Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021579.1 Corchorus olitorius cultivar O-4 contig21612, 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: 3415
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Found at i:154 original size:36 final size:36
Alignment explanation
Indices: 107--176 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
97 TTCAATAACC
* *
107 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
143 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
177 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:571 original size:25 final size:25
Alignment explanation
Indices: 537--626 Score: 171
Period size: 25 Copynumber: 3.6 Consensus size: 25
527 GCATTATACT
537 ACTTTCAACTAATTTTTTTTAGATA
1 ACTTTCAACTAATTTTTTTTAGATA
562 ACTTTCAACTAATTTTTTTTAGATA
1 ACTTTCAACTAATTTTTTTTAGATA
*
587 ACTTTCAACTATTTTTTTTTAGATA
1 ACTTTCAACTAATTTTTTTTAGATA
612 ACTTTCAACTAATTT
1 ACTTTCAACTAATTT
627 AATAACCTTA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 63 1.00
ACGTcount: A:0.31, C:0.13, G:0.03, T:0.52
Consensus pattern (25 bp):
ACTTTCAACTAATTTTTTTTAGATA
Found at i:827 original size:3 final size:3
Alignment explanation
Indices: 819--892 Score: 148
Period size: 3 Copynumber: 24.7 Consensus size: 3
809 GATACAACAC
819 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
867 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
893 ATATAAAACT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1373 original size:39 final size:40
Alignment explanation
Indices: 1319--1399 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
1309 ACACCTAAGA
*
1319 ATTTAATTAATGTAAGCACTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGCACTTCAGTTATTATATATATTAC
* * *
1358 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGCACTTCAGTTATTATATATATTAC
1398 AT
1 AT
1400 AGGAATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 29 0.78
40 8 0.22
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.48
Consensus pattern (40 bp):
ATTTAATTAATGTAAGCACTTCAGTTATTATATATATTAC
Found at i:1630 original size:2 final size:2
Alignment explanation
Indices: 1618--1668 Score: 75
Period size: 2 Copynumber: 25.0 Consensus size: 2
1608 AGTTTAGACT
* *
1618 TA TA TA GTA TA TA GA TA TA GA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1661 TA TA TA TA
1 TA TA TA TA
1669 CTCCCTCCAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1945 original size:2 final size:2
Alignment explanation
Indices: 1940--1969 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1930 GGACAGAGAG
1940 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1970 CTAGTTTTAG
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):
TA
Found at i:2106 original size:21 final size:21
Alignment explanation
Indices: 2032--2108 Score: 91
Period size: 22 Copynumber: 3.6 Consensus size: 21
2022 TATTTTTATG
*
2032 AAATTTTGATAATCACTCTATT
1 AAATTTTGATAATCAC-CTATA
* *
2054 AAATTTTGATAACCACCATATG
1 AAATTTTGATAATCACC-TATA
*
2076 AAATTTTGATAATTACCTATA
1 AAATTTTGATAATCACCTATA
*
2097 AAATTGTGATAA
1 AAATTTTGATAA
2109 ACTCCATAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
21 15 0.31
22 33 0.69
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.39
Consensus pattern (21 bp):
AAATTTTGATAATCACCTATA
Found at i:2116 original size:43 final size:44
Alignment explanation
Indices: 2028--2130 Score: 127
Period size: 43 Copynumber: 2.4 Consensus size: 44
2018 TGAATATTTT
* * *
2028 TATGAAATTTTGATAATCACTCTATTAAATTTTGATAACCACCA
1 TATGAAATTTTGATAATCACTCTATAAAATTGTGATAAACACCA
* *
2072 TATGAAATTTTGATAATTAC-CTATAAAATTGTGATAAACTCCA
1 TATGAAATTTTGATAATCACTCTATAAAATTGTGATAAACACCA
* **
2115 TAAGAAACATTGATAA
1 TATGAAATTTTGATAA
2131 CCTAACTATG
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
43 32 0.63
44 19 0.37
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.36
Consensus pattern (44 bp):
TATGAAATTTTGATAATCACTCTATAAAATTGTGATAAACACCA
Found at i:2189 original size:20 final size:21
Alignment explanation
Indices: 2160--2198 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2150 TAAACTTTCC
2160 TATGAATTTTG-TAATCTTCT
1 TATGAATTTTGATAATCTTCT
*
2180 TATGATTTTTGATAATCTT
1 TATGAATTTTGATAATCTT
2199 TGTGTGAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (21 bp):
TATGAATTTTGATAATCTTCT
Done.