Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010605.1 Corchorus capsularis cultivar CVL-1 contig10626, 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: 63277
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:317 original size:56 final size:55
Alignment explanation
Indices: 223--333 Score: 181
Period size: 56 Copynumber: 2.0 Consensus size: 55
213 GTCAAATATT
223 TACAAATACAAATGTAACATACATAAATTTATTTCTATGTATTTAA-GTA-CAAA
1 TACAAATACAAATGTAACATACATAAATTTATTTCTATGTATTTAATGTAGCAAA
276 TACAAATACAAATGTAACATTTTACATAAATTTATTTCTATGTATTTAATGTAGCAAA
1 TACAAATACAAATGTAACA---TACATAAATTTATTTCTATGTATTTAATGTAGCAAA
334 AAAAATTCTA
Statistics
Matches: 53, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
53 19 0.36
56 27 0.51
57 3 0.06
58 4 0.08
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.38
Consensus pattern (55 bp):
TACAAATACAAATGTAACATACATAAATTTATTTCTATGTATTTAATGTAGCAAA
Found at i:699 original size:17 final size:18
Alignment explanation
Indices: 677--730 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 18
667 TATACTAACC
677 TTCATTTTTAATT-AATA
1 TTCATTTTTAATTAAATA
* *
694 TTCATTATTATTTAAATA
1 TTCATTTTTAATTAAATA
* *
712 TTTA-TTTTAATTGAATA
1 TTCATTTTTAATTAAATA
729 TT
1 TT
731 TGTGATTTCT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
17 23 0.77
18 7 0.23
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (18 bp):
TTCATTTTTAATTAAATA
Found at i:3297 original size:16 final size:16
Alignment explanation
Indices: 3276--3309 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3266 TCTTTAGGCA
3276 ATTAATTTCTTTCTAG
1 ATTAATTTCTTTCTAG
*
3292 ATTAATTTTTTTCTAG
1 ATTAATTTCTTTCTAG
3308 AT
1 AT
3310 GTACTAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.59
Consensus pattern (16 bp):
ATTAATTTCTTTCTAG
Found at i:4202 original size:29 final size:29
Alignment explanation
Indices: 4165--4224 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
4155 CTTGACCGGA
*
4165 TTTGATAACGTTATATCCTTAATTGGTGTT
1 TTTGATAACGTTATATCCTGAATT-GTGTT
4195 TTTG-TAACGTTATATCCTGAATTGTGTT
1 TTTGATAACGTTATATCCTGAATTGTGTT
4223 TT
1 TT
4225 CAGGCAAACC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 7 0.24
29 18 0.62
30 4 0.14
ACGTcount: A:0.22, C:0.10, G:0.17, T:0.52
Consensus pattern (29 bp):
TTTGATAACGTTATATCCTGAATTGTGTT
Found at i:22799 original size:2 final size:2
Alignment explanation
Indices: 22792--22818 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
22782 AAATTCATTG
22792 TA TA 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 T
22819 GGATGATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24132 original size:29 final size:30
Alignment explanation
Indices: 24069--24148 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 30
24059 TCATCTGACG
* *
24069 TGGCATGCCACGTGTACAAAAAAATACCACG
1 TGGCATGCCACGTGTAC-AAAAAAGACCACA
*
24100 TGGCATGCCACGTGTACAAAAAGGA-CACA
1 TGGCATGCCACGTGTACAAAAAAGACCACA
*
24129 TGGCACGCCACGTGT-CAAAA
1 TGGCATGCCACGTGTACAAAA
24149 GTGACACGTG
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
28 5 0.11
29 17 0.38
30 6 0.13
31 17 0.38
ACGTcount: A:0.36, C:0.26, G:0.23, T:0.15
Consensus pattern (30 bp):
TGGCATGCCACGTGTACAAAAAAGACCACA
Found at i:24163 original size:28 final size:29
Alignment explanation
Indices: 24066--24163 Score: 101
Period size: 31 Copynumber: 3.3 Consensus size: 29
24056 CGGTCATCTG
* **
24066 ACGTGGCATGCCACGTGTACAAAAAAATACC
1 ACGTGGCACGCCACGTGTAC-AAAAAGGA-C
*
24097 ACGTGGCATGCCACGTGTACAAAAAGGAC
1 ACGTGGCACGCCACGTGTACAAAAAGGAC
*
24126 ACATGGCACGCCACGTGT-C-AAAAGTGAC
1 ACGTGGCACGCCACGTGTACAAAAAG-GAC
*
24154 ACGTGCCACG
1 ACGTGGCACG
24164 TGTCATTTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
27 5 0.08
28 12 0.20
29 17 0.28
30 6 0.10
31 20 0.33
ACGTcount: A:0.34, C:0.28, G:0.24, T:0.14
Consensus pattern (29 bp):
ACGTGGCACGCCACGTGTACAAAAAGGAC
Found at i:26367 original size:36 final size:36
Alignment explanation
Indices: 26327--26401 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
26317 GTGTAATATC
* *
26327 TATGTAATCTTGTTATCTTTGACAATGTGGATGCTT
1 TATGTAATATTGTTATATTTGACAATGTGGATGCTT
26363 TATGTAATATTGTTATATTTGACAATGTGGATGCTT
1 TATGTAATATTGTTATATTTGACAATGTGGATGCTT
26399 TAT
1 TAT
26402 ATAAATGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.25, C:0.08, G:0.19, T:0.48
Consensus pattern (36 bp):
TATGTAATATTGTTATATTTGACAATGTGGATGCTT
Found at i:27213 original size:20 final size:20
Alignment explanation
Indices: 27177--27220 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
27167 GTTATAGGTC
** *
27177 ATGGCTTTAGGGTTTAGGAA
1 ATGGCTTTAGGAATTAGAAA
27197 ATGGCTTTAGGAATTAGAAA
1 ATGGCTTTAGGAATTAGAAA
27217 ATGG
1 ATGG
27221 GTATTGTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.05, G:0.32, T:0.32
Consensus pattern (20 bp):
ATGGCTTTAGGAATTAGAAA
Found at i:27903 original size:62 final size:62
Alignment explanation
Indices: 27828--27954 Score: 254
Period size: 62 Copynumber: 2.0 Consensus size: 62
27818 ATACCCATCA
27828 GAAGCCCTTATTTAACTAACACAAACATGAGTATTTAATACATGGGTATCCCTAATTTAAGT
1 GAAGCCCTTATTTAACTAACACAAACATGAGTATTTAATACATGGGTATCCCTAATTTAAGT
27890 GAAGCCCTTATTTAACTAACACAAACATGAGTATTTAATACATGGGTATCCCTAATTTAAGT
1 GAAGCCCTTATTTAACTAACACAAACATGAGTATTTAATACATGGGTATCCCTAATTTAAGT
27952 GAA
1 GAA
27955 ATACCGGGTA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 65 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.31
Consensus pattern (62 bp):
GAAGCCCTTATTTAACTAACACAAACATGAGTATTTAATACATGGGTATCCCTAATTTAAGT
Found at i:32590 original size:22 final size:22
Alignment explanation
Indices: 32560--32602 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
32550 ACATGAAAAA
*
32560 TTTTCAAAGACTTAATTTAATT
1 TTTTAAAAGACTTAATTTAATT
*
32582 TTTTAAAAGATTTAATTTAAT
1 TTTTAAAAGACTTAATTTAAT
32603 GCTTCTTGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (22 bp):
TTTTAAAAGACTTAATTTAATT
Found at i:36450 original size:31 final size:30
Alignment explanation
Indices: 36415--36489 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 30
36405 ATATAGTAGA
*
36415 AATATTAAAAGTTAATTAAGGGTACAATAGG
1 AATATTAAAAGTTAATTAAGAGTACAAT-GG
*
36446 AATATTAAAAATTAATTAAGAGTACAATGG
1 AATATTAAAAGTTAATTAAGAGTACAATGG
36476 ACA-ATTCAAAAGTT
1 A-ATATT-AAAAGTT
36490 TCTCAAAACT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
30 6 0.15
31 33 0.85
ACGTcount: A:0.51, C:0.05, G:0.15, T:0.29
Consensus pattern (30 bp):
AATATTAAAAGTTAATTAAGAGTACAATGG
Found at i:56078 original size:2 final size:2
Alignment explanation
Indices: 56071--56111 Score: 55
Period size: 2 Copynumber: 19.5 Consensus size: 2
56061 AACCCTTAAC
*
56071 AT AT AT AT AT AT AT AT AT AT AT AT GCT ACT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT A-T AT AT AT AT AT A
56112 ATTACGAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 32 0.91
3 3 0.09
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:59367 original size:2 final size:2
Alignment explanation
Indices: 59362--59394 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
59352 TATGTGTGTG
59362 TA TA TA TA TA 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 TA T
59395 CTGTTGAGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.