Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024080.1 Corchorus olitorius cultivar O-4 contig24113, 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: 10223
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31
Found at i:1771 original size:11 final size:11
Alignment explanation
Indices: 1755--1792 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
1745 CTAAGGGTAA
1755 AGGAAAAAGCT
1 AGGAAAAAGCT
1766 AGGAAAAAGCT
1 AGGAAAAAGCT
**
1777 AGGAAGGAGCT
1 AGGAAAAAGCT
1788 AGGAA
1 AGGAA
1793 GTATCCTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.50, C:0.08, G:0.34, T:0.08
Consensus pattern (11 bp):
AGGAAAAAGCT
Found at i:2190 original size:21 final size:21
Alignment explanation
Indices: 2166--2257 Score: 132
Period size: 21 Copynumber: 4.4 Consensus size: 21
2156 CTTAGGGAAT
*
2166 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
2187 TCCAATGATCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
2208 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
2229 TCCAATGAGCTCGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
2250 TCCAATGA
1 TCCAATGA
2258 ACTTCTAGCA
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
20 3 0.05
21 62 0.95
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:5145 original size:30 final size:30
Alignment explanation
Indices: 5109--5682 Score: 857
Period size: 30 Copynumber: 19.1 Consensus size: 30
5099 TTAACTGATG
* * *
5109 AAGCAATGATCCTAAACCATGATAAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
5139 AAGCAATGATCCTCAACCAGGATTAAACTG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
5169 GAGCAAAT-ATCCTCAACCAGGATTAAAATG
1 AAGC-AATGATCCTCAACCAGGATTAAAATA
*
5199 GAGCAAAT-ATCCTCAACCAGGATTAAAATA
1 AAGC-AATGATCCTCAACCAGGATTAAAATA
* *
5229 AAGCAACGATCCTCAACCAGGATTAAAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
5259 ATGCAATGATCCTCAACCAGGATTAAAGTA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
5289 AAGCAATGATCCTCAACCAGGATTAAAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
5319 GAGCAAAT-ATCCTCAACCATGATTAAAATA
1 AAGC-AATGATCCTCAACCAGGATTAAAATA
*
5349 AAGCAATGATCCTCAACCAAGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
5379 AAACAATGATCCTTAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
5409 AAGCAATGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
5439 AAGCAATGATCCTTAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
5469 AAGCAATGATCCTTAACCAGGATTAAAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
5499 AAGCAATGATCCTCAACCAGGATTAAAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
5529 AAGCAATGATCCTCAACCAGAATTAAAGTA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
5559 AAGCAATGATCCTCAACCAGGATAAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
5589 AAGCAATGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
5619 AAGCAATGATCCTTAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
5649 AAGCAATGATCCTCAATCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
5679 AAGC
1 AAGC
5683 TGATAAAGCA
Statistics
Matches: 499, Mismatches: 41, Indels: 8
0.91 0.07 0.01
Matches are distributed among these distances:
29 5 0.01
30 488 0.98
31 6 0.01
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.21
Consensus pattern (30 bp):
AAGCAATGATCCTCAACCAGGATTAAAATA
Found at i:6051 original size:36 final size:36
Alignment explanation
Indices: 5947--6453 Score: 589
Period size: 36 Copynumber: 14.1 Consensus size: 36
5937 TCTGCGGTCG
* *
5947 ACTGAAATAAACTGCAGAGAAGATCGCCCTGGATCA
1 ACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCA
* * *
5983 ACTGAAGTAAA-TTAAGGAAAGATCGCCCTGGATCA
1 ACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCA
* * * *
6018 ACTGAAATAAATTAAAGAAAAGATCTCCTTGGATCA
1 ACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCA
* *
6054 ACTGAAA-CAACTGAAGAAAGGATCGCCCTGGATCA
1 ACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCA
6089 ACTTGAAATAAACTGAAGAAAAGATCGCCCTGGATCA
1 AC-TGAAATAAACTGAAGAAAAGATCGCCCTGGATCA
* * *
6126 ATTGAAATAAATTGAAGAAAAGATCACCCTGGATCA
1 ACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCA
* *
6162 ACTGAAATAAACAGAAGAAAGGATCGCCCTGGATCA
1 ACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCA
* *
6198 ACTTGAAATAAACTGAAGAAAGGATCACCCTGGATCA
1 AC-TGAAATAAACTGAAGAAAAGATCGCCCTGGATCA
6235 ACTTGAAATAAACTGAAGAAAAGATCGCCCTGGATCA
1 AC-TGAAATAAACTGAAGAAAAGATCGCCCTGGATCA
* *
6272 ATTGAAATAAACTGACA-AAAGGATCGCCCTGGATCAA
1 ACTGAAATAAACTGA-AGAAAAGATCGCCCTGGATC-A
* * * *
6309 ATTGAAATAAACTGAAG-AAAGACCACCCTGGGTCA
1 ACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCA
* * * *
6344 ACTGAAATAAATTG-AGGAAAGATCGCCTTGGATCT
1 ACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCA
** ** * * *
6379 GTTGAAACGAATTGAAG-AAAGACCGCCCTGGGTCA
1 ACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCA
6414 ACTGAAATAAACTGAAG--AAGATTCGCCCTGGATCA
1 ACTGAAATAAACTGAAGAAAAGA-TCGCCCTGGATCA
6449 ACTGA
1 ACTGA
6454 GAATTTCTTC
Statistics
Matches: 403, Mismatches: 58, Indels: 21
0.84 0.12 0.04
Matches are distributed among these distances:
34 6 0.01
35 132 0.33
36 153 0.38
37 112 0.28
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.19
Consensus pattern (36 bp):
ACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCA
Found at i:6204 original size:73 final size:71
Alignment explanation
Indices: 5947--6453 Score: 576
Period size: 73 Copynumber: 7.1 Consensus size: 71
5937 TCTGCGGTCG
* * * *
5947 ACTGAAATAAACTGCAGAGAAGATCGCCCTGGATCAACTGAAGTAAA-TTAAGGAAAGATCGCCC
1 ACTGAAATAAACTGAAGA-AAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCGCCC
6011 TGGATCA
65 TGGATCA
* * * * * *
6018 ACTGAAATAAATTAAAGAAAAGATCTCCTTGGATCAACTGAAA-CAACTGAAGAAAGGATCGCCC
1 ACTGAAATAAACTGAAG-AAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCGCCC
6082 TGGATCA
65 TGGATCA
* * *
6089 ACTTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAATTGAAATAAATTGAAGAAAAGATCACC
1 AC-TGAAATAAACTGAAG-AAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCGCC
6154 CTGGATCA
64 CTGGATCA
* * *
6162 ACTGAAATAAACAGAAGAAAGGATCGCCCTGGATCAACTTGAAATAAACTGAAGAAAGGATCACC
1 ACTGAAATAAACTGAAGAAA-GATCGCCCTGGATCAAC-TGAAATAAACTGAAGAAAAGATCGCC
6227 CTGGATCA
64 CTGGATCA
* *
6235 ACTTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAATTGAAATAAACTGACA-AAAGGATCGC
1 AC-TGAAATAAACTGAAG-AAAGATCGCCCTGGATCAACTGAAATAAACTGA-AGAAAAGATCGC
6299 CCTGGATCAA
63 CCTGGATC-A
* * * * * * *
6309 ATTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAATTG-AGGAAAGATCGCCTT
1 ACTGAAATAAACTGAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCGCCCT
*
6373 GGATCT
66 GGATCA
** ** * * *
6379 GTTGAAACGAATTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAG--AAGATTCGCCC
1 ACTGAAATAAACTGAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGA-TCGCCC
6442 TGGATCA
65 TGGATCA
6449 ACTGA
1 ACTGA
6454 GAATTTCTTC
Statistics
Matches: 377, Mismatches: 46, Indels: 27
0.84 0.10 0.06
Matches are distributed among these distances:
69 4 0.01
70 60 0.16
71 78 0.21
72 94 0.25
73 105 0.28
74 33 0.09
75 3 0.01
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.19
Consensus pattern (71 bp):
ACTGAAATAAACTGAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGATCGCCCT
GGATCA
Found at i:7344 original size:20 final size:19
Alignment explanation
Indices: 7306--7351 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
7296 CACCCTAGAG
7306 CTTTTTCCTTCATCATTTT
1 CTTTTTCCTTCATCATTTT
* **
7325 CATTTTTCCTTCTTTTTTTT
1 C-TTTTTCCTTCATCATTTT
7345 CTTTTTC
1 CTTTTTC
7352 TTTTTTTAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.70
Consensus pattern (19 bp):
CTTTTTCCTTCATCATTTT
Found at i:8168 original size:13 final size:13
Alignment explanation
Indices: 8152--8176 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8142 TAGGCCAAGT
8152 TTTCTTTTTCTTG
1 TTTCTTTTTCTTG
8165 TTTCTTTTTCTT
1 TTTCTTTTTCTT
8177 CTTCCGAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (13 bp):
TTTCTTTTTCTTG
Found at i:8462 original size:2 final size:2
Alignment explanation
Indices: 8455--8488 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
8445 GGACAGTAGA
8455 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8489 CATGTAATGG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:8476 original size:17 final size:17
Alignment explanation
Indices: 8454--8488 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
8444 TGGACAGTAG
8454 AATATATATATATATAT
1 AATATATATATATATAT
8471 AATATATATATATATAT
1 AATATATATATATATAT
8488 A
1 A
8489 CATGTAATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATATATATATATATAT
Found at i:8477 original size:15 final size:15
Alignment explanation
Indices: 8457--8486 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
8447 ACAGTAGAAT
8457 ATATATATATATATA
1 ATATATATATATATA
8472 ATATATATATATATA
1 ATATATATATATATA
8487 TACATGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATATATATATA
Done.