Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012582.1 Corchorus olitorius cultivar O-4 contig12615, 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: 10527
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Found at i:1013 original size:18 final size:18
Alignment explanation
Indices: 990--1044 Score: 92
Period size: 18 Copynumber: 3.1 Consensus size: 18
980 GTCAATCCTA
990 GGGAACTAACTTTGAATG
1 GGGAACTAACTTTGAATG
*
1008 GGGAACTGACTTTGAATG
1 GGGAACTAACTTTGAATG
*
1026 GGGAACTAGCTTTGAATG
1 GGGAACTAACTTTGAATG
1044 G
1 G
1045 ACTGACTTGG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.29, C:0.11, G:0.33, T:0.27
Consensus pattern (18 bp):
GGGAACTAACTTTGAATG
Found at i:2238 original size:15 final size:16
Alignment explanation
Indices: 2220--2253 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2210 TTTCCCAAGG
*
2220 TTATTTTTTTTAA-AA
1 TTATATTTTTTAATAA
2235 TTATATTTTTTAATAA
1 TTATATTTTTTAATAA
2251 TTA
1 TTA
2254 ATGGTCAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATATTTTTTAATAA
Found at i:4082 original size:42 final size:42
Alignment explanation
Indices: 4023--4113 Score: 173
Period size: 42 Copynumber: 2.2 Consensus size: 42
4013 TTTGCAGCCA
*
4023 TAATTGATGATGGGGAGCACTCTAATTGGCCATTAAAGATGC
1 TAATTAATGATGGGGAGCACTCTAATTGGCCATTAAAGATGC
4065 TAATTAATGATGGGGAGCACTCTAATTGGCCATTAAAGATGC
1 TAATTAATGATGGGGAGCACTCTAATTGGCCATTAAAGATGC
4107 TAATTAA
1 TAATTAA
4114 AAATACACTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (42 bp):
TAATTAATGATGGGGAGCACTCTAATTGGCCATTAAAGATGC
Found at i:4790 original size:11 final size:11
Alignment explanation
Indices: 4750--4783 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
4740 AGGAGTAGGG
4750 TCCTTCCTAGC
1 TCCTTCCTAGC
4761 TCCTTCCTAGC
1 TCCTTCCTAGC
4772 TCCTTCCTAGC
1 TCCTTCCTAGC
4783 T
1 T
4784 TTTTCCTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.09, C:0.44, G:0.09, T:0.38
Consensus pattern (11 bp):
TCCTTCCTAGC
Found at i:9915 original size:40 final size:40
Alignment explanation
Indices: 9862--10527 Score: 630
Period size: 41 Copynumber: 16.8 Consensus size: 40
9852 CAGGAAGATA
*
9862 TTGTTTACTTTTCCAGTTTGCCCTTCCCTACCGGAAGGTG
1 TTGTTTACTTTTCCAGTTTGCCCTTCCCCACCGGAAGGTG
* * ** * *
9902 TTGTTTGCCTTTCCCAGTTTGCCCTTCCGGATCGGAAGTTG
1 TTGTTT-ACTTTTCCAGTTTGCCCTTCCCCACCGGAAGGTG
* *
9943 TTGTTTAC-TTTCCTGTTTTGCCCTTCCCCAGCGGAAGGTG
1 TTGTTTACTTTTCCAG-TTTGCCCTTCCCCACCGGAAGGTG
* **
9983 TTGTTT--TTATCCCTAGTTTGCCCTTCCCCACTAGAAGGTG
1 TTGTTTACTT-TTCC-AGTTTGCCCTTCCCCACCGGAAGGTG
* * **
10023 TTGTTTACTTTTCCCAGTTTGCCTTTCCCGACCAAAAGGTG
1 TTGTTTACTTTT-CCAGTTTGCCCTTCCCCACCGGAAGGTG
* * * *
10064 TTATTTACTTTTCCTAGTTTGTCCTTCCCTACCGAAAGGTG
1 TTGTTTACTTTTCC-AGTTTGCCCTTCCCCACCGGAAGGTG
* *
10105 TTGTTTACTTTTCCCAGTTTGCCCTTCCCGACCGGAAGATG
1 TTGTTTACTTTT-CCAGTTTGCCCTTCCCCACCGGAAGGTG
* * * * *
10146 TTGTTTACCTTT---GTTTGCGCTTCTCGACCGGAAGGCG
1 TTGTTTACTTTTCCAGTTTGCCCTTCCCCACCGGAAGGTG
* * *
10183 TTGTTTACTTTTCCAGTTTGTCATTCCCTACCGGAAGGTG
1 TTGTTTACTTTTCCAGTTTGCCCTTCCCCACCGGAAGGTG
* * *
10223 TTGTTTA-TTTTCCTGTTTTGTCTTTCCCCACCGGAAGGTG
1 TTGTTTACTTTTCCAG-TTTGCCCTTCCCCACCGGAAGGTG
* * ** *
10263 TTCTTTTC-AATCTC-GTATTGCCCTTCCCCATCGGAAGGTG
1 TTGTTTACTTTTC-CAGT-TTGCCCTTCCCCACCGGAAGGTG
10303 TTGTTTACTTTTCCAGTTTG-------CCACCGGAAGGTG
1 TTGTTTACTTTTCCAGTTTGCCCTTCCCCACCGGAAGGTG
* **
10336 TTGTTTACTTTTCCAGTTTGCCTTTCCCCAATGGAAGGTG
1 TTGTTTACTTTTCCAGTTTGCCCTTCCCCACCGGAAGGTG
*
10376 TTGTTTACTTTTCCCAGTTTGCCCTTCCCCGCCGGAAGGTG
1 TTGTTTACTTTT-CCAGTTTGCCCTTCCCCACCGGAAGGTG
* * *
10417 TTGTTTACTTTTTCCAGTTTACCCTTCCCCACGGGAAGATG
1 TTGTTTAC-TTTTCCAGTTTGCCCTTCCCCACCGGAAGGTG
* * * *
10458 TTGTTT--TATTCCTGTTTTGCCCTTCCCAAACGGAAGGTG
1 TTGTTTACTTTTCCAG-TTTGCCCTTCCCCACCGGAAGGTG
*
10497 TTTTTTACTTTTCCCAGTTTGCCCTTCCCCA
1 TTGTTTACTTTT-CCAGTTTGCCCTTCCCCA
Statistics
Matches: 513, Mismatches: 81, Indels: 63
0.78 0.12 0.10
Matches are distributed among these distances:
33 32 0.06
37 32 0.06
38 6 0.01
39 38 0.07
40 174 0.34
41 218 0.42
42 13 0.03
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.41
Consensus pattern (40 bp):
TTGTTTACTTTTCCAGTTTGCCCTTCCCCACCGGAAGGTG
Found at i:10336 original size:33 final size:33
Alignment explanation
Indices: 10294--10398 Score: 129
Period size: 33 Copynumber: 2.9 Consensus size: 33
10284 CCTTCCCCAT
10294 CGGAAGGTGTTGTTTACTTTTCCAGTTTGCCAC
1 CGGAAGGTGTTGTTTACTTTTCCAGTTTGCCAC
*
10327 CGGAAGGTGTTGTTTACTTTTCCAGTTTGCCTTTCCC
1 CGGAAGGTGTTGTTTACTTTTCCAGTTTG-C---CAC
10364 CAATGGAAGGTGTTGTTTACTTTTCCCAGTTTGCC
1 C---GGAAGGTGTTGTTTACTTTT-CCAGTTTGCC
10399 CTTCCCCGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 12
0.83 0.01 0.16
Matches are distributed among these distances:
33 29 0.46
34 1 0.02
37 4 0.06
40 21 0.33
41 8 0.13
ACGTcount: A:0.14, C:0.22, G:0.23, T:0.41
Consensus pattern (33 bp):
CGGAAGGTGTTGTTTACTTTTCCAGTTTGCCAC
Found at i:10346 original size:153 final size:157
Alignment explanation
Indices: 9862--10527 Score: 550
Period size: 162 Copynumber: 4.2 Consensus size: 157
9852 CAGGAAGATA
* * * * * *
9862 TTGTTTACTTTTCCAGTTTGCCCTTCCCTACCGGAAGGTGTTGTTTGCCTTTCCCAGTTTGCCCT
1 TTGTTTACTTTTCCAGTTTGCCTTTCCCCACCGGAAGGTGTTGTTT-ACTTTTCCTGTTTGTCCT
** * * * * * * *
9927 TCCGGATCGGAAGTTGTTGTTTACT--TTCCTGTTTTGCCCTTCCCCAGCGGAAGGTGTTGTTTT
65 TCCCCACCGGAAGGTGTTCTTTACTAATCCCAG-TTTGCCCTTCCCCACCGGAAGATGTTG--TT
* * **
9990 TATCCCTAGTTTGCC-CTTCCCCACTAGAAGGTG
127 TA--CCTTGTTT-CCGCTTCTCCACCGGAAGGTG
* ** *
10023 TTGTTTACTTTTCCCAGTTTGCCTTTCCCGACCAAAAGGTGTTATTTACTTTTCCTAGTTTGTCC
1 TTGTTTACTTTT-CCAGTTTGCCTTTCCCCACCGGAAGGTGTTGTTTACTTTTCCT-GTTTGTCC
* * * ** *
10088 TTCCCTACCGAAAGGTGTTGTTTACTTTTCCCAGTTTGCCCTTCCCGACCGGAAGATGTTGTTTA
64 TTCCCCACCGGAAGGTGTTCTTTACTAATCCCAGTTTGCCCTTCCCCACCGGAAGATGTTGTTTA
* * *
10153 CCTTTGTTTGCGCTTCTCGACCGGAAGGCG
129 CC-TTGTTTCCGCTTCTCCACCGGAAGGTG
* * * *
10183 TTGTTTACTTTTCCAGTTTGTCATTCCCTACCGGAAGGTGTTGTTTA-TTTTCCTGTTTTGTCTT
1 TTGTTTACTTTTCCAGTTTGCCTTTCCCCACCGGAAGGTGTTGTTTACTTTTCCTG-TTTGTCCT
* * * *
10247 TCCCCACCGGAAGGTGTTCTTTTC-AATCTC-GTATTGCCCTTCCCCATCGGAAGGTGTTGTTTA
65 TCCCCACCGGAAGGTGTTCTTTACTAATCCCAGT-TTGCCCTTCCCCACCGGAAGATGTTGTTTA
10310 -C-T-TTTCCAG-TT-TGCCACCGGAAGGTG
129 CCTTGTTTCC-GCTTCT-CCACCGGAAGGTG
** * *
10336 TTGTTTACTTTTCCAGTTTGCCTTTCCCCAATGGAAGGTGTTGTTTACTTTTCCCAGTTTGCCCT
1 TTGTTTACTTTTCCAGTTTGCCTTTCCCCACCGGAAGGTGTTGTTTACTTTT-CCTGTTTGTCCT
* * ** * * *
10401 TCCCCGCCGGAAGGTGTTGTTTACTTTTTCCAGTTTACCCTTCCCCACGGGAAGATGTTGTTTTA
65 TCCCCACCGGAAGGTGTTCTTTACTAATCCCAGTTTGCCCTTCCCCACCGGAAGATGTTG-TTTA
*
10466 TTCC-TGTTTTGCC-CTTC-CCAAACGGAAGGTG
129 --CCTTG-TTT-CCGCTTCTCC-ACCGGAAGGTG
* *
10497 TTTTTTACTTTTCCCAGTTTGCCCTTCCCCA
1 TTGTTTACTTTT-CCAGTTTGCCTTTCCCCA
Statistics
Matches: 412, Mismatches: 68, Indels: 49
0.78 0.13 0.09
Matches are distributed among these distances:
152 1 0.00
153 59 0.14
154 33 0.08
155 27 0.07
156 9 0.02
157 31 0.08
158 34 0.08
159 34 0.08
160 32 0.08
161 48 0.12
162 76 0.18
163 24 0.06
164 4 0.01
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.41
Consensus pattern (157 bp):
TTGTTTACTTTTCCAGTTTGCCTTTCCCCACCGGAAGGTGTTGTTTACTTTTCCTGTTTGTCCTT
CCCCACCGGAAGGTGTTCTTTACTAATCCCAGTTTGCCCTTCCCCACCGGAAGATGTTGTTTACC
TTGTTTCCGCTTCTCCACCGGAAGGTG
Done.