Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006786.1 Corchorus capsularis cultivar CVL-1 contig06807, 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: 15756
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:226 original size:29 final size:29
Alignment explanation
Indices: 190--299 Score: 166
Period size: 29 Copynumber: 3.7 Consensus size: 29
180 TCTCGTTTTT
190 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
1 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
*
219 AAAAGTTAAGGGGCCAATTTGTCCCCAAA
1 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
248 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
1 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
* * *
277 TTGATAGTTAAGGGGCTAATTTG
1 --AAAAGTTAAGGGGCCAATTTG
300 GGTATTAAGC
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
29 56 0.76
31 18 0.24
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (29 bp):
AAAAGTTAAGGGGCCAATTTGTCCCAAAA
Found at i:1369 original size:2 final size:2
Alignment explanation
Indices: 1362--1398 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1352 ATTAAATGTA
*
1362 AT AT AT AT AT AT AT AT AT AT AT AT AT -T TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1399 GAATAAGAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:6701 original size:2 final size:2
Alignment explanation
Indices: 6694--6734 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
6684 ATTCCACAGC
*
6694 AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6735 GGGTTGAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7187 original size:2 final size:2
Alignment explanation
Indices: 7180--7219 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
7170 ATTTTGAAAC
7180 AT AT AT AT AT AT AT AT AT AT AT -T AT -T A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7219 A
1 A
7220 AAACAGATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 32 0.91
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8169 original size:24 final size:24
Alignment explanation
Indices: 8139--8195 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
8129 TTGCTTTTTC
8139 CTGTTGCTCATTCTTTTTCTTCTG
1 CTGTTGCTCATTCTTTTTCTTCTG
* *
8163 CTTTTGCTCATTCTTTTTCTTCTT
1 CTGTTGCTCATTCTTTTTCTTCTG
8187 CTGTTGCTC
1 CTGTTGCTC
8196 TCTTTCATAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.04, C:0.26, G:0.11, T:0.60
Consensus pattern (24 bp):
CTGTTGCTCATTCTTTTTCTTCTG
Found at i:14711 original size:36 final size:32
Alignment explanation
Indices: 14600--14722 Score: 142
Period size: 32 Copynumber: 3.8 Consensus size: 32
14590 CTTTTTAGAT
* * *
14600 TTAAGTTCTTTA-ATGACTTAATTACCTTGAA
1 TTAAGTTCTTTATTTTACTTAATTACCCTGAA
*
14631 TTAAGTTCTTTATTTTACTTAATTACCCAGAA
1 TTAAGTTCTTTATTTTACTTAATTACCCTGAA
*
14663 TTAAG-CCTTTTATTGACTTCACTTAATTACCCTGAA
1 TTAAGTTC-TTTATT---TT-ACTTAATTACCCTGAA
14699 TTAAGTTCTTTATTTTACTTAATT
1 TTAAGTTCTTTATTTTACTTAATT
14723 TCCTTTCCTG
Statistics
Matches: 78, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
31 13 0.17
32 34 0.44
33 2 0.03
35 2 0.03
36 26 0.33
37 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.07, T:0.48
Consensus pattern (32 bp):
TTAAGTTCTTTATTTTACTTAATTACCCTGAA
Found at i:14798 original size:36 final size:36
Alignment explanation
Indices: 14726--14889 Score: 197
Period size: 36 Copynumber: 4.6 Consensus size: 36
14716 CTTAATTTCC
* * * *
14726 TTTCC-TGAAATTAAGCCTGTGTCTT-TTTACTTAA
1 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAA
*
14760 TTTCCTTGAAATTAAGCCAGTCTTTCCTTTACCTAA
1 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAA
* * *
14796 TTTCCTTGAAATTAGGCCAATCTTTTCTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAA
* * *
14832 TTTCCTTGAAACTAAGCCAATCTTTTCTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAA
* *
14868 TTTCCTTGAAACTAGGCCAGTC
1 TTTCCTTGAAATTAAGCCAGTC
14890 CTTTATCGGT
Statistics
Matches: 115, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
34 5 0.04
35 16 0.14
36 94 0.82
ACGTcount: A:0.24, C:0.23, G:0.11, T:0.42
Consensus pattern (36 bp):
TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAA
Found at i:14914 original size:11 final size:11
Alignment explanation
Indices: 14898--15022 Score: 115
Period size: 11 Copynumber: 11.4 Consensus size: 11
14888 TCCTTTATCG
14898 GTCTAATTTCA
1 GTCTAATTTCA
*
14909 GTCTAATATCA
1 GTCTAATTTCA
**
14920 GTCTTTTTTCA
1 GTCTAATTTCA
*
14931 GTGTAATTTCA
1 GTCTAATTTCA
*
14942 GTGTAATTTCA
1 GTCTAATTTCA
* **
14953 GTATTCTTTCA
1 GTCTAATTTCA
*
14964 GTCTGATTTCA
1 GTCTAATTTCA
* * *
14975 ATTTAATATCA
1 GTCTAATTTCA
* *
14986 GTCTTATATCA
1 GTCTAATTTCA
14997 GTCTAATTTCA
1 GTCTAATTTCA
*
15008 GTCTAATATCA
1 GTCTAATTTCA
15019 GTCT
1 GTCT
15023 TTTTTTTTTC
Statistics
Matches: 91, Mismatches: 23, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 91 1.00
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.46
Consensus pattern (11 bp):
GTCTAATTTCA
Found at i:15022 original size:33 final size:32
Alignment explanation
Indices: 14885--15024 Score: 154
Period size: 33 Copynumber: 4.2 Consensus size: 32
14875 GAAACTAGGC
*
14885 CAGTCCTTTATCGGTCTAATTTCAGTCTAATAT
1 CAGT-CTTTATCAGTCTAATTTCAGTCTAATAT
* * * *
14918 CAGTCTTTTTTCAGTGTAATTTCAGTGTAATTT
1 CAGTC-TTTATCAGTCTAATTTCAGTCTAATAT
* * * * *
14951 CAGTATTCTTTCAGTCTGATTTCAATTTAATAT
1 CAGTCTT-TATCAGTCTAATTTCAGTCTAATAT
14984 CAGTCTTATATCAGTCTAATTTCAGTCTAATAT
1 CAGTCTT-TATCAGTCTAATTTCAGTCTAATAT
15017 CAGTCTTT
1 CAGTCTTT
15025 TTTTTTTCAG
Statistics
Matches: 88, Mismatches: 17, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
32 4 0.05
33 84 0.95
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.46
Consensus pattern (32 bp):
CAGTCTTTATCAGTCTAATTTCAGTCTAATAT
Found at i:15045 original size:26 final size:26
Alignment explanation
Indices: 15003--15056 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
14993 ATCAGTCTAA
15003 TTTCAGTCTAATATCAGTCTTTTTTT
1 TTTCAGTCTAATATCAGTCTTTTTTT
* *
15029 TTTCAGTCTATTTTCAGTCTTTTTTT
1 TTTCAGTCTAATATCAGTCTTTTTTT
15055 TT
1 TT
15057 AGTATTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.15, C:0.15, G:0.07, T:0.63
Consensus pattern (26 bp):
TTTCAGTCTAATATCAGTCTTTTTTT
Found at i:15053 original size:11 final size:11
Alignment explanation
Indices: 15026--15086 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
15016 TCAGTCTTTT
15026 TTTTTTCAGTC
1 TTTTTTCAGTC
*
15037 TATTTTCAGTC
1 TTTTTTCAGTC
* *
15048 TTTTTTTTTAGTA
1 --TTTTTTCAGTC
*
15061 TTCTTTCAGTC
1 TTTTTTCAGTC
*
15072 TTTCTTCAGT-
1 TTTTTTCAGTC
15082 TTTTT
1 TTTTT
15087 GCTTTAATTT
Statistics
Matches: 38, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
10 4 0.11
11 26 0.68
13 8 0.21
ACGTcount: A:0.11, C:0.15, G:0.08, T:0.66
Consensus pattern (11 bp):
TTTTTTCAGTC
Found at i:15067 original size:24 final size:25
Alignment explanation
Indices: 15016--15074 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
15006 CAGTCTAATA
*
15016 TCAGTCTTTTTTTTTTCAGTCTATTT
1 TCAGTC-TTTTTTTTTCAGTATATTT
15042 TCAGTCTTTTTTTTT-AGTAT-TCTT
1 TCAGTCTTTTTTTTTCAGTATAT-TT
15066 TCAGTCTTT
1 TCAGTCTTT
15075 CTTCAGTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 1 0.03
24 15 0.48
25 9 0.29
26 6 0.19
ACGTcount: A:0.12, C:0.15, G:0.08, T:0.64
Consensus pattern (25 bp):
TCAGTCTTTTTTTTTCAGTATATTT
Found at i:15189 original size:36 final size:36
Alignment explanation
Indices: 15100--15264 Score: 179
Period size: 36 Copynumber: 4.5 Consensus size: 36
15090 TTAATTTCCT
* * *
15100 TGAAATTAAGCCCTTTGTCTAATCTTACTTAATCATCTTT
1 TGAAATTAAG-TCTTTG-CTAATTTTACTTAAT--TCTTG
* * * * *
15140 TG-GATTAAATCTTTGCTGACTTTACTTAATTCTCG
1 TGAAATTAAGTCTTTGCTAATTTTACTTAATTCTTG
*
15175 TGAAATTAAGTCTTTGCCAATTTTACTTAATTCTTG
1 TGAAATTAAGTCTTTGCTAATTTTACTTAATTCTTG
* *
15211 TGAAATTAAGTCTTTACTAATTTTACTTAATTTTTG
1 TGAAATTAAGTCTTTGCTAATTTTACTTAATTCTTG
*
15247 TGAAATTAAGTCTATGCT
1 TGAAATTAAGTCTTTGCT
15265 TATCCTTACC
Statistics
Matches: 105, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
35 5 0.05
36 76 0.72
37 12 0.11
38 5 0.05
39 5 0.05
40 2 0.02
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.47
Consensus pattern (36 bp):
TGAAATTAAGTCTTTGCTAATTTTACTTAATTCTTG
Done.