Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003153.1 Hibiscus syriacus cultivar Beakdansim tig00006628_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: 80959
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3633 original size:253 final size:254
Alignment explanation
Indices: 3245--3733 Score: 713
Period size: 253 Copynumber: 1.9 Consensus size: 254
3235 CGGGTCGATC
* *
3245 GGTGAAACTTTATTTTAGTCGTCGGGTCGGTTTTTTTTAAGTGTGATATTCGGGTCGAGTTCGGG
1 GGTGAAACTTTATTTTAGTCGTCGGGTCGATTTTTTTTAAGTGTGATATTAGGGTCGAGTTCGGG
* ** *
3310 TTTAGGGTGAAAAACCATACCCGACCCGAAATGTATATAATTTTACCTTATATATATGAATAATT
66 TTTAGGGTGAAAAACCACACCCGACCCGAAATAAATATAAGTTTACCTTATATATATGAATAATT
3375 ACAATAATACCCCTCTATATATAATTTTTTCAATTAAGTCACTGTTTTTATTAAATAAAAATA-A
131 ACAATAATACCCCTCTATATATAATTTTTTCAATTAAGTCACTGTTTTTATTAAATAAAAATACA
*
3439 TTTTTTATTATTTCGGGTCGGGTCTCTAATTCATATATTCGGGTCGGTCAGATCGGTAG
196 TTTTTTATTATTTCGGGTCGAGTCTCTAATTCATATATTCGGGTCGGTCAGATCGGTAG
* * *
3498 GGTGAAACTTTA-TTTGGTCGGGTCGGGT-TATTTTTTTTAAGTGTGATATTAGGGTCGGGTTCG
1 GGTGAAACTTTATTTTAGTC--GTCGGGTCGATTTTTTTTAAGTGTGATATTAGGGTCGAGTTCG
* * * *
3561 GTTTTTAGGGTGAAATACACACCCACCCGGCCCGAAA-AAATATAAGTTTACCTTATATTTA-GA
64 G-GTTTAGGGTGAAA-A-AC-CACACCCGACCCGAAATAAATATAAGTTTACCTTATATATATGA
*
3624 A-AA-TACAATAATACCCCTCTATATATAATTTTTTCAATTAAGTCACTGTTTTTATTGAATAAA
125 ATAATTACAATAATACCCCTCTATATATAATTTTTTCAATTAAGTCACTGTTTTTATTAAATAAA
* *
3687 AATACTTTTTTTTATTATTTCGGGTCGAGTTTCTAATTCATATATTC
190 AATAC-ATTTTTTATTATTTCGGGTCGAGTCTCTAATTCATATATTC
3734 AAGTTGGGTC
Statistics
Matches: 211, Mismatches: 17, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
252 6 0.03
253 107 0.51
254 21 0.10
255 42 0.20
256 22 0.10
257 13 0.06
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (254 bp):
GGTGAAACTTTATTTTAGTCGTCGGGTCGATTTTTTTTAAGTGTGATATTAGGGTCGAGTTCGGG
TTTAGGGTGAAAAACCACACCCGACCCGAAATAAATATAAGTTTACCTTATATATATGAATAATT
ACAATAATACCCCTCTATATATAATTTTTTCAATTAAGTCACTGTTTTTATTAAATAAAAATACA
TTTTTTATTATTTCGGGTCGAGTCTCTAATTCATATATTCGGGTCGGTCAGATCGGTAG
Found at i:4146 original size:17 final size:17
Alignment explanation
Indices: 4126--4164 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
4116 AATTCCTGAT
4126 AGATTTCATTCATTCAC
1 AGATTTCATTCATTCAC
* *
4143 AGATTTCATTCCTTCAT
1 AGATTTCATTCATTCAC
4160 AGATT
1 AGATT
4165 CCAATTCTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.44
Consensus pattern (17 bp):
AGATTTCATTCATTCAC
Found at i:9026 original size:29 final size:29
Alignment explanation
Indices: 8973--9028 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
8963 TCCCAACACA
*
8973 TAGGTCGCCATGCCCTTCAGACGACCTTG
1 TAGGTCGCCATGCCCTCCAGACGACCTTG
* * *
9002 TAGGTCGCCATGCTCTCCGGGCGACCT
1 TAGGTCGCCATGCCCTCCAGACGACCT
9029 ACCCTTGCTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.14, C:0.36, G:0.27, T:0.23
Consensus pattern (29 bp):
TAGGTCGCCATGCCCTCCAGACGACCTTG
Found at i:9065 original size:23 final size:23
Alignment explanation
Indices: 9039--9103 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
9029 ACCCTTGCTC
9039 GCTCGCTCGGATGCCCTCGCATA
1 GCTCGCTCGGATGCCCTCGCATA
9062 GCTCGCTCGGATGCCCTCGCATA
1 GCTCGCTCGGATGCCCTCGCATA
* *
9085 GCTCGCTCGGCTACCCTCG
1 GCTCGCTCGGATGCCCTCG
9104 GATTCCCTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.11, C:0.42, G:0.26, T:0.22
Consensus pattern (23 bp):
GCTCGCTCGGATGCCCTCGCATA
Found at i:9104 original size:33 final size:33
Alignment explanation
Indices: 9067--9174 Score: 92
Period size: 33 Copynumber: 3.2 Consensus size: 33
9057 GCATAGCTCG
*
9067 CTCGGATGCCCTCGCATAGCTCGCTCGGCTACC
1 CTCGGATGCCCTCGCATAGCTCGCTCGGATACC
* * * **
9100 CTCGGATTCCCTTGGATAGC-CGCGGTCGGATGGC
1 CTCGGATGCCCTCGCATAGCTCGC--TCGGATACC
* * * **
9134 TTCGGATGCTCTCGCATAGCTCGGTCGGATGGC
1 CTCGGATGCCCTCGCATAGCTCGCTCGGATACC
9167 CTCGGATG
1 CTCGGATG
9175 TCCAGCGTGT
Statistics
Matches: 59, Mismatches: 13, Indels: 6
0.76 0.17 0.08
Matches are distributed among these distances:
32 3 0.05
33 33 0.56
34 21 0.36
35 2 0.03
ACGTcount: A:0.12, C:0.32, G:0.31, T:0.24
Consensus pattern (33 bp):
CTCGGATGCCCTCGCATAGCTCGCTCGGATACC
Found at i:19584 original size:12 final size:12
Alignment explanation
Indices: 19567--19591 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19557 GGCCTCTAAG
19567 ATAAGATTTTTA
1 ATAAGATTTTTA
19579 ATAAGATTTTTA
1 ATAAGATTTTTA
19591 A
1 A
19592 GAATGAGATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
ATAAGATTTTTA
Found at i:25149 original size:43 final size:43
Alignment explanation
Indices: 25088--25189 Score: 120
Period size: 43 Copynumber: 2.4 Consensus size: 43
25078 TATTTGCATA
* *
25088 GAAGACGTCGAGCA-ATCCAAGT-TTGTATGGAAATTTTT-TGAAT
1 GAAGACGTCGAG-AGATCCAA-TAATGCATGGAAATTTTTGTG-AT
* *
25131 GAAGACGTCGAGAGATCCAATAATGCATGTAAATTTTTGTGCT
1 GAAGACGTCGAGAGATCCAATAATGCATGGAAATTTTTGTGAT
25174 GAAGACGTCGAGAGAT
1 GAAGACGTCGAGAGAT
25190 TCTTTGAACG
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
42 2 0.04
43 48 0.92
44 2 0.04
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.28
Consensus pattern (43 bp):
GAAGACGTCGAGAGATCCAATAATGCATGGAAATTTTTGTGAT
Found at i:27718 original size:21 final size:21
Alignment explanation
Indices: 27679--27723 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
27669 ACTGTCTTGG
27679 AAAGTTTCAAAAATCTTG-TA
1 AAAGTTTCAAAAATCTTGTTA
**
27699 AAAGTTTCGAAACTTCTTGTTA
1 AAAGTTTC-AAAAATCTTGTTA
27721 AAA
1 AAA
27724 TACTCATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
21 8 0.38
22 5 0.24
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (21 bp):
AAAGTTTCAAAAATCTTGTTA
Found at i:28010 original size:27 final size:27
Alignment explanation
Indices: 27972--28026 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
27962 GATAAATAAG
*
27972 AATGAATATAAAATAGTATAGGTTTAA
1 AATGAATATAAAATAGTATACGTTTAA
27999 AATGAATATAAAATAGTATACGTTTAA
1 AATGAATATAAAATAGTATACGTTTAA
28026 A
1 A
28027 TATTCTCAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.53, C:0.02, G:0.13, T:0.33
Consensus pattern (27 bp):
AATGAATATAAAATAGTATACGTTTAA
Found at i:28229 original size:32 final size:33
Alignment explanation
Indices: 28181--28256 Score: 118
Period size: 32 Copynumber: 2.3 Consensus size: 33
28171 TTATTTTGAT
*
28181 TTTGTCCCTCTCATTTTCTATGATTAATTATAC
1 TTTGTCCCCCTCATTTTCTATGATTAATTATAC
* *
28214 TTTG-CCCCCTCATTTTTTATGATTAATTATAT
1 TTTGTCCCCCTCATTTTCTATGATTAATTATAC
28246 TTTGTCCCCCT
1 TTTGTCCCCCT
28257 TAAGTTGGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
32 29 0.74
33 10 0.26
ACGTcount: A:0.18, C:0.24, G:0.07, T:0.51
Consensus pattern (33 bp):
TTTGTCCCCCTCATTTTCTATGATTAATTATAC
Found at i:29729 original size:3 final size:3
Alignment explanation
Indices: 29723--29763 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
29713 TAATAATAAC
29723 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
29764 ATATAATACG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:30529 original size:179 final size:181
Alignment explanation
Indices: 30224--30580 Score: 589
Period size: 179 Copynumber: 2.0 Consensus size: 181
30214 AAAATTAAAT
* * *
30224 ATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAATTTT
1 ATTTTTTAATTCAAAAAAAGTTTACAAATAATTTAAATAATATATAATTATAAAATAAAAAATTT
30289 AGATAATTTTTTTAATTAATTAATATTAATTTAAGTTTAAAAGTTATTGGATCTTAAATTATTAA
66 AGATAATTTTTTTAATTAATTAATATTAATTTAAGTTTAAAAGTTATTGGATCTTAAATTATTAA
* *
30354 TTGGGTTTTAAATGGTTTGGGCTT-AG-CTCATATGTTATATAT-ATATAATA
131 TTAGGTTTTAAATGATTTGGG-TTGAGTC-CATATGTTATATATAATATAATA
30404 ATTTTTTAATT-AAAAAACAGTTTACAAATAATTTAAATAATATATAATTATAAAATAAAAAATT
1 ATTTTTTAATTCAAAAAA-AGTTTACAAATAATTTAAATAATATATAATTATAAAATAAAAAATT
* *
30468 TATATAA-TTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATCTTAAATTATTA
65 TAGATAATTTTTTTAATTAATTAATATTAATTTAAGTTTAAAAGTTATTGGATCTTAAATTATTA
30532 ATTAGGTTTTAAATGATTTGGGTTGAGTCCATATGTTATATATAATATA
130 ATTAGGTTTTAAATGATTTGGGTTGAGTCCATATGTTATATATAATATA
30581 TTTAATATTT
Statistics
Matches: 166, Mismatches: 7, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
178 2 0.01
179 98 0.59
180 66 0.40
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.46
Consensus pattern (181 bp):
ATTTTTTAATTCAAAAAAAGTTTACAAATAATTTAAATAATATATAATTATAAAATAAAAAATTT
AGATAATTTTTTTAATTAATTAATATTAATTTAAGTTTAAAAGTTATTGGATCTTAAATTATTAA
TTAGGTTTTAAATGATTTGGGTTGAGTCCATATGTTATATATAATATAATA
Found at i:31367 original size:23 final size:24
Alignment explanation
Indices: 31326--31371 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
31316 ATTGTGTTAC
* *
31326 ATAAAATATATCAATTAAATTATA
1 ATAAAATATATAAAATAAATTATA
31350 ATAAAA-ATATAAAATAAATTAT
1 ATAAAATATATAAAATAAATTAT
31372 TAAGTAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
ATAAAATATATAAAATAAATTATA
Found at i:31391 original size:28 final size:29
Alignment explanation
Indices: 31360--31415 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
31350 ATAAAAATAT
* *
31360 AAAATAAATTATTAAGTAAT-AATTATTA
1 AAAATAAATTACTAAATAATAAATTATTA
*
31388 AAAATACATTACTAAATAATAAATTATT
1 AAAATAAATTACTAAATAATAAATTATT
31416 TTTTAATGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (29 bp):
AAAATAAATTACTAAATAATAAATTATTA
Found at i:32408 original size:22 final size:22
Alignment explanation
Indices: 32383--32427 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
32373 CATGGTAGGT
*
32383 GGGATTCGTATATATATAATAA
1 GGGATTAGTATATATATAATAA
32405 GGGATTAGTATATATATAATAA
1 GGGATTAGTATATATATAATAA
32427 G
1 G
32428 CAAATGGGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.42, C:0.02, G:0.20, T:0.36
Consensus pattern (22 bp):
GGGATTAGTATATATATAATAA
Found at i:43675 original size:16 final size:16
Alignment explanation
Indices: 43654--43693 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
43644 TGTTTTAGTC
*
43654 TCTTATTACTCAATCT
1 TCTTATCACTCAATCT
*
43670 TCTTATCATTCAATCT
1 TCTTATCACTCAATCT
43686 TCTTATCA
1 TCTTATCA
43694 TTCCATCTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (16 bp):
TCTTATCACTCAATCT
Found at i:43694 original size:16 final size:16
Alignment explanation
Indices: 43663--43701 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
43653 CTCTTATTAC
43663 TCAATCTTCTTATCAT
1 TCAATCTTCTTATCAT
43679 TCAATCTTCTTATCAT
1 TCAATCTTCTTATCAT
*
43695 TCCATCT
1 TCAATCT
43702 GACATGCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.49
Consensus pattern (16 bp):
TCAATCTTCTTATCAT
Found at i:44131 original size:66 final size:66
Alignment explanation
Indices: 44025--44158 Score: 268
Period size: 66 Copynumber: 2.0 Consensus size: 66
44015 AAGACGAGAC
44025 AGATCGTGAGCTACTCAAGATTGATTAGTTCAAAATTCGATAAATAATCTATTCAAGTTCTTAAC
1 AGATCGTGAGCTACTCAAGATTGATTAGTTCAAAATTCGATAAATAATCTATTCAAGTTCTTAAC
44090 G
66 G
44091 AGATCGTGAGCTACTCAAGATTGATTAGTTCAAAATTCGATAAATAATCTATTCAAGTTCTTAAC
1 AGATCGTGAGCTACTCAAGATTGATTAGTTCAAAATTCGATAAATAATCTATTCAAGTTCTTAAC
44156 G
66 G
44157 AG
1 AG
44159 CTAAAACAAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.33
Consensus pattern (66 bp):
AGATCGTGAGCTACTCAAGATTGATTAGTTCAAAATTCGATAAATAATCTATTCAAGTTCTTAAC
G
Found at i:54489 original size:14 final size:13
Alignment explanation
Indices: 54456--54489 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
54446 CATAGTTGAA
*
54456 CAGTCTTCATATG
1 CAGTCTACATATG
54469 CAGTCTACATATG
1 CAGTCTACATATG
54482 CGAGTCTA
1 C-AGTCTA
54490 TAATGGGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (13 bp):
CAGTCTACATATG
Found at i:56949 original size:32 final size:32
Alignment explanation
Indices: 56913--57005 Score: 107
Period size: 31 Copynumber: 2.9 Consensus size: 32
56903 ATAAAATAGT
*
56913 CATTAAATTTTATCAAACTAGTACAAAATGAC
1 CATTAAACTTTATCAAACTAGTACAAAATGAC
* ** * * * *
56945 CATTAAGC-TTATTGAACCACTATAGAATGAC
1 CATTAAACTTTATCAAACTAGTACAAAATGAC
56976 CATTAAACTTTATCAAACTAGTACAAAATG
1 CATTAAACTTTATCAAACTAGTACAAAATG
57006 GTCGTTGAAT
Statistics
Matches: 45, Mismatches: 15, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
31 24 0.53
32 21 0.47
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.30
Consensus pattern (32 bp):
CATTAAACTTTATCAAACTAGTACAAAATGAC
Found at i:63694 original size:2 final size:2
Alignment explanation
Indices: 63687--63713 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
63677 TAATTTTTCG
63687 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
63714 GGGATTTGGA
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:65715 original size:110 final size:111
Alignment explanation
Indices: 65393--65901 Score: 745
Period size: 112 Copynumber: 4.6 Consensus size: 111
65383 TTGTCGGTTT
* * * * *
65393 GTGTTGATACATTATAAAAATATATTGATCAATAACAATATAACAGGTAAAAAAATGACAAAATC
1 GTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACAGGTAAAAAAATGACAAACT-
* * *
65458 GGTCTATAAATGACAAAACAGATAAAGCGCTATCAGATATATTAAAA
65 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
* *
65505 GTGTCGATACTTTATAAAAATATATATTGATCTATAACAATATAACAGGT-AAAAAATGACAAAA
1 GTGTCGATACTTTAT-AAAA-ATGTATTGATCCATAACAATATAACAGGTAAAAAAATGAC-AAA
* *
65569 CTGGTCTATAAATGACAAAACAGGTAAAGCGTTACCGGATATATTGAAA
63 CTGGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
* * *
65618 GTGTCCATACTTTATAAAAATGTATCGATCCATAGCAATATAACAGGTAAAAAAATGAC-AACTG
1 GTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACAGGTAAAAAAATGACAAACTG
* * * *
65682 GTCTACAAATGACAAAATAGGTAAAGCACTACCGGATATATTGAAA
66 GTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
* * *
65728 GTGTCGATACTTTATAAAAATGTATCGATCTATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACAGGTAAAAAAATGAC-AAACT
*
65793 GGTCTATAAATGACAAAACAAGTAAAGCGCTACCAGATATATTGAAA
65 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
65840 GTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACAGGT-AAAAAATGACAAAC
1 GTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACAGGTAAAAAAATGACAAAC
65902 CGATAAAGAG
Statistics
Matches: 362, Mismatches: 29, Indels: 14
0.89 0.07 0.03
Matches are distributed among these distances:
110 107 0.30
111 35 0.10
112 118 0.33
113 70 0.19
114 32 0.09
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.26
Consensus pattern (111 bp):
GTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACAGGTAAAAAAATGACAAACTG
GTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
Found at i:66488 original size:20 final size:20
Alignment explanation
Indices: 66460--66498 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
66450 GAAATAATAA
*
66460 TTATTATGTAACAGGTAAAT
1 TTATAATGTAACAGGTAAAT
*
66480 TTATAATGTAACCGGTAAA
1 TTATAATGTAACAGGTAAA
66499 AATATACTGG
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:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (20 bp):
TTATAATGTAACAGGTAAAT
Found at i:66504 original size:20 final size:20
Alignment explanation
Indices: 66465--66504 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
66455 AATAATTATT
**
66465 ATGTAACAGGTAAATTTATA
1 ATGTAACAGGTAAAAATATA
*
66485 ATGTAACCGGTAAAAATATA
1 ATGTAACAGGTAAAAATATA
66505 CTGGTTAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (20 bp):
ATGTAACAGGTAAAAATATA
Found at i:66759 original size:23 final size:23
Alignment explanation
Indices: 66729--66774 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
66719 ATATGTCAAA
*
66729 ATAAGCGCTACCTATTACATTAT
1 ATAAGCGCTACCTAATACATTAT
*
66752 ATAAGCGCTACCTAATATATTAT
1 ATAAGCGCTACCTAATACATTAT
66775 TGTACTTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.35
Consensus pattern (23 bp):
ATAAGCGCTACCTAATACATTAT
Found at i:67270 original size:18 final size:18
Alignment explanation
Indices: 67247--67281 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
67237 AGTATTGTCT
67247 ATTAAAAGTATTATTGAG
1 ATTAAAAGTATTATTGAG
*
67265 ATTAAAAGTATTCTTGA
1 ATTAAAAGTATTATTGA
67282 AATTTGGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.14, T:0.40
Consensus pattern (18 bp):
ATTAAAAGTATTATTGAG
Found at i:75949 original size:11 final size:11
Alignment explanation
Indices: 75935--75973 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
75925 ATTTAATAAA
75935 TTAATAATTAT
1 TTAATAATTAT
75946 TTAATAATT-T
1 TTAATAATTAT
75956 TT-A-AA-TAT
1 TTAATAATTAT
75964 TTAATAATTA
1 TTAATAATTA
75974 AATATTTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
7 1 0.04
8 5 0.21
9 2 0.08
10 5 0.21
11 11 0.46
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TTAATAATTAT
Found at i:76288 original size:50 final size:51
Alignment explanation
Indices: 76166--76290 Score: 171
Period size: 51 Copynumber: 2.5 Consensus size: 51
76156 GCAGTAAAGA
* **
76166 GCGCCCTCTGCACCGCGCTATACGATGATTTGGCGCCACGTGGAGTATAGC
1 GCGCCCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGAGTATAGC
* *
76217 GCGCCCCCTGCACCGCACTATACGGTGAGCTGGCGCCACGTGG-GTATAGC
1 GCGCCCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGAGTATAGC
** *
76267 GCGGTCCCTGCAGCGCGCTATACG
1 GCGCCCCCTGCACCGCGCTATACG
76291 CCACGTAGGG
Statistics
Matches: 65, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 27 0.42
51 38 0.58
ACGTcount: A:0.16, C:0.34, G:0.31, T:0.18
Consensus pattern (51 bp):
GCGCCCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGAGTATAGC
Found at i:77911 original size:110 final size:111
Alignment explanation
Indices: 77710--77922 Score: 374
Period size: 110 Copynumber: 1.9 Consensus size: 111
77700 ATTACAAAAA
* * *
77710 TTAATTCTTAATCTAATAATCATGTATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
77775 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTCGAGATAT
77821 TTAATTCTTAATCTAATAATCATGCATTAAATAAAT-AACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* *
77885 AATTAAAACGTTAAAATGTTATCGTATCAGCAAAGTGT
66 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGT
77923 AGATATATAT
Statistics
Matches: 97, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
110 63 0.65
111 34 0.35
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:78037 original size:16 final size:16
Alignment explanation
Indices: 77984--78037 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
77974 CTGCAAAAGA
*
77984 ATTATATTAGTAAAAT
1 ATTATAATAGTAAAAT
78000 ATTA-AATAAAGTAAAA-
1 ATTATAAT--AGTAAAAT
*
78016 A-CATAATAGTAAAAT
1 ATTATAATAGTAAAAT
78031 ATTATAA
1 ATTATAA
78038 AATACCTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
14 7 0.23
15 4 0.13
16 12 0.40
17 7 0.23
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (16 bp):
ATTATAATAGTAAAAT
Found at i:78288 original size:51 final size:50
Alignment explanation
Indices: 78184--78307 Score: 185
Period size: 51 Copynumber: 2.5 Consensus size: 50
78174 AGATATACAA
* * * **
78184 GTATAGCGCGCTGCAGGGGCCGCGCTATACCCACGTGGCGCCAGCTCACC
1 GTATAGCGCGGTGCAGGGGGCGCGCTATACCCACGTGGCACCAAATCACC
*
78234 GTATAGCGCGGTGCAGGGGGCGCGCTATACCTCACGTGGCACCAAATCATC
1 GTATAGCGCGGTGCAGGGGGCGCGCTATACC-CACGTGGCACCAAATCACC
78285 GTATAGCGCGGTGCAGGGGGCGC
1 GTATAGCGCGGTGCAGGGGGCGC
78308 TTTATTGCTA
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 29 0.43
51 38 0.57
ACGTcount: A:0.18, C:0.31, G:0.35, T:0.15
Consensus pattern (50 bp):
GTATAGCGCGGTGCAGGGGGCGCGCTATACCCACGTGGCACCAAATCACC
Found at i:80300 original size:194 final size:192
Alignment explanation
Indices: 79974--80359 Score: 677
Period size: 194 Copynumber: 2.0 Consensus size: 192
79964 GGTCAATTTG
79974 AACAATCTCGTAATACTCTTCTTCGCTACCCGGGCAAAGAAGTGACAATAATGAACAAGTCAACA
1 AACAATCTCGTAATACTCTTCTTCGCTACCCGGGCAAAGAAGTGACAATAATGAACAAGTCAACA
80039 TGGTACTTATTCATTCCCGCTCTACGAGATTGACAAGGATTTCCAAATGAACTGACAATAATTTT
66 TGGTACTTATTCATTCCCGCTCTACGAGATTGACAAGGATTTCCAAATGAACTGACAATAATTTT
* *
80104 TTGTTTGGAAACTTTGTTAGGTTGTTTCGAATAAG-CAATTGTCAAGCATCTGCAGAAAGAA
131 TTGTTTGGAAACTTTGTTAGGTTGTTTCGAATAAGTAAATTATCAAGCATCTGCAGAAAGAA
* * *
80165 AACAATCTCGTAATACTCTCTTCTTCGCTA-CCGGGGAAGGAAGTGACAAATAATGCACAAGTCA
1 AACAATCTCGTAATA--CTCTTCTTCGCTACCCGGGCAAAGAAGTGAC-AATAATGAACAAGTCA
80229 ACATGGTACTTACTTCATTCCCGCTCTACGAGATTGACAAGGATTTCCAAATGAACTGACAATAA
63 ACATGGTACTTA-TTCATTCCCGCTCTACGAGATTGACAAGGATTTCCAAATGAACTGACAATAA
80294 TTTTTTGTTTGGAAACTTTGTTAGGTTGTTTCGAATAAGTAAATTATCAAGCATCTGCAGAAAGA
127 TTTTTTGTTTGGAAACTTTGTTAGGTTGTTTCGAATAAGTAAATTATCAAGCATCTGCAGAAAGA
80359 A
192 A
80360 GTAGCAGGCT
Statistics
Matches: 185, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
191 15 0.08
192 15 0.08
193 40 0.22
194 91 0.49
195 24 0.13
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (192 bp):
AACAATCTCGTAATACTCTTCTTCGCTACCCGGGCAAAGAAGTGACAATAATGAACAAGTCAACA
TGGTACTTATTCATTCCCGCTCTACGAGATTGACAAGGATTTCCAAATGAACTGACAATAATTTT
TTGTTTGGAAACTTTGTTAGGTTGTTTCGAATAAGTAAATTATCAAGCATCTGCAGAAAGAA
Done.