Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017331.1 Corchorus olitorius cultivar O-4 contig17364, 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: 43949
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:311 original size:113 final size:113
Alignment explanation
Indices: 158--382 Score: 450
Period size: 113 Copynumber: 2.0 Consensus size: 113
148 TGAACTCTTT
158 AAAAAGCCAAATAAGTCCTTTTCTGATGGCTAAATGCTGAAATAAGGACTAAACGTTTCAAGATT
1 AAAAAGCCAAATAAGTCCTTTTCTGATGGCTAAATGCTGAAATAAGGACTAAACGTTTCAAGATT
223 TTCTCAAATAAGGATCAAAATACACAATTTCAACAAATTAGAATACAG
66 TTCTCAAATAAGGATCAAAATACACAATTTCAACAAATTAGAATACAG
271 AAAAAGCCAAATAAGTCCTTTTCTGATGGCTAAATGCTGAAATAAGGACTAAACGTTTCAAGATT
1 AAAAAGCCAAATAAGTCCTTTTCTGATGGCTAAATGCTGAAATAAGGACTAAACGTTTCAAGATT
336 TTCTCAAATAAGGATCAAAATACACAATTTCAACAAATTAGAATACA
66 TTCTCAAATAAGGATCAAAATACACAATTTCAACAAATTAGAATACA
383 TACTTAATAT
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 112 1.00
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (113 bp):
AAAAAGCCAAATAAGTCCTTTTCTGATGGCTAAATGCTGAAATAAGGACTAAACGTTTCAAGATT
TTCTCAAATAAGGATCAAAATACACAATTTCAACAAATTAGAATACAG
Found at i:7787 original size:22 final size:22
Alignment explanation
Indices: 7763--7948 Score: 150
Period size: 22 Copynumber: 8.5 Consensus size: 22
7753 TGAATATTTT
7763 TATGAAATTTTGATAA-CTACC
1 TATGAAATTTTGATAACCTACC
*
7784 TTATTAAATTTTGATAACC-ACGC
1 -TATGAAATTTTGATAACCTAC-C
* *
7807 TATGAAATTTTTATAA-TTACC
1 TATGAAATTTTGATAACCTACC
* *
7828 TATGAAATTGTGATAAACT-CC
1 TATGAAATTTTGATAACCTACC
* **
7849 ATATGAAACTTTGATAACCTAAA
1 -TATGAAATTTTGATAACCTACC
* * *
7872 TATGAAATTTTAATAAATCTTCC
1 TATGAAATTTTGAT-AACCTACC
* *
7895 TATGAAATTTTG-TAACCTTCT
1 TATGAAATTTTGATAACCTACC
* *
7916 TATG-ATTTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTACC
*
7937 TATGAGATTTTG
1 TATGAAATTTTG
7949 TTAGGTTGTA
Statistics
Matches: 129, Mismatches: 26, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
20 6 0.05
21 38 0.29
22 68 0.53
23 17 0.13
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTACC
Found at i:7941 original size:65 final size:65
Alignment explanation
Indices: 7763--7947 Score: 169
Period size: 65 Copynumber: 2.8 Consensus size: 65
7753 TGAATATTTT
* * * * * *
7763 TATGAAATTTTGAT-AACTACCTTATTAAATTTTGATAACCACGCTATGAAATTTTTATAATTAC
1 TATGAAATTGTGATAAACT-CCATATGAAATTTTGATAACCTCACTATGAAATTTTAATAATTAC
7827 C
65 C
* * * *
7828 TATGAAATTGTGATAAACTCCATATGAAACTTTGATAACCTAAATATGAAATTTTAATAAATCTT
1 TATGAAATTGTGATAAACTCCATATGAAATTTTGATAACCTCACTATGAAATTTTAAT-AAT-TA
7893 CC
64 CC
* * * * * * *
7895 TATGAAATTTTG-TAACCTTCTTATG-ATTTTTGATAACCTCCCTATGAGATTTT
1 TATGAAATTGTGATAAACTCCATATGAAATTTTGATAACCTCACTATGAAATTTT
7948 GTTAGGTTGT
Statistics
Matches: 97, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
65 66 0.68
66 17 0.18
67 14 0.14
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (65 bp):
TATGAAATTGTGATAAACTCCATATGAAATTTTGATAACCTCACTATGAAATTTTAATAATTACC
Found at i:10596 original size:119 final size:125
Alignment explanation
Indices: 10383--10625 Score: 340
Period size: 119 Copynumber: 2.0 Consensus size: 125
10373 CATTGTTTAA
*
10383 ACTTTTATAGTTTTACTCAACTAGAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC
1 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATC--ATATCC-T-TAAC
* *
10448 TATTTGATTTTTACCATTTTACTATTTTAA-TTAGAAAACTTATATATATTAGAATTTTTTAAAT
62 TATTTGATTTTTACCATTTTACTAATTTAATTTA-AAAACTTAGATATATTAGAATTTTTTAAAT
*
10512 ACTTTTATAGTTTTAGTCAACTAAAAACTCTATTTTTTATTTAATTAAATC-TAT-C-T-A-T-T
1 ACTTTTATAGTTTTACTCAACTAAAAACTCTA-TTTTTATTTAATTAAATCATATCCTTAACTAT
10571 TTG-TTTTTACCATTTTACTAATTTAATTTAAAAACTTAGATATATTAGAATTTTT
65 TTGATTTTTACCATTTTACTAATTTAATTTAAAAACTTAGATATATTAGAATTTTT
10626 AAAAATATTT
Statistics
Matches: 108, Mismatches: 4, Indels: 14
0.86 0.03 0.11
Matches are distributed among these distances:
119 46 0.43
120 7 0.06
121 1 0.01
122 1 0.01
123 1 0.01
126 1 0.01
127 3 0.03
129 30 0.28
130 18 0.17
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.51
Consensus pattern (125 bp):
ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCATATCCTTAACTATT
TGATTTTTACCATTTTACTAATTTAATTTAAAAACTTAGATATATTAGAATTTTTTAAAT
Found at i:11092 original size:17 final size:16
Alignment explanation
Indices: 11062--11118 Score: 64
Period size: 17 Copynumber: 3.6 Consensus size: 16
11052 CGTTCAAATG
11062 TCGGGTCA-TTTGGGT
1 TCGGGTCATTTTGGGT
11077 TCGGGTCAATTTTGGGT
1 TCGGGTC-ATTTTGGGT
* *
11094 T-GGGTCGTTTTCGGTT
1 TCGGGTCATTTT-GGGT
11110 TCGGGTCAT
1 TCGGGTCAT
11119 ACGATTCGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
15 11 0.31
16 10 0.29
17 14 0.40
ACGTcount: A:0.07, C:0.14, G:0.37, T:0.42
Consensus pattern (16 bp):
TCGGGTCATTTTGGGT
Found at i:12759 original size:16 final size:17
Alignment explanation
Indices: 12732--12777 Score: 76
Period size: 16 Copynumber: 2.8 Consensus size: 17
12722 GTCGGGTTGA
12732 TCGGGTTCGGGTCATTT
1 TCGGGTTCGGGTCATTT
*
12749 T-GGGTTTGGGTCATTT
1 TCGGGTTCGGGTCATTT
12765 TCGGGTTCGGGTC
1 TCGGGTTCGGGTC
12778 GTTTGGATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 15 0.58
17 11 0.42
ACGTcount: A:0.04, C:0.15, G:0.39, T:0.41
Consensus pattern (17 bp):
TCGGGTTCGGGTCATTT
Found at i:12840 original size:17 final size:17
Alignment explanation
Indices: 12800--12840 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
12790 GTACCCAAAA
12800 TTTCGGGTCATTTCTGG
1 TTTCGGGTCATTTCTGG
*
12817 GTT-GGGTCAGTTTC-GG
1 TTTCGGGTCA-TTTCTGG
12833 TTTCGGGT
1 TTTCGGGT
12841 TGGGCGGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.05, C:0.15, G:0.37, T:0.44
Consensus pattern (17 bp):
TTTCGGGTCATTTCTGG
Found at i:18464 original size:15 final size:15
Alignment explanation
Indices: 18444--18473 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
18434 ACCTGCTCAA
18444 ATATCTTATAAGAAT
1 ATATCTTATAAGAAT
18459 ATATCTTATAAGAAT
1 ATATCTTATAAGAAT
18474 TCAACATAAA
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:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (15 bp):
ATATCTTATAAGAAT
Found at i:29287 original size:59 final size:60
Alignment explanation
Indices: 29216--29329 Score: 203
Period size: 59 Copynumber: 1.9 Consensus size: 60
29206 AATGGTTATG
*
29216 TAACAAAGTTTATTGTTGATGCTTATGTAGCAAAGTTTGAGGGATGTACAAGGCATGATT
1 TAACAAAGTTTATTGTTGATGCTTATGTAACAAAGTTTGAGGGATGTACAAGGCATGATT
*
29276 TAAC-AAGTTTATTGTTGATGCTTATGTAACAGAGTTTGAGGGATGTACAAGGCA
1 TAACAAAGTTTATTGTTGATGCTTATGTAACAAAGTTTGAGGGATGTACAAGGCA
29330 AAAGTAGCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
59 48 0.92
60 4 0.08
ACGTcount: A:0.32, C:0.09, G:0.25, T:0.34
Consensus pattern (60 bp):
TAACAAAGTTTATTGTTGATGCTTATGTAACAAAGTTTGAGGGATGTACAAGGCATGATT
Found at i:32207 original size:23 final size:23
Alignment explanation
Indices: 32181--32227 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
32171 ATCTTTACAT
32181 AATGTTTTGGGTAATGCAAAGAC
1 AATGTTTTGGGTAATGCAAAGAC
32204 AATGTTTTGGGTAATGCAAAGAC
1 AATGTTTTGGGTAATGCAAAGAC
32227 A
1 A
32228 TTCATAGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.30
Consensus pattern (23 bp):
AATGTTTTGGGTAATGCAAAGAC
Found at i:37256 original size:31 final size:31
Alignment explanation
Indices: 37221--37282 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
37211 AGTTTCGTAA
* *
37221 AACTTTTTAAACGTCTATTGTACCCTTATTT
1 AACTTTTAAAACGTCTATTATACCCTTATTT
* *
37252 AACTTTTAAAATGTCTATTATATCCTTATTT
1 AACTTTTAAAACGTCTATTATACCCTTATTT
37283 GTCTAACATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.29, C:0.16, G:0.05, T:0.50
Consensus pattern (31 bp):
AACTTTTAAAACGTCTATTATACCCTTATTT
Done.