Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019739.1 Corchorus olitorius cultivar O-4 contig19772, 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: 35764
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:88 original size:22 final size:22
Alignment explanation
Indices: 60--110 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
50 TCGCGCTCTG
*
60 AAAATTTTGATAACCTC-CTCAT
1 AAAATTTTGATAACCACAC-CAT
82 AAAATTTTGATAACCACACCAT
1 AAAATTTTGATAACCACACCAT
104 AAAATTT
1 AAAATTT
111 CGCTAACTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 26 0.96
23 1 0.04
ACGTcount: A:0.43, C:0.20, G:0.04, T:0.33
Consensus pattern (22 bp):
AAAATTTTGATAACCACACCAT
Found at i:182 original size:22 final size:21
Alignment explanation
Indices: 156--238 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 21
146 CTCTATAAGT
156 AATTTTGATAACCTCTCCATA
1 AATTTTGATAACCTCTCCATA
*
177 ACATTTTCATAACCTC-CCTATGA
1 A-ATTTTGATAACCTCTCC-AT-A
*
200 AATTTTGTTAACCT-TCC-TA
1 AATTTTGATAACCTCTCCATA
*
219 GGATTTTTTGATAACCTCTC
1 --A-ATTTTGATAACCTCTC
239 TCCCTGTGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
19 1 0.02
20 1 0.02
21 4 0.08
22 39 0.80
23 4 0.08
ACGTcount: A:0.28, C:0.24, G:0.07, T:0.41
Consensus pattern (21 bp):
AATTTTGATAACCTCTCCATA
Found at i:323 original size:22 final size:22
Alignment explanation
Indices: 298--451 Score: 91
Period size: 22 Copynumber: 7.0 Consensus size: 22
288 TAAAATTTCA
298 ATAACCTTCGTATGAAATTTTG
1 ATAACCTTCGTATGAAATTTTG
* ** *
320 ATAACATTTTTATGAAAATTTG
1 ATAACCTTCGTATGAAATTTTG
*
342 GTAACC-TCTGTATGAAATTTTG
1 ATAACCTTC-GTATGAAATTTTG
* * *
364 ATAA-CTACATTATGAAGTTTTG
1 ATAACCTTC-GTATGAAATTTTG
* * * *
386 ATCACCTCCATATGAAGTTTTG
1 ATAACCTTCGTATGAAATTTTG
* *
408 GTAA--TTACAGTATGAAATTTTA
1 ATAACCTT-C-GTATGAAATTTTG
* * *
430 ATAACTTTCCTATGTAATTTTG
1 ATAACCTTCGTATGAAATTTTG
452 GCTTGATTGT
Statistics
Matches: 98, Mismatches: 27, Indels: 14
0.71 0.19 0.10
Matches are distributed among these distances:
20 1 0.01
21 3 0.03
22 88 0.90
23 4 0.04
24 2 0.02
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (22 bp):
ATAACCTTCGTATGAAATTTTG
Found at i:377 original size:44 final size:44
Alignment explanation
Indices: 269--434 Score: 124
Period size: 44 Copynumber: 3.8 Consensus size: 44
259 CGTTCTAATT
* *
269 AATTTTGATAA-TCACACTAT-AAAATTTCAATAACCT-TCGTATGA
1 AATTTTGATAACT-ACATTATGAAAATTT-GATAACCTCT-GTATGA
** *
313 AATTTTGATAAC-ATTTTTATGAAAATTTGGTAACCTCTGTATGA
1 AATTTTGATAACTA-CATTATGAAAATTTGATAACCTCTGTATGA
** * **
357 AATTTTGATAACTACATTATGAAGTTTTGATCACCTCCATATGA
1 AATTTTGATAACTACATTATGAAAATTTGATAACCTCTGTATGA
* * * * * *
401 AGTTTTGGTAATTACAGTATGAAATTTTAATAAC
1 AATTTTGATAACTACATTATGAAAATTTGATAAC
435 TTTCCTATGT
Statistics
Matches: 97, Mismatches: 20, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
43 1 0.01
44 87 0.90
45 9 0.09
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (44 bp):
AATTTTGATAACTACATTATGAAAATTTGATAACCTCTGTATGA
Found at i:19739 original size:16 final size:16
Alignment explanation
Indices: 19719--19752 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
19709 ATGAAAACTG
*
19719 GAAAGGAAAAA-AAAA
1 GAAAAGAAAAAGAAAA
19734 GAAAAGAAAAAGAAAA
1 GAAAAGAAAAAGAAAA
19750 GAA
1 GAA
19753 CACCTAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
GAAAAGAAAAAGAAAA
Found at i:19743 original size:11 final size:11
Alignment explanation
Indices: 19724--19752 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
19714 AACTGGAAAG
19724 GAAAA-AAAAA
1 GAAAAGAAAAA
19734 GAAAAGAAAAA
1 GAAAAGAAAAA
19745 GAAAAGAA
1 GAAAAGAA
19753 CACCTAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
GAAAAGAAAAA
Found at i:26180 original size:20 final size:20
Alignment explanation
Indices: 26144--26186 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
26134 CCATACAAAT
* *
26144 AATTAATCAATAAAAAAACG
1 AATTAAACAATAAAAAAAAG
26164 AATTAAACAA-AATAAAAAAG
1 AATTAAACAATAA-AAAAAAG
26184 AAT
1 AAT
26187 GAAAGTGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.70, C:0.07, G:0.05, T:0.19
Consensus pattern (20 bp):
AATTAAACAATAAAAAAAAG
Found at i:26786 original size:18 final size:18
Alignment explanation
Indices: 26763--26798 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
26753 CTTGAAAATT
26763 CTTTTTCTTTTCTTTGCA
1 CTTTTTCTTTTCTTTGCA
* *
26781 CTTTTTTTTTTTTTTGCA
1 CTTTTTCTTTTCTTTGCA
26799 ATAAACCTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.17, G:0.06, T:0.72
Consensus pattern (18 bp):
CTTTTTCTTTTCTTTGCA
Found at i:35054 original size:21 final size:22
Alignment explanation
Indices: 35014--35054 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
35004 AACAAACTCG
*
35014 TAACCCGAATAACCCGAGAAAA
1 TAACCCGAATAACCCAAGAAAA
*
35036 TAACCCG-ATGACCCAAGAA
1 TAACCCGAATAACCCAAGAA
35055 TATTATAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.46, C:0.29, G:0.15, T:0.10
Consensus pattern (22 bp):
TAACCCGAATAACCCAAGAAAA
Done.