Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 15 of 193
Found at i:5332574 original size:28 final size:26
Alignment explanation
Indices: 5332543--5332596 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 26
5332533 AAAAATTAAA
*
5332543 TTTTTAAATATATATAAATTATATAATT
1 TTTTTAAATATA-AAAAATTATA-AATT
5332571 TTTTTAAATATAAAAAATTATAAATT
1 TTTTTAAATATAAAAAATTATAAATT
5332597 ATAAAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 4 0.16
27 9 0.36
28 12 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TTTTTAAATATAAAAAATTATAAATT
Found at i:5332803 original size:12 final size:12
Alignment explanation
Indices: 5332786--5332811 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5332776 TTTATAGGAT
5332786 TTTTTTTTTTTG
1 TTTTTTTTTTTG
5332798 TTTTTTTTTTTG
1 TTTTTTTTTTTG
5332810 TT
1 TT
5332812 AATTATTGAT
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:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (12 bp):
TTTTTTTTTTTG
Found at i:5333150 original size:18 final size:18
Alignment explanation
Indices: 5333127--5333164 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
5333117 TTTTATAAAC
5333127 TTTTTAAAAT-TTTGTTTA
1 TTTTTAAAATATTT-TTTA
5333145 TTTTTAAAATATTTTTTA
1 TTTTTAAAATATTTTTTA
5333163 TT
1 TT
5333165 AATTTTTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTTTAAAATATTTTTTA
Found at i:5337165 original size:23 final size:23
Alignment explanation
Indices: 5337090--5337149 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
5337080 TTTGTTTTCT
* *
5337090 TAATACGGCTATGTCTTCTTTTA
1 TAATATGGTTATGTCTTCTTTTA
* *
5337113 GAACATGGTTATGTCTTCTTTTA
1 TAATATGGTTATGTCTTCTTTTA
5337136 TAATATGGTTATGT
1 TAATATGGTTATGT
5337150 TTGTTTCTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.48
Consensus pattern (23 bp):
TAATATGGTTATGTCTTCTTTTA
Found at i:5338238 original size:39 final size:39
Alignment explanation
Indices: 5338194--5338284 Score: 107
Period size: 39 Copynumber: 2.4 Consensus size: 39
5338184 TGGGACAAGT
* *
5338194 CTCTTCCAAGAGGTAT-GTCCAATATGAAAAGGGTTGTGA
1 CTCTTCCAAAAGGTATAATCCAATATG-AAAGGGTTGTGA
* *
5338233 CTCTT-CAAAAGGTGTCAATCCAATTTGAAAGGGTTGTGA
1 CTCTTCCAAAAGGTAT-AATCCAATATGAAAGGGTTGTGA
5338272 CTCTT-CAAAAGGT
1 CTCTTCCAAAAGGT
5338285 GTCCATTTAG
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
38 8 0.17
39 30 0.65
40 8 0.17
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (39 bp):
CTCTTCCAAAAGGTATAATCCAATATGAAAGGGTTGTGA
Found at i:5338244 original size:19 final size:19
Alignment explanation
Indices: 5338220--5338283 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
5338210 GTCCAATATG
5338220 AAAAGGGTTGTGACTCTTC
1 AAAAGGGTTGTGACTCTTC
* * *
5338239 AAAA-GG-TGTCAATCCAATTT
1 AAAAGGGTTGTGACT-C--TTC
*
5338259 GAAAGGGTTGTGACTCTTC
1 AAAAGGGTTGTGACTCTTC
5338278 AAAAGG
1 AAAAGG
5338284 TGTCCATTTA
Statistics
Matches: 32, Mismatches: 8, Indels: 10
0.64 0.16 0.20
Matches are distributed among these distances:
17 5 0.16
18 3 0.09
19 11 0.34
20 5 0.16
21 3 0.09
22 5 0.16
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (19 bp):
AAAAGGGTTGTGACTCTTC
Found at i:5338285 original size:39 final size:40
Alignment explanation
Indices: 5338211--5338287 Score: 138
Period size: 39 Copynumber: 1.9 Consensus size: 40
5338201 AAGAGGTATG
5338211 TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGGTGTCAA
1 TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGGTGTCAA
*
5338251 TCCAATTTG-AAAGGGTTGTGACTCTTCAAAAGGTGTC
1 TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGGTGTC
5338288 CATTTAGTGC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 28 0.78
40 8 0.22
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (40 bp):
TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGGTGTCAA
Found at i:5343181 original size:39 final size:39
Alignment explanation
Indices: 5343137--5343227 Score: 107
Period size: 39 Copynumber: 2.4 Consensus size: 39
5343127 TGGGACAAAT
* *
5343137 CTCTTCCAAGAGGTAT-GTCCAATATGAAAAGGGTTGTGA
1 CTCTTCCAAAAGGTATCATCCAATATG-AAAGGGTTGTGA
* *
5343176 CTCTT-CAAAAGGTGTCCATCCAATTTGAAAGGGTTGTGA
1 CTCTTCCAAAAGGTAT-CATCCAATATGAAAGGGTTGTGA
5343215 CTCTT-CAAAAGGT
1 CTCTTCCAAAAGGT
5343228 GTCCATTGAG
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
38 8 0.17
39 30 0.65
40 8 0.17
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (39 bp):
CTCTTCCAAAAGGTATCATCCAATATGAAAGGGTTGTGA
Found at i:5343228 original size:39 final size:40
Alignment explanation
Indices: 5343154--5343233 Score: 144
Period size: 39 Copynumber: 2.0 Consensus size: 40
5343144 AAGAGGTATG
5343154 TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGGTGTCCA
1 TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGGTGTCCA
*
5343194 TCCAATTTG-AAAGGGTTGTGACTCTTCAAAAGGTGTCCA
1 TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGGTGTCCA
5343233 T
1 T
5343234 TGAGTGCATA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (40 bp):
TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGGTGTCCA
Found at i:5344380 original size:2 final size:2
Alignment explanation
Indices: 5344373--5344398 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5344363 AATTTGGAAG
5344373 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
5344399 TTGAGTCGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5351558 original size:12 final size:11
Alignment explanation
Indices: 5351535--5351575 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
5351525 GAAATTTTGC
*
5351535 TTTCGTTTTTT
1 TTTCTTTTTTT
5351546 TTTCTTTTCTTT
1 TTTCTTTT-TTT
5351558 TTTCTTTTTTT
1 TTTCTTTTTTT
5351569 TTTCTTT
1 TTTCTTT
5351576 AAAGTCTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.85
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:5352797 original size:14 final size:14
Alignment explanation
Indices: 5352763--5352798 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
5352753 TTGTTTGACT
*
5352763 GAAAATAATTTTTA
1 GAAAATGATTTTTA
*
5352777 GAAAATGATTTTTG
1 GAAAATGATTTTTA
5352791 GAAAATGA
1 GAAAATGA
5352799 ATCACTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.17, T:0.36
Consensus pattern (14 bp):
GAAAATGATTTTTA
Found at i:5355358 original size:7 final size:7
Alignment explanation
Indices: 5355313--5355440 Score: 70
Period size: 7 Copynumber: 19.1 Consensus size: 7
5355303 AATTGAAAAC
5355313 GAGAAAG
1 GAGAAAG
*
5355320 G-CAAAG
1 GAGAAAG
5355326 GAGAAAG
1 GAGAAAG
* *
5355333 GGGGAAG
1 GAGAAAG
*
5355340 G-GAAAA
1 GAGAAAG
5355346 GA-AAAG
1 GAGAAAG
5355352 GAGAAAG
1 GAGAAAG
* *
5355359 GGGGAAG
1 GAGAAAG
* *
5355366 GGGGAAG
1 GAGAAAG
* *
5355373 GGGGAAG
1 GAGAAAG
* *
5355380 GGGGAAG
1 GAGAAAG
5355387 G-GAAAG
1 GAGAAAG
*
5355393 G-GGAAG
1 GAGAAAG
5355399 G-GAAAG
1 GAGAAAG
5355405 GAGAAAG
1 GAGAAAG
*
5355412 TAGAAAG
1 GAGAAAG
*
5355419 TAGAAAG
1 GAGAAAG
5355426 GAGAAAG
1 GAGAAAG
*
5355433 GAGGAAG
1 GAGAAAG
5355440 G
1 G
5355441 GGGAAGGGAA
Statistics
Matches: 102, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
6 29 0.28
7 73 0.72
ACGTcount: A:0.47, C:0.01, G:0.51, T:0.02
Consensus pattern (7 bp):
GAGAAAG
Found at i:5355395 original size:12 final size:12
Alignment explanation
Indices: 5355360--5355405 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
5355350 AGGAGAAAGG
*
5355360 GGGAAGGGGGAA
1 GGGAAAGGGGAA
*
5355372 GGGGGAAGGGGGAA
1 --GGGAAAGGGGAA
5355386 GGGAAAGGGGAA
1 GGGAAAGGGGAA
5355398 GGGAAAGG
1 GGGAAAGG
5355406 AGAAAGTAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 19 0.61
14 12 0.39
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (12 bp):
GGGAAAGGGGAA
Found at i:5355439 original size:60 final size:60
Alignment explanation
Indices: 5355323--5355458 Score: 166
Period size: 60 Copynumber: 2.2 Consensus size: 60
5355313 GAGAAAGGCA
* * * * *
5355323 AAGGAGAAAGGGGGAAGGGAAAAGAAAAGGAGAAAGGGGGAAGGGGGAAGGGGGAAGGGGG
1 AAGG-GAAAGGGGGAAGGGAAAAGAAAAGGAGAAAGGAGAAAGGAGAAAGGAGGAAGGGGG
* * *
5355384 AAGGGAAA-GGGGAAGGGAAAGGAGAAAGTAGAAAGTAGAAAGGAGAAAGGAGGAAGGGGG
1 AAGGGAAAGGGGGAAGGGAAAAGA-AAAGGAGAAAGGAGAAAGGAGAAAGGAGGAAGGGGG
5355444 AAGGGAAATGGGGGA
1 AAGGGAAA-GGGGGA
5355459 GAGGCTTCGG
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
59 14 0.22
60 41 0.64
61 4 0.06
62 5 0.08
ACGTcount: A:0.45, C:0.00, G:0.53, T:0.02
Consensus pattern (60 bp):
AAGGGAAAGGGGGAAGGGAAAAGAAAAGGAGAAAGGAGAAAGGAGAAAGGAGGAAGGGGG
Found at i:5355878 original size:19 final size:19
Alignment explanation
Indices: 5355850--5355910 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
5355840 AAGTTATATG
*
5355850 AAAATTAATAAATTTATAA
1 AAAATAAATAAATTTATAA
5355869 AAAATAAATAAATTT-TAA
1 AAAATAAATAAATTTATAA
* * * *
5355887 GAAATTCACTAATTTTATAA
1 -AAAATAAATAAATTTATAA
5355907 AAAA
1 AAAA
5355911 ATAGTACGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 3 0.09
19 28 0.82
20 3 0.09
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (19 bp):
AAAATAAATAAATTTATAA
Found at i:5356777 original size:19 final size:19
Alignment explanation
Indices: 5356721--5356792 Score: 63
Period size: 19 Copynumber: 3.7 Consensus size: 19
5356711 TGTAAGGTGT
* * * *
5356721 TCAATAATCTCTAAGAGAT
1 TCAATAATTTTTAAGAAAA
*
5356740 TCAATAATTTTGCAAGAAAA
1 TCAATAATTTT-TAAGAAAA
* *
5356760 TCAATCATTTTTAAGAAAT
1 TCAATAATTTTTAAGAAAA
*
5356779 TTAATAATTTTTAA
1 TCAATAATTTTTAA
5356793 TATATTAAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
19 27 0.64
20 15 0.36
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (19 bp):
TCAATAATTTTTAAGAAAA
Found at i:5356803 original size:19 final size:19
Alignment explanation
Indices: 5356732--5356808 Score: 55
Period size: 19 Copynumber: 4.0 Consensus size: 19
5356722 CAATAATCTC
* *
5356732 TAAGAGATTCAATAATTTT
1 TAAGAAATTAAATAATTTT
* * * *
5356751 GCAAGAAAATCAATCATTTT
1 -TAAGAAATTAAATAATTTT
*
5356771 TAAGAAATTTAATAATTTT
1 TAAGAAATTAAATAATTTT
* * *
5356790 TAATATATTAAATACTTTT
1 TAAGAAATTAAATAATTTT
5356809 ATAACAACTT
Statistics
Matches: 45, Mismatches: 12, Indels: 1
0.78 0.21 0.02
Matches are distributed among these distances:
19 30 0.67
20 15 0.33
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.43
Consensus pattern (19 bp):
TAAGAAATTAAATAATTTT
Found at i:5359332 original size:51 final size:51
Alignment explanation
Indices: 5359255--5359396 Score: 203
Period size: 51 Copynumber: 2.8 Consensus size: 51
5359245 GCTATAAACG
* * *
5359255 AAAGGATCCGATGACCAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGG-TCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGGATT
* *
5359307 AAAGGTCCGATGACTAAGTGCCATCGTGAGTAAATGAATCCATGATGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGGATT
* * *
5359358 AAAGGTCCGATGACTCAGTGTTATCGTGAGTATATGAAT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAAT
5359397 TTCTATACAG
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
51 76 0.94
52 5 0.06
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.27
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGGATT
Found at i:5366640 original size:20 final size:19
Alignment explanation
Indices: 5366599--5366701 Score: 66
Period size: 20 Copynumber: 5.3 Consensus size: 19
5366589 TAGACTTTAT
* *
5366599 TAATTATGTAAGCGATTGAA
1 TAATT-TGTAAGAGATTCAA
5366619 TAACTTTGTAAGATG-TTCAA
1 TAA-TTTGTAAGA-GATTCAA
* *
5366639 TAATCTCTAAGAGATTCAA
1 TAATTTGTAAGAGATTCAA
* *
5366658 TAATTTTGTAAGAAAATCAA
1 TAA-TTTGTAAGAGATTCAA
* * * *
5366678 TCA-TTATAAGAAATTTAA
1 TAATTTGTAAGAGATTCAA
5366696 TAATTT
1 TAATTT
5366702 TTAATATATT
Statistics
Matches: 65, Mismatches: 13, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
18 15 0.23
19 17 0.26
20 30 0.46
21 3 0.05
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.38
Consensus pattern (19 bp):
TAATTTGTAAGAGATTCAA
Found at i:5366678 original size:39 final size:38
Alignment explanation
Indices: 5366607--5366702 Score: 93
Period size: 39 Copynumber: 2.5 Consensus size: 38
5366597 ATTAATTATG
* * * *** *
5366607 TAAGCGATTGAATAACTTTGTAAGATGTTCAATAATCTC
1 TAAGAGATTCAATAATTTTGTAAGAAAATCAATAAT-TA
*
5366646 TAAGAGATTCAATAATTTTGTAAGAAAATCAATCATTA
1 TAAGAGATTCAATAATTTTGTAAGAAAATCAATAATTA
* *
5366684 TAAGAAATTTAATAATTTT
1 TAAGAGATTCAATAATTTT
5366703 TAATATATTA
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
38 18 0.38
39 29 0.62
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (38 bp):
TAAGAGATTCAATAATTTTGTAAGAAAATCAATAATTA
Found at i:5369322 original size:49 final size:50
Alignment explanation
Indices: 5369265--5369364 Score: 166
Period size: 52 Copynumber: 2.0 Consensus size: 50
5369255 TATATTTTTT
5369265 GAAGCCCTAGATCTAG-TTTTTTTCCCTTCTCATTGTAAACTCCTTGTTA
1 GAAGCCCTAGATCTAGTTTTTTTTCCCTTCTCATTGTAAACTCCTTGTTA
*
5369314 GAAGCCCTAGATCTAGTTTTTTTTTTCCCTTTTCATTGTAAACTCCTTGTT
1 GAAGCCCTAGATCTAG--TTTTTTTTCCCTTCTCATTGTAAACTCCTTGTT
5369365 TGATGTTAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
49 16 0.34
52 31 0.66
ACGTcount: A:0.19, C:0.23, G:0.12, T:0.46
Consensus pattern (50 bp):
GAAGCCCTAGATCTAGTTTTTTTTCCCTTCTCATTGTAAACTCCTTGTTA
Found at i:5380436 original size:20 final size:19
Alignment explanation
Indices: 5380407--5380477 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 19
5380397 TAAACTTTAT
* *
5380407 TAATTATGTAAGCGATTGAA
1 TAATTTTGTAAG-GATTCAA
*
5380427 TAATTTTGTAAGGTGTTCAA
1 TAATTTTGTAAGG-ATTCAA
* *
5380447 TAA-TCTCTAAGAGATTCAA
1 TAATTTTGTAAG-GATTCAA
5380466 TAATTTTGTAAG
1 TAATTTTGTAAG
5380478 AAAATCAATC
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 15 0.38
20 25 0.62
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (19 bp):
TAATTTTGTAAGGATTCAA
Found at i:5380486 original size:39 final size:38
Alignment explanation
Indices: 5380415--5380510 Score: 93
Period size: 39 Copynumber: 2.5 Consensus size: 38
5380405 ATTAATTATG
* * ****
5380415 TAAGCGATTGAATAATTTTGTAAGGTGTTCAATAATCTC
1 TAAGAGATTCAATAATTTTGTAAGAAAATCAATAAT-TC
* *
5380454 TAAGAGATTCAATAATTTTGTAAGAAAATCAATCATTT
1 TAAGAGATTCAATAATTTTGTAAGAAAATCAATAATTC
* *
5380492 TAAGAAATTTAATAATTTT
1 TAAGAGATTCAATAATTTT
5380511 TAATATATTC
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
38 18 0.38
39 29 0.62
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.40
Consensus pattern (38 bp):
TAAGAGATTCAATAATTTTGTAAGAAAATCAATAATTC
Found at i:5380524 original size:19 final size:19
Alignment explanation
Indices: 5380442--5380549 Score: 83
Period size: 19 Copynumber: 5.6 Consensus size: 19
5380432 TTGTAAGGTG
* * *
5380442 TTCAATAATCTCTAAGAGA
1 TTCAATAATTTTTAAGAAA
5380461 TTCAATAATTTTGTAAGAAA
1 TTCAATAATTTT-TAAGAAA
* *
5380481 ATCAATCA-TTTTAAGAAA
1 TTCAATAATTTTTAAGAAA
* * *
5380499 TTTAATAATTTTTAATATA
1 TTCAATAATTTTTAAGAAA
* * * *
5380518 TTCAATACCTTTATAACAAC
1 TTCAATA-ATTTTTAAGAAA
5380538 TTCAATAATTTT
1 TTCAATAATTTT
5380550 ATAAAAAAAA
Statistics
Matches: 68, Mismatches: 18, Indels: 6
0.74 0.20 0.07
Matches are distributed among these distances:
18 12 0.18
19 30 0.44
20 26 0.38
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.42
Consensus pattern (19 bp):
TTCAATAATTTTTAAGAAA
Found at i:5383131 original size:49 final size:50
Alignment explanation
Indices: 5383074--5383173 Score: 166
Period size: 52 Copynumber: 2.0 Consensus size: 50
5383064 TATATTTTTT
5383074 GAAGCCCTAGATCTAG-TTTTTTTCCCTTCTCATTGTAAACTCCTTGTTA
1 GAAGCCCTAGATCTAGTTTTTTTTCCCTTCTCATTGTAAACTCCTTGTTA
*
5383123 GAAGCCCTAGATCTAGTTTTTTTTTTCCCTTTTCATTGTAAACTCCTTGTT
1 GAAGCCCTAGATCTAG--TTTTTTTTCCCTTCTCATTGTAAACTCCTTGTT
5383174 TGATGTTAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
49 16 0.34
52 31 0.66
ACGTcount: A:0.19, C:0.23, G:0.12, T:0.46
Consensus pattern (50 bp):
GAAGCCCTAGATCTAGTTTTTTTTCCCTTCTCATTGTAAACTCCTTGTTA
Found at i:5386525 original size:18 final size:19
Alignment explanation
Indices: 5386502--5386537 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5386492 GAATATAGTA
5386502 AAATATA-AAAAAAAATGT
1 AAATATATAAAAAAAATGT
*
5386520 AAATATATAAAAGAAATG
1 AAATATATAAAAAAAATG
5386538 ATACACATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.22
Consensus pattern (19 bp):
AAATATATAAAAAAAATGT
Found at i:5390351 original size:16 final size:16
Alignment explanation
Indices: 5390312--5390352 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
5390302 TTAGGGTTTA
* *
5390312 AAAGTTTTAATTAATT
1 AAAGATTTATTTAATT
5390328 -AA-ATTTATTTAATT
1 AAAGATTTATTTAATT
5390342 AAAGATTTATT
1 AAAGATTTATT
5390353 CTCATTCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 10 0.48
15 4 0.19
16 7 0.33
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (16 bp):
AAAGATTTATTTAATT
Found at i:5394567 original size:19 final size:21
Alignment explanation
Indices: 5394540--5394588 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 21
5394530 ATAATATATC
*
5394540 AATACATTTAAAA-A-ATTAA
1 AATAAATTTAAAATACATTAA
5394559 AATAAATTTAAAATACATTAA
1 AATAAATTTAAAATACATTAA
5394580 AA-AAATTTA
1 AATAAATTTA
5394589 TATTAAGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 12 0.44
20 8 0.30
21 7 0.26
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (21 bp):
AATAAATTTAAAATACATTAA
Found at i:5394732 original size:12 final size:12
Alignment explanation
Indices: 5394712--5394801 Score: 75
Period size: 12 Copynumber: 7.8 Consensus size: 12
5394702 ATAAAATCCA
5394712 AACAACAAAAAT
1 AACAACAAAAAT
*
5394724 AACAGC---AA-
1 AACAACAAAAAT
*
5394732 AACAACATTAAA-
1 AACAACA-AAAAT
5394744 AACAACAAAAAT
1 AACAACAAAAAT
* *
5394756 AGCAACAAAAAC
1 AACAACAAAAAT
5394768 AACAACAAAAAT
1 AACAACAAAAAT
*
5394780 AAC-ACGAAAAT
1 AACAACAAAAAT
5394791 AACAACCAAAA
1 AACAA-CAAAA
5394802 CAGTAAAAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
8 5 0.08
9 2 0.03
11 13 0.21
12 38 0.61
13 4 0.06
ACGTcount: A:0.70, C:0.20, G:0.03, T:0.07
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:5394747 original size:20 final size:20
Alignment explanation
Indices: 5394698--5394863 Score: 72
Period size: 20 Copynumber: 7.9 Consensus size: 20
5394688 AAAACGCATA
*
5394698 AAAAATAA-AATCCAAACAAC
1 AAAAATAACAA-CAAAACAAC
*
5394718 AAAAATAACAGCAAAACAAC
1 AAAAATAACAACAAAACAAC
*
5394738 ATTAAA-AACAACAAAAATAGCAAC
1 A-AAAATAACAAC--AAA-A-CAAC
* *
5394762 AAAAACAACAACAAAAATAAC
1 AAAAATAACAAC-AAAACAAC
**
5394783 ACGAAAATAACAACCAAAACAGT
1 A--AAAATAACAA-CAAAACAAC
* **
5394806 AAAAA-AAGCACCAAAACAGT
1 AAAAATAA-CAACAAAACAAC
*
5394826 AAAAACAAC-ACAAAA-AAC
1 AAAAATAACAACAAAACAAC
*
5394844 AAAAAATAGCAATCAAAACA
1 -AAAAATAACAA-CAAAACA
5394864 GTAAAAAAAC
Statistics
Matches: 114, Mismatches: 16, Indels: 30
0.71 0.10 0.19
Matches are distributed among these distances:
18 1 0.01
19 12 0.11
20 40 0.35
21 21 0.18
22 5 0.04
23 23 0.20
24 12 0.11
ACGTcount: A:0.69, C:0.19, G:0.04, T:0.07
Consensus pattern (20 bp):
AAAAATAACAACAAAACAAC
Found at i:5394748 original size:32 final size:32
Alignment explanation
Indices: 5394711--5394803 Score: 105
Period size: 33 Copynumber: 2.8 Consensus size: 32
5394701 AATAAAATCC
* **
5394711 AAACAACAAAAATAACAGCAAAACAACATTAA
1 AAACAACAAAAATAACAACAAAACAACAACAA
*
5394743 AAACAACAAAAATAGCAACAAAAACAACAACAA
1 AAACAACAAAAATAACAAC-AAAACAACAACAA
*
5394776 AAATAACACGAAAATAACAACCAAAACA
1 AAACAACA--AAAATAACAA-CAAAACA
5394804 GTAAAAAAAG
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
32 17 0.33
33 18 0.35
35 15 0.29
36 1 0.02
ACGTcount: A:0.70, C:0.20, G:0.03, T:0.06
Consensus pattern (32 bp):
AAACAACAAAAATAACAACAAAACAACAACAA
Found at i:5394789 original size:24 final size:24
Alignment explanation
Indices: 5394744--5394801 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 24
5394734 CAACATTAAA
*
5394744 AACAACAAAAATAGCAACAAAAAC
1 AACAACAAAAATAACAACAAAAAC
* *
5394768 AACAACAAAAATAAC-ACGAAAAT
1 AACAACAAAAATAACAACAAAAAC
*
5394791 AACAACCAAAA
1 AACAACAAAAA
5394802 CAGTAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 16 0.53
24 14 0.47
ACGTcount: A:0.71, C:0.21, G:0.03, T:0.05
Consensus pattern (24 bp):
AACAACAAAAATAACAACAAAAAC
Found at i:5394802 original size:56 final size:56
Alignment explanation
Indices: 5394712--5394821 Score: 132
Period size: 56 Copynumber: 2.0 Consensus size: 56
5394702 ATAAAATCCA
** *
5394712 AACAACAAAAATAACAGCAAAACAACATTAAAAACAACAAAAATAGCAACAAAAAC
1 AACAACAAAAATAACAGCAAAACAACAACAAAAACAACAAAAAAAGCAACAAAAAC
* * ** *
5394768 AACAACAAAAATAACA-CGAAAATAACAACCAAAACAGTAAAAAAAGCACCAAAA
1 AACAACAAAAATAACAGC-AAAACAACAACAAAAACAACAAAAAAAGCAACAAAA
5394822 CAGTAAAAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
55 1 0.02
56 44 0.98
ACGTcount: A:0.69, C:0.20, G:0.05, T:0.06
Consensus pattern (56 bp):
AACAACAAAAATAACAGCAAAACAACAACAAAAACAACAAAAAAAGCAACAAAAAC
Found at i:5399175 original size:11 final size:11
Alignment explanation
Indices: 5399159--5399183 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5399149 ATCAATAAGA
5399159 TTTCTTTTCTC
1 TTTCTTTTCTC
5399170 TTTCTTTTCTC
1 TTTCTTTTCTC
5399181 TTT
1 TTT
5399184 TCCATTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTCTTTTCTC
Found at i:5401667 original size:51 final size:51
Alignment explanation
Indices: 5401580--5401917 Score: 507
Period size: 51 Copynumber: 6.6 Consensus size: 51
5401570 GCTATAAACA
*
5401580 AAAGAGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACAGATT
1 AAAG-GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
5401632 AAAGGTTCGGTGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
5401683 AAAGGTCCGGTGACTATGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
5401734 AAAGGTCCGATGACTAAATGTCATTGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
5401785 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTGCGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * * * *
5401836 AATGGTCCGATGAATAAGTGTCATCGTGAGT-AATGAATCCATGATGAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
5401886 AAAGGTCCGATGACTATGTGTCATTGTGAGTA
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTA
5401918 TTAAATGAAA
Statistics
Matches: 260, Mismatches: 25, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
50 41 0.16
51 215 0.83
52 4 0.02
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:5402422 original size:51 final size:51
Alignment explanation
Indices: 5402335--5402622 Score: 382
Period size: 51 Copynumber: 5.6 Consensus size: 51
5402325 GCTATAAACG
* * * *
5402335 AAAGAGTCTGATGACTAAGTGTTATCTTGAGTAAATGAATCCTTTACAGATT
1 AAAG-GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
5402387 AAAGGTTC-AGTGACTAAGTGTCATCATGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGA-TGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * *
5402438 AAAAGTCCGGTGACTATGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
5402489 AAAGGTCCGATGACTAAATGTCATCGTGAGTAAATGAATCCTTTGCGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* ** *
5402540 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGGCGAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
5402591 AAAGGTCCAATGACTATA-TGTCATTGTGAGTA
1 AAAGGTCCGATGACTA-AGTGTCATCGTGAGTA
5402623 TTAAATGAAA
Statistics
Matches: 212, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
50 1 0.00
51 206 0.97
52 5 0.02
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.31
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:5405102 original size:27 final size:27
Alignment explanation
Indices: 5405072--5405123 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
5405062 TTTGGGTTGG
5405072 TTATTTTGAAGTTTTCTTTTAAATAAA
1 TTATTTTGAAGTTTTCTTTTAAATAAA
5405099 TTATTTTGAAGTTTTCTTTTAAATA
1 TTATTTTGAAGTTTTCTTTTAAATA
5405124 TTTTCTCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.58
Consensus pattern (27 bp):
TTATTTTGAAGTTTTCTTTTAAATAAA
Found at i:5405469 original size:49 final size:49
Alignment explanation
Indices: 5405403--5405504 Score: 204
Period size: 49 Copynumber: 2.1 Consensus size: 49
5405393 TAATTTTTTC
5405403 ATGATCAGAGATAGCAGAAAGAGATTATTTAGGTTAAATGTAAAATTTG
1 ATGATCAGAGATAGCAGAAAGAGATTATTTAGGTTAAATGTAAAATTTG
5405452 ATGATCAGAGATAGCAGAAAGAGATTATTTAGGTTAAATGTAAAATTTG
1 ATGATCAGAGATAGCAGAAAGAGATTATTTAGGTTAAATGTAAAATTTG
5405501 ATGA
1 ATGA
5405505 ATAAAAACTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.43, C:0.04, G:0.23, T:0.30
Consensus pattern (49 bp):
ATGATCAGAGATAGCAGAAAGAGATTATTTAGGTTAAATGTAAAATTTG
Found at i:5407027 original size:17 final size:17
Alignment explanation
Indices: 5406995--5407027 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5406985 TTAAAAAAAG
5406995 AAAATATTGAAAAATTA
1 AAAATATTGAAAAATTA
5407012 AAAATATTGAAAAATT
1 AAAATATTGAAAAATT
5407028 TGTTTTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (17 bp):
AAAATATTGAAAAATTA
Found at i:5411931 original size:5 final size:5
Alignment explanation
Indices: 5411921--5411957 Score: 56
Period size: 5 Copynumber: 7.0 Consensus size: 5
5411911 CGTTTGTCAC
5411921 CTTTT CTTTT CTTTT CTTTT CTTGTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT C-T-TTT CTTTT CTTTT
5411958 AATATAGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 24 0.80
6 2 0.07
7 4 0.13
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (5 bp):
CTTTT
Found at i:5421463 original size:27 final size:26
Alignment explanation
Indices: 5421433--5421485 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
5421423 GGGCAATAGT
5421433 GTTTATGTTCAGAATTCTTGACC-TTAA
1 GTTTATG-T-AGAATTCTTGACCATTAA
* *
5421460 GTTTCTGTATAATTCTTGACCATTAA
1 GTTTATGTAGAATTCTTGACCATTAA
5421486 TTCAGAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 12 0.52
26 5 0.22
27 6 0.26
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.45
Consensus pattern (26 bp):
GTTTATGTAGAATTCTTGACCATTAA
Found at i:5423689 original size:2 final size:2
Alignment explanation
Indices: 5423682--5423715 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5423672 TAGCCATTTG
5423682 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
5423716 TGAAGTTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5425167 original size:2 final size:2
Alignment explanation
Indices: 5425162--5425206 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
5425152 CCGTAGCTAG
5425162 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
5425204 AT A
1 AT A
5425207 AAACAGCAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5436991 original size:20 final size:21
Alignment explanation
Indices: 5436966--5437005 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5436956 TTCATAAGTG
*
5436966 AAATAA-CTATTGATATTATT
1 AAATAATCTAATGATATTATT
*
5436986 AAATAATCTAATGGTATTAT
1 AAATAATCTAATGATATTAT
5437006 AAAAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (21 bp):
AAATAATCTAATGATATTATT
Found at i:5437124 original size:25 final size:24
Alignment explanation
Indices: 5437052--5437126 Score: 62
Period size: 25 Copynumber: 2.9 Consensus size: 24
5437042 GCTTCCTAAC
*
5437052 TAAAACAAAT-TATATTTAGAAAAAT
1 TAAAAAAAATCTA-ATTTA-AAAAAT
**
5437077 TTTAAAAAATCTAACTTCCTAAAAAAT
1 TAAAAAAAATCTAA-TT--TAAAAAAT
5437104 TAAAATAAAATCTAATTTAAAAA
1 TAAAA-AAAATCTAATTTAAAAA
5437127 TAGCTATAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
25 14 0.35
26 4 0.10
27 11 0.28
28 11 0.28
ACGTcount: A:0.59, C:0.08, G:0.01, T:0.32
Consensus pattern (24 bp):
TAAAAAAAATCTAATTTAAAAAAT
Found at i:5437600 original size:2 final size:2
Alignment explanation
Indices: 5437595--5437641 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
5437585 AATTCGTGTT
5437595 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5437637 T- TA TA
1 TA TA TA
5437642 GACTAGTATG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5440885 original size:21 final size:21
Alignment explanation
Indices: 5440863--5440909 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
5440853 TTTTTATGAT
5440863 TTTTAAT-AATTTTTATACAA
1 TTTTAATCAATTTTTATACAA
* *
5440883 TTTTAATCTATTTTTATAAAA
1 TTTTAATCAATTTTTATACAA
*
5440904 TCTTAA
1 TTTTAA
5440910 ATATTATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTAATCAATTTTTATACAA
Found at i:5445031 original size:9 final size:9
Alignment explanation
Indices: 5445019--5445188 Score: 64
Period size: 9 Copynumber: 18.6 Consensus size: 9
5445009 GCTTTATTAA
5445019 TTTTATAAT
1 TTTTATAAT
*
5445028 TTTTATCAT
1 TTTTATAAT
*
5445037 TTATTAGAAT
1 TT-TTATAAT
* *
5445047 TTATTAAAAAA
1 TT-TT-ATAAT
*
5445058 ATTTATAAT
1 TTTTATAAT
* * *
5445067 ATTAAT-TT
1 TTTTATAAT
5445075 TTTTATAAT
1 TTTTATAAT
5445084 TTTTATAAGT
1 TTTTATAA-T
** *
5445094 TCATATCAAA
1 TTTTAT-AAT
*
5445104 TTTCAT-A-
1 TTTTATAAT
5445111 TTTT-TAAT
1 TTTTATAAT
*
5445119 ATTTAATAAT
1 -TTTTATAAT
5445129 TTTTAT-AT
1 TTTTATAAT
5445137 TTGTTGAT-AT
1 TT-TT-ATAAT
*
5445147 TTTTGTAAT
1 TTTTATAAT
* *
5445156 TTTCATTAT
1 TTTTATAAT
5445165 TTTTATAAT
1 TTTTATAAT
*
5445174 TTGTTATGAT
1 TT-TTATAAT
5445184 TTTTA
1 TTTTA
5445189 ATCAATTTAT
Statistics
Matches: 119, Mismatches: 29, Indels: 26
0.68 0.17 0.15
Matches are distributed among these distances:
6 1 0.01
7 4 0.03
8 11 0.09
9 59 0.50
10 38 0.32
11 6 0.05
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.59
Consensus pattern (9 bp):
TTTTATAAT
Found at i:5447083 original size:44 final size:44
Alignment explanation
Indices: 5447020--5447145 Score: 195
Period size: 44 Copynumber: 2.9 Consensus size: 44
5447010 TATAGATCAC
5447020 CTAACTATTTTTTTTATGGAATTGTTTTTCAAATAAGGAATTAT
1 CTAACTATTTTTTTTATGGAATTGTTTTTCAAATAAGGAATTAT
5447064 CTAACTATTTTTTTTATGGAATTGTTTTTCAAATAAGGAATTAT
1 CTAACTATTTTTTTTATGGAATTGTTTTTCAAATAAGGAATTAT
* * *
5447108 CTAACTA--TTATTTATGGATTTGTGTTTT-AAATATGGAA
1 CTAACTATTTTTTTTATGGAATTGT-TTTTCAAATAAGGAA
5447146 AGAAAAAATT
Statistics
Matches: 78, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
42 23 0.29
43 4 0.05
44 51 0.65
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.49
Consensus pattern (44 bp):
CTAACTATTTTTTTTATGGAATTGTTTTTCAAATAAGGAATTAT
Found at i:5462710 original size:29 final size:29
Alignment explanation
Indices: 5462663--5462734 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 29
5462653 TTTTCTACTA
** *
5462663 TTTTTAAATTTTTTTATAACTTTCT-TTAT
1 TTTTTAAATTTTTAAATAA-TTTCTATCAT
*
5462692 TTTTTACATTTTTAAATAATTTCTATCAT
1 TTTTTAAATTTTTAAATAATTTCTATCAT
* *
5462721 TTTCTATATTTTTA
1 TTTTTAAATTTTTA
5462735 TAAATTTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
28 5 0.14
29 31 0.86
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.65
Consensus pattern (29 bp):
TTTTTAAATTTTTAAATAATTTCTATCAT
Found at i:5462725 original size:38 final size:37
Alignment explanation
Indices: 5462652--5462745 Score: 98
Period size: 38 Copynumber: 2.5 Consensus size: 37
5462642 AGCTTTTGCA
* * * *
5462652 ATTTTCTACTATTTTTAAATTTTTTTATAACTTTCTTT
1 ATTTTTTAC-ATTTTTAAATATTTCTATAACTTTCTAT
* *
5462690 ATTTTTTACATTTTTAAATAATTTCTATCATTTTCTAT
1 ATTTTTTACATTTTTAAAT-ATTTCTATAACTTTCTAT
*
5462728 ATTTTTATAAATTTTTAA
1 ATTTTT-TACATTTTTAA
5462746 TAGTGTTACG
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
37 10 0.21
38 27 0.57
39 10 0.21
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.63
Consensus pattern (37 bp):
ATTTTTTACATTTTTAAATATTTCTATAACTTTCTAT
Found at i:5465560 original size:26 final size:24
Alignment explanation
Indices: 5465531--5465578 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
5465521 TAACTTTTAC
*
5465531 ATTTTAGTAAAAAGTTCAAATTCACA
1 ATTTCAGTAAAAA-TT-AAATTCACA
*
5465557 ATTTCATTAAAAATTAAATTCA
1 ATTTCAGTAAAAATTAAATTCA
5465579 TATGTGTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 2 0.10
26 11 0.55
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.38
Consensus pattern (24 bp):
ATTTCAGTAAAAATTAAATTCACA
Found at i:5476207 original size:21 final size:21
Alignment explanation
Indices: 5476169--5476209 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5476159 TTTTCAATTT
* *
5476169 TGTCAAACTTGTATTTATTAA
1 TGTCAAAATTGTAATTATTAA
*
5476190 TGTCAAAATTTTAATTATTA
1 TGTCAAAATTGTAATTATTA
5476210 GTACTATACC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (21 bp):
TGTCAAAATTGTAATTATTAA
Found at i:5483356 original size:32 final size:33
Alignment explanation
Indices: 5483294--5483365 Score: 78
Period size: 32 Copynumber: 2.2 Consensus size: 33
5483284 TTATAAACTT
* *
5483294 ATAAATTGATTATTTAAATTTAGTAGCTCA-TG
1 ATAAATTAATTATTTAAATTTAGTAACTCATTG
5483326 ATAAATTAATTAATTT-AATTT-GATAACTCATTG
1 ATAAATTAATT-ATTTAAATTTAG-TAACTCATTG
*
5483359 ATTAATT
1 ATAAATT
5483366 TAACTCGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 1 0.03
32 21 0.62
33 12 0.35
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (33 bp):
ATAAATTAATTATTTAAATTTAGTAACTCATTG
Found at i:5502995 original size:24 final size:24
Alignment explanation
Indices: 5502975--5503021 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
5502965 CAGTTAAATT
5502975 CTATTTATTTGTTTCAATTAAACC
1 CTATTTATTTGTTTCAATTAAACC
* *
5502999 CTATTTATTTGTTTGAGTTAAAC
1 CTATTTATTTGTTTCAATTAAAC
5503022 TCTTAGTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.51
Consensus pattern (24 bp):
CTATTTATTTGTTTCAATTAAACC
Found at i:5507224 original size:3 final size:3
Alignment explanation
Indices: 5507218--5507262 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
5507208 TAAGGAAAAT
5507218 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A-A AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
5507263 CCATTTTCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:5507795 original size:11 final size:11
Alignment explanation
Indices: 5507779--5507804 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5507769 TGGTTATTGT
5507779 AAAATATTAAA
1 AAAATATTAAA
5507790 AAAATATTAAA
1 AAAATATTAAA
5507801 AAAA
1 AAAA
5507805 AAAAGAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAATATTAAA
Found at i:5510576 original size:29 final size:30
Alignment explanation
Indices: 5510505--5510569 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
5510495 GTAAATGATT
5510505 TTAAAATTATTTTTTAAAAATATAAAATTA
1 TTAAAATTATTTTTTAAAAATATAAAATTA
* *
5510535 TTAAAATTGTTTTTT-GAAATGATAAAATTA
1 TTAAAATTATTTTTTAAAAAT-ATAAAATTA
5510565 TTAAA
1 TTAAA
5510570 TAATTTTGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (30 bp):
TTAAAATTATTTTTTAAAAATATAAAATTA
Found at i:5511817 original size:9 final size:9
Alignment explanation
Indices: 5511801--5511839 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
5511791 GGGTTAATTG
5511801 TGTTTTAAT
1 TGTTTTAAT
*
5511810 TTTTTTAAT
1 TGTTTTAAT
5511819 TGTTTTAAT
1 TGTTTTAAT
**
5511828 TGCATTAAT
1 TGTTTTAAT
5511837 TGT
1 TGT
5511840 AGGTCCCAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.23, C:0.03, G:0.10, T:0.64
Consensus pattern (9 bp):
TGTTTTAAT
Found at i:5511901 original size:19 final size:18
Alignment explanation
Indices: 5511855--5511906 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
5511845 CCAAAATTTT
5511855 TTTAAATATATATTTTTTAA
1 TTTAAAT-TA-ATTTTTTAA
*
5511875 TTTTAATTAATTTTTTAA
1 TTTAAATTAATTTTTTAA
*
5511893 GTTTAAATTCATTT
1 -TTTAAATTAATTT
5511907 GCTGATGTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 9 0.32
19 13 0.46
20 6 0.21
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTAAATTAATTTTTTAA
Found at i:5512638 original size:12 final size:12
Alignment explanation
Indices: 5512596--5512639 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
5512586 ACTCAATTCC
*
5512596 ATTTTTCTTATT
1 ATTTTTATTATT
5512608 ATTTTTATTTATT
1 ATTTTTA-TTATT
*
5512621 -TATTTATTATT
1 ATTTTTATTATT
5512632 ATTTTTAT
1 ATTTTTAT
5512640 GAATATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 5 0.19
12 17 0.63
13 5 0.19
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (12 bp):
ATTTTTATTATT
Found at i:5512712 original size:67 final size:69
Alignment explanation
Indices: 5512603--5512767 Score: 239
Period size: 67 Copynumber: 2.4 Consensus size: 69
5512593 TCCATTTTTC
* *
5512603 TTATTATTTTTATTTATTTATTTATTATTATTTTTATGAATATAAATAAAT-A-TAAAATAATAT
1 TTATT-TTATTATTTATTTATTTATTATTATTTGTATGAATATAAATAAATAAGTAAAATAATAT
5512666 TAATT
65 TAATT
5512671 TTATTTTATTATTTATTTATTTATTTATTA-TTGTATGAATATAAATAAATAAATGTAAAATAAT
1 TTATTTTATTATTTATTTATTTA-TTATTATTTGTATGAATATAAATAAAT-AA-GTAAAATAAT
5512735 ATTAATT
63 ATTAATT
*
5512742 TTGTTTTATTATTTATTTA-TTATTAT
1 TTATTTTATTATTTATTTATTTATTAT
5512768 AAATAAATAA
Statistics
Matches: 89, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
67 36 0.40
68 11 0.12
69 5 0.06
70 3 0.03
71 34 0.38
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (69 bp):
TTATTTTATTATTTATTTATTTATTATTATTTGTATGAATATAAATAAATAAGTAAAATAATATT
AATT
Found at i:5519242 original size:24 final size:23
Alignment explanation
Indices: 5519207--5519272 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 23
5519197 TTGAGAAATA
*
5519207 ATTT-TTTAATTAAATTCTGTTT
1 ATTTGTTTAATTAAACTCTGTTT
5519229 ATTTGTTTCAATTAAACTCTGTTT
1 ATTTGTTT-AATTAAACTCTGTTT
*
5519253 ATTTGTTTGAGTTAAACTCT
1 ATTTGTTT-AATTAAACTCT
5519273 TGTTAGTCTA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
22 4 0.10
23 3 0.08
24 32 0.82
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.56
Consensus pattern (23 bp):
ATTTGTTTAATTAAACTCTGTTT
Found at i:5520288 original size:30 final size:30
Alignment explanation
Indices: 5520234--5520478 Score: 243
Period size: 30 Copynumber: 8.2 Consensus size: 30
5520224 AATTTTAAAG
* * *
5520234 AAGTTCGAGGGTCGAAAATATGATTTTGGAA
1 AAGTTTGAGGGTC-AAAATGTAATTTTGGAA
* * * **
5520265 AAGTTCGAGGGTTAAAATGTGATTTTAAAA
1 AAGTTTGAGGGTCAAAATGTAATTTTGGAA
*
5520295 AAATTTGAGGGGTCAAAATGTAATTTT-GAA
1 AAGTTTGA-GGGTCAAAATGTAATTTTGGAA
* * *
5520325 AAGTTTG-GAGGTTAAAATATGATTTTGGAA
1 AAGTTTGAG-GGTCAAAATGTAATTTTGGAA
*
5520355 AAGTTTG-GGATCAAAATGTAATTTTGGAA
1 AAGTTTGAGGGTCAAAATGTAATTTTGGAA
5520384 AAGTTT-AGGGGTCAAAATGTAATTTTGGAA
1 AAGTTTGA-GGGTCAAAATGTAATTTTGGAA
*
5520414 AAGTTTG-GGGTCATAATGTAATTTT-GAA
1 AAGTTTGAGGGTCAAAATGTAATTTTGGAA
* *
5520442 AA-TTTTAGGGGTTAAAATGTAATTTTGGAA
1 AAGTTTGA-GGGTCAAAATGTAATTTTGGAA
*
5520472 AATTTTG
1 AAGTTTG
5520479 GAGACCTTCA
Statistics
Matches: 181, Mismatches: 23, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
27 3 0.02
28 6 0.03
29 70 0.39
30 71 0.39
31 31 0.17
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.36
Consensus pattern (30 bp):
AAGTTTGAGGGTCAAAATGTAATTTTGGAA
Found at i:5520342 original size:29 final size:29
Alignment explanation
Indices: 5520242--5520479 Score: 255
Period size: 29 Copynumber: 8.0 Consensus size: 29
5520232 AGAAGTTCGA
* * *
5520242 GGGTCGAAAATATGATTTTGGAAAAGTTCG
1 GGGTC-AAAATGTAATTTTGGAAAAGTTTG
* * ** *
5520272 AGGGTTAAAATGTGATTTTAAAAAAATTTGAG
1 -GGGTCAAAATGTAATTTTGGAAAAGTTT--G
5520304 GGGTCAAAATGTAATTTT-GAAAAGTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTG
* * *
5520332 GAGGTTAAAATATGATTTTGGAAAAGTTTG
1 G-GGTCAAAATGTAATTTTGGAAAAGTTTG
*
5520362 GGATCAAAATGTAATTTTGGAAAAGTTTAG
1 GGGTCAAAATGTAATTTTGGAAAAGTTT-G
5520392 GGGTCAAAATGTAATTTTGGAAAAGTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTG
* *
5520421 GGGTCATAATGTAATTTT-GAAAATTTTAG
1 GGGTCAAAATGTAATTTTGGAAAAGTTT-G
* *
5520450 GGGTTAAAATGTAATTTTGGAAAATTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTG
5520479 G
1 G
5520480 AGACCTTCAG
Statistics
Matches: 178, Mismatches: 22, Indels: 16
0.82 0.10 0.07
Matches are distributed among these distances:
28 10 0.06
29 74 0.42
30 73 0.41
31 20 0.11
32 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.36
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTGGAAAAGTTTG
Found at i:5521144 original size:11 final size:11
Alignment explanation
Indices: 5521130--5521201 Score: 56
Period size: 11 Copynumber: 6.2 Consensus size: 11
5521120 TAATATTGAT
*
5521130 TTAAATTTTAA
1 TTAAATTTAAA
5521141 TTAAATTTAAA
1 TTAAATTTAAA
**
5521152 TTTAAA-GCAAA
1 -TTAAATTTAAA
5521163 TTTAAATTTAAAAA
1 -TTAAATTT--AAA
5521177 TTTAAATTTAAA
1 -TTAAATTTAAA
*
5521189 ATAAATTTAAA
1 TTAAATTTAAA
5521200 TT
1 TT
5521202 TAACAATGAA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
11 30 0.60
12 8 0.16
14 12 0.24
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:5521215 original size:18 final size:17
Alignment explanation
Indices: 5521128--5521221 Score: 113
Period size: 17 Copynumber: 5.6 Consensus size: 17
5521118 TTTAATATTG
* *
5521128 ATTTAAATTTTAATTAA
1 ATTTAAATTTAAAATAA
**
5521145 ATTTAAATTTAAAGCAA
1 ATTTAAATTTAAAATAA
5521162 ATTTAAATTT--AA-AA
1 ATTTAAATTTAAAATAA
5521176 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
*
5521193 ATTTAAATTTAACAATGA
1 ATTTAAATTTAA-AATAA
5521211 ATTTAAATTTA
1 ATTTAAATTTA
5521222 TTTAAACCCA
Statistics
Matches: 68, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
14 12 0.18
15 1 0.01
16 2 0.03
17 38 0.56
18 15 0.22
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:5521221 original size:6 final size:6
Alignment explanation
Indices: 5521128--5521204 Score: 79
Period size: 6 Copynumber: 13.0 Consensus size: 6
5521118 TTTAATATTG
* **
5521128 ATTTAA ATTTTA A-TTAA ATTTAA ATTTAA A-GCAA ATTTAA ATTTAAAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT--AA
*
5521176 ATTTAA ATTTAA A-ATAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
5521205 CAATGAATTT
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
5 11 0.19
6 41 0.71
8 6 0.10
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (6 bp):
ATTTAA
Found at i:5523170 original size:25 final size:24
Alignment explanation
Indices: 5523120--5523166 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
5523110 TCTGTTTATT
5523120 TTTATTTGTTTCAATTAAACTCTG
1 TTTATTTGTTTCAATTAAACTCTG
* *
5523144 TTTATTTGTTTGAATTTAACTCT
1 TTTATTTGTTTCAATTAAACTCT
5523167 TGTTAGTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.11, G:0.09, T:0.57
Consensus pattern (24 bp):
TTTATTTGTTTCAATTAAACTCTG
Found at i:5525886 original size:31 final size:33
Alignment explanation
Indices: 5525829--5525889 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
5525819 CATATATTTT
*
5525829 TATTGTATATTTATTTTTTTATGAATTTTTCCA
1 TATTGTATATATATTTTTTTATGAATTTTTCCA
*
5525862 TATTTTATATATA-TTTTTTA-GAATTTTT
1 TATTGTATATATATTTTTTTATGAATTTTT
5525890 AGATATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 8 0.31
32 7 0.27
33 11 0.42
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (33 bp):
TATTGTATATATATTTTTTTATGAATTTTTCCA
Found at i:5540379 original size:16 final size:16
Alignment explanation
Indices: 5540358--5540389 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5540348 TTGATTTACT
5540358 TTCAAGAGCCTAACCC
1 TTCAAGAGCCTAACCC
5540374 TTCAAGAGCCTAACCC
1 TTCAAGAGCCTAACCC
5540390 AATGTTGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.38, G:0.12, T:0.19
Consensus pattern (16 bp):
TTCAAGAGCCTAACCC
Found at i:5544567 original size:2 final size:2
Alignment explanation
Indices: 5544560--5544584 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5544550 CACACCATAA
5544560 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5544585 CCAATTAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5548570 original size:28 final size:26
Alignment explanation
Indices: 5548537--5548598 Score: 83
Period size: 25 Copynumber: 2.4 Consensus size: 26
5548527 TAAAAATATT
*
5548537 TTATATGATTTTTTTAAATATAAATGA
1 TTATAT-ATTTTTTTAAATATAAATAA
*
5548564 TTA-ATATTTTTTTAAATGTAAATAA
1 TTATATATTTTTTTAAATATAAATAA
5548589 TTA-ATATTTT
1 TTATATATTTT
5548599 GACAATTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 28 0.85
26 2 0.06
27 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (26 bp):
TTATATATTTTTTTAAATATAAATAA
Found at i:5548573 original size:24 final size:25
Alignment explanation
Indices: 5548544--5548598 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
5548534 ATTTTATATG
*
5548544 ATTTTTTTAAATATAAATGATTAAT
1 ATTTTTTTAAATATAAATAATTAAT
*
5548569 ATTTTTTTAAATGTAAATAATTAAT
1 ATTTTTTTAAATATAAATAATTAAT
5548594 ATTTT
1 ATTTT
5548599 GACAATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (25 bp):
ATTTTTTTAAATATAAATAATTAAT
Found at i:5549234 original size:28 final size:29
Alignment explanation
Indices: 5549172--5549234 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
5549162 CAAAATTACA
* *
5549172 TTTTATTTCTCTTAAAATGATAAATTTTT
1 TTTTAATTCTCTTAAAATGATAAATTTAT
*
5549201 TATTTAATTCT-TTAAAATTAT-AATTTAAT
1 T-TTTAATTCTCTTAAAATGATAAATTT-AT
5549230 TTTTA
1 TTTTA
5549235 TTCCCTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
28 9 0.31
29 12 0.41
30 8 0.28
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.59
Consensus pattern (29 bp):
TTTTAATTCTCTTAAAATGATAAATTTAT
Found at i:5554684 original size:19 final size:20
Alignment explanation
Indices: 5554660--5554697 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5554650 TACTAAATTG
5554660 ATATTTAAA-AAAAATTATA
1 ATATTTAAATAAAAATTATA
*
5554679 ATATTTAAATTAAAATTAT
1 ATATTTAAATAAAAATTAT
5554698 TAATTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATATTTAAATAAAAATTATA
Found at i:5557793 original size:20 final size:20
Alignment explanation
Indices: 5557768--5557855 Score: 83
Period size: 20 Copynumber: 4.4 Consensus size: 20
5557758 AATGAAGAAG
*
5557768 TGCCCCTGTTTGCACTTCGA
1 TGCCCCTGTATGCACTTCGA
* *
5557788 TGCCCCTACT-TGCACTTCGG
1 TGCCCCT-GTATGCACTTCGA
*
5557808 TGGCCCTGTATGCACACTT-G-
1 TGCCCCTGTATG--CACTTCGA
*
5557828 TGCCCCTGTATGCACTCCGA
1 TGCCCCTGTATGCACTTCGA
5557848 TGCCCCTG
1 TGCCCCTG
5557856 ATGGTATAGT
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
18 4 0.07
19 2 0.04
20 43 0.77
21 2 0.04
22 5 0.09
ACGTcount: A:0.11, C:0.38, G:0.22, T:0.30
Consensus pattern (20 bp):
TGCCCCTGTATGCACTTCGA
Found at i:5560190 original size:18 final size:18
Alignment explanation
Indices: 5560164--5560200 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5560154 ACCATTTTAT
* *
5560164 TCATTATTTTGAAAGATG
1 TCATAATTTTAAAAGATG
5560182 TCATAATTTTAAAAGATG
1 TCATAATTTTAAAAGATG
5560200 T
1 T
5560201 TTATTACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43
Consensus pattern (18 bp):
TCATAATTTTAAAAGATG
Found at i:5562688 original size:22 final size:20
Alignment explanation
Indices: 5562663--5562702 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
5562653 ATAAAAAACC
5562663 ATAAAATTCTTAAAAGTTTTGA
1 ATAAAATTC-TAAAA-TTTTGA
5562685 ATAAAATTCTAAAATTTT
1 ATAAAATTCTAAAATTTT
5562703 CTAAAAACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 5 0.28
22 9 0.50
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (20 bp):
ATAAAATTCTAAAATTTTGA
Found at i:5562852 original size:10 final size:10
Alignment explanation
Indices: 5562839--5562877 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
5562829 TTTTTATGGG
5562839 ATTTTTAATA
1 ATTTTTAATA
*
5562849 ATTTTTAAAA
1 ATTTTTAATA
5562859 ATTTTTAAATA
1 ATTTTT-AATA
5562870 ACTTTTTA
1 A-TTTTTA
5562878 TTCTTTTGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 15 0.60
11 5 0.20
12 5 0.20
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:5572013 original size:2 final size:2
Alignment explanation
Indices: 5572006--5572037 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5571996 CAAAAATTAA
5572006 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5572038 ATATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5572042 original size:2 final size:2
Alignment explanation
Indices: 5572037--5572099 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
5572027 TCTCTCTCTC
5572037 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5572079 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
5572100 TACTAGTTAC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5578331 original size:212 final size:212
Alignment explanation
Indices: 5577964--5578389 Score: 789
Period size: 212 Copynumber: 2.0 Consensus size: 212
5577954 ACAAAAGAAA
*
5577964 GGTAAACTCTTAACAGCAACGCGATTAGCGCGACTCAAACCATGATTACATTTGAGACAATGAAC
1 GGTAAACTCTTAACAGCAACACGATTAGCGCGACTCAAACCATGATTACATTTGAGACAATGAAC
*
5578029 ATTCTAACCATCAGGCTAACACACAAGTTTCAACCTCAAAAACTATTTTGATCAATCCTTTGACA
66 ATTCTAACCATCAAGCTAACACACAAGTTTCAACCTCAAAAACTATTTTGATCAATCCTTTGACA
5578094 AAAATAAGATAAAAACAAATTTTTGGCAAAGGACACCGAAACTAAACCGAGAAAAGCATCAATCA
131 AAAATAAGATAAAAACAAATTTTTGGCAAAGGACACCGAAACTAAACCGAGAAAAGCATCAATCA
5578159 CAAATAGAAAGGCGAAT
196 CAAATAGAAAGGCGAAT
*
5578176 GGTAAACTCTTAACAGCAACACGATTAGCGCGACTCAAATCATGATTACATTTGAGACAATGAAC
1 GGTAAACTCTTAACAGCAACACGATTAGCGCGACTCAAACCATGATTACATTTGAGACAATGAAC
*
5578241 ATTCTAACCATCAAGCTAACACACAAGTTTCAACCTCAAATACTATTTTGATCAATCCTTTGACA
66 ATTCTAACCATCAAGCTAACACACAAGTTTCAACCTCAAAAACTATTTTGATCAATCCTTTGACA
* *
5578306 AAAATAAGATAAAAACAATTTTTTGGCAAAGGACACCGAAACTAATCCGAGAAAAGCATCAATCA
131 AAAATAAGATAAAAACAAATTTTTGGCAAAGGACACCGAAACTAAACCGAGAAAAGCATCAATCA
*
5578371 CAAATAGAAAGGTGAAT
196 CAAATAGAAAGGCGAAT
5578388 GG
1 GG
5578390 GCTTTGGGAG
Statistics
Matches: 207, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
212 207 1.00
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.22
Consensus pattern (212 bp):
GGTAAACTCTTAACAGCAACACGATTAGCGCGACTCAAACCATGATTACATTTGAGACAATGAAC
ATTCTAACCATCAAGCTAACACACAAGTTTCAACCTCAAAAACTATTTTGATCAATCCTTTGACA
AAAATAAGATAAAAACAAATTTTTGGCAAAGGACACCGAAACTAAACCGAGAAAAGCATCAATCA
CAAATAGAAAGGCGAAT
Found at i:5594140 original size:28 final size:30
Alignment explanation
Indices: 5594095--5594155 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 30
5594085 CATATTAATA
*
5594095 TATATATTTTTTATAAATTAATA-CATAAAT
1 TATATATTTTTTACAAATTAATACCA-AAAT
*
5594125 TATATA-TTTTT-CAAATTGATACCAAAAT
1 TATATATTTTTTACAAATTAATACCAAAAT
5594153 TAT
1 TAT
5594156 CTCTCGTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 15 0.54
29 7 0.25
30 6 0.21
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.48
Consensus pattern (30 bp):
TATATATTTTTTACAAATTAATACCAAAAT
Found at i:5597198 original size:3 final size:3
Alignment explanation
Indices: 5597192--5597227 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
5597182 CTTCTACTTC
5597192 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
5597228 GTCACCTAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:5603050 original size:14 final size:14
Alignment explanation
Indices: 5603031--5603083 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
5603021 TACAATATCC
5603031 AAATAATAACAACA
1 AAATAATAACAACA
5603045 AAATAATAACAACA
1 AAATAATAACAACA
* *
5603059 TAATAATGA-AACA
1 AAATAATAACAACA
5603072 ACAATAA-AACAA
1 A-AATAATAACAA
5603084 TGAAAAAACA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 5 0.15
14 28 0.85
ACGTcount: A:0.70, C:0.13, G:0.02, T:0.15
Consensus pattern (14 bp):
AAATAATAACAACA
Found at i:5618209 original size:17 final size:18
Alignment explanation
Indices: 5618166--5618211 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
5618156 ATAACTTAAA
*
5618166 AAATAAAACAACATATATC
1 AAATAAAA-AACATATAGC
5618185 ATAA-AAAAAACAT-TAGC
1 A-AATAAAAAACATATAGC
5618202 AAATAAAAAA
1 AAATAAAAAA
5618212 ACGTAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
16 2 0.08
17 10 0.42
18 5 0.21
19 5 0.21
20 2 0.08
ACGTcount: A:0.70, C:0.11, G:0.02, T:0.17
Consensus pattern (18 bp):
AAATAAAAAACATATAGC
Found at i:5618209 original size:18 final size:19
Alignment explanation
Indices: 5618166--5618213 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
5618156 ATAACTTAAA
* *
5618166 AAATAAAACAACATATATC
1 AAATAAAAAAACATATAGC
*
5618185 ATA-AAAAAAACAT-TAGC
1 AAATAAAAAAACATATAGC
5618202 AAATAAAAAAAC
1 AAATAAAAAAAC
5618214 GTAATTTTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 5 0.21
18 17 0.71
19 2 0.08
ACGTcount: A:0.69, C:0.12, G:0.02, T:0.17
Consensus pattern (19 bp):
AAATAAAAAAACATATAGC
Found at i:5618378 original size:3 final size:3
Alignment explanation
Indices: 5618370--5618415 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
5618360 TAATTTTGCA
5618370 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5618416 GGTGAGTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5618787 original size:30 final size:31
Alignment explanation
Indices: 5618742--5618806 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
5618732 TTTTTTAATT
* *
5618742 AAATTTGACTTTCAACC-TTAAAAAAGATTC
1 AAATTTAACTATCAACCTTTAAAAAAGATTC
*
5618772 AAATTTAACTATCAACCTTTTGAAAAAGATTC
1 AAATTTAACTATCAACC-TTTAAAAAAGATTC
5618804 AAA
1 AAA
5618807 ATATTTGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 15 0.50
32 15 0.50
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.32
Consensus pattern (31 bp):
AAATTTAACTATCAACCTTTAAAAAAGATTC
Found at i:5619507 original size:15 final size:16
Alignment explanation
Indices: 5619487--5619520 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5619477 TTAAATCAAT
5619487 AAAT-AAAAATAAATA
1 AAATAAAAAATAAATA
*
5619502 AAATAAAAAATAACTA
1 AAATAAAAAATAAATA
5619518 AAA
1 AAA
5619521 ATATAGTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (16 bp):
AAATAAAAAATAAATA
Found at i:5620036 original size:92 final size:92
Alignment explanation
Indices: 5619863--5620038 Score: 230
Period size: 92 Copynumber: 1.9 Consensus size: 92
5619853 TGTTAACTCT
*
5619863 ATGTACCATAATAAAACACATAATGATAGTTCAAGTACTACATTAGATATTTTCAAAGTACAAAT
1 ATGTACCATAATAAAACACATAATGATAGTTCAAGTACTACATTAGACATTTTCAAAGTACAAAT
* **
5619928 ACTACATTGGGTATTTTATGAAAGTGC
66 ACTACATTAGACATTTTATGAAAGTGC
* * * * *
5619955 ATGTACTATAATAAAATATAT-ATAGATAGTTCAAGTATTACA-TAGGACATTTTCAAAGTACAT
1 ATGTACCATAATAAAACACATAAT-GATAGTTCAAGTACTACATTA-GACATTTTCAAAGTACAA
*
5620018 ATACTAGATTAGACATTTTAT
64 ATACTACATTAGACATTTTAT
5620039 AATATCTCTA
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
91 4 0.06
92 68 0.94
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (92 bp):
ATGTACCATAATAAAACACATAATGATAGTTCAAGTACTACATTAGACATTTTCAAAGTACAAAT
ACTACATTAGACATTTTATGAAAGTGC
Found at i:5624407 original size:34 final size:34
Alignment explanation
Indices: 5624364--5624433 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
5624354 ATGAGCATGG
5624364 CATCACCTAGATTGAGTGAAAGAAAAACATATGA
1 CATCACCTAGATTGAGTGAAAGAAAAACATATGA
5624398 CATCACCTAGATTGAGTGAAAGAAAAACATATGA
1 CATCACCTAGATTGAGTGAAAGAAAAACATATGA
5624432 CA
1 CA
5624434 GCAGGAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.47, C:0.16, G:0.17, T:0.20
Consensus pattern (34 bp):
CATCACCTAGATTGAGTGAAAGAAAAACATATGA
Found at i:5624821 original size:3 final size:3
Alignment explanation
Indices: 5624813--5624845 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5624803 CATCACATAT
5624813 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5624846 TGTTATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5628002 original size:16 final size:16
Alignment explanation
Indices: 5627981--5628031 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
5627971 ATTTGATTAA
5627981 TTTTAATATTTATATT
1 TTTTAATATTTATATT
**
5627997 TTTTAA-ATTTATAAA
1 TTTTAATATTTATATT
* *
5628012 TTTTAATCTCTATATT
1 TTTTAATATTTATATT
5628028 TTTT
1 TTTT
5628032 TCGATTTTTG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
15 13 0.46
16 15 0.54
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTAATATTTATATT
Found at i:5628014 original size:31 final size:32
Alignment explanation
Indices: 5627970--5628031 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
5627960 CATGCATCAT
* *
5627970 AATTTGATTAATTTTAATATTTATATTTTTTA
1 AATTTGATAAATTTTAATATCTATATTTTTTA
*
5628002 AATTT-ATAAATTTTAATCTCTATATTTTTT
1 AATTTGATAAATTTTAATATCTATATTTTTT
5628032 TCGATTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (32 bp):
AATTTGATAAATTTTAATATCTATATTTTTTA
Found at i:5628350 original size:16 final size:15
Alignment explanation
Indices: 5628331--5628364 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
5628321 CTTAATTAAT
5628331 AAATTTAAAAATTCTA
1 AAATTTAAAAATT-TA
*
5628347 AAATTTCAAAATTTA
1 AAATTTAAAAATTTA
5628362 AAA
1 AAA
5628365 AGTGATGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (15 bp):
AAATTTAAAAATTTA
Found at i:5631283 original size:44 final size:44
Alignment explanation
Indices: 5631168--5631290 Score: 192
Period size: 44 Copynumber: 2.8 Consensus size: 44
5631158 GTAAAACAAA
* *
5631168 TAATATTAAAATAACCTACACTAATCAAAGTTTATGTGAAAAAC
1 TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGAAAAAC
* * *
5631212 TAATATTAAAATAATCTACACTAATCAGAGTTTAAGTGGAAAAT
1 TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGAAAAAC
*
5631256 TAATATTAAAATAACCTACACTAATCAGGGTTTAA
1 TAATATTAAAATAACCTACACTAATCAGAGTTTAA
5631291 ATGAGAAATT
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 72 1.00
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGAAAAAC
Found at i:5634346 original size:27 final size:28
Alignment explanation
Indices: 5634302--5634372 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 28
5634292 TGACTTTTGG
5634302 AAATTT-GAGGGCAAAATGGTAATTTT-
1 AAATTTCGAGGGCAAAATGGTAATTTTA
** *
5634328 GGATTTCGAGGGCAAAATGGTGATTTTA
1 AAATTTCGAGGGCAAAATGGTAATTTTA
*
5634356 AAAGTTCGAGGGCAAAA
1 AAATTTCGAGGGCAAAA
5634373 ATATAATTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
26 4 0.11
27 19 0.51
28 14 0.38
ACGTcount: A:0.37, C:0.07, G:0.28, T:0.28
Consensus pattern (28 bp):
AAATTTCGAGGGCAAAATGGTAATTTTA
Found at i:5634381 original size:28 final size:29
Alignment explanation
Indices: 5634308--5634537 Score: 109
Period size: 30 Copynumber: 7.9 Consensus size: 29
5634298 TTGGAAATTT
* *
5634308 GAGGGC-AAAATGGTAATTTTG--GATTTC
1 GAGGGCAAAAAT-GTAATTTTGAAAAGTTC
*
5634335 GAGGGC-AAAATGGTGATTTT-AAAAGTTC
1 GAGGGCAAAAAT-GTAATTTTGAAAAGTTC
* *
5634363 GAGGGCAAAAATATAATTTTTGAGAAGTTC
1 GAGGGCAAAAATGTAA-TTTTGAAAAGTTC
* * *
5634393 GAGGACAAAAATGTAATTTTTGAGAAGTTT
1 GAGGGCAAAAATGTAA-TTTTGAAAAGTTC
* * * **
5634423 TAGGGTAAGAATGTGAATTTTGTGAAGTT-
1 GAGGGCAAAAATGT-AATTTTGAAAAGTTC
* * * *
5634452 TAGGGGTAAAAATGTAAATTTT-ATGAAGTTT
1 GA-GGGCAAAAATGT-AATTTTGA-AAAGTTC
** *
5634483 GAGGGTTAAAATGTAATTTTTGGAAAGTGT-
1 GAGGGCAAAAATGTAA-TTTTGAAAAGT-TC
*
5634513 AAGGGTC-AAAATGTAATTTTGAAAA
1 GAGGG-CAAAAATGTAATTTTGAAAA
5634538 AGTTTTTGGT
Statistics
Matches: 166, Mismatches: 24, Indels: 24
0.78 0.11 0.11
Matches are distributed among these distances:
27 19 0.11
28 12 0.07
29 21 0.13
30 110 0.66
31 4 0.02
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.33
Consensus pattern (29 bp):
GAGGGCAAAAATGTAATTTTGAAAAGTTC
Found at i:5634393 original size:30 final size:30
Alignment explanation
Indices: 5634357--5634421 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
5634347 GTGATTTTAA
*
5634357 AAGTTCGAGGGCAAAAATATAATTTTTGAG
1 AAGTTCGAGGACAAAAATATAATTTTTGAG
*
5634387 AAGTTCGAGGACAAAAATGTAATTTTTGAG
1 AAGTTCGAGGACAAAAATATAATTTTTGAG
5634417 AAGTT
1 AAGTT
5634422 TTAGGGTAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.31
Consensus pattern (30 bp):
AAGTTCGAGGACAAAAATATAATTTTTGAG
Found at i:5634436 original size:30 final size:29
Alignment explanation
Indices: 5634370--5634570 Score: 135
Period size: 30 Copynumber: 6.8 Consensus size: 29
5634360 TTCGAGGGCA
* ** **
5634370 AAAATATAATTTTTGAGAAGTTCGAGGACA
1 AAAATGTAATTTTTGAGAAGTTTTAGG-GT
5634400 AAAATGTAATTTTTGAGAAGTTTTAGGGT
1 AAAATGTAATTTTTGAGAAGTTTTAGGGT
*
5634429 AAGAATGTGAA-TTTTGTGAAG-TTTAGGGGT
1 AA-AATGT-AATTTTTGAGAAGTTTTA-GGGT
* *
5634459 AAAAATGTAAATTTT-ATGAAGTTTGAGGGTT
1 -AAAATGTAATTTTTGA-GAAGTTTTAGGG-T
* *
5634490 AAAATGTAATTTTTG-GAAAGTGTAAGGGT
1 AAAATGTAATTTTTGAG-AAGTTTTAGGGT
* * *
5634519 CAAAATGTAA-TTTTGAAAAAGTTTTTGGTT
1 -AAAATGTAATTTTTG-AGAAGTTTTAGGGT
* *
5634549 AAAATATAATTTTAGA-AAGTTT
1 AAAATGTAATTTTTGAGAAGTTT
5634571 AAGGATCAAA
Statistics
Matches: 139, Mismatches: 18, Indels: 30
0.74 0.10 0.16
Matches are distributed among these distances:
28 6 0.04
29 24 0.17
30 101 0.73
31 8 0.06
ACGTcount: A:0.38, C:0.01, G:0.22, T:0.38
Consensus pattern (29 bp):
AAAATGTAATTTTTGAGAAGTTTTAGGGT
Found at i:5634480 original size:90 final size:89
Alignment explanation
Indices: 5634369--5634533 Score: 201
Period size: 90 Copynumber: 1.8 Consensus size: 89
5634359 GTTCGAGGGC
* * *
5634369 AAAAATATAATTTTTGAGAAGTTCGAGGACAAAAATGTAATTTTT-GAGAAGTTTTAGGGT-AAG
1 AAAAATATAAATTTTGAGAAGTTCGAGGACAAAAATGTAATTTTTGGA-AAGTGTAAGGGTCAA-
5634432 AATGTGAATTTTGTGAAGTTTAGGGGT
64 AATGT-AATTTTGTGAAGTTTAGGGGT
* * ***
5634459 AAAAATGTAAATTTT-ATGAAGTTTGAGGGTTAAAATGTAATTTTTGGAAAGTGTAAGGGTCAAA
1 AAAAATATAAATTTTGA-GAAGTTCGAGGACAAAAATGTAATTTTTGGAAAGTGTAAGGGTCAAA
5634523 ATGTAATTTTG
65 ATGTAATTTTG
5634534 AAAAAGTTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
89 8 0.12
90 52 0.81
91 4 0.06
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (89 bp):
AAAAATATAAATTTTGAGAAGTTCGAGGACAAAAATGTAATTTTTGGAAAGTGTAAGGGTCAAAA
TGTAATTTTGTGAAGTTTAGGGGT
Found at i:5634541 original size:60 final size:58
Alignment explanation
Indices: 5634400--5634599 Score: 174
Period size: 60 Copynumber: 3.4 Consensus size: 58
5634390 TTCGAGGACA
* * *
5634400 AAAATGTAATTTTTG-AGAAGTTTTAGGG-TAAGAATGTGAATTTTGTG-AAGTTTAGGGGTA
1 AAAATGTAA-TTTTGAAAAAG-TTTAGGGTTAA-AATGT-AATTTTG-GAAAGTTTAAGGGTC
** *
5634460 AAAATGTAAATTTT-ATGAAGTTTGAGGGTTAAAATGTAATTTTTGGAAAGTGTAAGGGTC
1 AAAATGT-AATTTTGAAAAAGTTT-AGGGTTAAAATGTAA-TTTTGGAAAGTTTAAGGGTC
** * * *
5634520 AAAATGTAATTTTGAAAAAGTTTTTGGTTAAAATATAATTTTAGAAAGTTTAAGGATC
1 AAAATGTAATTTTGAAAAAGTTTAGGGTTAAAATGTAATTTTGGAAAGTTTAAGGGTC
* * *
5634578 AAAATATGATTTTTAAAAAGTT
1 AAAATGTAATTTTGAAAAAGTT
5634600 CAAGGACCTT
Statistics
Matches: 118, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
58 36 0.31
59 24 0.20
60 53 0.45
61 5 0.04
ACGTcount: A:0.39, C:0.01, G:0.21, T:0.39
Consensus pattern (58 bp):
AAAATGTAATTTTGAAAAAGTTTAGGGTTAAAATGTAATTTTGGAAAGTTTAAGGGTC
Found at i:5634581 original size:29 final size:29
Alignment explanation
Indices: 5634468--5634605 Score: 91
Period size: 30 Copynumber: 4.7 Consensus size: 29
5634458 TAAAAATGTA
* * * *
5634468 AATTTTATG-AAGTTTGAGGGTTAAAATGT
1 AATTTTA-GAAAGTTTAAGGATCAAAATAT
* * * *
5634497 AATTTTTGGAAAGTGTAAGGGTCAAAATGT
1 AA-TTTTAGAAAGTTTAAGGATCAAAATAT
* ** *
5634527 AATTTTGAAAAAGTTTTTGG-TTAAAATAT
1 AATTTT-AGAAAGTTTAAGGATCAAAATAT
5634556 AATTTTAGAAAGTTTAAGGATCAAAATAT
1 AATTTTAGAAAGTTTAAGGATCAAAATAT
* * *
5634585 GATTTTTAAAAAGTTCAAGGA
1 -AATTTTAGAAAGTTTAAGGA
5634606 CCTTCTGGAT
Statistics
Matches: 86, Mismatches: 18, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
28 10 0.12
29 28 0.33
30 48 0.56
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.38
Consensus pattern (29 bp):
AATTTTAGAAAGTTTAAGGATCAAAATAT
Found at i:5634590 original size:58 final size:59
Alignment explanation
Indices: 5634486--5634599 Score: 158
Period size: 58 Copynumber: 1.9 Consensus size: 59
5634476 GAAGTTTGAG
* * * *
5634486 GGTTAAAATGTAATTTTTGGAAAGTGTAAGGGTCAAAATGTAATTTTGAAAAAGTTTTT
1 GGTTAAAATATAATTTTTAGAAAGTGTAAGGATCAAAATATAATTTTGAAAAAGTTTTT
* * *
5634545 GGTTAAAATATAA-TTTTAGAAAGTTTAAGGATCAAAATATGATTTTTAAAAAGTT
1 GGTTAAAATATAATTTTTAGAAAGTGTAAGGATCAAAATATAATTTTGAAAAAGTT
5634600 CAAGGACCTT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
58 36 0.75
59 12 0.25
ACGTcount: A:0.41, C:0.02, G:0.18, T:0.39
Consensus pattern (59 bp):
GGTTAAAATATAATTTTTAGAAAGTGTAAGGATCAAAATATAATTTTGAAAAAGTTTTT
Found at i:5635560 original size:14 final size:14
Alignment explanation
Indices: 5635534--5635567 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
5635524 TAATAATGGT
5635534 AATATA-ATAAATA
1 AATATATATAAATA
*
5635547 AATATATATTAATA
1 AATATATATAAATA
5635561 AATATAT
1 AATATAT
5635568 GTATAGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATATATATAAATA
Found at i:5636106 original size:18 final size:18
Alignment explanation
Indices: 5636074--5636108 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5636064 GTTTAGGTGG
*
5636074 GTAATTGGTCATGGGTTT
1 GTAATTGGGCATGGGTTT
*
5636092 GTAATTGGGCTTGGGTT
1 GTAATTGGGCATGGGTT
5636109 ATTGGGTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.06, G:0.37, T:0.43
Consensus pattern (18 bp):
GTAATTGGGCATGGGTTT
Found at i:5636188 original size:17 final size:17
Alignment explanation
Indices: 5636168--5636270 Score: 125
Period size: 17 Copynumber: 6.0 Consensus size: 17
5636158 ATTAAATTTC
*
5636168 AAATTTAAATTCAAAAT
1 AAATTTAAATTTAAAAT
5636185 AAATTTAAATTTAAAAT
1 AAATTTAAATTTAAAAT
* **
5636202 AAATTTAAGCTAAAAAAT
1 AAATTTAA-ATTTAAAAT
* *
5636220 AAGTTTAAATTTTAAAT
1 AAATTTAAATTTAAAAT
*
5636237 AAATTTAAACTTAAAAT
1 AAATTTAAATTTAAAAT
*
5636254 AAATTAAAATTTAAAAT
1 AAATTTAAATTTAAAAT
5636271 TGGGTTCAAT
Statistics
Matches: 71, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
17 58 0.82
18 13 0.18
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (17 bp):
AAATTTAAATTTAAAAT
Found at i:5636201 original size:7 final size:6
Alignment explanation
Indices: 5636159--5636268 Score: 59
Period size: 6 Copynumber: 18.8 Consensus size: 6
5636149 GAACTTTTAA
* * *
5636159 TTAAAT TTCAAAT TTAAAT TCAAA- ATAAAT TTAAAT TTAAA- ATAAAT
1 TTAAAT TT-AAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
** * * * * *
5636206 TTAAGC TAAAAA ATAAGT TTAAATT TTAAA- -TAAAT TTAAAC TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT
* *
5636252 ATAAAT TAAAAT TTAAA
1 TTAAAT TTAAAT TTAAA
5636269 ATTGGGTTCA
Statistics
Matches: 75, Mismatches: 22, Indels: 14
0.68 0.20 0.13
Matches are distributed among these distances:
4 4 0.05
5 11 0.15
6 48 0.64
7 12 0.16
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (6 bp):
TTAAAT
Found at i:5636227 original size:35 final size:34
Alignment explanation
Indices: 5636168--5636270 Score: 134
Period size: 35 Copynumber: 3.0 Consensus size: 34
5636158 ATTAAATTTC
* *
5636168 AAATTTAAATTCAAAATAAATTTAAATTTAAAAT
1 AAATTTAAACTAAAAATAAATTTAAATTTAAAAT
* * *
5636202 AAATTTAAGCTAAAAAATAAGTTTAAATTTTAAAT
1 AAATTTAAACT-AAAAATAAATTTAAATTTAAAAT
* *
5636237 AAATTTAAACTTAAAATAAATTAAAATTTAAAAT
1 AAATTTAAACTAAAAATAAATTTAAATTTAAAAT
5636271 TGGGTTCAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
34 28 0.48
35 30 0.52
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (34 bp):
AAATTTAAACTAAAAATAAATTTAAATTTAAAAT
Found at i:5639847 original size:17 final size:17
Alignment explanation
Indices: 5639821--5639958 Score: 145
Period size: 17 Copynumber: 8.1 Consensus size: 17
5639811 AATCGTTTTA
* *
5639821 AAATTCATTTTAAAATT
1 AAATTTATTTTAAATTT
*
5639838 AAATTTATTTTAAAATT
1 AAATTTATTTTAAATTT
*
5639855 AAATTTATGTTAAATTT
1 AAATTTATTTTAAATTT
5639872 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
* * *
5639889 AGATTTGTTAT-AATTT
1 AAATTTATTTTAAATTT
5639905 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
* *
5639922 AGAA-TTAATGTAAATTTT
1 A-AATTTATTTTAAA-TTT
* *
5639940 AAAATTATTATAAATTT
1 AAATTTATTTTAAATTT
5639957 AA
1 AA
5639959 TAGAGTGTCC
Statistics
Matches: 103, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
16 13 0.13
17 76 0.74
18 14 0.14
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:5639883 original size:11 final size:11
Alignment explanation
Indices: 5639836--5639922 Score: 61
Period size: 11 Copynumber: 7.8 Consensus size: 11
5639826 CATTTTAAAA
*
5639836 TTAAATTTATT
1 TTAAATTTAAT
*
5639847 TTAAAATTAAAT
1 TT-AAATTTAAT
** *
5639859 TTATGTTAAAT
1 TTAAATTTAAT
*
5639870 TTAAATTTATT
1 TTAAATTTAAT
5639881 TTAAATTTAGAT
1 TTAAATTTA-AT
*
5639893 TT--GTTATAAT
1 TTAAATT-TAAT
*
5639903 TTAAATTTATT
1 TTAAATTTAAT
5639914 TTAAATTTA
1 TTAAATTTA
5639923 GAATTAATGT
Statistics
Matches: 59, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
10 6 0.10
11 39 0.66
12 14 0.24
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.56
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:5639927 original size:7 final size:6
Alignment explanation
Indices: 5639829--5639927 Score: 55
Period size: 6 Copynumber: 16.3 Consensus size: 6
5639819 TAAAATTCAT
* * *
5639829 TTTAAA ATTAAA TTT-AT TTTAAA ATTAAA TTT--A TGTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
* * *
5639875 TTT-AT TTTAAA TTTAGATT TGTTATAA TTTAAA TTT-AT TTTAAA TTTAGAA
1 TTTAAA TTTAAA TTTA-A-A T-TTA-AA TTTAAA TTTAAA TTTAAA TTTA-AA
5639926 TT
1 TT
5639928 AATGTAAATT
Statistics
Matches: 70, Mismatches: 13, Indels: 19
0.69 0.13 0.19
Matches are distributed among these distances:
4 2 0.03
5 14 0.20
6 38 0.54
7 10 0.14
8 2 0.03
9 4 0.06
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:5639940 original size:18 final size:18
Alignment explanation
Indices: 5639915--5639956 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
5639905 AAATTTATTT
* *
5639915 TAAA-TTTAGAATTAATG
1 TAAATTTTAAAATTAATA
*
5639932 TAAATTTTAAAATTATTA
1 TAAATTTTAAAATTAATA
5639950 TAAATTT
1 TAAATTT
5639957 AATAGAGTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (18 bp):
TAAATTTTAAAATTAATA
Found at i:5641942 original size:30 final size:29
Alignment explanation
Indices: 5641892--5641953 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
5641882 CAAACAGTCC
*
5641892 AAAAATTACATTTTGACCCCAAAATTTTA
1 AAAAATTACATTTTGACCCCAAAATTCTA
*
5641921 AAAAATTACCATTTT-ACCCCCAAACTTCTA
1 AAAAATTA-CATTTTGA-CCCCAAAATTCTA
5641951 AAA
1 AAA
5641954 TTCTATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 9 0.31
30 20 0.69
ACGTcount: A:0.45, C:0.23, G:0.02, T:0.31
Consensus pattern (29 bp):
AAAAATTACATTTTGACCCCAAAATTCTA
Found at i:5641953 original size:29 final size:29
Alignment explanation
Indices: 5641892--5642114 Score: 108
Period size: 29 Copynumber: 7.7 Consensus size: 29
5641882 CAAACAGTCC
* * *
5641892 AAAAATTA-CATTTTGACCCCAAAATTTT
1 AAAAATTACCATTTTAACCCCAAACTTCT
*
5641920 AAAAAATTACCATTTTACCCCCAAACTTCT
1 -AAAAATTACCATTTTAACCCCAAACTTCT
* * * *
5641950 -AAAATT-CTATTTTTAACCCC-GATTTCACC
1 AAAAATTACCA-TTTTAACCCCAAACTT--CT
* *
5641979 AAAAATTACTATTTTACCCCCAAACTT-T
1 AAAAATTACCATTTTAACCCCAAACTTCT
* * *
5642007 CCAAAATT-CCATTTTAACCCC-GATTTC-
1 -AAAAATTACCATTTTAACCCCAAACTTCT
*
5642034 ACCTAAAATTACCATTTTACCCCCAAACTT-T
1 A---AAAATTACCATTTTAACCCCAAACTTCT
* * * *
5642065 CCAAAATT-CCATTTTTAACCTCGAACCTCT
1 -AAAAATTACCA-TTTTAACCCCAAACTTCT
*
5642095 TAAAATT-CCATTTTAACCCC
1 AAAAATTACCATTTTAACCCC
5642115 GATTTCACAA
Statistics
Matches: 147, Mismatches: 29, Indels: 37
0.69 0.14 0.17
Matches are distributed among these distances:
27 8 0.05
28 38 0.26
29 48 0.33
30 44 0.30
31 9 0.06
ACGTcount: A:0.35, C:0.29, G:0.02, T:0.34
Consensus pattern (29 bp):
AAAAATTACCATTTTAACCCCAAACTTCT
Found at i:5641986 original size:58 final size:59
Alignment explanation
Indices: 5641921--5642084 Score: 278
Period size: 58 Copynumber: 2.8 Consensus size: 59
5641911 CAAAATTTTA
* *
5641921 AAAAATTACCATTTTACCCCCAAAC-TTCTAAAATTCTATTTTTAACCCCGATTTCACC
1 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
*
5641979 AAAAATTACTATTTTACCCCCAAACTTTCCAAAATTCCA-TTTTAACCCCGATTTCACC
1 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
*
5642037 TAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACC
1 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACC
5642085 TCGAACCTCT
Statistics
Matches: 99, Mismatches: 5, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
58 80 0.81
59 19 0.19
ACGTcount: A:0.35, C:0.30, G:0.01, T:0.34
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
Found at i:5641994 original size:30 final size:28
Alignment explanation
Indices: 5641950--5642196 Score: 137
Period size: 29 Copynumber: 8.5 Consensus size: 28
5641940 CCAAACTTCT
*
5641950 AAAATTCTATTTTTAACCCCGATTTCACC
1 AAAATTCCA-TTTTAACCCCGATTTCACC
* * *
5641979 AAAAATTACTATTTTACCCCCAAACTTT--CC
1 -AAAATT-CCATTTTAACCCC-GA-TTTCACC
5642009 AAAATTCCATTTTAACCCCGATTTCACC
1 AAAATTCCATTTTAACCCCGATTTCACC
* *
5642037 TAAAATTACCATTTTACCCCCAAACTTT--CC
1 -AAAATT-CCATTTTAACCCC-GA-TTTCACC
* ** **
5642067 AAAATTCCATTTTTAACCTCGAACCTC-TT
1 AAAATTCCA-TTTTAACCCCG-ATTTCACC
*
5642096 AAAATTCCATTTTAACCCCGATTTCACAA
1 AAAATTCCATTTTAACCCCGATTTCAC-C
*** * *
5642125 AAAATTACCATTTT-ACCCTCGAAGCCTCG
1 AAAATT-CCATTTTAACCC-CGATTTCACC
* *
5642154 AAAATTCCATTTTTAACCTCGATTTTACC
1 AAAATTCCA-TTTTAACCCCGATTTCACC
5642183 AAAATTACCATTTT
1 AAAATT-CCATTTT
5642197 GCCCCCGGGT
Statistics
Matches: 167, Mismatches: 31, Indels: 39
0.70 0.13 0.16
Matches are distributed among these distances:
26 3 0.02
27 4 0.02
28 30 0.18
29 70 0.42
30 49 0.29
31 5 0.03
32 6 0.04
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (28 bp):
AAAATTCCATTTTAACCCCGATTTCACC
Done.