Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 131 of 313
Found at i:42318769 original size:42 final size:42
Alignment explanation
Indices: 42318707--42318799 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 42
42318697 ATTGGCACTT
* * *
42318707 AGCCTGCGAGACATATAGTCTGAAATTGTTTCACCGGCATTA
1 AGCCTGCTAGACATAAAGTCTAAAATTGTTTCACCGGCATTA
42318749 AGCCTGCTAGACATAAAGTCTAAAATTGTTTCACCGGCATTA
1 AGCCTGCTAGACATAAAGTCTAAAATTGTTTCACCGGCATTA
*
42318791 AGTCTGCTA
1 AGCCTGCTA
42318800 AGCGCTAAGC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (42 bp):
AGCCTGCTAGACATAAAGTCTAAAATTGTTTCACCGGCATTA
Found at i:42321681 original size:15 final size:15
Alignment explanation
Indices: 42321645--42321695 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
42321635 TTAAAATGAT
42321645 AAAT-AAATGAATAA
1 AAATAAAATGAATAA
*
42321659 ATAA-AAAATGAAGAA
1 A-AATAAAATGAATAA
*
42321674 AAATAAAAAG-ATAA
1 AAATAAAATGAATAA
42321688 AAATAAAA
1 AAATAAAA
42321696 GATATGCTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 14 0.45
15 17 0.55
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (15 bp):
AAATAAAATGAATAA
Found at i:42326973 original size:49 final size:48
Alignment explanation
Indices: 42326897--42326999 Score: 122
Period size: 49 Copynumber: 2.1 Consensus size: 48
42326887 AAATCAATTT
* **
42326897 AAAT-ATATATTTTGAATTTAATGTTTTTATTTTTTATTTGTA-CAAA
1 AAATAATATATTTTGAATTTAATATTTTTATAATTTATTTGTACCAAA
*
42326943 AAATAATATATTTT-AATTTAAGTTTATTTTTATAATTTATTTGTACCATA
1 AAATAATATATTTTGAATTTAA---TATTTTTATAATTTATTTGTACCAAA
42326993 AAATAAT
1 AAATAAT
42327000 TTTAAAATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
46 11 0.23
47 9 0.19
49 18 0.38
50 10 0.21
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (48 bp):
AAATAATATATTTTGAATTTAATATTTTTATAATTTATTTGTACCAAA
Found at i:42331409 original size:303 final size:303
Alignment explanation
Indices: 42330875--42331440 Score: 828
Period size: 303 Copynumber: 1.9 Consensus size: 303
42330865 TAATTCTCAC
** * * * * * *
42330875 CAAATAATAAATTGTTAAAACCATTAAGTAAAAATTTATTATTTTTAAAATTTAATGTGTCATAT
1 CAAATAATAAATTGTTAAAACCATTAAGTAAAAATTTACCATTTCTAAAATCTAATGCGACAAAC
* * *
42330940 ATTTTATTATATATGTAATGTCATGTTAGATTATTTTTTTCTACATATTACTCATTAAAATTCAG
66 ATTTTATTATATATGTAATGTCATGTTAGATTATTTTTTTCTACATATTACTCACTAAAATCCAA
* * * * * * *
42331005 TTAATGGATTAACAAAAATTATTTTACGTTAAGATTGAAATTTTAAAATTCGAAAAGTATAGAGA
131 TTAATGGATTAACAAAAATCATTTTACGTTAAGACTGAAATTTCAAAATCCAAAAAGTACAAAGA
* * *
42331070 TTTAGAATGATCCAAATAGAGAATATAGAGTAAATCTACAACTGTATGAATAGTGCAAGACTAGT
196 TTTAGAATGATCCAAATAGAGAATATAGAATAAATCTACAACTGCATGAATAGTACAAGACTAGT
42331135 AATGGGTCATTTTTAGTTTTTTTTTTAAATTTTCAATATTCGT
261 AATGGGTCATTTTTAGTTTTTTTTTTAAATTTTCAATATTCGT
* *
42331178 CAAATAATAAATTGTTAAAACCGTTAAGTAAAATTTTACCATTTCTAAAATCTAATGCGACAAAC
1 CAAATAATAAATTGTTAAAACCATTAAGTAAAAATTTACCATTTCTAAAATCTAATGCGACAAAC
* *
42331243 ATTTTATTATATGTGTAATGTCATGTTAGATTATTATTTTTC-ATATATTACTCACTAAAATCCA
66 ATTTTATTATATATGTAATGTCATGTTAGATTATT-TTTTTCTACATATTACTCACTAAAATCCA
* *
42331307 ATTAATGGATTAACAAAAGTCATTTTACGTTAATACTGAAATTTCAAAATCCAAAAAGTACAAAG
130 ATTAATGGATTAACAAAAATCATTTTACGTTAAGACTGAAATTTCAAAATCCAAAAAGTACAAAG
* * * * *
42331372 ATTTAGAATGATCCAATTGGAGAATATGGAATAAATCTACAATTGCATGAATAGTATAAGACTAG
195 ATTTAGAATGATCCAAATAGAGAATATAGAATAAATCTACAACTGCATGAATAGTACAAGACTAG
42331437 TAAT
260 TAAT
42331441 TGCATGTAAC
Statistics
Matches: 230, Mismatches: 32, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
303 224 0.97
304 6 0.03
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (303 bp):
CAAATAATAAATTGTTAAAACCATTAAGTAAAAATTTACCATTTCTAAAATCTAATGCGACAAAC
ATTTTATTATATATGTAATGTCATGTTAGATTATTTTTTTCTACATATTACTCACTAAAATCCAA
TTAATGGATTAACAAAAATCATTTTACGTTAAGACTGAAATTTCAAAATCCAAAAAGTACAAAGA
TTTAGAATGATCCAAATAGAGAATATAGAATAAATCTACAACTGCATGAATAGTACAAGACTAGT
AATGGGTCATTTTTAGTTTTTTTTTTAAATTTTCAATATTCGT
Found at i:42332052 original size:36 final size:35
Alignment explanation
Indices: 42331972--42332052 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 35
42331962 AAAAAAACTT
*
42331972 TATAGAATTTTTAAAAATAAAAAAAAATTATAAAA
1 TATAAAATTTTTAAAAATAAAAAAAAATTATAAAA
*
42332007 -ATGACAAATTTATTAAAAATAGAAAAAAA-TATAAAA
1 TAT-A-AAATTT-TTAAAAATAAAAAAAAATTATAAAA
42332043 CTATAAAATT
1 -TATAAAATT
42332053 ACAAAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
34 2 0.05
35 1 0.03
36 17 0.44
37 17 0.44
38 2 0.05
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (35 bp):
TATAAAATTTTTAAAAATAAAAAAAAATTATAAAA
Found at i:42332339 original size:20 final size:20
Alignment explanation
Indices: 42332316--42332366 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
42332306 TTCAATTAAA
*
42332316 TAATTATT-TAAATAATTTTT
1 TAATTATTCAAAAT-ATTTTT
42332336 TAATTATTCAAAATATTTTT
1 TAATTATTCAAAATATTTTT
42332356 T-ATTATCTCAA
1 TAATTAT-TCAA
42332367 GATAAATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 5 0.18
20 19 0.68
21 4 0.14
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (20 bp):
TAATTATTCAAAATATTTTT
Found at i:42332360 original size:19 final size:22
Alignment explanation
Indices: 42332325--42332371 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
42332315 ATAATTATTT
42332325 AAATAATTTTTTAATTAT-TCA
1 AAATAATTTTTTAATTATCTCA
42332346 AAAT-ATTTTTT-ATTATCTCA
1 AAATAATTTTTTAATTATCTCA
*
42332366 AGATAA
1 AAATAA
42332372 ATATTTATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 5 0.22
20 13 0.57
21 5 0.22
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (22 bp):
AAATAATTTTTTAATTATCTCA
Found at i:42332699 original size:20 final size:20
Alignment explanation
Indices: 42332676--42332737 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 20
42332666 TTTACTATTG
42332676 TTTAAAATTCTTTATAATTT
1 TTTAAAATTCTTTATAATTT
* *
42332696 TTTATAA-TCTTTTATGA-TT
1 TTTAAAATTC-TTTATAATTT
* *
42332715 TCTAATATT-TTTATAATTT
1 TTTAAAATTCTTTATAATTT
42332734 TTTA
1 TTTA
42332738 TCAGTTTTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 7
0.70 0.15 0.15
Matches are distributed among these distances:
18 6 0.19
19 13 0.41
20 13 0.41
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTAAAATTCTTTATAATTT
Found at i:42332700 original size:10 final size:10
Alignment explanation
Indices: 42332676--42332754 Score: 63
Period size: 10 Copynumber: 8.1 Consensus size: 10
42332666 TTTACTATTG
* *
42332676 TTTAAAATTC
1 TTTATAATTT
42332686 TTTATAATTT
1 TTTATAATTT
*
42332696 TTTATAATCT
1 TTTATAATTT
*
42332706 TTTATGATTT
1 TTTATAATTT
* *
42332716 CTAAT-A-TT
1 TTTATAATTT
42332724 TTTATAATTT
1 TTTATAATTT
* *
42332734 TTTATCAGTT
1 TTTATAATTT
*
42332744 TTTATAGTTT
1 TTTATAATTT
42332754 T
1 T
42332755 AGTAAATTTT
Statistics
Matches: 53, Mismatches: 14, Indels: 4
0.75 0.20 0.06
Matches are distributed among these distances:
8 5 0.09
9 2 0.04
10 46 0.87
ACGTcount: A:0.28, C:0.05, G:0.04, T:0.63
Consensus pattern (10 bp):
TTTATAATTT
Found at i:42332754 original size:28 final size:28
Alignment explanation
Indices: 42332695--42332767 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
42332685 CTTTATAATT
* * *
42332695 TTTTATAATCTTTTATGATTTCTAATAT
1 TTTTATAATTTTTTATCATTTCTAATAG
*
42332723 TTTTATAATTTTTTATCAGTTT-TTATAG
1 TTTTATAATTTTTTATCA-TTTCTAATAG
*
42332751 TTTTAGTAAATTTTTAT
1 TTTTA-TAATTTTTTAT
42332768 TTTTTTTAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
28 25 0.66
29 13 0.34
ACGTcount: A:0.27, C:0.04, G:0.05, T:0.63
Consensus pattern (28 bp):
TTTTATAATTTTTTATCATTTCTAATAG
Found at i:42333618 original size:22 final size:22
Alignment explanation
Indices: 42333590--42333635 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
42333580 TTTATTTTTA
* *
42333590 TTTTTCTTTGCATGTAAAATTG
1 TTTTTCTTTACATGCAAAATTG
*
42333612 TTTTTCTTTACGTGCAAAATTG
1 TTTTTCTTTACATGCAAAATTG
42333634 TT
1 TT
42333636 GATGACAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.22, C:0.11, G:0.13, T:0.54
Consensus pattern (22 bp):
TTTTTCTTTACATGCAAAATTG
Found at i:42336641 original size:5 final size:6
Alignment explanation
Indices: 42336626--42336650 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
42336616 TCTATTTCAA
42336626 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
42336651 TCACCTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:42338679 original size:17 final size:17
Alignment explanation
Indices: 42338654--42338689 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
42338644 CTATTTCTTT
42338654 TTTACTGATGCCTTAAA
1 TTTACTGATGCCTTAAA
*
42338671 TTTATTGATGCCTTAAA
1 TTTACTGATGCCTTAAA
42338688 TT
1 TT
42338690 AGAGTTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.14, G:0.11, T:0.47
Consensus pattern (17 bp):
TTTACTGATGCCTTAAA
Found at i:42341503 original size:17 final size:17
Alignment explanation
Indices: 42341463--42341505 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
42341453 AAAATGAGTA
42341463 TTCATTTATTTATATTTT
1 TTCATTT-TTTATATTTT
42341481 TT-ATTTTTT-TATTTT
1 TTCATTTTTTATATTTT
42341496 TTACATTTTT
1 TT-CATTTTT
42341506 AATAAGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 8 0.35
16 3 0.13
17 10 0.43
18 2 0.09
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (17 bp):
TTCATTTTTTATATTTT
Found at i:42346846 original size:39 final size:39
Alignment explanation
Indices: 42346803--42346883 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
42346793 TAATTGTAAC
42346803 AATTATTATTATTATGAATCAGTATTTAGTGTGCTAGTG
1 AATTATTATTATTATGAATCAGTATTTAGTGTGCTAGTG
42346842 AATTATTATTATTATGAATCAGTATTTAGTGTGCTAGTG
1 AATTATTATTATTATGAATCAGTATTTAGTGTGCTAGTG
42346881 AAT
1 AAT
42346884 CCAACTGTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.32, C:0.05, G:0.17, T:0.46
Consensus pattern (39 bp):
AATTATTATTATTATGAATCAGTATTTAGTGTGCTAGTG
Found at i:42352063 original size:22 final size:23
Alignment explanation
Indices: 42352023--42352109 Score: 74
Period size: 22 Copynumber: 3.7 Consensus size: 23
42352013 TGACAATGTA
*
42352023 ATATATTTAGTATTATTAATTTG
1 ATATATTTAGTATTATTAATTTC
*
42352046 ATATATTTA-TATTGTTAATTTC
1 ATATATTTAGTATTATTAATTTC
*
42352068 ATATGTCATTACG-ATTAATTAATTTC
1 ATATAT--TTA-GTATT-ATTAATTTC
42352094 -TATATTGT-GTATTATT
1 ATATATT-TAGTATTATT
42352110 TTTAAATATA
Statistics
Matches: 52, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
22 20 0.38
23 13 0.25
24 4 0.08
25 7 0.13
26 8 0.15
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (23 bp):
ATATATTTAGTATTATTAATTTC
Found at i:42353201 original size:133 final size:133
Alignment explanation
Indices: 42353001--42353268 Score: 500
Period size: 133 Copynumber: 2.0 Consensus size: 133
42352991 AATCAAACTA
* *
42353001 AAAACTCAATCCACCATTCAACTAAATGTTAAACGGGCTTTGATGAGTTTTAGAAATATTATAAC
1 AAAACTCAATCCACCATTCAACTAAATGTTAAACCGGATTTGATGAGTTTTAGAAATATTATAAC
* *
42353066 ATTTTGTACTAGTTGATCGGTAGTATATTACTCTTTGAACAAGGCCTCATAGATATAGGAAATTT
66 ATTTTGTACTAATTGATCGGTAGTATATTACTCTTTGAACAAGGCCTCACAGATATAGGAAATTT
42353131 TTG
131 TTG
42353134 AAAACTCAATCCACCATTCAACTAAATGTTAAACCGGATTTGATGAGTTTTAGAAATATTATAAC
1 AAAACTCAATCCACCATTCAACTAAATGTTAAACCGGATTTGATGAGTTTTAGAAATATTATAAC
42353199 ATTTTGTACTAATTGATCGGTAGTATATTACTCTTTGAACAAGGCCTCACAGATATAGGAAATTT
66 ATTTTGTACTAATTGATCGGTAGTATATTACTCTTTGAACAAGGCCTCACAGATATAGGAAATTT
42353264 TTG
131 TTG
42353267 AA
1 AA
42353269 TTGCGTAACT
Statistics
Matches: 131, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
133 131 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (133 bp):
AAAACTCAATCCACCATTCAACTAAATGTTAAACCGGATTTGATGAGTTTTAGAAATATTATAAC
ATTTTGTACTAATTGATCGGTAGTATATTACTCTTTGAACAAGGCCTCACAGATATAGGAAATTT
TTG
Found at i:42354477 original size:29 final size:28
Alignment explanation
Indices: 42354444--42354498 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
42354434 CCTTAATACC
42354444 ATCAATTTTATCAACAAAAAAAAAACACT
1 ATCAATTTTATC-ACAAAAAAAAAACACT
* **
42354473 ATCAATTTTCTCTGAAAAAAAAAACA
1 ATCAATTTTATCACAAAAAAAAAACA
42354499 TAGCGAATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.56, C:0.16, G:0.02, T:0.25
Consensus pattern (28 bp):
ATCAATTTTATCACAAAAAAAAAACACT
Found at i:42363872 original size:4 final size:4
Alignment explanation
Indices: 42363863--42363894 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
42363853 TTAAACTAAG
42363863 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
42363895 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:42365030 original size:21 final size:20
Alignment explanation
Indices: 42364999--42365060 Score: 65
Period size: 21 Copynumber: 3.1 Consensus size: 20
42364989 TAAAAAAGGT
*
42364999 AATAGTAATAACAGTATTAA
1 AATAATAATAACAGTATTAA
*
42365019 ACATAATAATAATAGTA--AA
1 A-ATAATAATAACAGTATTAA
* *
42365038 AATAATGATAACATTATTAA
1 AATAATAATAACAGTATTAA
42365058 AAT
1 AAT
42365061 TAATTAATAG
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 12 0.35
19 3 0.09
20 6 0.18
21 13 0.38
ACGTcount: A:0.58, C:0.05, G:0.06, T:0.31
Consensus pattern (20 bp):
AATAATAATAACAGTATTAA
Found at i:42367585 original size:13 final size:13
Alignment explanation
Indices: 42367567--42367591 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42367557 TTAAAAATTC
42367567 AAAATAATTAATA
1 AAAATAATTAATA
42367580 AAAATAATTAAT
1 AAAATAATTAAT
42367592 TTATTCAACA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAATAATTAATA
Found at i:42376784 original size:4 final size:4
Alignment explanation
Indices: 42376777--42376805 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
42376767 TGTGTGTGTT
42376777 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
42376806 CAAAAACCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:42382476 original size:28 final size:25
Alignment explanation
Indices: 42382418--42382476 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 25
42382408 AAAATCAACC
*
42382418 ATTTATGAAATTAATATTTTAAAAA
1 ATTTATGAAATTAATATATTAAAAA
42382443 ATTTATGAAATTAATAAATAATTAAAAA
1 ATTTATGAAATTAAT--AT-ATTAAAAA
*
42382471 TTTTAT
1 ATTTAT
42382477 TGTAACTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 15 0.52
27 2 0.07
28 12 0.41
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (25 bp):
ATTTATGAAATTAATATATTAAAAA
Found at i:42382589 original size:18 final size:18
Alignment explanation
Indices: 42382566--42382629 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 18
42382556 AATGTTTTAT
42382566 TTAAATGAAAAATGGAAG
1 TTAAATGAAAAATGGAAG
* ** *
42382584 TTAAATTATAAAAATGTTTTAT
1 TTAAA-T-GAAAAATG--GAAG
42382606 TTAAATGAAAAATGGAAG
1 TTAAATGAAAAATGGAAG
42382624 TTAAAT
1 TTAAAT
42382630 TATAAAGGTT
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
18 12 0.35
19 1 0.03
20 14 0.41
21 1 0.03
22 6 0.18
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (18 bp):
TTAAATGAAAAATGGAAG
Found at i:42382596 original size:20 final size:20
Alignment explanation
Indices: 42382573--42382635 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
42382563 TATTTAAATG
42382573 AAAAATGGAAGTTAAATTAT
1 AAAAATGGAAGTTAAATTAT
** * *
42382593 AAAAATGTTTTATTTAAA-T-G
1 AAAAATG--GAAGTTAAATTAT
42382613 AAAAATGGAAGTTAAATTAT
1 AAAAATGGAAGTTAAATTAT
42382633 AAA
1 AAA
42382636 GGTTTTTTCC
Statistics
Matches: 31, Mismatches: 8, Indels: 8
0.66 0.17 0.17
Matches are distributed among these distances:
18 6 0.19
19 1 0.03
20 17 0.55
21 1 0.03
22 6 0.19
ACGTcount: A:0.54, C:0.00, G:0.13, T:0.33
Consensus pattern (20 bp):
AAAAATGGAAGTTAAATTAT
Found at i:42382611 original size:40 final size:40
Alignment explanation
Indices: 42382556--42382635 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
42382546 TATTTTTATT
42382556 AATGTTTTATTTAAATGAAAAATGGAAGTTAAATTATAAA
1 AATGTTTTATTTAAATGAAAAATGGAAGTTAAATTATAAA
42382596 AATGTTTTATTTAAATGAAAAATGGAAGTTAAATTATAAA
1 AATGTTTTATTTAAATGAAAAATGGAAGTTAAATTATAAA
42382636 GGTTTTTTCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (40 bp):
AATGTTTTATTTAAATGAAAAATGGAAGTTAAATTATAAA
Found at i:42392505 original size:16 final size:16
Alignment explanation
Indices: 42392468--42392507 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
42392458 TTAATAAAAT
* *
42392468 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
42392484 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
42392500 TAAAATTA
1 TAAAATTA
42392508 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:42392528 original size:9 final size:9
Alignment explanation
Indices: 42392514--42392557 Score: 56
Period size: 9 Copynumber: 5.1 Consensus size: 9
42392504 ATTATCAAAT
42392514 TATTAATTG
1 TATTAATTG
42392523 TATTAATTG
1 TATTAATTG
42392532 --TTAATTG
1 TATTAATTG
*
42392539 AATTAATTG
1 TATTAATTG
*
42392548 TATTCATTG
1 TATTAATTG
42392557 T
1 T
42392558 TGTCACAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 7 0.23
9 24 0.77
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (9 bp):
TATTAATTG
Found at i:42392535 original size:16 final size:16
Alignment explanation
Indices: 42392511--42392548 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
42392501 AAAATTATCA
* *
42392511 AATTATTAATTGTATT
1 AATTGTTAATTGAATT
42392527 AATTGTTAATTGAATT
1 AATTGTTAATTGAATT
42392543 AATTGT
1 AATTGT
42392549 ATTCATTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (16 bp):
AATTGTTAATTGAATT
Found at i:42392656 original size:68 final size:68
Alignment explanation
Indices: 42392545--42392680 Score: 202
Period size: 68 Copynumber: 2.0 Consensus size: 68
42392535 ATTGAATTAA
* * * * *
42392545 TTGTATTCATTGTTGTCACAAAACCTAACATTTGATTAGTAAAATAAACTTGATGTT-TTATTAT
1 TTGTATTAATTGTTGTAACAAAACCTAACATTTGATTAATAAAACAAACTTAATGTTATT-TTAT
42392609 TATT
65 TATT
*
42392613 TTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAATAAAACAAACTTAATGTTATTTTATT
1 TTGTATTAATTGTTGTAACAAAACCTAACATTTGATTAATAAAACAAACTTAATGTTATTTTATT
42392678 ATT
66 ATT
42392681 ATTATTTTGT
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
68 59 0.97
69 2 0.03
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (68 bp):
TTGTATTAATTGTTGTAACAAAACCTAACATTTGATTAATAAAACAAACTTAATGTTATTTTATT
ATT
Found at i:42392915 original size:16 final size:14
Alignment explanation
Indices: 42392876--42392908 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
42392866 AGTTGGACAA
*
42392876 ATAAAAAAAAACTT
1 ATAATAAAAAACTT
42392890 ATAATAAAAAACTT
1 ATAATAAAAAACTT
42392904 ATAAT
1 ATAAT
42392909 TTAAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (14 bp):
ATAATAAAAAACTT
Found at i:42398727 original size:78 final size:78
Alignment explanation
Indices: 42398634--42398872 Score: 372
Period size: 78 Copynumber: 3.1 Consensus size: 78
42398624 TTAACATTGT
* * * *
42398634 CATCATTCTTGGATTTGGTAGACTTGGGTGTGTCACCAGTGTCCCCACTTTTGGATTTGTTGCCT
1 CATCATCCTCGGATTTGGTAGACTTGGGTGTGTCACCAGTGTCCTCATTTTTGGATTTGTTGCCT
*
42398699 ACTTTTGAAGTGA
66 ACTTTTGAAGCGA
*
42398712 CATCCTCCTCGGATTTGGTAGACTTGGGTGTGTCACCAGTGTCCTCATTTTTGGATTTGTTGCCT
1 CATCATCCTCGGATTTGGTAGACTTGGGTGTGTCACCAGTGTCCTCATTTTTGGATTTGTTGCCT
42398777 A-TTTTCGAAGCGA
66 ACTTTT-GAAGCGA
* * *
42398790 CATCATCCTTGGATTTGGTAGACTTGGGAGTATCACCAGTGTCCTCATTTTTGGATTTGTTGCCT
1 CATCATCCTCGGATTTGGTAGACTTGGGTGTGTCACCAGTGTCCTCATTTTTGGATTTGTTGCCT
*
42398855 ACTTTTGAAGCGC
66 ACTTTTGAAGCGA
42398868 CATCA
1 CATCA
42398873 ACTGATCTAC
Statistics
Matches: 148, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
77 4 0.03
78 140 0.95
79 4 0.03
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.38
Consensus pattern (78 bp):
CATCATCCTCGGATTTGGTAGACTTGGGTGTGTCACCAGTGTCCTCATTTTTGGATTTGTTGCCT
ACTTTTGAAGCGA
Found at i:42398768 original size:42 final size:41
Alignment explanation
Indices: 42398722--42398848 Score: 97
Period size: 42 Copynumber: 3.2 Consensus size: 41
42398712 CATCCTCCTC
42398722 GGATTTGGTAGACTTGGGTGTGTCACCAGTGTCCTCATTTTT
1 GGATTTGGTAGACTTGGGTGT-TCACCAGTGTCCTCATTTTT
* * * * * **
42398764 GGATTT-GTTGCCTAT---T-TTCGA--AGCGACATCATCCTT
1 GGATTTGGTAGACT-TGGGTGTTC-ACCAGTGTCCTCATTTTT
*
42398800 GGATTTGGTAGACTTGGGAGTATCACCAGTGTCCTCATTTTT
1 GGATTTGGTAGACTTGGGTGT-TCACCAGTGTCCTCATTTTT
42398842 GGATTTG
1 GGATTTG
42398849 TTGCCTACTT
Statistics
Matches: 60, Mismatches: 15, Indels: 20
0.63 0.16 0.21
Matches are distributed among these distances:
36 17 0.28
37 7 0.12
38 2 0.03
39 1 0.02
40 2 0.03
41 7 0.12
42 24 0.40
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.39
Consensus pattern (41 bp):
GGATTTGGTAGACTTGGGTGTTCACCAGTGTCCTCATTTTT
Found at i:42404098 original size:36 final size:36
Alignment explanation
Indices: 42404051--42404122 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
42404041 AAATCATGTG
* * *
42404051 ATTCCCTTTAGGAGGAATCAAGATCGTTTCACCGCA
1 ATTCCCTTTAGGAGGAATCAAAACCGTTACACCGCA
42404087 ATTCCCTTTAGGAGGAATCAAAACCGTTACACCGCA
1 ATTCCCTTTAGGAGGAATCAAAACCGTTACACCGCA
42404123 TATGGACAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (36 bp):
ATTCCCTTTAGGAGGAATCAAAACCGTTACACCGCA
Found at i:42404165 original size:133 final size:133
Alignment explanation
Indices: 42404014--42404258 Score: 366
Period size: 133 Copynumber: 1.8 Consensus size: 133
42404004 ATCTCACGCA
** * * *
42404014 CGTGTAGATAGATGCTCACTTAAATGCAAATCATGTGATTCCCTTTAGGAGGAATCAAGATCGTT
1 CGTGTAGATAGACACTCACTTAAATGCAAATCATGCGATCCCCCTTAGGAGGAATCAAGATCGTT
* * *
42404079 -TCACCGCAATTCCCTTTAGGAGGAATCAAAACCGTTACACCGCATATGGACAGAAAAAGACTAG
66 AT-ACAGCAATTCCCTTTAGCAGGAATCAAAACCGTTACACCACATATGGACAGAAAAAGACTAG
42404143 CACG
130 CACG
**
42404147 CGTGTAGATAGACACTCACTTAAATGCAGCTCATGCGATCCCCCTTAGGAGGAATCAAGATCGTT
1 CGTGTAGATAGACACTCACTTAAATGCAAATCATGCGATCCCCCTTAGGAGGAATCAAGATCGTT
* *
42404212 ATACAGCACTTCCCTTTAGCAGGAATCAAGACCGTTACACCACATAT
66 ATACAGCAATTCCCTTTAGCAGGAATCAAAACCGTTACACCACATAT
42404259 ATATACACAA
Statistics
Matches: 99, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
133 98 0.99
134 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (133 bp):
CGTGTAGATAGACACTCACTTAAATGCAAATCATGCGATCCCCCTTAGGAGGAATCAAGATCGTT
ATACAGCAATTCCCTTTAGCAGGAATCAAAACCGTTACACCACATATGGACAGAAAAAGACTAGC
ACG
Found at i:42405162 original size:6 final size:6
Alignment explanation
Indices: 42405151--42405187 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
42405141 TATATCTCTG
42405151 TGTGTT TGTGTT TGTGTT TGTGTT TGTGTT TGTGTT T
1 TGTGTT TGTGTT TGTGTT TGTGTT TGTGTT TGTGTT T
42405188 TTGTGGGTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (6 bp):
TGTGTT
Found at i:42406404 original size:20 final size:20
Alignment explanation
Indices: 42406379--42406418 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
42406369 AATATTTTCC
*
42406379 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
42406399 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
42406419 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:42407889 original size:31 final size:31
Alignment explanation
Indices: 42407854--42407912 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
42407844 TAAATTGCCA
*
42407854 TTAACTTTTAATACCTAAATTACCCCTACTC
1 TTAACTTTTAATACCTAAACTACCCCTACTC
*
42407885 TTAACTTTTAATACCTAAACTATCCCTA
1 TTAACTTTTAATACCTAAACTACCCCTA
42407913 TTTACTCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.34, C:0.27, G:0.00, T:0.39
Consensus pattern (31 bp):
TTAACTTTTAATACCTAAACTACCCCTACTC
Found at i:42436700 original size:30 final size:30
Alignment explanation
Indices: 42436666--42436743 Score: 138
Period size: 30 Copynumber: 2.6 Consensus size: 30
42436656 TTAGCAATAA
42436666 AAAATAATAACAAAATTAACAAATCTCTCT
1 AAAATAATAACAAAATTAACAAATCTCTCT
*
42436696 AAAATAATAACAAAATTAACAAATCTCTTT
1 AAAATAATAACAAAATTAACAAATCTCTCT
*
42436726 AAAATAATAAAAAAATTA
1 AAAATAATAACAAAATTA
42436744 GCAATAAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.27
Consensus pattern (30 bp):
AAAATAATAACAAAATTAACAAATCTCTCT
Found at i:42438992 original size:28 final size:29
Alignment explanation
Indices: 42438931--42438992 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 29
42438921 ATTTTTTTAG
*
42438931 GTGACTAAAATGAAAGTGACTTAAAAGTTAT
1 GTGACCAAAATGAAAGTGA--TAAAAGTTAT
42438962 GTGACCAAAATGAAAGTG-TAAACA-TTAT
1 GTGACCAAAATGAAAGTGATAAA-AGTTAT
42438990 GTG
1 GTG
42438993 GGATGTATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 11 0.38
29 1 0.03
31 17 0.59
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.27
Consensus pattern (29 bp):
GTGACCAAAATGAAAGTGATAAAAGTTAT
Found at i:42445025 original size:40 final size:39
Alignment explanation
Indices: 42444961--42445051 Score: 137
Period size: 40 Copynumber: 2.3 Consensus size: 39
42444951 ATTTAGTGAG
*
42444961 TTAGAATTTTAAGATTTATAATTTTAAAGAAAAGGTTAAA
1 TTAG-ATTTTAAAATTTATAATTTTAAAGAAAAGGTTAAA
*
42445001 TTAAGATTTTAAAATTTATGATTTTAAAGAAAAGGTTAAA
1 TT-AGATTTTAAAATTTATAATTTTAAAGAAAAGGTTAAA
*
42445041 TTAGAATTTAA
1 TTAGATTTTAA
42445052 TGTCTAAAGG
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
39 8 0.17
40 37 0.79
41 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (39 bp):
TTAGATTTTAAAATTTATAATTTTAAAGAAAAGGTTAAA
Found at i:42446036 original size:21 final size:22
Alignment explanation
Indices: 42445986--42446044 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 22
42445976 TTTTTATTTT
* *
42445986 AAAAA-TTAAAAAAATTTTAAA
1 AAAAATTTAAAATATTTTTAAA
42446007 AAAAATTT-AAATATTTTTAAA
1 AAAAATTTAAAATATTTTTAAA
* *
42446028 ATAATTTTAAAATATTT
1 AAAAATTTAAAATATTT
42446045 CAAAATTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 22 0.69
22 10 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAAATTTAAAATATTTTTAAA
Found at i:42446040 original size:11 final size:11
Alignment explanation
Indices: 42445991--42446050 Score: 61
Period size: 11 Copynumber: 5.6 Consensus size: 11
42445981 ATTTTAAAAA
*
42445991 TTAAAAAAATT
1 TTAAAATAATT
* *
42446002 TTAAAAAAAAT
1 TTAAAATAATT
*
42446013 TT-AAATATTT
1 TTAAAATAATT
42446023 TTAAAATAATT
1 TTAAAATAATT
42446034 TTAAAAT-ATT
1 TTAAAATAATT
*
42446044 TCAAAAT
1 TTAAAAT
42446051 TAAAAAAAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
10 16 0.38
11 26 0.62
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (11 bp):
TTAAAATAATT
Found at i:42446069 original size:20 final size:19
Alignment explanation
Indices: 42446036--42446079 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
42446026 AAATAATTTT
42446036 AAAATATTTCAAAATTAAA
1 AAAATATTTCAAAATTAAA
*
42446055 AAAAGTATTTTAAAATTAAA
1 AAAA-TATTTCAAAATTAAA
42446075 AAAAT
1 AAAAT
42446080 TAAAATAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (19 bp):
AAAATATTTCAAAATTAAA
Found at i:42446795 original size:18 final size:18
Alignment explanation
Indices: 42446774--42446810 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
42446764 AATTATTGAA
42446774 ATATTAATCAATATTATT
1 ATATTAATCAATATTATT
**
42446792 ATATTTTTCAATATTATT
1 ATATTAATCAATATTATT
42446810 A
1 A
42446811 AACATACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATTAATCAATATTATT
Found at i:42447329 original size:33 final size:32
Alignment explanation
Indices: 42447265--42447330 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
42447255 TATCTATTTC
* *
42447265 ATATTTTTTAAAAATTAATTAAACAATAAAAA
1 ATATTTTATAAAAATTAATTAAACAACAAAAA
* * *
42447297 ATATTTTATACAAATTTATCTAAACACCAAAAA
1 ATATTTTATAAAAATTAAT-TAAACAACAAAAA
42447330 A
1 A
42447331 AATACACTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (32 bp):
ATATTTTATAAAAATTAATTAAACAACAAAAA
Found at i:42449498 original size:22 final size:22
Alignment explanation
Indices: 42449472--42449525 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
42449462 TGTTATAGAG
*
42449472 ATATATTAAAATATTTAAAAAA
1 ATATATTAAAATATGTAAAAAA
* * *
42449494 ATATATTTAAACATGTAACAAA
1 ATATATTAAAATATGTAAAAAA
42449516 AT-T-TTAAAAT
1 ATATATTAAAAT
42449526 TAATTATGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 5 0.19
21 1 0.04
22 20 0.77
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (22 bp):
ATATATTAAAATATGTAAAAAA
Found at i:42450860 original size:21 final size:21
Alignment explanation
Indices: 42450820--42450871 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
42450810 CATCATTAAA
*
42450820 TATTAT-AAATTATGATAAAT
1 TATTATAAAATTATGAGAAAT
*
42450840 TATTATAAAATTTTGAGAAAT
1 TATTATAAAATTATGAGAAAT
42450861 TATTA-AAAATT
1 TATTATAAAATT
42450872 CAAAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (21 bp):
TATTATAAAATTATGAGAAAT
Found at i:42450924 original size:14 final size:14
Alignment explanation
Indices: 42450905--42450954 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
42450895 TATAGAATAT
42450905 TATTAAAATAAAAA
1 TATTAAAATAAAAA
*
42450919 TATT--AATAAAAG
1 TATTAAAATAAAAA
*
42450931 TTTATAAAATAAAAA
1 TAT-TAAAATAAAAA
42450946 TATTAAAAT
1 TATTAAAAT
42450955 TTGTAGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
12 9 0.31
13 1 0.03
14 10 0.34
15 9 0.31
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (14 bp):
TATTAAAATAAAAA
Found at i:42451545 original size:18 final size:17
Alignment explanation
Indices: 42451522--42451586 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 17
42451512 TTATTTATTT
42451522 TTTATATTTTTATAATAA
1 TTTATATTTTT-TAATAA
* *
42451540 TTTATAAATTTCTAATAA
1 TTTAT-ATTTTTTAATAA
42451558 TCTT-TATGTTTTT-ATAA
1 T-TTATAT-TTTTTAATAA
42451575 TTTATATTTTTT
1 TTTATATTTTTT
42451587 TAAATTAGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
16 7 0.18
17 9 0.23
18 17 0.44
19 6 0.15
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTATATTTTTTAATAA
Found at i:42452954 original size:29 final size:29
Alignment explanation
Indices: 42452915--42452971 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
42452905 ATATTTGGGT
42452915 AAAAGTAGTAAGAAAAACCTATACTAAAA
1 AAAAGTAGTAAGAAAAACCTATACTAAAA
*
42452944 AAAAGTAGTAAGTAAAACCTATACTAAA
1 AAAAGTAGTAAGAAAAACCTATACTAAA
42452972 GTAAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.60, C:0.11, G:0.11, T:0.19
Consensus pattern (29 bp):
AAAAGTAGTAAGAAAAACCTATACTAAAA
Found at i:42457678 original size:42 final size:43
Alignment explanation
Indices: 42457576--42457734 Score: 144
Period size: 43 Copynumber: 3.7 Consensus size: 43
42457566 AATGTGATAT
* * * * * *
42457576 CGTGTAAGACCACGTCTGGGAC-GTTGGCATTGGTTTAAGATTTA
1 CGTGTAAGACCATGTCTGGGACAG-TGACATCGATATATGA-TTA
* ***
42457620 CGTGTAAGACCATGTCTGGGACATTGGTGTC-ATATATGATTA
1 CGTGTAAGACCATGTCTGGGACAGTGACATCGATATATGATTA
* * *
42457662 CGTGTAAGACCCTGTCTGGGACAGTGACATCGTTATTTGATTA
1 CGTGTAAGACCATGTCTGGGACAGTGACATCGATATATGATTA
*
42457705 CATGTAAGACCATGTCTGGGAC-GTTGACAT
1 CGTGTAAGACCATGTCTGGGACAG-TGACAT
42457735 TGTACGAGTT
Statistics
Matches: 95, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
42 30 0.32
43 40 0.42
44 25 0.26
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (43 bp):
CGTGTAAGACCATGTCTGGGACAGTGACATCGATATATGATTA
Found at i:42462228 original size:15 final size:16
Alignment explanation
Indices: 42462205--42462260 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
42462195 TTTTTATGTT
*
42462205 TTATATATATTATTTTA
1 TTATATATA-TATTATA
*
42462222 TTATATAATATAATATA
1 TTATAT-ATATATTATA
*
42462239 TTATAT-TGTATTATA
1 TTATATATATATTATA
42462254 TTATATA
1 TTATATA
42462261 AATTAAATAG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
15 13 0.39
17 17 0.52
18 3 0.09
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
TTATATATATATTATA
Found at i:42462244 original size:5 final size:5
Alignment explanation
Indices: 42462205--42462259 Score: 53
Period size: 5 Copynumber: 11.2 Consensus size: 5
42462195 TTTTTATGTT
* *
42462205 TTATA -TATA TTAT- TT-TA TTATA TAATATA ATATA TTATA TTGTA TTATA
1 TTATA TTATA TTATA TTATA TTATA T--TATA TTATA TTATA TTATA TTATA
42462254 TTATA T
1 TTATA T
42462260 AAATTAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
3 1 0.02
4 8 0.20
5 28 0.68
7 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:42462245 original size:27 final size:29
Alignment explanation
Indices: 42462206--42462261 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 29
42462196 TTTTATGTTT
*
42462206 TATATATATTATTTTATTATATAATATAA
1 TATATATATTATTGTATTATATAATATAA
*
42462235 TATAT-TA-TATTGTATTATATTATATAA
1 TATATATATTATTGTATTATATAATATAA
42462262 ATTAAATAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 18 0.72
28 2 0.08
29 5 0.20
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (29 bp):
TATATATATTATTGTATTATATAATATAA
Found at i:42462451 original size:19 final size:19
Alignment explanation
Indices: 42462415--42462450 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
42462405 TAAAAGAAAT
42462415 AAAGTAAAGTAAATAAAAG
1 AAAGTAAAGTAAATAAAAG
42462434 AAAGTAAAG-AAATAAAA
1 AAAGTAAAGTAAATAAAA
42462451 ACAAAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (19 bp):
AAAGTAAAGTAAATAAAAG
Found at i:42462494 original size:15 final size:17
Alignment explanation
Indices: 42462476--42462507 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42462466 CAGAATAGAA
42462476 AGAA-CAAA-GAAACAG
1 AGAAGCAAACGAAACAG
42462491 AGAAGCAAACGAAACAG
1 AGAAGCAAACGAAACAG
42462508 GGGAAGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 4 0.27
17 7 0.47
ACGTcount: A:0.62, C:0.16, G:0.22, T:0.00
Consensus pattern (17 bp):
AGAAGCAAACGAAACAG
Found at i:42463188 original size:12 final size:12
Alignment explanation
Indices: 42463171--42463213 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
42463161 ATGTGAAGTA
42463171 AGTATTAATATT
1 AGTATTAATATT
*
42463183 AGTATTAATATA
1 AGTATTAATATT
* *
42463195 ATTATTAGTATT
1 AGTATTAATATT
*
42463207 ATTATTA
1 AGTATTA
42463214 TTATGAGTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (12 bp):
AGTATTAATATT
Found at i:42463202 original size:18 final size:18
Alignment explanation
Indices: 42463179--42463217 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
42463169 TAAGTATTAA
42463179 TATTAGTATTAATATAAT
1 TATTAGTATTAATATAAT
* *
42463197 TATTAGTATTATTATTAT
1 TATTAGTATTAATATAAT
42463215 TAT
1 TAT
42463218 GAGTGGGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TATTAGTATTAATATAAT
Found at i:42464998 original size:23 final size:23
Alignment explanation
Indices: 42464955--42465008 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
42464945 ATAAAAAAAT
*
42464955 ATAATTATTGTTATTTTTTTAGTA
1 ATAA-TATTGTTATTTATTTAGTA
* *
42464979 ATAATATT-TTATTATATTTATTT
1 ATAATATTGTTATT-TATTTAGTA
42465002 ATAATAT
1 ATAATAT
42465009 ATATATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 5 0.19
23 17 0.65
24 4 0.15
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (23 bp):
ATAATATTGTTATTTATTTAGTA
Found at i:42470380 original size:16 final size:17
Alignment explanation
Indices: 42470359--42470395 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
42470349 AAAACCTTAC
42470359 TTATAAATGTTATA-TA
1 TTATAAATGTTATATTA
42470375 TTATAAATGTTATATTA
1 TTATAAATGTTATATTA
42470392 TTAT
1 TTAT
42470396 TGACTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (17 bp):
TTATAAATGTTATATTA
Found at i:42474691 original size:21 final size:21
Alignment explanation
Indices: 42474665--42474705 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
42474655 ATCTGCTCAA
* *
42474665 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
42474686 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
42474706 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:42484221 original size:939 final size:939
Alignment explanation
Indices: 42482403--42484281 Score: 3758
Period size: 939 Copynumber: 2.0 Consensus size: 939
42482393 TAAAAATAAT
42482403 TTTTAACAAAAAAAAATTGGATTTGGATATAATTACCTACGTAATTACTCCAATTCTTACCCTCG
1 TTTTAACAAAAAAAAATTGGATTTGGATATAATTACCTACGTAATTACTCCAATTCTTACCCTCG
42482468 CCTAAAAATTGAAAAGTGTAATTGGGATACTCCTATTACACCCAATTCAATGGGACTCACTACTT
66 CCTAAAAATTGAAAAGTGTAATTGGGATACTCCTATTACACCCAATTCAATGGGACTCACTACTT
42482533 ACAATGGTTATCCAAACATGTCACCATTGTGTAATTATAAGCAATTATATCTAAATCTAATTACT
131 ACAATGGTTATCCAAACATGTCACCATTGTGTAATTATAAGCAATTATATCTAAATCTAATTACT
42482598 AAGTAGCTTTCCAAACACTATCTAAATATATACATTTATACCTCAACCTCTAAGAAAGCATGGAA
196 AAGTAGCTTTCCAAACACTATCTAAATATATACATTTATACCTCAACCTCTAAGAAAGCATGGAA
42482663 TTATTATTATTATTTAAATTAAGAATCAAATCACTAAGAAAACATACTACTTTAAACCTAATTTA
261 TTATTATTATTATTTAAATTAAGAATCAAATCACTAAGAAAACATACTACTTTAAACCTAATTTA
42482728 ATCAATATATACAATGTTAGATATTATGTGACTCGAATCCCGTCACTTGTTAAAAAAATAAATAC
326 ATCAATATATACAATGTTAGATATTATGTGACTCGAATCCCGTCACTTGTTAAAAAAATAAATAC
42482793 AGTGGCAAAAAAAGAGGATCTGTGAGGGCGAAATGCCGTAGCCCGTCATAGATCCCCATTAAGCA
391 AGTGGCAAAAAAAGAGGATCTGTGAGGGCGAAATGCCGTAGCCCGTCATAGATCCCCATTAAGCA
42482858 CAAAACTGGACTAGGGTTGCGACCGGGGGTGTAGCCTTCATTGTACGGACCATGCAGCACAAGTT
456 CAAAACTGGACTAGGGTTGCGACCGGGGGTGTAGCCTTCATTGTACGGACCATGCAGCACAAGTT
42482923 GAATTCGTATAAAACTATTCTTCTTCTATTTGACTTTGATTAGAACAAAGTTTTTCAATCTCCTC
521 GAATTCGTATAAAACTATTCTTCTTCTATTTGACTTTGATTAGAACAAAGTTTTTCAATCTCCTC
42482988 TTTTGTCCGTAGTTTTTTCCTGAAATGATTTTCACATAAAATTATGTTCTTTTTTTTATTACTTT
586 TTTTGTCCGTAGTTTTTTCCTGAAATGATTTTCACATAAAATTATGTTCTTTTTTTTATTACTTT
42483053 GTGATCGTTTTACCACCATTATCGACATTTATTATAACACACAAATGTTGAAATCTTATTGTAAG
651 GTGATCGTTTTACCACCATTATCGACATTTATTATAACACACAAATGTTGAAATCTTATTGTAAG
42483118 GAGATTAAATATATACGGTAATTTTCAGAAATATTAAAATTAAAAAGGTTGTCGGATATGGCAAA
716 GAGATTAAATATATACGGTAATTTTCAGAAATATTAAAATTAAAAAGGTTGTCGGATATGGCAAA
42483183 GTGAAAAGGTATTCTTGAAATTATATTAATCTCAGCTGCTATTTCTGACTTTACTTCATGACAAT
781 GTGAAAAGGTATTCTTGAAATTATATTAATCTCAGCTGCTATTTCTGACTTTACTTCATGACAAT
42483248 GACCCCTCCTGTCTTAATTTGTTGAGCAAATTGAAGCAATATCATCACTATATGTTGATTCACCC
846 GACCCCTCCTGTCTTAATTTGTTGAGCAAATTGAAGCAATATCATCACTATATGTTGATTCACCC
42483313 CCACTTGTTGGAATTTTTTAACCCTAAAC
911 CCACTTGTTGGAATTTTTTAACCCTAAAC
42483342 TTTTAACAAAAAAAAATTGGATTTGGATATAATTACCTACGTAATTACTCCAATTCTTACCCTCG
1 TTTTAACAAAAAAAAATTGGATTTGGATATAATTACCTACGTAATTACTCCAATTCTTACCCTCG
42483407 CCTAAAAATTGAAAAGTGTAATTGGGATACTCCTATTACACCCAATTCAATGGGACTCACTACTT
66 CCTAAAAATTGAAAAGTGTAATTGGGATACTCCTATTACACCCAATTCAATGGGACTCACTACTT
42483472 ACAATGGTTATCCAAACATGTCACCATTGTGTAATTATAAGCAATTATATCTAAATCTAATTACT
131 ACAATGGTTATCCAAACATGTCACCATTGTGTAATTATAAGCAATTATATCTAAATCTAATTACT
42483537 AAGTAGCTTTCCAAACACTATCTAAATATATACATTTATACCTCAACCTCTAAGAAAGCATGGAA
196 AAGTAGCTTTCCAAACACTATCTAAATATATACATTTATACCTCAACCTCTAAGAAAGCATGGAA
42483602 TTATTATTATTATTTAAATTAAGAATCAAATCACTAAGAAAACATACTACTTTAAACCTAATTTA
261 TTATTATTATTATTTAAATTAAGAATCAAATCACTAAGAAAACATACTACTTTAAACCTAATTTA
42483667 ATCAATATATACAATGTTAGATATTATGTGACTCGAATCCCGTCACTTGTTAAAAAAATAAATAC
326 ATCAATATATACAATGTTAGATATTATGTGACTCGAATCCCGTCACTTGTTAAAAAAATAAATAC
42483732 AGTGGCAAAAAAAGAGGATCTGTGAGGGCGAAATGCCGTAGCCCGTCATAGATCCCCATTAAGCA
391 AGTGGCAAAAAAAGAGGATCTGTGAGGGCGAAATGCCGTAGCCCGTCATAGATCCCCATTAAGCA
42483797 CAAAACTGGACTAGGGTTGCGACCGGGGGTGTAGCCTTCATTGTACGGACCATGCAGCACAAGTT
456 CAAAACTGGACTAGGGTTGCGACCGGGGGTGTAGCCTTCATTGTACGGACCATGCAGCACAAGTT
42483862 GAATTCGTATAAAACTATTCTTCTTCTATTTGACTTTGATTAGAACAAAGTTTTTCAATCTCCTC
521 GAATTCGTATAAAACTATTCTTCTTCTATTTGACTTTGATTAGAACAAAGTTTTTCAATCTCCTC
42483927 TTTTGTCCGTAGTTTTTTCCTGAAATGATTTTCACATAAAATTATGTTCTTTTTTTTATTACTTT
586 TTTTGTCCGTAGTTTTTTCCTGAAATGATTTTCACATAAAATTATGTTCTTTTTTTTATTACTTT
42483992 GTGATCGTTTTACCACCATTATCGACATTTATTATAACACACAAATGTTGAAATCTTATTGTAAG
651 GTGATCGTTTTACCACCATTATCGACATTTATTATAACACACAAATGTTGAAATCTTATTGTAAG
42484057 GAGATTAAATATATACGGTAATTTTCAGAAATATTAAAATTAAAAAGGTTGTCGGATATGGCAAA
716 GAGATTAAATATATACGGTAATTTTCAGAAATATTAAAATTAAAAAGGTTGTCGGATATGGCAAA
42484122 GTGAAAAGGTATTCTTGAAATTATATTAATCTCAGCTGCTATTTCTGACTTTACTTCATGACAAT
781 GTGAAAAGGTATTCTTGAAATTATATTAATCTCAGCTGCTATTTCTGACTTTACTTCATGACAAT
42484187 GACCCCTCCTGTCTTAATTTGTTGAGCAAATTGAAGCAATATCATCACTATATGTTGATTCACCC
846 GACCCCTCCTGTCTTAATTTGTTGAGCAAATTGAAGCAATATCATCACTATATGTTGATTCACCC
42484252 CCACTTGTTGGAATTTTTTAACCCTAAAC
911 CCACTTGTTGGAATTTTTTAACCCTAAAC
42484281 T
1 T
42484282 CTCTCGAAAG
Statistics
Matches: 940, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
939 940 1.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (939 bp):
TTTTAACAAAAAAAAATTGGATTTGGATATAATTACCTACGTAATTACTCCAATTCTTACCCTCG
CCTAAAAATTGAAAAGTGTAATTGGGATACTCCTATTACACCCAATTCAATGGGACTCACTACTT
ACAATGGTTATCCAAACATGTCACCATTGTGTAATTATAAGCAATTATATCTAAATCTAATTACT
AAGTAGCTTTCCAAACACTATCTAAATATATACATTTATACCTCAACCTCTAAGAAAGCATGGAA
TTATTATTATTATTTAAATTAAGAATCAAATCACTAAGAAAACATACTACTTTAAACCTAATTTA
ATCAATATATACAATGTTAGATATTATGTGACTCGAATCCCGTCACTTGTTAAAAAAATAAATAC
AGTGGCAAAAAAAGAGGATCTGTGAGGGCGAAATGCCGTAGCCCGTCATAGATCCCCATTAAGCA
CAAAACTGGACTAGGGTTGCGACCGGGGGTGTAGCCTTCATTGTACGGACCATGCAGCACAAGTT
GAATTCGTATAAAACTATTCTTCTTCTATTTGACTTTGATTAGAACAAAGTTTTTCAATCTCCTC
TTTTGTCCGTAGTTTTTTCCTGAAATGATTTTCACATAAAATTATGTTCTTTTTTTTATTACTTT
GTGATCGTTTTACCACCATTATCGACATTTATTATAACACACAAATGTTGAAATCTTATTGTAAG
GAGATTAAATATATACGGTAATTTTCAGAAATATTAAAATTAAAAAGGTTGTCGGATATGGCAAA
GTGAAAAGGTATTCTTGAAATTATATTAATCTCAGCTGCTATTTCTGACTTTACTTCATGACAAT
GACCCCTCCTGTCTTAATTTGTTGAGCAAATTGAAGCAATATCATCACTATATGTTGATTCACCC
CCACTTGTTGGAATTTTTTAACCCTAAAC
Found at i:42485656 original size:29 final size:31
Alignment explanation
Indices: 42485591--42485658 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
42485581 ATCAAATATG
* * *
42485591 TACATGAACTTTGGTTTAATGTGCAATTTGC
1 TACATGAACTTTGATTTAATGTACAATTTAC
42485622 TACATGAACTTTGATTT-A-GTACAATTATAC
1 TACATGAACTTTGATTTAATGTACAATT-TAC
42485652 -ACATGAA
1 TACATGAA
42485659 ACTTGAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 14 0.42
30 3 0.09
31 16 0.48
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (31 bp):
TACATGAACTTTGATTTAATGTACAATTTAC
Found at i:42487739 original size:16 final size:18
Alignment explanation
Indices: 42487704--42487741 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
42487694 ATCTTTATTT
42487704 AAATAAAATACAATAGTA
1 AAATAAAATACAATAGTA
42487722 AAATAAAATA-AA-AGTA
1 AAATAAAATACAATAGTA
42487738 AAAT
1 AAAT
42487742 TTTTATAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
17 2 0.10
18 10 0.50
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATAAAATACAATAGTA
Found at i:42488965 original size:102 final size:103
Alignment explanation
Indices: 42488845--42489190 Score: 415
Period size: 102 Copynumber: 3.2 Consensus size: 103
42488835 AAAATATTAC
** *
42488845 GAAAAAAAATTAAAAAAAAAATTTTTGGGTGCTGGCCTGTCAATGGCCGACACCCAGTACACAGT
1 GAAAAAAAA-TACGAAAAAAATTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGT
42488910 ACAAAGAAAAAAAAATTA-TTTTTTTCGTGTCAGAATCA
65 ACAAAGAAAAAAAAATTATTTTTTTTCGTGTCAGAATCA
* * * * *
42488948 GAAAAAAAATACGAAAAAAAATTTTGGATGCTAGCCTGTCAATGGCCGGCACCTAGTACATAGTA
1 GAAAAAAAATACGAAAAAAATTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTA
*
42489013 CAAAGAAAAAAAATTTTAATTTTTTTTCGTGTCAGAATCA
66 CAAAGAAAAAAAA-ATT-ATTTTTTTTCGTGTCAGAATCA
* *
42489053 GATAAAAAATACGAAAAAAAATTAGAAAAAAAAATTTTTTGGTGCTGGCCTGTCAATGGCCGGCA
1 GAAAAAAAATAC------------G--AAAAAAATTTTTGGGTGCTGGCCTGTCAATGGCCGGCA
*
42489118 CCCAGTACACAGTACAAAGAAAAAAAAATTATTTTTTTTCATGTCAGAATCA
52 CCCAGTACACAGTACAAAGAAAAAAAAATTATTTTTTTTCGTGTCAGAATCA
*
42489170 GATAAAAAATACGAAAAAAAT
1 GAAAAAAAATACGAAAAAAAT
42489191 AAAAAAAAAA
Statistics
Matches: 208, Mismatches: 18, Indels: 34
0.80 0.07 0.13
Matches are distributed among these distances:
102 61 0.29
103 19 0.09
104 1 0.00
105 32 0.15
117 34 0.16
118 2 0.01
119 59 0.28
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.25
Consensus pattern (103 bp):
GAAAAAAAATACGAAAAAAATTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTA
CAAAGAAAAAAAAATTATTTTTTTTCGTGTCAGAATCA
Found at i:42489073 original size:221 final size:224
Alignment explanation
Indices: 42488729--42489189 Score: 788
Period size: 221 Copynumber: 2.1 Consensus size: 224
42488719 TGGATATACG
* * *
42488729 AAAAAAA-ACAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACA
1 AAAAAAATACGAAAAAAAATTTTGGATGCTAGCCTGTCAATGGCCGGCACCCAGTACACAGTACA
*
42488793 AAGAAAAAAAAATTTTAATTTTTTTTCGTGTCAAAATCAGATAAAATATTACGAAAAAAAATTA-
66 AAGAAAAAAAAATTTTAATTTTTTTTCGTGTCAAAATCAGATAAAATAATACGAAAAAAAATTAG
42488857 AAAAAAAAATTTTTGGGTGCTGGCCTGTCAATGGCCGACACCCAGTACACAGTACAAAGAAAAAA
131 AAAAAAAAATTTTTGGGTGCTGGCCTGTCAATGGCCGACACCCAGTACACAGTACAAAGAAAAAA
*
42488922 AAATTA-TTTTTTTCGTGTCAGAATCAGA
196 AAATTATTTTTTTTCATGTCAGAATCAGA
* *
42488950 AAAAAAATACGAAAAAAAATTTTGGATGCTAGCCTGTCAATGGCCGGCACCTAGTACATAGTACA
1 AAAAAAATACGAAAAAAAATTTTGGATGCTAGCCTGTCAATGGCCGGCACCCAGTACACAGTACA
*
42489015 AAG-AAAAAAAATTTTAATTTTTTTTCGTGTCAGAATCAGATAAAA-AATACGAAAAAAAATTAG
66 AAGAAAAAAAAATTTTAATTTTTTTTCGTGTCAAAATCAGATAAAATAATACGAAAAAAAATTAG
* *
42489078 AAAAAAAAATTTTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAAGAAAAAA
131 AAAAAAAAATTTTTGGGTGCTGGCCTGTCAATGGCCGACACCCAGTACACAGTACAAAGAAAAAA
42489143 AAATTATTTTTTTTCATGTCAGAATCAGA
196 AAATTATTTTTTTTCATGTCAGAATCAGA
*
42489172 TAAAAAATACGAAAAAAA
1 AAAAAAATACGAAAAAAA
42489190 TAAAAAAAAA
Statistics
Matches: 226, Mismatches: 11, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
220 16 0.07
221 117 0.52
222 93 0.41
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (224 bp):
AAAAAAATACGAAAAAAAATTTTGGATGCTAGCCTGTCAATGGCCGGCACCCAGTACACAGTACA
AAGAAAAAAAAATTTTAATTTTTTTTCGTGTCAAAATCAGATAAAATAATACGAAAAAAAATTAG
AAAAAAAAATTTTTGGGTGCTGGCCTGTCAATGGCCGACACCCAGTACACAGTACAAAGAAAAAA
AAATTATTTTTTTTCATGTCAGAATCAGA
Found at i:42489081 original size:117 final size:113
Alignment explanation
Indices: 42488724--42489204 Score: 585
Period size: 120 Copynumber: 4.2 Consensus size: 113
42488714 AAATATGGAT
* *
42488724 ATACGAAAAAAAACA-AAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACA
1 ATACGAAAAAAAATAGAAAAAAAATTTT-GGTGCTAGCCTGTCAATGGCCGGCACCCAGTACACA
* *
42488788 GTACAAAGAAAAAAAAATTTTAATTTTTTTTCGTGTCAAAATCAGATAAAATA
65 GTACAAAGAAAAAAAAA--TT-ATTTTTTTTCATGTCAGAATCAGATAAAA-A
* * * *
42488841 TTACGAAAAAAAATTAAAAAAAAAATTTTTGGGTGCTGGCCTGTCAATGGCCGACACCCAGTACA
1 ATACGAAAAAAAA-TAGAAAAAAAA-TTTT-GGTGCTAGCCTGTCAATGGCCGGCACCCAGTACA
* *
42488906 CAGTACAAAGAAAAAAAAATTA-TTTTTTTCGTGTCAGAATCAGAAAAAAA
63 CAGTACAAAGAAAAAAAAATTATTTTTTTTCATGTCAGAATCAGATAAAAA
* *
42488956 ATAC-----------GAAAAAAAATTTTGGATGCTAGCCTGTCAATGGCCGGCACCTAGTACATA
1 ATACGAAAAAAAATAGAAAAAAAATTTTGG-TGCTAGCCTGTCAATGGCCGGCACCCAGTACACA
* *
42489010 GTACAAAGAAAAAAAATTTTAATTTTTTTTCGTGTCAGAATCAGATAAAAA
65 GTACAAAGAAAAAAAA-ATT-ATTTTTTTTCATGTCAGAATCAGATAAAAA
*
42489061 ATACGAAAAAAAATTAGAAAAAAAAATTTTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGTAC
1 ATACGAAAAAAAA-TAG-AAAAAAAA--TTTTGGTGCTAGCCTGTCAATGGCCGGCACCCAGTAC
42489126 ACAGTACAAAGAAAAAAAAATTATTTTTTTTCATGTCAGAATCAGATAAAAA
62 ACAGTACAAAGAAAAAAAAATTATTTTTTTTCATGTCAGAATCAGATAAAAA
*
42489178 ATACG-AAAAAAATAAAAAAAAAATTTT
1 ATACGAAAAAAAATAGAAAAAAAATTTT
42489205 TGGCAGGCTG
Statistics
Matches: 323, Mismatches: 19, Indels: 49
0.83 0.05 0.13
Matches are distributed among these distances:
101 2 0.01
102 50 0.15
103 10 0.03
104 1 0.00
105 31 0.10
112 4 0.01
114 8 0.02
115 6 0.02
116 32 0.10
117 48 0.15
118 13 0.04
119 55 0.17
120 63 0.20
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (113 bp):
ATACGAAAAAAAATAGAAAAAAAATTTTGGTGCTAGCCTGTCAATGGCCGGCACCCAGTACACAG
TACAAAGAAAAAAAAATTATTTTTTTTCATGTCAGAATCAGATAAAAA
Found at i:42489365 original size:109 final size:109
Alignment explanation
Indices: 42489215--42489597 Score: 529
Period size: 109 Copynumber: 3.5 Consensus size: 109
42489205 TGGCAGGCTG
* *
42489215 TGTATTGTATACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAATTTTTTTTTATTTTTT
1 TGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCC-AAAAAATTTTTTTTTATTTTTT
42489280 TTCGTA-TTTTTTATCTGATTCTGACACGAAAAAAAAATTTTCTT
65 TTCGTATTTTTTTATCTGATTCTGACACGAAAAAAAAATTTTCTT
* *
42489324 TGTACTGTGGACTGGGTGCCGGCCATTAACAGGCCAGCACCC--AAAA--------T-TTTTTTT
1 TGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAATTTTTTTTTATTTTTTT
42489378 TCGTATTTTTTTATCTGATTCTGACACGAAAAAAAATTAAAATTTTTTTTTCTT
66 TCGTATTTTTTTATCTGATTCTGACACG---AAAAA--AAAA-----TTTTCTT
*
42489432 TGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAATTTTTTTTTTATTTTTTT
1 TGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAATTTTTTTTTATTTTTTT
42489497 TCGTATTTTTTTATCTGATTCTGACACGAAAAAAAAATTTTCTT
66 TCGTATTTTTTTATCTGATTCTGACACGAAAAAAAAATTTTCTT
*
42489541 TGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAATTTTTTTTTT
1 TGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAATTTTTTTTT
42489598 CGTATATCCG
Statistics
Matches: 245, Mismatches: 7, Indels: 44
0.83 0.02 0.15
Matches are distributed among these distances:
97 12 0.05
98 23 0.09
101 5 0.02
103 4 0.02
106 4 0.02
108 47 0.19
109 102 0.42
110 3 0.01
114 4 0.02
116 5 0.02
118 1 0.00
119 35 0.14
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (109 bp):
TGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAATTTTTTTTTATTTTTTT
TCGTATTTTTTTATCTGATTCTGACACGAAAAAAAAATTTTCTT
Found at i:42490867 original size:18 final size:17
Alignment explanation
Indices: 42490825--42490869 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
42490815 CGTTATGTCT
42490825 GCGACCGCGA-C-AAAC
1 GCGACCGCGACCGAAAC
*
42490840 GCG-GCGCGACCGAAAAC
1 GCGACCGCGACCG-AAAC
42490857 GCGACCGCGACCG
1 GCGACCGCGACCG
42490870 CAATTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
14 5 0.21
15 4 0.17
17 7 0.29
18 8 0.33
ACGTcount: A:0.27, C:0.40, G:0.33, T:0.00
Consensus pattern (17 bp):
GCGACCGCGACCGAAAC
Found at i:42497776 original size:14 final size:15
Alignment explanation
Indices: 42497749--42497781 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
42497739 AAGCGCATAT
42497749 TAAACTATTAAAAAA
1 TAAACTATTAAAAAA
42497764 TAAA-TATTTAAAAAA
1 TAAACTA-TTAAAAAA
42497779 TAA
1 TAA
42497782 TAATAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 2 0.12
15 15 0.88
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAACTATTAAAAAA
Found at i:42500746 original size:2 final size:2
Alignment explanation
Indices: 42500739--42500764 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42500729 CTCACACGAA
42500739 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
42500765 TAGCAAATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42508406 original size:23 final size:21
Alignment explanation
Indices: 42508353--42508406 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 21
42508343 TGCACACTTT
* *
42508353 ATTAGTTTCATATTTATTATT
1 ATTAATTTCATATTTATTATA
42508374 ATATATATTTCATATGTTATTAATA
1 AT-TA-ATTTCATAT-TTATT-ATA
42508399 ATTAATTT
1 ATTAATTT
42508407 AAAATAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 2 0.07
22 2 0.07
23 12 0.44
24 7 0.26
25 4 0.15
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (21 bp):
ATTAATTTCATATTTATTATA
Found at i:42512459 original size:12 final size:13
Alignment explanation
Indices: 42512436--42512464 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
42512426 TGATCCGCTC
42512436 ATATTAATTTTTT
1 ATATTAATTTTTT
42512449 ATATT-ATTTTTT
1 ATATTAATTTTTT
42512461 ATAT
1 ATAT
42512465 AAAACAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATATTAATTTTTT
Found at i:42526284 original size:17 final size:17
Alignment explanation
Indices: 42526262--42526295 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
42526252 ATGGTCTCTA
42526262 TTTTAAT-ATTTATAAAT
1 TTTTAATAATTT-TAAAT
42526279 TTTTAATAATTTTAAAT
1 TTTTAATAATTTTAAAT
42526296 AAATAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTAATAATTTTAAAT
Found at i:42527277 original size:19 final size:18
Alignment explanation
Indices: 42527253--42527298 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 18
42527243 TGATGGAGAT
42527253 AATAAAATAT-TCATAATAA
1 AATAAAATATGT-ATAA-AA
42527272 AATAAAA-ATGTATAAAA
1 AATAAAATATGTATAAAA
42527289 AATCAAAATA
1 AAT-AAAATA
42527299 AATGTTTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 5 0.21
18 10 0.42
19 9 0.38
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.26
Consensus pattern (18 bp):
AATAAAATATGTATAAAA
Found at i:42541599 original size:36 final size:36
Alignment explanation
Indices: 42541554--42541628 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
42541544 CTCAAACTCA
42541554 TTGGTGTGACATTAGAAATTAAAAGTATATATTCAT
1 TTGGTGTGACATTAGAAATTAAAAGTATATATTCAT
42541590 TTGGTGTGACATTAGAAATTAAAAGTATATATTCAT
1 TTGGTGTGACATTAGAAATTAAAAGTATATATTCAT
42541626 TTG
1 TTG
42541629 ATAGTCATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.40
Consensus pattern (36 bp):
TTGGTGTGACATTAGAAATTAAAAGTATATATTCAT
Found at i:42553147 original size:3 final size:3
Alignment explanation
Indices: 42553139--42553167 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
42553129 TCATGAACAC
42553139 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
42553168 GGATGAAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:42556959 original size:3 final size:3
Alignment explanation
Indices: 42556951--42556987 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
42556941 TACTCAACCC
42556951 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
42556988 GATGGTCCCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:42557798 original size:15 final size:15
Alignment explanation
Indices: 42557761--42557798 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
42557751 CGACGACGCG
*
42557761 GCTGCGGCGGCAGCA
1 GCTGCGGTGGCAGCA
42557776 GCTGCGGTGGCAGCA
1 GCTGCGGTGGCAGCA
42557791 GCTGCGGT
1 GCTGCGGT
42557799 AGGAGGAGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.11, C:0.29, G:0.47, T:0.13
Consensus pattern (15 bp):
GCTGCGGTGGCAGCA
Found at i:42558937 original size:12 final size:12
Alignment explanation
Indices: 42558920--42558945 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42558910 GCGTGTGAGG
42558920 CATGAACTCAAA
1 CATGAACTCAAA
42558932 CATGAACTCAAA
1 CATGAACTCAAA
42558944 CA
1 CA
42558946 GGGTTACAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.27, G:0.08, T:0.15
Consensus pattern (12 bp):
CATGAACTCAAA
Found at i:42561659 original size:16 final size:16
Alignment explanation
Indices: 42561638--42561672 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
42561628 GTTAAATTTG
*
42561638 TTATCAAATCAAATGC
1 TTATCAAATAAAATGC
*
42561654 TTATCAAATAAAATTC
1 TTATCAAATAAAATGC
42561670 TTA
1 TTA
42561673 AATTCGTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.37
Consensus pattern (16 bp):
TTATCAAATAAAATGC
Found at i:42562133 original size:17 final size:16
Alignment explanation
Indices: 42562108--42562147 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
42562098 TTAAAGAGTG
42562108 TTTTA-TTTTTCATAAT
1 TTTTATTTTTTCAT-AT
*
42562124 TTTTATTTTTTTATAT
1 TTTTATTTTTTCATAT
42562140 TTTTATTT
1 TTTTATTT
42562148 AAAATATGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTATTTTTTCATAT
Found at i:42567056 original size:30 final size:29
Alignment explanation
Indices: 42567020--42567076 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
42567010 ATAATTTAAA
*
42567020 AAAATTAAATCAAATTAAAATTTCATATTT
1 AAAATTAAATAAAATTAAAA-TTCATATTT
*
42567050 AAAATTACATAAAATTAAAATTCATAT
1 AAAATTAAATAAAATTAAAATTCATAT
42567077 ATAATTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (29 bp):
AAAATTAAATAAAATTAAAATTCATATTT
Found at i:42572312 original size:29 final size:28
Alignment explanation
Indices: 42572256--42572316 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
42572246 ACTTTTTAAT
42572256 AATTTTAATAAATTTTAATTTTACAAAA
1 AATTTTAATAAATTTTAATTTTACAAAA
* * **
42572284 CAATTTTTATAATTTTTAATTTTTTAAAA
1 -AATTTTAATAAATTTTAATTTTACAAAA
42572313 AATT
1 AATT
42572317 AAGTACTTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 4 0.14
29 24 0.86
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.52
Consensus pattern (28 bp):
AATTTTAATAAATTTTAATTTTACAAAA
Found at i:42572956 original size:31 final size:31
Alignment explanation
Indices: 42572918--42572976 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
42572908 GATACAAAAT
* *
42572918 GAAATAA-TAATATTAATAAGATTAGATTTAA
1 GAAATAATTAAT-TTAATAAAATAAGATTTAA
42572949 GAAATAATTAATTTAATAAAATAAGATT
1 GAAATAATTAATTTAATAAAATAAGATT
42572977 AATTTTATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 21 0.84
32 4 0.16
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (31 bp):
GAAATAATTAATTTAATAAAATAAGATTTAA
Found at i:42572979 original size:19 final size:18
Alignment explanation
Indices: 42572932--42572981 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
42572922 TAATAATATT
*
42572932 AATAAGATTAGATTTAAGA
1 AATAAGATTA-ATTTAAAA
42572951 AAT-A-ATTAATTTAATAA
1 AATAAGATTAATTTAA-AA
42572968 AATAAGATTAATTT
1 AATAAGATTAATTT
42572982 TATCAAACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 6 0.22
17 8 0.30
18 2 0.07
19 11 0.41
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (18 bp):
AATAAGATTAATTTAAAA
Found at i:42577432 original size:75 final size:74
Alignment explanation
Indices: 42577292--42577589 Score: 311
Period size: 75 Copynumber: 4.0 Consensus size: 74
42577282 GCCACATCCT
* * * *
42577292 TACCCATCTCTTTAGCATTTGAAGAATCTTCTATAAGCTTTGACATCAATTCAACGTTCTC-CTC
1 TACCCATCTCTTTAGCACTTGTAGAATCTTCTATAAGCTTTGATATCAATTCAATG-TC-CACTC
*
42577356 CTCAATATTCA
64 CTCCATATTCA
* * * *
42577367 TATCTATCTCTTTAGCACTTGGAGAATCTTCTATAAGCTTTGATATCAATTCGATGCTCCACTCC
1 TACCCATCTCTTTAGCACTTGTAGAATCTTCTATAAGCTTTGATATCAATTCAATG-TCCACTCC
42577432 TCCATATT-A
65 TCCATATTCA
* * * * *
42577441 TGACCCATCTCTTTAGGACTTGTAGAATCTTCTATAAGGCTTTGGTAACTATTCAATGTTCA-T-
1 T-ACCCATCTCTTTAGCACTTGTAGAATCTTCTATAA-GCTTTGATATCAATTCAATGTCCACTC
* *
42577504 CTCCATAGTCT
64 CTCCATATTCA
* * * * * *
42577515 TACCCATCTCTTTAGCACTTGTAGAATCTTCTATAAGATATGGTAGCAATTCAGTGTTCA--CCT
1 TACCCATCTCTTTAGCACTTGTAGAATCTTCTATAAGCTTTGATATCAATTCAATGTCCACTCCT
42577578 CCATATTCA
66 CCATATTCA
42577587 TAC
1 TAC
42577590 ATCATACCCA
Statistics
Matches: 190, Mismatches: 28, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
72 31 0.16
73 42 0.22
74 5 0.03
75 96 0.51
76 16 0.08
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.38
Consensus pattern (74 bp):
TACCCATCTCTTTAGCACTTGTAGAATCTTCTATAAGCTTTGATATCAATTCAATGTCCACTCCT
CCATATTCA
Found at i:42577565 original size:148 final size:150
Alignment explanation
Indices: 42577293--42577566 Score: 349
Period size: 148 Copynumber: 1.8 Consensus size: 150
42577283 CCACATCCTT
* *
42577293 ACCCATCTCTTTAGCATTTGAAGAATCTTCTATAAGCTTTGACATCAATTCAACGTTCTCCTCCT
1 ACCCATCTCTTTAGCACTTGAAGAATCTTCTATAAGCTTTGACAACAATTCAACGTTCTCCTCCT
* * * * * *
42577358 CAATATTCATATCTATCTCTTTAGCACTTGGAGAATCTTCTATAAGCTTTGATATCAATTCGATG
66 CAATAGTCATACCCATCTCTTTAGCACTTGGAGAATCTTCTATAAGATATGATAGCAATTCGATG
42577423 CTCCACTCCTCCATATTATG
131 CTCCACTCCTCCATATTATG
* * ** * *
42577443 ACCCATCTCTTTAGGACTTGTAGAATCTTCTATAAGGCTTTGGTAACTATTCAATGTTCAT-CT-
1 ACCCATCTCTTTAGCACTTGAAGAATCTTCTATAA-GCTTTGACAACAATTCAACGTTC-TCCTC
* * *
42577506 C-C-ATAGTCTTACCCATCTCTTTAGCACTTGTAGAATCTTCTATAAGATATGGTAGCAATTC
64 CTCAATAGTCATACCCATCTCTTTAGCACTTGGAGAATCTTCTATAAGATATGATAGCAATTC
42577567 AGTGTTCACC
Statistics
Matches: 105, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
148 50 0.48
149 1 0.01
150 33 0.31
151 20 0.19
152 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.38
Consensus pattern (150 bp):
ACCCATCTCTTTAGCACTTGAAGAATCTTCTATAAGCTTTGACAACAATTCAACGTTCTCCTCCT
CAATAGTCATACCCATCTCTTTAGCACTTGGAGAATCTTCTATAAGATATGATAGCAATTCGATG
CTCCACTCCTCCATATTATG
Found at i:42580534 original size:21 final size:20
Alignment explanation
Indices: 42580508--42580590 Score: 80
Period size: 20 Copynumber: 4.1 Consensus size: 20
42580498 AATATATTTA
*
42580508 TTTTTTAAATTTTAAAATAT
1 TTTTTTTAATTTTAAAATAT
42580528 TTTTTTTAATTTTAAAATAT
1 TTTTTTTAATTTTAAAATAT
* ** *
42580548 TTTTAAAATTCTTTTTTAAA-A-
1 TTTT---TTTAATTTTAAAATAT
42580569 TTTTTTTAATTTTAAAATAT
1 TTTTTTTAATTTTAAAATAT
42580589 TT
1 TT
42580591 AAAATTCTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
18 9 0.18
19 1 0.02
20 25 0.51
21 4 0.08
22 1 0.02
23 9 0.18
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTTTTAATTTTAAAATAT
Found at i:42580553 original size:11 final size:11
Alignment explanation
Indices: 42580537--42580577 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
42580527 TTTTTTTTAA
*
42580537 TTTTAAAATAT
1 TTTTAAAATTT
42580548 TTTTAAAATTCTT
1 TTTTAAAA-T-TT
42580561 TTTTAAAATTT
1 TTTTAAAATTT
42580572 TTTTAA
1 TTTTAA
42580578 TTTTAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 16 0.59
12 2 0.07
13 9 0.33
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTAAAATTT
Found at i:42580565 original size:13 final size:12
Alignment explanation
Indices: 42580537--42580575 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
42580527 TTTTTTTTAA
*
42580537 TTTTAAAA-TAT
1 TTTTAAAATTTT
42580548 TTTTAAAATTCTT
1 TTTTAAAATT-TT
42580561 TTTTAAAATTTT
1 TTTTAAAATTTT
42580573 TTT
1 TTT
42580576 AATTTTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 8 0.32
12 6 0.24
13 11 0.44
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTTAAAATTTT
Found at i:42580585 original size:41 final size:39
Alignment explanation
Indices: 42580528--42580605 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 39
42580518 TTTAAAATAT
42580528 TTTTTTTAATTTTAAAATATTTTTAAAATTCTTTTTTAAAA
1 TTTTTTTAATTTTAAAATA--TTTAAAATTCTTTTTTAAAA
42580569 TTTTTTTAATTTTAAAATATTTAAAATTCTTTTTTAA
1 TTTTTTTAATTTTAAAATATTTAAAATTCTTTTTTAA
42580606 TTTTTAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 18 0.49
41 19 0.51
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (39 bp):
TTTTTTTAATTTTAAAATATTTAAAATTCTTTTTTAAAA
Found at i:42580611 original size:29 final size:26
Alignment explanation
Indices: 42580562--42580616 Score: 83
Period size: 29 Copynumber: 2.0 Consensus size: 26
42580552 AAAATTCTTT
42580562 TTTAAAATTTTTTTAATTTTAAAATA
1 TTTAAAATTTTTTTAATTTTAAAATA
42580588 TTTAAAATTCTTTTTTAATTTTTAAAATA
1 TTTAAAA-T-TTTTTTAA-TTTTAAAATA
42580617 AATTTTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 7 0.27
27 1 0.04
28 8 0.31
29 10 0.38
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (26 bp):
TTTAAAATTTTTTTAATTTTAAAATA
Found at i:42580631 original size:23 final size:24
Alignment explanation
Indices: 42580591--42580642 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
42580581 TAAAATATTT
42580591 AAAATTCTTTTTTAATTT-TTAAA
1 AAAATTCTTTTTTAATTTATTAAA
42580614 ATAAATT-TTTTTGT-ATTTATTAAA
1 A-AAATTCTTTTT-TAATTTATTAAA
42580638 AAAAT
1 AAAAT
42580643 AGGCCGGGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
23 14 0.54
24 12 0.46
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
AAAATTCTTTTTTAATTTATTAAA
Found at i:42596254 original size:12 final size:12
Alignment explanation
Indices: 42596237--42596263 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
42596227 TATCTAATAT
42596237 AAATATTTTATA
1 AAATATTTTATA
42596249 AAATATTTTATA
1 AAATATTTTATA
42596261 AAA
1 AAA
42596264 ATTAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AAATATTTTATA
Found at i:42598496 original size:23 final size:23
Alignment explanation
Indices: 42598448--42598496 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
42598438 GAGTTGATTA
* **
42598448 TAATATCCCAAAAATTACTATTG
1 TAATACCCCAAAAATTACTACAG
*
42598471 TAATACCCCGAAAATTACTACAG
1 TAATACCCCAAAAATTACTACAG
42598494 TAA
1 TAA
42598497 GAAAGTAGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.45, C:0.20, G:0.06, T:0.29
Consensus pattern (23 bp):
TAATACCCCAAAAATTACTACAG
Found at i:42605376 original size:33 final size:32
Alignment explanation
Indices: 42605335--42605506 Score: 112
Period size: 33 Copynumber: 5.2 Consensus size: 32
42605325 TAGTGTTTAT
*
42605335 ATGTAAGACCATAGCTGGGCTATGGCATTCTG
1 ATGTAAGACCATAACTGGGCTATGGCATTCTG
* * *
42605367 ATGATAAGACCA-AACTGGGTTATGGCACTATG
1 ATG-TAAGACCATAACTGGGCTATGGCATTCTG
* ** * * * * *
42605399 AACGTAAGACCATATTTGGACCATGACAATGTTTAT
1 -ATGTAAGACCATAACTGGGCTATGGC-AT-TCT-G
** *
42605435 ATGTAAGACCATAGTTGGGCTATGGCGTTCTG
1 ATGTAAGACCATAACTGGGCTATGGCATTCTG
* * *
42605467 ATGATAAGACCATAACTGGGTTATGACATTATG
1 ATG-TAAGACCATAACTGGGCTATGGCATTCTG
42605500 AATGTAA
1 -ATGTAA
42605507 ATGATGAATT
Statistics
Matches: 104, Mismatches: 28, Indels: 15
0.71 0.19 0.10
Matches are distributed among these distances:
32 30 0.29
33 46 0.44
34 5 0.05
35 23 0.22
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (32 bp):
ATGTAAGACCATAACTGGGCTATGGCATTCTG
Found at i:42605404 original size:100 final size:101
Alignment explanation
Indices: 42605269--42605506 Score: 370
Period size: 100 Copynumber: 2.4 Consensus size: 101
42605259 GAATTGACGA
* * ** *
42605269 ATAAGACCATAACTGGGTTATGACACTATGAACGTAAGATCATGGTTGGACCATGGTAGTGTTTA
1 ATAAGACCATAACTGGGTTATGACACTATGAACGTAAGACCATAGTTGGACCATGACAATGTTTA
42605334 TATGTAAGACCATAGCTGGGCTATGGCATTCTGATG
66 TATGTAAGACCATAGCTGGGCTATGGCATTCTGATG
* *
42605370 ATAAGACCA-AACTGGGTTATGGCACTATGAACGTAAGACCATATTTGGACCATGACAATGTTTA
1 ATAAGACCATAACTGGGTTATGACACTATGAACGTAAGACCATAGTTGGACCATGACAATGTTTA
* *
42605434 TATGTAAGACCATAGTTGGGCTATGGCGTTCTGATG
66 TATGTAAGACCATAGCTGGGCTATGGCATTCTGATG
* *
42605470 ATAAGACCATAACTGGGTTATGACATTATGAATGTAA
1 ATAAGACCATAACTGGGTTATGACACTATGAACGTAA
42605507 ATGATGAATT
Statistics
Matches: 124, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
100 91 0.73
101 33 0.27
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (101 bp):
ATAAGACCATAACTGGGTTATGACACTATGAACGTAAGACCATAGTTGGACCATGACAATGTTTA
TATGTAAGACCATAGCTGGGCTATGGCATTCTGATG
Found at i:42606849 original size:11 final size:11
Alignment explanation
Indices: 42606833--42606862 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
42606823 TTGGGCTTCG
42606833 AAGGTCCATCT
1 AAGGTCCATCT
42606844 AAGGTCCATCT
1 AAGGTCCATCT
42606855 AAGGTCCA
1 AAGGTCCA
42606863 ATTCTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (11 bp):
AAGGTCCATCT
Found at i:42609118 original size:24 final size:24
Alignment explanation
Indices: 42609091--42609149 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 24
42609081 ATGACAATGA
42609091 TGATGAGGAAGATGAAGCA-GCAGG
1 TGATGAGGAAGATGAAG-ATGCAGG
*
42609115 TGAT---CAAGATGAAGATGCAGG
1 TGATGAGGAAGATGAAGATGCAGG
*
42609136 TGAGGAGGAAGATG
1 TGATGAGGAAGATG
42609150 GATCAGGTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
20 1 0.04
21 17 0.61
24 10 0.36
ACGTcount: A:0.37, C:0.07, G:0.41, T:0.15
Consensus pattern (24 bp):
TGATGAGGAAGATGAAGATGCAGG
Found at i:42609123 original size:21 final size:21
Alignment explanation
Indices: 42609099--42609138 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
42609089 GATGATGAGG
42609099 AAGATGAAGCA-GCAGGTGATC
1 AAGATGAAG-ATGCAGGTGATC
42609120 AAGATGAAGATGCAGGTGA
1 AAGATGAAGATGCAGGTGA
42609139 GGAGGAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.40, C:0.10, G:0.35, T:0.15
Consensus pattern (21 bp):
AAGATGAAGATGCAGGTGATC
Found at i:42609292 original size:18 final size:18
Alignment explanation
Indices: 42609269--42609312 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
42609259 CGATGATGGC
42609269 GAGGAAG-GTGAAGAAGAA
1 GAGGAAGAG-GAAGAAGAA
*
42609287 GAGGAAGAGGAGGAAGAA
1 GAGGAAGAGGAAGAAGAA
*
42609305 GATGAAGA
1 GAGGAAGA
42609313 AGAGGAAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.45, T:0.05
Consensus pattern (18 bp):
GAGGAAGAGGAAGAAGAA
Found at i:42609293 original size:9 final size:9
Alignment explanation
Indices: 42609281--42609321 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
42609271 GGAAGGTGAA
42609281 GAAGAAGAG
1 GAAGAAGAG
*
42609290 GAAGAGGAG
1 GAAGAAGAG
*
42609299 GAAGAAGAT
1 GAAGAAGAG
42609308 GAAGAAGAG
1 GAAGAAGAG
42609317 GAAGA
1 GAAGA
42609322 GCTTCAGCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.54, C:0.00, G:0.44, T:0.02
Consensus pattern (9 bp):
GAAGAAGAG
Found at i:42610903 original size:18 final size:19
Alignment explanation
Indices: 42610879--42610932 Score: 67
Period size: 18 Copynumber: 2.8 Consensus size: 19
42610869 TTTTCTTAAA
42610879 ATAATTTTTTTATAATTTT
1 ATAATTTTTTTATAATTTT
*
42610898 -TAATTTTTATGA-AATTTT
1 ATAATTTTT-TTATAATTTT
42610916 ATAATTTTTTTTATAAT
1 ATAA-TTTTTTTATAAT
42610933 GTACTCATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
18 14 0.48
19 7 0.24
20 8 0.28
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
ATAATTTTTTTATAATTTT
Found at i:42614527 original size:15 final size:16
Alignment explanation
Indices: 42614507--42614543 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
42614497 ACAAAATCAA
42614507 ATAAAA-TTACATAAT
1 ATAAAAGTTACATAAT
*
42614522 ATAAAAGTTACATTAT
1 ATAAAAGTTACATAAT
42614538 ATAAAA
1 ATAAAA
42614544 ATTAAATGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (16 bp):
ATAAAAGTTACATAAT
Found at i:42614755 original size:23 final size:23
Alignment explanation
Indices: 42614725--42614771 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
42614715 AATTACAAAC
42614725 ACAAAAATTTATAACATAATCCT
1 ACAAAAATTTATAACATAATCCT
42614748 ACAAAAATTTATAACATAATCCT
1 ACAAAAATTTATAACATAATCCT
42614771 A
1 A
42614772 AATTACTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (23 bp):
ACAAAAATTTATAACATAATCCT
Found at i:42614827 original size:23 final size:23
Alignment explanation
Indices: 42614799--42614932 Score: 177
Period size: 23 Copynumber: 5.8 Consensus size: 23
42614789 TTATAAAATA
42614799 ATTACAATATTCATACAAACAAT
1 ATTACAATATTCATACAAACAAT
42614822 ATTACAATATTCATACAAACAAT
1 ATTACAATATTCATACAAACAAT
* *
42614845 ACTACAATATCCATAC--A-AA-
1 ATTACAATATTCATACAAACAAT
42614864 ATTACAATATTCATACAAACAAT
1 ATTACAATATTCATACAAACAAT
*
42614887 ATTACAATATTCATACAAAATTACAAA
1 ATTACAATATTCATAC--AA--ACAAT
42614914 ATTACAATATTCATACAAA
1 ATTACAATATTCATACAAA
42614933 ATACTAATCC
Statistics
Matches: 98, Mismatches: 5, Indels: 16
0.82 0.04 0.13
Matches are distributed among these distances:
19 14 0.14
20 2 0.02
21 2 0.02
22 2 0.02
23 54 0.55
25 4 0.04
27 20 0.20
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (23 bp):
ATTACAATATTCATACAAACAAT
Found at i:42614879 original size:42 final size:42
Alignment explanation
Indices: 42614817--42614912 Score: 165
Period size: 42 Copynumber: 2.3 Consensus size: 42
42614807 ATTCATACAA
*
42614817 ACAATATTACAATATTCATACAAACAATACTACAATATCCAT
1 ACAAAATTACAATATTCATACAAACAATACTACAATATCCAT
* *
42614859 ACAAAATTACAATATTCATACAAACAATATTACAATATTCAT
1 ACAAAATTACAATATTCATACAAACAATACTACAATATCCAT
42614901 ACAAAATTACAA
1 ACAAAATTACAA
42614913 AATTACAATA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (42 bp):
ACAAAATTACAATATTCATACAAACAATACTACAATATCCAT
Found at i:42614930 original size:19 final size:19
Alignment explanation
Indices: 42614798--42615334 Score: 137
Period size: 19 Copynumber: 26.3 Consensus size: 19
42614788 ATTATAAAAT
42614798 AATTACAATATTCATACAAACA
1 AATTACAATATTCATAC--A-A
42614820 ATATTACAATATTCATACAAA
1 A-ATTACAATATTCATAC-AA
*
42614841 CAATACTACAATATCCATACAA
1 -AAT--TACAATATTCATACAA
42614863 AATTACAATATTCATACAAACA
1 AATTACAATATTCATAC--A-A
42614885 ATATTACAATATTCATACAAAATTACAA
1 A-ATTACAATA-T--T-C---A-TACAA
42614913 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
* * *
42614932 AA-TACTA-ATCCAAAACTATA
1 AATTACAATATTC-ATAC-A-A
*
42614952 AA-TACAAAATTAATT-ATAAAA
1 AATTAC--AA-T-ATTCATACAA
42614973 TAATTACAATATTCATACAA
1 -AATTACAATATTCATACAA
* *
42614993 CATTATAATATTCATACAA
1 AATTACAATATTCATACAA
** *
42615012 AA-TACTAATA-AAAAACTATA
1 AATTAC-AATATTCATAC-A-A
*
42615032 AA-TACATAATTAATT-ATAAAA
1 AATTAC--AA-T-ATTCATACAA
42615053 TAATTACAATATTCATACAA
1 -AATTACAATATTCATACAA
*
42615073 AATTACAAAATT--T-CAA
1 AATTACAATATTCATACAA
* *
42615089 TATTCATACAA-AAT--TACAA
1 -AAT--TACAATATTCATACAA
42615108 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
** * *
42615127 AA-TACTAAT-TAAAAACTGTA
1 AATTAC-AATATTCATAC--AA
*
42615147 AA-TACAAAATTAATT-ATAAAA
1 AATTAC--AA-T-ATTCATACAA
42615168 TAATTACAATATTCATA-AA
1 -AATTACAATATTCATACAA
42615187 AATTACAATATTCATACAAAAA
1 AATTACAATATTCATAC---AA
*
42615209 AATTACACTATTCATACAA
1 AATTACAATATTCATACAA
* * *
42615228 AA-TACTA-ATCCAAAACTATA
1 AATTACAATATTC-ATAC-A-A
* * *
42615248 AA-TACAAAATTAATTATAAA
1 AATTACAATATTCA-TA-CAA
42615268 GTAATTACAATATTCATACAA
1 --AATTACAATATTCATACAA
*
42615289 AATTATAATATTCATACAAA
1 AATTACAATATTCATAC-AA
*
42615309 AAGTTACAATATACATACAA
1 AA-TTACAATATTCATACAA
42615329 AATTAC
1 AATTAC
42615335 CCATTGGCGC
Statistics
Matches: 395, Mismatches: 51, Indels: 141
0.67 0.09 0.24
Matches are distributed among these distances:
16 8 0.02
17 11 0.03
18 46 0.12
19 109 0.28
20 52 0.13
21 40 0.10
22 41 0.10
23 64 0.16
24 3 0.01
25 2 0.01
26 2 0.01
27 10 0.03
28 2 0.01
29 1 0.00
30 1 0.00
31 3 0.01
ACGTcount: A:0.55, C:0.14, G:0.01, T:0.30
Consensus pattern (19 bp):
AATTACAATATTCATACAA
Found at i:42614933 original size:27 final size:27
Alignment explanation
Indices: 42614858--42615129 Score: 156
Period size: 27 Copynumber: 10.0 Consensus size: 27
42614848 ACAATATCCA
42614858 TACAAAATTACAATATTCATAC--AA-
1 TACAAAATTACAATATTCATACAAAAT
*
42614882 -ACAATATTACAATATTCATACAAAAT
1 TACAAAATTACAATATTCATACAAAAT
42614908 TACAAAATTACAATATTCATACAAAA-
1 TACAAAATTACAATATTCATACAAAAT
* * * **
42614934 TAC-TAATCCAAAACTATAAATACAAAAT
1 TACAAAAT-TACAA-TATTCATACAAAAT
** * * *
42614962 TA-ATTA-TAAAATAAT--TACAATATT
1 TACAAAATTACAATATTCATACAA-AAT
* *
42614986 CATACAACATTATAATATTCATACAAAA-
1 --TACAAAATTACAATATTCATACAAAAT
* **
42615014 TACTAATAA--AAAACTATAAATACATAATTAATT
1 TAC-AA-AATTACAA-TATTCATAC--AA--AA-T
*
42615047 ATAAAATAATTACAATATTCATACAAAAT
1 -TACAA-AATTACAATATTCATACAAAAT
*
42615076 TACAAAATTTCAATATTCATACAAAAT
1 TACAAAATTACAATATTCATACAAAAT
42615103 TACAAAATTACAATATTCATACAAAAT
1 TACAAAATTACAATATTCATACAAAAT
42615130 ACTAATTAAA
Statistics
Matches: 193, Mismatches: 28, Indels: 51
0.71 0.10 0.19
Matches are distributed among these distances:
23 25 0.13
24 2 0.01
25 7 0.04
26 18 0.09
27 93 0.48
28 16 0.08
29 4 0.02
30 7 0.04
31 2 0.01
32 2 0.01
33 5 0.03
34 9 0.05
35 3 0.02
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.31
Consensus pattern (27 bp):
TACAAAATTACAATATTCATACAAAAT
Found at i:42614958 original size:88 final size:84
Alignment explanation
Indices: 42614780--42615102 Score: 326
Period size: 80 Copynumber: 3.8 Consensus size: 84
42614770 TAAATTACTA
*
42614780 ACAA-ATTAATTATAAAATAATTACAATATTCATACAAACAATATTACAATATTCATACAAACAA
1 ACAATATTAATTATAAAATAATTACAATATTCATACAAACAAAATTACAATATTCATAC-AA-AA
*
42614844 TACTACAATATCC-ATAC-A-AAATT
64 TACT---A-ATCCAAAACTATAAA-T
* *
42614867 ACAATATTCA-TACAAACA-ATATTACAATATTCATACAAAATTACAAAATTACAATATTCATAC
1 ACAATATTAATTATAAA-ATA-ATTACAATATTCATAC--AA--ACAAAATTACAATATTCATAC
42614930 AAAATACTAATCCAAAACTATAAAT
60 AAAATACTAATCCAAAACTATAAAT
* *
42614955 ACAAAATTAATTATAAAATAATTACAATATTCATAC-AAC---ATTATAATATTCATACAAAATA
1 ACAATATTAATTATAAAATAATTACAATATTCATACAAACAAAATTACAATATTCATACAAAATA
**
42615016 CTAATAAAAAACTATAAAT
66 CTAATCCAAAACTATAAAT
*
42615035 AC-ATAATTAATTATAAAATAATTACAATATTCATACAAAATTACAAAATTTCAATATTCATACA
1 ACAAT-ATTAATTATAAAATAATTACAATATTCATAC--AA--ACAAAATTACAATATTCATACA
42615099 AAAT
61 AAAT
42615103 TACAAAATTA
Statistics
Matches: 202, Mismatches: 13, Indels: 41
0.79 0.05 0.16
Matches are distributed among these distances:
79 1 0.00
80 71 0.35
83 3 0.01
85 3 0.01
86 4 0.02
87 14 0.07
88 67 0.33
89 9 0.04
90 8 0.04
91 2 0.01
92 20 0.10
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (84 bp):
ACAATATTAATTATAAAATAATTACAATATTCATACAAACAAAATTACAATATTCATACAAAATA
CTAATCCAAAACTATAAAT
Found at i:42615064 original size:61 final size:61
Alignment explanation
Indices: 42614994--42615189 Score: 207
Period size: 61 Copynumber: 3.3 Consensus size: 61
42614984 TTCATACAAC
*
42614994 ATTATAATATTCATACAAAATACTAATAAAAAACTATAAATACATAATTAATTATAAAATA
1 ATTACAATATTCATACAAAATACTAATAAAAAACTATAAATACATAATTAATTATAAAATA
* * * * *
42615055 ATTACAATATTCATAC-AAA-A-T--TACAAAA-TTTCAATATTCATACA--AAAT-TACAA-A
1 ATTACAATATTCATACAAAATACTAATAAAAAACTAT-AA-ATACATA-ATTAATTATAAAATA
* * *
42615109 ATTACAATATTCATACAAAATACTAATTAAAAACTGTAAATACAAAATTAATTATAAAATA
1 ATTACAATATTCATACAAAATACTAATAAAAAACTATAAATACATAATTAATTATAAAATA
42615170 ATTACAATATTCATA-AAAAT
1 ATTACAATATTCATACAAAAT
42615190 TACAATATTC
Statistics
Matches: 109, Mismatches: 13, Indels: 27
0.73 0.09 0.18
Matches are distributed among these distances:
54 17 0.16
55 9 0.08
56 12 0.11
57 8 0.07
58 7 0.06
59 11 0.10
60 14 0.13
61 31 0.28
ACGTcount: A:0.57, C:0.11, G:0.01, T:0.32
Consensus pattern (61 bp):
ATTACAATATTCATACAAAATACTAATAAAAAACTATAAATACATAATTAATTATAAAATA
Found at i:42615081 original size:8 final size:8
Alignment explanation
Indices: 42615068--42615115 Score: 51
Period size: 8 Copynumber: 5.6 Consensus size: 8
42615058 ACAATATTCA
42615068 TACAAAAT
1 TACAAAAT
42615076 TACAAAAT
1 TACAAAAT
* *
42615084 TTCAATATT
1 TACAA-AAT
42615093 CATACAAAAT
1 --TACAAAAT
42615103 TACAAAAT
1 TACAAAAT
42615111 TACAA
1 TACAA
42615116 TATTCATACA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
8 25 0.76
9 2 0.06
10 2 0.06
11 4 0.12
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (8 bp):
TACAAAAT
Found at i:42615210 original size:22 final size:22
Alignment explanation
Indices: 42615164--42615229 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 22
42615154 AATTAATTAT
*
42615164 AAAATAATTACAATATTCAT--
1 AAAAAAATTACAATATTCATAC
42615184 --AAAAATTACAATATTCATAC
1 AAAAAAATTACAATATTCATAC
*
42615204 AAAAAAATTACACTATTCATAC
1 AAAAAAATTACAATATTCATAC
42615226 AAAA
1 AAAA
42615230 TACTAATCCA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
18 17 0.43
22 23 0.57
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAAAAATTACAATATTCATAC
Found at i:42615229 original size:101 final size:102
Alignment explanation
Indices: 42615076--42615331 Score: 372
Period size: 101 Copynumber: 2.5 Consensus size: 102
42615066 CATACAAAAT
* *
42615076 TACAAAATTTCAATATTCATACAAAATTACAAAATTACAATATTCATACAAAATACTAATTAAAA
1 TACAAAATTACAATATTCATAC--AA--A-AAAATTACAATATTCATACAAAATACTAATCAAAA
*
42615141 ACTGTAAATACAAAATTAATTATAAAATAATTACAATATTCA
61 ACTATAAATACAAAATTAATTATAAAATAATTACAATATTCA
* *
42615183 TA-AAAATTACAATATTCATACAAAAAAATTACACTATTCATACAAAATACTAATCCAAAACTAT
1 TACAAAATTACAATATTCATACAAAAAAATTACAATATTCATACAAAATACTAATCAAAAACTAT
*
42615247 AAATACAAAATTAATTATAAAGTAATTACAATATTCA
66 AAATACAAAATTAATTATAAAATAATTACAATATTCA
* * *
42615284 TACAAAATTATAATATTCATAC-AAAAAGTTACAATATACATACAAAAT
1 TACAAAATTACAATATTCATACAAAAAAATTACAATATTCATACAAAAT
42615332 TACCCATTGG
Statistics
Matches: 138, Mismatches: 10, Indels: 8
0.88 0.06 0.05
Matches are distributed among these distances:
101 97 0.70
102 19 0.14
104 2 0.01
106 18 0.13
107 2 0.01
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.30
Consensus pattern (102 bp):
TACAAAATTACAATATTCATACAAAAAAATTACAATATTCATACAAAATACTAATCAAAAACTAT
AAATACAAAATTAATTATAAAATAATTACAATATTCA
Found at i:42615380 original size:27 final size:27
Alignment explanation
Indices: 42615339--42615438 Score: 146
Period size: 27 Copynumber: 3.7 Consensus size: 27
42615329 AATTACCCAT
* *
42615339 TGGCGCCTCCCTATGAGACACTTTTAA
1 TGGCACCTCCCTATGAGGCACTTTTAA
*
42615366 TGGCACCTCCTTATGAGGCACTTTTAA
1 TGGCACCTCCCTATGAGGCACTTTTAA
*
42615393 TGGCACCTCCTTATGAGGCACTTTTAA
1 TGGCACCTCCCTATGAGGCACTTTTAA
**
42615420 TGGTGCCTCCCTATGAGGC
1 TGGCACCTCCCTATGAGGC
42615439 GCCACCCGAC
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 67 1.00
ACGTcount: A:0.20, C:0.28, G:0.21, T:0.31
Consensus pattern (27 bp):
TGGCACCTCCCTATGAGGCACTTTTAA
Found at i:42618888 original size:15 final size:15
Alignment explanation
Indices: 42618868--42618896 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
42618858 AAATTAAGGA
42618868 ATTAATAGAAAAAAG
1 ATTAATAGAAAAAAG
42618883 ATTAATAGAAAAAA
1 ATTAATAGAAAAAA
42618897 CTAATAGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (15 bp):
ATTAATAGAAAAAAG
Found at i:42622029 original size:52 final size:48
Alignment explanation
Indices: 42622010--42622212 Score: 265
Period size: 46 Copynumber: 4.3 Consensus size: 48
42622000 TGACAAGTGG
* *
42622010 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
42622056 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
42622108 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
42622154 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
42622200 AAAGTGATAAGTG
1 AAAGTGATAAGTG
42622213 GCTACACTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
46 100 0.69
52 44 0.31
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:42622064 original size:98 final size:98
Alignment explanation
Indices: 42621944--42622212 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
42621934 TTTGAGTACT
*
42621944 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
42622009 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
42622042 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
42622107 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
42622140 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
42622205 GATAAGTG
65 GAAAAGTG
42622213 GCTACACTTA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 149 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Done.