Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009184.1 Hibiscus syriacus cultivar Beakdansim tig00112757_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: 104462
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1296 original size:23 final size:23
Alignment explanation
Indices: 1250--1297 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1240 GTATGTATAT
*
1250 TTATATAACATAATACAAATACA
1 TTATATAACATAATACAAACACA
*
1273 TTATATACCATAATA-ATAACACA
1 TTATATAACATAATACA-AACACA
1296 TT
1 TT
1298 GACTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 21 0.95
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (23 bp):
TTATATAACATAATACAAACACA
Found at i:4217 original size:25 final size:25
Alignment explanation
Indices: 4185--4232 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
4175 TTTCTATACG
4185 ATTTTTT-AATAATAAAAGTTTTCT
1 ATTTTTTAAATAATAAAAGTTTTCT
*
4209 ATTTCTTTAAATAATAAAATTTTT
1 ATTT-TTTAAATAATAAAAGTTTT
4233 AGAGGGTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.19
25 3 0.14
26 14 0.67
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (25 bp):
ATTTTTTAAATAATAAAAGTTTTCT
Found at i:6718 original size:31 final size:32
Alignment explanation
Indices: 6674--6740 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
6664 CTATTTAAAA
*
6674 TTTTAAAAATTTTGGA-GGTTTAAATTATATT
1 TTTTAAAAATTTTGAATGGTTTAAATTATATT
** **
6705 TTTTAAATTTTTTGAATGGTTTAGTTTATATT
1 TTTTAAAAATTTTGAATGGTTTAAATTATATT
6737 TTTT
1 TTTT
6741 TTCTTCAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (32 bp):
TTTTAAAAATTTTGAATGGTTTAAATTATATT
Found at i:9574 original size:13 final size:13
Alignment explanation
Indices: 9556--9619 Score: 59
Period size: 13 Copynumber: 5.2 Consensus size: 13
9546 AATAGCACCA
9556 GTCAACGGGTCGG
1 GTCAACGGGTCGG
9569 GTCAACGGGTCGG
1 GTCAACGGGTCGG
*
9582 GT---CGGGTCAACG
1 GTCAACGGGTC--GG
9594 GT---CGGGTCGG
1 GTCAACGGGTCGG
9604 GTCAACGGGTCGG
1 GTCAACGGGTCGG
9617 GTC
1 GTC
9620 GTGACCGGTC
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
10 9 0.20
12 9 0.20
13 26 0.59
ACGTcount: A:0.12, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GTCAACGGGTCGG
Found at i:9584 original size:18 final size:18
Alignment explanation
Indices: 9561--9620 Score: 113
Period size: 18 Copynumber: 3.4 Consensus size: 18
9551 CACCAGTCAA
9561 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
9579 CGGGTCGGGTCAAC-GGT
1 CGGGTCGGGTCAACGGGT
9596 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
9614 CGGGTCG
1 CGGGTCG
9621 TGACCGGTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
17 17 0.41
18 24 0.59
ACGTcount: A:0.10, C:0.23, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:9643 original size:10 final size:10
Alignment explanation
Indices: 9623--9674 Score: 63
Period size: 9 Copynumber: 5.3 Consensus size: 10
9613 TCGGGTCGTG
9623 ACCGGTC-AA
1 ACCGGTCAAA
9632 ACCGGTCAAA
1 ACCGGTCAAA
9642 ACCGGTTCAAA
1 ACCGG-TCAAA
*
9653 ACCGGT-TAA
1 ACCGGTCAAA
*
9662 ACCGATCAAA
1 ACCGGTCAAA
9672 ACC
1 ACC
9675 AGTTTCGAGC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
9 14 0.38
10 13 0.35
11 10 0.27
ACGTcount: A:0.38, C:0.31, G:0.17, T:0.13
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:9653 original size:11 final size:11
Alignment explanation
Indices: 9630--9659 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
9620 GTGACCGGTC
9630 AAACCGG-TCA
1 AAACCGGTTCA
9640 AAACCGGTTCA
1 AAACCGGTTCA
9651 AAACCGGTT
1 AAACCGGTT
9660 AAACCGATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.37
11 12 0.63
ACGTcount: A:0.37, C:0.27, G:0.20, T:0.17
Consensus pattern (11 bp):
AAACCGGTTCA
Found at i:16836 original size:18 final size:18
Alignment explanation
Indices: 16797--16873 Score: 113
Period size: 17 Copynumber: 4.4 Consensus size: 18
16787 CACCAGTCAA
* *
16797 CGGGTCTGGTCAAC-GAT
1 CGGGTCGGGTCAACGGGT
*
16814 CGGGTCGTGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
16832 CGGGTCGGGTCAAC-GGT
1 CGGGTCGGGTCAACGGGT
16849 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
16867 CGGGTCG
1 CGGGTCG
16874 TGACCGATCA
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
17 29 0.54
18 25 0.46
ACGTcount: A:0.12, C:0.23, G:0.45, T:0.19
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:16843 original size:35 final size:35
Alignment explanation
Indices: 16797--16873 Score: 127
Period size: 35 Copynumber: 2.2 Consensus size: 35
16787 CACCAGTCAA
* *
16797 CGGGTCTGGTCAACGATCGGGTCGTGTCAACGGGT
1 CGGGTCGGGTCAACGATCGGGTCGGGTCAACGGGT
*
16832 CGGGTCGGGTCAACGGTCGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGATCGGGTCGGGTCAACGGGT
16867 CGGGTCG
1 CGGGTCG
16874 TGACCGATCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.12, C:0.23, G:0.45, T:0.19
Consensus pattern (35 bp):
CGGGTCGGGTCAACGATCGGGTCGGGTCAACGGGT
Found at i:16898 original size:10 final size:10
Alignment explanation
Indices: 16883--16930 Score: 71
Period size: 10 Copynumber: 4.8 Consensus size: 10
16873 GTGACCGATC
16883 AAACCGGTCA
1 AAACCGGTCA
16893 AAACCGGTTCA
1 AAACCGG-TCA
*
16904 AAACCGGT-T
1 AAACCGGTCA
16913 AAACCGGTCA
1 AAACCGGTCA
16923 AAACCGGT
1 AAACCGGT
16931 TTCCAGCGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 8 0.24
10 16 0.47
11 10 0.29
ACGTcount: A:0.38, C:0.27, G:0.21, T:0.15
Consensus pattern (10 bp):
AAACCGGTCA
Found at i:17972 original size:21 final size:22
Alignment explanation
Indices: 17948--17991 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
17938 GTCTATGAAG
17948 AGTCATAGGAGAAT-AAATATA
1 AGTCATAGGAGAATGAAATATA
* *
17969 AGTCATATGATAATGAAATATA
1 AGTCATAGGAGAATGAAATATA
17991 A
1 A
17992 TACTATGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.52, C:0.05, G:0.16, T:0.27
Consensus pattern (22 bp):
AGTCATAGGAGAATGAAATATA
Found at i:19002 original size:23 final size:23
Alignment explanation
Indices: 18972--19057 Score: 118
Period size: 23 Copynumber: 3.7 Consensus size: 23
18962 AATCTTATAT
18972 GGCACTACGGTGCATTTCTACAC
1 GGCACTACGGTGCATTTCTACAC
18995 GGCACTACGGTGCATTTCTACAC
1 GGCACTACGGTGCATTTCTACAC
* * **
19018 GGTACTACGGTGCAATTCTACGT
1 GGCACTACGGTGCATTTCTACAC
* *
19041 GACACTTCGGTGCATTT
1 GGCACTACGGTGCATTT
19058 ATACGAGTTG
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (23 bp):
GGCACTACGGTGCATTTCTACAC
Found at i:21014 original size:32 final size:32
Alignment explanation
Indices: 20948--21023 Score: 84
Period size: 32 Copynumber: 2.3 Consensus size: 32
20938 TCTTCGTCCT
* *
20948 AAATAAAAAATTTAGATACTATTATATTCTAA
1 AAATAAATAATTTAGATACTATTATATACTAA
*
20980 AAATAAATATTTTAGATACTATT-TAGTAAC-AA
1 AAATAAATAATTTAGATACTATTATA-T-ACTAA
21012 AAATGAAATAAT
1 AAAT-AAATAAT
21024 ATTATATCTA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
31 2 0.05
32 28 0.76
33 7 0.19
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (32 bp):
AAATAAATAATTTAGATACTATTATATACTAA
Found at i:22554 original size:20 final size:21
Alignment explanation
Indices: 22516--22557 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
22506 TTTCAATGTA
*
22516 TAAAATTATTTTTTTAATAATT
1 TAAAATTA-TTTTTAAATAATT
22538 TAAAATTA-TTTTAAATAATT
1 TAAAATTATTTTTAAATAATT
22558 ATATTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
22 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TAAAATTATTTTTAAATAATT
Found at i:22574 original size:18 final size:17
Alignment explanation
Indices: 22546--22583 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
22536 TTTAAAATTA
22546 TTTTAAATAATTAT-ATT
1 TTTTAAATAA-TATCATT
22563 TTTTACAATAATATCATT
1 TTTTA-AATAATATCATT
22581 TTT
1 TTT
22584 CACCTCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTAAATAATATCATT
Found at i:24691 original size:25 final size:25
Alignment explanation
Indices: 24662--24711 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
24652 GATTAGGGGT
24662 ACTGAAGCATAAACATGTAGGGATA
1 ACTGAAGCATAAACATGTAGGGATA
*
24687 ACTGAAGCATAAACATGTAGTGATA
1 ACTGAAGCATAAACATGTAGGGATA
24712 TGGTGCTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (25 bp):
ACTGAAGCATAAACATGTAGGGATA
Found at i:25766 original size:18 final size:19
Alignment explanation
Indices: 25743--25798 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 19
25733 ATCATTATCA
25743 TTTTATTATCATTCATAT-
1 TTTTATTATCATTCATATG
*
25761 TTTTATTCTCTTATTCATATG
1 TTTTATTATC--ATTCATATG
* *
25782 ATTCATTAT-ATTCATAT
1 TTTTATTATCATTCATAT
25799 CATATATCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
18 17 0.55
20 8 0.26
21 6 0.19
ACGTcount: A:0.27, C:0.12, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTTATTATCATTCATATG
Found at i:26998 original size:21 final size:19
Alignment explanation
Indices: 26972--27014 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
26962 GATTTCTGGG
*
26972 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAA-CGATACCC-TT
26993 CAAGGGGAACGATACCCTT
1 CAAGGGGAACGATACCCTT
27012 CAA
1 CAA
27015 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 7 0.33
21 9 0.43
ACGTcount: A:0.33, C:0.26, G:0.26, T:0.16
Consensus pattern (19 bp):
CAAGGGGAACGATACCCTT
Found at i:28860 original size:101 final size:100
Alignment explanation
Indices: 28680--28892 Score: 327
Period size: 101 Copynumber: 2.1 Consensus size: 100
28670 GGGTCTACGC
*
28680 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACATACTTGATCC
1 GGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACATACTTGATCC
* * *
28745 TTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CTAG-ATATATATATGATTCTTAAGGAATGATATGT
28781 GGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAG--ACATACTTGAT
28846 CCCTAGTATATATATATATGATTCTTAAGGAATGATATGT
64 CCCTAG---ATATATATATGATTCTTAAGGAATGATATGT
*
28886 AGTCCTT
1 GGTCCTT
28893 ATGGACATTA
Statistics
Matches: 102, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
101 51 0.50
103 15 0.15
105 36 0.35
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.37
Consensus pattern (100 bp):
GGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACATACTTGATCC
CTAGATATATATATGATTCTTAAGGAATGATATGT
Found at i:28942 original size:23 final size:23
Alignment explanation
Indices: 28909--28976 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
28899 ATTATTATAT
28909 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
28932 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* * * *
28955 GCCACTTCAGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
28977 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:31982 original size:21 final size:21
Alignment explanation
Indices: 31956--32000 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
31946 GATTTCTGGG
* *
31956 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
31977 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
31998 CAA
1 CAA
32001 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:32760 original size:16 final size:16
Alignment explanation
Indices: 32741--32777 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
32731 TGTGGAAGTC
32741 ATGATGTGTGCATGAT
1 ATGATGTGTGCATGAT
32757 ATGATGTGTGCATGAT
1 ATGATGTGTGCATGAT
32773 ATGAT
1 ATGAT
32778 ATATGTGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.27, C:0.05, G:0.30, T:0.38
Consensus pattern (16 bp):
ATGATGTGTGCATGAT
Found at i:33258 original size:25 final size:26
Alignment explanation
Indices: 33230--33278 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
33220 TATCACATGT
* *
33230 TCACATATCTCTTA-TTCTCATAGGA
1 TCACATAGCTCATACTTCTCATAGGA
33255 TCACATAGCTCATACTTCTCATAG
1 TCACATAGCTCATACTTCTCATAG
33279 ACATATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.29, C:0.27, G:0.08, T:0.37
Consensus pattern (26 bp):
TCACATAGCTCATACTTCTCATAGGA
Found at i:34366 original size:15 final size:15
Alignment explanation
Indices: 34343--34384 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
34333 ATATTAAATT
*
34343 TAACAAGAAACTAAC
1 TAACCAGAAACTAAC
34358 TAACCAGAAACTAAC
1 TAACCAGAAACTAAC
34373 TAACCAGAAACT
1 TAACCAGAAACT
34385 CACCTTTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.55, C:0.24, G:0.07, T:0.14
Consensus pattern (15 bp):
TAACCAGAAACTAAC
Found at i:36666 original size:18 final size:18
Alignment explanation
Indices: 36645--36683 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
36635 AGAACAGCAC
* * *
36645 GAGGTACAAGCTCTACCA
1 GAGGAACAAGCACGACCA
36663 GAGGAACAAGCACGACCA
1 GAGGAACAAGCACGACCA
36681 GAG
1 GAG
36684 CATCAAATGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.26, G:0.28, T:0.08
Consensus pattern (18 bp):
GAGGAACAAGCACGACCA
Found at i:46572 original size:2 final size:2
Alignment explanation
Indices: 46565--46610 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
46555 TTGTGAAATC
46565 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46607 AT AT
1 AT AT
46611 GTGTGTGTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46615 original size:2 final size:2
Alignment explanation
Indices: 46610--46654 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
46600 TATATATATA
* *
46610 TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG TG CG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
46652 TG T
1 TG T
46655 ATTGGTTATA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.02, C:0.02, G:0.47, T:0.49
Consensus pattern (2 bp):
TG
Found at i:47416 original size:182 final size:182
Alignment explanation
Indices: 47109--47593 Score: 749
Period size: 182 Copynumber: 2.7 Consensus size: 182
47099 GGGGTGTTAC
*
47109 ACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAAGCGGTCTCTA
1 ACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCGGTCTCTA
* ***
47174 TAGGACAAAATTGGTACAA-AGCGACCGGATATATTGAAAGT-ATCGATACTTTAATATAAGTAT
66 AAGGACAAAACCAGTA-AAGAGCGACCGGATATATTGAAAGTGA-CGATACTTTAATATAAGTAT
*
47237 AGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGAT
129 AGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCATATAAAGTGTCGAT
*
47291 ACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGAAAAAACCGGTCTCTA
1 ACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCGGTCTCTA
* * * * *
47356 AAGGAAAAAACCAGTATAGAGCGACTGAATATATTGAAAGTGACGATACTTTAATATAAGTATCG
66 AAGGACAAAACCAGTAAAGAGCGACCGGATATATTGAAAGTGACGATACTTTAATATAAGTATAG
47421 ACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCATATAAAGTGTCGAT
131 ACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCATATAAAGTGTCGAT
* * * *
47473 ACTTTATAAAAATGTATCGATCCATAACGATATAACAGGTAAAAATATGACAAAACCGATCTCAA
1 ACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCGGTCTCTA
* * * **
47538 AATGACAAAACCAGTAAAGCGCTACCGGATATATTGAAAGTGTTGATACTTTAATA
66 AAGGACAAAACCAGTAAAGAGCGACCGGATATATTGAAAGTGACGATACTTTAATA
47594 AGTACACGTA
Statistics
Matches: 275, Mismatches: 26, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
181 1 0.00
182 273 0.99
183 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (182 bp):
ACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCGGTCTCTA
AAGGACAAAACCAGTAAAGAGCGACCGGATATATTGAAAGTGACGATACTTTAATATAAGTATAG
ACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCATATAAAGTGTCGAT
Found at i:49988 original size:21 final size:21
Alignment explanation
Indices: 49964--50008 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
49954 AAGACAATCA
*
49964 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAAAGAAACTTGAG
*
49985 AGAGTCGAAAAGACACTTGAG
1 AGAGTCGAAAAGAAACTTGAG
50006 AGA
1 AGA
50009 CATAAGGGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.11, G:0.31, T:0.13
Consensus pattern (21 bp):
AGAGTCGAAAAGAAACTTGAG
Found at i:53908 original size:199 final size:200
Alignment explanation
Indices: 53457--53934 Score: 646
Period size: 200 Copynumber: 2.4 Consensus size: 200
53447 ACGTAAATAT
*
53457 GTGTCGATACATTT-TCTAAAAGTATCGA-CCCAAAAAACATCGAAACCAATAATTATAATGTAA
1 GTGTCGATACATTTAT-TAAAAGTATCGATCCC-AAAAACATCGAAACCGATAATTATAATGTAA
* * * * *
53520 T-TGGTAAATTAACAATGTAACTGGTATAAATATACTGGTTAATTAGAAAACAGGTCAACATAAT
64 TAT-GTAAATTTACAATGTAACTAGTATAAATATACCGGTTAATGAGAAAACAGGTCAACATAAA
* * *
53584 GTATCGACACTTGTGAAATTTGTGTCGATACTTATTGTCCAGAATGAATGTCCAAACTAGGTGCA
128 GTATCGACACTTGTGAAATTTGTGTCAATACTTATTGCCCAGAATAAATGTCCAAACTAGGTGCA
53649 CACATAAA
193 CACATAAA
53657 GTGTCGATACATTTATTAAAAGTATCGATCCCAATAAA-ATCGAAACCGATAATTATAATGTAAT
1 GTGTCGATACATTTATTAAAAGTATCGATCCCAA-AAACATCGAAACCGATAATTATAATGTAAT
* * * * *
53721 ATGTAAATTTACAATGTAACTAGTATAAATATACCGATTTTATGAGAAAATAGTTCAGCATAAAG
65 ATGTAAATTTACAATGTAACTAGTATAAATATACCG-GTTAATGAGAAAACAGGTCAACATAAAG
* * *
53786 TATCGACACTTGTTAAATTTGTGTCAATACATT-TTGCCCATAATAAATGT-CAAAC-GGGTGCA
129 TATCGACACTTGTGAAATTTGTGTCAATAC-TTATTGCCCAGAATAAATGTCCAAACTAGGTGCA
*
53848 CGCATAAA
193 CACATAAA
* * * *
53856 GTGTCGATACATTTATTAAAAGTATCGATCTCAAAAACATCGAAATCGATAATTACAATGTGATA
1 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
*
53921 GGTAAATTTACAAT
66 TGTAAATTTACAAT
53935 ATACCTAATA
Statistics
Matches: 248, Mismatches: 23, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
198 3 0.01
199 83 0.33
200 89 0.36
201 71 0.29
202 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (200 bp):
GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
TGTAAATTTACAATGTAACTAGTATAAATATACCGGTTAATGAGAAAACAGGTCAACATAAAGTA
TCGACACTTGTGAAATTTGTGTCAATACTTATTGCCCAGAATAAATGTCCAAACTAGGTGCACAC
ATAAA
Found at i:55153 original size:33 final size:34
Alignment explanation
Indices: 55111--55216 Score: 87
Period size: 33 Copynumber: 3.1 Consensus size: 34
55101 GTGGTAAGAA
* *
55111 ATTTATTTTTATGTTAGTAT-TTT-T-TAAATAGTT
1 ATTT-TTTTTATATTAATATATTTATGTAAATA-TT
55144 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATT-TTTTTTATATTAATATATTTATGTAAATATT
* * *
55179 A-TTTTTTTAT-TAAAATAATATTTATATAATTATT
1 ATTTTTTTTATAT-TAAT-ATATTTATGTAAATATT
55213 ATTT
1 ATTT
55217 ATTTAGAATT
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
32 1 0.02
33 27 0.44
34 21 0.34
35 6 0.10
36 6 0.10
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (34 bp):
ATTTTTTTTATATTAATATATTTATGTAAATATT
Found at i:55198 original size:36 final size:34
Alignment explanation
Indices: 55143--55221 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
55133 TTTAAATAGT
*
55143 TATTATTTTTTATATT--AAT-ATATTTATGTAAA
1 TATTATTTTTT-TATTAAAATAATATTTATATAAA
*
55175 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATTAAAATAATATTTATATAAA
*
55209 TATTATTTATTTA
1 TATTATTTTTTTA
55222 GAATTATAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
31 4 0.10
32 11 0.27
33 3 0.07
34 23 0.56
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
TATTATTTTTTTATTAAAATAATATTTATATAAA
Found at i:55231 original size:34 final size:32
Alignment explanation
Indices: 55133--55231 Score: 76
Period size: 34 Copynumber: 3.0 Consensus size: 32
55123 GTTAGTATTT
* * *
55133 TTTAAATAGTTATTATTTTTTATATTA-ATATA
1 TTTATATAATTATTATTTTTTAAATTATA-ATA
* * *
55165 TTTATGTAAATATTATTTTTTTATTAA-AATAATA
1 TTTATATAATTATTA-TTTTTTA--AATTATAATA
55199 TTTATATAATTATTATTTATTTAGAATTATAAT
1 TTTATATAATTATTATTT-TTTA-AATTATAAT
55232 TTTTTTTTGC
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
32 11 0.22
33 12 0.24
34 26 0.51
35 2 0.04
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (32 bp):
TTTATATAATTATTATTTTTTAAATTATAATA
Found at i:55382 original size:17 final size:17
Alignment explanation
Indices: 55360--55413 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
55350 AATGTTAATA
55360 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
55377 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
55394 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
55411 TTT
1 TTT
55414 TTATATGTAT
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:57017 original size:21 final size:21
Alignment explanation
Indices: 56991--57084 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
56981 TATGCCATCT
* *
56991 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
57012 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
*
57033 CCGCCA-GGTTACATGCCTATC
1 CCG-CAGGGTTACATGCCTAGC
57054 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
57075 CCGCAGGGTT
1 CCGCAGGGTT
57085 TTATACCATA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
20 2 0.03
21 63 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.26, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:57666 original size:33 final size:33
Alignment explanation
Indices: 57607--57703 Score: 106
Period size: 33 Copynumber: 2.9 Consensus size: 33
57597 AAATGTTTTT
* *
57607 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATA-AAAATATATTATTCAAAATTTAAAATA
* *
57641 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAAT-ATATTATTCAAAATTTAAAATA
* *
57674 AAAATATAAAGTATAGTATTCAAAATTTAA
1 AAAATA-AAAATATATTATTCAAAATTTAA
57704 CATTAAATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (33 bp):
AAAATAAAAATATATTATTCAAAATTTAAAATA
Found at i:57710 original size:34 final size:31
Alignment explanation
Indices: 57605--57710 Score: 104
Period size: 34 Copynumber: 3.2 Consensus size: 31
57595 GTAAATGTTT
*
57605 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATA-AAAATATATTATTC-AAATTT-AAA
*
57639 TAAAAATAAAAATAATATTATTCAAATTTAAA
1 TTAAAATAAAAAT-ATATTATTCAAATTTAAA
* *
57671 TTTAAAATATAAAGTATAGTATTCAAAATTTAACA
1 -TTAAAATA-AAAATATATTATTC-AAATTTAA-A
57706 TTAAA
1 TTAAA
57711 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.37
Consensus pattern (31 bp):
TTAAAATAAAAATATATTATTCAAATTTAAA
Found at i:58335 original size:128 final size:128
Alignment explanation
Indices: 58104--58859 Score: 1478
Period size: 128 Copynumber: 5.9 Consensus size: 128
58094 TTACCTGATT
58104 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
58169 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACACGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
58232 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
58297 TGACGAAATAATGGAAGGCGCACCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
58360 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
58425 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
58488 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
58553 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
58616 TACTGATATATCTAGTGT-CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
58680 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
58743 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
58808 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGTGCCTTCATGTGAATAGT
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
58860 ACTCCGATTA
Statistics
Matches: 623, Mismatches: 4, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
127 127 0.20
128 496 0.80
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:58943 original size:8 final size:8
Alignment explanation
Indices: 58930--58970 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
58920 TCACAATCTT
58930 TCAAATTC
1 TCAAATTC
58938 TCAAATTC
1 TCAAATTC
* *
58946 CCAAACTC
1 TCAAATTC
58954 T-AAATTC
1 TCAAATTC
58961 TCAAATTC
1 TCAAATTC
58969 TC
1 TC
58971 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:66993 original size:54 final size:54
Alignment explanation
Indices: 66926--67028 Score: 134
Period size: 54 Copynumber: 1.9 Consensus size: 54
66916 ATCATATTCG
* * * *
66926 TATGTCCTCGGTGGCGGTGACCGGGAGTCATCTCGTCCACCATATCTATCATCA
1 TATGGCCTCGGTGGCGGTGACCGGAAATCATCTCGTCCACCAAATCTATCATCA
* * * *
66980 TATGGCCTCGGTGGTGGTGATCGGAAATTATCTTGTCCACCAAATCTAT
1 TATGGCCTCGGTGGCGGTGACCGGAAATCATCTCGTCCACCAAATCTAT
67029 TAACATTACC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 41 1.00
ACGTcount: A:0.20, C:0.25, G:0.24, T:0.30
Consensus pattern (54 bp):
TATGGCCTCGGTGGCGGTGACCGGAAATCATCTCGTCCACCAAATCTATCATCA
Found at i:73339 original size:22 final size:24
Alignment explanation
Indices: 73294--73339 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
73284 ATAACATTTT
*
73294 TTATTATAATGACGAAATGGAATAC
1 TTATTATAATGACGAAA-GAAATAC
73319 TTATTATAATGAC-AAA-AAATA
1 TTATTATAATGACGAAAGAAATA
73340 ATGATACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
24 3 0.15
25 13 0.65
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.33
Consensus pattern (24 bp):
TTATTATAATGACGAAAGAAATAC
Found at i:73483 original size:27 final size:27
Alignment explanation
Indices: 73438--73489 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
73428 TGTTGACGCT
* * *
73438 ATATTTTAATTAATATGATTAATATCA
1 ATATTTGAATAAATATGATGAATATCA
*
73465 ATATTTGAATAAATGTGATGAATAT
1 ATATTTGAATAAATATGATGAATAT
73490 TAATTCAACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (27 bp):
ATATTTGAATAAATATGATGAATATCA
Found at i:74128 original size:97 final size:103
Alignment explanation
Indices: 73953--74139 Score: 260
Period size: 97 Copynumber: 1.9 Consensus size: 103
73943 AAAATATGTT
* *
73953 AAATCAAAATAAATAGTCTAATTAATTTATATTTACAATAAAAAATAAAACATTAAAATTTAAAC
1 AAATCAAAATAAATAGTCCAATTAATTTATATTTACAACAAAAAATAAAACATTAAAATTTAAAC
*
74018 TAAATTTACCAAACCACTCAAATACGATTTAATCTGTA
66 TAAACTTACCAAACCACTCAAATACGATTTAATCTGTA
* * * *
74056 AAATCAAGATAAATAGTCCAA-TAATTTATA-TTAC-CCAATAAA-AAAA-A-TATAATTTAAAC
1 AAATCAAAATAAATAGTCCAATTAATTTATATTTACAACAAAAAATAAAACATTAAAATTTAAAC
*
74115 TAAACTTACCAAACTACTCAAATAC
66 TAAACTTACCAAACCACTCAAATAC
74140 AACTTAATAT
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
97 34 0.45
98 1 0.01
99 4 0.05
100 5 0.07
101 4 0.05
102 9 0.12
103 19 0.25
ACGTcount: A:0.53, C:0.14, G:0.03, T:0.30
Consensus pattern (103 bp):
AAATCAAAATAAATAGTCCAATTAATTTATATTTACAACAAAAAATAAAACATTAAAATTTAAAC
TAAACTTACCAAACCACTCAAATACGATTTAATCTGTA
Found at i:74147 original size:97 final size:103
Alignment explanation
Indices: 73953--74160 Score: 259
Period size: 97 Copynumber: 2.1 Consensus size: 103
73943 AAAATATGTT
* *
73953 AAATCAAAATAAATAGTCTAATTAATTTATATTTACAATAAAAAATAAAACATTAAAATTTAAAC
1 AAATCAAAATAAATAGTCCAATTAATTTATATTTACAACAAAAAATAAAACATTAAAATTTAAAC
* * *
74018 TAAATTTACCAAACCACTCAAATACGATTTAATCTGTA
66 TAAACTTACCAAACCACTCAAATACAACTTAATCTGTA
* * * *
74056 AAATCAAGATAAATAGTCCAA-TAATTTATA-TTAC-CCAATAAA-AAAA-A-TATAATTTAAAC
1 AAATCAAAATAAATAGTCCAATTAATTTATATTTACAACAAAAAATAAAACATTAAAATTTAAAC
* *
74115 TAAACTTACCAAACTACTCAAATACAACTTAATATG-A
66 TAAACTTACCAAACCACTCAAATACAACTTAATCTGTA
74152 ATAATCAAA
1 A-AATCAAA
74161 TGGGGAAAAT
Statistics
Matches: 92, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
96 2 0.02
97 48 0.52
98 1 0.01
99 4 0.04
100 5 0.05
101 4 0.04
102 9 0.10
103 19 0.21
ACGTcount: A:0.53, C:0.14, G:0.03, T:0.30
Consensus pattern (103 bp):
AAATCAAAATAAATAGTCCAATTAATTTATATTTACAACAAAAAATAAAACATTAAAATTTAAAC
TAAACTTACCAAACCACTCAAATACAACTTAATCTGTA
Found at i:77215 original size:16 final size:16
Alignment explanation
Indices: 77179--77262 Score: 64
Period size: 16 Copynumber: 5.3 Consensus size: 16
77169 CGAAAACCAT
* *
77179 CCGAACCGAAAGTAAC
1 CCGAACCAAAAGCAAC
* *
77195 ACGAACCAATAGCAAC
1 CCGAACCAAAAGCAAC
*
77211 CCGAACCAAAATCAAC
1 CCGAACCAAAAGCAAC
* * *
77227 CTGAACCGAAATC-AC
1 CCGAACCAAAAGCAAC
*
77242 CCAAACCGAAAA-CAAC
1 CCGAACC-AAAAGCAAC
77258 CCGAA
1 CCGAA
77263 TTTAATTTAC
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
15 8 0.15
16 45 0.85
ACGTcount: A:0.48, C:0.35, G:0.12, T:0.06
Consensus pattern (16 bp):
CCGAACCAAAAGCAAC
Found at i:80513 original size:3 final size:3
Alignment explanation
Indices: 80505--80584 Score: 160
Period size: 3 Copynumber: 26.7 Consensus size: 3
80495 TGCATTGATC
80505 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
80553 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
80585 CTTTTCCTGT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:83894 original size:71 final size:71
Alignment explanation
Indices: 83778--83921 Score: 288
Period size: 71 Copynumber: 2.0 Consensus size: 71
83768 TACGTACTCC
83778 AATGAACATCATCTAGTTTCCTTTTGCAAAATTATACGAAATGTAAAAGGTAATTACAAATTAAA
1 AATGAACATCATCTAGTTTCCTTTTGCAAAATTATACGAAATGTAAAAGGTAATTACAAATTAAA
83843 AGTAGA
66 AGTAGA
83849 AATGAACATCATCTAGTTTCCTTTTGCAAAATTATACGAAATGTAAAAGGTAATTACAAATTAAA
1 AATGAACATCATCTAGTTTCCTTTTGCAAAATTATACGAAATGTAAAAGGTAATTACAAATTAAA
83914 AGTAGA
66 AGTAGA
83920 AA
1 AA
83922 ATAGCTTAAT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (71 bp):
AATGAACATCATCTAGTTTCCTTTTGCAAAATTATACGAAATGTAAAAGGTAATTACAAATTAAA
AGTAGA
Found at i:97544 original size:2 final size:2
Alignment explanation
Indices: 97537--97572 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
97527 CTTGTTCTCT
97537 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
97573 ATAATAATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:99117 original size:26 final size:26
Alignment explanation
Indices: 99087--99158 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 26
99077 AATTGTTACC
* *
99087 ATATAATTATCCTAGAACAATTGGAAA
1 ATATAATCACCCTAGAACAATT-GAAA
*
99114 TATAAAATCACCCTAGAACAATTGAAA
1 -ATATAATCACCCTAGAACAATTGAAA
99141 ATATAAAATCACCCTAGA
1 ATAT--AATCACCCTAGA
99159 TGTGTCCTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 3 0.08
27 4 0.11
28 31 0.82
ACGTcount: A:0.50, C:0.17, G:0.08, T:0.25
Consensus pattern (26 bp):
ATATAATCACCCTAGAACAATTGAAA
Found at i:99128 original size:28 final size:28
Alignment explanation
Indices: 99097--99158 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
99087 ATATAATTAT
*
99097 CCTAGAACAATTGGAAATATAAAATCAC
1 CCTAGAACAATTGAAAATATAAAATCAC
99125 CCTAGAACAATTGAAAATATAAAATCAC
1 CCTAGAACAATTGAAAATATAAAATCAC
99153 CCTAGA
1 CCTAGA
99159 TGTGTCCTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.50, C:0.19, G:0.10, T:0.21
Consensus pattern (28 bp):
CCTAGAACAATTGAAAATATAAAATCAC
Found at i:104023 original size:34 final size:34
Alignment explanation
Indices: 103953--104019 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 34
103943 TTTTTATATT
*
103953 TTTAATTTTGTAAAAAAATTATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATAAATATTATAAA
* *
103987 TTTAATTTT-TAAATAAA-TATATAATATTTTAAA
1 TTTAATTTTGTAAAAAAATTATA-AATATTATAAA
104020 ATTTGTAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
32 4 0.14
33 16 0.55
34 9 0.31
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (34 bp):
TTTAATTTTGTAAAAAAATTATAAATATTATAAA
Found at i:104045 original size:17 final size:17
Alignment explanation
Indices: 104001--104046 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
103991 ATTTTTAAAT
*
104001 AAATATATAATATTTTA
1 AAATATATAATATTATA
* *
104018 AAATTTGTAATATTATA
1 AAATATATAATATTATA
*
104035 CAATATATAATA
1 AAATATATAATA
104047 AGGACAATTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (17 bp):
AAATATATAATATTATA
Found at i:104192 original size:20 final size:20
Alignment explanation
Indices: 104167--104224 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
104157 ATCATATTCC
**
104167 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
104187 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
104207 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
104225 GTGAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.22, C:0.28, G:0.10, T:0.40
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Done.