Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 163 of 206
Found at i:49403989 original size:23 final size:22
Alignment explanation
Indices: 49403950--49404003 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
49403940 CCATAAATTG
49403950 TTTAGGGTTGTCAAATTTAGGGA
1 TTTAGGGTTGTCAAATTT-GGGA
** *
49403973 TTTAGGGTTGTTGAATTTTGGA
1 TTTAGGGTTGTCAAATTTGGGA
*
49403995 TTTTGGGTT
1 TTTAGGGTT
49404004 TTGGATAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 11 0.41
23 16 0.59
ACGTcount: A:0.19, C:0.02, G:0.31, T:0.48
Consensus pattern (22 bp):
TTTAGGGTTGTCAAATTTGGGA
Found at i:49404741 original size:20 final size:20
Alignment explanation
Indices: 49404714--49404781 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
49404704 TTATTATTTT
*
49404714 AATAATTTTAATGATTTTAA
1 AATAATTTTAATAATTTTAA
*
49404734 AATCATTTTAATAAATTTT-A
1 AATAATTTTAAT-AATTTTAA
*
49404754 ATTAATTTTAATAATTTTAA
1 AATAATTTTAATAATTTTAA
*
49404774 AATTATTT
1 AATAATTT
49404782 GCTGACGTGG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 6 0.15
20 29 0.73
21 5 0.12
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (20 bp):
AATAATTTTAATAATTTTAA
Found at i:49404753 original size:10 final size:9
Alignment explanation
Indices: 49404709--49404777 Score: 77
Period size: 9 Copynumber: 7.3 Consensus size: 9
49404699 TTTTATTATT
49404709 ATTTTAATA
1 ATTTTAATA
*
49404718 ATTTTAATG
1 ATTTTAATA
*
49404727 ATTTTAAAATC
1 ATTTT--AATA
49404738 ATTTTAATAA
1 ATTTTAAT-A
49404748 ATTTTAATTA
1 ATTTTAA-TA
49404758 ATTTTAATA
1 ATTTTAATA
49404767 ATTTTAA-A
1 ATTTTAATA
49404775 ATT
1 ATT
49404778 ATTTGCTGAC
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
8 4 0.08
9 25 0.47
10 15 0.28
11 9 0.17
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (9 bp):
ATTTTAATA
Found at i:49404959 original size:31 final size:30
Alignment explanation
Indices: 49404921--49404983 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 30
49404911 CCAATTTGAC
* * *
49404921 AAAAAAAAACGTTAGGGGCCAAAGTGATCCA
1 AAAAAAAAACATAAAGGGCCAAAGTGA-CCA
49404952 AAAAAAAAACATAAAGGGCCAAAGTGACCA
1 AAAAAAAAACATAAAGGGCCAAAGTGACCA
49404982 AA
1 AA
49404984 TAGTCAAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.56, C:0.16, G:0.19, T:0.10
Consensus pattern (30 bp):
AAAAAAAAACATAAAGGGCCAAAGTGACCA
Found at i:49410493 original size:5 final size:5
Alignment explanation
Indices: 49410483--49410521 Score: 60
Period size: 5 Copynumber: 7.6 Consensus size: 5
49410473 AGGTGCTCAT
*
49410483 GGGCC GGGCC GGGCC GGGCC GGGTTC GGGCC GGGCC GGG
1 GGGCC GGGCC GGGCC GGGCC GGG-CC GGGCC GGGCC GGG
49410522 TTCGGGCAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 27 0.87
6 4 0.13
ACGTcount: A:0.00, C:0.33, G:0.62, T:0.05
Consensus pattern (5 bp):
GGGCC
Found at i:49410513 original size:16 final size:16
Alignment explanation
Indices: 49410483--49410533 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
49410473 AGGTGCTCAT
*
49410483 GGGCCGGG-CCGGGCC
1 GGGCCGGGTTCGGGCC
49410498 GGGCCGGGTTCGGGCC
1 GGGCCGGGTTCGGGCC
*
49410514 GGGCCGGGTTCGGGCA
1 GGGCCGGGTTCGGGCC
49410530 GGGC
1 GGGC
49410534 TTGAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
15 8 0.24
16 25 0.76
ACGTcount: A:0.02, C:0.31, G:0.59, T:0.08
Consensus pattern (16 bp):
GGGCCGGGTTCGGGCC
Found at i:49415595 original size:39 final size:39
Alignment explanation
Indices: 49415541--49415618 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
49415531 ATCCTCACAT
49415541 TCACTTAAGATTGTTTATGGTGGTGATTGATTCTTTCAA
1 TCACTTAAGATTGTTTATGGTGGTGATTGATTCTTTCAA
*
49415580 TCACTTAAGTTTGTTTATGGTGGTGATTGATTCTTTCAA
1 TCACTTAAGATTGTTTATGGTGGTGATTGATTCTTTCAA
49415619 ATTAGCCAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.22, C:0.10, G:0.21, T:0.47
Consensus pattern (39 bp):
TCACTTAAGATTGTTTATGGTGGTGATTGATTCTTTCAA
Found at i:49421047 original size:22 final size:19
Alignment explanation
Indices: 49421022--49421065 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
49421012 TGATAATAAC
49421022 TAATATATAATTATATTTATTA
1 TAATATAT-ATTA-A-TTATTA
*
49421044 TAATGTATATTAATTATTA
1 TAATATATATTAATTATTA
49421063 TAA
1 TAA
49421066 ACTTGGTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
20 1 0.05
21 4 0.19
22 7 0.33
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TAATATATATTAATTATTA
Found at i:49421054 original size:16 final size:15
Alignment explanation
Indices: 49421022--49421060 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
49421012 TGATAATAAC
49421022 TAATATATAATTATAT
1 TAAT-TATAATTATAT
*
49421038 TTATTATAATGTATAT
1 TAATTATAAT-TATAT
49421054 TAATTAT
1 TAATTAT
49421061 TATAAACTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
TAATTATAATTATAT
Found at i:49423234 original size:31 final size:31
Alignment explanation
Indices: 49423196--49423256 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
49423186 TTATTTAATG
49423196 TTTCTTAGGATATTTAATGTTTTTTGGATTC
1 TTTCTTAGGATATTTAATGTTTTTTGGATTC
49423227 TTTCTTAGGATATTTAATGTTTTTTGGATT
1 TTTCTTAGGATATTTAATGTTTTTTGGATT
49423257 AGGTTCTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.20, C:0.05, G:0.16, T:0.59
Consensus pattern (31 bp):
TTTCTTAGGATATTTAATGTTTTTTGGATTC
Found at i:49424282 original size:144 final size:142
Alignment explanation
Indices: 49424098--49424383 Score: 423
Period size: 145 Copynumber: 2.0 Consensus size: 142
49424088 ATACAGTCAA
*
49424098 ATGCTCGTGTTAAAAAAAAAGAAAGAGCATATGTGCTCAAAAGAAA-TAGATGTACAAAAGAGCA
1 ATGCTCGTGTTAAAAAAAAAGAAAGAGCATATGTACTCAAAAGAAATTAGATGTACAAAAGAGCA
* * * *
49424162 TGTGAAAGTAAAATGAGTTGGTGCATTAAAGGTATTTATTTCGAAGGTCTGA-TGCAAGCTGAGT
66 TGTGAAAGCAAAATGAGTTGGTGCATTAAAGGTACTTATTCCGAAGGTCT-ATTGCAAGCTAAGT
*
49424226 CTAGGGTTTTTAG
130 CTAGGGGTTTTAG
* * *
49424239 ATGCTCGTGTTAAAAAAAGAAAAGAAATAGCATATGTACTCAAAAGAAATTAGTTGTATAAAAGA
1 ATGCTCGTGTT--AAAAA-AAAAGAAAGAGCATATGTACTCAAAAGAAATTAGATGTACAAAAGA
* *
49424304 GCATGTGAAAGCAAAATGAGTTGGTGTATTGAAGGTACTTATTCCGAAGGTCTATTGCAAGCTAA
63 GCATGTGAAAGCAAAATGAGTTGGTGCATTAAAGGTACTTATTCCGAAGGTCTATTGCAAGCTAA
49424369 GTCTAGGGGTTTTAG
128 GTCTAGGGGTTTTAG
49424384 CTTAAAATTA
Statistics
Matches: 129, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
141 11 0.09
143 5 0.04
144 29 0.22
145 84 0.65
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.28
Consensus pattern (142 bp):
ATGCTCGTGTTAAAAAAAAAGAAAGAGCATATGTACTCAAAAGAAATTAGATGTACAAAAGAGCA
TGTGAAAGCAAAATGAGTTGGTGCATTAAAGGTACTTATTCCGAAGGTCTATTGCAAGCTAAGTC
TAGGGGTTTTAG
Found at i:49426548 original size:13 final size:13
Alignment explanation
Indices: 49426530--49426554 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49426520 ATTATTTTTG
49426530 GTGTGAAAATTTC
1 GTGTGAAAATTTC
49426543 GTGTGAAAATTT
1 GTGTGAAAATTT
49426555 TATCGTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:49428403 original size:26 final size:27
Alignment explanation
Indices: 49428336--49428392 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
49428326 ACCGAAATAT
* *
49428336 CCCCTGTAGGGAAAAATGATCGTAATG
1 CCCCTGTAGAGTAAAATGATCGTAATG
49428363 CCCCTGTAGAGTAAAATGA-CTGTAATG
1 CCCCTGTAGAGTAAAATGATC-GTAATG
49428390 CCC
1 CCC
49428393 TGGTGGGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (27 bp):
CCCCTGTAGAGTAAAATGATCGTAATG
Found at i:49428462 original size:24 final size:24
Alignment explanation
Indices: 49428422--49428468 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
49428412 TTTGCCTCGA
*
49428422 GTCTGTGTTTGGTATGACTGATTT
1 GTCTGTGTTTGGAATGACTGATTT
*
49428446 GTCTGTGATTT-GAATGATTGATT
1 GTCTGTG-TTTGGAATGACTGATT
49428469 CTGAGTATGG
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:0.17, C:0.06, G:0.28, T:0.49
Consensus pattern (24 bp):
GTCTGTGTTTGGAATGACTGATTT
Found at i:49428580 original size:27 final size:26
Alignment explanation
Indices: 49428537--49428602 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 26
49428527 GGAAGTACTG
49428537 TACTGGTGGCTCTGCCACA-ATCACTAT
1 TACTGGTGGCT-TGCCACATAT-ACTAT
49428564 TACTGGTGGCTTGGCCACATATACTAT
1 TACTGGTGGCTT-GCCACATATACTAT
* *
49428591 TATTGGTAGCTT
1 TACTGGTGGCTT
49428603 TGCTGCGATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 1 0.03
27 32 0.91
28 2 0.06
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (26 bp):
TACTGGTGGCTTGCCACATATACTAT
Found at i:49428686 original size:32 final size:32
Alignment explanation
Indices: 49428640--49428869 Score: 145
Period size: 32 Copynumber: 7.4 Consensus size: 32
49428630 ATCGCGATGC
* * *
49428640 TACTGATGGTTTTGTGCCGATCATAGTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
** *
49428672 TACTGATGGCTTTGTATCGATCATCTTACTGT
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
* *
49428704 TACCGATGGCTGTGTGCC-ATTCAT-TTCACTGT
1 TACTGATGGCTTTGTGCCGA-TCATATT-ACTGT
* * * * *
49428736 TATTAATGGCTATGTGCCGATCATATCACTGC
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
* *
49428768 TACTGA-----TTGTGCTGATCATGA-TACCGT
1 TACTGATGGCTTTGTGCCGATCAT-ATTACTGT
* * * * * *
49428795 TATTGATGGCTGTGTGTCGGTCATATCACTGC
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
* * *
49428827 TACTAATGGCTTTGTGCCAATCACATTACTG-
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
*
49428858 TACTTATGGCTT
1 TACTGATGGCTT
49428870 GTAGCCATTT
Statistics
Matches: 147, Mismatches: 40, Indels: 23
0.70 0.19 0.11
Matches are distributed among these distances:
27 19 0.13
28 1 0.01
31 15 0.10
32 110 0.75
33 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.38
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACTGT
Found at i:49429946 original size:43 final size:42
Alignment explanation
Indices: 49429835--49429947 Score: 113
Period size: 43 Copynumber: 2.7 Consensus size: 42
49429825 GAAATTTATG
* *
49429835 TGTAAGACCATGTCTGGGACATTGGCATAATATATGATTTCA
1 TGTAAGACCACGTCTGGGACATTGGCATAATATATGATTACA
* * * **
49429877 TGTAAGACC-CTGTCTAGGATAATGGCATCGT-TAGTTGATTACA
1 TGTAAGACCAC-GTCTGGGACATTGGCATAATATA--TGATTACA
*
49429920 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACATTGGCAT
49429948 TGTACGAGCT
Statistics
Matches: 56, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
41 2 0.04
42 24 0.43
43 29 0.52
44 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGACATTGGCATAATATATGATTACA
Found at i:49434562 original size:226 final size:226
Alignment explanation
Indices: 49434168--49434617 Score: 740
Period size: 226 Copynumber: 2.0 Consensus size: 226
49434158 GCATGAATTG
* * * *
49434168 GGTATACGAGTTCTGCAGTATGTAACGTCATTCATAATAGTGGAATTTATAGCCCAAGAAATGGG
1 GGTATACGACTTCTGCAGTATGTAACGTCATTCATAACAGTGGAATTCATAACCCAAGAAATGGG
* *
49434233 TAAATGATATCCTCTCATTGGCATTACATGGTTGATGAATAGTAAACGTGGCCACGGGTCGTTCG
66 TAAATGATATCCTCTCATTGGCATTACATGGTTGATGAAAAGTAAACGTGGCCACGGGTCGTTCA
* *
49434298 TTTATGTGATGAATGACTTGATTACTATTTGATAGTAATTGACTTTTCATGAAGGAAGATGTAGT
131 TTTATGTGATGAATGACTTGATTACTATTTGATAGTAATTGACTTTTCATGAAGGAAAATGTACT
49434363 GGATACCATGAGATAAAATAAGATCATATTT
196 GGATACCATGAGATAAAATAAGATCATATTT
*
49434394 GGTATACGACTTCTGCAGTATGTAGCGTCATTCATAACAGTGGAATTCATAACCCAAGAAATGGG
1 GGTATACGACTTCTGCAGTATGTAACGTCATTCATAACAGTGGAATTCATAACCCAAGAAATGGG
*
49434459 TAAATGATATCTTCTCATTGGCATTACATGGTTGATGAAAAGTAAACGTGGCCACGGGTCGCTT-
66 TAAATGATATCCTCTCATTGGCATTACATGGTTGATGAAAAGTAAACGTGGCCACGGGTCG-TTC
* *
49434523 ATTTATGTGATGAATGATTTGATTATTATTTGATAGTAATTGACTTTTCATGAAGGAAAATGTAC
130 ATTTATGTGATGAATGACTTGATTACTATTTGATAGTAATTGACTTTTCATGAAGGAAAATGTAC
* * * *
49434588 TGGTTATCTTGAGATAAAATAGGATCATAT
195 TGGATACCATGAGATAAAATAAGATCATAT
49434618 GCGGAGAACG
Statistics
Matches: 207, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
226 205 0.99
227 2 0.01
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (226 bp):
GGTATACGACTTCTGCAGTATGTAACGTCATTCATAACAGTGGAATTCATAACCCAAGAAATGGG
TAAATGATATCCTCTCATTGGCATTACATGGTTGATGAAAAGTAAACGTGGCCACGGGTCGTTCA
TTTATGTGATGAATGACTTGATTACTATTTGATAGTAATTGACTTTTCATGAAGGAAAATGTACT
GGATACCATGAGATAAAATAAGATCATATTT
Found at i:49436373 original size:17 final size:17
Alignment explanation
Indices: 49436353--49436411 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
49436343 AGAAGATTTC
49436353 ATTTCAACATAAATTCA
1 ATTTCAACATAAATTCA
**** *
49436370 ATTTCAGTGCAAATTTA
1 ATTTCAACATAAATTCA
*
49436387 CATTTCAACTTAAATTCA
1 -ATTTCAACATAAATTCA
49436405 ATTTCAA
1 ATTTCAA
49436412 TAACAAATTT
Statistics
Matches: 31, Mismatches: 10, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
17 19 0.61
18 12 0.39
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.39
Consensus pattern (17 bp):
ATTTCAACATAAATTCA
Found at i:49438598 original size:19 final size:20
Alignment explanation
Indices: 49438561--49438604 Score: 81
Period size: 19 Copynumber: 2.2 Consensus size: 20
49438551 TCTTAAATTG
49438561 TTTTATTTATAAGATTATTA
1 TTTTATTTATAAGATTATTA
49438581 TTTTATTTATAA-ATTATTA
1 TTTTATTTATAAGATTATTA
49438600 TTTTA
1 TTTTA
49438605 ATAAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTTATTTATAAGATTATTA
Found at i:49438608 original size:16 final size:17
Alignment explanation
Indices: 49438568--49438610 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
49438558 TTGTTTTATT
49438568 TATAAGATTATTATTTTA
1 TATAA-ATTATTATTTTA
49438586 TTTATAAATTATTATTTTA
1 --TATAAATTATTATTTTA
49438605 -ATAAAT
1 TATAAAT
49438611 AAATTTCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 6 0.26
19 12 0.52
20 5 0.22
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TATAAATTATTATTTTA
Found at i:49438614 original size:20 final size:19
Alignment explanation
Indices: 49438569--49438615 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
49438559 TGTTTTATTT
**
49438569 ATAAGATTATTATTTTATTT
1 ATAA-ATTATTATTTTATAA
49438589 ATAAATTATTATTTTAATAA
1 ATAAATTATTATTTT-ATAA
49438609 ATAAATT
1 ATAAATT
49438616 TCATGTTAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
ATAAATTATTATTTTATAA
Found at i:49438703 original size:29 final size:29
Alignment explanation
Indices: 49438639--49438697 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
49438629 TGAGAAAAGT
*
49438639 ATATGTTCATTTATTTATAAATATTTTATA
1 ATAT-TTCATTTATTTATAAATATATTATA
49438669 ATATTTCATTTATTTTTATAAA-ATATTAT
1 ATATTTCATTTA--TTTATAAATATATTAT
49438698 GTATTTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 8 0.31
30 10 0.38
31 8 0.31
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (29 bp):
ATATTTCATTTATTTATAAATATATTATA
Found at i:49439019 original size:183 final size:187
Alignment explanation
Indices: 49438699--49439064 Score: 481
Period size: 183 Copynumber: 2.0 Consensus size: 187
49438689 AAATATTATG
*
49438699 TATTTTTATCAAAAAAAATAGCTTTTAAACATTTTTTTTTACTTTTTTAAAGTTTTTTTTAAGAA
1 TATTTTTATC-AAAAAAATAACTTTTAAACA-TTTTTTTTACTTTTTT--A-TTTTTTTTAAGAA
* *
49438764 TCAAATTGATAGAATATGTAAAATTGCAAGCTAAATTATTTGAATTTTAAGATTTAGGACTGACT
61 TCAAATTGACAGAATATGTAAAATTGCAAGCTAAATTATTTGAATTTTAAGATTTAGGACTAACT
* *
49438829 AATAGAATGTATAAATGTTGAAGGGATAAATTTATTATTATGCCAATAAAAAAGGTAATTGT
126 AATAGAATGTATAAATATTGAAGGGATAAATTTATTATTATACCAATAAAAAAGGTAATTGT
49438891 TATTTTTATC-AAAAAATAACTTTT-AA-A-TTTTTTTACTTTTTT-TTTATTTTTAAGAATCAA
1 TATTTTTATCAAAAAAATAACTTTTAAACATTTTTTTTACTTTTTTATTT-TTTTTAAGAATCAA
* * * * * * * * *
49438951 ATTGACAGAATGTGTAAAGTTGTAGGCTAATTTATTTGGATTTTTAGATTTAGGACTAATTGATA
65 ATTGACAGAATATGTAAAATTGCAAGCTAAATTATTTGAATTTTAAGATTTAGGACTAACTAATA
* * * *
49439016 GAATGTATAAATATTGGATGGCTAAATTTATTATTATACTAATAAAAAA
130 GAATGTATAAATATTGAAGGGATAAATTTATTATTATACCAATAAAAAA
49439065 AAGTCATTGT
Statistics
Matches: 155, Mismatches: 18, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
182 3 0.02
183 111 0.72
186 15 0.10
188 1 0.01
189 2 0.01
190 13 0.08
192 10 0.06
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.43
Consensus pattern (187 bp):
TATTTTTATCAAAAAAATAACTTTTAAACATTTTTTTTACTTTTTTATTTTTTTTAAGAATCAAA
TTGACAGAATATGTAAAATTGCAAGCTAAATTATTTGAATTTTAAGATTTAGGACTAACTAATAG
AATGTATAAATATTGAAGGGATAAATTTATTATTATACCAATAAAAAAGGTAATTGT
Found at i:49439536 original size:12 final size:12
Alignment explanation
Indices: 49439519--49439552 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
49439509 CCGGCCCGCC
49439519 TATATTAATTTT
1 TATATTAATTTT
49439531 TATATT-ATTTT
1 TATATTAATTTT
49439542 TATA-TAATTTT
1 TATATTAATTTT
49439553 AAAAATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 14 0.67
12 6 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATATTAATTTT
Found at i:49439574 original size:18 final size:18
Alignment explanation
Indices: 49439553--49439592 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
49439543 ATATAATTTT
*
49439553 AAAAATA-TATAATATATC
1 AAAAATACTA-AAAATATC
49439571 AAAAATACTAAAAATATC
1 AAAAATACTAAAAATATC
49439589 AAAA
1 AAAA
49439593 TAAATATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAAATACTAAAAATATC
Found at i:49439719 original size:30 final size:30
Alignment explanation
Indices: 49439675--49439737 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
49439665 ACTTAACAAG
*
49439675 CAAATGCTTCTAAAATAATAATAAAATTAA
1 CAAATGCTTCTAAAATAATAACAAAATTAA
49439705 CAAATGTCTT-TAAAATAATAACAAAATTAA
1 CAAATG-CTTCTAAAATAATAACAAAATTAA
49439735 CAA
1 CAA
49439738 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.90
31 3 0.10
ACGTcount: A:0.57, C:0.11, G:0.03, T:0.29
Consensus pattern (30 bp):
CAAATGCTTCTAAAATAATAACAAAATTAA
Found at i:49440516 original size:14 final size:14
Alignment explanation
Indices: 49440468--49440530 Score: 51
Period size: 14 Copynumber: 4.6 Consensus size: 14
49440458 TTATATAATT
*
49440468 TATATATTATAAAA
1 TATATATTTTAAAA
*
49440482 -ATAAAATTTTAGAAA
1 TAT-ATATTTTA-AAA
* *
49440497 T-T-TATTTTTAAT
1 TATATATTTTAAAA
49440509 TATATATTTTAAAA
1 TATATATTTTAAAA
49440523 TATATATT
1 TATATATT
49440531 CAGAATACGT
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
12 3 0.08
13 8 0.22
14 22 0.59
15 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (14 bp):
TATATATTTTAAAA
Found at i:49440693 original size:9 final size:9
Alignment explanation
Indices: 49440672--49440706 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 9
49440662 CTTAAGTACT
49440672 AAAATTTAGA
1 AAAATTTA-A
49440682 AAAATTTAAA
1 AAAATTT-AA
49440692 AAAATTTAA
1 AAAATTTAA
49440701 AAAATT
1 AAAATT
49440707 ATTTTATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 8 0.33
10 15 0.62
11 1 0.04
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (9 bp):
AAAATTTAA
Found at i:49452913 original size:36 final size:37
Alignment explanation
Indices: 49452873--49452964 Score: 116
Period size: 37 Copynumber: 2.5 Consensus size: 37
49452863 GTCTCCAAAT
*
49452873 TCACATTTCAATTCAATTTCACTTTTTCATTTTCAA-
1 TCACATTTCAATTCAATTTCACTTTTCCATTTTCAAG
* *
49452909 TCACAATTCAATTCAAAATTCACTTTTCCATTTTCAAG
1 TCACATTTCAATTC-AATTTCACTTTTCCATTTTCAAG
*
49452947 TCA-ATATTCATTTCAATT
1 TCACAT-TTCAATTCAATT
49452965 CCACACATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
36 13 0.28
37 24 0.51
38 10 0.21
ACGTcount: A:0.32, C:0.22, G:0.01, T:0.46
Consensus pattern (37 bp):
TCACATTTCAATTCAATTTCACTTTTCCATTTTCAAG
Found at i:49468875 original size:22 final size:22
Alignment explanation
Indices: 49468849--49468905 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
49468839 TAATGCCTAG
*
49468849 CAGGCTTTGTGCCAATGTTATT
1 CAGGCTTAGTGCCAATGTTATT
* **
49468871 TAGGCTTAGTGCCGGTGTTATT
1 CAGGCTTAGTGCCAATGTTATT
*
49468893 CAGGCTTAATGCC
1 CAGGCTTAGTGCC
49468906 TAGAAGGCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (22 bp):
CAGGCTTAGTGCCAATGTTATT
Found at i:49468927 original size:60 final size:60
Alignment explanation
Indices: 49468824--49468943 Score: 177
Period size: 60 Copynumber: 2.0 Consensus size: 60
49468814 ATTCAAATTA
* * * * *
49468824 GGTGTTATTCAAGCTTAATGCCTAGCAGGCTTTGTGCCAATGTTATTTAGGCTTAGTGCC
1 GGTGTTATTCAAGCTTAATGCCTAGAAGGCTTTATGCCAATGTTACTCAAGCTTAGTGCC
* *
49468884 GGTGTTATTCAGGCTTAATGCCTAGAAGGCTTTATGCCGATGTTACTCAAGCTTAGTGCC
1 GGTGTTATTCAAGCTTAATGCCTAGAAGGCTTTATGCCAATGTTACTCAAGCTTAGTGCC
49468944 TAGCAGGCTT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (60 bp):
GGTGTTATTCAAGCTTAATGCCTAGAAGGCTTTATGCCAATGTTACTCAAGCTTAGTGCC
Found at i:49468959 original size:76 final size:76
Alignment explanation
Indices: 49468872--49469068 Score: 238
Period size: 76 Copynumber: 2.6 Consensus size: 76
49468862 AATGTTATTT
*
49468872 AGGCTTAGTGCCGGTGTTATTCAGGCTTAATGCCTAGAAGGCTTTATGCC-GATGTTACTCAAGC
1 AGGCTTCGTGCCGGTGTTATTCAGGCTTAATGCCTAGAAGGCTTTATGCCAG-TGTTACTCAAGC
49468936 TTAGTGCCTAGC
65 TTAGTGCCTAGC
* * * * *
49468948 AGGCTTCGTGCCGGTGTTATTCAGGCTTAGTGCCTAGTAGGCTTTTTGCCAGTGTTATTTAAGCT
1 AGGCTTCGTGCCGGTGTTATTCAGGCTTAATGCCTAGAAGGCTTTATGCCAGTGTTACTCAAGCT
*
49469013 TAGTTCCTAGC
66 TAGTGCCTAGC
* * * * *
49469024 AGGC-TC-AGCATTGGTGTTATTCAGGCTTAACGCCAAGCAGGCTTT
1 AGGCTTCGTGC--CGGTGTTATTCAGGCTTAATGCCTAGAAGGCTTT
49469069 GTACTGGTGT
Statistics
Matches: 105, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
74 2 0.02
75 2 0.02
76 100 0.95
77 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (76 bp):
AGGCTTCGTGCCGGTGTTATTCAGGCTTAATGCCTAGAAGGCTTTATGCCAGTGTTACTCAAGCT
TAGTGCCTAGC
Found at i:49469078 original size:38 final size:38
Alignment explanation
Indices: 49468872--49469070 Score: 191
Period size: 38 Copynumber: 5.2 Consensus size: 38
49468862 AATGTTATTT
* * *
49468872 AGGCTTAGTGCCGGTGTTATTCAGGCTTAATGCCTAGA
1 AGGCTTTGTGCCGGTGTTATTCAGGCTTAGTGCCTAGC
* * * *
49468910 AGGCTTTATGCCGATGTTACTCAAGCTTAGTGCCTAGC
1 AGGCTTTGTGCCGGTGTTATTCAGGCTTAGTGCCTAGC
* *
49468948 AGGCTTCGTGCCGGTGTTATTCAGGCTTAGTGCCTAGT
1 AGGCTTTGTGCCGGTGTTATTCAGGCTTAGTGCCTAGC
* * * * *
49468986 AGGCTTTTTGCCAGTGTTATTTAAGCTTAGTTCCTAGC
1 AGGCTTTGTGCCGGTGTTATTCAGGCTTAGTGCCTAGC
** **** ** *
49469024 AGGCTCAGCATTGGTGTTATTCAGGCTTAACGCCAAGC
1 AGGCTTTGTGCCGGTGTTATTCAGGCTTAGTGCCTAGC
49469062 AGGCTTTGT
1 AGGCTTTGT
49469071 ACTGGTGTAC
Statistics
Matches: 124, Mismatches: 37, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
38 124 1.00
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.34
Consensus pattern (38 bp):
AGGCTTTGTGCCGGTGTTATTCAGGCTTAGTGCCTAGC
Found at i:49475425 original size:22 final size:22
Alignment explanation
Indices: 49475390--49475431 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
49475380 ATTTGAATTA
*
49475390 GGTGTGATTTAGGCTTAGTGCC
1 GGTGTGATTCAGGCTTAGTGCC
*
49475412 GGTGTTATTCAGGCTTAGTG
1 GGTGTGATTCAGGCTTAGTG
49475432 GCTAGCAGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.14, C:0.12, G:0.36, T:0.38
Consensus pattern (22 bp):
GGTGTGATTCAGGCTTAGTGCC
Found at i:49475451 original size:38 final size:38
Alignment explanation
Indices: 49475400--49475672 Score: 279
Period size: 38 Copynumber: 7.2 Consensus size: 38
49475390 GGTGTGATTT
49475400 AGGC-TTAGTGCCGGTGTTATTCAGGCTTAGTGGCTAGC
1 AGGCTTTA-TGCCGGTGTTATTCAGGCTTAGTGGCTAGC
*
49475438 AGGCTTTATGCCGGTGTTATTCAGACTTAGT-GCTTAGC
1 AGGCTTTATGCCGGTGTTATTCAGGCTTAGTGGC-TAGC
* * * *
49475476 AGGCTTTGTGCCGGTGCTATTTAGGCTTAGTGGTTAGC
1 AGGCTTTATGCCGGTGTTATTCAGGCTTAGTGGCTAGC
* *
49475514 AGGC-TCAGTGCCAGTGTTATTCAGGCTTAGTGGCTAGC
1 AGGCTTTA-TGCCGGTGTTATTCAGGCTTAGTGGCTAGC
* * *
49475552 AGGCTTCGA-GCCGGTGTTATTCAAGCTTAG-GGCCTAGT
1 AGGCTT-TATGCCGGTGTTATTCAGGCTTAGTGG-CTAGC
** * *
49475590 AGGCTTCGTTCCGGTGTTATTCAGGCTTAGTGCCTAGC
1 AGGCTTTATGCCGGTGTTATTCAGGCTTAGTGGCTAGC
* * * * *
49475628 AAGC-TCAGTGCCGGTGTTATTCAAGCTTAGCGCCTAGC
1 AGGCTTTA-TGCCGGTGTTATTCAGGCTTAGTGGCTAGC
49475666 AGGCTTT
1 AGGCTTT
49475673 GTGTCAGTGT
Statistics
Matches: 195, Mismatches: 29, Indels: 21
0.80 0.12 0.09
Matches are distributed among these distances:
37 7 0.04
38 180 0.92
39 7 0.04
40 1 0.01
ACGTcount: A:0.17, C:0.21, G:0.30, T:0.32
Consensus pattern (38 bp):
AGGCTTTATGCCGGTGTTATTCAGGCTTAGTGGCTAGC
Found at i:49475531 original size:76 final size:76
Alignment explanation
Indices: 49475400--49475671 Score: 327
Period size: 76 Copynumber: 3.6 Consensus size: 76
49475390 GGTGTGATTT
* * *
49475400 AGGCTTAGTGCCGGTGTTATTCAGGCTTAGTGGCTAGCAGGCTTTA-TGCCGGTGTTATTCAGAC
1 AGGCTTAGTGCCGGTGTTATTCAAGCTTAGTGGCTAGCAGGCTTCAGTGCCGGTGTTATTCAGGC
49475464 TTAGTGCTTAGC
66 TTAGTGC-TAGC
* * * * * *
49475476 AGGCTTTGTGCCGGTGCTATTTAGGCTTAGTGGTTAGCAGGC-TCAGTGCCAGTGTTATTCAGGC
1 AGGCTTAGTGCCGGTGTTATTCAAGCTTAGTGGCTAGCAGGCTTCAGTGCCGGTGTTATTCAGGC
49475540 TTAGTGGCTAGC
66 TTAGT-GCTAGC
* * * *
49475552 AGGCTTCGAGCCGGTGTTATTCAAGCTTAG-GGCCTAGTAGGCTTC-GTTCCGGTGTTATTCAGG
1 AGGCTTAGTGCCGGTGTTATTCAAGCTTAGTGG-CTAGCAGGCTTCAGTGCCGGTGTTATTCAGG
49475615 CTTAGTGCCTAGC
65 CTTAGTG-CTAGC
* * * *
49475628 AAGCTCAGTGCCGGTGTTATTCAAGCTTAGCGCCTAGCAGGCTT
1 AGGCTTAGTGCCGGTGTTATTCAAGCTTAGTGGCTAGCAGGCTT
49475672 TGTGTCAGTG
Statistics
Matches: 168, Mismatches: 22, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
75 5 0.03
76 158 0.94
77 5 0.03
ACGTcount: A:0.17, C:0.21, G:0.31, T:0.32
Consensus pattern (76 bp):
AGGCTTAGTGCCGGTGTTATTCAAGCTTAGTGGCTAGCAGGCTTCAGTGCCGGTGTTATTCAGGC
TTAGTGCTAGC
Found at i:49475581 original size:114 final size:114
Alignment explanation
Indices: 49475400--49475671 Score: 368
Period size: 114 Copynumber: 2.4 Consensus size: 114
49475390 GGTGTGATTT
* *
49475400 AGGCTTAGTGCCGGTGTTATTCAGGCTTAGTGGCTAGCAGGCTTTATGCCGGTGTTATTCAGACT
1 AGGCTCAGTGCCGGTGTTATTCAGGCTTAGTGGCTAGCAGGCTTGATGCCGGTGTTATTCAGACT
* * * * **
49475465 TAGTGCTTAGCAGGCTTTGTGCCGGTGCTATTTAGGCTTAGTGGTTAGC
66 TAGGGCCTAGCAGGCTTCGTGCCGGTGCTATTCAGGCTTAGTGCCTAGC
*
49475514 AGGCTCAGTGCCAGTGTTATTCAGGCTTAGTGGCTAGCAGGCTTCGA-GCCGGTGTTATTCA-AG
1 AGGCTCAGTGCCGGTGTTATTCAGGCTTAGTGGCTAGCAGGCTT-GATGCCGGTGTTATTCAGA-
* * *
49475577 CTTAGGGCCTAGTAGGCTTCGTTCCGGTGTTATTCAGGCTTAGTGCCTAGC
64 CTTAGGGCCTAGCAGGCTTCGTGCCGGTGCTATTCAGGCTTAGTGCCTAGC
* * * *
49475628 AAGCTCAGTGCCGGTGTTATTCAAGCTTAGCGCCTAGCAGGCTT
1 AGGCTCAGTGCCGGTGTTATTCAGGCTTAGTGGCTAGCAGGCTT
49475672 TGTGTCAGTG
Statistics
Matches: 139, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
113 1 0.01
114 137 0.99
115 1 0.01
ACGTcount: A:0.17, C:0.21, G:0.31, T:0.32
Consensus pattern (114 bp):
AGGCTCAGTGCCGGTGTTATTCAGGCTTAGTGGCTAGCAGGCTTGATGCCGGTGTTATTCAGACT
TAGGGCCTAGCAGGCTTCGTGCCGGTGCTATTCAGGCTTAGTGCCTAGC
Found at i:49479894 original size:50 final size:50
Alignment explanation
Indices: 49479779--49480027 Score: 291
Period size: 50 Copynumber: 4.8 Consensus size: 50
49479769 GATAATAACA
* * ** * *
49479779 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCGG
* *
49479830 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
49479880 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
49479930 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTTATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTC---TCATC-T-CGG
* *
49479985 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAACTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
49480028 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
50 92 0.54
51 33 0.19
53 4 0.02
54 1 0.01
55 2 0.01
56 38 0.22
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:49479965 original size:100 final size:104
Alignment explanation
Indices: 49479778--49480027 Score: 346
Period size: 100 Copynumber: 2.4 Consensus size: 104
49479768 TGATAATAAC
** * *
49479778 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-ACTCTCATCTCGGTGCCCATGCCATG
* *
49479843 TCCCAGACATGGTCTTATAGGGGACCTC-TCATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTTCATCTTAAGG
* * *
49479880 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCATGCCATGT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGAACTCTCATCTCGGTGCCCATGCCATGT
*
49479944 CCCAGACATGGTCTTACAGGGGACCTCTTATGATCTTAAGG
66 CCCAGACATGGTCTTACAGGGGACCTC-T-TCATCTTAAGG
*
49479985 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAACTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGAACTCT
49480028 TTACCCAAAT
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
100 48 0.37
101 36 0.27
103 4 0.03
104 1 0.01
105 2 0.02
106 40 0.31
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGAACTCTCATCTCGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTTCATCTTAAGG
Found at i:49480143 original size:13 final size:13
Alignment explanation
Indices: 49480122--49480152 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
49480112 GCTTAGATCA
*
49480122 TCATCAAATAAAT
1 TCATAAAATAAAT
49480135 TCATAAAATAAAT
1 TCATAAAATAAAT
49480148 TCATA
1 TCATA
49480153 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:49480400 original size:30 final size:30
Alignment explanation
Indices: 49480365--49480422 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
49480355 CCTCGACTCT
*
49480365 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
49480395 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
49480423 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:49484463 original size:41 final size:41
Alignment explanation
Indices: 49484417--49484506 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 41
49484407 AAATACATCA
*
49484417 TTTTCATTTGT-CATCCTTTT-TAGATAACATCCTTTTCAACC
1 TTTTCATTT-TACATCCTTTTCCA-ATAACATCCTTTTCAACC
*
49484458 TTTTCATTTTATATCCTTTTCCAATAACATCCTTTTCAACC
1 TTTTCATTTTACATCCTTTTCCAATAACATCCTTTTCAACC
49484499 TTTTCATT
1 TTTTCATT
49484507 GATTCGGTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 1 0.02
41 43 0.96
42 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.02, T:0.51
Consensus pattern (41 bp):
TTTTCATTTTACATCCTTTTCCAATAACATCCTTTTCAACC
Found at i:49484868 original size:39 final size:39
Alignment explanation
Indices: 49484825--49484902 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
49484815 ATAATTTAAC
49484825 TCAATTACATAATTCAAATAGCTTAACTTCATAGATTCT
1 TCAATTACATAATTCAAATAGCTTAACTTCATAGATTCT
49484864 TCAATTACATAATTCAAATAGCTTAACTTCATAGATTCT
1 TCAATTACATAATTCAAATAGCTTAACTTCATAGATTCT
49484903 AACTTATAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.38
Consensus pattern (39 bp):
TCAATTACATAATTCAAATAGCTTAACTTCATAGATTCT
Found at i:49488668 original size:20 final size:20
Alignment explanation
Indices: 49488643--49488683 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
49488633 TATGGATGAG
49488643 TATGCATGAATTATGAAGTT
1 TATGCATGAATTATGAAGTT
49488663 TATGCATGAATTATGAAGTT
1 TATGCATGAATTATGAAGTT
49488683 T
1 T
49488684 TATGGTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.20, T:0.41
Consensus pattern (20 bp):
TATGCATGAATTATGAAGTT
Found at i:49488976 original size:21 final size:21
Alignment explanation
Indices: 49488950--49488992 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
49488940 TTTTGACAAA
*
49488950 AATGTGTATTGGACTAAATTG
1 AATGTGAATTGGACTAAATTG
* *
49488971 AATGTGAATTGTATTAAATTG
1 AATGTGAATTGGACTAAATTG
49488992 A
1 A
49488993 GCTAAATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.02, G:0.21, T:0.40
Consensus pattern (21 bp):
AATGTGAATTGGACTAAATTG
Found at i:49489567 original size:25 final size:25
Alignment explanation
Indices: 49489506--49489568 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
49489496 CCGATAATTA
* *
49489506 GCTCACAACAGCTTCCGGTTACATG
1 GCTCACAAGAGCTTCCGGTTAAATG
* *
49489531 GCTCACATGAGCTTCCTGTTAAATG
1 GCTCACAAGAGCTTCCGGTTAAATG
49489556 GCTCGA-AAGAGCT
1 GCTC-ACAAGAGCT
49489569 ACCAGTTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 31 0.97
26 1 0.03
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (25 bp):
GCTCACAAGAGCTTCCGGTTAAATG
Found at i:49491178 original size:46 final size:46
Alignment explanation
Indices: 49491107--49491249 Score: 277
Period size: 46 Copynumber: 3.1 Consensus size: 46
49491097 CAACAAAGAA
*
49491107 ATCTCAAGTAATGAAGAGTCAAGGTGATAGTGATAATTATTGAACT
1 ATCTCAAGTAATGAAGAGTCGAGGTGATAGTGATAATTATTGAACT
49491153 ATCTCAAGTAATGAAGAGTCGAGGTGATAGTGATAATTATTGAACT
1 ATCTCAAGTAATGAAGAGTCGAGGTGATAGTGATAATTATTGAACT
49491199 ATCTCAAGTAATGAAGAGTCGAGGTGATAGTGATAATTATTGAACT
1 ATCTCAAGTAATGAAGAGTCGAGGTGATAGTGATAATTATTGAACT
49491245 ATCTC
1 ATCTC
49491250 TAAGACGATT
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
46 96 1.00
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (46 bp):
ATCTCAAGTAATGAAGAGTCGAGGTGATAGTGATAATTATTGAACT
Found at i:49495706 original size:26 final size:26
Alignment explanation
Indices: 49495677--49495736 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
49495667 TACACCAAGC
49495677 AAAATTTTGACAATTTTACCACTAGT
1 AAAATTTTGACAATTTTACCACTAGT
** * *
49495703 AAAATTTTTGATGATTTTGCCTCTAGT
1 AAAA-TTTTGACAATTTTACCACTAGT
49495730 AAAATTT
1 AAAATTT
49495737 CAAAAAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (26 bp):
AAAATTTTGACAATTTTACCACTAGT
Found at i:49504182 original size:2 final size:2
Alignment explanation
Indices: 49504175--49504207 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
49504165 AATCATATTC
*
49504175 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
49504208 AAGCATATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:49506111 original size:42 final size:43
Alignment explanation
Indices: 49506017--49506115 Score: 119
Period size: 42 Copynumber: 2.3 Consensus size: 43
49506007 TCCTAGACGT
* * * * *
49506017 GGTCTTACATGTAATCAAATAATGATGACACTGTCCCAGACAG
1 GGTCTTACACGTAATCAAATAACGATGACAATGTCCCAAACAC
* * *
49506060 GGTCTTACACGTAATCATAT-ACGATGCCAATGTCTCAAACAC
1 GGTCTTACACGTAATCAAATAACGATGACAATGTCCCAAACAC
49506102 GGTCTTACACGTAA
1 GGTCTTACACGTAA
49506116 ATCTCAAATC
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 30 0.62
43 18 0.38
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.26
Consensus pattern (43 bp):
GGTCTTACACGTAATCAAATAACGATGACAATGTCCCAAACAC
Found at i:49507697 original size:20 final size:20
Alignment explanation
Indices: 49507658--49507699 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
49507648 TTTATCACAC
* *
49507658 TAATATTTTTTTATAGTAAT
1 TAATATTTTTTTAAAATAAT
49507678 TAATATTTTTTTAAAATAAT
1 TAATATTTTTTTAAAATAAT
49507698 TA
1 TA
49507700 TATAACTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
TAATATTTTTTTAAAATAAT
Found at i:49510061 original size:4 final size:4
Alignment explanation
Indices: 49510054--49510091 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
49510044 CATATGTACG
*
49510054 TACA TACA TACA TACA TACA TACA TACA TACA AACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TA
49510092 AATTAATTAT
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:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
TACA
Found at i:49510305 original size:30 final size:30
Alignment explanation
Indices: 49510269--49510327 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
49510259 TTATCATGTA
49510269 AGACTTTTCATTATTTCCAATTTAGTCCCT
1 AGACTTTTCATTATTTCCAATTTAGTCCCT
49510299 AGACTTTTCATTATTTCCAATTTAGTCCC
1 AGACTTTTCATTATTTCCAATTTAGTCCC
49510328 CTTTTGCCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.24, C:0.24, G:0.07, T:0.46
Consensus pattern (30 bp):
AGACTTTTCATTATTTCCAATTTAGTCCCT
Found at i:49515503 original size:6 final size:6
Alignment explanation
Indices: 49515494--49515523 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
49515484 TCTATTTCTC
49515494 CATTTT CATTTT CATTTT CATTTT CATTTT
1 CATTTT CATTTT CATTTT CATTTT CATTTT
49515524 GGAGAAAGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67
Consensus pattern (6 bp):
CATTTT
Found at i:49534821 original size:44 final size:44
Alignment explanation
Indices: 49534770--49534959 Score: 134
Period size: 44 Copynumber: 4.3 Consensus size: 44
49534760 CAGTAAGTAT
49534770 AGCAAATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCAAAGAC
1 AGCAAATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCAAAGAC
* ** * * ** *
49534814 GGCAAATCTTATCTTTCAAAG-A-TAGTGGGAAGCAGATTTAAGCC
1 AGCAAATCTTATCTCCCTAAGCAGTAG-CGG-AGCAGATCAAAGAC
* * * * * * * * ** *
49534858 ACCGAACCTTGTCTCCCTAAGCAGCAGCAGAGTAGGTTGAAGAT
1 AGCAAATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCAAAGAC
* * *
49534902 AGCAGATCTTATCTCCCTAAGAAGTAGTGGAGCAGATCAAAGAC
1 AGCAAATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCAAAGAC
49534946 -GACAAATCTTATCT
1 AG-CAAATCTTATCT
49534960 TTCCAGGATA
Statistics
Matches: 102, Mismatches: 39, Indels: 10
0.68 0.26 0.07
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
44 91 0.89
45 2 0.02
46 2 0.02
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.23
Consensus pattern (44 bp):
AGCAAATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCAAAGAC
Found at i:49535005 original size:13 final size:13
Alignment explanation
Indices: 49534987--49535015 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
49534977 GCAGATTTAA
49534987 GTCACCGAGCCTT
1 GTCACCGAGCCTT
49535000 GTCACCGAGCCTT
1 GTCACCGAGCCTT
49535013 GTC
1 GTC
49535016 TCCCTGAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.38, G:0.24, T:0.24
Consensus pattern (13 bp):
GTCACCGAGCCTT
Found at i:49539835 original size:25 final size:25
Alignment explanation
Indices: 49539759--49539835 Score: 93
Period size: 25 Copynumber: 3.1 Consensus size: 25
49539749 TGTAAATCGA
* *
49539759 TAAGCTCATACGAGATGAGAATCAA
1 TAAGCTCATACGAGCTGAGAATCAG
* *
49539784 TAAGATCTTACGAGCTGA-AATCAG
1 TAAGCTCATACGAGCTGAGAATCAG
* *
49539808 TAAGCTCAAACAAGCTGAGAATCAG
1 TAAGCTCATACGAGCTGAGAATCAG
49539833 TAA
1 TAA
49539836 TCCCTAATGA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
24 19 0.44
25 24 0.56
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.21
Consensus pattern (25 bp):
TAAGCTCATACGAGCTGAGAATCAG
Found at i:49540198 original size:27 final size:26
Alignment explanation
Indices: 49540140--49540198 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
49540130 TTTAATTATC
* * *
49540140 AATCAACATTCCAAATTCATCATTTA
1 AATCAACATTACAAATTCATCAATGA
*
49540166 ACATCAACATTACAAGATTCATCAATGG
1 A-ATCAACATTACAA-ATTCATCAATGA
49540194 AATCA
1 AATCA
49540199 TTCAAAATCT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 1 0.04
27 16 0.59
28 10 0.37
ACGTcount: A:0.44, C:0.22, G:0.05, T:0.29
Consensus pattern (26 bp):
AATCAACATTACAAATTCATCAATGA
Found at i:49540754 original size:14 final size:14
Alignment explanation
Indices: 49540735--49540766 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
49540725 TTATAAAACA
49540735 AAAATTACTATATC
1 AAAATTACTATATC
49540749 AAAATTACTATATC
1 AAAATTACTATATC
49540763 AAAA
1 AAAA
49540767 ACCTTTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAATTACTATATC
Found at i:49549134 original size:18 final size:17
Alignment explanation
Indices: 49549111--49549153 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
49549101 AAACATAAAC
*
49549111 AAATAAAATTAACATTAA
1 AAATAAAATTAA-AATAA
**
49549129 AAATAAGCTTAAAATAA
1 AAATAAAATTAAAATAA
49549146 AAATAAAA
1 AAATAAAA
49549154 ATTTCAAAGT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (17 bp):
AAATAAAATTAAAATAA
Found at i:49550485 original size:35 final size:35
Alignment explanation
Indices: 49550436--49550505 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
49550426 AAAAGATCTC
*
49550436 AGTAATTTCACTTTCAGCTACACACTTTCTAATTA
1 AGTAAGTTCACTTTCAGCTACACACTTTCTAATTA
*
49550471 AGTAAGTTCCCTTTCAGCTACACACTTTCTAATTA
1 AGTAAGTTCACTTTCAGCTACACACTTTCTAATTA
49550506 TGTTATCTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.39
Consensus pattern (35 bp):
AGTAAGTTCACTTTCAGCTACACACTTTCTAATTA
Found at i:49555123 original size:50 final size:50
Alignment explanation
Indices: 49555069--49555170 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
49555059 TGATTAAACT
49555069 AGATTAATTTAACTAGATGTAAAATTGATCCCTAATGCAATTTTAATCTA
1 AGATTAATTTAACTAGATGTAAAATTGATCCCTAATGCAATTTTAATCTA
49555119 AGATTAATTTAACTAGATGTAAAATTGATCCCTAATGCAATTTTAATCTA
1 AGATTAATTTAACTAGATGTAAAATTGATCCCTAATGCAATTTTAATCTA
49555169 AG
1 AG
49555171 TATGCAAATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (50 bp):
AGATTAATTTAACTAGATGTAAAATTGATCCCTAATGCAATTTTAATCTA
Found at i:49558695 original size:20 final size:21
Alignment explanation
Indices: 49558656--49558728 Score: 57
Period size: 20 Copynumber: 3.6 Consensus size: 21
49558646 TAAATCAAGA
*
49558656 GCACTAAA-GTGCAA-ACAGGG
1 GCAC-AAATGTGCAATATAGGG
49558676 GCACAAATGTGCAAT-TAGGG
1 GCACAAATGTGCAATATAGGG
* *
49558696 ACACCAAA-GTG-TATATAGGG
1 GCA-CAAATGTGCAATATAGGG
*
49558716 GCACAGATGTGCA
1 GCACAAATGTGCA
49558729 GTCAGGGACA
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
19 8 0.20
20 29 0.71
21 4 0.10
ACGTcount: A:0.37, C:0.18, G:0.29, T:0.16
Consensus pattern (21 bp):
GCACAAATGTGCAATATAGGG
Found at i:49558705 original size:40 final size:40
Alignment explanation
Indices: 49558661--49558743 Score: 112
Period size: 40 Copynumber: 2.1 Consensus size: 40
49558651 CAAGAGCACT
*
49558661 AAAGTGCAAACAGGGGCACAAATGTGCAATTAGGGACACC
1 AAAGTGCAAACAGGGGCACAAATGTGCAATCAGGGACACC
* * * * *
49558701 AAAGTGTATATAGGGGCACAGATGTGCAGTCAGGGACACC
1 AAAGTGCAAACAGGGGCACAAATGTGCAATCAGGGACACC
49558741 AAA
1 AAA
49558744 TTTTATCCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.39, C:0.18, G:0.29, T:0.14
Consensus pattern (40 bp):
AAAGTGCAAACAGGGGCACAAATGTGCAATCAGGGACACC
Found at i:49558758 original size:40 final size:39
Alignment explanation
Indices: 49558674--49558772 Score: 108
Period size: 40 Copynumber: 2.5 Consensus size: 39
49558664 GTGCAAACAG
* * * *
49558674 GGGCACAAATGTGCAATTAGGGACACCAAAGTGTATATAG
1 GGGCAC-AATGTGCAGTCAGGGACACCAAAGTGTATACAA
* * *
49558714 GGGCACAGATGTGCAGTCAGGGACACCAAATTTTATCCAA
1 GGGCACA-ATGTGCAGTCAGGGACACCAAAGTGTATACAA
49558754 GGGCACAATTGTGCAGTCA
1 GGGCACAA-TGTGCAGTCA
49558773 ATTGTACATT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
39 2 0.04
40 48 0.96
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.20
Consensus pattern (39 bp):
GGGCACAATGTGCAGTCAGGGACACCAAAGTGTATACAA
Found at i:49562414 original size:4 final size:4
Alignment explanation
Indices: 49562405--49562440 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
49562395 TCGATTATGG
*
49562405 AATT AATT AATT AATT AATT AAGT AGATT AATT AAT
1 AATT AATT AATT AATT AATT AATT A-ATT AATT AAT
49562441 GGAAGAATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 26 0.90
5 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (4 bp):
AATT
Found at i:49565799 original size:41 final size:41
Alignment explanation
Indices: 49565748--49565853 Score: 133
Period size: 41 Copynumber: 2.6 Consensus size: 41
49565738 TCGAGTGTAC
* *
49565748 ACAGGGGCACGAATATGCTATTTAAGGGTACCA-AAGTACAA
1 ACAGGGGCACGTATATGCAATTTAAGGGTA-CAGAAGTACAA
* * * *
49565789 ACAGGGGCACGTATGTGCAATTCAGGGGTATAGAAGTACAA
1 ACAGGGGCACGTATATGCAATTTAAGGGTACAGAAGTACAA
*
49565830 ACAAGGGCACGTATATGCAATTTA
1 ACAGGGGCACGTATATGCAATTTA
49565854 GAGAATAATT
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 1 0.02
41 54 0.98
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (41 bp):
ACAGGGGCACGTATATGCAATTTAAGGGTACAGAAGTACAA
Found at i:49572672 original size:28 final size:28
Alignment explanation
Indices: 49572641--49572702 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
49572631 TTTTTTTAAT
* * *
49572641 TTAAAAATATATAATTTTTTAATTTTTC
1 TTAAAAATAAATAATATTATAATTTTTC
* *
49572669 TTAAAAATAAATTATATTATAATTTTTT
1 TTAAAAATAAATAATATTATAATTTTTC
49572697 TTAAAA
1 TTAAAA
49572703 TTTAAAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (28 bp):
TTAAAAATAAATAATATTATAATTTTTC
Found at i:49572714 original size:29 final size:28
Alignment explanation
Indices: 49572641--49572714 Score: 67
Period size: 28 Copynumber: 2.6 Consensus size: 28
49572631 TTTTTTTAAT
* * * *
49572641 TTAAAAATATATAATTTTTTAATTTTTC
1 TTAAAAATAAAAAATATTATAATTTTTC
** *
49572669 TTAAAAATAAATTATATTATAATTTTTT
1 TTAAAAATAAAAAATATTATAATTTTTC
*
49572697 TTAAAATTTAAAAAATAT
1 TTAAAA-ATAAAAAATAT
49572715 CAAAAAATTA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
28 29 0.78
29 8 0.22
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (28 bp):
TTAAAAATAAAAAATATTATAATTTTTC
Found at i:49577001 original size:28 final size:29
Alignment explanation
Indices: 49576953--49577010 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
49576943 GTTCATGTTC
49576953 TTTTTAGATGTGAAATAATTTTTATATTT
1 TTTTTAGATGTGAAATAATTTTTATATTT
* *
49576982 TTTTATAGAT-TGATAT-ATTTTTATGTTT
1 TTTT-TAGATGTGAAATAATTTTTATATTT
49577010 T
1 T
49577011 AAAATGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 12 0.46
29 9 0.35
30 5 0.19
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (29 bp):
TTTTTAGATGTGAAATAATTTTTATATTT
Found at i:49577860 original size:9 final size:9
Alignment explanation
Indices: 49577846--49577894 Score: 80
Period size: 9 Copynumber: 5.4 Consensus size: 9
49577836 TTTGGTTAAA
49577846 AATTAACCG
1 AATTAACCG
*
49577855 AATTAACCA
1 AATTAACCG
49577864 AATTAACCG
1 AATTAACCG
*
49577873 AATTACCCG
1 AATTAACCG
49577882 AATTAACCG
1 AATTAACCG
49577891 AATT
1 AATT
49577895 GAATCCCTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.45, C:0.22, G:0.08, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:49578020 original size:18 final size:18
Alignment explanation
Indices: 49577997--49578040 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
49577987 AATTTTTATG
*
49577997 ATTGGGTTGGGTTGGATA
1 ATTGGGTTGGGTTGAATA
49578015 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
49578033 CTTGGGTT
1 ATTGGGTT
49578041 TGGATTGGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.02, G:0.41, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:49578493 original size:20 final size:19
Alignment explanation
Indices: 49578460--49578521 Score: 65
Period size: 20 Copynumber: 3.3 Consensus size: 19
49578450 TTAGGGTTTA
49578460 AAGTTTTT-TATATTTTTT
1 AAGTTTTTATATATTTTTT
*
49578478 AAGTTTTCTATATATTCTTT
1 AAGTTTT-TATATATTTTTT
*
49578498 AGATTTTTTATA-ATTTTTT
1 A-AGTTTTTATATATTTTTT
*
49578517 GAGTT
1 AAGTT
49578522 GTAAAGTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
18 10 0.28
19 7 0.19
20 14 0.39
21 5 0.14
ACGTcount: A:0.24, C:0.03, G:0.08, T:0.65
Consensus pattern (19 bp):
AAGTTTTTATATATTTTTT
Found at i:49581662 original size:11 final size:11
Alignment explanation
Indices: 49581646--49581679 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
49581636 CTACTCCTTT
*
49581646 ATGTTGATGGC
1 ATGTTGATAGC
49581657 ATGTTGATAGC
1 ATGTTGATAGC
49581668 ATGTTGATAGC
1 ATGTTGATAGC
49581679 A
1 A
49581680 GTCAAAGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.26, C:0.09, G:0.29, T:0.35
Consensus pattern (11 bp):
ATGTTGATAGC
Found at i:49588821 original size:41 final size:42
Alignment explanation
Indices: 49588705--49588821 Score: 125
Period size: 41 Copynumber: 2.8 Consensus size: 42
49588695 TTGTATAAAA
* *
49588705 CACCGGCATAAAGCCTGCTAGGCACAAAGCCTG-ATACATTT
1 CACCGGCATCAAGCCTGCTAGGCATAAAGCCTGAATACATTT
* * **
49588746 CACTGGCA-CAAAGCCTGCTAGACATAAAATCTGAATTA-A-TT
1 CACCGGCATC-AAGCCTGCTAGGCATAAAGCCTGAA-TACATTT
*
49588787 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAA
1 CACCGGCATCAAGCCTGCTAGGCATAAAGCCTGAA
49588822 AATCTCAAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
41 56 0.92
42 3 0.05
43 2 0.03
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (42 bp):
CACCGGCATCAAGCCTGCTAGGCATAAAGCCTGAATACATTT
Found at i:49588983 original size:68 final size:64
Alignment explanation
Indices: 49588866--49589017 Score: 153
Period size: 64 Copynumber: 2.3 Consensus size: 64
49588856 TACAACATTA
* * *
49588866 AAATTCAGTTCAAAGAA-TTTGTAACCTATATTCGAACCATACACATATATATGTAAAATTCATA
1 AAATTCAGCTC-AAGAACTTTATAACCTATATTCGAACC--ACACACATATA--TAAAATTCATA
49588930 AATT
61 AATT
* * * ** * *
49588934 AAATTCAGCTCAAGAACTTTATAACCTATATTTGAATCACATATGTATATAAAATTCGTACATT
1 AAATTCAGCTCAAGAACTTTATAACCTATATTCGAACCACACACATATATAAAATTCATAAATT
*
49588998 AATTTCAGCTCAAGAACTTT
1 AAATTCAGCTCAAGAACTTT
49589018 CAAATATATA
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
64 32 0.43
66 9 0.12
67 5 0.07
68 28 0.38
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.35
Consensus pattern (64 bp):
AAATTCAGCTCAAGAACTTTATAACCTATATTCGAACCACACACATATATAAAATTCATAAATT
Found at i:49589046 original size:2 final size:2
Alignment explanation
Indices: 49589041--49589077 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
49589031 ATTCAAACCG
49589041 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49589078 TTCATAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:49592124 original size:25 final size:24
Alignment explanation
Indices: 49592095--49592144 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
49592085 ATTTTATTTT
* *
49592095 AATATTTATATTGATATTAAATAAA
1 AATATCTATATTAATATTAAA-AAA
49592120 AATATCTATATTAATATTAAAAAA
1 AATATCTATATTAATATTAAAAAA
49592144 A
1 A
49592145 TCAATTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (24 bp):
AATATCTATATTAATATTAAAAAA
Found at i:49592153 original size:20 final size:21
Alignment explanation
Indices: 49592108--49592154 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
49592098 ATTTATATTG
* *
49592108 ATATTAA-A-TAAAAATATCT
1 ATATTAATATTAAAAAAATCA
49592127 ATATTAATATTAAAAAAATCA
1 ATATTAATATTAAAAAAATCA
49592148 AT-TTAAT
1 ATATTAAT
49592155 TTTGGAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 7 0.29
20 6 0.25
21 11 0.46
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATTAATATTAAAAAAATCA
Found at i:49603258 original size:20 final size:19
Alignment explanation
Indices: 49603230--49603287 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 19
49603220 AAAATAAACA
* *
49603230 AAAACAATTACTTTATAAAT
1 AAAATAATTAATTTA-AAAT
*
49603250 AAAATAATTAATTTAATAT
1 AAAATAATTAATTTAAAAT
*
49603269 AAAATAATTAATTCAAAAT
1 AAAATAATTAATTTAAAAT
49603288 TTAGTAGTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 20 0.61
20 13 0.39
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATAATTAATTTAAAAT
Found at i:49607610 original size:19 final size:21
Alignment explanation
Indices: 49607567--49607619 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 21
49607557 AAGTTATTAA
49607567 TTTTTAAAATTA-TAAATATAG
1 TTTTT-AAATTATTAAATATAG
49607588 -TTTTAAATTATTAAAT-T-G
1 TTTTTAAATTATTAAATATAG
*
49607606 TTTTTCAATTATTA
1 TTTTTAAATTATTA
49607620 TCATTATACA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 1 0.03
19 19 0.66
20 9 0.31
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (21 bp):
TTTTTAAATTATTAAATATAG
Found at i:49613576 original size:17 final size:17
Alignment explanation
Indices: 49613554--49613601 Score: 96
Period size: 17 Copynumber: 2.8 Consensus size: 17
49613544 TCCAACAAAA
49613554 ACTACAGTAAGAAAATT
1 ACTACAGTAAGAAAATT
49613571 ACTACAGTAAGAAAATT
1 ACTACAGTAAGAAAATT
49613588 ACTACAGTAAGAAA
1 ACTACAGTAAGAAA
49613602 GTAAGATAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.54, C:0.12, G:0.12, T:0.21
Consensus pattern (17 bp):
ACTACAGTAAGAAAATT
Found at i:49617656 original size:28 final size:28
Alignment explanation
Indices: 49617616--49617673 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
49617606 TTCAGATAGG
49617616 AGGCGAATGTCCTTAAACTACTACTCCA
1 AGGCGAATGTCCTTAAACTACTACTCCA
49617644 AGGCGAATGTCCTTAAACTACTACTCCA
1 AGGCGAATGTCCTTAAACTACTACTCCA
49617672 AG
1 AG
49617674 AGTATGAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.24
Consensus pattern (28 bp):
AGGCGAATGTCCTTAAACTACTACTCCA
Found at i:49624611 original size:432 final size:433
Alignment explanation
Indices: 49623808--49624683 Score: 1634
Period size: 432 Copynumber: 2.0 Consensus size: 433
49623798 TTTGTGTTGT
49623808 ATTTC-AATTCGGTCTTTTGAATTTCTTTAATTTTGAGCAATACAATTTGTCATTGATTTCATCT
1 ATTTCAAATTCGGTCTTTTGAATTTCTTTAATTTTGAGCAATACAATTTGTCATTGATTTCATCT
49623872 GGGCCCAGATTAGATGCTGCGTTTTGGAGGGGCGGGGATTATTTCCCGCTTGGTCCCCCAAGTAA
66 GGGCCCAGATTAGATGCTGCGTTTTGGAGGGGCGGGGATTATTTCCCGCTTGGTCCCCCAAGTAA
49623937 TCCGCGCATTACATTCGGCCCATTTACTTTATTTTATTTTCATTTGGTTCTTTTAATTCTGTTTT
131 TCCGCGCATTACATTCGGCCCATTTACTTTATTTTATTTTCATTTGGTTCTTTTAATTCTGTTTT
*
49624002 TCATTTAATTTAATCCCTTTTGTATTTTTTATCAATTAATTTAGTAATAATATCATTATTATTTA
196 TAATTTAATTTAATCCCTTTTGTATTTTTTATCAATTAATTTAGTAATAATATCATTATTATTTA
49624067 TTAATTCTAGTATCATTCGTATTATCATTAAACTTGTTATTTCATATACGTTACTTATTTAGATT
261 TTAATTCTAGTATCATTCGTATTATCATTAAACTTGTTATTTCATATACGTTACTTATTTAGATT
49624132 AATGTATGTATATTATTTGGTATATTACACATATATTTTTATTTACTTC-GAAATTCATTTTAAT
326 AATGTATGTATATTATTTGGTATATTACACATATATTTTTATTTACTTCAG-AATTCATTTTAAT
* *
49624196 ATTATAATTTCACATAGTATTTCTTTTTATCTTCCTTTACATCG
390 ATTATAATTTCACATAGCATTTCTTTTTATCTTCCTTTAAATCG
*
49624240 ATTTCAAATTCGGTCTTTTGAATTTCTTTAATTTTGAGCAATACAGTTTGTCATTGATTTCATCT
1 ATTTCAAATTCGGTCTTTTGAATTTCTTTAATTTTGAGCAATACAATTTGTCATTGATTTCATCT
49624305 GGGCCCAGATTAGATGCTGCGTTTTGGAGGGGCGGGGATTATTTCCCGCTTGGTCCCCCAAGTAA
66 GGGCCCAGATTAGATGCTGCGTTTTGGAGGGGCGGGGATTATTTCCCGCTTGGTCCCCCAAGTAA
* *
49624370 TCCGTGCATTACATTCGGCCCCTTTACTTTATTTTATTTTCATTTGGTTCTTTTAATTCTGTTTT
131 TCCGCGCATTACATTCGGCCCATTTACTTTATTTTATTTTCATTTGGTTCTTTTAATTCTGTTTT
49624435 TAATTTAATTTAATCCCTTTTGTA-TTTTTATCAATTAATTTAGTAATAATATCATTATTATTTA
196 TAATTTAATTTAATCCCTTTTGTATTTTTTATCAATTAATTTAGTAATAATATCATTATTATTTA
*
49624499 TTAATTCTAGTATCATTCGTATTATCATTAAACTT-TTCATTTCATATACGTTATTTATTTAGAT
261 TTAATTCTAGTATCATTCGTATTATCATTAAACTTGTT-ATTTCATATACGTTACTTATTTAGAT
49624563 TAATGTATGTATATTATTTGGTATATTACACATATATTTTTATTTACTTCAGAATTCATTTTAAT
325 TAATGTATGTATATTATTTGGTATATTACACATATATTTTTATTTACTTCAGAATTCATTTTAAT
*
49624628 ATTATAATTTCACATAGCATTTCTTTTTATCTTCCTTTAAATCT
390 ATTATAATTTCACATAGCATTTCTTTTTATCTTCCTTTAAATCG
49624672 ATTTCAAATTCG
1 ATTTCAAATTCG
49624684 TATGTATATA
Statistics
Matches: 433, Mismatches: 8, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
431 2 0.00
432 221 0.51
433 210 0.48
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.48
Consensus pattern (433 bp):
ATTTCAAATTCGGTCTTTTGAATTTCTTTAATTTTGAGCAATACAATTTGTCATTGATTTCATCT
GGGCCCAGATTAGATGCTGCGTTTTGGAGGGGCGGGGATTATTTCCCGCTTGGTCCCCCAAGTAA
TCCGCGCATTACATTCGGCCCATTTACTTTATTTTATTTTCATTTGGTTCTTTTAATTCTGTTTT
TAATTTAATTTAATCCCTTTTGTATTTTTTATCAATTAATTTAGTAATAATATCATTATTATTTA
TTAATTCTAGTATCATTCGTATTATCATTAAACTTGTTATTTCATATACGTTACTTATTTAGATT
AATGTATGTATATTATTTGGTATATTACACATATATTTTTATTTACTTCAGAATTCATTTTAATA
TTATAATTTCACATAGCATTTCTTTTTATCTTCCTTTAAATCG
Found at i:49628491 original size:46 final size:46
Alignment explanation
Indices: 49628382--49628589 Score: 350
Period size: 46 Copynumber: 4.6 Consensus size: 46
49628372 TACATATGAT
* *
49628382 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAGA-CTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
49628425 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
49628471 CACTTATCACTTTGTTACTTGATCAGATAAGTGTAGTTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
49628517 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
49628563 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
49628590 AGTACTCAAA
Statistics
Matches: 154, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
43 10 0.06
44 5 0.03
45 22 0.14
46 117 0.76
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:49640035 original size:44 final size:44
Alignment explanation
Indices: 49639972--49640311 Score: 441
Period size: 44 Copynumber: 7.7 Consensus size: 44
49639962 AAATCACAAT
* *
49639972 GTCCTATCTCCCTGACCAGCTGTGGAATAGGTTGAAGATTGTAA
1 GTCCTATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGTAA
*
49640016 GTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAA
1 GTCCTATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGTAA
* *
49640060 GCCCTATCTCCCTGACCAGTAGTGGAATAGGTGGAAGATTGTAA
1 GTCCTATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGTAA
* * *
49640104 ATCCTAGCTCCCTGACCAGCAGTGAAATAGGTGGAAGATTGTAA
1 GTCCTATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGTAA
* * * *
49640148 ATCCTAGCTCCCTGACCAGCAGTGGAATAGGCGAAAGATTGTAA
1 GTCCTATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGTAA
** * * * *
49640192 AACCTAGCTCCCTGAACAGCAGTGGAATAGGCGAAAGATTGTAA
1 GTCCTATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGTAA
* * * *
49640236 GTCCTAACTCCCTGACTAGCAGTGGAATAGATGGAAGACTGT-A
1 GTCCTATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGTAA
*
49640279 GATCCTATCTCCCTGGA-CAGCAGTAGAATAGGT
1 G-TCCTATCTCCCT-GACCAGCAGTGGAATAGGT
49640312 CAAAAATTAC
Statistics
Matches: 267, Mismatches: 27, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
43 2 0.01
44 263 0.99
45 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (44 bp):
GTCCTATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGTAA
Found at i:49640335 original size:132 final size:130
Alignment explanation
Indices: 49639972--49640349 Score: 415
Period size: 132 Copynumber: 2.9 Consensus size: 130
49639962 AAATCACAAT
* * *
49639972 GTCCTATCTCCCTGACCAGCTGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGACCAGCA
1 GTCCTAACTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGTAA-TCCTATCTCCCTGACCAGCA
* * * * * * *
49640037 GTGGAATAGGTTGAAGATTGTAAG-CCCTATCTCCCTGACCAGTAGTGGAATAGGTGGAAGATTG
65 GTGGAATAGG-TCAAAAAT-TAAGAACCTATCTCCCTGAACAGTAGTGGAATAGGCGAAAGATTG
49640101 TAA
128 TAA
* * * *
49640104 ATCCTAGCTCCCTGACCAGCAGTGAAATAGGTGGAAGATTGTAAATCCTAGCTCCCTGACCAGCA
1 GTCCTAACTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGT-AATCCTATCTCCCTGACCAGCA
* * *
49640169 GTGGAATAGG-CGAAAGATTGTAA-AACCTAGCTCCCTGAACAGCAGTGGAATAGGCGAAAGATT
65 GTGGAATAGGTC-AAA-AAT-TAAGAACCTATCTCCCTGAACAGTAGTGGAATAGGCGAAAGATT
49640232 GTAA
127 GTAA
* * *
49640236 GTCCTAACTCCCTGACTAGCAGTGGAATAGATGGAAGACTGTAGATCCTATCTCCCTGGA-CAGC
1 GTCCTAACTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGTA-ATCCTATCTCCCT-GACCAGC
* * *
49640300 AGTAGAATAGGTCAAAAATTACAGATCTTATCTCCCT-AAGCAGTAGTGGA
64 AGTGGAATAGGTCAAAAATTA-AGAACCTATCTCCCTGAA-CAGTAGTGGA
49640350 GAAGAGCGAA
Statistics
Matches: 209, Mismatches: 27, Indels: 20
0.82 0.11 0.08
Matches are distributed among these distances:
130 2 0.01
131 8 0.04
132 194 0.93
133 5 0.02
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.24
Consensus pattern (130 bp):
GTCCTAACTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGTAATCCTATCTCCCTGACCAGCAG
TGGAATAGGTCAAAAATTAAGAACCTATCTCCCTGAACAGTAGTGGAATAGGCGAAAGATTGTAA
Found at i:49642377 original size:432 final size:433
Alignment explanation
Indices: 49641574--49642450 Score: 1652
Period size: 432 Copynumber: 2.0 Consensus size: 433
49641564 TTTTGTGTTG
49641574 TATTTC-AATTCGGTCTTTTGAATTTCTTTAATTTTGAGCAATACAATTTGTCATTGATTTCATC
1 TATTTCAAATTCGGTCTTTTGAATTTCTTTAATTTTGAGCAATACAATTTGTCATTGATTTCATC
49641638 TGGGCCCAGATTAGATGCTGCGTTTTGGAGGGGCGGGGATTATTTCCCGCTTGGTCCCCCAAGTA
66 TGGGCCCAGATTAGATGCTGCGTTTTGGAGGGGCGGGGATTATTTCCCGCTTGGTCCCCCAAGTA
49641703 ATCCGCGCATTACATTCGGCCCATTTACTTTATTTTATTTTCATTTGGTTCTTTTAATTCTGTTT
131 ATCCGCGCATTACATTCGGCCCATTTACTTTATTTTATTTTCATTTGGTTCTTTTAATTCTGTTT
*
49641768 TTCATTTAATTTAATCCCTTTTGTATTTTTTATCAATTAATTTAGTAATAATATCATTATTATTT
196 TTAATTTAATTTAATCCCTTTTGTATTTTTTATCAATTAATTTAGTAATAATATCATTATTATTT
49641833 ATTAATTCTAGTATCATTCGTATTATCATTAAACTTGTCATTTCATATACGTTACTTATTTAGAT
261 ATTAATTCTAGTATCATTCGTATTATCATTAAACTTGTCATTTCATATACGTTACTTATTTAGAT
49641898 TAATGTATGTATATTATTTGGTATATTACACATATATTTTTATTTACTTC-GAAATTCATTTTAA
326 TAATGTATGTATATTATTTGGTATATTACACATATATTTTTATTTACTTCAG-AATTCATTTTAA
* *
49641962 TATTATAATTTCACATAGTATTTCTTTTTATCTTCCTTTACATC
390 TATTATAATTTCACATAGCATTTCTTTTTATCTTCCTTTAAATC
*
49642006 TATTTCAAATTCGGTCTTTTGAATTTCTTTAATTTTGAGCAATACAGTTTGTCATTGATTTCATC
1 TATTTCAAATTCGGTCTTTTGAATTTCTTTAATTTTGAGCAATACAATTTGTCATTGATTTCATC
49642071 TGGGCCCAGATTAGATGCTGCGTTTTGGAGGGGCGGGGATTATTTCCCGCTTGGTCCCCCAAGTA
66 TGGGCCCAGATTAGATGCTGCGTTTTGGAGGGGCGGGGATTATTTCCCGCTTGGTCCCCCAAGTA
* *
49642136 ATCCGTGCATTACATTCGGCCCCTTTACTTTATTTTATTTTCATTTGGTTCTTTTAATTCTGTTT
131 ATCCGCGCATTACATTCGGCCCATTTACTTTATTTTATTTTCATTTGGTTCTTTTAATTCTGTTT
49642201 TTAATTTAATTTAATCCCTTTTGTA-TTTTTATCAATTAATTTAGTAATAATATCATTATTATTT
196 TTAATTTAATTTAATCCCTTTTGTATTTTTTATCAATTAATTTAGTAATAATATCATTATTATTT
* *
49642265 ATTAATTCTAGTATCATTCGTATTATCATTAAACTTTTCATTTCATATACGTTATTTATTTAGAT
261 ATTAATTCTAGTATCATTCGTATTATCATTAAACTTGTCATTTCATATACGTTACTTATTTAGAT
49642330 TAATGTATGTATATTATTTGGTATATTACACATATATTTTTATTTACTTCAGAATTCATTTTAAT
326 TAATGTATGTATATTATTTGGTATATTACACATATATTTTTATTTACTTCAGAATTCATTTTAAT
49642395 ATTATAATTTCACATAGCATTTCTTTTTATCTTCCTTTAAATC
391 ATTATAATTTCACATAGCATTTCTTTTTATCTTCCTTTAAATC
49642438 TATTTCAAATTCG
1 TATTTCAAATTCG
49642451 TATGTATATA
Statistics
Matches: 435, Mismatches: 8, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
432 225 0.52
433 210 0.48
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.48
Consensus pattern (433 bp):
TATTTCAAATTCGGTCTTTTGAATTTCTTTAATTTTGAGCAATACAATTTGTCATTGATTTCATC
TGGGCCCAGATTAGATGCTGCGTTTTGGAGGGGCGGGGATTATTTCCCGCTTGGTCCCCCAAGTA
ATCCGCGCATTACATTCGGCCCATTTACTTTATTTTATTTTCATTTGGTTCTTTTAATTCTGTTT
TTAATTTAATTTAATCCCTTTTGTATTTTTTATCAATTAATTTAGTAATAATATCATTATTATTT
ATTAATTCTAGTATCATTCGTATTATCATTAAACTTGTCATTTCATATACGTTACTTATTTAGAT
TAATGTATGTATATTATTTGGTATATTACACATATATTTTTATTTACTTCAGAATTCATTTTAAT
ATTATAATTTCACATAGCATTTCTTTTTATCTTCCTTTAAATC
Found at i:49643374 original size:21 final size:21
Alignment explanation
Indices: 49643348--49643391 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
49643338 CGACACTAAG
*
49643348 ACATTAAACAATCAATTCGGT
1 ACATTAAACAATCAATTCAGT
49643369 ACATTAAACAATCAATTCAGT
1 ACATTAAACAATCAATTCAGT
49643390 AC
1 AC
49643392 CAATTTTGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.45, C:0.20, G:0.07, T:0.27
Consensus pattern (21 bp):
ACATTAAACAATCAATTCAGT
Found at i:49644035 original size:20 final size:20
Alignment explanation
Indices: 49644007--49644052 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
49643997 AATATTATGA
* *
49644007 ACCACTCCATTTACTTTCTT
1 ACCATTCCATTTACTTACTT
49644027 ACCATTCCATTTACTTACTT
1 ACCATTCCATTTACTTACTT
*
49644047 TCCATT
1 ACCATT
49644053 TAATTTACCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.46
Consensus pattern (20 bp):
ACCATTCCATTTACTTACTT
Found at i:49644058 original size:20 final size:20
Alignment explanation
Indices: 49644015--49644060 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
49644005 GAACCACTCC
* *
49644015 ATTTACTTTCTTACCATTCC
1 ATTTACTTACTTACCATTCA
* *
49644035 ATTTACTTACTTTCCATTTA
1 ATTTACTTACTTACCATTCA
49644055 ATTTAC
1 ATTTAC
49644061 CTAGCATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTTACTTACTTACCATTCA
Found at i:49644809 original size:40 final size:40
Alignment explanation
Indices: 49644742--49644855 Score: 165
Period size: 40 Copynumber: 2.9 Consensus size: 40
49644732 CACACCAGAT
* * *
49644742 GCTCATAAGAGCTAGTCCGACCAAAACACACCAGAAAAAA
1 GCTCATAAGAGCTAATCCAACCGAAACACACCAGAAAAAA
* * *
49644782 GCTCATAGGAGCTAATCCAACCGAAACACACCAGACAGAA
1 GCTCATAAGAGCTAATCCAACCGAAACACACCAGAAAAAA
*
49644822 GCTCATAAGAGCTAATCCAATCGAAACACACCAG
1 GCTCATAAGAGCTAATCCAACCGAAACACACCAG
49644856 GCAGAGAGTA
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 66 1.00
ACGTcount: A:0.44, C:0.29, G:0.16, T:0.11
Consensus pattern (40 bp):
GCTCATAAGAGCTAATCCAACCGAAACACACCAGAAAAAA
Found at i:49645509 original size:18 final size:18
Alignment explanation
Indices: 49645486--49645523 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
49645476 CAAAATCACT
49645486 TAACAA-AATATTTTTAAA
1 TAACAACAATA-TTTTAAA
49645504 TAACAACTAATATTTTAAA
1 TAACAAC-AATATTTTAAA
49645523 T
1 T
49645524 TCATCATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 8 0.44
20 4 0.22
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (18 bp):
TAACAACAATATTTTAAA
Found at i:49651376 original size:24 final size:24
Alignment explanation
Indices: 49651306--49651377 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
49651296 GCGTTCTGTG
* *
49651306 GCAAATGATGAATTGACGGTAAAT
1 GCAAAGGATGAATTGACGGAAAAT
**
49651330 GCAAAGGATGAATTGACAAAAAAT
1 GCAAAGGATGAATTGACGGAAAAT
* * *
49651354 GCAATGGATTATTTGACGGAAAAT
1 GCAAAGGATGAATTGACGGAAAAT
49651378 TACCCAAGTA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.44, C:0.08, G:0.24, T:0.24
Consensus pattern (24 bp):
GCAAAGGATGAATTGACGGAAAAT
Found at i:49651556 original size:21 final size:21
Alignment explanation
Indices: 49651523--49651605 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
49651513 CAGTTTAAAC
* *
49651523 CTTATGGGTTTCCGTTCAGCT
1 CTTATGAGCTTCCGTTCAGCT
* *
49651544 CTTACGAGCTTCCGTTCAAC-
1 CTTATGAGCTTCCGTTCAGCT
* * *
49651564 CATTATGGGCTTCTGTTTAGCT
1 C-TTATGAGCTTCCGTTCAGCT
* *
49651586 CTCATGAGCTTCTGTTCAGC
1 CTTATGAGCTTCCGTTCAGC
49651606 GTTCGAGCTT
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
20 1 0.02
21 46 0.96
22 1 0.02
ACGTcount: A:0.14, C:0.27, G:0.20, T:0.39
Consensus pattern (21 bp):
CTTATGAGCTTCCGTTCAGCT
Found at i:49651603 original size:42 final size:41
Alignment explanation
Indices: 49651463--49651603 Score: 147
Period size: 42 Copynumber: 3.4 Consensus size: 41
49651453 GTTAACTCAA
* * *
49651463 ATGAGTTTCTGTTCAACCCTAATGGGTTTCCGTTTAGCTTTT
1 ATGAGCTTCTGTTCAA-CCTTATGGGTTTCCGTTTAGCTCTT
* * * *
49651505 TTGAGCTTCAGTTTAAACCTTATGGGTTTCCGTTCAGCTCTT
1 ATGAGCTTCTG-TTCAACCTTATGGGTTTCCGTTTAGCTCTT
* * * * *
49651547 ACGAGCTTCCGTTCAACCATTATGGGCTTCTGTTTAGCTCTC
1 ATGAGCTTCTGTTCAACC-TTATGGGTTTCCGTTTAGCTCTT
49651589 ATGAGCTTCTGTTCA
1 ATGAGCTTCTGTTCA
49651604 GCGTTCGAGC
Statistics
Matches: 80, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
41 6 0.08
42 70 0.88
43 4 0.05
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.41
Consensus pattern (41 bp):
ATGAGCTTCTGTTCAACCTTATGGGTTTCCGTTTAGCTCTT
Found at i:49659670 original size:13 final size:13
Alignment explanation
Indices: 49659652--49659678 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
49659642 TGCAGTAGGG
49659652 CCTTAGCCCATCA
1 CCTTAGCCCATCA
49659665 CCTTAGCCCATCA
1 CCTTAGCCCATCA
49659678 C
1 C
49659679 AGTATCAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.48, G:0.07, T:0.22
Consensus pattern (13 bp):
CCTTAGCCCATCA
Found at i:49671233 original size:32 final size:32
Alignment explanation
Indices: 49671196--49671261 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
49671186 AAATACCTAA
49671196 TATGTTTTTGACTCATATGAATCTTTTAATTT
1 TATGTTTTTGACTCATATGAATCTTTTAATTT
49671228 TATGTTTTTGACTCATATGAATCTTTTAATTT
1 TATGTTTTTGACTCATATGAATCTTTTAATTT
49671260 TA
1 TA
49671262 CAAAAATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.56
Consensus pattern (32 bp):
TATGTTTTTGACTCATATGAATCTTTTAATTT
Found at i:49671866 original size:21 final size:21
Alignment explanation
Indices: 49671840--49671892 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
49671830 TTACTATTAG
*
49671840 TCTCGAGACATGTTGAGCATA
1 TCTCGAGACATGTCGAGCATA
*
49671861 TCTCGAGAGATGTCGAGCATA
1 TCTCGAGACATGTCGAGCATA
49671882 TCTCGAGACAT
1 TCTCGAGACAT
49671893 AGACATCTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (21 bp):
TCTCGAGACATGTCGAGCATA
Found at i:49672259 original size:41 final size:41
Alignment explanation
Indices: 49672202--49672440 Score: 343
Period size: 41 Copynumber: 5.8 Consensus size: 41
49672192 GACCTTTCAG
* *
49672202 GGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAA
1 GGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCGA
49672243 GGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCGA
1 GGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCGA
* * * * *
49672284 GACTTTAGCGGCGTTTTTTAAGTAGCGCTGCTAATGCTCGG
1 GGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCGA
* * * * *
49672325 GGATTTAGCGGCATTTTTTAAGAAGCACCGCTAATGCTCGG
1 GGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCGA
*
49672366 GGCTTTAGCGGTGTTTTTGAAGAAGCGCCGCTAATGCTCGA
1 GGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCGA
* *
49672407 GGCTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAA
1 GGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAA
49672441 AACAATTTAT
Statistics
Matches: 176, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 176 1.00
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (41 bp):
GGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCGA
Found at i:49672824 original size:15 final size:14
Alignment explanation
Indices: 49672786--49672820 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
49672776 ACTATTTTAA
49672786 GGTTTAGGGAGTAT
1 GGTTTAGGGAGTAT
*
49672800 GGATTTAGGGATTAT
1 GG-TTTAGGGAGTAT
49672815 GGTTTA
1 GGTTTA
49672821 AGGGTTGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.23, C:0.00, G:0.37, T:0.40
Consensus pattern (14 bp):
GGTTTAGGGAGTAT
Found at i:49673034 original size:21 final size:21
Alignment explanation
Indices: 49673007--49673179 Score: 175
Period size: 21 Copynumber: 8.2 Consensus size: 21
49672997 GTTTAGGGTT
49673007 TTTATGGTTTATGGTTTATGG
1 TTTATGGTTTATGGTTTATGG
* * *
49673028 TATATGGTTTAAGGTTTAAGG
1 TTTATGGTTTATGGTTTATGG
* *
49673049 TTTATGGTATATGGTTTAAGG
1 TTTATGGTTTATGGTTTATGG
* *
49673070 TTTATGGATTATGGGTTTAGGG
1 TTTATGGTTTAT-GGTTTATGG
*
49673092 ATTATGGTTTATGGTTTATGG
1 TTTATGGTTTATGGTTTATGG
* * **
49673113 TTTATGGTTTAAGGGTTGGGG
1 TTTATGGTTTATGGTTTATGG
* *
49673134 TTTAAGGTTTAAGGTTTATGG
1 TTTATGGTTTATGGTTTATGG
** * *
49673155 TTTATGGGCTAGGGTTTAAGG
1 TTTATGGTTTATGGTTTATGG
49673176 TTTA
1 TTTA
49673180 GGGGTTAATG
Statistics
Matches: 125, Mismatches: 26, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
21 107 0.86
22 18 0.14
ACGTcount: A:0.20, C:0.01, G:0.32, T:0.47
Consensus pattern (21 bp):
TTTATGGTTTATGGTTTATGG
Found at i:49673179 original size:7 final size:7
Alignment explanation
Indices: 49673007--49673161 Score: 175
Period size: 7 Copynumber: 22.0 Consensus size: 7
49672997 GTTTAGGGTT
49673007 TTTATGG
1 TTTATGG
49673014 TTTATGG
1 TTTATGG
49673021 TTTATGG
1 TTTATGG
*
49673028 TATATGG
1 TTTATGG
*
49673035 TTTAAGG
1 TTTATGG
*
49673042 TTTAAGG
1 TTTATGG
49673049 TTTATGG
1 TTTATGG
*
49673056 TATATGG
1 TTTATGG
*
49673063 TTTAAGG
1 TTTATGG
49673070 TTTATGG
1 TTTATGG
*
49673077 ATTATGGG
1 TTTAT-GG
*
49673085 TTTAGGG
1 TTTATGG
*
49673092 ATTATGG
1 TTTATGG
49673099 TTTATGG
1 TTTATGG
49673106 TTTATGG
1 TTTATGG
49673113 TTTATGG
1 TTTATGG
*
49673120 TTTAAGG
1 TTTATGG
* **
49673127 GTTGGGG
1 TTTATGG
*
49673134 TTTAAGG
1 TTTATGG
*
49673141 TTTAAGG
1 TTTATGG
49673148 TTTATGG
1 TTTATGG
49673155 TTTATGG
1 TTTATGG
49673162 GCTAGGGTTT
Statistics
Matches: 125, Mismatches: 22, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
7 120 0.96
8 5 0.04
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.48
Consensus pattern (7 bp):
TTTATGG
Found at i:49673181 original size:14 final size:14
Alignment explanation
Indices: 49673007--49673210 Score: 151
Period size: 14 Copynumber: 14.4 Consensus size: 14
49672997 GTTTAGGGTT
*
49673007 TTTATGGTTTATGG
1 TTTAGGGTTTATGG
* *
49673021 TTTATGGTATATGG
1 TTTAGGGTTTATGG
* *
49673035 TTTAAGGTTTAAGG
1 TTTAGGGTTTATGG
* *
49673049 TTTATGGTATATGG
1 TTTAGGGTTTATGG
*
49673063 TTTAAGGTTTATGG
1 TTTAGGGTTTATGG
* *
49673077 ATTATGGGTTTAGGG
1 TTTA-GGGTTTATGG
* *
49673092 ATTATGGTTTATGG
1 TTTAGGGTTTATGG
*
49673106 TTTATGGTTTATGG
1 TTTAGGGTTTATGG
**
49673120 TTTAAGGG-TTGGGG
1 TTT-AGGGTTTATGG
* *
49673134 TTTAAGGTTTAAGG
1 TTTAGGGTTTATGG
*
49673148 TTTATGGTTTATGG
1 TTTAGGGTTTATGG
** *
49673162 GCTAGGGTTTAAGG
1 TTTAGGGTTTATGG
*
49673176 TTTAGGGGTTAATGG
1 TTTA-GGGTTTATGG
*
49673191 -TTAGGGGTTTAGGG
1 TTTA-GGGTTTATGG
49673205 TTTAGG
1 TTTAGG
49673211 AGTTAGGGGT
Statistics
Matches: 152, Mismatches: 33, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
13 3 0.02
14 123 0.81
15 26 0.17
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.46
Consensus pattern (14 bp):
TTTAGGGTTTATGG
Found at i:49673198 original size:29 final size:28
Alignment explanation
Indices: 49673139--49673230 Score: 87
Period size: 29 Copynumber: 3.2 Consensus size: 28
49673129 TGGGGTTTAA
* * *
49673139 GGTTTAAGGTTTA-TGGTTTATGGGCTAG
1 GGTTTAAGGTTTAGGGGTTAAT-GGTTAG
49673167 GGTTTAAGGTTTAGGGGTTAATGGTTAGG
1 GGTTTAAGGTTTAGGGGTTAATGGTTA-G
* * **
49673196 GGTTTAGGGTTTAGGAGTTAGGGGTTAAG
1 GGTTTAAGGTTTAGGGGTTAATGGTT-AG
49673225 GGTTTA
1 GGTTTA
49673231 TAAAATCTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
28 17 0.31
29 36 0.67
30 1 0.02
ACGTcount: A:0.20, C:0.01, G:0.40, T:0.39
Consensus pattern (28 bp):
GGTTTAAGGTTTAGGGGTTAATGGTTAG
Found at i:49673199 original size:7 final size:7
Alignment explanation
Indices: 49673177--49673228 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
49673167 GGTTTAAGGT
49673177 TTAGGGG
1 TTAGGGG
**
49673184 TTAATGG
1 TTAGGGG
49673191 TTAGGGG
1 TTAGGGG
*
49673198 TTTAGGGT
1 -TTAGGGG
*
49673206 TTAGGAG
1 TTAGGGG
49673213 TTAGGGG
1 TTAGGGG
*
49673220 TTAAGGG
1 TTAGGGG
49673227 TT
1 TT
49673229 TATAAAATCT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
7 29 0.83
8 6 0.17
ACGTcount: A:0.19, C:0.00, G:0.44, T:0.37
Consensus pattern (7 bp):
TTAGGGG
Found at i:49673199 original size:22 final size:23
Alignment explanation
Indices: 49673174--49673226 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
49673164 TAGGGTTTAA
*
49673174 GGTTTAGGGGTTAATG-GTTAGG
1 GGTTTAGGGGTTAAGGAGTTAGG
*
49673196 GGTTTA-GGGTTTAGGAGTTAGG
1 GGTTTAGGGGTTAAGGAGTTAGG
*
49673218 GGTTAAGGG
1 GGTTTAGGG
49673227 TTTATAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 7 0.27
22 17 0.65
23 2 0.08
ACGTcount: A:0.19, C:0.00, G:0.47, T:0.34
Consensus pattern (23 bp):
GGTTTAGGGGTTAAGGAGTTAGG
Found at i:49673273 original size:6 final size:6
Alignment explanation
Indices: 49673262--49673303 Score: 57
Period size: 6 Copynumber: 6.7 Consensus size: 6
49673252 CCAAATTATA
*
49673262 AAAAAT AAAAAT AAAAAT AAAAAT AAAATAC AAAAACT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA-AT AAAAA-T AAAA
49673304 TCATTCCACA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
6 23 0.72
7 9 0.28
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:49674063 original size:36 final size:36
Alignment explanation
Indices: 49673953--49674092 Score: 192
Period size: 35 Copynumber: 3.8 Consensus size: 36
49673943 GCTTCAGCCA
* *
49673953 ATTTGCTCCCTTGTTTCTTTTCTTTTCTTTTCTGTCG
1 ATTTGCTCCC-AGTTTATTTTCTTTTCTTTTCTGTCG
49673990 ATTTGCTCCCAGTTTATTTTCTTTT-TTTTCTGTCG
1 ATTTGCTCCCAGTTTATTTTCTTTTCTTTTCTGTCG
**
49674025 ATTTGCTCCCAGTTTATTTTCTTTTCTTTTCTACCG
1 ATTTGCTCCCAGTTTATTTTCTTTTCTTTTCTGTCG
* *
49674061 ATTTGCTCCCTCTGTTTCTTTTCTTTTCTTTT
1 ATTTGCT-CC-CAGTTTATTTTCTTTTCTTTT
49674093 TCGGCCGGTT
Statistics
Matches: 94, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
35 35 0.37
36 28 0.30
37 12 0.13
38 19 0.20
ACGTcount: A:0.06, C:0.24, G:0.09, T:0.61
Consensus pattern (36 bp):
ATTTGCTCCCAGTTTATTTTCTTTTCTTTTCTGTCG
Found at i:49674821 original size:7 final size:7
Alignment explanation
Indices: 49674809--49674842 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
49674799 ATTGTTGATA
49674809 CTGTTGT
1 CTGTTGT
49674816 CTGTTGT
1 CTGTTGT
49674823 CTGTTGT
1 CTGTTGT
49674830 CTGTTGT
1 CTGTTGT
*
49674837 TTGTTG
1 CTGTTG
49674843 ATGTGTTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.00, C:0.12, G:0.29, T:0.59
Consensus pattern (7 bp):
CTGTTGT
Found at i:49676142 original size:26 final size:26
Alignment explanation
Indices: 49676102--49676168 Score: 127
Period size: 26 Copynumber: 2.6 Consensus size: 26
49676092 TTGTATTAAT
49676102 ATCAAAAAATG-TGAGTACTACATGG
1 ATCAAAAAATGATGAGTACTACATGG
49676127 ATCAAAAAATGATGAGTACTACATGG
1 ATCAAAAAATGATGAGTACTACATGG
49676153 ATCAAAAAATGATGAG
1 ATCAAAAAATGATGAG
49676169 ATCGTTATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
25 11 0.27
26 30 0.73
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.22
Consensus pattern (26 bp):
ATCAAAAAATGATGAGTACTACATGG
Found at i:49676424 original size:23 final size:23
Alignment explanation
Indices: 49676355--49676427 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
49676345 GTATATTAAA
49676355 ATATAATTAAAATCATTTTGATT
1 ATATAATTAAAATCATTTTGATT
*** * * *
49676378 ATATAA-TATTTTTA-ATTGA-A
1 ATATAATTAAAATCATTTTGATT
49676398 ATATAATTAAAATCATTTTGATT
1 ATATAATTAAAATCATTTTGATT
49676421 ATATAAT
1 ATATAAT
49676428 ATTAATATAA
Statistics
Matches: 35, Mismatches: 12, Indels: 6
0.66 0.23 0.11
Matches are distributed among these distances:
20 6 0.17
21 8 0.23
22 8 0.23
23 13 0.37
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (23 bp):
ATATAATTAAAATCATTTTGATT
Found at i:49676454 original size:43 final size:41
Alignment explanation
Indices: 49676349--49676454 Score: 142
Period size: 43 Copynumber: 2.5 Consensus size: 41
49676339 TTTAAGGTAT
49676349 ATTAAAATATAATTAAAATCATTTTGATTATATAATATTTTTA
1 ATTAAAATATAATTAAAATCATTTTGATTATATAATA--TTTA
*
49676392 ATTGAAATATAATTAAAATCATTTTGATTATATAATA-TTA
1 ATTAAAATATAATTAAAATCATTTTGATTATATAATATTTA
*
49676432 ATATAAAACTATACATTTAAATC
1 AT-TAAAA-TATA-ATTAAAATC
49676455 CAAAATATAA
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
40 5 0.09
41 4 0.07
42 4 0.07
43 44 0.77
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (41 bp):
ATTAAAATATAATTAAAATCATTTTGATTATATAATATTTA
Found at i:49680356 original size:91 final size:91
Alignment explanation
Indices: 49680209--49680416 Score: 308
Period size: 91 Copynumber: 2.3 Consensus size: 91
49680199 TTGATTTTAG
* * *
49680209 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAATTTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
49680274 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
* *
49680301 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTGTATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
*
49680366 TGTAATAATAATTATTTTATATTATA
66 TGTAATAATAATTATTTTAAATTATA
* *
49680392 AAAATTCATATAAGAAAAATTATTA
1 TAAATTCATATAAGAAAATTTATTA
49680417 GTTATAATTA
Statistics
Matches: 105, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
91 89 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:49680556 original size:120 final size:120
Alignment explanation
Indices: 49680432--49681088 Score: 1156
Period size: 120 Copynumber: 5.5 Consensus size: 120
49680422 AATTATTTTA
* * *
49680432 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATATTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATCTTT
49680496 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
49680552 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
*
49680617 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATGAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
49680672 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
49680737 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
49680792 AATTTTATTAAATTATATATTTTAATTATAATTTATTTAATAATAATTATGTTAAATTATCTTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
49680857 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* * *
49680912 AATTATATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
* * *
49680977 ATAGTATCATATATTATGATTTCAGTAAATTCATATAAGAATATTGATTACTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
49681032 AA-TTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
49681089 ATGATTAAAT
Statistics
Matches: 521, Mismatches: 14, Indels: 4
0.97 0.03 0.01
Matches are distributed among these distances:
119 47 0.09
120 472 0.91
121 2 0.00
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:49680701 original size:18 final size:17
Alignment explanation
Indices: 49680673--49680707 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
49680663 ATTATGAAGA
*
49680673 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
49680690 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
49680708 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:49680947 original size:16 final size:16
Alignment explanation
Indices: 49680926--49680972 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
49680916 ATATTAAATT
49680926 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
49680942 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
49680957 AT-TATGTTAAATTATA
1 ATATAT-TTTAATTATA
49680973 TTTTATAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.42
16 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:49681064 original size:16 final size:16
Alignment explanation
Indices: 49681045--49681086 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
49681035 TTATTAAATT
*
49681045 ATATATTTTAATTATA
1 ATATATTTTAATAATA
49681061 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
49681076 AT-TATGTTTAA
1 ATATAT-TTTAA
49681087 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:49681071 original size:15 final size:15
Alignment explanation
Indices: 49681036--49681077 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
49681026 ACTAAGAATT
*
49681036 TATTAAATTAT-ATA
1 TATTTAATTATAATA
49681050 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
49681064 TATTTAATAATAAT
1 TATTTAATTATAAT
49681078 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Done.