Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024042.1 Corchorus olitorius cultivar O-4 contig24075, 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: 34818
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Found at i:2136 original size:16 final size:16
Alignment explanation
Indices: 2115--2146 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2105 TAAGTTCTTA
2115 CCAAACTTGATATAGG
1 CCAAACTTGATATAGG
2131 CCAAACTTGATATAGG
1 CCAAACTTGATATAGG
2147 AGGCTTGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (16 bp):
CCAAACTTGATATAGG
Found at i:5767 original size:69 final size:69
Alignment explanation
Indices: 5665--5820 Score: 197
Period size: 69 Copynumber: 2.3 Consensus size: 69
5655 TTCCAAGACT
* *** *
5665 AACTCGTTTCCATAC-AGGCAGTTTAAGCCTTGGTTCCATCCAAGCATTTGGGACTTTTCCATAA
1 AACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCAGCAGGGACTTTTCCACAA
*
5729 GTCA
66 GCCA
* * * *
5733 AACTCGTTTCCATACGAGTCAGTTTAAGCGTTGGTTCCATTCAAGTAGCAGGGGCTTTTCCACAA
1 AACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCAGCAGGGACTTTTCCACAA
5798 GCCA
66 GCCA
* *
5802 AACTTGTTTCCATATGAGT
1 AACTCGTTTCCATACGAGT
5821 TAAGTTTCAA
Statistics
Matches: 75, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
68 15 0.20
69 60 0.80
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (69 bp):
AACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCAGCAGGGACTTTTCCACAA
GCCA
Found at i:6086 original size:47 final size:47
Alignment explanation
Indices: 5840--6141 Score: 338
Period size: 47 Copynumber: 6.4 Consensus size: 47
5830 ATCCAGGTAA
** *
5840 TCTTTT-TCGCTTCCATACGAGTCTACAATTTAGTGACCCAAGTTGG
1 TCTTTTCTCGCTTCCACGCGAGTCTACAATTTAGTGACCAAAGTTGG
*
5886 TCTTTTCTCGCTTCCATC-CGAGTCTACAATTTAGTGGCCAAAGTTGG
1 TCTTTTCTCGCTTCCA-CGCGAGTCTACAATTTAGTGACCAAAGTTGG
* *
5933 TCTTTTCTCGCTTCCATGCAAGTCTACAATTTAGTGACCAAAGTTGG
1 TCTTTTCTCGCTTCCACGCGAGTCTACAATTTAGTGACCAAAGTTGG
* *
5980 TCTTTTCCCGCTTCCATGCGAGTCTACAATTTAGTGACCAAAGTTGG
1 TCTTTTCTCGCTTCCACGCGAGTCTACAATTTAGTGACCAAAGTTGG
* * ** * *
6027 TCTTTTCCCACTTCCACGCGAGTCTATGATTTGGTGACCAAAGTTGC
1 TCTTTTCTCGCTTCCACGCGAGTCTACAATTTAGTGACCAAAGTTGG
* * * * * * * ** * *
6074 TATTTTCTCACTTTCACGTGAGTTTGCAATATCTTTACAAAAGTTGG
1 TCTTTTCTCGCTTCCACGCGAGTCTACAATTTAGTGACCAAAGTTGG
* *
6121 TTTTTTCTCGCTTCCATGCGA
1 TCTTTTCTCGCTTCCACGCGA
6142 ATCTGCAAGA
Statistics
Matches: 220, Mismatches: 33, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
46 6 0.03
47 214 0.97
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (47 bp):
TCTTTTCTCGCTTCCACGCGAGTCTACAATTTAGTGACCAAAGTTGG
Found at i:6229 original size:3 final size:3
Alignment explanation
Indices: 6221--6275 Score: 94
Period size: 3 Copynumber: 18.7 Consensus size: 3
6211 AATAGGCCTA
*
6221 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6268 AAT AAT AA
1 AAT AAT AA
6276 AAAAAGAAGA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:6442 original size:13 final size:13
Alignment explanation
Indices: 6426--6464 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
6416 TTAGAGAGGT
6426 TGCAAAGAGGGGC
1 TGCAAAGAGGGGC
6439 TGCAAAGAGGGGC
1 TGCAAAGAGGGGC
6452 TGCAAAGAGGGGC
1 TGCAAAGAGGGGC
6465 AGCTGTAGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.46, T:0.08
Consensus pattern (13 bp):
TGCAAAGAGGGGC
Found at i:7900 original size:18 final size:18
Alignment explanation
Indices: 7873--7915 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
7863 AAAATCATCA
7873 CAAA-CAATCATATTTAT
1 CAAAGCAATCATATTTAT
7890 CAAAGCAATCATATTTAT
1 CAAAGCAATCATATTTAT
7908 CAAAGCAA
1 CAAAGCAA
7916 GGCAACAGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.49, C:0.19, G:0.05, T:0.28
Consensus pattern (18 bp):
CAAAGCAATCATATTTAT
Found at i:10289 original size:17 final size:17
Alignment explanation
Indices: 10267--10302 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
10257 GTCTCATTCA
10267 TTCTTGTACTTGAATTT
1 TTCTTGTACTTGAATTT
10284 TTCTTGTACTTGAATTT
1 TTCTTGTACTTGAATTT
10301 TT
1 TT
10303 GGATTGTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.11, G:0.11, T:0.61
Consensus pattern (17 bp):
TTCTTGTACTTGAATTT
Found at i:13481 original size:15 final size:15
Alignment explanation
Indices: 13457--13495 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
13447 TTATTTCCTT
13457 CTTTTT-TTTTCTTC
1 CTTTTTCTTTTCTTC
*
13471 CTTTTTCTTTTCTTT
1 CTTTTTCTTTTCTTC
*
13486 CTTTTCCTTT
1 CTTTTTCTTT
13496 CTATTTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
CTTTTTCTTTTCTTC
Found at i:15534 original size:24 final size:24
Alignment explanation
Indices: 15504--15563 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
15494 ACACTAAAGG
15504 CAAAGCCGAAACTGACAAAGCTTA
1 CAAAGCCGAAACTGACAAAGCTTA
*
15528 CATAGCCGAAACTGACAAAGCTTA
1 CAAAGCCGAAACTGACAAAGCTTA
*
15552 CAAAACCGAAAC
1 CAAAGCCGAAAC
15564 AAAAGGGAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.47, C:0.27, G:0.15, T:0.12
Consensus pattern (24 bp):
CAAAGCCGAAACTGACAAAGCTTA
Found at i:17824 original size:48 final size:48
Alignment explanation
Indices: 17761--17862 Score: 177
Period size: 48 Copynumber: 2.1 Consensus size: 48
17751 GTCTTAACTC
17761 CATTAATTGATGTTGTTAAGAGAATTAAAAGCTGGAAAATACTCCATG
1 CATTAATTGATGTTGTTAAGAGAATTAAAAGCTGGAAAATACTCCATG
* * *
17809 CGTTAATTGATGTTGTTAAGAGTATTAAAAGCTGGAAAATACTTCATG
1 CATTAATTGATGTTGTTAAGAGAATTAAAAGCTGGAAAATACTCCATG
17857 CATTAA
1 CATTAA
17863 AATTAAGTCT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (48 bp):
CATTAATTGATGTTGTTAAGAGAATTAAAAGCTGGAAAATACTCCATG
Found at i:21540 original size:19 final size:20
Alignment explanation
Indices: 21502--21545 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
21492 TGGAATTTGG
21502 GTTTTATGAAATTCAAATTA
1 GTTTTATGAAATTCAAATTA
21522 GCTTTTA-GAAATT-AAATTA
1 G-TTTTATGAAATTCAAATTA
21541 GTTTT
1 GTTTT
21546 CATATGCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.17
19 7 0.30
20 7 0.30
21 5 0.22
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (20 bp):
GTTTTATGAAATTCAAATTA
Found at i:21827 original size:43 final size:43
Alignment explanation
Indices: 21768--22090 Score: 442
Period size: 43 Copynumber: 7.7 Consensus size: 43
21758 CCAATAACCA
* * *
21768 AAAGTCCCCAAACACATATATAATACGGGGGCATCTCTATCCC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC
* * * *
21811 AAAGTCCTCAAACACATATATAACACAGAGACATCTATA-T-C
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC
*
21852 AAAGTCCCCAAACACATATATAACACAAGGGCATCTCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC
* * * *
21895 AAAGTCCTCAAACACATATATAACACAGAGACATCTATA-T-C
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC
*
21936 AAAGTCCACAAACAC--ATATAACACAGGGGCATCTCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC
*
21977 AAAGTCCCCAAACACATATATAACACAAGGGCATCTCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC
* *
22020 AAAGTCGCCAAACACATATATAACACATGGGCATCTCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC
* *
22063 AAAGTCCTCAAACACATTTATAACACAG
1 AAAGTCCCCAAACACATATATAACACAG
22091 AGACATTTCT
Statistics
Matches: 245, Mismatches: 29, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
39 19 0.08
40 1 0.00
41 65 0.27
42 2 0.01
43 158 0.64
ACGTcount: A:0.41, C:0.28, G:0.10, T:0.21
Consensus pattern (43 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC
Found at i:21909 original size:84 final size:84
Alignment explanation
Indices: 21768--22096 Score: 511
Period size: 84 Copynumber: 3.9 Consensus size: 84
21758 CCAATAACCA
* * *
21768 AAAGTCCCCAAACACATATATAATACGGGGGCATCTCTATCCCAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAGTCCTCAAACACATATATA
21833 ACACAGAGACATCTATATC
66 ACACAGAGACATCTATATC
*
21852 AAAGTCCCCAAACACATATATAACACAAGGGCATCTCTATTCCAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAGTCCTCAAACACATATATA
21917 ACACAGAGACATCTATATC
66 ACACAGAGACATCTATATC
* *
21936 AAAGTCCACAAACAC--ATATAACACAGGGGCATCTCTATTCCAAAGTCCCCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAGTCCTCAAACACATATATA
* *
21999 ACACA-AGGGCATCTCTATTCC
66 ACACAGA-GACATCTATA-T-C
* * *
22020 AAAGTCGCCAAACACATATATAACACATGGGCATCTCTATTCCAAAGTCCTCAAACACATTTATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAGTCCTCAAACACATATATA
22085 ACACAGAGACAT
66 ACACAGAGACAT
22097 TTCTCCTTAT
Statistics
Matches: 224, Mismatches: 15, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
81 1 0.00
82 59 0.26
83 1 0.00
84 108 0.48
86 54 0.24
87 1 0.00
ACGTcount: A:0.41, C:0.28, G:0.10, T:0.21
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAGTCCTCAAACACATATATA
ACACAGAGACATCTATATC
Found at i:21992 original size:125 final size:122
Alignment explanation
Indices: 21768--22096 Score: 453
Period size: 125 Copynumber: 2.6 Consensus size: 122
21758 CCAATAACCA
* *
21768 AAAGTCCCCAAACACATATATAATACGGGGGCATCTCTATCCCAAAGTCCTCAAACACATATATA
1 AAAGT-CCCAAACACATATATAACAC-AGGGCATCTCTAT-CCAAAGTCCTCAAACAC--ATATA
21833 ACACAGAGACATCTATATCAAAGTCCCCAAACACATATATAACACAAGGGCATCTCTATTCC
61 ACACAGAGACATCTATATCAAAGTCCCCAAACACATATATAACACAAGGGCATCTCTATTCC
* * *
21895 AAAGTCCTCAAACACATATATAACACAGAGACATCTATAT-CAAAGTCCACAAACACATATAACA
1 AAAGTCC-CAAACACATATATAACACAG-GGCATCTCTATCCAAAGTCCTCAAACACATATAACA
* * *
21959 CAGGGGCATCTCTATTCCAAAGTCCCCAAACACATATATAACACAAGGGCATCTCTATTCC
64 CAGAGACATCTATA-T-CAAAGTCCCCAAACACATATATAACACAAGGGCATCTCTATTCC
22020 AAAGTCGCCAAACACATATATAACACATGGGCATCTCTATTCCAAAGTCCTCAAACACATTTATA
1 AAAGTC-CCAAACACATATATAACACA-GGGCATCTCTA-TCCAAAGTCCTCAAACACA--TATA
22085 ACACAGAGACAT
61 ACACAGAGACAT
22097 TTCTCCTTAT
Statistics
Matches: 179, Mismatches: 13, Indels: 18
0.85 0.06 0.09
Matches are distributed among these distances:
123 19 0.11
124 1 0.01
125 92 0.51
126 6 0.03
127 47 0.26
129 14 0.08
ACGTcount: A:0.41, C:0.28, G:0.10, T:0.21
Consensus pattern (122 bp):
AAAGTCCCAAACACATATATAACACAGGGCATCTCTATCCAAAGTCCTCAAACACATATAACACA
GAGACATCTATATCAAAGTCCCCAAACACATATATAACACAAGGGCATCTCTATTCC
Found at i:34535 original size:43 final size:43
Alignment explanation
Indices: 34480--34757 Score: 375
Period size: 43 Copynumber: 6.6 Consensus size: 43
34470 TAACCAAAAT
* * *
34480 TCCCCAAACACATATATAACACAGGGGAATCTTTATCCCAAAG
1 TCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAG
* * * *
34523 TCCTCAAACACATATATAACACAGAGTCATCTATA-T-CAAAG
1 TCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAG
* *
34564 TCCCCAAACACATATATAACATAAGGGCATCTCTATTCCAAAG
1 TCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAG
* * * * *
34607 TCCTCAAACACATATATAACATAGAGACATCTATA-T-CAAAG
1 TCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAG
34648 TCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAG
1 TCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAG
34691 TCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAG
1 TCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAG
* * *
34734 TTCTCAAACACATTTATAACACAG
1 TCCCCAAACACATATATAACACAG
34758 TTATGGCAAA
Statistics
Matches: 206, Mismatches: 25, Indels: 8
0.86 0.10 0.03
Matches are distributed among these distances:
41 69 0.33
42 3 0.01
43 134 0.65
ACGTcount: A:0.41, C:0.27, G:0.09, T:0.23
Consensus pattern (43 bp):
TCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAG
Found at i:34621 original size:84 final size:84
Alignment explanation
Indices: 34480--34757 Score: 412
Period size: 84 Copynumber: 3.3 Consensus size: 84
34470 TAACCAAAAT
* * *
34480 TCCCCAAACACATATATAACACAGGGGAATCTTTATCCCAAAGTCCTCAAACACATATATAACAC
1 TCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAGTCCTCAAACACATATATAACAC
*
34545 AGAGTCATCTATATCAAAG
66 AGAGACATCTATATCAAAG
* * *
34564 TCCCCAAACACATATATAACATAAGGGCATCTCTATTCCAAAGTCCTCAAACACATATATAACAT
1 TCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAGTCCTCAAACACATATATAACAC
34629 AGAGACATCTATATCAAAG
66 AGAGACATCTATATCAAAG
*
34648 TCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAGTCCCCAAACACATATATAACAC
1 TCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAGTCCTCAAACACATATATAACAC
* * *
34713 AGGGGCATCTCTATTCCAAAG
66 AGAGACATCTATA-T-CAAAG
* * *
34734 TTCTCAAACACATTTATAACACAG
1 TCCCCAAACACATATATAACACAG
34758 TTATGGCAAA
Statistics
Matches: 175, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
84 148 0.85
85 1 0.01
86 26 0.15
ACGTcount: A:0.41, C:0.27, G:0.09, T:0.23
Consensus pattern (84 bp):
TCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAGTCCTCAAACACATATATAACAC
AGAGACATCTATATCAAAG
Found at i:34710 original size:127 final size:126
Alignment explanation
Indices: 34484--34757 Score: 399
Period size: 127 Copynumber: 2.2 Consensus size: 126
34474 CAAAATTCCC
* * *
34484 CAAACACATATATAACACAGGGGAATCTTTATCCCAAAGTCCTCAAACACATATATAACACAGAG
1 CAAACACATATATAACACAGGAGAATCTATAT-CCAAAGTCCCCAAACACATATATAACACAGAG
* *
34549 TCATCTATATCAAAGTCCCCAAACACATATATAACATAAGGGCATCTCTATTCCAAAGTCCT
65 GCATCTATATCAAAGTCCCCAAACACATATATAACACAAGGGCATCTCTATTCCAAAGTCCT
* *
34611 CAAACACATATATAACATA-GAGACATCTATAT-CAAAGTCCCCAAACACATATATAACACAGGG
1 CAAACACATATATAACACAGGAGA-ATCTATATCCAAAGTCCCCAAACACATATATAACACAGAG
* * *
34674 GCATCTCTATTCCAAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAGTTCT
65 GCATCTATA-T-CAAAGTCCCCAAACACATATATAACACAAGGGCATCTCTATTCCAAAGTCCT
*
34738 CAAACACATTTATAACACAG
1 CAAACACATATATAACACAG
34758 TTATGGCAAA
Statistics
Matches: 131, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
125 36 0.27
126 4 0.03
127 91 0.69
ACGTcount: A:0.41, C:0.26, G:0.09, T:0.23
Consensus pattern (126 bp):
CAAACACATATATAACACAGGAGAATCTATATCCAAAGTCCCCAAACACATATATAACACAGAGG
CATCTATATCAAAGTCCCCAAACACATATATAACACAAGGGCATCTCTATTCCAAAGTCCT
Done.