Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010007.1 Corchorus capsularis cultivar CVL-1 contig10028, 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: 46221
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:162 original size:19 final size:18
Alignment explanation
Indices: 134--177 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
124 TAGGGTAGTT
134 AAGA-AATGAGAAGGAGA
1 AAGAGAATGAGAAGGAGA
**
151 AGAGAGAATGAGTGGGAGA
1 A-AGAGAATGAGAAGGAGA
170 AAGAGAAT
1 AAGAGAAT
178 AAGGGTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 10 0.43
19 12 0.52
ACGTcount: A:0.52, C:0.00, G:0.39, T:0.09
Consensus pattern (18 bp):
AAGAGAATGAGAAGGAGA
Found at i:1123 original size:2 final size:2
Alignment explanation
Indices: 1116--1150 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1106 TTAATCAATA
*
1116 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1151 CTTCCTGCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:6787 original size:4 final size:4
Alignment explanation
Indices: 6780--6844 Score: 53
Period size: 4 Copynumber: 16.0 Consensus size: 4
6770 TTAATCAATG
* * * *
6780 ATTA ATTA ATTTA ATT- ACTA ATTA A-TA ATTA ATTAA GATTG ATTG ATTG
1 ATTA ATTA A-TTA ATTA ATTA ATTA ATTA ATTA ATT-A -ATTA ATTA ATTA
6829 ATTA ATTA ATTA ATTA
1 ATTA ATTA ATTA ATTA
6845 TTACTATTCA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
3 5 0.10
4 39 0.75
5 5 0.10
6 3 0.06
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.48
Consensus pattern (4 bp):
ATTA
Found at i:19760 original size:45 final size:46
Alignment explanation
Indices: 19709--19803 Score: 147
Period size: 45 Copynumber: 2.1 Consensus size: 46
19699 GTAACTTTTA
19709 TTTTATTTCCCATTATCGATAATCCCAATTAGTAACGCTAACC-AC
1 TTTTATTTCCCATTATCGATAATCCCAATTAGTAACGCTAACCAAC
*** *
19754 TTTTATTTCCCATTATCGATAATCGTGATTATTAACGCTAACCAAC
1 TTTTATTTCCCATTATCGATAATCCCAATTAGTAACGCTAACCAAC
19800 TTTT
1 TTTT
19804 TCAATCACGT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 39 0.87
46 6 0.13
ACGTcount: A:0.29, C:0.23, G:0.07, T:0.40
Consensus pattern (46 bp):
TTTTATTTCCCATTATCGATAATCCCAATTAGTAACGCTAACCAAC
Found at i:23576 original size:33 final size:33
Alignment explanation
Indices: 23531--23604 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 33
23521 AGGCGCGGTG
*
23531 CGGCACCAACCGTGGTGTGTC-GTCCTCCGGGGA
1 CGGCACCAACCGTGGTGTG-CAGTCCTCCGAGGA
23564 CGGCACGC-ACCGTGGTGTGCAGTCCTCCGAGGA
1 CGGCAC-CAACCGTGGTGTGCAGTCCTCCGAGGA
*
23597 CGACACCA
1 CGGCACCA
23605 CGCCTAGATC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
32 2 0.06
33 33 0.92
34 1 0.03
ACGTcount: A:0.16, C:0.35, G:0.34, T:0.15
Consensus pattern (33 bp):
CGGCACCAACCGTGGTGTGCAGTCCTCCGAGGA
Found at i:25175 original size:2 final size:2
Alignment explanation
Indices: 25168--25195 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25158 ACCAAATTAC
25168 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
25196 ATTGCAATTT
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:27239 original size:2 final size:2
Alignment explanation
Indices: 27232--27259 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
27222 ATATTGTAAG
27232 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27260 GTGCGCATAT
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):
AT
Found at i:32114 original size:2 final size:2
Alignment explanation
Indices: 32107--32131 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
32097 TCAATAGTTG
32107 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
32132 AGAAAAATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35346 original size:21 final size:21
Alignment explanation
Indices: 35313--35356 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
35303 TCCGGTTCAA
* *
35313 GTCCTACTGTATGTGGATTTT
1 GTCCCACTGTATGTAGATTTT
*
35334 GTCCCACTTTATGTAGATTTT
1 GTCCCACTGTATGTAGATTTT
35355 GT
1 GT
35357 ACTCTTTGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.16, G:0.20, T:0.48
Consensus pattern (21 bp):
GTCCCACTGTATGTAGATTTT
Found at i:35457 original size:42 final size:43
Alignment explanation
Indices: 35395--35482 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 43
35385 ATCGGATTCT
* * *
35395 ATTTGACAATTGTGAAGAGATAAGTTCGATTCC-TAAAAATAC
1 ATTTGACAATGGTGAAGAGATAAGTTCAATTCCGCAAAAATAC
* *
35437 ATTTGACAATGGTGAGGAGATAAGTTTAATTCCGCAAAAATAC
1 ATTTGACAATGGTGAAGAGATAAGTTCAATTCCGCAAAAATAC
35480 ATT
1 ATT
35483 CATTGCAAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
42 29 0.73
43 11 0.28
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (43 bp):
ATTTGACAATGGTGAAGAGATAAGTTCAATTCCGCAAAAATAC
Found at i:36748 original size:17 final size:17
Alignment explanation
Indices: 36726--36758 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
36716 CTCTCTCACT
*
36726 CTCTCACTCTCAACCCA
1 CTCTCACTCCCAACCCA
36743 CTCTCACTCCCAACCC
1 CTCTCACTCCCAACCC
36759 GAAAGAGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.58, G:0.00, T:0.21
Consensus pattern (17 bp):
CTCTCACTCCCAACCCA
Found at i:43335 original size:1 final size:1
Alignment explanation
Indices: 43287--43316 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
43277 GTCTTTCAGG
43287 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
43317 GCAATTCTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.