Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016661.1 Corchorus olitorius cultivar O-4 contig16694, 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: 8626
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Found at i:1172 original size:36 final size:36
Alignment explanation
Indices: 1125--1194 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
1115 TTCAATAACC
* * *
1125 TTACATCTTTTGTGATTTTGGTTATCTTATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
1161 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
1195 CCAAAATCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.20, C:0.10, G:0.09, T:0.61
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:2093 original size:204 final size:199
Alignment explanation
Indices: 1710--2117 Score: 699
Period size: 204 Copynumber: 2.0 Consensus size: 199
1700 GCTTAATAAC
1710 TTTATCAATGGTGAATGTTATTATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
1 TTTATCAATGGTGAATGTTATTATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
* **
1775 ATACAACACATTATTATTATATATAAAACTATACAAAAAAAAGTAGTTTAACATTAGTGGTTGAT
66 ATACAACACATTACTATTATATATAAAACTATACAAAAAAAAGTAGTCGAACATTAGTGGTTGAT
*
1840 TTATTAAATAAAATTATATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCAG
131 TTATTAAATAAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATCAG
1905 ATTTA
195 ATTTA
1910 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATT-ATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
*
1975 GATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTCGAACATTAGTGGT
65 GATACAACACATTACTATTATATATA-A-AACTATA-CAAAAAAAAGTAGTCGAACATTAGTGGT
* *
2040 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGTT
127 TGATTTATTAAATAAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT
*
2105 CCGATTTA
192 CAGATTTA
2113 TTTAT
1 TTTAT
2118 TATTAAGGAA
Statistics
Matches: 196, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
200 22 0.11
201 67 0.34
202 1 0.01
203 23 0.12
204 83 0.42
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (199 bp):
TTTATCAATGGTGAATGTTATTATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
ATACAACACATTACTATTATATATAAAACTATACAAAAAAAAGTAGTCGAACATTAGTGGTTGAT
TTATTAAATAAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCAGA
TTTA
Found at i:2278 original size:38 final size:39
Alignment explanation
Indices: 2228--2305 Score: 131
Period size: 38 Copynumber: 2.0 Consensus size: 39
2218 ACCTAAGAAT
*
2228 TTAATTAATGTAAGTATTTCAGTTATTATA-GTATTACA
1 TTAATTAATGTAAGTATTTCAGTTATTATATATATTACA
*
2266 TTAATTAATGTAAGTATTTTAGTTATTATATATATTACA
1 TTAATTAATGTAAGTATTTCAGTTATTATATATATTACA
2305 T
1 T
2306 AGGAATTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
38 29 0.78
39 8 0.22
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.50
Consensus pattern (39 bp):
TTAATTAATGTAAGTATTTCAGTTATTATATATATTACA
Found at i:2293 original size:21 final size:21
Alignment explanation
Indices: 2231--2293 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
2221 TAAGAATTTA
2231 ATTAATGTAAGTATTTCAGTT
1 ATTAATGTAAGTATTTCAGTT
*
2252 ATT-A--T-AGTATTACA-TT
1 ATTAATGTAAGTATTTCAGTT
*
2268 AATTAATGTAAGTATTTTAGTT
1 -ATTAATGTAAGTATTTCAGTT
2290 ATTA
1 ATTA
2294 TATATATTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
16 2 0.06
17 11 0.33
18 2 0.06
20 2 0.06
21 14 0.42
22 2 0.06
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.49
Consensus pattern (21 bp):
ATTAATGTAAGTATTTCAGTT
Found at i:2968 original size:21 final size:21
Alignment explanation
Indices: 2944--3006 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
2934 AAGAAATTTA
2944 ATTAATGTAAGTATTTCAGTT
1 ATTAATGTAAGTATTTCAGTT
*
2965 ATT-A--T-AGTATTACA-TT
1 ATTAATGTAAGTATTTCAGTT
*
2981 AATTAATGTAAGTATTTTAGTT
1 -ATTAATGTAAGTATTTCAGTT
3003 ATTA
1 ATTA
3007 TATATATTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
16 2 0.06
17 11 0.33
18 2 0.06
20 2 0.06
21 14 0.42
22 2 0.06
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.49
Consensus pattern (21 bp):
ATTAATGTAAGTATTTCAGTT
Found at i:2991 original size:38 final size:39
Alignment explanation
Indices: 2941--3018 Score: 131
Period size: 38 Copynumber: 2.0 Consensus size: 39
2931 CCTAAGAAAT
*
2941 TTAATTAATGTAAGTATTTCAGTTATTATA-GTATTACA
1 TTAATTAATGTAAGTATTTCAGTTATTATATATATTACA
*
2979 TTAATTAATGTAAGTATTTTAGTTATTATATATATTACA
1 TTAATTAATGTAAGTATTTCAGTTATTATATATATTACA
3018 T
1 T
3019 AGGAATTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
38 29 0.78
39 8 0.22
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.50
Consensus pattern (39 bp):
TTAATTAATGTAAGTATTTCAGTTATTATATATATTACA
Done.