Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014950.1 Corchorus capsularis cultivar CVL-1 contig14971, 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: 10964
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Found at i:160 original size:26 final size:27
Alignment explanation
Indices: 109--161 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
99 CAAAACCTGA
* * *
109 CCCGAACCCGATTAGCCGCCTAACTCG
1 CCCGAACCCGATAACCCGCCCAACTCG
136 CCCGAACCCG-TAACCCGCCCAACTCG
1 CCCGAACCCGATAACCCGCCCAACTCG
162 ATTTGACTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.23, C:0.49, G:0.17, T:0.11
Consensus pattern (27 bp):
CCCGAACCCGATAACCCGCCCAACTCG
Found at i:218 original size:16 final size:16
Alignment explanation
Indices: 199--302 Score: 86
Period size: 16 Copynumber: 6.5 Consensus size: 16
189 AACCTGCCCG
*
199 ACCCGAAACCCGACTA
1 ACCCGAAACCCGAATA
** * *
215 ACCCGTGACCCGATTG
1 ACCCGAAACCCGAATA
* *
231 ACCCGTAACCCAAATA
1 ACCCGAAACCCGAATA
*
247 ACCC-AAGACCCGTATA
1 ACCCGAA-ACCCGAATA
*
263 ACCCGAAACCCGTGA-A
1 ACCCGAAACCCG-AATA
*
279 ACCCGAAACCCGAATG
1 ACCCGAAACCCGAATA
295 ACCCGAAA
1 ACCCGAAA
303 AGTTGACCCG
Statistics
Matches: 70, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
15 2 0.03
16 65 0.93
17 3 0.04
ACGTcount: A:0.37, C:0.38, G:0.15, T:0.10
Consensus pattern (16 bp):
ACCCGAAACCCGAATA
Found at i:234 original size:32 final size:32
Alignment explanation
Indices: 198--302 Score: 97
Period size: 32 Copynumber: 3.3 Consensus size: 32
188 TAACCTGCCC
* *
198 GACCCGAAACCCGACTAACCCGTGACCCGATT
1 GACCCGAAACCCGAATAACCCGAGACCCGATT
* * *
230 GACCCGTAACCCAAATAACCCAAGACCCG-TAT
1 GACCCGAAACCCGAATAACCCGAGACCCGAT-T
* * * *
262 AACCCGAAACCCGTGA-AACCCGAAACCCGAAT
1 GACCCGAAACCCG-AATAACCCGAGACCCGATT
294 GACCCGAAA
1 GACCCGAAA
303 AGTTGACCCG
Statistics
Matches: 57, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
31 1 0.02
32 55 0.96
33 1 0.02
ACGTcount: A:0.36, C:0.38, G:0.16, T:0.10
Consensus pattern (32 bp):
GACCCGAAACCCGAATAACCCGAGACCCGATT
Found at i:463 original size:13 final size:14
Alignment explanation
Indices: 445--481 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
435 AATTTAAATT
445 ATAGAATAAAG-AA
1 ATAGAATAAAGAAA
*
458 ATAGAATATAGAAA
1 ATAGAATAAAGAAA
472 ATAGAATAAA
1 ATAGAATAAA
482 CTTGTTTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.19
Consensus pattern (14 bp):
ATAGAATAAAGAAA
Found at i:852 original size:16 final size:16
Alignment explanation
Indices: 833--1027 Score: 166
Period size: 16 Copynumber: 12.5 Consensus size: 16
823 ATGACCCATT
833 TGACCCGAGACCCGAA
1 TGACCCGAGACCCGAA
** *
849 TGACCCGA-AGTCTAA
1 TGACCCGAGACCCGAA
864 --ACCCGA-ACCCGAA
1 TGACCCGAGACCCGAA
* *
877 TAACCCGAGACCCGAT
1 TGACCCGAGACCCGAA
* **
893 TAACCCGAGAATCGAA
1 TGACCCGAGACCCGAA
* * *
909 TGACCCGAAATCCGAT
1 TGACCCGAGACCCGAA
*
925 TAACCCGAGACCCGAA
1 TGACCCGAGACCCGAA
* *
941 TAACCCGAGACCCGAT
1 TGACCCGAGACCCGAA
* *
957 TGACCCGAAACCCGAT
1 TGACCCGAGACCCGAA
* *
973 TGACCCGAAACCCGAT
1 TGACCCGAGACCCGAA
* *
989 TAACCCGA-ACCCAAA
1 TGACCCGAGACCCGAA
*
1004 TGACCCGAAACCCGAA
1 TGACCCGAGACCCGAA
1020 TGACCCGA
1 TGACCCGA
1028 AAAAACTAAC
Statistics
Matches: 148, Mismatches: 27, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.07
15 22 0.15
16 116 0.78
ACGTcount: A:0.35, C:0.36, G:0.18, T:0.11
Consensus pattern (16 bp):
TGACCCGAGACCCGAA
Found at i:935 original size:48 final size:47
Alignment explanation
Indices: 835--1027 Score: 203
Period size: 48 Copynumber: 4.1 Consensus size: 47
825 GACCCATTTG
* ** *
835 ACCCGAGACCCGAATGACCCGAAGTCTAA--ACCCG-AACCCGAATA
1 ACCCGAGACCCGAATAACCCGAACCCGAATGACCCGAAACCCGAATA
* ** * *
879 ACCCGAGACCCGATTAACCCGAGAATCGAATGACCCGAAATCCGATTA
1 ACCCGAGACCCGAATAACCCGA-ACCCGAATGACCCGAAACCCGAATA
* * *
927 ACCCGAGACCCGAATAACCCGAGACCCGATTGACCCGAAACCCGATTG
1 ACCCGAGACCCGAATAACCCGA-ACCCGAATGACCCGAAACCCGAATA
* * * *
975 ACCCGAAACCCGATTAACCCGAACCCAAATGACCCGAAACCCGAATG
1 ACCCGAGACCCGAATAACCCGAACCCGAATGACCCGAAACCCGAATA
1022 ACCCGA
1 ACCCGA
1028 AAAAACTAAC
Statistics
Matches: 128, Mismatches: 17, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
44 20 0.16
45 5 0.04
47 33 0.26
48 70 0.55
ACGTcount: A:0.35, C:0.36, G:0.18, T:0.10
Consensus pattern (47 bp):
ACCCGAGACCCGAATAACCCGAACCCGAATGACCCGAAACCCGAATA
Found at i:4801 original size:27 final size:26
Alignment explanation
Indices: 4765--4842 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 26
4755 AAGTAGACTT
*
4765 AAAACGACCAAAATGCCCCTGAATGTG-C
1 AAAATGACCAAAATGCCCCTG---GTGCC
*
4793 -AAATGACCAGAATGCCCCTGGTGCC
1 AAAATGACCAAAATGCCCCTGGTGCC
*
4818 AAAATGACCAAAATTCCCCTAGGTG
1 AAAATGACCAAAATGCCCCT-GGTG
4843 ACCTTAATAC
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
24 3 0.07
25 1 0.02
26 17 0.40
27 22 0.51
ACGTcount: A:0.36, C:0.28, G:0.19, T:0.17
Consensus pattern (26 bp):
AAAATGACCAAAATGCCCCTGGTGCC
Found at i:5004 original size:21 final size:22
Alignment explanation
Indices: 4969--5013 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
4959 CAAAAGTGTA
*
4969 AAAAGGGGGGACGGTATTTAGC
1 AAAAGGGGAGACGGTATTTAGC
*
4991 AAAAGGGGAG-CGGTGTTTAGC
1 AAAAGGGGAGACGGTATTTAGC
5012 AA
1 AA
5014 TCCAGTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.33, C:0.09, G:0.40, T:0.18
Consensus pattern (22 bp):
AAAAGGGGAGACGGTATTTAGC
Found at i:5237 original size:32 final size:32
Alignment explanation
Indices: 5196--5274 Score: 149
Period size: 32 Copynumber: 2.5 Consensus size: 32
5186 AGCCACGCGG
*
5196 AGCCTCCCCACTAGGACGGCTCTGCCACGGCT
1 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
5228 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
1 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
5260 AGCCGCCCCACTAGG
1 AGCCGCCCCACTAGG
5275 GTGGCAAGGC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.16, C:0.44, G:0.27, T:0.13
Consensus pattern (32 bp):
AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
Found at i:5955 original size:3 final size:3
Alignment explanation
Indices: 5947--5996 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
5937 GAAACAACCT
* *
5947 ATA ATA ATA TATA ATA ATA ATA A-A ATA ATA ATA ATA AGA GTA ATA
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5992 ATA AT
1 ATA AT
5997 GAACTAAGCA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:7221 original size:22 final size:23
Alignment explanation
Indices: 7179--7226 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
7169 TTTGATATTT
*
7179 TATAATTGTATTTTTATTAGTAG
1 TATAATTGTATTTTTAGTAGTAG
*
7202 TATATATT-TATTTTT-GTAGTCG
1 TATA-ATTGTATTTTTAGTAGTAG
7224 TAT
1 TAT
7227 TACTTAATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 8 0.36
23 11 0.50
24 3 0.14
ACGTcount: A:0.27, C:0.02, G:0.12, T:0.58
Consensus pattern (23 bp):
TATAATTGTATTTTTAGTAGTAG
Done.