Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010944.1 Corchorus olitorius cultivar O-4 contig10976, 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: 27738
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:6374 original size:27 final size:28
Alignment explanation
Indices: 6335--6408 Score: 69
Period size: 34 Copynumber: 2.5 Consensus size: 28
6325 ATTGTACCTA
* *
6335 AATTTTAGGAGTT-AAGTTGATGTGCAC
1 AATTTAAGTAGTTCAAGTTGATGTGCAC
6362 AATTTAAGTAGTTTGGTCCCAAGTTGATGTGCAC
1 AATTTAAGTAG--T--T--CAAGTTGATGTGCAC
6396 AATTTAAGTAGTT
1 AATTTAAGTAGTT
6409 TGGCCCATGA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
27 9 0.24
29 1 0.03
30 1 0.03
31 1 0.03
32 1 0.03
34 25 0.66
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (28 bp):
AATTTAAGTAGTTCAAGTTGATGTGCAC
Found at i:6391 original size:34 final size:33
Alignment explanation
Indices: 6348--6415 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 33
6338 TTTAGGAGTT
6348 AAGTTGATGTGCACAATTTAAGTAGTTTGGTCCC
1 AAGTTGATGTGCACAATTTAAGTAGTTTGG-CCC
6382 AAGTTGATGTGCACAATTTAAGTAGTTTGGCCC
1 AAGTTGATGTGCACAATTTAAGTAGTTTGGCCC
6415 A
1 A
6416 TGACTGACGT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 4 0.12
34 30 0.88
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.34
Consensus pattern (33 bp):
AAGTTGATGTGCACAATTTAAGTAGTTTGGCCC
Found at i:6480 original size:35 final size:35
Alignment explanation
Indices: 6434--6503 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
6424 GTAGTGGGAT
*
6434 AGTCTCATCTAGTAATTTCTCCACTCCAAGGGCCA
1 AGTCTCATCTAGTAATTTCTACACTCCAAGGGCCA
6469 AGTCTCATCTAGTAATTTCTACACTCCAAGGGCCA
1 AGTCTCATCTAGTAATTTCTACACTCCAAGGGCCA
6504 CTTGAGCTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.29
Consensus pattern (35 bp):
AGTCTCATCTAGTAATTTCTACACTCCAAGGGCCA
Found at i:6606 original size:61 final size:61
Alignment explanation
Indices: 6511--6628 Score: 236
Period size: 61 Copynumber: 1.9 Consensus size: 61
6501 CCACTTGAGC
6511 TTCTATTATGTCCTTTTAGAGTTTCTTATTTCCTTTATAAATATAGTTCTTTTTTTTTTGT
1 TTCTATTATGTCCTTTTAGAGTTTCTTATTTCCTTTATAAATATAGTTCTTTTTTTTTTGT
6572 TTCTATTATGTCCTTTTAGAGTTTCTTATTTCCTTTATAAATATAGTTCTTTTTTTT
1 TTCTATTATGTCCTTTTAGAGTTTCTTATTTCCTTTATAAATATAGTTCTTTTTTTT
6629 GTCATAAAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.19, C:0.12, G:0.08, T:0.62
Consensus pattern (61 bp):
TTCTATTATGTCCTTTTAGAGTTTCTTATTTCCTTTATAAATATAGTTCTTTTTTTTTTGT
Found at i:12490 original size:207 final size:208
Alignment explanation
Indices: 12113--12521 Score: 667
Period size: 207 Copynumber: 2.0 Consensus size: 208
12103 AATTCAAAAA
* ** * *
12113 AAATCTTCTGAAATTTGGTGGTTTTCGATTGCCGGTATATTTAATATCATATAATTTTTGATTCG
1 AAATCTTCTGAAATTTGGTAGTTTTCGATTGCCGGTATATTTAATATCATATAATTTTCAATCCA
*
12178 TATGTCCGATTAAAGTTATTTAAGTGTCGGTTAAAAGGTTATTGCATGATCTACGACTTTCATGA
66 TATGTCCGATTAAACTTATTTAAGTGTCGGTTAAAAGGTTATTGCATGATCTACGACTTTCATGA
* *
12243 ATGACCCAAAAGTTGAATTTGATATACGAGTTTCATGAAGGGCTCAAAAGGGAATTTTTATGTTT
131 AGGACCCAAAAGTTAAATTTGATATACGAGTTTCATGAAGGGCTCAAAAGGGAATTTTTATGTTT
*
12308 CAAGATTAAAGCT
196 AAAGATTAAAGCT
* * *
12321 AAATCTTCTGAAATTTGGTAG-TTTCGATTGTCGGTCTATTTAATATCATTTAATTTTCAATCCA
1 AAATCTTCTGAAATTTGGTAGTTTTCGATTGCCGGTATATTTAATATCATATAATTTTCAATCCA
* *
12385 TATGTCCGATTAAACTTATTTAAGTGTCGGTTAAAATGTTATTGCATGATCTACGATTTTCATGA
66 TATGTCCGATTAAACTTATTTAAGTGTCGGTTAAAAGGTTATTGCATGATCTACGACTTTCATGA
* *
12450 AGGACCCGAAAGTTAAATTTGATATACGAGTTTCATGAAGGGGTCAAAAGGGAATTTTTATGTTT
131 AGGACCCAAAAGTTAAATTTGATATACGAGTTTCATGAAGGGCTCAAAAGGGAATTTTTATGTTT
12515 AAAGATT
196 AAAGATT
12522 TCCAATAACA
Statistics
Matches: 185, Mismatches: 16, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
207 165 0.89
208 20 0.11
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (208 bp):
AAATCTTCTGAAATTTGGTAGTTTTCGATTGCCGGTATATTTAATATCATATAATTTTCAATCCA
TATGTCCGATTAAACTTATTTAAGTGTCGGTTAAAAGGTTATTGCATGATCTACGACTTTCATGA
AGGACCCAAAAGTTAAATTTGATATACGAGTTTCATGAAGGGCTCAAAAGGGAATTTTTATGTTT
AAAGATTAAAGCT
Found at i:13128 original size:23 final size:23
Alignment explanation
Indices: 13102--13156 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
13092 TTGTCTGATT
*
13102 AAGGTAATTCAGGTGTCTATTAA
1 AAGGTAATTCAGGTGTCGATTAA
*
13125 AAGGTAATGCAGGTGTCGATTAA
1 AAGGTAATTCAGGTGTCGATTAA
13148 AAGGTAATT
1 AAGGTAATT
13157 TCATGATCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.31
Consensus pattern (23 bp):
AAGGTAATTCAGGTGTCGATTAA
Found at i:15424 original size:16 final size:17
Alignment explanation
Indices: 15403--15438 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
15393 TCCTTTTCTC
*
15403 TTCCTTCT-TATTTGAT
1 TTCCTTCTCTATTTCAT
15419 TTCCTTCTCTATTTCAT
1 TTCCTTCTCTATTTCAT
15436 TTC
1 TTC
15439 TATACAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.11, C:0.25, G:0.03, T:0.61
Consensus pattern (17 bp):
TTCCTTCTCTATTTCAT
Found at i:16050 original size:17 final size:16
Alignment explanation
Indices: 16010--16060 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
16000 CATGTAATCT
*
16010 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
16026 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
* *
16043 TTAGATCATTAGTGATC
1 TT-GATCACTGGTGATC
16060 T
1 T
16061 GGGGAGTGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.10
17 26 0.87
18 1 0.03
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:16230 original size:2 final size:2
Alignment explanation
Indices: 16225--16307 Score: 72
Period size: 2 Copynumber: 43.0 Consensus size: 2
16215 AATCACTAGC
16225 TA TA TA TA TA TA TA TA T- TA T- TA TA CTA GTA -A TA CTA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA -TA TA TA -TA -TA TA
*
16266 TA TA TA -A TA TA TA T- TA TA -A TA TA TA TA TA TA TA -A TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16304 TA TA
1 TA TA
16308 AATAAGAATA
Statistics
Matches: 69, Mismatches: 3, Indels: 18
0.77 0.03 0.20
Matches are distributed among these distances:
1 7 0.10
2 53 0.77
3 9 0.13
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (2 bp):
TA
Found at i:16269 original size:31 final size:27
Alignment explanation
Indices: 16226--16301 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 27
16216 ATCACTAGCT
*
16226 ATATATATATATATATTATTATACTAGTA
1 ATATATATATATATAATA-TATACTA-TA
*
16255 ATACTACTATATATATAATATATATTATA
1 ATA-TA-TATATATATAATATATACTATA
16284 ATATATATATATATAATA
1 ATATATATATATATAATA
16302 AATATAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 13 0.30
28 2 0.05
29 8 0.19
30 8 0.19
31 12 0.28
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (27 bp):
ATATATATATATATAATATATACTATA
Found at i:16275 original size:9 final size:9
Alignment explanation
Indices: 16263--16308 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
16253 TAATACTACT
16263 ATATATATA
1 ATATATATA
*
16272 ATATATATT
1 ATATATATA
16281 ATA-ATATA
1 ATATATATA
16289 TATATATATA
1 -ATATATATA
*
16299 ATAAATATA
1 ATATATATA
16308 A
1 A
16309 ATAAGAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
8 4 0.12
9 23 0.72
10 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
ATATATATA
Found at i:16306 original size:29 final size:29
Alignment explanation
Indices: 16226--16307 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 29
16216 ATCACTAGCT
* *
16226 ATATATATATATATATTATTATACTAGTA
1 ATATATATATATATAATAATATACTAGTA
*
16255 ATACTACTATATATATAAT-ATATATTA-TA
1 ATA-TA-TATATATATAATAATATACTAGTA
16284 ATATATATATATATAATAAATATA
1 ATATATATATATATAAT-AATATA
16308 AATAAGAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
27 12 0.26
28 2 0.04
29 13 0.28
30 8 0.17
31 11 0.24
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (29 bp):
ATATATATATATATAATAATATACTAGTA
Found at i:20125 original size:168 final size:162
Alignment explanation
Indices: 19875--20192 Score: 420
Period size: 168 Copynumber: 1.9 Consensus size: 162
19865 ACGTTGCTGC
** *
19875 AGCCTGAAATCTCTCTTTCCATTGCCACTTATGCAGTCTCTTATGCAATTGAAAAGTGTCAAAAT
1 AGCCTGAAATCTCTCTTTCCATCACCACTTATGCAGTCTCTTATGCAATTGAAAAGAGTCAAAAT
* * *
19940 AGCTAACTGCAATATGTTGGAACAAATTTTTGAAGAGATGGGAGGTGCTAATAATAAGGTGCTAC
66 AGCTAAATGCAATATGTTGGAACAAATTTTT---GAGATGGAAGGTGCCAATAATAAGGTGCTAC
20005 TACCAAAGTTGGAATCATTGGAGATAAATGATTGTGAT
128 -A--AAAGTTGGAATCATTGGAGATAAATGATTGTGAT
* * ** * *
20043 AGCCTGAAATCTGTCTTTCCATCATCGGTTATGCAGTCTCTTGTGCAATTGAAAAGAGTCAGAAT
1 AGCCTGAAATCTCTCTTTCCATCACCACTTATGCAGTCTCTTATGCAATTGAAAAGAGTCAAAAT
* * * ** *
20108 AGTTAAATGCTATATGTTGGAGCAAATTTTTGAGATGGAAGGTGCCAATTGTGAGGTGCTACAAA
66 AGCTAAATGCAATATGTTGGAACAAATTTTTGAGATGGAAGGTGCCAATAATAAGGTGCTACAAA
20173 AGTTGGAATCATTGGAGATA
131 AGTTGGAATCATTGGAGATA
20193 CTTTCCTGTG
Statistics
Matches: 132, Mismatches: 18, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
162 22 0.17
164 1 0.01
165 26 0.20
168 83 0.63
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (162 bp):
AGCCTGAAATCTCTCTTTCCATCACCACTTATGCAGTCTCTTATGCAATTGAAAAGAGTCAAAAT
AGCTAAATGCAATATGTTGGAACAAATTTTTGAGATGGAAGGTGCCAATAATAAGGTGCTACAAA
AGTTGGAATCATTGGAGATAAATGATTGTGAT
Found at i:24374 original size:2 final size:2
Alignment explanation
Indices: 24367--24401 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
24357 AATTCGAGTG
24367 TA 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 TA T
24402 TTGAAAAGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.