Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015129.1 Corchorus capsularis cultivar CVL-1 contig15150, 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: 48958
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1630 original size:2 final size:2
Alignment explanation
Indices: 1623--1658 Score: 54
Period size: 2 Copynumber: 17.0 Consensus size: 2
1613 AGTAGGTTTA
1623 AT AT AT AT AT AT GAT AT AT GAT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT -AT AT AT -AT AT AT AT AT AT AT AT
1659 GACATATAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 28 0.88
3 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1655 original size:24 final size:24
Alignment explanation
Indices: 1621--1682 Score: 81
Period size: 24 Copynumber: 2.5 Consensus size: 24
1611 ATAGTAGGTT
*
1621 TAATATATATATATG-ATATATGA
1 TAATATATATATATGAATATAAGA
1644 TATATATATATATATGACATATAAGA
1 TA-ATATATATATATGA-ATATAAGA
*
1670 TAAGATATATATA
1 TAATATATATATA
1683 AGATGAGATG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 2 0.06
24 13 0.38
25 10 0.29
26 9 0.26
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (24 bp):
TAATATATATATATGAATATAAGA
Found at i:2708 original size:2 final size:2
Alignment explanation
Indices: 2703--2736 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2693 ATAATAATTA
*
2703 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2737 TCTTTTGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4886 original size:107 final size:103
Alignment explanation
Indices: 4718--4975 Score: 381
Period size: 107 Copynumber: 2.5 Consensus size: 103
4708 TAGCCTTAAC
*
4718 TTCACTAAGTTTAGTCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATTAATA
1 TTCACTAAGTTTAG-CCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTAATA
4783 ATTTATTATTATAGGGTTTTAGAAATAAAATACAAAACTAA
65 A--TATTATTATAGGGTTTTAGAAATAAAATACAAAACTAA
* * *
4824 TTTCACTAAATTTAGCCCCAAATTAAATTTTTATTTTTATTTTAAGGGTAAATTCCATAATTAAT
1 -TTCACTAAGTTTAG-CCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTAAT
* * *
4889 AATATTGTTATAGGGTTTTAGAAATAAAATATATAACTAA
64 AATATTATTATAGGGTTTTAGAAATAAAATACAAAACTAA
** *
4929 TTCACTAAGTTTAGCCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
4976 TAGAAAAATT
Statistics
Matches: 138, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
103 29 0.21
104 13 0.09
105 35 0.25
107 61 0.44
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.42
Consensus pattern (103 bp):
TTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTAATAA
TATTATTATAGGGTTTTAGAAATAAAATACAAAACTAA
Found at i:7187 original size:3 final size:3
Alignment explanation
Indices: 7179--7213 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
7169 GCTAGTTAGA
7179 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
7214 GAGAACCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12513 original size:15 final size:17
Alignment explanation
Indices: 12485--12519 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
12475 TGTATCTATC
12485 TATCTATCTATCTACTA
1 TATCTATCTATCTACTA
12502 TATCTA-CT-TCTACTA
1 TATCTATCTATCTACTA
12517 TAT
1 TAT
12520 AAAAAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
16 2 0.11
17 6 0.33
ACGTcount: A:0.29, C:0.23, G:0.00, T:0.49
Consensus pattern (17 bp):
TATCTATCTATCTACTA
Found at i:16980 original size:30 final size:29
Alignment explanation
Indices: 16911--16983 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
16901 GTAGTGTCTA
*
16911 GACGTTTTGCCACCCAAACTTCAATCTTG
1 GACGTTTTGCCCCCCAAACTTCAATCTTG
* *
16940 GACATTTTGCCCCCCAAACTTCAATTTTGG
1 GACGTTTTGCCCCCCAAACTTCAATCTT-G
16970 GACGTTTTGCCCCC
1 GACGTTTTGCCCCC
16984 TCAACCTAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 25 0.64
30 14 0.36
ACGTcount: A:0.21, C:0.33, G:0.15, T:0.32
Consensus pattern (29 bp):
GACGTTTTGCCCCCCAAACTTCAATCTTG
Found at i:17206 original size:29 final size:28
Alignment explanation
Indices: 17164--17234 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 28
17154 TTAGGTTGAG
*
17164 GGGGTAAAACGTCCCAAAATTGAAGTTCA
1 GGGGCAAAACGT-CCAAAATTGAAGTTCA
*
17193 GGGGCAAAATGTCCAAAATTGAAGTTC-
1 GGGGCAAAACGTCCAAAATTGAAGTTCA
17220 GGAGGACAAAACGTC
1 GG-GG-CAAAACGTC
17235 TAAACGCTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 2 0.05
28 17 0.46
29 18 0.49
ACGTcount: A:0.38, C:0.17, G:0.27, T:0.18
Consensus pattern (28 bp):
GGGGCAAAACGTCCAAAATTGAAGTTCA
Found at i:18438 original size:31 final size:31
Alignment explanation
Indices: 18400--18461 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
18390 TATATTAGAC
*
18400 AAATAAGGATATAATAGGTATTTTAAAAGTT
1 AAATAAGGATATAATAGGTATTTCAAAAGTT
*
18431 AAATAAGGGTATAATAGGTATTTCAAAAGTT
1 AAATAAGGATATAATAGGTATTTCAAAAGTT
18462 TCTCAAAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.47, C:0.02, G:0.18, T:0.34
Consensus pattern (31 bp):
AAATAAGGATATAATAGGTATTTCAAAAGTT
Found at i:18560 original size:31 final size:29
Alignment explanation
Indices: 18525--18591 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 29
18515 TACCATACAA
*
18525 GTCCCTCTACTTATAAAAAGGGATCAATTTG
1 GTCCCTCTAC-TATAAAAA-CGATCAATTTG
* *
18556 GTCCCCCTACTATAAAAACTATCAATTTG
1 GTCCCTCTACTATAAAAACGATCAATTTG
18585 GTCCCTC
1 GTCCCTC
18592 CAATTACAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 15 0.47
30 8 0.25
31 9 0.28
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (29 bp):
GTCCCTCTACTATAAAAACGATCAATTTG
Found at i:21055 original size:13 final size:13
Alignment explanation
Indices: 21023--21056 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
21013 TAAAAGTAAA
21023 TTTTTTTCCCATT
1 TTTTTTTCCCATT
*
21036 TTGTTTTTCCTATT
1 TT-TTTTTCCCATT
21050 TTTTTTT
1 TTTTTTT
21057 ACTTGGACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.06, C:0.15, G:0.03, T:0.76
Consensus pattern (13 bp):
TTTTTTTCCCATT
Found at i:22747 original size:11 final size:12
Alignment explanation
Indices: 22725--22763 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
22715 GTACTAACCT
*
22725 GATGAGGATGAG
1 GATGATGATGAG
22737 GAT-ATGATGAG
1 GATGATGATGAG
*
22748 GATGATGATGAT
1 GATGATGATGAG
22760 GATG
1 GATG
22764 GAGGTTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.33, C:0.00, G:0.41, T:0.26
Consensus pattern (12 bp):
GATGATGATGAG
Found at i:26619 original size:6 final size:7
Alignment explanation
Indices: 26580--26634 Score: 87
Period size: 7 Copynumber: 8.0 Consensus size: 7
26570 TAAGTACAGG
26580 ACCCTAAA
1 ACCCT-AA
26588 ACCCTAA
1 ACCCTAA
26595 ACCCTAA
1 ACCCTAA
26602 ACCCTAA
1 ACCCTAA
26609 ACCCT-A
1 ACCCTAA
26615 ACCCT-A
1 ACCCTAA
26621 ACCCTAA
1 ACCCTAA
26628 ACCCTAA
1 ACCCTAA
26635 CTGCCAACGT
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
6 12 0.26
7 29 0.63
8 5 0.11
ACGTcount: A:0.42, C:0.44, G:0.00, T:0.15
Consensus pattern (7 bp):
ACCCTAA
Found at i:28523 original size:14 final size:14
Alignment explanation
Indices: 28506--28536 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
28496 GATGGATATA
28506 TATCGTATAATTCT
1 TATCGTATAATTCT
28520 TATCGTATAATTCT
1 TATCGTATAATTCT
28534 TAT
1 TAT
28537 ATATTGTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.52
Consensus pattern (14 bp):
TATCGTATAATTCT
Found at i:38545 original size:5 final size:6
Alignment explanation
Indices: 38530--38555 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
38520 TCTACCTACC
38530 AAAAAT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AA
38556 TGCAGTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:39997 original size:11 final size:11
Alignment explanation
Indices: 39954--39991 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
39944 TTCCTATATA
*
39954 AAATAAATTAT
1 AAATTAATTAT
39965 CAAA-TAATTAT
1 -AAATTAATTAT
39976 AAATTAATTAT
1 AAATTAATTAT
39987 AAATT
1 AAATT
39992 TGTTATGGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Done.