Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017294.1 Corchorus olitorius cultivar O-4 contig17327, 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: 12589
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:223 original size:26 final size:26
Alignment explanation
Indices: 187--292 Score: 88
Period size: 26 Copynumber: 3.9 Consensus size: 26
177 TTAAGTGTGT
**
187 ACTTAAAATGACCAACGTGCCCCTGA
1 ACTTAAAATGACCAAAATGCCCCTGA
*
213 ACTTAAAATGATCAAAATGCCCCTGA
1 ACTTAAAATGACCAAAATGCCCCTGA
* *
239 A-TGTGTAAATGACTAAAATGCCCCTAGA
1 ACT-T-AAAATGACCAAAATGCCCCT-GA
* * *
267 TTCTTGAGAATGACCAAAATACCCCT
1 -ACTT-AAAATGACCAAAATGCCCCT
293 AGTTGATCCT
Statistics
Matches: 64, Mismatches: 11, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
25 1 0.02
26 25 0.39
27 17 0.27
28 2 0.03
29 18 0.28
30 1 0.02
ACGTcount: A:0.38, C:0.25, G:0.14, T:0.24
Consensus pattern (26 bp):
ACTTAAAATGACCAAAATGCCCCTGA
Found at i:732 original size:35 final size:35
Alignment explanation
Indices: 690--1029 Score: 476
Period size: 35 Copynumber: 9.7 Consensus size: 35
680 TGACTCCATA
* *
690 TTGAAGATGTTAAACCGAGTCATCTGGATTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGGATTCATCT
* *
725 TTGAAGATGCTACACCGAGTCATCCGAGA-TCATTT
1 TTGAAGATGCTACACCGAGTCATCTG-GATTCATCT
*
760 TTGAAGATGCTACACCGAGTCATCTGGATTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGGATTCATCT
*
795 TTGAAGATGCTACACCGAGTCAT-TTGAGTTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGGA-TTCATCT
*
830 TTGAAGATGCTGCACCGAGTCATCTGGATTCAAT-T
1 TTGAAGATGCTACACCGAGTCATCTGGATTC-ATCT
*
865 TCGAAGATGCTACACCGAGTCATCTGGATTCAATC-
1 TTGAAGATGCTACACCGAGTCATCTGGATTC-ATCT
* *
900 TCGAAGATGCTACACTGAGTCATCTGGATTCAAT-T
1 TTGAAGATGCTACACCGAGTCATCTGGATTC-ATCT
935 TTGAAGATGCTACACCGAGTCATCTGGATTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGGATTCATCT
* *
970 TTGAAGATGCTACACCAAGTCATCTGAATAT-ATCT
1 TTGAAGATGCTACACCGAGTCATCTGGAT-TCATCT
1005 TTGAAGATGCTACACCGAGTCATCT
1 TTGAAGATGCTACACCGAGTCATCT
1030 AAGAAGATGG
Statistics
Matches: 277, Mismatches: 19, Indels: 18
0.88 0.06 0.06
Matches are distributed among these distances:
34 7 0.03
35 262 0.95
36 8 0.03
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (35 bp):
TTGAAGATGCTACACCGAGTCATCTGGATTCATCT
Found at i:1145 original size:23 final size:23
Alignment explanation
Indices: 1118--1166 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
1108 ACGAGTTTGC
1118 CTAGAGACTGCCGGTTTTGCAAT
1 CTAGAGACTGCCGGTTTTGCAAT
1141 CTAGAGACTGCCGGTTTTGCAAT
1 CTAGAGACTGCCGGTTTTGCAAT
1164 CTA
1 CTA
1167 CCTCAGATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.31
Consensus pattern (23 bp):
CTAGAGACTGCCGGTTTTGCAAT
Found at i:5920 original size:379 final size:379
Alignment explanation
Indices: 5219--5953 Score: 1312
Period size: 379 Copynumber: 1.9 Consensus size: 379
5209 AAAGCCTTAC
*
5219 AAGCCCAAAAATAAAGACAAGGAAAACTAATCCCAAGTCCAACTAGGGAAAAATAAATAACAAAG
1 AAGCCCAAAAATAAAGACAAGGAAAACTAATCCCAAGTCCAACTAGGAAAAAATAAATAACAAAG
5284 CATAATTAAACAAGGATTGACTTAGTCAAACAAGGCCCAATCCTAATGTCATCTAAACATAACAA
66 CATAATTAAACAAGGATTGACTTAGTCAAACAAGGCCCAATCCTAATGTCATCTAAACATAACAA
* *
5349 TAAGCTTATCTAAGATAGAATAAAGCCCACAATAGCCGAAATTATACATTCAAGCACTAAGTCAT
131 TAAGCTAATCTAAGATAGAATAAAACCCACAATAGCCGAAATTATACATTCAAGCACTAAGTCAT
* *
5414 ATTGATTACAAGTAAGGTGATAATCTTGAAATCAATGGATGAATGCTTGCTCAAATCATGAACAA
196 ATCGATTACAAGTAAGGTGATAATCTTGAAATCAATGGATGAATGCTTGCTCAAATCATCAACAA
* * *
5479 ATCTCTTCAATTGCGCATCAATGACCTTCATATCATCTAGATGACTTCGAGCAAGGCCCATGAGT
261 AGCTCTTCAATTGCGCATCAATGACCTTCATATCATCTAGATGACTTCGAACAAGCCCCATGAGT
*
5544 GCATCCTTGAACCTCTTAGCTCTTGCTCTTGTCATCGGACCAATAGACATCTTT
326 GCATCCTTGAACCTATTAGCTCTTGCTCTTGTCATCGGACCAATAGACATCTTT
*
5598 AAGCCCAAAAATAAAGACAAGGAAAA-TCAAT-CCAAGTCCAACTAGGAAAAAATAAATAACAAG
1 AAGCCCAAAAATAAAGACAAGGAAAACT-AATCCCAAGTCCAACTAGGAAAAAATAAATAACAAA
5661 GCATAATTAAACAAGGATTAGACTTAGTCAAACAAGGCCCAATCCTAATGTCATCTAAACATAAC
65 GCATAATTAAACAAGGATT-GACTTAGTCAAACAAGGCCCAATCCTAATGTCATCTAAACATAAC
*
5726 AATAAGCTAATCTAAGATAGAATAAAACCCACAATAGCCGAAATTATACATTCAAGCCCTAAGTC
129 AATAAGCTAATCTAAGATAGAATAAAACCCACAATAGCCGAAATTATACATTCAAGCACTAAGTC
* * *
5791 ATATCGATTGCAAGTAAGGTGATAATCTTGGAATCAATGGATGAATGCTTGCTCAAATCATCACC
194 ATATCGATTACAAGTAAGGTGATAATCTTGAAATCAATGGATGAATGCTTGCTCAAATCATCAAC
5856 AAAGCTCTTCAATTGCGCATCAATGACCTTCATATCATCTAGATGACTTCGAACAAGCCCCATGA
259 AAAGCTCTTCAATTGCGCATCAATGACCTTCATATCATCTAGATGACTTCGAACAAGCCCCATGA
5921 GTGCATCCTTGAACCTATTAGCTCTTGCTCTTG
324 GTGCATCCTTGAACCTATTAGCTCTTGCTCTTG
5954 CTCTTGTCAT
Statistics
Matches: 340, Mismatches: 14, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
378 50 0.15
379 290 0.85
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.24
Consensus pattern (379 bp):
AAGCCCAAAAATAAAGACAAGGAAAACTAATCCCAAGTCCAACTAGGAAAAAATAAATAACAAAG
CATAATTAAACAAGGATTGACTTAGTCAAACAAGGCCCAATCCTAATGTCATCTAAACATAACAA
TAAGCTAATCTAAGATAGAATAAAACCCACAATAGCCGAAATTATACATTCAAGCACTAAGTCAT
ATCGATTACAAGTAAGGTGATAATCTTGAAATCAATGGATGAATGCTTGCTCAAATCATCAACAA
AGCTCTTCAATTGCGCATCAATGACCTTCATATCATCTAGATGACTTCGAACAAGCCCCATGAGT
GCATCCTTGAACCTATTAGCTCTTGCTCTTGTCATCGGACCAATAGACATCTTT
Found at i:9049 original size:19 final size:18
Alignment explanation
Indices: 9004--9055 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
8994 CATAGGTCTT
*
9004 TTAATAATAATTATTCAA
1 TTAATAATTATTATTCAA
* *
9022 TAAAATAATTATTATTTAA
1 T-TAATAATTATTATTCAA
9041 TTAATTAATTTATTA
1 TTAA-TAA-TTATTA
9056 ATTTCAGCCC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 3 0.11
19 18 0.67
20 6 0.22
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAATAATTATTATTCAA
Found at i:9426 original size:13 final size:13
Alignment explanation
Indices: 9408--9446 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
9398 AAGGTAACAA
9408 CAAAAATCATCAC
1 CAAAAATCATCAC
9421 CAAAAATCATCAC
1 CAAAAATCATCAC
9434 CAAAAATCATCAC
1 CAAAAATCATCAC
9447 TCATGCCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAATCATCAC
Done.