Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024807.1 Corchorus olitorius cultivar O-4 contig24840, 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: 20261
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Found at i:3068 original size:19 final size:18
Alignment explanation
Indices: 3035--3070 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3025 TTGAAATAAT
3035 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
3053 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
3071 TGAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:3078 original size:11 final size:10
Alignment explanation
Indices: 3035--3081 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
3025 TTGAAATAAT
3035 TCTTCAATGA
1 TCTTCAATGA
3045 TCTTCAA--A
1 TCTTCAATGA
*
3053 TCTTCAAATTA
1 TCTTC-AATGA
3064 TCTTCAATGA
1 TCTTCAATGA
3074 GTCTTCAA
1 -TCTTCAA
3082 ACACGAACTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 6 0.19
9 2 0.06
10 11 0.34
11 13 0.41
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.40
Consensus pattern (10 bp):
TCTTCAATGA
Found at i:6557 original size:3 final size:3
Alignment explanation
Indices: 6551--6580 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
6541 TGGTGGTATC
6551 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
6581 CTTGTAGCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:8231 original size:21 final size:21
Alignment explanation
Indices: 8207--8298 Score: 159
Period size: 21 Copynumber: 4.4 Consensus size: 21
8197 CTTAGGCAAT
*
8207 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
8228 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
8249 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
8270 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
8291 TCCAATGA
1 TCCAATGA
8299 TCTCCTAGCA
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
20 3 0.04
21 66 0.96
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:10661 original size:11 final size:11
Alignment explanation
Indices: 10645--10670 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
10635 CTTTGCCTAA
10645 AAAACTAGAAG
1 AAAACTAGAAG
10656 AAAACTAGAAG
1 AAAACTAGAAG
10667 AAAA
1 AAAA
10671 GATCTAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:12258 original size:17 final size:18
Alignment explanation
Indices: 12225--12260 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12215 CTCCTCTTGC
*
12225 ATGAAAACACTTCTTTTT
1 ATGAAAACAATTCTTTTT
12243 ATGAAAACAATT-TTTTT
1 ATGAAAACAATTCTTTTT
12260 A
1 A
12261 ACTACCCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (18 bp):
ATGAAAACAATTCTTTTT
Found at i:16265 original size:25 final size:27
Alignment explanation
Indices: 16237--16301 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 27
16227 TTCCTAAAAC
16237 CGCAGAACAAAAT-TTTTTTTTAT-GA
1 CGCAGAACAAAATCTTTTTTTTATCGA
* *
16262 CGCAGAA-AAACTCTTTTTTTTTTCGA
1 CGCAGAACAAAATCTTTTTTTTATCGA
*
16288 CGCAAAACACAAAT
1 CGCAGAACA-AAAT
16302 AGATTTATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
24 4 0.12
25 16 0.50
26 8 0.25
27 1 0.03
28 3 0.09
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (27 bp):
CGCAGAACAAAATCTTTTTTTTATCGA
Found at i:16408 original size:88 final size:89
Alignment explanation
Indices: 16231--16410 Score: 217
Period size: 88 Copynumber: 2.0 Consensus size: 89
16221 TTTTTTTTCC
* *
16231 TAAAACCGCAGAACAAAATTTTTTTTTATGACGCAGAAAAACTCTTTTTTTTTTCGACGCAAAAC
1 TAAAAACGCAGAACAAAATTTTTTTTTATGACGCAGAAAAACTCTTTTTTTTTTCAACGCAAAAC
* **** *
16296 ACAAATAGATTTATTTTGTTAAAA
66 ACAAATAGATTAAAAACGTCAAAA
16320 TAAAAACGCA-AACAAAATTTTTTTTTATGACGCA-AAAAACTCTTTTTTTTTTCAAAAACGCAA
1 TAAAAACGCAGAACAAAATTTTTTTTTATGACGCAGAAAAACTCTTTTTTTTTTC---AACGCAA
16383 AACACACAA-A-ATTAAAAACG-CAAAA
63 AACACA-AATAGATTAAAAACGTCAAAA
16408 TAA
1 TAA
16411 TTTTTATTTT
Statistics
Matches: 79, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
87 19 0.24
88 31 0.39
89 14 0.18
90 13 0.16
91 2 0.03
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.32
Consensus pattern (89 bp):
TAAAAACGCAGAACAAAATTTTTTTTTATGACGCAGAAAAACTCTTTTTTTTTTCAACGCAAAAC
ACAAATAGATTAAAAACGTCAAAA
Found at i:17547 original size:11 final size:11
Alignment explanation
Indices: 17531--17556 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
17521 CTTTGCCTAA
17531 AAAACTAGAAG
1 AAAACTAGAAG
17542 AAAACTAGAAG
1 AAAACTAGAAG
17553 AAAA
1 AAAA
17557 GATCTAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Done.