Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024911.1 Corchorus olitorius cultivar O-4 contig24944, 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: 30289
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Found at i:10375 original size:20 final size:20
Alignment explanation
Indices: 10350--10392 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
10340 GCCCAAGGCT
10350 TTGGTAAAGACATCTGCAAG
1 TTGGTAAAGACATCTGCAAG
10370 TTGGTAAAGACATCTGCAAG
1 TTGGTAAAGACATCTGCAAG
10390 TTG
1 TTG
10393 TGCTCCACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.28
Consensus pattern (20 bp):
TTGGTAAAGACATCTGCAAG
Found at i:13579 original size:15 final size:15
Alignment explanation
Indices: 13561--13611 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
13551 TCTGCAGTAG
*
13561 TATTTGCTGCGGTAA
1 TATTTGCTGCGGCAA
* *
13576 TATTTACTGCGGCAG
1 TATTTGCTGCGGCAA
*
13591 TATTTCCTGCGGCAA
1 TATTTGCTGCGGCAA
13606 TATTTG
1 TATTTG
13612 TTGATTTTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.39
Consensus pattern (15 bp):
TATTTGCTGCGGCAA
Found at i:14749 original size:29 final size:28
Alignment explanation
Indices: 14716--14797 Score: 98
Period size: 25 Copynumber: 3.0 Consensus size: 28
14706 GAACTACCTT
14716 CAACCTAATTTATCAGATGCAAGTTGTA
1 CAACCTAATTTATCAGATGCAAGTTGTA
* * **
14744 GCAACCTAATTTATCAGA-ACTACCT-T-
1 -CAACCTAATTTATCAGATGCAAGTTGTA
14770 CAACCTAATTTATCAGATGCAAGTTGTA
1 CAACCTAATTTATCAGATGCAAGTTGTA
14798 ACAAGTTCGG
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
25 17 0.40
26 3 0.07
27 2 0.05
28 3 0.07
29 17 0.40
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (28 bp):
CAACCTAATTTATCAGATGCAAGTTGTA
Found at i:14779 original size:25 final size:25
Alignment explanation
Indices: 14704--14786 Score: 94
Period size: 25 Copynumber: 3.2 Consensus size: 25
14694 TTTTTTATTG
14704 CAGAACTACCTTCAACCTAATTTAT
1 CAGAACTACCTTCAACCTAATTTAT
* * **
14729 CAGATGCAAGTTGTAGCAACCTAATTTAT
1 CAGA-ACTACCT-T--CAACCTAATTTAT
14758 CAGAACTACCTTCAACCTAATTTAT
1 CAGAACTACCTTCAACCTAATTTAT
14783 CAGA
1 CAGA
14787 TGCAAGTTGT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
25 21 0.46
26 3 0.07
27 2 0.04
28 3 0.07
29 17 0.37
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.30
Consensus pattern (25 bp):
CAGAACTACCTTCAACCTAATTTAT
Found at i:18649 original size:22 final size:22
Alignment explanation
Indices: 18621--18664 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
18611 AATCCATGAG
18621 AGGCATAAAAAAACTTACAGGA
1 AGGCATAAAAAAACTTACAGGA
* *
18643 AGGCATAAGAAAACTTATAGGA
1 AGGCATAAAAAAACTTACAGGA
18665 CTTGAAGGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.52, C:0.11, G:0.20, T:0.16
Consensus pattern (22 bp):
AGGCATAAAAAAACTTACAGGA
Found at i:20289 original size:31 final size:31
Alignment explanation
Indices: 20249--20308 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
20239 ATGTTCATGA
* *
20249 TTTGGGGTTACTAACTCCCTTTTTATTTTAT
1 TTTGAGGTTACTAACACCCTTTTTATTTTAT
* *
20280 TTTGAGGTTACTAACACTCTTTTTTTTTT
1 TTTGAGGTTACTAACACCCTTTTTATTTT
20309 TCAGAGGGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.57
Consensus pattern (31 bp):
TTTGAGGTTACTAACACCCTTTTTATTTTAT
Found at i:21784 original size:19 final size:18
Alignment explanation
Indices: 21760--21799 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
21750 TTGAAGATTT
*
21760 ATTGAAGATAATTTGAAGA
1 ATTGAAGACAA-TTGAAGA
*
21779 ATTGAAGACCATTGAAGA
1 ATTGAAGACAATTGAAGA
21797 ATT
1 ATT
21800 ATTTCAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (18 bp):
ATTGAAGACAATTGAAGA
Found at i:22412 original size:18 final size:17
Alignment explanation
Indices: 22385--22420 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
22375 TTTCACTTCA
22385 TCTATTTTTCTTCTAGT
1 TCTATTTTTCTTCTAGT
22402 TCTAGTTTTTCTTCTAGT
1 TCTA-TTTTTCTTCTAGT
22420 T
1 T
22421 TTTCCTAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (17 bp):
TCTATTTTTCTTCTAGT
Found at i:26189 original size:37 final size:38
Alignment explanation
Indices: 26147--26219 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
26137 TTAAAAACGG
26147 AAAATAAGA-AATTTTTTTTTCTAAAAACGCAAAAAAC
1 AAAATAAGAGAATTTTTTTTTCTAAAAACGCAAAAAAC
*
26184 AAAATAAGAGAATTTTTTTTTCTTAAAACGCAAAAA
1 AAAATAAGAGAATTTTTTTTTCTAAAAACGCAAAAA
26220 CTAAGAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 9 0.26
38 25 0.74
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.32
Consensus pattern (38 bp):
AAAATAAGAGAATTTTTTTTTCTAAAAACGCAAAAAAC
Found at i:28562 original size:129 final size:129
Alignment explanation
Indices: 28332--28578 Score: 485
Period size: 129 Copynumber: 1.9 Consensus size: 129
28322 GCTATTAAGC
28332 GAACTCGATAATCTTTTCTTGCTTGATCGGCTTGCTTTTCAAAAGCAAATTGGACATGTTGCTTT
1 GAACTCGATAATCTTTTCTTGCTTGATCGGCTTGCTTTTCAAAAGCAAATTGGACATGTTGCTTT
*
28397 TCATTTAGCAAATTGTCACATCTTTTTCTTGCTTGGTTATGAGCACTATTATGACCTCCAACAT
66 TCATTTAGCAAATCGTCACATCTTTTTCTTGCTTGGTTATGAGCACTATTATGACCTCCAACAT
28461 GAACTCGATAATCTTTTCTTGCTTGATCGGCTTGCTTTTCAAAAGCAAATTGGACATGTTGCTTT
1 GAACTCGATAATCTTTTCTTGCTTGATCGGCTTGCTTTTCAAAAGCAAATTGGACATGTTGCTTT
28526 TCATTTAGCAAATCGTCACATCTTTTTCTTGCTTGGTTATGAGCACTATTATG
66 TCATTTAGCAAATCGTCACATCTTTTTCTTGCTTGGTTATGAGCACTATTATG
28579 GTCCTACCAA
Statistics
Matches: 117, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
129 117 1.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.41
Consensus pattern (129 bp):
GAACTCGATAATCTTTTCTTGCTTGATCGGCTTGCTTTTCAAAAGCAAATTGGACATGTTGCTTT
TCATTTAGCAAATCGTCACATCTTTTTCTTGCTTGGTTATGAGCACTATTATGACCTCCAACAT
Found at i:28798 original size:10 final size:10
Alignment explanation
Indices: 28785--28822 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
28775 CTTTAAAAAA
*
28785 CTTTCCTCCC
1 CTTTCCTTCC
*
28795 CTTTCCTTTC
1 CTTTCCTTCC
28805 CTTTCCTTCC
1 CTTTCCTTCC
28815 CTTTCCTT
1 CTTTCCTT
28823 TAATTACTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (10 bp):
CTTTCCTTCC
Found at i:28804 original size:5 final size:5
Alignment explanation
Indices: 28794--28823 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
28784 ACTTTCCTCC
*
28794 CCTTT CCTTT CCTTT CCTTC CCTTT CCTTT
1 CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT
28824 AATTACTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (5 bp):
CCTTT
Found at i:30263 original size:2 final size:2
Alignment explanation
Indices: 30256--30289 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
30246 TAAAAACTAG
30256 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.