Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 16 of 126
Found at i:5393819 original size:98 final size:98
Alignment explanation
Indices: 5393489--5393806 Score: 406
Period size: 98 Copynumber: 3.2 Consensus size: 98
5393479 TCAATTCGCA
** * * * **
5393489 TGGTACTAAATTCGCCGTTACGGCTTAAATTTTTCCTTTCATGCTTCGGAGGTATAAGGTTCGCC
1 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTAAGGTATAAGGTTCGCC
* **
5393554 ATTACGACTTAAATC-TTTCCCTTTATGTCTTCG
66 ATTACGACTTAAA-CATTTCCCTTCAAATCTTCG
* * * *
5393587 TGGTACTGGATTCGTCATTGCGGCTTAAATCTTTCTCTTCATG-TCTCTAAGGTATAAGGTTTGC
1 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCT-TCTAAGGTATAAGGTTCGC
* *
5393651 CATTGCGAGTTAAACATTTCCCTTCAAATCTTCG
65 CATTACGACTTAAACATTTCCCTTCAAATCTTCG
* *
5393685 TGGTACTGGATTCGCCGTCGCGGCTTAAATCTTTCCCTTCATGCTTCTAAGGTACAAGGTTCGCC
1 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTAAGGTATAAGGTTCGCC
*
5393750 ATTACGACTTAAACATTTCCCTTCAAATCTTTG
66 ATTACGACTTAAACATTTCCCTTCAAATCTTCG
* * *
5393783 TGGTACCGGGTTTGCCGTTGCGGC
1 TGGTACTGGATTCGCCGTTGCGGC
5393807 CTCAACCTTT
Statistics
Matches: 188, Mismatches: 29, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
97 2 0.01
98 185 0.98
99 1 0.01
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.37
Consensus pattern (98 bp):
TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTAAGGTATAAGGTTCGCC
ATTACGACTTAAACATTTCCCTTCAAATCTTCG
Found at i:5393998 original size:49 final size:49
Alignment explanation
Indices: 5393892--5393998 Score: 124
Period size: 49 Copynumber: 2.2 Consensus size: 49
5393882 AGGTATCGGG
** * *
5393892 TTCACCGTTGCGGCCTTAACCTTTCCCTTCAAATATTCATGGTACTAGG
1 TTCACCGTTATGGCCTTAACCTTTCCCATCAAATATTCATGGTACTAGA
** * * *
5393941 TTCACCGTTATGGCCTTAACCTTTCCCATCTCATCTTTATGGTATTAGA
1 TTCACCGTTATGGCCTTAACCTTTCCCATCAAATATTCATGGTACTAGA
*
5393990 TTCGCCGTT
1 TTCACCGTT
5393999 GTGGTCTGAA
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.19, C:0.28, G:0.15, T:0.38
Consensus pattern (49 bp):
TTCACCGTTATGGCCTTAACCTTTCCCATCAAATATTCATGGTACTAGA
Found at i:5395891 original size:28 final size:28
Alignment explanation
Indices: 5395832--5395893 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
5395822 GAAGGAGATT
*
5395832 TTTTTTTAATAGTATGTCAGGCCTTATT
1 TTTTTTTAATAGTATGTCAGGCCTTATA
*
5395860 TTTTTTTAATAGTATGTCAGGTCTTGA-A
1 TTTTTTTAATAGTATGTCAGGCCTT-ATA
5395888 TTTTTT
1 TTTTTT
5395894 GTATTCTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 30 0.97
29 1 0.03
ACGTcount: A:0.21, C:0.08, G:0.15, T:0.56
Consensus pattern (28 bp):
TTTTTTTAATAGTATGTCAGGCCTTATA
Found at i:5396528 original size:17 final size:17
Alignment explanation
Indices: 5396505--5396615 Score: 125
Period size: 17 Copynumber: 6.4 Consensus size: 17
5396495 GGCTTTCATT
*
5396505 ATTTAAATTTAGAATAA
1 ATTTAAATTTAAAATAA
*
5396522 TTTTAAATTTAAATATAA
1 ATTTAAATTTAAA-ATAA
* * *
5396540 ATCTAAACTTAAATTAA
1 ATTTAAATTTAAAATAA
*
5396557 ATTTAAATTTTAAAACAA
1 ATTTAAA-TTTAAAATAA
5396575 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
5396592 ATTT-AATCTTAAAATAA
1 ATTTAAAT-TTAAAATAA
*
5396609 ATCTAAA
1 ATTTAAA
5396616 ATGGGTTTAG
Statistics
Matches: 78, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
16 3 0.04
17 45 0.58
18 30 0.38
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.41
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:5396566 original size:35 final size:34
Alignment explanation
Indices: 5396508--5396615 Score: 119
Period size: 35 Copynumber: 3.1 Consensus size: 34
5396498 TTTCATTATT
* * *
5396508 TAAATTTAGAATAATTTTAAATTTAAATATAAATC
1 TAAACTTAAAATAAATTTAAATTTAAA-ATAAATC
* * *
5396543 TAAACTTAAATTAAATTTAAATTTTAAAACAAATT
1 TAAACTTAAAATAAATTTAAA-TTTAAAATAAATC
*
5396578 TAAATTTAAAATAAATTT-AATCTTAAAATAAATC
1 TAAACTTAAAATAAATTTAAAT-TTAAAATAAATC
5396612 TAAA
1 TAAA
5396616 ATGGGTTTAG
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
33 1 0.02
34 16 0.26
35 38 0.62
36 6 0.10
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.40
Consensus pattern (34 bp):
TAAACTTAAAATAAATTTAAATTTAAAATAAATC
Found at i:5396570 original size:7 final size:6
Alignment explanation
Indices: 5396505--5396597 Score: 70
Period size: 6 Copynumber: 16.0 Consensus size: 6
5396495 GGCTTTCATT
* * * *
5396505 ATTTAA ATTTAGA A--TAA TTTTAA ATTTAA ATATAA ATCTAA ACTTAA
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
** *
5396552 A-TTAA ATTTAA ATTTTAA A-ACAA ATTTAA ATTTAA A-ATAA ATTTAA
1 ATTTAA ATTTAA A-TTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
5396598 TCTTAAAATA
Statistics
Matches: 68, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
4 1 0.01
5 14 0.21
6 45 0.66
7 8 0.12
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (6 bp):
ATTTAA
Found at i:5396580 original size:29 final size:29
Alignment explanation
Indices: 5396524--5396583 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
5396514 TAGAATAATT
*
5396524 TTAAATTTAAATATAAATCTAAACTTAAA
1 TTAAATTTAAATATAAAACTAAACTTAAA
* *
5396553 TTAAATTTAAATTTTAAAAC-AAATTTAAA
1 TTAAATTTAAA-TATAAAACTAAACTTAAA
5396582 TT
1 TT
5396584 TAAAATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (29 bp):
TTAAATTTAAATATAAAACTAAACTTAAA
Found at i:5398534 original size:30 final size:29
Alignment explanation
Indices: 5398500--5398575 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 29
5398490 TTAATAAATT
5398500 ATTTTTTTAATTTTTAAAAAATT-AAATAAA
1 ATTTTTTT-A-TTTTAAAAAATTAAAATAAA
*
5398530 ATTTTTATTATTTTAAAAAATTAAAATATA
1 ATTTTT-TTATTTTAAAAAATTAAAATAAA
*
5398560 ATTTTTTCATTATTAA
1 ATTTTTTTATT-TTAA
5398576 TTTAAAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
29 16 0.39
30 23 0.56
31 2 0.05
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (29 bp):
ATTTTTTTATTTTAAAAAATTAAAATAAA
Found at i:5398544 original size:29 final size:29
Alignment explanation
Indices: 5398503--5398565 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
5398493 ATAAATTATT
5398503 TTTTTAATTTTTAAAAAATT-AAATAAAA
1 TTTTTAATTTTTAAAAAATTAAAATAAAA
* *
5398531 TTTTTATTATTTTAAAAAATTAAAATATAA
1 TTTTTAAT-TTTTAAAAAATTAAAATAAAA
5398561 TTTTT
1 TTTTT
5398566 TCATTATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 7 0.23
29 12 0.39
30 12 0.39
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
TTTTTAATTTTTAAAAAATTAAAATAAAA
Found at i:5398996 original size:18 final size:17
Alignment explanation
Indices: 5398961--5399000 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
5398951 ATATATTTTA
*
5398961 TAAAA-ATTTAATTAAT
1 TAAAATATTTAAATAAT
5398977 TAAAATATTTAAAATAAT
1 TAAAATATTT-AAATAAT
5398995 TAAAAT
1 TAAAAT
5399001 CAAAATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 5 0.24
17 4 0.19
18 12 0.57
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAAATATTTAAATAAT
Found at i:5399761 original size:27 final size:28
Alignment explanation
Indices: 5399714--5399770 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
5399704 TTAATTTTTT
5399714 AATTTTTATTAAAAATAT-AAATTCTGA
1 AATTTTTATTAAAAATATAAAATTCTGA
* *
5399741 AATTTTTA-TAAAAATTTTAAAATTTTGA
1 AATTTTTATTAAAAA-TATAAAATTCTGA
5399769 AA
1 AA
5399771 ATTATTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 6 0.23
27 10 0.38
28 10 0.38
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.46
Consensus pattern (28 bp):
AATTTTTATTAAAAATATAAAATTCTGA
Found at i:5399975 original size:17 final size:17
Alignment explanation
Indices: 5399907--5399975 Score: 52
Period size: 17 Copynumber: 4.0 Consensus size: 17
5399897 ACTCGATTTG
5399907 AACTCAAAATTTAATAAATT
1 AACTCAAAA-TT--TAAATT
* ** *
5399927 AACTTAAAAAATAAAAT
1 AACTCAAAATTTAAATT
*
5399944 AACTC--AATTTTAATT
1 AACTCAAAATTTAAATT
5399959 AACTCAAAATTTAAATT
1 AACTCAAAATTTAAATT
5399976 TCTTTTTATT
Statistics
Matches: 37, Mismatches: 10, Indels: 7
0.69 0.19 0.13
Matches are distributed among these distances:
15 11 0.30
17 18 0.49
20 8 0.22
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (17 bp):
AACTCAAAATTTAAATT
Found at i:5404605 original size:3 final size:3
Alignment explanation
Indices: 5404597--5404641 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
5404587 TGTTAAAAAC
5404597 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5404642 AAAGGGATGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5406237 original size:96 final size:99
Alignment explanation
Indices: 5406061--5406257 Score: 276
Period size: 96 Copynumber: 2.0 Consensus size: 99
5406051 TACTACTAAC
* ** * * * *
5406061 AAATGTGAGGTATAATAATAAGACTTATTACATTCTAAAGAGAAAAATGGGATTCGAAACTTAAA
1 AAATGTGAGGTATAATAATAAAACCCATTACACTCTAAAGAGAAAAATAGAACTCGAAACTTAAA
*
5406126 AGACGATGTTGTTAAAAGTAATAAATAAATAATG
66 AGACGATATTGTTAAAAGTAATAAATAAATAATG
5406160 AAATGTGAGGTATAATAATAAAACCCATTACACTCT-AA-A-AAAAATAGAACT-GAAAACTTAA
1 AAATGTGAGGTATAATAATAAAACCCATTACACTCTAAAGAGAAAAATAGAACTCG-AAACTTAA
*
5406221 AAGATGATATTGTTAAAAGTAATAAATAAATAATG
65 AAGACGATATTGTTAAAAGTAATAAATAAATAATG
5406256 AA
1 AA
5406258 TACTTTTGGT
Statistics
Matches: 88, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
95 1 0.01
96 52 0.59
97 1 0.01
98 2 0.02
99 32 0.36
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.27
Consensus pattern (99 bp):
AAATGTGAGGTATAATAATAAAACCCATTACACTCTAAAGAGAAAAATAGAACTCGAAACTTAAA
AGACGATATTGTTAAAAGTAATAAATAAATAATG
Found at i:5410343 original size:14 final size:14
Alignment explanation
Indices: 5410313--5410342 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
5410303 CTTAAATAAC
5410313 AAATATTATTTTAA
1 AAATATTATTTTAA
5410327 AAATATT-TTTTAA
1 AAATATTATTTTAA
5410340 AAA
1 AAA
5410343 AATATATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AAATATTATTTTAA
Found at i:5411015 original size:21 final size:21
Alignment explanation
Indices: 5410991--5411032 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
5410981 TCTTCCAGTG
5410991 GAAAATCTGT-TTATTTTTTTA
1 GAAAATCT-TATTATTTTTTTA
*
5411012 GAAATTCTTAATTATTTTTTT
1 GAAAATCTT-ATTATTTTTTT
5411033 TCAATAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 1 0.06
21 7 0.39
22 10 0.56
ACGTcount: A:0.29, C:0.05, G:0.07, T:0.60
Consensus pattern (21 bp):
GAAAATCTTATTATTTTTTTA
Found at i:5411410 original size:53 final size:53
Alignment explanation
Indices: 5411330--5411435 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
5411320 CTGAAATTAA
5411330 GACATAGTTTTACCATTGTGTAAGGAACACACAGCCTTTCAGGACCCCTAATT
1 GACATAGTTTTACCATTGTGTAAGGAACACACAGCCTTTCAGGACCCCTAATT
*
5411383 GACATAGTTTTGCCATTGTGTAAGGAACACACAGCCTTTCAGGACCCCTAATT
1 GACATAGTTTTACCATTGTGTAAGGAACACACAGCCTTTCAGGACCCCTAATT
5411436 TTCCCATGGA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (53 bp):
GACATAGTTTTACCATTGTGTAAGGAACACACAGCCTTTCAGGACCCCTAATT
Found at i:5412126 original size:21 final size:21
Alignment explanation
Indices: 5412101--5412143 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
5412091 ATTACTGCAA
5412101 ACACTCCATTCTTGCAAGAAC
1 ACACTCCATTCTTGCAAGAAC
*
5412122 ACACTCCATTCTTGTAAGAAC
1 ACACTCCATTCTTGCAAGAAC
5412143 A
1 A
5412144 TTGGTAGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.30, G:0.09, T:0.26
Consensus pattern (21 bp):
ACACTCCATTCTTGCAAGAAC
Found at i:5414539 original size:127 final size:127
Alignment explanation
Indices: 5414313--5414567 Score: 433
Period size: 127 Copynumber: 2.0 Consensus size: 127
5414303 ATACACAAGG
*
5414313 TTTCTATATGACTGTAAAACTACGAATAAAGCCACACAAGGCTACGAGGTCTTCAATAAATAATA
1 TTTCTATATGACTGTAAAACTACAAATAAAGCCACACAAGGCTACGAGGTCTTCAATAAATAATA
*
5414378 CATTTACTAAAAAACTTAATTCAAAACAAACTTAGAAATCTTTCTCATACTTGATTGGTGAT
66 CATTTACTAAAAAACTTAATTCAAAACAAACTTAGAAATCTTTCTCATACTCGATTGGTGAT
* *
5414440 TTTCTATATGACTGTAAAACTACAAATTAAA-CCACACAATGCTACGAGGTTTTCAA-AAAGTAA
1 TTTCTATATGACTGTAAAACTACAAA-TAAAGCCACACAAGGCTACGAGGTCTTCAATAAA-TAA
*
5414503 TACATTTACTAAAAAACTTAATTCAAAACAAACTTAGAGATCTTTCTCATACTCGATTGGTGAT
64 TACATTTACTAAAAAACTTAATTCAAAACAAACTTAGAAATCTTTCTCATACTCGATTGGTGAT
5414567 T
1 T
5414568 CTTCGGGCCC
Statistics
Matches: 121, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
126 3 0.02
127 114 0.94
128 4 0.03
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (127 bp):
TTTCTATATGACTGTAAAACTACAAATAAAGCCACACAAGGCTACGAGGTCTTCAATAAATAATA
CATTTACTAAAAAACTTAATTCAAAACAAACTTAGAAATCTTTCTCATACTCGATTGGTGAT
Found at i:5415367 original size:24 final size:24
Alignment explanation
Indices: 5415339--5415398 Score: 93
Period size: 27 Copynumber: 2.4 Consensus size: 24
5415329 ACTAAAAACA
5415339 AAAGAAACATAGTTTTCCAGCCAC
1 AAAGAAACATAGTTTTCCAGCCAC
5415363 AAAGAAACATAATAGTTTTCCAGCCAC
1 AAAGAAAC---ATAGTTTTCCAGCCAC
5415390 AAAGAAACA
1 AAAGAAACA
5415399 AACTTCCTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
24 9 0.27
27 24 0.73
ACGTcount: A:0.48, C:0.22, G:0.12, T:0.18
Consensus pattern (24 bp):
AAAGAAACATAGTTTTCCAGCCAC
Found at i:5415384 original size:27 final size:27
Alignment explanation
Indices: 5415347--5415398 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
5415337 CAAAAGAAAC
5415347 ATAGTTTTCCAGCCACAAAGAAACATA
1 ATAGTTTTCCAGCCACAAAGAAACATA
5415374 ATAGTTTTCCAGCCACAAAGAAACA
1 ATAGTTTTCCAGCCACAAAGAAACA
5415399 AACTTCCTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.44, C:0.23, G:0.12, T:0.21
Consensus pattern (27 bp):
ATAGTTTTCCAGCCACAAAGAAACATA
Found at i:5424699 original size:86 final size:86
Alignment explanation
Indices: 5424499--5424804 Score: 416
Period size: 87 Copynumber: 3.5 Consensus size: 86
5424489 TGTAAATTTA
* * * *
5424499 TAATTAACGCACGCCACGAAGAAAATCGTTCTAAAAATGGAAATCCCTTTCGGGCTTTGGCTCAT
1 TAATTAACGCACGCCACGAAGAAAATCATTTTAAAAATGGAAATCCCTTTC-GGCTTGGGCTCGT
*
5424564 TCATAAATTTATAAACATGATG
65 TCGTAAATTTATAAACATGATG
* * * *
5424586 TACTTAACGCACTCCACGAAGAAAATCATTTTGAAAATGGACATCCCTTTCAGGCTTGGGCTCGT
1 TAATTAACGCACGCCACGAAGAAAATCATTTTAAAAATGGAAATCCCTTTC-GGCTTGGGCTCGT
5424651 TCGT-AATTTATAAACATGATG
65 TCGTAAATTTATAAACATGATG
* * * *
5424672 TAATTAATGCACGCCACGAAGAAAATCATTTCAAAAATGGAAATCCTTTTCGAGCTTGGGCTTGT
1 TAATTAACGCACGCCACGAAGAAAATCATTTTAAAAATGGAAATCCCTTTCG-GCTTGGGCTCGT
*
5424737 TTGTAAATTTATAAACATGATG
65 TCGTAAATTTATAAACATGATG
* * * *
5424759 TAATCAACACACGCCACGAAGAAAATCATTTCAAAAATCGAAATCC
1 TAATTAACGCACGCCACGAAGAAAATCATTTTAAAAATGGAAATCC
5424805 AATTAATAGG
Statistics
Matches: 194, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
85 1 0.01
86 75 0.39
87 118 0.61
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (86 bp):
TAATTAACGCACGCCACGAAGAAAATCATTTTAAAAATGGAAATCCCTTTCGGCTTGGGCTCGTT
CGTAAATTTATAAACATGATG
Found at i:5426903 original size:29 final size:30
Alignment explanation
Indices: 5426871--5426929 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
5426861 TATAATTTAA
5426871 TGTGTAATTGTATATAT-AAATTTTGATTT
1 TGTGTAATTGTATATATGAAATTTTGATTT
*
5426900 TGTGTAATTTTATATATGAAATTTTGATTT
1 TGTGTAATTGTATATATGAAATTTTGATTT
5426930 AATTTAATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.56
Consensus pattern (30 bp):
TGTGTAATTGTATATATGAAATTTTGATTT
Found at i:5426938 original size:30 final size:30
Alignment explanation
Indices: 5426849--5426938 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
5426839 AGTTTTAAAA
* *
5426849 TTATATATG-AATTATAATTTAATGTGTAATT
1 TTATATATGAAATTTTGATTTAAT-T-TAATT
* ** *
5426880 GTATATAT-AAATTTTGATTTTGTGTAATT
1 TTATATATGAAATTTTGATTTAATTTAATT
5426909 TTATATATGAAATTTTGATTTAATTTAATT
1 TTATATATGAAATTTTGATTTAATTTAATT
5426939 CTTGTAATTT
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
29 12 0.26
30 18 0.38
31 17 0.36
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (30 bp):
TTATATATGAAATTTTGATTTAATTTAATT
Found at i:5427108 original size:31 final size:30
Alignment explanation
Indices: 5427072--5427144 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
5427062 GACTAAATAA
5427072 AAATTAAAGTTTTAAGTATAT-ATTTGAACC
1 AAATTAAAGTTTTAAGTATATGA-TTGAACC
* * * *
5427102 ACAATTAAAATTTTACGTGTATGATTGTACC
1 A-AATTAAAGTTTTAAGTATATGATTGAACC
5427133 AAATTAAAGTTT
1 AAATTAAAGTTT
5427145 ATGTATACAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 11 0.31
31 24 0.67
32 1 0.03
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.40
Consensus pattern (30 bp):
AAATTAAAGTTTTAAGTATATGATTGAACC
Found at i:5427680 original size:30 final size:30
Alignment explanation
Indices: 5427644--5427704 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
5427634 AATTGAAAGA
5427644 TTATTTCTCAAATTTGACTTGAAATAGGAG
1 TTATTTCTCAAATTTGACTTGAAATAGGAG
5427674 TTATTTCTCAAATTTGACTTGAAATAGGAG
1 TTATTTCTCAAATTTGACTTGAAATAGGAG
5427704 T
1 T
5427705 CATAATTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (30 bp):
TTATTTCTCAAATTTGACTTGAAATAGGAG
Found at i:5429655 original size:24 final size:24
Alignment explanation
Indices: 5429598--5429656 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
5429588 TAGACTAATA
* *
5429598 AGAATTTAACTCAAATAAATAAAC
1 AGAATTTAATTAAAATAAATAAAC
5429622 AGAATTTAATTAAAATAAATAAAC
1 AGAATTTAATTAAAATAAATAAAC
*
5429646 AGAGTTTAATT
1 AGAATTTAATT
5429657 GAAAGATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.31
Consensus pattern (24 bp):
AGAATTTAATTAAAATAAATAAAC
Found at i:5430415 original size:5 final size:5
Alignment explanation
Indices: 5430407--5430431 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5430397 GTTCTTTGAA
5430407 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
5430432 TTTATTTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:5431047 original size:16 final size:17
Alignment explanation
Indices: 5431012--5431052 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
5431002 CGATATTACA
5431012 TTAAATATTATCCTTTT
1 TTAAATATTATCCTTTT
5431029 TTAAA-ATTAT-CTTTAT
1 TTAAATATTATCCTTT-T
*
5431045 TTAGATAT
1 TTAAATAT
5431053 GCGTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 4 0.19
16 10 0.48
17 7 0.33
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.56
Consensus pattern (17 bp):
TTAAATATTATCCTTTT
Found at i:5432471 original size:23 final size:22
Alignment explanation
Indices: 5432440--5432483 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
5432430 TATATATTTT
5432440 TTAAAAATTATT-TTATTTTAATA
1 TTAAAAATT-TTATT-TTTTAATA
*
5432463 TTAATAATTTTATTTTTTAAT
1 TTAAAAATTTTATTTTTTAAT
5432484 GAAATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTAAAAATTTTATTTTTTAATA
Found at i:5433030 original size:29 final size:29
Alignment explanation
Indices: 5432998--5433073 Score: 107
Period size: 30 Copynumber: 2.6 Consensus size: 29
5432988 ACTTTATAAA
*
5432998 ATTTTATAATTTTTTTTATAATTCTATAT
1 ATTTTATAATTTTTTTAATAATTCTATAT
* *
5433027 ATTTTATAATTTTTTACAATATTTCTATAT
1 ATTTTATAATTTTTT-TAATAATTCTATAT
*
5433057 ACTTTATAATTTTTTTA
1 ATTTTATAATTTTTTTA
5433074 CTATCTTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
29 16 0.39
30 25 0.61
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (29 bp):
ATTTTATAATTTTTTTAATAATTCTATAT
Found at i:5433084 original size:29 final size:28
Alignment explanation
Indices: 5433000--5433084 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 28
5432990 TTTATAAAAT
* *
5433000 TTTATAATTTTTTTTA-TAATTCTATATAT
1 TTTATAA-TTTTTTTACT-ATTTTATATAC
5433029 TTTATAA-TTTTTTACAATATTTCTATATAC
1 TTTATAATTTTTTTAC--TATTT-TATATAC
5433059 TTTATAATTTTTTTACTATCTTTATA
1 TTTATAATTTTTTTACTAT-TTTATA
5433085 AAATTTTACA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
27 7 0.15
29 17 0.35
30 16 0.33
31 8 0.17
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (28 bp):
TTTATAATTTTTTTACTATTTTATATAC
Found at i:5433098 original size:30 final size:30
Alignment explanation
Indices: 5432989--5433101 Score: 99
Period size: 30 Copynumber: 3.8 Consensus size: 30
5432979 ATCATTTCAA
5432989 CTTTATAAAATTTTATAATTTTTTTTA-TAAT
1 CTTTATAAAATTTTATAA-TTTTTTTACT-AT
* * *
5433020 -TCTAT-ATATTTTATAA-TTTTTTACAAT
1 CTTTATAAAATTTTATAATTTTTTTACTAT
* * * *
5433047 ATTTCTATATACTTTATAATTTTTTTACTAT
1 CTTTATA-AAATTTTATAATTTTTTTACTAT
*
5433078 CTTTATAAAATTTTACAATTTTTT
1 CTTTATAAAATTTTATAATTTTTT
5433102 CTAACTTTTA
Statistics
Matches: 65, Mismatches: 12, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
27 9 0.14
28 3 0.05
29 10 0.15
30 28 0.43
31 15 0.23
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (30 bp):
CTTTATAAAATTTTATAATTTTTTTACTAT
Found at i:5433135 original size:22 final size:22
Alignment explanation
Indices: 5433107--5433153 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
5433097 TTTTTCTAAC
* *
5433107 TTTTAAT-AAATTTTAAATAGTT
1 TTTTAATCAAAATTT-AATAATT
5433129 TTTTAATCAAAATTTAATAATT
1 TTTTAATCAAAATTTAATAATT
5433151 TTT
1 TTT
5433154 ATTGATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
TTTTAATCAAAATTTAATAATT
Found at i:5433994 original size:19 final size:19
Alignment explanation
Indices: 5433924--5433996 Score: 60
Period size: 19 Copynumber: 3.8 Consensus size: 19
5433914 TTCTCTTTCC
*
5433924 TTTTCCATATTTGATTCTCTA
1 TTTTCCATATAT-A-TCTCTA
*
5433945 TTTTCCATA-AAAT-TCTAA
1 TTTTCCATATATATCTCT-A
* * *
5433963 ATTTCCTTTTATATCTCTA
1 TTTTCCATATATATCTCTA
5433982 TTTTCCATATATATC
1 TTTTCCATATATATC
5433997 ATTTCTCTTT
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
17 3 0.08
18 8 0.20
19 17 0.43
20 3 0.08
21 9 0.22
ACGTcount: A:0.26, C:0.19, G:0.01, T:0.53
Consensus pattern (19 bp):
TTTTCCATATATATCTCTA
Found at i:5434062 original size:85 final size:85
Alignment explanation
Indices: 5433914--5434075 Score: 213
Period size: 85 Copynumber: 1.9 Consensus size: 85
5433904 ATATTTGTTA
* *
5433914 TTCTCTTTCCTTTTCCATATTTGATTCTCTATTTTCCATAAAATTCTAAATTTCCTTTTATATCT
1 TTCTCTTTCCTTTTCCATATTTGATTATCTATTTTCCATAAAATTCTAAATTTCCTTTCATATCT
* *
5433979 CTATTTTCCATATATATCAT
66 ATATTTTACATATATATCAT
* * *
5433999 TTCTCTTT-CTTTTCCCATATTTGATTATCTATTTTCCTTAAAATAT-T-CAGTTCTCTTTCATA
1 TTCTCTTTCCTTTT-CCATATTTGATTATCTATTTTCCATAAAAT-TCTAAATTTC-CTTTCATA
5434061 TCTATATTTTACATA
63 TCTATATTTTACATA
5434076 ATTGTTATCC
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
84 9 0.13
85 57 0.85
86 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.02, T:0.54
Consensus pattern (85 bp):
TTCTCTTTCCTTTTCCATATTTGATTATCTATTTTCCATAAAATTCTAAATTTCCTTTCATATCT
ATATTTTACATATATATCAT
Found at i:5434752 original size:24 final size:24
Alignment explanation
Indices: 5434701--5434746 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5434691 AGCAAACTGA
*
5434701 TATAAAAATAATATAATATTTTGG
1 TATAAAAATAATATAACATTTTGG
* *
5434725 TATAAAAATATTGTAACATTTT
1 TATAAAAATAATATAACATTTT
5434747 TTTATAGATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (24 bp):
TATAAAAATAATATAACATTTTGG
Found at i:5435893 original size:22 final size:22
Alignment explanation
Indices: 5435868--5435918 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
5435858 ACAGTTTGTC
5435868 ATGTTGTATTTTCATAGT-GTAT
1 ATGTTGTATTTTCATA-TCGTAT
**
5435890 ATGTCATATTTTCATATCGTAT
1 ATGTTGTATTTTCATATCGTAT
*
5435912 TTGTTGT
1 ATGTTGT
5435919 GTTTATTAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.22, C:0.08, G:0.16, T:0.55
Consensus pattern (22 bp):
ATGTTGTATTTTCATATCGTAT
Found at i:5437470 original size:13 final size:14
Alignment explanation
Indices: 5437442--5437479 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
5437432 ACGATACGAA
*
5437442 AATATGACATATAC
1 AATATGACAAATAC
5437456 AATATGA-AAATAC
1 AATATGACAAATAC
*
5437469 AACATGACAAA
1 AATATGACAAA
5437480 CTGTAAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.58, C:0.13, G:0.08, T:0.21
Consensus pattern (14 bp):
AATATGACAAATAC
Found at i:5437473 original size:22 final size:22
Alignment explanation
Indices: 5437430--5437473 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
5437420 AACACAGCAA
* **
5437430 ATACGATACGAAAATATGACAT
1 ATACAATACGAAAATACAACAT
*
5437452 ATACAATATGAAAATACAACAT
1 ATACAATACGAAAATACAACAT
5437474 GACAAACTGT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.55, C:0.14, G:0.09, T:0.23
Consensus pattern (22 bp):
ATACAATACGAAAATACAACAT
Found at i:5438280 original size:87 final size:87
Alignment explanation
Indices: 5438130--5438473 Score: 433
Period size: 87 Copynumber: 4.0 Consensus size: 87
5438120 GGCAACAGTG
* ** *
5438130 TTTCAGGCTTGGGCTCATTTGTAAATTTATGAACATGATGTAATTAACGCACGCCACGAAGAAAA
1 TTTCAGGCTTGGCCTCATTCATAAATTTATAAACATGATGTAATTAACGCACGCCACGAAGAAAA
* *
5438195 TCATTTCAAATATGGAAATCCT
66 TCATTTCAAAAATGGAAATCCC
* * ** *
5438217 TTTTAGGCTTGGTCTTGTTCATAAATTTATAAACATGATGTAATTAATGCACGCCACGAAGAAAA
1 TTTCAGGCTTGGCCTCATTCATAAATTTATAAACATGATGTAATTAACGCACGCCACGAAGAAAA
5438282 TCATTTC-AAAATGGAAATCCC
66 TCATTTCAAAAATGGAAATCCC
* * * * *
5438303 TTTCAGGCTTGGGCTCATTCATAAACTTAAAAACATGATGAAATTAACACACGCCACGAAGAAAA
1 TTTCAGGCTTGGCCTCATTCATAAATTTATAAACATGATGTAATTAACGCACGCCACGAAGAAAA
* **
5438368 TAATTTCAAAAAAAGAAATCCC
66 TCATTTCAAAAATGGAAATCCC
* ** * * *
5438390 TTTCGGGCTTGGCCTCATTTGTAAATTTATAAACGTGATGTAAGTT-AC-CACGCGATGAAGAAA
1 TTTCAGGCTTGGCCTCATTCATAAATTTATAAACATGATGTAA-TTAACGCACGCCACGAAGAAA
5438453 ATCATTTCAAAAATGGAAATC
65 ATCATTTCAAAAATGGAAATC
5438474 AGGTTAACAG
Statistics
Matches: 220, Mismatches: 35, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
86 105 0.48
87 113 0.51
88 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (87 bp):
TTTCAGGCTTGGCCTCATTCATAAATTTATAAACATGATGTAATTAACGCACGCCACGAAGAAAA
TCATTTCAAAAATGGAAATCCC
Found at i:5438419 original size:173 final size:173
Alignment explanation
Indices: 5438130--5438473 Score: 449
Period size: 173 Copynumber: 2.0 Consensus size: 173
5438120 GGCAACAGTG
** * ** * *
5438130 TTTCAGGCTTGGGCTCATTTGTAAATTTATGAACATGATGTAATTAACGCACGCCACGAAGAAAA
1 TTTCAGGCTTGGGCTCATTCATAAACTTAAAAACATGATGAAATTAACACACGCCACGAAGAAAA
* * ** * * * **
5438195 TCATTTCAAATATGGAAATCCTTTTTAGGCTTGGTCTTGTTCATAAATTTATAAACATGATGTAA
66 TAATTTCAAAAAAAGAAATCCCTTTCAGGCTTGGCCTCATTCATAAATTTATAAACATGATGTAA
*
5438260 -TTAATGCACGCCACGAAGAAAATCATTTC-AAAATGGAAATCCC
131 GTT-A-CCACGCCACGAAGAAAATCATTTCAAAAATGGAAATCCC
5438303 TTTCAGGCTTGGGCTCATTCATAAACTTAAAAACATGATGAAATTAACACACGCCACGAAGAAAA
1 TTTCAGGCTTGGGCTCATTCATAAACTTAAAAACATGATGAAATTAACACACGCCACGAAGAAAA
* ** *
5438368 TAATTTCAAAAAAAGAAATCCCTTTCGGGCTTGGCCTCATTTGTAAATTTATAAACGTGATGTAA
66 TAATTTCAAAAAAAGAAATCCCTTTCAGGCTTGGCCTCATTCATAAATTTATAAACATGATGTAA
* *
5438433 GTTACCACGCGATGAAGAAAATCATTTCAAAAATGGAAATC
131 GTTACCACGCCACGAAGAAAATCATTTCAAAAATGGAAATC
5438474 AGGTTAACAG
Statistics
Matches: 146, Mismatches: 23, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
172 21 0.14
173 123 0.84
174 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (173 bp):
TTTCAGGCTTGGGCTCATTCATAAACTTAAAAACATGATGAAATTAACACACGCCACGAAGAAAA
TAATTTCAAAAAAAGAAATCCCTTTCAGGCTTGGCCTCATTCATAAATTTATAAACATGATGTAA
GTTACCACGCCACGAAGAAAATCATTTCAAAAATGGAAATCCC
Found at i:5441640 original size:13 final size:13
Alignment explanation
Indices: 5441622--5441646 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5441612 TAACATTACT
5441622 AAAAATACTTTTC
1 AAAAATACTTTTC
5441635 AAAAATACTTTT
1 AAAAATACTTTT
5441647 AAACTAAAAA
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:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAAATACTTTTC
Found at i:5447619 original size:39 final size:39
Alignment explanation
Indices: 5447575--5447658 Score: 116
Period size: 39 Copynumber: 2.2 Consensus size: 39
5447565 CATTGTACTC
*
5447575 TTATTTTTATAAAAGTA-TGTTTTAATAAAAAGATATAAA
1 TTATTTTTATAAAAATATTGTTTTAAT-AAAAGATATAAA
* * *
5447614 TTATTTTTATAAAAATATTTTTTTAATAAAATATATTAA
1 TTATTTTTATAAAAATATTGTTTTAATAAAAGATATAAA
5447653 TTATTT
1 TTATTT
5447659 GAATTAATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 32 0.80
40 8 0.20
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (39 bp):
TTATTTTTATAAAAATATTGTTTTAATAAAAGATATAAA
Found at i:5447638 original size:16 final size:18
Alignment explanation
Indices: 5447617--5447650 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5447607 ATATAAATTA
5447617 TTTTT-ATAAAA-ATATT
1 TTTTTAATAAAATATATT
5447633 TTTTTAATAAAATATATT
1 TTTTTAATAAAATATATT
5447651 AATTATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 6 0.38
18 5 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTTAATAAAATATATT
Found at i:5450166 original size:18 final size:18
Alignment explanation
Indices: 5450143--5450185 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
5450133 GTTCAAGGTG
5450143 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
5450161 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
5450179 TAATTAA
1 TAATTAA
5450186 AGACCTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:5464757 original size:53 final size:53
Alignment explanation
Indices: 5464677--5464832 Score: 231
Period size: 60 Copynumber: 2.8 Consensus size: 53
5464667 GCAGGCAGAA
* *
5464677 GCTTATATATCTTTGAAAGAAAGCAACCAATGTTGCATGTTGTACTAAACCTT
1 GCTTATTTATCTTTGCAAGAAAGCAACCAATGTTGCATGTTGTACTAAACCTT
5464730 GCTTATTTATCTTTGCAAGAAAGCAACCAATGTTGCATGTTGTATGTTGTACTAAACCTT
1 GCTTATTTATCTTTGCAAGAAAGCAACCAATGTTGC-------ATGTTGTACTAAACCTT
5464790 GCTTATTTATCTTTGCAAGAAAGCAACCAATGTTGCATGTTGT
1 GCTTATTTATCTTTGCAAGAAAGCAACCAATGTTGCATGTTGT
5464833 GCAAAATCTT
Statistics
Matches: 94, Mismatches: 2, Indels: 14
0.85 0.02 0.13
Matches are distributed among these distances:
53 41 0.44
60 53 0.56
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (53 bp):
GCTTATTTATCTTTGCAAGAAAGCAACCAATGTTGCATGTTGTACTAAACCTT
Found at i:5464781 original size:60 final size:60
Alignment explanation
Indices: 5464706--5464832 Score: 245
Period size: 60 Copynumber: 2.1 Consensus size: 60
5464696 AAAGCAACCA
*
5464706 ATGTTGCATGTTGTACTAAACCTTGCTTATTTATCTTTGCAAGAAAGCAACCAATGTTGC
1 ATGTTGTATGTTGTACTAAACCTTGCTTATTTATCTTTGCAAGAAAGCAACCAATGTTGC
5464766 ATGTTGTATGTTGTACTAAACCTTGCTTATTTATCTTTGCAAGAAAGCAACCAATGTTGC
1 ATGTTGTATGTTGTACTAAACCTTGCTTATTTATCTTTGCAAGAAAGCAACCAATGTTGC
5464826 ATGTTGT
1 ATGTTGT
5464833 GCAAAATCTT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
60 66 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (60 bp):
ATGTTGTATGTTGTACTAAACCTTGCTTATTTATCTTTGCAAGAAAGCAACCAATGTTGC
Found at i:5471885 original size:30 final size:29
Alignment explanation
Indices: 5471638--5471889 Score: 253
Period size: 29 Copynumber: 8.5 Consensus size: 29
5471628 TAAAAGCAAA
*
5471638 TTTGGAAAGTTTTAGGGGTAAAAATGTCA-T
1 TTTGG-AAG-TTTAGGGGTAAAAATGTGATT
**
5471668 TTTGAGAAAATTAGGGGTAAAAATGTGATT
1 TTTG-GAAGTTTAGGGGTAAAAATGTGATT
*
5471698 TTTGAGAAG-TTCGAGGGTAAAAATGTGATT
1 TTTG-GAAGTTTAG-GGGTAAAAATGTGATT
* * *
5471728 TTTGGAAGTTCAGGGG-CAAAATGTAATT
1 TTTGGAAGTTTAGGGGTAAAAATGTGATT
*
5471756 TTTGAGAAGTTTAAGGGTAAAAATGTGATT
1 TTTG-GAAGTTTAGGGGTAAAAATGTGATT
*
5471786 TTTGGAAGTTTAGAGGTAAAAATGT-ATT
1 TTTGGAAGTTTAGGGGTAAAAATGTGATT
* *
5471814 TTTGAGAAGTTTAGAGGTCAAAATGTGA-T
1 TTTG-GAAGTTTAGGGGTAAAAATGTGATT
* *
5471843 TTTGGAAAAGTTTAGGGGTCAAAATATGATT
1 TTTGG--AAGTTTAGGGGTAAAAATGTGATT
*
5471874 TATGGATAGTTTAGGG
1 TTTGGA-AGTTTAGGG
5471890 ACCTTCTGGG
Statistics
Matches: 191, Mismatches: 19, Indels: 24
0.82 0.08 0.10
Matches are distributed among these distances:
28 22 0.12
29 82 0.43
30 81 0.42
31 6 0.03
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.35
Consensus pattern (29 bp):
TTTGGAAGTTTAGGGGTAAAAATGTGATT
Found at i:5475650 original size:28 final size:26
Alignment explanation
Indices: 5475595--5475653 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
5475585 ATCTCGATCG
*
5475595 AACCTAAACTTGAATCTCAAACTCCA
1 AACCTAAACTTGAATATCAAACTCCA
*
5475621 AACCATAAACTTTGAATATCGAAC-CTCA
1 AACC-TAAAC-TTGAATATCAAACTC-CA
5475649 AACCT
1 AACCT
5475654 TAATCTAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
26 4 0.14
27 7 0.25
28 17 0.61
ACGTcount: A:0.42, C:0.29, G:0.05, T:0.24
Consensus pattern (26 bp):
AACCTAAACTTGAATATCAAACTCCA
Found at i:5475883 original size:17 final size:18
Alignment explanation
Indices: 5475850--5475883 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5475840 ATTTCCCAAT
*
5475850 ATTATGAGTTTAAATTTG
1 ATTATGAGTTAAAATTTG
5475868 ATTATGA-TTAAAATTT
1 ATTATGAGTTAAAATTT
5475884 TATTGATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (18 bp):
ATTATGAGTTAAAATTTG
Found at i:5477273 original size:21 final size:22
Alignment explanation
Indices: 5477236--5477276 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5477226 GGCACTATGA
*
5477236 TTTAAATTATGAAAATTATTTT
1 TTTAAAATATGAAAATTATTTT
5477258 TTTAAAATAT-AAAATTATT
1 TTTAAAATATGAAAATTATT
5477277 AAATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TTTAAAATATGAAAATTATTTT
Found at i:5477280 original size:29 final size:30
Alignment explanation
Indices: 5477239--5477315 Score: 104
Period size: 29 Copynumber: 2.6 Consensus size: 30
5477229 ACTATGATTT
*
5477239 AAATTATGAAAATTATTTTTTTAAAAT-ATA
1 AAATTAT-TAAATTATTTTTTTAAAATAATA
*
5477269 AAATTATTAAATT-TTTTTTTGAAATAATA
1 AAATTATTAAATTATTTTTTTAAAATAATA
*
5477298 AAATTATTAAATAATTTT
1 AAATTATTAAATTATTTT
5477316 AATTTTTAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 11 0.26
29 20 0.48
30 11 0.26
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (30 bp):
AAATTATTAAATTATTTTTTTAAAATAATA
Found at i:5477315 original size:28 final size:28
Alignment explanation
Indices: 5477256--5477315 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
5477246 GAAAATTATT
**
5477256 TTTTTAAAATATAAAATTATTAAATTTT
1 TTTTTAAAATATAAAATTATTAAATTAA
*
5477284 TTTTTGAAATAATAAAATTATTAAA-TAA
1 TTTTTAAAAT-ATAAAATTATTAAATTAA
5477312 TTTT
1 TTTT
5477316 AATTTTTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (28 bp):
TTTTTAAAATATAAAATTATTAAATTAA
Found at i:5478422 original size:20 final size:20
Alignment explanation
Indices: 5478383--5478422 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5478373 TGATTCAAAA
* *
5478383 GTTAGGGTTTAGTTTTTTTT
1 GTTAGGGTTTAATTTGTTTT
*
5478403 GTTAGTGTTTAATTTGTTTT
1 GTTAGGGTTTAATTTGTTTT
5478423 AATTGTGTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.23, T:0.65
Consensus pattern (20 bp):
GTTAGGGTTTAATTTGTTTT
Found at i:5478492 original size:20 final size:20
Alignment explanation
Indices: 5478445--5478492 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
5478435 TGTGAGTCCC
* *
5478445 AATTTTTTTTTTAAAATTTT
1 AATTATTTTTTTAAAATTTA
*
5478465 AATTATTTTTTT-AAGTTTA
1 AATTATTTTTTTAAAATTTA
5478484 AATTCATTT
1 AATT-ATTT
5478493 ATTGACGTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (20 bp):
AATTATTTTTTTAAAATTTA
Found at i:5479180 original size:25 final size:24
Alignment explanation
Indices: 5479135--5479181 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
5479125 GACTTATTCA
*
5479135 TGATTTGGTCGTACATTAAATTAT
1 TGATTTGGTCGTACATAAAATTAT
* *
5479159 TGATTTGGGTCTTAGATAAAATT
1 TGATTT-GGTCGTACATAAAATT
5479182 TTATGTTTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 6 0.32
25 13 0.68
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.45
Consensus pattern (24 bp):
TGATTTGGTCGTACATAAAATTAT
Found at i:5480635 original size:17 final size:17
Alignment explanation
Indices: 5480605--5480637 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5480595 TGTGAATTCA
5480605 ATCAAAGTTAAATTAAT
1 ATCAAAGTTAAATTAAT
5480622 ATCACAAGTT-AATTAA
1 ATCA-AAGTTAAATTAA
5480638 GCATTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.52, C:0.09, G:0.06, T:0.33
Consensus pattern (17 bp):
ATCAAAGTTAAATTAAT
Found at i:5482745 original size:24 final size:24
Alignment explanation
Indices: 5482712--5482758 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
5482702 AGAAATAATC
*
5482712 TTTCAGTTAAACTCTGTTTATTTA
1 TTTCAATTAAACTCTGTTTATTTA
*
5482736 TTTCAATTAAATTCTGTTTATTT
1 TTTCAATTAAACTCTGTTTATTT
5482759 GTTTGAGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.11, G:0.06, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTA
Found at i:5488133 original size:3 final size:3
Alignment explanation
Indices: 5488127--5488158 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5488117 TGAGTGTTTG
5488127 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5488159 TACATATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5506810 original size:12 final size:12
Alignment explanation
Indices: 5506795--5506889 Score: 63
Period size: 12 Copynumber: 8.2 Consensus size: 12
5506785 CCAAACAAAT
*
5506795 AAAACAACAACA
1 AAAATAACAACA
**
5506807 AAAATAAC-AGT
1 AAAATAACAACA
*
5506818 AAAACAAC-A-A
1 AAAATAACAACA
*
5506828 TAAA-AACAACA
1 AAAATAACAACA
*
5506839 AAAATAACAGCA
1 AAAATAACAACA
*
5506851 AAAATAGCAACA
1 AAAATAACAACA
* *
5506863 AAAATAATAGCA
1 AAAATAACAACA
* *
5506875 AAAACAACACCA
1 AAAATAACAACA
5506887 AAA
1 AAA
5506890 CAGTAAAAAA
Statistics
Matches: 64, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
9 3 0.05
10 4 0.06
11 13 0.20
12 44 0.69
ACGTcount: A:0.71, C:0.18, G:0.04, T:0.07
Consensus pattern (12 bp):
AAAATAACAACA
Found at i:5506820 original size:23 final size:22
Alignment explanation
Indices: 5506793--5506856 Score: 76
Period size: 23 Copynumber: 2.9 Consensus size: 22
5506783 ATCCAAACAA
5506793 ATAAAACAACAACAAAAATAAC
1 ATAAAACAACAACAAAAATAAC
* *
5506815 AGTAAAACAACAATAAAAACAAC
1 A-TAAAACAACAACAAAAATAAC
* *
5506838 A-AAAATAACAGCAAAAATA
1 ATAAAACAACAACAAAAATA
5506857 GCAACAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
21 14 0.40
22 1 0.03
23 20 0.57
ACGTcount: A:0.72, C:0.16, G:0.03, T:0.09
Consensus pattern (22 bp):
ATAAAACAACAACAAAAATAAC
Found at i:5506841 original size:20 final size:20
Alignment explanation
Indices: 5506800--5506841 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
5506790 CAAATAAAAC
**
5506800 AACAACAAAAATAACAGTAA
1 AACAACAAAAATAACAACAA
5506820 AACAACAATAAA-AACAACAA
1 AACAACAA-AAATAACAACAA
5506840 AA
1 AA
5506842 ATAACAGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.74, C:0.17, G:0.02, T:0.07
Consensus pattern (20 bp):
AACAACAAAAATAACAACAA
Found at i:5506888 original size:24 final size:24
Alignment explanation
Indices: 5506832--5506889 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
5506822 CAACAATAAA
*
5506832 AACAACAAAAATAACAGCAAAAAT
1 AACAACAAAAATAACAGCAAAAAC
* *
5506856 AGCAACAAAAATAATAGCAAAAAC
1 AACAACAAAAATAACAGCAAAAAC
*
5506880 AACACCAAAA
1 AACAACAAAA
5506890 CAGTAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.69, C:0.19, G:0.05, T:0.07
Consensus pattern (24 bp):
AACAACAAAAATAACAGCAAAAAC
Found at i:5506898 original size:56 final size:53
Alignment explanation
Indices: 5506802--5506919 Score: 121
Period size: 56 Copynumber: 2.2 Consensus size: 53
5506792 AATAAAACAA
* *
5506802 CAACAAAAATAACAGTAAAACAACAATAAAAACAACAAAAATAACAGCAAAAATAG
1 CAACAAAAATAACAGAAAAACAACAACAAAAACAACAAAAA-AA-A-CAAAAATAG
* * ** *
5506858 CAACAAAAATAATAGCAAAAACAAC-ACCAAAACAGTAAAAAAAACCAAAATAG
1 CAACAAAAATAACAG-AAAAACAACAACAAAAACAACAAAAAAAACAAAAATAG
5506911 CAATCAAAA
1 CAA-CAAAA
5506920 TAGTTAAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
53 11 0.21
54 6 0.11
55 2 0.04
56 26 0.49
57 8 0.15
ACGTcount: A:0.69, C:0.18, G:0.05, T:0.08
Consensus pattern (53 bp):
CAACAAAAATAACAGAAAAACAACAACAAAAACAACAAAAAAAACAAAAATAG
Found at i:5506951 original size:20 final size:19
Alignment explanation
Indices: 5506924--5506969 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 19
5506914 TCAAAATAGT
5506924 TAAAAAAAAGTACCAAAACAG
1 TAAAAAAAA--ACCAAAACAG
5506945 TAAAAAAAAACCAAAACAG
1 TAAAAAAAAACCAAAACAG
5506964 TAAAAA
1 TAAAAA
5506970 CAGCAATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 16 0.64
21 9 0.36
ACGTcount: A:0.72, C:0.13, G:0.07, T:0.09
Consensus pattern (19 bp):
TAAAAAAAAACCAAAACAG
Found at i:5517743 original size:12 final size:11
Alignment explanation
Indices: 5517722--5517782 Score: 50
Period size: 12 Copynumber: 5.3 Consensus size: 11
5517712 AAAAATGCAT
*
5517722 AAAAATAACAA
1 AAAAACAACAA
5517733 CAAAAACAACAA
1 -AAAAACAACAA
5517745 AAATAACAACAA
1 AAA-AACAACAA
* * *
5517757 GACAACAATAA
1 AAAAACAACAA
*
5517768 AAATAACAGCAA
1 AAA-AACAACAA
5517780 AAA
1 AAA
5517783 TAGCACCAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
11 11 0.28
12 28 0.72
ACGTcount: A:0.74, C:0.16, G:0.03, T:0.07
Consensus pattern (11 bp):
AAAAACAACAA
Found at i:5517775 original size:20 final size:20
Alignment explanation
Indices: 5517722--5517764 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
5517712 AAAAATGCAT
*
5517722 AAAAATAACAACAAAAACAAC
1 AAAAATAACAAC-AAGACAAC
5517743 AAAAATAACAACAAGACAAC
1 AAAAATAACAACAAGACAAC
5517763 AA
1 AA
5517765 TAAAAATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.74, C:0.19, G:0.02, T:0.05
Consensus pattern (20 bp):
AAAAATAACAACAAGACAAC
Found at i:5517833 original size:30 final size:31
Alignment explanation
Indices: 5517760--5517839 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 31
5517750 ACAACAAGAC
* *
5517760 AACAATAAAAATAACAGCAAAAATAGCACCAA
1 AACAGTAAAAA-AATAGCAAAAATAGCACCAA
**
5517792 AACAGTAAAAAAA-AGCAAAAATAGCAATTAA
1 AACAGTAAAAAAATAGCAAAAATAGC-ACCAA
*
5517823 AATAGT-AAAAAATAGCA
1 AACAGTAAAAAAATAGCA
5517840 CCAAAACAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 18 0.43
31 14 0.33
32 10 0.24
ACGTcount: A:0.66, C:0.12, G:0.09, T:0.12
Consensus pattern (31 bp):
AACAGTAAAAAAATAGCAAAAATAGCACCAA
Found at i:5533897 original size:25 final size:25
Alignment explanation
Indices: 5533830--5533909 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
5533820 TAAAAGCCAA
* *
5533830 ACAGAATAC-AC-CATAAGCGCAACAG
1 ACAGAATACAACACA-AAG-GCGACAT
*
5533855 ACAGAATACAACACAAAGGCGATAT
1 ACAGAATACAACACAAAGGCGACAT
** * *
5533880 ACAGAATACGCCATAAAGGTGACAT
1 ACAGAATACAACACAAAGGCGACAT
5533905 ACAGA
1 ACAGA
5533910 GTCACATGTT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
25 38 0.84
26 5 0.11
27 2 0.04
ACGTcount: A:0.49, C:0.23, G:0.17, T:0.11
Consensus pattern (25 bp):
ACAGAATACAACACAAAGGCGACAT
Found at i:5535868 original size:13 final size:13
Alignment explanation
Indices: 5535852--5535881 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5535842 TTTTTCTACG
*
5535852 AAATTGAAAAATA
1 AAATTCAAAAATA
5535865 AAATTCAAAAATA
1 AAATTCAAAAATA
5535878 AAAT
1 AAAT
5535882 AAAATTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.23
Consensus pattern (13 bp):
AAATTCAAAAATA
Found at i:5540825 original size:17 final size:18
Alignment explanation
Indices: 5540816--5540896 Score: 87
Period size: 17 Copynumber: 4.6 Consensus size: 18
5540806 TAAATTTTAA
*
5540816 TTTAGTTTAAGTTTAAACT
1 TTTAATTTAAGTTTAAA-T
**
5540835 TTTCTTTTAAGTTTAAAT
1 TTTAATTTAAGTTTAAAT
5540853 TTTAA-TTAAGTTTAAA-
1 TTTAATTTAAGTTTAAAT
5540869 TTTAATTTGAA-TTTAAAT
1 TTTAATTT-AAGTTTAAAT
*
5540887 TTAAATTTAA
1 TTTAATTTAA
5540897 TTAAAAAATC
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
16 5 0.09
17 21 0.39
18 13 0.24
19 15 0.28
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.54
Consensus pattern (18 bp):
TTTAATTTAAGTTTAAAT
Found at i:5540884 original size:23 final size:22
Alignment explanation
Indices: 5540840--5540898 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
5540830 AAACTTTTCT
* * *
5540840 TTTAAGTTTAAATTTTAATTAAG
1 TTTAAATTT-AATTTGAATTAAA
5540863 TTTAAATTTAATTTGAATTTAAA
1 TTTAAATTTAATTTGAA-TTAAA
5540886 TTTAAATTTAATT
1 TTTAAATTTAATT
5540899 AAAAAATCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
22 7 0.22
23 25 0.78
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (22 bp):
TTTAAATTTAATTTGAATTAAA
Found at i:5542017 original size:16 final size:17
Alignment explanation
Indices: 5541982--5542023 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
5541972 TAGTTTTAAA
5541982 AAAGAAAATAAAGAGAG
1 AAAGAAAATAAAGAGAG
5541999 AAAGATAAA-AAAG-GAG
1 AAAGA-AAATAAAGAGAG
5542015 AAAAGAAAA
1 -AAAGAAAA
5542024 GAAAAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 6 0.26
17 14 0.61
18 3 0.13
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (17 bp):
AAAGAAAATAAAGAGAG
Found at i:5542766 original size:30 final size:31
Alignment explanation
Indices: 5542731--5542799 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 31
5542721 ATAAGTCCCT
* *
5542731 AAACTTTCTAAAAAGTATATTTTGA-CCCCA
1 AAACTTTCTAAAAAGTACATTTTAACCCCCA
*
5542761 AAACTTTCTAAAAATTACATTTTAACCCCCCA
1 AAACTTTCTAAAAAGTACATTTTAA-CCCCCA
5542793 AAACTTT
1 AAACTTT
5542800 TCGAAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 22 0.65
32 12 0.35
ACGTcount: A:0.41, C:0.23, G:0.03, T:0.33
Consensus pattern (31 bp):
AAACTTTCTAAAAAGTACATTTTAACCCCCA
Found at i:5542887 original size:60 final size:59
Alignment explanation
Indices: 5542831--5542999 Score: 250
Period size: 60 Copynumber: 2.9 Consensus size: 59
5542821 CGAACTTTCC
* *
5542831 AAAATCCCATTTTTAACCTCGATTTCACCAAAAATTACCGTTTTGCCCCCTTAACTTCTA
1 AAAATCCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTGCCCCC-GAACTTCTA
*
5542891 AAAATCCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTGCCCTCGAACTTCTA
1 AAAATCCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTGCCCCCGAACTTCTA
* * * * *
5542950 AAAATCCCATTTTTAACC-CAATTCCAACTAAAATTACCATTTTGCTCCCG
1 AAAATCCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTGCCCCCG
5543000 GGTATCCAAA
Statistics
Matches: 100, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
58 26 0.26
59 26 0.26
60 48 0.48
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.34
Consensus pattern (59 bp):
AAAATCCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTGCCCCCGAACTTCTA
Found at i:5542924 original size:30 final size:28
Alignment explanation
Indices: 5542884--5542967 Score: 71
Period size: 30 Copynumber: 2.9 Consensus size: 28
5542874 TGCCCCCTTA
*
5542884 ACTTCTAAAAATCCCATTTTTAACCTCG
1 ACTTCCAAAAATCCCATTTTTAACCTCG
* * **
5542912 ATTTCACCAAAAATTACCA-TTTTGCCCTCG
1 ACTT--CCAAAAA-TCCCATTTTTAACCTCG
*
5542942 AACTTCTAAAAATCCCATTTTTAACC
1 -ACTTCCAAAAATCCCATTTTTAACC
5542968 CAATTCCAAC
Statistics
Matches: 41, Mismatches: 10, Indels: 9
0.68 0.17 0.15
Matches are distributed among these distances:
28 7 0.17
29 12 0.29
30 15 0.37
31 7 0.17
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.35
Consensus pattern (28 bp):
ACTTCCAAAAATCCCATTTTTAACCTCG
Found at i:5547561 original size:12 final size:12
Alignment explanation
Indices: 5547544--5547576 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
5547534 TATATGTTTC
5547544 AAAAAATTATAT
1 AAAAAATTATAT
*
5547556 AAAAAATAATAT
1 AAAAAATTATAT
5547568 AAAAAATTA
1 AAAAAATTA
5547577 ATACTTCCGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
AAAAAATTATAT
Found at i:5554399 original size:24 final size:25
Alignment explanation
Indices: 5554367--5554414 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
5554357 CTTCTCAATC
*
5554367 AAACGCTCC-TCTTCCTCTCTTCCA
1 AAACCCTCCATCTTCCTCTCTTCCA
*
5554391 AAACCCTCCATTCTTTCTCTCTTC
1 AAACCCTCCA-TCTTCCTCTCTTC
5554415 TGTTCCACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
26 12 0.60
ACGTcount: A:0.17, C:0.44, G:0.02, T:0.38
Consensus pattern (25 bp):
AAACCCTCCATCTTCCTCTCTTCCA
Found at i:5554906 original size:16 final size:18
Alignment explanation
Indices: 5554887--5554921 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
5554877 AAGAGGAAAA
5554887 AGATGGA-AAA-GAAAGG
1 AGATGGAGAAATGAAAGG
5554903 AGATGGAGAAATGAAAGG
1 AGATGGAGAAATGAAAGG
5554921 A
1 A
5554922 AATGAGAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 3 0.18
18 7 0.41
ACGTcount: A:0.54, C:0.00, G:0.37, T:0.09
Consensus pattern (18 bp):
AGATGGAGAAATGAAAGG
Found at i:5554913 original size:18 final size:19
Alignment explanation
Indices: 5554892--5554935 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
5554882 GAAAAAGATG
*
5554892 GAAAAGAAAGGAGATG-GA
1 GAAAAGAAAGGAAATGAGA
*
5554910 GAAATGAAAGGAAATGAGA
1 GAAAAGAAAGGAAATGAGA
*
5554929 GGAAAGA
1 GAAAAGA
5554936 GTGTTGTCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.57, C:0.00, G:0.36, T:0.07
Consensus pattern (19 bp):
GAAAAGAAAGGAAATGAGA
Found at i:5561357 original size:1 final size:1
Alignment explanation
Indices: 5561351--5561375 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
5561341 TCGAAAACAG
5561351 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
5561376 CCTGATGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5563574 original size:19 final size:20
Alignment explanation
Indices: 5563535--5563574 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
5563525 AATAATTTCA
* *
5563535 CAAATCCTTCTTTGAGTACC
1 CAAATCCTTCTTTAAGAACC
5563555 CAAATCC-TCTTTAAGAACC
1 CAAATCCTTCTTTAAGAACC
5563574 C
1 C
5563575 TAATGGCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.30, C:0.33, G:0.07, T:0.30
Consensus pattern (20 bp):
CAAATCCTTCTTTAAGAACC
Found at i:5576062 original size:10 final size:9
Alignment explanation
Indices: 5576042--5576089 Score: 60
Period size: 9 Copynumber: 5.0 Consensus size: 9
5576032 TAATTATATT
5576042 ATTACAAAAA
1 ATTA-AAAAA
5576052 ATGTAAAAAA
1 AT-TAAAAAA
*
5576062 ATTTATAAAA
1 A-TTAAAAAA
5576072 ATTAAAAAA
1 ATTAAAAAA
5576081 ATTAAAAAA
1 ATTAAAAAA
5576090 TATTTAGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
9 16 0.47
10 15 0.44
11 3 0.09
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (9 bp):
ATTAAAAAA
Found at i:5576079 original size:29 final size:31
Alignment explanation
Indices: 5576042--5576104 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 31
5576032 TAATTATATT
*
5576042 ATTACAAAAAATGTAAAAAA-ATTTATAAA-A
1 ATTACAAAAAAT-TAAAAAATATTTAGAAATA
5576072 ATTA-AAAAAATTAAAAAATATTTAGAAATA
1 ATTACAAAAAATTAAAAAATATTTAGAAATA
5576102 ATT
1 ATT
5576105 TTTTATAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 7 0.23
29 15 0.50
30 8 0.27
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (31 bp):
ATTACAAAAAATTAAAAAATATTTAGAAATA
Found at i:5578685 original size:21 final size:21
Alignment explanation
Indices: 5578645--5578705 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 21
5578635 AGGTTTAGGG
**
5578645 TTTTTTTAAATTTCAT-ATAA
1 TTTTTTTAAATTTTTTAATAA
5578665 TTTTTTTAAATTTTTTAATAA
1 TTTTTTTAAATTTTTTAATAA
* * **
5578686 TGTTTTAAAAAGTTTTAATA
1 TTTTTTTAAATTTTTTAATA
5578706 GTATTTATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 14 0.41
21 20 0.59
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (21 bp):
TTTTTTTAAATTTTTTAATAA
Found at i:5584105 original size:37 final size:37
Alignment explanation
Indices: 5584064--5584137 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
5584054 TGCGCAAACC
5584064 TTACTCAAGAAAATCCAAAG-CCACCAAACTAAGTACA
1 TTACTCAAGAAAATCC-AAGTCCACCAAACTAAGTACA
**
5584101 TTACTCAAGACCATCCAAGTCCACCAAACTAAGTACA
1 TTACTCAAGAAAATCCAAGTCCACCAAACTAAGTACA
5584138 CCACTTGACT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 3 0.09
37 31 0.91
ACGTcount: A:0.45, C:0.30, G:0.08, T:0.18
Consensus pattern (37 bp):
TTACTCAAGAAAATCCAAGTCCACCAAACTAAGTACA
Found at i:5587685 original size:14 final size:14
Alignment explanation
Indices: 5587666--5587694 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5587656 TGTGCTAGAC
5587666 TTTTGTCTTTTTTT
1 TTTTGTCTTTTTTT
5587680 TTTTGTCTTTTTTT
1 TTTTGTCTTTTTTT
5587694 T
1 T
5587695 ACGAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (14 bp):
TTTTGTCTTTTTTT
Found at i:5589735 original size:5 final size:5
Alignment explanation
Indices: 5589725--5589753 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
5589715 CAAGAATAAT
5589725 CATCC CATCC CATCC CATCC CATCC CATC
1 CATCC CATCC CATCC CATCC CATCC CATC
5589754 TCATTAATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.59, G:0.00, T:0.21
Consensus pattern (5 bp):
CATCC
Found at i:5593142 original size:18 final size:19
Alignment explanation
Indices: 5593101--5593145 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
5593091 AATCATTTTA
* *
5593101 ATAA-TTTATTTTAATATT
1 ATAATTTTATTTGAATAAT
5593119 ATAATTTTATTTGAATAAT
1 ATAATTTTATTTGAATAAT
5593138 A-AATTTTA
1 ATAATTTTA
5593146 ATAGTAATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
ATAATTTTATTTGAATAAT
Found at i:5593617 original size:21 final size:23
Alignment explanation
Indices: 5593593--5593637 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
5593583 ATTTTTATTT
5593593 TAAAT-TTAAT-TATAA-AATATA
1 TAAATATTAATAT-TAATAATATA
5593614 TAAATATTAATATTAATAATATA
1 TAAATATTAATATTAATAATATA
5593637 T
1 T
5593638 TTTTAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 5 0.24
22 8 0.38
23 8 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TAAATATTAATATTAATAATATA
Found at i:5596902 original size:29 final size:28
Alignment explanation
Indices: 5596870--5597179 Score: 159
Period size: 29 Copynumber: 10.7 Consensus size: 28
5596860 GGATGCCCGG
*
5596870 GGGGTAAAATGGTATTTTTTGGTGAGATC
1 GGGGTAAAATGGTA-ATTTTGGTGAGATC
** *
5596899 GGGGTAAAATGG-AATTTTGGAAAGTTC
1 GGGGTAAAATGGTAATTTTGGTGAGATC
*
5596926 GAGGGTAAAATGGTAATTTTTGGTGAAATC
1 G-GGGTAAAATGGTAA-TTTTGGTGAGATC
* *
5596956 GGGGTTAAAAATGG-GATTTTGG-GAAGTTC
1 GGGG-T-AAAATGGTAATTTTGGTG-AGATC
* *
5596985 AGGGGTAAAATGGTAATTTTGGTGAAATTA
1 -GGGGTAAAATGGTAATTTTGGTGAGA-TC
* * * ** * *
5597015 GGGTTAAAAATGG-GATTTTAGAAAGTTTA
1 GGGGT-AAAATGGTAATTTTGGTGAG-ATC
* *
5597044 GGGGTAAAATGATAATTTTGGTGAAATC
1 GGGGTAAAATGGTAATTTTGGTGAGATC
* * *
5597072 GAGGTTAAAAATGG-GATTTTGG-GAAGTTC
1 G-GGGT-AAAATGGTAATTTTGGTG-AGATC
* *
5597101 AGGGGTAAAATGGTAATTTTTGATGAAATC
1 -GGGGTAAAATGGTAA-TTTTGGTGAGATC
* * *
5597131 GAGGTTAAAAATGG-GATTTTGG-GAAGTTC
1 G-GGGT-AAAATGGTAATTTTGGTG-AGATC
5597160 GGGGGTAAAATGGTAATTTT
1 -GGGGTAAAATGGTAATTTT
5597180 TGAACAATCC
Statistics
Matches: 208, Mismatches: 48, Indels: 50
0.68 0.16 0.16
Matches are distributed among these distances:
27 11 0.05
28 44 0.21
29 93 0.45
30 45 0.22
31 15 0.07
ACGTcount: A:0.33, C:0.03, G:0.32, T:0.33
Consensus pattern (28 bp):
GGGGTAAAATGGTAATTTTGGTGAGATC
Found at i:5596996 original size:59 final size:59
Alignment explanation
Indices: 5596870--5597181 Score: 454
Period size: 58 Copynumber: 5.4 Consensus size: 59
5596860 GGATGCCCGG
* * * *
5596870 GGGGTAAAATGGTATTTTTTGGTGAGATCGGGG-T-AAAATGGAATTTTGGAAAGTTC-
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGGAAGTTCA
5596926 GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGGAAGTTCA
1 G-GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGGAAGTTCA
** * * *
5596986 GGGGTAAAATGGTAA-TTTTGGTGAAATTAGGGTTAAAAATGGGATTTTAGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGGAAGTTCA
* *
5597044 GGGGTAAAATGATAA-TTTTGGTGAAATCGAGGTTAAAAATGGGATTTTGGGAAGTTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGGAAGTTCA
* * *
5597102 GGGGTAAAATGGTAATTTTTGATGAAATCGAGGTTAAAAATGGGATTTTGGGAAGTTCG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGGAAGTTCA
5597161 GGGGTAAAATGGTAATTTTTG
1 GGGGTAAAATGGTAATTTTTG
5597182 AACAATCCAG
Statistics
Matches: 232, Mismatches: 19, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
56 1 0.00
57 30 0.13
58 104 0.45
59 96 0.41
60 1 0.00
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.33
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGGAAGTTCA
Found at i:5599037 original size:28 final size:29
Alignment explanation
Indices: 5598983--5599037 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
5598973 ATTTGGGCCT
*
5598983 TAATTTGGGCCTGTTTTGGAATTGGACTC
1 TAATTTGGGCCTGTTTTGGAATGGGACTC
*
5599012 TAATTTGGGCCT-TTTTGTAATGGGAC
1 TAATTTGGGCCTGTTTTGGAATGGGAC
5599038 ACTTGTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.18, C:0.13, G:0.27, T:0.42
Consensus pattern (29 bp):
TAATTTGGGCCTGTTTTGGAATGGGACTC
Found at i:5599101 original size:17 final size:17
Alignment explanation
Indices: 5599095--5599155 Score: 104
Period size: 17 Copynumber: 3.6 Consensus size: 17
5599085 TAAATTTGAT
*
5599095 TAAATTTAAATTTAAAG
1 TAAATTTAAATTTAAAA
5599112 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
5599129 TAAATTTTAATTTAAAA
1 TAAATTTAAATTTAAAA
5599146 TAAATTTAAA
1 TAAATTTAAA
5599156 ATCCATTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:5599105 original size:6 final size:6
Alignment explanation
Indices: 5599094--5599155 Score: 67
Period size: 6 Copynumber: 10.8 Consensus size: 6
5599084 TTAAATTTGA
* * *
5599094 TTAAAT TTAAAT TTAAA- GTAAAT TTAAAT TTAAA- ATAAAT TTTAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
5599140 TTAAA- ATAAAT TTAAA
1 TTAAAT TTAAAT TTAAA
5599156 ATCCATTTAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
5 12 0.27
6 33 0.73
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (6 bp):
TTAAAT
Found at i:5599172 original size:34 final size:33
Alignment explanation
Indices: 5599093--5599178 Score: 84
Period size: 34 Copynumber: 2.5 Consensus size: 33
5599083 TTTAAATTTG
* * *
5599093 ATTAAATTTAAATTTAAAGTAAATTTAAATTTAA
1 ATTAAATTT-AATTTAAAATAAATTTAAAATCAA
* *
5599127 AATAAATTTTAATTTAAAATAAATTTAAAATCCA
1 ATTAAA-TTTAATTTAAAATAAATTTAAAATCAA
*
5599161 TTTAAACTTTAA-TTAAAA
1 ATTAAA-TTTAATTTAAAA
5599179 CCAAAGGCCC
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
33 6 0.14
34 34 0.79
35 3 0.07
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.42
Consensus pattern (33 bp):
ATTAAATTTAATTTAAAATAAATTTAAAATCAA
Found at i:5599177 original size:28 final size:28
Alignment explanation
Indices: 5599101--5599177 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 28
5599091 TGATTAAATT
*
5599101 TAAATTTAAA-GTAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAA-TTAAATTTAAAA
* *
5599129 TAAATTTTAATTTAAAATAAATTTAAAA
1 TAAATTTAAATTTAAATTAAATTTAAAA
**
5599157 TCCATTTAAACTTT-AATTAAA
1 TAAATTTAAA-TTTAAATTAAA
5599178 ACCAAAGGCC
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 33 0.82
29 7 0.17
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (28 bp):
TAAATTTAAATTTAAATTAAATTTAAAA
Found at i:5612162 original size:58 final size:58
Alignment explanation
Indices: 5612093--5612408 Score: 343
Period size: 59 Copynumber: 5.4 Consensus size: 58
5612083 CTTTGGATGC
* * *
5612093 TCGGGGGTAAAATGGTATTTTTTGGTGAGATCGGGGTAAAAATGGAATTTTGGAAAGT
1 TCGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGTTAAAAATGGAATTTTGGAAAGT
* ** * *
5612151 TCGGGGATAAAATTATAATTTTTGGTTAAATCAGGGTTAAAAAT-GAGATTTTGAAAAGT
1 TCGGGGGTAAAATGGTAATTTTTGGTGAAATC-GGGTTAAAAATGGA-ATTTTGGAAAGT
* * * ** *
5612210 TTGGGAGTAAAATGGTAA-TTTTGGTGAAATCAAGGTTAAAAATGGGTTTTTCGAAAGT
1 TCGGGGGTAAAATGGTAATTTTTGGTGAAATC-GGGTTAAAAATGGAATTTTGGAAAGT
* * * * *
5612268 TCGAGGGTAAAATGGTAATTTTTGATGAAATTAGGGTTAAAAATGGGATTTTGGGAAGT
1 TCGGGGGTAAAATGGTAATTTTTGGTGAAA-TCGGGTTAAAAATGGAATTTTGGAAAGT
* *
5612327 TCGGGGGTAAAATGGTATTTTTTGGTGAAATCGGGGTTAAAATTGGAATTTTAGG-AAGT
1 TCGGGGGTAAAATGGTAATTTTTGGTGAAATC-GGGTTAAAAATGGAATTTT-GGAAAGT
**
5612386 T-GGGGGTAAAATTATAATTTTTG
1 TCGGGGGTAAAATGGTAATTTTTG
5612409 AATAGTCCAG
Statistics
Matches: 214, Mismatches: 37, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
58 95 0.44
59 116 0.54
60 3 0.01
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (58 bp):
TCGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGTTAAAAATGGAATTTTGGAAAGT
Found at i:5612249 original size:29 final size:29
Alignment explanation
Indices: 5612093--5612378 Score: 100
Period size: 30 Copynumber: 9.8 Consensus size: 29
5612083 CTTTGGATGC
* * *
5612093 TCGGGGGTAAAATGGTATTTTTTGGTGAGA
1 TCGGGGTTAAAATGGTA-ATTTTGGTGAAA
*
5612123 TCGGGGTAAAAATGG-AATTTT-G-GAAA
1 TCGGGGTTAAAATGGTAATTTTGGTGAAA
* ** *
5612149 GTTCGGGGATAAAATTATAATTTTTGGTTAAA
1 --TCGGGGTTAAAATGGTAA-TTTTGGTGAAA
* *
5612181 TCAGGGTTAAAAAT-G-AGATTTT-G-AAAA
1 TCGGGGTT-AAAATGGTA-ATTTTGGTGAAA
*
5612208 GTTTGGGAG-TAAAATGGTAATTTTGGTGAAA
1 --TCGGG-GTTAAAATGGTAATTTTGGTGAAA
** *
5612239 TCAAGGTTAAAAATGGGT--TTTT--CGAAA
1 TCGGGGTT-AAAAT-GGTAATTTTGGTGAAA
*
5612266 GTTCGAGGG-TAAAATGGTAATTTTTGATGAAA
1 --TCG-GGGTTAAAATGGTAA-TTTTGGTGAAA
** * *
5612298 TTAGGGTTAAAAATGG-GATTTTGG-GAAGT
1 TCGGGGTT-AAAATGGTAATTTTGGTGAA-A
* *
5612327 TCGGGGGTAAAATGGTATTTTTTGGTGAAA
1 TCGGGGTTAAAATGGTA-ATTTTGGTGAAA
5612357 TCGGGGTTAAAATTGG-AATTTT
1 TCGGGGTTAAAA-TGGTAATTTT
5612379 AGGAAGTTGG
Statistics
Matches: 187, Mismatches: 36, Indels: 67
0.64 0.12 0.23
Matches are distributed among these distances:
26 3 0.02
27 11 0.06
28 37 0.20
29 45 0.24
30 59 0.32
31 25 0.13
32 7 0.04
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (29 bp):
TCGGGGTTAAAATGGTAATTTTGGTGAAA
Found at i:5612305 original size:117 final size:116
Alignment explanation
Indices: 5612093--5612409 Score: 393
Period size: 117 Copynumber: 2.7 Consensus size: 116
5612083 CTTTGGATGC
* * * *
5612093 TCGGGGGTAAAATGGTATTTTTTGGTGAGATCGGGGTAAAAATGGAATTTTGGAAAGTTCGGGGA
1 TCGGGAGTAAAATGGTATTTTTTGGTGAAATCGGGTTAAAAATGGAATTTTAGAAAGTTCGGGG-
* *
5612158 TAAAATTATAATTTTTGGTTAAATCAGGGTTAAAAATGAGATTTTGAAAAGT
65 TAAAATTATAATTTTTGATGAAATCAGGGTTAAAAATGAGATTTTGAAAAGT
* * * ** *
5612210 TTGGGAGTAAAATGGTA-ATTTTGGTGAAATCAAGGTTAAAAATGGGTTTTTCGAAAGTTCGAGG
1 TCGGGAGTAAAATGGTATTTTTTGGTGAAATC-GGGTTAAAAATGGAATTTTAGAAAGTTCG-GG
** * * **
5612274 GTAAAATGGTAATTTTTGATGAAATTAGGGTTAAAAATGGGATTTTGGGAAGT
64 GTAAAATTATAATTTTTGATGAAATCAGGGTTAAAAATGAGATTTTGAAAAGT
* * * *
5612327 TCGGGGGTAAAATGGTATTTTTTGGTGAAATCGGGGTTAAAATTGGAATTTTAGGAAGTTGGGGG
1 TCGGGAGTAAAATGGTATTTTTTGGTGAAATC-GGGTTAAAAATGGAATTTTAGAAAGTTCGGGG
5612392 TAAAATTATAATTTTTGA
65 TAAAATTATAATTTTTGA
5612410 ATAGTCCAGA
Statistics
Matches: 167, Mismatches: 30, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
116 12 0.07
117 117 0.70
118 38 0.23
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (116 bp):
TCGGGAGTAAAATGGTATTTTTTGGTGAAATCGGGTTAAAAATGGAATTTTAGAAAGTTCGGGGT
AAAATTATAATTTTTGATGAAATCAGGGTTAAAAATGAGATTTTGAAAAGT
Found at i:5612397 original size:28 final size:28
Alignment explanation
Indices: 5612305--5612398 Score: 82
Period size: 28 Copynumber: 3.2 Consensus size: 28
5612295 AAATTAGGGT
* *
5612305 TAAAAATGGGATTTTGGGAAGTTCGGGGG
1 TAAAATTGGAATTTTGGGAAGTT-GGGGG
* * * *
5612334 TAAAA-TGGTATTTTTTGGTGAAATCGGGGT
1 TAAAATTGG-A-ATTTTGG-GAAGTTGGGGG
*
5612364 TAAAATTGGAATTTTAGGAAGTTGGGGG
1 TAAAATTGGAATTTTGGGAAGTTGGGGG
5612392 TAAAATT
1 TAAAATT
5612399 ATAATTTTTG
Statistics
Matches: 51, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
28 18 0.35
29 10 0.20
30 16 0.31
31 7 0.14
ACGTcount: A:0.31, C:0.02, G:0.33, T:0.34
Consensus pattern (28 bp):
TAAAATTGGAATTTTGGGAAGTTGGGGG
Found at i:5619404 original size:39 final size:39
Alignment explanation
Indices: 5619340--5619417 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
5619330 AGTCAGTCTC
* *
5619340 GTGTTGGTAATAGATCTTGGAAATTTCCTAATACTTCTG
1 GTGTTGGTAACAGATATTGGAAATTTCCTAATACTTCTG
* *
5619379 GTGTTGGTAACGGATATTGGGAATTTCCTAATACTTCTG
1 GTGTTGGTAACAGATATTGGAAATTTCCTAATACTTCTG
5619418 CACAGATTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.24, C:0.13, G:0.23, T:0.40
Consensus pattern (39 bp):
GTGTTGGTAACAGATATTGGAAATTTCCTAATACTTCTG
Found at i:5622154 original size:20 final size:21
Alignment explanation
Indices: 5622129--5622168 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5622119 ATAAGTTAAC
5622129 AATCT-CCTAGGACTTAGTCA
1 AATCTCCCTAGGACTTAGTCA
5622149 AATCTCCCTAGGACTTAGTC
1 AATCTCCCTAGGACTTAGTC
5622169 TTATTCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (21 bp):
AATCTCCCTAGGACTTAGTCA
Found at i:5622587 original size:20 final size:21
Alignment explanation
Indices: 5622562--5622600 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5622552 CTCCTACTAA
*
5622562 CAAATCT-CTTATGACTTAAT
1 CAAATCTCCCTATGACTTAAT
5622582 CAAATCTCCCTATGACTTA
1 CAAATCTCCCTATGACTTA
5622601 GTCTAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (21 bp):
CAAATCTCCCTATGACTTAAT
Found at i:5626986 original size:26 final size:26
Alignment explanation
Indices: 5626935--5626990 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
5626925 ATTCATTCTA
*
5626935 ATTTTTATTAAAATAACATATTAATT
1 ATTTTTATTAAAATAACATATAAATT
* *
5626961 ATTTTTATTACCATTAACAT-TAAATT
1 ATTTTTATTA-AAATAACATATAAATT
5626987 ATTT
1 ATTT
5626991 ATTAAAGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 19 0.73
27 7 0.27
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (26 bp):
ATTTTTATTAAAATAACATATAAATT
Found at i:5628074 original size:9 final size:9
Alignment explanation
Indices: 5628060--5628110 Score: 59
Period size: 9 Copynumber: 5.7 Consensus size: 9
5628050 AACTTTAGAA
5628060 AATTGAGAG
1 AATTGAGAG
5628069 AATTGAGAG
1 AATTGAGAG
*
5628078 AGTTGAGAG
1 AATTGAGAG
* *
5628087 -TTTAGAGAT
1 AATT-GAGAG
5628096 AATTGAGAG
1 AATTGAGAG
5628105 AATTGA
1 AATTGA
5628111 ATTTGAGTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
8 2 0.06
9 31 0.89
10 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.27
Consensus pattern (9 bp):
AATTGAGAG
Found at i:5642041 original size:6 final size:6
Alignment explanation
Indices: 5642024--5642066 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
5642014 AGCCATTAGA
*
5642024 AGGAAG ATGAAG AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG A
1 AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG A
5642067 CTATTGCCTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.47, T:0.02
Consensus pattern (6 bp):
AGGAAG
Found at i:5666004 original size:44 final size:44
Alignment explanation
Indices: 5665912--5666005 Score: 120
Period size: 44 Copynumber: 2.1 Consensus size: 44
5665902 GCTATTTTGG
* *
5665912 CTTGCACCCACTCGATCTTGCATTTAGACTGTCCGCCGCTTCGG
1 CTTGCACCCACTCGATCTTGCATTTAGACTGTCCGCCCCTTCGA
* *
5665956 CTTGCACCCACTCGGGT-TTGTATTTAGACTGTCCGCCACCTT-GA
1 CTTGCACCCACTC-GATCTTGCATTTAGACTGTCCGCC-CCTTCGA
5666000 CTTGCA
1 CTTGCA
5666006 ATTCGAAAGG
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
44 39 0.89
45 5 0.11
ACGTcount: A:0.15, C:0.34, G:0.20, T:0.31
Consensus pattern (44 bp):
CTTGCACCCACTCGATCTTGCATTTAGACTGTCCGCCCCTTCGA
Found at i:5666067 original size:30 final size:30
Alignment explanation
Indices: 5666015--5666171 Score: 183
Period size: 30 Copynumber: 5.3 Consensus size: 30
5666005 AATTCGAAAG
* * *
5666015 GCTCACACTTT-GCTTGCTGTCTTCAACAA
1 GCTCGCACTTTGGCTTACTGTCTTTAACAA
*
5666044 GCTTGCACTTTGGCTTACTGTCTTTAACAA
1 GCTCGCACTTTGGCTTACTGTCTTTAACAA
* *
5666074 GCTCGCACTTTGGCTTACTGTCTTTGACAG
1 GCTCGCACTTTGGCTTACTGTCTTTAACAA
* *
5666104 GCTCGCACTTTGGCTTACTGTCTTTGACAG
1 GCTCGCACTTTGGCTTACTGTCTTTAACAA
* * * * *
5666134 GCTCACACTTT-GCTTGCTGTCTTCAATAG
1 GCTCGCACTTTGGCTTACTGTCTTTAACAA
5666163 GCTCGCACT
1 GCTCGCACT
5666172 CTACAGCTCG
Statistics
Matches: 114, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
29 31 0.27
30 83 0.73
ACGTcount: A:0.17, C:0.28, G:0.19, T:0.36
Consensus pattern (30 bp):
GCTCGCACTTTGGCTTACTGTCTTTAACAA
Found at i:5666112 original size:60 final size:59
Alignment explanation
Indices: 5666015--5666171 Score: 224
Period size: 60 Copynumber: 2.6 Consensus size: 59
5666005 AATTCGAAAG
* *
5666015 GCTCACACTTTGCTTGCTGTCTTCAACAAGCTTGCACTTTGGCTTACTGTCTTTAACAA
1 GCTCACACTTTGCTTGCTGTCTTCAACAGGCTCGCACTTTGGCTTACTGTCTTTAACAA
* * ** * *
5666074 GCTCGCACTTTGGCTTACTGTCTTTGACAGGCTCGCACTTTGGCTTACTGTCTTTGACAG
1 GCTCACACTTT-GCTTGCTGTCTTCAACAGGCTCGCACTTTGGCTTACTGTCTTTAACAA
*
5666134 GCTCACACTTTGCTTGCTGTCTTCAATAGGCTCGCACT
1 GCTCACACTTTGCTTGCTGTCTTCAACAGGCTCGCACT
5666172 CTACAGCTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
59 33 0.39
60 51 0.61
ACGTcount: A:0.17, C:0.28, G:0.19, T:0.36
Consensus pattern (59 bp):
GCTCACACTTTGCTTGCTGTCTTCAACAGGCTCGCACTTTGGCTTACTGTCTTTAACAA
Found at i:5666318 original size:44 final size:44
Alignment explanation
Indices: 5666270--5666357 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
5666260 CAACTCACAT
5666270 ATACTCCTCCTTCAGCTTATAGCTTGTTTGGGAGTCTCATAGAG
1 ATACTCCTCCTTCAGCTTATAGCTTGTTTGGGAGTCTCATAGAG
*
5666314 ATACTCCTCCTTCAGTTTATAGCTTGTTTGGGAGTCTCATAGAG
1 ATACTCCTCCTTCAGCTTATAGCTTGTTTGGGAGTCTCATAGAG
5666358 TTGAGTTGCT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (44 bp):
ATACTCCTCCTTCAGCTTATAGCTTGTTTGGGAGTCTCATAGAG
Found at i:5668818 original size:10 final size:10
Alignment explanation
Indices: 5668796--5668923 Score: 59
Period size: 10 Copynumber: 12.8 Consensus size: 10
5668786 AAAAATCAAT
5668796 AAAAATATT-
1 AAAAATATTA
5668805 -AAAATATTA
1 AAAAATATTA
*
5668814 AAAAATCTATA
1 AAAAATAT-TA
5668825 AAAAATA-TA
1 AAAAATATTA
5668834 GAAAAATA-TA
1 -AAAAATATTA
* **
5668844 AAAATTACAA
1 AAAAATATTA
5668854 AAAAAT-TTA
1 AAAAATATTA
* * * *
5668863 GAAAGTCTTT
1 AAAAATATTA
* *
5668873 CAAATTCATTA
1 AAAAAT-ATTA
*
5668884 AAAATTATTA
1 AAAAATATTA
*
5668894 AAAATATATAA
1 AAAA-ATATTA
*
5668905 AAAAATCGTTA
1 AAAAAT-ATTA
5668916 AAAAATAT
1 AAAAATAT
5668924 ACAAATATAA
Statistics
Matches: 90, Mismatches: 20, Indels: 17
0.71 0.16 0.13
Matches are distributed among these distances:
8 8 0.09
9 13 0.14
10 38 0.42
11 31 0.34
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (10 bp):
AAAAATATTA
Found at i:5668829 original size:29 final size:30
Alignment explanation
Indices: 5668786--5668946 Score: 92
Period size: 28 Copynumber: 5.5 Consensus size: 30
5668776 ATGATAAAAT
*
5668786 AAAAATCAAT-AAAAATATTA-AAATATTA
1 AAAAATCTATAAAAAATATTAGAAATATTA
*
5668814 AAAAATCTATAAAAAATA-TAGAAA-AATA
1 AAAAATCTATAAAAAATATTAGAAATATTA
* * *
5668842 TAAAAAT-TACAAAAAA-ATTTAGAAAGTCTTT
1 -AAAAATCTATAAAAAATA-TTAGAAA-TATTA
* * * *
5668873 CAAATTC-ATTAAAAATTATTAAAAATATATAA
1 AAAAATCTA-TAAAAAATATTAGAAATAT-T-A
*
5668905 AAAAATCGT-TAAAAAATA-TACAAATA-TA
1 AAAAATC-TATAAAAAATATTAGAAATATTA
5668933 AAAAATC-ATAAAAA
1 AAAAATCTATAAAAA
5668947 CTTATAAATA
Statistics
Matches: 101, Mismatches: 17, Indels: 31
0.68 0.11 0.21
Matches are distributed among these distances:
27 7 0.07
28 30 0.30
29 23 0.23
30 7 0.07
31 20 0.20
32 14 0.14
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (30 bp):
AAAAATCTATAAAAAATATTAGAAATATTA
Found at i:5668846 original size:28 final size:26
Alignment explanation
Indices: 5668781--5668848 Score: 64
Period size: 29 Copynumber: 2.4 Consensus size: 26
5668771 AAAAAATGAT
5668781 AAAATAAAAATCAATAAAAATATTAA
1 AAAATAAAAATCAATAAAAATATTAA
* * *
5668807 AATATTAAAAAATCTATAAAAAATATAGAA
1 AA-AAT-AAAAATCAAT-AAAAATAT-TAA
5668837 AAATATAAAAAT
1 AAA-ATAAAAAT
5668849 TACAAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
26 2 0.06
27 2 0.06
28 9 0.27
29 15 0.45
30 5 0.15
ACGTcount: A:0.71, C:0.03, G:0.01, T:0.25
Consensus pattern (26 bp):
AAAATAAAAATCAATAAAAATATTAA
Found at i:5668858 original size:19 final size:19
Alignment explanation
Indices: 5668784--5668859 Score: 59
Period size: 19 Copynumber: 4.0 Consensus size: 19
5668774 AAATGATAAA
5668784 ATAAAAA-T-CAATAAAAAT
1 ATAAAAATTACAA-AAAAAT
**
5668802 ATTAAAATATTA-AAAAATCT
1 A-TAAAA-ATTACAAAAAAAT
* * *
5668822 ATAAAAAATATAGAAAAAT
1 ATAAAAATTACAAAAAAAT
5668841 ATAAAAATTACAAAAAAAT
1 ATAAAAATTACAAAAAAAT
5668860 TTAGAAAGTC
Statistics
Matches: 44, Mismatches: 9, Indels: 9
0.71 0.15 0.15
Matches are distributed among these distances:
18 4 0.09
19 31 0.70
20 6 0.14
21 3 0.07
ACGTcount: A:0.70, C:0.04, G:0.01, T:0.25
Consensus pattern (19 bp):
ATAAAAATTACAAAAAAAT
Found at i:5670216 original size:20 final size:18
Alignment explanation
Indices: 5670193--5670241 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 18
5670183 GTTTTAAAGA
5670193 AATTTTATATGCTTTTATCC
1 AATTTTATATG-TTTTAT-C
*
5670213 AATTTTAAATATGTTTTATT
1 AATTTT--ATATGTTTTATC
5670233 AATTTTATA
1 AATTTTATA
5670242 AAAAATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 3 0.12
20 12 0.46
21 6 0.23
22 5 0.19
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (18 bp):
AATTTTATATGTTTTATC
Found at i:5670307 original size:16 final size:17
Alignment explanation
Indices: 5670286--5670318 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5670276 AATTTTACGA
*
5670286 ATTTTTTAT-ATTTTTT
1 ATTTTTAATAATTTTTT
5670302 ATTTTTAATAATTTTTT
1 ATTTTTAATAATTTTTT
5670319 TTTATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTTTTAATAATTTTTT
Found at i:5670319 original size:20 final size:19
Alignment explanation
Indices: 5670296--5670335 Score: 71
Period size: 20 Copynumber: 2.1 Consensus size: 19
5670286 ATTTTTTATA
5670296 TTTTTTATTTTTAATAATTT
1 TTTTTTATTTTTAAT-ATTT
5670316 TTTTTTATTTTTAATATTT
1 TTTTTTATTTTTAATATTT
5670335 T
1 T
5670336 ATGAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTTTATTTTTAATATTT
Found at i:5674248 original size:19 final size:18
Alignment explanation
Indices: 5674199--5674248 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
5674189 TTTAACTCTA
5674199 AAAAAATA-AAAATATAT
1 AAAAAATATAAAATATAT
* *
5674216 AAACAATCTCAAAATATAT
1 AAAAAATAT-AAAATATAT
5674235 AAAGAAATATAAAA
1 AAA-AAATATAAAA
5674249 GATACAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 6 0.23
19 16 0.62
20 4 0.15
ACGTcount: A:0.70, C:0.06, G:0.02, T:0.22
Consensus pattern (18 bp):
AAAAAATATAAAATATAT
Done.