Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009823.1 Corchorus olitorius cultivar O-4 contig09855, 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: 2714
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.26
Found at i:398 original size:23 final size:24
Alignment explanation
Indices: 368--412 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
358 TTCGTTAAGT
368 AATTCAAATC-AAATTCAAATCGA
1 AATTCAAATCAAAATTCAAATCGA
*
391 AATTCAAATCAAAATTTAAATC
1 AATTCAAATCAAAATTCAAATC
413 AAAAGTGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.53, C:0.16, G:0.02, T:0.29
Consensus pattern (24 bp):
AATTCAAATCAAAATTCAAATCGA
Found at i:416 original size:12 final size:12
Alignment explanation
Indices: 368--416 Score: 73
Period size: 12 Copynumber: 4.2 Consensus size: 12
358 TTCGTTAAGT
368 AATTCAAATC-A
1 AATTCAAATCAA
*
379 AATTCAAATCGA
1 AATTCAAATCAA
391 AATTCAAATCAA
1 AATTCAAATCAA
*
403 AATTTAAATCAA
1 AATTCAAATCAA
415 AA
1 AA
417 GTGAATTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
11 10 0.29
12 25 0.71
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (12 bp):
AATTCAAATCAA
Found at i:427 original size:16 final size:17
Alignment explanation
Indices: 406--438 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
396 AAATCAAAAT
406 TTAAAT-CAAAAGTGAA
1 TTAAATGCAAAAGTGAA
422 TTAAATGCAAAAGTGAA
1 TTAAATGCAAAAGTGAA
439 GAAACTGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.55, C:0.06, G:0.15, T:0.24
Consensus pattern (17 bp):
TTAAATGCAAAAGTGAA
Found at i:2434 original size:54 final size:54
Alignment explanation
Indices: 2352--2455 Score: 190
Period size: 54 Copynumber: 1.9 Consensus size: 54
2342 AGGAGAACAC
*
2352 CGGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAACACAATACAT
1 CGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAACACAATACAT
*
2406 CGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAAT
1 CGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAACACAAT
2456 CTTATTAAGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.29
Consensus pattern (54 bp):
CGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAACACAATACAT
Found at i:2572 original size:55 final size:55
Alignment explanation
Indices: 2473--2579 Score: 144
Period size: 55 Copynumber: 1.9 Consensus size: 55
2463 AGGAGAACCC
* * *
2473 CGGAAGACGGTTTGTTAGAAAGGATTTTCAAATGTCGATTGGAAGACAATCTCAT
1 CGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTCGATCGGAAGACAATCTCAT
* * *
2528 CGGAAGACGGTTTGCTAGAAAGAATTTTCAGGA-GTTGATCGGAAGACGATCT
1 CGGAAGACGGTTTGCTAGAAAGAATTTTCA-AATGTCGATCGGAAGACAATCT
2580 TGTCAAGAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
55 44 0.98
56 1 0.02
ACGTcount: A:0.32, C:0.13, G:0.28, T:0.27
Consensus pattern (55 bp):
CGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTCGATCGGAAGACAATCTCAT
Found at i:2601 original size:122 final size:120
Alignment explanation
Indices: 2279--2607 Score: 469
Period size: 121 Copynumber: 2.7 Consensus size: 120
2269 AGGATTTTAG
* * *
2279 ATACACCGGAAGACGGTTTGCTAAAAAGAATTTTCAAAAATTGATTGGAAGACAATCTTATTAAG
1 ATACATCGGAAGACGGTTTGCTAGAAAGAATTTTC-AAAGTTGATTGGAAGACAATCTTATTAAG
*
2344 GAGAACACCGGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAACACA
65 GAGAACACCGGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTCGATTGGAACACA
2400 ATACATCGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTTATTAAG
1 ATACATCGGAAGACGGTTTGCTAGAAAGAATTTTCAAA-GTTGATTGGAAGACAATCTTATTAAG
* * *
2465 GAGAACCCCGGAAGACGGTTTGTTAGAAAGGATTTTCAAATGTCGATTGGAAGACA
65 GAGAACACCGGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTCGATTGGAACACA
* * * * * *
2521 ATCTCATCGGAAGACGGTTTGCTAGAAAGAATTTTCAGGAGTTGATCGGAAGACGATCTTGTCAA
1 AT-ACATCGGAAGACGGTTTGCTAGAAAGAATTTTCA-AAGTTGATTGGAAGACAATCTTATTAA
* * * *
2586 GAAGTACACCAGAAGATGGTTT
64 GGAGAACACCGGAAGACGGTTT
2608 CTCAAAAATT
Statistics
Matches: 187, Mismatches: 18, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
120 3 0.02
121 112 0.60
122 71 0.38
123 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (120 bp):
ATACATCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAGTTGATTGGAAGACAATCTTATTAAGG
AGAACACCGGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTCGATTGGAACACA
Found at i:2634 original size:64 final size:64
Alignment explanation
Indices: 2550--2714 Score: 249
Period size: 64 Copynumber: 2.6 Consensus size: 64
2540 TGCTAGAAAG
* *
2550 AATTTTCAGGAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
1 AATTTACAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
* ** * *
2614 AATTTTCCTAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGTTTTCTCAAC
1 AATTTACAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
*
2678 AATTTACAGAAGTTGATCGGAAGATGATCTTAGTCAA
1 AATTTACAGAAGTTGATCGGAAGACGATCTT-GTCAA
Statistics
Matches: 91, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
64 86 0.95
65 5 0.05
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (64 bp):
AATTTACAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
Done.