Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold107
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1028272
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.29
Warning! 136574 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:1865 original size:49 final size:49
Alignment explanation
Indices: 1793--1892 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
1783 AAAATACTCA
1793 TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGAGATTGTAAGGTTT
1 TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGAGATTGTAAGGTTT
*
1842 TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTAAGGTTT
1 TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGAGATTGTAAGGTTT
1891 TT
1 TT
1893 TATTATTATT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (49 bp):
TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGAGATTGTAAGGTTT
Found at i:4531 original size:174 final size:176
Alignment explanation
Indices: 4197--4546 Score: 508
Period size: 176 Copynumber: 2.0 Consensus size: 176
4187 GTTTTAGCTA
* * *** * *
4197 TTTCGATGAATAATAATGTAAGATAGGCCAGAAAACAAGAATAAAAAAAATTAATTTTCATTTAG
1 TTTCGATGAAAAATAATGTAAAATAGAAAAGAAAACAAGAATAAAAAAAATTAAGTTTCATTAAG
* * *
4262 CACTTCCGTTTGCCCGTTTCCTGTCCCGGGACAAAAAAACCTTATATCGATGAGATCTCAAAAAC
66 CACTTCCGTTTGCCCGTTTCCTGTCCCGAGACAAAAAAACCATATATCGACGAGATCTCAAAAAC
* * * *
4327 GGTAAAGACTTCAACAACCAAACTTTGTAGGATTATAGACCTGTGT
131 AGTAAAGACTTAAACAACCAAACTTTGTAGGATGATAGACCAGTGT
*
4373 TTTCGATGAAAAATAATGTAAAATAGAAAAGTAAACAAG-ATAAAAAAAATTTAAGTTTCATTAA
1 TTTCGATGAAAAATAATGTAAAATAGAAAAGAAAACAAGAATAAAAAAAA-TTAAGTTTCATTAA
*
4437 GCACTTCCGTTTGTCCGTTTCCTGTCCCGAGAC-AAAAAA-CATATATCGACGAGATCTCAAAAA
65 GCACTTCCGTTTGCCCGTTTCCTGTCCCGAGACAAAAAAACCATATATCGACGAGATCTCAAAAA
**
4500 CAGTAGCGACTTAAACAACCAAACTTTGTAGGATGATAGACCAGTGT
130 CAGTAAAGACTTAAACAACCAAACTTTGTAGGATGATAGACCAGTGT
4547 ATGGACATGT
Statistics
Matches: 155, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
174 63 0.41
175 16 0.10
176 76 0.49
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (176 bp):
TTTCGATGAAAAATAATGTAAAATAGAAAAGAAAACAAGAATAAAAAAAATTAAGTTTCATTAAG
CACTTCCGTTTGCCCGTTTCCTGTCCCGAGACAAAAAAACCATATATCGACGAGATCTCAAAAAC
AGTAAAGACTTAAACAACCAAACTTTGTAGGATGATAGACCAGTGT
Found at i:6037 original size:36 final size:36
Alignment explanation
Indices: 5990--6066 Score: 145
Period size: 36 Copynumber: 2.1 Consensus size: 36
5980 AGCTCAGTAA
*
5990 ATTTGGAGCCATCAAAGTTTGAGTGAATAGTGATTT
1 ATTTGGAGCCATCAAAGTGTGAGTGAATAGTGATTT
6026 ATTTGGAGCCATCAAAGTGTGAGTGAATAGTGATTT
1 ATTTGGAGCCATCAAAGTGTGAGTGAATAGTGATTT
6062 ATTTG
1 ATTTG
6067 AGTATATGTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.30, C:0.08, G:0.26, T:0.36
Consensus pattern (36 bp):
ATTTGGAGCCATCAAAGTGTGAGTGAATAGTGATTT
Found at i:6196 original size:54 final size:54
Alignment explanation
Indices: 6116--6229 Score: 192
Period size: 54 Copynumber: 2.1 Consensus size: 54
6106 CCTTAGAATA
* * *
6116 AAATTAAACAAACTTGTCAAGCCATGAACAATTATGGAATGCTGTTATTATCAT
1 AAATTGAACAAACTTGTCAAGCCATGAACAATTATGGAATACTGTTATCATCAT
*
6170 AAATTGAACAAACTTGTCAAGCCATGAACAATTATTGAATACTGTTATCATCAT
1 AAATTGAACAAACTTGTCAAGCCATGAACAATTATGGAATACTGTTATCATCAT
6224 AAATTG
1 AAATTG
6230 GCATTGATTT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (54 bp):
AAATTGAACAAACTTGTCAAGCCATGAACAATTATGGAATACTGTTATCATCAT
Found at i:9818 original size:2 final size:2
Alignment explanation
Indices: 9811--10028 Score: 420
Period size: 2 Copynumber: 109.0 Consensus size: 2
9801 CAGACAACAA
9811 AC AC AC AC -C AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
9852 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
9894 AC AC AC AC AC AC AC AC NAC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC -AC AC AC AC AC AC AC AC AC AC AC AC AC
9937 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
9979 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
10021 AC AC AC AC
1 AC AC AC AC
10029 TTTTCCTTTT
Statistics
Matches: 214, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.00
2 211 0.99
3 2 0.01
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:13910 original size:2 final size:2
Alignment explanation
Indices: 13903--13945 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
13893 CGACTGGCGC
*
13903 AT AT AT AT AT AT AT AT AT AT AT AT NT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13945 A
1 A
13946 CACCACTGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17025 original size:16 final size:16
Alignment explanation
Indices: 17004--17034 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
16994 AGAACATTTT
17004 ACCTTCATTTTAAAAA
1 ACCTTCATTTTAAAAA
17020 ACCTTCATTTTAAAA
1 ACCTTCATTTTAAAA
17035 TATAGTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (16 bp):
ACCTTCATTTTAAAAA
Found at i:17495 original size:10 final size:10
Alignment explanation
Indices: 17479--17697 Score: 54
Period size: 10 Copynumber: 20.9 Consensus size: 10
17469 CCGTATGAAA
17479 ATCCCCTGTC
1 ATCCCCTGTC
*
17489 TTCCCCTGTC
1 ATCCCCTGTC
* *
17499 ACCCCCTGTGT
1 ATCCCCTGT-C
* * *
17510 TTTCACTGTC
1 ATCCCCTGTC
17520 ATCCCCTGTAC
1 ATCCCCTGT-C
17531 ATCCCCTGT-
1 ATCCCCTGTC
* *
17540 GTGCCACTGTAC
1 AT-CCCCTGT-C
*
17552 GGAGCCCCTGT-
1 --ATCCCCTGTC
*
17563 ATACCCTGTC
1 ATCCCCTGTC
17573 ATCCCCTGTGC
1 ATCCCCTGT-C
*
17584 -GCCCCTGTACAC
1 ATCCCCTGT---C
17596 ATCCCCCTGT-
1 AT-CCCCTGTC
* * *
17606 GTGCCACTGTA
1 AT-CCCCTGTC
*
17617 AGCCCCTGTC
1 ATCCCCTGTC
*
17627 ACCCCCTGT-
1 ATCCCCTGTC
*
17636 ACGCCCCTGTC
1 A-TCCCCTGTC
*
17647 ATCCCCTGTA
1 ATCCCCTGTC
* *
17657 AGCCACTGT-
1 ATCCCCTGTC
*
17666 ATACCCTTGTGC
1 AT-CCCCTGT-C
*
17678 ATGCCCCTGAC
1 AT-CCCCTGTC
17689 ATCCCCTGT
1 ATCCCCTGT
17698 ACGGCTTTTG
Statistics
Matches: 147, Mismatches: 43, Indels: 38
0.64 0.19 0.17
Matches are distributed among these distances:
9 10 0.07
10 96 0.65
11 20 0.14
12 8 0.05
13 6 0.04
14 7 0.05
ACGTcount: A:0.13, C:0.43, G:0.16, T:0.27
Consensus pattern (10 bp):
ATCCCCTGTC
Found at i:17603 original size:43 final size:43
Alignment explanation
Indices: 17523--17605 Score: 105
Period size: 42 Copynumber: 1.9 Consensus size: 43
17513 CACTGTCATC
* ** *
17523 CCCTGTACATCCCCTGTGTGCCACTGTACGGAGCCCCTGTATA
1 CCCTGTACATCCCCTGTGCGCCACTGTACACACCCCCTGTATA
*
17566 CCCTGT-CATCCCCTGTGCGCCCCTGTACACATCCCCCTGT
1 CCCTGTACATCCCCTGTGCGCCACTGTACACA-CCCCCTGT
17606 GTGCCACTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 21 0.62
43 13 0.38
ACGTcount: A:0.13, C:0.43, G:0.18, T:0.25
Consensus pattern (43 bp):
CCCTGTACATCCCCTGTGCGCCACTGTACACACCCCCTGTATA
Found at i:17635 original size:20 final size:20
Alignment explanation
Indices: 17612--17665 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
17602 CTGTGTGCCA
17612 CTGTAAGCCCCTGTCACCCC
1 CTGTAAGCCCCTGTCACCCC
* *
17632 CTGTACGCCCCTGTCATCCC
1 CTGTAAGCCCCTGTCACCCC
*
17652 CTGTAAGCCACTGT
1 CTGTAAGCCCCTGT
17666 ATACCCTTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.15, C:0.44, G:0.17, T:0.24
Consensus pattern (20 bp):
CTGTAAGCCCCTGTCACCCC
Found at i:18646 original size:2 final size:2
Alignment explanation
Indices: 18641--18694 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
18631 AAAATGATTA
18641 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
18683 AG AG AG AG AG AG
1 AG AG AG AG AG AG
18695 TTTGCATTGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:18894 original size:2 final size:2
Alignment explanation
Indices: 18887--18937 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
18877 GAGTTTATAC
18887 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
18929 AG AG AG AG A
1 AG AG AG AG A
18938 TTGCATTGAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19943 original size:2 final size:2
Alignment explanation
Indices: 19938--19986 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
19928 AAAAAATCAA
19938 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
19980 CT CT CT C
1 CT CT CT C
19987 ACATGATTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:20548 original size:20 final size:20
Alignment explanation
Indices: 20498--20586 Score: 90
Period size: 20 Copynumber: 4.3 Consensus size: 20
20488 AGTAAAAGAC
*
20498 CGTACAGGGGATGTCAGGGG
1 CGTACAGGGGATGACAGGGG
* *
20518 CATGCACAGGGGTAT-ACAGTGG
1 C--GTACAGGGG-ATGACAGGGG
*
20540 CTTACAGGGGATGACAGGGG
1 CGTACAGGGGATGACAGGGG
*
20560 CGTACAGGGGGTGACAGGGG
1 CGTACAGGGGATGACAGGGG
*
20580 CTTACAG
1 CGTACAG
20587 TGGCACACAG
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
19 2 0.04
20 38 0.68
22 14 0.25
23 2 0.04
ACGTcount: A:0.24, C:0.17, G:0.44, T:0.16
Consensus pattern (20 bp):
CGTACAGGGGATGACAGGGG
Found at i:20586 original size:10 final size:10
Alignment explanation
Indices: 20523--20586 Score: 58
Period size: 10 Copynumber: 6.4 Consensus size: 10
20513 AGGGGCATGC
20523 ACAGGGG-TAT
1 ACAGGGGCT-T
*
20533 ACAGTGGCTT
1 ACAGGGGCTT
* *
20543 ACAGGGGATG
1 ACAGGGGCTT
*
20553 ACAGGGGCGT
1 ACAGGGGCTT
* *
20563 ACAGGGGGTG
1 ACAGGGGCTT
20573 ACAGGGGCTT
1 ACAGGGGCTT
20583 ACAG
1 ACAG
20587 TGGCACACAG
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
10 40 0.98
11 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.44, T:0.16
Consensus pattern (10 bp):
ACAGGGGCTT
Found at i:20611 original size:23 final size:22
Alignment explanation
Indices: 20582--20672 Score: 73
Period size: 23 Copynumber: 4.2 Consensus size: 22
20572 GACAGGGGCT
*
20582 TACAGTGGCACACAGGGGTTGTG
1 TACAGTGGCACACAGGGG-TATG
**
20605 TACAGTGGCGGACAGGGG-ATG
1 TACAGTGGCACACAGGGGTATG
* * *
20626 -ACAG-GGTATACAGGGGCTCTG
1 TACAGTGGCACACAGGGG-TATG
*
20647 TACAGTGGCACACAGGAG-ATG
1 TACAGTGGCACACAGGGGTATG
20668 TACAG
1 TACAG
20673 GGGATGACAG
Statistics
Matches: 53, Mismatches: 11, Indels: 10
0.72 0.15 0.14
Matches are distributed among these distances:
19 9 0.17
20 4 0.08
21 11 0.21
22 4 0.08
23 25 0.47
ACGTcount: A:0.26, C:0.18, G:0.38, T:0.18
Consensus pattern (22 bp):
TACAGTGGCACACAGGGGTATG
Found at i:20651 original size:42 final size:43
Alignment explanation
Indices: 20593--20674 Score: 112
Period size: 42 Copynumber: 1.9 Consensus size: 43
20583 ACAGTGGCAC
* * ** *
20593 ACAGGGGTTGTGTACAGTGGCGGACAGGGGATG-ACAGGGTAT
1 ACAGGGGCTCTGTACAGTGGCACACAGGAGATGTACAGGGTAT
20635 ACAGGGGCTCTGTACAGTGGCACACAGGAGATGTACAGGG
1 ACAGGGGCTCTGTACAGTGGCACACAGGAGATGTACAGGG
20675 GATGACAGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
42 28 0.82
43 6 0.18
ACGTcount: A:0.26, C:0.16, G:0.41, T:0.17
Consensus pattern (43 bp):
ACAGGGGCTCTGTACAGTGGCACACAGGAGATGTACAGGGTAT
Found at i:20682 original size:63 final size:62
Alignment explanation
Indices: 20542--20682 Score: 144
Period size: 63 Copynumber: 2.2 Consensus size: 62
20532 TACAGTGGCT
* * *
20542 TACAGGGGATGACAGGGGCGTACAGGGGGTGACAGGGGCTTACAGTGGCACACAGGGGTTGTG
1 TACAGGGGATGACAGGGGCGTACAGGGGATGACAGGGGCTTACAGTGGCACACAGGAG-TATG
* ** * *
20605 TACAGTGGCGGACAGGGG-ATGACAGGGTAT-ACAGGGGCTCTGTACAGTGGCACACAGGAG-AT
1 TACAGGGGATGACAGGGGCGT-ACAGGGGATGACAGGGG--CT-TACAGTGGCACACAGGAGTAT
20667 G
62 G
20668 TACAGGGGATGACAG
1 TACAGGGGATGACAG
20683 TGAAAACACA
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
62 8 0.13
63 36 0.57
64 2 0.03
65 17 0.27
ACGTcount: A:0.26, C:0.16, G:0.43, T:0.16
Consensus pattern (62 bp):
TACAGGGGATGACAGGGGCGTACAGGGGATGACAGGGGCTTACAGTGGCACACAGGAGTATG
Found at i:22034 original size:2 final size:2
Alignment explanation
Indices: 22021--22089 Score: 129
Period size: 2 Copynumber: 34.5 Consensus size: 2
22011 AATTAAGTAC
*
22021 AG AG AC AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
22063 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
22090 CTTCATACTG
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.01, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:25745 original size:11 final size:10
Alignment explanation
Indices: 25710--25745 Score: 54
Period size: 11 Copynumber: 3.4 Consensus size: 10
25700 ATATAAAACG
25710 AAAGCATTAAA
1 AAAGCATT-AA
25721 AAAGCATTAA
1 AAAGCATTAA
25731 AAAGCAATTAA
1 AAAGC-ATTAA
25742 AAAG
1 AAAG
25746 TGAATCTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 7 0.29
11 17 0.71
ACGTcount: A:0.64, C:0.08, G:0.11, T:0.17
Consensus pattern (10 bp):
AAAGCATTAA
Found at i:26037 original size:316 final size:316
Alignment explanation
Indices: 25663--26294 Score: 1228
Period size: 316 Copynumber: 2.0 Consensus size: 316
25653 CAGTACACAA
25663 ATATCTATTTATAAAACTAAAACTGATTGGGCAGAAAATATAAAACGAAAGCATTAAAAAAGCAT
1 ATATCTATTTATAAAACTAAAACTGATTGGGCAGAAAATATAAAACGAAAGCATTAAAAAAGCAT
* *
25728 TAAAAAGCAATTAAAAAGTGAATCTGTCATTTTTGCAAAAAAAGGTGTCTCTCCTTCCTAAAAGA
66 TAAAAAGCAATTAAAAAGTAAATCTGTCATTTATGCAAAAAAAGGTGTCTCTCCTTCCTAAAAGA
25793 TTACGTAACCGCTAAGCACATTGAGAACAAATAGAAAAATATTAGAAATTAATATATAAAAGACG
131 TTACGTAACCGCTAAGCACATTGAGAACAAATAGAAAAATATTAGAAATTAATATATAAAAGACG
25858 GGCCAGCACCCAATCTCTATTAATATCTGAATTACCTTTCTGAAAAGCCTAAAAAGCCCTCCAAG
196 GGCCAGCACCCAATCTCTATTAATATCTGAATTACCTTTCTGAAAAGCCTAAAAAGCCCTCCAAG
25923 TGAATCCCGGTAACAGAACACCAATTTTGTAGTAAGTTACGATAAAATAATTATGT
261 TGAATCCCGGTAACAGAACACCAATTTTGTAGTAAGTTACGATAAAATAATTATGT
25979 ATATCTATTTATAAAACTAAAACTGATTGGGCAGAAAATATAAAACGAAAGCATTAAAAAAGCAT
1 ATATCTATTTATAAAACTAAAACTGATTGGGCAGAAAATATAAAACGAAAGCATTAAAAAAGCAT
26044 TAAAAAGCAATTAAAAAGTAAATCTGTCATTTATGCAAAAAAAGGTGTCTCTCCTTCCTAAAAGA
66 TAAAAAGCAATTAAAAAGTAAATCTGTCATTTATGCAAAAAAAGGTGTCTCTCCTTCCTAAAAGA
26109 TTACGTAACCGCTAAGCACATTGAGAACAAATAGAAAAATATTAGAAATTAATATATAAAAGACG
131 TTACGTAACCGCTAAGCACATTGAGAACAAATAGAAAAATATTAGAAATTAATATATAAAAGACG
*
26174 GGCCAGCACCCAATCTTTATTAATATCTGAATTACCTTTCTGAAAAGCCTAAAAAGCCCTCCAAG
196 GGCCAGCACCCAATCTCTATTAATATCTGAATTACCTTTCTGAAAAGCCTAAAAAGCCCTCCAAG
*
26239 TGAATCCCGGTAACAGAACCCCAATTTTGTAGTAAGTTACGATAAAATAATTATGT
261 TGAATCCCGGTAACAGAACACCAATTTTGTAGTAAGTTACGATAAAATAATTATGT
26295 GTTTATATCT
Statistics
Matches: 312, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
316 312 1.00
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.26
Consensus pattern (316 bp):
ATATCTATTTATAAAACTAAAACTGATTGGGCAGAAAATATAAAACGAAAGCATTAAAAAAGCAT
TAAAAAGCAATTAAAAAGTAAATCTGTCATTTATGCAAAAAAAGGTGTCTCTCCTTCCTAAAAGA
TTACGTAACCGCTAAGCACATTGAGAACAAATAGAAAAATATTAGAAATTAATATATAAAAGACG
GGCCAGCACCCAATCTCTATTAATATCTGAATTACCTTTCTGAAAAGCCTAAAAAGCCCTCCAAG
TGAATCCCGGTAACAGAACACCAATTTTGTAGTAAGTTACGATAAAATAATTATGT
Found at i:26061 original size:11 final size:10
Alignment explanation
Indices: 26026--26061 Score: 54
Period size: 11 Copynumber: 3.4 Consensus size: 10
26016 ATATAAAACG
26026 AAAGCATTAAA
1 AAAGCATT-AA
26037 AAAGCATTAA
1 AAAGCATTAA
26047 AAAGCAATTAA
1 AAAGC-ATTAA
26058 AAAG
1 AAAG
26062 TAAATCTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 7 0.29
11 17 0.71
ACGTcount: A:0.64, C:0.08, G:0.11, T:0.17
Consensus pattern (10 bp):
AAAGCATTAA
Found at i:42045 original size:14 final size:14
Alignment explanation
Indices: 42026--42053 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42016 GTCGCACAAA
42026 AATCTGTGCTAGTT
1 AATCTGTGCTAGTT
42040 AATCTGTGCTAGTT
1 AATCTGTGCTAGTT
42054 TTAGACTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.43
Consensus pattern (14 bp):
AATCTGTGCTAGTT
Found at i:42286 original size:21 final size:20
Alignment explanation
Indices: 42262--42324 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 20
42252 ACATTTTAAA
42262 CTGATACGTCTTCATTATATG
1 CTGATAC-TCTTCATTATATG
* * *
42283 CTGATACTTTATCTTTATATA
1 CTGATACTCT-TCATTATATG
**
42304 AAGATACTTCTTCATTATATG
1 CTGATAC-TCTTCATTATATG
42325 ATGGTAATTC
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 2 0.06
21 28 0.88
22 2 0.06
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.46
Consensus pattern (20 bp):
CTGATACTCTTCATTATATG
Found at i:43273 original size:2 final size:2
Alignment explanation
Indices: 43260--43304 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
43250 CCCCCTTCAC
*
43260 AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
43302 AG A
1 AG A
43305 CCGGTACCTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:47169 original size:1 final size:1
Alignment explanation
Indices: 47163--47212 Score: 55
Period size: 1 Copynumber: 50.0 Consensus size: 1
47153 ATGATTGTCG
* * * * *
47163 TTTTTTTTTGTTTTTTGTTTTGTTTTGTTTTTTTTTTTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
47213 GGGGGGGGGG
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (1 bp):
T
Found at i:47177 original size:10 final size:10
Alignment explanation
Indices: 47162--47213 Score: 70
Period size: 10 Copynumber: 5.1 Consensus size: 10
47152 GATGATTGTC
47162 GTTTTTTTTT
1 GTTTTTTTTT
47172 GTTTTTTGTTTT
1 G-TTTTT-TTTT
*
47184 GTTTTGTTTT
1 GTTTTTTTTT
47194 -TTTTTTTTT
1 GTTTTTTTTT
47203 GTTTTTTTTT
1 GTTTTTTTTT
47213 G
1 G
47214 GGGGGGGGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
9 8 0.22
10 15 0.41
11 9 0.24
12 5 0.14
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (10 bp):
GTTTTTTTTT
Found at i:47193 original size:24 final size:24
Alignment explanation
Indices: 47166--47213 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
47156 ATTGTCGTTT
47166 TTTTTTGTTTTTTGTTTTGTTTTG
1 TTTTTTGTTTTTTGTTTTGTTTTG
* *
47190 TTTTTTTTTTTTTGTTTTTTTTTG
1 TTTTTTGTTTTTTGTTTTGTTTTG
47214 GGGGGGGGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (24 bp):
TTTTTTGTTTTTTGTTTTGTTTTG
Found at i:47195 original size:19 final size:18
Alignment explanation
Indices: 47162--47212 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
47152 GATGATTGTC
*
47162 GTTTT-TTTTTGTTTTTT
1 GTTTTGTTTTTTTTTTTT
47179 GTTTTGTTTTGTTTTTTTT
1 GTTTTGTTTT-TTTTTTTT
*
47198 TTTTTGTTTTTTTTT
1 GTTTTGTTTTTTTTT
47213 GGGGGGGGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 5 0.17
18 9 0.30
19 16 0.53
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (18 bp):
GTTTTGTTTTTTTTTTTT
Found at i:58421 original size:16 final size:16
Alignment explanation
Indices: 58400--58435 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
58390 GCATGGTCAC
58400 GTTTTTGGATTTTAAT
1 GTTTTTGGATTTTAAT
58416 GTTTTTGGATTTTAAT
1 GTTTTTGGATTTTAAT
58432 GTTT
1 GTTT
58436 ACAGTGCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.17, C:0.00, G:0.19, T:0.64
Consensus pattern (16 bp):
GTTTTTGGATTTTAAT
Found at i:61419 original size:16 final size:16
Alignment explanation
Indices: 61398--61433 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
61388 GAAGCACTGT
61398 AAACATTAAAATCCAA
1 AAACATTAAAATCCAA
61414 AAACATTAAAATCCAA
1 AAACATTAAAATCCAA
61430 AAAC
1 AAAC
61434 GTGACCATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.64, C:0.19, G:0.00, T:0.17
Consensus pattern (16 bp):
AAACATTAAAATCCAA
Found at i:63291 original size:441 final size:442
Alignment explanation
Indices: 62445--63328 Score: 1299
Period size: 441 Copynumber: 2.0 Consensus size: 442
62435 ATGTTACCCA
* * *** ** * *
62445 GACCCAGACAAATTTTGTTATCTATTTCTTAATTTGACCTTGAGTGGTCACGGTCACGGTCATAT
1 GACCCAGACAAATTTTATCATCTATTTCTTAATTTGACCTTGAGTAAACAAAGTCAAGGTCAAAT
* *
62510 ATAAATCAATAGTACACCTAAGTGTATTATTATTGTTCTTTGTTAAAATTTTGAAGTCCTTCTGT
66 ATAAATCAATAGTACACATAAGTGTATTATTATTGTTCTTTGTTAAAAGTTTGAAGTCCTTCTGT
* * * * *
62575 CAAAGTATATTCAGGAGTTGAACAATGACGTTTTTCTAATTTGACCTTGAAATAAAATTTTTGGG
131 CAAAGTATATTCAGAAGTTGAACAATGAAGTTTTTCTAATTTGACCTTGAAATAAAAATTCTAGG
*
62640 TCAAGGTCAAAAATAATAATTTAATAAGGTTCAACTAGGTTATATACCATCTATCCGTGATACAA
196 TCAAGGT--AAAATAATAATTTAATAAGGTTCAACTAGGTTATATACCATCTATCCATGATACAA
* *
62705 GTTAAAAGTCTATATGTTAAAGGAGTCTTTTGTTATGGCCCGGACAATATTTTTTTATGAAAAGC
259 GTTAAAAGTCTATATCTTAAAGGAGTCTTGTGTTATGGCCCGGACAATATTTTTTTATGAAAAGC
* * * * **
62770 TTGACCTTGAAGAACAAAATAGGTCATGGTCAAAACTTTTTGTGGTGTGCACTCCTTCTCAATAC
324 TTGACCTTGAAGAACAAAATAGATCAAGATCAAAACTTTTGGTGGCATGCACTCCTTCTCAATAC
62835 CATCTACCTATGTTCCAAGATTGAAGTCTTAATGTCAAAGGGTATTAAAGTTAT
389 CATCTACCTATGTTCCAAGATTGAAGTCTTAATGTCAAAGGGTATTAAAGTTAT
* *
62889 GACCCAGACAAAATTTTATCATTTTTTTCTTAATTTGACCTTGAGTAAAACAAAGTCAAGGTCAA
1 GACCCAGAC-AAATTTTATCATCTATTTCTTAATTTGACCTTGAGT-AAACAAAGTCAAGGTCAA
* * *
62954 ATATTATTCAATAGTACACATAAGTGTATTATTATTGTTCTTTGTTTAAAGTTTGAAGTCCTTCT
64 ATATAAATCAATAGTACACATAAGTGTATTATTATTGTTCTTTGTTAAAAGTTTGAAGTCCTTCT
63019 GTCAAAGTATATTCAGAAGTTGAACAATGAAGTTTTTTCTAATTTGACCTTGAAATAAAAATTCT
129 GTCAAAGTATATTCAGAAGTTGAACAATGAAG-TTTTTCTAATTTGACCTTGAAATAAAAATTCT
* ** * * *
63084 AGGTCAAGGT-AAA-AAT-GTTTGGTAAGGTTCAACTAGGTTATCTACCATTTATCTATGATACA
193 AGGTCAAGGTAAAATAATAATTTAATAAGGTTCAACTAGGTTATATACCATCTATCCATGATACA
* * * *
63146 AGTTAAAAGTTTTTATCTTAAAGGAGTCTTGTGTTATTGTCCGGACAATA-TTTTTTATGAAAAG
258 AGTTAAAAGTCTATATCTTAAAGGAGTCTTGTGTTATGGCCCGGACAATATTTTTTTATGAAAAG
**
63210 CTTGACCTTGAAGAACAAAATAGATCAAGATCAAAACTTTTGGTGGCATGCACTTTTTCTCAATA
323 CTTGACCTTGAAGAACAAAATAGATCAAGATCAAAACTTTTGGTGGCATGCACTCCTTCTCAATA
* *
63275 CCATCTACCTATGTTCCAAGTTTGAAGTCTTAATGTCAAAGGGTATTTAAGTTA
388 CCATCTACCTATGTTCCAAGATTGAAGTCTTAATGTCAAAGGGTATTAAAGTTA
63329 CGGCATGTCC
Statistics
Matches: 393, Mismatches: 44, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
441 123 0.31
442 83 0.21
443 3 0.01
444 12 0.03
445 32 0.08
446 101 0.26
447 39 0.10
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (442 bp):
GACCCAGACAAATTTTATCATCTATTTCTTAATTTGACCTTGAGTAAACAAAGTCAAGGTCAAAT
ATAAATCAATAGTACACATAAGTGTATTATTATTGTTCTTTGTTAAAAGTTTGAAGTCCTTCTGT
CAAAGTATATTCAGAAGTTGAACAATGAAGTTTTTCTAATTTGACCTTGAAATAAAAATTCTAGG
TCAAGGTAAAATAATAATTTAATAAGGTTCAACTAGGTTATATACCATCTATCCATGATACAAGT
TAAAAGTCTATATCTTAAAGGAGTCTTGTGTTATGGCCCGGACAATATTTTTTTATGAAAAGCTT
GACCTTGAAGAACAAAATAGATCAAGATCAAAACTTTTGGTGGCATGCACTCCTTCTCAATACCA
TCTACCTATGTTCCAAGATTGAAGTCTTAATGTCAAAGGGTATTAAAGTTAT
Found at i:64159 original size:437 final size:429
Alignment explanation
Indices: 63352--64223 Score: 1250
Period size: 437 Copynumber: 2.0 Consensus size: 429
63342 CCTAACTACA
*
63352 TAACATAGGAGTAAATGATTGCCATATATAGGTGAATACTGTTAGAATGAACATAATTGCTTCTA
1 TAACATAGGAGTAAATGATTGCCATATATAGGTGAATACTGTTAGAATAAACATAATTGCTTCTA
* * * *
63417 TAACGTATCACAAAATATTTCACAGTAAAAAGTTATCATTAAAAGACTTTAGAGCCCCCTTAGTC
66 TAACGTATCACAAAATATTTCACAGTAAAAAGTTATCATTAAAAAACTTGAGAGCCCCCTCAGCC
* * * *
63482 CCTTATTTGAAGGGTCAGCCCTTGATGTCATAAGAATGTTCTTGTCAATTCAAACACATTTTGTT
131 CCTTATTTGAAGAGCCAGCCCTTGATGTCATAAGAAAGCTCTTGTCAATTCAAACACATTTTGTT
* ** * * *
63547 CAAGAAGTGTTTAGAAATTCTGTACTGTTCTCGAGATATCTTGAGAGAGTCGTATTAGGGGCCGA
196 CAACAAGTAATTACAAATTCTGTACCGTTATCGAGATATCTTGAGAGAGTCGTATTAGGGGCCGA
*
63612 CCCTGTAACTACCTTTAAGGACCGCATAACAAAGAAATTATGGTTGATTATTGTTAAGCTTAATA
261 CCCTGTAAC-ACCTTTAAGGACCGCATAACAAAGAAATTATGGTTGATTATTGTTAAGCTCAATA
63677 TTTTGAGCATATTTTGTTCAATATTGTTTATCAAAATGTTCCTCCATTTTGAGATATTGAGCATC
325 TTTTGAGCATATTTTGTTCAATATTGTTTATCAAAATGTTCCTCCATTTTGAGATATTGAGCAT-
* *
63742 AA-AGTTTTGGACATCTGGCCCCTTAAAATCCCGAATTACG
389 AAGAGTTTTGGACATCTGGCCCCTAAAAACCCCGAATTACG
* * *
63782 TAACATAGGAGTAAATTATTGCCATGTATAGGTGAATACTGTTGGAATAAACATAATTGCTTCTA
1 TAACATAGGAGTAAATGATTGCCATATATAGGTGAATACTGTTAGAATAAACATAATTGCTTCTA
* * *
63847 TAACGTATTACAAAATATTTTACAGTAAAAAGTTATCATTAAAAAACTTGAGAGTCCCCTCAGCC
66 TAACGTATCACAAAATATTTCACAGTAAAAAGTTATCATTAAAAAACTTGAGAGCCCCCTCAGCC
*
63912 CCTTATTTGAAGAGCCAGCCCCTTTTTCATGATTTCA-AATGAAAGCTCTTGTCAATTCAAACAC
131 CCTTATTTGAAGAGCCAG-CCC----T--TGATGTCATAA-GAAAGCTCTTGTCAATTCAAACAC
* * * * *
63976 TTTTTGTTCAACAAGTAATTACAAATTTTGTACCGTTATTGAGATATCTTGAGAGGGTCGTTTTA
188 ATTTTGTTCAACAAGTAATTACAAATTCTGTACCGTTATCGAGATATCTTGAGAGAGTCGTATTA
* *
64041 GGGGCCGACCCTGTTAGC-CCTTTTAAGGACTGCATAACAAAGAAATTATGGTTGATTATTGTTA
253 GGGGCCGACCCTG-TAACACC-TTTAAGGACCGCATAACAAAGAAATTATGGTTGATTATTGTTA
* *
64105 AGCTCAATATTTTGAGCTTCTTTTGTTCAATATTGCTTT-TCAAAAT-TGTCCTCCATTTTGAGA
316 AGCTCAATATTTTGAGCATATTTTGTTCAATATTG-TTTATCAAAATGT-TCCTCCATTTTGAGA
* * *
64168 TATTGAGCATAAGAGTTTTGGACTTCTGTCCCCTAAAAACCCCTAATTACG
379 TATTGAGCATAAGAGTTTTGGACATCTGGCCCCTAAAAACCCCGAATTACG
64219 TAACA
1 TAACA
64224 CATAATTACA
Statistics
Matches: 392, Mismatches: 37, Indels: 19
0.88 0.08 0.04
Matches are distributed among these distances:
430 135 0.34
431 3 0.01
435 1 0.00
436 7 0.02
437 240 0.61
438 6 0.02
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Consensus pattern (429 bp):
TAACATAGGAGTAAATGATTGCCATATATAGGTGAATACTGTTAGAATAAACATAATTGCTTCTA
TAACGTATCACAAAATATTTCACAGTAAAAAGTTATCATTAAAAAACTTGAGAGCCCCCTCAGCC
CCTTATTTGAAGAGCCAGCCCTTGATGTCATAAGAAAGCTCTTGTCAATTCAAACACATTTTGTT
CAACAAGTAATTACAAATTCTGTACCGTTATCGAGATATCTTGAGAGAGTCGTATTAGGGGCCGA
CCCTGTAACACCTTTAAGGACCGCATAACAAAGAAATTATGGTTGATTATTGTTAAGCTCAATAT
TTTGAGCATATTTTGTTCAATATTGTTTATCAAAATGTTCCTCCATTTTGAGATATTGAGCATAA
GAGTTTTGGACATCTGGCCCCTAAAAACCCCGAATTACG
Found at i:67286 original size:29 final size:29
Alignment explanation
Indices: 67228--67292 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
67218 TTAATGGTTT
* *
67228 ATAACCCCATTATAAAGAAACAAGGGAAG
1 ATAACTCCATTATAAAGAAACAAGAGAAG
* * *
67257 ATAACTCCATTATGAAGAAGCAAGATAAG
1 ATAACTCCATTATAAAGAAACAAGAGAAG
*
67286 ATGACTC
1 ATAACTC
67293 ATTTAACTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (29 bp):
ATAACTCCATTATAAAGAAACAAGAGAAG
Found at i:73580 original size:21 final size:21
Alignment explanation
Indices: 73556--73626 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
73546 CGATAAACCT
73556 GATAGGATTAACGCACGATAG
1 GATAGGATTAACGCACGATAG
*
73577 GATAGCATTAACGCACGATAG
1 GATAGGATTAACGCACGATAG
* * *
73598 AACAGTA-TACACGCACGATAG
1 GATAGGATTA-ACGCACGATAG
73619 GATAGGAT
1 GATAGGAT
73627 ATATATATAT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
20 2 0.05
21 39 0.95
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.18
Consensus pattern (21 bp):
GATAGGATTAACGCACGATAG
Found at i:76811 original size:10 final size:10
Alignment explanation
Indices: 76802--76852 Score: 57
Period size: 10 Copynumber: 5.1 Consensus size: 10
76792 ATATACTATT
*
76802 ATATTATATT
1 ATATTATATC
*
76812 AAATTATATC
1 ATATTATATC
*
76822 ATATTACATC
1 ATATTATATC
* *
76832 ATATCATGTC
1 ATATTATATC
76842 ATATTATATC
1 ATATTATATC
76852 A
1 A
76853 GTTAAGGTTG
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.41, C:0.12, G:0.02, T:0.45
Consensus pattern (10 bp):
ATATTATATC
Found at i:76817 original size:15 final size:15
Alignment explanation
Indices: 76799--76852 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
76789 TATATATACT
*
76799 ATTATATTATATTAA
1 ATTATATCATATTAA
*
76814 ATTATATCATATTAC
1 ATTATATCATATTAA
* * * *
76829 ATCATATCATGTCAT
1 ATTATATCATATTAA
76844 ATTATATCA
1 ATTATATCA
76853 GTTAAGGTTG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.46
Consensus pattern (15 bp):
ATTATATCATATTAA
Found at i:77597 original size:11 final size:11
Alignment explanation
Indices: 77581--77605 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
77571 TCTCAAAAAT
77581 AAATGCATGCA
1 AAATGCATGCA
77592 AAATGCATGCA
1 AAATGCATGCA
77603 AAA
1 AAA
77606 CAAAGTCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (11 bp):
AAATGCATGCA
Found at i:77761 original size:4 final size:4
Alignment explanation
Indices: 77752--77835 Score: 161
Period size: 4 Copynumber: 21.2 Consensus size: 4
77742 GAGTGCGAAG
77752 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
77800 AGAA AGAA AGAA AGAA A-AA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
77836 AAATACCTAT
Statistics
Matches: 79, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
3 3 0.04
4 76 0.96
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:78285 original size:15 final size:15
Alignment explanation
Indices: 78265--78294 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
78255 GAAAAAATCG
78265 TAATGTAATAATAAA
1 TAATGTAATAATAAA
78280 TAATGTAATAATAAA
1 TAATGTAATAATAAA
78295 CTGTATAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (15 bp):
TAATGTAATAATAAA
Found at i:78659 original size:20 final size:21
Alignment explanation
Indices: 78612--78660 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
78602 TTGTTTCATC
78612 TTGTTTGTTGGTTTGTTTGGGT
1 TTGTTT-TTGGTTTGTTTGGGT
**
78634 TT-TTTTTGGTTT-TTTTTGT
1 TTGTTTTTGGTTTGTTTGGGT
78653 TTGTTTTT
1 TTGTTTTT
78661 TTTTGCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 7 0.29
20 12 0.50
21 3 0.12
22 2 0.08
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (21 bp):
TTGTTTTTGGTTTGTTTGGGT
Found at i:78662 original size:16 final size:15
Alignment explanation
Indices: 78633--78684 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
78623 TTTGTTTGGG
*
78633 TTTTTTTTG-GTTTT
1 TTTTTTTTGTTTTTT
*
78647 TTTTGTTTGTTTTTT
1 TTTTTTTTGTTTTTT
*
78662 TTTGCTTTTGTTTTTGT
1 TTT-TTTTTGTTTTT-T
78679 TTTTTT
1 TTTTTT
78685 GTATTTTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
14 8 0.27
15 7 0.23
16 11 0.37
17 4 0.13
ACGTcount: A:0.00, C:0.02, G:0.13, T:0.85
Consensus pattern (15 bp):
TTTTTTTTGTTTTTT
Found at i:78662 original size:22 final size:22
Alignment explanation
Indices: 78632--78684 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 22
78622 GTTTGTTTGG
* *
78632 GTTTTTTTTGGTTTTTTTTGTTT
1 GTTTTTTTTGGCTTTTGTT-TTT
*
78655 GTTTTTTTTTGCTTTTGTTTTT
1 GTTTTTTTTGGCTTTTGTTTTT
78677 GTTTTTTT
1 GTTTTTTT
78685 GTATTTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 11 0.41
23 16 0.59
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (22 bp):
GTTTTTTTTGGCTTTTGTTTTT
Found at i:78670 original size:20 final size:20
Alignment explanation
Indices: 78647--78685 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
78637 TTTTGGTTTT
78647 TTTTGTTTGTT-TTTTTTTGC
1 TTTTGTTT-TTGTTTTTTTGC
78667 TTTTGTTTTTGTTTTTTTG
1 TTTTGTTTTTGTTTTTTTG
78686 TATTTTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (20 bp):
TTTTGTTTTTGTTTTTTTGC
Found at i:78684 original size:14 final size:13
Alignment explanation
Indices: 78633--78692 Score: 57
Period size: 14 Copynumber: 4.2 Consensus size: 13
78623 TTTGTTTGGG
*
78633 TTTTTTTTGGTTT
1 TTTTTTTTTGTTT
*
78646 TTTTTGTTTGTTTT
1 TTTTTTTTTG-TTT
78660 TTTTTGCTTTTGTTT
1 TTTTT--TTTTGTTT
78675 TTGTTTTTTTGTATT
1 TT-TTTTTTTGT-TT
78690 TTT
1 TTT
78693 AACTAAGTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
13 8 0.21
14 15 0.38
15 9 0.23
16 7 0.18
ACGTcount: A:0.02, C:0.02, G:0.13, T:0.83
Consensus pattern (13 bp):
TTTTTTTTTGTTT
Found at i:78692 original size:22 final size:21
Alignment explanation
Indices: 78634--78692 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 21
78624 TTGTTTGGGT
78634 TTTTTTTGGTTTTTTTTGTTTG
1 TTTTTTT-GTTTTTTTTGTTTG
78656 TTTTTTT-TTGCTTTTGTT-TTTG
1 TTTTTTTGTT--TTTT-TTGTTTG
*
78678 TTTTTTTGTATTTTT
1 TTTTTTTGTTTTTTT
78693 AACTAAGTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
20 3 0.09
21 4 0.12
22 22 0.69
23 3 0.09
ACGTcount: A:0.02, C:0.02, G:0.14, T:0.83
Consensus pattern (21 bp):
TTTTTTTGTTTTTTTTGTTTG
Found at i:82634 original size:64 final size:63
Alignment explanation
Indices: 82533--82660 Score: 247
Period size: 64 Copynumber: 2.0 Consensus size: 63
82523 ACTTGCAATT
82533 TCACTGTGTAAAGTCAGCACAACAGTCATAGCCGCAGGTTTCGCATTTTACTTCTGATTCTCA
1 TCACTGTGTAAAGTCAGCACAACAGTCATAGCCGCAGGTTTCGCATTTTACTTCTGATTCTCA
82596 NTCACTGTGTAAAGTCAGCACAACAGTCATAGCCGCAGGTTTCGCATTTTACTTCTGATTCTCA
1 -TCACTGTGTAAAGTCAGCACAACAGTCATAGCCGCAGGTTTCGCATTTTACTTCTGATTCTCA
82660 T
1 T
82661 GTACCCAAGA
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
63 1 0.02
64 63 0.98
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.32
Consensus pattern (63 bp):
TCACTGTGTAAAGTCAGCACAACAGTCATAGCCGCAGGTTTCGCATTTTACTTCTGATTCTCA
Found at i:94210 original size:11 final size:11
Alignment explanation
Indices: 94194--94230 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
94184 TTGAAGAAAA
94194 AAAAGTAATTG
1 AAAAGTAATTG
* *
94205 AAAAGTATTTT
1 AAAAGTAATTG
94216 AAAAGTAATTG
1 AAAAGTAATTG
94227 AAAA
1 AAAA
94231 TACATGCCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.30
Consensus pattern (11 bp):
AAAAGTAATTG
Found at i:100804 original size:21 final size:21
Alignment explanation
Indices: 100704--101054 Score: 185
Period size: 22 Copynumber: 15.9 Consensus size: 21
100694 TTTTTGAGGT
* *
100704 ATTTTCTGATATCAAAATATAA
1 ATTTT-TGATATCAAAAAATTA
* *
100726 ATATTTGATATC-AATAATTCGA
1 ATTTTTGATATCAAAAAATT--A
*
100748 ATTTTTGATATCAAAAAA-CA
1 ATTTTTGATATCAAAAAATTA
* *
100768 ATTCTGGATATC-AAAAATTA
1 ATTTTTGATATCAAAAAATTA
*
100788 ATTCTTGATATCAAAAAATCT-
1 ATTTTTGATATCAAAAAAT-TA
* *
100809 ATTTTGTGATATCAGAAAATCA
1 ATTTT-TGATATCAAAAAATTA
* *
100831 TTTTTTTGATATC-ACAAATTCGA
1 -ATTTTTGATATCAAAAAATT--A
* *
100854 ATTCTTGATATCAAAAAA-TG
1 ATTTTTGATATCAAAAAATTA
*
100874 ATTTTCTGATATCACAAAA-TA
1 ATTTT-TGATATCAAAAAATTA
*
100895 GATTTTCTGATATCAAGAATTAAAGTTG
1 -ATTTT-TGATATC-A-AA--AAA-TTA
* *
100923 ATTTTGGACATCAAAAAATTGA
1 ATTTTTGATATCAAAAAATT-A
* * * *
100945 AATCTTGATATCACAAAATCA
1 ATTTTTGATATCAAAAAATTA
* *
100966 TTTTTTGATATCAAAAAATCA
1 ATTTTTGATATCAAAAAATTA
*
100987 TTTTTTGATATCAAAAAATCATTTA
1 ATTTTTGATATC-AAAAA--A-TTA
*
101012 CATTTTCTGATATCAGAAAATCTA
1 -ATTTT-TGATATCAAAAAAT-TA
* *
101036 TTTTTTGATATCAGAAAAT
1 ATTTTTGATATCAAAAAAT
101055 AAGACTTACA
Statistics
Matches: 257, Mismatches: 44, Indels: 56
0.72 0.12 0.16
Matches are distributed among these distances:
19 5 0.02
20 31 0.12
21 66 0.26
22 97 0.38
23 19 0.07
24 7 0.03
25 3 0.01
26 16 0.06
27 12 0.05
28 1 0.00
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.39
Consensus pattern (21 bp):
ATTTTTGATATCAAAAAATTA
Found at i:100906 original size:43 final size:41
Alignment explanation
Indices: 100704--101010 Score: 140
Period size: 42 Copynumber: 7.1 Consensus size: 41
100694 TTTTTGAGGT
* * *
100704 ATTTTCTGATATCAAAATATAAATATT-TGATATCAATAATTCG
1 ATTTT-TGATATCAAAA-ATAGATATTCTGATATCAAAAAAT-G
* * *
100747 AATTTTTGATATCAAAAA-ACA-ATTCTGGATATCAAAAATTA
1 -ATTTTTGATATCAAAAATAGATATTCT-GATATCAAAAAATG
* ** * * * *
100788 ATTCTTGATATCAAAAAATCTATTTTGTGATATCAGAAAATC
1 ATTTTTGATATC-AAAAATAGATATTCTGATATCAAAAAATG
* *
100830 ATTTTTTTGATATCACAAATTCGA-ATTCTTGATATCAAAAAATG
1 A--TTTTTGATATCA-AAAATAGATATTC-TGATATCAAAAAATG
*
100874 ATTTTCTGATATCACAAAATAGATTTTCTGATATCAAGAATTAAAGTTG
1 ATTTT-TGATATCA-AAAATAGATATTCTGATATC-A-AA--AAA--TG
* * * * * *
100923 ATTTTGGACATCAAAAAATTGA-AATCTTGATATCACAAAATC
1 ATTTTTGATATC-AAAAATAGATATTC-TGATATCAAAAAATG
* * * *
100965 ATTTTTTGATATCAAAAA-ATCATTTTTTGATATCAAAAAATC
1 A-TTTTTGATATCAAAAATA-GATATTCTGATATCAAAAAATG
101007 ATTT
1 ATTT
101011 ACATTTTCTG
Statistics
Matches: 205, Mismatches: 36, Indels: 47
0.71 0.12 0.16
Matches are distributed among these distances:
40 14 0.07
41 11 0.05
42 53 0.26
43 49 0.24
44 42 0.20
45 2 0.01
46 1 0.00
47 6 0.03
48 19 0.09
49 8 0.04
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (41 bp):
ATTTTTGATATCAAAAATAGATATTCTGATATCAAAAAATG
Found at i:101015 original size:27 final size:28
Alignment explanation
Indices: 100985--101038 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
100975 ATCAAAAAAT
*
100985 CATTTTTTGATATCAAAAAATC-ATTTA
1 CATTTTCTGATATCAAAAAATCTATTTA
*
101012 CATTTTCTGATATCAGAAAATCTATTT
1 CATTTTCTGATATCAAAAAATCTATTT
101039 TTTGATATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (28 bp):
CATTTTCTGATATCAAAAAATCTATTTA
Found at i:101044 original size:91 final size:86
Alignment explanation
Indices: 100748--101054 Score: 262
Period size: 91 Copynumber: 3.5 Consensus size: 86
100738 AATAATTCGA
* * * *
100748 ATTTTTGATATCAAAAAA-C-AATTCTGGATATCAAAAATTAATTCTTGATATCAAAAAATCTAT
1 ATTTTTGATATCAAAAAATCTAATTCTTGATATCAAAAATCATTTTTTGATATCAAAAAATC-AT
* *
100811 TTTGTGATATCAGAAAATCATT
65 TTTCTGATATCAAAAAATCATT
* * * * * * *
100833 -TTTTTGATATCACAAATTCGAATTCTTGATATCAAAAAATGATTTTCTGATATCACAAAATAGA
1 ATTTTTGATATCAAAAAATCTAATTCTTGATATC-AAAAATCATTTTTTGATATCAAAAAAT-CA
* * *
100897 TTTTCTGATATCAAGAATTAAAGTT
64 TTTTCTGATATCAAAAAAT-CA-TT
* * *
100922 GATTTTGGACATCAAAAAAT-TGAAATCTTGATATCACAAAATCATTTTTTGATATCAAAAAATC
1 -ATTTTTGATATCAAAAAATCT-AATTCTTGATATCA-AAAATCATTTTTTGATATCAAAAAATC
*
100986 ATTTTTTGATATCAAAAAATCATTT
63 ATTTTCTGATATCAAAAAATCA-TT
* * *
101011 ACATTTTCTGATATCAGAAAATCTATTTTTTGATATCAGAAAAT
1 --ATTTT-TGATATCAAAAAATCTAATTCTTGATATCA-AAAAT
101055 AAGACTTACA
Statistics
Matches: 172, Mismatches: 37, Indels: 20
0.75 0.16 0.09
Matches are distributed among these distances:
84 15 0.09
85 1 0.01
86 12 0.07
87 38 0.22
88 1 0.01
89 5 0.03
90 23 0.13
91 76 0.44
92 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (86 bp):
ATTTTTGATATCAAAAAATCTAATTCTTGATATCAAAAATCATTTTTTGATATCAAAAAATCATT
TTCTGATATCAAAAAATCATT
Found at i:101531 original size:30 final size:29
Alignment explanation
Indices: 101492--101555 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
101482 AATTTCTGAT
101492 ATCAAAAAAT-ATAATTCTTGATATCAAAAA
1 ATCAAAAAATGAT-ATTC-TGATATCAAAAA
* * *
101522 ATCACAAAATGATTTTCTGATATCAGAAA
1 ATCAAAAAATGATATTCTGATATCAAAAA
101551 ATCAA
1 ATCAA
101556 TTTTTGGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 15 0.52
30 12 0.41
31 2 0.07
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.30
Consensus pattern (29 bp):
ATCAAAAAATGATATTCTGATATCAAAAA
Found at i:101593 original size:27 final size:24
Alignment explanation
Indices: 101533--101687 Score: 75
Period size: 22 Copynumber: 6.8 Consensus size: 24
101523 TCACAAAATG
101533 ATTTTCTGATATCAGAAAATCAAT
1 ATTTTCTGATATCAGAAAATCAAT
* *
101557 -TTTT-GGATATCAGAAAATGGATAGT
1 ATTTTCTGATATCAGAAAAT-CA-A-T
* *
101582 ATTTTCTGATATCA-AGAATTCGA-
1 ATTTTCTGATATCAGA-AAATCAAT
*
101605 A-TTTCTGATATCAAAAAATC---
1 ATTTTCTGATATCAGAAAATCAAT
* * * *
101625 ATTTCCTGATATTAGAAATTCGA-
1 ATTTTCTGATATCAGAAAATCAAT
* *
101648 ATTCT-TGATATCAAAAAATC---
1 ATTTTCTGATATCAGAAAATCAAT
*
101668 ATTTTCTGACATCAGAAAAT
1 ATTTTCTGATATCAGAAAAT
101688 ACCTCAAAAA
Statistics
Matches: 101, Mismatches: 19, Indels: 25
0.70 0.13 0.17
Matches are distributed among these distances:
20 5 0.05
21 27 0.27
22 41 0.41
23 10 0.10
24 1 0.01
25 2 0.02
26 5 0.05
27 10 0.10
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (24 bp):
ATTTTCTGATATCAGAAAATCAAT
Found at i:101635 original size:43 final size:44
Alignment explanation
Indices: 101582--101685 Score: 144
Period size: 43 Copynumber: 2.4 Consensus size: 44
101572 AATGGATAGT
101582 ATTTTCTGATATCAAG-AATTCGAATT-TCTGATATCAAAAAATC
1 ATTTTCTGATATCAAGAAATTCGAATTCT-TGATATCAAAAAATC
* *
101625 ATTTCCTGATAT-TAGAAATTCGAATTCTTGATATCAAAAAATC
1 ATTTTCTGATATCAAGAAATTCGAATTCTTGATATCAAAAAATC
*
101668 ATTTTCTGACATC-AGAAA
1 ATTTTCTGATATCAAGAAA
101686 ATACCTCAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
42 2 0.04
43 51 0.94
44 1 0.02
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (44 bp):
ATTTTCTGATATCAAGAAATTCGAATTCTTGATATCAAAAAATC
Found at i:101674 original size:22 final size:21
Alignment explanation
Indices: 101584--101687 Score: 86
Period size: 22 Copynumber: 4.9 Consensus size: 21
101574 TGGATAGTAT
* *
101584 TTTCTGATATCAAGAATTCGAA
1 TTTCTGATATCAAAAAATCG-A
101606 TTTCTGATATCAAAAAATC-A
1 TTTCTGATATCAAAAAATCGA
* * *
101626 TTTCCTGATATTAGAAATTCGA
1 TTT-CTGATATCAAAAAATCGA
*
101648 ATTCTTGATATCAAAAAATC-A
1 TTTC-TGATATCAAAAAATCGA
* *
101669 TTTTCTGACATCAGAAAAT
1 -TTTCTGATATCAAAAAAT
101688 ACCTCAAAAA
Statistics
Matches: 66, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
20 4 0.06
21 27 0.41
22 35 0.53
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (21 bp):
TTTCTGATATCAAAAAATCGA
Found at i:109949 original size:24 final size:23
Alignment explanation
Indices: 109912--109958 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
109902 GATCTTTTTT
* *
109912 TTTTTTTTGCTTTTGAATTATTG
1 TTTTTTGTGCTTTTGAATCATTG
109935 TTTTTTGTGCATTTTGAATCATTG
1 TTTTTTGTGC-TTTTGAATCATTG
109959 ACTTAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.15, C:0.06, G:0.15, T:0.64
Consensus pattern (23 bp):
TTTTTTGTGCTTTTGAATCATTG
Found at i:115037 original size:20 final size:20
Alignment explanation
Indices: 115012--115050 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
115002 AATTGTTTTG
* *
115012 GTATCATGTGATATGATATT
1 GTATCATATCATATGATATT
115032 GTATCATATCATATGATAT
1 GTATCATATCATATGATAT
115051 GATATTGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (20 bp):
GTATCATATCATATGATATT
Found at i:119969 original size:21 final size:21
Alignment explanation
Indices: 119943--120030 Score: 108
Period size: 21 Copynumber: 4.2 Consensus size: 21
119933 TACGCCATAG
119943 CATAGCATAGCATTGAAATCT
1 CATAGCATAGCATTGAAATCT
* *
119964 CATAGCATAGCATTAAAATAT
1 CATAGCATAGCATTGAAATCT
* *
119985 CATAGCATAGCATTGGAATCC
1 CATAGCATAGCATTGAAATCT
*
120006 CATACCATAGCA-T-ACAATCT
1 CATAGCATAGCATTGA-AATCT
120026 CATAG
1 CATAG
120031 AATTGCATCC
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
20 9 0.16
21 47 0.84
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.26
Consensus pattern (21 bp):
CATAGCATAGCATTGAAATCT
Found at i:120061 original size:10 final size:10
Alignment explanation
Indices: 120043--120076 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
120033 TTGCATCCGT
*
120043 CATATCATAC
1 CATAGCATAC
120053 CATAGCATAC
1 CATAGCATAC
*
120063 CATAGCATAG
1 CATAGCATAC
120073 CATA
1 CATA
120077 CAACATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.41, C:0.26, G:0.09, T:0.24
Consensus pattern (10 bp):
CATAGCATAC
Found at i:120066 original size:15 final size:15
Alignment explanation
Indices: 120043--120077 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
120033 TTGCATCCGT
*
120043 CATATCATACCATAG
1 CATACCATACCATAG
*
120058 CATACCATAGCATAG
1 CATACCATACCATAG
120073 CATAC
1 CATAC
120078 AACATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.40, C:0.29, G:0.09, T:0.23
Consensus pattern (15 bp):
CATACCATACCATAG
Found at i:120238 original size:5 final size:5
Alignment explanation
Indices: 120225--120258 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
120215 GTTCAAATCT
* *
120225 CATAG CATAC CATAG CATAG CATAG CATAC CATA
1 CATAG CATAG CATAG CATAG CATAG CATAG CATA
120259 TCATTAAGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.41, C:0.26, G:0.12, T:0.21
Consensus pattern (5 bp):
CATAG
Found at i:120240 original size:10 final size:10
Alignment explanation
Indices: 120225--120258 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
120215 GTTCAAATCT
120225 CATAGCATAC
1 CATAGCATAC
*
120235 CATAGCATAG
1 CATAGCATAC
120245 CATAGCATAC
1 CATAGCATAC
120255 CATA
1 CATA
120259 TCATTAAGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.41, C:0.26, G:0.12, T:0.21
Consensus pattern (10 bp):
CATAGCATAC
Found at i:120305 original size:21 final size:21
Alignment explanation
Indices: 120281--120360 Score: 99
Period size: 21 Copynumber: 3.8 Consensus size: 21
120271 TCATTCAATT
120281 TCTCATAGCATAGCATACAAA
1 TCTCATAGCATAGCATACAAA
*
120302 TCTCATAGCATAACATACAAA
1 TCTCATAGCATAGCATACAAA
* *
120323 TCTCATAGCATATCGTTA-AAA
1 TCTCATAGCATAGC-ATACAAA
* *
120344 TCGCATACCATAGCATA
1 TCTCATAGCATAGCATA
120361 GTATTAAATT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
20 2 0.04
21 47 0.92
22 2 0.04
ACGTcount: A:0.41, C:0.24, G:0.09, T:0.26
Consensus pattern (21 bp):
TCTCATAGCATAGCATACAAA
Found at i:122665 original size:8 final size:8
Alignment explanation
Indices: 122652--122677 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
122642 GAATATACAC
122652 TGCTTATA
1 TGCTTATA
122660 TGCTTATA
1 TGCTTATA
122668 TGCTTATA
1 TGCTTATA
122676 TG
1 TG
122678 TATGTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (8 bp):
TGCTTATA
Found at i:126541 original size:27 final size:27
Alignment explanation
Indices: 126503--126556 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
126493 TTCGAACTTT
126503 CGCCTTTGTCAATTTTATGTTTGTGGA
1 CGCCTTTGTCAATTTTATGTTTGTGGA
126530 CGCCTTTGTCAATTTTATGTTTGTGGA
1 CGCCTTTGTCAATTTTATGTTTGTGGA
126557 GCTCTCTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.48
Consensus pattern (27 bp):
CGCCTTTGTCAATTTTATGTTTGTGGA
Found at i:126678 original size:6 final size:6
Alignment explanation
Indices: 126667--126724 Score: 57
Period size: 6 Copynumber: 9.7 Consensus size: 6
126657 TTTTTTTCGG
* *
126667 TTTTGT TTTTGT TTTTGT TTTTGT TTTT-T TGGTTT-T TTTTGT TTGTCT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT T--TTTGT TTTTGT TTTTGT
*
126715 GTTTGT TTTT
1 TTTTGT TTTT
126725 TGCTGCTTTC
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
5 5 0.12
6 33 0.77
7 5 0.12
ACGTcount: A:0.00, C:0.02, G:0.17, T:0.81
Consensus pattern (6 bp):
TTTTGT
Found at i:126703 original size:22 final size:22
Alignment explanation
Indices: 126674--126726 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
126664 CGGTTTTGTT
* *
126674 TTTG-TTTTTGTT-TTTGTTTT
1 TTTGTTTTTTGTTGTTTGTCTG
* *
126694 TTTGGTTTTTTTTGTTTGTCTG
1 TTTGTTTTTTGTTGTTTGTCTG
126716 TTTGTTTTTTG
1 TTTGTTTTTTG
126727 CTGCTTTCTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 4 0.15
21 7 0.27
22 15 0.58
ACGTcount: A:0.00, C:0.02, G:0.19, T:0.79
Consensus pattern (22 bp):
TTTGTTTTTTGTTGTTTGTCTG
Found at i:136205 original size:11 final size:11
Alignment explanation
Indices: 136191--136215 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
136181 TTTTTGAGAT
136191 TTTTTTGTTTG
1 TTTTTTGTTTG
136202 TTTTTTGTTTG
1 TTTTTTGTTTG
136213 TTT
1 TTT
136216 GTATTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (11 bp):
TTTTTTGTTTG
Found at i:136212 original size:15 final size:15
Alignment explanation
Indices: 136190--136226 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
136180 GTTTTTGAGA
136190 TTTTTTTGTTTGT-T
1 TTTTTTTGTTTGTAT
136204 TTTTGTTTGTTTGTAT
1 TTTT-TTTGTTTGTAT
136220 TTTTTTT
1 TTTTTTT
136227 TTATTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.19
15 12 0.57
16 5 0.24
ACGTcount: A:0.03, C:0.00, G:0.14, T:0.84
Consensus pattern (15 bp):
TTTTTTTGTTTGTAT
Found at i:141828 original size:19 final size:19
Alignment explanation
Indices: 141800--141842 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
141790 AAAGCAGGTT
* *
141800 TAAATGATACATGAATAG-A
1 TAAATCATACACGAA-AGAA
141819 TAAATCATACACGAAAGAA
1 TAAATCATACACGAAAGAA
141838 TAAAT
1 TAAAT
141843 TTTAATATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.23
Consensus pattern (19 bp):
TAAATCATACACGAAAGAA
Found at i:143560 original size:2 final size:2
Alignment explanation
Indices: 143553--143597 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
143543 CACCTAATTA
143553 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
143595 AG A
1 AG A
143598 AATAATACTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:147227 original size:51 final size:51
Alignment explanation
Indices: 147172--147268 Score: 176
Period size: 51 Copynumber: 1.9 Consensus size: 51
147162 TTTTACAAGC
147172 ATTTAATGAGAAATCTCATGTTTTCAACATTTGCAAAATTGATTTACAAAT
1 ATTTAATGAGAAATCTCATGTTTTCAACATTTGCAAAATTGATTTACAAAT
* *
147223 ATTTAATGAGTAGTCTCATGTTTTCAACATTTGCAAAATTGATTTA
1 ATTTAATGAGAAATCTCATGTTTTCAACATTTGCAAAATTGATTTA
147269 AATCAAATCA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.41
Consensus pattern (51 bp):
ATTTAATGAGAAATCTCATGTTTTCAACATTTGCAAAATTGATTTACAAAT
Found at i:162584 original size:70 final size:69
Alignment explanation
Indices: 162501--162639 Score: 251
Period size: 70 Copynumber: 2.0 Consensus size: 69
162491 TCTTTGAAGT
* *
162501 AGCGATCTTGACGGTAGTTCTTATGACATCACCGCTTTAGTATATGGCGGGTCACTTTCTTGGTT
1 AGCGACCTTGACGGTAGTTCTTATGACATCACCGCTTTAGTATATAGCGGGTCACTTTCTTGGTT
162566 TTCA
66 TTCA
162570 NAGCGACCTTGACGGTAGTTCTTATGACATCACCGCTTTAGTATATAGCGGGTCACTTTCTTGGT
1 -AGCGACCTTGACGGTAGTTCTTATGACATCACCGCTTTAGTATATAGCGGGTCACTTTCTTGGT
162635 TTTCA
65 TTTCA
162640 TATCAGAGGT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.37
Consensus pattern (69 bp):
AGCGACCTTGACGGTAGTTCTTATGACATCACCGCTTTAGTATATAGCGGGTCACTTTCTTGGTT
TTCA
Found at i:180534 original size:194 final size:194
Alignment explanation
Indices: 180205--180583 Score: 749
Period size: 194 Copynumber: 2.0 Consensus size: 194
180195 CAACATGCGG
*
180205 CGAATCAAACTTCAGACAACTTTTAAAGATCTGTATTTGCTTATATACATGTACTTTGTTTCTTT
1 CGAATCAAACTTCAGACAACTTTTAAAGATCTGTATTTGCTTACATACATGTACTTTGTTTCTTT
180270 TACACAGTGTTTATACATCTAATATTGCACCATGGTCAGGTATCAATTTTTGTATTACGTCACAA
66 TACACAGTGTTTATACATCTAATATTGCACCATGGTCAGGTATCAATTTTTGTATTACGTCACAA
180335 GTATGACGCAGCTACGACGGAAGACCTAATCGTTGCTTGCAACGAGCTCGTCTCTGCAAAAAAA
131 GTATGACGCAGCTACGACGGAAGACCTAATCGTTGCTTGCAACGAGCTCGTCTCTGCAAAAAAA
180399 CGAATCAAACTTCAGACAACTTTTAAAGATCTGTATTTGCTTACATACATGTACTTTGTTTCTTT
1 CGAATCAAACTTCAGACAACTTTTAAAGATCTGTATTTGCTTACATACATGTACTTTGTTTCTTT
180464 TACACAGTGTTTATACATCTAATATTGCACCATGGTCAGGTATCAATTTTTGTATTACGTCACAA
66 TACACAGTGTTTATACATCTAATATTGCACCATGGTCAGGTATCAATTTTTGTATTACGTCACAA
180529 GTATGACGCAGCTACGACGGAAGACCTAATCGTTGCTTGCAACGAGCTCGTCTCT
131 GTATGACGCAGCTACGACGGAAGACCTAATCGTTGCTTGCAACGAGCTCGTCTCT
180584 AGTTTTTATT
Statistics
Matches: 184, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
194 184 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (194 bp):
CGAATCAAACTTCAGACAACTTTTAAAGATCTGTATTTGCTTACATACATGTACTTTGTTTCTTT
TACACAGTGTTTATACATCTAATATTGCACCATGGTCAGGTATCAATTTTTGTATTACGTCACAA
GTATGACGCAGCTACGACGGAAGACCTAATCGTTGCTTGCAACGAGCTCGTCTCTGCAAAAAAA
Found at i:181206 original size:28 final size:28
Alignment explanation
Indices: 181172--181227 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
181162 CCTGGATTTT
181172 ATACGAAGCTACCGATATGTACTTTATA
1 ATACGAAGCTACCGATATGTACTTTATA
181200 ATACGAAGCTACCGATATGTACTTTATA
1 ATACGAAGCTACCGATATGTACTTTATA
181228 CGAAACTCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (28 bp):
ATACGAAGCTACCGATATGTACTTTATA
Found at i:186236 original size:19 final size:19
Alignment explanation
Indices: 186217--186254 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
186207 CTAGATGAGG
186217 TAAATGATTTTAGAGCAGGT
1 TAAA-GATTTTAGAGCAGGT
*
186237 TAAAGTTTTTAGAGCAGG
1 TAAAGATTTTAGAGCAGG
186255 CGCTGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.34
Consensus pattern (19 bp):
TAAAGATTTTAGAGCAGGT
Found at i:186450 original size:15 final size:15
Alignment explanation
Indices: 186426--186457 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
186416 TATTGAATTG
186426 TATCAAATTATACAA
1 TATCAAATTATACAA
*
186441 TATCATATTATACAA
1 TATCAAATTATACAA
186456 TA
1 TA
186458 CAATTTTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (15 bp):
TATCAAATTATACAA
Found at i:195080 original size:59 final size:56
Alignment explanation
Indices: 195004--195170 Score: 261
Period size: 59 Copynumber: 3.0 Consensus size: 56
194994 CAAATATATA
* *
195004 TTATTAGGGTCTTCCGTTTCCGACGGAAGACCCTCTTGTTATTCTATTGTTTCTTTT
1 TTATTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTT-TTTT
195061 CCTTATTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTG---TTTT
1 --TTATTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTTTTTT
195116 TT-TTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTTTTTT
1 TTATTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTTTTTT
195171 NGCTGGCTGC
Statistics
Matches: 103, Mismatches: 2, Indels: 10
0.90 0.02 0.09
Matches are distributed among these distances:
52 46 0.45
53 2 0.02
55 8 0.08
59 47 0.46
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.48
Consensus pattern (56 bp):
TTATTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTTTTTT
Found at i:195123 original size:52 final size:52
Alignment explanation
Indices: 195007--195170 Score: 247
Period size: 52 Copynumber: 3.0 Consensus size: 52
194997 ATATATATTA
* *
195007 TTAGGGTCTTCCGTTTCCGACGGAAGACCCTCTTGTTATTCTATTGTTTCTTTTCCTT
1 TTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTG----TTTT--TT
195065 ATTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTTTTT
1 -TTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTTTTT
195118 TTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTTTTT
1 TTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTTTTT
195170 T
1 T
195171 NGCTGGCTGC
Statistics
Matches: 103, Mismatches: 2, Indels: 7
0.92 0.02 0.06
Matches are distributed among these distances:
52 53 0.51
53 2 0.02
55 4 0.04
59 44 0.43
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.48
Consensus pattern (52 bp):
TTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTTTTT
Found at i:197944 original size:2 final size:2
Alignment explanation
Indices: 197937--198001 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
197927 GTGCCTCAGA
*
197937 TC TC TC TC TG 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
197979 TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC T
198002 TTTAATCTTG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.00, C:0.48, G:0.02, T:0.51
Consensus pattern (2 bp):
TC
Found at i:201596 original size:32 final size:31
Alignment explanation
Indices: 201560--201636 Score: 91
Period size: 32 Copynumber: 2.5 Consensus size: 31
201550 CAAAAAAAAC
* * *
201560 TTGTTAAGTCGTACTTGAAATTAGTAAGGTTT
1 TTGTTAAGTCGTACTTAAAATCA-TAAGGATT
* **
201592 TTGTTAAGTTGTACTTAAAATCATTCGGATT
1 TTGTTAAGTCGTACTTAAAATCATAAGGATT
201623 TTGTTAAGTCGTAC
1 TTGTTAAGTCGTAC
201637 CAGGAATAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 18 0.47
32 20 0.53
ACGTcount: A:0.27, C:0.09, G:0.19, T:0.44
Consensus pattern (31 bp):
TTGTTAAGTCGTACTTAAAATCATAAGGATT
Found at i:202460 original size:31 final size:30
Alignment explanation
Indices: 202401--202465 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
202391 TCGGAAAGGT
* *
202401 TTTTGTTAAGTCGTACGTAAAATCATTCGGA
1 TTTTGTTAAGTCGTACCTAAAATAATTC-GA
** *
202432 TTTTGTTAAGTCGTACCTGGAGTAATTCGA
1 TTTTGTTAAGTCGTACCTAAAATAATTCGA
202462 TTTT
1 TTTT
202466 TTTTCATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 6 0.21
31 23 0.79
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.43
Consensus pattern (30 bp):
TTTTGTTAAGTCGTACCTAAAATAATTCGA
Found at i:203263 original size:31 final size:31
Alignment explanation
Indices: 203201--203269 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
203191 AAATCGGAAA
* *
203201 GGTTTTTGTTAAGTCGTACGTAAAATTATTC
1 GGTTTTTGTTAAGTCGTACGCAAAATAATTC
*
203232 GGTTTTTGTTAAGTCGTAC-CAGGAATAATTC
1 GGTTTTTGTTAAGTCGTACGCA-AAATAATTC
*
203263 GATTTTT
1 GGTTTTT
203270 TCATGTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 1 0.03
31 32 0.97
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.45
Consensus pattern (31 bp):
GGTTTTTGTTAAGTCGTACGCAAAATAATTC
Found at i:204036 original size:31 final size:31
Alignment explanation
Indices: 203934--204044 Score: 114
Period size: 32 Copynumber: 3.5 Consensus size: 31
203924 CCAAAAATTA
* *
203934 TTGTTAAGTCGTACTTGAACTCATTTGGATTTTT
1 TTGTTAAGTCGTACTTGAAATCATTAGGA---TT
* ** *
203968 TTGTTAAGTCGTTCTTGAAATCAGGAAGGTTT
1 TTGTTAAGTCGTACTTGAAATCA-TTAGGATT
* *
204000 TTGTTAAGTCGTACTTAAAATCATTCGGATT
1 TTGTTAAGTCGTACTTGAAATCATTAGGATT
204031 TTGTTAAGTCGTAC
1 TTGTTAAGTCGTAC
204045 CAGGAATAAT
Statistics
Matches: 64, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
31 18 0.28
32 23 0.36
34 21 0.33
35 2 0.03
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.44
Consensus pattern (31 bp):
TTGTTAAGTCGTACTTGAAATCATTAGGATT
Found at i:204057 original size:31 final size:31
Alignment explanation
Indices: 203998--204063 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
203988 TCAGGAAGGT
* * *
203998 TTTTGTTAAGTCGTACTTAAAATCATTCGGA
1 TTTTGTTAAGTCGTACTCAAAATAATTCGAA
*
204029 TTTTGTTAAGTCGTAC-CAGGAATAATTCGAA
1 TTTTGTTAAGTCGTACTCA-AAATAATTCGAA
204060 TTTT
1 TTTT
204064 CATTTTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 1 0.03
31 29 0.97
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (31 bp):
TTTTGTTAAGTCGTACTCAAAATAATTCGAA
Found at i:205382 original size:437 final size:433
Alignment explanation
Indices: 204627--205578 Score: 1194
Period size: 437 Copynumber: 2.2 Consensus size: 433
204617 TTAACTAGGA
* * * *
204627 CTTTTGTTTGATTTCAAGAAAAAGGGGCTGGCCCGTCAAATTAGGGGCCAAAAGGGCTCAAAATT
1 CTTTTATTTGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGCCAAAAGGGCTC-AAAGT
* ** * *
204692 ATTTTTGCAATAACTCTTTACTGAAAAATAATTTGTAATCGATCATAGAACCAAAAGTGTTCATT
65 CTTTTTAAAATAACTCTTTACTGAAAAATAATTTATAATCAATCATAGAACCAAAAGTGTTCATT
* *
204757 GTACATCTGTTTATCTACAAAGAACCATACCTAAGTCATATGTTACGTAATTATGGGTTTCAAGG
130 GTACAGCTGTTTATCTACAAAGAACCATACCTAAGTCATATGTTACGTAATTAGGGGTTTCAAGG
* ** * * * *
204822 GGCCAGAAGTCCAAAATTTTGATCTTTAATATCTAGAAAAGGAGAAATATTTTGATAAGCATTGT
195 GACCAGAAGTAAAAAACTTTGATCATTAATATCTAGAAAAAGAGAAATATTTTGAAAAGCATTGT
* * ** * *
204887 AGAACTAAAAATGCTTAGAATAATGTTTTTAACAATATGCTACCTAAATAATTTTTGTTGGTGGC
260 AGAACTAAAAATGCTCAAAATAATGTTTTTAACAATATGAAACCTAAAAAAATTTTGTTGGTGGC
* * * * *
204952 CCCAGTAAGGATTTTAAGGGTCGGCCCCTAAAACACATTTGTTCAGATATCTTTAGAACGGTCAA
325 CCCAGTAAAGAGTTAAAGGGTCGGCCCCTAAAACACAGTTGTTCAGATATCTCTAGAACGGT-AA
* *
205017 CAATTTCCG-AACACTTGTTGAACAAAATGTGTTTATATTTACAAGAC
389 CAA-TT-CGAAACACTTGTTGAAAAAAATATGTTTAT-TTTACAAGAC
* * *
205064 CTTTTATTTGATATCTAGAAATAA-GGGTTGGCCCCTCAAATTAGGGGCCAAGAGGGCTCTAAAG
1 CTTTTATTTGATATCAAGAAA-AAGGGGCTGGCCCCTCAAATTAGGGGCCAAAAGGGCTC-AAAG
* * * *
205128 TCTTTTTAAAATAACTCTTTACTGAAAAATAATTTATTATCAATTATAGAAGCAACAA-TGTTTA
64 TCTTTTTAAAATAACTCTTTACTGAAAAATAATTTATAATCAATCATAGAACCAA-AAGTGTTCA
* * *
205192 TTGTACAGCTGTTTATCTATACAGTACCATACCTAAGTCATATGTTACGTAATTAGGGGTTTCAA
128 TTGTACAGCTGTTTATCTACAAAGAACCATACCTAAGTCATATGTTACGTAATTAGGGGTTTCAA
*
205257 GGGACCAGAAGTAAAAAACTTTGATCATTAATATCTAGAAAAAGAGAAATATTTTGAAAAGTATT
193 GGGACCAGAAGTAAAAAACTTTGATCATTAATATCTAGAAAAAGAGAAATATTTTGAAAAGCATT
* ** *
205322 GTAGAAC-AAAAGTTGCTCAAAATAATGTTATTT-ATGATATGAAATCTAAAAAAATTTTGTTGG
258 GTAGAACTAAAA-ATGCTCAAAATAATGTT-TTTAACAATATGAAACCTAAAAAAATTTTGTTGG
* * *
205385 TGGCCCCAGTAAAGAGTTAAAGGGTGGGCCCCTAAAACAGAGTTGTTCGGATATCTCTAGAACGG
321 TGGCCCCAGTAAAGAGTTAAAGGGTCGGCCCCTAAAACACAGTTGTTCAGATATCTCTAGAACGG
* * * * * *
205450 TTAGAATTCGTAAATACTTGTTGAAAAAAATATGTTTGTTTTTCGAGAC
386 TAACAATTCG-AAACACTTGTTGAAAAAAATATGTTTATTTTACAAGAC
* ** * * *
205499 CTTTCATTTGATATCAAGAAAAAGGGGCCAGCCCCTCAAATAAAGAGCCAAAAGGGCTACAAAGT
1 CTTTTATTTGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGCCAAAAGGGCT-CAAAGT
* *
205564 CTTTTCATAATAACT
65 CTTTTTAAAATAACT
205579 TATTTTTAAG
Statistics
Matches: 440, Mismatches: 67, Indels: 18
0.84 0.13 0.03
Matches are distributed among these distances:
434 4 0.01
435 74 0.17
436 31 0.07
437 324 0.74
438 7 0.02
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.32
Consensus pattern (433 bp):
CTTTTATTTGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGCCAAAAGGGCTCAAAGTC
TTTTTAAAATAACTCTTTACTGAAAAATAATTTATAATCAATCATAGAACCAAAAGTGTTCATTG
TACAGCTGTTTATCTACAAAGAACCATACCTAAGTCATATGTTACGTAATTAGGGGTTTCAAGGG
ACCAGAAGTAAAAAACTTTGATCATTAATATCTAGAAAAAGAGAAATATTTTGAAAAGCATTGTA
GAACTAAAAATGCTCAAAATAATGTTTTTAACAATATGAAACCTAAAAAAATTTTGTTGGTGGCC
CCAGTAAAGAGTTAAAGGGTCGGCCCCTAAAACACAGTTGTTCAGATATCTCTAGAACGGTAACA
ATTCGAAACACTTGTTGAAAAAAATATGTTTATTTTACAAGAC
Found at i:235495 original size:4 final size:4
Alignment explanation
Indices: 235488--235531 Score: 61
Period size: 4 Copynumber: 11.0 Consensus size: 4
235478 GGGACAGACA
* * *
235488 GACG GACG GACG GACG GATG GACG GACA GACG GACT GACG GACG
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG
235532 CAGAGGAAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.27, C:0.23, G:0.45, T:0.05
Consensus pattern (4 bp):
GACG
Found at i:266084 original size:54 final size:53
Alignment explanation
Indices: 266014--266119 Score: 140
Period size: 54 Copynumber: 2.0 Consensus size: 53
266004 AAATAATAAT
* * *
266014 AAGAAACAGTAGAATAACAGAAGGGTTTTCCGTTGAAAAACGGAAAACCCTAAA
1 AAGAAACAGTACAATAACAGAAGGGTCTTCCGCTG-AAAACGGAAAACCCTAAA
* * * *
266068 AAGAAACATTACAATAATAGAAGGGTCTTCCGCTGAAGACGGAAGACCCTAA
1 AAGAAACAGTACAATAACAGAAGGGTCTTCCGCTGAAAACGGAAAACCCTAA
266120 TTACTTGCAA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
53 15 0.33
54 30 0.67
ACGTcount: A:0.45, C:0.17, G:0.21, T:0.17
Consensus pattern (53 bp):
AAGAAACAGTACAATAACAGAAGGGTCTTCCGCTGAAAACGGAAAACCCTAAA
Found at i:268705 original size:13 final size:13
Alignment explanation
Indices: 268687--268711 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
268677 TTCTACGGGC
268687 TTAGTGGCTGCTG
1 TTAGTGGCTGCTG
268700 TTAGTGGCTGCT
1 TTAGTGGCTGCT
268712 AGCTTCAGCC
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:0.08, C:0.16, G:0.36, T:0.40
Consensus pattern (13 bp):
TTAGTGGCTGCTG
Found at i:268770 original size:2 final size:2
Alignment explanation
Indices: 268763--268802 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
268753 GATGAATGAA
268763 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
268803 ATTGAATACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:275809 original size:146 final size:146
Alignment explanation
Indices: 275171--276008 Score: 1189
Period size: 146 Copynumber: 5.7 Consensus size: 146
275161 CTTCCTCAAT
* * * * * * * * *
275171 TGACCTTTGGTCAAGGTCATGACATACTCTCAGGTTATGAGCATTC-TAGATGTGAATTAAGAAC
1 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTG-TGTGAAGTAAGAAC
* * * * * * ** *
275235 TTCCAATATTTGTCCATTAGAAAGATATGGACTGAACACGAGTTTTATAC-TTTTCTGCAAGTGA
65 TTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTGCACTTTTTCTGCCAGTGA
*
275299 CCTTGACCTTGCCCAAA
130 CCTTGACCTTGCCCGAA
* * * * *
275316 TGACCTTGGGTCAAGGTCATGACAAACCCTTAGCTTATAAGCAATCTTTGTGTGAACTGAGAACT
1 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACT
* *
275381 TCCAATGTTTCTCCATAAGAAAGATATGGACCGGACAAGAATTTTGCACTTTTTTCTGCCATTGA
66 TCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTGCAC-TTTTTCTGCCAGTGA
* *
275446 CCTTGACCTTGTCCAAA
130 CCTTGACCTTGCCCGAA
275463 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACT
1 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACT
* * *
275528 TCCAATGTTTCTCCATTAA-AAAGATATGGACCAGACACGAATTTTGCAATTTTTTCTGTCAGTG
66 TCCAATGTTTCTCCA-TAAGAAAGATATGGACCGGACACGAATTTTGC-ACTTTTTCTGCCAGTG
275592 ACCTTGACCTTGCCCGAA
129 ACCTTGACCTTGCCCGAA
* *
275610 TGACCTTGGGTTAAGGTCATGACACACCCTTAGGTCATTAGCAATCTTTGTGTGAAGTTAA-AAC
1 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAG-TAAGAAC
***
275674 TTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTGCACTTTTTCTGTTGGTGA
65 TTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTGCACTTTTTCTGCCAGTGA
275739 CCTTGACCTTGCCCGAA
130 CCTTGACCTTGCCCGAA
* ** * * *
275756 TGACCATGCTTTAAGGTCATGACACACCCTCAGGTCATAAGCATTCTTTGTGTGAAGTAAGAACT
1 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACT
*
275821 TCTAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTGCACTTTTTCTGCCAGTGAC
66 TCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTGCACTTTTTCTGCCAGTGAC
275886 CTTGACCTTGCCCGAA
131 CTTGACCTTGCCCGAA
* *
275902 TGACCTTGGTTCAAGGTCATGACACATCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACT
1 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACT
*
275967 TCCAATGTTTCTTCATAAGAAAGATATGGACCGGACACGAAT
66 TCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAAT
276009 CGAACAGACA
Statistics
Matches: 627, Mismatches: 58, Indels: 15
0.90 0.08 0.02
Matches are distributed among these distances:
145 95 0.15
146 267 0.43
147 258 0.41
148 7 0.01
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (146 bp):
TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACT
TCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTGCACTTTTTCTGCCAGTGAC
CTTGACCTTGCCCGAA
Found at i:276034 original size:4 final size:4
Alignment explanation
Indices: 276019--276081 Score: 108
Period size: 4 Copynumber: 15.8 Consensus size: 4
276009 CGAACAGACA
* *
276019 GACG GACA GACG GACG GACG GACG GACG GACG GACG GACG GACG GACA
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG
276067 GACG GACG GACG GAC
1 GACG GACG GACG GAC
276082 AAGGTGATTC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.29, C:0.25, G:0.46, T:0.00
Consensus pattern (4 bp):
GACG
Found at i:283879 original size:24 final size:24
Alignment explanation
Indices: 283847--283896 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
283837 GCGTAACGCC
283847 CATCCCAATCAATACTGGGATCAA
1 CATCCCAATCAATACTGGGATCAA
*
283871 CATCCCAATCTATACTGGGATCAA
1 CATCCCAATCAATACTGGGATCAA
283895 CA
1 CA
283897 ACCCTCACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.30, G:0.12, T:0.22
Consensus pattern (24 bp):
CATCCCAATCAATACTGGGATCAA
Found at i:284333 original size:51 final size:51
Alignment explanation
Indices: 284290--284403 Score: 158
Period size: 51 Copynumber: 2.2 Consensus size: 51
284280 TTCATCTACT
* *
284290 TCGGTCTCCTCCCGTCTGAAGCTCTCTCGAGGGGTAGTCGCTTCCTCGTCC
1 TCGGACTCCTCCCGTCTGAAGCTCTCTCGAGGGGTAGTCGCTTCATCGTCC
* * * *
284341 TCGGACTCCTCCTGTCTGAAGCTCTCTGGAGGGGTAG-CGGCGTCCTCGTCC
1 TCGGACTCCTCCCGTCTGAAGCTCTCTCGAGGGGTAGTC-GCTTCATCGTCC
284392 TCGGACTCCTCC
1 TCGGACTCCTCC
284404 AGGCAGATGC
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
50 1 0.02
51 57 0.98
ACGTcount: A:0.09, C:0.37, G:0.27, T:0.27
Consensus pattern (51 bp):
TCGGACTCCTCCCGTCTGAAGCTCTCTCGAGGGGTAGTCGCTTCATCGTCC
Found at i:284895 original size:5 final size:5
Alignment explanation
Indices: 284885--284925 Score: 82
Period size: 5 Copynumber: 8.2 Consensus size: 5
284875 GAATGCACGT
284885 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC A
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC A
284926 ATGTCCCTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATC
Found at i:290259 original size:1 final size:1
Alignment explanation
Indices: 290253--290307 Score: 56
Period size: 1 Copynumber: 55.0 Consensus size: 1
290243 ACCTTCACAT
* * * * * *
290253 AAAAAAAAAACAAAAAAAAAAAACAAAACAAAAACAAACAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
290308 CCCGACATTC
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:290269 original size:11 final size:11
Alignment explanation
Indices: 290253--290307 Score: 74
Period size: 11 Copynumber: 4.8 Consensus size: 11
290243 ACCTTCACAT
290253 AAAAAAAAAAC
1 AAAAAAAAAAC
290264 AAAAAAAAAAAAC
1 --AAAAAAAAAAC
*
290277 AAAACAAAAAC
1 AAAAAAAAAAC
*
290288 AAACAAAAAAC
1 AAAAAAAAAAC
290299 AAAAAAAAA
1 AAAAAAAAA
290308 CCCGACATTC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
11 27 0.71
13 11 0.29
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:291424 original size:2 final size:2
Alignment explanation
Indices: 291417--291475 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
291407 GGAATCTGAA
291417 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
291459 TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC T
291476 TCCAGAAGCA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:299299 original size:9 final size:9
Alignment explanation
Indices: 299285--299322 Score: 76
Period size: 9 Copynumber: 4.2 Consensus size: 9
299275 AATATTATTG
299285 CAAATATGT
1 CAAATATGT
299294 CAAATATGT
1 CAAATATGT
299303 CAAATATGT
1 CAAATATGT
299312 CAAATATGT
1 CAAATATGT
299321 CA
1 CA
299323 GTTTGTACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.32
Consensus pattern (9 bp):
CAAATATGT
Found at i:300019 original size:10 final size:10
Alignment explanation
Indices: 300002--300048 Score: 69
Period size: 10 Copynumber: 4.8 Consensus size: 10
299992 TCCCACTGGG
300002 TTTTTTTGTT
1 TTTTTTTGTT
*
300012 TGTTTTTG-T
1 TTTTTTTGTT
*
300021 TTTGTTTGTT
1 TTTTTTTGTT
300031 TTTTTTTGTT
1 TTTTTTTGTT
300041 TTTTTTTG
1 TTTTTTTG
300049 CAATTTTTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
9 7 0.22
10 25 0.78
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:300025 original size:15 final size:15
Alignment explanation
Indices: 300005--300048 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
299995 CACTGGGTTT
300005 TTTTGTTTGTTTTTG
1 TTTTGTTTGTTTTTG
300020 TTTTGTTTGTTTTT-
1 TTTTGTTTGTTTTTG
*
300034 TTTTGTTTTTTTTTG
1 TTTTGTTTGTTTTTG
300049 CAATTTTTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 13 0.48
15 14 0.52
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (15 bp):
TTTTGTTTGTTTTTG
Found at i:300030 original size:19 final size:18
Alignment explanation
Indices: 300001--300045 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 18
299991 ATCCCACTGG
300001 GTTTTTTTGTTTGTTTTT
1 GTTTTTTTGTTTGTTTTT
*
300019 GTTTTGTTTGTTTTTTTTT
1 GTTTT-TTTGTTTGTTTTT
300038 GTTTTTTT
1 GTTTTTTT
300046 TTGCAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 8 0.32
19 17 0.68
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (18 bp):
GTTTTTTTGTTTGTTTTT
Found at i:301943 original size:330 final size:329
Alignment explanation
Indices: 301342--302000 Score: 1309
Period size: 330 Copynumber: 2.0 Consensus size: 329
301332 TTTGATTATC
301342 TTTTATTTTCTTTGATGTAATTGTGGATATCACTTGAGGATGCAATAGTTATAAGCAATGCTTTT
1 TTTTATTTTCTTTGATGTAATTGTGGATATCACTTGAGGATGCAATAGTTATAAGCAATGCTTTT
301407 TTTCTTTTCTTTGTCCTGTTATAAAATCTGCTTATGATGTGTTTCTATTTATTCCAGTGTATTTG
66 TTTCTTTTCTTTGTCCTGTTATAAAATCTGCTTATGATGTGTTTCTATTTATTCCAGTGTATTTG
301472 TGAAAAGTGACACAGACGACAGAAAGGGGTTCTCTAGCGATCATTTCTAGCCAAGGATTATGCTC
131 TGAAAAGTGACACAGACGACAGAAAGGGGTTCTCTAGCGATCATTTCTAGCCAAGGATTATGCTC
301537 GTGAATTGTAGAAACGTGAACTGTTGATCATAAACTCTATAACTGTGTCCTTAACCATATATTTA
196 GTGAATTGTAGAAACGTGAACTGTTGATCATAAACTCTATAACTGTGTCCTTAACCATATATTTA
301602 TTTTATTTGTATATCAATGCTCAGTATTCATGTACATAAAAAGAATTATAATAAATAGGTGATCT
261 TTTTATTTGTATATCAATGCTCAGTATTCATGTACATAAAAAGAATTATAATAAATAGGTGATCT
301667 ACCA
326 ACCA
301671 NTTTTATTTTCTTTGATGTAATTGTGGATATCACTTGAGGATGCAATAGTTATAAGCAATGCTTT
1 -TTTTATTTTCTTTGATGTAATTGTGGATATCACTTGAGGATGCAATAGTTATAAGCAATGCTTT
301736 TTTTCTTTTCTTTGTCCTGTTATAAAATCTGCTTATGATGTGTTTCTATTTATTCCAGTGTATTT
65 TTTTCTTTTCTTTGTCCTGTTATAAAATCTGCTTATGATGTGTTTCTATTTATTCCAGTGTATTT
301801 GTGAAAAGTGACACAGACGACAGAAAGGGGTTCTCTAGCGATCATTTCTAGCCAAGGATTATGCT
130 GTGAAAAGTGACACAGACGACAGAAAGGGGTTCTCTAGCGATCATTTCTAGCCAAGGATTATGCT
301866 CGTGAATTGTAGAAACGTGAACTGTTGATCATAAACTCTATAACTGTGTCCTTAACCATATATTT
195 CGTGAATTGTAGAAACGTGAACTGTTGATCATAAACTCTATAACTGTGTCCTTAACCATATATTT
301931 ATTTTATTTGTATATCAATGCTCAGTATTCATGTACATAAAAAGAATTATAATAAATAGGTGATC
260 ATTTTATTTGTATATCAATGCTCAGTATTCATGTACATAAAAAGAATTATAATAAATAGGTGATC
301996 TACCA
325 TACCA
302001 GTATTAGTTA
Statistics
Matches: 329, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
330 329 1.00
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (329 bp):
TTTTATTTTCTTTGATGTAATTGTGGATATCACTTGAGGATGCAATAGTTATAAGCAATGCTTTT
TTTCTTTTCTTTGTCCTGTTATAAAATCTGCTTATGATGTGTTTCTATTTATTCCAGTGTATTTG
TGAAAAGTGACACAGACGACAGAAAGGGGTTCTCTAGCGATCATTTCTAGCCAAGGATTATGCTC
GTGAATTGTAGAAACGTGAACTGTTGATCATAAACTCTATAACTGTGTCCTTAACCATATATTTA
TTTTATTTGTATATCAATGCTCAGTATTCATGTACATAAAAAGAATTATAATAAATAGGTGATCT
ACCA
Found at i:309458 original size:27 final size:26
Alignment explanation
Indices: 309429--309483 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 26
309419 GGGGGGGTGT
* *
309429 TTGTTTTTGTTTTTTTGTTTTTTGTTT
1 TTGTTTTTGTTTTTGT-TTTTTTGGTT
309456 TTGTTTTTGTTTTTGTTTTTTTGGTT
1 TTGTTTTTGTTTTTGTTTTTTTGGTT
309482 TT
1 TT
309484 CAGTTTTGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (26 bp):
TTGTTTTTGTTTTTGTTTTTTTGGTT
Found at i:309483 original size:6 final size:6
Alignment explanation
Indices: 309428--309475 Score: 69
Period size: 6 Copynumber: 7.5 Consensus size: 6
309418 GGGGGGGGTG
309428 TTTGTT TTTGTTTT TTTGTTT TTTGTT TTTGTT TTTGTT TTTGTT TTT
1 TTTGTT TTTG--TT TTTG-TT TTTGTT TTTGTT TTTGTT TTTGTT TTT
309476 TTGGTTTTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
6 27 0.68
7 7 0.17
8 6 0.15
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTGTT
Found at i:309490 original size:27 final size:27
Alignment explanation
Indices: 309431--309495 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 27
309421 GGGGGTGTTT
* *
309431 GTTTTTGTTTTTTTGTTTTTTGTTTTT
1 GTTTTTGTTTTTTTGTTTTTGGTTTTA
309458 GTTTTTGTTTTTGTT-TTTTTGGTTTTCA
1 GTTTTTGTTTTT-TTGTTTTTGGTTTT-A
309486 GTTTTGTGTT
1 GTTTT-TGTT
309496 GCATGTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 22 0.67
28 7 0.21
29 4 0.12
ACGTcount: A:0.02, C:0.02, G:0.18, T:0.78
Consensus pattern (27 bp):
GTTTTTGTTTTTTTGTTTTTGGTTTTA
Found at i:309491 original size:33 final size:33
Alignment explanation
Indices: 309428--309495 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
309418 GGGGGGGGTG
**
309428 TTTGTTTTTGTTTTTTTGTTTTTTGTTTTTGTT
1 TTTGTTTTTGTTTTTTTGTTTTCAGTTTTTGTT
309461 TTTGTTTTTGTTTTTTTGGTTTTCAGTTTTGTGTT
1 TTTGTTTTTGTTTTTTT-GTTTTCAGTTTT-TGTT
309496 GCATGTTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 17 0.55
34 10 0.32
35 4 0.13
ACGTcount: A:0.01, C:0.01, G:0.18, T:0.79
Consensus pattern (33 bp):
TTTGTTTTTGTTTTTTTGTTTTCAGTTTTTGTT
Found at i:310632 original size:21 final size:21
Alignment explanation
Indices: 310526--310621 Score: 183
Period size: 21 Copynumber: 4.6 Consensus size: 21
310516 TCAATCACCC
310526 CAAGGCTATGCCGCACCCCAA
1 CAAGGCTATGCCGCACCCCAA
*
310547 CAAGGCTATGCTGCACCCCAA
1 CAAGGCTATGCCGCACCCCAA
310568 CAAGGCTATGCCGCACCCCAA
1 CAAGGCTATGCCGCACCCCAA
310589 CAAGGCTATGCCGCACCCCAA
1 CAAGGCTATGCCGCACCCCAA
310610 CAAGGCTATGCC
1 CAAGGCTATGCC
310622 CCATCTCAAC
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 73 1.00
ACGTcount: A:0.28, C:0.41, G:0.20, T:0.11
Consensus pattern (21 bp):
CAAGGCTATGCCGCACCCCAA
Found at i:311924 original size:21 final size:21
Alignment explanation
Indices: 311900--311939 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
311890 CATCATTACG
311900 AAATTTGTTATCATT-TTTATC
1 AAATTT-TTATCATTCTTTATC
*
311921 AAATTTTTTTCATTCTTTA
1 AAATTTTTATCATTCTTTA
311940 ATGTCGTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.10, G:0.03, T:0.60
Consensus pattern (21 bp):
AAATTTTTATCATTCTTTATC
Found at i:315127 original size:21 final size:21
Alignment explanation
Indices: 315103--315212 Score: 143
Period size: 21 Copynumber: 5.2 Consensus size: 21
315093 AGGGTACCCC
*
315103 CCGCCCCAACAGGGCTATGGT
1 CCGCCCCAACAGGGGTATGGT
*
315124 CCGCCCCAACAGGGTTATGGT
1 CCGCCCCAACAGGGGTATGGT
*
315145 CCGCCCCAACAGGGTTATGGT
1 CCGCCCCAACAGGGGTATGGT
*
315166 CCGCCACC-ACAGGGGTACGGT
1 CCGCC-CCAACAGGGGTATGGT
*
315187 CCGCCACC-ACAGGGGTACGGT
1 CCGCC-CCAACAGGGGTATGGT
315208 CCGCC
1 CCGCC
315213 GCCACAAGGC
Statistics
Matches: 85, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
21 83 0.98
22 2 0.02
ACGTcount: A:0.18, C:0.38, G:0.30, T:0.14
Consensus pattern (21 bp):
CCGCCCCAACAGGGGTATGGT
Found at i:320928 original size:11 final size:11
Alignment explanation
Indices: 320909--320940 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
320899 TTTTAAAAAA
320909 TGGCTTAAAGG
1 TGGCTTAAAGG
*
320920 TGTCTTAAAGG
1 TGGCTTAAAGG
320931 TGGCTTAAAG
1 TGGCTTAAAG
320941 AAGTTTGGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.28, C:0.09, G:0.31, T:0.31
Consensus pattern (11 bp):
TGGCTTAAAGG
Found at i:320988 original size:11 final size:11
Alignment explanation
Indices: 320972--321000 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
320962 ATAAGTCCTC
320972 CTTAAAGGTGG
1 CTTAAAGGTGG
320983 CTTAAAGGTGG
1 CTTAAAGGTGG
320994 CTTAAAG
1 CTTAAAG
321001 ACAGTCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.28
Consensus pattern (11 bp):
CTTAAAGGTGG
Found at i:321022 original size:11 final size:11
Alignment explanation
Indices: 321006--321081 Score: 109
Period size: 11 Copynumber: 7.0 Consensus size: 11
320996 TAAAGACAGT
*
321006 CTTTAAGCCGC
1 CTTTAAGCCAC
*
321017 CTTTAAG-GAC
1 CTTTAAGCCAC
*
321027 CTTTAAGCCAT
1 CTTTAAGCCAC
*
321038 CTTTAAGTCAC
1 CTTTAAGCCAC
321049 CTTTAAGCCAC
1 CTTTAAGCCAC
321060 CTTTAAGCCAC
1 CTTTAAGCCAC
321071 CTTTAAGCCAC
1 CTTTAAGCCAC
321082 ATTGAAACTT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
10 8 0.14
11 49 0.86
ACGTcount: A:0.26, C:0.32, G:0.12, T:0.30
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:321147 original size:10 final size:10
Alignment explanation
Indices: 321123--321161 Score: 60
Period size: 11 Copynumber: 3.7 Consensus size: 10
321113 TAAAGACCGT
321123 CTTTAAGCTAC
1 CTTTAAGC-AC
321134 CTTTAAGCAC
1 CTTTAAGCAC
321144 CTTTAAGCCAC
1 CTTTAAG-CAC
321155 CTTTAAG
1 CTTTAAG
321162 GAGAACTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.33
Consensus pattern (10 bp):
CTTTAAGCAC
Found at i:326972 original size:19 final size:19
Alignment explanation
Indices: 326950--326986 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
326940 CTTTTTTTTT
326950 TCTTTTTGA-ATTTTATTAG
1 TCTTTTT-ATATTTTATTAG
326969 TCTTTTTATATTTTATTA
1 TCTTTTTATATTTTATTA
326987 TTTTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (19 bp):
TCTTTTTATATTTTATTAG
Found at i:329223 original size:2 final size:2
Alignment explanation
Indices: 329216--329254 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
329206 CTGATTTCAA
329216 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
329255 GCAGTTCTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:333068 original size:1 final size:1
Alignment explanation
Indices: 333064--333093 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
333054 CCCCCCCCCC
*
333064 AAAAAAAAAAAAAATAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
333094 CAAACCAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.97, C:0.00, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:333084 original size:15 final size:15
Alignment explanation
Indices: 333064--333092 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
333054 CCCCCCCCCC
333064 AAAAAAAAAAAAAAT
1 AAAAAAAAAAAAAAT
333079 AAAAAAAAAAAAAA
1 AAAAAAAAAAAAAA
333093 ACAAACCAAA
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:0.97, C:0.00, G:0.00, T:0.03
Consensus pattern (15 bp):
AAAAAAAAAAAAAAT
Found at i:343394 original size:1 final size:1
Alignment explanation
Indices: 343390--343423 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
343380 TTGGTTGTTG
343390 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
343424 GTAGTTGGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.