Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016216.1 Corchorus capsularis cultivar CVL-1 contig16237, 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: 12560
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:1289 original size:70 final size:70
Alignment explanation
Indices: 1176--1654 Score: 665
Period size: 70 Copynumber: 6.8 Consensus size: 70
1166 TGGATCAATC
* * ** * *
1176 GGAAACAACTGATGAAAAACCTTCCTGGGTCGACTGAATCGATCATTCTGACATAAAATTGCATA
1 GGAAACAACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGATA
1241 AACGT
66 AACGT
*
1246 GGAAACTACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATAT-TGACATAAACTTGGAT
1 GGAAACAACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCAT-TCTGACATAAACTTGGAT
1310 AAACGT
65 AAACGT
* * *
1316 GGAAACTACTGAAGAAAGACCACCCTGGGTTGACCGAATCGATCATTCTGACATAAACTTGGATA
1 GGAAACAACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGATA
*
1381 AATGT
66 AACGT
* * **
1386 GGAAACTACTGAAGAAAAACCACCCTGGGTTAACTGAATCGATCATTCTGACATAAACTTGGATA
1 GGAAACAACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGATA
1451 AAC-T
66 AACGT
* * * *
1455 TGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAATTTCGAAT
1 GGAAACAACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTT-GGAT
*
1520 AAACTT
65 AAACGT
* * * *
1526 GAAAACAATTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAAATTGGATA
1 GGAAACAACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGATA
*
1591 AACTT
66 AACGT
* * * *
1596 GAAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCACTCTAACATAAACT
1 GGAAACAACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACT
1655 GAAGAAAGAC
Statistics
Matches: 374, Mismatches: 31, Indels: 8
0.91 0.08 0.02
Matches are distributed among these distances:
69 55 0.15
70 261 0.70
71 58 0.16
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (70 bp):
GGAAACAACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGATA
AACGT
Found at i:1681 original size:49 final size:49
Alignment explanation
Indices: 1602--1703 Score: 159
Period size: 49 Copynumber: 2.1 Consensus size: 49
1592 ACTTGAAAAC
* *
1602 AACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCACTCTAACATA
1 AACTGAAGAAAGACCGCCCTAGGTCAACTGAATCGATCACTCTAACATA
* * *
1651 AACTGAAGAAAGACCGCCCTAGGTCAACTGAATCGATCATTTTGACATA
1 AACTGAAGAAAGACCGCCCTAGGTCAACTGAATCGATCACTCTAACATA
1700 AACT
1 AACT
1704 TGGATAAACT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.21
Consensus pattern (49 bp):
AACTGAAGAAAGACCGCCCTAGGTCAACTGAATCGATCACTCTAACATA
Found at i:1735 original size:69 final size:70
Alignment explanation
Indices: 1651--1844 Score: 257
Period size: 69 Copynumber: 2.7 Consensus size: 70
1641 CTCTAACATA
* *
1651 AACTGAAGAAAGACCGCCCTAGGTCAACTGAATCGATCATTTTGACATAAACTT-GGATAAACTT
1 AACTGAAGAAAGACCGCCCT-GGTCAACTGAATCGATCATTCTGACATAAACTTCGAATAAACTT
1715 G-AAAC
65 GAAAAC
** *
1720 AACTGAAGAAAGACCGCATTGGGTCGACTGAATCGATCATTCTGACATAAACTTCGAATAAACTT
1 AACTGAAGAAAGACCGCCCT-GGTCAACTGAATCGATCATTCTGACATAAACTTCGAATAAACTT
1785 GAAAAC
65 GAAAAC
* * * *
1791 AATTCAAGAAAGACCGCCCTGGAAACTACTGAATCGATCATTCTGACATAAACT
1 AACTGAAGAAAGACCGCCCTGG--TCAACTGAATCGATCATTCTGACATAAACT
1845 GAAGAAAGAC
Statistics
Matches: 109, Mismatches: 12, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
69 49 0.45
70 12 0.11
71 20 0.18
72 28 0.26
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (70 bp):
AACTGAAGAAAGACCGCCCTGGTCAACTGAATCGATCATTCTGACATAAACTTCGAATAAACTTG
AAAAC
Found at i:1824 original size:190 final size:190
Alignment explanation
Indices: 1461--1868 Score: 631
Period size: 190 Copynumber: 2.1 Consensus size: 190
1451 AACTTGAAAC
* *
1461 AACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAATTTCGAATAAACTT
1 AACTGAAGAAAGACCGCCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTCGAATAAACTT
* * *
1526 GAAAACAATTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAAATTGGATA
66 GAAAACAACTGAAGAAAGACCGCACTGGGTCGACTGAATCGATCATTCTGACATAAAATTGAATA
* **
1591 AACTTGAAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCACTCTAACATA
131 AACTTGAAAACAACTCAAGAAAGACCGCCCTGGAACGACTGAATCGATCACTCTAACATA
* * *
1651 AACTGAAGAAAGACCGCCCTAGGTCAACTGAATCGATCATTTTGACATAAACTT-GGATAAACTT
1 AACTGAAGAAAGACCGCCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTCGAATAAACTT
* *
1715 G-AAACAACTGAAGAAAGACCGCATTGGGTCGACTGAATCGATCATTCTGACATAAACTTCGAAT
66 GAAAACAACTGAAGAAAGACCGCACTGGGTCGACTGAATCGATCATTCTGACATAAAATT-GAAT
* * * *
1779 AAACTTGAAAACAATTCAAGAAAGACCGCCCTGGAAACTACTGAATCGATCATTCTGACATA
130 AAACTTGAAAACAACTCAAGAAAGACCGCCCTGG-AACGACTGAATCGATCACTCTAACATA
1841 AACTGAAGAAAGACCGCCCTGGGTCAAC
1 AACTGAAGAAAGACCGCCCTGGGTCAAC
1869 CGAAATAAAC
Statistics
Matches: 198, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
188 54 0.27
189 45 0.23
190 99 0.50
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (190 bp):
AACTGAAGAAAGACCGCCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTCGAATAAACTT
GAAAACAACTGAAGAAAGACCGCACTGGGTCGACTGAATCGATCATTCTGACATAAAATTGAATA
AACTTGAAAACAACTCAAGAAAGACCGCCCTGGAACGACTGAATCGATCACTCTAACATA
Found at i:1885 original size:35 final size:35
Alignment explanation
Indices: 1838--1971 Score: 119
Period size: 35 Copynumber: 3.8 Consensus size: 35
1828 TCATTCTGAC
*
1838 ATAAACTGAAGAAAGACCGCCCTGGGTCAACCGAA
1 ATAAACTAAAGAAAGACCGCCCTGGGTCAACCGAA
* * * * * *
1873 ATAAACTAAAGAAACACAAG-CCTCGATCATTCCGAC
1 ATAAACTAAAGAAAGAC-CGCCCTGGGTCA-ACCGAA
* * * *
1909 ATAAACTGAAGAAAGACCACCCTAGGTCAACTGAA
1 ATAAACTAAAGAAAGACCGCCCTGGGTCAACCGAA
*
1944 ATAAACTTAAA-TAAGACCGCCCTGGGTC
1 ATAAAC-TAAAGAAAGACCGCCCTGGGTC
1972 GATTGAAGTA
Statistics
Matches: 75, Mismatches: 20, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
35 45 0.60
36 30 0.40
ACGTcount: A:0.42, C:0.25, G:0.17, T:0.16
Consensus pattern (35 bp):
ATAAACTAAAGAAAGACCGCCCTGGGTCAACCGAA
Found at i:1914 original size:36 final size:36
Alignment explanation
Indices: 1824--1922 Score: 103
Period size: 35 Copynumber: 2.8 Consensus size: 36
1814 AACTACTGAA
* * *
1824 TCGATCATTCTGACATAAACTGAAGAAAGACCGCCC
1 TCGATCATTCCGACATAAACTGAAGAAACACAGCCC
* * * * *
1860 TGGGTCA-ACCGAAATAAACTAAAGAAACACAAG-CC
1 TCGATCATTCCGACATAAACTGAAGAAACAC-AGCCC
1895 TCGATCATTCCGACATAAACTGAAGAAA
1 TCGATCATTCCGACATAAACTGAAGAAA
1923 GACCACCCTA
Statistics
Matches: 48, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
35 25 0.52
36 23 0.48
ACGTcount: A:0.42, C:0.24, G:0.16, T:0.17
Consensus pattern (36 bp):
TCGATCATTCCGACATAAACTGAAGAAACACAGCCC
Found at i:2993 original size:13 final size:13
Alignment explanation
Indices: 2975--3012 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
2965 CGTCATTCAT
2975 TTTTTTTCTTCTC
1 TTTTTTTCTTCTC
2988 TTTTTTTCTTCTC
1 TTTTTTTCTTCTC
3001 TCTTTTTT-TTCT
1 T-TTTTTTCTTCT
3013 TTTCTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 18 0.75
14 6 0.25
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTTTCTTCTC
Found at i:3011 original size:16 final size:15
Alignment explanation
Indices: 2974--3021 Score: 66
Period size: 16 Copynumber: 3.3 Consensus size: 15
2964 TCGTCATTCA
2974 TTTTTTTTC-TTCTC
1 TTTTTTTTCTTTCTC
2988 -TTTTTTTCTTCTCTC
1 TTTTTTTTCTT-TCTC
3003 TTTTTTTTCTTT-TC
1 TTTTTTTTCTTTCTC
3017 TTTTT
1 TTTTT
3022 ACATGCACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
13 8 0.26
14 8 0.26
15 5 0.16
16 10 0.32
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTTTTCTTTCTC
Found at i:3020 original size:13 final size:13
Alignment explanation
Indices: 2975--3021 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 13
2965 CGTCATTCAT
*
2975 TTTTTTTCTTCTC
1 TTTTTTTCTTTTC
2988 TTTTTTTCTTCTCTC
1 TTTTTTTCTT-T-TC
3003 TTTTTTTTCTTTTC
1 -TTTTTTTCTTTTC
3017 TTTTT
1 TTTTT
3022 ACATGCACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 15 0.50
14 2 0.07
15 3 0.10
16 10 0.33
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTTTCTTTTC
Found at i:3786 original size:45 final size:46
Alignment explanation
Indices: 3713--3818 Score: 180
Period size: 46 Copynumber: 2.3 Consensus size: 46
3703 TTTGAAATCA
3713 TTTTTGGAAAACCATTTTATCAAAAACCTTTTG-AAAACCATGACTC
1 TTTTT-GAAAACCATTTTATCAAAAACCTTTTGCAAAACCATGACTC
3759 TTTTTGAAAAACCATTTTATC-AAAACCTTTTGCAAAACCATGACTC
1 TTTTTG-AAAACCATTTTATCAAAAACCTTTTGCAAAACCATGACTC
3805 TTTTTGAAAACCAT
1 TTTTTGAAAACCAT
3819 GATTTGATTT
Statistics
Matches: 58, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
45 20 0.34
46 38 0.66
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.36
Consensus pattern (46 bp):
TTTTTGAAAACCATTTTATCAAAAACCTTTTGCAAAACCATGACTC
Found at i:3871 original size:19 final size:19
Alignment explanation
Indices: 3849--3893 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
3839 CCATCGTTGT
3849 TTTTTTCTCTTTT-TCTTTC-
1 TTTTTTCT-TTTTAT-TTTCA
3868 TTTTTTCTTTTTATTTTCA
1 TTTTTTCTTTTTATTTTCA
3887 TTTTTTC
1 TTTTTTC
3894 CACTTATCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTTCTTTTTATTTTCA
Found at i:3957 original size:13 final size:14
Alignment explanation
Indices: 3941--3978 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
3931 GGCCAAGTTT
3941 TTTTTTCTTTT-TC
1 TTTTTTCTTTTCTC
3954 TTTTTTCTTTTCTC
1 TTTTTTCTTTTCTC
3968 TTTTTT-TTTTC
1 TTTTTTCTTTTC
3979 AGAATGGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 16 0.67
14 8 0.33
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTTCTTTTCTC
Found at i:3958 original size:7 final size:7
Alignment explanation
Indices: 3941--3977 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
3931 GGCCAAGTTT
3941 TTTTTTC
1 TTTTTTC
3948 -TTTTTC
1 TTTTTTC
3954 TTTTTTC
1 TTTTTTC
*
3961 TTTTCTC
1 TTTTTTC
3968 TTTTTT-
1 TTTTTTC
3974 TTTT
1 TTTT
3978 CAGAATGGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
6 10 0.37
7 17 0.63
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTC
Found at i:3978 original size:18 final size:18
Alignment explanation
Indices: 3938--3978 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
3928 TTAGGCCAAG
3938 TTTTT-TTTTCTTTTTCT
1 TTTTTCTTTTCTTTTTCT
3955 TTTTTCTTTTCTCTTTT-T
1 TTTTTCTTTTCT-TTTTCT
3973 TTTTTC
1 TTTTTC
3979 AGAATGGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.23
18 13 0.59
19 4 0.18
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTTCTTTTCTTTTTCT
Done.