Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 125 of 259
Found at i:40488401 original size:27 final size:27
Alignment explanation
Indices: 40488162--40488397 Score: 194
Period size: 27 Copynumber: 8.8 Consensus size: 27
40488152 CTCGATTTAC
* * **
40488162 AAAATTACTAAAATA-CCCTCGGTTTAC
1 AAAATTACCAAAATACCCCT-AGTTTGT
* **
40488189 AAAATTACCAAAATA-CCCTCGATCAGT
1 AAAATTACCAAAATACCCCTAG-TTTGT
* *
40488216 AAAATTACCAAAATA-CCCTAGTCTAT
1 AAAATTACCAAAATACCCCTAGTTTGT
* * * *
40488242 AAAATTGCTAAAATACCCTTGGTTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
** *
40488269 AAAATTACTGAAATA-CCCTCAATTTGT
1 AAAATTACCAAAATACCCCT-AGTTTGT
*
40488296 AAAATTACCAAAATACTCCTAGTTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
* *
40488323 AAAATTACCAAAATACCACTGGTTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
* * *
40488350 GAAATTACCGAAATA-CCCTCAATTTGT
1 AAAATTACCAAAATACCCCT-AGTTTGT
*
40488377 AAAATTACCAGAATACCCCTA
1 AAAATTACCAAAATACCCCTA
40488398 ATTTACAAAG
Statistics
Matches: 168, Mismatches: 35, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
26 23 0.14
27 138 0.82
28 7 0.04
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.29
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTAGTTTGT
Found at i:40488418 original size:81 final size:80
Alignment explanation
Indices: 40488156--40488422 Score: 313
Period size: 81 Copynumber: 3.3 Consensus size: 80
40488146 TTTACCCTCG
** * * **
40488156 ATTTACAAAATTACTAAAATACCCTCGGTTTACAAAATTACCAAAATACCCTCGATCAGTAAAAT
1 ATTTACAAAATTACTAAAATACCCT-GGTTTGTAAAATTACCGAAATACCCTCAATTTGTAAAAT
40488221 TACCAAAATA-CCCTA
65 TACCAAAATACCCCTA
* * * * *
40488236 GTCTATAAAATTGCTAAAATACCCTTGGTTTGTAAAATTACTGAAATACCCTCAATTTGTAAAAT
1 ATTTACAAAATTACTAAAATACCC-TGGTTTGTAAAATTACCGAAATACCCTCAATTTGTAAAAT
*
40488301 TACCAAAATACTCCTA
65 TACCAAAATACCCCTA
* ** * *
40488317 GTTTGTAAAATTACCAAAATACCACTGGTTTGTGAAATTACCGAAATACCCTCAATTTGTAAAAT
1 ATTTACAAAATTACTAAAATACC-CTGGTTTGTAAAATTACCGAAATACCCTCAATTTGTAAAAT
*
40488382 TACCAGAATACCCCTA
65 TACCAAAATACCCCTA
*
40488398 ATTTACAAAGTTAC-AGAAATACCCT
1 ATTTACAAAATTACTA-AAATACCCT
40488423 TGACTTTCTA
Statistics
Matches: 159, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
80 65 0.41
81 93 0.58
82 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (80 bp):
ATTTACAAAATTACTAAAATACCCTGGTTTGTAAAATTACCGAAATACCCTCAATTTGTAAAATT
ACCAAAATACCCCTA
Found at i:40488494 original size:27 final size:27
Alignment explanation
Indices: 40488433--40488484 Score: 88
Period size: 27 Copynumber: 1.9 Consensus size: 27
40488423 TGACTTTCTA
40488433 AAAATTA-TGGAAATACCATTGGTTTAC
1 AAAATTACT-GAAATACCATTGGTTTAC
40488460 AAAATTACTGAAATACCATTGGTTT
1 AAAATTACTGAAATACCATTGGTTT
40488485 GTAGATTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (27 bp):
AAAATTACTGAAATACCATTGGTTTAC
Found at i:40488596 original size:28 final size:27
Alignment explanation
Indices: 40488538--40488626 Score: 108
Period size: 27 Copynumber: 3.3 Consensus size: 27
40488528 ACCCCTATTA
* *
40488538 GGTAAAAAGACTGTAAAGCCCCTGTAG
1 GGTAAAGAGACCGTAAAGCCCCTGTAG
40488565 GGTAAAGAGACCGTAAAGCCCCCTGTAG
1 GGTAAAGAGACCGTAAAG-CCCCTGTAG
* * *
40488593 GGTAAAGTGACCGTAATA-CCCTTGTAT
1 GGTAAAGAGACCGTAA-AGCCCCTGTAG
40488620 GGTAAAG
1 GGTAAAG
40488627 TGACGAATAT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
27 30 0.55
28 24 0.44
29 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.27, T:0.20
Consensus pattern (27 bp):
GGTAAAGAGACCGTAAAGCCCCTGTAG
Found at i:40488626 original size:27 final size:27
Alignment explanation
Indices: 40488550--40488630 Score: 101
Period size: 28 Copynumber: 3.0 Consensus size: 27
40488540 TAAAAAGACT
* *
40488550 GTAAAGCCCCTGTAGGGTAAAGAGACC
1 GTAAACCCCCTGTAGGGTAAAGTGACC
40488577 GTAAAGCCCCCTGTAGGGTAAAGTGACC
1 GTAAA-CCCCCTGTAGGGTAAAGTGACC
* *
40488605 GTAATA-CCCTTGTATGGTAAAGTGAC
1 GTAA-ACCCCCTGTAGGGTAAAGTGAC
40488631 GAATATGCCC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
27 23 0.48
28 24 0.50
29 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (27 bp):
GTAAACCCCCTGTAGGGTAAAGTGACC
Found at i:40489462 original size:26 final size:26
Alignment explanation
Indices: 40489433--40489582 Score: 221
Period size: 26 Copynumber: 5.8 Consensus size: 26
40489423 GAGGAAGTGC
*
40489433 AAAAGGGCTTATGCCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* **
40489459 AAAAGGGATTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
40489485 AAAATGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* **
40489511 AAAAGGGCTTATGCCCTAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
40489537 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
40489563 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
40489583 ATTAAAGAGG
Statistics
Matches: 109, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
25 10 0.09
26 99 0.91
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:40489516 original size:52 final size:52
Alignment explanation
Indices: 40489433--40489582 Score: 257
Period size: 52 Copynumber: 2.9 Consensus size: 52
40489423 GAGGAAGTGC
* *
40489433 AAAAGGGCTTATGCCCTAGTTTACCGAAAAGGGATTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
* *
40489485 AAAATGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCTAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
40489537 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTT
40489583 ATTAAAGAGG
Statistics
Matches: 92, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
51 9 0.10
52 83 0.90
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (52 bp):
AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
Found at i:40489774 original size:42 final size:42
Alignment explanation
Indices: 40489727--40489818 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
40489717 TAGTCTCCCC
* ** *
40489727 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
40489769 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
40489811 AAATGGGC
1 AAATGGGC
40489819 CTATGGGCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:40489877 original size:31 final size:31
Alignment explanation
Indices: 40489842--40489920 Score: 115
Period size: 31 Copynumber: 2.5 Consensus size: 31
40489832 TATTTACAGT
40489842 AAAGGTTTCGGCCCAGTGAAATGATTCATGA
1 AAAGGTTTCGGCCCAGTGAAATGATTCATGA
* *
40489873 AAAGGCTTT-GGCCCAGTGATATGATTTATGA
1 AAAGG-TTTCGGCCCAGTGAAATGATTCATGA
*
40489904 AAAGGCTTCGGCCCAGT
1 AAAGGTTTCGGCCCAGT
40489921 AATCGTTAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
30 2 0.05
31 38 0.88
32 3 0.07
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (31 bp):
AAAGGTTTCGGCCCAGTGAAATGATTCATGA
Found at i:40494815 original size:21 final size:22
Alignment explanation
Indices: 40494782--40494825 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
40494772 ATAAGATAAT
*
40494782 AAACATATTTAA-TAATACATGA
1 AAACATATGTAATTAATA-ATGA
40494804 AAACATA-GTAATTAATAATGA
1 AAACATATGTAATTAATAATGA
40494825 A
1 A
40494826 TTTTGAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (22 bp):
AAACATATGTAATTAATAATGA
Found at i:40494997 original size:16 final size:15
Alignment explanation
Indices: 40494961--40495015 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
40494951 AATAATGTGA
40494961 ATAATAATATACATG
1 ATAATAATATACATG
*
40494976 AAAATATATATA-ATAG
1 ATAATA-ATATACAT-G
*
40494992 ATAATAATA-ATATG
1 ATAATAATATACATG
40495006 A-AATAATATA
1 ATAATAATATA
40495016 TTGTTAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
13 7 0.21
14 4 0.12
15 12 0.35
16 11 0.32
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (15 bp):
ATAATAATATACATG
Found at i:40495157 original size:5 final size:5
Alignment explanation
Indices: 40495147--40495226 Score: 53
Period size: 5 Copynumber: 16.4 Consensus size: 5
40495137 AAATATGAAG
* *
40495147 TAATA TAATA TAATA AAATA TAA-A TAAATAA TAATA TAAAA T-ATA TAATA
1 TAATA TAATA TAATA TAATA TAATA T-AAT-A TAATA TAATA TAATA TAATA
* * *
40495197 -CATA T-ATA TTAAAA TAAAA TAATA T-ATA TA
1 TAATA TAATA -TAATA TAATA TAATA TAATA TA
40495227 CAATTTAAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 16
0.72 0.08 0.19
Matches are distributed among these distances:
4 15 0.25
5 38 0.63
6 5 0.08
7 2 0.03
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (5 bp):
TAATA
Found at i:40495178 original size:28 final size:26
Alignment explanation
Indices: 40495149--40495217 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
40495139 ATATGAAGTA
40495149 ATATAATATAATAAAATATAAATAAAT
1 ATATAATATAATAAAATAT-AATAAAT
* *
40495176 A-ATAATATAA-AATATATAATACAT
1 ATATAATATAATAAAATATAATAAAT
* *
40495200 ATATATTAAAATAAAATA
1 ATATAATATAATAAAATA
40495218 ATATATATAC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
24 7 0.20
25 13 0.37
26 14 0.40
27 1 0.03
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (26 bp):
ATATAATATAATAAAATATAATAAAT
Found at i:40495180 original size:89 final size:89
Alignment explanation
Indices: 40494983--40495182 Score: 203
Period size: 89 Copynumber: 2.2 Consensus size: 89
40494973 ATGAAAATAT
* * *
40494983 ATATAATAGATAATAATAATATGAAATAATATATTGTTAAAATGTCAAATAATATAATAATATAA
1 ATATAAT--ATAATAATAATAAGAAATAATATATTGTTAAAATATCAAATAATATAATAATAGAA
* * *
40495048 AAATATATAAATATTATGTGATAAAA
64 AAATATATAAATATAATATAATAAAA
* * * *
40495074 ATATAATATAATAAATAATAAGTAATGATATA-TGTTAAAATAT-ATATTAATATGATAATAGAA
1 ATATAATATAAT-AATAATAAGAAATAATATATTGTTAAAATATCA-AATAATATAATAATAGAA
40495137 AAATATGA-AGTAATATAATATAAT-AAA
64 AAATAT-ATA--AATATAATATAATAAAA
40495164 ATATAA-ATAAATAATAATA
1 ATATAATAT-AATAATAATA
40495183 TAAAATATAT
Statistics
Matches: 93, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
88 1 0.01
89 46 0.49
90 29 0.31
91 17 0.18
ACGTcount: A:0.58, C:0.01, G:0.07, T:0.34
Consensus pattern (89 bp):
ATATAATATAATAATAATAAGAAATAATATATTGTTAAAATATCAAATAATATAATAATAGAAAA
ATATATAAATATAATATAATAAAA
Found at i:40495193 original size:35 final size:33
Alignment explanation
Indices: 40495109--40495226 Score: 83
Period size: 33 Copynumber: 3.3 Consensus size: 33
40495099 TGATATATGT
* * *
40495109 TAAAATATATATTAATATGATAATAGAAAAATATGAAG
1 TAAAATATATAATAA-AT-ATAA-ATAAAAATA--AAA
* *
40495147 TAATATAATATAATAAAATATAAATAAATAATAATA
1 TAAAAT-ATATAAT-AAATATAAATAAA-AATAAAA
* * *
40495183 TAAAATATATAATACATATATATTAAAATAAAA
1 TAAAATATATAATAAATATAAATAAAAATAAAA
*
40495216 TAATATATATA
1 TAAAATATATA
40495227 CAATTTAAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
33 16 0.24
34 10 0.15
35 7 0.11
36 6 0.09
37 4 0.06
38 13 0.20
39 8 0.12
40 2 0.03
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (33 bp):
TAAAATATATAATAAATATAAATAAAAATAAAA
Found at i:40498479 original size:27 final size:27
Alignment explanation
Indices: 40498445--40498622 Score: 173
Period size: 27 Copynumber: 6.6 Consensus size: 27
40498435 TAAACTGTAC
40498445 AGCACTAAGTGTGCGATATGACTATGT
1 AGCACTAAGTGTGCGATATGACTATGT
* * *
40498472 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATATGACTATGT
* *
40498498 ATGCACTAAGTGTGCGAAATGA-TCATGC
1 A-GCACTAAGTGTGCGATATGACT-ATGT
* *
40498526 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TATGACTATGT
* * *
40498554 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATATGACTATGT
* * *
40498581 GGCACTAAGTGTGCGAGT-TGATTATAT
1 AGCACTAAGTGTGCGA-TATGACTATGT
*
40498608 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40498623 GGCTCAATAT
Statistics
Matches: 129, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
26 1 0.01
27 105 0.81
28 22 0.17
29 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATATGACTATGT
Found at i:40498560 original size:82 final size:81
Alignment explanation
Indices: 40498446--40498596 Score: 223
Period size: 82 Copynumber: 1.9 Consensus size: 81
40498436 AAACTGTACA
* *
40498446 GCACTAAGTGTGCGATATGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGATATGACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
40498510 TGCGAAATGATCATGCG
65 TGCGAAATGATCATGCG
* ** *
40498527 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGA-TATGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
40498592 TGCGA
65 TGCGA
40498597 GTTGATTATA
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
81 16 0.26
82 46 0.74
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGATATGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAAATGATCATGCG
Found at i:40498613 original size:82 final size:81
Alignment explanation
Indices: 40498442--40498622 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
40498432 GATTAAACTG
* *
40498442 TACAGCACTAAGTGTGCGATATGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATATGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
40498507 GTGTGCGAAATGATCA
66 GTGTGCGAAATGATCA
* * * ** *
40498523 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGA-TATGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
** *
40498587 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAAATGATCA
* *
40498605 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
40498623 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATATGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAAATGATCA
Found at i:40501141 original size:45 final size:45
Alignment explanation
Indices: 40500996--40501208 Score: 188
Period size: 45 Copynumber: 4.9 Consensus size: 45
40500986 TAATTGAACA
* * * * * *
40500996 ATGCCAACGTCCCAGACGTGGTCTTACATGATATCTC--ATATCA
1 ATGCCAACGTCCCAGACATGGTCTTACACGAAAACACATATATCG
* * * * *
40501039 AAGCC-ACTATCCCAGACAGGGTCTTACA-GGAATCA-A-ATA-CG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGAAAACACATATATCG
* * * * * *
40501080 ATGTCGATGTCCCAGACATGGTCTTACACGTAACCACATATATTG
1 ATGCCAACGTCCCAGACATGGTCTTACACGAAAACACATATATCG
40501125 ATGCCAACGTCCCAGACATGGTCTTACACGAAAACACATATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGAAAACACATATATCG
** *
40501170 ATGCCAACGTCCCAGATGTGGTCTTACATGAAAACACAT
1 ATGCCAACGTCCCAGACATGGTCTTACACGAAAACACAT
40501209 CAGAATCCTA
Statistics
Matches: 138, Mismatches: 25, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
41 22 0.16
42 15 0.11
43 22 0.16
44 3 0.02
45 76 0.55
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.23
Consensus pattern (45 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGAAAACACATATATCG
Found at i:40507985 original size:44 final size:44
Alignment explanation
Indices: 40507937--40508032 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 44
40507927 CCAGACAGGA
* *
40507937 TCTTACACTTAAATCTC-AAATCGATGCCAACATCCCAAATGTGG
1 TCTTACACTTAAATCTCAAAAT-AATGCCAACATCCCAAACGTGG
* * *
40507981 TCTTACACTTACATCTCAAAATAATGCCAACGTCCCACACGTGG
1 TCTTACACTTAAATCTCAAAATAATGCCAACATCCCAAACGTGG
40508025 TCTTACAC
1 TCTTACAC
40508033 GATAACATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 42 0.91
45 4 0.09
ACGTcount: A:0.32, C:0.30, G:0.10, T:0.27
Consensus pattern (44 bp):
TCTTACACTTAAATCTCAAAATAATGCCAACATCCCAAACGTGG
Found at i:40510656 original size:33 final size:34
Alignment explanation
Indices: 40510613--40510683 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 34
40510603 TCTTTGTATG
*
40510613 CACATCTGATACTGTACTGAAATGGGCTAAGGCC
1 CACATCTGATACTATACTGAAATGGGCTAAGGCC
** * *
40510647 CACAT-TGATACTATTTTGTATTGGGCTAAGGCC
1 CACATCTGATACTATACTGAAATGGGCTAAGGCC
40510680 CACA
1 CACA
40510684 ATAATATTGC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 27 0.84
34 5 0.16
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (34 bp):
CACATCTGATACTATACTGAAATGGGCTAAGGCC
Found at i:40525458 original size:27 final size:27
Alignment explanation
Indices: 40525428--40525686 Score: 164
Period size: 27 Copynumber: 9.6 Consensus size: 27
40525418 ATATTGAGTC
*
40525428 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
** *
40525455 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTATATAATCAACT
*
40525482 CGCACACTTAGTGCT-TCATAGTCAAACT
1 CGCACACTTAGTGCTAT-ATAATC-AACT
*** ** *
40525510 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTATATAATCAACT
* **
40525537 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTAT-ATAATCAACT
* * * * *
40525564 CGTACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTATATAATCAACT
*** ** *
40525591 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTATATAATCAACT
* * **
40525618 CGCAAACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTAT-ATAATCAACT
* * * *
40525645 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTATATAATCAACT
40525672 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40525687 GTACAATTTA
Statistics
Matches: 186, Mismatches: 39, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
27 162 0.87
28 24 0.13
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:40525594 original size:54 final size:54
Alignment explanation
Indices: 40525428--40525685 Score: 266
Period size: 54 Copynumber: 4.8 Consensus size: 54
40525418 ATATTGAGTC
* * * * * *
40525428 CGCACACTCAGTGCTAT-ATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGC-ATCATAGTCAATTCGCACACTTAGTGCAACATAGTCAAAT
* * ** * *
40525482 CGCACACTTAGTGCTTCATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCATCATAGTC-AATTCGCACACTTAGTGCAACATAGTCAAAT
* * *
40525537 CGCACACTTAGTGCATCATATTCATTTCGTACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCATCATAGTCAATTCGCACACTTAGTGCAACATAGTCAAAT
** * * * * **
40525591 CGCACACTTAGTGCCGCATGGTCAATTCGCAAACTTAGTGCATCATATTCATTT
1 CGCACACTTAGTGCATCATAGTCAATTCGCACACTTAGTGCAACATAGTCAAAT
* *
40525645 CGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGC
1 CGCACACTTAGTGCATCATAGTCAATTCGCACACTTAGTGC
40525686 TGTACAATTT
Statistics
Matches: 168, Mismatches: 34, Indels: 4
0.82 0.17 0.02
Matches are distributed among these distances:
53 1 0.01
54 121 0.72
55 46 0.27
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (54 bp):
CGCACACTTAGTGCATCATAGTCAATTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:40525627 original size:81 final size:81
Alignment explanation
Indices: 40525481--40525685 Score: 365
Period size: 81 Copynumber: 2.5 Consensus size: 81
40525471 CGTAATCAAA
** *
40525481 TCGCACACTTAGTGCTTCATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATTCGCACACTT
1 TCGCACACTTAGTGCAACATAGTCAAA-TCGCACACTTAGTGCCGCATGGTCAATTCGCAAACTT
40525546 AGTGCATCATATTCATT
65 AGTGCATCATATTCATT
*
40525563 TCGTACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCGCATGGTCAATTCGCAAACTTA
1 TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCGCATGGTCAATTCGCAAACTTA
40525628 GTGCATCATATTCATT
66 GTGCATCATATTCATT
40525644 TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGC
1 TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGC
40525686 TGTACAATTT
Statistics
Matches: 118, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
81 94 0.80
82 24 0.20
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (81 bp):
TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCCGCATGGTCAATTCGCAAACTTA
GTGCATCATATTCATT
Found at i:40529459 original size:17 final size:17
Alignment explanation
Indices: 40529433--40529472 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
40529423 TTTTAAACAA
*
40529433 TATATTTTATTATTT-AT
1 TATATATTATT-TTTAAT
40529450 TATATATTATTTTTAAT
1 TATATATTATTTTTAAT
40529467 TATATA
1 TATATA
40529473 CCTATCTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATATATTATTTTTAAT
Found at i:40538771 original size:20 final size:20
Alignment explanation
Indices: 40538717--40538764 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
40538707 GTAATTTGTC
40538717 AAATAAAGGAATTTTTATGA
1 AAATAAAGGAATTTTTATGA
40538737 AAATAAAGGAATTTTTATGA
1 AAATAAAGGAATTTTTATGA
40538757 AAATAAAG
1 AAATAAAG
40538765 TTATTTTGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (20 bp):
AAATAAAGGAATTTTTATGA
Found at i:40540196 original size:14 final size:13
Alignment explanation
Indices: 40540165--40540192 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
40540155 CGGGTGGCCC
40540165 ATATTAATTTTTT
1 ATATTAATTTTTT
40540178 ATATTAATTTTTT
1 ATATTAATTTTTT
40540191 AT
1 AT
40540193 TATTTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATATTAATTTTTT
Found at i:40540354 original size:29 final size:30
Alignment explanation
Indices: 40540322--40540383 Score: 101
Period size: 29 Copynumber: 2.1 Consensus size: 30
40540312 ACTTAACAAG
40540322 CAAATG-CTTCTAAAATAATAA-AAAATTAA
1 CAAATGCCTT-TAAAATAATAAGAAAATTAA
40540351 CAAATGCCTTTAAAATAATAAGAAAATTAA
1 CAAATGCCTTTAAAATAATAAGAAAATTAA
40540381 CAA
1 CAA
40540384 TAAAATAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 17 0.55
30 14 0.45
ACGTcount: A:0.58, C:0.11, G:0.05, T:0.26
Consensus pattern (30 bp):
CAAATGCCTTTAAAATAATAAGAAAATTAA
Found at i:40540971 original size:9 final size:9
Alignment explanation
Indices: 40540957--40540994 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
40540947 TTAGTTTTTA
40540957 AACTCGAAT
1 AACTCGAAT
40540966 AACTCGAAT
1 AACTCGAAT
*
40540975 AATTCGAAT
1 AACTCGAAT
40540984 AACTCGAAT
1 AACTCGAAT
40540993 AA
1 AA
40540995 TTTGAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.24
Consensus pattern (9 bp):
AACTCGAAT
Found at i:40540983 original size:18 final size:18
Alignment explanation
Indices: 40540960--40541003 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
40540950 GTTTTTAAAC
40540960 TCGAATAACTCGAATAAT
1 TCGAATAACTCGAATAAT
40540978 TCGAATAACTCGAATAAT
1 TCGAATAACTCGAATAAT
*
40540996 TTGAATAA
1 TCGAATAA
40541004 ACCAAATAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (18 bp):
TCGAATAACTCGAATAAT
Found at i:40541001 original size:9 final size:9
Alignment explanation
Indices: 40540960--40541003 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
40540950 GTTTTTAAAC
*
40540960 TCGAATAAC
1 TCGAATAAT
40540969 TCGAATAAT
1 TCGAATAAT
*
40540978 TCGAATAAC
1 TCGAATAAT
40540987 TCGAATAAT
1 TCGAATAAT
*
40540996 TTGAATAA
1 TCGAATAA
40541004 ACCAAATAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
TCGAATAAT
Found at i:40541011 original size:18 final size:18
Alignment explanation
Indices: 40540960--40541012 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
40540950 GTTTTTAAAC
*
40540960 TCGAATAACTCGAATAAT
1 TCGAATAACTCAAATAAT
*
40540978 TCGAATAACTCGAATAAT
1 TCGAATAACTCAAATAAT
*
40540996 TTGAATAAAC-CAAATAA
1 TCGAAT-AACTCAAATAA
40541013 CAAACTCTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 29 0.91
19 3 0.09
ACGTcount: A:0.49, C:0.15, G:0.09, T:0.26
Consensus pattern (18 bp):
TCGAATAACTCAAATAAT
Found at i:40541011 original size:27 final size:27
Alignment explanation
Indices: 40540957--40541013 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
40540947 TTAGTTTTTA
** *
40540957 AACTCGAATAACTCGAATAATTCGAAT
1 AACTCGAATAACTCGAATAAACCAAAT
* *
40540984 AACTCGAATAATTTGAATAAACCAAAT
1 AACTCGAATAACTCGAATAAACCAAAT
40541011 AAC
1 AAC
40541014 AAACTCTAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.49, C:0.18, G:0.09, T:0.25
Consensus pattern (27 bp):
AACTCGAATAACTCGAATAAACCAAAT
Found at i:40541742 original size:19 final size:19
Alignment explanation
Indices: 40541715--40541752 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40541705 AAAGTTAATA
* *
40541715 ACAACTTTGATTACGGTGG
1 ACAAATTTGATTACAGTGG
40541734 ACAAATTTGATTACAGTGG
1 ACAAATTTGATTACAGTGG
40541753 GTGACAGTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.32
Consensus pattern (19 bp):
ACAAATTTGATTACAGTGG
Found at i:40542698 original size:24 final size:22
Alignment explanation
Indices: 40542670--40542739 Score: 68
Period size: 26 Copynumber: 2.9 Consensus size: 22
40542660 TAAATTCCAT
40542670 TTTATATATCTATTTTCCATATA
1 TTTAT-TATCTATTTTCCATATA
*
40542693 TGTTATTATCTTTCCTTTCCCATATA
1 T-TTATTATCTAT--TTT-CCATATA
*
40542719 TTTGATTTTCTATTTTCCATA
1 TTT-ATTATCTATTTTCCATA
40542740 AAATATTCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
23 12 0.31
24 7 0.18
25 5 0.13
26 15 0.38
ACGTcount: A:0.23, C:0.17, G:0.03, T:0.57
Consensus pattern (22 bp):
TTTATTATCTATTTTCCATATA
Found at i:40542752 original size:86 final size:84
Alignment explanation
Indices: 40542600--40542771 Score: 247
Period size: 86 Copynumber: 2.0 Consensus size: 84
40542590 AATCTTTATC
* *
40542600 TTCCATATATGTTATTCTCTTTCCTTTACCATATTTGATTCTCTATTTTTCATAAAATATTAAAT
1 TTCCATATATGTTATTATCTTTCCTTTACCATATTTGATTCTCTATTTTCCATAAAATATTAAAT
*
40542665 TCCATTTTATAT-ATCTATT
66 TCCATTTCATATCA-CTATT
* * *
40542684 TTCCATATATGTTATTATCTTTCCTTTCCCATATATTTGATTTTCTATTTTCCATAAAATATTCA
1 TTCCATATATGTTATTATCTTTCCTTTACC--ATATTTGATTCTCTATTTTCCATAAAATATTAA
*
40542749 ATTCCCTTTCATATCACTATT
64 ATTCCATTTCATATCACTATT
40542770 TT
1 TT
40542772 ACACAGTTGT
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
84 28 0.36
86 49 0.63
87 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.02, T:0.53
Consensus pattern (84 bp):
TTCCATATATGTTATTATCTTTCCTTTACCATATTTGATTCTCTATTTTCCATAAAATATTAAAT
TCCATTTCATATCACTATT
Found at i:40542783 original size:86 final size:86
Alignment explanation
Indices: 40542606--40542803 Score: 242
Period size: 86 Copynumber: 2.3 Consensus size: 86
40542596 TATCTTCCAT
* *
40542606 ATATGTTATTCTCTTTCCTTTACC--ATATTTGATTCTCTATTTTTCATAAAATATTAAATTCCA
1 ATATGTTATTCTCTTTCCTTTCCCATATATTTGATTCTCTATTTTCCATAAAATATTAAATTCCA
* * *
40542669 TTTTATATATCTATTTTCCAT
66 TTTCATATATCTATTTTACAC
* * * *
40542690 ATATGTTATTATCTTTCCTTTCCCATATATTTGATTTTCTATTTTCCATAAAATATTCAATTCCC
1 ATATGTTATTCTCTTTCCTTTCCCATATATTTGATTCTCTATTTTCCATAAAATATTAAATTCCA
40542755 TTTCATATCA-CTATTTTACAC
66 TTTCATAT-ATCTATTTTACAC
* * *
40542776 AGT-TGTTATTCTTTTTCTTTTCCTATAT
1 A-TATGTTATTCTCTTTCCTTTCCCATAT
40542804 TTCACTTTTC
Statistics
Matches: 97, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
84 22 0.23
86 73 0.75
87 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.03, T:0.54
Consensus pattern (86 bp):
ATATGTTATTCTCTTTCCTTTCCCATATATTTGATTCTCTATTTTCCATAAAATATTAAATTCCA
TTTCATATATCTATTTTACAC
Found at i:40543937 original size:16 final size:15
Alignment explanation
Indices: 40543918--40543970 Score: 67
Period size: 16 Copynumber: 3.6 Consensus size: 15
40543908 AAAATAAAAT
40543918 AATAATACAATATCTA
1 AATAATA-AATATCTA
40543934 AATAATGAAATATC-A
1 AATAAT-AAATATCTA
40543949 AATAAT--ATATCTA
1 AATAATAAATATCTA
40543962 AATAATAAA
1 AATAATAAA
40543971 CAAAAGTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
12 5 0.15
13 7 0.21
15 8 0.24
16 12 0.36
17 1 0.03
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (15 bp):
AATAATAAATATCTA
Found at i:40545805 original size:42 final size:42
Alignment explanation
Indices: 40545758--40545879 Score: 154
Period size: 42 Copynumber: 2.9 Consensus size: 42
40545748 TTTATGTAAA
* *
40545758 AAAACGCTGCTAAAGAACATGACTTTTAGCGGCACTTTCAAG
1 AAAACGCTGCTAAAAAACGTGACTTTTAGCGGCACTTTCAAG
* * * **
40545800 AAAACGCCGCTAAATAACGTGACTTTTAGCAGCACTTTCTTG
1 AAAACGCTGCTAAAAAACGTGACTTTTAGCGGCACTTTCAAG
* * *
40545842 AAAATGCTGCTAAAAAACGTGACCTTTAGCGGCGCTTT
1 AAAACGCTGCTAAAAAACGTGACTTTTAGCGGCACTTT
40545880 TTCTACAAAT
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (42 bp):
AAAACGCTGCTAAAAAACGTGACTTTTAGCGGCACTTTCAAG
Found at i:40545900 original size:42 final size:42
Alignment explanation
Indices: 40545805--40545965 Score: 166
Period size: 42 Copynumber: 3.8 Consensus size: 42
40545795 TCAAGAAAAC
* * * *
40545805 GCCGCTAAATAACGTGACTTTTAGCAGCACTTTCTTGA-AAAT
1 GCCGCTAAAGAACGTGACCTTTAGCAGCGCTTT-TTTACAAAT
* * *
40545847 GCTGCTAAAAAACGTGACCTTTAGCGGCGCTTTTTCTACAAAT
1 GCCGCTAAAGAACGTGACCTTTAGCAGCGCTTTTT-TACAAAT
* *
40545890 GCCGCTAAA-AATGTGACCTTTAGCAGCGCTTTTTGTACAAAC
1 GCCGCTAAAGAACGTGACCTTTAGCAGCGCTTTTT-TACAAAT
* *
40545932 GCCTCTAAAGAACCTGACCTTTAG-AGGCGCTTTT
1 GCCGCTAAAGAACGTGACCTTTAGCA-GCGCTTTT
40545966 CTTCAAAATG
Statistics
Matches: 101, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
41 2 0.02
42 67 0.66
43 32 0.32
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (42 bp):
GCCGCTAAAGAACGTGACCTTTAGCAGCGCTTTTTTACAAAT
Found at i:40545954 original size:85 final size:85
Alignment explanation
Indices: 40545805--40545965 Score: 211
Period size: 85 Copynumber: 1.9 Consensus size: 85
40545795 TCAAGAAAAC
* * *
40545805 GCCGCTAAATAACGTGACTTTTAGCAGCACTTTCTTGAAAATGCTGCTAAAAAACGTGACCTTTA
1 GCCGCTAAATAACGTGACCTTTAGCAGCACTTTCTTGAAAACGCTGCTAAAAAACCTGACCTTTA
*
40545870 GCGGCGCTTTTTCTACAAAT
66 GAGGCGCTTTTTCTACAAAT
* * *
40545890 GCCGCTAAA-AATGTGACCTTTAGCAGCGCTTT-TTGTACAAACGCCT-CTAAAGAACCTGACCT
1 GCCGCTAAATAACGTGACCTTTAGCAGCACTTTCTTG-A-AAACG-CTGCTAAAAAACCTGACCT
40545952 TTAGAGGCGCTTTT
63 TTAGAGGCGCTTTT
40545966 CTTCAAAATG
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
83 3 0.05
84 21 0.32
85 40 0.61
86 2 0.03
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (85 bp):
GCCGCTAAATAACGTGACCTTTAGCAGCACTTTCTTGAAAACGCTGCTAAAAAACCTGACCTTTA
GAGGCGCTTTTTCTACAAAT
Found at i:40545975 original size:85 final size:86
Alignment explanation
Indices: 40545758--40545975 Score: 216
Period size: 84 Copynumber: 2.6 Consensus size: 86
40545748 TTTATGTAAA
* * * * * * * *
40545758 AAAACGCTGCTAAAGAACATGACTTTTAGCGGCAC--TTTCAAGAAAACGCCGCTAAATAACGTG
1 AAAACGCTGCTAAAAAACCTGACCTTTAGAGGCGCTTTTTCTACAAAATGCCGCTAAATAACGTG
*
40545821 ACTTTTAGCAGCACTTTCTTG
66 ACCTTTAGCAGCACTTTCTTG
* * * *
40545842 AAAATGCTGCTAAAAAACGTGACCTTTAGCGGCGCTTTTTCTAC-AAATGCCGCTAAA-AATGTG
1 AAAACGCTGCTAAAAAACCTGACCTTTAGAGGCGCTTTTTCTACAAAATGCCGCTAAATAACGTG
*
40545905 ACCTTTAGCAGCGCTTT-TTG
66 ACCTTTAGCAGCACTTTCTTG
* *
40545925 TACAAACGCCT-CTAAAGAACCTGACCTTTAGAGGCGC-TTTTCTTCAAAATG
1 -A-AAACG-CTGCTAAAAAACCTGACCTTTAGAGGCGCTTTTTCTACAAAATG
40545976 TAGCTAAAGG
Statistics
Matches: 112, Mismatches: 16, Indels: 11
0.81 0.12 0.08
Matches are distributed among these distances:
83 3 0.03
84 58 0.52
85 44 0.39
86 7 0.06
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (86 bp):
AAAACGCTGCTAAAAAACCTGACCTTTAGAGGCGCTTTTTCTACAAAATGCCGCTAAATAACGTG
ACCTTTAGCAGCACTTTCTTG
Found at i:40545982 original size:85 final size:85
Alignment explanation
Indices: 40545808--40545983 Score: 198
Period size: 85 Copynumber: 2.1 Consensus size: 85
40545798 AGAAAACGCC
* * * *
40545808 GCTAAATAACGTGACTTTTAGCAGCACTTTCTTGAAAATGCTGCTAAAAAACGTGACCTTTAGCG
1 GCTAAATAACGTGACCTTTAGCAGCACTTTCTTGAAAACGCTGCTAAAAAACCTGACCTTTAGAG
*
40545873 GCGCTTTTTCTACAAATGCC
66 GCGCTTTTTCTACAAATGCA
* * *
40545893 GCTAAA-AATGTGACCTTTAGCAGCGCTTT-TTGTACAAACGCCT-CTAAAGAACCTGACCTTTA
1 GCTAAATAACGTGACCTTTAGCAGCACTTTCTTG-A-AAACG-CTGCTAAAAAACCTGACCTTTA
* *
40545955 GAGGCGC-TTTTCTTCAAAATGTA
63 GAGGCGCTTTTTCTAC-AAATGCA
40545978 GCTAAA
1 GCTAAA
40545984 GGTCACGTTC
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
83 3 0.04
84 28 0.36
85 44 0.57
86 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (85 bp):
GCTAAATAACGTGACCTTTAGCAGCACTTTCTTGAAAACGCTGCTAAAAAACCTGACCTTTAGAG
GCGCTTTTTCTACAAATGCA
Found at i:40546881 original size:13 final size:14
Alignment explanation
Indices: 40546855--40546883 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
40546845 ACTAACGACG
40546855 AATTAAACCATTAT
1 AATTAAACCATTAT
40546869 AATTAAA-CATTAT
1 AATTAAACCATTAT
40546882 AA
1 AA
40546884 ATATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:40551999 original size:9 final size:9
Alignment explanation
Indices: 40551985--40552095 Score: 120
Period size: 9 Copynumber: 12.6 Consensus size: 9
40551975 TATTTATGTA
40551985 TTATGTAAG
1 TTATGTAAG
40551994 TTATGTAAG
1 TTATGTAAG
*
40552003 TTATGTGAG
1 TTATGTAAG
* *
40552012 GTATGTGAG
1 TTATGTAAG
40552021 TTATGTAAG
1 TTATGTAAG
40552030 TTATGTAAG
1 TTATGTAAG
*
40552039 TTATGATATG
1 TTATG-TAAG
* * *
40552049 ATATAT-AT
1 TTATGTAAG
40552057 TTATGT-A-
1 TTATGTAAG
40552064 TTATGTAAG
1 TTATGTAAG
*
40552073 TTATGTAAA
1 TTATGTAAG
40552082 TTATGTAAG
1 TTATGTAAG
40552091 TTATG
1 TTATG
40552096 AAATTTAAAC
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.07
8 6 0.07
9 68 0.79
10 6 0.07
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:40553182 original size:24 final size:24
Alignment explanation
Indices: 40553155--40553207 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
40553145 AATGTTTTAT
40553155 AATATAATATAAATTTTAGATACA
1 AATATAATATAAATTTTAGATACA
* *
40553179 AATATAATATTAATTTTAGTTACA
1 AATATAATATAAATTTTAGATACA
40553203 AATAT
1 AATAT
40553208 TATAACATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (24 bp):
AATATAATATAAATTTTAGATACA
Found at i:40554591 original size:47 final size:47
Alignment explanation
Indices: 40554522--40554617 Score: 165
Period size: 47 Copynumber: 2.0 Consensus size: 47
40554512 CGTTTTATCA
* *
40554522 AAAGTAGAAGTATTTAATCATTAATATTGCCTTGTTACAATATAACC
1 AAAGTAGAAGTATTTAATCATTAATACTGCCTTGTTACAACATAACC
*
40554569 AAAGTAGAAGTATTTAATCATTAATACTGCCTTGTTACAACATTACC
1 AAAGTAGAAGTATTTAATCATTAATACTGCCTTGTTACAACATAACC
40554616 AA
1 AA
40554618 TCACGTAGCA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (47 bp):
AAAGTAGAAGTATTTAATCATTAATACTGCCTTGTTACAACATAACC
Found at i:40555336 original size:16 final size:17
Alignment explanation
Indices: 40555317--40555351 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
40555307 ATTATTTATT
40555317 ATATAAATT-AAAAACA
1 ATATAAATTAAAAAACA
40555333 ATATAAATTAAAAAACA
1 ATATAAATTAAAAAACA
40555350 AT
1 AT
40555352 CAGTTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (17 bp):
ATATAAATTAAAAAACA
Found at i:40555669 original size:8 final size:8
Alignment explanation
Indices: 40555654--40555699 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 8
40555644 CCCCTTAATG
40555654 CCTT-AAC
1 CCTTAAAC
40555661 CCTTAAAC
1 CCTTAAAC
*
40555669 CCCTAAAC
1 CCTTAAAC
*
40555677 CCCTAAAC
1 CCTTAAAC
*
40555685 CCTAAAAC
1 CCTTAAAC
40555693 CC-TAAAC
1 CCTTAAAC
40555700 TCCAACCTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
7 8 0.24
8 26 0.76
ACGTcount: A:0.39, C:0.43, G:0.00, T:0.17
Consensus pattern (8 bp):
CCTTAAAC
Found at i:40555683 original size:16 final size:16
Alignment explanation
Indices: 40555658--40555699 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
40555648 TTAATGCCTT
*
40555658 AACCCTTAAACCCCTA
1 AACCCCTAAACCCCTA
40555674 AACCCCTAAA-CCCTA
1 AACCCCTAAACCCCTA
*
40555689 AAACCCTAAAC
1 AACCCCTAAAC
40555700 TCCAACCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.43, C:0.43, G:0.00, T:0.14
Consensus pattern (16 bp):
AACCCCTAAACCCCTA
Found at i:40555689 original size:7 final size:7
Alignment explanation
Indices: 40555658--40556002 Score: 68
Period size: 7 Copynumber: 47.4 Consensus size: 7
40555648 TTAATGCCTT
40555658 AACCCTTA
1 AACCC-TA
40555666 AACCCCTA
1 AA-CCCTA
40555674 AACCCCTA
1 AA-CCCTA
40555682 AACCCTAA
1 AACCCT-A
40555690 AACCCTA
1 AACCCTA
40555697 AACTCC--
1 AAC-CCTA
*
40555703 AACCTTTA
1 AACC-CTA
*
40555711 AACCATA
1 AACCCTA
*
40555718 AACCATA
1 AACCCTA
*
40555725 ATCCCTA
1 AACCCTA
* *
40555732 ATCTCTA
1 AACCCTA
40555739 AACCCATA
1 AACCC-TA
* *
40555747 ATCCATA
1 AACCCTA
* *
40555754 ATCCATA
1 AACCCTA
*
40555761 AACCTTA
1 AACCCTA
*** *
40555768 AAATATT
1 AACCCTA
*
40555775 AACTCATA
1 AAC-CCTA
*
40555783 AACCATA
1 AACCCTA
*
40555790 AACCCCTG
1 AA-CCCTA
*
40555798 AACCTTA
1 AACCCTA
*
40555805 AACCC-C
1 AACCCTA
40555811 AACCCTTA
1 AACCC-TA
40555819 AACCCTA
1 AACCCTA
40555826 AACCCATA
1 AACCC-TA
* *
40555834 ATCCATA
1 AACCCTA
*
40555841 AACCTTA
1 AACCCTA
*** *
40555848 AAATATT
1 AACCCTA
*
40555855 AACTCATA
1 AAC-CCTA
**
40555863 AACTATA
1 AACCCTA
40555870 AACCCCTA
1 AA-CCCTA
*
40555878 AACCTTA
1 AACCCTA
*
40555885 AACCC-C
1 AACCCTA
40555891 AACCCTTA
1 AACCC-TA
*
40555899 AACCTTA
1 AACCCTA
40555906 AACCCATA
1 AACCC-TA
*
40555914 ATCCCTA
1 AACCCTA
40555921 AACCCATA
1 AACCC-TA
** *
40555929 ATTCATA
1 AACCCTA
*
40555936 AACCTTA
1 AACCCTA
*** *
40555943 AAATATT
1 AACCCTA
*
40555950 AACTCATA
1 AAC-CCTA
* *
40555958 AATCATA
1 AACCCTA
40555965 AACCCTA
1 AACCCTA
* *
40555972 AATCATA
1 AACCCTA
*
40555979 TACCCTA
1 AACCCTA
*
40555986 AACCATA
1 AACCCTA
40555993 AACCCTA
1 AACCCTA
40556000 AAC
1 AAC
40556003 TATAATGATA
Statistics
Matches: 247, Mismatches: 71, Indels: 39
0.69 0.20 0.11
Matches are distributed among these distances:
5 1 0.00
6 13 0.05
7 150 0.61
8 80 0.32
9 3 0.01
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.23
Consensus pattern (7 bp):
AACCCTA
Found at i:40555747 original size:22 final size:22
Alignment explanation
Indices: 40555713--40555764 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
40555703 AACCTTTAAA
*
40555713 CCATAAA-CCATAATCCCTAAT
1 CCATAAACCCATAATCCATAAT
40555734 CTC-TAAACCCATAATCCATAAT
1 C-CATAAACCCATAATCCATAAT
40555756 CCATAAACC
1 CCATAAACC
40555765 TTAAAATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 6 0.22
22 21 0.78
ACGTcount: A:0.42, C:0.35, G:0.00, T:0.23
Consensus pattern (22 bp):
CCATAAACCCATAATCCATAAT
Found at i:40555838 original size:80 final size:80
Alignment explanation
Indices: 40555749--40555924 Score: 316
Period size: 80 Copynumber: 2.2 Consensus size: 80
40555739 AACCCATAAT
*
40555749 CCATAATCCATAAACCTTAAAATATTAACTCATAAACCATAAACCCCTGAACCTTAAACCCCAAC
1 CCATAATCCATAAACCTTAAAATATTAACTCATAAACCATAAACCCCTAAACCTTAAACCCCAAC
40555814 CCTTAAACCCTAAAC
66 CCTTAAACCCTAAAC
*
40555829 CCATAATCCATAAACCTTAAAATATTAACTCATAAACTATAAACCCCTAAACCTTAAACCCCAAC
1 CCATAATCCATAAACCTTAAAATATTAACTCATAAACCATAAACCCCTAAACCTTAAACCCCAAC
*
40555894 CCTTAAACCTTAAAC
66 CCTTAAACCCTAAAC
*
40555909 CCATAATCCCTAAACC
1 CCATAATCCATAAACC
40555925 CATAATTCAT
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 92 1.00
ACGTcount: A:0.44, C:0.34, G:0.01, T:0.22
Consensus pattern (80 bp):
CCATAATCCATAAACCTTAAAATATTAACTCATAAACCATAAACCCCTAAACCTTAAACCCCAAC
CCTTAAACCCTAAAC
Found at i:40555846 original size:29 final size:28
Alignment explanation
Indices: 40555709--40556007 Score: 130
Period size: 29 Copynumber: 10.4 Consensus size: 28
40555699 CTCCAACCTT
* * * *
40555709 TAAACCATAAACCATAATCCCTAATCTC
1 TAAACCATAAACCATAAACCATAAACCC
* * *
40555737 TAAACCCATAATCCATAATCCATAAACCT
1 TAAA-CCATAAACCATAAACCATAAACCC
** *
40555766 TAAAATATTAACTCATAAACCATAAACCCC
1 TAAACCATAAAC-CATAAACCATAAA-CCC
* * ** * *
40555796 TGAACCTTAAACCCCAACCCTTAAACCC
1 TAAACCATAAACCATAAACCATAAACCC
* * ***
40555824 TAAACCCATAATCCATAAACCTTAAAATA
1 TAAA-CCATAAACCATAAACCATAAACCC
* * * *
40555853 TTAACTCATAAACTATAAACCCCTAAACCT
1 TAAAC-CATAAACCATAAA-CCATAAACCC
** * * *
40555883 TAAACCCCAACCCTTAAACCTTAAACCC
1 TAAACCATAAACCATAAACCATAAACCC
* * ** *
40555911 ATAATCCCTAAACCCATAATTCATAAACCT
1 -TAAACCATAAA-CCATAAACCATAAACCC
** * *
40555941 TAAAATATTAACTCATAAATCATAAACCC
1 TAAACCATAAAC-CATAAACCATAAACCC
* * *
40555970 TAAATCATATACCCTAAACCATAAACCC
1 TAAACCATAAACCATAAACCATAAACCC
*
40555998 TAAACTATAA
1 TAAACCATAA
40556008 TGATAATTAA
Statistics
Matches: 194, Mismatches: 68, Indels: 18
0.69 0.24 0.06
Matches are distributed among these distances:
28 45 0.23
29 118 0.61
30 31 0.16
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.24
Consensus pattern (28 bp):
TAAACCATAAACCATAAACCATAAACCC
Found at i:40555895 original size:21 final size:22
Alignment explanation
Indices: 40555870--40555924 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
40555860 ATAAACTATA
40555870 AACCCCTAAACCTTAAACCC-C
1 AACCCCTAAACCTTAAACCCAC
* *
40555891 AACCCTTAAACCTTAAACCCAT
1 AACCCCTAAACCTTAAACCCAC
*
40555913 AATCCCTAAACC
1 AACCCCTAAACC
40555925 CATAATTCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 19 0.66
22 10 0.34
ACGTcount: A:0.40, C:0.42, G:0.00, T:0.18
Consensus pattern (22 bp):
AACCCCTAAACCTTAAACCCAC
Found at i:40555937 original size:15 final size:15
Alignment explanation
Indices: 40555904--40555939 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
40555894 CCTTAAACCT
*
40555904 TAAACCCATAATCCC
1 TAAACCCATAATCCA
*
40555919 TAAACCCATAATTCA
1 TAAACCCATAATCCA
40555934 TAAACC
1 TAAACC
40555940 TTAAAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.22
Consensus pattern (15 bp):
TAAACCCATAATCCA
Found at i:40555973 original size:14 final size:14
Alignment explanation
Indices: 40555919--40556001 Score: 78
Period size: 14 Copynumber: 5.8 Consensus size: 14
40555909 CCATAATCCC
*
40555919 TAAACCCATAATTCA
1 TAAACCC-TAAATCA
*
40555934 TAAACCTTAAAAT-A
1 TAAACCCT-AAATCA
* *
40555948 TTAACTCATAAATCA
1 TAAAC-CCTAAATCA
40555963 TAAACCCTAAATCA
1 TAAACCCTAAATCA
* *
40555977 TATACCCTAAACCA
1 TAAACCCTAAATCA
40555991 TAAACCCTAAA
1 TAAACCCTAAA
40556002 CTATAATGAT
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
14 40 0.71
15 16 0.29
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAACCCTAAATCA
Found at i:40556518 original size:155 final size:152
Alignment explanation
Indices: 40556330--40556825 Score: 527
Period size: 155 Copynumber: 3.3 Consensus size: 152
40556320 ACAAAGCACA
*
40556330 GCTAAAGCTCGATCTATAGCGACGTTTTTCAAAAAGCGCCGCTAATGCCACTAAGGCTCAATAAA
1 GCTAAAGCTCGATCTATAGCGACGTTTTTCAAAAAGCGCCGCTAATGCCACTAAGGCTCAACAAA
* *
40556395 AAATGATGGCGTGTTGATGAATTAATTTGCGGCGTTTTTTAAAAAATGCCACTAATGCTCTATCT
66 AAATGATGGCGTGTTGATGAATTATTTTGCGGCGTTTTTTAAAAAATGCCACTAATGCTCGATCT
40556460 ATAGTAGCATTTATCATAAAGAGCC
131 ATAGTAGCATTT-TCA-AAAG-GCC
* * *
40556485 GCTAAAGCTCGATCTATAGCGACATTTTTCAAAAAGCGCAGCTAATGCCACTATGGCTCAACAAA
1 GCTAAAGCTCGATCTATAGCGACGTTTTTCAAAAAGCGCCGCTAATGCCACTAAGGCTCAACAAA
** * * ** * * *
40556550 AAACAACT-GCGTGTTGATGAATTATTTTGTGGCATTTTTTAAAAAGCGTCGCTCATGCTCGATC
66 AAATGA-TGGCGTGTTGATGAATTATTTTGCGGCGTTTTTTAAAAAATGCCACTAATGCTCGATC
*
40556614 --TA-TAG------C----GGTC
130 TATAGTAGCATTTTCAAAAGGCC
* * * * *
40556624 GCTAAAGCTCGATTTATAGCTATGTTTTCCGAAAAGCGCCGCTAATGCCACTAAGGCTCAACAAA
1 GCTAAAGCTCGATCTATAGCGACGTTTTTCAAAAAGCGCCGCTAATGCCACTAAGGCTCAACAAA
* *
40556689 AAATGACGGCGTGTTGATGAATTATTTTGCGGCGTTTTTTAAAAAATGCTACTAATGCTCGATCT
66 AAATGATGGCGTGTTGATGAATTATTTTGCGGCGTTTTTTAAAAAATGCCACTAATGCTCGATCT
**
40556754 ATAGCGGCATTTTTCAAAAAGCGCC
131 ATAGTAGCA-TTTTC-AAAAG-GCC
** * * * * *
40556779 GCTAATTCTCAATCTATAGTGGCGCTTTTCTAAAAA-CACCGCTAATG
1 GCTAAAGCTCGATCTATAGCGACGTTTTTC-AAAAAGCGCCGCTAATG
40556826 TTTGATCTAT
Statistics
Matches: 272, Mismatches: 50, Indels: 38
0.76 0.14 0.11
Matches are distributed among these distances:
139 111 0.41
140 1 0.00
141 2 0.01
142 1 0.00
145 1 0.00
149 1 0.00
152 3 0.01
153 2 0.01
154 1 0.00
155 144 0.53
156 5 0.02
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (152 bp):
GCTAAAGCTCGATCTATAGCGACGTTTTTCAAAAAGCGCCGCTAATGCCACTAAGGCTCAACAAA
AAATGATGGCGTGTTGATGAATTATTTTGCGGCGTTTTTTAAAAAATGCCACTAATGCTCGATCT
ATAGTAGCATTTTCAAAAGGCC
Found at i:40556625 original size:24 final size:24
Alignment explanation
Indices: 40556597--40556643 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
40556587 TTTAAAAAGC
* *
40556597 GTCGCTCATGCTCGATCTATAGCG
1 GTCGCTAAAGCTCGATCTATAGCG
*
40556621 GTCGCTAAAGCTCGATTTATAGC
1 GTCGCTAAAGCTCGATCTATAGC
40556644 TATGTTTTCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (24 bp):
GTCGCTAAAGCTCGATCTATAGCG
Found at i:40556747 original size:139 final size:139
Alignment explanation
Indices: 40556330--40556761 Score: 499
Period size: 139 Copynumber: 3.0 Consensus size: 139
40556320 ACAAAGCACA
*
40556330 GCTAAAGCTCGATCTATAGCGACGTTTTTCAAAAAGCGCCGCTAATGCCACTAAGGCTCAATAAA
1 GCTAAAGCTCGATCTATAGCGACGTTTTTCAAAAAGCGCCGCTAATGCCACTAAGGCTCAACAAA
* * * *
40556395 AAATGATGGCGTGTTGATGAATTAATTTGCGGCGTTTTTTAAAAAATGCCACTAATGCTCTATCT
66 AAATGACGGCGTGTTGATGAATTATTTTGCGGCGTTTTTTAAAAAATGCTACTAATGCTCGATC-
40556460 ATAGTAGCATTTATCATAAAGAGCC
130 -TA-TAG-------C-----G-GCC
* * *
40556485 GCTAAAGCTCGATCTATAGCGACATTTTTCAAAAAGCGCAGCTAATGCCACTATGGCTCAACAAA
1 GCTAAAGCTCGATCTATAGCGACGTTTTTCAAAAAGCGCCGCTAATGCCACTAAGGCTCAACAAA
** * * * * *
40556550 AAACAACTGCGTGTTGATGAATTATTTTGTGGCATTTTTT-AAAAA-GCGTCGCTCATGCTCGAT
66 AAATGACGGCGTGTTGATGAATTATTTTGCGGCGTTTTTTAAAAAATGC-T-ACTAATGCTCGAT
*
40556613 CTATAGCGGTC
129 CTATAGCGGCC
* * * * *
40556624 GCTAAAGCTCGATTTATAGCTATGTTTTCCGAAAAGCGCCGCTAATGCCACTAAGGCTCAACAAA
1 GCTAAAGCTCGATCTATAGCGACGTTTTTCAAAAAGCGCCGCTAATGCCACTAAGGCTCAACAAA
40556689 AAATGACGGCGTGTTGATGAATTATTTTGCGGCGTTTTTTAAAAAATGCTACTAATGCTCGATCT
66 AAATGACGGCGTGTTGATGAATTATTTTGCGGCGTTTTTTAAAAAATGCTACTAATGCTCGATCT
40556754 ATAGCGGC
131 ATAGCGGC
40556762 ATTTTTCAAA
Statistics
Matches: 241, Mismatches: 32, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
139 114 0.47
140 7 0.03
141 2 0.01
145 1 0.00
152 3 0.01
153 4 0.02
154 5 0.02
155 105 0.44
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (139 bp):
GCTAAAGCTCGATCTATAGCGACGTTTTTCAAAAAGCGCCGCTAATGCCACTAAGGCTCAACAAA
AAATGACGGCGTGTTGATGAATTATTTTGCGGCGTTTTTTAAAAAATGCTACTAATGCTCGATCT
ATAGCGGCC
Found at i:40556784 original size:40 final size:39
Alignment explanation
Indices: 40556740--40556850 Score: 132
Period size: 40 Copynumber: 2.8 Consensus size: 39
40556730 AAAAATGCTA
* *
40556740 CTAATGCTCGATCTATAGCGGCATTTTTCAAAAAGCGCCG
1 CTAATGCTCGATCTATAGCGGCGTTTTTCAAAAA-CACCG
* * * *
40556780 CTAATTCTCAATCTATAGTGGCGCTTTTCTAAAAACACCG
1 CTAATGCTCGATCTATAGCGGCGTTTTTC-AAAAACACCG
* *
40556820 CTAATGTTTGATCTATAGCGGCGTTTTTCAA
1 CTAATGCTCGATCTATAGCGGCGTTTTTCAA
40556851 TGCTTGATCT
Statistics
Matches: 58, Mismatches: 12, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
39 2 0.03
40 51 0.88
41 5 0.09
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (39 bp):
CTAATGCTCGATCTATAGCGGCGTTTTTCAAAAACACCG
Found at i:40556852 original size:27 final size:27
Alignment explanation
Indices: 40556822--40556874 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
40556812 AAACACCGCT
* *
40556822 AATGTTTGATCTATAGCGGCGTTTTTC
1 AATGCTTGATCTATAGCGGCATTTTTC
40556849 AATGCTTGATCTATAGCGGCATTTTT
1 AATGCTTGATCTATAGCGGCATTTTT
40556875 TGTACAAACG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.43
Consensus pattern (27 bp):
AATGCTTGATCTATAGCGGCATTTTTC
Found at i:40559820 original size:46 final size:46
Alignment explanation
Indices: 40559694--40559845 Score: 155
Period size: 46 Copynumber: 3.3 Consensus size: 46
40559684 GAATCTATTA
* * * *
40559694 GCTACAATATAGTGGTAGCTTTGGCTACATCT-CAGGGGTAGCTTCG
1 GCTACAATACAGTGGTAGCTTCGGCTACAT-TACAGTGGTAGCTTTG
* *
40559740 GCTAC-ATCTCAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTTG
1 GCTACAAT-ACAGTGGTAGCTTCGGCTACATTACAGTGGTAGCTTTG
* ** * *
40559786 GCTACAATACAGTGGTAGCTTCGACTATGTTACAGTGATAGCTTTA
1 GCTACAATACAGTGGTAGCTTCGGCTACATTACAGTGGTAGCTTTG
* *
40559832 GCTATATTACAGTG
1 GCTACAATACAGTG
40559846 TGGCACTTTG
Statistics
Matches: 88, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
45 3 0.03
46 83 0.94
47 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (46 bp):
GCTACAATACAGTGGTAGCTTCGGCTACATTACAGTGGTAGCTTTG
Found at i:40559822 original size:23 final size:23
Alignment explanation
Indices: 40559694--40559808 Score: 144
Period size: 23 Copynumber: 5.0 Consensus size: 23
40559684 GAATCTATTA
* *
40559694 GCTACAATATAGTGGTAGCTTTG
1 GCTACAATACAGTGGTAGCTTCG
* *
40559717 GCTAC-ATCTCAGGGGTAGCTTCG
1 GCTACAAT-ACAGTGGTAGCTTCG
*
40559740 GCTAC-ATCTCAGTGGTAGCTTCG
1 GCTACAAT-ACAGTGGTAGCTTCG
*
40559763 GCTACAATACAGTGGTAGCTTTG
1 GCTACAATACAGTGGTAGCTTCG
40559786 GCTACAATACAGTGGTAGCTTCG
1 GCTACAATACAGTGGTAGCTTCG
40559809 ACTATGTTAC
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
22 2 0.02
23 78 0.95
24 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.30
Consensus pattern (23 bp):
GCTACAATACAGTGGTAGCTTCG
Found at i:40559822 original size:69 final size:69
Alignment explanation
Indices: 40559694--40559829 Score: 177
Period size: 69 Copynumber: 2.0 Consensus size: 69
40559684 GAATCTATTA
* * * *
40559694 GCTACAATATAGTGGTAGCTTTGGCTACATCTCAGGGGTAGCTTCGGCTACATCTCAGTGGTAGC
1 GCTACAATACAGTGGTAGCTTTGGCTACATCACAGGGGTAGCTTCGACTACATCTCAGTGATAGC
40559759 TTCG
66 TTCG
* **
40559763 GCTACAATACAGTGGTAGCTTTGGCTACAAT-ACAGTGGTAGCTTCGACTATGT-TACAGTGATA
1 GCTACAATACAGTGGTAGCTTTGGCTAC-ATCACAGGGGTAGCTTCGACTACATCT-CAGTGATA
40559826 GCTT
64 GCTT
40559830 TAGCTATATT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
68 1 0.02
69 55 0.95
70 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.31
Consensus pattern (69 bp):
GCTACAATACAGTGGTAGCTTTGGCTACATCACAGGGGTAGCTTCGACTACATCTCAGTGATAGC
TTCG
Found at i:40559836 original size:23 final size:23
Alignment explanation
Indices: 40559704--40559845 Score: 92
Period size: 23 Copynumber: 6.2 Consensus size: 23
40559694 GCTACAATAT
* *
40559704 AGTGGTAGCTTTGGCTACATCT-C
1 AGTGGTAGCTTTAGCTATAT-TAC
* ** *
40559727 AGGGGTAGCTTCGGCTACATCT-C
1 AGTGGTAGCTTTAGCTATAT-TAC
** * *
40559750 AGTGGTAGCTTCGGCTACAATAC
1 AGTGGTAGCTTTAGCTATATTAC
* * *
40559773 AGTGGTAGCTTTGGCTACAATAC
1 AGTGGTAGCTTTAGCTATATTAC
* *
40559796 AGTGGTAGC-TTCGACTATGTTAC
1 AGTGGTAGCTTTAG-CTATATTAC
*
40559819 AGTGATAGCTTTAGCTATATTAC
1 AGTGGTAGCTTTAGCTATATTAC
40559842 AGTG
1 AGTG
40559846 TGGCACTTTG
Statistics
Matches: 104, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
22 4 0.04
23 97 0.93
24 3 0.03
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (23 bp):
AGTGGTAGCTTTAGCTATATTAC
Found at i:40559843 original size:69 final size:69
Alignment explanation
Indices: 40559693--40559845 Score: 175
Period size: 69 Copynumber: 2.2 Consensus size: 69
40559683 AGAATCTATT
* * * *
40559693 AGCTACAATATAGTGGTAGCTTTGGCTACATCTCAGGGGTAGCTTCGGCTACATCTCAGTGGTAG
1 AGCTACAATACAGTGGTAGCTTTGGCTACATCACAGGGGTAGCTTCGACTACATCTCAGTGATAG
40559758 CTTC
66 CTTC
* * **
40559762 GGCTACAATACAGTGGTAGCTTTGGCTACAAT-ACAGTGGTAGCTTCGACTATGT-TACAGTGAT
1 AGCTACAATACAGTGGTAGCTTTGGCTAC-ATCACAGGGGTAGCTTCGACTACATCT-CAGTGAT
*
40559825 AGCTTT
64 AGCTTC
* *
40559831 AGCTATATTACAGTG
1 AGCTACAATACAGTG
40559846 TGGCACTTTG
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
68 1 0.01
69 67 0.96
70 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (69 bp):
AGCTACAATACAGTGGTAGCTTTGGCTACATCACAGGGGTAGCTTCGACTACATCTCAGTGATAG
CTTC
Found at i:40559911 original size:25 final size:25
Alignment explanation
Indices: 40559836--40559911 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
40559826 GCTTTAGCTA
40559836 TATTACAGTGTGGCACTTTGTGCCT
1 TATTACAGTGTGGCACTTTGTGCCT
* * * *
40559861 TATT-CCGTGT--TAGC-TT-CGACT
1 TATTACAGTGTGGCA-CTTTGTGCCT
40559882 ATATTACAGTGTGGCACTTTGTGCCT
1 -TATTACAGTGTGGCACTTTGTGCCT
40559908 TATT
1 TATT
40559912 CCGTGTATCC
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
21 3 0.08
22 7 0.19
23 6 0.17
24 6 0.17
25 11 0.31
26 3 0.08
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.42
Consensus pattern (25 bp):
TATTACAGTGTGGCACTTTGTGCCT
Found at i:40560332 original size:36 final size:36
Alignment explanation
Indices: 40560292--40560366 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
40560282 ATGAGATATG
40560292 AAATTAAAGGTCATTGAGTCTATTTTCATAGAAAGA
1 AAATTAAAGGTCATTGAGTCTATTTTCATAGAAAGA
40560328 AAATTAAAGGTCATTGAGTCTATTTTCATAGAAAGA
1 AAATTAAAGGTCATTGAGTCTATTTTCATAGAAAGA
40560364 AAA
1 AAA
40560367 CGGTGTGAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (36 bp):
AAATTAAAGGTCATTGAGTCTATTTTCATAGAAAGA
Found at i:40562489 original size:37 final size:37
Alignment explanation
Indices: 40562439--40562518 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
40562429 CTTATTACGA
* *
40562439 AGTCTTACCCGGACATAA-TCTCCACACGAAGTTATCG
1 AGTCTTACCCGGACAAAATTC-CCACACGAAGTCATCG
*
40562476 AGTCTTACCCGGACAAAATTCCCACACGCAGTCATCG
1 AGTCTTACCCGGACAAAATTCCCACACGAAGTCATCG
*
40562513 GGTCTT
1 AGTCTT
40562519 TAGAGTCCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (37 bp):
AGTCTTACCCGGACAAAATTCCCACACGAAGTCATCG
Found at i:40562708 original size:47 final size:47
Alignment explanation
Indices: 40562649--40562899 Score: 328
Period size: 47 Copynumber: 5.4 Consensus size: 47
40562639 TATCACATTT
* * *
40562649 ATACAC-T-TTCACATTCGTCACATCGGCCATTAGGCCTTATCTCAC
1 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCAC
* * *
40562694 ATACACATGCTCACATTCATCACATTGGCCACTCGGCCTTATCACAC
1 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCAC
* * *
40562741 ATACACCTGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
1 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCAC
*
40562788 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCAT
1 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCAC
** * *
40562835 ATATGCATGTTCACATTCATCACATTGGCCATTCGGCCCTATTCACAC
1 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTA-TCTCAC
*
40562883 ATATACACT-TTCACATT
1 ATACACA-TGTTCACATT
40562900 TATTCAATTA
Statistics
Matches: 182, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
45 6 0.03
46 1 0.01
47 156 0.86
48 18 0.10
49 1 0.01
ACGTcount: A:0.26, C:0.32, G:0.10, T:0.31
Consensus pattern (47 bp):
ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCAC
Found at i:40562938 original size:94 final size:93
Alignment explanation
Indices: 40562656--40562929 Score: 241
Period size: 94 Copynumber: 2.9 Consensus size: 93
40562646 TTTATACACT
* * * * * * *
40562656 TTCACATTCGTCACATCGGCCATTAGGCCTTATCTCACATACACATGCTCACATTCATCACATTG
1 TTCACATTCATCACATTGGCCATTCGGCCCTATCACACATACACATGTTCACATTCATCACATTA
* * * * * * ** *
40562721 GCCACTCGGCCTTATCACACATACACCTG
66 GACATTC-GACATACCACATATATGCATG
* * *
40562750 TTCACTTTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTG
1 TTCACATTCATCACATTGGCCATTCGGCCCTATCACACATACACATGTTCACATTCATCACATTA
* * * * *
40562815 GCCATTCGGCCTTATCTCATATATGCATG
66 GACATTC-GACATACCACATATATGCATG
* *
40562844 TTCACATTCATCACATTGGCCATTCGGCCCTATTCACACATATACACT-TTCACATTTATTCA-A
1 TTCACATTCATCACATTGGCCATTCGGCCCTA-TCACACATACACA-TGTTCACATTCA-TCACA
40562907 TTAGAC-TTC-ACATACCACATATA
63 TTAGACATTCGACATACCACATATA
40562930 CTATCATGTA
Statistics
Matches: 155, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
92 10 0.06
94 115 0.74
95 26 0.17
96 4 0.03
ACGTcount: A:0.27, C:0.31, G:0.10, T:0.32
Consensus pattern (93 bp):
TTCACATTCATCACATTGGCCATTCGGCCCTATCACACATACACATGTTCACATTCATCACATTA
GACATTCGACATACCACATATATGCATG
Found at i:40562938 original size:141 final size:140
Alignment explanation
Indices: 40562649--40562930 Score: 326
Period size: 141 Copynumber: 2.0 Consensus size: 140
40562639 TATCACATTT
*
40562649 ATACAC-T-TTCACATTCGTCACATCGGCCATTAGGCCTTATCTCACATACACATGCTCACATTC
1 ATACACATGTTCACATTCATCACATCGGCCATTAGGCCTTATCTCACATACACATGCTCACATTC
* * *
40562712 ATCACATTGGCCACTCGGCCTTATCACACATACACCTGTTCACTTTCATCACATTGGCCATTCGG
66 ATCACATTGGCCACTCGGCCCTATCACACATACACCTGTTCACTTTCATCACATTAGACATTC-G
* * *
40562777 CCTTATCACAC
130 ACATACCACAC
* * * ** *
40562788 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTC
1 ATACACATGTTCACATTCATCACATCGGCCATTAGGCCTTATCTCACATACACATGCTCACATTC
* *
40562853 ATCACATTGGCCATTCGGCCCTATTCACACATATACACT-TTCACATTT-ATTCA-ATTAGAC-T
66 ATCACATTGGCCACTCGGCCCTA-TCACACATACAC-CTGTTCAC-TTTCA-TCACATTAGACAT
*
40562914 TC-ACATACCACAT
127 TCGACATACCACAC
40562927 ATAC
1 ATAC
40562931 TATCATGTAC
Statistics
Matches: 121, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
139 17 0.14
140 1 0.01
141 73 0.60
142 22 0.18
143 8 0.07
ACGTcount: A:0.27, C:0.32, G:0.10, T:0.32
Consensus pattern (140 bp):
ATACACATGTTCACATTCATCACATCGGCCATTAGGCCTTATCTCACATACACATGCTCACATTC
ATCACATTGGCCACTCGGCCCTATCACACATACACCTGTTCACTTTCATCACATTAGACATTCGA
CATACCACAC
Found at i:40565643 original size:40 final size:40
Alignment explanation
Indices: 40565586--40566006 Score: 638
Period size: 40 Copynumber: 10.6 Consensus size: 40
40565576 CCAGCATGAT
* * *
40565586 TGCTCTTCGGGATTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
40565626 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
40565666 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
40565706 TGCTCTTC-GGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
40565745 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
40565785 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
40565825 TGCTCTTC-GGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
40565864 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * * *
40565904 TGCTCTTCGGGGCTTAGCCCGGATATATCAACTTGCACAAA
1 TGCTCTTCGGGACTTAGCCCGGATACATC-ACTAGCACGAA
* **
40565945 TGC-CTTC-GGATCTTAGTCCGGATATGGTCACTTAGCAC-AA
1 TGCTCTTCGGGA-CTTAGCCCGGATA-CATCAC-TAGCACGAA
*
40565985 AGC-CTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGGACTTAGCCCGGA
40566007 CATCATTCGA
Statistics
Matches: 356, Mismatches: 18, Indels: 14
0.92 0.05 0.04
Matches are distributed among these distances:
39 79 0.22
40 255 0.72
41 22 0.06
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:40565810 original size:119 final size:119
Alignment explanation
Indices: 40565586--40566006 Score: 650
Period size: 119 Copynumber: 3.5 Consensus size: 119
40565576 CCAGCATGAT
* * * *
40565586 TGCTCTTCGGGATTTAGCACGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATA
1 TGCTCTTC-GGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA
40565651 CATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
65 CATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
40565706 TGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATAC
1 TGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATAC
*
40565771 ATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
66 ATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
40565825 TGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATAT
1 TGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATAC
* * * *
40565890 ATCACTAGCACGAATGCTCTTCGGGGCTTAGCCCGGATATATCAACTTGCACAAA
66 ATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATC-ACTAGCACGAA
* ** *
40565945 TGC-CTTCGGATCTTAGTCCGGATATGGTCACTTAGCAC-AAAGC-CTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGA-CTTAGCCCGGATA-CATCAC-TAGCACGAATGCTCTTCGGGACTTAGCCCGGA
40566007 CATCATTCGA
Statistics
Matches: 282, Mismatches: 15, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
119 217 0.77
120 51 0.18
121 8 0.03
122 6 0.02
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (119 bp):
TGCTCTTCGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATAC
ATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:40565877 original size:159 final size:159
Alignment explanation
Indices: 40565586--40566006 Score: 670
Period size: 159 Copynumber: 2.6 Consensus size: 159
40565576 CCAGCATGAT
* *
40565586 TGCTCTTCGGGATTTAGCACGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATA
40565651 CATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGG
66 CATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGG
40565716 ACTTAGCCCGGATACATCACTAGCACGAA
131 ACTTAGCCCGGATACATCACTAGCACGAA
*
40565745 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATA
40565810 CATCACTAGCACGAATGCTCTTC-GGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGG
66 CATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTC-G
*
40565874 GACTTAGCCCGGATATATCACTAGCACGAA
130 GACTTAGCCCGGATACATCACTAGCACGAA
* * * * *
40565904 TGCTCTTCGGGGCTTAGCCCGGATATATCAACTTGCACAAATGC-CTTCGGATCTTAGTCCGGAT
1 TGCTCTTCGGGACTTAGCCCGGATATATC-ACTAGCACGAATGCTCTTCGGAACTTAGCCCGGAT
** *
40565968 ATGGTCACTTAGCAC-AAAGC-CTTCGGGACTTAGCCCGGA
65 A-CATCAC-TAGCACGAATGCTCTTCGGGACTTAGCCCGGA
40566007 CATCATTCGA
Statistics
Matches: 244, Mismatches: 13, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
158 39 0.16
159 165 0.68
160 34 0.14
161 6 0.02
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (159 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATA
CATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGG
ACTTAGCCCGGATACATCACTAGCACGAA
Found at i:40567852 original size:37 final size:37
Alignment explanation
Indices: 40567802--40567881 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
40567792 CTTATTACGA
* *
40567802 AGTCTTACCCGGACATAA-TCTCCACACGAAGTTATCG
1 AGTCTTACCCGGACAAAATTC-CCACACGAAGTCATCG
*
40567839 AGTCTTACCCGGACAAAATTCCCACACGCAGTCATCG
1 AGTCTTACCCGGACAAAATTCCCACACGAAGTCATCG
*
40567876 GGTCTT
1 AGTCTT
40567882 TAGAGTCCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (37 bp):
AGTCTTACCCGGACAAAATTCCCACACGAAGTCATCG
Found at i:40568071 original size:47 final size:47
Alignment explanation
Indices: 40568012--40568262 Score: 328
Period size: 47 Copynumber: 5.4 Consensus size: 47
40568002 TATCACATTT
* * *
40568012 ATACAC-T-TTCACATTCGTCACATCGGCCATTAGGCCTTATCTCAC
1 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCAC
* * *
40568057 ATACACATGCTCACATTCATCACATTGGCCACTCGGCCTTATCACAC
1 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCAC
* * *
40568104 ATACACCTGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
1 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCAC
*
40568151 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCAT
1 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCAC
** * *
40568198 ATATGCATGTTCACATTCATCACATTGGCCATTCGGCCCTATTCACAC
1 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTA-TCTCAC
*
40568246 ATATACACT-TTCACATT
1 ATACACA-TGTTCACATT
40568263 TATTCAATTA
Statistics
Matches: 182, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
45 6 0.03
46 1 0.01
47 156 0.86
48 18 0.10
49 1 0.01
ACGTcount: A:0.26, C:0.32, G:0.10, T:0.31
Consensus pattern (47 bp):
ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCAC
Found at i:40568301 original size:94 final size:93
Alignment explanation
Indices: 40568019--40568292 Score: 241
Period size: 94 Copynumber: 2.9 Consensus size: 93
40568009 TTTATACACT
* * * * * * *
40568019 TTCACATTCGTCACATCGGCCATTAGGCCTTATCTCACATACACATGCTCACATTCATCACATTG
1 TTCACATTCATCACATTGGCCATTCGGCCCTATCACACATACACATGTTCACATTCATCACATTA
* * * * * * ** *
40568084 GCCACTCGGCCTTATCACACATACACCTG
66 GACATTC-GACATACCACATATATGCATG
* * *
40568113 TTCACTTTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTG
1 TTCACATTCATCACATTGGCCATTCGGCCCTATCACACATACACATGTTCACATTCATCACATTA
* * * * *
40568178 GCCATTCGGCCTTATCTCATATATGCATG
66 GACATTC-GACATACCACATATATGCATG
* *
40568207 TTCACATTCATCACATTGGCCATTCGGCCCTATTCACACATATACACT-TTCACATTTATTCA-A
1 TTCACATTCATCACATTGGCCATTCGGCCCTA-TCACACATACACA-TGTTCACATTCA-TCACA
40568270 TTAGAC-TTC-ACATACCACATATA
63 TTAGACATTCGACATACCACATATA
40568293 CTATCATGTA
Statistics
Matches: 155, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
92 10 0.06
94 115 0.74
95 26 0.17
96 4 0.03
ACGTcount: A:0.27, C:0.31, G:0.10, T:0.32
Consensus pattern (93 bp):
TTCACATTCATCACATTGGCCATTCGGCCCTATCACACATACACATGTTCACATTCATCACATTA
GACATTCGACATACCACATATATGCATG
Found at i:40568301 original size:141 final size:140
Alignment explanation
Indices: 40568012--40568293 Score: 326
Period size: 141 Copynumber: 2.0 Consensus size: 140
40568002 TATCACATTT
*
40568012 ATACAC-T-TTCACATTCGTCACATCGGCCATTAGGCCTTATCTCACATACACATGCTCACATTC
1 ATACACATGTTCACATTCATCACATCGGCCATTAGGCCTTATCTCACATACACATGCTCACATTC
* * *
40568075 ATCACATTGGCCACTCGGCCTTATCACACATACACCTGTTCACTTTCATCACATTGGCCATTCGG
66 ATCACATTGGCCACTCGGCCCTATCACACATACACCTGTTCACTTTCATCACATTAGACATTC-G
* * *
40568140 CCTTATCACAC
130 ACATACCACAC
* * * ** *
40568151 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTC
1 ATACACATGTTCACATTCATCACATCGGCCATTAGGCCTTATCTCACATACACATGCTCACATTC
* *
40568216 ATCACATTGGCCATTCGGCCCTATTCACACATATACACT-TTCACATTT-ATTCA-ATTAGAC-T
66 ATCACATTGGCCACTCGGCCCTA-TCACACATACAC-CTGTTCAC-TTTCA-TCACATTAGACAT
*
40568277 TC-ACATACCACAT
127 TCGACATACCACAC
40568290 ATAC
1 ATAC
40568294 TATCATGTAC
Statistics
Matches: 121, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
139 17 0.14
140 1 0.01
141 73 0.60
142 22 0.18
143 8 0.07
ACGTcount: A:0.27, C:0.32, G:0.10, T:0.32
Consensus pattern (140 bp):
ATACACATGTTCACATTCATCACATCGGCCATTAGGCCTTATCTCACATACACATGCTCACATTC
ATCACATTGGCCACTCGGCCCTATCACACATACACCTGTTCACTTTCATCACATTAGACATTCGA
CATACCACAC
Found at i:40569545 original size:21 final size:22
Alignment explanation
Indices: 40569505--40569545 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
40569495 TCACCTCATG
* *
40569505 TTTTATTATTCTTAATTCATTC
1 TTTTATTATTCTAAACTCATTC
40569527 TTTTATT-TTCTAAACTCAT
1 TTTTATTATTCTAAACTCAT
40569546 AGTGCTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTTATTATTCTAAACTCATTC
Found at i:40574565 original size:27 final size:26
Alignment explanation
Indices: 40574533--40574765 Score: 83
Period size: 27 Copynumber: 8.7 Consensus size: 26
40574523 ACCCCAATTG
40574533 TAAAATTACCAAAGTACCCCCGGTTTA
1 TAAAATTACCAAA-TACCCCCGGTTTA
**** * *
40574560 TAAAATTACCGAAATA-CTGTTGATTG
1 TAAAATTACC-AAATACCCCCGGTTTA
** * ** *
40574586 TAAAATTATTAAAATACCCTCGACTTG
1 TAAAATTA-CCAAATACCCCCGGTTTA
*
40574613 TAAAATTACCAAAGTACCCCCAGTTTA
1 TAAAATTACCAAA-TACCCCCGGTTTA
** * *
40574640 TAAAATTACCGAAATA-CCGTGGATTG
1 TAAAATTACC-AAATACCCCCGGTTTA
* * * *
40574666 TAAAATTACTGAAATACCCTCGATTTG
1 TAAAATTAC-CAAATACCCCCGGTTTA
* * * *
40574693 TAAAATTATCGAAATACCCTCAGTTTG
1 TAAAATTA-CCAAATACCCCCGGTTTA
* * * ** *
40574720 CAAAATTACTGAAATACCCTCAATTTG
1 TAAAATTAC-CAAATACCCCCGGTTTA
*
40574747 TAAAATTACTAAAATACCC
1 TAAAATTAC-CAAATACCC
40574766 TTGTAGGGTA
Statistics
Matches: 160, Mismatches: 37, Indels: 18
0.74 0.17 0.08
Matches are distributed among these distances:
26 40 0.25
27 113 0.71
28 7 0.04
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (26 bp):
TAAAATTACCAAATACCCCCGGTTTA
Found at i:40574625 original size:80 final size:80
Alignment explanation
Indices: 40574530--40574766 Score: 323
Period size: 80 Copynumber: 3.0 Consensus size: 80
40574520 GATACCCCAA
* * * *
40574530 TTGTAAAATTACCAAAGTACCCCCGGTTTATAAAATTACCGAAATACTGTTGATTGTAAAATTAT
1 TTGTAAAATTACCAAAGTACCCCCAGTTTATAAAATTACCGAAATACCGTCGATTGTAAAATTAC
40574595 TAAAATACCCTCGAC
66 TAAAATACCCTCGAC
*
40574610 TTGTAAAATTACCAAAGTACCCCCAGTTTATAAAATTACCGAAATACCGTGGATTGTAAAATTAC
1 TTGTAAAATTACCAAAGTACCCCCAGTTTATAAAATTACCGAAATACCGTCGATTGTAAAATTAC
* *
40574675 TGAAATACCCTCGAT
66 TAAAATACCCTCGAC
* * ** * * *
40574690 TTGTAAAATTATCGAAA-TACCCTCAGTTTGCAAAATTACTGAAATACCCTCAATTTGTAAAATT
1 TTGTAAAATTA-CCAAAGTACCCCCAGTTTATAAAATTACCGAAATACCGTCGA-TTGTAAAATT
40574754 ACTAAAATACCCT
64 ACTAAAATACCCT
40574767 TGTAGGGTAG
Statistics
Matches: 140, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
80 114 0.81
81 26 0.19
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (80 bp):
TTGTAAAATTACCAAAGTACCCCCAGTTTATAAAATTACCGAAATACCGTCGATTGTAAAATTAC
TAAAATACCCTCGAC
Found at i:40574657 original size:54 final size:53
Alignment explanation
Indices: 40574530--40574766 Score: 194
Period size: 54 Copynumber: 4.4 Consensus size: 53
40574520 GATACCCCAA
* * * * ** * *
40574530 TTGTAAAATTACC-AAAGTACCCCCGGTTTATAAAATTACCGAAATACTGT-TGA
1 TTGTAAAATTACCGAAA-TACCCTC-GATTGTAAAATTACTGAAATACCCTCAGT
*** * *
40574583 TTGTAAAATTATTAAAATACCCTCGACTTGTAAAATTAC-CAAAGTACCCCCAGT
1 TTGTAAAATTACCGAAATACCCTCGA-TTGTAAAATTACTGAAA-TACCCTCAGT
* * *
40574637 TTATAAAATTACCGAAATACCGTGGATTGTAAAATTACTGAAATACCCTC-GAT
1 TTGTAAAATTACCGAAATACCCTCGATTGTAAAATTACTGAAATACCCTCAG-T
* * * *
40574690 TTGTAAAATTATCGAAATACCCTCAGTTTGCAAAATTACTGAAATACCCTCAAT
1 TTGTAAAATTACCGAAATACCCTC-GATTGTAAAATTACTGAAATACCCTCAGT
**
40574744 TTGTAAAATTACTAAAATACCCT
1 TTGTAAAATTACCGAAATACCCT
40574767 TGTAGGGTAG
Statistics
Matches: 147, Mismatches: 29, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
52 5 0.03
53 70 0.48
54 72 0.49
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (53 bp):
TTGTAAAATTACCGAAATACCCTCGATTGTAAAATTACTGAAATACCCTCAGT
Found at i:40574766 original size:27 final size:27
Alignment explanation
Indices: 40574583--40574766 Score: 185
Period size: 27 Copynumber: 6.9 Consensus size: 27
40574573 ATACTGTTGA
* * * *
40574583 TTGTAAAATTATTAAAATACCCTCGAC
1 TTGTAAAATTACTGAAATACCCTCAAT
* * *
40574610 TTGTAAAATTAC-CAAAGTACCCCCAGT
1 TTGTAAAATTACTGAAA-TACCCTCAAT
* * * **
40574637 TTATAAAATTACCGAAATACCGTGGA-
1 TTGTAAAATTACTGAAATACCCTCAAT
*
40574663 TTGTAAAATTACTGAAATACCCTCGAT
1 TTGTAAAATTACTGAAATACCCTCAAT
*
40574690 TTGTAAAATTA-TCGAAATACCCTCAGT
1 TTGTAAAATTACT-GAAATACCCTCAAT
*
40574717 TTGCAAAATTACTGAAATACCCTCAAT
1 TTGTAAAATTACTGAAATACCCTCAAT
*
40574744 TTGTAAAATTACTAAAATACCCT
1 TTGTAAAATTACTGAAATACCCT
40574767 TGTAGGGTAG
Statistics
Matches: 129, Mismatches: 23, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
26 26 0.20
27 99 0.77
28 4 0.03
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.31
Consensus pattern (27 bp):
TTGTAAAATTACTGAAATACCCTCAAT
Found at i:40574781 original size:54 final size:54
Alignment explanation
Indices: 40574669--40575104 Score: 345
Period size: 54 Copynumber: 8.1 Consensus size: 54
40574659 TGGATTGTAA
* ** * * * ** * *
40574669 AATTACTGAAATACCCTCGATTTGTAAAATTATCGAAATACCCTCAGT-TTGCAA
1 AATTACTGAAATACCCTCTATGGGTAAAATTACCAAAATACCCT-TGTAGGGTAG
* ** *
40574723 AATTACTGAAATACCCTCAATTTGTAAAATTACTAAAATACCCTTGTAGGGTAG
1 AATTACTGAAATACCCTCTATGGGTAAAATTACCAAAATACCCTTGTAGGGTAG
* * *
40574777 AATTACTAAAATACCAT-TATAGGGTAGAATTACCAAAATACCCTTGTAGGGTAG
1 AATTACTGAAATACCCTCTAT-GGGTAAAATTACCAAAATACCCTTGTAGGGTAG
* * * * *
40574831 AATTACTGAAATA-CCTTTGTAGGTAGAAA-TACCGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCTCTATGGGTA-AAATTACCAAAATACCCTTGTAGGGTAG
* * * * *
40574884 AATTACTAAAATACCC-CTATAGGGTAGAATTATCGAAATACCCTTGTAGGGTAA
1 AATTACTGAAATACCCTCTAT-GGGTAAAATTACCAAAATACCCTTGTAGGGTAG
* * *
40574938 AAATA-TCGAAATA-CCTTTGTAGGGTAGAAA-TACCAAAATACCCTTGTAGGGTAG
1 AATTACT-GAAATACCCTCTAT-GGGTA-AAATTACCAAAATACCCTTGTAGGGTAG
* * * * *
40574992 AATTACTGAAATACCC-CTGTAAGGTAGAATTA-CAGAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCTCTAT-GGGTAAAATTACCA-AAATACCCTTGTAGGGTAG
* * * * * *
40575046 AATTACTGAAATACCCTATA-GGGTAGAATTACCGAGATACCCTTGTGGGGTAA
1 AATTACTGAAATACCCTCTATGGGTAAAATTACCAAAATACCCTTGTAGGGTAG
40575099 AATTAC
1 AATTAC
40575105 CATTTTACCC
Statistics
Matches: 312, Mismatches: 54, Indels: 33
0.78 0.14 0.08
Matches are distributed among these distances:
53 85 0.27
54 221 0.71
55 6 0.02
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (54 bp):
AATTACTGAAATACCCTCTATGGGTAAAATTACCAAAATACCCTTGTAGGGTAG
Found at i:40574905 original size:107 final size:107
Alignment explanation
Indices: 40574758--40575104 Score: 475
Period size: 107 Copynumber: 3.2 Consensus size: 107
40574748 AAAATTACTA
**
40574758 AAATACCCTTGTAGGGTAGAATTACTAAAATACCATTATAGGGTAGAATTACCAAAATACCCTTG
1 AAATACCCTTGTAGGGTAGAATTACTAAAATACCCCTATAGGGTAGAATTA-CAAAATACCCTTG
40574823 TAGGGTAGAATTACTGAAATACCTTTGTA-GGTAGAAATACCG
65 TAGGGTAGAATTACTGAAATACCTTTGTAGGGTAGAAATACCG
* *
40574865 AAATACCCCTGTAGGGTAGAATTACTAAAATACCCCTATAGGGTAGAATTATCGAAATACCCTTG
1 AAATACCCTTGTAGGGTAGAATTACTAAAATACCCCTATAGGGTAGAATTA-CAAAATACCCTTG
* * *
40574930 TAGGGTAAAAATA-TCGAAATACCTTTGTAGGGTAGAAATACCA
65 TAGGGTAGAATTACT-GAAATACCTTTGTAGGGTAGAAATACCG
* * * * *
40574973 AAATACCCTTGTAGGGTAGAATTACTGAAATACCCCTGTAAGGTAGAATTACAGAAATACCCCTA
1 AAATACCCTTGTAGGGTAGAATTACTAAAATACCCCTATAGGGTAGAATTACA-AAATACCCTTG
* * *
40575038 TAGGGTAGAATTACTGAAATACC-CTATAGGGTAGAATTACCG
65 TAGGGTAGAATTACTGAAATACCTTTGTAGGGTAGAAATACCG
* * *
40575080 AGATACCCTTGTGGGGTAAAATTAC
1 AAATACCCTTGTAGGGTAGAATTAC
40575105 CATTTTACCC
Statistics
Matches: 212, Mismatches: 24, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
106 1 0.00
107 123 0.58
108 87 0.41
109 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (107 bp):
AAATACCCTTGTAGGGTAGAATTACTAAAATACCCCTATAGGGTAGAATTACAAAATACCCTTGT
AGGGTAGAATTACTGAAATACCTTTGTAGGGTAGAAATACCG
Found at i:40575065 original size:161 final size:161
Alignment explanation
Indices: 40574758--40575100 Score: 519
Period size: 161 Copynumber: 2.1 Consensus size: 161
40574748 AAAATTACTA
* * *
40574758 AAATACCCTTGTAGGGTAGAATTACTAAAATACCATTATAGGGTAGAATTACCAAAATACCCTTG
1 AAATACCCTTGTAGGGTAAAAATACTAAAATACCATTATAGGGTAGAAATACCAAAATACCCTTG
** * *
40574823 TAGGGTAGAATTACTGAAATACCTTTGTAGGTAGAAATACCGAAATACCCCTGTAGGGTAGAATT
66 TAGGGTAGAATTACTGAAATACCCCTGTAGGTAGAAATACAGAAATACCCCTATAGGGTAGAATT
*
40574888 ACTAAAATACCCCTATAGGGTAGAATTATCG
131 ACTAAAATACCCCTATAGGGTAGAATTACCG
* * *
40574919 AAATACCCTTGTAGGGTAAAAATA-TCGAAATACCTTTGTAGGGTAGAAATACCAAAATACCCTT
1 AAATACCCTTGTAGGGTAAAAATACT-AAAATACCATTATAGGGTAGAAATACCAAAATACCCTT
*
40574983 GTAGGGTAGAATTACTGAAATACCCCTGTAAGGTAGAATTACAGAAATACCCCTATAGGGTAGAA
65 GTAGGGTAGAATTACTGAAATACCCCTGT-AGGTAGAAATACAGAAATACCCCTATAGGGTAGAA
*
40575048 TTACTGAAATA-CCCTATAGGGTAGAATTACCG
129 TTACTAAAATACCCCTATAGGGTAGAATTACCG
* *
40575080 AGATACCCTTGTGGGGTAAAA
1 AAATACCCTTGTAGGGTAAAA
40575101 TTACCATTTT
Statistics
Matches: 165, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
160 1 0.01
161 122 0.74
162 42 0.25
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (161 bp):
AAATACCCTTGTAGGGTAAAAATACTAAAATACCATTATAGGGTAGAAATACCAAAATACCCTTG
TAGGGTAGAATTACTGAAATACCCCTGTAGGTAGAAATACAGAAATACCCCTATAGGGTAGAATT
ACTAAAATACCCCTATAGGGTAGAATTACCG
Found at i:40575105 original size:27 final size:27
Alignment explanation
Indices: 40574758--40575105 Score: 403
Period size: 27 Copynumber: 13.0 Consensus size: 27
40574748 AAAATTACTA
**
40574758 AAATACCCTTGTAGGGTAGAATTACTA
1 AAATACCCTTGTAGGGTAGAATTACCG
* * *
40574785 AAATACCATTATAGGGTAGAATTACCA
1 AAATACCCTTGTAGGGTAGAATTACCG
*
40574812 AAATACCCTTGTAGGGTAGAATTACTG
1 AAATACCCTTGTAGGGTAGAATTACCG
* *
40574839 AAATACCTTTGTA-GGTAGAAATACCG
1 AAATACCCTTGTAGGGTAGAATTACCG
* **
40574865 AAATACCCCTGTAGGGTAGAATTACTA
1 AAATACCCTTGTAGGGTAGAATTACCG
* * *
40574892 AAATACCCCTATAGGGTAGAATTATCG
1 AAATACCCTTGTAGGGTAGAATTACCG
* * *
40574919 AAATACCCTTGTAGGGTAAAAATATCG
1 AAATACCCTTGTAGGGTAGAATTACCG
* * *
40574946 AAATACCTTTGTAGGGTAGAAATACCA
1 AAATACCCTTGTAGGGTAGAATTACCG
*
40574973 AAATACCCTTGTAGGGTAGAATTACTG
1 AAATACCCTTGTAGGGTAGAATTACCG
* * *
40575000 AAATACCCCTGTAAGGTAGAATTACAG
1 AAATACCCTTGTAGGGTAGAATTACCG
* * *
40575027 AAATACCCCTATAGGGTAGAATTACTG
1 AAATACCCTTGTAGGGTAGAATTACCG
*
40575054 AAATACCC-TATAGGGTAGAATTACCG
1 AAATACCCTTGTAGGGTAGAATTACCG
* * *
40575080 AGATACCCTTGTGGGGTAAAATTACC
1 AAATACCCTTGTAGGGTAGAATTACC
40575106 ATTTTACCCC
Statistics
Matches: 277, Mismatches: 42, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
26 46 0.17
27 231 0.83
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (27 bp):
AAATACCCTTGTAGGGTAGAATTACCG
Found at i:40575711 original size:6 final size:6
Alignment explanation
Indices: 40575700--40575774 Score: 82
Period size: 6 Copynumber: 12.3 Consensus size: 6
40575690 TTGCGTTCAC
*
40575700 ATTCTG ATTCTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* *
40575749 ATTCTC ATTTTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG ATTCTG A-TTCTG AT
40575775 AATGTTTCTT
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
5 3 0.05
6 50 0.86
7 4 0.07
8 1 0.02
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:40578338 original size:29 final size:29
Alignment explanation
Indices: 40578281--40578382 Score: 143
Period size: 29 Copynumber: 3.6 Consensus size: 29
40578271 TACCTGTATC
* *
40578281 TGGCCCATTAAGCCC-AATCATATTTATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
* *
40578309 TGGCCCATTAGGCCCAAATCACCTATATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
*
40578338 TGGCCCATTAGGCCCAAATAACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
*
40578367 TGGCCCGTTAGGCCCA
1 TGGCCCATTAGGCCCA
40578383 GTCACACTCA
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
28 14 0.22
29 51 0.78
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.26
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTTATA
Found at i:40578344 original size:57 final size:58
Alignment explanation
Indices: 40578272--40578382 Score: 161
Period size: 58 Copynumber: 1.9 Consensus size: 58
40578262 AAATTCACAT
* * * *
40578272 ACCTGTATCTGGCCCATTAAGCCC-AATCATATTTATATGGCCCATTAGGCCCAAATC
1 ACCTATATATGGCCCATTAAGCCCAAATAACATTTATATGGCCCATTAGGCCCAAATC
* *
40578329 ACCTATATATGGCCCATTAGGCCCAAATAACATTTATATGGCCCGTTAGGCCCA
1 ACCTATATATGGCCCATTAAGCCCAAATAACATTTATATGGCCCATTAGGCCCA
40578383 GTCACACTCA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
57 21 0.45
58 26 0.55
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (58 bp):
ACCTATATATGGCCCATTAAGCCCAAATAACATTTATATGGCCCATTAGGCCCAAATC
Found at i:40578626 original size:16 final size:16
Alignment explanation
Indices: 40578605--40578648 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
40578595 GTAGTCAAAC
*
40578605 TTTCAGCTTTTCAGTA
1 TTTCAGCTTTTCAGCA
* *
40578621 TTTCAGCATTTCGGCA
1 TTTCAGCTTTTCAGCA
*
40578637 TTTCGGCTTTTC
1 TTTCAGCTTTTC
40578649 CCGATTCATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.48
Consensus pattern (16 bp):
TTTCAGCTTTTCAGCA
Found at i:40585643 original size:29 final size:28
Alignment explanation
Indices: 40585580--40585694 Score: 106
Period size: 29 Copynumber: 4.0 Consensus size: 28
40585570 TTCACATACC
* * *
40585580 TGTATCTGGCCCATTAAGCCCAATCATA
1 TGTATATGGCCCATTAGGCCCAATCACA
* * *
40585608 TTTATATGGCCTATTAGGCCCAAATCACC
1 TGTATATGGCCCATTAGGCCC-AATCACA
*
40585637 TGTATATGGCCCATTAGGCTCGAATCACA
1 TGTATATGGCCCATTAGGC-CCAATCACA
* * *
40585666 TTTATATGGCCCCTGT-GGCCCAGTCACA
1 TGTATATGGCCCAT-TAGGCCCAATCACA
40585694 T
1 T
40585695 TCATATTCAT
Statistics
Matches: 70, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
28 25 0.36
29 43 0.61
30 2 0.03
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (28 bp):
TGTATATGGCCCATTAGGCCCAATCACA
Found at i:40585924 original size:8 final size:8
Alignment explanation
Indices: 40585911--40585954 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
40585901 TTAACCAAAC
*
40585911 TTTCAGCT
1 TTTCAGCA
40585919 TTTCAGCA
1 TTTCAGCA
*
40585927 TTTCGGCA
1 TTTCAGCA
*
40585935 TTTCGGCA
1 TTTCAGCA
40585943 TTTCAGCA
1 TTTCAGCA
40585951 TTTC
1 TTTC
40585955 GGCTTTTACT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.16, C:0.25, G:0.16, T:0.43
Consensus pattern (8 bp):
TTTCAGCA
Found at i:40588490 original size:38 final size:38
Alignment explanation
Indices: 40588397--40588492 Score: 106
Period size: 38 Copynumber: 2.5 Consensus size: 38
40588387 GATGGGGGCA
* *
40588397 ATTTGCTCAACACTTCAAAGCTTCAAGATGGTGGCAAG
1 ATTTGCTCAACACTTCAAAGCATCAAGATGGTGGAAAG
* * *
40588435 A-TTCCTTTAACACTTCAAAGCATCAATATGGAT-GAAAG
1 ATTTGC-TCAACACTTCAAAGCATCAAGATGG-TGGAAAG
*
40588473 ATTTGCTCAACATTTCAAAG
1 ATTTGCTCAACACTTCAAAG
40588493 ATTCGAGGAG
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
37 3 0.06
38 40 0.85
39 4 0.09
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (38 bp):
ATTTGCTCAACACTTCAAAGCATCAAGATGGTGGAAAG
Found at i:40589437 original size:57 final size:58
Alignment explanation
Indices: 40589288--40589457 Score: 177
Period size: 57 Copynumber: 2.9 Consensus size: 58
40589278 CTTTCAGCTT
* * *
40589288 TAAC-TTTTGCTTAAGCCATCCAATGAAGGATTTTCAA-CTTAACGAG-TATTATCTCTCAC
1 TAACATTTTGCTTAAACCATCCAATGAAGGATTTT-AAGCTTAATGAGCT-TT-T-TTTCAC
* * * * *
40589347 TAACTTTTTTCTTAAACCATCAAATGAAGGATTTTTAGCTTAATGAGCTTTTTTTCCC
1 TAACATTTTGCTTAAACCATCCAATGAAGGATTTTAAGCTTAATGAGCTTTTTTTCAC
* * *
40589405 TAA-ATTTTGCTTAAACCATCCAATGTAGGATTTTAAGGTTAATAAGCTTTTTT
1 TAACATTTTGCTTAAACCATCCAATGAAGGATTTTAAGCTTAATGAGCTTTTTT
40589458 ATTTTTGCCC
Statistics
Matches: 94, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
57 43 0.46
58 7 0.07
59 6 0.06
60 37 0.39
61 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (58 bp):
TAACATTTTGCTTAAACCATCCAATGAAGGATTTTAAGCTTAATGAGCTTTTTTTCAC
Found at i:40591585 original size:18 final size:19
Alignment explanation
Indices: 40591562--40591597 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
40591552 GGCTCAGAAT
*
40591562 CCCACACG-CCCATGTGGA
1 CCCACACGACCCAGGTGGA
40591580 CCCACACGACCCAGGTGG
1 CCCACACGACCCAGGTGG
40591598 TCGATCTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.22, C:0.44, G:0.25, T:0.08
Consensus pattern (19 bp):
CCCACACGACCCAGGTGGA
Found at i:40592974 original size:24 final size:24
Alignment explanation
Indices: 40592946--40592995 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
40592936 AATATTAATT
*
40592946 ATTTATAATATTTAATTAGATTAA
1 ATTTATAAAATTTAATTAGATTAA
*
40592970 ATTTATAAAATTTAATTATATTAA
1 ATTTATAAAATTTAATTAGATTAA
40592994 AT
1 AT
40592996 AAACTATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
ATTTATAAAATTTAATTAGATTAA
Found at i:40593006 original size:24 final size:24
Alignment explanation
Indices: 40592950--40593020 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 24
40592940 TTAATTATTT
* **
40592950 ATAATATTTAATTAGATTAAATTT
1 ATAATATTTAATTATATTAAATAA
*
40592974 ATAAAATTTAATTATATTAAATAA
1 ATAATATTTAATTATATTAAATAA
*
40592998 ACT-ATATTTTAAATAT-TTAAATA
1 A-TAATA-TTTAATTATATTAAATA
40593021 TAACCATTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
24 30 0.77
25 9 0.23
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (24 bp):
ATAATATTTAATTATATTAAATAA
Found at i:40610472 original size:31 final size:31
Alignment explanation
Indices: 40610434--40610495 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
40610424 TACTTGGGTA
40610434 TAGCTAGTCTAATCATTTTGAGTATGACATG
1 TAGCTAGTCTAATCATTTTGAGTATGACATG
40610465 TAGCTAGTCTAATCATTTTGAGTATGACATG
1 TAGCTAGTCTAATCATTTTGAGTATGACATG
40610496 CATAGGGACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (31 bp):
TAGCTAGTCTAATCATTTTGAGTATGACATG
Found at i:40618908 original size:56 final size:56
Alignment explanation
Indices: 40618822--40618941 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
40618812 ACAAGGGATG
40618822 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
40618878 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
40618934 ATGGGCAA
1 ATGGGCAA
40618942 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:40620443 original size:47 final size:47
Alignment explanation
Indices: 40620389--40620936 Score: 802
Period size: 47 Copynumber: 11.6 Consensus size: 47
40620379 TATTTGAATA
* *
40620389 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
40620436 AATGTGAAAGTGTATGTATGTGATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
40620483 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
40620532 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
40620579 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
40620628 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
40620675 AATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
*
40620722 AATGTGAACATGTGTATGTA--TGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-A-GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
40620769 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
40620816 AATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
40620863 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
40620910 GATGTGGAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
40620937 TCCCGAAGGG
Statistics
Matches: 464, Mismatches: 27, Indels: 20
0.91 0.05 0.04
Matches are distributed among these distances:
45 5 0.01
46 1 0.00
47 361 0.78
49 96 0.21
50 1 0.00
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:40620814 original size:22 final size:22
Alignment explanation
Indices: 40620787--40620908 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
40620777 CATGTGTATG
40620787 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * *
40620809 TGTGATGAATG-TGAACAT-GCATATA
1 TGTGAT-AAGGCCG-A-ATGGC-CA-A
*
40620834 TGAGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * ***
40620856 TGTGATGAATG-TGAAAGTGTATATA
1 TGTGAT-AAGGCCG-AA-TGGCCA-A
40620881 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
40620903 TGTGAT
1 TGTGAT
40620909 GGATGTGGAA
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 21 0.30
23 17 0.24
24 17 0.24
25 15 0.21
ACGTcount: A:0.34, C:0.11, G:0.30, T:0.25
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:40623772 original size:21 final size:20
Alignment explanation
Indices: 40623739--40623778 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
40623729 ATAAATTTAA
40623739 AAAGAAAAAGAGAGTGAGAG
1 AAAGAAAAAGAGAGTGAGAG
*
40623759 AAAGAAAAATGAGATTGAGA
1 AAAGAAAAA-GAGAGTGAGA
40623779 TTGAAAAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.60, C:0.00, G:0.30, T:0.10
Consensus pattern (20 bp):
AAAGAAAAAGAGAGTGAGAG
Found at i:40625881 original size:3 final size:3
Alignment explanation
Indices: 40625873--40625929 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
40625863 ACTACCAGCC
40625873 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
40625921 ATT ATT ATT
1 ATT ATT ATT
40625930 TTCTTTTAGC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:40626752 original size:21 final size:20
Alignment explanation
Indices: 40626700--40626758 Score: 68
Period size: 18 Copynumber: 3.0 Consensus size: 20
40626690 TGAAAAAAAT
* *
40626700 GAAAGAAAAAGAAATTGA-A
1 GAAAGAAAAAGAGAGTGAGA
40626719 -AAAGAAAAAGAGAGTGAGA
1 GAAAGAAAAAGAGAGTGAGA
*
40626738 GAAAGAAAAACGAGATTGAGA
1 GAAAGAAAAA-GAGAGTGAGA
40626759 TTGAAAAAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 15 0.44
19 1 0.03
20 9 0.26
21 9 0.26
ACGTcount: A:0.63, C:0.02, G:0.27, T:0.08
Consensus pattern (20 bp):
GAAAGAAAAAGAGAGTGAGA
Found at i:40628532 original size:31 final size:31
Alignment explanation
Indices: 40628467--40628535 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 31
40628457 AACTTAATTT
*
40628467 CAGCTCAACGAGCTCAATCTTGGATTTTGCC
1 CAGCTCAACGAGCTCAATCTTGGATTATGCC
* *
40628498 CAGCTCAATGGAGCTCAAT-TTGGCTTGATG-C
1 CAGCTCAA-CGAGCTCAATCTTGGATT-ATGCC
40628529 CAGCTCA
1 CAGCTCA
40628536 TTGAGTTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 22 0.67
32 11 0.33
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.28
Consensus pattern (31 bp):
CAGCTCAACGAGCTCAATCTTGGATTATGCC
Found at i:40633772 original size:49 final size:49
Alignment explanation
Indices: 40633678--40633809 Score: 131
Period size: 49 Copynumber: 2.7 Consensus size: 49
40633668 CACATCAAAG
* * * *
40633678 TCGATGTCATGTCCCAGACAGGTCTTACATTGACTGTCATATATCGAGGC
1 TCGATGCCGTGTCCCAGACAGGTCTTACACTGACTCTCATATATCG-GGC
** * * * * **
40633728 T-GATGTTGTGTCCCAGATAGGTCTTACACTGGCTCTTATTTATCGGTT
1 TCGATGCCGTGTCCCAGACAGGTCTTACACTGACTCTCATATATCGGGC
*
40633776 TCGATGCCGTGTCCCAAACAGGTCTTACACTGAC
1 TCGATGCCGTGTCCCAGACAGGTCTTACACTGAC
40633810 ACATAACAAG
Statistics
Matches: 66, Mismatches: 15, Indels: 3
0.79 0.18 0.04
Matches are distributed among these distances:
48 2 0.03
49 63 0.95
50 1 0.02
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (49 bp):
TCGATGCCGTGTCCCAGACAGGTCTTACACTGACTCTCATATATCGGGC
Found at i:40634578 original size:20 final size:20
Alignment explanation
Indices: 40634553--40634591 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40634543 AAAATTTCAA
40634553 TTATTTCAC-ACATTTACAAC
1 TTATTTCACAAC-TTTACAAC
*
40634573 TTATTTTACAACTTTACAA
1 TTATTTCACAACTTTACAA
40634592 AATTGCCCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.44
Consensus pattern (20 bp):
TTATTTCACAACTTTACAAC
Found at i:40639126 original size:16 final size:16
Alignment explanation
Indices: 40639105--40639136 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40639095 AATTGAGTTG
*
40639105 AGAAAATTATTTAATT
1 AGAAAATTAATTAATT
40639121 AGAAAATTAATTAATT
1 AGAAAATTAATTAATT
40639137 TAAATTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (16 bp):
AGAAAATTAATTAATT
Found at i:40646849 original size:47 final size:47
Alignment explanation
Indices: 40646781--40647300 Score: 778
Period size: 47 Copynumber: 11.1 Consensus size: 47
40646771 GAAATGATAG
* * *
40646781 TAAGGCCAAATGGTCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
*
40646828 TAAGGCCTAATAGCCGGTGTGATGAATGTGAAAGTGTATATAG-GTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT-GTGTGA
40646875 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
* *
40646922 TAAGGCCAAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
40646969 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAG-GTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT-GTGTGA
*
40647016 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
40647063 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAG-GTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT-GTGTGA
* *
40647110 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
*
40647157 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
* *
40647204 TAAGGCCTAATGGCCGATGTG-TGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
* * * * * * * * * **
40647250 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
40647297 TAAG
1 TAAG
40647301 TCCCGAAGGG
Statistics
Matches: 440, Mismatches: 26, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
46 41 0.09
47 397 0.90
48 2 0.00
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
Found at i:40646918 original size:23 final size:23
Alignment explanation
Indices: 40646891--40646965 Score: 57
Period size: 23 Copynumber: 3.2 Consensus size: 23
40646881 CTAATAGCCG
40646891 ATGTGATGAATGTGAAAGTGTAT
1 ATGTGATGAATGTGAAAGTGTAT
* ***
40646914 ATGTG-TGATAAG-GCCAAA-TGGCCG
1 ATGTGATGA-ATGTG--AAAGT-GTAT
40646938 ATGTGATGAATGTGAAAGTGTAT
1 ATGTGATGAATGTGAAAGTGTAT
40646961 ATGTG
1 ATGTG
40646966 TGATAAGGCC
Statistics
Matches: 37, Mismatches: 8, Indels: 14
0.63 0.14 0.24
Matches are distributed among these distances:
22 4 0.11
23 17 0.46
24 12 0.32
25 4 0.11
ACGTcount: A:0.32, C:0.05, G:0.32, T:0.31
Consensus pattern (23 bp):
ATGTGATGAATGTGAAAGTGTAT
Found at i:40647475 original size:37 final size:37
Alignment explanation
Indices: 40647419--40647497 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
40647409 CCGAGCTCTA
* * * *
40647419 AAGACCCGATGACTACGTGTGGGGATTTTGTCTGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
40647456 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
40647493 AAGAC
1 AAGAC
40647498 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:40652782 original size:13 final size:12
Alignment explanation
Indices: 40652746--40652784 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
40652736 GGTTTTCTCC
*
40652746 AAAATGAAAATG
1 AAAATGAAAATA
40652758 AAAATGAGAAATA
1 AAAATGA-AAATA
40652771 AAACATGAAAATA
1 AAA-ATGAAAATA
40652784 A
1 A
40652785 CCTAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 7 0.29
13 13 0.54
14 4 0.17
ACGTcount: A:0.69, C:0.03, G:0.13, T:0.15
Consensus pattern (12 bp):
AAAATGAAAATA
Found at i:40663264 original size:40 final size:39
Alignment explanation
Indices: 40663220--40663404 Score: 187
Period size: 40 Copynumber: 4.6 Consensus size: 39
40663210 GCTCCTCGTT
* *
40663220 CAAATGCCTTCAGGACATAGCCC-GATTATAGTAATTTGCA
1 CAAATGCCTTC-GGACTTAGCCCGGATT-TAGTAATTCGCA
* *
40663260 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTC-GGACTTAGCCCGGATTTAGTAATTCGCA
* *
40663300 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGATTTAGTAAT-TCGCA
* * * * *
40663339 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGT-AATTCGCA
40663380 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTC-GGACTTAGCCCGGA
40663405 CATCATTCAA
Statistics
Matches: 122, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
38 1 0.01
39 35 0.29
40 70 0.57
41 15 0.12
42 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGACTTAGCCCGGATTTAGTAATTCGCA
Found at i:40663320 original size:79 final size:79
Alignment explanation
Indices: 40663220--40663402 Score: 194
Period size: 79 Copynumber: 2.3 Consensus size: 79
40663210 GCTCCTCGTT
* * * *
40663220 CAAATGCCTTCAGGACATAGCCCGATTATAGTAAT-TTGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTC-GGGCTTAGCCCGAAT-TAGT-ATCTCGCACAAATGCCTTC-GGATCTTAACCC
* *
40663283 GGATTTAGTAAC-TCGCA
62 GGATATAGTAACTTAGCA
**
40663300 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 CAAATGCCTTCGGGCTTAGCCC-GAATTAGTATCTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
40663365 TATGGTCACTTAGCA
65 TATAGTAACTTAGCA
40663380 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGG-CTTAGCCCG
40663403 GACATCATTC
Statistics
Matches: 88, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
78 5 0.06
79 53 0.60
80 30 0.34
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGGCTTAGCCCGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAACCCGGAT
ATAGTAACTTAGCA
Found at i:40671131 original size:40 final size:40
Alignment explanation
Indices: 40671087--40671270 Score: 243
Period size: 39 Copynumber: 4.7 Consensus size: 40
40671077 GCTCCTCGTT
* *
40671087 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
40671127 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
40671166 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * *
40671205 CAAATGCCTTC-GGATCTTAGTCCGG-ATATGGTAACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGTAAC-TCGCA
40671246 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40671271 CATCATTCAA
Statistics
Matches: 130, Mismatches: 8, Indels: 11
0.87 0.05 0.07
Matches are distributed among these distances:
38 2 0.02
39 74 0.57
40 43 0.33
41 11 0.08
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:40673538 original size:48 final size:47
Alignment explanation
Indices: 40673475--40673801 Score: 350
Period size: 48 Copynumber: 6.8 Consensus size: 47
40673465 TGCACCCTAG
* *
40673475 GTGCCAATATCATGGCCCGAAGCCAAATCAATAAAGCTCACCCCTGAA
1 GTGCTAATATCATGGCCCGAAGCCAAATCAATGAAGCTCACCCC-GAA
* * * * * *
40673523 GTGATAATATTATGGCCCAAATCCAAATCAATGAAGCTCGCACCTGAA
1 GTGCTAATATCATGGCCCGAAGCCAAATCAATGAAGCTCAC-CCCGAA
* * * * *
40673571 GTGCTAATATCATGGCCCAAATCCAAATAAATGAATCTCGCACCCGAA
1 GTGCTAATATCATGGCCCGAAGCCAAATCAATGAAGCTCAC-CCCGAA
* *
40673619 GTGCTAATATCATGGCTCGAAGCCAAATCAATGAAGCTTGCA-CCCAAA
1 GTGCTAATATCATGGCCCGAAGCCAAATCAATGAAGC-T-CACCCCGAA
* *
40673667 GTGCTAATATCATGGCCCGAAGCCAAATCAATGAAGCTCATACCCAAA
1 GTGCTAATATCATGGCCCGAAGCCAAATCAATGAAGCTCA-CCCCGAA
* * ** * * *
40673715 GTGCCAATATCATGGCCCAAATTCAAATCAATAAAGCTCGCACCTGAA
1 GTGCTAATATCATGGCCCGAAGCCAAATCAATGAAGCTCAC-CCCGAA
* *
40673763 GTGCTAATATCATAGCCCGAAGCCAAATAAATGAAGCTC
1 GTGCTAATATCATGGCCCGAAGCCAAATCAATGAAGCTC
40673802 CTAATGACAT
Statistics
Matches: 236, Mismatches: 37, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
46 2 0.01
47 1 0.00
48 229 0.97
49 3 0.01
50 1 0.00
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (47 bp):
GTGCTAATATCATGGCCCGAAGCCAAATCAATGAAGCTCACCCCGAA
Found at i:40673634 original size:96 final size:96
Alignment explanation
Indices: 40673475--40673801 Score: 440
Period size: 96 Copynumber: 3.4 Consensus size: 96
40673465 TGCACCCTAG
* * * * *
40673475 GTGCCAATATCATGGCCCGAAGCCAAATCAATAAAGCTCAC-CCCTGAAGTGATAATATTATGGC
1 GTGCTAATATCATGGCCCGAAGCCAAATAAATGAAGCTCACACCC-GAAGTGCTAATATCATGGC
40673539 CCAAATCCAAATCAATGAAGCTCGCACCTGAA
65 CCAAATCCAAATCAATGAAGCTCGCACCTGAA
* * * * *
40673571 GTGCTAATATCATGGCCCAAATCCAAATAAATGAATCTCGCACCCGAAGTGCTAATATCATGGCT
1 GTGCTAATATCATGGCCCGAAGCCAAATAAATGAAGCTCACACCCGAAGTGCTAATATCATGGCC
* * * **
40673636 CGAAGCCAAATCAATGAAGCTTGCACCCAAA
66 CAAATCCAAATCAATGAAGCTCGCACCTGAA
* * * *
40673667 GTGCTAATATCATGGCCCGAAGCCAAATCAATGAAGCTCATACCCAAAGTGCCAATATCATGGCC
1 GTGCTAATATCATGGCCCGAAGCCAAATAAATGAAGCTCACACCCGAAGTGCTAATATCATGGCC
* *
40673732 CAAATTCAAATCAATAAAGCTCGCACCTGAA
66 CAAATCCAAATCAATGAAGCTCGCACCTGAA
*
40673763 GTGCTAATATCATAGCCCGAAGCCAAATAAATGAAGCTC
1 GTGCTAATATCATGGCCCGAAGCCAAATAAATGAAGCTC
40673802 CTAATGACAT
Statistics
Matches: 197, Mismatches: 33, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
96 194 0.98
97 3 0.02
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (96 bp):
GTGCTAATATCATGGCCCGAAGCCAAATAAATGAAGCTCACACCCGAAGTGCTAATATCATGGCC
CAAATCCAAATCAATGAAGCTCGCACCTGAA
Done.