Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018487.1 Corchorus olitorius cultivar O-4 contig18520, 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: 39574
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:1138 original size:11 final size:12
Alignment explanation
Indices: 1112--1138 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1102 ACCCTTGCCT
1112 AAAACTAGAAGA
1 AAAACTAGAAGA
1124 AAAACTAGAAGA
1 AAAACTAGAAGA
1136 AAA
1 AAA
1139 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.07, G:0.15, T:0.07
Consensus pattern (12 bp):
AAAACTAGAAGA
Found at i:6076 original size:18 final size:18
Alignment explanation
Indices: 6053--6088 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
6043 GATGATGTAA
6053 AACTCTTCTTGGTCAAAT
1 AACTCTTCTTGGTCAAAT
6071 AACTCTTCTTGGTCAAAT
1 AACTCTTCTTGGTCAAAT
6089 GAATTTCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (18 bp):
AACTCTTCTTGGTCAAAT
Found at i:6242 original size:2 final size:2
Alignment explanation
Indices: 6235--6259 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6225 CTCTTAATTA
6235 GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT G
6260 ATTACCAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:6816 original size:21 final size:21
Alignment explanation
Indices: 6787--6834 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
6777 AGTTCTAATC
6787 AACT-AAGAACCCTAATTTTG
1 AACTCAAGAACCCTAATTTTG
6807 AACTCAAGAACCCTAATTTTG
1 AACTCAAGAACCCTAATTTTG
*
6828 AATTCAA
1 AACTCAA
6835 TCAGCTCCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (21 bp):
AACTCAAGAACCCTAATTTTG
Found at i:12835 original size:29 final size:30
Alignment explanation
Indices: 12803--12862 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
12793 AACAAGCTTC
12803 TGAACT-CCAATTCTGGCCAAATAAACCCT
1 TGAACTACCAATTCTGGCCAAATAAACCCT
* * * *
12832 TGAACTATCAATTTTGGTCAGATAAACCCT
1 TGAACTACCAATTCTGGCCAAATAAACCCT
12862 T
1 T
12863 CTGCTATGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (30 bp):
TGAACTACCAATTCTGGCCAAATAAACCCT
Found at i:13164 original size:29 final size:30
Alignment explanation
Indices: 13121--13181 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
13111 CTTATCCAGG
* *
13121 CAAAATTGGTAGTTCAGGGGCTTATTTGAC
1 CAAAATTGGAAGTTCAAGGGCTTATTTGAC
*
13151 CAAAATT-GAAGTTCAAGGGCTTGTTTGAC
1 CAAAATTGGAAGTTCAAGGGCTTATTTGAC
13180 CA
1 CA
13182 TTGACAGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
CAAAATTGGAAGTTCAAGGGCTTATTTGAC
Found at i:14942 original size:18 final size:20
Alignment explanation
Indices: 14916--14955 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
14906 GCAAGCTTCA
*
14916 TGTCTCCTTCCT-AA-AAGT
1 TGTCACCTTCCTGAAGAAGT
14934 TGTCACCTTCCTGAAGAAGT
1 TGTCACCTTCCTGAAGAAGT
14954 TG
1 TG
14956 AAATCGCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 2 0.11
20 6 0.32
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (20 bp):
TGTCACCTTCCTGAAGAAGT
Found at i:24830 original size:22 final size:22
Alignment explanation
Indices: 24788--24830 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
24778 TTTCTAATTA
**
24788 ATTGTTTTCTTTAATTTTCTTG
1 ATTGTTTTCTTTAATAGTCTTG
24810 ATTGTTTTC-TTAGATAGTCTT
1 ATTGTTTTCTTTA-ATAGTCTT
24831 AATTACTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.16, C:0.09, G:0.12, T:0.63
Consensus pattern (22 bp):
ATTGTTTTCTTTAATAGTCTTG
Found at i:25759 original size:19 final size:18
Alignment explanation
Indices: 25726--25761 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
25716 CCATGATAAT
25726 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
25744 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
25762 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:29647 original size:11 final size:11
Alignment explanation
Indices: 29631--29660 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
29621 ACCTGTTCAT
29631 GGGCCGGGTTC
1 GGGCCGGGTTC
29642 GGGCCGGGTTC
1 GGGCCGGGTTC
29653 GGGCCGGG
1 GGGCCGGG
29661 CCTAGCCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.27, G:0.60, T:0.13
Consensus pattern (11 bp):
GGGCCGGGTTC
Found at i:31965 original size:25 final size:25
Alignment explanation
Indices: 31931--31979 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
31921 CCAAACAATC
31931 TTGAACACTCTCGCTCGGTCTCTAT
1 TTGAACACTCTCGCTCGGTCTCTAT
*
31956 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAACACTCTCGCTCGGTCTCTA
31980 CAAACTAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.14, C:0.33, G:0.18, T:0.35
Consensus pattern (25 bp):
TTGAACACTCTCGCTCGGTCTCTAT
Found at i:33602 original size:25 final size:25
Alignment explanation
Indices: 33568--33616 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
33558 TCAAACAATC
*
33568 TTGAGCACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGATCTCTAT
33593 TTGAGCACTCTCGCTCGATCTCTA
1 TTGAGCACTCTCGCTCGATCTCTA
33617 CAAACTAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.14, C:0.33, G:0.18, T:0.35
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGATCTCTAT
Found at i:37071 original size:2 final size:2
Alignment explanation
Indices: 37023--37057 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
37013 AATTATTGTT
37023 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37058 AACAACAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:39199 original size:18 final size:19
Alignment explanation
Indices: 39176--39221 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 19
39166 TTTAATTAAG
*
39176 GTTAATTAGTGTTAATTA-
1 GTTAATTAGTATTAATTAC
39194 GTTAATTAGTATTAATTAC
1 GTTAATTAGTATTAATTAC
39213 TGTTAATTA
1 -GTTAATTA
39222 ACTAATTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 17 0.68
20 8 0.32
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.50
Consensus pattern (19 bp):
GTTAATTAGTATTAATTAC
Found at i:39200 original size:28 final size:28
Alignment explanation
Indices: 39177--39248 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
39167 TTAATTAAGG
*
39177 TTAATTAGTGTTAATTAGTTAATTAGTA
1 TTAATTACTGTTAATTAGTTAATTAGTA
** *
39205 TTAATTACTGTTAATTAACTAATTTGTTA
1 TTAATTACTGTTAATTAGTTAATTAG-TA
*
39234 TTAATTAGTGTTAAT
1 TTAATTACTGTTAAT
39249 CAGTGCTAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
28 22 0.58
29 16 0.42
ACGTcount: A:0.35, C:0.03, G:0.11, T:0.51
Consensus pattern (28 bp):
TTAATTACTGTTAATTAGTTAATTAGTA
Done.