Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021370.1 Corchorus olitorius cultivar O-4 contig21403, 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: 8249
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Found at i:1412 original size:3 final size:3
Alignment explanation
Indices: 1404--1555 Score: 295
Period size: 3 Copynumber: 50.3 Consensus size: 3
1394 TCTCTTCTAT
1404 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1452 ATA ATA ATA ATA ATA ATA ATA ATA TATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA
1498 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1546 ATA ATA ATA A
1 ATA ATA ATA A
1556 AAGAAAGCTT
Statistics
Matches: 148, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
3 145 0.98
4 3 0.02
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2121 original size:2 final size:2
Alignment explanation
Indices: 2114--2145 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2104 GTACTTGGTG
*
2114 TA TA TA TA TA TA TT TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2146 GGGAGATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2422 original size:14 final size:13
Alignment explanation
Indices: 2405--2455 Score: 75
Period size: 14 Copynumber: 3.7 Consensus size: 13
2395 ATATTTGTCC
2405 ATATATAGTATATT
1 ATATATA-TATATT
2419 ATATATTATATATT
1 ATATA-TATATATT
2433 ATATTATATATATT
1 ATA-TATATATATT
2447 ATATATATA
1 ATATATATA
2456 AAGCCTTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.17
14 25 0.71
15 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (13 bp):
ATATATATATATT
Found at i:2423 original size:7 final size:7
Alignment explanation
Indices: 2413--2452 Score: 64
Period size: 7 Copynumber: 5.7 Consensus size: 7
2403 CCATATATAG
2413 TATATTA
1 TATATTA
2420 TATATTA
1 TATATTA
2427 TATATTA
1 TATATTA
2434 TAT-TATA
1 TATAT-TA
2441 TATATTA
1 TATATTA
2448 TATAT
1 TATAT
2453 ATAAAGCCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 1 0.03
7 29 0.94
8 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TATATTA
Found at i:2428 original size:19 final size:19
Alignment explanation
Indices: 2406--2443 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2396 TATTTGTCCA
2406 TATATAGTATATTATATAT
1 TATATAGTATATTATATAT
*
2425 TATATATTATATTATATAT
1 TATATAGTATATTATATAT
2444 ATTATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
TATATAGTATATTATATAT
Found at i:2471 original size:2 final size:2
Alignment explanation
Indices: 2405--2455 Score: 58
Period size: 2 Copynumber: 27.5 Consensus size: 2
2395 ATATTTGTCC
2405 AT AT AT AGT AT AT -T AT AT AT -T AT AT AT -T AT AT -T AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2444 AT -T AT AT AT AT A
1 AT AT AT AT AT AT A
2456 AAGCCTTAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
1 5 0.12
2 36 0.84
3 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3316 original size:22 final size:24
Alignment explanation
Indices: 3285--3328 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
3275 AAACTCGTAA
*
3285 CCCGAATGACCCGAGAA-ATTAAT
1 CCCGAATGACCCAAGAATATTAAT
3308 CCCG-ATGACCCAAGAATATTA
1 CCCGAATGACCCAAGAATATTA
3329 TAAATTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.39, C:0.27, G:0.16, T:0.18
Consensus pattern (24 bp):
CCCGAATGACCCAAGAATATTAAT
Found at i:4867 original size:372 final size:377
Alignment explanation
Indices: 4122--4871 Score: 1312
Period size: 372 Copynumber: 2.0 Consensus size: 377
4112 ATGTCATTTA
*
4122 AGAAATATATTTTAAAAATTCTAATATATCTAATTTTTTTTAATTAAATTAGTAAAATGATAAAA
1 AGAAATATATTTTAAAAATTCTAATATATCTAATGTTTTTTAATTAAATTAGTAAAATGATAAAA
*
4187 ATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTATTTTTTTTTTTGA
66 ATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTATGTTTTTTTTTGA
* * * *
4252 CCAAAAAAAAATAGATTTTTTAAGTTGAGTAAAACTATAAAAGTATATTTAAAAAATTCTAATAT
131 CC--AAAAAAATAGAGTTCTTAAGGTAAGTAAAACTATAAAAGTATATTTAAAAAATTCTAATAT
*
4317 ATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAGGATATTAGATT
194 ATACAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAGGATATTAGATT
* * *
4382 TAATTAAATAAAACTAGAGTTTTTAGTTGAGTAAAACTATAAAAGTCTAAATAATGGCATTTAAG
259 TAATTAAATAAAAATAGAGTTTTTAGTTGAGCAAAACTATAAAAGTCTAAACAATGGCATTTAAG
* *
4447 AAATATATTCAAAAAATAAGGGTATAATGGGCAATTCGAAATTTTTACAAGAGG
324 AAATATATTCAAAAAATAAGGGTATAATGGGCAATTCAAAAGTTTTACAAGAGG
4501 AGAAATATATTTTAAAAATTCTAATATATCTAA-GTTTTTTAATTAAATTAGTAAAATGATAAAA
1 AGAAATATATTTTAAAAATTCTAATATATCTAATGTTTTTTAATTAAATTAGTAAAATGATAAAA
4565 ATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTA-GTTTTTTTTT-A
66 ATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTATGTTTTTTTTTGA
4628 CC-AAAAAATAGAGTTCTT-AGGTAAGTAAAACTATAAAAGTATATTTAAAAAATTCTAATATAT
131 CCAAAAAAATAGAGTTCTTAAGGTAAGTAAAACTATAAAAGTATATTTAAAAAATTCTAATATAT
4691 ACAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAGGATATTAGATTTA
196 ACAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAGGATATTAGATTTA
4756 ATTAAATAAAAATAGAGTTTTTAGTTGAGCAAAACTATAAAAGTCTAAACAATGGCATTTAAGAA
261 ATTAAATAAAAATAGAGTTTTTAGTTGAGCAAAACTATAAAAGTCTAAACAATGGCATTTAAGAA
* * *
4821 ATATATTCGAAAAATAAGGGTATCATGGGCGATTCAAAAGTTTTACAAGAG
326 ATATATTCAAAAAATAAGGGTATAATGGGCAATTCAAAAGTTTTACAAGAG
4872 ATTGTACTTT
Statistics
Matches: 356, Mismatches: 15, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
372 215 0.60
373 14 0.04
376 3 0.01
377 9 0.03
378 82 0.23
379 33 0.09
ACGTcount: A:0.47, C:0.04, G:0.12, T:0.37
Consensus pattern (377 bp):
AGAAATATATTTTAAAAATTCTAATATATCTAATGTTTTTTAATTAAATTAGTAAAATGATAAAA
ATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTATGTTTTTTTTTGA
CCAAAAAAATAGAGTTCTTAAGGTAAGTAAAACTATAAAAGTATATTTAAAAAATTCTAATATAT
ACAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAGGATATTAGATTTA
ATTAAATAAAAATAGAGTTTTTAGTTGAGCAAAACTATAAAAGTCTAAACAATGGCATTTAAGAA
ATATATTCAAAAAATAAGGGTATAATGGGCAATTCAAAAGTTTTACAAGAGG
Found at i:6971 original size:15 final size:15
Alignment explanation
Indices: 6951--6980 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6941 ACCCCTTTTT
6951 ACATGAACCAAGTAA
1 ACATGAACCAAGTAA
6966 ACATGAACCAAGTAA
1 ACATGAACCAAGTAA
6981 GAATCGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.20, G:0.13, T:0.13
Consensus pattern (15 bp):
ACATGAACCAAGTAA
Done.