Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 127 of 211
Found at i:40091238 original size:139 final size:139
Alignment explanation
Indices: 40090972--40091228 Score: 369
Period size: 139 Copynumber: 1.9 Consensus size: 139
40090962 GTTTTTAGTC
* * *
40090972 ATTTTAAAGCAAAATTTTAAATTTTTTAAAATAAAGTTTTGATCTTTTTCAACTATTTCAAAATA
1 ATTTTAAAGCAAAAGTTTAAATATTTTAAAACAAAGTTTTGATCTTTTTCAACTATTTCAAAATA
* * *
40091037 AAGTTTTGATTTTTAAGAAAAATGGTGATTTTTTTTTAAAAGAGAAAGGTTAGATTTAAAAAAAA
66 AAGCTTTGATTTTTAAGAAAAATGGTGA-TTTTTTTTAAAACAGAAAGCTTAGATTTAAAAAAAA
40091102 ACATTTAGCT
130 ACATTTAGCT
* * * *
40091112 ATTTTAAAGGAAAAGTTTAAA-ATTTTAGAACAATGTTTTGATCTTTTTCAACTGTTTCAAAATA
1 ATTTTAAAGCAAAAGTTTAAATATTTTAAAACAAAGTTTTGATCTTTTTCAACTATTTCAAAATA
* *
40091176 AAGCTTTGATTTTTAAGAAAAATTGTGA-TTTTTTTAAAACA-AAA-CTTTGATTT
66 AAGCTTTGATTTTTAAGAAAAATGGTGATTTTTTTTAAAACAGAAAGCTTAGATTT
40091229 TGCAAAAAAA
Statistics
Matches: 105, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
135 7 0.07
136 3 0.03
137 12 0.11
139 64 0.61
140 19 0.18
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (139 bp):
ATTTTAAAGCAAAAGTTTAAATATTTTAAAACAAAGTTTTGATCTTTTTCAACTATTTCAAAATA
AAGCTTTGATTTTTAAGAAAAATGGTGATTTTTTTTAAAACAGAAAGCTTAGATTTAAAAAAAAA
CATTTAGCT
Found at i:40091808 original size:16 final size:17
Alignment explanation
Indices: 40091779--40091824 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
40091769 ATAATTTTTA
*
40091779 TTTATTTTTATTTCATC
1 TTTATTTATATTTCATC
*
40091796 TTTATTTAT-TTTCATG
1 TTTATTTATATTTCATC
*
40091812 TCTATTTATATTT
1 TTTATTTATATTT
40091825 ATGGTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.70
Consensus pattern (17 bp):
TTTATTTATATTTCATC
Found at i:40103022 original size:24 final size:24
Alignment explanation
Indices: 40102990--40103037 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
40102980 ATGAAGAATG
40102990 AATGAAAAATTATGAATTCTTGAT
1 AATGAAAAATTATGAATTCTTGAT
*
40103014 AATGCAAAATTATGAATTCTTGAT
1 AATGAAAAATTATGAATTCTTGAT
40103038 CTCATTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (24 bp):
AATGAAAAATTATGAATTCTTGAT
Found at i:40103639 original size:19 final size:18
Alignment explanation
Indices: 40103611--40103646 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
40103601 TTGCCTACAC
40103611 AAAAAAAAACTAAAAAAT
1 AAAAAAAAACTAAAAAAT
40103629 AAAAAATAAACTAAAAAA
1 AAAAAA-AAACTAAAAAA
40103647 AGATAGAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.83, C:0.06, G:0.00, T:0.11
Consensus pattern (18 bp):
AAAAAAAAACTAAAAAAT
Found at i:40104118 original size:42 final size:42
Alignment explanation
Indices: 40104054--40104316 Score: 334
Period size: 42 Copynumber: 6.3 Consensus size: 42
40104044 AAGGAAAGCA
* *
40104054 TTCATTGCATTTAGTGGCCCAGGTGTAGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
40104096 TTCACTGCATTTAGAGGCCCAGGCGTAGAGGTCCGTTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* **
40104138 TTCATTGCATTTAGAAG-CTTGGTTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGG-TGTGGAGGTCCATTTACTT
* *
40104180 TACATTGCATTTAGAGGCCC-GAGTGTGGAGGTCAATTTACTT
1 TTCATTGCATTTAGAGGCCCAG-GTGTGGAGGTCCATTTACTT
** * *
40104222 TTCATTGCATTTAGAATCGCAAGTGTGGAGG-CTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTC-CATTTACTT
*
40104264 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
40104306 TTCATTGCATT
1 TTCATTGCATT
40104317 GTATATGAAG
Statistics
Matches: 191, Mismatches: 24, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
41 4 0.02
42 184 0.96
43 3 0.02
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Found at i:40106087 original size:69 final size:69
Alignment explanation
Indices: 40105976--40106246 Score: 243
Period size: 69 Copynumber: 3.9 Consensus size: 69
40105966 TATTCACACT
* * *
40105976 TATAAGATCAAGGCTTGCAAGCG-AAAAG-CTACAACCCCCAAAACAGTTAGCAATAGCAAAGCT
1 TATAAGATCAAGGCTCGC-AGCGAAAAAGTC-GCAACCCCCAAAACAGTTAGCAAGAGCAAAGCT
40106039 CCTAGC
64 CCTAGC
* * * *
40106045 TATAAGATCAAGGCTTGCAG-GAAAAGAGTCGCAACCCCCAAAATAGTTAACAAAAGCAAAGCTC
1 TATAAGATCAAGGCTCGCAGCGAAAA-AGTCGCAACCCCCAAAACAGTTAGCAAGAGCAAAGCTC
* *
40106109 CCAAC
65 CTAGC
* * * * * *
40106114 TATCAGATCAAGGCTCACAG-GTGAAAAG-C-C-ACTGCTCTAGAACAGTTAGCAAGAGCAAAGC
1 TATAAGATCAAGGCTCGCAGCG-AAAAAGTCGCAAC--CCCCAAAACAGTTAGCAAGAGCAAAGC
40106175 TCCTAGC
63 TCCTAGC
* * * * *
40106182 TGTAAGGTCAAGGCTCGTAAGCG-AAAAGTCGCAGCTCCCAAAACAGTTAGCAAGAGCAAAGCTC
1 TATAAGATCAAGGCTCG-CAGCGAAAAAGTCGCAACCCCCAAAACAGTTAGCAAGAGCAAAGCTC
40106246 C
65 C
40106247 CAGTTGTATT
Statistics
Matches: 163, Mismatches: 28, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
66 2 0.01
67 2 0.01
68 50 0.31
69 102 0.63
70 6 0.04
71 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (69 bp):
TATAAGATCAAGGCTCGCAGCGAAAAAGTCGCAACCCCCAAAACAGTTAGCAAGAGCAAAGCTCC
TAGC
Found at i:40106552 original size:58 final size:58
Alignment explanation
Indices: 40106425--40106601 Score: 266
Period size: 58 Copynumber: 3.1 Consensus size: 58
40106415 CTGTAGTATC
* * *
40106425 AGTATAAAACAGACCGCAAATTCATATTCCTAGCTTATAA-TTTGAGAAAAATCTCTA
1 AGTAAAAAATAGATCGCAAATTCATATTCCTAGCTTATAATTTTGAGAAAAATCTCTA
* *
40106482 TGTAAAAAATAGATCGCGAATTCATATTCCTAGCTTATAATTTTGAGAAAAATCTCTA
1 AGTAAAAAATAGATCGCAAATTCATATTCCTAGCTTATAATTTTGAGAAAAATCTCTA
* * * *
40106540 AGTAGAAAATAGATCGCAAATTCATGTTCCCAGCTTATAATTTCGAGAAAAATCTCTA
1 AGTAAAAAATAGATCGCAAATTCATATTCCTAGCTTATAATTTTGAGAAAAATCTCTA
40106598 AGTA
1 AGTA
40106602 TCAGACGGCT
Statistics
Matches: 108, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
57 35 0.32
58 73 0.68
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (58 bp):
AGTAAAAAATAGATCGCAAATTCATATTCCTAGCTTATAATTTTGAGAAAAATCTCTA
Found at i:40111958 original size:25 final size:25
Alignment explanation
Indices: 40111928--40111984 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
40111918 AATACACCTA
40111928 TTAGAGATTAGAACTCATAACACAT
1 TTAGAGATTAGAACTCATAACACAT
40111953 TTAGAGATTAGAACTCATAACACAT
1 TTAGAGATTAGAACTCATAACACAT
40111978 TTAGAGA
1 TTAGAGA
40111985 ATTTTTTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (25 bp):
TTAGAGATTAGAACTCATAACACAT
Found at i:40115590 original size:24 final size:23
Alignment explanation
Indices: 40115533--40115594 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
40115523 TACCCTATTT
*
40115533 TGGACAACATTTATACATCAAAT
1 TGGACAACATTTATACATCAAAA
* *
40115556 TGGACAACATTTATATCCTTAAAA
1 TGGACAACATTTATA-CATCAAAA
*
40115580 TGGACAGCA-TTATAC
1 TGGACAACATTTATAC
40115595 GTCTAAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 1 0.03
23 20 0.59
24 13 0.38
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (23 bp):
TGGACAACATTTATACATCAAAA
Found at i:40119851 original size:22 final size:20
Alignment explanation
Indices: 40119826--40119868 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
40119816 AAACAGTTGT
*
40119826 TTATCTCACAAAGTTTATAGCA
1 TTAT-TCACAAAGGTT-TAGCA
*
40119848 TTATTCTCAAAGGTTTAGCA
1 TTATTCACAAAGGTTTAGCA
40119868 T
1 T
40119869 GTTCAGATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 9 0.47
22 4 0.21
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.40
Consensus pattern (20 bp):
TTATTCACAAAGGTTTAGCA
Found at i:40123459 original size:13 final size:13
Alignment explanation
Indices: 40123441--40123465 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40123431 CTTAACCTTT
40123441 TCTATTTGAACTA
1 TCTATTTGAACTA
40123454 TCTATTTGAACT
1 TCTATTTGAACT
40123466 TCCTACTTAC
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:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (13 bp):
TCTATTTGAACTA
Found at i:40128742 original size:66 final size:65
Alignment explanation
Indices: 40128630--40128767 Score: 172
Period size: 66 Copynumber: 2.1 Consensus size: 65
40128620 GCAATTTGCT
* * ** *
40128630 CAACTTAAAGCGGAGGCAGCATTGAGAGAAGCAGAGGCTCAAAGAAAATATGAA-GAACTCTAGC
1 CAACTTAAAGCAGAGGCAACAGCGAGAGAAGCAGAGGCTC-AAGAAAATAT-AACGAACTCCAGC
40128694 TA
64 TA
*
40128696 CAACTTAAAGCAGAGGCAATAGCGAGAGAAGCAGAGGCATGC-AGAAAATATAACGAACTCCAGC
1 CAACTTAAAGCAGAGGCAACAGCGAGAGAAGCAGAGGC-T-CAAGAAAATATAACGAACTCCAGC
40128760 TA
64 TA
40128762 CAACTT
1 CAACTT
40128768 CAAAATATGA
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
65 2 0.03
66 59 0.94
67 1 0.02
68 1 0.02
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.14
Consensus pattern (65 bp):
CAACTTAAAGCAGAGGCAACAGCGAGAGAAGCAGAGGCTCAAGAAAATATAACGAACTCCAGCTA
Found at i:40129158 original size:42 final size:42
Alignment explanation
Indices: 40129096--40129243 Score: 163
Period size: 42 Copynumber: 3.5 Consensus size: 42
40129086 GTTTTTACTA
* * *
40129096 AAAGCGCCGCTAAAGAACATGACCTTTAACGGTGTTT-TGGCG
1 AAAGCGCCGCTAAAGGACATGTCCTTTAACGGCGTTTGTGG-G
* * **
40129138 ACAGCGTCGCTAAAGGACATGTCCTTTAGTGGCGTTTGTGGG
1 AAAGCGCCGCTAAAGGACATGTCCTTTAACGGCGTTTGTGGG
* ** *
40129180 AAAGCGCCGCTAAAGGTCATGTCCTTTAGTGGCATTTGTGGG
1 AAAGCGCCGCTAAAGGACATGTCCTTTAACGGCGTTTGTGGG
* *
40129222 AAAGTGCCGCTAAAGGTCATGT
1 AAAGCGCCGCTAAAGGACATGT
40129244 TCTATAGTGA
Statistics
Matches: 93, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
42 90 0.97
43 3 0.03
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (42 bp):
AAAGCGCCGCTAAAGGACATGTCCTTTAACGGCGTTTGTGGG
Found at i:40129285 original size:41 final size:42
Alignment explanation
Indices: 40129145--40129291 Score: 188
Period size: 42 Copynumber: 3.5 Consensus size: 42
40129135 GCGACAGCGT
* * *
40129145 CGCTAAAGGACATGTCCTTTAGTGGCGTTTGTGGGAAAGCGC
1 CGCTAAAGGTCATGTCCTATAGTGGCGTTTGTGGGAAAGTGC
* *
40129187 CGCTAAAGGTCATGTCCTTTAGTGGCATTTGTGGGAAAGTGC
1 CGCTAAAGGTCATGTCCTATAGTGGCGTTTGTGGGAAAGTGC
* * * * *
40129229 CGCTAAAGGTCATGTTCTATAGTGACGTTTATGGG-AGGTGT
1 CGCTAAAGGTCATGTCCTATAGTGGCGTTTGTGGGAAAGTGC
*
40129270 CGCTAAAGGTCATGTTCTATAG
1 CGCTAAAGGTCATGTCCTATAG
40129292 CTTCATTTTT
Statistics
Matches: 95, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
41 26 0.27
42 69 0.73
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.31
Consensus pattern (42 bp):
CGCTAAAGGTCATGTCCTATAGTGGCGTTTGTGGGAAAGTGC
Found at i:40129548 original size:29 final size:30
Alignment explanation
Indices: 40129507--40129565 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
40129497 TTTTGTTCAA
40129507 TGTGCAATATTATATA-TAAAT-TTCAATTT
1 TGTGCAATATTATATATTAAATGTT-AATTT
* *
40129536 TGTGTAATTTTATATATTAAATGTTAATTT
1 TGTGCAATATTATATATTAAATGTTAATTT
40129566 GATCTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 14 0.54
30 10 0.38
31 2 0.08
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.53
Consensus pattern (30 bp):
TGTGCAATATTATATATTAAATGTTAATTT
Found at i:40129574 original size:30 final size:29
Alignment explanation
Indices: 40129516--40129576 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
40129506 ATGTGCAATA
*
40129516 TTATATATAAATTTCAATTTTGTGTAATT
1 TTATATATAAATTTCAATTTTGTCTAATT
40129545 TTATATATTAAATGTT-AA-TTTGATCTAATT
1 TTATATA-TAAAT-TTCAATTTTG-TCTAATT
40129575 TT
1 TT
40129577 CAAAAATCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 11 0.39
30 15 0.54
31 2 0.07
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.56
Consensus pattern (29 bp):
TTATATATAAATTTCAATTTTGTCTAATT
Found at i:40131387 original size:22 final size:22
Alignment explanation
Indices: 40131362--40131403 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
40131352 CAATTTAATC
* *
40131362 TAATTTAATATATATTTCATTT
1 TAATATAATACATATTTCATTT
*
40131384 TAATATCATACATATTTCAT
1 TAATATAATACATATTTCAT
40131404 GTGTTATTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (22 bp):
TAATATAATACATATTTCATTT
Found at i:40132267 original size:18 final size:19
Alignment explanation
Indices: 40132239--40132290 Score: 88
Period size: 18 Copynumber: 2.8 Consensus size: 19
40132229 AGAATTTCTG
40132239 AAAATTCAAAAAATACATA
1 AAAATTCAAAAAATACATA
*
40132258 AAAATT-AAAAAACACATA
1 AAAATTCAAAAAATACATA
40132276 AAAATTCAAAAAATA
1 AAAATTCAAAAAATA
40132291 AAATATAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 17 0.57
19 13 0.43
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (19 bp):
AAAATTCAAAAAATACATA
Found at i:40135734 original size:2 final size:2
Alignment explanation
Indices: 40135727--40135760 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
40135717 CCGTCAAAAC
40135727 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
40135761 GGAACCGAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40140848 original size:20 final size:19
Alignment explanation
Indices: 40140820--40140871 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
40140810 AATTACGGTT
*
40140820 TTAATTGAGAAATTTGTAAAA
1 TTAA-TGAGAAATGTGT-AAA
* *
40140841 TTCATGAGTAAATGTGTGAA
1 TTAATGAG-AAATGTGTAAA
40140861 TTAATGAGAAA
1 TTAATGAGAAA
40140872 AATGGTCTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 3 0.12
20 13 0.50
21 10 0.38
ACGTcount: A:0.44, C:0.02, G:0.19, T:0.35
Consensus pattern (19 bp):
TTAATGAGAAATGTGTAAA
Found at i:40141286 original size:20 final size:20
Alignment explanation
Indices: 40141249--40141286 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40141239 CTTGAAATTC
*
40141249 AAATTACTGATTATATGATT
1 AAATTACTGATTACATGATT
*
40141269 AAATTACTGTTTACATGA
1 AAATTACTGATTACATGA
40141287 ATGAAAGTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (20 bp):
AAATTACTGATTACATGATT
Found at i:40141608 original size:23 final size:23
Alignment explanation
Indices: 40141582--40141641 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
40141572 CTCATTGGAA
40141582 CTTACCATTTCAGCTAGT-ATGAG
1 CTTACCATTTCAGCTAGTCA-GAG
*
40141605 CTTA-C-TGTTCAGCTCGTCAGAG
1 CTTACCAT-TTCAGCTAGTCAGAG
*
40141627 CTTACCATTTTAGCT
1 CTTACCATTTCAGCT
40141642 TAATAGAGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
21 1 0.03
22 17 0.55
23 12 0.39
24 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.37
Consensus pattern (23 bp):
CTTACCATTTCAGCTAGTCAGAG
Found at i:40141851 original size:20 final size:21
Alignment explanation
Indices: 40141821--40141861 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
40141811 TATGAATAAG
40141821 ATATGTGTTTATACAGATGAA
1 ATATGTGTTTATACAGATGAA
*
40141842 ATAT-TGTTTATACGGATGAA
1 ATATGTGTTTATACAGATGAA
40141862 CCACTGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.39
Consensus pattern (21 bp):
ATATGTGTTTATACAGATGAA
Found at i:40141869 original size:20 final size:20
Alignment explanation
Indices: 40141826--40141873 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
40141816 ATAAGATATG
* *
40141826 TGTTTATACAGATGAAATAT
1 TGTTTATACAGATGAAACAC
* *
40141846 TGTTTATACGGATGAACCAC
1 TGTTTATACAGATGAAACAC
40141866 TGTTTATA
1 TGTTTATA
40141874 TGAATGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (20 bp):
TGTTTATACAGATGAAACAC
Found at i:40142826 original size:13 final size:13
Alignment explanation
Indices: 40142808--40142832 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40142798 ATATGTTTGG
40142808 ATATGAAATTGAT
1 ATATGAAATTGAT
40142821 ATATGAAATTGA
1 ATATGAAATTGA
40142833 GATTGAATTT
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:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (13 bp):
ATATGAAATTGAT
Found at i:40147719 original size:20 final size:19
Alignment explanation
Indices: 40147691--40147742 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
40147681 AATTACGGTT
*
40147691 TTAATTGAGAAATTTGTAAAA
1 TTAA-TGAGAAATGTGT-AAA
* *
40147712 TTCATGAGTAAATGTGTGAA
1 TTAATGAG-AAATGTGTAAA
40147732 TTAATGAGAAA
1 TTAATGAGAAA
40147743 AATAGGCTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 3 0.12
20 13 0.50
21 10 0.38
ACGTcount: A:0.44, C:0.02, G:0.19, T:0.35
Consensus pattern (19 bp):
TTAATGAGAAATGTGTAAA
Found at i:40148494 original size:24 final size:23
Alignment explanation
Indices: 40148458--40148580 Score: 67
Period size: 23 Copynumber: 5.3 Consensus size: 23
40148448 TCGATATATC
* *
40148458 AGCTCGTAAGAGCTTACTGTTTT
1 AGCTCATATGAGCTTACTGTTTT
**
40148481 CAGCTCAT-TGGAGCTTACCATTTT
1 -AGCTCATAT-GAGCTTACTGTTTT
* *
40148505 AGCTCGTATGAGCTTACTG-TTC
1 AGCTCATATGAGCTTACTGTTTT
* **
40148527 AGCTCGTCA-GAGCTTACCATTTT
1 AGCTCAT-ATGAGCTTACTGTTTT
40148550 AGCTCA-ATAGAGCATT-CTGTTTATT
1 AGCTCATAT-GAGC-TTACTG-TT-TT
40148575 AGCTCA
1 AGCTCA
40148581 AGAGGAGTTT
Statistics
Matches: 76, Mismatches: 14, Indels: 17
0.71 0.13 0.16
Matches are distributed among these distances:
21 1 0.01
22 17 0.22
23 27 0.36
24 23 0.30
25 8 0.11
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.37
Consensus pattern (23 bp):
AGCTCATATGAGCTTACTGTTTT
Found at i:40148543 original size:45 final size:46
Alignment explanation
Indices: 40148458--40148554 Score: 142
Period size: 45 Copynumber: 2.1 Consensus size: 46
40148448 TCGATATATC
**
40148458 AGCTCGTAAGAGCTTACTGTTTTCAGCTCATTGGAGCTTACCATTTT
1 AGCTCGTAAGAGCTTACTG-TTTCAGCTCATCAGAGCTTACCATTTT
* *
40148505 AGCTCGTATGAGCTTACTG-TTCAGCTCGTCAGAGCTTACCATTTT
1 AGCTCGTAAGAGCTTACTGTTTCAGCTCATCAGAGCTTACCATTTT
40148550 AGCTC
1 AGCTC
40148555 AATAGAGCAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
45 28 0.61
47 18 0.39
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.36
Consensus pattern (46 bp):
AGCTCGTAAGAGCTTACTGTTTCAGCTCATCAGAGCTTACCATTTT
Found at i:40148562 original size:23 final size:22
Alignment explanation
Indices: 40148458--40148554 Score: 81
Period size: 23 Copynumber: 4.2 Consensus size: 22
40148448 TCGATATATC
**
40148458 AGCTCGTAAGAGCTTACTGTTTT
1 AGCTCGT-AGAGCTTACCATTTT
* *
40148481 CAGCTCATTGGAGCTTACCATTTT
1 -AGCTC-GTAGAGCTTACCATTTT
*
40148505 AGCTCGTATGAGCTTA-C-TGTTC
1 AGCTCGTA-GAGCTTACCAT-TTT
40148527 AGCTCGTCAGAGCTTACCATTTT
1 AGCTCGT-AGAGCTTACCATTTT
40148550 AGCTC
1 AGCTC
40148555 AATAGAGCAT
Statistics
Matches: 59, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
21 1 0.02
22 18 0.31
23 21 0.36
24 18 0.31
25 1 0.02
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.36
Consensus pattern (22 bp):
AGCTCGTAGAGCTTACCATTTT
Found at i:40170144 original size:45 final size:45
Alignment explanation
Indices: 40170076--40170178 Score: 143
Period size: 45 Copynumber: 2.3 Consensus size: 45
40170066 TTGGACTATC
* * * * *
40170076 CACCATGTTTGTTTGCCATTTGGATTGTTCATCATTTATGTTGTT
1 CACCATGTGTGTTTGCCAATTGGACTATTCACCATTTATGTTGTT
* *
40170121 CTCCATGTGTGTTTGCCAATTGGACTATTCGCCATTTATGTTGTT
1 CACCATGTGTGTTTGCCAATTGGACTATTCACCATTTATGTTGTT
40170166 CACCATGTGTGTT
1 CACCATGTGTGTT
40170179 CACCATTGCA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.16, C:0.18, G:0.19, T:0.47
Consensus pattern (45 bp):
CACCATGTGTGTTTGCCAATTGGACTATTCACCATTTATGTTGTT
Found at i:40190778 original size:44 final size:44
Alignment explanation
Indices: 40190607--40191297 Score: 275
Period size: 44 Copynumber: 15.7 Consensus size: 44
40190597 GTGAAACACC
* * * *
40190607 AGATCGTATCTCCCTAAGCAGTAGTGGAGCGGATCGAAGAC-GG
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTGT
* * * * ***
40190650 CGAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACC
1 AG-ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACTGT
* * * * * * *
40190695 AAACCTTATCTCCCTGAGTAGTAGTGGAGAAGGTTGAAGATTGT
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTGT
* * *
40190739 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGC
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTGT
* * * * * * ***
40190783 AAATCTTATCTTTCC-AA-TA-TAGTGGGAAGCACATTTAAGCCACC
1 AGATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACTGT
* * * * * * * * *
40190827 AAACCTTGTCTCCCTGAGCAGCAGTAGAGAAGGTTGAAGATTGT
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTGT
* * *
40190871 AGATCTTATCTCCCAAAGCAGTAGTGGAGCAGATCGAAGACGGT
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTGT
* * * * ***
40190915 -GAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCACATTTAAGCCACC
1 AG-ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACTGT
* * * * * * *
40190959 AAACCTTATCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGT
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTGT
* *
40191003 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGT
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTGT
** * * * ***
40191047 -GAATCTTATCTTTCTAAG-A-TAGTGGGAAGCACATTTAAGCCACC
1 AG-ATCTTATCTCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACTGT
* * * * * * *
40191091 AAACCTTATCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGT
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTGT
* *
40191135 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC-GG
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTGT
* * * * ***
40191178 CGAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACC
1 AG-ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACTGT
* * * * ** * * *
40191223 AAACCTTGTCTCCCTGAGCAGCGGTGGAGAAGGTTGAAGATTGT
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTGT
40191267 AGATCTTATCTCCCTAAGCAGTAGTGGAGCA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCA
40191298 AATCGATATC
Statistics
Matches: 449, Mismatches: 163, Indels: 71
0.66 0.24 0.10
Matches are distributed among these distances:
42 20 0.04
43 32 0.07
44 356 0.79
45 26 0.06
46 15 0.03
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (44 bp):
AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTGT
Found at i:40190844 original size:132 final size:132
Alignment explanation
Indices: 40190607--40191303 Score: 1241
Period size: 132 Copynumber: 5.3 Consensus size: 132
40190597 GTGAAACACC
* *
40190607 AGATCGTATCTCCCTAAGCAGTAGTGGAGCGGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
* * *
40190672 GTGGGAAGCAGATTTAAGCCACCAAACCTTATCTCCCTGAGTAGTAGTGGAGAAGGTTGAAGATT
66 GTGGGAAGCACATTTAAGCCACCAAACCTTATCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATT
40190737 GT
131 GT
* *
40190739 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAATATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
* *
40190804 GTGGGAAGCACATTTAAGCCACCAAACCTTGTCTCCCTGAGCAGCAGTAGAGAAGGTTGAAGATT
66 GTGGGAAGCACATTTAAGCCACCAAACCTTATCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATT
40190869 GT
131 GT
* *
40190871 AGATCTTATCTCCCAAAGCAGTAGTGGAGCAGATCGAAGACGGTGAATCTTATCTTTCCAAGATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
40190936 GTGGGAAGCACATTTAAGCCACCAAACCTTATCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATT
66 GTGGGAAGCACATTTAAGCCACCAAACCTTATCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATT
40191001 GT
131 GT
* *
40191003 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAATCTTATCTTTCTAAGATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
40191068 GTGGGAAGCACATTTAAGCCACCAAACCTTATCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATT
66 GTGGGAAGCACATTTAAGCCACCAAACCTTATCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATT
40191133 GT
131 GT
40191135 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
* * *
40191200 GTGGGAAGCAGATTTAAGCCACCAAACCTTGTCTCCCTGAGCAGCGGTGGAGAAGGTTGAAGATT
66 GTGGGAAGCACATTTAAGCCACCAAACCTTATCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATT
40191265 GT
131 GT
*
40191267 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGA
40191304 TATCTTTCCA
Statistics
Matches: 542, Mismatches: 23, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
132 542 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (132 bp):
AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
GTGGGAAGCACATTTAAGCCACCAAACCTTATCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATT
GT
Found at i:40191406 original size:118 final size:118
Alignment explanation
Indices: 40191185--40191397 Score: 299
Period size: 118 Copynumber: 1.8 Consensus size: 118
40191175 CGGCGAATCT
* *
40191185 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAACCTTGTCTCCCTGAGCAGCGGTGG
1 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAACCTTGTCTCCCTAAGCAGCAGTGG
* ***
40191250 AGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGA
66 AGAAGGTCG-AGATCCCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGA
* *
40191304 TATCTTTCCAAGATAGTGGGAAGCAGATTT-AGCCACCAAGCCTTGTCTCCCTAAGCAGTAGTGG
1 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAACCTTGTCTCCCTAAGCAGCAGTGG
* *
40191368 AGCAGGTCG-TA-CCCA-ATCTTATCTCCCTAA
66 AGAAGGTCGAGATCCCAGATCTTATCTCCCTAA
40191398 AGTTGCAGTG
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
114 15 0.18
115 1 0.01
116 1 0.01
118 37 0.44
119 30 0.36
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (118 bp):
TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAACCTTGTCTCCCTAAGCAGCAGTGG
AGAAGGTCGAGATCCCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGA
Found at i:40199738 original size:14 final size:13
Alignment explanation
Indices: 40199719--40199751 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
40199709 TAAAAAATTC
40199719 AAAAAAATTGTGA
1 AAAAAAATTGTGA
40199732 GAAAAAAATTGTGA
1 -AAAAAAATTGTGA
40199746 AAAAAA
1 AAAAAA
40199752 GGAAAGGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.18
Consensus pattern (13 bp):
AAAAAAATTGTGA
Found at i:40211962 original size:111 final size:110
Alignment explanation
Indices: 40211768--40211990 Score: 392
Period size: 111 Copynumber: 2.0 Consensus size: 110
40211758 AAATTGTACC
* * *
40211768 TTTCCAATTCGTCTAGGATAAACGCTTCGACCAAGTAGTCTTCTCCATTATCCTCAAGCTCATAT
1 TTTCCAATTCGTCTAGGATAAAAGCTTCGACCAAGTAGTCTTCTCCATTATCCTAAAGCTCACAT
40211833 CTGCCGAGTGTGGGCTCACTTTGAACCAAAAAAATTTGCACAAAAA
66 CTGCCGAGTGTGGGCTCACTTTGAACC-AAAAAATTTGCACAAAAA
40211879 TTTCCAATTCGTCTAGGATAAAAGCTTCGACCAAGTAGTCTTCTCCATTATCCTAAAGCTCACAT
1 TTTCCAATTCGTCTAGGATAAAAGCTTCGACCAAGTAGTCTTCTCCATTATCCTAAAGCTCACAT
* *
40211944 CTGTCGAGTGTGGGCTCACTTTGAACCAAAAAATTTTCACAAAAA
66 CTGCCGAGTGTGGGCTCACTTTGAACCAAAAAATTTGCACAAAAA
40211989 TT
1 TT
40211991 ACTAGTGGCG
Statistics
Matches: 107, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
110 19 0.18
111 88 0.82
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (110 bp):
TTTCCAATTCGTCTAGGATAAAAGCTTCGACCAAGTAGTCTTCTCCATTATCCTAAAGCTCACAT
CTGCCGAGTGTGGGCTCACTTTGAACCAAAAAATTTGCACAAAAA
Found at i:40212307 original size:61 final size:58
Alignment explanation
Indices: 40212198--40212309 Score: 152
Period size: 61 Copynumber: 1.9 Consensus size: 58
40212188 ATCACTTTAA
* * *
40212198 TATTCAATTAATATAATACTTACCAAGATAAATATTAGATTAAATTTAATACTAAATC
1 TATTAAATTAATAGAATACTTACCAAGATAAATATTAAATTAAATTTAATACTAAATC
* *
40212256 TATTAAATTAATAGAATACTTATCTACAATATAAATATTAAATTAGATTTAATA
1 TATTAAATTAATAGAATACTTA-C--CAAGATAAATATTAAATTAAATTTAATA
40212310 TTAAGATAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
58 20 0.43
59 1 0.02
61 25 0.54
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (58 bp):
TATTAAATTAATAGAATACTTACCAAGATAAATATTAAATTAAATTTAATACTAAATC
Found at i:40218846 original size:51 final size:54
Alignment explanation
Indices: 40218759--40218910 Score: 143
Period size: 56 Copynumber: 2.8 Consensus size: 54
40218749 ATATATGGCA
* * *
40218759 TAAGACCATGGATGAAAGA-GGCTATGGCAGTC-TGGTATATGGTA-CAT-A-GCG
1 TAAGACCATGGATGAAAGATGTC-ATGGCA-ACATGGTAAATGGTATCATAAGGCG
* * *
40218810 TAAGACCATGGATGAAAGATGTCATGGCAACATGGTACATGGCAATGATAAGGGCG
1 TAAGACCATGGATGAAAGATGTCATGGCAACATGGTAAATGG-TATCATAA-GGCG
* * * *
40218866 TAAGACAATTGATGAAAGATGTCATGACAACAAGGTAAATGGTAT
1 TAAGACCATGGATGAAAGATGTCATGGCAACATGGTAAATGGTAT
40218911 AAGATATACG
Statistics
Matches: 83, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
50 1 0.01
51 34 0.41
52 3 0.04
53 2 0.02
54 1 0.01
55 2 0.02
56 40 0.48
ACGTcount: A:0.37, C:0.12, G:0.28, T:0.22
Consensus pattern (54 bp):
TAAGACCATGGATGAAAGATGTCATGGCAACATGGTAAATGGTATCATAAGGCG
Found at i:40223458 original size:130 final size:130
Alignment explanation
Indices: 40223192--40223447 Score: 413
Period size: 130 Copynumber: 2.0 Consensus size: 130
40223182 CCTTAGCTAA
* * * *
40223192 ATTTTTAAGGATTTCTTATAAATGAGTAGTTTGTTTAGAAATTTAAATTGCAAAAAACCAAACAA
1 ATTTTTAAGGATTTCTTATAAATGAGTAGTCTGTTCAGAAATTTAAACTGCAAAAAACCAAAAAA
*
40223257 TTAGTGACTTAAGGCCCTTGCTGTAAGAATGATTAAATTTTAAAGTTCACTTTTTTAGAAAATAC
66 TTAGTGACTTAAGGCCCTTGCTGTAAGAATGATTAAATTTTAAAATTCACTTTTTTAGAAAATAC
* * *
40223322 ATTTTTAAGGATTTCTTGTAAATGAGTAGTCTGTTCAGAAATTTGAACTGCGAAAAACCAAAAAA
1 ATTTTTAAGGATTTCTTATAAATGAGTAGTCTGTTCAGAAATTTAAACTGCAAAAAACCAAAAAA
* * *
40223387 TTAGTGACTTAAGGCCCTTGTTGTAAGAGTGATTAAATTTTAAAATTCAGTTTTTTAGAAA
66 TTAGTGACTTAAGGCCCTTGCTGTAAGAATGATTAAATTTTAAAATTCACTTTTTTAGAAA
40223448 GTTTTATTTT
Statistics
Matches: 115, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
130 115 1.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.37
Consensus pattern (130 bp):
ATTTTTAAGGATTTCTTATAAATGAGTAGTCTGTTCAGAAATTTAAACTGCAAAAAACCAAAAAA
TTAGTGACTTAAGGCCCTTGCTGTAAGAATGATTAAATTTTAAAATTCACTTTTTTAGAAAATAC
Found at i:40224798 original size:28 final size:28
Alignment explanation
Indices: 40224759--40224816 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
40224749 AATAAAAAAA
40224759 TTCATTACATTAATATACTTTGTATAAT
1 TTCATTACATTAATATACTTTGTATAAT
*
40224787 TTCATTATATTAATATACTTTGTATAAT
1 TTCATTACATTAATATACTTTGTATAAT
40224815 TT
1 TT
40224817 TTGTCATATG
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:0.34, C:0.09, G:0.03, T:0.53
Consensus pattern (28 bp):
TTCATTACATTAATATACTTTGTATAAT
Found at i:40228494 original size:27 final size:27
Alignment explanation
Indices: 40228309--40228499 Score: 170
Period size: 27 Copynumber: 7.1 Consensus size: 27
40228299 ACATGCCAGA
* * *
40228309 AAAAGGAAGCCTTTGTAGCGATCTAAG
1 AAAAGGAAGCCTTTGTGGCTATCTATG
* **
40228336 AAAAGAAAGCCTTTGTGTTTATCTATG
1 AAAAGGAAGCCTTTGTGGCTATCTATG
* * **
40228363 AAAAGAAAGCCTTTGTGGCGATCTAAC
1 AAAAGGAAGCCTTTGTGGCTATCTATG
* * * * *
40228390 AAATGAAAGTCTTTATGGCT-TTTAATG
1 AAAAGGAAGCCTTTGTGGCTATCT-ATG
*
40228417 AAAAGGAAGCCTTTATGGCTATCTATG
1 AAAAGGAAGCCTTTGTGGCTATCTATG
* *
40228444 AAAAGAAAACCTTTGTGGCTATCTATG
1 AAAAGGAAGCCTTTGTGGCTATCTATG
* *
40228471 ACAAGGAAGCCTTCGTGG-TGATCTATG
1 AAAAGGAAGCCTTTGTGGCT-ATCTATG
40228498 AA
1 AA
40228500 GGGAATGCCC
Statistics
Matches: 131, Mismatches: 30, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
26 3 0.02
27 126 0.96
28 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (27 bp):
AAAAGGAAGCCTTTGTGGCTATCTATG
Found at i:40228499 original size:54 final size:54
Alignment explanation
Indices: 40228309--40228495 Score: 214
Period size: 54 Copynumber: 3.5 Consensus size: 54
40228299 ACATGCCAGA
* **
40228309 AAAAGGAAGCCTTTGTAGCGATCTAAGAAAAGAAAGCCTTTGTGTTTATCTATG
1 AAAAGGAAGCCTTTGTGGCGATCTAAGAAAAGAAAGCCTTTGTGGCTATCTATG
* * * * * *
40228363 AAAAGAAAGCCTTTGTGGCGATCTAACAAATGAAAGTCTTTATGGCT-TTTAATG
1 AAAAGGAAGCCTTTGTGGCGATCTAAGAAAAGAAAGCCTTTGTGGCTATCT-ATG
* * * *
40228417 AAAAGGAAGCCTTTATGGCTATCTATGAAAAGAAAACCTTTGTGGCTATCTATG
1 AAAAGGAAGCCTTTGTGGCGATCTAAGAAAAGAAAGCCTTTGTGGCTATCTATG
* * *
40228471 ACAAGGAAGCCTTCGTGGTGATCTA
1 AAAAGGAAGCCTTTGTGGCGATCTA
40228496 TGAAGGGAAT
Statistics
Matches: 107, Mismatches: 24, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
53 2 0.02
54 103 0.96
55 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29
Consensus pattern (54 bp):
AAAAGGAAGCCTTTGTGGCGATCTAAGAAAAGAAAGCCTTTGTGGCTATCTATG
Found at i:40238216 original size:49 final size:49
Alignment explanation
Indices: 40238162--40238255 Score: 172
Period size: 49 Copynumber: 1.9 Consensus size: 49
40238152 AGGCAATTGA
40238162 AGCATCTGCATTTTCTCTCAACCTCTTT-TGGTACTTCTTAGTAACAGGG
1 AGCATCTGCATTTTCTCTCAACCT-TTTCTGGTACTTCTTAGTAACAGGG
40238211 AGCATCTGCATTTTCTCTCAACCTTTTCTGGTACTTCTTAGTAAC
1 AGCATCTGCATTTTCTCTCAACCTTTTCTGGTACTTCTTAGTAAC
40238256 TGGCTTCTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
48 3 0.07
49 41 0.93
ACGTcount: A:0.20, C:0.26, G:0.14, T:0.40
Consensus pattern (49 bp):
AGCATCTGCATTTTCTCTCAACCTTTTCTGGTACTTCTTAGTAACAGGG
Found at i:40249184 original size:27 final size:25
Alignment explanation
Indices: 40249139--40249199 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 25
40249129 ATTTAATTTC
* *
40249139 AAAAAATTT-AATTACTAAACTAAA
1 AAAAAATTTAAATAACTAAAATAAA
40249163 AAATAATATTTAAATAACTAAAATAAA
1 AAA-AA-ATTTAAATAACTAAAATAAA
40249190 AAAAAATTTA
1 AAAAAATTTA
40249200 TATTTGGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 3 0.09
25 7 0.22
26 6 0.19
27 16 0.50
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (25 bp):
AAAAAATTTAAATAACTAAAATAAA
Found at i:40258510 original size:34 final size:34
Alignment explanation
Indices: 40258467--40258533 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
40258457 CCATGTTCTG
40258467 CACCAATCAACTCAACAGTACATTATACAAATTT
1 CACCAATCAACTCAACAGTACATTATACAAATTT
*
40258501 CACCAATCAAGTCAACAGTACATTATACAAATT
1 CACCAATCAACTCAACAGTACATTATACAAATT
40258534 CCAATTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.45, C:0.25, G:0.04, T:0.25
Consensus pattern (34 bp):
CACCAATCAACTCAACAGTACATTATACAAATTT
Found at i:40280694 original size:21 final size:22
Alignment explanation
Indices: 40280668--40280721 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
40280658 ATTCAACTAT
*
40280668 TATTAAACTTAAT-CACTTTAA
1 TATTAAACTTAATACAATTTAA
*
40280689 TATTAAA-TTAATATAATTTAA
1 TATTAAACTTAATACAATTTAA
40280710 TATTAAATCTTA
1 TATTAAA-CTTA
40280722 TTAAAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 5 0.18
21 20 0.71
23 3 0.11
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (22 bp):
TATTAAACTTAATACAATTTAA
Found at i:40280701 original size:11 final size:11
Alignment explanation
Indices: 40280685--40280717 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
40280675 CTTAATCACT
40280685 TTAATATTAAA
1 TTAATATTAAA
*
40280696 TTAATA-TAAT
1 TTAATATTAAA
40280706 TTAATATTAAA
1 TTAATATTAAA
40280717 T
1 T
40280718 CTTATTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:40280988 original size:18 final size:18
Alignment explanation
Indices: 40280962--40280996 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40280952 CCGCTGTTGA
*
40280962 CCATCGGGATGTCATCGG
1 CCATCGGGATGCCATCGG
*
40280980 CCATTGGGATGCCATCG
1 CCATCGGGATGCCATCG
40280997 TCGCAGCCAC
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:0.17, C:0.29, G:0.31, T:0.23
Consensus pattern (18 bp):
CCATCGGGATGCCATCGG
Found at i:40287585 original size:13 final size:12
Alignment explanation
Indices: 40287567--40287600 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
40287557 TACATAATAT
40287567 AAATATTATAAAC
1 AAATA-TATAAAC
40287580 AAATATA-AAAC
1 AAATATATAAAC
40287591 AAATATATAA
1 AAATATATAA
40287601 GGAGATAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 11 0.55
12 4 0.20
13 5 0.25
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (12 bp):
AAATATATAAAC
Found at i:40288676 original size:25 final size:24
Alignment explanation
Indices: 40288562--40288676 Score: 60
Period size: 25 Copynumber: 4.7 Consensus size: 24
40288552 TACAAGATAA
*
40288562 AAAT-TAAATTAA-ATTAAATATT
1 AAATATAATTTAATATTAAATATT
* * *
40288584 AAGATAATCACTTTAATGTTAAATTAAT
1 AA-AT-AT-AATTTAATATTAAA-TATT
* *
40288612 AAA-ATACTATTAAGA-TAAATATT
1 AAATATAAT-TTAATATTAAATATT
*
40288635 AAATTTAATTTAATATTAAACTATT
1 AAATATAATTTAATATTAAA-TATT
*
40288660 AAA-ATAATATTATTATT
1 AAATATAAT-TTAATATT
40288677 GGAATAACTA
Statistics
Matches: 70, Mismatches: 12, Indels: 19
0.69 0.12 0.19
Matches are distributed among these distances:
22 2 0.03
23 13 0.19
24 18 0.26
25 21 0.30
26 5 0.07
27 6 0.09
28 5 0.07
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (24 bp):
AAATATAATTTAATATTAAATATT
Found at i:40291323 original size:5 final size:5
Alignment explanation
Indices: 40291313--40291349 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
40291303 TTTTTAGAGT
*
40291313 AATAA AATAA AATAA CATAA AATAA AAT-A AATAA AAT
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AAT
40291350 TCAAGAGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 4 0.14
5 25 0.86
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (5 bp):
AATAA
Found at i:40291334 original size:15 final size:14
Alignment explanation
Indices: 40291313--40291349 Score: 65
Period size: 15 Copynumber: 2.6 Consensus size: 14
40291303 TTTTTAGAGT
40291313 AATAAAATAAAATA
1 AATAAAATAAAATA
40291327 ACATAAAATAAAATA
1 A-ATAAAATAAAATA
40291342 AATAAAAT
1 AATAAAAT
40291350 TCAAGAGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (14 bp):
AATAAAATAAAATA
Found at i:40303254 original size:7 final size:7
Alignment explanation
Indices: 40303242--40303270 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
40303232 TTTCCATTTC
40303242 AAATCCA
1 AAATCCA
40303249 AAATCCA
1 AAATCCA
40303256 AAATCCA
1 AAATCCA
40303263 AAATCCA
1 AAATCCA
40303270 A
1 A
40303271 TCTCATCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.59, C:0.28, G:0.00, T:0.14
Consensus pattern (7 bp):
AAATCCA
Found at i:40312710 original size:14 final size:14
Alignment explanation
Indices: 40312691--40312717 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40312681 CTAAATATGA
40312691 TAATCCAATTCAAT
1 TAATCCAATTCAAT
40312705 TAATCCAATTCAA
1 TAATCCAATTCAA
40312718 CATCTTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (14 bp):
TAATCCAATTCAAT
Found at i:40320441 original size:35 final size:35
Alignment explanation
Indices: 40320400--40320484 Score: 152
Period size: 35 Copynumber: 2.4 Consensus size: 35
40320390 GATTTTCTTC
*
40320400 CAAATTATTATTCATTCATTCATAATGATATGGTA
1 CAAATTATTATTCATTCATTCATAATCATATGGTA
40320435 CAAATTATTATTCATTCATTCATAATCATATGGTA
1 CAAATTATTATTCATTCATTCATAATCATATGGTA
*
40320470 CAAATAATTATTCAT
1 CAAATTATTATTCAT
40320485 GAATTTATAC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (35 bp):
CAAATTATTATTCATTCATTCATAATCATATGGTA
Found at i:40321234 original size:15 final size:15
Alignment explanation
Indices: 40321216--40321257 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
40321206 ATCAAATAAA
40321216 AAAATAAAAAATGTG
1 AAAATAAAAAATGTG
*
40321231 AAAA-ACAAAAAAGTG
1 AAAATA-AAAAATGTG
*
40321246 AAAATGAAAAAT
1 AAAATAAAAAAT
40321258 AAAAAATGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
14 1 0.05
15 21 0.95
ACGTcount: A:0.71, C:0.02, G:0.12, T:0.14
Consensus pattern (15 bp):
AAAATAAAAAATGTG
Found at i:40321282 original size:17 final size:17
Alignment explanation
Indices: 40321215--40321280 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 17
40321205 AATCAAATAA
40321215 AAAAATAAAAAATG-TG
1 AAAAATAAAAAATGATG
*
40321231 AAAAACAAAAAAGTGAAAATG
1 AAAAATAAAAAA-TG---ATG
40321252 AAAAATAAAAAATGATG
1 AAAAATAAAAAATGATG
40321269 AAAAAGTAAAAA
1 AAAAA-TAAAAA
40321281 TGGAGAGGCT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
16 11 0.26
17 10 0.24
18 6 0.14
20 2 0.05
21 13 0.31
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.14
Consensus pattern (17 bp):
AAAAATAAAAAATGATG
Found at i:40322596 original size:44 final size:44
Alignment explanation
Indices: 40322528--40322779 Score: 319
Period size: 44 Copynumber: 5.7 Consensus size: 44
40322518 AATCACAAAA
* * *
40322528 CCTAGCTCCCTAACCAGTAGTGGAATAGGTTGAAGATTGTAAGT
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGT
*
40322572 CCTATCTCCCTAACCAGCAGTGGAATAGGTTGAAGATTGTAAGT
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGT
* * * * * *
40322616 CCTATCTCCATGGCCAGTAGAGGAATAGGTAGAAGATTGCAAGT
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGT
* * *
40322660 CCTAACTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGTAAGC
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGT
* * * *
40322704 CCTAGT-TCCCTGACCAGCAATGGAATAGGTGGAAGACTGTAAGC
1 CCTA-TCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGT
40322748 CCTAGT-TCCCTGACCAGCAGTGGAATAGGTTG
1 CCTA-TCTCCCTGACCAGCAGTGGAATAGGTTG
40322780 GGAAATTACA
Statistics
Matches: 185, Mismatches: 22, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
44 185 1.00
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (44 bp):
CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGT
Found at i:40323145 original size:44 final size:43
Alignment explanation
Indices: 40323048--40323164 Score: 119
Period size: 44 Copynumber: 2.7 Consensus size: 43
40323038 GAAGATGGCA
* * *
40323048 AATCTTATCTCCCTGAGGTTGTAGTAGAGCAGATTGAAGCCGAT
1 AATCTTATCT-CCTGAAGTTGTAGTAGAGCAGATTAAAGCCAAT
* * * *
40323092 AATCCTATCTCCATGAAGTTGTAGTGGAGCGGATTAAAG-TAAT
1 AATCTTATCTCC-TGAAGTTGTAGTAGAGCAGATTAAAGCCAAT
*
40323135 AGATCTTATCTCTCTGAAGTTGCAGTAGAG
1 A-ATCTTATCTC-CTGAAGTTGTAGTAGAG
40323165 TGGATCGCAT
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
43 5 0.08
44 54 0.90
45 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (43 bp):
AATCTTATCTCCTGAAGTTGTAGTAGAGCAGATTAAAGCCAAT
Found at i:40323306 original size:50 final size:50
Alignment explanation
Indices: 40323252--40323534 Score: 281
Period size: 50 Copynumber: 5.7 Consensus size: 50
40323242 ACAGTGGAAC
*
40323252 AGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACATCAGTGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * * ** *
40323302 AGATTAAAGCTACAACAGCGAATCTTAC-T-CCCGA-AGTGATGCAGTGGAAC
1 AGATTAAAGCCACATCAGTGAATCTTACTTCCCCGACA-T--TGCAGTTAAAA
* * *
40323352 AGATTAAAGCCACATCAGTGAATCATGCTTCCCCGAAATTGCAGTTAAAA
1 AGATTAAAGCCACATCAGTGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * * ** *
40323402 AGATTAAAGCTACAACAGTGAATCTTAC-TCCCC-AGCTAATGCAGTGCAAC
1 AGATTAAAGCCACATCAGTGAATCTTACTTCCCCGA-C-ATTGCAGTTAAAA
* * *
40323452 AGATTAAAGCCACATCGGTGAATCTTTCTTCCCCGACATTACAGTTAAAA
1 AGATTAAAGCCACATCAGTGAATCTTACTTCCCCGACATTGCAGTTAAAA
* *
40323502 AGATTAAAGCTACAAT-AGCGAATCTTACTTCCC
1 AGATTAAAGCCAC-ATCAGTGAATCTTACTTCCC
40323535 AGGCAGTGTA
Statistics
Matches: 185, Mismatches: 37, Indels: 22
0.76 0.15 0.09
Matches are distributed among these distances:
47 1 0.01
48 7 0.04
49 6 0.03
50 154 0.83
51 9 0.05
52 7 0.04
53 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (50 bp):
AGATTAAAGCCACATCAGTGAATCTTACTTCCCCGACATTGCAGTTAAAA
Found at i:40323395 original size:100 final size:100
Alignment explanation
Indices: 40323222--40323599 Score: 485
Period size: 100 Copynumber: 3.8 Consensus size: 100
40323212 GAGAATAGCA
* *
40323222 AATCTTACTCCCCAGGC-AATACAGTGGAACAGATTAAAGCCACATCAGTGAATCTTGCTTCCCC
1 AATCTTACT-CCCAAGCTAATGCAGTGGAACAGATTAAAGCCACATCAGTGAATCTTGCTTCCCC
40323286 GACATTGCAGTTAAAAAGATTAAAGCTACAACAGCG
65 GACATTGCAGTTAAAAAGATTAAAGCTACAACAGCG
* *
40323322 AATCTTACTCCCGAAG-TGATGCAGTGGAACAGATTAAAGCCACATCAGTGAATCATGCTTCCCC
1 AATCTTACTCCC-AAGCTAATGCAGTGGAACAGATTAAAGCCACATCAGTGAATCTTGCTTCCCC
* *
40323386 GAAATTGCAGTTAAAAAGATTAAAGCTACAACAGTG
65 GACATTGCAGTTAAAAAGATTAAAGCTACAACAGCG
* * * *
40323422 AATCTTACTCCCCAGCTAATGCAGTGCAACAGATTAAAGCCACATCGGTGAATCTTTCTTCCCCG
1 AATCTTACTCCCAAGCTAATGCAGTGGAACAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCG
* *
40323487 ACATTACAGTTAAAAAGATTAAAGCTACAATAGCG
66 ACATTGCAGTTAAAAAGATTAAAGCTACAACAGCG
* * * * * * * **
40323522 AATCTTACTTCCCAGGC-AGTGTAGTGGAACCA-ATTGAAGCTACAGCAGCGAATCTTATTTCCC
1 AATCTTAC-TCCCAAGCTAATGCAGTGGAA-CAGATTAAAGCCACATCAGTGAATCTTGCTTCCC
**
40323585 CGACATCACAGTTAA
64 CGACATTGCAGTTAA
40323600 GCAGATCAAA
Statistics
Matches: 244, Mismatches: 29, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
99 5 0.02
100 231 0.95
101 8 0.03
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (100 bp):
AATCTTACTCCCAAGCTAATGCAGTGGAACAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCG
ACATTGCAGTTAAAAAGATTAAAGCTACAACAGCG
Found at i:40328524 original size:90 final size:90
Alignment explanation
Indices: 40328371--40328540 Score: 322
Period size: 90 Copynumber: 1.9 Consensus size: 90
40328361 ATGAATGATC
40328371 TACTTATAGATAATATGACATTTCAAAAGCCTCGTTGGTGAAGGAAAAAATTTTGGATAACCTTT
1 TACTTATAGATAATATGACATTTCAAAAGCCTCGTTGGTGAAGGAAAAAATTTTGGATAACCTTT
40328436 GATGGGATAAGGACTTATATATCCT
66 GATGGGATAAGGACTTATATATCCT
*
40328461 TACTTATAGATAATATGACATTTCAAAAGCCTCGTTGGTGAAGGAAGAAATTTTGGATAACCTTT
1 TACTTATAGATAATATGACATTTCAAAAGCCTCGTTGGTGAAGGAAAAAATTTTGGATAACCTTT
*
40328526 GATGGGATAATGACT
66 GATGGGATAAGGACT
40328541 AAGTGTAAAT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
90 78 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (90 bp):
TACTTATAGATAATATGACATTTCAAAAGCCTCGTTGGTGAAGGAAAAAATTTTGGATAACCTTT
GATGGGATAAGGACTTATATATCCT
Found at i:40338951 original size:42 final size:42
Alignment explanation
Indices: 40338904--40338988 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
40338894 ATGTATATGA
40338904 TAATTTTGGCTGTAAGATCAAGCGTATAACTCTTTCGTTATT
1 TAATTTTGGCTGTAAGATCAAGCGTATAACTCTTTCGTTATT
40338946 TAATTTTGGCTGTAAGATCAAGCGTATAACTCTTTCGTTATT
1 TAATTTTGGCTGTAAGATCAAGCGTATAACTCTTTCGTTATT
40338988 T
1 T
40338989 GGTTGCCATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.44
Consensus pattern (42 bp):
TAATTTTGGCTGTAAGATCAAGCGTATAACTCTTTCGTTATT
Found at i:40343743 original size:21 final size:23
Alignment explanation
Indices: 40343712--40343755 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
40343702 TATTCACATT
*
40343712 TAGATTTAAATTTTAAA-ATAAA
1 TAGATTTAAATTTCAAATATAAA
40343734 TAGA-TTAAATTTCAAATATAAA
1 TAGATTTAAATTTCAAATATAAA
40343756 AAAATATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (23 bp):
TAGATTTAAATTTCAAATATAAA
Found at i:40344640 original size:22 final size:23
Alignment explanation
Indices: 40344605--40344648 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
40344595 ATTAGCAAAC
40344605 AAATATATAAATAT-AAATAAAT
1 AAATATATAAATATAAAATAAAT
* *
40344627 AAATATCTATATATAAAATAAA
1 AAATATATAAATATAAAATAAA
40344649 ATATAAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
AAATATATAAATATAAAATAAAT
Found at i:40344642 original size:14 final size:14
Alignment explanation
Indices: 40344605--40344656 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
40344595 ATTAGCAAAC
40344605 AAATATATAAATAT
1 AAATATATAAATAT
*
40344619 AAATAAATAAATAT
1 AAATATATAAATAT
**
40344633 CTATATATAAA-AT
1 AAATATATAAATAT
40344646 AAA-ATATAAAT
1 AAATATATAAAT
40344657 TGAATAATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
12 7 0.23
13 3 0.10
14 21 0.68
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATATATAAATAT
Found at i:40345116 original size:20 final size:20
Alignment explanation
Indices: 40345091--40345143 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
40345081 TTAAAGGAGC
* *
40345091 AATTAAATCCATTTGATTAA
1 AATTAAATCAAATTGATTAA
*
40345111 AATTAAATCAAATTGATTAG
1 AATTAAATCAAATTGATTAA
* *
40345131 AATAAAATAAAAT
1 AATTAAATCAAAT
40345144 CAGGATATGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.34
Consensus pattern (20 bp):
AATTAAATCAAATTGATTAA
Found at i:40349680 original size:54 final size:54
Alignment explanation
Indices: 40349588--40349937 Score: 301
Period size: 54 Copynumber: 6.5 Consensus size: 54
40349578 GCATGAAGTT
* * * **
40349588 TGCTTACAAAATTTTAAAAATATTAC-AGTCCGCTGATTTACGATCACGACCTTC
1 TGCTTACAAGATTTTAAGAATCTTACGA-TCCATTGATTTACGATCACGACCTTC
* * * * * *
40349642 TGCTAACAAGATTTTTAGAATCTTACGACCCGTTGATTTACGATCAGGATCTTC
1 TGCTTACAAGATTTTAAGAATCTTACGATCCATTGATTTACGATCACGACCTTC
* * * * ** *
40349696 TACTTACAAGATTTTAAGCATTTTAAAGAT-TGTTGATTTACGATCACGACCTTT
1 TGCTTACAAGATTTTAAGAATCTT-ACGATCCATTGATTTACGATCACGACCTTC
* * * * *
40349750 TGCTTAGATGAATTTAAGAATCTTGC-AGTTCATTGATTTACGATCACGACCTTC
1 TGCTTACAAGATTTTAAGAATCTTACGA-TCCATTGATTTACGATCACGACCTTC
* * * * *
40349804 TGCTTAAAAGATTTTAAAAATCTTACGATCCACTGATTTATGATCACAACCTTC
1 TGCTTACAAGATTTTAAGAATCTTACGATCCATTGATTTACGATCACGACCTTC
* * * * * * * * *
40349858 TACTTATAAGATTTTAAGAATCTCAAGGTCTATTGAATTATGATCACGACGTTC
1 TGCTTACAAGATTTTAAGAATCTTACGATCCATTGATTTACGATCACGACCTTC
* *
40349912 TGCTTACAAGATTTTTAGAATATTAC
1 TGCTTACAAGATTTTAAGAATCTTAC
40349938 AGTTTGTTGA
Statistics
Matches: 234, Mismatches: 57, Indels: 10
0.78 0.19 0.03
Matches are distributed among these distances:
52 1 0.00
53 1 0.00
54 227 0.97
55 5 0.02
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (54 bp):
TGCTTACAAGATTTTAAGAATCTTACGATCCATTGATTTACGATCACGACCTTC
Found at i:40349950 original size:162 final size:162
Alignment explanation
Indices: 40349588--40349951 Score: 417
Period size: 162 Copynumber: 2.2 Consensus size: 162
40349578 GCATGAAGTT
* * * *
40349588 TGCTTACAAAATTTTAAAAATATTACAGTCCGCTGATTTACGATCACGACCTTCTGCTAACAAGA
1 TGCTTACAAGATTTTAAGAATATTACAGTTCGTTGATTTACGATCACGACCTTCTGCTAACAAGA
* * ** ** * *
40349653 TTTTTAGAATCTTACGACCCGTTGATTTACGATCAGGATCTTCTACTTACAAGATTTTAAGCATT
66 TTTTAAAAATCTTACGACCCACTGATTTACGATCACAACCTTCTACTTACAAGATTTTAAGCAAT
* * * *
40349718 TTAAAGATTGTTGATTTACGATCACGACCTTT
131 CTAAAGATTATTGAATTACGATCACGACCTTC
* * * * * *
40349750 TGCTTAGATGAATTTAAGAATCTTGCAGTTCATTGATTTACGATCACGACCTTCTGCTTAA-AAG
1 TGCTTACAAGATTTTAAGAATATTACAGTTCGTTGATTTACGATCACGACCTTCTGC-TAACAAG
* * *
40349814 ATTTTAAAAATCTTACGATCCACTGATTTATGATCACAACCTTCTACTTATAAGATTTTAAG-AA
65 ATTTTAAAAATCTTACGACCCACTGATTTACGATCACAACCTTCTACTTACAAGATTTTAAGCAA
* * * *
40349878 TCTCAAGGTCTATTGAATTATGATCACGACGTTC
130 TCTAAAGAT-TATTGAATTACGATCACGACCTTC
* *
40349912 TGCTTACAAGATTTTTAGAATATTACAGTTTGTTGATTTA
1 TGCTTACAAGATTTTAAGAATATTACAGTTCGTTGATTTA
40349952 AGATTCTCAA
Statistics
Matches: 163, Mismatches: 37, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
161 7 0.04
162 153 0.94
163 3 0.02
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (162 bp):
TGCTTACAAGATTTTAAGAATATTACAGTTCGTTGATTTACGATCACGACCTTCTGCTAACAAGA
TTTTAAAAATCTTACGACCCACTGATTTACGATCACAACCTTCTACTTACAAGATTTTAAGCAAT
CTAAAGATTATTGAATTACGATCACGACCTTC
Found at i:40360120 original size:43 final size:43
Alignment explanation
Indices: 40360073--40360156 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
40360063 AATTTAACTT
40360073 TTTTTAACATTAAC-GACCACCATGTTTAAGTTGGATCAAAAAC
1 TTTTTAACATTAACAG-CCACCATGTTTAAGTTGGATCAAAAAC
* *
40360116 TTTTTAACATTAACAGTCACCATGTTTAGGTTGGATCAAAA
1 TTTTTAACATTAACAGCCACCATGTTTAAGTTGGATCAAAA
40360157 CCTACAGCCT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 37 0.97
44 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.35
Consensus pattern (43 bp):
TTTTTAACATTAACAGCCACCATGTTTAAGTTGGATCAAAAAC
Found at i:40362643 original size:9 final size:9
Alignment explanation
Indices: 40362631--40362659 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
40362621 AATTTATAAA
40362631 AAAAATTAT
1 AAAAATTAT
40362640 AAAAATTAT
1 AAAAATTAT
40362649 -AAAATTAT
1 AAAAATTAT
40362657 AAA
1 AAA
40362660 TTTTTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:40362648 original size:21 final size:20
Alignment explanation
Indices: 40362612--40362652 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
40362602 AAGCCCTTTT
*
40362612 AAAATTTAAAATTTATAAAA
1 AAAATTTAAAAATTATAAAA
40362632 AAAATTATAAAAATTATAAAA
1 AAAATT-TAAAAATTATAAAA
40362653 TTATAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAATTTAAAAATTATAAAA
Found at i:40362807 original size:13 final size:13
Alignment explanation
Indices: 40362789--40362827 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
40362779 ATTTTAAAAA
40362789 TTTTATAACTTTT
1 TTTTATAACTTTT
40362802 TTTTATAACTTTT
1 TTTTATAACTTTT
*
40362815 GTTTATAA-TTTT
1 TTTTATAACTTTT
40362827 T
1 T
40362828 ATGATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 4 0.17
13 20 0.83
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (13 bp):
TTTTATAACTTTT
Found at i:40362826 original size:22 final size:20
Alignment explanation
Indices: 40362801--40362846 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
40362791 TTATAACTTT
*
40362801 TTTTTATAACTTTTGTTTATAA
1 TTTTTATAA-TTTT-TTAATAA
*
40362823 TTTTTATGATTTTTTAATAA
1 TTTTTATAATTTTTTAATAA
40362843 TTTT
1 TTTT
40362847 AAAATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.45
21 4 0.18
22 8 0.36
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.67
Consensus pattern (20 bp):
TTTTTATAATTTTTTAATAA
Found at i:40365347 original size:22 final size:22
Alignment explanation
Indices: 40365298--40365340 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
40365288 AATTTTCCTC
*
40365298 ATTATTATGCTATTATCTTTGT
1 ATTATTATGCTATTATATTTGT
*
40365320 ATTATTATTGTTATTATATTT
1 ATTATTA-TGCTATTATATTT
40365341 TGTTATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.26, C:0.05, G:0.07, T:0.63
Consensus pattern (22 bp):
ATTATTATGCTATTATATTTGT
Found at i:40365369 original size:3 final size:3
Alignment explanation
Indices: 40365361--40365387 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
40365351 CTAGTTTAAA
40365361 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
40365388 GATTTATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:40365724 original size:6 final size:6
Alignment explanation
Indices: 40365713--40365753 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
40365703 TAATTCTAAA
40365713 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
40365754 TTCTTTATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:40365929 original size:46 final size:46
Alignment explanation
Indices: 40365878--40365977 Score: 130
Period size: 46 Copynumber: 2.2 Consensus size: 46
40365868 AATTTTAAAT
* **
40365878 ACATACATACATATATTCTTCGTATTTTATAA-CTTTATGTATATAC
1 ACATACATACATATATT-TTCATATTTTATAATCTTTAAATATATAC
* * *
40365924 ACATACTTACATATATTTTTATATTTTATAATTTTTAAATATATAC
1 ACATACATACATATATTTTCATATTTTATAATCTTTAAATATATAC
40365970 ACATACAT
1 ACATACAT
40365978 GTATGTCTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
45 12 0.26
46 34 0.74
ACGTcount: A:0.38, C:0.13, G:0.02, T:0.47
Consensus pattern (46 bp):
ACATACATACATATATTTTCATATTTTATAATCTTTAAATATATAC
Found at i:40371025 original size:9 final size:9
Alignment explanation
Indices: 40371002--40371054 Score: 61
Period size: 9 Copynumber: 5.6 Consensus size: 9
40370992 GAATGTTAAA
*
40371002 AAAAACAAAC
1 AAAAA-AAAG
40371012 AAAAAATAAG
1 AAAAAA-AAG
40371022 AAAAGAAAAG
1 AAAA-AAAAG
40371032 AAAAAAAAG
1 AAAAAAAAG
*
40371041 AAGAAAAAG
1 AAAAAAAAG
40371050 AAAAA
1 AAAAA
40371055 GGAGAGGCCA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
9 18 0.47
10 18 0.47
11 2 0.05
ACGTcount: A:0.83, C:0.04, G:0.11, T:0.02
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:40371543 original size:100 final size:105
Alignment explanation
Indices: 40371420--40371628 Score: 252
Period size: 108 Copynumber: 2.0 Consensus size: 105
40371410 CATTGTGATA
** * * *
40371420 ATCTTATTCATTTCGTATCTTAGCAAAATTTTCTA-T-CTTAATTGA-T-TTT-GAGCTTTGTTC
1 ATCTTATTCATTTCGTATCTTAGCAAAATTCGCTATTGATTAATTGATTGTTTAGAGCTCTGCTC
40371480 TCAATAAAATTTCATCTTAT-CCATTGTGATAATCCTTTTC
66 TCAATAAAATTTCATCTT-TCCCATTGTGATAATCCTTTTC
* *
40371520 ATCTTATTCATTTTG-AGTCTTAGCAAAATTCGCTATTTTGATTAATTTATTTGTTTAGAGCTCT
1 ATCTTATTCATTTCGTA-TCTTAGCAAAATTCGCTA--TTGATTAATTGA-TTGTTTAGAGCTCT
*
40371584 GCTCTCAATAAAATTTCATCTTTCCCATTGTGATAATCTTTTTC
62 GCTCTCAATAAAATTTCATCTTTCCCATTGTGATAATCCTTTTC
40371628 A
1 A
40371629 AGCATTTTCT
Statistics
Matches: 91, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
99 1 0.01
100 30 0.33
103 1 0.01
104 7 0.08
106 1 0.01
107 4 0.04
108 47 0.52
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.48
Consensus pattern (105 bp):
ATCTTATTCATTTCGTATCTTAGCAAAATTCGCTATTGATTAATTGATTGTTTAGAGCTCTGCTC
TCAATAAAATTTCATCTTTCCCATTGTGATAATCCTTTTC
Found at i:40372733 original size:89 final size:89
Alignment explanation
Indices: 40372506--40372733 Score: 305
Period size: 89 Copynumber: 2.6 Consensus size: 89
40372496 AAATTGTAGA
* * * * *
40372506 GGAGTAGACTAGAAGCAACATATCTTGTCTTCCTGTACTGGCAGTGAAGCAGATCGAAGACACAA
1 GGAGCAGACTAAAAGCAACAGATCTTGTCTTCCTGTACTGGCAGTGAAGCAGACCAAAGACACAA
40372571 GCCTGAACTCCCCGAGTTTACAGC
66 GCCTGAACTCCCCGAGTTTACAGC
* * * * * *
40372595 AGAGCAAACTAAAAGCAGCAGATCTTGTCTTCCTGTACCGACAGCGAAGCAGACCAAAGACACAA
1 GGAGCAGACTAAAAGCAACAGATCTTGTCTTCCTGTACTGGCAGTGAAGCAGACCAAAGACACAA
* * *
40372660 TCCT-AACCTCCCTGAGTTTGCAGC
66 GCCTGAA-CTCCCCGAGTTTACAGC
*
40372684 GGAGCAGACTAAAAGTAACAGATCTTGTCTTCCTGTACTGGCAGTGAAGC
1 GGAGCAGACTAAAAGCAACAGATCTTGTCTTCCTGTACTGGCAGTGAAGC
40372734 GGATCAAAAA
Statistics
Matches: 117, Mismatches: 21, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
88 2 0.02
89 115 0.98
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (89 bp):
GGAGCAGACTAAAAGCAACAGATCTTGTCTTCCTGTACTGGCAGTGAAGCAGACCAAAGACACAA
GCCTGAACTCCCCGAGTTTACAGC
Found at i:40373283 original size:41 final size:41
Alignment explanation
Indices: 40373230--40373429 Score: 238
Period size: 41 Copynumber: 4.8 Consensus size: 41
40373220 AAAGGACAGA
* *
40373230 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAG
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCAAG
*
40373271 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAG
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCAAG
* * *
40373312 TATTATCTCTCTGAAGTTGCAGTAGAGCAGATCATATGAAG
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCAAG
* * * * * * * *
40373353 TCTCATTTCCCTGAAGTTGTAGTGGAGCAGACTGAAGATAGCAAA
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-T-CACAT--CAAG
40373398 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGAT
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGAT
40373430 TAAAGCTATA
Statistics
Matches: 135, Mismatches: 20, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
41 102 0.76
42 1 0.01
43 3 0.02
44 1 0.01
45 28 0.21
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (41 bp):
TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCAAG
Found at i:40375120 original size:3 final size:3
Alignment explanation
Indices: 40375112--40375194 Score: 57
Period size: 3 Copynumber: 27.3 Consensus size: 3
40375102 ATTATCTTTG
* * *
40375112 TAT TAT TAT TAT TAT TA- TAT T-T TGTT TATT TAT CTAGT T-T AAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TA-T TAT -TA-T TAT TAT TAT
*
40375158 TAT TAAT CA- TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
40375195 TATTCATTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
2 6 0.09
3 47 0.73
4 10 0.16
5 1 0.02
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:40375707 original size:46 final size:46
Alignment explanation
Indices: 40375656--40375757 Score: 125
Period size: 46 Copynumber: 2.2 Consensus size: 46
40375646 GTAATTTTAA
* **
40375656 ATACATACATACATATATTCTTCGTATTTTATAA-CTTTATGTATAT
1 ATACATACATACATATATT-TTCATATTTTATAATCTTTAAATATAT
* * *
40375702 ATACATACTTACATATATTTTTATATTTTATAATTTTTAAATATAT
1 ATACATACATACATATATTTTCATATTTTATAATCTTTAAATATAT
*
40375748 ACACATACAT
1 ATACATACAT
40375758 GTATTTCTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
45 12 0.26
46 35 0.74
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (46 bp):
ATACATACATACATATATTTTCATATTTTATAATCTTTAAATATAT
Found at i:40375763 original size:42 final size:41
Alignment explanation
Indices: 40375633--40375763 Score: 113
Period size: 42 Copynumber: 3.1 Consensus size: 41
40375623 ACACTTGCAC
** *
40375633 ATTTTTGTATTTCGTAA-TTTTAAATACAT-ACATACATAT
1 ATTTTTGTATTTTATAATTTTTAAATATATAACATACATAT
* * * *
40375672 ATTCTTCGTATTTTATAACTTTATGTATATATACATACTTACATAT
1 ATT-TTTGTATTTTATAA-TTT-T-TAAATATATA-ACATACATAT
* *
40375718 ATTTTTATATTTTATAATTTTTAAATATATACACATACATGT
1 ATTTTTGTATTTTATAATTTTTAAATATATA-ACATACATAT
40375760 ATTT
1 ATTT
40375764 CTTTTTACCC
Statistics
Matches: 71, Mismatches: 14, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
39 3 0.04
40 11 0.15
42 22 0.31
43 2 0.03
44 9 0.13
45 12 0.17
46 12 0.17
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.51
Consensus pattern (41 bp):
ATTTTTGTATTTTATAATTTTTAAATATATAACATACATAT
Found at i:40379964 original size:2 final size:2
Alignment explanation
Indices: 40379957--40379981 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40379947 TAGTTGTAGG
40379957 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
40379982 GCCACCCAGG
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:40383254 original size:7 final size:6
Alignment explanation
Indices: 40383218--40383252 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
40383208 TTAAAAGAAA
* *
40383218 GAAAGG GAAAGG GAAAAG GAAAAG GAAAAG GAAAA
1 GAAAAG GAAAAG GAAAAG GAAAAG GAAAAG GAAAA
40383253 AGAACACAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (6 bp):
GAAAAG
Found at i:40384515 original size:31 final size:31
Alignment explanation
Indices: 40384478--40384546 Score: 113
Period size: 31 Copynumber: 2.2 Consensus size: 31
40384468 ATTAAAGCCC
40384478 AATGACTTAAATAAAATTTTTTGAATAG-TT
1 AATGACTTAAATAAAATTTTTTGAATAGTTT
*
40384508 AAGTGACTTAAATGAAATTTTTTGAATAGTTT
1 AA-TGACTTAAATAAAATTTTTTGAATAGTTT
40384540 AATGACT
1 AATGACT
40384547 ATTTTGTAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
30 2 0.06
31 30 0.83
32 4 0.11
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.42
Consensus pattern (31 bp):
AATGACTTAAATAAAATTTTTTGAATAGTTT
Found at i:40385947 original size:27 final size:25
Alignment explanation
Indices: 40385900--40385949 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
40385890 AGAATTATCA
*
40385900 ATTAAAAATAAAAAACTTGAAAACT
1 ATTAAAAATAAAAAACATGAAAACT
*
40385925 ATTATAAAATAAAGAAAGATGAAAA
1 ATTA-AAAATAAA-AAACATGAAAA
40385950 GAATAAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 8 0.38
27 9 0.43
ACGTcount: A:0.66, C:0.04, G:0.08, T:0.22
Consensus pattern (25 bp):
ATTAAAAATAAAAAACATGAAAACT
Found at i:40385969 original size:19 final size:20
Alignment explanation
Indices: 40385932--40385976 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
40385922 ACTATTATAA
40385932 AATAAAGAAAGATGAAAAG-
1 AATAAAGAAAGATGAAAAGC
*
40385951 AATAAAGAAAATATG-AAAGC
1 AATAAAG-AAAGATGAAAAGC
40385971 AATAAA
1 AATAAA
40385977 TAATGTACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.69, C:0.02, G:0.16, T:0.13
Consensus pattern (20 bp):
AATAAAGAAAGATGAAAAGC
Found at i:40398057 original size:9 final size:10
Alignment explanation
Indices: 40398043--40398082 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
40398033 ATTATTTTTT
40398043 AAAATT-TAA
1 AAAATTATAA
*
40398052 AAAATTATTA
1 AAAATTATAA
40398062 AAAATT-T-A
1 AAAATTATAA
40398070 AAAATTATAA
1 AAAATTATAA
40398080 AAA
1 AAA
40398083 GAGTATTTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
8 7 0.26
9 8 0.30
10 12 0.44
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAATTATAA
Found at i:40398082 original size:18 final size:19
Alignment explanation
Indices: 40398043--40398082 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
40398033 ATTATTTTTT
*
40398043 AAAATTTAAAAAATTATTA
1 AAAATTTAAAAAATTATAA
40398062 AAAATTT-AAAAATTATAA
1 AAAATTTAAAAAATTATAA
40398080 AAA
1 AAA
40398083 GAGTATTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATTTAAAAAATTATAA
Found at i:40401490 original size:5 final size:5
Alignment explanation
Indices: 40401480--40401504 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
40401470 CTAAAATTAT
40401480 GAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA
40401505 TGTTCAACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:40409199 original size:23 final size:23
Alignment explanation
Indices: 40409173--40409217 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
40409163 AAATATTAAA
* * *
40409173 ATTTGAAAAATTGGGTTTTGTTT
1 ATTTCAAAAATTAGGTCTTGTTT
*
40409196 ATTTCAAAGATTAGGTCTTGTT
1 ATTTCAAAAATTAGGTCTTGTT
40409218 CTTGTTTTTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.04, G:0.20, T:0.49
Consensus pattern (23 bp):
ATTTCAAAAATTAGGTCTTGTTT
Found at i:40414834 original size:25 final size:25
Alignment explanation
Indices: 40414764--40414839 Score: 59
Period size: 25 Copynumber: 3.0 Consensus size: 25
40414754 GACAAATGCA
*
40414764 TTTCACAAGATTAGTCATAAAGGC-
1 TTTCACAAGATTAGCCATAAAGGCT
* * *
40414788 -TTC-CCAGCTTATACGCCTTAAAGGCT
1 TTTCACAAG-AT-TA-GCCATAAAGGCT
*
40414814 TTTCACAAGATTAGCCATAAAAGCT
1 TTTCACAAGATTAGCCATAAAGGCT
40414839 T
1 T
40414840 CTAAGATAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 11
0.67 0.14 0.19
Matches are distributed among these distances:
22 3 0.08
23 4 0.11
24 2 0.05
25 20 0.53
26 2 0.05
27 4 0.11
28 3 0.08
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.30
Consensus pattern (25 bp):
TTTCACAAGATTAGCCATAAAGGCT
Found at i:40414860 original size:25 final size:25
Alignment explanation
Indices: 40414827--40414884 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
40414817 CACAAGATTA
* *
40414827 GCCATAAAAGCTT-CTAAGATAATAT
1 GCCACAAAAGCTTCCT-AGATAATAC
*
40414852 TCCACAAAAGCTTCCTAGATAATAC
1 GCCACAAAAGCTTCCTAGATAATAC
40414877 GCCACAAA
1 GCCACAAA
40414885 CACTTTTCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 26 0.93
26 2 0.07
ACGTcount: A:0.43, C:0.24, G:0.10, T:0.22
Consensus pattern (25 bp):
GCCACAAAAGCTTCCTAGATAATAC
Found at i:40416920 original size:58 final size:59
Alignment explanation
Indices: 40416850--40416968 Score: 213
Period size: 59 Copynumber: 2.0 Consensus size: 59
40416840 AAAGCTACCA
40416850 ATAATGCGATAGAATTACCAATCTCC-TCATACTCCCAATGTAGTGCACTAATAATAAT
1 ATAATGCGATAGAATTACCAATCTCCTTCATACTCCCAATGTAGTGCACTAATAATAAT
* *
40416908 ATAATGCGATAGAATTGCCAATCTCCTTGATACTCCCAATGTAGTGCACTAATAATAAT
1 ATAATGCGATAGAATTACCAATCTCCTTCATACTCCCAATGTAGTGCACTAATAATAAT
40416967 AT
1 AT
40416969 TGTGGATTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
58 25 0.43
59 33 0.57
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (59 bp):
ATAATGCGATAGAATTACCAATCTCCTTCATACTCCCAATGTAGTGCACTAATAATAAT
Found at i:40420575 original size:14 final size:14
Alignment explanation
Indices: 40420538--40420588 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
40420528 GAAACCAGTT
*
40420538 AAAACAATTATAG-
1 AAAACAATTACAGC
40420551 AAATACAAATTACAGTC
1 AAA-AC-AATTACAG-C
40420568 -AAACAATTACAGC
1 AAAACAATTACAGC
40420581 AAAACAAT
1 AAAACAAT
40420589 CAAACTAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
13 4 0.12
14 17 0.53
15 9 0.28
16 2 0.06
ACGTcount: A:0.59, C:0.16, G:0.06, T:0.20
Consensus pattern (14 bp):
AAAACAATTACAGC
Found at i:40435493 original size:36 final size:36
Alignment explanation
Indices: 40435453--40435582 Score: 161
Period size: 36 Copynumber: 3.6 Consensus size: 36
40435443 TGGGCACACG
* *
40435453 CAAGATACGATAGTTCGCTGGACCTATCTCCTGATT
1 CAAGATACGACAGTTCGCTGGACCTATCTCATGATT
* * *
40435489 CAAGATACGACAATTCGCAGGACCTACCTCATGATT
1 CAAGATACGACAGTTCGCTGGACCTATCTCATGATT
* * *
40435525 CAAGATACAACAGTTCGCTGGACCTATCTTATGATA
1 CAAGATACGACAGTTCGCTGGACCTATCTCATGATT
* * *
40435561 CATGTTACGACAGTCCGCTGGA
1 CAAGATACGACAGTTCGCTGGA
40435583 TTTGTTCTCT
Statistics
Matches: 79, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 79 1.00
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.26
Consensus pattern (36 bp):
CAAGATACGACAGTTCGCTGGACCTATCTCATGATT
Found at i:40439770 original size:24 final size:24
Alignment explanation
Indices: 40439741--40439804 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 24
40439731 GTGATTATAA
*
40439741 AATTAAAATACT-AAATTATATTAG
1 AATTAAAATA-TAAAATTAAATTAG
*
40439765 AATTAAAATATAAAATTAAATTCG
1 AATTAAAATATAAAATTAAATTAG
*
40439789 AATTTTAAATATAAAA
1 AA-TTAAAATATAAAA
40439805 ACTAAAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
23 1 0.03
24 22 0.63
25 12 0.34
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (24 bp):
AATTAAAATATAAAATTAAATTAG
Found at i:40443726 original size:43 final size:43
Alignment explanation
Indices: 40443673--40443911 Score: 309
Period size: 43 Copynumber: 5.6 Consensus size: 43
40443663 TTTTAGAAAT
*
40443673 AAACGCCGCTATAGACCATGACCTTTAGCGGCACTTTTCCCAC
1 AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* *
40443716 AAACACCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* * *
40443759 AAATGCCGCTATAGACCATGACCTTTAGCGGC-ATTTTTCCAC
1 AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* *
40443801 AAACGCCGATATAGACCATGACCTTTAGCAGCGCTTTTCCCAC
1 AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* * * * ** *
40443844 AAACGCAGCTAAAGGCTATGACCTTTAGCGGCGCTTTTGTCAG
1 AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* * *
40443887 AAATGTCGCTAAAGACCATGACCTT
1 AAACGCCGCTATAGACCATGACCTT
40443912 CAGTAACGCT
Statistics
Matches: 168, Mismatches: 27, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
42 37 0.22
43 131 0.78
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:40443840 original size:85 final size:86
Alignment explanation
Indices: 40443673--40443946 Score: 316
Period size: 85 Copynumber: 3.2 Consensus size: 86
40443663 TTTTAGAAAT
*
40443673 AAACGCCGCTATAGACCATGACCTTTAGCGGCACTTTTCCCACAAACACCGCTAAAGACCATGAC
1 AAACGCCGCTATAGACCATGACCTTTAGCGGCACTTTTCCCACAAACACCGATAAAGACCATGAC
*
40443738 CTTTAGCGGCGCTTTTCCCAC
66 CTTTAGCAGCGCTTTTCCCAC
* * * *
40443759 AAATGCCGCTATAGACCATGACCTTTAGCGGCA-TTTTTCCACAAACGCCGATATAGACCATGAC
1 AAACGCCGCTATAGACCATGACCTTTAGCGGCACTTTTCCCACAAACACCGATAAAGACCATGAC
40443823 CTTTAGCAGCGCTTTTCCCAC
66 CTTTAGCAGCGCTTTTCCCAC
* * * * * ** * *** *
40443844 AAACGCAGCTAAAGGCTATGACCTTTAGCGGCGCTTTTGTCAGAAATGTCGCTAAAGACCATGAC
1 AAACGCCGCTATAGACCATGACCTTTAGCGGCACTTTTCCCACAAACACCGATAAAGACCATGAC
* * * **
40443909 CTTCAGTAACGCTTTTTTATCAC
66 CTTTAGCAGCGC--TTTTCCCAC
40443932 AAACGCCGCTATAGA
1 AAACGCCGCTATAGA
40443947 ACAAACTTTT
Statistics
Matches: 158, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
85 74 0.47
86 65 0.41
88 19 0.12
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.25
Consensus pattern (86 bp):
AAACGCCGCTATAGACCATGACCTTTAGCGGCACTTTTCCCACAAACACCGATAAAGACCATGAC
CTTTAGCAGCGCTTTTCCCAC
Found at i:40443903 original size:128 final size:128
Alignment explanation
Indices: 40443673--40443911 Score: 370
Period size: 128 Copynumber: 1.9 Consensus size: 128
40443663 TTTTAGAAAT
* * *
40443673 AAACGCCGCTATAGACCATGACCTTTAGCGGCACTTTTCCCACAAACACCGCTAAAGACCATGAC
1 AAACGCCGATATAGACCATGACCTTTAGCAGCACTTTTCCCACAAACACAGCTAAAGACCATGAC
*
40443738 CTTTAGCGGCGCTTTTCCCACAAATGCCGCTATAGACCATGACCTTTAGCGGCATTTTTCCAC
66 CTTTAGCGGCGCTTTTCCCACAAATGCCGCTAAAGACCATGACCTTTAGCGGCATTTTTCCAC
* * * *
40443801 AAACGCCGATATAGACCATGACCTTTAGCAGCGCTTTTCCCACAAACGCAGCTAAAGGCTATGAC
1 AAACGCCGATATAGACCATGACCTTTAGCAGCACTTTTCCCACAAACACAGCTAAAGACCATGAC
** * *
40443866 CTTTAGCGGCGCTTTTGTCAGAAATGTCGCTAAAGACCATGACCTT
66 CTTTAGCGGCGCTTTTCCCACAAATGCCGCTAAAGACCATGACCTT
40443912 CAGTAACGCT
Statistics
Matches: 99, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
128 99 1.00
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (128 bp):
AAACGCCGATATAGACCATGACCTTTAGCAGCACTTTTCCCACAAACACAGCTAAAGACCATGAC
CTTTAGCGGCGCTTTTCCCACAAATGCCGCTAAAGACCATGACCTTTAGCGGCATTTTTCCAC
Found at i:40445619 original size:39 final size:39
Alignment explanation
Indices: 40445565--40445644 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
40445555 GTATAATGTG
40445565 CATAGTCAACACAGTTAGCAGTTTAACTTTTATGATTTC
1 CATAGTCAACACAGTTAGCAGTTTAACTTTTATGATTTC
40445604 CATAGTCAACACAGTTAGCAGTTTAACTTTTATGATTTC
1 CATAGTCAACACAGTTAGCAGTTTAACTTTTATGATTTC
40445643 CA
1 CA
40445645 AACACATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (39 bp):
CATAGTCAACACAGTTAGCAGTTTAACTTTTATGATTTC
Found at i:40447880 original size:3 final size:3
Alignment explanation
Indices: 40447872--40447913 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
40447862 AAGATATAAA
40447872 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
40447914 GGGCGATGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:40449016 original size:29 final size:29
Alignment explanation
Indices: 40448947--40449009 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
40448937 TACTAATTAA
* **
40448947 TCTAAACCCTAAACCCCTAACCCCTATTC
1 TCTAAACCCTAAACCCCTAACACCTAACC
*
40448976 TCTAAACCCTAAACCCCTAACACTTAACC
1 TCTAAACCCTAAACCCCTAACACCTAACC
40449005 TCTAA
1 TCTAA
40449010 CTCCTAACCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.35, C:0.41, G:0.00, T:0.24
Consensus pattern (29 bp):
TCTAAACCCTAAACCCCTAACACCTAACC
Found at i:40449538 original size:41 final size:40
Alignment explanation
Indices: 40449434--40449590 Score: 163
Period size: 41 Copynumber: 3.9 Consensus size: 40
40449424 GATGGTTTTT
****
40449434 GCGGCGCTTTTTAAAAAACGCCGCTAAA-AATAGAGCATTA
1 GCGGCGC-TTTTAAAAAACGCCGCTAAAGCCCCGAGCATTA
** *
40449474 GCGGCGCTTATTGGAAAACGCCGCTAAAGCCCTGAGCATTA
1 GCGGCGCTT-TTAAAAAACGCCGCTAAAGCCCCGAGCATTA
* * * *
40449515 GCGGTGCTTCTTAAAAAATGCCGCTAAAACCCCGAGCACTA
1 GCGGCGCTT-TTAAAAAACGCCGCTAAAGCCCCGAGCATTA
*
40449556 GTGGCGCTTTTCAAAAAACGCCGCTAAAGCCCCGA
1 GCGGCGCTTTT-AAAAAACGCCGCTAAAGCCCCGA
40449591 AAGCTCAGAA
Statistics
Matches: 96, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
39 2 0.02
40 25 0.26
41 69 0.72
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (40 bp):
GCGGCGCTTTTAAAAAACGCCGCTAAAGCCCCGAGCATTA
Found at i:40453022 original size:57 final size:57
Alignment explanation
Indices: 40452840--40453022 Score: 249
Period size: 57 Copynumber: 3.2 Consensus size: 57
40452830 AACCAATTTG
* * *
40452840 ATATAACATTAAAATGAATTATGTGAAATTAGTATGATCTTATAGATTGATAATAGA
1 ATATGACATTGAAATGAATTATGTGAAATTTGTATGATCTTATAGATTGATAATAGA
* * *
40452897 ATACGACATTGAAATGAATCATGTGAAATTTGTATGATCCTATAGATTGATAATAGA
1 ATATGACATTGAAATGAATTATGTGAAATTTGTATGATCTTATAGATTGATAATAGA
* * * ** *
40452954 ATGTGACATTGAAATGAATTATGTGAAATTTGTATGATATTATGGATTGATGGTGGA
1 ATATGACATTGAAATGAATTATGTGAAATTTGTATGATCTTATAGATTGATAATAGA
*
40453011 ATATGAAATTGA
1 ATATGACATTGA
40453023 GGTGAGTTGT
Statistics
Matches: 109, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 109 1.00
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.36
Consensus pattern (57 bp):
ATATGACATTGAAATGAATTATGTGAAATTTGTATGATCTTATAGATTGATAATAGA
Found at i:40466580 original size:29 final size:29
Alignment explanation
Indices: 40466537--40466693 Score: 147
Period size: 29 Copynumber: 5.4 Consensus size: 29
40466527 TCTCACCATG
*
40466537 AAGACGTCCTTTTAATAGAGATAGCCACA
1 AAGACATCCTTTTAATAGAGATAGCCACA
* * * * *
40466566 AATACATCCTCTTAACAAAGATAGTCACA
1 AAGACATCCTTTTAATAGAGATAGCCACA
*
40466595 AAGACTTCCTTTTAATAGAGATAGCCACA
1 AAGACATCCTTTTAATAGAGATAGCCACA
* * *
40466624 AAGGCATACATTTAACTA-AGATAGCCACA
1 AAGACATCCTTTTAA-TAGAGATAGCCACA
* * *
40466653 AAGGCATCCTTTTAACAAAGATCA-CCACA
1 AAGACATCCTTTTAATAGAGAT-AGCCACA
* *
40466682 AAGGCTTCCTTT
1 AAGACATCCTTT
40466694 CAGAGATTAC
Statistics
Matches: 105, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
28 1 0.01
29 101 0.96
30 3 0.03
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.25
Consensus pattern (29 bp):
AAGACATCCTTTTAATAGAGATAGCCACA
Found at i:40466606 original size:58 final size:58
Alignment explanation
Indices: 40466537--40466684 Score: 174
Period size: 58 Copynumber: 2.6 Consensus size: 58
40466527 TCTCACCATG
* * * *
40466537 AAGACGTCCTTTTAATAGAGATAGCCACAAATACAT-CCTCTTAACAAAGATAGTCACA
1 AAGACATCCTTTTAATAGAGATAGCCACAAAGACATACAT-TTAACAAAGATAGCCACA
* * *
40466595 AAGACTTCCTTTTAATAGAGATAGCCACAAAGGCATACATTTAACTAAGATAGCCACA
1 AAGACATCCTTTTAATAGAGATAGCCACAAAGACATACATTTAACAAAGATAGCCACA
* * *
40466653 AAGGCATCCTTTTAACAAAGATCA-CCACAAAG
1 AAGACATCCTTTTAATAGAGAT-AGCCACAAAG
40466685 GCTTCCTTTC
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
58 75 0.96
59 3 0.04
ACGTcount: A:0.42, C:0.22, G:0.13, T:0.23
Consensus pattern (58 bp):
AAGACATCCTTTTAATAGAGATAGCCACAAAGACATACATTTAACAAAGATAGCCACA
Found at i:40468689 original size:51 final size:51
Alignment explanation
Indices: 40468632--40468816 Score: 200
Period size: 51 Copynumber: 3.6 Consensus size: 51
40468622 GGTTCACATC
* * *
40468632 GTAGCCTGCACATAGTATTACACATGTGACCATTAGCATTCGATACCCGTA
1 GTAGCCTGCACATAGTACTACACATGTGACCATTAACATTCGATACACGTA
* * * *
40468683 GTAGCCTGCACATAGTACTACACATGTG---ATTGAAACTATCCGGTACGCATA
1 GTAGCCTGCACATAGTACTACACATGTGACCATT--AAC-ATTCGATACACGTA
* * * *
40468734 GTAGCTTGCACATAGTACTACACATGCGACC--TATCATTTTGATACACGTA
1 GTAGCCTGCACATAGTACTACACATGTGACCATTAACA-TTCGATACACGTA
40468784 GTAGCCTGCACATAGTACTACACATGTGACCAT
1 GTAGCCTGCACATAGTACTACACATGTGACCAT
40468817 CACCTTCACT
Statistics
Matches: 109, Mismatches: 16, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
48 3 0.03
49 1 0.01
50 41 0.38
51 63 0.58
52 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (51 bp):
GTAGCCTGCACATAGTACTACACATGTGACCATTAACATTCGATACACGTA
Found at i:40468836 original size:101 final size:99
Alignment explanation
Indices: 40468627--40468812 Score: 257
Period size: 101 Copynumber: 1.8 Consensus size: 99
40468617 TGTTTGGTTC
* * * *
40468627 ACATCGTAGCCTGCACATAGTATTACACATGTGACCATTAGCATTCGATACCCGTAGTAGCCTGC
1 ACATAGTAGCCTGCACATAGTACTACACATGCGACCA-TAGCATTCGATACACGTAGTAGCCTGC
*
40468692 ACATAGTACTACACATGTGATTGAAACTATCCGGT
65 ACATAGTACTACACATGTGAATGAAACTATCCGGT
* * *
40468727 ACGCATAGTAGCTTGCACATAGTACTACACATGCGACC-TATCATTTTGATACACGTAGTAGCCT
1 A--CATAGTAGCCTGCACATAGTACTACACATGCGACCATAGCA-TTCGATACACGTAGTAGCCT
40468791 GCACATAGTACTACACATGTGA
63 GCACATAGTACTACACATGTGA
40468813 CCATCACCTT
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
100 5 0.07
101 40 0.53
102 31 0.41
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (99 bp):
ACATAGTAGCCTGCACATAGTACTACACATGCGACCATAGCATTCGATACACGTAGTAGCCTGCA
CATAGTACTACACATGTGAATGAAACTATCCGGT
Found at i:40471557 original size:51 final size:50
Alignment explanation
Indices: 40471477--40471815 Score: 323
Period size: 51 Copynumber: 6.7 Consensus size: 50
40471467 TATCGATGAA
* * *
40471477 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCG-TAAATATTGGT
* * * *
40471528 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCG-AGAAGTTTTGAG-
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGTA-AA-TATTG-GT
* ** * *
40471579 CACGTGTGTAGTACTGTGTGAAATCTACTACGTGTGTCGGTAAACTA-TGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGT-ACCGTAAA-TATTGGT
* * * * * *
40471630 TACATGTGTGGTACTAAGTGAAGGCTACTATG-GATACCGGAAATATTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG-TACCGTAAATA-TTGGT
* *
40471681 CACGTATGTAGTACTATGTGAAGGCTACTACGTG-AGCCGTAAA-ACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA-CCGTAAATA-TTGGT
* * * *
40471731 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACTGTAAA-ACTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGTAAATATTGGT
40471780 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
40471816 TCGAATGATA
Statistics
Matches: 235, Mismatches: 41, Indels: 26
0.78 0.14 0.09
Matches are distributed among these distances:
49 42 0.18
50 55 0.23
51 130 0.55
52 7 0.03
53 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGTAAATATTGGT
Found at i:40471653 original size:102 final size:102
Alignment explanation
Indices: 40471477--40471814 Score: 379
Period size: 102 Copynumber: 3.3 Consensus size: 102
40471467 TATCGATGAA
* *
40471477 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAA-TAATGGTCACATGTGTAGTA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTGTCGGTAAACT-ATGGTCACATGTGTAGTA
*
40471541 CTAAGTGAAGGCTACTATGTG-TACCGAGAAGT-TTTGAG-
65 CTAAGTGAAGGCTACTATG-GATACCG-GAAATATTTG-GT
** * *
40471579 CACGTGTGTAGTACTGTGTGAAATCTACTACGTGTGTCGGTAAACTATGGTTACATGTGTGGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTGTCGGTAAACTATGGTCACATGTGTAGTAC
40471644 TAAGTGAAGGCTACTATGGATACCGGAAATATTTGGT
66 TAAGTGAAGGCTACTATGGATACCGGAAATATTTGGT
* * * * * *
40471681 CACGTATGTAGTACTATGTGAAGGCTACTACGTGAG-CCGTAAAACT-TGATCACGTGTGTAGTA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTGTCGGT-AAACTATGGTCACATGTGTAGTA
* * * * * *
40471744 CTATGTGAAGGCTACTACGTGA-ACTGTAAA-A-CTGAT
65 CTAAGTGAAGGCTACTATG-GATACCGGAAATATTTGGT
*
40471780 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGT
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGT
40471815 ATCGAATGAT
Statistics
Matches: 205, Mismatches: 25, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
99 36 0.18
100 1 0.00
101 45 0.22
102 122 0.60
103 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (102 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTGTCGGTAAACTATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATGGATACCGGAAATATTTGGT
Found at i:40477226 original size:51 final size:50
Alignment explanation
Indices: 40477168--40477341 Score: 208
Period size: 51 Copynumber: 3.4 Consensus size: 50
40477158 ATCGTACCCA
* * **
40477168 GCACATAGTACTACACATGTGATCATTAGCATTCAATACACGTAGTAGCCT
1 GCACATAGTACTACACACGTGATCA-TAACATTCGGTACACGTAGTAGCCT
* *
40477219 GCACATAGTACTACACACGTGATCGA-AACTATCCGGTACGCGTAGTAGCCT
1 GCACATAGTACTACACACGTGATC-ATAAC-ATTCGGTACACGTAGTAGCCT
* * * *
40477270 GCACATAGTACTACACATGCGA-CCTATCATTCTGGTACACGTAGTAGCCT
1 GCACATAGTACTACACACGTGATCATAACATTC-GGTACACGTAGTAGCCT
40477320 GCACATAGTACTACACACGTGA
1 GCACATAGTACTACACACGTGA
40477342 CCATCACTTT
Statistics
Matches: 105, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
49 3 0.03
50 41 0.39
51 60 0.57
52 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (50 bp):
GCACATAGTACTACACACGTGATCATAACATTCGGTACACGTAGTAGCCT
Found at i:40503633 original size:11 final size:11
Alignment explanation
Indices: 40503596--40503636 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
40503586 ACTTACTAAT
40503596 TTTTCACA-CA
1 TTTTCACATCA
40503606 TTTTCAC-TGCA
1 TTTTCACAT-CA
*
40503617 TATTCACATCA
1 TTTTCACATCA
40503628 TTTTCACAT
1 TTTTCACAT
40503637 TATAATCACT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 7 0.27
11 18 0.69
12 1 0.04
ACGTcount: A:0.27, C:0.27, G:0.02, T:0.44
Consensus pattern (11 bp):
TTTTCACATCA
Found at i:40517071 original size:49 final size:48
Alignment explanation
Indices: 40517010--40517116 Score: 153
Period size: 49 Copynumber: 2.2 Consensus size: 48
40517000 AACATGCTCA
* *
40517010 CACACTTGTCTTATCAGAATGGCT-GAGAAACATAAAATATTTTCTCACC
1 CACACTTATCTTATCAGAATGG-TAGAGAAACATAAAA-ATGTTCTCACC
* *
40517059 CACACTTATCTTATCAGAATGGTAGAGGAACATAAAAATGTTCTCGCC
1 CACACTTATCTTATCAGAATGGTAGAGAAACATAAAAATGTTCTCACC
40517107 CACACTTATC
1 CACACTTATC
40517117 AGAATCTTGT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
48 20 0.38
49 33 0.62
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (48 bp):
CACACTTATCTTATCAGAATGGTAGAGAAACATAAAAATGTTCTCACC
Found at i:40517575 original size:13 final size:13
Alignment explanation
Indices: 40517536--40517581 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
40517526 GCGCTCACAT
40517536 AAAACATATCTTGA
1 AAAACATATCTT-A
** *
40517550 AAGTCATAACTTA
1 AAAACATATCTTA
40517563 AAAACATATCTTA
1 AAAACATATCTTA
40517576 AAAACA
1 AAAACA
40517582 GAGGTTTGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
13 17 0.65
14 9 0.35
ACGTcount: A:0.54, C:0.15, G:0.04, T:0.26
Consensus pattern (13 bp):
AAAACATATCTTA
Found at i:40532783 original size:44 final size:44
Alignment explanation
Indices: 40532588--40533300 Score: 215
Period size: 44 Copynumber: 16.4 Consensus size: 44
40532578 GATCTACTCT
* * * * *
40532588 CTGCAACTTCAAAGAGATAAGA-TTG-TGATTTTAATCCGCTCCA
1 CTGCAACTTCAGAGAGATAAGACTTGCTTA-CTTAGTCTGCTCCA
* * *
40532631 CTGCAACTTCA-AGGAGATAAGA-TT-ATTGGCCTTA-ACTTGCTCCA
1 CTGCAACTTCAGA-GAGATAAGACTTGCTT--ACTTAGTC-TGCTCCA
* * * ** * * *
40532675 TTGTAACTTCAGGGAGATAAGGTTTGCCGT-CTTCAGCCTGCCCCA
1 CTGCAACTTCAGAGAGATAAGACTTG-CTTACTT-AGTCTGCTCCA
40532720 CTGCAACTTCAG-GAGGATAAGACTTGCTTACTTAGTCTGCTCCA
1 CTGCAACTTCAGAGA-GATAAGACTTGCTTACTTAGTCTGCTCCA
* * * * * *
40532764 TTGCAACTTCAGAGAGATAAGACTAG-ATGC-GA-TCTGCT-CT
1 CTGCAACTTCAGAGAGATAAGACTTGCTTACTTAGTCTGCTCCA
** * * * *
40532804 CTGCAACTTCAGAGAGATAAGATCCAAGATTTC-AATTC-GCTCCA
1 CTGCAACTTCAGAGAGATAAGA--CTTGCTTACTTAGTCTGCTCCA
* * * * * **
40532848 CTACAACTTTAG-GTAGATAGGA-TT-ATTGGCTTTAACCTGCTCCA
1 CTGCAACTTCAGAG-AGATAAGACTTGCTT-AC-TTAGTCTGCTCCA
* ** *
40532892 CTGCAACTTCAGGGAGATAAGGTTTGC-CATCTTCAGTCTGC-CTCA
1 CTGCAACTTCAGAGAGATAAGACTTGCTTA-CTT-AGTCTGCTC-CA
40532937 CTGCAACTTCAG-GAGGATAAGACTTGCTTACTTAGTCTGCTCCA
1 CTGCAACTTCAGAGA-GATAAGACTTGCTTACTTAGTCTGCTCCA
* * * * *
40532981 CTGCAACTTCA-AGGAGATAAGACTAG-ATGC-GA-TCTGCT-CT
1 CTGCAACTTCAGA-GAGATAAGACTTGCTTACTTAGTCTGCTCCA
* ** * * *
40533021 CTGTAACTTCAGAGAGATAAGAACCAAGATT--TTAATCCGCTCCA
1 CTGCAACTTCAGAGAGATAAG-A-CTTGCTTACTTAGTCTGCTCCA
* * * * * **
40533065 CTACAACTTTAGGGAGATAAGA-TT-ATTGGCTTTAACCTGCTCCA
1 CTGCAACTTCAGAGAGATAAGACTTGCTT-AC-TTAGTCTGCTCCA
* * ** * *
40533109 TTGCAACTTCAGGGAGATAAGGTTTGC-CATCTTCAGTCTAC-CTCA
1 CTGCAACTTCAGAGAGATAAGACTTGCTTA-CTT-AGTCTGCTC-CA
* * *
40533154 TTGCAACTTCAGAAAGATAGGACTTGCTTACTTAGTCTGCTCCA
1 CTGCAACTTCAGAGAGATAAGACTTGCTTACTTAGTCTGCTCCA
* * * * * * *
40533198 CTGCAACTTCAGGGAGACAAGACTAG-ATGC-GA-TCTGCT-CT
1 CTGCAACTTCAGAGAGATAAGACTTGCTTACTTAGTCTGCTCCA
* * *
40533238 CTGTAACTTCAGAGAGATAAGATCTGTTG-TT--TTAATCCGCTCCA
1 CTGCAACTTCAGAGAGATAAGA-C--TTGCTTACTTAGTCTGCTCCA
*
40533282 CTGCAACTTCAGGGAGATA
1 CTGCAACTTCAGAGAGATA
40533301 GGATCATTGG
Statistics
Matches: 502, Mismatches: 109, Indels: 117
0.69 0.15 0.16
Matches are distributed among these distances:
40 67 0.13
41 22 0.04
42 12 0.02
43 54 0.11
44 236 0.47
45 107 0.21
46 3 0.01
47 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (44 bp):
CTGCAACTTCAGAGAGATAAGACTTGCTTACTTAGTCTGCTCCA
Found at i:40532941 original size:217 final size:217
Alignment explanation
Indices: 40532537--40533314 Score: 1141
Period size: 217 Copynumber: 3.6 Consensus size: 217
40532527 CTAGTGCTGC
* * * * *
40532537 AGTCTACTCCACAGCAA-TGTCAGGGAGATAAGACTAGATGCGATCTACTCTCTGCAACTTCAAA
1 AGTCTGCTCCACTGCAACT-TCAGAGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGA
*** * * * *
40532601 GAGATAAGAT-TGTGATTTTAATCCGCTCCACTGCAACTTCAAGGAGATAAGATTATTGGCCTTA
65 GAGATAAGATCCAAGATTTTAATCCGCTCCACTACAACTTTAGGGAGATAAGATTATTGGCTTTA
* * * * *
40532665 ACTTGCTCCATTGTAACTTCAGGGAGATAAGGTTTGCCGTCTTCAGCCTGCCCCACTGCAACTTC
130 ACCTGCTCCATTGCAACTTCAGGGAGATAAGGTTTGCCATCTTCAGTCTGCCTCACTGCAACTTC
40532730 AGGAGGATAAGACTTGCTTACTT
195 AGGAGGATAAGACTTGCTTACTT
*
40532753 AGTCTGCTCCATTGCAACTTCAGAGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAG
1 AGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAG
* * * *
40532818 AGATAAGATCCAAGATTTCAATTCGCTCCACTACAACTTTAGGTAGATAGGATTATTGGCTTTAA
66 AGATAAGATCCAAGATTTTAATCCGCTCCACTACAACTTTAGGGAGATAAGATTATTGGCTTTAA
*
40532883 CCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGCCATCTTCAGTCTGCCTCACTGCAACTTCA
131 CCTGCTCCATTGCAACTTCAGGGAGATAAGGTTTGCCATCTTCAGTCTGCCTCACTGCAACTTCA
40532948 GGAGGATAAGACTTGCTTACTT
196 GGAGGATAAGACTTGCTTACTT
*
40532970 AGTCTGCTCCACTGCAACTTCA-AGGAGATAAGACTAGATGCGATCTGCTCTCTGTAACTTCAGA
1 AGTCTGCTCCACTGCAACTTCAGA-GAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGA
*
40533034 GAGATAAGAACCAAGATTTTAATCCGCTCCACTACAACTTTAGGGAGATAAGATTATTGGCTTTA
65 GAGATAAGATCCAAGATTTTAATCCGCTCCACTACAACTTTAGGGAGATAAGATTATTGGCTTTA
* *
40533099 ACCTGCTCCATTGCAACTTCAGGGAGATAAGGTTTGCCATCTTCAGTCTACCTCATTGCAACTTC
130 ACCTGCTCCATTGCAACTTCAGGGAGATAAGGTTTGCCATCTTCAGTCTGCCTCACTGCAACTTC
* * *
40533164 AGAAAGATAGGACTTGCTTACTT
195 AGGAGGATAAGACTTGCTTACTT
* * *
40533187 AGTCTGCTCCACTGCAACTTCAGGGAGACAAGACTAGATGCGATCTGCTCTCTGTAACTTCAGAG
1 AGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAG
*** * * * *
40533252 AGATAAGATCTGTTG-TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATCATTGGCTTT
66 AGATAAGATC-CAAGATTTTAATCCGCTCCACTACAACTTTAGGGAGATAAGATTATTGGCTTT
40533315 CGATCTGTTC
Statistics
Matches: 511, Mismatches: 46, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
216 67 0.13
217 443 0.87
218 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (217 bp):
AGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAG
AGATAAGATCCAAGATTTTAATCCGCTCCACTACAACTTTAGGGAGATAAGATTATTGGCTTTAA
CCTGCTCCATTGCAACTTCAGGGAGATAAGGTTTGCCATCTTCAGTCTGCCTCACTGCAACTTCA
GGAGGATAAGACTTGCTTACTT
Found at i:40546405 original size:34 final size:34
Alignment explanation
Indices: 40546367--40546433 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
40546357 GTATTTCTTG
*
40546367 ATTGGTACGGGCCGGGTACCAATTGGGTATTACA
1 ATTGGTACGGGCCGGGTACAAATTGGGTATTACA
40546401 ATTGGTACGGGCCGGGTACAAATTGGGTATTAC
1 ATTGGTACGGGCCGGGTACAAATTGGGTATTAC
40546434 CATAACATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.24, C:0.16, G:0.33, T:0.27
Consensus pattern (34 bp):
ATTGGTACGGGCCGGGTACAAATTGGGTATTACA
Done.