Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005980.1 Corchorus capsularis cultivar CVL-1 contig05998, 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: 26827
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3213 original size:17 final size:17
Alignment explanation
Indices: 3169--3219 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
3159 ATACTCATTT
3169 AAAATAGTCTTCTTCTC
1 AAAATAGTCTTCTTCTC
* * *
3186 -CATTCAATCTTCTTCTC
1 AAAAT-AGTCTTCTTCTC
3203 AAAATAGTCTTCTTCTC
1 AAAATAGTCTTCTTCTC
3220 TATTCAGTCA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
16 2 0.08
17 22 0.85
18 2 0.08
ACGTcount: A:0.25, C:0.27, G:0.04, T:0.43
Consensus pattern (17 bp):
AAAATAGTCTTCTTCTC
Found at i:3228 original size:17 final size:17
Alignment explanation
Indices: 3174--3228 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
3164 CATTTAAAAT
*
3174 AGTCTTCTTCTCCATTC
1 AGTCTTCTTCTCAATTC
* *
3191 AATCTTCTTCTCAAAAT-
1 AGTCTTCTTCTC-AATTC
*
3208 AGTCTTCTTCTCTATTC
1 AGTCTTCTTCTCAATTC
3225 AGTC
1 AGTC
3229 ACCGAGAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
16 2 0.07
17 26 0.87
18 2 0.07
ACGTcount: A:0.20, C:0.29, G:0.05, T:0.45
Consensus pattern (17 bp):
AGTCTTCTTCTCAATTC
Found at i:3761 original size:22 final size:22
Alignment explanation
Indices: 3735--3779 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3725 CAAAAATGTC
* * *
3735 AAAAGGGGGGCGGTAAGTAGCA
1 AAAAGGAGGACGGTAAATAGCA
3757 AAAAGGAGGACGGTAAATAGCA
1 AAAAGGAGGACGGTAAATAGCA
3779 A
1 A
3780 CTCTCTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.09, G:0.38, T:0.09
Consensus pattern (22 bp):
AAAAGGAGGACGGTAAATAGCA
Found at i:4894 original size:2 final size:2
Alignment explanation
Indices: 4883--4912 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4873 ATAATCAAAT
4883 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4913 TAAACCACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9843 original size:2 final size:2
Alignment explanation
Indices: 9836--9863 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9826 GGTTGAACCT
9836 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9864 GTTTGAAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18688 original size:21 final size:21
Alignment explanation
Indices: 18650--18689 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
18640 GGCGCCCACA
* *
18650 TGGTTTGTCTGAAGACCCATG
1 TGGTTTGCCTGAACACCCATG
*
18671 TGGTTTGCCTGATCACCCA
1 TGGTTTGCCTGAACACCCA
18690 GTTAGGTAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (21 bp):
TGGTTTGCCTGAACACCCATG
Found at i:23769 original size:32 final size:32
Alignment explanation
Indices: 23732--23822 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 32
23722 GGCTTAAGTC
*
23732 GAGTTCGAATTAAATTTGGGTCGGGTTGATTT
1 GAGTTCGAATTAAATTTGGGTCAGGTTGATTT
** *
23764 GAGTTCGGGTTAAATTTGGGTCAGGTTGATTC
1 GAGTTCGAATTAAATTTGGGTCAGGTTGATTT
* ** * *
23796 GGGTTCGGGTCAATTTTGGGTCAGGTT
1 GAGTTCGAATTAAATTTGGGTCAGGTT
23823 AACTCGGGTT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.18, C:0.09, G:0.35, T:0.38
Consensus pattern (32 bp):
GAGTTCGAATTAAATTTGGGTCAGGTTGATTT
Found at i:23773 original size:16 final size:15
Alignment explanation
Indices: 23745--23805 Score: 50
Period size: 16 Copynumber: 3.9 Consensus size: 15
23735 TTCGAATTAA
*
23745 ATTTGGGTCGGGTTG
1 ATTTGGTTCGGGTTG
*
23760 ATTTGAGTTCGGGTTAA
1 ATTTG-GTTCGGGTT-G
* *
23777 ATTTGGGTCAGGTTG
1 ATTTGGTTCGGGTTG
*
23792 ATTCGGGTTCGGGT
1 ATT-TGGTTCGGGT
23806 CAATTTTGGG
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
15 8 0.23
16 22 0.63
17 5 0.14
ACGTcount: A:0.13, C:0.08, G:0.39, T:0.39
Consensus pattern (15 bp):
ATTTGGTTCGGGTTG
Found at i:23830 original size:32 final size:32
Alignment explanation
Indices: 23743--23836 Score: 107
Period size: 32 Copynumber: 2.9 Consensus size: 32
23733 AGTTCGAATT
* * * * * *
23743 AAATTTGGGTCGGGTTGATTTGAGTTCGGGTT
1 AAATTTGGGTCAGGTTAACTCGGGTTCGGGTC
* *
23775 AAATTTGGGTCAGGTTGATTCGGGTTCGGGTC
1 AAATTTGGGTCAGGTTAACTCGGGTTCGGGTC
*
23807 AATTTTGGGTCAGGTTAACTCGGGTTCGGG
1 AAATTTGGGTCAGGTTAACTCGGGTTCGGG
23837 CTCGGATTGG
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.16, C:0.11, G:0.37, T:0.36
Consensus pattern (32 bp):
AAATTTGGGTCAGGTTAACTCGGGTTCGGGTC
Found at i:24097 original size:15 final size:15
Alignment explanation
Indices: 24034--24104 Score: 63
Period size: 16 Copynumber: 4.5 Consensus size: 15
24024 TTTTTTCAGG
24034 TTCGGGTTT-AGTTTT
1 TTCGGGTTTGAG-TTT
* *
24049 TTCGTGTTTCAGATTT
1 TTCGGGTTTGAG-TTT
* *
24065 TGCGGGTTCTGATTTT
1 TTCGGGTT-TGAGTTT
24081 TTCGGGTTTGAGCTTT
1 TTCGGGTTTGAG-TTT
24097 TTCGGGTT
1 TTCGGGTT
24105 CGGATTCAGG
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
15 11 0.24
16 32 0.71
17 2 0.04
ACGTcount: A:0.07, C:0.11, G:0.28, T:0.54
Consensus pattern (15 bp):
TTCGGGTTTGAGTTT
Found at i:24103 original size:32 final size:32
Alignment explanation
Indices: 24045--24110 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 32
24035 TCGGGTTTAG
* *
24045 TTTTTTCGTGTTTCAGATTTTGCGGGTTCTGA
1 TTTTTTCGGGTTTCAGATTTTGCGGGTTCGGA
* * *
24077 TTTTTTCGGGTTTGAGCTTTTTCGGGTTCGGA
1 TTTTTTCGGGTTTCAGATTTTGCGGGTTCGGA
24109 TT
1 TT
24111 CAGGCGGGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.08, C:0.12, G:0.27, T:0.53
Consensus pattern (32 bp):
TTTTTTCGGGTTTCAGATTTTGCGGGTTCGGA
Found at i:24177 original size:14 final size:15
Alignment explanation
Indices: 24158--24186 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
24148 GGTTCGGATT
24158 CGGGTTTTT-TCGGG
1 CGGGTTTTTCTCGGG
24172 CGGGTTTTTCTCGGG
1 CGGGTTTTTCTCGGG
24187 TCGAGTTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.00, C:0.17, G:0.41, T:0.41
Consensus pattern (15 bp):
CGGGTTTTTCTCGGG
Found at i:24590 original size:229 final size:229
Alignment explanation
Indices: 24189--24650 Score: 906
Period size: 229 Copynumber: 2.0 Consensus size: 229
24179 TTCTCGGGTC
24189 GAGTTCATTTTGCCAACTCTAGTTGGTACACACCCTCTGGGAAGTCTTATCATGGATATTCGACT
1 GAGTTCATTTTGCCAACTCTAGTTGGTACACACCCTCTGGGAAGTCTTATCATGGATATTCGACT
24254 TTTGTTGAGCAGGGGGTGGCATTGTTCTTTACAGCATACCTACAGAGAAGGTAACTTTTGTGCTG
66 TTTGTTGAGCAGGGGGTGGCATTGTTCTTTACAGCATACCTACAGAGAAGGTAACTTTTGTGCTG
24319 ATTGGTTGGCTAATGCTGCTTGTGTTCTGGACGACGACTTTGAGCTACTATCTAATCCGCCTGAT
131 ATTGGTTGGCTAATGCTGCTTGTGTTCTGGACGACGACTTTGAGCTACTATCTAATCCGCCTGAT
*
24384 GGGCTAAAGACCTTGTTGGACGCTGATGCTAGGG
196 GGGCTAAAGACCTTGTTGGACGCTGATCCTAGGG
*
24418 GAGTTCATTTTGCCACCTCTAGTTGGTACACACCCTCTGGGAAGTCTTATCATGGATATTCGACT
1 GAGTTCATTTTGCCAACTCTAGTTGGTACACACCCTCTGGGAAGTCTTATCATGGATATTCGACT
24483 TTTGTTGAGCAGGGGGTGGCATTGTTCTTTACAGCATACCTACAGAGAAGGTAACTTTTGTGCTG
66 TTTGTTGAGCAGGGGGTGGCATTGTTCTTTACAGCATACCTACAGAGAAGGTAACTTTTGTGCTG
24548 ATTGGTTGGCTAATGCTGCTTGTGTTCTGGACGACGACTTTGAGCTACTATCTAATCCGCCTGAT
131 ATTGGTTGGCTAATGCTGCTTGTGTTCTGGACGACGACTTTGAGCTACTATCTAATCCGCCTGAT
24613 GGGCTAAAGACCTTGTTGGACGCTGATCCTAGGG
196 GGGCTAAAGACCTTGTTGGACGCTGATCCTAGGG
24647 GAGT
1 GAGT
24651 ATCCTTCCCT
Statistics
Matches: 231, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
229 231 1.00
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.33
Consensus pattern (229 bp):
GAGTTCATTTTGCCAACTCTAGTTGGTACACACCCTCTGGGAAGTCTTATCATGGATATTCGACT
TTTGTTGAGCAGGGGGTGGCATTGTTCTTTACAGCATACCTACAGAGAAGGTAACTTTTGTGCTG
ATTGGTTGGCTAATGCTGCTTGTGTTCTGGACGACGACTTTGAGCTACTATCTAATCCGCCTGAT
GGGCTAAAGACCTTGTTGGACGCTGATCCTAGGG
Found at i:26161 original size:19 final size:19
Alignment explanation
Indices: 26128--26179 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
26118 AAACCACAGC
26128 AAAAATTACATTTATCAAG-CA
1 AAAAATTA-A-TTAT-AAGTCA
26149 AAAAATTAATTATAAGTCA
1 AAAAATTAATTATAAGTCA
*
26168 AATAAAATAATT
1 AA-AAATTAATT
26180 GCACGTTGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 3 0.11
19 8 0.29
20 9 0.32
21 8 0.29
ACGTcount: A:0.58, C:0.08, G:0.04, T:0.31
Consensus pattern (19 bp):
AAAAATTAATTATAAGTCA
Done.