Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016154.1 Corchorus capsularis cultivar CVL-1 contig16175, 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: 14046
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Found at i:390 original size:15 final size:16
Alignment explanation
Indices: 370--403 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
360 GATTGCTTTC
*
370 TTAGTTA-ATTTACTT
1 TTAGTTAGATTTAATT
385 TTAGTTAGATTTAATT
1 TTAGTTAGATTTAATT
401 TTA
1 TTA
404 ATTCTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (16 bp):
TTAGTTAGATTTAATT
Found at i:1147 original size:65 final size:65
Alignment explanation
Indices: 1041--1211 Score: 245
Period size: 65 Copynumber: 2.6 Consensus size: 65
1031 TCTCAAAGAG
* *
1041 TCAGAAACCTCCGGGTAGCAATTCTGATAGCATCC-AGGCATGCTATAAGGCCTTCGGGCACAAC
1 TCAGAAACCTCCGGGTAGCAATTCTGATAGCCTCCGA-GCATGCTATAAGGCCTCCGGGCACAAC
1105 A
65 A
* * * *
1106 TCAGAAACCTCCGGGTAGCAATTCTAATAGCCTCCGAGCATGTTATAAGTCCTCCGTGCACAACA
1 TCAGAAACCTCCGGGTAGCAATTCTGATAGCCTCCGAGCATGCTATAAGGCCTCCGGGCACAACA
* * *
1171 CCAGAAACCTCCGGGTAGCAATTTTGATAGCCTCCGGGCAT
1 TCAGAAACCTCCGGGTAGCAATTCTGATAGCCTCCGAGCAT
1212 ACTTCGAAGA
Statistics
Matches: 95, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
65 94 0.99
66 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (65 bp):
TCAGAAACCTCCGGGTAGCAATTCTGATAGCCTCCGAGCATGCTATAAGGCCTCCGGGCACAACA
Found at i:1319 original size:36 final size:36
Alignment explanation
Indices: 1243--1331 Score: 97
Period size: 36 Copynumber: 2.4 Consensus size: 36
1233 AGAATGGTTC
* * * *
1243 TGAAGACAGATCCTAAAAGAAATTTGAGAATGGATC
1 TGAAGACAGTTCCTAAAAGAAATTCGAGAATGAATA
* * *
1279 TGAAGACAGTTCCTAAATGACATTCGAGAGTGAATA
1 TGAAGACAGTTCCTAAAAGAAATTCGAGAATGAATA
*
1315 TGAAGATAGTTCACTAA
1 TGAAGACAGTTC-CTAA
1332 GATGGATCTG
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 40 0.91
37 4 0.09
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (36 bp):
TGAAGACAGTTCCTAAAAGAAATTCGAGAATGAATA
Found at i:1346 original size:61 final size:61
Alignment explanation
Indices: 1272--1448 Score: 273
Period size: 61 Copynumber: 2.9 Consensus size: 61
1262 AAATTTGAGA
* *
1272 ATGGATCTGAAGACAGTTCCTAAATGACATTCGAGAGTGAATATGAAGATAGTTCACTAAG
1 ATGGATCTGAAGACAGTTCCTAAATGATATTTGAGAGTGAATATGAAGATAGTTCACTAAG
* * *
1333 ATGGATCTGAAGACAGTTCCTAAATGATATTTGAGAGTGAATATAAAGACAATTCACTAAG
1 ATGGATCTGAAGACAGTTCCTAAATGATATTTGAGAGTGAATATGAAGATAGTTCACTAAG
* * * *
1394 ATGGATCTGAAGACAGTTCCTAAAAGATATTTGAGAATGGATCTGAAGATAGTTC
1 ATGGATCTGAAGACAGTTCCTAAATGATATTTGAGAGTGAATATGAAGATAGTTC
1449 CTGAAAGATA
Statistics
Matches: 104, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 104 1.00
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (61 bp):
ATGGATCTGAAGACAGTTCCTAAATGATATTTGAGAGTGAATATGAAGATAGTTCACTAAG
Found at i:1434 original size:36 final size:36
Alignment explanation
Indices: 1390--1468 Score: 124
Period size: 36 Copynumber: 2.2 Consensus size: 36
1380 GACAATTCAC
1390 TAAG-ATGGATCTGAAGACAGTTCCTAAAAGATATT
1 TAAGAATGGATCTGAAGACAGTTCCTAAAAGATATT
* * *
1425 TGAGAATGGATCTGAAGATAGTTCCTGAAAGATATT
1 TAAGAATGGATCTGAAGACAGTTCCTAAAAGATATT
1461 TAAGAATG
1 TAAGAATG
1469 AGTATGAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 3 0.08
36 36 0.92
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.29
Consensus pattern (36 bp):
TAAGAATGGATCTGAAGACAGTTCCTAAAAGATATT
Found at i:1477 original size:36 final size:36
Alignment explanation
Indices: 1390--1480 Score: 114
Period size: 36 Copynumber: 2.6 Consensus size: 36
1380 GACAATTCAC
*
1390 TAAG-ATGGATCTGAAGACAGTTCCTAAAAGATATT
1 TAAGAATGGATATGAAGACAGTTCCTAAAAGATATT
* * * *
1425 TGAGAATGGATCTGAAGATAGTTCCTGAAAGATATT
1 TAAGAATGGATATGAAGACAGTTCCTAAAAGATATT
1461 TAAGAAT-GAGTATGAAGACA
1 TAAGAATGGA-TATGAAGACA
1481 ACTCAAATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
35 5 0.10
36 43 0.90
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (36 bp):
TAAGAATGGATATGAAGACAGTTCCTAAAAGATATT
Found at i:1688 original size:55 final size:56
Alignment explanation
Indices: 1591--1714 Score: 178
Period size: 55 Copynumber: 2.2 Consensus size: 56
1581 AGATTTAGAC
* * *
1591 CGAAGACGGTCATCCTTTCCAGTTTTCAGTAGTTTTAAGTAGTTACTCAAATTGAT
1 CGAAGACGATCATCCTTTCCAGTTTCCAGCAGTTTTAAGTAGTTACTCAAATTGAT
* * * *
1647 CGAAGACGATCATCC-TTCCAGTTTCCAGCAGTTTTTAGTAGTTATTCAAGTTGGT
1 CGAAGACGATCATCCTTTCCAGTTTCCAGCAGTTTTAAGTAGTTACTCAAATTGAT
1702 CGAAGACGATCAT
1 CGAAGACGATCAT
1715 TTTTCTAAGA
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
55 47 0.77
56 14 0.23
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (56 bp):
CGAAGACGATCATCCTTTCCAGTTTCCAGCAGTTTTAAGTAGTTACTCAAATTGAT
Found at i:1994 original size:26 final size:27
Alignment explanation
Indices: 1965--2036 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
1955 GGTCACCTAT
1965 GGGCATTTTGGTTATTTTGGCACA-AG
1 GGGCATTTTGGTTATTTTGGCACATAG
*
1991 GGGCATTCTGGTTA-TTT-GCACACTTAG
1 GGGCATTTTGGTTATTTTGGCACA--TAG
*
2018 GGGCATTTTGGTCATTTTG
1 GGGCATTTTGGTTATTTTG
2037 AGTCCACTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
24 5 0.13
25 3 0.08
26 13 0.34
27 14 0.37
28 3 0.08
ACGTcount: A:0.17, C:0.14, G:0.29, T:0.40
Consensus pattern (27 bp):
GGGCATTTTGGTTATTTTGGCACATAG
Found at i:5908 original size:22 final size:22
Alignment explanation
Indices: 5882--5930 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
5872 TTCAAATAAA
*
5882 ATGTAATAAATATGCTGCAATC
1 ATGTAATAAACATGCTGCAATC
5904 ATGTAATAAACATGCTGCAATC
1 ATGTAATAAACATGCTGCAATC
5926 ATGTA
1 ATGTA
5931 TTTAAAGCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (22 bp):
ATGTAATAAACATGCTGCAATC
Found at i:10211 original size:96 final size:96
Alignment explanation
Indices: 10044--10242 Score: 344
Period size: 96 Copynumber: 2.1 Consensus size: 96
10034 TCAAAAGAAA
* * *
10044 TTAAAATGGTAATCAAAGAGTTTTCAAGGTAAGTATTTTCAAAAAGAAAGTTTTTTTTAAGCAAC
1 TTAAAATGGGAATCAAAGAGTTTTCAAGGTAAGCATTTACAAAAAGAAAGTTTTTTTTAAGCAAC
*
10109 TCCAAAAGAAGACTTTTGGAAAATAAAGGTT
66 TCCAAAAGAAGACTTTTGGAAAATAAAGGCT
*
10140 TTAAAATGGGAATCAAAGAGTTTTCAAGGTAAGCATTTACAAAAAGAATGTTTTTTTTAAGCAAC
1 TTAAAATGGGAATCAAAGAGTTTTCAAGGTAAGCATTTACAAAAAGAAAGTTTTTTTTAAGCAAC
*
10205 TTCAAAAGAAGACTTTTGGAAAATAAAGGCT
66 TCCAAAAGAAGACTTTTGGAAAATAAAGGCT
10236 TTAAAAT
1 TTAAAAT
10243 ATCCAAGAGA
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
96 97 1.00
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.32
Consensus pattern (96 bp):
TTAAAATGGGAATCAAAGAGTTTTCAAGGTAAGCATTTACAAAAAGAAAGTTTTTTTTAAGCAAC
TCCAAAAGAAGACTTTTGGAAAATAAAGGCT
Found at i:13453 original size:21 final size:21
Alignment explanation
Indices: 13424--13466 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
13414 ACTTAGGAAC
13424 CCTAGTTTGAACCACTTAAAT
1 CCTAGTTTGAACCACTTAAAT
* * *
13445 CCTATTTTGTACCACTTGAAT
1 CCTAGTTTGAACCACTTAAAT
13466 C
1 C
13467 AAAAGGGTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.37
Consensus pattern (21 bp):
CCTAGTTTGAACCACTTAAAT
Done.