Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013235.1 Corchorus olitorius cultivar O-4 contig13268, 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: 8064
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Found at i:110 original size:68 final size:68
Alignment explanation
Indices: 1--171 Score: 315
Period size: 68 Copynumber: 2.5 Consensus size: 68
*
1 AAGCCTCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAACGAGTTTGGCTTGTG
1 AAGCCTCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAACGAGTTTGGCTTGCG
66 AGA
66 AGA
*
69 AAGCCTTTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAACGAGTTTGGCTTGCG
1 AAGCCTCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAACGAGTTTGGCTTGCG
134 AGA
66 AGA
*
137 AAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAAC
1 AAGCCTCTGCTGCTTGGATGGAACCAAGGCTTAAC
172 GGGTCTGACT
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 99 1.00
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.25
Consensus pattern (68 bp):
AAGCCTCTGCTGCTTGGATGGAACCAAGGCTTAACTGGCTCGTATGGAAACGAGTTTGGCTTGCG
AGA
Found at i:804 original size:50 final size:50
Alignment explanation
Indices: 741--847 Score: 160
Period size: 50 Copynumber: 2.1 Consensus size: 50
731 TAAAATGCCC
* **
741 TTTGAAAAACGAATTTTGATCTTGGACTCACAAATGGAACGCAATCTTAT
1 TTTGAAAAACGAATTTTGATATCAGACTCACAAATGGAACGCAATCTTAT
* *
791 TTTGAAAATCGAATTTTGATATCAGACTCACAAATGGAATGCAATCTTAT
1 TTTGAAAAACGAATTTTGATATCAGACTCACAAATGGAACGCAATCTTAT
*
841 TATGAAA
1 TTTGAAA
848 CTTCTTGTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (50 bp):
TTTGAAAAACGAATTTTGATATCAGACTCACAAATGGAACGCAATCTTAT
Found at i:1119 original size:13 final size:14
Alignment explanation
Indices: 1101--1129 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1091 GCTTCTTTTC
1101 TTCA-TTTTTTCAT
1 TTCATTTTTTTCAT
1114 TTCATTTTTTTCAT
1 TTCATTTTTTTCAT
1128 TT
1 TT
1130 TTCATTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (14 bp):
TTCATTTTTTTCAT
Found at i:1121 original size:22 final size:23
Alignment explanation
Indices: 1096--1154 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 23
1086 CTAAAGCTTC
1096 TTTTCTTCATTTTTTCA-TTTCA
1 TTTTCTTCATTTTTTCATTTTCA
*
1118 TTTTTTTCA-TTTTTCATTTTCA
1 TTTTCTTCATTTTTTCATTTTCA
*
1140 TTTTCATCATTTTTT
1 TTTTCTTCATTTTTT
1155 TTGTATGCAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.22
22 20 0.62
23 5 0.16
ACGTcount: A:0.14, C:0.15, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTTCTTCATTTTTTCATTTTCA
Found at i:1528 original size:27 final size:27
Alignment explanation
Indices: 1498--1550 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1488 TCTTTTCTTT
1498 TTTGTTTGT-TTTT-TTTTATTTGTTTTA
1 TTTGTTT-TATTTTGTTTTA-TTGTTTTA
1525 TTTGTTTTATTTTGTTTTATTGTTTT
1 TTTGTTTTATTTTGTTTTATTGTTTT
1551 TTTTTGCATC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 1 0.04
27 18 0.75
28 5 0.21
ACGTcount: A:0.08, C:0.00, G:0.11, T:0.81
Consensus pattern (27 bp):
TTTGTTTTATTTTGTTTTATTGTTTTA
Found at i:1532 original size:18 final size:19
Alignment explanation
Indices: 1497--1556 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 19
1487 TTCTTTTCTT
*
1497 TTTTGTTTGT-TTTTTTTTA
1 TTTTGTTT-TATTTGTTTTA
1516 -TTTGTTTTATTTGTTTTA
1 TTTTGTTTTATTTGTTTTA
*
1534 TTTTGTTTTA-TTGTTTTT
1 TTTTGTTTTATTTGTTTTA
1552 TTTTG
1 TTTTG
1557 CATCTTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
17 1 0.03
18 27 0.73
19 9 0.24
ACGTcount: A:0.07, C:0.00, G:0.12, T:0.82
Consensus pattern (19 bp):
TTTTGTTTTATTTGTTTTA
Found at i:1551 original size:9 final size:9
Alignment explanation
Indices: 1498--1550 Score: 65
Period size: 9 Copynumber: 5.9 Consensus size: 9
1488 TCTTTTCTTT
1498 TTTGTTTGT-
1 TTTGTTT-TA
*
1507 TTTTTTTTA
1 TTTGTTTTA
1516 TTTGTTTTA
1 TTTGTTTTA
1525 TTTGTTTTA
1 TTTGTTTTA
1534 TTTTGTTTTA
1 -TTTGTTTTA
1544 -TTGTTTT
1 TTTGTTTT
1551 TTTTTGCATC
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
8 8 0.20
9 23 0.57
10 9 0.22
ACGTcount: A:0.08, C:0.00, G:0.11, T:0.81
Consensus pattern (9 bp):
TTTGTTTTA
Found at i:2507 original size:75 final size:75
Alignment explanation
Indices: 2384--2535 Score: 259
Period size: 75 Copynumber: 2.0 Consensus size: 75
2374 TGGATTCAGT
*
2384 CACCTCGAAATCATTGCTTTGACTAAAACTAATTTTGAAACATCTTTTGATCAAAACTCATCATT
1 CACCTCGAAATCATCGCTTTGACTAAAACTAATTTTGAAACATCTTTTGATCAAAACTCATCATT
**
2449 TTTTTGCTCA
66 CCTTTGCTCA
* *
2459 CACCTCGAAATCATCGCTTTGACTAAAACTGATTTTGAAACATCTTTTGATTAAAACTCATCATT
1 CACCTCGAAATCATCGCTTTGACTAAAACTAATTTTGAAACATCTTTTGATCAAAACTCATCATT
2524 CCTTTGCTCA
66 CCTTTGCTCA
2534 CA
1 CA
2536 GTCTAGATAA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.37
Consensus pattern (75 bp):
CACCTCGAAATCATCGCTTTGACTAAAACTAATTTTGAAACATCTTTTGATCAAAACTCATCATT
CCTTTGCTCA
Found at i:7494 original size:33 final size:33
Alignment explanation
Indices: 7395--7526 Score: 138
Period size: 33 Copynumber: 3.8 Consensus size: 33
7385 AAAAACTGAA
* ****
7395 TGGGAACTTTTCCCAATTTGAAAACTTAAAAGTTAA
1 TGGGAAC-TTTCCCAA-TTAAAAACTTAAAA-CCGG
7431 TGGGAACTTTCCCAATTTTTAAAAACTTAAAACCGG
1 TGGGAACTTTCCCAA---TTAAAAACTTAAAACCGG
* * *
7467 TGGGAACTTTCCCGATTAAAAATTTAAAACTGG
1 TGGGAACTTTCCCAATTAAAAACTTAAAACCGG
7500 TGGGAACTTTCCCAATTAAAAACTTAA
1 TGGGAACTTTCCCAATTAAAAACTTAA
7527 TGAAATTCTT
Statistics
Matches: 84, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
33 41 0.49
35 8 0.10
36 21 0.25
37 14 0.17
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (33 bp):
TGGGAACTTTCCCAATTAAAAACTTAAAACCGG
Found at i:7566 original size:18 final size:19
Alignment explanation
Indices: 7543--7578 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
7533 TCTTTTTTGA
7543 TTTTTG-AGTTTTGAAAAT
1 TTTTTGTAGTTTTGAAAAT
*
7561 TTTTTGTATTTTTGAAAA
1 TTTTTGTAGTTTTGAAAA
7579 CCTTTTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (19 bp):
TTTTTGTAGTTTTGAAAAT
Done.