Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018663.1 Corchorus olitorius cultivar O-4 contig18696, 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: 23314
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1422 original size:37 final size:38
Alignment explanation
Indices: 1380--1455 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 38
1370 CTAGAATTAA
*
1380 GTCCA-TTCAACAAGGAATTCCCTCTCCGTGTCTATTT
1 GTCCATTTCAACAAGGAATTCCCTCTCCATGTCTATTT
* * *
1417 GTCCATTTTCAGCGAGGAATTCTCTCTCCATGTCTATTT
1 GTCCA-TTTCAACAAGGAATTCCCTCTCCATGTCTATTT
1456 TGCCTATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 5 0.15
39 28 0.85
ACGTcount: A:0.20, C:0.28, G:0.14, T:0.38
Consensus pattern (38 bp):
GTCCATTTCAACAAGGAATTCCCTCTCCATGTCTATTT
Found at i:3860 original size:22 final size:22
Alignment explanation
Indices: 3811--3860 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
3801 ATCATAGTGT
* *
3811 GCTTATCAAATTTTCATATGAA
1 GCTTATCAAAATTTCATAAGAA
** *
3833 ATTTATCAAAATTTCATAAGGA
1 GCTTATCAAAATTTCATAAGAA
3855 GCTTAT
1 GCTTAT
3861 TAAATTTTTA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (22 bp):
GCTTATCAAAATTTCATAAGAA
Found at i:11416 original size:168 final size:168
Alignment explanation
Indices: 11138--11477 Score: 653
Period size: 168 Copynumber: 2.0 Consensus size: 168
11128 AAACTGCAGT
11138 CTATAAGGCATAAAGCTGTAGAAAGTTTAATTCTACCTGTTCCTAGTACTTCTGCAGATTTAGAT
1 CTATAAGGCATAAAGCTGTAGAAAGTTTAATTCTACCTGTTCCTAGTACTTCTGCAGATTTAGAT
*
11203 GATTCTAATGGTGTTTTTCATGCTCAACCTTCATCCCAAGATCCTGTTGTGATTCTTCCCACTTC
66 GATTCTAATGGTGTTTTTCATGCTCAACCTTCATCCCAAGATCCTGCTGTGATTCTTCCCACTTC
*
11268 ATCATCACCACAAATTGAATCATCTCCTCCAATTCAAA
131 ATCATCACCACAAATTGAACCATCTCCTCCAATTCAAA
11306 CTATAAGGCATAAAGCTGTAGAAAGTTTAATTCTACCTGTTCCTAGTACTTCTGCAGATTTAGAT
1 CTATAAGGCATAAAGCTGTAGAAAGTTTAATTCTACCTGTTCCTAGTACTTCTGCAGATTTAGAT
11371 GATTCTAATGGTGTTTTTCATGCTCAACCTTCATCCCAAGATCCTGCTGTGATTCTTCCCACTTC
66 GATTCTAATGGTGTTTTTCATGCTCAACCTTCATCCCAAGATCCTGCTGTGATTCTTCCCACTTC
*
11436 ATCATCACCACAAATTGAACCATCTCCTCCAATTTAAA
131 ATCATCACCACAAATTGAACCATCTCCTCCAATTCAAA
11474 CTAT
1 CTAT
11478 CTCACCTGTT
Statistics
Matches: 169, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
168 169 1.00
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (168 bp):
CTATAAGGCATAAAGCTGTAGAAAGTTTAATTCTACCTGTTCCTAGTACTTCTGCAGATTTAGAT
GATTCTAATGGTGTTTTTCATGCTCAACCTTCATCCCAAGATCCTGCTGTGATTCTTCCCACTTC
ATCATCACCACAAATTGAACCATCTCCTCCAATTCAAA
Found at i:14933 original size:23 final size:23
Alignment explanation
Indices: 14905--14948 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
14895 TAAAATGCAC
14905 CAAAACAGTCACCACTAACCCAT
1 CAAAACAGTCACCACTAACCCAT
14928 CAAAACAGTCACCACTAACCC
1 CAAAACAGTCACCACTAACCC
14949 TCTTCCTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.43, C:0.41, G:0.05, T:0.11
Consensus pattern (23 bp):
CAAAACAGTCACCACTAACCCAT
Found at i:19045 original size:2 final size:2
Alignment explanation
Indices: 19038--19080 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
19028 TAAGATTTTA
19038 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
19080 A
1 A
19081 CTAGTTAAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20665 original size:58 final size:58
Alignment explanation
Indices: 20571--20685 Score: 169
Period size: 58 Copynumber: 2.0 Consensus size: 58
20561 ATTAATCAAA
* *
20571 TATCAAGTGACATGTTCTTTATTAGATGTATAAAAAAAGACGTTTTCGGACCAAGGCT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGGCT
* * *
20629 TATCAAGTGACATGTTTTTTTATTAGATGCCT-AAAAAAGACGTTTTAGGACCGAGGC
1 TATCAAGTGACATG-TTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGGC
20686 ATGATGCTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 37 0.73
59 14 0.27
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGGCT
Found at i:22907 original size:204 final size:198
Alignment explanation
Indices: 22535--22941 Score: 715
Period size: 204 Copynumber: 2.0 Consensus size: 198
22525 GCTTAATAAC
22535 TTTATCAATGGTGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
1 TTTATCAATGGTGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
*
22600 ATACAACACATTATTATTATATATAAAACTATACAAAAAAAGTAGCTGAACATTAGTGGTTGATT
66 ATACAACACATTACTATTATATATAAAACTATACAAAAAAAGTAGCTGAACATTAGTGGTTGATT
*
22665 TATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGA
131 TATTAAATTAAATTAGATCAATGGCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATCCGA
22730 TTTA
195 TTTA
*
22734 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTTTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAA-TTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* *
22799 GATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGT
65 GATACAACACATTACTATTATATATA-A-AACTATA-C-AAAAAAAGTAGCTGAACATTAGTGGT
22864 TGATTTATTAAATTAAATTAGATCAATGGCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT
126 TGATTTATTAAATTAAATTAGATCAATGGCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT
22929 CCGATTTA
191 CCGATTTA
22937 TTTAT
1 TTTAT
22942 TATTAAGGAA
Statistics
Matches: 198, Mismatches: 5, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
199 24 0.12
200 64 0.32
201 1 0.01
202 7 0.04
203 19 0.10
204 83 0.42
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (198 bp):
TTTATCAATGGTGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
ATACAACACATTACTATTATATATAAAACTATACAAAAAAAGTAGCTGAACATTAGTGGTTGATT
TATTAAATTAAATTAGATCAATGGCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCCGAT
TTA
Found at i:23047 original size:25 final size:24
Alignment explanation
Indices: 23013--23059 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
23003 ACGTTTGCAC
23013 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
23038 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
23060 TGTAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:23104 original size:39 final size:38
Alignment explanation
Indices: 23050--23125 Score: 143
Period size: 39 Copynumber: 2.0 Consensus size: 38
23040 ATACCTAAGA
23050 ATTTAATTAATGTAAGTATTTTAGTTATTATAGTATATC
1 ATTTAATTAATGTAAGTATTTTAGTTATTATA-TATATC
23089 ATTTAATTAATGTAAGTATTTTAGTTATTATATATAT
1 ATTTAATTAATGTAAGTATTTTAGTTATTATATATAT
23126 TACATAGGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
38 5 0.14
39 32 0.86
ACGTcount: A:0.37, C:0.01, G:0.09, T:0.53
Consensus pattern (38 bp):
ATTTAATTAATGTAAGTATTTTAGTTATTATATATATC
Found at i:23111 original size:18 final size:18
Alignment explanation
Indices: 23051--23111 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 18
23041 TACCTAAGAA
23051 TTTAATTAATGTAAGTAT
1 TTTAATTAATGTAAGTAT
*
23069 TTTAGTT-AT-TATAGTATAT
1 TTTAATTAATGTA-AG--TAT
23088 CATTTAATTAATGTAAGTAT
1 --TTTAATTAATGTAAGTAT
23108 TTTA
1 TTTA
23112 GTTATTATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 14
0.68 0.04 0.28
Matches are distributed among these distances:
16 2 0.06
17 4 0.12
18 10 0.29
19 3 0.09
20 3 0.09
21 6 0.18
22 4 0.12
23 2 0.06
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (18 bp):
TTTAATTAATGTAAGTAT
Found at i:23126 original size:18 final size:18
Alignment explanation
Indices: 23066--23126 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 18
23056 TTAATGTAAG
23066 TATTTTAGTTATTATAGTA
1 TATTTTAGTTATTATA-TA
* * *
23085 TATCATTTAATTAATGTA-A
1 TAT--TTTAGTTATTATATA
23104 GTATTTTAGTTATTATATA
1 -TATTTTAGTTATTATATA
23123 TATT
1 TATT
23127 ACATAGGAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 9
0.68 0.13 0.19
Matches are distributed among these distances:
18 14 0.44
19 5 0.16
20 3 0.09
21 10 0.31
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.56
Consensus pattern (18 bp):
TATTTTAGTTATTATATA
Done.