Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009717.1 Corchorus capsularis cultivar CVL-1 contig09738, 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: 26097
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:1561 original size:22 final size:22
Alignment explanation
Indices: 1528--1569 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1518 GAGAATCTTT
*
1528 TTATAAATTTTTTTTAACCTTC
1 TTATAAATTTTTGTTAACCTTC
1550 TTATGAAA-TTTTGTTAACCT
1 TTAT-AAATTTTTGTTAACCT
1570 CTCTAAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.29, C:0.12, G:0.05, T:0.55
Consensus pattern (22 bp):
TTATAAATTTTTGTTAACCTTC
Found at i:1739 original size:22 final size:23
Alignment explanation
Indices: 1714--1795 Score: 84
Period size: 22 Copynumber: 3.7 Consensus size: 23
1704 AAAATCTCCT
*
1714 TATG-AATTGTT-AGTAATTACAC
1 TATGAAATTGTTGA-TAATCACAC
1736 TATGAAATT-TTGATAATCACAC
1 TATGAAATTGTTGATAATCACAC
* * *
1758 TATGAAATTG-TGATAACCTCGC
1 TATGAAATTGTTGATAATCACAC
1780 TATGAAATT-TTGATAA
1 TATGAAATTGTTGATAA
1796 ATCTTCCTAC
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
22 47 0.90
23 5 0.10
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (23 bp):
TATGAAATTGTTGATAATCACAC
Found at i:1812 original size:23 final size:23
Alignment explanation
Indices: 1762--1841 Score: 81
Period size: 23 Copynumber: 3.5 Consensus size: 23
1752 TCACACTATG
* * **
1762 AAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAACCTCCCTACA
* *
1784 AAATTTTGATAAATCTTCCTACA
1 AAATTTTGATAAACCTCCCTACA
*
1807 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCTACA
*
1830 AAAATTTGATAA
1 AAATTTTGATAA
1842 CTTTCTTATG
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 9 0.19
23 38 0.81
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTACA
Found at i:1862 original size:45 final size:45
Alignment explanation
Indices: 1757--1863 Score: 110
Period size: 45 Copynumber: 2.4 Consensus size: 45
1747 GATAATCACA
* * *
1757 CTATGAAATTGTGAT-AACCTCGCTATGAAATTTTGATAAATCTTC
1 CTATGAAATT-TGATAAACCTCCCTATAAAAATTTGATAAATCTTC
** *
1802 CTACAAAATTTTGATAAACCTCCCTATAAAAATTTGATAACT-TTC
1 CTATGAAA-TTTGATAAACCTCCCTATAAAAATTTGATAAATCTTC
*
1847 TTATGAAATCTTGATAA
1 CTATGAAAT-TTGATAA
1864 CTAAAAATTT
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
44 1 0.02
45 25 0.50
46 24 0.48
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.37
Consensus pattern (45 bp):
CTATGAAATTTGATAAACCTCCCTATAAAAATTTGATAAATCTTC
Found at i:1897 original size:22 final size:22
Alignment explanation
Indices: 1868--2048 Score: 160
Period size: 22 Copynumber: 8.5 Consensus size: 22
1858 TGATAACTAA
*
1868 AAATTTTGATAAGCTCCCTATG
1 AAATTTTGATAACCTCCCTATG
** **
1890 ATTTTTTGATAACCTCATTATG
1 AAATTTTGATAACCTCCCTATG
* *
1912 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCTCCCTATG
*
1934 AAATTTTGATAACC-CTCTTATG
1 AAATTTTGATAACCTC-CCTATG
* **
1956 AAATTTTGA-AAACTAAACTATG
1 AAATTTTGATAACCT-CCCTATG
* *
1978 AAATTTTGATAACCTTCATATG
1 AAATTTTGATAACCTCCCTATG
*
2000 AAATTTTGATATCCTCCC--TG
1 AAATTTTGATAACCTCCCTATG
*
2020 -AATTTTGATATCCT-CC-ATG
1 AAATTTTGATAACCTCCCTATG
2039 AAATTTTGAT
1 AAATTTTGAT
2049 TACTCCATAA
Statistics
Matches: 128, Mismatches: 25, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
18 2 0.02
19 16 0.12
20 11 0.09
21 4 0.03
22 91 0.71
23 4 0.03
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAACCTCCCTATG
Found at i:1931 original size:44 final size:43
Alignment explanation
Indices: 1736--2007 Score: 175
Period size: 44 Copynumber: 6.3 Consensus size: 43
1726 GTAATTACAC
* * * * **
1736 TATGAAATTTTGATAATCACACTATGAAATTGTGATAACCTCGC
1 TATGAAATTTTG-TAAACTCCCTATGAAATTTTGATAACCTCAT
* ** **
1780 TATGAAATTTTGATAAATCTTCCTACAAAATTTTGATAAACCTCCC
1 TATGAAATTTTG-TAAA-CTCCCTATGAAATTTTGAT-AACCTCAT
* * * * *
1826 TATAAAAATTTG-ATAACTTTCTTATGAAATCTTGATAA-CT-A-
1 TATGAAATTTTGTA-AAC-TCCCTATGAAATTTTGATAACCTCAT
* **
1867 -A--AAATTTTGATAAGCTCCCTATGATTTTTTGATAACCTCAT
1 TATGAAATTTTG-TAAACTCCCTATGAAATTTTGATAACCTCAT
*
1908 TATGAAATTTTGTTAATCTCCCTATGAAATTTTGATAACCCTC-T
1 TATGAAATTTTG-TAAACTCCCTATGAAATTTTGATAA-CCTCAT
* **
1952 TATGAAATTTTGAAAACTAAACTATGAAATTTTGATAACCTTCA-
1 TATGAAATTTTGTAAACT-CCCTATGAAATTTTGATAACC-TCAT
1996 TATGAAATTTTG
1 TATGAAATTTTG
2008 ATATCCTCCC
Statistics
Matches: 182, Mismatches: 30, Indels: 32
0.75 0.12 0.13
Matches are distributed among these distances:
38 22 0.12
39 4 0.02
40 3 0.02
42 1 0.01
43 8 0.04
44 94 0.52
45 33 0.18
46 17 0.09
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (43 bp):
TATGAAATTTTGTAAACTCCCTATGAAATTTTGATAACCTCAT
Found at i:2056 original size:19 final size:20
Alignment explanation
Indices: 1975--2048 Score: 96
Period size: 19 Copynumber: 3.6 Consensus size: 20
1965 AAACTAAACT
* *
1975 ATGAAATTTTGATAACCTTCAT
1 ATGAAATTTTGATATCC-TC-C
1997 ATGAAATTTTGATATCCTCC
1 ATGAAATTTTGATATCCTCC
*
2017 CTG-AATTTTGATATCCTCC
1 ATGAAATTTTGATATCCTCC
2036 ATGAAATTTTGAT
1 ATGAAATTTTGAT
2049 TACTCCATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 18 0.38
20 11 0.23
21 2 0.04
22 16 0.34
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (20 bp):
ATGAAATTTTGATATCCTCC
Found at i:2355 original size:22 final size:22
Alignment explanation
Indices: 2129--2383 Score: 127
Period size: 22 Copynumber: 11.6 Consensus size: 22
2119 AGAAATACCA
2129 CTATGAAATTTTTG-TAATCACAT
1 CTATGAAA-TTTTGATAATCAC-T
* * * * *
2152 -TTTGAAAATGTGATAACCTCT
1 CTATGAAATTTTGATAATCACT
*
2173 TTATGAAATTTTGATAA-C-CT
1 CTATGAAATTTTGATAATCACT
** * * * *
2193 CTTCACAAAATTTTGTTGACCCCT
1 C-T-ATGAAATTTTGATAATCACT
*
2217 CTATGAAATTCTGATAATCACAT
1 CTATGAAATTTTGATAATCAC-T
* * * *
2240 -TATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAATCACT
* *
2261 CTTTGAAATTTTGATAA-CAACA
1 CTATGAAATTTTGATAATC-ACT
*
2283 CTATGAAATTTTGATAATC-TT
1 CTATGAAATTTTGATAATCACT
2304 CATAT-AAATTTTGATAATCCGATCT
1 C-TATGAAATTTTGATAAT-C-A-CT
*
2329 CTATGAAATTTCGATAATCACT
1 CTATGAAATTTTGATAATCACT
*
2351 CTATGAGA-TTTGATAA-C-CTT
1 CTATGAAATTTTGATAATCAC-T
*
2371 CTATCAAATTTTG
1 CTATGAAATTTTG
2384 GTATTCCTTA
Statistics
Matches: 176, Mismatches: 38, Indels: 38
0.70 0.15 0.15
Matches are distributed among these distances:
19 1 0.01
20 10 0.06
21 32 0.18
22 107 0.61
23 5 0.03
24 7 0.04
25 14 0.08
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCACT
Found at i:2435 original size:22 final size:21
Alignment explanation
Indices: 2406--2545 Score: 88
Period size: 22 Copynumber: 6.4 Consensus size: 21
2396 AAATTGAGAC
2406 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TCATATGAAA
* *
2427 TTTTGATAACCACATTATAAAA
1 TTTTGATAACCTCA-TATGAAA
**
2449 TTTTGATAACCTCCCCATGAAA
1 TTTTGATAACCT-CATATGAAA
* * *
2471 -TATCAGTAACCTCCTAATGAAA
1 TTTTGA-TAACCTCAT-ATGAAA
* *
2493 TTTTGTTAACCACACTATGAAA
1 TTTTGATAACCTCA-TATGAAA
* *
2515 TTCTT-ATAACCTCGTTATGACA
1 TT-TTGATAACCTC-ATATGAAA
2537 TTTTGATAA
1 TTTTGATAA
2546 TCTCTTTGAT
Statistics
Matches: 91, Mismatches: 18, Indels: 19
0.71 0.14 0.15
Matches are distributed among these distances:
21 13 0.14
22 72 0.79
23 6 0.07
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.37
Consensus pattern (21 bp):
TTTTGATAACCTCATATGAAA
Found at i:3410 original size:38 final size:37
Alignment explanation
Indices: 3363--3440 Score: 102
Period size: 38 Copynumber: 2.1 Consensus size: 37
3353 TGTTGAAGAT
3363 AAAGACAAAAAACAAAATTAAATACAACGATTGGAAAC
1 AAAGACAAAAAACAAAATTAAATACAACG-TTGGAAAC
* ** **
3401 AAAGGCAAAAGGCAAAATTAAATAGGACGTTGGAAAC
1 AAAGACAAAAAACAAAATTAAATACAACGTTGGAAAC
3438 AAA
1 AAA
3441 AAGCCAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
37 11 0.31
38 24 0.69
ACGTcount: A:0.59, C:0.12, G:0.17, T:0.13
Consensus pattern (37 bp):
AAAGACAAAAAACAAAATTAAATACAACGTTGGAAAC
Found at i:3664 original size:2 final size:2
Alignment explanation
Indices: 3657--3690 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
3647 TTCGTACTTT
*
3657 TA TA TA TA GTA TA GA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA T
3691 GTGCGTGTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4086 original size:6 final size:6
Alignment explanation
Indices: 4048--4082 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
4038 CTCATTCTAG
* *
4048 TTAAAA TTAAAA TTAAAA TTAAAA ATAAAT TTAAA
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAA
4083 TTTATATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
TTAAAA
Found at i:4277 original size:2 final size:2
Alignment explanation
Indices: 4270--4302 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4260 GTATTCTCCT
4270 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4303 TAAATTACCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14045 original size:3 final size:3
Alignment explanation
Indices: 14037--14081 Score: 54
Period size: 3 Copynumber: 14.0 Consensus size: 3
14027 TCTCCCTCAA
*
14037 AAT AAT AAT AAT AAT AAT AATT AAT ATAT ATAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AA-T AAT A-AT A-AT AAT AAT AAT AAT
14082 TTTATTCTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 28 0.74
4 10 0.26
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:15985 original size:20 final size:20
Alignment explanation
Indices: 15960--15998 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
15950 TAAAGATTTC
15960 TAATTTTTATT-TTATTTTTA
1 TAATTTTT-TTATTATTTTTA
15980 TAATTTTTTTATTATTTTT
1 TAATTTTTTTATTATTTTT
15999 TAAGTTTGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (20 bp):
TAATTTTTTTATTATTTTTA
Found at i:19152 original size:15 final size:16
Alignment explanation
Indices: 19127--19158 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
19117 AATGTCCATT
19127 TTTTGAATTATTTAAA
1 TTTTGAATTATTTAAA
19143 TTTT-AATTATTTAAA
1 TTTTGAATTATTTAAA
19158 T
1 T
19159 CTAATCTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TTTTGAATTATTTAAA
Found at i:25818 original size:22 final size:21
Alignment explanation
Indices: 25774--25817 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
25764 CAGTTCTGGA
25774 TTGCTAAACACCACCCCCCTT
1 TTGCTAAACACCACCCCCCTT
* *
25795 TTGCTAAATACCGCCCCCCTT
1 TTGCTAAACACCACCCCCCTT
25816 TT
1 TT
25818 TACACTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.43, G:0.07, T:0.30
Consensus pattern (21 bp):
TTGCTAAACACCACCCCCCTT
Found at i:25950 original size:25 final size:25
Alignment explanation
Indices: 25892--25946 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
25882 AATCCTAAAC
*
25892 TTCATTTCTAACAACTTCTTCAAAT
1 TTCATTTCTAACAACATCTTCAAAT
25917 TTCATTTCTAACAA-ATCTTCAAA-
1 TTCATTTCTAACAACATCTTCAAAT
25940 TTCATTT
1 TTCATTT
25947 TTCTTCATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 7 0.24
24 8 0.28
25 14 0.48
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.45
Consensus pattern (25 bp):
TTCATTTCTAACAACATCTTCAAAT
Found at i:25985 original size:26 final size:26
Alignment explanation
Indices: 25956--26023 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
25946 TTTCTTCATT
25956 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
25982 TTAATCATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
26008 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
26024 AAACTAAGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:25986 original size:15 final size:15
Alignment explanation
Indices: 25956--26023 Score: 62
Period size: 15 Copynumber: 5.1 Consensus size: 15
25946 TTTCTTCATT
25956 TTAATCATAAACTAA
1 TTAATCATAAACTAA
25971 TTAA--AT--ACTAA
1 TTAATCATAAACTAA
25982 TTAATCATAAACTAA
1 TTAATCATAAACTAA
*
25997 TT-A-GAT--ACTAA
1 TTAATCATAAACTAA
*
26008 TTAAACATAAACTAA
1 TTAATCATAAACTAA
26023 T
1 T
26024 AAACTAAGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
11 16 0.37
12 1 0.02
13 8 0.19
14 1 0.02
15 17 0.40
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (15 bp):
TTAATCATAAACTAA
Done.