Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020029.1 Corchorus olitorius cultivar O-4 contig20062, 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: 42623
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:440 original size:15 final size:15
Alignment explanation
Indices: 416--446 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
406 ATATAAATAA
*
416 TATTGTAATTTTAAC
1 TATTGGAATTTTAAC
431 TATTGGAATTTTAAC
1 TATTGGAATTTTAAC
446 T
1 T
447 TGTTGATGTT
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:0.32, C:0.06, G:0.10, T:0.52
Consensus pattern (15 bp):
TATTGGAATTTTAAC
Found at i:513 original size:123 final size:124
Alignment explanation
Indices: 358--604 Score: 478
Period size: 123 Copynumber: 2.0 Consensus size: 124
348 ACATATTGAT
358 AAAATCCAAATCCAAGTCAGATTTTATCACGCTCTTGCCTTCGTAATCATATAAATAATATTGTA
1 AAAATCCAAATCCAAGTCAGATTTTATCACGCTCTTGCCTTCGTAATCATATAAATAATATTGTA
423 ATTTTAACTATTGGAATTTTAACTTGTTGATGTTCCTTGAC-TTTTTTTTAACCTTAAC
66 ATTTTAACTATTGGAATTTTAACTTGTTGATGTTCCTTGACGTTTTTTTTAACCTTAAC
*
481 AAAATCCAAATCCAAGTCGGATTTTATCACGCTCTTGCCTTCGTAATCATATAAATAATATTGTA
1 AAAATCCAAATCCAAGTCAGATTTTATCACGCTCTTGCCTTCGTAATCATATAAATAATATTGTA
546 ATTTTAACTATTGGAATTTTAACTTGTTGATGTTCCTTGACGTTTTTTTTAACCTTAAC
66 ATTTTAACTATTGGAATTTTAACTTGTTGATGTTCCTTGACGTTTTTTTTAACCTTAAC
605 GTTTTTTTTT
Statistics
Matches: 122, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
123 105 0.86
124 17 0.14
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (124 bp):
AAAATCCAAATCCAAGTCAGATTTTATCACGCTCTTGCCTTCGTAATCATATAAATAATATTGTA
ATTTTAACTATTGGAATTTTAACTTGTTGATGTTCCTTGACGTTTTTTTTAACCTTAAC
Found at i:563 original size:15 final size:15
Alignment explanation
Indices: 539--569 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
529 ATATAAATAA
*
539 TATTGTAATTTTAAC
1 TATTGGAATTTTAAC
554 TATTGGAATTTTAAC
1 TATTGGAATTTTAAC
569 T
1 T
570 TGTTGATGTT
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:0.32, C:0.06, G:0.10, T:0.52
Consensus pattern (15 bp):
TATTGGAATTTTAAC
Found at i:785 original size:6 final size:6
Alignment explanation
Indices: 771--804 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
761 ATTTAGACTT
*
771 ATATTG ATATAG ATATAG ATATAG ATATAG ATAT
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATAT
805 TTTTGAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (6 bp):
ATATAG
Found at i:3830 original size:36 final size:36
Alignment explanation
Indices: 3780--3863 Score: 150
Period size: 36 Copynumber: 2.3 Consensus size: 36
3770 CTGATTTTAC
* *
3780 AACTATAAACATTACTAGCTACAACTATAAACTTTG
1 AACTAAAAATATTACTAGCTACAACTATAAACTTTG
3816 AACTAAAAATATTACTAGCTACAACTATAAACTTTG
1 AACTAAAAATATTACTAGCTACAACTATAAACTTTG
3852 AACTAAAAATAT
1 AACTAAAAATAT
3864 CAACATCTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.49, C:0.17, G:0.05, T:0.30
Consensus pattern (36 bp):
AACTAAAAATATTACTAGCTACAACTATAAACTTTG
Found at i:5356 original size:2 final size:2
Alignment explanation
Indices: 5349--5383 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5339 ATTAATCTTA
5349 AT AT AT AT AT AT AT AT 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 AT AT A
5384 ACTAGGAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15907 original size:19 final size:18
Alignment explanation
Indices: 15874--15909 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
15864 TGAAAATAAT
15874 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
15892 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
15910 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:20812 original size:30 final size:30
Alignment explanation
Indices: 20749--20812 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
20739 AACCTGCAAA
*
20749 TTTTTTTCATTGTGTTACCTAGTACTCTTT
1 TTTTTTTCATTGTGTTACCTAGTACTCTAT
**
20779 TTTTTTTTTTTGTGTTACCTAGTACT-TGAT
1 TTTTTTTCATTGTGTTACCTAGTACTCT-AT
20809 TTTT
1 TTTT
20813 ATTTAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.12, C:0.12, G:0.11, T:0.64
Consensus pattern (30 bp):
TTTTTTTCATTGTGTTACCTAGTACTCTAT
Found at i:20870 original size:19 final size:19
Alignment explanation
Indices: 20846--20883 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
20836 TTTTATTTAA
20846 TTTTGATTTGAGATATTTT
1 TTTTGATTTGAGATATTTT
*
20865 TTTTGATTTTAGATATTTT
1 TTTTGATTTGAGATATTTT
20884 AAAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.13, T:0.66
Consensus pattern (19 bp):
TTTTGATTTGAGATATTTT
Found at i:22843 original size:2 final size:2
Alignment explanation
Indices: 22800--22826 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
22790 TTACTAATAA
22800 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
22827 AAATGATAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26741 original size:17 final size:17
Alignment explanation
Indices: 26719--26755 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
26709 AAAACCACGC
26719 CCTAGCATGCCATATGA
1 CCTAGCATGCCATATGA
26736 CCTAGCATGCCATATGA
1 CCTAGCATGCCATATGA
26753 CCT
1 CCT
26756 GAAAATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.24
Consensus pattern (17 bp):
CCTAGCATGCCATATGA
Found at i:37175 original size:38 final size:38
Alignment explanation
Indices: 37079--37226 Score: 226
Period size: 38 Copynumber: 3.9 Consensus size: 38
37069 GGCTGTGCAT
* *
37079 AGTGGACCCGTACCTCAGGGGGTTAAACTGATGGTAAAG
1 AGTGGACCCATACCTCAGGGGGTTAAACTGTTGGT-AAG
*
37118 AGTGGACCCATACCACAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCATACCTCAGGGGGTTAAACTGTTGGTAAG
* *
37156 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCATACCTCAGGGGGTTAAACTGTTGGTAAG
*
37194 AGTGGACCCATGCCTCAGGGGGTT-AACTGTTGG
1 AGTGGACCCATACCTCAGGGGGTTAAACTGTTGG
37227 CTAGACTCGA
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
37 9 0.09
38 61 0.60
39 32 0.31
ACGTcount: A:0.24, C:0.19, G:0.34, T:0.22
Consensus pattern (38 bp):
AGTGGACCCATACCTCAGGGGGTTAAACTGTTGGTAAG
Found at i:37267 original size:6 final size:6
Alignment explanation
Indices: 37256--37281 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
37246 CGTTAACAGA
37256 TGATTG TGATTG TGATTG TGATTG TG
1 TGATTG TGATTG TGATTG TGATTG TG
37282 GTGTAGCCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (6 bp):
TGATTG
Found at i:41830 original size:16 final size:16
Alignment explanation
Indices: 41809--41839 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41799 TCAAGTTGTA
*
41809 TAGTAATCTTATTAAT
1 TAGTAACCTTATTAAT
41825 TAGTAACCTTATTAA
1 TAGTAACCTTATTAA
41840 CTGAGCTTTT
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:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (16 bp):
TAGTAACCTTATTAAT
Found at i:42339 original size:202 final size:198
Alignment explanation
Indices: 41848--42623 Score: 1047
Period size: 202 Copynumber: 3.9 Consensus size: 198
41838 AACTGAGCTT
* *
41848 TTTCATAATTAATTAAATATTAAATATTAATACATATTCCCTAAGGCGACACATGTCAACCCTTA
1 TTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTA
* ** * * * * *
41913 CACATCGCCCGTGCAGTCTGCTAAACTCTACTGACGGTGTATTCTATAATTTTTCTTATATGATT
66 AACCCCACACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTATATAATTTTTCTTATAGGATT
* * * *
41978 ATTATACAATACATTGTAAGTGTAAATTTTGGACTCCATAAACGGGTTAAAAGGTTGACACATA-
131 ATTATACAATACACTATCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAAA-GTTGACACATAC
*
42042 CTCA
195 CCCA
* * ** * *
42046 TTTCACAATTAATTAAATATTTAATATTAATAAATATTCCCTAAGTAGACATATGCCAACCCTTA
1 TTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTA
*
42111 AACCCCACACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTATATCATTTTTCTTATAGGGAT
66 AACCCCACACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTATATAATTTTTCTTATA-GGAT
** * *
42176 TATTATACAATACACTATTGGTGTAAATTTTGGACTCTATAAGCGGGTTAGAAAGTTGCCACATA
130 TATTATACAATACACTATCAGTGTAAATTTTGGACTCCATAAGCGGGTTA-AAAGTTGACACATA
42241 CCCCA
194 CCCCA
* *
42246 TTTCATAATTAATTAAATATATTTAATATCAATACATATTCCCTAAGGGGACACATGTTAACCCT
1 TTTCATAATTAATT-AA-ATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCT
* * * * * *
42311 TAAATCCCGCACATGCAGTCGGCTAAACTCCACTGACTGTGTATTATATAATTTTTCTTATAGTA
64 TAAACCCCACACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTATATAATTTTTCTTATAGGA
*
42376 ATATTATACAATACACTGACGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACA
129 TTATTATACAATACACT-A--TCAGTGTAAATTTTGGACTCCATAAGCGGGTTAA-AAGTTGACA
42441 CATACCCCA
190 CATACCCCA
* *
42450 TTTCATAATTAATTCAATATTTAATATTAATACATATTCCCTAATGGGACACATGTCAACCCTTA
1 TTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTA
* * * *
42515 AACCCCACACGTGCATTCTGCTAAACT---CTAATGGTGTATTGTATAATTTTTCTTATAGGGAT
66 AACCCCACACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTATATAATTTTTCTTATA-GGAT
* *
42577 TATTATTCAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGG
130 TATTATACAATACACTATCAGTGTAAATTTTGGACTCCATAAGCGGG
Statistics
Matches: 507, Mismatches: 61, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
197 30 0.06
198 110 0.22
199 83 0.16
200 36 0.07
201 20 0.04
202 165 0.33
203 2 0.00
204 61 0.12
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.34
Consensus pattern (198 bp):
TTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTA
AACCCCACACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTATATAATTTTTCTTATAGGATT
ATTATACAATACACTATCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAAAGTTGACACATACC
CCA
Done.