Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013258.1 Corchorus olitorius cultivar O-4 contig13291, 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: 14078
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Found at i:659 original size:22 final size:22
Alignment explanation
Indices: 634--697 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
624 TATGTTCAGT
634 ATTTGACTTTTCTCATACTGAC
1 ATTTGACTTTTCTCATACTGAC
*
656 ATTTG-----TCT-ATAGTTGA-
1 ATTTGACTTTTCTCATA-CTGAC
672 -TTTGACTTTTCTCATACTGAC
1 ATTTGACTTTTCTCATACTGAC
693 ATTTG
1 ATTTG
698 TCTATAGTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 18
0.61 0.04 0.35
Matches are distributed among these distances:
15 4 0.13
16 3 0.10
17 6 0.19
20 6 0.19
21 3 0.10
22 9 0.29
ACGTcount: A:0.22, C:0.17, G:0.12, T:0.48
Consensus pattern (22 bp):
ATTTGACTTTTCTCATACTGAC
Found at i:684 original size:37 final size:37
Alignment explanation
Indices: 634--712 Score: 158
Period size: 37 Copynumber: 2.1 Consensus size: 37
624 TATGTTCAGT
634 ATTTGACTTTTCTCATACTGACATTTGTCTATAGTTG
1 ATTTGACTTTTCTCATACTGACATTTGTCTATAGTTG
671 ATTTGACTTTTCTCATACTGACATTTGTCTATAGTTG
1 ATTTGACTTTTCTCATACTGACATTTGTCTATAGTTG
708 ATTTG
1 ATTTG
713 TTGAGAGAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.22, C:0.15, G:0.14, T:0.49
Consensus pattern (37 bp):
ATTTGACTTTTCTCATACTGACATTTGTCTATAGTTG
Found at i:1801 original size:57 final size:57
Alignment explanation
Indices: 1723--1875 Score: 191
Period size: 57 Copynumber: 2.7 Consensus size: 57
1713 GAAGGAGATT
* *
1723 CAAAGTCAGACACTTATGAGGCAAAGCCCGAAGGAGAAGCAAAGCCTAACTATGGTG
1 CAAAGCCAGACACTTACGAGGCAAAGCCCGAAGGAGAAGCAAAGCCTAACTATGGTG
* * * * * *
1780 CAAAGCCGGATACTTACGAGGCAAAGCTCGAAGTAGAAGTAAAGGCTAACTATGGTG
1 CAAAGCCAGACACTTACGAGGCAAAGCCCGAAGGAGAAGCAAAGCCTAACTATGGTG
* * * *
1837 CAAAGCCAGACACTTACAAGTCAAAGTCAGAA-GAGAAGC
1 CAAAGCCAGACACTTACGAGGCAAAGCCCGAAGGAGAAGC
1876 CTACTACCTA
Statistics
Matches: 79, Mismatches: 17, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
56 5 0.06
57 74 0.94
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.14
Consensus pattern (57 bp):
CAAAGCCAGACACTTACGAGGCAAAGCCCGAAGGAGAAGCAAAGCCTAACTATGGTG
Found at i:2098 original size:60 final size:60
Alignment explanation
Indices: 2033--2502 Score: 759
Period size: 60 Copynumber: 8.1 Consensus size: 60
2023 CCTACAAGCC
* *
2033 AAAGCCTGAAGAGAAGCCTACCACTTATGAAACCAAAGATTACAAGCCAAAGACAGAAGA
1 AAAGCCTGAAGAGAAGCCTACCACTTATGAAACCAAAGATTACAAGCCAAAGCCTGAAGA
* *
2093 AAAGCCTGAAGAGAAGCCTACCACTTATGAAACCAAAGATTACAAGTCAAAGCCGGAAGA
1 AAAGCCTGAAGAGAAGCCTACCACTTATGAAACCAAAGATTACAAGCCAAAGCCTGAAGA
* *
2153 AAAGCCTGAAGAGAAGCCTACCACTTATGAAACCAAAGATTACAAGTCAAAACCTGAAGA
1 AAAGCCTGAAGAGAAGCCTACCACTTATGAAACCAAAGATTACAAGCCAAAGCCTGAAGA
*
2213 AAAGCCTGAAGAGAAGCCTACCACTTATGAAACCAAAGACTACAAGCCAAA-CCTGAAGA
1 AAAGCCTGAAGAGAAGCCTACCACTTATGAAACCAAAGATTACAAGCCAAAGCCTGAAGA
*
2272 AAAGCCTGAAGAGAAGCCTACCACTTATGAAACCAAAG---ACTA--C-AAGCC-----A
1 AAAGCCTGAAGAGAAGCCTACCACTTATGAAACCAAAGATTACAAGCCAAAGCCTGAAGA
2321 AAA-CCTGAAGAGAAGCCTACCACTTATGAAACCAAAGATTACAAGCCAAAGCCTGAAGA
1 AAAGCCTGAAGAGAAGCCTACCACTTATGAAACCAAAGATTACAAGCCAAAGCCTGAAGA
2380 AAAGCCTGAAGAGAAGCCTACCACTTATGAAACCAAAGATTACAAGCCAAAGCCTGAAGA
1 AAAGCCTGAAGAGAAGCCTACCACTTATGAAACCAAAGATTACAAGCCAAAGCCTGAAGA
* *
2440 AAAGCCTGAAGAGAAGCCTACCACTTATGAAACCAAAGATTACAAGCCAAAGTCAGAAGA
1 AAAGCCTGAAGAGAAGCCTACCACTTATGAAACCAAAGATTACAAGCCAAAGCCTGAAGA
2500 AAA
1 AAA
2503 CTCTGGTTAT
Statistics
Matches: 386, Mismatches: 11, Indels: 26
0.91 0.03 0.06
Matches are distributed among these distances:
48 34 0.09
49 4 0.01
51 3 0.01
53 3 0.01
54 8 0.02
56 3 0.01
59 50 0.13
60 281 0.73
ACGTcount: A:0.46, C:0.23, G:0.18, T:0.13
Consensus pattern (60 bp):
AAAGCCTGAAGAGAAGCCTACCACTTATGAAACCAAAGATTACAAGCCAAAGCCTGAAGA
Found at i:2260 original size:30 final size:30
Alignment explanation
Indices: 2226--2319 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 30
2216 GCCTGAAGAG
2226 AAGCCTACCACTTATGAAACCAAAGACTAC
1 AAGCCTACCACTTATGAAACCAAAGACTAC
* * * * * *
2256 AAGCCAAAC-CTGAAGAAAAGCCTGAAG---AG
1 AAGCCTACCACTTATG-AAA-CC-AAAGACTAC
2285 AAGCCTACCACTTATGAAACCAAAGACTAC
1 AAGCCTACCACTTATGAAACCAAAGACTAC
2315 AAGCC
1 AAGCC
2320 AAAACCTGAA
Statistics
Matches: 45, Mismatches: 12, Indels: 14
0.63 0.17 0.20
Matches are distributed among these distances:
27 3 0.07
28 2 0.04
29 15 0.33
30 20 0.44
31 2 0.04
32 3 0.07
ACGTcount: A:0.45, C:0.28, G:0.15, T:0.13
Consensus pattern (30 bp):
AAGCCTACCACTTATGAAACCAAAGACTAC
Found at i:2378 original size:167 final size:169
Alignment explanation
Indices: 2152--2490 Score: 628
Period size: 167 Copynumber: 2.0 Consensus size: 169
2142 AAGCCGGAAG
*
2152 AAAAGCCTGAAGAGAAGCCTACCACTTATGAAACCAAAGATTACAAGTCAAAACCTGAAGAAAAG
1 AAAAGCCTGAAGAGAAGCCTACCACTTATGAAACCAAAGATTACAAGCCAAAACCTGAAGAAAAG
2217 CCTGAAGAGAAGCCTACCACTTATGAAACCAAAGACTACAAGCCAAA-CCTGAAGAAAAGCCTGA
66 CCTGAAGAGAAGCCTACCACTTATGAAACCAAAGACTACAAGCCAAAGCCTGAAGAAAAGCCTGA
2281 AGAGAAGCCTACCACTTATGAAACCAAAGACTACAAGCC
131 AGAGAAGCCTACCACTTATGAAACCAAAGACTACAAGCC
*
2320 AAAA-CCTGAAGAGAAGCCTACCACTTATGAAACCAAAGATTACAAGCCAAAGCCTGAAGAAAAG
1 AAAAGCCTGAAGAGAAGCCTACCACTTATGAAACCAAAGATTACAAGCCAAAACCTGAAGAAAAG
*
2384 CCTGAAGAGAAGCCTACCACTTATGAAACCAAAGATTACAAGCCAAAGCCTGAAGAAAAGCCTGA
66 CCTGAAGAGAAGCCTACCACTTATGAAACCAAAGACTACAAGCCAAAGCCTGAAGAAAAGCCTGA
*
2449 AGAGAAGCCTACCACTTATGAAACCAAAGATTACAAGCC
131 AGAGAAGCCTACCACTTATGAAACCAAAGACTACAAGCC
2488 AAA
1 AAA
2491 GTCAGAAGAA
Statistics
Matches: 166, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
167 104 0.63
168 62 0.37
ACGTcount: A:0.46, C:0.24, G:0.17, T:0.13
Consensus pattern (169 bp):
AAAAGCCTGAAGAGAAGCCTACCACTTATGAAACCAAAGATTACAAGCCAAAACCTGAAGAAAAG
CCTGAAGAGAAGCCTACCACTTATGAAACCAAAGACTACAAGCCAAAGCCTGAAGAAAAGCCTGA
AGAGAAGCCTACCACTTATGAAACCAAAGACTACAAGCC
Found at i:2385 original size:12 final size:12
Alignment explanation
Indices: 2368--2398 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2358 ATTACAAGCC
2368 AAAGCCTGAAGA
1 AAAGCCTGAAGA
2380 AAAGCCTGAAGA
1 AAAGCCTGAAGA
*
2392 GAAGCCT
1 AAAGCCT
2399 ACCACTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.19, G:0.26, T:0.10
Consensus pattern (12 bp):
AAAGCCTGAAGA
Found at i:2445 original size:12 final size:12
Alignment explanation
Indices: 2428--2458 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2418 ATTACAAGCC
2428 AAAGCCTGAAGA
1 AAAGCCTGAAGA
2440 AAAGCCTGAAGA
1 AAAGCCTGAAGA
*
2452 GAAGCCT
1 AAAGCCT
2459 ACCACTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.19, G:0.26, T:0.10
Consensus pattern (12 bp):
AAAGCCTGAAGA
Done.