Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011957.1 Corchorus capsularis cultivar CVL-1 contig11978, 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: 5155
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Found at i:62 original size:33 final size:33
Alignment explanation
Indices: 20--129 Score: 157
Period size: 33 Copynumber: 3.3 Consensus size: 33
10 TGAAAACAAA
20 TCTGATTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTG-TTTTGGTTGATCATAGCATTGCAAATAAT
*
54 TCTGTTTTGGTTGATCAGAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
* * ** *
87 TTTGTTTTGGTTGATTATAGCATTAAAAAAAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
120 TCTGTTTTGG
1 TCTGTTTTGG
130 GTGAAAAGAA
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
33 64 0.94
34 4 0.06
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.44
Consensus pattern (33 bp):
TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
Found at i:4201 original size:53 final size:53
Alignment explanation
Indices: 4138--4430 Score: 276
Period size: 54 Copynumber: 5.5 Consensus size: 53
4128 CGGTCATACA
*
4138 AAGAAATTTTCAATGGTCAGAGTTGACCCCCAGATGAT-CAGTGAGGTCATTTC
1 AAGAAATTTTCAATGGTCAGAGTTGACCCCCAGATGATCCAATGA-GTCATTTC
* * * *
4191 AAGAAGTTTTCAATGG-GAGAGTTGA--CCCAGATGATCCTATGCAGTTA-TTC
1 AAGAAATTTTCAATGGTCAGAGTTGACCCCCAGATGATCCAATG-AGTCATTTC
* * * * *
4241 GAAGAAATTTTCAATGGTCAGAGTTGACCCCTAGATAATCTAGTGCAGTCATTCC
1 -AAGAAATTTTCAATGGTCAGAGTTGACCCCCAGATGATCCAATG-AGTCATTTC
* * * *
4296 AAGAAGTTTTCAATGGTCAAAGTTGA-CCCTAGATGATCCAATGTGGTCA-TTC
1 AAGAAATTTTCAATGGTCAGAGTTGACCCCCAGATGATCCAATG-AGTCATTTC
* * *
4348 AAAGAAATTTTCAATCGTCAGAGTTGACCACCAGATGATCCAATGACGTCATTTT
1 -AAGAAATTTTCAATGGTCAGAGTTGACCCCCAGATGATCCAATGA-GTCATTTC
* * *
4403 AAGAAGTTTTTTCGATGATCAGAGTTGA
1 AAGAA--ATTTTCAATGGTCAGAGTTGA
4431 TCTCAATTCA
Statistics
Matches: 194, Mismatches: 33, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
50 13 0.07
51 21 0.11
52 19 0.10
53 56 0.29
54 64 0.33
55 4 0.02
56 17 0.09
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (53 bp):
AAGAAATTTTCAATGGTCAGAGTTGACCCCCAGATGATCCAATGAGTCATTTC
Found at i:4300 original size:54 final size:54
Alignment explanation
Indices: 4138--4387 Score: 282
Period size: 53 Copynumber: 4.7 Consensus size: 54
4128 CGGTCATACA
* *
4138 AAGAAATTTTCAATGGTCAGAGTTGACCCCCAGATGATC-AGTG-AGGTCATTTC
1 AAGAAATTTTCAATGGTCAGAGTTGACCCCTAGATGATCTAGTGCA-GTCATTCC
* * * *
4191 AAGAAGTTTTCAATGG-GAGAGTTGA-CCC-AGATGATCCTA-TGCAGTTATTCG
1 AAGAAATTTTCAATGGTCAGAGTTGACCCCTAGATGAT-CTAGTGCAGTCATTCC
*
4242 AAGAAATTTTCAATGGTCAGAGTTGACCCCTAGATAATCTAGTGCAGTCATTCC
1 AAGAAATTTTCAATGGTCAGAGTTGACCCCTAGATGATCTAGTGCAGTCATTCC
* * * * ** *
4296 AAGAAGTTTTCAATGGTCAAAGTTGA-CCCTAGATGATCCAATGTGGTCATTCA
1 AAGAAATTTTCAATGGTCAGAGTTGACCCCTAGATGATCTAGTGCAGTCATTCC
*
4349 AAGAAATTTTCAATCGTCAGAGTTGACCACC-AGATGATC
1 AAGAAATTTTCAATGGTCAGAGTTGACC-CCTAGATGATC
4388 CAATGACGTC
Statistics
Matches: 167, Mismatches: 21, Indels: 17
0.81 0.10 0.08
Matches are distributed among these distances:
50 7 0.04
51 26 0.16
52 18 0.11
53 65 0.39
54 49 0.29
55 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (54 bp):
AAGAAATTTTCAATGGTCAGAGTTGACCCCTAGATGATCTAGTGCAGTCATTCC
Found at i:4399 original size:107 final size:104
Alignment explanation
Indices: 4117--4412 Score: 380
Period size: 107 Copynumber: 2.8 Consensus size: 104
4107 GGTGTTTAAA
* *
4117 ATGATCCATTGCGGTCATACAAAGAAATTTTCAATGGTCAGAGTTGACCCCCAGATGAT-CAGTG
1 ATGATCCAATGCGGTCATTCAAAGAAATTTTCAATGGTCAGAGTTGA-CCCCAGATGATCCAGTG
* * *
4181 AGGTCATTTCAAGAAGTTTTCAATGGGAGAGTTGACCCAG
65 ACGTCATTTCAAGAAGTTTTCAATGGCAAAGTTGACCCAG
* * * * * *
4221 ATGATCCTATGCAGTTATTCGAAGAAATTTTCAATGGTCAGAGTTGACCCCTAGATAATCTAGTG
1 ATGATCCAATGCGGTCATTCAAAGAAATTTTCAATGGTCAGAGTTGACCCC-AGATGATCCAGTG
*
4286 -CAGTCATTCCAAGAAGTTTTCAATGGTCAAAGTTGACCCTAG
65 AC-GTCATTTCAAGAAGTTTTCAATGG-CAAAGTTGACCC-AG
* * *
4328 ATGATCCAATGTGGTCATTCAAAGAAATTTTCAATCGTCAGAGTTGACCACCAGATGATCCAATG
1 ATGATCCAATGCGGTCATTCAAAGAAATTTTCAATGGTCAGAGTTGACC-CCAGATGATCCAGTG
*
4393 ACGTCATTTTAAGAAGTTTT
65 ACGTCATTTCAAGAAGTTTT
4413 TTCGATGATC
Statistics
Matches: 162, Mismatches: 23, Indels: 11
0.83 0.12 0.06
Matches are distributed among these distances:
103 4 0.02
104 47 0.29
105 27 0.17
106 10 0.06
107 71 0.44
108 3 0.02
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (104 bp):
ATGATCCAATGCGGTCATTCAAAGAAATTTTCAATGGTCAGAGTTGACCCCAGATGATCCAGTGA
CGTCATTTCAAGAAGTTTTCAATGGCAAAGTTGACCCAG
Found at i:4450 original size:35 final size:35
Alignment explanation
Indices: 4411--4515 Score: 160
Period size: 35 Copynumber: 3.1 Consensus size: 35
4401 TTAAGAAGTT
4411 TTTTCGATGATCAGAGTTGATCTCAATTCAAGAAG
1 TTTTCGATGATCAGAGTTGATCTCAATTCAAGAAG
* * *
4446 TTTTCCATGATCGGAGTTGATCTCATTTCAAGAAG
1 TTTTCGATGATCAGAGTTGATCTCAATTCAAGAAG
*
4481 TTTTCGATGATCAGAGTTGATC-CAGTT-AAGAAG
1 TTTTCGATGATCAGAGTTGATCTCAATTCAAGAAG
4514 TT
1 TT
4516 CAAGATTTGA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 8 0.12
34 4 0.06
35 52 0.81
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (35 bp):
TTTTCGATGATCAGAGTTGATCTCAATTCAAGAAG
Done.