Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013441.1 Corchorus olitorius cultivar O-4 contig13474, 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: 30182
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:6625 original size:62 final size:61
Alignment explanation
Indices: 6553--6674 Score: 147
Period size: 61 Copynumber: 2.0 Consensus size: 61
6543 GTATGCATTC
* *
6553 GAATAAAATATACAGTAA-GTTGGAAATTTTTTATTTTCTTTTATGTGTTGGGTATTGTATTT
1 GAATAAAATATA-AGGAATGTTAGAAA-TTTTTATTTTCTTTTATGTGTTGGGTATTGTATTT
* * * * * *
6615 GAATAGAATATATGGAATGTTAGTAATTTTTGTTTTGTTTTATGTGTTGGGTTTTGTATT
1 GAATAAAATATAAGGAATGTTAGAAATTTTTATTTTCTTTTATGTGTTGGGTATTGTATT
6675 CAAATATAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
61 34 0.67
62 17 0.33
ACGTcount: A:0.26, C:0.02, G:0.20, T:0.52
Consensus pattern (61 bp):
GAATAAAATATAAGGAATGTTAGAAATTTTTATTTTCTTTTATGTGTTGGGTATTGTATTT
Found at i:7334 original size:24 final size:24
Alignment explanation
Indices: 7315--7365 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
7305 GCTGGTGAGC
*
7315 ATGCAGATGGTGAGAATGGTGAAA
1 ATGCAGAAGGTGAGAATGGTGAAA
*
7339 ATGCAGAAGGTGAGAATGTTGAAA
1 ATGCAGAAGGTGAGAATGGTGAAA
7363 ATG
1 ATG
7366 GTGAAAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.35, T:0.22
Consensus pattern (24 bp):
ATGCAGAAGGTGAGAATGGTGAAA
Found at i:10377 original size:18 final size:18
Alignment explanation
Indices: 10354--10388 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
10344 TCTTGTTGTT
*
10354 CTGACATTTTTTGATGTA
1 CTGACATTTTGTGATGTA
10372 CTGACATTTTGTGATGT
1 CTGACATTTTGTGATGT
10389 TCACAGCCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.11, G:0.20, T:0.49
Consensus pattern (18 bp):
CTGACATTTTGTGATGTA
Found at i:14160 original size:8 final size:8
Alignment explanation
Indices: 14147--14172 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
14137 TGGTTGTTGT
14147 TGTGGCAG
1 TGTGGCAG
14155 TGTGGCAG
1 TGTGGCAG
14163 TGTGGCAG
1 TGTGGCAG
14171 TG
1 TG
14173 CGTGTTTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.50, T:0.27
Consensus pattern (8 bp):
TGTGGCAG
Found at i:18518 original size:17 final size:17
Alignment explanation
Indices: 18479--18526 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
18469 GTAATCTTTG
*
18479 ATCACCGGTGATCTCGC
1 ATCACTGGTGATCTCGC
*
18496 ATCACTGGTGATCTTGC
1 ATCACTGGTGATCTCGC
*
18513 ATCACTAGTGATCT
1 ATCACTGGTGATCT
18527 GGGGGTGATC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.31
Consensus pattern (17 bp):
ATCACTGGTGATCTCGC
Found at i:19237 original size:38 final size:38
Alignment explanation
Indices: 19186--19261 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
19176 AAACAGGTTA
19186 AACAGCTGGAATCTTCAATTGGATTATGTGGATTATGT
1 AACAGCTGGAATCTTCAATTGGATTATGTGGATTATGT
19224 AACAGCTGGAATCTTCAATTGGATTATGTGGATTATGT
1 AACAGCTGGAATCTTCAATTGGATTATGTGGATTATGT
19262 GCTTTGTGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.37
Consensus pattern (38 bp):
AACAGCTGGAATCTTCAATTGGATTATGTGGATTATGT
Found at i:21606 original size:22 final size:22
Alignment explanation
Indices: 21578--21621 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
21568 AACGCGCAAC
21578 GGCTTGATGGCCTTGCTAATCA
1 GGCTTGATGGCCTTGCTAATCA
*
21600 GGCTTGATGGCCTTGTTAATCA
1 GGCTTGATGGCCTTGCTAATCA
21622 AATTGTTCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.34
Consensus pattern (22 bp):
GGCTTGATGGCCTTGCTAATCA
Found at i:26442 original size:29 final size:27
Alignment explanation
Indices: 26406--26507 Score: 107
Period size: 28 Copynumber: 3.6 Consensus size: 27
26396 GATCACCTAA
26406 GGGCATTTTGGTCATTTTCAAAAATCCAG
1 GGGCATTTTGGTCATTTTC--AAATCCAG
* *
26435 GGGCATTTTGGTCATTTTTCACATTCAG
1 GGGCATTTTGGTCA-TTTTCAAATCCAG
* *
26463 GGGCATTTTGGTCATTTTTACA-CCTAGG
1 GGGCATTTTGGTCATTTTCAAATCC-A-G
*
26491 GGGCATTTTAGTCATTT
1 GGGCATTTTGGTCATTT
26508 GTGCTTCAGG
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
26 1 0.02
27 8 0.12
28 37 0.57
29 14 0.22
30 5 0.08
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.40
Consensus pattern (27 bp):
GGGCATTTTGGTCATTTTCAAATCCAG
Found at i:26518 original size:27 final size:27
Alignment explanation
Indices: 26434--26539 Score: 115
Period size: 28 Copynumber: 3.9 Consensus size: 27
26424 CAAAAATCCA
26434 GGGGCATTTTGGTCATTTTTCACATTCA-
1 GGGGCATTTTGGTCATTTTT-AC-TTCAG
**
26462 GGGGCATTTTGGTCATTTTTACACCTAG
1 GGGGCATTTTGGTCATTTTTACTTC-AG
* * *
26490 GGGGCATTTTAGTCATTTGTGCTTCAG
1 GGGGCATTTTGGTCATTTTTACTTCAG
* *
26517 GGGGCATTATGGTCATTTCTACT
1 GGGGCATTTTGGTCATTTTTACT
26540 CCATTGCTCA
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
26 1 0.02
27 24 0.37
28 40 0.62
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.41
Consensus pattern (27 bp):
GGGGCATTTTGGTCATTTTTACTTCAG
Found at i:26661 original size:21 final size:20
Alignment explanation
Indices: 26633--26681 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
26623 TGTTGTGTTC
**
26633 TTTTGCATATTTGTATCACA
1 TTTTGCATATTAATATCACA
*
26653 TTTTCGCATATTAATTTCACA
1 TTTT-GCATATTAATATCACA
26674 TTTTGCAT
1 TTTTGCAT
26682 TTACATAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.51
Consensus pattern (20 bp):
TTTTGCATATTAATATCACA
Done.