Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023244.1 Corchorus olitorius cultivar O-4 contig23277, 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: 47623
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:6579 original size:14 final size:13
Alignment explanation
Indices: 6560--6591 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
6550 ACTGTTTTGG
6560 CTTCATTTGAACT
1 CTTCATTTGAACT
6573 CCTTCATTTGAACT
1 -CTTCATTTGAACT
6587 CTTCA
1 CTTCA
6592 AAGACCCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.22, C:0.28, G:0.06, T:0.44
Consensus pattern (13 bp):
CTTCATTTGAACT
Found at i:7977 original size:35 final size:35
Alignment explanation
Indices: 7928--8001 Score: 139
Period size: 35 Copynumber: 2.1 Consensus size: 35
7918 ATCTTTTACT
*
7928 TTTCATCACTCTTGTTTTTACAAGGTGTAATCTTG
1 TTTCATCACCCTTGTTTTTACAAGGTGTAATCTTG
7963 TTTCATCACCCTTGTTTTTACAAGGTGTAATCTTG
1 TTTCATCACCCTTGTTTTTACAAGGTGTAATCTTG
7998 TTTC
1 TTTC
8002 GGCAATTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.49
Consensus pattern (35 bp):
TTTCATCACCCTTGTTTTTACAAGGTGTAATCTTG
Found at i:11776 original size:42 final size:42
Alignment explanation
Indices: 11729--11809 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
11719 ATCTGCATCA
* * *
11729 TTTAAAATTAGGGAATTCATGTATTTTTCCTATTATTATGTT
1 TTTAAAATTAGGGAATTCATGTATTCTTCATACTATTATGTT
*
11771 TTTAAAATTAGGGAATTCGTGTATTCTTCATACTATTAT
1 TTTAAAATTAGGGAATTCATGTATTCTTCATACTATTAT
11810 TATTATTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.49
Consensus pattern (42 bp):
TTTAAAATTAGGGAATTCATGTATTCTTCATACTATTATGTT
Found at i:15903 original size:84 final size:89
Alignment explanation
Indices: 15810--15996 Score: 224
Period size: 84 Copynumber: 2.1 Consensus size: 89
15800 TTTCTTACTT
* * *
15810 CAATAATAAT-AATAATCAAGGTGCAGCAAAGC-AGG-AGA-AAA-AGCAGCAGGAAGTTTCAAG
1 CAATAATAATCAA-AATCAAGATGCAGCAAAGCAAGGAAGAGAAAGAGCAGCAGAAAGTTGCAAG
15870 GCCAAGCAT-GGTTGGTACGTCCAA
65 GCCAAGCATAGGTTGGTACGTCCAA
* *
15894 CAATAATAATCAAGATCAAGATGCAGCAAAGCAGAGGAAAGAGAAAGAGCAGCAGAAAGTTGCAT
1 CAATAATAATCAAAATCAAGATGCAGCAAAGCA-AGG-AAGAGAAAGAGCAGCAGAAAGTTGCAA
*
15959 GGCCAAGCATGCAGGTTGGTTCGTCCAA
64 GGCCAAGCAT--AGGTTGGTACGTCCAA
*
15987 CAATACTAAT
1 CAATAATAAT
15997 TCTGCTAACT
Statistics
Matches: 86, Mismatches: 7, Indels: 11
0.83 0.07 0.11
Matches are distributed among these distances:
84 27 0.31
85 2 0.02
86 3 0.03
88 3 0.03
89 3 0.03
90 25 0.29
93 23 0.27
ACGTcount: A:0.42, C:0.17, G:0.25, T:0.17
Consensus pattern (89 bp):
CAATAATAATCAAAATCAAGATGCAGCAAAGCAAGGAAGAGAAAGAGCAGCAGAAAGTTGCAAGG
CCAAGCATAGGTTGGTACGTCCAA
Found at i:16517 original size:17 final size:17
Alignment explanation
Indices: 16495--16535 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
16485 TTACCATTAA
*
16495 TTCTTTTCGTTTATACT
1 TTCTTTCCGTTTATACT
*
16512 TTCTTTCCGTTTATCCT
1 TTCTTTCCGTTTATACT
16529 TTCTTTC
1 TTCTTTC
16536 TGTTGGATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.07, C:0.24, G:0.05, T:0.63
Consensus pattern (17 bp):
TTCTTTCCGTTTATACT
Found at i:35826 original size:28 final size:28
Alignment explanation
Indices: 35786--35840 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
35776 CATATGAAAC
*
35786 AATCTCATGACTGTAATCT-TTGTCCAAA
1 AATCTCATCACTGTAAT-TATTGTCCAAA
35814 AATCTCATCACTGTAATTATTGTCCAA
1 AATCTCATCACTGTAATTATTGTCCAA
35841 TCTTTACAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 1 0.04
28 24 0.96
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (28 bp):
AATCTCATCACTGTAATTATTGTCCAAA
Found at i:46013 original size:178 final size:177
Alignment explanation
Indices: 45642--46015 Score: 461
Period size: 178 Copynumber: 2.1 Consensus size: 177
45632 GTTTGACTAA
* * * *
45642 ACGGTCTATTTAACATTATATAATTTTCTCTTCAGTTATCCGATTAAGGTGATTTAAGTGTCTAT
1 ACGGTCTAATTAATATTATATAATTTTCTC-TCAGTTATCCGATTAAGATGATTCAAGTGTCTAT
* *
45707 TAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCAAATACTAAATTTTATGTTTCAAG
65 TAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCAAATACCAAATTTAATGTTTCAAG
* * *
45772 TATAAAAAATACTTCCGAAAAATTTGTTGTTTCGGTTAACGTGAATAG
130 TATAAAAAATACTTCCGAAAAATTAGTTATTTCGATTAACGTGAATAG
* * * * * * *
45820 ACGGTCCACTTAATATTATATAACTTTTGCTC-CAGTTGTCTGATTGAGATGATTCAAGTGTTTC
1 ACGGTCTAATTAATATTATATAA-TTTT-CTCTCAGTTATCCGATTAAGATGATTCAAGTGTCTA
* *
45884 TTGAAAGGTTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAA-ACCAAATTTAATG-TTCA
64 TTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTC-AAATACCAAATTTAATGTTTCA
* *
45947 AGGTATATAAAATGCTTCC-AAAGAATTAGTTATTTCGATTAACG-GAAATAG
128 A-GTATAAAAAATACTTCCGAAA-AATTAGTTATTTCGATTAACGTG-AATAG
*
45998 ATGGTCTAATTAATATTA
1 ACGGTCTAATTAATATTA
46016 CAAAAGTGGA
Statistics
Matches: 168, Mismatches: 22, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
177 9 0.05
178 149 0.89
179 7 0.04
180 3 0.02
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (177 bp):
ACGGTCTAATTAATATTATATAATTTTCTCTCAGTTATCCGATTAAGATGATTCAAGTGTCTATT
AAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCAAATACCAAATTTAATGTTTCAAGT
ATAAAAAATACTTCCGAAAAATTAGTTATTTCGATTAACGTGAATAG
Found at i:47541 original size:128 final size:119
Alignment explanation
Indices: 47270--47585 Score: 361
Period size: 128 Copynumber: 2.6 Consensus size: 119
47260 ATGTAGCTAG
* *
47270 TGCCTCGTTAAAAACCTTAAG-CTGGAAAACCCAATGGGACAAAACC-AGTCATAAGGAAAAAAG
1 TGCCTCATTAAAAACCTTAAGTC-GGAAAACCCAATGGGACAAAACCGA-TCATAAGGGAAAAAG
** * * *
47333 AGTGCAGCATATCAAGTCCATTTGTCTTCTGGACAAATATTACATGTGCTCTTTAT
64 AGTGCAGCATATCAAGTCCATTTGTCTTCAAGACAAACATTAAATGTGCTCATTAT
** *
47389 TGCCTCATTAAAAACCTTGTGTCGGAAAACCCAATGGGACAAAACCGAACATAAGGGAAAAAGAG
1 TGCCTCATTAAAAACCTTAAGTCGGAAAACCCAATGGGACAAAACCGATCATAAGGGAAAAAGAG
* *
47454 TGCTAGAGCA-ATTTAAGTCCATGTAAATGTCTTCAAGACAATTACATCTAAATGTGCT-ATTGT
66 TGC---AGCATA-TCAAGTCCAT-T---TGTCTTCAAGACAA--ACAT-TAAATGTGCTCATTAT
**
47517 TGCCTCATTAAAAACCTTAAGTCGGAAAACCCTGTGGGACAAAACCGATCATAAGGGAAAAAGAG
1 TGCCTCATTAAAAACCTTAAGTCGGAAAACCCAATGGGACAAAACCGATCATAAGGGAAAAAGAG
47582 TGCA
66 TGCA
47586 ACGCACTTTA
Statistics
Matches: 167, Mismatches: 17, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
119 59 0.35
120 2 0.01
121 1 0.01
122 13 0.08
123 1 0.01
125 1 0.01
126 12 0.07
128 69 0.41
129 9 0.05
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (119 bp):
TGCCTCATTAAAAACCTTAAGTCGGAAAACCCAATGGGACAAAACCGATCATAAGGGAAAAAGAG
TGCAGCATATCAAGTCCATTTGTCTTCAAGACAAACATTAAATGTGCTCATTAT
Done.