Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011659.1 Corchorus capsularis cultivar CVL-1 contig11680, 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: 22709
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:1857 original size:156 final size:154
Alignment explanation
Indices: 1467--1857 Score: 357
Period size: 156 Copynumber: 2.5 Consensus size: 154
1457 GTAGACCATT
* * ** * *
1467 TTGGCTAAGTTTCATCTCAAACGGACTTAAGATGAAAAACTTATGCAAGTTTTTCAGTTAAGGAC
1 TTGGCAAAGTTTCACCTCAATTGGACTTAAGATGAAAAACTTATGCTAGTTTTTCAGTTAACGAC
* * * * *
1532 AATTTGGGGTGAGAAACCACTTCATCATGATAGGGAGTTCGGTTTTACTTAGAATTTTTTCCATA
66 -ATTTGAGGTGAGAAACCACTTCACCATCATAGGGAGCTCGGTTTTACTTAGAATTTTTCCCATA
* *
1597 GTCATACGGAGATAATCTAAGCCTAC
130 GTCATACGGAGAGAACCTAAGCC-AC
* * ** * *
1623 TGGTGG-AAA-ATTAACCT-TTTTGGACTT-AGAATGAGAAACTTATGCTAGTTTTTCATTTAAC
1 T--TGGCAAAGTTTCACCTCAATTGGACTTAAG-ATGAAAAACTTATGCTAGTTTTTCAGTTAAC
* * * *
1684 GACAATTCAGGGAGAGAAACCTAGTTCACCATCA-AGGGGAGCTCGGTTTTACTT-GAAATTTTT
63 GACATTTGA-GGTGAGAAACC-ACTTCACCATCATA-GGGAGCTCGGTTTTACTTAG-AATTTTT
* * *
1747 CCCATAGTC-TCATGGGGAGAGCCTAAGTCC-C
124 CCCATAGTCAT-ACGGAGAGAACCTAAG-CCAC
* * *
1778 TTGGCAAAGTTTCAGCTCAATTGGACTTAAGGTGAAAAACTTATGCTAGTTTTTCAGTTAATGAC
1 TTGGCAAAGTTTCACCTCAATTGGACTTAAGATGAAAAACTTATGCTAGTTTTTCAGTTAACGAC
1843 AGTTTGAGGTGAGAA
66 A-TTTGAGGTGAGAA
1858 GCTCGGTTTA
Statistics
Matches: 183, Mismatches: 38, Indels: 28
0.73 0.15 0.11
Matches are distributed among these distances:
153 3 0.02
154 8 0.04
155 56 0.31
156 104 0.57
157 9 0.05
158 3 0.02
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.32
Consensus pattern (154 bp):
TTGGCAAAGTTTCACCTCAATTGGACTTAAGATGAAAAACTTATGCTAGTTTTTCAGTTAACGAC
ATTTGAGGTGAGAAACCACTTCACCATCATAGGGAGCTCGGTTTTACTTAGAATTTTTCCCATAG
TCATACGGAGAGAACCTAAGCCAC
Found at i:4283 original size:25 final size:24
Alignment explanation
Indices: 4251--4297 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
4241 GGGGATCATC
*
4251 TTTTTTCTTTAACAGCAAAGTTCCT
1 TTTTTTC-TCAACAGCAAAGTTCCT
*
4276 TTTTTTCTCGACAGCAAAGTTC
1 TTTTTTCTCAACAGCAAAGTTC
4298 ATCTTCTTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (24 bp):
TTTTTTCTCAACAGCAAAGTTCCT
Found at i:4407 original size:8 final size:8
Alignment explanation
Indices: 4394--4420 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
4384 ATAGTAAAAT
4394 AAAAAGAA
1 AAAAAGAA
4402 AAAAAGAA
1 AAAAAGAA
4410 AAAAAGAA
1 AAAAAGAA
4418 AAA
1 AAA
4421 CAAAGAAGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:7244 original size:135 final size:135
Alignment explanation
Indices: 6998--7283 Score: 450
Period size: 135 Copynumber: 2.1 Consensus size: 135
6988 AAGACTTGGA
* * *
6998 GGGG-AAAACCAACAACTGCTTGGTGCCCAGCCCGGTGCTCTGCCTTTTCAACAAGTCAACCATC
1 GGGGCAAAACCAACAACTGCTTGGTGCCCAGCCCGGTCCTCTCCCCTTTCAACAAGTCAACCATC
* *
7062 AGGTGAATAACCCACAAGTCATGGCTCAGATTGGTCTCATCGATGAAAGACTTGGGGGGCAAGGA
66 AGGTGAACAACCAACAAGTCATGGCTCAGATTGGTCTCATCGATGAAAGACTTGGGGGGCAAGGA
7127 CTCGG
131 CTCGG
*
7132 GGGGCAAAACCAACAACTGCTTGGTGCCTAGCCCGGTCCTCTTCCCCTTT-AACAAGTCAACCAT
1 GGGGCAAAACCAACAACTGCTTGGTGCCCAGCCCGGTCCTC-TCCCCTTTCAACAAGTCAACCAT
* * * * *
7196 CAGGTGAACAATCAACATGTCATGGCTCAGGTTGGTCTGATCGATGAAAGATTTGGGGGGCAAGG
65 CAGGTGAACAACCAACAAGTCATGGCTCAGATTGGTCTCATCGATGAAAGACTTGGGGGGCAAGG
7261 ACTCGG
130 ACTCGG
7267 GGGGCAAAACCAACAAC
1 GGGGCAAAACCAACAAC
7284 CACTTAGTGC
Statistics
Matches: 139, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
134 4 0.03
135 129 0.93
136 6 0.04
ACGTcount: A:0.28, C:0.26, G:0.27, T:0.20
Consensus pattern (135 bp):
GGGGCAAAACCAACAACTGCTTGGTGCCCAGCCCGGTCCTCTCCCCTTTCAACAAGTCAACCATC
AGGTGAACAACCAACAAGTCATGGCTCAGATTGGTCTCATCGATGAAAGACTTGGGGGGCAAGGA
CTCGG
Found at i:10194 original size:21 final size:21
Alignment explanation
Indices: 10159--10211 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
10149 ACAACAGCTC
* *
10159 ATGGAGTCGACTGCTCGAA-TA
1 ATGGAGTCAAATGCTC-AACTA
10180 ATGGAGTCAAATGCTCAACTTA
1 ATGGAGTCAAATGCTCAAC-TA
10202 A-GGAGTCAAA
1 ATGGAGTCAAA
10212 CGACTTACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 2 0.07
21 23 0.82
22 3 0.11
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (21 bp):
ATGGAGTCAAATGCTCAACTA
Found at i:13713 original size:156 final size:156
Alignment explanation
Indices: 13329--13713 Score: 369
Period size: 156 Copynumber: 2.5 Consensus size: 156
13319 CATTTTGGCT
* ** **
13329 AAGTTTCATCTCAAACGGACTTAAGATGAAAAACTTA--CATAAGTTTTTCAGTTAAGGACCGTT
1 AAGTTTCACCTCAATTGGACTTAAGATGAAAAACTTATGC-T-AGTTTTTCAGTTAAGGACAATT
* * * * * *
13392 TGGGGTGAGAAACCACTTGATCATGATAGGGAGTTCGGTTTTACTTAGAATTTTTTCCATAGTCT
64 TGAGGTGAGAAACCACTTCACCATCATAGGGAGCTCGGTTTTACTTAGAATTTTTCCCATAGTCT
* *
13457 TATGGAGATAATCTAAGCCTACTGGTGGAA
129 CATGGAGAGAATCTAAGCC-ACT-GTGGAA
* ** * *
13487 AA--TTAACCT-TTTTGGACTT-AGAATGAGAAACTTATGCTAGTTTTTCATTTAAGGACAA-TT
1 AAGTTTCACCTCAATTGGACTTAAG-ATGAAAAACTTATGCTAGTTTTTCAGTTAAGGACAATTT
* * * *
13547 CAGGGAGAGAAACCTAGTTCACCATCA-AGGGGAGCTCTGTTTTACTT-GAAATTTTTCCCATAG
65 GA-GGTGAGAAACC-ACTTCACCATCATA-GGGAGCTCGGTTTTACTTAG-AATTTTTCCCATAG
* *
13610 TCTCATGGGGAGAGTCTAAGTCC-CT-TGGAA
126 TCTCATGGAGAGAATCTAAG-CCACTGTGGAA
* *
13640 AAGTTTCAGCTCAATTGGACTTAAGGTGAAAAACTTATGCTAGTTTTTCAGTTAAGGACAATTTG
1 AAGTTTCACCTCAATTGGACTTAAGATGAAAAACTTATGCTAGTTTTTCAGTTAAGGACAATTTG
13705 AGGTGAGAA
66 AGGTGAGAA
13714 GCCCGGTTTA
Statistics
Matches: 181, Mismatches: 33, Indels: 28
0.75 0.14 0.12
Matches are distributed among these distances:
153 7 0.04
154 4 0.02
155 53 0.29
156 107 0.59
157 8 0.04
158 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.33
Consensus pattern (156 bp):
AAGTTTCACCTCAATTGGACTTAAGATGAAAAACTTATGCTAGTTTTTCAGTTAAGGACAATTTG
AGGTGAGAAACCACTTCACCATCATAGGGAGCTCGGTTTTACTTAGAATTTTTCCCATAGTCTCA
TGGAGAGAATCTAAGCCACTGTGGAA
Found at i:15493 original size:32 final size:32
Alignment explanation
Indices: 15450--15512 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
15440 CACGTCATCT
15450 ATGAGACTAACCAATTAAACCTTGACATGTCC
1 ATGAGACTAACCAATTAAACCTTGACATGTCC
* *
15482 ATGAGATTAACCAATTAAATCTTGACATGTC
1 ATGAGACTAACCAATTAAACCTTGACATGTC
15513 AAATGACCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.29
Consensus pattern (32 bp):
ATGAGACTAACCAATTAAACCTTGACATGTCC
Found at i:16759 original size:14 final size:14
Alignment explanation
Indices: 16740--16769 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
16730 ACGAGTCGAG
*
16740 TATTTGGGTTTGGT
1 TATTTGGGTTAGGT
16754 TATTTGGGTTAGGT
1 TATTTGGGTTAGGT
16768 TA
1 TA
16770 GTTTCGGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.00, G:0.33, T:0.53
Consensus pattern (14 bp):
TATTTGGGTTAGGT
Found at i:20598 original size:33 final size:33
Alignment explanation
Indices: 20549--20624 Score: 134
Period size: 33 Copynumber: 2.3 Consensus size: 33
20539 TTACAGCTAT
*
20549 ATATCTACTCATCCCATGTTTGATTTGTTGAGCG
1 ATATCTA-TTATCCCATGTTTGATTTGTTGAGCG
20583 ATATCTATTATCCCATGTTTGATTTGTTGAGCG
1 ATATCTATTATCCCATGTTTGATTTGTTGAGCG
20616 ATATCTATT
1 ATATCTATT
20625 GGCACTGGCA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
33 34 0.83
34 7 0.17
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.45
Consensus pattern (33 bp):
ATATCTATTATCCCATGTTTGATTTGTTGAGCG
Done.