Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024494.1 Corchorus olitorius cultivar O-4 contig24527, 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: 17373
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1256 original size:21 final size:21
Alignment explanation
Indices: 1229--1276 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1219 TGGAATGGCA
*
1229 ATGGCACAGGCATAGCCGGTG
1 ATGGCACAGGCATAACCGGTG
* * *
1250 GTGGCACGGGCTTAACCGGTG
1 ATGGCACAGGCATAACCGGTG
1271 ATGGCA
1 ATGGCA
1277 TGGTGAATGG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.23, G:0.40, T:0.17
Consensus pattern (21 bp):
ATGGCACAGGCATAACCGGTG
Found at i:4508 original size:29 final size:28
Alignment explanation
Indices: 4448--4511 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
4438 AAAAACTCTT
* * ***
4448 TTTTTTTCAAAAGCGCAACAGAAAATTT
1 TTTTTTTCAAAAACGCAACACAAAACAA
4476 TTTTTTTCAAAAACGCAACAACAAAACAA
1 TTTTTTTCAAAAACGCAAC-ACAAAACAA
4505 TTTTTTT
1 TTTTTTT
4512 TTAAAATTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 18 0.60
29 12 0.40
ACGTcount: A:0.41, C:0.16, G:0.06, T:0.38
Consensus pattern (28 bp):
TTTTTTTCAAAAACGCAACACAAAACAA
Found at i:5736 original size:9 final size:10
Alignment explanation
Indices: 5705--5738 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
5695 TAAAGAGAAT
5705 TATGTGAAGG
1 TATGTGAAGG
5715 TATGTGAAGG
1 TATGTGAAGG
5725 TATGTG-AGG
1 TATGTGAAGG
5734 TATGT
1 TATGT
5739 TACAGGAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.26, C:0.00, G:0.38, T:0.35
Consensus pattern (10 bp):
TATGTGAAGG
Found at i:8650 original size:15 final size:15
Alignment explanation
Indices: 8620--8670 Score: 75
Period size: 15 Copynumber: 3.3 Consensus size: 15
8610 AAGTGGAATC
*
8620 TTTATTTGCATTAGTT
1 TTTATTTTC-TTAGTT
*
8636 TTTGTTTTCTTAGTT
1 TTTATTTTCTTAGTT
8651 TTTATTTTCTTAGTT
1 TTTATTTTCTTAGTT
8666 TTTAT
1 TTTAT
8671 GCATTAGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
15 25 0.78
16 7 0.22
ACGTcount: A:0.14, C:0.06, G:0.10, T:0.71
Consensus pattern (15 bp):
TTTATTTTCTTAGTT
Found at i:14220 original size:75 final size:75
Alignment explanation
Indices: 14069--14213 Score: 281
Period size: 75 Copynumber: 1.9 Consensus size: 75
14059 TTATCTGGAC
*
14069 TGTGAGCAAAGGAATGATGAGTTTTAATCAAAAGATGTTTCAAAATCAGTTTTAGTCAAAGCAAT
1 TGTGAGCAAAGAAATGATGAGTTTTAATCAAAAGATGTTTCAAAATCAGTTTTAGTCAAAGCAAT
14134 GATTTCAAGG
66 GATTTCAAGG
14144 TGTGAGCAAAGAAATGATGAGTTTTAATCAAAAGATGTTTCAAAATCAGTTTTAGTCAAAGCAAT
1 TGTGAGCAAAGAAATGATGAGTTTTAATCAAAAGATGTTTCAAAATCAGTTTTAGTCAAAGCAAT
14209 GATTT
66 GATTT
14214 TGAGGTGACT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.32
Consensus pattern (75 bp):
TGTGAGCAAAGAAATGATGAGTTTTAATCAAAAGATGTTTCAAAATCAGTTTTAGTCAAAGCAAT
GATTTCAAGG
Found at i:14627 original size:27 final size:25
Alignment explanation
Indices: 14597--14654 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 25
14587 ATTCCCTGAT
14597 AAAAAAGAAAAACAA-AAAGAAGAGAAA
1 AAAAAAGAAAAA-AAGAAA-AA-AGAAA
*
14624 AAAAGAGAAAAAAAGAAAAAAGAAA
1 AAAAAAGAAAAAAAGAAAAAAGAAA
14649 AAAAAA
1 AAAAAA
14655 CACTTGGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 10 0.36
26 4 0.14
27 14 0.50
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (25 bp):
AAAAAAGAAAAAAAGAAAAAAGAAA
Found at i:14629 original size:10 final size:10
Alignment explanation
Indices: 14610--14644 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
14600 AAAGAAAAAC
14610 AAAAAGAAGAG
1 AAAAA-AAGAG
14621 AAAAAAAGAG
1 AAAAAAAGAG
14631 AAAAAAAGA-
1 AAAAAAAGAG
14640 AAAAA
1 AAAAA
14645 GAAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 5 0.21
10 14 0.58
11 5 0.21
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAG
Found at i:14642 original size:17 final size:16
Alignment explanation
Indices: 14597--14653 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 16
14587 ATTCCCTGAT
14597 AAAAAAGAAAAACA-AA
1 AAAAAAGAAAAA-AGAA
*
14613 AAGAAGAGAAAAAAAGAGA
1 AA-AAAAG-AAAAAAGA-A
14632 AAAAAAGAAAAAAGAA
1 AAAAAAGAAAAAAGAA
14648 AAAAAA
1 AAAAAA
14654 ACACTTGGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
16 9 0.26
17 13 0.37
18 10 0.29
19 3 0.09
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAAAGAA
Found at i:15503 original size:21 final size:21
Alignment explanation
Indices: 15477--15572 Score: 140
Period size: 21 Copynumber: 4.6 Consensus size: 21
15467 AAGATGCTAG
15477 AAGCTCATTGGAGCAA-GTTCC
1 AAGCTCATTGGAG-AAGGTTCC
*
15498 AAGCTCATTGGAGCAGGTTCC
1 AAGCTCATTGGAGAAGGTTCC
*
15519 AAGTTCATTGGAGAAGGTTCC
1 AAGCTCATTGGAGAAGGTTCC
* *
15540 AAGATCATTGGAGAAGGTTTC
1 AAGCTCATTGGAGAAGGTTCC
15561 AAGCTCATTGGA
1 AAGCTCATTGGA
15573 AATGCCTAAG
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 1 0.01
21 67 0.99
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (21 bp):
AAGCTCATTGGAGAAGGTTCC
Found at i:16509 original size:21 final size:21
Alignment explanation
Indices: 16483--16574 Score: 125
Period size: 21 Copynumber: 4.4 Consensus size: 21
16473 TGCTAGAAGT
16483 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
16504 TCATTGGAGCAA-GTTCCAAGT
1 TCATTGGAG-AAGGTTCCAAGC
*
16525 TCATTGGAGAAGGTTCCAAGA
1 TCATTGGAGAAGGTTCCAAGC
*
16546 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
16567 TCATTGGA
1 TCATTGGA
16575 AATGCCTAAG
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
20 2 0.03
21 64 0.97
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Done.