Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012060.1 Corchorus olitorius cultivar O-4 contig12093, 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: 14952
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Found at i:1194 original size:88 final size:83
Alignment explanation
Indices: 1091--1266 Score: 262
Period size: 88 Copynumber: 2.1 Consensus size: 83
1081 CCAACTATGG
*
1091 CAATTTGGAAACCGAAAGTGGACTTTATGCTTAGCAATTGATTATTTACCAATTAATTTAAATAA
1 CAATTTGGAAACCGAAAGTGGACTTTAGGCTTAGCAATTGATTATTTACCAATTAA-TT---TAA
* *
1156 ATTGCCTTTTGTTTTTTGGAAA
62 ATTGCCTTTTGGTTTTTAGAAA
* *
1178 CAATTTGGGAATCCGAAAGTTGACTTTAGGCTTAGCAATTGATTATTTACCAATTAATTTAAATT
1 CAATTT-GGAAACCGAAAGTGGACTTTAGGCTTAGCAATTGATTATTTACCAATTAATTTAAATT
1243 GCCTTTTGGTTTTTAGAAA
65 GCCTTTTGGTTTTTAGAAA
1262 CAATT
1 CAATT
1267 AAGGAATTGA
Statistics
Matches: 83, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
84 28 0.34
87 8 0.10
88 47 0.57
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.40
Consensus pattern (83 bp):
CAATTTGGAAACCGAAAGTGGACTTTAGGCTTAGCAATTGATTATTTACCAATTAATTTAAATTG
CCTTTTGGTTTTTAGAAA
Found at i:1429 original size:2 final size:2
Alignment explanation
Indices: 1422--1452 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1412 GGGTTAGTTT
1422 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1453 TTCACATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2355 original size:35 final size:36
Alignment explanation
Indices: 2316--2608 Score: 270
Period size: 35 Copynumber: 8.2 Consensus size: 36
2306 TCAAAAAGAA
*
2316 TCCCA-CCAGTTTTTAAGTTTTCAAATTGGGAAAGT
1 TCCCATCCAGTTTTAAAGTTTTCAAATTGGGAAAGT
* * * * *
2351 TCCCATTCAATTTTCAAAGTTTTTACATAGGGAAAGT
1 TCCCATCCAGTTTT-AAAGTTTTCAAATTGGGAAAGT
2388 TCCCA-CCAGTTTTTAAA-TTTTCAAATTGGGAAAGT
1 TCCCATCCAG-TTTTAAAGTTTTCAAATTGGGAAAGT
* * * *
2423 TCTCATTCAGTGTTCAAAGTTTTTAAATTGGGAAAGT
1 TCCCATCCAGT-TTTAAAGTTTTCAAATTGGGAAAGT
*
2460 TCCCA-CCAGTTTTTAAGTTTTCAAATT-GGAAAGT
1 TCCCATCCAGTTTTAAAGTTTTCAAATTGGGAAAGT
2494 TCCCATCCAGTTTTCAAAGTTTTCAAATT-GGAAAGT
1 TCCCATCCAGTTTT-AAAGTTTTCAAATTGGGAAAGT
* *
2530 T-CCAT-CAGGTTT--AG-TTTCAATTTAGGGAAAGTT
1 TCCCATCCAGTTTTAAAGTTTTCAAATT-GGGAAAG-T
*
2563 TCCGTCATTTTCAGTTTT--AGTTTTCAAAGTTGGGAAAGT
1 TCC--CA--TCCAGTTTTAAAGTTTTCAAA-TTGGGAAAGT
2602 TCCCATC
1 TCCCATC
2609 AAAAGCATTT
Statistics
Matches: 213, Mismatches: 26, Indels: 38
0.77 0.09 0.14
Matches are distributed among these distances:
30 8 0.04
31 2 0.01
32 6 0.03
33 2 0.01
34 19 0.09
35 52 0.24
36 46 0.22
37 50 0.23
38 1 0.00
39 12 0.06
40 13 0.06
41 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (36 bp):
TCCCATCCAGTTTTAAAGTTTTCAAATTGGGAAAGT
Found at i:2409 original size:72 final size:72
Alignment explanation
Indices: 2316--2532 Score: 339
Period size: 72 Copynumber: 3.0 Consensus size: 72
2306 TCAAAAAGAA
* *
2316 TCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCCATTCAATTTTCAAAGTTTTTACATAG
1 TCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCCATTCAGTTTTCAAAGTTTTTAAATAG
2381 GGAAAGT
66 GGAAAGT
* * * *
2388 TCCCACCAGTTTTTAAATTTTCAAATTGGGAAAGTTCTCATTCAGTGTTCAAAGTTTTTAAATTG
1 TCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCCATTCAGTTTTCAAAGTTTTTAAATAG
2453 GGAAAGT
66 GGAAAGT
* * *
2460 TCCCACCAGTTTTTAAGTTTTCAAATT-GGAAAGTTCCCATCCAGTTTTCAAAGTTTTCAAAT-T
1 TCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCCATTCAGTTTTCAAAGTTTTTAAATAG
2523 GGAAAGT
66 GGAAAGT
2530 TCC
1 TCC
2533 ATCAGGTTTA
Statistics
Matches: 133, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
70 10 0.08
71 31 0.23
72 92 0.69
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (72 bp):
TCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCCATTCAGTTTTCAAAGTTTTTAAATAG
GGAAAGT
Found at i:2521 original size:36 final size:36
Alignment explanation
Indices: 2316--2532 Score: 264
Period size: 36 Copynumber: 6.1 Consensus size: 36
2306 TCAAAAAGAA
*
2316 TCCCACCAGTTTT-TAAGTTTTCAAATTGGGAAAGT
1 TCCCACCAGTTTTCAAAGTTTTCAAATTGGGAAAGT
* * * * *
2351 TCCCATTCAATTTTCAAAGTTTTTACATAGGGAAAGT
1 TCCCA-CCAGTTTTCAAAGTTTTCAAATTGGGAAAGT
*
2388 TCCCACCAGTTTTTAAA-TTTTCAAATTGGGAAAGT
1 TCCCACCAGTTTTCAAAGTTTTCAAATTGGGAAAGT
* * * *
2423 TCTCATTCAGTGTTCAAAGTTTTTAAATTGGGAAAGT
1 TCCCA-CCAGTTTTCAAAGTTTTCAAATTGGGAAAGT
*
2460 TCCCACCAGTTTT-TAAGTTTTCAAATT-GGAAAGT
1 TCCCACCAGTTTTCAAAGTTTTCAAATTGGGAAAGT
2494 TCCCATCCAGTTTTCAAAGTTTTCAAATT-GGAAAGT
1 TCCCA-CCAGTTTTCAAAGTTTTCAAATTGGGAAAGT
2530 TCC
1 TCC
2533 ATCAGGTTTA
Statistics
Matches: 153, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
34 12 0.08
35 44 0.29
36 53 0.35
37 44 0.29
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (36 bp):
TCCCACCAGTTTTCAAAGTTTTCAAATTGGGAAAGT
Found at i:8921 original size:194 final size:194
Alignment explanation
Indices: 8633--9205 Score: 898
Period size: 194 Copynumber: 2.9 Consensus size: 194
8623 ACGCGCATAT
* * * * * *
8633 GTTTGGTCACAAAATGTACCATTCCCACTATATGCACGTTGGCGCCAAAATGGCTAACGTTTTTG
1 GTTTGGCCACAAAAAGTATCATTCCCACCATATCCATGTTGGCGCCAAAATGGCTAACGTTTTTG
8698 TGACGATATTTCGTAGCCACTAATTAGTTGAATTGTTAGTGACACAACTTGTCGTCACAAATTGT
66 TGACGATATTTCGTAGCCACTAATTAGTTGAATTGTTAGTGACACAACTTGTCGTCACAAATTGT
8763 ACACACAAAAGTGACGAGGTAAGTTTTCGTCACAAGAAAATGAAACTAGTAGTGACCAATATAG
131 ACACACAAAAGTGACGAGGTAAGTTTTCGTCACAAGAAAATGAAACTAGTAGTGACCAATATAG
* *
8827 GTTTGGCCACAAAAAGTATCATTCCCGCCATATCCATGTTGGCGCCAAATTGGCTAACGTTTTTG
1 GTTTGGCCACAAAAAGTATCATTCCCACCATATCCATGTTGGCGCCAAAATGGCTAACGTTTTTG
* *
8892 TGACGATATTTCGTAGCCACTAATTAGTTGAATTGTTAGTGACACAATTTGTCGTCACAAATTTT
66 TGACGATATTTCGTAGCCACTAATTAGTTGAATTGTTAGTGACACAACTTGTCGTCACAAATTGT
*
8957 ACACACAAAAGTGATGAGGTAAGTTTTCGTCACAAGAAAATGAAACTAGTAGTGACCAATATAG
131 ACACACAAAAGTGACGAGGTAAGTTTTCGTCACAAGAAAATGAAACTAGTAGTGACCAATATAG
*
9021 GTTTGGCCACAAAAAGTATCATTCCCACCATATCCATGTTGGCGCCAAAATGACTAACGTTTTTG
1 GTTTGGCCACAAAAAGTATCATTCCCACCATATCCATGTTGGCGCCAAAATGGCTAACGTTTTTG
* * * * *
9086 TGACGATATTGT-GTAGCCCCTAATTAATTCAATTGTTAGTGACACAACTTGTCATCACAAAATG
66 TGACGATATT-TCGTAGCCACTAATTAGTTGAATTGTTAGTGACACAACTTGTCGTCACAAATTG
* ** * *
9150 TTACACACAAATGTGACGAGGTACTTTTTTTGTCACAA-ACAAATGAAACTTGTAGT
130 -TACACACAAAAGTGACGAGGTA-AGTTTTCGTCACAAGA-AAATGAAACTAGTAGT
9206 TTTGTGACAA
Statistics
Matches: 348, Mismatches: 27, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
194 300 0.86
195 22 0.06
196 26 0.07
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (194 bp):
GTTTGGCCACAAAAAGTATCATTCCCACCATATCCATGTTGGCGCCAAAATGGCTAACGTTTTTG
TGACGATATTTCGTAGCCACTAATTAGTTGAATTGTTAGTGACACAACTTGTCGTCACAAATTGT
ACACACAAAAGTGACGAGGTAAGTTTTCGTCACAAGAAAATGAAACTAGTAGTGACCAATATAG
Done.