Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 168 of 190
Found at i:49096325 original size:11 final size:11
Alignment explanation
Indices: 49096305--49096355 Score: 54
Period size: 10 Copynumber: 4.9 Consensus size: 11
49096295 TTTAAAATAA
49096305 TTATAATTTTT
1 TTATAATTTTT
49096316 TTAT-ATTTTT
1 TTATAATTTTT
* **
49096326 TTAAAATAATT
1 TTATAATTTTT
49096337 TTA-AATTTTT
1 TTATAATTTTT
49096347 TTAT-ATTTT
1 TTATAATTTT
49096356 CATCAATGGC
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
10 22 0.67
11 11 0.33
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATAATTTTT
Found at i:49096328 original size:30 final size:31
Alignment explanation
Indices: 49096292--49096355 Score: 112
Period size: 30 Copynumber: 2.1 Consensus size: 31
49096282 CTCAAATCCA
49096292 TTTTTTAAAATAATTAT-AATTTTTTTATAT
1 TTTTTTAAAATAATTATAAATTTTTTTATAT
*
49096322 TTTTTTAAAATAATTTTAAATTTTTTTATAT
1 TTTTTTAAAATAATTATAAATTTTTTTATAT
49096353 TTT
1 TTT
49096356 CATCAATGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (31 bp):
TTTTTTAAAATAATTATAAATTTTTTTATAT
Found at i:49097449 original size:7 final size:7
Alignment explanation
Indices: 49097437--49097461 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
49097427 AGTCGATTGA
49097437 TATTTAG
1 TATTTAG
49097444 TATTTAG
1 TATTTAG
49097451 TATTTAG
1 TATTTAG
49097458 TATT
1 TATT
49097462 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:49098134 original size:18 final size:18
Alignment explanation
Indices: 49098113--49098147 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
49098103 AGGTATGTTT
* *
49098113 CCTAGCCCTTATATGTAC
1 CCTAACCCTTACATGTAC
49098131 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
49098148 TCCTTTTCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:49098465 original size:27 final size:24
Alignment explanation
Indices: 49098406--49098461 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
49098396 ATGCCGAACC
*
49098406 GGAAGAACCAAAACCACCACCGGA
1 GGAAGAACCAAAACCACCACCAGA
* *
49098430 GGAAGAACCACAATCACCACCAGA
1 GGAAGAACCAAAACCACCACCAGA
49098454 GGAAGAAC
1 GGAAGAAC
49098462 AACCGCCGCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.46, C:0.30, G:0.21, T:0.02
Consensus pattern (24 bp):
GGAAGAACCAAAACCACCACCAGA
Found at i:49098746 original size:28 final size:29
Alignment explanation
Indices: 49098691--49099027 Score: 389
Period size: 28 Copynumber: 11.7 Consensus size: 29
49098681 AAAACCCTAA
* *
49098691 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAAACCTAACCTAAATTAACTAAAAAC
*
49098720 CCTAAACCTAACCTAAATTAACAAAAAAC
1 CCTAAACCTAACCTAAATTAACTAAAAAC
* *
49098749 CCTAAACCTAACCTAAATTAATTAAAAAT
1 CCTAAACCTAACCTAAATTAACTAAAAAC
*
49098778 CCT-AATCTAACCTAAATTAACTAAAAAC
1 CCTAAACCTAACCTAAATTAACTAAAAAC
*
49098806 CCTAAACCTAACCTAAATTAACAAAAAAC
1 CCTAAACCTAACCTAAATTAACTAAAAAC
*
49098835 ACTAAACCTAACCTAAATTAAATTAACTAAAAAC
1 CCTAAACCTAACC-----TAAATTAACTAAAAAC
* * *
49098869 CAT-AATCTAACTTAAATTAACTAAAAAC
1 CCTAAACCTAACCTAAATTAACTAAAAAC
** *
49098897 CCT-AATTTAATCTAAATTAACTAAAAAC
1 CCTAAACCTAACCTAAATTAACTAAAAAC
* * *
49098925 CCT-AATCTAACCTAAATTAATTTAAAAC
1 CCTAAACCTAACCTAAATTAACTAAAAAC
* * *
49098953 CCT-AATCTAACCAAAATTAATTAAAAAC
1 CCTAAACCTAACCTAAATTAACTAAAAAC
*
49098981 CCTAAACCTAACCTAAATTAATTAAAAAC
1 CCTAAACCTAACCTAAATTAACTAAAAAC
*
49099010 CC-AAAACTAACCTAAATT
1 CCTAAACCTAACCTAAATT
49099028 TTTTTGGCTT
Statistics
Matches: 271, Mismatches: 30, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
28 133 0.49
29 115 0.42
33 7 0.03
34 16 0.06
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.25
Consensus pattern (29 bp):
CCTAAACCTAACCTAAATTAACTAAAAAC
Found at i:49098758 original size:24 final size:24
Alignment explanation
Indices: 49098694--49098759 Score: 62
Period size: 29 Copynumber: 2.6 Consensus size: 24
49098684 ACCCTAACCT
**
49098694 AACCCT-AACCTAAATTAATTAAA
1 AACCCTAAACCTAAATTAACAAAA
49098717 AACCCTAAACCTAACCTAAATTAACAAAA
1 AACCCT--A---AACCTAAATTAACAAAA
49098746 AACCCTAAACCTAA
1 AACCCTAAACCTAA
49098760 CCTAAATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
23 6 0.17
24 7 0.20
27 1 0.03
29 21 0.60
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (24 bp):
AACCCTAAACCTAAATTAACAAAA
Found at i:49098815 original size:57 final size:57
Alignment explanation
Indices: 49098691--49099027 Score: 417
Period size: 57 Copynumber: 5.8 Consensus size: 57
49098681 AAAACCCTAA
* * *
49098691 CCTAACCCTAACCTAAATTAATTAAAAACCCTAAACCTAACCTAAATTAACAAAAAAC
1 CCTAAACCTAACCTAAATTAATTAAAAACCCT-AATCTAACCTAAATTAACTAAAAAC
*
49098749 CCTAAACCTAACCTAAATTAATTAAAAATCCTAATCTAACCTAAATTAACTAAAAAC
1 CCTAAACCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAACTAAAAAC
** * *
49098806 CCTAAACCTAACCTAAATTAACAAAAAACACTAAACCTAACCTAAATTAAATTAACTAAAAAC
1 CCTAAACCTAACCTAAATTAATTAAAAACCCT-AATCTAACC-----TAAATTAACTAAAAAC
* * * * * *
49098869 CAT-AATCTAACTTAAATTAACTAAAAACCCTAATTTAATCTAAATTAACTAAAAAC
1 CCTAAACCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAACTAAAAAC
* * * *
49098925 CCT-AATCTAACCTAAATTAATTTAAAACCCTAATCTAACCAAAATTAATTAAAAAC
1 CCTAAACCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAACTAAAAAC
* *
49098981 CCTAAACCTAACCTAAATTAATTAAAAACCCAAAACTAACCTAAATT
1 CCTAAACCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATT
49099028 TTTTTGGCTT
Statistics
Matches: 242, Mismatches: 30, Indels: 15
0.84 0.10 0.05
Matches are distributed among these distances:
56 67 0.28
57 89 0.37
58 38 0.16
61 6 0.02
62 24 0.10
63 18 0.07
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.25
Consensus pattern (57 bp):
CCTAAACCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAACTAAAAAC
Found at i:49099166 original size:10 final size:10
Alignment explanation
Indices: 49099151--49099175 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
49099141 TTTTGGCTTA
49099151 ATAATTTTAC
1 ATAATTTTAC
49099161 ATAATTTTAC
1 ATAATTTTAC
49099171 ATAAT
1 ATAAT
49099176 GTTAGATCTG
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:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:49102513 original size:125 final size:126
Alignment explanation
Indices: 49102287--49102625 Score: 599
Period size: 126 Copynumber: 2.7 Consensus size: 126
49102277 CCCAAACTTG
*
49102287 CTACTGTAGCAAAACCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTCG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTCG
* *
49102352 TAGAAATGATTTTATACTATTTGCTCAGAAACATCAG-AAAAAAATTATTTCTTACATGAC
66 TAGAAACGATTTTATACTATTTGCTCAGAAAAATCAGAAAAAAAATTATTTCTTACATGAC
**
49102412 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATAATCG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTCG
49102477 TAGAAACGATTTTATACTATTTGCTCAGAAAAATCAGAAAAAAAATTATTTCTTACATGAC
66 TAGAAACGATTTTATACTATTTGCTCAGAAAAATCAGAAAAAAAATTATTTCTTACATGAC
* * *
49102538 CTACTGTAGCAAAGTCGTGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTCG
49102603 TAGAAACGATTTTATACTATTTG
66 TAGAAACGATTTTATACTATTTG
49102626 ACCAGAGACG
Statistics
Matches: 203, Mismatches: 10, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
125 97 0.48
126 106 0.52
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (126 bp):
CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTCG
TAGAAACGATTTTATACTATTTGCTCAGAAAAATCAGAAAAAAAATTATTTCTTACATGAC
Found at i:49102924 original size:23 final size:23
Alignment explanation
Indices: 49102898--49102946 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
49102888 TTTGTTTAAA
*
49102898 CACATTTCTTTTCCCGTCTCCCC
1 CACATTTCTTTTCCCGTCCCCCC
49102921 CACATTTCTTTTCCCGTCCCCCC
1 CACATTTCTTTTCCCGTCCCCCC
49102944 CAC
1 CAC
49102947 TCCCAACTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.10, C:0.51, G:0.04, T:0.35
Consensus pattern (23 bp):
CACATTTCTTTTCCCGTCCCCCC
Found at i:49103214 original size:20 final size:20
Alignment explanation
Indices: 49103189--49103229 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
49103179 AAGTTTGTTT
49103189 TATTTTTTCTTTCTCTGATA
1 TATTTTTTCTTTCTCTGATA
49103209 TATTTTTTCTTTCTCTGATA
1 TATTTTTTCTTTCTCTGATA
49103229 T
1 T
49103230 CCCAGTACAG
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:0.15, C:0.15, G:0.05, T:0.66
Consensus pattern (20 bp):
TATTTTTTCTTTCTCTGATA
Found at i:49104335 original size:13 final size:13
Alignment explanation
Indices: 49104319--49104368 Score: 68
Period size: 13 Copynumber: 3.9 Consensus size: 13
49104309 ATAGCCATTA
*
49104319 TTTCTTACATTTG
1 TTTCTTACATTTC
49104332 TTTCTATA-ATTTC
1 TTTCT-TACATTTC
49104345 TTTCTTACA-TTC
1 TTTCTTACATTTC
49104357 TTTCTTACATTT
1 TTTCTTACATTT
49104369 GTATTTATCT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 14 0.42
13 17 0.52
14 2 0.06
ACGTcount: A:0.18, C:0.18, G:0.02, T:0.62
Consensus pattern (13 bp):
TTTCTTACATTTC
Found at i:49104359 original size:12 final size:12
Alignment explanation
Indices: 49104314--49104367 Score: 56
Period size: 12 Copynumber: 4.3 Consensus size: 12
49104304 TATGCATAGC
*
49104314 CATTATTTCTTA
1 CATTCTTTCTTA
*
49104326 CATTTGTTTCTATA
1 CA-TTCTTTCT-TA
49104340 -ATTTCTTTCTTA
1 CA-TTCTTTCTTA
49104352 CATTCTTTCTTA
1 CATTCTTTCTTA
49104364 CATT
1 CATT
49104368 TGTATTTATC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
12 18 0.49
13 17 0.46
14 2 0.05
ACGTcount: A:0.20, C:0.19, G:0.02, T:0.59
Consensus pattern (12 bp):
CATTCTTTCTTA
Found at i:49109468 original size:24 final size:27
Alignment explanation
Indices: 49109417--49109475 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
49109407 CATATAACTC
*
49109417 CAATTCAATCATAATTTCTCACATTTT
1 CAATTCAATCATAATTTCTCACACTTT
*
49109444 CAATTCAATCAT-TTTTC-CAC-CTTT
1 CAATTCAATCATAATTTCTCACACTTT
49109468 CAA-TCAAT
1 CAATTCAAT
49109476 AATTAATCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 5 0.17
24 6 0.20
25 3 0.10
26 4 0.13
27 12 0.40
ACGTcount: A:0.32, C:0.25, G:0.00, T:0.42
Consensus pattern (27 bp):
CAATTCAATCATAATTTCTCACACTTT
Found at i:49109485 original size:23 final size:24
Alignment explanation
Indices: 49109441--49109485 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
49109431 TTTCTCACAT
* **
49109441 TTTCAATTCAATCATTTTTCCACC
1 TTTCAATTCAATAATTAATCCACC
49109465 TTTCAA-TCAATAATTAATCCA
1 TTTCAATTCAATAATTAATCCA
49109486 AAAATTCACA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.42
Consensus pattern (24 bp):
TTTCAATTCAATAATTAATCCACC
Found at i:49109633 original size:3 final size:3
Alignment explanation
Indices: 49109625--49109649 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
49109615 TAATTCTCAC
49109625 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
49109650 AATAATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:49109654 original size:3 final size:3
Alignment explanation
Indices: 49109648--49109683 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
49109638 CATCATCATC
49109648 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
49109684 CTTACCTCAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:49110339 original size:13 final size:14
Alignment explanation
Indices: 49110320--49110355 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
49110310 CTAGTTTTTC
49110320 CTTTCTTTCTCTTT
1 CTTTCTTTCTCTTT
*
49110334 -TTTCTTTTTCTTT
1 CTTTCTTTCTCTTT
49110347 CTTTCTTTC
1 CTTTCTTTC
49110356 GCCCCTGTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (14 bp):
CTTTCTTTCTCTTT
Found at i:49110448 original size:24 final size:24
Alignment explanation
Indices: 49110398--49110442 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
49110388 ATTCTGTTTC
49110398 TTTC-TTTCTTTTATTTCATTTGT
1 TTTCTTTTCTTTTATTTCATTTGT
49110421 TTTCTTTTCTTTTATTTCATTT
1 TTTCTTTTCTTTTATTTCATTT
49110443 TATTTCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.09, C:0.13, G:0.02, T:0.76
Consensus pattern (24 bp):
TTTCTTTTCTTTTATTTCATTTGT
Found at i:49110459 original size:24 final size:24
Alignment explanation
Indices: 49110398--49110457 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
49110388 ATTCTGTTTC
49110398 TTTCTTT-CTTTTATTTCATTTGT
1 TTTCTTTACTTTTATTTCATTTGT
*
49110421 TTTCTTTTCTTTTATTTCATTT-T
1 TTTCTTTACTTTTATTTCATTTGT
49110444 ATTTCATTTACTTT
1 -TTTC-TTTACTTT
49110458 ATGTTATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
23 8 0.24
24 18 0.55
25 7 0.21
ACGTcount: A:0.12, C:0.13, G:0.02, T:0.73
Consensus pattern (24 bp):
TTTCTTTACTTTTATTTCATTTGT
Found at i:49110942 original size:9 final size:9
Alignment explanation
Indices: 49110928--49110976 Score: 66
Period size: 9 Copynumber: 5.6 Consensus size: 9
49110918 AATTTGAATA
49110928 AATAATTAT
1 AATAATTAT
49110937 AATAATTAT
1 AATAATTAT
49110946 AATAATTAT
1 AATAATTAT
49110955 -ATAGA-TAT
1 AATA-ATTAT
*
49110963 AATATTTAT
1 AATAATTAT
49110972 AATAA
1 AATAA
49110977 CTTGAATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 6 0.17
9 29 0.83
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (9 bp):
AATAATTAT
Found at i:49112273 original size:134 final size:133
Alignment explanation
Indices: 49112059--49112310 Score: 459
Period size: 134 Copynumber: 1.9 Consensus size: 133
49112049 AGAAGCACGG
*
49112059 CAAAGTCAAAGCACAAATACTTTAAATTTCTAGCTGTTAAAGTAAAAATTCAAAGTGATCAGGTG
1 CAAAGTCAAAGCACAAATACTTTAAATTTCTAGCTGTTAAAGTAAAAATTCAAAGTGATCAAGTG
*
49112124 TTTATAAAACATATTGGGACAAACTTTATGATTGCAGATCCGCTTATTAAGGGAATAATAGGAGC
66 TTTATAAAACATATTGGGACAAA-TCTATGATTGCAGATCCGCTTATTAAGGGAATAATAGGAGC
49112189 ACAT
130 ACAT
*
49112193 CAAAGTCAAAGCACAAATACTTTAAATTTCTGGCTGTTAAAGTAAAAATTCAAAGTGATCAAGTG
1 CAAAGTCAAAGCACAAATACTTTAAATTTCTAGCTGTTAAAGTAAAAATTCAAAGTGATCAAGTG
*
49112258 TTTATAAAACATATTGGGACAAATCTATGATTGCAGATCCGTTTATTAAGGGA
66 TTTATAAAACATATTGGGACAAATCTATGATTGCAGATCCGCTTATTAAGGGA
49112311 TTACCACCCA
Statistics
Matches: 114, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
133 28 0.25
134 86 0.75
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (133 bp):
CAAAGTCAAAGCACAAATACTTTAAATTTCTAGCTGTTAAAGTAAAAATTCAAAGTGATCAAGTG
TTTATAAAACATATTGGGACAAATCTATGATTGCAGATCCGCTTATTAAGGGAATAATAGGAGCA
CAT
Found at i:49119551 original size:2 final size:2
Alignment explanation
Indices: 49119544--49119585 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
49119534 ACAACACCAA
49119544 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
49119586 TCTTAAGTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49125047 original size:47 final size:47
Alignment explanation
Indices: 49124995--49125085 Score: 130
Period size: 47 Copynumber: 1.9 Consensus size: 47
49124985 TACGTACTCA
* * *
49124995 TATATATATTTTATATATTT-TGTAATTTATATACATGTTTATATATC
1 TATATATATTTTATATTTTTATG-AATATATATACATGCTTATATATC
*
49125042 TATATATATTTTCTATTTTTATGAATATATATACATGCTTATAT
1 TATATATATTTTATATTTTTATGAATATATATACATGCTTATAT
49125086 TTTTTAAAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 37 0.95
48 2 0.05
ACGTcount: A:0.34, C:0.05, G:0.04, T:0.56
Consensus pattern (47 bp):
TATATATATTTTATATTTTTATGAATATATATACATGCTTATATATC
Found at i:49125424 original size:24 final size:24
Alignment explanation
Indices: 49125392--49125443 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
49125382 TCATTTTTAC
49125392 TTATCTTTGTTGCTATTGCTCGTA
1 TTATCTTTGTTGCTATTGCTCGTA
49125416 TTATCTTTGTTGCTATTGCTCGTA
1 TTATCTTTGTTGCTATTGCTCGTA
49125440 TTAT
1 TTAT
49125444 TTTTATTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.13, C:0.15, G:0.15, T:0.56
Consensus pattern (24 bp):
TTATCTTTGTTGCTATTGCTCGTA
Found at i:49125795 original size:108 final size:108
Alignment explanation
Indices: 49125511--49125826 Score: 494
Period size: 109 Copynumber: 2.9 Consensus size: 108
49125501 AAAGAAAATT
* *
49125511 TTTCAAAGTAAGGCAATATTTTGTGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
1 TTTCAAAGTAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
49125576 CGATCTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAATAA
66 CGAT-TTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAATAA
* * *
49125620 TTCCAAAGTAAAGCAATGTTTTGCGTTTGGAAA-TCTGAGAAAACGTGCCCTAATGTGTTGGGTT
1 TTTCAAAGTAAGGCAATGTTTTGCGTTTGGAAATTC-GAGAAAACGTGCCCTAATGTGCTGGGTT
49125684 TCGATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAA-AA
65 TCGA-TTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAATAA
* * * *
49125728 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCAAGAAAACGTGCTCTAATGTGCTGGATTT
1 TTTCAAAGTAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
*
49125793 CGA-TTTCTCGTTGGACCAAATAGCCAAATATCCT
66 CGATTTTCTCGTTCGACCAAATAGCCAAATATCCT
49125827 CTTATATCTT
Statistics
Matches: 191, Mismatches: 13, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
106 30 0.16
108 62 0.32
109 98 0.51
110 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (108 bp):
TTTCAAAGTAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
CGATTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAATAA
Found at i:49129373 original size:11 final size:11
Alignment explanation
Indices: 49129357--49129428 Score: 76
Period size: 11 Copynumber: 6.4 Consensus size: 11
49129347 CACATTCAAT
49129357 AAAAAAAAGAG
1 AAAAAAAAGAG
49129368 AAAAAAAAGAG
1 AAAAAAAAGAG
*
49129379 AAAAAAAAAAAG
1 -AAAAAAAAGAG
*
49129391 AAAAAGAAGA-
1 AAAAAAAAGAG
49129401 AAAAAGAAAGAAG
1 AAAAA-AAAG-AG
49129414 AAAAGAAAA-AG
1 AAAA-AAAAGAG
49129425 AAAA
1 AAAA
49129429 GAAGAGGCCA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
10 5 0.10
11 28 0.54
12 11 0.21
13 7 0.13
14 1 0.02
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAG
Found at i:49129385 original size:14 final size:14
Alignment explanation
Indices: 49129357--49129434 Score: 60
Period size: 14 Copynumber: 5.8 Consensus size: 14
49129347 CACATTCAAT
49129357 AAAAAAAAGAG---
1 AAAAAAAAGAGAAA
49129368 AAAAAAAAGAGAAA
1 AAAAAAAAGAGAAA
49129382 AAAAAAAAGA-AAA
1 AAAAAAAAGAGAAA
49129395 AGAAGAAAAA-AGAAA
1 A-AA-AAAAAGAGAAA
* *
49129410 GAAGAAAAGA-AAA
1 AAAAAAAAGAGAAA
*
49129423 AGAAAAGAAGAG
1 A-AAAAAAAGAG
49129435 GCCAATGTGA
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
11 11 0.21
13 11 0.21
14 23 0.43
15 8 0.15
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAGAAA
Found at i:49129387 original size:23 final size:23
Alignment explanation
Indices: 49129357--49129428 Score: 85
Period size: 23 Copynumber: 3.1 Consensus size: 23
49129347 CACATTCAAT
49129357 AAAAAAAAGAGAAAAAAAAGAGA
1 AAAAAAAAGAGAAAAAAAAGAGA
* *
49129380 AAAAAAAAAAGAAAAAGAAGA-A
1 AAAAAAAAGAGAAAAAAAAGAGA
*
49129402 AAAAGAAAGAAGAAAAGAAAA-AGA
1 AAAAAAAAG-AGAAAA-AAAAGAGA
49129426 AAA
1 AAA
49129429 GAAGAGGCCA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
22 8 0.20
23 26 0.63
24 7 0.17
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (23 bp):
AAAAAAAAGAGAAAAAAAAGAGA
Found at i:49130732 original size:44 final size:45
Alignment explanation
Indices: 49130678--49130902 Score: 235
Period size: 45 Copynumber: 5.0 Consensus size: 45
49130668 GTGAAAATAG
* *
49130678 CAGATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACAC
1 CAGACCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACAC
* * * *
49130723 CAG-CCTTGCCTTCCTGTACTGACAGCGGAGCA-AACTGAAGATAG
1 CAGACCTTGCCTTCCTGTACTGACAGCGAAGCAGATC-GAAGACAC
* * *
49130767 CAGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACAC
1 CAGACCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACAC
* * * * *
49130812 TAG-CCTTGCCTTCTTGTACTGACAGCGGAA-CAGA-CTAAAGATAG
1 CAGACCTTGCCTTCCTGTACTGACAGC-GAAGCAGATC-GAAGACAC
* * *
49130856 CAGATCTTGCCTTCCTGTACTAACAGCGAAGCAGATCGAGGACAC
1 CAGACCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACAC
49130901 CA
1 CA
49130903 TAGTTTGCAG
Statistics
Matches: 143, Mismatches: 29, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
43 3 0.02
44 68 0.48
45 69 0.48
46 3 0.02
ACGTcount: A:0.28, C:0.27, G:0.24, T:0.21
Consensus pattern (45 bp):
CAGACCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACAC
Found at i:49130789 original size:45 final size:44
Alignment explanation
Indices: 49130669--49130891 Score: 238
Period size: 44 Copynumber: 5.0 Consensus size: 44
49130659 AACAGATCAG
* *
49130669 TGAAAATAGCAGATCTTGCCTTCCTGTACTGACGGCGAAGCAGA
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGA
* * * * *
49130713 TCGAAGACACCAG-CCTTGCCTTCCTGTACTGACAGCGGAGCAAA
1 T-GAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGA
* *
49130757 CTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGTGAAGCAGA
1 -TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGA
* * *
49130802 TCGAAGACA-CTAG-CCTTGCCTTCTTGTACTGACAGCGGAA-CAGA
1 T-GAAGATAGC-AGATCTTGCCTTCCTGTACTGACAGC-GAAGCAGA
* *
49130846 CTAAAGATAGCAGATCTTGCCTTCCTGTACTAACAGCGAAGCAGA
1 -TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGA
49130891 T
1 T
49130892 CGAGGACACC
Statistics
Matches: 145, Mismatches: 24, Indels: 20
0.77 0.13 0.11
Matches are distributed among these distances:
44 73 0.50
45 72 0.50
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.22
Consensus pattern (44 bp):
TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGA
Found at i:49130830 original size:89 final size:89
Alignment explanation
Indices: 49130669--49130902 Score: 378
Period size: 89 Copynumber: 2.6 Consensus size: 89
49130659 AACAGATCAG
*
49130669 TGAAAATAGCAGATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
49130734 TCCTGTACTGACAGCGGAGCAAAC
66 TCCTGTACTGACAGCGGAACAAAC
* *
49130758 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACACTAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
49130823 TCTTGTACTGACAGCGGAACAGAC
66 TCCTGTACTGACAGCGGAACAAAC
* * * *
49130847 TAAAGATAGCAGATCTTGCCTTCCTGTACTAACAGCGAAGCAGATCGAGGACACCA
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACCA
49130903 TAGTTTGCAG
Statistics
Matches: 133, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
89 133 1.00
ACGTcount: A:0.29, C:0.26, G:0.24, T:0.21
Consensus pattern (89 bp):
TGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACCAGCCTTGCCT
TCCTGTACTGACAGCGGAACAAAC
Found at i:49130982 original size:44 final size:42
Alignment explanation
Indices: 49130934--49131281 Score: 174
Period size: 44 Copynumber: 8.0 Consensus size: 42
49130924 AAAGATAACA
*
49130934 AATCTTATCTCCCTAAGCAGTAGTGGATCAGATCGAAGATGGTG
1 AATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAT--TG
* **
49130978 AATCTTATCTTCCC-AAG-A-TAGTGGAGAAGCATATTTAAGCCATT-
1 AATCTTATC-TCCCTAAGCAGTAGT-G-G-AGCAGATCGAAG--ATTG
* * * * * *
49131022 AGTCCTATCTCCCTAAGCAGTGGTGGAGTAGGTTGAAGATTG
1 AATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATTG
49131064 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTG
1 -A-ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAT--TG
**
49131110 AATCTTATCTTCCC-AAG-A-TAGTGGAGAAGCAGATTTAAGCCATT-
1 AATCTTATC-TCCCTAAGCAGTAGT-G-G-AGCAGATCGAAG--ATTG
** * * * * *
49131154 AGCCCTATCTCCTTAAGCAGTAGTGGAGTAGGTTGAAGATTG
1 AATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATTG
* * * ** *
49131196 CAGATCCTGTCTCCCTAAGCAGTAGTAGAATAGGTCGAAGATTG
1 -A-ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATTG
* * *
49131240 CAGAT-TCTGTCTCCCTAAGCAGTAGTGAAGCAAATCGAAGAT
1 -A-ATCT-TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAT
49131282 AGTGAATATT
Statistics
Matches: 237, Mismatches: 40, Indels: 54
0.72 0.12 0.16
Matches are distributed among these distances:
41 6 0.03
42 8 0.03
43 30 0.13
44 147 0.62
45 33 0.14
46 9 0.04
47 4 0.02
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (42 bp):
AATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATTG
Found at i:49131162 original size:132 final size:132
Alignment explanation
Indices: 49130935--49131221 Score: 511
Period size: 132 Copynumber: 2.2 Consensus size: 132
49130925 AAGATAACAA
*
49130935 ATCTTATCTCCCTAAGCAGTAGTGGATCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGT
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGT
* * *
49131000 GGAGAAGCATATTTAAGCCATTAGTCCTATCTCCCTAAGCAGTGGTGGAGTAGGTTGAAGATTGC
66 GGAGAAGCAGATTTAAGCCATTAGCCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGC
49131065 AG
131 AG
49131067 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGT
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGT
*
49131132 GGAGAAGCAGATTTAAGCCATTAGCCCTATCTCCTTAAGCAGTAGTGGAGTAGGTTGAAGATTGC
66 GGAGAAGCAGATTTAAGCCATTAGCCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGC
49131197 AG
131 AG
* *
49131199 ATCCTGTCTCCCTAAGCAGTAGT
1 ATCTTATCTCCCTAAGCAGTAGT
49131222 AGAATAGGTC
Statistics
Matches: 148, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 148 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (132 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGT
GGAGAAGCAGATTTAAGCCATTAGCCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGC
AG
Found at i:49131347 original size:50 final size:50
Alignment explanation
Indices: 49131284--49131428 Score: 128
Period size: 50 Copynumber: 2.9 Consensus size: 50
49131274 TCGAAGATAG
* *
49131284 TGAATATTACTTCCCTTGCGGTGCAGTGGAACAGATTGAAGCTACAACGA
1 TGAATCTTACTTCCCTAGCGGTGCAGTGGAACAGATTGAAGCTACAACGA
* * * ** * ** * ** *
49131334 TGAATCTTGCTTCCCCAACATTGCAATTAAAAAGATTGAAGCCGCAACGG
1 TGAATCTTACTTCCCTAGCGGTGCAGTGGAACAGATTGAAGCTACAACGA
* * * *
49131384 TGAATTTTACTTCCCTAGTGGTGTAGTGGGACAGATTGAAGCTAC
1 TGAATCTTACTTCCCTAGCGGTGCAGTGGAACAGATTGAAGCTAC
49131429 GACAGCGAAT
Statistics
Matches: 66, Mismatches: 29, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
50 66 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (50 bp):
TGAATCTTACTTCCCTAGCGGTGCAGTGGAACAGATTGAAGCTACAACGA
Found at i:49131456 original size:100 final size:100
Alignment explanation
Indices: 49131283--49131476 Score: 291
Period size: 100 Copynumber: 1.9 Consensus size: 100
49131273 ATCGAAGATA
* *
49131283 GTGAATATTACTTCCCTTGCGGTGCAGTGGAACAGATTGAAGCTACAACGATGAATCTTGCTTCC
1 GTGAATATTACTTCCCTAGCGGTGCAGTGGAACAGATTGAAGCTACAACGACGAATCTTGCTTCC
49131348 CCAACATTGCAATTAAAAAGATTGAAGCCGCAACG
66 CCAACATTGCAATTAAAAAGATTGAAGCCGCAACG
* * * * *
49131383 GTGAATTTTACTTCCCTAGTGGTGTAGTGGGACAGATTGAAGCTACGAC-AGCGAATCTTGCTTC
1 GTGAATATTACTTCCCTAGCGGTGCAGTGGAACAGATTGAAGCTACAACGA-CGAATCTTGCTTC
* *
49131447 CCCGACATTGCAGTTAAAAAGATTGAAGCC
65 CCCAACATTGCAATTAAAAAGATTGAAGCC
49131477 ATACATTACA
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
99 1 0.01
100 83 0.99
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (100 bp):
GTGAATATTACTTCCCTAGCGGTGCAGTGGAACAGATTGAAGCTACAACGACGAATCTTGCTTCC
CCAACATTGCAATTAAAAAGATTGAAGCCGCAACG
Found at i:49131625 original size:44 final size:44
Alignment explanation
Indices: 49131484--49131911 Score: 220
Period size: 44 Copynumber: 9.9 Consensus size: 44
49131474 GCCATACATT
* * * ****
49131484 ACAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGA-TCGCGTC
1 ACAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC
* ** *
49131527 -CAG-TCTTATCTCCCTGAAGTTGCAGTGGAGAAGACGAAAGA-A
1 ACAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA-ATC
* *
49131569 ACTA-ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATC
1 AC-AGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC
** ** * ***
49131613 ACAGATCTTATCTATCTGAAGTTGCAGTATAGCTGA-TCGCATC
1 ACAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC
* ** *
49131656 -CAG-TCTTATCTCCCTGAAGTTGTAGTGGAGCAGACAGAAGAAGC
1 ACAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAA-AATC
* * * * *
49131700 -CA-ATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTGAAACC
1 ACAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC
* ** * ***
49131742 ATAGATCTTATCTTTCTGAAGTTGCAGTAGAGCAGA-TCGCATC
1 ACAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC
* * * *
49131785 -CAG-TCTTATCTCCCTGAAGTTGTAGTGGAGCAGGTTGAAGATA
1 ACAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAATC
* * * * ** *
49131828 ACA-ATCTTATCTCCCTAAAGTTACAGTGGAGAAAATTGAAGCTG
1 ACAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAATC
** * * *
49131872 TTA-ATCCTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAA
1 ACAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
49131912 CCACGAACCT
Statistics
Matches: 287, Mismatches: 81, Indels: 34
0.71 0.20 0.08
Matches are distributed among these distances:
41 78 0.27
42 12 0.04
43 16 0.06
44 181 0.63
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (44 bp):
ACAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC
Found at i:49131714 original size:129 final size:127
Alignment explanation
Indices: 49131484--49131858 Score: 534
Period size: 129 Copynumber: 2.9 Consensus size: 127
49131474 GCCATACATT
* * *
49131484 ACAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCGTCCAGTCTTATCTCCCTGAAGTTG
1 ACAGATCTTATCTATCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTG
* * * * *
49131549 CAGTGGAGAAGACGAAAGAAACTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATC
66 TAGTGGAGCAGACG-AAG-AACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACC
* *
49131613 ACAGATCTTATCTATCTGAAGTTGCAGTATAGCTGATCGCATCCAGTCTTATCTCCCTGAAGTTG
1 ACAGATCTTATCTATCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTG
*
49131678 TAGTGGAGCAGACAGAAGAAGCCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTGAAACC
66 TAGTGGAGCAGAC-GAAGAA-CCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACC
* *
49131742 ATAGATCTTATCTTTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTG
1 ACAGATCTTATCTATCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTG
** * * *
49131807 TAGTGGAGCAGGTTGAAGATAACAATCTTATCTCCCTAAAGTTACAGTGGAG
66 TAGTGGAGCA-GACGAAGA-ACCAATCCTATCTCCCTAAAGTTGCAGTGGAG
49131859 AAAATTGAAG
Statistics
Matches: 222, Mismatches: 20, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
128 2 0.01
129 217 0.98
130 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (127 bp):
ACAGATCTTATCTATCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTG
TAGTGGAGCAGACGAAGAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACC
Found at i:49131805 original size:85 final size:84
Alignment explanation
Indices: 49131486--49131823 Score: 256
Period size: 85 Copynumber: 4.0 Consensus size: 84
49131476 CATACATTAC
* * * **
49131486 AGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCGTCCAGTCTTATCTCCCTGAAGTTGCA
1 AGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATAGAATCCAGTCTTATCTCCCTGAAGTTGCA
* **
49131551 GTGGAGAAGACGAAAGAAA-CT
66 GTGGAG-CG--GATTGAAACCT
* * * * **
49131572 A-ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTATCTGAAGTT
1 AGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGA-TAGAATC-CAG-TCTTATCTCCCTGAAGTT
** * * * *
49131636 GCAGTATAGCTGATCGCATCC-
63 GCAGTGGAGCGGATTGAAACCT
* * * * *
49131657 AG-TCTTATCTCCCTGAAGTTGTAGTGGAGCAGACAGA-AGAAGCCAATCCTATCTCCCTAAAGT
1 AGATCTTATCTCCCTGAAGTTGCAGT--AG-AG-CAGATAGAATCCAGTCTTATCTCCCTGAAGT
49131720 TGCAGTGGAGCGGATTGAAACCAT
62 TGCAGTGGAGCGGATTGAAACC-T
** * * *
49131744 AGATCTTATCTTTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGTA
1 AGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATAGAATCCAGTCTTATCTCCCTGAAGTTGCA
49131809 GTGGAGCAGG-TTGAA
66 GTGGAGC-GGATTGAA
49131824 GATAACAATC
Statistics
Matches: 192, Mismatches: 46, Indels: 29
0.72 0.17 0.11
Matches are distributed among these distances:
84 4 0.02
85 119 0.62
86 11 0.06
87 10 0.05
88 45 0.23
89 3 0.02
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (84 bp):
AGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATAGAATCCAGTCTTATCTCCCTGAAGTTGCA
GTGGAGCGGATTGAAACCT
Found at i:49133460 original size:31 final size:31
Alignment explanation
Indices: 49133422--49133497 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 31
49133412 CAAATTTAGT
49133422 TATATATATATACATAAATACATTTTCATAA-
1 TATATATATATACATAAATA-ATTTTCATAAC
* * * *
49133453 TATATATATGTACATATATATTTTTTATAAC
1 TATATATATATACATAAATAATTTTCATAAC
49133484 T-TATATATATACAT
1 TATATATATATACAT
49133498 TCATACATAC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
30 20 0.51
31 19 0.49
ACGTcount: A:0.43, C:0.08, G:0.01, T:0.47
Consensus pattern (31 bp):
TATATATATATACATAAATAATTTTCATAAC
Found at i:49133593 original size:47 final size:47
Alignment explanation
Indices: 49133515--49133605 Score: 130
Period size: 47 Copynumber: 1.9 Consensus size: 47
49133505 TACGTACTCA
* *
49133515 TATATATATTTTATATATTTTGTAATTTATATACATGTTTATATATC
1 TATATATATTTTATATATTTTGTAATATATATACATGCTTATATATC
* *
49133562 TATATATATTTTCTAT-TTTTATGAATATATATACATGCTTATAT
1 TATATATATTTTATATATTTTGT-AATATATATACATGCTTATAT
49133606 TTTTTAAAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
46 5 0.13
47 34 0.87
ACGTcount: A:0.34, C:0.05, G:0.04, T:0.56
Consensus pattern (47 bp):
TATATATATTTTATATATTTTGTAATATATATACATGCTTATATATC
Found at i:49134329 original size:108 final size:107
Alignment explanation
Indices: 49134012--49134325 Score: 486
Period size: 109 Copynumber: 2.9 Consensus size: 107
49134002 ATACTTAAAA
* * *
49134012 AAAAATTCAAAGTAAGGCAATATTTTGTGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGG
1 AAAATTTCAAAGTAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGG
49134077 GTTTCGATCTTTCTCGTTCGACCAAATAGCCAAATATCCTTTC
66 GTTTCGAT-TTTCTCGTTCGACCAAATAGCCAAATATCCTTTC
* * *
49134120 AATATTTCCAAAGTAAGGCAATGTTTTGCGTTTGGGAATTCGAGAAAACGTGCCCTAATGTGTTG
1 AAAATTT-CAAAGTAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTG
*
49134185 GGTTTCGATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
65 GGTTTCGA-TTTTCTCGTTCGACCAAATAGCCAAATATCCTTTC
* * *
49134229 AAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCAAGAAAACGTGCTCTAATGTGCTGG
1 AAAATTTCAAAGTAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGG
* *
49134294 GTTTCGA-TTTCTCATTGGACCAAATAGCCAAA
66 GTTTCGATTTTCTCGTTCGACCAAATAGCCAAA
49134326 AATACTCTTA
Statistics
Matches: 189, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
106 23 0.12
108 65 0.34
109 100 0.53
110 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (107 bp):
AAAATTTCAAAGTAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGG
GTTTCGATTTTCTCGTTCGACCAAATAGCCAAATATCCTTTC
Found at i:49134949 original size:32 final size:32
Alignment explanation
Indices: 49134913--49134973 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
49134903 AAATAAACAC
49134913 ATAATTATTCATTT-AATA-TTATAACTATTCAA
1 ATAA-TATT-ATTTAAATAGTTATAACTATTCAA
*
49134945 ATAATATTATTTAAATAGTTATAATTATT
1 ATAATATTATTTAAATAGTTATAACTATT
49134974 TTTCAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 4 0.15
31 8 0.31
32 14 0.54
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (32 bp):
ATAATATTATTTAAATAGTTATAACTATTCAA
Found at i:49136094 original size:29 final size:29
Alignment explanation
Indices: 49136054--49136113 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
49136044 GTAGATACAA
* *
49136054 TTTAAAGGATTAAATTA-ATATTTTATTAT
1 TTTAAAGGATTAAAATATA-ATTTTATCAT
*
49136083 TTTAAAGTATTAAAATATAATTTTATCAT
1 TTTAAAGGATTAAAATATAATTTTATCAT
49136112 TT
1 TT
49136114 ATTAACTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 26 0.96
30 1 0.04
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (29 bp):
TTTAAAGGATTAAAATATAATTTTATCAT
Found at i:49138370 original size:29 final size:29
Alignment explanation
Indices: 49138312--49138371 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
49138302 ACTTATTCAC
* *
49138312 ATATATTTAAATATAAATATAGTATATAT
1 ATATATTTAAATATAAATAAAATATATAT
* *
49138341 ATATATTTAAA-ATATATGAAAATATTTAT
1 ATATATTTAAATATAAAT-AAAATATATAT
49138370 AT
1 AT
49138372 TAAATTGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (29 bp):
ATATATTTAAATATAAATAAAATATATAT
Found at i:49142612 original size:50 final size:50
Alignment explanation
Indices: 49142537--49142634 Score: 187
Period size: 50 Copynumber: 2.0 Consensus size: 50
49142527 TGACCAATAT
49142537 AATTATATTTAACCATATATACCATGTAACCAAGTAATCAACTAACTTAC
1 AATTATATTTAACCATATATACCATGTAACCAAGTAATCAACTAACTTAC
*
49142587 AATTATGTTTAACCATATATACCATGTAACCAAGTAATCAACTAACTT
1 AATTATATTTAACCATATATACCATGTAACCAAGTAATCAACTAACTT
49142635 TTATGTCTAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (50 bp):
AATTATATTTAACCATATATACCATGTAACCAAGTAATCAACTAACTTAC
Found at i:49144415 original size:24 final size:22
Alignment explanation
Indices: 49144366--49144418 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
49144356 ACTAATGAAT
* *
49144366 AGAGAGCACTGAAGTGCTATAC
1 AGAGAGCACAGAAGTGCTAAAC
*
49144388 AGAGAGCACAGATGTGCTAAAC
1 AGAGAGCACAGAAGTGCTAAAC
*
49144410 GGAGAGCAC
1 AGAGAGCAC
49144419 CAACGTGCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.38, C:0.19, G:0.30, T:0.13
Consensus pattern (22 bp):
AGAGAGCACAGAAGTGCTAAAC
Found at i:49144426 original size:22 final size:22
Alignment explanation
Indices: 49144366--49144429 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
49144356 ACTAATGAAT
* * *
49144366 AGAGAGCACTGAAGTGCTATAC
1 AGAGAGCACAGACGTGCTAAAC
*
49144388 AGAGAGCACAGATGTGCTAAAC
1 AGAGAGCACAGACGTGCTAAAC
*
49144410 GGAGAGCACCA-ACGTGCTAA
1 AGAGAGCA-CAGACGTGCTAA
49144430 TAATCAGAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
22 34 0.94
23 2 0.06
ACGTcount: A:0.38, C:0.20, G:0.28, T:0.14
Consensus pattern (22 bp):
AGAGAGCACAGACGTGCTAAAC
Found at i:49147400 original size:11 final size:11
Alignment explanation
Indices: 49147384--49147427 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
49147374 AAACTTTCTA
*
49147384 ATTTCACTTTT
1 ATTTCAATTTT
49147395 ATTTC-ATTTT
1 ATTTCAATTTT
*
49147405 AATTTCAATTTA
1 -ATTTCAATTTT
49147417 ATTTCAATTTT
1 ATTTCAATTTT
49147428 GCCATTAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 4 0.14
11 20 0.71
12 4 0.14
ACGTcount: A:0.27, C:0.11, G:0.00, T:0.61
Consensus pattern (11 bp):
ATTTCAATTTT
Found at i:49147410 original size:22 final size:23
Alignment explanation
Indices: 49147382--49147427 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
49147372 AGAAACTTTC
* *
49147382 TAATTTCACTTTTATTTC-ATTT
1 TAATTTCAATTTAATTTCAATTT
49147404 TAATTTCAATTTAATTTCAATTT
1 TAATTTCAATTTAATTTCAATTT
49147427 T
1 T
49147428 GCCATTAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.61
Consensus pattern (23 bp):
TAATTTCAATTTAATTTCAATTT
Found at i:49149593 original size:24 final size:20
Alignment explanation
Indices: 49149538--49149576 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
49149528 CAGGAAAACT
49149538 TGAAAAATTGTAGTTATGAG
1 TGAAAAATTGTAGTTATGAG
49149558 TGAAAAATTGTAGTTATGA
1 TGAAAAATTGTAGTTATGA
49149577 AGATAGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.23, T:0.36
Consensus pattern (20 bp):
TGAAAAATTGTAGTTATGAG
Found at i:49152976 original size:18 final size:15
Alignment explanation
Indices: 49152931--49152964 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
49152921 ATTCTTCCAG
*
49152931 TTTTCTTCTTCTTCT
1 TTTTCTTTTTCTTCT
49152946 TTTTCTTTTTCTTCT
1 TTTTCTTTTTCTTCT
49152961 TTTT
1 TTTT
49152965 GCTGATTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTCTTTTTCTTCT
Found at i:49153738 original size:15 final size:15
Alignment explanation
Indices: 49153699--49153731 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
49153689 CGAGAAGCTA
49153699 TTATAGAAAACTAAT
1 TTATAGAAAACTAAT
49153714 TTATAGAAAACTAAT
1 TTATAGAAAACTAAT
49153729 TTA
1 TTA
49153732 GTAAAAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (15 bp):
TTATAGAAAACTAAT
Found at i:49158752 original size:30 final size:30
Alignment explanation
Indices: 49158702--49158835 Score: 92
Period size: 30 Copynumber: 4.5 Consensus size: 30
49158692 AGGGCCTAAG
** * *
49158702 CCTTCAAAGTTTTGAAAATTTTATTTATAC
1 CCTTCAATTTTTTTAAAATTTTATTTAGAC
* **
49158732 CCTT-ACTTTTTTTAAAAATTTTAACTAGAC
1 CCTTCAATTTTTTT-AAAATTTTATTTAGAC
* *
49158762 CCTTCAATTTTTTTAAAATTATTA-TTAAAT
1 CCTTCAATTTTTTTAAAATT-TTATTTAGAC
* * ** * * *
49158792 CTTTGAAAATTTTCAAAATTTCAATTAGAC
1 CCTTCAATTTTTTTAAAATTTTATTTAGAC
49158822 CCTTCAATTTTTTT
1 CCTTCAATTTTTTT
49158836 TTTTTGTAAA
Statistics
Matches: 76, Mismatches: 24, Indels: 8
0.70 0.22 0.07
Matches are distributed among these distances:
29 7 0.09
30 58 0.76
31 11 0.14
ACGTcount: A:0.34, C:0.14, G:0.04, T:0.49
Consensus pattern (30 bp):
CCTTCAATTTTTTTAAAATTTTATTTAGAC
Found at i:49161226 original size:2 final size:2
Alignment explanation
Indices: 49161215--49161255 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
49161205 AAAACCTAGC
49161215 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
49161255 T
1 T
49161256 TAGATTTTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:49161894 original size:2 final size:2
Alignment explanation
Indices: 49161887--49161911 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
49161877 TTCTATTGAT
49161887 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 T
49161912 GTATGTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:49162535 original size:13 final size:13
Alignment explanation
Indices: 49162517--49162542 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49162507 CATTAAATTC
49162517 TTCTTTTTTTTTT
1 TTCTTTTTTTTTT
49162530 TTCTTTTTTTTTT
1 TTCTTTTTTTTTT
49162543 ATCATCAAAA
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:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TTCTTTTTTTTTT
Found at i:49174605 original size:9 final size:9
Alignment explanation
Indices: 49174587--49174626 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
49174577 TTTGGTTAAA
49174587 AATTAACCG
1 AATTAACCG
*
49174596 AATTACCCG
1 AATTAACCG
49174605 AATTAACCG
1 AATTAACCG
*
49174614 AATTAACCT
1 AATTAACCG
49174623 AATT
1 AATT
49174627 GAATCATACA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.42, C:0.23, G:0.07, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:49184166 original size:20 final size:20
Alignment explanation
Indices: 49184127--49184167 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
49184117 GTTGAATTGG
*
49184127 TTTATTAAATTTTTTATATT
1 TTTATTAAATTTTTAATATT
49184147 TTTATT-AATTTTTAATTATT
1 TTTATTAAATTTTTAA-TATT
49184167 T
1 T
49184168 ATATAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTATTAAATTTTTAATATT
Found at i:49184174 original size:19 final size:18
Alignment explanation
Indices: 49184127--49184175 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 18
49184117 GTTGAATTGG
49184127 TTTATTAAATTTTTTATATT
1 TTTATT-AA-TTTTTATATT
49184147 TTTATTAATTTTTA-ATT
1 TTTATTAATTTTTATATT
49184164 ATTTATATAATT
1 -TTTAT-TAATT
49184176 ATTGTTGATC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 3 0.11
18 11 0.41
19 7 0.26
20 6 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTATTAATTTTTATATT
Found at i:49185391 original size:41 final size:40
Alignment explanation
Indices: 49185346--49185478 Score: 162
Period size: 40 Copynumber: 3.3 Consensus size: 40
49185336 AAACAGGCTT
**
49185346 TTAGCGGCGTTTGTATAAAAAACGCCGCTAAAGATCGAGCA
1 TTAGCGGCGTTT-TATGGAAAACGCCGCTAAAGATCGAGCA
* *
49185387 TTAGCGGCGCTTTT-TGGAAAACGCTGCTAAAGATCGAGTA
1 TTAGCGGCG-TTTTATGGAAAACGCCGCTAAAGATCGAGCA
* * * *
49185427 TTAGTGGCGATTTATGGAAAACGCCGCTAAA-AACAAGCA
1 TTAGCGGCGTTTTATGGAAAACGCCGCTAAAGATCGAGCA
49185466 TTAGCGGCGTTTT
1 TTAGCGGCGTTTT
49185479 CCAGAAAGCG
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
39 19 0.24
40 46 0.59
41 10 0.13
42 3 0.04
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (40 bp):
TTAGCGGCGTTTTATGGAAAACGCCGCTAAAGATCGAGCA
Found at i:49185599 original size:41 final size:41
Alignment explanation
Indices: 49185529--49185656 Score: 156
Period size: 41 Copynumber: 3.1 Consensus size: 41
49185519 TTGTGAGCTT
*
49185529 TCAGGGC-TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGC
1 TCAGGGCTTTTAGCGGCGTTTTT-AAAAAGCGCCGCTAATGC
* * *
49185570 TCAGGGCTTTTAGCGGCGTTTTTATAAAGCGCCGCAAATGT
1 TCAGGGCTTTTAGCGGCGTTTTTAAAAAGCGCCGCTAATGC
*
49185611 TCTA---TTTTTAGCGGCGTTTTCTAAAAAGCGCCGCTAATGC
1 TC-AGGGCTTTTAGCGGCGTTTT-TAAAAAGCGCCGCTAATGC
49185651 TCAGGG
1 TCAGGG
49185657 ATTTAAAATA
Statistics
Matches: 74, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
39 16 0.22
40 18 0.24
41 24 0.32
42 16 0.22
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (41 bp):
TCAGGGCTTTTAGCGGCGTTTTTAAAAAGCGCCGCTAATGC
Found at i:49185857 original size:14 final size:14
Alignment explanation
Indices: 49185835--49185953 Score: 78
Period size: 14 Copynumber: 8.4 Consensus size: 14
49185825 TATCACTATA
* *
49185835 GTTTTGGGTTTTTG
1 GTTTAGGGTTTATG
*
49185849 GTTTAGGGTATATG
1 GTTTAGGGTTTATG
* *
49185863 GTTTAGAGTTTAAG
1 GTTTAGGGTTTATG
* *
49185877 ATTTA-GGTGTTACCG
1 GTTTAGGGT-TTA-TG
* *
49185892 TTTTAAGGTTTATG
1 GTTTAGGGTTTATG
* *
49185906 GATTATGGGTTTAGG
1 GTTTA-GGGTTTATG
* *
49185921 GGTTATGGTTTATG
1 GTTTAGGGTTTATG
*
49185935 GTTTATGGTTTATG
1 GTTTAGGGTTTATG
49185949 GTTTA
1 GTTTA
49185954 AAAGTTAGGG
Statistics
Matches: 82, Mismatches: 19, Indels: 8
0.75 0.17 0.07
Matches are distributed among these distances:
13 2 0.02
14 58 0.71
15 19 0.23
16 3 0.04
ACGTcount: A:0.18, C:0.02, G:0.31, T:0.50
Consensus pattern (14 bp):
GTTTAGGGTTTATG
Found at i:49185911 original size:7 final size:7
Alignment explanation
Indices: 49185893--49185953 Score: 77
Period size: 7 Copynumber: 8.6 Consensus size: 7
49185883 GTGTTACCGT
*
49185893 TTTAAGG
1 TTTATGG
49185900 TTTATGG
1 TTTATGG
*
49185907 ATTATGGG
1 TTTAT-GG
*
49185915 TTTAGGG
1 TTTATGG
*
49185922 GTTATGG
1 TTTATGG
49185929 TTTATGG
1 TTTATGG
49185936 TTTATGG
1 TTTATGG
49185943 TTTATGG
1 TTTATGG
49185950 TTTA
1 TTTA
49185954 AAAGTTAGGG
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
7 41 0.89
8 5 0.11
ACGTcount: A:0.18, C:0.00, G:0.31, T:0.51
Consensus pattern (7 bp):
TTTATGG
Found at i:49185972 original size:7 final size:7
Alignment explanation
Indices: 49185893--49186026 Score: 67
Period size: 7 Copynumber: 18.6 Consensus size: 7
49185883 GTGTTACCGT
49185893 TTTAAGG
1 TTTAAGG
*
49185900 TTTATGG
1 TTTAAGG
* *
49185907 ATTATGGG
1 TTTA-AGG
*
49185915 TTTAGGG
1 TTTAAGG
* *
49185922 GTTATGG
1 TTTAAGG
*
49185929 TTTATGG
1 TTTAAGG
*
49185936 TTTATGG
1 TTTAAGG
*
49185943 TTTATGG
1 TTTAAGG
*
49185950 TTTAAAAG
1 TTT-AAGG
*
49185958 -TTAGGG
1 TTTAAGG
49185964 TTTAAGG
1 TTTAAGG
49185971 TTTAGAGG
1 TTTA-AGG
*
49185979 -TT-ATG
1 TTTAAGG
49185984 TGTTAAGGG
1 T-TTAA-GG
*
49185993 TTTATGGG
1 TTTA-AGG
49186001 TTTAAGG
1 TTTAAGG
49186008 TTTTAAGG
1 -TTTAAGG
49186016 TTTAAGG
1 TTTAAGG
49186023 TTTA
1 TTTA
49186027 GATTAACTAG
Statistics
Matches: 101, Mismatches: 16, Indels: 20
0.74 0.12 0.15
Matches are distributed among these distances:
5 2 0.02
6 2 0.02
7 68 0.67
8 27 0.27
9 2 0.02
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.46
Consensus pattern (7 bp):
TTTAAGG
Found at i:49185975 original size:14 final size:14
Alignment explanation
Indices: 49185893--49186026 Score: 74
Period size: 14 Copynumber: 9.3 Consensus size: 14
49185883 GTGTTACCGT
*
49185893 TTTAAGGTTTATGG
1 TTTAAGGTTTAGGG
* *
49185907 ATTATGGGTTTAGGG
1 TTTA-AGGTTTAGGG
* * *
49185922 GTTATGGTTTATGG
1 TTTAAGGTTTAGGG
* *
49185936 TTTATGGTTTATGG
1 TTTAAGGTTTAGGG
*
49185950 TTTAAAAG-TTAGGG
1 TTT-AAGGTTTAGGG
49185964 TTTAAGGTTTAGAGG
1 TTTAAGGTTTAG-GG
* *
49185979 -TTATGTGTTAAGGG
1 TTTAAG-GTTTAGGG
* *
49185993 TTTATGGGTTTAAGGT
1 TTTA-AGGTTT-AGGG
*
49186009 TTTAAGGTTTAAGG
1 TTTAAGGTTTAGGG
49186023 TTTA
1 TTTA
49186027 GATTAACTAG
Statistics
Matches: 93, Mismatches: 19, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
13 3 0.03
14 51 0.55
15 31 0.33
16 8 0.09
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.46
Consensus pattern (14 bp):
TTTAAGGTTTAGGG
Found at i:49186012 original size:8 final size:8
Alignment explanation
Indices: 49185986--49186026 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
49185976 AGGTTATGTG
49185986 TTAAGGGT
1 TTAAGGGT
*
49185994 TTATGGGT
1 TTAAGGGT
*
49186002 TTAAGGTT
1 TTAAGGGT
49186010 TTAA-GGT
1 TTAAGGGT
49186017 TTAA-GGT
1 TTAAGGGT
49186024 TTA
1 TTA
49186027 GATTAACTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
7 12 0.41
8 17 0.59
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.46
Consensus pattern (8 bp):
TTAAGGGT
Found at i:49186299 original size:14 final size:14
Alignment explanation
Indices: 49186289--49186319 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
49186279 GATTTAAGGT
*
49186289 TTAAGTGTTAAGAG
1 TTAAGGGTTAAGAG
49186303 TTAAGGGTTAAGAG
1 TTAAGGGTTAAGAG
49186317 TTA
1 TTA
49186320 GGGATTTAGG
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:0.35, C:0.00, G:0.29, T:0.35
Consensus pattern (14 bp):
TTAAGGGTTAAGAG
Found at i:49186974 original size:19 final size:19
Alignment explanation
Indices: 49186950--49187017 Score: 73
Period size: 19 Copynumber: 3.3 Consensus size: 19
49186940 ATCAACGGCG
49186950 TTTTTATAAAATCCCTCCT
1 TTTTTATAAAATCCCTCCT
*
49186969 TTTTTATAAAATTCCACTGGCGCCG
1 TTTTTATAAAA-TCC-CT----CCT
49186994 TTTTTATAAAATCCCTCCT
1 TTTTTATAAAATCCCTCCT
49187013 TTTTT
1 TTTTT
49187018 CCCCCTTCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
19 18 0.44
20 3 0.07
21 2 0.05
23 2 0.05
24 3 0.07
25 13 0.32
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.47
Consensus pattern (19 bp):
TTTTTATAAAATCCCTCCT
Found at i:49189736 original size:18 final size:18
Alignment explanation
Indices: 49189713--49189749 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
49189703 TGCCTACGTG
49189713 TATATATATATTAGATTA
1 TATATATATATTAGATTA
49189731 TATATATATATTAGATTA
1 TATATATATATTAGATTA
49189749 T
1 T
49189750 TCAAAATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (18 bp):
TATATATATATTAGATTA
Found at i:49190607 original size:27 final size:26
Alignment explanation
Indices: 49190577--49190633 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
49190567 AATTTTGAGG
*
49190577 TTTACAATTTT-TAATTTTTATTAATT
1 TTTAC-ATTTTCTAACTTTTATTAATT
* *
49190603 ATTTACGTTTTCTCACTTTTATTAATT
1 -TTTACATTTTCTAACTTTTATTAATT
49190630 TTTA
1 TTTA
49190634 TTATTATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTACATTTTCTAACTTTTATTAATT
Found at i:49190918 original size:43 final size:43
Alignment explanation
Indices: 49190820--49191115 Score: 409
Period size: 43 Copynumber: 6.9 Consensus size: 43
49190810 ATGATATGTT
* * * * * *
49190820 TTTAGCGGCGTTTTTGCGG-GAAGCGTCGCTAAAAGT-TTGTTC
1 TTTAGCGGCGTTTGTG-GGAAAAGCGCCGCTAAAGGTCATGGTC
* *
49190862 TATAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
*
49190905 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* *
49190948 TTTAGCGGCGTTTGTGGAAAAAGCGACGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* *
49190991 TTTAGCGGCGTTTGTGGGAAAAGCGACGCTAAAGGTCCTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* *
49191034 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCGTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* *
49191077 TATAGCGGCGTTTGTGGG-AAAGTGCCGCTAAAGGTCATG
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATG
49191116 ACTTTTAGCG
Statistics
Matches: 230, Mismatches: 22, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
41 2 0.01
42 47 0.20
43 181 0.79
ACGTcount: A:0.21, C:0.18, G:0.34, T:0.27
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:49192669 original size:112 final size:113
Alignment explanation
Indices: 49192429--49193028 Score: 808
Period size: 114 Copynumber: 5.3 Consensus size: 113
49192419 AAAATAAGCA
* * * *
49192429 TTAGCGGCGTTTATTTGAAAGCGCCGCAAAAAGCCTAAGCCAAACGGTACCGTTTTCTGAGTTTT
1 TTAGCGGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
** * *
49192494 TGGGGGTCTTTAGCGGCGTTTCTATAAAGCGCCGCTAATTCTCAGGTCT
66 T-GGGGTCTTTAGCGGCGTTTCTGCAATGCGCCGCTAATGCTCAGGTCT
* * * * * *
49192543 GTAGCGGCGGTTTTTTAACAGCGCCGCAAAAAGCCTAAACCCAACAGTACCGTTTTCTGAG-TTT
1 TTAGCGGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
* * *
49192607 TGGGGTCTTTAGCGACGTTTCTGCACTGCGCCGCTAATGCTGAGGTCT
66 TGGGGTCTTTAGCGGCGTTTCTGCAATGCGCCGCTAATGCTCAGGTCT
* * *
49192655 TTAGCGGCGTTTTTTTAAAAGCGCCGCAACAAGCCTAAACCCAACGGCACCGTTTTCTGAATTTT
1 TTAGCGGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
* * * * * * *
49192720 TGGGGGCCTTTCGCGGCATTTTTGTAATGCGCCGCTAATTCTTAGGTCTT
66 T-GGGGTCTTTAGCGGCGTTTCTGCAATGCGCCGCTAATGCTCAGGTC-T
* * *
49192770 TTAGCGGCGTTTTGTTAAAAGCGCCGCAAAAAGCCTAAGCCAAACGACACCGTTTTCTGAGTTTT
1 TTAGCGGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
* * * *
49192835 TGGGGTCTTTAGCGGCGTTTTTTCAAAGCGCCGCTAATGCTCAGGTGT
66 TGGGGTCTTTAGCGGCGTTTCTGCAATGCGCCGCTAATGCTCAGGTCT
* *
49192883 TTAGCAGCGTTTTTTTAAAAGTGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
1 TTAGCGGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
49192948 TGGGGTCTTTAGCGGCGTTTCTG-AATAAGCGCCGCTAATGCTCAGGTCT
66 TGGGGTCTTTAGCGGCGTTTCTGCAAT--GCGCCGCTAATGCTCAGGTCT
*
49192997 TTAGCGGCGTTTTTTAAAAAGCGCCGCAAAAA
1 TTAGCGGCGTTTTTTTAAAAGCGCCGCAAAAA
49193029 CATTTTATCT
Statistics
Matches: 423, Mismatches: 58, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
112 96 0.23
113 90 0.21
114 176 0.42
115 61 0.14
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (113 bp):
TTAGCGGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
TGGGGTCTTTAGCGGCGTTTCTGCAATGCGCCGCTAATGCTCAGGTCT
Found at i:49193797 original size:92 final size:89
Alignment explanation
Indices: 49193627--49193879 Score: 368
Period size: 92 Copynumber: 2.8 Consensus size: 89
49193617 ATGTTTAGGG
* *
49193627 GTTAGGGATTTAGG-GTTAGATTAATTAGTG-TTTTTAATTGATATATTAAATAATGTTTAGGGG
1 GTTAGGG-TTTAGGATTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAATGTTTAGGGG
49193690 TTAGGGGTTAGTGATTCGGGGTCGA
65 TTAGGGGTTAGTGATTCGGGGTCGA
49193715 GTTAGGGTTTAGGATTTAGATTAATTAGTGTTTTTTAATTTATATATTAATAAATAATGTTTAGG
1 GTTAGGGTTTAGGATTTAGATTAATTAGTGTTTTTTAATTTATATA-T--TAAATAATGTTTAGG
*
49193780 GGTTTGGGGTTAGTGATTCGGGGTCGA
63 GGTTAGGGGTTAGTGATTCGGGGTCGA
* * ** *
49193807 GTTAGGGTTTAGGATTTAGATTGATTAGTGTTTTATAATTTATATAACAAA-AAGTGTTTAGGGT
1 GTTAGGGTTTAGGATTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAA-TGTTTAGGGG
49193871 TTAGGGGTT
65 TTAGGGGTT
49193880 TGGGGTTTGG
Statistics
Matches: 150, Mismatches: 9, Indels: 11
0.88 0.05 0.06
Matches are distributed among these distances:
87 6 0.04
88 24 0.16
89 34 0.23
90 1 0.01
92 85 0.57
ACGTcount: A:0.27, C:0.02, G:0.28, T:0.43
Consensus pattern (89 bp):
GTTAGGGTTTAGGATTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAATGTTTAGGGGT
TAGGGGTTAGTGATTCGGGGTCGA
Found at i:49193874 original size:7 final size:7
Alignment explanation
Indices: 49193862--49193928 Score: 50
Period size: 7 Copynumber: 9.4 Consensus size: 7
49193852 AACAAAAAGT
49193862 GTTTAGG
1 GTTTAGG
49193869 GTTTAGGG
1 GTTTA-GG
*
49193877 GTTTGGG
1 GTTTAGG
*
49193884 GTTTGGG
1 GTTTAGG
*
49193891 GTTTGGG
1 GTTTAGG
49193898 GTTT-GG
1 GTTTAGG
49193904 TGTTT-GG
1 -GTTTAGG
49193911 TGTTTGAGG
1 -GTTT-AGG
49193920 G-TTAGG
1 GTTTAGG
49193926 GTT
1 GTT
49193929 AAGAGTTAGT
Statistics
Matches: 54, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
6 6 0.11
7 39 0.72
8 7 0.13
9 2 0.04
ACGTcount: A:0.06, C:0.00, G:0.49, T:0.45
Consensus pattern (7 bp):
GTTTAGG
Found at i:49193893 original size:14 final size:14
Alignment explanation
Indices: 49193862--49193922 Score: 77
Period size: 14 Copynumber: 4.2 Consensus size: 14
49193852 AACAAAAAGT
*
49193862 GTTTAGGGTTTAGGG
1 GTTTGGGGTTT-GGG
49193877 GTTTGGGGTTTGGG
1 GTTTGGGGTTTGGG
*
49193891 GTTTGGGGTTTGGT
1 GTTTGGGGTTTGGG
*
49193905 GTTTGGTGTTTGAGG
1 GTTTGGGGTTTG-GG
49193920 GTT
1 GTT
49193923 AGGGTTAAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
14 27 0.66
15 14 0.34
ACGTcount: A:0.05, C:0.00, G:0.49, T:0.46
Consensus pattern (14 bp):
GTTTGGGGTTTGGG
Found at i:49193900 original size:21 final size:21
Alignment explanation
Indices: 49193862--49193922 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
49193852 AACAAAAAGT
*
49193862 GTTTAGGGTTTAGGGGTTTGGG
1 GTTTGGGGTTT-GGGGTTTGGG
*
49193884 GTTTGGGGTTTGGGGTTTGGT
1 GTTTGGGGTTTGGGGTTTGGG
*
49193905 GTTTGGTGTTTGAGGGTT
1 GTTTGGGGTTTG-GGGTT
49193923 AGGGTTAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 20 0.57
22 15 0.43
ACGTcount: A:0.05, C:0.00, G:0.49, T:0.46
Consensus pattern (21 bp):
GTTTGGGGTTTGGGGTTTGGG
Found at i:49193964 original size:17 final size:18
Alignment explanation
Indices: 49193942--49193980 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
49193932 AGTTAGTGAT
49193942 TTAAGGTTT-AGATCAGA
1 TTAAGGTTTAAGATCAGA
*
49193959 TTAAGGTTTAAGCTCAGA
1 TTAAGGTTTAAGATCAGA
49193977 TTAA
1 TTAA
49193981 TTATTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.36
Consensus pattern (18 bp):
TTAAGGTTTAAGATCAGA
Found at i:49194328 original size:21 final size:20
Alignment explanation
Indices: 49194289--49194333 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
49194279 AATTTGGACC
49194289 AAAATATAAGAAAAAATAAA
1 AAAATATAAGAAAAAATAAA
49194309 AAAATATAA-AAAGGAAATAAA
1 AAAATATAAGAAA--AAATAAA
49194330 AAAA
1 AAAA
49194334 CTAATAATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.13
20 9 0.39
21 11 0.48
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (20 bp):
AAAATATAAGAAAAAATAAA
Found at i:49199017 original size:66 final size:66
Alignment explanation
Indices: 49198941--49199069 Score: 206
Period size: 66 Copynumber: 2.0 Consensus size: 66
49198931 AGCAAATTAC
*
49198941 ACAACTTAAAGCAGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAG
1 ACAACTTAAAGCAGAGGCAACAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCAG
49199005 TT
65 TT
* * *
49199007 ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCA
1 ACAACTTAAAGCAGAGGCAACAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCA
49199070 ACAACAGCTT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
66 54 0.93
67 4 0.07
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.16
Consensus pattern (66 bp):
ACAACTTAAAGCAGAGGCAACAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGT
T
Found at i:49199102 original size:66 final size:66
Alignment explanation
Indices: 49198941--49199105 Score: 179
Period size: 66 Copynumber: 2.5 Consensus size: 66
49198931 AGCAAATTAC
* * * * * **
49198941 ACAACTTAAAGCAGAGGCAACATCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGT
1 ACAACTTAAAGCAAATGCAGCAGCAAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAAC
*
49199006 T
66 A
* * *
49199007 ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAG-TATGAAGAACTCCAA
1 ACAACTTAAAGCAAATGCAGCAGCAAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAA
49199071 CA
65 CA
* * * *
49199073 ACAGCTTAGAGCAAATGCGGCGGCAAGAGAAGC
1 ACAACTTAAAGCAAATGCAGCAGCAAGAGAAGC
49199106 AGAGACGGCA
Statistics
Matches: 85, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
66 81 0.95
67 4 0.05
ACGTcount: A:0.42, C:0.19, G:0.25, T:0.14
Consensus pattern (66 bp):
ACAACTTAAAGCAAATGCAGCAGCAAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAAC
A
Found at i:49199163 original size:21 final size:21
Alignment explanation
Indices: 49199136--49199193 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
49199126 TACAGGTTGC
49199136 AGCGAGGGAAGTAGAGGCTAA
1 AGCGAGGGAAGTAGAGGCTAA
* * **
49199157 AGTGAGGGAAATAGAGGCTGC
1 AGCGAGGGAAGTAGAGGCTAA
*
49199178 AGCGAGGGAAGCAGAG
1 AGCGAGGGAAGTAGAG
49199194 CAGCGTCAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.36, C:0.10, G:0.45, T:0.09
Consensus pattern (21 bp):
AGCGAGGGAAGTAGAGGCTAA
Found at i:49199620 original size:43 final size:43
Alignment explanation
Indices: 49199564--49199688 Score: 119
Period size: 43 Copynumber: 2.9 Consensus size: 43
49199554 GTTTTTGGTC
* * *
49199564 AAAGCGTCGCTAAAGATTAGGGTCTTTTGCGACGTTTGT-G-G
1 AAAGCGCCACTAAAGATTAGGGTCTTTAGCGACGTTTGTAGTG
* * * *
49199605 AAAAGGCGCCACTAAAGCTCATGGTCTTTAGCGGCGTTTGTAGTG
1 -AAA-GCGCCACTAAAGATTAGGGTCTTTAGCGACGTTTGTAGTG
* * * *
49199650 AAAGCGCCACTAAAGATTCGGTTCTTTAGTGGCGTTTGT
1 AAAGCGCCACTAAAGATTAGGGTCTTTAGCGACGTTTGT
49199689 TGTCTATACG
Statistics
Matches: 67, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
42 3 0.04
43 59 0.88
44 4 0.06
45 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (43 bp):
AAAGCGCCACTAAAGATTAGGGTCTTTAGCGACGTTTGTAGTG
Found at i:49201611 original size:2 final size:2
Alignment explanation
Indices: 49201604--49201638 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
49201594 AAATTAAAGT
*
49201604 TA TA TA TA TA TA TA TA TA AA 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 T
49201639 TCGAACTACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:49201729 original size:29 final size:27
Alignment explanation
Indices: 49201665--49201729 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 27
49201655 GTAACATGTG
*
49201665 TATAATTACACTAAATCAAAATTTATG
1 TATAATTACACTAAATCAAAATTTATA
*
49201692 TATCAAATTACACAGTAAATTAAAATTTATA
1 TAT--AATTACAC--TAAATCAAAATTTATA
49201723 TATAATT
1 TATAATT
49201730 TTGATATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 3 0.09
29 12 0.38
31 17 0.53
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.38
Consensus pattern (27 bp):
TATAATTACACTAAATCAAAATTTATA
Found at i:49208817 original size:42 final size:42
Alignment explanation
Indices: 49208749--49208940 Score: 217
Period size: 42 Copynumber: 4.6 Consensus size: 42
49208739 AGCTGAATAA
** *
49208749 AAGCTCATGAGAGCTAAACAAAAACCCATAAGGGTTAAACAG
1 AAGCTCAAAAGAGCTAAACAGAAACCCATAAGGGTTAAACAG
** * * *
49208791 AAGCTTGTAAA-AGCTGAACGGAAACCCATAAGGGTTAAATAG
1 AAGC-TCAAAAGAGCTAAACAGAAACCCATAAGGGTTAAACAG
*
49208833 AAGCTCAAAAGAGCTGAACAGAAACCCATAAGGGTTAAACAG
1 AAGCTCAAAAGAGCTAAACAGAAACCCATAAGGGTTAAACAG
* * *
49208875 AAGCTCAAAAGAGCTAAACAGAAACTCATATGAGTTAAACAG
1 AAGCTCAAAAGAGCTAAACAGAAACCCATAAGGGTTAAACAG
* **
49208917 AATCTTGTAAA-AGCTAAACAGAAA
1 AAGC-TCAAAAGAGCTAAACAGAAA
49208941 GTAAAACACG
Statistics
Matches: 128, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
41 4 0.03
42 118 0.92
43 6 0.05
ACGTcount: A:0.48, C:0.17, G:0.19, T:0.16
Consensus pattern (42 bp):
AAGCTCAAAAGAGCTAAACAGAAACCCATAAGGGTTAAACAG
Found at i:49208873 original size:21 final size:21
Alignment explanation
Indices: 49208752--49208918 Score: 109
Period size: 21 Copynumber: 8.0 Consensus size: 21
49208742 TGAATAAAAG
* * *
49208752 CTCATGAGAGCTAAACAAAAA
1 CTCATAAGAGTTAAACAGAAA
* * *
49208773 CCCATAAGGGTTAAACAGAAG
1 CTCATAAGAGTTAAACAGAAA
** * * * *
49208794 CTTGTAAAAGCTGAACGGAAA
1 CTCATAAGAGTTAAACAGAAA
* * * *
49208815 CCCATAAGGGTTAAATAGAAG
1 CTCATAAGAGTTAAACAGAAA
* * *
49208836 CTCAAAAGAGCTGAACAGAAA
1 CTCATAAGAGTTAAACAGAAA
* * *
49208857 CCCATAAGGGTTAAACAGAAG
1 CTCATAAGAGTTAAACAGAAA
* *
49208878 CTCAAAAGAGCTAAACAGAAA
1 CTCATAAGAGTTAAACAGAAA
*
49208899 CTCATATGAGTTAAACAGAA
1 CTCATAAGAGTTAAACAGAA
49208919 TCTTGTAAAA
Statistics
Matches: 100, Mismatches: 46, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
21 100 1.00
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.16
Consensus pattern (21 bp):
CTCATAAGAGTTAAACAGAAA
Found at i:49210094 original size:7 final size:7
Alignment explanation
Indices: 49210082--49210114 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
49210072 AAAAAAATTA
49210082 ATAAAAT
1 ATAAAAT
49210089 ATAAAAT
1 ATAAAAT
49210096 ATAAAAT
1 ATAAAAT
49210103 ATAAAAT
1 ATAAAAT
49210110 ATAAA
1 ATAAA
49210115 TAAATGTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
ATAAAAT
Found at i:49217484 original size:2 final size:2
Alignment explanation
Indices: 49217477--49217506 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
49217467 TAATATCATT
49217477 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
49217507 TATATTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:49230986 original size:18 final size:18
Alignment explanation
Indices: 49230963--49230997 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
49230953 TATATAATAT
49230963 TTTTTTAAATATATTTAA
1 TTTTTTAAATATATTTAA
*
49230981 TTTTTTAATTATATTTA
1 TTTTTTAAATATATTTA
49230998 TATCATATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTTTAAATATATTTAA
Found at i:49234371 original size:20 final size:18
Alignment explanation
Indices: 49234333--49234382 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 18
49234323 AACATTTCCT
49234333 TTAATTAATTTAAAAAAA
1 TTAATTAATTTAAAAAAA
*
49234351 TTAATTCATTTAATTAAAAA
1 TTAATTAATTTAA--AAAAA
*
49234371 TCAATTAATTTA
1 TTAATTAATTTA
49234383 CTTGGCTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 12 0.44
20 15 0.56
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAATTAATTTAAAAAAA
Found at i:49238915 original size:22 final size:22
Alignment explanation
Indices: 49238890--49238931 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
49238880 ATGTTTTTTA
*
49238890 AATTTTGT-TTTTAATTTAATTT
1 AATTTT-TCTTTTAATATAATTT
49238912 AATTTTTCTTTTAATATAAT
1 AATTTTTCTTTTAATATAAT
49238932 ATATTTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
AATTTTTCTTTTAATATAATTT
Found at i:49240791 original size:32 final size:32
Alignment explanation
Indices: 49240755--49240904 Score: 147
Period size: 32 Copynumber: 4.7 Consensus size: 32
49240745 ATGTTTTATA
*
49240755 TATTTCCGAATTGAATTGTATAGGTATAGACC
1 TATTTCCGAATTGAATTGTATAGGTATACACC
** *
49240787 TATTTTTGAATTGAATTGTATATGTATACACC
1 TATTTCCGAATTGAATTGTATAGGTATACACC
* * * * * ***
49240819 TATTGCTGAAATGAATTATATATGTATACTTA
1 TATTTCCGAATTGAATTGTATAGGTATACACC
* * *
49240851 TATTGCCGAATTTAATTGTATAGGTATACACA
1 TATTTCCGAATTGAATTGTATAGGTATACACC
* *
49240883 TATTGCCGAATTGATTTGTATA
1 TATTTCCGAATTGAATTGTATA
49240905 TATATTTATG
Statistics
Matches: 98, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 98 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (32 bp):
TATTTCCGAATTGAATTGTATAGGTATACACC
Found at i:49247468 original size:23 final size:23
Alignment explanation
Indices: 49247442--49247486 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
49247432 ATCTTTAAAA
*
49247442 TTTATACATATTCGATAAAAGAG
1 TTTATACATATTCAATAAAAGAG
* *
49247465 TTTATATATATTTAATAAAAGA
1 TTTATACATATTCAATAAAAGA
49247487 ACATGTCTCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (23 bp):
TTTATACATATTCAATAAAAGAG
Found at i:49257399 original size:5 final size:5
Alignment explanation
Indices: 49257391--49257416 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
49257381 GAGATGGAAT
49257391 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
49257417 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:49257416 original size:26 final size:26
Alignment explanation
Indices: 49257365--49257416 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
49257355 TGAAGTTTTC
* * *
49257365 TCGAATCGAGTCGAGTGAGATGGAAT
1 TCGAATCGAATCGAATGAGATCGAAT
49257391 TCGAATCGAATCGAATCGA-ATCGAAT
1 TCGAATCGAATCGAAT-GAGATCGAAT
49257417 ATATTTGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (26 bp):
TCGAATCGAATCGAATGAGATCGAAT
Found at i:49258346 original size:9 final size:9
Alignment explanation
Indices: 49258332--49258368 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
49258322 TATAGTTTGA
49258332 TATTCGAAT
1 TATTCGAAT
49258341 TATTCGAAT
1 TATTCGAAT
*
49258350 TATTCGAGT
1 TATTCGAAT
49258359 TATTCGAAT
1 TATTCGAAT
49258368 T
1 T
49258369 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:49258438 original size:9 final size:9
Alignment explanation
Indices: 49258421--49258451 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
49258411 TCGAGTTGAT
49258421 TCGAATAAC
1 TCGAATAAC
*
49258430 TCGATTAAC
1 TCGAATAAC
49258439 TCGAATAAC
1 TCGAATAAC
49258448 TCGA
1 TCGA
49258452 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:49258713 original size:22 final size:22
Alignment explanation
Indices: 49258680--49258740 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 22
49258670 GCCCGGCCCG
*
49258680 TTTTTAATTAAAATTAAAATTAT
1 TTTTTAA-TAAAATTAAAATTAA
49258703 TTTTTAATAAAATTAAAATTAA
1 TTTTTAATAAAATTAAAATTAA
* *
49258725 TTGTTATTAAAATTAA
1 TTTTTAATAAAATTAA
49258741 TTGTTAGTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 28 0.80
23 7 0.20
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTTTAATAAAATTAAAATTAA
Found at i:49258733 original size:16 final size:16
Alignment explanation
Indices: 49258714--49258755 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
49258704 TTTTAATAAA
49258714 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
49258730 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
*
49258746 AGTAAAATTA
1 ATTAAAATTA
49258756 TCAAATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (16 bp):
ATTAAAATTAATTGTT
Found at i:49258860 original size:68 final size:68
Alignment explanation
Indices: 49258744--49258953 Score: 370
Period size: 68 Copynumber: 3.1 Consensus size: 68
49258734 AAATTAATTG
* *
49258744 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTATCATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
49258807 TGA
66 TGA
*
49258810 TTAGGAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
49258875 TGA
66 TGA
*
49258878 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
49258943 TGA
66 TGA
49258946 TTAGTAAA
1 TTAGTAAA
49258954 ACAAACTTGA
Statistics
Matches: 137, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
66 25 0.18
68 112 0.82
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.46
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:49258861 original size:9 final size:9
Alignment explanation
Indices: 49258828--49258855 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
49258818 TTTATCAAAT
49258828 TATTAATTG
1 TATTAATTG
49258837 TATTAATTG
1 TATTAATTG
49258846 TATTAATTG
1 TATTAATTG
49258855 T
1 T
49258856 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:49258908 original size:9 final size:9
Alignment explanation
Indices: 49258896--49258923 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
49258886 TTTATCAAAT
49258896 TATTAATTG
1 TATTAATTG
49258905 TATTAATTG
1 TATTAATTG
49258914 TATTAATTG
1 TATTAATTG
49258923 T
1 T
49258924 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:49259015 original size:16 final size:16
Alignment explanation
Indices: 49258994--49259029 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
49258984 TTTGGTTCGC
49258994 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
49259010 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
49259026 TGTA
1 TGTA
49259030 ATAGCTAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:49259094 original size:44 final size:45
Alignment explanation
Indices: 49259010--49259100 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
49259000 GGATTAGAGG
* * *
49259010 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
49259055 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
49259099 TG
1 TG
49259101 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:49263115 original size:171 final size:171
Alignment explanation
Indices: 49262825--49263173 Score: 680
Period size: 171 Copynumber: 2.0 Consensus size: 171
49262815 AACCAACCGG
49262825 TTTCGAACCCAATTACCAACCCAATAAAAATAAAACTAAAGTCTAACTCTTAAGTATCTACCCAA
1 TTTC-AACCCAATTACCAACCCAATAAAAATAAAACTAAAGTCTAACTCTTAAGTATCTACCCAA
49262890 TTACACATGTTTTATTTTTTAGGTTTAATGCAAATGGAAATTTTTTGGAGAGAAGAAATGGATAT
65 TTACACATGTTTTATTTTTTAGGTTTAATGCAAATGGAAATTTTTTGGAGAGAAGAAATGGATAT
49262955 AAATGGAGAATATTAAAGACTTACATTTCAACTATGTGTTAA
130 AAATGGAGAATATTAAAGACTTACATTTCAACTATGTGTTAA
*
49262997 TTTCAACCCAATTACCAACCCAATAGAAATAAAACTAAAGTCTAACTCTTAAGTATCTACCCAAT
1 TTTCAACCCAATTACCAACCCAATAAAAATAAAACTAAAGTCTAACTCTTAAGTATCTACCCAAT
49263062 TACACATGTTTTATTTTTTAGGTTTAATGCAAATGGAAATTTTTTGGAGAGAAGAAATGGATATA
66 TACACATGTTTTATTTTTTAGGTTTAATGCAAATGGAAATTTTTTGGAGAGAAGAAATGGATATA
49263127 AATGGAGAATATTAAAGACTTACATTTCAACTATGTGTTAA
131 AATGGAGAATATTAAAGACTTACATTTCAACTATGTGTTAA
49263168 TTTCAA
1 TTTCAA
49263174 GAATTATGTA
Statistics
Matches: 176, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
171 172 0.98
172 4 0.02
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (171 bp):
TTTCAACCCAATTACCAACCCAATAAAAATAAAACTAAAGTCTAACTCTTAAGTATCTACCCAAT
TACACATGTTTTATTTTTTAGGTTTAATGCAAATGGAAATTTTTTGGAGAGAAGAAATGGATATA
AATGGAGAATATTAAAGACTTACATTTCAACTATGTGTTAA
Found at i:49263195 original size:17 final size:17
Alignment explanation
Indices: 49263175--49263237 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
49263165 TAATTTCAAG
49263175 AATTATGTAATGTTTTT
1 AATTATGTAATGTTTTT
* ***
49263192 AATTATGTAGTGATTCAA
1 AATTATGTAATG-TTTTT
*
49263210 AGACTTATGTAATATTTTT
1 A-A-TTATGTAATGTTTTT
49263229 AATTATGTA
1 AATTATGTA
49263238 GTGATTCAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 18 0.53
18 4 0.12
19 4 0.12
20 8 0.24
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.49
Consensus pattern (17 bp):
AATTATGTAATGTTTTT
Found at i:49263199 original size:37 final size:37
Alignment explanation
Indices: 49263172--49263246 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
49263162 TGTTAATTTC
* *
49263172 AAGAATTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAGTAATTCA
* *
49263209 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAGTAATTCA
49263246 A
1 A
49263247 TTCGGGTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (37 bp):
AAGAATTATGTAATATTTTTAATTATGTAGTAATTCA
Found at i:49263259 original size:9 final size:9
Alignment explanation
Indices: 49263245--49263275 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
49263235 GTAGTGATTC
*
49263245 AATTCGGGT
1 AATTCGGTT
49263254 AATTCGGTT
1 AATTCGGTT
49263263 AATTCGGTT
1 AATTCGGTT
49263272 AATT
1 AATT
49263276 TTTAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:49265383 original size:3 final size:3
Alignment explanation
Indices: 49265365--49265414 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
49265355 TATTTTGTTC
* *
49265365 ATT ATT -TT AAT ATT ATT ATC ATT -TT CATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT
49265409 ATT ATT
1 ATT ATT
49265415 GTCATTACTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 34 0.85
4 2 0.05
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:49266795 original size:16 final size:17
Alignment explanation
Indices: 49266765--49266797 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
49266755 TTGTTTATTA
*
49266765 TTTAATAAATGTAATAT
1 TTTAATAAATATAATAT
49266782 TTTAAT-AATATAATAT
1 TTTAATAAATATAATAT
49266798 AATAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTTAATAAATATAATAT
Found at i:49268216 original size:24 final size:24
Alignment explanation
Indices: 49268174--49268224 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
49268164 AATCAAAGTC
** *
49268174 AAATATATTATGTTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
49268198 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
49268222 AAA
1 AAA
49268225 CATCCTAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:49272612 original size:24 final size:24
Alignment explanation
Indices: 49272570--49272621 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
49272560 AACCAAAGTC
** *
49272570 AAATATATTATGTTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
49272594 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
49272618 AAAT
1 AAAT
49272622 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:49277113 original size:25 final size:27
Alignment explanation
Indices: 49277085--49277136 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
49277075 ATATAACAAG
*
49277085 TCATAATTC-ATATTTTAAAAA-AAAT
1 TCATAATTCAAAATTTTAAAAATAAAT
49277110 TCATAATTCAAAATTTTAAAAATAAAT
1 TCATAATTCAAAATTTTAAAAATAAAT
49277137 GATAAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 9 0.38
26 11 0.46
27 4 0.17
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (27 bp):
TCATAATTCAAAATTTTAAAAATAAAT
Found at i:49277190 original size:48 final size:51
Alignment explanation
Indices: 49277129--49277259 Score: 146
Period size: 52 Copynumber: 2.6 Consensus size: 51
49277119 AAAATTTTAA
* * *
49277129 AAATAAATGATAAATATTTTACATAT-T-TTT-AAAATGATTTTTGGGTAC
1 AAATAAATAATAAATATTTAAAATATATATTTGAAAATGATTTTTGGGTAC
* **
49277177 AAATAAATAATAAATAATTTAAAATATATATTTGAAAATTATTTTTTTGTAC
1 AAATAAATAATAAAT-ATTTAAAATATATATTTGAAAATGATTTTTGGGTAC
*
49277229 AAATAAAAAATAAA-ATTTAAAAT-TAATATTT
1 AAATAAATAATAAATATTTAAAATAT-ATATTT
49277260 TTGATACCAG
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
48 14 0.20
49 10 0.14
50 16 0.23
51 3 0.04
52 28 0.39
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.42
Consensus pattern (51 bp):
AAATAAATAATAAATATTTAAAATATATATTTGAAAATGATTTTTGGGTAC
Found at i:49279245 original size:2 final size:2
Alignment explanation
Indices: 49279238--49279277 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
49279228 AATTTTATTT
49279238 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
49279278 CGTACATAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:49280445 original size:13 final size:14
Alignment explanation
Indices: 49280427--49280460 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
49280417 TTTAGGCCAG
49280427 TTGGGCTA-GGGTA
1 TTGGGCTAGGGGTA
49280440 TTGGGCTAGGGGTA
1 TTGGGCTAGGGGTA
*
49280454 TTTGGCT
1 TTGGGCT
49280461 TAGTGGGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.12, C:0.09, G:0.44, T:0.35
Consensus pattern (14 bp):
TTGGGCTAGGGGTA
Found at i:49284751 original size:18 final size:20
Alignment explanation
Indices: 49284723--49284761 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
49284713 TTATAAATAT
49284723 TTAATTATTATA-TTTAAAA
1 TTAATTATTATATTTTAAAA
49284742 TTAA-TATTATATTTTAAAA
1 TTAATTATTATATTTTAAAA
49284761 T
1 T
49284762 ATTAACAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAATTATTATATTTTAAAA
Found at i:49284952 original size:13 final size:13
Alignment explanation
Indices: 49284931--49284978 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
49284921 ACACTTAAAT
49284931 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
* *
49284944 TTCTCAAAAGTAC
1 TTTTCAAAAGCAC
* *
49284957 TTTTCCACAGCAC
1 TTTTCAAAAGCAC
49284970 TTTTCAAAA
1 TTTTCAAAA
49284979 ACATTACTAA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.33
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Done.