Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009255.1 Corchorus capsularis cultivar CVL-1 contig09276, 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: 19964
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Found at i:169 original size:15 final size:14
Alignment explanation
Indices: 118--210 Score: 58
Period size: 11 Copynumber: 7.1 Consensus size: 14
108 TTATGATTAG
*
118 TTTTAATTAGTTAA
1 TTTTAATTAGTTTA
** *
132 TTAAAATTA-CTTA
1 TTTTAATTAGTTTA
*
145 GTTT-ATTAGTTTA
1 TTTTAATTAGTTTA
158 TGTTTAATTAG--TA
1 T-TTTAATTAGTTTA
*
171 -TCTAATTAGTTTA
1 TTTTAATTAGTTTA
184 TTATTAATTAG--TA
1 TT-TTAATTAGTTTA
197 -TTTAATTAGTTTA
1 TTTTAATTAGTTTA
210 T
1 T
211 GATTAAAATG
Statistics
Matches: 58, Mismatches: 11, Indels: 20
0.65 0.12 0.22
Matches are distributed among these distances:
11 16 0.28
12 5 0.09
13 14 0.24
14 11 0.19
15 12 0.21
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (14 bp):
TTTTAATTAGTTTA
Found at i:178 original size:26 final size:26
Alignment explanation
Indices: 149--216 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
139 TACTTAGTTT
149 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
*
175 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
*
201 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
217 AATGAAGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 1 0.03
26 37 0.97
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAGTATCTA
Found at i:264 original size:24 final size:25
Alignment explanation
Indices: 225--284 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
215 AAAATGAAGG
*
225 AAAATGAA-TTTGAAG-ATTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
248 AAAATGAAGTTTGAAGAAGTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
* *
273 GAAATTAAGTTT
1 AAAATGAAGTTT
285 AGGGTTTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 8 0.25
24 7 0.22
25 17 0.53
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (25 bp):
AAAATGAAGTTTGAAGAAGTTGTTA
Found at i:396 original size:21 final size:22
Alignment explanation
Indices: 354--398 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
344 GCAAAAGTGT
* **
354 AAAAAGGGGGGCGGTATTTAGC
1 AAAAAGGGGGACGGTAAATAGC
376 AAAAA-GGGGACGGTAAATAGC
1 AAAAAGGGGGACGGTAAATAGC
397 AA
1 AA
399 TCCAAATATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.42, C:0.09, G:0.36, T:0.13
Consensus pattern (22 bp):
AAAAAGGGGGACGGTAAATAGC
Found at i:6203 original size:42 final size:42
Alignment explanation
Indices: 6156--6241 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
6146 TGTACTCTTC
* *
6156 AAATGAGCTCATTTCCACAAAAGAAGTTACAAAATTAGGAAT
1 AAATGAGCTCATTTCCACAAAAGAAGTTACAAAATCAAGAAT
6198 AAATGAGCTCATTTCCACAAAAGAAGTTACAAAATCAAGAAT
1 AAATGAGCTCATTTCCACAAAAGAAGTTACAAAATCAAGAAT
6240 AA
1 AA
6242 GTAAAAGACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.50, C:0.15, G:0.13, T:0.22
Consensus pattern (42 bp):
AAATGAGCTCATTTCCACAAAAGAAGTTACAAAATCAAGAAT
Found at i:7023 original size:24 final size:24
Alignment explanation
Indices: 6996--7048 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
6986 AAATTTTATC
6996 TATATTAAAATTTAATCCGTTTTG
1 TATATTAAAATTTAATCCGTTTTG
7020 TATATTAAAATTTAATCCGTTTTG
1 TATATTAAAATTTAATCCGTTTTG
7044 TATAT
1 TATAT
7049 AATTAATCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.51
Consensus pattern (24 bp):
TATATTAAAATTTAATCCGTTTTG
Found at i:7119 original size:39 final size:39
Alignment explanation
Indices: 7062--7138 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
7052 TAATCAAATT
* * *
7062 GAATTCTTTTAGTCCAATTCCAATTATGTATTACGGGTA
1 GAATTCTTTTAGTACAATTCAAATTATATATTACGGGTA
*
7101 GAATT-TTATTAGTACAATTCAAATTATATTTTACGGGT
1 GAATTCTT-TTAGTACAATTCAAATTATATATTACGGGT
7139 TCTATTAGTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 2 0.06
39 31 0.94
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (39 bp):
GAATTCTTTTAGTACAATTCAAATTATATATTACGGGTA
Found at i:7145 original size:34 final size:34
Alignment explanation
Indices: 7107--7173 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
7097 GGTAGAATTT
*
7107 TATTAGTACAATT-CAAATTATATTTTACGGGTTC
1 TATTAGTACAATTGC-AATTATATATTACGGGTTC
*
7141 TATTAGTCCAATTGCAATTATATATTACGGGTT
1 TATTAGTACAATTGCAATTATATATTACGGGTT
7174 AAGTGTAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 29 0.97
35 1 0.03
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.43
Consensus pattern (34 bp):
TATTAGTACAATTGCAATTATATATTACGGGTTC
Found at i:19604 original size:19 final size:18
Alignment explanation
Indices: 19580--19615 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
19570 TGAAGATTTC
19580 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
19599 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
19616 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Done.