Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012896.1 Corchorus olitorius cultivar O-4 contig12929, 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: 2815
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Found at i:1847 original size:2 final size:2
Alignment explanation
Indices: 1840--1869 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1830 TTATATGCGA
1840 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
1870 TGTATTGCAT
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:2406 original size:235 final size:220
Alignment explanation
Indices: 1957--2815 Score: 1174
Period size: 235 Copynumber: 3.9 Consensus size: 220
1947 GTTATGCTAT
* * * *
1957 AAATCCAGTATCCCCAAAGTTATATACTTTATACCCAAATAATTTCTCATCATCCCCAAATAATC
1 AAATTCAGTATCCCCAAACTAATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATC
* * *
2022 ATAAGCACCATCCCCAAACTT-TTTAGAGATTAACA-ATTTT-TTATATACCCAAAATTGGCTTT
66 ATATGCACCATCCCCAAA-TTCTTTAGAGATTGACATTTTTTCTTATATACCCAAAATTGGCTTT
* * * * *
2084 AAACGTGTTTTGAT-CATATTTTCATCCTAATTAATTGAAT-AAACACAGTCCATATGAATTTAG
130 AAAAGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAAAC-CCGTCTATATGAATTTAG
*
2147 TGCCATCAAATAATTAAACAAAATGCA
194 TGCCATCTAATAATTAAACAAAATGCA
* *
2174 AAATTCAGTATCCCCAAATTAATATACTTTATACCTAAATCATTTCTCATCATCCCCAAATAATC
1 AAATTCAGTATCCCCAAACTAATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATC
* *
2239 ATATGCACCATCCCCAAATTTTTTAGAGATTGGCATTTTTTCTTATATACCCAAATTCTGTAGAG
66 ATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTTCTTATATACCC--A------A-A-
* *
2304 ATTGGCTTTAAAAAGTGCTTTAATCAATATTTTCATCCTAATTAATTGAATAAACCCCGTCTATA
121 ATTGGCTTT-AAAAGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAAACCCGTC----
*
2369 TATATGATTTTAGTGCCATCTAATAATTAAACAAAATGC-
181 TATATGAATTTAGTGCCATCTAATAATTAAACAAAATGCA
* *
2408 AAATTCAGTATCCCCAAAGTAATATACTTTAAACCCAAATCATTTCTCATCATCCCCAAAATAAT
1 AAATTCAGTATCCCCAAACTAATATACTTTATACCCAAATCATTTCTCATCATCCCC-AAATAAT
* *
2473 CATATGCACCATCCCCAAATTCATTAGAGATTCACATTTTTTCTTATATACCCAAAATTGGCTTT
65 CATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTTCTTATATACCCAAAATTGGCTTT
* *
2538 AAAAAGTGTTTTAATCCATATTTTCATCCTAATTAATTGAATAAAACTCGTCTATATGAATTTAG
130 -AAAAGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAAACCCGTCTATATGAATTTAG
* *
2603 TGTCATCTAATAATGAAACAAAATGCA
194 TGCCATCTAATAATTAAACAAAATGCA
* *
2630 AAATTCAGCATCCCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATC
1 AAATTCAGTATCCCCAAACTAATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATC
* * * *
2695 ATAAGAACCATACCCAAATTCTTTAGAGATTGACAATTTTT-TTATATACCCAAAATTGGCTTTA
66 ATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTTCTTATATACCCAAAATTGGCTTTA
* *
2759 GACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAAACCCGTCTATATGA
131 AAAGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAAACCCGTCTATATGA
Statistics
Matches: 574, Mismatches: 46, Indels: 42
0.87 0.07 0.06
Matches are distributed among these distances:
216 2 0.00
217 89 0.16
218 4 0.01
219 64 0.11
220 22 0.04
221 80 0.14
222 53 0.09
225 57 0.10
226 1 0.00
227 2 0.00
228 1 0.00
229 9 0.02
230 11 0.02
231 29 0.05
232 3 0.01
233 1 0.00
234 54 0.09
235 92 0.16
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.35
Consensus pattern (220 bp):
AAATTCAGTATCCCCAAACTAATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATC
ATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTTCTTATATACCCAAAATTGGCTTTA
AAAGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAAACCCGTCTATATGAATTTAGTG
CCATCTAATAATTAAACAAAATGCA
Done.