Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012898.1 Corchorus capsularis cultivar CVL-1 contig12919, 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: 17520
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Found at i:725 original size:2 final size:2
Alignment explanation
Indices: 718--750 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
708 AACTGATTCA
*
718 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
751 CTACATATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1005 original size:45 final size:46
Alignment explanation
Indices: 941--1031 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 46
931 TTATAGAGTA
941 GTGGAATTACTAAAAGATCCCTA-CCCCGAATTAATGATAACCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCCGAATTAATGATAACCTGG
986 GTGGAATTACTAAAAGATCCCTACCCCCGAATTAATGATAACCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCCGAATTAATGATAACCTGG
1032 AGAAGTAATC
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 23 0.51
46 22 0.49
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (46 bp):
GTGGAATTACTAAAAGATCCCTACCCCCGAATTAATGATAACCTGG
Found at i:1366 original size:166 final size:167
Alignment explanation
Indices: 1090--1415 Score: 483
Period size: 166 Copynumber: 2.0 Consensus size: 167
1080 CCTAAATTTT
* * * * ** * **
1090 AATAGAGTAGTGGAATTACTAAAAGATCCCTACCAAGCCTTGCTTTTGGAGTTAGACAACTTATT
1 AATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGCATTGATGATGGAGTTAGACAACTAACA
*
1155 TTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTACTAATTTTTTATTCTTGAGGGGATTA
66 TTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATGTACTAATTTTTTATTCTTGAGGGGATTA
*
1220 AATAAATAATCTTTTTGGTCATTTCTCAATGGACTTG
131 AATAAATAAACTTTTTGGTCATTTCTCAATGGACTTG
* * * *
1257 AATAGAGTAGTGGAATTAATAAATGATCCCCATCAAGGATTGATGAT-GAGTTAGAGAACTAACA
1 AATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGCATTGATGATGGAGTTAGACAACTAACA
*
1321 TTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATGTCCTAATTTTTTATTCTTGAGGGGATTA
66 TTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATGTACTAATTTTTTATTCTTGAGGGGATTA
* *
1386 AATCACTAAACTTTTTGGTCATTTCTCAAT
131 AATAAATAAACTTTTTGGTCATTTCTCAAT
1416 TGACAAATGA
Statistics
Matches: 141, Mismatches: 18, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
166 103 0.73
167 38 0.27
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (167 bp):
AATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGCATTGATGATGGAGTTAGACAACTAACA
TTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATGTACTAATTTTTTATTCTTGAGGGGATTA
AATAAATAAACTTTTTGGTCATTTCTCAATGGACTTG
Found at i:3376 original size:3 final size:3
Alignment explanation
Indices: 3363--3401 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
3353 AATTGAAATG
3363 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3402 GGCTAATTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:7211 original size:2 final size:2
Alignment explanation
Indices: 7204--7233 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
7194 TATAGGGTTC
7204 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7234 GTTAATTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12241 original size:28 final size:28
Alignment explanation
Indices: 12210--12263 Score: 92
Period size: 28 Copynumber: 1.9 Consensus size: 28
12200 TTTTCATATG
12210 TTTTGGT-AAAGGTTAAAAATAAATTTCT
1 TTTTGGTGAAA-GTTAAAAATAAATTTCT
12238 TTTTGGTGAAAGTTAAAAATAAATTT
1 TTTTGGTGAAAGTTAAAAATAAATTT
12264 TTAACCAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 22 0.88
29 3 0.12
ACGTcount: A:0.41, C:0.02, G:0.15, T:0.43
Consensus pattern (28 bp):
TTTTGGTGAAAGTTAAAAATAAATTTCT
Found at i:17040 original size:168 final size:164
Alignment explanation
Indices: 16685--17118 Score: 559
Period size: 168 Copynumber: 2.6 Consensus size: 164
16675 TGAGTCATTT
16685 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAAT-CCCTCAAGAATCAAAAGTTAGGACAT
* * * ** ** *
16750 TTAAGTAATT-TGCCAAGTAGGTAAAGACGAAAAAGATTAATTCTCTAGCTCATCATTAATCCTT
64 TTAAGT-ATTCTGCCAAGTAGGAAAAGACGAAAAA-AATAATTCTCTAACTCAAAAGGAAGCCTT
* *
16814 GATGGGGATCTTTTATTAATTCCACTACTCTATTCAAA
127 GATAGGGATCTTTTAGTAATTCCACTACTCTATTCAAA
* * * * *
16852 -TCCATCGAGAAATTACCAAAAAGATTACTTATTTAATCTCCTAAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATC-CCTCAAGAATCAAAAGTTAGGACAT
* *
16916 TTAAGTATTCTGTCAAAGTAGGAAAAAACGAAAAAAATAAGTTCTCTAACTCCAAAAGGAAGCCT
64 TTAAGTATTCTG-CCAAGTAGGAAAAGACGAAAAAAATAA-TTCTCTAACT-CAAAAGGAAGCCT
*
16981 TGGTAGGGATCTTTTAGTAATTCCACTACTCTATT-AAA
126 TGATAGGGATCTTTTAGTAATTCCACTACTCTATTCAAA
*
17019 GTCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCCCTTCAAGAATTAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAGT-TAGTTATTTAATCCC-TCAAGAATCAAAAGTTAGGACAT
* *
17084 TTAAGTAATCTGCCAAGTGGGAAAAGACGAAAAAA
64 TTAAGTATTCTGCCAAGTAGGAAAAGACGAAAAAA
17119 TTAGTTATCT
Statistics
Matches: 230, Mismatches: 29, Indels: 16
0.84 0.11 0.06
Matches are distributed among these distances:
165 4 0.02
166 68 0.30
167 54 0.23
168 104 0.45
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.29
Consensus pattern (164 bp):
GTCAATTGAGAAATGACCAAAAAGTTAGTTATTTAATCCCTCAAGAATCAAAAGTTAGGACATTT
AAGTATTCTGCCAAGTAGGAAAAGACGAAAAAAATAATTCTCTAACTCAAAAGGAAGCCTTGATA
GGGATCTTTTAGTAATTCCACTACTCTATTCAAA
Done.