Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 96 of 259
Found at i:31264465 original size:21 final size:23
Alignment explanation
Indices: 31264420--31264466 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
31264410 TCACCTGCAA
* *
31264420 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
31264443 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
31264464 TAA
1 TAA
31264467 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:31277299 original size:15 final size:16
Alignment explanation
Indices: 31277279--31277320 Score: 77
Period size: 15 Copynumber: 2.7 Consensus size: 16
31277269 TAGCTTCTTC
31277279 TTTTTTTTTCACG-AA
1 TTTTTTTTTCACGAAA
31277294 TTTTTTTTTCACGAAA
1 TTTTTTTTTCACGAAA
31277310 TTTTTTTTTCA
1 TTTTTTTTTCA
31277321 ACTTGATATC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.19, C:0.12, G:0.05, T:0.64
Consensus pattern (16 bp):
TTTTTTTTTCACGAAA
Found at i:31277377 original size:12 final size:12
Alignment explanation
Indices: 31277357--31277402 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
31277347 AAAGGAAACC
*
31277357 AATTATTTTTTG
1 AATTTTTTTTTG
31277369 AATTTTTTTTTG
1 AATTTTTTTTTG
*
31277381 AATTTTTTTTTC
1 AATTTTTTTTTG
*
31277393 AAATTTTTTT
1 AATTTTTTTT
31277403 GAAGAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.72
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:31277387 original size:13 final size:13
Alignment explanation
Indices: 31277362--31277402 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
31277352 AAACCAATTA
31277362 TTTTTTGAA-TTT
1 TTTTTTGAATTTT
31277374 TTTTTTGAATTTT
1 TTTTTTGAATTTT
**
31277387 TTTTTCAAATTTT
1 TTTTTTGAATTTT
31277400 TTT
1 TTT
31277403 GAAGAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 9 0.35
13 17 0.65
ACGTcount: A:0.17, C:0.02, G:0.05, T:0.76
Consensus pattern (13 bp):
TTTTTTGAATTTT
Found at i:31279937 original size:21 final size:23
Alignment explanation
Indices: 31279892--31279938 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
31279882 TCACCTGCAA
* *
31279892 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
31279915 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
31279936 TAA
1 TAA
31279939 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:31282093 original size:23 final size:25
Alignment explanation
Indices: 31282062--31282107 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
31282052 TTATCTTTAT
31282062 TTTCTTGC-TGT-TCAATCTTTTAAA
1 TTTCTTGCTTGTGTCAAT-TTTTAAA
31282086 TTTC-TGCTTGTGTCAATTTTTA
1 TTTCTTGCTTGTGTCAATTTTTA
31282108 TTAGCTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 3 0.15
24 12 0.60
25 5 0.25
ACGTcount: A:0.17, C:0.15, G:0.11, T:0.57
Consensus pattern (25 bp):
TTTCTTGCTTGTGTCAATTTTTAAA
Found at i:31292655 original size:10 final size:10
Alignment explanation
Indices: 31292640--31292688 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
31292630 TTGGGTTAAG
31292640 ATTGAGCTGA
1 ATTGAGCTGA
31292650 ATTGAGCTTGA
1 ATTGAGC-TGA
31292661 A-TGAGCTGA
1 ATTGAGCTGA
* *
31292670 CTTGAGCTCA
1 ATTGAGCTGA
*
31292680 AGTGAGCTG
1 ATTGAGCTG
31292689 GAAACGAGCT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 3 0.09
10 25 0.78
11 4 0.12
ACGTcount: A:0.27, C:0.14, G:0.31, T:0.29
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:31294754 original size:13 final size:12
Alignment explanation
Indices: 31294719--31294751 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
31294709 TTGTAGATTC
*
31294719 AAAAAAAAATCG
1 AAAAAAAAATTG
31294731 AAAAAAAAATTG
1 AAAAAAAAATTG
31294743 AAAAAAAAA
1 AAAAAAAAA
31294752 ATTTGCATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.82, C:0.03, G:0.06, T:0.09
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:31304135 original size:30 final size:30
Alignment explanation
Indices: 31304101--31304197 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
31304091 TAAACTAAAA
*
31304101 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
31304131 TGAGCTGAGGCTAAACTCTTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
31304161 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
31304190 ATGAGCTA
1 -TGAGCTA
31304198 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:31306393 original size:12 final size:12
Alignment explanation
Indices: 31306378--31306408 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
31306368 TTCTTTTTGC
31306378 TTTTCAAAGGCT
1 TTTTCAAAGGCT
31306390 TTTTCAAAGGCT
1 TTTTCAAAGGCT
31306402 TTTTCAA
1 TTTTCAA
31306409 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:31309201 original size:30 final size:30
Alignment explanation
Indices: 31309167--31309263 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
31309157 TAAACTAAAA
*
31309167 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
31309197 TGAGCTGAGGCTAAACTCTTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
31309227 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
31309256 ATGAGCTA
1 -TGAGCTA
31309264 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:31311605 original size:11 final size:11
Alignment explanation
Indices: 31311586--31311630 Score: 72
Period size: 11 Copynumber: 4.0 Consensus size: 11
31311576 TAGTAGTTTC
31311586 TTCAAAAAAAA
1 TTCAAAAAAAA
*
31311597 TTGAAAAAAAAA
1 TT-CAAAAAAAA
31311609 TTCAAAAAAAA
1 TTCAAAAAAAA
31311620 TTCAAAAAAAA
1 TTCAAAAAAAA
31311631 ATTGGTTTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 21 0.68
12 10 0.32
ACGTcount: A:0.73, C:0.07, G:0.02, T:0.18
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:31311606 original size:12 final size:12
Alignment explanation
Indices: 31311589--31311634 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
31311579 TAGTTTCTTC
31311589 AAAAAAAATTGA
1 AAAAAAAATTGA
*
31311601 AAAAAAAATT-C
1 AAAAAAAATTGA
*
31311612 AAAAAAAATTCA
1 AAAAAAAATTGA
31311624 AAAAAAAATTG
1 AAAAAAAATTG
31311635 GTTTCCTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
11 10 0.33
12 20 0.67
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.17
Consensus pattern (12 bp):
AAAAAAAATTGA
Found at i:31311616 original size:23 final size:23
Alignment explanation
Indices: 31311586--31311633 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
31311576 TAGTAGTTTC
*
31311586 TTCAAAAAAAATTGAAAAAAAAA
1 TTCAAAAAAAATTCAAAAAAAAA
31311609 TTCAAAAAAAATTCAAAAAAAAA
1 TTCAAAAAAAATTCAAAAAAAAA
31311632 TT
1 TT
31311634 GGTTTCCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.21
Consensus pattern (23 bp):
TTCAAAAAAAATTCAAAAAAAAA
Found at i:31311693 original size:15 final size:15
Alignment explanation
Indices: 31311670--31311709 Score: 71
Period size: 15 Copynumber: 2.6 Consensus size: 15
31311660 GATATCAAGT
31311670 TGAAAAAAAAATTTCG
1 TGAAAAAAAAA-TTCG
31311686 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
31311701 TGAAAAAAA
1 TGAAAAAAA
31311710 GAAGAAGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.20
Consensus pattern (15 bp):
TGAAAAAAAAATTCG
Found at i:31317440 original size:18 final size:18
Alignment explanation
Indices: 31317419--31317461 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
31317409 CCTTTCCCCC
*
31317419 TTCTTTCATTTGTTTATT
1 TTCTTTCATTTATTTATT
*
31317437 TTCTTTCGTTTATTTATT
1 TTCTTTCATTTATTTATT
*
31317455 TGCTTTC
1 TTCTTTC
31317462 TTTTTATGCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.09, C:0.14, G:0.07, T:0.70
Consensus pattern (18 bp):
TTCTTTCATTTATTTATT
Found at i:31322914 original size:24 final size:25
Alignment explanation
Indices: 31322861--31322914 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
31322851 AACAAATTCT
* *
31322861 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
31322886 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
31322909 TTTTTT
1 TTTTTT
31322915 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:31333050 original size:13 final size:13
Alignment explanation
Indices: 31333032--31333056 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31333022 TGGTCATCAT
31333032 GGTGTGAACACAA
1 GGTGTGAACACAA
31333045 GGTGTGAACACA
1 GGTGTGAACACA
31333057 TGATCAATAC
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:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:31339545 original size:19 final size:18
Alignment explanation
Indices: 31339509--31339548 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
31339499 TTTCCACTCG
*
31339509 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
31339527 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
31339546 TTT
1 TTT
31339549 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:31339680 original size:18 final size:17
Alignment explanation
Indices: 31339621--31339681 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
31339611 GCACTCTTTC
*
31339621 TTTTCTTTCTCCAATCTTT
1 TTTTCTTT-TTCAAT-TTT
*
31339640 TTCTCTTTTTCAATTTT
1 TTTTCTTTTTCAATTTT
*
31339657 TGTTTCTTTTTCAGTTTCT
1 T-TTTCTTTTTCAATTT-T
31339676 TTTTCT
1 TTTTCT
31339682 CTCGTCACTC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 4 0.11
18 23 0.64
19 9 0.25
ACGTcount: A:0.08, C:0.20, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTTCTTTTTCAATTTT
Found at i:31340629 original size:13 final size:13
Alignment explanation
Indices: 31340611--31340660 Score: 75
Period size: 13 Copynumber: 3.8 Consensus size: 13
31340601 ACTAGCTCTC
31340611 TTTTTTTACAATT
1 TTTTTTTACAATT
*
31340624 TTTTTTCACAATT
1 TTTTTTTACAATT
31340637 TTTTTTT-CAATT
1 TTTTTTTACAATT
31340649 TTTTTTTCACAA
1 TTTTTTT-ACAA
31340661 CTTCATATCC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
12 12 0.36
13 18 0.55
14 3 0.09
ACGTcount: A:0.22, C:0.12, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTTTTTACAATT
Found at i:31340657 original size:12 final size:12
Alignment explanation
Indices: 31340611--31340654 Score: 70
Period size: 12 Copynumber: 3.6 Consensus size: 12
31340601 ACTAGCTCTC
31340611 TTTTTTTACAAT
1 TTTTTTTACAAT
31340623 TTTTTTTCACAAT
1 TTTTTTT-ACAAT
*
31340636 TTTTTTTTCAAT
1 TTTTTTTACAAT
31340648 TTTTTTT
1 TTTTTTT
31340655 TCACAACTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 18 0.60
13 12 0.40
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTTTTACAAT
Found at i:31340742 original size:11 final size:11
Alignment explanation
Indices: 31340699--31340741 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
31340689 GGAAACTAGT
*
31340699 TTTTTTTCAAA
1 TTTTTTTCGAA
*
31340710 TTTTTTTTGAA
1 TTTTTTTCGAA
*
31340721 TTTTTTTCGAG
1 TTTTTTTCGAA
31340732 TTTTTTTCGA
1 TTTTTTTCGA
31340742 GAAACTACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.16, C:0.07, G:0.09, T:0.67
Consensus pattern (11 bp):
TTTTTTTCGAA
Found at i:31349396 original size:15 final size:15
Alignment explanation
Indices: 31349371--31349417 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
31349361 AGAAAAGAAT
31349371 AAAGAAAATGAAAATG
1 AAAG-AAATGAAAATG
*
31349387 AAAGAAATGAAAAAG
1 AAAGAAATGAAAATG
31349402 AAA-AATATGAAAATG
1 AAAGAA-ATGAAAATG
31349417 A
1 A
31349418 GATTTCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 22 0.79
16 4 0.14
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (15 bp):
AAAGAAATGAAAATG
Found at i:31349462 original size:12 final size:12
Alignment explanation
Indices: 31349445--31349520 Score: 50
Period size: 12 Copynumber: 6.3 Consensus size: 12
31349435 AGAGTGAAGC
31349445 AAAAAGAGATTG
1 AAAAAGAGATTG
*
31349457 AAAAAGAAATTG
1 AAAAAGAGATTG
*
31349469 --AAAGAGA-AG
1 AAAAAGAGATTG
*
31349478 AAAAAGAAAGAGTGG
1 AAAAAG--AGA-TTG
*
31349493 AAAAAGAAATTG
1 AAAAAGAGATTG
* *
31349505 AAAGAGAGCTTG
1 AAAAAGAGATTG
31349517 AAAA
1 AAAA
31349521 GAAATCGAGT
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
9 1 0.02
10 6 0.12
11 4 0.08
12 25 0.52
13 5 0.10
15 7 0.15
ACGTcount: A:0.62, C:0.01, G:0.25, T:0.12
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:31349486 original size:15 final size:15
Alignment explanation
Indices: 31349468--31349501 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
31349458 AAAAGAAATT
31349468 GAAAGAGAAGAAAAA
1 GAAAGAGAAGAAAAA
**
31349483 GAAAGAGTGGAAAAA
1 GAAAGAGAAGAAAAA
31349498 GAAA
1 GAAA
31349502 TTGAAAGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (15 bp):
GAAAGAGAAGAAAAA
Found at i:31351404 original size:10 final size:10
Alignment explanation
Indices: 31351380--31351428 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
31351370 AGCTCGTTTC
*
31351380 CAGCTCACTT
1 CAGCTCAATT
* *
31351390 GAGCTCAAGT
1 CAGCTCAATT
31351400 CAGCTC-ATT
1 CAGCTCAATT
31351409 CGAGCTCAATT
1 C-AGCTCAATT
31351420 CAGCTCAAT
1 CAGCTCAAT
31351429 CTTAACCCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 3 0.09
10 25 0.78
11 4 0.12
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.27
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:31351405 original size:20 final size:20
Alignment explanation
Indices: 31351380--31351426 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
31351370 AGCTCGTTTC
31351380 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGCTCAAGT
*
31351400 CAGCTCATTCGAGCTCAATT
1 CAGCTCATTCGAGCTCAAGT
31351420 CAGCTCA
1 CAGCTCA
31351427 ATCTTAACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGCTCAAGT
Found at i:31354835 original size:30 final size:30
Alignment explanation
Indices: 31354801--31354897 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
31354791 AGCTCACTCC
*
31354801 TAGCTCATA-TTTAGCTCATGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
31354831 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
31354861 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
31354891 TAGCTCA
1 TAGCTCA
31354898 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:31365060 original size:24 final size:25
Alignment explanation
Indices: 31365007--31365060 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
31364997 AACAAATTCT
* *
31365007 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
31365032 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
31365055 TTTTTT
1 TTTTTT
31365061 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:31367106 original size:27 final size:27
Alignment explanation
Indices: 31367051--31367128 Score: 72
Period size: 27 Copynumber: 2.9 Consensus size: 27
31367041 ATGCAATTTT
***
31367051 TTTTTTTTGCAA-TTTTTTTTTC-CTTC
1 TTTTTTTTG-AACTTTTTTTTTCGAAAC
*
31367077 TTTTTTTTCGGA-TTTTTTTTTCGAAAC
1 TTTTTTTT-GAACTTTTTTTTTCGAAAC
*
31367104 TTTTTTTTTAACTTTTTTTTTCGAA
1 TTTTTTTTGAACTTTTTTTTTCGAA
31367129 GCTACGATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
26 20 0.47
27 23 0.53
ACGTcount: A:0.13, C:0.12, G:0.06, T:0.69
Consensus pattern (27 bp):
TTTTTTTTGAACTTTTTTTTTCGAAAC
Found at i:31373181 original size:6 final size:6
Alignment explanation
Indices: 31373168--31373203 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
31373158 TCAATTTTTT
* *
31373168 TCTCAA TATCAA TATCAA TCTCAA TCTCAA TCTCAA
1 TCTCAA TCTCAA TCTCAA TCTCAA TCTCAA TCTCAA
31373204 ATTCTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.39, C:0.28, G:0.00, T:0.33
Consensus pattern (6 bp):
TCTCAA
Found at i:31373255 original size:21 final size:20
Alignment explanation
Indices: 31373211--31373255 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
31373201 CAAATTCTTT
*
31373211 TTTCTTTTTCTCACTCTCAT
1 TTTCTTTTTCTCACTCTCAA
* *
31373231 TTTCTTTTTTTCTTCTCTCAA
1 TTTCTTTTTCTC-ACTCTCAA
31373252 TTTC
1 TTTC
31373256 ATTCAAGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.09, C:0.27, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCTTTTTCTCACTCTCAA
Found at i:31374092 original size:28 final size:29
Alignment explanation
Indices: 31374060--31374130 Score: 83
Period size: 28 Copynumber: 2.4 Consensus size: 29
31374050 TTTCAATCAC
**
31374060 TCTTTTTTTTTTCAATT-TTGA-TTTTTTT
1 TCTTTTTTTTTT-AATTCTAAATTTTTTTT
31374088 TCTTTTTTTTTTAATTCTAAATTTTTTTT
1 TCTTTTTTTTTTAATTCTAAATTTTTTTT
31374117 TCTTCTTCTTTTTT
1 TCTT-TT-TTTTTT
31374131 TTTCAATACT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
27 4 0.11
28 14 0.38
29 11 0.30
30 2 0.05
31 6 0.16
ACGTcount: A:0.11, C:0.10, G:0.01, T:0.77
Consensus pattern (29 bp):
TCTTTTTTTTTTAATTCTAAATTTTTTTT
Found at i:31374193 original size:12 final size:12
Alignment explanation
Indices: 31374176--31374218 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
31374166 AATATAAACT
31374176 TTTTTTTTTGAA
1 TTTTTTTTTGAA
**
31374188 TTTTTTTTCAAA
1 TTTTTTTTTGAA
31374200 TTTTTTTTTTGAA
1 -TTTTTTTTTGAA
31374213 TTTTTT
1 TTTTTT
31374219 ATATATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.16, C:0.02, G:0.05, T:0.77
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:31374193 original size:13 final size:13
Alignment explanation
Indices: 31374175--31374218 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
31374165 GAATATAAAC
31374175 TTTTTTTTTTGAA
1 TTTTTTTTTTGAA
**
31374188 -TTTTTTTTCAAA
1 TTTTTTTTTTGAA
31374200 TTTTTTTTTTGAA
1 TTTTTTTTTTGAA
31374213 TTTTTT
1 TTTTTT
31374219 ATATATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.16, C:0.02, G:0.05, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTTGAA
Found at i:31374228 original size:25 final size:25
Alignment explanation
Indices: 31374175--31374230 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
31374165 GAATATAAAC
*
31374175 TTTTTTTTTTGAATTTTTTTTCAAA
1 TTTTTTTTTTGAATTTTTTATCAAA
*
31374200 TTTTTTTTTTGAATTTTTTAT-ATA
1 TTTTTTTTTTGAATTTTTTATCAAA
31374224 TTTTTTT
1 TTTTTTT
31374231 ACAATACCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 9 0.31
25 20 0.69
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.77
Consensus pattern (25 bp):
TTTTTTTTTTGAATTTTTTATCAAA
Found at i:31380977 original size:21 final size:21
Alignment explanation
Indices: 31380951--31380994 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
31380941 CCAATACGTC
31380951 CCTTTCATCTCGAGTATTCCT
1 CCTTTCATCTCGAGTATTCCT
31380972 CCTTTCATCTCGAGTATTCCT
1 CCTTTCATCTCGAGTATTCCT
31380993 CC
1 CC
31380995 ATTTAAGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.36, G:0.09, T:0.41
Consensus pattern (21 bp):
CCTTTCATCTCGAGTATTCCT
Found at i:31381163 original size:45 final size:44
Alignment explanation
Indices: 31381099--31381261 Score: 159
Period size: 45 Copynumber: 3.6 Consensus size: 44
31381089 ATGTAACCGC
*
31381099 CCATAAGTGAACTCAGACTCAACTCACGATCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCACGATCTCGGGC-TTCGCAT
* * * *
31381144 CCATAAGTGAACTCGGACTCAACTCACGAGCTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCACGATCTCGG--GCTTCGCAT
* *** *
31381189 ACATCTCTCGAACTCGGACTCAACTCAACGAGT-TCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTC-ACGA-TCTCGGGC-TTCGCAT
31381236 CCATAAGTGAACTCGGACTCAACTCA
1 CCATAAGTGAACTCGGACTCAACTCA
31381262 ACGAGTTCGG
Statistics
Matches: 93, Mismatches: 18, Indels: 14
0.74 0.14 0.11
Matches are distributed among these distances:
45 40 0.43
46 38 0.41
47 15 0.16
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (44 bp):
CCATAAGTGAACTCGGACTCAACTCACGATCTCGGGCTTCGCAT
Found at i:31381248 original size:46 final size:45
Alignment explanation
Indices: 31381099--31381272 Score: 176
Period size: 46 Copynumber: 3.8 Consensus size: 45
31381089 ATGTAACCGC
* * *
31381099 CCATAAGTGAACTCAGACTCAACTCACGA-TCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCACGAGT-TCGGACATTCGCAT
* *
31381144 CCATAAGTGAACTCGGACTCAACTCACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCACGAGTTCGGACATTCGC-A--T
* ***
31381189 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTC-ACGAGTTCGGACATTCGCAT
31381236 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTC-ACGAGTTCGGA
31381273 TGCCCAAATA
Statistics
Matches: 106, Mismatches: 14, Indels: 17
0.77 0.10 0.12
Matches are distributed among these distances:
42 1 0.01
43 3 0.03
45 37 0.35
46 46 0.43
47 14 0.13
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCACGAGTTCGGACATTCGCAT
Found at i:31381291 original size:46 final size:44
Alignment explanation
Indices: 31381149--31381291 Score: 107
Period size: 46 Copynumber: 3.1 Consensus size: 44
31381139 CGCATCCATA
* *
31381149 AGTGAACTCGGACTCAACTC-ACGAGCTCGGATGCCTAGTTACATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA---A-ATC-CT
* * *
31381197 --CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC--ATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCAAATCC-T
31381240 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCC-AA-ATCCT
31381287 AGTGA
1 AGTGA
31381292 CATGTCACTT
Statistics
Matches: 76, Mismatches: 8, Indels: 24
0.70 0.07 0.22
Matches are distributed among these distances:
42 1 0.01
43 4 0.05
44 4 0.05
46 50 0.66
47 10 0.13
48 4 0.05
49 3 0.04
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATCCT
Found at i:31384696 original size:25 final size:23
Alignment explanation
Indices: 31384668--31384728 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 23
31384658 AAAGAAAAAA
*
31384668 GAAAAGAAGAAAAAGAGAAGACTGT
1 GAAAAGAAGAAAAAGACAAGA-T-T
31384693 G-AAAGAA-AAGAAA-ACAAGATT
1 GAAAAGAAGAA-AAAGACAAGATT
31384714 GAAAA-AAGAAAAAGA
1 GAAAAGAAGAAAAAGA
31384729 AATTGATCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 11
0.72 0.02 0.26
Matches are distributed among these distances:
21 7 0.23
22 7 0.23
23 7 0.23
24 9 0.29
25 1 0.03
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.07
Consensus pattern (23 bp):
GAAAAGAAGAAAAAGACAAGATT
Found at i:31388888 original size:33 final size:33
Alignment explanation
Indices: 31388850--31388912 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
31388840 GATTACTCAC
31388850 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
31388883 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
31388913 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:31388958 original size:14 final size:14
Alignment explanation
Indices: 31388909--31388965 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
31388899 TCAAGCTCTC
31388909 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
31388922 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
31388936 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
31388950 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
31388964 TT
1 TT
31388966 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:31389029 original size:6 final size:6
Alignment explanation
Indices: 31388927--31389016 Score: 65
Period size: 6 Copynumber: 14.7 Consensus size: 6
31388917 TCTTTTTTCG
* * * **
31388927 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * *
31388978 CGATTT CTTTTT CTTTTT CGTTTT CTTTTT -GTTTT CTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTT
31389017 CAATTTCTTT
Statistics
Matches: 62, Mismatches: 19, Indels: 6
0.71 0.22 0.07
Matches are distributed among these distances:
5 4 0.06
6 46 0.74
7 9 0.15
8 3 0.05
ACGTcount: A:0.06, C:0.19, G:0.03, T:0.72
Consensus pattern (6 bp):
CTTTTT
Found at i:31389048 original size:63 final size:63
Alignment explanation
Indices: 31388927--31389049 Score: 140
Period size: 63 Copynumber: 2.0 Consensus size: 63
31388917 TCTTTTTTCG
* * ** * *
31388927 CTTTTTCTTTTTCAATTTTCTTTTCTTCATTTTCTTTTTCTCTCACTTTTTCGATTTCTTTTT
1 CTTTTTCGTTTTCAATTTTCTTTTCTTCAATTTCTTTTTCAATCACTTTCTCCATTTCTTTTT
* * * *
31388990 CTTTTTCGTTTTC-TTTTTGTTTTCTTTCAATTTCTTTTTCAATCTCTTTCTCCTTTTCTT
1 CTTTTTCGTTTTCAATTTTCTTTTC-TTCAATTTCTTTTTCAATCACTTTCTCCATTTCTT
31389050 GCTCAATGGA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
62 9 0.18
63 40 0.82
ACGTcount: A:0.07, C:0.21, G:0.02, T:0.69
Consensus pattern (63 bp):
CTTTTTCGTTTTCAATTTTCTTTTCTTCAATTTCTTTTTCAATCACTTTCTCCATTTCTTTTT
Found at i:31395680 original size:12 final size:11
Alignment explanation
Indices: 31395579--31395677 Score: 119
Period size: 11 Copynumber: 8.6 Consensus size: 11
31395569 AAGTAAGTGA
31395579 AAAAAAAGTTTC
1 AAAAAAA-TTTC
* *
31395591 GACAAAAAGTTC
1 -AAAAAAATTTC
31395603 AAAAAAAAGTTTC
1 -AAAAAAA-TTTC
*
31395616 GAAAAAAAGTTC
1 -AAAAAAATTTC
31395628 AAAAAAATTTC
1 AAAAAAATTTC
31395639 AAAAAAATTTC
1 AAAAAAATTTC
31395650 -AAAAAATTTC
1 AAAAAAATTTC
31395660 AAAAAAATTTC
1 AAAAAAATTTC
31395671 AAAAAAA
1 AAAAAAA
31395678 ATTGAAACTA
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
10 10 0.13
11 38 0.50
12 12 0.16
13 16 0.21
ACGTcount: A:0.63, C:0.09, G:0.06, T:0.22
Consensus pattern (11 bp):
AAAAAAATTTC
Found at i:31397760 original size:16 final size:15
Alignment explanation
Indices: 31397741--31397784 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
31397731 AGAAGATTGT
31397741 AAAAAAATAAAAGAA
1 AAAAAAATAAAAGAA
31397756 GAAAAAAAT--AAGAA
1 -AAAAAAATAAAAGAA
31397770 AAAGAAAATAAAAGA
1 AAA-AAAATAAAAGA
31397785 GAGCAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.12
14 10 0.40
16 12 0.48
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (15 bp):
AAAAAAATAAAAGAA
Found at i:31400869 original size:93 final size:93
Alignment explanation
Indices: 31400754--31400924 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
31400744 GCCCAGAAGT
* *
31400754 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAAATCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAAATCAA
31400819 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* * *
31400847 GAACTCGGACTCAGCTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAAATCAA
*
31400912 CGAGTTCGGATGC
66 CGAGCTCGGATGC
31400925 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAAATCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:31400921 original size:46 final size:46
Alignment explanation
Indices: 31400750--31400921 Score: 188
Period size: 46 Copynumber: 3.7 Consensus size: 46
31400740 ACCCGCCCAG
* *
31400750 AAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCAT
1 AAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCAT
* * *
31400796 AAGTGAACTCGGACTCAAATCAACGAGCTCGG--ATGC-CTAGTTACAT
1 AAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--TCCAT
*** * *
31400842 CTCTCGAACTCGGACTCAGCTCAACGAGTTCGGACATTCGCATCCAT
1 AAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCAT
*
31400889 AAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 AAGTGAACTCGGACTCAACTCAACGAGCTCGGA
31400922 TGCTCAACCA
Statistics
Matches: 103, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 64 0.62
47 30 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.21
Consensus pattern (46 bp):
AAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCAT
Found at i:31403375 original size:15 final size:15
Alignment explanation
Indices: 31403306--31403382 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
31403296 CAAAGATAAC
*
31403306 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
31403320 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
31403335 GAGAAA-CCCGAAATA
1 AAGAAATCCAG-AATA
31403350 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
31403365 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
31403380 AAG
1 AAG
31403383 GAACCCAAGA
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
14 11 0.22
15 36 0.71
16 4 0.08
ACGTcount: A:0.57, C:0.14, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:31406486 original size:46 final size:45
Alignment explanation
Indices: 31406317--31406478 Score: 168
Period size: 46 Copynumber: 3.5 Consensus size: 45
31406307 ACCCGCCCAG
*
31406317 AAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCAT
1 AAGTGAACTCGGACTCAACTCAACGAGCTC-GGCATTCGCATCCAT
* * *
31406363 AAGTGAACTCGGACTCAAATCAACGAGCTCGG-ATGC-CTAGT-TAT
1 AAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGC-A-TCCAT
** * *
31406407 ATCTCTCGAACTCGGACTCAGCTCAACGAGTTCGGACATTCGCATCCAT
1 A--AGT-GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCATCCAT
31406456 AAGTGAACTCGGACTCAACTCAA
1 AAGTGAACTCGGACTCAACTCAA
31406479 TGAGTTCGAA
Statistics
Matches: 93, Mismatches: 14, Indels: 18
0.74 0.11 0.14
Matches are distributed among these distances:
43 1 0.01
44 6 0.06
45 3 0.03
46 48 0.52
47 26 0.28
48 1 0.01
49 7 0.08
50 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (45 bp):
AAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCAT
Found at i:31406507 original size:46 final size:46
Alignment explanation
Indices: 31406317--31406499 Score: 142
Period size: 46 Copynumber: 4.0 Consensus size: 46
31406307 ACCCGCCCAG
* * * * *
31406317 AAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCAT
1 AAGTGAACTCGGACTCAACTCAACGAGTTCGGACATGCGCAACCAT
* * ***
31406363 AAGTGAACTCGGACTCAAATCAACGAGCTCGG--ATGC-CTAGTTAT
1 AAGTGAACTCGGACTCAACTCAACGAGTTCGGACATGCGC-AACCAT
** * * *
31406407 ATCTCTCGAACTCGGACTCAGCTCAACGAGTTCGGACATTCGCATCCAT
1 A--AGT-GAACTCGGACTCAACTCAACGAGTTCGGACATGCGCAACCAT
* *
31406456 AAGTGAACTCGGACTCAACTCAATGAGTTC-GA-ATGCTCAACCAT
1 AAGTGAACTCGGACTCAACTCAACGAGTTCGGACATGCGCAACCAT
31406500 CCTAGTGACA
Statistics
Matches: 108, Mismatches: 22, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
43 1 0.01
44 15 0.14
45 2 0.02
46 56 0.52
47 26 0.24
49 7 0.06
50 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
AAGTGAACTCGGACTCAACTCAACGAGTTCGGACATGCGCAACCAT
Found at i:31410453 original size:68 final size:67
Alignment explanation
Indices: 31410381--31410530 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
31410371 CATCATGTGT
* * * *
31410381 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
31410443 ATGTAG
62 ATGTAG
** * *
31410449 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
31410514 AG
66 AG
31410516 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
31410531 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:31410486 original size:64 final size:64
Alignment explanation
Indices: 31410405--31410588 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
31410395 AGACATTATG
* *
31410405 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
31410469 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
31410534 AA
63 AA
* * * *
31410536 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
31410589 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:31422091 original size:15 final size:15
Alignment explanation
Indices: 31422067--31422143 Score: 54
Period size: 15 Copynumber: 5.3 Consensus size: 15
31422057 GAATGAAGTG
* *
31422067 GAAAAAGAAAGATAA
1 GAAAATGAAAAATAA
*
31422082 GAAAATGAAAAAGAA
1 GAAAATGAAAAATAA
* *
31422097 AAAAATGAGAAA-AA
1 GAAAATGAAAAATAA
*
31422111 GAAAGT-AAAAAT-A
1 GAAAATGAAAAATAA
*
31422124 GAAAAAGAAAGAA-AA
1 GAAAATGAAA-AATAA
31422139 GAAAA
1 GAAAA
31422144 AATGAGAGAA
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
13 9 0.19
14 9 0.19
15 30 0.62
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.06
Consensus pattern (15 bp):
GAAAATGAAAAATAA
Found at i:31422144 original size:24 final size:24
Alignment explanation
Indices: 31422090--31422167 Score: 69
Period size: 24 Copynumber: 3.4 Consensus size: 24
31422080 AAGAAAATGA
31422090 AAAAGAAAAAAATGAG--AA-AAAG
1 AAAAG-AAAAAATGAGAAAAGAAAG
*
31422112 -AAAGTAAAAAT-AGAAAAAGAAAG
1 AAAAGAAAAAATGAG-AAAAGAAAG
*
31422135 AAAAGAAAAAATGAGAGAAGAAA-
1 AAAAGAAAAAATGAGAAAAGAAAG
31422158 AACAAGAAAA
1 AA-AAGAAAA
31422168 TGAAAATGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
19 2 0.04
20 6 0.13
21 4 0.09
22 2 0.04
23 6 0.13
24 24 0.52
25 2 0.04
ACGTcount: A:0.76, C:0.01, G:0.18, T:0.05
Consensus pattern (24 bp):
AAAAGAAAAAATGAGAAAAGAAAG
Found at i:31422185 original size:57 final size:56
Alignment explanation
Indices: 31422067--31422189 Score: 135
Period size: 57 Copynumber: 2.2 Consensus size: 56
31422057 GAATGAAGTG
* *
31422067 GAAAAAGAAAGATAAGAAAATGAAAAAGAAAAAAATGAGAAAAAGAAAGTAAAAATA
1 GAAAAAGAAAGAAAAGAAAATGAAAAAGAAAAAAA-GAGAAAAAGAAAATAAAAATA
* * * *
31422124 GAAAAAGAAAGAAAAGAAAAAATGAGAGAAGAAAAACA-AGAAAATGAAAATGAAAAT-
1 GAAAAAGAAAGAAAAG--AAAATGA-AAAAGAAAAAAAGAGAAAAAGAAAATAAAAATA
31422181 G-AAAAGAAA
1 GAAAAAGAAA
31422190 AGCTTGATTG
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
56 8 0.14
57 16 0.28
58 16 0.28
59 7 0.12
60 10 0.18
ACGTcount: A:0.73, C:0.01, G:0.19, T:0.07
Consensus pattern (56 bp):
GAAAAAGAAAGAAAAGAAAATGAAAAAGAAAAAAAGAGAAAAAGAAAATAAAAATA
Found at i:31423273 original size:45 final size:45
Alignment explanation
Indices: 31423178--31423338 Score: 211
Period size: 45 Copynumber: 3.6 Consensus size: 45
31423168 CAGTATTTCA
* *
31423178 CCTGCTAGGCTCGAA-GCTCG-ATA-TCATTTCACCGACATTATAG
1 CCTGCTAGGCTCAAAGGCTCGAATAGT-ATCTCACCGACATTATAG
* * * *
31423221 CCTGCTAGGCTCGAAGGCCCGAATAGTATCTCACTGGCATTATAG
1 CCTGCTAGGCTCAAAGGCTCGAATAGTATCTCACCGACATTATAG
*
31423266 CCTGCTAGGCTCAAAGGCTCGAATAGTATCTCACCGACATCATAG
1 CCTGCTAGGCTCAAAGGCTCGAATAGTATCTCACCGACATTATAG
* *
31423311 CCTGCTAGGTTCAAAAGCTCGAATAGTA
1 CCTGCTAGGCTCAAAGGCTCGAATAGTA
31423339 CCGTACTATA
Statistics
Matches: 104, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
43 15 0.14
44 4 0.04
45 84 0.81
46 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (45 bp):
CCTGCTAGGCTCAAAGGCTCGAATAGTATCTCACCGACATTATAG
Found at i:31425091 original size:30 final size:30
Alignment explanation
Indices: 31424995--31425079 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
31424985 TAAACTAAAA
* *
31424995 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* * * * *
31425025 TGAGCTGAGATTAAACTCCTAAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
*
31425055 TGAGCTAAGGTTTAGCTCGTGAGCT
1 TGAGCTAAGATTTAGCTCGTGAGCT
31425080 GAATATGAGC
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
Found at i:31426078 original size:20 final size:20
Alignment explanation
Indices: 31426055--31426120 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
31426045 AGCTCCGTGC
31426055 AGCTCAACTCAGCTTATTTG
1 AGCTCAACTCAGCTTATTTG
*** **
31426075 AGCTCGTTTCAGCTCGTTTG
1 AGCTCAACTCAGCTTATTTG
*
31426095 AGCTCAAC-CGAGCTTACTTTC
1 AGCTCAACTC-AGCTTA-TTTG
31426116 AGCTC
1 AGCTC
31426121 CTTCTTTCTT
Statistics
Matches: 33, Mismatches: 11, Indels: 3
0.70 0.23 0.06
Matches are distributed among these distances:
19 1 0.03
20 24 0.73
21 8 0.24
ACGTcount: A:0.20, C:0.29, G:0.18, T:0.33
Consensus pattern (20 bp):
AGCTCAACTCAGCTTATTTG
Found at i:31429171 original size:10 final size:10
Alignment explanation
Indices: 31429156--31429212 Score: 69
Period size: 10 Copynumber: 5.6 Consensus size: 10
31429146 CACCTGAGCA
31429156 CGTTTCAGCT
1 CGTTTCAGCT
31429166 CGTTTCAGCT
1 CGTTTCAGCT
*
31429176 CGTTTGAGCT
1 CGTTTCAGCT
* *
31429186 TGATTTTAGCT
1 CG-TTTCAGCT
31429197 CGTTTCAGCT
1 CGTTTCAGCT
*
31429207 TGTTTC
1 CGTTTC
31429213 TTTTCCATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
10 32 0.80
11 8 0.20
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.46
Consensus pattern (10 bp):
CGTTTCAGCT
Found at i:31434084 original size:21 final size:21
Alignment explanation
Indices: 31434054--31434102 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
31434044 GAGTGTGCTC
*
31434054 GATTT-AGCTC-AGACAAGTTG
1 GATTTGAGCTCGA-ACAAGCTG
*
31434074 GATTTGAGCTCGAATAAGCTG
1 GATTTGAGCTCGAACAAGCTG
31434095 GATTTGAG
1 GATTTGAG
31434103 TTGGACGGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 5 0.20
21 19 0.76
22 1 0.04
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.31
Consensus pattern (21 bp):
GATTTGAGCTCGAACAAGCTG
Found at i:31439225 original size:14 final size:14
Alignment explanation
Indices: 31439203--31439250 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
31439193 ACCTAAACCG
* *
31439203 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
31439217 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
*
31439231 ACCCTTTTGTTCCT
1 ACCATTTTGTTCCT
31439245 ACCATT
1 ACCATT
31439251 CCATTCGTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.19, C:0.29, G:0.06, T:0.46
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:31439666 original size:30 final size:30
Alignment explanation
Indices: 31439632--31439696 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
31439622 TTTCAACTTA
*
31439632 TTTTTCACTCTCAAATTT-ATTTTCATTCTC
1 TTTTTCAATCTC-AATTTCATTTTCATTCTC
* * *
31439662 TTTTTCAATCTCATTTTCTTTTTCATTTTC
1 TTTTTCAATCTCAATTTCATTTTCATTCTC
31439692 TTTTT
1 TTTTT
31439697 GCTTTTCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 4 0.13
30 26 0.87
ACGTcount: A:0.15, C:0.20, G:0.00, T:0.65
Consensus pattern (30 bp):
TTTTTCAATCTCAATTTCATTTTCATTCTC
Found at i:31439696 original size:18 final size:18
Alignment explanation
Indices: 31439650--31439702 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
31439640 TCTCAAATTT
*
31439650 ATTTTCATTCTCTTTTTC
1 ATTTTCATTTTCTTTTTC
* *
31439668 AATCTCATTTTCTTTTTC
1 ATTTTCATTTTCTTTTTC
*
31439686 ATTTTCTTTTTGCTTTT
1 ATTTTCATTTT-CTTTT
31439703 CAAAGGCTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 23 0.82
19 5 0.18
ACGTcount: A:0.11, C:0.19, G:0.02, T:0.68
Consensus pattern (18 bp):
ATTTTCATTTTCTTTTTC
Found at i:31439703 original size:12 final size:12
Alignment explanation
Indices: 31439672--31439696 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31439662 TTTTTCAATC
31439672 TCATTTTCTTTT
1 TCATTTTCTTTT
31439684 TCATTTTCTTTT
1 TCATTTTCTTTT
31439696 T
1 T
31439697 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:31439714 original size:12 final size:12
Alignment explanation
Indices: 31439699--31439726 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
31439689 TTCTTTTTGC
31439699 TTTTCAAAGGCT
1 TTTTCAAAGGCT
31439711 TTTTCAAAGGCT
1 TTTTCAAAGGCT
31439723 TTTT
1 TTTT
31439727 GAAGTTCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.50
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:31439787 original size:5 final size:5
Alignment explanation
Indices: 31439777--31439833 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
31439767 CTCTTGCTTC
*
31439777 TCTTT TCTTT T-TATT TCGTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
31439824 TCTTT TCTTT
1 TCTTT TCTTT
31439834 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:31439817 original size:15 final size:14
Alignment explanation
Indices: 31439777--31439833 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
31439767 CTCTTGCTTC
*
31439777 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
31439792 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
31439807 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
31439824 TCTTTTCTTT
1 TCTTTTCTTT
31439834 GTTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:31439834 original size:21 final size:21
Alignment explanation
Indices: 31439777--31439844 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
31439767 CTCTTGCTTC
* *
31439777 TCTTTTCTTTT-TATTTCGTTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
31439798 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
31439819 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
31439839 CTCTTT
1 -TCTTT
31439845 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.18
21 27 0.69
22 5 0.13
ACGTcount: A:0.01, C:0.18, G:0.04, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:31441993 original size:20 final size:20
Alignment explanation
Indices: 31441970--31442008 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31441960 CACAACCAAA
* *
31441970 TACCAAATTTTTAAAAATTT
1 TACCAAATTCTCAAAAATTT
31441990 TACCAAATTCTCAAAAATT
1 TACCAAATTCTCAAAAATT
31442009 ACGAAAATCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (20 bp):
TACCAAATTCTCAAAAATTT
Found at i:31450690 original size:12 final size:12
Alignment explanation
Indices: 31450675--31450705 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
31450665 TTCTTTTTGC
31450675 TTTTCAAAGGCT
1 TTTTCAAAGGCT
31450687 TTTTCAAAGGCT
1 TTTTCAAAGGCT
31450699 TTTTCAA
1 TTTTCAA
31450706 TTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:31450782 original size:6 final size:6
Alignment explanation
Indices: 31450766--31450815 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
31450756 TTTCTTTTTA
*
31450766 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
31450815 T
1 T
31450816 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:31450798 original size:37 final size:37
Alignment explanation
Indices: 31450755--31450825 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
31450745 CTTGCCTCTC
31450755 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
31450792 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
31450826 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:31450826 original size:16 final size:16
Alignment explanation
Indices: 31450751--31450811 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
31450741 GCCTCTTGCC
*
31450751 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
31450767 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
31450783 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
31450799 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
31450812 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:31451773 original size:13 final size:12
Alignment explanation
Indices: 31451734--31451766 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
31451724 TCAAAAATAT
31451734 TTTTTTTTTGAA
1 TTTTTTTTTGAA
31451746 TTTTTTTTTGAA
1 TTTTTTTTTGAA
31451758 TTTTTTTTT
1 TTTTTTTTT
31451767 CAAATTTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:31453486 original size:19 final size:19
Alignment explanation
Indices: 31453432--31453478 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
31453422 TAAACTAAAA
31453432 TGAGCTAAATTTTAGCTCG
1 TGAGCTAAATTTTAGCTCG
31453451 TGAGCTAAATTTTAGCTCG
1 TGAGCTAAATTTTAGCTCG
31453470 TGAGCTAAA
1 TGAGCTAAA
31453479 GTTGAGCTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (19 bp):
TGAGCTAAATTTTAGCTCG
Found at i:31454920 original size:24 final size:24
Alignment explanation
Indices: 31454851--31454931 Score: 94
Period size: 24 Copynumber: 3.4 Consensus size: 24
31454841 TTGGAGGCCT
*
31454851 AGCCTCTTTTAAT-AACTGGGGCAA
1 AGCC-CTTTTGATAAACTGGGGCAA
*
31454875 AGCCCTTTTGATTAACTGGGGCAA
1 AGCCCTTTTGATAAACTGGGGCAA
*
31454899 AGCCCTTTTCGGTAAACT-GGGCAA
1 AGCCCTTTT-GATAAACTGGGGCAA
*
31454923 AACCCTTTT
1 AGCCCTTTT
31454932 TTGCACTTTC
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
23 7 0.14
24 38 0.75
25 6 0.12
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (24 bp):
AGCCCTTTTGATAAACTGGGGCAA
Found at i:31455005 original size:21 final size:21
Alignment explanation
Indices: 31454980--31455038 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
31454970 TATAATGAGT
*
31454980 ATATCATGTGCATCTCATAAC
1 ATATCATGTGCATATCATAAC
**
31455001 ATATCATGTGCATATCATGTC
1 ATATCATGTGCATATCATAAC
31455022 ATATCATGT-CATATCAT
1 ATATCATGTGCATATCAT
31455039 GTATATCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
20 8 0.23
21 27 0.77
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.37
Consensus pattern (21 bp):
ATATCATGTGCATATCATAAC
Found at i:31455024 original size:10 final size:10
Alignment explanation
Indices: 31454980--31455046 Score: 82
Period size: 10 Copynumber: 6.6 Consensus size: 10
31454970 TATAATGAGT
31454980 ATATCATGTGC
1 ATATCATGT-C
* **
31454991 ATCTCATAAC
1 ATATCATGTC
31455001 ATATCATGTGC
1 ATATCATGT-C
31455012 ATATCATGTC
1 ATATCATGTC
31455022 ATATCATGTC
1 ATATCATGTC
31455032 ATATCATGT-
1 ATATCATGTC
31455041 ATATCA
1 ATATCA
31455047 AAATCTCATG
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
9 6 0.12
10 27 0.55
11 16 0.33
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.37
Consensus pattern (10 bp):
ATATCATGTC
Found at i:31457326 original size:12 final size:12
Alignment explanation
Indices: 31457309--31457362 Score: 69
Period size: 12 Copynumber: 4.6 Consensus size: 12
31457299 TATACAAGTC
31457309 AAAAAAATTCGA
1 AAAAAAATTCGA
31457321 AAAAAAATTC-A
1 AAAAAAATTCGA
31457332 AAAAAATATTCG-
1 AAAAAA-ATTCGA
31457344 AAAAAAA-TCTGA
1 AAAAAAATTC-GA
31457356 AAAAAAA
1 AAAAAAA
31457363 GTGTTTAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.05
11 9 0.24
12 27 0.71
ACGTcount: A:0.70, C:0.07, G:0.06, T:0.17
Consensus pattern (12 bp):
AAAAAAATTCGA
Found at i:31459493 original size:12 final size:12
Alignment explanation
Indices: 31459478--31459519 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
31459468 ATTGTAGATT
31459478 AAAAAAATTGAA
1 AAAAAAATTGAA
*
31459490 AAAAAAATCGAA
1 AAAAAAATTGAA
*
31459502 AAAAAAATTTAA
1 AAAAAAATTGAA
31459514 AAAAAA
1 AAAAAA
31459520 CAAATTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (12 bp):
AAAAAAATTGAA
Found at i:31461817 original size:17 final size:18
Alignment explanation
Indices: 31461778--31461819 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
31461768 AAGAAGAAAA
31461778 ACAAAA-AGATGAGTGAT
1 ACAAAAGAGATGAGTGAT
*
31461795 AAAAAAGAGA-GAGTGAT
1 ACAAAAGAGATGAGTGAT
*
31461812 TCAAAAGA
1 ACAAAAGA
31461820 AAAAGAAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (18 bp):
ACAAAAGAGATGAGTGAT
Found at i:31465749 original size:20 final size:20
Alignment explanation
Indices: 31465726--31465772 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
31465716 GGGTTAAGAT
*
31465726 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
31465746 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
31465766 TGAGCTG
1 TGAGCTG
31465773 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:31466117 original size:24 final size:24
Alignment explanation
Indices: 31466085--31466132 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
31466075 AGAGGAGGGG
*
31466085 AATGATGTGAGCTTGCCTATGAAC
1 AATGATGTGAGCTTGCCTACGAAC
31466109 AATGATGTGAGCTTGCCTACGAAC
1 AATGATGTGAGCTTGCCTACGAAC
31466133 CAAATGGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (24 bp):
AATGATGTGAGCTTGCCTACGAAC
Found at i:31467923 original size:21 final size:19
Alignment explanation
Indices: 31467897--31467959 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 19
31467887 TCTTGTAAAG
31467897 AGAAAATAAAGAAAAGAAAA
1 AGAAAATAAA-AAAAGAAAA
* *
31467917 AGCAAAAGCAAAAGAAGAAAA
1 AG-AAAA-TAAAAAAAGAAAA
31467938 AGAAAATGAAATAAAAAGAAAA
1 AGAAAAT--AA-AAAAAGAAAA
31467960 GAGAGGCAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
20 6 0.18
21 16 0.47
22 12 0.35
ACGTcount: A:0.76, C:0.03, G:0.16, T:0.05
Consensus pattern (19 bp):
AGAAAATAAAAAAAGAAAA
Found at i:31467929 original size:12 final size:11
Alignment explanation
Indices: 31467904--31467959 Score: 55
Period size: 12 Copynumber: 5.2 Consensus size: 11
31467894 AAGAGAAAAT
31467904 AAAGAAAAGAA
1 AAAGAAAAGAA
*
31467915 AAAGCAAAAGCA
1 AAAG-AAAAGAA
31467927 AAAG--AAGAA
1 AAAGAAAAGAA
31467936 AAAGAAAATGAA
1 AAAGAAAA-GAA
*
31467948 ATA-AAAAGAA
1 AAAGAAAAGAA
31467958 AA
1 AA
31467960 GAGAGGCAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
9 8 0.22
10 4 0.11
11 10 0.27
12 15 0.41
ACGTcount: A:0.77, C:0.04, G:0.16, T:0.04
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:31468026 original size:12 final size:12
Alignment explanation
Indices: 31468009--31468038 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
31467999 TTGAGAGAAC
31468009 TTGAAAAAGCCT
1 TTGAAAAAGCCT
31468021 TTGAAAAAGCCT
1 TTGAAAAAGCCT
31468033 TTGAAA
1 TTGAAA
31468039 GAAAAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:31468113 original size:29 final size:29
Alignment explanation
Indices: 31468032--31468121 Score: 76
Period size: 29 Copynumber: 3.1 Consensus size: 29
31468022 TGAAAAAGCC
* * * *
31468032 TTTGAAAGAAAAAAGAAAATTAAAAGAAA
1 TTTGAGAGTAAAAAGAAGATGAAAAGAAA
* * *
31468061 -ATGAGATTGAAAAAG-AGAACGAAAAGAAA
1 TTTGAGAGT-AAAAAGAAG-ATGAAAAGAAA
31468090 TTTGAGAGTAAAAAGAAGATGAAAAAGAAA
1 TTTGAGAGTAAAAAGAAGATG-AAAAGAAA
31468120 TT
1 TT
31468122 GAAACAAAAG
Statistics
Matches: 46, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
28 5 0.11
29 23 0.50
30 18 0.39
ACGTcount: A:0.62, C:0.01, G:0.20, T:0.17
Consensus pattern (29 bp):
TTTGAGAGTAAAAAGAAGATGAAAAGAAA
Found at i:31470270 original size:30 final size:31
Alignment explanation
Indices: 31470236--31470332 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
31470226 AGCTCACTCC
*
31470236 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
31470266 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
31470296 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
31470326 TAGCTCA
1 TAGCTCA
31470333 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:31471264 original size:22 final size:20
Alignment explanation
Indices: 31471232--31471280 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
31471222 GCCGAATTTA
31471232 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
31471255 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
31471275 TGAACA
1 TGAACA
31471281 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:31473911 original size:58 final size:58
Alignment explanation
Indices: 31473843--31473960 Score: 236
Period size: 58 Copynumber: 2.0 Consensus size: 58
31473833 ACAGTCCTCC
31473843 CACGACTTCAAATTCTTTTGAATGATGGCCCAGAGCAAAGTAGATAGGACTCTATTGA
1 CACGACTTCAAATTCTTTTGAATGATGGCCCAGAGCAAAGTAGATAGGACTCTATTGA
31473901 CACGACTTCAAATTCTTTTGAATGATGGCCCAGAGCAAAGTAGATAGGACTCTATTGA
1 CACGACTTCAAATTCTTTTGAATGATGGCCCAGAGCAAAGTAGATAGGACTCTATTGA
31473959 CA
1 CA
31473961 ACTTCTGTTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27
Consensus pattern (58 bp):
CACGACTTCAAATTCTTTTGAATGATGGCCCAGAGCAAAGTAGATAGGACTCTATTGA
Found at i:31477714 original size:14 final size:14
Alignment explanation
Indices: 31477695--31477736 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
31477685 AAGGAATGGT
31477695 CGAAATGGTATGAA
1 CGAAATGGTATGAA
31477709 CGAAATGGTATGAA
1 CGAAATGGTATGAA
* **
31477723 TGAAGGGGTATGAA
1 CGAAATGGTATGAA
31477737 TGAATTGGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.40, C:0.05, G:0.33, T:0.21
Consensus pattern (14 bp):
CGAAATGGTATGAA
Found at i:31484513 original size:39 final size:39
Alignment explanation
Indices: 31484396--31484657 Score: 320
Period size: 39 Copynumber: 6.6 Consensus size: 39
31484386 GCTCCTCGTT
* * *
31484396 CAAATGCCTTCAGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTC-GGGCTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
31484436 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
31484476 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
31484515 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
31484554 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
* * *
31484593 CAAATGCCTTCGGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGG-GCTTAGCCCGGA-ATTAGT-ATC-TCGCA
31484634 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
31484658 CATCATTCAA
Statistics
Matches: 202, Mismatches: 12, Indels: 17
0.87 0.05 0.07
Matches are distributed among these distances:
39 134 0.66
40 57 0.28
41 11 0.05
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
Found at i:31492509 original size:79 final size:78
Alignment explanation
Indices: 31492407--31492629 Score: 247
Period size: 79 Copynumber: 2.8 Consensus size: 78
31492397 GCTCCTCGTT
* *
31492407 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
31492472 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
* *
31492487 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCTGG
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAAT-TCGCACAAATGCCTTCGGGACTTAGCCCGG
*
31492550 AATTAGTATCTCGCA
64 AATTAGTAACTCGCA
** * * * *
31492565 CAAATGCCTTCGAATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCG-GGCTTAGCCCGG-TATAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCCG
31492628 GA
63 GA
31492630 CATCATTCAA
Statistics
Matches: 122, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
78 45 0.37
79 56 0.46
80 20 0.16
81 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:31492524 original size:39 final size:40
Alignment explanation
Indices: 31492407--31492629 Score: 248
Period size: 39 Copynumber: 5.7 Consensus size: 40
31492397 GCTCCTCGTT
* *
31492407 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
31492447 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
31492487 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
*
31492526 CAAATGCCTTCGGG-CTTAGCCTGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* * *
31492565 CAAATGCCTTC-GAATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
31492606 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
31492630 CATCATTCAA
Statistics
Matches: 162, Mismatches: 13, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
38 1 0.01
39 88 0.54
40 62 0.38
41 11 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:31507557 original size:12 final size:13
Alignment explanation
Indices: 31507509--31507625 Score: 71
Period size: 12 Copynumber: 8.5 Consensus size: 13
31507499 AAAACAAATG
31507509 AGAGAAAAAGAAA
1 AGAGAAAAAGAAA
* *
31507522 AGAATGTAAAAGTGAA
1 AG-A-GAAAAAG-AAA
*
31507538 AGACAAAAA-AAA
1 AGAGAAAAAGAAA
*
31507550 AGAGAAAAA-TAA
1 AGAGAAAAAGAAA
*
31507562 AGAAAAAATAGCAAA
1 AGAGAAAA-AG-AAA
31507577 AGAGAGTGAAAAGAAA
1 AGAGA---AAAAGAAA
31507593 ATGAG-AAAAGAAA
1 A-GAGAAAAAGAAA
31507606 AGATGAAAAAGAAA
1 AGA-GAAAAAGAAA
31507620 AG-GAAA
1 AGAGAAA
31507626 GTGAGAAAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 25
0.70 0.09 0.21
Matches are distributed among these distances:
12 25 0.30
13 13 0.16
14 15 0.18
15 13 0.16
16 8 0.10
17 5 0.06
18 3 0.04
ACGTcount: A:0.70, C:0.02, G:0.21, T:0.07
Consensus pattern (13 bp):
AGAGAAAAAGAAA
Found at i:31507602 original size:13 final size:13
Alignment explanation
Indices: 31507583--31507621 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
31507573 CAAAAGAGAG
31507583 TGAAAAGAAAATGA
1 TGAAAAGAAAA-GA
31507597 -GAAAAGAAAAGA
1 TGAAAAGAAAAGA
31507609 TGAAAAAGAAAAG
1 TG-AAAAGAAAAG
31507622 GAAAGTGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 2 0.09
13 11 0.48
14 10 0.43
ACGTcount: A:0.69, C:0.00, G:0.23, T:0.08
Consensus pattern (13 bp):
TGAAAAGAAAAGA
Found at i:31507617 original size:14 final size:15
Alignment explanation
Indices: 31507584--31507621 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
31507574 AAAAGAGAGT
31507584 GAAAAG-AAA-ATGA
1 GAAAAGAAAAGATGA
31507597 GAAAAGAAAAGATGA
1 GAAAAGAAAAGATGA
31507612 -AAAAGAAAAG
1 GAAAAGAAAAG
31507622 GAAAGTGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 13 0.57
15 4 0.17
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.05
Consensus pattern (15 bp):
GAAAAGAAAAGATGA
Found at i:31523236 original size:17 final size:16
Alignment explanation
Indices: 31523207--31523250 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
31523197 CTTTTTGCTC
31523207 TCTTTTATTTTCTTT-T
1 TCTTTTATTTT-TTTCT
31523223 TC--TTATTTTTTTCT
1 TCTTTTATTTTTTTCT
31523237 TCTTTTATTTTTTT
1 TCTTTTATTTTTTT
31523251 ACAATCTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.12
14 10 0.40
16 12 0.48
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.82
Consensus pattern (16 bp):
TCTTTTATTTTTTTCT
Found at i:31525328 original size:11 final size:11
Alignment explanation
Indices: 31525312--31525409 Score: 117
Period size: 11 Copynumber: 8.6 Consensus size: 11
31525302 TAGTTTCAAT
31525312 TTTTTTTGAAA
1 TTTTTTTGAAA
31525323 TTTTTTTGAAA
1 TTTTTTTGAAA
31525334 -TTTTTTGAAA
1 TTTTTTTGAAA
31525344 TTTTTTTGAAA
1 TTTTTTTGAAA
*
31525355 TTTTTTTGAAC
1 TTTTTTTGAAA
31525366 TTTTTTTCGAAA
1 TTTTTTT-GAAA
*
31525378 CTTTTTTTTGAAC
1 --TTTTTTTGAAA
* *
31525391 TTTTGTCGAAA
1 TTTTTTTGAAA
31525402 CTTTTTTT
1 -TTTTTTT
31525410 TCACTTACTT
Statistics
Matches: 74, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
10 10 0.14
11 46 0.62
12 8 0.11
13 3 0.04
14 7 0.09
ACGTcount: A:0.22, C:0.06, G:0.09, T:0.62
Consensus pattern (11 bp):
TTTTTTTGAAA
Found at i:31525410 original size:24 final size:24
Alignment explanation
Indices: 31525311--31525410 Score: 111
Period size: 21 Copynumber: 4.3 Consensus size: 24
31525301 CTAGTTTCAA
* *
31525311 TTTTTTTTGAAATTTTTTTGAAA-
1 TTTTTTTTGAACTTTTTTCGAAAC
* *
31525334 --TTTTTTGAAATTTTTTTGAAA-
1 TTTTTTTTGAACTTTTTTCGAAAC
31525355 -TTTTTTTGAACTTTTTTTCGAAAC
1 TTTTTTTTGAAC-TTTTTTCGAAAC
*
31525379 TTTTTTTTGAACTTTTGTCGAAAC
1 TTTTTTTTGAACTTTTTTCGAAAC
31525403 TTTTTTTT
1 TTTTTTTT
31525411 CACTTACTTG
Statistics
Matches: 70, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
21 21 0.30
22 9 0.13
23 10 0.14
24 19 0.27
25 11 0.16
ACGTcount: A:0.22, C:0.06, G:0.09, T:0.63
Consensus pattern (24 bp):
TTTTTTTTGAACTTTTTTCGAAAC
Found at i:31531878 original size:6 final size:6
Alignment explanation
Indices: 31531869--31531957 Score: 63
Period size: 6 Copynumber: 14.5 Consensus size: 6
31531859 TGAAAGAAAC
* ** ** *
31531869 AAAAAG AAAACG AAAAAG AAAAAG AAATCG -AAAAG TGAGAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
* * *
31531916 AAAATG AAGAAAG AAAATTG AAAAAG AAAAGCG AAAAAG AAA
1 AAAAAG AA-AAAG AAAA-AG AAAAAG AAAA-AG AAAAAG AAA
31531958 TTGAAAGAGA
Statistics
Matches: 62, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
5 3 0.05
6 44 0.71
7 15 0.24
ACGTcount: A:0.71, C:0.03, G:0.20, T:0.06
Consensus pattern (6 bp):
AAAAAG
Found at i:31531886 original size:12 final size:12
Alignment explanation
Indices: 31531869--31531957 Score: 63
Period size: 13 Copynumber: 7.2 Consensus size: 12
31531859 TGAAAGAAAC
*
31531869 AAAAAGAAAACG
1 AAAAAGAAAAAG
31531881 AAAAAGAAAAAG
1 AAAAAGAAAAAG
**
31531893 AAATCG-AAAAG
1 AAAAAGAAAAAG
** *
31531904 TGAGAGAAAAAG
1 AAAAAGAAAAAG
*
31531916 AAAATGAAGAAAG
1 AAAAAGAA-AAAG
*
31531929 AAAATTGAAAAAG
1 AAAA-AGAAAAAG
*
31531942 AAAAGCGAAAAAG
1 AAAA-AGAAAAAG
31531955 AAA
1 AAA
31531958 TTGAAAGAGA
Statistics
Matches: 61, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
11 7 0.11
12 24 0.39
13 26 0.43
14 4 0.07
ACGTcount: A:0.71, C:0.03, G:0.20, T:0.06
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:31531939 original size:25 final size:25
Alignment explanation
Indices: 31531909--31531963 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
31531899 AAAAGTGAGA
*
31531909 GAAAAAGAAAA-TGAAGAAAGAAAATT
1 GAAAAAGAAAAGCGAA-AAAG-AAATT
31531935 GAAAAAGAAAAGCGAAAAAGAAATT
1 GAAAAAGAAAAGCGAAAAAGAAATT
31531960 GAAA
1 GAAA
31531964 GAGAGCTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 9 0.33
26 15 0.56
27 3 0.11
ACGTcount: A:0.69, C:0.02, G:0.20, T:0.09
Consensus pattern (25 bp):
GAAAAAGAAAAGCGAAAAAGAAATT
Found at i:31531963 original size:12 final size:12
Alignment explanation
Indices: 31531909--31531981 Score: 58
Period size: 13 Copynumber: 5.9 Consensus size: 12
31531899 AAAAGTGAGA
*
31531909 GAAAAAGAAAAT
1 GAAAAAGAAATT
31531921 GAAGAAAGAAAATT
1 GAA-AAAG-AAATT
**
31531935 GAAAAAGAAAAGC
1 GAAAAAG-AAATT
31531948 GAAAAAGAAATT
1 GAAAAAGAAATT
* **
31531960 GAAAGAGAGCTT
1 GAAAAAGAAATT
31531972 G-AAAAGAAAT
1 GAAAAAGAAAT
31531982 CAAGTGAAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
11 6 0.12
12 16 0.33
13 19 0.40
14 7 0.15
ACGTcount: A:0.64, C:0.03, G:0.22, T:0.11
Consensus pattern (12 bp):
GAAAAAGAAATT
Found at i:31531979 original size:62 final size:61
Alignment explanation
Indices: 31531841--31531980 Score: 144
Period size: 61 Copynumber: 2.3 Consensus size: 61
31531831 AGAAAAGGAG
* *
31531841 AAGAGA-TTGAAAAGAAATTGAAAGAAACAAAAAGAAAACGAAAAAGAAAAAGAAATCGAA
1 AAGAGAGTTGAAAAGAAAATGAAAGAAACAAAAAGAAAAAGAAAAAGAAAAAGAAATCGAA
* * * * * *
31531901 AAGTGAG-AGAAAAAGAAAATG-AAGAAAGAAAATTGAAAAAGAAAAGCGAAAAAGAAATTG-A
1 AAGAGAGTTG-AAAAGAAAATGAAAGAAACAAAA-AGAAAAAGAAAA-AGAAAAAGAAATCGAA
31531962 AAGAGAGCTTGAAAAGAAA
1 AAGAGAG-TTGAAAAGAAA
31531981 TCAAGTGAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
60 16 0.25
61 27 0.42
62 20 0.31
63 1 0.02
ACGTcount: A:0.66, C:0.04, G:0.21, T:0.09
Consensus pattern (61 bp):
AAGAGAGTTGAAAAGAAAATGAAAGAAACAAAAAGAAAAAGAAAAAGAAAAAGAAATCGAA
Found at i:31532001 original size:33 final size:33
Alignment explanation
Indices: 31531960--31532022 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
31531950 AAAAGAAATT
31531960 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
31531993 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
31532023 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:31533805 original size:20 final size:20
Alignment explanation
Indices: 31533782--31533835 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
31533772 AGTTTTCCCC
*
31533782 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
31533802 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
31533822 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
31533836 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:31533817 original size:30 final size:30
Alignment explanation
Indices: 31533782--31533855 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
31533772 AGTTTTCCCC
31533782 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
31533812 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
31533842 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
31533856 TGACTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:31533845 original size:20 final size:20
Alignment explanation
Indices: 31533782--31533846 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
31533772 AGTTTTCCCC
* * * *
31533782 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
31533802 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
31533821 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
31533842 AGCTC
1 AGCTC
31533847 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:31536581 original size:17 final size:16
Alignment explanation
Indices: 31536561--31536592 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
31536551 TTTCACAGTC
31536561 TTTCTCTTTTTCTTTCT
1 TTTCT-TTTTTCTTTCT
31536578 TTTCTTTTTTCTTTC
1 TTTCTTTTTTCTTTC
31536593 ACACTCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTCTTTTTTCTTTCT
Found at i:31540073 original size:46 final size:45
Alignment explanation
Indices: 31540020--31540195 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 45
31540010 TATTTGGGCA
31540020 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
31540066 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
31540113 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
31540159 CCCGAGA-TCGTTGAGTTGAGTCTGAGTTCACTTATGG
1 TCCGA-ACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
31540196 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 66 0.61
47 32 0.30
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:31540175 original size:93 final size:93
Alignment explanation
Indices: 31540016--31540187 Score: 292
Period size: 93 Copynumber: 1.8 Consensus size: 93
31540006 AGGATATTTG
* *
31540016 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
31540081 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
*
31540109 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGA-TCGTTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGA-ACTCGTTGA
*
31540173 GTTGAGTCTGAGTTC
65 GTTGAGTCCGAGTTC
31540188 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
93 73 0.99
94 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:31540326 original size:21 final size:21
Alignment explanation
Indices: 31540301--31540344 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
31540291 CTACTTAAAT
31540301 GGAGGAATACTCGAGATGAAA
1 GGAGGAATACTCGAGATGAAA
31540322 GGAGGAATACTCGAGATGAAA
1 GGAGGAATACTCGAGATGAAA
31540343 GG
1 GG
31540345 GACGTATTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.09, G:0.36, T:0.14
Consensus pattern (21 bp):
GGAGGAATACTCGAGATGAAA
Found at i:31546953 original size:13 final size:12
Alignment explanation
Indices: 31546935--31546992 Score: 55
Period size: 14 Copynumber: 4.6 Consensus size: 12
31546925 ACGGTATTGT
*
31546935 AAAAAAAATAT-
1 AAAAAAAATTTA
31546946 AAAAAAAATTTGAA
1 AAAAAAAATTT--A
31546960 AAAAAAAATTTTGA
1 AAAAAAAA-TTT-A
*
31546974 AAAAAAAATTCA
1 AAAAAAAATTTA
31546986 AAAAAAA
1 AAAAAAA
31546993 GTTTGTATTC
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
11 10 0.25
12 8 0.20
13 2 0.05
14 17 0.43
15 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.03, T:0.19
Consensus pattern (12 bp):
AAAAAAAATTTA
Found at i:31546983 original size:14 final size:15
Alignment explanation
Indices: 31546946--31546981 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
31546936 AAAAAAATAT
31546946 AAAAAAAA-TTTGAA
1 AAAAAAAATTTTGAA
31546960 AAAAAAAATTTTGAA
1 AAAAAAAATTTTGAA
31546975 AAAAAAA
1 AAAAAAA
31546982 TTCAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (15 bp):
AAAAAAAATTTTGAA
Found at i:31546990 original size:14 final size:14
Alignment explanation
Indices: 31546946--31546992 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
31546936 AAAAAAATAT
*
31546946 AAAAAAAATTTGAA
1 AAAAAAAATTTAAA
**
31546960 AAAAAAAATTTTGA
1 AAAAAAAATTTAAA
*
31546974 AAAAAAAATTCAAA
1 AAAAAAAATTTAAA
31546988 AAAAA
1 AAAAA
31546993 GTTTGTATTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.19
Consensus pattern (14 bp):
AAAAAAAATTTAAA
Found at i:31547083 original size:29 final size:32
Alignment explanation
Indices: 31547036--31547106 Score: 103
Period size: 29 Copynumber: 2.3 Consensus size: 32
31547026 AGTATTGAAG
* *
31547036 AAAAAAAAGAAGAAGAAAAAATTCAGAATT-A
1 AAAAAAAAGAAGAAGAAAAAAATCAAAATTGA
31547067 AAAAAAAAGAAG-A-AAAAAAATCAAAATTGA
1 AAAAAAAAGAAGAAGAAAAAAATCAAAATTGA
31547097 AAAAAAAAGA
1 AAAAAAAAGA
31547107 GTGATTGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
29 13 0.35
30 12 0.32
31 12 0.32
ACGTcount: A:0.76, C:0.03, G:0.11, T:0.10
Consensus pattern (32 bp):
AAAAAAAAGAAGAAGAAAAAAATCAAAATTGA
Done.