Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016325.1 Corchorus capsularis cultivar CVL-1 contig16346, 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: 2979
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Found at i:737 original size:38 final size:39
Alignment explanation
Indices: 661--753 Score: 143
Period size: 38 Copynumber: 2.4 Consensus size: 39
651 TGGTCCCTTT
* *
661 CAGGTCACCTTTCAGCAATAATCGAAAAGTTGACTGGAAA
1 CAGGTCATCTTTCAACAATAATC-AAAAGTTGACTGGAAA
*
701 CAGGTCGTCTTTCAACAATAATC-AAAGTTGACTGGAAA
1 CAGGTCATCTTTCAACAATAATCAAAAGTTGACTGGAAA
739 CAGGTCATCTTTCAA
1 CAGGTCATCTTTCAA
754 GTTATCAGAG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
38 29 0.59
40 20 0.41
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.26
Consensus pattern (39 bp):
CAGGTCATCTTTCAACAATAATCAAAAGTTGACTGGAAA
Found at i:874 original size:74 final size:76
Alignment explanation
Indices: 790--1083 Score: 251
Period size: 77 Copynumber: 3.9 Consensus size: 76
780 GTTATCAAAG
* ** *
790 TTGACTGGAAACAGGTCATCTTTCAGCAA-TTATCTTA-CGACTGGAAACAGGTCGTCTTTCAGC
1 TTGACTGGAAACAGGTCATCTTTCAACAAGTTATCAAAGCGACTGGAAACAGGTCATCTTTCAGC
*
853 ACTTATTAGGT
66 AATTATTAGGT
* *
864 TTGACTGGAAACAGGTCATCTTTCAATAAGTTATCAAAGTTGACTGGAAACAGGTCATCTTTCAG
1 TTGACTGGAAACAGGTCATCTTTCAACAAGTTATCAAAG-CGACTGGAAACAGGTCATCTTTCAG
929 CAATTATCT---T
65 CAATTAT-TAGGT
** * * * * *****
939 ACGACTGAAAAACAGGTCGTCTTTCAAC-ACTTGTTCGGTTTGACTGGAAACAGGTCATCTTTCA
1 TTGACTG-GAAACAGGTCATCTTTCAACAAGTT-ATCAAAGCGACTGGAAACAGGTCATCTTTCA
** * *
1003 ATAAGTTATCAAAG-
64 GCAA-TTAT-TAGGT
* * *
1017 TTGACTGGAAACAGATCATCTTTCAACAAGTTATCAAGATCAACTGGAAACAGGTCATCTTTCAG
1 TTGACTGGAAACAGGTCATCTTTCAACAAGTTATCAA-AGCGACTGGAAACAGGTCATCTTTCAG
1082 CA
65 CA
1084 GTTTTCGGTT
Statistics
Matches: 173, Mismatches: 35, Indels: 20
0.76 0.15 0.09
Matches are distributed among these distances:
74 27 0.16
75 41 0.24
76 24 0.14
77 48 0.28
78 33 0.19
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (76 bp):
TTGACTGGAAACAGGTCATCTTTCAACAAGTTATCAAAGCGACTGGAAACAGGTCATCTTTCAGC
AATTATTAGGT
Found at i:918 original size:39 final size:39
Alignment explanation
Indices: 765--1080 Score: 278
Period size: 39 Copynumber: 8.3 Consensus size: 39
755 TTATCAGAGA
*
765 TCATCTTTTCAATAAGTTATCAAAGTTGACTGGAAACAGG
1 TCATC-TTTCAACAAGTTATCAAAGTTGACTGGAAACAGG
* ** *
805 TCATCTTTCAGCAA-TTATCTTA--CGACTGGAAACAGG
1 TCATCTTTCAACAAGTTATCAAAGTTGACTGGAAACAGG
* * * * *
841 TCGTCTTTCAGC-ACTTAT-TAGGTTTGACTGGAAACAGG
1 TCATCTTTCAACAAGTTATCAAAG-TTGACTGGAAACAGG
*
879 TCATCTTTCAATAAGTTATCAAAGTTGACTGGAAACAGG
1 TCATCTTTCAACAAGTTATCAAAGTTGACTGGAAACAGG
* ** * *
918 TCATCTTTCAGCAA-TTATCTTA--CGACTGAAAAACAGG
1 TCATCTTTCAACAAGTTATCAAAGTTGACTG-GAAACAGG
* * * *
955 TCGTCTTTCAAC-ACTTGTTC--GGTTTGACTGGAAACAGG
1 TCATCTTTCAACAAGTT-ATCAAAG-TTGACTGGAAACAGG
* *
993 TCATCTTTCAATAAGTTATCAAAGTTGACTGGAAACAGA
1 TCATCTTTCAACAAGTTATCAAAGTTGACTGGAAACAGG
**
1032 TCATCTTTCAACAAGTTATC-AAGATCAACTGGAAACAGG
1 TCATCTTTCAACAAGTTATCAAAG-TTGACTGGAAACAGG
1071 TCATCTTTCA
1 TCATCTTTCA
1081 GCAGTTTTCG
Statistics
Matches: 223, Mismatches: 37, Indels: 33
0.76 0.13 0.11
Matches are distributed among these distances:
35 2 0.01
36 34 0.15
37 19 0.09
38 58 0.26
39 102 0.46
40 8 0.04
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (39 bp):
TCATCTTTCAACAAGTTATCAAAGTTGACTGGAAACAGG
Found at i:990 original size:114 final size:113
Alignment explanation
Indices: 765--1051 Score: 493
Period size: 114 Copynumber: 2.5 Consensus size: 113
755 TTATCAGAGA
765 TCATCTTTTCAATAAGTTATCAAAGTTGACTGGAAACAGGTCATCTTTCAGCAATTATCTTACGA
1 TCATC-TTTCAATAAGTTATCAAAGTTGACTGGAAACAGGTCATCTTTCAGCAATTATCTTACGA
* *
830 CTGGAAACAGGTCGTCTTTCAGCACTTATTAGGTTTGACTGGAAACAGG
65 CTGAAAACAGGTCGTCTTTCAACACTTATTAGGTTTGACTGGAAACAGG
879 TCATCTTTCAATAAGTTATCAAAGTTGACTGGAAACAGGTCATCTTTCAGCAATTATCTTACGAC
1 TCATCTTTCAATAAGTTATCAAAGTTGACTGGAAACAGGTCATCTTTCAGCAATTATCTTACGAC
* *
944 TGAAAAACAGGTCGTCTTTCAACACTTGTTCGGTTTGACTGGAAACAGG
66 TG-AAAACAGGTCGTCTTTCAACACTTATTAGGTTTGACTGGAAACAGG
* *
993 TCATCTTTCAATAAGTTATCAAAGTTGACTGGAAACAGATCATCTTTCAACAAGTTATC
1 TCATCTTTCAATAAGTTATCAAAGTTGACTGGAAACAGGTCATCTTTCAGCAA-TTATC
1052 AAGATCAACT
Statistics
Matches: 165, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
113 62 0.38
114 98 0.59
115 5 0.03
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Consensus pattern (113 bp):
TCATCTTTCAATAAGTTATCAAAGTTGACTGGAAACAGGTCATCTTTCAGCAATTATCTTACGAC
TGAAAACAGGTCGTCTTTCAACACTTATTAGGTTTGACTGGAAACAGG
Found at i:1135 original size:15 final size:15
Alignment explanation
Indices: 1116--1206 Score: 65
Period size: 15 Copynumber: 5.5 Consensus size: 15
1106 GGGCACTCCA
1116 ACAACTTTTCAATTT
1 ACAACTTTTCAATTT
* *
1131 GCAACTTTACAGCATTT
1 ACAACTTTTCA--ATTT
1148 AAACAACTTTTCAATTT
1 --ACAACTTTTCAATTT
* *
1165 ACAACTTTACAGCATTCC
1 ACAACTTTTCA--ATT-T
*
1183 AGCAAATTTTCAATTT
1 A-CAACTTTTCAATTT
1199 ACAACTTT
1 ACAACTTT
1207 ACAGTAATCC
Statistics
Matches: 58, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
15 25 0.43
16 1 0.02
17 14 0.24
18 1 0.02
19 17 0.29
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.38
Consensus pattern (15 bp):
ACAACTTTTCAATTT
Found at i:1153 original size:34 final size:34
Alignment explanation
Indices: 1115--1210 Score: 147
Period size: 34 Copynumber: 2.8 Consensus size: 34
1105 GGGGCACTCC
* *
1115 AACAACTTTTCAATTTGCAACTTTACAGCATTTA
1 AACAACTTTTCAATTTACAACTTTACAGCATTCA
*
1149 AACAACTTTTCAATTTACAACTTTACAGCATTCC
1 AACAACTTTTCAATTTACAACTTTACAGCATTCA
* *
1183 AGCAAATTTTCAATTTACAACTTTACAG
1 AACAACTTTTCAATTTACAACTTTACAG
1211 TAATCCTTCG
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 57 1.00
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.36
Consensus pattern (34 bp):
AACAACTTTTCAATTTACAACTTTACAGCATTCA
Found at i:1281 original size:47 final size:47
Alignment explanation
Indices: 1220--1367 Score: 217
Period size: 47 Copynumber: 3.1 Consensus size: 47
1210 GTAATCCTTC
* * * * *
1220 GACCAAAGTTGGTCTTTTCTCACTTCTATGCAAAGT-TACAATTTGGT
1 GACCACAGTCGGTCTTTTCTCGCTTCCATGC-GAGTCTACAATTTGGT
*
1267 GACCACAGTCGGTCTTTTCTCGCTTCCACGCGAGTCTACAATTTGGT
1 GACCACAGTCGGTCTTTTCTCGCTTCCATGCGAGTCTACAATTTGGT
*
1314 GACCACAGTCGGTCTTTTCTCGCTTCCATTCGAGTCTACAATTTGGT
1 GACCACAGTCGGTCTTTTCTCGCTTCCATGCGAGTCTACAATTTGGT
1361 GACCACA
1 GACCACA
1368 ATTGGTTTCC
Statistics
Matches: 92, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
46 3 0.03
47 89 0.97
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (47 bp):
GACCACAGTCGGTCTTTTCTCGCTTCCATGCGAGTCTACAATTTGGT
Found at i:1536 original size:33 final size:33
Alignment explanation
Indices: 1498--1659 Score: 109
Period size: 33 Copynumber: 5.3 Consensus size: 33
1488 TAGGTCTTTC
* *
1498 TCAATTTCAATATCGACCGCAGACTTGTCCTAT
1 TCAATTTCAATATCGACCGCAAACTAGTCCTAT
* *
1531 TCAATTTC---A--GACCTCAAAC-AGT-CTTT
1 TCAATTTCAATATCGACCGCAAACTAGTCCTAT
*
1557 CTCAATTTCAATATCGACCGCAAACTGGTCCTAT
1 -TCAATTTCAATATCGACCGCAAACTAGTCCTAT
* *
1591 TCAATTTC---A--GACCTCAAAC-AGT-CTTT
1 TCAATTTCAATATCGACCGCAAACTAGTCCTAT
* * *
1617 CTCAATTTCAATATCGACCACAGACTGGTCCTAT
1 -TCAATTTCAATATCGACCGCAAACTAGTCCTAT
*
1651 CCAATTTCA
1 TCAATTTCA
1660 GACCTCATTT
Statistics
Matches: 98, Mismatches: 15, Indels: 32
0.68 0.10 0.22
Matches are distributed among these distances:
26 6 0.06
27 20 0.20
28 17 0.17
30 4 0.04
32 17 0.17
33 28 0.29
34 6 0.06
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.32
Consensus pattern (33 bp):
TCAATTTCAATATCGACCGCAAACTAGTCCTAT
Found at i:1561 original size:27 final size:27
Alignment explanation
Indices: 1531--1626 Score: 95
Period size: 27 Copynumber: 3.3 Consensus size: 27
1521 CTTGTCCTAT
1531 TCAATTTCAGACCTCAAACAGTCTTTC
1 TCAATTTCAGACCTCAAACAGTCTTTC
* * *
1558 TCAATTTCAATATCGACCGCAAACTGGTCCTAT-
1 TCAATTTC---A--GACCTCAAAC-AGT-CTTTC
1591 TCAATTTCAGACCTCAAACAGTCTTTC
1 TCAATTTCAGACCTCAAACAGTCTTTC
1618 TCAATTTCA
1 TCAATTTCA
1627 ATATCGACCA
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
26 3 0.05
27 19 0.35
28 9 0.16
30 2 0.04
32 9 0.16
33 10 0.18
34 3 0.05
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.33
Consensus pattern (27 bp):
TCAATTTCAGACCTCAAACAGTCTTTC
Found at i:1563 original size:60 final size:60
Alignment explanation
Indices: 1467--1666 Score: 328
Period size: 60 Copynumber: 3.3 Consensus size: 60
1457 CTTTCTCAGA
* * * *
1467 TATTCAATTTCAGGCCTTAAATAGGTCTTTCTCAATTTCAATATCGACCGCAGACTTGTCC
1 TATTCAATTTCAGACCTCAAACA-GTCTTTCTCAATTTCAATATCGACCGCAGACTGGTCC
*
1528 TATTCAATTTCAGACCTCAAACAGTCTTTCTCAATTTCAATATCGACCGCAAACTGGTCC
1 TATTCAATTTCAGACCTCAAACAGTCTTTCTCAATTTCAATATCGACCGCAGACTGGTCC
*
1588 TATTCAATTTCAGACCTCAAACAGTCTTTCTCAATTTCAATATCGACCACAGACTGGTCC
1 TATTCAATTTCAGACCTCAAACAGTCTTTCTCAATTTCAATATCGACCGCAGACTGGTCC
*
1648 TATCCAATTTCAGACCTCA
1 TATTCAATTTCAGACCTCA
1667 TTTCTCAATT
Statistics
Matches: 131, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
60 111 0.85
61 20 0.15
ACGTcount: A:0.29, C:0.28, G:0.10, T:0.33
Consensus pattern (60 bp):
TATTCAATTTCAGACCTCAAACAGTCTTTCTCAATTTCAATATCGACCGCAGACTGGTCC
Done.