Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012150.1 Corchorus capsularis cultivar CVL-1 contig12171, 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: 68404
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:1099 original size:28 final size:28
Alignment explanation
Indices: 1068--1128 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
1058 ACAAAATTAA
1068 AAGTTCAAAGACTAATTGGTAAATTTA-G
1 AAGTTCAAAGACTAATTGGTAAA-TTAGG
* * *
1096 AAGTTTAAGGTCTAATTGGTAAATTAGG
1 AAGTTCAAAGACTAATTGGTAAATTAGG
1124 AAGTT
1 AAGTT
1129 TAAGATTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 3 0.10
28 26 0.90
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.34
Consensus pattern (28 bp):
AAGTTCAAAGACTAATTGGTAAATTAGG
Found at i:1129 original size:28 final size:28
Alignment explanation
Indices: 1079--1132 Score: 92
Period size: 28 Copynumber: 1.9 Consensus size: 28
1069 AGTTCAAAGA
1079 CTAATTGGTAAATTTAGAAGTTTAAGGT
1 CTAATTGGTAAATTTAGAAGTTTAAGGT
1107 CTAATTGGTAAA-TTAGGAAGTTTAAG
1 CTAATTGGTAAATTTA-GAAGTTTAAG
1133 ATTGTGACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 3 0.12
28 22 0.88
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (28 bp):
CTAATTGGTAAATTTAGAAGTTTAAGGT
Found at i:1791 original size:13 final size:13
Alignment explanation
Indices: 1773--1797 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1763 TTGGAATTCC
1773 AAATAATATTTAT
1 AAATAATATTTAT
1786 AAATAATATTTA
1 AAATAATATTTA
1798 GAACATTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:2013 original size:5 final size:5
Alignment explanation
Indices: 2003--2037 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
1993 TAATATCTAG
*
2003 TTATA TTATA TTATA TAATA TTATA -TATA TTATA T
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA T
2038 AAGTCGTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TTATA
Found at i:2371 original size:38 final size:38
Alignment explanation
Indices: 2329--2414 Score: 109
Period size: 38 Copynumber: 2.3 Consensus size: 38
2319 AGCCTTTACT
* * *
2329 ATTTTGACCACCATCAGTCGCAATGGTTAGCCTTGGTC
1 ATTTTGACCACCATCAATCACAATGGTTAGCCTTAGTC
* ** *
2367 ATTTTGGCCACCATCAATCATGATTGTTAGCCTTAGTC
1 ATTTTGACCACCATCAATCACAATGGTTAGCCTTAGTC
2405 ATTTTGACCA
1 ATTTTGACCA
2415 ATTTTTATCA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.35
Consensus pattern (38 bp):
ATTTTGACCACCATCAATCACAATGGTTAGCCTTAGTC
Found at i:2475 original size:32 final size:32
Alignment explanation
Indices: 2434--2495 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
2424 ATGTTAGATC
2434 GTGATAATTAACCTTAGCCATTTTGGCCACTT
1 GTGATAATTAACCTTAGCCATTTTGGCCACTT
*
2466 GTGATAATTAACCTTAGTCATTTTGGCCAC
1 GTGATAATTAACCTTAGCCATTTTGGCCAC
2496 CTTGAATCGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (32 bp):
GTGATAATTAACCTTAGCCATTTTGGCCACTT
Found at i:2867 original size:37 final size:37
Alignment explanation
Indices: 2817--2889 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
2807 ATTATGCCTC
*
2817 TATTGCTATCCATAGATTTATCATCAACCCATTGATA
1 TATTGCTATCCATAGATGTATCATCAACCCATTGATA
* *
2854 TATTGTTATCCATAGATGTATCATCACCCCATTGAT
1 TATTGCTATCCATAGATGTATCATCAACCCATTGAT
2890 TAGTTATGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (37 bp):
TATTGCTATCCATAGATGTATCATCAACCCATTGATA
Found at i:4536 original size:29 final size:30
Alignment explanation
Indices: 4485--4541 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
4475 AATTCCCAAG
*
4485 TCTCACCTAAACTTAGAGCTTCTTTGAGCC
1 TCTCACATAAACTTAGAGCTTCTTTGAGCC
* *
4515 TCTCACAT-AACTTGGAGTTTCTTTGAG
1 TCTCACATAAACTTAGAGCTTCTTTGAG
4542 GCTCACCTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.37
Consensus pattern (30 bp):
TCTCACATAAACTTAGAGCTTCTTTGAGCC
Found at i:5233 original size:72 final size:72
Alignment explanation
Indices: 5140--5284 Score: 193
Period size: 72 Copynumber: 2.0 Consensus size: 72
5130 GCTTTTGCAA
* * *
5140 ACAAACCATCAAGATCAATTTTTGACAATCTAAAAATTTCAGCAGAAAATTTTGCATCCAAACCA
1 ACAAACCATCAAGATCAATTTTTGACAATCTAAAAACTTCAGCAGAAAACTTTGCATCAAAACCA
5205 AAATCCC
66 AAATCCC
* * * * *
5212 ACAAACCTTCAA-ACTCAATTTTTGACAATCTCAAGACTTCAGCAGTAAACTTTGCATCAAAACT
1 ACAAACCATCAAGA-TCAATTTTTGACAATCTAAAAACTTCAGCAGAAAACTTTGCATCAAAACC
*
5276 AGAATCCC
65 AAAATCCC
5284 A
1 A
5285 TAAAACAAGA
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
71 1 0.02
72 62 0.98
ACGTcount: A:0.42, C:0.25, G:0.08, T:0.26
Consensus pattern (72 bp):
ACAAACCATCAAGATCAATTTTTGACAATCTAAAAACTTCAGCAGAAAACTTTGCATCAAAACCA
AAATCCC
Found at i:6198 original size:12 final size:12
Alignment explanation
Indices: 6181--6205 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6171 CCTCTATCAT
6181 CTTGCAATCCTC
1 CTTGCAATCCTC
6193 CTTGCAATCCTC
1 CTTGCAATCCTC
6205 C
1 C
6206 GTCCCATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.44, G:0.08, T:0.32
Consensus pattern (12 bp):
CTTGCAATCCTC
Found at i:8922 original size:16 final size:16
Alignment explanation
Indices: 8901--8934 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
8891 CTCTGAATTA
8901 GTCATAAATCACTATC
1 GTCATAAATCACTATC
8917 GTCATAAATCACTATC
1 GTCATAAATCACTATC
8933 GT
1 GT
8935 TAGATCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.24, G:0.09, T:0.32
Consensus pattern (16 bp):
GTCATAAATCACTATC
Found at i:17335 original size:23 final size:23
Alignment explanation
Indices: 17309--17352 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
17299 TTTTATTTTA
17309 AAGTGAAA-AATT-ATTCAATACAT
1 AAGT-AAATAATTAATT-AATACAT
17332 AAGTAAATAATTAATTAATAC
1 AAGTAAATAATTAATTAATAC
17353 CAATAAAGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 3 0.16
23 13 0.68
24 3 0.16
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.32
Consensus pattern (23 bp):
AAGTAAATAATTAATTAATACAT
Found at i:21346 original size:27 final size:26
Alignment explanation
Indices: 21315--21369 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
21305 ATTTGTACGG
*
21315 GTCGTACATTTAGAGGTCACGTATGGA
1 GTCGTAC-GTTAGAGGTCACGTATGGA
* *
21342 GTCGTACGTTGGAGGTCACGTGTGGA
1 GTCGTACGTTAGAGGTCACGTATGGA
21368 GT
1 GT
21370 GCCAGCTGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 18 0.72
27 7 0.28
ACGTcount: A:0.20, C:0.15, G:0.36, T:0.29
Consensus pattern (26 bp):
GTCGTACGTTAGAGGTCACGTATGGA
Found at i:25973 original size:30 final size:30
Alignment explanation
Indices: 25937--25997 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
25927 TCTGATTGAA
25937 TGCTATTTCTTCTACTGTAAAAACGAGATC
1 TGCTATTTCTTCTACTGTAAAAACGAGATC
* * * *
25967 TGCTATTTCTTTTGCTGTAGAAGCGAGATC
1 TGCTATTTCTTCTACTGTAAAAACGAGATC
25997 T
1 T
25998 ACCATGTCAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (30 bp):
TGCTATTTCTTCTACTGTAAAAACGAGATC
Found at i:28247 original size:17 final size:17
Alignment explanation
Indices: 28209--28247 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
28199 ACAGTGCAAC
*
28209 AAAAACAAAACGAAAAT
1 AAAAACAAAACAAAAAT
*
28226 GAAAACAAAACAAAAAT
1 AAAAACAAAACAAAAAT
28243 AAAAA
1 AAAAA
28248 ACAGAAAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.79, C:0.10, G:0.05, T:0.05
Consensus pattern (17 bp):
AAAAACAAAACAAAAAT
Found at i:29840 original size:3 final size:3
Alignment explanation
Indices: 29832--29894 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
29822 TCAAGCTTTA
29832 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29880 TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT
29895 ATCAGATGAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:32781 original size:30 final size:29
Alignment explanation
Indices: 32714--32785 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
32704 TACACCGACC
****
32714 GTCAAATAAGCCCCTGAACTATTATTTCA
1 GTCAAATAAGCCCCTGAACTATTAAAAAA
* *
32743 GCCAAATAAGCCCCTGAACTCTTAAAAAAA
1 GTCAAATAAGCCCCTGAACTATT-AAAAAA
32773 GTCAAATAAGCCC
1 GTCAAATAAGCCC
32786 TGTTGTCAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 21 0.60
30 14 0.40
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.22
Consensus pattern (29 bp):
GTCAAATAAGCCCCTGAACTATTAAAAAA
Found at i:37764 original size:2 final size:2
Alignment explanation
Indices: 37757--37790 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
37747 TAGTCGATGC
37757 AT AT AT AT AT AT AT AT AT AT 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
37791 TACTATAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41291 original size:17 final size:17
Alignment explanation
Indices: 41269--41302 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
41259 TCCAACACAA
41269 AGCTTGGCAGCTTCATT
1 AGCTTGGCAGCTTCATT
41286 AGCTTGGCAGCTTCATT
1 AGCTTGGCAGCTTCATT
41303 TCCAATGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.35
Consensus pattern (17 bp):
AGCTTGGCAGCTTCATT
Found at i:42331 original size:15 final size:15
Alignment explanation
Indices: 42311--42340 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
42301 CGGTTGCCAT
42311 TGCCTAGGGCAAGGG
1 TGCCTAGGGCAAGGG
42326 TGCCTAGGGCAAGGG
1 TGCCTAGGGCAAGGG
42341 ATATGTTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.47, T:0.13
Consensus pattern (15 bp):
TGCCTAGGGCAAGGG
Found at i:53142 original size:17 final size:17
Alignment explanation
Indices: 53120--53155 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
53110 AACATTAGCA
53120 AGCATCAATTTCTTTTT
1 AGCATCAATTTCTTTTT
53137 AGCATCAATTTCTTTTT
1 AGCATCAATTTCTTTTT
53154 AG
1 AG
53156 AAGGTATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (17 bp):
AGCATCAATTTCTTTTT
Found at i:54880 original size:18 final size:18
Alignment explanation
Indices: 54859--54900 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
54849 TTGCTTTTAG
54859 CATTTTAC-TACTTTATTC
1 CATTTTACTTACTTT-TTC
*
54877 CATTTTACTTACTTTTTG
1 CATTTTACTTACTTTTTC
54895 CATTTT
1 CATTTT
54901 CCATAGATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.19, C:0.19, G:0.02, T:0.60
Consensus pattern (18 bp):
CATTTTACTTACTTTTTC
Found at i:58972 original size:57 final size:57
Alignment explanation
Indices: 58884--59000 Score: 234
Period size: 57 Copynumber: 2.1 Consensus size: 57
58874 CCGAGAAATT
58884 ATTACATGGACTGGTTTCACCACATCATTCATGGTCTCGGCCAATAACATTGTTATG
1 ATTACATGGACTGGTTTCACCACATCATTCATGGTCTCGGCCAATAACATTGTTATG
58941 ATTACATGGACTGGTTTCACCACATCATTCATGGTCTCGGCCAATAACATTGTTATG
1 ATTACATGGACTGGTTTCACCACATCATTCATGGTCTCGGCCAATAACATTGTTATG
58998 ATT
1 ATT
59001 TCTTCGATTC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.34
Consensus pattern (57 bp):
ATTACATGGACTGGTTTCACCACATCATTCATGGTCTCGGCCAATAACATTGTTATG
Found at i:67899 original size:14 final size:15
Alignment explanation
Indices: 67872--67908 Score: 67
Period size: 14 Copynumber: 2.5 Consensus size: 15
67862 TTCTTCAGCA
67872 ATGGGTTTTCAAGTT
1 ATGGGTTTTCAAGTT
67887 ATGGGTTTT-AAGTT
1 ATGGGTTTTCAAGTT
67901 ATGGGTTT
1 ATGGGTTT
67909 CAGCAATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.19, C:0.03, G:0.30, T:0.49
Consensus pattern (15 bp):
ATGGGTTTTCAAGTT
Done.