Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017081.1 Corchorus olitorius cultivar O-4 contig17114, 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: 35731
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:73 original size:18 final size:18
Alignment explanation
Indices: 27--74 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
17 GTTTAGGTGG
*
27 TGGTGCTGGTGGTGGACT
1 TGGTGCTGGTGGCGGACT
**
45 TGGTGGAGGTGGCGG-CAT
1 TGGTGCTGGTGGCGGAC-T
63 TGGTGCTGGTGG
1 TGGTGCTGGTGG
75 AGGAGGTGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 1 0.04
18 23 0.96
ACGTcount: A:0.06, C:0.10, G:0.54, T:0.29
Consensus pattern (18 bp):
TGGTGCTGGTGGCGGACT
Found at i:137 original size:30 final size:30
Alignment explanation
Indices: 64--137 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 30
54 TGGCGGCATT
* * *
64 GGTGCTGGTGGAGGAGGTGGTCTTGGTGGG
1 GGTGCTGGAGGAGGAGGGGGTCTTGGTGGA
* *
94 GGAGCAGGAGGAGGAGGGGGTCTTGGTGGA
1 GGTGCTGGAGGAGGAGGGGGTCTTGGTGGA
* *
124 GGTGGTGGCGGAGG
1 GGTGCTGGAGGAGG
138 CTTAGGAGGT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.12, C:0.07, G:0.62, T:0.19
Consensus pattern (30 bp):
GGTGCTGGAGGAGGAGGGGGTCTTGGTGGA
Found at i:151 original size:30 final size:29
Alignment explanation
Indices: 117--235 Score: 113
Period size: 30 Copynumber: 4.2 Consensus size: 29
107 GAGGGGGTCT
* *
117 TGGTGGAGGTGGTGGCGGAGGCTTAGGAGG
1 TGGTGCAGGTGGTGG-GGAGGCTTTGGAGG
*
147 TGGTGC---TGGT--GGTGGCTTTGGAGG
1 TGGTGCAGGTGGTGGGGAGGCTTTGGAGG
*
171 TGGTGCAGGTGGTGGTGGAGGCCTTGGAGG
1 TGGTGCAGGTGGTGG-GGAGGCTTTGGAGG
* * *
201 TGGTGCAGGGGGTGGAGGAGGATTTGGTGG
1 TGGTGCAGGTGGTGG-GGAGGCTTTGGAGG
231 TGGTG
1 TGGTG
236 GTGGAGTTGG
Statistics
Matches: 73, Mismatches: 10, Indels: 12
0.77 0.11 0.13
Matches are distributed among these distances:
24 18 0.25
27 8 0.11
30 47 0.64
ACGTcount: A:0.10, C:0.07, G:0.58, T:0.25
Consensus pattern (29 bp):
TGGTGCAGGTGGTGGGGAGGCTTTGGAGG
Found at i:163 original size:24 final size:24
Alignment explanation
Indices: 136--185 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
126 TGGTGGCGGA
*
136 GGCTTAGGAGGTGGTGCTGGTGGT
1 GGCTTAGGAGGTGGTGCAGGTGGT
*
160 GGCTTTGGAGGTGGTGCAGGTGGT
1 GGCTTAGGAGGTGGTGCAGGTGGT
184 GG
1 GG
186 TGGAGGCCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.08, C:0.08, G:0.56, T:0.28
Consensus pattern (24 bp):
GGCTTAGGAGGTGGTGCAGGTGGT
Found at i:205 original size:24 final size:24
Alignment explanation
Indices: 115--205 Score: 58
Period size: 24 Copynumber: 3.5 Consensus size: 24
105 AGGAGGGGGT
* * *
115 CTTGGTGGAGGTGGTGGCGGAGG-
1 CTTGGAGGTGGTGGTGGTGGAGGC
* *
138 CTTAGGAGGTGGTGCTGGTGGTGGC
1 CTT-GGAGGTGGTGGTGGTGGAGGC
*
163 TTTGGAGGTGGTGCAGGTGGTGGTGGAGGC
1 CTTGGA---GGT---GGTGGTGGTGGAGGC
193 CTTGGAGGTGGTG
1 CTTGGAGGTGGTG
206 CAGGGGGTGG
Statistics
Matches: 51, Mismatches: 9, Indels: 15
0.68 0.12 0.20
Matches are distributed among these distances:
23 3 0.06
24 22 0.43
25 2 0.04
27 6 0.12
30 18 0.35
ACGTcount: A:0.09, C:0.09, G:0.56, T:0.26
Consensus pattern (24 bp):
CTTGGAGGTGGTGGTGGTGGAGGC
Found at i:241 original size:42 final size:42
Alignment explanation
Indices: 195--282 Score: 104
Period size: 42 Copynumber: 2.1 Consensus size: 42
185 GTGGAGGCCT
* ** * *
195 TGGAGGTGGTGCAGGGGGTGGAGGAGGATTTGGTGGTGGTGG
1 TGGAGGTGGAGCAGGAAGTGGAGGAGGATTTGGAGCTGGTGG
* * *
237 TGGAGTTGGAGGAGGAAGTGGGGGAGGATTTGGAGCTGGTGG
1 TGGAGGTGGAGCAGGAAGTGGAGGAGGATTTGGAGCTGGTGG
279 TGGA
1 TGGA
283 TTTGGAAAAG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.16, C:0.02, G:0.59, T:0.23
Consensus pattern (42 bp):
TGGAGGTGGAGCAGGAAGTGGAGGAGGATTTGGAGCTGGTGG
Found at i:5941 original size:7 final size:7
Alignment explanation
Indices: 5929--5958 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
5919 TATTACCCAC
5929 AAAGAAG
1 AAAGAAG
5936 AAAGAAG
1 AAAGAAG
5943 AAAGAAG
1 AAAGAAG
5950 AAAGAAG
1 AAAGAAG
5957 AA
1 AA
5959 GAAAAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (7 bp):
AAAGAAG
Found at i:8538 original size:2 final size:2
Alignment explanation
Indices: 8531--8588 Score: 68
Period size: 2 Copynumber: 30.5 Consensus size: 2
8521 TCGATTGAAT
*
8531 TA TA TA TA TA TA TA TA TA TA -A TA TA -A TA TA -A TA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
8570 TA TA TA TA TG TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA T
8589 GTAATTGAGA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
1 3 0.06
2 44 0.94
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (2 bp):
TA
Found at i:17789 original size:12 final size:12
Alignment explanation
Indices: 17771--17834 Score: 58
Period size: 12 Copynumber: 5.1 Consensus size: 12
17761 GATGGATTCC
17771 AGGTTGATTTGG
1 AGGTTGATTTGG
* *
17783 GGGTTGATTAGG
1 AGGTTGATTTGG
*
17795 AGGTTGGTTT-G
1 AGGTTGATTTGG
17806 ATGGTTGATCTGGTGG
1 A-GGTTGAT-T--TGG
17822 AGGTTGATTTGG
1 AGGTTGATTTGG
17834 A
1 A
17835 TTCATCTTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
11 2 0.05
12 27 0.66
13 1 0.02
14 1 0.02
15 8 0.20
16 2 0.05
ACGTcount: A:0.16, C:0.02, G:0.44, T:0.39
Consensus pattern (12 bp):
AGGTTGATTTGG
Found at i:17798 original size:24 final size:26
Alignment explanation
Indices: 17771--17833 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 26
17761 GATGGATTCC
17771 AGGTTGATTTGGGGGTTGAT-T-AGG
1 AGGTTGATTTGGGGGTTGATCTGAGG
* ** *
17795 AGGTTGGTTTGATGGTTGATCTGGTGG
1 AGGTTGATTTGGGGGTTGATCT-GAGG
17822 AGGTTGATTTGG
1 AGGTTGATTTGG
17834 ATTCATCTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
24 17 0.57
25 1 0.03
27 12 0.40
ACGTcount: A:0.14, C:0.02, G:0.44, T:0.40
Consensus pattern (26 bp):
AGGTTGATTTGGGGGTTGATCTGAGG
Found at i:18898 original size:2 final size:2
Alignment explanation
Indices: 18891--18924 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
18881 GATAAGATTT
18891 TA TA TA 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 TA TA TA
18925 CTAGAAATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20727 original size:23 final size:27
Alignment explanation
Indices: 20683--20731 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 27
20673 ATAAATTTTA
20683 ATATGTAGTTATGATTTCTTAAAAATT
1 ATATGTAGTTATGATTTCTTAAAAATT
20710 ATATGTA-TTAT-A-TT-TTAAAAAT
1 ATATGTAGTTATGATTTCTTAAAAAT
20732 AATGTGGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 8 0.36
24 2 0.09
25 1 0.05
26 4 0.18
27 7 0.32
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (27 bp):
ATATGTAGTTATGATTTCTTAAAAATT
Found at i:22098 original size:13 final size:12
Alignment explanation
Indices: 22076--22111 Score: 63
Period size: 13 Copynumber: 2.9 Consensus size: 12
22066 AAGACATTGA
22076 AATAGTATTAAT
1 AATAGTATTAAT
22088 AATAGTAATTAAT
1 AATAGT-ATTAAT
22101 AATAGTATTAA
1 AATAGTATTAA
22112 CATTACAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (12 bp):
AATAGTATTAAT
Found at i:22606 original size:156 final size:155
Alignment explanation
Indices: 22323--22600 Score: 386
Period size: 157 Copynumber: 1.8 Consensus size: 155
22313 TTATTTTATG
*
22323 AATATATTTCTTAAATATCATTGTTTAAATTTTATAGTTTTACTCAACTAAAAACTCTATTTATA
1 AATATATTTCTTAAATATCATTGTTTAAATTTTACAGTTTTACTCAACTAAAAACTCTATTTATA
* * ** * *
22388 TTAAATTGAATCTGATATCTTTATATATCTATTTTATTTTTACCATTTTACTATTTTTAATTAAA
66 TTAAATTAAATCTAATATCTTTATATAAATATTTTATTTTTACCAATTTAC-ATTTTAAATTAAA
22453 AATTTTAGATTTATTAGAATTTTTTA
130 AATTTTAGATTTATTAGAATTTTTTA
* * *
22479 AATATATTTCTTAAATGA-CATTGTTTAAACTTTTACAGTTTTATTCTACTAAAAACTCTATTTT
1 AATATATTTCTTAAAT-ATCATTGTTTAAA-TTTTACAGTTTTACTCAACTAAAAACTCTATTTA
*
22543 TATTTAATTAAAT-TCAATAT-TTT-TATAAATATTTTATTTTTACCAATTTA-ATTTTAAA
64 TATTAAATTAAATCT-AATATCTTTATATAAATATTTTATTTTTACCAATTTACATTTTAAA
22601 AAATTAGAGA
Statistics
Matches: 108, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
153 7 0.06
155 24 0.22
156 31 0.29
157 46 0.43
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.52
Consensus pattern (155 bp):
AATATATTTCTTAAATATCATTGTTTAAATTTTACAGTTTTACTCAACTAAAAACTCTATTTATA
TTAAATTAAATCTAATATCTTTATATAAATATTTTATTTTTACCAATTTACATTTTAAATTAAAA
ATTTTAGATTTATTAGAATTTTTTA
Found at i:25707 original size:6 final size:6
Alignment explanation
Indices: 25691--25720 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
25681 ACCCGGGAAC
*
25691 CGGAGG AGGAGG CGGAGG CGGAGG CGGAGG
1 CGGAGG CGGAGG CGGAGG CGGAGG CGGAGG
25721 TGGAAGCACC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.20, C:0.13, G:0.67, T:0.00
Consensus pattern (6 bp):
CGGAGG
Found at i:27407 original size:2 final size:2
Alignment explanation
Indices: 27400--27430 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
27390 AGAAAAATAC
27400 AT AT AT 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 AT AT AT A
27431 GTTATAGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35380 original size:25 final size:25
Alignment explanation
Indices: 35314--35380 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
35304 TGTGTCACTA
*
35314 TAAAAAAAGTAGGCTATGCAAGACC
1 TAAAAAAAATAGGCTATGCAAGACC
* *
35339 TAGAATAAGA-AGGCTATGCAAGACC
1 TA-AAAAAAATAGGCTATGCAAGACC
*
35364 TAAAAAAAATAGACTAT
1 TAAAAAAAATAGGCTAT
35381 AAGAATCTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
24 5 0.15
25 25 0.74
26 4 0.12
ACGTcount: A:0.51, C:0.13, G:0.18, T:0.18
Consensus pattern (25 bp):
TAAAAAAAATAGGCTATGCAAGACC
Done.