Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015337.1 Corchorus capsularis cultivar CVL-1 contig15358, 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: 33765
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:465 original size:31 final size:31
Alignment explanation
Indices: 423--490 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
413 GATTGGACTC
* * *
423 AATTGATCCAATCTTGTGAGTACATGAACTA
1 AATTGACCCAATCTTGTGAATACAGGAACTA
*
454 AATTGACCCAATCTTGTGAATACAGGGACTA
1 AATTGACCCAATCTTGTGAATACAGGAACTA
485 AATTGA
1 AATTGA
491 TGCTTATTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (31 bp):
AATTGACCCAATCTTGTGAATACAGGAACTA
Found at i:1473 original size:224 final size:224
Alignment explanation
Indices: 1076--1489 Score: 632
Period size: 224 Copynumber: 1.8 Consensus size: 224
1066 TTAATTAAAG
* **
1076 TTTTGCTACATGACCAGAAAAAATAGTTTGGAAATTTTGTCATCCATAACATGTTGTTACACGAT
1 TTTTGCTAAATGACCAGAAAAAATAGTTCCGAAATTTTGTCATCCATAACATGTTGTTACACGAT
* * *
1141 TGGTCTAGCAGATTGGTCCCATCACTATTTAAGTGGGATTTTGCTACAAAACATGGGATGACCCC
66 TGGTCCAGCAGATTAGTCCCACCACTATTTAAGTGGGATTTTGCTACAAAACATGGGATGACCCC
* *
1206 ACATGACACATCATGTGAGACAAAATTCTGGTCAATCTTTCTGATTGTTTAGAATTTTCCGAAAA
131 ACATGACAAATCATGTGAGACAAAATTCTGGTCAATCTTTCTGAATGTTTAGAATTTTCCGAAAA
1271 ATATTAAATATAGCAAATTAATTAAAAAA
196 ATATTAAATATAGCAAATTAATTAAAAAA
* * * ** *
1300 TTTTGCTAAATGACCAG-AAAAATTGTTCCGAAATTTTGGTCCTCCATGATGTGTTGTTACATGA
1 TTTTGCTAAATGACCAGAAAAAATAGTTCCGAAATTTT-GTCATCCATAACATGTTGTTACACGA
* * * *
1364 TTGGTCCAGTAGATTAGTTCCACCACTATTTAAGTGGGGTTTTGCTACAAAATATGGGATGACCC
65 TTGGTCCAGCAGATTAGTCCCACCACTATTTAAGTGGGATTTTGCTACAAAACATGGGATGACCC
* *
1429 CACATGACAAATCATGTGGGACAAAATTCTGGTCAATTTTTCTGAATGTTTAGAATTTTCC
130 CACATGACAAATCATGTGAGACAAAATTCTGGTCAATCTTTCTGAATGTTTAGAATTTTCC
1490 TTTCCTATAT
Statistics
Matches: 169, Mismatches: 20, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
223 17 0.10
224 152 0.90
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (224 bp):
TTTTGCTAAATGACCAGAAAAAATAGTTCCGAAATTTTGTCATCCATAACATGTTGTTACACGAT
TGGTCCAGCAGATTAGTCCCACCACTATTTAAGTGGGATTTTGCTACAAAACATGGGATGACCCC
ACATGACAAATCATGTGAGACAAAATTCTGGTCAATCTTTCTGAATGTTTAGAATTTTCCGAAAA
ATATTAAATATAGCAAATTAATTAAAAAA
Found at i:3850 original size:6 final size:6
Alignment explanation
Indices: 3839--3867 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
3829 CAAGCTAGGG
3839 CGGGGC CGGGGC CGGGGC CGGGGC CGGGG
1 CGGGGC CGGGGC CGGGGC CGGGGC CGGGG
3868 GCACTTTCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.69, T:0.00
Consensus pattern (6 bp):
CGGGGC
Found at i:4486 original size:65 final size:67
Alignment explanation
Indices: 4415--4539 Score: 191
Period size: 68 Copynumber: 1.9 Consensus size: 67
4405 GAAATTATCA
*
4415 TATAAAATAATAATAACTAATTAATAA-TT-AAAAAAAATTGGGACAGAAAATAGGCTCATCGTG
1 TATAAAATAATAATAACTAATTAATAATTTAAAAAAAAATTGGGACAGAAAACAGGCTCATCGTG
4478 TG
66 TG
* * *
4480 TATAAAATAATTATAACTAATTATTAATTTTAAAAAAAAATTGGGACGGAAAACAGGCTC
1 TATAAAATAATAATAACTAATTAATAA-TTTAAAAAAAAATTGGGACAGAAAACAGGCTC
4540 GTCGCACGCG
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
65 25 0.47
67 2 0.04
68 26 0.49
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.29
Consensus pattern (67 bp):
TATAAAATAATAATAACTAATTAATAATTTAAAAAAAAATTGGGACAGAAAACAGGCTCATCGTG
TG
Found at i:8071 original size:45 final size:45
Alignment explanation
Indices: 7997--8086 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
7987 GATTACTTCT
7997 CCAGCTCATCATTAATCCGGGATAAGGATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATCCGGGATAAGGATCTTTTAGTAATTCCAC
* *
8042 CCAGCTCATCATTAAT-CTGGAGTAGGGATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATCCGGGA-TAAGGATCTTTTAGTAATTCCAC
8087 TACTCTATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 4 0.10
45 38 0.90
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (45 bp):
CCAGCTCATCATTAATCCGGGATAAGGATCTTTTAGTAATTCCAC
Found at i:8744 original size:14 final size:14
Alignment explanation
Indices: 8725--8777 Score: 79
Period size: 14 Copynumber: 3.7 Consensus size: 14
8715 ATTTGTTATT
8725 TTTATAATATTCAA
1 TTTATAATATTCAA
* *
8739 TTTATAATATTTATT
1 TTTATAATATTCA-A
8754 TTTATAATATTCAA
1 TTTATAATATTCAA
8768 TTTATAATAT
1 TTTATAATAT
8778 AATAATAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTATAATATTCAA
Found at i:8753 original size:29 final size:29
Alignment explanation
Indices: 8720--8777 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
8710 CAATAATTTG
8720 TTATTTTTATAATATTCAATTTATAATAT
1 TTATTTTTATAATATTCAATTTATAATAT
8749 TTATTTTTATAATATTCAATTTATAATAT
1 TTATTTTTATAATATTCAATTTATAATAT
8778 AATAATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (29 bp):
TTATTTTTATAATATTCAATTTATAATAT
Found at i:16195 original size:5 final size:5
Alignment explanation
Indices: 16185--16222 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
16175 CTATTGACTC
16185 TCTTT TCTTT TCTTT TCTTT T-TTT TCTTT T-TTT T-TTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
16223 AAAGAAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 12 0.38
5 20 0.62
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (5 bp):
TCTTT
Found at i:16200 original size:10 final size:9
Alignment explanation
Indices: 16187--16222 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
16177 ATTGACTCTC
16187 TTTTCTTTT
1 TTTTCTTTT
16196 CTTTTCTTTT
1 -TTTTCTTTT
16206 TTTTCTTTT
1 TTTTCTTTT
16215 TTTT-TTTT
1 TTTTCTTTT
16223 AAAGAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 4 0.15
9 13 0.50
10 9 0.35
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:16211 original size:14 final size:14
Alignment explanation
Indices: 16185--16222 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
16175 CTATTGACTC
16185 TCTTTTCTTTTCTTT
1 TCTTTT-TTTTCTTT
16200 TCTTTTTTTTCTTT
1 TCTTTTTTTTCTTT
16214 T-TTTTTTTT
1 TCTTTTTTTT
16223 AAAGAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 8 0.35
14 9 0.39
15 6 0.26
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (14 bp):
TCTTTTTTTTCTTT
Found at i:21479 original size:31 final size:28
Alignment explanation
Indices: 21418--21488 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 28
21408 CGAAAAGATC
*
21418 AGGCACTAATTTGACCTTTTCATAGTTT
1 AGGCACTAATTTGACCTTTTCAAAGTTT
*
21446 AGGCACTTATTTGACCCTTTTGGCAAAGTTT
1 AGGCACTAATTTGA-CCTTTT--CAAAGTTT
*
21477 AGGACCCTAATT
1 AGG-CACTAATT
21489 GAGATTTTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 13 0.37
29 6 0.17
31 10 0.29
32 6 0.17
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (28 bp):
AGGCACTAATTTGACCTTTTCAAAGTTT
Done.