Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024886.1 Corchorus olitorius cultivar O-4 contig24919, 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: 5291
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:562 original size:11 final size:11
Alignment explanation
Indices: 546--570 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
536 AAAATCAATT
546 TGTGATTGTAG
1 TGTGATTGTAG
557 TGTGATTGTAG
1 TGTGATTGTAG
568 TGT
1 TGT
571 TGCAGAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.36, T:0.48
Consensus pattern (11 bp):
TGTGATTGTAG
Found at i:4154 original size:131 final size:128
Alignment explanation
Indices: 4017--4454 Score: 433
Period size: 131 Copynumber: 3.3 Consensus size: 128
4007 TGAAATGCGG
* * *
4017 GAATGACGAAACTGACCTTTTCACCGAAAAGGTATTTTTGGAAAGTAGAATAAACTGAAATGCAA
1 GAATGACGAAACTGACCCTTTCACCGAAAGGGTATTTTTGGAAAGTAGAATAAACTGAAATGCGA
*
4082 AAATGATGAAACTGACCTTTTCACCGAAAGGGTATTTTTGGAAATCAAAAGTAAACTCAAATGCA
66 AAATGATGAAACTGACC-TTTCACCGAAAGGGTATTTTTGGAAATCAAAA-TAAACTTAAATG-A
4147 A
128 A
* * * * *
4148 GAATGAC-AGAATTGACCCTTTGACCGAAAGGGCATTTTGGGAAAAGTA-AACT-AACTTAGACA
1 GAATGACGA-AACTGACCCTTTCACCGAAAGGGTATTTTTGG-AAAGTAGAA-TAAAC-T-GAAA
* * * * *
4210 TG-GAAAA-GTTGAAACTGACCCTTCGACCGGAAGGGTATTTTTGGAAAACAAAATTGAACTTAG
61 TGCGAAAATGATGAAACTGACCTTTC-ACCGAAAGGGTATTTTTGGAAATCAAAA-TAAACTTA-
4273 ATATGAA
123 A-ATGAA
* * * * *
4280 AAAT-ATGAAACTGACCC-TTCGACCGGAAGGGTATTTTTGGAAAGTAGAATAAACTTAGATGCG
1 GAATGACGAAACTGACCCTTTC-ACCGAAAGGGTATTTTTGGAAAGTAGAATAAACTGAAATGCG
* * * *
4343 AAGATGATGAAACTGACCCTTTCACCGAAAGGGTAATTTTGGAAATGAAAATACTGAACTTGAAT
65 AAAATGATGAAACTGA-CCTTTCACCGAAAGGGTATTTTTGGAAATCAAAATA---AACTTAAAT
4408 GTAA
126 G-AA
* *
4412 -AAAGACGAAACTGACCCTTTGACCGAAAGGGTATTTTTGGAAA
1 GAATGACGAAACTGACCCTTTCACCGAAAGGGTATTTTTGGAAA
4455 TGAAAATACT
Statistics
Matches: 249, Mismatches: 37, Indels: 41
0.76 0.11 0.13
Matches are distributed among these distances:
129 4 0.02
130 19 0.08
131 151 0.61
132 60 0.24
133 15 0.06
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.25
Consensus pattern (128 bp):
GAATGACGAAACTGACCCTTTCACCGAAAGGGTATTTTTGGAAAGTAGAATAAACTGAAATGCGA
AAATGATGAAACTGACCTTTCACCGAAAGGGTATTTTTGGAAATCAAAATAAACTTAAATGAA
Found at i:4174 original size:66 final size:64
Alignment explanation
Indices: 4018--4598 Score: 426
Period size: 65 Copynumber: 8.8 Consensus size: 64
4008 GAAATGCGGG
* * * * * *
4018 AATGACGAAACTGACCTTTTCACCGAAAAGGTATTTTTGGAAA-GTAGAATAAACTGAAATGCAA
1 AATGATGAAACTGACCCTTTGACCGAAAGGGTATTTTTGGAAATG-AAAATAAACTTAAATGC-A
4082 A
64 A
* * * *
4083 AATGATGAAACTGACCTTTTCACCGAAAGGGTATTTTTGGAAATCAAAAGTAAACTCAAATGCAA
1 AATGATGAAACTGACCCTTTGACCGAAAGGGTATTTTTGGAAATGAAAA-TAAACTTAAATGCAA
* * * * * *
4148 GAATGA-CAGAATTGACCCTTTGACCGAAAGGGCATTTTGGGAAAAGTAAACT-AACTTAGACAT
1 -AATGATGA-AACTGACCCTTTGACCGAAAGGGTATTTTTGGAAATG-AAAATAAACTTA-A-AT
*
4211 GGAA
61 GCAA
* * * ** * *
4215 AA-GTTGAAACTGACCCTTCGACCGGAAGGGTATTTTTGGAAAACAAAATTGAACTTAGATATGA
1 AATGATGAAACTGACCCTTTGACCGAAAGGGTATTTTTGGAAATGAAAA-TAAACTTA-A-ATGC
4279 AA
63 AA
* * * *
4281 AAT-ATGAAACTGACCCTTCGACCGGAAGGGTATTTTTGGAAA-GTAGAATAAACTTAGATGCGA
1 AATGATGAAACTGACCCTTTGACCGAAAGGGTATTTTTGGAAATG-AAAATAAACTTAAATGC-A
4344 A
64 A
* * * * *
4345 GATGATGAAACTGACCCTTTCACCGAAAGGGTAATTTTGGAAATGAAAATACTGAACTTGAATGT
1 AATGATGAAACTGACCCTTTGACCGAAAGGGTATTTTTGGAAATGAAAATA---AACTTAAATGC
4410 AA
63 AA
* * **
4412 AAAGACGAAACTGACCCTTTGACCGAAAGGGTATTTTTGGAAATGAAAATACTATGTTGAAATGC
1 AATGATGAAACTGACCCTTTGACCGAAAGGGTATTTTTGGAAATGAAAATA--AACTT-AAATGC
4477 AA
63 AA
* * * *
4479 AA-GACGGAAA-TGACCCTTCGACCAAAAGGGTA-CTTTGGAAATTTGAAAATGCTAAACTTAAA
1 AATGA-TGAAACTGACCCTTTGACCGAAAGGGTATTTTTGGAAA--TGAAAA---TAAACTTAAA
4541 TGCAA
60 TGCAA
* * * * * * *
4546 AA-GACGAAAATGACTCTTCGACCAAAAGGGTATTTCTGGAAAGAGAAAATAAA
1 AATGATGAAACTGACCCTTTGACCGAAAGGGTATTTTTGGAAA-TGAAAATAAA
4599 ACTTTACTTT
Statistics
Matches: 424, Mismatches: 65, Indels: 55
0.78 0.12 0.10
Matches are distributed among these distances:
63 3 0.01
64 11 0.03
65 140 0.33
66 138 0.33
67 112 0.26
68 18 0.04
70 2 0.00
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (64 bp):
AATGATGAAACTGACCCTTTGACCGAAAGGGTATTTTTGGAAATGAAAATAAACTTAAATGCAA
Found at i:4574 original size:133 final size:135
Alignment explanation
Indices: 4351--4596 Score: 322
Period size: 133 Copynumber: 1.8 Consensus size: 135
4341 CGAAGATGAT
* * * *
4351 GAAACTGACCCTTTCACCGAAAGGGTAATTTTGGAAATGAAAATACTGAACTTGAATGTAAAAAG
1 GAAACTGACCCTTTCACCAAAAGGGTAACTTTGGAAATGAAAATACTAAACTTAAATGTAAAAAG
* * * * *
4416 ACGAAACTGACCCTTTGACCGAAAGGGTATTTTTGGAAA-TGAAAATACTATGTTGAAATGCAAA
66 ACGAAAATGACCCTTCGACCAAAAGGGTATTTCTGGAAAGAGAAAATACTATGTTGAAATGCAAA
4480 AGACG
131 AGACG
* *
4485 GAAA-TGACCC-TTCGACCAAAAGGGT-ACTTTGGAAATTTGAAAATGCTAAACTTAAATG-CAA
1 GAAACTGACCCTTTC-ACCAAAAGGGTAACTTTGGAAA--TGAAAATACTAAACTTAAATGTAAA
*
4546 AAGACGAAAATGACTCTTCGACCAAAAGGGTATTTCTGGAAAGAGAAAATA
63 AAGACGAAAATGACCCTTCGACCAAAAGGGTATTTCTGGAAAGAGAAAATA
4597 AAACTTTACT
Statistics
Matches: 96, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
132 12 0.12
133 55 0.57
134 29 0.30
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (135 bp):
GAAACTGACCCTTTCACCAAAAGGGTAACTTTGGAAATGAAAATACTAAACTTAAATGTAAAAAG
ACGAAAATGACCCTTCGACCAAAAGGGTATTTCTGGAAAGAGAAAATACTATGTTGAAATGCAAA
AGACG
Done.