Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012065.1 Corchorus capsularis cultivar CVL-1 contig12086, 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: 93409
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5161 original size:2 final size:2
Alignment explanation
Indices: 5154--5195 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5144 CCCTCTAATT
5154 TA TA TA 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 TA TA TA
5196 GTAATAGCAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10564 original size:59 final size:62
Alignment explanation
Indices: 10499--10776 Score: 388
Period size: 66 Copynumber: 4.5 Consensus size: 62
10489 TTGATGCGTT
10499 CGTCTCCCTCGAGACCGTTTTACCAAAATAAAAACGATCCTTGAATCGTAA-A-AA-ACGAA
1 CGTCTCCCTCGAGACCGTTTTACCAAAATAAAAACGATCCTTGAATCGTAATAGAAGACGAA
*
10558 CGTCTCCCTCGAGACCGTTTTACCAAAATAAAAACGATCCTTGAATCGTAACTTAGGTAAGACGG
1 CGTCTCCCTCGAGACCGTTTTACCAAAATAAAAACGATCCTTGAATCGTAA--TA-G-AAGACGA
10623 A
62 A
* * *
10624 TGTCTCCCTCGAGACCGTTTTACCAAAATCAAAACGATCCTTGAATCGTAACTTAGGTAAGACGG
1 CGTCTCCCTCGAGACCGTTTTACCAAAATAAAAACGATCCTTGAATCGTAA--TA-G-AAGACGA
10689 A
62 A
10690 CGTCTCCCTCGAGACCGTTTTACCAAAATAAAAACGATCCTTGAATCGTAA-A-AA-ACGAA
1 CGTCTCCCTCGAGACCGTTTTACCAAAATAAAAACGATCCTTGAATCGTAATAGAAGACGAA
* *
10749 CGTCTCCCTCGAGACCATTTTGCCAAAA
1 CGTCTCCCTCGAGACCGTTTTACCAAAA
10777 ATTGTACGAT
Statistics
Matches: 204, Mismatches: 8, Indels: 14
0.90 0.04 0.06
Matches are distributed among these distances:
59 81 0.40
60 2 0.01
62 1 0.00
63 1 0.00
65 2 0.01
66 117 0.57
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.24
Consensus pattern (62 bp):
CGTCTCCCTCGAGACCGTTTTACCAAAATAAAAACGATCCTTGAATCGTAATAGAAGACGAA
Found at i:14676 original size:20 final size:20
Alignment explanation
Indices: 14651--14693 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
14641 ACGAAGCGGG
14651 AAACCCGCTCGAACTCCAAA
1 AAACCCGCTCGAACTCCAAA
14671 AAACCCGCTCGAACTCCAAA
1 AAACCCGCTCGAACTCCAAA
14691 AAA
1 AAA
14694 TCCGAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.44, C:0.37, G:0.09, T:0.09
Consensus pattern (20 bp):
AAACCCGCTCGAACTCCAAA
Found at i:21456 original size:7 final size:7
Alignment explanation
Indices: 21439--21472 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
21429 TCAATCTTGT
21439 CAAAAAA
1 CAAAAAA
21446 -AAAAAA
1 CAAAAAA
21452 CAAAAAA
1 CAAAAAA
21459 CAAAAAA
1 CAAAAAA
21466 CAAAAAA
1 CAAAAAA
21473 AACAAAGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
CAAAAAA
Found at i:22843 original size:18 final size:19
Alignment explanation
Indices: 22820--22866 Score: 78
Period size: 18 Copynumber: 2.5 Consensus size: 19
22810 AAATTTAAAG
22820 GAAATTGTTAAACGAAG-A
1 GAAATTGTTAAACGAAGAA
22838 GAAATTGTTAAACGAAGAA
1 GAAATTGTTAAACGAAGAA
22857 GAAAATTGTT
1 G-AAATTGTT
22867 GAAATGTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 17 0.63
19 2 0.07
20 8 0.30
ACGTcount: A:0.49, C:0.04, G:0.21, T:0.26
Consensus pattern (19 bp):
GAAATTGTTAAACGAAGAA
Found at i:28306 original size:15 final size:15
Alignment explanation
Indices: 28286--28316 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28276 ATTCTCCCAC
28286 TTAATACACCACTGA
1 TTAATACACCACTGA
*
28301 TTAATACACTACTGA
1 TTAATACACCACTGA
28316 T
1 T
28317 AAGATCAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.23, G:0.06, T:0.32
Consensus pattern (15 bp):
TTAATACACCACTGA
Found at i:29887 original size:68 final size:68
Alignment explanation
Indices: 29778--29914 Score: 274
Period size: 68 Copynumber: 2.0 Consensus size: 68
29768 AAATGTTTCG
29778 AGATTTTCTCAAATAAGGATCAAAATACACAATTTCAACAAATTAGAATACATACTTAATATTTT
1 AGATTTTCTCAAATAAGGATCAAAATACACAATTTCAACAAATTAGAATACATACTTAATATTTT
29843 TTT
66 TTT
29846 AGATTTTCTCAAATAAGGATCAAAATACACAATTTCAACAAATTAGAATACATACTTAATATTTT
1 AGATTTTCTCAAATAAGGATCAAAATACACAATTTCAACAAATTAGAATACATACTTAATATTTT
29911 TTT
66 TTT
29914 A
1 A
29915 AGAATATAAG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.36
Consensus pattern (68 bp):
AGATTTTCTCAAATAAGGATCAAAATACACAATTTCAACAAATTAGAATACATACTTAATATTTT
TTT
Found at i:30319 original size:5 final size:5
Alignment explanation
Indices: 30309--30346 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
30299 GCAATAAACC
* *
30309 TTTCT TTTCT TTTCT TTTCG TTTCT TTTTT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
30347 ATACCCTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:30332 original size:20 final size:20
Alignment explanation
Indices: 30309--30346 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
30299 GCAATAAACC
30309 TTTCTTTTCTTTTCTTTTCG
1 TTTCTTTTCTTTTCTTTTCG
*
30329 TTTCTTTTTTTTTCTTTT
1 TTTCTTTTCTTTTCTTTT
30347 ATACCCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.82
Consensus pattern (20 bp):
TTTCTTTTCTTTTCTTTTCG
Found at i:31197 original size:3 final size:3
Alignment explanation
Indices: 31144--31184 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
31134 TTTTGGCACA
31144 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
31185 ATAACTTTAT
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:35301 original size:83 final size:85
Alignment explanation
Indices: 35130--35303 Score: 300
Period size: 83 Copynumber: 2.1 Consensus size: 85
35120 ATAAAAATTT
*
35130 GAAATCAATTAAATAAAAAAATAGTGTTTTCAGTTGCAAAAGTTTATTTTAAAAAAAATTGTAAA
1 GAAATCAATTAAAT-AAAAAATAGTGTTTTCAGTTGCAAAAATTTATTTTAAAAAAAATTGTAAA
35195 AGTTTAAACAATGTCATTCAA
65 AGTTTAAACAATGTCATTCAA
35216 GAAATCAATTAAAT-AAAAATAGT-TATTTCAGTTGCAAAAATTTATTTT-AAAAAAATTGTAAA
1 GAAATCAATTAAATAAAAAATAGTGT-TTTCAGTTGCAAAAATTTATTTTAAAAAAAATTGTAAA
35278 AGTTTAAACAATGTCATTCAA
65 AGTTTAAACAATGTCATTCAA
35299 GAAAT
1 GAAAT
35304 ATATTTTTAA
Statistics
Matches: 86, Mismatches: 1, Indels: 5
0.93 0.01 0.05
Matches are distributed among these distances:
83 41 0.48
84 31 0.36
86 14 0.16
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (85 bp):
GAAATCAATTAAATAAAAAATAGTGTTTTCAGTTGCAAAAATTTATTTTAAAAAAAATTGTAAAA
GTTTAAACAATGTCATTCAA
Found at i:35431 original size:70 final size:70
Alignment explanation
Indices: 35348--35502 Score: 215
Period size: 70 Copynumber: 2.2 Consensus size: 70
35338 TAATTAAAAT
* * * * *
35348 AGTAAAATGGTAAAATACAATAGTTATAAGGATATTAGATTTAATTATATAAACA-AAGAGTTTT
1 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAA-AGAAGAGTTTT
35412 TAGTTG
65 TAGTTG
* *
35418 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAGTAGAGTTTTT
1 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAGAAGAGTTTTT
35483 AGTTG
66 AGTTG
35488 AGTAAAACTA-TAAAA
1 AGTAAAA-TAGTAAAA
35503 ACCTAAACAA
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
69 1 0.01
70 73 0.96
71 2 0.03
ACGTcount: A:0.50, C:0.02, G:0.13, T:0.35
Consensus pattern (70 bp):
AGTAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAGAAGAGTTTTT
AGTTG
Found at i:36379 original size:6 final size:6
Alignment explanation
Indices: 36368--36402 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
36358 GAAAGAAAGG
36368 AATTAA AATTAA AATTAA AATTAA AATTAA AATTA
1 AATTAA AATTAA AATTAA AATTAA AATTAA AATTA
36403 TTATTAATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
AATTAA
Found at i:43988 original size:98 final size:98
Alignment explanation
Indices: 43882--44080 Score: 371
Period size: 98 Copynumber: 2.0 Consensus size: 98
43872 TCAGTCAAAC
43882 TTGGTCAACAACCGGATAAAATCGGTTAGACCGACAGTTGAACCGTAATCTGACCGGATTGAACC
1 TTGGTCAACAACCGGATAAAATCGGTTAGACCGACAGTTGAACCGTAATCTGACCGGATTGAACC
43947 GGTTTGATAATTGAAAAAATTTGTAAAAAACAT
66 GGTTTGATAATTGAAAAAATTTGTAAAAAACAT
*
43980 TTGGTCAACAACCGGATAAAATCGGTTAGACCGGCAGTTGAACCGTAATCTGACCGGATTGAACC
1 TTGGTCAACAACCGGATAAAATCGGTTAGACCGACAGTTGAACCGTAATCTGACCGGATTGAACC
* *
44045 GGTTTGATAATTGAAAAAATTTGTACAAAACTT
66 GGTTTGATAATTGAAAAAATTTGTAAAAAACAT
44078 TTG
1 TTG
44081 AAGGTGGTGA
Statistics
Matches: 98, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 98 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.27
Consensus pattern (98 bp):
TTGGTCAACAACCGGATAAAATCGGTTAGACCGACAGTTGAACCGTAATCTGACCGGATTGAACC
GGTTTGATAATTGAAAAAATTTGTAAAAAACAT
Found at i:46840 original size:35 final size:35
Alignment explanation
Indices: 46794--46876 Score: 157
Period size: 35 Copynumber: 2.4 Consensus size: 35
46784 TGATTATGGT
46794 GAAGAGGTTTTCTGCTTTTCACCAAAAGAAAAAAA
1 GAAGAGGTTTTCTGCTTTTCACCAAAAGAAAAAAA
46829 GAAGAGGTTTTCTGCTTTTCACCAAAAGAAAAAAA
1 GAAGAGGTTTTCTGCTTTTCACCAAAAGAAAAAAA
*
46864 GAAGAGATTTTCT
1 GAAGAGGTTTTCT
46877 ACAGATGTGG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 47 1.00
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (35 bp):
GAAGAGGTTTTCTGCTTTTCACCAAAAGAAAAAAA
Found at i:50741 original size:239 final size:238
Alignment explanation
Indices: 50373--50870 Score: 755
Period size: 239 Copynumber: 2.1 Consensus size: 238
50363 ATGTAACAAC
* * * *
50373 AACGTCACAATAATAGGTGACATATATTTCGCCATGAAATACTACAGAATAGCGCCACAAAAAAA
1 AACGTCACACTAATAGGTGACATAGATTTCGCCATGAAATACTACACAATAACGCCACAAAAAAA
* *
50438 ATTGATCGTCACAAAATAAAAGAAAATTGCTGATGATTCGTGACGAAAATGAGAACGTCACACTA
66 ATTGATCGTCACAAAATAAAAGAAAATTGCTGATGATTCGTGACAAAAATAAGAACGTCACACTA
*
50503 ATAGGCGACCTTGATTTCGTCATGGAATATCACACAATAACGCCAC-CAAAAAATATTGATCATC
131 ATAGGCGACCTTGATTTCGTCATGGAATATCACACAATAACACCACACAAAAAATATTGATCATC
*
50567 ACAAAATAAAAGAAAATTGTTGATGATTCGTGACGAAAATGAG
196 ACAAAATAAAAGAAAATTGCTGATGATTCGTGACGAAAATGAG
* * *
50610 AACGTCACACTAATAGGTGACATAGATTTCGTCATGGAATATTACACAATAACGCCACCAAAAAA
1 AACGTCACACTAATAGGTGACATAGATTTCGCCATGAAATACTACACAATAACGCCA-CAAAAAA
*
50675 ATGTTGATCGTCACAAAATAAAAGAAAATTGCTGATGATTCGTGACAAAAATAAGAACGTCACAC
65 A-ATTGATCGTCACAAAATAAAAGAAAATTGCTGATGATTCGTGACAAAAATAAGAACGTCACAC
* * * * * * * *
50740 TAATAGGTGACGTTGATTTCGTCATGTAATATTAGACTATAACACCACACAAAAAATGTTGATCG
129 TAATAGGCGACCTTGATTTCGTCATGGAATATCACACAATAACACCACACAAAAAATATTGATCA
* *
50805 TCACAAAATAAAAGAAAATTGCTGATGATTCGTGACGGAAATTAG
194 TCACAAAATAAAAGAAAATTGCTGATGATTCGTGACGAAAATGAG
* *
50850 AACGGCACACTATTAGGTGAC
1 AACGTCACACTAATAGGTGAC
50871 GTAAATTACG
Statistics
Matches: 234, Mismatches: 24, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
237 50 0.21
238 8 0.03
239 101 0.43
240 75 0.32
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24
Consensus pattern (238 bp):
AACGTCACACTAATAGGTGACATAGATTTCGCCATGAAATACTACACAATAACGCCACAAAAAAA
ATTGATCGTCACAAAATAAAAGAAAATTGCTGATGATTCGTGACAAAAATAAGAACGTCACACTA
ATAGGCGACCTTGATTTCGTCATGGAATATCACACAATAACACCACACAAAAAATATTGATCATC
ACAAAATAAAAGAAAATTGCTGATGATTCGTGACGAAAATGAG
Found at i:50745 original size:120 final size:119
Alignment explanation
Indices: 50373--50870 Score: 719
Period size: 120 Copynumber: 4.2 Consensus size: 119
50363 ATGTAACAAC
* * * * * * *
50373 AACGTCACAATAATAGGTGACATATATTTCGCCATGAAATACTACAGAATAGCGCCACAAAAAAA
1 AACGTCACACTAATAGGTGACATAGATTTCGTCATGGAATATTACACAATAACGCCACAAAAAAA
50438 -ATTGATCGTCACAAAATAAAAGAAAATTGCTGATGATTCGTGACGAAAATGAG
66 TATTGATCGTCACAAAATAAAAGAAAATTGCTGATGATTCGTGACGAAAATGAG
* * * * *
50491 AACGTCACACTAATAGGCGACCTTGATTTCGTCATGGAATATCACACAATAACGCCACCAAAAAA
1 AACGTCACACTAATAGGTGACATAGATTTCGTCATGGAATATTACACAATAACGCCACAAAAAAA
* *
50556 TATTGATCATCACAAAATAAAAGAAAATTGTTGATGATTCGTGACGAAAATGAG
66 TATTGATCGTCACAAAATAAAAGAAAATTGCTGATGATTCGTGACGAAAATGAG
50610 AACGTCACACTAATAGGTGACATAGATTTCGTCATGGAATATTACACAATAACGCCACCAAAAAA
1 AACGTCACACTAATAGGTGACATAGATTTCGTCATGGAATATTACACAATAACGCCA-CAAAAAA
* * *
50675 ATGTTGATCGTCACAAAATAAAAGAAAATTGCTGATGATTCGTGACAAAAATAAG
65 ATATTGATCGTCACAAAATAAAAGAAAATTGCTGATGATTCGTGACGAAAATGAG
* * * * * *
50730 AACGTCACACTAATAGGTGACGTTGATTTCGTCATGTAATATTAGACTATAACACCACACAAAAA
1 AACGTCACACTAATAGGTGACATAGATTTCGTCATGGAATATTACACAATAACGCCACA-AAAAA
* * *
50795 ATGTTGATCGTCACAAAATAAAAGAAAATTGCTGATGATTCGTGACGGAAATTAG
65 ATATTGATCGTCACAAAATAAAAGAAAATTGCTGATGATTCGTGACGAAAATGAG
* *
50850 AACGGCACACTATTAGGTGAC
1 AACGTCACACTAATAGGTGAC
50871 GTAAATTACG
Statistics
Matches: 342, Mismatches: 35, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
118 53 0.15
119 106 0.31
120 183 0.54
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24
Consensus pattern (119 bp):
AACGTCACACTAATAGGTGACATAGATTTCGTCATGGAATATTACACAATAACGCCACAAAAAAA
TATTGATCGTCACAAAATAAAAGAAAATTGCTGATGATTCGTGACGAAAATGAG
Found at i:53513 original size:2 final size:2
Alignment explanation
Indices: 53506--53539 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
53496 TAAGTATGTG
53506 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
53540 CCTCAATACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:57034 original size:69 final size:69
Alignment explanation
Indices: 56934--57062 Score: 186
Period size: 69 Copynumber: 1.9 Consensus size: 69
56924 TCTGTCGTAT
* * *
56934 GCATTATGCTTACTTACTATTACATTATTGCAACATATTTATTAGATTTTATTTGAAATTCTGTC
1 GCATTATGCTTACATACTATTACATTATTGCAACATATTTATTACATTTTATTTAAAATTCTGTC
56999 CAGA
66 CAGA
* * * * *
57003 GCATTGTGTTTACATACTATTATATTATTGCATCATATTTTTTACATTTTATTTAAAATT
1 GCATTATGCTTACATACTATTACATTATTGCAACATATTTATTACATTTTATTTAAAATT
57063 TATTATAAGA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 52 1.00
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.49
Consensus pattern (69 bp):
GCATTATGCTTACATACTATTACATTATTGCAACATATTTATTACATTTTATTTAAAATTCTGTC
CAGA
Found at i:57509 original size:44 final size:44
Alignment explanation
Indices: 57461--57544 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
57451 TAGGAGCCTA
*
57461 AAATCAACTTTATCATTTCGA-GATTATTTTATGGTAGGAGATTG
1 AAATCAACTTGATCATTT-GAGGATTATTTTATGGTAGGAGATTG
* *
57505 AAATCAACTTGATCATTTTAGGATTATTTTGTGGTAGGAG
1 AAATCAACTTGATCATTTGAGGATTATTTTATGGTAGGAG
57545 TGTTTTCTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 1 0.03
44 35 0.97
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.40
Consensus pattern (44 bp):
AAATCAACTTGATCATTTGAGGATTATTTTATGGTAGGAGATTG
Found at i:73477 original size:13 final size:13
Alignment explanation
Indices: 73459--73486 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
73449 ATGGATAGAC
73459 TCGAGTTCGGAGA
1 TCGAGTTCGGAGA
73472 TCGAGTTCGGAGA
1 TCGAGTTCGGAGA
73485 TC
1 TC
73487 TTTCACCGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.18, G:0.36, T:0.25
Consensus pattern (13 bp):
TCGAGTTCGGAGA
Found at i:78371 original size:4 final size:4
Alignment explanation
Indices: 78364--78389 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
78354 CTTTTTTTTA
78364 TTTC TTTC TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TT
78390 GTTTTTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:78737 original size:49 final size:49
Alignment explanation
Indices: 78683--78781 Score: 155
Period size: 49 Copynumber: 2.0 Consensus size: 49
78673 AATGAGATTA
* *
78683 ATGCCTCCTAATTAAAGTCTC-AAGTTCGAATCTTGTATATAATGAAAAT
1 ATGCCTCCTAATTAAAGTCTCGAA-TTCGAATCTTGTAAATAATAAAAAT
*
78732 ATGCCTTCTAATTAAAGTCTCGAATTCGAATCTTGTAAATAATAAAAAT
1 ATGCCTCCTAATTAAAGTCTCGAATTCGAATCTTGTAAATAATAAAAAT
78781 A
1 A
78782 GATGTTAGGA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
49 44 0.96
50 2 0.04
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.34
Consensus pattern (49 bp):
ATGCCTCCTAATTAAAGTCTCGAATTCGAATCTTGTAAATAATAAAAAT
Found at i:79234 original size:2 final size:2
Alignment explanation
Indices: 79227--79276 Score: 56
Period size: 2 Copynumber: 27.5 Consensus size: 2
79217 TATACTAGCA
*
79227 AT AT AT AT A- AT AT A- AT A- AT AT -T AT TT 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
79265 AT AT -T AT AT AT A
1 AT AT AT AT AT AT A
79277 ATAGTAGTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
1 5 0.12
2 36 0.88
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:79256 original size:17 final size:20
Alignment explanation
Indices: 79228--79279 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
79218 ATACTAGCAA
79228 TATATATAATATA-ATAATAT
1 TATATATAATATATAT-ATAT
*
79248 TATTTATATATATATATATAT
1 TATATATA-ATATATATATAT
79269 TATATATAATA
1 TATATATAATA
79280 GTAGTAATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 10 0.36
21 16 0.57
22 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TATATATAATATATATATAT
Found at i:81831 original size:21 final size:21
Alignment explanation
Indices: 81805--81851 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
81795 TCCATCACCT
81805 CCTCATCAGAACACCTAAACA
1 CCTCATCAGAACACCTAAACA
*
81826 CCTCATCAGAAGACCTAAACA
1 CCTCATCAGAACACCTAAACA
81847 CCTCA
1 CCTCA
81852 ACCACTAGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.40, C:0.38, G:0.06, T:0.15
Consensus pattern (21 bp):
CCTCATCAGAACACCTAAACA
Found at i:85273 original size:23 final size:21
Alignment explanation
Indices: 85231--85273 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
85221 ACACTTTTTT
*
85231 TAAAATAAAAATAAATAGTAG
1 TAAAATAAAAATAAACAGTAG
*
85252 TAAAATACATAAATGAACAGTA
1 TAAAATA-A-AAATAAACAGTA
85274 AGGAATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
22 1 0.06
23 10 0.56
ACGTcount: A:0.63, C:0.05, G:0.09, T:0.23
Consensus pattern (21 bp):
TAAAATAAAAATAAACAGTAG
Found at i:85585 original size:16 final size:16
Alignment explanation
Indices: 85564--85596 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
85554 GTTCCTATAA
*
85564 AAATTATATTTTTTTT
1 AAATTATATTTCTTTT
85580 AAATTATATTTCTTTT
1 AAATTATATTTCTTTT
85596 A
1 A
85597 TAGAAGGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (16 bp):
AAATTATATTTCTTTT
Found at i:91603 original size:3 final size:3
Alignment explanation
Indices: 91595--91623 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
91585 AGACACAGAA
91595 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
91624 AACCCCGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Done.