Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01001681.1 Corchorus olitorius cultivar O-4 contig01681, 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: 5104
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--32 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1 TA TA TA TA TA TA TA 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
33 GACACACACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39 original size:2 final size:2
Alignment explanation
Indices: 34--68 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
24 ATATATATAG
34 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
69 TATTGGACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2468 original size:22 final size:22
Alignment explanation
Indices: 2439--2519 Score: 103
Period size: 22 Copynumber: 3.7 Consensus size: 22
2429 TGAATATTTT
2439 TATGAAATTTTGATAACTATCC
1 TATGAAATTTTGATAACTATCC
* * *
2461 TATTAAATTTTGATAACCACCC
1 TATGAAATTTTGATAACTATCC
2483 TATGAAATTTTGATAA-T-TGCC
1 TATGAAATTTTGATAACTAT-CC
*
2504 TATGAAATTGTGATAA
1 TATGAAATTTTGATAA
2520 AATCCACTTG
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
21 17 0.33
22 34 0.67
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACTATCC
Found at i:2532 original size:43 final size:44
Alignment explanation
Indices: 2439--2555 Score: 118
Period size: 43 Copynumber: 2.7 Consensus size: 44
2429 TGAATATTTT
* * *
2439 TATGAAATTTTGATAACTATCCTATTAAATTTTGATAACCACCC
1 TATGAAATTTTGATAACTATCCTATGAAATTGTGATAACAACCC
2483 TATGAAATTTTGATAA-T-TGCCTATGAAATTGTGATAA-AATCCAC
1 TATGAAATTTTGATAACTAT-CCTATGAAATTGTGATAACAA-CC-C
* *
2527 T-TGAAAGTTTGATAACCTA-ACTATGAAAT
1 TATGAAATTTTGATAA-CTATCCTATGAAAT
2556 CTTAATAAAC
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
42 2 0.03
43 32 0.52
44 27 0.44
45 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (44 bp):
TATGAAATTTTGATAACTATCCTATGAAATTGTGATAACAACCC
Found at i:2595 original size:21 final size:23
Alignment explanation
Indices: 2547--2596 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
2537 GATAACCTAA
2547 CTATGAAATCTTAATAAACCTTC
1 CTATGAAATCTTAATAAACCTTC
* * *
2570 ATATGAAA-CTT-ATTAATCTTC
1 CTATGAAATCTTAATAAACCTTC
2591 CTATGA
1 CTATGA
2597 TTTTTTATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 13 0.57
22 3 0.13
23 7 0.30
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.38
Consensus pattern (23 bp):
CTATGAAATCTTAATAAACCTTC
Found at i:3292 original size:52 final size:52
Alignment explanation
Indices: 3230--3393 Score: 164
Period size: 52 Copynumber: 3.2 Consensus size: 52
3220 CTCTACATGG
3230 AGTATACATCCAGATAGAATACCCTTACGTGACACTCAGTTTCATAGCCGTT
1 AGTATACATCCAGATAGAATACCCTTACGTGACACTCAGTTTCATAGCCGTT
* * ** ** * *
3282 AGTATACATCCAAATCGAGCATTC-TACGACTCAACACTC--TCTACAT-G--G--
1 AGTATACATCCAGATAGAATACCCTTACG--T-GACACTCAGT-TTCATAGCCGTT
3330 AGTATACATCCAGATAGAATACCCTTACGTGACACTCAGTTTCATAGCCGTT
1 AGTATACATCCAGATAGAATACCCTTACGTGACACTCAGTTTCATAGCCGTT
3382 AGTATACATCCA
1 AGTATACATCCA
3394 AATCGAGCAT
Statistics
Matches: 84, Mismatches: 16, Indels: 24
0.68 0.13 0.19
Matches are distributed among these distances:
46 6 0.07
47 5 0.06
48 20 0.24
49 4 0.05
50 2 0.02
51 4 0.05
52 32 0.38
53 5 0.06
54 6 0.07
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.27
Consensus pattern (52 bp):
AGTATACATCCAGATAGAATACCCTTACGTGACACTCAGTTTCATAGCCGTT
Found at i:3341 original size:48 final size:48
Alignment explanation
Indices: 3191--3341 Score: 121
Period size: 48 Copynumber: 3.1 Consensus size: 48
3181 GGGCACATTA
*
3191 CCAAATCGAGCATTCTATGACTCAACACTCTCTACATGGAGTATACAT
1 CCAAATCGAGCATTCTACGACTCAACACTCTCTACATGGAGTATACAT
* * ** ** * *
3239 CCAGATAGAATACCCTTACG--T-GACACTCAGT-TTCATAGCCGTTAGTATACAT
1 CCAAATCGAGCATTC-TACGACTCAACACTC--TCTACAT-G--G--AGTATACAT
3291 CCAAATCGAGCATTCTACGACTCAACACTCTCTACATGGAGTATACAT
1 CCAAATCGAGCATTCTACGACTCAACACTCTCTACATGGAGTATACAT
3339 CCA
1 CCA
3342 GATAGAATAC
Statistics
Matches: 74, Mismatches: 17, Indels: 24
0.64 0.15 0.21
Matches are distributed among these distances:
46 6 0.08
47 5 0.07
48 23 0.31
49 3 0.04
50 2 0.03
51 4 0.05
52 20 0.27
53 5 0.07
54 6 0.08
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.26
Consensus pattern (48 bp):
CCAAATCGAGCATTCTACGACTCAACACTCTCTACATGGAGTATACAT
Found at i:3364 original size:100 final size:100
Alignment explanation
Indices: 3191--3422 Score: 455
Period size: 100 Copynumber: 2.3 Consensus size: 100
3181 GGGCACATTA
*
3191 CCAAATCGAGCATTCTATGACTCAACACTCTCTACATGGAGTATACATCCAGATAGAATACCCTT
1 CCAAATCGAGCATTCTACGACTCAACACTCTCTACATGGAGTATACATCCAGATAGAATACCCTT
3256 ACGTGACACTCAGTTTCATAGCCGTTAGTATACAT
66 ACGTGACACTCAGTTTCATAGCCGTTAGTATACAT
3291 CCAAATCGAGCATTCTACGACTCAACACTCTCTACATGGAGTATACATCCAGATAGAATACCCTT
1 CCAAATCGAGCATTCTACGACTCAACACTCTCTACATGGAGTATACATCCAGATAGAATACCCTT
3356 ACGTGACACTCAGTTTCATAGCCGTTAGTATACAT
66 ACGTGACACTCAGTTTCATAGCCGTTAGTATACAT
3391 CCAAATCGAGCATTCTACGACTCAACACTCTC
1 CCAAATCGAGCATTCTACGACTCAACACTCTC
3423 CAATTTGCCT
Statistics
Matches: 131, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 131 1.00
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.27
Consensus pattern (100 bp):
CCAAATCGAGCATTCTACGACTCAACACTCTCTACATGGAGTATACATCCAGATAGAATACCCTT
ACGTGACACTCAGTTTCATAGCCGTTAGTATACAT
Done.