Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 84 of 290
Found at i:28024218 original size:42 final size:43
Alignment explanation
Indices: 28024135--28024228 Score: 111
Period size: 42 Copynumber: 2.2 Consensus size: 43
28024125 TCCCAGACGT
* * *
28024135 GGTCTTACATGTAATCAAACATCGATGCCATTGTCCCAGACAG
1 GGTCTTACACGGAATCAAACATCGATGCCATTGTCCAAGACAG
* * *
28024178 GGTCTTACACGGAATCAGATAT-GATGCCGA-TGTCCAAGACAT
1 GGTCTTACACGGAATCAAACATCGATGCC-ATTGTCCAAGACAG
28024220 GGTCTTACA
1 GGTCTTACA
28024229 TGTAAAATAG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
42 25 0.57
43 19 0.43
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (43 bp):
GGTCTTACACGGAATCAAACATCGATGCCATTGTCCAAGACAG
Found at i:28040252 original size:40 final size:40
Alignment explanation
Indices: 28040197--28040898 Score: 1125
Period size: 40 Copynumber: 17.6 Consensus size: 40
28040187 AGTGGTATAC
* *
28040197 CCGGGATAAGTCCCGAAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
28040237 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
28040277 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
* *
28040317 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATAT
1 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
*
28040357 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
* *
28040397 CCGGGCTAAGCCCCAAAGAGCATTTGTGCTAGTGATGTAT
1 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
*
28040437 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
* *
28040477 CTGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
28040517 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
* * *
28040557 CCGGGCTAAGTCCCGAAGAGTATTCGTGCTAGTGATATAT
1 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
28040597 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
* * *
28040637 CCGGGCTAAGTCCCGAAGAGTATTCGTGCTAGTGATATAT
1 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
28040677 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
* * *
28040717 CCGGGCTAAGTCCCGAAGAGGATTCGTGCTAGTGATATAT
1 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
28040757 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
*
28040797 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATATAT
1 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
*** * * * * *
28040837 CCATTCTAAACCCCGAAGAGCATTCGTGATGGTGTTATAT
1 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
** *
28040877 CCGGGCTGGGTCCCGAAGAGCA
1 CCGGGCTAAGCCCCGAAGAGCA
28040899 ATCATGCTGG
Statistics
Matches: 615, Mismatches: 47, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 615 1.00
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
Found at i:28040587 original size:23 final size:23
Alignment explanation
Indices: 28040561--28040667 Score: 58
Period size: 23 Copynumber: 5.2 Consensus size: 23
28040551 ATGTATCCGG
28040561 GCTAAGTCCCGAAGAGTATTCGT
1 GCTAAGTCCCGAAGAGTATTCGT
* * *
28040584 GCT-AGT---G-ATA-TATCCGG
1 GCTAAGTCCCGAAGAGTATTCGT
* *
28040601 GCTAAGCCCCGAAGAGCATTCGT
1 GCTAAGTCCCGAAGAGTATTCGT
* * *
28040624 GCT-AGT---G-A-TGTATCCGG
1 GCTAAGTCCCGAAGAGTATTCGT
28040641 GCTAAGTCCCGAAGAGTATTCGT
1 GCTAAGTCCCGAAGAGTATTCGT
28040664 GCTA
1 GCTA
28040668 GTGATATATC
Statistics
Matches: 56, Mismatches: 16, Indels: 24
0.58 0.17 0.25
Matches are distributed among these distances:
17 16 0.29
18 8 0.14
19 2 0.04
21 2 0.04
22 8 0.14
23 20 0.36
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (23 bp):
GCTAAGTCCCGAAGAGTATTCGT
Found at i:28041115 original size:25 final size:25
Alignment explanation
Indices: 28041074--28041123 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
28041064 TGTGCAAATA
28041074 CGAATGAATAAGAGCACTATGTGTG
1 CGAATGAATAAGAGCACTATGTGTG
* *
28041099 CGAATG-ATTAGAGGCACTGTGTGTG
1 CGAATGAATAAGA-GCACTATGTGTG
28041124 TGCGAATTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.30, C:0.12, G:0.32, T:0.26
Consensus pattern (25 bp):
CGAATGAATAAGAGCACTATGTGTG
Found at i:28045031 original size:22 final size:22
Alignment explanation
Indices: 28045004--28045126 Score: 58
Period size: 22 Copynumber: 5.3 Consensus size: 22
28044994 ATGTGCATAT
28045004 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* * *
28045026 ATGTGATGAATG-TGAACAT-GCATA
1 ATGTGAT-AAGGCCG-A-ATGGC-CA
*
28045050 TATGTGATAAGGCCAAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
* *
28045073 ATGTGATGAATGTG-AGCAT-G-CA
1 ATGTGAT-AA-G-GCCGAATGGCCA
28045095 TATGTGTGATAAGGCCGAATGGCCA
1 -A--TGTGATAAGGCCGAATGGCCA
28045120 ATGTGAT
1 ATGTGAT
28045127 GAATATGAAC
Statistics
Matches: 73, Mismatches: 12, Indels: 32
0.62 0.10 0.27
Matches are distributed among these distances:
22 24 0.33
23 17 0.23
24 16 0.22
25 16 0.22
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.25
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:28045048 original size:47 final size:47
Alignment explanation
Indices: 28044988--28045172 Score: 280
Period size: 47 Copynumber: 3.9 Consensus size: 47
28044978 GATAATTGTG
**
28044988 ATGTGAATGTGCATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGA
*
28045035 ATGTGAACATGCATATATGTGATAAGGCCAAATGGCCAATGTGATGA
1 ATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGA
* *
28045082 ATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGA
* * ** *
28045129 ATATGAACATGCATATATGTGGTAAATCCGAATGGCTAATGTGA
1 ATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGA
28045173 AATATATGTA
Statistics
Matches: 125, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 125 1.00
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.27
Consensus pattern (47 bp):
ATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGA
Found at i:28045427 original size:37 final size:37
Alignment explanation
Indices: 28045377--28045526 Score: 248
Period size: 37 Copynumber: 4.1 Consensus size: 37
28045367 GGAAATATAT
28045377 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
28045414 TCCGGGTAAGACCCGATGACTACGTGTGAAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
28045451 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
28045488 TCCGGGTAAGACCCGAT-AGCTTCGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGA-CTACGTGTGGAGATTATG
28045525 TC
1 TC
28045527 TGAGCTAAAG
Statistics
Matches: 108, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
36 1 0.01
37 107 0.99
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:28050843 original size:27 final size:27
Alignment explanation
Indices: 28050804--28050912 Score: 96
Period size: 27 Copynumber: 4.0 Consensus size: 27
28050794 TTAGAATATT
*
28050804 TTAATTTACTAAAATTACCGAAATACCC
1 TTAATTT-GTAAAATTACCGAAATACCC
* *
28050832 TTAATTTGTAAAAATACTGAAATACCC
1 TTAATTTGTAAAATTACCGAAATACCC
** * *
28050859 TCGATTTGTAAAATTACTGAAACA-CC
1 TTAATTTGTAAAATTACCGAAATACCC
* *
28050885 TTCGACTTGTAAAATTACC-AAAGTACCC
1 TT-AATTTGTAAAATTACCGAAA-TACCC
28050913 CCGATTTACA
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
26 6 0.09
27 52 0.78
28 9 0.13
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.31
Consensus pattern (27 bp):
TTAATTTGTAAAATTACCGAAATACCC
Found at i:28051174 original size:27 final size:27
Alignment explanation
Indices: 28050908--28051173 Score: 320
Period size: 27 Copynumber: 9.9 Consensus size: 27
28050898 ATTACCAAAG
* * *
28050908 TACCCCCGATTTACAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* * * *
28050935 TACCCCCGATTTACATAATTCCCGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
28050962 TACCCCCGATTTACATAATTA-TCGTTT
1 TACCCTCGATTTACAGAATTACT-GTTT
* * *
28050989 TACCCTCGACTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
28051016 TACCCTCGATTTACAGAATTATTATTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
28051043 TACCCTCGATTTATAGAATTA-TCGTTT
1 TACCCTCGATTTACAGAATTACT-GTTT
*
28051070 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
28051097 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
28051124 TACCCTTGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
28051151 TACCCTCGATTTACAAAATTACT
1 TACCCTCGATTTACAGAATTACT
28051174 AAAATACCAT
Statistics
Matches: 210, Mismatches: 25, Indels: 8
0.86 0.10 0.03
Matches are distributed among these distances:
26 1 0.00
27 209 1.00
ACGTcount: A:0.27, C:0.24, G:0.09, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTGTTT
Found at i:28051181 original size:27 final size:27
Alignment explanation
Indices: 28051070--28051318 Score: 92
Period size: 27 Copynumber: 9.1 Consensus size: 27
28051060 ATTATCGTTT
* *****
28051070 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAAAATTACTAAAA
* * ****
28051097 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTAAAA
* * ***
28051124 TACCCTTGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAAAATTACTAAAA
28051151 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCGATTTACAAAATTACTAAAA
* * * ** **
28051178 TACCATTGGTTTGTAAAATTACCGAAA
1 TACCCTCGATTTACAAAATTACTAAAA
* ** *
28051205 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACTAAAA
* *
28051232 TACCC-CTAATTTACAAAGTTAC-AGAAA
1 TACCCTC-GATTTACAAAATTACTA-AAA
* * *
28051259 TACCATTGACTTT-CTAAAAATTA-TAGAAT
1 TACCCTCGA-TTTAC--AAAATTACTA-AAA
* * *
28051288 TACCATTGGTTTACAAAATTACTAAAA
1 TACCCTCGATTTACAAAATTACTAAAA
28051315 TACC
1 TACC
28051319 TTTGGTTTGT
Statistics
Matches: 181, Mismatches: 32, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
26 2 0.01
27 152 0.84
28 8 0.04
29 19 0.10
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.35
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACTAAAA
Found at i:28051323 original size:27 final size:27
Alignment explanation
Indices: 28051160--28051326 Score: 97
Period size: 27 Copynumber: 6.1 Consensus size: 27
28051150 TTACCCTCGA
28051160 TTTACAAAATTACTAAAATACCATTGG
1 TTTACAAAATTACTAAAATACCATTGG
** ** * ***
28051187 TTTGTAAAATTACCGAAATACCCTCAA
1 TTTACAAAATTACTAAAATACCATTGG
** * ** **
28051214 TTTGTAAAATTACCAAAATACCCCTAA
1 TTTACAAAATTACTAAAATACCATTGG
* *
28051241 TTTACAAAGTTAC-AGAAATACCATTGAC
1 TTTACAAAATTACTA-AAATACCATTG-G
*
28051269 TTT-CTAAAAATTA-TAGAATTACCATTGG
1 TTTAC--AAAATTACTA-AAATACCATTGG
*
28051297 TTTACAAAATTACTAAAATACCTTTGG
1 TTTACAAAATTACTAAAATACCATTGG
28051324 TTT
1 TTT
28051327 GTAGATTTAC
Statistics
Matches: 110, Mismatches: 23, Indels: 14
0.75 0.16 0.10
Matches are distributed among these distances:
26 1 0.01
27 82 0.75
28 8 0.07
29 19 0.17
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.34
Consensus pattern (27 bp):
TTTACAAAATTACTAAAATACCATTGG
Found at i:28051444 original size:27 final size:27
Alignment explanation
Indices: 28051367--28051444 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
28051357 AAGTGACTAA
* *
28051367 AATACCCCTAT-TAGGTAAAAAGACCGG
1 AATACCCCTGTAT-GGTAAAATGACCGG
* * *
28051394 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTATGGTAAAATGACCGG
28051421 AATACCCCTGTATGGTAAAATGAC
1 AATACCCCTGTATGGTAAAATGAC
28051445 GAATATGCCC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
26 1 0.02
27 39 0.95
28 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.21
Consensus pattern (27 bp):
AATACCCCTGTATGGTAAAATGACCGG
Found at i:28052275 original size:26 final size:26
Alignment explanation
Indices: 28052246--28052395 Score: 221
Period size: 26 Copynumber: 5.8 Consensus size: 26
28052236 GAGGAAGTGC
*
28052246 AAAAGGGCTTATGCCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* **
28052272 AAAAGGGCTTATGCCCCAATTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
28052298 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
28052324 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
28052350 AAAAGGATTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
28052376 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
28052396 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:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:28052324 original size:52 final size:52
Alignment explanation
Indices: 28052246--28052392 Score: 251
Period size: 52 Copynumber: 2.8 Consensus size: 52
28052236 GAGGAAGTGC
*
28052246 AAAAGGGCTTATGCCCTAGTTTACCGAAAAGGGCTTATGCCCCAATTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAATTTATTG
*
28052298 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAATTTATTG
**
28052350 AAAAGGATTTATGCCCCAGTTTACCGAAAAGGGCTT-TGCCCCA
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCA
28052393 GTTATTAAAG
Statistics
Matches: 91, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 7 0.08
52 84 0.92
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.27
Consensus pattern (52 bp):
AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAATTTATTG
Found at i:28052605 original size:42 final size:42
Alignment explanation
Indices: 28052540--28052631 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
28052530 TAGTCTCCCC
* ** *
28052540 AAATGGGCTTGCACACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCACACATCCATTGACATTACATGTGATATTG
*
28052582 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCACACATCCATTGACATTACATGTGATATTG
28052624 AAATGGGC
1 AAATGGGC
28052632 CTATAGGCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (42 bp):
AAATGGGCTTGCACACATCCATTGACATTACATGTGATATTG
Found at i:28052693 original size:31 final size:31
Alignment explanation
Indices: 28052655--28052733 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
28052645 CGTTTACAAT
*
28052655 AAAGGCTTCAGCCCAGTGAAATGATTTATGA
1 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
* *
28052686 AAAGGCTTTGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
28052717 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
28052734 AATCGTTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGAAATGATTTATGA
Found at i:28054097 original size:28 final size:27
Alignment explanation
Indices: 28054064--28054119 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
28054054 TTAGAATACT
*
28054064 TTAGTTTACTAAAATTACCGAAATACCC
1 TTAGTTT-CTAAAAATACCGAAATACCC
* *
28054092 TTAGTTTGTAAAAATACTGAAATACCC
1 TTAGTTTCTAAAAATACCGAAATACCC
28054119 T
1 T
28054120 CGATTTGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (27 bp):
TTAGTTTCTAAAAATACCGAAATACCC
Found at i:28054103 original size:27 final size:28
Alignment explanation
Indices: 28054073--28054172 Score: 100
Period size: 27 Copynumber: 3.7 Consensus size: 28
28054063 TTTAGTTTAC
28054073 TAAAATTACCGAAATACCCTTAG-TTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
* * *
28054100 TAAAAATACTGAAATACCC-TCGATTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
** * *
28054127 TAAAATTACTAAAATA-CCTTCGACTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
28054154 TAAAATTACC-AAAGTACCC
1 TAAAATTACCGAAA-TACCC
28054173 CCAATTTACA
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
26 7 0.11
27 53 0.85
28 2 0.03
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (28 bp):
TAAAATTACCGAAATACCCTTAGATTTG
Found at i:28054198 original size:27 final size:27
Alignment explanation
Indices: 28054176--28054377 Score: 230
Period size: 27 Copynumber: 7.5 Consensus size: 27
28054166 AGTACCCCCA
*
28054176 ATTTACATAATTATCGTTTTACCC-CTG
1 ATTTACAGAATTATCGTTTTACCCTC-G
* *
28054203 ATTTACAGAATTACCATTTTACCCTCG
1 ATTTACAGAATTATCGTTTTACCCTCG
*
28054230 ATTTACAGAATTA-CTATTTTACCCTCG
1 ATTTACAGAATTATC-GTTTTACCCTCG
* * *
28054257 ATTCATAGAATTATAGTTTTACCCTCG
1 ATTTACAGAATTATCGTTTTACCCTCG
*
28054284 ATTTACAGAATTACCGTTTTACCCTCG
1 ATTTACAGAATTATCGTTTTACCCTCG
* * *
28054311 ATTTATAGAATTA-CTATTTTACCCTTG
1 ATTTACAGAATTATC-GTTTTACCCTCG
* *
28054338 ATTTACAGAATTATTGTTTTACCCTTG
1 ATTTACAGAATTATCGTTTTACCCTCG
*
28054365 ATTTACAAAATTA
1 ATTTACAGAATTA
28054378 CTAAAATACA
Statistics
Matches: 152, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
26 2 0.01
27 149 0.98
28 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (27 bp):
ATTTACAGAATTATCGTTTTACCCTCG
Found at i:28054226 original size:54 final size:54
Alignment explanation
Indices: 28054176--28054380 Score: 263
Period size: 54 Copynumber: 3.8 Consensus size: 54
28054166 AGTACCCCCA
* *
28054176 ATTTACATAATTATCGTTTTACCC-CTGATTTACAGAATTACCATTTTACCCTCG
1 ATTTACAGAATTATCGTTTTACCCTC-GATTTACAGAATTACTATTTTACCCTCG
* * *
28054230 ATTTACAGAATTA-CTATTTTACCCTCGATTCATAGAATTA-TAGTTTTACCCTCG
1 ATTTACAGAATTATC-GTTTTACCCTCGATTTACAGAATTACTA-TTTTACCCTCG
* * *
28054284 ATTTACAGAATTACCGTTTTACCCTCGATTTATAGAATTACTATTTTACCCTTG
1 ATTTACAGAATTATCGTTTTACCCTCGATTTACAGAATTACTATTTTACCCTCG
* * *
28054338 ATTTACAGAATTATTGTTTTACCCTTGATTTACAAAATTACTA
1 ATTTACAGAATTATCGTTTTACCCTCGATTTACAGAATTACTA
28054381 AAATACACTT
Statistics
Matches: 133, Mismatches: 13, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
53 2 0.02
54 127 0.95
55 4 0.03
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (54 bp):
ATTTACAGAATTATCGTTTTACCCTCGATTTACAGAATTACTATTTTACCCTCG
Found at i:28054242 original size:81 final size:81
Alignment explanation
Indices: 28054176--28054378 Score: 300
Period size: 81 Copynumber: 2.5 Consensus size: 81
28054166 AGTACCCCCA
* *
28054176 ATTTACATAATTATCGTTTTACCCCTGATTTACAGAATTACCATTTTACCCTCGATTTACAGAAT
1 ATTTACAGAATTATAGTTTTACCCCTGATTTACAGAATTACCATTTTACCCTCGATTTACAGAAT
28054241 TACTATTTTACCCTCG
66 TACTATTTTACCCTCG
* * * *
28054257 ATTCATAGAATTATAGTTTTA-CCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTATAGAA
1 ATTTACAGAATTATAGTTTTACCCCT-GATTTACAGAATTACCATTTTACCCTCGATTTACAGAA
*
28054321 TTACTATTTTACCCTTG
65 TTACTATTTTACCCTCG
* * *
28054338 ATTTACAGAATTATTGTTTTACCCTTGATTTACAAAATTAC
1 ATTTACAGAATTATAGTTTTACCCCTGATTTACAGAATTAC
28054379 TAAAATACAC
Statistics
Matches: 108, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
80 4 0.04
81 101 0.94
82 3 0.03
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (81 bp):
ATTTACAGAATTATAGTTTTACCCCTGATTTACAGAATTACCATTTTACCCTCGATTTACAGAAT
TACTATTTTACCCTCG
Found at i:28054391 original size:27 final size:27
Alignment explanation
Indices: 28054357--28054609 Score: 154
Period size: 27 Copynumber: 9.3 Consensus size: 27
28054347 ATTATTGTTT
* *
28054357 TACCCTTGATTTACAAAATTACTAAAA
1 TACCCTTGATTTGCAAAATTACCAAAA
* * *
28054384 TACACTTGGTTTGTAAAATTACCAAAA
1 TACCCTTGATTTGCAAAATTACCAAAA
* *
28054411 TACCCCT-AGTTTGTAAAATTACCAAAA
1 TACCCTTGA-TTTGCAAAATTACCAAAA
* * **
28054438 TGCCCTTGGTTTGTGAAATTACCAAAA
1 TACCCTTGATTTGCAAAATTACCAAAA
** *
28054465 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTTGATTTGCAAAATTACCAAAA
* * * *
28054492 TACCCCTGATTTACAAAGTTA-TAGAAA
1 TACCCTTGATTTGCAAAATTACCA-AAA
*
28054519 TACCCTTGACTTT-CTAAAAATTA-TAGAAA
1 TACCCTTGA-TTTGC--AAAATTACCA-AAA
* * ** *
28054548 TACCATTGGTTAACAAAATTACTAAAA
1 TACCCTTGATTTGCAAAATTACCAAAA
* * * * *
28054575 TACCTTTGGTTTGTAGATTTACCAAAA
1 TACCCTTGATTTGCAAAATTACCAAAA
*
28054602 CACCCTTG
1 TACCCTTG
28054610 TAGGATGAAA
Statistics
Matches: 180, Mismatches: 38, Indels: 16
0.77 0.16 0.07
Matches are distributed among these distances:
26 1 0.01
27 152 0.84
28 7 0.04
29 20 0.11
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.32
Consensus pattern (27 bp):
TACCCTTGATTTGCAAAATTACCAAAA
Found at i:28054404 original size:81 final size:81
Alignment explanation
Indices: 28054114--28054405 Score: 219
Period size: 81 Copynumber: 3.6 Consensus size: 81
28054104 AATACTGAAA
** * * * * *** * *
28054114 TACCCTCGATTTGTAAAATTACTAAAATAC-CTTCGACTTGTAAAATTACCAAAGTACCCCCAAT
1 TACCCTCGATTTACAAAATTACCAAAATACAC-TCGATTTATAAAATTACTATTTTACCCTCGAT
* * *
28054178 TTACATAATTATCGTTT
65 TCACAGAATTATAGTTT
* *** * * *
28054195 TACCC-CTGATTTACAGAATTACCATTTTACCCTCGATTTACAGAATTACTATTTTACCCTCGAT
1 TACCCTC-GATTTACAAAATTACCAAAATACACTCGATTTATAAAATTACTATTTTACCCTCGAT
*
28054259 TCATAGAATTATAGTTT
65 TCACAGAATTATAGTTT
* **** * * *
28054276 TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTATAGAATTACTATTTTACCCTTGATT
1 TACCCTCGATTTACAAAATTACCAAAATACACTCGATTTATAAAATTACTATTTTACCCTCGATT
* *
28054341 TACAGAATTATTGTTT
66 CACAGAATTATAGTTT
* * * * *
28054357 TACCCTTGATTTACAAAATTACTAAAATACACTTGGTTTGTAAAATTAC
1 TACCCTCGATTTACAAAATTACCAAAATACACTCGATTTATAAAATTAC
28054406 CAAAATACCC
Statistics
Matches: 169, Mismatches: 39, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
80 1 0.01
81 166 0.98
82 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.39
Consensus pattern (81 bp):
TACCCTCGATTTACAAAATTACCAAAATACACTCGATTTATAAAATTACTATTTTACCCTCGATT
CACAGAATTATAGTTT
Found at i:28054415 original size:54 final size:53
Alignment explanation
Indices: 28054357--28054494 Score: 177
Period size: 54 Copynumber: 2.5 Consensus size: 53
28054347 ATTATTGTTT
** *
28054357 TACCCTTGATTTACAAAATTACTAAAATACACTTGGTTTGTAAAATTACCAAAA
1 TACCCTT-ATTTGTAAAATTACCAAAATACACTTGGTTTGTAAAATTACCAAAA
* * * *
28054411 TACCCCTAGTTTGTAAAATTACCAAAATGCCCTTGGTTTGTGAAATTACCAAAA
1 TACCCTTA-TTTGTAAAATTACCAAAATACACTTGGTTTGTAAAATTACCAAAA
*
28054465 TACCCTCAATTTGTAAAATTACCAAAATAC
1 TACCCT-TATTTGTAAAATTACCAAAATAC
28054495 CCCTGATTTA
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
53 1 0.01
54 70 0.97
55 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.32
Consensus pattern (53 bp):
TACCCTTATTTGTAAAATTACCAAAATACACTTGGTTTGTAAAATTACCAAAA
Found at i:28054670 original size:27 final size:27
Alignment explanation
Indices: 28054640--28054731 Score: 114
Period size: 27 Copynumber: 3.4 Consensus size: 27
28054630 ACCCCTATTA
* *
28054640 GGTAAAAAGACCGTAACGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
* *
28054667 GGTAAAGTGACCATAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
* *
28054694 GGTAAAGTGACCGTAATA-CCCCTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAG
28054721 GGTAAAATGAC
1 GGTAAAATGAC
28054732 GAATATGCCC
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
27 56 0.98
28 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.20
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAG
Found at i:28055560 original size:26 final size:26
Alignment explanation
Indices: 28055531--28055706 Score: 228
Period size: 26 Copynumber: 6.8 Consensus size: 26
28055521 GAGGAAGTGC
**
28055531 AAAAGGGCTTATGCCTTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
28055557 AAAAGGGCTTATGCCTTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
28055583 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* *
28055609 AAAAGAGCTTATGCCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* * **
28055635 AAAGGGGCTTATGCGCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
28055661 AAAAGGGTTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
28055687 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
28055707 ATTAAAGAGG
Statistics
Matches: 130, Mismatches: 20, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
25 10 0.08
26 120 0.92
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:28055612 original size:52 final size:52
Alignment explanation
Indices: 28055531--28055706 Score: 255
Period size: 52 Copynumber: 3.4 Consensus size: 52
28055521 GAGGAAGTGC
** ** *
28055531 AAAAGGGCTTATGCCTTAGTTTACCGAAAAGGGCTTATGCCTTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCTAGTTTACCG
*
28055583 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGAGCTTATGCCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCTAGTTTACCG
* * * *
28055635 AAAGGGGCTTATGCGCCAGTTTATTGAAAAGGGTTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCTAGTTTACCG
28055687 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
28055707 ATTAAAGAGG
Statistics
Matches: 111, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
51 9 0.08
52 102 0.92
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (52 bp):
AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCTAGTTTACCG
Found at i:28055910 original size:42 final size:42
Alignment explanation
Indices: 28055851--28055942 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
28055841 TAGTCTCCCC
* ** *
28055851 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
28055893 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
28055935 AAATGGGC
1 AAATGGGC
28055943 CTATAGGCCA
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:28056004 original size:31 final size:31
Alignment explanation
Indices: 28055966--28056036 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
28055956 CGTTTACAGT
28055966 AAAGGCTTCAG-CGCAGTGAAATGATTTATGA
1 AAAGGCTTCAGCCG-AGTGAAATGATTTATGA
** *
28055997 AAAGGCTTTGGCCGAGTGATATGATTTATGA
1 AAAGGCTTCAGCCGAGTGAAATGATTTATGA
28056028 AAAGGCTTC
1 AAAGGCTTC
28056037 GGCCCAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 33 0.94
32 2 0.06
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCAGCCGAGTGAAATGATTTATGA
Found at i:28058295 original size:28 final size:27
Alignment explanation
Indices: 28058262--28058360 Score: 103
Period size: 27 Copynumber: 3.6 Consensus size: 27
28058252 TTAGAATACT
* *
28058262 TTAGTTTACTAAAATTACCGAAATACCC
1 TTAGTTT-GTAAAATTACTGAAATACCC
*
28058290 TTAGTTTGTAAAAATACTGAAATACCC
1 TTAGTTTGTAAAATTACTGAAATACCC
*
28058317 -TCGATTTGTAAAATTACTGAAATA-CC
1 TTAG-TTTGTAAAATTACTGAAATACCC
**
28058343 TTCAACTTGTAAAATTAC
1 TT-AGTTTGTAAAATTAC
28058361 CAAAGTACCC
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
26 4 0.07
27 49 0.82
28 7 0.12
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.34
Consensus pattern (27 bp):
TTAGTTTGTAAAATTACTGAAATACCC
Found at i:28058353 original size:54 final size:54
Alignment explanation
Indices: 28058266--28058389 Score: 135
Period size: 54 Copynumber: 2.3 Consensus size: 54
28058256 AATACTTTAG
** * *
28058266 TTTACTAAAATTACCGAAATACCCTTAGTTTGTAAAAATACTGAAA-TACCCTCGA
1 TTTA-TAAAATTACCGAAATACCCTTAACTTGTAAAAATAC-CAAAGTACCCCCGA
* * *
28058321 TTTGTAAAATTACTGAAATA-CCTTCAACTTGTAAAATTACCAAAGTACCCCCGA
1 TTTATAAAATTACCGAAATACCCTT-AACTTGTAAAAATACCAAAGTACCCCCGA
*
28058375 TTTATAGAATTACCG
1 TTTATAAAATTACCG
28058390 TTTTACCCCC
Statistics
Matches: 57, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
53 7 0.12
54 47 0.82
55 3 0.05
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (54 bp):
TTTATAAAATTACCGAAATACCCTTAACTTGTAAAAATACCAAAGTACCCCCGA
Found at i:28058577 original size:27 final size:27
Alignment explanation
Indices: 28058366--28058576 Score: 253
Period size: 27 Copynumber: 7.8 Consensus size: 27
28058356 ATTACCAAAG
* * *
28058366 TACCCCCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAAAATTACCGTTT
* * *
28058393 TACCCCCGATTTACATAATCACCGTTT
1 TACCCTCGATTTACAAAATTACCGTTT
* * *
28058420 TACCCCCGATTTACATAATTATCGTTT
1 TACCCTCGATTTACAAAATTACCGTTT
*
28058447 TACCCTCGACTTACAAAATTACCGTTT
1 TACCCTCGATTTACAAAATTACCGTTT
* *
28058474 TACCCTCAATTTACAAAATTACCATTT
1 TACCCTCGATTTACAAAATTACCGTTT
* *
28058501 TACCCTCGATTTATAGAATTACTC-TTT
1 TACCCTCGATTTACAAAATTAC-CGTTT
* * *
28058528 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACCGTTT
28058555 TACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTACAAAATTAC
28058577 TAAAATACCC
Statistics
Matches: 162, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
27 161 0.99
28 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.07, T:0.38
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACCGTTT
Found at i:28058585 original size:27 final size:27
Alignment explanation
Indices: 28058447--28058776 Score: 114
Period size: 27 Copynumber: 12.1 Consensus size: 27
28058437 ATTATCGTTT
* *****
28058447 TACCCTCGACTTACAAAATTACCGTTT
1 TACCCTCGATTTACAAAATTACTAAAA
* * ***
28058474 TACCCTCAATTTACAAAATTACCATTT
1 TACCCTCGATTTACAAAATTACTAAAA
* * ****
28058501 TACCCTCGATTTATAGAATTACTCTTT
1 TACCCTCGATTTACAAAATTACTAAAA
* * ****
28058528 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTAAAA
28058555 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCGATTTACAAAATTACTAAAA
* * **
28058582 TACCCTTGGTTTGTAAAATTACTAAAA
1 TACCCTCGATTTACAAAATTACTAAAA
* ** *
28058609 TACCC-CTAGTTTGTAAAATTACCAAAA
1 TACCCTCGA-TTTACAAAATTACTAAAA
* * *** * *
28058636 TACCCTTGGTTTGTGAAACTA-TCGAAA
1 TACCCTCGATTTACAAAATTACT-AAAA
** ** *
28058663 TACCCTTAATTTGTAAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACTAAAA
*
28058690 TACCC-CTGATTTACAAAGTTAC-AGAAA
1 TACCCTC-GATTTACAAAATTACTA-AAA
*
28058717 TACCCTTGACTTT-CTAAAAATTA-TAGAAA
1 TACCCTCGA-TTTAC--AAAATTACTA-AAA
* * *
28058746 TACCATTGGTTTACAAAATTACTAAAA
1 TACCCTCGATTTACAAAATTACTAAAA
28058773 TACC
1 TACC
28058777 TTTGGTTTGT
Statistics
Matches: 243, Mismatches: 47, Indels: 26
0.77 0.15 0.08
Matches are distributed among these distances:
26 1 0.00
27 215 0.88
28 8 0.03
29 19 0.08
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.35
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACTAAAA
Found at i:28058587 original size:81 final size:81
Alignment explanation
Indices: 28058366--28058576 Score: 280
Period size: 81 Copynumber: 2.6 Consensus size: 81
28058356 ATTACCAAAG
* * * * * * *
28058366 TACCCCCGATTTATAGAATTACCGTTTTACCCCCGATTTACATAATCACCGTTTTACCCCCGATT
1 TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTACAAAATTACCATTTTACCCTCGATT
*
28058431 TACATAATTATCGTTT
66 TACAGAATTATCGTTT
* * *
28058447 TACCCTCGACTTACAAAATTACCGTTTTACCCTCAATTTACAAAATTACCATTTTACCCTCGATT
1 TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTACAAAATTACCATTTTACCCTCGATT
*
28058512 TATAGAATTACTC-TTT
66 TACAGAATTA-TCGTTT
* *
28058528 TACCCTTGATTTACAGAATTACTGTTTTACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTACAAAATTAC
28058577 TAAAATACCC
Statistics
Matches: 112, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
81 110 0.98
82 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.07, T:0.38
Consensus pattern (81 bp):
TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTACAAAATTACCATTTTACCCTCGATT
TACAGAATTATCGTTT
Found at i:28058602 original size:54 final size:54
Alignment explanation
Indices: 28058488--28058649 Score: 146
Period size: 54 Copynumber: 3.0 Consensus size: 54
28058478 CTCAATTTAC
* * **** * **
28058488 AAAATTACCATTTTACCCTCGATTTATAGAATTACTCTTTTACCCTTGATTTAC
1 AAAATTACTATTTTACCCTCGATTTATAAAATTACTAAAATACCCTTGGTTTGT
* * *
28058542 AGAATTACTGTTTTACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTGT
1 AAAATTACTATTTTACCCTCGATTTATAAAATTACTAAAATACCCTTGGTTTGT
*** * * *
28058596 AAAATTACTAAAATACCC-CTAGTTTGTAAAATTACCAAAATACCCTTGGTTTGT
1 AAAATTACTATTTTACCCTCGA-TTTATAAAATTACTAAAATACCCTTGGTTTGT
28058650 GAAACTATCG
Statistics
Matches: 86, Mismatches: 21, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
53 2 0.02
54 84 0.98
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38
Consensus pattern (54 bp):
AAAATTACTATTTTACCCTCGATTTATAAAATTACTAAAATACCCTTGGTTTGT
Found at i:28058602 original size:81 final size:82
Alignment explanation
Indices: 28058382--28058604 Score: 216
Period size: 81 Copynumber: 2.7 Consensus size: 82
28058372 CGATTTATAG
* * * * **** * * *
28058382 AATTACCGTTTTACCCCCGATTTACATAATCACCGTTTTACCCCCGATTTACATAATTA-TCGTT
1 AATTACCGTTTTACCCTCAATTTACAAAATTACCAAAATACCCTCGATTTATAAAATTACTCGTT
28058446 TTACCCTCGACTTACAA
66 TTACCCTCGACTTACAA
*** *
28058463 AATTACCGTTTTACCCTCAATTTACAAAATTACCATTTTACCCTCGATTTATAGAATTACTC-TT
1 AATTACCGTTTTACCCTCAATTTACAAAATTACCAAAATACCCTCGATTTATAAAATTACTCGTT
* * *
28058527 TTACCCTTGATTTACAG
66 TTACCCTCGACTTACAA
* * * * * *
28058544 AATTACTGTTTTACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACT
1 AATTACCGTTTTACCCTCAATTTACAAAATTACCAAAATACCCTCGATTTATAAAATTACT
28058605 AAAATACCCC
Statistics
Matches: 120, Mismatches: 21, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
81 118 0.98
82 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.39
Consensus pattern (82 bp):
AATTACCGTTTTACCCTCAATTTACAAAATTACCAAAATACCCTCGATTTATAAAATTACTCGTT
TTACCCTCGACTTACAA
Found at i:28058640 original size:81 final size:78
Alignment explanation
Indices: 28058555--28058807 Score: 213
Period size: 81 Copynumber: 3.1 Consensus size: 78
28058545 ATTACTGTTT
*
28058555 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACTAAAATACCCCTAGTT
1 TACCCTTGATTT-CAAAATTA-TAAAATACCCTTGGTTTGTAAAATTACTAAAATACCCCT-GTT
28058620 TGTAAAATTACCAAAA
63 TGTAAAATTACCAAAA
* ** * * ** * *
28058636 TACCCTTGGTTTGTGAAACTATCGAAATACCCTTAATTTGTAAAATTACCAAAATACCCCTGATT
1 TACCCTTGATTT-CAAAATTAT-AAAATACCCTTGGTTTGTAAAATTACTAAAATACCCCTGTTT
28058701 -TACAAAGTTA-CAGAAA
64 GTA-AAA-TTACCA-AAA
* ** **
28058717 TACCCTTGACTTTCTAAAAATTATAGAAATACCATTGGTTTACAAAATTACTAAAATACCTTTGG
1 TACCCTTGA-TTTC--AAAATTATA-AAATACCCTTGGTTTGTAAAATTACTAAAATACCCCT-G
* *
28058782 TTTGTAGATTTACCAAAA
61 TTTGTAAAATTACCAAAA
*
28058800 CACCCTTG
1 TACCCTTG
28058808 TAGGATGAAA
Statistics
Matches: 133, Mismatches: 28, Indels: 20
0.73 0.15 0.11
Matches are distributed among these distances:
79 2 0.02
80 9 0.07
81 63 0.47
82 3 0.02
83 48 0.36
84 6 0.05
85 2 0.02
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.33
Consensus pattern (78 bp):
TACCCTTGATTTCAAAATTATAAAATACCCTTGGTTTGTAAAATTACTAAAATACCCCTGTTTGT
AAAATTACCAAAA
Found at i:28058717 original size:54 final size:53
Alignment explanation
Indices: 28058569--28058807 Score: 182
Period size: 54 Copynumber: 4.4 Consensus size: 53
28058559 CTCGATTTAC
* * *
28058569 AAAATTACTAAAATACCCTTGGTTTGTA-AAATTACTA-AAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCTTGG-TT-TACAAATTAC-AGAAATACCCTTAATTTGT
** *
28058623 AAAATTACCAAAATACCCTTGGTTTGTGAAACTATC-GAAATACCCTTAATTTGT
1 AAAATTACCAAAATACCCTTGGTTT-ACAAATTA-CAGAAATACCCTTAATTTGT
* * * *
28058677 AAAATTACCAAAATACCCCTGATTTACAAAGTTACAGAAATACCCTTGACTTTCT
1 AAAATTACCAAAATACCCTTGGTTTACAAA-TTACAGAAATACCCTT-AATTTGT
* * * **
28058732 AAAAATTA-TAGAAATACCATTGGTTTACAAAATTACTA-AAATACCTTTGGTTTGT
1 -AAAATTACCA-AAATACCCTTGGTTTAC-AAATTAC-AGAAATACCCTTAATTTGT
* * *
28058787 AGATTTACCAAAACACCCTTG
1 AAAATTACCAAAATACCCTTG
28058808 TAGGATGAAA
Statistics
Matches: 148, Mismatches: 25, Indels: 24
0.75 0.13 0.12
Matches are distributed among these distances:
52 1 0.01
53 6 0.04
54 91 0.61
55 12 0.08
56 34 0.23
57 4 0.03
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (53 bp):
AAAATTACCAAAATACCCTTGGTTTACAAATTACAGAAATACCCTTAATTTGT
Found at i:28058781 original size:27 final size:27
Alignment explanation
Indices: 28058568--28058785 Score: 165
Period size: 27 Copynumber: 8.0 Consensus size: 27
28058558 CCTCGATTTA
28058568 CAAAATTACTAAAATACCCTTGGTTTG
1 CAAAATTACTAAAATACCCTTGGTTTG
* * *
28058595 TAAAATTACTAAAATACCCCTAGTTTG
1 CAAAATTACTAAAATACCCTTGGTTTG
* *
28058622 TAAAATTACCAAAATACCCTTGGTTTG
1 CAAAATTACTAAAATACCCTTGGTTTG
** * * **
28058649 TGAAACTA-TCGAAATACCCTTAATTTG
1 CAAAATTACT-AAAATACCCTTGGTTTG
* * * * *
28058676 TAAAATTACCAAAATACCCCTGATTTA
1 CAAAATTACTAAAATACCCTTGGTTTG
* *
28058703 CAAAGTTAC-AGAAATACCCTTGACTTT-
1 CAAAATTACTA-AAATACCCTTG-GTTTG
* *
28058730 CTAAAAATTA-TAGAAATACCATTGGTTTA
1 C--AAAATTACTA-AAATACCCTTGGTTTG
*
28058759 CAAAATTACTAAAATACCTTTGGTTTG
1 CAAAATTACTAAAATACCCTTGGTTTG
28058786 TAGATTTACC
Statistics
Matches: 154, Mismatches: 28, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
26 1 0.01
27 126 0.82
28 8 0.05
29 19 0.12
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (27 bp):
CAAAATTACTAAAATACCCTTGGTTTG
Found at i:28058868 original size:27 final size:27
Alignment explanation
Indices: 28058846--28058929 Score: 107
Period size: 27 Copynumber: 3.1 Consensus size: 27
28058836 TAGGTAAAAA
*
28058846 GACCATAAAGCCCCTGTAGGGTAAAGT
1 GACCGTAAAGCCCCTGTAGGGTAAAGT
* *
28058873 GGCCGTAAAGCCCCTGTAGAGTAAAGT
1 GACCGTAAAGCCCCTGTAGGGTAAAGT
* *
28058900 GACCGTAATA-CCCCTGTATGGTAAATT
1 GACCGTAA-AGCCCCTGTAGGGTAAAGT
28058927 GAC
1 GAC
28058930 GAATATGCCC
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
27 48 0.98
28 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.21
Consensus pattern (27 bp):
GACCGTAAAGCCCCTGTAGGGTAAAGT
Found at i:28059761 original size:26 final size:26
Alignment explanation
Indices: 28059732--28059881 Score: 212
Period size: 26 Copynumber: 5.8 Consensus size: 26
28059722 GAGGAAGTGC
**
28059732 AAAAGGGCTTATGCCTTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
28059758 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
28059784 AAAAGGGCTTATGCCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* **
28059810 AAAAGGGCTTATGCCCCAATTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
28059836 AAAAGGGTTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
28059862 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
28059882 ATTAAAGAGG
Statistics
Matches: 108, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
25 10 0.09
26 98 0.91
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:28059810 original size:52 final size:52
Alignment explanation
Indices: 28059732--28059881 Score: 257
Period size: 52 Copynumber: 2.9 Consensus size: 52
28059722 GAGGAAGTGC
*
28059732 AAAAGGGCTTATGCCTTAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCTAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
*
28059784 AAAAGGGCTTATGCCCTAGTTTACCGAAAAGGGCTTATGCCCCAATTTATTG
1 AAAAGGGCTTATGCCCTAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
* *
28059836 AAAAGGGTTTATGCCCCAGTTTACCGAAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCTAGTTTACCGAAAAGGGCTTATGCCCCAGTT
28059882 ATTAAAGAGG
Statistics
Matches: 93, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
51 9 0.10
52 84 0.90
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (52 bp):
AAAAGGGCTTATGCCCTAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
Found at i:28060085 original size:42 final size:42
Alignment explanation
Indices: 28060026--28060117 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
28060016 TAGTCTCCCC
* ** *
28060026 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
28060068 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
28060110 AAATGGGC
1 AAATGGGC
28060118 CTATAGGCCA
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:28060179 original size:31 final size:31
Alignment explanation
Indices: 28060141--28060219 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
28060131 CGTTTACAGC
**
28060141 AAAGGCTTCAGCCCAGTGAAATGATTTATGA
1 AAAGGCTTTGGCCCAGTGAAATGATTTATGA
*
28060172 AAAGGCTTTGGCCCAGTGATATGATTTATGA
1 AAAGGCTTTGGCCCAGTGAAATGATTTATGA
28060203 AAAGGCTTTGGCCCAGT
1 AAAGGCTTTGGCCCAGT
28060220 AATCGTTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.28
Consensus pattern (31 bp):
AAAGGCTTTGGCCCAGTGAAATGATTTATGA
Found at i:28081319 original size:27 final size:27
Alignment explanation
Indices: 28081277--28081350 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
28081267 AAAATTAACT
** *
28081277 AAATGACCAAAATACCCCTGAGGTGT-A
1 AAATGACCATTATACCCCT-AAGTGTCA
* * *
28081304 AAATTACCATTTTACCCCTAATTGTCA
1 AAATGACCATTATACCCCTAAGTGTCA
28081331 AAATGACCATTATACCCCTA
1 AAATGACCATTATACCCCTA
28081351 GGGGTAGGTT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
26 4 0.11
27 34 0.89
ACGTcount: A:0.38, C:0.26, G:0.09, T:0.27
Consensus pattern (27 bp):
AAATGACCATTATACCCCTAAGTGTCA
Found at i:28082989 original size:40 final size:40
Alignment explanation
Indices: 28082891--28083313 Score: 584
Period size: 40 Copynumber: 10.6 Consensus size: 40
28082881 TCCTCGTTCA
* * * * *
28082891 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
28082930 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
28082970 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
28083010 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
28083050 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
28083090 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
28083130 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
28083170 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * *
28083210 AAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGG-ATTTAATAACTCGCACG
** * * * *
28083250 AATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
28083290 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
28083314 CAGCATTCAA
Statistics
Matches: 355, Mismatches: 23, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
39 39 0.11
40 304 0.86
41 12 0.03
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:28083322 original size:41 final size:41
Alignment explanation
Indices: 28083245--28083322 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
28083235 TTTGTATCTC
* * *
28083245 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
28083286 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
28083323 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:28091720 original size:40 final size:40
Alignment explanation
Indices: 28091672--28092019 Score: 561
Period size: 40 Copynumber: 8.7 Consensus size: 40
28091662 GCAAACACAT
* * * *
28091672 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
* *
28091712 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
1 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
* **
28091752 TTGCCTTCGGGTCTTAGCCCGGATATATCGTCTCGCATAA
1 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
* *
28091792 TTGCCTTCGGGTCATAGCCCGGATATATTATCTCGCATAA
1 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
* *
28091832 TTGCCTTCGGGTCATAGCCCGGATATATTATCTCGCATAA
1 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
28091872 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
*
28091912 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
*
28091952 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
28091992 TTGCCTTCGGGTCATAGCCCGGATATAT
1 TTGCCTTCGGGTCATAGCCCGGATATAT
28092020 TCCAATGCTC
Statistics
Matches: 294, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 294 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.30
Consensus pattern (40 bp):
TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
Found at i:28101418 original size:48 final size:48
Alignment explanation
Indices: 28101345--28101519 Score: 246
Period size: 48 Copynumber: 3.6 Consensus size: 48
28101335 GCTAAATGTT
* * * * *
28101345 CCAGTGTAAGTCCATGCCTGAGACATGGGATCGACGATGATATGTGTG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATGTGTG
* *
28101393 CCAGTGTAAGACCCTGTCTGGGACATGGCATCGGTGATGATATGTGTG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATGTGTG
28101441 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATGTG-G
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATGTGTG
*
28101488 ATTCA-TGTAAGACCATGTCTGGGACATGGCAT
1 --CCAGTGTAAGACCATGTCTGGGACATGGCAT
28101520 TGATACTTTA
Statistics
Matches: 115, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
47 1 0.01
48 112 0.97
49 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (48 bp):
CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATGTGTG
Found at i:28104701 original size:28 final size:29
Alignment explanation
Indices: 28104656--28104715 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
28104646 ATTTATTTTA
*
28104656 CAATTTAACCCATCAATTTACACTTTTCT
1 CAATTTAACCCATCAATTGACACTTTTCT
* *
28104685 CAATTTAATCCC-T-AATTGACATTTTTGT
1 CAATTTAA-CCCATCAATTGACACTTTTCT
28104713 CAA
1 CAA
28104716 AAATCATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 15 0.56
29 9 0.33
30 3 0.11
ACGTcount: A:0.32, C:0.23, G:0.03, T:0.42
Consensus pattern (29 bp):
CAATTTAACCCATCAATTGACACTTTTCT
Found at i:28110520 original size:42 final size:43
Alignment explanation
Indices: 28110460--28110572 Score: 124
Period size: 43 Copynumber: 2.7 Consensus size: 43
28110450 TGAGACATCG
* * *
28110460 TGTAAGACCATGTCTGGGACATCGGCATC-ATATT-TGATTTCA
1 TGTAAGACCCTGTCTGGGACATCGGCATCGATATTAAG-TTACA
* **
28110502 TGTAAGACCCTGTTTGGGACAGAGGCATCGATATTAAGTTACA
1 TGTAAGACCCTGTCTGGGACATCGGCATCGATATTAAGTTACA
*
28110545 TGTAAGACCAC-GTCCGGGACATCGGCAT
1 TGTAAGACC-CTGTCTGGGACATCGGCAT
28110573 TGTACTTGTT
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
42 25 0.43
43 31 0.53
44 2 0.03
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (43 bp):
TGTAAGACCCTGTCTGGGACATCGGCATCGATATTAAGTTACA
Found at i:28110550 original size:43 final size:42
Alignment explanation
Indices: 28110460--28110565 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 42
28110450 TGAGACATCG
** * *
28110460 TGTAAGACCATGTCTGGGACATCGGCATCATATTTGATTTCA
1 TGTAAGACCATGTCTGGGACAGAGGCATCATATTAGATTACA
* *
28110502 TGTAAGACCCTGTTTGGGACAGAGGCATCGATATTA-AGTTACA
1 TGTAAGACCATGTCTGGGACAGAGGCATC-ATATTAGA-TTACA
* *
28110545 TGTAAGACCACGTCCGGGACA
1 TGTAAGACCATGTCTGGGACA
28110566 TCGGCATTGT
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
42 26 0.50
43 26 0.50
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACAGAGGCATCATATTAGATTACA
Found at i:28119648 original size:47 final size:46
Alignment explanation
Indices: 28119559--28119667 Score: 121
Period size: 47 Copynumber: 2.3 Consensus size: 46
28119549 GATTAATAAG
* **
28119559 AGCCAGTGTAAGACCATGTCTAAGACATGTCATCAGTGTTGATATGAT
1 AGCCAGTGTAAGA-CATGTCTAAGACATGGCATCAGCATTGATAT-AT
** *
28119607 AGCCAGTGTAAGACATGTCTGGGACATGGCATCGGCATTGATATAT
1 AGCCAGTGTAAGACATGTCTAAGACATGGCATCAGCATTGATATAT
28119653 -GTCCTAGTGTAAGAC
1 AG-CC-AGTGTAAGAC
28119668 CATATTTGGG
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
45 1 0.02
46 4 0.08
47 35 0.66
48 13 0.25
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (46 bp):
AGCCAGTGTAAGACATGTCTAAGACATGGCATCAGCATTGATATAT
Found at i:28119834 original size:90 final size:90
Alignment explanation
Indices: 28119740--28119904 Score: 217
Period size: 90 Copynumber: 1.8 Consensus size: 90
28119730 GGCATTGATA
* * * * ***
28119740 TGAGATTTCGTGTAAGACCATGTCTGGGACATGGCATC-A-ATGTGAGGTCTTGTGTAAGACCAT
1 TGAGATTTCATATAAGACCATATCTGGGACATGGCATCTATATGT-A-GACCCATGTAAGACCAT
28119803 GTCTGGGACATGACATCGACACCGATG
64 GTCTGGGACATGACATCGACACCGATG
* *
28119830 TGAGATTTCATATAAGACCATATTTGGGATATGGCATCTATATGTAGACCCATGTAAGACCATGT
1 TGAGATTTCATATAAGACCATATCTGGGACATGGCATCTATATGTAGACCCATGTAAGACCATGT
28119895 CTGGGACATG
66 CTGGGACATG
28119905 GCTTTGGAAT
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
90 58 0.91
91 2 0.03
92 4 0.06
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (90 bp):
TGAGATTTCATATAAGACCATATCTGGGACATGGCATCTATATGTAGACCCATGTAAGACCATGT
CTGGGACATGACATCGACACCGATG
Found at i:28119906 original size:42 final size:44
Alignment explanation
Indices: 28119707--28119906 Score: 162
Period size: 42 Copynumber: 4.6 Consensus size: 44
28119697 ATGTGATTTT
* * *
28119707 ATGTAAGACCATATCTGGGATATGGCAT-TGATA--TGAGATTTC
1 ATGTAAGACCATGTCTGGGACATGGCATCT-ATATGTGAGATCTC
* * *
28119749 GTGTAAGACCATGTCTGGGACATGGCATC-A-ATGTGAGGTCTT
1 ATGTAAGACCATGTCTGGGACATGGCATCTATATGTGAGATCTC
* * * * *
28119791 GTGTAAGACCATGTCTGGGACATGACATCGACACCGATGTGAGATTTC
1 ATGTAAGACCATGTCTGGGACATGGCATC--TA--TATGTGAGATCTC
* * * * *
28119839 ATATAAGACCATATTTGGGATATGGCATCTATATGT-AGA-CCC
1 ATGTAAGACCATGTCTGGGACATGGCATCTATATGTGAGATCTC
28119881 ATGTAAGACCATGTCTGGGACATGGC
1 ATGTAAGACCATGTCTGGGACATGGC
28119907 TTTGGAATTC
Statistics
Matches: 125, Mismatches: 24, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
40 1 0.01
41 1 0.01
42 82 0.66
43 3 0.02
44 4 0.03
45 1 0.01
46 1 0.01
48 32 0.26
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.28
Consensus pattern (44 bp):
ATGTAAGACCATGTCTGGGACATGGCATCTATATGTGAGATCTC
Found at i:28144035 original size:39 final size:39
Alignment explanation
Indices: 28143981--28144111 Score: 163
Period size: 39 Copynumber: 3.4 Consensus size: 39
28143971 AATTAAAAGT
*
28143981 GGAATTATATTCGGACTTAAGGTCCGTAGGCTATATGCG
1 GGAATTATATCCGGACTTAAGGTCCGTAGGCTATATGCG
28144020 GGAATTATATCCGGACTTAAGGTCCGTAGGCTATATGCG
1 GGAATTATATCCGGACTTAAGGTCCGTAGGCTATATGCG
* * * ** * ** * *
28144059 GGAATCATATTCGAACTTCGGGTTCGCCGGCTATGTGCT
1 GGAATTATATCCGGACTTAAGGTCCGTAGGCTATATGCG
28144098 GGAATTATATCCGG
1 GGAATTATATCCGG
28144112 GCTAATAGTC
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (39 bp):
GGAATTATATCCGGACTTAAGGTCCGTAGGCTATATGCG
Found at i:28152508 original size:19 final size:19
Alignment explanation
Indices: 28152484--28152521 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
28152474 AAGTCCCTAT
28152484 ACATGCCATAATTTTAAAA
1 ACATGCCATAATTTTAAAA
28152503 ACATGCCATAATTTTAAAA
1 ACATGCCATAATTTTAAAA
28152522 TACTTGCGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (19 bp):
ACATGCCATAATTTTAAAA
Found at i:28159812 original size:28 final size:28
Alignment explanation
Indices: 28159724--28159814 Score: 112
Period size: 27 Copynumber: 3.2 Consensus size: 28
28159714 ATCCATACTT
* * *
28159724 ATTCATTTGGCCCCTTTAGGCCCAATCTC
1 ATTCATATGG-CCCATTAGGCCCAATCAC
28159753 ATTCATATGGCCCATT-GGCCCAATCAC
1 ATTCATATGGCCCATTAGGCCCAATCAC
* * *
28159780 TTTCATATGGCCCGTTAGGCCTAATCAC
1 ATTCATATGGCCCATTAGGCCCAATCAC
28159808 ATTCATA
1 ATTCATA
28159815 GTCATGCAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
27 24 0.44
28 21 0.39
29 9 0.17
ACGTcount: A:0.23, C:0.31, G:0.14, T:0.32
Consensus pattern (28 bp):
ATTCATATGGCCCATTAGGCCCAATCAC
Found at i:28173793 original size:27 final size:26
Alignment explanation
Indices: 28173762--28173939 Score: 142
Period size: 27 Copynumber: 6.6 Consensus size: 26
28173752 TAAATTGTAC
*
28173762 AGCACTAAGTGTGCGATTCTACTTTGT
1 AGCACTAAGTGTGCGATT-TACTATGT
* * * *
28173789 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTTACTATGT
* * *
28173815 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTTACTATGT
*
28173843 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTT-ACTATGT
* *
28173871 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTT-ACTATGT
* * *
28173898 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTTACTATGT
*
28173925 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28173940 GGCTCAATAT
Statistics
Matches: 125, Mismatches: 20, Indels: 12
0.80 0.13 0.08
Matches are distributed among these distances:
26 1 0.01
27 100 0.80
28 24 0.19
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTTACTATGT
Found at i:28173823 original size:54 final size:54
Alignment explanation
Indices: 28173762--28173939 Score: 166
Period size: 54 Copynumber: 3.3 Consensus size: 54
28173752 TAAATTGTAC
* *
28173762 AGCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATT-TACTTTGTAGCACTAAGTGTGCGAATTGAATATGAT
* ** ** * *
28173817 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTTGACTATG-T
1 AGCACTAAGTGTGCG-ATTTACTTTGTAGCACTAAGTGTGCGA-ATTGAATATGAT
* * *
28173871 AGCACTAAGTGTGCGATTTGA-TTACGTAGCACTAAGTGTGCGAGTTGATTAT-AT
1 AGCACTAAGTGTGCGATTT-ACTT-TGTAGCACTAAGTGTGCGAATTGAATATGAT
*
28173925 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28173940 GGCTCAATAT
Statistics
Matches: 100, Mismatches: 17, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
54 59 0.59
55 41 0.41
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (54 bp):
AGCACTAAGTGTGCGATTTACTTTGTAGCACTAAGTGTGCGAATTGAATATGAT
Found at i:28173886 original size:55 final size:54
Alignment explanation
Indices: 28173790--28173939 Score: 167
Period size: 55 Copynumber: 2.8 Consensus size: 54
28173780 CTACTTTGTT
** * *
28173790 GCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAGTTGAATATGTA-GCACTAAGTGTGCGAATTGACCACGCA
* * ** *
28173844 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAG-TTGAATATGTAGCACTAAGTGTGCGAATTGACCACGCA
* * *
28173899 GCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCG
28173940 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
54 37 0.45
55 44 0.54
56 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAATTGACCACGCA
Found at i:28173886 original size:82 final size:81
Alignment explanation
Indices: 28173763--28173918 Score: 208
Period size: 82 Copynumber: 1.9 Consensus size: 81
28173753 AAATTGTACA
* * *
28173763 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
28173827 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
28173844 GCACTAAGTGTGCGAGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGT
1 GCACTAAGTGTGCGA-TTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGT
*
28173908 GTGCGAGTTGA
64 GTGCGAATTGA
28173919 TTATATAGCA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
81 16 0.25
82 48 0.74
83 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:28173930 original size:82 final size:81
Alignment explanation
Indices: 28173759--28173939 Score: 204
Period size: 82 Copynumber: 2.2 Consensus size: 81
28173749 GATTAAATTG
* * *
28173759 TACAGCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
28173824 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
28173840 TGCGGCACTAAGTGTGCGAGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCAC
1 TACAGCACTAAGTGTGCGA-TTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCAC
* **
28173903 TAAGTGTGCGAGTTGATTA
63 TAAGTGTGCGAATTGACCA
* *
28173922 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
28173940 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
81 19 0.23
82 63 0.77
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:28173950 original size:27 final size:27
Alignment explanation
Indices: 28173844--28173950 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
28173834 TGACCATGCG
* * * *
28173844 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAG-CTCAATATATA
** * * **
28173872 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
28173899 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
28173926 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
28173951 CATTCGTGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 53 0.78
28 15 0.22
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:28177962 original size:28 final size:28
Alignment explanation
Indices: 28177874--28177964 Score: 112
Period size: 27 Copynumber: 3.2 Consensus size: 28
28177864 ATCCATACTT
* * *
28177874 ATTCATTTGGCCCCTTTAGGCCCAATCTC
1 ATTCATATGG-CCCATTAGGCCCAATCAC
28177903 ATTCATATGGCCCATT-GGCCCAATCAC
1 ATTCATATGGCCCATTAGGCCCAATCAC
* * *
28177930 TTTCATATGGCCCGTTAGGCCTAATCAC
1 ATTCATATGGCCCATTAGGCCCAATCAC
28177958 ATTCATA
1 ATTCATA
28177965 GTCATGCAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
27 24 0.44
28 21 0.39
29 9 0.17
ACGTcount: A:0.23, C:0.31, G:0.14, T:0.32
Consensus pattern (28 bp):
ATTCATATGGCCCATTAGGCCCAATCAC
Found at i:28182916 original size:16 final size:17
Alignment explanation
Indices: 28182885--28182918 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
28182875 AAACAACATG
*
28182885 AAATAATTAAATATAAA
1 AAATAATTAAAGATAAA
28182902 AAATAA-TAAAGATAAA
1 AAATAATTAAAGATAAA
28182918 A
1 A
28182919 CTAAAGTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
AAATAATTAAAGATAAA
Found at i:28187743 original size:16 final size:16
Alignment explanation
Indices: 28187722--28187753 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28187712 TTTGTTTTTA
28187722 ATATAAATGAATCTAT
1 ATATAAATGAATCTAT
*
28187738 ATATAAATGTATCTAT
1 ATATAAATGAATCTAT
28187754 GCTACGATGA
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:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (16 bp):
ATATAAATGAATCTAT
Found at i:28199123 original size:45 final size:45
Alignment explanation
Indices: 28199073--28199158 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
28199063 CCAAAACATG
* * *
28199073 TGTCACATTTATCACGAACTCAGACCATAACTCAATGAGTTCGAA
1 TGTCACATATATCACGAACTCAAACCACAACTCAATGAGTTCGAA
* *
28199118 TGTCACATATATCATGAACTCAAACCACCACTCAATGAGTT
1 TGTCACATATATCACGAACTCAAACCACAACTCAATGAGTT
28199159 TAGATTACAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.27
Consensus pattern (45 bp):
TGTCACATATATCACGAACTCAAACCACAACTCAATGAGTTCGAA
Found at i:28205830 original size:27 final size:27
Alignment explanation
Indices: 28205800--28205977 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28205790 ATATTGAGTC
* * * *
28205800 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
28205827 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28205854 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
28205882 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
28205909 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
28205936 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28205963 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28205978 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:28205939 original size:82 final size:81
Alignment explanation
Indices: 28205821--28205976 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28205811 TGCTATATAA
* *
28205821 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
28205886 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
28205903 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
28205967 CACTTAGTGC
65 CACTTAGTGC
28205977 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28214019 original size:27 final size:27
Alignment explanation
Indices: 28213989--28214166 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28213979 ATATTGAGTC
* * * *
28213989 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
28214016 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28214043 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
28214071 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
28214098 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
28214125 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28214152 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28214167 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:28214128 original size:82 final size:81
Alignment explanation
Indices: 28214010--28214165 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28214000 TGCTATATAA
* *
28214010 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
28214075 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
28214092 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
28214156 CACTTAGTGC
65 CACTTAGTGC
28214166 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28225080 original size:27 final size:27
Alignment explanation
Indices: 28225047--28225226 Score: 186
Period size: 27 Copynumber: 6.7 Consensus size: 27
28225037 GGATAAGTTG
*
28225047 TAGAATTACTGAAATACCCCTGTAAGA
1 TAGAATTACTGAAATACCCCTGTAGGA
*
28225074 TAGAATTAC-GAAAATACCCTTGTAGGA
1 TAGAATTACTG-AAATACCCCTGTAGGA
* *
28225101 TAGAATTATTGAAATACCCCTGTAGGG
1 TAGAATTACTGAAATACCCCTGTAGGA
28225128 TAGAATTA-TCGAAATACCCCTGTAGGA
1 TAGAATTACT-GAAATACCCCTGTAGGA
** * * *
28225155 TAGAATTACCAAAATACCCTTATAGGG
1 TAGAATTACTGAAATACCCCTGTAGGA
* * *
28225182 TAGAAATACCT-AAATACCCCTATAGGG
1 TAGAATTA-CTGAAATACCCCTGTAGGA
* *
28225209 TAGAATTACCGAGATACC
1 TAGAATTACTGAAATACC
28225227 TTTGTGGGGT
Statistics
Matches: 130, Mismatches: 17, Indels: 12
0.82 0.11 0.08
Matches are distributed among these distances:
26 3 0.02
27 125 0.96
28 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (27 bp):
TAGAATTACTGAAATACCCCTGTAGGA
Found at i:28225186 original size:81 final size:80
Alignment explanation
Indices: 28225046--28225226 Score: 247
Period size: 81 Copynumber: 2.2 Consensus size: 80
28225036 TGGATAAGTT
* * * *
28225046 GTAGAATTACTGAAATACCCCTGTAAGATAGAATTACGAAAATACCCTTGTAGGATAGAATTA-T
1 GTAGAATTAC-GAAATACCCCTGTAAGATAGAATTACCAAAATACCCTTATAGGATAGAAATACC
*
28225110 TGAAATACCCCTGTAGG
65 T-AAATACCCCTATAGG
* *
28225127 GTAGAATTATCGAAATACCCCTGTAGGATAGAATTACCAAAATACCCTTATAGGGTAGAAATACC
1 GTAGAATTA-CGAAATACCCCTGTAAGATAGAATTACCAAAATACCCTTATAGGATAGAAATACC
28225192 TAAATACCCCTATAGG
65 TAAATACCCCTATAGG
*
28225208 GTAGAATTACCGAGATACC
1 GTAGAATTA-CGAAATACC
28225227 TTTGTGGGGT
Statistics
Matches: 89, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
81 87 0.98
82 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (80 bp):
GTAGAATTACGAAATACCCCTGTAAGATAGAATTACCAAAATACCCTTATAGGATAGAAATACCT
AAATACCCCTATAGG
Found at i:28236131 original size:24 final size:24
Alignment explanation
Indices: 28236102--28236149 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
28236092 AATTGGTGGT
* *
28236102 ATATGATATATGGATAAAATTTTA
1 ATATGAAATATGCATAAAATTTTA
28236126 ATATGAAATATGCATAAAATTTTA
1 ATATGAAATATGCATAAAATTTTA
28236150 TTTATTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (24 bp):
ATATGAAATATGCATAAAATTTTA
Found at i:28237440 original size:37 final size:37
Alignment explanation
Indices: 28237348--28237451 Score: 118
Period size: 37 Copynumber: 2.8 Consensus size: 37
28237338 TTGGTAACAG
*
28237348 TAACAATATCAATGGCATGCTTATCATGCTTTTAGTT
1 TAACAATATCAATGGCATGCTTATCATGCTTCTAGTT
* * * *** *
28237385 TAATAATTTTAGCAGCATGCTTATCATGCTTCTGGTT
1 TAACAATATCAATGGCATGCTTATCATGCTTCTAGTT
*
28237422 TAACAATCTCAATGGCATGCTTAATCATGC
1 TAACAATATCAATGGCATGCTT-ATCATGC
28237452 ATTCATTAAT
Statistics
Matches: 52, Mismatches: 14, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
37 45 0.87
38 7 0.13
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.38
Consensus pattern (37 bp):
TAACAATATCAATGGCATGCTTATCATGCTTCTAGTT
Found at i:28238496 original size:20 final size:20
Alignment explanation
Indices: 28238459--28238497 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
28238449 TAAACTGAGC
*
28238459 ACATACAAATTTTCTCAAAA
1 ACATACAAAATTTCTCAAAA
28238479 ACATAACAAAATTT-TCAAA
1 ACAT-ACAAAATTTCTCAAA
28238498 GTTTCAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.28
Consensus pattern (20 bp):
ACATACAAAATTTCTCAAAA
Found at i:28240214 original size:12 final size:12
Alignment explanation
Indices: 28240190--28240227 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
28240180 ATTCTGTCAC
*
28240190 CTCATTCTGATT
1 CTCATTTTGATT
*
28240202 CTGATTTTGATT
1 CTCATTTTGATT
28240214 CTCATTTTGATT
1 CTCATTTTGATT
28240226 CT
1 CT
28240228 AGTTATGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.16, C:0.18, G:0.11, T:0.55
Consensus pattern (12 bp):
CTCATTTTGATT
Found at i:28240236 original size:24 final size:24
Alignment explanation
Indices: 28240190--28240236 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
28240180 ATTCTGTCAC
*
28240190 CTCATTCTGATTCTGATTTTGATT
1 CTCATTCTGATTCTGATTATGATT
*
28240214 CTCATTTTGATTCT-AGTTATGAT
1 CTCATTCTGATTCTGA-TTATGAT
28240237 AATGTTTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.19, C:0.15, G:0.13, T:0.53
Consensus pattern (24 bp):
CTCATTCTGATTCTGATTATGATT
Found at i:28240329 original size:27 final size:27
Alignment explanation
Indices: 28240291--28240826 Score: 123
Period size: 27 Copynumber: 19.9 Consensus size: 27
28240281 CTGCCCCTAG
28240291 TTTGTAAAATTACCAAAATA-CCTCTGA
1 TTTGTAAAATTACCAAAATACCCTC-GA
* ***
28240318 TTTGTGAAATTATTGAAATACCCTCGA
1 TTTGTAAAATTACCAAAATACCCTCGA
** *
28240345 CCTGTAAAATTACTAAAATACCCTCGA
1 TTTGTAAAATTACCAAAATACCCTCGA
* * *
28240372 CTTGTAAAATTACCAAAGTACCATCGA
1 TTTGTAAAATTACCAAAATACCCTCGA
** * ******
28240399 TTTACAGAATTATTGTTTTACCCTCGA
1 TTTGTAAAATTACCAAAATACCCTCGA
** *** *
28240426 TTTAAAAAATTACCATTTTACCCTTGA
1 TTTGTAAAATTACCAAAATACCCTCGA
** **** *
28240453 TTTAAAAAATTACCGTTTTACTCTCGA
1 TTTGTAAAATTACCAAAATACCCTCGA
* * ***** *
28240480 TTTATAGAATTACTGTTTTACCTTCGA
1 TTTGTAAAATTACCAAAATACCCTCGA
* ***
28240507 TTTATAAAATTACCATTTTACCCTCGA
1 TTTGTAAAATTACCAAAATACCCTCGA
** ***** *
28240534 TTTACAAAATTACTGTTTTATCCTCGA
1 TTTGTAAAATTACCAAAATACCCTCGA
** ****
28240561 TTTACAAAATTACCGTTTTACCCTCGA
1 TTTGTAAAATTACCAAAATACCCTCGA
* * ***
28240588 TTTATAGAATTACCATTTTACCCTCGA
1 TTTGTAAAATTACCAAAATACCCTCGA
** * * ****
28240615 TTTACAGAATTATCGTTTTACCCTCGA
1 TTTGTAAAATTACCAAAATACCCTCGA
** ***
28240642 TTTACAAAAATTACCATTTTACCCTC-A
1 TTT-GTAAAATTACCAAAATACCCTCGA
** * ***
28240669 GTTTACAAAATTATCATTTTACCCTCGA
1 -TTTGTAAAATTACCAAAATACCCTCGA
* **
28240697 -TTGTGAAATTACTGAAATACCC-CTG-
1 TTTGTAAAATTACCAAAATACCCTC-GA
** * *
28240722 TAGGATAGAATTACCAAAATACCC-CTA
1 TTTG-TAAAATTACCAAAATACCCTCGA
*
28240749 GTTTGTAAAATTACCAAAATACCC-CTA
1 -TTTGTAAAATTACCAAAATACCCTCGA
* * *
28240776 GTTTGTAAAATTATCGAAATACCCTCAA
1 -TTTGTAAAATTACCAAAATACCCTCGA
28240804 TTTGTAAAATTACCAAAATACCC
1 TTTGTAAAATTACCAAAATACCC
28240827 CTAATTTACT
Statistics
Matches: 413, Mismatches: 86, Indels: 20
0.80 0.17 0.04
Matches are distributed among these distances:
25 1 0.00
26 15 0.04
27 368 0.89
28 29 0.07
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.36
Consensus pattern (27 bp):
TTTGTAAAATTACCAAAATACCCTCGA
Found at i:28240421 original size:54 final size:54
Alignment explanation
Indices: 28240363--28240698 Score: 386
Period size: 54 Copynumber: 6.2 Consensus size: 54
28240353 ATTACTAAAA
* * *** * * **
28240363 TACCCTCGACTTGTAAAATTACCAAAGTACCATCGATTTACAGAATTATTGTTT
1 TACCCTCGATTTATAAAATTACCATTTTACCCTCGATTTACAAAATTACCGTTT
* * *
28240417 TACCCTCGATTTAAAAAATTACCATTTTACCCTTGATTTAAAAAATTACCGTTT
1 TACCCTCGATTTATAAAATTACCATTTTACCCTCGATTTACAAAATTACCGTTT
* * ** * * *
28240471 TACTCTCGATTTATAGAATTACTGTTTTACCTTCGATTTATAAAATTACCATTT
1 TACCCTCGATTTATAAAATTACCATTTTACCCTCGATTTACAAAATTACCGTTT
* ** *
28240525 TACCCTCGATTTACAAAATTACTGTTTTATCCTCGATTTACAAAATTACCGTTT
1 TACCCTCGATTTATAAAATTACCATTTTACCCTCGATTTACAAAATTACCGTTT
* * *
28240579 TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTATCGTTT
1 TACCCTCGATTTATAAAATTACCATTTTACCCTCGATTTACAAAATTACCGTTT
* * *
28240633 TACCCTCGATTTACAAAAATTACCATTTTACCCTC-AGTTTACAAAATTATCATTT
1 TACCCTCGATTTA-TAAAATTACCATTTTACCCTCGA-TTTACAAAATTACCGTTT
28240688 TACCCTCGATT
1 TACCCTCGATT
28240699 GTGAAATTAC
Statistics
Matches: 241, Mismatches: 39, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
54 195 0.81
55 46 0.19
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.40
Consensus pattern (54 bp):
TACCCTCGATTTATAAAATTACCATTTTACCCTCGATTTACAAAATTACCGTTT
Found at i:28240435 original size:81 final size:81
Alignment explanation
Indices: 28240350--28240602 Score: 204
Period size: 81 Copynumber: 3.1 Consensus size: 81
28240340 CTCGACCTGT
* ** *
28240350 AAAATTACTAAAATACCCTCGACTTGTAAAATTACCAAAGTAC-CATCGATTTACAGAATTATTG
1 AAAATTACCAAAATACCCTCGACTTAAAAAATTACCAAAGTACTC-TCGATTTACAGAATTACTG
28240414 TTTTACCCTCGATTTAA
65 TTTTACCCTCGATTTAA
*** * * **** *
28240431 AAAATTACCATTTTACCCTTGATTTAAAAAATTACCGTTTTACTCTCGATTTATAGAATTACTGT
1 AAAATTACCAAAATACCCTCGACTTAAAAAATTACCAAAGTACTCTCGATTTACAGAATTACTGT
* *
28240496 TTTACCTTCGATTTAT
66 TTTACCCTCGATTTAA
*** * * ***** * *
28240512 AAAATTACCATTTTACCCTCGATTTACAAAATTACTGTTTTA-TCCTCGATTTACAAAATTACCG
1 AAAATTACCAAAATACCCTCGACTTAAAAAATTACCAAAGTACT-CTCGATTTACAGAATTACTG
*
28240576 TTTTACCCTCGATTTAT
65 TTTTACCCTCGATTTAA
*
28240593 AGAATTACCA
1 AAAATTACCA
28240603 TTTTACCCTC
Statistics
Matches: 146, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
80 1 0.01
81 144 0.99
82 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.39
Consensus pattern (81 bp):
AAAATTACCAAAATACCCTCGACTTAAAAAATTACCAAAGTACTCTCGATTTACAGAATTACTGT
TTTACCCTCGATTTAA
Found at i:28240603 original size:81 final size:80
Alignment explanation
Indices: 28240390--28240698 Score: 397
Period size: 81 Copynumber: 3.8 Consensus size: 80
28240380 ATTACCAAAG
* ** * *
28240390 TACCATCGATTTACAGAATTATTGTTTTACCCTCGATTTAAAAAATTACCATTTTACCCTTGATT
1 TACC-TCGATTTACAAAATTACCGTTTTACCCTCGATTTATAAAATTACCATTTTACCCTCGATT
* *
28240455 TAAAAAATTACCGTTT
65 TACAAAATTACTGTTT
* * * *
28240471 TACTCTCGATTTATAGAATTACTGTTTTACCTTCGATTTATAAAATTACCATTTTACCCTCGATT
1 TAC-CTCGATTTACAAAATTACCGTTTTACCCTCGATTTATAAAATTACCATTTTACCCTCGATT
28240536 TACAAAATTACTGTTT
65 TACAAAATTACTGTTT
*
28240552 TATCCTCGATTTACAAAATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATT
1 TA-CCTCGATTTACAAAATTACCGTTTTACCCTCGATTTATAAAATTACCATTTTACCCTCGATT
*
28240617 TACAGAATTA-TCGTTT
65 TACAAAATTACT-GTTT
* * *
28240633 TACCCTCGATTTACAAAAATTACCATTTTACCCTC-AGTTTACAAAATTATCATTTTACCCTCGA
1 TA-CCTCGATTTAC-AAAATTACCGTTTTACCCTCGA-TTTATAAAATTACCATTTTACCCTCGA
28240697 TT
63 TT
28240699 GTGAAATTAC
Statistics
Matches: 205, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
80 1 0.00
81 157 0.77
82 47 0.23
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (80 bp):
TACCTCGATTTACAAAATTACCGTTTTACCCTCGATTTATAAAATTACCATTTTACCCTCGATTT
ACAAAATTACTGTTT
Found at i:28240771 original size:54 final size:54
Alignment explanation
Indices: 28240688--28240829 Score: 155
Period size: 54 Copynumber: 2.6 Consensus size: 54
28240678 ATTATCATTT
* * ** *
28240688 TACCCTCGA-TTGTGAAATTACTGAAATACCCCT-GTAGGATAGAATTACCAAAA
1 TACCCTCAATTTGTAAAATTACCAAAATACCCCTAGTAGG-TAAAATTACCAAAA
* ** * *
28240741 TACCC-CTAGTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTATCGAAA
1 TACCCTC-AATTTGTAAAATTACCAAAATACCCCTAGTAGGTAAAATTACCAAAA
28240795 TACCCTCAATTTGTAAAATTACCAAAATACCCCTA
1 TACCCTCAATTTGTAAAATTACCAAAATACCCCTA
28240830 ATTTACTAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
52 1 0.01
53 5 0.07
54 64 0.86
55 4 0.05
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.29
Consensus pattern (54 bp):
TACCCTCAATTTGTAAAATTACCAAAATACCCCTAGTAGGTAAAATTACCAAAA
Found at i:28240849 original size:27 final size:27
Alignment explanation
Indices: 28240730--28240833 Score: 156
Period size: 27 Copynumber: 3.9 Consensus size: 27
28240720 TGTAGGATAG
*
28240730 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAATTTGTAA
*
28240757 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAATTTGTAA
* *
28240784 AATTATCGAAATA-CCCTCAATTTGTAA
1 AATTACCAAAATACCCCT-AATTTGTAA
28240811 AATTACCAAAATACCCCTAATTT
1 AATTACCAAAATACCCCTAATTT
28240834 ACTAAATTAC
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
26 4 0.06
27 62 0.89
28 4 0.06
ACGTcount: A:0.41, C:0.22, G:0.06, T:0.31
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAATTTGTAA
Found at i:28240904 original size:27 final size:27
Alignment explanation
Indices: 28240865--28240916 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
28240855 TGACTTTCTA
28240865 AAAATTATAGAAATACCATTGGTTTAC
1 AAAATTATAGAAATACCATTGGTTTAC
*
28240892 AAAATTACT-GAAATACCCTTGGTTT
1 AAAATTA-TAGAAATACCATTGGTTT
28240917 GTAGATTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (27 bp):
AAAATTATAGAAATACCATTGGTTTAC
Found at i:28241034 original size:27 final size:27
Alignment explanation
Indices: 28240970--28241034 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
28240960 ACCCCTAATA
*
28240970 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
* * * *
28240997 GGCAAAGTGACCGTAATA-CCCTTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAG
28241024 GGTAAAATGAC
1 GGTAAAATGAC
28241035 GAATATGCCC
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
27 29 0.97
28 1 0.03
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAG
Found at i:28241907 original size:27 final size:26
Alignment explanation
Indices: 28241863--28241914 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
28241853 CTCGCTGCAA
*
28241863 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
28241890 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
28241915 GCAGTCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:28242143 original size:6 final size:6
Alignment explanation
Indices: 28242134--28242255 Score: 97
Period size: 6 Copynumber: 19.8 Consensus size: 6
28242124 TTGCATTCAT
* * *
28242134 ATTCTG ATTCTG -TTACCTC ATACTG ATTCTG ATTCTG -TTACCTA ATTCTG
1 ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG
* *
28242184 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG -TCACCTC ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG
* * *
28242233 ATTTTG ATTCTC ATTTTG ATTCT
1 ATTCTG ATTCTG ATTCTG ATTCT
28242256 AGTTATGATA
Statistics
Matches: 91, Mismatches: 16, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
5 5 0.05
6 76 0.84
7 6 0.07
8 4 0.04
ACGTcount: A:0.18, C:0.20, G:0.12, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:28242162 original size:25 final size:25
Alignment explanation
Indices: 28242134--28242235 Score: 128
Period size: 25 Copynumber: 4.4 Consensus size: 25
28242124 TTGCATTCAT
*
28242134 ATTCTGATTCTGTTACCTCATACTG
1 ATTCTGATTCTGTTACCTCATTCTG
*
28242159 ATTCTGATTCTGTTACCTAATTCTG
1 ATTCTGATTCTGTTACCTCATTCTG
28242184 ATTCTGATTCTG-------ATTCTG
1 ATTCTGATTCTGTTACCTCATTCTG
*
28242202 ATTCTGATTCTGTCACCTCATTCTG
1 ATTCTGATTCTGTTACCTCATTCTG
28242227 ATTCTGATT
1 ATTCTGATT
28242236 TTGATTCTCA
Statistics
Matches: 68, Mismatches: 2, Indels: 14
0.81 0.02 0.17
Matches are distributed among these distances:
18 18 0.26
25 50 0.74
ACGTcount: A:0.19, C:0.22, G:0.13, T:0.47
Consensus pattern (25 bp):
ATTCTGATTCTGTTACCTCATTCTG
Found at i:28242210 original size:43 final size:43
Alignment explanation
Indices: 28242134--28242260 Score: 157
Period size: 43 Copynumber: 2.9 Consensus size: 43
28242124 TTGCATTCAT
* *
28242134 ATTCTGATTCTG-TTACCTCATACTGATTCTGATTCTGTTACCTA
1 ATTCTGATTCTGATT--CTGATTCTGATTCTGATTCTGTTACCTA
* *
28242178 ATTCTGATTCTGATTCTGATTCTGATTCTGATTCTGTCACCTC
1 ATTCTGATTCTGATTCTGATTCTGATTCTGATTCTGTTACCTA
* * *
28242221 ATTCTGATTCTGATTTTGATTCTCATTTTGATTCTAGTTA
1 ATTCTGATTCTGATTCTGATTCTGATTCTGATTCT-GTTA
28242261 TGATAATGTT
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
43 56 0.77
44 15 0.21
45 2 0.03
ACGTcount: A:0.19, C:0.20, G:0.13, T:0.49
Consensus pattern (43 bp):
ATTCTGATTCTGATTCTGATTCTGATTCTGATTCTGTTACCTA
Found at i:28242264 original size:24 final size:24
Alignment explanation
Indices: 28242178--28242264 Score: 79
Period size: 24 Copynumber: 3.6 Consensus size: 24
28242168 CTGTTACCTA
* *
28242178 ATTCTGATTCTGATTCTGATTCTG
1 ATTCTGATTATGATTCTCATTCTG
* *
28242202 ATTCTGATTCTG-TCACCTCATTCTG
1 ATTCTGATTATGAT--TCTCATTCTG
* *
28242227 ATTCTGATTTTGATTCTCATTTTG
1 ATTCTGATTATGATTCTCATTCTG
28242251 ATTCT-AGTTATGAT
1 ATTCTGA-TTATGAT
28242265 AATGTTTCTT
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
23 2 0.04
24 31 0.58
25 19 0.36
26 1 0.02
ACGTcount: A:0.18, C:0.17, G:0.14, T:0.51
Consensus pattern (24 bp):
ATTCTGATTATGATTCTCATTCTG
Found at i:28256205 original size:28 final size:28
Alignment explanation
Indices: 28256161--28256225 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
28256151 ATCTACTAGA
*
28256161 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATAACCATT
* *
28256189 ATACCCCTATGTGTGCAAAATAACCTTT
1 ATACCCCTATGTATGCAAAATAACCATT
28256217 ATACCCCTA
1 ATACCCCTA
28256226 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATAACCATT
Found at i:28256389 original size:27 final size:27
Alignment explanation
Indices: 28256331--28256420 Score: 119
Period size: 27 Copynumber: 3.2 Consensus size: 27
28256321 AGGAAGCGTC
28256331 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* *
28256359 CTGGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
28256386 CTGGTGGCACTGCCACAAGATATCTGTAT
1 CTGGTGGCACTGCCACAA-ATATCTGT-T
28256415 CTGGTG
1 CTGGTG
28256421 ACTCTGTCAC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 24 0.44
28 24 0.44
29 7 0.13
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:28257542 original size:11 final size:10
Alignment explanation
Indices: 28257514--28257547 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
28257504 AGCCTGTAAG
28257514 TATTCTGAAT
1 TATTCTGAAT
*
28257524 TTTTCTGAAT
1 TATTCTGAAT
28257534 ATATTCTGAAT
1 -TATTCTGAAT
28257545 TAT
1 TAT
28257548 CTATCTGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (10 bp):
TATTCTGAAT
Found at i:28277130 original size:16 final size:15
Alignment explanation
Indices: 28277101--28277131 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
28277091 TAAAATAATT
28277101 ATAAAATATAATATA
1 ATAAAATATAATATA
28277116 ATAAAATAATAATATA
1 ATAAAAT-ATAATATA
28277132 TACTAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
ATAAAATATAATATA
Found at i:28279649 original size:27 final size:27
Alignment explanation
Indices: 28279610--28279895 Score: 412
Period size: 27 Copynumber: 10.6 Consensus size: 27
28279600 TAAATTGTAC
*
28279610 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
* ** *
28279637 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAGTTGACTATGT
* * *
28279663 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAGTTGACTATGT
*
28279691 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
28279719 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
28279746 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
28279773 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
28279800 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
* * *
28279827 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
* *
28279854 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
28279881 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28279896 GACTCAATAT
Statistics
Matches: 236, Mismatches: 20, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
27 212 0.90
28 24 0.10
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:28288282 original size:14 final size:14
Alignment explanation
Indices: 28288260--28288289 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28288250 AAGAGAGAAT
28288260 GATGATGAATAAGG
1 GATGATGAATAAGG
*
28288274 GATGCTGAATAAGG
1 GATGATGAATAAGG
28288288 GA
1 GA
28288290 ATGAAGGGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.03, G:0.37, T:0.20
Consensus pattern (14 bp):
GATGATGAATAAGG
Found at i:28296305 original size:25 final size:25
Alignment explanation
Indices: 28296258--28296340 Score: 80
Period size: 25 Copynumber: 3.3 Consensus size: 25
28296248 TTGGAGGCCT
* *
28296258 AGCCTCTTTTAAT-AACTGGGGCAA
1 AGCCTTTTTTGATAAACTGGGGCAA
28296282 AGCCTTTTTTGATAAACTGGGGCAA
1 AGCCTTTTTTGATAAACTGGGGCAA
* * * *
28296307 TA-CCCTTTTCGGTAAATTGGGGCAA
1 -AGCCTTTTTTGATAAACTGGGGCAA
28296332 AGCTCTTTT
1 AGC-CTTTT
28296341 AGCACTTCTT
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
24 12 0.25
25 31 0.65
26 5 0.10
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (25 bp):
AGCCTTTTTTGATAAACTGGGGCAA
Found at i:28296400 original size:21 final size:21
Alignment explanation
Indices: 28296375--28296415 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28296365 CCCAACCCAT
*
28296375 GCATATAATGAGTATATCATA
1 GCATATAATGAGCATATCATA
* *
28296396 GCATATCATGTGCATATCAT
1 GCATATAATGAGCATATCAT
28296416 GTCCTATCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (21 bp):
GCATATAATGAGCATATCATA
Found at i:28296889 original size:27 final size:27
Alignment explanation
Indices: 28296564--28296888 Score: 409
Period size: 27 Copynumber: 12.0 Consensus size: 27
28296554 TAAGGGTATC
*
28296564 CAGTAATTCTATCCTACAGGGGTATTT
1 CAGTAATTCTACCCTACAGGGGTATTT
* * *
28296591 CGGTATTTCTACCCTACAAGGGTATTT
1 CAGTAATTCTACCCTACAGGGGTATTT
*
28296618 C-GATAATTCTACCCTATAGGGGTATTT
1 CAG-TAATTCTACCCTACAGGGGTATTT
* *
28296645 CAATAATTCTACCCTACAAGGGTATTT
1 CAGTAATTCTACCCTACAGGGGTATTT
* * *
28296672 TAGTAATTCCACCCTACACGGGTATTT
1 CAGTAATTCTACCCTACAGGGGTATTT
28296699 CAGTAATTCTACCCTACAGGGGTATTT
1 CAGTAATTCTACCCTACAGGGGTATTT
28296726 CAGTAATTCTACCCTACAGGGGTATTT
1 CAGTAATTCTACCCTACAGGGGTATTT
*
28296753 CAGTAATTCTACCCTACATGGGTATTT
1 CAGTAATTCTACCCTACAGGGGTATTT
* *
28296780 CGGTAATTCTACCTTACAGGGGTATTT
1 CAGTAATTCTACCCTACAGGGGTATTT
* ** *
28296807 TAGTAATAATACCCTATAGGGGTATTT
1 CAGTAATTCTACCCTACAGGGGTATTT
* ** *
28296834 CGGTAATAATACCCTATAGGGGTATTT
1 CAGTAATTCTACCCTACAGGGGTATTT
* ** *
28296861 CGGTAATAATACCCTATAGGGGTATTT
1 CAGTAATTCTACCCTACAGGGGTATTT
28296888 C
1 C
28296889 GAAAATTTTG
Statistics
Matches: 267, Mismatches: 29, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
26 1 0.00
27 266 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (27 bp):
CAGTAATTCTACCCTACAGGGGTATTT
Found at i:28297028 original size:81 final size:81
Alignment explanation
Indices: 28296914--28297337 Score: 614
Period size: 81 Copynumber: 5.2 Consensus size: 81
28296904 CGGGGGTAAA
* ** * * ** * *
28296914 TGGTAATTTTGTAAATTGGGGGTACTTTGGTAATTTTACAAGTCGAGGGTATTTTAGTAATTTTA
1 TGGTAATTTTGTAAACTAAGGGTATTTTAGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTA
28296979 CAAACTAGGGGTATTT
66 CAAACTAGGGGTATTT
*
28296995 TGGTAATTTTGTAAACTAAGGGTATTTTAGTAATTTTACAAACCAAGAGTATTTTGGTAATTTTA
1 TGGTAATTTTGTAAACTAAGGGTATTTTAGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTA
28297060 CAAACTAGGGGTATTT
66 CAAACTAGGGGTATTT
*
28297076 TGGTAATTTTGTAAACTAAGGGTATTTTAGTAATTTTACAAACCAAGGGTATTCTGGTAATTTTA
1 TGGTAATTTTGTAAACTAAGGGTATTTTAGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTA
*
28297141 CAAACCAGGGGTATTT
66 CAAACTAGGGGTATTT
** * * * * * *
28297157 TGGTAATTTTACAATCTAGGGGTATTTTGGTAATTTTATAAACAAAGGGTATTTTAGTAATTTTA
1 TGGTAATTTTGTAAACTAAGGGTATTTTAGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTA
**
28297222 CAAACTAATGGTATTT
66 CAAACTAGGGGTATTT
* * *
28297238 TGGTAATTTTGTAAACCAAGGGTATTTTAGTAATTTTACAAACCAAAGGTATTTTGGTAAATTTA
1 TGGTAATTTTGTAAACTAAGGGTATTTTAGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTA
*
28297303 CAAACCAGGGGTATTT
66 CAAACTAGGGGTATTT
28297319 TGGTAATTTTGTAAACTAA
1 TGGTAATTTTGTAAACTAA
28297338 AGTATTCTAA
Statistics
Matches: 303, Mismatches: 40, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 303 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (81 bp):
TGGTAATTTTGTAAACTAAGGGTATTTTAGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTA
CAAACTAGGGGTATTT
Found at i:28297334 original size:27 final size:27
Alignment explanation
Indices: 28296932--28297328 Score: 454
Period size: 27 Copynumber: 14.7 Consensus size: 27
28296922 TTGTAAATTG
* **
28296932 GGGGTACTTTGGTAATTTTACAAGTC-
1 GGGGTATTTTGGTAATTTTACAAACCA
* *
28296958 GAGGGTATTTTAGTAATTTTACAAACTA
1 G-GGGTATTTTGGTAATTTTACAAACCA
** *
28296986 GGGGTATTTTGGTAATTTTGTAAACTA
1 GGGGTATTTTGGTAATTTTACAAACCA
* *
28297013 AGGGTATTTTAGTAATTTTACAAACCA
1 GGGGTATTTTGGTAATTTTACAAACCA
* * *
28297040 AGAGTATTTTGGTAATTTTACAAACTA
1 GGGGTATTTTGGTAATTTTACAAACCA
** *
28297067 GGGGTATTTTGGTAATTTTGTAAACTA
1 GGGGTATTTTGGTAATTTTACAAACCA
* *
28297094 AGGGTATTTTAGTAATTTTACAAACCA
1 GGGGTATTTTGGTAATTTTACAAACCA
* *
28297121 AGGGTATTCTGGTAATTTTACAAACCA
1 GGGGTATTTTGGTAATTTTACAAACCA
* *
28297148 GGGGTATTTTGGTAATTTTACAATCTA
1 GGGGTATTTTGGTAATTTTACAAACCA
* *
28297175 GGGGTATTTTGGTAATTTTATAAACAA
1 GGGGTATTTTGGTAATTTTACAAACCA
* * *
28297202 AGGGTATTTTAGTAATTTTACAAACTA
1 GGGGTATTTTGGTAATTTTACAAACCA
** **
28297229 ATGGTATTTTGGTAATTTTGTAAACCA
1 GGGGTATTTTGGTAATTTTACAAACCA
* *
28297256 AGGGTATTTTAGTAATTTTACAAACCA
1 GGGGTATTTTGGTAATTTTACAAACCA
** *
28297283 AAGGTATTTTGGTAAATTTACAAACCA
1 GGGGTATTTTGGTAATTTTACAAACCA
28297310 GGGGTATTTTGGTAATTTT
1 GGGGTATTTTGGTAATTTT
28297329 GTAAACTAAA
Statistics
Matches: 316, Mismatches: 53, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
26 1 0.00
27 314 0.99
28 1 0.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (27 bp):
GGGGTATTTTGGTAATTTTACAAACCA
Found at i:28300172 original size:24 final size:26
Alignment explanation
Indices: 28300139--28300187 Score: 75
Period size: 24 Copynumber: 1.9 Consensus size: 26
28300129 TTCGCTAGAG
28300139 AAAAACCAAAAATAAA-AAAATAACC
1 AAAAACCAAAAATAAATAAAATAACC
28300164 AAAAA-CAAAAATAAATTAAAATAA
1 AAAAACCAAAAATAAA-TAAAATAA
28300188 AAAACCAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.45
25 5 0.23
26 7 0.32
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12
Consensus pattern (26 bp):
AAAAACCAAAAATAAATAAAATAACC
Found at i:28301494 original size:30 final size:30
Alignment explanation
Indices: 28301459--28301516 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
28301449 GTGTTAAACC
28301459 ATTTTAATGATTTTGTTTATTTTCATTTCT
1 ATTTTAATGATTTTGTTTATTTTCATTTCT
*
28301489 ATTTTAATGATTTTGTTTGTTTTCATTT
1 ATTTTAATGATTTTGTTTATTTTCATTT
28301517 GTACAATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.19, C:0.05, G:0.09, T:0.67
Consensus pattern (30 bp):
ATTTTAATGATTTTGTTTATTTTCATTTCT
Found at i:28305565 original size:20 final size:20
Alignment explanation
Indices: 28305523--28305566 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
28305513 TATTGTGCCA
*
28305523 TATTTATTGTTGTTGTATAT
1 TATTTATTATTGTTGTATAT
*
28305543 TATTTATTCATTGTTTTAT-T
1 TATTTATT-ATTGTTGTATAT
28305563 TATT
1 TATT
28305567 ATATCAATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.20, C:0.02, G:0.09, T:0.68
Consensus pattern (20 bp):
TATTTATTATTGTTGTATAT
Found at i:28307687 original size:43 final size:42
Alignment explanation
Indices: 28307625--28307717 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
28307615 CCAGATATGA
* * ** *
28307625 TCTTACATGTTATCACATATCAATGCCTTTGTCCTAGACAGGG
1 TCTTACACGTAATCACATAT-AATGCCAATGTCCCAGACAGGG
* * *
28307668 TCTTACACGTAATCTCATATGATGCCAATGTCCCAGACATGG
1 TCTTACACGTAATCACATATAATGCCAATGTCCCAGACAGGG
28307710 TCTTACAC
1 TCTTACAC
28307718 AAAACCACAC
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 25 0.60
43 17 0.40
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (42 bp):
TCTTACACGTAATCACATATAATGCCAATGTCCCAGACAGGG
Found at i:28312497 original size:38 final size:38
Alignment explanation
Indices: 28312436--28312548 Score: 154
Period size: 38 Copynumber: 2.9 Consensus size: 38
28312426 ATTTGATGTG
*
28312436 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGTAAAA
1 TATCCGGG-TTAAA-TCCCGCAGGCTTCGTGCTGGTAAAA
**
28312476 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAAA
* * *
28312514 TATCCGGGATAAATCCCGCAGGCCTAGTGCTGGTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTA
28312549 TTATATTCGG
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
38 54 0.81
39 5 0.07
40 8 0.12
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.26
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAAA
Found at i:28312549 original size:38 final size:38
Alignment explanation
Indices: 28312452--28312559 Score: 162
Period size: 38 Copynumber: 2.8 Consensus size: 38
28312442 GGCTTAAAGA
** *
28312452 CCCGCAGGCTTCGTGCTGGTAAAATATCCGGGTTAAAT
1 CCCGCAGGCTTCGTGCTGGTATTATATCCGGGATAAAT
28312490 CCCGCAGGCTTCGTGCTGGTATTATATCCGGGATAAAT
1 CCCGCAGGCTTCGTGCTGGTATTATATCCGGGATAAAT
* * *
28312528 CCCGCAGGCCTAGTGCTGGTATTATATTCGGG
1 CCCGCAGGCTTCGTGCTGGTATTATATCCGGG
28312560 CCTTCGTGCC
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 64 1.00
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.28
Consensus pattern (38 bp):
CCCGCAGGCTTCGTGCTGGTATTATATCCGGGATAAAT
Found at i:28312676 original size:43 final size:43
Alignment explanation
Indices: 28312552--28312663 Score: 224
Period size: 43 Copynumber: 2.6 Consensus size: 43
28312542 GCTGGTATTA
28312552 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
28312595 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
28312638 TATTCGGGCCTTCGTGCCTAGCAGGC
1 TATTCGGGCCTTCGTGCCTAGCAGGC
28312664 GTAATGCCGG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 69 1.00
ACGTcount: A:0.10, C:0.27, G:0.34, T:0.29
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
Found at i:28325998 original size:24 final size:26
Alignment explanation
Indices: 28325966--28326039 Score: 89
Period size: 27 Copynumber: 2.9 Consensus size: 26
28325956 GTTGGTCATT
* *
28325966 AAAGCATAACGCATGAATAAAT-A-C
1 AAAGAATAATGCATGAATAAATGACC
* *
28325990 AAAGAATAATGCATGAACAAGTTGACC
1 AAAGAATAATGCATGAATAA-ATGACC
28326017 AAAGAATAATGCATGAATAAATG
1 AAAGAATAATGCATGAATAAATG
28326040 CAATGTTAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
24 17 0.41
25 1 0.02
26 3 0.07
27 20 0.49
ACGTcount: A:0.53, C:0.12, G:0.16, T:0.19
Consensus pattern (26 bp):
AAAGAATAATGCATGAATAAATGACC
Found at i:28327248 original size:38 final size:38
Alignment explanation
Indices: 28327203--28327304 Score: 129
Period size: 37 Copynumber: 2.7 Consensus size: 38
28327193 GGCTTAAAGA
* *
28327203 CCCGCAGGCTATATGCTGGAATTATATCCGGGATAAAT
1 CCCGCAGGCTATATGCTGGTATTATATCCAGGATAAAT
* *
28327241 CCCGCAGGCT-TCGTGCT-GTATTATATCCAGGTTAAAT
1 CCCGCAGGCTAT-ATGCTGGTATTATATCCAGGATAAAT
28327278 CCCGCAGGCCTA-ATGCTGGTATTATAT
1 CCCGCAGG-CTATATGCTGGTATTATAT
28327305 TTGAGCTTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
37 30 0.55
38 25 0.45
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.29
Consensus pattern (38 bp):
CCCGCAGGCTATATGCTGGTATTATATCCAGGATAAAT
Found at i:28345134 original size:27 final size:26
Alignment explanation
Indices: 28345112--28345163 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
28345102 AAAGCCCGTT
* *
28345112 ACAATATCATTTGGGTCATAGCCCATA
1 ACAAAATCAATTGGG-CATAGCCCATA
*
28345139 ACAAAATCAATTGGGCCTAGCCCAT
1 ACAAAATCAATTGGGCATAGCCCAT
28345164 CTTAGCCTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (26 bp):
ACAAAATCAATTGGGCATAGCCCATA
Found at i:28345733 original size:27 final size:27
Alignment explanation
Indices: 28345659--28345908 Score: 134
Period size: 27 Copynumber: 9.3 Consensus size: 27
28345649 GGCAAAACTC
* * ** *
28345659 ATTTTACCCTACAGGGGTATGCCGGTC
1 ATTTTACACTACAAGGGTATTTCGGTA
28345686 ATTTTACACTACAAGGGTATTTCGGTA
1 ATTTTACACTACAAGGGTATTTCGGTA
** *
28345713 ATTTTATGCTACAAGGGTATTTCGATA
1 ATTTTACACTACAAGGGTATTTCGGTA
* * * *
28345740 ATTTTACA-AATCAGGGGTGTTTTGGTA
1 ATTTTACACTA-CAAGGGTATTTCGGTA
* * *
28345767 ATTTTACA-AATCGAGGGTATTTAGGTA
1 ATTTTACACTA-CAAGGGTATTTCGGTA
* * *
28345794 ATTTTACA-AATTAAGGGTATTTCGATA
1 ATTTTACACTA-CAAGGGTATTTCGGTA
* * * *
28345821 ATTTTACA-AATCGATGGTGTTTCGGTA
1 ATTTTACACTA-CAAGGGTATTTCGGTA
* * **
28345848 ATTTTACA-AATCGAGGGTATTTTAGTA
1 ATTTTACACTA-CAAGGGTATTTCGGTA
* * ** *
28345875 ATTTCACAAT-TGAGGGTATTTTGGTA
1 ATTTTACACTACAAGGGTATTTCGGTA
28345901 ATTTTACA
1 ATTTTACA
28345909 AATCGAAGGT
Statistics
Matches: 184, Mismatches: 37, Indels: 5
0.81 0.16 0.02
Matches are distributed among these distances:
26 22 0.12
27 162 0.88
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.39
Consensus pattern (27 bp):
ATTTTACACTACAAGGGTATTTCGGTA
Found at i:28345794 original size:81 final size:80
Alignment explanation
Indices: 28345699--28346040 Score: 354
Period size: 80 Copynumber: 4.2 Consensus size: 80
28345689 TTACACTACA
* * * *
28345699 AGGGTATTTCGGTAATTTTATGCTA-CAAGGGTATTTCGATAATTTTACAAATC-AGGGGTGTTT
1 AGGGTATTTAGGTAATTTTA--CAATTAAGGGTATTTCGATAATTTTACAAATCGA-AGGTGTTT
*
28345762 TGGTAATTTTACAAATCG
63 CGGTAATTTTACAAATCG
*
28345780 AGGGTATTTAGGTAATTTTACAAATTAAGGGTATTTCGATAATTTTACAAATCGATGGTGTTTCG
1 AGGGTATTTAGGTAATTTTAC-AATTAAGGGTATTTCGATAATTTTACAAATCGAAGGTGTTTCG
28345845 GTAATTTTACAAATCG
65 GTAATTTTACAAATCG
* * * *
28345861 AGGGTATTTTA-GTAATTTCACAATTGAGGGTATTTTGGTAATTTTACAAATCGAAGGTGTTTCG
1 AGGGTA-TTTAGGTAATTTTACAATTAAGGGTATTTCGATAATTTTACAAATCGAAGGTGTTTCG
* * *
28345925 ATAATTTCACAAATTG
65 GTAATTTTACAAATCG
* * * * * * * *
28345941 AGGGTATTTCGATAATTTTACAAATTGAA-AGTATTT-TAGTAATTTCAC-AATTGAGGGTATTT
1 AGGGTATTTAGGTAATTTTAC-AATT-AAGGGTATTTCGA-TAATTTTACAAATCGAAGGTGTTT
*
28346003 CGATAATTTTACAAATCG
63 CGGTAATTTTACAAATCG
* *
28346021 AGGGTGTTTCGGTAATTTTA
1 AGGGTATTTAGGTAATTTTA
28346041 TAAATCAAAG
Statistics
Matches: 225, Mismatches: 28, Indels: 17
0.83 0.10 0.06
Matches are distributed among these distances:
79 4 0.02
80 112 0.50
81 103 0.46
82 6 0.03
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (80 bp):
AGGGTATTTAGGTAATTTTACAATTAAGGGTATTTCGATAATTTTACAAATCGAAGGTGTTTCGG
TAATTTTACAAATCG
Found at i:28345928 original size:107 final size:107
Alignment explanation
Indices: 28345728--28346065 Score: 421
Period size: 107 Copynumber: 3.1 Consensus size: 107
28345718 ATGCTACAAG
* * * *
28345728 GGTATTTCGATAATTTTACAAATC-AGGGGTGTTTTGGTAATTTTACAAATCGAGGGTATTTAGG
1 GGTATTTCGATAATTTTACAAATCGA-GGGTATTTTAGTAATTTCAC-AATTGAGGGTATTTAGG
* * *
28345792 TAATTTTACAAAT-TAAGGGTATTTCGATAATTTTACAAATCGAT
64 TAATTTTACAAATCGAA-GGTGTTTCGATAATTTTACAAATCGAA
* * *
28345836 GGTGTTTCGGTAATTTTACAAATCGAGGGTATTTTAGTAATTTCACAATTGAGGGTATTTTGGTA
1 GGTATTTCGATAATTTTACAAATCGAGGGTATTTTAGTAATTTCACAATTGAGGGTATTTAGGTA
* * *
28345901 ATTTTACAAATCGAAGGTGTTTCGATAATTTCACAAATTGAG
66 ATTTTACAAATCGAAGGTGTTTCGATAATTTTACAAATCGAA
* ** * *
28345943 GGTATTTCGATAATTTTACAAATTGAAAGTATTTTAGTAATTTCACAATTGAGGGTATTTCGATA
1 GGTATTTCGATAATTTTACAAATCGAGGGTATTTTAGTAATTTCACAATTGAGGGTATTTAGGTA
* * * *
28346008 ATTTTACAAATCGAGGGTGTTTCGGTAATTTTATAAATCAAA
66 ATTTTACAAATCGAAGGTGTTTCGATAATTTTACAAATCGAA
28346050 GGTATTTC-AGTAATTT
1 GGTATTTCGA-TAATTT
28346066 CACTTTATTA
Statistics
Matches: 201, Mismatches: 26, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
106 1 0.00
107 158 0.79
108 41 0.20
109 1 0.00
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (107 bp):
GGTATTTCGATAATTTTACAAATCGAGGGTATTTTAGTAATTTCACAATTGAGGGTATTTAGGTA
ATTTTACAAATCGAAGGTGTTTCGATAATTTTACAAATCGAA
Found at i:28345930 original size:27 final size:27
Alignment explanation
Indices: 28345726--28346065 Score: 332
Period size: 27 Copynumber: 12.7 Consensus size: 27
28345716 TTATGCTACA
28345726 AGGGTATTTCGATAATTTTACAAATC-
1 AGGGTATTTCGATAATTTTACAAATCG
* * *
28345752 AGGGGTGTTTTGGTAATTTTACAAATCG
1 A-GGGTATTTCGATAATTTTACAAATCG
* * **
28345780 AGGGTATTTAGGTAATTTTACAAATTA
1 AGGGTATTTCGATAATTTTACAAATCG
28345807 AGGGTATTTCGATAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
* * *
28345834 ATGGTGTTTCGGTAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
* * *
28345861 AGGGTATTT-TAGTAATTTCAC-AATTG
1 AGGGTATTTCGA-TAATTTTACAAATCG
* *
28345887 AGGGTATTTTGGTAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
* * * *
28345914 AAGGTGTTTCGATAATTTCACAAATTG
1 AGGGTATTTCGATAATTTTACAAATCG
*
28345941 AGGGTATTTCGATAATTTTACAAATTG
1 AGGGTATTTCGATAATTTTACAAATCG
** * * *
28345968 AAAGTATTT-TAGTAATTTCAC-AATTG
1 AGGGTATTTCGA-TAATTTTACAAATCG
28345994 AGGGTATTTCGATAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
* * * *
28346021 AGGGTGTTTCGGTAATTTTATAAATCA
1 AGGGTATTTCGATAATTTTACAAATCG
*
28346048 AAGGTATTTC-AGTAATTT
1 AGGGTATTTCGA-TAATTT
28346066 CACTTTATTA
Statistics
Matches: 256, Mismatches: 49, Indels: 17
0.80 0.15 0.05
Matches are distributed among these distances:
26 43 0.17
27 212 0.83
28 1 0.00
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (27 bp):
AGGGTATTTCGATAATTTTACAAATCG
Found at i:28346426 original size:28 final size:28
Alignment explanation
Indices: 28346395--28346468 Score: 130
Period size: 28 Copynumber: 2.6 Consensus size: 28
28346385 CCCAATTTCG
*
28346395 TTCACATGGCCCATCAGGCCCAACCACA
1 TTCATATGGCCCATCAGGCCCAACCACA
*
28346423 TTCATATGGCCCATCAGGCCCAATCACA
1 TTCATATGGCCCATCAGGCCCAACCACA
28346451 TTCATATGGCCCATCAGG
1 TTCATATGGCCCATCAGG
28346469 AGCAACTACT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.27, C:0.36, G:0.16, T:0.20
Consensus pattern (28 bp):
TTCATATGGCCCATCAGGCCCAACCACA
Found at i:28351635 original size:50 final size:51
Alignment explanation
Indices: 28351489--28351696 Score: 165
Period size: 50 Copynumber: 4.2 Consensus size: 51
28351479 GCTAAATGAC
* * * * * * * * *
28351489 CTTGAATATTCGACCACATAGGTTTGTACATATATGATTTTATA-TTGGAT
1 CTTGTATATTCGGCCATATAAGTATGCACATATGTGATATTATATTTGAAT
* * * *
28351539 CTTGTATATTCGGCTATA-AAGGTATGCACAAATGTCATATTGTATTTGAAT
1 CTTGTATATTCGGCCATATAA-GTATGCACATATGTGATATTATATTTGAAT
* * * *
28351590 -TTGTATATTCAGCCATATAAGTAAGCACATATGTGATGTTATATTT-TAT
1 CTTGTATATTCGGCCATATAAGTATGCACATATGTGATATTATATTTGAAT
* * * * * *
28351639 CTTGCATATTTGGCCACATATGTATGCATATATGTGATATTATA-TTGGAT
1 CTTGTATATTCGGCCATATAAGTATGCACATATGTGATATTATATTTGAAT
28351689 CTTGTATA
1 CTTGTATA
28351697 CTTAGCCAAA
Statistics
Matches: 122, Mismatches: 31, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
49 5 0.04
50 110 0.90
51 7 0.06
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (51 bp):
CTTGTATATTCGGCCATATAAGTATGCACATATGTGATATTATATTTGAAT
Found at i:28360534 original size:50 final size:50
Alignment explanation
Indices: 28360443--28360620 Score: 123
Period size: 50 Copynumber: 3.6 Consensus size: 50
28360433 CATATATGAT
* ** *
28360443 GTTATATTGGATCTTGTATATTCAGGTATAAAGGTATGCACAAATGTGAC
1 GTTATATTGAATCTTGTATATTCAGCCATAAAGGTAAGCACAAATGTGAC
* *
28360493 GTTATATTTGAAT-TTGTATATTCAGCCATATAA-GTAAGCACATATGTGAT
1 GTTATA-TTGAATCTTGTATATTCAGCCATA-AAGGTAAGCACAAATGTGAC
* ** * * ** * * *
28360543 GTTAGGT-TTG-ATCTTGCATATTTGGCCACATAGGTGTGCATATATGTGAT
1 GTTA--TATTGAATCTTGTATATTCAGCCATAAAGGTAAGCACAAATGTGAC
*
28360593 ATTATATTTG-ATCTTGTATATTCAGCCA
1 GTTATA-TTGAATCTTGTATATTCAGCCA
28360621 AATGAGTGAT
Statistics
Matches: 102, Mismatches: 18, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
48 1 0.01
49 3 0.03
50 90 0.88
51 7 0.07
52 1 0.01
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (50 bp):
GTTATATTGAATCTTGTATATTCAGCCATAAAGGTAAGCACAAATGTGAC
Done.