Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chrUn_random
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 10571689
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.28
Warning! 1662808 characters in sequence are not A, C, G, or T
File 15 of 30
Found at i:5134208 original size:25 final size:27
Alignment explanation
Indices: 5134176--5134227 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
5134166 CCGATCTTCC
*
5134176 TTTCTTCCC-CTTT-TTCTTTTTTCTT
1 TTTCTTCCCTCTTTCTTCTTTTCTCTT
5134201 TTTCTTCCCTCTTTCTTCTTTTCTCTT
1 TTTCTTCCCTCTTTCTTCTTTTCTCTT
5134228 CCTCTTTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 9 0.38
26 4 0.17
27 11 0.46
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTCTTCCCTCTTTCTTCTTTTCTCTT
Found at i:5134219 original size:20 final size:20
Alignment explanation
Indices: 5134190--5134238 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
5134180 TTCCCCTTTT
*
5134190 TCTTTTTTCTTTT-TCTTCCC
1 TCTTTCTTCTTTTCTCTT-CC
5134210 TCTTTCTTCTTTTCTCTTCC
1 TCTTTCTTCTTTTCTCTTCC
5134230 TCTTTCTTC
1 TCTTTCTTC
5134239 CTCACCGGCG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (20 bp):
TCTTTCTTCTTTTCTCTTCC
Found at i:5134866 original size:6 final size:6
Alignment explanation
Indices: 5134842--5134909 Score: 63
Period size: 6 Copynumber: 11.7 Consensus size: 6
5134832 CTTTTTTATT
* * *
5134842 TTTTTCA TTATTT- TTTTTA TTTTTA -ATTTA TTTCTA -TTTT- TTTATA
1 TTTTT-A TT-TTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
5134888 TTTTTA TTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTT
5134910 CTTTCATTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
5 13 0.26
6 32 0.64
7 2 0.04
8 3 0.06
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:5134898 original size:39 final size:38
Alignment explanation
Indices: 5134838--5134914 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 38
5134828 TTCCCTTTTT
5134838 TATTTTTTTCATTATTTTTTTTATTTTTAATTTATTTC
1 TATTTTTTTCATTATTTTTTTTATTTTTAATTTATTTC
* * *
5134876 TATTTTTTT-ATATTTTTATTTTTATTTTTATTTTCTTTC
1 TATTTTTTTCAT-TATTT-TTTTTATTTTTAATTTATTTC
5134915 ATTATTATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
37 2 0.06
38 13 0.38
39 19 0.56
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (38 bp):
TATTTTTTTCATTATTTTTTTTATTTTTAATTTATTTC
Found at i:5134899 original size:28 final size:27
Alignment explanation
Indices: 5134834--5134929 Score: 97
Period size: 27 Copynumber: 3.4 Consensus size: 27
5134824 TCATTTCCCT
5134834 TTTTTATTTT-TTTCATTATTTTTTT-TA
1 TTTTTATTTTATTTC--TATTTTTTTATA
*
5134861 TTTTTAATTTATTTCTATTTTTTTATA
1 TTTTTATTTTATTTCTATTTTTTTATA
*
5134888 TTTTTATTTTTATTTTTATTTTCTTTCATTA
1 TTTTTA-TTTTATTTCTATTTT-TTT-A-TA
5134919 TTATTTATTTT
1 TT-TTTATTTT
5134930 GTTTTTTAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
26 9 0.15
27 17 0.29
28 17 0.29
29 3 0.05
30 1 0.02
31 8 0.14
32 4 0.07
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (27 bp):
TTTTTATTTTATTTCTATTTTTTTATA
Found at i:5134925 original size:54 final size:53
Alignment explanation
Indices: 5134834--5134936 Score: 129
Period size: 54 Copynumber: 1.9 Consensus size: 53
5134824 TCATTTCCCT
* *
5134834 TTTTTATTTTTTTCATTATTTTTTTTATTTTTAATTTATTTCTATTTTTTTATA
1 TTTTTATTTTTTTCATTATTTTTTTCATTATTAATTTATTT-TATTTTTTTATA
* *
5134888 TTTTTATTTTTATT-TTTATTTTCTTTCATTATT-ATTTATTTTGTTTTTT
1 TTTTTATTTTT-TTCATTATTTT-TTTCATTATTAATTTATTTTATTTTTT
5134937 AAAAGAGGTG
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
53 7 0.16
54 26 0.60
55 10 0.23
ACGTcount: A:0.17, C:0.04, G:0.01, T:0.79
Consensus pattern (53 bp):
TTTTTATTTTTTTCATTATTTTTTTCATTATTAATTTATTTTATTTTTTTATA
Found at i:5138590 original size:52 final size:52
Alignment explanation
Indices: 5138502--5138601 Score: 137
Period size: 52 Copynumber: 1.9 Consensus size: 52
5138492 TCCTTAGTCA
* * *
5138502 TGTCAAGATGTGAACAGTACAATGAGTATACTGATAAAAATATTAATAATCT
1 TGTCAAGATGTGAACAGTACAATGAATATACCGATAAAAATAATAATAATCT
* * * *
5138554 TGTCAAGATGTGAACGGTACATTGAATCTACCGATAAAAGTAATAATA
1 TGTCAAGATGTGAACAGTACAATGAATATACCGATAAAAATAATAATA
5138602 GCCAGGTCAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 41 1.00
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTCAAGATGTGAACAGTACAATGAATATACCGATAAAAATAATAATAATCT
Found at i:5139715 original size:52 final size:52
Alignment explanation
Indices: 5139647--5139756 Score: 136
Period size: 52 Copynumber: 2.1 Consensus size: 52
5139637 TTTTATTAGT
* *
5139647 CATGTCAGAATGTGAACGGTACA-A-TGAGTCTATTGATAAAAATATTAATAGC
1 CATGTCAGAATGTGAAC-G-ACATAGTGAGTATACTGATAAAAATATTAATAGC
* *
5139699 CATGTCA-AGATGTGAACGACATAGTGGGTATACTGATAAGAATATTAATAGC
1 CATGTCAGA-ATGTGAACGACATAGTGAGTATACTGATAAAAATATTAATAGC
5139751 CATGTC
1 CATGTC
5139757 CAGGTTTGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
50 3 0.06
51 3 0.06
52 45 0.88
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (52 bp):
CATGTCAGAATGTGAACGACATAGTGAGTATACTGATAAAAATATTAATAGC
Found at i:5141590 original size:102 final size:102
Alignment explanation
Indices: 5141422--5141618 Score: 218
Period size: 102 Copynumber: 1.9 Consensus size: 102
5141412 AAAAAAATAT
* *
5141422 CATTGCAACCAAAATATGAGGGGTAAAGCTCACAACTGAAGTAAGAGTGACGAGCAATGTTCAAA
1 CATTGCAACCAAAATATGAGCGGTAAAGCTCACAACTGAAGTAAGAGTGACGAACAATGTTCAAA
*
5141487 GAAT-AAGAGATAAAGCTTACAACCAATAGTGTAATGC
66 GAATGAA-AGACAAAGCTTACAACCAATAGTGTAATGC
** * *** * * * *
5141524 CATTGCAGTCAAAGTATGAGCGGTAAAGCTTGTAACTTAATTAAGAGTGATGAACTATGGTT-AA
1 CATTGCAACCAAAATATGAGCGGTAAAGCTCACAACTGAAGTAAGAGTGACGAACAAT-GTTCAA
* * *
5141588 AGAATGAACGACAAAGCTTGCAACGAATAGT
65 AGAATGAAAGACAAAGCTTACAACCAATAGT
5141619 ATAGAATAAT
Statistics
Matches: 77, Mismatches: 16, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
102 72 0.94
103 5 0.06
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.22
Consensus pattern (102 bp):
CATTGCAACCAAAATATGAGCGGTAAAGCTCACAACTGAAGTAAGAGTGACGAACAATGTTCAAA
GAATGAAAGACAAAGCTTACAACCAATAGTGTAATGC
Found at i:5142835 original size:35 final size:35
Alignment explanation
Indices: 5142796--5142871 Score: 89
Period size: 35 Copynumber: 2.2 Consensus size: 35
5142786 TTTACTTGTA
* ** *
5142796 TTAGTTGTTCCGTATGGGGTAGTACTCTATTTATT
1 TTAGTTCTTCCGTATGAAGTAATACTCTATTTATT
* * *
5142831 TTAGTTCTTCTGTATGAAGTAATACTTTATTTGTT
1 TTAGTTCTTCCGTATGAAGTAATACTCTATTTATT
5142866 TTAGTT
1 TTAGTT
5142872 TTTTTGCATG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (35 bp):
TTAGTTCTTCCGTATGAAGTAATACTCTATTTATT
Found at i:5142883 original size:35 final size:35
Alignment explanation
Indices: 5142818--5142886 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
5142808 TATGGGGTAG
*
5142818 TACTCTATTTATTTTAGTTCTTCTGTATGAAGTAA
1 TACTCTATTTATTTTAGTTCTTCTGCATGAAGTAA
* * * *
5142853 TACTTTATTTGTTTTAGTTTTTTTGCATGAAGTA
1 TACTCTATTTATTTTAGTTCTTCTGCATGAAGTA
5142887 GTGTGTTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.23, C:0.09, G:0.13, T:0.55
Consensus pattern (35 bp):
TACTCTATTTATTTTAGTTCTTCTGCATGAAGTAA
Found at i:5142973 original size:23 final size:23
Alignment explanation
Indices: 5142941--5142984 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
5142931 CTTGTAAAGA
*
5142941 TTGTTTTCATTATTCTCTATAGG
1 TTGTTCTCATTATTCTCTATAGG
5142964 TTGTTCTCATTATTCTCTATA
1 TTGTTCTCATTATTCTCTATA
5142985 CAATATTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.16, G:0.09, T:0.57
Consensus pattern (23 bp):
TTGTTCTCATTATTCTCTATAGG
Found at i:5153562 original size:22 final size:22
Alignment explanation
Indices: 5153537--5153580 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
5153527 TTTAAAACCA
5153537 CTTTAAAACCAAAACCTCTTAT
1 CTTTAAAACCAAAACCTCTTAT
*
5153559 CTTTAAAACTAAAACCTCTTAT
1 CTTTAAAACCAAAACCTCTTAT
5153581 ACCAATAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.25, G:0.00, T:0.34
Consensus pattern (22 bp):
CTTTAAAACCAAAACCTCTTAT
Found at i:5165414 original size:51 final size:50
Alignment explanation
Indices: 5165358--5165479 Score: 154
Period size: 51 Copynumber: 2.4 Consensus size: 50
5165348 GGACAAAATG
* * *
5165358 AGACATGCTTAGGCATGTAATATATAACAAGATGTGATGAGGCACGTAACT
1 AGACATGCTAAGGCATGTAAAATATAACAAGATGTGATGAAGCACGTAA-T
* *
5165409 AGACATGCTAATGCATGTAAAATATACCAAGATGTGATGAAGCACGTAAT
1 AGACATGCTAAGGCATGTAAAATATAACAAGATGTGATGAAGCACGTAAT
* * *
5165459 AGGACATCCTAAAGAATGTAA
1 A-GACATGCTAAGGCATGTAA
5165480 TTTGTTATAA
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
50 2 0.03
51 60 0.97
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (50 bp):
AGACATGCTAAGGCATGTAAAATATAACAAGATGTGATGAAGCACGTAAT
Found at i:5168527 original size:67 final size:67
Alignment explanation
Indices: 5168448--5168603 Score: 217
Period size: 67 Copynumber: 2.3 Consensus size: 67
5168438 TTACAATGGC
* * *
5168448 TTTTCACAGGCTCAGCCACAACCTTTAATAATGG-TTTTTACCAAGATCAACCAAAATCCAAAGT
1 TTTTCAAAGGCTCAACCACAACCTTTAATAATGGTTTTTTA-CAAGATCAACCAAAACCCAAAGT
5168512 -GAT
65 AG-T
* * * *
5168515 TTTTCAAAGGCTCAACCACAACCTTTCATAATGGTTTTTTATAGGCTCAACCAAAACCCAAAGTA
1 TTTTCAAAGGCTCAACCACAACCTTTAATAATGGTTTTTTACAAGATCAACCAAAACCCAAAGTA
5168580 GT
66 GT
5168582 TTTTCAAAGGCTCAACCACAAC
1 TTTTCAAAGGCTCAACCACAAC
5168604 TTACAACAAT
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
67 73 0.91
68 7 0.09
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.28
Consensus pattern (67 bp):
TTTTCAAAGGCTCAACCACAACCTTTAATAATGGTTTTTTACAAGATCAACCAAAACCCAAAGTA
GT
Found at i:5168530 original size:32 final size:32
Alignment explanation
Indices: 5168494--5168599 Score: 99
Period size: 32 Copynumber: 3.2 Consensus size: 32
5168484 TTTACCAAGA
5168494 TCAACCAAAATCCAAAGTGATTTTTCAAAGGC
1 TCAACCAAAATCCAAAGTGATTTTTCAAAGGC
* * * * *
5168526 TCAACCACAACCTTTCATAA-TGGTTTTTTATAGGC
1 TCAACCA-AA--ATCCA-AAGTGATTTTTCAAAGGC
*
5168561 TCAACCAAAACCCAAAGT-AGTTTTTCAAAGGC
1 TCAACCAAAATCCAAAGTGA-TTTTTCAAAGGC
5168593 TCAACCA
1 TCAACCA
5168600 CAACTTACAA
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
31 2 0.04
32 27 0.47
33 2 0.04
34 2 0.04
35 22 0.39
36 2 0.04
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.27
Consensus pattern (32 bp):
TCAACCAAAATCCAAAGTGATTTTTCAAAGGC
Found at i:5168620 original size:67 final size:67
Alignment explanation
Indices: 5168448--5168642 Score: 211
Period size: 67 Copynumber: 2.9 Consensus size: 67
5168438 TTACAATGGC
* * * * *
5168448 TTTTCACAGGCTCAGCCACAACCTTTA-ATAATGGTTTTTACCA-A-GATCAACCAAAATCCAAA
1 TTTTCAAAGGCTCAACCACAACC-TTACACAATGATTTTT--CATAGGATCAACCAAAACCCAAA
5168510 GTGAT
63 GTGAT
* * * * *
5168515 TTTTCAAAGGCTCAACCACAACCTTTCATAATGGTTTTTTATAGGCTCAACCAAAACCCAAAGT-
1 TTTTCAAAGGCTCAACCACAACCTTACACAATGATTTTTCATAGGATCAACCAAAACCCAAAGTG
5168579 AGT
66 A-T
*
5168582 TTTTCAAAGGCTCAACCACAA-CTTACAACAATGATTTTTCATTGGATCAACCAAAACCCAA
1 TTTTCAAAGGCTCAACCACAACCTTAC-ACAATGATTTTTCATAGGATCAACCAAAACCCAA
5168643 CAACTAACTT
Statistics
Matches: 111, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
65 1 0.01
66 8 0.07
67 102 0.92
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.28
Consensus pattern (67 bp):
TTTTCAAAGGCTCAACCACAACCTTACACAATGATTTTTCATAGGATCAACCAAAACCCAAAGTG
AT
Found at i:5171045 original size:20 final size:20
Alignment explanation
Indices: 5171017--5171055 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5171007 CTTCAAGCAC
* *
5171017 TATTCTCAATTATCATCAAG
1 TATTATCAATCATCATCAAG
5171037 TATTATCAATCATCATCAA
1 TATTATCAATCATCATCAA
5171056 ACATTCATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (20 bp):
TATTATCAATCATCATCAAG
Found at i:5179372 original size:20 final size:19
Alignment explanation
Indices: 5179347--5179386 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
5179337 AACTTATGCC
5179347 TATCTACCAATAGATAGCAA
1 TATCTACCAATAGATA-CAA
* *
5179367 TATCTATCTATAGATACAA
1 TATCTACCAATAGATACAA
5179386 T
1 T
5179387 TTAGGGGCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (19 bp):
TATCTACCAATAGATACAA
Found at i:5181832 original size:2 final size:2
Alignment explanation
Indices: 5181825--5181875 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
5181815 AACCAACACG
5181825 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5181867 TA TA TA TA T
1 TA TA TA TA T
5181876 CTAACGACGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5190531 original size:28 final size:27
Alignment explanation
Indices: 5190500--5190552 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
5190490 TTTGGAGTAT
*
5190500 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTT-CCACCTC
*
5190528 AGGGGCAAAATTGTAATTTTCCACC
1 AGGGGCAAAATGGTAATTTTCCACC
5190553 ACCAGGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (27 bp):
AGGGGCAAAATGGTAATTTTCCACCTC
Found at i:5190558 original size:28 final size:28
Alignment explanation
Indices: 5190500--5190558 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
5190490 TTTGGAGTAT
* *
5190500 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTTGCCACCCC
*
5190528 AGGGGCAAAATTGTAATTTT-CCACCACC
1 AGGGGCAAAATGGTAATTTTGCCACC-CC
5190556 AGG
1 AGG
5190559 ATATTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (28 bp):
AGGGGCAAAATGGTAATTTTGCCACCCC
Found at i:5193431 original size:19 final size:19
Alignment explanation
Indices: 5193407--5193468 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
5193397 AAAATATTAA
**
5193407 TATTTTAATATTTTAATAT
1 TATTTTAATATTAAAATAT
* *
5193426 TATTTTATTCTTAAAATAT
1 TATTTTAATATTAAAATAT
5193445 TATTTT-AT-TTCAAAATAT
1 TATTTTAATATT-AAAATAT
*
5193463 TCTTTT
1 TATTTT
5193469 CACTTGTCAC
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
17 2 0.06
18 13 0.36
19 21 0.58
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTTTAATATTAAAATAT
Found at i:5193461 original size:18 final size:19
Alignment explanation
Indices: 5193421--5193468 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
5193411 TTAATATTTT
*
5193421 AATATTATTTTATTCTTAA
1 AATATTATTTTATTCTCAA
5193440 AATATTATTTTATT-TCAA
1 AATATTATTTTATTCTCAA
*
5193458 AATATTCTTTT
1 AATATTATTTT
5193469 CACTTGTCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (19 bp):
AATATTATTTTATTCTCAA
Found at i:5195848 original size:171 final size:169
Alignment explanation
Indices: 5195436--5196616 Score: 1208
Period size: 172 Copynumber: 6.9 Consensus size: 169
5195426 AAAACCTTCT
* * * * *
5195436 GTTGACAAGAAAAGTCCATTTATGGTCACTCCTACCTTC-AGAATCCTTATTAC-CTGCTTAAAA
1 GTTGATAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGA-AAGCCTTATTACTC-GCTTAAAA
* * * *
5195499 TGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTACACATTTTTGATTAAGAA-AGGTT
64 TGGTTTTATAATCTCATTATTGATTTTAAGTTGAATTTTT-TACATTTTTGGTTAA-AACAGATT
* *** *
5195563 ATAATTAAATGTTTGCCTTGGGAAACGTGAAGCGAGAGCCATC
127 ATAATTGAATGTTTGCCTCAAGAAACGTGAAGCGAAAGCCATC
* * * * *
5195606 GTTGACAAGGAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGTCTTATTATTCACATT-AAAT
1 GTTGATAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGC-TTAAAAT
* * * *
5195670 GGTTTTATAATCTCATTATTGAATTTAAGTTGAGTTGTTTTACATTTTTTGTTTAAAA-AGATCA
65 GGTTTTATAATCTCATTATTGATTTTAAGTTGAATT-TTTTACA-TTTTTGGTTAAAACAGATTA
* * * * * * *
5195734 TAATTGAATGTTTACCTCAAGTAACGCGAGGCTAAACCCCTC
128 TAATTGAATGTTTGCCTCAAGAAACGTGAAGCGAAAGCCATC
* * * **
5195776 TGTTGGTAGGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCCTATTACTCGCTTCGAAT
1 -GTTGATAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTAAAAT
* * * * *
5195841 GGTTTTATAATTTGA-TATTGATTTTAAGCTGAAGTTTTTTATATTTTTGGTTAAAACAAATTAT
65 GGTTTTATAATCTCATTATTGATTTTAAGTTGAA-TTTTTTACATTTTTGGTTAAAACAGATTAT
* *
5195905 AATTGAATGTTTGCCTTAAGAAACGTGAAGCGAAAGCAATC
129 AATTGAATGTTTGCCTCAAGAAACGTGAAGCGAAAGCCATC
* * ** *
5195946 GATTGATAAGAAAAGTCAATTTATTA-TCACTCATGCTTTTAAAAGCCTTATTACTCGCTTCAAA
1 G-TTGATAAGAAAAGTCCATTTA-TAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTAAAA
* * * *
5196010 TGGTTTTATAAGCTTATTATGGATTTTAAGTTGAATTTTCTTACATTTTTGGTTAAAACATATTA
64 TGGTTTTATAATCTCATTATTGATTTTAAGTTGAATTTT-TTACATTTTTGGTTAAAACAGATTA
*** * * * *
5196075 TAATTGAATGTTTGCCTTTGGAAACATGAAACGAAAGCTAAC
128 TAATTGAATGTTTGCCTCAAGAAACGTGAAGCGAAAGCCATC
** * * * * **
5196117 GATTGGCAAGAAAAGTCCATTTTAGAGTGACTCATGCCTTGGAAAGCCTTATTACTCACTTTGAA
1 G-TTGATAAGAAAAGTCCA-TTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTAAAA
* * * * * *
5196182 TGGTTTTATAATCTGATTATTGATTTTAAGCTGAATTTTTTAACCTTCTTGGTTAAAATAGGTTA
64 TGGTTTTATAATCTCATTATTGATTTTAAGTTGAATTTTTT-ACATTTTTGGTTAAAACAGATTA
* * *
5196247 TAATTGAATGTTTACCTCGAA-AAACATGAAGCGAAATCCATCC
128 TAATTGAATGTTTGCCTC-AAGAAACGTGAAGCGAAAGCCAT-C
* * * *
5196290 ATTGATAAGAAAAAATCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTTGCTTTAAAT
1 GTTGATAAG-AAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTAAAAT
* * * * * * *
5196355 GGTTTTAAAATGTCATTATTGATTTTAAGTTGAATTTTCTTACAATATTAGTTGAAACAGATTAC
65 GGTTTTATAATCTCATTATTGATTTTAAGTTGAATTTT-TTACATTTTTGGTTAAAACAGATTAT
* *
5196420 AATTGAATGTTTGCCTCGAGAAACGTGAAGCGAATGCCATC
129 AATTGAATGTTTGCCTCAAGAAACGTGAAGCGAAAGCCATC
* * * *
5196461 GATTGAGAAGAAAAGTCCATTTATAGTCACTGATGCCTTCAAAAACCTTATTACTCGCTTAAAAT
1 G-TTGATAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTAAAAT
* * * * * * *
5196526 GGTTTTATAATTTGATTATTGACTTTAAGTTGACTTTTTTTTATATTTTTTGTTAAAACATATTA
65 GGTTTTATAATCTCATTATTGATTTTAAGTTGA--ATTTTTTACATTTTTGGTTAAAACAGATTA
*
5196591 TAATTGAATGTTTACCTCAAGAAACG
128 TAATTGAATGTTTGCCTCAAGAAACG
5196617 GGAGGCTAAA
Statistics
Matches: 835, Mismatches: 152, Indels: 46
0.81 0.15 0.04
Matches are distributed among these distances:
169 13 0.02
170 249 0.30
171 260 0.31
172 298 0.36
173 15 0.02
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.38
Consensus pattern (169 bp):
GTTGATAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTAAAATG
GTTTTATAATCTCATTATTGATTTTAAGTTGAATTTTTTACATTTTTGGTTAAAACAGATTATAA
TTGAATGTTTGCCTCAAGAAACGTGAAGCGAAAGCCATC
Found at i:5202076 original size:43 final size:43
Alignment explanation
Indices: 5202018--5202099 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
5202008 TCATCATCAC
* *
5202018 CAGCTCATGCGCACTCCCTACTCGCACATAACCGGGTCATCTT
1 CAGCTCATGCCCACTCCCTACTCGCACATAACCGAGTCATCTT
* * *
5202061 CAGCTTATGCCCACTCCCTACTTGCACATAGCCGAGTCA
1 CAGCTCATGCCCACTCCCTACTCGCACATAACCGAGTCA
5202100 ATATAATTAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.22, C:0.39, G:0.16, T:0.23
Consensus pattern (43 bp):
CAGCTCATGCCCACTCCCTACTCGCACATAACCGAGTCATCTT
Found at i:5202920 original size:19 final size:20
Alignment explanation
Indices: 5202886--5202923 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
5202876 GAAGAAGACC
5202886 AGCTGCTGGAAAATTCAAGA
1 AGCTGCTGGAAAATTCAAGA
5202906 AGCTGCTGG-AAATTCAAG
1 AGCTGCTGGAAAATTCAAG
5202924 GTATTTATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (20 bp):
AGCTGCTGGAAAATTCAAGA
Found at i:5203875 original size:171 final size:169
Alignment explanation
Indices: 5203329--5205141 Score: 1943
Period size: 171 Copynumber: 10.6 Consensus size: 169
5203319 ACAAAAACTC
* * *
5203329 TCCGTTGAC-AGAAAAAGTCCATTTATGGTCACTCAT-ACTTACAAAAGCCTTATTAC-CTGCTT
1 TCCGTTGACAAG-AAAAGTCCATTTATAGTCACTCATGCCTT-CGAAAGCCTTATTACTC-GCTT
* * *
5203391 AAAATGGTTTTATAATATCATAATTGATTTTAAGTTGAATTTTTTTACA-TTTTTGATTAAGAA-
63 -AAATGGTTTTATAATCTCATTATTGATTTTAAGCTGAATTTTTTTACATTTTTTG-TTAA-AAC
* * ** * *
5203454 AGGTTATAATTCAATGTTTGTCTTGAGAAATGTGAAGCAGAAGCCA
125 AGATTATAATTGAATGTTTACCTTGAGAAACGTGAAGCA-AAACCA
* * * *
5203500 T-CGATTGACAAAAAAAGTCTATTTATAGTCATTCATGCCTTCGAAAGCCTTATTACTGGCTTTA
1 TCCG-TTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGC-TTA
*
5203564 AATGGTTTTATAATCT-AGTTATTGA-TTTAAGCTGAATTTTTTTACATTTTTGGTTAAAACAGA
64 AATGGTTTTATAATCTCA-TTATTGATTTTAAGCTGAATTTTTTTACATTTTTTGTTAAAACAGA
* *
5203627 TTATAATTGAATGTTTACCTCGAGAAAAGTGAAGCGAAAACCA
128 TTATAATTGAATGTTTACCTTGAGAAACGTGAAGC-AAAACCA
* * *
5203670 TCCATTGACAAGAATAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTTGCATTAA
1 TCCGTTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGC-TTAA
* * *
5203735 ATGGTTTTATAATCTGATTATTGATTTTGAGGTGAATTTTTTTACATTTTTTGTTAAAACAGATT
65 ATGGTTTTATAATCTCATTATTGATTTTAAGCTGAATTTTTTTACATTTTTTGTTAAAACAGATT
* *
5203800 ATAATTGAATGCTTACCTTGGGAAACGTGAAGCTAAAACTC-
130 ATAATTGAATGTTTACCTTGAGAAACGTGAAGC-AAAAC-CA
* **
5203841 TCCGTTGACAGGAAAAGTGAATTTATTA-TCACTCATGCCTTC-AGAAGCCTTATTACTCGCTTA
1 TCCGTTGACAAGAAAAGTCCATTTA-TAGTCACTCATGCCTTCGA-AAGCCTTATTACTCGCTTA
* * * *
5203904 ATATGGTTTTATAACCTCCTAATTGATTTTAAGCTGAATTTTTTTACCTTTTCTT-TTAAGAA-A
64 A-ATGGTTTTATAATCTCATTATTGATTTTAAGCTGAATTTTTTTACATTTT-TTGTTAA-AACA
* * * * *
5203967 GGTTATAATTGAATGTTTACCTTGAGCAATGTAAACCAAAAGCCA
126 GATTATAATTGAATGTTTACCTTGAGAAACGTGAAGCAAAA-CCA
* * * *
5204012 T-CGATTGAGAAGAAAAGTCCATTTAAAGTCACTCATGCCTATAG-AAGCCTTATTACTCGCTGA
1 TCCG-TTGACAAGAAAAGTCCATTTATAGTCACTCATGCCT-TCGAAAGCCTTATTACTCGCT-T
* * * * ** *
5204075 AAAT-GTTTTTTAGTCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTCAGCTAAGAA-AG
63 AAATGGTTTTATAATCTCATTATTGATTTTAAGCTGAATTTTTTTACATTTTTTGTTAA-AACAG
* * * *
5204138 GTTATAATTGAATGTTTACCTTGAGAAACATGAAGCGAAAGCTA
127 ATTATAATTGAATGTTTACCTTGAGAAACGTGAAGC-AAAACCA
* * *
5204182 TCCATTGACAAGAAAAGTCCATTTATAGTCACTCATACCTTCGAAACCCTTATTACTCGCTTTAA
1 TCCGTTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGC-TTAA
* * * * **
5204247 ATGGTTATATAATCTGATTATTGATTTTAAGCTGAATTGTTTTATATTTTGGGTTAAAACAGATT
65 ATGGTTTTATAATCTCATTATTGATTTTAAGCTGAATTTTTTTACATTTTTTGTTAAAACAGATT
* * *
5204312 ATAATTGCATGTTTGCCTCATGA-AAA-GTGAAGCAGAAGCCA
130 ATAATTGAATGTTTACCT--TGAGAAACGTGAAGCA-AAACCA
* * *
5204353 TCCATTGACAAGAATAGTCCATTTATAGTCACTCATGCCTTCGAAAGCTTTATTACTCGCTTCAA
1 TCCGTTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTT-AA
* * * * * *
5204418 ATGGTTTTATCATCTGATTGTTGATTTTAAGTTGAATTTTTTTGCATTTTTTGTTAAAACAAATT
65 ATGGTTTTATAATCTCATTATTGATTTTAAGCTGAATTTTTTTACATTTTTTGTTAAAACAGATT
* *
5204483 ACAATTGAATGCTTT-CCTTGAGAAACGTGAGGCTAAAACTC-
130 ATAATTGAATG-TTTACCTTGAGAAACGTGAAGC-AAAAC-CA
** * * *
5204524 TCTATTGACAAGAAAAGTCCATTTATAGTCACTCCTACCTTC-AGAAGCCTTATTAC-CTTCTTA
1 TCCGTTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGA-AAGCCTTATTACTC-GCTT-
* * * **
5204587 AAATGGTTTTATAATCTCATAATTGATTTTCAGTTGAATTTTTTTACATTTTCGGTTAAGAA-AG
63 AAATGGTTTTATAATCTCATTATTGATTTTAAGCTGAATTTTTTTACATTTTTTGTTAA-AACAG
* * * * *
5204651 GTTATAATTAAATGTTTGCCTTGGGAAATGTGAAGCAAAAGCCA
127 ATTATAATTGAATGTTTACCTTGAGAAACGTGAAGCAAAA-CCA
* *
5204695 T-CGATTGACAAGGAAAGTCCATTTATAGTCACTCATACCTTCGAAAGCCTTATTACTCGCATTA
1 TCCG-TTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGC-TTA
* *
5204759 AATGGTTTTATAATCTCATTATTGATTTTAAGCTGAGTTTTTTTACATTTTTTGTTTAAACAGAT
64 AATGGTTTTATAATCTCATTATTGATTTTAAGCTGAATTTTTTTACATTTTTTGTTAAAACAGAT
* ** * *
5204824 CATAATTGAATGTTTACCTCAAGAAACGTGAGGCTAAAACCC
129 TATAATTGAATGTTTACCTTGAGAAACGTGAAGC-AAAACCA
* * * * * * *
5204866 TCTGTAGGCAGGAAAAGTCCATTTATAGCCACTCATGCCTTCGGAAGCCTTATTACTCGCTTCGA
1 TCCGTTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTT-AA
* * * *
5204931 ATGGTTTTATAATTTGATTATTGATTTTAAGCTGAATTTTTTTACATTTTTGGTTAAAAGAGATT
65 ATGGTTTTATAATCTCATTATTGATTTTAAGCTGAATTTTTTTACATTTTTTGTTAAAACAGATT
* * * **
5204996 GTAATTGAATTTTTGCCTCAAGAAACGTGAAGCAAAAGCCA
130 ATAATTGAATGTTTACCTTGAGAAACGTGAAGCAAAA-CCA
*
5205037 T-CGATTGACAAGAAAAGTCCATTTATTA-TCACTCATGCCTTCAAAAGCCTTATTACTCGCTTT
1 TCCG-TTGACAAGAAAAGTCCATTTA-TAGTCACTCATGCCTTCGAAAGCCTTATTACTCGC-TT
* *
5205100 AAATGCTTTTATAATCTCATTATTGATTTTAAGTTGAATTTT
63 AAATGGTTTTATAATCTCATTATTGATTTTAAGCTGAATTTT
5205142 CTTANNNNNN
Statistics
Matches: 1389, Mismatches: 194, Indels: 118
0.82 0.11 0.07
Matches are distributed among these distances:
169 7 0.01
170 317 0.23
171 1023 0.74
172 39 0.03
173 3 0.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (169 bp):
TCCGTTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTAAA
TGGTTTTATAATCTCATTATTGATTTTAAGCTGAATTTTTTTACATTTTTTGTTAAAACAGATTA
TAATTGAATGTTTACCTTGAGAAACGTGAAGCAAAACCA
Found at i:5204305 original size:512 final size:512
Alignment explanation
Indices: 5203322--5205141 Score: 2217
Period size: 512 Copynumber: 3.6 Consensus size: 512
5203312 GGGTATCACA
* * * *
5203322 AAAACTCTCCGTTGACAGAAAAAGTCCATTTATGGTCACTCAT-ACTTACAAAAGCCTTATTAC-
1 AAAACTCTCCGTTGACAGGAAAAGTCCATTTATAGTCACTCATGCCTT-CAGAAGCCTTATTACT
* * * *
5203385 CTGCTTAAAATGGTTTTATAATATCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTA
65 C-GCTTCAAATGGTTTTATAATCTCATAATTGATTTTAAGCTGAATTTTTTTACATTTTTGTTTA
* * * * * * * *
5203450 AGAA-AGGTTATAATTCAATGTTTGTCTTGAGAAATGTGAAGCAGAAGCCATCGATTGACAAAAA
129 A-AACAGATTATAATTGAATGTTTGCCTTGAGAAACGTAAACCAAAAGCCATCGATTGACAAGAA
* * * *
5203514 AAGTCTATTTATAGTCATTCATGCCTTC-GAAAGCCTTATTACTGGCTTTAAATGGTTTTATAAT
193 AAGTCCATTTATAGTCACTCATGCCTTCAG-AAGCCTTATTACTCGCTTAAAATGGTTTTATAAT
* * * *
5203578 CT-AGTTATTGA-TTTAAGCTGAATTTTTTTACATTTTTGGTTAA-AACAGATTATAATTGAATG
257 CTCA-TAATTGATTTTAAGTTGAATTTTTTTACATTTTCGGTTAAGAA-AGGTTATAATTGAATG
* * *
5203640 TTTACCTCGAGAAAAGTGAAGCGAAAACCATCCATTGACAAGAATAGTCCATTTATAGTCACTCA
320 TTTACCTTGAGAAAA-TGAAGCGAAAGCCATCCATTGACAAGAAAAGTCCATTTATAGTCACTCA
* * * *
5203705 TGCCTTCGAAAGCCTTATTACTTGCATTAAATGGTTTTATAATCTGATTATTGATTTTGAGGTGA
384 TACCTTCGAAAGCCTTATTACTCGCATTAAATGGTTTTATAATCTGATTATTGATTTTAAGCTGA
* ***
5203770 ATTTTTTTACATTTTTTGTTAAAACAGATTATAATTGAATGCTTACCTTGGGAAACGTGAAGCT
449 ATTTTTTTACATTTTTTGTTAAAACAGATTATAATTGAATGTTTACCTCAAGAAACGTGAAGCT
**
5203834 AAAACTCTCCGTTGACAGGAAAAGTGAATTTATTA-TCACTCATGCCTTCAGAAGCCTTATTACT
1 AAAACTCTCCGTTGACAGGAAAAGTCCATTTA-TAGTCACTCATGCCTTCAGAAGCCTTATTACT
* * *
5203898 CGCTT-AATATGGTTTTATAACCTCCTAATTGATTTTAAGCTGAATTTTTTTACCTTTTCT-TTT
65 CGCTTCAA-ATGGTTTTATAATCTCATAATTGATTTTAAGCTGAATTTTTTTACATTTT-TGTTT
* * * * *
5203961 AAGAA-AGGTTATAATTGAATGTTTACCTTGAGCAATGTAAACCAAAAGCCATCGATTGAGAAGA
128 AA-AACAGATTATAATTGAATGTTTGCCTTGAGAAACGTAAACCAAAAGCCATCGATTGACAAGA
* * * *
5204025 AAAGTCCATTTAAAGTCACTCATGCCTAT-AGAAGCCTTATTACTCGCTGAAAAT-GTTTTTTAG
192 AAAGTCCATTTATAGTCACTCATGCCT-TCAGAAGCCTTATTACTCGCTTAAAATGGTTTTATAA
* *
5204088 TCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTCAGCTAAGAAAGGTTATAATTGAATGT
256 TCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTCGGTTAAGAAAGGTTATAATTGAATGT
*
5204153 TTACCTTGAGAAACATGAAGCGAAAGCTATCCATTGACAAGAAAAGTCCATTTATAGTCACTCAT
321 TTACCTTGAGAAA-ATGAAGCGAAAGCCATCCATTGACAAGAAAAGTCCATTTATAGTCACTCAT
* * *
5204218 ACCTTCGAAACCCTTATTACTCGCTTTAAATGGTTATATAATCTGATTATTGATTTTAAGCTGAA
385 ACCTTCGAAAGCCTTATTACTCGCATTAAATGGTTTTATAATCTGATTATTGATTTTAAGCTGAA
* * ** * * * *
5204283 TTGTTTTATATTTTGGGTTAAAACAGATTATAATTGCATGTTTGCCTCATGAAAAGTGAAGC-
450 TTTTTTTACATTTTTTGTTAAAACAGATTATAATTGAATGTTTACCTCAAGAAACGTGAAGCT
* * * * *
5204345 AGAAGC-CATCCATTGACAAGAATAGTCCATTTATAGTCACTCATGCCTTC-GAAAGCTTTATTA
1 A-AAACTC-TCCGTTGACAGGAAAAGTCCATTTATAGTCACTCATGCCTTCAG-AAGCCTTATTA
* * ** * *
5204408 CTCGCTTCAAATGGTTTTATCATCTGATTGTTGATTTTAAGTTGAATTTTTTTGCATTTTT-TGT
63 CTCGCTTCAAATGGTTTTATAATCTCATAATTGATTTTAAGCTGAATTTTTTTACATTTTTGT-T
* * ** * *
5204472 TAAAACAAATTACAATTGAATGCTTT-CCTTGAGAAACGTGAGGCTAAAA-CTC-TCTATTGACA
127 TAAAACAGATTATAATTGAATG-TTTGCCTTGAGAAACGT-AAACCAAAAGC-CATCGATTGACA
* * *
5204534 AGAAAAGTCCATTTATAGTCACTCCTACCTTCAGAAGCCTTATTAC-CTTCTTAAAATGGTTTTA
189 AGAAAAGTCCATTTATAGTCACTCATGCCTTCAGAAGCCTTATTACTC-GCTTAAAATGGTTTTA
* *
5204598 TAATCTCATAATTGATTTTCAGTTGAATTTTTTTACATTTTCGGTTAAGAAAGGTTATAATTAAA
253 TAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTCGGTTAAGAAAGGTTATAATTGAA
* * * * * *
5204663 TGTTTGCCTTGGGAAATGTGAAGCAAAAGCCATCGATTGACAAGGAAAGTCCATTTATAGTCACT
318 TGTTTACCTTGAGAAA-ATGAAGCGAAAGCCATCCATTGACAAGAAAAGTCCATTTATAGTCACT
*
5204728 CATACCTTCGAAAGCCTTATTACTCGCATTAAATGGTTTTATAATCTCATTATTGATTTTAAGCT
382 CATACCTTCGAAAGCCTTATTACTCGCATTAAATGGTTTTATAATCTGATTATTGATTTTAAGCT
* * * *
5204793 GAGTTTTTTTACATTTTTTGTTTAAACAGATCATAATTGAATGTTTACCTCAAGAAACGTGAGGC
447 GAATTTTTTTACATTTTTTGTTAAAACAGATTATAATTGAATGTTTACCTCAAGAAACGTGAAGC
5204858 T
512 T
* * * * * *
5204859 AAAACCCTCTGTAGGCAGGAAAAGTCCATTTATAGCCACTCATGCCTTCGGAAGCCTTATTACTC
1 AAAACTCTCCGTTGACAGGAAAAGTCCATTTATAGTCACTCATGCCTTCAGAAGCCTTATTACTC
* * * * *
5204924 GCTTCGAATGGTTTTATAATTTGATTATTGATTTTAAGCTGAATTTTTTTACATTTTTGGTTAAA
66 GCTTCAAATGGTTTTATAATCTCATAATTGATTTTAAGCTGAATTTTTTTACATTTTTGTTTAAA
* * * ** * *
5204989 AGAGATTGTAATTGAATTTTTGCCTCAAGAAACGTGAAGCAAAAGCCATCGATTGACAAGAAAAG
131 ACAGATTATAATTGAATGTTTGCCTTGAGAAACGTAAACCAAAAGCCATCGATTGACAAGAAAAG
* * *
5205054 TCCATTTATTA-TCACTCATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGCTTTTATAATCTC
196 TCCATTTA-TAGTCACTCATGCCTTCAGAAGCCTTATTACTCGCTTAAAATGGTTTTATAATCTC
*
5205118 ATTATTGATTTTAAGTTGAATTTT
260 ATAATTGATTTTAAGTTGAATTTT
5205142 CTTANNNNNN
Statistics
Matches: 1120, Mismatches: 155, Indels: 65
0.84 0.12 0.05
Matches are distributed among these distances:
511 29 0.03
512 602 0.54
513 483 0.43
514 6 0.01
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (512 bp):
AAAACTCTCCGTTGACAGGAAAAGTCCATTTATAGTCACTCATGCCTTCAGAAGCCTTATTACTC
GCTTCAAATGGTTTTATAATCTCATAATTGATTTTAAGCTGAATTTTTTTACATTTTTGTTTAAA
ACAGATTATAATTGAATGTTTGCCTTGAGAAACGTAAACCAAAAGCCATCGATTGACAAGAAAAG
TCCATTTATAGTCACTCATGCCTTCAGAAGCCTTATTACTCGCTTAAAATGGTTTTATAATCTCA
TAATTGATTTTAAGTTGAATTTTTTTACATTTTCGGTTAAGAAAGGTTATAATTGAATGTTTACC
TTGAGAAAATGAAGCGAAAGCCATCCATTGACAAGAAAAGTCCATTTATAGTCACTCATACCTTC
GAAAGCCTTATTACTCGCATTAAATGGTTTTATAATCTGATTATTGATTTTAAGCTGAATTTTTT
TACATTTTTTGTTAAAACAGATTATAATTGAATGTTTACCTCAAGAAACGTGAAGCT
Found at i:5209975 original size:171 final size:170
Alignment explanation
Indices: 5209536--5211618 Score: 2380
Period size: 171 Copynumber: 12.2 Consensus size: 170
5209526 TCAAGAAAGT
* * **
5209536 TTATAATTAAATGTTTGCCTCTA-GAAACGTGAAGCGAAAGGCATTGATTGACAAGAAAAGTCCA
1 TTATAATTGAATGTTTGCCTC-AGGAAACGTGAAGCGAAAGCCATCCATTGACAAGAAAAGTCCA
* *
5209600 TTTATAGTCACTCATG-CTTACGAAAGCCTTATTAC-CTGCATTAAATGGTTTTATTATCTCATT
65 TTTATAGTCACTCATGCCTT-CGAAAGCCTTATTACTC-GCTTTAAATGGTTTTATAATCTCATT
* * * *
5209663 ATTGATTTTTAA-TTTAGTTTTCTTAC--TTTTCGATTAAAATATA
128 ATTGA-TTTTAAGTTGAATTTT-TTACATTTTTTG-TTAAAACATA
* *
5209706 TTATAATTGAATGTTTGCCTC-GAGAAACGTGAAGCGAAAGCCATCCAATGAAAAGAAAAGTCCA
1 TTATAATTGAATGTTTGCCTCAG-GAAACGTGAAGCGAAAGCCATCCATTGACAAGAAAAGTCCA
* * * * * * *
5209770 TTAATAGTCACCCAAGCCTTCAAAAGCGTTATTACTGGCTTTAAATGGATTTATAATCTCATTAT
65 TTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATTAT
*
5209835 TGATTTTAAGTTTAATTTTTTAACATTTTTTGTTAAAACATA
130 TGATTTTAAGTTGAATTTTTT-ACATTTTTTGTTAAAACATA
* * * * ** * * ** * *
5209877 TCATAATTGAATGCTTACCTCAGGAAACGTGAGGTTAAAACCCTCTGTTGATAGGAAAAGTCCAT
1 TTATAATTGAATGTTTGCCTCAGGAAACGTGAAGCGAAAGCCATCCATTGACAAGAAAAGTCCAT
* * * *
5209942 TTACAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTCAAATGGTTTTATAATTTGATTATT
66 TTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATTATT
** * * * *
5210007 GATTTTAAACTAAATTTTTTTTCATTTTTGGTTAAAACAGA
131 GATTTTAAGTTGAA-TTTTTTACATTTTTTGTTAAAACATA
* **
5210048 TTATAATTGAATGTTTGCCTC-GAGAAATGTGAAGCGAAAGCCATTGATTGACAAGAAAAGTCCA
1 TTATAATTGAATGTTTGCCTCAG-GAAACGTGAAGCGAAAGCCATCCATTGACAAGAAAAGTCCA
* * * * * *
5210112 TTTCTTGTCACTCTTGCCTTCAAAAGCGTTATTACTCGCTTTAAATGGTTTTATAAGCTCATTAT
65 TTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATTAT
* * * *
5210177 TGATTTTGAGTTGAATTGTTTTACATTTTTTGTGAAAATAGA
130 TGATTTTAAGTTGAATT-TTTTACATTTTTTGTTAAAACATA
* ** * * *
5210219 TTATAATTGAATGTTTGCCTCTGGAAATATGAAGCGAAAGCCATCGATTGGCAAGAAAAGTCTAT
1 TTATAATTGAATGTTTGCCTCAGGAAACGTGAAGCGAAAGCCATCCATTGACAAGAAAAGTCCAT
* * *
5210284 TTATAGTCACTCATACCTTCGAAAGCCTTATTACTCGCTTTGAATGGTTTTATAATCTGATTATT
66 TTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATTATT
* * * *
5210349 GATTTTAAGCTGAATGTTTTAACATTTTTCGTTAAAA-TTGA
131 GATTTTAAGTTGAAT-TTTTTACATTTTTTGTTAAAACAT-A
* * * *
5210390 TTTTAATTGAATGTTTGCCTCAAGAAACATGAAGCGAAAGCCATCCATTGATAAGAAAAGTCCAT
1 TTATAATTGAATGTTTGCCTCAGGAAACGTGAAGCGAAAGCCATCCATTGACAAGAAAAGTCCAT
* * * *
5210455 TTATAGTCACTCATGCCTTCGAAAGCCTTATTATTCGCTTCAAATGGTTTTATAATTTGATTATT
66 TTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATTATT
** * * * *
5210520 GATTTTAAACTAAATTTTTTTTCATTTTTGGTTAAAACAGA
131 GATTTTAAGTTGAA-TTTTTTACATTTTTTGTTAAAACATA
* **
5210561 TTATAATTGAATGTTTGCCTC-GAGAAATGTGAAGCGAAAGCCATTGATTGACAAGAAAAGTCCA
1 TTATAATTGAATGTTTGCCTCAG-GAAACGTGAAGCGAAAGCCATCCATTGACAAGAAAAGTCCA
* * * * * *
5210625 TTTCTTGTCACTCTTGCCTTCAAAAGCGTTATTACTCGCTTTAAATGGTTTTATAAGCTCATTAT
65 TTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATTAT
* * * *
5210690 TGATTTTGAGTTGAATTGTTTTACATTTTTTGTGAAAATAGA
130 TGATTTTAAGTTGAATT-TTTTACATTTTTTGTTAAAACATA
* ** * * *
5210732 TTATAATTGAATGTTTGCCTCTGGAAATATGAAGCGAAAGCCATCGATTGGCAAGAAAAGTCTAT
1 TTATAATTGAATGTTTGCCTCAGGAAACGTGAAGCGAAAGCCATCCATTGACAAGAAAAGTCCAT
* * *
5210797 TTATAGTCACTCATACCTTCGAAAGCCTTATTACTCGCTTTGAATGGTTTTATAATCTGATTATT
66 TTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATTATT
* * * *
5210862 GATTTTAAGCTGAATGTTTTAACATTTTTCGTTAAAA-TTGA
131 GATTTTAAGTTGAAT-TTTTTACATTTTTTGTTAAAACAT-A
* * * *
5210903 TTTTAATTGAATGTTTGCCTCAAGAAACATGAAGCGAAAGCCATCCATTGATAAGAAAAGTCCAT
1 TTATAATTGAATGTTTGCCTCAGGAAACGTGAAGCGAAAGCCATCCATTGACAAGAAAAGTCCAT
* * * * *
5210968 TTATAGTCACTCATGCCTTCGTAAGCCTTATTATTCGATTTAAATGATTTTATAATCTCGTTATT
66 TTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATTATT
5211033 GATTTTAAGTTGAATTTTCTTACATTTTTTGTTAAGAA-AGT-
131 GATTTTAAGTTGAATTTT-TTACATTTTTTGTTAA-AACA-TA
* * *
5211074 TTATAATTAAATGTTTGCCTCAAGAAACATGAAGCGAAAGCCATCCATTGACAAGAAAAGTCCAT
1 TTATAATTGAATGTTTGCCTCAGGAAACGTGAAGCGAAAGCCATCCATTGACAAGAAAAGTCCAT
* * * *
5211139 TTGTAGCCACTCATGTCTTCGAAAGCCTTATTACTCGCTTTAAATGATTTTATAATCTCATTATT
66 TTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATTATT
* * *
5211204 GATTTCAAGTTGAATTTTCTTACATTTTTGGTTAAAAAAGT-
131 GATTTTAAGTTGAATTTT-TTACATTTTTTGTTAAAACA-TA
* * * * ** * * *
5211245 TTATAAATAAATGTTTGTCTCAAGAAACGTGAAGTAAAAGCCATTCATTGAGAAGAAAAGTCCGT
1 TTATAATTGAATGTTTGCCTCAGGAAACGTGAAGCGAAAGCCATCCATTGACAAGAAAAGTCCAT
* * * *
5211310 TTATAGTAACTCATGCCTTCGAAAACCTTATTACTTGCTTTAAATGGTTTTAAAATCTCATTATT
66 TTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATTATT
* * * * * *
5211375 GATTTTAAGTTGAATTATCTTATATTATTAGTTGAAATATA
131 GATTTTAAGTTGAATT-TTTTACATTTTTTGTTAAAACATA
* * *
5211416 TTATAATTGAATGTTTGCTTC-GAGAAACGTGAAGCGAAAACCATCCAATGGA-AAGAAAAGTCC
1 TTATAATTGAATGTTTGCCTCAG-GAAACGTGAAGCGAAAGCCATCC-ATTGACAAGAAAAGTCC
* * * * *
5211479 ATTAATAGTCACCCAAGCCTTCGAAAGCCTTATTAGTTGCTTTAAATGGTTTTATAATCTCATTA
64 ATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATTA
* *
5211544 TTGATTTTAAGTTTAATTTTTTTACATTTTTTGTTAGAACATA
129 TTGATTTTAAGTTGAA-TTTTTTACATTTTTTGTTAAAACATA
* * *
5211587 TCATAATTGAATGCTTACCTCAGGAAACGTGA
1 TTATAATTGAATGTTTGCCTCAGGAAACGTGA
5211619 GGCTAAATGT
Statistics
Matches: 1631, Mismatches: 250, Indels: 63
0.84 0.13 0.03
Matches are distributed among these distances:
169 8 0.00
170 131 0.08
171 1464 0.90
172 27 0.02
173 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.38
Consensus pattern (170 bp):
TTATAATTGAATGTTTGCCTCAGGAAACGTGAAGCGAAAGCCATCCATTGACAAGAAAAGTCCAT
TTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATTATT
GATTTTAAGTTGAATTTTTTACATTTTTTGTTAAAACATA
Found at i:5210465 original size:513 final size:512
Alignment explanation
Indices: 5209492--5211618 Score: 2672
Period size: 513 Copynumber: 4.1 Consensus size: 512
5209482 TTACATCATA
* * * * * * *
5209492 ATTGATTTT-AAGTTAATTTTTTTTACATTTTCGATCAAGAA-AGTTTATAATTAAATGTTTGCC
1 ATTGATTTTAAACTAAATTTTTTTT-CATTTTTGGTTAA-AACAGATTATAATTGAATGTTTGCC
* * *
5209555 TCTAGAAACGTGAAGCGAAAGGCATTGATTGACAAGAAAAGTCCATTTATAGTCACTCATG-CTT
64 TCGAGAAACGTGAAGCGAAAGCCATTGATTGACAAGAAAAGTCCATTTCTAGTCACTCATGCCTT
* * * * * * * *
5209619 ACGAAAGCCTTATTAC-CTGCATTAAATGGTTTTATTATCTCATTATTGATTTTTAATTTAGTTT
129 -CAAAAGCCTTATTACTC-GCTTTAAATGGTTTTATAAGCTCATTATTGATTTTGAGTTGAATTT
* * * *
5209683 TCTTAC--TTTTCGATTAAAATATATTATAATTGAATGTTTGCCTC-GAGAAACGTGAAGCGAAA
192 TCTTACATTTTTTG-TGAAAATAGATTATAATTGAATGTTTGCCTCTG-GAAACATGAAGCGAAA
* * ** * * * * *
5209745 GCCATCCAATGAAAAGAAAAGTCCATTAATAGTCACCCA-AGCCTTCAAAAGCGTTATTACTGGC
255 GCCATCGATTGGCAAGAAAAGTCCATTTATAGTCACTCATA-CCTTCGAAAGCCTTATTACTCGC
* * * * *
5209809 TTTAAATGGATTTATAATCTCATTATTGATTTTAAGTTTAATTTTTTAACATTTTTTGTTAAAAC
319 TTTAAATGGTTTTATAATCTCATTATTGATTTTAAGCTGAATGTTTTAACATTTTTCGTTAAAA-
* * * * * * * ** * ** *
5209874 ATATCATAATTGAATGCTTACCTCAGGAAACGTGAGGTTAAAACCCTCTGTTGATAGGAAAAGTC
383 TTATTATAATTGAATGTTTGCCTCAAGAAACATGAAGCGAAAACCATCCATTGATAAGAAAAGTC
* *
5209939 CATTTACAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTCAAATGGTTTTATAATTTGATT
448 CATTTATAGTCACTCATGCCTTCGAAAGCCTTATTATTCGCTTCAAATGGTTTTATAATTTGATT
5210004 ATTGATTTTAAACTAAATTTTTTTTCATTTTTGGTTAAAACAGATTATAATTGAATGTTTGCCTC
1 ATTGATTTTAAACTAAATTTTTTTTCATTTTTGGTTAAAACAGATTATAATTGAATGTTTGCCTC
* * *
5210069 GAGAAATGTGAAGCGAAAGCCATTGATTGACAAGAAAAGTCCATTTCTTGTCACTCTTGCCTTCA
66 GAGAAACGTGAAGCGAAAGCCATTGATTGACAAGAAAAGTCCATTTCTAGTCACTCATGCCTTCA
*
5210134 AAAGCGTTATTACTCGCTTTAAATGGTTTTATAAGCTCATTATTGATTTTGAGTTGAATTGTT-T
131 AAAGCCTTATTACTCGCTTTAAATGGTTTTATAAGCTCATTATTGATTTTGAGTTGAATT-TTCT
*
5210198 TACATTTTTTGTGAAAATAGATTATAATTGAATGTTTGCCTCTGGAAATATGAAGCGAAAGCCAT
195 TACATTTTTTGTGAAAATAGATTATAATTGAATGTTTGCCTCTGGAAACATGAAGCGAAAGCCAT
* *
5210263 CGATTGGCAAGAAAAGTCTATTTATAGTCACTCATACCTTCGAAAGCCTTATTACTCGCTTTGAA
260 CGATTGGCAAGAAAAGTCCATTTATAGTCACTCATACCTTCGAAAGCCTTATTACTCGCTTTAAA
* *
5210328 TGGTTTTATAATCTGATTATTGATTTTAAGCTGAATGTTTTAACATTTTTCGTTAAAATTGATTT
325 TGGTTTTATAATCTCATTATTGATTTTAAGCTGAATGTTTTAACATTTTTCGTTAAAATT-ATTA
*
5210393 TAATTGAATGTTTGCCTCAAGAAACATGAAGCGAAAGCCATCCATTGATAAGAAAAGTCCATTTA
389 TAATTGAATGTTTGCCTCAAGAAACATGAAGCGAAAACCATCCATTGATAAGAAAAGTCCATTTA
5210458 TAGTCACTCATGCCTTCGAAAGCCTTATTATTCGCTTCAAATGGTTTTATAATTTGATT
454 TAGTCACTCATGCCTTCGAAAGCCTTATTATTCGCTTCAAATGGTTTTATAATTTGATT
5210517 ATTGATTTTAAACTAAATTTTTTTTCATTTTTGGTTAAAACAGATTATAATTGAATGTTTGCCTC
1 ATTGATTTTAAACTAAATTTTTTTTCATTTTTGGTTAAAACAGATTATAATTGAATGTTTGCCTC
* * *
5210582 GAGAAATGTGAAGCGAAAGCCATTGATTGACAAGAAAAGTCCATTTCTTGTCACTCTTGCCTTCA
66 GAGAAACGTGAAGCGAAAGCCATTGATTGACAAGAAAAGTCCATTTCTAGTCACTCATGCCTTCA
*
5210647 AAAGCGTTATTACTCGCTTTAAATGGTTTTATAAGCTCATTATTGATTTTGAGTTGAATTGTT-T
131 AAAGCCTTATTACTCGCTTTAAATGGTTTTATAAGCTCATTATTGATTTTGAGTTGAATT-TTCT
*
5210711 TACATTTTTTGTGAAAATAGATTATAATTGAATGTTTGCCTCTGGAAATATGAAGCGAAAGCCAT
195 TACATTTTTTGTGAAAATAGATTATAATTGAATGTTTGCCTCTGGAAACATGAAGCGAAAGCCAT
* *
5210776 CGATTGGCAAGAAAAGTCTATTTATAGTCACTCATACCTTCGAAAGCCTTATTACTCGCTTTGAA
260 CGATTGGCAAGAAAAGTCCATTTATAGTCACTCATACCTTCGAAAGCCTTATTACTCGCTTTAAA
* *
5210841 TGGTTTTATAATCTGATTATTGATTTTAAGCTGAATGTTTTAACATTTTTCGTTAAAATTGATTT
325 TGGTTTTATAATCTCATTATTGATTTTAAGCTGAATGTTTTAACATTTTTCGTTAAAATT-ATTA
*
5210906 TAATTGAATGTTTGCCTCAAGAAACATGAAGCGAAAGCCATCCATTGATAAGAAAAGTCCATTTA
389 TAATTGAATGTTTGCCTCAAGAAACATGAAGCGAAAACCATCCATTGATAAGAAAAGTCCATTTA
* * * * *
5210971 TAGTCACTCATGCCTTCGTAAGCCTTATTATTCGATTTAAATGATTTTATAATCTCG-TT
454 TAGTCACTCATGCCTTCGAAAGCCTTATTATTCGCTTCAAATGGTTTTATAAT-TTGATT
** * * * * * *
5211030 ATTGATTTTAAGTTGAATTTTCTTACATTTTTTGTTAAGAA-AGTTTATAATTAAATGTTTGCCT
1 ATTGATTTTAAACTAAATTTTTTTTCATTTTTGGTTAA-AACAGATTATAATTGAATGTTTGCCT
* * ** * * *
5211094 CAAGAAACATGAAGCGAAAGCCATCCATTGACAAGAAAAGTCCATTTGTAGCCACTCATGTCTTC
65 CGAGAAACGTGAAGCGAAAGCCATTGATTGACAAGAAAAGTCCATTTCTAGTCACTCATGCCTTC
* * * **
5211159 GAAAGCCTTATTACTCGCTTTAAATGATTTTATAATCTCATTATTGATTTCAAGTTGAATTTTCT
130 AAAAGCCTTATTACTCGCTTTAAATGGTTTTATAAGCTCATTATTGATTTTGAGTTGAATTTTCT
* * * * * * * ** * **
5211224 TACATTTTTGGTTAAAAAAGTTTATAAATAAATGTTTGTCTCAAGAAACGTGAAGTAAAAGCCAT
195 TACATTTTTTGTGAAAATAGATTATAATTGAATGTTTGCCTCTGGAAACATGAAGCGAAAGCCA-
* * * * *
5211289 TC-ATTGAG-AAGAAAAGTCCGTTTATAGTAACTCATGCCTTCGAAAACCTTATTACTTGCTTTA
259 TCGATTG-GCAAGAAAAGTCCATTTATAGTCACTCATACCTTCGAAAGCCTTATTACTCGCTTTA
* * * * * *
5211352 AATGGTTTTAAAATCTCATTATTGATTTTAAGTTGAAT-TATCTT-ATATTATTAGTTGAAATAT
323 AATGGTTTTATAATCTCATTATTGATTTTAAGCTGAATGT-T-TTAACATTTTTCGTTAAAAT-T
* * * *
5211415 ATTATAATTGAATGTTTGCTTCGAGAAACGTGAAGCGAAAACCATCCAATGGA-AAGAAAAGTCC
385 ATTATAATTGAATGTTTGCCTCAAGAAACATGAAGCGAAAACCATCC-ATTGATAAGAAAAGTCC
* * * * * *
5211479 ATTAATAGTCACCCAAGCCTTCGAAAGCCTTATTAGTT-GCTTTAAATGGTTTTATAATCTCATT
449 ATTTATAGTCACTCATGCCTTCGAAAGCCTTATTA-TTCGCTTCAAATGGTTTTATAATTTGATT
** * * * * * * * *
5211543 ATTGATTTTAAGTTTAATTTTTTTACATTTTTTGTTAGAACATATCATAATTGAATGCTTACCTC
1 ATTGATTTTAAACTAAATTTTTTTTCATTTTTGGTTAAAACAGATTATAATTGAATGTTTGCCTC
5211608 -AGGAAACGTGA
66 GA-GAAACGTGA
5211619 GGCTAAATGT
Statistics
Matches: 1450, Mismatches: 142, Indels: 45
0.89 0.09 0.03
Matches are distributed among these distances:
511 2 0.00
512 156 0.11
513 1269 0.88
514 23 0.02
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (512 bp):
ATTGATTTTAAACTAAATTTTTTTTCATTTTTGGTTAAAACAGATTATAATTGAATGTTTGCCTC
GAGAAACGTGAAGCGAAAGCCATTGATTGACAAGAAAAGTCCATTTCTAGTCACTCATGCCTTCA
AAAGCCTTATTACTCGCTTTAAATGGTTTTATAAGCTCATTATTGATTTTGAGTTGAATTTTCTT
ACATTTTTTGTGAAAATAGATTATAATTGAATGTTTGCCTCTGGAAACATGAAGCGAAAGCCATC
GATTGGCAAGAAAAGTCCATTTATAGTCACTCATACCTTCGAAAGCCTTATTACTCGCTTTAAAT
GGTTTTATAATCTCATTATTGATTTTAAGCTGAATGTTTTAACATTTTTCGTTAAAATTATTATA
ATTGAATGTTTGCCTCAAGAAACATGAAGCGAAAACCATCCATTGATAAGAAAAGTCCATTTATA
GTCACTCATGCCTTCGAAAGCCTTATTATTCGCTTCAAATGGTTTTATAATTTGATT
Found at i:5212450 original size:20 final size:20
Alignment explanation
Indices: 5212393--5212455 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
5212383 TATATACCCA
*
5212393 TCATCATCATC-TCACCAAC
1 TCATCATCATCATCACCAGC
* *
5212412 CCATTATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
5212432 TCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
5212452 TCAT
1 TCAT
5212456 GCGCACTTCC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
19 9 0.24
20 29 0.76
ACGTcount: A:0.30, C:0.40, G:0.03, T:0.27
Consensus pattern (20 bp):
TCATCATCATCATCACCAGC
Found at i:5212502 original size:43 final size:43
Alignment explanation
Indices: 5212441--5212602 Score: 200
Period size: 43 Copynumber: 3.8 Consensus size: 43
5212431 CTCATCATCA
* * * ** **
5212441 TCATCACCAGCTCATGCGCACTTCCTACTCGCACATGGCTGGG
1 TCATCACCAGGTTATGCGCACTCCCTACTCGCACATAACCAGG
*
5212484 TCATCACCAGGTTATGCGCACTCCCTACTCGCACATAACCAGA
1 TCATCACCAGGTTATGCGCACTCCCTACTCGCACATAACCAGG
* *
5212527 TCATCACCGGGTTATGTGCACTCCCTACTCGCACATAACCAGG
1 TCATCACCAGGTTATGCGCACTCCCTACTCGCACATAACCAGG
**
5212570 TCATC-CTTGGCTTATGCGCACTCCCTACTCGCA
1 TCATCACCAGG-TTATGCGCACTCCCTACTCGCA
5212603 TATAGCCGAG
Statistics
Matches: 104, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
42 3 0.03
43 101 0.97
ACGTcount: A:0.22, C:0.37, G:0.17, T:0.24
Consensus pattern (43 bp):
TCATCACCAGGTTATGCGCACTCCCTACTCGCACATAACCAGG
Found at i:5228589 original size:171 final size:171
Alignment explanation
Indices: 5228291--5229603 Score: 1397
Period size: 171 Copynumber: 7.7 Consensus size: 171
5228281 NNNNNNNNNN
* * * *
5228291 TAATTAAATGTTTGCCTCTAGAAACGTGAAGCAAAAGCCATCGATTGACAAGAAAAGTCCATTTA
1 TAATTGAATGTTTGCCTCTAGAAAAGTGAAGCGAAAGCCATCCATTGACAAGAAAAGTCCATTTA
* * * * *
5228356 TTGTCACTCATGCCTTCAAAAGACTTATTACTAGCATTAAATGGTTTTATAATCTAATTATTGAT
66 TAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCATTAAATGGTTTTATAATCTGATTATTGAT
* *
5228421 TTTAAGTTGAATTGTTTTACATTTTTAGTTAAAACAGAGTA
131 TTTAAGTTGAATTTTTTTACATTTTTAGTTAAAACAGATTA
* *
5228462 TAATTGAATGTTTGCCTCGAGAAAAGTGAAGCGAAAGCCATCCATTGACAAGAATAGTCCATTTA
1 TAATTGAATGTTTGCCTCTAGAAAAGTGAAGCGAAAGCCATCCATTGACAAGAAAAGTCCATTTA
* * * *
5228527 TAGTCATTCATGCCTTCGAAAGCCTTATTCCTCGCTTTAAATGGTTTTATAACCTGATTATTGAT
66 TAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCATTAAATGGTTTTATAATCTGATTATTGAT
* * *
5228592 TTTAAGCTGAATTTTTTTAC-TTTTTTGATTAAAACAAATTA
131 TTTAAGTTGAATTTTTTTACATTTTTAG-TTAAAACAGATTA
* * * * * *
5228633 TAATTGAATGTTTTCCTCGAGAAAAGTGAGGTGAAAGCCATCCATTGATAAGAATAGTCCATTTA
1 TAATTGAATGTTTGCCTCTAGAAAAGTGAAGCGAAAGCCATCCATTGACAAGAAAAGTCCATTTA
* * *
5228698 TAGTCACACATGCCTTCGAAAGCCTTATTACTTGCATTAAATGGTTTTATAATCTAATTATTGAT
66 TAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCATTAAATGGTTTTATAATCTGATTATTGAT
* * *
5228763 TTTAAGGTGAATTATTTTT-CATTGTTT-GTTAAAATAGATTG
131 TTTAAGTTGAATT-TTTTTACATT-TTTAGTTAAAACAGATTA
** * * * * * * * ** *
5228804 TAATTGAATGTTTATCTCAAGAAACGTG-AGTCTAAAGCTC-TTCGTTGATAGGAAAAGTGAATG
1 TAATTGAATGTTTGCCTCTAGAAAAGTGAAG-CGAAAGC-CATCCATTGACAAGAAAAGTCCATT
* * * * * *
5228867 TATAGTCTA-TCATGCTTTCAAAAACAC-TATTAGTCAC-TTAAAATGGTTTTATAATCTCG-TA
64 TATAGTC-ACTCATGCCTTCGAAAGC-CTTATTACTCGCATT-AAATGGTTTTATAATCT-GATT
* *
5228928 ATTGATTTTAAGTTGAATTTTTTTACATTTTCAAG-TAAGAA-AGGTTA
125 ATTGATTTTAAGTTGAATTTTTTTACATTTT-TAGTTAA-AACAGATTA
* * *
5228975 TAATTAAATGTTTGCCTCTAGAAACGTGAAGCGAAAGCCATCGATTGACAAGAAAAGTCCATTTA
1 TAATTGAATGTTTGCCTCTAGAAAAGTGAAGCGAAAGCCATCCATTGACAAGAAAAGTCCATTTA
* * *
5229040 TTGTCACTCATGCCTTCGAAAGCCTTATTACTCGCATGAAATAGTTTTATAATCTGATTATTGAT
66 TAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCATTAAATGGTTTTATAATCTGATTATTGAT
* * *
5229105 TTTGAGTTGAATTTTTTTTACATTTTTGGTTAAAACAGAGTA
131 TTTAAGTTGAA-TTTTTTTACATTTTTAGTTAAAACAGATTA
* * *
5229147 TAATTGAATATTTGCCTCTAGAAAAGTGAAGCGAAAGCCATCCATTGACAAGAATAGTCTATTTA
1 TAATTGAATGTTTGCCTCTAGAAAAGTGAAGCGAAAGCCATCCATTGACAAGAAAAGTCCATTTA
* * * *
5229212 TAGTCGCTCATGCCTTCGAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATTATTGAT
66 TAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCATTAAATGGTTTTATAATCTGATTATTGAT
* *
5229277 TGTAAGTTGAATTTTTTTACATTCTTTA-TTAAAACAAATTA
131 TTTAAGTTGAATTTTTTTACATT-TTTAGTTAAAACAGATTA
* * * * * * * * * * * * *
5229318 TAATTGAATATTTACGTTTGGAAATGT-AAGGCTAAAACTC-TTCGTTGAC-AGGATAGCTCTAT
1 TAATTGAATGTTTGCCTCTAGAAAAGTGAA-GCGAAAGC-CATCCATTGACAAGAAAAG-TCCAT
* * * * * * *
5229380 TTATGGTCACTCATACCTTC-AGAAGTCTTATTACTC-CCTTAAAGTAGTTTTATAATCTTATAA
63 TTATAGTCACTCATGCCTTCGA-AAGCCTTATTACTCGCATTAAA-TGGTTTTATAATCTGATTA
* * *
5229443 TTAATTTTAAGTTGAATTTTTTTACA-TTTTCGATTAAGAA-AGTTTA
126 TTGATTTTAAGTTGAATTTTTTTACATTTTTAG-TTAA-AACAGATTA
* * * * *
5229489 TAATTAAATGTTTGCCTCTACAAATGTGAAGCGAAAGGCATCGATTGACAAGAAAAGTCCATTTA
1 TAATTGAATGTTTGCCTCTAGAAAAGTGAAGCGAAAGCCATCCATTGACAAGAAAAGTCCATTTA
* *
5229554 TAGGCACTCATGCCTACGAAAGCCTTATTAC-CTGCATTAAATGGTTTTAT
66 TAGTCACTCATGCCTTCGAAAGCCTTATTACTC-GCATTAAATGGTTTTAT
5229604 TGTCACGACC
Statistics
Matches: 951, Mismatches: 153, Indels: 76
0.81 0.13 0.06
Matches are distributed among these distances:
169 3 0.00
170 38 0.04
171 723 0.76
172 184 0.19
173 3 0.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (171 bp):
TAATTGAATGTTTGCCTCTAGAAAAGTGAAGCGAAAGCCATCCATTGACAAGAAAAGTCCATTTA
TAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCATTAAATGGTTTTATAATCTGATTATTGAT
TTTAAGTTGAATTTTTTTACATTTTTAGTTAAAACAGATTA
Found at i:5229436 original size:514 final size:511
Alignment explanation
Indices: 5228335--5229603 Score: 1627
Period size: 514 Copynumber: 2.5 Consensus size: 511
5228325 AAGCCATCGA
* * * * *
5228335 TTGACAAGAAAAGTCCATTTATTGTCACTCATGCCTTCAAAAGACTTATTACTAGCATTAAATGG
1 TTGACAGGAAAAGTCAATTTATAGTCACTCATGCCTTC-AAAGACTTATTACT-CCCTTAAATGG
* * *
5228400 TTTTATAATCTAATTATTGATTTTAAGTTGAATTGTTTTACATTTT-TAGTTAA-AACAGAG-TA
64 TTTTATAATCTAATAATTGATTTTAAGTTGAATTTTTTTACATTTTCAAG-TAAGAA-AG-GTTA
* * * *
5228462 TAATTGAATGTTTGCCTCGAGAAAAGTGAAGCGAAAGCCATCCATTGACAAGAATAGTCCATTTA
126 TAATTAAATGTTTGCCTCTAGAAAAGTGAAGCGAAAGCCATCGATTGACAAGAAAAGTCCATTTA
* * *
5228527 TAGTCATTCATGCCTTCGAAAGCCTTATTCCTCGCTTTAAATGGTTTTATAACCTGATTATTGAT
191 TAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCATTAAATGGTTTTATAACCTGATTATTGAT
* * * *
5228592 TTTAAGCTGAATTTTTTTACTTTTTTGATTAAAACAAATTATAATTGAATGTTTTCCTCGAGAAA
256 TTTAAGCTGAATTTTTTTACATTTTTGATTAAAACAAAGTATAATTGAATATTTGCCTCGAGAAA
* * *
5228657 AGTGAGGTGAAAGCCATCCATTGATAAGAATAGTCCATTTATAGTCACACATGCCTTCGAAAGCC
321 AGTGAAGCGAAAGCCATCCATTGACAAGAATAGTCCATTTATAGTCACACATGCCTTCGAAAGCC
** * *
5228722 TTATTACTTGCATTAAATGGTTTTATAATCTAATTATTGATTTTAAGGTGAATTATTTTTCATTG
386 TTATTACTCACATTAAATGGTTTTATAATCTAATTATTGATTGTAAGGTGAATTATTTTTCATTC
* * * * * * * *
5228787 TTTGTTAAAATAGATTGTAATTGAATGTTTATCTCAAGAAACGTGAGTCTAAAGCTCTTCG
451 TTTATTAAAACAAATTATAATTGAATATTTATCTCAAGAAACGTAAGGCTAAAACTCTTCG
* * * * * * * *
5228848 TTGATAGGAAAAGTGAATGTATAGTCTA-TCATGCTTTCAAAAACACTATTAGTCACTTAAAATG
1 TTGACAGGAAAAGTCAATTTATAGTC-ACTCATGCCTTCAAAGAC-TTATTACTCCCTT-AAATG
**
5228912 GTTTTATAATCTCGTAATTGATTTTAAGTTGAATTTTTTTACATTTTCAAGTAAGAAAGGTTATA
63 GTTTTATAATCTAATAATTGATTTTAAGTTGAATTTTTTTACATTTTCAAGTAAGAAAGGTTATA
* *
5228977 ATTAAATGTTTGCCTCTAGAAACGTGAAGCGAAAGCCATCGATTGACAAGAAAAGTCCATTTATT
128 ATTAAATGTTTGCCTCTAGAAAAGTGAAGCGAAAGCCATCGATTGACAAGAAAAGTCCATTTATA
* * *
5229042 GTCACTCATGCCTTCGAAAGCCTTATTACTCGCATGAAATAGTTTTATAATCTGATTATTGATTT
193 GTCACTCATGCCTTCGAAAGCCTTATTACTCGCATTAAATGGTTTTATAACCTGATTATTGATTT
* * * * *
5229107 TGAGTTGAATTTTTTTTACATTTTTGGTTAAAACAGAGTATAATTGAATATTTGCCTCTAGAAAA
258 TAAGCTGAA-TTTTTTTACATTTTTGATTAAAACAAAGTATAATTGAATATTTGCCTCGAGAAAA
* * *
5229172 GTGAAGCGAAAGCCATCCATTGACAAGAATAGTCTATTTATAGTCGCTCATGCCTTCGAAAGCCT
322 GTGAAGCGAAAGCCATCCATTGACAAGAATAGTCCATTTATAGTCACACATGCCTTCGAAAGCCT
* * *
5229237 TATTACTCACTTTAAATGGTTTTATAATCTCATTATTGATTGTAAGTTGAATT-TTTTTACATTC
387 TATTACTCACATTAAATGGTTTTATAATCTAATTATTGATTGTAAGGTGAATTATTTTT-CATTC
*** *
5229301 TTTATTAAAACAAATTATAATTGAATATTTA-CGTTTGGAAATGTAAGGCTAAAACTCTTCG
451 TTTATTAAAACAAATTATAATTGAATATTTATC-TCAAGAAACGTAAGGCTAAAACTCTTCG
* * * * * *
5229362 TTGACAGG-ATAGCTCTATTTATGGTCACTCATACCTTCAGAAGTCTTATTACTCCCTTAAAGTA
1 TTGACAGGAAAAG-TCAATTTATAGTCACTCATGCCTTCA-AAGACTTATTACTCCCTTAAA-TG
* * * * *
5229426 GTTTTATAATCTTATAATTAATTTTAAGTTGAATTTTTTTACATTTTCGATTAAGAAAGTTTATA
63 GTTTTATAATCTAATAATTGATTTTAAGTTGAATTTTTTTACATTTTCAAGTAAGAAAGGTTATA
* * *
5229491 ATTAAATGTTTGCCTCTACAAATGTGAAGCGAAAGGCATCGATTGACAAGAAAAGTCCATTTATA
128 ATTAAATGTTTGCCTCTAGAAAAGTGAAGCGAAAGCCATCGATTGACAAGAAAAGTCCATTTATA
* *
5229556 GGCACTCATGCCTACGAAAGCCTTATTAC-CTGCATTAAATGGTTTTAT
193 GTCACTCATGCCTTCGAAAGCCTTATTACTC-GCATTAAATGGTTTTAT
5229604 TGTCACGACC
Statistics
Matches: 650, Mismatches: 92, Indels: 27
0.85 0.12 0.04
Matches are distributed among these distances:
512 8 0.01
513 231 0.36
514 408 0.63
515 3 0.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (511 bp):
TTGACAGGAAAAGTCAATTTATAGTCACTCATGCCTTCAAAGACTTATTACTCCCTTAAATGGTT
TTATAATCTAATAATTGATTTTAAGTTGAATTTTTTTACATTTTCAAGTAAGAAAGGTTATAATT
AAATGTTTGCCTCTAGAAAAGTGAAGCGAAAGCCATCGATTGACAAGAAAAGTCCATTTATAGTC
ACTCATGCCTTCGAAAGCCTTATTACTCGCATTAAATGGTTTTATAACCTGATTATTGATTTTAA
GCTGAATTTTTTTACATTTTTGATTAAAACAAAGTATAATTGAATATTTGCCTCGAGAAAAGTGA
AGCGAAAGCCATCCATTGACAAGAATAGTCCATTTATAGTCACACATGCCTTCGAAAGCCTTATT
ACTCACATTAAATGGTTTTATAATCTAATTATTGATTGTAAGGTGAATTATTTTTCATTCTTTAT
TAAAACAAATTATAATTGAATATTTATCTCAAGAAACGTAAGGCTAAAACTCTTCG
Found at i:5232631 original size:171 final size:171
Alignment explanation
Indices: 5232317--5233042 Score: 881
Period size: 171 Copynumber: 4.2 Consensus size: 171
5232307 GGGTTTTACA
* * * * * * *
5232317 TTTATTATCTCATTATTGATTTTAAGTTTAATTTTCTTACATTTTCGATTAAAATAAATTATAAT
1 TTTATAATCTAATTATTGATTTTAAGTTTAATTTTTTTACATTTTTGCTTAAAACAGATTATAAT
* ** * * *
5232382 TGAATGTTTACCTCGAGAAACGTGAAGCGAAAACCATCCAATGGA-AAGAAAAATCCATTAATAG
66 TGAATGTTTACCTCAAGAAACGTGAAGCGAAAACCAT-TGATTGACAAGAAAACTCCATTTATAG
* * *
5232446 TCACCCAAGCCTTCGAAAGCCTTATTACTTGCTTTAAAA-GGT
130 TCACTCATGCCTTCGAAAGCCTTATTACTCG-TTTAAAATGGT
* *
5232488 TTTATAATCTCATTATTGATTTTAAGTTTAATTTTTTTACATTTTCT-CTTAAAACAGATCATAA
1 TTTATAATCTAATTATTGATTTTAAGTTTAATTTTTTTACATTTT-TGCTTAAAACAGATTATAA
* ** * * * * * *
5232552 TTGAATGCTTACCTCAAGAAACGTGGGGCTAAAACCTTTTG-TTGATAGGAAAAGTCCATTTACA
65 TTGAATGTTTACCTCAAGAAACGTGAAGCGAAAACC-ATTGATTGACAAGAAAACTCCATTTATA
* * ** * *
5232616 ATCACTCATGCCTTCGAAAACCTTATTACTCACTTCAAATAGT
129 GTCACTCATGCCTTCGAAAGCCTTATTACTCGTTTAAAATGGT
* * * **
5232659 TTTATAATTTGATTATTGCTTTTAA-ACTAATTTTTTTTACATTTTTGGC-TAAAACAGATTATA
1 TTTATAATCTAATTATTGATTTTAAGTTTAA-TTTTTTTACATTTTT-GCTTAAAACAGATTATA
* * *
5232722 ATTGAATGTTTACCTCGAGAAATGTGAAGCGAAAGCCATTGATTGACAAGAAAACTCCATTTATA
64 ATTGAATGTTTACCTCAAGAAACGTGAAGCGAAAACCATTGATTGACAAGAAAACTCCATTTATA
*
5232787 GTCACTCATGCCTTCGAAAGCCTTATTACCCGTTTAAAATGGT
129 GTCACTCATGCCTTCGAAAGCCTTATTACTCGTTTAAAATGGT
* * * * *
5232830 TTTATAATCTAATTATTGATTTTATGTTGAATTTTTTAATATTTTTGGTTAAAACAGATTATAAT
1 TTTATAATCTAATTATTGATTTTAAGTTTAATTTTTTTACATTTTTGCTTAAAACAGATTATAAT
*
5232895 TGAATGTTTACCTCGAA-AAACGTGAAGCGAAAGCCATTGATTGACAAGAAAACTCCATTTATAG
66 TGAATGTTTACCTC-AAGAAACGTGAAGCGAAAACCATTGATTGACAAGAAAACTCCATTTATAG
5232959 TCACTCATGCCTTCGAAAGCCTTATTACTCGTTTAAAATGGT
130 TCACTCATGCCTTCGAAAGCCTTATTACTCGTTTAAAATGGT
* * *
5233001 TTTATAATCTAATTATTGATTTTATGTTGAATTTTCTTACAT
1 TTTATAATCTAATTATTGATTTTAAGTTTAATTTTTTTACAT
5233043 NNNNNNNNNN
Statistics
Matches: 474, Mismatches: 70, Indels: 22
0.84 0.12 0.04
Matches are distributed among these distances:
170 16 0.03
171 453 0.96
172 5 0.01
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.39
Consensus pattern (171 bp):
TTTATAATCTAATTATTGATTTTAAGTTTAATTTTTTTACATTTTTGCTTAAAACAGATTATAAT
TGAATGTTTACCTCAAGAAACGTGAAGCGAAAACCATTGATTGACAAGAAAACTCCATTTATAGT
CACTCATGCCTTCGAAAGCCTTATTACTCGTTTAAAATGGT
Found at i:5239641 original size:60 final size:60
Alignment explanation
Indices: 5239526--5239674 Score: 217
Period size: 60 Copynumber: 2.5 Consensus size: 60
5239516 CGAAATGCAT
* *
5239526 TCTCGCTACAGCGAGAAACTTTCTGTTTTCTGGGTTGCAATTTCGCTGCAACGAGATTGAA
1 TCTCGCTGCAGCGAGAAACTTTCTG-TTTCTGGGTTGAAATTTCGCTGCAACGAGATTGAA
* * * **
5239587 TCTCGCTGCAGTGAGAAACATTCTGTTTCTGGGTTGAAATTTTGCTGCTGCGAGATTGAA
1 TCTCGCTGCAGCGAGAAACTTTCTGTTTCTGGGTTGAAATTTCGCTGCAACGAGATTGAA
*
5239647 TCTCGCTGCAGCGAAAAACTTTCTGTTT
1 TCTCGCTGCAGCGAGAAACTTTCTGTTT
5239675 TGGTCTCCTA
Statistics
Matches: 78, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
60 56 0.72
61 22 0.28
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.34
Consensus pattern (60 bp):
TCTCGCTGCAGCGAGAAACTTTCTGTTTCTGGGTTGAAATTTCGCTGCAACGAGATTGAA
Found at i:5243848 original size:42 final size:42
Alignment explanation
Indices: 5243789--5243930 Score: 203
Period size: 42 Copynumber: 3.4 Consensus size: 42
5243779 TGTTGATTTG
*
5243789 GACCCGGCTATGTGCGAGTAAGAGTGCACATAAGCCGTTGTT
1 GACCCGGCTATGTGCGAGTAAGAGTGCACATAAGCCGTTGCT
* *
5243831 GACCCAGCTATGTGCGAGTAAGAGTGCACATAAGCCGTTACT
1 GACCCGGCTATGTGCGAGTAAGAGTGCACATAAGCCGTTGCT
** **
5243873 GACCCGGCTATGTATGAGTTGGAGTGCACATAAGCCGTTGCT
1 GACCCGGCTATGTGCGAGTAAGAGTGCACATAAGCCGTTGCT
* *
5243915 GACCTGGCTATATGCG
1 GACCCGGCTATGTGCG
5243931 CATAAGCCGT
Statistics
Matches: 87, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 87 1.00
ACGTcount: A:0.24, C:0.23, G:0.30, T:0.24
Consensus pattern (42 bp):
GACCCGGCTATGTGCGAGTAAGAGTGCACATAAGCCGTTGCT
Found at i:5245012 original size:22 final size:23
Alignment explanation
Indices: 5244984--5245027 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
5244974 GGTCGAAAAC
*
5244984 TCGCTGCAGTGAGAATG-CATTT
1 TCGCTGCAGCGAGAATGACATTT
5245006 TCGCTGCAGCGAGAATGACATT
1 TCGCTGCAGCGAGAATGACATT
5245028 GTAGCTTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (23 bp):
TCGCTGCAGCGAGAATGACATTT
Found at i:5246282 original size:171 final size:170
Alignment explanation
Indices: 5245987--5249880 Score: 3812
Period size: 171 Copynumber: 22.8 Consensus size: 170
5245977 GGGTCGTGAC
* * *
5245987 AAGTCCATTTATAGTCACTAAGGCCTTCGAAAGCCTTATTACTCACTTTAAATGGTTTTATAATC
1 AAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATC
* * * * * *
5246052 TGATTATTGATTTTAAGCTAAATTTTTTTACTTTTTTTGTTAAAATAGATTACAATTGAATGTTT
66 TCATTATTGATTTTAAGTTGAATTTTTTTACTTTTTTGGTTAAAACAGATTATAATTGAATGTTT
* * * *
5246117 TCCTTGACAAAAGTGAAGCGAAAGCCATCCATTGACAAAA
131 GCCTTGAGAAACGTGAAGCGAAAGCCATCCATTGATAAAA
** * * * *
5246157 ATAGTCCATTTGCAGTCACTTATACCTTTGAAAGCCTTATTACTTGCTTTAAATGGTTTTATAAT
1 A-AGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAAT
* * * *
5246222 CTGATTATTGATTTTAAGCTGAATTTTTTTGCTTTTTTGGTTTAAACAGATTATAATTGAATGTT
65 CTCATTATTGATTTTAAGTTGAATTTTTTTACTTTTTTGGTTAAAACAGATTATAATTGAATGTT
* * *
5246287 TGCCATGAGAAAAGTGAAGCGAAAGCCATCCATTGACAAGAA
130 TGCCTTGAGAAACGTGAAGCGAAAGCCATCCATTGATAA-AA
* ** * * *
5246329 TAGTCCATTTATAGTCGTTTATGCCTTCGAAAGCCTTATTACTCACTTTAAATGGTTTTATAAGC
1 AAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATC
* * *
5246394 TCATTATTGATTTTAAGTTGAATTTTTTTACGTTCTTT-GTTAAAACAGATTATAATTGATTATT
66 TCATTATTGATTTTAAGTTGAATTTTTTTAC-TTTTTTGGTTAAAACAGATTATAATTGAATGTT
* * ** * ** * *
5246458 TACCTCTG-GAAACGTGAGGTTAAAACTTTCCGTTGACAGAAA
130 TGCCT-TGAGAAACGTGAAGCGAAAGCCATCCATTGATA-AAA
* * * * **
5246500 AAGTTCATTTATGGTCACTCATGCCTTC-AGAAGCCTTATTACTCACTTAAAATTATTTTATAAT
1 AAGTCCATTTATAGTCACTCATGCCTTCGA-AAGCCTTATTACTCGCTTTAAATGGTTTTATAAT
* * * * *
5246564 CTCATAATTGATTTTAAGTTGAATGTTTTTA-TATTTTCGGTTAAGAA-AGGTTATAATTAAATG
65 CTCATTATTGATTTTAAGTTGAATTTTTTTACT-TTTTTGGTTAA-AACAGATTATAATTGAATG
* * * * *
5246627 TTTG-CTTCTAGCAATGTGAAGCGAAAGCCATCGATTGACAAGAA
128 TTTGCCTT-GAGAAACGTGAAGCGAAAGCCATCCATTGATAA-AA
* * * * *
5246671 AAGTTCATTTATTGTTACTCATGCCTTCGAAAGCCTTATTACTCGCATTAAATAGTTTTATAATC
1 AAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATC
* * * * *
5246736 -CGATTATTGATTTTGAGTTGAATTTTTTTTCCCATTTTTGGTTAAAATAGAATATAATTGAATG
66 TC-ATTATTGATTTTAAGTTGAA-TTTTTTT-ACTTTTTTGGTTAAAACAGATTATAATTGAATG
* *
5246800 TTTGCCTTCGA-AAACGTGAAGTGAAAGCTC-TCGATTGATAAGAA
128 TTTGCCTT-GAGAAACGTGAAGCGAAAGC-CATCCATTGATAA-AA
** * * * *
5246844 ATTTCCGTTTATAGTCACTCATTCCTTCAAAAGCCTTATTAC-CTGCTTAAAATGGTTTTATAAT
1 AAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTC-GCTTTAAATGGTTTTATAAT
* * * *
5246908 CTCATAATTGATTTTAAGTTGAATTTTTTTACTTTTTTGTTTAAGAA-AGGTTATAATTGAGTGT
65 CTCATTATTGATTTTAAGTTGAATTTTTTTACTTTTTTGGTTAA-AACAGATTATAATTGAATGT
* * * * * *
5246972 TCGCCTCGA-AAAGCATGAAGGGAAAGCCATCCATTAACTAGAA
129 TTGCCTTGAGAAA-CGTGAAGCGAAAGCCATCCATTGA-TAAAA
* * * *
5247015 AAGTCCATTTATAGTCGCTCATGCCTTCGAAAGGCTTATTACTCGTTTTAAATAGTTTTATAATC
1 AAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATC
* ** * ** * * *
5247080 TCATTATTCATTCCAAGTTGAATTTTCTTACAATTGTAGTTAAAACATATTATAATTGAATGTTT
66 TCATTATTGATTTTAAGTTGAATTTTTTTACTTTTTTGGTTAAAACAGATTATAATTGAATGTTT
* * *
5247145 GCCTTGAGAAATGTGAAGCGAAAGCCATCGATTGACAAGAA
131 GCCTTGAGAAACGTGAAGCGAAAGCCATCCATTGATAA-AA
* * * * *
5247186 AAGTTCATTTATTGTCACTCATGCCTACGAAAGCCTTATTACTTG-TATTAAATGGTTTTATTAT
1 AAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCT-TTAAATGGTTTTATAAT
* * * *
5247250 CTCATTATTGATTTTAAGTTGAATTTTCTTACATTTTCGATTAAAACAGATTATAATTGAATGTT
65 CTCATTATTGATTTTAAGTTGAATTTTTTTACTTTTTTGGTTAAAACAGATTATAATTGAATGTT
* * * * * *
5247315 TGCCTCGGGAAACGTGAAGCAAAAGCCATCCATAGGTATGAA
130 TGCCTTGAGAAACGTGAAGCGAAAGCCATCCATTGATA-AAA
*
5247357 AAGTCCATTTATAGTCACTCATGCCTTTGAAAGACC-TATTACTCGCTTTAAATGGTTTTATAAT
1 AAGTCCATTTATAGTCACTCATGCCTTCGAAAG-CCTTATTACTCGCTTTAAATGGTTTTATAAT
* * **
5247421 CTCATTATTGATTGTAAGTTGAATTTTTTTACCTTTTTT-GTTAAAACAAATTACCATTGAATGT
65 CTCATTATTGATTTTAAGTTGAATTTTTTTA-CTTTTTTGGTTAAAACAGATTATAATTGAATGT
* * * * * * * *
5247485 TTTCCTTGGGAAACGTGAGGCTAAAACCCTCCGTTGATAGGAA
129 TTGCCTTGAGAAACGTGAAGCGAAAGCCATCCATTGATA-AAA
* * * *
5247528 AAGTCCATTTATGGTCACTCATACCTTC-AGAAGCCTTATTACTTGCTTAAAATGGTTTTATAAT
1 AAGTCCATTTATAGTCACTCATGCCTTCGA-AAGCCTTATTACTCGCTTTAAATGGTTTTATAAT
* * * * *
5247592 CTCATAATTGATTTTAAGTTAAATTTTTTTAC-ATTTCGGTTAAGAAAAG-TTATAATTGAATGT
65 CTCATTATTGATTTTAAGTTGAATTTTTTTACTTTTTTGGTTAA-AACAGATTATAATTGAATGT
* * * ** * * *
5247655 TCGCCTCGAGAAACTTGGCGAGAAAGCCATCCATTAATTAGAA
129 TTGCCTTGAGAAACGTGAAGCGAAAGCCATCCATTGA-TAAAA
**
5247698 AAGTCCATTTATAGTTGCTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATC
1 AAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATC
* * ** *
5247763 TCATTATTCATTTCAAGTTGAATTTACTTA-TATTTTTAGTTAAAACAGATTATAATTGAATGTT
66 TCATTATTGATTTTAAGTTGAATTTTTTTACT-TTTTTGGTTAAAACAGATTATAATTGAATGTT
* * * * *
5247827 TGCCTCGAGAAACGTGAAGGGAAAGCTATCCATTAACAAGAA
130 TGCCTTGAGAAACGTGAAGCGAAAGCCATCCATTGATAA-AA
* * * * * *
5247869 AAATCCATTTATTGTCACTCATGCCTACGAAAGCCTTATTACTTGCATTAAATAGTTTTACT-AT
1 AAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTA-TAAT
* * * *
5247933 CTCATTATTGATTTTAAGTTGAATTTCTTTACATTTTCGATTAAAACAGATTATAATTGAATGTT
65 CTCATTATTGATTTTAAGTTGAATTTTTTTACTTTTTTGGTTAAAACAGATTATAATTGAATGTT
* * * * * *
5247998 TGCCTCGGGAAACGTGAAGCAAAAGCCATCCATAGGTATGAA
130 TGCCTTGAGAAACGTGAAGCGAAAGCCATCCATTGATA-AAA
*
5248040 AAGTCCATTTATAGTCACTCATGCCTTTGAAAGACC-TATTACTCGCTTTAAATGGTTTTATAAT
1 AAGTCCATTTATAGTCACTCATGCCTTCGAAAG-CCTTATTACTCGCTTTAAATGGTTTTATAAT
* * **
5248104 CTCATTATTGATTGTAAGTTGAATTTTTTTACCTTTTTT-GTTAAAACAAATTACCATTGAATGT
65 CTCATTATTGATTTTAAGTTGAATTTTTTTA-CTTTTTTGGTTAAAACAGATTATAATTGAATGT
* * * * * * * *
5248168 TTTCCTTGGGAAACGTGAGGCTAAAACCCTCCGTTGATAGGAA
129 TTGCCTTGAGAAACGTGAAGCGAAAGCCATCCATTGATA-AAA
* * * *
5248211 AAGTCCATTTATGGTCACTCATACCTTC-AGAAGCCTTATTACTTGCTTAAAATGGTTTTATAAT
1 AAGTCCATTTATAGTCACTCATGCCTTCGA-AAGCCTTATTACTCGCTTTAAATGGTTTTATAAT
* * * * *
5248275 CTCATAATTGATTTTAAGTTAAATTTTTTTAC-ATTTCGGTTAAGAAAAG-TTATAATTGAATGT
65 CTCATTATTGATTTTAAGTTGAATTTTTTTACTTTTTTGGTTAA-AACAGATTATAATTGAATGT
* * * ** * * *
5248338 TCGCCTCGAGAAACTTGGCGAGAAAGCCATCCATTAATTAGAA
129 TTGCCTTGAGAAACGTGAAGCGAAAGCCATCCATTGA-TAAAA
**
5248381 AAGTCCATTTATAGTTGCTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATC
1 AAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATC
* * ** *
5248446 TCATTATTCATTTCAAGTTGAATTTACTTA-TATTTTTAGTTAAAACAGATTATAATTGAATGTT
66 TCATTATTGATTTTAAGTTGAATTTTTTTACT-TTTTTGGTTAAAACAGATTATAATTGAATGTT
* * * * *
5248510 TGCCTCGAGAAACGTGAAGGGAAAGCTATCCATTAACAAGAA
130 TGCCTTGAGAAACGTGAAGCGAAAGCCATCCATTGATAA-AA
* * * * * *
5248552 AAATCCATTTATTGTCACTCATGCCTACGAAAGCCTTATTACTTGCATTAAATAGTTTTACT-AT
1 AAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTA-TAAT
* * *
5248616 CTCATTATTGATTTTAAGTTGAA-TTTCTTACATTTTCGGTTAAAACAGATTATAATTGAATGTT
65 CTCATTATTGATTTTAAGTTGAATTTTTTTACTTTTTTGGTTAAAACAGATTATAATTGAATGTT
* * **
5248680 TGCC-TCAGGAAACATGAAGCGAAAGCCATCCATTGGCAAGAA
130 TGCCTTGA-GAAACGTGAAGCGAAAGCCATCCATTGATAA-AA
* * * * *
5248722 AAATCCATTTATAGTCACTCATGCCTTTGAAAGCCTTATTACTCACGTTAAATGGTTTTACAATC
1 AAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATC
* * *
5248787 TCATTATTGATTGTAAGTTGATTTTTTTTTTTTACATTTTTT-GTTAAAACAGATTATAATTTAA
66 TCATTATTGATTTTAAGTTGA----ATTTTTTTAC-TTTTTTGGTTAAAACAGATTATAATTGAA
* * * * * * **
5248851 TGTTTTCC-TCAGGAAACGTGAGGCTAAAACTC-TCCGTTGATAGGA
126 TGTTTGCCTTGA-GAAACGTGAAGCGAAAGC-CATCCATTGATAAAA
* * ** * * * * *
5248896 AAG-CCATTTATGGTCACCCATATCTTC-AGAAGCCTTATTAC-CTACATAAAATGATTTTGTAA
1 AAGTCCATTTATAGTCACTCATGCCTTCGA-AAGCCTTATTACTC-GCTTTAAATGGTTTTATAA
* * * * *
5248958 TCTCATAATTGCTTTTAAGTTGAATTTTTTTACATTTTTAGTTAAGAA-AGGTTATAATT-AATT
64 TCTCATTATTGATTTTAAGTTGAATTTTTTTACTTTTTTGGTTAA-AACAGATTATAATTGAA-T
* * *
5249021 GTTTGCCTTGAGAAACGTGAAGCGAAAGCTATCGATTGACAAGAA
127 GTTTGCCTTGAGAAACGTGAAGCGAAAGCCATCCATTGATAA-AA
* * * *
5249066 AAATCTATTTATAGTCACTCATACCTTCGAAAGCCTTATTACTCACTTTAAATGGTTTTATAATC
1 AAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATC
* * *
5249131 TCATTACTGATTTTAAGTTG-ATTTTTCTTACATTTTTGGTTAAAACATATTATAATTGAATGTT
66 TCATTATTGATTTTAAGTTGAATTTTT-TTACTTTTTTGGTTAAAACAGATTATAATTGAATGTT
* * * * *
5249195 TGCCTCGAGAAACATAAAGCGAAAGTCGTCCATTGATAAGAA
130 TGCCTTGAGAAACGTGAAGCGAAAGCCATCCATTGATAA-AA
* * * *
5249237 AAGTCCATTTATAGTCACTCATGCCTACGAAAGCCTTATTACTTGCATTAAAT-GTTTTATTATC
1 AAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATC
* * * * **
5249301 TCATTATT-ACTTTTAAGTTGAATTTTCTTACATTTTCT-ATTAAAATATTTTATAATTGAATGT
66 TCATTATTGA-TTTTAAGTTGAATTTTTTTAC-TTTTTTGGTTAAAACAGATTATAATTGAATGT
* * * *
5249364 TTGCCTTTG-GAAACGTGAAGCAAAATCCATCCATTGGTTAGAA
129 TTGCC-TTGAGAAACGTGAAGCGAAAGCCATCCATT-GATAAAA
** * *
5249407 AAGTCCATTTATAGTCACTCATGCCTTTTAAAACCTTATTACTCGCTTTAAATAGTTTTATAATC
1 AAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATC
** * * *
5249472 GAATTATTGATTTTAAGTTGAATATTTTTACATATTTTT--TTAAAACAGATTATAATTGATTGC
66 TCATTATTGATTTTAAGTTGAATTTTTTTAC-T-TTTTTGGTTAAAACAGATTATAATTGAATGT
* * * * * * *
5249535 TTACCTTAAGAAACGTGAGGCTAAAAACCCTCCGTTGATAAGAA
129 TTGCCTTGAGAAACGTGAAGC-GAAAGCCATCCATTGATAA-AA
* * * * * * *
5249579 AAGTCCACTTATAGTCGCTCATGCCTT-TAGAAGCCTAATTACTTGCTTAAAATGGTTTTATAAC
1 AAGTCCATTTATAGTCACTCATGCCTTCGA-AAGCCTTATTACTCGCTTTAAATGGTTTTATAAT
* * * * * *
5249643 CTCATAATTTATTTTAAGTTGAATTGTTTTACATTTTTGGTTAAGAA-AGGTTACAATTGAATGT
65 CTCATTATTGATTTTAAGTTGAATTTTTTTACTTTTTTGGTTAA-AACAGATTATAATTGAATGT
* * ** *
5249707 TTACCTTGAGAAACGTGAAGTGAAAGCCATTGATTGAAAACAA
129 TTGCCTTGAGAAACGTGAAGCGAAAGCCATCCATTGATAA-AA
* * * **
5249750 AAATCTATTTATAATCACTCATGCCTTCGAAAGCCTTATTACAGGCTTTAAATGGTTTTATAATC
1 AAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATC
* * * * * * *
5249815 TCGTTATTGATTTTAAGTTGAATTTTCTTACATTTTTGGTTAAAAAAGTTTATAACTAAATGTTT
66 TCATTATTGATTTTAAGTTGAATTTTTTTACTTTTTTGGTTAAAACAGATTATAATTGAATGTTT
5249880 G
131 G
5249881 NNNNNNNNNN
Statistics
Matches: 3070, Mismatches: 551, Indels: 205
0.80 0.14 0.05
Matches are distributed among these distances:
168 7 0.00
169 63 0.02
170 584 0.19
171 1957 0.64
172 193 0.06
173 191 0.06
174 10 0.00
175 60 0.02
176 5 0.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (170 bp):
AAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATC
TCATTATTGATTTTAAGTTGAATTTTTTTACTTTTTTGGTTAAAACAGATTATAATTGAATGTTT
GCCTTGAGAAACGTGAAGCGAAAGCCATCCATTGATAAAA
Found at i:5247868 original size:683 final size:683
Alignment explanation
Indices: 5245987--5249880 Score: 4900
Period size: 683 Copynumber: 5.7 Consensus size: 683
5245977 GGGTCGTGAC
* * * *
5245987 AAGTCCATTTATAGTCACTAAGGCCTTCGAAAGCCTTATTACTCACTTTAAATGGTTTTATAATC
1 AAGTCCATTTATAGTCACTCATGCCTTTGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATC
* * * * * * *
5246052 TGATTATTGATTTTAAGCTAAATTTTTTTACTTTTTTTGTTAAAATAGATTACAATTGAATGTTT
66 TCATTATTGATTGTAAGTTGAATTTTTTTACCTTTTTTGTTAAAACAAATTACAATTGAATGTTT
** * * * * * * * * ** *
5246117 TCCTTGACAAAAGTGAAGCGAAAGCCATCCATTGACA-AAAATAGTCCATTTGCAGTCACTTATA
131 TCCTTGGGAAACGTGAGGCTAAAACCCTCCGTTGATAGGAAA-AGTCCATTTATAGTCACTCATA
* * * * *
5246181 CCTT-TGAAAGCCTTATTACTTGCTTTAAATGGTTTTATAATCTGATTATTGATTTTAAGCTGAA
195 CCTTCAG-AAGCCTTATTACTTGCTTAAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAA
* * * * * * *
5246245 TTTTTTTGCTTTTTTGGTTTA-AACAGATTATAATTGAATGTTTGCCAT-GAGAAAAGTGAAGCG
259 TTTTTTTAC-ATTTTGGTTAAGAAAAG-TTATAATTGAATGTTCGCC-TCGAGAAACGTGAAGAG
* * * *
5246308 AAAGCCATCCATTGACAAGAATAGTCCATTTATAGTCGTTTATGCCTTCGAAAGCCTTATTACTC
321 AAAGCCATCCATTAACAAGAAAAGTCCATTTATAGTCGCTCATGCCTTCGAAAGCCTTATTACTC
* * * * * *
5246373 ACTTTAAATGGTTTTATAAGCTCATTATTGATTTTAAGTTGAATTTTTTTACGTTCTTT-GTTAA
386 GCTTTAAATGGTTTTATAATCTCATTATTCATTTCAAGTTGAATTTTCTTACATT-TTTAGTTAA
* * * * * * *
5246437 AACAGATTATAATTGATTATTTACCTCTG-GAAACGTG-AGGTTAAAACTTTCCGTTGAC-AGAA
450 AACAGATTATAATTGAATGTTTGCCTC-GAGAAACGTGAAGG-GAAAGCTATCCATTGACAAG-A
* * *
5246499 AAAGTTCATTTATGGTCACTCATGCCTTC-AGAAGCCTTATTAC-T-CACTTAAAATTA-TTTTA
512 AAAGTCCATTTATTGTCACTCATGCCTACGA-AAGCCTTATTACTTGCA-TT-AAA-TAGTTTTA
* * * * * *
5246560 TAATCTCATAATTGATTTTAAGTTGAATGTTT-TTATATTTTCGGTTAAGAA-AGGTTATAATTA
573 TTATCTCATTATTGATTTTAAGTTGAAT-TTTCTTACATTTTCGATTAA-AACAGATTATAATTG
* ** * * * * ** *
5246623 AATGTTTGCTTCTAGCAATGTGAAGCGAAAGCCATCGATTGACAAGAA
636 AATGTTTGCCTCGGGAAACGTGAAGCAAAAGCCATCCATTGGTATGAA
* * * * * *
5246671 AAGTTCATTTATTGTTACTCATGCCTTCGAAAGCCTTATTACTCGCATTAAATAGTTTTATAATC
1 AAGTCCATTTATAGTCACTCATGCCTTTGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATC
* * * * * *
5246736 -CGATTATTGATTTTGAGTTGAATTTTTTTTCCCATTTTTGGTTAAAATAGAA-TATAATTGAAT
66 TC-ATTATTGATTGTAAGTTGAA-TTTTTTTACC-TTTTTTGTTAAAACA-AATTACAATTGAAT
* * * * * * * ** *
5246799 GTTTGCCTTCGAAAACGTGAAG-TGAAA-GCTCTCGATTGATAAGAAATTTCCGTTTATAGTCAC
127 GTTTTCCTTGGGAAACGTGAGGCTAAAACCCTC-CG-TTGATAGGAAAAGTCCATTTATAGTCAC
* * *
5246862 TCATTCCTTCAAAAGCCTTATTACCTGCTTAAAATGGTTTTATAATCTCATAATTGATTTTAAGT
190 TCATACCTTCAGAAGCCTTATTACTTGCTTAAAATGGTTTTATAATCTCATAATTGATTTTAAGT
* * * * *
5246927 TGAATTTTTTTACTTTTTTGTTTAAGAAAGGTTATAATTGAGTGTTCGCCTCGA-AAAGCATGAA
255 TGAATTTTTTTAC-ATTTTGGTTAAGAAAAGTTATAATTGAATGTTCGCCTCGAGAAA-CGTGAA
* * *
5246991 GGGAAAGCCATCCATTAACTAGAAAAGTCCATTTATAGTCGCTCATGCCTTCGAAAGGCTTATTA
318 GAGAAAGCCATCCATTAACAAGAAAAGTCCATTTATAGTCGCTCATGCCTTCGAAAGCCTTATTA
* * * * *
5247056 CTCGTTTTAAATAGTTTTATAATCTCATTATTCATTCCAAGTTGAATTTTCTTACAATTGTAGTT
383 CTCGCTTTAAATGGTTTTATAATCTCATTATTCATTTCAAGTTGAATTTTCTTACATTTTTAGTT
* * * * * *
5247121 AAAACATATTATAATTGAATGTTTGCCTTGAGAAATGTGAAGCGAAAGCCATCGATTGACAAGAA
448 AAAACAGATTATAATTGAATGTTTGCCTCGAGAAACGTGAAGGGAAAGCTATCCATTGACAAGAA
* * *
5247186 AAGTTCATTTATTGTCACTCATGCCTACGAAAGCCTTATTACTTGTATTAAATGGTTTTATTATC
513 AAGTCCATTTATTGTCACTCATGCCTACGAAAGCCTTATTACTTGCATTAAATAGTTTTATTATC
5247251 TCATTATTGATTTTAAGTTGAATTTTCTTACATTTTCGATTAAAACAGATTATAATTGAATGTTT
578 TCATTATTGATTTTAAGTTGAATTTTCTTACATTTTCGATTAAAACAGATTATAATTGAATGTTT
*
5247316 GCCTCGGGAAACGTGAAGCAAAAGCCATCCATAGGTATGAA
643 GCCTCGGGAAACGTGAAGCAAAAGCCATCCATTGGTATGAA
5247357 AAGTCCATTTATAGTCACTCATGCCTTTGAAAGACC-TATTACTCGCTTTAAATGGTTTTATAAT
1 AAGTCCATTTATAGTCACTCATGCCTTTGAAAG-CCTTATTACTCGCTTTAAATGGTTTTATAAT
*
5247421 CTCATTATTGATTGTAAGTTGAATTTTTTTACCTTTTTTGTTAAAACAAATTACCATTGAATGTT
65 CTCATTATTGATTGTAAGTTGAATTTTTTTACCTTTTTTGTTAAAACAAATTACAATTGAATGTT
*
5247486 TTCCTTGGGAAACGTGAGGCTAAAACCCTCCGTTGATAGGAAAAGTCCATTTATGGTCACTCATA
130 TTCCTTGGGAAACGTGAGGCTAAAACCCTCCGTTGATAGGAAAAGTCCATTTATAGTCACTCATA
*
5247551 CCTTCAGAAGCCTTATTACTTGCTTAAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAAAT
195 CCTTCAGAAGCCTTATTACTTGCTTAAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAAT
* * **
5247616 TTTTTTACATTTCGGTTAAGAAAAGTTATAATTGAATGTTCGCCTCGAGAAACTTGGCGAGAAAG
260 TTTTTTACATTTTGGTTAAGAAAAGTTATAATTGAATGTTCGCCTCGAGAAACGTGAAGAGAAAG
** *
5247681 CCATCCATTAATTAGAAAAGTCCATTTATAGTTGCTCATGCCTTCGAAAGCCTTATTACTCGCTT
325 CCATCCATTAACAAGAAAAGTCCATTTATAGTCGCTCATGCCTTCGAAAGCCTTATTACTCGCTT
* *
5247746 TAAATGGTTTTATAATCTCATTATTCATTTCAAGTTGAATTTACTTATATTTTTAGTTAAAACAG
390 TAAATGGTTTTATAATCTCATTATTCATTTCAAGTTGAATTTTCTTACATTTTTAGTTAAAACAG
* *
5247811 ATTATAATTGAATGTTTGCCTCGAGAAACGTGAAGGGAAAGCTATCCATTAACAAGAAAAATCCA
455 ATTATAATTGAATGTTTGCCTCGAGAAACGTGAAGGGAAAGCTATCCATTGACAAGAAAAGTCCA
*
5247876 TTTATTGTCACTCATGCCTACGAAAGCCTTATTACTTGCATTAAATAGTTTTACTATCTCATTAT
520 TTTATTGTCACTCATGCCTACGAAAGCCTTATTACTTGCATTAAATAGTTTTATTATCTCATTAT
5247941 TGATTTTAAGTTGAA-TTTCTTTACATTTTCGATTAAAACAGATTATAATTGAATGTTTGCCTCG
585 TGATTTTAAGTTGAATTTTC-TTACATTTTCGATTAAAACAGATTATAATTGAATGTTTGCCTCG
*
5248005 GGAAACGTGAAGCAAAAGCCATCCATAGGTATGAA
649 GGAAACGTGAAGCAAAAGCCATCCATTGGTATGAA
5248040 AAGTCCATTTATAGTCACTCATGCCTTTGAAAGACC-TATTACTCGCTTTAAATGGTTTTATAAT
1 AAGTCCATTTATAGTCACTCATGCCTTTGAAAG-CCTTATTACTCGCTTTAAATGGTTTTATAAT
*
5248104 CTCATTATTGATTGTAAGTTGAATTTTTTTACCTTTTTTGTTAAAACAAATTACCATTGAATGTT
65 CTCATTATTGATTGTAAGTTGAATTTTTTTACCTTTTTTGTTAAAACAAATTACAATTGAATGTT
*
5248169 TTCCTTGGGAAACGTGAGGCTAAAACCCTCCGTTGATAGGAAAAGTCCATTTATGGTCACTCATA
130 TTCCTTGGGAAACGTGAGGCTAAAACCCTCCGTTGATAGGAAAAGTCCATTTATAGTCACTCATA
*
5248234 CCTTCAGAAGCCTTATTACTTGCTTAAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAAAT
195 CCTTCAGAAGCCTTATTACTTGCTTAAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAAT
* * **
5248299 TTTTTTACATTTCGGTTAAGAAAAGTTATAATTGAATGTTCGCCTCGAGAAACTTGGCGAGAAAG
260 TTTTTTACATTTTGGTTAAGAAAAGTTATAATTGAATGTTCGCCTCGAGAAACGTGAAGAGAAAG
** *
5248364 CCATCCATTAATTAGAAAAGTCCATTTATAGTTGCTCATGCCTTCGAAAGCCTTATTACTCGCTT
325 CCATCCATTAACAAGAAAAGTCCATTTATAGTCGCTCATGCCTTCGAAAGCCTTATTACTCGCTT
* *
5248429 TAAATGGTTTTATAATCTCATTATTCATTTCAAGTTGAATTTACTTATATTTTTAGTTAAAACAG
390 TAAATGGTTTTATAATCTCATTATTCATTTCAAGTTGAATTTTCTTACATTTTTAGTTAAAACAG
* *
5248494 ATTATAATTGAATGTTTGCCTCGAGAAACGTGAAGGGAAAGCTATCCATTAACAAGAAAAATCCA
455 ATTATAATTGAATGTTTGCCTCGAGAAACGTGAAGGGAAAGCTATCCATTGACAAGAAAAGTCCA
*
5248559 TTTATTGTCACTCATGCCTACGAAAGCCTTATTACTTGCATTAAATAGTTTTACTATCTCATTAT
520 TTTATTGTCACTCATGCCTACGAAAGCCTTATTACTTGCATTAAATAGTTTTATTATCTCATTAT
* *
5248624 TGATTTTAAGTTGAA-TTTCTTACATTTTCGGTTAAAACAGATTATAATTGAATGTTTGCCTCAG
585 TGATTTTAAGTTGAATTTTCTTACATTTTCGATTAAAACAGATTATAATTGAATGTTTGCCTCGG
* * * *
5248688 GAAACATGAAGCGAAAGCCATCCATTGGCAAGAA
650 GAAACGTGAAGCAAAAGCCATCCATTGGTATGAA
* * * *
5248722 AAATCCATTTATAGTCACTCATGCCTTTGAAAGCCTTATTACTCACGTTAAATGGTTTTACAATC
1 AAGTCCATTTATAGTCACTCATGCCTTTGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATC
* * * * *
5248787 TCATTATTGATTGTAAGTTGATTTTTTTTTTTTACATTTTTTGTTAAAACAGATTATAATTTAAT
66 TCATTATTGATTGTAAGTTGA----ATTTTTTTACCTTTTTTGTTAAAACAAATTACAATTGAAT
** * * *
5248852 GTTTTCCTCAGGAAACGTGAGGCTAAAACTCTCCGTTGATAGG-AAAG-CCATTTATGGTCACCC
127 GTTTTCCTTGGGAAACGTGAGGCTAAAACCCTCCGTTGATAGGAAAAGTCCATTTATAGTCACTC
* * * * * * *
5248915 ATATCTTCAGAAGCCTTATTACCTACATAAAATGATTTTGTAATCTCATAATTGCTTTTAAGTTG
192 ATACCTTCAGAAGCCTTATTACTTGCTTAAAATGGTTTTATAATCTCATAATTGATTTTAAGTTG
* * * * *
5248980 AATTTTTTTACATTTTTAGTTAAGAAAGGTTATAATT-AATTGTTTGCCTTGAGAAACGTGAAGC
257 AATTTTTTTACA-TTTTGGTTAAGAAAAGTTATAATTGAA-TGTTCGCCTCGAGAAACGTGAAGA
* * * * * * *
5249044 GAAAGCTATCGATTGACAAGAAAAATCTATTTATAGTCACTCATACCTTCGAAAGCCTTATTACT
320 GAAAGCCATCCATTAACAAGAAAAGTCCATTTATAGTCGCTCATGCCTTCGAAAGCCTTATTACT
* * * * * *
5249109 CACTTTAAATGGTTTTATAATCTCATTACTGATTTTAAGTTGATTTTTCTTACATTTTTGGTTAA
385 CGCTTTAAATGGTTTTATAATCTCATTATTCATTTCAAGTTGAATTTTCTTACATTTTTAGTTAA
* * * * * *
5249174 AACATATTATAATTGAATGTTTGCCTCGAGAAACATAAAGCGAAAG-TCGTCCATTGATAAGAAA
450 AACAGATTATAATTGAATGTTTGCCTCGAGAAACGTGAAGGGAAAGCT-ATCCATTGACAAGAAA
*
5249238 AGTCCATTTATAGTCACTCATGCCTACGAAAGCCTTATTACTTGCATTAAAT-GTTTTATTATCT
514 AGTCCATTTATTGTCACTCATGCCTACGAAAGCCTTATTACTTGCATTAAATAGTTTTATTATCT
* * **
5249302 CATTATT-ACTTTTAAGTTGAATTTTCTTACATTTTCTATTAAAATATTTTATAATTGAATGTTT
579 CATTATTGA-TTTTAAGTTGAATTTTCTTACATTTTCGATTAAAACAGATTATAATTGAATGTTT
** *
5249366 GCCTTTGGAAACGTGAAGCAAAATCCATCCATTGGT-TAGAA
643 GCCTCGGGAAACGTGAAGCAAAAGCCATCCATTGGTAT-GAA
* * *
5249407 AAGTCCATTTATAGTCACTCATGCCTTTTAAAACCTTATTACTCGCTTTAAATAGTTTTATAATC
1 AAGTCCATTTATAGTCACTCATGCCTTTGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATC
** * * * * * * *
5249472 GAATTATTGATTTTAAGTTGAATATTTTTACATATTTTT-TTAAAACAGATTATAATTGATTGCT
66 TCATTATTGATTGTAAGTTGAATTTTTTTACCT-TTTTTGTTAAAACAAATTACAATTGAATGTT
* ** * * *
5249536 TACCTTAAGAAACGTGAGGCTAAAAACCCTCCGTTGATAAGAAAAGTCCACTTATAGTCGCTCAT
130 TTCCTTGGGAAACGTGAGGCT-AAAACCCTCCGTTGATAGGAAAAGTCCATTTATAGTCACTCAT
* * * * *
5249601 GCCTTTAGAAGCCTAATTACTTGCTTAAAATGGTTTTATAACCTCATAATTTATTTTAAGTTGAA
194 ACCTTCAGAAGCCTTATTACTTGCTTAAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAA
* * * ** * *
5249666 TTGTTTTACATTTTTGGTTAAGAAAGGTTACAATTGAATGTTTACCTTGAGAAACGTGAAGTGAA
259 TTTTTTTACA-TTTTGGTTAAGAAAAGTTATAATTGAATGTTCGCCTCGAGAAACGTGAAGAGAA
** * * * * * **
5249731 AGCCATTGATTGAA-AACAAAAATCTATTTATAATCACTCATGCCTTCGAAAGCCTTATTACAGG
323 AGCCATCCATT-AACAAGAAAAGTCCATTTATAGTCGCTCATGCCTTCGAAAGCCTTATTACTCG
* * * *
5249795 CTTTAAATGGTTTTATAATCTCGTTATTGATTTTAAGTTGAATTTTCTTACATTTTTGGTTAAAA
387 CTTTAAATGGTTTTATAATCTCATTATTCATTTCAAGTTGAATTTTCTTACATTTTTAGTTAAAA
* * * *
5249860 AAGTTTATAACTAAATGTTTG
452 CAGATTATAATTGAATGTTTG
5249881 NNNNNNNNNN
Statistics
Matches: 2865, Mismatches: 300, Indels: 90
0.88 0.09 0.03
Matches are distributed among these distances:
681 52 0.02
682 177 0.06
683 986 0.34
684 588 0.21
685 448 0.16
686 595 0.21
687 18 0.01
688 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (683 bp):
AAGTCCATTTATAGTCACTCATGCCTTTGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATC
TCATTATTGATTGTAAGTTGAATTTTTTTACCTTTTTTGTTAAAACAAATTACAATTGAATGTTT
TCCTTGGGAAACGTGAGGCTAAAACCCTCCGTTGATAGGAAAAGTCCATTTATAGTCACTCATAC
CTTCAGAAGCCTTATTACTTGCTTAAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATT
TTTTTACATTTTGGTTAAGAAAAGTTATAATTGAATGTTCGCCTCGAGAAACGTGAAGAGAAAGC
CATCCATTAACAAGAAAAGTCCATTTATAGTCGCTCATGCCTTCGAAAGCCTTATTACTCGCTTT
AAATGGTTTTATAATCTCATTATTCATTTCAAGTTGAATTTTCTTACATTTTTAGTTAAAACAGA
TTATAATTGAATGTTTGCCTCGAGAAACGTGAAGGGAAAGCTATCCATTGACAAGAAAAGTCCAT
TTATTGTCACTCATGCCTACGAAAGCCTTATTACTTGCATTAAATAGTTTTATTATCTCATTATT
GATTTTAAGTTGAATTTTCTTACATTTTCGATTAAAACAGATTATAATTGAATGTTTGCCTCGGG
AAACGTGAAGCAAAAGCCATCCATTGGTATGAA
Found at i:5258912 original size:42 final size:42
Alignment explanation
Indices: 5258852--5258986 Score: 173
Period size: 42 Copynumber: 3.2 Consensus size: 42
5258842 TTGGACTCGG
* * *
5258852 CTATGTGCGAGTAAGAGTGCACATAAGCCATTGCTGACCTGA
1 CTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTGACCCGA
*
5258894 CTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTGACCCGG
1 CTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTGACCCGA
* * * *
5258936 CTATGTGTGAGT-GCAAGTGCACATAAGCCGTTGTTGACCCGG
1 CTATGTGCGAGTAG-GAGTGCACATAAGCCGTTGCTGACCCGA
*
5258978 CTATATGCG
1 CTATGTGCG
5258987 CATAAGCCGT
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
41 1 0.01
42 82 0.99
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24
Consensus pattern (42 bp):
CTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTGACCCGA
Found at i:5259042 original size:26 final size:26
Alignment explanation
Indices: 5259006--5259067 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
5258996 TTGCATATGA
5259006 GATGATGATGATGGGATGGTGTGCAT
1 GATGATGATGATGGGATGGTGTGCAT
5259032 GATGATGATGATGGGATGGTGTGCAT
1 GATGATGATGATGGGATGGTGTGCAT
*
5259058 GTTGATGATG
1 GATGATGATG
5259068 GGTATATGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.23, C:0.03, G:0.42, T:0.32
Consensus pattern (26 bp):
GATGATGATGATGGGATGGTGTGCAT
Found at i:5262955 original size:18 final size:18
Alignment explanation
Indices: 5262918--5262956 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5262908 CAAAACCAAG
* *
5262918 CTTTTTCTTCCTTTTTCT
1 CTTTTTCTTCCTTCTCCT
*
5262936 CTTTTTCTTTCTTCTCCT
1 CTTTTTCTTCCTTCTCCT
5262954 CTT
1 CTT
5262957 GGGGTTTAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (18 bp):
CTTTTTCTTCCTTCTCCT
Found at i:5263926 original size:28 final size:28
Alignment explanation
Indices: 5263883--5263941 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
5263873 ATAATTTCAT
*
5263883 AGGGGCAAAATGGTAATTTTGCCACC-CC
1 AGGGGCAAAATAGTAATTTT-CCACCACC
*
5263911 AGGGGCGAAATAGTAATTTTCCACCACC
1 AGGGGCAAAATAGTAATTTTCCACCACC
5263939 AGG
1 AGG
5263942 ACACTTGTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 5 0.18
28 23 0.82
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (28 bp):
AGGGGCAAAATAGTAATTTTCCACCACC
Found at i:5267762 original size:2 final size:2
Alignment explanation
Indices: 5267757--5267795 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5267747 TCTATGTATG
5267757 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5267796 NNNNNNNNNN
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5267997 original size:43 final size:43
Alignment explanation
Indices: 5267950--5268042 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 43
5267940 CAGCTCATAT
** * * *
5267950 GCACTCCCCACTAGCACATGGCTGGGTCATCATCGGCTTATGC
1 GCACTCCCCACTAGCACATAACCGGGTCAACATCCGCTTATGC
* *
5267993 GCACT-CCCACTCGTACATAACCGGGTCAACATCCGCTTATGC
1 GCACTCCCCACTAGCACATAACCGGGTCAACATCCGCTTATGC
5268035 GCACTCCC
1 GCACTCCC
5268043 AATCGCAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 35 0.83
43 7 0.17
ACGTcount: A:0.20, C:0.39, G:0.19, T:0.22
Consensus pattern (43 bp):
GCACTCCCCACTAGCACATAACCGGGTCAACATCCGCTTATGC
Found at i:5268019 original size:42 final size:42
Alignment explanation
Indices: 5267973--5268063 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 42
5267963 GCACATGGCT
* * * * *
5267973 GGGTCATCATCGGCTTATGCGCACTCCCACTCGTACATAACC
1 GGGTCAACATCCGCTTATGCGCACTCCCAATCGCAAATAACC
5268015 GGGTCAACATCCGCTTATGCGCACTCCCAATCGCAAATAACC
1 GGGTCAACATCCGCTTATGCGCACTCCCAATCGCAAATAACC
*
5268057 AGGTCAA
1 GGGTCAA
5268064 TATCATTACA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.26, C:0.34, G:0.19, T:0.21
Consensus pattern (42 bp):
GGGTCAACATCCGCTTATGCGCACTCCCAATCGCAAATAACC
Found at i:5269733 original size:62 final size:62
Alignment explanation
Indices: 5269612--5269736 Score: 162
Period size: 62 Copynumber: 2.0 Consensus size: 62
5269602 TTAAAATATG
** * * *
5269612 AATCTATTAAAGTAAGATAAAATGTACCTTGTATTTCGAGATTCTTATTTTTGGACACCACC
1 AATCTATTAAAGTAAGATAAAACATACCTTGTATTTCGAGATGCTCATTTTTAGACACCACC
* * *
5269674 AATCTTTTAAAGTAAGATAAAACATACCTTTTATTTTGAGATGCTCATTTTCTAG-CACCACC
1 AATCTATTAAAGTAAGATAAAACATACCTTGTATTTCGAGATGCTCATTTT-TAGACACCACC
5269736 A
1 A
5269737 CAATAGTAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
62 52 0.96
63 2 0.04
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (62 bp):
AATCTATTAAAGTAAGATAAAACATACCTTGTATTTCGAGATGCTCATTTTTAGACACCACC
Found at i:5270090 original size:29 final size:29
Alignment explanation
Indices: 5270048--5270262 Score: 309
Period size: 29 Copynumber: 7.6 Consensus size: 29
5270038 CTCTGGCCTC
*
5270048 AAATTAAGACAAAACATATTTTCTTGTCT
1 AAATTAAGACAAAACATGTTTTCTTGTCT
5270077 AAATTAAGACAAAACATGTTTTCTTGTCT
1 AAATTAAGACAAAACATGTTTTCTTGTCT
*
5270106 AAATTAAGACAAAACATGTTTTCTTATCT
1 AAATTAAGACAAAACATGTTTTCTTGTCT
5270135 AAATTAAGACAAAAACATGTTTTCTTGTCT
1 AAATTAAGAC-AAAACATGTTTTCTTGTCT
* *
5270165 AAATTAAAAC-AAACATGTTTTCTTGTTT
1 AAATTAAGACAAAACATGTTTTCTTGTCT
5270193 AAATTAAG-----ACATGTTTTCTTGTCT
1 AAATTAAGACAAAACATGTTTTCTTGTCT
*
5270217 AAATTAAGACAAAACATGTTTTCTTGGCT
1 AAATTAAGACAAAACATGTTTTCTTGTCT
* *
5270246 AACTTAAAAC-AAACATG
1 AAATTAAGACAAAACATG
5270263 GAAAAGATGC
Statistics
Matches: 170, Mismatches: 10, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
24 23 0.14
28 31 0.18
29 89 0.52
30 27 0.16
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.37
Consensus pattern (29 bp):
AAATTAAGACAAAACATGTTTTCTTGTCT
Found at i:5270258 original size:111 final size:113
Alignment explanation
Indices: 5270048--5270258 Score: 309
Period size: 111 Copynumber: 1.8 Consensus size: 113
5270038 CTCTGGCCTC
*
5270048 AAATTAAGACAAAACATATTTTCTTGTCTAAATTAAGACAAAACATGTTTTCTTGTCTAAATTAA
1 AAATTAAAACAAAACATATTTTCTTGTCTAAATTAAG----AACATGTTTTCTTGTCTAAATTAA
* *
5270113 GACAAAACATGTTTTCTTATCTAAATTAAGACAAAAACATGTTTTCTTGTCT
62 GACAAAACATGTTTTCTTAGCTAAATTAAAACAAAAACATGTTTTCTTGTCT
* *
5270165 AAATTAAAAC-AAACATGTTTTCTTGTTTAAATTAAG-ACATGTTTTCTTGTCTAAATTAAGACA
1 AAATTAAAACAAAACATATTTTCTTGTCTAAATTAAGAACATGTTTTCTTGTCTAAATTAAGACA
* *
5270228 AAACATGTTTTCTTGGCTAACTTAAAACAAA
66 AAACATGTTTTCTTAGCTAAATTAAAACAAA
5270259 CATGGAAAAG
Statistics
Matches: 87, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
111 54 0.62
116 24 0.28
117 9 0.10
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.37
Consensus pattern (113 bp):
AAATTAAAACAAAACATATTTTCTTGTCTAAATTAAGAACATGTTTTCTTGTCTAAATTAAGACA
AAACATGTTTTCTTAGCTAAATTAAAACAAAAACATGTTTTCTTGTCT
Found at i:5271191 original size:17 final size:17
Alignment explanation
Indices: 5271161--5271193 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5271151 TTCTTGATAA
5271161 AATAAAACTCCTTATTG
1 AATAAAACTCCTTATTG
5271178 AATAATAACT-CTTATT
1 AATAA-AACTCCTTATT
5271194 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (17 bp):
AATAAAACTCCTTATTG
Found at i:5271399 original size:28 final size:28
Alignment explanation
Indices: 5271368--5271510 Score: 180
Period size: 29 Copynumber: 5.0 Consensus size: 28
5271358 AAATATTTTA
* *
5271368 TCTTGTCTAAATTGAGACAAATATGTTT
1 TCTTGTCTAAATTAAGACAAACATGTTT
* * *
5271396 TCTTGACTAAATTAAGACAAAAAATATTTT
1 TCTTGTCTAAATTAAGAC-AAACAT-GTTT
*
5271426 TCTTGTCTTAAATTAA-AGCAAACATATTT
1 TCTTGTC-TAAATTAAGA-CAAACATGTTT
5271455 TCTTGTCTAAATTAAGAACAAACATGTTT
1 TCTTGTCTAAATTAAG-ACAAACATGTTT
5271484 TCTTGTCTAAATTAAGACAAACATGTT
1 TCTTGTCTAAATTAAGACAAACATGTT
5271511 AAAGCTGTCA
Statistics
Matches: 101, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
28 35 0.35
29 41 0.41
30 16 0.16
31 9 0.09
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATGTTT
Found at i:5271438 original size:59 final size:57
Alignment explanation
Indices: 5271345--5271510 Score: 201
Period size: 59 Copynumber: 2.8 Consensus size: 57
5271335 TCTTGTCTGT
*
5271345 AATTAAGACAAAAAAATATTTTATCTTGTCTAAATTGAGACAAATATGTTTTCTTGACTA
1 AATTAAGAC-AAAAAATATTTT-TCTTGTCTAAATT-AGACAAACATGTTTTCTTGACTA
* * *
5271405 AATTAAGACAAAAAATATTTTTCTTGTCTTAAATTAAAGCAAACATATTTTCTTGTCTA
1 AATTAAGACAAAAAATATTTTTCTTGTC-TAAATTAGA-CAAACATGTTTTCTTGACTA
* *
5271464 AATTAAGA-ACAAACAT-GTTTTCTTGTCTAAATTAAGACAAACATGTT
1 AATTAAGACA-AAAAATATTTTTCTTGTCTAAATT-AGACAAACATGTT
5271511 AAAGCTGTCA
Statistics
Matches: 94, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
57 15 0.16
58 22 0.23
59 48 0.51
60 9 0.10
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (57 bp):
AATTAAGACAAAAAATATTTTTCTTGTCTAAATTAGACAAACATGTTTTCTTGACTA
Found at i:5271460 original size:29 final size:28
Alignment explanation
Indices: 5271335--5271507 Score: 177
Period size: 29 Copynumber: 5.9 Consensus size: 28
5271325 TTAAGATAAC
* *
5271335 TCTTGTCTGTAATTAAGACAAAAAAATATTTT
1 TCTTGTCT-AAATTAAGAC--AAACATA-TTT
* * *
5271367 ATCTTGTCTAAATTGAGACAAATATGTTT
1 -TCTTGTCTAAATTAAGACAAACATATTT
* *
5271396 TCTTGACTAAATTAAGACAAAAAATATTTT
1 TCTTGTCTAAATTAAGAC-AAACATA-TTT
5271426 TCTTGTCTTAAATTAA-AGCAAACATATTT
1 TCTTGTC-TAAATTAAGA-CAAACATATTT
*
5271455 TCTTGTCTAAATTAAGAACAAACATGTTT
1 TCTTGTCTAAATTAAG-ACAAACATATTT
5271484 TCTTGTCTAAATTAAGACAAACAT
1 TCTTGTCTAAATTAAGACAAACAT
5271508 GTTAAAGCTG
Statistics
Matches: 123, Mismatches: 11, Indels: 17
0.81 0.07 0.11
Matches are distributed among these distances:
28 32 0.26
29 44 0.36
30 22 0.18
31 9 0.07
32 8 0.07
33 8 0.07
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATATTT
Found at i:5276330 original size:26 final size:26
Alignment explanation
Indices: 5276270--5276341 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
5276260 TCCAACCGAG
* * *
5276270 AGGAAAAAGAAAAAAAAAGA-GAGAA
1 AGGAAAAGGAAAGAAAGAGAGGAGAA
*
5276295 A-GAGATAGGAAAGAAAGAGAGGAGAA
1 AGGA-AAAGGAAAGAAAGAGAGGAGAA
*
5276321 AGGAAAAGGAAGGAAAGAGAG
1 AGGAAAAGGAAAGAAAGAGAG
5276342 AAAAGCTTGG
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
24 2 0.05
25 13 0.34
26 21 0.55
27 2 0.05
ACGTcount: A:0.64, C:0.00, G:0.35, T:0.01
Consensus pattern (26 bp):
AGGAAAAGGAAAGAAAGAGAGGAGAA
Found at i:5304596 original size:68 final size:67
Alignment explanation
Indices: 5304444--5304674 Score: 184
Period size: 68 Copynumber: 3.4 Consensus size: 67
5304434 AATGCCCTAA
* * * * * *
5304444 AATATGTATATGATGTGAATTCCATATA-CAATATGAGATGATCAAGTATGCATGATGTATACTA
1 AATAGGTATATGATGTAAATTCCATATACCACT-TGAGATGATTAAGTATGCATAAT-TATGCTA
*
5304508 TAAG
64 TGAG
* * * *
5304512 -ATGGAGTTTATAATGTAAATTCCATATACCACTTAAGATGATTAAGTATGCATAATTAATGCTA
1 AATAG-GTATATGATGTAAATTCCATATACCACTTGAGATGATTAAGTATGCATAATT-ATGCTA
5304576 TGAG
64 TGAG
* * * * * *
5304580 AATAGGTATATGATGTATATTTCGTATACTACTTGAGATGATTGAGT-TAGCATAA-T-TGCCAT
1 AATAGGTATATGATGTAAATTCCATATACCACTTGAGATGATTAAGTAT-GCATAATTATGCTAT
*
5304642 GAC
65 GAG
* * * *
5304645 ATTATGTATATGATCTAAATTTCATATACC
1 AATAGGTATATGATGTAAATTCCATATACC
5304675 TTATGAGATG
Statistics
Matches: 130, Mismatches: 28, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
65 31 0.24
67 5 0.04
68 88 0.68
69 6 0.05
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.36
Consensus pattern (67 bp):
AATAGGTATATGATGTAAATTCCATATACCACTTGAGATGATTAAGTATGCATAATTATGCTATG
AG
Found at i:5304848 original size:31 final size:31
Alignment explanation
Indices: 5304813--5304925 Score: 109
Period size: 31 Copynumber: 3.6 Consensus size: 31
5304803 ATCATAAAAT
*
5304813 GCCCAAGGTGCAATGGGGCTGTACATTGCCA
1 GCCCAAGGTGCAATGGGGCTATACATTGCCA
* ** *
5304844 GCCCAAGGTGCAATGGGGTTATATGTTGCTA
1 GCCCAAGGTGCAATGGGGCTATACATTGCCA
** *** *
5304875 GTTCAAGGTGCAATGGAATTATACATTACCA
1 GCCCAAGGTGCAATGGGGCTATACATTGCCA
* *
5304906 ACCCAAGGTGTAATGGGGCT
1 GCCCAAGGTGCAATGGGGCT
5304926 GCACATGGCT
Statistics
Matches: 62, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (31 bp):
GCCCAAGGTGCAATGGGGCTATACATTGCCA
Found at i:5310355 original size:17 final size:17
Alignment explanation
Indices: 5310333--5310365 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5310323 ATAATAATAA
5310333 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
5310350 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
5310366 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:5318595 original size:24 final size:24
Alignment explanation
Indices: 5318568--5318621 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
5318558 CCTATCGAGA
* *
5318568 CCTCGCAAGGCTCTCGTATCAGTT
1 CCTCACAAGGCTCTCATATCAGTT
*
5318592 CCTCACCAGGCTCTCATATCAGTT
1 CCTCACAAGGCTCTCATATCAGTT
5318616 CCTCAC
1 CCTCAC
5318622 CTAACCTGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.19, C:0.39, G:0.15, T:0.28
Consensus pattern (24 bp):
CCTCACAAGGCTCTCATATCAGTT
Found at i:5318622 original size:24 final size:24
Alignment explanation
Indices: 5318575--5318622 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
5318565 AGACCTCGCA
*
5318575 AGGCTCTCGTATCAGTTCCTCACC
1 AGGCTCTCATATCAGTTCCTCACC
5318599 AGGCTCTCATATCAGTTCCTCACC
1 AGGCTCTCATATCAGTTCCTCACC
5318623 TAACCTGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.19, C:0.38, G:0.15, T:0.29
Consensus pattern (24 bp):
AGGCTCTCATATCAGTTCCTCACC
Found at i:5319934 original size:10 final size:10
Alignment explanation
Indices: 5319906--5319934 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
5319896 TAAATCCATT
5319906 TTTCATAAAA
1 TTTCATAAAA
5319916 TTT-ATAAAA
1 TTTCATAAAA
5319925 TTTCATAAAA
1 TTTCATAAAA
5319935 ACTACCTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (10 bp):
TTTCATAAAA
Found at i:5320968 original size:28 final size:29
Alignment explanation
Indices: 5320936--5320990 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
5320926 TGGAGCAAAT
5320936 TTTTC-AAAATTACACTTTTGCCCTAAAC
1 TTTTCAAAAATTACACTTTTGCCCTAAAC
*
5320964 TTTTCAAAAATTACATTTTTGCCCTAA
1 TTTTCAAAAATTACACTTTTGCCCTAA
5320991 CTATTGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.42
Consensus pattern (29 bp):
TTTTCAAAAATTACACTTTTGCCCTAAAC
Found at i:5321000 original size:28 final size:29
Alignment explanation
Indices: 5320941--5321000 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
5320931 CAAATTTTTC
*
5320941 AAAATTACACTTTTGCCCTAAACTTTTCA
1 AAAATTACACTTTTGCCCTAAACTATTCA
* *
5320970 AAAATTACATTTTTGCCCT-AACTATTGA
1 AAAATTACACTTTTGCCCTAAACTATTCA
5320998 AAA
1 AAA
5321001 CTTGCCATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 10 0.36
29 18 0.64
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.37
Consensus pattern (29 bp):
AAAATTACACTTTTGCCCTAAACTATTCA
Found at i:5329995 original size:21 final size:21
Alignment explanation
Indices: 5329953--5329995 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5329943 CTTGTACCGG
*
5329953 TGGTGGAACTAAAGGAGTAAC
1 TGGTGGAACTAAAGGAGGAAC
* * *
5329974 TGGTGGTACTATAGGTGGAAC
1 TGGTGGAACTAAAGGAGGAAC
5329995 T
1 T
5329996 TGACCAGTCG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.09, G:0.35, T:0.26
Consensus pattern (21 bp):
TGGTGGAACTAAAGGAGGAAC
Found at i:5334306 original size:5 final size:5
Alignment explanation
Indices: 5334289--5334321 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
5334279 TAAGAATTAG
*
5334289 AAATT AAAAT AAATT AAATT AAATT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAATT AAA
5334322 ATTTGTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (5 bp):
AAATT
Found at i:5334402 original size:34 final size:32
Alignment explanation
Indices: 5334350--5334435 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 32
5334340 AAAGAAATTA
*
5334350 AAATAAAATATATAATATAAAAAATTATATTAAAG
1 AAATAAAATA-A-AATATAAAAAATTATAAT-AAG
* *
5334385 AAATGAAAATAAAATATATAAGATTATAATAAG
1 AAAT-AAAATAAAATATAAAAAATTATAATAAG
5334418 AAATAAAAATAAAATATA
1 AAAT-AAAATAAAATATA
5334436 TGGCATTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
33 20 0.43
34 15 0.33
35 5 0.11
36 6 0.13
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (32 bp):
AAATAAAATAAAATATAAAAAATTATAATAAG
Found at i:5334687 original size:15 final size:15
Alignment explanation
Indices: 5334648--5334691 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
5334638 TGTTATTTTC
5334648 CCTGCAATCACATTA
1 CCTGCAATCACATTA
* *
5334663 CTTGCGATCACATTA
1 CCTGCAATCACATTA
*
5334678 CCTGTAATCACATT
1 CCTGCAATCACATT
5334692 GTATTGTAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.32
Consensus pattern (15 bp):
CCTGCAATCACATTA
Found at i:5339201 original size:28 final size:27
Alignment explanation
Indices: 5339162--5339215 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
5339152 ATGTCTTGGT
**
5339162 GGTGGAAAATTACTGTTTTGCCCCTAG
1 GGTGGAAAATTACCATTTTGCCCCTAG
5339189 GGTGGCAAAATTACCATTTTGCCCCTA
1 GGTGG-AAAATTACCATTTTGCCCCTA
5339216 TGCTCTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (27 bp):
GGTGGAAAATTACCATTTTGCCCCTAG
Found at i:5343103 original size:19 final size:19
Alignment explanation
Indices: 5343079--5343116 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5343069 ACTTCTAAAC
5343079 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
5343098 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
5343117 AGTCAAAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:5343782 original size:25 final size:24
Alignment explanation
Indices: 5343754--5343814 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 24
5343744 TGGACTTCTC
5343754 CCATTTCTT-TTTAATTGGACCATGT
1 CCATTT-TTCTTT-ATTGGACCATGT
5343779 CCATTTTTCCTTTATTGGACCATGT
1 CCATTTTT-CTTTATTGGACCATGT
5343804 CCATTTTTCTT
1 CCATTTTTCTT
5343815 GTTTGTTGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
24 5 0.15
25 26 0.76
26 3 0.09
ACGTcount: A:0.16, C:0.23, G:0.10, T:0.51
Consensus pattern (24 bp):
CCATTTTTCTTTATTGGACCATGT
Found at i:5343834 original size:27 final size:27
Alignment explanation
Indices: 5343757--5343844 Score: 101
Period size: 27 Copynumber: 3.3 Consensus size: 27
5343747 ACTTCTCCCA
5343757 TTTCTT-TTTAATTGGACCATGTCCATT
1 TTTCTTGTTT-ATTGGACCATGTCCATT
*
5343784 TTTC--CTTTATTGGACCATGTCCATT
1 TTTCTTGTTTATTGGACCATGTCCATT
* * *
5343809 TTTCTTGTTTGTTGGGCCATGCCCATT
1 TTTCTTGTTTATTGGACCATGTCCATT
*
5343836 TTCCTTGTT
1 TTTCTTGTT
5343845 ATTTTCTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
25 21 0.40
26 3 0.06
27 29 0.55
ACGTcount: A:0.12, C:0.22, G:0.15, T:0.51
Consensus pattern (27 bp):
TTTCTTGTTTATTGGACCATGTCCATT
Found at i:5343860 original size:5 final size:5
Alignment explanation
Indices: 5343846--5343920 Score: 111
Period size: 5 Copynumber: 15.6 Consensus size: 5
5343836 TTCCTTGTTA
* *
5343846 TTTTC TTTTC CTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTCC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
5343896 TTTTC TTTTC -TTTC -TTTC -TTTC TTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTT
5343921 CTCTCCCACC
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
4 12 0.18
5 53 0.82
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:5344099 original size:33 final size:34
Alignment explanation
Indices: 5344055--5344134 Score: 92
Period size: 33 Copynumber: 2.3 Consensus size: 34
5344045 ATTTTTCAAT
*
5344055 AGCTAAGGCTGCTTAT-TTTTGCTTCAAAA-TCAGC
1 AGCTAA-GCTGC-TATGTTTTGCCTCAAAATTCAGC
* *
5344089 AGCTATGCTGCTATGTTTTTCCTCAAAATTTCAGC
1 AGCTAAGCTGCTATGTTTTGCCTCAAAA-TTCAGC
5344124 AGCTAAGCTGC
1 AGCTAAGCTGC
5344135 ACCTTTCCCT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
32 3 0.08
33 16 0.41
34 5 0.13
35 15 0.38
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (34 bp):
AGCTAAGCTGCTATGTTTTGCCTCAAAATTCAGC
Found at i:5347971 original size:28 final size:28
Alignment explanation
Indices: 5347892--5347972 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 28
5347882 CATGGGCAAT
* *
5347892 TTTGGATTTGGTTTAGGTGCCTTAGCACC
1 TTTGGATTTGG-TTAAGTGCCTTAACACC
* *
5347921 TTTAGATTTTGGTTAAGTACCTTAACACC
1 TTTGGA-TTTGGTTAAGTGCCTTAACACC
* *
5347950 TTTGGATTTGGCTACGTGCCTTA
1 TTTGGATTTGGTTAAGTGCCTTA
5347973 CCACACGTGG
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
28 14 0.33
29 24 0.56
30 5 0.12
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.42
Consensus pattern (28 bp):
TTTGGATTTGGTTAAGTGCCTTAACACC
Found at i:5351408 original size:120 final size:117
Alignment explanation
Indices: 5351197--5351433 Score: 447
Period size: 120 Copynumber: 2.0 Consensus size: 117
5351187 ATATTTATGA
5351197 TAATATCTATTTACTCATTGGGATTGTAAAATCTCACCCACCTCCTTTTCAAATATTTCAGGCCT
1 TAATATCTATTTACTCATTGGGATTGTAAAATCTCACCCACCTCCTTTTCAAATATTTCAGGCCT
5351262 GTGGTAGCTTGTAAATACCGATTTTGTCGAGGATTTCAGTTGACCCCTCTAT
66 GTGGTAGCTTGTAAATACCGATTTTGTCGAGGATTTCAGTTGACCCCTCTAT
5351314 NTAATATCTATTTACTCATTGGGATTGTAAAAATCTCACCCACCTCCTTTTCCAAATATTTCAGG
1 -TAATATCTATTTACTCATTGGGATTGT-AAAATCTCACCCACCTCCTTTT-CAAATATTTCAGG
5351379 CCTGTGGTAGCTTGTAAATACCGATTTTGTCGAGGATTTCAGTTGACCCCTCTAT
63 CCTGTGGTAGCTTGTAAATACCGATTTTGTCGAGGATTTCAGTTGACCCCTCTAT
5351434 CTCACAGATA
Statistics
Matches: 117, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
118 27 0.23
119 22 0.19
120 68 0.58
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.37
Consensus pattern (117 bp):
TAATATCTATTTACTCATTGGGATTGTAAAATCTCACCCACCTCCTTTTCAAATATTTCAGGCCT
GTGGTAGCTTGTAAATACCGATTTTGTCGAGGATTTCAGTTGACCCCTCTAT
Found at i:5357611 original size:17 final size:17
Alignment explanation
Indices: 5357586--5357619 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5357576 ACAAATGAAA
*
5357586 TTGATTTTATATGATAT
1 TTGAATTTATATGATAT
5357603 TTGAATTTATATGATAT
1 TTGAATTTATATGATAT
5357620 CTATTTTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (17 bp):
TTGAATTTATATGATAT
Found at i:5357887 original size:28 final size:27
Alignment explanation
Indices: 5357855--5357941 Score: 111
Period size: 28 Copynumber: 3.1 Consensus size: 27
5357845 TTCTAATAAT
*
5357855 AATACTTATAATCTACTAGGACTGGATG
1 AATACTTTTAA-CTACTAGGACTGGATG
* *
5357883 AATACTTTTAACTAACTAGGATTGGGTG
1 AATACTTTTAACT-ACTAGGACTGGATG
* *
5357911 AATACTTTTAACCACTAGGAGTGGATG
1 AATACTTTTAACTACTAGGACTGGATG
5357938 AATA
1 AATA
5357942 ATAAAGAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
27 18 0.35
28 34 0.65
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.32
Consensus pattern (27 bp):
AATACTTTTAACTACTAGGACTGGATG
Found at i:5359599 original size:250 final size:251
Alignment explanation
Indices: 5359093--5359646 Score: 711
Period size: 250 Copynumber: 2.2 Consensus size: 251
5359083 GTCAGGTTTT
* * * * * *
5359093 ACAAGGATTGTCAAAATATTAACGTAAATGTGTGAGATTTAATATAACAAATCAATTATATCAAA
1 ACAAGCATTGTCAAAATATTGACGTAAATATGTGATATTTAATATAACAAGTCAATGATATCAAA
* *
5359158 TTAACATAATTTTTAGGAAAATTAAACATTTAAATTGTTATTCTCAAGTTTAAAGTGTTTTACTA
66 TAAACATAATTTTTAGG-AAATTAAACATTTAAATTGTTATTCTCAAGTTTAAAGTATTTTACTA
* * *
5359223 CTTACAAATTTTAATCTATGCATGAATGATAGTAAGAATAAAAAGAATTATGGTGAAAATTAGTT
130 CTTACAAATTTTAATCTATGCATGAATAATAGTAAGAATAAAAAGAATTACGGTGAAAATTAGTA
* * ** * *
5359288 GTTGAAAAACCTTGACATAAAGTGATAGGAATTAGCTTAAAACATTATAAAAGTGGA
195 GTAGAAAAACCTTGACATAAACTGATAAAAATTAACGTAAAACATTATAAAAGTGGA
* * * * *
5359345 ACAAGCATTTTCAAAATGTTGACGTAAATATGTGATATTTAATGTAACAAGTCAATGATGTCTAA
1 ACAAGCATTGTCAAAATATTGACGTAAATATGTGATATTTAATATAACAAGTCAATGATATCAAA
* * *
5359410 TAAACATAATTTTTGAGG-AATTAAACATTTGAATTGTTATTCTCGAGTTTAAGGTATTTTA-TA
66 TAAACATAATTTTT-AGGAAATTAAACATTTAAATTGTTATTCTCAAGTTTAAAGTATTTTACTA
* * *
5359473 GCTTATAAATTTTAATCTATGCATGAATAATAGTGAGGAT-AAAAGAATTACGGTGAAAATTAGT
130 -CTTACAAATTTTAATCTATGCATGAATAATAGTAAGAATAAAAAGAATTACGGTGAAAATTAGT
* * * *
5359537 AGTAGAAAAACCTTGACGTAAACTGGTAAAAATTAACGTAAAACATTAT-AAGGATTGA
194 AGTAGAAAAACCTTGACATAAACTGATAAAAATTAACGTAAAACATTATAAAAG-TGGA
* * ** *
5359595 ACAAGCATTGTAAAAATATTGATGTAAATACATGATATTTAACATAACAAGT
1 ACAAGCATTGTCAAAATATTGACGTAAATATGTGATATTTAATATAACAAGT
5359647 AAAATCCTAC
Statistics
Matches: 259, Mismatches: 40, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
249 3 0.01
250 112 0.43
251 74 0.29
252 67 0.26
253 3 0.01
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.34
Consensus pattern (251 bp):
ACAAGCATTGTCAAAATATTGACGTAAATATGTGATATTTAATATAACAAGTCAATGATATCAAA
TAAACATAATTTTTAGGAAATTAAACATTTAAATTGTTATTCTCAAGTTTAAAGTATTTTACTAC
TTACAAATTTTAATCTATGCATGAATAATAGTAAGAATAAAAAGAATTACGGTGAAAATTAGTAG
TAGAAAAACCTTGACATAAACTGATAAAAATTAACGTAAAACATTATAAAAGTGGA
Found at i:5362851 original size:28 final size:28
Alignment explanation
Indices: 5362819--5362897 Score: 115
Period size: 28 Copynumber: 2.8 Consensus size: 28
5362809 TTCTGGTGGT
*
5362819 GGAAAATTACAATTTTGCCCCTAGGGTG
1 GGAAAATTACAATTTTGCCCCTAAGGTG
5362847 GGAAAATTACAATTTTGCCCCTAAGGTG
1 GGAAAATTACAATTTTGCCCCTAAGGTG
* *
5362875 GCAAAATTATC-ATTTTACCCCTA
1 GGAAAATTA-CAATTTTGCCCCTA
5362898 TACTCCAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
28 46 0.98
29 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (28 bp):
GGAAAATTACAATTTTGCCCCTAAGGTG
Found at i:5364291 original size:20 final size:21
Alignment explanation
Indices: 5364246--5364292 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
5364236 AGATGTCTAA
*
5364246 AATAATTATTTGAAATGAAAT
1 AATAATTATTTGAAATAAAAT
* *
5364267 TATAATTGTTTG-AATAAAAT
1 AATAATTATTTGAAATAAAAT
5364287 AATAAT
1 AATAAT
5364293 ATTCAATGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (21 bp):
AATAATTATTTGAAATAAAAT
Found at i:5368506 original size:19 final size:19
Alignment explanation
Indices: 5368482--5368519 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5368472 TGCCAAACCC
*
5368482 TCAAATTATACACCAATAA
1 TCAAATCATACACCAATAA
*
5368501 TCAAATCATACTCCAATAA
1 TCAAATCATACACCAATAA
5368520 GTTAAATGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (19 bp):
TCAAATCATACACCAATAA
Found at i:5372179 original size:15 final size:15
Alignment explanation
Indices: 5372159--5372209 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
5372149 TTCTTAAAAC
5372159 AACTTTAAAATCAAA
1 AACTTTAAAATCAAA
*
5372174 AACTTTAAAATCCAA
1 AACTTTAAAATCAAA
*
5372189 AGCTTTAAAATCAAA
1 AACTTTAAAATCAAA
*
5372204 ATCTTT
1 AACTTT
5372210 GATCTTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.51, C:0.16, G:0.02, T:0.31
Consensus pattern (15 bp):
AACTTTAAAATCAAA
Found at i:5372603 original size:20 final size:21
Alignment explanation
Indices: 5372558--5372604 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
5372548 AGATGTCTAA
*
5372558 AATAATTATTTGAAATGAAAT
1 AATAATTATTTGAAATAAAAT
* *
5372579 TATAATTGTTTG-AATAAAAT
1 AATAATTATTTGAAATAAAAT
5372599 AATAAT
1 AATAAT
5372605 ATTCAATNNN
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (21 bp):
AATAATTATTTGAAATAAAAT
Found at i:5378019 original size:122 final size:121
Alignment explanation
Indices: 5377784--5378026 Score: 337
Period size: 122 Copynumber: 2.0 Consensus size: 121
5377774 TATGTCCATA
5377784 TATTGATAATCTTTATAAATTTCATGATCATGAAAACTACAAATTACAAACTAGCTTTCTATCAT
1 TATTGATAATCTTTATAAATTTCATGATCATGAAAACTACAAATTACAAACTAGCTTTCTATCAT
* * * *
5377849 ACGCACACTATTAGAACATTAATTTCAACATGTTTAATTCTCCTTTGGTGGTATGT
66 ACGCACACTATTAGAACAGTAATTTCAACATATGTAATTCTCCCTTGGTGGTATGT
* * *
5377905 NTATTGATAATCTTTATATATTTCATGATCATGAAAACTACAACTTACAAACTAGGTTTCTATCA
1 -TATTGATAATCTTTATAAATTTCATGATCATGAAAACTACAAATTACAAACTAGCTTTCTATCA
* *** *
5377970 TATGCATTTTATTAGTACAGTAATTTTC-ACATATGTAA-TCTACCCTTGGTGGTATGT
65 TACGCACACTATTAGAACAGTAA-TTTCAACATATGTAATTCT-CCCTTGGTGGTATGT
5378027 CAAAATCATC
Statistics
Matches: 107, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
121 3 0.03
122 100 0.93
123 4 0.04
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (121 bp):
TATTGATAATCTTTATAAATTTCATGATCATGAAAACTACAAATTACAAACTAGCTTTCTATCAT
ACGCACACTATTAGAACAGTAATTTCAACATATGTAATTCTCCCTTGGTGGTATGT
Found at i:5381037 original size:10 final size:10
Alignment explanation
Indices: 5381007--5381040 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
5380997 CCTCACCAAA
5381007 CATAAAATAT
1 CATAAAATAT
5381017 CACTAAAATAT
1 CA-TAAAATAT
*
5381028 CATGAAATAT
1 CATAAAATAT
5381038 CAT
1 CAT
5381041 CAATTTCAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.53, C:0.15, G:0.03, T:0.29
Consensus pattern (10 bp):
CATAAAATAT
Found at i:5382708 original size:76 final size:76
Alignment explanation
Indices: 5382612--5382771 Score: 232
Period size: 76 Copynumber: 2.1 Consensus size: 76
5382602 TGCGATCTAT
* * *
5382612 TTTAATTTTGGATGATTCATAAAAAATAGGAAATTGTTTCCTACTTTAAAAGCAATTCCTAAAAT
1 TTTAATTTTGGATGATTCATAAAAAATAGGAAATTATTTCCTACTTTAAAAGAAATTCAT-AAAT
5382677 TAAAGATAG-AA
65 TAAAGATAGTAA
* * *
5382688 TTTAATTTTGGGTGTTTCATAAAGAATAGGAAATTATTTCCTACTTTAAAAGAAATTCATAAATT
1 TTTAATTTTGGATGATTCATAAAAAATAGGAAATTATTTCCTACTTTAAAAGAAATTCATAAATT
* *
5382753 AAGGATAGTAT
66 AAAGATAGTAA
5382764 TTTAATTT
1 TTTAATTT
5382772 GGAAAATTAT
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
75 12 0.16
76 63 0.84
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.39
Consensus pattern (76 bp):
TTTAATTTTGGATGATTCATAAAAAATAGGAAATTATTTCCTACTTTAAAAGAAATTCATAAATT
AAAGATAGTAA
Found at i:5395523 original size:2 final size:2
Alignment explanation
Indices: 5395516--5395558 Score: 77
Period size: 2 Copynumber: 21.0 Consensus size: 2
5395506 TATTTTTCAG
5395516 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
5395559 ANCTATAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5395610 original size:2 final size:2
Alignment explanation
Indices: 5395603--5395646 Score: 79
Period size: 2 Copynumber: 21.5 Consensus size: 2
5395593 AAGTTATTTT
5395603 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
5395646 T
1 T
5395647 GAAATGCGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5397722 original size:73 final size:72
Alignment explanation
Indices: 5397584--5397765 Score: 201
Period size: 73 Copynumber: 2.5 Consensus size: 72
5397574 AACAGAGAAG
* *
5397584 ACTTAGTCAACTAAGAAGTAAGTTAGTCGATTAAGAGCCTACTGCCAAAAATCTAGACTTCAAGA
1 ACTTAGTCAACTAAGAAGGAAGTTAGTCGACTAAGAGCCTACTGCCAAAAATCTAGAC-TCAAGA
5397649 TAGAA-ACA
65 TA-AAGACA
* * * * *
5397657 ACTTAATCGACTAAGAAGGAAGTTAGTGGACTAAGAGCTTACTGCCAAAAA-CTGGGA-TCAGAA
1 ACTTAGTCAACTAAGAAGGAAGTTAGTCGACTAAGAGCCTACTGCCAAAAATCT-AGACTC--AA
5397720 GATAAAGACA
63 GATAAAGACA
* *
5397730 ACTTAGTCAACTAAG-AGCGTAGTTAGTCGACGAAGA
1 ACTTAGTCAACTAAGAAG-GAAGTTAGTCGACTAAGA
5397766 TCATTCTGTC
Statistics
Matches: 92, Mismatches: 12, Indels: 10
0.81 0.11 0.09
Matches are distributed among these distances:
71 2 0.02
72 6 0.07
73 84 0.91
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.21
Consensus pattern (72 bp):
ACTTAGTCAACTAAGAAGGAAGTTAGTCGACTAAGAGCCTACTGCCAAAAATCTAGACTCAAGAT
AAAGACA
Found at i:5401943 original size:13 final size:13
Alignment explanation
Indices: 5401925--5401949 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5401915 AGAGAAATTG
5401925 TGATTTTATAAAA
1 TGATTTTATAAAA
5401938 TGATTTTATAAA
1 TGATTTTATAAA
5401950 TTTTCTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:5412560 original size:352 final size:352
Alignment explanation
Indices: 5411913--5412620 Score: 1308
Period size: 352 Copynumber: 2.0 Consensus size: 352
5411903 AAATCAATTG
*
5411913 CATAAGGATATTCTATGTAGTGTCACAAGTTTGAGTCAAAAATGGAAAGCCAAAAACTAAATAAA
1 CATAAGGATAGTCTATGTAGTGTCACAAGTTTGAGTCAAAAATGGAAAGCCAAAAACTAAATAAA
5411978 TATATATTTATGAAAATAGTGAAACTATTTGCACCAAATTATGAAATTATAAGTTAAATTAATTA
66 TATATATTTATGAAAATAGTGAAACTATTTGCACCAAATTATGAAATTATAAGTTAAATTAATTA
5412043 AATTGTCATAAAAAACACATTATCTCAAAGAAACTATTTCATTCTTAATTAAAAAACAATGAAGC
131 AATTGTCATAAAAAACACATTATCTCAAAGAAACTATTTCATTCTTAATTAAAAAACAATGAAGC
* *
5412108 TATTTGATTTGAATAAATTAAAGGCTAAGTTTAGTGGTTATTAATTTTCTATATATTTAGGTTTT
196 TATTTGATTTAAATAAATTAAAGGCTAAGTTTAGTGGTTATTAATTTTCTATATATTTAGATTTT
*
5412173 GCTATTCCTACTTGTTTGTTTTTTTTCAATCAATCAGTAAATTTCATTAATACCATTATACTAAA
261 GCTATTCCTACTTGTTTGTTTTTTCTCAATCAATCAGTAAATTTCATTAATACCATTATACTAAA
5412238 CCTTTATAAATACTAATAATTGTTATT
326 CCTTTATAAATACTAATAATTGTTATT
5412265 CATAAGGATAGTCTATGTAGTGTCACAAGTTTGAGTCAAAAATGGAAAGCCAAAAACTAAATAAA
1 CATAAGGATAGTCTATGTAGTGTCACAAGTTTGAGTCAAAAATGGAAAGCCAAAAACTAAATAAA
* *
5412330 TATATATTTATGAAAATAGTGAATCTATTTGCTCCAAATTATGAAATTATAAGTTAAATTAATTA
66 TATATATTTATGAAAATAGTGAAACTATTTGCACCAAATTATGAAATTATAAGTTAAATTAATTA
*
5412395 AATTGTCATAAAAAACACATTATCTCAAAGAAACTATTTCATTCTTAGTTAAAAAACAATGAAGC
131 AATTGTCATAAAAAACACATTATCTCAAAGAAACTATTTCATTCTTAATTAAAAAACAATGAAGC
* *
5412460 TATTTGATTTAAATAAATTAAAGGCTATGTTTAGTGGTTATTAATTTTCTCTATATTTAGATTTT
196 TATTTGATTTAAATAAATTAAAGGCTAAGTTTAGTGGTTATTAATTTTCTATATATTTAGATTTT
* * *
5412525 GCTATTCCTATTTGTTTGTTTTTTCTCAGTCAATCAGTAAATTTCATTACTACCATTATACTAAA
261 GCTATTCCTACTTGTTTGTTTTTTCTCAATCAATCAGTAAATTTCATTAATACCATTATACTAAA
5412590 CCTTTATAAATACTAATAATTGTTATT
326 CCTTTATAAATACTAATAATTGTTATT
5412617 CATA
1 CATA
5412621 TTTTTCTTTT
Statistics
Matches: 344, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
352 344 1.00
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39
Consensus pattern (352 bp):
CATAAGGATAGTCTATGTAGTGTCACAAGTTTGAGTCAAAAATGGAAAGCCAAAAACTAAATAAA
TATATATTTATGAAAATAGTGAAACTATTTGCACCAAATTATGAAATTATAAGTTAAATTAATTA
AATTGTCATAAAAAACACATTATCTCAAAGAAACTATTTCATTCTTAATTAAAAAACAATGAAGC
TATTTGATTTAAATAAATTAAAGGCTAAGTTTAGTGGTTATTAATTTTCTATATATTTAGATTTT
GCTATTCCTACTTGTTTGTTTTTTCTCAATCAATCAGTAAATTTCATTAATACCATTATACTAAA
CCTTTATAAATACTAATAATTGTTATT
Found at i:5417464 original size:206 final size:207
Alignment explanation
Indices: 5417097--5417477 Score: 586
Period size: 206 Copynumber: 1.8 Consensus size: 207
5417087 GGGTTGAGTC
* * *
5417097 GAATTCGGTTGGTATCAGAGCAAAGGGAAAGATAACCTTATTCCTGGGAACTCTCGCATATGATC
1 GAATTCGGTTGGTATCAAAGCAAAGGGAAAGATAACCCTATTCCTGAGAACTCTCGCATATGATC
* *
5417162 TATGGCGAAGTATAACTCTCCACCCAGGAGCTTAGAAGAGGAAGGAAAGGACTGCTCCCGATGCG
66 TATGGCGAAGTATAACTCTCCACCCAGGAGCTTAGAAGAAGAAGGAAAGGACTGCTCCAGATGCG
* *
5417227 TCCTGGAGTGAAGTGCACCTCTTGTCGAGTGCTCTGATAGGTACCATTACATGCCACCATGCCTT
131 TCCTGGAGTGAAGTGCACATCTTGCCGAGTGCTCTGATAGGTACCATTACATGCCACCATGCCTT
5417292 GAGGGGTGCGCA
196 GAGGGGTGCGCA
* *
5417304 GAATTCTG-TGGTATCAAAGCAAAGGGAAAGATAACCCTATTCCTGAGAACTCTCGTATATGATC
1 GAATTCGGTTGGTATCAAAGCAAAGGGAAAGATAACCCTATTCCTGAGAACTCTCGCATATGATC
* * * * * *
5417368 TATGGCGTAGTATGACTCTCCGCCCAGGAGCTTGGAAGAAGAGGGAAGGGACTGCTCCTAG-TGC
66 TATGGCGAAGTATAACTCTCCACCCAGGAGCTTAGAAGAAGAAGGAAAGGACTGCTCC-AGATGC
* *
5417432 GTCTTGGAGTGAAGTGCACATCTTGCCGAGTGCTTTGATAGGTACC
130 GTCCTGGAGTGAAGTGCACATCTTGCCGAGTGCTCTGATAGGTACC
5417478 CTTGAATGCC
Statistics
Matches: 156, Mismatches: 17, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
206 148 0.95
207 8 0.05
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.24
Consensus pattern (207 bp):
GAATTCGGTTGGTATCAAAGCAAAGGGAAAGATAACCCTATTCCTGAGAACTCTCGCATATGATC
TATGGCGAAGTATAACTCTCCACCCAGGAGCTTAGAAGAAGAAGGAAAGGACTGCTCCAGATGCG
TCCTGGAGTGAAGTGCACATCTTGCCGAGTGCTCTGATAGGTACCATTACATGCCACCATGCCTT
GAGGGGTGCGCA
Found at i:5421324 original size:13 final size:13
Alignment explanation
Indices: 5421306--5421330 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5421296 GGAAAATGGG
5421306 ATTTTATAAAATA
1 ATTTTATAAAATA
5421319 ATTTTATAAAAT
1 ATTTTATAAAAT
5421331 TTTTGAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:5436826 original size:11 final size:11
Alignment explanation
Indices: 5436812--5436841 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5436802 AATAATATTT
5436812 TATTAATAAAA
1 TATTAATAAAA
*
5436823 TATTATTAAAA
1 TATTAATAAAA
5436834 TATTAATA
1 TATTAATA
5436842 TTTTGACTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATTAATAAAA
Found at i:5437913 original size:41 final size:40
Alignment explanation
Indices: 5437857--5437971 Score: 131
Period size: 41 Copynumber: 2.7 Consensus size: 40
5437847 ATTTTGTATG
*
5437857 ATTTTACTTATTTGTTAGGTAAAATTTGCATGATGTAATT
1 ATTTTACTTATTTGTTAGGTAAAATTTGCATGATGTAATC
*
5437897 ATTTTTACTTATTTGTTAAGTAAAATTTATAAAATGCATGATGTAATC
1 A-TTTTACTTATTTGTTAGGTAAAA--T-T----TGCATGATGTAATC
*
5437945 ATTTTACATATTTGTTAGGTAAAATTT
1 ATTTTACTTATTTGTTAGGTAAAATTT
5437972 ATAAAATGCA
Statistics
Matches: 63, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
40 2 0.03
41 22 0.35
43 1 0.02
44 2 0.03
45 1 0.02
47 21 0.33
48 14 0.22
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.49
Consensus pattern (40 bp):
ATTTTACTTATTTGTTAGGTAAAATTTGCATGATGTAATC
Found at i:5437967 original size:47 final size:47
Alignment explanation
Indices: 5437883--5438014 Score: 210
Period size: 47 Copynumber: 2.8 Consensus size: 47
5437873 AGGTAAAATT
*
5437883 TGCATGATGTAATTATTTTTACTTATTTGTTAAGTAAAATTTATAAAA
1 TGCATGATGTAATCA-TTTTACTTATTTGTTAAGTAAAATTTATAAAA
* *
5437931 TGCATGATGTAATCATTTTACATATTTGTTAGGTAAAATTTATAAAA
1 TGCATGATGTAATCATTTTACTTATTTGTTAAGTAAAATTTATAAAA
**
5437978 TGCATGGCGTAATCATTTTACTTATTTGTTAAGTAAA
1 TGCATGATGTAATCATTTTACTTATTTGTTAAGTAAA
5438015 CTTGTATGCA
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
47 63 0.82
48 14 0.18
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.45
Consensus pattern (47 bp):
TGCATGATGTAATCATTTTACTTATTTGTTAAGTAAAATTTATAAAA
Found at i:5458334 original size:2 final size:2
Alignment explanation
Indices: 5458327--5458365 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5458317 AATTCAAACC
5458327 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5458366 NNNNNNNNNN
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5460539 original size:21 final size:21
Alignment explanation
Indices: 5460514--5460614 Score: 69
Period size: 21 Copynumber: 4.5 Consensus size: 21
5460504 TGAGATAGGA
5460514 TAAATTTAAATTTAATTTGTT
1 TAAATTTAAATTTAATTTGTT
*
5460535 TAAATTTAAATTATCTATCCATTGTATT
1 TAAATTTAAA-T-T-TA---ATT-TGTT
* * * *
5460563 TAAA-TTAAAATAAAGATTGAT
1 TAAATTTAAATTTAA-TTTGTT
*
5460584 TATATTTAAATTTAATTTGTT
1 TAAATTTAAATTTAATTTGTT
5460605 TAAATTTAAA
1 TAAATTTAAA
5460615 CGTAATATCC
Statistics
Matches: 59, Mismatches: 12, Indels: 18
0.66 0.13 0.20
Matches are distributed among these distances:
21 29 0.49
22 10 0.17
23 1 0.02
24 3 0.05
25 1 0.02
27 8 0.14
28 7 0.12
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.50
Consensus pattern (21 bp):
TAAATTTAAATTTAATTTGTT
Found at i:5461739 original size:31 final size:31
Alignment explanation
Indices: 5461672--5461746 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
5461662 TTCAAGTTTA
* *
5461672 AGGTTATACTTTAACCATTGAAAGGTAGAGT
1 AGGTTATACCTTAACCATTGAAAGGTAAAGT
*
5461703 TGGTTATACCTTAACCATTGAAAAGGTAAAG-
1 AGGTTATACCTTAACCATTG-AAAGGTAAAGT
*
5461734 AGGTTAAACCTTA
1 AGGTTATACCTTA
5461747 GCTTTGAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
31 29 0.76
32 9 0.24
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (31 bp):
AGGTTATACCTTAACCATTGAAAGGTAAAGT
Found at i:5464259 original size:18 final size:18
Alignment explanation
Indices: 5464236--5464272 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
5464226 TAGAAATTAA
5464236 AAGGTTTATTTTATATAT
1 AAGGTTTATTTTATATAT
*
5464254 AAGGTTTATTTTATTTAT
1 AAGGTTTATTTTATATAT
5464272 A
1 A
5464273 TTTTATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (18 bp):
AAGGTTTATTTTATATAT
Found at i:5472659 original size:19 final size:19
Alignment explanation
Indices: 5472635--5472672 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5472625 CTGCCAAACC
*
5472635 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
5472654 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
5472673 AGTTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:5484436 original size:15 final size:15
Alignment explanation
Indices: 5484397--5484442 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
5484387 AGATTAGAGA
*
5484397 TTTTGGTTTTAAA-A
1 TTTTGGTTTTAAAGT
*
5484411 CTTTGGATTTTAAAGT
1 TTTTGG-TTTTAAAGT
5484427 TTTTGGTTTTAAAGT
1 TTTTGGTTTTAAAGT
5484442 T
1 T
5484443 GTTTTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 5 0.19
15 17 0.63
16 5 0.19
ACGTcount: A:0.24, C:0.02, G:0.17, T:0.57
Consensus pattern (15 bp):
TTTTGGTTTTAAAGT
Found at i:5493044 original size:37 final size:38
Alignment explanation
Indices: 5492945--5493048 Score: 102
Period size: 42 Copynumber: 2.7 Consensus size: 38
5492935 ATTGTAAGGA
* * * * *
5492945 AAATCTGATACTCTTCTCTTTCTTAGAATCTATAAAAG
1 AAATTTGATCCTCTTTTCTTCCTTAGAATATATAAAAG
**
5492983 AAAGTTAAATCCTTCTCTTCTCTTCCTTAGAATATAT-AAAG
1 AAA-TTTGATCC-TCT-TT-TCTTCCTTAGAATATATAAAAG
5493024 AAATTTGATCCTCTTTTCTTCCTTA
1 AAATTTGATCCTCTTTTCTTCCTTA
5493049 AAATCTACGA
Statistics
Matches: 53, Mismatches: 9, Indels: 9
0.75 0.13 0.13
Matches are distributed among these distances:
37 9 0.17
38 5 0.09
39 7 0.13
40 9 0.17
41 8 0.15
42 15 0.28
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.42
Consensus pattern (38 bp):
AAATTTGATCCTCTTTTCTTCCTTAGAATATATAAAAG
Found at i:5493318 original size:21 final size:19
Alignment explanation
Indices: 5493287--5493328 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
5493277 ATTAAAAAGA
5493287 TTAAAAAGATGGGAATCAG
1 TTAAAAAGATGGGAATCAG
*
5493306 TTAAGAAATGATGGTAATCAG
1 TTAA-AAA-GATGGGAATCAG
5493327 TT
1 TT
5493329 TGAAGGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 3 0.15
21 13 0.65
ACGTcount: A:0.43, C:0.05, G:0.24, T:0.29
Consensus pattern (19 bp):
TTAAAAAGATGGGAATCAG
Found at i:5495138 original size:10 final size:10
Alignment explanation
Indices: 5495123--5495182 Score: 68
Period size: 10 Copynumber: 6.0 Consensus size: 10
5495113 GGAGTTCAAG
5495123 GAGAGAGAAA
1 GAGAGAGAAA
*
5495133 GAGAGAAAAA
1 GAGAGAGAAA
5495143 GAGAGA-AAA
1 GAGAGAGAAA
*
5495152 GAAAGAGGAAA
1 GAGAGA-GAAA
*
5495163 GAGAAAGAAA
1 GAGAGAGAAA
*
5495173 GGGAGAGAAA
1 GAGAGAGAAA
5495183 AAGGAGGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
9 8 0.19
10 27 0.64
11 7 0.17
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (10 bp):
GAGAGAGAAA
Found at i:5495162 original size:22 final size:23
Alignment explanation
Indices: 5495128--5495172 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
5495118 TCAAGGAGAG
*
5495128 AGAAAGAGAGAAAAAGAGAGAAA
1 AGAAAGAGAGAAAAAGAAAGAAA
*
5495151 AGAAAGAG-GAAAGAGAAAGAAA
1 AGAAAGAGAGAAAAAGAAAGAAA
5495173 GGGAGAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (23 bp):
AGAAAGAGAGAAAAAGAAAGAAA
Found at i:5495190 original size:30 final size:30
Alignment explanation
Indices: 5495124--5495192 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
5495114 GAGTTCAAGG
5495124 AGAGAGAAAGAGAGAAAAAGAGAGAAAAGAA
1 AGAG-GAAAGAGAGAAAAAGAGAGAAAAGAA
*
5495155 AGAGGAAAGAGA-AAGAAAGGGAGAGAAA-AA
1 AGAGGAAAGAGAGAA-AAAGAGAGA-AAAGAA
*
5495185 GGAGGAAA
1 AGAGGAAA
5495193 CTGAGGAGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 2 0.06
30 25 0.74
31 7 0.21
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (30 bp):
AGAGGAAAGAGAGAAAAAGAGAGAAAAGAA
Found at i:5509015 original size:129 final size:129
Alignment explanation
Indices: 5508785--5509044 Score: 434
Period size: 129 Copynumber: 2.0 Consensus size: 129
5508775 CATGCTGATG
*
5508785 AGTCACTCTACTGGGTTATAGTTGAGTCTTTCACTTCCGTAATATGTAAAAGTTATGTCTAAACA
1 AGTCACTCTACTAGGTTATAGTTGAGTCTTTCACTTCCGTAATATGTAAAAGTTATGTCTAAACA
5508850 GATTATGTGGGCATTACGTTACTCTATATTTACGTAATGAATTGTTTAGATGTTTTAAGAAACT
66 GATTATGTGGGCATTACGTTACTCTATATTTACGTAATGAATTGTTTAGATGTTTTAAGAAACT
* * *
5508914 AGTCACTCTGCTAGGTTATAGTTGAGT-TTTACGCTTCCGTAATATGTAAAAGTTATGTCTAAAT
1 AGTCACTCTACTAGGTTATAGTTGAGTCTTT-CACTTCCGTAATATGTAAAAGTTATGTCTAAAC
* *
5508978 AGATTATGTGGGCATTGCGTTAGC-CTATATTTACGTAATGAATTGTTTATATGTTTTAAGAAAC
65 AGATTATGTGGGCATTACGTTA-CTCTATATTTACGTAATGAATTGTTTAGATGTTTTAAGAAAC
5509042 T
129 T
5509043 AG
1 AG
5509045 CCTATGTATG
Statistics
Matches: 123, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
128 3 0.02
129 119 0.97
130 1 0.01
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (129 bp):
AGTCACTCTACTAGGTTATAGTTGAGTCTTTCACTTCCGTAATATGTAAAAGTTATGTCTAAACA
GATTATGTGGGCATTACGTTACTCTATATTTACGTAATGAATTGTTTAGATGTTTTAAGAAACT
Found at i:5509811 original size:1 final size:1
Alignment explanation
Indices: 5509805--5509868 Score: 110
Period size: 1 Copynumber: 64.0 Consensus size: 1
5509795 TTGTATTCTC
**
5509805 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAATTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5509869 CAAATCCCTA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
1 61 1.00
ACGTcount: A:0.03, C:0.00, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:5512771 original size:130 final size:129
Alignment explanation
Indices: 5512539--5512799 Score: 450
Period size: 130 Copynumber: 2.0 Consensus size: 129
5512529 CATGTTGATG
* *
5512539 AGTCACTCTACTGGGTTATAGTTGAGTATTTCGCTTCCGTAATATGTAAAAGTTATGTCTAAACA
1 AGTCACTCTACTAGGTTATAGTTGAGTATTACGCTTCCGTAATATGTAAAAGTTATGTCTAAACA
5512604 GATTATGTGGGCATTGCGTTACCCTATATTTACGTAATGAATTATTTAGATGTTTTAAAAAACT
66 GATTATGTGGGCATTGCGTTACCCTATATTTACGTAATGAATTATTTAGATGTTTTAAAAAACT
* *
5512668 AGTCACTCTGCTAGGTTATAGTTGAGTCTTAACGCTTCCGTAATATGTAAAAGTTATGTCTAAAC
1 AGTCACTCTACTAGGTTATAGTTGAGTATT-ACGCTTCCGTAATATGTAAAAGTTATGTCTAAAC
* * *
5512733 AGATTATGTGGGTATTGCGTTACCCTATATTTACGTAATGAATTGTTTAGATGTTTTAAGAAACT
65 AGATTATGTGGGCATTGCGTTACCCTATATTTACGTAATGAATTATTTAGATGTTTTAAAAAACT
5512798 AG
1 AG
5512800 CCTATGTATG
Statistics
Matches: 124, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
129 27 0.22
130 97 0.78
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (129 bp):
AGTCACTCTACTAGGTTATAGTTGAGTATTACGCTTCCGTAATATGTAAAAGTTATGTCTAAACA
GATTATGTGGGCATTGCGTTACCCTATATTTACGTAATGAATTATTTAGATGTTTTAAAAAACT
Found at i:5515728 original size:19 final size:19
Alignment explanation
Indices: 5515704--5515741 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5515694 CTGCCAAACC
*
5515704 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
5515723 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
5515742 AGTTTAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:5522234 original size:34 final size:35
Alignment explanation
Indices: 5522180--5522297 Score: 157
Period size: 35 Copynumber: 3.4 Consensus size: 35
5522170 CTTACTCAGC
* ***
5522180 TCATGTGCATTCCCTACACGCACAGGGCAATATCA
1 TCATGTGCACTCCCTACACGCACATTTCAATATCA
5522215 TCATGTGCACT-CCTACACGCACATTTCAATATCA
1 TCATGTGCACTCCCTACACGCACATTTCAATATCA
* *
5522249 TCATATGCACTCCCTACATGCACATTTCAATATCA
1 TCATGTGCACTCCCTACACGCACATTTCAATATCA
* *
5522284 TCACGTGTACTCCC
1 TCATGTGCACTCCC
5522298 GCCAACATCA
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
34 30 0.41
35 43 0.59
ACGTcount: A:0.28, C:0.33, G:0.11, T:0.28
Consensus pattern (35 bp):
TCATGTGCACTCCCTACACGCACATTTCAATATCA
Found at i:5523983 original size:35 final size:35
Alignment explanation
Indices: 5523937--5524004 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
5523927 CTCCAGTTCG
5523937 AATGGCGTTGTAACAATAGTTTATATTAAATCTCA
1 AATGGCGTTGTAACAATAGTTTATATTAAATCTCA
*
5523972 AATGGCGTTGTAATAATAGTTTATATTAAATCT
1 AATGGCGTTGTAACAATAGTTTATATTAAATCT
5524005 TTTAAGAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.40
Consensus pattern (35 bp):
AATGGCGTTGTAACAATAGTTTATATTAAATCTCA
Found at i:5524814 original size:23 final size:23
Alignment explanation
Indices: 5524777--5524841 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
5524767 AACACAACTA
5524777 TTGAAACA-AAGCAGATACATCTG
1 TTGAAACATAA-CAGATACATCTG
* * * *
5524800 TTGAAATATAACAGACATATTTG
1 TTGAAACATAACAGATACATCTG
*
5524823 TTGAAACATAGCAGATACA
1 TTGAAACATAACAGATACA
5524842 ACTTCTCAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
23 31 0.94
24 2 0.06
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (23 bp):
TTGAAACATAACAGATACATCTG
Found at i:5527906 original size:30 final size:31
Alignment explanation
Indices: 5527872--5527930 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
5527862 CCCTAGAGAG
5527872 AGAAAATCAA-AGAAAAAGTGTGA-ATTTTCA
1 AGAAAATCAAGAGAAAAA-TGTGAGATTTTCA
* *
5527902 AGAAAATTAAGTGAAAAATGTGAGATTTT
1 AGAAAATCAAGAGAAAAATGTGAGATTTT
5527931 TTCTATTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.51, C:0.03, G:0.19, T:0.27
Consensus pattern (31 bp):
AGAAAATCAAGAGAAAAATGTGAGATTTTCA
Found at i:5530939 original size:7 final size:7
Alignment explanation
Indices: 5530908--5530961 Score: 60
Period size: 7 Copynumber: 7.7 Consensus size: 7
5530898 ACTAAGCTTT
5530908 TTTCTTCC
1 TTTC-TCC
5530916 TTTCTCTC
1 TTTCTC-C
5530924 TTT-TCC
1 TTTCTCC
5530930 TTTCTCC
1 TTTCTCC
5530937 TTTCT-C
1 TTTCTCC
5530943 TCTT-TCC
1 T-TTCTCC
5530950 TTTCTCC
1 TTTCTCC
5530957 TTTCT
1 TTTCT
5530962 TTCTTTCCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
6 9 0.22
7 24 0.59
8 8 0.20
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (7 bp):
TTTCTCC
Found at i:5530950 original size:20 final size:20
Alignment explanation
Indices: 5530908--5530981 Score: 112
Period size: 20 Copynumber: 3.6 Consensus size: 20
5530898 ACTAAGCTTT
5530908 TTTCTTCCTTTCTCTCTTTTCC
1 TTTC-TCCTTTCTCTC-TTTCC
5530930 TTTCTCCTTTCTCTCTTTCC
1 TTTCTCCTTTCTCTCTTTCC
*
5530950 TTTCTCCTTTCTTTCTTTCC
1 TTTCTCCTTTCTCTCTTTCC
*
5530970 TTTCTCTTTTCT
1 TTTCTCCTTTCT
5530982 TTCAACTGAT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
20 35 0.70
21 11 0.22
22 4 0.08
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTCTCCTTTCTCTCTTTCC
Found at i:5533884 original size:15 final size:15
Alignment explanation
Indices: 5533866--5533918 Score: 74
Period size: 14 Copynumber: 3.6 Consensus size: 15
5533856 TTATTTTTCC
5533866 CTTTTTCTTTTTTTT
1 CTTTTTCTTTTTTTT
5533881 C-TTTTCTTTTTTTTT
1 CTTTTTC-TTTTTTTT
*
5533896 CTTTTT-TTTTTTGT
1 CTTTTTCTTTTTTTT
5533910 CTTTTTCTT
1 CTTTTTCTT
5533919 CTTCTTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
14 18 0.53
15 12 0.35
16 4 0.12
ACGTcount: A:0.00, C:0.13, G:0.02, T:0.85
Consensus pattern (15 bp):
CTTTTTCTTTTTTTT
Found at i:5533892 original size:12 final size:12
Alignment explanation
Indices: 5533875--5533929 Score: 60
Period size: 13 Copynumber: 4.6 Consensus size: 12
5533865 CCTTTTTCTT
5533875 TTTTTTCTTTTC
1 TTTTTTCTTTTC
5533887 -TTTTT-TTTTC
1 TTTTTTCTTTTC
* *
5533897 TTTTTTTTTTTG
1 TTTTTTCTTTTC
5533909 TCTTTTTCTTCTTC
1 T-TTTTTCTT-TTC
5533923 TTTTTTC
1 TTTTTTC
5533930 CTTCACTTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
10 5 0.14
11 10 0.28
12 5 0.14
13 13 0.36
14 3 0.08
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.84
Consensus pattern (12 bp):
TTTTTTCTTTTC
Done.