Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019388.1 Corchorus olitorius cultivar O-4 contig19421, 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: 53459
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:272 original size:33 final size:32
Alignment explanation
Indices: 231--302 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
221 CTTCCATTCA
*
231 TCAA-AGAGTAAAATGTCTTAAACTTTAAAAAT
1 TCAAGAGAGTAAAATATCTTAAA-TTTAAAAAT
* *
263 TCAAGAGAGTAAAATATCTTGAATTTGAAAAT
1 TCAAGAGAGTAAAATATCTTAAATTTAAAAAT
*
295 TCATGAGA
1 TCAAGAGA
303 CAAAAAACTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 19 0.54
33 16 0.46
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (32 bp):
TCAAGAGAGTAAAATATCTTAAATTTAAAAAT
Found at i:10491 original size:60 final size:60
Alignment explanation
Indices: 10392--10812 Score: 592
Period size: 60 Copynumber: 7.0 Consensus size: 60
10382 GTGCTTCATC
* * * * *
10392 TGGATCAGACCACGTTATGAATTCATCTGAATACCGGGGATCAAACTTCAGCCATGAATA
1 TGGACCAGACCAAGTTATGGATTCATCTGATTACTGGGGATCAAACTTCAGCCATGAATA
*
10452 TGGACGAGACCAAGTTATGGATTCATCTGATTA-TCGGGGATCAAACTTCAGCCATGAATA
1 TGGACCAGACCAAGTTATGGATTCATCTGATTACT-GGGGATCAAACTTCAGCCATGAATA
* * * * * *
10512 TGAACCAGGCCAAGTTATGGATTCATCTGGTTATTGGGGATCAAGCTTAAGCCATGAATA
1 TGGACCAGACCAAGTTATGGATTCATCTGATTACTGGGGATCAAACTTCAGCCATGAATA
*
10572 TGGACGAGACCAAGTTATGGATTCATCTGATTACTGGGGATCAAACTTCAGCCATGAATA
1 TGGACCAGACCAAGTTATGGATTCATCTGATTACTGGGGATCAAACTTCAGCCATGAATA
** * *
10632 TGGACCAGGTCAAGTTATGGATTCATTTGGTTACTGGGGATCAAACTTCAGCCATGAATA
1 TGGACCAGACCAAGTTATGGATTCATCTGATTACTGGGGATCAAACTTCAGCCATGAATA
* *
10692 TGGACCACACCAAGTTATGGATTCATCTGAATACTGGGGATCAAACTTCAGCCATGAATA
1 TGGACCAGACCAAGTTATGGATTCATCTGATTACTGGGGATCAAACTTCAGCCATGAATA
* * * * * * *
10752 CGTACCGGACCAAATTATGGATTCATTTGATTACTGGGGATCAAACATCGGCCATGAATA
1 TGGACCAGACCAAGTTATGGATTCATCTGATTACTGGGGATCAAACTTCAGCCATGAATA
10812 T
1 T
10813 AGATATGAAC
Statistics
Matches: 319, Mismatches: 40, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
60 318 1.00
61 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (60 bp):
TGGACCAGACCAAGTTATGGATTCATCTGATTACTGGGGATCAAACTTCAGCCATGAATA
Found at i:11292 original size:20 final size:20
Alignment explanation
Indices: 11267--11306 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
11257 TAATCGTGTC
*
11267 AAGACACGATTAACACGTTT
1 AAGACACGAGTAACACGTTT
*
11287 AAGACACGAGTGACACGTTT
1 AAGACACGAGTAACACGTTT
11307 TAATTAACGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (20 bp):
AAGACACGAGTAACACGTTT
Found at i:11613 original size:24 final size:24
Alignment explanation
Indices: 11585--11639 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
11575 TCGTGTCTGA
11585 ATCGTGTCGGACACGATTAAGAAT
1 ATCGTGTCGGACACGATTAAGAAT
11609 ATCGTGTCGGACACGATTAAGAAT
1 ATCGTGTCGGACACGATTAAGAAT
11633 ATCGTGT
1 ATCGTGT
11640 TTCGTGTCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.27
Consensus pattern (24 bp):
ATCGTGTCGGACACGATTAAGAAT
Found at i:11947 original size:49 final size:49
Alignment explanation
Indices: 11884--11980 Score: 167
Period size: 49 Copynumber: 2.0 Consensus size: 49
11874 AGATATTTTT
*
11884 ACTCTAATCATATATTATATATATAGTATAGTTAATTGAAATATTTGAC
1 ACTCTAATCATATATTATATATATAATATAGTTAATTGAAATATTTGAC
* *
11933 ACTCTAATTATATATTATATATATAATTTAGTTAATTGAAATATTTGA
1 ACTCTAATCATATATTATATATATAATATAGTTAATTGAAATATTTGA
11981 AAAATTATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.45
Consensus pattern (49 bp):
ACTCTAATCATATATTATATATATAATATAGTTAATTGAAATATTTGAC
Found at i:12196 original size:21 final size:21
Alignment explanation
Indices: 12170--12214 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
12160 CAATGGTTTT
12170 CTCCATTCATAAAGACTCGAA
1 CTCCATTCATAAAGACTCGAA
12191 CTCCATTCATAAAGACTCGAA
1 CTCCATTCATAAAGACTCGAA
12212 CTC
1 CTC
12215 GAGAACTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.36, C:0.31, G:0.09, T:0.24
Consensus pattern (21 bp):
CTCCATTCATAAAGACTCGAA
Found at i:20205 original size:13 final size:13
Alignment explanation
Indices: 20187--20231 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 13
20177 GAGTGAGAGG
20187 TACTTTTTATGTA
1 TACTTTTTATGTA
*
20200 TACTTTTTTTTGGTA
1 TAC-TTTTTAT-GTA
20215 TTACTTTTTATGTA
1 -TACTTTTTATGTA
20229 TAC
1 TAC
20232 ACGTATCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 6 0.22
14 9 0.33
15 9 0.33
16 3 0.11
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (13 bp):
TACTTTTTATGTA
Found at i:35439 original size:3 final size:3
Alignment explanation
Indices: 35431--35462 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
35421 AAAATATATG
*
35431 ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
35463 ATATATATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:36497 original size:6 final size:6
Alignment explanation
Indices: 36479--36535 Score: 87
Period size: 6 Copynumber: 9.3 Consensus size: 6
36469 TTAGTAAGTA
* *
36479 ATTAGT AATTAGT ATTAGT ATTAGT ATTCGT ATTAAT ATTAGT ATTAGT
1 ATTAGT -ATTAGT ATTAGT ATTAGT ATTAGT ATTAGT ATTAGT ATTAGT
36528 ATTAGT AT
1 ATTAGT AT
36536 ATTAGTATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
6 40 0.87
7 6 0.13
ACGTcount: A:0.35, C:0.02, G:0.14, T:0.49
Consensus pattern (6 bp):
ATTAGT
Found at i:36676 original size:16 final size:16
Alignment explanation
Indices: 36655--36710 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
36645 GGGTGTTTCA
36655 AATATTATTTATTATT
1 AATATTATTTATTATT
*
36671 AATATTAATTATTAATT
1 AATATTATTTATT-ATT
*
36688 ATTA-TATTATATTATT
1 AATATTATT-TATTATT
*
36704 AGTATTA
1 AATATTA
36711 GTATTAGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
16 21 0.64
17 12 0.36
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
AATATTATTTATTATT
Found at i:36681 original size:13 final size:14
Alignment explanation
Indices: 36658--36697 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
36648 TGTTTCAAAT
*
36658 ATTATTTATTATTA
1 ATTATTAATTATTA
36672 A-TATTAATTATTA
1 ATTATTAATTATTA
36685 ATTATTATATTAT
1 ATTATTA-ATTAT
36698 ATTATTAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 12 0.52
14 6 0.26
15 5 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATTATTAATTATTA
Found at i:36683 original size:20 final size:21
Alignment explanation
Indices: 36656--36818 Score: 89
Period size: 24 Copynumber: 7.3 Consensus size: 21
36646 GGTGTTTCAA
36656 ATATTATTTATTATTAATATT
1 ATATTATTTATTATTAATATT
*
36677 A-ATTATTAATTATT-ATATT
1 ATATTATTTATTATTAATATT
* *
36696 ATATTA-TTAGTATTAGTATT
1 ATATTATTTATTATTAATATT
* *
36716 AGTATTAGTATTAGTATTAGTATT
1 A-TATTA-T-TTATTATTAATATT
* *
36740 AGTATTAGTATTAGTATTAGTATT
1 A-TATTA-T-TTATTATTAATATT
* *
36764 AGTATTAGTATTAGTATTAGTATT
1 A-TATTA-T-TTATTATTAATATT
* *
36788 AGTATTAGTATTAGTATTAGTATT
1 A-TATTA-T-TTATTATTAATATT
36812 AGTATTA
1 A-TATTA
36819 GTATTAGTAT
Statistics
Matches: 132, Mismatches: 4, Indels: 9
0.91 0.03 0.06
Matches are distributed among these distances:
19 12 0.09
20 21 0.16
21 6 0.05
24 93 0.70
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.53
Consensus pattern (21 bp):
ATATTATTTATTATTAATATT
Found at i:36701 original size:13 final size:13
Alignment explanation
Indices: 36656--36716 Score: 58
Period size: 12 Copynumber: 4.8 Consensus size: 13
36646 GGTGTTTCAA
36656 ATATTAT-TTATT
1 ATATTATATTATT
* *
36668 AT-TAATATTAAT
1 ATATTATATTATT
36680 -TATTA-ATTATT
1 ATATTATATTATT
36691 ATATTATATTATT
1 ATATTATATTATT
36704 AGTATTAGTATTA
1 A-TATTA-TATTA
36717 GTATTAGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
11 9 0.23
12 13 0.33
13 7 0.18
14 5 0.13
15 5 0.13
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.57
Consensus pattern (13 bp):
ATATTATATTATT
Found at i:36711 original size:6 final size:6
Alignment explanation
Indices: 36700--36863 Score: 321
Period size: 6 Copynumber: 27.5 Consensus size: 6
36690 TATATTATAT
36700 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
36748 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
36796 TATTAG TATTAG TATTAG TATTAG TATTAG TA-TAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
36843 TATTAG TATTAG TATTAG TAT
1 TATTAG TATTAG TATTAG TAT
36864 ATTAGTATAT
Statistics
Matches: 157, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.03
6 152 0.97
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
TATTAG
Found at i:37038 original size:12 final size:12
Alignment explanation
Indices: 37023--37066 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
37013 TATATTACAT
*
37023 TATTATTAGTAG
1 TATTAGTAGTAG
*
37035 TATTAGTATTAG
1 TATTAGTAGTAG
* *
37047 TATTAGTATTAA
1 TATTAGTAGTAG
37059 TATTAGTA
1 TATTAGTA
37067 CAAGTTGATC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (12 bp):
TATTAGTAGTAG
Found at i:37041 original size:6 final size:6
Alignment explanation
Indices: 37032--37066 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
37022 TTATTATTAG
*
37032 TAGTAT TAGTAT TAGTAT TAGTAT TAATAT TAGTA
1 TAGTAT TAGTAT TAGTAT TAGTAT TAGTAT TAGTA
37067 CAAGTTGATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (6 bp):
TAGTAT
Found at i:37053 original size:18 final size:18
Alignment explanation
Indices: 36996--37066 Score: 63
Period size: 18 Copynumber: 3.8 Consensus size: 18
36986 TAATATTTAT
*
36996 TATTAATTATTAATTATTA-
1 TATTAA-TATT-AGTATTAG
* *
37015 TATTACATTATTATTAGTAG
1 TATTA-A-TATTAGTATTAG
*
37035 TATTAGTATTAGTATTAG
1 TATTAATATTAGTATTAG
37053 TATTAATATTAGTA
1 TATTAATATTAGTA
37067 CAAGTTGATC
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
18 23 0.51
19 11 0.24
20 11 0.24
ACGTcount: A:0.38, C:0.01, G:0.08, T:0.52
Consensus pattern (18 bp):
TATTAATATTAGTATTAG
Found at i:37880 original size:6 final size:6
Alignment explanation
Indices: 37869--37947 Score: 126
Period size: 6 Copynumber: 13.5 Consensus size: 6
37859 ATGTAGTATA
* *
37869 TATTAG TATTAG TATTAG TATTAG TATTAG TACTGG TATTAG TA-TAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
37916 TA-TAG TATTAG TATTAG TATTAG TATTAG TAT
1 TATTAG TATTAG TATTAG TATTAG TATTAG TAT
37948 ATTAGTATAT
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
5 10 0.15
6 58 0.85
ACGTcount: A:0.33, C:0.01, G:0.18, T:0.48
Consensus pattern (6 bp):
TATTAG
Found at i:37914 original size:46 final size:42
Alignment explanation
Indices: 37857--37960 Score: 147
Period size: 46 Copynumber: 2.4 Consensus size: 42
37847 GTTTCAAATA
37857 ATATGTAGTATATATTAGTATTAGTATTAGTATTAGTATTAGT
1 ATAT-TAGTATATATTAGTATTAGTATTAGTATTAGTATTAGT
37900 ACTGGTATTAGTATAGTA-TAGTATTAGTATTAGTATTAGTATTAGT
1 A----TATTAGTATA-TATTAGTATTAGTATTAGTATTAGTATTAGT
37946 ATATTAGTATATATT
1 ATATTAGTATATATT
37961 TGGACTTTTC
Statistics
Matches: 55, Mismatches: 0, Indels: 13
0.81 0.00 0.19
Matches are distributed among these distances:
41 2 0.04
42 11 0.20
43 1 0.02
46 36 0.65
47 5 0.09
ACGTcount: A:0.35, C:0.01, G:0.16, T:0.48
Consensus pattern (42 bp):
ATATTAGTATATATTAGTATTAGTATTAGTATTAGTATTAGT
Found at i:38115 original size:3 final size:3
Alignment explanation
Indices: 38107--38142 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
38097 TAGTATATAT
38107 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
38143 TATTTTAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:51356 original size:31 final size:31
Alignment explanation
Indices: 51294--51381 Score: 158
Period size: 31 Copynumber: 2.8 Consensus size: 31
51284 TAAACAATAC
*
51294 TTCTCAACTGTATTCTAAAAATTCATTATAAA
1 TTCTCAATTGTATTCTAAAAATT-ATTATAAA
51326 TTCTCAATTGTATTCTAAAAATTATTATAAA
1 TTCTCAATTGTATTCTAAAAATTATTATAAA
51357 TTCTCAATTGTATTCTAAAAATTAT
1 TTCTCAATTGTATTCTAAAAATTAT
51382 AAAATCCTTT
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 33 0.60
32 22 0.40
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.44
Consensus pattern (31 bp):
TTCTCAATTGTATTCTAAAAATTATTATAAA
Done.