Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold474
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: 172927
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.33
Warning! 1681 characters in sequence are not A, C, G, or T
Found at i:488 original size:29 final size:30
Alignment explanation
Indices: 447--508 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
437 TAAAAATTTT
*
447 AAAAATTCAAAAAAATATT-ATAATTTTTTAA
1 AAAAATT-AAAAAAATATTGA-AATTATTTAA
*
478 AAAAATT-AAAAATTATTGAAATTATTTAA
1 AAAAATTAAAAAAATATTGAAATTATTTAA
507 AA
1 AA
509 CTTCTAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 20 0.71
30 1 0.04
31 7 0.25
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (30 bp):
AAAAATTAAAAAAATATTGAAATTATTTAA
Found at i:17265 original size:3 final size:3
Alignment explanation
Indices: 17257--17287 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
17247 CTATTATATT
17257 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
17288 AGCAAGACAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:26317 original size:5 final size:5
Alignment explanation
Indices: 26307--26332 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
26297 CCATTCATTG
26307 TACTA TACTA TACTA TACTA TACTA T
1 TACTA TACTA TACTA TACTA TACTA T
26333 CACCATTATC
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:0.00, T:0.42
Consensus pattern (5 bp):
TACTA
Found at i:26674 original size:2 final size:2
Alignment explanation
Indices: 26667--26698 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
26657 TGCTACATAA
26667 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
26699 TAGTTTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32464 original size:18 final size:19
Alignment explanation
Indices: 32443--32485 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 19
32433 TTAAAATTAC
32443 TAAAAATATCTTT-ATTTT
1 TAAAAATATCTTTAATTTT
*
32461 T-AAAATATTTTTAATTTT
1 TAAAAATATCTTTAATTTT
32479 TAAAAAT
1 TAAAAAT
32486 TAATTAATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 10 0.45
18 7 0.32
19 5 0.23
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
TAAAAATATCTTTAATTTT
Found at i:32492 original size:18 final size:18
Alignment explanation
Indices: 32456--32493 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
32446 AAATATCTTT
*
32456 ATTTTTAAAATATTTTTA
1 ATTTTTAAAATATTATTA
32474 ATTTTTAAAA-ATTAATTA
1 ATTTTTAAAATATT-ATTA
32492 AT
1 AT
32494 GACTAGTGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTTTAAAATATTATTA
Found at i:32959 original size:22 final size:23
Alignment explanation
Indices: 32934--32978 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
32924 ATATCGGCTA
* *
32934 AATTAGTCATATATGT-TTTTTT
1 AATTAGTCAAATAGGTCTTTTTT
*
32956 AATTGGTCAAATAGGTCTTTTTT
1 AATTAGTCAAATAGGTCTTTTTT
32979 TTTTGAAGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (23 bp):
AATTAGTCAAATAGGTCTTTTTT
Found at i:38336 original size:2 final size:2
Alignment explanation
Indices: 38329--38359 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
38319 TACATATTGT
38329 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38360 TGTAAAACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39375 original size:17 final size:17
Alignment explanation
Indices: 39349--39389 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
39339 GATATCTTTA
* *
39349 AAAATCTTTATAAATAT
1 AAAATATTTATAAAAAT
39366 AAAATATTTATAAAAAT
1 AAAATATTTATAAAAAT
39383 ATAAATA
1 A-AAATA
39390 AAATTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAATATTTATAAAAAT
Found at i:39539 original size:38 final size:38
Alignment explanation
Indices: 39460--39532 Score: 92
Period size: 38 Copynumber: 1.9 Consensus size: 38
39450 AAAATTTTTA
* ** * * *
39460 AAAATTATTAGAATTTGTAAAATATTGTAGAAAATTAT
1 AAAATCATTAGAAACTGTAAAAGATTGTAAAAAAATAT
39498 AAAATCATTAGAAACTGTAAAAGATTGTAAAAAAA
1 AAAATCATTAGAAACTGTAAAAGATTGTAAAAAAA
39533 ATTAAAAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 29 1.00
ACGTcount: A:0.55, C:0.03, G:0.11, T:0.32
Consensus pattern (38 bp):
AAAATCATTAGAAACTGTAAAAGATTGTAAAAAAATAT
Found at i:40281 original size:18 final size:18
Alignment explanation
Indices: 40258--40292 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
40248 TTAGTATTGA
*
40258 TTTTAAAAATTAAAAAAC
1 TTTTAAAAAATAAAAAAC
40276 TTTTAAAAAATAAAAAA
1 TTTTAAAAAATAAAAAA
40293 AATAACAGTT
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:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
TTTTAAAAAATAAAAAAC
Found at i:40293 original size:19 final size:18
Alignment explanation
Indices: 40258--40293 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
40248 TTAGTATTGA
*
40258 TTTTAAAAATTAAAAAAC
1 TTTTAAAAATAAAAAAAC
40276 TTTTAAAAAATAAAAAAA
1 TTTT-AAAAATAAAAAAA
40294 ATAACAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
TTTTAAAAATAAAAAAAC
Found at i:57447 original size:43 final size:42
Alignment explanation
Indices: 57396--57615 Score: 236
Period size: 43 Copynumber: 5.3 Consensus size: 42
57386 TTTCTTTAAA
57396 AAACGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTACCAC
1 AAACGCCGCTAAAGACCA-GACCTTTAGCGGCGCTTTTACCAC
* * * *
57439 AAACGCCGCTAAAGATCATGACCTTTAGCGACGCTTTTTCGAC
1 AAACGCCGCTAAAGACCA-GACCTTTAGCGGCGCTTTTACCAC
* *
57482 AAACGTCGCTAAAAACCATGACCTTTAGCGGCGCTTTTACCAC
1 AAACGCCGCTAAAGACCA-GACCTTTAGCGGCGCTTTTACCAC
*
57525 AAACGCCGCT--A-A--A-ACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAGACCTTTAGCGGCGCTTTTACCAC
* * * * * * * *
57561 AAGCGCCACTAAAGAACAAACCTTTAGCGACGCTTCTAGCAA
1 AAACGCCGCTAAAGACCAGACCTTTAGCGGCGCTTTTACCAC
57603 AAACGCCGCTAAA
1 AAACGCCGCTAAA
57616 AACATAATCT
Statistics
Matches: 149, Mismatches: 22, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
36 30 0.20
38 2 0.01
39 1 0.01
40 1 0.01
41 2 0.01
42 29 0.19
43 84 0.56
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (42 bp):
AAACGCCGCTAAAGACCAGACCTTTAGCGGCGCTTTTACCAC
Found at i:57549 original size:36 final size:36
Alignment explanation
Indices: 57502--57573 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
57492 AAAAACCATG
*
57502 ACCTTTAGCGGCGCTTTTACCACAAACGCCGCTAAA
1 ACCTTTAGCGGCGCTTTTACCACAAACGCCACTAAA
* *
57538 ACCTTTAGCGGCGCTTTTCCCACAAGCGCCACTAAA
1 ACCTTTAGCGGCGCTTTTACCACAAACGCCACTAAA
57574 GAACAAACCT
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:0.26, C:0.35, G:0.17, T:0.22
Consensus pattern (36 bp):
ACCTTTAGCGGCGCTTTTACCACAAACGCCACTAAA
Found at i:61948 original size:14 final size:13
Alignment explanation
Indices: 61931--61966 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
61921 ATAAACCGTA
61931 AACCCTTAACCCC
1 AACCCTTAACCCC
61944 TAACCCTTAAACCCC
1 -AACCCTT-AACCCC
61959 AACCCTTA
1 AACCCTTA
61967 TAACTGTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.05
14 14 0.67
15 6 0.29
ACGTcount: A:0.33, C:0.47, G:0.00, T:0.19
Consensus pattern (13 bp):
AACCCTTAACCCC
Found at i:62687 original size:14 final size:14
Alignment explanation
Indices: 62670--62719 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
62660 ATAAACCGTA
*
62670 AACCCTTAATCCCT
1 AACCCTTAAACCCT
* *
62684 AACCCCTAACCCCT
1 AACCCTTAAACCCT
*
62698 AACCCTTAAACCCC
1 AACCCTTAAACCCT
62712 AACCCTTA
1 AACCCTTA
62720 TAACTGTCCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.32, C:0.48, G:0.00, T:0.20
Consensus pattern (14 bp):
AACCCTTAAACCCT
Found at i:63714 original size:41 final size:41
Alignment explanation
Indices: 63669--63912 Score: 355
Period size: 41 Copynumber: 5.9 Consensus size: 41
63659 TATGATAAAT
* *
63669 CTGAGCATTAGCGGCGCTTCTTAAAAAATGCCGCTAAAGCC
1 CTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCC
* *
63710 CTGAGCATTAACGGTGCTTCTTCAAAAACGCCGCTAAAGCC
1 CTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCC
*
63751 CTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAACC
1 CTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCC
* *
63792 CTGAGAATTATTAGCGGCGC-TCTTCAAAAACGCCGCTAAAACC
1 CTGAG---CATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCC
* * *
63835 CTGAGAATTAGCGACGCTTCTTTAAAAACGCCGCTAAAGCC
1 CTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCC
*
63876 CTGAGCATTAGCGGTGCTTCTTCAAAAACGCCGCTAA
1 CTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAA
63913 TGCTCATTTT
Statistics
Matches: 183, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
40 10 0.05
41 134 0.73
43 28 0.15
44 11 0.06
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (41 bp):
CTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCC
Found at i:63837 original size:125 final size:126
Alignment explanation
Indices: 63675--63912 Score: 388
Period size: 125 Copynumber: 1.9 Consensus size: 126
63665 AAATCTGAGC
* * * **
63675 ATTAGCGGCGCTTCTTAAAAAATGCCGCTAAAGCCCTGAGCATTAACGGTGCTTCTTCAAAAACG
1 ATTAGCGGCGCTTCTTAAAAAACGCCGCTAAAACCCTGAGAATTAACGACGCTTCTTCAAAAACG
63740 CCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAACCCTGAGAATT
66 CCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAACCCTGAGAATT
* * *
63801 ATTAGCGGCGC-TCTTCAAAAACGCCGCTAAAACCCTGAGAATTAGCGACGCTTCTTTAAAAACG
1 ATTAGCGGCGCTTCTTAAAAAACGCCGCTAAAACCCTGAGAATTAACGACGCTTCTTCAAAAACG
*
63865 CCGCTAAAGCCCTGAGCATTAGCGGTGCTTCTTCAAAAACGCCGCTAA
66 CCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAA
63913 TGCTCATTTT
Statistics
Matches: 103, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
125 92 0.89
126 11 0.11
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (126 bp):
ATTAGCGGCGCTTCTTAAAAAACGCCGCTAAAACCCTGAGAATTAACGACGCTTCTTCAAAAACG
CCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAACCCTGAGAATT
Found at i:63976 original size:40 final size:40
Alignment explanation
Indices: 63899--64015 Score: 148
Period size: 40 Copynumber: 3.0 Consensus size: 40
63889 GTGCTTCTTC
* *
63899 AAAAA-CGCCGCTAATGCTC-ATTTTTAGCGGCGTTTTTT
1 AAAAAGCGCCGCTAATGCTCGATTTTTAGTGGCATTTTTT
* *
63937 AAAAAGCGCCGCTAATACTCGATCTTTAGTGGCATTTTTT
1 AAAAAGCGCCGCTAATGCTCGATTTTTAGTGGCATTTTTT
* * * *
63977 TAAAAGCGTCGCTAATGCTTGATTTTTAGTGGTATTTTT
1 AAAAAGCGCCGCTAATGCTCGATTTTTAGTGGCATTTTT
64016 CATCCAAACG
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
38 5 0.07
39 13 0.19
40 49 0.73
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (40 bp):
AAAAAGCGCCGCTAATGCTCGATTTTTAGTGGCATTTTTT
Found at i:67046 original size:16 final size:16
Alignment explanation
Indices: 67012--67064 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
67002 ATGGCATCAG
67012 TCATGCAATACTCAAT
1 TCATGCAATACTCAAT
*
67028 TCATG-AATACATCATT
1 TCATGCAATAC-TCAAT
* * *
67044 TCATACCATACTCAAA
1 TCATGCAATACTCAAT
67060 TCATG
1 TCATG
67065 AGTATATAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 5 0.17
16 20 0.69
17 4 0.14
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.32
Consensus pattern (16 bp):
TCATGCAATACTCAAT
Found at i:67310 original size:40 final size:41
Alignment explanation
Indices: 67255--67381 Score: 156
Period size: 41 Copynumber: 3.2 Consensus size: 41
67245 GCTAGTTTGG
* *
67255 CACCCAGTGCCTCATCGGAT-AATTCGAAGTAGTAAATTGA
1 CACCCAGTGTCTCATCGGATAAATCCGAAGTAGTAAATTGA
*
67295 CACCCAGTGTCTCATCGAATAAATCCGAAGTAGTAAATTGA
1 CACCCAGTGTCTCATCGGATAAATCCGAAGTAGTAAATTGA
* * * *
67336 CACCTAGTGTCTCATCGGTTAAA-CTG-A--AGTAAATTGG
1 CACCCAGTGTCTCATCGGATAAATCCGAAGTAGTAAATTGA
67373 CACCCAGTG
1 CACCCAGTG
67382 CCTTATCGAC
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
37 17 0.22
39 1 0.01
40 20 0.26
41 39 0.51
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (41 bp):
CACCCAGTGTCTCATCGGATAAATCCGAAGTAGTAAATTGA
Found at i:68227 original size:15 final size:16
Alignment explanation
Indices: 68207--68236 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
68197 GCCGTGGTTT
68207 TTTTTCTTT-TTTCTC
1 TTTTTCTTTCTTTCTC
68222 TTTTTCTTTCTTTCT
1 TTTTTCTTTCTTTCT
68237 TTCCTGTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTCTTTCTTTCTC
Found at i:68246 original size:19 final size:19
Alignment explanation
Indices: 68209--68246 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
68199 CGTGGTTTTT
*
68209 TTTCTTTTTTCTCTTTTTC
1 TTTCTTTTTTCTCTGTTTC
68228 TTTCTTTCTTTC-CTGTTTC
1 TTTCTTT-TTTCTCTGTTTC
68247 GTTTTGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.00, C:0.24, G:0.03, T:0.74
Consensus pattern (19 bp):
TTTCTTTTTTCTCTGTTTC
Found at i:70488 original size:18 final size:18
Alignment explanation
Indices: 70465--70508 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
70455 TTAATAGGGT
*
70465 ATTTCAATTC-ATAATTCA
1 ATTTCAATTCAAT-ATACA
*
70483 ATTTCAAATCAATATACA
1 ATTTCAATTCAATATACA
70501 ATTTCAAT
1 ATTTCAAT
70509 CTATTCCAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTTCAATTCAATATACA
Found at i:70792 original size:13 final size:14
Alignment explanation
Indices: 70773--70828 Score: 58
Period size: 14 Copynumber: 3.8 Consensus size: 14
70763 ATTTCCCCTT
70773 TCTTTTTCTTTCTC
1 TCTTTTTCTTTCTC
*
70787 TCTTTTTCGTTTCAC
1 TCTTTTTC-TTTCTC
* *
70802 TTCTCTGTTCTTTCTT
1 -TCT-TTTTCTTTCTC
70818 TCTTTTTCTTT
1 TCTTTTTCTTT
70829 TTTCTTTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
14 15 0.44
15 8 0.24
16 7 0.21
17 4 0.12
ACGTcount: A:0.02, C:0.25, G:0.04, T:0.70
Consensus pattern (14 bp):
TCTTTTTCTTTCTC
Found at i:70826 original size:21 final size:22
Alignment explanation
Indices: 70802--70845 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
70792 TTCGTTTCAC
*
70802 TTCTCTGTTC-TTTCTTTCTTT
1 TTCTCTGTTCTTTTATTTCTTT
* *
70823 TTCTTTTTTCTTTTATTTCTTT
1 TTCTCTGTTCTTTTATTTCTTT
70845 T
1 T
70846 ACTTTCTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.77
Consensus pattern (22 bp):
TTCTCTGTTCTTTTATTTCTTT
Found at i:70856 original size:10 final size:9
Alignment explanation
Indices: 70812--70859 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
70802 TTCTCTGTTC
*
70812 TTTCTTTCTT
1 TTTCTTT-TA
70822 TTTC-TTT-
1 TTTCTTTTA
70829 TTTCTTTTA
1 TTTCTTTTA
70838 TTTCTTTTA
1 TTTCTTTTA
70847 CTTTCTTTTA
1 -TTTCTTTTA
70857 TTT
1 TTT
70860 TATGTTATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
7 4 0.11
8 4 0.11
9 14 0.40
10 13 0.37
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTCTTTTA
Found at i:71734 original size:209 final size:208
Alignment explanation
Indices: 71358--71758 Score: 529
Period size: 210 Copynumber: 1.9 Consensus size: 208
71348 TAGAATAAGG
* **
71358 TTACTACTCTGCTTCTACTTGACATTAATTAGAATAAGGTTTTCAACCTATAAATAGATGTAGTT
1 TTACTACTCTGCTTCTACTTGACATTAATTAGAATAAGGTTTTCAACATATAAATAGATGTAGCC
* * * * ** *
71423 GAAGCTCCTCTTGTATCATTCGAATTCGACATTAGTGAATTTTCTTCTCCTCTATTCGTGGTTTT
66 GAAACTCCTCTTGTATAATTCGAATTCAACAATAGTGAATTTTCTTCTCCTCTACCCGTAGTTTT
* * *
71488 TTCCCGAAAGGGTTTCTACGTAAAATCTGTGTGTTCTTA-TTTTTTTTTCTTATTGCTTTGCGAT
131 TTCCCGAAAGGGTTTCCACGTAAAATCTATGTGTTCTTATTTTTTTTTTCTTATTACTTTGCGAT
71552 CGTTTTATGCTGC
196 CGTTTTATGCTGC
* * * * *
71565 TTACTACAT-TGCTTCTATTTGATATTGATTAGAATAAGGGTTTTCAATATATAAATATAGATTT
1 TTACTAC-TCTGCTTCTACTTGACATTAATTAGAATAA-GGTTTTCAACATAT-AA-ATAGATGT
* * *
71629 AGCCGAAACTCCTCTTGTATAATTTGAATTCAACAATAGTGAATTTTCTTCTTCTCTGCCCGTAG
62 AGCCGAAACTCCTCTTGTATAATTCGAATTCAACAATAGTGAATTTTCTTCTCCTCTACCCGTAG
* * *
71694 -TTTTTCTCGAAAGGGTTTCCACGTAAAATTTATTTGTTCTTATTTTTTTTTTCTTATTACTTTG
127 TTTTTTCCCGAAAGGGTTTCCACGTAAAATCTATGTGTTCTTATTTTTTTTTTCTTATTACTTTG
71758 C
192 C
71759 AATCATTCTA
Statistics
Matches: 165, Mismatches: 24, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
207 32 0.19
208 13 0.08
209 39 0.24
210 81 0.49
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.46
Consensus pattern (208 bp):
TTACTACTCTGCTTCTACTTGACATTAATTAGAATAAGGTTTTCAACATATAAATAGATGTAGCC
GAAACTCCTCTTGTATAATTCGAATTCAACAATAGTGAATTTTCTTCTCCTCTACCCGTAGTTTT
TTCCCGAAAGGGTTTCCACGTAAAATCTATGTGTTCTTATTTTTTTTTTCTTATTACTTTGCGAT
CGTTTTATGCTGC
Found at i:76174 original size:15 final size:16
Alignment explanation
Indices: 76154--76183 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
76144 CGGGCAGATA
76154 AAAGT-ATTTTTAAAC
1 AAAGTAATTTTTAAAC
76169 AAAGTAATTTTTAAA
1 AAAGTAATTTTTAAA
76184 AAAATTCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (16 bp):
AAAGTAATTTTTAAAC
Found at i:84582 original size:20 final size:20
Alignment explanation
Indices: 84549--84587 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
84539 ACAAAACTAA
84549 TCCCATTGACTAAACAAATCC
1 TCCCATTGACTAAA-AAATCC
84570 TCCCATT-ACTAAAAAATC
1 TCCCATTGACTAAAAAATC
84588 TAATACTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 6 0.33
21 7 0.39
ACGTcount: A:0.41, C:0.31, G:0.03, T:0.26
Consensus pattern (20 bp):
TCCCATTGACTAAAAAATCC
Found at i:86639 original size:8 final size:8
Alignment explanation
Indices: 86626--86655 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
86616 ATAAAATTTT
86626 TTAAATAA
1 TTAAATAA
86634 TTAAATAA
1 TTAAATAA
86642 TTAAATAA
1 TTAAATAA
*
86650 CTAAAT
1 TTAAAT
86656 TGTAACTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (8 bp):
TTAAATAA
Found at i:98799 original size:4 final size:4
Alignment explanation
Indices: 98790--98841 Score: 61
Period size: 4 Copynumber: 12.8 Consensus size: 4
98780 TTCATCGAGC
* *
98790 ATTT ATTT ATTT ATTC ATTTT ATTT -TATT ATTT ATTT ATTT ATTT ACTT
1 ATTT ATTT ATTT ATTT A-TTT ATTT AT-TT ATTT ATTT ATTT ATTT ATTT
98839 ATT
1 ATT
98842 ATTCCTTTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 1 0.02
4 36 0.88
5 4 0.10
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:100007 original size:2 final size:2
Alignment explanation
Indices: 100000--100042 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
99990 TTTCTCATGT
100000 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
100042 T
1 T
100043 AAACGAAGGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:100263 original size:85 final size:85
Alignment explanation
Indices: 100120--100325 Score: 412
Period size: 85 Copynumber: 2.4 Consensus size: 85
100110 CTAAGCACCC
100120 CACGAAAATAGATGACAACCCAAACACCTAACTTCTAAGACCAGTGGAGTAAGTGAATGGCTTAG
1 CACGAAAATAGATGACAACCCAAACACCTAACTTCTAAGACCAGTGGAGTAAGTGAATGGCTTAG
100185 AACGTCACTCAATTTTTTTA
66 AACGTCACTCAATTTTTTTA
100205 CACGAAAATAGATGACAACCCAAACACCTAACTTCTAAGACCAGTGGAGTAAGTGAATGGCTTAG
1 CACGAAAATAGATGACAACCCAAACACCTAACTTCTAAGACCAGTGGAGTAAGTGAATGGCTTAG
100270 AACGTCACTCAATTTTTTTA
66 AACGTCACTCAATTTTTTTA
100290 CACGAAAATAGATGACAACCCAAACACCTAACTTCT
1 CACGAAAATAGATGACAACCCAAACACCTAACTTCT
100326 GTTACTCAAT
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 121 1.00
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.23
Consensus pattern (85 bp):
CACGAAAATAGATGACAACCCAAACACCTAACTTCTAAGACCAGTGGAGTAAGTGAATGGCTTAG
AACGTCACTCAATTTTTTTA
Found at i:103168 original size:8 final size:9
Alignment explanation
Indices: 103137--103165 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
103127 AAAATTTTTA
103137 TTTAAAATT
1 TTTAAAATT
103146 TTTAAAATT
1 TTTAAAATT
103155 TTTAAAATT
1 TTTAAAATT
103164 TT
1 TT
103166 AAATTAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTAAAATT
Found at i:112331 original size:3 final size:3
Alignment explanation
Indices: 112323--112356 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
112313 TAAGATATAT
112323 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
112357 CTGACCTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:119157 original size:24 final size:24
Alignment explanation
Indices: 119129--119175 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
119119 TAGAAGATTT
*
119129 AGTATTTATTAGTATAATATATTA
1 AGTATTTATTAGCATAATATATTA
*
119153 AGTATTTATTAGCATAATTTATT
1 AGTATTTATTAGCATAATATATT
119176 TGACTTACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.51
Consensus pattern (24 bp):
AGTATTTATTAGCATAATATATTA
Found at i:121629 original size:13 final size:13
Alignment explanation
Indices: 121611--121762 Score: 78
Period size: 13 Copynumber: 11.5 Consensus size: 13
121601 CATATCTATC
*
121611 CATATAAACATTT
1 CATATAATCATTT
*
121624 CATATAATTATTT
1 CATATAATCATTT
121637 CCATATAATCGA-TT
1 -CATATAATC-ATTT
*
121651 CATATAATTATTT
1 CATATAATCATTT
* *
121664 CGT-TTATCTATTT
1 CATATAATC-ATTT
* *
121677 CTGTATAACTGA-TT
1 C-ATATAA-TCATTT
* *
121691 CATATAACCATTA
1 CATATAATCATTT
121704 CATAT-ATCTATTT
1 CATATAATC-ATTT
* *
121717 CTATATAACCAATT
1 C-ATATAATCATTT
*
121731 CTTATAATCATTT
1 CATATAATCATTT
* *
121744 CACATAACCATTT
1 CATATAATCATTT
*
121757 CGTATA
1 CATATA
121763 GCCATTTAAA
Statistics
Matches: 103, Mismatches: 25, Indels: 22
0.69 0.17 0.15
Matches are distributed among these distances:
12 7 0.07
13 66 0.64
14 23 0.22
15 6 0.06
16 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.03, T:0.44
Consensus pattern (13 bp):
CATATAATCATTT
Found at i:121652 original size:27 final size:27
Alignment explanation
Indices: 121609--121664 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
121599 TACATATCTA
121609 TCCATATAAACATTTCATATAATTATT
1 TCCATATAAACATTTCATATAATTATT
*
121636 TCCATATAATCGA-TTCATATAATTATT
1 TCCATATAAAC-ATTTCATATAATTATT
121663 TC
1 TC
121665 GTTTATCTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.38, C:0.16, G:0.02, T:0.45
Consensus pattern (27 bp):
TCCATATAAACATTTCATATAATTATT
Found at i:121657 original size:40 final size:40
Alignment explanation
Indices: 121611--121750 Score: 133
Period size: 40 Copynumber: 3.5 Consensus size: 40
121601 CATATCTATC
* *
121611 CATATAAACATTTCATATAAT-TATTTCCATATAATCGATT
1 CATATAATCATTTCATATAATCTATTTCTATATAA-CGATT
* * * *
121651 CATATAATTATTTCGT-TTATCTATTTCTGTATAACTGATT
1 CATATAATCATTTCATATAATCTATTTCTATATAAC-GATT
* * *
121691 CATATAACCATTACATAT-ATCTATTTCTATATAACCAATT
1 CATATAATCATTTCATATAATCTATTTCTATATAA-CGATT
* *
121731 CTTATAATCATTTCACATAA
1 CATATAATCATTTCATATAA
121751 CCATTTCGTA
Statistics
Matches: 79, Mismatches: 16, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
39 4 0.05
40 72 0.91
41 3 0.04
ACGTcount: A:0.36, C:0.16, G:0.03, T:0.44
Consensus pattern (40 bp):
CATATAATCATTTCATATAATCTATTTCTATATAACGATT
Found at i:121757 original size:80 final size:79
Alignment explanation
Indices: 121611--121762 Score: 171
Period size: 80 Copynumber: 1.9 Consensus size: 79
121601 CATATCTATC
* * * * *** * *
121611 CATATAAACATTTCATATAATTATTTCCATATAATCGATTCATATAATTATTTCGTTTATCTATT
1 CATATAAACATTACATATAATTATTTCCATATAACCAATTCATATAATCATTTCACATAACCATT
121676 TCTGTATAACTGATT
66 TC-GTATAACTGATT
* * *
121691 CATATAACCATTACATAT-ATCTATTTCTATATAACCAATTCTTATAATCATTTCACATAACCAT
1 CATATAAACATTACATATAAT-TATTTCCATATAACCAATTCATATAATCATTTCACATAACCAT
121755 TTCGTATA
65 TTCGTATA
121763 GCCATTTAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
79 7 0.12
80 52 0.88
ACGTcount: A:0.36, C:0.17, G:0.03, T:0.44
Consensus pattern (79 bp):
CATATAAACATTACATATAATTATTTCCATATAACCAATTCATATAATCATTTCACATAACCATT
TCGTATAACTGATT
Found at i:126022 original size:22 final size:23
Alignment explanation
Indices: 125969--126024 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
125959 CCCGTTTTTA
* * *
125969 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
125992 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
126014 ATTAAAATTAA
1 ATTAAAATTAA
126025 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:126037 original size:16 final size:16
Alignment explanation
Indices: 126000--126039 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
125990 TTAATAAAAT
* *
126000 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
126016 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
126032 TAAAATTA
1 TAAAATTA
126040 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:126215 original size:23 final size:24
Alignment explanation
Indices: 126168--126213 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
126158 AAATAAACTT
126168 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
*
126192 AAAATATAAAA-TATATATATTT
1 AAAATAAAAAACTAT-TATATTT
126214 AATATTTTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:130803 original size:213 final size:213
Alignment explanation
Indices: 130436--132796 Score: 4609
Period size: 213 Copynumber: 11.1 Consensus size: 213
130426 TAAGACACAA
* * * * * *
130436 AAGAGATTTCAATTTAAAAAAGCTGTCAAGAAAGCAAACAA-AGTTTTCACAGTCGTTCA-AGCT
1 AAGAGATTTCAATTTACAAAAGCTGTCAGGAAGGCAAACAAGA-TTTTTACAGTTGTTCATA-TT
* * *
130499 CAAATACTTAAGACCAACAAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTA
64 CAAATCCTTAAGACCAATAAGATTGCCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTA
130564 AATCAAGTTCATACAACCTCTCCATGGTGTCTATGATTTCCGGGAAAATCTCCAATCTCAAGCAA
129 AATCAAGTTCATACAACCTCTCCATGGTGTCTATGATTTCCGGGAAAATCTCCAATCTCAAGCAA
130629 CCATGAAGACGGAATGTTGT
194 CCATGAAGACGGAATGTTGT
130649 AAGAGATTTCAATTTACAAAAGCTGTCAGGAAGGCAAACAAGATTTTTACAGTTGTTCATATTCA
1 AAGAGATTTCAATTTACAAAAGCTGTCAGGAAGGCAAACAAGATTTTTACAGTTGTTCATATTCA
130714 AATCCTTAAGACCAATAAGATTGCCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAA
66 AATCCTTAAGACCAATAAGATTGCCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAA
130779 TCAAGTTCATACAACCTCTCCATGGTGTCTATGATTTCCGGGAAAATCTCCAATCTCAAGCAACC
131 TCAAGTTCATACAACCTCTCCATGGTGTCTATGATTTCCGGGAAAATCTCCAATCTCAAGCAACC
130844 ATGAAGACGGAATGTTGT
196 ATGAAGACGGAATGTTGT
130862 AAGAGATTTCAATTTACAAAAGCTGTCAGGAAGGCAAACAAGATTTTTACAGTTGTTCATATTCA
1 AAGAGATTTCAATTTACAAAAGCTGTCAGGAAGGCAAACAAGATTTTTACAGTTGTTCATATTCA
130927 AATCCTTAAGACCAATAAGATTGCCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAA
66 AATCCTTAAGACCAATAAGATTGCCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAA
130992 TCAAGTTCATACAACCTCTCCATGGTGTCTATGATTTCCGGGAAAATCTCCAATCTCAAGCAACC
131 TCAAGTTCATACAACCTCTCCATGGTGTCTATGATTTCCGGGAAAATCTCCAATCTCAAGCAACC
131057 ATGAAGACGGAATGTTGT
196 ATGAAGACGGAATGTTGT
131075 AAGAGATTTCAATTTACAAAAGCTGTCAGGAAGGCAAACAAGATTTTTACAGTTGTTCATATTCA
1 AAGAGATTTCAATTTACAAAAGCTGTCAGGAAGGCAAACAAGATTTTTACAGTTGTTCATATTCA
131140 AATCCTTAAGACCAATAAGATTGCCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAA
66 AATCCTTAAGACCAATAAGATTGCCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAA
131205 TCAAGTTCATACAACCTCTCCATGGTGTCTATGATTTCCGGGAAAATCTCCAATCTCAAGCAACC
131 TCAAGTTCATACAACCTCTCCATGGTGTCTATGATTTCCGGGAAAATCTCCAATCTCAAGCAACC
131270 ATGAAGACGGAATGTTGT
196 ATGAAGACGGAATGTTGT
131288 AAGAGATTTCAATTTACAAAAGCTGTCAGGAAGGCAAACAAGATTTTTACAGTTGTTCATATTCA
1 AAGAGATTTCAATTTACAAAAGCTGTCAGGAAGGCAAACAAGATTTTTACAGTTGTTCATATTCA
131353 AATCCTTAAGACCAATAAGATTGCCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAA
66 AATCCTTAAGACCAATAAGATTGCCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAA
131418 TCAAGTTCATACAACCTCTCCATGGTGTCTATGATTTCCGGGAAAATCTCCAATCTCAAGCAACC
131 TCAAGTTCATACAACCTCTCCATGGTGTCTATGATTTCCGGGAAAATCTCCAATCTCAAGCAACC
131483 ATGAAGACGGAATGTTGT
196 ATGAAGACGGAATGTTGT
131501 AAGAGATTTCAATTTACAAAAGCTGTCAGGAAGGCAAACAAGATTTTTACAGTTGTTCATATTCA
1 AAGAGATTTCAATTTACAAAAGCTGTCAGGAAGGCAAACAAGATTTTTACAGTTGTTCATATTCA
131566 AATCCTTAAGACCAATAAGATTGCCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAA
66 AATCCTTAAGACCAATAAGATTGCCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAA
131631 TCAAGTTCATACAACCTCTCCATGGTGTCTATGATTTCCGGGAAAATCTCCAATCTCAAGCAACC
131 TCAAGTTCATACAACCTCTCCATGGTGTCTATGATTTCCGGGAAAATCTCCAATCTCAAGCAACC
131696 ATGAAGACGGAATGTTGT
196 ATGAAGACGGAATGTTGT
131714 AAGAGATTTCAATTTACAAAAGCTGTCAGGAAGGCAAACAAGATTTTTACAGTTGTTCATATTCA
1 AAGAGATTTCAATTTACAAAAGCTGTCAGGAAGGCAAACAAGATTTTTACAGTTGTTCATATTCA
131779 AATCCTTAAGACCAATAAGATTGCCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAA
66 AATCCTTAAGACCAATAAGATTGCCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAA
131844 TCAAGTTCATACAACCTCTCCATGGTGTCTATGATTTCCGGGAAAATCTCCAATCTCAAGCAACC
131 TCAAGTTCATACAACCTCTCCATGGTGTCTATGATTTCCGGGAAAATCTCCAATCTCAAGCAACC
131909 ATGAAGACGGAATGTTGT
196 ATGAAGACGGAATGTTGT
131927 AAGAGATTTCAATTTACAAAAGCTGTCAGGAAGGCAAACAAGATTTTTACAGTTGTTCATATTCA
1 AAGAGATTTCAATTTACAAAAGCTGTCAGGAAGGCAAACAAGATTTTTACAGTTGTTCATATTCA
131992 AATCCTTAAGACCAATAAGATTGCCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAA
66 AATCCTTAAGACCAATAAGATTGCCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAA
132057 TCAAGTTCATACAACCTCTCCATGGTGTCTATGATTTCCGGGAAAATCTCCAATCTCAAGCAACC
131 TCAAGTTCATACAACCTCTCCATGGTGTCTATGATTTCCGGGAAAATCTCCAATCTCAAGCAACC
132122 ATGAAGACGGAATGTTGT
196 ATGAAGACGGAATGTTGT
132140 AAGAGATTTCAATTTACAAAAGCTGTCAGGAAGGCAAACAAGATTTTTACAGTTGTTCATATTCA
1 AAGAGATTTCAATTTACAAAAGCTGTCAGGAAGGCAAACAAGATTTTTACAGTTGTTCATATTCA
132205 AATCCTTAAGACCAATAAGATTGCCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAA
66 AATCCTTAAGACCAATAAGATTGCCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAA
132270 TCAAGTTCATACAACCTCTCCATGGTGTCTATGATTTCCGGGAAAATCTCCAATCTCAAGCAACC
131 TCAAGTTCATACAACCTCTCCATGGTGTCTATGATTTCCGGGAAAATCTCCAATCTCAAGCAACC
132335 ATGAAGACGGAATGTTGT
196 ATGAAGACGGAATGTTGT
132353 AAGAGATTTCAATTTACAAAAGCTGTCAGGAAGGCAAACAAGATTTTTACAGTTGTTCATATTCA
1 AAGAGATTTCAATTTACAAAAGCTGTCAGGAAGGCAAACAAGATTTTTACAGTTGTTCATATTCA
132418 AATCCTTAAGACCAATAAGATTGCCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAA
66 AATCCTTAAGACCAATAAGATTGCCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAA
132483 TCAAGTTCATACAACCTCTCCATGGTGTCTATGATTTCCGGGAAAATCTCCAATCTCAAGCAACC
131 TCAAGTTCATACAACCTCTCCATGGTGTCTATGATTTCCGGGAAAATCTCCAATCTCAAGCAACC
132548 ATGAAGACGGAATGTTGT
196 ATGAAGACGGAATGTTGT
132566 AAGAGATTTCAATTTACAAAAGCTGTCAGGAAGGCAAACAAGATTTTTACAGTTGTTCATATTCA
1 AAGAGATTTCAATTTACAAAAGCTGTCAGGAAGGCAAACAAGATTTTTACAGTTGTTCATATTCA
132631 AATCCTTAAGACCAATAAGATTGCCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAA
66 AATCCTTAAGACCAATAAGATTGCCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAA
132696 TCAAGTTCATACAACCTCTCCATGGTGTCTATGATTTCCGGGAAAATCTCCAATCTCAAGCAACC
131 TCAAGTTCATACAACCTCTCCATGGTGTCTATGATTTCCGGGAAAATCTCCAATCTCAAGCAACC
132761 ATGAAGACGGAATGTTGT
196 ATGAAGACGGAATGTTGT
132779 AAGAGATTTCAATTTACA
1 AAGAGATTTCAATTTACA
132797 TTCAAATTTA
Statistics
Matches: 2137, Mismatches: 9, Indels: 4
0.99 0.00 0.00
Matches are distributed among these distances:
213 2135 1.00
214 2 0.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (213 bp):
AAGAGATTTCAATTTACAAAAGCTGTCAGGAAGGCAAACAAGATTTTTACAGTTGTTCATATTCA
AATCCTTAAGACCAATAAGATTGCCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAA
TCAAGTTCATACAACCTCTCCATGGTGTCTATGATTTCCGGGAAAATCTCCAATCTCAAGCAACC
ATGAAGACGGAATGTTGT
Found at i:137530 original size:68 final size:66
Alignment explanation
Indices: 137448--137589 Score: 230
Period size: 68 Copynumber: 2.1 Consensus size: 66
137438 TCAAGTTTGT
* *
137448 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAACTAATACAATTAATAATTTGAT
1 TTTACTAATAAAATGTTAGATTTTATTACAACAATTAATACAA-TAA-ACAATTAATAATTTGAT
137513 AAA
64 AAA
*
137516 TTTACTAATAAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
1 TTTACTAATAAAATGTTAGATTTTATTACAACAATTAATACAATAAACAATTAATAATTTGATAA
*
137581 T
66 A
137582 TTTACTAA
1 TTTACTAA
137590 CAATTAATTT
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
66 27 0.39
67 2 0.03
68 41 0.59
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (66 bp):
TTTACTAATAAAATGTTAGATTTTATTACAACAATTAATACAATAAACAATTAATAATTTGATAA
A
Found at i:137599 original size:16 final size:16
Alignment explanation
Indices: 137578--137619 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
137568 AATAATTTGA
*
137578 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
137594 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
137610 TAGTTTTAAT
1 TAATTTTAAT
137620 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:137603 original size:22 final size:23
Alignment explanation
Indices: 137593--137648 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
137583 TTACTAACAA
* * *
137593 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
137615 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
137638 TTAATTTTAAT
1 TTAATTTTAAT
137649 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:138502 original size:47 final size:47
Alignment explanation
Indices: 138433--138533 Score: 202
Period size: 47 Copynumber: 2.1 Consensus size: 47
138423 TACTATTTCA
138433 TTAAAAACTGATTGACTGTTTACAGGGATAAGAAAGCTTAAATAAGC
1 TTAAAAACTGATTGACTGTTTACAGGGATAAGAAAGCTTAAATAAGC
138480 TTAAAAACTGATTGACTGTTTACAGGGATAAGAAAGCTTAAATAAGC
1 TTAAAAACTGATTGACTGTTTACAGGGATAAGAAAGCTTAAATAAGC
138527 TTAAAAA
1 TTAAAAA
138534 TAATAATAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.28
Consensus pattern (47 bp):
TTAAAAACTGATTGACTGTTTACAGGGATAAGAAAGCTTAAATAAGC
Found at i:141038 original size:18 final size:18
Alignment explanation
Indices: 141002--141038 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
140992 AAATAATTTA
*
141002 AAAATATTTTTTATTTTT
1 AAAATATTTTTTATGTTT
*
141020 AAAATATTTTTTGTGTTT
1 AAAATATTTTTTATGTTT
141038 A
1 A
141039 TTAAAAACCG
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:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
AAAATATTTTTTATGTTT
Found at i:151543 original size:20 final size:21
Alignment explanation
Indices: 151515--151563 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
151505 ATATATCTTT
*
151515 ATTTTATTTGATTTTAAT-AA
1 ATTTGATTTGATTTTAATCAA
151535 ATTTGATTTGATTTTAATCAA
1 ATTTGATTTGATTTTAATCAA
151556 A-TTGATTT
1 ATTTGATTT
151564 AATTGCCTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 24 0.89
21 3 0.11
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57
Consensus pattern (21 bp):
ATTTGATTTGATTTTAATCAA
Found at i:151999 original size:30 final size:32
Alignment explanation
Indices: 151946--152004 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
151936 TATTTGACAA
151946 TTTAAATATAAATTATTTGATTTACATTTTAT
1 TTTAAATATAAATTATTTGATTTACATTTTAT
* *
151978 TTTATATATAAA-TATTT-ATTTATATTT
1 TTTAAATATAAATTATTTGATTTACATTT
152005 ATATATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 9 0.36
31 5 0.20
32 11 0.44
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (32 bp):
TTTAAATATAAATTATTTGATTTACATTTTAT
Found at i:152001 original size:18 final size:19
Alignment explanation
Indices: 151973--152012 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
151963 TGATTTACAT
151973 TTTATTTTATATATAAATA
1 TTTATTTTATATATAAATA
* *
151992 TTTA-TTTATATTTATATA
1 TTTATTTTATATATAAATA
152010 TTT
1 TTT
152013 TATTCGCTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATTTTATATATAAATA
Found at i:152202 original size:31 final size:30
Alignment explanation
Indices: 152161--152218 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
152151 AGTGTACCAC
152161 TTTAAATATAAATTATTGATTTACATTTTAT
1 TTTAAATATAAA-TATTGATTTACATTTTAT
* * *
152192 TTTATATATAAATATTTATTTATATTT
1 TTTAAATATAAATATTGATTTACATTT
152219 ATATATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (30 bp):
TTTAAATATAAATATTGATTTACATTTTAT
Found at i:152215 original size:18 final size:19
Alignment explanation
Indices: 152187--152226 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
152177 TGATTTACAT
152187 TTTATTTTATATATAAATA
1 TTTATTTTATATATAAATA
* *
152206 TTTA-TTTATATTTATATA
1 TTTATTTTATATATAAATA
152224 TTT
1 TTT
152227 TATTCGCTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATTTTATATATAAATA
Found at i:152331 original size:214 final size:215
Alignment explanation
Indices: 151946--152379 Score: 861
Period size: 214 Copynumber: 2.0 Consensus size: 215
151936 TATTTGACAA
151946 TTTAAATATAAATTATTTGATTTACATTTTATTTTATATATAAATATTTATTTATATTTATATAT
1 TTTAAATATAAATTATTTGATTTACATTTTATTTTATATATAAATATTTATTTATATTTATATAT
152011 TTTATTCGCTAGCGTGTTTTGTCCAACAAAAATCAACTGCTATTAATGTTAAATACACTTACATC
66 TTTATTCGCTAGCGTGTTTTGTCCAACAAAAATCAACTGCTATTAATGTTAAATACACTTACATC
152076 TTGTGAAAAAGAAGATTACTGGCTCTTTCTTAAAAAGTTACAGTTTAGTTTGGCGTGAGGAACAA
131 TTGTGAAAAAGAAGATTACTGGCTCTTTCTTAAAAAGTTACAGTTTAGTTTGGCGTGAGGAACAA
152141 GGACATTAAAAGTGTACCAC
196 GGACATTAAAAGTGTACCAC
152161 TTTAAATATAAATTA-TTGATTTACATTTTATTTTATATATAAATATTTATTTATATTTATATAT
1 TTTAAATATAAATTATTTGATTTACATTTTATTTTATATATAAATATTTATTTATATTTATATAT
152225 TTTATTCGCTAGCGTGTTTTGTCCAACAAAAATCAACTGCTATTAATGTTAAATACACTTACATC
66 TTTATTCGCTAGCGTGTTTTGTCCAACAAAAATCAACTGCTATTAATGTTAAATACACTTACATC
152290 TTGTGAAAAAGAAGATTACTGGCTCTTTCTTAAAAAGTTACAGTTTAGTTTGGCGTGAGGAACAA
131 TTGTGAAAAAGAAGATTACTGGCTCTTTCTTAAAAAGTTACAGTTTAGTTTGGCGTGAGGAACAA
152355 GGACATTAAAAGTGTACCAC
196 GGACATTAAAAGTGTACCAC
152375 TTTAA
1 TTTAA
152380 GACCGCCGAA
Statistics
Matches: 219, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
214 204 0.93
215 15 0.07
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (215 bp):
TTTAAATATAAATTATTTGATTTACATTTTATTTTATATATAAATATTTATTTATATTTATATAT
TTTATTCGCTAGCGTGTTTTGTCCAACAAAAATCAACTGCTATTAATGTTAAATACACTTACATC
TTGTGAAAAAGAAGATTACTGGCTCTTTCTTAAAAAGTTACAGTTTAGTTTGGCGTGAGGAACAA
GGACATTAAAAGTGTACCAC
Found at i:153771 original size:20 final size:18
Alignment explanation
Indices: 153720--153774 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 18
153710 TAATTAACTT
*
153720 TTTAAAATATTAAAA--A
1 TTTAAAAAATTAAAATTA
153736 TTTAAAAAATTAAAATTA
1 TTTAAAAAATTAAAATTA
153754 TTTAAAAAATATACAAATTA
1 TTTAAAAAAT-TA-AAATTA
153774 T
1 T
153775 AAGTAAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
16 14 0.41
18 11 0.32
19 2 0.06
20 7 0.21
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
TTTAAAAAATTAAAATTA
Found at i:165062 original size:3 final size:3
Alignment explanation
Indices: 165054--165087 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
165044 TAAGATATAT
165054 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
165088 CTGACCTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:166520 original size:13 final size:13
Alignment explanation
Indices: 166504--166528 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
166494 CATGGCTCAA
166504 ATTTAAAATAAAT
1 ATTTAAAATAAAT
166517 ATTTAAAATAAA
1 ATTTAAAATAAA
166529 GAATGACCTA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATTTAAAATAAAT
Found at i:170057 original size:24 final size:24
Alignment explanation
Indices: 170029--170075 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
170019 TAGAAGATTT
*
170029 AGTATTTATTAGTATAATATATTA
1 AGTATTTATTAGCATAATATATTA
*
170053 AGTATTTATTAGCATAATTTATT
1 AGTATTTATTAGCATAATATATT
170076 TGACTTACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.51
Consensus pattern (24 bp):
AGTATTTATTAGCATAATATATTA
Found at i:171166 original size:17 final size:17
Alignment explanation
Indices: 171144--171181 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
171134 TCGAATTGCC
171144 TAAATTTGTTTTCACTG
1 TAAATTTGTTTTCACTG
171161 TAAATTTGTTTTCACTG
1 TAAATTTGTTTTCACTG
171178 TAAA
1 TAAA
171182 AGACACACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.50
Consensus pattern (17 bp):
TAAATTTGTTTTCACTG
Found at i:172276 original size:13 final size:13
Alignment explanation
Indices: 172260--172284 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
172250 TTCAGAAGTG
172260 CTTTTGAAAAGCA
1 CTTTTGAAAAGCA
172273 CTTTTGAAAAGC
1 CTTTTGAAAAGC
172285 GAAAAATTCC
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
CTTTTGAAAAGCA
Done.