Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 35 of 204
Found at i:12493584 original size:22 final size:21
Alignment explanation
Indices: 12493559--12493599 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
12493549 TACTTGTTTT
12493559 AATATTATTAATATCATTATAC
1 AATATTATTAATAT-ATTATAC
*
12493581 AATATTATTATTATATTAT
1 AATATTATTAATATATTAT
12493600 TATTGATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATTATTAATATATTATAC
Found at i:12493715 original size:20 final size:20
Alignment explanation
Indices: 12493690--12493728 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
12493680 TGTTATTACA
12493690 TACATATTTTAT-TATTTATG
1 TACATA-TTTATGTATTTATG
12493710 TACATATTTATGTATTTAT
1 TACATATTTATGTATTTAT
12493729 ATACTTCCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (20 bp):
TACATATTTATGTATTTATG
Found at i:12494283 original size:25 final size:25
Alignment explanation
Indices: 12494255--12494304 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
12494245 AATATTCAAT
12494255 GTTTAATATTTTGATAAATTGTGCC
1 GTTTAATATTTTGATAAATTGTGCC
12494280 GTTTAATATTTTGATAAATTGTGCC
1 GTTTAATATTTTGATAAATTGTGCC
12494305 CTAACGTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (25 bp):
GTTTAATATTTTGATAAATTGTGCC
Found at i:12504088 original size:36 final size:35
Alignment explanation
Indices: 12504044--12504113 Score: 113
Period size: 36 Copynumber: 2.0 Consensus size: 35
12504034 CATTTCACAA
* *
12504044 TTTTAAGATTACTTTTTAAGTATACTAACCATTATT
1 TTTTAAGATTACTTTTTAAGT-TACCAACAATTATT
12504080 TTTTAAGATTACTTTTTAAGTTACCAACAATTAT
1 TTTTAAGATTACTTTTTAAGTTACCAACAATTAT
12504114 ATTTAAAGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 11 0.34
36 21 0.66
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.49
Consensus pattern (35 bp):
TTTTAAGATTACTTTTTAAGTTACCAACAATTATT
Found at i:12516386 original size:120 final size:120
Alignment explanation
Indices: 12516247--12516934 Score: 1139
Period size: 120 Copynumber: 5.7 Consensus size: 120
12516237 AGTAGATTAC
*
12516247 AAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTA
1 AAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAATATTA
12516312 AGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTT
66 AGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTT
* * * *
12516367 AGATTATATTTTATAGTATTATAAATTATGATTATAGTAAATTCATATAAGAATATTTAATATTA
1 AAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAATATTA
*
12516432 AGAATTTTATTAAATTATATATTTTTAATAAATTATATTTTTAATAATAATTATTTT
66 AGAATTTTATTAAATTATATATTTTTATTAAATTATA--TTTAATAATAATTATTTT
* *
12516489 AAATTATATTTTATAGTGTTATATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAACAT
1 AAATTATATTTTATAGT-AT-TATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAATAT
* *
12516554 TAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAAAAATAATTAATTT
64 TAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTT
12516611 AAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTC---TAAGAATATTTAATATTA
1 AAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAATATTA
* *
12516673 AGAATTTTATTAAATTATATATTTTTACTAAATTATATTTTTAATAATTATTATTTT
66 AGAATTTTATTAAATTATATATTTTTATTAAATTATA--TTTAATAATAATTATTTT
*
12516730 AAATTATATTTTATAGTATTATATATTATGATTTTATTAAATTCATTTAAGAATATTTAATATTA
1 AAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAATATTA
*
12516795 AGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTT
66 AGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTT
* * * *
12516850 AAATTATATTTTATAGTGTTATATATTATGATCTTAGAAAATTCATTTAAGAATATTTAATACTA
1 AAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAATATTA
12516915 AGAATTTTATTAAATTATAT
66 AGAATTTTATTAAATTATAT
12516935 TTAATAATAA
Statistics
Matches: 531, Mismatches: 28, Indels: 18
0.92 0.05 0.03
Matches are distributed among these distances:
117 53 0.10
119 58 0.11
120 219 0.41
121 1 0.00
122 121 0.23
123 1 0.00
124 78 0.15
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (120 bp):
AAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAATATTA
AGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTT
Found at i:12516457 original size:18 final size:17
Alignment explanation
Indices: 12516436--12516478 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
12516426 ATATTAAGAA
*
12516436 TTTTATTAAATTATATAT
1 TTTTAATAAATTATAT-T
12516454 TTTTAATAAATTATA-T
1 TTTTAATAAATTATATT
12516470 TTTTAATAA
1 TTTTAATAA
12516479 TAATTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 10 0.42
18 14 0.58
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTAATAAATTATATT
Found at i:12516486 original size:16 final size:16
Alignment explanation
Indices: 12516448--12516488 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
12516438 TTATTAAATT
12516448 ATATATTTTTAATAAA
1 ATATATTTTTAATAAA
*
12516464 TTATATTTTTAATAATA
1 ATATATTTTTAATAA-A
12516481 AT-TATTTT
1 ATATATTTT
12516489 AAATTATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 20 0.91
17 2 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATATATTTTTAATAAA
Found at i:12516572 original size:17 final size:18
Alignment explanation
Indices: 12516547--12516592 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
12516537 TTAAGAATAT
12516547 TTAACATTA-AGAATTTTA
1 TTAA-ATTATAGAATTTTA
* *
12516565 TTAAATTATATATTTTTA
1 TTAAATTATAGAATTTTA
12516583 TTAAATTATA
1 TTAAATTATA
12516593 TTTAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
TTAAATTATAGAATTTTA
Found at i:12516721 original size:15 final size:15
Alignment explanation
Indices: 12516690--12516741 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
12516680 TATTAAATTA
*
12516690 TATATTTTTACTAAAT
1 TATATTTTTAAT-AAT
12516706 TATATTTTTAATAAT
1 TATATTTTTAATAAT
12516721 TAT-TATTTT-A-AAT
1 TATAT-TTTTAATAAT
12516734 TATATTTT
1 TATATTTT
12516742 ATAGTATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
13 9 0.27
14 3 0.09
15 10 0.30
16 11 0.33
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
TATATTTTTAATAAT
Found at i:12516750 original size:28 final size:29
Alignment explanation
Indices: 12516701--12516756 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
12516691 ATATTTTTAC
12516701 TAAATTATATTTTTAATAATTAT-TATTT
1 TAAATTATATTTTTAATAATTATATATTT
*
12516729 TAAATTATATTTTATAGT-ATTATATATT
1 TAAATTATATTTT-TAATAATTATATATT
12516757 ATGATTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (29 bp):
TAAATTATATTTTTAATAATTATATATTT
Found at i:12516922 original size:61 final size:60
Alignment explanation
Indices: 12516254--12516924 Score: 385
Period size: 61 Copynumber: 11.1 Consensus size: 60
12516244 TACAAATTAT
* *
12516254 ATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGA
1 ATTTTATAGTATTATATATTATGA-TTTATTAAATTCATTTAAGAATATTTAATATTAAGA
* * * * * *
12516315 ATTTTATTA-AATTATATA-T-T--TTTATTAAATTATATTTAATAATAATT-ATTTTAGATTA
1 ATTTTA-TAGTATTATATATTATGATTTATTAAATT-CATTTAAGAATATTTAATATTA-A-GA
* * *
12516373 TATTTTATAGTATTATAAATTATGATTATAGTAAATTCATATAAGAATATTTAATATTAAGA
1 -ATTTTATAGTATTATATATTATGATT-TATTAAATTCATTTAAGAATATTTAATATTAAGA
* * * ** * * * * *
12516435 ATTTTATTA-AATTATATATTTTTAATAAATTATATT--TTTAATAATAATT-ATTTTAAATTA
1 ATTTTA-TAGTATTATATA-TTATGATTTATTAAATTCATTTAAGAATATTTAATATT-AA-GA
* * *
12516495 TATTTTATAGTGTTATATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAACATTAAGA
1 -ATTTTATAGT-AT-TATATATTATGA-TTTATTAAATTCATTTAAGAATATTTAATATTAAGA
* * * * *
12516559 ATTTTATTA-AATTATATA-T-T--TTTATTAAATTATATTTAAAAATAATTAAT-TTAAATTA
1 ATTTTA-TAGTATTATATATTATGATTTATTAAATT-CATTTAAGAATATTTAATATT-AA-GA
*
12516617 TATTTTATAGTATTATATATTATGATTTTAGTAAATTC---TAAGAATATTTAATATTAAGA
1 -ATTTTATAGTATTATATATTATGA-TTTATTAAATTCATTTAAGAATATTTAATATTAAGA
* * * ** * * * *
12516676 ATTTTATTA-AATTATATATTTTTACTAAATTATATT--TTTAATAAT-TATT-ATTTTAAATTA
1 ATTTTA-TAGTATTATATATTATGA-TTTATTAAATTCATTTAAGAATAT-TTAATATT-AA-GA
12516736 TATTTTATAGTATTATATATTATGATTTTATTAAATTCATTTAAGAATATTTAATATTAAGA
1 -ATTTTATAGTATTATATATTATGA-TTTATTAAATTCATTTAAGAATATTTAATATTAAGA
* * * * * *
12516798 ATTTTATTA-AATTATATA-T-T--TTTATTAAATTATATTTAATAATAATT-ATGTTAAATTA
1 ATTTTA-TAGTATTATATATTATGATTTATTAAATT-CATTTAAGAATATTTAATATT-AA-GA
* ** *
12516856 TATTTTATAGTGTTATATATTATGATCTTAGAAAATTCATTTAAGAATATTTAATACTAAGA
1 -ATTTTATAGTATTATATATTATGAT-TTATTAAATTCATTTAAGAATATTTAATATTAAGA
12516918 ATTTTAT
1 ATTTTAT
12516925 TAAATTATAT
Statistics
Matches: 456, Mismatches: 94, Indels: 120
0.68 0.14 0.18
Matches are distributed among these distances:
56 42 0.09
57 42 0.09
58 43 0.09
59 68 0.15
60 26 0.06
61 97 0.21
62 20 0.04
63 60 0.13
64 42 0.09
65 13 0.03
66 3 0.01
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (60 bp):
ATTTTATAGTATTATATATTATGATTTATTAAATTCATTTAAGAATATTTAATATTAAGA
Found at i:12522798 original size:13 final size:13
Alignment explanation
Indices: 12522780--12522805 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12522770 ATCATGGATA
12522780 TCTCTTCTTTTTT
1 TCTCTTCTTTTTT
12522793 TCTCTTCTTTTTT
1 TCTCTTCTTTTTT
12522806 CCTTAGATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TCTCTTCTTTTTT
Found at i:12528915 original size:23 final size:24
Alignment explanation
Indices: 12528876--12528922 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
12528866 CATGGATAGT
12528876 AATAAAAATTATATAAAAATATTC
1 AATAAAAATTATATAAAAATATTC
* *
12528900 AATAAAAATT-TGTAAATATATTC
1 AATAAAAATTATATAAAAATATTC
12528923 TTAATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.36
Consensus pattern (24 bp):
AATAAAAATTATATAAAAATATTC
Found at i:12540709 original size:16 final size:16
Alignment explanation
Indices: 12540684--12540717 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12540674 GTTCGCTGTG
12540684 ATGGAATAGACGCGTA
1 ATGGAATAGACGCGTA
* *
12540700 ATGGATTAGAGGCGTA
1 ATGGAATAGACGCGTA
12540716 AT
1 AT
12540718 AGCAATTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.09, G:0.32, T:0.24
Consensus pattern (16 bp):
ATGGAATAGACGCGTA
Found at i:12540971 original size:18 final size:17
Alignment explanation
Indices: 12540950--12540984 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12540940 TTATTATTAA
*
12540950 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
12540968 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
12540985 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:12541049 original size:22 final size:24
Alignment explanation
Indices: 12541004--12541050 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
12540994 TCAACATTCT
12541004 TATATGAATTTACTAAAATCATAA
1 TATATGAATTTACTAAAATCATAA
12541028 TATATG-ATATTA-TAAAAT-ATAA
1 TATATGAAT-TTACTAAAATCATAA
12541050 T
1 T
12541051 TTGAAATAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.23
23 8 0.36
24 9 0.41
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (24 bp):
TATATGAATTTACTAAAATCATAA
Found at i:12541076 original size:120 final size:120
Alignment explanation
Indices: 12540925--12541206 Score: 458
Period size: 120 Copynumber: 2.4 Consensus size: 120
12540915 ATAATTTAAT
* *
12540925 TATATTTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTA
1 TATAATTTAAAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTA
* * *
12540990 ATAATCAACATTCTTATATGAATTTACTAAAATCATAATATATGATATTATAAAA
66 ATAATAAACATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA
* *
12541045 TATAATTTGAAATAACTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTA
1 TATAATTTAAAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTA
* * *
12541110 GTATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA
66 ATAATAAACATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA
*
12541165 TATAATTTAAAATAATTATTATTAAATATAATTTAA-TAAAAT
1 TATAATTTAAAATAATTATTATTAAATATATTTTAATTAAAAT
12541207 TCTTAACATT
Statistics
Matches: 149, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
119 6 0.04
120 143 0.96
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
TATAATTTAAAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTA
ATAATAAACATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA
Found at i:12541091 original size:18 final size:17
Alignment explanation
Indices: 12541070--12541104 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12541060 CTATTATTAA
*
12541070 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
12541088 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
12541105 TCTTAGTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:12541102 original size:59 final size:57
Alignment explanation
Indices: 12540910--12541109 Score: 160
Period size: 59 Copynumber: 3.4 Consensus size: 57
12540900 TAATATCAAT
* * * * *
12540910 AATAAATAATTTAATTATATT-TTAA-CATAATTATTATTAAATATATTTTAATTAA
1 AATATATAATTTAATAAAATTCTTAATAATAACTATTATTAAATATATTTTAATTAA
* * * *
12540965 AATATATAATTTAATAAAATTCTTAATAATCAAC-ATTCTTATATGA-ATTTACTAAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAAT-AACTATTATTAAAT-ATATTT--T--AATTAA
* * *
12541026 AATATATGATATT-ATAAAATATAATTTGA-AATAACTATTATTAAATATATTTTAATTAA
1 AATATATAAT-TTAATAAAAT-T--CTTAATAATAACTATTATTAAATATATTTTAATTAA
12541085 AATATATAATTTAATAAAATTCTTA
1 AATATATAATTTAATAAAATTCTTA
12541110 GTATTAAATA
Statistics
Matches: 111, Mismatches: 19, Indels: 29
0.70 0.12 0.18
Matches are distributed among these distances:
55 18 0.16
56 6 0.05
57 14 0.13
58 6 0.05
59 21 0.19
61 21 0.19
62 7 0.06
63 15 0.14
64 3 0.03
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (57 bp):
AATATATAATTTAATAAAATTCTTAATAATAACTATTATTAAATATATTTTAATTAA
Found at i:12541165 original size:61 final size:61
Alignment explanation
Indices: 12540965--12541155 Score: 187
Period size: 61 Copynumber: 3.2 Consensus size: 61
12540955 TTTTAATTAA
* * *
12540965 AATATATAATTTAATAAAATTCTTAATAATCAACATTCTTATATGAATTTACTAAAATCAT
1 AATATATAATTTAATAAAATTCTTAGTAATAAATATTCTTATATGAATTTACTAAAATCAT
* * * * * * * * *
12541026 AATATATGATATT-ATAAAATATAATTTGAAATAACTATTATTAAAT-ATATTT--T--AATTAA
1 AATATATAAT-TTAATAAAAT-T-CTTAGTAATAAATATTCTTATATGA-ATTTACTAAAATCAT
*
12541085 AATATATAATTTAATAAAATTCTTAGTATTAAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATAATTTAATAAAATTCTTAGTAATAAATATTCTTATATGAATTTACTAAAATCAT
12541146 AATATATAAT
1 AATATATAAT
12541156 ACTATAAAAT
Statistics
Matches: 98, Mismatches: 22, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
57 20 0.20
58 4 0.04
59 21 0.21
61 31 0.32
62 4 0.04
63 18 0.18
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAGTAATAAATATTCTTATATGAATTTACTAAAATCAT
Found at i:12541220 original size:14 final size:14
Alignment explanation
Indices: 12541203--12541248 Score: 51
Period size: 12 Copynumber: 3.3 Consensus size: 14
12541193 TAATTTAATA
12541203 AAATTCTTAACATT
1 AAATTCTTAACATT
*
12541217 AAATATTCTT-ATA-T
1 -AA-ATTCTTAACATT
12541231 AAATTCTTAACATT
1 AAATTCTTAACATT
12541245 AAAT
1 AAAT
12541249 ATAATTGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
12 6 0.23
13 4 0.15
14 6 0.23
15 4 0.15
16 6 0.23
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATTCTTAACATT
Found at i:12541226 original size:16 final size:15
Alignment explanation
Indices: 12541201--12541247 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
12541191 TATAATTTAA
12541201 TAAAATTCTTAACAT
1 TAAAATTCTTAACAT
*
12541216 TAAATATTCTT-ATA-
1 TAAA-ATTCTTAACAT
12541230 T-AAATTCTTAACAT
1 TAAAATTCTTAACAT
12541244 TAAA
1 TAAA
12541248 TATAATTGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
12 6 0.23
13 4 0.15
14 2 0.08
15 8 0.31
16 6 0.23
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.43
Consensus pattern (15 bp):
TAAAATTCTTAACAT
Found at i:12544196 original size:14 final size:14
Alignment explanation
Indices: 12544177--12544207 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12544167 GGCTTCCTCT
12544177 TATAAGCATTTTAA
1 TATAAGCATTTTAA
*
12544191 TATAAGTATTTTAA
1 TATAAGCATTTTAA
12544205 TAT
1 TAT
12544208 TATTTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (14 bp):
TATAAGCATTTTAA
Found at i:12544640 original size:18 final size:19
Alignment explanation
Indices: 12544608--12544657 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
12544598 ATAAGGACTG
12544608 AAAAATAA-ATATTAC-AAA
1 AAAAATAATAT-TTACTAAA
*
12544626 AAAAATTATATTTACTAAA
1 AAAAATAATATTTACTAAA
*
12544645 AATAATAATATTT
1 AAAAATAATATTT
12544658 GTAATAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAATAATATTTACTAAA
Found at i:12545000 original size:2 final size:2
Alignment explanation
Indices: 12544995--12545025 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12544985 TTTTTCCAGC
12544995 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12545026 AAATTAGCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12547753 original size:20 final size:20
Alignment explanation
Indices: 12547728--12547768 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
12547718 AAATATTTTC
*
12547728 AAGTAAATCATTTTACAGAA
1 AAGTAAAACATTTTACAGAA
*
12547748 AAGTAAAACATTTTCCAGAA
1 AAGTAAAACATTTTACAGAA
12547768 A
1 A
12547769 TCATTTTACG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.12, G:0.10, T:0.27
Consensus pattern (20 bp):
AAGTAAAACATTTTACAGAA
Found at i:12547771 original size:34 final size:35
Alignment explanation
Indices: 12547717--12547783 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
12547707 CAAACACCAG
*
12547717 AAAATATTTTCAAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCAAGTAAATCATTTTACAGAAAAGT
* *
12547752 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCAAGTAAATCATTTTACAGAAAA
12547784 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCAAGTAAATCATTTTACAGAAAAGT
Found at i:12547775 original size:14 final size:14
Alignment explanation
Indices: 12547752--12547791 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
12547742 ACAGAAAAGT
*
12547752 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
12547766 AAATCATTTTACGG
1 AAAACATTTTACAG
12547780 AAAACATTTTAC
1 AAAACATTTTAC
12547792 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:12553355 original size:16 final size:17
Alignment explanation
Indices: 12553332--12553370 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
12553322 TATCTCAATG
*
12553332 AGAAAATCCAAGTCCAA
1 AGAAAATCCAAATCCAA
12553349 A-AAAATCCAAATCCAA
1 AGAAAATCCAAATCCAA
12553365 AGAAAA
1 AGAAAA
12553371 CTCGATTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.62, C:0.21, G:0.08, T:0.10
Consensus pattern (17 bp):
AGAAAATCCAAATCCAA
Found at i:12555102 original size:6 final size:6
Alignment explanation
Indices: 12555093--12555119 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
12555083 GTTATATATT
12555093 AATTTA AATTTA AATTTA AATTTA AAT
1 AATTTA AATTTA AATTTA AATTTA AAT
12555120 CTATAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTTA
Found at i:12561137 original size:124 final size:124
Alignment explanation
Indices: 12560813--12561205 Score: 524
Period size: 125 Copynumber: 3.2 Consensus size: 124
12560803 GGCCAAACAT
* * * * *
12560813 GAACTACTGTAGAAAAATAGCGTCCATGTGGGAGCTTTTTTTAGTAATTTTGCTGACT-GTGTAT
1 GAACTACTGTAGAAAAAAAGTGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGA-TAGTGCAT
* * *
12560877 CCTGCTTGAAGCATTTTTGACACTAATTTTTCAAAATTGTCTTCTCAAAATTATTTTTCAG
65 CCTGCTTGAAGCGTTTTTGACACT-ATTTTTCAGAATCGTCTTCTCAAAATTATTTTTCAG
* *
12560938 GAACTACTGTGGAAAAAAAGTGTCCACGTGGGAGCTTTTTTCAGTAATTTTACTGATAGTGCATC
1 GAACTACTGTAGAAAAAAAGTGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGATAGTGCATC
* * *
12561003 CTGCTTGAAGCGTTTTTGAAACTATTTTTCCAGAATCGTGTTCTTAAAATTATTTTTCAG
66 CTGCTTGAAGCGTTTTTGACACTATTTTT-CAGAATCGTCTTCTCAAAATTATTTTTCAG
* * * *
12561063 GAACTACTGTAGAAAAAGAGTGTCCACATGGTAG-TTTTTTCAGTAATTTTGCTGATAGTACATC
1 GAACTACTGTAGAAAAAAAGTGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGATAGTGCATC
* * *
12561127 CTGCTTGAAGCGTTTTTGACATTATCTTTTCAGAACCGTCTTCTCAAAATTAATTTTTC-T
66 CTGCTTGAAGCGTTTTTGACACTAT-TTTTCAGAATCGTCTTCTCAAAATT-ATTTTTCAG
12561187 GAAGCTACTGTA-AAAAAAA
1 GAA-CTACTGTAGAAAAAAA
12561206 TTGAATCCTT
Statistics
Matches: 237, Mismatches: 26, Indels: 11
0.86 0.09 0.04
Matches are distributed among these distances:
124 85 0.36
125 152 0.64
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (124 bp):
GAACTACTGTAGAAAAAAAGTGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGATAGTGCATC
CTGCTTGAAGCGTTTTTGACACTATTTTTCAGAATCGTCTTCTCAAAATTATTTTTCAG
Found at i:12561318 original size:34 final size:32
Alignment explanation
Indices: 12561273--12561400 Score: 127
Period size: 34 Copynumber: 3.9 Consensus size: 32
12561263 TTTAAAAAAA
*
12561273 TAAATCCTAATTTAATTAATTTTCTTAAAAACTC
1 TAAACCCTAATTTAATT-ATTTT-TTAAAAACTC
* *
12561307 TAAACCCTAATTTAATTTATTTATTTAAAACCCC
1 TAAACCCTAATTTAA-TTATTT-TTTAAAAACTC
*
12561341 TAAAACCTAATTTAATTATTATTTTAAAAAAACTC
1 TAAACCCTAATTTAATTATT-TTTT--AAAAACTC
*
12561376 TAAACCTTAATTT-A-TA-TTTTTAAAA
1 TAAACCCTAATTTAATTATTTTTTAAAA
12561401 TTCTTAAACC
Statistics
Matches: 81, Mismatches: 8, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
29 4 0.05
31 4 0.05
32 1 0.01
33 10 0.12
34 42 0.52
35 20 0.25
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (32 bp):
TAAACCCTAATTTAATTATTTTTTAAAAACTC
Found at i:12572711 original size:27 final size:27
Alignment explanation
Indices: 12572648--12572722 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 27
12572638 GTATAGGGGT
* *
12572648 GTGGTGCCTATCTGATAGGCAGCACCA
1 GTGGTACCTATCTGATAGGCGGCACCA
*** **
12572675 GTGACCCCTATCTGATAGGCGGCACTG
1 GTGGTACCTATCTGATAGGCGGCACCA
12572702 GTGGTACCTATCTGATAGGCG
1 GTGGTACCTATCTGATAGGCG
12572723 CCACACCTTG
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.20, C:0.25, G:0.31, T:0.24
Consensus pattern (27 bp):
GTGGTACCTATCTGATAGGCGGCACCA
Found at i:12572836 original size:40 final size:40
Alignment explanation
Indices: 12572791--12572871 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
12572781 TTTGATTAAA
*
12572791 AAGAGCTATGAATGTATGTTTGTATTTATTTTATATTTTC
1 AAGAGCTATGAAGGTATGTTTGTATTTATTTTATATTTTC
12572831 AAGAGCTATGAAGGTATGTTTGTATTTATTTTATATTTTC
1 AAGAGCTATGAAGGTATGTTTGTATTTATTTTATATTTTC
12572871 A
1 A
12572872 TTCATTCATA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.28, C:0.05, G:0.16, T:0.51
Consensus pattern (40 bp):
AAGAGCTATGAAGGTATGTTTGTATTTATTTTATATTTTC
Found at i:12579714 original size:14 final size:14
Alignment explanation
Indices: 12579695--12579735 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
12579685 AAAATTATAT
12579695 TATAAACATGAAGA
1 TATAAACATGAAGA
* *
12579709 TATAAA-A-AAAGT
1 TATAAACATGAAGA
12579721 TATAAACATGAAGA
1 TATAAACATGAAGA
12579735 T
1 T
12579736 GTATGTGTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 4
0.72 0.14 0.14
Matches are distributed among these distances:
12 9 0.43
13 2 0.10
14 10 0.48
ACGTcount: A:0.59, C:0.05, G:0.12, T:0.24
Consensus pattern (14 bp):
TATAAACATGAAGA
Found at i:12580091 original size:22 final size:22
Alignment explanation
Indices: 12580041--12580093 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
12580031 TTAATATAAC
12580041 TTATTTATAAAAAATAACTTTA
1 TTATTTATAAAAAATAACTTTA
* * *
12580063 -AAGTTATAACAAA-AACTTATA
1 TTATTTATAAAAAATAACTT-TA
12580084 TTATTTATAA
1 TTATTTATAA
12580094 GAAGTGTTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
20 5 0.21
21 12 0.50
22 7 0.29
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.42
Consensus pattern (22 bp):
TTATTTATAAAAAATAACTTTA
Found at i:12580165 original size:22 final size:24
Alignment explanation
Indices: 12580129--12580172 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
12580119 CTTATGTGTT
*
12580129 TATATTATATATTATAATAAATAA
1 TATATTATATATTATAAAAAATAA
12580153 TATATT-TAT-TTATAAAAAAT
1 TATATTATATATTATAAAAAAT
12580173 GTTATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 3 0.16
24 6 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TATATTATATATTATAAAAAATAA
Found at i:12580178 original size:22 final size:22
Alignment explanation
Indices: 12580128--12580186 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
12580118 ACTTATGTGT
*
12580128 TTATATTATATATTATAATAAATA
1 TTATATT-TAT-TTATAAAAAATA
* *
12580152 ATATATTTATTTATAAAAAATG
1 TTATATTTATTTATAAAAAATA
12580174 TTATAATTT-TTTA
1 TTAT-ATTTATTTA
12580187 CTTGAACTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 17 0.57
23 7 0.23
24 6 0.20
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TTATATTTATTTATAAAAAATA
Found at i:12583265 original size:2 final size:2
Alignment explanation
Indices: 12583258--12583294 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
12583248 AGCGAAAAAT
12583258 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
12583295 TGGAGAGTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12586617 original size:14 final size:15
Alignment explanation
Indices: 12586594--12586626 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
12586584 TTTTTACCGC
*
12586594 TTTTGTTAATTTGGT
1 TTTTGTTAATTTGAT
12586609 TTTTG-TAATTTGAT
1 TTTTGTTAATTTGAT
12586623 TTTT
1 TTTT
12586627 AATCAAAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.70
Consensus pattern (15 bp):
TTTTGTTAATTTGAT
Found at i:12587260 original size:11 final size:11
Alignment explanation
Indices: 12587246--12587275 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
12587236 AATTTTTTTT
12587246 TGTTTTTTTAC
1 TGTTTTTTTAC
*
12587257 TGTTTTGTTAC
1 TGTTTTTTTAC
12587268 TGTTTTTT
1 TGTTTTTT
12587276 CATTGTTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.07, G:0.13, T:0.73
Consensus pattern (11 bp):
TGTTTTTTTAC
Found at i:12591991 original size:35 final size:35
Alignment explanation
Indices: 12591945--12592017 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
12591935 AATTTGAGAC
12591945 TTCTAAGCATATGTTTTTCCTCTATAAATGAATAA
1 TTCTAAGCATATGTTTTTCCTCTATAAATGAATAA
12591980 TTCTAAGCATATGTTTTTCCTCTATAAATGAATAA
1 TTCTAAGCATATGTTTTTCCTCTATAAATGAATAA
12592015 TTC
1 TTC
12592018 AACTTAAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (35 bp):
TTCTAAGCATATGTTTTTCCTCTATAAATGAATAA
Found at i:12593101 original size:69 final size:69
Alignment explanation
Indices: 12593019--12593158 Score: 217
Period size: 69 Copynumber: 2.0 Consensus size: 69
12593009 GTTCTGGATA
** *
12593019 AAAGTACAAGTACTATGACTGATTCTCAAGTAGTGTTGGATGAGGATTCACCAACCATGGACGCA
1 AAAGTACAAGTACTATGAAGGATTCCCAAGTAGTGTTGGATGAGGATTCACCAACCATGGACGCA
12593084 GTTG
66 GTTG
* * * *
12593088 AAAGTAGAAGTACTATGAAGGATTCCCTAGTGGTGTTGGATGAGGATTCACCAACCATGGATGCA
1 AAAGTACAAGTACTATGAAGGATTCCCAAGTAGTGTTGGATGAGGATTCACCAACCATGGACGCA
12593153 GTTG
66 GTTG
12593157 AA
1 AA
12593159 GTTGCCATTA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (69 bp):
AAAGTACAAGTACTATGAAGGATTCCCAAGTAGTGTTGGATGAGGATTCACCAACCATGGACGCA
GTTG
Found at i:12595116 original size:30 final size:28
Alignment explanation
Indices: 12595080--12595153 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 28
12595070 ATTATTTTTT
12595080 ATTTTTTTAATTTTAAAATACTTTTATT-AA
1 ATTTTTTTAATTTTAAAAT--TTTT-TTAAA
*
12595110 ATTTTTTAAATTTTAAAATTTTTTTAAA
1 ATTTTTTTAATTTTAAAATTTTTTTAAA
12595138 ATACTTTTTTAATTTT
1 AT--TTTTTTAATTTT
12595154 TTTAAATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
27 2 0.05
28 8 0.21
30 29 0.74
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (28 bp):
ATTTTTTTAATTTTAAAATTTTTTTAAA
Found at i:12595134 original size:18 final size:18
Alignment explanation
Indices: 12595111--12595177 Score: 80
Period size: 18 Copynumber: 3.5 Consensus size: 18
12595101 TTTTATTAAA
12595111 TTTTTTAAATTTTAAAAT
1 TTTTTTAAATTTTAAAAT
**
12595129 TTTTTTAAAATACTTTTTTAAT
1 TTTTTT--AA-A-TTTTAAAAT
12595151 TTTTTTAAATTTTAAAAT
1 TTTTTTAAATTTTAAAAT
12595169 TTTTTTAAA
1 TTTTTTAAA
12595178 ATACTTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
18 22 0.54
19 1 0.02
20 4 0.10
21 1 0.02
22 13 0.32
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTTAAATTTTAAAAT
Found at i:12595147 original size:13 final size:11
Alignment explanation
Indices: 12595120--12595179 Score: 60
Period size: 11 Copynumber: 5.8 Consensus size: 11
12595110 ATTTTTTAAA
12595120 TTTTAAAATTT
1 TTTTAAAATTT
12595131 TTTTAAAATACTT
1 TTTTAAAAT--TT
12595144 TTTT--AATTT
1 TTTTAAAATTT
12595153 TTTT-AAA---
1 TTTTAAAATTT
12595160 TTTTAAAATTT
1 TTTTAAAATTT
12595171 TTTTAAAAT
1 TTTTAAAAT
12595180 ACTTTTTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
7 4 0.10
8 3 0.07
9 6 0.14
10 2 0.05
11 21 0.50
13 6 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATTT
Found at i:12595166 original size:40 final size:40
Alignment explanation
Indices: 12595090--12595195 Score: 185
Period size: 40 Copynumber: 2.6 Consensus size: 40
12595080 ATTTTTTTAA
*
12595090 TTTTAAAATACTTTTATTAAATTTTTTAAATTTTAAAATTT
1 TTTTAAAATACTTTT-TTAATTTTTTTAAATTTTAAAATTT
12595131 TTTTAAAATACTTTTTTAATTTTTTTAAATTTTAAAATTT
1 TTTTAAAATACTTTTTTAATTTTTTTAAATTTTAAAATTT
12595171 TTTTAAAATACTTTTTTTAATTTTT
1 TTTTAAAATAC-TTTTTTAATTTTT
12595196 ATTTTAATTT
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
40 35 0.56
41 28 0.44
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (40 bp):
TTTTAAAATACTTTTTTAATTTTTTTAAATTTTAAAATTT
Found at i:12608055 original size:43 final size:41
Alignment explanation
Indices: 12608000--12608112 Score: 138
Period size: 43 Copynumber: 2.7 Consensus size: 41
12607990 TTCAGTGATA
* * *
12608000 CGGGTAATCAGCACATAGCAACCCCTTTCACAATCAAGGATAT
1 CGGGGAATCAGCACTTAGCAACCCCTTT-ACAATCAAGAAT-T
* *
12608043 -GGTGGAATCAGCACTTAGCAACCACCTTTAGAATCAATAATT
1 CGG-GGAATCAGCACTTAGCAACC-CCTTTACAATCAAGAATT
12608085 CGGGGAATCAGCACTTAGCAACCCCTTT
1 CGGGGAATCAGCACTTAGCAACCCCTTT
12608113 TTGATCAGTG
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
41 5 0.08
42 23 0.37
43 29 0.47
44 5 0.08
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.23
Consensus pattern (41 bp):
CGGGGAATCAGCACTTAGCAACCCCTTTACAATCAAGAATT
Found at i:12608132 original size:41 final size:42
Alignment explanation
Indices: 12608005--12608151 Score: 138
Period size: 41 Copynumber: 3.5 Consensus size: 42
12607995 TGATACGGGT
* * * ** *
12608005 AATCAGCACATAGCAACCCCTTTCACAATCAAGGATAT-GGTGG
1 AATCAGCACTTAGCAACCCCTTTTAGAATCAATAAT-TCAG-GG
*
12608048 AATCAGCACTTAGCAACCACC-TTTAGAATCAATAATTCGGGG
1 AATCAGCACTTAGCAACC-CCTTTTAGAATCAATAATTCAGGG
* * *
12608090 AATCAGCACTTAGCAACCCCTTTTTG-ATCAGTGATTCAGGG
1 AATCAGCACTTAGCAACCCCTTTTAGAATCAATAATTCAGGG
* *
12608131 AATCTGCACTTGGCAACCCCT
1 AATCAGCACTTAGCAACCCCT
12608152 AACATTCAAT
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
41 33 0.37
42 25 0.28
43 30 0.33
44 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (42 bp):
AATCAGCACTTAGCAACCCCTTTTAGAATCAATAATTCAGGG
Found at i:12612258 original size:26 final size:26
Alignment explanation
Indices: 12612229--12612278 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
12612219 AGGATACGGT
12612229 GGAATCAT-CACTTAGCAACCCCTTGG
1 GGAATC-TGCACTTAGCAACCCCTTGG
12612255 GGAATCTGCACTTAGCAACCCCTT
1 GGAATCTGCACTTAGCAACCCCTT
12612279 TTTGATCAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (26 bp):
GGAATCTGCACTTAGCAACCCCTTGG
Found at i:12612310 original size:41 final size:41
Alignment explanation
Indices: 12612253--12612360 Score: 171
Period size: 41 Copynumber: 2.6 Consensus size: 41
12612243 GCAACCCCTT
* *
12612253 GGGGAATCTGCACTTAGCAACCCCTTTTTGATCAGTGATTC
1 GGGGAATCTACACTTAGCAACCCCTTTTTGATAAGTGATTC
* * *
12612294 GGGGAATCTCCACTTAGCATCCCCTTTTTGATAAGTGGTTC
1 GGGGAATCTACACTTAGCAACCCCTTTTTGATAAGTGATTC
12612335 GGGGAATCTACACTTAGCAACCCCTT
1 GGGGAATCTACACTTAGCAACCCCTT
12612361 ACATTCAATG
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 61 1.00
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.31
Consensus pattern (41 bp):
GGGGAATCTACACTTAGCAACCCCTTTTTGATAAGTGATTC
Found at i:12612622 original size:30 final size:30
Alignment explanation
Indices: 12612588--12612644 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
12612578 AAAAGCATAC
12612588 TTTCAAAAAATTA-CATTTTTGCCCCTAAAA
1 TTTCAAAAAATTATCA-TTTTGCCCCTAAAA
* *
12612618 TTTCATAAAATTATGATTTTGCCCCTA
1 TTTCAAAAAATTATCATTTTGCCCCTA
12612645 GACTCGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.96
31 1 0.04
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.40
Consensus pattern (30 bp):
TTTCAAAAAATTATCATTTTGCCCCTAAAA
Found at i:12620844 original size:27 final size:27
Alignment explanation
Indices: 12620806--12620882 Score: 120
Period size: 27 Copynumber: 2.9 Consensus size: 27
12620796 TAGTATTGGC
12620806 GCCTATCTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
12620833 GCCTACCTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
12620860 GCC-ATTCTGAGAGGCGCCAATGG
1 GCCTA-TCTGGGAGGCGCCAATGG
12620883 GCGGGGCTTG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 1 0.02
27 45 0.98
ACGTcount: A:0.17, C:0.25, G:0.39, T:0.19
Consensus pattern (27 bp):
GCCTATCTGGGAGGCGCCAATGGTGGT
Found at i:12621106 original size:11 final size:11
Alignment explanation
Indices: 12621092--12621127 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
12621082 AATTTAATTT
*
12621092 ATTAGTAATAA
1 ATTACTAATAA
12621103 ATTACTAATAA
1 ATTACTAATAA
*
12621114 GTTACTAATAA
1 ATTACTAATAA
12621125 ATT
1 ATT
12621128 TATAACATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.39
Consensus pattern (11 bp):
ATTACTAATAA
Found at i:12621253 original size:27 final size:27
Alignment explanation
Indices: 12621217--12621312 Score: 123
Period size: 27 Copynumber: 3.8 Consensus size: 27
12621207 ATATACCGAC
12621217 ATTACAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTATAAT
12621244 ATTACAATATTCATAC--AA--A-AA-
1 ATTACAATATTCATACAAAATTATAAT
* *
12621265 ATTGCAATATTCATATAAAATTATAAT
1 ATTACAATATTCATACAAAATTATAAT
*
12621292 ATTACAATATTCATACTAAAT
1 ATTACAATATTCATACAAAAT
12621313 ATAGATAATT
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
21 14 0.24
22 2 0.03
23 3 0.05
25 3 0.05
26 2 0.03
27 34 0.59
ACGTcount: A:0.51, C:0.11, G:0.01, T:0.36
Consensus pattern (27 bp):
ATTACAATATTCATACAAAATTATAAT
Found at i:12621285 original size:48 final size:48
Alignment explanation
Indices: 12621164--12621307 Score: 177
Period size: 48 Copynumber: 3.0 Consensus size: 48
12621154 AATTAATTAT
*
12621164 AAAATAATTACAATATTCATACAAAAAATTACAATATTACAATA-T-ATAC
1 AAAA-AATTACAATATTCAT--AAAAAATTATAATATTACAATATTCATAC
** * *
12621213 -CGACATTACAATATTCATACAAAATTATAATATTACAATATTCATAC
1 AAAAAATTACAATATTCATAAAAAATTATAATATTACAATATTCATAC
* *
12621260 AAAAAATTGCAATATTCATATAAAATTATAATATTACAATATTCATAC
1 AAAAAATTACAATATTCATAAAAAATTATAATATTACAATATTCATAC
12621308 TAAATATAGA
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
45 20 0.24
46 1 0.01
47 18 0.22
48 43 0.52
ACGTcount: A:0.52, C:0.13, G:0.01, T:0.33
Consensus pattern (48 bp):
AAAAAATTACAATATTCATAAAAAATTATAATATTACAATATTCATAC
Found at i:12621416 original size:11 final size:12
Alignment explanation
Indices: 12621399--12621443 Score: 90
Period size: 12 Copynumber: 3.8 Consensus size: 12
12621389 TATGAATTTT
12621399 TATTTTTAAATA
1 TATTTTTAAATA
12621411 TATTTTTAAATA
1 TATTTTTAAATA
12621423 TATTTTTAAATA
1 TATTTTTAAATA
12621435 TATTTTTAA
1 TATTTTTAA
12621444 TATNNNNNNN
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTTTTAAATA
Found at i:12621862 original size:20 final size:21
Alignment explanation
Indices: 12621820--12621863 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
12621810 NNNNTTTTTA
12621820 TTTTTTATTTTTAAAATACTT
1 TTTTTTATTTTTAAAATACTT
12621841 TTTTTTATTTTTAAAA-A-TT
1 TTTTTTATTTTTAAAATACTT
12621860 TTTT
1 TTTT
12621864 GGTGTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.26
20 1 0.04
21 16 0.70
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTTATTTTTAAAATACTT
Found at i:12622097 original size:27 final size:27
Alignment explanation
Indices: 12622025--12622086 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
12622015 GGTCTAGTAA
*
12622025 TGGCGCCTCTCTATAAGGCACCTTCAT
1 TGGCGCCTCTCTATGAGGCACCTTCAT
12622052 TGGCGCCTCTCTATGAGGCACCTTCAT
1 TGGCGCCTCTCTATGAGGCACCTTCAT
12622079 TGGCGCCT
1 TGGCGCCT
12622087 ACCTGATAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.15, C:0.34, G:0.23, T:0.29
Consensus pattern (27 bp):
TGGCGCCTCTCTATGAGGCACCTTCAT
Found at i:12622163 original size:12 final size:12
Alignment explanation
Indices: 12622148--12622179 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12622138 CGTATTTTTT
12622148 TTAAAAAAATTA
1 TTAAAAAAATTA
12622160 TTAAAAAAA-TA
1 TTAAAAAAATTA
12622171 -TAAAAAAAT
1 TTAAAAAAAT
12622180 ATTTTATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 8 0.42
11 2 0.11
12 9 0.47
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
TTAAAAAAATTA
Found at i:12636214 original size:30 final size:31
Alignment explanation
Indices: 12636178--12636237 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
12636168 ACTCTAGTAA
12636178 CTTAAAT-AAAACTTTTAAATAGTTCAATGG
1 CTTAAATGAAAACTTTTAAATAGTTCAATGG
* *
12636208 CTTAAATGAAAATTTTTTAATAGTTCAATG
1 CTTAAATGAAAACTTTTAAATAGTTCAATG
12636238 ACCATTTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (31 bp):
CTTAAATGAAAACTTTTAAATAGTTCAATGG
Found at i:12638619 original size:21 final size:21
Alignment explanation
Indices: 12638595--12638635 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12638585 CCCGCCCATA
*
12638595 TTATTTTTTAA-AATATTTATT
1 TTATTATTTAATAAT-TTTATT
12638616 TTATTATTTAATAATTTTAT
1 TTATTATTTAATAATTTTAT
12638636 ATGTTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTATTATTTAATAATTTTATT
Found at i:12652755 original size:72 final size:72
Alignment explanation
Indices: 12652636--12652771 Score: 175
Period size: 72 Copynumber: 1.9 Consensus size: 72
12652626 ATTCATACCC
*** * * *
12652636 CCATGATGGGGTGAAACATGAGCAGGAGAGGGAGACTGAGATAAAACAGGACCAGGTGAGGCAGT
1 CCATGATGGGGTGAAACATGAGCAGGAGAAACAGACTGAGAGAAAACAGAACCAGGTGAAGCAGT
12652701 CCTATCA
66 CCTATCA
* * *
12652708 CCATGATGGGGTGAAACA-GAAGCAGGAGAAACAGGCTGAGGGGAAACAGAACCAGGTGAAGCAG
1 CCATGATGGGGTGAAACATG-AGCAGGAGAAACAGACTGAGAGAAAACAGAACCAGGTGAAGCAG
12652772 GCAGGTATTC
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
71 1 0.02
72 53 0.98
ACGTcount: A:0.37, C:0.16, G:0.36, T:0.11
Consensus pattern (72 bp):
CCATGATGGGGTGAAACATGAGCAGGAGAAACAGACTGAGAGAAAACAGAACCAGGTGAAGCAGT
CCTATCA
Found at i:12663354 original size:6 final size:7
Alignment explanation
Indices: 12663338--12663389 Score: 81
Period size: 7 Copynumber: 7.6 Consensus size: 7
12663328 TCTTTGAAGC
12663338 TTTTTAT
1 TTTTTAT
12663345 TTTTTAT
1 TTTTTAT
12663352 TTTTTAT
1 TTTTTAT
12663359 TTTTTAT
1 TTTTTAT
12663366 TTTTT-T
1 TTTTTAT
12663372 ATTTTTA-
1 -TTTTTAT
12663379 TTTTTAT
1 TTTTTAT
12663386 TTTT
1 TTTT
12663390 GCAAGAGTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
6 7 0.17
7 35 0.83
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTAT
Found at i:12664849 original size:13 final size:13
Alignment explanation
Indices: 12664798--12664860 Score: 76
Period size: 13 Copynumber: 4.9 Consensus size: 13
12664788 AGTTTGGCAA
12664798 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
12664811 TAC-TTTGAAAAG
1 TGCTTTTGAAAAG
*
12664823 TGC-TGTGTAAAAG
1 TGCTTTTG-AAAAG
*
12664836 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
12664849 TGCTTTTGAAAA
1 TGCTTTTGAAAA
12664861 TTTTGGTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
12 14 0.33
13 25 0.60
14 3 0.07
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.37
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:12670627 original size:12 final size:12
Alignment explanation
Indices: 12670603--12670663 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
12670593 CAAATAAATG
*
12670603 AAAGAAAAAGAA
1 AAAGAAAGAGAA
*
12670615 AAAGAAAGTGAAA
1 AAAGAAAGAG-AA
* *
12670628 CGAAACATAAGGGAA
1 --AAAGA-AAGAGAA
12670643 AAAGAAAGAGAA
1 AAAGAAAGAGAA
12670655 AAAGAAAGA
1 AAAGAAAGA
12670664 AAAGTTAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
12 23 0.59
13 6 0.15
15 6 0.15
16 4 0.10
ACGTcount: A:0.70, C:0.03, G:0.23, T:0.03
Consensus pattern (12 bp):
AAAGAAAGAGAA
Found at i:12671228 original size:206 final size:204
Alignment explanation
Indices: 12670831--12671256 Score: 703
Period size: 206 Copynumber: 2.1 Consensus size: 204
12670821 AATTTTAGTA
* * *
12670831 TTAGGGATTAAATTGATAGATTTTTAAGTTAGAAGTGAAAAAGTATTGAATTGTAGAATAAGTTG
1 TTAGGGATTAAATTGATAGATTTTTAAGTTAGAAGTGAAAAAGTATTGAATTATAGAATAAATTA
*
12670896 TAAATTTTGAGTAATAGGGACTAAATTGTAAAATTTGAAATTTAGGGATTTAAGTGAAATTAGAG
66 TAAATTTTGAGTAATAGGGACTAAATTGTAAAATTTAAAATTTAGGGATTTAAGTGAAATTAGAG
*
12670961 AGTTAAAACTAGTTTAAAGTGAAAATTGAATGAAAATATAGAATTAATTGTGAAGAAATAAAATT
131 AGTTAAAACTAGTTTAAAGTGAAAATTGAATGAAAATATAGAATTAATTGTAAAGAAATAAAATT
12671026 AGTCTCGGT
196 AGTCTCGGT
* *
12671035 TTTGGGATTAATTTGATAGATTTTTAAGTTAGAAGTGAAAAA-TGATTGAATTATAGAATAAATT
1 TTAGGGATTAAATTGATAGATTTTTAAGTTAGAAGTGAAAAAGT-ATTGAATTATAGAATAAATT
12671099 ATAAATTTTGAGT-ATCAGGGACTAAATTGTGAAAATTTTAAAATTTAGGGATTTAAGTGAAATT
65 ATAAATTTTGAGTAAT-AGGGACTAAATTGT-AAAA-TTTAAAATTTAGGGATTTAAGTGAAATT
* * *
12671163 AGAGAGTTAAATCTAGTTTAAAGTGGAAATTGAATGAAAATATAGAATTGATTGTAAAGAAATAA
127 AGAGAGTTAAAACTAGTTTAAAGTGAAAATTGAATGAAAATATAGAATTAATTGTAAAGAAATAA
12671228 AATTAGTCTCGGT
192 AATTAGTCTCGGT
*
12671241 TTAGGGACTAAATTGA
1 TTAGGGATTAAATTGA
12671257 AATTTAGACA
Statistics
Matches: 205, Mismatches: 13, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
203 3 0.01
204 84 0.41
205 4 0.02
206 114 0.56
ACGTcount: A:0.42, C:0.02, G:0.20, T:0.35
Consensus pattern (204 bp):
TTAGGGATTAAATTGATAGATTTTTAAGTTAGAAGTGAAAAAGTATTGAATTATAGAATAAATTA
TAAATTTTGAGTAATAGGGACTAAATTGTAAAATTTAAAATTTAGGGATTTAAGTGAAATTAGAG
AGTTAAAACTAGTTTAAAGTGAAAATTGAATGAAAATATAGAATTAATTGTAAAGAAATAAAATT
AGTCTCGGT
Found at i:12671631 original size:2 final size:2
Alignment explanation
Indices: 12671574--12671622 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
12671564 ATTGAATTGG
12671574 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12671616 TA TA TA T
1 TA TA TA T
12671623 TGCATATATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12671862 original size:37 final size:39
Alignment explanation
Indices: 12671817--12671906 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 39
12671807 TTCGTGGAGG
12671817 CATTGGGTGCCAA-T-TTACTTCGGT-TTAACCGATGAGA
1 CATTGGGTGCCAATTATTACTTC-GTATTAACCGATGAGA
* * *
12671854 CATTGGGTGTCAATTTATTACTTCGTATTATCCGATGAGG
1 CATTGGGTGCCAA-TTATTACTTCGTATTAACCGATGAGA
*
12671894 CACTGGGTGCCAA
1 CATTGGGTGCCAA
12671907 ATTGGTGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
37 12 0.27
39 3 0.07
40 29 0.66
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (39 bp):
CATTGGGTGCCAATTATTACTTCGTATTAACCGATGAGA
Found at i:12673388 original size:36 final size:36
Alignment explanation
Indices: 12673347--12673537 Score: 229
Period size: 36 Copynumber: 5.0 Consensus size: 36
12673337 GGTAGCTTTA
12673347 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
12673383 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGAT-A-----AG---T
12673428 AGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 -GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
12673465 GTTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
** *
12673501 GCTATTCTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
12673537 G
1 G
12673538 GTAGCTTAGC
Statistics
Matches: 136, Mismatches: 9, Indels: 20
0.82 0.05 0.12
Matches are distributed among these distances:
36 98 0.72
37 2 0.01
40 2 0.01
42 2 0.01
45 2 0.01
46 30 0.22
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:12673448 original size:82 final size:82
Alignment explanation
Indices: 12673311--12673501 Score: 337
Period size: 82 Copynumber: 2.3 Consensus size: 82
12673301 TTTGAGTACT
*
12673311 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
12673376 GATAAGTGCTACACTTA
66 GATAAGTGCTACACTTA
*
12673393 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
* *
12673458 GATAAGTGTTATACTTA
66 GATAAGTGCTACACTTA
*
12673475 TCTGATCAAGTGAAAAAGTGATAAGTG
1 TCTGATCAAGAGAAAAAGTGATAAGTG
12673502 CTATTCTTAT
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 104 1.00
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.29
Consensus pattern (82 bp):
TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGTGCTACACTTA
Found at i:12683276 original size:13 final size:13
Alignment explanation
Indices: 12683240--12683286 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
12683230 AAACCAAACC
*
12683240 TTTCAAAAGCACT
1 TTTCAAAAACACT
* *
12683253 TTTCCACAACACT
1 TTTCAAAAACACT
*
12683266 TTTCAAAAACACA
1 TTTCAAAAACACT
12683279 TTTCAAAA
1 TTTCAAAA
12683287 GCAATGAAGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.43, C:0.26, G:0.02, T:0.30
Consensus pattern (13 bp):
TTTCAAAAACACT
Found at i:12685080 original size:22 final size:22
Alignment explanation
Indices: 12685055--12685097 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12685045 ATAAACTAGT
* *
12685055 AGCAATATAATAGCAAAATGGC
1 AGCAAAATAACAGCAAAATGGC
*
12685077 AGCAAAATAACATCAAAATGG
1 AGCAAAATAACAGCAAAATGG
12685098 TAACAAGCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.53, C:0.14, G:0.16, T:0.16
Consensus pattern (22 bp):
AGCAAAATAACAGCAAAATGGC
Found at i:12690502 original size:92 final size:92
Alignment explanation
Indices: 12690345--12690527 Score: 339
Period size: 92 Copynumber: 2.0 Consensus size: 92
12690335 AGTTGTTTAT
*
12690345 ATTATTAGATGAATTTAGCTGCATCTATGCATCTATATGATGCTTTTATTCTGTTGTTCATGATG
1 ATTATTAGATGAATTTAGCTGCATCTATGCATCTATATGATGCTTTTATTCTGTTGCTCATGATG
12690410 GATGAGATGGAGATGACTAGCACAGCC
66 GATGAGATGGAGATGACTAGCACAGCC
* *
12690437 ATTATTAGGTGAATTTAGCTGCATCTATGTATCTATATGATGCTTTTATTCTGTTGCTCATGATG
1 ATTATTAGATGAATTTAGCTGCATCTATGCATCTATATGATGCTTTTATTCTGTTGCTCATGATG
12690502 GATGAGATGGAGATGACTAGCACAGC
66 GATGAGATGGAGATGACTAGCACAGC
12690528 TATGAAAGAG
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 88 1.00
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (92 bp):
ATTATTAGATGAATTTAGCTGCATCTATGCATCTATATGATGCTTTTATTCTGTTGCTCATGATG
GATGAGATGGAGATGACTAGCACAGCC
Found at i:12694000 original size:20 final size:21
Alignment explanation
Indices: 12693962--12694010 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
12693952 GAAGTATCGC
*
12693962 AAATT-TATTTTGTAAGAA-T
1 AAATTCTATTTTATAAGAATT
*
12693981 AAATTCTATTTTATAGGAATT
1 AAATTCTATTTTATAAGAATT
12694002 ATAATTCTA
1 A-AATTCTA
12694011 CCAGTTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.20
20 11 0.44
21 2 0.08
22 7 0.28
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (21 bp):
AAATTCTATTTTATAAGAATT
Found at i:12716475 original size:99 final size:99
Alignment explanation
Indices: 12716304--12716504 Score: 402
Period size: 99 Copynumber: 2.0 Consensus size: 99
12716294 TATTAGATAA
12716304 TACTGTTTCATATTATTAATACACAGGCTCGCTTTGTTTATATTATAATAAATTGTTAATAATCA
1 TACTGTTTCATATTATTAATACACAGGCTCGCTTTGTTTATATTATAATAAATTGTTAATAATCA
12716369 TTGCCATCTGACGTTGTAGAAACTAAAGATTAAC
66 TTGCCATCTGACGTTGTAGAAACTAAAGATTAAC
12716403 TACTGTTTCATATTATTAATACACAGGCTCGCTTTGTTTATATTATAATAAATTGTTAATAATCA
1 TACTGTTTCATATTATTAATACACAGGCTCGCTTTGTTTATATTATAATAAATTGTTAATAATCA
12716468 TTGCCATCTGACGTTGTAGAAACTAAAGATTAAC
66 TTGCCATCTGACGTTGTAGAAACTAAAGATTAAC
12716502 TAC
1 TAC
12716505 CTCAGGAAGT
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 102 1.00
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.39
Consensus pattern (99 bp):
TACTGTTTCATATTATTAATACACAGGCTCGCTTTGTTTATATTATAATAAATTGTTAATAATCA
TTGCCATCTGACGTTGTAGAAACTAAAGATTAAC
Found at i:12728983 original size:15 final size:14
Alignment explanation
Indices: 12728959--12728997 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
12728949 ATATATTTCA
12728959 AATATTTATTTTTG
1 AATATTTATTTTTG
12728973 AATATTTTATTTTT-
1 AATA-TTTATTTTTG
12728987 AATTATTTATT
1 AA-TATTTATT
12728998 AAGTTATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (14 bp):
AATATTTATTTTTG
Found at i:12730317 original size:39 final size:39
Alignment explanation
Indices: 12730274--12730352 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
12730264 ATCAATGGCT
12730274 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGATTAC
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGATTAC
* * *
12730313 ACAATTAGAAGTTGTATACAATTAGAACTTTAAGATTAC
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGATTAC
12730352 A
1 A
12730353 TTATCATATC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (39 bp):
ACAATTAAAAGCTGTATACAATTAGAACTCTAAGATTAC
Found at i:12735397 original size:39 final size:39
Alignment explanation
Indices: 12735354--12735432 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
12735344 ATCACTGGCT
12735354 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGATTAC
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGATTAC
*
12735393 ACAATTAGAAGCTGTATACAATTAGAACTCTAAGATTAC
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGATTAC
12735432 A
1 A
12735433 TAATCATATC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (39 bp):
ACAATTAAAAGCTGTATACAATTAGAACTCTAAGATTAC
Found at i:12735415 original size:17 final size:17
Alignment explanation
Indices: 12735353--12735419 Score: 62
Period size: 17 Copynumber: 3.6 Consensus size: 17
12735343 CATCACTGGC
*
12735353 TACAATTAAAAGCTGTA
1 TACAATTAGAAGCTGTA
*
12735370 TACAATTAGAACTCTAAGATTA
1 TACAATTAGAA-GCT--G--TA
*
12735392 CACAATTAGAAGCTGTA
1 TACAATTAGAAGCTGTA
12735409 TACAATTAGAA
1 TACAATTAGAA
12735420 CTCTAAGATT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
17 22 0.55
18 2 0.05
19 1 0.03
20 1 0.03
21 2 0.05
22 12 0.30
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.28
Consensus pattern (17 bp):
TACAATTAGAAGCTGTA
Found at i:12737501 original size:22 final size:22
Alignment explanation
Indices: 12737460--12737502 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12737450 ACAGCAGAAC
* *
12737460 AGGTTTTTAGCGGCATTTTTTT
1 AGGTCTTTAGCGGCACTTTTTT
*
12737482 AGGTCTTTAGCGGCGCTTTTT
1 AGGTCTTTAGCGGCACTTTTT
12737503 AACGCCACTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.14, G:0.26, T:0.49
Consensus pattern (22 bp):
AGGTCTTTAGCGGCACTTTTTT
Found at i:12737647 original size:43 final size:42
Alignment explanation
Indices: 12737573--12737885 Score: 389
Period size: 43 Copynumber: 7.4 Consensus size: 42
12737563 ACGTCACTAA
*
12737573 CTTTTGCGGCGCTTACGTAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTA-G-AAAAAAACGCCGCTAAAGATCATGTT
* *
12737617 CTTTAGCGGCGCTTAAAAAACAAACGCCGCTAAAGATCATGCT
1 CTTTAGCGGCGCTTAGAAAA-AAACGCCGCTAAAGATCATGTT
* * *
12737660 CTTTAGCGGCGCTTAGAAAACAAACGCCCCTAAAGATCACGCT
1 CTTTAGCGGCGCTTAGAAAA-AAACGCCGCTAAAGATCATGTT
* *
12737703 CTTTAGCGGCGCTTAG--AAAAACGCCCCTAAAGATCATGCT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
*
12737743 CTTTAGCGGCGCTTATAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
* *
12737785 CTTTAGCGGCGCTTAGGAAAAAGCGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
* ** * *
12737827 CTTTTAGCGGCGCTTTGGAAGGAAACGCCGCTAAA-AGTAATATT
1 C-TTTAGCGGCGC-TTAGAAAAAAACGCCGCTAAAGA-TCATGTT
*
12737871 CTATAGCGGCGCTTA
1 CTTTAGCGGCGCTTA
12737886 TTTCACAAAC
Statistics
Matches: 241, Mismatches: 22, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
40 36 0.15
41 2 0.01
42 68 0.28
43 99 0.41
44 36 0.15
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
Found at i:12737833 original size:125 final size:126
Alignment explanation
Indices: 12737593--12737841 Score: 394
Period size: 125 Copynumber: 2.0 Consensus size: 126
12737583 GCTTACGTAA
* *
12737593 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAAAAAACAAACGCCGCTAAAGATCATG
1 AAAAACGCCCCTAAAGATCATGCTCTTTAGCGGCGCTTAAAAAACAAACGCCGCTAAAGATCATG
12737658 CTCTTTAGCGGCGCTTAGAAAACAAACGCCCCTAAAGATCACGCTCTTTAGCGGCGCTTAG
66 CTCTTTAGCGGCGCTTAGAAAACAAACGCCCCTAAAGATCACGCTCTTTAGCGGCGCTTAG
*
12737719 AAAAACGCCCCTAAAGATCATGCTCTTTAGCGGCGCTTATAAAA-AAACGCCGCTAAAGATCATG
1 AAAAACGCCCCTAAAGATCATGCTCTTTAGCGGCGCTTAAAAAACAAACGCCGCTAAAGATCATG
* * * * * *
12737783 TTCTTTAGCGGCGCTTAGGAAA-AAGCGCCGCTAAAGATCATGTTCTTTTAGCGGCGCTT
66 CTCTTTAGCGGCGCTTAGAAAACAAACGCCCCTAAAGATCACGCTC-TTTAGCGGCGCTT
12737842 TGGAAGGAAA
Statistics
Matches: 113, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
124 19 0.17
125 53 0.47
126 41 0.36
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.23
Consensus pattern (126 bp):
AAAAACGCCCCTAAAGATCATGCTCTTTAGCGGCGCTTAAAAAACAAACGCCGCTAAAGATCATG
CTCTTTAGCGGCGCTTAGAAAACAAACGCCCCTAAAGATCACGCTCTTTAGCGGCGCTTAG
Found at i:12737880 original size:168 final size:169
Alignment explanation
Indices: 12737573--12737885 Score: 443
Period size: 168 Copynumber: 1.9 Consensus size: 169
12737563 ACGTCACTAA
*
12737573 CTTTTGCGGCGCTTACGTAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAAAAAAC
1 CTTTAGCGGCGCTTAC-TAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAAAAAAC
* *
12737638 AAACGCCGCTAAAGATCATGCTCTTTAGCGGCGCTTAGAAAACAAACGCCCCTAAAGATCACGCT
65 AAACGCCGCTAAAGATCATGCTCTTTAGCGGCGCTTAGAAAACAAACGCCCCTAAAGATAACACT
*
12737703 CTTTAGCGGCGCTTAGAAAAACGCCCCTAAAGATCATGCT
130 CTATAGCGGCGCTTAGAAAAACGCCCCTAAAGATCATGCT
**
12737743 CTTTAGCGGCGCTTA-TAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAA-A
1 CTTTAGCGGCGCTTACTAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAAAAAACA
* * * * ** * * *
12737806 AGCGCCGCTAAAGATCATGTTCTTTTAGCGGCGCTTTGGAAGGAAACGCCGCTAAA-AGTAATAT
66 AACGCCGCTAAAGATCATGCTC-TTTAGCGGCGCTTAGAAAACAAACGCCCCTAAAGA-TAACAC
12737870 TCTATAGCGGCGCTTA
129 TCTATAGCGGCGCTTA
12737886 TTTCACAAAC
Statistics
Matches: 126, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
167 22 0.17
168 90 0.71
170 14 0.11
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (169 bp):
CTTTAGCGGCGCTTACTAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAAAAAACA
AACGCCGCTAAAGATCATGCTCTTTAGCGGCGCTTAGAAAACAAACGCCCCTAAAGATAACACTC
TATAGCGGCGCTTAGAAAAACGCCCCTAAAGATCATGCT
Found at i:12738341 original size:21 final size:21
Alignment explanation
Indices: 12738317--12738385 Score: 102
Period size: 21 Copynumber: 3.3 Consensus size: 21
12738307 GCTTCTATTG
*
12738317 CTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
*
12738338 CTGCTTCTCTCGCTGTAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
12738359 CTGCTTCCCTCGCTGCCGCCT
1 CTGCTTCTCTCGCTGCAGCCT
12738380 CTGCTT
1 CTGCTT
12738386 TAAGTTGCTG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.01, C:0.43, G:0.20, T:0.35
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:12746105 original size:16 final size:17
Alignment explanation
Indices: 12746084--12746182 Score: 73
Period size: 16 Copynumber: 5.9 Consensus size: 17
12746074 GATTTAGGAA
12746084 TAAGTTATGTA-TTATG
1 TAAGTTATGTAGTTATG
*
12746100 TAAGTTATGTAAGTTGTG
1 TAAGTTATGT-AGTTATG
* *
12746118 TAAGTTGTGTAAGTTGTG
1 TAAGTTATGT-AGTTATG
* *
12746136 T-A-TTATGAAACTTATG
1 TAAGTTATG-TAGTTATG
* *
12746152 TACGTTATGT-CTTATG
1 TAAGTTATGTAGTTATG
12746168 TAAGTTATGTA-TTAT
1 TAAGTTATGTAGTTAT
12746183 TATGTAAGTA
Statistics
Matches: 68, Mismatches: 9, Indels: 12
0.76 0.10 0.13
Matches are distributed among these distances:
16 39 0.57
17 2 0.03
18 27 0.40
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.47
Consensus pattern (17 bp):
TAAGTTATGTAGTTATG
Found at i:12746109 original size:9 final size:9
Alignment explanation
Indices: 12746084--12746191 Score: 86
Period size: 9 Copynumber: 12.6 Consensus size: 9
12746074 GATTTAGGAA
12746084 TAAGTTATG
1 TAAGTTATG
12746093 T-A-TTATG
1 TAAGTTATG
12746100 TAAGTTATG
1 TAAGTTATG
*
12746109 TAAGTTGTG
1 TAAGTTATG
*
12746118 TAAGTTGTG
1 TAAGTTATG
*
12746127 TAAGTTGTG
1 TAAGTTATG
12746136 T-A-TTATG
1 TAAGTTATG
* *
12746143 AAACTTATG
1 TAAGTTATG
*
12746152 TACGTTATG
1 TAAGTTATG
*
12746161 T--CTTATG
1 TAAGTTATG
12746168 TAAGTTATG
1 TAAGTTATG
12746177 TATTA-TTATG
1 TA--AGTTATG
12746187 TAAGT
1 TAAGT
12746192 AGGGATGTAG
Statistics
Matches: 82, Mismatches: 8, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
7 16 0.20
8 5 0.06
9 53 0.65
10 7 0.09
11 1 0.01
ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:12746282 original size:12 final size:12
Alignment explanation
Indices: 12746265--12746309 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
12746255 ATGTTATGTA
12746265 TTATTATGTAAG
1 TTATTATGTAAG
*
12746277 TTATTATGTAGG
1 TTATTATGTAAG
12746289 TTATTATGTAAG
1 TTATTATGTAAG
*
12746301 TCATTATGT
1 TTATTATGT
12746310 TGGTTATGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.29, C:0.02, G:0.18, T:0.51
Consensus pattern (12 bp):
TTATTATGTAAG
Found at i:12746297 original size:24 final size:24
Alignment explanation
Indices: 12746258--12746316 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
12746248 TTTATGGATG
*
12746258 TTATGTA--TTATTATGTAAGTTA
1 TTATGTAGGTTATTATGTAAGTCA
12746280 TTATGTAGGTTATTATGTAAGTCA
1 TTATGTAGGTTATTATGTAAGTCA
*
12746304 TTATGTTGGTTAT
1 TTATGTAGGTTAT
12746317 GTAAGTTGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
22 7 0.21
24 26 0.79
ACGTcount: A:0.27, C:0.02, G:0.19, T:0.53
Consensus pattern (24 bp):
TTATGTAGGTTATTATGTAAGTCA
Found at i:12746318 original size:21 final size:22
Alignment explanation
Indices: 12746268--12746322 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 22
12746258 TTATGTATTA
*
12746268 TTATGTAAGTTATTATGTAGGTT
1 TTATGTAAGTCATTATGTAGG-T
*
12746291 ATTATGTAAGTCATTATGTTGG-
1 -TTATGTAAGTCATTATGTAGGT
12746313 TTATGTAAGT
1 TTATGTAAGT
12746323 TGTGATATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 10 0.34
24 19 0.66
ACGTcount: A:0.27, C:0.02, G:0.22, T:0.49
Consensus pattern (22 bp):
TTATGTAAGTCATTATGTAGGT
Found at i:12748404 original size:45 final size:45
Alignment explanation
Indices: 12748315--12748404 Score: 103
Period size: 45 Copynumber: 2.0 Consensus size: 45
12748305 GCGATTTAGG
* * * *
12748315 GATTTCGGATTTCAAGAAATTAGGCAAGAAAGGAGGCGATTTTCA
1 GATTTCGGAATTCAAGAAATTAGGCAAGAAAGGACGCCAATTTCA
*
12748360 GATTTGGGAATTCAAGAAATT-GGCAAG-AAGGACGCAACAATTTCA
1 GATTTCGGAATTCAAGAAATTAGGCAAGAAAGGACGC--CAATTTCA
12748405 CAGAGAAAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
43 7 0.18
44 6 0.16
45 25 0.66
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.24
Consensus pattern (45 bp):
GATTTCGGAATTCAAGAAATTAGGCAAGAAAGGACGCCAATTTCA
Found at i:12749599 original size:7 final size:7
Alignment explanation
Indices: 12749584--12749634 Score: 66
Period size: 7 Copynumber: 7.3 Consensus size: 7
12749574 TAAATTAAGC
*
12749584 ACCCTAA
1 ACCCCAA
12749591 ACCCCAA
1 ACCCCAA
12749598 ACCCCAA
1 ACCCCAA
12749605 ACCCCAA
1 ACCCCAA
*
12749612 ACCCTAA
1 ACCCCAA
**
12749619 ACCTTAA
1 ACCCCAA
12749626 ACCCCAA
1 ACCCCAA
12749633 AC
1 AC
12749635 TTTTAAACCC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.43, C:0.49, G:0.00, T:0.08
Consensus pattern (7 bp):
ACCCCAA
Found at i:12749648 original size:7 final size:7
Alignment explanation
Indices: 12749584--12749656 Score: 65
Period size: 7 Copynumber: 10.3 Consensus size: 7
12749574 TAAATTAAGC
12749584 ACCCTAA
1 ACCCTAA
*
12749591 ACCCCAA
1 ACCCTAA
*
12749598 ACCCCAA
1 ACCCTAA
*
12749605 ACCCCAA
1 ACCCTAA
12749612 ACCCTAA
1 ACCCTAA
*
12749619 ACCTTAA
1 ACCCTAA
*
12749626 ACCCCAA
1 ACCCTAA
**
12749633 ACTTTTAA
1 AC-CCTAA
12749641 ACCCTAA
1 ACCCTAA
*
12749648 ACCCAAA
1 ACCCTAA
12749655 AC
1 AC
12749657 ACCATAATCG
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
7 50 0.93
8 4 0.07
ACGTcount: A:0.44, C:0.44, G:0.00, T:0.12
Consensus pattern (7 bp):
ACCCTAA
Found at i:12751859 original size:49 final size:45
Alignment explanation
Indices: 12751789--12751891 Score: 161
Period size: 49 Copynumber: 2.2 Consensus size: 45
12751779 GGACGGTGGA
12751789 GGAGAGGGAAAGAATCAGAGTAGGAGGAGGGATGGTGGGGAAGAGGG
1 GGAGAGGGAAAGAATCAGAGTAGGAGGAGGGATGGTGGGGAAGA--G
*
12751836 GGAGAGGGAGAGAGAATCAGAGTAGGGGGAGGGATGGTGGGGAAGAG
1 GGAGAGGGA-A-AGAATCAGAGTAGGAGGAGGGATGGTGGGGAAGAG
12751883 GGAGAGGGA
1 GGAGAGGGA
12751892 TGGGAGGGGG
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
47 19 0.36
48 1 0.02
49 33 0.62
ACGTcount: A:0.33, C:0.02, G:0.57, T:0.08
Consensus pattern (45 bp):
GGAGAGGGAAAGAATCAGAGTAGGAGGAGGGATGGTGGGGAAGAG
Found at i:12752231 original size:30 final size:31
Alignment explanation
Indices: 12752196--12752255 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
12752186 ACAAGAATTG
* *
12752196 TTAAATTTTAATTTTGATCTCTATA-TTTAC
1 TTAAATTTGAATTTTAATCTCTATACTTTAC
*
12752226 TTAAATTTGGATTTTAATCTCTATACTTTA
1 TTAAATTTGAATTTTAATCTCTATACTTTA
12752256 ATTTTGACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.30, C:0.10, G:0.05, T:0.55
Consensus pattern (31 bp):
TTAAATTTGAATTTTAATCTCTATACTTTAC
Found at i:12753280 original size:45 final size:45
Alignment explanation
Indices: 12753223--12753377 Score: 238
Period size: 45 Copynumber: 3.4 Consensus size: 45
12753213 AGTATACAGT
* **
12753223 AATCAATAACAGTAACAGTAACAGTATTCAACACACAAAGTGTTG
1 AATCAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCG
* * * *
12753268 AACCTGTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCCG
1 AATCAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCG
*
12753313 AGTCAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCG
1 AATCAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCG
12753358 AATCAGTAACAGTAACAGTA
1 AATCAGTAACAGTAACAGTA
12753378 GTCGGCACAT
Statistics
Matches: 97, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 97 1.00
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (45 bp):
AATCAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCG
Found at i:12755243 original size:8 final size:8
Alignment explanation
Indices: 12755221--12755274 Score: 58
Period size: 8 Copynumber: 7.0 Consensus size: 8
12755211 TCTTGAAAAT
12755221 TATATAAA
1 TATATAAA
12755229 -ATATAAA
1 TATATAAA
*
12755236 TTTATAAA
1 TATATAAA
*
12755244 AATATAAA
1 TATATAAA
*
12755252 -ATAAAAA
1 TATATAAA
*
12755259 TTTATAAA
1 TATATAAA
12755267 TATATAAA
1 TATATAAA
12755275 ATAATAATTA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
7 13 0.35
8 24 0.65
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
TATATAAA
Found at i:12755249 original size:23 final size:23
Alignment explanation
Indices: 12755222--12755283 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
12755212 CTTGAAAATT
*
12755222 ATATAAAATATAAATTTATAAAA
1 ATATAAAATAAAAATTTATAAAA
*
12755245 ATATAAAATAAAAATTTATAAAT
1 ATATAAAATAAAAATTTATAAAA
*
12755268 ATATAAAATAATAATT
1 ATATAAAATAAAAATT
12755284 AATTAAAGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
ATATAAAATAAAAATTTATAAAA
Found at i:12755253 original size:17 final size:18
Alignment explanation
Indices: 12755216--12755253 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
12755206 TATTTTCTTG
12755216 AAAA-TTATATAAAATAT
1 AAAATTTATATAAAATAT
12755233 -AAATTTATA-AAAATAT
1 AAAATTTATATAAAATAT
12755249 AAAAT
1 AAAAT
12755254 AAAAATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAATTTATATAAAATAT
Found at i:12755938 original size:14 final size:14
Alignment explanation
Indices: 12755921--12755964 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
12755911 AAATAAAAAA
12755921 TAAAAAAATTATTT
1 TAAAAAAATTATTT
**
12755935 TAAAAAAATTAAAAT
1 TAAAAAAATT-ATTT
12755950 TAAAAAAATATATTT
1 TAAAAAAAT-TATTT
12755965 ATTATATTCG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 10 0.42
15 13 0.54
16 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TAAAAAAATTATTT
Found at i:12755941 original size:35 final size:35
Alignment explanation
Indices: 12755889--12755956 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
12755879 AATAAACACC
*
12755889 AAAAATTTATTTT-AAAAATAAAAAATAAAAAATA
1 AAAAAATTATTTTAAAAAATAAAAAATAAAAAATA
* *
12755923 AAAAAATTATTTTAAAAAAATTAAAATTAAAAAA
1 AAAAAATTATTTT-AAAAAATAAAAAATAAAAAA
12755957 ATATATTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 12 0.41
36 17 0.59
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (35 bp):
AAAAAATTATTTTAAAAAATAAAAAATAAAAAATA
Found at i:12755948 original size:8 final size:7
Alignment explanation
Indices: 12755902--12755927 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
12755892 AATTTATTTT
12755902 AAAAATA
1 AAAAATA
12755909 AAAAATA
1 AAAAATA
12755916 AAAAATA
1 AAAAATA
12755923 AAAAA
1 AAAAA
12755928 ATTATTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:12755948 original size:29 final size:30
Alignment explanation
Indices: 12755908--12755964 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
12755898 TTTTAAAAAT
12755908 AAAAAATAAAAAATAAAAAAAT-TATTTTA
1 AAAAAATAAAAAATAAAAAAATATATTTTA
* *
12755937 AAAAAATTAAAATTAAAAAAATATATTT
1 AAAAAATAAAAAATAAAAAAATATATTT
12755965 ATTATATTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (30 bp):
AAAAAATAAAAAATAAAAAAATATATTTTA
Found at i:12755952 original size:15 final size:15
Alignment explanation
Indices: 12755908--12755958 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
12755898 TTTTAAAAAT
* *
12755908 AAAAAATAAAAAATA
1 AAAAAATTAAAATTA
**
12755923 AAAAAATT-ATTTTA
1 AAAAAATTAAAATTA
12755937 AAAAAATTAAAATTA
1 AAAAAATTAAAATTA
12755952 AAAAAAT
1 AAAAAAT
12755959 ATATTTATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAAAATTAAAATTA
Found at i:12758289 original size:2 final size:2
Alignment explanation
Indices: 12758282--12758317 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
12758272 TTAGCCTAAC
12758282 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
12758318 TTAACTATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12763131 original size:18 final size:19
Alignment explanation
Indices: 12763116--12763150 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12763106 CTAAAATAGT
12763116 AACAA-AATTA-ACAATAA
1 AACAATAATTATACAATAA
12763133 AACAATAATTATACAATA
1 AACAATAATTATACAATA
12763151 TCCAAACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.23
Consensus pattern (19 bp):
AACAATAATTATACAATAA
Found at i:12764923 original size:19 final size:19
Alignment explanation
Indices: 12764899--12764935 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
12764889 ACTTTGAGAT
12764899 TTTTTTATTTTTAAAATTA
1 TTTTTTATTTTTAAAATTA
*
12764918 TTTTTTATTTTTTAAATT
1 TTTTTTATTTTTAAAATT
12764936 TAAAGAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTTTATTTTTAAAATTA
Found at i:12765094 original size:2 final size:2
Alignment explanation
Indices: 12765087--12765130 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
12765077 NNNNNNNNNN
12765087 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
12765129 AT
1 AT
12765131 GTAGATATAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12766442 original size:19 final size:20
Alignment explanation
Indices: 12766402--12766453 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
12766392 TTTTTAAATA
12766402 AAAATTATAAAAATACTCTTT
1 AAAATTA-AAAAATACTCTTT
12766423 AAAATTAAAAAATGA-T-TTT
1 AAAATTAAAAAAT-ACTCTTT
*
12766442 AAAAATAAAAAA
1 AAAATTAAAAAA
12766454 AATCAAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 14 0.48
20 7 0.24
21 8 0.28
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (20 bp):
AAAATTAAAAAATACTCTTT
Found at i:12769381 original size:21 final size:20
Alignment explanation
Indices: 12769357--12769400 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
12769347 CATAAACTAA
12769357 AATAAAGTATTAAAATTTATC
1 AATAAAGTA-TAAAATTTATC
* * *
12769378 AATACAGTATATATTTTATC
1 AATAAAGTATAAAATTTATC
12769398 AAT
1 AAT
12769401 CTAAAATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (20 bp):
AATAAAGTATAAAATTTATC
Found at i:12780888 original size:11 final size:11
Alignment explanation
Indices: 12780868--12780974 Score: 81
Period size: 11 Copynumber: 10.4 Consensus size: 11
12780858 TAAAAATTAA
12780868 AAAAAGTATTTT
1 AAAAA-TATTTT
12780880 AAAAATATTTT
1 AAAAATATTTT
12780891 --AAA-A-TTT
1 AAAAATATTTT
*
12780898 AAAAA-AATTT
1 AAAAATATTTT
12780908 AAAAATATTTT
1 AAAAATATTTT
12780919 AAAAATATTTT
1 AAAAATATTTT
12780930 --AAA-A--TT
1 AAAAATATTTT
*
12780936 AAAAAAATTTAAT
1 AAAAATATTT--T
*
12780949 AAAAGTATTTT
1 AAAAATATTTT
*
12780960 AAAAGTATTTT
1 AAAAATATTTT
12780971 AAAA
1 AAAA
12780975 TTAAAAAAAA
Statistics
Matches: 81, Mismatches: 3, Indels: 23
0.76 0.03 0.21
Matches are distributed among these distances:
6 2 0.02
7 3 0.04
8 5 0.06
9 11 0.14
10 8 0.10
11 38 0.47
12 5 0.06
13 9 0.11
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:12780904 original size:10 final size:10
Alignment explanation
Indices: 12780891--12780952 Score: 58
Period size: 10 Copynumber: 6.3 Consensus size: 10
12780881 AAAATATTTT
12780891 AAAATTTAAA
1 AAAATTTAAA
12780901 AAAATTTAAA
1 AAAATTTAAA
*
12780911 AATATTTTAAA
1 AA-AATTTAAA
* *
12780922 AATATTT--T
1 AAAATTTAAA
12780930 AAAA-TTAAA
1 AAAATTTAAA
12780939 AAAATTTAATA
1 AAAATTTAA-A
12780950 AAA
1 AAA
12780953 GTATTTTAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
7 2 0.05
8 3 0.07
9 4 0.10
10 19 0.46
11 13 0.32
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:12780952 original size:30 final size:29
Alignment explanation
Indices: 12780901--12780963 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
12780891 AAAATTTAAA
*
12780901 AAAATTTAAAAATATTTTAAAAATATTTT
1 AAAATTTAAAAAAATTTTAAAAATATTTT
*
12780930 AAAA-TTAAAAAAATTTAATAAAAGTATTTT
1 AAAATTTAAAAAAATTT--TAAAAATATTTT
12780960 AAAA
1 AAAA
12780964 GTATTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 11 0.37
29 4 0.13
30 15 0.50
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (29 bp):
AAAATTTAAAAAAATTTTAAAAATATTTT
Found at i:12780952 original size:41 final size:41
Alignment explanation
Indices: 12780841--12780999 Score: 216
Period size: 41 Copynumber: 3.9 Consensus size: 41
12780831 ACCAAAAATT
12780841 TATTTTAAAAATTAAAATAAAAATTAA-AAAAAGTATTTTAAAAA
1 TATTTT-AAAATT-AAA-AAAAATTAATAAAAA-TATTTTAAAAA
*
12780885 TATTTTAAAATTTAAAAAAATT--TAAAAATATTTTAAAAA
1 TATTTTAAAATTAAAAAAAATTAATAAAAATATTTTAAAAA
* * *
12780924 TATTTTAAAATTAAAAAAATTTAATAAAAGTATTTTAAAAG
1 TATTTTAAAATTAAAAAAAATTAATAAAAATATTTTAAAAA
*
12780965 TATTTTAAAATTAAAAAAAAATAATAAAAATATTT
1 TATTTTAAAATTAAAAAAAATTAATAAAAATATTT
12781000 ATTATATTCG
Statistics
Matches: 104, Mismatches: 8, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
39 31 0.30
40 5 0.05
41 54 0.52
42 2 0.02
43 6 0.06
44 6 0.06
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (41 bp):
TATTTTAAAATTAAAAAAAATTAATAAAAATATTTTAAAAA
Found at i:12783308 original size:126 final size:127
Alignment explanation
Indices: 12782995--12783335 Score: 621
Period size: 126 Copynumber: 2.7 Consensus size: 127
12782985 CGTCTCTGGT
* * * *
12782995 CAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCTTCA
1 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
* *
12783060 TGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTTTCTGATTTTTCTGAG
66 TGGACGCGATTTTGCTACAGTAGGTCATATAAGAAATAATTTTTTTTTCTGATGTTTCTGAG
12783122 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
1 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
12783187 TGGACGCGATTTTGCTACAGTAGGTCATATAAGAAATAA-TTTTTTTTCTGATGTTTCTGAG
66 TGGACGCGATTTTGCTACAGTAGGTCATATAAGAAATAATTTTTTTTTCTGATGTTTCTGAG
12783248 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
1 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
12783313 TGGACGCGATTTTGCTACAGTAG
66 TGGACGCGATTTTGCTACAGTAG
12783336 CAAATTTGGG
Statistics
Matches: 208, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
126 109 0.52
127 99 0.48
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.33
Consensus pattern (127 bp):
CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
TGGACGCGATTTTGCTACAGTAGGTCATATAAGAAATAATTTTTTTTTCTGATGTTTCTGAG
Found at i:12786460 original size:10 final size:10
Alignment explanation
Indices: 12786445--12786469 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12786435 CAGATCTAAC
12786445 ATTATGTAAA
1 ATTATGTAAA
12786455 ATTATGTAAA
1 ATTATGTAAA
12786465 ATTAT
1 ATTAT
12786470 TAAGCTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (10 bp):
ATTATGTAAA
Found at i:12786598 original size:26 final size:26
Alignment explanation
Indices: 12786565--12786619 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
12786555 TAAAGTGTTC
12786565 AAAATATGTAAAATTATTAAGCCAAA
1 AAAATATGTAAAATTATTAAGCCAAA
12786591 AAAATATGTAAAATTATTAAGCCAAA
1 AAAATATGTAAAATTATTAAGCCAAA
12786617 AAA
1 AAA
12786620 TTTAGGTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.25
Consensus pattern (26 bp):
AAAATATGTAAAATTATTAAGCCAAA
Found at i:12787208 original size:310 final size:309
Alignment explanation
Indices: 12786618--12788133 Score: 2489
Period size: 310 Copynumber: 4.9 Consensus size: 309
12786608 TAAGCCAAAA
* * *
12786618 AATTTAGGTTAGTTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGC
1 AATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGT
* * * * *
12786683 TAGGTTTAGGGTTTTTTGTAAATTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGGTTT
66 TA-GATTAGGGTTTTTAGTTAATTTAGGTTA-GATTAGGGTTTTTAATTAATTTAGGTTA-GATT
** * * *
12786748 AGGGTTTTTTGTTAATTTAGGTTAGGTTTAGGGTTTTTAATTATTTTAGGTTAGATTATGGTTTT
128 AGGGTTTTTAATTAATTTAGGTTA-GATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTT
* *
12786813 TAATTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGGTTTAGGGTTTTTAATTATT
192 TAATTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTA-GATTAGGGTTTTTAATTAAT
* *
12786878 TTAGGTTA-GATTATGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATT
256 TTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATT
*
12786931 AATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTACGGGTTTTTAGTTAATTTTAG
1 AATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTA-GGGTTTTTAATTAA-TTTAG
* *
12786996 GTTAGATTAGGGTTTTTAATTAATATAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTA
64 GTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTA
*
12787061 -GGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTA
129 GGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTA
12787125 ATTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTA
194 ATTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTA
*
12787190 GGTTAGGTTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAATT
259 GGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATT
*
12787241 AATTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGG
1 AATTTAGGTTA-GATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGG
* *
12787306 TTAGATTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTCGATTAG
65 TTAGATTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAG
* *
12787371 GGTTTTTAGTTAATTTAGGTTCGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAA
130 GGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAA
* * * *
12787436 TTAATTTAGGTTCGATTAGGGTTTTTAATTAATTTAGGTTCGATTAGGGTTTTTAGTTAATTTAT
195 TTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAG
* *
12787501 GTTAGGTTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGATTTTAATT
260 GTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATT
12787551 AATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGT
1 AATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGT
* * *
12787616 TAGGTCTAGGGTTTTTAGTTAATTTAGGTTAGGTTAGGGTTTTTAATTAATTTAGGTTAGGTTTA
66 TAGAT-TAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTA-GATTA
12787681 GGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTA-GGTTTTTA
129 GGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTA
*
12787745 GTTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTA
194 ATTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTA
12787810 GGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATT
259 GGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATT
* *
12787861 AACTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGT
1 AATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGT
* *
12787926 TAGATTAGGGTTTTAAATTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGG
66 TAGATTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGG
* *
12787991 GTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGGTTTAGGGTTTTTAG
131 GTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTA-GATTAGGGTTTTTAA
* *
12788056 TTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGGTTTAAGGTTTTTAATTAATTTA
195 TTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTA-GATTAGGGTTTTTAATTAATTTA
*
12788121 GGTTAGGGTTAGG
259 GGTTAGGTTTAGG
12788134 TTAGGGTTTT
Statistics
Matches: 1131, Mismatches: 62, Indels: 22
0.93 0.05 0.02
Matches are distributed among these distances:
308 55 0.05
309 203 0.18
310 613 0.54
311 143 0.13
312 4 0.00
313 69 0.06
314 36 0.03
315 8 0.01
ACGTcount: A:0.26, C:0.01, G:0.23, T:0.50
Consensus pattern (309 bp):
AATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGT
TAGATTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGG
GTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAAT
TAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGG
TTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAATT
Found at i:12788135 original size:28 final size:28
Alignment explanation
Indices: 12786618--12788126 Score: 2437
Period size: 28 Copynumber: 53.4 Consensus size: 28
12786608 TAAGCCAAAA
* *
12786618 AATTTAGGTTAGTTTAGGGTTTTTAGTT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
12786646 AATTTAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
* * ** *
12786674 AATTTAGGCTAGGTTTAGGGTTTTTTGTA
1 AATTTAGGTTA-GATTAGGGTTTTTAATT
*
12786703 AATTTAGGTTAGGTTTAGGGTTTTTAATT
1 AATTTAGGTTA-GATTAGGGTTTTTAATT
* **
12786732 AATTTAGGTTAGGTTTAGGGTTTTTTGTT
1 AATTTAGGTTA-GATTAGGGTTTTTAATT
*
12786761 AATTTAGGTTAGGTTTAGGGTTTTTAATT
1 AATTTAGGTTA-GATTAGGGTTTTTAATT
* *
12786790 ATTTTAGGTTAGATTATGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
12786818 AATTTAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
*
12786846 AATTTAGGTTAGGTTTAGGGTTTTTAATT
1 AATTTAGGTTA-GATTAGGGTTTTTAATT
* *
12786875 ATTTTAGGTTAGATTATGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
12786903 AATTTAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
12786931 AATTTAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
*
12786959 AATTTAGGTTAGATTACGGGTTTTTAGTT
1 AATTTAGGTTAGATTA-GGGTTTTTAATT
12786988 AATTTTAGGTTAGATTAGGGTTTTTAATT
1 AA-TTTAGGTTAGATTAGGGTTTTTAATT
*
12787017 AATATAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
12787045 AATTTAGGTTAGATTA-GGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
*
12787072 AATTTAGGTTAGATTAGGGTTTTTAGTT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
12787100 AATTTAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
12787128 AATTTAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
12787156 AATTTAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
* *
12787184 AATTTAGGTTAGGTTTAGGGTTTTTAGTT
1 AATTTAGGTTA-GATTAGGGTTTTTAATT
12787213 AATTTAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
*
12787241 AATTTAGGTTAGGTTTAGGGTTTTTAATT
1 AATTTAGGTTA-GATTAGGGTTTTTAATT
12787270 AATTTAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
*
12787298 AATTTAGGTTAGATTAGGGTTTTTAGTT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
*
12787326 AATTTAGGTTAGATTAGGGTTTTTAGTT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
* *
12787354 AATTTAGGTTCGATTAGGGTTTTTAGTT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
*
12787382 AATTTAGGTTCGATTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
12787410 AATTTAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
*
12787438 AATTTAGGTTCGATTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
* *
12787466 AATTTAGGTTCGATTAGGGTTTTTAGTT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
* * *
12787494 AATTTATGTTAGGTTTAGGGTTTTTAGTT
1 AATTTAGGTTA-GATTAGGGTTTTTAATT
*
12787523 AATTTAGGTTAGATTAGGGATTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
12787551 AATTTAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
12787579 AATTTAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
* *
12787607 AATTTAGGTTAGGTCTAGGGTTTTTAGTT
1 AATTTAGGTTAGAT-TAGGGTTTTTAATT
*
12787636 AATTTAGGTTAGGTTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
*
12787664 AATTTAGGTTAGGTTTAGGGTTTTTAATT
1 AATTTAGGTTA-GATTAGGGTTTTTAATT
12787693 AATTTAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
*
12787721 AATTTAGGTTAGATTA-GGTTTTTAGTT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
12787748 AATTTAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
12787776 AATTTAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
*
12787804 AATTTAGGTTAGGTTTAGGGTTTTTAATT
1 AATTTAGGTTA-GATTAGGGTTTTTAATT
12787833 AATTTAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
* *
12787861 AACTTAGGTTAGATTAGGGTTTTTAGTT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
12787889 AATTTAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
*
12787917 AATTTAGGTTAGATTAGGGTTTTAAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
12787945 AATTTAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
12787973 AATTTAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
12788001 AATTTAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
* *
12788029 AATTTAGGTTAGGTTTAGGGTTTTTAGTT
1 AATTTAGGTTA-GATTAGGGTTTTTAATT
12788058 AATTTAGGTTAGATTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATT
* *
12788086 AATTTAGGTTAGGTTTAAGGTTTTTAATT
1 AATTTAGGTTA-GATTAGGGTTTTTAATT
12788115 AATTTAGGTTAG
1 AATTTAGGTTAG
12788127 GGTTAGGTTA
Statistics
Matches: 1394, Mismatches: 73, Indels: 28
0.93 0.05 0.02
Matches are distributed among these distances:
27 53 0.04
28 961 0.69
29 366 0.26
30 14 0.01
ACGTcount: A:0.26, C:0.01, G:0.23, T:0.50
Consensus pattern (28 bp):
AATTTAGGTTAGATTAGGGTTTTTAATT
Found at i:12788234 original size:26 final size:25
Alignment explanation
Indices: 12788203--12788251 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
12788193 CTTAAAAAAT
12788203 TTCTATGCGTATTACATCAAATAAAC
1 TTCTAT-CGTATTACATCAAATAAAC
** *
12788229 TTCTATTTTATTGCATCAAATAA
1 TTCTATCGTATTACATCAAATAA
12788252 TAAATTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (25 bp):
TTCTATCGTATTACATCAAATAAAC
Done.