Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022843.1 Corchorus olitorius cultivar O-4 contig22876, 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: 16474
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Found at i:4041 original size:19 final size:19
Alignment explanation
Indices: 4017--4059 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
4007 TCTAGAAATG
4017 GAAAAAGAG-AAAAAAATCA
1 GAAAAA-AGTAAAAAAATCA
*
4036 GAAAAAAGTGAAAAAATCA
1 GAAAAAAGTAAAAAAATCA
4055 GAAAA
1 GAAAA
4060 TCAAAAGAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.09
19 20 0.91
ACGTcount: A:0.72, C:0.05, G:0.16, T:0.07
Consensus pattern (19 bp):
GAAAAAAGTAAAAAAATCA
Found at i:7677 original size:16 final size:16
Alignment explanation
Indices: 7656--7687 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
7646 CCCAAACCTG
7656 AAAATGACCCAAATCC
1 AAAATGACCCAAATCC
*
7672 AAAATGACCCGAATCC
1 AAAATGACCCAAATCC
7688 GATCAACACG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.31, G:0.09, T:0.12
Consensus pattern (16 bp):
AAAATGACCCAAATCC
Found at i:9380 original size:15 final size:16
Alignment explanation
Indices: 9327--9378 Score: 81
Period size: 16 Copynumber: 3.3 Consensus size: 16
9317 AACCGAAAAC
9327 GACCCAACCCATAATT
1 GACCCAACCCATAATT
9343 GACCCAACCCATAATT
1 GACCCAACCCATAATT
9359 GACCCGAACCCA-AA-T
1 GACCC-AACCCATAATT
9374 GACCC
1 GACCC
9379 GACATTTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
15 6 0.17
16 23 0.66
17 6 0.17
ACGTcount: A:0.37, C:0.40, G:0.10, T:0.13
Consensus pattern (16 bp):
GACCCAACCCATAATT
Found at i:10476 original size:40 final size:40
Alignment explanation
Indices: 10384--10461 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
10374 ATAACTAGGA
* * *
10384 GCTAAATCTAGATTTAATTTATTACTTTAATTATTAGGGG
1 GCTAAACCTGGATTTAATTTATTACCTTAATTATTAGGGG
*
10424 GCTAAACCTGGATTTAATTTATTTCCTTAATTATTAGG
1 GCTAAACCTGGATTTAATTTATTACCTTAATTATTAGG
10462 AGGGTCAAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (40 bp):
GCTAAACCTGGATTTAATTTATTACCTTAATTATTAGGGG
Found at i:16261 original size:67 final size:68
Alignment explanation
Indices: 16076--16376 Score: 305
Period size: 67 Copynumber: 4.5 Consensus size: 68
16066 TTTTCTCTTC
* * * *
16076 CCAGAAATACCCTTTCGGTCGAAGGGTCA-TTTTCGTC-TTTTGCATTTAAGTTTATTATTTTCT
1 CCAGAAATACCCTTTCGGTCAAAGGGTCAGTTTT-GTCTTTTTGCATTCAAGTTTAGTAGTTT-T
**
16139 CTTTT
64 GATTT
* * * *
16144 CAAAAAATACCATTTCGGTCAAAGGGGTCAGTCTTGTCTTTTTGCATTCAAGTTTAGTA-TTTTG
1 CCAGAAATACCCTTTCGGTCAAA-GGGTCAGTTTTGTCTTTTTGCATTCAAGTTTAGTAGTTTTG
16208 ATTT
65 ATTT
* * *
16212 CCAGAAATACCCTTTCGGTCAAAGGGTCGGTTTTGTCTTTTTGTATTCAATTTTAGTA-TTTTCG
1 CCAGAAATACCCTTTCGGTCAAAGGGTCAGTTTTGTCTTTTTGCATTCAAGTTTAGTAGTTTT-G
*
16276 -TTC
65 ATTT
* ** *
16279 CCAGAGATACCCTTTCGGTTGAAGGGTCAGTTTTGTCTTTTTGTATTC-AGTTT--TAGTTTTGA
1 CCAGAAATACCCTTTCGGTCAAAGGGTCAGTTTTGTCTTTTTGCATTCAAGTTTAGTAGTTTTGA
16341 TTT
66 TTT
* * *
16344 TCA-AAAGTACCCTTTCGGTGAAAAGGTCAGTTT
1 CCAGAAA-TACCCTTTCGGTCAAAGGGTCAGTTT
16377 CATCAGGTTG
Statistics
Matches: 198, Mismatches: 28, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
64 5 0.03
65 31 0.16
66 4 0.02
67 81 0.41
68 44 0.22
69 12 0.06
70 21 0.11
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.44
Consensus pattern (68 bp):
CCAGAAATACCCTTTCGGTCAAAGGGTCAGTTTTGTCTTTTTGCATTCAAGTTTAGTAGTTTTGA
TTT
Found at i:16423 original size:134 final size:134
Alignment explanation
Indices: 16076--16441 Score: 334
Period size: 134 Copynumber: 2.7 Consensus size: 134
16066 TTTTCTCTTC
* * * * * * * *
16076 CCAGAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTT-TTGCATTTAAGTTTATTATTTTCTC
1 CCAGAAATACCCTTTCGGTCAAAAGGTCAGTTTCATCTTGTTGCATTCAAGTCTAGTA-CTT-TC
* * *
16140 TTTTCAAAAAATACCATTTCGGTCAAAGGGGTCAGTCTTGTCTTTTTGCATTCAAGTTTAGTATT
64 TTTCCAAAGAATACCCTTTCGGTCAAAGGGGTCAGTCTTGTCTTTTTGCATTCAAGTTTAG-ATT
16205 TTGATTT
128 TTGATTT
* * ** * * * * * *
16212 CCAGAAATACCCTTTCGGTCAAAGGGTCGGTTTTGTCTTTTTGTATTCAATTTTAGTATTTTCGT
1 CCAGAAATACCCTTTCGGTCAAAAGGTCAGTTTCATCTTGTTGCATTCAAGTCTAGTACTTTCTT
* ** * *
16277 TCC-CAGAGATACCCTTTCGGTTGAA-GGGTCAGTTTTGTCTTTTTGTATTC-AGTTTTAG-TTT
66 TCCAAAGA-ATACCCTTTCGGTCAAAGGGGTCAGTCTTGTCTTTTTGCATTCAAG-TTTAGATTT
16338 TGATTT
129 TGATTT
* * *
16344 TCA-AAAGTACCCTTTCGGTGAAAAGGTCAGTTTCATCAGGTTGTTGCATTTAAGTCTAGT-CTT
1 CCAGAAA-TACCCTTTCGGTCAAAAGGTCAGTTTCATC---TTGTTGCATTCAAGTCTAGTACTT
16407 TCTTTCCAAAGAATACCCTTTCGGTC-AAGGGGTCA
62 TCTTTCCAAAGAATACCCTTTCGGTCAAAGGGGTCA
16442 TTTATGTCAT
Statistics
Matches: 189, Mismatches: 32, Indels: 20
0.78 0.13 0.08
Matches are distributed among these distances:
131 3 0.02
132 36 0.19
133 4 0.02
134 57 0.30
135 37 0.20
136 38 0.20
137 14 0.07
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (134 bp):
CCAGAAATACCCTTTCGGTCAAAAGGTCAGTTTCATCTTGTTGCATTCAAGTCTAGTACTTTCTT
TCCAAAGAATACCCTTTCGGTCAAAGGGGTCAGTCTTGTCTTTTTGCATTCAAGTTTAGATTTTG
ATTT
Done.