Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022782.1 Corchorus olitorius cultivar O-4 contig22815, 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: 68898
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3482 original size:45 final size:47
Alignment explanation
Indices: 3432--3529 Score: 137
Period size: 49 Copynumber: 2.1 Consensus size: 47
3422 TGTGAGTTTA
*
3432 TTTGTGTATTTGGGAAG-TAGATGA-TAATTTATGGTAGTTTCTTAG
1 TTTGTGTATTTGGGAAGATAGAGGATTAATTTATGGTAGTTTCTTAG
* *
3477 TTTGTGTATTTGGTAAGTACTAGAGGATTTATTTATGGTAGTTTCTTAG
1 TTTGTGTATTTGGGAAG-A-TAGAGGATTAATTTATGGTAGTTTCTTAG
3526 TTTG
1 TTTG
3530 AGTTGATTTC
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
45 16 0.35
48 6 0.13
49 24 0.52
ACGTcount: A:0.22, C:0.03, G:0.26, T:0.49
Consensus pattern (47 bp):
TTTGTGTATTTGGGAAGATAGAGGATTAATTTATGGTAGTTTCTTAG
Found at i:3904 original size:31 final size:31
Alignment explanation
Indices: 3844--3939 Score: 92
Period size: 31 Copynumber: 3.2 Consensus size: 31
3834 AGACAATTTG
*
3844 TTGTTCTAAATTTTGAAAATT--TAAGGGCAAA
1 TTGTCCTAAA-TTTGAAAATTCATAA-GGCAAA
*
3875 TTGTCCTAAATTTGAAAATTCATAAGGCAAG
1 TTGTCCTAAATTTGAAAATTCATAAGGCAAA
* * *
3906 TTGTTCT-GATTTG-AAGTTCATAAGGCAAA
1 TTGTCCTAAATTTGAAAATTCATAAGGCAAA
*
3935 ATGTC
1 TTGTC
3940 TTTGAACGTT
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
29 17 0.31
30 15 0.27
31 20 0.36
32 3 0.05
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.36
Consensus pattern (31 bp):
TTGTCCTAAATTTGAAAATTCATAAGGCAAA
Found at i:12821 original size:80 final size:79
Alignment explanation
Indices: 12688--12849 Score: 297
Period size: 80 Copynumber: 2.0 Consensus size: 79
12678 GTAAAACAAA
* *
12688 TTTGGATCCACTTATATAAACTAAACCAAAAGCTTAGGTGACAACGATTTCAATTTTTCTTTAGT
1 TTTGGATCCACTTATATAAACCAAACCAAAACCTTAGGTGACAACGATTTCAATTTTTCTTTAGT
12753 CTATGTACAAGTTAG
66 C-ATGTACAAGTTAG
12768 TTTGGATCCACTTATATAAACCAAACCAAAACCTTAGGTGACAACGATTTCAATTTTTCTTTAGT
1 TTTGGATCCACTTATATAAACCAAACCAAAACCTTAGGTGACAACGATTTCAATTTTTCTTTAGT
12833 CATGTACAAGTTAG
66 CATGTACAAGTTAG
12847 TTT
1 TTT
12850 TATTCGAGCC
Statistics
Matches: 80, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
79 16 0.20
80 64 0.80
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.36
Consensus pattern (79 bp):
TTTGGATCCACTTATATAAACCAAACCAAAACCTTAGGTGACAACGATTTCAATTTTTCTTTAGT
CATGTACAAGTTAG
Found at i:17370 original size:2 final size:2
Alignment explanation
Indices: 17365--17395 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17355 AGAAAAACAA
17365 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
17396 AGCAATTTCT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:22694 original size:111 final size:111
Alignment explanation
Indices: 22541--22752 Score: 327
Period size: 111 Copynumber: 1.9 Consensus size: 111
22531 TCTTCCTCGC
* *
22541 CATCATCATTTCTATCATTCCCATCTTTCTTGTCCTCGAATTTATCCTTAAAAAATTTCCGGAAA
1 CATCATCATTTCTATCATTCCCATCTTTCCTGTCCTCAAATTTATCCTTAAAAAATTTCCGGAAA
*
22606 AAACCATCCTTATCATCATCTTCAGCAGATTTTGAAATTCTTTCCT
66 AAACCATCCTTATCATCATCTTCAACAGATTTTGAAATTCTTTCCT
* *
22652 CATCATCAATTT-TATCATTCCCGTCTTTCCTGTCTTCAAATTTATCCTTAAAAAATTTCCGGAA
1 CATCATC-ATTTCTATCATTCCCATCTTTCCTGTCCTCAAATTTATCCTTAAAAAATTTCCGGAA
* * * *
22716 AAATCCATCTTTGTCATCATCTTCAACTGATTTTGAA
65 AAAACCATCCTTATCATCATCTTCAACAGATTTTGAA
22753 GCTTTTTCTT
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
111 87 0.96
112 4 0.04
ACGTcount: A:0.28, C:0.25, G:0.07, T:0.40
Consensus pattern (111 bp):
CATCATCATTTCTATCATTCCCATCTTTCCTGTCCTCAAATTTATCCTTAAAAAATTTCCGGAAA
AAACCATCCTTATCATCATCTTCAACAGATTTTGAAATTCTTTCCT
Found at i:27733 original size:24 final size:25
Alignment explanation
Indices: 27700--27756 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
27690 GTCAACCTTG
*
27700 AATTT-TTTAATGT-TTAATTCTTA
1 AATTTATTTAATGTCTTAATTATTA
*
27723 AATTTATTTAATGTCTTAATTATTC
1 AATTTATTTAATGTCTTAATTATTA
27748 AATTTATTT
1 AATTTATTT
27757 TACAATCCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.27
25 17 0.57
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60
Consensus pattern (25 bp):
AATTTATTTAATGTCTTAATTATTA
Found at i:30628 original size:1 final size:1
Alignment explanation
Indices: 30622--30646 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
30612 TGTTGTTGTG
30622 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
30647 CATTTTAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:40247 original size:42 final size:42
Alignment explanation
Indices: 40185--40266 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
40175 TTCTGCTCCT
* *
40185 GCCCCACCCTCAGAACCTGATCGCTGGGGTAGTGGGAGCAAA
1 GCCCCACCCTCACAACCTGATCGCTGGGGTAGTGGCAGCAAA
* *
40227 GCCCCACCTTCACAATCTGATCGCTGGGGTAGTGGCAGCA
1 GCCCCACCCTCACAACCTGATCGCTGGGGTAGTGGCAGCA
40267 GGGCTCCACC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.22, C:0.32, G:0.29, T:0.17
Consensus pattern (42 bp):
GCCCCACCCTCACAACCTGATCGCTGGGGTAGTGGCAGCAAA
Found at i:41256 original size:67 final size:67
Alignment explanation
Indices: 41148--41282 Score: 270
Period size: 67 Copynumber: 2.0 Consensus size: 67
41138 ACCTCACTGC
41148 AGGCCAGAAAATCTCCATTTTTGAGCCTAAGGAGCTAAGATTTAAGTCAAATAAAAATAATCTCA
1 AGGCCAGAAAATCTCCATTTTTGAGCCTAAGGAGCTAAGATTTAAGTCAAATAAAAATAATCTCA
41213 AA
66 AA
41215 AGGCCAGAAAATCTCCATTTTTGAGCCTAAGGAGCTAAGATTTAAGTCAAATAAAAATAATCTCA
1 AGGCCAGAAAATCTCCATTTTTGAGCCTAAGGAGCTAAGATTTAAGTCAAATAAAAATAATCTCA
41280 AA
66 AA
41282 A
1 A
41283 TTAATCAATC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.44, C:0.16, G:0.15, T:0.25
Consensus pattern (67 bp):
AGGCCAGAAAATCTCCATTTTTGAGCCTAAGGAGCTAAGATTTAAGTCAAATAAAAATAATCTCA
AA
Found at i:42358 original size:124 final size:126
Alignment explanation
Indices: 42142--42397 Score: 410
Period size: 124 Copynumber: 2.0 Consensus size: 126
42132 ATTTAAGAAA
42142 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGT---AATAAAA
*
42207 TAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAA
63 T--GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
42272 G
126 G
*
42273 TATATTTAAGAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGT-A-AAAAT-
1 TATATTTAAAAAATTCTAATATATATAAG-TTTTTTAATTAAAATAGTAAAATGGTAATAAAATG
*
42335 TATAATGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
65 TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
42397 T
1 T
42398 TTAAACAATG
Statistics
Matches: 121, Mismatches: 3, Indels: 9
0.91 0.02 0.07
Matches are distributed among these distances:
124 61 0.50
127 5 0.04
128 1 0.01
131 28 0.23
132 26 0.21
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (126 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAATAAAATGT
ATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
Found at i:57544 original size:13 final size:13
Alignment explanation
Indices: 57526--57552 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
57516 AAACAACTGA
57526 AAAGCACTTCTGG
1 AAAGCACTTCTGG
57539 AAAGCACTTCTGG
1 AAAGCACTTCTGG
57552 A
1 A
57553 TTTTCCGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (13 bp):
AAAGCACTTCTGG
Found at i:64355 original size:123 final size:125
Alignment explanation
Indices: 64155--64409 Score: 381
Period size: 123 Copynumber: 2.0 Consensus size: 125
64145 CATTGTTTAA
* *
64155 ACTTTTATAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATAA-
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATAAT
*
64219 -TTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
66 TTTTTTACAATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
* *
64278 ACTTTTACAGTTTTACTCAACTAAAAGCTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATA--
64343 TATTTTATTTTTATC-ATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAAT
64 -A--TT-TTTTTA-CAATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAAT
64407 AT
124 AT
64409 A
1 A
64410 TTTCTTAAAT
Statistics
Matches: 119, Mismatches: 4, Indels: 10
0.89 0.03 0.08
Matches are distributed among these distances:
123 59 0.50
126 1 0.01
131 58 0.49
132 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (125 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATAAT
TTTTTTACAATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:64398 original size:131 final size:123
Alignment explanation
Indices: 64155--64409 Score: 402
Period size: 131 Copynumber: 2.0 Consensus size: 123
64145 CATTGTTTAA
*
64155 ACTTTTATAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATAAT
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATAAT
64220 TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
66 TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
* *
64278 ACTTTTACAGTTTTACTCAACTAAAAGCTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATAT-CTT-TA--
*
64343 TATTTTATTTTTATCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATA
62 TA----ATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATA
64408 T
123 T
64409 A
1 A
64410 TTTCTTAAAT
Statistics
Matches: 120, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
123 53 0.44
124 3 0.03
125 2 0.02
127 2 0.02
131 60 0.50
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (123 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATAAT
TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:64431 original size:14 final size:13
Alignment explanation
Indices: 64395--64433 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
64385 TATATATTAG
64395 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
64408 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
64422 AATTTTTTAAAT
1 AATTTTTTAAAT
64434 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Found at i:65848 original size:15 final size:15
Alignment explanation
Indices: 65828--65861 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
65818 ACAATACCTC
65828 TTTAGTC-TTTACTCA
1 TTTAGTCATTTA-TCA
65843 TTTAGTCATTTATCA
1 TTTAGTCATTTATCA
65858 TTTA
1 TTTA
65862 TAATAAGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.24, C:0.15, G:0.06, T:0.56
Consensus pattern (15 bp):
TTTAGTCATTTATCA
Done.