Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015156.1 Corchorus olitorius cultivar O-4 contig15189, 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: 26912
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:2469 original size:42 final size:42
Alignment explanation
Indices: 2422--2506 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
2412 AGTGTATAGA
*
2422 AACAATACACTGTCAGTGCATCAAATATTAATCCATATTTTT
1 AACAATACACTGTCAGTGCATCAAATATTAATCCATATGTTT
2464 AACAATACACTGTCAGTGCATCAAATATTAATCCATATGTTT
1 AACAATACACTGTCAGTGCATCAAATATTAATCCATATGTTT
2506 A
1 A
2507 TTAGTTTATA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.34
Consensus pattern (42 bp):
AACAATACACTGTCAGTGCATCAAATATTAATCCATATGTTT
Found at i:2731 original size:22 final size:23
Alignment explanation
Indices: 2706--2750 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
2696 TTTTAACTCA
2706 TTATTTTTTATTTA-AAATATAT
1 TTATTTTTTATTTATAAATATAT
*
2728 TTATTTTTTATTTATTAATATAT
1 TTATTTTTTATTTATAAATATAT
2751 ATCTATATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TTATTTTTTATTTATAAATATAT
Found at i:2993 original size:157 final size:158
Alignment explanation
Indices: 2830--3269 Score: 626
Period size: 166 Copynumber: 2.8 Consensus size: 158
2820 TTTTCGGATG
* * * *
2830 TATTTCTTAAATGCCATTGTTTAAACTTTTTTAGTTTTACTCAACTAAAAACTCTACTTTTATTT
1 TATTTCTTAAATGACATTGTTTAAACTTTTATAGTTTTATTCTACTAAAAACTCTA-TTTTATTT
*
2895 AATT-ATTAAATCTAATATCTTTATAACTATTTTATTTTCACCATTTTACTATTTTAAGT-AAAA
65 AATTAATTAAATCTAATATTTTTATAACTATTTTATTTTCACCATTTTACTATTTTAAGTAAAAA
*
2958 AACTTAGATATATTAGAATTTTTTAAATA
130 AACTTAGATATATTAGAATTTTATAAATA
*
2987 TATTTCTTAAATGACATTGTTTAAACTTTTACAGTTTTATTCTACTAAAAACTCTATATTTATTT
1 TATTTCTTAAATGACATTGTTTAAACTTTTATAGTTTTATTCTACTAAAAACTCTAT-TTTATTT
* *
3052 AACTTTTATTTAATTAAATCTAATATTTTTATAACTATTTTACTTTCATCATTTTACTATTTTAA
65 -A-----A-TTAATTAAATCTAATATTTTTATAACTATTTTATTTTCACCATTTTACTATTTTAA
*
3117 TTAAAAAAACTTAGATATATTAGAATTTTATAAATA
123 GTAAAAAAACTTAGATATATTAGAATTTTATAAATA
3153 TATTTCTTAAATGACATTGTTTAAACTTTTATAGTTTTATTCTACTAAAAACTCTATTTTTATTT
1 TATTTCTTAAATGACATTGTTTAAACTTTTATAGTTTTATTCTACTAAAAACTCTA-TTTTATTT
* *
3218 AATTAATT---TC-AATATTTTTATAAATATTTTATTTTTACCATTTTA--ATTTTAA
65 AATTAATTAAATCTAATATTTTTATAACTATTTTATTTTCACCATTTTACTATTTTAA
3270 AAAGTTGGAG
Statistics
Matches: 257, Mismatches: 15, Indels: 26
0.86 0.05 0.09
Matches are distributed among these distances:
153 7 0.03
155 31 0.12
156 3 0.01
157 58 0.23
158 1 0.00
159 6 0.02
160 1 0.00
163 1 0.00
164 2 0.01
165 52 0.20
166 94 0.37
167 1 0.00
ACGTcount: A:0.36, C:0.10, G:0.03, T:0.51
Consensus pattern (158 bp):
TATTTCTTAAATGACATTGTTTAAACTTTTATAGTTTTATTCTACTAAAAACTCTATTTTATTTA
ATTAATTAAATCTAATATTTTTATAACTATTTTATTTTCACCATTTTACTATTTTAAGTAAAAAA
ACTTAGATATATTAGAATTTTATAAATA
Found at i:4037 original size:30 final size:30
Alignment explanation
Indices: 4001--4062 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
3991 AAACCAACTT
4001 TTGTTGAATTTTCTGTTAACTTTTGTTGAA
1 TTGTTGAATTTTCTGTTAACTTTTGTTGAA
4031 TTGTTGAATTTTCTGTTAACTTTTGTTGAA
1 TTGTTGAATTTTCTGTTAACTTTTGTTGAA
4061 TT
1 TT
4063 TTCTGTTAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.19, C:0.06, G:0.16, T:0.58
Consensus pattern (30 bp):
TTGTTGAATTTTCTGTTAACTTTTGTTGAA
Found at i:4175 original size:38 final size:38
Alignment explanation
Indices: 4124--4198 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
4114 GATATCCTGG
* * *
4124 CTGTTTTTGTGTACCCAGTTTGGGGGTCAGCATAGATT
1 CTGTTCTTGTGTACCCAATTTGGGGGTCAACATAGATT
*
4162 CTGTTCTTGTGTACCCAATTTGGGGGTTAACATAGAT
1 CTGTTCTTGTGTACCCAATTTGGGGGTCAACATAGAT
4199 ATGGTTGCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.19, C:0.16, G:0.27, T:0.39
Consensus pattern (38 bp):
CTGTTCTTGTGTACCCAATTTGGGGGTCAACATAGATT
Found at i:8559 original size:2 final size:2
Alignment explanation
Indices: 8552--8577 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8542 CAAAGTTCTG
8552 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
8578 GCTGGACAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:14380 original size:2 final size:2
Alignment explanation
Indices: 14373--14409 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
14363 TTAGTAGTAG
14373 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14410 TTTCTCCATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16942 original size:17 final size:17
Alignment explanation
Indices: 16920--16953 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
16910 GTGTCGGTGA
16920 GCACACAGATGGATTTC
1 GCACACAGATGGATTTC
16937 GCACACAGATGGATTTC
1 GCACACAGATGGATTTC
16954 TGTAACACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (17 bp):
GCACACAGATGGATTTC
Found at i:17098 original size:91 final size:91
Alignment explanation
Indices: 16943--17124 Score: 346
Period size: 91 Copynumber: 2.0 Consensus size: 91
16933 TTTCGCACAC
16943 AGATGGATTTCTGTAACACAATCTGCAAACAACGTCTGGCTCTCTGGCTCAAAAGATTACAGACT
1 AGATGGATTTCTGTAACACAATCTGCAAACAACGTCTGGCTCTCTGGCTCAAAAGATTACAGACT
*
17008 GGAAGATTAGTACAAATGAGTTCAAT
66 GGAAAATTAGTACAAATGAGTTCAAT
*
17034 AGATGGATTTCTGTAACACAATCTGCAAACAACGTCTGGTTCTCTGGCTCAAAAGATTACAGACT
1 AGATGGATTTCTGTAACACAATCTGCAAACAACGTCTGGCTCTCTGGCTCAAAAGATTACAGACT
17099 GGAAAATTAGTACAAATGAGTTCAAT
66 GGAAAATTAGTACAAATGAGTTCAAT
17125 GCTTATTTTT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 89 1.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (91 bp):
AGATGGATTTCTGTAACACAATCTGCAAACAACGTCTGGCTCTCTGGCTCAAAAGATTACAGACT
GGAAAATTAGTACAAATGAGTTCAAT
Found at i:17862 original size:15 final size:16
Alignment explanation
Indices: 17837--17866 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17827 AATAATTATT
17837 TTTAGATTATAATATA
1 TTTAGATTATAATATA
17853 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
17867 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:17906 original size:37 final size:35
Alignment explanation
Indices: 17826--17906 Score: 85
Period size: 36 Copynumber: 2.3 Consensus size: 35
17816 AACTTACTTC
*
17826 TAATAATTATTTTTAGATTATAATATATTTAATTA
1 TAATAATTATTTTTAGATTATAAAATATTTAATTA
* * *
17861 TAAT-ATTATTATTTATATTCATAAAACT-TTTTATTT
1 TAATAATTATT-TTTAGATT-ATAAAA-TATTTAATTA
17897 TAATAATTAT
1 TAATAATTAT
17907 GTAAAGATGT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
34 6 0.16
35 11 0.29
36 15 0.39
37 6 0.16
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (35 bp):
TAATAATTATTTTTAGATTATAAAATATTTAATTA
Found at i:18658 original size:2 final size:2
Alignment explanation
Indices: 18651--18675 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18641 TGATTTTAAT
18651 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
18676 GATCATTTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20768 original size:15 final size:15
Alignment explanation
Indices: 20748--20777 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20738 CACCATCTGC
*
20748 AATAACTTCTTCAGG
1 AATAACCTCTTCAGG
20763 AATAACCTCTTCAGG
1 AATAACCTCTTCAGG
20778 TGCTTGTTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.30
Consensus pattern (15 bp):
AATAACCTCTTCAGG
Found at i:20846 original size:15 final size:15
Alignment explanation
Indices: 20826--20917 Score: 112
Period size: 15 Copynumber: 5.9 Consensus size: 15
20816 CATCATCCTC
* *
20826 AACTTCTTCAGCATT
1 AACTTCTGCACCATT
*
20841 AACTTCTTCACCATT
1 AACTTCTGCACCATT
*
20856 AACTTCTGGACCATT
1 AACTTCTGCACCATT
20871 AACTTCTGCACCATT
1 AACTTCTGCACCATT
20886 AACTTCTGCTTCACCATT
1 AACTTCTG---CACCATT
*
20904 AACTTTTGCACCAT
1 AACTTCTGCACCAT
20918 CACCATTACC
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
15 55 0.80
18 14 0.20
ACGTcount: A:0.26, C:0.30, G:0.07, T:0.37
Consensus pattern (15 bp):
AACTTCTGCACCATT
Found at i:20917 original size:48 final size:45
Alignment explanation
Indices: 20826--20917 Score: 121
Period size: 48 Copynumber: 2.0 Consensus size: 45
20816 CATCATCCTC
* * *
20826 AACTTCTTCAGCATTAACTTCTTCACCATTAACTTCTGGACCATT
1 AACTTCTGCACCATTAACTTCTTCACCATTAACTTCTGCACCATT
*
20871 AACTTCTGCACCATTAACTTCTGCTTCACCATTAACTTTTGCACCAT
1 AACTTCTGCACCATTAAC-T-T-CTTCACCATTAACTTCTGCACCAT
20918 CACCATTACC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
45 16 0.40
46 1 0.03
47 1 0.03
48 22 0.55
ACGTcount: A:0.26, C:0.30, G:0.07, T:0.37
Consensus pattern (45 bp):
AACTTCTGCACCATTAACTTCTTCACCATTAACTTCTGCACCATT
Found at i:21191 original size:18 final size:18
Alignment explanation
Indices: 21170--21227 Score: 84
Period size: 18 Copynumber: 3.3 Consensus size: 18
21160 TCACCATTCT
21170 CATCAACTTGGCCATTTC
1 CATCAACTTGGCCATTTC
* *
21188 CATCAA-AT-GCAATTTC
1 CATCAACTTGGCCATTTC
21204 CATCAACTTGGCCATTTC
1 CATCAACTTGGCCATTTC
21222 CATCAA
1 CATCAA
21228 ATGAACTTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
16 13 0.38
17 2 0.06
18 19 0.56
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.31
Consensus pattern (18 bp):
CATCAACTTGGCCATTTC
Done.