Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 125 of 132
Found at i:38471389 original size:23 final size:23
Alignment explanation
Indices: 38471356--38471401 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
38471346 ATACTAAAAG
38471356 AGAAGAATATATTTGTTCATAAT
1 AGAAGAATATATTTGTTCATAAT
*
38471379 AGAAGACTATATTTGTTCATAAT
1 AGAAGAATATATTTGTTCATAAT
38471402 GAGTAGAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (23 bp):
AGAAGAATATATTTGTTCATAAT
Found at i:38473018 original size:2 final size:2
Alignment explanation
Indices: 38473013--38473041 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
38473003 GTGTGTGTGT
38473013 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
38473042 CTAAGTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:38476307 original size:13 final size:13
Alignment explanation
Indices: 38476289--38476313 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38476279 AAGTCGATGG
38476289 AAACGAGGCTTAA
1 AAACGAGGCTTAA
38476302 AAACGAGGCTTA
1 AAACGAGGCTTA
38476314 TGAGTTACTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (13 bp):
AAACGAGGCTTAA
Found at i:38478417 original size:17 final size:17
Alignment explanation
Indices: 38478384--38478416 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
38478374 AATTCAATTG
38478384 ATATATTTAAATATTTT
1 ATATATTTAAATATTTT
38478401 ATATA-TTAAATATTTT
1 ATATATTTAAATATTTT
38478417 TTTAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATATTTAAATATTTT
Found at i:38480364 original size:6 final size:6
Alignment explanation
Indices: 38480353--38480377 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
38480343 TTTCAGCCGG
38480353 CTGAGC CTGAGC CTGAGC CTGAGC C
1 CTGAGC CTGAGC CTGAGC CTGAGC C
38480378 GCAGTCGCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.36, G:0.32, T:0.16
Consensus pattern (6 bp):
CTGAGC
Found at i:38480821 original size:6 final size:6
Alignment explanation
Indices: 38480810--38480892 Score: 141
Period size: 6 Copynumber: 13.8 Consensus size: 6
38480800 GGCCATTAAA
38480810 TATGTT TATGTT TATGTT TATGTT TATGTT TATGTT TATGTT TATGTT
1 TATGTT TATGTT TATGTT TATGTT TATGTT TATGTT TATGTT TATGTT
*
38480858 TATGTT TATGTT TATGTT CT-TATT TATGTT TATGT
1 TATGTT TATGTT TATGTT -TATGTT TATGTT TATGT
38480893 ATGCAAATAT
Statistics
Matches: 73, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
5 1 0.01
6 71 0.97
7 1 0.01
ACGTcount: A:0.17, C:0.01, G:0.16, T:0.66
Consensus pattern (6 bp):
TATGTT
Found at i:38483963 original size:733 final size:733
Alignment explanation
Indices: 38482557--38484028 Score: 2926
Period size: 733 Copynumber: 2.0 Consensus size: 733
38482547 TGTACGATGC
38482557 ATCCCAATCACCGAATAATTGTTCCATTGCCATCTGTTTCGTAATCCATGCTTTTCGATATGAAA
1 ATCCCAATCACCGAATAATTGTTCCATTGCCATCTGTTTCGTAATCCATGCTTTTCGATATGAAA
38482622 CTCGATAATGGAATCGTACTTGCATCTCGACAATCAGTGTAGAAACTTTGATGGTCGGATCGTCC
66 CTCGATAATGGAATCGTACTTGCATCTCGACAATCAGTGTAGAAACTTTGATGGTCGGATCGTCC
38482687 TTCACCATTGGCATGATATGTGTGCAGATAGTTTTGGAATCGAGTTTTCGATGATCTTCTGACAA
131 TTCACCATTGGCATGATATGTGTGCAGATAGTTTTGGAATCGAGTTTTCGATGATCTTCTGACAA
38482752 ACGTGTTGAACTGCATGTGTGAGGCCCGACAAATTTTTTTATCTCCCACTTTTGCGACTTCTGGA
196 ACGTGTTGAACTGCATGTGTGAGGCCCGACAAATTTTTTTATCTCCCACTTTTGCGACTTCTGGA
38482817 TAAATGCAGCTCGTACCCGCCAATTGCAGCCTTCTGTCGAACACTCTCCAATATATAATGTCGGT
261 TAAATGCAGCTCGTACCCGCCAATTGCAGCCTTCTGTCGAACACTCTCCAATATATAATGTCGGT
38482882 TTAGACACAACGACTTTGTAGTCCACTGACAAATTCATGCTATATCGCTTAATGGCAAATACGCA
326 TTAGACACAACGACTTTGTAGTCCACTGACAAATTCATGCTATATCGCTTAATGGCAAATACGCA
*
38482947 CTCTTCCTTCGAGTCAAACCTTTGACCCACGAATAACTGTTCAGGTTCTGGTGTAAGCGCCAATC
391 CTCTTCCTTCGAGTCAAACCTTTGACCCACGAACAACTGTTCAGGTTCTGGTGTAAGCGCCAATC
38483012 GGTGAGCAGGCATTATATCAGGGTACTCTTCAAAATCGGCTGCATATGCCGCATCAGGGTCTATA
456 GGTGAGCAGGCATTATATCAGGGTACTCTTCAAAATCGGCTGCATATGCCGCATCAGGGTCTATA
38483077 ACTGACATGTGTGACCCAGCAGGATAATTGTGCATCACAATACGTCGACCATCCGGGACCTCGTC
521 ACTGACATGTGTGACCCAGCAGGATAATTGTGCATCACAATACGTCGACCATCCGGGACCTCGTC
38483142 ATTTAGGCCTTCCTCATCGATATCATCCGAGACCTCGTCCATGTCGGGATCACTACCAATATCGT
586 ATTTAGGCCTTCCTCATCGATATCATCCGAGACCTCGTCCATGTCGGGATCACTACCAATATCGT
38483207 CCTCGTGATCAGAAGGATCACTACTATCATCTCCATCATCACCATCCGTATCATTATCGGGTGCA
651 CCTCGTGATCAGAAGGATCACTACTATCATCTCCATCATCACCATCCGTATCATTATCGGGTGCA
38483272 ACATTAAGATCGATATTA
716 ACATTAAGATCGATATTA
38483290 ATCCCAATCACCGAATAATTGTTCCATTGCCATCTGTTTCGTAATCCATGCTTTTCGATATGAAA
1 ATCCCAATCACCGAATAATTGTTCCATTGCCATCTGTTTCGTAATCCATGCTTTTCGATATGAAA
38483355 CTCGATAATGGAATCGTACTTGCATCTCGACAATCAGTGTAGAAACTTTGATGGTCGGATCGTCC
66 CTCGATAATGGAATCGTACTTGCATCTCGACAATCAGTGTAGAAACTTTGATGGTCGGATCGTCC
38483420 TTCACCATTGGCATGATATGTGTGCAGATAGTTTTGGAATCGAGTTTTCGATGATCTTCTGACAA
131 TTCACCATTGGCATGATATGTGTGCAGATAGTTTTGGAATCGAGTTTTCGATGATCTTCTGACAA
38483485 ACGTGTTGAACTGCATGTGTGAGGCCCGACAAATTTTTTTATCTCCCACTTTTGCGACTTCTGGA
196 ACGTGTTGAACTGCATGTGTGAGGCCCGACAAATTTTTTTATCTCCCACTTTTGCGACTTCTGGA
38483550 TAAATGCAGCTCGTACCCGCCAATTGCAGCCTTCTGTCGAACACTCTCCAATATATAATGTCGGT
261 TAAATGCAGCTCGTACCCGCCAATTGCAGCCTTCTGTCGAACACTCTCCAATATATAATGTCGGT
38483615 TTAGACACAACGACTTTGTAGTCCACTGACAAATTCATGCTATATCGCTTAATGGCAAATACGCA
326 TTAGACACAACGACTTTGTAGTCCACTGACAAATTCATGCTATATCGCTTAATGGCAAATACGCA
38483680 CTCTTCCTTCGAGTCAAACCTTTGACCCACGAACAACTGTTCAGGTTCTGGTGTAAGCGCCAATC
391 CTCTTCCTTCGAGTCAAACCTTTGACCCACGAACAACTGTTCAGGTTCTGGTGTAAGCGCCAATC
38483745 GGTGAGCAGGCATTATATCAGGGTACTCTTCAAAATCGGCTGCATATGCCGCATCAGGGTCTATA
456 GGTGAGCAGGCATTATATCAGGGTACTCTTCAAAATCGGCTGCATATGCCGCATCAGGGTCTATA
38483810 ACTGACATGTGTGACCCAGCAGGATAATTGTGCATCACAATACGTCGACCATCCGGGACCTCGTC
521 ACTGACATGTGTGACCCAGCAGGATAATTGTGCATCACAATACGTCGACCATCCGGGACCTCGTC
*
38483875 ATTTAGGCCTTCCTCATCGATATCATCCGGGACCTCGTCCATGTCGGGATCACTACCAATATCGT
586 ATTTAGGCCTTCCTCATCGATATCATCCGAGACCTCGTCCATGTCGGGATCACTACCAATATCGT
38483940 CCTCGTGATCAGAAGGATCACTACTATCATCTCCATCATCACCATCCGTATCATTATCGGGTGCA
651 CCTCGTGATCAGAAGGATCACTACTATCATCTCCATCATCACCATCCGTATCATTATCGGGTGCA
38484005 ACATTAAGATCGATATTA
716 ACATTAAGATCGATATTA
38484023 ATCCCA
1 ATCCCA
38484029 CTGATCCCGC
Statistics
Matches: 737, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
733 737 1.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (733 bp):
ATCCCAATCACCGAATAATTGTTCCATTGCCATCTGTTTCGTAATCCATGCTTTTCGATATGAAA
CTCGATAATGGAATCGTACTTGCATCTCGACAATCAGTGTAGAAACTTTGATGGTCGGATCGTCC
TTCACCATTGGCATGATATGTGTGCAGATAGTTTTGGAATCGAGTTTTCGATGATCTTCTGACAA
ACGTGTTGAACTGCATGTGTGAGGCCCGACAAATTTTTTTATCTCCCACTTTTGCGACTTCTGGA
TAAATGCAGCTCGTACCCGCCAATTGCAGCCTTCTGTCGAACACTCTCCAATATATAATGTCGGT
TTAGACACAACGACTTTGTAGTCCACTGACAAATTCATGCTATATCGCTTAATGGCAAATACGCA
CTCTTCCTTCGAGTCAAACCTTTGACCCACGAACAACTGTTCAGGTTCTGGTGTAAGCGCCAATC
GGTGAGCAGGCATTATATCAGGGTACTCTTCAAAATCGGCTGCATATGCCGCATCAGGGTCTATA
ACTGACATGTGTGACCCAGCAGGATAATTGTGCATCACAATACGTCGACCATCCGGGACCTCGTC
ATTTAGGCCTTCCTCATCGATATCATCCGAGACCTCGTCCATGTCGGGATCACTACCAATATCGT
CCTCGTGATCAGAAGGATCACTACTATCATCTCCATCATCACCATCCGTATCATTATCGGGTGCA
ACATTAAGATCGATATTA
Found at i:38484618 original size:25 final size:25
Alignment explanation
Indices: 38484584--38484633 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
38484574 TTTGTTTCCT
38484584 TTCCTTCTTCAAAAATTTACTGTTA
1 TTCCTTCTTCAAAAATTTACTGTTA
38484609 TTCCTTCTTCAAAAATTTACTGTTA
1 TTCCTTCTTCAAAAATTTACTGTTA
38484634 AACAGATCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.20, G:0.04, T:0.48
Consensus pattern (25 bp):
TTCCTTCTTCAAAAATTTACTGTTA
Found at i:38484706 original size:27 final size:27
Alignment explanation
Indices: 38484668--38484728 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
38484658 GCATTGACAA
38484668 AGGCACCACTAGTGCCGCCTACCCAGT
1 AGGCACCACTAGTGCCGCCTACCCAGT
**
38484695 AGGCACCACTAGTGCCGCCTACCTGGT
1 AGGCACCACTAGTGCCGCCTACCCAGT
38484722 AGGCACC
1 AGGCACC
38484729 TCTTGTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.21, C:0.39, G:0.25, T:0.15
Consensus pattern (27 bp):
AGGCACCACTAGTGCCGCCTACCCAGT
Found at i:38485322 original size:14 final size:15
Alignment explanation
Indices: 38485287--38485328 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
38485277 AACGGAAAGA
38485287 ATATATTATTTTAGT
1 ATATATTATTTTAGT
*
38485302 ATATATTATTTT-TT
1 ATATATTATTTTAGT
*
38485316 TTATATTATTTTA
1 ATATATTATTTTA
38485329 ATAAAAAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
ATATATTATTTTAGT
Found at i:38487127 original size:18 final size:18
Alignment explanation
Indices: 38487106--38487140 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38487096 CTTATTATTA
38487106 TCATCCTTCTTCCCACCT
1 TCATCCTTCTTCCCACCT
* *
38487124 TCATCTTTCTTCTCACC
1 TCATCCTTCTTCCCACC
38487141 ATCTTTCTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.46, G:0.00, T:0.43
Consensus pattern (18 bp):
TCATCCTTCTTCCCACCT
Found at i:38490797 original size:14 final size:14
Alignment explanation
Indices: 38490774--38490807 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
38490764 CATTGCTTCT
38490774 CAAAAACACTTTTG
1 CAAAAACACTTTTG
*
38490788 CAAAAGCACTTTTG
1 CAAAAACACTTTTG
*
38490802 GAAAAA
1 CAAAAA
38490808 AAAAACACTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.24
Consensus pattern (14 bp):
CAAAAACACTTTTG
Found at i:38492691 original size:22 final size:22
Alignment explanation
Indices: 38492666--38492714 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
38492656 AAGTACATAT
* *
38492666 AAATATATTTTTTTCAAAACAA
1 AAATACATTTTTTTAAAAACAA
*
38492688 AAATTACATTTTTTTAAAAATAA
1 AAA-TACATTTTTTTAAAAACAA
38492711 AAAT
1 AAAT
38492715 TTATGAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (22 bp):
AAATACATTTTTTTAAAAACAA
Found at i:38492698 original size:23 final size:23
Alignment explanation
Indices: 38492672--38492715 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
38492662 ATATAAATAT
*
38492672 ATTTTTTTCAAAACAAAAATTAC
1 ATTTTTTTAAAAACAAAAATTAC
*
38492695 ATTTTTTTAAAAATAAAAATT
1 ATTTTTTTAAAAACAAAAATT
38492716 TATGAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTTTTTTAAAAACAAAAATTAC
Found at i:38492739 original size:16 final size:16
Alignment explanation
Indices: 38492698--38492767 Score: 68
Period size: 18 Copynumber: 4.0 Consensus size: 16
38492688 AAATTACATT
*
38492698 TTTTTAAAAATAAAAA
1 TTTTAAAAAATAAAAA
*
38492714 TTTATGAAAAAATAAAAC
1 TTT-T-AAAAAATAAAAA
38492732 TTTTAAAAAATAAGAATGA
1 TTTTAAAAAATAA-AA--A
38492751 TTTTAAAAATATAAAAA
1 TTTTAAAAA-ATAAAAA
38492768 AATTCAAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
16 12 0.27
17 5 0.11
18 13 0.29
19 11 0.24
20 4 0.09
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.33
Consensus pattern (16 bp):
TTTTAAAAAATAAAAA
Found at i:38493837 original size:21 final size:20
Alignment explanation
Indices: 38493813--38493857 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
38493803 AACGTGGTCG
38493813 TTTTGTGCAAAATAATTTAAA
1 TTTTGTG-AAAATAATTTAAA
* *
38493834 TTTTTTGAGAATTAATTTAAA
1 TTTTGTGA-AAATAATTTAAA
38493855 TTT
1 TTT
38493858 CGTGTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.51
Consensus pattern (20 bp):
TTTTGTGAAAATAATTTAAA
Found at i:38495874 original size:27 final size:28
Alignment explanation
Indices: 38495842--38495907 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 28
38495832 TTTTATATAA
* *
38495842 AATTTTTAAATAA-ATTTA-ATTTTTTT
1 AATTTTTAAATAATATTTATAATTTTTG
*
38495868 AATTTTTAAAATAATTTTTATAATTTTTG
1 AATTTTT-AAATAATATTTATAATTTTTG
38495897 AATTTTTAAAT
1 AATTTTTAAAT
38495908 TTTAAAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.21
27 6 0.18
28 8 0.24
29 13 0.38
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (28 bp):
AATTTTTAAATAATATTTATAATTTTTG
Found at i:38499233 original size:2 final size:2
Alignment explanation
Indices: 38499226--38499277 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
38499216 AGACAATGTC
38499226 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
38499268 AT AT AT AT AT
1 AT AT AT AT AT
38499278 CACATACTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38502904 original size:2 final size:2
Alignment explanation
Indices: 38502891--38502928 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
38502881 AATTGCTTAA
*
38502891 AT AT AC 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
38502929 TTGTGATCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:38504840 original size:17 final size:19
Alignment explanation
Indices: 38504806--38504847 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
38504796 ACTTTTAATC
38504806 ATTTAATTTGATAATT-AA
1 ATTTAATTTGATAATTAAA
* *
38504824 ATTTATTTTGAT-CTTAAA
1 ATTTAATTTGATAATTAAA
38504842 ATTTAA
1 ATTTAA
38504848 AAAAATACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52
Consensus pattern (19 bp):
ATTTAATTTGATAATTAAA
Found at i:38529181 original size:17 final size:15
Alignment explanation
Indices: 38529148--38529178 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
38529138 GATTTTACAG
38529148 AGAGATGAAGTTTAT
1 AGAGATGAAGTTTAT
38529163 AGAGATGAAGTTTAT
1 AGAGATGAAGTTTAT
38529178 A
1 A
38529179 TAGGGAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.32
Consensus pattern (15 bp):
AGAGATGAAGTTTAT
Found at i:38540842 original size:18 final size:18
Alignment explanation
Indices: 38540811--38540845 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38540801 ATATTTAAGT
**
38540811 AAAGTGTTTTATGAAAGC
1 AAAGTGTTACATGAAAGC
38540829 AAAGTGTTACATGAAAG
1 AAAGTGTTACATGAAAG
38540846 TGAATTCAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.06, G:0.23, T:0.29
Consensus pattern (18 bp):
AAAGTGTTACATGAAAGC
Found at i:38544701 original size:21 final size:22
Alignment explanation
Indices: 38544672--38544716 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
38544662 TTATCTTTTC
*
38544672 TAAAGTTAAAAGTCAAAACCAT
1 TAAAGTTAAAAGGCAAAACCAT
*
38544694 TAAA-TTAAAAGGCAAAATCAT
1 TAAAGTTAAAAGGCAAAACCAT
38544715 TA
1 TA
38544717 TATTGTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.56, C:0.11, G:0.09, T:0.24
Consensus pattern (22 bp):
TAAAGTTAAAAGGCAAAACCAT
Found at i:38546128 original size:30 final size:31
Alignment explanation
Indices: 38546088--38546200 Score: 104
Period size: 30 Copynumber: 3.5 Consensus size: 31
38546078 GTTTTGGTTT
*
38546088 TTTACCAAAATAAAATATAAAAAA-TATTTA
1 TTTACTAAAATAAAATATAAAAAATTATTTA
* *
38546118 TTTACTAAAATAATATACAAAAATTATTTATTTTA
1 TTTACTAAAATAAAATATAAAAA--A-TTA-TTTA
* *
38546153 TTTGACTAAAATAATAT-TAAAAAATTATTAA
1 TTT-ACTAAAATAAAATATAAAAAATTATTTA
*
38546184 TTTAATAAAAATAAAAT
1 TTTACT-AAAATAAAAT
38546201 GAAATAAATA
Statistics
Matches: 69, Mismatches: 7, Indels: 13
0.78 0.08 0.15
Matches are distributed among these distances:
30 22 0.32
31 15 0.22
32 4 0.06
33 1 0.01
34 2 0.03
35 12 0.17
36 13 0.19
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (31 bp):
TTTACTAAAATAAAATATAAAAAATTATTTA
Found at i:38546153 original size:35 final size:36
Alignment explanation
Indices: 38546114--38546186 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 36
38546104 ATAAAAAATA
*
38546114 TTTATTT-ACTAAAATAATA-TACAAAAATTATTTAT
1 TTTATTTGACTAAAATAATATTA-AAAAATTATTAAT
38546149 TTTATTTGACTAAAATAATATTAAAAAATTATTAAT
1 TTTATTTGACTAAAATAATATTAAAAAATTATTAAT
38546185 TT
1 TT
38546187 AATAAAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
35 7 0.20
36 26 0.74
37 2 0.06
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (36 bp):
TTTATTTGACTAAAATAATATTAAAAAATTATTAAT
Found at i:38546199 original size:36 final size:36
Alignment explanation
Indices: 38546123--38546200 Score: 86
Period size: 36 Copynumber: 2.2 Consensus size: 36
38546113 ATTTATTTAC
* * *** *
38546123 TAAAATAATATACAAAAATTATTTATTTTATTTGAC
1 TAAAATAATATACAAAAATTATTAATTTAATAAAAA
38546159 TAAAATAATATTA-AAAAATTATTAATTTAATAAAAA
1 TAAAATAATA-TACAAAAATTATTAATTTAATAAAAA
38546195 TAAAAT
1 TAAAAT
38546201 GAAATAAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
36 33 0.94
37 2 0.06
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (36 bp):
TAAAATAATATACAAAAATTATTAATTTAATAAAAA
Found at i:38549467 original size:14 final size:15
Alignment explanation
Indices: 38549430--38549472 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
38549420 GGTTTAATGG
* *
38549430 TTTAAAGTTTTGAAT
1 TTTAAGGTTTTGAAA
*
38549445 TTTATGGTTTT-AAA
1 TTTAAGGTTTTGAAA
38549459 TTTAAGGTTTTGAA
1 TTTAAGGTTTTGAA
38549473 GAAAAGGGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.53
Consensus pattern (15 bp):
TTTAAGGTTTTGAAA
Found at i:38549545 original size:14 final size:14
Alignment explanation
Indices: 38549520--38549564 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
38549510 TCTAATTTAG
38549520 GGTTAAGAGTTTATA
1 GGTTAAG-GTTTATA
*
38549535 GTTTAAGGTTTA-A
1 GGTTAAGGTTTATA
*
38549548 GGTTATGGTTTATA
1 GGTTAAGGTTTATA
38549562 GGT
1 GGT
38549565 ATGAAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 11 0.42
14 9 0.35
15 6 0.23
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.44
Consensus pattern (14 bp):
GGTTAAGGTTTATA
Found at i:38549893 original size:45 final size:45
Alignment explanation
Indices: 38549827--38549915 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
38549817 AAGAGTATAA
*
38549827 TATTGCGGTACCTCGTCAAACTGAGGCTGATATCCTTGGCTTGAG
1 TATTGCGGTACCTCGTAAAACTGAGGCTGATATCCTTGGCTTGAG
** *
38549872 TATTGCGGTGGCTCGTAAAACTGAGGCTGATATCTTTGGCTTGA
1 TATTGCGGTACCTCGTAAAACTGAGGCTGATATCCTTGGCTTGA
38549916 TGAGCTAGGC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (45 bp):
TATTGCGGTACCTCGTAAAACTGAGGCTGATATCCTTGGCTTGAG
Found at i:38551798 original size:30 final size:30
Alignment explanation
Indices: 38551704--38551798 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 30
38551694 CCAAAATGAG
38551704 TTATTTACTAAAATGGTACAAAATAAATAT
1 TTATTTACTAAAATGGTACAAAATAAATAT
* * * * * **
38551734 TTATATACCAAAATGGTATCCACA-CACCA-
1 TTATTTACTAAAATGGTA-CAAAATAAATAT
*
38551763 TTATTTACTAAAATGATACAAAATAAATAT
1 TTATTTACTAAAATGGTACAAAATAAATAT
38551793 TTATTT
1 TTATTT
38551799 TGTACCATTT
Statistics
Matches: 47, Mismatches: 15, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
28 3 0.06
29 17 0.36
30 24 0.51
31 3 0.06
ACGTcount: A:0.46, C:0.13, G:0.05, T:0.36
Consensus pattern (30 bp):
TTATTTACTAAAATGGTACAAAATAAATAT
Found at i:38552568 original size:14 final size:13
Alignment explanation
Indices: 38552551--38552606 Score: 51
Period size: 14 Copynumber: 4.2 Consensus size: 13
38552541 TCTCATTCTC
38552551 CTTCTCCTTTCTTT
1 CTTCTCC-TTCTTT
*
38552565 CTTCTCCTTCTTC
1 CTTCTCCTTCTTT
*
38552578 CTTTTTCCTTCTTT
1 C-TTCTCCTTCTTT
* *
38552592 -TTTTCTTTCTTT
1 CTTCTCCTTCTTT
38552604 CTT
1 CTT
38552607 TCAATACCCG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
12 11 0.31
13 8 0.22
14 17 0.47
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (13 bp):
CTTCTCCTTCTTT
Found at i:38552588 original size:20 final size:20
Alignment explanation
Indices: 38552546--38552589 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
38552536 CTCATTCTCA
*
38552546 TTCTCCTTCTCCTTTCTTTC
1 TTCTCCTTCTCCTTTCTTCC
38552566 TTCTCCTTCTTCCTTT-TTCC
1 TTCTCCTTC-TCCTTTCTTCC
38552586 TTCT
1 TTCT
38552590 TTTTTTCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (20 bp):
TTCTCCTTCTCCTTTCTTCC
Found at i:38553680 original size:13 final size:12
Alignment explanation
Indices: 38553657--38553690 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
38553647 AGTTACGTTA
38553657 TTTTA-TTTTAT
1 TTTTATTTTTAT
38553668 TTTTACTTTTTAT
1 TTTTA-TTTTTAT
38553681 TTTTATTTTT
1 TTTTATTTTT
38553691 CTCTCCATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 5 0.24
12 5 0.24
13 11 0.52
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTATTTTTAT
Found at i:38553690 original size:6 final size:6
Alignment explanation
Indices: 38553657--38553690 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
38553647 AGTTACGTTA
38553657 TTTTA- TTTTAT TTTTACT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTA-T TTTTAT TTTTAT TTTT
38553691 CTCTCCATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.19
6 16 0.59
7 6 0.22
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTAT
Found at i:38554284 original size:8 final size:8
Alignment explanation
Indices: 38554271--38554298 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
38554261 TATAAAAATT
38554271 AAACCCGA
1 AAACCCGA
38554279 AAACCCGA
1 AAACCCGA
38554287 AAACCCGA
1 AAACCCGA
38554295 AAAC
1 AAAC
38554299 AAAGAACCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.54, C:0.36, G:0.11, T:0.00
Consensus pattern (8 bp):
AAACCCGA
Found at i:38554486 original size:24 final size:24
Alignment explanation
Indices: 38554470--38554544 Score: 132
Period size: 24 Copynumber: 3.1 Consensus size: 24
38554460 AGTTTGACTC
38554470 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
38554494 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
* *
38554518 AAACAATTAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAATTG
38554542 AAA
1 AAA
38554545 GATTATTTCT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.55, C:0.09, G:0.12, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:38558668 original size:17 final size:18
Alignment explanation
Indices: 38558637--38558672 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
38558627 TGTTCTTCGA
*
38558637 TAAATTTATTTAATTAAT
1 TAAATTTATTCAATTAAT
38558655 TAAA-TTATTCAATTAAT
1 TAAATTTATTCAATTAAT
38558672 T
1 T
38558673 TGACATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
TAAATTTATTCAATTAAT
Found at i:38559347 original size:13 final size:13
Alignment explanation
Indices: 38559329--38559393 Score: 78
Period size: 13 Copynumber: 5.0 Consensus size: 13
38559319 TTAAACCAAG
*
38559329 CTTTTCAAAAGTA
1 CTTTTCAAAAGCA
*
38559342 CTTTTCAAAATCA
1 CTTTTCAAAAGCA
*
38559355 CTTTTCCAAAGCA
1 CTTTTCAAAAGCA
*
38559368 CTTTTTAAAAGCA
1 CTTTTCAAAAGCA
38559381 -TTTCTCAAAAGCA
1 CTTT-TCAAAAGCA
38559394 ATGCTAAACT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
12 3 0.07
13 41 0.93
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (13 bp):
CTTTTCAAAAGCA
Found at i:38603791 original size:31 final size:31
Alignment explanation
Indices: 38603755--38603823 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
38603745 TTATAATATG
* * *
38603755 GTCACTAAACTATTTGAAAATTTTTATTTAA
1 GTCACTAAACTATGTGAAAATTGTCATTTAA
* *
38603786 GTCACTAAATTATGTGAAAGTTGTCATTTAA
1 GTCACTAAACTATGTGAAAATTGTCATTTAA
38603817 GTCACTA
1 GTCACTA
38603824 GGCTATTAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.41
Consensus pattern (31 bp):
GTCACTAAACTATGTGAAAATTGTCATTTAA
Found at i:38609724 original size:16 final size:16
Alignment explanation
Indices: 38609713--38609750 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
38609703 GGAATAAAGG
38609713 TGTAATGAAATAGAGC
1 TGTAATGAAATAGAGC
*
38609729 TGTAATGGAATAGAGC
1 TGTAATGAAATAGAGC
38609745 TGTAAT
1 TGTAAT
38609751 CAGTAATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.29
Consensus pattern (16 bp):
TGTAATGAAATAGAGC
Found at i:38609821 original size:39 final size:43
Alignment explanation
Indices: 38609732--38609836 Score: 112
Period size: 46 Copynumber: 2.5 Consensus size: 43
38609722 ATAGAGCTGT
*
38609732 AATGGAATAGAGCTGTAATCAGTAATTCAATTGTTTGGTTGATTGA
1 AATGGAATAGAGCTGTAAT-AATAATTC-ATTG-TTGGTTGATTGA
* *
38609778 AATGGAATAGAGCTGTAATAAT-ATTC-TTG-TGTTTGGTTG-
1 AATGGAATAGAGCTGTAATAATAATTCATTGTTGGTTGATTGA
38609817 AATGGAAT-GATGCTGTAATA
1 AATGGAATAGA-GCTGTAATA
38609837 GTATAAGAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
38 2 0.04
39 17 0.31
40 8 0.15
42 3 0.05
44 4 0.07
45 2 0.04
46 19 0.35
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.37
Consensus pattern (43 bp):
AATGGAATAGAGCTGTAATAATAATTCATTGTTGGTTGATTGA
Found at i:38609953 original size:26 final size:26
Alignment explanation
Indices: 38609913--38610013 Score: 94
Period size: 26 Copynumber: 3.7 Consensus size: 26
38609903 CTTATTAAAT
*
38609913 TTTAATAAGATTATTATTAAATATAA
1 TTTAATAAAATTATTATTAAATATAA
* *
38609939 TTTAATAAAAATATTAATTAATTTAATTATAT
1 TTTAAT--AAA-ATT-ATT-A-TTAAATATAA
* *
38609971 TTTAATATAATTATTATTAAATAAAA
1 TTTAATAAAATTATTATTAAATATAA
*
38609997 TTTAATAAAATAATTAT
1 TTTAATAAAATTATTAT
38610014 AATTTAATAA
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
26 28 0.47
27 1 0.02
28 5 0.08
29 6 0.10
30 5 0.08
31 1 0.02
32 14 0.23
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (26 bp):
TTTAATAAAATTATTATTAAATATAA
Found at i:38609984 original size:58 final size:57
Alignment explanation
Indices: 38609906--38610066 Score: 204
Period size: 58 Copynumber: 2.8 Consensus size: 57
38609896 GATTATGCTT
*
38609906 ATTAAATTTTAATA-AGATTATTATTAAATATAATTTAATAAAAAT-ATTAATTAATTTA
1 ATTATATTTTAATATA-ATTATTATTAAATATAATTTAATAAAAATAATT-A-TAATTTA
*
38609964 ATTATATTTTAATATAATTATTATTAAATAAAATTTAAT-AAAATAATTATAATTTA
1 ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATTATAATTTA
* *
38610020 ATAATATTTTTAATATAATTATTATTAAAATATGAA-TTAGTAAAAAT
1 ATTATA-TTTTAATATAATTATTATT-AAATAT-AATTTAATAAAAAT
38610067 TATAATATAT
Statistics
Matches: 92, Mismatches: 5, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
56 12 0.13
57 25 0.27
58 47 0.51
59 8 0.09
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (57 bp):
ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATTATAATTTA
Found at i:38610051 original size:26 final size:28
Alignment explanation
Indices: 38609911--38610052 Score: 109
Period size: 32 Copynumber: 5.0 Consensus size: 28
38609901 TGCTTATTAA
38609911 ATTTTAATA-AGATTATTATT-A-AATAT
1 ATTTTAATATA-ATTATTATTAATAATAT
* * *
38609937 AATTTAATAAAAATATTAATTAATTTAATTAT
1 ATTTTAATATAATTATT-ATTAA--TAA-TAT
38609969 ATTTTAATATAATTATTATTAAATAA-A-
1 ATTTTAATATAATTATTATT-AATAATAT
* *
38609996 ATTTAATAAAATAATTATAATTTAATAATAT
1 ATTT--TAATATAATTATTA-TTAATAATAT
38610027 -TTTTAATATAATTATTATTAA-AATAT
1 ATTTTAATATAATTATTATTAATAATAT
38610053 GAATTAGTAA
Statistics
Matches: 94, Mismatches: 9, Indels: 26
0.73 0.07 0.20
Matches are distributed among these distances:
26 18 0.19
27 12 0.13
28 14 0.15
29 17 0.18
30 9 0.10
31 5 0.05
32 19 0.20
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.49
Consensus pattern (28 bp):
ATTTTAATATAATTATTATTAATAATAT
Found at i:38610069 original size:25 final size:24
Alignment explanation
Indices: 38610040--38610090 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
38610030 TAATATAATT
*
38610040 ATTATTAAAATATGA-ATTAGTAAAA
1 ATTA-TAAAATATAATATTAG-AAAA
*
38610065 ATTATAATATATAATATTAGAAAA
1 ATTATAAAATATAATATTAGAAAA
38610089 AT
1 AT
38610091 AATATATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (24 bp):
ATTATAAAATATAATATTAGAAAA
Found at i:38619965 original size:49 final size:49
Alignment explanation
Indices: 38619893--38619990 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 49
38619883 CTGCTGCCTT
*
38619893 CTAATTTACAGCAAAGCACTCCATTGTGCGCATTAATTAGCAGTTAATA
1 CTAATTTACAGCAAAGCACTCCATTGTACGCATTAATTAGCAGTTAATA
*
38619942 CTAATTTACAGCAACGCACTCCATTGTACGCATTAATTAGCAGTTAATA
1 CTAATTTACAGCAAAGCACTCCATTGTACGCATTAATTAGCAGTTAATA
38619991 AGTTTGCATG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31
Consensus pattern (49 bp):
CTAATTTACAGCAAAGCACTCCATTGTACGCATTAATTAGCAGTTAATA
Found at i:38621997 original size:22 final size:22
Alignment explanation
Indices: 38621958--38622003 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
38621948 ATGAAATGAT
* * *
38621958 AACAAAATAGTAAGAAAACAAC
1 AACAAAACAATAAAAAAACAAC
*
38621980 AACAAAACAATAAAAAAATAAC
1 AACAAAACAATAAAAAAACAAC
38622002 AA
1 AA
38622004 TTTTATTTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.74, C:0.13, G:0.04, T:0.09
Consensus pattern (22 bp):
AACAAAACAATAAAAAAACAAC
Found at i:38630168 original size:25 final size:25
Alignment explanation
Indices: 38630140--38630192 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
38630130 ATAAATCGAG
38630140 TTTTTTCCTCAATTAAACTCTT-TTA
1 TTTTTTCC-CAATTAAACTCTTATTA
* * *
38630165 TTTTTTTCCAGTTAAATTCTTATTA
1 TTTTTTCCCAATTAAACTCTTATTA
38630190 TTT
1 TTT
38630193 CAATGATATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.23, C:0.15, G:0.02, T:0.60
Consensus pattern (25 bp):
TTTTTTCCCAATTAAACTCTTATTA
Found at i:38630950 original size:31 final size:31
Alignment explanation
Indices: 38630896--38630975 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 31
38630886 ATATTAAATT
*
38630896 AATAATGATAAAATTATACTTTAATTCC-TTCAAA
1 AATAAT-A-AAAATTATAATTTAA--CCTTTCAAA
*
38630930 AATAATAAAAATT-TAATTTAACCTTTTAAA
1 AATAATAAAAATTATAATTTAACCTTTCAAA
*
38630960 ATTAATAAAAA-TATAA
1 AATAATAAAAATTATAA
38630976 ACTATTAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
29 3 0.07
30 18 0.44
31 7 0.17
32 6 0.15
33 1 0.02
34 6 0.15
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.38
Consensus pattern (31 bp):
AATAATAAAAATTATAATTTAACCTTTCAAA
Found at i:38634271 original size:15 final size:16
Alignment explanation
Indices: 38634246--38634276 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
38634236 ATATAAGCAA
38634246 AAATATTTTTAAGAAT
1 AAATATTTTTAAGAAT
38634262 AAAT-TTTTTAAGAAT
1 AAATATTTTTAAGAAT
38634277 CTGATAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
AAATATTTTTAAGAAT
Found at i:38638293 original size:30 final size:30
Alignment explanation
Indices: 38638252--38638318 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
38638242 CACGATGGTC
* *
38638252 GATATTTGGGTGGTGGTGG-AACAGACGACG
1 GATAATTGGGTGGTGG-GGAAACAGAAGACG
38638282 GATAATTGGGTGGTGGGGAAACAGAAGACG
1 GATAATTGGGTGGTGGGGAAACAGAAGACG
38638312 GATAATT
1 GATAATT
38638319 TTGAACTCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 2 0.06
30 32 0.94
ACGTcount: A:0.30, C:0.07, G:0.40, T:0.22
Consensus pattern (30 bp):
GATAATTGGGTGGTGGGGAAACAGAAGACG
Found at i:38638471 original size:108 final size:108
Alignment explanation
Indices: 38638282--38638503 Score: 336
Period size: 108 Copynumber: 2.1 Consensus size: 108
38638272 ACAGACGACG
* * *
38638282 GATAATTGGGTGGTGGGGAAACAGAAGACGGATAATTTTGAACTCCATAACCAGGTGCATAAGAC
1 GATAATGGGGTGGTGGGGAAACAGAAGACGGATAATCTTGAACTACATAACCAGGTGCATAAGAC
* *
38638347 TGTTGGTATTGTGGTGGATATTCATCCATAGGATGATTTTGAT
66 TGTTGGTATTGTGGTGGATATCCATCCATAGGAGGATTTTGAT
* * * * * **
38638390 GATAATGGGGTGGTGGGGGAACAGACGGCGGATAATCTTGAGCTACATAACTAGGTGCATAAGGT
1 GATAATGGGGTGGTGGGGAAACAGAAGACGGATAATCTTGAACTACATAACCAGGTGCATAAGAC
38638455 TGTTGGTATTGTGGTGGATATCCATCCATAGGAGGATTTTGAT
66 TGTTGGTATTGTGGTGGATATCCATCCATAGGAGGATTTTGAT
38638498 GATAAT
1 GATAAT
38638504 TGGTCCGCAA
Statistics
Matches: 102, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
108 102 1.00
ACGTcount: A:0.28, C:0.11, G:0.31, T:0.30
Consensus pattern (108 bp):
GATAATGGGGTGGTGGGGAAACAGAAGACGGATAATCTTGAACTACATAACCAGGTGCATAAGAC
TGTTGGTATTGTGGTGGATATCCATCCATAGGAGGATTTTGAT
Found at i:38638998 original size:30 final size:32
Alignment explanation
Indices: 38638963--38639033 Score: 87
Period size: 30 Copynumber: 2.3 Consensus size: 32
38638953 CAGAGCCCCC
*
38638963 AAAATTTTGGAAAATTGTT-GTTAGG-CCT-TT
1 AAAATTTTGGAAAATT-TTAATTAGGTCCTATT
38638993 AAAATTTAT-GAAAATTTTAATTAGGTCCTATT
1 AAAATTT-TGGAAAATTTTAATTAGGTCCTATT
38639025 AAAATTTTG
1 AAAATTTTG
38639034 CAAATTATCA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
29 2 0.06
30 19 0.54
31 5 0.14
32 9 0.26
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.44
Consensus pattern (32 bp):
AAAATTTTGGAAAATTTTAATTAGGTCCTATT
Found at i:38640306 original size:29 final size:29
Alignment explanation
Indices: 38640247--38640306 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
38640237 TGTTATAAAG
* *
38640247 AATGGATCAAATTAGTCCCTCTATTACTA
1 AATGGATCAAATTAGTCCCTATACTACTA
* *
38640276 AATGGATCAATTTAGTCCCTATACTATTA
1 AATGGATCAAATTAGTCCCTATACTACTA
38640305 AA
1 AA
38640307 AAAAATCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (29 bp):
AATGGATCAAATTAGTCCCTATACTACTA
Found at i:38643577 original size:152 final size:150
Alignment explanation
Indices: 38643370--38643764 Score: 384
Period size: 152 Copynumber: 2.6 Consensus size: 150
38643360 GGAAGGTGTG
* ** * * *
38643370 GGTTCGAGTGTGCTGAAGCGTATTATCTTCTTATTTATGAGTTTGG-AGGGGTTATGAGTAGTTC
1 GGTTCAAGTGTGCTGAAGCACATTATCCTCTTATTTATG-GGTTGGAAGGGATTATGAGTAGTTC
* * * * * * *
38643434 TAGACATTGTATCAAAAAATTAATAAGTACTGTCGATTGAGTTTTAGCTTAATTGATATGGGTAT
65 TA-ATATTGTGTCAAAAAATTAATAAGTACTGTCGATTAAGTTTTAACTCAATTAACATGGGTAT
*
38643499 TGTTG-TCAATACAGGAGAACGTA
129 TATTGCT-AATACAGGAGAAC-TA
* * * *
38643522 GGTTCAAGTGTGCTGAAGCACATTGTCCTCTTATTTATGGGTTGGAAGGGATTATGGGTAATACT
1 GGTTCAAGTGTGCTGAAGCACATTATCCTCTTATTTATGGGTTGGAAGGGATTATGAGTAGTTCT
* * *
38643587 AAGTATTATGTCAAAATAA-TAATAAGTATTGTCGATTAAGTTTTAACTCGATTAACATGGGTAT
66 AA-TATTGTGTCAAAA-AATTAATAAGTACTGTCGATTAAGTTTTAACTCAATTAACATGGGTAT
* * *
38643651 TATTGCTAATGCAGGAGGACTT
129 TATTGCTAATACAGGAGAACTA
* * * * * * *
38643673 GAGTTCAAGTGCGTTAAAGCACATTATCCTCCTATTTATGTGTT-GAGAGAGACTATGAGTAGTT
1 G-GTTCAAGTGTGCTGAAGCACATTATCCTCTTATTTATGGGTTGGA-AGGGATTATGAGTAGTT
*
38643737 TTAAATATTGTGTCAAAAAATTTAATAA
64 CT-AATATTGTGTCAAAAAA-TTAATAA
38643765 ATATTGAATG
Statistics
Matches: 197, Mismatches: 37, Indels: 17
0.78 0.15 0.07
Matches are distributed among these distances:
151 12 0.06
152 174 0.88
153 11 0.06
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (150 bp):
GGTTCAAGTGTGCTGAAGCACATTATCCTCTTATTTATGGGTTGGAAGGGATTATGAGTAGTTCT
AATATTGTGTCAAAAAATTAATAAGTACTGTCGATTAAGTTTTAACTCAATTAACATGGGTATTA
TTGCTAATACAGGAGAACTA
Found at i:38659530 original size:3 final size:3
Alignment explanation
Indices: 38659522--38659565 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
38659512 AGATAAATAG
38659522 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
38659566 GAGCTTTGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:38665059 original size:19 final size:19
Alignment explanation
Indices: 38665035--38665108 Score: 69
Period size: 19 Copynumber: 3.8 Consensus size: 19
38665025 ATCCAGGTAA
*
38665035 AATTTTTATGATTTTTTAT
1 AATTTTTATGATTTTATAT
* *
38665054 AATTTTTATAAATTTATAT
1 AATTTTTATGATTTTATAT
* * *
38665073 CAATTTTAAT-ATTTGAAAT
1 -AATTTTTATGATTTTATAT
38665092 AATATTTTATGATTTTA
1 AAT-TTTTATGATTTTA
38665109 ATAGGTTTTT
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
18 3 0.07
19 27 0.63
20 13 0.30
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.58
Consensus pattern (19 bp):
AATTTTTATGATTTTATAT
Found at i:38665128 original size:20 final size:21
Alignment explanation
Indices: 38665103--38665150 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
38665093 ATATTTTATG
* * *
38665103 ATTTTAATAGGTTTTTA-AGA
1 ATTTTAACACGTTTTTATAAA
38665123 ATTTTAACACGTTTTTATAAA
1 ATTTTAACACGTTTTTATAAA
38665144 ATTTTAA
1 ATTTTAA
38665151 ATAATTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (21 bp):
ATTTTAACACGTTTTTATAAA
Found at i:38665244 original size:20 final size:20
Alignment explanation
Indices: 38665219--38665260 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
38665209 TTTACAAGTT
*
38665219 TTAATTTTTATAAGTTTATA
1 TTAATTTTAATAAGTTTATA
**
38665239 TTAATTTTAATACTTTTATA
1 TTAATTTTAATAAGTTTATA
38665259 TT
1 TT
38665261 TTAAACCACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
TTAATTTTAATAAGTTTATA
Found at i:38671082 original size:19 final size:19
Alignment explanation
Indices: 38671046--38671083 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
38671036 TTAAAATTAA
* *
38671046 ATAATTGGATGATCATTTT
1 ATAATTGGATAATAATTTT
38671065 ATAATTGGATAATAATTTT
1 ATAATTGGATAATAATTTT
38671084 TTTAATAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (19 bp):
ATAATTGGATAATAATTTT
Found at i:38671148 original size:33 final size:34
Alignment explanation
Indices: 38671080--38671148 Score: 104
Period size: 36 Copynumber: 2.0 Consensus size: 34
38671070 TGGATAATAA
38671080 TTTTTTTAATAATTAGATTACCATTTTGCAACAATT
1 TTTTTTTAATAATTAGATTACCATTTTG--ACAATT
*
38671116 TTTTTTTAATAATTAGGTTACCATTTTG-CAATT
1 TTTTTTTAATAATTAGATTACCATTTTGACAATT
38671149 AACTTTAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 5 0.16
36 27 0.84
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.52
Consensus pattern (34 bp):
TTTTTTTAATAATTAGATTACCATTTTGACAATT
Found at i:38678334 original size:11 final size:11
Alignment explanation
Indices: 38678298--38678371 Score: 53
Period size: 11 Copynumber: 6.8 Consensus size: 11
38678288 AGGACTATCC
*
38678298 ATAATATTTTT
1 ATAATATTTAT
* * *
38678309 AAAATTTTTAA
1 ATAATATTTAT
38678320 ATAATATTTAT
1 ATAATATTTAT
38678331 ATAATA-TTATT
1 ATAATATTTA-T
*
38678342 TTAATATTTA-
1 ATAATATTTAT
* *
38678352 ATAAAATTTTT
1 ATAATATTTAT
*
38678363 ATATTATTT
1 ATAATATTT
38678372 TAATGTTTAT
Statistics
Matches: 47, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
10 10 0.21
11 34 0.72
12 3 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
ATAATATTTAT
Found at i:38678335 original size:33 final size:31
Alignment explanation
Indices: 38678298--38678372 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 31
38678288 AGGACTATCC
* *
38678298 ATAATATTTTTAAAATTTTTAAATAATATTTAT
1 ATAATATTTTT-AAATATTT-AATAAAATTTAT
* *
38678331 ATAATATTATTTTAATATTTAATAAAATTTTT
1 ATAATATT-TTTAAATATTTAATAAAATTTAT
*
38678363 ATATTATTTT
1 ATAATATTTT
38678373 AATGTTTATA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 2 0.06
32 17 0.47
33 14 0.39
34 3 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (31 bp):
ATAATATTTTTAAATATTTAATAAAATTTAT
Found at i:38696054 original size:31 final size:31
Alignment explanation
Indices: 38696019--38696077 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
38696009 ACCCAATAAC
38696019 TTAAATAAAAACTTACGAA-TAGTTCAATGAT
1 TTAAATAAAAACTTACGAATTA-TTCAATGAT
* *
38696050 TTAAATGAAAACTTCCGAATTATTCAAT
1 TTAAATAAAAACTTACGAATTATTCAAT
38696078 ATCCATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 23 0.92
32 2 0.08
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.34
Consensus pattern (31 bp):
TTAAATAAAAACTTACGAATTATTCAATGAT
Found at i:38701524 original size:29 final size:32
Alignment explanation
Indices: 38701487--38701568 Score: 84
Period size: 30 Copynumber: 2.7 Consensus size: 32
38701477 TTAAATAAAA
*
38701487 AAATCAATAATTAAAA-CATATAAA-A-TTATT
1 AAAT-AATAATTAAAATAATATAAATATTTATT
* *
38701517 AAATAATAAATAAAATAATATAAATATTTTTT
1 AAATAATAATTAAAATAATATAAATATTTATT
38701549 AAA-AA-AATTAAAATTAATAT
1 AAATAATAATTAAAA-TAATAT
38701569 GGGCGAGCCT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
29 10 0.23
30 18 0.41
31 9 0.20
32 7 0.16
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (32 bp):
AAATAATAATTAAAATAATATAAATATTTATT
Found at i:38702713 original size:21 final size:21
Alignment explanation
Indices: 38702646--38702720 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
38702636 TTAAATTCAC
* *
38702646 GAATCTTAAATCTTAAACTTT
1 GAATCTTAAATCTAAAATTTT
* **
38702667 GAATATTAAA-CTCAAAATCAT
1 GAATCTTAAATCT-AAAATTTT
38702688 GAATCTTAAATCTAAAATTTT
1 GAATCTTAAATCTAAAATTTT
* *
38702709 AAATCTCAAATC
1 GAATCTTAAATC
38702721 ATGAACTCAA
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 2 0.05
21 38 0.90
22 2 0.05
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (21 bp):
GAATCTTAAATCTAAAATTTT
Found at i:38702886 original size:36 final size:34
Alignment explanation
Indices: 38702820--38702886 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
38702810 TTTTGAGTTC
*
38702820 GAAAAAAATTATCAAAATTATATATCAATTACAT
1 GAAAAAAATTATCAAAATTATAAATCAATTACAT
*
38702854 GAAAAAAATTACTGAAATATTATTAAAT-AATTA
1 GAAAAAAATTA-TCAAA-ATTA-TAAATCAATTA
38702887 AAAAAATCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 11 0.39
35 4 0.14
36 9 0.32
37 4 0.14
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (34 bp):
GAAAAAAATTATCAAAATTATAAATCAATTACAT
Found at i:38707475 original size:20 final size:21
Alignment explanation
Indices: 38707430--38707475 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
38707420 CTTCCAATAA
*
38707430 AAAATAAAATTATTAAATATT
1 AAAATAAAATTAATAAATATT
*
38707451 AAAATAAAA-TAATATATATT
1 AAAATAAAATTAATAAATATT
*
38707471 TAAAT
1 AAAAT
38707476 TTTTTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAATAAAATTAATAAATATT
Found at i:38714699 original size:3 final size:3
Alignment explanation
Indices: 38714691--38714733 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
38714681 ATCTCTGTGC
38714691 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
38714734 TCATCACCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:38715677 original size:203 final size:202
Alignment explanation
Indices: 38715328--38715728 Score: 694
Period size: 203 Copynumber: 2.0 Consensus size: 202
38715318 GACATCAAGG
* **
38715328 ATGAGCTGTCCAACCAAATTAACTCATATAATTTAATTTAGATTCGAATTGTGTTAGTTACATTT
1 ATGAGCTGTCCAACCAAATTAACTCATATAATTTAATTTAGATTCAAATTGTACTAGTTACATTT
*
38715393 TTATTAAATAGAAGAAGAGTGAAAAGATTTTTTGAGTTCCCCGGAATAAAGTTATATTTTTATAG
66 CTATTAAATAGAAGAAGAGTGAAAAGATTTTTTGAGTTCCCCGGAATAAAGTTATATTTTTATAG
* *
38715458 TAGTAAAATTAAAATTTCAACATTCTAATAATTTATTTTTTTTATAATTTTTAAATAATTAAATC
131 TAGTAAAATTAAAATTTCAACATTCCAATAATTTA-TTTTTTTATAATTTTTAAATAATTAAATA
38715523 ATTTAAGA
195 ATTTAAGA
*
38715531 ATGAGCTGTCTAACCAAATTAACTCATATAATTTAATTTAGATTCAAATTGTACTAGTTACATTT
1 ATGAGCTGTCCAACCAAATTAACTCATATAATTTAATTTAGATTCAAATTGTACTAGTTACATTT
* *
38715596 CTGTTAAATAGAGGAAGAGTGAAAAGATTTTTTGAGTTCCCCGGAATAAAGTTATATTTTTATAG
66 CTATTAAATAGAAGAAGAGTGAAAAGATTTTTTGAGTTCCCCGGAATAAAGTTATATTTTTATAG
* *
38715661 TAGTAAAATTAAAATTTCAACATTCCAATAGTTTATTTTTTTATAATTTTTAAATGATTAAATAA
131 TAGTAAAATTAAAATTTCAACATTCCAATAATTTATTTTTTTATAATTTTTAAATAATTAAATAA
38715726 TTT
196 TTT
38715729 TTTTCTCATT
Statistics
Matches: 187, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
202 31 0.17
203 156 0.83
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (202 bp):
ATGAGCTGTCCAACCAAATTAACTCATATAATTTAATTTAGATTCAAATTGTACTAGTTACATTT
CTATTAAATAGAAGAAGAGTGAAAAGATTTTTTGAGTTCCCCGGAATAAAGTTATATTTTTATAG
TAGTAAAATTAAAATTTCAACATTCCAATAATTTATTTTTTTATAATTTTTAAATAATTAAATAA
TTTAAGA
Found at i:38715744 original size:30 final size:31
Alignment explanation
Indices: 38715695--38715753 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
38715685 CCAATAGTTT
* *
38715695 ATTTTTTTATAATT-TTTAAATGATTAAATA
1 ATTTTTTTATAATTCTTAAAAAGATTAAATA
* *
38715725 ATTTTTTTCTCATTCTTAAAAAGATTAAA
1 ATTTTTTTATAATTCTTAAAAAGATTAAA
38715754 GTGTAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 12 0.50
31 12 0.50
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (31 bp):
ATTTTTTTATAATTCTTAAAAAGATTAAATA
Found at i:38716339 original size:10 final size:9
Alignment explanation
Indices: 38716314--38716338 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
38716304 ATTTTATTAA
38716314 TTTAAAATT
1 TTTAAAATT
38716323 TTTAAAATT
1 TTTAAAATT
38716332 TTTAAAA
1 TTTAAAA
38716339 AACAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
TTTAAAATT
Found at i:38721553 original size:50 final size:50
Alignment explanation
Indices: 38721408--38721609 Score: 293
Period size: 50 Copynumber: 4.1 Consensus size: 50
38721398 GTGTCTTCAT
* *
38721408 CATCAAACTTAAAGAGCGACCACCAGCTTTTATGTTGTAACGTGGCAATCG
1 CATCAACCTTAAA-TGCGACCACCAGCTTTTATGTTGTAACGTGGCAATCG
38721459 CATCAACC-TAAATGCGACCACCAGCTTTTATGTTGTAACGTGGCAATCG
1 CATCAACCTTAAATGCGACCACCAGCTTTTATGTTGTAACGTGGCAATCG
* * *
38721508 CATCAACCTTACATGCAACAACCAGCTTTTATGTTGTAACGTGGCAATCG
1 CATCAACCTTAAATGCGACCACCAGCTTTTATGTTGTAACGTGGCAATCG
* * * *
38721558 CATCAACCTTATATGCGACCACCAGC--TTACGATGTAACGTGGCAATTG
1 CATCAACCTTAAATGCGACCACCAGCTTTTATGTTGTAACGTGGCAATCG
38721606 CATC
1 CATC
38721610 TTCTTTAGCC
Statistics
Matches: 139, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
48 23 0.17
49 44 0.32
50 65 0.47
51 7 0.05
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (50 bp):
CATCAACCTTAAATGCGACCACCAGCTTTTATGTTGTAACGTGGCAATCG
Found at i:38728051 original size:133 final size:134
Alignment explanation
Indices: 38727858--38728140 Score: 487
Period size: 133 Copynumber: 2.1 Consensus size: 134
38727848 ACCAAAGATA
38727858 ATAACATTATTTTTTTGGTGAATTATAAGATAAAAGATAAAGTCCTAATAGCAATGCAATTAACG
1 ATAACATTATTTTTTTGGTGAATTATAAGATAAAAGATAAAGTCCTAATAGCAATGCAATTAACG
* * *
38727923 CGACTCAAACTCAAACCACACTTGGGGTGATAAACATCCTAATCATCAGGCCAACATACGGATTC
66 CGACTCAAACTCAAACCACACTTGGAGTGATAAACATCCTAACCATCAGGCCAACATACAGATTC
38727988 AAAT
131 AAAT
* *
38727992 ATAACATTATTTTTTTGGTGAATTATAAGAT-AAAGATAAAGTCTTAATAGCAATGCAATTAGCG
1 ATAACATTATTTTTTTGGTGAATTATAAGATAAAAGATAAAGTCCTAATAGCAATGCAATTAACG
* **
38728056 CGACTCAAACTCAGACCACACTTGGAGTGATAAACATTTTAACCATCAGGCCAACATACAGATTC
66 CGACTCAAACTCAAACCACACTTGGAGTGATAAACATCCTAACCATCAGGCCAACATACAGATTC
38728121 AAAT
131 AAAT
38728125 ATAACATTATTTTTTT
1 ATAACATTATTTTTTT
38728141 TATATAATAT
Statistics
Matches: 141, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
133 110 0.78
134 31 0.22
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (134 bp):
ATAACATTATTTTTTTGGTGAATTATAAGATAAAAGATAAAGTCCTAATAGCAATGCAATTAACG
CGACTCAAACTCAAACCACACTTGGAGTGATAAACATCCTAACCATCAGGCCAACATACAGATTC
AAAT
Found at i:38730761 original size:34 final size:34
Alignment explanation
Indices: 38730685--38730763 Score: 122
Period size: 34 Copynumber: 2.3 Consensus size: 34
38730675 TTGAAGGTCC
*
38730685 ACTCGAAAAATGAGAGGGTTTGGAGAAAATATAA
1 ACTCGAAAAATGAGAGGATTTGGAGAAAATATAA
* * *
38730719 AATAGAAAAATGAGAGGATTTGGAGAAAATATAG
1 ACTCGAAAAATGAGAGGATTTGGAGAAAATATAA
38730753 ACTCGAAAAAT
1 ACTCGAAAAAT
38730764 AGGCTTGGAC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.51, C:0.05, G:0.24, T:0.20
Consensus pattern (34 bp):
ACTCGAAAAATGAGAGGATTTGGAGAAAATATAA
Found at i:38734731 original size:25 final size:24
Alignment explanation
Indices: 38734703--38734767 Score: 80
Period size: 22 Copynumber: 2.8 Consensus size: 24
38734693 TATGTTGTTG
*
38734703 TTTTGTTATTATTATTATGCTATGA
1 TTTTGTTATTATTATT-TGATATGA
*
38734728 TTTTGTTATTA-TA-TTGATATTA
1 TTTTGTTATTATTATTTGATATGA
*
38734750 TTTTGTTGTTATTATTTG
1 TTTTGTTATTATTATTTG
38734768 GATAATATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 16 0.46
23 3 0.09
24 5 0.14
25 11 0.31
ACGTcount: A:0.22, C:0.02, G:0.12, T:0.65
Consensus pattern (24 bp):
TTTTGTTATTATTATTTGATATGA
Found at i:38734761 original size:11 final size:11
Alignment explanation
Indices: 38734711--38734762 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
38734701 TGTTTTGTTA
*
38734711 TTATTATTATG
1 TTATTATTTTG
* *
38734722 CTATGATTTTG
1 TTATTATTTTG
*
38734733 TTATTATATTG
1 TTATTATTTTG
*
38734744 ATATTATTTTG
1 TTATTATTTTG
*
38734755 TTGTTATT
1 TTATTATT
38734763 ATTTGGATAA
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.23, C:0.02, G:0.12, T:0.63
Consensus pattern (11 bp):
TTATTATTTTG
Found at i:38735627 original size:16 final size:17
Alignment explanation
Indices: 38735598--38735631 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
38735588 TCGATTTATA
38735598 ATTTTTTTAAATGATTTT
1 ATTTTTTT-AATGATTTT
38735616 ATTTTTTT-ATGATTTT
1 ATTTTTTTAATGATTTT
38735632 TAATTATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
18 8 0.50
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
ATTTTTTTAATGATTTT
Found at i:38740136 original size:21 final size:20
Alignment explanation
Indices: 38740098--38740137 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
38740088 ATCAGAGAAG
*
38740098 AAAAAACGGGAAGAAAAATC
1 AAAAAACGGGAAAAAAAATC
38740118 AAAAAACGGGAAAAGAAAAT
1 AAAAAACGGGAAAA-AAAAT
38740138 TCGGAGGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.68, C:0.07, G:0.20, T:0.05
Consensus pattern (20 bp):
AAAAAACGGGAAAAAAAATC
Found at i:38740982 original size:12 final size:12
Alignment explanation
Indices: 38740954--38740997 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
38740944 ATTCGACTTA
38740954 AATAAAAATG-T
1 AATAAAAATGTT
38740965 --TAAAAATGTT
1 AATAAAAATGTT
38740975 AATAAAAATGTT
1 AATAAAAATGTT
38740987 AAATAAAAATG
1 -AATAAAAATG
38740998 CCATAAATCC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.28
10 1 0.03
12 10 0.34
13 10 0.34
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (12 bp):
AATAAAAATGTT
Found at i:38740982 original size:13 final size:13
Alignment explanation
Indices: 38740965--38740997 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
38740955 ATAAAAATGT
38740965 TAAAAATGTT-AA
1 TAAAAATGTTAAA
38740977 TAAAAATGTTAAA
1 TAAAAATGTTAAA
38740990 TAAAAATG
1 TAAAAATG
38740998 CCATAAATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (13 bp):
TAAAAATGTTAAA
Found at i:38741057 original size:13 final size:14
Alignment explanation
Indices: 38741039--38741067 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
38741029 TTTTTTTATC
38741039 TAAATTTAT-TTTT
1 TAAATTTATATTTT
38741052 TAAATTTATATTTT
1 TAAATTTATATTTT
38741066 TA
1 TA
38741068 CTCAAAATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TAAATTTATATTTT
Found at i:38743363 original size:26 final size:26
Alignment explanation
Indices: 38743334--38743387 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
38743324 AGAAGCAGGA
*
38743334 TAGGATGATTTCTTCGAAAAGGAAGG
1 TAGGATGATTTCTTCCAAAAGGAAGG
38743360 TAGGATGATTTCTTCCAAAAGGAAGG
1 TAGGATGATTTCTTCCAAAAGGAAGG
38743386 TA
1 TA
38743388 TGAACATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.35, C:0.09, G:0.28, T:0.28
Consensus pattern (26 bp):
TAGGATGATTTCTTCCAAAAGGAAGG
Found at i:38747185 original size:11 final size:11
Alignment explanation
Indices: 38747169--38747198 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
38747159 TGGATTTCAA
38747169 TCTTCTTCTTT
1 TCTTCTTCTTT
38747180 TCTTCTTCTTT
1 TCTTCTTCTTT
38747191 TCTTCTTC
1 TCTTCTTC
38747199 CTACTGATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (11 bp):
TCTTCTTCTTT
Found at i:38748467 original size:27 final size:27
Alignment explanation
Indices: 38748414--38748468 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
38748404 ATAAGATTAT
** * * *
38748414 TAAAAAAATGTTTTAATGTTATTTCAA
1 TAAAAAAATGTTAAAATATGATGTCAA
38748441 TAAAAAAATGTTAAAATATGATGTCAA
1 TAAAAAAATGTTAAAATATGATGTCAA
38748468 T
1 T
38748469 CCATATGCTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (27 bp):
TAAAAAAATGTTAAAATATGATGTCAA
Found at i:38748581 original size:26 final size:26
Alignment explanation
Indices: 38748548--38748615 Score: 136
Period size: 26 Copynumber: 2.6 Consensus size: 26
38748538 TTTTTTATTT
38748548 AAAAATGTTACTTCAAAATCACAAAA
1 AAAAATGTTACTTCAAAATCACAAAA
38748574 AAAAATGTTACTTCAAAATCACAAAA
1 AAAAATGTTACTTCAAAATCACAAAA
38748600 AAAAATGTTACTTCAA
1 AAAAATGTTACTTCAA
38748616 TCATTAATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.56, C:0.15, G:0.04, T:0.25
Consensus pattern (26 bp):
AAAAATGTTACTTCAAAATCACAAAA
Found at i:38753343 original size:13 final size:13
Alignment explanation
Indices: 38753325--38753349 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38753315 AGTTTTTTTT
38753325 TTTTTAATTAATG
1 TTTTTAATTAATG
38753338 TTTTTAATTAAT
1 TTTTTAATTAAT
38753350 AAATATATTA
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:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATG
Found at i:38758725 original size:30 final size:30
Alignment explanation
Indices: 38758687--38758750 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
38758677 ATAATAGTAA
38758687 TTTTAATAACTTAA-AATTAAATTAAAAAT
1 TTTTAATAACTTAATAATTAAATTAAAAAT
* * * *
38758716 TTTTAAATAATTTAATCATTAAATTATAATT
1 TTTT-AATAACTTAATAATTAAATTAAAAAT
38758747 TTTT
1 TTTT
38758751 TAGTTAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 4 0.14
30 9 0.31
31 16 0.55
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (30 bp):
TTTTAATAACTTAATAATTAAATTAAAAAT
Found at i:38773264 original size:2 final size:2
Alignment explanation
Indices: 38773257--38773321 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
38773247 GTTCTTTCTT
38773257 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
38773299 TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC T
38773322 TATCTCTTTC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:38782045 original size:6 final size:6
Alignment explanation
Indices: 38782034--38782078 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
38782024 TACTCCCTCC
*
38782034 CTCACT CTCACT CTCACT CTCACT CTCACT CTCACT CTCAGT CTC
1 CTCACT CTCACT CTCACT CTCACT CTCACT CTCACT CTCACT CTC
38782079 TCACACACAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.16, C:0.49, G:0.02, T:0.33
Consensus pattern (6 bp):
CTCACT
Found at i:38783766 original size:18 final size:18
Alignment explanation
Indices: 38783743--38783777 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38783733 TAACTTTTCT
*
38783743 TTTCTTATATATTGAAAA
1 TTTCTTATATACTGAAAA
*
38783761 TTTCTTGTATACTGAAA
1 TTTCTTATATACTGAAA
38783778 TTGAATTCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.49
Consensus pattern (18 bp):
TTTCTTATATACTGAAAA
Found at i:38788999 original size:2 final size:2
Alignment explanation
Indices: 38788992--38789034 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
38788982 TAAGCAATCG
38788992 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
38789034 A
1 A
38789035 GGGAGATTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38794191 original size:23 final size:23
Alignment explanation
Indices: 38794133--38794192 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 23
38794123 AAAAAAAAAT
* * * *
38794133 AAATTATCTCTTAA-AAATGATG
1 AAATTATATATTAATAAATAATA
*
38794155 AAATTATAAATTAATAAATAATA
1 AAATTATATATTAATAAATAATA
*
38794178 AAATTATATTTTAAT
1 AAATTATATATTAAT
38794193 CTTCTAACTT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 11 0.37
23 19 0.63
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (23 bp):
AAATTATATATTAATAAATAATA
Found at i:38798906 original size:6 final size:6
Alignment explanation
Indices: 38798881--38798928 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
38798871 ATAAAAAGCA
38798881 TGCC-T TGCC-T TGCC-T TGCCTT TGCCTT TGCCTT TGCCTT TGCCTT
1 TGCCTT TGCCTT TGCCTT TGCCTT TGCCTT TGCCTT TGCCTT TGCCTT
38798926 TGC
1 TGC
38798929 TCCTTTGCCC
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 14 0.33
6 28 0.67
ACGTcount: A:0.00, C:0.35, G:0.19, T:0.46
Consensus pattern (6 bp):
TGCCTT
Found at i:38805683 original size:23 final size:24
Alignment explanation
Indices: 38805640--38805684 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
38805630 AATTATAGTA
38805640 AAAGAAATTGTTACAAGTGAATTG
1 AAAGAAATTGTTACAAGTGAATTG
*
38805664 AAAGAAATT-TTACAATTGAAT
1 AAAGAAATTGTTACAAGTGAAT
38805685 CAATTAACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.49, C:0.04, G:0.16, T:0.31
Consensus pattern (24 bp):
AAAGAAATTGTTACAAGTGAATTG
Found at i:38818866 original size:2 final size:2
Alignment explanation
Indices: 38818859--38818893 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
38818849 AATCAATGCT
38818859 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38818894 CTCTTTGAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38827588 original size:31 final size:31
Alignment explanation
Indices: 38827523--38827587 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
38827513 GAGAATTATT
38827523 AAAATTTTGATGGATCTAATTGAAAATTTTA
1 AAAATTTTGATGGATCTAATTGAAAATTTTA
*
38827554 AAAATTTTG-TGAGAT-TAA-TGAGAATTTCTA
1 AAAATTTTGATG-GATCTAATTGAAAATTT-TA
38827584 AAAA
1 AAAA
38827588 AAATTAGAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
29 8 0.26
30 11 0.35
31 12 0.39
ACGTcount: A:0.45, C:0.03, G:0.14, T:0.38
Consensus pattern (31 bp):
AAAATTTTGATGGATCTAATTGAAAATTTTA
Found at i:38827627 original size:122 final size:118
Alignment explanation
Indices: 38827416--38827684 Score: 271
Period size: 122 Copynumber: 2.2 Consensus size: 118
38827406 AATTTTTGGG
* * *
38827416 TTAATTAAAATTTTAAAAATTTTCGTGAGATTAGTGAGAATTTTTAAAAAATTTGAGTTTAATTA
1 TTAATTAAAATTTTAAAAATTTTCGTGAGATTAATGAGAATTTTAAAAAAATTAGAGTTTAATTA
** *
38827481 AATTCTTTTACAAAAAATTTAAAAGGCATAATGAGAATTATT-AAAATTTTGATGG-A
66 AA-TAATTTACAAAAAA--TAAAAGGCATAATGAG-ATTATTAAAAATTTAGA-GGAA
38827537 TCTAATTGAAAATTTTAAAAATTTT-GTGAGATTAATGAGAATTTCTAAAAAAAATTAGAAGAGT
1 T-TAATT-AAAATTTTAAAAATTTTCGTGAGATTAATGAGAATTT-T-AAAAAAATT---AGAGT
* * *
38827601 TTAATTAAA-AATTT-CAAGAGAA-AAAAGGTATAATGAGATTTTTCAAAAATTTAGAGGAA
59 TTAATTAAATAATTTACAA-AAAATAAAAGGCATAATGAGATTATT-AAAAATTTAGAGGAA
*
38827660 TTAATTAAAATTTTCAAAAAATTTC
1 TTAATTAAAATTTT-AAAAATTTTC
38827685 AAGAGAATAT
Statistics
Matches: 125, Mismatches: 10, Indels: 24
0.79 0.06 0.15
Matches are distributed among these distances:
121 14 0.11
122 52 0.42
123 29 0.23
124 11 0.09
125 6 0.05
127 13 0.10
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.38
Consensus pattern (118 bp):
TTAATTAAAATTTTAAAAATTTTCGTGAGATTAATGAGAATTTTAAAAAAATTAGAGTTTAATTA
AATAATTTACAAAAAATAAAAGGCATAATGAGATTATTAAAAATTTAGAGGAA
Found at i:38832487 original size:21 final size:18
Alignment explanation
Indices: 38832463--38832573 Score: 50
Period size: 21 Copynumber: 5.7 Consensus size: 18
38832453 AAATTGTTAA
38832463 AAAAACATAAAAAATATCTAT
1 AAAAA-ATAAAAAATAT-T-T
*
38832484 AAAAATTGAAAAAATATTT
1 AAAAAAT-AAAAAATATTT
*
38832503 -AAAATTATAAAAA-ATTT
1 AAAAAATA-AAAAATATTT
* *
38832520 AAATAATTGAACAAA-A-TT
1 AAA-AAAT-AAAAAATATTT
38832538 AAAAAATGTAAACAAATATTT
1 AAAAAA--TAAA-AAATATTT
38832559 AAAAATTATAAAAAA
1 AAAAA--ATAAAAAA
38832574 ATCTAAGATC
Statistics
Matches: 74, Mismatches: 4, Indels: 25
0.72 0.04 0.24
Matches are distributed among these distances:
17 7 0.09
18 20 0.27
19 14 0.19
20 7 0.09
21 25 0.34
23 1 0.01
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.28
Consensus pattern (18 bp):
AAAAAATAAAAAATATTT
Found at i:38832505 original size:19 final size:19
Alignment explanation
Indices: 38832471--38832565 Score: 83
Period size: 18 Copynumber: 4.9 Consensus size: 19
38832461 AAAAAAACAT
38832471 AAAAAATATCTATAAAAATTG
1 AAAAAATAT-T-TAAAAATTG
38832492 AAAAAATATTT-AAAATT-
1 AAAAAATATTTAAAAATTG
38832509 ATAAAAA-ATTTAAATAATTG
1 A-AAAAATATTTAAA-AATTG
* *
38832529 AACAAA-A-TTAAAAAATG
1 AAAAAATATTTAAAAATTG
38832546 TAAACAAATATTTAAAAATT
1 -AAA-AAATATTTAAAAATT
38832566 ATAAAAAAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 16
0.76 0.05 0.20
Matches are distributed among these distances:
17 9 0.15
18 20 0.32
19 13 0.21
20 3 0.05
21 17 0.27
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (19 bp):
AAAAAATATTTAAAAATTG
Found at i:38832506 original size:10 final size:9
Alignment explanation
Indices: 38832470--38832573 Score: 59
Period size: 9 Copynumber: 10.8 Consensus size: 9
38832460 TAAAAAAACA
38832470 TAAAAAATAT
1 TAAAAAAT-T
38832480 CTATAAAAATT
1 -TA-AAAAATT
*
38832491 GAAAAAATAT
1 TAAAAAAT-T
*
38832501 T-TAAAATT
1 TAAAAAATT
38832509 ATAAAAAATT
1 -TAAAAAATT
*
38832519 TAAATAATT
1 TAAAAAATT
*
38832528 GAACAAAA-T
1 TAA-AAAATT
*
38832537 TAAAAAATG
1 TAAAAAATT
38832546 TAAACAAATAT
1 TAAA-AAAT-T
*
38832557 TTAAAAATT
1 TAAAAAATT
38832566 ATAAAAAA
1 -TAAAAAA
38832574 ATCTAAGATC
Statistics
Matches: 72, Mismatches: 12, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
8 5 0.07
9 30 0.42
10 25 0.35
11 6 0.08
12 6 0.08
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (9 bp):
TAAAAAATT
Found at i:38832516 original size:28 final size:28
Alignment explanation
Indices: 38832484--38832573 Score: 78
Period size: 28 Copynumber: 3.2 Consensus size: 28
38832474 AAATATCTAT
38832484 AAAAATTGAAAAAATATTTAAAATTATA
1 AAAAATTGAAAAAATATTTAAAATTATA
* * ** *
38832512 AAAAATTTAAATAAT-TGAACAAAAT-TA
1 AAAAATTGAAAAAATATTTA-AAATTATA
38832539 AAAAA-TGTAAACAAATATTTAAAAATTATA
1 AAAAATTG-AAA-AAATATTT-AAAATTATA
38832569 AAAAA
1 AAAAA
38832574 ATCTAAGATC
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
26 1 0.02
27 12 0.26
28 20 0.43
29 5 0.11
30 8 0.17
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (28 bp):
AAAAATTGAAAAAATATTTAAAATTATA
Found at i:38832575 original size:21 final size:19
Alignment explanation
Indices: 38832471--38832573 Score: 86
Period size: 19 Copynumber: 5.3 Consensus size: 19
38832461 AAAAAAACAT
*
38832471 AAAAAATATCTATAAAAATTG
1 AAAAAATAT-T-TAAAAATTA
38832492 AAAAAATATTT-AAAATTA
1 AAAAAATATTTAAAAATTA
* *
38832510 TAAAAA-ATTTAAATAATTG
1 AAAAAATATTTAAA-AATTA
* *
38832529 AACAAA-ATTAAAAAATGTA
1 AAAAAATATTTAAAAAT-TA
*
38832548 AACAAATATTTAAAAATTA
1 AAAAAATATTTAAAAATTA
38832567 TAAAAAA
1 -AAAAAA
38832574 ATCTAAGATC
Statistics
Matches: 68, Mismatches: 9, Indels: 11
0.77 0.10 0.12
Matches are distributed among these distances:
17 4 0.06
18 16 0.24
19 24 0.35
20 15 0.22
21 9 0.13
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (19 bp):
AAAAAATATTTAAAAATTA
Found at i:38833665 original size:18 final size:17
Alignment explanation
Indices: 38833623--38833665 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
38833613 TTTTTAAGTT
38833623 TATAATTTTTTATATTA
1 TATAATTTTTTATATTA
* *
38833640 TGTTATTTTTATATATTA
1 TATAATTTTT-TATATTA
38833658 TATAATTT
1 TATAATTT
38833666 AGAACACATT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
TATAATTTTTTATATTA
Found at i:38840892 original size:32 final size:32
Alignment explanation
Indices: 38840817--38840895 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 32
38840807 GAAGTGACCA
*
38840817 AAATCTGAAATGATTTGAACTCAAAACAATCT
1 AAATCTGAAATGATCTGAACTCAAAACAATCT
* * *
38840849 AAATTTAAAATGATCTGAATTCAAAATCAAT-T
1 AAATCTGAAATGATCTGAACTCAAAA-CAATCT
38840881 CAAA-CTGAAATGATC
1 -AAATCTGAAATGATC
38840896 CAAAATTGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
32 32 0.82
33 7 0.18
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.29
Consensus pattern (32 bp):
AAATCTGAAATGATCTGAACTCAAAACAATCT
Found at i:38845687 original size:31 final size:31
Alignment explanation
Indices: 38845652--38845721 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
38845642 GTTATAAAAT
*
38845652 AGTCACTGAACTAT-TCAAAAGTTTTCATTTA
1 AGTCACTGAAATATAT-AAAAGTTTTCATTTA
* * *
38845683 AGTCACTAAAATATATGAAAGTTTTTATTTA
1 AGTCACTGAAATATATAAAAGTTTTCATTTA
38845714 AGTCACTG
1 AGTCACTG
38845722 GGCTGTTAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (31 bp):
AGTCACTGAAATATATAAAAGTTTTCATTTA
Found at i:38854517 original size:77 final size:77
Alignment explanation
Indices: 38854426--38854580 Score: 238
Period size: 77 Copynumber: 2.0 Consensus size: 77
38854416 CCCTCTCAAT
* * * *
38854426 AATATTATCTCCAACATTTAAACCTGAATTCTTTACTTACAATGCAATATGTTTTACCATTAGTG
1 AATATTATCTCCAACATCTAAAACTGAATTCTCTACTTACAATGCAATATGTTTTACCATTAATG
*
38854491 ATATAGCTAAAA
66 ATAAAGCTAAAA
* *
38854503 AATATTATCTCCAACATCTAAAACTGAATTCTCTACTTACAATGCAATATGTTTTTCCCTTAATG
1 AATATTATCTCCAACATCTAAAACTGAATTCTCTACTTACAATGCAATATGTTTTACCATTAATG
*
38854568 ATAAAGCTGAAA
66 ATAAAGCTAAAA
38854580 A
1 A
38854581 GCACATGCAA
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
77 70 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (77 bp):
AATATTATCTCCAACATCTAAAACTGAATTCTCTACTTACAATGCAATATGTTTTACCATTAATG
ATAAAGCTAAAA
Found at i:38855418 original size:45 final size:45
Alignment explanation
Indices: 38855354--38855491 Score: 258
Period size: 45 Copynumber: 3.1 Consensus size: 45
38855344 AAATATAAAC
* *
38855354 CAGAGCTAACTCTTTAAAAGGAATGACATACCTTGTAAGCAATCA
1 CAGAGCTAACTCTGTAAAAGAAATGACATACCTTGTAAGCAATCA
38855399 CAGAGCTAACTCTGTAAAAGAAATGACATACCTTGTAAGCAATCA
1 CAGAGCTAACTCTGTAAAAGAAATGACATACCTTGTAAGCAATCA
38855444 CAGAGCTAACTCTGTAAAAGAAATGACATACCTTGTAAGCAATCA
1 CAGAGCTAACTCTGTAAAAGAAATGACATACCTTGTAAGCAATCA
38855489 CAG
1 CAG
38855492 TTCTCGGATT
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 91 1.00
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.22
Consensus pattern (45 bp):
CAGAGCTAACTCTGTAAAAGAAATGACATACCTTGTAAGCAATCA
Found at i:38855436 original size:21 final size:21
Alignment explanation
Indices: 38855411--38855481 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 21
38855401 GAGCTAACTC
38855411 TGTAAAAGAAATGACATACCT
1 TGTAAAAGAAATGACATACCT
* * *
38855432 TGT--AAGCAATCACAGAGCTAACT
1 TGTAAAAGAAATGAC--A--TACCT
38855455 CTGTAAAAGAAATGACATACCT
1 -TGTAAAAGAAATGACATACCT
38855477 TGTAA
1 TGTAA
38855482 GCAATCACAG
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
19 8 0.22
21 9 0.24
22 4 0.11
23 4 0.11
24 4 0.11
26 8 0.22
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.24
Consensus pattern (21 bp):
TGTAAAAGAAATGACATACCT
Found at i:38868385 original size:6 final size:6
Alignment explanation
Indices: 38868374--38868398 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
38868364 TAAGAAAGAA
38868374 GGTGAG GGTGAG GGTGAG GGTGAG G
1 GGTGAG GGTGAG GGTGAG GGTGAG G
38868399 TATTTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.68, T:0.16
Consensus pattern (6 bp):
GGTGAG
Found at i:38871381 original size:20 final size:20
Alignment explanation
Indices: 38871356--38871400 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
38871346 CTATTTGATG
*
38871356 TACTCATATCTCTTGATACA
1 TACTCATATCTCTTAATACA
38871376 TACTCATATCTCTTAATACA
1 TACTCATATCTCTTAATACA
38871396 T-CTCA
1 TACTCA
38871401 CTACCCGTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.31, C:0.27, G:0.02, T:0.40
Consensus pattern (20 bp):
TACTCATATCTCTTAATACA
Found at i:38878582 original size:61 final size:61
Alignment explanation
Indices: 38878512--38878634 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
38878502 TTGAATCATT
38878512 ACTGTCATACAAGCGCTAAAGAAATAGTAAGGGTGCATCAATCTTGTATTGGAAAAGAAAA
1 ACTGTCATACAAGCGCTAAAGAAATAGTAAGGGTGCATCAATCTTGTATTGGAAAAGAAAA
38878573 ACTGTCATACAAGCGCTAAAGAAATAGTAAGGGTGCATCAATCTTGTATTGGAAAAGAAAA
1 ACTGTCATACAAGCGCTAAAGAAATAGTAAGGGTGCATCAATCTTGTATTGGAAAAGAAAA
38878634 A
1 A
38878635 AAGTTTTGGG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (61 bp):
ACTGTCATACAAGCGCTAAAGAAATAGTAAGGGTGCATCAATCTTGTATTGGAAAAGAAAA
Found at i:38879784 original size:18 final size:18
Alignment explanation
Indices: 38879761--38879796 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
38879751 TAAATAGTTC
* *
38879761 AAATTATTTGAATTAATT
1 AAATTATTCGAATCAATT
38879779 AAATTATTCGAATCAATT
1 AAATTATTCGAATCAATT
38879797 TGAATAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (18 bp):
AAATTATTCGAATCAATT
Found at i:38892991 original size:30 final size:31
Alignment explanation
Indices: 38892919--38892997 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 31
38892909 ATTAAAAGGT
*
38892919 ATAATGAGAA-TTT-TAAAAAATTTAAGGGGC
1 ATAATGA-AATTTTCTAAAAAATTCAAGGGGC
* *
38892949 CTAATTAAATTTTTCTAAAAAATTCAA-GGG-
1 ATAATGAAA-TTTTCTAAAAAATTCAAGGGGC
38892979 ATAATGAAATTTTCTAAAA
1 ATAATGAAATTTTCTAAAA
38892998 GTTTTGGGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
29 12 0.29
30 12 0.29
31 6 0.15
32 11 0.27
ACGTcount: A:0.47, C:0.06, G:0.13, T:0.34
Consensus pattern (31 bp):
ATAATGAAATTTTCTAAAAAATTCAAGGGGC
Found at i:38900009 original size:22 final size:22
Alignment explanation
Indices: 38899983--38900029 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
38899973 TTATATAAAA
38899983 AATAAATATGA-TCAAAACTTAT
1 AATAAA-ATGATTCAAAACTTAT
*
38900005 AATAAAATTATTCAAAACTTAT
1 AATAAAATGATTCAAAACTTAT
38900027 AAT
1 AAT
38900030 CTAGAATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (22 bp):
AATAAAATGATTCAAAACTTAT
Found at i:38908531 original size:21 final size:21
Alignment explanation
Indices: 38908507--38908565 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 21
38908497 TTAAAAAATA
38908507 AAAATATATATAAATATTTTT
1 AAAATATATATAAATATTTTT
*
38908528 AAAA-ATATA-ATAATTTTTTT
1 AAAATATATATA-AATATTTTT
* * *
38908548 AAATTTTATATTAATATT
1 AAAATATATATAAATATT
38908566 AAATAAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
19 1 0.03
20 16 0.53
21 13 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AAAATATATATAAATATTTTT
Found at i:38908546 original size:20 final size:22
Alignment explanation
Indices: 38908505--38908550 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 22
38908495 TTTTAAAAAA
38908505 TAAAAATATATATAAATATTTT
1 TAAAAATATATATAAATATTTT
*
38908527 TAAAAATATA-AT-AATTTTTT
1 TAAAAATATATATAAATATTTT
38908547 TAAA
1 TAAA
38908551 TTTTATATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.48
21 2 0.09
22 10 0.43
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TAAAAATATATATAAATATTTT
Found at i:38908591 original size:6 final size:6
Alignment explanation
Indices: 38908582--38908615 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
38908572 AATAAAAATT
* *
38908582 ACCCCA ACCCCA ACCCCA ACCCAA ACCCAA ACCC
1 ACCCCA ACCCCA ACCCCA ACCCCA ACCCCA ACCC
38908616 AAACGCGATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.38, C:0.62, G:0.00, T:0.00
Consensus pattern (6 bp):
ACCCCA
Found at i:38908599 original size:12 final size:12
Alignment explanation
Indices: 38908582--38908619 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
38908572 AATAAAAATT
*
38908582 ACCCCAACCCCA
1 ACCCCAACCCAA
38908594 ACCCCAACCCAA
1 ACCCCAACCCAA
*
38908606 ACCCAAACCCAA
1 ACCCCAACCCAA
38908618 AC
1 AC
38908620 GCGATGAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.42, C:0.58, G:0.00, T:0.00
Consensus pattern (12 bp):
ACCCCAACCCAA
Found at i:38908610 original size:17 final size:17
Alignment explanation
Indices: 38908584--38908617 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38908574 TAAAAATTAC
* *
38908584 CCCAACCCCAACCCCAA
1 CCCAAACCCAAACCCAA
38908601 CCCAAACCCAAACCCAA
1 CCCAAACCCAAACCCAA
38908618 ACGCGATGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.59, G:0.00, T:0.00
Consensus pattern (17 bp):
CCCAAACCCAAACCCAA
Done.