Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 4 of 208
Found at i:1315673 original size:20 final size:19
Alignment explanation
Indices: 1315650--1315713 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 19
1315640 AATTCAAAAA
1315650 AAAAAATCAAAATCAAAATC
1 AAAAAA-CAAAATCAAAATC
* **
1315670 AAAAAAGAAAAGAAAAAATC
1 AAAAAACAAAA-TCAAAATC
1315690 AAAGTAAA-AAAATCAAAATC
1 AAA--AAACAAAATCAAAATC
1315710 AAAA
1 AAAA
1315714 TAAAAAAAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 4 0.11
20 24 0.67
21 4 0.11
22 3 0.08
ACGTcount: A:0.75, C:0.09, G:0.05, T:0.11
Consensus pattern (19 bp):
AAAAAACAAAATCAAAATC
Found at i:1315709 original size:46 final size:42
Alignment explanation
Indices: 1315649--1315741 Score: 141
Period size: 42 Copynumber: 2.1 Consensus size: 42
1315639 AAATTCAAAA
1315649 AAAAAAATCAAAATCAAAATCAAAAAAGAAAAGAAAAAATCAAAGT
1 AAAAAAATCAAAATCAAAAT---AAAA-AAAAGAAAAAATCAAAGT
1315695 AAAAAAATCAAAATCAAAATAAAAAAAAGAAAAAATCAAAGT
1 AAAAAAATCAAAATCAAAATAAAAAAAAGAAAAAATCAAAGT
*
1315737 CAAAA
1 AAAAA
1315742 GTAAAAAAAG
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
42 22 0.48
43 4 0.09
46 20 0.43
ACGTcount: A:0.75, C:0.09, G:0.05, T:0.11
Consensus pattern (42 bp):
AAAAAAATCAAAATCAAAATAAAAAAAAGAAAAAATCAAAGT
Found at i:1315717 original size:20 final size:20
Alignment explanation
Indices: 1315658--1315721 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
1315648 AAAAAAAATC
1315658 AAAATCAAAATCAAAA-AAGA
1 AAAATCAAAATCAAAATAA-A
* *
1315678 AAAGA-AAAAATCAAAGTAAA
1 AAA-ATCAAAATCAAAATAAA
1315698 AAAATCAAAATCAAAATAAA
1 AAAATCAAAATCAAAATAAA
1315718 AAAA
1 AAAA
1315722 AGAAAAAATC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
19 1 0.03
20 33 0.89
21 3 0.08
ACGTcount: A:0.77, C:0.08, G:0.05, T:0.11
Consensus pattern (20 bp):
AAAATCAAAATCAAAATAAA
Found at i:1315741 original size:20 final size:19
Alignment explanation
Indices: 1315677--1315749 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 19
1315667 ATCAAAAAAG
1315677 AAAAGAAAAAATCAAAGTA
1 AAAAGAAAAAATCAAAGTA
*
1315696 AAAA-AATCAAAATCAAAATAAAA
1 AAAAGAA--AAAATCAAAGT---A
*
1315719 AAAAGAAAAAATCAAAGTC
1 AAAAGAAAAAATCAAAGTA
1315738 AAAAGTAAAAAA
1 AAAAG-AAAAAA
1315750 AGAAATCAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
18 2 0.05
19 9 0.20
20 16 0.36
22 10 0.23
23 5 0.11
24 2 0.05
ACGTcount: A:0.75, C:0.07, G:0.07, T:0.11
Consensus pattern (19 bp):
AAAAGAAAAAATCAAAGTA
Found at i:1315746 original size:29 final size:28
Alignment explanation
Indices: 1315696--1315775 Score: 108
Period size: 28 Copynumber: 2.8 Consensus size: 28
1315686 AATCAAAGTA
*
1315696 AAAAAATCAAAATCAAAATAAAAAAAAG
1 AAAAAATCAAAGTCAAAATAAAAAAAAG
1315724 AAAAAATCAAAGTCAAAAGT-AAAAAAAG
1 AAAAAATCAAAGTCAAAA-TAAAAAAAAG
* *
1315752 AAATCAATCAAAGTTAAAATAAAA
1 AAA-AAATCAAAGTCAAAATAAAA
1315776 TATGAAAAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
28 29 0.63
29 17 0.37
ACGTcount: A:0.72, C:0.07, G:0.06, T:0.14
Consensus pattern (28 bp):
AAAAAATCAAAGTCAAAATAAAAAAAAG
Found at i:1316158 original size:7 final size:7
Alignment explanation
Indices: 1316146--1316178 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1316136 GATTTCAAAA
1316146 AAAAATG
1 AAAAATG
1316153 AAAAATG
1 AAAAATG
*
1316160 -AGAATG
1 AAAAATG
1316166 AAAAATG
1 AAAAATG
1316173 AAAAAT
1 AAAAAT
1316179 AGAGAGGCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (7 bp):
AAAAATG
Found at i:1316167 original size:13 final size:13
Alignment explanation
Indices: 1316149--1316173 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1316139 TTCAAAAAAA
1316149 AATGAAAAATGAG
1 AATGAAAAATGAG
1316162 AATGAAAAATGA
1 AATGAAAAATGA
1316174 AAAATAGAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.20, T:0.16
Consensus pattern (13 bp):
AATGAAAAATGAG
Found at i:1317551 original size:87 final size:87
Alignment explanation
Indices: 1317400--1317574 Score: 278
Period size: 87 Copynumber: 2.0 Consensus size: 87
1317390 AGATCAGTGA
* * *
1317400 AGATGAAAAACAAAGCCTTGCCTTCATCGGTTGTAGTGAAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGAAGCTGGTTAAAGATAGCAGATCTTGC
1317465 CTTCCTGCGTTAATAGCGAAGC
66 CTTCCTGCGTTAATAGCGAAGC
* * * *
1317487 AGATCAAAAACGAAGCCTTGCCTCCATCGGTTGCAGTGGAGTTGGTTGAAGATAGCAGATCTTGC
1 AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGAAGCTGGTTAAAGATAGCAGATCTTGC
*
1317552 CTTCCTGTGTTAATAGCGAAGC
66 CTTCCTGCGTTAATAGCGAAGC
1317574 A
1 A
1317575 TCTTGCTTTC
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 80 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (87 bp):
AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGAAGCTGGTTAAAGATAGCAGATCTTGC
CTTCCTGCGTTAATAGCGAAGC
Found at i:1317578 original size:29 final size:29
Alignment explanation
Indices: 1317545--1317603 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
1317535 AAGATAGCAG
* * *
1317545 ATCTTGCCTTCCTGTGTTAATAGCGAAGC
1 ATCTTGCCTTCCTGCGTCAACAGCGAAGC
*
1317574 ATCTTGCTTTCCTGCGTCAACAGCGAAGC
1 ATCTTGCCTTCCTGCGTCAACAGCGAAGC
1317603 A
1 A
1317604 GATCGAAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (29 bp):
ATCTTGCCTTCCTGCGTCAACAGCGAAGC
Found at i:1317655 original size:116 final size:116
Alignment explanation
Indices: 1317458--1317674 Score: 335
Period size: 116 Copynumber: 1.9 Consensus size: 116
1317448 AAGATAGCAG
* * *
1317458 ATCTTGCCTTCCTGCGTTAATAGCGAAGCAGATCAAAAACGAAGCCTTGCCTCCATCGGTTGCAG
1 ATCTTGCCTTCCTGCGTCAACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAG
* * * *
1317523 TGGAGTTGGTTGAAGATAGCAGATCTTGCCTTCCTGTGTTAATAGCGAAGC
66 TGGAGCTAGTTAAAGATAACAGATCTTGCCTTCCTGTGTTAATAGCGAAGC
* * *
1317574 ATCTTGCTTTCCTGCGTCAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAG
1 ATCTTGCCTTCCTGCGTCAACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAG
*
1317639 TGGAGCTAGTTAAAGATAATAGATCTTGCCTTCCTG
66 TGGAGCTAGTTAAAGATAACAGATCTTGCCTTCCTG
1317675 CATCGACAGT
Statistics
Matches: 90, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
116 90 1.00
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.28
Consensus pattern (116 bp):
ATCTTGCCTTCCTGCGTCAACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAG
TGGAGCTAGTTAAAGATAACAGATCTTGCCTTCCTGTGTTAATAGCGAAGC
Found at i:1317856 original size:44 final size:44
Alignment explanation
Indices: 1317794--1317910 Score: 116
Period size: 44 Copynumber: 2.7 Consensus size: 44
1317784 TTACAAGTCT
* *
1317794 TATCTCCCT-AAGTAGTAGTGGAGCAGA-CAGAAGAAATTA-ATCC
1 TATCTCTCTGAAGTTGTAGTGGAGCAGATCA-AAGAAA-TAGATCC
* * * *
1317837 TATCTCAT-TGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCT
1 TATCTC-TCTGAAGTTGTAGTGGAGCAGATCAAAGAAATAGATCC
*
1317881 TATCTCTCTGAAGTTGTAGTAGAGCAGATC
1 TATCTCTCTGAAGTTGTAGTGGAGCAGATC
1317911 GCATCAAGTC
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
43 10 0.17
44 49 0.82
45 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (44 bp):
TATCTCTCTGAAGTTGTAGTGGAGCAGATCAAAGAAATAGATCC
Found at i:1328549 original size:22 final size:22
Alignment explanation
Indices: 1328507--1328550 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1328497 AATTACAAAT
**
1328507 TATTTGAGAATTTATGGTTTTA
1 TATTTGAGAATTTATACTTTTA
1328529 TATTTGAGAATTTATACTTTTA
1 TATTTGAGAATTTATACTTTTA
1328551 GACGAGTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.55
Consensus pattern (22 bp):
TATTTGAGAATTTATACTTTTA
Found at i:1338462 original size:12 final size:12
Alignment explanation
Indices: 1338445--1338471 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1338435 TTGCTTGATC
1338445 TGGTAGAAGATT
1 TGGTAGAAGATT
1338457 TGGTAGAAGATT
1 TGGTAGAAGATT
1338469 TGG
1 TGG
1338472 CCGGTTCTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (12 bp):
TGGTAGAAGATT
Found at i:1345182 original size:18 final size:20
Alignment explanation
Indices: 1345140--1345178 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1345130 ATGCATTGTT
*
1345140 TTATATTTTTTTAATATATA
1 TTATATTATTTTAATATATA
1345160 TTATATTATTTTAATATAT
1 TTATATTATTTTAATATAT
1345179 TATAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATATTATTTTAATATATA
Found at i:1347824 original size:31 final size:31
Alignment explanation
Indices: 1347788--1347848 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
1347778 CAGTGATTTG
*
1347788 AATAAAA-ACTTTTGAATAGTTCA-ATGACTAA
1 AATAAAATA-TTTGGAATAGTT-AGATGACTAA
1347819 AATAAAATATTTGGAATAGTTAGATGACTA
1 AATAAAATATTTGGAATAGTTAGATGACTA
1347849 TTTTGTATCC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 1 0.04
31 25 0.93
32 1 0.04
ACGTcount: A:0.48, C:0.07, G:0.13, T:0.33
Consensus pattern (31 bp):
AATAAAATATTTGGAATAGTTAGATGACTAA
Found at i:1352383 original size:13 final size:13
Alignment explanation
Indices: 1352355--1352412 Score: 55
Period size: 13 Copynumber: 4.3 Consensus size: 13
1352345 TTATATTTAG
*
1352355 TTATA-TAATAAA
1 TTATATTAATAAT
*
1352367 TTATATTAATATT
1 TTATATTAATAAT
*
1352380 TTATTATTTTAATAAA
1 TTA-TA--TTAATAAT
1352396 TTATATTAATAAT
1 TTATATTAATAAT
1352409 TTAT
1 TTAT
1352413 TATTTTAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
12 5 0.14
13 19 0.51
14 2 0.05
15 2 0.05
16 9 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTATATTAATAAT
Found at i:1352391 original size:16 final size:15
Alignment explanation
Indices: 1352333--1352422 Score: 59
Period size: 16 Copynumber: 6.2 Consensus size: 15
1352323 ACATACATAC
1352333 ATATTTAATTAT-TT-
1 ATATTT-ATTATATTA
1352347 ATATTTAGTTATA-TA
1 ATATTTA-TTATATTA
*
1352362 ATA--AATTATATTA
1 ATATTTATTATATTA
*
1352375 ATATTTTATTATTTTA
1 ATA-TTTATTATATTA
*
1352391 ATA--AATTATATTA
1 ATATTTATTATATTA
*
1352404 ATAATTTATTATTTTA
1 AT-ATTTATTATATTA
1352420 ATA
1 ATA
1352423 AATTATTTAG
Statistics
Matches: 59, Mismatches: 7, Indels: 19
0.69 0.08 0.22
Matches are distributed among these distances:
12 5 0.08
13 17 0.29
14 12 0.20
15 4 0.07
16 21 0.36
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (15 bp):
ATATTTATTATATTA
Found at i:1352393 original size:29 final size:29
Alignment explanation
Indices: 1352360--1352437 Score: 131
Period size: 29 Copynumber: 2.7 Consensus size: 29
1352350 TTTAGTTATA
1352360 TAATAAATTATATTAATATTTTATTATTT
1 TAATAAATTATATTAATATTTTATTATTT
*
1352389 TAATAAATTATATTAATAATTTATTATTT
1 TAATAAATTATATTAATATTTTATTATTT
*
1352418 TAATAAATTAT-TTAGTATTT
1 TAATAAATTATATTAATATTT
1352438 CAATTTTATT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
28 7 0.15
29 39 0.85
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (29 bp):
TAATAAATTATATTAATATTTTATTATTT
Found at i:1352423 original size:16 final size:16
Alignment explanation
Indices: 1352366--1352429 Score: 71
Period size: 16 Copynumber: 4.2 Consensus size: 16
1352356 TATATAATAA
*
1352366 ATTATATTAATATTTT
1 ATTATATTAATAATTT
*
1352382 ATTATTTTAATAA---
1 ATTATATTAATAATTT
1352395 ATTATATTAATAATTT
1 ATTATATTAATAATTT
* *
1352411 ATTATTTTAATAAATT
1 ATTATATTAATAATTT
1352427 ATT
1 ATT
1352430 TAGTATTTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
13 12 0.30
16 28 0.70
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTATATTAATAATTT
Found at i:1352427 original size:13 final size:13
Alignment explanation
Indices: 1352382--1352430 Score: 62
Period size: 13 Copynumber: 3.5 Consensus size: 13
1352372 TTAATATTTT
1352382 ATTATTTTAATAA
1 ATTATTTTAATAA
*
1352395 ATTATATTAATAA
1 ATTATTTTAATAA
1352408 TTTATTATTTTAATAA
1 ---ATTATTTTAATAA
1352424 ATTATTT
1 ATTATTT
1352431 AGTATTTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 19 0.61
16 12 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
ATTATTTTAATAA
Found at i:1352478 original size:15 final size:17
Alignment explanation
Indices: 1352449--1352485 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
1352439 AATTTTATTT
1352449 TAATAATGAATTTTAAA
1 TAATAATGAATTTTAAA
1352466 -AATAATG-ATTTTAAA
1 TAATAATGAATTTTAAA
1352481 TAATA
1 TAATA
1352486 TTCTTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
TAATAATGAATTTTAAA
Found at i:1360207 original size:11 final size:11
Alignment explanation
Indices: 1360177--1360267 Score: 53
Period size: 11 Copynumber: 9.4 Consensus size: 11
1360167 ATTTTTAAAA
*
1360177 TTTTAAAACAC
1 TTTTAAAATAC
1360188 TTTTAAAATAC
1 TTTTAAAATAC
*
1360199 TTTTTAAAT--
1 TTTTAAAATAC
*
1360208 TTTT----TAA
1 TTTTAAAATAC
*
1360215 TTTTAAAATAT
1 TTTTAAAATAC
1360226 TTTTAAAATA-
1 TTTTAAAATAC
1360236 TTTT---A-A-
1 TTTTAAAATAC
*
1360242 TTTTAAAATAT
1 TTTTAAAATAC
1360253 TTTTAAAATAC
1 TTTTAAAATAC
1360264 TTTT
1 TTTT
1360268 TTTAAAAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 22
0.71 0.04 0.24
Matches are distributed among these distances:
5 1 0.02
6 5 0.08
7 5 0.08
9 5 0.08
10 5 0.08
11 44 0.68
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:1360221 original size:27 final size:26
Alignment explanation
Indices: 1360188--1360290 Score: 124
Period size: 27 Copynumber: 4.0 Consensus size: 26
1360178 TTTAAAACAC
*
1360188 TTTTAAAATACTTTTTAAATTTTTTAA
1 TTTTAAAATA-TTTTTAAATATTTTAA
1360215 TTTTAAAATATTTTTAAAATATTTTAA
1 TTTTAAAATATTTTT-AAATATTTTAA
*
1360242 TTTTAAAATATTTTTAAAATACTTT--
1 TTTTAAAATATTTTT-AAATATTTTAA
*
1360267 TTTTAAAAAATTTTT-AAT-TTTTAA
1 TTTTAAAATATTTTTAAATATTTTAA
1360291 AATAAAATTT
Statistics
Matches: 69, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
22 3 0.04
23 3 0.04
25 14 0.20
26 5 0.07
27 44 0.64
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (26 bp):
TTTTAAAATATTTTTAAATATTTTAA
Found at i:1360258 original size:17 final size:16
Alignment explanation
Indices: 1360199--1360255 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 16
1360189 TTTAAAATAC
* *
1360199 TTTTTAAATTTTTTAA
1 TTTTAAAATATTTTAA
1360215 TTTTAAAATA---T--
1 TTTTAAAATATTTTAA
1360226 TTTTAAAATATTTTAA
1 TTTTAAAATATTTTAA
1360242 TTTTAAAATATTTT
1 TTTTAAAATATTTT
1360256 TAAAATACTT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
11 10 0.29
13 1 0.03
14 1 0.03
16 22 0.65
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTAAAATATTTTAA
Found at i:1369799 original size:18 final size:19
Alignment explanation
Indices: 1369757--1369799 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 19
1369747 CCCCCCCCCC
1369757 TTTATTCACATAAAAAATA
1 TTTATTCACATAAAAAATA
*
1369776 TATATT-AC-TAAAAAATAA
1 TTTATTCACATAAAAAAT-A
1369794 TTTATT
1 TTTATT
1369800 TTTTTAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 8 0.38
18 8 0.38
19 5 0.24
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTATTCACATAAAAAATA
Found at i:1373642 original size:48 final size:45
Alignment explanation
Indices: 1373590--1374255 Score: 309
Period size: 48 Copynumber: 14.6 Consensus size: 45
1373580 CTCCACCACC
* * * *
1373590 GCCTTATGTGTATAAATCTCCACCACCACCACCTAAACATGAGGAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACC--AACA-AAGGAGAA
* *
1373638 GCCTTATGAATACAAGTCTCCACCACCACCACCACCAAAGGAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAACAAAGGAGAA
* * * ******* *
1373683 GCCTTATGAGTACAAGTCTCCACCCCCACCATCACCTTCTCCTCCACC
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAAC--AAAGGAGA-A
* * * * * ***** * *
1373731 TCCTTATGAGTACAAATCTCCACCACCTCCATCACCTTCTCCACCACC
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAAC-AAAGGA-GA-A
* * * * *
1373779 TCCTTATGTGTATAAGTCTCCACCACCTCCACCAAAGCATGAGGAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACC-AA-CA-AAGGAGAA
* *
1373827 GCCTTATGAATACAAGTCTCCACCACCACCA-C--CGAAGGAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAACAAAGGAGAA
* *
1373869 GCCTTATGAATACAAGTCTCCACCACCACCACC--GAAA-GAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAACAAAGGAGAA
* * * * ***** * *
1373911 GCCTTATGAATACAAGTCTCCACCACCTCCATCACCTTCTCCACCACC
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAAC-AAAGGA-GA-A
* * * * *
1373959 TCCTTATGTGTATAAGTCTCCACCACCTCCACCAAAGCATGAGGAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACC-AA-CA-AAGGAGAA
* *
1374007 GCCTTATGAATACAAGTCTCCACCACCACCA-C--CGAAGGAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAACAAAGGAGAA
* *
1374049 GCCTTATGAATACAAGTCTCCACCACCACCACC--GAAA-GAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAACAAAGGAGAA
* * * * ***** * *
1374091 GCCTTATGAATACAAGTCTCCACCACCTCCATCACCTTCTCCACCACC
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAAC-AAAGGA-GA-A
* * * * * *
1374139 TCCTTATGTGTATAAGTCTCCTCCACCTCCACCAAAGCATGAGGAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACC-AA-CA-AAGGAGAA
* *
1374187 GCCTTATGAATACAAGTCTCCACCACCACCA-C--CGAAGGAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAACAAAGGAGAA
*
1374229 GCCTTATGAATACAAGTCTCCACCACC
1 GCCTTATGAGTACAAGTCTCCACCACC
1374256 TCCATCTCCA
Statistics
Matches: 482, Mismatches: 109, Indels: 60
0.74 0.17 0.09
Matches are distributed among these distances:
42 182 0.38
43 9 0.02
45 40 0.08
46 5 0.01
47 8 0.02
48 226 0.47
49 6 0.01
50 6 0.01
ACGTcount: A:0.31, C:0.36, G:0.13, T:0.20
Consensus pattern (45 bp):
GCCTTATGAGTACAAGTCTCCACCACCACCACCAACAAAGGAGAA
Found at i:1373758 original size:27 final size:26
Alignment explanation
Indices: 1373720--1373808 Score: 71
Period size: 27 Copynumber: 3.5 Consensus size: 26
1373710 ACCATCACCT
*
1373720 TCTCCTCCACCTCCTTATGAGTACAAA
1 TCTCCACCACCTCCTTATG-GTACAAA
* **
1373747 TCTCCACCACCTCC--AT--CAC-CT
1 TCTCCACCACCTCCTTATGGTACAAA
* *
1373768 TCTCCACCACCTCCTTATGTGTATAAG
1 TCTCCACCACCTCCTTATG-GTACAAA
1373795 TCTCCACCACCTCC
1 TCTCCACCACCTCC
1373809 ACCAAAGCAT
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
21 14 0.29
22 2 0.04
23 2 0.04
25 2 0.04
26 1 0.02
27 27 0.56
ACGTcount: A:0.21, C:0.45, G:0.06, T:0.28
Consensus pattern (26 bp):
TCTCCACCACCTCCTTATGGTACAAA
Found at i:1373866 original size:42 final size:42
Alignment explanation
Indices: 1373820--1374255 Score: 395
Period size: 42 Copynumber: 9.8 Consensus size: 42
1373810 CCAAAGCATG
1373820 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
1373862 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
* * **
1373904 AAGAGAAGCCTTATGAATACAAGTCTCCACCACCTCCATCACCTTC
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCA---CCACCACC-GA
*** * ** ** * *
1373950 TCCACCACCTCCTTATGTGTATAAGTCTCCACCACCTCCACCAAAGCA
1 AGGA-GA-AGCCTTATGAATACAAGTCTCCACCACCACCACC---G-A
1373998 TGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
1 --AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
1374042 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
* * **
1374084 AAGAGAAGCCTTATGAATACAAGTCTCCACCACCTCCATCACCTTC
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCA---CCACCACC-GA
*** * ** ** * * *
1374130 TCCACCACCTCCTTATGTGTATAAGTCTCCTCCACCTCCACCAAAGCA
1 AGGA-GA-AGCCTTATGAATACAAGTCTCCACCACCACCACC---G-A
1374178 TGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
1 --AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
1374222 AGGAGAAGCCTTATGAATACAAGTCTCCACCACC
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACC
1374256 TCCATCTCCA
Statistics
Matches: 314, Mismatches: 58, Indels: 44
0.75 0.14 0.11
Matches are distributed among these distances:
42 180 0.57
44 2 0.01
45 28 0.09
46 2 0.01
47 2 0.01
48 96 0.31
49 2 0.01
50 2 0.01
ACGTcount: A:0.33, C:0.35, G:0.14, T:0.19
Consensus pattern (42 bp):
AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
Found at i:1373968 original size:180 final size:180
Alignment explanation
Indices: 1373542--1374255 Score: 1115
Period size: 180 Copynumber: 3.9 Consensus size: 180
1373532 CACCTCCTCC
* * * * * * * *
1373542 GCCTTATGAGTATAAGTCACCACCACCGCCTTCTCCTTCTCCACCACCGCCTTATGTGTATAAAT
1 GCCTTATGAATACAAGTCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTATGTGTATAAGT
*
1373607 CTCCACCACCACCACCTAAA-CATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACC
66 CTCCACCACCTCCACC-AAAGCATGAGGAGAAGCCTTATGAATACAAGTCT---CCACCACCACC
* * * ******* *
1373671 ACCAAAGGAGAAGCCTTATGAGTACAAGTCTCCACCCCCACCATCACCTTCTCCTCCACC
127 ACCGAAGGAGAAGCCTTATGAATACAAGTCTCCA---CCACCACCACC--GAAAGAGA-A
* * *
1373731 TCCTTATGAGTACAAATCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTATGTGTATAAGT
1 GCCTTATGAATACAAGTCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTATGTGTATAAGT
1373796 CTCCACCACCTCCACCAAAGCATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCG
66 CTCCACCACCTCCACCAAAGCATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCG
1373861 AAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAAAGAGAA
131 AAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAAAGAGAA
1373911 GCCTTATGAATACAAGTCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTATGTGTATAAGT
1 GCCTTATGAATACAAGTCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTATGTGTATAAGT
1373976 CTCCACCACCTCCACCAAAGCATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCG
66 CTCCACCACCTCCACCAAAGCATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCG
1374041 AAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAAAGAGAA
131 AAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAAAGAGAA
1374091 GCCTTATGAATACAAGTCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTATGTGTATAAGT
1 GCCTTATGAATACAAGTCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTATGTGTATAAGT
*
1374156 CTCCTCCACCTCCACCAAAGCATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCG
66 CTCCACCACCTCCACCAAAGCATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCG
1374221 AAGGAGAAGCCTTATGAATACAAGTCTCCACCACC
131 AAGGAGAAGCCTTATGAATACAAGTCTCCACCACC
1374256 TCCATCTCCA
Statistics
Matches: 499, Mismatches: 25, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
180 341 0.68
181 1 0.00
183 10 0.02
186 43 0.09
188 3 0.01
189 101 0.20
ACGTcount: A:0.31, C:0.37, G:0.13, T:0.20
Consensus pattern (180 bp):
GCCTTATGAATACAAGTCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTATGTGTATAAGT
CTCCACCACCTCCACCAAAGCATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCG
AAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAAAGAGAA
Found at i:1374291 original size:138 final size:138
Alignment explanation
Indices: 1374042--1374307 Score: 417
Period size: 138 Copynumber: 1.9 Consensus size: 138
1374032 CCACCACCGA
1374042 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAAAGAGAAGCCTTATGAATACAAG
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAAAGAGAAGCCTTATGAATACAAG
* * * * ** * *
1374107 TCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTATGTGTATAAGTCTCCTCCACCTCCACC
66 TCTCCACCACCTCCATCACCATCACCACCACCACCATATGACTATAAATCTCCACCACCTCCACC
1374172 AAAGCATG
131 AAAGCATG
*
1374180 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAAGGAGAAGCCTTATGAATACAAG
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAAAGAGAAGCCTTATGAATACAAG
* *
1374245 TCTCCACCACCTCCATCTCCATCACCACCTCCACCATACT-ACTATAAATCTCCACCACCTCCA
66 TCTCCACCACCTCCATCACCATCACCACCACCACCATA-TGACTATAAATCTCCACCACCTCCA
1374308 TCACCATCAC
Statistics
Matches: 116, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
138 115 0.99
139 1 0.01
ACGTcount: A:0.32, C:0.37, G:0.11, T:0.20
Consensus pattern (138 bp):
AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAAAGAGAAGCCTTATGAATACAAG
TCTCCACCACCTCCATCACCATCACCACCACCACCATATGACTATAAATCTCCACCACCTCCACC
AAAGCATG
Found at i:1374301 original size:48 final size:48
Alignment explanation
Indices: 1374239--1374837 Score: 502
Period size: 48 Copynumber: 12.4 Consensus size: 48
1374229 GCCTTATGAA
* * *
1374239 TACAAGTCTCCACCACCTCCATCTCCATCACCACCTCCACCATACTAC
1 TACAAGTCTCCACCACCTCCATCACCATCACCACCACCTCCATACTAC
* *
1374287 TATAAATCTCCACCACCTCCATCACCATCACCACCACCTCCATACTAC
1 TACAAGTCTCCACCACCTCCATCACCATCACCACCACCTCCATACTAC
* * * * * ** * * *
1374335 TACAAGTCCCCACCACCACCACCAAAGCATGAAGAACAACCACCATATTAC
1 TACAAGTCTCCACCACCTCCATC--ACCAT-CACCACCACCTCCATACTAC
* * * * *
1374386 TACAAGTCACCTCCTCCTCCATCTCCATCACCACCTCCTCCATACTAC
1 TACAAGTCTCCACCACCTCCATCACCATCACCACCACCTCCATACTAC
* *
1374434 TACAAGTCCCCACCACCTCCTTCACCATCACCACCACCTCCATACTAC
1 TACAAGTCTCCACCACCTCCATCACCATCACCACCACCTCCATACTAC
* ** * * * *
1374482 TACAAGTCTCCACCACCACCAAAACACGT-A-GAGCAACCCCCATACTAC
1 TACAAGTCTCCACCACCTCCATCAC-CATCACCA-CCACCTCCATACTAC
* * * *
1374530 TACAAGTCTCCTCCACCTCCATCACCCTCACCACCACCACCTTACTAC
1 TACAAGTCTCCACCACCTCCATCACCATCACCACCACCTCCATACTAC
* * * * * *
1374578 TATAAATCTCCACCACCACCTTCACCATCTCCACCACCTCCTTACTAC
1 TACAAGTCTCCACCACCTCCATCACCATCACCACCACCTCCATACTAC
* * *
1374626 TACAAGTCCCCACCACCTCCATCTCCATCACCACCTCCTCCATACTAC
1 TACAAGTCTCCACCACCTCCATCACCATCACCACCACCTCCATACTAC
* * * * * ** * *
1374674 TACAAATCTCCACCACCACCACCAAAGCATGAAGAACAACCCCCATACTAC
1 TACAAGTCTCCACCACCTCCATC--ACCAT-CACCACCACCTCCATACTAC
* * * * * *
1374725 TACAAGTCTCCACCACCACCTTCACCATCTCCTCCACCACCTTACTAC
1 TACAAGTCTCCACCACCTCCATCACCATCACCACCACCTCCATACTAC
* * ** * ** *
1374773 TACAAATCTCCACCACCACCCCCA-CATTACGTCTCACCACCATACTAC
1 TACAAGTCTCCACCACCTCCATCACCATCACCAC-CACCTCCATACTAC
*
1374821 TACAAATCTCCACCACC
1 TACAAGTCTCCACCACC
1374838 ACCAGTGAAG
Statistics
Matches: 437, Mismatches: 103, Indels: 22
0.78 0.18 0.04
Matches are distributed among these distances:
47 9 0.02
48 345 0.79
49 10 0.02
50 7 0.02
51 66 0.15
ACGTcount: A:0.30, C:0.48, G:0.03, T:0.19
Consensus pattern (48 bp):
TACAAGTCTCCACCACCTCCATCACCATCACCACCACCTCCATACTAC
Found at i:1374340 original size:96 final size:96
Alignment explanation
Indices: 1374239--1374837 Score: 556
Period size: 96 Copynumber: 6.2 Consensus size: 96
1374229 GCCTTATGAA
* * *
1374239 TACAAGTCTCCACCACCTCCATCTCCATCACCACCTCCACCATACTACTATAAATCTCCACCACC
1 TACAAGTCTCCACCACCTCCATCACCATCACCACCACCACCATACTACTACAAATCTCCACCACC
*
1374304 TCCATCACCATCACCACCACCTCCATACTAC
66 ACCATCACCATCACCACCACCTCCATACTAC
* * * * * ** * * * * *
1374335 TACAAGTCCCCACCACCACCACCAAAGCATGAAGAACAACCACCATATTACTACAAGTCACCTCC
1 TACAAGTCTCCACCACCTCCATC--ACCAT-CACCACCACCACCATACTACTACAAATCTCCACC
* * * *
1374400 TCCTCCATCTCCATCACCACCTCCTCCATACTAC
63 ACCACCATCACCATCACCACCACCTCCATACTAC
* * * *
1374434 TACAAGTCCCCACCACCTCCTTCACCATCACCACCACCTCCATACTACTACAAGTCTCCACCACC
1 TACAAGTCTCCACCACCTCCATCACCATCACCACCACCACCATACTACTACAAATCTCCACCACC
** * * * *
1374499 ACCAAAACACGT-A-GAGCAACCCCCATACTAC
66 ACCATCAC-CATCACCA-CCACCTCCATACTAC
* * * *
1374530 TACAAGTCTCCTCCACCTCCATCACCCTCACCACCACCACCTTACTACTATAAATCTCCACCACC
1 TACAAGTCTCCACCACCTCCATCACCATCACCACCACCACCATACTACTACAAATCTCCACCACC
* * *
1374595 ACCTTCACCATCTCCACCACCTCCTTACTAC
66 ACCATCACCATCACCACCACCTCCATACTAC
* * * *
1374626 TACAAGTCCCCACCACCTCCATCTCCATCACCACCTCCTCCATACTACTACAAATCTCCACCACC
1 TACAAGTCTCCACCACCTCCATCACCATCACCACCACCACCATACTACTACAAATCTCCACCACC
* * * ** * *
1374691 ACCACCAAAGCATGAAGAACAACCCCCATACTAC
66 ACCATC--ACCAT-CACCACCACCTCCATACTAC
* * * * *
1374725 TACAAGTCTCCACCACCACCTTCACCATCTCCTCCACCACCTTACTACTACAAATCTCCACCACC
1 TACAAGTCTCCACCACCTCCATCACCATCACCACCACCACCATACTACTACAAATCTCCACCACC
** * ** *
1374790 ACCCCCA-CATTACGTCTCACCACCATACTAC
66 ACCATCACCATCACCAC-CACCTCCATACTAC
*
1374821 TACAAATCTCCACCACC
1 TACAAGTCTCCACCACC
1374838 ACCAGTGAAG
Statistics
Matches: 400, Mismatches: 92, Indels: 22
0.78 0.18 0.04
Matches are distributed among these distances:
95 5 0.01
96 231 0.58
97 8 0.02
98 7 0.02
99 149 0.37
ACGTcount: A:0.30, C:0.48, G:0.03, T:0.19
Consensus pattern (96 bp):
TACAAGTCTCCACCACCTCCATCACCATCACCACCACCACCATACTACTACAAATCTCCACCACC
ACCATCACCATCACCACCACCTCCATACTAC
Found at i:1374414 original size:147 final size:144
Alignment explanation
Indices: 1374239--1374642 Score: 592
Period size: 144 Copynumber: 2.8 Consensus size: 144
1374229 GCCTTATGAA
*
1374239 TACAAGTCTCCACCACCTCCATCTCCATCACCACCTCCACCATACTACTATAAATCTCCACCACC
1 TACAAGTCTCCTCCACCTCCATCTCCATCACCACCTCCACCATACTACTATAAATCTCCACCACC
* *
1374304 TCCATCACCATCACCACCACCTCCATACTACTACAAGTCCCCACCACCACCACCAAAGCATGAAG
66 TCCTTCACCATCACCACCACCTCCATACTACTACAAGTCCCCACCACCACCA--AAA-CACGAAG
*
1374369 AACAACCACCATATTAC
128 AACAACCACCATACTAC
* * * * * *
1374386 TACAAGTCACCTCCTCCTCCATCTCCATCACCACCTCCTCCATACTACTACAAGTCCCCACCACC
1 TACAAGTCTCCTCCACCTCCATCTCCATCACCACCTCCACCATACTACTATAAATCTCCACCACC
* * *
1374451 TCCTTCACCATCACCACCACCTCCATACTACTACAAGTCTCCACCACCACCAAAACACGTAGAGC
66 TCCTTCACCATCACCACCACCTCCATACTACTACAAGTCCCCACCACCACCAAAACACGAAGAAC
*
1374516 AACCCCCATACTAC
131 AACCACCATACTAC
* * * *
1374530 TACAAGTCTCCTCCACCTCCATCACCCTCACCACCACCACCTTACTACTATAAATCTCCACCACC
1 TACAAGTCTCCTCCACCTCCATCTCCATCACCACCTCCACCATACTACTATAAATCTCCACCACC
* * *
1374595 ACCTTCACCATCTCCACCACCTCCTTACTACTACAAGTCCCCACCACC
66 TCCTTCACCATCACCACCACCTCCATACTACTACAAGTCCCCACCACC
1374643 TCCATCTCCA
Statistics
Matches: 229, Mismatches: 28, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
144 118 0.52
145 3 0.01
147 108 0.47
ACGTcount: A:0.30, C:0.48, G:0.03, T:0.19
Consensus pattern (144 bp):
TACAAGTCTCCTCCACCTCCATCTCCATCACCACCTCCACCATACTACTATAAATCTCCACCACC
TCCTTCACCATCACCACCACCTCCATACTACTACAAGTCCCCACCACCACCAAAACACGAAGAAC
AACCACCATACTAC
Found at i:1374783 original size:24 final size:23
Alignment explanation
Indices: 1374756--1374837 Score: 69
Period size: 24 Copynumber: 3.4 Consensus size: 23
1374746 TCACCATCTC
1374756 CTCCACCACCTTACTACTACAAAT
1 CTCCACCACC-TACTACTACAAAT
** * *
1374780 CTCCACCACC-ACCCCCAC-ATT
1 CTCCACCACCTACTACTACAAAT
1374801 ACGTCTCACCACCATACTACTACAAAT
1 -C-TC-CACCACC-TACTACTACAAAT
1374828 CTCCACCACC
1 CTCCACCACC
1374838 ACCAGTGAAG
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
21 2 0.05
22 6 0.14
23 2 0.05
24 24 0.55
25 2 0.05
26 6 0.14
27 2 0.05
ACGTcount: A:0.30, C:0.49, G:0.01, T:0.20
Consensus pattern (23 bp):
CTCCACCACCTACTACTACAAAT
Found at i:1376008 original size:36 final size:36
Alignment explanation
Indices: 1375961--1376040 Score: 106
Period size: 36 Copynumber: 2.2 Consensus size: 36
1375951 GTACTACTAT
* * * *
1375961 AAGTCTCCACCTCCACCGGCTCCCACTTACGTTTAC
1 AAGTCACCACCTCCACCAGCACCAACTTACGTTTAC
* *
1375997 AAGTCACCACCTCCACCATCACCAACTTATGTTTAC
1 AAGTCACCACCTCCACCAGCACCAACTTACGTTTAC
1376033 AAGTCACC
1 AAGTCACC
1376041 TCCACCTCCT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.26, C:0.41, G:0.09, T:0.24
Consensus pattern (36 bp):
AAGTCACCACCTCCACCAGCACCAACTTACGTTTAC
Found at i:1376149 original size:150 final size:150
Alignment explanation
Indices: 1375952--1376223 Score: 490
Period size: 150 Copynumber: 1.8 Consensus size: 150
1375942 GCCACCACCG
1375952 TACTACTATAAGTCTCCACCTCCACCGGCTCCCACTTACGTTTACAAGTCACCACCTCCACCATC
1 TACTACTATAAGTCTCCACCTCCACCGGCTCCCACTTACGTTTACAAGTCACCACCTCCACCATC
* * *
1376017 ACCAACTTATGTTTACAAGTCACCTCCACCTCCTGTGTACTACTACAAGTCTCCACCACCACCAA
66 ACCAACTTATGTTTACAAGTCACCTCCACCACCTGTGTACTACTACAAATCACCACCACCACCAA
1376082 AGCATGTGGAACAACCCCCA
131 AGCATGTGGAACAACCCCCA
*
1376102 TACTACTATAAGTCTCCACCTCCACCGGCTCCCACTTATGTTTACAAGTCACCACCTCCACCATC
1 TACTACTATAAGTCTCCACCTCCACCGGCTCCCACTTACGTTTACAAGTCACCACCTCCACCATC
* *
1376167 GCCGACTTATGTTTACAAGTCACCTCCACCACCTGTGTACTACTACAAATCACCACC
66 ACCAACTTATGTTTACAAGTCACCTCCACCACCTGTGTACTACTACAAATCACCACC
1376224 TCCTCCCACT
Statistics
Matches: 116, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
150 116 1.00
ACGTcount: A:0.27, C:0.40, G:0.09, T:0.24
Consensus pattern (150 bp):
TACTACTATAAGTCTCCACCTCCACCGGCTCCCACTTACGTTTACAAGTCACCACCTCCACCATC
ACCAACTTATGTTTACAAGTCACCTCCACCACCTGTGTACTACTACAAATCACCACCACCACCAA
AGCATGTGGAACAACCCCCA
Found at i:1376158 original size:36 final size:36
Alignment explanation
Indices: 1376111--1376199 Score: 115
Period size: 36 Copynumber: 2.5 Consensus size: 36
1376101 ATACTACTAT
* * *
1376111 AAGTCTCCACCTCCACCGGCTCCCACTTATGTTTAC
1 AAGTCACCACCTCCACCAGCGCCCACTTATGTTTAC
* *
1376147 AAGTCACCACCTCCACCATCGCCGACTTATGTTTAC
1 AAGTCACCACCTCCACCAGCGCCCACTTATGTTTAC
* *
1376183 AAGTCACCTCCACCACC
1 AAGTCACCACCTCCACC
1376200 TGTGTACTAC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.24, C:0.43, G:0.10, T:0.24
Consensus pattern (36 bp):
AAGTCACCACCTCCACCAGCGCCCACTTATGTTTAC
Found at i:1376334 original size:48 final size:47
Alignment explanation
Indices: 1376282--1376567 Score: 203
Period size: 48 Copynumber: 6.0 Consensus size: 47
1376272 GCAGCCCCCG
* * * *
1376282 TACTACTACAAATCTCCTCCACCACCATCGCCATCTCCTCCTCCACCA
1 TACTACTACAAATCCCCACCACCACCA-CACCATCTCCTCCACCACCA
* * *** *
1376330 TACTATTACAAGTCCCCACCACCACCAGTTCACTCTCCACCACCACCA
1 TACTACTACAAATCCCCACCACCACCACACCA-TCTCCTCCACCACCA
* * * * *** * *
1376378 TACTACTACAAGTCCCCACCACCACCAAAACATGTGGAGCAACCTCCA
1 TACTACTACAAATCCCCACCACCACCACACCATCT-CCTCCACCACCA
* * * *
1376426 TACTACTACAAATCTCCTCCTCCACCATCGCCATCTCCTCCACCACCA
1 TACTACTACAAATCCCCACCACCACCA-CACCATCTCCTCCACCACCA
* * * ***** *
1376474 TACTACTACAAATCCCCACCACCACCAAAACATGTAGAAGAGCCCCCA
1 TACTACTACAAATCCCCACCACCACCACACCATCTCCTCCA-CCACCA
* * *
1376522 TACTACTACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCAC
1 TACTACTACAAATCCCCACCACCACCA-CACCATCTCCTCCACCAC
1376568 NNNNNNNNNN
Statistics
Matches: 176, Mismatches: 57, Indels: 10
0.72 0.23 0.04
Matches are distributed among these distances:
47 9 0.05
48 158 0.90
49 9 0.05
ACGTcount: A:0.30, C:0.46, G:0.05, T:0.19
Consensus pattern (47 bp):
TACTACTACAAATCCCCACCACCACCACACCATCTCCTCCACCACCA
Found at i:1376404 original size:144 final size:144
Alignment explanation
Indices: 1376239--1376500 Score: 434
Period size: 144 Copynumber: 1.8 Consensus size: 144
1376229 CCACTTATGT
* * * *
1376239 CTACAAGTCTCCACCACCACCAAAGCATGTAGAGCAGCCCCCGTACTACTACAAATCTCCTCCAC
1 CTACAAGTCCCCACCACCACCAAAACATGTAGAGCAACCCCCATACTACTACAAATCTCCTCCAC
* * *
1376304 CACCATCGCCATCTCCTCCTCCACCATACTATTACAAGTCCCCACCACCACCAGTTCACTCTCCA
66 CACCATCGCCATCTCCTCCACCACCATACTACTACAAATCCCCACCACCACCAGTTCACTCTCCA
1376369 CCACCACCATACTA
131 CCACCACCATACTA
* * *
1376383 CTACAAGTCCCCACCACCACCAAAACATGTGGAGCAACCTCCATACTACTACAAATCTCCTCCTC
1 CTACAAGTCCCCACCACCACCAAAACATGTAGAGCAACCCCCATACTACTACAAATCTCCTCCAC
1376448 CACCATCGCCATCTCCTCCACCACCATACTACTACAAATCCCCACCACCACCA
66 CACCATCGCCATCTCCTCCACCACCATACTACTACAAATCCCCACCACCACCA
1376501 AAACATGTAG
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
144 108 1.00
ACGTcount: A:0.30, C:0.46, G:0.06, T:0.18
Consensus pattern (144 bp):
CTACAAGTCCCCACCACCACCAAAACATGTAGAGCAACCCCCATACTACTACAAATCTCCTCCAC
CACCATCGCCATCTCCTCCACCACCATACTACTACAAATCCCCACCACCACCAGTTCACTCTCCA
CCACCACCATACTA
Found at i:1376523 original size:144 final size:144
Alignment explanation
Indices: 1376239--1376548 Score: 415
Period size: 144 Copynumber: 2.2 Consensus size: 144
1376229 CCACTTATGT
* * *
1376239 CTACAAGTCTCCACCACCACCAAAGCATGTAGAGCAGCCCCCGTACTACTACAAATCTCCTCCAC
1 CTACAAGTCTCCACCACCACCAAAACATGTAGAGCAACCCCCATACTACTACAAATCTCCTCCAC
* * * *** *
1376304 CACCATCGCCATCTCCTCCTCCACCATACTATTACAAGTCCCCACCACCACCAGTTCACTCTCCA
66 CACCATCGCCATCTCCTCCACCACCATACTACTACAAATCCCCACCACCACCAAAACACTCTACA
*
1376369 CCACCACCATACTA
131 ACACCACCATACTA
* * * *
1376383 CTACAAGTCCCCACCACCACCAAAACATGTGGAGCAACCTCCATACTACTACAAATCTCCTCCTC
1 CTACAAGTCTCCACCACCACCAAAACATGTAGAGCAACCCCCATACTACTACAAATCTCCTCCAC
* *
1376448 CACCATCGCCATCTCCTCCACCACCATACTACTACAAATCCCCACCACCACCAAAACA-TGTAGA
66 CACCATCGCCATCTCCTCCACCACCATACTACTACAAATCCCCACCACCACCAAAACACTCTACA
* *
1376512 AGAGCCCCCATACTA
131 ACA-CCACCATACTA
* *
1376527 CTACAAATCTCCTCCACCACCA
1 CTACAAGTCTCCACCACCACCA
1376549 TCACCATCTC
Statistics
Matches: 143, Mismatches: 22, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
143 4 0.03
144 139 0.97
ACGTcount: A:0.31, C:0.45, G:0.06, T:0.18
Consensus pattern (144 bp):
CTACAAGTCTCCACCACCACCAAAACATGTAGAGCAACCCCCATACTACTACAAATCTCCTCCAC
CACCATCGCCATCTCCTCCACCACCATACTACTACAAATCCCCACCACCACCAAAACACTCTACA
ACACCACCATACTA
Found at i:1376560 original size:96 final size:96
Alignment explanation
Indices: 1376327--1376567 Score: 326
Period size: 96 Copynumber: 2.5 Consensus size: 96
1376317 TCCTCCTCCA
* * * * * *
1376327 CCATACTATTACAAGTCCCCACCACCACCAGTTCA-C-TCTCCACCACCACCATACTACTACAAG
1 CCATACTACTACAAATCTCCTCCACCACCA--TCACCATCTCCTCCACCACCATACTACTACAAA
* *
1376390 TCCCCACCACCACCAAAACATGTGGAGCAACCT
64 TCCCCACCACCACCAAAACATGTGAAGCAACCC
* *
1376423 CCATACTACTACAAATCTCCTCCTCCACCATCGCCATCTCCTCCACCACCATACTACTACAAATC
1 CCATACTACTACAAATCTCCTCCACCACCATCACCATCTCCTCCACCACCATACTACTACAAATC
*
1376488 CCCACCACCACCAAAACATGTAGAAG-AGCCC
66 CCCACCACCACCAAAACATGT-GAAGCAACCC
*
1376519 CCATACTACTACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCAC
1 CCATACTACTACAAATCTCCTCCACCACCATCACCATCTCCTCCACCAC
1376568 NNNNNNNNNN
Statistics
Matches: 128, Mismatches: 14, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
94 2 0.02
95 1 0.01
96 122 0.95
97 3 0.02
ACGTcount: A:0.31, C:0.46, G:0.05, T:0.18
Consensus pattern (96 bp):
CCATACTACTACAAATCTCCTCCACCACCATCACCATCTCCTCCACCACCATACTACTACAAATC
CCCACCACCACCAAAACATGTGAAGCAACCC
Found at i:1376753 original size:48 final size:48
Alignment explanation
Indices: 1376677--1377260 Score: 346
Period size: 48 Copynumber: 12.2 Consensus size: 48
1376667 NGAGCAACCT
* * *
1376677 CCATACTACTACAAATCTCCTCCTCCACCATCGCCATCTCCTCCACCA
1 CCATACTACTACAAATCCCCACCACCACCATCGCCATCTCCTCCACCA
*** * ***** *
1376725 CCATACTACTACAAATCCCCACCACCACCA-AAACATGTAGAAGAGCCC
1 CCATACTACTACAAATCCCCACCACCACCATCGCCATCTCCTCCA-CCA
* * * *
1376773 CCATACTACTACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCA
1 CCATACTACTACAAATCCCCACCACCACCATCGCCATCTCCTCCACCA
* * *** * *** * *
1376821 CCATACTACTACAAGTCCCCACCACCGCCA-AAACATGTGGAGCAACCT
1 CCATACTACTACAAATCCCCACCACCACCATCGCCATCT-CCTCCACCA
*
1376869 CCATACTACTACAAATCACCC-CCACCACCATCGCCATCTCCTCCTCCA
1 CCATACTACTACAAATC-CCCACCACCACCATCGCCATCTCCTCCACCA
* * * ***** *
1376917 CCATACTACTACAAGTCCCCACCACCACCGA-AG-CATGTAGAGGAGCCC
1 CCATACTACTACAAATCCCCACCACCACC-ATCGCCATCTCCTCCA-CCA
* *
1376965 CCATACTACTACAAGTCTCCC-CCACCACCATCGCCATCTCCTCCTCCA
1 CCATACTACTACAAATC-CCCACCACCACCATCGCCATCTCCTCCACCA
* * * * *
1377013 CCATACTATTACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCA
1 CCATACTACTACAAATCCCCACCACCACCATCGCCATCTCCTCCACCA
* ** * ***** *
1377061 CCATACTACTACAAGTCCCCACCACCACCGA--AACATGTAGAGGAGCCC
1 CCATACTACTACAAATCCCCACCACCACC-ATCGCCATCTCCTCCA-CCA
* * * *
1377109 CCATAC-ATCTACAAATCTCCTCCACCACCATCGCCATCTCTTCCTCCA
1 CCATACTA-CTACAAATCCCCACCACCACCATCGCCATCTCCTCCACCA
* * * ***** *
1377157 CCATACTACTACAAGTCCCCACCACCACCGA-AG-CATGTAGAGGAGCCC
1 CCATACTACTACAAATCCCCACCACCACC-ATCGCCATCTCCTCCA-CCA
* *
1377205 CCATACTACTACAAGTCTCCC-CCACCACCATCGCCATCTCCTCCTCCA
1 CCATACTACTACAAATC-CCCACCACCACCATCGCCATCTCCTCCACCA
1377253 CCATACTA
1 CCATACTA
1377261 TTNNNNNNNN
Statistics
Matches: 393, Mismatches: 120, Indels: 46
0.70 0.21 0.08
Matches are distributed among these distances:
47 32 0.08
48 327 0.83
49 34 0.09
ACGTcount: A:0.29, C:0.46, G:0.07, T:0.18
Consensus pattern (48 bp):
CCATACTACTACAAATCCCCACCACCACCATCGCCATCTCCTCCACCA
Found at i:1376841 original size:96 final size:96
Alignment explanation
Indices: 1376677--1377042 Score: 545
Period size: 96 Copynumber: 3.8 Consensus size: 96
1376667 NGAGCAACCT
* * *
1376677 CCATACTACTACAAATCTCCTCCTCCACCATCGCCATCTCCTCCACCACCATACTACTACAAATC
1 CCATACTACTACAAATCTCCCCCACCACCATCGCCATCTCCTCCTCCACCATACTACTACAAATC
1376742 CCCACCACCACCAAAACATGTAGAAGAGCCC
66 CCCACCACCACCAAAACATGTAGAAGAGCCC
* * *
1376773 CCATACTACTACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTC
1 CCATACTACTACAAATCTCCCCCACCACCATCGCCATCTCCTCCTCCACCATACTACTACAAATC
* * * *
1376838 CCCACCACCGCCAAAACATGT-GGAGCAACCT
66 CCCACCACCACCAAAACATGTAGAAG-AGCCC
* *
1376869 CCATACTACTACAAATCACCCCCACCACCATCGCCATCTCCTCCTCCACCATACTACTACAAGTC
1 CCATACTACTACAAATCTCCCCCACCACCATCGCCATCTCCTCCTCCACCATACTACTACAAATC
* * *
1376934 CCCACCACCACCGAAGCATGTAGAGGAGCCC
66 CCCACCACCACCAAAACATGTAGAAGAGCCC
* *
1376965 CCATACTACTACAAGTCTCCCCCACCACCATCGCCATCTCCTCCTCCACCATACTATTACAAATC
1 CCATACTACTACAAATCTCCCCCACCACCATCGCCATCTCCTCCTCCACCATACTACTACAAATC
* *
1377030 TCCTCCACCACCA
66 CCCACCACCACCA
1377043 TCACCATCTC
Statistics
Matches: 243, Mismatches: 25, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
95 3 0.01
96 238 0.98
97 2 0.01
ACGTcount: A:0.30, C:0.46, G:0.06, T:0.18
Consensus pattern (96 bp):
CCATACTACTACAAATCTCCCCCACCACCATCGCCATCTCCTCCTCCACCATACTACTACAAATC
CCCACCACCACCAAAACATGTAGAAGAGCCC
Found at i:1376995 original size:192 final size:192
Alignment explanation
Indices: 1376668--1377026 Score: 610
Period size: 192 Copynumber: 1.9 Consensus size: 192
1376658 NNNNNNNNNN
* * *
1376668 GAGCAACCTCCATACTACTACAAATCTCCTCCTCCACCATCGCCATCTCCTCCACCACCATACTA
1 GAGCAACCTCCATACTACTACAAATCACCCCCACCACCATCGCCATCTCCTCCACCACCATACTA
*
1376733 CTACAAATCCCCACCACCACCAAAACATGTAGAAGAGCCCCCATACTACTACAAATCTCCTCCAC
66 CTACAAATCCCCACCACCACCAAAACATGTAGAAGAGCCCCCATACTACTACAAATCTCCCCCAC
1376798 CACCATCACCATCTCCTCCTCCACCATACTACTACAAGTCCCCACCACCGCCAAAACATGTG
131 CACCATCACCATCTCCTCCTCCACCATACTACTACAAGTCCCCACCACCGCCAAAACATGTG
*
1376860 GAGCAACCTCCATACTACTACAAATCACCCCCACCACCATCGCCATCTCCTCCTCCACCATACTA
1 GAGCAACCTCCATACTACTACAAATCACCCCCACCACCATCGCCATCTCCTCCACCACCATACTA
* * * * *
1376925 CTACAAGTCCCCACCACCACCGAAGCATGTAGAGGAGCCCCCATACTACTACAAGTCTCCCCCAC
66 CTACAAATCCCCACCACCACCAAAACATGTAGAAGAGCCCCCATACTACTACAAATCTCCCCCAC
* *
1376990 CACCATCGCCATCTCCTCCTCCACCATACTATTACAA
131 CACCATCACCATCTCCTCCTCCACCATACTACTACAA
1377027 ATCTCCTCCA
Statistics
Matches: 155, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
192 155 1.00
ACGTcount: A:0.30, C:0.45, G:0.07, T:0.18
Consensus pattern (192 bp):
GAGCAACCTCCATACTACTACAAATCACCCCCACCACCATCGCCATCTCCTCCACCACCATACTA
CTACAAATCCCCACCACCACCAAAACATGTAGAAGAGCCCCCATACTACTACAAATCTCCCCCAC
CACCATCACCATCTCCTCCTCCACCATACTACTACAAGTCCCCACCACCGCCAAAACATGTG
Found at i:1377013 original size:24 final size:24
Alignment explanation
Indices: 1376981--1377063 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
1376971 TACTACAAGT
* *
1376981 CTCCCCCACCACCATCGCCATCTC
1 CTCCTCCACCACCATCACCATCTC
* * **
1377005 CTCCTCCACCATACTATTA-CAAAT-
1 CTCCTCCACC--ACCATCACCATCTC
1377029 CTCCTCCACCACCATCACCATCTC
1 CTCCTCCACCACCATCACCATCTC
1377053 CTCCTCCACCA
1 CTCCTCCACCA
1377064 TACTACTACA
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
22 5 0.11
23 3 0.07
24 30 0.67
25 3 0.07
26 4 0.09
ACGTcount: A:0.23, C:0.54, G:0.01, T:0.22
Consensus pattern (24 bp):
CTCCTCCACCACCATCACCATCTC
Found at i:1377051 original size:21 final size:21
Alignment explanation
Indices: 1376980--1377064 Score: 71
Period size: 21 Copynumber: 3.8 Consensus size: 21
1376970 CTACTACAAG
* *
1376980 TCTCCCCCACCACCATCGCCA
1 TCTCCTCCACCACCATCACCA
* *
1377001 TCTCCTCCTCCACCATACTATTACAAA
1 TCTCCTCCACCACCAT-C----AC-CA
1377028 TCTCCTCCACCACCATCACCA
1 TCTCCTCCACCACCATCACCA
*
1377049 TCTCCTCCTCCACCAT
1 TCTCCTCCACCACCAT
1377065 ACTACTACAA
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
21 30 0.59
22 3 0.06
26 2 0.04
27 16 0.31
ACGTcount: A:0.22, C:0.53, G:0.01, T:0.24
Consensus pattern (21 bp):
TCTCCTCCACCACCATCACCA
Found at i:1377065 original size:96 final size:96
Alignment explanation
Indices: 1376677--1377089 Score: 427
Period size: 96 Copynumber: 4.3 Consensus size: 96
1376667 NGAGCAACCT
* * *
1376677 CCATACTACTACAAATCTCCTCCTCCACCATCGCCATCTCCTCCACCACCATACTACTACAAATC
1 CCATACTACTACAAATCTCCCCCACCACCATCGCCATCTCCTCCTCCACCATACTACTACAAATC
* * * * ** * *
1376742 CCCACCACCACCAAAACATGTAGAAGAGCCC
66 CCCACCACCACCACACCATCTACATCATCCA
* * *
1376773 CCATACTACTACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTC
1 CCATACTACTACAAATCTCCCCCACCACCATCGCCATCTCCTCCTCCACCATACTACTACAAATC
* * * * ** * * *
1376838 CCCACCACCGCCAAAACATGTGGAGCAACCT
66 CCCACCACCACCACACCATCTACATCATCCA
* *
1376869 CCATACTACTACAAATCACCCCCACCACCATCGCCATCTCCTCCTCCACCATACTACTACAAGTC
1 CCATACTACTACAAATCTCCCCCACCACCATCGCCATCTCCTCCTCCACCATACTACTACAAATC
* * * ** * *
1376934 CCCACCACCACCGA-AGCATGTAGAGGAGCCC
66 CCCACCACCACC-ACACCATCTACATCATCCA
* *
1376965 CCATACTACTACAAGTCTCCCCCACCACCATCGCCATCTCCTCCTCCACCATACTATTACAAATC
1 CCATACTACTACAAATCTCCCCCACCACCATCGCCATCTCCTCCTCCACCATACTACTACAAATC
* * * *
1377030 TCCTCCACCACCATCACCATCT-CCTCCTCCA
66 CCCACCACCACCA-CACCATCTACATCATCCA
*
1377061 CCATACTACTACAAGTC-CCCACCACCACC
1 CCATACTACTACAAATCTCCC-CCACCACC
1377090 GAAACATGTA
Statistics
Matches: 279, Mismatches: 34, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
95 4 0.01
96 269 0.96
97 6 0.02
ACGTcount: A:0.29, C:0.47, G:0.06, T:0.18
Consensus pattern (96 bp):
CCATACTACTACAAATCTCCCCCACCACCATCGCCATCTCCTCCTCCACCATACTACTACAAATC
CCCACCACCACCACACCATCTACATCATCCA
Found at i:1377067 original size:192 final size:191
Alignment explanation
Indices: 1376669--1377089 Score: 565
Period size: 192 Copynumber: 2.2 Consensus size: 191
1376659 NNNNNNNNNG
* * *
1376669 AGCAACCTCCATACTACTACAAATCTCCTCCTCCACCATCGCCATCTCCTCCACCACCATACTAC
1 AGCAACCACCATACTACTACAAATC-CCCCCACCACCATCGCCATCTCCTCCACCACCATACTAC
*
1376734 TACAAATCCCCACCACCACCAAAACATGTAGAAGAGCCCCCATACTACTACAAATCTCCTCCACC
65 TACAAATCCCCACCACCACCAAAACATGTAGAAGAGCCCCCATACTACTACAAATCTCCCCCACC
* * * *
1376799 ACCATCACCATCTCCTCCTCCACCATACTACTACAAGTCCCCACCACCGCCAAAACATGTGG
130 ACCATCACCATCTCCTCCTCCACCATACTACTACAAATCCCCACCACCACCAAAACATCTGC
* *
1376861 AGCAACCTCCATACTACTACAAATCACCCCCACCACCATCGCCATCTCCTCCTCCACCATACTAC
1 AGCAACCACCATACTACTACAAATC-CCCCCACCACCATCGCCATCTCCTCCACCACCATACTAC
* * * * *
1376926 TACAAGTCCCCACCACCACCGAAGCATGTAGAGGAGCCCCCATACTACTACAAGTCTCCCCCACC
65 TACAAATCCCCACCACCACCAAAACATGTAGAAGAGCCCCCATACTACTACAAATCTCCCCCACC
* * * * * *
1376991 ACCATCGCCATCTCCTCCTCCACCATACTATTACAAATCTCCTCCACCACCATCACCATCT-C
130 ACCATCACCATCTCCTCCTCCACCATACTACTACAAATCCCCACCACCACCA-AAACATCTGC
** ** *
1377053 CTCCTCCACCATACTACTACAAGTCCCCACCACCACC
1 AGCAACCACCATACTACTACAAATCCCC-CCACCACC
1377090 GAAACATGTA
Statistics
Matches: 201, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
191 3 0.01
192 193 0.96
193 5 0.02
ACGTcount: A:0.29, C:0.47, G:0.06, T:0.18
Consensus pattern (191 bp):
AGCAACCACCATACTACTACAAATCCCCCCACCACCATCGCCATCTCCTCCACCACCATACTACT
ACAAATCCCCACCACCACCAAAACATGTAGAAGAGCCCCCATACTACTACAAATCTCCCCCACCA
CCATCACCATCTCCTCCTCCACCATACTACTACAAATCCCCACCACCACCAAAACATCTGC
Found at i:1377113 original size:96 final size:96
Alignment explanation
Indices: 1377013--1377260 Score: 426
Period size: 96 Copynumber: 2.6 Consensus size: 96
1377003 TCCTCCTCCA
*
1377013 CCATACTATTACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTC
1 CCATACTATTACAAATCTCCTCCACCACCATCGCCATCTCCTCCTCCACCATACTACTACAAGTC
1377078 CCCACCACCACCGAAACATGTAGAGGAGCCC
66 CCCACCACCACCGAAACATGTAGAGGAGCCC
*
1377109 CCATAC-ATCTACAAATCTCCTCCACCACCATCGCCATCTCTTCCTCCACCATACTACTACAAGT
1 CCATACTAT-TACAAATCTCCTCCACCACCATCGCCATCTCCTCCTCCACCATACTACTACAAGT
*
1377173 CCCCACCACCACCGAAGCATGTAGAGGAGCCC
65 CCCCACCACCACCGAAACATGTAGAGGAGCCC
* * *
1377205 CCATACTACTACAAGTCTCCCCCACCACCATCGCCATCTCCTCCTCCACCATACTA
1 CCATACTATTACAAATCTCCTCCACCACCATCGCCATCTCCTCCTCCACCATACTA
1377261 TTNNNNNNNN
Statistics
Matches: 143, Mismatches: 7, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
95 2 0.01
96 140 0.98
97 1 0.01
ACGTcount: A:0.28, C:0.45, G:0.07, T:0.19
Consensus pattern (96 bp):
CCATACTATTACAAATCTCCTCCACCACCATCGCCATCTCCTCCTCCACCATACTACTACAAGTC
CCCACCACCACCGAAACATGTAGAGGAGCCC
Found at i:1377123 original size:240 final size:240
Alignment explanation
Indices: 1376773--1377262 Score: 874
Period size: 240 Copynumber: 2.0 Consensus size: 240
1376763 AGAAGAGCCC
*
1376773 CCATACTACTACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTC
1 CCATACTATTACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTC
* * *
1376838 CCCACCACCGCCAAAACATGTGGAGCAACCTCCATACTACTACAAATCACCCCCACCACCATCGC
66 CCCACCACCACCAAAACATGTAGAGCAACCCCCATACTACTACAAATCACCCCCACCACCATCGC
1376903 CATCTCCTCCTCCACCATACTACTACAAGTCCCCACCACCACCGAAGCATGTAGAGGAGCCCCCA
131 CATCTCCTCCTCCACCATACTACTACAAGTCCCCACCACCACCGAAGCATGTAGAGGAGCCCCCA
1376968 TACTACTACAAGTCTCCCCCACCACCATCGCCATCTCCTCCTCCA
196 TACTACTACAAGTCTCCCCCACCACCATCGCCATCTCCTCCTCCA
1377013 CCATACTATTACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTC
1 CCATACTATTACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTC
* * * * *
1377078 CCCACCACCACCGAAACATGTAGAGGAGCCCCCATAC-ATCTACAAATCTCCTCCACCACCATCG
66 CCCACCACCACCAAAACATGTAGAGCAACCCCCATACTA-CTACAAATCACCCCCACCACCATCG
*
1377142 CCATCTCTTCCTCCACCATACTACTACAAGTCCCCACCACCACCGAAGCATGTAGAGGAGCCCCC
130 CCATCTCCTCCTCCACCATACTACTACAAGTCCCCACCACCACCGAAGCATGTAGAGGAGCCCCC
1377207 ATACTACTACAAGTCTCCCCCACCACCATCGCCATCTCCTCCTCCA
195 ATACTACTACAAGTCTCCCCCACCACCATCGCCATCTCCTCCTCCA
1377253 CCATACTATT
1 CCATACTATT
1377263 NNNNNNNNNN
Statistics
Matches: 239, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
239 1 0.00
240 238 1.00
ACGTcount: A:0.28, C:0.46, G:0.07, T:0.19
Consensus pattern (240 bp):
CCATACTATTACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTC
CCCACCACCACCAAAACATGTAGAGCAACCCCCATACTACTACAAATCACCCCCACCACCATCGC
CATCTCCTCCTCCACCATACTACTACAAGTCCCCACCACCACCGAAGCATGTAGAGGAGCCCCCA
TACTACTACAAGTCTCCCCCACCACCATCGCCATCTCCTCCTCCA
Found at i:1377209 original size:144 final size:143
Alignment explanation
Indices: 1376677--1377233 Score: 448
Period size: 144 Copynumber: 3.9 Consensus size: 143
1376667 NGAGCAACCT
* * *
1376677 CCATACTACTACAAATCTCCTCCTCCACCATCGCCATCTCCTCCACCACCATACTACTACAAATC
1 CCATACTACTACAAATCTCCCCCACCACCATCGCCATCTCCTCCTCCACCATACTACTACAAATC
* * * * * * * *
1376742 CCCACCACCACCAAAACATGT-AGAAGAGCCCCCATACTACTACAAATCTCCTCCACCACC-ATC
66 CCCACCACCACCACACCATCTCAG--CAGCCACCATACTACTACAAGTCCCCACCACCACCGA--
* * ****** *
1376805 ACCATCT-CCTCCTCCA
127 AACATGTAGAGGAGCCC
* * *** * *** ** *
1376821 CCATACTACTACAAGTC-CCCACCACCGCCA-AAACATGTGGAGCAACCTCCATACTACTACAAA
1 CCATACTACTACAAATCTCCC-CCACCACCATCGCCATCT-CCTCCTCCACCATACTACTACAAA
* ** **
1376884 TCACCC-CCACCACCATCGCCATCTCCTCCTCCACCATACTACTACAAGTCCCCACCACCACCGA
64 TC-CCCACCACCACCA-CACCATCTCAGCAGCCACCATACTACTACAAGTCCCCACCACCACCGA
*
1376948 AGCATGTAGAGGAGCCC
127 AACATGTAGAGGAGCCC
* *
1376965 CCATACTACTACAAGTCTCCCCCACCACCATCGCCATCTCCTCCTCCACCATACTATTACAAATC
1 CCATACTACTACAAATCTCCCCCACCACCATCGCCATCTCCTCCTCCACCATACTACTACAAATC
* * ** **
1377030 TCCTCCACCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTCCCCACCACCACCGAAAC
66 CCCACCACCACCA-CACCATCTCAGCAGCCACCATACTACTACAAGTCCCCACCACCACCGAAAC
1377095 ATGTAGAGGAGCCC
130 ATGTAGAGGAGCCC
* * *
1377109 CCATAC-ATCTACAAATCTCCTCCACCACCATCGCCATCTCTTCCTCCACCATACTACTACAAGT
1 CCATACTA-CTACAAATCTCCCCCACCACCATCGCCATCTCCTCCTCCACCATACTACTACAAAT
* * * * *
1377173 CCCCACCACCACCGA-AGCATGTAGAGGAGCCCCCATACTACTACAAGTCTCCC-CCACCACC
65 CCCCACCACCACC-ACACCATCT-CAGCAGCCACCATACTACTACAAGTC-CCCACCACCACC
1377234 ATCGCCATCT
Statistics
Matches: 333, Mismatches: 66, Indels: 28
0.78 0.15 0.07
Matches are distributed among these distances:
143 19 0.06
144 295 0.89
145 19 0.06
ACGTcount: A:0.29, C:0.46, G:0.07, T:0.18
Consensus pattern (143 bp):
CCATACTACTACAAATCTCCCCCACCACCATCGCCATCTCCTCCTCCACCATACTACTACAAATC
CCCACCACCACCACACCATCTCAGCAGCCACCATACTACTACAAGTCCCCACCACCACCGAAACA
TGTAGAGGAGCCC
Found at i:1377566 original size:21 final size:21
Alignment explanation
Indices: 1377491--1377574 Score: 62
Period size: 21 Copynumber: 3.7 Consensus size: 21
1377481 CTATTACAAG
* *
1377491 TCCCCACCACCACTAGTCCAT
1 TCCCCACCACCACCAGTCCAC
1377512 TCCCCACCACCACCA-TACTACTAC
1 TCCCCACCACCACCAGT-C--C-AC
*
1377536 AAGTCTCCACCACCACCAGTCCAC
1 ---TCCCCACCACCACCAGTCCAC
*
1377560 TCCCCACCCCCACCA
1 TCCCCACCACCACCA
1377575 TACTATTACA
Statistics
Matches: 50, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
20 1 0.02
21 28 0.56
23 1 0.02
24 3 0.06
25 1 0.02
27 15 0.30
28 1 0.02
ACGTcount: A:0.26, C:0.56, G:0.04, T:0.14
Consensus pattern (21 bp):
TCCCCACCACCACCAGTCCAC
Found at i:1377631 original size:144 final size:140
Alignment explanation
Indices: 1377428--1378122 Score: 560
Period size: 144 Copynumber: 4.8 Consensus size: 140
1377418 AGAGGAGCCC
* * * *
1377428 CCATAC-ATCTACAAATCTCCTCCACCACCATCGCCATCTCCTCCACCACCATACTATTACAAGT
1 CCATACTAT-TACAAATCCCCACCACCACCATC-CC-TCTCCACCACCACCATACTATTACAAAT
* *
1377492 CCCCACCACCACTAGTCCATTCCCCACCACCACCATACTACTACAAGTCTCCACCACCACCAGTC
63 CCCCACCACCACCA-TCCA-TCCCCACCACCACCATACTACTACAAATCTCCACCACCACCAGTC
*
1377557 CACTCCCCACCCCCA
126 CACTCTCCACCCCCA
* * * * * *
1377572 CCATACTATTACAAGTCTCCACCACCACCTTCTCCTTCACCACCTCCACCATACTATTACAAGTC
1 CCATACTATTACAAATCCCCACCACCACCATC-CC-TCTCCACCACCACCATACTATTACAAATC
** *** ** * * *
1377637 CCCACCACCACCAAAACA-CGTAGAGGAGCCCCCATAC-ATTTACAAATCTCCTCCACCACCA-T
64 CCCACCACCACC-ATCCATC-CCCACCA-CCACCATACTA-CTACAAATCTCCACCACCACCAGT
* *
1377699 -CACCATCTCCTCCTCCA
125 CCA-C-TCTCCACCCCCA
* *
1377716 CCATATTATTACAAGTCCCCACCACCACCAGTCCACTCTCCACCACCACCATACTATTACAAATC
1 CCATACTATTACAAATCCCCACCACCACCA-TCC-CTCTCCACCACCACCATACTATTACAAATC
* * * * * * *
1377781 CCCTCCTCCGCCATCGCCATCTCCTCCTCCACCATACTACTACAAATCCCCACCACCACCAGTCC
64 CCCACCACCACCAT--CCATCCCCACCACCACCATACTACTACAAATCTCCACCACCACCAGTCC
1377846 ACTCTCCACCCCCA
127 ACTCTCCACCCCCA
* * * *
1377860 CCATACTACTACAAATCCCCACCACCACCAGTTCACTCTCCACCCCCACCATACTACTACAAATC
1 CCATACTATTACAAATCCCCACCACCACCA--TCCCTCTCCACCACCACCATACTATTACAAATC
* * * * * * **
1377925 CCCACCACCACCATCTCCTTCACCACCTCCACCATACTACTACAAATCACCCCCACCTCCAGTGA
64 CCCACCACCACCA--TCCATCCCCACCACCACCATACTACTACAAATCTCCACCACCACCAGTCC
** * *
1377990 AGGCTCCAGCACCTA
127 ACTCTCCA-CCCCCA
* * * * * * * *
1378005 CC-TACCATTACAACTCCCCTCCTCCACCATCACCATCTCCTCCTCCCCCATACTACTACAAATC
1 CCATACTATTACAAATCCCCACCACCACCATC-CC-TCTCCACCACCACCATACTATTACAAATC
1378069 TCCC-CCACCACCAGTCCACTCTCCC-CCACCACCATACTACTACAAATCTCCACC
64 -CCCACCACCACCA-TCCA-TC-CCCACCACCACCATACTACTACAAATCTCCACC
1378123 TCTTCCATCT
Statistics
Matches: 444, Mismatches: 83, Indels: 48
0.77 0.14 0.08
Matches are distributed among these distances:
142 5 0.01
143 10 0.02
144 400 0.90
145 25 0.06
146 4 0.01
ACGTcount: A:0.28, C:0.50, G:0.03, T:0.19
Consensus pattern (140 bp):
CCATACTATTACAAATCCCCACCACCACCATCCCTCTCCACCACCACCATACTATTACAAATCCC
CACCACCACCATCCATCCCCACCACCACCATACTACTACAAATCTCCACCACCACCAGTCCACTC
TCCACCCCCA
Found at i:1377881 original size:27 final size:27
Alignment explanation
Indices: 1377809--1377981 Score: 109
Period size: 21 Copynumber: 7.1 Consensus size: 27
1377799 ATCTCCTCCT
1377809 CCACCATACTACTACAAATCCCCACCA
1 CCACCATACTACTACAAATCCCCACCA
* *
1377836 CCACCAGT-C--C-AC---TCTCCACCC
1 CCACCA-TACTACTACAAATCCCCACCA
1377857 CCACCATACTACTACAAATCCCCACCA
1 CCACCATACTACTACAAATCCCCACCA
* *
1377884 CCACCAGT--T-C-AC---TCTCCACCC
1 CCACCA-TACTACTACAAATCCCCACCA
1377905 CCACCATACTACTACAAATCCCCACCA
1 CCACCATACTACTACAAATCCCCACCA
* * *
1377932 CCACCAT-CT-C--C--TTCACCACCT
1 CCACCATACTACTACAAATCCCCACCA
1377953 CCACCATACTACTACAAATCACCC-CCA
1 CCACCATACTACTACAAATC-CCCACCA
1377980 CC
1 CC
1377982 TCCAGTGAAG
Statistics
Matches: 109, Mismatches: 14, Indels: 46
0.64 0.08 0.27
Matches are distributed among these distances:
20 2 0.02
21 41 0.38
22 3 0.03
23 4 0.04
24 8 0.07
25 4 0.04
26 3 0.03
27 40 0.37
28 4 0.04
ACGTcount: A:0.30, C:0.53, G:0.01, T:0.16
Consensus pattern (27 bp):
CCACCATACTACTACAAATCCCCACCA
Found at i:1378152 original size:48 final size:49
Alignment explanation
Indices: 1377428--1378159 Score: 482
Period size: 48 Copynumber: 15.2 Consensus size: 49
1377418 AGAGGAGCCC
* * * * * *
1377428 CCATAC-ATCTACAAATCTCCTCCACCACCA-TCGCCATCTCCTCCACCA
1 CCATACTA-CTACAAATCCCCACCACCACCAGTCTCCCTCTCCACCTCCA
* * * ** * *
1377476 CCATACTATTACAAGTCCCCACCACCACTAGTC-CATTCCCCACCACCA
1 CCATACTACTACAAATCCCCACCACCACCAGTCTCCCTCTCCACCTCCA
* * * * *
1377524 CCATACTACTACAAGTCTCCACCACCACCAGTC-CACTCCCCACCCCCA
1 CCATACTACTACAAATCCCCACCACCACCAGTCTCCCTCTCCACCTCCA
* * * * * *
1377572 CCATACTATTACAAGTCTCCACCACCACC-TTCTCCTTCACCACCTCCA
1 CCATACTACTACAAATCCCCACCACCACCAGTCTCCCTCTCCACCTCCA
* * ** * * **** *
1377620 CCATACTATTACAAGTCCCCACCACCACCAAAAC-ACGTAGAGGAGC-CC-
1 CCATACTACTACAAATCCCCACCACCACC-AGTCTCCCT-CTCCACCTCCA
* * * * * *
1377668 CCATAC-ATTTACAAATCTCCTCCACCACCA-TCACCATCTCCTCCTCCA
1 CCATACTA-CTACAAATCCCCACCACCACCAGTCTCCCTCTCCACCTCCA
* * * * *
1377716 CCATATTATTACAAGTCCCCACCACCACCAGTC-CACTCTCCACCACCA
1 CCATACTACTACAAATCCCCACCACCACCAGTCTCCCTCTCCACCTCCA
* * * * * * *
1377764 CCATACTATTACAAATCCCCTCCTCCGCCA-TCGCCATCTCCTCCTCCA
1 CCATACTACTACAAATCCCCACCACCACCAGTCTCCCTCTCCACCTCCA
* *
1377812 CCATACTACTACAAATCCCCACCACCACCAGTC-CACTCTCCACCCCCA
1 CCATACTACTACAAATCCCCACCACCACCAGTCTCCCTCTCCACCTCCA
* *
1377860 CCATACTACTACAAATCCCCACCACCACCAGT-TCACTCTCCACCCCCA
1 CCATACTACTACAAATCCCCACCACCACCAGTCTCCCTCTCCACCTCCA
* *
1377908 CCATACTACTACAAATCCCCACCACCACCA-TCTCCTTCACCACCTCCA
1 CCATACTACTACAAATCCCCACCACCACCAGTCTCCCTCTCCACCTCCA
* ***** * *
1377956 CCATACTACTACAAATCACCC-CCACCTCCAGT-GAAGGCTCCAGCACCTA
1 CCATACTACTACAAATC-CCCACCACCACCAGTCTCCCTCTCCACCTCC-A
* * * * * * * * *
1378005 CC-TACCATTACAACTCCCCTCCTCCACCA-TCACCATCTCCTCCTCCC
1 CCATACTACTACAAATCCCCACCACCACCAGTCTCCCTCTCCACCTCCA
* * *
1378052 CCATACTACTACAAATCTCCC-CCACCACCAGTC-CACTCTCCCCCACCA
1 CCATACTACTACAAATC-CCCACCACCACCAGTCTCCCTCTCCACCTCCA
* * ** * *
1378100 CCATACTACTACAAATCTCCACCTCTTCCA-TCTCCCTCACCACCTCCT
1 CCATACTACTACAAATCCCCACCACCACCAGTCTCCCTCTCCACCTCCA
1378148 CCATACTACTAC
1 CCATACTACTAC
1378160 CACTCACCTC
Statistics
Matches: 547, Mismatches: 111, Indels: 52
0.77 0.16 0.07
Matches are distributed among these distances:
46 2 0.00
47 21 0.04
48 496 0.91
49 24 0.04
50 4 0.01
ACGTcount: A:0.27, C:0.50, G:0.03, T:0.20
Consensus pattern (49 bp):
CCATACTACTACAAATCCCCACCACCACCAGTCTCCCTCTCCACCTCCA
Found at i:1381578 original size:2 final size:2
Alignment explanation
Indices: 1381566--1381611 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
1381556 ATTCCTCCCC
*
1381566 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1381607 AT AT A
1 AT AT A
1381612 AAAGGAGTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1384593 original size:15 final size:15
Alignment explanation
Indices: 1384569--1384598 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1384559 TAAAATTTTG
1384569 GGGTCATTTCAAGTT
1 GGGTCATTTCAAGTT
*
1384584 GGGTCGTTTCAAGTT
1 GGGTCATTTCAAGTT
1384599 CCGATTCTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.13, G:0.30, T:0.40
Consensus pattern (15 bp):
GGGTCATTTCAAGTT
Found at i:1389832 original size:28 final size:31
Alignment explanation
Indices: 1389777--1389834 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 31
1389767 TTTATATATG
1389777 TAATTATATTAAAATAAATAGAAGTAATTAC
1 TAATTATATTAAAATAAATAGAAGTAATTAC
* *
1389808 TAATT-TATTCAAA-AATTAGAA-TAATTA
1 TAATTATATTAAAATAAATAGAAGTAATTA
1389835 AATTTAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 6 0.24
29 7 0.28
30 7 0.28
31 5 0.20
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.38
Consensus pattern (31 bp):
TAATTATATTAAAATAAATAGAAGTAATTAC
Found at i:1397307 original size:33 final size:33
Alignment explanation
Indices: 1397252--1397327 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 33
1397242 CAGGCACAAT
**
1397252 CAAGTGCTAATATGTACAGCCAACC-GACACAGC
1 CAAGTGCTAATACATACAGCCAACCTG-CACAGC
* *
1397285 CAAGTGCTAATCCATACGGCCAACCTGCACAGC
1 CAAGTGCTAATACATACAGCCAACCTGCACAGC
**
1397318 CTGGTGCTAA
1 CAAGTGCTAA
1397328 CGCATATGAC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
33 35 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.32, G:0.20, T:0.17
Consensus pattern (33 bp):
CAAGTGCTAATACATACAGCCAACCTGCACAGC
Found at i:1398025 original size:6 final size:6
Alignment explanation
Indices: 1398014--1398044 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1398004 AGTATGGGTA
*
1398014 GCATGG GCATGG GCATGG GCATGG GAATGG G
1 GCATGG GCATGG GCATGG GCATGG GCATGG G
1398045 TGGTGGACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.13, G:0.52, T:0.16
Consensus pattern (6 bp):
GCATGG
Found at i:1400254 original size:33 final size:33
Alignment explanation
Indices: 1400217--1400287 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
1400207 AATATGTACA
1400217 GCCAACC-GACACAGCCAAGTGCTAATC-CATATG
1 GCCAACCTG-CACAGCCAAGTGCTAA-CGCATATG
**
1400250 GCCAACCTGCACAGCCTGGTGCTAACGCATATG
1 GCCAACCTGCACAGCCAAGTGCTAACGCATATG
*
1400283 ACCAA
1 GCCAA
1400288 GTTGGACAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 1 0.03
33 31 0.94
34 1 0.03
ACGTcount: A:0.31, C:0.34, G:0.20, T:0.15
Consensus pattern (33 bp):
GCCAACCTGCACAGCCAAGTGCTAACGCATATG
Found at i:1406452 original size:27 final size:27
Alignment explanation
Indices: 1406414--1406469 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
1406404 CACTCTCTAA
1406414 CATCTTCAAGTTCTTCATCACCATTTT
1 CATCTTCAAGTTCTTCATCACCATTTT
*
1406441 CATCTTCAAGTTCTTCATGACCATTTT
1 CATCTTCAAGTTCTTCATCACCATTTT
1406468 CA
1 CA
1406470 GTGGAAATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.23, C:0.29, G:0.05, T:0.43
Consensus pattern (27 bp):
CATCTTCAAGTTCTTCATCACCATTTT
Found at i:1409541 original size:3 final size:3
Alignment explanation
Indices: 1409526--1409560 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
1409516 AATTTAATAC
*
1409526 TAT TAT CAT TAT TAT TAT TAAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT T
1409561 TACTCCTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1409551 original size:13 final size:13
Alignment explanation
Indices: 1409533--1409558 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1409523 TACTATTATC
1409533 ATTATTATTATTA
1 ATTATTATTATTA
1409546 ATTATTATTATTA
1 ATTATTATTATTA
1409559 TTTACTCCTA
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTATTATTATTA
Found at i:1412801 original size:87 final size:87
Alignment explanation
Indices: 1412692--1412860 Score: 209
Period size: 87 Copynumber: 1.9 Consensus size: 87
1412682 TAAGTCTATT
* * ** *
1412692 TTTTTTGCACTTAATTGAGTACTTAAACTTTTAAAATGTATCAAAAAGGTCCTC-AAATTTCTTC
1 TTTTTTGCACTCAATTGAGTACTTAAACTTTCAAAATACATCAAAAAGATCCTCAAAATTT-TTC
*
1412756 AAACAAAAGCGATTAAGCCCCTGC
65 AAA-AAAAGCAATTAAGCCCCTGC
* **
1412780 TTTTTT-CACTCAATT-AGGTACTTGAACTTTCAAAATACATCAAAAAGATTTTCAAAATTTTTC
1 TTTTTTGCACTCAATTGA-GTACTTAAACTTTCAAAATACATCAAAAAGATCCTCAAAATTTTTC
1412843 AAAAAAAGCAATTAAGCC
65 AAAAAAAGCAATTAAGCC
1412861 GCTACTCTTT
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
86 15 0.21
87 43 0.61
88 12 0.17
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.34
Consensus pattern (87 bp):
TTTTTTGCACTCAATTGAGTACTTAAACTTTCAAAATACATCAAAAAGATCCTCAAAATTTTTCA
AAAAAAGCAATTAAGCCCCTGC
Found at i:1413231 original size:9 final size:9
Alignment explanation
Indices: 1413219--1413314 Score: 58
Period size: 8 Copynumber: 10.6 Consensus size: 9
1413209 ACTTTTTAAA
1413219 ATTTTATAT
1 ATTTTATAT
1413228 ATTTT-TAT
1 ATTTTATAT
1413236 ATTTCTATAT
1 ATTT-TATAT
1413246 ATTTTATA-
1 ATTTTATAT
* *
1413254 ATTTTTTTACG
1 A-TTTTATA-T
*
1413265 ATTTTTATAAA
1 A-TTTTAT-AT
*
1413276 ATTTTACA-
1 ATTTTATAT
1413284 ATTTT-TAT
1 ATTTTATAT
*
1413292 ATTTTTTAT
1 ATTTTATAT
1413301 GATTTT-TAT
1 -ATTTTATAT
1413310 ATTTT
1 ATTTT
1413315 TTCTAATTTT
Statistics
Matches: 73, Mismatches: 5, Indels: 19
0.75 0.05 0.20
Matches are distributed among these distances:
7 1 0.01
8 23 0.32
9 23 0.32
10 17 0.23
11 8 0.11
12 1 0.01
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (9 bp):
ATTTTATAT
Found at i:1413290 original size:56 final size:56
Alignment explanation
Indices: 1413194--1413316 Score: 153
Period size: 56 Copynumber: 2.2 Consensus size: 56
1413184 TATTTCTTTA
* * *
1413194 TATAATTTTCTTACTACTTTTTAAAATTTTATATATTTTTATATTTCTATAT-ATTT
1 TATAATTTTTTTACGACTTTTTAAAATTTTACATATTTTTATATTT-TATATGATTT
* *
1413250 TATAATTTTTTTACGATTTTTATAAAATTTTACA-ATTTTTATATTTTTTATGATTT
1 TATAATTTTTTTACGACTTTT-TAAAATTTTACATATTTTTATATTTTATATGATTT
1413306 T-TATATTTTTT
1 TATA-ATTTTTT
1413317 CTAATTTTTA
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
55 6 0.10
56 42 0.71
57 11 0.19
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (56 bp):
TATAATTTTTTTACGACTTTTTAAAATTTTACATATTTTTATATTTTATATGATTT
Found at i:1413331 original size:37 final size:36
Alignment explanation
Indices: 1413211--1413332 Score: 108
Period size: 37 Copynumber: 3.3 Consensus size: 36
1413201 TTCTTACTAC
* * * *
1413211 TTTTTAAAATTTTATAT-ATTTTTATATTTCTATATA
1 TTTTTAATATTTTTTATGATTTTTATATTTTTCTA-A
* *
1413247 TTTTATAAT-TTTTTTACGATTTTTATAAAATTTTAC-AA
1 TTTT-TAATATTTTTTATGATTTTTAT---ATTTTTCTAA
1413285 TTTTT-ATATTTTTTATGATTTTTATATTTTTTCTAA
1 TTTTTAATATTTTTTATGATTTTTATA-TTTTTCTAA
1413321 TTTTTAATATTT
1 TTTTTAATATTT
1413333 AAAATTTTTA
Statistics
Matches: 69, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
34 1 0.01
35 5 0.07
36 19 0.28
37 34 0.49
38 5 0.07
39 1 0.01
40 4 0.06
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.66
Consensus pattern (36 bp):
TTTTTAATATTTTTTATGATTTTTATATTTTTCTAA
Found at i:1413342 original size:9 final size:9
Alignment explanation
Indices: 1413211--1413343 Score: 87
Period size: 9 Copynumber: 14.8 Consensus size: 9
1413201 TTCTTACTAC
1413211 TTTTTA-AA
1 TTTTTATAA
*
1413219 ATTTTATATA
1 TTTTTATA-A
1413229 TTTTTAT-A
1 TTTTTATAA
*
1413237 TTTCTAT-A
1 TTTTTATAA
1413245 TATTTTATAA
1 T-TTTTATAA
*
1413255 TTTTTTTACGA
1 TTTTTATA--A
1413266 TTTTTATAAA
1 TTTTTAT-AA
* *
1413276 ATTTTACAA
1 TTTTTATAA
*
1413285 TTTTTATAT
1 TTTTTATAA
*
1413294 TTTTTATGA
1 TTTTTATAA
*
1413303 TTTTTATAT
1 TTTTTATAA
*
1413312 TTTTTCTAA
1 TTTTTATAA
1413321 -TTTT-TAA
1 TTTTTATAA
* *
1413328 TATTTAAAA
1 TTTTTATAA
1413337 TTTTTAT
1 TTTTTAT
1413344 TAAAATTTAA
Statistics
Matches: 95, Mismatches: 21, Indels: 17
0.71 0.16 0.13
Matches are distributed among these distances:
7 3 0.03
8 21 0.22
9 48 0.51
10 15 0.16
11 7 0.07
12 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:1413346 original size:19 final size:20
Alignment explanation
Indices: 1413320--1413363 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
1413310 ATTTTTTCTA
*
1413320 ATTT-TTAATATTTAA-AAT
1 ATTTATTAAAATTTAATAAT
*
1413338 TTTTATTAAAATTTAATAAT
1 ATTTATTAAAATTTAATAAT
1413358 ATTTAT
1 ATTTAT
1413364 AGCTTTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 3 0.14
19 10 0.48
20 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTATTAAAATTTAATAAT
Found at i:1413519 original size:89 final size:89
Alignment explanation
Indices: 1413422--1413596 Score: 262
Period size: 89 Copynumber: 2.0 Consensus size: 89
1413412 TAAAAAGCAT
* * * *
1413422 GGGCTTAATTGCTTTTTTTGAAAAAGCTTGAGGGTCTTTTTGAA-CCATTTTGAAAGTTCAAGTA
1 GGGCTTAATTACTTTTTTCGAAAAAACTTGAGGG-CTTTTTGAATCCATTTTGAAAGTTCAAATA
*
1413486 CTCAATTGAGTGCAAAAAAAAATAG
65 CTCAAATGAGTGCAAAAAAAAATAG
* * *
1413511 GGGCTTAATTACTTTTTTCGAAAAAATTTGAGGGCTTTTTTAATGCATTTTGAAAGTTCAAATAC
1 GGGCTTAATTACTTTTTTCGAAAAAACTTGAGGGCTTTTTGAATCCATTTTGAAAGTTCAAATAC
1413576 TCAAATGAGTGCAAAAAAAAA
66 TCAAATGAGTGCAAAAAAAAA
1413597 AGTAGGGACT
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
88 8 0.10
89 69 0.90
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (89 bp):
GGGCTTAATTACTTTTTTCGAAAAAACTTGAGGGCTTTTTGAATCCATTTTGAAAGTTCAAATAC
TCAAATGAGTGCAAAAAAAAATAG
Found at i:1413616 original size:89 final size:86
Alignment explanation
Indices: 1413433--1413617 Score: 237
Period size: 89 Copynumber: 2.1 Consensus size: 86
1413423 GGCTTAATTG
* * *
1413433 CTTTTTTTGAAAAAGCTTGAGGGTCTTTTTGAACCATTTTGAAAGTTCAAGTACTCAATTGAGTG
1 CTTTTTTTGAAAAAACTTGAGGGTCTTTTTGAACCATTTTGAAAGTTCAAATACTCAAATGAGTG
*
1413498 CAAAAAAAAATAGGGGCTTAATTA
66 CAAAAAAAAATAGGGACTT-A--A
* * * *
1413522 CTTTTTTCGAAAAAATTTGAGGG-CTTTTTTAATGCATTTTGAAAGTTCAAATACTCAAATGAGT
1 CTTTTTTTGAAAAAACTTGAGGGTCTTTTTGAA-CCATTTTGAAAGTTCAAATACTCAAATGAGT
1413586 GCAAAAAAAAAAGTAGGGACTTAA
65 GC-AAAAAAAAA-TAGGGACTTAA
1413610 CTTTTTTT
1 CTTTTTTT
1413618 TTTTTTTAAA
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
88 16 0.19
89 50 0.60
90 10 0.12
91 8 0.10
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (86 bp):
CTTTTTTTGAAAAAACTTGAGGGTCTTTTTGAACCATTTTGAAAGTTCAAATACTCAAATGAGTG
CAAAAAAAAATAGGGACTTAA
Found at i:1438355 original size:20 final size:20
Alignment explanation
Indices: 1438330--1438370 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1438320 TTCAATGTCG
1438330 CGACACCCACTTGATATTTT
1 CGACACCCACTTGATATTTT
*
1438350 CGACACCCACTTGATTTTTT
1 CGACACCCACTTGATATTTT
1438370 C
1 C
1438371 TTAAATTGAA
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:0.22, C:0.32, G:0.10, T:0.37
Consensus pattern (20 bp):
CGACACCCACTTGATATTTT
Found at i:1443068 original size:12 final size:12
Alignment explanation
Indices: 1443051--1443076 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1443041 ATCACAGAAA
1443051 TCGCAAATGCAC
1 TCGCAAATGCAC
1443063 TCGCAAATGCAC
1 TCGCAAATGCAC
1443075 TC
1 TC
1443077 TCCATCTGAA
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:0.31, C:0.35, G:0.15, T:0.19
Consensus pattern (12 bp):
TCGCAAATGCAC
Found at i:1443091 original size:6 final size:6
Alignment explanation
Indices: 1443080--1443124 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
1443070 TGCACTCTCC
1443080 ATCTGA ATCTGA ATCTGA ATCTGA ATCTGA ATCTGA ATCTGA ATC
1 ATCTGA ATCTGA ATCTGA ATCTGA ATCTGA ATCTGA ATCTGA ATC
1443125 AGGTGGCTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (6 bp):
ATCTGA
Found at i:1447078 original size:23 final size:24
Alignment explanation
Indices: 1447051--1447095 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1447041 TTTAGATTTT
*
1447051 ATTTTATAA-TTTTAAAAATATAA
1 ATTTTAGAATTTTTAAAAATATAA
*
1447074 ATTTTAGAATTTTTATAAATAT
1 ATTTTAGAATTTTTAAAAATAT
1447096 TTGGGTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
ATTTTAGAATTTTTAAAAATATAA
Found at i:1448882 original size:30 final size:30
Alignment explanation
Indices: 1448841--1448898 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
1448831 CACGGGCAGG
* *
1448841 CACATGGGCGTGTGGCCAGCCCGTGTGGCT
1 CACAGGGGCGTGTGGCCAACCCGTGTGGCT
1448871 CACAGGGGCGTGTGGCCAACCCGTGTGG
1 CACAGGGGCGTGTGGCCAACCCGTGTGG
1448899 AAATAGCCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.12, C:0.29, G:0.41, T:0.17
Consensus pattern (30 bp):
CACAGGGGCGTGTGGCCAACCCGTGTGGCT
Found at i:1450679 original size:46 final size:46
Alignment explanation
Indices: 1450626--1450865 Score: 329
Period size: 46 Copynumber: 5.0 Consensus size: 46
1450616 ACATTGCTAT
1450626 AACTCAGTATGGTTTTCTTCATTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAATACCATACCTACTTTTCAC
1450672 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTG----A--A-A--TACCATACCTACTTTTCAC
* *
1450727 AACTCAGTATGGTTTTCTTCATTGAAAAATCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAATACCATACCTACTTTTCAC
* *
1450773 AACTCAGTATGGTTTTCTAT-ATCGAAATACCACACCTACTTTTCAC
1 AACTCAGTATGGTTTTCT-TCATTGAAATACCATACCTACTTTTCAC
* *
1450819 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAATACCATACCTACTTTTCAC
1450865 A
1 A
1450866 TTTTGCCATG
Statistics
Matches: 173, Mismatches: 10, Indels: 22
0.84 0.05 0.11
Matches are distributed among these distances:
45 1 0.01
46 122 0.71
47 1 0.01
48 1 0.01
49 1 0.01
50 1 0.01
51 1 0.01
52 1 0.01
53 1 0.01
55 43 0.25
ACGTcount: A:0.30, C:0.26, G:0.08, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCATTGAAATACCATACCTACTTTTCAC
Found at i:1452110 original size:17 final size:17
Alignment explanation
Indices: 1452088--1452123 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1452078 ATTCTTTTTT
*
1452088 TAAATCACAAAATTTAC
1 TAAATCACAAAATTCAC
1452105 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAC
1452122 TA
1 TA
1452124 GTTCAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (17 bp):
TAAATCACAAAATTCAC
Found at i:1461473 original size:22 final size:22
Alignment explanation
Indices: 1461432--1461473 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1461422 TGAATAAACC
* * *
1461432 AAATAAACTTTATTTCTGTATA
1 AAATAAACTTAATATATGTATA
1461454 AAATAAACTTAATATATGTA
1 AAATAAACTTAATATATGTA
1461474 AACTGAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (22 bp):
AAATAAACTTAATATATGTATA
Found at i:1461583 original size:31 final size:31
Alignment explanation
Indices: 1461548--1461608 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
1461538 ACTAAATATT
* *
1461548 CTTAAATGACATTACACCCATTTGAGCAATC
1 CTTAAATGACAATACACCCATATGAGCAATC
1461579 CTTAAATGACAATACACCCATATGAGCAAT
1 CTTAAATGACAATACACCCATATGAGCAAT
1461609 ATGCTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.39, C:0.25, G:0.10, T:0.26
Consensus pattern (31 bp):
CTTAAATGACAATACACCCATATGAGCAATC
Found at i:1461728 original size:21 final size:21
Alignment explanation
Indices: 1461693--1461735 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1461683 TATAGATACC
* *
1461693 TAACTATTCCGAACTTTTACT
1 TAACTATTCCAAACTTGTACT
*
1461714 TAACTATTCTAAACTTGTACT
1 TAACTATTCCAAACTTGTACT
1461735 T
1 T
1461736 TAACAACCAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44
Consensus pattern (21 bp):
TAACTATTCCAAACTTGTACT
Found at i:1463642 original size:104 final size:101
Alignment explanation
Indices: 1463496--1463683 Score: 245
Period size: 104 Copynumber: 1.8 Consensus size: 101
1463486 TTATAGTTAT
*
1463496 TTATTTTGTTAGTAATTTATGAGATTAGGTTACAAATAGTTAGTGTTTAG-TATAGAGTTTTGTG
1 TTATTTTGTTAGTAATTTAT-AGATTAGGTTACAAATAGTTAGTGCTTAGTTAT-GAGTTTTGTG
* *
1463560 CTTTTTTAGTAATGTATTTTTTTCAAAAATAATTCTATAG
64 ATTTTTT--TAATGTAATTTTTTCAAAAATAATTCTATAG
* * * *
1463600 TTATTTTGTTAGTAATTTAT-GATTAAGTTATATAAATTGTTAGTGCTTAGTTATGTGTTTTGTG
1 TTATTTTGTTAGTAATTTATAGATT-AGGT-TACAAATAGTTAGTGCTTAGTTATGAGTTTTGTG
1463664 ATTTTTTTAATGTAATTTTT
64 ATTTTTTTAATGTAATTTTT
1463684 ATATAACGTA
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
102 16 0.22
103 3 0.04
104 52 0.70
105 3 0.04
ACGTcount: A:0.28, C:0.03, G:0.16, T:0.54
Consensus pattern (101 bp):
TTATTTTGTTAGTAATTTATAGATTAGGTTACAAATAGTTAGTGCTTAGTTATGAGTTTTGTGAT
TTTTTTAATGTAATTTTTTCAAAAATAATTCTATAG
Found at i:1468235 original size:23 final size:23
Alignment explanation
Indices: 1468192--1468237 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1468182 TGTAAAACCG
*
1468192 AATAATTGTCACATGTTTATTAT
1 AATAATTGTCACATGTATATTAT
*
1468215 AATAGTTG-CACATGTAATATTAT
1 AATAATTGTCACATGT-ATATTAT
1468238 TAACTTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (23 bp):
AATAATTGTCACATGTATATTAT
Found at i:1471307 original size:89 final size:89
Alignment explanation
Indices: 1471207--1471678 Score: 694
Period size: 89 Copynumber: 5.3 Consensus size: 89
1471197 CTTTGATTTT
* ** * *
1471207 ACGCCAATACATGAAGACAAGATCTGCTATCTTTTATCTAC-TCTGCCACTAGTATGGGAACACA
1 ACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTC-GCCACCAGTATGGGAAGACA
* * * *
1471271 AGATCTACTAATTTTGATCTATTTC
65 AGATCTGCTATTTTTTATCTACTTC
* * *
1471296 ACGCCAATACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACCACCAATATGGGAAGACAA
1 ACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAA
*
1471361 GATCTGCTTGTTTTTTATCTACTTC
66 GATCTGC-TATTTTTTATCTACTTC
*
1471386 ACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAA
1 ACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAA
* *
1471451 GATCTGCTGTTTTTGATCTACTTC
66 GATCTGCTATTTTTTATCTACTTC
* *
1471475 ACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCGCCAGTATGGGAAGACAA
1 ACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAA
* * *
1471540 GATCTGCTTTTTTTTATGTACTTT
66 GATCTGCTATTTTTTATCTACTTC
* *
1471564 ACGCCAATACATGAAGACAAGATCTGCTTTATTCGATCTACTTCGCCACCAATATGGGAAGACAA
1 ACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAA
*
1471629 TATCTGCTTATTTTTTATCTACTTC
66 GATCTGC-TATTTTTTATCTACTTC
1471654 ACGCCAATACATGAAGACAAGATCT
1 ACGCCAATACATGAAGACAAGATCT
1471679 ATTTTCTTTT
Statistics
Matches: 351, Mismatches: 29, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
89 229 0.65
90 122 0.35
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.32
Consensus pattern (89 bp):
ACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAA
GATCTGCTATTTTTTATCTACTTC
Found at i:1471515 original size:179 final size:178
Alignment explanation
Indices: 1471207--1471686 Score: 728
Period size: 179 Copynumber: 2.7 Consensus size: 178
1471197 CTTTGATTTT
* ** * *
1471207 ACGCCAATACATGAAGACAAGATCTGCTATCTTTTATCTAC-TCTGCCACTAGTATGGGAACACA
1 ACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTC-GCCACCAGTATGGGAAGACA
* * * * *
1471271 AGATCTACTAATTTTGATCTATTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTTGATCTA
65 AGATCTGCTATTTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTA
1471336 CTTCACCACCAATATGGGAAGACAAGATCTGCTTGTTTTTTATCTACTTC
130 CTTCACCACCAATATGGGAAGACAAGATCTGCTT-TTTTTTATCTACTTC
*
1471386 ACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAA
1 ACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAA
*
1471451 GATCTGCTGTTTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTAC
66 GATCTGCTATTTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTAC
* * * * *
1471516 TTCGCCGCCAGTATGGGAAGACAAGATCTGCTTTTTTTTATGTACTTT
131 TTCACCACCAATATGGGAAGACAAGATCTGCTTTTTTTTATCTACTTC
* *
1471564 ACGCCAATACATGAAGACAAGATCTGCTTTATTCGATCTACTTCGCCACCAATATGGGAAGACAA
1 ACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAA
* * *
1471629 TATCTGCTTATTTTTTATCTACTTCACGCCAATACATGAAGACAAGATCTATTTTCTT
66 GATCTGC-TATTTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTT
1471687 TTCAACCTGC
Statistics
Matches: 275, Mismatches: 24, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
178 81 0.29
179 192 0.70
180 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (178 bp):
ACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAA
GATCTGCTATTTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTAC
TTCACCACCAATATGGGAAGACAAGATCTGCTTTTTTTTATCTACTTC
Found at i:1472962 original size:15 final size:14
Alignment explanation
Indices: 1472942--1472971 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1472932 GCCTCTCCAC
1472942 TTTCTTTTTTTCTTT
1 TTTCTTTTTTT-TTT
1472957 TTTCTTTTTTTTTT
1 TTTCTTTTTTTTTT
1472971 T
1 T
1472972 GACTCAAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTCTTTTTTTTTT
Found at i:1477623 original size:18 final size:18
Alignment explanation
Indices: 1477600--1477638 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1477590 GATATAAAAG
1477600 TATATATAAAAATGCTTA
1 TATATATAAAAATGCTTA
1477618 TATATATAAAAATGCTTA
1 TATATATAAAAATGCTTA
1477636 TAT
1 TAT
1477639 GTACAAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (18 bp):
TATATATAAAAATGCTTA
Found at i:1477646 original size:18 final size:18
Alignment explanation
Indices: 1477600--1477647 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
1477590 GATATAAAAG
*
1477600 TATATATAAAAATGCTTA
1 TATATACAAAAATGCTTA
*
1477618 TATATATAAAAATGCTTA
1 TATATACAAAAATGCTTA
*
1477636 TATGTACAAAAA
1 TATATACAAAAA
1477648 CATGTGTATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.35
Consensus pattern (18 bp):
TATATACAAAAATGCTTA
Found at i:1477951 original size:21 final size:22
Alignment explanation
Indices: 1477861--1477952 Score: 61
Period size: 21 Copynumber: 4.3 Consensus size: 22
1477851 GTATTTTTAT
* *
1477861 GTAA-AATAATAAA-TATAGTA
1 GTAATAATAATAAATTACAATA
* * *
1477881 TTAATAATAATAAGTAACAATA
1 GTAATAATAATAAATTACAATA
1477903 GT-ATAATAAAATAAAATTAACAA-A
1 GTAATAAT--AAT-AAATT-ACAATA
1477927 -TAATAATAATAAATTA-AATA
1 GTAATAATAATAAATTACAATA
1477947 GTAATA
1 GTAATA
1477953 TAACTTCGAA
Statistics
Matches: 55, Mismatches: 8, Indels: 17
0.69 0.10 0.21
Matches are distributed among these distances:
19 2 0.04
20 5 0.09
21 23 0.42
22 8 0.15
23 4 0.07
24 9 0.16
25 4 0.07
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.30
Consensus pattern (22 bp):
GTAATAATAATAAATTACAATA
Found at i:1478542 original size:24 final size:23
Alignment explanation
Indices: 1478491--1478542 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
1478481 TATTTTAGGT
*
1478491 AAAATAAAAATGAGAAAATAAAAG
1 AAAATAAAAA-GAGAAAATAAAAC
1478515 AAAATAAAAA-AGAAATATATAAAC
1 AAAATAAAAAGAGAAA-ATA-AAAC
1478539 AAAA
1 AAAA
1478543 AAAGTAATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 5 0.20
23 3 0.12
24 17 0.68
ACGTcount: A:0.77, C:0.02, G:0.08, T:0.13
Consensus pattern (23 bp):
AAAATAAAAAGAGAAAATAAAAC
Found at i:1480494 original size:24 final size:24
Alignment explanation
Indices: 1480465--1480511 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1480455 TCCATGAAAA
*
1480465 ATTAATGATTAATAACCAATCACC
1 ATTAATGATAAATAACCAATCACC
* *
1480489 ATTAATGATAAATTATCAATCAC
1 ATTAATGATAAATAACCAATCAC
1480512 GTTTTAATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.47, C:0.17, G:0.04, T:0.32
Consensus pattern (24 bp):
ATTAATGATAAATAACCAATCACC
Found at i:1484830 original size:43 final size:44
Alignment explanation
Indices: 1484755--1484841 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 44
1484745 TTTTCTAAAA
1484755 GTCGACAACTAAATTTTTTGTTTTTTCAAAAAAACGGTTTCGAC
1 GTCGACAACTAAATTTTTTGTTTTTTCAAAAAAACGGTTTCGAC
1484799 GTCGACAACTAAA-TTTTTGTTTTTTCAAAAAAACGGTTTCGAC
1 GTCGACAACTAAATTTTTTGTTTTTTCAAAAAAACGGTTTCGAC
1484842 ACCTACTCGT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 30 0.70
44 13 0.30
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (44 bp):
GTCGACAACTAAATTTTTTGTTTTTTCAAAAAAACGGTTTCGAC
Found at i:1490277 original size:19 final size:19
Alignment explanation
Indices: 1490253--1490290 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
1490243 TTTTTTTTCC
1490253 ATTTAATT-TTTCAATTTAA
1 ATTTAATTGTTT-AATTTAA
1490272 ATTTAATTGTTTAATTTAA
1 ATTTAATTGTTTAATTTAA
1490291 TTTCAGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (19 bp):
ATTTAATTGTTTAATTTAA
Found at i:1491643 original size:18 final size:18
Alignment explanation
Indices: 1491598--1491643 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1491588 AGTTTTTTTT
1491598 TTTTCAATTTAAGTTTAA
1 TTTTCAATTTAAGTTTAA
*
1491616 TTGTT-AATTTAATTTTAA
1 TT-TTCAATTTAAGTTTAA
*
1491634 TTTTCTATTT
1 TTTTCAATTT
1491644 CATAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 2 0.08
18 20 0.83
19 2 0.08
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.63
Consensus pattern (18 bp):
TTTTCAATTTAAGTTTAA
Found at i:1492220 original size:20 final size:20
Alignment explanation
Indices: 1492135--1492213 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
1492125 ATTAACTATG
*
1492135 AGGTTCGAGATTTAGGGTTCG
1 AGGTTCGAGATTT-GGGTTCA
* * * * *
1492156 GGGTTTGAGACTTAGGTT-T
1 AGGTTCGAGATTTGGGTTCA
1492175 AGAGTTCGAGATTTGGGTTCA
1 AG-GTTCGAGATTTGGGTTCA
*
1492196 AGGTTCGAGGTTTGGGTT
1 AGGTTCGAGATTTGGGTT
1492214 ATGGGTTTGG
Statistics
Matches: 45, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
19 1 0.02
20 32 0.71
21 12 0.27
ACGTcount: A:0.18, C:0.08, G:0.38, T:0.37
Consensus pattern (20 bp):
AGGTTCGAGATTTGGGTTCA
Found at i:1496963 original size:25 final size:25
Alignment explanation
Indices: 1496911--1496964 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
1496901 TGGATTGGTG
*
1496911 ATTTAATATAATTATAATTATAATT
1 ATTTAATATAATTATAATTATAAAT
1496936 ATTTAATAT-A-TATAATTAATATAAT
1 ATTTAATATAATTATAATT-ATA-AAT
1496961 ATTT
1 ATTT
1496965 TTTAGAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 7 0.27
24 4 0.15
25 15 0.58
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTTAATATAATTATAATTATAAAT
Found at i:1497621 original size:24 final size:24
Alignment explanation
Indices: 1497594--1497644 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
1497584 AAAAAAGATC
* *
1497594 AAAGTAGAACGAAATA-GAGAAGAA
1 AAAG-AGAACGAAAAAGGAGAAAAA
*
1497618 AAAGAGAATGAAAAAGGAGAAAAA
1 AAAGAGAACGAAAAAGGAGAAAAA
1497642 AAA
1 AAA
1497645 ATTAGGGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.69, C:0.02, G:0.24, T:0.06
Consensus pattern (24 bp):
AAAGAGAACGAAAAAGGAGAAAAA
Found at i:1497637 original size:13 final size:11
Alignment explanation
Indices: 1497568--1497643 Score: 52
Period size: 11 Copynumber: 6.7 Consensus size: 11
1497558 AAATAAATGA
1497568 AAGAAAAAGA-
1 AAGAAAAAGAG
1497578 ATAGAAAAA-A-
1 A-AGAAAAAGAG
*
1497588 AAGATCAAAGTAG
1 AAGA-AAAAG-AG
*
1497601 AACGAAATAGAG
1 AA-GAAAAAGAG
1497613 AAGAAAAAGAG
1 AAGAAAAAGAG
1497624 AATGAAAAAGGAG
1 AA-GAAAAA-GAG
1497637 AA-AAAAA
1 AAGAAAAA
1497644 AATTAGGGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 15
0.74 0.05 0.21
Matches are distributed among these distances:
9 3 0.06
10 6 0.11
11 22 0.41
12 11 0.20
13 10 0.19
14 2 0.04
ACGTcount: A:0.70, C:0.03, G:0.21, T:0.07
Consensus pattern (11 bp):
AAGAAAAAGAG
Found at i:1499363 original size:25 final size:24
Alignment explanation
Indices: 1499280--1499414 Score: 145
Period size: 25 Copynumber: 5.6 Consensus size: 24
1499270 TTATTATGCA
* *
1499280 CTAATGAACAGAGAGCACTAAAGTG
1 CTAAT-AACAGAGAGCACCAACGTG
*
1499305 CT-AT-ACAGAGAGCA-CAGATGTG
1 CTAATAACAGAGAGCACCA-ACGTG
**
1499327 CT-A-AACAGAGAGCACTGACGTG
1 CTAATAACAGAGAGCACCAACGTG
1499349 CTAATAATCAGAGAGCACCAACGTG
1 CTAATAA-CAGAGAGCACCAACGTG
1499374 CTAATAATCAGAGAGCACCAACGTG
1 CTAATAA-CAGAGAGCACCAACGTG
1499399 CTAATAATCAGAGAGC
1 CTAATAA-CAGAGAGC
1499415 GCGCTAAAGT
Statistics
Matches: 97, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
21 1 0.01
22 33 0.34
23 1 0.01
24 4 0.04
25 58 0.60
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.16
Consensus pattern (24 bp):
CTAATAACAGAGAGCACCAACGTG
Found at i:1499400 original size:50 final size:49
Alignment explanation
Indices: 1499280--1499414 Score: 165
Period size: 50 Copynumber: 2.8 Consensus size: 49
1499270 TTATTATGCA
* *
1499280 CTAATGAACAGAGAGCACTAAAGTGCT-AT-A-CAGAGAGCACAGATGTG
1 CTAAT-AACAGAGAGCACTAACGTGCTAATAATCAGAGAGCACAGACGTG
*
1499327 CT-A-AACAGAGAGCACTGACGTGCTAATAATCAGAGAGCACCA-ACGTG
1 CTAATAACAGAGAGCACTAACGTGCTAATAATCAGAGAGCA-CAGACGTG
*
1499374 CTAATAATCAGAGAGCACCAACGTGCTAATAATCAGAGAGC
1 CTAATAA-CAGAGAGCACTAACGTGCTAATAATCAGAGAGC
1499415 GCGCTAAAGT
Statistics
Matches: 76, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
44 19 0.25
45 2 0.03
46 2 0.03
47 17 0.22
48 3 0.04
49 2 0.03
50 31 0.41
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.16
Consensus pattern (49 bp):
CTAATAACAGAGAGCACTAACGTGCTAATAATCAGAGAGCACAGACGTG
Found at i:1505925 original size:19 final size:18
Alignment explanation
Indices: 1505901--1505954 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
1505891 TTTTTTTTCC
1505901 ATTTAAGTTTTCAATTTAA
1 ATTTAAGTTTTCAATTT-A
*
1505920 ATTTAA-TTGTTTAATTTA
1 ATTTAAGTT-TTCAATTTA
* *
1505938 ATTTCAGTTTTCTATTT
1 ATTTAAGTTTTCAATTT
1505955 CATAAATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
18 14 0.48
19 15 0.52
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.59
Consensus pattern (18 bp):
ATTTAAGTTTTCAATTTA
Found at i:1506843 original size:20 final size:20
Alignment explanation
Indices: 1506801--1506861 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
1506791 GAGATTTAGG
* *
1506801 GTTCGGAGTTCGAGGCTCAA
1 GTTCAGAGTTCGAGGTTCAA
* **
1506821 GTTTAGAGTTCGAGGTTTGA
1 GTTCAGAGTTCGAGGTTCAA
* *
1506841 GTTCAGGGTTTGAGGTTCAA
1 GTTCAGAGTTCGAGGTTCAA
1506861 G
1 G
1506862 ATAAAAAATT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.20, C:0.11, G:0.36, T:0.33
Consensus pattern (20 bp):
GTTCAGAGTTCGAGGTTCAA
Found at i:1512396 original size:3 final size:3
Alignment explanation
Indices: 1512390--1512469 Score: 160
Period size: 3 Copynumber: 26.7 Consensus size: 3
1512380 AGGTAAGTAG
1512390 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1512438 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1512470 GTGTGAATTA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1512790 original size:23 final size:22
Alignment explanation
Indices: 1512763--1512847 Score: 113
Period size: 21 Copynumber: 4.0 Consensus size: 22
1512753 CTTTGCCGAC
1512763 CAGGCACTTTATGTGTCGTATCT
1 CAGGCACTTTATGTGTCGTAT-T
1512786 CAGGCACTTTATGTGTCGTA-T
1 CAGGCACTTTATGTGTCGTATT
* **
1512807 CAGGCACCTCGTGTGTCGT-TT
1 CAGGCACTTTATGTGTCGTATT
1512828 CAGGCAC-TTATGTGTCGTAT
1 CAGGCACTTTATGTGTCGTAT
1512848 ACTGATCTGG
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
20 9 0.16
21 26 0.47
23 20 0.36
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.36
Consensus pattern (22 bp):
CAGGCACTTTATGTGTCGTATT
Found at i:1512813 original size:44 final size:41
Alignment explanation
Indices: 1512763--1512847 Score: 116
Period size: 44 Copynumber: 2.0 Consensus size: 41
1512753 CTTTGCCGAC
* *
1512763 CAGGCACTTTATGTGTCGTATCTCAGGCACTTTATGTGTCGTAT
1 CAGGCACCTCATGTGTCGT-T-TCAGGCAC-TTATGTGTCGTAT
*
1512807 CAGGCACCTCGTGTGTCGTTTCAGGCACTTATGTGTCGTAT
1 CAGGCACCTCATGTGTCGTTTCAGGCACTTATGTGTCGTAT
1512848 ACTGATCTGG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 13 0.34
42 8 0.21
43 1 0.03
44 16 0.42
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.36
Consensus pattern (41 bp):
CAGGCACCTCATGTGTCGTTTCAGGCACTTATGTGTCGTAT
Found at i:1519845 original size:25 final size:24
Alignment explanation
Indices: 1519793--1519846 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
1519783 TAGATTGGTG
*
1519793 ATTTAATATAAATATAATTATAATT
1 ATTTAATAT-AATATAATTATAAAT
1519818 ATTTAATAT-ATATAATTAATATAAT
1 ATTTAATATAATATAATT-ATA-AAT
1519843 ATTT
1 ATTT
1519847 TTTAGGAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 8 0.31
24 3 0.12
25 15 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
ATTTAATATAATATAATTATAAAT
Found at i:1524296 original size:6 final size:6
Alignment explanation
Indices: 1524285--1524330 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
1524275 AGCTGAGTAC
1524285 CCTGTG CCTGTG CCTGTG CCTGTG CCTGTG CCTGTG CCTGTG CCTG
1 CCTGTG CCTGTG CCTGTG CCTGTG CCTGTG CCTGTG CCTGTG CCTG
1524331 CGCCATGTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.00, C:0.35, G:0.33, T:0.33
Consensus pattern (6 bp):
CCTGTG
Found at i:1535787 original size:14 final size:14
Alignment explanation
Indices: 1535768--1535800 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
1535758 AAACATAAAG
1535768 AAAAAGCCAAAATT
1 AAAAAGCCAAAATT
1535782 AAAAAGCCAAAATT
1 AAAAAGCCAAAATT
1535796 AAAAA
1 AAAAA
1535801 ATAAACCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.70, C:0.12, G:0.06, T:0.12
Consensus pattern (14 bp):
AAAAAGCCAAAATT
Found at i:1536613 original size:22 final size:24
Alignment explanation
Indices: 1536588--1536634 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
1536578 AAAATTATAT
*
1536588 TATTAAATTAAA-TTA-AAAAAAA
1 TATTAAATCAAATTTATAAAAAAA
*
1536610 TATTTAATCAAATTTATAAAAAAA
1 TATTAAATCAAATTTATAAAAAAA
1536634 T
1 T
1536635 TAATAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.48
23 3 0.14
24 8 0.38
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
TATTAAATCAAATTTATAAAAAAA
Found at i:1536734 original size:3 final size:3
Alignment explanation
Indices: 1536726--1536771 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1536716 AACTTTATAT
1536726 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1536772 ACTACTTACT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1537731 original size:3 final size:3
Alignment explanation
Indices: 1537723--1537764 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1537713 TTTGCCCTAA
1537723 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1537765 GGAACTAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1541393 original size:22 final size:22
Alignment explanation
Indices: 1541357--1541399 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1541347 TAGTGAAAAA
*
1541357 AAAACAATAAGAAAATAACAAC
1 AAAACAATAAAAAAATAACAAC
* *
1541379 AAAACAGTAAAAAAATTACAA
1 AAAACAATAAAAAAATAACAA
1541400 TTTTTTTTGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.72, C:0.12, G:0.05, T:0.12
Consensus pattern (22 bp):
AAAACAATAAAAAAATAACAAC
Found at i:1542778 original size:21 final size:20
Alignment explanation
Indices: 1542739--1542777 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1542729 ATTTTAATAA
1542739 AAATTAAGTGAATTAAAAAC
1 AAATTAAGTGAATTAAAAAC
1542759 AAATTGAAGTG-ATTAAAAA
1 AAATT-AAGTGAATTAAAAA
1542778 AATGTACCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.59, C:0.03, G:0.13, T:0.26
Consensus pattern (20 bp):
AAATTAAGTGAATTAAAAAC
Found at i:1543161 original size:27 final size:26
Alignment explanation
Indices: 1543120--1543184 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
1543110 ATATGTCACG
*
1543120 TTAATAAATAATTTAAAA-ATTATAAAA
1 TTAAAAAAT-ATTTAAAATA-TATAAAA
* *
1543147 TTATAAAAATATTTAATATATATAAAT
1 TTA-AAAAATATTTAAAATATATAAAA
1543174 TTAAAAAATAT
1 TTAAAAAATAT
1543185 AGCATAAAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
26 8 0.24
27 19 0.58
28 6 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
TTAAAAAATATTTAAAATATATAAAA
Found at i:1546767 original size:2 final size:2
Alignment explanation
Indices: 1546762--1546803 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1546752 AAATCTTTTA
1546762 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1546804 TCTAATTTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1554751 original size:23 final size:23
Alignment explanation
Indices: 1554710--1554763 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
1554700 TTACTATTCA
1554710 TTAATTATAGAAAATATATAATTT
1 TTAA-TATAGAAAATATATAATTT
1554734 TTAATATA-AAAATAATATAATTT
1 TTAATATAGAAAAT-ATATAATTT
1554757 TTAATAT
1 TTAATAT
1554764 GTGTTAGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
22 5 0.17
23 20 0.69
24 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
TTAATATAGAAAATATATAATTT
Found at i:1562303 original size:19 final size:18
Alignment explanation
Indices: 1562276--1562329 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 18
1562266 TACATTGAAG
1562276 AATCAAAAAAAAATGTTAA
1 AATCAAAAAAAAATG-TAA
* **
1562295 AATCTAAAATTAATGTAA
1 AATCAAAAAAAAATGTAA
1562313 AA-CAAAAAAAAAT-TAA
1 AATCAAAAAAAAATGTAA
1562329 A
1 A
1562330 GACCAAATTG
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 4 0.14
17 8 0.28
18 5 0.17
19 12 0.41
ACGTcount: A:0.69, C:0.06, G:0.04, T:0.22
Consensus pattern (18 bp):
AATCAAAAAAAAATGTAA
Found at i:1564635 original size:30 final size:27
Alignment explanation
Indices: 1564571--1564637 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 27
1564561 TCACAAATTT
*
1564571 AAAATTTAGTCTCTGTATTTTTATTTC
1 AAAATTTAGTCTCTGTATTTTTAGTTC
1564598 AAGAATTTAGTCTCTCTGT-TTTTTAGAGTTC
1 AA-AATTTAG--TCTCTGTATTTTT--AGTTC
1564629 AAAATTTAG
1 AAAATTTAG
1564638 GTCTATTTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
27 2 0.06
28 7 0.21
29 5 0.15
30 14 0.41
31 6 0.18
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.49
Consensus pattern (27 bp):
AAAATTTAGTCTCTGTATTTTTAGTTC
Found at i:1567053 original size:138 final size:138
Alignment explanation
Indices: 1566886--1567199 Score: 481
Period size: 138 Copynumber: 2.3 Consensus size: 138
1566876 GAGGACACAT
1566886 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTAAATATTTTACCGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTAAATATTTTACCGAATTTATT
* * * *
1566951 AATATAAACTGTTATATTAATTAATA-CTGCTCAGAATATAAAAGAAATGAAAATTAATATTAT-
66 AATATAAACAGTTATATTAATTAATATC-GATCAAAATATAAAAGAAATGAAAAATAATATT-TG
* *
1567014 TTTGGAAATA
129 TTTGAAAAGA
* * * *
1567024 ATATAATTAATATATAAATTTGATTCATACAAAATATTAATTGTATATGTTTTACTGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTAAATATTTTACCGAATTTATT
* *
1567089 AATATAAACAGTTATATTAATTAATATCGATCAAAATATAAAAGATATGAAAAATATTATTTGTT
66 AATATAAACAGTTATATTAATTAATATCGATCAAAATATAAAAGAAATGAAAAATAATATTTGTT
1567154 TGAAAAGA
131 TGAAAAGA
1567162 ATAT-ATTAATATATGAATTTGATTCATACAAAATATTA
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTA
1567200 CAAAATATTA
Statistics
Matches: 161, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
137 34 0.21
138 126 0.78
139 1 0.01
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (138 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTAAATATTTTACCGAATTTATT
AATATAAACAGTTATATTAATTAATATCGATCAAAATATAAAAGAAATGAAAAATAATATTTGTT
TGAAAAGA
Done.