Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014676.1 Corchorus capsularis cultivar CVL-1 contig14697, 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: 9633
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Found at i:853 original size:36 final size:36
Alignment explanation
Indices: 802--973 Score: 145
Period size: 36 Copynumber: 4.8 Consensus size: 36
792 TAAAATAAAT
* *
802 AACTGAAGAAAGACCACCCTGGATCATTCCAAACCG
1 AACTGAAGAACGACCACCCTCGATCATTCCAAACCG
* **
838 AATTGAAGAACGACCACCCTCGATCATTCC--GTCG
1 AACTGAAGAACGACCACCCTCGATCATTCCAAACCG
* * * * * **
872 TAAACTGAAGAAAGACCACCCTGGGTCA-GCTGAAA-TA
1 --AACTGAAGAACGACCACCCTCGATCATTC-CAAACCG
* * *
909 AACTGAAGAACGACCACCCTCGATCATTCTAGACTG
1 AACTGAAGAACGACCACCCTCGATCATTCCAAACCG
*
945 AACTGAAGAACAACCACCCTCGATCATTC
1 AACTGAAGAACGACCACCCTCGATCATTC
974 TGACACAAAT
Statistics
Matches: 107, Mismatches: 22, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
34 2 0.02
35 26 0.24
36 79 0.74
ACGTcount: A:0.36, C:0.30, G:0.17, T:0.17
Consensus pattern (36 bp):
AACTGAAGAACGACCACCCTCGATCATTCCAAACCG
Found at i:974 original size:36 final size:36
Alignment explanation
Indices: 802--1128 Score: 142
Period size: 36 Copynumber: 9.2 Consensus size: 36
792 TAAAATAAAT
* * * **
802 AACTGAAGAA-AGACCACCCTGGATCATTCCAAACCG
1 AACTGAAGAACA-ACCACCCTCGATCATTCTAGACTA
* * * *
838 AATTGAAGAACGACCACCCTCGATCATTC-CGTCGTA
1 AACTGAAGAACAACCACCCTCGATCATTCTAGAC-TA
* * * *
874 AACTGAAGAA-AGACCACCCTGGGTCA-GCT-GAAATA
1 AACTGAAGAACA-ACCACCCTCGATCATTCTAG-ACTA
* *
909 AACTGAAGAACGACCACCCTCGATCATTCTAGACTG
1 AACTGAAGAACAACCACCCTCGATCATTCTAGACTA
*
945 AACTGAAGAACAACCACCCTCGATCATTCT-GACACA
1 AACTGAAGAACAACCACCCTCGATCATTCTAGAC-TA
* * * * * *
981 AATTGACGAA-AGACCACCCTGGGTCA-ACT-GAAATA
1 AACTGAAGAACA-ACCACCCTCGATCATTCTAG-ACTA
** * * *
1016 AGTTGAAGAACGACCATCCTCGATCATTCT-GACACA
1 AACTGAAGAACAACCACCCTCGATCATTCTAGAC-TA
* * * *
1052 AACTGAAGAA-AGACCACCCTAGGTCA-ACT-GAAATA
1 AACTGAAGAACA-ACCACCCTCGATCATTCTAG-ACTA
* * * *
1087 AACCGAAGAACGACCACCCTCTATCATTCCAGCAC-A
1 AACTGAAGAACAACCACCCTCGATCATTCTAG-ACTA
1123 AACTGA
1 AACTGA
1129 TGCAAGACCA
Statistics
Matches: 213, Mismatches: 59, Indels: 38
0.69 0.19 0.12
Matches are distributed among these distances:
35 79 0.37
36 131 0.62
37 3 0.01
ACGTcount: A:0.38, C:0.29, G:0.17, T:0.17
Consensus pattern (36 bp):
AACTGAAGAACAACCACCCTCGATCATTCTAGACTA
Found at i:1023 original size:71 final size:71
Alignment explanation
Indices: 948--1172 Score: 317
Period size: 71 Copynumber: 3.2 Consensus size: 71
938 TAGACTGAAC
* * *
948 TGAAGAACAACCACCCTCGATCATTCTGACACAAATTGACGAAAGACCACCCTGGGTCAACTGAA
1 TGAAGAACGACCACCCTCGATCATTCTGACACAAACTGAAGAAAGACCACCCTGGGTCAACTGAA
*
1013 ATAAGT
66 ATAAAT
* *
1019 TGAAGAACGACCATCCTCGATCATTCTGACACAAACTGAAGAAAGACCACCCTAGGTCAACTGAA
1 TGAAGAACGACCACCCTCGATCATTCTGACACAAACTGAAGAAAGACCACCCTGGGTCAACTGAA
*
1084 ATAAAC
66 ATAAAT
* * * * *
1090 CGAAGAACGACCACCCTCTATCATTC-CAGCACAAACTGATGCAAGACCACCCTGGGTCAACTGA
1 TGAAGAACGACCACCCTCGATCATTCTGA-CACAAACTGAAGAAAGACCACCCTGGGTCAACTGA
1154 AATAAAT
65 AATAAAT
*
1161 TGAAGAATGACC
1 TGAAGAACGACC
1173 GCCATGGATC
Statistics
Matches: 136, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
70 1 0.01
71 135 0.99
ACGTcount: A:0.39, C:0.28, G:0.16, T:0.17
Consensus pattern (71 bp):
TGAAGAACGACCACCCTCGATCATTCTGACACAAACTGAAGAAAGACCACCCTGGGTCAACTGAA
ATAAAT
Found at i:1045 original size:107 final size:107
Alignment explanation
Indices: 798--1071 Score: 347
Period size: 107 Copynumber: 2.6 Consensus size: 107
788 ACTCTAAAAT
* * * * * *
798 AAAT-AACTGAAGAAAGACCACCCTGGATCATTCCAAACCGAATTGAAGAACGACCACCCTCGAT
1 AAATAAACTGAAGAACGACCACCCTCGATCATTCTAGACCGAACTGAAGAACAACCACCCTCGAT
* ** *
862 CATTCCGTCGTAAACTGAAGAAAGACCACCCTGGGTCAGCTG
66 CATTCCGACACAAACTGAAGAAAGACCACCCTGGGTCAACTG
*
904 AAATAAACTGAAGAACGACCACCCTCGATCATTCTAGACTGAACTGAAGAACAACCACCCTCGAT
1 AAATAAACTGAAGAACGACCACCCTCGATCATTCTAGACCGAACTGAAGAACAACCACCCTCGAT
* * *
969 CATTCTGACACAAATTGACGAAAGACCACCCTGGGTCAACTG
66 CATTCCGACACAAACTGAAGAAAGACCACCCTGGGTCAACTG
** * *
1011 AAATAAGTTGAAGAACGACCATCCTCGATCATTCT-GACACAAACTGAAGAA-AGACCACCCT
1 AAATAAACTGAAGAACGACCACCCTCGATCATTCTAGAC-CGAACTGAAGAACA-ACCACCCT
1072 AGGTCAACTG
Statistics
Matches: 146, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
106 8 0.05
107 138 0.95
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.18
Consensus pattern (107 bp):
AAATAAACTGAAGAACGACCACCCTCGATCATTCTAGACCGAACTGAAGAACAACCACCCTCGAT
CATTCCGACACAAACTGAAGAAAGACCACCCTGGGTCAACTG
Found at i:3620 original size:26 final size:27
Alignment explanation
Indices: 3591--3641 Score: 79
Period size: 26 Copynumber: 1.9 Consensus size: 27
3581 AAAAAACTTA
3591 AAAACCTTTT-T-GAAAACTCATTTTGG
1 AAAACCTTTTCTCGAAAAC-CATTTTGG
3617 AAAACCTTTTCTCGAAAACCATTTT
1 AAAACCTTTTCTCGAAAACCATTTT
3642 TTTGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 10 0.43
27 7 0.30
28 6 0.26
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (27 bp):
AAAACCTTTTCTCGAAAACCATTTTGG
Found at i:3633 original size:14 final size:12
Alignment explanation
Indices: 3591--3642 Score: 50
Period size: 14 Copynumber: 3.9 Consensus size: 12
3581 AAAAAACTTA
3591 AAAACCTTTTTG
1 AAAACCTTTTTG
*
3603 AAAACTCATTTTGG
1 AAAAC-C-TTTTTG
3617 AAAACCTTTTCTCG
1 AAAACCTTTT-T-G
3631 AAAACCATTTTT
1 AAAACC-TTTTT
3643 TTGAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
12 9 0.27
13 2 0.06
14 18 0.55
15 4 0.12
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (12 bp):
AAAACCTTTTTG
Found at i:3805 original size:42 final size:42
Alignment explanation
Indices: 3711--3806 Score: 135
Period size: 41 Copynumber: 2.3 Consensus size: 42
3701 TTGCAATTCT
* * *
3711 TTTTATTC-TCTTTTTGCGACCTCTTTCTTTTTTAGGCCCAG
1 TTTTATTCTTCTTTTTGCGACATCTTTCTTTTTTAGACCCAA
3752 TTTTATT-TTCTTTTTGCGACATCTTTCTTTTTTTAGACCCAA
1 TTTTATTCTTCTTTTTGCGACATCTTTC-TTTTTTAGACCCAA
3794 TTTT-TTCTTCTTT
1 TTTTATTCTTCTTT
3807 AATGGGAATT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
41 27 0.55
42 22 0.45
ACGTcount: A:0.11, C:0.21, G:0.08, T:0.59
Consensus pattern (42 bp):
TTTTATTCTTCTTTTTGCGACATCTTTCTTTTTTAGACCCAA
Found at i:6919 original size:35 final size:35
Alignment explanation
Indices: 6823--7305 Score: 754
Period size: 35 Copynumber: 13.9 Consensus size: 35
6813 TTTTTACTAA
* *
6823 ACTTAATTACCCTGAATTAAGTTGCTTA-TTACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* *
6857 ACTTAATTA-TCTGAATTAAGTTGATTACTGAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* * *
6891 ACTTAATTACCCTTAATTAAGTTTATTACTGACTG
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
6926 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
6961 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
*
6996 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* * *
7031 ACTTAATTACCCTGAATTAAGTTTATTACCGACTG
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* * *
7066 ACTTAATTACCCTGAATTAAGTTTATTACCGACTG
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
7101 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* *
7136 ACTTAATTACCCAGAATTAAATTGATTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* * * * *
7171 AGTTACTTACCCTGAATTAAGTTTATTACCGACTG
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
7206 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
*
7241 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
7276 ACTTAATTACCCTGAATTAAGTTGATTACT
1 ACTTAATTACCCTGAATTAAGTTGATTACT
7306 ACTGATTATC
Statistics
Matches: 413, Mismatches: 34, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
33 16 0.04
34 22 0.05
35 375 0.91
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.40
Consensus pattern (35 bp):
ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
Found at i:7071 original size:21 final size:21
Alignment explanation
Indices: 7042--7106 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
7032 CTTAATTACC
7042 CTGAATTAAGTTTATTACCGA
1 CTGAATTAAGTTTATTACCGA
*
7063 CTGACTT-A----ATTACC--
1 CTGAATTAAGTTTATTACCGA
7077 CTGAATTAAGTTTATTACCGA
1 CTGAATTAAGTTTATTACCGA
*
7098 CTGACTTAA
1 CTGAATTAA
7107 TTACCCTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 14
0.67 0.06 0.27
Matches are distributed among these distances:
14 6 0.18
15 1 0.03
16 6 0.18
19 6 0.18
20 1 0.03
21 14 0.41
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.37
Consensus pattern (21 bp):
CTGAATTAAGTTTATTACCGA
Found at i:7076 original size:16 final size:16
Alignment explanation
Indices: 7055--7111 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
7045 AATTAAGTTT
7055 ATTACCGACTGACTTA
1 ATTACCGACTGACTTA
* * * *
7071 ATTACCCTGAATTAAGTTT
1 ATTA-CC-G-ACTGACTTA
7090 ATTACCGACTGACTTA
1 ATTACCGACTGACTTA
7106 ATTACC
1 ATTACC
7112 CTGAATTAAG
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
16 15 0.50
17 3 0.10
18 3 0.10
19 9 0.30
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.35
Consensus pattern (16 bp):
ATTACCGACTGACTTA
Done.