Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001949.1 Hibiscus syriacus cultivar Beakdansim tig00003943_pilon, whole genome shotgun sequence
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: 104373
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:636 original size:20 final size:20
Alignment explanation
Indices: 611--665 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
601 AAAACCCGAA
611 GAGTGTATCGATACACTCCT
1 GAGTGTATCGATACACTCCT
631 GAGTGTATC-AGTACACTCCT
1 GAGTGTATCGA-TACACTCCT
* *
651 AAATGTATCGATACA
1 GAGTGTATCGATACA
666 AATTCAAGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (20 bp):
GAGTGTATCGATACACTCCT
Found at i:6421 original size:22 final size:22
Alignment explanation
Indices: 6393--6451 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
6383 GGGAGTGTGA
6393 GTGTATCGGTACACTCTCAAGG
1 GTGTATCGGTACACTCTCAAGG
*
6415 GTGTATCGATACACTCTCAAGG
1 GTGTATCGGTACACTCTCAAGG
*
6437 GTGCATCGGTACACT
1 GTGTATCGGTACACT
6452 GTGTGTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (22 bp):
GTGTATCGGTACACTCTCAAGG
Found at i:7563 original size:2 final size:2
Alignment explanation
Indices: 7556--7586 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
7546 TGTCAAAAAG
7556 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7587 CTTTTATAGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10408 original size:81 final size:81
Alignment explanation
Indices: 10302--10468 Score: 244
Period size: 81 Copynumber: 2.1 Consensus size: 81
10292 TGTTTAAAAA
* * * * *
10302 TAAAAGATTAATGGGCTAGTTGTGCATTTGGCATAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATCATGCAAGTTAGATGAAAG
*
10367 GTTAAATACCTTTGAG
66 GCTAAATACCTTTGAG
* *
10383 TAAAAGATTAATTGCCTAGCTGTGCATTTGGTAGAAAGGTGTCAATCATGCAAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATCATGCAAGTTAGATGAAAG
* *
10448 GCTAAATGCCTTTGGG
66 GCTAAATACCTTTGAG
10464 TAAAA
1 TAAAA
10469 ACTAAAGGAA
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 76 1.00
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.31
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATCATGCAAGTTAGATGAAAG
GCTAAATACCTTTGAG
Found at i:23174 original size:19 final size:18
Alignment explanation
Indices: 23150--23216 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 18
23140 CCGGTTTTCA
23150 ACCGGTTCTG-ACCTGTTTG
1 ACCGG-TCTGAACC-GTTTG
23169 ACCGGT-TCGAACCGGTTTG
1 ACCGGTCT-GAACC-GTTTG
23188 ACCGGTCTGAACCGATTTG
1 ACCGGTCTGAACCG-TTTG
*
23207 ATCGGTCTGA
1 ACCGGTCTGA
23217 CCCGACCCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.02
18 3 0.07
19 37 0.88
20 1 0.02
ACGTcount: A:0.16, C:0.25, G:0.28, T:0.30
Consensus pattern (18 bp):
ACCGGTCTGAACCGTTTG
Found at i:23221 original size:19 final size:19
Alignment explanation
Indices: 23165--23221 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 19
23155 TTCTGACCTG
*
23165 TTTGACCGGT-TCGAACCGG
1 TTTGACCGGTCT-GAACCGA
23184 TTTGACCGGTCTGAACCGA
1 TTTGACCGGTCTGAACCGA
* *
23203 TTTGATCGGTCTGACCCGA
1 TTTGACCGGTCTGAACCGA
23222 CCCAACCGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 33 0.97
20 1 0.03
ACGTcount: A:0.18, C:0.26, G:0.28, T:0.28
Consensus pattern (19 bp):
TTTGACCGGTCTGAACCGA
Found at i:23240 original size:22 final size:22
Alignment explanation
Indices: 23215--23257 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
23205 TGATCGGTCT
23215 GACCCGACCCAACCGTTGACCC
1 GACCCGACCCAACCGTTGACCC
*
23237 GACCCGACCCGACCGTTGACC
1 GACCCGACCCAACCGTTGACC
23258 GTTGACCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.49, G:0.21, T:0.09
Consensus pattern (22 bp):
GACCCGACCCAACCGTTGACCC
Found at i:23259 original size:7 final size:7
Alignment explanation
Indices: 23247--23276 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
23237 GACCCGACCC
23247 GACCGTT
1 GACCGTT
23254 GACCGTT
1 GACCGTT
23261 GACCGTT
1 GACCGTT
23268 GACCGTT
1 GACCGTT
23275 GA
1 GA
23277 GTTTCTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.17, C:0.27, G:0.30, T:0.27
Consensus pattern (7 bp):
GACCGTT
Found at i:30425 original size:9 final size:9
Alignment explanation
Indices: 30403--30481 Score: 68
Period size: 9 Copynumber: 8.3 Consensus size: 9
30393 CCGGTTTTCA
30403 ACCGGTTCTG
1 ACCGGTT-TG
30413 ACCGGTTTG
1 ACCGGTTTG
*
30422 ACCGGTTTCA
1 ACCGGTTT-G
* *
30432 ACAGGTTCG
1 ACCGGTTTG
30441 AACCGGTTTG
1 -ACCGGTTTG
*
30451 ACCGGTCTG
1 ACCGGTTTG
*
30460 AACCGATTTG
1 -ACCGGTTTG
*
30470 ACCGGTCTG
1 ACCGGTTTG
30479 ACC
1 ACC
30482 CGACCCGACC
Statistics
Matches: 55, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
9 28 0.51
10 27 0.49
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.27
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:30427 original size:19 final size:19
Alignment explanation
Indices: 30402--30479 Score: 79
Period size: 19 Copynumber: 4.1 Consensus size: 19
30392 ACCGGTTTTC
*
30402 AACCGGTTCTGACCGGTTTG
1 AACCGGTT-TGACCGGTCTG
* *
30422 -ACCGGTTTCAACAGGT-TCG
1 AACCGGTTT-GACCGGTCT-G
30441 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
30460 AACCGATTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
30479 A
1 A
30480 CCCGACCCGA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
18 2 0.04
19 38 0.78
20 9 0.18
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:30438 original size:29 final size:29
Alignment explanation
Indices: 30392--30456 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 29
30382 AATCGATTTA
*
30392 ACCGGTTTTCAACCGGTTCTG-ACCGGTTTG
1 ACCGG-TTTCAACAGGTTC-GAACCGGTTTG
30422 ACCGGTTTCAACAGGTTCGAACCGGTTTG
1 ACCGGTTTCAACAGGTTCGAACCGGTTTG
30451 ACCGGT
1 ACCGGT
30457 CTGAACCGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 1 0.03
29 27 0.82
30 5 0.15
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.29
Consensus pattern (29 bp):
ACCGGTTTCAACAGGTTCGAACCGGTTTG
Found at i:30484 original size:19 final size:19
Alignment explanation
Indices: 30440--30484 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
30430 CAACAGGTTC
*
30440 GAACCGGTTTGACCGGTCT
1 GAACCGATTTGACCGGTCT
30459 GAACCGATTTGACCGGTCT
1 GAACCGATTTGACCGGTCT
*
30478 GACCCGA
1 GAACCGA
30485 CCCGACCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.20, C:0.29, G:0.29, T:0.22
Consensus pattern (19 bp):
GAACCGATTTGACCGGTCT
Found at i:30488 original size:5 final size:5
Alignment explanation
Indices: 30478--30567 Score: 99
Period size: 5 Copynumber: 16.8 Consensus size: 5
30468 TGACCGGTCT
* *
30478 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
*
30527 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCC GACC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACCC GACC
30568 GTTGACCGTT
Statistics
Matches: 73, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
5 61 0.84
7 12 0.16
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:30510 original size:27 final size:27
Alignment explanation
Indices: 30495--30574 Score: 160
Period size: 27 Copynumber: 3.0 Consensus size: 27
30485 CCCGACCGTT
30495 GACCCGACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCCGACCGTTGACCC
30522 GACCCGACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCCGACCGTTGACCC
30549 GACCCGACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCCGACCGTTGACC
30575 GTTGACCGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.19, C:0.51, G:0.23, T:0.07
Consensus pattern (27 bp):
GACCCGACCCGACCCGACCGTTGACCC
Found at i:30574 original size:22 final size:22
Alignment explanation
Indices: 30478--30562 Score: 125
Period size: 22 Copynumber: 3.6 Consensus size: 22
30468 TGACCGGTCT
30478 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
30500 GACCCGACCCGACCGTTGACCCGACCC
1 GACCCGACCCGACCGTT-----GACCC
30527 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
30549 GACCCGACCCGACC
1 GACCCGACCCGACC
30563 CGACCGTTGA
Statistics
Matches: 58, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
22 36 0.62
27 22 0.38
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:34948 original size:33 final size:33
Alignment explanation
Indices: 34902--34972 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
34892 ACAAGGTTTA
* *
34902 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
*
34934 TGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
34967 CGATAA
1 CGATAA
34973 TTGAAACAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 3 0.09
33 31 0.91
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.32
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTCCAAGTT
Found at i:34992 original size:21 final size:21
Alignment explanation
Indices: 34967--35008 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
34957 CTTCCAAGTT
*
34967 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAATTTA
*
34988 CGATAATTGAAATAAAATTTA
1 CGATAATTGAAACAAAATTTA
35009 AAAATAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAATTTA
Found at i:37687 original size:7 final size:7
Alignment explanation
Indices: 37677--37702 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
37667 ATAAAATAAA
37677 AAATTCT
1 AAATTCT
37684 AAATTCT
1 AAATTCT
37691 AAATTCT
1 AAATTCT
37698 AAATT
1 AAATT
37703 ATACCCTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (7 bp):
AAATTCT
Found at i:43447 original size:2 final size:2
Alignment explanation
Indices: 43440--43467 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
43430 GAATATAAGA
43440 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
43468 TGTTTTGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46911 original size:25 final size:24
Alignment explanation
Indices: 46866--46915 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
46856 ACATATAATT
* *
46866 CTTACTAATGCATTCATAATCTATA
1 CTTACTAATGCATACACAATC-ATA
46891 CTTACTATAT-CATACACAATCATA
1 CTTACTA-ATGCATACACAATCATA
46915 C
1 C
46916 ATTCTGTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 4 0.18
25 16 0.73
26 2 0.09
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.36
Consensus pattern (24 bp):
CTTACTAATGCATACACAATCATA
Found at i:47010 original size:23 final size:23
Alignment explanation
Indices: 46980--47043 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
46970 ATCTTATATA
46980 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
47003 AATTGCACCGTAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
* * *
47026 AAATACACCAAAGTGCCA
1 AATTGCACCGAAGTGCCA
47044 TATAAGGTTG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.33, C:0.27, G:0.23, T:0.17
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:48767 original size:21 final size:21
Alignment explanation
Indices: 48737--48800 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
48727 TCTGGTTCGG
* *
48737 TTGAAGGGGTATCGATTCCCC
1 TTGAATGGGTACCGATTCCCC
*
48758 TTGAATGGGTACCGATTCCCA
1 TTGAATGGGTACCGATTCCCC
48779 TTGAATGGGTACCGATTCCCC
1 TTGAATGGGTACCGATTCCCC
48800 T
1 T
48801 AGCCTAGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.30
Consensus pattern (21 bp):
TTGAATGGGTACCGATTCCCC
Found at i:53232 original size:23 final size:23
Alignment explanation
Indices: 53192--53235 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
53182 TATATATTTA
**
53192 AATTAATTTCAAACAAAAAATCT
1 AATTAATTAAAAACAAAAAATCT
*
53215 AATTAATTAAAAATAAAAAAT
1 AATTAATTAAAAACAAAAAAT
53236 AAACGTGCAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.30
Consensus pattern (23 bp):
AATTAATTAAAAACAAAAAATCT
Found at i:54596 original size:14 final size:14
Alignment explanation
Indices: 54577--54610 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
54567 AATTATTTAG
54577 TTTTTTTTTGAGGT
1 TTTTTTTTTGAGGT
54591 TTTTTTTTTGAGGT
1 TTTTTTTTTGAGGT
54605 TTTTTT
1 TTTTTT
54611 CTCCAACATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.06, C:0.00, G:0.18, T:0.76
Consensus pattern (14 bp):
TTTTTTTTTGAGGT
Found at i:55580 original size:26 final size:25
Alignment explanation
Indices: 55522--55580 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
55512 AGTATTATTT
**
55522 TTTAAAAGTATTTTAAAAAAAATGC
1 TTTAAAAGTATTTTAAAAAAAATAA
*
55547 TATAAAAAGTATTTTAAAAAAACATAA
1 T-TTAAAAGTATTTTAAAAAAA-ATAA
55574 TTTAAAA
1 TTTAAAA
55581 TGTAACTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 1 0.04
26 24 0.86
27 3 0.11
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (25 bp):
TTTAAAAGTATTTTAAAAAAAATAA
Found at i:60382 original size:35 final size:36
Alignment explanation
Indices: 60296--60383 Score: 117
Period size: 36 Copynumber: 2.5 Consensus size: 36
60286 AACTCAAGCA
*
60296 AAATAATGAACTCAAATTAGAAAAATTTTCAATGTT
1 AAATTATGAACTCAAATTAGAAAAATTTTCAATGTT
* *
60332 AAATTATGAACTCAAATTAGAAAACTTTT-AGTGTT
1 AAATTATGAACTCAAATTAGAAAAATTTTCAATGTT
*
60367 GAATTAT-AACTTCAAAT
1 AAATTATGAAC-TCAAAT
60384 AATAAAAAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
34 3 0.06
35 17 0.36
36 27 0.57
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.35
Consensus pattern (36 bp):
AAATTATGAACTCAAATTAGAAAAATTTTCAATGTT
Found at i:60696 original size:36 final size:36
Alignment explanation
Indices: 60649--60741 Score: 107
Period size: 36 Copynumber: 2.6 Consensus size: 36
60639 GGGCAAAATA
*
60649 ATGAACTCAAATTAGAAAAAATTTCAGTGTTGAATT
1 ATGAACTCAAATCAGAAAAAATTTCAGTGTTGAATT
** * *
60685 ATGAACTCAAATCAGAAAACTTTTTAGTTTTGAATT
1 ATGAACTCAAATCAGAAAAAATTTCAGTGTTGAATT
* *
60721 AT-CACTTCAAATCATAAAAAA
1 ATGAAC-TCAAATCAGAAAAAA
60742 ACATGTATTT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
35 2 0.04
36 45 0.96
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (36 bp):
ATGAACTCAAATCAGAAAAAATTTCAGTGTTGAATT
Found at i:60926 original size:362 final size:348
Alignment explanation
Indices: 60075--61018 Score: 912
Period size: 362 Copynumber: 2.6 Consensus size: 348
60065 AACATTTTCT
* * * * * * * *
60075 AGTGCTCAATTAATGCACCGTTTAAGCTACATTTCAGAGGTCATTTATTGCATCAAAAATGTAAC
1 AGTGCTCAATTAATGCACCGTTCAA-CTACTTTTCAGAGG-CAATTACTACAACAATAATGCAA-
* * * * * *
60140 AG-TTGACTTATTTT-GTTGGTCATTTAATGCAGAGTTCAAGCAACTTTTCAGAAAACGGGTGAA
63 AGATTGACTT-TTTTAG-AGATCATTTAATGAAGAATTCAAGCAACTTTTCAAAAAAAGGGTGAA
* * *
60203 ATAG-AAGTGCATTATCATCTTC-AGCAACTTTTGAGTGATATATCAACTCAAATAAGAAAACGT
126 ATAGTGA-TGCATTATCATTTTCTA-CAAC-TTTAAGTGATATATCAACTCAAATAAGAAAA---
* * *
60266 GGTTTTAACTCAGGCATTTTAACTCAAGCAAAATAATGAACTCAAATTAGAAAAATTTTCAATGT
185 ------AAGT---G-ATTTTAACTCAGGCAAAATAATGAACTCAAATTAGAAAAAATTTCAATGT
*
60331 TAAATTATGAACTCAAATTAGAAAACTTTTAGTGTTGAATTATAACTTCAAATAATAAAAAACAT
240 TAAATTATGAACTCAAATCAGAAAACTTTTAGTGTTGAATTATAACTTCAAATAATAAAAAACAT
* **
60396 GTATTTCAACCAGGCAAAATTATTCACTGTTTCAACTACTTTTT
305 GTATTTCAACCAGGCAAAATTATTCACTGTTTCAACTACATTCC
* ** * * * *
60440 AGTGCTCAATTAATGTATTGTTCATCTACTTTTCAGAGGCCATTACTACAATAATAATGCAACGA
1 AGTGCTCAATTAATGCACCGTTCAACTACTTTTCAGAGGCAATTACTACAACAATAATGCAAAGA
* * * **
60505 TTGACTTTTTTAGAGGTTATTTAATGTAGAATTCAAGCAACTTTTCAGGAAAAGGGTGAAATAGT
66 TTGACTTTTTTAGAGATCATTTAATGAAGAATTCAAGCAACTTTTCAAAAAAAGGGTGAAATAGT
* * * *
60570 GGTGCATTATCATTTTCTACAACTTTTAAGTGATATTTCAACTCAAATCAG-AAAACGTGATTTT
131 GATGCATTATCATTTTCTACAAC-TTTAAGTGATATATCAACTCAAATAAGAAAAAAGTGATTTT
* * *
60634 AACTCGGGCAAAATAATGAACTCAAATTAGAAAAAATTTCAGTGTTGAATTATGAACTCAAATCA
195 AACTCAGGCAAAATAATGAACTCAAATTAGAAAAAATTTCAATGTTAAATTATGAACTCAAATCA
* * * * ** **
60699 GAAAACTTTTTAGTTTTGAATTATCACTTCAAATCATAAAAAAACATGTATTTTAATTAGGTGAA
260 GAAAAC-TTTTAGTGTTGAATTATAACTTCAAATAAT-AAAAAACATGTATTTCAACCAGGCAAA
* **
60764 ATTATTCATTGTCTT-AGTTACATTCC
323 ATTATTCACTGT-TTCAACTACATTCC
* * * * *
60790 ATTGCTCAATTAATGCACCGTTTCAACTACTTTTCAGAGGTAATTTATTGCAGCAATAATGCAAT
1 AGTGCTCAATTAATGCACCG-TTCAACTACTTTTCAGAGGCAA-TTACTACAACAATAATGCAA-
*
60855 AG-TTGGCTTTTTTCAGAGATCATTTAATGAAGAATTCAAGCAACTTTTCAAAAAAAAAAAAAAA
63 AGATTGACTTTTTT-AGAGATCATTTAATGAAGAATTCAAGCAACTTTTC--------AAAAAAA
* *
60919 CGGGTGAAATAGTGATGCATTATCATTTTCTGCAACTTTCAGTGATATATCAACTCAAATAAGAA
119 -GGGTGAAATAGTGATGCATTATCATTTTCTACAACTTTAAGTGATATATCAACTCAAATAAGAA
* * *
60984 AAAAGTGTTTTTAACTCAGGTAAAATAATGCACTC
183 AAAAGTGATTTTAACTCAGGCAAAATAATGAACTC
61019 TCAACCGACC
Statistics
Matches: 481, Mismatches: 77, Indels: 45
0.80 0.13 0.07
Matches are distributed among these distances:
348 70 0.15
349 28 0.06
350 55 0.11
351 21 0.04
352 28 0.06
353 33 0.07
361 32 0.07
362 157 0.33
363 24 0.05
364 13 0.03
365 20 0.04
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (348 bp):
AGTGCTCAATTAATGCACCGTTCAACTACTTTTCAGAGGCAATTACTACAACAATAATGCAAAGA
TTGACTTTTTTAGAGATCATTTAATGAAGAATTCAAGCAACTTTTCAAAAAAAGGGTGAAATAGT
GATGCATTATCATTTTCTACAACTTTAAGTGATATATCAACTCAAATAAGAAAAAAGTGATTTTA
ACTCAGGCAAAATAATGAACTCAAATTAGAAAAAATTTCAATGTTAAATTATGAACTCAAATCAG
AAAACTTTTAGTGTTGAATTATAACTTCAAATAATAAAAAACATGTATTTCAACCAGGCAAAATT
ATTCACTGTTTCAACTACATTCC
Found at i:77203 original size:132 final size:132
Alignment explanation
Indices: 76974--77392 Score: 434
Period size: 132 Copynumber: 3.2 Consensus size: 132
76964 TTTTTGATTT
* ** * * ** *
76974 AACTCCTTATGTGATAGAATCGAGCGAAGAAAAGTGAAGCTGATCTAAC-CTATATGCGACGGA-
1 AACTCCTTATGTGAT-GGAT-GAGTTAAGAAAAGTGAGGCTAATCCGACTCCATATGCGAC-GAC
* * * *
77037 TGGGCCAAGAAATATAAAGCTGATCCAACCCCTTATACGATGGAT-AGGCTAAGAAATGTGATGT
63 TAGGCCAAGAAATGTAAAGCTGATCCAACACCTTATGCGATGGATGA-GCTAAGAAATGTGATGT
77101 TGATCC
127 TGATCC
* * * *
77107 AACTCCTTATGCGATGGGTGAG-TAAGGAAAAGTGAGGCTGATCCGACTCCATATGTGACAGAC-
1 AACTCCTTATGTGATGGATGAGTTAA-GAAAAGTGAGGCTAATCCGACTCCATATGCGAC-GACT
* * * * * *
77170 AGGTCAAGAAATGTAAAGCTAATACGACTCCTTATGCAATGGATGAGCTAAGAAATGTGATGTTG
64 AGGCCAAGAAATGTAAAGCTGATCCAACACCTTATGCGATGGATGAGCTAAGAAATGTGATGTTG
*
77235 ATCA
129 ATCC
* * * ** * *
77239 AACTCCTTATATGATGGACGAGTTAAGAAAAGTGAGGCTAATCTGACTTTATATGCGACGTCTGG
1 AACTCCTTATGTGATGGATGAGTTAAGAAAAGTGAGGCTAATCCGACTCCATATGCGACGACTAG
* * * * *
77304 GCCAAAAAATGTAAAGCTGATCCAACAACTTATGCGATGGATGTGCTAAGAAATGTGATGCTAAT
66 GCCAAGAAATGTAAAGCTGATCCAACACCTTATGCGATGGATGAGCTAAGAAATGTGATGTTGAT
77369 CC
131 CC
77371 AACTCCTTATGTGATGGATGAG
1 AACTCCTTATGTGATGGATGAG
77393 CCGAGGTTGA
Statistics
Matches: 235, Mismatches: 45, Indels: 13
0.80 0.15 0.04
Matches are distributed among these distances:
130 2 0.01
131 23 0.10
132 192 0.82
133 18 0.08
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (132 bp):
AACTCCTTATGTGATGGATGAGTTAAGAAAAGTGAGGCTAATCCGACTCCATATGCGACGACTAG
GCCAAGAAATGTAAAGCTGATCCAACACCTTATGCGATGGATGAGCTAAGAAATGTGATGTTGAT
CC
Found at i:77390 original size:44 final size:44
Alignment explanation
Indices: 76974--77393 Score: 231
Period size: 44 Copynumber: 9.5 Consensus size: 44
76964 TTTTTGATTT
* * * * * *
76974 AACTCCTTATGTGATAGAATCGAGCGAAGAAAAGTGAAGCTGATCT
1 AACTCCTTATGCGAT-GGAT-GAGCTAAGAAATGTGATGCTGATCC
* * * * * *
77020 AA--CCTATATGCGACGGATGGGCCAAGAAATATAAAGCTGATCC
1 AACTCCT-TATGCGATGGATGAGCTAAGAAATGTGATGCTGATCC
* * *
77063 AACCCCTTATACGATGGAT-AGGCTAAGAAATGTGATGTTGATCC
1 AACTCCTTATGCGATGGATGA-GCTAAGAAATGTGATGCTGATCC
* * *
77107 AACTCCTTATGCGATGGGTGAG-TAAGGAAAAGTGAGGCTGATCC
1 AACTCCTTATGCGATGGATGAGCTAA-GAAATGTGATGCTGATCC
* * * ** * * * * * *
77151 GACTCCATATGTGACAGA-CAGGTCAAGAAATGTAAAGCTAATAC
1 AACTCCTTATGCGATGGATGAGCT-AAGAAATGTGATGCTGATCC
* * * *
77195 GACTCCTTATGCAATGGATGAGCTAAGAAATGTGATGTTGATCA
1 AACTCCTTATGCGATGGATGAGCTAAGAAATGTGATGCTGATCC
** * * * * * *
77239 AACTCCTTATATGATGGACGAGTTAAGAAAAGTGAGGCTAATCT
1 AACTCCTTATGCGATGGATGAGCTAAGAAATGTGATGCTGATCC
* * * ** * * * * *
77283 GACT-TTATATGCGACGTCTGGGCCAAAAAATGTAAAGCTGATCC
1 AACTCCT-TATGCGATGGATGAGCTAAGAAATGTGATGCTGATCC
** * *
77327 AACAACTTATGCGATGGATGTGCTAAGAAATGTGATGCTAATCC
1 AACTCCTTATGCGATGGATGAGCTAAGAAATGTGATGCTGATCC
*
77371 AACTCCTTATGTGATGGATGAGC
1 AACTCCTTATGCGATGGATGAGC
77394 CGAGGTTGAA
Statistics
Matches: 271, Mismatches: 92, Indels: 24
0.70 0.24 0.06
Matches are distributed among these distances:
43 27 0.10
44 226 0.83
45 16 0.06
46 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (44 bp):
AACTCCTTATGCGATGGATGAGCTAAGAAATGTGATGCTGATCC
Found at i:78620 original size:13 final size:12
Alignment explanation
Indices: 78604--78695 Score: 103
Period size: 13 Copynumber: 7.2 Consensus size: 12
78594 TTTCCCTTTA
78604 TTTCTTCTTTCTT
1 TTTCTT-TTTCTT
78617 TTTCTTTTTCCTT
1 TTTCTTTTT-CTT
*
78630 TTTCTTTTCCTT
1 TTTCTTTTTCTT
* *
78642 TTCCTTTTCCTT
1 TTTCTTTTTCTT
78654 TTTCTTTTTCCTT
1 TTTCTTTTT-CTT
78667 TTTCTTTTTCTTTT
1 TTTCTTTTTC--TT
78681 TTTCTTTTTTCTT
1 TTTC-TTTTTCTT
78694 TT
1 TT
78696 CCTTCACTTC
Statistics
Matches: 70, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
12 25 0.36
13 33 0.47
14 6 0.09
15 6 0.09
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTCTTTTTCTT
Found at i:78622 original size:6 final size:6
Alignment explanation
Indices: 78604--78695 Score: 103
Period size: 6 Copynumber: 14.3 Consensus size: 6
78594 TTTCCCTTTA
* * *
78604 TTTCTT CTTTCTT TTTCTT TTTCCTT TTTCTT TTCCTT TTCCTT TTCCTT
1 TTTCTT -TTTCTT TTTCTT TTT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
78654 TTTCTT TTTCCTT TTTCTT TTTCTTTT TTTCTTT TTTCTT TT
1 TTTCTT TTT-CTT TTTCTT TTTC--TT TTTC-TT TTTCTT TT
78696 CCTTCACTTC
Statistics
Matches: 79, Mismatches: 2, Indels: 9
0.88 0.02 0.10
Matches are distributed among these distances:
6 48 0.61
7 25 0.32
8 6 0.08
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTCTT
Found at i:79690 original size:17 final size:15
Alignment explanation
Indices: 79659--79696 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 15
79649 AATACTCGGA
79659 TCGAATGGACTCGAC
1 TCGAATGGACTCGAC
79674 TCGAACTGGAGCTCGAC
1 TCGAA-TGGA-CTCGAC
79691 TCGAAT
1 TCGAAT
79697 TCTTAATGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.24
16 5 0.24
17 11 0.52
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (15 bp):
TCGAATGGACTCGAC
Found at i:80188 original size:81 final size:81
Alignment explanation
Indices: 80053--80215 Score: 308
Period size: 81 Copynumber: 2.0 Consensus size: 81
80043 TCAGCAATAC
* *
80053 TCGAGCTCGACTCGGCTCATTTACCCCCCTAGCCATGGTGCAGTCACCACATGTAGAGGTAATGG
1 TCGAGCTCGACTCGGCTCATTTACACCCCTAACCATGGTGCAGTCACCACATGTAGAGGTAATGG
80118 AGGCTCGTGAATCTTG
66 AGGCTCGTGAATCTTG
80134 TCGAGCTCGACTCGGCTCATTTACACCCCTAACCATGGTGCAGTCACCACATGTAGAGGTAATGG
1 TCGAGCTCGACTCGGCTCATTTACACCCCTAACCATGGTGCAGTCACCACATGTAGAGGTAATGG
80199 AGGCTCGTGAATCTTG
66 AGGCTCGTGAATCTTG
80215 T
1 T
80216 ATGCATATAT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (81 bp):
TCGAGCTCGACTCGGCTCATTTACACCCCTAACCATGGTGCAGTCACCACATGTAGAGGTAATGG
AGGCTCGTGAATCTTG
Found at i:82808 original size:16 final size:16
Alignment explanation
Indices: 82783--82813 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
82773 AAAAAGAATA
*
82783 AATGTCAAGAATGTAG
1 AATGTAAAGAATGTAG
82799 AATGTAAAGAATGTA
1 AATGTAAAGAATGTA
82814 AATAATGCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.23, T:0.26
Consensus pattern (16 bp):
AATGTAAAGAATGTAG
Found at i:92177 original size:23 final size:21
Alignment explanation
Indices: 92146--92200 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
92136 AATGACATGC
*
92146 AAAACTAAAACAAGTATATAAAT
1 AAAAATAAAACAAG-ATA-AAAT
* *
92169 AAAAATAAAATAAGATAAGAT
1 AAAAATAAAACAAGATAAAAT
92190 AAGAAATAAAA
1 AA-AAATAAAA
92201 AGTAAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.18
22 11 0.39
23 12 0.43
ACGTcount: A:0.71, C:0.04, G:0.07, T:0.18
Consensus pattern (21 bp):
AAAAATAAAACAAGATAAAAT
Found at i:92381 original size:2 final size:2
Alignment explanation
Indices: 92370--92409 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
92360 TTTTCAAAAC
92370 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
92410 TTAAAATGCT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:92495 original size:2 final size:2
Alignment explanation
Indices: 92488--92514 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
92478 ACCTTTAAAC
92488 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 T
92515 TAAAAACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:98091 original size:20 final size:21
Alignment explanation
Indices: 98054--98093 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
98044 ATTAAAAAAT
98054 ATATATTATCTTAATTTATTAA
1 ATATATTATCTT-ATTTATTAA
*
98076 ATATATTTTCTT-TTTATT
1 ATATATTATCTTATTTATT
98094 TCAACTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
ATATATTATCTTATTTATTAA
Found at i:98166 original size:30 final size:29
Alignment explanation
Indices: 98057--98174 Score: 98
Period size: 30 Copynumber: 4.0 Consensus size: 29
98047 AAAAAATATA
98057 TATTATCTTAA-TTTATTAAATATATTTT-C
1 TATTATCTTAACTTTA--AAATATATTTTAC
* * *
98086 TTTTTAT-TTCAACTTCAAAATATATTTTAG
1 -TATTATCTT-AACTTTAAAATATATTTTAC
* * *
98116 TCTTATTTTTAACTTAAAAATATATTTTAC
1 TATTA-TCTTAACTTTAAAATATATTTTAC
*
98146 TATTATCTTAATTTTTAAAATATATTTTA
1 TATTATCTTAA-CTTTAAAATATATTTTA
98175 AATTAAATCC
Statistics
Matches: 72, Mismatches: 10, Indels: 12
0.77 0.11 0.13
Matches are distributed among these distances:
29 22 0.31
30 45 0.62
31 5 0.07
ACGTcount: A:0.36, C:0.08, G:0.01, T:0.56
Consensus pattern (29 bp):
TATTATCTTAACTTTAAAATATATTTTAC
Found at i:98214 original size:151 final size:151
Alignment explanation
Indices: 98021--98295 Score: 376
Period size: 151 Copynumber: 1.8 Consensus size: 151
98011 AATTCACATA
* * * *
98021 TTAAATTAGATTCACATCTTAAAATTAAAAAATATATATTATCTTAATTTATTAAATATATTTTC
1 TTAAATTAAATCCACATCTTAAAATTAAAAAATATATATTATCTTAATTTATCAAATATATTTTA
* *
98086 TTTTTA-TTTCAACTTCAAAATATATTTTAGTCTTATTTTTAACTTAAAAATATATTTTACTATT
66 TTCTTATTTTCAACTTAAAAATATATTTTAGTCTTA-TTTTAACTTAAAAATATATTTTACTATT
98150 ATCTTAATTTTTAAAATATATT
130 ATCTTAATTTTTAAAATATATT
* * *
98172 TTAAATTAAATCCACATAC-TAACATT-AAAAATATATTTTTATCTTAATTTATCAAATATGTTT
1 TTAAATTAAATCCACAT-CTTAAAATTAAAAAATATA-TATTATCTTAATTTATCAAATATATTT
* ** * *
98235 TATTCTTATTTTTATTTTAAAAATATATTTTAGTCTTATTTTAGCTTAAAAATATTTTTTA
64 TATTCTTATTTTCAACTTAAAAATATATTTTAGTCTTATTTTAACTTAAAAATATATTTTA
98296 TCTTTAAATT
Statistics
Matches: 107, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
150 9 0.08
151 72 0.67
152 26 0.24
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (151 bp):
TTAAATTAAATCCACATCTTAAAATTAAAAAATATATATTATCTTAATTTATCAAATATATTTTA
TTCTTATTTTCAACTTAAAAATATATTTTAGTCTTATTTTAACTTAAAAATATATTTTACTATTA
TCTTAATTTTTAAAATATATT
Found at i:98266 original size:30 final size:29
Alignment explanation
Indices: 98225--98296 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
98215 TTAATTTATC
* **
98225 AAATATGTTTTATTCTTATTTTTATTTTAA
1 AAATATATTTTATTCTTA-TTTTAGCTTAA
*
98255 AAATATATTTTAGTCTTATTTTAGCTTAA
1 AAATATATTTTATTCTTATTTTAGCTTAA
*
98284 AAATATTTTTTAT
1 AAATATATTTTAT
98297 CTTTAAATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 20 0.56
30 16 0.44
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (29 bp):
AAATATATTTTATTCTTATTTTAGCTTAA
Found at i:98334 original size:30 final size:30
Alignment explanation
Indices: 98291--98349 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
98281 TAAAAATATT
**
98291 TTTTATCTTTAAATTATGATATATATTTTAC
1 TTTTATCTTTAAATTAAAATATAT-TTTTAC
98322 TTTTAT-TTTAAATTAAAATATATTTTTA
1 TTTTATCTTTAAATTAAAATATATTTTTA
98350 AAAGCTAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 5 0.19
30 15 0.58
31 6 0.23
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (30 bp):
TTTTATCTTTAAATTAAAATATATTTTTAC
Found at i:98412 original size:28 final size:27
Alignment explanation
Indices: 98376--98455 Score: 88
Period size: 28 Copynumber: 2.9 Consensus size: 27
98366 TAAGATGTAT
* * *
98376 TTTTTAAGTTAAAATAAGATTAAAAATA
1 TTTTAAAGTTAAAATAAAAAT-AAAATA
*
98404 TTTTAAAGTTCAAATAAAAATAAAATA
1 TTTTAAAGTTAAAATAAAAATAAAATA
*
98431 TATTTATAAGTTAATATAAAAATAA
1 T-TTTA-AAGTTAAAATAAAAATAA
98456 TTATAAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
27 7 0.16
28 21 0.48
29 16 0.36
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.38
Consensus pattern (27 bp):
TTTTAAAGTTAAAATAAAAATAAAATA
Found at i:98433 original size:29 final size:30
Alignment explanation
Indices: 98335--98455 Score: 106
Period size: 29 Copynumber: 4.1 Consensus size: 30
98325 TATTTTAAAT
* *
98335 TAAAATATATTTTTAAAAGCTAAGATAAGAA
1 TAAAATATATTTTT-AAAGTTAAGATAAAAA
* * * * * *
98366 TAAGATGTATTTTTTAAGTTAAAATAAGAT
1 TAAAATATATTTTTAAAGTTAAGATAAAAA
98396 TAAAA-ATA-TTTTAAAGTTCAA-ATAAAAA
1 TAAAATATATTTTTAAAGTT-AAGATAAAAA
* *
98424 TAAAATATATTTAT-AAGTTAATATAAAAA
1 TAAAATATATTTTTAAAGTTAAGATAAAAA
98453 TAA
1 TAA
98456 TTATAAAAAA
Statistics
Matches: 74, Mismatches: 12, Indels: 10
0.77 0.12 0.10
Matches are distributed among these distances:
28 21 0.28
29 22 0.30
30 19 0.26
31 12 0.16
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (30 bp):
TAAAATATATTTTTAAAGTTAAGATAAAAA
Found at i:101683 original size:2 final size:2
Alignment explanation
Indices: 101676--101716 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
101666 ATTTAAACAA
101676 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
101717 AGACTAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:104162 original size:113 final size:113
Alignment explanation
Indices: 103817--104371 Score: 548
Period size: 113 Copynumber: 4.9 Consensus size: 113
103807 AAATTAAGGC
103817 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * * * ** *
103881 TGAACCCT-TCGGAAAGTTGATGTTGATCTATCTCCTTCTGTGAT-AGAGTC-AAC-A
66 TGAACTCTACCTG---G-TAATGTTGATCCA--T-C--GAGTGATGA-ATTCAAACAA
* *
103935 AAGGTTGAACAAATTC-T-TC-TTATTAA---CTTCTT-C-TCTTCAGATAAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * *
103992 TGAACTCTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAACAA
66 TGAACTCTAC-CTGGTAATGTTGATCCATCGAGTGATGAATTCAAACAA
** *
104041 AAAATTGAACAAATTCTTCTCATTATGAATTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* *
104106 TGAACTCTACCTGGTAATGTTGATCCATCAAATGATGAATTCAAACAA
66 TGAACTCTACCTGGTAATGTTGATCCATCGAGTGATGAATTCAAACAA
* * * * *
104154 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATAACTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * * * *
104219 TGAACT-TTCTCTGGCAATGCTAATCCATCGGGTGATGAATT-AAAGAAA
66 TGAACTCTAC-CTGGTAATGTTGATCCATCGAGTGATGAATTCAAA-CAA
*
104267 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCCTTCTTCAGATGAGTTCTTCTC
1 AAGGTTGAACAAATTCTTCTCATTATGAA--T-TTCTT-CTTCCTTCTTCAGATGAGTTCTTCTC
* * *
104332 ATTATTAACTCTACCTGG-CATGTTGATCCATTGAGTGATG
62 ATTATGAACTCTACCTGGTAATGTTGATCCATCGAGTGATG
104372 GA
Statistics
Matches: 367, Mismatches: 49, Indels: 44
0.80 0.11 0.10
Matches are distributed among these distances:
104 8 0.02
105 4 0.01
106 16 0.04
107 2 0.01
108 2 0.01
109 15 0.04
110 1 0.00
111 30 0.08
112 15 0.04
113 157 0.43
114 32 0.09
115 6 0.02
116 24 0.07
117 37 0.10
118 18 0.05
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTCTACCTGGTAATGTTGATCCATCGAGTGATGAATTCAAACAA
Found at i:104189 original size:17 final size:17
Alignment explanation
Indices: 104167--104225 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 17
104157 GTTGAACAAG
104167 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
*
104184 TTCTTCTTCATTCTTCAGATAAC
1 TTCTTC-TCATT-AT--G--AAC
104207 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
104224 TT
1 TT
104226 TCTCTGGCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
17 11 0.32
18 5 0.15
19 2 0.06
21 2 0.06
22 5 0.15
23 9 0.26
ACGTcount: A:0.22, C:0.24, G:0.05, T:0.49
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Done.