Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011021.1 Corchorus capsularis cultivar CVL-1 contig11042, 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: 7160
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Found at i:2914 original size:17 final size:17
Alignment explanation
Indices: 2892--2924 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2882 ATGAAAGAGT
*
2892 TGTTTTTGGAATAAAAC
1 TGTTTTTGAAATAAAAC
2909 TGTTTTTGAAATAAAA
1 TGTTTTTGAAATAAAA
2925 AGGATGCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
TGTTTTTGAAATAAAAC
Found at i:4144 original size:15 final size:16
Alignment explanation
Indices: 4122--4160 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
4112 TTTTGAAACG
*
4122 AGAAAAAATGTTTTTC
1 AGAAAAAATGATTTTC
4138 A-AAAAAA-GATTTTC
1 AGAAAAAATGATTTTC
4152 AGAAAAAAT
1 AGAAAAAAT
4161 TGGTTTCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
14 7 0.35
15 12 0.60
16 1 0.05
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.28
Consensus pattern (16 bp):
AGAAAAAATGATTTTC
Found at i:4212 original size:11 final size:11
Alignment explanation
Indices: 4196--4225 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
4186 TGCGTGGCGA
4196 AAAAAAAGAAG
1 AAAAAAAGAAG
4207 AAAAAAAGAAG
1 AAAAAAAGAAG
4218 AAAAAAAG
1 AAAAAAAG
4226 TAGGAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAG
Found at i:4657 original size:16 final size:16
Alignment explanation
Indices: 4636--4671 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
4626 GGTCGCCAAA
4636 TCTTTTGAGAAAAGTT
1 TCTTTTGAGAAAAGTT
4652 TCTTTTGAGAAAAGTT
1 TCTTTTGAGAAAAGTT
4668 TCTT
1 TCTT
4672 GATTTTGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.08, G:0.17, T:0.47
Consensus pattern (16 bp):
TCTTTTGAGAAAAGTT
Found at i:5602 original size:104 final size:104
Alignment explanation
Indices: 5326--5670 Score: 554
Period size: 104 Copynumber: 3.3 Consensus size: 104
5316 TCTTTCATAA
* *
5326 AAGTTTTCAGAGGTCAGAGTTGATCTAATATCAAGAAGTTTCCAGAGGTCAGAGTTGATCTCATA
1 AAGTTTTCAGAGGTCAGAGTTGATCTCAT-TCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCAT-
5391 T-CAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA-TTCAGAGG
64 TCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCA-A-G
*
5432 AAGTTTTCAGAGGTCAGAGTTGATCTCAATCCAAGAAG-TTTCAAGAGGTCAGAGTTGATCTCAT
1 AAGTTTTCAGAGGTCAGAGTTGATCTC-ATTCAAGAAGTTTTC-AGAGGTCAGAGTTGATCTCAT
5496 TCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAG
64 TCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAG
*
5537 AAGTTTTCAGAGGTCAGAGTTG-TCTCATTGCAAGAAGTTTTCAGAGATCAGAGTTGATCTCATT
1 AAGTTTTCAGAGGTCAGAGTTGATCTCATT-CAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATT
*
5601 CCAAGAAGTTTTCAGAGGGCAGAGTTGATCTCATTTCAAG
65 CCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAG
5641 AAGTTTTCAGAGGTCAGAGTTGATCTCATT
1 AAGTTTTCAGAGGTCAGAGTTGATCTCATT
5671 TTCAGTATTT
Statistics
Matches: 226, Mismatches: 6, Indels: 15
0.91 0.02 0.06
Matches are distributed among these distances:
103 2 0.01
104 93 0.41
105 38 0.17
106 87 0.38
107 6 0.03
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (104 bp):
AAGTTTTCAGAGGTCAGAGTTGATCTCATTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTC
CAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAG
Found at i:5671 original size:35 final size:35
Alignment explanation
Indices: 5326--5671 Score: 545
Period size: 35 Copynumber: 9.9 Consensus size: 35
5316 TCTTTCATAA
* *
5326 AAGTTTTCAGAGGTCAGAGTTGATCTAATATCAAG
1 AAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAG
* *
5361 AAGTTTCCAGAGGTCAGAGTTGATCTCATATCAAG
1 AAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAG
5396 AAGTTTTCAGAGGTCAGAGTTGATCTCA-TTCAGAGG
1 AAGTTTTCAGAGGTCAGAGTTGATCTCATTTCA-A-G
* *
5432 AAGTTTTCAGAGGTCAGAGTTGATCTCAATCCAAG
1 AAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAG
*
5467 AAG-TTTCAAGAGGTCAGAGTTGATCTCATTCCAAG
1 AAGTTTTC-AGAGGTCAGAGTTGATCTCATTTCAAG
5502 AAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAG
1 AAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAG
*
5537 AAGTTTTCAGAGGTCAGAGTTG-TCTCATTGCAAG
1 AAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAG
* *
5571 AAGTTTTCAGAGATCAGAGTTGATCTCATTCCAAG
1 AAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAG
*
5606 AAGTTTTCAGAGGGCAGAGTTGATCTCATTTCAAG
1 AAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAG
5641 AAGTTTTCAGAGGTCAGAGTTGATCTCATTT
1 AAGTTTTCAGAGGTCAGAGTTGATCTCATTT
5672 TCAGTATTTT
Statistics
Matches: 291, Mismatches: 14, Indels: 12
0.92 0.04 0.04
Matches are distributed among these distances:
34 39 0.13
35 215 0.74
36 34 0.12
37 3 0.01
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.32
Consensus pattern (35 bp):
AAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAG
Found at i:5693 original size:35 final size:35
Alignment explanation
Indices: 5620--6188 Score: 834
Period size: 35 Copynumber: 16.5 Consensus size: 35
5610 TTTCAGAGGG
* * * *
5620 CAGAGTTGATCTCA-TTTCAAGAAGTTTTCAGA-GGT
1 CAGAGTTGATCGCATTTTC-AGTAGTTTCCA-ACGAT
* * *
5655 CAGAGTTGATCTCATTTTCAGTATTTTCCAATGAT
1 CAGAGTTGATCGCATTTTCAGTAGTTTCCAACGAT
*
5690 CAGAGTTGATCGCATTTTCAGTATTTTCCAACGAT
1 CAGAGTTGATCGCATTTTCAGTAGTTTCCAACGAT
* *
5725 CAGAGTTGATCACATTTTCAGTATTTTCCAACGAT
1 CAGAGTTGATCGCATTTTCAGTAGTTTCCAACGAT
5760 CAGAGTTGATCGCATTTTCAGTAGTTTCCAACGAT
1 CAGAGTTGATCGCATTTTCAGTAGTTTCCAACGAT
*
5795 CAGAGTTGATCACATTTTCAGTAGTTTCCAACGAT
1 CAGAGTTGATCGCATTTTCAGTAGTTTCCAACGAT
*
5830 CAGAG-T--T-GCATTTTCAGTAGTTCCCAACGAT
1 CAGAGTTGATCGCATTTTCAGTAGTTTCCAACGAT
*
5861 CAGAGTTGATCGCATTTTCAGTATTTTCCAACGAT
1 CAGAGTTGATCGCATTTTCAGTAGTTTCCAACGAT
5896 CAGAGTTGATCGCATTTTCAGTAGTTTCCAACGAT
1 CAGAGTTGATCGCATTTTCAGTAGTTTCCAACGAT
* *
5931 CAGAGTTGATCACATTTTCAGTATTTTCCAACGAT
1 CAGAGTTGATCGCATTTTCAGTAGTTTCCAACGAT
* *
5966 CAGAGTTGATCACATTTTCAGAAGTTTCCAACGAT
1 CAGAGTTGATCGCATTTTCAGTAGTTTCCAACGAT
6001 CAGAGTTGATCGCATTTTCAGTAGTTTCCAACGAT
1 CAGAGTTGATCGCATTTTCAGTAGTTTCCAACGAT
6036 CAGAG-T--T-GCATTTTCAGTAGTTTCCAACGAT
1 CAGAGTTGATCGCATTTTCAGTAGTTTCCAACGAT
*
6067 CAGAGTTGATCGCATTTTCAGTATTTTCCAACGAT
1 CAGAGTTGATCGCATTTTCAGTAGTTTCCAACGAT
*
6102 CAGAGTTGATCGCATTTTCAGTAGTTTTCAACGAT
1 CAGAGTTGATCGCATTTTCAGTAGTTTCCAACGAT
* *
6137 CAGAGTTGATCACATTTTCAGTAGTTTCCAACAAT
1 CAGAGTTGATCGCATTTTCAGTAGTTTCCAACGAT
* * *
6172 TAGAGGTGATCTCATTT
1 CAGAGTTGATCGCATTT
6189 CAAGAAATTT
Statistics
Matches: 494, Mismatches: 30, Indels: 20
0.91 0.06 0.04
Matches are distributed among these distances:
31 56 0.11
32 4 0.01
34 5 0.01
35 425 0.86
36 4 0.01
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (35 bp):
CAGAGTTGATCGCATTTTCAGTAGTTTCCAACGAT
Found at i:5694 original size:70 final size:70
Alignment explanation
Indices: 5480--6213 Score: 801
Period size: 70 Copynumber: 10.6 Consensus size: 70
5470 TTTCAAGAGG
* * * *
5480 TCAGAGTTGATCTCA-TTCCAAGAAGTTTTCAGA-GGTCAGAGTTGATCTCA-TTTCAAGAAGTT
1 TCAGAGTTGATCTCATTTTC-AGAAGTTTCCA-ACGATCAGAGTTGATCTCATTTTC-AGTA-TT
*
5542 TT-CAGA-GG
62 TTCCA-ACGA
* * * *
5550 TCAGAGTTG-TCTCA-TTGCAAGAAGTTTTCAGA-GATCAGAGTTGATCTCA-TTCCAAGAAGTT
1 TCAGAGTTGATCTCATTTTC-AGAAGTTTCCA-ACGATCAGAGTTGATCTCATTTTC-AGTA-TT
*
5611 TT-CAGA-GG
62 TTCCA-ACGA
* * *
5619 GCAGAGTTGATCTCA-TTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATCTCATTTTCAGTATTTT
1 TCAGAGTTGATCTCATTTTC-AGAAGTTTCCA-ACGATCAGAGTTGATCTCATTTTCAGTATTTT
*
5682 CCAATGA
64 CCAACGA
* * * *
5689 TCAGAGTTGATCGCATTTTCAGTATTTTCCAACGATCAGAGTTGATCACATTTTCAGTATTTTCC
1 TCAGAGTTGATCTCATTTTCAGAAGTTTCCAACGATCAGAGTTGATCTCATTTTCAGTATTTTCC
5754 AACGA
66 AACGA
* * * *
5759 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGATCAGAGTTGATCACATTTTCAGTAGTTTCC
1 TCAGAGTTGATCTCATTTTCAGAAGTTTCCAACGATCAGAGTTGATCTCATTTTCAGTATTTTCC
5824 AACGA
66 AACGA
* * *
5829 TCAGAGTTG----CATTTTCAGTAGTTCCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTCC
1 TCAGAGTTGATCTCATTTTCAGAAGTTTCCAACGATCAGAGTTGATCTCATTTTCAGTATTTTCC
5890 AACGA
66 AACGA
* * *
5895 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGATCAGAGTTGATCACATTTTCAGTATTTTCC
1 TCAGAGTTGATCTCATTTTCAGAAGTTTCCAACGATCAGAGTTGATCTCATTTTCAGTATTTTCC
5960 AACGA
66 AACGA
* * *
5965 TCAGAGTTGATCACATTTTCAGAAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTCC
1 TCAGAGTTGATCTCATTTTCAGAAGTTTCCAACGATCAGAGTTGATCTCATTTTCAGTATTTTCC
6030 AACGA
66 AACGA
* *
6035 TCAGAGTTG----CATTTTCAGTAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTCC
1 TCAGAGTTGATCTCATTTTCAGAAGTTTCCAACGATCAGAGTTGATCTCATTTTCAGTATTTTCC
6096 AACGA
66 AACGA
* * * * *
6101 TCAGAGTTGATCGCATTTTCAGTAGTTTTCAACGATCAGAGTTGATCACATTTTCAGTAGTTTCC
1 TCAGAGTTGATCTCATTTTCAGAAGTTTCCAACGATCAGAGTTGATCTCATTTTCAGTATTTTCC
*
6166 AACAA
66 AACGA
* * * * *
6171 TTAGAGGTGATCTCA-TTTCAAGAAATTTCCGATGATCAGAGTT
1 TCAGAGTTGATCTCATTTTC-AGAAGTTTCCAACGATCAGAGTT
6214 AATCCAGAGG
Statistics
Matches: 607, Mismatches: 42, Indels: 30
0.89 0.06 0.04
Matches are distributed among these distances:
66 127 0.21
69 75 0.12
70 398 0.66
71 7 0.01
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (70 bp):
TCAGAGTTGATCTCATTTTCAGAAGTTTCCAACGATCAGAGTTGATCTCATTTTCAGTATTTTCC
AACGA
Found at i:5880 original size:171 final size:174
Alignment explanation
Indices: 5620--6168 Score: 864
Period size: 171 Copynumber: 3.2 Consensus size: 174
5610 TTTCAGAGGG
* * * * * *
5620 CAGAGTTGATCTCA-TTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATCTCATTTTCAGTATTTTC
1 CAGAGTTGATCACATTTTC-AGTAGTTTCCA-ACGATCAGAGTT-ATCGCATTTTCAGTAGTTTC
* *
5683 CAATGATCAGAGTTGATCGCATTTTCAGTATTTTCCAACGATCAGAGTTGATCACATTTTCAGTA
63 CAACGATCAGAGTTGATCGCATTTTCAGTATTTTCCAACGATCAGAGTTGATCGCATTTTCAGTA
5748 TTTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGAT
128 TTTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGAT
*
5795 CAGAGTTGATCACATTTTCAGTAGTTTCCAACGATCAGAG-T-T-GCATTTTCAGTAGTTCCCAA
1 CAGAGTTGATCACATTTTCAGTAGTTTCCAACGATCAGAGTTATCGCATTTTCAGTAGTTTCCAA
*
5857 CGATCAGAGTTGATCGCATTTTCAGTATTTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTT
66 CGATCAGAGTTGATCGCATTTTCAGTATTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTT
* *
5922 TCCAACGATCAGAGTTGATCACATTTTCAGTATTTTCCAACGAT
131 TCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGAT
*
5966 CAGAGTTGATCACATTTTCAGAAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTCCA
1 CAGAGTTGATCACATTTTCAGTAGTTTCCAACGATCAGAGTT-ATCGCATTTTCAGTAGTTTCCA
*
6031 ACGATCAGAG-T--T-GCATTTTCAGTAGTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATT
65 ACGATCAGAGTTGATCGCATTTTCAGTATTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATT
*
6092 TTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTTCAACGAT
130 TTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGAT
6137 CAGAGTTGATCACATTTTCAGTAGTTTCCAAC
1 CAGAGTTGATCACATTTTCAGTAGTTTCCAAC
6169 AATTAGAGGT
Statistics
Matches: 348, Mismatches: 20, Indels: 16
0.91 0.05 0.04
Matches are distributed among these distances:
171 280 0.80
172 3 0.01
174 4 0.01
175 57 0.16
176 4 0.01
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (174 bp):
CAGAGTTGATCACATTTTCAGTAGTTTCCAACGATCAGAGTTATCGCATTTTCAGTAGTTTCCAA
CGATCAGAGTTGATCGCATTTTCAGTATTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTT
TCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGAT
Found at i:5899 original size:206 final size:206
Alignment explanation
Indices: 5654--6213 Score: 953
Period size: 206 Copynumber: 2.7 Consensus size: 206
5644 TTTTCAGAGG
* *
5654 TCAGAGTTGATCTCATTTTCAGTATTTTCCAATGATCAGAGTTGATCGCATTTTCAGTATTTTCC
1 TCAGAGTTGATCGCATTTTCAGTATTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTCC
* *
5719 AACGATCAGAGTTGATCACATTTTCAGTATTTTCCAACGATCAGAGTTGATCGCATTTTCAGTAG
66 AACGATCAGAGTTGATCACATTTTCAGTATTTTCCAACGATCAGAGTTGATCACATTTTCAGAAG
5784 TTTCCAACGATCAGAGTTGATCACATTTTCAGTAGTTTCCAACGATCAGAGTTGCATTTTCAGTA
131 TTTCCAACGATCAGAGTTGATCACATTTTCAGTAGTTTCCAACGATCAGAGTTGCATTTTCAGTA
5849 GTTCCCAACGA
196 GTTCCCAACGA
*
5860 TCAGAGTTGATCGCATTTTCAGTATTTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTCC
1 TCAGAGTTGATCGCATTTTCAGTATTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTCC
5925 AACGATCAGAGTTGATCACATTTTCAGTATTTTCCAACGATCAGAGTTGATCACATTTTCAGAAG
66 AACGATCAGAGTTGATCACATTTTCAGTATTTTCCAACGATCAGAGTTGATCACATTTTCAGAAG
*
5990 TTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGATCAGAGTTGCATTTTCAGTA
131 TTTCCAACGATCAGAGTTGATCACATTTTCAGTAGTTTCCAACGATCAGAGTTGCATTTTCAGTA
*
6055 GTTTCCAACGA
196 GTTCCCAACGA
6066 TCAGAGTTGATCGCATTTTCAGTATTTTCCAACGATCAGAGTTGATCGCATTTTCAGTAGTTTT-
1 TCAGAGTTGATCGCATTTTCAGTATTTTCCAACGATCAGAGTTGATCGCATTTTCAGTA-TTTTC
* * * * *
6130 CAACGATCAGAGTTGATCACATTTTCAGTAGTTTCCAACAATTAGAGGTGATCTCA-TTTCAAGA
65 CAACGATCAGAGTTGATCACATTTTCAGTATTTTCCAACGATCAGAGTTGATCACATTTTC-AGA
* * *
6194 AATTTCCGATGATCAGAGTT
129 AGTTTCCAACGATCAGAGTT
6214 AATCCAGAGG
Statistics
Matches: 336, Mismatches: 16, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
205 4 0.01
206 329 0.98
207 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (206 bp):
TCAGAGTTGATCGCATTTTCAGTATTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTCC
AACGATCAGAGTTGATCACATTTTCAGTATTTTCCAACGATCAGAGTTGATCACATTTTCAGAAG
TTTCCAACGATCAGAGTTGATCACATTTTCAGTAGTTTCCAACGATCAGAGTTGCATTTTCAGTA
GTTCCCAACGA
Done.