Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023781.1 Corchorus olitorius cultivar O-4 contig23814, 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: 28770
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:2177 original size:20 final size:20
Alignment explanation
Indices: 2152--2222 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
2142 AGCCAGGCTG
2152 CTGGGCCTGCGCTGGCGCGC
1 CTGGGCCTGCGCTGGCGCGC
*
2172 CTGGGCCTGCGCTGGCCCGC
1 CTGGGCCTGCGCTGGCGCGC
2192 CT--GCCTG-GCCTGGCGCGC
1 CTGGGCCTGCG-CTGGCGCGC
2210 CTGGGCCTGCGCT
1 CTGGGCCTGCGCT
2223 AGGCCCGCGT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
17 1 0.02
18 15 0.33
20 28 0.62
21 1 0.02
ACGTcount: A:0.00, C:0.42, G:0.41, T:0.17
Consensus pattern (20 bp):
CTGGGCCTGCGCTGGCGCGC
Found at i:2205 original size:38 final size:40
Alignment explanation
Indices: 2163--2243 Score: 139
Period size: 38 Copynumber: 2.1 Consensus size: 40
2153 TGGGCCTGCG
2163 CTGGCGCGCCTGGGCCTGCGCT-GGCCCGCCTGCCT-GGC
1 CTGGCGCGCCTGGGCCTGCGCTAGGCCCGCCTGCCTGGGC
*
2201 CTGGCGCGCCTGGGCCTGCGCTAGGCCCGCGTGCCTGGGC
1 CTGGCGCGCCTGGGCCTGCGCTAGGCCCGCCTGCCTGGGC
2241 CTG
1 CTG
2244 CACAAGCAGG
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
38 22 0.55
39 12 0.30
40 6 0.15
ACGTcount: A:0.01, C:0.42, G:0.41, T:0.16
Consensus pattern (40 bp):
CTGGCGCGCCTGGGCCTGCGCTAGGCCCGCCTGCCTGGGC
Found at i:4035 original size:39 final size:39
Alignment explanation
Indices: 3969--4125 Score: 246
Period size: 39 Copynumber: 4.1 Consensus size: 39
3959 GTACCTTCAT
*
3969 GGGGTTAAACTGA-TGGTAAGAGTGGACCCATGCCTCAG
1 GGGGTTAAACTGATTGGTAAGAGTGGACCCGTGCCTCAG
* *
4007 GGGGTTAAACTGATTGGTAAGACTGGACCCGTGCCTTAG
1 GGGGTTAAACTGATTGGTAAGAGTGGACCCGTGCCTCAG
*
4046 GGGGTTAAACTGATTGGTAAGAGTGGACCCGTGCCTTAG
1 GGGGTTAAACTGATTGGTAAGAGTGGACCCGTGCCTCAG
* *
4085 GGGATTAAACTG-TTGGTAAGAGTGGACCCCTGCCTCAG
1 GGGGTTAAACTGATTGGTAAGAGTGGACCCGTGCCTCAG
4123 GGG
1 GGG
4126 TTAGCCGTTG
Statistics
Matches: 111, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
38 40 0.36
39 71 0.64
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.24
Consensus pattern (39 bp):
GGGGTTAAACTGATTGGTAAGAGTGGACCCGTGCCTCAG
Found at i:4111 original size:77 final size:77
Alignment explanation
Indices: 3969--4125 Score: 244
Period size: 77 Copynumber: 2.0 Consensus size: 77
3959 GTACCTTCAT
*
3969 GGGGTTAAACTGATGGTAAGAGTGGACCCATGCCTCAGGGGGTTAAACTGATTGGTAAGACTGGA
1 GGGGTTAAACTGATGGTAAGAGTGGACCCATGCCTCAGGGGATTAAACTGATTGGTAAGACTGGA
* *
4034 CCCGTGCCTTAG
66 CCCCTGCCTCAG
* * *
4046 GGGGTTAAACTGATTGGTAAGAGTGGACCCGTGCCTTAGGGGATTAAACTG-TTGGTAAGAGTGG
1 GGGGTTAAACTGA-TGGTAAGAGTGGACCCATGCCTCAGGGGATTAAACTGATTGGTAAGACTGG
4110 ACCCCTGCCTCAG
65 ACCCCTGCCTCAG
4123 GGG
1 GGG
4126 TTAGCCGTTG
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
77 39 0.53
78 34 0.47
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.24
Consensus pattern (77 bp):
GGGGTTAAACTGATGGTAAGAGTGGACCCATGCCTCAGGGGATTAAACTGATTGGTAAGACTGGA
CCCCTGCCTCAG
Found at i:5162 original size:40 final size:41
Alignment explanation
Indices: 5084--5170 Score: 158
Period size: 40 Copynumber: 2.1 Consensus size: 41
5074 AGAGATCAAT
5084 TAAATTCTACATTGGAGAAAAGAAAAAGGATTACTCACTCA
1 TAAATTCTACATTGGAGAAAAGAAAAAGGATTACTCACTCA
5125 TAAATTCTACATTGGAGAAAAG-AAAAGGATTACTCACTCA
1 TAAATTCTACATTGGAGAAAAGAAAAAGGATTACTCACTCA
*
5165 TGAATT
1 TAAATT
5171 GAGTGAGCAT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 23 0.51
41 22 0.49
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (41 bp):
TAAATTCTACATTGGAGAAAAGAAAAAGGATTACTCACTCA
Found at i:6839 original size:23 final size:23
Alignment explanation
Indices: 6813--6915 Score: 129
Period size: 23 Copynumber: 4.5 Consensus size: 23
6803 TTTAAATAGG
6813 TTATCAAAATTTTATAGGGAAGT
1 TTATCAAAATTTTATAGGGAAGT
*
6836 TTATCAAAATTTTATAAGGAAGT
1 TTATCAAAATTTTATAGGGAAGT
*
6859 TTATTAAAATTTTATA-GGAAGGT
1 TTATCAAAATTTTATAGGGAA-GT
* * * *
6882 TTATCAAAATTTCATAGTG-TGA
1 TTATCAAAATTTTATAGGGAAGT
6904 TTATCAAAATTT
1 TTATCAAAATTT
6916 CACAATGTGA
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
22 17 0.24
23 53 0.75
24 1 0.01
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.42
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAAGT
Found at i:6910 original size:22 final size:22
Alignment explanation
Indices: 6882--6976 Score: 93
Period size: 22 Copynumber: 4.3 Consensus size: 22
6872 ATAGGAAGGT
*
6882 TTATCAAAATTTCATAGTGTGA
1 TTATCAAAATTTCATAATGTGA
*
6904 TTATCAAAATTTCACAATGTGA
1 TTATCAAAATTTCATAATGTGA
* * * *
6926 TTA-CTAACATTTCATATTGGGG
1 TTATC-AAAATTTCATAATGTGA
* * *
6948 TTTTCAAAATTTTATAATGTGC
1 TTATCAAAATTTCATAATGTGA
6970 TTATCAA
1 TTATCAA
6977 CGTTATCAAA
Statistics
Matches: 57, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
21 1 0.02
22 55 0.96
23 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (22 bp):
TTATCAAAATTTCATAATGTGA
Found at i:7009 original size:22 final size:22
Alignment explanation
Indices: 6978--7123 Score: 98
Period size: 22 Copynumber: 6.6 Consensus size: 22
6968 GCTTATCAAC
6978 GTTATCAAAATTTCATAGTGAG
1 GTTATCAAAATTTCATAGTGAG
* * *
7000 GTCATCAAAATTCCATAG-GCAT
1 GTTATCAAAATTTCATAGTG-AG
* * * *
7022 GTTAACAAAATTTAATAGTAAAT
1 GTTATCAAAATTTCATAGT-GAG
* * * **
7045 TTTTTCGAAATTTCATAGTGTC
1 GTTATCAAAATTTCATAGTGAG
*
7067 ATTATCAAAATTTCATA-TGAAG
1 GTTATCAAAATTTCATAGTG-AG
* * *
7089 GTTATTAAAATTTCATTGGGAG
1 GTTATCAAAATTTCATAGTGAG
*
7111 GTCATCAAAATTT
1 GTTATCAAAATTT
7124 TAATATGGTA
Statistics
Matches: 92, Mismatches: 27, Indels: 10
0.71 0.21 0.08
Matches are distributed among these distances:
21 3 0.03
22 72 0.78
23 17 0.18
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGTGAG
Found at i:8028 original size:21 final size:19
Alignment explanation
Indices: 7981--8038 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
7971 CTGTTTGGCA
7981 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* * *
8000 ATTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA--C
8021 ACTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
8039 TTAGAGCAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.31
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:15799 original size:30 final size:30
Alignment explanation
Indices: 15763--15823 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
15753 GACTCCACGT
15763 CCTCAATCCGATGGCAACTTTTATCAACGA
1 CCTCAATCCGATGGCAACTTTTATCAACGA
* * *
15793 CCTCAATCTGATGGCACCTTTTATCAGCGA
1 CCTCAATCCGATGGCAACTTTTATCAACGA
15823 C
1 C
15824 AAAGGAAGCC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (30 bp):
CCTCAATCCGATGGCAACTTTTATCAACGA
Found at i:21084 original size:107 final size:105
Alignment explanation
Indices: 20860--21117 Score: 360
Period size: 107 Copynumber: 2.5 Consensus size: 105
20850 TTTTTCTAAC
* ** *
20860 CCTTAAAATAAAATTTTAATTTTCATTT-GGGCTAAACTTAGTG-AATTAGTTATATATTTAATT
1 CCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTAATT
* *
20923 TCTAAAACTCTATAACAATATTATTAATTATGGAATTTAA
66 TCTAAAACCCTATAACAATATTATTAATTATGAAATTTAA
* * *
20963 CCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTATT
1 CCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTAATT
* *
21028 TTTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT-A
66 TCTAAAACCCTATAACAAT--ATTATTAATTATGAAATTTAA
*
21069 CTCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAAT
1 C-CTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAAT
21118 CAAGGCTAAA
Statistics
Matches: 138, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
103 24 0.17
104 15 0.11
105 34 0.25
106 2 0.01
107 63 0.46
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (105 bp):
CCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTAATT
TCTAAAACCCTATAACAATATTATTAATTATGAAATTTAA
Found at i:25670 original size:29 final size:29
Alignment explanation
Indices: 25628--25842 Score: 216
Period size: 29 Copynumber: 7.4 Consensus size: 29
25618 TTAGTCTCTA
25628 ATGGTCATTTTTGCATATCCAGGGGCATT
1 ATGGTCATTTTTGCATATCCAGGGGCATT
25657 ATGGTCATTTTTGCATATCCAGGGGCATT
1 ATGGTCATTTTTGCATATCCAGGGGCATT
* *
25686 TTGGTCATTTTTGCATATCCAAGGGCATT
1 ATGGTCATTTTTGCATATCCAGGGGCATT
* ** * * *
25715 ATGGTCGTTTTCACGTATCCCA-TGGCTTT
1 ATGGTCATTTTTGCATAT-CCAGGGGCATT
* ** * * *
25744 TTTATCATTTTTGCACATTCAGGAGCATT
1 ATGGTCATTTTTGCATATCCAGGGGCATT
* * ** *
25773 TTGGTCATTTTTGCACATCCAATGGTATT
1 ATGGTCATTTTTGCATATCCAGGGGCATT
* *
25802 TTGGTCATTTTTGCACATCCAAGGGGCATT
1 ATGGTCATTTTTGCATATCC-AGGGGCATT
25832 ATGGTCATTTT
1 ATGGTCATTTT
25843 GGTTTTATTC
Statistics
Matches: 151, Mismatches: 32, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
28 2 0.01
29 130 0.86
30 19 0.13
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.41
Consensus pattern (29 bp):
ATGGTCATTTTTGCATATCCAGGGGCATT
Found at i:25843 original size:58 final size:58
Alignment explanation
Indices: 25629--25842 Score: 245
Period size: 58 Copynumber: 3.7 Consensus size: 58
25619 TAGTCTCTAA
* * ** *
25629 TGGTCATTTTTGCATATCCAGGGGCATTATGGTCATTTTTGCATATCCAGGGGCATTT
1 TGGTCATTTTTGCACATCCAGGGGCATTATGGTCATTTTTGCACATCCAATGGTATTT
* * * *
25687 TGGTCATTTTTGCATATCCAAGGGCATTATGGTC-GTTTT-CACGTATCCCATGGCT-TTT
1 TGGTCATTTTTGCACATCCAGGGGCATTATGGTCATTTTTGCAC--ATCCAATGG-TATTT
** * * *
25745 TTATCATTTTTGCACATTCAGGAGCATTTTGGTCATTTTTGCACATCCAATGGTATTT
1 TGGTCATTTTTGCACATCCAGGGGCATTATGGTCATTTTTGCACATCCAATGGTATTT
25803 TGGTCATTTTTGCACATCCAAGGGGCATTATGGTCATTTT
1 TGGTCATTTTTGCACATCC-AGGGGCATTATGGTCATTTT
25843 GGTTTTATTC
Statistics
Matches: 128, Mismatches: 21, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
56 2 0.02
57 5 0.04
58 96 0.75
59 22 0.17
60 3 0.02
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.42
Consensus pattern (58 bp):
TGGTCATTTTTGCACATCCAGGGGCATTATGGTCATTTTTGCACATCCAATGGTATTT
Found at i:25843 original size:87 final size:87
Alignment explanation
Indices: 25628--25842 Score: 247
Period size: 87 Copynumber: 2.5 Consensus size: 87
25618 TTAGTCTCTA
* * *
25628 ATGGTCATTTTTGCATATCCAGGGGCATTATGGTCATTTTTGCATATCCAGGGGCATTTTGGTCA
1 ATGGTCATTTTTGCACATCCAGGGGCATTATGGTCATTTTTGCACATCCAGGAGCATTTTGGTCA
*
25693 TTTTTGCATATCCAAGGGCATT
66 TTTTTGCACATCCAAGGGCATT
* * * * ** *
25715 ATGGTC-GTTTT-CACGTATCCCA-TGGCTTTTTTATCATTTTTGCACATTCAGGAGCATTTTGG
1 ATGGTCATTTTTGCAC--AT-CCAGGGGCATTATGGTCATTTTTGCACATCCAGGAGCATTTTGG
* *
25777 TCATTTTTGCACATCCAATGGTATT
63 TCATTTTTGCACATCCAAGGGCATT
*
25802 TTGGTCATTTTTGCACATCCAAGGGGCATTATGGTCATTTT
1 ATGGTCATTTTTGCACATCC-AGGGGCATTATGGTCATTTT
25843 GGTTTTATTC
Statistics
Matches: 101, Mismatches: 20, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
85 2 0.02
86 6 0.06
87 70 0.69
88 20 0.20
89 3 0.03
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.41
Consensus pattern (87 bp):
ATGGTCATTTTTGCACATCCAGGGGCATTATGGTCATTTTTGCACATCCAGGAGCATTTTGGTCA
TTTTTGCACATCCAAGGGCATT
Done.