Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022901.1 Corchorus olitorius cultivar O-4 contig22934, 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: 21773
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Found at i:2372 original size:12 final size:12
Alignment explanation
Indices: 2355--2384 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2345 ACCAACAAAG
2355 GCCCAAAAGCAA
1 GCCCAAAAGCAA
2367 GCCCAAAAGCAA
1 GCCCAAAAGCAA
*
2379 GTCCAA
1 GCCCAA
2385 GTACAAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.33, G:0.17, T:0.03
Consensus pattern (12 bp):
GCCCAAAAGCAA
Found at i:2711 original size:28 final size:28
Alignment explanation
Indices: 2680--2743 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
2670 AATGATCGAG
* *
2680 ATGCCCTTGAATGTGCAAAATGA-CCAAA
1 ATGCCCCTGAACGTGC-AAATGACCCAAA
*
2708 ATGCCCCTGGACGTGCAAATGACCCAAA
1 ATGCCCCTGAACGTGCAAATGACCCAAA
2736 ATGCCCCT
1 ATGCCCCT
2744 AGATGACCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 6 0.19
28 26 0.81
ACGTcount: A:0.33, C:0.30, G:0.19, T:0.19
Consensus pattern (28 bp):
ATGCCCCTGAACGTGCAAATGACCCAAA
Found at i:2756 original size:28 final size:27
Alignment explanation
Indices: 2697--2760 Score: 67
Period size: 28 Copynumber: 2.4 Consensus size: 27
2687 TGAATGTGCA
* **
2697 AAATGACCAAAATGCCCCTGGACGTGC
1 AAATGACCAAAATGCCCCTAGACGACC
*
2724 AAATGACCCAAAATGCCCCTAGATGACC
1 AAATGA-CCAAAATGCCCCTAGACGACC
*
2752 TAATG-CCAA
1 AAATGACCAA
2761 TTAAGAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
26 4 0.13
27 6 0.19
28 21 0.68
ACGTcount: A:0.38, C:0.30, G:0.17, T:0.16
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTAGACGACC
Found at i:9981 original size:242 final size:240
Alignment explanation
Indices: 9553--10026 Score: 858
Period size: 242 Copynumber: 2.0 Consensus size: 240
9543 TTCTCGTGAC
9553 CTACTTGAGGAACAAACAATTAGTAGCAAAACTAGAGTGAATCAAAGGTAAGTGATCATAAAACC
1 CTACTTGAGGAACAAACAATTAGTAGCAAAACTAGAGTGAATCAAAGGTAAGTGATCATAAAACC
9618 AAAACAAACCAATTTGCAGCACCCTTATGTCGATGTAAGTAGCTTCAATTTGCTGCAAAATCACA
66 AAAACAAACCAATTTGCAGCACCCTTATGTCGATGTAAGTAGCTTCAATTTGCTGCAAAATCACA
** *
9683 ATCAAACAACACAAATTGCAAATCACCCAATTCAAGCTTAAAATCCTATCTTGTACCATTTATTT
131 ATCAAACAACACAAATTGCAAATCACCCAATTCAAGCTTAAAATCCTATCTTGTACCACCTA--G
9748 TTTTTTAACTTGAAATTGGTGAACTCCAAACTGAACTCTCTTAAATA
194 TTTTTTAACTTGAAATTGGTGAACTCCAAACTGAACTCTCTTAAATA
* *
9795 CTACTTGAGGAACAAACAATTAGTAGCAAAACTAGAGTGAATCAAAGGTAAGTTATCTTAAAACC
1 CTACTTGAGGAACAAACAATTAGTAGCAAAACTAGAGTGAATCAAAGGTAAGTGATCATAAAACC
*
9860 AAAACAAACCAGTTTGCAGCACCCTTATGTCGATGTAAGTAGCTTCAATTTGCTGCAAAATCACA
66 AAAACAAACCAATTTGCAGCACCCTTATGTCGATGTAAGTAGCTTCAATTTGCTGCAAAATCACA
*
9925 ATCAAACAACACAAATTGCAAATCACCCAATTCAAGCTTAAAATCCTATTTTGTACCACCTAGTT
131 ATCAAACAACACAAATTGCAAATCACCCAATTCAAGCTTAAAATCCTATCTTGTACCACCTAGTT
*
9990 TTTTAACTTGAAGTTGGTGAACTCCAAACTGAACTCT
196 TTTTAACTTGAAATTGGTGAACTCCAAACTGAACTCT
10027 TTCAAATTAA
Statistics
Matches: 224, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
240 38 0.17
242 186 0.83
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.28
Consensus pattern (240 bp):
CTACTTGAGGAACAAACAATTAGTAGCAAAACTAGAGTGAATCAAAGGTAAGTGATCATAAAACC
AAAACAAACCAATTTGCAGCACCCTTATGTCGATGTAAGTAGCTTCAATTTGCTGCAAAATCACA
ATCAAACAACACAAATTGCAAATCACCCAATTCAAGCTTAAAATCCTATCTTGTACCACCTAGTT
TTTTAACTTGAAATTGGTGAACTCCAAACTGAACTCTCTTAAATA
Found at i:12267 original size:21 final size:21
Alignment explanation
Indices: 12243--12283 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
12233 CCTTAGGCAA
12243 CTCCAATGAGCTTGAAACTTT
1 CTCCAATGAGCTTGAAACTTT
12264 CTCCAATGAGCTTGAAACTT
1 CTCCAATGAGCTTGAAACTT
12284 CTTTGTGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (21 bp):
CTCCAATGAGCTTGAAACTTT
Found at i:21132 original size:23 final size:21
Alignment explanation
Indices: 21089--21141 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
21079 GATAAGAAGT
*
21089 AGCACAAGTTGTCGACCAAAGGA
1 AGCA-AAGTTATCGACCAAA-GA
*
21112 AGCAAAGTTATCGACTTAAAGA
1 AGCAAAGTTATCGAC-CAAAGA
*
21134 AACAAAGT
1 AGCAAAGT
21142 CGATAACAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 19 0.73
23 7 0.27
ACGTcount: A:0.45, C:0.17, G:0.21, T:0.17
Consensus pattern (21 bp):
AGCAAAGTTATCGACCAAAGA
Done.