Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015855.1 Corchorus olitorius cultivar O-4 contig15888, 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: 14274
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:1519 original size:7 final size:7
Alignment explanation
Indices: 1490--1530 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
1480 GATCATCTGC
*
1490 TGTCCGC
1 TGTCCGT
1497 TGTCCGT
1 TGTCCGT
1504 TGTCCGT
1 TGTCCGT
*
1511 TGTCTGT
1 TGTCCGT
1518 TGTCCGT
1 TGTCCGT
*
1525 TTTCCG
1 TGTCCG
1531 CTCCGTTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.00, C:0.29, G:0.27, T:0.44
Consensus pattern (7 bp):
TGTCCGT
Found at i:1524 original size:14 final size:14
Alignment explanation
Indices: 1485--1525 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1475 GACGTGATCA
* *
1485 TCTGCTGTCCGCTG
1 TCTGTTGTCCGTTG
*
1499 TCCGTTGTCCGTTG
1 TCTGTTGTCCGTTG
1513 TCTGTTGTCCGTT
1 TCTGTTGTCCGTT
1526 TTCCGCTCCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.00, C:0.29, G:0.27, T:0.44
Consensus pattern (14 bp):
TCTGTTGTCCGTTG
Found at i:4721 original size:81 final size:80
Alignment explanation
Indices: 4603--4923 Score: 387
Period size: 80 Copynumber: 4.0 Consensus size: 80
4593 ATATATTATT
* * *
4603 TTCGTATCTTAACAAAATTACTAAAAGGCCCAATATATTTTTCACAAGAATTGAGATAACTGGTC
1 TTCGTACCTTACCAAAATTACTAAAAGGCCCAATATATTTTTCACAAGAATTGAGATAACTAGTC
4668 TA-TTTTAGTCTTTTC
66 TATTTTTA-TCTTTTC
* * * *
4683 TTCGTACCTTACCAAGATTACTTAAAAGGCCCATTATATATTTCACAAGAATTGAGATAATTAGT
1 TTCGTACCTTACCAAAATTAC-TAAAAGGCCCAATATATTTTTCACAAGAATTGAGATAACTAGT
* *
4748 TTATTTTTGTCTTTTC
65 CTATTTTTATCTTTTC
* ** ** * *
4764 TTCGTAGCTTACCAAAATTACTAAAAGATCCAATATATTTTTCGTAAGAATTGAAAT-ACTAGCC
1 TTCGTACCTTACCAAAATTACTAAAAGGCCCAATATATTTTTCACAAGAATTGAGATAACTAGTC
*
4828 TATTTTTATTTTTTC
66 TATTTTTATCTTTTC
* * * * * *
4843 TTCGTACCTTACCAAAAATACTAAAA-GCTCCAATCTATTTCTCAAAAGAATAGAGATAAATAGT
1 TTCGTACCTTACCAAAATTACTAAAAGGC-CCAATATATTTTTCACAAGAATTGAGATAACTAGT
4907 CTATTTTTATCTTTTC
65 CTATTTTTATCTTTTC
4923 T
1 T
4924 CTTACTCCCT
Statistics
Matches: 201, Mismatches: 36, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
79 63 0.31
80 67 0.33
81 67 0.33
82 4 0.02
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.40
Consensus pattern (80 bp):
TTCGTACCTTACCAAAATTACTAAAAGGCCCAATATATTTTTCACAAGAATTGAGATAACTAGTC
TATTTTTATCTTTTC
Found at i:5219 original size:14 final size:14
Alignment explanation
Indices: 5200--5230 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5190 ATAGGTCTAT
*
5200 TTTTAAAATTTAGA
1 TTTTAAAATTTAAA
5214 TTTTAAAATTTAAA
1 TTTTAAAATTTAAA
5228 TTT
1 TTT
5231 AGCAGGCCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (14 bp):
TTTTAAAATTTAAA
Found at i:12597 original size:23 final size:23
Alignment explanation
Indices: 12535--12606 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
12525 TAGTAATTGA
12535 TTTTTTTTT-ATCATCAAATT-AT
1 TTTTTTTTTGA-CATCAAATTAAT
* *
12557 TGTTTTTGGTTGAAATCAAATTAAT
1 T-TTTTT-TTTGACATCAAATTAAT
* *
12582 TTTTTTTTTGCCATCAAATAAAT
1 TTTTTTTTTGACATCAAATTAAT
12605 TT
1 TT
12607 ATTTATTAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
22 1 0.03
23 20 0.50
24 15 0.38
25 4 0.10
ACGTcount: A:0.29, C:0.08, G:0.07, T:0.56
Consensus pattern (23 bp):
TTTTTTTTTGACATCAAATTAAT
Found at i:12840 original size:109 final size:109
Alignment explanation
Indices: 12715--12929 Score: 349
Period size: 109 Copynumber: 2.0 Consensus size: 109
12705 TCTAAACTTG
12715 AAAAACCTTGACCTGAAATATTTAAAATACCCTTTTTAATTTTAAAATTTTAGTATTCCTTTAAA
1 AAAAACCTTGACCTGAAATATTTAAAATACCCTTTTTAATTTTAAAATTTTAGTATTCCTTTAAA
*
12780 GGATAAACATGTATTTTTATTTCATTTAGATTAATTAATTATTC
66 GGATAAACATGTATTTTTATTTCATTTAGATTAATCAATTATTC
* * * * *
12824 AAAAATCTTGATCTGAAATATTTAAAATATCCTTTTTAATTTTTAAATTTTAGTATTTCTTTAAA
1 AAAAACCTTGACCTGAAATATTTAAAATACCCTTTTTAATTTTAAAATTTTAGTATTCCTTTAAA
* * *
12889 GGGTAAATATGTTTTTTTATTTCATTTAGATTAATCAATTA
66 GGATAAACATGTATTTTTATTTCATTTAGATTAATCAATTA
12930 ATTGTGAAGT
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
109 97 1.00
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (109 bp):
AAAAACCTTGACCTGAAATATTTAAAATACCCTTTTTAATTTTAAAATTTTAGTATTCCTTTAAA
GGATAAACATGTATTTTTATTTCATTTAGATTAATCAATTATTC
Found at i:13619 original size:23 final size:23
Alignment explanation
Indices: 13589--13634 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
13579 TTACACTTTC
13589 GTTTGAAGACCAATAAATCAATA
1 GTTTGAAGACCAATAAATCAATA
*
13612 GTTTGAAGATCAATAAATCAATA
1 GTTTGAAGACCAATAAATCAATA
13635 TATCATTCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.28
Consensus pattern (23 bp):
GTTTGAAGACCAATAAATCAATA
Done.