Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010250.1 Corchorus olitorius cultivar O-4 contig10282, 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: 8342
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Found at i:1153 original size:15 final size:16
Alignment explanation
Indices: 1126--1159 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
1116 ATAGTTATGT
1126 AATCAATTTATAATTA
1 AATCAATTTATAATTA
1142 AATCAA-TTATAATTA
1 AATCAATTTATAATTA
1157 AAT
1 AAT
1160 TAGAATGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (16 bp):
AATCAATTTATAATTA
Found at i:1674 original size:24 final size:24
Alignment explanation
Indices: 1625--1674 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
1615 TTTACACGGT
* **
1625 TAATCAATCAATTTTTTTGGCAAC
1 TAATCAATCAATTTATTTGAAAAC
1649 TAATCAATCAA-TTATTTGAAATAC
1 TAATCAATCAATTTATTTGAAA-AC
1673 TA
1 TA
1675 TTTACATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (24 bp):
TAATCAATCAATTTATTTGAAAAC
Found at i:3583 original size:16 final size:16
Alignment explanation
Indices: 3562--3592 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3552 TTGAAAAATA
3562 TTACTAAATATTTATT
1 TTACTAAATATTTATT
*
3578 TTACTAAATCTTTAT
1 TTACTAAATATTTAT
3593 AATATGTAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (16 bp):
TTACTAAATATTTATT
Found at i:4031 original size:7 final size:7
Alignment explanation
Indices: 4019--4044 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4009 TTCATAATTA
4019 ATTAAAT
1 ATTAAAT
4026 ATTAAAT
1 ATTAAAT
4033 ATTAAAT
1 ATTAAAT
4040 ATTAA
1 ATTAA
4045 TAAATATTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATTAAAT
Found at i:4429 original size:199 final size:200
Alignment explanation
Indices: 3933--4839 Score: 1171
Period size: 199 Copynumber: 4.5 Consensus size: 200
3923 CTTTATAATA
* * * * * *
3933 AGGATCATTATACAATACACTATCAATGTAAATTTTGGACTCCATAAGCAGGTTAAGAAATTGAC
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGAC
* * *
3998 ACATACCTTGTTTCATAATTAATTAAATATTAAATATTAAATATTAATAAATATTCCCTAAGGGG
66 ACATACCCTATTTCATAATTAATTAAATA-T-AA-A-T--ATATTAATACATATTCCCTAAGGGG
* * * * * *
4063 ACACATGTCAACCCTTAAATCATGCATGTGCAGTCTGCTAAATTTCACTGACGGTGTATTGTATA
125 ACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTGACGATGTATTGTATA
4128 A-TTTTTTTAT
190 ATTTTTTTTAT
* * * *
4138 AAGATTGTTATACAATACACTATCAGTGTAAATTTTGAACTCCATAAGCGAGTTAAGAAGTTGAC
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGAC
* *
4203 ACATACTCTATTTCATAATTAATTAAATATAAA-ATATTTATACATATTCCCTAAGGGGACACAT
66 ACATACCCTATTTCATAATTAATTAAATATAAATATATTAATACATATTCCCTAAGGGGACACAT
* *
4267 GTCAACCCTTAAGCCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTT
131 GTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTGACGATGTATTGTATAATTTTT
4332 TTTAT
196 TTTAT
* *
4337 AGGATTGTTATACAATACACTGTCAGTGTAAATTTTGAACTCTATAAGCGGGTTAAGAAGTTGAC
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGAC
*
4402 AAATACCCTATTTCATAATTAATTAAATATAAATTATATTAATACATATTCCCTAA-GGGACACA
66 ACATACCCTATTTCATAATTAATTAAATATAAA-TATATTAATACATATTCCCTAAGGGGACACA
* * * * *
4466 TGTCAACCCTT-AAGCCTGCGCCTGCAGTCGGATAAACTCCACTGACGATGTATTGTATAATTTT
130 TGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTGACGATGTATTGTATAATTTT
*
4530 TTTTAA
195 TTTTAT
* * * *
4536 ATGAAATTATTATACAATACACTGTCAATGTAAATTTTGGACTCCATAAGCAGGTTAAGAAGTTG
1 A-G-GATTATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTG
* ** * *
4601 ACACATACCCCATTTCATAATTAATTAAATATTTA-ATATTAAAACATATTCCCTAAGGGGATAC
64 ACACATACCCTATTTCATAATTAATTAAATATAAATATATTAATACATATTCCCTAAGGGGACAC
* * * * *
4665 ATGTCAACCCTTAAACTCCCGCACATGCAGTCTGCTAAACTCCATTGACAATGTATTGCATAATT
129 ATGTCAACCCTTAAAC-CCTGCACGTGCAGTCTGCTAAACTCCACTGACGATGTATTGTATAATT
*
4730 TTTCTTAT
193 TTTTTTAT
* * ** * *
4738 AGGATTATTATACAATACACAGTAAGAATAAATTTTGGAA-TCCATAAGTGGGTTATGAAGTTGA
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTT-GAACTCCATAAGCGGGTTAAGAAGTTGA
*
4802 CACATACCGC-ATTTCATAATTAATTAAATATATATATA
65 CACATACC-CTATTTCATAATTAATTAAATATAAATATA
4840 GATATATATA
Statistics
Matches: 623, Mismatches: 68, Indels: 26
0.87 0.09 0.04
Matches are distributed among these distances:
198 83 0.13
199 173 0.28
200 118 0.19
201 115 0.18
202 48 0.08
203 2 0.00
204 1 0.00
205 83 0.13
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (200 bp):
AGGATTATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGAC
ACATACCCTATTTCATAATTAATTAAATATAAATATATTAATACATATTCCCTAAGGGGACACAT
GTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTGACGATGTATTGTATAATTTTT
TTTAT
Found at i:4599 original size:400 final size:402
Alignment explanation
Indices: 3933--4838 Score: 1227
Period size: 401 Copynumber: 2.2 Consensus size: 402
3923 CTTTATAATA
* * * * * *
3933 AGGATCATTATACAATACACTATCAATGTAAATTTTGGACTCCATAAGCAGGTTAAGAAATTGAC
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGAC
* *
3998 ACATACCTTGTTTCATAATTAATTAAATATTAAATATTAAATATTAATAAATATTCCCTAAGGGG
66 ACATACCCTATTTCATAATTAATTAAATA-T-AATATT-AATATTAATAAATATTCCCTAAGGGG
* ** * * * * *
4063 ACACATGTCAACCCTTAAATCATGCATGTGCAGTCTGCTAAATTTCACTGACGGTGTATTGTATA
128 ACACATGTCAACCCTTAAAGCATGCACCTGCAGTCGGATAAACTCCACTGACGATGTATTGTATA
* *
4128 ATTTTTTTATAAGATTGTTATACAATACACTATCAGTGTAAATTTTGAACTCCATAAGCGAGTTA
193 ATTTTTTTATAAGATTATTATACAATACACTATCAATGTAAATTTTGAACTCCATAAGCGAGTTA
* * * *
4193 AGAAGTTGACACATACTCTATTTCATAATTAATTAAATATAAAATATTTATACATATTCCCTAAG
258 AGAAGTTGACACATACCCCATTTCATAATTAATTAAATATAAAATATTAAAACATATTCCCTAAG
* * * **
4258 GGGACACATGTCAACCCTTAAGC-CCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTG
323 GGGACACATGTCAACCCTTAAACTCCCGCACATGCAGTCTGCTAAACTCCACTGACAATGTATTG
* *
4322 TATAATTTTTTTTAT
388 CATAATTTTTCTTAT
* *
4337 AGGATTGTTATACAATACACTGTCAGTGTAAATTTTGAACTCTATAAGCGGGTTAAGAAGTTGAC
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGAC
* *
4402 AAATACCCTATTTCATAATTAATTAAATATAA-ATT-ATATTAATACATATTCCCTAA-GGGACA
66 ACATACCCTATTTCATAATTAATTAAATATAATATTAATATTAATAAATATTCCCTAAGGGGACA
* *
4464 CATGTCAACCCTT-AAGCCTGCGCCTGCAGTCGGATAAACTCCACTGACGATGTATTGTATAATT
131 CATGTCAACCCTTAAAGCATGCACCTGCAGTCGGATAAACTCCACTGACGATGTATTGTATAATT
* *
4528 TTTTT-TAAATGAAATTATTATACAATACACTGTCAATGTAAATTTTGGACTCCATAAGC-AGGT
196 TTTTTAT-AA-G--ATTATTATACAATACACTATCAATGTAAATTTTGAACTCCATAAGCGA-GT
**
4591 TAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAAAACATATTCCCTA
256 TAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATAAAATATTAAAACATATTCCCTA
* *
4656 AGGGGATACATGTCAACCCTTAAACTCCCGCACATGCAGTCTGCTAAACTCCATTGACAATGTAT
321 AGGGGACACATGTCAACCCTTAAACTCCCGCACATGCAGTCTGCTAAACTCCACTGACAATGTAT
4721 TGCATAATTTTTCTTAT
386 TGCATAATTTTTCTTAT
* * ** * *
4738 AGGATTATTATACAATACACAGTAAGAATAAATTTTGGAA-TCCATAAGTGGGTTATGAAGTTGA
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTT-GAACTCCATAAGCGGGTTAAGAAGTTGA
4802 CACATACCGC-ATTTCATAATTAATTAAATATATATAT
65 CACATACC-CTATTTCATAATTAATTAAATATA-ATAT
4839 AGATATATAT
Statistics
Matches: 442, Mismatches: 50, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
396 1 0.00
397 48 0.11
398 20 0.05
399 21 0.05
400 126 0.29
401 133 0.30
402 7 0.02
403 3 0.01
404 83 0.19
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (402 bp):
AGGATTATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGAC
ACATACCCTATTTCATAATTAATTAAATATAATATTAATATTAATAAATATTCCCTAAGGGGACA
CATGTCAACCCTTAAAGCATGCACCTGCAGTCGGATAAACTCCACTGACGATGTATTGTATAATT
TTTTTATAAGATTATTATACAATACACTATCAATGTAAATTTTGAACTCCATAAGCGAGTTAAGA
AGTTGACACATACCCCATTTCATAATTAATTAAATATAAAATATTAAAACATATTCCCTAAGGGG
ACACATGTCAACCCTTAAACTCCCGCACATGCAGTCTGCTAAACTCCACTGACAATGTATTGCAT
AATTTTTCTTAT
Found at i:4836 original size:2 final size:2
Alignment explanation
Indices: 4829--4859 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4819 AATTAATTAA
*
4829 AT AT AT AT AT AG AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4860 CACTAAATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:6095 original size:201 final size:194
Alignment explanation
Indices: 5746--6112 Score: 500
Period size: 201 Copynumber: 1.9 Consensus size: 194
5736 GATCAATTTG
* * * *
5746 TTTAATATTAATACATATTCCTTAAGGGGACGCATGTCAACCCTTAAATCCTGCACGTGCAGTCT
1 TTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAATCCCGCACGTGCAGTCG
* * * * *
5811 GCTAAAATCTACTGACGGGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTTTTAG
66 GCTAAAATCCACTGACGGGTATTATATAAATTTTCTTATAGGATTATTATACAATACACTGTCAG
*
5876 TATAAATTGCGAACTCCATAAGCGGGTTAAGAAGTTGACACATACGGCATTTCATAATTAAATA
131 TATAAATTGCGAACTCCATAAACGGGTTAAGAAGTTGACACATACGGCATTTCATAATTAAATA
* *
5940 TTTAATGTTAATACATATTCCCTAAGGGTACACATGTCAACCCTTAAAGTTAAACCCCGCACGTG
1 TTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAA--T----CCCGCACGTG
* *
6005 CAGTCGGCTAAACTCCATTGACGGTGTATTATATAAATTTTCTTATAGGATTATTATACAATACA
60 CAGTCGGCTAAAATCCACTGACGG-GTATTATATAAATTTTCTTATAGGATTATTATACAATACA
* ** * *
6070 CTGTCAGTGTAAATTTTGGACTCCATAAACGGGTTATGAAGTT
124 CTGTCAGTATAAATTGCGAACTCCATAAACGGGTTAAGAAGTT
6113 TTTGTGTAAA
Statistics
Matches: 147, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
194 44 0.30
196 1 0.01
200 29 0.20
201 73 0.50
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Consensus pattern (194 bp):
TTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAATCCCGCACGTGCAGTCG
GCTAAAATCCACTGACGGGTATTATATAAATTTTCTTATAGGATTATTATACAATACACTGTCAG
TATAAATTGCGAACTCCATAAACGGGTTAAGAAGTTGACACATACGGCATTTCATAATTAAATA
Found at i:7782 original size:21 final size:21
Alignment explanation
Indices: 7756--7830 Score: 116
Period size: 21 Copynumber: 3.6 Consensus size: 21
7746 CTTAGGCAAT
* *
7756 TCCAATAAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
7777 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
7798 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
7819 TCCAATGAGCTT
1 TCCAATGAGCTT
7831 CTAGCATCTT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
20 3 0.06
21 48 0.94
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Done.