Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010883.1 Corchorus olitorius cultivar O-4 contig10915, 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: 6506
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:1015 original size:43 final size:43
Alignment explanation
Indices: 967--1206 Score: 214
Period size: 52 Copynumber: 5.0 Consensus size: 43
957 AAAGAAGAAG
967 AAGTATTCAATTTAAGTTTTTCAAATTGGGAAAGTTCCCATCA
1 AAGTATTCAATTTAAGTTTTTCAAATTGGGAAAGTTCCCATCA
*
1010 AAGTATTCAATTTAAATTTTTCAAATTGGGAAAGTTCCCATCAATTTTCA
1 AAGTATTCAATTTAAGTTTTTCAAATTGGGAAAGTT-CC--C-A---TCA
1060 AAGTATTCAATTTAAGTTTTTCAAATTGGGAAAGTTCCCATCAA
1 AAGTATTCAATTTAAGTTTTTCAAATTGGGAAAGTTCCCATC-A
1104 TTTTTAGAGTATTCAATTT-AGCTCCTTTTCAAATTGGGAAAGTTCCAATCAATTTTCA
1 -----A-AGTATTCAATTTAAG-T--TTTTCAAATTGGGAAAGTTCC---C-A---TCA
1162 AAGTATTCAATTT-AGCTGGTTTTCAAATTGGGAAAGTTCCCATCA
1 AAGTATTCAATTTAAG-T--TTTTCAAATTGGGAAAGTTCCCATCA
1207 GTTTTCAAAG
Statistics
Matches: 169, Mismatches: 4, Indels: 46
0.77 0.02 0.21
Matches are distributed among these distances:
43 37 0.22
44 3 0.02
45 3 0.02
46 2 0.01
47 2 0.01
48 1 0.01
49 6 0.04
50 51 0.30
52 58 0.34
53 1 0.01
55 1 0.01
56 1 0.01
58 1 0.01
59 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (43 bp):
AAGTATTCAATTTAAGTTTTTCAAATTGGGAAAGTTCCCATCA
Found at i:1066 original size:50 final size:51
Alignment explanation
Indices: 1007--1264 Score: 360
Period size: 52 Copynumber: 5.0 Consensus size: 51
997 AAAGTTCCCA
**
1007 TCAAAGTATTCAATTTAAAT-TTTTCAAATTGGGAAAGTTCCCATCAATTT
1 TCAAAGTATTCAATTTAGCTGTTTTCAAATTGGGAAAGTTCCCATCAATTT
1057 TCAAAGTATTCAATTTAAG-T-TTTTCAAATTGGGAAAGTTCCCATCAATTT
1 TCAAAGTATTCAATTT-AGCTGTTTTCAAATTGGGAAAGTTCCCATCAATTT
* * * *
1107 TTAGAGTATTCAATTTAGCTCCTTTTCAAATTGGGAAAGTTCCAATCAATTT
1 TCAAAGTATTCAATTTAGCT-GTTTTCAAATTGGGAAAGTTCCCATCAATTT
*
1159 TCAAAGTATTCAATTTAGCTGGTTTTCAAATTGGGAAAGTTCCCATCAGTTT
1 TCAAAGTATTCAATTTAGCT-GTTTTCAAATTGGGAAAGTTCCCATCAATTT
* * *
1211 TCAAAGTGTTCAATTTAGCTGGTTTTTAAATTGGGAAAGTTCCCACCAGATTT
1 TCAAAGTATTCAATTTAGCT-GTTTTCAAATTGGGAAAGTTCCCATCA-ATTT
1264 T
1 T
1265 AGTTTTCAAT
Statistics
Matches: 189, Mismatches: 14, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
49 2 0.01
50 62 0.33
51 1 0.01
52 120 0.63
53 4 0.02
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (51 bp):
TCAAAGTATTCAATTTAGCTGTTTTCAAATTGGGAAAGTTCCCATCAATTT
Found at i:1245 original size:104 final size:102
Alignment explanation
Indices: 967--1253 Score: 378
Period size: 104 Copynumber: 2.9 Consensus size: 102
957 AAAGAAGAAG
*
967 AAGTATTCAATTTAAGTTTTTCAAATTGGGAAAGTT-CC--C-A---TCAAAGTATTCAATTTAA
1 AAGTATTCAATTTAAGTTTTTCAAATTGGGAAAGTTCCCATCAATTTTCAAAGTATTCAATTTAG
* * *
1025 AT--TTTTCAAATTGGGAAAGTTCCCATCAATTTTCA
66 CTCCTTTTTAAATTGGGAAAGTTCCAATCAATTTTCA
* *
1060 AAGTATTCAATTTAAGTTTTTCAAATTGGGAAAGTTCCCATCAATTTTTAGAGTATTCAATTTAG
1 AAGTATTCAATTTAAGTTTTTCAAATTGGGAAAGTTCCCATCAATTTTCAAAGTATTCAATTTAG
*
1125 CTCCTTTTCAAATTGGGAAAGTTCCAATCAATTTTCA
66 CTCCTTTTTAAATTGGGAAAGTTCCAATCAATTTTCA
* *
1162 AAGTATTCAATTT-AGCTGGTTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAAGTGTTCAATT
1 AAGTATTCAATTTAAG-T--TTTTCAAATTGGGAAAGTTCCCATCAATTTTCAAAGTATTCAATT
**
1226 TAGCTGGTTTTTAAATTGGGAAAGTTCC
63 TAGCTCCTTTTTAAATTGGGAAAGTTCC
1254 CACCAGATTT
Statistics
Matches: 170, Mismatches: 12, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
93 36 0.21
94 2 0.01
96 1 0.01
97 1 0.01
100 16 0.09
101 2 0.01
102 46 0.27
104 66 0.39
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (102 bp):
AAGTATTCAATTTAAGTTTTTCAAATTGGGAAAGTTCCCATCAATTTTCAAAGTATTCAATTTAG
CTCCTTTTTAAATTGGGAAAGTTCCAATCAATTTTCA
Found at i:6165 original size:74 final size:73
Alignment explanation
Indices: 6070--6214 Score: 211
Period size: 74 Copynumber: 2.0 Consensus size: 73
6060 TTATCTGGAC
* * * * *
6070 TGTGAGCAAAGGAATGGTGAGTTTTGATTAAAAGATGTTTCAAAATCAGTTTTTAGTCAAAGCAA
1 TGTGAGCAAAGGAATGATGAGTTTTAATCAAAAAATGTTTCAAAATCAG-TTTTAGTCAAACCAA
*
6135 TGGTTTCGG
65 TGATTTCGG
6144 TGTGAGCAAAGGGAA-GATGAGTTTTAATCAAAAAATGTTTCAAAATCAGTTTTAGTCAAACCAA
1 TGTGAGCAAA-GGAATGATGAGTTTTAATCAAAAAATGTTTCAAAATCAGTTTTAGTCAAACCAA
6208 TGATTTC
65 TGATTTC
6215 AAGGTGACTG
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
73 20 0.31
74 40 0.62
75 4 0.06
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.32
Consensus pattern (73 bp):
TGTGAGCAAAGGAATGATGAGTTTTAATCAAAAAATGTTTCAAAATCAGTTTTAGTCAAACCAAT
GATTTCGG
Done.