Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023667.1 Corchorus olitorius cultivar O-4 contig23700, 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: 22893
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Found at i:4996 original size:9 final size:9
Alignment explanation
Indices: 4982--5015 Score: 54
Period size: 8 Copynumber: 4.0 Consensus size: 9
4972 TGTCACTCTT
4982 AAAATAAAA
1 AAAATAAAA
4991 AAAAT-AAA
1 AAAATAAAA
4999 AAAATAAAA
1 AAAATAAAA
5008 AAAA-AAAA
1 AAAATAAAA
5016 CGAGGTTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 12 0.50
9 12 0.50
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (9 bp):
AAAATAAAA
Found at i:5004 original size:17 final size:16
Alignment explanation
Indices: 4982--5015 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
4972 TGTCACTCTT
4982 AAAATAAAAAAAATAAA
1 AAAATAAAAAAAA-AAA
4999 AAAATAAAAAAAAAAA
1 AAAATAAAAAAAAAAA
5015 A
1 A
5016 CGAGGTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (16 bp):
AAAATAAAAAAAAAAA
Found at i:7552 original size:21 final size:20
Alignment explanation
Indices: 7518--7556 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
7508 CTATTCTTTA
*
7518 TTTTTTTCTTTTTTCTTCCC
1 TTTTTTTCTATTTTCTTCCC
7538 TTTTCTTTCTATTTTCTTC
1 TTTT-TTTCTATTTTCTTC
7557 TTCATCTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTTTTCTATTTTCTTCCC
Found at i:7576 original size:37 final size:35
Alignment explanation
Indices: 7533--7601 Score: 120
Period size: 37 Copynumber: 1.9 Consensus size: 35
7523 TTCTTTTTTC
7533 TTCCCTTTTCTTTCTATTTTCTTCTTCATCTCCTTCG
1 TTCCCTTTTCTTTCTATTTTC--CTTCATCTCCTTCG
7570 TTCCCTTTTCTTTCTATTTTCCTTCATCTCCT
1 TTCCCTTTTCTTTCTATTTTCCTTCATCTCCT
7602 GCGATCTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
35 11 0.34
37 21 0.66
ACGTcount: A:0.06, C:0.33, G:0.01, T:0.59
Consensus pattern (35 bp):
TTCCCTTTTCTTTCTATTTTCCTTCATCTCCTTCG
Found at i:7998 original size:17 final size:17
Alignment explanation
Indices: 7976--8011 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
7966 TTTGTGGAGC
*
7976 TATTGATGGGAGCTCGA
1 TATTGATGGGAGCCCGA
7993 TATTGATGGGAGCCCGA
1 TATTGATGGGAGCCCGA
8010 TA
1 TA
8012 AAGGTCTGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.25, C:0.14, G:0.33, T:0.28
Consensus pattern (17 bp):
TATTGATGGGAGCCCGA
Found at i:13774 original size:131 final size:131
Alignment explanation
Indices: 13532--14101 Score: 754
Period size: 131 Copynumber: 4.3 Consensus size: 131
13522 TAAACTAAAG
* * *** *
13532 TGCGAAAATGATGGAACTGACCCTTTC-ACCGAAAGGGTATTTTTGGAAAGACAAAACCAAACCT
1 TGCGAAAAT-ATGAAACTGACCC-TTCGACCGGAAGGGTATTTTTGGAAAGACAAAATTGAACTT
* * * * *
13596 AGATGTGAAAAATATGAAAATGACCCTTCGACCGAAAGGGTAGTTTTGGAAAACAAAATTGAACT
64 AGATG-CAAAAAGATGAAACTGACCCTTCGACCGGAAGGGTATTTTTGGAAAACAAAATTGAACT
13661 TAGATA
128 TAG--A
* * *
13667 TG-GCAAATATGAAACAGACCCTTCGACTGGAAGGGTATTTTTGGAAA-ACAAAATTGAACTTAG
1 TGCGAAAATATGAAACTGACCCTTCGACCGGAAGGGTATTTTTGGAAAGACAAAATTGAACTTAG
* * * * *
13730 ATGCGAAAAGATGAAGCTGACCCTTCGACTGGAAGGGTAATTTTGGAAATAGAAAATTGAACTTA
66 ATGCAAAAAGATGAAACTGACCCTTCGACCGGAAGGGTATTTTTGGAAA-ACAAAATTGAACTTA
*
13795 TA
130 GA
* * *
13797 TGCGAAAAGATGAAACTGACCCTTCGACCGGAAGGGTATTTTTGGAAATAGAAAATTGAACTTAG
1 TGCGAAAATATGAAACTGACCCTTCGACCGGAAGGGTATTTTTGGAAAGACAAAATTGAACTTAG
* *
13862 ATGCAAAAAGATGAAATTGACCCTTCGACCGGAATGGTATTTTTGGAAAACAAAATTGAACTTAG
66 ATGCAAAAAGATGAAACTGACCCTTCGACCGGAAGGGTATTTTTGGAAAACAAAATTGAACTTAG
*
13927 G
131 A
13928 TGCGAAAATATGAAACTGACCCTTCGACCGGAAGGGTATTTTTGGAAA-ACAAAATTGAACTTA-
1 TGCGAAAATATGAAACTGACCCTTCGACCGGAAGGGTATTTTTGGAAAGACAAAATTGAACTTAG
* * * * * *
13991 TTGCAAAAATATGAAACTGACACTTAGACCGGAAGGGTATTTTTGGACATAGAAAATTGAACTTA
66 ATGCAAAAAGATGAAACTGACCCTTCGACCGGAAGGGTATTTTTGGA-AAACAAAATTGAACTTA
14056 GA
130 GA
14058 TGCGAAAATATGAAACTGACCCTTCGACCGGAAGGGTATTTTTG
1 TGCGAAAATATGAAACTGACCCTTCGACCGGAAGGGTATTTTTG
14102 TACATAGAAA
Statistics
Matches: 386, Mismatches: 44, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
129 41 0.11
130 77 0.20
131 140 0.36
132 90 0.23
133 31 0.08
134 5 0.01
135 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.25
Consensus pattern (131 bp):
TGCGAAAATATGAAACTGACCCTTCGACCGGAAGGGTATTTTTGGAAAGACAAAATTGAACTTAG
ATGCAAAAAGATGAAACTGACCCTTCGACCGGAAGGGTATTTTTGGAAAACAAAATTGAACTTAG
A
Found at i:14113 original size:66 final size:65
Alignment explanation
Indices: 13532--14101 Score: 750
Period size: 66 Copynumber: 8.7 Consensus size: 65
13522 TAAACTAAAG
* * *** *
13532 TGCGAAAATGATGGAACTGACCCTTTC-ACCGAAAGGGTATTTTTGGAAAGACAAAACCAAACCT
1 TGCGAAAAT-ATGAAACTGACCC-TTCGACCGGAAGGGTATTTTTGGAAA-ACAAAATTGAACTT
13596 AGA
63 AGA
* * * *
13599 TGTGAAAAATATGAAAATGACCCTTCGACCGAAAGGGTAGTTTTGGAAAACAAAATTGAACTTAG
1 TGCG-AAAATATGAAACTGACCCTTCGACCGGAAGGGTATTTTTGGAAAACAAAATTGAACTTAG
13664 ATA
65 --A
* * *
13667 TG-GCAAATATGAAACAGACCCTTCGACTGGAAGGGTATTTTTGGAAAACAAAATTGAACTTAGA
1 TGCGAAAATATGAAACTGACCCTTCGACCGGAAGGGTATTTTTGGAAAACAAAATTGAACTTAGA
* * * * * *
13731 TGCGAAAAGATGAAGCTGACCCTTCGACTGGAAGGGTAATTTTGGAAATAGAAAATTGAACTTAT
1 TGCGAAAATATGAAACTGACCCTTCGACCGGAAGGGTATTTTTGGAAA-ACAAAATTGAACTTAG
13796 A
65 A
* *
13797 TGCGAAAAGATGAAACTGACCCTTCGACCGGAAGGGTATTTTTGGAAATAGAAAATTGAACTTAG
1 TGCGAAAATATGAAACTGACCCTTCGACCGGAAGGGTATTTTTGGAAA-ACAAAATTGAACTTAG
13862 A
65 A
* * * * *
13863 TGCAAAAAGATGAAATTGACCCTTCGACCGGAATGGTATTTTTGGAAAACAAAATTGAACTTAGG
1 TGCGAAAATATGAAACTGACCCTTCGACCGGAAGGGTATTTTTGGAAAACAAAATTGAACTTAGA
*
13928 TGCGAAAATATGAAACTGACCCTTCGACCGGAAGGGTATTTTTGGAAAACAAAATTGAACTTA-T
1 TGCGAAAATATGAAACTGACCCTTCGACCGGAAGGGTATTTTTGGAAAACAAAATTGAACTTAGA
* * * * *
13992 TGCAAAAATATGAAACTGACACTTAGACCGGAAGGGTATTTTTGGACATAGAAAATTGAACTTAG
1 TGCGAAAATATGAAACTGACCCTTCGACCGGAAGGGTATTTTTGGA-AAACAAAATTGAACTTAG
14057 A
65 A
14058 TGCGAAAATATGAAACTGACCCTTCGACCGGAAGGGTATTTTTG
1 TGCGAAAATATGAAACTGACCCTTCGACCGGAAGGGTATTTTTG
14102 TACATAGAAA
Statistics
Matches: 451, Mismatches: 44, Indels: 17
0.88 0.09 0.03
Matches are distributed among these distances:
64 46 0.10
65 129 0.29
66 232 0.51
67 36 0.08
68 8 0.02
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.25
Consensus pattern (65 bp):
TGCGAAAATATGAAACTGACCCTTCGACCGGAAGGGTATTTTTGGAAAACAAAATTGAACTTAGA
Found at i:14806 original size:18 final size:18
Alignment explanation
Indices: 14783--14818 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
14773 AGACAATAAA
14783 GCCCAAAACAAATCCAAG
1 GCCCAAAACAAATCCAAG
* *
14801 GCCCAAAGCAAATTCAAG
1 GCCCAAAACAAATCCAAG
14819 TTACTACTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.31, G:0.14, T:0.08
Consensus pattern (18 bp):
GCCCAAAACAAATCCAAG
Found at i:19252 original size:29 final size:29
Alignment explanation
Indices: 19210--19268 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
19200 ATGGTATGGA
19210 TCTATGCATGTAGACTCTCTCCCCCACAC
1 TCTATGCATGTAGACTCTCTCCCCCACAC
19239 TCTATGCATGTAGACTCTCTCCCCCACAC
1 TCTATGCATGTAGACTCTCTCCCCCACAC
19268 T
1 T
19269 TAAAAGACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.20, C:0.41, G:0.10, T:0.29
Consensus pattern (29 bp):
TCTATGCATGTAGACTCTCTCCCCCACAC
Done.