Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 38 of 66
Found at i:13326589 original size:59 final size:57
Alignment explanation
Indices: 13326468--13326592 Score: 135
Period size: 59 Copynumber: 2.2 Consensus size: 57
13326458 TCTTGTCTTT
* * **
13326468 AATTAAGACGAAACATATTATCTTATCTAAATTGAGACTAACATCTTTTCTTGTATA
1 AATTAAGACGAAACATATTATCTTATCTAAATTAAGACAAACATCTTTTCTTACATA
* * * * *
13326525 GATTAAGA-GAAAACATATTTTTCTTCTCTTAAATTAAGACAAACATGTTTTCTTACCTA
1 AATTAAGACG-AAACATA-TTATCTTATC-TAAATTAAGACAAACATCTTTTCTTACATA
13326584 AATTAAGAC
1 AATTAAGAC
13326593 AATACATGTA
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
56 1 0.02
57 14 0.26
58 8 0.15
59 31 0.57
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (57 bp):
AATTAAGACGAAACATATTATCTTATCTAAATTAAGACAAACATCTTTTCTTACATA
Found at i:13332050 original size:36 final size:39
Alignment explanation
Indices: 13331992--13332086 Score: 126
Period size: 36 Copynumber: 2.5 Consensus size: 39
13331982 TTGCCTATAT
*
13331992 GCGATGTGGGGGTTGCACATAATGGCAT-TAG-T-TGTGC
1 GCGATGTGGGGGTTGCACATAATGAC-TCTAGCTATGTGC
* *
13332029 GTGATGTAGGGG-TGCACATAATGACTCTAGCTATGTGC
1 GCGATGTGGGGGTTGCACATAATGACTCTAGCTATGTGC
13332067 GCGATGTGGGGGTTGCACAT
1 GCGATGTGGGGGTTGCACAT
13332087 GAGCTAGGTG
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
35 1 0.02
36 15 0.31
37 11 0.22
38 15 0.31
39 7 0.14
ACGTcount: A:0.20, C:0.15, G:0.37, T:0.28
Consensus pattern (39 bp):
GCGATGTGGGGGTTGCACATAATGACTCTAGCTATGTGC
Found at i:13337403 original size:2 final size:2
Alignment explanation
Indices: 13337391--13337424 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
13337381 AAGCTATTGG
*
13337391 TA TA CA 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
13337425 AGAAAAGTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:13338648 original size:68 final size:68
Alignment explanation
Indices: 13338564--13338824 Score: 278
Period size: 68 Copynumber: 3.9 Consensus size: 68
13338554 ACATGTTTAC
* ** * * *
13338564 TCATCTCATAAGGTATATGGAATTTACATCATATACATGTTCCAATGGCATTTATCATGCTTACT
1 TCATCTCATATGGTATATGGAATTTACATCATATACATAATCCTATGGCATTCATCATGCATACT
13338629 CAA
66 CAA
* * * * *
13338632 TCATCTCATGTAGTATATGGAATATACATCATATACATAA--CTCATGGCATTAATCATACATAC
1 TCATCTCATATGGTATATGGAATTTACATCATATACATAATCCT-ATGGCATTCATCATGCATAC
*
13338695 TTAA
65 TCAA
* * * * *
13338699 TCA-CTGCATATGGTATATGGAATTTACATCATATACACAATCTTATAGTATACATCATGCATAC
1 TCATCT-CATATGGTATATGGAATTTACATCATATACATAATCCTATGGCATTCATCATGCATAC
13338763 TTC-A
65 -TCAA
* * * *
13338767 TCATCTCGTATGGTATATGGAATTTACATCATAAACATATTCTTATGGCATTCATCAT
1 TCATCTCATATGGTATATGGAATTTACATCATATACATAATCCTATGGCATTCATCAT
13338825 ACCAAACATG
Statistics
Matches: 158, Mismatches: 29, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
66 3 0.02
67 53 0.34
68 98 0.62
69 4 0.03
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.36
Consensus pattern (68 bp):
TCATCTCATATGGTATATGGAATTTACATCATATACATAATCCTATGGCATTCATCATGCATACT
CAA
Found at i:13338795 original size:135 final size:136
Alignment explanation
Indices: 13338570--13338826 Score: 320
Period size: 135 Copynumber: 1.9 Consensus size: 136
13338560 TTACTCATCT
*** * ** *
13338570 CATAAGGTATATGGAATTTACATCATATACATGTTCCAATGGCATTTATCATGCTTACTCAATCA
1 CATAAGGTATATGGAATTTACATCATATACACAATCCAATAGCATACATCATGCATACTCAATCA
* *
13338635 TCTCATGTAGTATATGGAATATACATCATATACATA-ACTCATGGCATTAATCATACATACTTAA
66 TCTCATATAGTATATGGAATATACATCATAAACATATACTCATGGCATTAATCATACATACTTAA
13338699 TCACTG
131 TCACTG
* ** *
13338705 CATATGGTATATGGAATTTACATCATATACACAATCTTATAGTATACATCATGCATACTTC-ATC
1 CATAAGGTATATGGAATTTACATCATATACACAATCCAATAGCATACATCATGCATAC-TCAATC
* * * * * *
13338769 ATCTCGTATGGTATATGGAATTTACATCATAAACATATTCTTATGGCATTCATCATAC
65 ATCTCATATAGTATATGGAATATACATCATAAACATATACTCATGGCATTAATCATAC
13338827 CAAACATGCA
Statistics
Matches: 101, Mismatches: 19, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
135 82 0.81
136 19 0.19
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (136 bp):
CATAAGGTATATGGAATTTACATCATATACACAATCCAATAGCATACATCATGCATACTCAATCA
TCTCATATAGTATATGGAATATACATCATAAACATATACTCATGGCATTAATCATACATACTTAA
TCACTG
Found at i:13339704 original size:16 final size:16
Alignment explanation
Indices: 13339685--13339715 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13339675 ATAAAAAATA
13339685 AAAAAAATCAAAATCC
1 AAAAAAATCAAAATCC
*
13339701 AAAAGAATCAAAATC
1 AAAAAAATCAAAATC
13339716 TAAATTTTGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.16, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAAAAATCAAAATCC
Found at i:13345108 original size:20 final size:20
Alignment explanation
Indices: 13345083--13345127 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
13345073 ATCTTACCTT
*
13345083 TTTTC-ACTTGTTTCCTTGAA
1 TTTTCAACTT-TTCCCTTGAA
13345103 TTTTCAGACTTTTCCCTTGAA
1 TTTTCA-ACTTTTCCCTTGAA
13345124 TTTT
1 TTTT
13345128 TCCACCTAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 13 0.59
22 4 0.18
ACGTcount: A:0.16, C:0.20, G:0.09, T:0.56
Consensus pattern (20 bp):
TTTTCAACTTTTCCCTTGAA
Found at i:13348461 original size:11 final size:11
Alignment explanation
Indices: 13348445--13348472 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
13348435 CACTGTAGTT
13348445 TTTAAAACAAC
1 TTTAAAACAAC
13348456 TTTAAAACAAC
1 TTTAAAACAAC
13348467 TTTAAA
1 TTTAAA
13348473 CCCAAAAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (11 bp):
TTTAAAACAAC
Found at i:13350810 original size:21 final size:21
Alignment explanation
Indices: 13350772--13350822 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
13350762 AATCTTACCT
*
13350772 TTTTCCACTTGTTTCCTTGAA
1 TTTTCCACTTGTTCCCTTGAA
13350793 TTTTCACACTT-TTCCCTTGAA
1 TTTTC-CACTTGTTCCCTTGAA
13350814 TTTTTCCAC
1 -TTTTCCAC
13350823 CTAGGGTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.16, C:0.27, G:0.06, T:0.51
Consensus pattern (21 bp):
TTTTCCACTTGTTCCCTTGAA
Found at i:13352021 original size:21 final size:21
Alignment explanation
Indices: 13351996--13352065 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
13351986 TATTCATTGT
13351996 ATTTAAATTTAAATTGTTTAA
1 ATTTAAATTTAAATTGTTTAA
* ** *
13352017 ATTTAAA-TAAAGATTAATTAT
1 ATTTAAATTTAA-ATTGTTTAA
* *
13352038 CTTTAAATTTAATTTGTTTAA
1 ATTTAAATTTAAATTGTTTAA
13352059 ATTTAAA
1 ATTTAAA
13352066 ACTAATATCC
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
20 3 0.08
21 30 0.83
22 3 0.08
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.50
Consensus pattern (21 bp):
ATTTAAATTTAAATTGTTTAA
Found at i:13356547 original size:35 final size:35
Alignment explanation
Indices: 13356505--13356735 Score: 252
Period size: 35 Copynumber: 6.5 Consensus size: 35
13356495 GAAGTTCAAT
*** *
13356505 TAACTTAATTATTTAATTTAATCAATTAGGCCTAA
1 TAACTTAATTAAACAATTTAATTAATTAGGCCTAA
*
13356540 TAACTTAATTAAACAATTTAATTAATTAAGCCTAA
1 TAACTTAATTAAACAATTTAATTAATTAGGCCTAA
* *
13356575 CAAATTAATTAAACAATTTTAATTAATTAGGCCTAA
1 TAACTTAATTAAACAA-TTTAATTAATTAGGCCTAA
* * *
13356611 TGACTTAATTAAACAATTATAATCAATTAGGCCCAA
1 TAACTTAATTAAACAATT-TAATTAATTAGGCCTAA
* * *
13356647 TGACTTCTTAATTAAACAATTTAATAAATTAGGCCCAA
1 T-A--ACTTAATTAAACAATTTAATTAATTAGGCCTAA
* *
13356685 TGACTTAATTAAACAATTTAATTAATTA-GAC--A
1 TAACTTAATTAAACAATTTAATTAATTAGGCCTAA
*
13356717 CAACTTAATTAAACAATTT
1 TAACTTAATTAAACAATTT
13356736 TAATCAAGTG
Statistics
Matches: 169, Mismatches: 22, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
32 18 0.11
34 2 0.01
35 70 0.41
36 47 0.28
38 17 0.10
39 15 0.09
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.36
Consensus pattern (35 bp):
TAACTTAATTAAACAATTTAATTAATTAGGCCTAA
Found at i:13356724 original size:19 final size:17
Alignment explanation
Indices: 13356689--13356728 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
13356679 GCCCAATGAC
*
13356689 TTAATTAAACAATTTAA
1 TTAATTAAACAACTTAA
13356706 TTAATTAGACACAACTTAA
1 TTAATTA-A-ACAACTTAA
13356725 TTAA
1 TTAA
13356729 ACAATTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 1 0.05
19 12 0.60
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.38
Consensus pattern (17 bp):
TTAATTAAACAACTTAA
Found at i:13358753 original size:2 final size:2
Alignment explanation
Indices: 13358741--13358774 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
13358731 ACCATAAACC
*
13358741 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13358775 CAATCATCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13358862 original size:42 final size:42
Alignment explanation
Indices: 13358815--13358940 Score: 162
Period size: 42 Copynumber: 3.0 Consensus size: 42
13358805 CAGCTCATAT
13358815 GCATCGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
1 GCATCGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
* * * * *
13358857 GCATCGACTTATGTGCACTCCCACTCGTACATAGTCGAGCCA
1 GCATCGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
** * * *
13358899 GCATCGGCTTATGCACACTCCTACTTGCACATAGCCAGGTCA
1 GCATCGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
13358941 ATATCATTAC
Statistics
Matches: 69, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.22, C:0.34, G:0.21, T:0.23
Consensus pattern (42 bp):
GCATCGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
Found at i:13358969 original size:2 final size:2
Alignment explanation
Indices: 13358962--13358992 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
13358952 CAACATTATT
*
13358962 TA TA TA TA TA TA TC 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 T
13358993 CAACATAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13366827 original size:43 final size:43
Alignment explanation
Indices: 13366768--13366897 Score: 199
Period size: 43 Copynumber: 3.0 Consensus size: 43
13366758 TTTTATGATA
*
13366768 ATGATGACCAAGCTATGTGCGATGTGGGAGTGCACATGAGCTG
1 ATGATGACCCAGCTATGTGCGATGTGGGAGTGCACATGAGCTG
* * *
13366811 ATGATGACCCAGCTATGTACGGTGTGGGAGTACACATGAGCTG
1 ATGATGACCCAGCTATGTGCGATGTGGGAGTGCACATGAGCTG
*
13366854 ATGATGACCCGGCTATGTGC-ATGTAGGGAGTGCACATGAGCTG
1 ATGATGACCCAGCTATGTGCGATGT-GGGAGTGCACATGAGCTG
13366897 A
1 A
13366898 GTGTGGCGAG
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
42 3 0.04
43 75 0.96
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.23
Consensus pattern (43 bp):
ATGATGACCCAGCTATGTGCGATGTGGGAGTGCACATGAGCTG
Found at i:13368448 original size:35 final size:35
Alignment explanation
Indices: 13368381--13368451 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
13368371 TTTCACCAAG
* * * *
13368381 CTTTTACAATGGCTTTTACCGGGCTTAGCCAAAAC
1 CTTTCACAATGGCTTTTACCGGGATCAACCAAAAC
* *
13368416 CTTTCACAATGGTTTTTACTGGGATCAACCAAAAC
1 CTTTCACAATGGCTTTTACCGGGATCAACCAAAAC
13368451 C
1 C
13368452 CAACAACTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.31
Consensus pattern (35 bp):
CTTTCACAATGGCTTTTACCGGGATCAACCAAAAC
Found at i:13369404 original size:17 final size:18
Alignment explanation
Indices: 13369382--13369426 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
13369372 TCTCCCCCTA
13369382 AGTGTGTGCTTCCCTC-T
1 AGTGTGTGCTTCCCTCTT
13369399 AGTGTGTG-TTCCCTCTT
1 AGTGTGTGCTTCCCTCTT
*
13369416 AGTATGTGCTT
1 AGTGTGTGCTT
13369427 ATTATACTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 7 0.28
17 16 0.64
18 2 0.08
ACGTcount: A:0.09, C:0.22, G:0.24, T:0.44
Consensus pattern (18 bp):
AGTGTGTGCTTCCCTCTT
Found at i:13370836 original size:15 final size:16
Alignment explanation
Indices: 13370807--13370839 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
13370797 TCAATAAAAT
*
13370807 AAATTATTTTCTTATA
1 AAATAATTTTCTTATA
13370823 AAATAATTTT-TTATA
1 AAATAATTTTCTTATA
13370838 AA
1 AA
13370840 GCTATCGGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
AAATAATTTTCTTATA
Found at i:13373057 original size:19 final size:19
Alignment explanation
Indices: 13373033--13373070 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
13373023 AGTTCTAAAC
*
13373033 CTCAAATCATACTCCAATA
1 CTCAAATCAAACTCCAATA
13373052 CTCAAATCAAACTCCAATA
1 CTCAAATCAAACTCCAATA
13373071 AGTCAAATGG
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:0.45, C:0.32, G:0.00, T:0.24
Consensus pattern (19 bp):
CTCAAATCAAACTCCAATA
Found at i:13376146 original size:205 final size:202
Alignment explanation
Indices: 13375789--13376195 Score: 591
Period size: 205 Copynumber: 2.0 Consensus size: 202
13375779 TTGCTCGCAG
* * *
13375789 GGGAGGTGAGAAAACTGATATTCAGCCTTGCGAGGTTTCGGTTGGCATTTTGGGTAATGAATGTC
1 GGGAGGTGAGAAAACTGATATTAAGCCTTGCGAGGTTTCGGTTGGCATTCTAGGTAATGAATGTC
*
13375854 TATAAGGACATCGCGGCAGTTGTCACGGGCTCGAAAGGAGTACCGGGTCGTGACAATTCAGTTGG
66 TATAAGGACATCGCGGCAGTTGTCACGGGCTCGAAAAGAGTACCGGGTCGTGACAATTCAGTTGG
* * ** *
13375919 TATCAGAGCTTTTGGTTTTAAAGTTGTTTTAAAAATTTACAGTGTCAGTGTGGCCCCAAGTTAAG
131 TATCAGAGCTTTTAGATTTAAAGTCATTTTAAAAA-TTACAATGTCAGTGTGGCCCCAAGTTAAG
13375984 TTAGGTTA
195 TTAGGTTA
* * *
13375992 GNGGAGGTGAGAAAATTGATATTAAAGCCTTGTGGGGTTTCGGTTGGCATTCTAGGTAATGAATG
1 G-GGAGGTGAGAAAACTGATATT-AAGCCTTGCGAGGTTTCGGTTGGCATTCTAGGTAATGAATG
** * ** * *
13376057 TCTATCGGGATATCGCGGTGGTTGTCATGGGCTCGAAAAGAGTACTGGGTCGTGACAATTC-GAT
64 TCTATAAGGACATCGCGGCAGTTGTCACGGGCTCGAAAAGAGTACCGGGTCGTGACAATTCAG-T
*
13376121 TGGTATCAGAGCTTTTAGATTTAAAGTCATTTTAAAAATTACAATGTCAGTTTGGCCCCAAGTTA
128 TGGTATCAGAGCTTTTAGATTTAAAGTCATTTTAAAAATTACAATGTCAGTGTGGCCCCAAGTTA
13376186 AGTTAGGTTA
193 AGTTAGGTTA
13376196 AGTTAAGTTG
Statistics
Matches: 181, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
203 1 0.01
204 56 0.31
205 124 0.69
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (202 bp):
GGGAGGTGAGAAAACTGATATTAAGCCTTGCGAGGTTTCGGTTGGCATTCTAGGTAATGAATGTC
TATAAGGACATCGCGGCAGTTGTCACGGGCTCGAAAAGAGTACCGGGTCGTGACAATTCAGTTGG
TATCAGAGCTTTTAGATTTAAAGTCATTTTAAAAATTACAATGTCAGTGTGGCCCCAAGTTAAGT
TAGGTTA
Found at i:13383492 original size:37 final size:37
Alignment explanation
Indices: 13383438--13383522 Score: 118
Period size: 37 Copynumber: 2.3 Consensus size: 37
13383428 AGGCTTTGAA
* * *
13383438 GCCAAGTATC-GAGACCACTAGGTCTCTATACTTTGT
1 GCCAAGTATCAAAAACCACTAGATCTCTATACTTTGT
13383474 GCCAAGTATCAAAAACCACTAGATCTCTATACTTTGT
1 GCCAAGTATCAAAAACCACTAGATCTCTATACTTTGT
* *
13383511 GCTAGGTATCAA
1 GCCAAGTATCAA
13383523 GACTTTTGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 10 0.23
37 33 0.77
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (37 bp):
GCCAAGTATCAAAAACCACTAGATCTCTATACTTTGT
Found at i:13383647 original size:11 final size:11
Alignment explanation
Indices: 13383631--13383689 Score: 56
Period size: 10 Copynumber: 5.6 Consensus size: 11
13383621 ATTAAATGAA
13383631 ATTCAAA-AAT
1 ATTCAAACAAT
13383641 CATTCAAACAAT
1 -ATTCAAACAAT
*
13383653 -TCCAAACAA-
1 ATTCAAACAAT
13383662 ATTCAAA-AAT
1 ATTCAAACAAT
13383672 CATTCAAACAAT
1 -ATTCAAACAAT
13383684 -TTCAAA
1 ATTCAAA
13383690 ACTTATCCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
9 2 0.05
10 19 0.46
11 14 0.34
12 6 0.15
ACGTcount: A:0.54, C:0.20, G:0.00, T:0.25
Consensus pattern (11 bp):
ATTCAAACAAT
Found at i:13383667 original size:31 final size:31
Alignment explanation
Indices: 13383629--13383689 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
13383619 CCATTAAATG
13383629 AAATTCAAAAATCATTCAAACAATTCCAAAC
1 AAATTCAAAAATCATTCAAACAATTCCAAAC
*
13383660 AAATTCAAAAATCATTCAAACAATTTCAAA
1 AAATTCAAAAATCATTCAAACAATTCCAAA
13383690 ACTTATCCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.56, C:0.20, G:0.00, T:0.25
Consensus pattern (31 bp):
AAATTCAAAAATCATTCAAACAATTCCAAAC
Found at i:13384873 original size:30 final size:29
Alignment explanation
Indices: 13384819--13384881 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 29
13384809 ACTATTAGTA
*
13384819 ATAAGGACTTATTTGGCAAAAATAAAAGT
1 ATAAAGACTTATTTGGCAAAAATAAAAGT
13384848 ATAAAGACTTATTTGG-ATTAAAATAAAAGT
1 ATAAAGACTTATTTGGCA--AAAATAAAAGT
13384878 ATAA
1 ATAA
13384882 GAGCTCAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
28 1 0.03
29 15 0.48
30 15 0.48
ACGTcount: A:0.51, C:0.05, G:0.14, T:0.30
Consensus pattern (29 bp):
ATAAAGACTTATTTGGCAAAAATAAAAGT
Found at i:13401015 original size:42 final size:42
Alignment explanation
Indices: 13400942--13401072 Score: 163
Period size: 42 Copynumber: 3.1 Consensus size: 42
13400932 TGTTGGTGTG
* ** * *
13400942 GACCCGGCTATGTGCGAGTAGAAGTGTGCATAAGCCGATGAT
1 GACCCGACTATGCACGAGTAGGAGTGCGCATAAGCCGATGAT
* *
13400984 GACTCGACTATGCACGAGTAGGAGTGCGCATAAGTCGATGAT
1 GACCCGACTATGCACGAGTAGGAGTGCGCATAAGCCGATGAT
** * *
13401026 GACCCGACTATGTGCAAGTAGGAGTACGCATAAGCCGATGAT
1 GACCCGACTATGCACGAGTAGGAGTGCGCATAAGCCGATGAT
13401068 GACCC
1 GACCC
13401073 AGCCATGTGC
Statistics
Matches: 76, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.28, C:0.21, G:0.31, T:0.20
Consensus pattern (42 bp):
GACCCGACTATGCACGAGTAGGAGTGCGCATAAGCCGATGAT
Found at i:13409718 original size:18 final size:18
Alignment explanation
Indices: 13409675--13409718 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
13409665 CACTCAAACT
*
13409675 AAATTTA-AAAAATTTAA
1 AAATTTACAAAAATATAA
* *
13409692 ATATATACAAAAATATAA
1 AAATTTACAAAAATATAA
13409710 AAATTTACA
1 AAATTTACA
13409719 TGAACTGACT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATTTACAAAAATATAA
Found at i:13410184 original size:67 final size:67
Alignment explanation
Indices: 13410105--13410280 Score: 230
Period size: 67 Copynumber: 2.6 Consensus size: 67
13410095 GCTTAGCCAA
* *
13410105 AACCTTTCACAATAGTTTTT-ACCAGGATCAACCAAAACTCAAAGTGATTTTTCAAAGGCTCAAC
1 AACCTTTCACAATGGTTTTTCA-CAGGATCAACCAAAACCCAAAGTGATTTTTCAAAGGCTCAAC
13410169 CAC
65 CAC
* * * * *
13410172 AACCTTTCACAATGGTTTTTCACAAGCTCAACAAAAACCCAAAGTGGTTTTTCAAAGGCTTAACC
1 AACCTTTCACAATGGTTTTTCACAGGATCAACCAAAACCCAAAGTGATTTTTCAAAGGCTCAACC
*
13410237 AT
66 AC
* *
13410239 AACC-TACAACAATGGTTTTTCACGGGATCAACCAAAACCCAA
1 AACCTTTC-ACAATGGTTTTTCACAGGATCAACCAAAACCCAA
13410281 CAACTAACTT
Statistics
Matches: 94, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
66 2 0.02
67 91 0.97
68 1 0.01
ACGTcount: A:0.38, C:0.26, G:0.11, T:0.26
Consensus pattern (67 bp):
AACCTTTCACAATGGTTTTTCACAGGATCAACCAAAACCCAAAGTGATTTTTCAAAGGCTCAACC
AC
Found at i:13410193 original size:35 final size:33
Alignment explanation
Indices: 13410101--13410277 Score: 123
Period size: 35 Copynumber: 5.2 Consensus size: 33
13410091 CCAAGCTTAG
* * *
13410101 CCAAAACCTTTCACAATAGTTTTT-ACCAGGATCAA
1 CCAAAACC--TCACAATGGTTTTTCA-AAGGCTCAA
*
13410136 CCAAAA-CTCA-AAGTGATTTTTCAAAGGCTCAA
1 CCAAAACCTCACAA-TGGTTTTTCAAAGGCTCAA
*
13410168 CCACAACCTTTCACAATGGTTTTTCACAA-GCTCAA
1 CCAAAACC--TCACAATGGTTTTTCA-AAGGCTCAA
* *
13410203 CAAAAACC-CA-AAGTGGTTTTTCAAAGGCTTAA
1 CCAAAACCTCACAA-TGGTTTTTCAAAGGCTCAA
* ** *
13410235 CCATAACCTACAACAATGGTTTTTCACGGGATCAA
1 CCAAAACCT-C-ACAATGGTTTTTCAAAGGCTCAA
13410270 CCAAAACC
1 CCAAAACC
13410278 CAACAACTAA
Statistics
Matches: 113, Mismatches: 16, Indels: 26
0.73 0.10 0.17
Matches are distributed among these distances:
31 6 0.05
32 44 0.39
33 2 0.02
34 2 0.02
35 53 0.47
36 6 0.05
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.25
Consensus pattern (33 bp):
CCAAAACCTCACAATGGTTTTTCAAAGGCTCAA
Found at i:13411897 original size:20 final size:20
Alignment explanation
Indices: 13411872--13411964 Score: 67
Period size: 20 Copynumber: 5.0 Consensus size: 20
13411862 ATAAAACAAT
*
13411872 ATTAATAATTTGTTATTAAA
1 ATTAATAATTTATTATTAAA
*
13411892 ATTAATATTTTATTATT-AA
1 ATTAATAATTTATTATTAAA
* *
13411911 A-T--T-A-TTA--ATNAAT
1 ATTAATAATTTATTATTAAA
*
13411924 ATTAATAATTTGTTAATTAAA
1 ATTAATAATTTATT-ATTAAA
*
13411945 ATTAATATTTTATTATTAAA
1 ATTAATAATTTATTATTAAA
13411965 TTATTAATAT
Statistics
Matches: 54, Mismatches: 10, Indels: 18
0.66 0.12 0.22
Matches are distributed among these distances:
12 2 0.04
13 2 0.04
14 4 0.07
16 2 0.04
17 1 0.02
18 3 0.06
19 3 0.06
20 21 0.39
21 16 0.30
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
ATTAATAATTTATTATTAAA
Found at i:13411956 original size:53 final size:51
Alignment explanation
Indices: 13411869--13411973 Score: 192
Period size: 53 Copynumber: 2.0 Consensus size: 51
13411859 TTAATAAAAC
13411869 AATATTAATAATTTGTTATTAAAATTAATATTTTATTATTAAATTATTAAT
1 AATATTAATAATTTGTTATTAAAATTAATATTTTATTATTAAATTATTAAT
13411920 NAATATTAATAATTTGTTAATTAAAATTAATATTTTATTATTAAATTATTAAT
1 -AATATTAATAATTTGTT-ATTAAAATTAATATTTTATTATTAAATTATTAAT
13411973 A
1 A
13411974 TGATTTTTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
52 18 0.35
53 34 0.65
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (51 bp):
AATATTAATAATTTGTTATTAAAATTAATATTTTATTATTAAATTATTAAT
Found at i:13412456 original size:11 final size:11
Alignment explanation
Indices: 13412429--13412457 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
13412419 TATTCATATC
13412429 AATTTTATTTT
1 AATTTTATTTT
13412440 AA-TTTATTTT
1 AATTTTATTTT
13412450 AATTTTAT
1 AATTTTAT
13412458 ATCTATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
AATTTTATTTT
Found at i:13412466 original size:17 final size:17
Alignment explanation
Indices: 13412424--13412472 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
13412414 TAAAATATTC
*
13412424 ATATCAATTTT-ATTTT
1 ATATCTATTTTAATTTT
*
13412440 A-ATTTATTTTAATTTT
1 ATATCTATTTTAATTTT
13412456 ATATCTATTTTAATTTT
1 ATATCTATTTTAATTTT
13412473 TTCTTTTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 7 0.25
16 7 0.25
17 14 0.50
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (17 bp):
ATATCTATTTTAATTTT
Found at i:13412466 original size:32 final size:35
Alignment explanation
Indices: 13412397--13412472 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 35
13412387 TCATTTTTTA
13412397 TATTTATAATTTATTATTAAAATATTCATATCAATTT
1 TATTT-TAATTTATTATT-AAATATTCATATCAATTT
* *
13412434 TATTTTAATTTATT-TT-AAT-TTTATATCTATTT
1 TATTTTAATTTATTATTAAATATTCATATCAATTT
13412466 TAATTTT
1 T-ATTTT
13412473 TTCTTTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
32 12 0.33
33 8 0.22
35 2 0.06
36 9 0.25
37 5 0.14
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (35 bp):
TATTTTAATTTATTATTAAATATTCATATCAATTT
Found at i:13414982 original size:36 final size:36
Alignment explanation
Indices: 13414935--13415029 Score: 138
Period size: 35 Copynumber: 2.7 Consensus size: 36
13414925 AAGCTTAACC
* **
13414935 ACTTAATTAAACAATTTTAATCAATTAGGCCCAATG
1 ACTTAATTAAACAATTTTAATCAATTAAGCCCAACA
* *
13414971 ACTTAATTAAACAA-TATAATTAATTAAGCCCAACA
1 ACTTAATTAAACAATTTTAATCAATTAAGCCCAACA
13415006 ACTTAATTAAACAATTTTAATCAA
1 ACTTAATTAAACAATTTTAATCAA
13415030 ATACTTTAGA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
35 30 0.59
36 21 0.41
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (36 bp):
ACTTAATTAAACAATTTTAATCAATTAAGCCCAACA
Found at i:13428393 original size:17 final size:18
Alignment explanation
Indices: 13428371--13428404 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13428361 TTAAATCCTG
13428371 GCTTTTG-AAAATTGACA
1 GCTTTTGCAAAATTGACA
*
13428388 GCTTTTGCATAATTGAC
1 GCTTTTGCAAAATTGAC
13428405 CAAATCTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (18 bp):
GCTTTTGCAAAATTGACA
Found at i:13429981 original size:24 final size:24
Alignment explanation
Indices: 13429949--13429998 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
13429939 GAACTATTAA
13429949 ATATATATATTATGCCTTGGGGAC
1 ATATATATATTATGCCTTGGGGAC
*
13429973 ATATATATATTGTGCCTTGGGGAC
1 ATATATATATTATGCCTTGGGGAC
13429997 AT
1 AT
13429999 CAATGATATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (24 bp):
ATATATATATTATGCCTTGGGGAC
Found at i:13431937 original size:35 final size:34
Alignment explanation
Indices: 13431873--13431942 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 34
13431863 TTAGTTGTTG
* *
13431873 GGTTTTGGTTGATCCTGGTAAAAACCATTGTGAAA
1 GGTTTTGGCTGAGCCTGGTAAAAACCATTGT-AAA
**
13431908 GGTTTTGGCTGAGCCTGGTAAAAGTCATTGTAAA
1 GGTTTTGGCTGAGCCTGGTAAAAACCATTGTAAA
13431942 G
1 G
13431943 CTTGGTGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 4 0.13
35 27 0.87
ACGTcount: A:0.27, C:0.11, G:0.29, T:0.33
Consensus pattern (34 bp):
GGTTTTGGCTGAGCCTGGTAAAAACCATTGTAAA
Found at i:13436081 original size:20 final size:20
Alignment explanation
Indices: 13436056--13436101 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
13436046 CTTATAAACC
13436056 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
13436076 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
13436096 TCAAAT
1 TCAAAT
13436102 GGGGACAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:13454729 original size:8 final size:8
Alignment explanation
Indices: 13454673--13454745 Score: 58
Period size: 8 Copynumber: 8.8 Consensus size: 8
13454663 GAAGTTTCAA
13454673 TATTTTTT
1 TATTTTTT
*
13454681 TCTTTTCTT
1 TATTTT-TT
13454690 T-TTTTTT
1 TATTTTTT
* *
13454697 TCATTTATA
1 T-ATTTTTT
* *
13454706 TATTTATA
1 TATTTTTT
13454714 TATATTTTT
1 TAT-TTTTT
13454723 TATTTTTT
1 TATTTTTT
13454731 TATTTTTTT
1 TA-TTTTTT
13454740 TATTTT
1 TATTTT
13454746 AAGAAAAATT
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
7 3 0.05
8 30 0.55
9 22 0.40
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.79
Consensus pattern (8 bp):
TATTTTTT
Found at i:13459294 original size:41 final size:41
Alignment explanation
Indices: 13459249--13459329 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
13459239 TAGTTGGTAA
*
13459249 TTGAATATATTACTTGCTCAAATTTTAGGAATTTAGAGTAC
1 TTGAATATATTACTTGCTCAAATTTTAGGAATCTAGAGTAC
* * **
13459290 TTGAATTTATTACTTGTTTGAATTTTAGGAATCTAGAGTA
1 TTGAATATATTACTTGCTCAAATTTTAGGAATCTAGAGTA
13459330 AAGTTGTGCC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.44
Consensus pattern (41 bp):
TTGAATATATTACTTGCTCAAATTTTAGGAATCTAGAGTAC
Found at i:13460389 original size:32 final size:33
Alignment explanation
Indices: 13460350--13460451 Score: 100
Period size: 32 Copynumber: 3.1 Consensus size: 33
13460340 AACCTTTAGA
13460350 AATGGTTTTTCACGGGATCAACCAAAACCCAA-
1 AATGGTTTTTCACGGGATCAACCAAAACCCAAC
* ** * * *
13460382 AGTGGTTTTTCAAAGGCTTAACCACAACCTACAAC
1 AATGGTTTTTCACGGGATCAACCAAAACC--CAAC
*
13460417 AATTGTTTTT-ACCGGGATCAACCAAAACCCAAC
1 AATGGTTTTTCA-CGGGATCAACCAAAACCCAAC
13460450 AA
1 AA
13460452 CAAACTTTTC
Statistics
Matches: 53, Mismatches: 13, Indels: 7
0.73 0.18 0.10
Matches are distributed among these distances:
32 23 0.43
33 6 0.11
34 4 0.08
35 20 0.38
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24
Consensus pattern (33 bp):
AATGGTTTTTCACGGGATCAACCAAAACCCAAC
Found at i:13469151 original size:60 final size:61
Alignment explanation
Indices: 13469043--13469192 Score: 194
Period size: 60 Copynumber: 2.5 Consensus size: 61
13469033 ATAGGAGACC
* * * * * *
13469043 AAAATAGAAGGTTTTTCGCTGCAGCGAGATTCAATCTCGTTGCAGCGAAATTTCTACCCAG
1 AAAACAGAAAGTTTCTCGCTGTAGCGAGATTCAATCTCGTTGCAGCGAAATTGCAACCCAG
* *
13469104 -AAACAGAATGTTTCTCGCTGTAGCGAGATTCAATCTGGTTGCAGCGAAATTGCAACCCAG
1 AAAACAGAAAGTTTCTCGCTGTAGCGAGATTCAATCTCGTTGCAGCGAAATTGCAACCCAG
* * *
13469164 AAAATAGAAAGTTTCTCACTGTAGTGAGA
1 AAAACAGAAAGTTTCTCGCTGTAGCGAGA
13469193 ATGCATTTCA
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
60 53 0.69
61 24 0.31
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (61 bp):
AAAACAGAAAGTTTCTCGCTGTAGCGAGATTCAATCTCGTTGCAGCGAAATTGCAACCCAG
Found at i:13471384 original size:21 final size:22
Alignment explanation
Indices: 13471360--13471408 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
13471350 TTTACTTATT
13471360 TTTAATTGTTTTTA-TAA-TTAG
1 TTTAATTG-TTTTAGTAAGTTAG
*
13471381 TTT-ATTGTTTTAGTAAGTTAT
1 TTTAATTGTTTTAGTAAGTTAG
13471402 TTTAATT
1 TTTAATT
13471409 TTATGTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 5 0.21
20 7 0.29
21 9 0.38
22 3 0.12
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (22 bp):
TTTAATTGTTTTAGTAAGTTAG
Found at i:13478224 original size:11 final size:11
Alignment explanation
Indices: 13478208--13478235 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
13478198 AGTTTTTGGA
13478208 TTTAAAGTTGT
1 TTTAAAGTTGT
13478219 TTTAAAGTTGT
1 TTTAAAGTTGT
13478230 TTTAAA
1 TTTAAA
13478236 ATTTACAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (11 bp):
TTTAAAGTTGT
Found at i:13478533 original size:15 final size:15
Alignment explanation
Indices: 13478513--13478551 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
13478503 TGGTCCATCC
13478513 CGAATTCCTATTAAT
1 CGAATTCCTATTAAT
*
13478528 CGAATTCTTATTAAT
1 CGAATTCCTATTAAT
*
13478543 AGAATTCCT
1 CGAATTCCT
13478552 CCGAACTTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (15 bp):
CGAATTCCTATTAAT
Found at i:13494926 original size:33 final size:33
Alignment explanation
Indices: 13494884--13494953 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
13494874 TTGGCAAAGA
*
13494884 TGGCCCATGCTTAACAAAGTAAGATTGATAATG
1 TGGCCCATGCTGAACAAAGTAAGATTGATAATG
*
13494917 TGGCCCATGCTGAACAAAGTAAGATTGGTAATG
1 TGGCCCATGCTGAACAAAGTAAGATTGATAATG
13494950 TGGC
1 TGGC
13494954 TTGAAAAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.26
Consensus pattern (33 bp):
TGGCCCATGCTGAACAAAGTAAGATTGATAATG
Found at i:13496417 original size:2 final size:2
Alignment explanation
Indices: 13496336--13496401 Score: 87
Period size: 2 Copynumber: 32.0 Consensus size: 2
13496326 TTAGAAACGT
* * *
13496336 TA TA TA TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA CA TGN TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
13496379 CTA TA TA TA TA TA TA TA TA TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA
13496402 CATGTAAGCT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
2 53 0.95
3 3 0.05
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:13505971 original size:15 final size:16
Alignment explanation
Indices: 13505945--13505978 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
13505935 TTCTCAAAAA
13505945 TTTTATTGATTAATAT
1 TTTTATTGATTAATAT
*
13505961 TTTTATT-ATTATTAT
1 TTTTATTGATTAATAT
13505976 TTT
1 TTT
13505979 GTTAAATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTTATTGATTAATAT
Found at i:13510120 original size:26 final size:26
Alignment explanation
Indices: 13510091--13510140 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
13510081 TATAGGCGGG
*
13510091 GTAGTCGCCACTTGTTTCACATAATC
1 GTAGTCGCCACTTGTCTCACATAATC
* *
13510117 GTAGTTGTCACTTGTCTCACATAA
1 GTAGTCGCCACTTGTCTCACATAA
13510141 CCATGGTCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (26 bp):
GTAGTCGCCACTTGTCTCACATAATC
Found at i:13525558 original size:27 final size:30
Alignment explanation
Indices: 13525500--13525559 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
13525490 GGCCGGCCAT
*
13525500 AAAGAAAGAACAAGAGAGAAAACAGAGAGA
1 AAAGAAAGAACAAGAGAGAAAACAAAGAGA
*
13525530 AAAGGAAGAA-AAGAGA-AAAACAAAG-GA
1 AAAGAAAGAACAAGAGAGAAAACAAAGAGA
13525557 AAA
1 AAA
13525560 CTAGAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 5 0.18
28 8 0.29
29 6 0.21
30 9 0.32
ACGTcount: A:0.70, C:0.05, G:0.25, T:0.00
Consensus pattern (30 bp):
AAAGAAAGAACAAGAGAGAAAACAAAGAGA
Found at i:13531314 original size:17 final size:18
Alignment explanation
Indices: 13531267--13531313 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
13531257 TTAAAAAAAC
* *
13531267 ATTTATTAATTTTCCTTA
1 ATTTATTAATTTTACTAA
*
13531285 A-TTATAAATTTTACTAA
1 ATTTATTAATTTTACTAA
13531302 ATTTATTAATTT
1 ATTTATTAATTT
13531314 ATTTAATTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTATTAATTTTACTAA
Found at i:13531548 original size:115 final size:114
Alignment explanation
Indices: 13531289--13531570 Score: 282
Period size: 115 Copynumber: 2.4 Consensus size: 114
13531279 TCCTTAATTA
* * * * *
13531289 TAAATTTTACTAAATTTATTAATTTATTTAATTGCTTAATTGCTAAGACATTACATAACTTAATT
1 TAAAATTTACT-AATTTACTAATTTAATTAATTGCTTAATTACTAAAACATTACATAACTTAATT
* * * *
13531354 AACTAAATTATTTGATTAATTAATTAACACCTTAATTTATTTAAATAGTTT
65 AACTAAATTATTTCATTAATTAA-TAAAACCTTAATTAATCTAAATAGTTT
* * * ** * * **
13531405 T-TACTTTAAGTAATATTACTAATTTAATTAATTGCTTAATTACTAAAACATCT-TTTCATTTGC
1 TAAAATTT-ACTAAT-TTACTAATTTAATTAATTGCTTAATTACTAAAACAT-TACATAACTTAA
* *
13531468 TTAGCTAAATTATTTCATTAATTTAA-AAAATCTTAATTAATCTAAATAGTTT
63 TTAACTAAATTATTTCATTAA-TTAATAAAACCTTAATTAATCTAAATAGTTT
* *
13531520 TAAAATTTACTATATTTACTAATTTAATTAATTGATTAATTACTAATACAT
1 TAAAATTTACTA-ATTTACTAATTTAATTAATTGCTTAATTACTAAAACAT
13531571 AATTCTTTTT
Statistics
Matches: 136, Mismatches: 24, Indels: 13
0.79 0.14 0.08
Matches are distributed among these distances:
115 67 0.49
116 64 0.47
117 5 0.04
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (114 bp):
TAAAATTTACTAATTTACTAATTTAATTAATTGCTTAATTACTAAAACATTACATAACTTAATTA
ACTAAATTATTTCATTAATTAATAAAACCTTAATTAATCTAAATAGTTT
Found at i:13532757 original size:17 final size:17
Alignment explanation
Indices: 13532727--13532765 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
13532717 CAAGCCAAAG
*
13532727 ATAAAAAATTTGAATAT
1 ATAAAAAATATGAATAT
13532744 -TAAAAACATATGAATAT
1 ATAAAAA-ATATGAATAT
13532761 ATAAA
1 ATAAA
13532766 CCATTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 6 0.32
17 9 0.47
18 4 0.21
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (17 bp):
ATAAAAAATATGAATAT
Found at i:13535287 original size:16 final size:16
Alignment explanation
Indices: 13535266--13535299 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
13535256 GGAATAATTA
*
13535266 TTATTTATTTTTATTT
1 TTATTTATTATTATTT
13535282 TTATTTATTATTATTT
1 TTATTTATTATTATTT
13535298 TT
1 TT
13535300 TGTTTCTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (16 bp):
TTATTTATTATTATTT
Found at i:13542305 original size:13 final size:13
Alignment explanation
Indices: 13542287--13542311 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13542277 GGAAAATGGG
13542287 ATTTTATAAAATA
1 ATTTTATAAAATA
13542300 ATTTTATAAAAT
1 ATTTTATAAAAT
13542312 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:13545824 original size:6 final size:6
Alignment explanation
Indices: 13545807--13545849 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
13545797 AAAGGAATAA
*
13545807 TTATTAT TTATTT TTATTT TTATTT ATTATTT TT-TTT CTATTT
1 TTATT-T TTATTT TTATTT TTATTT -TTATTT TTATTT TTATTT
13545850 CTCTTTCTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
5 4 0.12
6 18 0.55
7 11 0.33
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (6 bp):
TTATTT
Found at i:13545836 original size:19 final size:18
Alignment explanation
Indices: 13545811--13545849 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
13545801 GAATAATTAT
*
13545811 TATTTATT-TTTATTTT-
1 TATTTATTATTTTTTTTC
13545827 TATTTATTATTTTTTTTC
1 TATTTATTATTTTTTTTC
13545845 TATTT
1 TATTT
13545850 CTCTTTCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 7 0.35
18 5 0.25
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (18 bp):
TATTTATTATTTTTTTTC
Found at i:13545848 original size:14 final size:13
Alignment explanation
Indices: 13545806--13545840 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
13545796 CAAAGGAATA
13545806 ATTATTATTTATTT
1 ATTATT-TTTATTT
13545820 -TTATTTTTATTT
1 ATTATTTTTATTT
13545832 ATTATTTTT
1 ATTATTTTT
13545841 TTTCTATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
ATTATTTTTATTT
Found at i:13546138 original size:70 final size:69
Alignment explanation
Indices: 13546055--13546185 Score: 199
Period size: 70 Copynumber: 1.9 Consensus size: 69
13546045 TCGACAACAT
* *
13546055 AAAGCCCCATTTGTCTTTCACAATCCGACAGCAAAAAACCTCTATTTTTTCCTGCACAAACCAAC
1 AAAGCCCCATTTGTCTTTCACAATCCGACAACAAAAAACCTCCA-TTTTTCCTGCACAAACCAAC
13546120 AGCAC
65 AGCAC
* * * *
13546125 AAAGCCCCCTTTGTCTTTCACAATCCGGCAACAAACAGCCTCCATTTTTCCTGCACAAACC
1 AAAGCCCCATTTGTCTTTCACAATCCGACAACAAAAAACCTCCATTTTTCCTGCACAAACC
13546186 GACTGCAACA
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
69 17 0.31
70 38 0.69
ACGTcount: A:0.31, C:0.35, G:0.09, T:0.24
Consensus pattern (69 bp):
AAAGCCCCATTTGTCTTTCACAATCCGACAACAAAAAACCTCCATTTTTCCTGCACAAACCAACA
GCAC
Found at i:13549886 original size:11 final size:11
Alignment explanation
Indices: 13549870--13549894 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
13549860 CGATTTGACA
13549870 TTAATATTATT
1 TTAATATTATT
13549881 TTAATATTATT
1 TTAATATTATT
13549892 TTA
1 TTA
13549895 TCCAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTAATATTATT
Found at i:13558324 original size:5 final size:5
Alignment explanation
Indices: 13558318--13558367 Score: 82
Period size: 5 Copynumber: 10.0 Consensus size: 5
13558308 TTATACAACC
* *
13558318 TAACC TAACT TAACT TAACT TAACT TAACT TAACT TATCT TAACT TAACT
1 TAACT TAACT TAACT TAACT TAACT TAACT TAACT TAACT TAACT TAACT
13558368 AGACTTGGGG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.40
Consensus pattern (5 bp):
TAACT
Found at i:13558475 original size:22 final size:22
Alignment explanation
Indices: 13558418--13558484 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
13558408 TTTAAACCAG
*
13558418 CTTTAAACCCAAAAACTCTAAT
1 CTTTAAAACCAAAAACTCTAAT
* ** *
13558440 CTTTAAAAATCAAAAGTTCTGAT
1 CTTT-AAAACCAAAAACTCTAAT
**
13558463 CTTTAAAACCAAATGCTCTAAT
1 CTTTAAAACCAAAAACTCTAAT
13558485 ACCAACCAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
22 18 0.51
23 17 0.49
ACGTcount: A:0.43, C:0.21, G:0.04, T:0.31
Consensus pattern (22 bp):
CTTTAAAACCAAAAACTCTAAT
Found at i:13561311 original size:28 final size:28
Alignment explanation
Indices: 13561266--13561422 Score: 165
Period size: 28 Copynumber: 5.5 Consensus size: 28
13561256 TTTTTGTAAC
*
13561266 AAGTGGAGGAATACTCTTAACCCACTAG
1 AAGTGGATGAATACTCTTAACCCACTAG
* *
13561294 AAATGGATGAATATTCTTACTCTTAACCCACCAG
1 AAGTGGATG-A-A----TACTCTTAACCCACTAG
*
13561328 AAGGGGATGAATACTCTTAACCCACTAG
1 AAGTGGATGAATACTCTTAACCCACTAG
* * *
13561356 AAGGGGATGAATACTTTTAA-CCATTAG
1 AAGTGGATGAATACTCTTAACCCACTAG
*
13561383 AAGTGGATGAATACTCTTAA-TCACTAG
1 AAGTGGATGAATACTCTTAACCCACTAG
*
13561410 GAGTGGATGAATA
1 AAGTGGATGAATA
13561423 GGAAAGAGAT
Statistics
Matches: 110, Mismatches: 13, Indels: 13
0.81 0.10 0.10
Matches are distributed among these distances:
27 41 0.37
28 42 0.38
29 1 0.01
30 1 0.01
32 1 0.01
33 1 0.01
34 23 0.21
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.26
Consensus pattern (28 bp):
AAGTGGATGAATACTCTTAACCCACTAG
Found at i:13561320 original size:34 final size:34
Alignment explanation
Indices: 13561277--13561346 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 34
13561267 AGTGGAGGAA
* * *
13561277 TACTCTTAACCCACTAGAAATGGATGAATATTCT
1 TACTCTTAACCCACCAGAAAGGGATGAATACTCT
*
13561311 TACTCTTAACCCACCAGAAGGGGATGAATACTCT
1 TACTCTTAACCCACCAGAAAGGGATGAATACTCT
13561345 TA
1 TA
13561347 ACCCACTAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (34 bp):
TACTCTTAACCCACCAGAAAGGGATGAATACTCT
Found at i:13561391 original size:27 final size:27
Alignment explanation
Indices: 13561311--13561422 Score: 143
Period size: 27 Copynumber: 4.1 Consensus size: 27
13561301 TGAATATTCT
*
13561311 TACTCTTAACCCACCAGAAGGGGATGAA
1 TACTCTTAA-CCACTAGAAGGGGATGAA
13561339 TACTCTTAACCCACTAGAAGGGGATGAA
1 TACTCTTAA-CCACTAGAAGGGGATGAA
* * *
13561367 TACTTTTAACCATTAGAAGTGGATGAA
1 TACTCTTAACCACTAGAAGGGGATGAA
* * *
13561394 TACTCTTAATCACTAGGAGTGGATGAA
1 TACTCTTAACCACTAGAAGGGGATGAA
13561421 TA
1 TA
13561423 GGAAAGAGAT
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
27 41 0.54
28 35 0.46
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.26
Consensus pattern (27 bp):
TACTCTTAACCACTAGAAGGGGATGAA
Found at i:13561884 original size:3 final size:3
Alignment explanation
Indices: 13561876--13561911 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
13561866 ATATATATAT
13561876 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
13561912 AAAAAATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:13570179 original size:22 final size:22
Alignment explanation
Indices: 13570145--13570186 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
13570135 GTTTTGGTGA
*
13570145 TTTTTATGAATTACATGACTAG
1 TTTTTAGGAATTACATGACTAG
* *
13570167 TTTTTAGGCATTACGTGACT
1 TTTTTAGGAATTACATGACT
13570187 GACTTTAGAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (22 bp):
TTTTTAGGAATTACATGACTAG
Found at i:13570199 original size:21 final size:21
Alignment explanation
Indices: 13570169--13570228 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
13570159 ATGACTAGTT
*
13570169 TTTAGGCATTACGTGACTGAC
1 TTTAGACATTACGTGACTGAC
*
13570190 TTTAGACATTGCGTGACTGAC
1 TTTAGACATTACGTGACTGAC
13570211 TTT-GAGCATTACGTGACT
1 TTTAGA-CATTACGTGACT
13570229 AGTTTTTGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
20 2 0.06
21 33 0.94
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (21 bp):
TTTAGACATTACGTGACTGAC
Found at i:13570252 original size:26 final size:25
Alignment explanation
Indices: 13570216--13570346 Score: 141
Period size: 23 Copynumber: 5.4 Consensus size: 25
13570206 CTGACTTTGA
*
13570216 GCATTACGTGACTAGTTTTTGATAAG
1 GCATTGCGTGACTAG-TTTTGATAAG
13570242 GCATTGCGTGACTAGTTTTTGATAAG
1 GCATTGCGTGACTAG-TTTTGATAAG
*
13570268 GCATTGCATGACTAG--TTGAT-AG
1 GCATTGCGTGACTAGTTTTGATAAG
* *
13570290 GCATTGCGTGACTTG-TTAG-TAAG
1 GCATTGCGTGACTAGTTTTGATAAG
* *
13570313 GTATTGCGTGACTAG-TTAG-TAAG
1 GCATTGCGTGACTAGTTTTGATAAG
13570336 GCATTGCGTGA
1 GCATTGCGTGA
13570347 TTAATTAGTA
Statistics
Matches: 95, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
22 16 0.17
23 40 0.42
26 39 0.41
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.35
Consensus pattern (25 bp):
GCATTGCGTGACTAGTTTTGATAAG
Found at i:13570319 original size:23 final size:23
Alignment explanation
Indices: 13570238--13570372 Score: 123
Period size: 23 Copynumber: 5.8 Consensus size: 23
13570228 TAGTTTTTGA
* *
13570238 TAAGGCATTGCGTGACTAGTTTTTG
1 TAAGGCATTGCGTGACT--TGTTAG
* *
13570263 ATAAGGCATTGCATGACTAGTT-G
1 -TAAGGCATTGCGTGACTTGTTAG
13570286 -ATAGGCATTGCGTGACTTGTTAG
1 TA-AGGCATTGCGTGACTTGTTAG
* *
13570309 TAAGGTATTGCGTGACTAGTTAG
1 TAAGGCATTGCGTGACTTGTTAG
*
13570332 TAAGGCATTGCGTGA-TTAATTAG
1 TAAGGCATTGCGTGACTT-GTTAG
* *
13570355 TAAAGCATTGTGTGACTT
1 TAAGGCATTGCGTGACTT
13570373 AGGCATTACT
Statistics
Matches: 92, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.01
22 18 0.20
23 52 0.57
24 5 0.05
26 16 0.17
ACGTcount: A:0.26, C:0.11, G:0.27, T:0.36
Consensus pattern (23 bp):
TAAGGCATTGCGTGACTTGTTAG
Found at i:13570355 original size:46 final size:45
Alignment explanation
Indices: 13570216--13570371 Score: 136
Period size: 46 Copynumber: 3.3 Consensus size: 45
13570206 CTGACTTTGA
* * *
13570216 GCATTACGTGACTAGTTTTTGATAAGGCATTGCGTGACTAGTTTTTGATAAG
1 GCATTGCGTGACTAG---TTGAT-AGGCATTGCGTGACT--TATTAG-TAAG
* *
13570268 GCATTGCATGACTAGTTGATAGGCATTGCGTGACTTGTTAGTAAG
1 GCATTGCGTGACTAGTTGATAGGCATTGCGTGACTTATTAGTAAG
* *
13570313 GTATTGCGTGACTAGTT-AGTAAGGCATTGCGTGA-TTAATTAGTAAA
1 GCATTGCGTGACTAGTTGA-T-AGGCATTGCGTGACTT-ATTAGTAAG
*
13570359 GCATTGTGTGACT
1 GCATTGCGTGACT
13570372 TAGGCATTAC
Statistics
Matches: 91, Mismatches: 10, Indels: 12
0.81 0.09 0.11
Matches are distributed among these distances:
44 1 0.01
45 22 0.24
46 35 0.38
48 15 0.16
49 5 0.05
52 13 0.14
ACGTcount: A:0.26, C:0.12, G:0.27, T:0.36
Consensus pattern (45 bp):
GCATTGCGTGACTAGTTGATAGGCATTGCGTGACTTATTAGTAAG
Found at i:13570415 original size:22 final size:22
Alignment explanation
Indices: 13570383--13570453 Score: 90
Period size: 22 Copynumber: 3.3 Consensus size: 22
13570373 AGGCATTACT
*
13570383 TAAAAATCAGTCACGCAATGCC
1 TAAAAACCAGTCACGCAATGCC
*
13570405 TAAAAACCAGTTACGCAATGCC
1 TAAAAACCAGTCACGCAATGCC
** *
13570427 T-AAAACCAACCACGTAATGCC
1 TAAAAACCAGTCACGCAATGCC
13570448 TAAAAA
1 TAAAAA
13570454 TCAATCTTGC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.40
22 25 0.60
ACGTcount: A:0.45, C:0.27, G:0.11, T:0.17
Consensus pattern (22 bp):
TAAAAACCAGTCACGCAATGCC
Found at i:13570433 original size:21 final size:21
Alignment explanation
Indices: 13570385--13570452 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
13570375 GCATTACTTA
*
13570385 AAAATCAGTCACGCAATGCCT
1 AAAACCAGTCACGCAATGCCT
*
13570406 AAAAACCAGTTACGCAATGCCT
1 -AAAACCAGTCACGCAATGCCT
** *
13570428 AAAACCAACCACGTAATGCCT
1 AAAACCAGTCACGCAATGCCT
13570449 AAAA
1 AAAA
13570453 ATCAATCTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
21 21 0.52
22 19 0.47
ACGTcount: A:0.44, C:0.28, G:0.12, T:0.16
Consensus pattern (21 bp):
AAAACCAGTCACGCAATGCCT
Found at i:13576382 original size:59 final size:59
Alignment explanation
Indices: 13576318--13576436 Score: 222
Period size: 59 Copynumber: 2.0 Consensus size: 59
13576308 AAACGCAAAC
13576318 CCTGTAAAATT-TACAAATTATAAGATCAAGAACGTAACAAAACCTCAGCAAAATTTTCA
1 CCTGTAAAATTAT-CAAATTATAAGATCAAGAACGTAACAAAACCTCAGCAAAATTTTCA
13576377 CCTGTAAAATTATCAAATTATAAGATCAAGAACGTAACAAAACCTCAGCAAAATTTTCA
1 CCTGTAAAATTATCAAATTATAAGATCAAGAACGTAACAAAACCTCAGCAAAATTTTCA
13576436 C
1 C
13576437 TTGAAACCAT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
59 58 0.98
60 1 0.02
ACGTcount: A:0.47, C:0.19, G:0.08, T:0.25
Consensus pattern (59 bp):
CCTGTAAAATTATCAAATTATAAGATCAAGAACGTAACAAAACCTCAGCAAAATTTTCA
Found at i:13580201 original size:41 final size:42
Alignment explanation
Indices: 13580127--13580209 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 42
13580117 AAGACCTTGT
13580127 ATTAGAACAGGAGTAGCATTACGTAGTTTTCATTTTGTTGAA
1 ATTAGAACAGGAGTAGCATTACGTAGTTTTCATTTTGTTGAA
* * * *
13580169 ATTAGAACATG-GTAGGATTAGGTGGTTTTCATTTTGTTGAA
1 ATTAGAACAGGAGTAGCATTACGTAGTTTTCATTTTGTTGAA
13580210 TATAAATGCA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 27 0.73
42 10 0.27
ACGTcount: A:0.29, C:0.07, G:0.24, T:0.40
Consensus pattern (42 bp):
ATTAGAACAGGAGTAGCATTACGTAGTTTTCATTTTGTTGAA
Found at i:13582132 original size:14 final size:14
Alignment explanation
Indices: 13582077--13582132 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
13582067 TATTTATTTT
* *
13582077 TTAAAATTACAAAT
1 TTAAAATTATAAAA
*
13582091 TTAAACTTATAAAA
1 TTAAAATTATAAAA
* *
13582105 TTAATATT-TTAAA
1 TTAAAATTATAAAA
*
13582118 TTAAAATTAAAAAA
1 TTAAAATTATAAAA
13582132 T
1 T
13582133 ATTAATATTT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
13 11 0.34
14 21 0.66
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (14 bp):
TTAAAATTATAAAA
Found at i:13586415 original size:33 final size:33
Alignment explanation
Indices: 13586377--13586450 Score: 114
Period size: 33 Copynumber: 2.2 Consensus size: 33
13586367 CTCCTTCTTT
13586377 CTTTCTTCTGTTTCTCTCCTTC-GTTCTTTTTTC
1 CTTTCTTCTGTTTCTC-CCTTCTGTTCTTTTTTC
*
13586410 CTTTCTTCTGTTTCTCCCTTCTGTTCTTTTTTT
1 CTTTCTTCTGTTTCTCCCTTCTGTTCTTTTTTC
13586443 CTTCTCTT
1 CTT-TCTT
13586451 TCTCTTTTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
32 5 0.13
33 29 0.76
34 4 0.11
ACGTcount: A:0.00, C:0.30, G:0.05, T:0.65
Consensus pattern (33 bp):
CTTTCTTCTGTTTCTCCCTTCTGTTCTTTTTTC
Found at i:13588833 original size:2 final size:2
Alignment explanation
Indices: 13588826--13588852 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13588816 CTGATTATTG
13588826 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
13588853 ACTANNNNNN
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:13599896 original size:30 final size:31
Alignment explanation
Indices: 13599862--13599945 Score: 100
Period size: 31 Copynumber: 2.7 Consensus size: 31
13599852 AAAAGGGGTG
*
13599862 AAATTGTAAT-TATGAACAAG-TTGAAGGATC
1 AAATTGTAATATATGAA-AAGTTTGAAGGACC
*
13599892 AAATTGTAATATATGAAATGTTTGAAGGACC
1 AAATTGTAATATATGAAAAGTTTGAAGGACC
* * *
13599923 AAATTGTAAAAGATAAAAAGTTT
1 AAATTGTAATATATGAAAAGTTT
13599946 AGAGGGGTCA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
30 12 0.26
31 34 0.74
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.31
Consensus pattern (31 bp):
AAATTGTAATATATGAAAAGTTTGAAGGACC
Found at i:13602258 original size:25 final size:25
Alignment explanation
Indices: 13602230--13602289 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
13602220 CAGTCTGTGA
*
13602230 TTATACGTGGAAGGGCCACGGGTTG
1 TTATACGTGGAAGGGCCACGAGTTG
* * *
13602255 TTATGCATGGCAGGGCCACGAGTTG
1 TTATACGTGGAAGGGCCACGAGTTG
*
13602280 ATATACGTGG
1 TTATACGTGG
13602290 TTGCAACCAC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.22, C:0.17, G:0.37, T:0.25
Consensus pattern (25 bp):
TTATACGTGGAAGGGCCACGAGTTG
Found at i:13607523 original size:151 final size:151
Alignment explanation
Indices: 13607238--13607767 Score: 603
Period size: 151 Copynumber: 3.5 Consensus size: 151
13607228 TCCTTGAATA
* * * * *
13607238 GGTCAATTGCAATAATAGATATTAATATGTTATTTGATAATCAAATATGGAATTGTTGAACATAA
1 GGTCAACTACAATAACAGATATTATTATGTTATTCGATAATCAAATATGGAATTGTTGAACATAA
* * * * * * *
13607303 ACCATAAAAACTGTCCTTACTGGTGGATCATTACCACTGTGCATCAGAGTAGGTTCTGTCAGTCA
66 ACCATAAGAACTGTCCTTACTGGTGGCTCGTTACCACTGTGCATCTGAGCAGGTCCTGTCAGTCG
* * *
13607368 TTGAGGAGCTATCGTTACATG
131 TTGAGGAGATGTCGTCACATG
* * * * * ** *
13607389 GGCCAACTGCAATAGCAGATATTATTGTGTTATTTGATAATCTCATATTGAATTGTTGAACATAA
1 GGTCAACTACAATAACAGATATTATTATGTTATTCGATAATCAAATATGGAATTGTTGAACATAA
* * * * *
13607454 ATCATTAGAACTGTCCTTA-TAGATGGCTCGTTACCACTGTGCGTCTGAGCAGGTCCTGTCAGTT
66 ACCATAAGAACTGTCCTTACT-GGTGGCTCGTTACCACTGTGCATCTGAGCAGGTCCTGTCAGTC
*
13607518 GTTGAGGAGATGTCGTCACATA
130 GTTGAGGAGATGTCGTCACATG
* * * * *
13607540 GGTCAACTATAATAACAAATATTATTATGTTATTCAATAATCATATATGAAATTGTTGAACATAA
1 GGTCAACTACAATAACAGATATTATTATGTTATTCGATAATCAAATATGGAATTGTTGAACATAA
* * * * * * * **
13607605 ACCGTTAGAACCGTCCTTACTGGTGGCTCGTTACCATTGTGCCATTTAAGCAAGTCCTGTTGGTC
66 ACCATAAGAACTGTCCTTACTGGTGGCTCGTTACCACTGTG-CATCTGAGCAGGTCCTGTCAGTC
* * *
13607670 GTTGAGTAGATGTTGTCGCATG
130 GTTGAGGAGATGTCGTCACATG
* *
13607692 GGTCAACTACAATAATAGATATTATTGTGTTATTCGATAATCAAATATGGAATTGTTGAACATAA
1 GGTCAACTACAATAACAGATATTATTATGTTATTCGATAATCAAATATGGAATTGTTGAACATAA
13607757 ACCATAAGAAC
66 ACCATAAGAAC
13607768 CATTCTTATG
Statistics
Matches: 314, Mismatches: 62, Indels: 5
0.82 0.16 0.01
Matches are distributed among these distances:
150 1 0.00
151 211 0.67
152 102 0.32
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (151 bp):
GGTCAACTACAATAACAGATATTATTATGTTATTCGATAATCAAATATGGAATTGTTGAACATAA
ACCATAAGAACTGTCCTTACTGGTGGCTCGTTACCACTGTGCATCTGAGCAGGTCCTGTCAGTCG
TTGAGGAGATGTCGTCACATG
Found at i:13608905 original size:11 final size:11
Alignment explanation
Indices: 13608889--13608915 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
13608879 CCCTTGCTGC
13608889 GCAATGGGTTT
1 GCAATGGGTTT
13608900 GCAATGGGTTT
1 GCAATGGGTTT
13608911 GCAAT
1 GCAAT
13608916 ATTTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.11, G:0.33, T:0.33
Consensus pattern (11 bp):
GCAATGGGTTT
Found at i:13616896 original size:27 final size:26
Alignment explanation
Indices: 13616843--13616915 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
13616833 TAACACATTA
* *
13616843 TCAACATGGCGTGTAACAAATTTTTTT
1 TCAACATGGCATGTAACAAA-TTGTTT
13616870 TCAACATGGCATGTAACAACA-TGTTT
1 TCAACATGGCATGTAACAA-ATTGTTT
* * *
13616896 TCAACAAGACATGTAGCAAA
1 TCAACATGGCATGTAACAAA
13616916 ATTTTAGAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
25 1 0.03
26 20 0.50
27 18 0.45
28 1 0.03
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (26 bp):
TCAACATGGCATGTAACAAATTGTTT
Found at i:13617556 original size:21 final size:21
Alignment explanation
Indices: 13617532--13617579 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
13617522 CATTATGACA
13617532 CTGGAGAATGAAATTGCGACG
1 CTGGAGAATGAAATTGCGACG
*
13617553 CTGGAGAATGACATTGCGACG
1 CTGGAGAATGAAATTGCGACG
13617574 CTGGAG
1 CTGGAG
13617580 GATAATGCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.17, G:0.35, T:0.19
Consensus pattern (21 bp):
CTGGAGAATGAAATTGCGACG
Found at i:13620311 original size:77 final size:77
Alignment explanation
Indices: 13620206--13620369 Score: 211
Period size: 77 Copynumber: 2.1 Consensus size: 77
13620196 TATATTGTTT
* * * * **
13620206 CACGCTCCAGTTTCACCTATGTCATTGACATCTTGTCCTGACACGCTGAGTCATTGTAGTATTAT
1 CACGCTCCAATTTCACCTATGTCATTGACATCTTGTCATGACACACTAAGTCATTACAGTATTAT
13620271 AGGGTAACACGC
66 AGGGTAACACGC
* * **
13620283 CACGCTCCAATTTCACCTATGTCGTTGACATCTTGTCATGCCACACTAAGTTGTTACAGTATTAT
1 CACGCTCCAATTTCACCTATGTCATTGACATCTTGTCATGACACACTAAGTCATTACAGTATTAT
* *
13620348 AGGGTGACATGC
66 AGGGTAACACGC
*
13620360 CACACTCCAA
1 CACGCTCCAA
13620370 AGATATCGTT
Statistics
Matches: 74, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
77 74 1.00
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (77 bp):
CACGCTCCAATTTCACCTATGTCATTGACATCTTGTCATGACACACTAAGTCATTACAGTATTAT
AGGGTAACACGC
Found at i:13620610 original size:77 final size:75
Alignment explanation
Indices: 13620224--13620813 Score: 422
Period size: 77 Copynumber: 7.8 Consensus size: 75
13620214 AGTTTCACCT
* * * * * * * *
13620224 ATGTCATTGACATCTTGTCCTGACACGC-TGAGTCATTGTAGTATTATAGGGTAACACGCCACGC
1 ATGTCGTTGACATCTTGTCGTGACACACATAAGTCGTTGCAGTATTATAGGGTGACACGCCACAC
*
13620288 TCCAATTTCACCT
66 TCCAATTT-A--G
* * * * *
13620301 ATGTCGTTGACATCTTGTCATGCCACAC-TAAGTTGTTACAGTATTATAGGGTGACATGCCACAC
1 ATGTCGTTGACATCTTGTCGTGACACACATAAGTCGTTGCAGTATTATAGGGTGACACGCCACAC
13620365 TCCAA---AG
66 TCCAATTTAG
* * * * * * *
13620372 ATATCGTTGACATCTTGTCGTGACACGA-ATGAGTTGTTGCAATATTGTAGGGCGACATGCCACA
1 ATGTCGTTGACATCTTGTCGTGACAC-ACATAAGTCGTTGCAGTATTATAGGGTGACACGCCACA
* *
13620436 CTCAAATTGTTAA
65 CTCCAA-T-TTAG
* * * *
13620449 ATGTCATTAACATCTTTTCGTGACATGCCACCAT--GTCGTTGTAGTATTAT-GGGTGACACGCC
1 ATGTCGTTGACATCTTGTCGTGACA---CA-CATAAGTCGTTGCAGTATTATAGGGTGACACGCC
*
13620511 ACTCTCCAA---AG
62 ACACTCCAATTTAG
* * *
13620522 ATGTTGTTGACATCTTGTTGTGACACACATAAGTCATTGCAGTATTATAGGGTGACACGCCACAC
1 ATGTCGTTGACATCTTGTCGTGACACACATAAGTCGTTGCAGTATTATAGGGTGACACGCCACAC
13620587 TCCAATTGTTAG
66 TCCAA-T-TTAG
* * * * * * *
13620599 ATGTCGCTGACATCTTGTTGTGACACATCGTCATGTCGTTGCAGTATTATAAGATGACATGCCAC
1 ATGTCGTTGACATCTTGTCGTGACACA-CAT-AAGTCGTTGCAGTATTATAGGGTGACACGCCAC
**
13620664 TTTCCAA---AG
64 ACTCCAATTTAG
* * * * * * *
13620673 ATATCGTTGACATCTTGTCATGACACGCATGAGTCGTTGCAGTATTATAGAGTGATACGCCACAT
1 ATGTCGTTGACATCTTGTCGTGACACACATAAGTCGTTGCAGTATTATAGGGTGACACGCCACAC
* *
13620738 TACAATTGTTAA
66 TCCAA-T-TTAG
* *
13620750 ATGTCGTTGACATCTTGTCGTGACATGTCGCCAT--GTCGTTGCAGTATTATAAGGTGACACGCC
1 ATGTCGTTGACATCTTGTCGTGACA---C-ACATAAGTCGTTGCAGTATTATAGGGTGACACGCC
13620813 A
62 A
13620814 TGCTTCAAAG
Statistics
Matches: 406, Mismatches: 76, Indels: 60
0.75 0.14 0.11
Matches are distributed among these distances:
69 3 0.01
70 2 0.00
71 37 0.09
72 87 0.21
73 24 0.06
74 24 0.06
77 130 0.32
78 19 0.05
79 73 0.18
80 2 0.00
81 5 0.01
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.32
Consensus pattern (75 bp):
ATGTCGTTGACATCTTGTCGTGACACACATAAGTCGTTGCAGTATTATAGGGTGACACGCCACAC
TCCAATTTAG
Found at i:13620670 original size:79 final size:79
Alignment explanation
Indices: 13620301--13620813 Score: 308
Period size: 72 Copynumber: 6.8 Consensus size: 79
13620291 AATTTCACCT
* * * * * * * *
13620301 ATGTCGTTGACATCTTGTCATGCCACA-C-T-AAGTTGTTACAGTATTATAGGGTGACATGCCAC
1 ATGTCGTTGACATCTTGTCGTGACACATCATCATGTCGTTGCAGTATTATAAGATGACACGCCAC
*
13620363 ACTCCAA-----AG
66 ATTCCAATTGTTAG
* * * * * * ** *
13620372 ATATCGTTGACATCTTGTCGTGACACGA--ATGA-GTTGTTGCAATATTGTAGGGCGACATGCCA
1 ATGTCGTTGACATCTTGTCGTGACAC-ATCATCATGTCGTTGCAGTATTATAAGATGACACGCCA
* * *
13620434 CACTCAAATTGTTAA
65 CATTCCAATTGTTAG
* * * *** * * * *
13620449 ATGTCATTAACATCTTTTCGTGACATGCCACCATGTCGTTGTAGTATTAT-GGGTGACACGCCAC
1 ATGTCGTTGACATCTTGTCGTGACACATCATCATGTCGTTGCAGTATTATAAGATGACACGCCAC
13620513 -TCTCCAA-----AG
66 AT-TCCAATTGTTAG
* * * * * *
13620522 ATGTTGTTGACATCTTGTTGTGACACA-CAT-AAGTCATTGCAGTATTATAGGGTGACACGCCAC
1 ATGTCGTTGACATCTTGTCGTGACACATCATCATGTCGTTGCAGTATTATAAGATGACACGCCAC
*
13620585 ACTCCAATTGTTAG
66 ATTCCAATTGTTAG
* * * *
13620599 ATGTCGCTGACATCTTGTTGTGACACATCGTCATGTCGTTGCAGTATTATAAGATGACATGCCAC
1 ATGTCGTTGACATCTTGTCGTGACACATCATCATGTCGTTGCAGTATTATAAGATGACACGCCAC
*
13620664 TTTCCAA-----AG
66 ATTCCAATTGTTAG
* * * * *
13620673 ATATCGTTGACATCTTGTCATGACAC-GCATGA-GTCGTTGCAGTATTAT-AGAGTGATACGCCA
1 ATGTCGTTGACATCTTGTCGTGACACATCATCATGTCGTTGCAGTATTATAAGA-TGACACGCCA
* *
13620735 CATTACAATTGTTAA
65 CATTCCAATTGTTAG
** ** *
13620750 ATGTCGTTGACATCTTGTCGTGACATGTCGCCATGTCGTTGCAGTATTATAAGGTGACACGCCA
1 ATGTCGTTGACATCTTGTCGTGACACATCATCATGTCGTTGCAGTATTATAAGATGACACGCCA
13620814 TGCTTCAAAG
Statistics
Matches: 343, Mismatches: 69, Indels: 52
0.74 0.15 0.11
Matches are distributed among these distances:
71 41 0.12
72 86 0.25
73 25 0.07
74 24 0.07
77 73 0.21
78 22 0.06
79 70 0.20
80 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (79 bp):
ATGTCGTTGACATCTTGTCGTGACACATCATCATGTCGTTGCAGTATTATAAGATGACACGCCAC
ATTCCAATTGTTAG
Found at i:13620733 original size:151 final size:151
Alignment explanation
Indices: 13620230--13620856 Score: 676
Period size: 151 Copynumber: 4.2 Consensus size: 151
13620220 ACCTATGTCA
* * * *
13620230 TTGACATCTTGTCCTGACACGC-TGAGTCATTGTAGTATTATAGGGTAACACGCCACGCTCCAAT
1 TTGACATCTTGTCGTGACACGCATGAGTCATTGCAGTATTATAGGGTGACACGCCACACTCCAAT
* * * * * * * * *
13620294 T-TCACCTATGTCGTTGACATCTTGTCATG-C-CA-CACTAAGTTGTTACAGTATTATAGGGTGA
66 TGTTA--AATGTCGTTGACATCTTGTCGTGACACATCGCCATGTCGTTGCAGTATTATAAGGTGA
* *
13620355 CATGCCACACTCCAAAGATATCG
129 CACGCCACTCTCCAAAGATATCG
* ** * * * * *
13620378 TTGACATCTTGTCGTGACACGAATGAGTTGTTGCAATATTGTAGGGCGACATGCCACACTCAAAT
1 TTGACATCTTGTCGTGACACGCATGAGTCATTGCAGTATTATAGGGTGACACGCCACACTCCAAT
* * * *** * * *
13620443 TGTTAAATGTCATTAACATCTTTTCGTGACATGCCACCATGTCGTTGTAGTATTAT-GGGTGACA
66 TGTTAAATGTCGTTGACATCTTGTCGTGACACATCGCCATGTCGTTGCAGTATTATAAGGTGACA
* *
13620507 CGCCACTCTCCAAAGATGTTG
131 CGCCACTCTCCAAAGATATCG
* * *
13620528 TTGACATCTTGTTGTGACACACATAAGTCATTGCAGTATTATAGGGTGACACGCCACACTCCAAT
1 TTGACATCTTGTCGTGACACGCATGAGTCATTGCAGTATTATAGGGTGACACGCCACACTCCAAT
* * * * *
13620593 TGTTAGATGTCGCTGACATCTTGTTGTGACACATCGTCATGTCGTTGCAGTATTATAAGATGACA
66 TGTTAAATGTCGTTGACATCTTGTCGTGACACATCGCCATGTCGTTGCAGTATTATAAGGTGACA
* *
13620658 TGCCACTTTCCAAAGATATCG
131 CGCCACTCTCCAAAGATATCG
* * * * * *
13620679 TTGACATCTTGTCATGACACGCATGAGTCGTTGCAGTATTATAGAGTGATACGCCACATTACAAT
1 TTGACATCTTGTCGTGACACGCATGAGTCATTGCAGTATTATAGGGTGACACGCCACACTCCAAT
**
13620744 TGTTAAATGTCGTTGACATCTTGTCGTGACATGTCGCCATGTCGTTGCAGTATTATAAGGTGACA
66 TGTTAAATGTCGTTGACATCTTGTCGTGACACATCGCCATGTCGTTGCAGTATTATAAGGTGACA
* *
13620809 CGCCA-TGCTTCAAAGATATCA
131 CGCCACT-CTCCAAAGATATCG
*
13620830 TTGACATCTTGTTGTGACACGC-TGAGT
1 TTGACATCTTGTCGTGACACGCATGAGT
13620857 TGTTCTTGTT
Statistics
Matches: 392, Mismatches: 80, Indels: 12
0.81 0.17 0.02
Matches are distributed among these distances:
148 38 0.10
149 34 0.09
150 131 0.33
151 189 0.48
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (151 bp):
TTGACATCTTGTCGTGACACGCATGAGTCATTGCAGTATTATAGGGTGACACGCCACACTCCAAT
TGTTAAATGTCGTTGACATCTTGTCGTGACACATCGCCATGTCGTTGCAGTATTATAAGGTGACA
CGCCACTCTCCAAAGATATCG
Found at i:13620798 original size:301 final size:298
Alignment explanation
Indices: 13620227--13620849 Score: 777
Period size: 301 Copynumber: 2.1 Consensus size: 298
13620217 TTCACCTATG
** * * * *
13620227 TCATTGACATCTTGTCCTGACACGCTGAGTCATTGTAGTATTATAGGGTAACACGCCACGCTCCA
1 TCATTGACATCTTGTTGTGACACACTAAGTCATTGCAGTATTATAGGGTAACACGCCACACTCCA
* * * * * *
13620292 ATTTCACCTATGTCGTTGACATCTTGTCATGCCACACTAAGTTGTTACAGTATTATAGGGTGACA
66 ATTTCA-CGATGTCGCTGACATCTTGTCATGACACACTAAGTCGTTACAGTATTATAAGATGACA
* * *
13620357 TGCCACACTCCAAAGATATCGTTGACATCTTGTCGTGACACGAATGAGTTGTTGCAATATTGTAG
130 TGCCACACTCCAAAGATATCGTTGACATCTTGTCATGACACGAATGAGTCGTTGCAATATTATAG
* * *
13620422 GGCGACATGCCACACTCAAATTGTTAAATGTCATTAACATCTTTTCGTGACATGCCACCATGTCG
195 AGCGACACGCCACACTCAAATTGTTAAATGTCATTAACATCTTGTCGTGACATGCCACCATGTCG
* * *
13620487 TTGTAGTATTAT-GGGTGACACGCCACT-CTCCAAAGATG
260 TTGCAGTATTATAAGGTGACACGCCA-TGCTCCAAAGATA
** *
13620525 TTGTTGACATCTTGTTGTGACACACATAAGTCATTGCAGTATTATAGGGTGACACGCCACACTCC
1 TCATTGACATCTTGTTGTGACACAC-TAAGTCATTGCAGTATTATAGGGTAACACGCCACACTCC
* ** * *
13620590 AATTGTTA-GATGTCGCTGACATCTTGTTGTGACACATCGTCATGTCGTTGCAGTATTATAAGAT
65 AATT-TCACGATGTCGCTGACATCTTGTCATGACACA-C-T-AAGTCGTTACAGTATTATAAGAT
** * *
13620654 GACATGCCACTTTCCAAAGATATCGTTGACATCTTGTCATGACACGCATGAGTCGTTGCAGTATT
126 GACATGCCACACTCCAAAGATATCGTTGACATCTTGTCATGACACGAATGAGTCGTTGCAATATT
* * * * * * *
13620719 ATAGAGTGATACGCCACA-TTACAATTGTTAAATGTCGTTGACATCTTGTCGTGACATGTCGCCA
191 ATAGAGCGACACGCCACACTCA-AATTGTTAAATGTCATTAACATCTTGTCGTGACATGCCACCA
*
13620783 TGTCGTTGCAGTATTATAAGGTGACACGCCATGCTTCAAAGATA
255 TGTCGTTGCAGTATTATAAGGTGACACGCCATGCTCCAAAGATA
13620827 TCATTGACATCTTGTTGTGACAC
1 TCATTGACATCTTGTTGTGACAC
13620850 GCTGAGTTGT
Statistics
Matches: 274, Mismatches: 43, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
298 43 0.16
299 40 0.15
300 5 0.02
301 144 0.53
302 42 0.15
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (298 bp):
TCATTGACATCTTGTTGTGACACACTAAGTCATTGCAGTATTATAGGGTAACACGCCACACTCCA
ATTTCACGATGTCGCTGACATCTTGTCATGACACACTAAGTCGTTACAGTATTATAAGATGACAT
GCCACACTCCAAAGATATCGTTGACATCTTGTCATGACACGAATGAGTCGTTGCAATATTATAGA
GCGACACGCCACACTCAAATTGTTAAATGTCATTAACATCTTGTCGTGACATGCCACCATGTCGT
TGCAGTATTATAAGGTGACACGCCATGCTCCAAAGATA
Found at i:13620868 original size:24 final size:24
Alignment explanation
Indices: 13620836--13620884 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
13620826 ATCATTGACA
13620836 TCTTGTTGTGACACGCTGAGTTGT
1 TCTTGTTGTGACACGCTGAGTTGT
* *
13620860 TCTTGTTGTGACATGTTGAGTTGT
1 TCTTGTTGTGACACGCTGAGTTGT
13620884 T
1 T
13620885 GCAGTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.12, G:0.29, T:0.47
Consensus pattern (24 bp):
TCTTGTTGTGACACGCTGAGTTGT
Found at i:13622612 original size:52 final size:52
Alignment explanation
Indices: 13622550--13622652 Score: 161
Period size: 52 Copynumber: 2.0 Consensus size: 52
13622540 GCACATGACA
* * *
13622550 ATGATAGTGGTGTGCTATGTGAGTGCACACACTGATGATATATGCCATGTGC
1 ATGATAGTGGTGTGCTATGTCAGTGCACACACTAATGATATATGACATGTGC
* *
13622602 ATGATAGTGGTGTGTTGTGTCAGTGCACACACTAATGATATATGACATGTG
1 ATGATAGTGGTGTGCTATGTCAGTGCACACACTAATGATATATGACATGTG
13622653 TGATGTGGGA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32
Consensus pattern (52 bp):
ATGATAGTGGTGTGCTATGTCAGTGCACACACTAATGATATATGACATGTGC
Found at i:13623005 original size:72 final size:72
Alignment explanation
Indices: 13622908--13623041 Score: 198
Period size: 73 Copynumber: 1.9 Consensus size: 72
13622898 ATTCTTTAAT
* * *
13622908 TTGATAGCCCTGGTTTTCGCTGCAGTG-AAATTCATTCTCCCTACAGCGAGAAACTCTCGGGTGC
1 TTGATAGCCCAGATTTTCGCTGCAGTGAAAATGCATTCTCCCTACAGCGAGAAACTCTCGGGTGC
13622972 TGGGGGC
66 TGGGGGC
* * *
13622979 TTGACTAGCCCAGATTTTCGCTGCAGTGAAAATGCATTCTTCCTGCAGTGAGAAACTCTCGGG
1 TTGA-TAGCCCAGATTTTCGCTGCAGTGAAAATGCATTCTCCCTACAGCGAGAAACTCTCGGG
13623042 CTATTGGTTC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
71 4 0.07
72 21 0.38
73 30 0.55
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (72 bp):
TTGATAGCCCAGATTTTCGCTGCAGTGAAAATGCATTCTCCCTACAGCGAGAAACTCTCGGGTGC
TGGGGGC
Found at i:13625597 original size:151 final size:151
Alignment explanation
Indices: 13625319--13625700 Score: 462
Period size: 151 Copynumber: 2.5 Consensus size: 151
13625309 CCGTCATTGC
* * * * *
13625319 CTGTCGTTGAATGAGTCAACTACCATAACAAATATTACTGTGTTATTCGCTAATCAAATATGTAA
1 CTGTCGTCGAATGAGTCAACTGCAATAACAAATATTACTGTGTTATTCGATAATCAAATATGGAA
*
13625384 TTGTTGAACATAAACCATATGAAGCATCTTTACTGGTGGATTGTTACCACTATGCATCTGAGTAG
66 TTGTTGAACATAAACCATAAGAAGCATCTTTACTGGTGGATTGTTACCACTATGCATCTGAGTAG
* * * *
13625449 GTCCCGTCGGTCGTTGATGAG
131 GTCCCATCGATCATTGAGGAG
* * * * * *
13625470 TTGTCGTGGTATGAGTTAACTGCAATAACAAATATTACTGTGTTATTTGATAATCATATATGGAA
1 CTGTCGTCGAATGAGTCAACTGCAATAACAAATATTACTGTGTTATTCGATAATCAAATATGGAA
* * * * * * *
13625535 TTCTTGAACCTAAATCATAAGAA-CTATCTTTACTGGTGGTTTGTTACCACTGTGCGTTTGAGTA
66 TTGTTGAACATAAACCATAAGAAGC-ATCTTTACTGGTGGATTGTTACCACTATGCATCTGAGTA
*
13625599 GGTCCTATCGATCATTGAGGAG
130 GGTCCCATCGATCATTGAGGAG
* * * * * *
13625621 CTGTCGTCGCATGGGTCAACTGTAATAATAGATATTA-TTTAGTTATTCGATAATCAAATATGGA
1 CTGTCGTCGAATGAGTCAACTGCAATAACAAATATTACTGT-GTTATTCGATAATCAAATATGGA
13625685 ATTGTTGAACATAAAC
65 ATTGTTGAACATAAAC
13625701 TGTTAGAACC
Statistics
Matches: 192, Mismatches: 37, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
150 3 0.02
151 189 0.98
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (151 bp):
CTGTCGTCGAATGAGTCAACTGCAATAACAAATATTACTGTGTTATTCGATAATCAAATATGGAA
TTGTTGAACATAAACCATAAGAAGCATCTTTACTGGTGGATTGTTACCACTATGCATCTGAGTAG
GTCCCATCGATCATTGAGGAG
Found at i:13628367 original size:23 final size:23
Alignment explanation
Indices: 13628324--13628381 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
13628314 AAATTTATGC
*
13628324 CGTGTTACATATTCAAGCCAT-G
1 CGTGTCACATATTCAAGCCATAG
* *
13628346 ACGTGTCACATATTCCATCCATAG
1 -CGTGTCACATATTCAAGCCATAG
*
13628370 CGTGCCACATAT
1 CGTGTCACATAT
13628382 ATTCTCACCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 29 0.97
24 1 0.03
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.29
Consensus pattern (23 bp):
CGTGTCACATATTCAAGCCATAG
Found at i:13628508 original size:22 final size:24
Alignment explanation
Indices: 13628480--13628533 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 24
13628470 CACAACCGTG
*
13628480 TCACATATTTCT-ACCATG-CCTC
1 TCACATATTTCTCACCATGACATC
*
13628502 TCACATA-TTCTCACCATGACATG
1 TCACATATTTCTCACCATGACATC
13628525 TCACATATT
1 TCACATATT
13628534 CAGACCATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 4 0.15
22 13 0.48
23 9 0.33
24 1 0.04
ACGTcount: A:0.28, C:0.31, G:0.06, T:0.35
Consensus pattern (24 bp):
TCACATATTTCTCACCATGACATC
Found at i:13628532 original size:23 final size:23
Alignment explanation
Indices: 13628478--13628753 Score: 199
Period size: 23 Copynumber: 12.3 Consensus size: 23
13628468 GTCACAACCG
13628478 TGTCACATATT-TCTACCATGCC-
1 TGTCACATATTCTC-ACCATGCCA
* *
13628500 TCTCACATATTCTCACCATGACA
1 TGTCACATATTCTCACCATGCCA
** *
13628523 TGTCACATATTCAGACCATGGCA
1 TGTCACATATTCTCACCATGCCA
* * *
13628546 TGTCAC--ATCCTCA-CATTGGCG
1 TGTCACATATTCTCACCA-TGCCA
* * * *
13628567 TGTCACATATTATCACAATGTCG
1 TGTCACATATTCTCACCATGCCA
* * *
13628590 TTTCACATATTCCCTCCATG---
1 TGTCACATATTCTCACCATGCCA
* *
13628610 GGTCACATATTCTCACTATGCCA
1 TGTCACATATTCTCACCATGCCA
* *
13628633 TGTCACACATTCTCACTATGCCA
1 TGTCACATATTCTCACCATGCCA
*
13628656 TGTCACACATTCTCACCATGCCA
1 TGTCACATATTCTCACCATGCCA
* *
13628679 TGTCACACATTCTCACCATGCCG
1 TGTCACATATTCTCACCATGCCA
* * * ***
13628702 TCTCACACATTCTCATCATGTTG
1 TGTCACATATTCTCACCATGCCA
* * *
13628725 TGTCAAACATTCCCACCATGCCA
1 TGTCACATATTCTCACCATGCCA
13628748 TGTCAC
1 TGTCAC
13628754 GAACTCTAAA
Statistics
Matches: 205, Mismatches: 40, Indels: 17
0.78 0.15 0.06
Matches are distributed among these distances:
20 17 0.08
21 14 0.07
22 17 0.08
23 156 0.76
24 1 0.00
ACGTcount: A:0.25, C:0.33, G:0.11, T:0.31
Consensus pattern (23 bp):
TGTCACATATTCTCACCATGCCA
Found at i:13628677 original size:46 final size:46
Alignment explanation
Indices: 13628478--13629048 Score: 210
Period size: 46 Copynumber: 11.9 Consensus size: 46
13628468 GTCACAACCG
* * * *
13628478 TGTCACATATT-TCTACCATGCC-TCTCACATATTCTCACCATGACA
1 TGTCACACATTCTC-ACCATGCCATGTCACACATTCTCACCATGCCA
* ** * * * *
13628523 TGTCACATATTCAGACCATGGCATGT--CACATCCTCA-CATTGGCG
1 TGTCACACATTCTCACCATGCCATGTCACACATTCTCACCA-TGCCA
* * * * * * * * *
13628567 TGTCACATATTATCACAATGTCGTTTCACATATTCCCTCCATG---
1 TGTCACACATTCTCACCATGCCATGTCACACATTCTCACCATGCCA
* * * *
13628610 GGTCACATATTCTCACTATGCCATGTCACACATTCTCACTATGCCA
1 TGTCACACATTCTCACCATGCCATGTCACACATTCTCACCATGCCA
*
13628656 TGTCACACATTCTCACCATGCCATGTCACACATTCTCACCATGCCG
1 TGTCACACATTCTCACCATGCCATGTCACACATTCTCACCATGCCA
* * *** * *
13628702 TCTCACACATTCTCATCATGTTGTGTCAAACATTCCCACCATGCCA
1 TGTCACACATTCTCACCATGCCATGTCACACATTCTCACCATGCCA
* * * * * *
13628748 TGTCACGA-ACTCTAAACCTTGTTGTGTCATAACTATGTCACAAATTCTCACCATGTCG
1 TGTCAC-ACATTCT-CACC-----ATG-C----C-ATGTCACACATTCTCACCATGCCA
* * * * * *
13628806 TCTCATAAATTCTCACCATGCCATGTCACAAACTCTAAACCCTATCGTGTCACAA
1 TGTCACACATTCTCACCATGCCATGTCACACATTCT-CA-CC-A---TG-C-C-A
* *
13628861 TCGTGTCACACATTCTCACCATG--ATGTCTAACACATTCTCACTATGCCG
1 ---TGTCACACATTCTCACCATGCCATGTC--ACACATTCTCACCATGCCA
** * * * * *
13628910 CATCACACATTCCCACCATTCCATGTCACAACCTTGTCATGTCATAGCCA
1 TGTCACACATTCTCACCATGCCATGTCAC-ACATTCTCA--CCAT-GCCA
* * * *
13628960 TGTCACATATTCTCACCATGCTATGTCACACATTCTCACCATGTCG
1 TGTCACACATTCTCACCATGCCATGTCACACATTCTCACCATGCCA
* * * * *
13629006 TGTCACAGATTCTCGCCATGACGTGTCACACATTCCCACCATG
1 TGTCACACATTCTCACCATGCCATGTCACACATTCTCACCATG
13629049 GTATGTTAGA
Statistics
Matches: 385, Mismatches: 98, Indels: 85
0.68 0.17 0.15
Matches are distributed among these distances:
43 35 0.09
44 30 0.08
45 18 0.05
46 168 0.44
47 17 0.04
48 7 0.02
49 10 0.03
50 27 0.07
51 2 0.01
52 8 0.02
54 1 0.00
55 1 0.00
56 6 0.02
57 5 0.01
58 50 0.13
ACGTcount: A:0.26, C:0.33, G:0.11, T:0.30
Consensus pattern (46 bp):
TGTCACACATTCTCACCATGCCATGTCACACATTCTCACCATGCCA
Found at i:13628840 original size:81 final size:81
Alignment explanation
Indices: 13628704--13628908 Score: 229
Period size: 81 Copynumber: 2.5 Consensus size: 81
13628694 CCATGCCGTC
* * * * * *
13628704 TCACACATTCTCATCATGTTGTGTCAAACATTCCCACCATGCCATGTCACGAACTCTAAACCTTG
1 TCACACATTCTCACCATGTCGTCTCAAACATTCCCACCATGCCATGTCACAAACTCTAAACCCTA
* *
13628769 TTGTGTCATAA-CTATG
66 TCGTGTCACAATC-ATG
* *
13628785 TCACAAATTCTCACCATGTCGTCTCATAA-ATTCTCACCATGCCATGTCACAAACTCTAAACCCT
1 TCACACATTCTCACCATGTCGTCTCA-AACATTCCCACCATGCCATGTCACAAACTCTAAACCCT
*
13628849 ATCGTGTCACAATCGTG
65 ATCGTGTCACAATCATG
* *
13628866 TCACACATTCTCACCATGAT-GTCT-AACACATTCTCACTATGCC
1 TCACACATTCTCACCATG-TCGTCTCAA-ACATTCCCACCATGCC
13628909 GCATCACACA
Statistics
Matches: 106, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
79 1 0.01
80 2 0.02
81 99 0.93
82 4 0.04
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.30
Consensus pattern (81 bp):
TCACACATTCTCACCATGTCGTCTCAAACATTCCCACCATGCCATGTCACAAACTCTAAACCCTA
TCGTGTCACAATCATG
Found at i:13628938 original size:23 final size:23
Alignment explanation
Indices: 13628864--13629048 Score: 140
Period size: 23 Copynumber: 7.9 Consensus size: 23
13628854 GTCACAATCG
13628864 TGTCACACATTCTCACCATG--A
1 TGTCACACATTCTCACCATGCCA
* *
13628885 TGTCTAACACATTCTCACTATGCCG
1 TGTC--ACACATTCTCACCATGCCA
** * *
13628910 CATCACACATTCCCACCATTCCA
1 TGTCACACATTCTCACCATGCCA
* * *
13628933 TGTCACAACCTTGTCATGTCATAGCCA
1 TGTCAC-ACATTCTCA--CCAT-GCCA
* *
13628960 TGTCACATATTCTCACCATGCTA
1 TGTCACACATTCTCACCATGCCA
* *
13628983 TGTCACACATTCTCACCATGTCG
1 TGTCACACATTCTCACCATGCCA
* * * *
13629006 TGTCACAGATTCTCGCCATGACG
1 TGTCACACATTCTCACCATGCCA
*
13629029 TGTCACACATTCCCACCATG
1 TGTCACACATTCTCACCATG
13629049 GTATGTTAGA
Statistics
Matches: 126, Mismatches: 30, Indels: 14
0.74 0.18 0.08
Matches are distributed among these distances:
21 4 0.03
23 93 0.74
24 9 0.07
25 2 0.02
26 9 0.07
27 9 0.07
ACGTcount: A:0.25, C:0.35, G:0.11, T:0.29
Consensus pattern (23 bp):
TGTCACACATTCTCACCATGCCA
Found at i:13629204 original size:81 final size:81
Alignment explanation
Indices: 13629117--13629275 Score: 239
Period size: 81 Copynumber: 2.0 Consensus size: 81
13629107 TTTGTCACAA
* *
13629117 ATTCTCACCACATCGTGTCACACATTCCC-ACTATGGCATGTCACAAACTCTAAAACCTACCGTA
1 ATTCTCACCACACCATGTCACACATTCCCAAC-ATGGCATGTCACAAACTCTAAAACCTACCGTA
13629181 TCACAACCGTGTCATAG
65 TCACAACCGTGTCATAG
* * * *
13629198 ATTCTCACCATACCATGTCACACATTCCCAACATGGCATGTCACAAACTCTAAATCCTGCCGTGT
1 ATTCTCACCACACCATGTCACACATTCCCAACATGGCATGTCACAAACTCTAAAACCTACCGTAT
*
13629263 CACGACCGTGTCA
66 CACAACCGTGTCA
13629276 CATATGGCTT
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
81 68 0.97
82 2 0.03
ACGTcount: A:0.30, C:0.34, G:0.12, T:0.25
Consensus pattern (81 bp):
ATTCTCACCACACCATGTCACACATTCCCAACATGGCATGTCACAAACTCTAAAACCTACCGTAT
CACAACCGTGTCATAG
Found at i:13631454 original size:20 final size:20
Alignment explanation
Indices: 13631397--13631459 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
13631387 TATATACCCA
*
13631397 TCATCATCATC-TCACCAAC
1 TCATCATCATCATCACCAGC
*
13631416 CCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
13631436 TCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
13631456 TCAT
1 TCAT
13631460 GCGCACTCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.30, C:0.41, G:0.03, T:0.25
Consensus pattern (20 bp):
TCATCATCATCATCACCAGC
Found at i:13631506 original size:43 final size:43
Alignment explanation
Indices: 13631458--13631576 Score: 168
Period size: 43 Copynumber: 2.8 Consensus size: 43
13631448 TCACCAGCTC
** * *
13631458 ATGCGCACTCCCTACTCGCACATGGCTGGGTCATCAC-CGGGTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATC-CTCGGCTT
13631501 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
* *
13631544 ATGCGCACTCCCTACTCGCACATAGCCGAGTCA
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCA
13631577 ACATAATTAC
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
42 1 0.01
43 68 0.99
ACGTcount: A:0.19, C:0.38, G:0.21, T:0.22
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
Found at i:13639609 original size:38 final size:40
Alignment explanation
Indices: 13639511--13639616 Score: 135
Period size: 38 Copynumber: 2.7 Consensus size: 40
13639501 CACTCCCGGC
*
13639511 TCATGTACATCCCCCCACATCGTGCACATAGCCGACACCA
1 TCATGTACATCCCCCCACATCGTGCACATAGCAGACACCA
* * ** *
13639551 TCATGTGCATCCCCCCACATCGTGCACA-ATCAG-TGCTA
1 TCATGTACATCCCCCCACATCGTGCACATAGCAGACACCA
*
13639589 TCGTGTACATCCCCCCACATCGTGCACA
1 TCATGTACATCCCCCCACATCGTGCACA
13639617 CGGGCACTAT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
38 28 0.48
39 3 0.05
40 27 0.47
ACGTcount: A:0.25, C:0.41, G:0.14, T:0.21
Consensus pattern (40 bp):
TCATGTACATCCCCCCACATCGTGCACATAGCAGACACCA
Found at i:13643284 original size:2 final size:2
Alignment explanation
Indices: 13643277--13643317 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
13643267 TGCCAACCAA
13643277 AT 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 AT A
13643318 NNNNNNNNNN
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13650111 original size:20 final size:23
Alignment explanation
Indices: 13650080--13650125 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
13650070 TATTTCTATG
13650080 AAAACTTATAATAC-T-AAATAT
1 AAAACTTATAATACATAAAATAT
*
13650101 AAAAC-TATAATGCATAAAATAT
1 AAAACTTATAATACATAAAATAT
13650123 AAA
1 AAA
13650126 TAGTTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
21 6 0.27
22 9 0.41
ACGTcount: A:0.61, C:0.09, G:0.02, T:0.28
Consensus pattern (23 bp):
AAAACTTATAATACATAAAATAT
Found at i:13660967 original size:18 final size:18
Alignment explanation
Indices: 13660944--13660982 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
13660934 TAAGTGAAGA
13660944 ATTTTA-AAATAAAATAAT
1 ATTTTATAAATAAAA-AAT
*
13660962 ATTTTATTAATAAAAAAT
1 ATTTTATAAATAAAAAAT
13660980 ATT
1 ATT
13660983 AAAATATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTTTATAAATAAAAAAT
Found at i:13664687 original size:20 final size:20
Alignment explanation
Indices: 13664662--13664707 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
13664652 TTTTGACCCC
13664662 ATTTGACTTATT-AGAGTATA
1 ATTTGACTTATTGA-AGTATA
*
13664682 ATTTGACTTATTGAAGTATG
1 ATTTGACTTATTGAAGTATA
13664702 ATTTGA
1 ATTTGA
13664708 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGAAGTATA
Found at i:13664783 original size:28 final size:27
Alignment explanation
Indices: 13664752--13664804 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
13664742 TTTGGAGTAT
*
13664752 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTT-CCACCTC
*
13664780 AGGGGCAAAATTGTAATTTTCCACC
1 AGGGGCAAAATGGTAATTTTCCACC
13664805 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:13664810 original size:28 final size:28
Alignment explanation
Indices: 13664752--13664810 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
13664742 TTTGGAGTAT
* *
13664752 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTTGCCACCCC
*
13664780 AGGGGCAAAATTGTAATTTT-CCACCACC
1 AGGGGCAAAATGGTAATTTTGCCACC-CC
13664808 AGG
1 AGG
13664811 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:13672053 original size:2 final size:2
Alignment explanation
Indices: 13672042--13672087 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
13672032 GGGAGGCTTT
13672042 TA TA -A 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
13672083 TA TA T
1 TA TA T
13672088 CTGGTTGGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13672440 original size:13 final size:13
Alignment explanation
Indices: 13672422--13672446 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13672412 AGGATCTTAT
13672422 TTTTTGGTCATTG
1 TTTTTGGTCATTG
13672435 TTTTTGGTCATT
1 TTTTTGGTCATT
13672447 AGGTTCAGGC
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:0.08, C:0.08, G:0.20, T:0.64
Consensus pattern (13 bp):
TTTTTGGTCATTG
Found at i:13690390 original size:18 final size:20
Alignment explanation
Indices: 13690356--13690392 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
13690346 TAAACTCTAG
13690356 GAGAAGAAGAAAGAAAAAGA
1 GAGAAGAAGAAAGAAAAAGA
13690376 GAGAA-AAGAAA-AAAAAG
1 GAGAAGAAGAAAGAAAAAG
13690393 CTTGGTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 6 0.35
20 5 0.29
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (20 bp):
GAGAAGAAGAAAGAAAAAGA
Found at i:13690899 original size:42 final size:42
Alignment explanation
Indices: 13690836--13690924 Score: 151
Period size: 42 Copynumber: 2.1 Consensus size: 42
13690826 TGATGTGGAT
*
13690836 CCGGCTATGTGTGAGTAGGAGTGCACATAAGTCGTTACTGAC
1 CCGGCTATGTGTGAGTAGGAGTGCACATAAGTCATTACTGAC
* *
13690878 CCGGCTATGTGTGAGTGGGAGTGCACATAAGTCATTGCTGAC
1 CCGGCTATGTGTGAGTAGGAGTGCACATAAGTCATTACTGAC
13690920 CCGGC
1 CCGGC
13690925 CATATGCAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.25
Consensus pattern (42 bp):
CCGGCTATGTGTGAGTAGGAGTGCACATAAGTCATTACTGAC
Found at i:13690937 original size:42 final size:42
Alignment explanation
Indices: 13690853--13690950 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 42
13690843 TGTGTGAGTA
* * * **
13690853 GGAGTGCACATAAGTCGTTACTGACCCGGCTATGTGTGAGTG
1 GGAGTGCACATAAGTCATTACTGACCCGGCCATATGCAAGTG
*
13690895 GGAGTGCACATAAGTCATTGCTGACCCGGCCATATGCAAGTG
1 GGAGTGCACATAAGTCATTACTGACCCGGCCATATGCAAGTG
* *
13690937 GGAGTACGCATAAG
1 GGAGTGCACATAAG
13690951 CTGTTGCATA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.22
Consensus pattern (42 bp):
GGAGTGCACATAAGTCATTACTGACCCGGCCATATGCAAGTG
Found at i:13694097 original size:21 final size:22
Alignment explanation
Indices: 13694068--13694119 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
13694058 CTCAAGAAAC
*
13694068 AAGTCAAGAGTCAATCCTAGAG
1 AAGTCAAGAGTCAACCCTAGAG
13694090 AAGT-AAGAGTCAACCCTAGAG
1 AAGTCAAGAGTCAACCCTAGAG
13694111 AAGCTCAAG
1 AAG-TCAAG
13694120 TTTATCCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 19 0.70
22 5 0.19
23 3 0.11
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.15
Consensus pattern (22 bp):
AAGTCAAGAGTCAACCCTAGAG
Found at i:13696769 original size:21 final size:21
Alignment explanation
Indices: 13696745--13696818 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
13696735 AGAAAAACAG
13696745 ATAAAATCTATATTTAAAAGA
1 ATAAAATCTATATTTAAAAGA
* * **
13696766 AT-AAA-CCAAATCAAAAAGA
1 ATAAAATCTATATTTAAAAGA
* *
13696785 ATAAAATCAATATTTAATAGA
1 ATAAAATCTATATTTAAAAGA
13696806 ATAAAATCTATAT
1 ATAAAATCTATAT
13696819 AGTTCCACAT
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
19 12 0.29
20 6 0.15
21 23 0.56
ACGTcount: A:0.59, C:0.08, G:0.04, T:0.28
Consensus pattern (21 bp):
ATAAAATCTATATTTAAAAGA
Found at i:13714167 original size:27 final size:25
Alignment explanation
Indices: 13714107--13714166 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
13714097 GTGGTCGCAA
**
13714107 CCACATATATCAACTTGTGGCCTAG
1 CCACATATATCAACCCGTGGCCTAG
*
13714132 CCACATATATCAACCCGTGGCCTCG
1 CCACATATATCAACCCGTGGCCTAG
*
13714157 CCACGTATAT
1 CCACATATAT
13714167 ATATCACAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.27, C:0.33, G:0.15, T:0.25
Consensus pattern (25 bp):
CCACATATATCAACCCGTGGCCTAG
Found at i:13718125 original size:7 final size:7
Alignment explanation
Indices: 13718113--13718167 Score: 58
Period size: 7 Copynumber: 7.9 Consensus size: 7
13718103 CCTACTAGCT
13718113 TTTCTTC
1 TTTCTTC
13718120 TTTCTTC
1 TTTCTTC
** *
13718127 CCTCTCC
1 TTTCTTC
13718134 TTT-TTC
1 TTTCTTC
13718140 TTTCCTTC
1 TTT-CTTC
*
13718148 TTTCTCC
1 TTTCTTC
13718155 TTTCTTC
1 TTTCTTC
13718162 TTTCTT
1 TTTCTT
13718168 TTTGCTTTCA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
6 5 0.13
7 27 0.71
8 6 0.16
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (7 bp):
TTTCTTC
Found at i:13727859 original size:33 final size:33
Alignment explanation
Indices: 13727773--13728021 Score: 223
Period size: 33 Copynumber: 7.1 Consensus size: 33
13727763 TCAACTCAGC
* * *
13727773 TCATGTGCACTACCACACCGCACATAGCTAATATCC
1 TCATGTGCACTCCCACACCGCACATGGC-AA-AT-A
* *
13727809 TCATGTGCACTCTCACACCGCACATAGCAAATA
1 TCATGTGCACTCCCACACCGCACATGGCAAATA
*
13727842 TCATGTGGACTCCCACACCGCACATGGCAAATA
1 TCATGTGCACTCCCACACCGCACATGGCAAATA
* *
13727875 TCATGTGCACTCCCACACAGCACATGGCATATA
1 TCATGTGCACTCCCACACCGCACATGGCAAATA
* *
13727908 TCATGGGCACTCCCACACCTCACATGGCATATATCATCATCA
1 TCATGTGCACTCCCACACCGCACATGGC----A--A--AT-A
* * *
13727950 TCATGTGCACTACCACACCGCACA--CCACATCCCCA
1 TCATGTGCACTCCCACACCGCACATGGCAAAT----A
13727985 TCATGTGCACTCCCACACCGCACATGGCAAATA
1 TCATGTGCACTCCCACACCGCACATGGCAAATA
13728018 TCAT
1 TCAT
13728022 CATCGTGTGC
Statistics
Matches: 178, Mismatches: 21, Indels: 31
0.77 0.09 0.13
Matches are distributed among these distances:
32 2 0.01
33 90 0.51
34 2 0.01
35 27 0.15
36 27 0.15
37 5 0.03
40 1 0.01
41 2 0.01
42 22 0.12
ACGTcount: A:0.30, C:0.37, G:0.13, T:0.20
Consensus pattern (33 bp):
TCATGTGCACTCCCACACCGCACATGGCAAATA
Done.