Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009317.1 Corchorus capsularis cultivar CVL-1 contig09338, 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: 16555
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:220 original size:28 final size:28
Alignment explanation
Indices: 189--244 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
179 TATGTTTTGC
* *
189 TTTTGGAACAAAATAATTCCTTATGTTT
1 TTTTGGAACAAAATAATCCCTTACGTTT
* *
217 TTTTGGGACAAATTAATCCCTTACGTTT
1 TTTTGGAACAAAATAATCCCTTACGTTT
245 CAAAAATGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (28 bp):
TTTTGGAACAAAATAATCCCTTACGTTT
Found at i:1125 original size:180 final size:179
Alignment explanation
Indices: 849--1177 Score: 525
Period size: 180 Copynumber: 1.8 Consensus size: 179
839 ATTATATTTA
* * * **
849 CCATTGTTTAAATGTTTATAGTTTTACTTAACTAAAAACTCTATTTTTATTTAATTTAATCTAAT
1 CCATTGTTTAAATGTTTACAATTTTACTCAACTAAAAACTCTATTTTTATTTAATCAAATCTAAT
*
914 ATATTTATAAATATTTTATTTTTATCATTTTACTATTTTAATTAAAAAACTTAGATATATTAAAA
66 ATATTTATAAATATTTTATTTTTACCATTTTACTATTTTAATTAAAAAA-TTAGATATATTAAAA
*
979 TTTTTTAAATATATTTCTTACCCTTATTTTTCAAATATATTTCTTAAATG
130 TTTTTTAAATACATTTCTTACCCTTATTTTTCAAATATATTTCTTAAATG
* *
1029 CCATTGTTTAAAAT-TTTACAATTTTACTCAATTAAGAACTCTATTTTTATTTAATCAAATCTAA
1 CCATTGTTT-AAATGTTTACAATTTTACTCAACTAAAAACTCTATTTTTATTTAATCAAATCTAA
* * *
1093 TATATTTATAATTATTTTGTTTTTACCATTTTACTATTTTAATTAAAAAATTAGATATATTAGAA
65 TATATTTATAAATATTTTATTTTTACCATTTTACTATTTTAATTAAAAAATTAGATATATTAAAA
1158 TTTTTTAAATACATTTCTTA
130 TTTTTTAAATACATTTCTTA
1178 AATTACATTA
Statistics
Matches: 136, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
179 33 0.24
180 99 0.73
181 4 0.03
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.51
Consensus pattern (179 bp):
CCATTGTTTAAATGTTTACAATTTTACTCAACTAAAAACTCTATTTTTATTTAATCAAATCTAAT
ATATTTATAAATATTTTATTTTTACCATTTTACTATTTTAATTAAAAAATTAGATATATTAAAAT
TTTTTAAATACATTTCTTACCCTTATTTTTCAAATATATTTCTTAAATG
Found at i:1811 original size:33 final size:32
Alignment explanation
Indices: 1771--1864 Score: 124
Period size: 29 Copynumber: 3.0 Consensus size: 32
1761 ACTAAATACT
1771 AAAAAAATCCCTTATGTTTTTCTTTTGGGACAA
1 AAAAAAATCCCTTATGTTTTT-TTTTGGGACAA
* *
1804 AAAAAAATCCCTAATGTTTTATTTTGGGAC--
1 AAAAAAATCCCTTATGTTTTTTTTTGGGACAA
*
1834 -AAAAAATCTCTTATGTTTTTTTTT-GGACAA
1 AAAAAAATCCCTTATGTTTTTTTTTGGGACAA
1864 A
1 A
1865 TTAGTCCCGT
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
28 4 0.08
29 21 0.40
32 9 0.17
33 19 0.36
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (32 bp):
AAAAAAATCCCTTATGTTTTTTTTTGGGACAA
Found at i:1829 original size:32 final size:33
Alignment explanation
Indices: 1771--1839 Score: 113
Period size: 32 Copynumber: 2.1 Consensus size: 33
1761 ACTAAATACT
* *
1771 AAAAAAATCCCTTATGTTTTTCTTTTGGGACAA
1 AAAAAAATCCCTAATGTTTTTATTTTGGGACAA
1804 AAAAAAATCCCTAATG-TTTTATTTTGGGACAA
1 AAAAAAATCCCTAATGTTTTTATTTTGGGACAA
1836 AAAA
1 AAAA
1840 TCTCTTATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 19 0.56
33 15 0.44
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.35
Consensus pattern (33 bp):
AAAAAAATCCCTAATGTTTTTATTTTGGGACAA
Found at i:2046 original size:29 final size:29
Alignment explanation
Indices: 2009--2075 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
1999 CTCATTTTCG
* *
2009 AAACGTAAGGGATTAATTTGTCCCGAAA-A
1 AAACATAAGGGATT-ATTTGTCCCAAAACA
2038 AAACATAAGGGATTATTTGTCCCAAAAGCA
1 AAACATAAGGGATTATTTGTCCCAAAA-CA
2068 AAACATAA
1 AAACATAA
2076 TAGATTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 12 0.35
29 13 0.38
30 9 0.26
ACGTcount: A:0.46, C:0.15, G:0.16, T:0.22
Consensus pattern (29 bp):
AAACATAAGGGATTATTTGTCCCAAAACA
Found at i:2883 original size:15 final size:15
Alignment explanation
Indices: 2859--2930 Score: 54
Period size: 11 Copynumber: 5.4 Consensus size: 15
2849 AAATTACTTA
2859 GTTT-ATTAGTTTAT
1 GTTTAATTAGTTTAT
2873 GTTTAATTAG--TA-
1 GTTTAATTAGTTTAT
*
2885 -TCTAATTAGTTTAT
1 GTTTAATTAGTTTAT
*
2899 GATTAATTAG--TA-
1 GTTTAATTAGTTTAT
2911 -TTTAATTAGTTTAT
1 GTTTAATTAGTTTAT
*
2925 GATTAA
1 GTTTAA
2931 AATGAAGGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 17
0.67 0.08 0.26
Matches are distributed among these distances:
11 16 0.36
13 8 0.18
14 4 0.09
15 16 0.36
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.54
Consensus pattern (15 bp):
GTTTAATTAGTTTAT
Found at i:2892 original size:26 final size:26
Alignment explanation
Indices: 2863--2930 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
2853 TACTTAGTTT
*
2863 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGATTAATTAGTATCTA
*
2889 ATTAGTTTATGATTAATTAGTATTTA
1 ATTAGTTTATGATTAATTAGTATCTA
2915 ATTAGTTTATGATTAA
1 ATTAGTTTATGATTAA
2931 AATGAAGGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.53
Consensus pattern (26 bp):
ATTAGTTTATGATTAATTAGTATCTA
Found at i:2974 original size:24 final size:25
Alignment explanation
Indices: 2940--2998 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
2930 AAATGAAGGA
*
2940 AAATGAA-TTTGAAG-ATTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
2963 AAATGAAGTTTGAAGAAGTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
2988 AAATGAAGTTT
1 AAATGAAGTTT
2999 AGGGTTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 7 0.21
24 7 0.21
25 19 0.58
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.36
Consensus pattern (25 bp):
AAATGAAGTTTGAAGAAGTTGTTAG
Found at i:11766 original size:24 final size:24
Alignment explanation
Indices: 11739--11786 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
11729 AAAACATTAT
11739 TTTTTTATAGTTTAGTGACAAAAA
1 TTTTTTATAGTTTAGTGACAAAAA
11763 TTTTTTATAGTTTAGTGACAAAAA
1 TTTTTTATAGTTTAGTGACAAAAA
11787 CAAAAGTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (24 bp):
TTTTTTATAGTTTAGTGACAAAAA
Found at i:11860 original size:15 final size:14
Alignment explanation
Indices: 11840--11870 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
11830 TTAAAAATAA
11840 TAATAATAATTATAG
1 TAATAATAA-TATAG
11855 TAATAATAATATAG
1 TAATAATAATATAG
11869 TA
1 TA
11871 CATGCCATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (14 bp):
TAATAATAATATAG
Found at i:13138 original size:6 final size:6
Alignment explanation
Indices: 13123--13154 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
13113 AAATAATACC
*
13123 CCATTA CCATTT CCATTT CCATTT CCATTT CC
1 CCATTT CCATTT CCATTT CCATTT CCATTT CC
13155 TTCCATTACC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.38, G:0.00, T:0.44
Consensus pattern (6 bp):
CCATTT
Done.