Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 111 of 318
Found at i:35521433 original size:319 final size:319
Alignment explanation
Indices: 35520854--35521490 Score: 1139
Period size: 319 Copynumber: 2.0 Consensus size: 319
35520844 GTATGCTATG
*
35520854 GTTTGTTCACGTCCAGATTTATCATATGCAGTCATTGCAGTTAGCGGATACATGGCGAATCCCGA
1 GTTTGTTCACGTCCAGATTTATCATATGCAGTCATTGCAGTTAGCAGATACATGGCGAATCCCGA
* *
35520919 TAAAGAACACTGGAAAGCAGTTCAGTGGATTTTAAGATACTTACGAGGTATTACTGATGTCTGCT
66 TAAAGAACACTGGAAAGCAATTCAGTGGATTTTAAGATACTTACAAGGTATTACTGATGTCTGCT
*
35520984 TACAGTTTGGAAGAACTAGAGATGGAGTCATTGGATATGTTGATGTTGATTTTGTTGGAGACCTT
131 TACAGTTTGGAAGAACTAGAGATGGAGTCATTGGATATGTTGATGTTGATTTTGCTGGAGACCTT
*
35521049 GATAGAAGAAGATCTCTCACAGGTTGTGTCTTTACAATCAAAGGTTGTGCAATCAGTTAGAAAGC
196 GATAGAAGAAGATCTCTCACAGGTTATGTCTTTACAATCAAAGGTTGTGCAATCAGTTAGAAAGC
*
35521114 AACTTTGCAAACTACAGTCACTTTTTCTACCACTGAAGCTGAGCACATGGCGATTACTA
261 AACTTTGCAAACTACAGTCACTTTGTCTACCACTGAAGCTGAGCACATGGCGATTACTA
*
35521173 GTTTGTTTACGTCCAGATTTATCATATGCAGTCATTGCAGTTAGCAGATACATGGCGAATCCCGA
1 GTTTGTTCACGTCCAGATTTATCATATGCAGTCATTGCAGTTAGCAGATACATGGCGAATCCCGA
*
35521238 TAAAGAACACTGGAAAGCAATTCAGTGGATTTTAAGATACTTACAAGGTGTTACTGATGTCTGCT
66 TAAAGAACACTGGAAAGCAATTCAGTGGATTTTAAGATACTTACAAGGTATTACTGATGTCTGCT
*
35521303 TACAGTTTGGAAGAACTAGAGATGGAGTCATTGGATGTGTTGATGTTGATTTTGCTGGAGACCTT
131 TACAGTTTGGAAGAACTAGAGATGGAGTCATTGGATATGTTGATGTTGATTTTGCTGGAGACCTT
**
35521368 GATAGAAGAAGATCTCTCACAGGTTATGTCTTTACAATCGGAGGTTGTGCAATCAGTTAGAAAGC
196 GATAGAAGAAGATCTCTCACAGGTTATGTCTTTACAATCAAAGGTTGTGCAATCAGTTAGAAAGC
* * * *
35521433 AACTTTGTAAACTACAGTCGCTTTGTCTACCATTGAAGCTGAGTACATGGCGATTACT
261 AACTTTGCAAACTACAGTCACTTTGTCTACCACTGAAGCTGAGCACATGGCGATTACT
35521491 GAGGCTTGTA
Statistics
Matches: 303, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
319 303 1.00
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.31
Consensus pattern (319 bp):
GTTTGTTCACGTCCAGATTTATCATATGCAGTCATTGCAGTTAGCAGATACATGGCGAATCCCGA
TAAAGAACACTGGAAAGCAATTCAGTGGATTTTAAGATACTTACAAGGTATTACTGATGTCTGCT
TACAGTTTGGAAGAACTAGAGATGGAGTCATTGGATATGTTGATGTTGATTTTGCTGGAGACCTT
GATAGAAGAAGATCTCTCACAGGTTATGTCTTTACAATCAAAGGTTGTGCAATCAGTTAGAAAGC
AACTTTGCAAACTACAGTCACTTTGTCTACCACTGAAGCTGAGCACATGGCGATTACTA
Found at i:35522312 original size:24 final size:22
Alignment explanation
Indices: 35522284--35522343 Score: 84
Period size: 22 Copynumber: 2.6 Consensus size: 22
35522274 TTTCTGGCGA
35522284 GTTTCAAATATATAACCAATAGTT
1 GTTTCAAA-A-ATAACCAATAGTT
*
35522308 GTTTCTAAAATAACCAATAGTT
1 GTTTCAAAAATAACCAATAGTT
*
35522330 GTTTCTAAAATAAC
1 GTTTCAAAAATAAC
35522344 ACCATCGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 27 0.77
23 1 0.03
24 7 0.20
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (22 bp):
GTTTCAAAAATAACCAATAGTT
Found at i:35522321 original size:22 final size:22
Alignment explanation
Indices: 35522295--35522343 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
35522285 TTTCAAATAT
35522295 ATAACCAATAGTTGTTTCTAAA
1 ATAACCAATAGTTGTTTCTAAA
35522317 ATAACCAATAGTTGTTTCTAAA
1 ATAACCAATAGTTGTTTCTAAA
35522339 ATAAC
1 ATAAC
35522344 ACCATCGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.35
Consensus pattern (22 bp):
ATAACCAATAGTTGTTTCTAAA
Found at i:35523192 original size:3 final size:3
Alignment explanation
Indices: 35523186--35523231 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
35523176 ATCATCATCT
35523186 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
35523232 AACTGATGTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:35526408 original size:21 final size:21
Alignment explanation
Indices: 35526359--35526431 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
35526349 AGGAAATAAC
* *
35526359 ATGTGAACATTATAGGAATTCT
1 ATGTGAACA-CATAGGAATTAT
*
35526381 AATGTGAACACATAGGAGTTAT
1 -ATGTGAACACATAGGAATTAT
* *
35526403 ATGTGAACCCATAGAAATTAT
1 ATGTGAACACATAGGAATTAT
*
35526424 ATATGAAC
1 ATGTGAAC
35526432 CTTAACTACT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 25 0.58
22 9 0.21
23 9 0.21
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (21 bp):
ATGTGAACACATAGGAATTAT
Found at i:35530888 original size:20 final size:20
Alignment explanation
Indices: 35530865--35530907 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
35530855 AAACTTATAA
*
35530865 ATATTATAAAATATAAAAAT
1 ATATAATAAAATATAAAAAT
** *
35530885 ATATAATAAGTTATAAAATT
1 ATATAATAAAATATAAAAAT
35530905 ATA
1 ATA
35530908 AAATTTAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
ATATAATAAAATATAAAAAT
Found at i:35530916 original size:7 final size:8
Alignment explanation
Indices: 35530854--35530917 Score: 60
Period size: 8 Copynumber: 7.5 Consensus size: 8
35530844 AAATCATAAA
35530854 AAAACTTAT
1 AAAA-TTAT
35530863 AAATATTAT
1 AAA-ATTAT
35530872 AAAA-TAT
1 AAAATTAT
35530879 AAAAATATAT
1 -AAAAT-TAT
35530889 AATAAGTTAT
1 AA-AA-TTAT
35530899 AAAATTAT
1 AAAATTAT
35530907 AAAATT-T
1 AAAATTAT
35530914 AAAA
1 AAAA
35530918 AAAATTATTA
Statistics
Matches: 49, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
7 8 0.16
8 15 0.31
9 14 0.29
10 11 0.22
11 1 0.02
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (8 bp):
AAAATTAT
Found at i:35531017 original size:12 final size:12
Alignment explanation
Indices: 35531000--35531025 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35530990 ATAAACTTAT
35531000 AAAAATTATAAA
1 AAAAATTATAAA
35531012 AAAAATTATAAA
1 AAAAATTATAAA
35531024 AA
1 AA
35531026 CTTGAACTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAAATTATAAA
Found at i:35531025 original size:9 final size:9
Alignment explanation
Indices: 35530853--35531013 Score: 82
Period size: 9 Copynumber: 17.6 Consensus size: 9
35530843 AAAATCATAA
35530853 AAAAACTTAT
1 AAAAA-TTAT
*
35530863 AAATATTAT
1 AAAAATTAT
35530872 -AAAA-TAT
1 AAAAATTAT
35530879 AAAAATATAT
1 AAAAAT-TAT
*
35530889 AATAAGTTAT
1 AA-AAATTAT
35530899 -AAAATTAT
1 AAAAATTAT
* *
35530907 AAAATTTAAA
1 AAAAATT-AT
35530917 AAAAATTATT
1 AAAAATTA-T
*
35530927 AGAAATCT-T
1 AAAAAT-TAT
* * *
35530936 GAAAGTAAT
1 AAAAATTAT
*
35530945 AAAAATGTAAA
1 AAAAAT-T-AT
*
35530956 AAAAAATAT
1 AAAAATTAT
35530965 AAAAA--AT
1 AAAAATTAT
*
35530972 TAAAATTAT
1 AAAAATTAT
*
35530981 TAAAATTAT
1 AAAAATTAT
*
35530990 ATAAACTTAT
1 A-AAAATTAT
35531000 AAAAATTAT
1 AAAAATTAT
35531009 AAAAA
1 AAAAA
35531014 AAATTATAAA
Statistics
Matches: 114, Mismatches: 23, Indels: 29
0.69 0.14 0.17
Matches are distributed among these distances:
7 9 0.08
8 13 0.11
9 49 0.43
10 33 0.29
11 10 0.09
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:35540522 original size:16 final size:15
Alignment explanation
Indices: 35540503--35540553 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
35540493 TTCATATTGG
35540503 TAATTTTTAATTTGAA
1 TAATTTTTAATTT-AA
*
35540519 TAA-TTTTAATTTAG
1 TAATTTTTAATTTAA
* *
35540533 TTATTTTTTATTTAAA
1 TAATTTTTAATTT-AA
35540549 TAATT
1 TAATT
35540554 CTCCTTTTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 3 0.11
15 17 0.61
16 8 0.29
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (15 bp):
TAATTTTTAATTTAA
Found at i:35541080 original size:47 final size:47
Alignment explanation
Indices: 35541011--35541104 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
35541001 GGTTAAAGTC
*
35541011 TACCAAAATATTATTGAAGGGACTCTTGAAGAAGCTTAGTTGACTTG
1 TACCAAAATATTATTGAAGGGACTCTTGAAGAAGCTTAGTCGACTTG
35541058 TACCAAAATATTATTGAAGGGACTCTTGAAGAAGCTTAGTCGACTTG
1 TACCAAAATATTATTGAAGGGACTCTTGAAGAAGCTTAGTCGACTTG
35541105 CAAAATATAG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (47 bp):
TACCAAAATATTATTGAAGGGACTCTTGAAGAAGCTTAGTCGACTTG
Found at i:35543139 original size:17 final size:17
Alignment explanation
Indices: 35543113--35543155 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
35543103 GTAAAAATTA
*
35543113 AATA-TTTTATTGAGAT
1 AATATTTTTATTAAGAT
35543129 AATATTTTTATTAAGAT
1 AATATTTTTATTAAGAT
35543146 --TATTTTTATT
1 AATATTTTTATT
35543156 TAGTAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 10 0.40
16 4 0.16
17 11 0.44
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (17 bp):
AATATTTTTATTAAGAT
Found at i:35549635 original size:13 final size:13
Alignment explanation
Indices: 35549617--35549647 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
35549607 AATAAATATT
35549617 ATTGATACATACA
1 ATTGATACATACA
*
35549630 ATTGATATATACA
1 ATTGATACATACA
35549643 ATTGA
1 ATTGA
35549648 AAGAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (13 bp):
ATTGATACATACA
Found at i:35553543 original size:36 final size:36
Alignment explanation
Indices: 35553492--35553563 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
35553482 TTTTCAACAC
**
35553492 TTAATTTTTTCAGTTTATCAAACACATTCTAAAACT
1 TTAATTTTTTCAGTTTATCAAACACACCCTAAAACT
*
35553528 TTAATTTTTTTAGTTTATCAAACACACCCTAAAACT
1 TTAATTTTTTCAGTTTATCAAACACACCCTAAAACT
35553564 CTTGTCAAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.36, C:0.18, G:0.03, T:0.43
Consensus pattern (36 bp):
TTAATTTTTTCAGTTTATCAAACACACCCTAAAACT
Found at i:35553882 original size:31 final size:31
Alignment explanation
Indices: 35553846--35553904 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
35553836 ACTTGGTTAG
**
35553846 TGAACTATTTGCAAG-TTTTCATTTAAATCAC
1 TGAACTATTTAAAAGTTTTTC-TTTAAATCAC
35553877 TGAACTATTTAAAAGTTTTTCTTTAAAT
1 TGAACTATTTAAAAGTTTTTCTTTAAAT
35553905 TATTGGATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.46
Consensus pattern (31 bp):
TGAACTATTTAAAAGTTTTTCTTTAAATCAC
Found at i:35560369 original size:17 final size:17
Alignment explanation
Indices: 35560347--35560393 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
35560337 TATTCTAATT
35560347 TTATAAATTAAAAATAA
1 TTATAAATTAAAAATAA
*
35560364 TTATAAA-GAAAAATAA
1 TTATAAATTAAAAATAA
*
35560380 TT-T-TATTAAAAATA
1 TTATAAATTAAAAATA
35560394 TATCAATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 1 0.04
15 8 0.31
16 10 0.38
17 7 0.27
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
TTATAAATTAAAAATAA
Found at i:35560401 original size:23 final size:21
Alignment explanation
Indices: 35560374--35560435 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 21
35560364 TTATAAAGAA
35560374 AAATAATTTTATTAAAAATATAT
1 AAATAATTTTA-TAAAAAT-TAT
*
35560397 CAATATATTTGTA-AAAAATTAT
1 AAATA-ATTT-TATAAAAATTAT
*
35560419 AAATAGTTTTAATAAAA
1 AAATAATTTT-ATAAAA
35560436 TAATATTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
20 1 0.03
21 4 0.12
22 11 0.34
23 10 0.31
24 4 0.12
25 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (21 bp):
AAATAATTTTATAAAAATTAT
Found at i:35567695 original size:3 final size:3
Alignment explanation
Indices: 35567687--35567723 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
35567677 CTTTCAACTT
35567687 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
35567724 CTTCCAACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:35568054 original size:5 final size:5
Alignment explanation
Indices: 35568044--35568068 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
35568034 TACCCAGTAT
35568044 GAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA
35568069 TGACAAGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:35572239 original size:37 final size:37
Alignment explanation
Indices: 35572178--35572323 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
35572168 TACGTATGAT
* *
35572178 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
35572213 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
35572250 CACTTATCACTTTATTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
35572287 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
35572324 TAAAGCTATC
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 90 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:35572340 original size:46 final size:46
Alignment explanation
Indices: 35572287--35572555 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
35572277 TAAGTGTAGC
* **
35572287 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
35572333 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
35572379 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
35572431 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
35572477 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
35572529 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
35572556 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:35572406 original size:52 final size:52
Alignment explanation
Indices: 35572330--35572549 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
35572320 TAGCTAAAGC
* *
35572330 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
35572383 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
35572435 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
35572481 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
35572533 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
35572550 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:35572452 original size:98 final size:98
Alignment explanation
Indices: 35572287--35572555 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
35572277 TAAGTGTAGC
* * *
35572287 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
35572352 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
35572386 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
35572451 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
35572484 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
35572549 GATCAGA
66 GATCAGA
35572556 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:35574685 original size:49 final size:47
Alignment explanation
Indices: 35574632--35574777 Score: 168
Period size: 49 Copynumber: 3.0 Consensus size: 47
35574622 TGCTTTATCA
* *
35574632 TATAACTGGAGGCCT-AGCCTCTTTTAGTAACTGGGGCAAAAGCCCTTTT
1 TATAACTGG-GGCATAAGCC-CTTTTA-TAACTGGGGCATAAGCCCTTTT
* *
35574681 TATAACTGGGGCATAAGCCCTTCATCACAACTGGGGCATAAGCCCTTTAT
1 TATAACTGGGGCATAAGCCCTT--TTATAACTGGGGCATAAGCCCTTT-T
* * *
35574731 CACAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTT
1 TATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTT
35574778 GCACTTCCTC
Statistics
Matches: 85, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
47 1 0.01
48 29 0.34
49 32 0.38
50 23 0.27
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (47 bp):
TATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTT
Found at i:35574686 original size:24 final size:24
Alignment explanation
Indices: 35574633--35574777 Score: 161
Period size: 25 Copynumber: 6.0 Consensus size: 24
35574623 GCTTTATCAT
*
35574633 ATAACTGGAGGCCT-AGCCTCTTTT-
1 ATAACTGG-GGCATAAGCC-CTTTTC
* *
35574657 AGTAACTGGGGCAAAAGCCCTTTTT
1 A-TAACTGGGGCATAAGCCCTTTTC
*
35574682 ATAACTGGGGCATAAGCCCTTCATC
1 ATAACTGGGGCATAAGCCCTT-TTC
*
35574707 ACAACTGGGGCATAAGCCCTTTATC
1 ATAACTGGGGCATAAGCCCTTT-TC
* *
35574732 ACAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTC
35574755 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
35574778 GCACTTCCTC
Statistics
Matches: 106, Mismatches: 9, Indels: 12
0.83 0.07 0.09
Matches are distributed among these distances:
23 19 0.18
24 33 0.31
25 54 0.51
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTC
Found at i:35574849 original size:9 final size:9
Alignment explanation
Indices: 35574835--35574891 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
35574825 ATCTCATGTG
35574835 CATATCATA
1 CATATCATA
*
35574844 CATATCATGTG
1 CATATCA--TA
35574855 CATATCATA
1 CATATCATA
* *
35574864 CATGTCATGTG
1 CATATCA--TA
35574875 CATATCATA
1 CATATCATA
35574884 CATATCAT
1 CATATCAT
35574892 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:35574851 original size:20 final size:20
Alignment explanation
Indices: 35574823--35574893 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
35574813 GCATTTATGA
*
35574823 ACATCTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
35574843 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
35574863 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
35574883 ACATATCATGT
1 ACATATCATGT
35574894 TTATCAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:35574858 original size:11 final size:11
Alignment explanation
Indices: 35574828--35574882 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
35574818 TATGAACATC
35574828 TCATGTGCATA
1 TCATGTGCATA
*
35574839 TCA--TACATA
1 TCATGTGCATA
35574848 TCATGTGCATA
1 TCATGTGCATA
* *
35574859 TCA--TACATG
1 TCATGTGCATA
35574868 TCATGTGCATA
1 TCATGTGCATA
35574879 TCAT
1 TCAT
35574883 ACATATCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:35574958 original size:25 final size:25
Alignment explanation
Indices: 35574930--35574977 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
35574920 ATATATAAAC
* * *
35574930 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
35574955 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
35574978 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:35576199 original size:27 final size:27
Alignment explanation
Indices: 35576140--35576214 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
35576130 CATATTCGTT
35576140 ATTTTACCATACAGGGGTATTACGGTC
1 ATTTTACCATACAGGGGTATTACGGTC
* *
35576167 ACTTTACCCTACAGGGGCT-TTACGGTC
1 ATTTTACCATACAGGGG-TATTACGGTC
* *
35576194 TTTTTACC-TGATAGGGGTATT
1 ATTTTACCAT-ACAGGGGTATT
35576215 TTAGTCATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
26 2 0.05
27 37 0.93
28 1 0.03
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (27 bp):
ATTTTACCATACAGGGGTATTACGGTC
Found at i:35576285 original size:27 final size:27
Alignment explanation
Indices: 35576255--35576484 Score: 147
Period size: 27 Copynumber: 8.4 Consensus size: 27
35576245 GTAAATCTAC
*
35576255 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTAT
* *
35576282 AAACCAATGGTATTTCTA-TAATTTTTAG
1 AAACCAAGGGTATTTC-AGTAA-TTTTAT
* * * *
35576310 AAAGTCAAGGGTATTTCTGTAACTTTGT
1 AAA-CCAAGGGTATTTCAGTAATTTTAT
* * **
35576338 AAATCAGGGGTATTTTGGTAATTTTAT
1 AAACCAAGGGTATTTCAGTAATTTTAT
*** * * *
35576365 AAATTGAGGGTATTTCGGTAATTTCAC
1 AAACCAAGGGTATTTCAGTAATTTTAT
* ** *
35576392 AAACCAATGGTATTTTGGTAATTTTAC
1 AAACCAAGGGTATTTCAGTAATTTTAT
* * ** *
35576419 AAACTAGGGGTATTTTGGTAATTTTAC
1 AAACCAAGGGTATTTCAGTAATTTTAT
* * *
35576446 AAACTAAGGGTATTTTAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTAT
* *
35576473 AAATCGAGGGTA
1 AAACCAAGGGTA
35576485 AAACAGTAAT
Statistics
Matches: 163, Mismatches: 36, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
27 135 0.83
28 14 0.09
29 14 0.09
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.40
Consensus pattern (27 bp):
AAACCAAGGGTATTTCAGTAATTTTAT
Found at i:35576404 original size:54 final size:54
Alignment explanation
Indices: 35576345--35576484 Score: 183
Period size: 54 Copynumber: 2.6 Consensus size: 54
35576335 TGTAAATCAG
35576345 GGGTATTTTGGTAATTTTATAAATTGAGGGTATTTCGGTAATTTCACAAACCAA
1 GGGTATTTTGGTAATTTTATAAATTGAGGGTATTTCGGTAATTTCACAAACCAA
* * * * * *
35576399 TGGTATTTTGGTAATTTTACAAACT-AGGGGTATTTTGGTAATTTTACAAACTAA
1 GGGTATTTTGGTAATTTTATAAATTGA-GGGTATTTCGGTAATTTCACAAACCAA
* * *
35576453 GGGTATTTTAGTAATTTTGTAAATCGAGGGTA
1 GGGTATTTTGGTAATTTTATAAATTGAGGGTA
35576485 AAACAGTAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
53 1 0.01
54 70 0.97
55 1 0.01
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTATAAATTGAGGGTATTTCGGTAATTTCACAAACCAA
Found at i:35576673 original size:27 final size:27
Alignment explanation
Indices: 35576463--35576665 Score: 237
Period size: 27 Copynumber: 7.5 Consensus size: 27
35576453 GGGTATTTTA
* *
35576463 GTAATTTTGTAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * **
35576490 GTAATTCTGTAAATCAATGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
35576517 GTAATTCTATAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
35576544 GTAATTCTATAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
35576571 GTAATTCTGTAAGTCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * * *
35576598 ATAATTATGTAAATC-AGGGGTAGAATG
1 GTAATTCTGTAAATCGA-GGGTAAAACG
* * *
35576625 GTAATTATGTAAATCGGGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
35576652 GTAATTTTGTAAAT
1 GTAATTCTGTAAAT
35576666 TGGGGGTACT
Statistics
Matches: 154, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
26 1 0.01
27 153 0.99
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.30
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAACG
Found at i:35576727 original size:27 final size:27
Alignment explanation
Indices: 35576679--35576768 Score: 103
Period size: 27 Copynumber: 3.3 Consensus size: 27
35576669 GGGTACTTTG
* * *
35576679 GTAATTTTACAAGTTGAAGGTATTTCA
1 GTAATTTTACAAATCGAGGGTATTTCA
35576706 GTAATTTTACAAATCGAGGGTATTTCA
1 GTAATTTTACAAATCGAGGGTATTTCA
* *
35576733 GTATTTTTACAAA-CTAAGGGTATTTC-
1 GTAATTTTACAAATC-GAGGGTATTTCA
35576759 GATAATTTTA
1 G-TAATTTTA
35576769 GTAAACTAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
26 2 0.04
27 53 0.96
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (27 bp):
GTAATTTTACAAATCGAGGGTATTTCA
Found at i:35579779 original size:23 final size:24
Alignment explanation
Indices: 35579733--35579787 Score: 94
Period size: 23 Copynumber: 2.3 Consensus size: 24
35579723 CAGCAACTAA
35579733 TAAATTTGTCCCAACTAAGACACAT
1 TAAA-TTGTCCCAACTAAGACACAT
35579758 TAAATTGTCCCAAC-AAGACACAT
1 TAAATTGTCCCAACTAAGACACAT
35579781 TAAATTG
1 TAAATTG
35579788 ATGCATGAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 16 0.53
24 10 0.33
25 4 0.13
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.27
Consensus pattern (24 bp):
TAAATTGTCCCAACTAAGACACAT
Found at i:35582747 original size:31 final size:28
Alignment explanation
Indices: 35582712--35582780 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 28
35582702 TATTTTGTGC
35582712 TTTTTTTTTGAATATTTATCAAATTTTATAA
1 TTTTTTTTTGAAT-TTTAT-AAATTTTA-AA
**
35582743 TTTTTTATTTTTATTTTATAAATTTTAAA
1 TTTTTT-TTTGAATTTTATAAATTTTAAA
*
35582772 TTATTTTTT
1 TTTTTTTTT
35582781 AACGTAACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 3 0.09
29 7 0.21
30 8 0.24
31 11 0.32
32 5 0.15
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (28 bp):
TTTTTTTTTGAATTTTATAAATTTTAAA
Found at i:35583531 original size:19 final size:19
Alignment explanation
Indices: 35583496--35583552 Score: 71
Period size: 18 Copynumber: 3.0 Consensus size: 19
35583486 AAGGAAAATC
*
35583496 AAAATAATTTTAAAAAATTT
1 AAAATAATTTT-TAAAATTT
*
35583516 AAAATAATTTTTAAAATTC
1 AAAATAATTTTTAAAATTT
*
35583535 AAAAT-ATTTATAAAATTT
1 AAAATAATTTTTAAAATTT
35583553 CCAAAATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.33
19 11 0.33
20 11 0.33
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATAATTTTTAAAATTT
Found at i:35583548 original size:18 final size:19
Alignment explanation
Indices: 35583490--35583551 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
35583480 ATTACAAAGG
*
35583490 AAAA-TCAAAATAATTTTAA
1 AAAATTCAAAATAA-TTTAT
* *
35583509 AAAATTTAAAATAATTTTT
1 AAAATTCAAAATAATTTAT
35583528 AAAATTCAAAAT-ATTTAT
1 AAAATTCAAAATAATTTAT
35583546 AAAATT
1 AAAATT
35583552 TCCAAAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
18 11 0.30
19 18 0.49
20 8 0.22
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATTCAAAATAATTTAT
Found at i:35583561 original size:18 final size:17
Alignment explanation
Indices: 35583521--35583564 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
35583511 AATTTAAAAT
*
35583521 AATTTTTAAAATTCAAA
1 AATTTATAAAATTCAAA
*
35583538 ATATTTATAAAATTTCCAA
1 A-ATTTATAAAA-TTCAAA
35583557 AATTTATA
1 AATTTATA
35583565 TTTTTTAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 16 0.70
19 6 0.26
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTTATAAAATTCAAA
Found at i:35583763 original size:16 final size:17
Alignment explanation
Indices: 35583733--35583765 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
35583723 CTTTAAAAAA
35583733 GTTTTCAAATATATATG
1 GTTTTCAAATATATATG
*
35583750 GTTTT-AAATTTATATG
1 GTTTTCAAATATATATG
35583766 CTCTAACATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.52
Consensus pattern (17 bp):
GTTTTCAAATATATATG
Found at i:35602038 original size:21 final size:23
Alignment explanation
Indices: 35602007--35602077 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
35601997 AAGATTAAAT
* *
35602007 CATAATAATCATTCAAAC-CA-A
1 CATAATCATCAGTCAAACTCACA
* *
35602028 CTTAATCATCAGTCATACTCACA
1 CATAATCATCAGTCAAACTCACA
*
35602051 CATAATCATCAGTCATACTCACA
1 CATAATCATCAGTCAAACTCACA
35602074 CATA
1 CATA
35602078 CATTAGTGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
21 14 0.33
22 2 0.05
23 27 0.63
ACGTcount: A:0.42, C:0.28, G:0.03, T:0.27
Consensus pattern (23 bp):
CATAATCATCAGTCAAACTCACA
Found at i:35602056 original size:23 final size:23
Alignment explanation
Indices: 35602030--35602077 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
35602020 CAAACCAACT
35602030 TAATCATCAGTCATACTCACACA
1 TAATCATCAGTCATACTCACACA
35602053 TAATCATCAGTCATACTCACACA
1 TAATCATCAGTCATACTCACACA
35602076 TA
1 TA
35602078 CATTAGTGTT
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:0.40, C:0.29, G:0.04, T:0.27
Consensus pattern (23 bp):
TAATCATCAGTCATACTCACACA
Found at i:35608362 original size:25 final size:24
Alignment explanation
Indices: 35608328--35608379 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
35608318 GAACTTTCCT
*
35608328 TTTTCATTTCATTTTATTTAATTTC
1 TTTTCATTTCATTTCATTT-ATTTC
* * *
35608353 TTTTCCTTTCCTTTCCTTTATTTC
1 TTTTCATTTCATTTCATTTATTTC
35608377 TTT
1 TTT
35608380 GTTTTCCTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTTCATTTCATTTCATTTATTTC
Found at i:35608860 original size:43 final size:43
Alignment explanation
Indices: 35608813--35608898 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
35608803 AAAAAAAAGA
*
35608813 GTGAAGGATAAAAAATTTGTAATTGTTTGAAAAACCTCAAAAC
1 GTGAAGGATAAAAAATTTGTAATGGTTTGAAAAACCTCAAAAC
*
35608856 GTGAATGATAAAAAATTTGTAATGGTTTGAAAAACCTCAAAAC
1 GTGAAGGATAAAAAATTTGTAATGGTTTGAAAAACCTCAAAAC
35608899 TAAGTATTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.28
Consensus pattern (43 bp):
GTGAAGGATAAAAAATTTGTAATGGTTTGAAAAACCTCAAAAC
Found at i:35610345 original size:17 final size:18
Alignment explanation
Indices: 35610323--35610364 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
35610313 GATATTATTT
35610323 ATTAAATTAATTTTC-CA
1 ATTAAATTAATTTTCTCA
35610340 ATTAAA-TAATTTTCTCA
1 ATTAAATTAATTTTCTCA
*
35610357 AGTAAATT
1 ATTAAATT
35610365 TTAATTCCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 8 0.36
17 13 0.59
18 1 0.05
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAAATTAATTTTCTCA
Found at i:35611466 original size:172 final size:172
Alignment explanation
Indices: 35611180--35611523 Score: 607
Period size: 172 Copynumber: 2.0 Consensus size: 172
35611170 GCCTTAAAGG
*
35611180 TAGCTTGGGGGATACACTTGATTTCACTTGGATTAAATAAGAACTATTTTATTTCCTTTCCAAAT
1 TAGCTTGGGCGATACACTTGATTTCACTTGGATTAAATAAGAACTATTTTATTTCCTTTCCAAAT
* * *
35611245 TCATGCGTCAATAGCTACTGCTATTTCATTTCCTTGTTCTTGCAAAATTTATTTAATTGCTTTTC
66 TCATGCGTCAATAGCTACTGCAATTCCATTTCCTTGCTCTTGCAAAATTTATTTAATTGCTTTTC
*
35611310 AAGTCTCTTCCTTTCCCAATTTCCACCATTTTCATTTAAACT
131 AAGTCTCTTCCTTTCCCAATTTCCACCATTTTCATTCAAACT
*
35611352 TAGCTTGGGCGATACACTTGGTTTCACTTGGATTAAATAAGAACTATTTTATTTCCTTTCCAAAT
1 TAGCTTGGGCGATACACTTGATTTCACTTGGATTAAATAAGAACTATTTTATTTCCTTTCCAAAT
* * *
35611417 TCATGCGTGAATAGCTACTGCAATTCCATTTCCTTGCTCTTGCAAAATTTGTTTATTTGCTTTTC
66 TCATGCGTCAATAGCTACTGCAATTCCATTTCCTTGCTCTTGCAAAATTTATTTAATTGCTTTTC
35611482 AAGTCTCTTCCTTTCCCAATTTCCACCATTTTCATTCAAACT
131 AAGTCTCTTCCTTTCCCAATTTCCACCATTTTCATTCAAACT
35611524 CATTCCATAG
Statistics
Matches: 163, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
172 163 1.00
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.43
Consensus pattern (172 bp):
TAGCTTGGGCGATACACTTGATTTCACTTGGATTAAATAAGAACTATTTTATTTCCTTTCCAAAT
TCATGCGTCAATAGCTACTGCAATTCCATTTCCTTGCTCTTGCAAAATTTATTTAATTGCTTTTC
AAGTCTCTTCCTTTCCCAATTTCCACCATTTTCATTCAAACT
Found at i:35613661 original size:30 final size:30
Alignment explanation
Indices: 35613625--35613682 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
35613615 AAGACGAATT
* *
35613625 CCACACGGGCTGAG-CACATGCCCGTGTGAG
1 CCACACGGGCT-AGCCACACGCCCATGTGAG
35613655 CCACACGGGCTAGCCACACGCCCATGTG
1 CCACACGGGCTAGCCACACGCCCATGTG
35613683 GCAGCCCGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.21, C:0.38, G:0.29, T:0.12
Consensus pattern (30 bp):
CCACACGGGCTAGCCACACGCCCATGTGAG
Found at i:35621522 original size:16 final size:16
Alignment explanation
Indices: 35621503--35621533 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
35621493 AAACTGAGAA
35621503 AAAAATAAAAATAAAT
1 AAAAATAAAAATAAAT
35621519 AAAAATAAAAATAAA
1 AAAAATAAAAATAAA
35621534 GAACACATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAATAAAAATAAAT
Found at i:35632241 original size:23 final size:24
Alignment explanation
Indices: 35632191--35632242 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
35632181 TTGTTTTATT
* * *
35632191 TTTATTTTTATTTTTTTGCCCTTA
1 TTTATTGTTATTTTATTGCCATTA
35632215 -TTATTGTTATTTTATT-CCATTA
1 TTTATTGTTATTTTATTGCCATTA
35632237 TTTATT
1 TTTATT
35632243 TGTTTATTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.17, C:0.10, G:0.04, T:0.69
Consensus pattern (24 bp):
TTTATTGTTATTTTATTGCCATTA
Found at i:35632307 original size:18 final size:18
Alignment explanation
Indices: 35632277--35632362 Score: 102
Period size: 18 Copynumber: 4.7 Consensus size: 18
35632267 TAAAATTTAG
*
35632277 ATTATTCATTATTATTATT
1 ATTATT-ATTATTATTGTT
35632296 ATTATTATTATTATTGTT
1 ATTATTATTATTATTGTT
*
35632314 ATTGTTATTATTATTGTT
1 ATTATTATTATTATTGTT
* *
35632332 ATTGTTATTATCA-TGTT
1 ATTATTATTATTATTGTT
*
35632349 CATCATTATTATTA
1 -ATTATTATTATTA
35632363 CTATTTATGC
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
17 4 0.07
18 50 0.83
19 6 0.10
ACGTcount: A:0.28, C:0.05, G:0.06, T:0.62
Consensus pattern (18 bp):
ATTATTATTATTATTGTT
Found at i:35632362 original size:3 final size:3
Alignment explanation
Indices: 35632277--35632342 Score: 87
Period size: 3 Copynumber: 21.7 Consensus size: 3
35632267 TAAAATTTAG
* *
35632277 ATT ATT CATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT GTT ATT
1 ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
35632323 ATT ATT GTT ATT GTT ATT AT
1 ATT ATT ATT ATT ATT ATT AT
35632343 CATGTTCATC
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
3 51 0.94
4 3 0.06
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:35632384 original size:28 final size:29
Alignment explanation
Indices: 35632339--35632394 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
35632329 GTTATTGTTA
* *
35632339 TTATCATGTTCATCATTATTATT-ACTAT
1 TTATCATGTTCAACATTATGATTCACTAT
35632367 TTATGCATGTT-AACATTATGATTCACTA
1 TTAT-CATGTTCAACATTATGATTCACTA
35632395 ATATCATTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.30, C:0.14, G:0.07, T:0.48
Consensus pattern (29 bp):
TTATCATGTTCAACATTATGATTCACTAT
Found at i:35639830 original size:81 final size:80
Alignment explanation
Indices: 35639675--35639833 Score: 196
Period size: 81 Copynumber: 2.0 Consensus size: 80
35639665 AATTTTCTTT
* * *
35639675 TATTCTTTTCATTTCATTCATAATCATATCATACAGATAATTATTCTTAGATTCTTTTGTTCTTT
1 TATTCTTTTCATTTCATTCATAATCATACCATACAGATAATTATTCTTAGATTATTTTGTCCTTT
*
35639740 ACATTTTCTTTCAAA
66 ACATCTTCTTTCAAA
* * *
35639755 TATTCTTTT-ATTCTTCATTCATGATCATACCATATA-ACTAATTATTCTTATATTATTTTGTCC
1 TATTCTTTTCA-T-TTCATTCATAATCATACCATACAGA-TAATTATTCTTAGATTATTTTGTCC
**
35639818 TTTGGATCTTCTTTCA
63 TTTACATCTTCTTTCA
35639834 TCCCTATAAC
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
79 1 0.01
80 11 0.16
81 55 0.82
ACGTcount: A:0.26, C:0.17, G:0.04, T:0.53
Consensus pattern (80 bp):
TATTCTTTTCATTTCATTCATAATCATACCATACAGATAATTATTCTTAGATTATTTTGTCCTTT
ACATCTTCTTTCAAA
Found at i:35644287 original size:44 final size:44
Alignment explanation
Indices: 35644224--35644333 Score: 130
Period size: 44 Copynumber: 2.5 Consensus size: 44
35644214 CATGGAAAAT
* ** * *
35644224 CTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCGTTAAC
1 CTTATCTCCCTAAAGTTGCAGTGGAACAGATTAAAACCATTAAC
* *
35644268 CTTATCTCCTTAAAGTTGCAGTGGAACAGATTAAAACCATTAAT
1 CTTATCTCCCTAAAGTTGCAGTGGAACAGATTAAAACCATTAAC
* * *
35644312 CTTATCTCTCTGAAGCTGCAGT
1 CTTATCTCCCTAAAGTTGCAGT
35644334 AGAGCAGGTT
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (44 bp):
CTTATCTCCCTAAAGTTGCAGTGGAACAGATTAAAACCATTAAC
Found at i:35644756 original size:89 final size:89
Alignment explanation
Indices: 35644575--35644838 Score: 298
Period size: 89 Copynumber: 3.0 Consensus size: 89
35644565 AATGGAGAAT
* **
35644575 CTTATCTCCCTGAAGTTGCAATGGAGTAGACTAAAGCCA-CGAATCTTATC-CCCTTGAAGTTAC
1 CTTATCTCCATGAAGTTGCAATGGAGTAGACTAAAGAAAGCGAATCTTATCTCCC-TGAAGTTAC
* * * * *
35644638 AATGGAACAGATTAAAGCCACACAT
65 AATGGAGCAGATTAAAGCTATAAAC
** * * * *
35644663 CTTATCTCTTTGAAGTTGCAGTGGAGCAGACTAAAGAAAGCAAATCTTATCTCTCTGAAGTTACA
1 CTTATCTCCATGAAGTTGCAATGGAGTAGACTAAAGAAAGCGAATCTTATCTCCCTGAAGTTACA
*
35644728 ATAGAGCAGATTAAAGCTATAAAC
66 ATGGAGCAGATTAAAGCTATAAAC
* * * * * *
35644752 CTTATCTCCATGAAATTGCAATGGAGTAGATTGAAGATAGCGAATCTCATTTCCCTGAAGTTACA
1 CTTATCTCCATGAAGTTGCAATGGAGTAGACTAAAGAAAGCGAATCTTATCTCCCTGAAGTTACA
* *
35644817 GTGGGGCAGATTAAAGCTATAA
66 ATGGAGCAGATTAAAGCTATAA
35644839 GTCACAAATC
Statistics
Matches: 145, Mismatches: 29, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
88 33 0.23
89 110 0.76
90 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (89 bp):
CTTATCTCCATGAAGTTGCAATGGAGTAGACTAAAGAAAGCGAATCTTATCTCCCTGAAGTTACA
ATGGAGCAGATTAAAGCTATAAAC
Found at i:35644783 original size:44 final size:44
Alignment explanation
Indices: 35644572--35644833 Score: 211
Period size: 44 Copynumber: 5.9 Consensus size: 44
35644562 GAAAATGGAG
* * * *
35644572 AATCTTATCTCCCTGAAGTTGCAATGGAGTAGACTAAAGCCACG
1 AATCTTATCTCCTTGAAGTTGCAATGGAGCAGATTAAAGCCACA
* * *
35644616 AATCTTATCCCCTTGAAGTTACAATGGAACAGATTAAAGCCACA
1 AATCTTATCTCCTTGAAGTTGCAATGGAGCAGATTAAAGCCACA
* * * * **
35644660 CATCTTATCTCTTTGAAGTTGCAGTGGAGCAGACTAAAGAAAGCA
1 AATCTTATCTCCTTGAAGTTGCAATGGAGCAGATTAAAGCCA-CA
* * * *
35644705 AATCTTATCT-CTCTGAAGTTACAATAGAGCAGATTAAAGCTATA
1 AATCTTATCTCCT-TGAAGTTGCAATGGAGCAGATTAAAGCCACA
* * * * * ** *
35644749 AACCTTATCTCCATGAAATTGCAATGGAGTAGATTGAAGATAGCG
1 AATCTTATCTCCTTGAAGTTGCAATGGAGCAGATTAAAGCCA-CA
* * * * * *
35644794 AATCTCATTTCCCTGAAGTTACAGTGGGGCAGATTAAAGC
1 AATCTTATCTCCTTGAAGTTGCAATGGAGCAGATTAAAGC
35644834 TATAAGTCAC
Statistics
Matches: 168, Mismatches: 46, Indels: 7
0.76 0.21 0.03
Matches are distributed among these distances:
44 104 0.62
45 64 0.38
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (44 bp):
AATCTTATCTCCTTGAAGTTGCAATGGAGCAGATTAAAGCCACA
Found at i:35646609 original size:12 final size:12
Alignment explanation
Indices: 35646564--35646603 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
35646554 CAAAATTTAG
*
35646564 ATTATTCATTATT
1 ATTATT-ATTGTT
35646577 ATTATTATTGTT
1 ATTATTATTGTT
35646589 ATTATTATTGTT
1 ATTATTATTGTT
35646601 ATT
1 ATT
35646604 TATATTATCG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 20 0.77
13 6 0.23
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.65
Consensus pattern (12 bp):
ATTATTATTGTT
Found at i:35646631 original size:3 final size:3
Alignment explanation
Indices: 35646564--35646603 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
35646554 CAAAATTTAG
* *
35646564 ATT ATT CATT ATT ATT ATT ATT GTT ATT ATT ATT GTT ATT
1 ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
35646604 TATATTATCG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:35648437 original size:3 final size:3
Alignment explanation
Indices: 35648429--35648469 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
35648419 TAAATCCTTT
35648429 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
35648470 GTTATTAAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:35651642 original size:16 final size:17
Alignment explanation
Indices: 35651623--35651654 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
35651613 TTTTAAAAAT
35651623 TAATATAAT-TAACTTG
1 TAATATAATATAACTTG
35651639 TAATATAATATAACTT
1 TAATATAATATAACTT
35651655 TTATAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (17 bp):
TAATATAATATAACTTG
Found at i:35653143 original size:17 final size:17
Alignment explanation
Indices: 35653122--35653166 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
35653112 AGTTTTTCAC
35653122 ATATTATATATTTTAAA
1 ATATTATATATTTTAAA
* **
35653139 CTATTATCCATTTTAAA
1 ATATTATATATTTTAAA
*
35653156 ATTTTATATAT
1 ATATTATATAT
35653167 ATTATTTACT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATTATATATTTTAAA
Found at i:35653179 original size:26 final size:26
Alignment explanation
Indices: 35653150--35653214 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
35653140 TATTATCCAT
* *
35653150 TTTAAAATTTTATATATATTATTTAC
1 TTTAAAATATTATATATAATATTTAC
* *
35653176 TTTAAACTATTATATATAATATTTAT
1 TTTAAAATATTATATATAATATTTAC
* *
35653202 TTTGAATTATTAT
1 TTTAAAATATTAT
35653215 TTTTTATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (26 bp):
TTTAAAATATTATATATAATATTTAC
Found at i:35653276 original size:27 final size:27
Alignment explanation
Indices: 35653246--35653313 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
35653236 AAAAAAATTG
* *
35653246 TTTTGTATATTTTTTAT-TTAAATTTCT
1 TTTTATATATTATTTATCTTAAA-TTCT
35653273 TTTTATATATTATTTATCTTAAATTC-
1 TTTTATATATTATTTATCTTAAATTCT
*
35653299 TTTTATATTTTATTT
1 TTTTATATATTATTT
35653314 TAAGGTGTCT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 14 0.38
27 18 0.49
28 5 0.14
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.69
Consensus pattern (27 bp):
TTTTATATATTATTTATCTTAAATTCT
Found at i:35653315 original size:27 final size:26
Alignment explanation
Indices: 35653240--35653315 Score: 84
Period size: 27 Copynumber: 2.9 Consensus size: 26
35653230 TTTTTAAAAA
* *
35653240 AAATTGTTTTGTATATT-TTTTATTT
1 AAATTCTTTTATATATTATTTTATTT
35653265 AAATTTCTTTTTATATATTA-TTTATCTT
1 AAA-TTC-TTTTATATATTATTTTAT-TT
*
35653293 AAATTCTTTTATATTTTATTTTA
1 AAATTCTTTTATATATTATTTTA
35653316 AGGTGTCTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
25 3 0.07
26 13 0.30
27 22 0.51
28 5 0.12
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.66
Consensus pattern (26 bp):
AAATTCTTTTATATATTATTTTATTT
Found at i:35653382 original size:26 final size:26
Alignment explanation
Indices: 35653240--35653433 Score: 159
Period size: 26 Copynumber: 7.7 Consensus size: 26
35653230 TTTTTAAAAA
* *
35653240 AAATTGTTTTGTATATTTTTTA-TTT
1 AAATTGTTTTATATATTATTTATTTT
* *
35653265 AAATTTCTTTTTATATATTATTTATCTT
1 AAA-TT-GTTTTATATATTATTTATTTT
*
35653293 AAATT-CTTT-TATA-T-TTTATTTT
1 AAATTGTTTTATATATTATTTATTTT
** *
35653315 AAGGTGTCTTATATATTATTTATTTT
1 AAATTGTTTTATATATTATTTATTTT
* * *
35653341 AAGTTGCTTTGTATATTATTTATTTT
1 AAATTGTTTTATATATTATTTATTTT
* * **
35653367 AATTTGTTTTACATATTACGTATTTT
1 AAATTGTTTTATATATTATTTATTTT
* * *
35653393 AAATTG-TTT-TATACTATTTACTTC
1 AAATTGTTTTATATATTATTTATTTT
35653417 AAATTGTTTTATATATT
1 AAATTGTTTTATATATT
35653434 TTTTGTTTCG
Statistics
Matches: 132, Mismatches: 28, Indels: 17
0.75 0.16 0.10
Matches are distributed among these distances:
22 10 0.08
23 3 0.02
24 23 0.17
25 13 0.10
26 62 0.47
27 16 0.12
28 5 0.04
ACGTcount: A:0.27, C:0.05, G:0.06, T:0.61
Consensus pattern (26 bp):
AAATTGTTTTATATATTATTTATTTT
Found at i:35653427 original size:50 final size:52
Alignment explanation
Indices: 35653335--35653433 Score: 130
Period size: 50 Copynumber: 1.9 Consensus size: 52
35653325 ATATATTATT
* * * * *
35653335 TATTTTAAGTTGCTTTGTATATTATTTATTTTAATTTGTTTTACATATTACG
1 TATTTTAAATTGCTTTGTATACTATTTACTTCAAATTGTTTTACATATTACG
*
35653387 TATTTTAAATTG-TTT-TATACTATTTACTTCAAATTGTTTTATATATT
1 TATTTTAAATTGCTTTGTATACTATTTACTTCAAATTGTTTTACATATT
35653434 TTTTGTTTCG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 27 0.66
51 3 0.07
52 11 0.27
ACGTcount: A:0.27, C:0.06, G:0.07, T:0.60
Consensus pattern (52 bp):
TATTTTAAATTGCTTTGTATACTATTTACTTCAAATTGTTTTACATATTACG
Found at i:35656976 original size:22 final size:22
Alignment explanation
Indices: 35656954--35657000 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
35656944 ATGCTTTTTA
35656954 TATTTCAATATTATTACAATTAT
1 TATTT-AATATTATTACAATTAT
*
35656977 TATTTATTATTATTACTAA-TAT
1 TATTTAATATTATTAC-AATTAT
35656999 TA
1 TA
35657001 GGGTATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTTAATATTATTACAATTAT
Found at i:35658831 original size:45 final size:45
Alignment explanation
Indices: 35658767--35658858 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
35658757 AGTTATTTTA
35658767 AATTTCAAGTTAAAAAATGAATATTTCATATTTACTTTTAAGATC
1 AATTTCAAGTTAAAAAATGAATATTTCATATTTACTTTTAAGATC
35658812 AATTTCAAGTTAAAAAATGAATATTTCATATTTACTTTTAAGATC
1 AATTTCAAGTTAAAAAATGAATATTTCATATTTACTTTTAAGATC
35658857 AA
1 AA
35658859 ACGTTTGAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (45 bp):
AATTTCAAGTTAAAAAATGAATATTTCATATTTACTTTTAAGATC
Found at i:35660274 original size:24 final size:25
Alignment explanation
Indices: 35660238--35660292 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 25
35660228 TGACTAGTTC
35660238 AAAATAAATAAATTATTTAAAAA-ATA
1 AAAATAAATAAA-TA-TTAAAAATATA
35660264 AAAAT-AA-AAATATTAAAAATTATA
1 AAAATAAATAAATATTAAAAA-TATA
35660288 AAAAT
1 AAAAT
35660293 CAGTTCAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 7 0.26
23 2 0.07
24 11 0.41
25 2 0.07
26 5 0.19
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (25 bp):
AAAATAAATAAATATTAAAAATATA
Found at i:35660735 original size:14 final size:15
Alignment explanation
Indices: 35660716--35660746 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
35660706 ATTTTTATAA
35660716 TTTTTAAT-ATTTAT
1 TTTTTAATAATTTAT
35660730 TTTTTAATAATTTAT
1 TTTTTAATAATTTAT
35660745 TT
1 TT
35660747 ACTTTAAATC
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:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTAATAATTTAT
Found at i:35663067 original size:22 final size:22
Alignment explanation
Indices: 35663039--35663091 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
35663029 TAATACCAAA
35663039 CCCCATACCCCCACTACAACAG
1 CCCCATACCCCCACTACAACAG
*
35663061 CCCCATACCTCCACTACAACAG
1 CCCCATACCCCCACTACAACAG
*
35663083 TCCCATACC
1 CCCCATACC
35663092 GTCTGACACC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.30, C:0.53, G:0.04, T:0.13
Consensus pattern (22 bp):
CCCCATACCCCCACTACAACAG
Found at i:35663400 original size:26 final size:25
Alignment explanation
Indices: 35663367--35663420 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 25
35663357 CTTGGTTCTA
35663367 TTTTTATTTT-TATTTAGTTTTTTTC
1 TTTTTATTTTCT-TTTAGTTTTTTTC
*
35663392 TTTTGTATTTTCTTTTATTTTTTTTC
1 TTTT-TATTTTCTTTTAGTTTTTTTC
35663418 TTT
1 TTT
35663421 CTCTTCGCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 4 0.15
26 21 0.81
27 1 0.04
ACGTcount: A:0.09, C:0.06, G:0.04, T:0.81
Consensus pattern (25 bp):
TTTTTATTTTCTTTTAGTTTTTTTC
Found at i:35664353 original size:3 final size:3
Alignment explanation
Indices: 35664331--35664388 Score: 53
Period size: 3 Copynumber: 18.3 Consensus size: 3
35664321 TTTTTATTTA
* * * *
35664331 TAT TAT TGT TAG TAT CAT TAT TAT TAT TAT CTCCAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -T--AT TAT TAT TAT TAT
35664379 TAT TAT TAT T
1 TAT TAT TAT T
35664389 CTCTTGTTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
3 40 0.91
4 1 0.02
5 1 0.02
6 2 0.05
ACGTcount: A:0.29, C:0.09, G:0.03, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:35664427 original size:20 final size:19
Alignment explanation
Indices: 35664390--35664441 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
35664380 ATTATTATTC
35664390 TCTTGTTATA-T-TACTAT
1 TCTTGTTATATTATACTAT
35664407 TCTTGTTATATTATCACTAT
1 TCTTGTTATATTAT-ACTAT
* *
35664427 TTTTCTTACTATTAT
1 TCTTGTTA-TATTAT
35664442 TATTACTACA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 10 0.34
18 1 0.03
19 1 0.03
20 11 0.38
21 6 0.21
ACGTcount: A:0.23, C:0.13, G:0.04, T:0.60
Consensus pattern (19 bp):
TCTTGTTATATTATACTAT
Found at i:35664757 original size:15 final size:15
Alignment explanation
Indices: 35664737--35664767 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
35664727 TATTATTTTC
35664737 TATTTATTACTATTA
1 TATTTATTACTATTA
35664752 TATTTATTACTATTA
1 TATTTATTACTATTA
35664767 T
1 T
35664768 TAATATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTTATTACTATTA
Found at i:35664868 original size:15 final size:15
Alignment explanation
Indices: 35664850--35664887 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
35664840 CCCACTTAGC
35664850 TATTATTACTATTAT
1 TATTATTACTATTAT
*
35664865 TATTTTTACTATTAT
1 TATTATTACTATTAT
*
35664880 GATTATTA
1 TATTATTA
35664888 TTAATCTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.61
Consensus pattern (15 bp):
TATTATTACTATTAT
Found at i:35665919 original size:20 final size:19
Alignment explanation
Indices: 35665894--35665937 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
35665884 AAATATAACG
35665894 ATATATAAAAA-TAATACTAT
1 ATATATAAAAAGT-ATA-TAT
35665914 ATATATAAAAAGTATATAT
1 ATATATAAAAAGTATATAT
35665933 ATATA
1 ATATA
35665938 CATGTATAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.35
20 14 0.61
21 1 0.04
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (19 bp):
ATATATAAAAAGTATATAT
Found at i:35666148 original size:12 final size:12
Alignment explanation
Indices: 35666127--35666164 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
35666117 TACTACATAA
*
35666127 ATATACATATAT
1 ATATAAATATAT
35666139 ATATAAATATAT
1 ATATAAATATAT
*
35666151 AT-TAAAAATAT
1 ATATAAATATAT
35666162 ATA
1 ATA
35666165 CATAATAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (12 bp):
ATATAAATATAT
Found at i:35666161 original size:13 final size:13
Alignment explanation
Indices: 35666133--35666191 Score: 50
Period size: 13 Copynumber: 4.6 Consensus size: 13
35666123 ATAAATATAC
*
35666133 ATATATA-TATAA
1 ATATATATTAAAA
35666145 ATATATATTAAAA
1 ATATATATTAAAA
* *
35666158 ATATATACATAATA
1 ATATATA-TTAAAA
*
35666172 AT-GATATTAAAA
1 ATATATATTAAAA
*
35666184 GTATATAT
1 ATATATAT
35666192 GTGATATAGT
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
12 12 0.33
13 18 0.50
14 6 0.17
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (13 bp):
ATATATATTAAAA
Found at i:35666188 original size:26 final size:25
Alignment explanation
Indices: 35666133--35666368 Score: 179
Period size: 25 Copynumber: 9.6 Consensus size: 25
35666123 ATAAATATAC
*
35666133 ATATATATATAAATAT-ATATTAAAA
1 ATATATACAT-AATATGATATTAAAA
35666158 ATATATACATAATAATGATATTAAAA
1 ATATATACATAAT-ATGATATTAAAA
* ** * *
35666184 GTATATATGTGATAT-AGTGTTAAAA
1 ATATATACATAATATGA-TATTAAAA
* *
35666209 ATACT-TGCATAATATAGTTATTAAAAA
1 ATA-TATACATAATAT-GATATT-AAAA
35666236 ATATATACATAATAT-A-A-T-AAA
1 ATATATACATAATATGATATTAAAA
* * *
35666257 GTATATAAATAATATGATATTAACA
1 ATATATACATAATATGATATTAAAA
** *
35666282 ATGCATACATAATATAATTATTAAAA
1 ATATATACATAATATGA-TATTAAAA
35666308 ATATATACATAATAT-A-A-T-AAA
1 ATATATACATAATATGATATTAAAA
* *
35666329 ATATATAAATAATATGATATTAACA
1 ATATATACATAATATGATATTAAAA
*
35666354 ATACATACATAATAT
1 ATATATACATAATAT
35666369 AGTTAAAAAA
Statistics
Matches: 164, Mismatches: 30, Indels: 34
0.72 0.13 0.15
Matches are distributed among these distances:
21 33 0.20
22 3 0.02
23 4 0.02
24 7 0.04
25 58 0.35
26 43 0.26
27 16 0.10
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (25 bp):
ATATATACATAATATGATATTAAAA
Found at i:35666334 original size:72 final size:73
Alignment explanation
Indices: 35666150--35666369 Score: 275
Period size: 72 Copynumber: 3.0 Consensus size: 73
35666140 TATAAATATA
** * * *
35666150 TATT-AAAAATATATACATAATAATGATATTAAAAGTATATATGTGATAT-AGTGTTAAAAATAC
1 TATTAAAAAATATATACATAAT-AT-A-A-TAAAA-TATATAAATAATATGA-TATTAACAATAC
* * *
35666213 TTGCATAATATAGT
60 ATACATAATATAAT
* *
35666227 TATTAAAAAATATATACATAATATAATAAAGTATATAAATAATATGATATTAACAATGCATACAT
1 TATTAAAAAATATATACATAATATAATAAAATATATAAATAATATGATATTAACAATACATACAT
35666292 AATATAAT
66 AATATAAT
35666300 TATT-AAAAATATATACATAATATAATAAAATATATAAATAATATGATATTAACAATACATACAT
1 TATTAAAAAATATATACATAATATAATAAAATATATAAATAATATGATATTAACAATACATACAT
35666364 AATATA
66 AATATA
35666370 GTTAAAAAAT
Statistics
Matches: 129, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
72 64 0.50
73 35 0.27
74 5 0.04
75 1 0.01
76 1 0.01
77 6 0.05
78 17 0.13
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (73 bp):
TATTAAAAAATATATACATAATATAATAAAATATATAAATAATATGATATTAACAATACATACAT
AATATAAT
Found at i:35666336 original size:38 final size:37
Alignment explanation
Indices: 35666292--35666410 Score: 89
Period size: 38 Copynumber: 2.9 Consensus size: 37
35666282 ATGCATACAT
35666292 AATATAATTATTAAAAATATATACATAATATAATAAA
1 AATATAATTATTAAAAATATATACATAATATAATAAA
* *
35666329 ATATATAAATAATATGATATTAACAATACATACATAATATAGTTAAA
1 A-ATAT-AAT--TAT--TA--AA-AATATATACATAATATA-ATAAA
*
35666376 AA-ATAA-TATTAAAAAATGATATACATGATATAATA
1 AATATAATTATT-AAAAAT-ATATACATAATATAATA
35666411 TTAATATACA
Statistics
Matches: 65, Mismatches: 5, Indels: 24
0.69 0.05 0.26
Matches are distributed among these distances:
37 6 0.09
38 18 0.28
39 4 0.06
40 1 0.02
41 6 0.09
43 2 0.03
44 2 0.03
45 4 0.06
46 17 0.26
47 5 0.08
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.34
Consensus pattern (37 bp):
AATATAATTATTAAAAATATATACATAATATAATAAA
Found at i:35666408 original size:72 final size:71
Alignment explanation
Indices: 35666216--35666392 Score: 230
Period size: 72 Copynumber: 2.4 Consensus size: 71
35666206 AAAATACTTG
* * * *
35666216 CATAATATAGTTATTAAAAAATATATACATAATATAATAAAGTATATAAATAATATGATATTAAC
1 CATAATATAATTA-T-AAAAATATATAAAAAATATAATAAAATATATAAATAATATGATATTAAC
*
35666281 AATGCATA
64 AATACATA
* *
35666289 CATAATATAATTATTAAAAATATATACATAATATAATAAAATATATAAATAATATGATATTAACA
1 CATAATATAATTA-TAAAAATATATAAAAAATATAATAAAATATATAAATAATATGATATTAACA
35666354 ATACATA
65 ATACATA
*
35666361 CATAATATAGTTA-AAAAATAATATTAAAAAAT
1 CATAATATAATTATAAAAAT-ATA-TAAAAAAT
35666393 GATATACATG
Statistics
Matches: 96, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
70 6 0.06
71 3 0.03
72 73 0.76
73 14 0.15
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (71 bp):
CATAATATAATTATAAAAATATATAAAAAATATAATAAAATATATAAATAATATGATATTAACAA
TACATA
Found at i:35681040 original size:22 final size:24
Alignment explanation
Indices: 35681002--35681055 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 24
35680992 TAAATACTTT
35681002 AATTTTTAATATAATTTT-AGTTAA
1 AATTTTTAATATAATTTTGA-TTAA
*
35681026 TATTTTTAAT-T-ATTTTGATTAA
1 AATTTTTAATATAATTTTGATTAA
35681048 AATTTTTA
1 AATTTTTA
35681056 CACTAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 16 0.59
23 2 0.07
24 9 0.33
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (24 bp):
AATTTTTAATATAATTTTGATTAA
Found at i:35681239 original size:16 final size:13
Alignment explanation
Indices: 35681208--35681233 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35681198 CTTCTCCTTT
35681208 TAAAGTTATTATA
1 TAAAGTTATTATA
35681221 TAAAGTTATTATA
1 TAAAGTTATTATA
35681234 AGATAATGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TAAAGTTATTATA
Found at i:35683756 original size:9 final size:9
Alignment explanation
Indices: 35683742--35683803 Score: 56
Period size: 9 Copynumber: 6.6 Consensus size: 9
35683732 TCCATGCTTT
35683742 TTTTTATAA
1 TTTTTATAA
35683751 TTTTTATAAA
1 TTTTTAT-AA
35683761 TTTTT-TATA
1 TTTTTATA-A
35683770 TTTTTA-AA
1 TTTTTATAA
*
35683778 TTTAATTTTTAA
1 -TT--TTTATAA
35683790 TTTTTATAA
1 TTTTTATAA
35683799 TTTTT
1 TTTTT
35683804 TGAATTACTT
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
8 2 0.05
9 28 0.64
10 7 0.16
11 5 0.11
12 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTTTATAA
Found at i:35683766 original size:20 final size:20
Alignment explanation
Indices: 35683741--35683804 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
35683731 ATCCATGCTT
35683741 TTTTTTATAATTTTTATAAA
1 TTTTTTATAATTTTTATAAA
35683761 TTTTTTAT-A-TTTT-TAAA
1 TTTTTTATAATTTTTATAAA
*
35683778 TTTAATTTTTAATTTTTAT-AA
1 TTT--TTTATAATTTTTATAAA
35683799 TTTTTT
1 TTTTTT
35683805 GAATTACTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
17 7 0.18
18 4 0.11
19 8 0.21
20 9 0.24
21 9 0.24
22 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTTTATAATTTTTATAAA
Found at i:35683784 original size:22 final size:21
Alignment explanation
Indices: 35683762--35683801 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
35683752 TTTTATAAAT
35683762 TTTTTATATTTTTA-AATTTAA
1 TTTTTA-ATTTTTATAATTTAA
35683783 TTTTTAATTTTTATAATTT
1 TTTTTAATTTTTATAATTT
35683802 TTTGAATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTAATTTTTATAATTTAA
Found at i:35684357 original size:18 final size:18
Alignment explanation
Indices: 35684320--35684357 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
35684310 CAAATTTCTC
*
35684320 TATTTTTTAATATTTTTT
1 TATTTTTTAATATTTATT
35684338 TATTTTATTAAT-TTTATT
1 TATTTT-TTAATATTTATT
35684356 TA
1 TA
35684358 ATAAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TATTTTTTAATATTTATT
Found at i:35685350 original size:19 final size:19
Alignment explanation
Indices: 35685313--35685350 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
35685303 AGCAATTTAA
*
35685313 TTTTTTTTATGTCTTTTCT
1 TTTTTTTTATGTCTCTTCT
35685332 TTTTTTTTCAT-TCTCTTCT
1 TTTTTTTT-ATGTCTCTTCT
35685351 GAATCTCGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.05, C:0.16, G:0.03, T:0.76
Consensus pattern (19 bp):
TTTTTTTTATGTCTCTTCT
Found at i:35688484 original size:28 final size:28
Alignment explanation
Indices: 35688444--35688500 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
35688434 GTGCCTCTGG
*
35688444 TTAGACTAGAGCCGATGATGAACTTGTC
1 TTAGACTAGAGCCGATGATGAACCTGTC
35688472 TTAGACTAGAGCCGATGATGAACCTGTC
1 TTAGACTAGAGCCGATGATGAACCTGTC
35688500 T
1 T
35688501 CAGGACATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (28 bp):
TTAGACTAGAGCCGATGATGAACCTGTC
Found at i:35692918 original size:48 final size:48
Alignment explanation
Indices: 35692854--35693001 Score: 215
Period size: 48 Copynumber: 3.1 Consensus size: 48
35692844 TTGATGTACA
*
35692854 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTAAAATATGTATG
1 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
* * *
35692902 ATATATATATATGTGGTAAAGTCGAAAGGCTAATGTGAAATATGTATG
1 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
** ** *
35692950 AGCCATGCATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATG
1 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
35692998 AGAT
1 AGAT
35693002 GTGTATATAT
Statistics
Matches: 86, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 86 1.00
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.30
Consensus pattern (48 bp):
AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
Found at i:35695166 original size:33 final size:32
Alignment explanation
Indices: 35695129--35695255 Score: 78
Period size: 33 Copynumber: 3.8 Consensus size: 32
35695119 TCGGTTACGG
35695129 TCTTATCATCAGAATGCCATAGCCCAACCATGA
1 TCTTA-CATCAGAATGCCATAGCCCAACCATGA
* * * * *
35695162 TCTTACATATAAACACTGCCATGGTCCAACCATGG
1 TCTTACAT-CAGA-A-TGCCATAGCCCAACCATGA
* * * **
35695197 TCTTACATCTATAGTGCCATAACCCAATTAT-A
1 TCTTACATC-AGAATGCCATAGCCCAACCATGA
35695229 GTCCTGT-CATCAGAATGCCATAGCCCA
1 -T-CT-TACATCAGAATGCCATAGCCCA
35695256 GCTATAGTCT
Statistics
Matches: 70, Mismatches: 17, Indels: 14
0.69 0.17 0.14
Matches are distributed among these distances:
32 3 0.04
33 33 0.47
34 7 0.10
35 27 0.39
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (32 bp):
TCTTACATCAGAATGCCATAGCCCAACCATGA
Found at i:35696764 original size:110 final size:108
Alignment explanation
Indices: 35696617--35696844 Score: 282
Period size: 110 Copynumber: 2.1 Consensus size: 108
35696607 TATCAGTATT
* * *
35696617 TAAAAAAAA-TTGTACTGGCCTGTAGATGGCCGGCACCAGGTACTTTTTTCATATCCCAATGCAA
1 TAAAAAAAATTTGTACTAGCCTGTAGATAGCCGGCACCAGGTACTTTTTTCATATCCCAAT-AAA
* * * * *
35696681 ATTTTTTCTTTTGTTTTGGCCTTTTAATGG-TCGGCACCAAACTAG
65 AATCTTT-TTTGGTTCTGGCCTTCTAATGGCT-GGCACCAAACTAG
* * * *
35696726 -AAAAAAAATTTAGTGCTAGCCTGTGGATAGCTGGCACCAGGTACTTTTTTCATGTCCCAATAAA
1 TAAAAAAAATTT-GTACTAGCCTGTAGATAGCCGGCACCAGGTACTTTTTTCATATCCCAATAAA
*
35696790 AATCTTTTTTGGTTCTGGCCTTCTAATGGCTGGCATCAAACTAG
65 AATCTTTTTTGGTTCTGGCCTTCTAATGGCTGGCACCAAACTAG
35696834 TAAAAAAAATT
1 TAAAAAAAATT
35696845 GGTTCTGGTC
Statistics
Matches: 102, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
108 39 0.38
109 20 0.20
110 43 0.42
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (108 bp):
TAAAAAAAATTTGTACTAGCCTGTAGATAGCCGGCACCAGGTACTTTTTTCATATCCCAATAAAA
ATCTTTTTTGGTTCTGGCCTTCTAATGGCTGGCACCAAACTAG
Found at i:35696858 original size:45 final size:46
Alignment explanation
Indices: 35696798--35696916 Score: 154
Period size: 45 Copynumber: 2.6 Consensus size: 46
35696788 AAAATCTTTT
* *
35696798 TTGGTTCTGGCCTTCTAATGGCTGGCATCAAACTAGT-AAAAAAAA
1 TTGGTTCTGGCCTTCTAATGGCCGGCACCAAACTAGTAAAAAAAAA
* *
35696843 TTGGTTCTGGTCTTCTAATGGCCGGCACCAGACTAGTAAAAAAAAA
1 TTGGTTCTGGCCTTCTAATGGCCGGCACCAAACTAGTAAAAAAAAA
*
35696889 TTGGTGT-TGGCCTGT-AAATGGCCGGCAC
1 TTGGT-TCTGGCCT-TCTAATGGCCGGCAC
35696917 TAGGTATTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
45 33 0.51
46 30 0.46
47 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (46 bp):
TTGGTTCTGGCCTTCTAATGGCCGGCACCAAACTAGTAAAAAAAAA
Found at i:35696872 original size:108 final size:107
Alignment explanation
Indices: 35696617--35696873 Score: 252
Period size: 108 Copynumber: 2.3 Consensus size: 107
35696607 TATCAGTATT
* *
35696617 TAAAAAAAATTGTACTGGCCTGTAGATGGCCGGCACCAGGTACTTTTTTCATATCCCAATGCAAA
1 TAAAAAAAATTGTACTGG-CTTTA-ATGGCCGGCACCAGGTACTTTTTTCATATCCCAATGAAAA
* * * * *
35696682 TTTTTTCTTTTGTTTTGGCCTTTTAATGGTCGGCACCAAACTAG
64 ATCTTTCTTTGGTTCTGGCCTTCTAATGGTCGGCACCAAACTAG
* * ** * * *
35696726 -AAAAAAAATTTAGTGCTAGCCTGTGGATAGCTGGCACCAGGTACTTTTTTCATGTCCCAAT-AA
1 TAAAAAAAA-TT-GTACT-GGCT-TTAATGGCCGGCACCAGGTACTTTTTTCATATCCCAATGAA
*
35696789 AAATCTTT-TTTGGTTCTGGCCTTCTAATGG-CTGGCATCAAACTAG
62 AAATCTTTCTTTGGTTCTGGCCTTCTAATGGTC-GGCACCAAACTAG
*
35696834 TAAAAAAAATTGGTTCTGGTCTTCTAATGGCCGGCACCAG
1 TAAAAAAAATT-GTACTGG-CTT-TAATGGCCGGCACCAG
35696874 ACTAGTAAAA
Statistics
Matches: 118, Mismatches: 22, Indels: 17
0.75 0.14 0.11
Matches are distributed among these distances:
107 3 0.03
108 59 0.50
109 17 0.14
110 38 0.32
111 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (107 bp):
TAAAAAAAATTGTACTGGCTTTAATGGCCGGCACCAGGTACTTTTTTCATATCCCAATGAAAAAT
CTTTCTTTGGTTCTGGCCTTCTAATGGTCGGCACCAAACTAG
Found at i:35696982 original size:152 final size:154
Alignment explanation
Indices: 35696705--35697038 Score: 392
Period size: 153 Copynumber: 2.2 Consensus size: 154
35696695 TTTGGCCTTT
* * ** *
35696705 TAATGGTCGGCACCAAACTAG-AAAAAAAATTTAGTGCTAGCCTGTGGATAGCTGGCACCAGGTA
1 TAATGGCCGGCACC-AACTAGTAAAAAAAAATTAGTGCTAGCCTGTAAATAGCCGGCACCAGGTA
* * *
35696769 CTTTTTTCATGTCCCAATAAAAATCTTTTTTGGTTCTGGCCTTCTAATGGCTGGCATCAAACTAG
65 CTTTTTTCATGTCCCAATAAAAATCTTTTTTGGTTCTAGCCTTCTAATGGCCGGCACCAAACTAG
* * *
35696834 TAAAAAAAA-TTGGTTCTGGTCTTC
130 TAAAAAAAATTTGGTGCTGGGCATC
* * * * *
35696858 TAATGGCCGGCACCAGACTAGTAAAAAAAAATTGGTGTTGGCCTGTAAATGGCCGGCACTAGGTA
1 TAATGGCCGGCACCA-ACTAGTAAAAAAAAATTAGTGCTAGCCTGTAAATAGCCGGCACCAGGTA
* * * * * *
35696923 -TTTTTTCGTGTTCTAAT-ACAATTTTTTTTTGTTCTAGCCTTCTAATGGCCGGCACCAAACTAG
65 CTTTTTTCATGTCCCAATAAAAATCTTTTTTGGTTCTAGCCTTCTAATGGCCGGCACCAAACTAG
*
35696986 TAAAAAAAATTTGGTGCTGGGCATG
130 TAAAAAAAATTTGGTGCTGGGCATC
*
35697011 TATTGGCCGGCACCAA--AGTAAAAAAAAA
1 TAATGGCCGGCACCAACTAGTAAAAAAAAA
35697039 AATCAAATTT
Statistics
Matches: 154, Mismatches: 24, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
150 12 0.08
152 51 0.33
153 57 0.37
154 34 0.22
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (154 bp):
TAATGGCCGGCACCAACTAGTAAAAAAAAATTAGTGCTAGCCTGTAAATAGCCGGCACCAGGTAC
TTTTTTCATGTCCCAATAAAAATCTTTTTTGGTTCTAGCCTTCTAATGGCCGGCACCAAACTAGT
AAAAAAAATTTGGTGCTGGGCATC
Found at i:35700231 original size:74 final size:73
Alignment explanation
Indices: 35700153--35700386 Score: 257
Period size: 73 Copynumber: 3.2 Consensus size: 73
35700143 GAAAAAAAAT
35700153 TGAAATGA-ACAAATATAATA-TAAATGAATTGAGAAAAAAAATTAAATTTACATGGAAAGAAAG
1 TGAAATGAGA-AAATATAATATTAAATGAATTGAG--AAAAAATTAAATTTACATGGAAAGAAAG
35700216 ATAAATTTAAA
63 ATAAATTTAAA
* * * * **
35700227 TGAAATGAGAAAA-AAAATATTTAAAAG-ATATGAGAAAAAATTAAATTAAAATTAAAAGAAAGA
1 TGAAATGAGAAAATATAATA-TTAAATGAAT-TGAGAAAAAATTAAATTTACATGGAAAGAAAGA
35700290 TAAATTTAAA
64 TAAATTTAAA
* * *
35700300 TGAAACGAGGAAAATATTTAA-ATTAAATGAA-TGAGGAAAAAATTAAATTTGCATGGAAAGATA
1 TGAAATGA-GAAAATA--TAATATTAAATGAATTGA-GAAAAAATTAAATTTACATGGAAAGAAA
35700363 GAT-AATTTAAA
62 GATAAATTTAAA
35700374 TGAAATGAGAAAA
1 TGAAATGAGAAAA
35700387 AATTAAATTT
Statistics
Matches: 134, Mismatches: 16, Indels: 21
0.78 0.09 0.12
Matches are distributed among these distances:
73 52 0.39
74 36 0.27
75 42 0.31
76 2 0.01
77 2 0.01
ACGTcount: A:0.59, C:0.02, G:0.14, T:0.25
Consensus pattern (73 bp):
TGAAATGAGAAAATATAATATTAAATGAATTGAGAAAAAATTAAATTTACATGGAAAGAAAGATA
AATTTAAA
Found at i:35700275 original size:25 final size:25
Alignment explanation
Indices: 35700216--35700399 Score: 75
Period size: 25 Copynumber: 7.4 Consensus size: 25
35700206 GGAAAGAAAG
*
35700216 ATAAATTTAAATGAAATGAGAAAAA
1 ATAAATTTAAAAGAAATGAGAAAAA
*
35700241 A-AATATTTAAAAGATATGAGAAAAA
1 ATAA-ATTTAAAAGAAATGAGAAAAA
* *
35700266 ATTAAA-TTAAAATTAAA--AG-AAAG
1 A-TAAATTTAAAA-GAAATGAGAAAAA
* *
35700289 ATAAATTTAAATGAAACGAGGAAAATA
1 ATAAATTTAAAAGAAATGA-GAAAA-A
* *
35700316 TTTAAA-TTAAATG-AATGAGGAAAAA
1 -ATAAATTTAAAAGAAATGA-GAAAAA
** * * * *
35700341 ATTAAATTTGCATGGAA--AG-ATAG
1 A-TAAATTTAAAAGAAATGAGAAAAA
*
35700364 AT-AATTTAAATGAAATGAGAAAAA
1 ATAAATTTAAAAGAAATGAGAAAAA
35700388 ATTAAATTTAAA
1 A-TAAATTTAAA
35700400 TAAAAATAAT
Statistics
Matches: 120, Mismatches: 20, Indels: 37
0.68 0.11 0.21
Matches are distributed among these distances:
21 10 0.08
22 8 0.07
23 14 0.12
24 9 0.08
25 35 0.29
26 29 0.24
27 11 0.09
28 4 0.03
ACGTcount: A:0.59, C:0.01, G:0.13, T:0.27
Consensus pattern (25 bp):
ATAAATTTAAAAGAAATGAGAAAAA
Found at i:35700328 original size:27 final size:25
Alignment explanation
Indices: 35700290--35700348 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 25
35700280 AAAAGAAAGA
*
35700290 TAAATTTAAATGAAACGAGGAAAATATT
1 TAAA-TTAAATG-AACGAGGAAAA-AAT
*
35700318 TAAATTAAATGAATGAGGAAAAAAT
1 TAAATTAAATGAACGAGGAAAAAAT
35700343 TAAATT
1 TAAATT
35700349 TGCATGGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 8 0.28
26 10 0.34
27 7 0.24
28 4 0.14
ACGTcount: A:0.56, C:0.02, G:0.14, T:0.29
Consensus pattern (25 bp):
TAAATTAAATGAACGAGGAAAAAAT
Found at i:35700373 original size:47 final size:46
Alignment explanation
Indices: 35700322--35700488 Score: 195
Period size: 47 Copynumber: 3.7 Consensus size: 46
35700312 AATATTTAAA
**
35700322 TTAAATG-AATGAGGAAAAAATTAAATTTGCATGGAAAGATAGATAAT
1 TTAAATGAAATGA-GAAAAAATTAAATTTAAATGG-AAGATAGATAAT
35700369 TTAAATGAAATGAGAAAAAATTAAATTTAAAT--AA-A-A-ATAAT
1 TTAAATGAAATGAGAAAAAATTAAATTTAAATGGAAGATAGATAAT
* * *
35700410 ATAAATGAAATGAGAAAAAAAATTAAATTAAAATGGGAAGATAGATAAA
1 TTAAATGAAATGAG--AAAAAATTAAATTTAAAT-GGAAGATAGATAAT
35700459 TTAAATGAAATGAGAAAAAA-TAAATTTAAA
1 TTAAATGAAATGAGAAAAAATTAAATTTAAA
35700489 AGATAAAAAA
Statistics
Matches: 104, Mismatches: 7, Indels: 19
0.80 0.05 0.15
Matches are distributed among these distances:
41 18 0.17
42 1 0.01
43 18 0.17
44 2 0.02
46 11 0.11
47 31 0.30
48 6 0.06
49 17 0.16
ACGTcount: A:0.60, C:0.01, G:0.14, T:0.26
Consensus pattern (46 bp):
TTAAATGAAATGAGAAAAAATTAAATTTAAATGGAAGATAGATAAT
Found at i:35700451 original size:90 final size:89
Alignment explanation
Indices: 35700319--35700512 Score: 261
Period size: 90 Copynumber: 2.2 Consensus size: 89
35700309 GAAAATATTT
* *** *
35700319 AAAT-TAAATG-AATGAGGAAAAAATTAAATTTGCATGGAAAGATAGATAATTTAAATGAAATGA
1 AAATATAAATGAAATGAGAAAAAAATTAAATTAAAATGGAAAGATAGATAAATTAAATGAAATGA
35700382 GAAAAAATTAAATTTAAATA-A-AAA
66 GAAAAAA-TAAATTTAAA-AGATAAA
* *
35700406 TAATATAAATGAAATGAGAAAAAAAATTAAATTAAAATGGGAAGATAGATAAATTAAATGAAATG
1 AAATATAAATGAAATGAG-AAAAAAATTAAATTAAAATGGAAAGATAGATAAATTAAATGAAATG
35700471 AGAAAAAATAAATTTAAAAGATAAA
65 AGAAAAAATAAATTTAAAAGATAAA
*
35700496 AAATATAAATTAAATGA
1 AAATATAAATGAAATGA
35700513 AATGGAAATA
Statistics
Matches: 93, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
87 3 0.03
88 7 0.08
89 17 0.18
90 66 0.71
ACGTcount: A:0.61, C:0.01, G:0.13, T:0.25
Consensus pattern (89 bp):
AAATATAAATGAAATGAGAAAAAAATTAAATTAAAATGGAAAGATAGATAAATTAAATGAAATGA
GAAAAAATAAATTTAAAAGATAAA
Found at i:35700505 original size:41 final size:42
Alignment explanation
Indices: 35700319--35700512 Score: 148
Period size: 41 Copynumber: 4.4 Consensus size: 42
35700309 GAAAATATTT
*
35700319 AAAT-TAAATG-AATGAGGAAAAAATTAAATTTGCATGGAAAGATAGA
1 AAATATAAATGAAATGA-GAAAAAATTAAATTT--A---AAAGATAAA
* *
35700365 TAATTTAAATGAAATGAGAAAAAATTAAATTTAAATA-A-AAA
1 AAATATAAATGAAATGAGAAAAAATTAAATTTAAA-AGATAAA
* * *
35700406 TAATATAAATGAAATGAGAAAAAAAATTAAATTAAAATGGGAAGATAGAT
1 AAATATAAATGAAATGAG--AAAAAATTAAATT-TAA----AAGATA-AA
35700456 AAAT-TAAATGAAATGAGAAAAAA-TAAATTTAAAAGATAAA
1 AAATATAAATGAAATGAGAAAAAATTAAATTTAAAAGATAAA
*
35700496 AAATATAAATTAAATGA
1 AAATATAAATGAAATGA
35700513 AATGGAAATA
Statistics
Matches: 125, Mismatches: 9, Indels: 33
0.75 0.05 0.20
Matches are distributed among these distances:
40 5 0.04
41 36 0.29
42 3 0.02
43 14 0.11
44 2 0.02
45 3 0.02
46 9 0.07
47 28 0.22
48 7 0.06
49 14 0.11
50 4 0.03
ACGTcount: A:0.61, C:0.01, G:0.13, T:0.25
Consensus pattern (42 bp):
AAATATAAATGAAATGAGAAAAAATTAAATTTAAAAGATAAA
Found at i:35700520 original size:6 final size:5
Alignment explanation
Indices: 35700502--35700585 Score: 69
Period size: 5 Copynumber: 15.6 Consensus size: 5
35700492 TAAAAAATAT
* * *
35700502 AAATT AAATG AAATGG AAATAG GAATGG AAATGG AAATA AAATG AAATG
1 AAATG AAATG AAAT-G AAAT-G AAAT-G AAAT-G AAATG AAATG AAATG
* *
35700551 AAATG AAATGG AAATG AAATTG GAATG ATATG AAA
1 AAATG AAAT-G AAATG AAA-TG AAATG AAATG AAA
35700586 AAAAAAATTA
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
5 37 0.57
6 28 0.43
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (5 bp):
AAATG
Found at i:35700521 original size:11 final size:11
Alignment explanation
Indices: 35700507--35700575 Score: 79
Period size: 12 Copynumber: 6.2 Consensus size: 11
35700497 AATATAAATT
35700507 AAATGAAATGG
1 AAATGAAATGG
*
35700518 AAATAGGAATGG
1 AAAT-GAAATGG
*
35700530 AAATGGAAAT-A
1 AAAT-GAAATGG
35700541 AAATGAAAT-G
1 AAATGAAATGG
35700551 AAATGAAATGG
1 AAATGAAATGG
35700562 AAATGAAATTGG
1 AAATGAAA-TGG
35700574 AA
1 AA
35700576 TGATATGAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
10 14 0.28
11 17 0.34
12 19 0.38
ACGTcount: A:0.57, C:0.00, G:0.25, T:0.19
Consensus pattern (11 bp):
AAATGAAATGG
Found at i:35700577 original size:11 final size:10
Alignment explanation
Indices: 35700508--35700578 Score: 52
Period size: 11 Copynumber: 6.5 Consensus size: 10
35700498 ATATAAATTA
35700508 AATGAAATGG
1 AATGAAATGG
*
35700518 AAATAGGAATGG
1 -AAT-GAAATGG
**
35700530 AAATGGAAATAA
1 -AAT-GAAATGG
*
35700542 AATGAAATGA
1 AATGAAATGG
35700552 AATGAAATGG
1 AATGAAATGG
35700562 AAATGAAATTGG
1 -AATGAAA-TGG
35700574 AATGA
1 AATGA
35700579 TATGAAAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
10 15 0.30
11 18 0.36
12 17 0.34
ACGTcount: A:0.55, C:0.00, G:0.25, T:0.20
Consensus pattern (10 bp):
AATGAAATGG
Found at i:35700583 original size:16 final size:15
Alignment explanation
Indices: 35700502--35700585 Score: 69
Period size: 16 Copynumber: 5.2 Consensus size: 15
35700492 TAAAAAATAT
*
35700502 AAATTAAATGAAATGG
1 AAATGAAATGAAAT-G
*
35700518 AAATAGGAATGGAAATGG
1 AAAT-GAAAT-GAAAT-G
*
35700536 AAATAAAATGAAATG
1 AAATGAAATGAAATG
35700551 AAATGAAATGGAAATG
1 AAATGAAAT-GAAATG
* *
35700567 AAATTGGAATGATATG
1 AAA-TGAAATGAAATG
35700583 AAA
1 AAA
35700586 AAAAAAATTA
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
15 9 0.16
16 26 0.46
17 11 0.19
18 11 0.19
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (15 bp):
AAATGAAATGAAATG
Found at i:35700820 original size:20 final size:22
Alignment explanation
Indices: 35700782--35700827 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
35700772 AAATTGATAA
35700782 AAATAAAATATGAAAAAAATT-
1 AAATAAAATATGAAAAAAATTG
35700803 AAATAAAATATG-AAAAAATTG
1 AAATAAAATATGAAAAAAATTG
35700824 AAAT
1 AAAT
35700828 GACCTTGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.24
Consensus pattern (22 bp):
AAATAAAATATGAAAAAAATTG
Found at i:35700901 original size:15 final size:15
Alignment explanation
Indices: 35700852--35700904 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
35700842 GACTACTTCT
35700852 AATTAATATGAAAAA
1 AATTAATATGAAAAA
*
35700867 ATATGAA-ATGAATTAAAA
1 A-ATTAATATG-A--AAAA
35700885 AATTAATATGAAAAA
1 AATTAATATGAAAAA
35700900 AATTA
1 AATTA
35700905 TATTAGGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
15 13 0.42
16 5 0.16
17 5 0.16
18 8 0.26
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (15 bp):
AATTAATATGAAAAA
Found at i:35700951 original size:5 final size:5
Alignment explanation
Indices: 35700941--35701062 Score: 50
Period size: 5 Copynumber: 22.4 Consensus size: 5
35700931 GAAAAAAATT
* * *
35700941 AATGA AATGA AATGTTA AAAGAA ATATGA ATATGA AATGA AATGTA ATTTGT
1 AATGA AATGA AATG--A AATG-A A-ATGA A-ATGA AATGA AATG-A A-ATGA
* * *
35700993 AATGA ATATGA AATTA AATTA AATGTTA AATGA ATATAA AATGA AATG-
1 AATGA A-ATGA AATGA AATGA AATG--A AATGA A-ATGA AATGA AATGA
* *
35701041 -ATGA TTATGA AATGG AATGA AA
1 AATGA -AATGA AATGA AATGA AA
35701063 GTTTAAAAAA
Statistics
Matches: 91, Mismatches: 14, Indels: 24
0.71 0.11 0.19
Matches are distributed among these distances:
3 3 0.03
5 49 0.54
6 26 0.29
7 13 0.14
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.30
Consensus pattern (5 bp):
AATGA
Found at i:35701006 original size:28 final size:29
Alignment explanation
Indices: 35700942--35701040 Score: 98
Period size: 28 Copynumber: 3.4 Consensus size: 29
35700932 AAAAAAATTA
* *
35700942 ATGAAATGAAATGTTAAAAG-AAATATGAAT
1 ATGAAATGAAATG-TAAATGTTAA-ATGAAT
*
35700972 ATGAAATGAAATGT-AAT-TTGTAATGAAT
1 ATGAAATGAAATGTAAATGTT-AAATGAAT
*
35701000 ATGAAATTAAAT-TAAATGTTAAATGAAT
1 ATGAAATGAAATGTAAATGTTAAATGAAT
*
35701028 ATAAAATGAAATG
1 ATGAAATGAAATG
35701041 ATGATTATGA
Statistics
Matches: 57, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
27 1 0.02
28 39 0.68
29 4 0.07
30 13 0.23
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (29 bp):
ATGAAATGAAATGTAAATGTTAAATGAAT
Found at i:35701179 original size:5 final size:5
Alignment explanation
Indices: 35701169--35701236 Score: 64
Period size: 5 Copynumber: 12.6 Consensus size: 5
35701159 TAGATAATTT
* *
35701169 AAATG AAATG AAAATG AAAATG TAAATA AAATG AAATG AAATG CACATG
1 AAATG AAATG -AAATG -AAATG -AAATG AAATG AAATG AAATG -AAATG
*
35701218 AAATTG GAATG AAATG AAA
1 AAA-TG AAATG AAATG AAA
35701237 AAAAACAGAA
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
5 30 0.57
6 23 0.43
ACGTcount: A:0.59, C:0.03, G:0.18, T:0.21
Consensus pattern (5 bp):
AAATG
Found at i:35701185 original size:6 final size:6
Alignment explanation
Indices: 35701169--35701209 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
35701159 TAGATAATTT
*
35701169 AAATG- AAATGA AAATGA AAATGT AAAT-A AAATG- AAATGA AA
1 AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA AA
35701210 TGCACATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
5 14 0.45
6 17 0.55
ACGTcount: A:0.66, C:0.00, G:0.15, T:0.20
Consensus pattern (6 bp):
AAATGA
Found at i:35701185 original size:11 final size:10
Alignment explanation
Indices: 35701169--35701236 Score: 64
Period size: 11 Copynumber: 6.3 Consensus size: 10
35701159 TAGATAATTT
35701169 AAATGAAATG
1 AAATGAAATG
35701179 AAAATGAAAATG
1 -AAATG-AAATG
*
35701191 TAAATAAAATG
1 -AAATGAAATG
35701202 AAATGAAATG
1 AAATGAAATG
*
35701212 CACATGAAATTG
1 -AAATGAAA-TG
*
35701224 GAATGAAATG
1 AAATGAAATG
35701234 AAA
1 AAA
35701237 AAAAACAGAA
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
10 13 0.28
11 23 0.49
12 11 0.23
ACGTcount: A:0.59, C:0.03, G:0.18, T:0.21
Consensus pattern (10 bp):
AAATGAAATG
Found at i:35701199 original size:17 final size:17
Alignment explanation
Indices: 35701169--35701237 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
35701159 TAGATAATTT
35701169 AAATGAAATGAAAATGA
1 AAATGAAATGAAAATGA
35701186 AAATGTAAAT-AAAATG-
1 AAATG-AAATGAAAATGA
* *
35701202 AAATGAAATGCACATGA
1 AAATGAAATGAAAATGA
* *
35701219 AATTGGAATG-AAATGA
1 AAATGAAATGAAAATGA
35701235 AAA
1 AAA
35701238 AAAACAGAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
15 4 0.09
16 16 0.37
17 19 0.44
18 4 0.09
ACGTcount: A:0.59, C:0.03, G:0.17, T:0.20
Consensus pattern (17 bp):
AAATGAAATGAAAATGA
Found at i:35704997 original size:50 final size:51
Alignment explanation
Indices: 35704821--35705002 Score: 312
Period size: 51 Copynumber: 3.6 Consensus size: 51
35704811 AAATAATTTG
*
35704821 TTTTACTAGTCTGGTGCCGGCCATTAGAAGGCCAGAACCAAATTTTGTTTT
1 TTTTACTAGCCTGGTGCCGGCCATTAGAAGGCCAGAACCAAATTTTGTTTT
* *
35704872 TTTTACTAGCCTGGTGCCTGCCATTAGAAGGCCAGAACCAAATTCTGTTTT
1 TTTTACTAGCCTGGTGCCGGCCATTAGAAGGCCAGAACCAAATTTTGTTTT
*
35704923 TTTTACTAGCCTGGTACCGGCCATTAGAAGGCCAGAACCAAATTTTG-TTT
1 TTTTACTAGCCTGGTGCCGGCCATTAGAAGGCCAGAACCAAATTTTGTTTT
*
35704973 TTTTACTAGCCTGGTGCCGACCATTAGAAG
1 TTTTACTAGCCTGGTGCCGGCCATTAGAAG
35705003 CCCAAGGCAA
Statistics
Matches: 123, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
50 31 0.25
51 92 0.75
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (51 bp):
TTTTACTAGCCTGGTGCCGGCCATTAGAAGGCCAGAACCAAATTTTGTTTT
Found at i:35707212 original size:3 final size:3
Alignment explanation
Indices: 35707204--35707228 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
35707194 CATAATACTA
35707204 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
35707229 AAAACAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:35727186 original size:66 final size:66
Alignment explanation
Indices: 35727103--35727235 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
35727093 TTGTTGACAT
*
35727103 ATCAAACATTTAGATAGGAATTCTGAAATATCACTTTTCATTATCAGCTACTGGTACATCTCTTT
1 ATCAAACATTTAGATAGGAATTCTGAAATATCACTTTTCATTATCAGCTACTAGTACATCTCTTT
35727168 C
66 C
*
35727169 ATCAAACATTTAGATAGGAATTCTGAAATATCACTTTTCATTATCAGCTACTAGTACATCTTTTT
1 ATCAAACATTTAGATAGGAATTCTGAAATATCACTTTTCATTATCAGCTACTAGTACATCTCTTT
35727234 C
66 C
35727235 A
1 A
35727236 AGTCATTGTA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (66 bp):
ATCAAACATTTAGATAGGAATTCTGAAATATCACTTTTCATTATCAGCTACTAGTACATCTCTTT
C
Found at i:35729808 original size:27 final size:26
Alignment explanation
Indices: 35729767--35729839 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 26
35729757 ATACATGATA
35729767 ATATTAAAAGTATGTACACAATATATAAT
1 ATATTAAAA--ATGTACA-AATATATAAT
* *
35729796 ATATTAAAAATGTATATATATATAAT
1 ATATTAAAAATGTACAAATATATAAT
* *
35729822 ATTTATAAAAATATACAA
1 ATAT-TAAAAATGTACAA
35729840 GGCATAATGT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
26 12 0.32
27 16 0.43
29 9 0.24
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (26 bp):
ATATTAAAAATGTACAAATATATAAT
Found at i:35734030 original size:22 final size:22
Alignment explanation
Indices: 35734002--35734054 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
35733992 CTCAGAGAAT
**
35734002 TTTTTTTTTGCAAAATCTTAAA
1 TTTTTTTCAGCAAAATCTTAAA
35734024 TTTTTTTCAGCAAAATCTTAAA
1 TTTTTTTCAGCAAAATCTTAAA
*
35734046 CTTTTTTCA
1 TTTTTTTCA
35734055 AGATACAGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.30, C:0.13, G:0.04, T:0.53
Consensus pattern (22 bp):
TTTTTTTCAGCAAAATCTTAAA
Done.