Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 46 of 425
Found at i:12315521 original size:22 final size:22
Alignment explanation
Indices: 12315486--12315528 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
12315476 AACATTGAAC
*
12315486 TTACTCAAAGAAAACAACTAAG
1 TTACTCAAAGAAAAAAACTAAG
12315508 TTAC-CAAAGAAAAAAAACTAA
1 TTACTCAAAG-AAAAAAACTAA
12315529 AATATCATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.60, C:0.16, G:0.07, T:0.16
Consensus pattern (22 bp):
TTACTCAAAGAAAAAAACTAAG
Found at i:12317660 original size:43 final size:43
Alignment explanation
Indices: 12317613--12317704 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 43
12317603 ATTTTAGGAA
*
12317613 TATTTTTATTTTATCTTTTAATAGTTTATTAGAATAAGGAAAC
1 TATTTTTATTTTATATTTTAATAGTTTATTAGAATAAGGAAAC
* * *
12317656 TA-TTTTCTTTTATATTTTAGTAGTTTATTAGAATAAGGGAAC
1 TATTTTTATTTTATATTTTAATAGTTTATTAGAATAAGGAAAC
12317698 TATTTTT
1 TATTTTT
12317705 CCAATTAGGA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 38 0.86
43 6 0.14
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.53
Consensus pattern (43 bp):
TATTTTTATTTTATATTTTAATAGTTTATTAGAATAAGGAAAC
Found at i:12321506 original size:19 final size:18
Alignment explanation
Indices: 12321477--12321516 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
12321467 GTATATATTT
12321477 TAAATTTATTTAGGTAGA
1 TAAATTTATTTAGGTAGA
12321495 TAAATCTTATTTAGGTAGA
1 TAAAT-TTATTTAGGTAGA
12321514 TAA
1 TAA
12321517 GTTTCATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.40, C:0.03, G:0.15, T:0.42
Consensus pattern (18 bp):
TAAATTTATTTAGGTAGA
Found at i:12322841 original size:22 final size:22
Alignment explanation
Indices: 12322813--12322864 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
12322803 AAATTTTTTG
*
12322813 TTGTTGTTGTTTTGCTGTCATT
1 TTGTTGTTGTTTTGCTATCATT
*
12322835 TTGTTGTTGTTTTGTTATCATT
1 TTGTTGTTGTTTTGCTATCATT
*
12322857 TTATTGTT
1 TTGTTGTT
12322865 ATATTTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.08, C:0.06, G:0.19, T:0.67
Consensus pattern (22 bp):
TTGTTGTTGTTTTGCTATCATT
Found at i:12322874 original size:22 final size:22
Alignment explanation
Indices: 12322816--12322883 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
12322806 TTTTTTGTTG
* * * *
12322816 TTGTTGTTTTGCTGTCATTTTG
1 TTGTTATTTTGTTATCATTTTA
*
12322838 TTGTTGTTTTGTTATCATTTTA
1 TTGTTATTTTGTTATCATTTTA
*
12322860 TTGTTATATTT-TTATTATTTTA
1 TTGTTAT-TTTGTTATCATTTTA
12322882 TT
1 TT
12322884 ATTTTTGTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
22 37 0.93
23 3 0.08
ACGTcount: A:0.13, C:0.04, G:0.13, T:0.69
Consensus pattern (22 bp):
TTGTTATTTTGTTATCATTTTA
Found at i:12322886 original size:17 final size:17
Alignment explanation
Indices: 12322857--12322889 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12322847 TGTTATCATT
12322857 TTATTGTTATATTTTTA
1 TTATTGTTATATTTTTA
12322874 TTATT-TTATTATTTTT
1 TTATTGTTA-TATTTTT
12322890 GTTTAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (17 bp):
TTATTGTTATATTTTTA
Found at i:12323344 original size:29 final size:30
Alignment explanation
Indices: 12323297--12323381 Score: 154
Period size: 29 Copynumber: 2.9 Consensus size: 30
12323287 AAATATGTTA
12323297 TAAGTTTTTGTATTTTTTATTTATTTTTAG
1 TAAGTTTTTGTATTTTTTATTTATTTTTAG
12323327 TAAGTTTTTGTA-TTTTTATTTATTTTTAG
1 TAAGTTTTTGTATTTTTTATTTATTTTTAG
*
12323356 TAAGTTTTTGTATTTTTTATATATTT
1 TAAGTTTTTGTATTTTTTATTTATTT
12323382 AGAACTTAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
29 29 0.55
30 24 0.45
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.69
Consensus pattern (30 bp):
TAAGTTTTTGTATTTTTTATTTATTTTTAG
Found at i:12324006 original size:23 final size:23
Alignment explanation
Indices: 12323971--12324015 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
12323961 TATATAATAA
* *
12323971 ATATATATTTTTTATTTTTAATT
1 ATATATATATTTTAATTTTAATT
*
12323994 ATATTTATATTTTAATTTTAAT
1 ATATATATATTTTAATTTTAAT
12324016 ATAATCAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
ATATATATATTTTAATTTTAATT
Found at i:12325530 original size:26 final size:26
Alignment explanation
Indices: 12325494--12325603 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
12325484 TGATACAAAT
12325494 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
* *
12325520 TGATAATAGGTTAGGTAAATATTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
* *
12325546 TGATAATGGGTTAGGTCAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
12325572 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
12325598 TGATAA
1 TGATAA
12325604 GAATTTCATG
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:12333424 original size:21 final size:23
Alignment explanation
Indices: 12333377--12333430 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
12333367 CATTCAAGAT
**
12333377 AAAATAATATATAAAACTCTTTA
1 AAAATAATATATAAAACTAATTA
*
12333400 AAAATAATATAT-AAAC-AATTC
1 AAAATAATATATAAAACTAATTA
12333421 AAAAT-ATATA
1 AAAATAATATA
12333431 ATGTGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.18
21 7 0.25
22 4 0.14
23 12 0.43
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAATAATATATAAAACTAATTA
Found at i:12333662 original size:15 final size:15
Alignment explanation
Indices: 12333638--12333683 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
12333628 ATATAAATAG
*
12333638 AAATAAAAATATAAT
1 AAATAGAAATATAAT
12333653 AAATAGAAATATAAT
1 AAATAGAAATATAAT
12333668 AATAGTAGAAATATAA
1 AA-A-TAGAAATATAA
12333684 ATAGATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 16 0.57
16 1 0.04
17 11 0.39
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (15 bp):
AAATAGAAATATAAT
Found at i:12333671 original size:23 final size:23
Alignment explanation
Indices: 12333605--12333671 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 23
12333595 TATAAGAAAA
*
12333605 ATAAT-AAT-GAAA-ATAATATT
1 ATAATAAATAGAAATATAATAAT
12333625 AGTATATAAATAGAAATA-AA-AAT
1 A-TA-ATAAATAGAAATATAATAAT
12333648 ATAATAAATAGAAATATAATAAT
1 ATAATAAATAGAAATATAATAAT
12333671 A
1 A
12333672 GTAGAAATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
20 1 0.03
21 15 0.38
22 6 0.15
23 10 0.26
24 6 0.15
25 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (23 bp):
ATAATAAATAGAAATATAATAAT
Found at i:12333703 original size:15 final size:14
Alignment explanation
Indices: 12333630--12333715 Score: 59
Period size: 15 Copynumber: 5.9 Consensus size: 14
12333620 ATATTAGTAT
*
12333630 ATAAATAGAAATA-
1 ATAAATAAAAATAG
*
12333643 AAAATATAATAAATAG
1 ATAA-ATAA-AAATAG
*
12333659 A-AATATAATAATAG
1 ATAA-ATAAAAATAG
* *
12333673 TAGAAATATAAATAG
1 -ATAAATAAAAATAG
12333688 ATAAATAAAAATTAG
1 ATAAATAAAAA-TAG
*
12333703 ATAAATAACAATA
1 ATAAATAAAAATA
12333716 ATATTAGAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
13 3 0.05
14 19 0.32
15 34 0.58
16 3 0.05
ACGTcount: A:0.66, C:0.01, G:0.07, T:0.26
Consensus pattern (14 bp):
ATAAATAAAAATAG
Found at i:12335027 original size:31 final size:31
Alignment explanation
Indices: 12334978--12335049 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
12334968 CAAAGATTAA
* ** * * *
12334978 GTACCAACTTAAGGAAAAATGTCAAGTTTTG
1 GTACCAAATTAAAAAAAAAGGTCAAATTTAG
12335009 GTACCAAATTAAAAAAAAAGGTCAAATTTAG
1 GTACCAAATTAAAAAAAAAGGTCAAATTTAG
*
12335040 ATACCAAATT
1 GTACCAAATT
12335050 GAACTAAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.26
Consensus pattern (31 bp):
GTACCAAATTAAAAAAAAAGGTCAAATTTAG
Found at i:12336661 original size:18 final size:19
Alignment explanation
Indices: 12336623--12336663 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
12336613 TTGGTTCATG
12336623 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
12336642 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
12336660 TTTC
1 TTTC
12336664 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:12337218 original size:25 final size:26
Alignment explanation
Indices: 12337190--12337261 Score: 78
Period size: 24 Copynumber: 2.9 Consensus size: 26
12337180 CACATATAAC
12337190 ATATAAATTCAATTCAATTCAATCA-
1 ATATAAATTCAATTCAATTCAATCAT
* *
12337215 ATATAAATTCAA-TAAATTC-ATTAT
1 ATATAAATTCAATTCAATTCAATCAT
* * *
12337239 ATATAAAATCAATCCATTTCAAT
1 ATATAAATTCAATTCAATTCAAT
12337262 TATAAAACAC
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
23 3 0.08
24 17 0.45
25 16 0.42
26 2 0.05
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.38
Consensus pattern (26 bp):
ATATAAATTCAATTCAATTCAATCAT
Found at i:12338034 original size:18 final size:18
Alignment explanation
Indices: 12338013--12338049 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12338003 AATAATAATT
*
12338013 ATAATAAAAATTTATTTA
1 ATAACAAAAATTTATTTA
*
12338031 ATAACAAATATTTATTTA
1 ATAACAAAAATTTATTTA
12338049 A
1 A
12338050 CACTTTTACC
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:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAACAAAAATTTATTTA
Found at i:12338127 original size:11 final size:12
Alignment explanation
Indices: 12338108--12338141 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
12338098 TATATATATA
12338108 TATATAATAACT
1 TATATAATAACT
12338120 TA-ATAATATACT
1 TATATAATA-ACT
12338132 TATATAATAA
1 TATATAATAA
12338142 GTAAACATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 6 0.30
12 8 0.40
13 6 0.30
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (12 bp):
TATATAATAACT
Found at i:12338542 original size:3 final size:3
Alignment explanation
Indices: 12338534--12338592 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
12338524 TATTTTAACT
12338534 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12338582 TAA TAA TAA TA
1 TAA TAA TAA TA
12338593 GTTTAATATA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:12340024 original size:21 final size:22
Alignment explanation
Indices: 12339998--12340042 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
12339988 TATTTTTATT
* *
12339998 TAATTT-TGAAAATTAAAAAAG
1 TAATTTATCAAAAATAAAAAAG
*
12340019 TAATTTATCAAAAATGAAAAAG
1 TAATTTATCAAAAATAAAAAAG
12340041 TA
1 TA
12340043 TGCTTTGCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.31
Consensus pattern (22 bp):
TAATTTATCAAAAATAAAAAAG
Found at i:12340499 original size:42 final size:41
Alignment explanation
Indices: 12340423--12340663 Score: 189
Period size: 43 Copynumber: 5.7 Consensus size: 41
12340413 CTTTTTCCAT
* * *
12340423 AAACGCCGCTATAGAACATGACTTTTA-TCGATGCTTTACCTC
1 AAACGCCGCTAAAGAACATGACCTTTAGT-GACGCTTT-CCTC
* * *
12340465 AAACGCCGCTAAAGAACATGACCTTTAGTTATGCTTTTCTCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGTGACGC-TTTC-CTC
* ** * * * **
12340508 AAACACTACTAAATAACATGGCCTTTAGTGGCGCATTTTTTAC
1 AAACGCCGCTAAAGAACATGACCTTTAGTGACGC-TTTCCT-C
*
12340551 AAACGCACGCTAAAGAACATGACCTTTAATGACGCTTTTCCTAC
1 AAACGC-CGCTAAAGAACATGACCTTTAGTGACGC-TTTCCT-C
* * * * *
12340595 AAACGCCGCTATAGAACA-GACCTTTAGCGGCACTTTTCTC
1 AAACGCCGCTAAAGAACATGACCTTTAGTGACGCTTTCCTC
12340635 ACGAACGCCGCTAAAGAACATGACCTTTA
1 A--AACGCCGCTAAAGAACATGACCTTTA
12340664 AAAAATATTT
Statistics
Matches: 158, Mismatches: 33, Indels: 15
0.77 0.16 0.07
Matches are distributed among these distances:
40 2 0.01
41 5 0.03
42 57 0.36
43 60 0.38
44 34 0.22
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (41 bp):
AAACGCCGCTAAAGAACATGACCTTTAGTGACGCTTTCCTC
Found at i:12340575 original size:87 final size:85
Alignment explanation
Indices: 12340464--12340664 Score: 235
Period size: 87 Copynumber: 2.3 Consensus size: 85
12340454 TGCTTTACCT
* * * * *
12340464 CAAACGCCGCTAAAGAACATGACCTTTAGTTATGCTTTT-CTCACAAACACTACTAAATAACATG
1 CAAACGCCGCTAAAGAACATGACCTTTAATGACGCTTTTCCT-ACAAACACCACTAAAGAACA-G
* * * *
12340528 GCCTTTAGTGGCGCATTTT-TTA
64 ACCTTTAGCGGCAC-TTTTCTCA
* * *
12340550 CAAACGCACGCTAAAGAACATGACCTTTAATGACGCTTTTCCTACAAACGCCGCTATAGAACAGA
1 CAAACGC-CGCTAAAGAACATGACCTTTAATGACGCTTTTCCTACAAACACCACTAAAGAACAGA
12340615 CCTTTAGCGGCACTTTTCTCA
65 CCTTTAGCGGCACTTTTCTCA
*
12340636 CGAACGCCGCTAAAGAACATGACCTTTAA
1 CAAACGCCGCTAAAGAACATGACCTTTAA
12340665 AAAATATTTT
Statistics
Matches: 99, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
85 26 0.26
86 27 0.27
87 44 0.44
88 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (85 bp):
CAAACGCCGCTAAAGAACATGACCTTTAATGACGCTTTTCCTACAAACACCACTAAAGAACAGAC
CTTTAGCGGCACTTTTCTCA
Found at i:12340631 original size:129 final size:128
Alignment explanation
Indices: 12340392--12340663 Score: 298
Period size: 129 Copynumber: 2.1 Consensus size: 128
12340382 ACCCCTCTAT
* * * * * * * *
12340392 AGAACATAAACTTTAGCGGCGC-TTTTTCCATAAACGCCGCTATAGAACATGACTTTTATCGATG
1 AGAACATGACCTTTAGTGGCGCATTTTT-TACAAACGCCGCTAAAGAACATGACTTTAATCGACG
** ** *
12340456 CTTTACCTCAAACGCCGCTAAAGAACATGACCTTTAGTTATGCTTTTCTCACAAACACTACTAA
65 CTTTACCTCAAACGCCGCTAAAGAACATGACCTTTAGCGACACTTTTCTCACAAACACCACTAA
* *
12340520 ATAACATGGCCTTTAGTGGCGCATTTTTTACAAACGCACGCTAAAGAACATGACCTTTAAT-GAC
1 AGAACATGACCTTTAGTGGCGCATTTTTTACAAACGC-CGCTAAAGAACATGA-CTTTAATCGAC
* * * * * *
12340584 GCTTTTCCTACAAACGCCGCTATAGAACA-GACCTTTAGCGGCACTTTTCTCACGAACGCCGCTA
64 GCTTTACCT-CAAACGCCGCTAAAGAACATGACCTTTAGCGACACTTTTCTCACAAACACCACTA
12340648 A
128 A
12340649 AGAACATGACCTTTA
1 AGAACATGACCTTTA
12340664 AAAAATATTT
Statistics
Matches: 117, Mismatches: 23, Indels: 7
0.80 0.16 0.05
Matches are distributed among these distances:
128 24 0.21
129 69 0.59
130 24 0.21
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (128 bp):
AGAACATGACCTTTAGTGGCGCATTTTTTACAAACGCCGCTAAAGAACATGACTTTAATCGACGC
TTTACCTCAAACGCCGCTAAAGAACATGACCTTTAGCGACACTTTTCTCACAAACACCACTAA
Found at i:12340872 original size:12 final size:12
Alignment explanation
Indices: 12340857--12340909 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
12340847 CAAGTTATCT
*
12340857 TAAATATTAAAA
1 TAAAAATTAAAA
*
12340869 TAAAAATAAAAA
1 TAAAAATTAAAA
*
12340881 TAAAAATTTAGAA
1 TAAAAA-TTAAAA
* *
12340894 TCAAAACTAAAA
1 TAAAAATTAAAA
12340906 TAAA
1 TAAA
12340910 TATCAATAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
12 23 0.72
13 9 0.28
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.25
Consensus pattern (12 bp):
TAAAAATTAAAA
Found at i:12348045 original size:26 final size:26
Alignment explanation
Indices: 12348002--12348074 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 26
12347992 TCTCATCCCT
* ** **
12348002 ATTTTACCCCCAACAAAATTTTGATG
1 ATTTTACCCCTAGTAAAATTTTGACA
12348028 ATTTTACCCCTAGTAAAATTTTGACA
1 ATTTTACCCCTAGTAAAATTTTGACA
* * *
12348054 ATTTTGCCTCTGGTAAAATTT
1 ATTTTACCCCTAGTAAAATTT
12348075 CGAGAAAATA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.40
Consensus pattern (26 bp):
ATTTTACCCCTAGTAAAATTTTGACA
Found at i:12350981 original size:46 final size:46
Alignment explanation
Indices: 12350929--12351339 Score: 538
Period size: 46 Copynumber: 9.0 Consensus size: 46
12350919 GCTTTCTGAA
12350929 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
12350975 ATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
12351021 ATAAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
12351067 ATGAAATGTGTAAGACCATGGTTGAAAGATACTATGGCAACATTAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
12351113 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAGGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
12351159 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGA-
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
** * ** * ** * *
12351204 CGGGAATGAATAAAACCATGGTTGAAAGATACCATGGCAATGTAAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*** * * *
12351250 ATGAAATGAACAAGACCATGGTTGAAAGATACCATGACAACCTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * * * * *
12351296 A-GAAAATGAGTAAAACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG
12351340 TCAAAGATAA
Statistics
Matches: 324, Mismatches: 39, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
45 36 0.11
46 288 0.89
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
Found at i:12353418 original size:19 final size:19
Alignment explanation
Indices: 12353396--12353432 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
12353386 AACACTGTCA
12353396 CCCACCGTAATCAAATTTG
1 CCCACCGTAATCAAATTTG
12353415 CCCACCGTAATCAAATTT
1 CCCACCGTAATCAAATTT
12353433 TTTATTAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.08, T:0.27
Consensus pattern (19 bp):
CCCACCGTAATCAAATTTG
Found at i:12355995 original size:25 final size:25
Alignment explanation
Indices: 12355967--12356018 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
12355957 TTTGGCTTAA
**
12355967 CATTTACTAAGCAATATCGGATATT
1 CATTTACTAAGCAATATCAAATATT
* *
12355992 CATTTATTAGGCAATATCAAATATT
1 CATTTACTAAGCAATATCAAATATT
12356017 CA
1 CA
12356019 AATTATTCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (25 bp):
CATTTACTAAGCAATATCAAATATT
Found at i:12371287 original size:23 final size:23
Alignment explanation
Indices: 12371260--12371306 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
12371250 TAAGAAGACT
* *
12371260 ATAGGGACTTAGATTATAATTTA
1 ATAGGGACCTAGATCATAATTTA
12371283 ATAGGGACCTAGATCATAATTTA
1 ATAGGGACCTAGATCATAATTTA
12371306 A
1 A
12371307 CCTTTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (23 bp):
ATAGGGACCTAGATCATAATTTA
Found at i:12371350 original size:26 final size:26
Alignment explanation
Indices: 12371314--12371366 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
12371304 TAACCTTTTA
12371314 TTTTTAATATAGTTTTAACAATCATT
1 TTTTTAATATAGTTTTAACAATCATT
12371340 TTTTTAATATAGTTTTAACAATCATT
1 TTTTTAATATAGTTTTAACAATCATT
12371366 T
1 T
12371367 GTAAGGAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.08, G:0.04, T:0.55
Consensus pattern (26 bp):
TTTTTAATATAGTTTTAACAATCATT
Found at i:12376954 original size:18 final size:18
Alignment explanation
Indices: 12376931--12376991 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
12376921 TTTGTTTATT
12376931 GTTATTCAATAACAATCA
1 GTTATTCAATAACAATCA
* * * *
12376949 GTTATTTAGTATCAAACA
1 GTTATTCAATAACAATCA
12376967 ---A-TCAATAACAATCA
1 GTTATTCAATAACAATCA
12376981 GTTATTCAATA
1 GTTATTCAATA
12376992 TCAAACAATC
Statistics
Matches: 31, Mismatches: 8, Indels: 8
0.66 0.17 0.17
Matches are distributed among these distances:
14 9 0.29
15 1 0.03
17 1 0.03
18 20 0.65
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (18 bp):
GTTATTCAATAACAATCA
Found at i:12377020 original size:32 final size:32
Alignment explanation
Indices: 12376936--12377012 Score: 136
Period size: 32 Copynumber: 2.4 Consensus size: 32
12376926 TTATTGTTAT
* *
12376936 TCAATAACAATCAGTTATTTAGTATCAAACAA
1 TCAATAACAATCAGTTATTCAATATCAAACAA
12376968 TCAATAACAATCAGTTATTCAATATCAAACAA
1 TCAATAACAATCAGTTATTCAATATCAAACAA
12377000 TCAATAACAATCA
1 TCAATAACAATCA
12377013 ATAATTCAGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.49, C:0.18, G:0.04, T:0.29
Consensus pattern (32 bp):
TCAATAACAATCAGTTATTCAATATCAAACAA
Found at i:12378773 original size:30 final size:30
Alignment explanation
Indices: 12378739--12378795 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
12378729 ACTTAACAAG
*
12378739 CAAATACCATTAAAATAATAACAAAATTAA
1 CAAATACCATTAAAATAATAAAAAAATTAA
* *
12378769 CAAATGCCTTTAAAATAATAAAAAAAT
1 CAAATACCATTAAAATAATAAAAAAAT
12378796 AAGTTTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.61, C:0.12, G:0.02, T:0.25
Consensus pattern (30 bp):
CAAATACCATTAAAATAATAAAAAAATTAA
Found at i:12379299 original size:20 final size:20
Alignment explanation
Indices: 12379276--12379338 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
12379266 TTAATTTATT
*
12379276 TTTAATAATAATAATCATAA
1 TTTAATAATAATAATAATAA
*
12379296 TTTAATAA-AATAAATTATAA
1 TTTAATAATAAT-AATAATAA
*
12379316 TTTGATAGTATAATAATAATAA
1 TTTAATA--ATAATAATAATAA
12379338 T
1 T
12379339 AATGATAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 3 0.08
20 21 0.58
22 9 0.25
23 3 0.08
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (20 bp):
TTTAATAATAATAATAATAA
Found at i:12383996 original size:25 final size:24
Alignment explanation
Indices: 12383923--12383997 Score: 60
Period size: 25 Copynumber: 3.0 Consensus size: 24
12383913 TTAAATAGTC
*
12383923 GTGGATGGTTCCGTGCGAAGGTACA
1 GTGGATGGTTCTGTG-GAAGGTACA
* * * **
12383948 ATGGATGGTATTTGTGGGAGGGTATT
1 GTGGATGGT-TCTGT-GGAAGGTACA
12383974 GTGGATGGTTCTGTGGAAAGGTAC
1 GTGGATGGTTCTGTGG-AAGGTAC
12383998 CGTAGGAGTG
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
24 2 0.05
25 17 0.46
26 17 0.46
27 1 0.03
ACGTcount: A:0.20, C:0.08, G:0.41, T:0.31
Consensus pattern (24 bp):
GTGGATGGTTCTGTGGAAGGTACA
Found at i:12385430 original size:36 final size:36
Alignment explanation
Indices: 12385345--12385433 Score: 97
Period size: 36 Copynumber: 2.5 Consensus size: 36
12385335 AAAACCGTTC
* *
12385345 ATTGATGATATAAAATGCAAAAAGTGTAGACTATCT
1 ATTGATGATATAAAATGCAAAAAGTATAAACTATCT
* * * * * *
12385381 GTTGACGAGATAAAATGGAAGAAGTATAAACTATTT
1 ATTGATGATATAAAATGCAAAAAGTATAAACTATCT
*
12385417 ATTGGTGATATAAAATG
1 ATTGATGATATAAAATG
12385434 TAAGCAATGC
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.44, C:0.06, G:0.20, T:0.30
Consensus pattern (36 bp):
ATTGATGATATAAAATGCAAAAAGTATAAACTATCT
Found at i:12386573 original size:80 final size:78
Alignment explanation
Indices: 12386456--12386686 Score: 268
Period size: 80 Copynumber: 2.9 Consensus size: 78
12386446 CTATGGGAAC
* *
12386456 CCTTCACGAGCTCTCTTTGCCTCACAATATTCATTATACGGATATACAAACATGTAAAGGGGCAT
1 CCTTCAC-AGCTCTCTTTGCCTCACAATATTCATTATACGGATATACAAACATGCAAA-GGGTAT
*
12386521 AACCAGTCGC-GGAA-AT
64 AACCA--C-CAGCAAGAT
* * *
12386537 CCTTCACAGCTCTCTTTGCCTCACAATATTCGTTATACGAATATACAAACATGCAAAAAGGTATA
1 CCTTCACAGCTCTCTTTGCCTCACAATATTCATTATACGGATATACAAACATGC-AAAGGGTATA
12386602 ACCACCAGCAAGGAT
65 ACCACCAGCAA-GAT
* * * * * *
12386617 CCTTTATAGGATCCCTTTGTCTCACAATATTCATTATATGGATATACAAACATGCAAAGGGTATA
1 CCTTCACA-GCTCTCTTTGCCTCACAATATTCATTATACGGATATACAAACATGCAAAGGGTATA
12386682 ACCAC
65 ACCAC
12386687 TCACGGGAAC
Statistics
Matches: 130, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
77 1 0.01
78 4 0.03
80 75 0.58
81 50 0.38
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.27
Consensus pattern (78 bp):
CCTTCACAGCTCTCTTTGCCTCACAATATTCATTATACGGATATACAAACATGCAAAGGGTATAA
CCACCAGCAAGAT
Found at i:12388816 original size:16 final size:16
Alignment explanation
Indices: 12388795--12388826 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12388785 TTTCGAACCT
12388795 TGATTTATTTTATTTA
1 TGATTTATTTTATTTA
12388811 TGATTTATTTTATTTA
1 TGATTTATTTTATTTA
12388827 CGTCCTATAT
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:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (16 bp):
TGATTTATTTTATTTA
Found at i:12389797 original size:2 final size:2
Alignment explanation
Indices: 12389790--12389855 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
12389780 AGATATAATG
12389790 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
12389832 TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC
12389856 CCCGTTGCCA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:12390885 original size:13 final size:13
Alignment explanation
Indices: 12390867--12390892 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12390857 AATTAAGAAG
12390867 GTTTTGGTTTTTT
1 GTTTTGGTTTTTT
12390880 GTTTTGGTTTTTT
1 GTTTTGGTTTTTT
12390893 TATTCTGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (13 bp):
GTTTTGGTTTTTT
Found at i:12393475 original size:22 final size:23
Alignment explanation
Indices: 12393444--12393486 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
12393434 TTACATATTC
*
12393444 AATCACATTATT-TCTTTTAAAA
1 AATCACATTATTGTCATTTAAAA
*
12393466 AATCATATTATTGTCATTTAA
1 AATCACATTATTGTCATTTAA
12393487 TTTAATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.47
Consensus pattern (23 bp):
AATCACATTATTGTCATTTAAAA
Found at i:12395794 original size:2 final size:2
Alignment explanation
Indices: 12395787--12395815 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12395777 GGTCTGATAA
12395787 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
12395816 AGAAGAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12395821 original size:3 final size:3
Alignment explanation
Indices: 12395813--12395837 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12395803 AGAGAGAGAG
12395813 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
12395838 ATCCAAGCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:12400865 original size:2 final size:2
Alignment explanation
Indices: 12400858--12400885 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12400848 CAAAGTTTGA
12400858 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
12400886 TGCATGTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12402051 original size:25 final size:25
Alignment explanation
Indices: 12402023--12402087 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
12402013 GAAATTTTTT
*
12402023 ATTTAAATAATAATATTTAATTCGA
1 ATTTAAATAATAATATTTAATTCAA
12402048 ATTTAAATAATAATATTTAATTCAA
1 ATTTAAATAATAATATTTAATTCAA
12402073 ATTTAAATAATAATA
1 ATTTAAATAATAATA
12402088 CTTAGATAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (25 bp):
ATTTAAATAATAATATTTAATTCAA
Found at i:12406671 original size:29 final size:29
Alignment explanation
Indices: 12406616--12406678 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
12406606 TTGATCTTAT
* * *
12406616 TTGATTCTTTTAATAGTACAGATACTAAA
1 TTGATTCATTTAATAGTAAAGAGACTAAA
*
12406645 TTGATTCATTTAATAGTAGAAG-GACTAAT
1 TTGATTCATTTAATAGTA-AAGAGACTAAA
12406674 TTGAT
1 TTGAT
12406679 AAAATCCCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 27 0.93
30 2 0.07
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (29 bp):
TTGATTCATTTAATAGTAAAGAGACTAAA
Found at i:12408510 original size:18 final size:18
Alignment explanation
Indices: 12408487--12408528 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
12408477 CTTAAAGAAT
*
12408487 TTACAATATTCTCTAAGA
1 TTACAATATCCTCTAAGA
*
12408505 TTACAATATCCTTTAAGA
1 TTACAATATCCTCTAAGA
12408523 TTACAA
1 TTACAA
12408529 AATATTTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (18 bp):
TTACAATATCCTCTAAGA
Found at i:12410106 original size:31 final size:29
Alignment explanation
Indices: 12410071--12410140 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 29
12410061 ATCCCAAAAT
12410071 TATACATGAAC-TATGATTTAATATGCAATTG
1 TATACATGAACGT-TGATTT--TATGCAATTG
** * *
12410102 TATACACAAACGTTGATTTTGTGCAATTT
1 TATACATGAACGTTGATTTTATGCAATTG
12410131 TATACATGAA
1 TATACATGAA
12410141 ATTTTGATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
29 16 0.50
31 15 0.47
32 1 0.03
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (29 bp):
TATACATGAACGTTGATTTTATGCAATTG
Found at i:12410329 original size:31 final size:30
Alignment explanation
Indices: 12410284--12410377 Score: 91
Period size: 31 Copynumber: 3.1 Consensus size: 30
12410274 AATGTGTATG
*
12410284 ATTAAATCAAAATTAAAGTTTCAAGTATACA
1 ATTAAA-CCAAATTAAAGTTTCAAGTATACA
* * * ** *
12410315 TTTGAACCACAATTAAAGTGTCCCGTATATA
1 ATTAAACCA-AATTAAAGTTTCAAGTATACA
*
12410346 ATTAAACCAAATTAAAG-TTCATGTATACA
1 ATTAAACCAAATTAAAGTTTCAAGTATACA
12410375 ATT
1 ATT
12410378 GCACATTAAA
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
29 11 0.22
30 10 0.20
31 28 0.57
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.33
Consensus pattern (30 bp):
ATTAAACCAAATTAAAGTTTCAAGTATACA
Found at i:12414966 original size:42 final size:43
Alignment explanation
Indices: 12414908--12415009 Score: 129
Period size: 42 Copynumber: 2.4 Consensus size: 43
12414898 GATTTATGTA
*
12414908 TAAGACCATGTCTGGGACATAA-GCATCG-TATCTG-ATTTCATG
1 TAAGACCATGTCTGGGACA-AAGGCATCGATAT-TGAATTACATG
*
12414950 TAAGACCCTGTCTGGGACAAAGGCATCGATATTGAATTACATG
1 TAAGACCATGTCTGGGACAAAGGCATCGATATTGAATTACATG
* *
12414993 TAAGACCACGTCCGGGA
1 TAAGACCATGTCTGGGA
12415010 TGTCGGTATT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
41 2 0.04
42 26 0.50
43 24 0.46
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (43 bp):
TAAGACCATGTCTGGGACAAAGGCATCGATATTGAATTACATG
Found at i:12418386 original size:19 final size:18
Alignment explanation
Indices: 12418349--12418386 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
12418339 TAATTTACTG
*
12418349 TAAGGTAGTCAATTATCA
1 TAAGGTAGTCAAATATCA
12418367 TAAGGTAGTCAACATATCA
1 TAAGGTAGTCAA-ATATCA
12418386 T
1 T
12418387 TCAAGTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (18 bp):
TAAGGTAGTCAAATATCA
Found at i:12419257 original size:26 final size:28
Alignment explanation
Indices: 12419219--12419271 Score: 67
Period size: 26 Copynumber: 1.9 Consensus size: 28
12419209 TTATCTTATA
12419219 TACTTAGATTAA-TAAC-TAATTAATTT
1 TACTTAGATTAATTAACATAATTAATTT
12419245 TACTTAG-TCTAATTAACATTAATTAAT
1 TACTTAGAT-TAATTAACA-TAATTAAT
12419272 CAAACATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
25 1 0.04
26 10 0.43
27 4 0.17
29 8 0.35
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (28 bp):
TACTTAGATTAATTAACATAATTAATTT
Found at i:12419593 original size:2 final size:2
Alignment explanation
Indices: 12419582--12419616 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
12419572 AGCAGGATGT
12419582 TA TA -A 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
12419617 ACATCTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:12422929 original size:2 final size:2
Alignment explanation
Indices: 12422922--12422958 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
12422912 CGAATCCTTC
12422922 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12422959 TGTATCATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12431164 original size:47 final size:47
Alignment explanation
Indices: 12431111--12431204 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
12431101 CTAATGGGAC
12431111 GTACTAGGACTTTCTTTCTTCCTTTTTAATGAGACTGGATAAATAGA
1 GTACTAGGACTTTCTTTCTTCCTTTTTAATGAGACTGGATAAATAGA
12431158 GTACTAGGACTTTCTTTCTTCCTTTTTAATGAGACTGGATAAATAGA
1 GTACTAGGACTTTCTTTCTTCCTTTTTAATGAGACTGGATAAATAGA
12431205 TGCTCCATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (47 bp):
GTACTAGGACTTTCTTTCTTCCTTTTTAATGAGACTGGATAAATAGA
Found at i:12443472 original size:16 final size:15
Alignment explanation
Indices: 12443451--12443480 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
12443441 ATATCTTTTT
12443451 ATTTTTTTATTATTTA
1 ATTTTTTT-TTATTTA
12443467 ATTTTTTTTTATTT
1 ATTTTTTTTTATTT
12443481 TCGCTCAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (15 bp):
ATTTTTTTTTATTTA
Found at i:12447257 original size:24 final size:24
Alignment explanation
Indices: 12447224--12447271 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
12447214 AATGTATTAT
*
12447224 TAATATCTGAAATAATTAATAAAA
1 TAATACCTGAAATAATTAATAAAA
12447248 TAATACCTGAAATAATTAATAAAA
1 TAATACCTGAAATAATTAATAAAA
12447272 AATTATAAAT
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:0.58, C:0.06, G:0.04, T:0.31
Consensus pattern (24 bp):
TAATACCTGAAATAATTAATAAAA
Found at i:12451829 original size:56 final size:57
Alignment explanation
Indices: 12451762--12451876 Score: 189
Period size: 56 Copynumber: 2.0 Consensus size: 57
12451752 CTATGGCAAC
12451762 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGA-AAAGTGA-AAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAA-TGACAAGTGA
* *
12451818 AAGTGATAAGTGATAGTTTCGGCTACACTTATCTGATCAATGACAAATGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGACAAGTGA
12451875 AA
1 AA
12451877 AGTGGTAGCT
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
56 44 0.80
57 11 0.20
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (57 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGACAAGTGA
Found at i:12451908 original size:31 final size:31
Alignment explanation
Indices: 12451870--12452049 Score: 236
Period size: 31 Copynumber: 5.8 Consensus size: 31
12451860 ACAAATGACA
*
12451870 AGTGAAAAGTGGTAGCTTTAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
* *
12451901 AGTGAAAAGTGGTAGCTTTAACTACCTGATC
1 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
*
12451932 AGTGAAAAGTGGTAG-TTCAGGCTACTTGATC
1 AGTGAAAAGTGGTAGCTTCA-GCTACCTGATC
* *
12451963 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
* * * *
12451994 AGTGAAAAATGGTAGCTCCGGCTACCTGATT
1 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
* *
12452025 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCAGCTAC
12452050 AAGTGACAAA
Statistics
Matches: 135, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
30 3 0.02
31 130 0.96
32 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.27
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
Found at i:12452111 original size:30 final size:30
Alignment explanation
Indices: 12452075--12452133 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
12452065 AGTGATTTCC
*
12452075 GTATAAGACCATATTTGGGATATGGCATCT
1 GTATAAGACCATATCTGGGATATGGCATCT
12452105 GTATAAGACCATATCTGGGATATGGCATC
1 GTATAAGACCATATCTGGGATATGGCATC
12452134 AGTGAGATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.31
Consensus pattern (30 bp):
GTATAAGACCATATCTGGGATATGGCATCT
Found at i:12452214 original size:42 final size:42
Alignment explanation
Indices: 12452108--12452265 Score: 165
Period size: 42 Copynumber: 3.7 Consensus size: 42
12452098 GGCATCTGTA
* * * * *
12452108 TAAGACCATATCTGGGATATGGCATCAGTGAGATATGTGATTTGTG
1 TAAGACCATAGCTGGGCTATGGCATC---GATATATG-AATATGTG
*
12452154 TAAGACCATAGCTAGGCTATGGCATCGATATATGAATATGTG
1 TAAGACCATAGCTGGGCTATGGCATCGATATATGAATATGTG
* *
12452196 TAAGACCATAGCTGGGCTATGGCATC-ATTATGTGAAGATGTG
1 TAAGACCATAGCTGGGCTATGGCATCGA-TATATGAATATGTG
* **
12452238 TAAGACCATAGTTGAACTATGGCATCGA
1 TAAGACCATAGCTGGGCTATGGCATCGA
12452266 GAAAACGAAG
Statistics
Matches: 98, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
41 1 0.01
42 66 0.67
43 8 0.08
46 23 0.23
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (42 bp):
TAAGACCATAGCTGGGCTATGGCATCGATATATGAATATGTG
Found at i:12454463 original size:30 final size:30
Alignment explanation
Indices: 12454388--12454463 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
12454378 ATGTTGATGA
* *
12454388 TATTTTATAATTATTTAATTAGAAAAATAT
1 TATTTTATTATTATTTAATAAGAAAAATAT
* * **
12454418 TATTTTATTAATATTTAATAAGATATTTAT
1 TATTTTATTATTATTTAATAAGAAAAATAT
12454448 TATTATT-TTATTATTT
1 TATT-TTATTATTATTT
12454464 TATTTAGTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 36 0.95
31 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (30 bp):
TATTTTATTATTATTTAATAAGAAAAATAT
Found at i:12457833 original size:20 final size:20
Alignment explanation
Indices: 12457804--12457845 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
12457794 AAAAATTATA
*
12457804 ATATTGTTTTATGAATA-AGT
1 ATATTATTTTAT-AATATAGT
12457824 ATATTATTTTATAATATAGT
1 ATATTATTTTATAATATAGT
12457844 AT
1 AT
12457846 GGACACATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (20 bp):
ATATTATTTTATAATATAGT
Found at i:12463090 original size:70 final size:70
Alignment explanation
Indices: 12462977--12463116 Score: 262
Period size: 70 Copynumber: 2.0 Consensus size: 70
12462967 ATTGAAAAGT
*
12462977 GTAATTGGGGTGACCTAATTACACCCAATTTAGTGGGACCCATCAATTACAATGATTACCTAAAC
1 GTAATTGGGGTGACCTAATTACACCCAATTTAGTGAGACCCATCAATTACAATGATTACCTAAAC
12463042 ATGTC
66 ATGTC
*
12463047 GTAATTGGGGTGACCTAATTACACCCAATTTGGTGAGACCCATCAATTACAATGATTACCTAAAC
1 GTAATTGGGGTGACCTAATTACACCCAATTTAGTGAGACCCATCAATTACAATGATTACCTAAAC
12463112 ATGTC
66 ATGTC
12463117 ACTCTTATGT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (70 bp):
GTAATTGGGGTGACCTAATTACACCCAATTTAGTGAGACCCATCAATTACAATGATTACCTAAAC
ATGTC
Found at i:12463432 original size:22 final size:24
Alignment explanation
Indices: 12463378--12463432 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 24
12463368 TAAACTTAAT
*
12463378 AAAATTTAA-TTAAGTTCTATAAA
1 AAAATCTAATTTAAGTTCTATAAA
* *
12463401 AATATGTAATTTAA-TTC-ATAAA
1 AAAATCTAATTTAAGTTCTATAAA
12463423 AAAATCTAAT
1 AAAATCTAAT
12463433 AGTTAACATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 13 0.48
23 10 0.37
24 4 0.15
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.38
Consensus pattern (24 bp):
AAAATCTAATTTAAGTTCTATAAA
Found at i:12464616 original size:6 final size:6
Alignment explanation
Indices: 12464605--12464646 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
12464595 CATTACCCTT
12464605 TCTCCA TCTCCA TCTCCA TCTCCA TCTCCA TCTCCA TCTCCA
1 TCTCCA TCTCCA TCTCCA TCTCCA TCTCCA TCTCCA TCTCCA
12464647 ACGATAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.17, C:0.50, G:0.00, T:0.33
Consensus pattern (6 bp):
TCTCCA
Found at i:12469121 original size:5 final size:5
Alignment explanation
Indices: 12469113--12469153 Score: 64
Period size: 5 Copynumber: 8.0 Consensus size: 5
12469103 AATCTATGTG
*
12469113 AATAA AATAA AATAA AATAA AATAA AGAAAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA A-ATAA AATAA AATAA
12469154 CACACAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 29 0.88
6 4 0.12
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (5 bp):
AATAA
Found at i:12469133 original size:15 final size:16
Alignment explanation
Indices: 12469113--12469153 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
12469103 AATCTATGTG
*
12469113 AATAAAATAAA-ATAA
1 AATAAAATAAAGAAAA
12469128 AATAAAATAAAGAAAA
1 AATAAAATAAAGAAAA
12469144 AATAAAATAA
1 AATAAAATAA
12469154 CACACAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (16 bp):
AATAAAATAAAGAAAA
Found at i:12474361 original size:49 final size:49
Alignment explanation
Indices: 12474289--12474386 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
12474279 TTATAAATTA
12474289 CAAAAAAAGTAAAATTTTAAACTCGAGGTATCGAAATTTTAAAATAGAT
1 CAAAAAAAGTAAAATTTTAAACTCGAGGTATCGAAATTTTAAAATAGAT
12474338 CAAAAAAAGTAAAATTTTAAACTCGAGGTATCGAAATTTTAAAATAGAT
1 CAAAAAAAGTAAAATTTTAAACTCGAGGTATCGAAATTTTAAAATAGAT
12474387 TTATTGAGAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (49 bp):
CAAAAAAAGTAAAATTTTAAACTCGAGGTATCGAAATTTTAAAATAGAT
Found at i:12475934 original size:97 final size:97
Alignment explanation
Indices: 12475818--12476014 Score: 394
Period size: 97 Copynumber: 2.0 Consensus size: 97
12475808 ACTTGAATTA
12475818 GAACCTGCATTAAAAATAGACATTTATAAGTTCAAACAAACTTAGTGAATATTAACCCAAATCAC
1 GAACCTGCATTAAAAATAGACATTTATAAGTTCAAACAAACTTAGTGAATATTAACCCAAATCAC
12475883 CTTGGCATATTTATCGTTGCATTCCTCAACTT
66 CTTGGCATATTTATCGTTGCATTCCTCAACTT
12475915 GAACCTGCATTAAAAATAGACATTTATAAGTTCAAACAAACTTAGTGAATATTAACCCAAATCAC
1 GAACCTGCATTAAAAATAGACATTTATAAGTTCAAACAAACTTAGTGAATATTAACCCAAATCAC
12475980 CTTGGCATATTTATCGTTGCATTCCTCAACTT
66 CTTGGCATATTTATCGTTGCATTCCTCAACTT
12476012 GAA
1 GAA
12476015 GATTCTAGAT
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 100 1.00
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (97 bp):
GAACCTGCATTAAAAATAGACATTTATAAGTTCAAACAAACTTAGTGAATATTAACCCAAATCAC
CTTGGCATATTTATCGTTGCATTCCTCAACTT
Found at i:12476905 original size:23 final size:23
Alignment explanation
Indices: 12476879--12476977 Score: 126
Period size: 23 Copynumber: 4.3 Consensus size: 23
12476869 CAGGGGTATT
*
12476879 ACAGAATATGCCACAAGGGCATC
1 ACAGAATATGCCACAAAGGCATC
* *
12476902 ACAGAATATGTCACAAAAGCATC
1 ACAGAATATGCCACAAAGGCATC
* *
12476925 ACGGAATATGCCACAAAGGCTTC
1 ACAGAATATGCCACAAAGGCATC
* **
12476948 ACAGAATATGCTACAAAGGTTTC
1 ACAGAATATGCCACAAAGGCATC
12476971 ACAGAAT
1 ACAGAAT
12476978 TCTATGTTTA
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 66 1.00
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.18
Consensus pattern (23 bp):
ACAGAATATGCCACAAAGGCATC
Found at i:12480009 original size:5 final size:5
Alignment explanation
Indices: 12480001--12480040 Score: 62
Period size: 5 Copynumber: 7.6 Consensus size: 5
12479991 TATAAGTAAA
12480001 TATAT TATAT TATAT TATAT TATAT TATTAT TATTAT TAT
1 TATAT TATAT TATAT TATAT TATAT TA-TAT TA-TAT TAT
12480041 TATAAACATA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 23 0.68
6 11 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TATAT
Found at i:12480031 original size:3 final size:3
Alignment explanation
Indices: 12480003--12480043 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
12479993 TAAGTAAATA
12480003 TAT TA- TAT TA- TAT TA- TAT TA- TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12480044 AAACATAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 8 0.24
3 26 0.76
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:12480041 original size:15 final size:15
Alignment explanation
Indices: 12480003--12480043 Score: 54
Period size: 13 Copynumber: 3.0 Consensus size: 15
12479993 TAAGTAAATA
12480003 TATTA-TATTA-TAT
1 TATTATTATTATTAT
12480016 TA-TATTA-TATTAT
1 TATTATTATTATTAT
12480029 TATTATTATTATTAT
1 TATTATTATTATTAT
12480044 AAACATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 4 0.17
13 9 0.38
14 5 0.21
15 6 0.25
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TATTATTATTATTAT
Found at i:12487693 original size:30 final size:30
Alignment explanation
Indices: 12487659--12487715 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
12487649 ACTTAACAAG
12487659 CAAATACCTCTAAAATAATAACAAAATCAA
1 CAAATACCTCTAAAATAATAACAAAATCAA
* *
12487689 CAAATGCCTTTAAAATAATAACAAAAT
1 CAAATACCTCTAAAATAATAACAAAAT
12487716 TAATAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.58, C:0.18, G:0.02, T:0.23
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATCAA
Found at i:12490063 original size:19 final size:20
Alignment explanation
Indices: 12490039--12490083 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
12490029 ATAATAAAAT
*
12490039 AATAACAT-AAATAACTAAA
1 AATAACATGAAATAAATAAA
12490058 AATAACATGAAATAAATAAA
1 AATAACATGAAATAAATAAA
12490078 AATAAC
1 AATAAC
12490084 TATTTTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.69, C:0.09, G:0.02, T:0.20
Consensus pattern (20 bp):
AATAACATGAAATAAATAAA
Found at i:12500729 original size:10 final size:10
Alignment explanation
Indices: 12500704--12500735 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
12500694 ATACTATAAA
12500704 TAAAAAGAA-
1 TAAAAAGAAG
12500713 T-AAAAGAAG
1 TAAAAAGAAG
12500722 TAAAAAGAAG
1 TAAAAAGAAG
12500732 TAAA
1 TAAA
12500736 TTTAATAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 7 0.33
9 2 0.10
10 12 0.57
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (10 bp):
TAAAAAGAAG
Found at i:12505680 original size:11 final size:10
Alignment explanation
Indices: 12505664--12505711 Score: 55
Period size: 9 Copynumber: 4.8 Consensus size: 10
12505654 CGTCGTTCAC
12505664 CTTTCTTCTTT
1 CTTTCTT-TTT
12505675 CTTTCTATTTT
1 CTTTCT-TTTT
12505686 CTTTC-TTTT
1 CTTTCTTTTT
*
12505695 CTTTCTTCTT
1 CTTTCTTTTT
12505705 -TTTCTTT
1 CTTTCTTT
12505712 CAATTTGCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 15 0.45
10 3 0.09
11 14 0.42
12 1 0.03
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (10 bp):
CTTTCTTTTT
Found at i:12505692 original size:22 final size:21
Alignment explanation
Indices: 12505664--12505712 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 21
12505654 CGTCGTTCAC
12505664 CTTTC-TTCTTTCTTTCTATTTT
1 CTTTCTTTCTTTC-TTCT-TTTT
12505686 CTTTCTTTTCTTTCTTCTTTTT
1 CTTTC-TTTCTTTCTTCTTTTT
12505708 CTTTC
1 CTTTC
12505713 AATTTGCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 14 0.56
23 4 0.16
24 7 0.28
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.73
Consensus pattern (21 bp):
CTTTCTTTCTTTCTTCTTTTT
Found at i:12507620 original size:5 final size:5
Alignment explanation
Indices: 12507610--12507650 Score: 82
Period size: 5 Copynumber: 8.2 Consensus size: 5
12507600 ATATTTAAAA
12507610 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A
12507651 GGCACAATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:12507834 original size:16 final size:16
Alignment explanation
Indices: 12507800--12507852 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
12507790 ATGACATCAG
12507800 TCATGCAATACTCAAT
1 TCATGCAATACTCAAT
*
12507816 TCATG-AATACATCATT
1 TCATGCAATAC-TCAAT
* *
12507832 TCATACCATACTCAAT
1 TCATGCAATACTCAAT
12507848 TCATG
1 TCATG
12507853 AGTATATAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 5 0.17
16 21 0.70
17 4 0.13
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
TCATGCAATACTCAAT
Found at i:12509834 original size:57 final size:57
Alignment explanation
Indices: 12509739--12509848 Score: 132
Period size: 57 Copynumber: 1.9 Consensus size: 57
12509729 AATTTCACAT
* * *
12509739 ACCTGTATCTGTCCCATTAAGCCTAATCATATTCATATGACCCATTAGGCCCAAATC
1 ACCTGTATCTGGCCCATTAAGCCAAATCACATTCATATGACCCATTAGGCCCAAATC
* * * * *
12509796 ACCTGTAT-TGGCCCATTAGGCCCAAATCACATTTATATGGCTCGTTAGGCCCA
1 ACCTGTATCTGGCCCATTAAG-CCAAATCACATTCATATGACCCATTAGGCCCA
12509849 GTCACATTCA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
56 10 0.23
57 34 0.77
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (57 bp):
ACCTGTATCTGGCCCATTAAGCCAAATCACATTCATATGACCCATTAGGCCCAAATC
Found at i:12509846 original size:29 final size:29
Alignment explanation
Indices: 12509763--12509861 Score: 103
Period size: 28 Copynumber: 3.5 Consensus size: 29
12509753 CATTAAGCCT
* * *
12509763 AATCATATTCATATGACCCATTAGGCCCA
1 AATCACATTTATATGGCCCATTAGGCCCA
* *
12509792 AATCACCTGTAT-TGGCCCATTAGGCCCA
1 AATCACATTTATATGGCCCATTAGGCCCA
* *
12509820 AATCACATTTATATGGCTCGTTAGGCCC-
1 AATCACATTTATATGGCCCATTAGGCCCA
* *
12509848 AGTCACATTCATAT
1 AATCACATTTATAT
12509862 TCATGCTCAC
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
28 37 0.64
29 21 0.36
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.29
Consensus pattern (29 bp):
AATCACATTTATATGGCCCATTAGGCCCA
Found at i:12510113 original size:24 final size:23
Alignment explanation
Indices: 12510069--12510115 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
12510059 CCGTAGCCAA
*
12510069 ACTTTTGACTTTTCGGCATTTCG
1 ACTTTTCACTTTTCGGCATTTCG
* *
12510092 ACTTTTCAGCTTTTTGGTATTTCG
1 ACTTTTCA-CTTTTCGGCATTTCG
12510116 GCATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.13, C:0.19, G:0.17, T:0.51
Consensus pattern (23 bp):
ACTTTTCACTTTTCGGCATTTCG
Found at i:12510121 original size:8 final size:8
Alignment explanation
Indices: 12510079--12510133 Score: 56
Period size: 8 Copynumber: 6.9 Consensus size: 8
12510069 ACTTTTGACT
12510079 TTTCGGCA
1 TTTCGGCA
* *
12510087 TTTCGACT
1 TTTCGGCA
* *
12510095 TTTCAGCT
1 TTTCGGCA
* *
12510103 TTTTGGTA
1 TTTCGGCA
12510111 TTTCGGCA
1 TTTCGGCA
12510119 TTTCGGCA
1 TTTCGGCA
12510127 TTTCGGC
1 TTTCGGC
12510134 TTTTGCCGAT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
8 37 1.00
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.45
Consensus pattern (8 bp):
TTTCGGCA
Found at i:12511953 original size:20 final size:21
Alignment explanation
Indices: 12511919--12511972 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
12511909 TGATGATATT
*
12511919 TTATGATTA-TTTAATTAGATA
1 TTAT-ATTATTTTAATAAGATA
12511940 -TATATTATTTTAATAAGATA
1 TTATATTATTTTAATAAGATA
*
12511960 TTTTATTATTTTA
1 TTATATTATTTTA
12511973 TTATTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.14
20 14 0.48
21 11 0.38
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (21 bp):
TTATATTATTTTAATAAGATA
Found at i:12511978 original size:11 final size:11
Alignment explanation
Indices: 12511962--12511989 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
12511952 ATAAGATATT
12511962 TTATTATTTTA
1 TTATTATTTTA
12511973 TTATTATTTTA
1 TTATTATTTTA
12511984 TTATTA
1 TTATTA
12511990 ATTATTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:12514173 original size:23 final size:23
Alignment explanation
Indices: 12514139--12514291 Score: 141
Period size: 23 Copynumber: 6.5 Consensus size: 23
12514129 CTTGATATAT
12514139 GGCT-TTTCGTGAGCTTCCCGATA
1 GGCTCTTT-GTGAGCTTCCCGATA
12514162 GGCTCTTTGTGAGCTTCCCGATA
1 GGCTCTTTGTGAGCTTCCCGATA
12514185 GGCTCTTTGTGAGCTTCCCGATA
1 GGCTCTTTGTGAGCTTCCCGATA
** *
12514208 GTGCTCGCT-TGAACTTCCCGATATA
1 G-GCTCTTTGTGAGCTTCCCG--ATA
* ** *
12514233 TGGCT-ATTCAGAGCTTCCTGATA
1 -GGCTCTTTGTGAGCTTCCCGATA
* *
12514256 GGTTCTTCGTGAGCTTCCCGATA
1 GGCTCTTTGTGAGCTTCCCGATA
*
12514279 TGGTTCTTTGTGA
1 -GGCTCTTTGTGA
12514292 ACTACCTAAT
Statistics
Matches: 107, Mismatches: 15, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
22 3 0.03
23 69 0.64
24 20 0.19
25 14 0.13
26 1 0.01
ACGTcount: A:0.15, C:0.24, G:0.25, T:0.36
Consensus pattern (23 bp):
GGCTCTTTGTGAGCTTCCCGATA
Found at i:12514199 original size:46 final size:46
Alignment explanation
Indices: 12514135--12514291 Score: 156
Period size: 46 Copynumber: 3.3 Consensus size: 46
12514125 GCGTCTTGAT
12514135 ATATGGCTTTTCGTGAGCTTCCCGATAGGCTCTTTGTGAGCTTCCCG
1 ATATGGCTTTT-GTGAGCTTCCCGATAGGCTCTTTGTGAGCTTCCCG
** *
12514182 ATA-GGCTCTTTGTGAGCTTCCCGATAGTGCTCGCT-TGAACTTCCCG
1 ATATGGCT-TTTGTGAGCTTCCCGATAG-GCTCTTTGTGAGCTTCCCG
* ** * * *
12514228 ATATATGGCTATTCAGAGCTTCCTGATAGGTTCTTCGTGAGCTTCCCG
1 --ATATGGCTTTTGTGAGCTTCCCGATAGGCTCTTTGTGAGCTTCCCG
*
12514276 ATATGGTTCTTTGTGA
1 ATATGGCT-TTTGTGA
12514292 ACTACCTAAT
Statistics
Matches: 87, Mismatches: 16, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
46 37 0.43
47 18 0.21
48 28 0.32
49 4 0.05
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (46 bp):
ATATGGCTTTTGTGAGCTTCCCGATAGGCTCTTTGTGAGCTTCCCG
Found at i:12515797 original size:28 final size:30
Alignment explanation
Indices: 12515742--12515797 Score: 80
Period size: 28 Copynumber: 1.9 Consensus size: 30
12515732 TCCCTAAATT
*
12515742 TCAAAATTCTCACAATTTAGTCCCTAATAC
1 TCAAAATTCTCACAATTTAGTCCATAATAC
*
12515772 TCAAAATT-T-ACAATTTATTCCATAAT
1 TCAAAATTCTCACAATTTAGTCCATAAT
12515798 TCAATACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 15 0.62
29 1 0.04
30 8 0.33
ACGTcount: A:0.39, C:0.21, G:0.02, T:0.38
Consensus pattern (30 bp):
TCAAAATTCTCACAATTTAGTCCATAATAC
Found at i:12516042 original size:17 final size:18
Alignment explanation
Indices: 12516009--12516049 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
12515999 TTGAACCCTA
12516009 ACTTTTTCTCCTTTCTTTC
1 ACTTTTTCT-CTTTCTTTC
*
12516028 CCTTTTTCT-TTTCTTTC
1 ACTTTTTCTCTTTCTTTC
12516045 ACTTT
1 ACTTT
12516050 GCTTCTCTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 12 0.60
19 8 0.40
ACGTcount: A:0.05, C:0.29, G:0.00, T:0.66
Consensus pattern (18 bp):
ACTTTTTCTCTTTCTTTC
Found at i:12516128 original size:22 final size:21
Alignment explanation
Indices: 12516082--12516128 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
12516072 TTTGTTTCTT
*
12516082 TTATTTCATTTCTTTTATTTA
1 TTATTTCATTTCTTGTATTTA
12516103 TTATTTCATTTACTTAGTA-TTA
1 TTATTTCATTT-CTT-GTATTTA
12516125 TTAT
1 TTAT
12516129 AATAATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 11 0.48
22 10 0.43
23 2 0.09
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (21 bp):
TTATTTCATTTCTTGTATTTA
Found at i:12516140 original size:5 final size:5
Alignment explanation
Indices: 12516130--12516181 Score: 88
Period size: 5 Copynumber: 10.6 Consensus size: 5
12516120 TATTATTATA
*
12516130 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATTAT AT-AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
12516179 ATA
1 ATA
12516182 CTTAAATATT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
4 4 0.09
5 41 0.91
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATAAT
Found at i:12516190 original size:12 final size:12
Alignment explanation
Indices: 12516132--12516190 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 12
12516122 TTATTATAAT
12516132 AATATAATA-T-
1 AATATAATATTA
12516142 AATATAATA-T-
1 AATATAATATTA
12516152 AATATAATA-T-
1 AATATAATATTA
12516162 AATATAATATTA
1 AATATAATATTA
*
12516174 TATAT-ATACTTA
1 AATATAATA-TTA
12516186 AATAT
1 AATAT
12516191 TAAGTAATAC
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
10 29 0.66
11 4 0.09
12 11 0.25
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (12 bp):
AATATAATATTA
Found at i:12519940 original size:23 final size:23
Alignment explanation
Indices: 12519910--12519958 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
12519900 TATTGGTATC
12519910 AGGGCTACAGTTTAGTCGGTTCT
1 AGGGCTACAGTTTAGTCGGTTCT
* *
12519933 AGGGCTACGGTTTAGTTGGTTCT
1 AGGGCTACAGTTTAGTCGGTTCT
12519956 AGG
1 AGG
12519959 ACTAACGTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.16, C:0.14, G:0.35, T:0.35
Consensus pattern (23 bp):
AGGGCTACAGTTTAGTCGGTTCT
Found at i:12522248 original size:17 final size:17
Alignment explanation
Indices: 12522226--12522261 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
12522216 TTGCGGGTTA
*
12522226 AAGACTCAGACGTGCCG
1 AAGACTCAGACGAGCCG
12522243 AAGACTCAGACGAGCCG
1 AAGACTCAGACGAGCCG
12522260 AA
1 AA
12522262 AACTACTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.28, G:0.28, T:0.08
Consensus pattern (17 bp):
AAGACTCAGACGAGCCG
Found at i:12532209 original size:53 final size:53
Alignment explanation
Indices: 12532070--12532267 Score: 175
Period size: 53 Copynumber: 3.7 Consensus size: 53
12532060 ATTAGGGTTT
* * * ** * * * *
12532070 AAGGATACCAAGTAAGACCATGCCAATGCATGTAATTGGTAAGTTTTACAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGGCATGGCATTGATAA-CTTCATAAGGC
* * * *
12532124 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAACTATGAT-AGGC
1 AAGGATACCATGTAAGACCATGTCAAGGCATGGCATTGAT-AACT-TCATAAGGC
* * * * * *
12532178 AA-GATCCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGGCATGGCATTGATAACTTCATAAGGC
*
12532230 AAGGATACCACGTAAGACCATGTCAAGGCATGGCATTG
1 AAGGATACCATGTAAGACCATGTCAAGGCATGGCATTG
12532268 GTAAGTTTAA
Statistics
Matches: 114, Mismatches: 26, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
51 3 0.03
52 8 0.07
53 61 0.54
54 38 0.33
55 4 0.04
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGTCAAGGCATGGCATTGATAACTTCATAAGGC
Found at i:12543087 original size:5 final size:5
Alignment explanation
Indices: 12543074--12543221 Score: 179
Period size: 5 Copynumber: 29.2 Consensus size: 5
12543064 ATATTTAAAA
* * *
12543074 ATAAT ATAAC ATAAT ATAAT ATAAT ATAGT ATGAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
* * * *
12543124 ATAATAT ATAAT ATAAT ATAGT ATGAT ATAAT ATAAT ATGAT ATAAT ATGAT
1 AT-A-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
* * * *
12543176 ATAAT ATAAT ATGAT ATGAT ATGAT ATGAT ATAAT ATAAT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A
12543222 GGCACAATTA
Statistics
Matches: 125, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
5 119 0.95
6 2 0.02
7 4 0.03
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:12543420 original size:32 final size:32
Alignment explanation
Indices: 12543378--12543462 Score: 134
Period size: 32 Copynumber: 2.7 Consensus size: 32
12543368 CAGTTATGCA
12543378 ATACTCAATTTATGAATATATCATTTCATACC
1 ATACTCAATTTATGAATATATCATTTCATACC
* *
12543410 ATACTTAATTTATGAATACATCATTTCATACC
1 ATACTCAATTTATGAATATATCATTTCATACC
* *
12543442 ATACTCAATTCATGAGTATAT
1 ATACTCAATTTATGAATATAT
12543463 AACTCATATA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.40
Consensus pattern (32 bp):
ATACTCAATTTATGAATATATCATTTCATACC
Found at i:12544678 original size:22 final size:21
Alignment explanation
Indices: 12544632--12544678 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
12544622 TTTGTTTCTT
*
12544632 TTATTTCATTTCTTTTATTTA
1 TTATTTCATTTCTTGTATTTA
12544653 TTATTTCATTTACTTAGTA-TTA
1 TTATTTCATTT-CTT-GTATTTA
12544675 TTAT
1 TTAT
12544679 AATAATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 11 0.48
22 10 0.43
23 2 0.09
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (21 bp):
TTATTTCATTTCTTGTATTTA
Found at i:12544760 original size:39 final size:39
Alignment explanation
Indices: 12544686--12544761 Score: 95
Period size: 37 Copynumber: 1.9 Consensus size: 39
12544676 TATAATAATA
12544686 TAATATAATATAATTTTATATATATACTTAAATATTAAG
1 TAATATAATATAATTTTATATATATACTTAAATATTAAG
*
12544725 TAATAT-ATAT-ATTATTAT-TTTATACTTATACATATTA
1 TAATATAATATAATT-TTATATATATACTTA-A-ATATTA
12544762 TTTTTACACT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
37 12 0.36
38 9 0.27
39 12 0.36
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.50
Consensus pattern (39 bp):
TAATATAATATAATTTTATATATATACTTAAATATTAAG
Found at i:12547022 original size:40 final size:40
Alignment explanation
Indices: 12546960--12547137 Score: 227
Period size: 40 Copynumber: 4.5 Consensus size: 40
12546950 AAGCCAAGTA
* * * *
12546960 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
** *
12546999 CCTTCGGGACAAAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
12547039 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
12547079 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
12547119 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
12547138 TTATCATCCA
Statistics
Matches: 124, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
39 12 0.10
40 112 0.90
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:12555012 original size:38 final size:38
Alignment explanation
Indices: 12554968--12555126 Score: 155
Period size: 38 Copynumber: 4.1 Consensus size: 38
12554958 CGGGATTTAA
* *
12554968 CCGGATATAGCTACTCGCTCGAATGCCTTCGGAC-AAGC
1 CCGGATATAG-TACTCGCACAAATGCCTTCGGACTAAGC
*
12555006 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGT-ACTCGCACAAATGCCTTC-GGACTAAGC
* *
12555046 CCGGATATA-AACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTACTCGCACAAATGCCTTC-GGACTAAGC
* * *
12555084 CC-GA-ACTAGTCACTAGCGCAAATGCCTTCGGGACTTAGC
1 CCGGATA-TAGT-ACTCGCACAAATGCCTTC-GGACTAAGC
12555123 CCGG
1 CCGG
12555127 TTATCATCCA
Statistics
Matches: 107, Mismatches: 7, Indels: 12
0.85 0.06 0.10
Matches are distributed among these distances:
36 1 0.01
37 5 0.05
38 56 0.52
39 32 0.30
40 13 0.12
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.21
Consensus pattern (38 bp):
CCGGATATAGTACTCGCACAAATGCCTTCGGACTAAGC
Found at i:12558118 original size:38 final size:38
Alignment explanation
Indices: 12558022--12558220 Score: 251
Period size: 38 Copynumber: 5.4 Consensus size: 38
12558012 AAACCAAGTA
* *
12558022 CCTTCGGGATTTA--CCGGATATAGCACTCGC-C-AATG
1 CCTTCGGGACTTAGCCCGGATATAGTACT-GCACAAATG
12558057 CCTTCGGGAC-TAGCCCGGATATAGTAACTGCAC-AATG
1 CCTTCGGGACTTAGCCCGGATATAGT-ACTGCACAAATG
12558094 CCTTCGGGACTTAGCCCGGATATAGTAACTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGT-ACTGCACAAATG
12558133 CCTTC-GGACTTAG-CCGG--ATAGTACTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTACTGCACAAATG
12558167 CCTTCGGGACTTAGCCCGGA-ACTAGTACTAGC-CAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTACT-GCACAAATG
12558205 CCTTCGGGACTTAGCC
1 CCTTCGGGACTTAGCC
12558221 GGTTATCATC
Statistics
Matches: 151, Mismatches: 2, Indels: 19
0.88 0.01 0.11
Matches are distributed among these distances:
34 19 0.13
35 22 0.15
36 16 0.11
37 23 0.15
38 60 0.40
39 11 0.07
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (38 bp):
CCTTCGGGACTTAGCCCGGATATAGTACTGCACAAATG
Found at i:12558174 original size:73 final size:74
Alignment explanation
Indices: 12558022--12558222 Score: 258
Period size: 73 Copynumber: 2.8 Consensus size: 74
12558012 AAACCAAGTA
* * *
12558022 CCTTCGGGATTTA--CCGGATATAGCACTCGCC-AATGCCTTCGGGAC-TAGCCCGGATATAGTA
1 CCTTCGGGACTTAGCCCGGATATAGTACTAGCCAAATGCCTTCGGGACTTAG-CCGGA-ATAGTA
12558083 ACTGCACAATG
64 ACTGCACAATG
12558094 CCTTCGGGACTTAGCCCGGATATAGTAACT-GCACAAATGCCTTC-GGACTTAGCCGG-ATAGT-
1 CCTTCGGGACTTAGCCCGGATATAGT-ACTAGC-CAAATGCCTTCGGGACTTAGCCGGAATAGTA
12558155 ACTGCACAAATG
64 ACTGCAC-AATG
12558167 CCTTCGGGACTTAGCCCGGA-ACTAGTACTAGCCAAATGCCTTCGGGACTTAGCCGG
1 CCTTCGGGACTTAGCCCGGATA-TAGTACTAGCCAAATGCCTTCGGGACTTAGCCGG
12558223 TTATCATCCA
Statistics
Matches: 117, Mismatches: 2, Indels: 19
0.85 0.01 0.14
Matches are distributed among these distances:
72 34 0.29
73 47 0.40
74 12 0.10
75 12 0.10
76 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (74 bp):
CCTTCGGGACTTAGCCCGGATATAGTACTAGCCAAATGCCTTCGGGACTTAGCCGGAATAGTAAC
TGCACAATG
Found at i:12565811 original size:40 final size:40
Alignment explanation
Indices: 12565712--12565882 Score: 243
Period size: 39 Copynumber: 4.5 Consensus size: 40
12565702 AAACCAAGTA
* *
12565712 CCTTCGGGATTTA--CCGGATATAG-CACTCGC-C-AATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
12565747 CCTTCGGGAC-TAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
12565786 CCTTCGGGACTTAGCCCGGATATAGTAACT-GCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
12565825 CCTTCGGGACTTAGCCCGGA-ACTAGT-ACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
12565864 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
12565883 CTTGCCGGTT
Statistics
Matches: 126, Mismatches: 2, Indels: 12
0.90 0.01 0.09
Matches are distributed among these distances:
34 2 0.02
35 9 0.07
36 10 0.08
37 6 0.05
38 5 0.04
39 75 0.60
40 19 0.15
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:12568194 original size:29 final size:29
Alignment explanation
Indices: 12568161--12568320 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 29
12568151 GTGACGAGAT
12568161 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
12568190 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
12568219 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
12568248 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
* ** * *
12568277 TGGCACTATGTGTGCGGGCT-TAAATCACA
1 TGGCACTAAGTGTGCATGCTGGAAAT-ATA
12568306 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
12568321 GAAATCGAGT
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 108 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:12576282 original size:29 final size:29
Alignment explanation
Indices: 12576249--12576408 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 29
12576239 GTGACGAGAT
12576249 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
12576278 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
12576307 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
12576336 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
* ** * *
12576365 TGGCACTATGTGTGCGGGCT-TAAATCACA
1 TGGCACTAAGTGTGCATGCTGGAAAT-ATA
12576394 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
12576409 GAAATCGAGT
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 108 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:12582626 original size:25 final size:27
Alignment explanation
Indices: 12582589--12582641 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
12582579 TCAAACATGC
12582589 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
12582615 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
12582641 A
1 A
12582642 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:12584156 original size:26 final size:26
Alignment explanation
Indices: 12584126--12584181 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
12584116 TGAAATTCCC
12584126 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
12584152 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
12584178 ATCA
1 ATCA
12584182 AATTGTATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.27, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:12590356 original size:7 final size:7
Alignment explanation
Indices: 12590344--12590369 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
12590334 CTTGGCCCGA
12590344 CGGAGGC
1 CGGAGGC
12590351 CGGAGGC
1 CGGAGGC
12590358 CGGAGGC
1 CGGAGGC
12590365 CGGAG
1 CGGAG
12590370 CCCAGAGGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.27, G:0.58, T:0.00
Consensus pattern (7 bp):
CGGAGGC
Found at i:12591003 original size:12 final size:12
Alignment explanation
Indices: 12590988--12591079 Score: 75
Period size: 12 Copynumber: 7.5 Consensus size: 12
12590978 TTATATCATT
12590988 TATATTTTATTA
1 TATATTTTATTA
12591000 TATATTTTGATTTA
1 TATATTTT-A-TTA
*
12591014 TACATTTTATTA
1 TATATTTTATTA
12591026 TATATTATT-TTA
1 TATATT-TTATTA
*
12591038 TTATATATTATTCA
1 -TATATTTTATT-A
*
12591052 CTATA--TTATTG
1 -TATATTTTATTA
12591063 T-TATTTTATTA
1 TATATTTTATTA
12591074 TATATT
1 TATATT
12591080 ATAATTATTC
Statistics
Matches: 65, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
9 2 0.03
10 1 0.02
11 6 0.09
12 30 0.46
13 11 0.17
14 15 0.23
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (12 bp):
TATATTTTATTA
Found at i:12591034 original size:3 final size:3
Alignment explanation
Indices: 12591020--12591104 Score: 68
Period size: 3 Copynumber: 27.3 Consensus size: 3
12591010 TTTATACATT
* *
12591020 TTA TTA TATA TTA TT- TTA TTA TATA TTA TTCA CTA -TA TTA TTG TTA
1 TTA TTA T-TA TTA TTA TTA TTA T-TA TTA TT-A TTA TTA TTA TTA TTA
*
12591066 TT- TTA TTA TATA TTA TAA TTA TTCA TTA TTCA TTA TTA T
1 TTA TTA TTA T-TA TTA TTA TTA TT-A TTA TT-A TTA TTA T
12591105 ATAATTTTAA
Statistics
Matches: 68, Mismatches: 5, Indels: 18
0.75 0.05 0.20
Matches are distributed among these distances:
2 6 0.09
3 45 0.66
4 17 0.25
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:12591280 original size:107 final size:109
Alignment explanation
Indices: 12591157--12591379 Score: 423
Period size: 108 Copynumber: 2.1 Consensus size: 109
12591147 TTATATATCA
12591157 TTATTAAAATTTAGTATGTAATACACTAAAATTTATGATAAA-ATTTATTCCTATTATATAATAT
1 TTATTAAAATTTAGTATGTAATACACTAAAATTTATGATAAAGATTTATTCCTATTATATAATAT
12591221 TATTCTATAAAACATATTAAATTATTACATCATATAGTATA-TT
66 TATTCTATAAAACATATTAAATTATTACATCATATAGTATATTT
*
12591264 TTATTAAAATTTAGTATGTAATACACTAAAATTTATGATAAAGTTTTATTCCTATTATATAATAT
1 TTATTAAAATTTAGTATGTAATACACTAAAATTTATGATAAAGATTTATTCCTATTATATAATAT
12591329 TATTCTATAAAACATATTAAATTATTACATCATATAGTATATTT
66 TATTCTATAAAACATATTAAATTATTACATCATATAGTATATTT
12591373 TTATTAA
1 TTATTAA
12591380 TCATATATAA
Statistics
Matches: 113, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
107 42 0.37
108 62 0.55
109 9 0.08
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (109 bp):
TTATTAAAATTTAGTATGTAATACACTAAAATTTATGATAAAGATTTATTCCTATTATATAATAT
TATTCTATAAAACATATTAAATTATTACATCATATAGTATATTT
Found at i:12591394 original size:22 final size:23
Alignment explanation
Indices: 12591350--12591395 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
12591340 ACATATTAAA
*
12591350 TTATTACATCATATAGTATATTT
1 TTATTACATCATATAGTAAATTT
*
12591373 TTATTA-ATCATATA-TAAAATT
1 TTATTACATCATATAGTAAATTT
12591394 TT
1 TT
12591396 CTTCTTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 8 0.38
23 6 0.29
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (23 bp):
TTATTACATCATATAGTAAATTT
Found at i:12594801 original size:12 final size:12
Alignment explanation
Indices: 12594784--12594922 Score: 59
Period size: 12 Copynumber: 11.0 Consensus size: 12
12594774 TATATGAAAA
12594784 ATTATTATATAT
1 ATTATTATATAT
* *
12594796 ATTATTTTATTT
1 ATTATTATATAT
* *
12594808 GTGTATTATTTGTTAT
1 AT-TATTA--T-ATAT
*
12594824 ATCATT-TATAT
1 ATTATTATATAT
*
12594835 TTTATTATATAT
1 ATTATTATATAT
* *
12594847 TTTGATTTATACAT
1 ATT-A-TTATATAT
*
12594861 TTTATTATATATT
1 ATTATTATATA-T
12594874 ATTTTATTATATAT
1 A--TTATTATATAT
*
12594888 ATTATTCA-CTAT
1 ATTATT-ATATAT
*
12594900 ATTATTGT-TAT
1 ATTATTATATAT
*
12594911 TTTATTATATAT
1 ATTATTATATAT
12594923 TATAATTATT
Statistics
Matches: 96, Mismatches: 18, Indels: 26
0.69 0.13 0.19
Matches are distributed among these distances:
11 16 0.17
12 43 0.45
13 8 0.08
14 12 0.12
15 14 0.15
16 3 0.03
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.63
Consensus pattern (12 bp):
ATTATTATATAT
Found at i:12594856 original size:24 final size:24
Alignment explanation
Indices: 12594830--12594923 Score: 77
Period size: 27 Copynumber: 3.8 Consensus size: 24
12594820 TTATATCATT
12594830 TATATTTTATTATATATTTTGATTTA
1 TATATTTTATTATATATTTT-A-TTA
*
12594856 TACATTTTATTATATATTATTTTATTA
1 TATATTTTA-T-TATA-TATTTTATTA
* *
12594883 TATATATTATTCACTATA--TTATTG
1 TATATTTTATT-A-TATATTTTATTA
12594907 T-TATTTTATTATATATT
1 TATATTTTATTATATATT
12594924 ATAATTATTC
Statistics
Matches: 56, Mismatches: 5, Indels: 17
0.72 0.06 0.22
Matches are distributed among these distances:
21 4 0.07
22 1 0.02
23 8 0.14
24 6 0.11
25 1 0.02
26 12 0.21
27 13 0.23
28 5 0.09
29 6 0.11
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (24 bp):
TATATTTTATTATATATTTTATTA
Found at i:12594876 original size:3 final size:3
Alignment explanation
Indices: 12594862--12594948 Score: 65
Period size: 3 Copynumber: 28.3 Consensus size: 3
12594852 TTTATACATT
* *
12594862 TTA TTA TATA TTA TT- TTA TTA -TA TATA TTA TTCA CTA -TA TTA TTG
1 TTA TTA T-TA TTA TTA TTA TTA TTA T-TA TTA TT-A TTA TTA TTA TTA
*
12594907 TTA TT- TTA TTA TATA TTA TAA TTA TTCA TTA TTCA TTA TTA T
1 TTA TTA TTA TTA T-TA TTA TTA TTA TT-A TTA TT-A TTA TTA T
12594949 ATAATTTTAA
Statistics
Matches: 69, Mismatches: 5, Indels: 20
0.73 0.05 0.21
Matches are distributed among these distances:
2 8 0.12
3 44 0.64
4 17 0.25
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:12594890 original size:14 final size:14
Alignment explanation
Indices: 12594830--12594890 Score: 81
Period size: 15 Copynumber: 4.4 Consensus size: 14
12594820 TTATATCATT
12594830 TATATTTTATTATA
1 TATATTTTATTATA
*
12594844 TAT-TTTGATT-TA
1 TATATTTTATTATA
*
12594856 TACATTTTATTATA
1 TATATTTTATTATA
12594870 TATTATTTTATTATA
1 TA-TATTTTATTATA
12594885 TATATT
1 TATATT
12594891 ATTCACTATA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
12 4 0.10
13 12 0.30
14 11 0.28
15 13 0.32
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (14 bp):
TATATTTTATTATA
Found at i:12594923 original size:12 final size:12
Alignment explanation
Indices: 12594830--12594923 Score: 77
Period size: 12 Copynumber: 7.5 Consensus size: 12
12594820 TTATATCATT
12594830 TATATTTTATTA
1 TATATTTTATTA
12594842 TATATTTTGATTTA
1 TATATTTT-A-TTA
*
12594856 TACATTTTATTATA
1 TATATTTTA-T-TA
12594870 TATTATTTTATTA
1 TA-TATTTTATTA
*
12594883 TATATATTATTCA
1 TATATTTTATT-A
*
12594896 CTATA--TTATTG
1 -TATATTTTATTA
12594907 T-TATTTTATTA
1 TATATTTTATTA
12594918 TATATT
1 TATATT
12594924 ATAATTATTC
Statistics
Matches: 68, Mismatches: 5, Indels: 18
0.75 0.05 0.20
Matches are distributed among these distances:
9 2 0.03
10 1 0.01
11 6 0.09
12 25 0.37
13 9 0.13
14 19 0.28
15 6 0.09
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (12 bp):
TATATTTTATTA
Done.