Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 16 of 199
Found at i:4942562 original size:16 final size:16
Alignment explanation
Indices: 4942541--4942573 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
4942531 AATAATTTCT
*
4942541 AAAAAAATGTATATGA
1 AAAAAAATGCATATGA
4942557 AAAAAAATGCATATGA
1 AAAAAAATGCATATGA
4942573 A
1 A
4942574 TTAGAAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.64, C:0.03, G:0.12, T:0.21
Consensus pattern (16 bp):
AAAAAAATGCATATGA
Found at i:4944575 original size:44 final size:44
Alignment explanation
Indices: 4944453--4944894 Score: 350
Period size: 45 Copynumber: 9.9 Consensus size: 44
4944443 ATTTGTTGTA
*
4944453 TTTGATCTACTTCACGCC-GATACATGAAGACAAGATCTGCTTTTC
1 TTTGATCTACTTCACGCCAG-TATATGAAGACAAGATCTGC-TTTC
* * * ** * * *
4944498 TTTAATCT-GTTCCACCACCAGTATGGGGAGACAAGATCTGGTATC
1 TTTGATCTACTT-CA-CGCCAGTATATGAAGACAAGATCTGCTTTC
* * **
4944543 TTTGATCTACTTCACGCCAGTACATGAAGACAATATCTATTTTTC
1 TTTGATCTACTTCACGCCAGTATATGAAGACAAGATCT-GCTTTC
** * * * ** * * *
4944588 TTCAATCTGCTCCACCACCAGTATGGGGAGACAAGATCTGGTATC
1 TTTGATCTACTTCA-CGCCAGTATATGAAGACAAGATCTGCTTTC
*
4944633 TTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTC
1 TTTGATCTACTTCACGCCAGTATATGAAGACAAGATCTGCTTTC
* * * * ** *
4944677 TTTGACCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTG-TTATC
1 TTTGATCTACTTC-ACGCCAGTATATGAAGACAAGATCTGCTT-TC
4944722 TTTGATCTACTTCACGCCAGTATATGAAGACAAGATCTGCTTTC
1 TTTGATCTACTTCACGCCAGTATATGAAGACAAGATCTGCTTTC
* * * * ** * * *
4944766 TTTGACCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATC
1 TTTGATCTACTTC-ACGCCAGTATATGAAGACAAGATCTGCTTTC
*
4944811 TTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTC
1 TTTGATCTACTTCACGCCAGTATATGAAGACAAGATCTGCTTTC
* * * * **
4944855 TTTGACCTGCTTCGCCACCAGTATGGGAAGACAAGATCTG
1 TTTGATCTACTTC-ACGCCAGTATATGAAGACAAGATCTG
4944895 TTACTTTTCA
Statistics
Matches: 301, Mismatches: 85, Indels: 22
0.74 0.21 0.05
Matches are distributed among these distances:
44 124 0.41
45 138 0.46
46 38 0.13
47 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.30
Consensus pattern (44 bp):
TTTGATCTACTTCACGCCAGTATATGAAGACAAGATCTGCTTTC
Found at i:4944735 original size:89 final size:89
Alignment explanation
Indices: 4944426--4944894 Score: 681
Period size: 89 Copynumber: 5.2 Consensus size: 89
4944416 ATTCCACCAT
* * * * * *
4944426 CAGTATGGGGAGACAATATTTGTTGTATTTGATCTACTTCACGCC-GATACATGAAGACAAGATC
1 CAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAG-TACATGAAGACAAGATC
* * *
4944490 TGCTTTTCTTTAATCTG-TTCCACCAC
65 TGC-TTTCTTTGACCTGCTT-CGCCAC
* *
4944516 CAGTATGGGGAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAATATCT
1 CAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCT
** ** * * *
4944581 ATTTTTCTTCAATCTGCTCCACCAC
66 -GCTTTCTTTGACCTGCTTCGCCAC
*
4944606 CAGTATGGGGAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCT
1 CAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCT
4944671 GCTTTCTTTGACCTGCTTCGCCAC
66 GCTTTCTTTGACCTGCTTCGCCAC
* * *
4944695 CAGTATGGGAAGGCAAGATCTGTTATCTTTGATCTACTTCACGCCAGTATATGAAGACAAGATCT
1 CAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCT
4944760 GCTTTCTTTGACCTGCTTCGCCAC
66 GCTTTCTTTGACCTGCTTCGCCAC
*
4944784 CAGTATGGGAAGGCAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCT
1 CAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCT
4944849 GCTTTCTTTGACCTGCTTCGCCAC
66 GCTTTCTTTGACCTGCTTCGCCAC
4944873 CAGTATGGGAAGACAAGATCTG
1 CAGTATGGGAAGACAAGATCTG
4944895 TTACTTTTCA
Statistics
Matches: 351, Mismatches: 25, Indels: 7
0.92 0.07 0.02
Matches are distributed among these distances:
89 210 0.60
90 139 0.40
91 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.30
Consensus pattern (89 bp):
CAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCT
GCTTTCTTTGACCTGCTTCGCCAC
Found at i:4952988 original size:20 final size:20
Alignment explanation
Indices: 4952963--4953002 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
4952953 TAAAGGTCTT
4952963 TAATGCATATGATGCGATGC
1 TAATGCATATGATGCGATGC
4952983 TAATGCATATGATGCGATGC
1 TAATGCATATGATGCGATGC
4953003 ATGAGGTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (20 bp):
TAATGCATATGATGCGATGC
Found at i:4956758 original size:15 final size:15
Alignment explanation
Indices: 4956738--4956769 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
4956728 AATAATTTCT
4956738 AAAAAAATGTATATG
1 AAAAAAATGTATATG
4956753 AAAAAAATGTATATG
1 AAAAAAATGTATATG
4956768 AA
1 AA
4956770 TTAGAAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (15 bp):
AAAAAAATGTATATG
Found at i:4957818 original size:5 final size:5
Alignment explanation
Indices: 4957774--4957801 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
4957764 TTTGTTTTTG
4957774 ATAAA ATAAA ATAAA ATAAA ATAAA ATA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATA
4957802 GACTGAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:4960549 original size:16 final size:17
Alignment explanation
Indices: 4960517--4960549 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4960507 AATGTATTCT
*
4960517 AAATTACATATATATAA
1 AAATAACATATATATAA
4960534 AAATAACATA-ATATAA
1 AAATAACATATATATAA
4960550 GCCAGAACCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATAACATATATATAA
Found at i:4967478 original size:84 final size:86
Alignment explanation
Indices: 4967314--4967478 Score: 210
Period size: 86 Copynumber: 1.9 Consensus size: 86
4967304 AGGGTTTTAA
* * * * *
4967314 TTTTTTTGTAGTATTATTTATTTGTATGTTTGTCACTTAATTATGAAAAAACTAAATAAATACTG
1 TTTTTTTGTAGTATTATTTATTTGTATGCTTCTCAATTAAGTATGAAAAAACTAAATAAATACTA
*
4967379 AAATGATATATTTGAGAAGTT
66 AAATGATATAGTTGAGAAGTT
* *
4967400 TTTTTTTGTATTATTATTTATTTGTATGCTTCTTAATT-AGTAT-AAAAAAC-AAATTAAATACT
1 TTTTTTTGTAGTATTATTTATTTGTATGCTTCTCAATTAAGTATGAAAAAACTAAA-TAAATACT
* *
4967462 AAAATGGTATGGTTGAG
65 AAAATGATATAGTTGAG
4967479 GTTTTCAGGG
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
83 3 0.04
84 28 0.41
85 4 0.06
86 33 0.49
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.47
Consensus pattern (86 bp):
TTTTTTTGTAGTATTATTTATTTGTATGCTTCTCAATTAAGTATGAAAAAACTAAATAAATACTA
AAATGATATAGTTGAGAAGTT
Found at i:4974707 original size:31 final size:31
Alignment explanation
Indices: 4974618--4974708 Score: 91
Period size: 31 Copynumber: 2.9 Consensus size: 31
4974608 CACAAAAATT
* *
4974618 CTATTGGTGCCGCCT-A-ATAGTGCCCTTCCTT
1 CTATTGGTGCCGCTTGACAT-GTGCCC-TCCTC
*
4974649 CTACTGGTGCCGCTTGACA-GACT-CCCTCCTC
1 CTATTGGTGCCGCTTGACATG--TGCCCTCCTC
4974680 CTATTGGTGCCGCTTGACATGTGCCCTCC
1 CTATTGGTGCCGCTTGACATGTGCCCTCC
4974709 AACCTTGGTG
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
30 1 0.02
31 42 0.84
32 5 0.10
33 2 0.04
ACGTcount: A:0.12, C:0.36, G:0.21, T:0.31
Consensus pattern (31 bp):
CTATTGGTGCCGCTTGACATGTGCCCTCCTC
Found at i:4979425 original size:25 final size:25
Alignment explanation
Indices: 4979396--4979457 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
4979386 CAGCTCTTTT
*
4979396 GAGCTTACCGTTATTCAGCTTGGAA
1 GAGCTTACCGTTATTCAGCTCGGAA
* * *
4979421 TAGCTTACTGTTATTCAGCTCGGAG
1 GAGCTTACCGTTATTCAGCTCGGAA
4979446 GAGCTTACCGTT
1 GAGCTTACCGTT
4979458 TATAGCTCGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (25 bp):
GAGCTTACCGTTATTCAGCTCGGAA
Found at i:4982653 original size:50 final size:48
Alignment explanation
Indices: 4982593--4982771 Score: 206
Period size: 50 Copynumber: 3.7 Consensus size: 48
4982583 GTGAGTATGC
4982593 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGTTCGAGGAGTG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-GTTCGAGGAGTG
* ** *
4982642 CTAGTGTAAGACCATGTCTGGGACATGGCATCAGCACGGACAAAGAAGAGT-
1 C-AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTTC---GAGGAGTG
*
4982693 CAGTGTAAGACCATGTTTGGGACATGGCATCGG--C-TT-GAGATGAGTG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTTCGAG--GAGTG
4982739 CCAGTGTAAGACCATGTCTGGGACATGGCATCG
1 -CAGTGTAAGACCATGTCTGGGACATGGCATCG
4982772 ACACTGATAT
Statistics
Matches: 112, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
43 2 0.02
45 4 0.04
47 31 0.28
48 1 0.01
49 3 0.03
50 64 0.57
51 1 0.01
52 6 0.05
ACGTcount: A:0.27, C:0.20, G:0.32, T:0.21
Consensus pattern (48 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTTCGAGGAGTG
Found at i:4982807 original size:48 final size:47
Alignment explanation
Indices: 4982592--4982817 Score: 188
Period size: 50 Copynumber: 4.7 Consensus size: 47
4982582 AGTGAGTATG
* ** * *
4982592 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGTTCGAGGAGTG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATC-G-AC-CTGAGATGAGTC
* ** *
4982642 CTAGTGTAAGACCATGTCTGGGACATGGCATCAGCACGGACAAAGAAGAGT-
1 CCAGTGTAAGACCATGTCTGGGACATGGCATC-G-AC---CTGAGATGAGTC
* * * *
4982693 -CAGTGTAAGACCATGTTTGGGACATGGCATCGGCTTGAGATGAGTG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGACCTGAGATGAGTC
* *
4982739 CCAGTGTAAGACCATGTCTGGGACATGGCATCGACACTGATATGTGATC
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGAC-CTGAGATGAG-TC
* *
4982788 CCA-TGTAAGACCATATCTGGGATATGGCAT
1 CCAGTGTAAGACCATGTCTGGGACATGGCAT
4982818 TGGCAGGACA
Statistics
Matches: 148, Mismatches: 22, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
45 7 0.05
47 32 0.22
48 33 0.22
49 5 0.03
50 64 0.43
52 7 0.05
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (47 bp):
CCAGTGTAAGACCATGTCTGGGACATGGCATCGACCTGAGATGAGTC
Found at i:4982943 original size:53 final size:52
Alignment explanation
Indices: 4982827--4982943 Score: 128
Period size: 53 Copynumber: 2.2 Consensus size: 52
4982817 TTGGCAGGAC
* * * * * * *
4982827 AGGAAACATCCCATGTAAGACCATTCCAAGGCATGGCATTGGTGAGTTCATA
1 AGGAAAGATACCACGTAAGACCATTCCAAGACATGGCAATGGTAAGTTCAAA
*
4982879 AGGCAAGGATACCACGTAAGACCATGT-CAAGACATGGCAATGGTAAGTTTCAAA
1 AGG-AAAGATACCACGTAAGACCAT-TCCAAGACATGGCAATGGTAAG-TTCAAA
4982933 AGGAAAGATAC
1 AGGAAAGATAC
4982944 TTGAGTAATC
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
52 3 0.06
53 41 0.77
54 9 0.17
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.20
Consensus pattern (52 bp):
AGGAAAGATACCACGTAAGACCATTCCAAGACATGGCAATGGTAAGTTCAAA
Found at i:4983365 original size:47 final size:47
Alignment explanation
Indices: 4983311--4983402 Score: 175
Period size: 47 Copynumber: 2.0 Consensus size: 47
4983301 GAAAGCTTAG
*
4983311 TAATAAGCTAAATTCATTACTAATGATTGTTATTTTACATGTGAACT
1 TAATAAGCTAAATTCATTACTAATGATTGTTATTATACATGTGAACT
4983358 TAATAAGCTAAATTCATTACTAATGATTGTTATTATACATGTGAA
1 TAATAAGCTAAATTCATTACTAATGATTGTTATTATACATGTGAA
4983403 ACAAGTAGAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (47 bp):
TAATAAGCTAAATTCATTACTAATGATTGTTATTATACATGTGAACT
Found at i:4985986 original size:17 final size:18
Alignment explanation
Indices: 4985964--4986001 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
4985954 ATTGAGTTCT
4985964 AATAGCTA-AAAATATTA
1 AATAGCTATAAAATATTA
*
4985981 AATAGCTATAAAATTTTA
1 AATAGCTATAAAATATTA
4985999 AAT
1 AAT
4986002 TGGAGGTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (18 bp):
AATAGCTATAAAATATTA
Found at i:4989459 original size:22 final size:20
Alignment explanation
Indices: 4989434--4989495 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
4989424 TTCTCAACAA
4989434 AAATTACAAAATAGTTCAAAAT
1 AAATTACAAAA-A-TTCAAAAT
*
4989456 AAATTTCAAAAATTCAAAAT
1 AAATTACAAAAATTCAAAAT
* *
4989476 -ATTTATAAAAATTCCAAAAT
1 AAATTACAAAAATT-CAAAAT
4989496 TTATATTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
19 10 0.29
20 14 0.40
21 1 0.03
22 10 0.29
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.31
Consensus pattern (20 bp):
AAATTACAAAAATTCAAAAT
Found at i:4989487 original size:19 final size:18
Alignment explanation
Indices: 4989463--4989500 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
4989453 AATAAATTTC
4989463 AAAAATTCAAAATATTTAT
1 AAAAATTCAAAA-ATTTAT
*
4989482 AAAAATTCCAAAATTTAT
1 AAAAATTCAAAAATTTAT
4989500 A
1 A
4989501 TTTTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAAATTCAAAAATTTAT
Found at i:4992848 original size:15 final size:15
Alignment explanation
Indices: 4992828--4992859 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
4992818 CCAAGATAAG
4992828 TTTGTTTAAATTGAA
1 TTTGTTTAAATTGAA
4992843 TTTGTTTAAATTGAA
1 TTTGTTTAAATTGAA
4992858 TT
1 TT
4992860 ATAAGTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (15 bp):
TTTGTTTAAATTGAA
Found at i:5002098 original size:43 final size:43
Alignment explanation
Indices: 5002045--5002228 Score: 201
Period size: 43 Copynumber: 4.3 Consensus size: 43
5002035 TTTTAGAAAT
5002045 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTACCAC
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTACCAC
* * *
5002088 AAACGCCGCTATAGATCAGGATCTTTAGCGGCGCTTTT-CTAAC
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTAC-CAC
* * **
5002131 AAACGCCGCTATAGCT-TTAGATATTTAGCGGCGCTTTTACCAC
1 AAACGCCGCTATAGATCAT-GACCTTTAGCGGCGCTTTTACCAC
* * ** * **
5002174 AAACGCCACTATAGATCAAAGACCTTTAGCAACGCTTTGATTAC
1 AAACGCCGCTATAGATC-ATGACCTTTAGCGGCGCTTTTACCAC
5002218 AAACGCCGCTA
1 AAACGCCGCTA
5002229 AAAACACCAT
Statistics
Matches: 116, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
42 1 0.01
43 87 0.75
44 28 0.24
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTACCAC
Found at i:5002190 original size:86 final size:87
Alignment explanation
Indices: 5002068--5002228 Score: 243
Period size: 86 Copynumber: 1.9 Consensus size: 87
5002058 GATCATGACC
* * * ** **
5002068 TTTAGCGGCGCTTTTACCACAAACGCCGCTATAGATC-AGGATCTTTAGCGGCGCTTTTCTAACA
1 TTTAGCGGCGCTTTTACCACAAACGCCACTATAGATCAAAGACCTTTAGCAACGCTTTGATAACA
5002132 AACGCCGCTATAGCTTTAGATA
66 AACGCCGCTATAGCTTTAGATA
*
5002154 TTTAGCGGCGCTTTTACCACAAACGCCACTATAGATCAAAGACCTTTAGCAACGCTTTGATTACA
1 TTTAGCGGCGCTTTTACCACAAACGCCACTATAGATCAAAGACCTTTAGCAACGCTTTGATAACA
5002219 AACGCCGCTA
66 AACGCCGCTA
5002229 AAAACACCAT
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
86 36 0.55
87 30 0.45
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (87 bp):
TTTAGCGGCGCTTTTACCACAAACGCCACTATAGATCAAAGACCTTTAGCAACGCTTTGATAACA
AACGCCGCTATAGCTTTAGATA
Found at i:5002321 original size:16 final size:16
Alignment explanation
Indices: 5002300--5002333 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5002290 AAATATTAAA
*
5002300 TATTAAAATCAAACAT
1 TATTAAAATCAAAAAT
*
5002316 TATTAATATCAAAAAT
1 TATTAAAATCAAAAAT
5002332 TA
1 TA
5002334 ATTAGTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (16 bp):
TATTAAAATCAAAAAT
Found at i:5004845 original size:15 final size:15
Alignment explanation
Indices: 5004810--5004847 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
5004800 GTCCCTTAAT
5004810 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
*
5004824 T-AATCCATAATCTC
1 TAAATCCATAATCCC
5004838 TAAATCCATA
1 TAAATCCATA
5004848 TATATAGTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 11 0.52
15 8 0.38
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:5005146 original size:17 final size:17
Alignment explanation
Indices: 5005120--5005163 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
5005110 CCAACCCTTA
*
5005120 ATTAAACCATAATCCCT
1 ATTAATCCATAATCCCT
5005137 ATTAATCCATAATCCCT
1 ATTAATCCATAATCCCT
5005154 A--AATCCATAA
1 ATTAATCCATAA
5005164 ATACTCCCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 9 0.35
17 17 0.65
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (17 bp):
ATTAATCCATAATCCCT
Found at i:5005213 original size:315 final size:308
Alignment explanation
Indices: 5004638--5005241 Score: 790
Period size: 315 Copynumber: 1.9 Consensus size: 308
5004628 AAACCCATAA
* * *
5004638 ATTATATATCTTTTACAATTACATAATAACATATTTAAAATATAAATAAAAAATCTAAACCCTAA
1 ATTATATATCTTTTACAACTACATAATAACATATTTAAAATATAAATAAAAAACCAAAACCCTAA
*
5004703 CCCGACCCCTAAAACCTTAAACCCTAAATCCCTAACTCTTAACCACTAACGTCTAACCCCTAAAC
66 CCCGACCCCTAAAACCTTAAACCCTAAATCCCTAACTCTTAACCACTAACATCTAACCCCTAAAC
* *
5004768 TCTTAACCCCTAAACCTTAAATCTCGACCAACGTCCCTTAATTAAACCATAATCCCTAATCCATA
131 CCCTAACCCCTAAACCTTAAA-CTC-ACCAAC--CCCTTAATTAAACCATAATCCCTAATCCATA
* * ** * *
5004833 ATCTCTAAATCCATATATATAGTACTCCCTAAACCTTTAAATATGAACCCCTAAACCGGCCTTAA
192 ATCCCTAAATCCATATATATACTACTAACTAAACCTTAAAATATGAACCCCTAAACCGACCTTAA
** *
5004898 ATATTAAAT-TTATCATATACTCTAAACTAATTAAAAATCCTAAACAATTTT
257 ATATTAAATAAAATCATATACCCTAAACTAATTAAAAATCCTAAACAATTTT
* *
5004949 ATTAT-TATCTTTTACAACTACATAATAACATATTTTAAATATAATAATAATCTAAACCCAAAAC
1 ATTATATATCTTTTACAACTACATAATAACATATTTAAAATAT-A-AATAA---AAAACCAAAAC
5005013 CCTAACCCGACCCCTAAAACCTTAAACCCTAAATCCCTAACTCTTAACCCCTAGCTAACATCTAA
61 CCTAACCCGACCCCTAAAACCTTAAACCCTAAATCCCTAACTCTTAA--CC-A-CTAACATCTAA
* *
5005078 CTCCTAAACCCCTAACCCCTAAGCCTTAAA-TC-CCAA-CCCTTAATTAAACCATAATCCCTATT
122 CCCCTAAACCCCTAACCCCTAAACCTTAAACTCACCAACCCCTTAATTAAACCATAATCCC---T
* * *
5005140 AATCCATAATCCCTAAATCCATA-A-ATACTCCCTAACTAAAACCTTAAAATATGAACTCTTAAA
184 AATCCATAATCCCTAAATCCATATATATACT-ACTAACT-AAACCTTAAAATATGAACCCCTAAA
*
5005203 CCGACCTTAAATCTTAAATAAAATCATATACCCTAAACT
247 CCGACCTTAAATATTAAATAAAATCATATACCCTAAACT
5005242 GAGAACCCTA
Statistics
Matches: 255, Mismatches: 23, Indels: 25
0.84 0.08 0.08
Matches are distributed among these distances:
310 35 0.14
311 6 0.02
312 27 0.11
313 4 0.02
314 5 0.02
315 121 0.47
316 16 0.06
317 4 0.02
318 1 0.00
319 36 0.14
ACGTcount: A:0.41, C:0.28, G:0.02, T:0.29
Consensus pattern (308 bp):
ATTATATATCTTTTACAACTACATAATAACATATTTAAAATATAAATAAAAAACCAAAACCCTAA
CCCGACCCCTAAAACCTTAAACCCTAAATCCCTAACTCTTAACCACTAACATCTAACCCCTAAAC
CCCTAACCCCTAAACCTTAAACTCACCAACCCCTTAATTAAACCATAATCCCTAATCCATAATCC
CTAAATCCATATATATACTACTAACTAAACCTTAAAATATGAACCCCTAAACCGACCTTAAATAT
TAAATAAAATCATATACCCTAAACTAATTAAAAATCCTAAACAATTTT
Found at i:5008869 original size:12 final size:12
Alignment explanation
Indices: 5008852--5008877 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5008842 TTTTTTATTC
5008852 AAACGCCGCTAA
1 AAACGCCGCTAA
5008864 AAACGCCGCTAA
1 AAACGCCGCTAA
5008876 AA
1 AA
5008878 GCTCGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:5011621 original size:49 final size:50
Alignment explanation
Indices: 5011563--5011690 Score: 159
Period size: 50 Copynumber: 2.6 Consensus size: 50
5011553 TATGTGATTT
* *
5011563 CACATGCCCGTGTG-TCCCACACGACCTACCTGATTTGCCCATGTAATAG
1 CACATGCCCGTGTGCCCCCACACGGCCTACCTGATTTGCCCATGTAATAG
* * * * * * *
5011612 CACACGCCCGTCTGCCCCCATATGGCCTAACTGATTTGCCCGTGTAATCG
1 CACATGCCCGTGTGCCCCCACACGGCCTACCTGATTTGCCCATGTAATAG
*
5011662 CACATGCTCGTGTGCCCCCACACGGCCTA
1 CACATGCCCGTGTGCCCCCACACGGCCTA
5011691 ACACACGGCC
Statistics
Matches: 64, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
49 12 0.19
50 52 0.81
ACGTcount: A:0.20, C:0.38, G:0.20, T:0.23
Consensus pattern (50 bp):
CACATGCCCGTGTGCCCCCACACGGCCTACCTGATTTGCCCATGTAATAG
Found at i:5014032 original size:15 final size:15
Alignment explanation
Indices: 5013995--5014023 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5013985 TATTTTTACT
5013995 AAAGT-ACTAAAGTA
1 AAAGTAACTAAAGTA
5014009 AAAGTAACTAAAGTA
1 AAAGTAACTAAAGTA
5014024 CAATTAACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.59, C:0.07, G:0.14, T:0.21
Consensus pattern (15 bp):
AAAGTAACTAAAGTA
Found at i:5020021 original size:2 final size:2
Alignment explanation
Indices: 5020014--5020071 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
5020004 AGTGAAAGTG
5020014 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
5020056 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
5020072 GGATTTTTAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5021848 original size:84 final size:84
Alignment explanation
Indices: 5021726--5021927 Score: 359
Period size: 84 Copynumber: 2.4 Consensus size: 84
5021716 TGTCTTCTGA
* * * *
5021726 TCAACTTGCTAAAGAGGTGGAGGATAAATATTCCAGAATTGCTGCCTGGAAACCTTTTGTTGGCA
1 TCAACTTGCTAAGGAGCTGGAGGATAAATATTCTAGAATTGCTGCCTGGAAACCTTTTGTTGACA
5021791 AAACTCCCCAATCATCTTC
66 AAACTCCCCAATCATCTTC
5021810 TCAACTTGCTAAGGAGCTGGAGGATAAATATTCTAGAATTGCTGCCTGGAAACCTTTTGTTGACA
1 TCAACTTGCTAAGGAGCTGGAGGATAAATATTCTAGAATTGCTGCCTGGAAACCTTTTGTTGACA
5021875 AAACTCCCCAATCATCTTC
66 AAACTCCCCAATCATCTTC
*
5021894 TCAACTTGCTAAGGAGCTGGAGGATACATATTCT
1 TCAACTTGCTAAGGAGCTGGAGGATAAATATTCT
5021928 GCTCTATCTG
Statistics
Matches: 113, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 113 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (84 bp):
TCAACTTGCTAAGGAGCTGGAGGATAAATATTCTAGAATTGCTGCCTGGAAACCTTTTGTTGACA
AAACTCCCCAATCATCTTC
Found at i:5041345 original size:8 final size:8
Alignment explanation
Indices: 5041332--5041360 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
5041322 TAATAAATAA
5041332 ATTAAATT
1 ATTAAATT
5041340 ATTAAATT
1 ATTAAATT
5041348 ATTAAA-T
1 ATTAAATT
5041355 ATTAAA
1 ATTAAA
5041361 ATAATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
ATTAAATT
Found at i:5042558 original size:11 final size:10
Alignment explanation
Indices: 5042516--5042557 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
5042506 GCAATTAATT
5042516 AATT-TTAAA
1 AATTATTAAA
5042525 AATTATTTAAA
1 AATTA-TTAAA
* *
5042536 ATTTAATAAA
1 AATTATTAAA
5042546 AATTATTAAA
1 AATTATTAAA
5042556 AA
1 AA
5042558 AAATTTAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
9 4 0.15
10 14 0.52
11 9 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
AATTATTAAA
Found at i:5043379 original size:2 final size:2
Alignment explanation
Indices: 5043374--5043428 Score: 78
Period size: 2 Copynumber: 28.0 Consensus size: 2
5043364 TTTTTTAGTA
5043374 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
5043415 A- AC AT AT CAT AT AT
1 AT AT AT AT -AT AT AT
5043429 TCTATATTGT
Statistics
Matches: 49, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
1 2 0.04
2 45 0.92
3 2 0.04
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5047899 original size:17 final size:18
Alignment explanation
Indices: 5047874--5047911 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
5047864 TTTAGTTTTA
*
5047874 TTTATTTTTCA-AATAAT
1 TTTAATTTTCATAATAAT
*
5047891 TTTAATTTTCATAATACT
1 TTTAATTTTCATAATAAT
5047909 TTT
1 TTT
5047912 TAAGCTCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTAATTTTCATAATAAT
Found at i:5052605 original size:145 final size:145
Alignment explanation
Indices: 5052342--5052636 Score: 563
Period size: 145 Copynumber: 2.0 Consensus size: 145
5052332 TTTTTCAAAG
*
5052342 ATATTGTTGAAGAAGGTGATCTTGTTTGTCATTTGCAGCCATGGAAGCTTTATGTTGTTGCTTTC
1 ATATTGTTGAAGAAGGTGATCTTGTTTGTCATTTGCAGCCATGGAAGCTTTATGCTGTTGCTTTC
*
5052407 TCTTTGGATGACTGCTGCAACTACAACCCCTCTGTGATATGATTCTGGGCTGAGATCCTGCATCA
66 TCTTTGGATGACTGCCGCAACTACAACCCCTCTGTGATATGATTCTGGGCTGAGATCCTGCATCA
5052472 GCAATAACTTATATT
131 GCAATAACTTATATT
5052487 ATATTGTTGAAGAAGGTGATCTTGTTTGTCATTTGCAGCCATGGAAGCTTTATGCTGTTGCTTTC
1 ATATTGTTGAAGAAGGTGATCTTGTTTGTCATTTGCAGCCATGGAAGCTTTATGCTGTTGCTTTC
*
5052552 TCTTTGGATGACTGCCGCAACTACAACCCCTCTGTGATATGATTCTTGGCTGAGATCCTGCATCA
66 TCTTTGGATGACTGCCGCAACTACAACCCCTCTGTGATATGATTCTGGGCTGAGATCCTGCATCA
5052617 GCAATAACTTATATT
131 GCAATAACTTATATT
5052632 ATATT
1 ATATT
5052637 ATATATTATG
Statistics
Matches: 147, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
145 147 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (145 bp):
ATATTGTTGAAGAAGGTGATCTTGTTTGTCATTTGCAGCCATGGAAGCTTTATGCTGTTGCTTTC
TCTTTGGATGACTGCCGCAACTACAACCCCTCTGTGATATGATTCTGGGCTGAGATCCTGCATCA
GCAATAACTTATATT
Found at i:5057748 original size:5 final size:5
Alignment explanation
Indices: 5057738--5057764 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
5057728 AATTAAACTA
5057738 TTTAT TTTAT TTTAT TTTAT TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TT
5057765 GAATCCAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:5060582 original size:24 final size:22
Alignment explanation
Indices: 5060554--5060607 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 22
5060544 ATTCTTTTCC
**
5060554 ATTAAAACCTTTTAAATAATGATA
1 ATTAAAA--TTTTAAATAAAAATA
5060578 ATTAATTAATTTTAAATAAAAATA
1 ATTAA--AATTTTAAATAAAAATA
5060602 ATTAAA
1 ATTAAA
5060608 TGAATTTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
22 1 0.04
24 23 0.88
26 2 0.08
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (22 bp):
ATTAAAATTTTAAATAAAAATA
Found at i:5060615 original size:24 final size:24
Alignment explanation
Indices: 5060563--5060614 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
5060553 CATTAAAACC
** *
5060563 TTTTAAATAATGATAATTAATTAA
1 TTTTAAATAAAAATAATTAATGAA
5060587 TTTTAAATAAAAATAATTAAATGAA
1 TTTTAAATAAAAATAATT-AATGAA
5060612 TTT
1 TTT
5060615 ATCTCAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (24 bp):
TTTTAAATAAAAATAATTAATGAA
Found at i:5062020 original size:18 final size:18
Alignment explanation
Indices: 5061997--5062039 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
5061987 GAACAGGTTT
5061997 TTAATTAAATAATTTT-AA
1 TTAATTAAA-AATTTTAAA
5062015 TTAATTAAAAATTTTAAA
1 TTAATTAAAAATTTTAAA
5062033 TTAATTA
1 TTAATTA
5062040 CACCTTAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTAATTAAAAATTTTAAA
Found at i:5077585 original size:15 final size:15
Alignment explanation
Indices: 5077565--5077594 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5077555 CACCCTAATC
5077565 ACAGATATAGAAATA
1 ACAGATATAGAAATA
*
5077580 ACAGATATAGTAATA
1 ACAGATATAGAAATA
5077595 TCGTGCATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.13, T:0.23
Consensus pattern (15 bp):
ACAGATATAGAAATA
Found at i:5082180 original size:38 final size:38
Alignment explanation
Indices: 5082138--5082217 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
5082128 AGTATGGGAT
* *
5082138 TATGTGCTTGTGTGCCAGTATGCACTTCGTGTACCAGG
1 TATGTGCTTATGCGCCAGTATGCACTTCGTGTACCAGG
* * *
5082176 TATGTGCTTATGCGCCAGTATGTACTTTGTGTGCCAGG
1 TATGTGCTTATGCGCCAGTATGCACTTCGTGTACCAGG
5082214 TATG
1 TATG
5082218 CGTTTTATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.16, C:0.19, G:0.29, T:0.36
Consensus pattern (38 bp):
TATGTGCTTATGCGCCAGTATGCACTTCGTGTACCAGG
Found at i:5082193 original size:19 final size:20
Alignment explanation
Indices: 5082171--5082217 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
5082161 ACTTCGTGTA
*
5082171 CCAGGTATGTGC-TTATGCG
1 CCAGGTATGTACTTTATGCG
* *
5082190 CCA-GTATGTACTTTGTGTG
1 CCAGGTATGTACTTTATGCG
5082209 CCAGGTATG
1 CCAGGTATG
5082218 CGTTTTATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 7 0.30
19 11 0.48
20 5 0.22
ACGTcount: A:0.17, C:0.19, G:0.30, T:0.34
Consensus pattern (20 bp):
CCAGGTATGTACTTTATGCG
Found at i:5084446 original size:29 final size:30
Alignment explanation
Indices: 5084393--5084452 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
5084383 TCCGAGCCTT
*
5084393 GGGGCAAAAATGTAATTATGTAAAAATTTA
1 GGGGCAAAAATGTAATTATGTAAAAAGTTA
*
5084423 GGGGCAAAATTGTAATT-T-TAAAAAAGTTA
1 GGGGCAAAAATGTAATTATGT-AAAAAGTTA
5084452 G
1 G
5084453 AGTCGAGGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 1 0.04
29 10 0.37
30 16 0.59
ACGTcount: A:0.45, C:0.03, G:0.22, T:0.30
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGTAAAAAGTTA
Found at i:5084680 original size:13 final size:13
Alignment explanation
Indices: 5084662--5084692 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5084652 TTCCAGCAAC
5084662 TATGAATTTATTT
1 TATGAATTTATTT
5084675 TATGAATTTATTT
1 TATGAATTTATTT
*
5084688 GATGA
1 TATGA
5084693 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:5084901 original size:50 final size:54
Alignment explanation
Indices: 5084785--5084934 Score: 209
Period size: 50 Copynumber: 2.8 Consensus size: 54
5084775 ACATTTGGGT
*
5084785 AAAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATC
1 AAAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC-TAAGATC
* * *
5084840 ATAAGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCA-CC-GAGA-C
1 A-AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTAAGATC
*
5084892 -GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
1 AAAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
5084935 NNNNNNNNNN
Statistics
Matches: 87, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
50 40 0.46
52 1 0.01
53 3 0.03
55 3 0.03
56 40 0.46
ACGTcount: A:0.28, C:0.23, G:0.29, T:0.21
Consensus pattern (54 bp):
AAAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTAAGATC
Found at i:5091131 original size:13 final size:13
Alignment explanation
Indices: 5091113--5091143 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5091103 TTCCAGCAAC
5091113 TATGAATTTATTT
1 TATGAATTTATTT
5091126 TATGAATTTATTT
1 TATGAATTTATTT
*
5091139 GATGA
1 TATGA
5091144 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:5091352 original size:50 final size:50
Alignment explanation
Indices: 5091238--5091479 Score: 286
Period size: 50 Copynumber: 4.7 Consensus size: 50
5091228 ATTTGGGTAA
* * *
5091238 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--AAGA-C--G
* *
5091294 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* * * *
5091344 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* * * *
5091394 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
**
5091444 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
5091480 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
50 92 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
Found at i:5091430 original size:100 final size:103
Alignment explanation
Indices: 5091238--5091487 Score: 353
Period size: 100 Copynumber: 2.4 Consensus size: 103
5091228 ATTTGGGTAA
5091238 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATAAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATAAGAGGTCCC
* * *
5091303 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* * * *
5091344 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATAAGAGGTCCCCTA
*
5091406 TAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* *
5091444 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
5091488 GTTATTATCA
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
100 50 0.38
101 39 0.30
105 2 0.02
106 40 0.31
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATAAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
Found at i:5096911 original size:27 final size:27
Alignment explanation
Indices: 5096879--5097051 Score: 195
Period size: 27 Copynumber: 6.4 Consensus size: 27
5096869 CCTAAAATAG
*
5096879 GGTAAAATAACCGAAATACCCCCATAA
1 GGTAAAATGACCGAAATACCCCCATAA
* * *
5096906 GATAAAATGATCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAA
* * *
5096933 GGTAAAATAACCAAAATACCCTCAT-A
1 GGTAAAATGACCGAAATACCCCCATAA
**
5096959 GAGTAAAATGACCGAAATAAACCCATAA
1 G-GTAAAATGACCGAAATACCCCCATAA
* * *
5096987 GGTAAAATGATCGGAATACCCCCATAT
1 GGTAAAATGACCGAAATACCCCCATAA
* * *
5097014 GGTAAAATGACTGAAATACCCTCATAG
1 GGTAAAATGACCGAAATACCCCCATAA
5097041 GGTAAAATGAC
1 GGTAAAATGAC
5097052 TGTTATACCC
Statistics
Matches: 119, Mismatches: 25, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
26 1 0.01
27 116 0.97
28 2 0.02
ACGTcount: A:0.46, C:0.21, G:0.15, T:0.18
Consensus pattern (27 bp):
GGTAAAATGACCGAAATACCCCCATAA
Found at i:5097018 original size:81 final size:81
Alignment explanation
Indices: 5096875--5097051 Score: 264
Period size: 81 Copynumber: 2.2 Consensus size: 81
5096865 AGACCCTAAA
* **
5096875 ATAGGGTAAAATAACCGAAATACCCCCATAAGATAAAATGATCGAAATACCCCCATAGGGTAAAA
1 ATAGGGTAAAATGACCGAAATAAACCCATAAGATAAAATGATCGAAATACCCCCATAGGGTAAAA
5096940 TAACCAAAATACCCTC
66 TAACCAAAATACCCTC
* * * *
5096956 ATAGAGTAAAATGACCGAAATAAACCCATAAGGTAAAATGATCGGAATACCCCCATATGGTAAAA
1 ATAGGGTAAAATGACCGAAATAAACCCATAAGATAAAATGATCGAAATACCCCCATAGGGTAAAA
* **
5097021 TGACTGAAATACCCTC
66 TAACCAAAATACCCTC
5097037 ATAGGGTAAAATGAC
1 ATAGGGTAAAATGAC
5097052 TGTTATACCC
Statistics
Matches: 85, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 85 1.00
ACGTcount: A:0.46, C:0.20, G:0.15, T:0.19
Consensus pattern (81 bp):
ATAGGGTAAAATGACCGAAATAAACCCATAAGATAAAATGATCGAAATACCCCCATAGGGTAAAA
TAACCAAAATACCCTC
Found at i:5105091 original size:26 final size:26
Alignment explanation
Indices: 5105044--5105101 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
5105034 CTGAACAAAT
*
5105044 TTTTGGCGATTTTACCCCTAGTAAAA
1 TTTTGACGATTTTACCCCTAGTAAAA
*
5105070 TTTTGACGAATTTT-CCCTTAGTAAAA
1 TTTTGACG-ATTTTACCCCTAGTAAAA
5105096 TTTTGA
1 TTTTGA
5105102 GAAAATATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 24 0.83
27 5 0.17
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.43
Consensus pattern (26 bp):
TTTTGACGATTTTACCCCTAGTAAAA
Found at i:5108210 original size:27 final size:27
Alignment explanation
Indices: 5108155--5108211 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
5108145 ACAACTTTAC
* *
5108155 CAATTAATTAAATTCATTTTCAAACTT
1 CAATTAATTAAATTAATTTTCAAAATT
5108182 CAATTAATT-AATTAATTATT-AATAATT
1 CAATTAATTAAATTAATT-TTCAA-AATT
5108209 CAA
1 CAA
5108212 AAAATTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.44
Consensus pattern (27 bp):
CAATTAATTAAATTAATTTTCAAAATT
Found at i:5116119 original size:22 final size:21
Alignment explanation
Indices: 5116089--5116193 Score: 71
Period size: 19 Copynumber: 5.2 Consensus size: 21
5116079 TTTTTATTTT
5116089 AAAA-ATTTTAAAAAATTAAA
1 AAAATATTTTAAAAAATTAAA
***
5116109 AAAAGTATTTTAAAAATATTTTT
1 AAAA-TATTTTAAAAA-ATTAAA
5116132 AAAATATTTT--AAAATTAAA
1 AAAATATTTTAAAAAATTAAA
*** *
5116151 AAAAT-TAAAAAAAAATT-TA
1 AAAATATTTTAAAAAATTAAA
*
5116170 AAAGTATTTT--AAAATTAAA
1 AAAATATTTTAAAAAATTAAA
5116189 AAAAT
1 AAAAT
5116194 TTAAAAAAAG
Statistics
Matches: 62, Mismatches: 16, Indels: 15
0.67 0.17 0.16
Matches are distributed among these distances:
18 7 0.11
19 18 0.29
20 14 0.23
22 16 0.26
23 7 0.11
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
AAAATATTTTAAAAAATTAAA
Found at i:5116166 original size:30 final size:32
Alignment explanation
Indices: 5116131--5116249 Score: 80
Period size: 38 Copynumber: 3.5 Consensus size: 32
5116121 AAAATATTTT
5116131 TAAAATATTTTAAAATTAAAAAAATTAAAAAAAAA
1 TAAAATATTTTAAAATTAAAAAAATT---AAAAAA
*
5116166 TTTAAAAGTATTTTAAAATTAAAAAAATT-TAAAA
1 --TAAAA-TATTTTAAAATTAAAAAAATTAAAAAA
* * ***
5116200 -AAAGTATTTTAAAAATATTTTAAATTAAAAAA
1 TAAAATATTTTAAAATTA-AAAAAATTAAAAAA
5116232 TTAAAAAGTATTTTAAAA
1 -T-AAAA-TATTTTAAAA
5116250 AATATTTTAA
Statistics
Matches: 67, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
30 12 0.18
31 8 0.12
32 4 0.06
34 4 0.06
35 3 0.04
36 10 0.15
37 5 0.07
38 21 0.31
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (32 bp):
TAAAATATTTTAAAATTAAAAAAATTAAAAAA
Found at i:5116191 original size:39 final size:38
Alignment explanation
Indices: 5116132--5116310 Score: 218
Period size: 39 Copynumber: 4.6 Consensus size: 38
5116122 AAATATTTTT
5116132 AAAATATTTTAAAATTAAAAAAATTAAAAAAAAATTTA
1 AAAATATTTTAAAATTAAAAAAATTAAAAAAAAATTTA
* *
5116170 AAAGTATTTTAAAATTAAAAAAATTTAAAAAAAGTATTTTA
1 AAAATATTTTAAAATTAAAAAAA-TTAAAAAAA--AATTTA
** *
5116211 AAAATATTTT-AAATT-AAAAAATTAAAAAGTATTTTAA
1 AAAATATTTTAAAATTAAAAAAATTAAAAAAAAATTT-A
* ** *
5116248 AAAATATTTTAAATTTAAAAAAATTAAAAAAGTATGTAA
1 AAAATATTTTAAAATTAAAAAAATTAAAAAAAAAT-TTA
5116287 AAAATATTTTAAAATTAAAAAAAT
1 AAAATATTTTAAAATTAAAAAAAT
5116311 ATATATATTT
Statistics
Matches: 122, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
36 5 0.04
37 11 0.09
38 33 0.27
39 53 0.43
40 6 0.05
41 14 0.11
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.35
Consensus pattern (38 bp):
AAAATATTTTAAAATTAAAAAAATTAAAAAAAAATTTA
Found at i:5116227 original size:78 final size:79
Alignment explanation
Indices: 5116100--5116310 Score: 270
Period size: 78 Copynumber: 2.7 Consensus size: 79
5116090 AAAATTTTAA
* *
5116100 AAAATTAAAAAAAGTATTTTAAAAA-TATTTTTAAAATATTTTAAAATTAAAAAAATTAAAAAAA
1 AAAATT-AAAAAA--ATTTAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAA
*
5116164 AATTT-AAAAGTATTTT
63 AATTTAAAAAATATTTT
** *
5116180 AAAATTAAAAAAATTTAAAAAAAGTATTTTAAAAATATTTT-AAATT-AAAAAATTAAAAAGTAT
1 AAAATTAAAAAAATTT-AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAAAA
5116243 TTTAAAAAATATTTT
65 TTTAAAAAATATTTT
* * *
5116258 AAATTTAAAAAAA-TTAAAAAAGTATGTAAAAAATATTTTAAAATTAAAAAAAT
1 AAAATTAAAAAAATTTAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAT
5116311 ATATATATTT
Statistics
Matches: 117, Mismatches: 9, Indels: 12
0.85 0.07 0.09
Matches are distributed among these distances:
76 22 0.19
77 28 0.24
78 39 0.33
79 22 0.19
80 6 0.05
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (79 bp):
AAAATTAAAAAAATTTAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAAAAT
TTAAAAAATATTTT
Found at i:5116250 original size:13 final size:12
Alignment explanation
Indices: 5116184--5116300 Score: 71
Period size: 12 Copynumber: 9.5 Consensus size: 12
5116174 TATTTTAAAA
5116184 TTAAAAAA-ATT
1 TTAAAAAATATT
*
5116195 TAAAAAAAGTATT
1 TTAAAAAA-TATT
5116208 TT-AAAAATATT
1 TTAAAAAATATT
**
5116219 TTAAATTAAA-AAA
1 TTAAA--AAATATT
*
5116232 TTAAAAAGTATT
1 TTAAAAAATATT
5116244 TTAAAAAATATT
1 TTAAAAAATATT
* **
5116256 TTAAATTTAAAAAAA
1 TTAAA---AAATATT
5116271 TTAAAAAAGTA-T
1 TTAAAAAA-TATT
*
5116283 GTAAAAAATATT
1 TTAAAAAATATT
5116295 TTAAAA
1 TTAAAA
5116301 TTAAAAAAAT
Statistics
Matches: 80, Mismatches: 15, Indels: 21
0.69 0.13 0.18
Matches are distributed among these distances:
11 17 0.21
12 40 0.50
13 11 0.14
14 3 0.04
15 9 0.11
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (12 bp):
TTAAAAAATATT
Found at i:5116262 original size:77 final size:77
Alignment explanation
Indices: 5116086--5116308 Score: 265
Period size: 77 Copynumber: 2.9 Consensus size: 77
5116076 CCATTTTTAT
* * *
5116086 TTTAAAAAT-TTTAAAAAATTAAAAAAAGTATTTTAAAAA-TATTTTTAAAATATTTTAAAATTA
1 TTTAAAAATATTT-TAAAATT-AAAAAA--ATTTAAAAAAGTATTTTAAAAATATTTTAAAATT-
5116149 AAAAAATTAAAAAAAAA
61 AAAAAATTAAAAAAAAA
*
5116166 TTTAAAAGTATTTTAAAATTAAAAAAATTTAAAAAAAGTATTTTAAAAATATTTT-AAATTAAAA
1 TTTAAAAATATTTTAAAATTAAAAAAATTT-AAAAAAGTATTTTAAAAATATTTTAAAATTAAAA
** *
5116230 AATTAAAAAGTAT
65 AATTAAAAAAAAA
* * *
5116243 TTTAAAAAATATTTTAAATTTAAAAAAA-TTAAAAAAGTATGTAAAAAATATTTTAAAATTAAAA
1 TTT-AAAAATATTTTAAAATTAAAAAAATTTAAAAAAGTATTTTAAAAATATTTTAAAATTAAAA
5116307 AA
65 AA
5116309 ATATATATAT
Statistics
Matches: 127, Mismatches: 11, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
76 22 0.17
77 34 0.27
78 32 0.25
79 22 0.17
80 14 0.11
81 3 0.02
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (77 bp):
TTTAAAAATATTTTAAAATTAAAAAAATTTAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAA
ATTAAAAAAAAA
Found at i:5116263 original size:19 final size:19
Alignment explanation
Indices: 5116241--5116312 Score: 58
Period size: 18 Copynumber: 3.7 Consensus size: 19
5116231 ATTAAAAAGT
5116241 ATTTTAAAAAATATTTTAA
1 ATTTTAAAAAATATTTTAA
**
5116260 A-TTTAAAAAA-ATTAAAAA
1 ATTTTAAAAAATATT-TTAA
*
5116278 AGTATGTAAAAAATATTTTAA
1 A-T-TTTAAAAAATATTTTAA
* *
5116299 AATTAAAAAAATAT
1 ATTTTAAAAAATAT
5116313 ATATATTTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
17 3 0.08
18 12 0.30
19 11 0.28
21 11 0.28
22 3 0.08
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (19 bp):
ATTTTAAAAAATATTTTAA
Found at i:5116801 original size:23 final size:23
Alignment explanation
Indices: 5116750--5116802 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
5116740 AGTGTTATTG
5116750 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
5116773 -TACAGTGGTAG-TTACGGCTACAT
1 AT-CAGTGGTAGCTT-CGGCTACAT
5116796 ATCAGTG
1 ATCAGTG
5116803 TGGCACTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 3 0.11
23 23 0.85
24 1 0.04
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:5119639 original size:17 final size:15
Alignment explanation
Indices: 5119605--5119634 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5119595 ATTTTTGTAT
*
5119605 TATTTTAATATTAAA
1 TATTTTAAAATTAAA
5119620 TATTTTAAAATTAAA
1 TATTTTAAAATTAAA
5119635 AATATATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTTTAAAATTAAA
Found at i:5123575 original size:27 final size:27
Alignment explanation
Indices: 5123545--5123598 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
5123535 TAGGAAAATG
5123545 ATGGAACCATTGAGTTGGAATTTATGA
1 ATGGAACCATTGAGTTGGAATTTATGA
5123572 ATGGAACCATTGAGTTGGAATTTATGA
1 ATGGAACCATTGAGTTGGAATTTATGA
5123599 GATAATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.33
Consensus pattern (27 bp):
ATGGAACCATTGAGTTGGAATTTATGA
Found at i:5127700 original size:105 final size:105
Alignment explanation
Indices: 5127458--5127723 Score: 336
Period size: 115 Copynumber: 2.4 Consensus size: 105
5127448 AACTAATAAT
* * *
5127458 TAATTTATAATAGTTACTAACAAAATAACTTTCAAATAAATTAAAAATATTAAAAGATTACATTC
1 TAATTTATAATAGTTACTAACAAAATAACTTTAAAATAAATTAAAAATAATAAAAAATTACATTC
* *
5127523 ATAATCTAACAAATCACAATAAACCTTAAACCCTAAACAAA
66 ATAACCTAACAAATCACAATAAACATTAAA-CCTAAACAAA
* * * *
5127564 CAATTAACCTAACCACAAAACTTACTAACAAAATAACTTTAAAATAAATTAAAAATTAATAAAAA
1 TAATT----T----ATAATAGTTACTAACAAAATAACTTTAAAATAAATTAAAAA-TAATAAAAA
5127629 ATTACATTCATAACCTAACAAATCACAATAAACATTAAA-CTAAACAAA
57 ATTACATTCATAACCTAACAAATCACAATAAACATTAAACCTAAACAAA
* *
5127677 TAATTTATAATAGTAACTGACAAAATAACTTTAAAATAAATTAAAAA
1 TAATTTATAATAGTTACTAACAAAATAACTTTAAAATAAATTAAAAA
5127724 CAACATAAAA
Statistics
Matches: 136, Mismatches: 15, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
105 36 0.26
106 4 0.03
109 1 0.01
110 1 0.01
113 13 0.10
114 37 0.27
115 44 0.32
ACGTcount: A:0.56, C:0.15, G:0.02, T:0.27
Consensus pattern (105 bp):
TAATTTATAATAGTTACTAACAAAATAACTTTAAAATAAATTAAAAATAATAAAAAATTACATTC
ATAACCTAACAAATCACAATAAACATTAAACCTAAACAAA
Found at i:5127873 original size:22 final size:22
Alignment explanation
Indices: 5127833--5127885 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
5127823 ATCCTTGTTT
* *
5127833 TTTCTTCTCCTTTCTTTCTTTC
1 TTTCTTCTCCTCTCTTTCTTCC
5127855 TTTCTTCTCC-CTCTCTTCTTCC
1 TTTCTTCTCCTCTCT-TTCTTCC
5127877 TTCTCTTCT
1 TT-TCTTCT
5127886 GCTATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 3 0.11
22 18 0.67
23 6 0.22
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTCTTCTCCTCTCTTTCTTCC
Found at i:5127883 original size:12 final size:11
Alignment explanation
Indices: 5127833--5127885 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
5127823 ATCCTTGTTT
5127833 TTTCTTC-TCC
1 TTTCTTCTTCC
*
5127843 TTTCTTTCTTTC
1 TTTC-TTCTTCC
*
5127855 TTTCTTCTCCC
1 TTTCTTCTTCC
*
5127866 TCTCTTCTTCC
1 TTTCTTCTTCC
5127877 TTCTCTTCT
1 TT-TCTTCT
5127886 GCTATTTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 4 0.12
11 18 0.53
12 12 0.35
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTCTTCTTCC
Found at i:5133023 original size:31 final size:29
Alignment explanation
Indices: 5132985--5133061 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
5132975 ATTAATGCTC
*
5132985 AGTGACTAAAATGTTACAACACAATAACATA
1 AGTGACTAAAATGTAACAACAC-A-AACATA
* ***
5133016 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACAACACAAACATA
5133045 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
5133062 CTGAGACAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 22 0.55
30 1 0.03
31 17 0.43
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.23
Consensus pattern (29 bp):
AGTGACTAAAATGTAACAACACAAACATA
Found at i:5134009 original size:27 final size:30
Alignment explanation
Indices: 5133978--5134042 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 30
5133968 TATTTTCCCC
*
5133978 ATAAAAATATTTTTAAAAA-A-GAAAATT-
1 ATAAAAATATATTTAAAAATATGAAAATTG
*
5134005 ATAAAAAAATATTTAAAAATATGAAAATTG
1 ATAAAAATATATTTAAAAATATGAAAATTG
*
5134035 ATACAAAT
1 ATAAAAAT
5134043 TTATAAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 17 0.55
28 1 0.03
29 7 0.23
30 6 0.19
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.31
Consensus pattern (30 bp):
ATAAAAATATATTTAAAAATATGAAAATTG
Found at i:5134074 original size:9 final size:9
Alignment explanation
Indices: 5134039--5134075 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
5134029 AAATTGATAC
5134039 AAAT-TTAT
1 AAATATTAT
5134047 AAATATTATT
1 AAATATTA-T
5134057 AAA-ATTAT
1 AAATATTAT
5134065 AAATATTAT
1 AAATATTAT
5134074 AA
1 AA
5134076 TAAATCTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.31
9 14 0.54
10 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
AAATATTAT
Found at i:5134106 original size:9 final size:9
Alignment explanation
Indices: 5133999--5134213 Score: 96
Period size: 10 Copynumber: 22.4 Consensus size: 9
5133989 TTTAAAAAAG
5133999 AAAATTATAAA
1 AAAATTAT--A
*
5134010 AAAATATTTA
1 AAAAT-TATA
*
5134020 AAAA-TATG
1 AAAATTATA
5134028 AAAATTGATA
1 AAAATT-ATA
*
5134038 CAAATTTATA
1 -AAAATTATA
* *
5134048 AATATTATT
1 AAAATTATA
5134057 AAAATTATA
1 AAAATTATA
*
5134066 AATATTATA
1 AAAATTATA
5134075 ATAAATCTA-A
1 A-AAAT-TATA
* *
5134085 CAAATTCTAA
1 AAAATTAT-A
5134095 AAAATTAT-
1 AAAATTATA
5134103 AAAATTAATA
1 AAAATT-ATA
*
5134113 AAAATATTTA
1 AAAAT-TATA
*
5134123 AAATTTTATA
1 AAA-ATTATA
*
5134133 AAAACATATTA
1 AAAA-TTA-TA
*
5134144 AAATTCTATA
1 AAAAT-TATA
*
5134154 AAAATCATA
1 AAAATTATA
5134163 AAAATTTATA
1 AAAA-TTATA
* *
5134173 AAAAGTATT
1 AAAATTATA
5134182 AAAATTGATA
1 AAAATT-ATA
*
5134192 TAAAA-AATA
1 -AAAATTATA
*
5134201 AAAATCATA
1 AAAATTATA
5134210 AAAA
1 AAAA
5134214 CTTGAACTGG
Statistics
Matches: 153, Mismatches: 32, Indels: 40
0.68 0.14 0.18
Matches are distributed among these distances:
8 17 0.11
9 54 0.35
10 55 0.36
11 25 0.16
12 2 0.01
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (9 bp):
AAAATTATA
Found at i:5134114 original size:19 final size:18
Alignment explanation
Indices: 5134019--5134213 Score: 89
Period size: 19 Copynumber: 10.2 Consensus size: 18
5134009 AAAAATATTT
5134019 AAAAA-TATGAAAATTGATA
1 AAAAATTAT-AAAATT-ATA
* *
5134038 CAAATTTATAAATATTAT-
1 AAAAATTATAAA-ATTATA
*
5134056 TAAAATTATAAATATTATA
1 AAAAATTATAAA-ATTATA
* *
5134075 ATAAATCTA-ACAAATTCTA
1 AAAAAT-TATA-AAATTATA
5134094 AAAAATTATAAAATTAATA
1 AAAAATTATAAAATT-ATA
5134113 AAAATATT-TAAAATTTTATA
1 AAAA-ATTATAAAA--TTATA
*
5134133 AAAACA-TATTAAAATTCTA
1 AAAA-ATTA-TAAAATTATA
*
5134152 TAAAAATCATAAAAATT-TA
1 -AAAAATTAT-AAAATTATA
*
5134171 TAAAAAGTATTAAAATTGATA
1 -AAAAATTA-TAAAATT-ATA
* *
5134192 TAAAAAATA-AAAATCATA
1 -AAAAATTATAAAATTATA
5134210 AAAA
1 AAAA
5134214 CTTGAACTGG
Statistics
Matches: 142, Mismatches: 16, Indels: 38
0.72 0.08 0.19
Matches are distributed among these distances:
17 4 0.03
18 26 0.18
19 62 0.44
20 33 0.23
21 17 0.12
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (18 bp):
AAAAATTATAAAATTATA
Found at i:5134144 original size:21 final size:21
Alignment explanation
Indices: 5134102--5134197 Score: 87
Period size: 21 Copynumber: 4.8 Consensus size: 21
5134092 TAAAAAATTA
* *
5134102 TAAAA-TTAATAAAAATAT-T
1 TAAAATTTTATAAAAACATAT
5134121 TAAAATTTTATAAAAACATAT
1 TAAAATTTTATAAAAACATAT
*
5134142 TAAAATTCTATAAAAATCATA-
1 TAAAATTTTATAAAAA-CATAT
*
5134163 -AAAA-TTTATAAAAA-GTAT
1 TAAAATTTTATAAAAACATAT
*
5134181 TAAAATTGATATAAAAA
1 TAAAATT-TTATAAAAA
5134198 ATAAAAATCA
Statistics
Matches: 64, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
17 2 0.03
19 18 0.28
20 16 0.25
21 24 0.38
22 4 0.06
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.34
Consensus pattern (21 bp):
TAAAATTTTATAAAAACATAT
Found at i:5134684 original size:20 final size:20
Alignment explanation
Indices: 5134634--5134690 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
5134624 TAAGAATTCT
5134634 AATATGTTTTTTTTAATTATA
1 AATAT-TTTTTTTTAATTATA
* *
5134655 AATATGTTTTTTTAATTTTA
1 AATATTTTTTTTTAATTATA
* *
5134675 TA-ATTTTTTTGTAATT
1 AATATTTTTTTTTAATT
5134691 TATTTCAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 12 0.39
20 14 0.45
21 5 0.16
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (20 bp):
AATATTTTTTTTTAATTATA
Found at i:5134771 original size:9 final size:9
Alignment explanation
Indices: 5134757--5134824 Score: 50
Period size: 10 Copynumber: 7.3 Consensus size: 9
5134747 TATAGCAATA
5134757 TTAATATTT
1 TTAATATTT
*
5134766 TTAATACTT
1 TTAATATTT
*
5134775 TTAGT-TTT
1 TTAATATTT
5134783 TATAATATTTT
1 T-TAATA-TTT
5134794 TTAA-ATTT
1 TTAATATTT
**
5134802 TTCTTGATTT
1 TTAAT-ATTT
5134812 TTAATCATTT
1 TTAAT-ATTT
5134822 TTA
1 TTA
5134825 TATAGGAAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 9
0.71 0.14 0.14
Matches are distributed among these distances:
8 8 0.18
9 16 0.36
10 17 0.38
11 4 0.09
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.65
Consensus pattern (9 bp):
TTAATATTT
Found at i:5135212 original size:24 final size:25
Alignment explanation
Indices: 5135184--5135232 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
5135174 TTATATTATT
*
5135184 ATTTTGAAAT-AAAAAATATATAAA
1 ATTTTAAAATCAAAAAATATATAAA
* *
5135208 ATTTTAAAATCATAAGATATATAAA
1 ATTTTAAAATCAAAAAATATATAAA
5135233 TTAATAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (25 bp):
ATTTTAAAATCAAAAAATATATAAA
Found at i:5135386 original size:17 final size:16
Alignment explanation
Indices: 5135360--5135397 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
5135350 TATATGTTTA
5135360 TATATTTTTATAAATT
1 TATATTTTTATAAATT
*
5135376 TATAGTTTTTATTAATT
1 TATA-TTTTTATAAATT
5135393 TATAT
1 TATAT
5135398 ATTATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (16 bp):
TATATTTTTATAAATT
Found at i:5144810 original size:5 final size:6
Alignment explanation
Indices: 5144792--5144817 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5144782 TGTTAAACTC
5144792 AACAAA AACAAA AACAAA AACAAA AA
1 AACAAA AACAAA AACAAA AACAAA AA
5144818 AACACCCTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
AACAAA
Found at i:5147562 original size:35 final size:34
Alignment explanation
Indices: 5147494--5147567 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 34
5147484 GGTGAGTTCA
* *
5147494 ATTTAGGACAATATGTAGTTTATATCGTGAACTT
1 ATTTAGGACAATATGTAGTTTATACCGTAAACTT
* * *
5147528 ATTTAGGATTAATATGTAGTTTATCCCTTAAACTT
1 ATTTAGGA-CAATATGTAGTTTATACCGTAAACTT
5147563 ATTTA
1 ATTTA
5147568 AAAGTACTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 8 0.24
35 26 0.76
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (34 bp):
ATTTAGGACAATATGTAGTTTATACCGTAAACTT
Found at i:5151720 original size:40 final size:41
Alignment explanation
Indices: 5151631--5151722 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 41
5151621 TCCTTTTCCG
* **
5151631 GGAAATCGCGTCCACGTCAGCGCGATATCAGGGTACGTGTCA
1 GGAAATCGCGTCCACGTCAGCGCGAGATCA-GGTACGTGGAA
* *
5151673 GGAAATCGCGTCCACGTCAGCGTGAGAT--GCTGACGTGGAA
1 GGAAATCGCGTCCACGTCAGCGCGAGATCAGGT-ACGTGGAA
5151713 GGAAATCGCG
1 GGAAATCGCG
5151723 CCCATTTCGA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
39 2 0.05
40 16 0.36
42 26 0.59
ACGTcount: A:0.25, C:0.24, G:0.34, T:0.17
Consensus pattern (41 bp):
GGAAATCGCGTCCACGTCAGCGCGAGATCAGGTACGTGGAA
Found at i:5155842 original size:17 final size:17
Alignment explanation
Indices: 5155822--5155882 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
5155812 ATTTCGAGAC
5155822 TTATGTAATGTTTTTAA
1 TTATGTAATGTTTTTAA
* ***
5155839 TTATGTAGTGATTCAAAGA
1 TTATGTAATG-TTTTTA-A
*
5155858 CTTATGTAATATTTTTAA
1 -TTATGTAATGTTTTTAA
5155876 TTATGTA
1 TTATGTA
5155883 GTGATTCAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 16 0.50
18 4 0.12
19 4 0.12
20 8 0.25
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.51
Consensus pattern (17 bp):
TTATGTAATGTTTTTAA
Found at i:5155859 original size:37 final size:37
Alignment explanation
Indices: 5155818--5155891 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
5155808 GTTAATTTCG
*
5155818 AGACTTATGTAATGTTTTTAATTATGTAGTGATTCAA
1 AGACTTATGTAATATTTTTAATTATGTAGTGATTCAA
5155855 AGACTTATGTAATATTTTTAATTATGTAGTGATTCAA
1 AGACTTATGTAATATTTTTAATTATGTAGTGATTCAA
5155892 TTCGAGTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.46
Consensus pattern (37 bp):
AGACTTATGTAATATTTTTAATTATGTAGTGATTCAA
Found at i:5155904 original size:9 final size:10
Alignment explanation
Indices: 5155890--5155947 Score: 56
Period size: 9 Copynumber: 6.4 Consensus size: 10
5155880 GTAGTGATTC
5155890 AATTCGAG-T
1 AATTCGAGTT
**
5155899 AATTCG-GGC
1 AATTCGAGTT
5155908 AATTCG-GTT
1 AATTCGAGTT
5155917 AATTC-AGTT
1 AATTCGAGTT
5155926 AATTCG-GTT
1 AATTCGAGTT
5155935 AATTCGA-TT
1 AATTCGAGTT
5155944 AATT
1 AATT
5155948 TTTAATCAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
8 1 0.02
9 41 0.98
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (10 bp):
AATTCGAGTT
Found at i:5155921 original size:27 final size:27
Alignment explanation
Indices: 5155885--5155947 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
5155875 ATTATGTAGT
5155885 GATTCAATTCGAG-TAATTCGGGCAATTC
1 GATT-AATTC-AGTTAATTCGGGCAATTC
* **
5155913 GGTTAATTCAGTTAATTCGGTTAATTC
1 GATTAATTCAGTTAATTCGGGCAATTC
5155940 GATTAATT
1 GATTAATT
5155948 TTTAATCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 2 0.07
27 25 0.83
28 3 0.10
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.40
Consensus pattern (27 bp):
GATTAATTCAGTTAATTCGGGCAATTC
Found at i:5160728 original size:34 final size:35
Alignment explanation
Indices: 5160689--5160755 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
5160679 TTCATTCTCT
5160689 TTCTTTCCATTT-TCTT-TTC-TCTGTTGGCCGAACC
1 TTCTTT-CATTTCTCTTCTTCTTCT-TTGGCCGAACC
*
5160723 TTCTTTCTTTTCTCTTCTTCTTCTTTGGCCGAA
1 TTCTTTCATTTCTCTTCTTCTTCTTTGGCCGAA
5160756 TATTTTTCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
33 4 0.14
34 10 0.34
35 12 0.41
36 3 0.10
ACGTcount: A:0.07, C:0.28, G:0.10, T:0.54
Consensus pattern (35 bp):
TTCTTTCATTTCTCTTCTTCTTCTTTGGCCGAACC
Found at i:5161406 original size:27 final size:27
Alignment explanation
Indices: 5161375--5161555 Score: 197
Period size: 27 Copynumber: 6.7 Consensus size: 27
5161365 AACTTGAGAT
*
5161375 TCAAAGGGTAAAATGACTAAAATACCC
1 TCAAAGGGTAAAATGACTGAAATACCC
*
5161402 TCAAAGGGTAAAAT-AATCGAAATACCC
1 TCAAAGGGTAAAATGACT-GAAATACCC
* *
5161429 TCGAAGGGTAAAATGACTGAAATATCC
1 TCAAAGGGTAAAATGACTGAAATACCC
* *
5161456 TCGAAGGGTAAAATAACTGAAATACCC
1 TCAAAGGGTAAAATGACTGAAATACCC
*
5161483 TCGAAGGGTAAAATGA-TCGAAATACCC
1 TCAAAGGGTAAAATGACT-GAAATACCC
* *
5161510 TCATAA-GGTAAAATGGCCGAAATACCC
1 TCA-AAGGGTAAAATGACTGAAATACCC
* ** *
5161537 CCGTAGAGTAAAATGACTG
1 TCAAAGGGTAAAATGACTG
5161556 TTATACCCCT
Statistics
Matches: 131, Mismatches: 17, Indels: 12
0.82 0.11 0.08
Matches are distributed among these distances:
26 4 0.03
27 123 0.94
28 4 0.03
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.19
Consensus pattern (27 bp):
TCAAAGGGTAAAATGACTGAAATACCC
Found at i:5161442 original size:54 final size:53
Alignment explanation
Indices: 5161378--5161555 Score: 225
Period size: 54 Copynumber: 3.3 Consensus size: 53
5161368 TTGAGATTCA
*
5161378 AAGGGTAAAATGACTAAAATACCCTCAAAGGGTAAAATAATCGAAATACCCTCG
1 AAGGGTAAAATGACTGAAATACCCTCAAAGGGTAAAATAA-CGAAATACCCTCG
* *
5161432 AAGGGTAAAATGACTGAAATATCCTCGAAGGGTAAAATAACTGAAATACCCTCG
1 AAGGGTAAAATGACTGAAATACCCTCAAAGGGTAAAATAAC-GAAATACCCTCG
** *
5161486 AAGGGTAAAATGA-TCGAAATACCCTCATAA-GGTAAAATGGCCGAAATACCCCCG
1 AAGGGTAAAATGACT-GAAATACCCTCA-AAGGGTAAAAT-AACGAAATACCCTCG
* *
5161540 TAGAGTAAAATGACTG
1 AAGGGTAAAATGACTG
5161556 TTATACCCCT
Statistics
Matches: 109, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
53 2 0.02
54 103 0.94
55 4 0.04
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.19
Consensus pattern (53 bp):
AAGGGTAAAATGACTGAAATACCCTCAAAGGGTAAAATAACGAAATACCCTCG
Found at i:5161563 original size:81 final size:81
Alignment explanation
Indices: 5161382--5161555 Score: 233
Period size: 81 Copynumber: 2.1 Consensus size: 81
5161372 GATTCAAAGG
* * *
5161382 GTAAAATGACTAAAATACCCTCAAAGGGTAAAATAATCGAAATACCCTCGAAGGGTAAAATGACT
1 GTAAAATGACTGAAATACCCTCAAAGGGTAAAATAATCGAAATACCCTCGAAAGGTAAAATGACC
* * *
5161447 GAAATATCCTCGAAGG
66 GAAATACCCCCGAAGA
* * * *
5161463 GTAAAATAACTGAAATACCCTCGAAGGGTAAAATGATCGAAATACCCTC-ATAAGGTAAAATGGC
1 GTAAAATGACTGAAATACCCTCAAAGGGTAAAATAATCGAAATACCCTCGA-AAGGTAAAATGAC
*
5161527 CGAAATACCCCCGTAGA
65 CGAAATACCCCCGAAGA
5161544 GTAAAATGACTG
1 GTAAAATGACTG
5161556 TTATACCCCT
Statistics
Matches: 80, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
80 1 0.01
81 79 0.99
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.20
Consensus pattern (81 bp):
GTAAAATGACTGAAATACCCTCAAAGGGTAAAATAATCGAAATACCCTCGAAAGGTAAAATGACC
GAAATACCCCCGAAGA
Found at i:5161721 original size:26 final size:26
Alignment explanation
Indices: 5161691--5161771 Score: 74
Period size: 26 Copynumber: 3.1 Consensus size: 26
5161681 TAGAGGAAGT
*
5161691 ATACTGTTTCTGGCAGCTTTGCTACG
1 ATACTGTTTCTGGCAGCTTTGCTGCG
* * *
5161717 ATACTGATAT-TGGCAGCTCTGTTGCG
1 ATACTG-TTTCTGGCAGCTTTGCTGCG
* ** *
5161743 ATGCTACTACTGGCAGCTTTGCTGCG
1 ATACTGTTTCTGGCAGCTTTGCTGCG
5161769 ATA
1 ATA
5161772 TTGGTGTGTT
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
26 39 0.95
27 2 0.05
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.35
Consensus pattern (26 bp):
ATACTGTTTCTGGCAGCTTTGCTGCG
Found at i:5164333 original size:16 final size:16
Alignment explanation
Indices: 5164312--5164366 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
5164302 TGAATTACTG
*
5164312 ATTACAGCTTTATTCC
1 ATTACAGCTCTATTCC
*
5164328 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCC
5164344 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
5164360 ATTACAG
1 ATTACAG
5164367 TGAACCAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.29, C:0.25, G:0.07, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:5165475 original size:28 final size:28
Alignment explanation
Indices: 5165435--5165492 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
5165425 AATATCAAAA
5165435 TCCTGATTAGACCTGATCATGGGTCGGG
1 TCCTGATTAGACCTGATCATGGGTCGGG
*
5165463 TCCTGATTAGACCTGATCGTGGGTCGGG
1 TCCTGATTAGACCTGATCATGGGTCGGG
5165491 TC
1 TC
5165493 GAGTGTCCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.16, C:0.22, G:0.33, T:0.29
Consensus pattern (28 bp):
TCCTGATTAGACCTGATCATGGGTCGGG
Found at i:5167092 original size:21 final size:22
Alignment explanation
Indices: 5167057--5167098 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
5167047 ATAAAAAATT
5167057 ATTTTTAAAACTTTTTACAATC
1 ATTTTTAAAACTTTTTACAATC
*
5167079 ATTTTTATAA-TTTTTACAAT
1 ATTTTTAAAACTTTTTACAAT
5167099 TTTTTTACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTTTTAAAACTTTTTACAATC
Found at i:5167104 original size:21 final size:22
Alignment explanation
Indices: 5167053--5167105 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
5167043 CTTTATAAAA
5167053 AATTATTTTTAAAACTTTTTAC
1 AATTATTTTTAAAACTTTTTAC
* *
5167075 AATCATTTTTATAA-TTTTTAC
1 AATTATTTTTAAAACTTTTTAC
5167096 AATT-TTTTTA
1 AATTATTTTTA
5167106 CATTTTTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 6 0.21
21 10 0.36
22 12 0.43
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (22 bp):
AATTATTTTTAAAACTTTTTAC
Found at i:5167226 original size:21 final size:20
Alignment explanation
Indices: 5167192--5167257 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
5167182 ATTTAGATGT
5167192 TTTTTTCTAGATTTTTTATATA
1 TTTTTT-TA-ATTTTTTATATA
*
5167214 TTTTTTTGAATTTTCTATATA
1 TTTTTTT-AATTTTTTATATA
*
5167235 TTTATTTTCA-TTTTTATAT-
1 TTT-TTTTAATTTTTTATATA
5167254 TTTT
1 TTTT
5167258 AATATGTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 1 0.03
19 3 0.08
20 8 0.21
21 16 0.41
22 11 0.28
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (20 bp):
TTTTTTTAATTTTTTATATA
Found at i:5168415 original size:46 final size:43
Alignment explanation
Indices: 5168350--5168441 Score: 105
Period size: 43 Copynumber: 2.1 Consensus size: 43
5168340 ATAGGACTGT
* *
5168350 AATGGAATAGAATTATAATAAGTAATTCAAT-TGTTTGGTTGAGTGG
1 AATGGAATAGAACTATAAT-AGT-ATTC--TCTGTTTGGTTGAATGG
* *
5168396 AATGGAATAGTACTGTAATAGTATTCTCTGTTTGGTTGAATGG
1 AATGGAATAGAACTATAATAGTATTCTCTGTTTGGTTGAATGG
5168439 AAT
1 AAT
5168442 AAAGATTGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
42 1 0.02
43 17 0.41
44 4 0.10
45 3 0.07
46 16 0.39
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.38
Consensus pattern (43 bp):
AATGGAATAGAACTATAATAGTATTCTCTGTTTGGTTGAATGG
Found at i:5169951 original size:42 final size:42
Alignment explanation
Indices: 5169892--5169974 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
5169882 GGTGGCTAAG
* *
5169892 TACACTGTATTGGAATCACCATTAATTTGCAAAATATTAATT
1 TACACTATATTAGAATCACCATTAATTTGCAAAATATTAATT
* ** *
5169934 TACACTATATTAGAATCATCATTCGTTTGCAAAATTTTAAT
1 TACACTATATTAGAATCACCATTAATTTGCAAAATATTAAT
5169975 ATTGTATTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.40
Consensus pattern (42 bp):
TACACTATATTAGAATCACCATTAATTTGCAAAATATTAATT
Found at i:5172776 original size:267 final size:266
Alignment explanation
Indices: 5172378--5173143 Score: 943
Period size: 267 Copynumber: 2.9 Consensus size: 266
5172368 AATCAATGGT
* *
5172378 ATCCTAAATCTAAAAGGTAAACCAATCGTGACAAAGATTTGGGGAAGAGAG------ATTTAAGT
1 ATCCTAAATCTAAAAGGTAAACCACTCGTGACAAAGATTTGGGGAAGAGAGACACACATATAAGT
* * * *
5172437 CAAATGGATAAAATGGACTCTATGCTATTTGTGTGATTGTATCCATAATTCAGAAAGTAATGAAT
66 CAAATGGATAAAATGGACTCCATGCAATTTGTATGATTGTATCCATAATTCAGAAAGCAATGAAT
5172502 GGATCCTAAATCTAAAAGATAAACCACTCAAGACAAAGATTTAGGGAAGAGAGACACCATATAAG
131 GGATCCTAAATCTAAAAGATAAACCACTCAAGACAAAGATTTAGGGAAGAGAGACACCATATAAG
* * *
5172567 CCAAATGGAAAAAAGCGGACTCCTTGCGATTCATATGATCATATCTGTAACTCAGAGAGTGACCA
196 CCAAATGGAAAAAAGC-GACTCCATGAGATTCATATGATCATATCTGTAACTCAAAGAGTGACCA
5172632 TT-G-GG
260 TTGGAGG
5172637 ATCCTAAATCTAAAAGGTAAACCACTCGTGACAAAAGATTTGGGGAAGAGAGACACAACATATAA
1 ATCCTAAATCTAAAAGGTAAACCACTCGTGAC-AAAGATTTGGGGAAGAGAGACAC-ACATATAA
* **
5172702 GTCAAATGGATAAAATGGACTCCATGCCATTCATATGATTGTATCCATAATTCAGAAAGCAATGA
64 GTCAAATGGATAAAATGGACTCCATGCAATTTGTATGATTGTATCCATAATTCAGAAAGCAATGA
*
5172767 ATGGATCCTAAATCTAAAAGATAAACCACTCAAGACAAAGATTTAGGGAAAAGAGACACCATATA
129 ATGGATCCTAAATCTAAAAGATAAACCACTCAAGACAAAGATTTAGGGAAGAGAGACACCATATA
* * *
5172832 AGCCAAATGGAAAAAAGCAGACTCCATGAG-TTCGTCTG-TCATATCTGTAACTCAAAGAGTGAT
194 AGCCAAATGGAAAAAAGC-GACTCCATGAGATTCATATGATCATATCTGTAACTCAAAGAGTGAC
5172895 CATTGGATGG
258 CATTGGA-GG
* ** * *
5172905 ATCCTAAATCTAAAAGATAAACCACTCAAGACAAAGATTTAGGGAAGAGAGACAC-CACCATAAG
1 ATCCTAAATCTAAAAGGTAAACCACTCGTGACAAAGATTTGGGGAAGAGAGACACACA-TATAAG
* * *** ** ** * ** * *
5172969 CCAAATGGAAAAAAACAAACTCCATGCAATTTGTATGATCATATCTGTAACTCAGTGATCATTG-
65 TCAAATGG-ATAAAATGGACTCCATGCAATTTGTATGATTGTATCCATAATTCAGAAAGCAATGA
* ** *
5173033 --GGATCCTAAATCTAAAAGGT-AACCTACTCCTGACAAAAGATTTGGGGAAGAGAGACACAACA
129 ATGGATCCTAAATCTAAAAGATAAACC-ACTCAAGAC-AAAGATTTAGGGAAGAGAGACAC--CA
* * *
5173095 TATAAGTCAAATGGATAAAA-CGACTCCATGTGATTCATATGATCATATC
190 TATAAGCCAAATGGAAAAAAGCGACTCCATGAGATTCATATGATCATATC
5173144 CGAAATTCAG
Statistics
Matches: 440, Mismatches: 48, Indels: 30
0.85 0.09 0.06
Matches are distributed among these distances:
259 31 0.07
260 19 0.04
263 4 0.01
264 26 0.06
265 60 0.14
266 26 0.06
267 243 0.55
268 31 0.07
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (266 bp):
ATCCTAAATCTAAAAGGTAAACCACTCGTGACAAAGATTTGGGGAAGAGAGACACACATATAAGT
CAAATGGATAAAATGGACTCCATGCAATTTGTATGATTGTATCCATAATTCAGAAAGCAATGAAT
GGATCCTAAATCTAAAAGATAAACCACTCAAGACAAAGATTTAGGGAAGAGAGACACCATATAAG
CCAAATGGAAAAAAGCGACTCCATGAGATTCATATGATCATATCTGTAACTCAAAGAGTGACCAT
TGGAGG
Found at i:5172780 original size:134 final size:131
Alignment explanation
Indices: 5172308--5173204 Score: 782
Period size: 134 Copynumber: 6.8 Consensus size: 131
5172298 CCAAAGGAGA
** * * ** *
5172308 TCAAATGGATAAAAACAAACTCCATGCGATTTGTAAGATTGTATCCATAACTCAGAAAGCAATCA
1 TCAAATGGAT-AAAACGGACTCCATGCGATTCGTATGATCATATCCATAACTCAGAAAGCAATGA
* * ** * *
5172373 ATGGTATCCTAAATCTAAAAGGTAAACCAATCGTGACAAAGATTTGGGGAAGAGAG-----ATTT
65 ATGG-ATCCTAAATCTAAAAGATAAACCACTCAAGACAAAGATTTAGGGAAGAGAGACACCATAT
5172433 AAG
129 AAG
* * * * * ** * *
5172436 TCAAATGGATAAAATGGACTCTATGCTATTTGTGTGATTGTATCCATAATTCAGAAAGTAATGAA
1 TCAAATGGATAAAACGGACTCCATGCGATTCGTATGATCATATCCATAACTCAGAAAGCAATGAA
5172501 TGGATCCTAAATCTAAAAGATAAACCACTCAAGACAAAGATTTAGGGAAGAGAGACACCATATAA
66 TGGATCCTAAATCTAAAAGATAAACCACTCAAGACAAAGATTTAGGGAAGAGAGACACCATATAA
5172566 G
131 G
* * * * ** * ** **
5172567 CCAAATGGAAAAAAGCGGACTCCTTGCGATTCATATGATCATATCTGTAACTCAGAGAGTGACCA
1 TCAAATGGATAAAA-CGGACTCCATGCGATTCGTATGATCATATCCATAACTCAGAAAGCAATGA
* * ** *
5172632 TTGGGATCCTAAATCTAAAAGGTAAACCACTCGTGACAAAAGATTTGGGGAAGAGAGACACAACA
65 AT-GGATCCTAAATCTAAAAGATAAACCACTCAAGAC-AAAGATTTAGGGAAGAGAGACAC--CA
5172697 TATAAG
126 TATAAG
* * * ** *
5172703 TCAAATGGATAAAATGGACTCCATGCCATTCATATGATTGTATCCATAATTCAGAAAGCAATGAA
1 TCAAATGGATAAAACGGACTCCATGCGATTCGTATGATCATATCCATAACTCAGAAAGCAATGAA
*
5172768 TGGATCCTAAATCTAAAAGATAAACCACTCAAGACAAAGATTTAGGGAAAAGAGACACCATATAA
66 TGGATCCTAAATCTAAAAGATAAACCACTCAAGACAAAGATTTAGGGAAGAGAGACACCATATAA
5172833 G
131 G
* * * * * **
5172834 CCAAATGGAAAAAAGCAGACTCCATGAG-TTCGTCTG-TCATATCTGTAACTCA-AAGAGTGATC
1 TCAAATGGATAAAA-CGGACTCCATGCGATTCGTATGATCATATCCATAACTCAGAA-A--G--C
* *
5172896 ATTGGATGGATCCTAAATCTAAAAGATAAACCACTCAAGACAAAGATTTAGGGAAGAGAGACACC
60 AATGAATGGATCCTAAATCTAAAAGATAAACCACTCAAGACAAAGATTTAGGGAAGAGAGACACC
*
5172961 ACCATAAG
125 A-TATAAG
* * ** * * ** ** * *
5172969 CCAAATGGAAAAAAACAAACTCCATGCAATTTGTATGATCATATCTGTAACTCAGTGATCATTG-
1 TCAAATGG-ATAAAACGGACTCCATGCGATTCGTATGATCATATCCATAACTCAGAAAGCAATGA
* ** *
5173033 --GGATCCTAAATCTAAAAGGT-AACCTACTCCTGACAAAAGATTTGGGGAAGAGAGACACAACA
65 ATGGATCCTAAATCTAAAAGATAAACC-ACTCAAGAC-AAAGATTTAGGGAAGAGAGACAC--CA
5173095 TATAAG
126 TATAAG
* * * *
5173101 TCAAATGGATAAAAC-GACTCCATGTGATTCATATGATCATATCCGA-AATTCAGAAAGTAATGA
1 TCAAATGGATAAAACGGACTCCATGCGATTCGTATGATCATATCC-ATAACTCAGAAAGCAATGA
* * *
5173164 ATGGGATCCT-AATCTCAAAAGA-GAGCCACTCATGACAAAGA
65 AT-GGATCCTAAATCT-AAAAGATAAACCACTCAAGACAAAGA
5173205 AAGGATATCT
Statistics
Matches: 629, Mismatches: 108, Indels: 60
0.79 0.14 0.08
Matches are distributed among these distances:
126 46 0.07
127 48 0.08
128 10 0.02
129 6 0.01
130 71 0.11
131 72 0.11
132 62 0.10
133 72 0.11
134 132 0.21
135 61 0.10
136 32 0.05
137 17 0.03
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.23
Consensus pattern (131 bp):
TCAAATGGATAAAACGGACTCCATGCGATTCGTATGATCATATCCATAACTCAGAAAGCAATGAA
TGGATCCTAAATCTAAAAGATAAACCACTCAAGACAAAGATTTAGGGAAGAGAGACACCATATAA
G
Found at i:5175789 original size:31 final size:31
Alignment explanation
Indices: 5175751--5175815 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
5175741 CAATAGTTTC
*
5175751 AAAATTTT-ATCTAAATCTTTTA-AATTTTTTA
1 AAAATTTTAAT-TAAATCATTTATAA-TTTTTA
5175782 AAAATTTTAATTAAATCATTTATAATTTTTA
1 AAAATTTTAATTAAATCATTTATAATTTTTA
5175813 AAA
1 AAA
5175816 GTTATCGTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 27 0.87
32 4 0.13
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.51
Consensus pattern (31 bp):
AAAATTTTAATTAAATCATTTATAATTTTTA
Found at i:5176243 original size:26 final size:27
Alignment explanation
Indices: 5176213--5176275 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
5176203 ATAAAAAATA
5176213 ACCAAAATATTA-AACTTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTTATTT
*
5176239 ACCAAAATATTATAATTTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTTATTT
5176266 ACCAAAATAT
1 ACCAAAATAT
5176276 ACCAAAAACG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 12 0.34
27 23 0.66
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (27 bp):
ACCAAAATATTATAACTTTTTTTATTT
Found at i:5184784 original size:17 final size:17
Alignment explanation
Indices: 5184755--5184795 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
5184745 ACTTTCCCTC
5184755 AAAC-TTTTATTCCCCA
1 AAACTTTTTATTCCCCA
* *
5184771 AAACTTTTTTTTCCCCT
1 AAACTTTTTATTCCCCA
5184788 AAACTTTT
1 AAACTTTT
5184796 ACTTCTCACC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.46
Consensus pattern (17 bp):
AAACTTTTTATTCCCCA
Found at i:5190209 original size:28 final size:27
Alignment explanation
Indices: 5190161--5190215 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
5190151 TAGGCGCCAA
5190161 TGAATAAAAAAATAATATATATATTTTT
1 TGAATAAAAAAATAATATATAT-TTTTT
* *
5190189 TGAAT-AAAATATAATTTTATATTTTTT
1 TGAATAAAAAAATAA-TATATATTTTTT
5190216 AATATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (27 bp):
TGAATAAAAAAATAATATATATTTTTT
Found at i:5190213 original size:25 final size:27
Alignment explanation
Indices: 5190161--5190219 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 27
5190151 TAGGCGCCAA
5190161 TGAATAAAAAAATAATATATATATTTTT
1 TGAAT-AAAAAATAATATATATATTTTT
* *
5190189 TGAATAAAATATAAT-TTTATATTTTT
1 TGAATAAAAAATAATATATATATTTTT
5190215 T-AATA
1 TGAATA
5190220 TTTTTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 4 0.14
26 11 0.38
27 9 0.31
28 5 0.17
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.47
Consensus pattern (27 bp):
TGAATAAAAAATAATATATATATTTTT
Found at i:5190318 original size:27 final size:27
Alignment explanation
Indices: 5190288--5190352 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
5190278 CCTATCAGGT
5190288 AGGCGCCAATGAAGGTGCCTCATAAAG
1 AGGCGCCAATGAAGGTGCCTCATAAAG
**
5190315 AGGCGCCAATGAAGGTGCCTCATTGAG
1 AGGCGCCAATGAAGGTGCCTCATAAAG
*
5190342 AGGCACCAATG
1 AGGCGCCAATG
5190353 GTTGGCCTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.31, C:0.23, G:0.31, T:0.15
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCATAAAG
Found at i:5190495 original size:14 final size:13
Alignment explanation
Indices: 5190478--5190528 Score: 59
Period size: 14 Copynumber: 3.8 Consensus size: 13
5190468 GAGAAAAAAA
5190478 AAGAGAGAAAGGAG
1 AAGA-AGAAAGGAG
5190492 AAGAAGAGAAGGAG
1 AAGAAGA-AAGGAG
*
5190506 AAGAAG-AAGAAG
1 AAGAAGAAAGGAG
5190518 AAGAAAGAAAG
1 AAG-AAGAAAG
5190529 AAAAAAGGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 8 0.24
13 6 0.18
14 19 0.58
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (13 bp):
AAGAAGAAAGGAG
Found at i:5190496 original size:3 final size:3
Alignment explanation
Indices: 5190490--5190522 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
5190480 GAGAGAAAGG
*
5190490 AGA AGA AG- AGA AGG AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
5190523 AGAAAGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:5190826 original size:22 final size:22
Alignment explanation
Indices: 5190798--5190936 Score: 179
Period size: 22 Copynumber: 5.9 Consensus size: 22
5190788 GGATTAGTAA
5190798 TTTGTATGAATATTGTAATTTT
1 TTTGTATGAATATTGTAATTTT
5190820 TTTGTATGAATATTGTAATATTATAGT
1 TTTGTATGAATATTGT-A-ATT-T--T
5190847 TTTGTATGAATATTGTAATTTT
1 TTTGTATGAATATTGTAATTTT
5190869 TTTGTATGAATATTGTAATTTTGTAAT
1 TTTGTATGAATATTGTAA--TT-T--T
5190896 TTTGTATGAATATTGTAATTTT
1 TTTGTATGAATATTGTAATTTT
*
5190918 TTTATATGAATATTGTAAT
1 TTTGTATGAATATTGTAAT
5190937 ATTAGGGGTT
Statistics
Matches: 106, Mismatches: 1, Indels: 20
0.83 0.01 0.16
Matches are distributed among these distances:
22 54 0.51
23 1 0.01
24 7 0.07
25 7 0.07
26 1 0.01
27 36 0.34
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56
Consensus pattern (22 bp):
TTTGTATGAATATTGTAATTTT
Found at i:5190851 original size:49 final size:49
Alignment explanation
Indices: 5190790--5190940 Score: 250
Period size: 49 Copynumber: 3.1 Consensus size: 49
5190780 ATAGTTTTGG
5190790 ATTAGTAA-TTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAAT
1 ATTA-TAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAAT
*
5190839 ATTATAGTTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAAT
1 ATTATAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAAT
* * *
5190888 TTTGTAATTTTGTATGAATATTGTAATTTTTTTATATGAATATTGTAAT
1 ATTATAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAAT
5190937 ATTA
1 ATTA
5190941 GGGGTTTTTG
Statistics
Matches: 94, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
48 2 0.02
49 92 0.98
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (49 bp):
ATTATAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAAT
Found at i:5190917 original size:19 final size:19
Alignment explanation
Indices: 5190678--5190893 Score: 118
Period size: 19 Copynumber: 11.5 Consensus size: 19
5190668 TTTAGATTAG
*
5190678 AATTTTGTATGAATATTCT
1 AATTTTGTATGAATATTGT
*
5190697 AACTTTT-T-TGTATATTGT
1 AA-TTTTGTATGAATATTGT
*
5190715 AATTTTTTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
5190734 AATGTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
5190753 AATTATTTTAT-AATTAAATTTGT
1 AATT-TTGTATGAA-T--A-TTGT
* * *
5190776 -ATTTATAGTTTTGGAT-TAGT
1 AATTT-T-G-TATGAATATTGT
5190796 AA-TTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
5190814 AATTTT-TTTG--TA-TG-
1 AATTTTGTATGAATATTGT
* *
5190828 AATATTG--T-AATATTAT
1 AATTTTGTATGAATATTGT
*
5190844 AGTTTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
5190863 AATTTTTTTGTATGAATATTGT
1 AA---TTTTGTATGAATATTGT
5190885 AATTTTGTA
1 AATTTTGTA
5190894 ATTTTGTATG
Statistics
Matches: 150, Mismatches: 21, Indels: 52
0.67 0.09 0.23
Matches are distributed among these distances:
13 1 0.01
14 7 0.05
15 3 0.02
16 7 0.05
17 9 0.06
18 21 0.14
19 53 0.35
20 15 0.10
21 2 0.01
22 24 0.16
23 4 0.03
24 3 0.02
25 1 0.01
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.55
Consensus pattern (19 bp):
AATTTTGTATGAATATTGT
Found at i:5191050 original size:12 final size:12
Alignment explanation
Indices: 5191033--5191060 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
5191023 CAATTTCAAA
5191033 TTGTAGACAATT
1 TTGTAGACAATT
5191045 TTGTAGACAATT
1 TTGTAGACAATT
5191057 TTGT
1 TTGT
5191061 GATTCAAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.07, G:0.18, T:0.46
Consensus pattern (12 bp):
TTGTAGACAATT
Found at i:5193984 original size:13 final size:13
Alignment explanation
Indices: 5193966--5194007 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
5193956 TATTTTTTTT
5193966 CTTCTTTTCCTTC
1 CTTCTTTTCCTTC
5193979 CTTCTTTTCCTT-
1 CTTCTTTTCCTTC
*
5193991 CTGC--TTCCTTC
1 CTTCTTTTCCTTC
5194002 CTTCTT
1 CTTCTT
5194008 ATTTCTTCCG
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 6 0.25
11 3 0.12
12 3 0.12
13 12 0.50
ACGTcount: A:0.00, C:0.38, G:0.02, T:0.60
Consensus pattern (13 bp):
CTTCTTTTCCTTC
Found at i:5196220 original size:2 final size:2
Alignment explanation
Indices: 5196213--5196238 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5196203 TAACAAATTC
5196213 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
5196239 GACTTAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5197799 original size:2 final size:2
Alignment explanation
Indices: 5197792--5197816 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5197782 ACATGTGCAT
5197792 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 T
5197817 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5203116 original size:14 final size:14
Alignment explanation
Indices: 5203076--5203116 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
5203066 CTATATTTTG
*
5203076 TTTAATTTTGA-AA
1 TTTAATTTTGATAT
5203089 TTTAATTTAT-ATAT
1 TTTAATTT-TGATAT
5203103 TTTAATTTTGATAT
1 TTTAATTTTGATAT
5203117 AATTTGGTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 10 0.42
14 14 0.58
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (14 bp):
TTTAATTTTGATAT
Found at i:5212063 original size:22 final size:22
Alignment explanation
Indices: 5212038--5212080 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
5212028 ACTTAAATTT
5212038 TTAAATT-TAAAAAATAAAAAGA
1 TTAAATTCT-AAAAATAAAAAGA
5212060 TTAAATTCCTAAAAATAAAAA
1 TTAAATT-CTAAAAATAAAAA
5212081 TATAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 11 0.58
24 1 0.05
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (22 bp):
TTAAATTCTAAAAATAAAAAGA
Found at i:5214148 original size:16 final size:17
Alignment explanation
Indices: 5214115--5214150 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
5214105 GAATACCTAT
5214115 AAAATTATCTTTTAAAA
1 AAAATTATCTTTTAAAA
5214132 AAAATTATCTTTTAAAA
1 AAAATTATCTTTTAAAA
5214149 AA
1 AA
5214151 GATAATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAATTATCTTTTAAAA
Found at i:5218162 original size:5 final size:5
Alignment explanation
Indices: 5218147--5218181 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
5218137 GTGTGTCATT
5218147 TAAAA -AAAA TAAAA TAAAA TAAAA TAAAA CTAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA -TAAAA
5218182 AGGGACATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.14
5 19 0.68
6 5 0.18
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (5 bp):
TAAAA
Found at i:5219964 original size:54 final size:54
Alignment explanation
Indices: 5219874--5219983 Score: 184
Period size: 54 Copynumber: 2.0 Consensus size: 54
5219864 CATTAGAGGA
* *
5219874 TTAGTGGTGGGGTTAATTGTTGGAGCTTCTGGTTTGATTCTTGGCCTAGGTTTG
1 TTAGTGGTGGGGTTAATTGTTGGAGCTTCTGCTTTGATTCTTGGCCTAGGTGTG
* *
5219928 TTAGTGGTGGGGTTAATTGTTGGAGCTTGTGCTTTGATTTTTGGCCTAGGTGTG
1 TTAGTGGTGGGGTTAATTGTTGGAGCTTCTGCTTTGATTCTTGGCCTAGGTGTG
5219982 TT
1 TT
5219984 CTTGTGGTTC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.11, C:0.08, G:0.35, T:0.45
Consensus pattern (54 bp):
TTAGTGGTGGGGTTAATTGTTGGAGCTTCTGCTTTGATTCTTGGCCTAGGTGTG
Found at i:5224138 original size:2 final size:2
Alignment explanation
Indices: 5224133--5224196 Score: 105
Period size: 2 Copynumber: 32.5 Consensus size: 2
5224123 TACGGAATGA
5224133 AT AT AT AT AT AT AT AT 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 AT AT AT AT
5224175 AT A- AT A- AT AT AT AT ACT AT AT A
1 AT AT AT AT AT AT AT AT A-T AT AT A
5224197 GTAGTAGTAG
Statistics
Matches: 59, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.03
2 55 0.93
3 2 0.03
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5225508 original size:26 final size:26
Alignment explanation
Indices: 5225479--5225528 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
5225469 AAATAACATA
* *
5225479 GAAAGCAATTTAAA-TAGGTAATATAT
1 GAAA-CAACTTAAAGTAGCTAATATAT
5225505 GAAACAACTTAAAGTAGCTAATAT
1 GAAACAACTTAAAGTAGCTAATAT
5225529 CAAACATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.50, C:0.08, G:0.14, T:0.28
Consensus pattern (26 bp):
GAAACAACTTAAAGTAGCTAATATAT
Found at i:5227340 original size:44 final size:44
Alignment explanation
Indices: 5227314--5227614 Score: 170
Period size: 44 Copynumber: 6.7 Consensus size: 44
5227304 GTTTTAATTT
* *
5227314 GCTCCACTGTAACTTTAGGGAGATAAGATTAGTAGCTTCAATAC
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAATAC
*
5227358 GCTCCACTGCAACTTCAGGGAGATAATG-TTTGTTA-CTTCAACCTA-
1 GCTCCACTGCAACTTCAGGGAGATAA-GATTAG-TAGCTTCAA--TAC
* * * * * *
5227403 -CTCCACTGCAACTTCAAGGAGATAAGTTTTGTTATCTTTAGT-C
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAG-TAGCTTCAATAC
* * *
5227446 TGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTAGGTTTAATTC
1 -GCTCCACTGCAACTTCAGGGAGATAAGA----TTA--GTAGCTTCAATAC
* * * * * * *
5227497 GAC-CTACTGCAACTTCAGAGG-TATAGGATTTA-TCGTTTTAATCC
1 G-CTCCACTGCAACTTCAG-GGAGATAAGA-TTAGTAGCTTCAATAC
* * * * *
5227541 TCTCCACTGCAACTTTAGGGAGATAGGATTAATTGCTTCAAT-C
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAATAC
*
5227584 TGCTCCACTGCAACTTTAGGGAGATAAGATT
1 -GCTCCACTGCAACTTCAGGGAGATAAGATT
5227615 GGTATCCTCT
Statistics
Matches: 207, Mismatches: 28, Indels: 44
0.74 0.10 0.16
Matches are distributed among these distances:
43 9 0.04
44 127 0.61
45 32 0.15
46 2 0.01
47 3 0.01
49 2 0.01
50 27 0.13
51 5 0.02
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAATAC
Found at i:5227462 original size:45 final size:45
Alignment explanation
Indices: 5227313--5227482 Score: 177
Period size: 44 Copynumber: 3.8 Consensus size: 45
5227303 CGTTTTAATT
* * * * * *
5227313 TGCTCCACTGTAACTTTAGGGAGATAAGATTAG-TAGCTTCAATAC
1 TGCTCCACTGCAACTTCAGGGAGATAAGTTTTGTTATCTTCAA-CC
5227358 -GCTCCACTGCAACTTCAGGGAGATAA-TGTTTGTTA-CTTCAACC
1 TGCTCCACTGCAACTTCAGGGAGATAAGT-TTTGTTATCTTCAACC
* * * **
5227401 TACTCCACTGCAACTTCAAGGAGATAAGTTTTGTTATCTTTAGTC
1 TGCTCCACTGCAACTTCAGGGAGATAAGTTTTGTTATCTTCAACC
**
5227446 TGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTAT
1 TGCTCCACTGCAACTTCAGGGAGATAAGTTTTGTTAT
5227483 GGTAGGTTTA
Statistics
Matches: 106, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
43 1 0.01
44 64 0.60
45 41 0.39
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (45 bp):
TGCTCCACTGCAACTTCAGGGAGATAAGTTTTGTTATCTTCAACC
Found at i:5227930 original size:88 final size:88
Alignment explanation
Indices: 5227823--5228424 Score: 555
Period size: 88 Copynumber: 6.8 Consensus size: 88
5227813 TTCTGCAACT
* * ** * *
5227823 TCAGGGAGATAAGGTTTGTGTTTTTAATTTGCTTCACTGTCAGTACAGGAAGACAAGATCTGCAA
1 TCAGGAAGATAAGGCTTGTGTTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTGCAA
* *
5227888 TCTTCAACTTACTCCACTTCTGC
66 TCTTCAACCTACTCCACTGCTGC
* * * * ** * *
5227911 TCAGAAAGATAAGGCTTGTGTTTTTGATCTGTTTCACTACCAGTGTAGGAAGATAAGACCTGCAA
1 TCAGGAAGATAAGGCTTGTGTTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTGCAA
* * * *
5227976 TCTTTAACCTATTTCACTGCTAC
66 TCTTCAACCTACTCCACTGCTGC
* * * *
5227999 TTAAGG-AGATAAGGCTTGT-TATTTCGATCTGTTTCACTGCCAATACAGGAAGACAAGATTTGC
1 -TCAGGAAGATAAGGCTTGTGT-TTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTGC
*
5228062 AATCTTCAACCTACTCCACTGCTTC
64 AATCTTCAACCTACTCCACTGCTGC
* * * *
5228087 TCTGGAAGATAAGG-TTGGTGTTTTCGATCTGCTTCACTGCCAGTATAGGAAGACAAAATCTTCA
1 TCAGGAAGATAAGGCTT-GTGTTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTGCA
5228151 ATCTTCAACCTACTCCACTGCTGC
65 ATCTTCAACCTACTCCACTGCTGC
* * *
5228175 TCAGGAAGATAAGGCTGGTGTTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATTTGTAA
1 TCAGGAAGATAAGGCTTGTGTTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTGCAA
* * * *
5228240 ACTTTAACCCACTCCACTACTGC
66 TCTTCAACCTACTCCACTGCTGC
* ** * ** ** * * * * **
5228263 TCAGGGAGATAAGGCAGGTGTCTTCGATCTATTTTGCTGCCAATACAGGAAGAAAAAATTTGTTA
1 TCAGGAAGATAAGGCTTGTGTTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTGCAA
* * *
5228328 TCTTCAACCTGCTCCGCTG-TAAAC
66 TCTTCAACCTACTCCACTGCT--GC
* *** * * * * * **
5228352 TCAGGGAGGCGAGGCTGGTGTCTTCGATCTACTTCACTGCCAATGCAGGAAGACAAGATCTGTTA
1 TCAGGAAGATAAGGCTTGTGTTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTGCAA
5228417 TCTTCAAC
66 TCTTCAAC
5228425 TTGCTCCGCC
Statistics
Matches: 425, Mismatches: 81, Indels: 15
0.82 0.16 0.03
Matches are distributed among these distances:
87 7 0.02
88 350 0.82
89 68 0.16
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (88 bp):
TCAGGAAGATAAGGCTTGTGTTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTGCAA
TCTTCAACCTACTCCACTGCTGC
Done.