Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008241.1 Corchorus capsularis cultivar CVL-1 contig08262, 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: 28903
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:4937 original size:10 final size:10
Alignment explanation
Indices: 4922--4958 Score: 65
Period size: 10 Copynumber: 3.6 Consensus size: 10
4912 TTCTTGTCGA
4922 ATTTTTTTTT
1 ATTTTTTTTT
4932 ATTTTTTTTT
1 ATTTTTTTTT
4942 ATTTTTTTTAT
1 ATTTTTTTT-T
4953 ATTTTT
1 ATTTTT
4959 CGATATAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 19 0.73
11 7 0.27
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (10 bp):
ATTTTTTTTT
Found at i:4938 original size:9 final size:9
Alignment explanation
Indices: 4924--4958 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
4914 CTTGTCGAAT
4924 TTTTTTTTA
1 TTTTTTTTA
4933 TTTTTTTTTA
1 -TTTTTTTTA
4943 TTTTTTTTA
1 TTTTTTTTA
*
4952 TATTTTT
1 TTTTTTT
4959 CGATATAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:4939 original size:11 final size:11
Alignment explanation
Indices: 4923--4958 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
4913 TCTTGTCGAA
4923 TTTTTTTTTA-
1 TTTTTTTTTAT
4933 TTTTTTTTTAT
1 TTTTTTTTTAT
*
4944 TTTTTTTATAT
1 TTTTTTTTTAT
4955 TTTT
1 TTTT
4959 CGATATAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTTTTTTTAT
Found at i:5059 original size:8 final size:8
Alignment explanation
Indices: 5031--5064 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
5021 GAATCGGCTA
5031 TGAATTTT
1 TGAATTTT
*
5039 TGAAGTTTC
1 TGAA-TTTT
5048 TGAATTTT
1 TGAATTTT
5056 TGAATTTT
1 TGAATTTT
5064 T
1 T
5065 CAAAAAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:6022 original size:33 final size:32
Alignment explanation
Indices: 5980--6080 Score: 96
Period size: 33 Copynumber: 3.1 Consensus size: 32
5970 AGCTAAAGGA
*
5980 TCATATGGCCGGTTGTGGCCGGGCATGGCCGA-G
1 TCATGTGGCCGG-TGTGGCCGGGCATGGCC-ATG
* *
6013 TCATGTGGCCGGCTGTGGCTGGGCTTGGCCATG
1 TCATGTGGCCGG-TGTGGCCGGGCATGGCCATG
** **
6046 TCGCGTGGCCGGTGATGGCCGGGCATCTCCATG
1 TCATGTGGCCGGTG-TGGCCGGGCATGGCCATG
6079 TC
1 TC
6081 GCATGGCCGG
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
32 3 0.05
33 53 0.95
ACGTcount: A:0.09, C:0.27, G:0.41, T:0.24
Consensus pattern (32 bp):
TCATGTGGCCGGTGTGGCCGGGCATGGCCATG
Found at i:6081 original size:33 final size:33
Alignment explanation
Indices: 6041--6109 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
6031 CTGGGCTTGG
*
6041 CCATGTCGCGTGGCCGGTGATGGC-CGGGCATCT
1 CCATGTCGCATGGCCGGTG-TGGCGCGGGCATCT
* *
6074 CCATGTCGCATGGCCGGTGTTGCGTGGGCATCT
1 CCATGTCGCATGGCCGGTGTGGCGCGGGCATCT
6107 CCA
1 CCA
6110 AATTTCGTGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 3 0.09
33 29 0.91
ACGTcount: A:0.10, C:0.30, G:0.36, T:0.23
Consensus pattern (33 bp):
CCATGTCGCATGGCCGGTGTGGCGCGGGCATCT
Found at i:6836 original size:22 final size:23
Alignment explanation
Indices: 6795--6838 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
6785 AATGCTGTGA
6795 TAAAATCTTTTATTTTTGTTTTC
1 TAAAATCTTTTATTTTTGTTTTC
*
6818 TAAAGTCTTTTA-TTTTGTTTT
1 TAAAATCTTTTATTTTTGTTTT
6839 GAAAACTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.66
Consensus pattern (23 bp):
TAAAATCTTTTATTTTTGTTTTC
Found at i:9393 original size:34 final size:37
Alignment explanation
Indices: 9350--9426 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 37
9340 GTCAAGCCAA
*
9350 GAGAGGTGCTTGC-T-TCCAACTTGGCT-CAATGTTG
1 GAGAGGTGCTTGCTTGTCCAACGTGGCTCCAATGTTG
9384 GAGAGGTGCTTGCTTGGCTCCAACGTGGCTCCAATGTTG
1 GAGAGGTGCTTGCTT-G-TCCAACGTGGCTCCAATGTTG
9423 GAGA
1 GAGA
9427 CATGTCCACA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
34 13 0.35
35 1 0.03
38 11 0.30
39 12 0.32
ACGTcount: A:0.18, C:0.21, G:0.32, T:0.29
Consensus pattern (37 bp):
GAGAGGTGCTTGCTTGTCCAACGTGGCTCCAATGTTG
Found at i:18411 original size:33 final size:32
Alignment explanation
Indices: 18340--18413 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 32
18330 AAAACAAATA
**
18340 TGTTTTGGTTGATCATAGCATTAAAAATAATT
1 TGTTTTGGTTGATCATAGCATTAAAAATAACC
**
18372 TCGTTTTGGTTGATCATAGCATTGCAAATAAACC
1 T-GTTTTGGTTGATCATAGCATTAAAAAT-AACC
18406 TGTTTTGG
1 TGTTTTGG
18414 GTGACGAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 1 0.03
33 32 0.89
34 3 0.08
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (32 bp):
TGTTTTGGTTGATCATAGCATTAAAAATAACC
Found at i:20232 original size:33 final size:33
Alignment explanation
Indices: 20171--20234 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
20161 AGCACTAGTG
* * *
20171 ACCGGCCATGCGACTTGGAGAAGCCCGGCCAAC
1 ACCGGCCACGCGACATGGACAAGCCCGGCCAAC
* *
20204 ACCGGCCACGCGACATGGACATGTCCGGCCA
1 ACCGGCCACGCGACATGGACAAGCCCGGCCA
20235 CAATCGGCCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.23, C:0.38, G:0.30, T:0.09
Consensus pattern (33 bp):
ACCGGCCACGCGACATGGACAAGCCCGGCCAAC
Found at i:22840 original size:23 final size:23
Alignment explanation
Indices: 22807--23015 Score: 136
Period size: 23 Copynumber: 9.1 Consensus size: 23
22797 AAGTTGATGG
* *
22807 AATGCTCAAAAGTTGTGAATTGA
1 AATGCTGAAAAGTTGTAAATTGA
22830 AATGCTGAAAAGTTGTAAATTCTGAA
1 AATGCTGAAAAGTTGTAAA-T-TG-A
* *
22856 AAGTTGTTGAAATGTTGTAAAGTTGTA
1 AA--TGCTGAAAAGTTGTAAA-TTG-A
22883 AAT--TGAAAAGTTG----TTGA
1 AATGCTGAAAAGTTGTAAATTGA
*
22900 AATGCTGTAAAGTTGTAAATTGA
1 AATGCTGAAAAGTTGTAAATTGA
22923 AATGCTGAAAAGTTGTAAATTGAA
1 AATGCTGAAAAGTTGTAAATTG-A
* * *
22947 AAGTTGTTGAAATGTTATAAAGTTGTA
1 AA--TGCTGAAAAGTTGTAAA-TTG-A
22974 AAT--TGAAAAGTTG----TTGA
1 AATGCTGAAAAGTTGTAAATTGA
* *
22991 AATGTTGTAAAGTTGTAAATTGA
1 AATGCTGAAAAGTTGTAAATTGA
23014 AA
1 AA
23016 AGTTGTTGAA
Statistics
Matches: 149, Mismatches: 16, Indels: 42
0.72 0.08 0.20
Matches are distributed among these distances:
17 8 0.05
18 6 0.04
19 18 0.12
23 65 0.44
24 4 0.03
25 4 0.03
26 17 0.11
27 11 0.07
28 16 0.11
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.35
Consensus pattern (23 bp):
AATGCTGAAAAGTTGTAAATTGA
Found at i:22895 original size:34 final size:34
Alignment explanation
Indices: 22826--23028 Score: 266
Period size: 34 Copynumber: 6.2 Consensus size: 34
22816 AAGTTGTGAA
* *
22826 TTGAAATGCTGAAAAGTTGTAAATTCTGAAAAGTTG
1 TTGAAATGTTGTAAAGTTGTAAA-T-TGAAAAGTTG
22862 TTGAAATGTTGTAAAGTTGTAAATTGAAAAGTTG
1 TTGAAATGTTGTAAAGTTGTAAATTGAAAAGTTG
*
22896 TTGAAATGCTGTAAAGTTGTAAATTG-AAA--TG
1 TTGAAATGTTGTAAAGTTGTAAATTGAAAAGTTG
*
22927 CTG--A------AAAGTTGTAAATTGAAAAGTTG
1 TTGAAATGTTGTAAAGTTGTAAATTGAAAAGTTG
*
22953 TTGAAATGTTATAAAGTTGTAAATTGAAAAGTTG
1 TTGAAATGTTGTAAAGTTGTAAATTGAAAAGTTG
22987 TTGAAATGTTGTAAAGTTGTAAATTGAAAAGTTG
1 TTGAAATGTTGTAAAGTTGTAAATTGAAAAGTTG
23021 TTGAAATG
1 TTGAAATG
23029 CGCCGCTTGG
Statistics
Matches: 150, Mismatches: 6, Indels: 24
0.83 0.03 0.13
Matches are distributed among these distances:
23 14 0.09
24 3 0.02
26 4 0.03
28 1 0.01
29 1 0.01
31 4 0.03
33 3 0.02
34 98 0.65
35 1 0.01
36 21 0.14
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (34 bp):
TTGAAATGTTGTAAAGTTGTAAATTGAAAAGTTG
Found at i:22938 original size:57 final size:57
Alignment explanation
Indices: 22862--22981 Score: 204
Period size: 57 Copynumber: 2.1 Consensus size: 57
22852 TGAAAAGTTG
* * *
22862 TTGAAATGTTGTAAAGTTGTAAATTGAAAAGTTGTTGAAATGCTGTAAAGTTGTAAA
1 TTGAAATGCTGAAAAGTTGTAAATTGAAAAGTTGTTGAAATGCTATAAAGTTGTAAA
*
22919 TTGAAATGCTGAAAAGTTGTAAATTGAAAAGTTGTTGAAATGTTATAAAGTTGTAAA
1 TTGAAATGCTGAAAAGTTGTAAATTGAAAAGTTGTTGAAATGCTATAAAGTTGTAAA
22976 TTGAAA
1 TTGAAA
22982 AGTTGTTGAA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.41, C:0.02, G:0.22, T:0.36
Consensus pattern (57 bp):
TTGAAATGCTGAAAAGTTGTAAATTGAAAAGTTGTTGAAATGCTATAAAGTTGTAAA
Found at i:22988 original size:91 final size:93
Alignment explanation
Indices: 22796--23015 Score: 363
Period size: 91 Copynumber: 2.4 Consensus size: 93
22786 CGAAAACTGT
* * ** *
22796 AAAGTTGATGGAATGCTCAAAAGTTGTGAATTGAAATGCTGAAAAGTTGTAAATTCTGAAAAGTT
1 AAAGTTGTTGAAATGCTGTAAAGTTGTAAATTGAAATGCTGAAAAGTTGTAAATTCTGAAAAGTT
*
22861 GTTGAAATGTTGTAAAGTTGTAAATTGA
66 GTTGAAATGTTATAAAGTTGTAAATTGA
22889 AAAGTTGTTGAAATGCTGTAAAGTTGTAAATTGAAATGCTGAAAAGTTGTAAA-T-TGAAAAGTT
1 AAAGTTGTTGAAATGCTGTAAAGTTGTAAATTGAAATGCTGAAAAGTTGTAAATTCTGAAAAGTT
22952 GTTGAAATGTTATAAAGTTGTAAATTGA
66 GTTGAAATGTTATAAAGTTGTAAATTGA
*
22980 AAAGTTGTTGAAATGTTGTAAAGTTGTAAATTGAAA
1 AAAGTTGTTGAAATGCTGTAAAGTTGTAAATTGAAA
23016 AGTTGTTGAA
Statistics
Matches: 120, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
91 71 0.59
92 1 0.01
93 48 0.40
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.35
Consensus pattern (93 bp):
AAAGTTGTTGAAATGCTGTAAAGTTGTAAATTGAAATGCTGAAAAGTTGTAAATTCTGAAAAGTT
GTTGAAATGTTATAAAGTTGTAAATTGA
Found at i:23113 original size:39 final size:38
Alignment explanation
Indices: 23053--23243 Score: 156
Period size: 39 Copynumber: 5.0 Consensus size: 38
23043 AACTGAAAAC
*
23053 TGCTGAAAGATGACATGTTTCCAGTCGATCTTGATAACT
1 TGCTGAAAGATGACCTGTTTCCAGTCGATCTTGATAA-T
* * * * * * *
23092 TGTTGAAAGATTACCTATTTCCAGTCAAAAC-TAATAAG
1 TGCTGAAAGATGACCTGTTTCCAGTC-GATCTTGATAAT
* * * **
23130 TGCTGAAAGACGACCAGTTTCCAATCG-T-AAGATAAT
1 TGCTGAAAGATGACCTGTTTCCAGTCGATCTTGATAAT
* *
23166 TGCTGAAAGATGACATGTTTCCAGACGATCTTGATAACT
1 TGCTGAAAGATGACCTGTTTCCAGTCGATCTTGATAA-T
* * *
23205 TGTTGAAAGATGACCTGTTTCTAGTC-AACTTTGATAAT
1 TGCTGAAAGATGACCTGTTTCCAGTCGATC-TTGATAAT
23243 T
1 T
23244 TGGAACATGA
Statistics
Matches: 115, Mismatches: 31, Indels: 13
0.72 0.19 0.08
Matches are distributed among these distances:
36 26 0.23
37 1 0.01
38 29 0.25
39 57 0.50
40 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Consensus pattern (38 bp):
TGCTGAAAGATGACCTGTTTCCAGTCGATCTTGATAAT
Found at i:23318 original size:38 final size:38
Alignment explanation
Indices: 23266--23410 Score: 177
Period size: 40 Copynumber: 3.8 Consensus size: 38
23256 TCTGATAACT
*
23266 TGAAAGATGGCCTGTTTCCAGTCAACTTTGAATATTGC
1 TGAAAGATGACCTGTTTCCAGTCAACTTTGAATATTGC
* *
23304 TGAAAGATGACCTGTTTCAAGTCAACTTTTCGATTATTGC
1 TGAAAGATGACCTGTTTCCAGTCAAC-TTT-GAATATTGC
* * *
23344 TGAAAGGTGACCTGTTTCTAGTCAACTTCG-ATGATTG-
1 TGAAAGATGACCTGTTTCCAGTCAACTTTGAAT-ATTGC
* *
23381 TGAAAGATGACTTGTTTCCAATCAACTTTG
1 TGAAAGATGACCTGTTTCCAGTCAACTTTG
23411 GGACTTCTTT
Statistics
Matches: 92, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
37 26 0.28
38 29 0.32
39 5 0.05
40 32 0.35
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (38 bp):
TGAAAGATGACCTGTTTCCAGTCAACTTTGAATATTGC
Found at i:23355 original size:40 final size:39
Alignment explanation
Indices: 23266--23409 Score: 179
Period size: 38 Copynumber: 3.7 Consensus size: 39
23256 TCTGATAACT
* * *
23266 TGAAAGATGGCCTGTTTCCAGTCAACTTT-GAATATTGC
1 TGAAAGATGACCTGTTTCAAGTCAACTTTCGATTATTGC
23304 TGAAAGATGACCTGTTTCAAGTCAACTTTTCGATTATTGC
1 TGAAAGATGACCTGTTTCAAGTCAAC-TTTCGATTATTGC
* * *
23344 TGAAAGGTGACCTGTTTCTAGTCAAC-TTCGATGATTG-
1 TGAAAGATGACCTGTTTCAAGTCAACTTTCGATTATTGC
*
23381 TGAAAGATGACTTGTTTCCAA-TCAACTTT
1 TGAAAGATGACCTGTTT-CAAGTCAACTTT
23410 GGGACTTCTT
Statistics
Matches: 93, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
37 20 0.22
38 38 0.41
39 3 0.03
40 32 0.34
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.36
Consensus pattern (39 bp):
TGAAAGATGACCTGTTTCAAGTCAACTTTCGATTATTGC
Found at i:27756 original size:10 final size:10
Alignment explanation
Indices: 27743--27788 Score: 67
Period size: 10 Copynumber: 4.6 Consensus size: 10
27733 AGTTATATCG
27743 AAAAATATAA
1 AAAAATATAA
27753 AAAAATATATA
1 AAAAATATA-A
27764 AAAAATA-AA
1 AAAAATATAA
*
27773 AAAAATAAAA
1 AAAAATATAA
27783 AAAAAT
1 AAAAAT
27789 TTCGACCAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 8 0.24
10 18 0.53
11 8 0.24
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (10 bp):
AAAAATATAA
Found at i:27775 original size:9 final size:9
Alignment explanation
Indices: 27743--27786 Score: 61
Period size: 9 Copynumber: 4.8 Consensus size: 9
27733 AGTTATATCG
*
27743 AAAAATATA
1 AAAAAAATA
27752 AAAAAATATA
1 AAAAAA-ATA
*
27762 TAAAAAATA
1 AAAAAAATA
27771 AAAAAAATA
1 AAAAAAATA
27780 AAAAAAA
1 AAAAAAA
27787 ATTTCGACCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
9 23 0.74
10 8 0.26
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (9 bp):
AAAAAAATA
Done.