Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022368.1 Corchorus olitorius cultivar O-4 contig22401, 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: 14319
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:1404 original size:10 final size:9
Alignment explanation
Indices: 1361--1418 Score: 50
Period size: 10 Copynumber: 6.4 Consensus size: 9
1351 TAAAAGTAAT
1361 TAAGAAAAA
1 TAAGAAAAA
*
1370 TAAACAAAAA
1 T-AAGAAAAA
1380 TAA-AAGAAA
1 TAAGAA-AAA
1389 -AAGAAAAA
1 TAAGAAAAA
1397 TAACGAAAAA
1 TAA-GAAAAA
*
1407 TAA-AAAGA
1 TAAGAAAAA
1415 TAAG
1 TAAG
1419 GGTAAGAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
8 14 0.34
9 10 0.24
10 17 0.41
ACGTcount: A:0.76, C:0.03, G:0.10, T:0.10
Consensus pattern (9 bp):
TAAGAAAAA
Found at i:1404 original size:16 final size:17
Alignment explanation
Indices: 1375--1412 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1365 AAAAATAAAC
1375 AAAAATAAAAGAAAAAG
1 AAAAATAAAAGAAAAAG
* *
1392 AAAAAT-AACGAAAAAT
1 AAAAATAAAAGAAAAAG
1408 AAAAA
1 AAAAA
1413 GATAAGGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.82, C:0.03, G:0.08, T:0.08
Consensus pattern (17 bp):
AAAAATAAAAGAAAAAG
Found at i:3122 original size:76 final size:76
Alignment explanation
Indices: 2986--3136 Score: 198
Period size: 76 Copynumber: 2.0 Consensus size: 76
2976 CAAGGACCCT
* *
2986 GACTCCACCTGGGTGCCCACATGGTTGCCTTGAACACCCATGTGGTTTGCTTGAGAACCCAGGTG
1 GACTCCACCTGGGTGCCCACATGGTTGCCTTGAACACCCATGTGGTTTGCCTGAGAACCCAGATG
3051 GGCAGTGTCAC
66 GGCAGTGTCAC
* * * **
3062 GACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAGACCCATGT-GTTTCGCCTGATCACCCAGA
1 GACTCCACCTGGGTGCCCACATGG-TTGCCTTGAACACCCATGTGGTTT-GCCTGAGAACCCAGA
*
3125 TGGGCTGTGTCA
64 TGGGCAGTGTCA
3137 TAGCTCATCA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
75 4 0.06
76 57 0.88
77 4 0.06
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.25
Consensus pattern (76 bp):
GACTCCACCTGGGTGCCCACATGGTTGCCTTGAACACCCATGTGGTTTGCCTGAGAACCCAGATG
GGCAGTGTCAC
Found at i:4120 original size:27 final size:26
Alignment explanation
Indices: 4066--4114 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
4056 ATGATTTAGG
*
4066 GGTTACTAACTCCCTTTTTCTTTTGA
1 GGTTACTAACGCCCTTTTTCTTTTGA
*
4092 GGTTACTAACGCTCTTTTT-TTTT
1 GGTTACTAACGCCCTTTTTCTTTT
4115 CAGAGGGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.14, C:0.20, G:0.12, T:0.53
Consensus pattern (26 bp):
GGTTACTAACGCCCTTTTTCTTTTGA
Found at i:6435 original size:16 final size:17
Alignment explanation
Indices: 6414--6447 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
6404 CAACTCCTTC
6414 AAAACTTGA-GAATTTG
1 AAAACTTGAGGAATTTG
6430 AAAACTTGAGGAATTTG
1 AAAACTTGAGGAATTTG
6447 A
1 A
6448 TGGAAAAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (17 bp):
AAAACTTGAGGAATTTG
Found at i:7989 original size:24 final size:24
Alignment explanation
Indices: 7957--8015 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
7947 CTTGGCTGTC
* *
7957 GTTGCAATCCTGGATTTGATTGAG
1 GTTGCAATCCTAGATTTGACTGAG
* *
7981 GTTGCAATCTTAGATTTGGCTGAG
1 GTTGCAATCCTAGATTTGACTGAG
*
8005 GTTGGAATCCT
1 GTTGCAATCCT
8016 CTACTTGATT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.20, C:0.14, G:0.29, T:0.37
Consensus pattern (24 bp):
GTTGCAATCCTAGATTTGACTGAG
Done.