Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008200.1 Corchorus capsularis cultivar CVL-1 contig08221, 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: 2085
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Found at i:762 original size:8 final size:8
Alignment explanation
Indices: 751--790 Score: 66
Period size: 8 Copynumber: 5.2 Consensus size: 8
741 TTCTTCTCTT
751 TTTTTTCA
1 TTTTTTCA
759 TTTTTTCA
1 TTTTTTCA
767 TTTTTTCA
1 TTTTTTCA
775 -TTTTTCA
1 TTTTTTCA
782 -TTTTTCA
1 TTTTTTCA
789 TT
1 TT
791 GCACTTGGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 14 0.45
8 17 0.55
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTTTCA
Found at i:772 original size:16 final size:16
Alignment explanation
Indices: 751--790 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
741 TTCTTCTCTT
751 TTTTTTCATTTTTTCA
1 TTTTTTCATTTTTTCA
767 TTTTTTCA-TTTTTCA
1 TTTTTTCATTTTTTCA
782 -TTTTTCATT
1 TTTTTTCATT
791 GCACTTGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.30
15 8 0.35
16 8 0.35
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTTCATTTTTTCA
Found at i:788 original size:7 final size:7
Alignment explanation
Indices: 752--790 Score: 60
Period size: 7 Copynumber: 5.3 Consensus size: 7
742 TCTTCTCTTT
752 TTTTTCA
1 TTTTTCA
759 TTTTTTCA
1 -TTTTTCA
767 TTTTTTCA
1 -TTTTTCA
775 TTTTTCA
1 TTTTTCA
782 TTTTTCA
1 TTTTTCA
789 TT
1 TT
791 GCACTTGGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 16 0.52
8 15 0.48
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTCA
Found at i:845 original size:12 final size:13
Alignment explanation
Indices: 817--845 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
807 AGTTAACCCG
817 AAAACTCTTTTCA
1 AAAACTCTTTTCA
830 AAAACTCTTTTCA
1 AAAACTCTTTTCA
843 AAA
1 AAA
846 GTTTTGACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (13 bp):
AAAACTCTTTTCA
Found at i:1163 original size:20 final size:22
Alignment explanation
Indices: 1130--1186 Score: 93
Period size: 20 Copynumber: 2.7 Consensus size: 22
1120 CTCTCTTTTT
1130 TTTTGATT-ATTTTTTTATTGA
1 TTTTGATTGATTTTTTTATTGA
1151 -TTT-ATTGATTTTTTTATTGA
1 TTTTGATTGATTTTTTTATTGA
1171 TTTTGATTGATTTTTT
1 TTTTGATTGATTTTTT
1187 CTTTTCTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
19 3 0.09
20 16 0.48
21 3 0.09
22 11 0.33
ACGTcount: A:0.18, C:0.00, G:0.11, T:0.72
Consensus pattern (22 bp):
TTTTGATTGATTTTTTTATTGA
Found at i:1173 original size:12 final size:12
Alignment explanation
Indices: 1125--1186 Score: 53
Period size: 12 Copynumber: 5.5 Consensus size: 12
1115 GTTCTCTCTC
1125 TTTTTTT-TTGA
1 TTTTTTTATTGA
1136 TTATTTTT-TT-A
1 TT-TTTTTATTGA
**
1147 TTGATTTATTGA
1 TTTTTTTATTGA
1159 TTTTTTTATTGA
1 TTTTTTTATTGA
*
1171 --TTTTGATTGA
1 TTTTTTTATTGA
1181 TTTTTT
1 TTTTTT
1187 CTTTTCTTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
10 12 0.29
11 7 0.17
12 22 0.54
ACGTcount: A:0.16, C:0.00, G:0.10, T:0.74
Consensus pattern (12 bp):
TTTTTTTATTGA
Found at i:1498 original size:13 final size:13
Alignment explanation
Indices: 1482--1527 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
1472 AATGAGTTTC
*
1482 GAAAACCATTTTT
1 GAAAAACATTTTT
*
1495 GAAAAACATCTTT
1 GAAAAACATTTTT
1508 GAAAAATCATTTTTT
1 GAAAAA-CA-TTTTT
1523 GAAAA
1 GAAAA
1528 TCATCATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 17 0.61
14 2 0.07
15 9 0.32
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.35
Consensus pattern (13 bp):
GAAAAACATTTTT
Found at i:1528 original size:14 final size:14
Alignment explanation
Indices: 1490--1531 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
1480 TCGAAAACCA
*
1490 TTTTTGAAAAACA-
1 TTTTTGAAAATCAT
*
1503 TCTTTGAAAAATCAT
1 TTTTTG-AAAATCAT
1518 TTTTTGAAAATCAT
1 TTTTTGAAAATCAT
1532 CATTTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 5 0.21
14 14 0.58
15 5 0.21
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (14 bp):
TTTTTGAAAATCAT
Found at i:1535 original size:17 final size:15
Alignment explanation
Indices: 1490--1539 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 15
1480 TCGAAAACCA
1490 TTTTTGAAAAA-CA-
1 TTTTTGAAAAATCAT
*
1503 TCTTTGAAAAATCAT
1 TTTTTGAAAAATCAT
1518 TTTTTGAAAATCATCAT
1 TTTTTGAAAA--ATCAT
1535 TTTTT
1 TTTTT
1540 TTTGAAAACC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 10 0.32
14 2 0.06
15 9 0.29
17 10 0.32
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.48
Consensus pattern (15 bp):
TTTTTGAAAAATCAT
Found at i:1631 original size:7 final size:7
Alignment explanation
Indices: 1621--1663 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
1611 CTTTTTTTCA
1621 TCATTTT
1 TCATTTT
1628 TCATTCATT
1 TCATT--TT
1637 T--TTTT
1 TCATTTT
1642 TCATTTT
1 TCATTTT
1649 TCATTTT
1 TCATTTT
1656 TCATTTT
1 TCATTTT
1663 T
1 T
1664 TTTGGGAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
5 3 0.09
7 26 0.81
9 3 0.09
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (7 bp):
TCATTTT
Found at i:1635 original size:11 final size:11
Alignment explanation
Indices: 1614--1653 Score: 57
Period size: 10 Copynumber: 3.8 Consensus size: 11
1604 TATTTTTCTT
1614 TTTTTCA-TCA
1 TTTTTCATTCA
1624 TTTTTCATTCA
1 TTTTTCATTCA
*
1635 TTTTT-TTTCA
1 TTTTTCATTCA
1645 TTTTTCATT
1 TTTTTCATT
1654 TTTCATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 16 0.62
11 10 0.38
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTTCATTCA
Found at i:1645 original size:21 final size:22
Alignment explanation
Indices: 1612--1653 Score: 68
Period size: 21 Copynumber: 1.9 Consensus size: 22
1602 TTTATTTTTC
1612 TTTTTTTCATCATTTTTCATTCA
1 TTTTTTT-ATCATTTTTCATTCA
1635 TTTTTTT-TCATTTTTCATT
1 TTTTTTTATCATTTTTCATT
1654 TTTCATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
23 7 0.37
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTTTTATCATTTTTCATTCA
Found at i:1658 original size:24 final size:24
Alignment explanation
Indices: 1605--1666 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
1595 AAGTGCCTTT
1605 ATTTTTC-TTTTTTTCATCATTTTTC
1 ATTTTTCATTTTTTT--TCATTTTTC
1630 A---TTCATTTTTTTTCATTTTTC
1 ATTTTTCATTTTTTTTCATTTTTC
1651 ATTTTTCATTTTTTTT
1 ATTTTTCATTTTTTTT
1667 GGGAATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
21 10 0.30
22 3 0.09
23 7 0.21
24 12 0.36
25 1 0.03
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (24 bp):
ATTTTTCATTTTTTTTCATTTTTC
Done.