Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010052.1 Corchorus olitorius cultivar O-4 contig10084, 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: 2840
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Found at i:781 original size:30 final size:30
Alignment explanation
Indices: 747--809 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
737 TCTCATAGAA
747 TGTGAG-TTTCTCTTGTAATTTATTTGTTTG
1 TGTGAGTTTTCT-TTGTAATTTATTTGTTTG
777 TGTGAGTTTTCTTTGTAATTTATTTGTTTG
1 TGTGAGTTTTCTTTGTAATTTATTTGTTTG
807 TGT
1 TGT
810 AATTTGTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 27 0.84
31 5 0.16
ACGTcount: A:0.13, C:0.05, G:0.21, T:0.62
Consensus pattern (30 bp):
TGTGAGTTTTCTTTGTAATTTATTTGTTTG
Found at i:1231 original size:78 final size:78
Alignment explanation
Indices: 1063--1224 Score: 288
Period size: 78 Copynumber: 2.1 Consensus size: 78
1053 TTTTTTTAAT
* *
1063 TAAAATAGTAAAATGGTAAACTAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGA
1128 GTTTTCAGTTGAG
66 GTTTTCAGTTGAG
*
1141 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAATATAGA
1 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGA
*
1206 GTTTTTAGTTGAG
66 GTTTTCAGTTGAG
1219 TAAAAT
1 TAAAAT
1225 TATAAAAGTT
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.50, C:0.01, G:0.14, T:0.35
Consensus pattern (78 bp):
TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGA
GTTTTCAGTTGAG
Found at i:1415 original size:10 final size:10
Alignment explanation
Indices: 1400--1463 Score: 92
Period size: 10 Copynumber: 6.4 Consensus size: 10
1390 AATACTCCCA
* *
1400 ATATACATAC
1 ATATATATAT
* *
1410 ATATACATAC
1 ATATATATAT
1420 ATATATATAT
1 ATATATATAT
1430 ATATATATAT
1 ATATATATAT
1440 ATATATATAT
1 ATATATATAT
1450 ATATATATAT
1 ATATATATAT
1460 ATAT
1 ATAT
1464 TAGTTTTAAC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 52 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (10 bp):
ATATATATAT
Found at i:1417 original size:6 final size:6
Alignment explanation
Indices: 1400--1463 Score: 92
Period size: 6 Copynumber: 10.7 Consensus size: 6
1390 AATACTCCCA
* * * *
1400 ATATAC ATACAT ATACAT ACATAT ATATAT ATATAT ATATAT ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
1448 ATATAT ATATAT ATAT
1 ATATAT ATATAT ATAT
1464 TAGTTTTAAC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (6 bp):
ATATAT
Found at i:1427 original size:4 final size:4
Alignment explanation
Indices: 1400--1463 Score: 92
Period size: 4 Copynumber: 16.0 Consensus size: 4
1390 AATACTCCCA
* * * *
1400 ATAT ACAT ACAT ATAC ATAC ATAT ATAT ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
1448 ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT
1464 TAGTTTTAAC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 56 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (4 bp):
ATAT
Found at i:1550 original size:22 final size:22
Alignment explanation
Indices: 1521--1580 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
1511 TGAATATTTT
*
1521 TATGAAATTTTGATAACTACCC
1 TATGAAATTTTGATAACCACCC
* * *
1543 TATTAAATTTTGACAACCACGC
1 TATGAAATTTTGATAACCACCC
1565 TATGAAATTTTGATAA
1 TATGAAATTTTGATAA
1581 TTACATATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACCC
Found at i:1648 original size:23 final size:21
Alignment explanation
Indices: 1591--1667 Score: 64
Period size: 23 Copynumber: 3.5 Consensus size: 21
1581 TTACATATTT
* *
1591 CTTCCATATGAAACTTTGATAGC
1 CTTCC-TATGAAA-TTTAATAAC
**
1614 CTAACTATGAAATTTCAATAAAC
1 CTTCCTATGAAATTT-AAT-AAC
**
1637 CTTCCTATGAAATTTTGTAAC
1 CTTCCTATGAAATTTAATAAC
1658 CTTCCTATGA
1 CTTCCTATGA
1668 TTTTTGATAA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
21 16 0.36
22 10 0.23
23 18 0.41
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (21 bp):
CTTCCTATGAAATTTAATAAC
Found at i:1660 original size:21 final size:22
Alignment explanation
Indices: 1591--1708 Score: 87
Period size: 22 Copynumber: 5.4 Consensus size: 22
1581 TTACATATTT
* *
1591 CTTCCATATGAAACTTTGATAGC
1 CTTCC-TATGAAATTTTGATAAC
** **
1614 CTAACTATGAAATTTCAATAAAC
1 CTTCCTATGAAATTTTGAT-AAC
1637 CTTCCTATGAAATTTTG-TAAC
1 CTTCCTATGAAATTTTGATAAC
* *
1658 CTTCCTATG-ATTTTTGATAAA
1 CTTCCTATGAAATTTTGATAAC
* * * * *
1679 CTCCCTGTGAGATTTTGTTAAT
1 CTTCCTATGAAATTTTGATAAC
1701 CTTCCTAT
1 CTTCCTAT
1709 AATTTTTTCA
Statistics
Matches: 72, Mismatches: 20, Indels: 7
0.73 0.20 0.07
Matches are distributed among these distances:
20 6 0.08
21 22 0.31
22 26 0.36
23 18 0.25
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (22 bp):
CTTCCTATGAAATTTTGATAAC
Done.