Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 127 of 193
Found at i:40080389 original size:17 final size:20
Alignment explanation
Indices: 40080347--40080394 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 20
40080337 TATAATAAAC
*
40080347 ATTAATATTAAGTAATGATT
1 ATTAATATTAAGTAATGATA
40080367 ATTAATATTAA-TAAT-A-A
1 ATTAATATTAAGTAATGATA
40080384 ATTAATATTAA
1 ATTAATATTAA
40080395 AAAAGGGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 11 0.41
18 1 0.04
19 4 0.15
20 11 0.41
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (20 bp):
ATTAATATTAAGTAATGATA
Found at i:40081334 original size:161 final size:162
Alignment explanation
Indices: 40081154--40081491 Score: 552
Period size: 162 Copynumber: 2.1 Consensus size: 162
40081144 GCTTTTCAAT
40081154 TTAGTCCTTTGACTGTTTGACTGTACCAGAGGCTGCCACGTGCCA-TTTTTGGATTATTTATGCA
1 TTAGTCCTTTGACTGTTTGACTGTACCAGAGGCTGCCACGTGCCACTTTTTGGATTATTTATGCA
40081218 TTTAGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTATTTAATTACAA
66 TTTAGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTATTTAATTACAA
* * *
40081283 AATTGGCCCAAGAATTTTTCATGGTTTATAAA
131 AATTGGCCCAAGAATTTTTCAAGATTTACAAA
* *
40081315 TTAGTCCTTTGACTGTTTGACTGTACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGCA
1 TTAGTCCTTTGACTGTTTGACTGTACCAGAGGCTGCCACGTGCCACTTTTTGGATTATTTATGCA
* *** * *
40081380 TTTAGTCCTTTTTATTTTTAATTTTTTTTAATTTAATCCCCAAATCGACTTTTATTTAATTACAA
66 TTTAGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTATTTAATTACAA
*
40081445 AATTGGCCCAAGAATTTTTCAAGATTTACAAC
131 AATTGGCCCAAGAATTTTTCAAGATTTACAAA
*
40081477 TTAATCCTTTGACTG
1 TTAGTCCTTTGACTG
40081492 CTGGATGCCT
Statistics
Matches: 163, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
161 44 0.27
162 119 0.73
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.43
Consensus pattern (162 bp):
TTAGTCCTTTGACTGTTTGACTGTACCAGAGGCTGCCACGTGCCACTTTTTGGATTATTTATGCA
TTTAGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTATTTAATTACAA
AATTGGCCCAAGAATTTTTCAAGATTTACAAA
Found at i:40081655 original size:29 final size:28
Alignment explanation
Indices: 40081619--40081724 Score: 88
Period size: 29 Copynumber: 3.6 Consensus size: 28
40081609 CCCCGAAACT
40081619 TTCAAAAATTACCATTTTACCCCCAAATC
1 TTCAAAAATT-CCATTTTACCCCCAAATC
* * * **
40081648 TTCTAAAATTTCATTTTTAACCCCGATTTC
1 TTCAAAAATTCCA-TTTT-ACCCCCAAATC
**
40081678 ACCAAAAATTACCATTTTACCCCCAAA-C
1 TTCAAAAATT-CCATTTTACCCCCAAATC
*
40081706 TTTCCAAAATTCCATTTTA
1 -TTCAAAAATTCCATTTTA
40081725 ACCTCGATTT
Statistics
Matches: 58, Mismatches: 15, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
28 11 0.19
29 26 0.45
30 19 0.33
31 2 0.03
ACGTcount: A:0.35, C:0.28, G:0.01, T:0.36
Consensus pattern (28 bp):
TTCAAAAATTCCATTTTACCCCCAAATC
Found at i:40081759 original size:58 final size:59
Alignment explanation
Indices: 40081621--40081758 Score: 210
Period size: 59 Copynumber: 2.4 Consensus size: 59
40081611 CCGAAACTTT
* *
40081621 CAAAAATTACCATTTTACCCCCAAATCTTCTAAAATTTCATTTTTAACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCCCAAATCTTCCAAAATTCCATTTTTAACCCCGATTTCAC
*
40081680 CAAAAATTACCATTTTACCCCCAAA-CTTTCCAAAATTCCA-TTTTAACCTCGATTTCAC
1 CAAAAATTACCATTTTACCCCCAAATC-TTCCAAAATTCCATTTTTAACCCCGATTTCAC
*
40081738 C-AAAATTACCATTTTGCCCCC
1 CAAAAATTACCATTTTACCCCC
40081759 CGAGTATCCA
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
57 19 0.26
58 19 0.26
59 36 0.49
ACGTcount: A:0.33, C:0.31, G:0.02, T:0.33
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCCCAAATCTTCCAAAATTCCATTTTTAACCCCGATTTCAC
Found at i:40081773 original size:58 final size:58
Alignment explanation
Indices: 40081621--40081781 Score: 200
Period size: 59 Copynumber: 2.8 Consensus size: 58
40081611 CCGAAACTTT
* *
40081621 CAAAAATTACCATTTTACCCCCAAATCT-TCTAAAATTTCATTTTTAACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCCCAAA-CTATCCAAAATTCCA-TTTTAACCCCGATTTCAC
* *
40081680 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTAACCTCGATTTCAC
1 CAAAAATTACCATTTTACCCCCAAACTATCCAAAATTCCATTTTAACCCCGATTTCAC
* ** * *
40081738 C-AAAATTACCATTTTGCCCCCCGAGTATCCAAAAATCCCATTTT
1 CAAAAATTACCATTTTACCCCCAAACTATCC-AAAATTCCATTTT
40081782 TTTTCACCCC
Statistics
Matches: 91, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
57 24 0.26
58 32 0.35
59 35 0.38
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCCCAAACTATCCAAAATTCCATTTTAACCCCGATTTCAC
Found at i:40083677 original size:101 final size:100
Alignment explanation
Indices: 40083443--40083725 Score: 320
Period size: 101 Copynumber: 2.8 Consensus size: 100
40083433 CAGTGACGGT
* * * * * * *
40083443 ACTGAATTGAAATGTAATTATATAAAACGTTCAGGGACCTGATAAAACAATTTCCTTTTTAGATT
1 ACTGAACTGAAGTGTGATTATATAAAACGTTCAGGGACTTGATGAAACAATTCCCCTTTTAGATT
* * * *
40083508 AACTGAAAAAAAGGGGTGTCGCCTGACATAGTGACGGC
66 GACTG--AAAAA-GGGTGTCGACTGACATAATGACGAC
* *
40083546 A-TCGAACTAAAGTGTGA-T-TATAAAACGTTCAGGGACTTGATGAATCAATTACCCCTTTTAGA
1 ACT-GAACTGAAGTGTGATTATATAAAACGTTCAGGGACTTGATGAAACAATT-CCCCTTTTAGA
*
40083608 TTGACCGAAAAAGGGTGTCGACTGACATAATGACGAC
64 TTGACTGAAAAAGGGTGTCGACTGACATAATGACGAC
* * *
40083645 ACTGAACTGAAGTGTGATTATATAAAATGTTCAGGGACTTGATGAAGCAATTGCCCCTTTTATAT
1 ACTGAACTGAAGTGTGATTATATAAAACGTTCAGGGACTTGATGAAACAATT-CCCCTTTTAGAT
* *
40083710 TGGCTGAAAAGGGGTG
65 TGACTGAAAAAGGGTG
40083726 CCACTTTATA
Statistics
Matches: 153, Mismatches: 22, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
99 36 0.24
100 7 0.05
101 83 0.54
102 16 0.10
103 11 0.07
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (100 bp):
ACTGAACTGAAGTGTGATTATATAAAACGTTCAGGGACTTGATGAAACAATTCCCCTTTTAGATT
GACTGAAAAAGGGTGTCGACTGACATAATGACGAC
Found at i:40084112 original size:17 final size:16
Alignment explanation
Indices: 40084098--40084132 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
40084088 TCAGTAAAGA
40084098 ATAATTATTTTTAAAAT
1 ATAATT-TTTTTAAAAT
*
40084115 ATAATTTTTTAAAAAT
1 ATAATTTTTTTAAAAT
40084131 AT
1 AT
40084133 TTTAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATAATTTTTTTAAAAT
Found at i:40084153 original size:10 final size:11
Alignment explanation
Indices: 40084121--40084146 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
40084111 AAATATAATT
40084121 TTTTAAAAATA
1 TTTTAAAAATA
40084132 TTTTAAAAATA
1 TTTTAAAAATA
40084143 TTTT
1 TTTT
40084147 TAAATATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAAATA
Found at i:40085150 original size:11 final size:11
Alignment explanation
Indices: 40085114--40085149 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
40085104 TTATATTTAA
40085114 AAAATAATTTT
1 AAAATAATTTT
*
40085125 AAATTAATTTT
1 AAAATAATTTT
40085136 AAAAT-ATTTT
1 AAAATAATTTT
40085146 AAAA
1 AAAA
40085150 AATAATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AAAATAATTTT
Found at i:40085621 original size:29 final size:29
Alignment explanation
Indices: 40085578--40085642 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
40085568 CACTTGTTTG
*
40085578 AATGTGGTACCTGAAGTTTCAAAATGTTC
1 AATGTGGTACCTGAAGTTTCAAAATGTCC
* *
40085607 AATGTGGTACTTGAAGTTTCAGAATGTCC
1 AATGTGGTACCTGAAGTTTCAAAATGTCC
40085636 AATGTGG
1 AATGTGG
40085643 ACCAATTATG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (29 bp):
AATGTGGTACCTGAAGTTTCAAAATGTCC
Found at i:40087658 original size:23 final size:23
Alignment explanation
Indices: 40087626--40087676 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
40087616 TTTAAAATTA
*
40087626 AATAATCAAAATATAAATTTATT
1 AATAACCAAAATATAAATTTATT
*
40087649 AATAACCAAAATATAAATTTTTT
1 AATAACCAAAATATAAATTTATT
40087672 AATAA
1 AATAA
40087677 TTTAGTTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (23 bp):
AATAACCAAAATATAAATTTATT
Found at i:40087811 original size:22 final size:22
Alignment explanation
Indices: 40087783--40087829 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
40087773 TGATGTAACA
40087783 TATAATTAA-TATTAAAATAAAT
1 TATAATTAATTA-TAAAATAAAT
* *
40087805 TATAATTTATTATAAAATATAT
1 TATAATTAATTATAAAATAAAT
40087827 TAT
1 TAT
40087830 TATGACAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TATAATTAATTATAAAATAAAT
Found at i:40089776 original size:22 final size:22
Alignment explanation
Indices: 40089748--40089794 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
40089738 TGTTGTAACA
40089748 TATAA-TTAGTATTAAAATAAAT
1 TATAATTTAGTA-TAAAATAAAT
* *
40089770 TATAATTTATTATAAAATATAT
1 TATAATTTAGTATAAAATAAAT
40089792 TAT
1 TAT
40089795 TATGACAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TATAATTTAGTATAAAATAAAT
Found at i:40098648 original size:3 final size:3
Alignment explanation
Indices: 40098640--40098666 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
40098630 ATGGTTTATG
40098640 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
40098667 TATGAAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:40112447 original size:25 final size:25
Alignment explanation
Indices: 40112399--40112464 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 25
40112389 TTTTGATAAA
* * *
40112399 ATAAATAAATTATATATTATATTCAT
1 ATAAATATATT-TAAATTACATTCAT
*
40112425 GTAAATATATTTAAATTACATTCAT
1 ATAAATATATTTAAATTACATTCAT
40112450 ATAATTATATATTTA
1 ATAA--ATATATTTA
40112465 TATTTAATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
25 15 0.45
26 9 0.27
27 9 0.27
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (25 bp):
ATAAATATATTTAAATTACATTCAT
Found at i:40115188 original size:2 final size:2
Alignment explanation
Indices: 40115181--40115218 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
40115171 AATAAGATAA
40115181 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40115219 TGTAATTATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40115527 original size:32 final size:31
Alignment explanation
Indices: 40115461--40115530 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
40115451 AATAGTCTAT
* * *
40115461 ATTTTTATATTTTTTAAAAAATTAAATTTAA
1 ATTTATATAATTTTTAAAAAATTAAATATAA
40115492 ATTTATATAATTTTTAAAAAGATTAAAGTATAA
1 ATTTATATAATTTTTAAAAA-ATTAAA-TATAA
*
40115525 TTTTAT
1 ATTTAT
40115531 TTTCATTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 18 0.55
32 6 0.18
33 9 0.27
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (31 bp):
ATTTATATAATTTTTAAAAAATTAAATATAA
Found at i:40116979 original size:24 final size:24
Alignment explanation
Indices: 40116952--40116998 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
40116942 ACTCCTGAAT
*
40116952 CCAATTGCTTGA-TTTGTCTAATGG
1 CCAATTGATTGACTTT-TCTAATGG
*
40116976 CCAATTTATTGACTTTTCTAATG
1 CCAATTGATTGACTTTTCTAATG
40116999 TTGATGGGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.45
Consensus pattern (24 bp):
CCAATTGATTGACTTTTCTAATGG
Found at i:40146809 original size:24 final size:24
Alignment explanation
Indices: 40146781--40146830 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
40146771 TGAAGCTATC
*
40146781 CATGTGTAGGCCATTGTTGAGCTA
1 CATGTGTAGGCCATTGTTGAGATA
40146805 CATGTGTAGGCCATTGTTGAGATA
1 CATGTGTAGGCCATTGTTGAGATA
40146829 CA
1 CA
40146831 AGTGAGGGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (24 bp):
CATGTGTAGGCCATTGTTGAGATA
Found at i:40153442 original size:17 final size:18
Alignment explanation
Indices: 40153420--40153457 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
40153410 TTATCTTAAC
*
40153420 ATTATTTTAATATT-TAT
1 ATTATTATAATATTATAT
*
40153437 ATTATTATAGTATTATAT
1 ATTATTATAATATTATAT
40153455 ATT
1 ATT
40153458 TAGTATAGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
ATTATTATAATATTATAT
Found at i:40163356 original size:18 final size:18
Alignment explanation
Indices: 40163318--40163359 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
40163308 AGTGTATTTT
*
40163318 AAAAGCACTTTTGACATA
1 AAAAGCACTTTTGACACA
*
40163336 AAAAGCACTTTTGA-ACC
1 AAAAGCACTTTTGACACA
40163353 AAAAGCA
1 AAAAGCA
40163360 ATGCTAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (18 bp):
AAAAGCACTTTTGACACA
Found at i:40163763 original size:13 final size:13
Alignment explanation
Indices: 40163745--40163807 Score: 65
Period size: 13 Copynumber: 4.8 Consensus size: 13
40163735 CTTAAACCAA
40163745 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
40163758 ACTTTTCAAAA-T
1 ACTTTTCAAAAGT
* *
40163770 CACTTTTCCAAAGC
1 -ACTTTTCAAAAGT
* *
40163784 ATTTTTTAAAAGT
1 ACTTTTCAAAAGT
*
40163797 ACTTCTCAAAA
1 ACTTTTCAAAA
40163808 CAATGCTAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
12 1 0.03
13 38 0.97
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (13 bp):
ACTTTTCAAAAGT
Found at i:40165003 original size:29 final size:29
Alignment explanation
Indices: 40164936--40165003 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
40164926 TAGCATTTAG
* *
40164936 ATTTGATTCTTTTTAATAGTACAAGGATTA
1 ATTTGA-TCTTTTTAATAATACAAGGACTA
* * * *
40164966 AATTAATCTTTTTAATAATAGATGGACTA
1 ATTTGATCTTTTTAATAATACAAGGACTA
40164995 ATTTGATCT
1 ATTTGATCT
40165004 AGTCTATGTA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
29 26 0.87
30 4 0.13
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.46
Consensus pattern (29 bp):
ATTTGATCTTTTTAATAATACAAGGACTA
Found at i:40168459 original size:11 final size:11
Alignment explanation
Indices: 40168440--40168472 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
40168430 GTTTTGTTTA
40168440 ATTTAATTTTT
1 ATTTAATTTTT
*
40168451 ATTTGATTTTT
1 ATTTAATTTTT
40168462 ATTTAATTTTT
1 ATTTAATTTTT
40168473 TTATTTAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (11 bp):
ATTTAATTTTT
Found at i:40168535 original size:5 final size:5
Alignment explanation
Indices: 40168525--40168552 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
40168515 TTTGATTATT
40168525 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
40168553 TGTTAGTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:40168770 original size:19 final size:18
Alignment explanation
Indices: 40168728--40168772 Score: 65
Period size: 17 Copynumber: 2.5 Consensus size: 18
40168718 ATTTATTTTG
40168728 TATTATTTTGATAAATAA
1 TATTATTTTGATAAATAA
*
40168746 -ATTATTTTGATATATAA
1 TATTATTTTGATAAATAA
40168763 TTATTATTTT
1 -TATTATTTT
40168773 TGTATTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 16 0.67
19 8 0.33
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (18 bp):
TATTATTTTGATAAATAA
Found at i:40168774 original size:47 final size:46
Alignment explanation
Indices: 40168702--40168793 Score: 123
Period size: 47 Copynumber: 2.0 Consensus size: 46
40168692 TGAGGATACC
* *
40168702 ATTTTGGTATATAAATATTTATTTTGTATTATTTTGATAAATAAATT
1 ATTTTGATATATAAATATTTATTTTGTATTATATTGATAAA-AAATT
* *
40168749 ATTTTGATATATAATTA-TTATTTTTGTATTATATTGGTAAAAAAT
1 ATTTTGATATATAAATATTTA-TTTTGTATTATATTGATAAAAAAT
40168794 CATAAAAATC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
46 7 0.17
47 33 0.82
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (46 bp):
ATTTTGATATATAAATATTTATTTTGTATTATATTGATAAAAAATT
Found at i:40169242 original size:3 final size:3
Alignment explanation
Indices: 40169234--40169274 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
40169224 ACCAAAAAGT
40169234 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
40169275 CAAAGATGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:40169875 original size:16 final size:16
Alignment explanation
Indices: 40169806--40169904 Score: 69
Period size: 16 Copynumber: 6.4 Consensus size: 16
40169796 AATCCTAAAT
*
40169806 CTTAAAAACCTAATAC
1 CTTAAAAACCTAAAAC
* * *
40169822 CCT-AAAACATTAAAC
1 CTTAAAAACCTAAAAC
* *
40169837 CTTAAAAATCTTAAAC
1 CTTAAAAACCTAAAAC
* *
40169853 ATT--AAACCTAAAGC
1 CTTAAAAACCTAAAAC
* *
40169867 CTTAAAAACCCAAAAT
1 CTTAAAAACCTAAAAC
*
40169883 CTTAAAAACCTTAAAC
1 CTTAAAAACCTAAAAC
*
40169899 CCTAAA
1 CTTAAA
40169905 TTATGAACCG
Statistics
Matches: 61, Mismatches: 19, Indels: 6
0.71 0.22 0.07
Matches are distributed among these distances:
14 10 0.16
15 11 0.18
16 40 0.66
ACGTcount: A:0.52, C:0.24, G:0.01, T:0.23
Consensus pattern (16 bp):
CTTAAAAACCTAAAAC
Found at i:40170098 original size:26 final size:26
Alignment explanation
Indices: 40170058--40170109 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
40170048 CCCTAAACCA
*
40170058 AAATACAAACATAAAAATTATTAATT
1 AAATACAAACATAAAAATAATTAATT
** *
40170084 AAATACAAATTTAAACATAATTAATT
1 AAATACAAACATAAAAATAATTAATT
40170110 TCAAATTCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.33
Consensus pattern (26 bp):
AAATACAAACATAAAAATAATTAATT
Found at i:40175735 original size:417 final size:408
Alignment explanation
Indices: 40174929--40175737 Score: 1213
Period size: 417 Copynumber: 2.0 Consensus size: 408
40174919 TTCGGAAGGA
* *
40174929 TTTTTTTGTGTGTTTCTCAACGAAAGAGTTCAAGACGTTTTTGTACTAGAGCTAAATTCACTAGG
1 TTTTTTTGTGTGTTTCTCAACGAAAGAGTTCAAGACATTTTTGTACTAGAGCTAAATTCACTAAG
* * * * *
40174994 CAATGGCATAATTAGTGTTGTCAATGATGCAAACACAAGGTAGAACCTTTCATTCAAAAGAGTTT
66 CAATGACAAAACTAGTGTTGTCAAGGATGCAAACACAAGGTAGAACCTTGCATTCAAAAGAGTTT
* * ** *
40175059 TTATTGTGTTTGTGTGTCTCATTCTAAAGGGTTTGAGACATTTTTTTACTAAAACTAAATTCATT
131 TTATTGTGTTTGTGTGTCTCATCCGAAAGGGTTCAAGACATTTTTGTACTAAAACTAAATTCATT
* * *
40175124 AGGCAATGGCAGAAAGGGTGCAAAGACAAGCTAGAACCCTTATATTGTCTTGCATTTGAAAGAGT
196 AGGCAATGGCAGAAAGGGCGCAAAGACAAGCTAGAACCCTTAAATTGTCTTGCATTCGAAAGAGT
*
40175189 TTTTTTGTGTCTCTCATTCGAAAGGGTTTAAGACATTTTTGTAGTAGAGCTAAATTCACTAAGCA
261 TTTTTTGTGTCTCTCATTCGAAAGGGTTTAAGACATTTTAGTAGTAGAGCTAAATTCACTAAGCA
* * *
40175254 ATGACACAATTAGTGTTGTTAAGGGTGCAAAGTCAAGCTAGAACCCTTATCTTGTCTTGCATTCG
326 ATGACACAACTAGTGTTGTTAAGGGTGCAAAGCCAAGCTAAAACCCTTATCTTGTCTTGCATTCG
40175319 AAAGGTTTTTTTTTTTTT
391 AAAGGTTTTTTTTTTTTT
* * * *
40175337 TTTTTTCTGTGTGTCTCTCTCATTCGAAAGGGTTCGAGACATTTTTGTAGTAGAGCTAAATTCAC
1 TTTTTT-TGTGTGT-T-TCTCA-ACGAAAGAGTTCAAGACATTTTTGTACTAGAGCTAAATTCAC
* * *
40175402 TAAGCAATGACAAAACTAGTGTTGTCAAGGATGCAAATACGAGGTAGAACCTTGCATTCAAAAGG
62 TAAGCAATGACAAAACTAGTGTTGTCAAGGATGCAAACACAAGGTAGAACCTTGCATTCAAAAGA
* *
40175467 GTTTTTTTTGTGTTTGTGTGTGTCTCATCCGAAAGGGTTCAAGATATTTTTGTACTAAAACTAAA
127 GTTTTTATTGTG-TT-TGTGTGTCTCATCCGAAAGGGTTCAAGACATTTTTGTACTAAAACTAAA
* *
40175532 TTCATTAGGCAATTGCAGAAAGGGCGCAAAGCCAAGCTAGAACCCTTAAATTGTCTTGCATTCGA
190 TTCATTAGGCAATGGCAGAAAGGGCGCAAAGACAAGCTAGAACCCTTAAATTGTCTTGCATTCGA
* * *
40175597 AAGAGTTTTGTGTGTGTGTGTGTCATTCGAAAGGGTTTGAGACATTTTAGTAGTAGAGCTAAATT
255 AAGAGTTTT-T-T-TGTGTCTCTCATTCGAAAGGGTTTAAGACATTTTAGTAGTAGAGCTAAATT
* * *
40175662 CACTAGGCAATGACACAACTAGTGTTGTTAAGGGTGCAAAGCCGAGCTAAAACCCTTATTTTGTC
317 CACTAAGCAATGACACAACTAGTGTTGTTAAGGGTGCAAAGCCAAGCTAAAACCCTTATCTTGTC
40175727 TTGCATTCGAA
382 TTGCATTCGAA
40175738 TTTTTCTGTG
Statistics
Matches: 356, Mismatches: 36, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
408 6 0.02
409 7 0.02
410 1 0.00
411 5 0.01
412 104 0.29
413 2 0.01
414 112 0.31
415 1 0.00
416 1 0.00
417 117 0.33
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (408 bp):
TTTTTTTGTGTGTTTCTCAACGAAAGAGTTCAAGACATTTTTGTACTAGAGCTAAATTCACTAAG
CAATGACAAAACTAGTGTTGTCAAGGATGCAAACACAAGGTAGAACCTTGCATTCAAAAGAGTTT
TTATTGTGTTTGTGTGTCTCATCCGAAAGGGTTCAAGACATTTTTGTACTAAAACTAAATTCATT
AGGCAATGGCAGAAAGGGCGCAAAGACAAGCTAGAACCCTTAAATTGTCTTGCATTCGAAAGAGT
TTTTTTGTGTCTCTCATTCGAAAGGGTTTAAGACATTTTAGTAGTAGAGCTAAATTCACTAAGCA
ATGACACAACTAGTGTTGTTAAGGGTGCAAAGCCAAGCTAAAACCCTTATCTTGTCTTGCATTCG
AAAGGTTTTTTTTTTTTT
Found at i:40175807 original size:139 final size:136
Alignment explanation
Indices: 40175551--40176013 Score: 545
Period size: 139 Copynumber: 3.4 Consensus size: 136
40175541 CAATTGCAGA
* *
40175551 AAGGGCGCAAAGCCAAGCTAGAACCCTTAAATTGTCTTGCATTCGAAAGAGTTTTGTGTGTGTGT
1 AAGGGCGCAAAGCCAAGCTAGAACCCTTATATTGTCTTGCATTCGAAA-A-TTTTGTGTTTGT-T
* * *
40175616 GTGTCATTCGAAAGGGTTTGAGACATTTTAGTAGTAGAGCTAAATTCACTAGGCAATGACACAAC
63 GTCTCATTCGAAAGGGTTCGAGACATTTT-GTACTAGAGCTAAATTCACTAGGCAATGACACAAC
40175681 TAGTGTTGTT
127 TAGTGTTGTT
* * * * ** *
40175691 AAGGGTGCAAAGCCGAGCTAAAACCCTTATTTTGTCTTGCATTCGAATTTTTCTGTGTTTGTCTC
1 AAGGGCGCAAAGCCAAGCTAGAACCCTTATATTGTCTTGCATTCGAAAATTT-TGTGTTTGT-TG
* *
40175756 TCTCATTCGAAAGGATTCGAGACACTTTTGTACTAGAGCTAAATTCACTAGGCAATGGCACAACT
64 TCTCATTCGAAAGGGTTCGAGACA-TTTTGTACTAGAGCTAAATTCACTAGGCAATGACACAACT
40175821 AGTGTTGTT
128 AGTGTTGTT
* * * ** * *
40175830 AAGGGCGCAGAGCCGAGCTAGAA-CCTTAATATTGTCTTGCATTAGAAAAGATT-TCTTTCTTGT
1 AAGGGCGCAAAGCCAAGCTAGAACCCTT-ATATTGTCTTGCATTCGAAAATTTTGTGTTTGTTGT
* *
40175893 CTCATTCGAAAGGGTTCGAGACATTTT-TATGCTACAGCTAAAGTCACTAGGCAATGACACAACT
65 CTCATTCGAAAGGGTTCGAGACATTTTGTA--CTAGAGCTAAATTCACTAGGCAATGACACAACT
* *
40175957 AATATTGTT
128 AGTGTTGTT
* * * * *
40175966 AAGGACGCAAAACCAAGGTAGAACCCTTATATTGTTTTGCATTTGAAA
1 AAGGGCGCAAAGCCAAGCTAGAACCCTTATATTGTCTTGCATTCGAAA
40176014 GGATTTTTTT
Statistics
Matches: 277, Mismatches: 40, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
134 2 0.01
135 4 0.01
136 97 0.35
137 9 0.03
138 8 0.03
139 111 0.40
140 46 0.17
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (136 bp):
AAGGGCGCAAAGCCAAGCTAGAACCCTTATATTGTCTTGCATTCGAAAATTTTGTGTTTGTTGTC
TCATTCGAAAGGGTTCGAGACATTTTGTACTAGAGCTAAATTCACTAGGCAATGACACAACTAGT
GTTGTT
Found at i:40175954 original size:136 final size:136
Alignment explanation
Indices: 40175551--40176019 Score: 530
Period size: 136 Copynumber: 3.4 Consensus size: 136
40175541 CAATTGCAGA
* * *
40175551 AAGGGCGCAAAGCCAAGCTAGAACCCTTAAATTGTCTTGCATTCGAAAGAGTTTTGTGTGTGTGT
1 AAGGGCGCAAAGCCAAGCTAGAACCCTTATATTGTCTTGCATTCGAAA-AGATTTGT-T-TGTCT
* *
40175616 GTGTCATTCGAAAGGGTTTGAGACATTTTAGTAG-TAGAGCTAAATTCACTAGGCAATGACACAA
63 GTCTCATTCGAAAGGGTTCGAGACATTTTA-T-GCTAGAGCTAAATTCACTAGGCAATGACACAA
40175680 CTAGTGTTGTT
126 CTAGTGTTGTT
* * * * **** *
40175691 AAGGGTGCAAAGCCGAGCTAAAACCCTTATTTTGTCTTGCATTCGAATTTTTCTGTGTTTGTCTC
1 AAGGGCGCAAAGCCAAGCTAGAACCCTTATATTGTCTTGCATTCGAAAAGAT-T-TGTTTGTCTG
* * * *
40175756 TCTCATTCGAAAGGATTCGAGACACTTTTGTACTAGAGCTAAATTCACTAGGCAATGGCACAACT
64 TCTCATTCGAAAGGGTTCGAGACA-TTTTATGCTAGAGCTAAATTCACTAGGCAATGACACAACT
40175821 AGTGTTGTT
128 AGTGTTGTT
* * * * *
40175830 AAGGGCGCAGAGCCGAGCTAGAA-CCTTAATATTGTCTTGCATTAGAAAAGATTTCTTTCT-TGT
1 AAGGGCGCAAAGCCAAGCTAGAACCCTT-ATATTGTCTTGCATTCGAAAAGATTTGTTTGTCTGT
* *
40175893 CTCATTCGAAAGGGTTCGAGACATTTTTATGCTACAGCTAAAGTCACTAGGCAATGACACAACTA
65 CTCATTCGAAAGGGTTCGAGACA-TTTTATGCTAGAGCTAAATTCACTAGGCAATGACACAACTA
* *
40175958 ATATTGTT
129 GTGTTGTT
* * * * * *
40175966 AAGGACGCAAAACCAAGGTAGAACCCTTATATTGTTTTGCATTTGAAAGGATTT
1 AAGGGCGCAAAGCCAAGCTAGAACCCTTATATTGTCTTGCATTCGAAAAGATTT
40176020 TTTTTTTTGC
Statistics
Matches: 278, Mismatches: 45, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
136 107 0.38
137 9 0.03
138 5 0.02
139 106 0.38
140 48 0.17
141 3 0.01
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (136 bp):
AAGGGCGCAAAGCCAAGCTAGAACCCTTATATTGTCTTGCATTCGAAAAGATTTGTTTGTCTGTC
TCATTCGAAAGGGTTCGAGACATTTTATGCTAGAGCTAAATTCACTAGGCAATGACACAACTAGT
GTTGTT
Found at i:40178595 original size:13 final size:14
Alignment explanation
Indices: 40178569--40178597 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
40178559 GAAAATTAAA
40178569 TATTAAATTTTTAT
1 TATTAAATTTTTAT
40178583 TATTAAA-TTTTAT
1 TATTAAATTTTTAT
40178596 TA
1 TA
40178598 GTGCTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTAAATTTTTAT
Found at i:40180224 original size:31 final size:30
Alignment explanation
Indices: 40180189--40180272 Score: 73
Period size: 31 Copynumber: 2.7 Consensus size: 30
40180179 TTTATCATAT
40180189 ATTAACATATAATTTTATCAT-TTTTAGAAAG
1 ATTAA-ATATAATTTTATCATATTTT-GAAAG
*
40180220 ATTAAATAATTAAATTTA-CATATTTTGAAAG
1 ATTAAAT-A-TAATTTTATCATATTTTGAAAG
* * *
40180251 GTAAAAATACAATTTTATCATA
1 AT-TAAATATAATTTTATCATA
40180273 AATTAATTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
30 8 0.19
31 20 0.47
32 15 0.35
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (30 bp):
ATTAAATATAATTTTATCATATTTTGAAAG
Found at i:40180740 original size:2 final size:2
Alignment explanation
Indices: 40180665--40180726 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
40180655 AAGAATCTCG
40180665 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40180707 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
40180727 GCAAAGTGTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40185155 original size:139 final size:139
Alignment explanation
Indices: 40184905--40185159 Score: 320
Period size: 139 Copynumber: 1.8 Consensus size: 139
40184895 CATTTAATAG
* *
40184905 TTAAATTAACGATTTTAGTAACAAAATGACCTATTTGATATAACCTTGATAGTTTAGGGATAAAT
1 TTAAATTAACGATTTTAGTAACAAAATGAACTATTTGATATAACATTGATAGTTTAGGGATAAAT
* ** * * *
40184970 TTAGAATGGTTTAAAGTTTATGGAGTAATTTAGAATGAGGGTCATAGTTTGTGGATGCTTTGTGC
66 TTAGAATAGTTTAAAGTTTATGGACCAATTTAAAATAAGAGTCATAGTTTGTGGATGCTTTGTGC
40185035 AATTAACTC
131 AATTAACTC
* * * *
40185044 TTAAATTAACGATTTTAGTAATAGAA-GAACTTTATTGATATAACATTGATAG-TTAGAGGATGT
1 TTAAATTAACGATTTTAGTAACAAAATGAACTAT-TTGATATAACATTGATAGTTTAG-GGAT-A
* *
40185107 AA-TTATAATATTTTAAAAGTTTA-GGACCAATTTAAAATAAGAGTCATAGTTTG
63 AATTTAGAATAGTTT-AAAGTTTATGGACCAATTTAAAATAAGAGTCATAGTTTG
40185160 GGGACGTTTA
Statistics
Matches: 98, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
138 9 0.09
139 79 0.81
140 10 0.10
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.38
Consensus pattern (139 bp):
TTAAATTAACGATTTTAGTAACAAAATGAACTATTTGATATAACATTGATAGTTTAGGGATAAAT
TTAGAATAGTTTAAAGTTTATGGACCAATTTAAAATAAGAGTCATAGTTTGTGGATGCTTTGTGC
AATTAACTC
Found at i:40191723 original size:29 final size:29
Alignment explanation
Indices: 40191666--40191722 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
40191656 TGGTTTAATC
* *
40191666 TGCAATTGTATGCATGAACTTTGATTTTG
1 TGCAATTGTATACATAAACTTTGATTTTG
*
40191695 TGCAATTGTATACATAAAATTTTGATTT
1 TGCAATTGTATACAT-AAACTTTGATTT
40191723 GATCAAATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.46
Consensus pattern (29 bp):
TGCAATTGTATACATAAACTTTGATTTTG
Found at i:40198292 original size:17 final size:17
Alignment explanation
Indices: 40198247--40198294 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
40198237 TATTTTGTTT
* * *
40198247 AATAATATTTTTATCTC
1 AATAGTATTTTTGTCCC
*
40198264 AAAAGTACTTTTTGTCCC
1 AATAGTA-TTTTTGTCCC
40198282 AATAGTATTTTTG
1 AATAGTATTTTTG
40198295 AGAAGCGATA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.48
Consensus pattern (17 bp):
AATAGTATTTTTGTCCC
Found at i:40201573 original size:43 final size:43
Alignment explanation
Indices: 40201512--40201646 Score: 191
Period size: 43 Copynumber: 3.1 Consensus size: 43
40201502 GCAAAAAATA
*
40201512 CCGCTAAAGAACATGGTCTTTAGCGGTGCTTTACCCACAAACG
1 CCGCTAAAGAACATGGTCTTTAGCGGCGCTTTACCCACAAACG
* * * *
40201555 CCGCTAAAGAATATGGTCTTTAGCGGCGCTTTTCTCACAAATG
1 CCGCTAAAGAACATGGTCTTTAGCGGCGCTTTACCCACAAACG
* *
40201598 CCACTAAAAAACATGGTCTTTAGCGGCGC-TTACTCCACAAACG
1 CCGCTAAAGAACATGGTCTTTAGCGGCGCTTTAC-CCACAAACG
40201641 CCGCTA
1 CCGCTA
40201647 TAGATAGTGT
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
42 3 0.04
43 76 0.96
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.24
Consensus pattern (43 bp):
CCGCTAAAGAACATGGTCTTTAGCGGCGCTTTACCCACAAACG
Found at i:40201661 original size:43 final size:41
Alignment explanation
Indices: 40201524--40201688 Score: 131
Period size: 43 Copynumber: 3.9 Consensus size: 41
40201514 GCTAAAGAAC
*
40201524 ATGGTCTTTAGCGGTGCTTTAC-CCACAAACGCCGCTAAAGAAT
1 ATGGTCTTTAGCGGCGC-TTACTCCACAAACGCCGCT-AAG-AT
* * * * *
40201567 ATGGTCTTTAGCGGCGCTT-TTCTCACAAATGCCACTAAAAAAC
1 ATGGTCTTTAGCGGCGCTTACTC-CACAAACGCCGCT--AAGAT
40201610 ATGGTCTTTAGCGGCGCTTACTCCACAAACGCCGCTATAGAT
1 ATGGTCTTTAGCGGCGCTTACTCCACAAACGCCGCTA-AGAT
* * * **
40201652 AGTGTTCTTT-GGGGCGTTTTTTCCACAAACG-CGCTAA
1 A-TGGTCTTTAGCGGCGCTTACTCCACAAACGCCGCTAA
40201689 AATTAACAGA
Statistics
Matches: 100, Mismatches: 16, Indels: 15
0.76 0.12 0.11
Matches are distributed among these distances:
40 1 0.01
41 6 0.06
42 23 0.23
43 65 0.65
44 5 0.05
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.28
Consensus pattern (41 bp):
ATGGTCTTTAGCGGCGCTTACTCCACAAACGCCGCTAAGAT
Found at i:40201674 original size:86 final size:85
Alignment explanation
Indices: 40201515--40201680 Score: 221
Period size: 86 Copynumber: 1.9 Consensus size: 85
40201505 AAAAATACCG
* *
40201515 CTAAAGAACATGGTCTTTAGCGGTGCTTTACCCACAAACGCCGCTAAAGAATATGGTCTTTAGCG
1 CTAAAAAACATGGTCTTTAGCGGCGCTTTACCCACAAACGCCGCTAAAGAATATGGTCTTTAGCG
40201580 GCGCTTTTCTCACAAATGCCA
66 GCGCTTTTC-CACAAATGCCA
* *
40201601 CTAAAAAACATGGTCTTTAGCGGCGC-TTACTCCACAAACGCCGCTATAG-ATAGTGTTCTTT-G
1 CTAAAAAACATGGTCTTTAGCGGCGCTTTAC-CCACAAACGCCGCTAAAGAATA-TGGTCTTTAG
* *
40201663 GGGCGTTTTTTCCACAAA
64 CGGCG-CTTTTCCACAAA
40201681 CGCGCTAAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
85 18 0.25
86 53 0.75
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (85 bp):
CTAAAAAACATGGTCTTTAGCGGCGCTTTACCCACAAACGCCGCTAAAGAATATGGTCTTTAGCG
GCGCTTTTCCACAAATGCCA
Found at i:40204398 original size:41 final size:41
Alignment explanation
Indices: 40204341--40204566 Score: 240
Period size: 41 Copynumber: 5.5 Consensus size: 41
40204331 AATCAACAGG
* * ** *
40204341 ATTGCTCTGACCTTTAGCGGGGTTTTTACATAAGCACCACT
1 ATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGCCACT
* *
40204382 ATTGCTCTGACCTTTAGCAGCGCTTGCCCATAAGCGCCACT
1 ATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGCCACT
* * * *
40204423 ATTGTTAC-GACCTTTAGCGGCGTTTTCCCATAAGCGTCGCT
1 ATTGCT-CTGACCTTTAGCGGCGCTTTCCCATAAGCGCCACT
* * *
40204464 ATTGCTCTGACCTTTAGCGGTGCTTTTCCATAAGCGCCGCT
1 ATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGCCACT
* * * * *
40204505 ATTGCTCTGACCTTTAGTGACGCTTTCCCATTAGCGTCGCT
1 ATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGCCACT
* *
40204546 ATTGCTCT-ATCTTTTGCGGCG
1 ATTGCTCTGACCTTTAGCGGCG
40204567 TTTATATAAA
Statistics
Matches: 155, Mismatches: 28, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
40 10 0.06
41 144 0.93
42 1 0.01
ACGTcount: A:0.17, C:0.28, G:0.21, T:0.34
Consensus pattern (41 bp):
ATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGCCACT
Found at i:40204495 original size:82 final size:82
Alignment explanation
Indices: 40204341--40204553 Score: 266
Period size: 82 Copynumber: 2.6 Consensus size: 82
40204331 AATCAACAGG
* ** ** *
40204341 ATTGCTCTGACCTTTAGCGGGGTTTTTACATAAGCACCACTATTGCTCTGACCTTTAGCAGCGCT
1 ATTGCTCTGACCTTTAGCGGCGTTTTCCCATAAGCGTCGCTATTGCTCTGACCTTTAGCAGCGCT
40204406 TGCCCATAAGCGCCACT
66 TGCCCATAAGCGCCACT
* * *
40204423 ATTGTTAC-GACCTTTAGCGGCGTTTTCCCATAAGCGTCGCTATTGCTCTGACCTTTAGCGGTGC
1 ATTGCT-CTGACCTTTAGCGGCGTTTTCCCATAAGCGTCGCTATTGCTCTGACCTTTAGCAGCGC
** *
40204487 TTTTCCATAAGCGCCGCT
65 TTGCCCATAAGCGCCACT
* * * *
40204505 ATTGCTCTGACCTTTAGTGACGCTTTCCCATTAGCGTCGCTATTGCTCT
1 ATTGCTCTGACCTTTAGCGGCGTTTTCCCATAAGCGTCGCTATTGCTCT
40204554 ATCTTTTGCG
Statistics
Matches: 112, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
81 1 0.01
82 110 0.98
83 1 0.01
ACGTcount: A:0.17, C:0.29, G:0.20, T:0.34
Consensus pattern (82 bp):
ATTGCTCTGACCTTTAGCGGCGTTTTCCCATAAGCGTCGCTATTGCTCTGACCTTTAGCAGCGCT
TGCCCATAAGCGCCACT
Found at i:40205423 original size:22 final size:22
Alignment explanation
Indices: 40205404--40205450 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
40205394 AAAAAAATCA
40205404 ACTATTTTAAGAGTTGAAATAAT
1 ACTATTTTAA-AGTTGAAATAAT
* *
40205427 ACTCTTTTGAAGTTGAAATAAT
1 ACTATTTTAAAGTTGAAATAAT
40205449 AC
1 AC
40205451 AGGAAGACGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (22 bp):
ACTATTTTAAAGTTGAAATAAT
Found at i:40207974 original size:31 final size:31
Alignment explanation
Indices: 40207916--40207975 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
40207906 TGTGGGGTTT
**
40207916 ATTAGGGAAATATGTTATTTTTTAAAAAGTA
1 ATTAGGGAAATATGTTATTTTAAAAAAAGTA
* *
40207947 ATTAGGGAATTATGTTGATTTAAAAAAAA
1 ATTAGGGAAATATGTT-ATTTTAAAAAAA
40207976 AGATCGATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 15 0.62
32 9 0.38
ACGTcount: A:0.45, C:0.00, G:0.17, T:0.38
Consensus pattern (31 bp):
ATTAGGGAAATATGTTATTTTAAAAAAAGTA
Found at i:40210576 original size:159 final size:159
Alignment explanation
Indices: 40210286--40210824 Score: 925
Period size: 159 Copynumber: 3.4 Consensus size: 159
40210276 AAAAATCTGG
* *
40210286 TATCTAGTGAGTTGATGAACACAATTTGATATGTTTATGGATAGCCATTGATGAATTTATTCGGT
1 TATCTAGTGAGTTGATGAACACAATTTGATATGTTTATGGATTGCCATTGATGAATTTATTCGAT
* * *
40210351 TCTTTTGTTGATTTAAAGCATGTGAAAATGAGTTTACATGTAAGAATGTGAAAGCATCTTCTGCT
66 TCTTTTGTTGATTTAAAGCATGTGAAAATGAGTGTACTTGTAAGAATGTGAAAGCATCTTCGGCT
40210416 CGAATGAATGTTTTTGGATACTTTTCTCA
131 CGAATGAATGTTTTTGGATACTTTTCTCA
* *
40210445 TATCTAGTGAGTTGATGAACACAATTTGATATGTTTATGGATTGCCATAGATGTATTTATTCGAT
1 TATCTAGTGAGTTGATGAACACAATTTGATATGTTTATGGATTGCCATTGATGAATTTATTCGAT
*
40210510 TCTTTTGTTGATTTAAAGCATGTGAAAATGAGTGTACTTGTAAGAATGTGAAAGCACCTTCGGCT
66 TCTTTTGTTGATTTAAAGCATGTGAAAATGAGTGTACTTGTAAGAATGTGAAAGCATCTTCGGCT
40210575 CGAATGAATGTTTTTGGATACTTTTCTCA
131 CGAATGAATGTTTTTGGATACTTTTCTCA
* * *
40210604 TATCTATTGAGTTGATGAACACAATTTGATATGTTTATGGATTGCCATTGCTGAATTTATTTGAT
1 TATCTAGTGAGTTGATGAACACAATTTGATATGTTTATGGATTGCCATTGATGAATTTATTCGAT
* * * *
40210669 TCTTTTGTTGATTTAAAGCATGTGAAAACGAGTGTACTTGTAAGAATGAGAAAGCATTTTCGGCC
66 TCTTTTGTTGATTTAAAGCATGTGAAAATGAGTGTACTTGTAAGAATGTGAAAGCATCTTCGGCT
40210734 CGAATGAATGTTTTTGGATACTTTTCTCA
131 CGAATGAATGTTTTTGGATACTTTTCTCA
*
40210763 TATCTAGTGAGTTGATGAACACAATTTGATATGTTTATGAATTGCCATTTGATGAATTTATT
1 TATCTAGTGAGTTGATGAACACAATTTGATATGTTTATGGATTGCCA-TTGATGAATTTATT
40210825 TGGTTCTGAT
Statistics
Matches: 358, Mismatches: 21, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
159 345 0.96
160 13 0.04
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (159 bp):
TATCTAGTGAGTTGATGAACACAATTTGATATGTTTATGGATTGCCATTGATGAATTTATTCGAT
TCTTTTGTTGATTTAAAGCATGTGAAAATGAGTGTACTTGTAAGAATGTGAAAGCATCTTCGGCT
CGAATGAATGTTTTTGGATACTTTTCTCA
Found at i:40212884 original size:31 final size:31
Alignment explanation
Indices: 40212849--40212907 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
40212839 TTTGATACCC
*
40212849 GAGTTTAGCTTCAATGTTCAATTTGGTACTT
1 GAGTTTAGCTTCAATGTTCAACTTGGTACTT
* * *
40212880 GAGTTTGGCTTCGATGTTTAACTTGGTA
1 GAGTTTAGCTTCAATGTTCAACTTGGTA
40212908 GCTGAGGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.20, C:0.12, G:0.24, T:0.44
Consensus pattern (31 bp):
GAGTTTAGCTTCAATGTTCAACTTGGTACTT
Found at i:40213127 original size:29 final size:29
Alignment explanation
Indices: 40213091--40213153 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
40213081 CATTGAAGCT
40213091 AAACTTAGGTACTTAACTAGGACAAAAGA
1 AAACTTAGGTACTTAACTAGGACAAAAGA
40213120 AAACTTAGGTACTTAACTAGGACAAAAGA
1 AAACTTAGGTACTTAACTAGGACAAAAGA
40213149 AAACT
1 AAACT
40213154 AAGTATCCGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.49, C:0.14, G:0.16, T:0.21
Consensus pattern (29 bp):
AAACTTAGGTACTTAACTAGGACAAAAGA
Found at i:40215930 original size:16 final size:16
Alignment explanation
Indices: 40215895--40215937 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
40215885 AGTAGGCATG
*
40215895 AAAATAAAT-GACAAA
1 AAAATAAATAAACAAA
*
40215910 TAAATAAATAAACAAA
1 AAAATAAATAAACAAA
*
40215926 AAAATCAATAAA
1 AAAATAAATAAA
40215938 TTAAATGCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.74, C:0.07, G:0.02, T:0.16
Consensus pattern (16 bp):
AAAATAAATAAACAAA
Found at i:40229846 original size:31 final size:31
Alignment explanation
Indices: 40229806--40229865 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
40229796 CCCCTAATTT
* *
40229806 TTTTGAAAATTTTAATTAAATCCCCTAAAAAA
1 TTTTGAAAATTTTAAATAAATACCC-AAAAAA
40229838 TTTT-AAAATTTTAAATAAATACCCAAAA
1 TTTTGAAAATTTTAAATAAATACCCAAAA
40229866 CTTAATAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 4 0.15
31 18 0.69
32 4 0.15
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.37
Consensus pattern (31 bp):
TTTTGAAAATTTTAAATAAATACCCAAAAAA
Found at i:40231774 original size:131 final size:131
Alignment explanation
Indices: 40231526--40231761 Score: 375
Period size: 131 Copynumber: 1.8 Consensus size: 131
40231516 TATGTTATAA
* * *
40231526 TATTATATATTACTATAACTTAGAGGTGCTCATGAGTCGGGTTGGGTCGGGCCTAAGTATTGTAT
1 TATTATATATTACTATAAATTAGAAGTGCTCATGAGTAGGGTTGGGTCGGGCCTAAGTATTGTAT
40231591 TAACATACTTTATGTTTACTTAAGTCCAACCTGAAATATGAGCCTAAAATTTTGCTCAAACTTGC
66 TAACATACTTTATGTTTACTTAAGTCCAACCTGAAATATGAGCCTAAAATTTTGCTCAAACTTGC
40231656 C
131 C
* * *
40231657 TATTATATATTACTATAAATTAGAAGTGCTTATGGGTAGGGTTGTGTCGGGCCTAAGTA-TGATA
1 TATTATATATTACTATAAATTAGAAGTGCTCATGAGTAGGGTTGGGTCGGGCCTAAGTATTG-TA
* * *
40231721 TTAACATATTTTATGTTTGCTTAAGTCCGACCTGAAATATG
65 TTAACATACTTTATGTTTACTTAAGTCCAACCTGAAATATG
40231762 GGTTTAAAAT
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
130 2 0.02
131 93 0.98
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.37
Consensus pattern (131 bp):
TATTATATATTACTATAAATTAGAAGTGCTCATGAGTAGGGTTGGGTCGGGCCTAAGTATTGTAT
TAACATACTTTATGTTTACTTAAGTCCAACCTGAAATATGAGCCTAAAATTTTGCTCAAACTTGC
C
Found at i:40231878 original size:22 final size:21
Alignment explanation
Indices: 40231835--40231882 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
40231825 TCGCCCATGT
40231835 TATTT-TTTTAATTTTTTAAA
1 TATTTATTTTAATTTTTTAAA
* *
40231855 TATTTATTTTATTTTATTTTAA
1 TATTTATTTTAATTT-TTTAAA
40231877 TATTTA
1 TATTTA
40231883 ATATTTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 5 0.21
21 8 0.33
22 11 0.46
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
TATTTATTTTAATTTTTTAAA
Found at i:40232283 original size:17 final size:18
Alignment explanation
Indices: 40232255--40232290 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
40232245 TTATAAATCT
40232255 AATTTATATATATAATAA
1 AATTTATATATATAATAA
*
40232273 AATTTAT-TATATTATAA
1 AATTTATATATATAATAA
40232290 A
1 A
40232291 CATAAAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AATTTATATATATAATAA
Found at i:40236685 original size:51 final size:52
Alignment explanation
Indices: 40236626--40236727 Score: 147
Period size: 51 Copynumber: 2.0 Consensus size: 52
40236616 ATTTAGCACA
40236626 TGCAATATCACGCCTTTG-TCTCGATGCAT-GAAAAAGACATAA-ACCTTATAG
1 TGCAATATCACGCCTTTGAT-TCGATGCATAG-AAAAGACATAATACCTTATAG
* *
40236677 TGCAATATCACGCCTTTGATTCGATGTATAGAAAAGATATAATACCTTATA
1 TGCAATATCACGCCTTTGATTCGATGCATAGAAAAGACATAATACCTTATA
40236728 TAATGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
51 36 0.78
52 10 0.22
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (52 bp):
TGCAATATCACGCCTTTGATTCGATGCATAGAAAAGACATAATACCTTATAG
Found at i:40236868 original size:101 final size:102
Alignment explanation
Indices: 40236681--40236873 Score: 250
Period size: 101 Copynumber: 1.9 Consensus size: 102
40236671 TTATAGTGCA
* * ***
40236681 ATATCACGCCTTTGATTCGATGTATAGAAAAGATATAATACCTTATATAATGATTTTGGTGCTAA
1 ATATCAAGCCTTTGATTCGATGTATAGAAAAGATACAATACCTTATATAATGATTTCAATGCTAA
40236746 TACATTGGTTGTGATTTAAGTTCATTTAGAGCGCGCG
66 TACATTGGTTGTGATTTAAGTTCATTTAGAGCGCGCG
* *
40236783 ATATCAAGCCTTTG-TTCCGATGTAT-GAAAA-ATACATTAACCTTATATGATGATTTCAATGCT
1 ATATCAAGCCTTTGATT-CGATGTATAGAAAAGATACAAT-ACCTTATATAATGATTTCAATGCT
* *
40236845 AATGCATTTGTT-TGATTTAAAGTTCATTT
64 AATACATTGGTTGTGATTT-AAGTTCATTT
40236874 TGTTGACATA
Statistics
Matches: 79, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
100 11 0.14
101 47 0.59
102 21 0.27
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (102 bp):
ATATCAAGCCTTTGATTCGATGTATAGAAAAGATACAATACCTTATATAATGATTTCAATGCTAA
TACATTGGTTGTGATTTAAGTTCATTTAGAGCGCGCG
Found at i:40240134 original size:26 final size:28
Alignment explanation
Indices: 40240086--40240139 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 28
40240076 TAAAATGAAA
** *
40240086 ATAAAATTATTTAAATTCTTAATTATTT
1 ATAAAATTATTTAAATTAATAATAATTT
40240114 ATAAAA-T-TTTAAATTAATAATAATTT
1 ATAAAATTATTTAAATTAATAATAATTT
40240140 TATTACATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 16 0.70
27 1 0.04
28 6 0.26
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (28 bp):
ATAAAATTATTTAAATTAATAATAATTT
Found at i:40247391 original size:12 final size:12
Alignment explanation
Indices: 40247371--40247405 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
40247361 AGAATCATTC
*
40247371 ATAAATATAAAT
1 ATAATTATAAAT
*
40247383 ATAATTATAATT
1 ATAATTATAAAT
40247395 ATAATTATAAA
1 ATAATTATAAA
40247406 GTCTAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATTATAAAT
Found at i:40248609 original size:13 final size:13
Alignment explanation
Indices: 40248581--40248622 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
40248571 TTTCTCAAAA
40248581 AAAGTCAACGGGTC
1 AAAGTCAAC-GGTC
40248595 AAAGTCAACGGTC
1 AAAGTCAACGGTC
*
40248608 AAAGTCAACTGTC
1 AAAGTCAACGGTC
40248621 AA
1 AA
40248623 CGGTCAATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
13 18 0.67
14 9 0.33
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.17
Consensus pattern (13 bp):
AAAGTCAACGGTC
Found at i:40248621 original size:7 final size:7
Alignment explanation
Indices: 40248584--40248643 Score: 52
Period size: 7 Copynumber: 8.7 Consensus size: 7
40248574 CTCAAAAAAA
40248584 GTCAACGG
1 GTCAAC-G
*
40248592 GTCAA-A
1 GTCAACG
40248598 GTCAACG
1 GTCAACG
*
40248605 GTCAA-A
1 GTCAACG
*
40248611 GTCAACT
1 GTCAACG
40248618 GTCAACG
1 GTCAACG
*
40248625 GTCAATG
1 GTCAACG
*
40248632 ATCAACG
1 GTCAACG
40248639 GTCAA
1 GTCAA
40248644 TGGGTCGATC
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
6 10 0.24
7 26 0.63
8 5 0.12
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:40248623 original size:20 final size:21
Alignment explanation
Indices: 40248598--40248643 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
40248588 ACGGGTCAAA
*
40248598 GTCAACGGTCAAAG-TCAACT
1 GTCAACGGTCAAAGATCAACG
*
40248618 GTCAACGGTCAATGATCAACG
1 GTCAACGGTCAAAGATCAACG
40248639 GTCAA
1 GTCAA
40248644 TGGGTCGATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.20
Consensus pattern (21 bp):
GTCAACGGTCAAAGATCAACG
Found at i:40254504 original size:6 final size:6
Alignment explanation
Indices: 40254493--40254533 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
40254483 GGAATCATTC
* * *
40254493 ATAAAT ATAAAT ATAAAT ATAATT ATAATT ATAATT ATAAA
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAA
40254534 GTCTAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (6 bp):
ATAAAT
Found at i:40254510 original size:12 final size:12
Alignment explanation
Indices: 40254493--40254533 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
40254483 GGAATCATTC
*
40254493 ATAAATATAAAT
1 ATAAATATAATT
40254505 ATAAATATAATT
1 ATAAATATAATT
*
40254517 ATAATTATAATT
1 ATAAATATAATT
40254529 ATAAA
1 ATAAA
40254534 GTCTAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
ATAAATATAATT
Found at i:40255726 original size:20 final size:19
Alignment explanation
Indices: 40255701--40255755 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
40255691 TTTCTCGAAA
40255701 AAAGTCAACGGGTCAAAGTC
1 AAAGTCAAC-GGTCAAAGTC
*
40255721 AAAGTCAACGGTTAAAGTC
1 AAAGTCAACGGTCAAAGTC
* *
40255740 AACTGTCAATGGTCAA
1 AA-AGTCAACGGTCAA
40255756 TGGTCAATGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.20
Consensus pattern (19 bp):
AAAGTCAACGGTCAAAGTC
Found at i:40255739 original size:19 final size:20
Alignment explanation
Indices: 40255701--40255741 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
40255691 TTTCTCGAAA
40255701 AAAGTCAACGGGTCAAAGTC
1 AAAGTCAACGGGTCAAAGTC
*
40255721 AAAGTCAAC-GGTTAAAGTC
1 AAAGTCAACGGGTCAAAGTC
40255740 AA
1 AA
40255742 CTGTCAATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.17
Consensus pattern (20 bp):
AAAGTCAACGGGTCAAAGTC
Found at i:40255754 original size:7 final size:7
Alignment explanation
Indices: 40255744--40255807 Score: 67
Period size: 7 Copynumber: 9.1 Consensus size: 7
40255734 AAAGTCAACT
40255744 GTCAATG
1 GTCAATG
40255751 GTCAATG
1 GTCAATG
40255758 GTCAATG
1 GTCAATG
40255765 GTCAATG
1 GTCAATG
*
40255772 GTTAACT-
1 GTCAA-TG
*
40255779 GTCAACG
1 GTCAATG
40255786 GTCAATG
1 GTCAATG
* * *
40255793 ATTAACG
1 GTCAATG
40255800 GTCAATG
1 GTCAATG
40255807 G
1 G
40255808 GTCGATCGGG
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
7 44 0.98
8 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (7 bp):
GTCAATG
Found at i:40255761 original size:14 final size:14
Alignment explanation
Indices: 40255724--40255807 Score: 73
Period size: 14 Copynumber: 6.1 Consensus size: 14
40255714 CAAAGTCAAA
* *
40255724 GTCAACGGTTAA-A
1 GTCAACGGTCAATG
*
40255737 GTCAACTGTCAATG
1 GTCAACGGTCAATG
*
40255751 GTCAATGGTCAATG
1 GTCAACGGTCAATG
* *
40255765 GTCAATGGTTAACT-
1 GTCAACGGTCAA-TG
40255779 GTCAACGGTCAATG
1 GTCAACGGTCAATG
* *
40255793 ATTAACGGTCAATG
1 GTCAACGGTCAATG
40255807 G
1 G
40255808 GTCGATCGGG
Statistics
Matches: 57, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
13 11 0.19
14 45 0.79
15 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (14 bp):
GTCAACGGTCAATG
Found at i:40255797 original size:21 final size:21
Alignment explanation
Indices: 40255737--40255804 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
40255727 AACGGTTAAA
* * * *
40255737 GTCAACTGTCAATGGTCAATG
1 GTCAACGGTCAATGATTAACG
* * *
40255758 GTCAATGGTCAATGGTTAACT
1 GTCAACGGTCAATGATTAACG
40255779 GTCAACGGTCAATGATTAACG
1 GTCAACGGTCAATGATTAACG
40255800 GTCAA
1 GTCAA
40255805 TGGGTCGATC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.28
Consensus pattern (21 bp):
GTCAACGGTCAATGATTAACG
Found at i:40255906 original size:23 final size:23
Alignment explanation
Indices: 40255853--40255906 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
40255843 TTCAATTAGT
* **
40255853 TTGGGTTAAAGGTTTGGGTTTGG
1 TTGGTTTAAAGGTTTGGGTTTAA
** *
40255876 TTTTTTTAAGGGTTTGGGTTTAA
1 TTGGTTTAAAGGTTTGGGTTTAA
40255899 TTGGTTTA
1 TTGGTTTA
40255907 GTGATTGGGC
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.15, C:0.00, G:0.33, T:0.52
Consensus pattern (23 bp):
TTGGTTTAAAGGTTTGGGTTTAA
Found at i:40259413 original size:22 final size:22
Alignment explanation
Indices: 40259385--40259426 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
40259375 TCGTTGTCAT
*
40259385 TAAATTAATATTAAGTTTATAC
1 TAAATTAATATTAAATTTATAC
40259407 TAAATTAATATTAAATTTAT
1 TAAATTAATATTAAATTTAT
40259427 GTTTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TAAATTAATATTAAATTTATAC
Found at i:40259423 original size:11 final size:11
Alignment explanation
Indices: 40259383--40259423 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
40259373 ACTCGTTGTC
40259383 ATTAAATTAAT
1 ATTAAATTAAT
* *
40259394 ATTAAGTTTAT
1 ATTAAATTAAT
*
40259405 ACTAAATTAAT
1 ATTAAATTAAT
40259416 ATTAAATT
1 ATTAAATT
40259424 TATGTTTTAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (11 bp):
ATTAAATTAAT
Found at i:40271496 original size:27 final size:27
Alignment explanation
Indices: 40271451--40271561 Score: 123
Period size: 27 Copynumber: 4.1 Consensus size: 27
40271441 TATTTCGGAA
* *
40271451 ACCAACAGAGGTACATCGATACAAGGG
1 ACCAACAAAGGTACGTCGATACAAGGG
* * * *
40271478 ATCAACAAAGATACGTCGATCCAAGAG
1 ACCAACAAAGGTACGTCGATACAAGGG
* * *
40271505 ACCAACAGAGGTACGTCGATCCGAGGG
1 ACCAACAAAGGTACGTCGATACAAGGG
* *
40271532 ACCAACAAAGGTATGTTGATACAAGGG
1 ACCAACAAAGGTACGTCGATACAAGGG
40271559 ACC
1 ACC
40271562 GTGATTTTTA
Statistics
Matches: 68, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 68 1.00
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.14
Consensus pattern (27 bp):
ACCAACAAAGGTACGTCGATACAAGGG
Found at i:40273432 original size:26 final size:25
Alignment explanation
Indices: 40273385--40273462 Score: 70
Period size: 26 Copynumber: 3.1 Consensus size: 25
40273375 GTTTTGTCCA
*
40273385 ATTTACTAATTTATATTAATTTTCG
1 ATTTACTAATTTATACTAATTTTCG
* *
40273410 ATTTAACTAATTTAATACTATTTTTCAA
1 ATTT-ACTAATTT-ATACTAATTTTC-G
* *
40273438 ATTGA-TACTTTA-ACTAATTTTCG
1 ATTTACTAATTTATACTAATTTTCG
40273461 AT
1 AT
40273463 AAACCGACGA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
23 2 0.05
24 9 0.21
25 5 0.12
26 13 0.30
27 11 0.26
28 3 0.07
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.51
Consensus pattern (25 bp):
ATTTACTAATTTATACTAATTTTCG
Found at i:40276307 original size:15 final size:17
Alignment explanation
Indices: 40276287--40276320 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40276277 AAACAATTAA
40276287 TTCAT-ATTC-ATTAGT
1 TTCATAATTCGATTAGT
40276302 TTCATAATTCGATTAGT
1 TTCATAATTCGATTAGT
40276319 TT
1 TT
40276321 GATTGGAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 4 0.24
17 8 0.47
ACGTcount: A:0.26, C:0.12, G:0.09, T:0.53
Consensus pattern (17 bp):
TTCATAATTCGATTAGT
Found at i:40280824 original size:120 final size:120
Alignment explanation
Indices: 40280608--40280842 Score: 319
Period size: 120 Copynumber: 2.0 Consensus size: 120
40280598 ATATGCACAG
* * * * *
40280608 ATACCGTATCGATGGCTTAGATACCACATATGTTGCGAATCCTCAACATCTCGTTTGAGCAGCAT
1 ATACCGTATCGATGGCTGAGATACCACATATGTTGCGAATCATCAACAGCTCGTGTGAGCAGAAT
* *
40280673 CGTATACTGGTAACAGAGTTGATACAGACATGAGAATGAAATTCTGGATTCTAGC
66 CGTATACTAGTAACAGAGTTGATACAAACATGAGAATGAAATTCTGGATTCTAGC
* * ** **
40280728 ATACCGTATCGATGGCTGGGGTACCGTATATGTTGC-AAGTCATTGACAGCTCGTGTGAGCAGAA
1 ATACCGTATCGATGGCTGAGATACCACATATGTTGCGAA-TCATCAACAGCTCGTGTGAGCAGAA
* *
40280792 TCTTATACTAGTAACAGAGTTGATACAAACATGAGGATGAAATTCTGGATT
65 TCGTATACTAGTAACAGAGTTGATACAAACATGAGAATGAAATTCTGGATT
40280843 ATAGATAGTG
Statistics
Matches: 99, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
119 2 0.02
120 97 0.98
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.29
Consensus pattern (120 bp):
ATACCGTATCGATGGCTGAGATACCACATATGTTGCGAATCATCAACAGCTCGTGTGAGCAGAAT
CGTATACTAGTAACAGAGTTGATACAAACATGAGAATGAAATTCTGGATTCTAGC
Found at i:40281097 original size:21 final size:22
Alignment explanation
Indices: 40281057--40281099 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
40281047 CAGCAAATGA
*
40281057 TTTTAAAATTATTAAAATTATT
1 TTTTAAAAATATTAAAATTATT
*
40281079 TTTTAAAAATA-TAACATTATT
1 TTTTAAAAATATTAAAATTATT
40281100 AAAATTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTTAAAAATATTAAAATTATT
Found at i:40281114 original size:11 final size:11
Alignment explanation
Indices: 40281098--40281139 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
40281088 TATAACATTA
40281098 TTAAAATTATT
1 TTAAAATTATT
*
40281109 TTAAAATTAAT
1 TTAAAATTATT
40281120 TTAAAATTAATTT
1 TTAAAATT-A-TT
40281133 TTAAAAT
1 TTAAAAT
40281140 ATAAAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 18 0.67
12 1 0.04
13 8 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TTAAAATTATT
Found at i:40281153 original size:51 final size:50
Alignment explanation
Indices: 40281051--40281155 Score: 158
Period size: 51 Copynumber: 2.1 Consensus size: 50
40281041 CCACGTCAGC
* *
40281051 AAATGATTTTAAAATTATTAAAATTATTTTTTAAAAATATAACATTATTA
1 AAATGATTTTAAAATTATTAAAATTAATTTTTAAAAATATAAAATTATTA
*
40281101 AAATTATTTTAAAATTAATTTAAAATTAATTTTT-AAAATATAAAATTATTA
1 AAATGATTTTAAAATT-A-TTAAAATTAATTTTTAAAAATATAAAATTATTA
40281152 AAAT
1 AAAT
40281156 CATCATCATC
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
50 15 0.30
51 21 0.42
52 14 0.28
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (50 bp):
AAATGATTTTAAAATTATTAAAATTAATTTTTAAAAATATAAAATTATTA
Found at i:40282195 original size:10 final size:10
Alignment explanation
Indices: 40282180--40282229 Score: 63
Period size: 10 Copynumber: 5.3 Consensus size: 10
40282170 ATATTTTAAA
40282180 AAATAATTTT
1 AAATAATTTT
40282190 AAATAATTTT
1 AAATAATTTT
40282200 --AT-ATTTT
1 AAATAATTTT
40282207 AAAATAATTTT
1 -AAATAATTTT
40282218 -AATAATTTT
1 AAATAATTTT
40282227 AAA
1 AAA
40282230 ATCATTTGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
7 5 0.14
8 2 0.06
9 9 0.26
10 14 0.40
11 5 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
AAATAATTTT
Found at i:40282219 original size:28 final size:28
Alignment explanation
Indices: 40282156--40282227 Score: 119
Period size: 30 Copynumber: 2.5 Consensus size: 28
40282146 GATGATGATG
40282156 ATTTTAATAATTTTATATTTTAAAAAATA
1 ATTTTAATAATTTTATATTTT-AAAAATA
40282185 ATTTTAAATAATTTTATATTTT-AAAATA
1 ATTTT-AATAATTTTATATTTTAAAAATA
40282213 ATTTTAATAATTTTA
1 ATTTTAATAATTTTA
40282228 AAATCATTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
27 10 0.24
28 11 0.26
29 5 0.12
30 16 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
ATTTTAATAATTTTATATTTTAAAAATA
Found at i:40287777 original size:4 final size:4
Alignment explanation
Indices: 40287768--40287805 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
40287758 AGGTAACTTT
*
40287768 CATA CATA CATA CATA CATA CATA CATA CATA CGTA CA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CA
40287806 GAAGCCAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.47, C:0.26, G:0.03, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:40289563 original size:167 final size:167
Alignment explanation
Indices: 40289229--40289560 Score: 612
Period size: 166 Copynumber: 2.0 Consensus size: 167
40289219 CGTTAAATTC
40289229 ATTAGTTATGTTATTTTAAAATTTTGATGCGATAAACATATTATAATATCTACAATATCATATTA
1 ATTAGTTATGTTATTTTAAAATTTTGATGCGATAAACATATTATAATATCTACAATATCATATTA
* * *
40289294 TTATTTTTATTTTAATATATTACTCAAAGATATAAGTTATTAAAATAATAAAATTATATTTTTAT
66 TTATTTTTATTTTAATAAATTACTCAAAGATATAAATTATTAAAATAATAAAATTACATTTTTAT
*
40289359 TATTGTAAATATACAATTTACTTTTCCGCCTCCCCCA
131 TATCGTAAATATACAATTTACTTTTCCGCCTCCCCCA
40289396 ATTAGTTATGTTATTTTAAAATTTTGATGCGATAAACATATTATAATATCTACAATATCATATTA
1 ATTAGTTATGTTATTTTAAAATTTTGATGCGATAAACATATTATAATATCTACAATATCATATTA
40289461 TT-TTTTTATTTTAATAAATTACTCAAAGATATAAATTATTAAAATAATAAAATTACATTTTTAT
66 TTATTTTTATTTTAATAAATTACTCAAAGATATAAATTATTAAAATAATAAAATTACATTTTTAT
*
40289525 TATCGTAAATATACAATTTATTTTTCCGCCTCCCCC
131 TATCGTAAATATACAATTTACTTTTCCGCCTCCCCC
40289561 CAAAATTTTT
Statistics
Matches: 160, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
166 93 0.58
167 67 0.42
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (167 bp):
ATTAGTTATGTTATTTTAAAATTTTGATGCGATAAACATATTATAATATCTACAATATCATATTA
TTATTTTTATTTTAATAAATTACTCAAAGATATAAATTATTAAAATAATAAAATTACATTTTTAT
TATCGTAAATATACAATTTACTTTTCCGCCTCCCCCA
Found at i:40290411 original size:29 final size:29
Alignment explanation
Indices: 40290378--40290433 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
40290368 TTAGATTGTT
40290378 TTTAATAATATAA-GGACTAAATTGATTTA
1 TTTAATAATA-AATGGACTAAATTGATTTA
* *
40290407 TTTAATAATAAATGGATTAATTTGATT
1 TTTAATAATAAATGGACTAAATTGATT
40290434 ATGTCTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.45
Consensus pattern (29 bp):
TTTAATAATAAATGGACTAAATTGATTTA
Found at i:40292633 original size:3 final size:3
Alignment explanation
Indices: 40292625--40292654 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
40292615 GCTTTGTTAT
40292625 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
40292655 GCAGCTAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:40293550 original size:23 final size:24
Alignment explanation
Indices: 40293522--40293577 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
40293512 CATTAAAATT
** *
40293522 TTTTAAAA-AAACTATATATATAA
1 TTTTAAAATAAAAAATATATAAAA
40293545 TTTTAATAATAAAAAATATATAAAA
1 TTTTAA-AATAAAAAATATATAAAA
40293570 TTATTAAA
1 TT-TTAAA
40293578 TTGTAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 6 0.22
24 2 0.07
25 15 0.56
26 4 0.15
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (24 bp):
TTTTAAAATAAAAAATATATAAAA
Found at i:40301466 original size:3 final size:3
Alignment explanation
Indices: 40301458--40301492 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
40301448 ATACTAATGC
40301458 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG TATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG -ATG A
40301493 AAACATGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:40305447 original size:219 final size:219
Alignment explanation
Indices: 40305030--40305454 Score: 483
Period size: 219 Copynumber: 1.9 Consensus size: 219
40305020 CAATCCGTTG
*
40305030 GGATTAATTTAAAAAATATTACTAATTAGAATCTAAGATTAATTAATTTTTTATTTTTTAACAAT
1 GGATTAATTTAAAAAATATTACTAATTAAAATCTAAGATTAATTAATTTTTTATTTTTTAACAAT
* * * * * * *
40305095 TTTATTATACGTTATGATCATAATGCTTAAAATTACTCATAACCCATTTTCAACTAATAAATGGG
66 TTTATTATAAGTTATGATCACAATACTTAAAACTACTAATAACCCATTCTCAACTAATAAATAGG
* ** * * * * **
40305160 AGTATAATGTGTTTCAATGCACTCGAACTCACATCCTCTTACATTAACAACAATACTCATGTTAA
131 AGGATAATACGTTTCAACGCACTCAAACCCACATACTCTTACATTAACAACAATACTCATACTAA
*
40305225 TCGAGCTAAAAACTTAATCTACTA
196 TCGAACTAAAAACTTAATCTACTA
* ** * *
40305249 GGATTAATTTAAAAAATATTACTAATTAAAATTTGGGATTAGTTTATTTTTTATTTTTTAACAAT
1 GGATTAATTTAAAAAATATTACTAATTAAAATCTAAGATTAATTAATTTTTTATTTTTTAACAAT
* * * * * ***
40305314 TTTATTATAAGTTTTGATTACAATATTTAGAACTATTAATAGGTCATTCTCAACTCAA-AAATAG
66 TTTATTATAAGTTATGATCACAATACTTAAAACTACTAATAACCCATTCTCAACT-AATAAATAG
* * *** * * *
40305378 GAGGATAATACGTTTCAACGCATTCAAACCCACATACTCTTACTTTGTTAATAATATTTATACTA
130 GAGGATAATACGTTTCAACGCACTCAAACCCACATACTCTTACATTAACAACAATACTCATACTA
40305443 ATCGAACTAAAA
195 ATCGAACTAAAA
40305455 TTCGATCGAC
Statistics
Matches: 166, Mismatches: 39, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
219 164 0.99
220 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (219 bp):
GGATTAATTTAAAAAATATTACTAATTAAAATCTAAGATTAATTAATTTTTTATTTTTTAACAAT
TTTATTATAAGTTATGATCACAATACTTAAAACTACTAATAACCCATTCTCAACTAATAAATAGG
AGGATAATACGTTTCAACGCACTCAAACCCACATACTCTTACATTAACAACAATACTCATACTAA
TCGAACTAAAAACTTAATCTACTA
Found at i:40307494 original size:6 final size:6
Alignment explanation
Indices: 40307485--40307513 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
40307475 CCTTTGCCCT
40307485 TGCCTG TGCCTG TGCCTG TGCCTG TGCCT
1 TGCCTG TGCCTG TGCCTG TGCCTG TGCCT
40307514 CTCTTTCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.34, G:0.31, T:0.34
Consensus pattern (6 bp):
TGCCTG
Found at i:40323788 original size:4 final size:4
Alignment explanation
Indices: 40323779--40323823 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
40323769 AACATATATT
* * * *
40323779 CATA CATA CATA CATG CATG CATG CATA AATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C
40323824 GATAAGAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.44, C:0.24, G:0.07, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:40326356 original size:67 final size:67
Alignment explanation
Indices: 40326274--40326603 Score: 651
Period size: 67 Copynumber: 4.9 Consensus size: 67
40326264 AAAAATTATA
*
40326274 TTTTAAATCCTTCAAAGATAAACAAATTTATAAATTAATATATAATAAAATTTTCTCAGTTGAAC
1 TTTTCAATCCTTCAAAGATAAACAAATTTATAAATTAATATATAATAAAATTTTCTCAGTTGAAC
40326339 TT
66 TT
40326341 TTTTCAATCCTTCAAAGATAAACAAATTTATAAATTAATATATAATAAAATTTTCTCAGTTGAAC
1 TTTTCAATCCTTCAAAGATAAACAAATTTATAAATTAATATATAATAAAATTTTCTCAGTTGAAC
40326406 TT
66 TT
40326408 TTTTCAATCCTTCAAAGATAAACAAATTTATAAATTAATATATAATAAAATTTTCTCAGTTGAAC
1 TTTTCAATCCTTCAAAGATAAACAAATTTATAAATTAATATATAATAAAATTTTCTCAGTTGAAC
40326473 TT
66 TT
40326475 TTTTCAATCCTTCAAAGATAAACAAATTTATAAATTAATATATAATAAAATTTTCTCAGTTGAAC
1 TTTTCAATCCTTCAAAGATAAACAAATTTATAAATTAATATATAATAAAATTTTCTCAGTTGAAC
40326540 TT
66 TT
40326542 TTTTCAATCCTTCAAAGATAAACAAATTTATAAATTAATATATAATAAAATTTTCTCAGTTG
1 TTTTCAATCCTTCAAAGATAAACAAATTTATAAATTAATATATAATAAAATTTTCTCAGTTG
40326604 TATTTTTCTC
Statistics
Matches: 262, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 262 1.00
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.40
Consensus pattern (67 bp):
TTTTCAATCCTTCAAAGATAAACAAATTTATAAATTAATATATAATAAAATTTTCTCAGTTGAAC
TT
Found at i:40327360 original size:18 final size:18
Alignment explanation
Indices: 40327327--40327376 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
40327317 AAGTCTTTTG
*
40327327 TTTAATAATA-TTTTTAT
1 TTTAAAAATATTTTTTAT
40327344 TTTAAAAATATTTTTTAT
1 TTTAAAAATATTTTTTAT
* *
40327362 CTCAAAAATACTTTT
1 TTTAAAAATA-TTTT
40327377 GAGAAACAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 9 0.32
18 15 0.54
19 4 0.14
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAAAAATATTTTTTAT
Found at i:40332250 original size:30 final size:30
Alignment explanation
Indices: 40332216--40332272 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
40332206 TAGTGACTTG
40332216 AATAAAAAC-TTTATAATAGTTCAATGATTA
1 AATAAAAACTTTTA-AATAGTTCAATGATTA
40332246 AATAAAAACTTTTAAATAGTTCAATGA
1 AATAAAAACTTTTAAATAGTTCAATGA
40332273 CAATTTTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.35
Consensus pattern (30 bp):
AATAAAAACTTTTAAATAGTTCAATGATTA
Found at i:40354195 original size:60 final size:60
Alignment explanation
Indices: 40354062--40354195 Score: 153
Period size: 60 Copynumber: 2.2 Consensus size: 60
40354052 GACAAATTTG
* * * *
40354062 AATAGTTAGATAACCATTTTGTAACTTTTCACAGTTGGATGATCAAAAAAAAAATTTACT
1 AATAGTTAGGTGACCATTTTGTAACTTTTCACAATTGAATGATCAAAAAAAAAATTTACT
* * * * * * *
40354122 AATAATAAAGTGACCATTTTGTAATTTTTCATAATTGAATGA-CTAAAAAAGAAATTTATT
1 AATAGTTAGGTGACCATTTTGTAACTTTTCACAATTGAATGATC-AAAAAAAAAATTTACT
40354182 AATAGTTAGGTGAC
1 AATAGTTAGGTGAC
40354196 TACTAGTGTA
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
59 1 0.02
60 58 0.98
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.36
Consensus pattern (60 bp):
AATAGTTAGGTGACCATTTTGTAACTTTTCACAATTGAATGATCAAAAAAAAAATTTACT
Found at i:40354474 original size:31 final size:31
Alignment explanation
Indices: 40354386--40354484 Score: 77
Period size: 31 Copynumber: 3.3 Consensus size: 31
40354376 TATTTTTTTA
*
40354386 AAAATATTTATATTATATTATATTAATA-T-TT
1 AAAATATTTATA-TAT-TTATTTTAATATTATT
* *
40354417 AATAAT-TTTACACA-TT-TTTT-AT-TTATT
1 AA-AATATTTATATATTTATTTTAATATTATT
40354444 AAAATATTTATATATTTATTTTAATATTATT
1 AAAATATTTATATATTTATTTTAATATTATT
**
40354475 TTAATATTTA
1 AAAATATTTA
40354485 CATTAGAATA
Statistics
Matches: 53, Mismatches: 7, Indels: 16
0.70 0.09 0.21
Matches are distributed among these distances:
26 6 0.11
27 13 0.25
28 4 0.08
29 4 0.08
30 3 0.06
31 20 0.38
32 3 0.06
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (31 bp):
AAAATATTTATATATTTATTTTAATATTATT
Found at i:40355191 original size:52 final size:51
Alignment explanation
Indices: 40355109--40355206 Score: 144
Period size: 53 Copynumber: 1.9 Consensus size: 51
40355099 TCACTTTTAA
*
40355109 TTTTTAGGGTTTGAATGAATTTTTCTGGGAATTTGATTTTGTTTGTTTGTTTG
1 TTTTTAGGGTTTGAATGAATTTTTCTGGGAATTT-AATTTG-TTGTTTGTTTG
* *
40355162 TTTTTGGGGTTTGAATTAA-TTTTCTGGGAATTTAATTTGTTGTTT
1 TTTTTAGGGTTTGAATGAATTTTTCTGGGAATTTAATTTGTTGTTT
40355207 AGGCGCTGAG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
50 6 0.14
51 5 0.12
52 14 0.33
53 17 0.40
ACGTcount: A:0.16, C:0.02, G:0.23, T:0.58
Consensus pattern (51 bp):
TTTTTAGGGTTTGAATGAATTTTTCTGGGAATTTAATTTGTTGTTTGTTTG
Found at i:40365259 original size:12 final size:13
Alignment explanation
Indices: 40365223--40365269 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
40365213 TTTATCATTA
*
40365223 CTTTTGATAAGTG
1 CTTTTGAAAAGTG
*
40365236 CTTTTAAAAAGTG
1 CTTTTGAAAAGTG
*
40365249 C-TTTGAAAAGTA
1 CTTTTGAAAAGTG
*
40365261 ATTTTGAAA
1 CTTTTGAAA
40365270 GATATTTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.40
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:40367815 original size:26 final size:27
Alignment explanation
Indices: 40367754--40367823 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 27
40367744 TTGAAATCTG
* *
40367754 AAAAGTAGATGGACTAAATTCCGAGAAAT
1 AAAAGTACAAGGACTAAATTCC--GAAAT
*
40367783 AAAAGTACAATGACTAAATTCC-AAAT
1 AAAAGTACAAGGACTAAATTCCGAAAT
*
40367809 AACAGTACAAGGACT
1 AAAAGTACAAGGACT
40367824 TATGACATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
26 17 0.47
29 19 0.53
ACGTcount: A:0.50, C:0.14, G:0.16, T:0.20
Consensus pattern (27 bp):
AAAAGTACAAGGACTAAATTCCGAAAT
Found at i:40375219 original size:4 final size:4
Alignment explanation
Indices: 40375196--40375275 Score: 61
Period size: 4 Copynumber: 19.8 Consensus size: 4
40375186 TTTTACGATG
* * * * * ** *
40375196 TAAA TAAG TAAG TAAG TAAA TAAA TAAAA TAAA TAAC TAAC TAGC TAAC
1 TAAA TAAA TAAA TAAA TAAA TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
* *
40375245 TAAA TAAA TAAA TAAT TAAA TAAC TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
40375276 TATTTTTAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
4 61 0.94
5 4 0.06
ACGTcount: A:0.62, C:0.06, G:0.05, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:40375253 original size:24 final size:24
Alignment explanation
Indices: 40375197--40375275 Score: 68
Period size: 28 Copynumber: 3.1 Consensus size: 24
40375187 TTTACGATGT
* * * *
40375197 AAATAAGTAAGTAAGTAAATAAAT
1 AAATAAATAACTAAATAACTAAAT
40375221 AAAATAAATAACTAACTAGCTAACTAAAT
1 -AAATAAATAACTAA--A--TAACTAAAT
*
40375250 AAATAAATAATTAAATAACTAAAT
1 AAATAAATAACTAAATAACTAAAT
40375274 AA
1 AA
40375276 TATTTTTAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
24 11 0.24
25 12 0.27
26 1 0.02
28 13 0.29
29 8 0.18
ACGTcount: A:0.63, C:0.06, G:0.05, T:0.25
Consensus pattern (24 bp):
AAATAAATAACTAAATAACTAAAT
Found at i:40375435 original size:16 final size:15
Alignment explanation
Indices: 40375414--40375444 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
40375404 TAACCACTGG
40375414 AAATAAATAAATATAT
1 AAATAAATAAA-ATAT
40375430 AAATAAATAAAATAT
1 AAATAAATAAAATAT
40375445 TTTTTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATAAATAAAATAT
Found at i:40377024 original size:14 final size:14
Alignment explanation
Indices: 40377005--40377039 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
40376995 TACAATATCC
*
40377005 AAATAATAACAATA
1 AAATAATAAAAATA
40377019 AAATAATAAAAATA
1 AAATAATAAAAATA
*
40377033 TAATAAT
1 AAATAAT
40377040 GATATAGCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATAATAAAAATA
Found at i:40378758 original size:26 final size:26
Alignment explanation
Indices: 40378729--40378781 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
40378719 ATGCTATAAA
40378729 TGGTTTGTGCATATATAGCATCTGTC
1 TGGTTTGTGCATATATAGCATCTGTC
40378755 TGGTTTGTGCATATATAGCATCTGTC
1 TGGTTTGTGCATATATAGCATCTGTC
40378781 T
1 T
40378782 TTTCGTGGTA
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:0.19, C:0.15, G:0.23, T:0.43
Consensus pattern (26 bp):
TGGTTTGTGCATATATAGCATCTGTC
Found at i:40391672 original size:22 final size:22
Alignment explanation
Indices: 40391647--40391690 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
40391637 GTAACCACGT
40391647 AACAATTTAATTGAAAAGTCAA
1 AACAATTTAATTGAAAAGTCAA
40391669 AACAATTTAATTGAAAAGTCAA
1 AACAATTTAATTGAAAAGTCAA
40391691 TGTTATTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.27
Consensus pattern (22 bp):
AACAATTTAATTGAAAAGTCAA
Found at i:40393712 original size:6 final size:6
Alignment explanation
Indices: 40393701--40393765 Score: 69
Period size: 6 Copynumber: 10.8 Consensus size: 6
40393691 CCTCACATAT
* * * * *
40393701 ATATAC ATATAC ATATAC ACATAC ACATAC AAATAC ATATGA- GTATAG
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATAT-AC ATATAC
40393749 ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATA
40393766 GTGAAAGTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
5 1 0.02
6 49 0.96
7 1 0.02
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.29
Consensus pattern (6 bp):
ATATAC
Found at i:40400420 original size:16 final size:15
Alignment explanation
Indices: 40400399--40400433 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
40400389 AATTTAAATG
*
40400399 ATAAAAATATTTTAAA
1 ATAAAAAT-TTATAAA
40400415 ATAAAAATTTATAAA
1 ATAAAAATTTATAAA
40400430 ATAA
1 ATAA
40400434 TAACTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
ATAAAAATTTATAAA
Found at i:40402293 original size:35 final size:35
Alignment explanation
Indices: 40402254--40402338 Score: 152
Period size: 35 Copynumber: 2.4 Consensus size: 35
40402244 GGGTTTGACC
40402254 CTATTCGATATCGAATTTAGTGAAATTTGATACGA
1 CTATTCGATATCGAATTTAGTGAAATTTGATACGA
40402289 CTATTCGATATCGAATTTAGTGAAATTTGATACGA
1 CTATTCGATATCGAATTTAGTGAAATTTGATACGA
**
40402324 CTATTAAATATCGAA
1 CTATTCGATATCGAA
40402339 AGGTCTCATA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (35 bp):
CTATTCGATATCGAATTTAGTGAAATTTGATACGA
Found at i:40405004 original size:56 final size:56
Alignment explanation
Indices: 40404918--40405031 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 56
40404908 CACATTTATT
40404918 TCTCGAACTTAAAATCTCGAAGTTTTTAAAATTTCAATCTCGTTATTGGTTTTTCA
1 TCTCGAACTTAAAATCTCGAAGTTTTTAAAATTTCAATCTCGTTATTGGTTTTTCA
*
40404974 TCTCGAACTTAAAATCTCGAAGTTTTTAAAATTTTAATCTCGTTATTGGTTTTTCA
1 TCTCGAACTTAAAATCTCGAAGTTTTTAAAATTTCAATCTCGTTATTGGTTTTTCA
40405030 TC
1 TC
40405032 CAATTAACTT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.28, C:0.16, G:0.11, T:0.46
Consensus pattern (56 bp):
TCTCGAACTTAAAATCTCGAAGTTTTTAAAATTTCAATCTCGTTATTGGTTTTTCA
Found at i:40414634 original size:4 final size:4
Alignment explanation
Indices: 40414625--40414666 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
40414615 AATCAAAGAA
40414625 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
40414667 GTATTAAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:40415713 original size:19 final size:19
Alignment explanation
Indices: 40415689--40415726 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
40415679 TATATATTTA
40415689 AAAAATATAATATTTTATT
1 AAAAATATAATATTTTATT
40415708 AAAAATATAATATTTTATT
1 AAAAATATAATATTTTATT
40415727 TTTATATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAAAATATAATATTTTATT
Found at i:40416295 original size:29 final size:29
Alignment explanation
Indices: 40416223--40416288 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 29
40416213 TTTATCAAAT
* *
40416223 ACAAATACTAGATTGGACCAAAACATAAC
1 ACAAATACTAGATTAGACCAAAAAATAAC
* *
40416252 AGAAGTACTAGATTAGACCAAAAAATAAC
1 ACAAATACTAGATTAGACCAAAAAATAAC
40416281 ACAAATAC
1 ACAAATAC
40416289 CATATTAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.55, C:0.18, G:0.11, T:0.17
Consensus pattern (29 bp):
ACAAATACTAGATTAGACCAAAAAATAAC
Found at i:40419233 original size:39 final size:39
Alignment explanation
Indices: 40419190--40419884 Score: 714
Period size: 39 Copynumber: 18.1 Consensus size: 39
40419180 CTTTTCACTT
* * * **
40419190 TCTTCTAGTTCACGTGCCTCCTTCTCTTTCTTCTCTTTC
1 TCTTCTCGTTCACGAGCTTCCTTCAATTTCTTCTCTTTC
* * **
40419229 TCTTCTCGTTCACGTGCCTCCTTCTCTTTCTTCTCTTTC
1 TCTTCTCGTTCACGAGCTTCCTTCAATTTCTTCTCTTTC
*
40419268 TCTTCTCGTTCAC--G-TGCC-TC-----CTTCTCTTTC
1 TCTTCTCGTTCACGAGCTTCCTTCAATTTCTTCTCTTTC
* * *
40419298 TCTTCTCGTTCACAAGCTTCCTTCAATCTCTTCTCATTC
1 TCTTCTCGTTCACGAGCTTCCTTCAATTTCTTCTCTTTC
* *
40419337 TCTTCTCGTTCATGAGCTTCCTTCAATTTCTTCTCTTGC
1 TCTTCTCGTTCACGAGCTTCCTTCAATTTCTTCTCTTTC
* * * ** *
40419376 TCTTCTCGTTCATGTGCCTCCTTCTCTTCCTTCTCTTTC
1 TCTTCTCGTTCACGAGCTTCCTTCAATTTCTTCTCTTTC
** * **
40419415 TCTTCTCGTTCACGAGCTTCCTTCTCTTCCTTCTCAATC
1 TCTTCTCGTTCACGAGCTTCCTTCAATTTCTTCTCTTTC
** * *
40419454 TCTTCTCGTTCACGAATTTCCTTCAATCTCTTCTCATTC
1 TCTTCTCGTTCACGAGCTTCCTTCAATTTCTTCTCTTTC
** * * *
40419493 TCTTCTCGTTCACGAATTTCCTTCAATCTCCTCTCATTC
1 TCTTCTCGTTCACGAGCTTCCTTCAATTTCTTCTCTTTC
*
40419532 TCTTCTCGTTCACGAGCTTCCTTCAATTCCTTCTCTTTC
1 TCTTCTCGTTCACGAGCTTCCTTCAATTTCTTCTCTTTC
* * * **
40419571 TCTTCTCGTTCATGTGCGTCCTTCTCTTTCTTCTCTTTC
1 TCTTCTCGTTCACGAGCTTCCTTCAATTTCTTCTCTTTC
* * * * * * * *
40419610 TCTTCTTGCTCACAAGCCTCCCTCAATCTCTTCTCATTA
1 TCTTCTCGTTCACGAGCTTCCTTCAATTTCTTCTCTTTC
*
40419649 TCTTCTCGTTCACGAGCTTCCTTCAAGTTCTTCTCTTTC
1 TCTTCTCGTTCACGAGCTTCCTTCAATTTCTTCTCTTTC
* * * *
40419688 TCTTCTCGTTCACGAGCCTCCATCAATCTCTTCTCATTC
1 TCTTCTCGTTCACGAGCTTCCTTCAATTTCTTCTCTTTC
* * * *
40419727 TCTTCTCGTTCACGAGCCTCCCTCAATCTCTTCTCATTC
1 TCTTCTCGTTCACGAGCTTCCTTCAATTTCTTCTCTTTC
* *
40419766 TCTTCCCGTTCACAAGCTTCCTTCAATTTCTTCTCTTTC
1 TCTTCTCGTTCACGAGCTTCCTTCAATTTCTTCTCTTTC
* * *
40419805 TCTTCTAGTTCACGTGCCTCC-TC--TTTCTTC-CTTCTC
1 TCTTCTCGTTCACGAGCTTCCTTCAATTTCTTCTCTT-TC
*
40419841 TCTTCTCGTTCATGAGCTTCCTTCAATTTCTTCTCTTTC
1 TCTTCTCGTTCACGAGCTTCCTTCAATTTCTTCTCTTTC
40419880 TCTTC
1 TCTTC
40419885 CTGCTCAACA
Statistics
Matches: 559, Mismatches: 83, Indels: 28
0.83 0.12 0.04
Matches are distributed among these distances:
30 23 0.04
32 1 0.00
33 3 0.01
34 2 0.00
35 5 0.01
36 28 0.05
37 3 0.01
38 2 0.00
39 489 0.87
40 3 0.01
ACGTcount: A:0.10, C:0.36, G:0.07, T:0.46
Consensus pattern (39 bp):
TCTTCTCGTTCACGAGCTTCCTTCAATTTCTTCTCTTTC
Found at i:40422849 original size:2 final size:2
Alignment explanation
Indices: 40422842--40422866 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40422832 AATATTCGTT
40422842 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
40422867 TTTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:40423322 original size:27 final size:25
Alignment explanation
Indices: 40423273--40423324 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
40423263 CCTACAATTT
*
40423273 TAAAAAATTATATCAAATCTTAAAA
1 TAAAAAATTATATCAAATATTAAAA
*
40423298 TAAAAAATATATATTAAATTATTAAAA
1 TAAAAAAT-TATATCAAA-TATTAAAA
40423325 ATCATAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 8 0.35
26 8 0.35
27 7 0.30
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (25 bp):
TAAAAAATTATATCAAATATTAAAA
Found at i:40424832 original size:18 final size:19
Alignment explanation
Indices: 40424809--40424845 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40424799 TTTTCATCAT
*
40424809 ATTATTT-ATTATTTTTTA
1 ATTATTTAATAATTTTTTA
40424827 ATTATTTAATAATTTTTTA
1 ATTATTTAATAATTTTTTA
40424846 TTACAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTATTTAATAATTTTTTA
Found at i:40424848 original size:18 final size:17
Alignment explanation
Indices: 40424808--40424848 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
40424798 TTTTTCATCA
*
40424808 TATTATTTATTATTTTT
1 TATTATTTATAATTTTT
40424825 TAATTATTTAATAATTTTT
1 T-ATTATTT-ATAATTTTT
40424844 TATTA
1 TATTA
40424849 CAATAATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 11 0.52
19 9 0.43
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TATTATTTATAATTTTT
Found at i:40425243 original size:5 final size:5
Alignment explanation
Indices: 40425233--40425257 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
40425223 TATTTAATGT
40425233 ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA
40425258 TTTAGACACT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:40430531 original size:5 final size:5
Alignment explanation
Indices: 40430521--40430589 Score: 52
Period size: 5 Copynumber: 13.2 Consensus size: 5
40430511 TTAACTGCTT
* *
40430521 ATTTA ATTTA ATTT- ATTT- TTTTA TATATA ATTTA ATTTA ATTTTA ACTGTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA -ATTTA ATTTA ATTTA A-TTTA A-T-TTA
*
40430573 ATATA ATTGTA ATTTA A
1 ATTTA ATT-TA ATTTA A
40430590 AATATTTTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
4 7 0.13
5 26 0.50
6 15 0.29
7 4 0.08
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (5 bp):
ATTTA
Found at i:40434176 original size:390 final size:389
Alignment explanation
Indices: 40433419--40434510 Score: 1507
Period size: 390 Copynumber: 2.8 Consensus size: 389
40433409 GAGAATGGAA
*
40433419 GGAAGAGAAGAAGCAATTAATCAGAAAGTTCAACAAGATACAAAACTGGGAACTTTTACATCAAT
1 GGAAGAGACGAAGCAATTAATCAGAAAGTTCAACAAGATACAAAACTGGGAACTTTTACATCAAT
* * *
40433484 ATCATTTCCAATAGGAACAACAAAAATGGATGGATAAAGG-T-TCGGTCATGAATTTCTGAAGTC
66 CTCATTTTCAATAGGAACAACAAAAATGGATGGATCAAGGTTCTCGGTCATGAATTTCTGAAGTC
* * * * * *
40433547 T-TGTGTCAATTTGAGAGCTAGATAATAACTAACCTATGAGATTCATATTTTCATTCGTCATGAA
131 TCT-TATTACTTCGAGAGCTAGATAATTACTAA-CTATGAGATTCATATTTTTATTCGTCATGAA
*
40433611 AGCAACATGATCCAACATGTAGTGAATTATAGCTTGTGTTAAATGAACATACCAGTTTTGGTCAT
194 AGCAACATGATCCAACATGTAGTGAATTATAGCTTATGTTAAATGAACATACCAGTTTTGGTCAT
** * * * **
40433676 TAATCATACACAATTTAGTTTCATTATAAGTTTCTAGCGAATTCCAGCACTGTCACTCAAAAATT
259 TAATCATACACAAGATAGTTTCATCATAAGTTTCTAGCAAACTCCAGCACCATCACTCAAAAATT
* *
40433741 CTTAATTCTGAAGTTGCACAGAAAATTCAATTTAACTTCCTAACACACATATATGATG-GAACAA
324 CTTAATTCTGAACTTACACAGAAAATTCAATTTAACTTCCTAACACACATATATGA-GAGAACAA
40433805 AC
388 AC
* * * *
40433807 GGAAGTGTCGAAGCAATTATTCAGAAAGTT-AACAATATACAAAACTGGGAACTTTTACATCAAT
1 GGAAGAGACGAAGCAATTAATCAGAAAGTTCAACAAGATACAAAACTGGGAACTTTTACATCAAT
* *
40433871 CTCATTTTTAATAGGAACAACAAAAATGAATGGATCAAGGTTCATCCGGTCATGAATTTCTGAAG
66 CTCATTTTCAATAGGAACAACAAAAATGGATGGATCAAGGTTC-T-CGGTCATGAATTTCTGAAG
*
40433936 TCTCTTATTACTTCGAGAGCTAGATAATTACTAGA-TATGAGATTCATATTTTTATTCATCATGA
129 TCTCTTATTACTTCGAGAGCTAGATAATTACTA-ACTATGAGATTCATATTTTTATTCGTCATGA
* *
40434000 GAGCAACATGATCCAACACGTAGTGAATTATAGCTTATGTTAAATGAACATACC-GCTTTTGGTC
193 AAGCAACATGATCCAACATGTAGTGAATTATAGCTTATGTTAAATGAACATACCAG-TTTTGGTC
* * *
40434064 ATTAATCATACACAAGATAGTTTGATCATTAGTTTCTAGCAAACTCCAGCCCCATCACTCAAAAA
257 ATTAATCATACACAAGATAGTTTCATCATAAGTTTCTAGCAAACTCCAGCACCATCACTCAAAAA
*
40434129 TTCTTAATTCTGAACTTACACAGAAAATTCAATTTAACTTGCTAACACACATATATGAGAGAACA
322 TTCTTAATTCTGAACTTACACAGAAAATTCAATTTAACTTCCTAACACACATATATGAGAGAACA
*
40434194 AAG
387 AAC
* * **
40434197 GGAAGAGACAAAGCAATTAATCAGAAAGTTCATCAAGATACAAAACTGGGAACTTTTACATTGAT
1 GGAAGAGACGAAGCAATTAATCAGAAAGTTCAACAAGATACAAAACTGGGAACTTTTACATCAAT
*
40434262 CTCATTTTCAATAGGAACAACAAAAAAGGATGGATCAAGGTTCCTTCGGTCATGAATTTCTGAAG
66 CTCATTTTCAATAGGAACAACAAAAATGGATGGATCAAGGTT-C-TCGGTCATGAATTTCTGAAG
* * * * *
40434327 TCTCATATTACTTCGAGAGCAAGATAATTACTAACCTATGAGATTCATATTTTTATTTGCCATAA
129 TCTCTTATTACTTCGAGAGCTAGATAATTACTAA-CTATGAGATTCATATTTTTATTCGTCATGA
*
40434392 AAGCAAACATCATCCAACATGTAGTGAATTATAGCTTATGTTAAATGAACATACC--------T-
193 AAGC-AACATGATCCAACATGTAGTGAATTATAGCTTATGTTAAATGAACATACCAGTTTTGGTC
* * * * * *
40434448 -TTAATCCTACACAATATAGTTTCATTATAAGTTTCTAGCGAACTCCAGCTCCGTCACTCAAAA
257 ATTAATCATACACAAGATAGTTTCATCATAAGTTTCTAGCAAACTCCAGCACCATCACTCAAAA
40434511 TTTCCAAAAT
Statistics
Matches: 628, Mismatches: 63, Indels: 31
0.87 0.09 0.04
Matches are distributed among these distances:
383 55 0.09
385 1 0.00
387 68 0.11
388 27 0.04
389 2 0.00
390 231 0.37
391 164 0.26
392 32 0.05
393 48 0.08
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (389 bp):
GGAAGAGACGAAGCAATTAATCAGAAAGTTCAACAAGATACAAAACTGGGAACTTTTACATCAAT
CTCATTTTCAATAGGAACAACAAAAATGGATGGATCAAGGTTCTCGGTCATGAATTTCTGAAGTC
TCTTATTACTTCGAGAGCTAGATAATTACTAACTATGAGATTCATATTTTTATTCGTCATGAAAG
CAACATGATCCAACATGTAGTGAATTATAGCTTATGTTAAATGAACATACCAGTTTTGGTCATTA
ATCATACACAAGATAGTTTCATCATAAGTTTCTAGCAAACTCCAGCACCATCACTCAAAAATTCT
TAATTCTGAACTTACACAGAAAATTCAATTTAACTTCCTAACACACATATATGAGAGAACAAAC
Found at i:40440928 original size:15 final size:15
Alignment explanation
Indices: 40440908--40440938 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40440898 ACTCTGCAAA
40440908 AAAAGAAAAAAAGAG
1 AAAAGAAAAAAAGAG
*
40440923 AAAAGAAAAAGAGAG
1 AAAAGAAAAAAAGAG
40440938 A
1 A
40440939 GCATAAACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAAAGAG
Found at i:40449868 original size:204 final size:199
Alignment explanation
Indices: 40449585--40449961 Score: 538
Period size: 204 Copynumber: 1.9 Consensus size: 199
40449575 ATAGTTTTGT
*
40449585 CTTAAACTAAGATAGAACACAATTTCTCAGCTAAAGATGCCCTATGTATTTTCCGACCGTGCCAC
1 CTTAAACTAAGACAGAACACAATTTCTCAGCTAAAGATGCCCTATGTATTTTCCGACCGTGCCAC
* * * ** *
40449650 GGCCAGATATTGTATCCGTCTGGCTTGAACGGTAATCTCTCCCCAGAATTCTACATTCCCAACAT
66 AGCCAGATATTGTATCCGTCCGGCTTGAACAGTAATCTCTCCAAAGAATTCTACATTCCCAAAAT
*
40449715 GCAGCTTAAGTACAACAATCTCAACTCTAGACTGTCCTACGTGAACAAAGCCGAGTTATGATCCA
131 GCAGCTT-AG-ACAACAATCTCAACTATAGACTGTCCTACGTGAACAAAGCCGAGTTATGATCCA
40449780 ATTGGC
194 ATTGGC
* *
40449786 CTTAATCTAAGACAGAACACACAATTTCTTAGCTAAAGACTGCCCTATGTATTTTCCGACCGTGC
1 CTTAAACTAAGACAG-A-ACACAATTTCTCAGCTAAAGA-TGCCCTATGTATTTTCCGACCGTGC
* * * * *
40449851 CATATCCAGATATTGTATCTGTCCGGCTTGAACAGTAATCTCTCCAAAGAATTCTATATTTCCAA
63 CACAGCCAGATATTGTATCCGTCCGGCTTGAACAGTAATCTCTCCAAAGAATTCTACATTCCCAA
* * * *
40449916 AATGCAGCTTAGGCAACAATCTCGACTATAGACTGTTCTATGTGAA
128 AATGCAGCTTAGACAACAATCTCAACTATAGACTGTCCTACGTGAA
40449962 TAAAACCTAG
Statistics
Matches: 154, Mismatches: 19, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
201 13 0.08
202 30 0.19
203 22 0.14
204 89 0.58
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.29
Consensus pattern (199 bp):
CTTAAACTAAGACAGAACACAATTTCTCAGCTAAAGATGCCCTATGTATTTTCCGACCGTGCCAC
AGCCAGATATTGTATCCGTCCGGCTTGAACAGTAATCTCTCCAAAGAATTCTACATTCCCAAAAT
GCAGCTTAGACAACAATCTCAACTATAGACTGTCCTACGTGAACAAAGCCGAGTTATGATCCAAT
TGGC
Done.