Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014673.1 Corchorus capsularis cultivar CVL-1 contig14694, 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: 36918
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:210 original size:59 final size:59
Alignment explanation
Indices: 136--257 Score: 199
Period size: 59 Copynumber: 2.1 Consensus size: 59
126 TTGAGTCATA
* *
136 TGATAGTTTTTGCATGAGTTGCATGAAAACCTAGGATTACAATTTGATTGTTGATGGAT
1 TGATAGTTTTTGCATGAGTTGCATGAAAACCTAGGATAAAAATTTGATTGTTGATGGAT
* **
195 TGATAGTTTTTGCATGAGTTGCATGAGAACCTAGGATAAAAATTTGATTGTTTTTGGAT
1 TGATAGTTTTTGCATGAGTTGCATGAAAACCTAGGATAAAAATTTGATTGTTGATGGAT
254 TGAT
1 TGAT
258 CTTTTATTCC
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.29, C:0.07, G:0.24, T:0.40
Consensus pattern (59 bp):
TGATAGTTTTTGCATGAGTTGCATGAAAACCTAGGATAAAAATTTGATTGTTGATGGAT
Found at i:1510 original size:19 final size:18
Alignment explanation
Indices: 1486--1522 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1476 TTGAAGATTT
1486 CTTGAAGATAATTTGAAGA
1 CTTGAAGATAA-TTGAAGA
*
1505 CTTGAAGATCATTGAAGA
1 CTTGAAGATAATTGAAGA
1523 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (18 bp):
CTTGAAGATAATTGAAGA
Found at i:8954 original size:11 final size:11
Alignment explanation
Indices: 8914--8959 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
8904 TGTCATCGGA
8914 CTTAATGGCAT
1 CTTAATGGCAT
*
8925 CTTCAAAGG-AT
1 CTT-AATGGCAT
*
8936 C-AAATGGCAT
1 CTTAATGGCAT
8946 CTTAATGGCAT
1 CTTAATGGCAT
8957 CTT
1 CTT
8960 CTTGGTGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
9 4 0.14
10 3 0.11
11 17 0.61
12 4 0.14
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (11 bp):
CTTAATGGCAT
Found at i:13000 original size:27 final size:27
Alignment explanation
Indices: 12964--13019 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
12954 TAACTATTTA
*
12964 TTTTGGGACAAATTGGCCCCTTAACTT
1 TTTTGGGACAAATTGACCCCTTAACTT
12991 TTTTGGGACAAATTGACCCCTTAACTT
1 TTTTGGGACAAATTGACCCCTTAACTT
13018 TT
1 TT
13020 AAAAACGAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.39
Consensus pattern (27 bp):
TTTTGGGACAAATTGACCCCTTAACTT
Found at i:20485 original size:18 final size:18
Alignment explanation
Indices: 20462--20497 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
20452 TGTGGGAAGC
20462 ACATGAGATTCTGATGTG
1 ACATGAGATTCTGATGTG
*
20480 ACATGAGATTCTGTTGTG
1 ACATGAGATTCTGATGTG
20498 GAAGTCACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.11, G:0.28, T:0.36
Consensus pattern (18 bp):
ACATGAGATTCTGATGTG
Found at i:31440 original size:6 final size:6
Alignment explanation
Indices: 31429--31453 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
31419 ACAACATTAA
31429 TGTAAT TGTAAT TGTAAT TGTAAT T
1 TGTAAT TGTAAT TGTAAT TGTAAT T
31454 TAAACGAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (6 bp):
TGTAAT
Found at i:35200 original size:15 final size:15
Alignment explanation
Indices: 35180--35265 Score: 93
Period size: 15 Copynumber: 5.5 Consensus size: 15
35170 TTTGAGTTGG
35180 ATTTGGG-CTAGGTTA
1 ATTTGGGTC-AGGTTA
*
35195 ATTTGGGTTCGGGTTA
1 ATTTGGG-TCAGGTTA
35211 ATTTGGGTCAGGTTA
1 ATTTGGGTCAGGTTA
* *
35226 ATTTGGATTCGGGTTGA
1 ATTTGG-GTCAGGTT-A
35243 ATTTGGGTCAGGTTA
1 ATTTGGGTCAGGTTA
*
35258 ATTCGGGT
1 ATTTGGGT
35266 TCGGGTTCTG
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
15 28 0.47
16 24 0.40
17 8 0.13
ACGTcount: A:0.17, C:0.07, G:0.35, T:0.41
Consensus pattern (15 bp):
ATTTGGGTCAGGTTA
Found at i:35211 original size:16 final size:16
Alignment explanation
Indices: 35190--35272 Score: 107
Period size: 16 Copynumber: 5.2 Consensus size: 16
35180 ATTTGGGCTA
35190 GGTTAATTTGGGTTCG
1 GGTTAATTTGGGTTCG
*
35206 GGTTAATTTGGG-TCA
1 GGTTAATTTGGGTTCG
*
35221 GGTTAATTTGGATTCG
1 GGTTAATTTGGGTTCG
*
35237 GGTTGAATTTGGG-TCA
1 GGTT-AATTTGGGTTCG
*
35253 GGTTAATTCGGGTTCG
1 GGTTAATTTGGGTTCG
35269 GGTT
1 GGTT
35273 CTGTTTGGGT
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
15 20 0.35
16 30 0.53
17 7 0.12
ACGTcount: A:0.16, C:0.07, G:0.36, T:0.41
Consensus pattern (16 bp):
GGTTAATTTGGGTTCG
Found at i:35251 original size:32 final size:32
Alignment explanation
Indices: 35175--35272 Score: 146
Period size: 32 Copynumber: 3.1 Consensus size: 32
35165 TCGGGTTTGA
*
35175 GTTGGATTTGGG-CTAGGTTAATTTGGGTTCGG
1 GTTGAATTTGGGTC-AGGTTAATTTGGGTTCGG
*
35207 GTT-AATTTGGGTCAGGTTAATTTGGATTCGG
1 GTTGAATTTGGGTCAGGTTAATTTGGGTTCGG
*
35238 GTTGAATTTGGGTCAGGTTAATTCGGGTTCGG
1 GTTGAATTTGGGTCAGGTTAATTTGGGTTCGG
35270 GTT
1 GTT
35273 CTGTTTGGGT
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
31 27 0.45
32 33 0.55
ACGTcount: A:0.15, C:0.07, G:0.37, T:0.41
Consensus pattern (32 bp):
GTTGAATTTGGGTCAGGTTAATTTGGGTTCGG
Found at i:35769 original size:26 final size:26
Alignment explanation
Indices: 35733--35784 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
35723 ACTATTTATA
*
35733 AAAAATTTATATGTAATTAAAATTTT
1 AAAAATATATATGTAATTAAAATTTT
* * *
35759 AAAAATATATATTTTATTAAATTTTT
1 AAAAATATATATGTAATTAAAATTTT
35785 TAAATTTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
AAAAATATATATGTAATTAAAATTTT
Done.