Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012781.1 Corchorus olitorius cultivar O-4 contig12814, 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: 6960
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Found at i:1114 original size:11 final size:11
Alignment explanation
Indices: 1100--1139 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
1090 TTTTCATATA
1100 TTTTTTCCCTT
1 TTTTTTCCCTT
1111 TTTTTT-CCTT
1 TTTTTTCCCTT
1121 TTCTTTTCCCTCT
1 TT-TTTTCCCT-T
1134 TTTTTT
1 TTTTTT
1140 TTTCTTCTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 6 0.23
11 10 0.38
12 7 0.27
13 3 0.12
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTTTCCCTT
Found at i:2119 original size:51 final size:49
Alignment explanation
Indices: 2060--2288 Score: 159
Period size: 51 Copynumber: 4.6 Consensus size: 49
2050 AAAGTGGCAT
*
2060 TTTTATTTACAAATTATTTCAAAGTTTC-ATCTTTTAGCTTAAACATTTCA
1 TTTTATTTACAAATTA-TTCAAAG-TTCAATCTTTTAGCTTAAAGATTTCA
* * * * *
2110 TCTTTATTTACGAATTA---AAAGTTTC-ATCTTTTGGCTTAATGATTCCGT
1 T-TTTATTTACAAATTATTCAAAG-TTCAATCTTTTAGCTTAAAGATTTC-A
* *
2158 TTTTATTTACAAATTAATTAAAAGTTCAATCTTTTAG-TTCAAAGATCTCA
1 TTTTATTTACAAATT-ATTCAAAGTTCAATCTTTTAGCTT-AAAGATTTCA
* * * *
2208 TTTTAAATTACAAATTAATCACAAGTTCAATCTTTTAG-TTCGAAGA-TCCGA
1 TTTT-ATTTACAAATTATTCA-AAGTTCAATCTTTTAGCTT-AAAGATTTC-A
* *
2259 TTTTTAATTACAAATTAATCACAAGTTCAA
1 -TTTTATTTACAAATTATTCA-AAGTTCAA
2289 CCATTTAGTT
Statistics
Matches: 149, Mismatches: 18, Indels: 23
0.78 0.09 0.12
Matches are distributed among these distances:
47 38 0.26
48 2 0.01
50 14 0.09
51 91 0.61
52 4 0.03
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.44
Consensus pattern (49 bp):
TTTTATTTACAAATTATTCAAAGTTCAATCTTTTAGCTTAAAGATTTCA
Found at i:2163 original size:47 final size:47
Alignment explanation
Indices: 2061--2174 Score: 129
Period size: 47 Copynumber: 2.3 Consensus size: 47
2051 AAGTGGCATT
*
2061 TTTATTTACAAATTATTTCAAAGTTTCATCTTTTAGCTTAAACATTTCATC
1 TTTATTTACAAATTA----AAAGTTTCATCTTTTAGCTTAAACATTCCATC
* * ** * *
2112 TTTATTTACGAATTAAAAGTTTCATCTTTTGGCTTAATGATTCCGTT
1 TTTATTTACAAATTAAAAGTTTCATCTTTTAGCTTAAACATTCCATC
2159 TTTATTTACAAATTAA
1 TTTATTTACAAATTAA
2175 TTAAAAGTTC
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
47 41 0.75
51 14 0.25
ACGTcount: A:0.31, C:0.13, G:0.07, T:0.49
Consensus pattern (47 bp):
TTTATTTACAAATTAAAAGTTTCATCTTTTAGCTTAAACATTCCATC
Found at i:2296 original size:51 final size:51
Alignment explanation
Indices: 2153--2301 Score: 212
Period size: 51 Copynumber: 2.9 Consensus size: 51
2143 GCTTAATGAT
* * *
2153 TCCG-TTTTTATTTACAAATTAATTAAAAGTTCAATCTTTTAGTTCAAAGA
1 TCCGATTTTTAATTACAAATTAATCACAAGTTCAATCTTTTAGTTCAAAGA
* *
2203 TCTC-ATTTTAAATTACAAATTAATCACAAGTTCAATCTTTTAGTTCGAAGA
1 TC-CGATTTTTAATTACAAATTAATCACAAGTTCAATCTTTTAGTTCAAAGA
* *
2254 TCCGATTTTTAATTACAAATTAATCACAAGTTCAACCATTTAGTTCAA
1 TCCGATTTTTAATTACAAATTAATCACAAGTTCAATCTTTTAGTTCAA
2302 GGCTTTACTT
Statistics
Matches: 87, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
50 3 0.03
51 84 0.97
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.40
Consensus pattern (51 bp):
TCCGATTTTTAATTACAAATTAATCACAAGTTCAATCTTTTAGTTCAAAGA
Found at i:2364 original size:49 final size:52
Alignment explanation
Indices: 2311--2424 Score: 146
Period size: 50 Copynumber: 2.2 Consensus size: 52
2301 AGGCTTTACT
*
2311 TTTATTATAAATTTACCC-AAGTTTCAATCTTTCTC-ATCCAAAGATTA-A-A
1 TTTATTATAAATTTACCCGAAGTTCCAATCTTTCTCAAT-CAAAGATTACATA
* * *
2360 TTTATTATTACTTTACCCGAAGTTCCAATCTTTTTCAATCAAAGATTACATA
1 TTTATTATAAATTTACCCGAAGTTCCAATCTTTCTCAATCAAAGATTACATA
*
2412 TTTATTATGAATT
1 TTTATTATAAATT
2425 CATTAAAGCC
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
49 16 0.29
50 24 0.44
51 3 0.05
52 12 0.22
ACGTcount: A:0.34, C:0.17, G:0.05, T:0.44
Consensus pattern (52 bp):
TTTATTATAAATTTACCCGAAGTTCCAATCTTTCTCAATCAAAGATTACATA
Found at i:3858 original size:16 final size:16
Alignment explanation
Indices: 3823--3859 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
3813 ACTACTGGCC
*
3823 GAATCAAGCCAAGGCA
1 GAATCAAGCCAAAGCA
*
3839 GAATCAAGCCAAAGCG
1 GAATCAAGCCAAAGCA
3855 GAATC
1 GAATC
3860 TAATCTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.24, G:0.24, T:0.08
Consensus pattern (16 bp):
GAATCAAGCCAAAGCA
Found at i:5115 original size:2 final size:2
Alignment explanation
Indices: 5108--5134 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5098 CCTAATTAAT
5108 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5135 TTAATGTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6136 original size:13 final size:13
Alignment explanation
Indices: 6118--6142 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6108 TTGGAATTCC
6118 AAATAATATTTAT
1 AAATAATATTTAT
6131 AAATAATATTTA
1 AAATAATATTTA
6143 GAACATTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Done.