Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 158 of 202
Found at i:49380479 original size:21 final size:21
Alignment explanation
Indices: 49380440--49380480 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
49380430 TAGAAACAGG
* **
49380440 AATGATCTTAATGGCAATCCA
1 AATGATCATAATGAAAATCCA
49380461 AATGATCATAATGAAAATCC
1 AATGATCATAATGAAAATCC
49380481 TCTCATTAGA
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:0.44, C:0.17, G:0.12, T:0.27
Consensus pattern (21 bp):
AATGATCATAATGAAAATCCA
Found at i:49383508 original size:93 final size:93
Alignment explanation
Indices: 49383349--49383537 Score: 342
Period size: 93 Copynumber: 2.0 Consensus size: 93
49383339 GGTAAGGCAT
*
49383349 TTTATTGCTTCCTAGATGCTTATTCAGGATATAATCAAATTTCTATAGCACTTGAAGATCAAGAG
1 TTTATTGCTTCCTAGATGCTTATTCAGGATATAATCAAATTTCTATAGCACTTAAAGATCAAGAG
*
49383414 AAAATAACTTTCACGTGTCCATATGGTA
66 AAAACAACTTTCACGTGTCCATATGGTA
*
49383442 TTTATTGCTTCCTAGATGGTTATTCAGGATATAATCAAATTTCTATAGCACTTAAAGATCAAGAG
1 TTTATTGCTTCCTAGATGCTTATTCAGGATATAATCAAATTTCTATAGCACTTAAAGATCAAGAG
*
49383507 AAGACAACTTTCACGTGTCCATATGGTA
66 AAAACAACTTTCACGTGTCCATATGGTA
49383535 TTT
1 TTT
49383538 TTCTATTCAG
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (93 bp):
TTTATTGCTTCCTAGATGCTTATTCAGGATATAATCAAATTTCTATAGCACTTAAAGATCAAGAG
AAAACAACTTTCACGTGTCCATATGGTA
Found at i:49388406 original size:16 final size:16
Alignment explanation
Indices: 49388376--49388407 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
49388366 CGGTTTCCAT
49388376 TAAAAAAAGGAAAAAA
1 TAAAAAAAGGAAAAAA
49388392 TAAAGAAAAGGAAAAA
1 TAAA-AAAAGGAAAAA
49388408 GGAGAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (16 bp):
TAAAAAAAGGAAAAAA
Found at i:49390493 original size:2 final size:2
Alignment explanation
Indices: 49390486--49390521 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
49390476 TTCTTAGGAT
49390486 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
49390522 GTCCTGAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:49410801 original size:152 final size:152
Alignment explanation
Indices: 49410525--49410821 Score: 594
Period size: 152 Copynumber: 2.0 Consensus size: 152
49410515 CTTACCATAG
49410525 AAATTTTAGAATTTTTGGTCTAGCCAATTAATACATTTTATTCATTAAATAATCCTCTATTTCAC
1 AAATTTTAGAATTTTTGGTCTAGCCAATTAATACATTTTATTCATTAAATAATCCTCTATTTCAC
49410590 TGCTTGATAGCTCTGACCCCTCTTCACTAAAAATTAATTATCTCTTTGCACAGAATTCAAATGAT
66 TGCTTGATAGCTCTGACCCCTCTTCACTAAAAATTAATTATCTCTTTGCACAGAATTCAAATGAT
49410655 GTCCCTATTTGTTTCATGCACA
131 GTCCCTATTTGTTTCATGCACA
49410677 AAATTTTAGAATTTTTGGTCTAGCCAATTAATACATTTTATTCATTAAATAATCCTCTATTTCAC
1 AAATTTTAGAATTTTTGGTCTAGCCAATTAATACATTTTATTCATTAAATAATCCTCTATTTCAC
49410742 TGCTTGATAGCTCTGACCCCTCTTCACTAAAAATTAATTATCTCTTTGCACAGAATTCAAATGAT
66 TGCTTGATAGCTCTGACCCCTCTTCACTAAAAATTAATTATCTCTTTGCACAGAATTCAAATGAT
49410807 GTCCCTATTTGTTTC
131 GTCCCTATTTGTTTC
49410822 TCTTGAAAAT
Statistics
Matches: 145, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
152 145 1.00
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (152 bp):
AAATTTTAGAATTTTTGGTCTAGCCAATTAATACATTTTATTCATTAAATAATCCTCTATTTCAC
TGCTTGATAGCTCTGACCCCTCTTCACTAAAAATTAATTATCTCTTTGCACAGAATTCAAATGAT
GTCCCTATTTGTTTCATGCACA
Found at i:49411324 original size:45 final size:45
Alignment explanation
Indices: 49411255--49411444 Score: 163
Period size: 45 Copynumber: 4.2 Consensus size: 45
49411245 TACACGGTGG
* *
49411255 ATCAGCACACAGC-ACCACAC-TTATAGTCAATAGTACTC-GGTGAA
1 ATCAGCACATAGCAACCAC-CTTTATAATCAATAGTA-TCGGGTGAA
* * *
49411299 ATCAGCACATAGCAACCACCTTTATACTCAATGGTACCGGGTGAA
1 ATCAGCACATAGCAACCACCTTTATAATCAATAGTATCGGGTGAA
* * * * * *
49411344 TTCAGCACATAGCAATCA-CTTATATAACCATTGGTATCCGGTGAA
1 ATCAGCACATAGCAACCACCTT-TATAATCAATAGTATCGGGTGAA
* ** * * * *
49411389 ATCAGCACATAGCAATCACCTTTATTTTCATTAATATCTGGTGGA
1 ATCAGCACATAGCAACCACCTTTATAATCAATAGTATCGGGTGAA
49411434 ATCAGCACATA
1 ATCAGCACATA
49411445 ACATCCATCT
Statistics
Matches: 122, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
44 17 0.14
45 102 0.84
46 3 0.02
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.26
Consensus pattern (45 bp):
ATCAGCACATAGCAACCACCTTTATAATCAATAGTATCGGGTGAA
Found at i:49415714 original size:2 final size:2
Alignment explanation
Indices: 49415707--49415739 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
49415697 GCTGATACTG
49415707 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
49415740 AGATTTTCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49421373 original size:98 final size:98
Alignment explanation
Indices: 49421199--49421395 Score: 322
Period size: 98 Copynumber: 2.0 Consensus size: 98
49421189 GTATAATAAA
* *
49421199 ACTTAAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATATGTTAGGGCACGATT
1 ACTTAAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
* * *
49421264 CCTCTAGAATCCCAAACTTGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCATTT
* *
49421297 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTAAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
*
49421362 CCTTTAAAATCCCAAACTCGGAATATTTCATTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCATTT
49421395 A
1 A
49421396 TTATTTTTAA
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
98 91 1.00
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.28
Consensus pattern (98 bp):
ACTTAAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTCTAAAATCCCAAACTCGGAATATTTCATTT
Found at i:49421944 original size:27 final size:24
Alignment explanation
Indices: 49421913--49421964 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 24
49421903 TACAACACAT
49421913 AATATAATTATGAAAATAAGGAAAAAA
1 AATAT-ATT-TGAAAA-AAGGAAAAAA
*
49421940 AATATATTTTAAAAAAGGAAAAAA
1 AATATATTTGAAAAAAGGAAAAAA
49421964 A
1 A
49421965 GGTGAGTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 11 0.46
25 5 0.21
26 3 0.12
27 5 0.21
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (24 bp):
AATATATTTGAAAAAAGGAAAAAA
Found at i:49422040 original size:23 final size:24
Alignment explanation
Indices: 49422012--49422058 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
49422002 ATATATATAT
49422012 GAAAATATTC-ATTTAAAAAAAAG
1 GAAAATATTCGATTTAAAAAAAAG
*
49422035 GAAAATATTCGTTTTTAAAAAAAA
1 GAAAATATTCG-ATTTAAAAAAAA
49422059 TATATATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.48
25 11 0.52
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (24 bp):
GAAAATATTCGATTTAAAAAAAAG
Found at i:49422720 original size:19 final size:19
Alignment explanation
Indices: 49422696--49422768 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
49422686 AATCATATAT
49422696 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
** *
49422715 TCTAAGATTATATATCATC
1 TCTAAGATTGCATATCATA
**
49422734 TCTTGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
49422753 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
49422769 CTCAAAAATT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:49423079 original size:44 final size:44
Alignment explanation
Indices: 49423018--49423545 Score: 261
Period size: 44 Copynumber: 12.2 Consensus size: 44
49423008 ACTAGATGCG
* * *
49423018 ATCTGCT-CTCTGTAACTTCAGAGAGATAAGATTTGTAATTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAATTTTA
* * * ***
49423061 ATCCGCTCCACTGTAACTTCAGGGAGATAGGA-TTGTCGGCTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGT-AATTTTA
* * * ** *
49423105 ATCTGCTCTACTGCAACTTTAGGAAGATAAGATTTGCCATCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAAT-TTTA
* * * * *
49423150 GTCTGC-CTCACTGTAACTTCA-GGAGGATAAGACTTGCTTA-CTTA
1 ATCTGCTC-CACTGCAACTTCAGGGA-GATAAGATTTG-TAATTTTA
* * * ***
49423194 GTAT-TG-TCCACCGCAACTTCAGGGAGATAAGACTAG--A-TGCG
1 --ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAATTTTA
* * * *
49423235 ATCTGCT-CTCTGTAACTTCAGAGAGATAAGATCTGTAATTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAATTTTA
* * ***
49423278 ATCCGCTCCACTGCAACTTCAGGGAGATATGA-TTGTCGGCTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGT-AATTTTA
* ** *
49423322 ATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAAT-TTTA
* * * * * *
49423367 GTCTGC-CTCACTGTAACTTTA-GAAGGATAAGACTTGCTAA-CTTA
1 ATCTGCTC-CACTGCAACTTCAGGGA-GATAAGATTTG-TAATTTTA
* * * ***
49423411 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAG--A-TGCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAATTTTA
* * * *
49423452 ATTTGCT-CTCTGCAACTTCAGAGG-GATAAGATCTGTGATTTTA
1 ATCTGCTCCACTGCAACTTCAG-GGAGATAAGATTTGTAATTTTA
* * *
49423495 ATCCGCTCCACTGCAACTTCAGGGAGATAGGA-TTGTCAACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGT-AATTTTA
49423539 ATCTGCT
1 ATCTGCT
49423546 TCCCACTATC
Statistics
Matches: 357, Mismatches: 96, Indels: 63
0.69 0.19 0.12
Matches are distributed among these distances:
39 2 0.01
40 44 0.12
41 10 0.03
42 2 0.01
43 31 0.09
44 193 0.54
45 72 0.20
46 3 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAATTTTA
Found at i:49423355 original size:217 final size:216
Alignment explanation
Indices: 49422980--49423545 Score: 961
Period size: 217 Copynumber: 2.6 Consensus size: 216
49422970 TGCTTCAATC
*
49422980 TTGTCCACCGCAACTTTAGGGAGATAAGACTAGATGCGATCTGCTCTCTGTAACTTCAGAGAGAT
1 TTGTCCACCGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGTAACTTCAGAGAGAT
* *
49423045 AAGATTTGTAATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTGTCGGCTTTAATCTG
66 AAGATCTGTAATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGTCGGCTTTAATCTG
* * *
49423110 CTCTACTGCAACTTTAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGTAACTTCAGGAG
131 CTCCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGTAACTTCAGAAG
*
49423175 GATAAGACTTGCTTACTTAGT
196 GATAAGACTTGCTAACTTAGT
49423196 ATTGTCCACCGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGTAACTTCAGAGAGA
1 -TTGTCCACCGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGTAACTTCAGAGAGA
*
49423261 TAAGATCTGTAATTTTAATCCGCTCCACTGCAACTTCAGGGAGATATGATTGTCGGCTTTAATCT
65 TAAGATCTGTAATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGTCGGCTTTAATCT
*
49423326 GCTCCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGTAACTTTAGAA
130 GCTCCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGTAACTTCAGAA
49423391 GGATAAGACTTGCTAACTTAGT
195 GGATAAGACTTGCTAACTTAGT
* * * * *
49423413 CTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATTTGCTCTCTGCAACTTCAGAGGGA
1 TTG-TCCACCGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGTAACTTCAGAGAGA
* **
49423478 TAAGATCTGTGATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGTCAACTTTAATCT
65 TAAGATCTGTAATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGTCGGCTTTAATCT
49423543 GCT
130 GCT
49423546 TCCCACTATC
Statistics
Matches: 330, Mismatches: 18, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
216 2 0.01
217 328 0.99
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (216 bp):
TTGTCCACCGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGTAACTTCAGAGAGAT
AAGATCTGTAATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGTCGGCTTTAATCTG
CTCCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGTAACTTCAGAAG
GATAAGACTTGCTAACTTAGT
Found at i:49423616 original size:44 final size:44
Alignment explanation
Indices: 49423568--49423746 Score: 125
Period size: 44 Copynumber: 4.1 Consensus size: 44
49423558 GGAAATATAT
* *
49423568 GATTTGTCGTATTCGATCTGCTCCACTACTGCTTAGGGAGATAA
1 GATTTGTCGTCTTCAATCTGCTCCACTACTGCTTAGGGAGATAA
* * * * * * * * *
49423612 GATTT-ACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAAACAA
1 GATTTGTC-GTCTTCAATCTGCTCCACTACTGCTTAGGGAGATAA
* * * * *
49423656 GGCTTGGT-GGCTTAAATCTGCTTCCCACTA-T-CTT-GGAAAGATAA
1 -GATTTGTCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-GAGATAA
*
49423700 GATTTGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAA
1 GATTTGTCGTCTTCAATCTGCTCCACTACTGCTTAGGGAGATAA
49423744 GAT
1 GAT
49423747 CTACAATTTT
Statistics
Matches: 94, Mismatches: 31, Indels: 20
0.65 0.21 0.14
Matches are distributed among these distances:
42 6 0.06
43 10 0.11
44 67 0.71
45 7 0.07
46 4 0.04
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (44 bp):
GATTTGTCGTCTTCAATCTGCTCCACTACTGCTTAGGGAGATAA
Found at i:49423689 original size:132 final size:132
Alignment explanation
Indices: 49423538--49423993 Score: 716
Period size: 132 Copynumber: 3.5 Consensus size: 132
49423528 TGTCAACTTT
* * * *
49423538 AATCTGCTTCCCACTATCTTGGAAATATATGATTTGTCGTATTCGATCTGCTCCACTACTGCTTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTA
* * * *
49423603 GGGAGATAAGATTTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAAACAAGGCTTGGTGGCT
66 GGGAGATAAGATCTACAATTTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCT
49423668 TA
131 TA
*
49423670 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTA
49423735 GGGAGATAAGATCTACAATTTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCT
66 GGGAGATAAGATCTACAATTTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCT
49423800 TA
131 TA
* * ** * *
49423802 AATCTGCTTCCCAATATCTTGGAAATATAAGATTCACCGTCTTTGATATGCTCCACTACTGCTTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTA
* * *
49423867 GGGAGATAAAATCTACAATTTTCAACCTTCTTCGCTACTGCTCAGGGAGACAAGGCTTGGTGGCT
66 GGGAGATAAGATCTACAATTTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCT
49423932 TA
131 TA
* *
49423934 AATTTGCTTCCCACTATCTTGGATAGATAAGATTCG-CTGTCTTCGATCTGCTCCACTACT
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGTC-GTCTTCGATCTGCTCCACTACT
49423994 TACAATCTTC
Statistics
Matches: 299, Mismatches: 24, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
131 1 0.00
132 298 1.00
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (132 bp):
AATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTA
GGGAGATAAGATCTACAATTTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCT
TA
Found at i:49423828 original size:264 final size:246
Alignment explanation
Indices: 49423538--49424136 Score: 822
Period size: 264 Copynumber: 2.4 Consensus size: 246
49423528 TGTCAACTTT
* * *
49423538 AATCTGCTTCCCACTATCTTGGAAATATATGATTTGTCGTATTCGATCTGCTCCACTACTGCTTA
1 AATCTGCTTCCCACTATCTTGGAAATATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTA
* * *
49423603 GGGAGATAAGATTTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAAACAAGGCTTGGTGGCT
66 GGGAGATAAGATCTACAATTTTCAACCTACTCCGCTACTGCTCAGGGAAACAAGGCTTGGTGGCT
*
49423668 TAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTG-TCGTCTTCGATCTGCTCCACTACTGC
131 TAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCT-GTCTTCGATCTGCTCCACTA---C
*
49423732 TTAGGGAGATAAGATCTACAATTTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTG
192 --------------T-TACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTG
49423797 GCTTA
242 GCTTA
* ** * *
49423802 AATCTGCTTCCCAATATCTTGGAAATATAAGATTCACCGTCTTTGATATGCTCCACTACTGCTTA
1 AATCTGCTTCCCACTATCTTGGAAATATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTA
* * * *
49423867 GGGAGATAAAATCTACAATTTTCAACCTTCTTCGCTACTGCTCAGGGAGACAAGGCTTGGTGGCT
66 GGGAGATAAGATCTACAATTTTCAACCTACTCCGCTACTGCTCAGGGAAACAAGGCTTGGTGGCT
* *
49423932 TAAATTTGCTTCCCACTATCTTGGATAGATAAGATTCGCTGTCTTCGATCTGCTCCACTACTTAC
131 TAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCTGTCTTCGATCTGCTCCACTACTTAC
49423997 AATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTA
196 AATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTA
* * *
49424048 AATTTGCTTCCCACTATCTTGGAAAGATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGTTTA
1 AATCTGCTTCCCACTATCTTGGAAATATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTA
49424113 GGGAGATAAGATCTACAATTTTCA
66 GGGAGATAAGATCTACAATTTTCA
49424137 CTGATCTGTT
Statistics
Matches: 306, Mismatches: 28, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
246 133 0.43
247 1 0.00
261 1 0.00
264 170 0.56
265 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (246 bp):
AATCTGCTTCCCACTATCTTGGAAATATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTA
GGGAGATAAGATCTACAATTTTCAACCTACTCCGCTACTGCTCAGGGAAACAAGGCTTGGTGGCT
TAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCTGTCTTCGATCTGCTCCACTACTTAC
AATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTA
Found at i:49424080 original size:114 final size:114
Alignment explanation
Indices: 49423880--49424107 Score: 404
Period size: 114 Copynumber: 2.0 Consensus size: 114
49423870 AGATAAAATC
* *
49423880 TACAATTTTCAACCTTCTTCGCTACTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATTTGCTTCC
1 TACAATCTTCAACCTTCTCCGCTACTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATTTGCTTCC
*
49423945 CACTATCTTGGATAGATAAGATTCG-CTGTCTTCGATCTGCTCCACTACT
66 CACTATCTTGGAAAGATAAGATTCGTC-GTCTTCGATCTGCTCCACTACT
*
49423994 TACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATTTGCTTCC
1 TACAATCTTCAACCTTCTCCGCTACTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATTTGCTTCC
49424059 CACTATCTTGGAAAGATAAGATTCGTCGTCTTCGATCTGCTCCACTACT
66 CACTATCTTGGAAAGATAAGATTCGTCGTCTTCGATCTGCTCCACTACT
49424108 GTTTAGGGAG
Statistics
Matches: 109, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
114 108 0.99
115 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (114 bp):
TACAATCTTCAACCTTCTCCGCTACTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATTTGCTTCC
CACTATCTTGGAAAGATAAGATTCGTCGTCTTCGATCTGCTCCACTACT
Found at i:49425370 original size:20 final size:20
Alignment explanation
Indices: 49425342--49425384 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
49425332 TTGCCTCTCC
*
49425342 TTTTACTTTTACTTTTACTT
1 TTTTACTTTTACCTTTACTT
* *
49425362 TTTTCCTTTTTCCTTTACTT
1 TTTTACTTTTACCTTTACTT
49425382 TTT
1 TTT
49425385 CCTCTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTACTTTTACCTTTACTT
Found at i:49425377 original size:21 final size:21
Alignment explanation
Indices: 49425348--49425393 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
49425338 CTCCTTTTAC
*
49425348 TTTTACTTTTACTTTTTTC-CT
1 TTTTAC-TTTACTTTTTCCTCT
*
49425369 TTTTCCTTTACTTTTTCCTCT
1 TTTTACTTTACTTTTTCCTCT
49425390 TTTT
1 TTTT
49425394 TTTTTGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTACTTTACTTTTTCCTCT
Found at i:49429651 original size:98 final size:98
Alignment explanation
Indices: 49429477--49429673 Score: 331
Period size: 98 Copynumber: 2.0 Consensus size: 98
49429467 GTACAATAAA
* * *
49429477 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAACCACACCCAATACGTTAGAGCACAATT
*
49429542 CCTCTAGAATCCCAAACTCAGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCAGAATATTTCCTTT
*
49429575 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAACCACACCCAATACGTTAGAGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAACCACACCCAATACGTTAGAGCACAATT
* *
49429640 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCAGAATATTTCCTTT
49429673 A
1 A
49429674 TTATTTTTAA
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 92 1.00
ACGTcount: A:0.38, C:0.26, G:0.09, T:0.27
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAACCACACCCAATACGTTAGAGCACAATT
CCTCTAAAATCCCAAACTCAGAATATTTCCTTT
Found at i:49430992 original size:19 final size:19
Alignment explanation
Indices: 49430965--49431039 Score: 105
Period size: 19 Copynumber: 3.8 Consensus size: 19
49430955 AAATTAAATC
*
49430965 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
49430984 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
**
49431005 TCTTGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
49431024 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
49431040 CTCAAAAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 32 0.65
21 17 0.35
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:49431000 original size:21 final size:21
Alignment explanation
Indices: 49430976--49431038 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
49430966 CTAGGATTGC
49430976 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
**
49430997 ATATCATATCTTGGATTGC--
1 ATATCATATCTAAGATTGCAT
49431016 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
49431037 AT
1 AT
49431039 CCTCAAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 17 0.47
21 19 0.53
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:49437122 original size:19 final size:19
Alignment explanation
Indices: 49437098--49437140 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
49437088 CGATTTAATT
49437098 TTGGATATAATTGAATATC
1 TTGGATATAATTGAATATC
*
49437117 TTGGATATGATTGAATATC
1 TTGGATATAATTGAATATC
49437136 TTGGA
1 TTGGA
49437141 AATGATTGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.42
Consensus pattern (19 bp):
TTGGATATAATTGAATATC
Found at i:49437145 original size:19 final size:19
Alignment explanation
Indices: 49437107--49437148 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
49437097 TTTGGATATA
*
49437107 ATTGAATATCTTGGATATG
1 ATTGAATATCTTGGAAATG
49437126 ATTGAATATCTTGGAAATG
1 ATTGAATATCTTGGAAATG
49437145 ATTG
1 ATTG
49437149 TAATTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.40
Consensus pattern (19 bp):
ATTGAATATCTTGGAAATG
Found at i:49440575 original size:44 final size:44
Alignment explanation
Indices: 49440508--49440686 Score: 279
Period size: 44 Copynumber: 4.1 Consensus size: 44
49440498 GTAGATAAAA
* *
49440508 TAATATTAAAATAACCTACACTAATTAGAGTTTAAATGAGAAAC
1 TAATATTAAAATAACCTACACTAATCAAAGTTTAAATGAGAAAC
* * *
49440552 TAATATTAAAATAACCTATACTAATCAGAGTTTAAATGGGAAAC
1 TAATATTAAAATAACCTACACTAATCAAAGTTTAAATGAGAAAC
*
49440596 TAATATTAAAATAACCTACAATAATCAAAGTTTAAAT-AGGAAAC
1 TAATATTAAAATAACCTACACTAATCAAAGTTTAAATGA-GAAAC
*
49440640 TAATATTAAAATAACCTACACTAATCAAAGTTTAAGTGAGAAAC
1 TAATATTAAAATAACCTACACTAATCAAAGTTTAAATGAGAAAC
49440684 TAA
1 TAA
49440687 AAACAGAGTT
Statistics
Matches: 124, Mismatches: 9, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
44 123 0.99
45 1 0.01
ACGTcount: A:0.51, C:0.12, G:0.09, T:0.28
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACTAATCAAAGTTTAAATGAGAAAC
Found at i:49452190 original size:44 final size:45
Alignment explanation
Indices: 49452113--49452200 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 45
49452103 ATAACTGTAA
* ** *
49452113 ATTAAATTATAGTTATTTTTAAATGTGCGATTATCA-AAATTTTT
1 ATTAAATTATAATTATTTTTAAATGAACAATTATCACAAATTTTT
*
49452157 ATTAAATTATAATTATTTTTAAATGAATAATTATCACAAATTTT
1 ATTAAATTATAATTATTTTTAAATGAACAATTATCACAAATTTT
49452201 AATTTACATC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
44 31 0.82
45 7 0.18
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.49
Consensus pattern (45 bp):
ATTAAATTATAATTATTTTTAAATGAACAATTATCACAAATTTTT
Found at i:49452701 original size:14 final size:14
Alignment explanation
Indices: 49452650--49452703 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
49452640 AAAAAATATA
49452650 TATTTA-TA-TTA-
1 TATTTATTATTTAC
49452661 TATTATATTATATTAC
1 TATT-TATTAT-TTAC
*
49452677 TATTTACTATTTAC
1 TATTTATTATTTAC
*
49452691 TATTTTTTATTTA
1 TATTTATTATTTA
49452704 TTAAATTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
11 4 0.11
12 2 0.06
13 2 0.06
14 15 0.43
15 8 0.23
16 4 0.11
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (14 bp):
TATTTATTATTTAC
Found at i:49454581 original size:20 final size:20
Alignment explanation
Indices: 49454544--49454581 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
49454534 AAAAACTCAT
* *
49454544 CAAAACCTAGTTTTCGACGA
1 CAAAACCTAGATTCCGACGA
49454564 CAAAACCTAGATTCCGAC
1 CAAAACCTAGATTCCGAC
49454582 AAGCTTCTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.29, G:0.13, T:0.21
Consensus pattern (20 bp):
CAAAACCTAGATTCCGACGA
Found at i:49455750 original size:59 final size:60
Alignment explanation
Indices: 49455597--49455765 Score: 223
Period size: 59 Copynumber: 2.8 Consensus size: 60
49455587 AGCACCGAAT
* * *
49455597 TTTTTAACGAATAACTGTAAATTAAATTATAATTATAATCATCACACTTTATCATCAAAA
1 TTTTTAACTAATAACTGTAAATTAAATTATAATTATAATCATCACAATTTATCAGCAAAA
* * * *
49455657 CTTTTAACTAATAACTGTAAATTAAATTATAATTATAGTCATCACAATTTA-GAGCCAAA
1 TTTTTAACTAATAACTGTAAATTAAATTATAATTATAATCATCACAATTTATCAGCAAAA
** * * *
49455716 TTTTTAACTAATAGTTGTGAATTAAATTATAATTATAATTATCTCAATTT
1 TTTTTAACTAATAACTGTAAATTAAATTATAATTATAATCATCACAATTT
49455766 TTCCTATATT
Statistics
Matches: 95, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
59 48 0.51
60 47 0.49
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (60 bp):
TTTTTAACTAATAACTGTAAATTAAATTATAATTATAATCATCACAATTTATCAGCAAAA
Found at i:49455953 original size:6 final size:6
Alignment explanation
Indices: 49455930--49456010 Score: 137
Period size: 6 Copynumber: 13.5 Consensus size: 6
49455920 TACTTAAATA
*
49455930 ATAATT ATAAGTC A-AATT ATAATT ATAATT ATAATT ATAATT ATAATT
1 ATAATT ATAA-TT ATAATT ATAATT ATAATT ATAATT ATAATT ATAATT
49455978 ATAATT ATAATT ATAATT ATAATT ATAATT ATA
1 ATAATT ATAATT ATAATT ATAATT ATAATT ATA
49456011 TGATCACAAT
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
5 2 0.03
6 67 0.94
7 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (6 bp):
ATAATT
Found at i:49459067 original size:17 final size:17
Alignment explanation
Indices: 49459037--49459091 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 17
49459027 TGCAATTTGT
49459037 AATAA-AATACATAAATA
1 AATAATAATA-ATAAATA
*
49459054 GATAATAATAATAAATA
1 AATAATAATAATAAATA
49459071 AATAAATAA-AATAAATA
1 AAT-AATAATAATAAATA
49459088 AATA
1 AATA
49459092 GATGCCCGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
16 1 0.03
17 24 0.71
18 9 0.26
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (17 bp):
AATAATAATAATAAATA
Found at i:49459072 original size:4 final size:4
Alignment explanation
Indices: 49459041--49459091 Score: 54
Period size: 4 Copynumber: 13.2 Consensus size: 4
49459031 ATTTGTAATA
* *
49459041 AAAT ACAT AAAT AGAT -AAT -AAT -AAT AAAT AAAT AAAT AAAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT
49459087 AAAT A
1 AAAT A
49459092 GATGCCCGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 8 0.20
4 29 0.71
5 4 0.10
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:49460832 original size:94 final size:95
Alignment explanation
Indices: 49460666--49461195 Score: 236
Period size: 94 Copynumber: 5.8 Consensus size: 95
49460656 GTGTTACTTC
* * * *
49460666 AATCTACTCCACTGCAATTTCAGGGAGATTAGACTTATAGCTTTAATCTACTCCACTGTAACTTC
1 AATCTACTCCACTACAACTTCAGGGAGATAAGACTTATAGCTTTAATCTACTCCACTGCAACTTC
*
49460731 AGGGAGATGAGATTTGTAATTTTTCGTTTT
66 AGGGAGATAAGATTTGTAATTTTTCGTTTT
* * * * *
49460761 AATCTATTCTACTACAACTTCAGGGA-ATAAGATTTGTAGCCTTT-ATCTGCTCCACTGCAACTT
1 AATCTACTCCACTACAACTTCAGGGAGATAAGACTTATAG-CTTTAATCTACTCCACTGCAACTT
* * * * * * * *
49460824 TATGGAGATAAGATTTGTTACTTGTAGCTTC
65 CAGGGAGATAAGATTTGTAATTTTTCGTTTT
* * * * * * * * * * * * * *
49460855 AAT-AAGTTCCA-TGCAACTTTAAGGAAATGAGATTTGTAGCTTTAATTTGCTCTAGTACAACTT
1 AATCTA-CTCCACTACAACTTCAGGGAGATAAGACTTATAGCTTTAATCTACTCCACTGCAACTT
* * * * *
49460918 TAGAGAGATAAG----G---TTTATAGCTTT
65 CAGGGAGATAAGATTTGTAATTTTTCGTTTT
* * * * * * ** *
49460942 AATCTGCTCTACTGCAACTTCAGAGAGATAAGA-TTCACTATCTTCAATCTACTTTACTGTAACT
1 AATCTACTCCACTACAACTTCAGGGAGATAAGACTT-A-TAGCTTTAATCTACTCCACTGCAACT
*
49461006 TCAGGAAGATAAGATTTGTAA-----C--TTT
64 TCAGGGAGATAAGATTTGTAATTTTTCGTTTT
* * * * * * * *
49461031 AATCTACTCCACTACGACTTCAGGGAGATAAGATTTGT-GTTTTTAGTTTACTCCACTACAAGTT
1 AATCTACTCCACTACAACTTCAGGGAGATAAGACTTATAG-CTTTAATCTACTCCACTGCAACTT
* *
49461095 CAGGGAGATAAGATTAGT-A----TC--TTC
65 CAGGGAGATAAGATTTGTAATTTTTCGTTTT
* * * * * * *
49461119 AATCTAATCCACTGCAACCTCAGGGAG--AAGATTTCTGGCTTTAATCTACTCCACTACAACTTC
1 AATCTACTCCACTACAACTTCAGGGAGATAAGACTTATAGCTTTAATCTACTCCACTGCAACTTC
49461182 AGGGAGATAAGATT
66 AGGGAGATAAGATT
49461196 CACCACGATG
Statistics
Matches: 333, Mismatches: 83, Indels: 47
0.72 0.18 0.10
Matches are distributed among these distances:
86 43 0.13
87 18 0.05
88 74 0.22
89 59 0.18
90 3 0.01
93 17 0.05
94 93 0.28
95 26 0.08
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (95 bp):
AATCTACTCCACTACAACTTCAGGGAGATAAGACTTATAGCTTTAATCTACTCCACTGCAACTTC
AGGGAGATAAGATTTGTAATTTTTCGTTTT
Found at i:49461051 original size:44 final size:44
Alignment explanation
Indices: 49460666--49461610 Score: 422
Period size: 44 Copynumber: 20.8 Consensus size: 44
49460656 GTGTTACTTC
* * * * * *
49460666 AATCTACTCCACTGCAATTTCAGGGAGATTAGACTTATAGCTTT
1 AATCTACTCCACTACAACTTCAGGGAGATAAGATTTGTATCTTT
** *
49460710 AATCTACTCCACTGTAACTTCAGGGAGATGAGATTTGTAATTTTTCGTTTT
1 AATCTACTCCACTACAACTTCAGGGAGATAAGATTTGT-A----TC--TTT
* * *
49460761 AATCTATTCTACTACAACTTCAGGGA-ATAAGATTTGTAGCCTTT
1 AATCTACTCCACTACAACTTCAGGGAGATAAGATTTGTA-TCTTT
* * * *
49460805 -ATCTGCTCCACTGCAACTTTATGGAGATAAGATTTGT-TACTTGT
1 AATCTACTCCACTACAACTTCAGGGAGATAAGATTTGTAT-CTT-T
* * * * * * * *
49460849 AGCTTCAATAAGTTCCA-TGCAACTTTAAGGAAATGAGATTTGTAGCTTT
1 A--ATC--T-A-CTCCACTACAACTTCAGGGAGATAAGATTTGTATCTTT
* * * * * * * * *
49460898 AATTTGCTCTAGTACAACTTTAGAGAGATAAGGTTTATAGCTTT
1 AATCTACTCCACTACAACTTCAGGGAGATAAGATTTGTATCTTT
* * * * ** *
49460942 AATCTGCTCTACTGCAACTTCAGAGAGATAAGATTCACTATCTTC
1 AATCTACTCCACTACAACTTCAGGGAGATAAGATT-TGTATCTTT
** ** * *
49460987 AATCTACTTTACTGTAACTTCAGGAAGATAAGATTTGTAACTTT
1 AATCTACTCCACTACAACTTCAGGGAGATAAGATTTGTATCTTT
* * *
49461031 AATCTACTCCACTACGACTTCAGGGAGATAAGATTTGTGTTTTT
1 AATCTACTCCACTACAACTTCAGGGAGATAAGATTTGTATCTTT
* * * * *
49461075 AGTTTACTCCACTACAAGTTCAGGGAGATAAGATTAGTATCTTC
1 AATCTACTCCACTACAACTTCAGGGAGATAAGATTTGTATCTTT
* * * * **
49461119 AATCTAATCCACTGCAACCTCAGGGAG--AAGATTTCTGGCTTT
1 AATCTACTCCACTACAACTTCAGGGAGATAAGATTTGTATCTTT
* *
49461161 AATCTACTCCACTACAACTTCAGGGAGATAAGATTCACCACG-ATGACTTC
1 AATCTACTCCACTACAACTTCAGGGAGATAAGATT-----TGTAT--CTTT
** * * *
49461211 AATC--CGTCCCACTACAACTTCAAGGGTATAGGATTTGTGGTTTGTAGCATT
1 AATCTAC-T-CCACTACAACTTC-AGGG---A-GA--TAAGATTTGTATCTTT
* * * * * * *
49461262 AATCTATTCCATTGCAATTTCAGGGAAATAAGATTCGCTATCTTC
1 AATCTACTCCACTACAACTTCAGGGAGATAAGATTTG-TATCTTT
* * * *
49461307 AATCTGCTCCACTGCATCTTCAGGGAGATAACATTTGTTATCTTT
1 AATCTACTCCACTACAACTTCAGGGAGATAAGATTTG-TATCTTT
* * * * *
49461352 AACCTGCTCCACTACAATTTTAGGGAGATAAGGTTTGTAGT-TTT
1 AATCTACTCCACTACAACTTCAGGGAGATAAGATTTGTA-TCTTT
* * * * * * *
49461396 AATCTGCTCTACTGCCACTTCAGAGAGATAAGATTCAT-TGTCTTC
1 AATCTACTCCACTACAACTTCAGGGAGATAAGATT--TGTATCTTT
* * * *
49461441 AATTCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGTAGCTTT
1 AA-TCTACTCCACTACAACTTCAGGGAGATAAGATTTGTATCTTT
* * * * * *
49461486 AATTTGCTCTACTGCAACTTTAGAGAGATAAGATTTGCTAT-TTT
1 AATCTACTCCACTACAACTTCAGGGAGATAAGATTTG-TATCTTT
* ** * * *
49461530 CAATCTGCTCCACTGTAACTTTAGGGAGATAAGATTAGT-TCTTC
1 -AATCTACTCCACTACAACTTCAGGGAGATAAGATTTGTATCTTT
* * * * * *
49461574 AATTTGCTCCACTGCAATTTCAAGGAGGTAAGATTTG
1 AATCTACTCCACTACAACTTCAGGGAGATAAGATTTG
49461611 CCATGGTGAC
Statistics
Matches: 689, Mismatches: 161, Indels: 103
0.72 0.17 0.11
Matches are distributed among these distances:
42 34 0.05
43 56 0.08
44 283 0.41
45 152 0.22
46 34 0.05
47 4 0.01
48 1 0.00
49 6 0.01
50 60 0.09
51 49 0.07
52 2 0.00
53 1 0.00
54 1 0.00
55 2 0.00
57 4 0.01
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (44 bp):
AATCTACTCCACTACAACTTCAGGGAGATAAGATTTGTATCTTT
Found at i:49461456 original size:46 final size:46
Alignment explanation
Indices: 49461302--49461609 Score: 233
Period size: 45 Copynumber: 6.9 Consensus size: 46
49461292 AGATTCGCTA
* * * * *
49461302 TCTTCAA-TCTGCTCCACTGCATCTTCAGGGAGATAACATTTGTTA
1 TCTTCAATTCTGCTCCACTGCAACTTCAGAGAGATAAGATTTATTG
* * * * * * * * *
49461347 TCTTTAA-CCTGCTCCACTACAATTTTAGGGAGATAAGGTTTGTAG
1 TCTTCAATTCTGCTCCACTGCAACTTCAGAGAGATAAGATTTATTG
* * * *
49461392 T-TTTAA-TCTGCTCTACTGCCACTTCAGAGAGATAAGATTCATTG
1 TCTTCAATTCTGCTCCACTGCAACTTCAGAGAGATAAGATTTATTG
* *
49461436 TCTTCAATTCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGTAG
1 TCTTCAATTCTGCTCCACTGCAACTTCAGAGAGATAAGATTTATTG
* * * ** *
49461482 -CTTTAATT-TGCTCTACTGCAACTTTAGAGAGATAAGATTTGCTA
1 TCTTCAATTCTGCTCCACTGCAACTTCAGAGAGATAAGATTTATTG
* * * * *
49461526 TTTTCAA-TCTGCTCCACTGTAACTTTAGGGAGATAAGA-TTAGT-
1 TCTTCAATTCTGCTCCACTGCAACTTCAGAGAGATAAGATTTATTG
* *
49461569 TCTTCAATT-TGCTCCACTGCAATTTCA-AGGAGGTAAGATTT
1 TCTTCAATTCTGCTCCACTGCAACTTCAGA-GAGATAAGATTT
49461610 GCCATGGTGA
Statistics
Matches: 210, Mismatches: 46, Indels: 15
0.77 0.17 0.06
Matches are distributed among these distances:
43 29 0.14
44 71 0.34
45 77 0.37
46 33 0.16
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.36
Consensus pattern (46 bp):
TCTTCAATTCTGCTCCACTGCAACTTCAGAGAGATAAGATTTATTG
Found at i:49468617 original size:15 final size:14
Alignment explanation
Indices: 49468595--49468642 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
49468585 TACACTTTTT
*
49468595 AGTTTAGGGTTTAT
1 AGTTTAGGGTTTAA
* *
49468609 GGTTTTAGGATTTAA
1 AG-TTTAGGGTTTAA
49468624 AGTTTAGGGTTTAA
1 AGTTTAGGGTTTAA
49468638 GAGTT
1 -AGTT
49468643 AGTATTTAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
14 12 0.44
15 15 0.56
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (14 bp):
AGTTTAGGGTTTAA
Found at i:49468682 original size:14 final size:14
Alignment explanation
Indices: 49468596--49468678 Score: 60
Period size: 14 Copynumber: 5.9 Consensus size: 14
49468586 ACACTTTTTA
*
49468596 GTTTAGGGTTTATG
1 GTTTAGGGTTTAAG
* *
49468610 GTTTTAGGATTTAAA
1 G-TTTAGGGTTTAAG
49468625 GTTTAGGGTTTAAG
1 GTTTAGGGTTTAAG
**
49468639 AG-TTAGTATTTAAG
1 -GTTTAGGGTTTAAG
** * *
49468653 GTTTAATGTCTATG
1 GTTTAGGGTTTAAG
49468667 GTTTAGGGTTTA
1 GTTTAGGGTTTA
49468679 TGGTGTAATG
Statistics
Matches: 52, Mismatches: 14, Indels: 6
0.72 0.19 0.08
Matches are distributed among these distances:
13 1 0.02
14 39 0.75
15 12 0.23
ACGTcount: A:0.24, C:0.01, G:0.28, T:0.47
Consensus pattern (14 bp):
GTTTAGGGTTTAAG
Found at i:49468870 original size:7 final size:7
Alignment explanation
Indices: 49468843--49468893 Score: 57
Period size: 7 Copynumber: 7.1 Consensus size: 7
49468833 GTATGATTAT
*
49468843 GGTTTGG
1 GGTTTAG
*
49468850 GGTTTAA
1 GGTTTAG
49468857 GGTTTAG
1 GGTTTAG
49468864 GGTTTAG
1 GGTTTAG
*
49468871 GATTTTAG
1 G-GTTTAG
49468879 GGTTTAG
1 GGTTTAG
*
49468886 AGTTTAG
1 GGTTTAG
49468893 G
1 G
49468894 TAATGCAATA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
7 30 0.83
8 6 0.17
ACGTcount: A:0.18, C:0.00, G:0.39, T:0.43
Consensus pattern (7 bp):
GGTTTAG
Found at i:49468882 original size:22 final size:22
Alignment explanation
Indices: 49468852--49468893 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
49468842 TGGTTTGGGG
*
49468852 TTTAAGGTTTAGGGTTTAGGAT
1 TTTAAGGTTTAGAGTTTAGGAT
*
49468874 TTTAGGGTTTAGAGTTTAGG
1 TTTAAGGTTTAGAGTTTAGG
49468894 TAATGCAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.45
Consensus pattern (22 bp):
TTTAAGGTTTAGAGTTTAGGAT
Found at i:49469312 original size:39 final size:39
Alignment explanation
Indices: 49469256--49469333 Score: 113
Period size: 41 Copynumber: 2.0 Consensus size: 39
49469246 CATTATATTC
49469256 AATTTTAAAATTGAACAATT-AAATAATGTCATATTAAA
1 AATTTTAAAATTGAACAATTAAAATAATGTCATATTAAA
* *
49469294 AATTTTAAAAATTTAACAATTAAAAATAATGTCATTTTAA
1 AATTTT-AAAATTGAACAATT-AAAATAATGTCATATTAA
49469334 TGTATCAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
38 6 0.17
39 13 0.37
41 16 0.46
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.38
Consensus pattern (39 bp):
AATTTTAAAATTGAACAATTAAAATAATGTCATATTAAA
Found at i:49469535 original size:124 final size:126
Alignment explanation
Indices: 49469393--49469671 Score: 350
Period size: 126 Copynumber: 2.2 Consensus size: 126
49469383 CGTTTGGACC
* * * * *
49469393 AAAAATGCCACAACAATGTCTTAAAAATTATAC-AAAACGGCGCCGTTTGGTTACAGGAATTTGA
1 AAAAACGCCACAACAATGTATTAAAAATTATACAAAAACGACGCCGTTTGCTTACAGGAATTTAA
* *
49469457 -TTTTTAGTGGCATTTTTCTCCACAAT-GCCGCAAAAGGTATGGAATAGCGGCG-TTTGTTAT
66 CTTTTTAGTGGCATTTTTCT-CACAATCGCCGCAAAAGGTAAGCAATAGCGGCGTTTTG-TAT
** * * * * *
49469517 AAAAACGCCGTAACAATGTATTAAAAAGTGTACAAAAACTACGTCGTTTGCTTACAGGATTTTAA
1 AAAAACGCCACAACAATGTATTAAAAATTATACAAAAACGACGCCGTTTGCTTACAGGAATTTAA
* * *
49469582 CTTTTTAGTGGCATTTTTCTCAGAATCGCCGCAAAAGGTAAGCATTAGCGGCGTTTTGTCT
66 CTTTTTAGTGGCATTTTTCTCACAATCGCCGCAAAAGGTAAGCAATAGCGGCGTTTTGTAT
*
49469643 AAAAACGCTACAACAATGTATTAAAAATT
1 AAAAACGCCACAACAATGTATTAAAAATT
49469672 GTTCAGAATG
Statistics
Matches: 130, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
124 27 0.21
125 30 0.23
126 69 0.53
127 4 0.03
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Consensus pattern (126 bp):
AAAAACGCCACAACAATGTATTAAAAATTATACAAAAACGACGCCGTTTGCTTACAGGAATTTAA
CTTTTTAGTGGCATTTTTCTCACAATCGCCGCAAAAGGTAAGCAATAGCGGCGTTTTGTAT
Found at i:49469795 original size:20 final size:20
Alignment explanation
Indices: 49469772--49469812 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
49469762 TGCACTCAGC
49469772 CCCTAATTCCCCTTCCAAAT
1 CCCTAATTCCCCTTCCAAAT
*
49469792 CCCTAATTCCCCTTCTAAAT
1 CCCTAATTCCCCTTCCAAAT
49469812 C
1 C
49469813 TCTTCCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.44, G:0.00, T:0.32
Consensus pattern (20 bp):
CCCTAATTCCCCTTCCAAAT
Found at i:49470680 original size:13 final size:13
Alignment explanation
Indices: 49470664--49470704 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
49470654 GCTATAAGTT
49470664 TTGGTTAATGTTG
1 TTGGTTAATGTTG
49470677 TTGGTTAATGTT-
1 TTGGTTAATGTTG
*
49470689 CTGGTTAATGTTG
1 TTGGTTAATGTTG
49470702 TTG
1 TTG
49470705 CAAGTTCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.15, C:0.02, G:0.29, T:0.54
Consensus pattern (13 bp):
TTGGTTAATGTTG
Found at i:49470695 original size:12 final size:13
Alignment explanation
Indices: 49470665--49470701 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
49470655 CTATAAGTTT
*
49470665 TGGTTAATGTTGT
1 TGGTTAATGTTGC
49470678 TGGTTAATGTT-C
1 TGGTTAATGTTGC
49470690 TGGTTAATGTTG
1 TGGTTAATGTTG
49470702 TTGCAAGTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.16, C:0.03, G:0.30, T:0.51
Consensus pattern (13 bp):
TGGTTAATGTTGC
Found at i:49471398 original size:33 final size:33
Alignment explanation
Indices: 49471358--49471423 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
49471348 GTCAATTTTT
*
49471358 TTAATTTCCATTTTAAAATTGCCGCAAAAACAA
1 TTAATTTCCATTTTAAAATTGCAGCAAAAACAA
49471391 TTAATTTCCATTTTAAAATTGCAGCAAAAACAA
1 TTAATTTCCATTTTAAAATTGCAGCAAAAACAA
49471424 CTCTTTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (33 bp):
TTAATTTCCATTTTAAAATTGCAGCAAAAACAA
Found at i:49471751 original size:20 final size:20
Alignment explanation
Indices: 49471728--49471766 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
49471718 AGAACGAAAA
*
49471728 TATCTATATTATAATATTTG
1 TATCTATATAATAATATTTG
*
49471748 TATCTATATAATATTATTT
1 TATCTATATAATAATATTT
49471767 TAGTGTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (20 bp):
TATCTATATAATAATATTTG
Found at i:49471854 original size:9 final size:9
Alignment explanation
Indices: 49471836--49472134 Score: 139
Period size: 9 Copynumber: 33.0 Consensus size: 9
49471826 AAATATATAT
49471836 CATAACTTA
1 CATAACTTA
*
49471845 CATAATTTA
1 CATAACTTA
*
49471854 CATAACTCA
1 CATAACTTA
49471863 CATAACTTA
1 CATAACTTA
49471872 CATAACTTA
1 CATAACTTA
49471881 -ATAACTTA
1 CATAACTTA
* *
49471889 TATATATCATA
1 CATA-A-CTTA
49471900 CCATAACTTA
1 -CATAACTTA
* *
49471910 AATAACTCA
1 CATAACTTA
*
49471919 AATAACTTA
1 CATAACTTA
*
49471928 CTTAACTTA
1 CATAACTTA
49471937 C-TAACTTA
1 CATAACTTA
* *
49471945 TAT-ACAT-
1 CATAACTTA
* *
49471952 CATATCATA
1 CATAACTTA
*
49471961 TCATAATTTA
1 -CATAACTTA
*
49471971 CATAACTCA
1 CATAACTTA
49471980 CATAACTTA
1 CATAACTTA
* *
49471989 CTTAGCTTA
1 CATAACTTA
*
49471998 -ATAGCTTA
1 CATAACTTA
* *
49472006 TATATATCATA
1 CATA-A-CTTA
*
49472017 TCATAATTTA
1 -CATAACTTA
**
49472027 CATAACTCG
1 CATAACTTA
49472036 CATAACTTA
1 CATAACTTA
*
49472045 CCTAACTTA
1 CATAACTTA
*
49472054 -ACAACTTA
1 CATAACTTA
* * *
49472062 TGTATATCATA
1 --CATAACTTA
49472073 TCATAACTTA
1 -CATAACTTA
*
49472083 CATAACTTG
1 CATAACTTA
49472092 CATAA--TA
1 CATAACTTA
*
49472099 CATAA-ATA
1 CATAACTTA
* * *
49472107 TATATCATA
1 CATAACTTA
*
49472116 TCATAAGTTA
1 -CATAACTTA
49472126 CATAACTTA
1 CATAACTTA
49472135 ATTATACTTA
Statistics
Matches: 218, Mismatches: 54, Indels: 36
0.71 0.18 0.12
Matches are distributed among these distances:
7 8 0.04
8 39 0.18
9 129 0.59
10 23 0.11
11 13 0.06
12 6 0.03
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.36
Consensus pattern (9 bp):
CATAACTTA
Found at i:49471915 original size:56 final size:56
Alignment explanation
Indices: 49471845--49472089 Score: 328
Period size: 56 Copynumber: 4.3 Consensus size: 56
49471835 TCATAACTTA
* *
49471845 CATAATTTACATAACTCACATAACTTACATAACTTAATAACTTATATATATCATAC
1 CATAATTTACATAACTCACATAACTTACTTAACTTAATAACTTATATATATCATAT
* * * *
49471901 CATAACTTAAATAACTCAAATAACTTACTTAACTTACTAACTTATATACATCATATCATAT
1 CATAATTTACATAACTCACATAACTTACTTAACTTAATAAC-T-TAT--AT-ATATCATAT
* *
49471962 CATAATTTACATAACTCACATAACTTACTTAGCTTAATAGCTTATATATATCATAT
1 CATAATTTACATAACTCACATAACTTACTTAACTTAATAACTTATATATATCATAT
* * * *
49472018 CATAATTTACATAACTCGCATAACTTACCTAACTTAACAACTTATGTATATCATAT
1 CATAATTTACATAACTCACATAACTTACTTAACTTAATAACTTATATATATCATAT
*
49472074 CATAACTTACATAACT
1 CATAATTTACATAACT
49472090 TGCATAATAC
Statistics
Matches: 165, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
56 110 0.67
57 3 0.02
58 3 0.02
59 3 0.02
60 3 0.02
61 43 0.26
ACGTcount: A:0.42, C:0.20, G:0.02, T:0.36
Consensus pattern (56 bp):
CATAATTTACATAACTCACATAACTTACTTAACTTAATAACTTATATATATCATAT
Found at i:49471924 original size:65 final size:61
Alignment explanation
Indices: 49471832--49472077 Score: 209
Period size: 61 Copynumber: 4.0 Consensus size: 61
49471822 TACAAAATAT
* * *
49471832 ATATCATAACTTACATAATTTACATAACTCACATAACTTACATAACTTA-ATAACTTATATATAT
1 ATATCATAACTTACATAACTCACATAACTCACATAACTTAC-TAACTTATAT-AC--AT-CATAT
49471896 C
61 C
* * * * *
49471897 ATACCATAACTTAAATAACTCAAATAACTTACTTAACTTACTAACTTATATACATCATATC
1 ATATCATAACTTACATAACTCACATAACTCACATAACTTACTAACTTATATACATCATATC
* * * * * *
49471958 ATATCATAATTTACATAACTCACATAACTTACTTAGCTTAATAGC-T-TAT--AT-ATATC
1 ATATCATAACTTACATAACTCACATAACTCACATAACTTACTAACTTATATACATCATATC
* * * * * *
49472014 ATATCATAATTTACATAACTCGCATAACTTACCTAACTTAAC-AACTTATGTATATCATATC
1 ATATCATAACTTACATAACTCACATAACTCACATAACTT-ACTAACTTATATACATCATATC
49472075 ATA
1 ATA
49472078 ACTTACATAA
Statistics
Matches: 153, Mismatches: 21, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
56 43 0.28
57 4 0.03
58 2 0.01
59 3 0.02
60 3 0.02
61 51 0.33
62 2 0.01
64 9 0.06
65 36 0.24
ACGTcount: A:0.42, C:0.20, G:0.02, T:0.37
Consensus pattern (61 bp):
ATATCATAACTTACATAACTCACATAACTCACATAACTTACTAACTTATATACATCATATC
Found at i:49471978 original size:117 final size:116
Alignment explanation
Indices: 49471828--49472077 Score: 358
Period size: 117 Copynumber: 2.1 Consensus size: 116
49471818 AACTTACAAA
* *
49471828 ATATATATCATAACTTACATAATTTACATAACTCACATAACTTACATAACTTAATAACTTATATA
1 ATATATATCATATCATACATAATTTACATAACTCACATAACTTACATAACTTAATAACTTATATA
*
49471893 TATCATACCATAACTTAAATAACTCAAATAACTTACTTAACTT-ACTAACTT
66 TATCATACCATAACTTAAATAACTCAAATAACTTACCTAACTTAAC-AACTT
* * * *
49471944 ATATACATCATATCATATCATAATTTACATAACTCACATAACTTACTTAGCTTAATAGCTTATAT
1 ATATATATCATATCATA-CATAATTTACATAACTCACATAACTTACATAACTTAATAACTTATAT
* * * **
49472009 ATATCATATCATAATTTACATAACTCGCATAACTTACCTAACTTAACAACTT
65 ATATCATACCATAACTTAAATAACTCAAATAACTTACCTAACTTAACAACTT
*
49472061 ATGTATATCATATCATA
1 ATATATATCATATCATA
49472078 ACTTACATAA
Statistics
Matches: 118, Mismatches: 14, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
116 14 0.12
117 102 0.86
118 2 0.02
ACGTcount: A:0.42, C:0.19, G:0.02, T:0.37
Consensus pattern (116 bp):
ATATATATCATATCATACATAATTTACATAACTCACATAACTTACATAACTTAATAACTTATATA
TATCATACCATAACTTAAATAACTCAAATAACTTACCTAACTTAACAACTT
Found at i:49478000 original size:43 final size:43
Alignment explanation
Indices: 49477952--49478163 Score: 288
Period size: 43 Copynumber: 5.0 Consensus size: 43
49477942 AGATCATTCT
* * *
49477952 TATAAAAGCGTCGCTAAAGAACATAACCTTTAGCGGCATTTGC
1 TATAAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTGC
*
49477995 TATAAAAGCGCCACTAAAGAACATGACCTTTAGCGGCGTTT-C
1 TATAAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTGC
*
49478037 TTATAAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTAGC
1 -TATAAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTGC
*
49478081 TATAAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGCCTAT-C
1 TATAAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCG--TTTGC
* * *
49478125 T-TTAAA-CGCCGCTAAAGGACATGATCTTTAGCGGCGTTT
1 TATAAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTT
49478164 ATGTGAGAAA
Statistics
Matches: 153, Mismatches: 12, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
40 2 0.01
42 29 0.19
43 118 0.77
44 3 0.02
45 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.25
Consensus pattern (43 bp):
TATAAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTGC
Found at i:49478098 original size:86 final size:87
Alignment explanation
Indices: 49477948--49478162 Score: 321
Period size: 86 Copynumber: 2.5 Consensus size: 87
49477938 CTAAAGATCA
* * * *
49477948 TTCTTATAAAAGCGTCGCTAAAGAACATAACCTTTAGCGGCATTTGCTATAAAAGCGCCACTAAA
1 TTCTTATAAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTAGCTATAAAAGCGCCACTAAA
49478013 GAACATGACCTTTAGCGGCG-T
66 GAACATGACCTTTAGCGGCGCT
*
49478034 TTCTTATAAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTAGCTATAAAAGCGCCGCTAAA
1 TTCTTATAAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTAGCTATAAAAGCGCCACTAAA
49478099 GAACATGACCTTTAGCGGCGCCT
66 GAACATGACCTTTAGCGGCG-CT
* * *
49478122 ATCTT-T-AAA-CGCCGCTAAAGGACATGATCTTTAGCGGCGTT
1 TTCTTATAAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTT
49478163 TATGTGAGAA
Statistics
Matches: 119, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
85 30 0.25
86 83 0.70
87 1 0.01
88 5 0.04
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.25
Consensus pattern (87 bp):
TTCTTATAAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTAGCTATAAAAGCGCCACTAAA
GAACATGACCTTTAGCGGCGCT
Found at i:49478358 original size:4 final size:4
Alignment explanation
Indices: 49478349--49478385 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
49478339 AAGGACAAGA
* *
49478349 AAAT AAAT AAAT AAAT AAAT ACAT AAAT AAAT GAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
49478386 TAGAGGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:49478500 original size:19 final size:19
Alignment explanation
Indices: 49478462--49478519 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 19
49478452 ATGCAATTTG
49478462 TAATAAAATACATAAATAGA
1 TAATAAAATA-ATAAATAGA
49478482 TAATAATAATAAT-AATAGA
1 TAATAA-AATAATAAATAGA
49478501 TAAATAAAATAAATAAATA
1 T-AATAAAAT-AATAAATA
49478520 TATGCCCGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
19 10 0.29
20 16 0.47
21 8 0.24
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (19 bp):
TAATAAAATAATAAATAGA
Found at i:49478574 original size:18 final size:19
Alignment explanation
Indices: 49478552--49478602 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
49478542 GAAAAGATTT
49478552 GAATATAAAAAAAGTAAAA
1 GAATATAAAAAAAGTAAAA
*
49478571 -AATACTAAATAAA-TAAAA
1 GAATA-TAAAAAAAGTAAAA
49478589 GAAT-TAAAATAAAG
1 GAATATAAAA-AAAG
49478603 AAAGGACCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
17 4 0.15
18 12 0.46
19 10 0.38
ACGTcount: A:0.71, C:0.02, G:0.08, T:0.20
Consensus pattern (19 bp):
GAATATAAAAAAAGTAAAA
Found at i:49484904 original size:10 final size:10
Alignment explanation
Indices: 49484889--49484913 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
49484879 CATGTAAAAT
49484889 ATAAAAAACA
1 ATAAAAAACA
49484899 ATAAAAAACA
1 ATAAAAAACA
49484909 ATAAA
1 ATAAA
49484914 TGAATCACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.08, G:0.00, T:0.12
Consensus pattern (10 bp):
ATAAAAAACA
Found at i:49492836 original size:17 final size:17
Alignment explanation
Indices: 49492800--49492846 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
49492790 AATTTAGAAT
*
49492800 AATTTT-TGAATTAGTG
1 AATTTTGTGATTTAGTG
*
49492816 AATTTTGTGATTTATTG
1 AATTTTGTGATTTAGTG
49492833 AATTTTGTGATTTA
1 AATTTTGTGATTTA
49492847 AAAAGAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
16 6 0.21
17 22 0.79
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.55
Consensus pattern (17 bp):
AATTTTGTGATTTAGTG
Found at i:49494148 original size:45 final size:46
Alignment explanation
Indices: 49494052--49494235 Score: 282
Period size: 46 Copynumber: 4.0 Consensus size: 46
49494042 CATGGAAAAG
* * *
49494052 TGTGAAACGTAGGTATGGTATTTTAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
* *
49494098 TGTGAAAATTAGGTATGGTGTTTCAATGAAG-AAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
49494143 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
* *
49494189 TGTAAAAAGTAGGTATGGTATTTTC-GTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGT-GTTTCAGTGAAGAAAACCATACTGAGT
49494235 T
1 T
49494236 ATAGCATTGT
Statistics
Matches: 127, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
45 43 0.34
46 80 0.63
47 4 0.03
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.30
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
Found at i:49494207 original size:91 final size:92
Alignment explanation
Indices: 49494052--49494235 Score: 282
Period size: 91 Copynumber: 2.0 Consensus size: 92
49494042 CATGGAAAAG
* * * *
49494052 TGTGAAACGTAGGTATGGTATTTTAGTGAAGAAAACCATACTGAGTTGTGAAAATTAGGTATGGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTGTAAAAAGTAGGTATGGT
49494117 -GTTTCAATGAAG-AAACCATACTGAGT
66 AGTTTC-ATGAAGAAAACCATACTGAGT
*
49494143 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTGTAAAAAGTAGGTATGGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTGTAAAAAGTAGGTATGGT
* *
49494208 ATTTTCGTGAAGAAAACCATACTGAGT
66 AGTTTCATGAAGAAAACCATACTGAGT
49494235 T
1 T
49494236 ATAGCATTGT
Statistics
Matches: 84, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
91 65 0.77
92 19 0.23
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.30
Consensus pattern (92 bp):
TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTGTAAAAAGTAGGTATGGT
AGTTTCATGAAGAAAACCATACTGAGT
Found at i:49496136 original size:6 final size:6
Alignment explanation
Indices: 49496125--49496159 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
49496115 ATGGATCTTA
49496125 ACATAC ACATAC ACATAC ACATAC ACATAC ACATA
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATA
49496160 TATCACATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.31, G:0.00, T:0.17
Consensus pattern (6 bp):
ACATAC
Found at i:49497064 original size:15 final size:16
Alignment explanation
Indices: 49497044--49497075 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
49497034 TTTAATTGAA
49497044 AGAGAAG-AGAAAAAG
1 AGAGAAGAAGAAAAAG
49497059 AGAGAAGAAGAAAAAG
1 AGAGAAGAAGAAAAAG
49497075 A
1 A
49497076 AAAAAACAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (16 bp):
AGAGAAGAAGAAAAAG
Found at i:49503853 original size:15 final size:17
Alignment explanation
Indices: 49503814--49503855 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
49503804 AGTACCCTTA
*
49503814 AATACATAATCAATTTC
1 AATAAATAATCAATTTC
49503831 AGATAAATAAT-AATTT-
1 A-ATAAATAATCAATTTC
49503847 AATAAATAA
1 AATAAATAA
49503856 ATTAGTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 8 0.35
16 1 0.04
17 6 0.26
18 8 0.35
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (17 bp):
AATAAATAATCAATTTC
Found at i:49506695 original size:18 final size:18
Alignment explanation
Indices: 49506672--49506706 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
49506662 GTTTTTGGAT
49506672 AAATTTTGTAA-AATTTTG
1 AAATTTT-TAAGAATTTTG
49506690 AAATTTTTAAGAATTTT
1 AAATTTTTAAGAATTTT
49506707 CCCAAAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (18 bp):
AAATTTTTAAGAATTTTG
Found at i:49510493 original size:23 final size:21
Alignment explanation
Indices: 49510430--49510497 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 21
49510420 AATTCGGTTG
*
49510430 TTATGGATGACGATAATCAAT
1 TTATGCATGACGATAATCAAT
* *
49510451 TTCT-CATGGTCGGATAATCAAT
1 TTATGCAT-GAC-GATAATCAAT
49510473 CCTTATGCATGACGATAATCAAT
1 --TTATGCATGACGATAATCAAT
49510496 TT
1 TT
49510498 GGTTGTTATG
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
20 2 0.05
21 7 0.19
22 10 0.27
23 10 0.27
24 5 0.14
25 3 0.08
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (21 bp):
TTATGCATGACGATAATCAAT
Found at i:49510655 original size:22 final size:21
Alignment explanation
Indices: 49510630--49510670 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
49510620 AATATATAAA
* *
49510630 TATAATATTAATATATAAATTG
1 TATAAAATTAAAATA-AAATTG
49510652 TATAAAATTAAAATAAAAT
1 TATAAAATTAAAATAAAAT
49510671 AAAGTAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
TATAAAATTAAAATAAAATTG
Found at i:49513386 original size:19 final size:19
Alignment explanation
Indices: 49513362--49513399 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
49513352 AAAGTTAATA
*
49513362 ACAAATTTGATTACGGTGG
1 ACAAATTTGACTACGGTGG
49513381 ACAAATTTGACTACGGTGG
1 ACAAATTTGACTACGGTGG
49513400 GTGACAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (19 bp):
ACAAATTTGACTACGGTGG
Found at i:49518052 original size:19 final size:19
Alignment explanation
Indices: 49518029--49518079 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
49518019 TGCACACACG
* *
49518029 ATTCCACTAATCTCACATA
1 ATTCCACTAATCACACAGA
* *
49518048 GTTCCACTAATCAGACAGA
1 ATTCCACTAATCACACAGA
49518067 ATTCCACTAATCA
1 ATTCCACTAATCA
49518080 AACATCATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.37, C:0.29, G:0.06, T:0.27
Consensus pattern (19 bp):
ATTCCACTAATCACACAGA
Found at i:49519415 original size:38 final size:38
Alignment explanation
Indices: 49519347--49519463 Score: 153
Period size: 38 Copynumber: 3.1 Consensus size: 38
49519337 AACTTTTAAT
* * * *
49519347 ACACCAGCACTAAGCTTGCTAGGCACAAAGCCCGAATA
1 ACACCGGCACCAAGCCTGCTAGGCACAAAGCCTGAATA
* * * *
49519385 ACACTGGCACCAAGCCTGCTAGTCATAAAGCCTGAACA
1 ACACCGGCACCAAGCCTGCTAGGCACAAAGCCTGAATA
*
49519423 ACACCGGCACCAAGCCTGCTAGGCACAAAGCTTGAATA
1 ACACCGGCACCAAGCCTGCTAGGCACAAAGCCTGAATA
49519461 ACA
1 ACA
49519464 ATATAATTCA
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 66 1.00
ACGTcount: A:0.36, C:0.32, G:0.19, T:0.14
Consensus pattern (38 bp):
ACACCGGCACCAAGCCTGCTAGGCACAAAGCCTGAATA
Found at i:49521115 original size:18 final size:18
Alignment explanation
Indices: 49521092--49521152 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
49521082 TTCATGGTGG
49521092 AAGAAAGAAGAAAATAAA
1 AAGAAAGAAGAAAATAAA
*
49521110 AAGAAAGAAGAGAGATAAA
1 AAGAAAGAAGA-AAATAAA
*
49521129 AA-AAAGGAAGGAAAA-GAA
1 AAGAAA-GAA-GAAAATAAA
49521147 AAGAAA
1 AAGAAA
49521153 TGTAGTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
18 18 0.50
19 16 0.44
20 2 0.06
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (18 bp):
AAGAAAGAAGAAAATAAA
Found at i:49521534 original size:19 final size:21
Alignment explanation
Indices: 49521504--49521547 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
49521494 TCAAATAATG
49521504 TTTTTTCAATTTTTCGAT-TA
1 TTTTTTCAATTTTTCGATATA
*
49521524 TTTTTTC-ATTTTTTGATATA
1 TTTTTTCAATTTTTCGATATA
49521544 TTTT
1 TTTT
49521548 AAAATTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.18, C:0.07, G:0.05, T:0.70
Consensus pattern (21 bp):
TTTTTTCAATTTTTCGATATA
Found at i:49522238 original size:12 final size:12
Alignment explanation
Indices: 49522221--49522249 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
49522211 TAAACTTGAA
49522221 TTATTAATTAAC
1 TTATTAATTAAC
49522233 TTATTAATTAAC
1 TTATTAATTAAC
49522245 TTATT
1 TTATT
49522250 TAGGTCCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (12 bp):
TTATTAATTAAC
Found at i:49524444 original size:44 final size:44
Alignment explanation
Indices: 49524381--49524470 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
49524371 CTTAATAGAG
49524381 ATAGACACCATAAGATCTCATACCACAATCCCCAGAACAATACA
1 ATAGACACCATAAGATCTCATACCACAATCCCCAGAACAATACA
49524425 ATAGACACCATAAGATCTCATACCACAATCCCCAGAACAATACA
1 ATAGACACCATAAGATCTCATACCACAATCCCCAGAACAATACA
49524469 AT
1 AT
49524471 GGCAAGAGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.46, C:0.31, G:0.07, T:0.17
Consensus pattern (44 bp):
ATAGACACCATAAGATCTCATACCACAATCCCCAGAACAATACA
Found at i:49527765 original size:21 final size:22
Alignment explanation
Indices: 49527741--49527785 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
49527731 AGAAAAAGAG
49527741 AAATACAAAAAAG-AATAG-ATC
1 AAAT-CAAAAAAGAAATAGAATC
*
49527762 AAATCAAGAAAGAAATAGAATC
1 AAATCAAAAAAGAAATAGAATC
49527784 AA
1 AA
49527786 CAATTTGTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 9 0.43
22 5 0.24
ACGTcount: A:0.67, C:0.09, G:0.11, T:0.13
Consensus pattern (22 bp):
AAATCAAAAAAGAAATAGAATC
Found at i:49530642 original size:35 final size:34
Alignment explanation
Indices: 49530596--49530791 Score: 257
Period size: 35 Copynumber: 5.7 Consensus size: 34
49530586 AAATGATACA
*
49530596 TGAACAGGAGAGATTCCCTGCAACAACATAATGCG
1 TGAACAGGAGAGATTCCCTGCAACAA-ATAATGTG
* * * *
49530631 TGAACAGGAGAGATTCCCTACAAGAAATGATGTA
1 TGAACAGGAGAGATTCCCTGCAACAAATAATGTG
*
49530665 TGAACAGGAGAGTTTCCCTGCAACAAAATAATGTG
1 TGAACAGGAGAGATTCCCTGCAAC-AAATAATGTG
* * *
49530700 TGAACAGGAGAGATTCCCTACAAGAAATGATGTG
1 TGAACAGGAGAGATTCCCTGCAACAAATAATGTG
*
49530734 TGAACAGGAGAGATTCCCTGCAACAAAATAATGCG
1 TGAACAGGAGAGATTCCCTGCAAC-AAATAATGTG
* *
49530769 TGAACAGGAAATATTCCCTGCAA
1 TGAACAGGAGAGATTCCCTGCAA
49530792 GAAAAGACAA
Statistics
Matches: 139, Mismatches: 20, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
34 57 0.41
35 82 0.59
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (34 bp):
TGAACAGGAGAGATTCCCTGCAACAAATAATGTG
Found at i:49530696 original size:69 final size:69
Alignment explanation
Indices: 49530583--49530795 Score: 345
Period size: 69 Copynumber: 3.1 Consensus size: 69
49530573 CAGGTCCAAA
** *
49530583 AAGAAATGATACATGAACAGGAGAGATTCCCTGCAACAACATAATGCGTGAACAGGAGAGATTCC
1 AAGAAATGATGTATGAACAGGAGAGATTCCCTGCAACAAAATAATGCGTGAACAGGAGAGATTCC
49530648 CTAC
66 CTAC
* *
49530652 AAGAAATGATGTATGAACAGGAGAGTTTCCCTGCAACAAAATAATGTGTGAACAGGAGAGATTCC
1 AAGAAATGATGTATGAACAGGAGAGATTCCCTGCAACAAAATAATGCGTGAACAGGAGAGATTCC
49530717 CTAC
66 CTAC
* * *
49530721 AAGAAATGATGTGTGAACAGGAGAGATTCCCTGCAACAAAATAATGCGTGAACAGGAAATATTCC
1 AAGAAATGATGTATGAACAGGAGAGATTCCCTGCAACAAAATAATGCGTGAACAGGAGAGATTCC
*
49530786 CTGC
66 CTAC
49530790 AAGAAA
1 AAGAAA
49530796 AGACAAGTGA
Statistics
Matches: 133, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 133 1.00
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.19
Consensus pattern (69 bp):
AAGAAATGATGTATGAACAGGAGAGATTCCCTGCAACAAAATAATGCGTGAACAGGAGAGATTCC
CTAC
Found at i:49531071 original size:13 final size:13
Alignment explanation
Indices: 49531053--49531091 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
49531043 AGTTTTCAAA
49531053 TTTTCAAATTAAG
1 TTTTCAAATTAAG
49531066 TTTTCAAAACTTAAG
1 TTTTC-AAA-TTAAG
*
49531081 CTTTCAAATTA
1 TTTTCAAATTA
49531092 CAAATATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 8 0.35
14 6 0.26
15 9 0.39
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.44
Consensus pattern (13 bp):
TTTTCAAATTAAG
Found at i:49536983 original size:20 final size:20
Alignment explanation
Indices: 49536958--49536995 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
49536948 GGGAACAATT
*
49536958 TTTCAATCGATTTAAAAATG
1 TTTCAATCGACTTAAAAATG
*
49536978 TTTCAATTGACTTAAAAA
1 TTTCAATCGACTTAAAAA
49536996 ATTTTAAACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (20 bp):
TTTCAATCGACTTAAAAATG
Found at i:49537367 original size:14 final size:15
Alignment explanation
Indices: 49537339--49537369 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
49537329 TAGGTGTTGA
49537339 CATTAAAATATTAAT
1 CATTAAAATATTAAT
49537354 CATTAAAA-ATTAAT
1 CATTAAAATATTAAT
49537368 CA
1 CA
49537370 ACCAAATACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (15 bp):
CATTAAAATATTAAT
Found at i:49544745 original size:25 final size:25
Alignment explanation
Indices: 49544692--49544763 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 25
49544682 AAGCTCTTTC
* *
49544692 GAGCCATATAACAGGAAG-TTCATGT
1 GAGCCAT-TAACAGGAAGCTCCATGA
49544717 GAGCCATGTAACAGGAAGCTCCA-GA
1 GAGCCAT-TAACAGGAAGCTCCATGA
*
49544742 GAGCCATTAATCGGGAAGCTCC
1 GAGCCATTAA-CAGGAAGCTCC
49544764 TGAAAGAGCC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
24 3 0.07
25 35 0.85
26 3 0.07
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.18
Consensus pattern (25 bp):
GAGCCATTAACAGGAAGCTCCATGA
Found at i:49544912 original size:25 final size:26
Alignment explanation
Indices: 49544717--49544917 Score: 89
Period size: 25 Copynumber: 7.8 Consensus size: 26
49544707 AAGTTCATGT
* * *
49544717 GAGCCATGTAA-CAGGAAGCTCCAGA
1 GAGCCATATAATCGGGAAGCTCCAAA
49544742 GAGCCAT-TAATCGGGAAGCTCCTGAAA
1 GAGCCATATAATCGGGAAGCTCC--AAA
* * * *
49544769 GAGCC-TTTAATTGGGAAGGTTCAAA
1 GAGCCATATAATCGGGAAGCTCCAAA
* * * * *
49544794 CGAACCA-AT-ATCGGAAAGGTTCAAGT
1 -GAGCCATATAATCGGGAAGCTCCAA-A
** *
49544820 GAGCCA-AT-ATTAGGAAGCTCCAGA
1 GAGCCATATAATCGGGAAGCTCCAAA
*
49544844 GAGCCA-ATTAATCGGGAAGCTCATGAAA
1 GAGCCATA-TAATCGGGAAGCTC--CAAA
* * *
49544872 AAGCC-TTTAATTGGGAAGCTCCAAA
1 GAGCCATATAATCGGGAAGCTCCAAA
*
49544897 GAGCCATAT-ATCGGGACGCTC
1 GAGCCATATAATCGGGAAGCTC
49544918 ATTAGAGTTG
Statistics
Matches: 133, Mismatches: 30, Indels: 26
0.70 0.16 0.14
Matches are distributed among these distances:
24 10 0.08
25 67 0.50
26 18 0.14
27 32 0.24
28 6 0.05
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.19
Consensus pattern (26 bp):
GAGCCATATAATCGGGAAGCTCCAAA
Found at i:49556281 original size:25 final size:24
Alignment explanation
Indices: 49556253--49556310 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
49556243 ACATAAATGG
*
49556253 GAAGCTCTTTCGAGCCATATAACGA
1 GAAGCTCTGT-GAGCCATATAACGA
* *
49556278 GAAGCTCATGTGAGCCATGTAACGG
1 GAAGCTC-TGTGAGCCATATAACGA
49556303 GAAGCTCT
1 GAAGCTCT
49556311 AGAGAACCGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 1 0.03
25 26 0.90
26 2 0.07
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.22
Consensus pattern (24 bp):
GAAGCTCTGTGAGCCATATAACGA
Found at i:49556379 original size:25 final size:25
Alignment explanation
Indices: 49556350--49556407 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
49556340 AGAGCCTTTA
49556350 ATCGGGAAGGTTCAAACGAACCAAT
1 ATCGGGAAGGTTCAAACGAACCAAT
* * *
49556375 ATCGGAAAGGTTCAAGCGAGCCAAT
1 ATCGGGAAGGTTCAAACGAACCAAT
49556400 ATCGGGAA
1 ATCGGGAA
49556408 ACTCATGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.38, C:0.19, G:0.28, T:0.16
Consensus pattern (25 bp):
ATCGGGAAGGTTCAAACGAACCAAT
Found at i:49556455 original size:25 final size:27
Alignment explanation
Indices: 49556392--49556465 Score: 75
Period size: 25 Copynumber: 2.9 Consensus size: 27
49556382 AGGTTCAAGC
* *
49556392 GAGCCA-ATATCGGGAAACTCATGAAA
1 GAGCCATATATTGGGAAGCTCATGAAA
*
49556418 GAGCC-TTTAATTGGGAAGCTC-T-AAA
1 GAGCCATAT-ATTGGGAAGCTCATGAAA
*
49556443 GAGCCATATATTGGGACGCTCAT
1 GAGCCATATATTGGGAAGCTCAT
49556466 TAGAGTTGTG
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
25 19 0.49
26 10 0.26
27 10 0.26
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (27 bp):
GAGCCATATATTGGGAAGCTCATGAAA
Found at i:49562173 original size:33 final size:32
Alignment explanation
Indices: 49562120--49562181 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
49562110 ATCAACACGC
*
49562120 TTTTATTTTAGCGACCAAATTAACCACTTTTT
1 TTTTATTTTAACGACCAAATTAACCACTTTTT
*
49562152 TTTTTTTTTAACGAACCAAATTAACCACTT
1 TTTTATTTTAACG-ACCAAATTAACCACTT
49562182 AAAATATGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.31, C:0.19, G:0.05, T:0.45
Consensus pattern (32 bp):
TTTTATTTTAACGACCAAATTAACCACTTTTT
Found at i:49562538 original size:24 final size:23
Alignment explanation
Indices: 49562493--49562548 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 23
49562483 ATCACATATT
* *
49562493 TTAATAAAATAAGTTATATCAAA
1 TTAATAAAAAAAGTTACATCAAA
*
49562516 TTAATGAAAAAAAGTTACCTC-AA
1 TTAAT-AAAAAAAGTTACATCAAA
49562539 -TAATAAAAAA
1 TTAATAAAAAA
49562549 TATACACTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 6 0.21
22 4 0.14
23 7 0.24
24 12 0.41
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.29
Consensus pattern (23 bp):
TTAATAAAAAAAGTTACATCAAA
Found at i:49572125 original size:12 final size:12
Alignment explanation
Indices: 49572108--49572137 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
49572098 CCTCACATGC
49572108 CCATGTGCCAGG
1 CCATGTGCCAGG
*
49572120 CCATGTGCTAGG
1 CCATGTGCCAGG
49572132 CCATGT
1 CCATGT
49572138 AAAAGCCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (12 bp):
CCATGTGCCAGG
Found at i:49573400 original size:25 final size:25
Alignment explanation
Indices: 49573362--49573454 Score: 80
Period size: 25 Copynumber: 3.7 Consensus size: 25
49573352 TCCTGTACAT
**
49573362 GTATGCTCAGACGAGCTATGAATCG
1 GTATGCTCTCACGAGCTATGAATCG
* * *
49573387 GTATGCTCTCACGAGCTGTAAATTG
1 GTATGCTCTCACGAGCTATGAATCG
* * *
49573412 GTAGGTTCAT-ACGAGCTGTGAATCG
1 GTATGCTC-TCACGAGCTATGAATCG
* *
49573437 GTAAGCTCTCATGAGCTA
1 GTATGCTCTCACGAGCTA
49573455 AAATCAGTAA
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
24 1 0.02
25 51 0.96
26 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (25 bp):
GTATGCTCTCACGAGCTATGAATCG
Found at i:49577334 original size:17 final size:18
Alignment explanation
Indices: 49577312--49577358 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
49577302 TTATTTTTAT
49577312 ATATTTTTATATAATTA-
1 ATATTTTTATATAATTAC
* *
49577329 ATATTTTGATA-ATTTAC
1 ATATTTTTATATAATTAC
*
49577346 ATATTTATATATA
1 ATATTTTTATATA
49577359 TCGTAAATGC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 4 0.17
17 19 0.79
18 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
ATATTTTTATATAATTAC
Found at i:49589002 original size:49 final size:50
Alignment explanation
Indices: 49588934--49589036 Score: 163
Period size: 51 Copynumber: 2.1 Consensus size: 50
49588924 TCTTATAGAG
* * *
49588934 AACATATGGAAAGTGTT-AAACACGTTATATTCTTTCCAAAAAGAATTAT
1 AACATATGGAAAGTATTAAAAAACATTATATTCTTTCCAAAAAGAATTAT
49588983 AACATATGGAAAGTATTAAAAAAACATTATATTCTTTCCAAAAAGAATTAT
1 AACATATGGAAAGTATT-AAAAAACATTATATTCTTTCCAAAAAGAATTAT
49589034 AAC
1 AAC
49589037 TATCATGTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
49 16 0.33
51 33 0.67
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.31
Consensus pattern (50 bp):
AACATATGGAAAGTATTAAAAAACATTATATTCTTTCCAAAAAGAATTAT
Found at i:49591059 original size:17 final size:16
Alignment explanation
Indices: 49591039--49591081 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 16
49591029 TTGGGTTGAG
49591039 AAAATAATTTAATTAGAA
1 AAAATAATTTAA-TA-AA
*
49591057 AAATTAATTTAATAAA
1 AAAATAATTTAATAAA
49591073 AAAATAATT
1 AAAATAATT
49591082 AACTAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 10 0.43
17 2 0.09
18 11 0.48
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (16 bp):
AAAATAATTTAATAAA
Found at i:49591066 original size:18 final size:15
Alignment explanation
Indices: 49591039--49591081 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 15
49591029 TTGGGTTGAG
49591039 AAAATAATTTAATTAGA
1 AAAATAATTTAA-TA-A
49591056 AAAATTAATTTAATAAA
1 AAAA-TAATTTAAT-AA
49591073 AAAATAATT
1 AAAATAATT
49591082 AACTAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.21
17 10 0.42
18 9 0.38
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (15 bp):
AAAATAATTTAATAA
Found at i:49593156 original size:19 final size:16
Alignment explanation
Indices: 49593112--49593156 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 16
49593102 ACTTTCCCTC
49593112 AAACTTTTATTCCCCA
1 AAACTTTTATTCCCCA
49593128 AAACTTTTTATTTTCCCCA
1 AAAC-TTTTA--TTCCCCA
49593147 TAAACTTTTA
1 -AAACTTTTA
49593157 CTTCTCACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 4 0.16
17 5 0.20
19 12 0.48
20 4 0.16
ACGTcount: A:0.31, C:0.24, G:0.00, T:0.44
Consensus pattern (16 bp):
AAACTTTTATTCCCCA
Found at i:49593673 original size:5 final size:5
Alignment explanation
Indices: 49593663--49593714 Score: 52
Period size: 5 Copynumber: 10.2 Consensus size: 5
49593653 GAACAAATAT
* * *
49593663 ATTCG ATTCG ATTCG AATCG ATTCG AATTCC ATCTC- ACTCG ATTCG ATTCG
1 ATTCG ATTCG ATTCG ATTCG ATTCG -ATTCG AT-TCG ATTCG ATTCG ATTCG
49593714 A
1 A
49593715 GAAAACTTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
4 2 0.05
5 31 0.79
6 6 0.15
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (5 bp):
ATTCG
Found at i:49606262 original size:21 final size:22
Alignment explanation
Indices: 49606244--49606286 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
49606234 GCATTTAATT
49606244 AATT-TTTTAAAAAATTTAAAA
1 AATTATTTTAAAAAATTTAAAA
*
49606265 AATTATTTTTAAAAA-TTAAAA
1 AATTATTTTAAAAAATTTAAAA
49606286 A
1 A
49606287 CTATTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AATTATTTTAAAAAATTTAAAA
Found at i:49606301 original size:19 final size:19
Alignment explanation
Indices: 49606279--49606327 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
49606269 ATTTTTAAAA
*
49606279 ATTAAAAACTATTAAAATT
1 ATTAAAAAATATTAAAATT
* *
49606298 ATTAAAAAGTA-TAAATTT
1 ATTAAAAAATATTAAAATT
49606316 A-TAAAAAATATT
1 ATTAAAAAATATT
49606328 TTGAATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 8 0.31
18 8 0.31
19 10 0.38
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (19 bp):
ATTAAAAAATATTAAAATT
Found at i:49608656 original size:23 final size:23
Alignment explanation
Indices: 49608618--49608661 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
49608608 ATTTTATCAA
*
49608618 ATTTTTGAAACATTTTCATTGAT
1 ATTTTTGAAACATTTTAATTGAT
* *
49608641 ATTTTTGAAGCTTTTTAATTG
1 ATTTTTGAAACATTTTAATTG
49608662 TAATTGGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.07, G:0.11, T:0.55
Consensus pattern (23 bp):
ATTTTTGAAACATTTTAATTGAT
Found at i:49614135 original size:325 final size:323
Alignment explanation
Indices: 49613533--49614494 Score: 1358
Period size: 325 Copynumber: 3.0 Consensus size: 323
49613523 TTTTTTAAAA
*
49613533 AATTGGTTAATAAAACAATTCATGGATTACATTAATATACTTTGTATAATTGTCCTCATGTGGTT
1 AATTGGTTAAT-AAACAATTCATGGATTACATTAATATACTTTGTATAATTGACCTCATGTGGTT
*
49613598 TTTGAATGCAAAGAAAAATAGAAAGAAATATTGGCTCATGATCTTTCGTAACTTGATACATCAAA
65 TTTGAATGCAAAGAAAAATAGAAAGAAATATTGGCTCATGATC-TTCGTAATTTGATACATCAAA
** *
49613663 TTAGGCTCTCTGTTACACTTGATGAGCTTATTCTCAATCAATTTAAATGTTTTTATCATGTTTTT
129 TTAGGCTCTCCATTACACTTGATGAGCTTATTCTCAAGCAATTTAAATGTTTTTATCATGTTTTT
* * * *
49613728 AGTTAGTTTTTGTTTTAATAAGTGAATTGGTGTGTTTTAAGCTATTTTTTATACCCGAATTGGCC
194 AGTTAGTTTTTGTTTTAATAAGTGAATTAGTGTGTTTTATG-TAATTTTTATACCTGAATTGGCC
* *
49613793 AAATGCGCCATAGGGAACCTAATGGTTGATTAAGTGTTGTAATGAGTCAATGGATTACAATAACA
258 AAATGCGCCATAGGGAACCTAACGGTTGATTAAGTGTTGTAAGGAGTCAATGGATTACAATAACA
49613858 T
323 T
* * *
49613859 AATTGGTTAATAGAGCAATTCATGGATTACATTAATATAC-TTGTATAATTGACCTCATATAGTT
1 AATTGGTTAATA-AACAATTCATGGATTACATTAATATACTTTGTATAATTGACCTCATGTGGTT
*
49613923 TTTGAATACAAAGAAAAATAG-AAGAAAATATTGGCTCATGATCTGTCGTAATTTGATACATCAA
65 TTTGAATGCAAAGAAAAATAGAAAG-AAATATTGGCTCATGATCT-TCGTAATTTGATACATCAA
*
49613987 ATTAGGCTCTCCATTACACTTGATGAGCTTATTCTCAAGCAATTTAAATGTTTTTATCGTGTTTT
128 ATTAGGCTCTCCATTACACTTGATGAGCTTATTCTCAAGCAATTTAAATGTTTTTATCATGTTTT
* * * * *
49614052 TAGTTGGTTTTTGTTTTAATAAGTGAACTAGTGTGTTTTATGATAATTTTGAAACCTAAATTGGC
193 TAGTTAGTTTTTGTTTTAATAAGTGAATTAGTGTGTTTTATG-TAATTTTTATACCTGAATTGGC
* * * * * ** * * * *
49614117 CAAATACGGCAAAGGGAACTTAACAGTTGATTAAGTACTATAGGGAGTCAATGGATTACATTAAT
257 CAAATGCGCCATAGGGAACCTAACGGTTGATTAAGTGTTGTAAGGAGTCAATGGATTACAATAAC
49614182 AT
322 AT
* * * ** *
49614184 AATTGGTTAATAACACAATTCACGAATTACA-TAATATACTTTGTATAATTGAACAAACGTGGTT
1 AATTGGTTAATAA-ACAATTCATGGATTACATTAATATACTTTGTATAATTGACCTCATGTGGTT
*
49614248 TTTGAATGCAAAGCAAAATAGAAAGAAATATTGGCTCATGATCTTCCGTAATTTGATACATCAAA
65 TTTGAATGCAAAGAAAAATAGAAAGAAATATTGGCTCATGATCTT-CGTAATTTGATACATCAAA
* * * * *
49614313 TTAGGCTCTCCATTACACTTTATGAGCTTATTTTCGAGCAATTTAACTG-TTTTATCATATTTTT
129 TTAGGCTCTCCATTACACTTGATGAGCTTATTCTCAAGCAATTTAAATGTTTTTATCATGTTTTT
* *
49614377 AGTTAGTTTTTATTTTAATAAGTGAATTAGTGTGTTTTATGTTATTCTTTATA-CTCGAATTGGC
194 AGTTAGTTTTTGTTTTAATAAGTGAATTAGTGTGTTTTATGTAATT-TTTATACCT-GAATTGGC
* *
49614441 CAAATGCGCCATACGAAACCTAACGGTTGATTAAGTGTTGTAAGGAGTCAATGG
257 CAAATGCGCCATAGGGAACCTAACGGTTGATTAAGTGTTGTAAGGAGTCAATGG
49614495 TGGCCCGAAC
Statistics
Matches: 559, Mismatches: 68, Indels: 20
0.86 0.11 0.03
Matches are distributed among these distances:
323 6 0.01
324 119 0.21
325 394 0.70
326 40 0.07
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (323 bp):
AATTGGTTAATAAACAATTCATGGATTACATTAATATACTTTGTATAATTGACCTCATGTGGTTT
TTGAATGCAAAGAAAAATAGAAAGAAATATTGGCTCATGATCTTCGTAATTTGATACATCAAATT
AGGCTCTCCATTACACTTGATGAGCTTATTCTCAAGCAATTTAAATGTTTTTATCATGTTTTTAG
TTAGTTTTTGTTTTAATAAGTGAATTAGTGTGTTTTATGTAATTTTTATACCTGAATTGGCCAAA
TGCGCCATAGGGAACCTAACGGTTGATTAAGTGTTGTAAGGAGTCAATGGATTACAATAACAT
Found at i:49615308 original size:31 final size:32
Alignment explanation
Indices: 49615249--49615313 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
49615239 AGCAAATTAC
49615249 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
49615281 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
49615312 AA
1 AA
49615314 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:49620426 original size:31 final size:32
Alignment explanation
Indices: 49620370--49620429 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
49620360 AAATTACAAA
*
49620370 AGTAATTGAATCCTAATAAAAACTCTTTAAAG
1 AGTAATTAAATCCTAATAAAAACTCTTTAAAG
49620402 AGTAATTAAATCCTAAT-AAAACTCTTTA
1 AGTAATTAAATCCTAATAAAAACTCTTTA
49620430 CAATTATCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 11 0.41
32 16 0.59
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (32 bp):
AGTAATTAAATCCTAATAAAAACTCTTTAAAG
Found at i:49620709 original size:70 final size:70
Alignment explanation
Indices: 49620596--49620735 Score: 280
Period size: 70 Copynumber: 2.0 Consensus size: 70
49620586 TTGGTCTAGT
49620596 GAATTACATTCCCGTATTTGTCAATGTCACGAACATGATGAATTAAATTTGTAGCAACAAAGTCT
1 GAATTACATTCCCGTATTTGTCAATGTCACGAACATGATGAATTAAATTTGTAGCAACAAAGTCT
49620661 TGGAC
66 TGGAC
49620666 GAATTACATTCCCGTATTTGTCAATGTCACGAACATGATGAATTAAATTTGTAGCAACAAAGTCT
1 GAATTACATTCCCGTATTTGTCAATGTCACGAACATGATGAATTAAATTTGTAGCAACAAAGTCT
49620731 TGGAC
66 TGGAC
49620736 AAAAGCATTC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (70 bp):
GAATTACATTCCCGTATTTGTCAATGTCACGAACATGATGAATTAAATTTGTAGCAACAAAGTCT
TGGAC
Found at i:49622500 original size:20 final size:19
Alignment explanation
Indices: 49622475--49622524 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
49622465 GATCATTAGT
49622475 TTAATTAATTTAAGGTTTAA
1 TTAATTAATTT-AGGTTTAA
* * *
49622495 TTAATTAAATTATGTTTGA
1 TTAATTAATTTAGGTTTAA
49622514 TTAATTTAATT
1 TTAA-TTAATT
49622525 ATATATAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (19 bp):
TTAATTAATTTAGGTTTAA
Found at i:49622516 original size:19 final size:19
Alignment explanation
Indices: 49622475--49622526 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
49622465 GATCATTAGT
* *
49622475 TTAATTAATTTAAGGTTTAA
1 TTAATTAAATT-ATGTTTAA
*
49622495 TTAATTAAATTATGTTTGA
1 TTAATTAAATTATGTTTAA
*
49622514 TTAATTTAATTAT
1 TTAATTAAATTAT
49622527 ATATAATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 18 0.64
20 10 0.36
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (19 bp):
TTAATTAAATTATGTTTAA
Found at i:49642336 original size:34 final size:34
Alignment explanation
Indices: 49642270--49642337 Score: 118
Period size: 35 Copynumber: 2.0 Consensus size: 34
49642260 ACTTACACAT
49642270 AACATTTACGCATAATAAAACTCAAACAAAAAAA
1 AACATTTACGCATAATAAAACTCAAACAAAAAAA
*
49642304 AACATTATACGCATAATAAACCTCAAACAAAAAA
1 AACATT-TACGCATAATAAAACTCAAACAAAAAA
49642338 TATCAAAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 6 0.19
35 26 0.81
ACGTcount: A:0.60, C:0.19, G:0.03, T:0.18
Consensus pattern (34 bp):
AACATTTACGCATAATAAAACTCAAACAAAAAAA
Found at i:49644194 original size:18 final size:18
Alignment explanation
Indices: 49644171--49644205 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
49644161 TTCTCATAAC
*
49644171 TTATAACTATAAAAAATA
1 TTATAACTAAAAAAAATA
*
49644189 TTATAATTAAAAAAAAT
1 TTATAACTAAAAAAAAT
49644206 GCTAATGTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
TTATAACTAAAAAAAATA
Found at i:49647040 original size:13 final size:13
Alignment explanation
Indices: 49647022--49647059 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
49647012 TAAGTAAAAA
49647022 GCGAACCCTTTGT
1 GCGAACCCTTTGT
*
49647035 GCGAA-CCTTAGT
1 GCGAACCCTTTGT
49647047 GCGAACCCTTTGT
1 GCGAACCCTTTGT
49647060 ATGTGAAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.18, C:0.29, G:0.24, T:0.29
Consensus pattern (13 bp):
GCGAACCCTTTGT
Found at i:49647499 original size:21 final size:19
Alignment explanation
Indices: 49647451--49647501 Score: 52
Period size: 21 Copynumber: 2.7 Consensus size: 19
49647441 GCCCTAGGTA
49647451 ATATGCAAA-C-ATTGTAT
1 ATATGCAAACCTATTGTAT
* *
49647468 ACATGTAAACCTATTTGTAGT
1 ATATGCAAACCTA-TTGTA-T
49647489 ATATGCAAACCTA
1 ATATGCAAACCTA
49647502 AATGTTTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 7 0.27
18 1 0.04
19 1 0.04
20 5 0.19
21 12 0.46
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (19 bp):
ATATGCAAACCTATTGTAT
Found at i:49647824 original size:34 final size:34
Alignment explanation
Indices: 49647742--49647830 Score: 81
Period size: 34 Copynumber: 2.6 Consensus size: 34
49647732 AACACTATAC
* * * *
49647742 TATGATATGCGAACCCTAGGAATATGCGACCCTG
1 TATGTTATGCGAACCCTAGGTATACGCGACCCTA
* ***
49647776 TATGATT-TGTGAACCCTAGGTATACGCGAGTTTA
1 TATG-TTATGCGAACCCTAGGTATACGCGACCCTA
*
49647810 TATGTTATGCGAACCGTAGGT
1 TATGTTATGCGAACCCTAGGT
49647831 TAGTGTGAGC
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
33 2 0.05
34 40 0.93
35 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (34 bp):
TATGTTATGCGAACCCTAGGTATACGCGACCCTA
Found at i:49649830 original size:16 final size:16
Alignment explanation
Indices: 49649796--49649833 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
49649786 TGTTAATAAA
*
49649796 TTTTA-TTTCTTTTAG
1 TTTTATTTTATTTTAG
*
49649811 TTTTATTTTATTTTAT
1 TTTTATTTTATTTTAG
49649827 TTTTATT
1 TTTTATT
49649834 ATTTTTCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.79
Consensus pattern (16 bp):
TTTTATTTTATTTTAG
Found at i:49659125 original size:123 final size:125
Alignment explanation
Indices: 49658862--49659129 Score: 282
Period size: 123 Copynumber: 2.2 Consensus size: 125
49658852 ATAAAACACA
* *
49658862 CTGATTTAA-AAAATATATAAGTACATAAAGAGATGTGTATACCATAAAATATATTATATATGAA
1 CTGATTTAATAAAA-ATATAAGTACATAAAGAAATGTGTATACCACAAAATATATTATATATGAA
* * * *
49658926 TTTTTTTTACTTTTGATAAATCATAAAACACAGTTCAATAATCCATCAAATTTGGTTTACTC
65 TTATTTTGACTTTTAATAAATCATAAAACACAATTCAATAATCCAT-AAATTTGGTTTACTC
* *
49658988 CTGATTTAAT-AAAATATAAGTACTTGAAGAAATGTGTA-A-CACAAAATATA-TATTATATGAA
1 CTGATTTAATAAAAATATAAGTACATAAAGAAATGTGTATACCACAAAATATATTA-TATATGAA
* * * * *
49659049 TTATTTTGACTTTTAATCAA-CTATAAAACACATTATTTAGTAATTCAT-AA-TTGGTTTATTC
65 TTATTTTGACTTTTAATAAATC-ATAAAACACA--ATTCAATAATCCATAAATTTGGTTTACTC
* **
49659110 CTTATTTTTTAAAAATATAA
1 CTGATTTAATAAAAATATAA
49659130 ACATGTGGAG
Statistics
Matches: 120, Mismatches: 16, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
122 20 0.17
123 55 0.46
124 1 0.01
125 32 0.27
126 12 0.10
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (125 bp):
CTGATTTAATAAAAATATAAGTACATAAAGAAATGTGTATACCACAAAATATATTATATATGAAT
TATTTTGACTTTTAATAAATCATAAAACACAATTCAATAATCCATAAATTTGGTTTACTC
Found at i:49662474 original size:39 final size:39
Alignment explanation
Indices: 49662429--49662510 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 39
49662419 TAATACTTTA
**
49662429 TTTTATATTTATTATTAAATTAAAAAATTT-TTTTAAAAT
1 TTTTATAAATATT-TTAAATTAAAAAATTTATTTTAAAAT
* * * *
49662468 TTTTATAAATATTTTGAATTATAAAATTTATTTTGAATT
1 TTTTATAAATATTTTAAATTAAAAAATTTATTTTAAAAT
49662507 TTTT
1 TTTT
49662511 GTAATTTTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
38 14 0.39
39 22 0.61
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (39 bp):
TTTTATAAATATTTTAAATTAAAAAATTTATTTTAAAAT
Found at i:49662693 original size:16 final size:14
Alignment explanation
Indices: 49662658--49662696 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
49662648 TGACTTGAAT
*
49662658 AATTCGAATAACTC
1 AATTCGATTAACTC
49662672 AATTCGATTAACTC
1 AATTCGATTAACTC
49662686 GAAATTCGATT
1 --AATTCGATT
49662697 TTTTTCGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
16 9 0.41
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (14 bp):
AATTCGATTAACTC
Found at i:49667685 original size:9 final size:9
Alignment explanation
Indices: 49667671--49667701 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
49667661 GTTAAACGAA
49667671 TCGAGTTAT
1 TCGAGTTAT
*
49667680 TCGAGTTAA
1 TCGAGTTAT
49667689 TCGAGTTAT
1 TCGAGTTAT
49667698 TCGA
1 TCGA
49667702 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:49668040 original size:30 final size:31
Alignment explanation
Indices: 49667995--49668054 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
49667985 AAACCTTTTA
49667995 TTTTCCCCCAAAATTTTTATTCCC-TCCCAC
1 TTTTCCCCCAAAATTTTTATTCCCTTCCCAC
* *
49668025 TTTTTCCCTAAAATTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAATTTTTATTCCCTTCCCA
49668055 TCCCACCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.35, G:0.00, T:0.45
Consensus pattern (31 bp):
TTTTCCCCCAAAATTTTTATTCCCTTCCCAC
Found at i:49672625 original size:85 final size:85
Alignment explanation
Indices: 49672477--49672661 Score: 298
Period size: 85 Copynumber: 2.2 Consensus size: 85
49672467 AACACTCCAC
* * *
49672477 ATACTTGTGTTATTGCAGGTATGTCACAGGATCATCCCAAATTGGATTCTAACCTTATCTCTAAT
1 ATACTTGTGTTGTTGCAGGTATGCCACAGGATCATCCCAAATTGAATTCTAACCTTATCTCTAAT
* *
49672542 ATTGTCTTACGTATGATGAA
66 ATTGTCTTACATATGATAAA
* *
49672562 ATACTTGTGTTGTTGCAGGTATGCCACAGGATCATCCTAAATTGAATTCTAACCTTATTTCTAAT
1 ATACTTGTGTTGTTGCAGGTATGCCACAGGATCATCCCAAATTGAATTCTAACCTTATCTCTAAT
*
49672627 ATTGTCTTACATATGGTAAA
66 ATTGTCTTACATATGATAAA
49672647 ATACTTGTGTTGTTG
1 ATACTTGTGTTGTTG
49672662 TAAAGAAAGG
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 92 1.00
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (85 bp):
ATACTTGTGTTGTTGCAGGTATGCCACAGGATCATCCCAAATTGAATTCTAACCTTATCTCTAAT
ATTGTCTTACATATGATAAA
Found at i:49681762 original size:23 final size:23
Alignment explanation
Indices: 49681732--49681777 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
49681722 CAAATACGCA
*
49681732 GAAAAACCTAATTTTTAGGCTTT
1 GAAAAACCTAATTTCTAGGCTTT
49681755 GAAAAACCTAATTTCTAGGCTTT
1 GAAAAACCTAATTTCTAGGCTTT
49681778 CTTAGGATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (23 bp):
GAAAAACCTAATTTCTAGGCTTT
Found at i:49682173 original size:23 final size:23
Alignment explanation
Indices: 49682147--49682194 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
49682137 ATTCATGTTT
49682147 AATGTGCTTATTTCAGTGGAGAA
1 AATGTGCTTATTTCAGTGGAGAA
49682170 AATGTGCTTATTTCAGTGGAGAA
1 AATGTGCTTATTTCAGTGGAGAA
49682193 AA
1 AA
49682195 AGTCCCTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.33
Consensus pattern (23 bp):
AATGTGCTTATTTCAGTGGAGAA
Found at i:49688993 original size:5 final size:5
Alignment explanation
Indices: 49688983--49689038 Score: 85
Period size: 5 Copynumber: 10.6 Consensus size: 5
49688973 TATCATTGTC
49688983 TTTAT TTTAT TTTAT TTTAT TTTAT TTTATT TTTATT TCTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA-T TTTA-T T-TTAT TTTAT
49689031 TTTAT TTT
1 TTTAT TTT
49689039 TTCATTCATT
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
5 36 0.73
6 10 0.20
7 3 0.06
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:49690397 original size:17 final size:17
Alignment explanation
Indices: 49690368--49690400 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
49690358 CTTATGTGAC
49690368 TCGACTCGCTCGACACT
1 TCGACTCGCTCGACACT
49690385 TCGATCTCG-TCGACAC
1 TCGA-CTCGCTCGACAC
49690401 ACCGGAGTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.18, C:0.39, G:0.18, T:0.24
Consensus pattern (17 bp):
TCGACTCGCTCGACACT
Found at i:49700748 original size:15 final size:14
Alignment explanation
Indices: 49700696--49700824 Score: 79
Period size: 14 Copynumber: 9.2 Consensus size: 14
49700686 AAGCTGTGAA
*
49700696 TTTAATTTTTACAT
1 TTTAATTTTTATAT
*
49700710 TTTAATTTGGT-TAT
1 TTTAATTT-TTATAT
49700724 TTTAATTTTTATAT
1 TTTAATTTTTATAT
*
49700738 TTTTATGTTTTATAT
1 TTTAAT-TTTTATAT
* * *
49700753 TTTGAAATTTGAAAT
1 TTT-AATTTTTATAT
* *
49700768 TTGAAATTTTA-AT
1 TTTAATTTTTATAT
49700781 TTTAA-TTTTATA-
1 TTTAATTTTTATAT
* *
49700793 -TTAATTATTAAAT
1 TTTAATTTTTATAT
*
49700806 TATTAAATTTTGATAT
1 T-TT-AATTTTTATAT
49700822 TTT
1 TTT
49700825 CAAAATATCA
Statistics
Matches: 89, Mismatches: 16, Indels: 19
0.72 0.13 0.15
Matches are distributed among these distances:
11 4 0.04
12 10 0.11
13 8 0.09
14 33 0.37
15 24 0.27
16 10 0.11
ACGTcount: A:0.32, C:0.01, G:0.05, T:0.62
Consensus pattern (14 bp):
TTTAATTTTTATAT
Found at i:49701962 original size:8 final size:8
Alignment explanation
Indices: 49701949--49701977 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
49701939 AGTTTATTGG
49701949 AAAATTAT
1 AAAATTAT
49701957 AAAATTAT
1 AAAATTAT
49701965 AAAATTAT
1 AAAATTAT
49701973 AAAAT
1 AAAAT
49701978 AGTATAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
AAAATTAT
Done.