Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017383.1 Corchorus olitorius cultivar O-4 contig17416, 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: 20624
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:626 original size:60 final size:60
Alignment explanation
Indices: 559--678 Score: 197
Period size: 60 Copynumber: 2.0 Consensus size: 60
549 CATACTTATA
*
559 TTCTAAATGCAACTAATAAAAACATTTTTGCAAACGAC-AACTAATGTTAAATTGATGGAG
1 TTCTAAATGCAACAAATAAAAACA-TTTTGCAAACGACAAACTAATGTTAAATTGATGGAG
* *
619 TTCTAAATGCAACAAATGAAAACATTTTGCAAATGACAAACTAATGTTAAATTGATGGAG
1 TTCTAAATGCAACAAATAAAAACATTTTGCAAACGACAAACTAATGTTAAATTGATGGAG
679 GATTGCTAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 12 0.21
60 44 0.79
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.29
Consensus pattern (60 bp):
TTCTAAATGCAACAAATAAAAACATTTTGCAAACGACAAACTAATGTTAAATTGATGGAG
Found at i:910 original size:29 final size:28
Alignment explanation
Indices: 878--1010 Score: 115
Period size: 29 Copynumber: 4.7 Consensus size: 28
868 AAATGAACTT
* *
878 AAAATGATCAAAATGCTCCTGAATATGCA
1 AAAATGACCAAAATGCCCCTGAATATG-A
* *
907 AAAATGACCATAATGCCCCTGAATGTGA
1 AAAATGACCAAAATGCCCCTGAATATGA
* ** * *
935 ATAATGACCAAAATGCCCCCTGGGTTTTTA
1 AAAATGACCAAAATG-CCCCT-GAATATGA
* *
965 AAAATGACTAAAATGCCCCTGAATGTG-
1 AAAATGACCAAAATGCCCCTGAATATGA
* *
992 CAAATGACTAAAATGCCCC
1 AAAATGACCAAAATGCCCC
1011 CCCTAGATTT
Statistics
Matches: 85, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
27 18 0.21
28 17 0.20
29 33 0.39
30 17 0.20
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTGAATATGA
Found at i:947 original size:57 final size:56
Alignment explanation
Indices: 878--1010 Score: 149
Period size: 58 Copynumber: 2.3 Consensus size: 56
868 AAATGAACTT
* * *
878 AAAATGATCAAAATGCTCCTGAATATGCAAAAATGACCATAATGCCCCTGAATGTG
1 AAAATGACCAAAATGCCCCTGAATATGCAAAAATGACCAAAATGCCCCTGAATGTG
** * ** *
934 AATAATGACCAAAATGCCCCCTGGGTTTTTAAAAATGACTAAAATGCCCCTGAATGTG
1 AA-AATGACCAAAATG-CCCCTGAATATGCAAAAATGACCAAAATGCCCCTGAATGTG
* *
992 CAAATGACTAAAATGCCCC
1 AAAATGACCAAAATGCCCC
1011 CCCTAGATTT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
56 6 0.09
57 24 0.38
58 34 0.53
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (56 bp):
AAAATGACCAAAATGCCCCTGAATATGCAAAAATGACCAAAATGCCCCTGAATGTG
Found at i:1027 original size:58 final size:58
Alignment explanation
Indices: 906--1042 Score: 170
Period size: 58 Copynumber: 2.4 Consensus size: 58
896 CTGAATATGC
* * *
906 AAAAATGACCATAATGCCCCTGAATGTGAATAATGACCAAAATGCCCCCTGGGTTTTT
1 AAAAATGACCAAAATGCCCCTGAATGTGAATAATGACCAAAATGCCCCCTGAGATTTT
* * *
964 AAAAATGACTAAAATGCCCCTGAATGTGCA-AATGACTAAAATGCCCCCCCT-AGATTTT
1 AAAAATGACCAAAATGCCCCTGAATGTGAATAATGACCAAAATG--CCCCCTGAGATTTT
* *
1022 GAAAATGACCGAAATGCCCCT
1 AAAAATGACCAAAATGCCCCT
1043 AGTTGATCCT
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
57 12 0.18
58 50 0.74
59 6 0.09
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.23
Consensus pattern (58 bp):
AAAAATGACCAAAATGCCCCTGAATGTGAATAATGACCAAAATGCCCCCTGAGATTTT
Found at i:3351 original size:25 final size:25
Alignment explanation
Indices: 3318--3369 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
3308 AATTAAGAAA
3318 TATATTGATCAAAATGCAATAGTAC
1 TATATTGATCAAAATGCAATAGTAC
3343 TATATTGATCAAAATGCAATAGTAC
1 TATATTGATCAAAATGCAATAGTAC
3368 TA
1 TA
3370 AATGGAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (25 bp):
TATATTGATCAAAATGCAATAGTAC
Found at i:3503 original size:29 final size:29
Alignment explanation
Indices: 3467--3603 Score: 208
Period size: 29 Copynumber: 4.8 Consensus size: 29
3457 AACCTAGAGC
* *
3467 ATGC-AAAATGACCAAAATGTCCTTGAAT
1 ATGCAAAAATGACCAAAATGCCCCTGAAT
*
3495 ATACAAAAATGACCAAAATGCCCCTGAAT
1 ATGCAAAAATGACCAAAATGCCCCTGAAT
3524 ATGCAAAAATGACCAAAATGCCCCTGAAT
1 ATGCAAAAATGACCAAAATGCCCCTGAAT
* *
3553 GTGCAAAAATGACCAAAATGCCCCTGAAC
1 ATGCAAAAATGACCAAAATGCCCCTGAAT
3582 ATGC--AAATGACCAAAATGCCCC
1 ATGCAAAAATGACCAAAATGCCCC
3604 CTGTATGACC
Statistics
Matches: 101, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
27 18 0.18
28 3 0.03
29 80 0.79
ACGTcount: A:0.44, C:0.25, G:0.14, T:0.18
Consensus pattern (29 bp):
ATGCAAAAATGACCAAAATGCCCCTGAAT
Found at i:4187 original size:30 final size:30
Alignment explanation
Indices: 4092--4397 Score: 247
Period size: 30 Copynumber: 9.7 Consensus size: 30
4082 AACTCTTAAT
* * * *
4092 GCAATAATCCTACATCAGGATTAACTGATGAA
1 GCAATGATCCTAAACCAGGATTAA--AATGAA
* * *
4124 GCAATGATCCTAAACCAAGATAAAAAATAAA
1 GCAATGATCCTAAACCAGGAT-TAAAATGAA
* *
4155 GCAATGATCCTAATCCAGTATTAAAATGAA
1 GCAATGATCCTAAACCAGGATTAAAATGAA
* * *
4185 GCAATGATCCTCAACCATGATTAAAATAAA
1 GCAATGATCCTAAACCAGGATTAAAATGAA
* *
4215 GCAATGATCTTAAACCGGGATTAAAATGAA
1 GCAATGATCCTAAACCAGGATTAAAATGAA
*
4245 ACAATGATCCTAAACCAGGATTGAGAAAT-AA
1 GCAATGATCCTAAACCAGGATT-A-AAATGAA
* *
4276 ACAAGGATCCTAAACCAGGATTCGAGAAAT-AA
1 GCAATGATCCTAAACCAGGATT--A-AAATGAA
* *
4308 ACGATGATCCTAAACCAGGATTGCAAATAAACTGATAAA
1 GCAATGATCCTAAACCAGGATT----A-AAA-TG---AA
* *
4347 GTAATGATCCTAAACCAGGATTGAAATGAA
1 GCAATGATCCTAAACCAGGATTAAAATGAA
*
4377 GCAACGATCCTAAACCAGGAT
1 GCAATGATCCTAAACCAGGAT
4398 CGAAATTGAC
Statistics
Matches: 226, Mismatches: 37, Indels: 24
0.79 0.13 0.08
Matches are distributed among these distances:
30 97 0.43
31 46 0.20
32 50 0.22
33 4 0.02
34 7 0.03
35 1 0.00
39 21 0.09
ACGTcount: A:0.46, C:0.18, G:0.16, T:0.21
Consensus pattern (30 bp):
GCAATGATCCTAAACCAGGATTAAAATGAA
Found at i:4997 original size:172 final size:171
Alignment explanation
Indices: 4499--5237 Score: 1060
Period size: 172 Copynumber: 4.3 Consensus size: 171
4489 TTTTAGACAG
* * * ** *
4499 GAATTTTTGATG--AAAAACTTGATTAAATGAAATGGTACCTGGAAATTTTTACCGATTGCCCAG
1 GAATTTTTGACGAAAAAAACTTGATGAAATGAAATGGTACCCGG-AGGTTTTACCGATTGCCCGG
* * *
4562 AGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTACTCGAAGGACTTACCAATGTAAA
65 AGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCTCGGAGGACTTACCAATGCAAA
* * *
4627 CTCTGAATAGAGACCTTGACCAAGGATTTTAAACTTTAATAT
130 CTCTGAATAGAGACCTTGACCAAGGATTTTAAACATGAACAT
* ** * *
4669 GAATCTTCAATG--AAAAACTT-AGTGAAATGAAATGGTACCCGGAGGTTTTACCGATTGCCTGG
1 GAATTTTTGACGAAAAAAACTTGA-TGAAATGAAATGGTACCCGGAGGTTTTACCGATTGCCCGG
* * *
4731 AGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAACGTAAA
65 AGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCTCGGAGGACTTACCAATGCAAA
*
4796 CTCTGAATAGAGACCTTGACCAAGGATTTTAAACAGGAACAT
130 CTCTGAATAGAGACCTTGACCAAGGATTTTAAACATGAACAT
* * *
4838 GGATTTTTGACGAAAAAAACTTGATGAAAGGAAATGGTACCCGGAGGTTTTACCGTTTGCCCGGA
1 GAATTTTTGACGAAAAAAACTTGATGAAATGAAATGGTACCCGGAGGTTTTACCGATTGCCCGGA
* *
4903 GGACTTATCAGAATTAATACCCAGAAGTTTCGTGAATTTGTGC-CAGGAGGACTTACCAATGCAA
66 GGACTTATCAGAATTAATACCCGGAGGTTTC-TGAATTTGTGCTC-GGAGGACTTACCAATGCAA
*
4967 ACTCTGAATAGAGACCTTTACCAAGGATTTTAAACATGAACAT
129 ACTCTGAATAGAGACCTTGACCAAGGATTTTAAACATGAACAT
*
5010 GAATTTTTGACGAAAAAAACTTGATGAAAGGAAATGGTACCCGGAGGTTTTACCGATTGCCCGGA
1 GAATTTTTGACGAAAAAAACTTGATGAAATGAAATGGTACCCGGAGGTTTTACCGATTGCCCGGA
*
5075 GGACTTACCAGAATTAATACCCGGAGGTTTCATGAATTTGTGCTCGGAGGACTTACCAATGCAAA
66 GGACTTATCAGAATTAATACCCGGAGGTTTC-TGAATTTGTGCTCGGAGGACTTACCAATGCAAA
* * *
5140 CTCTGAATAGAGACCTTGACCAAGGATTTTAAACTTAAATAT
130 CTCTGAATAGAGACCTTGACCAAGGATTTTAAACATGAACAT
* * * *
5182 GGATTTTTGATGAAAAAAA-ATGATGAAATGAAATGGTACCCAGAGGTTTTACCGAT
1 GAATTTTTGACGAAAAAAACTTGATGAAATGAAATGGTACCCGGAGGTTTTACCGAT
5238 ATGGAAATAA
Statistics
Matches: 516, Mismatches: 46, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
169 123 0.24
170 35 0.07
171 110 0.21
172 247 0.48
173 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (171 bp):
GAATTTTTGACGAAAAAAACTTGATGAAATGAAATGGTACCCGGAGGTTTTACCGATTGCCCGGA
GGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCTCGGAGGACTTACCAATGCAAAC
TCTGAATAGAGACCTTGACCAAGGATTTTAAACATGAACAT
Found at i:6941 original size:8 final size:8
Alignment explanation
Indices: 6925--7055 Score: 198
Period size: 8 Copynumber: 16.5 Consensus size: 8
6915 TTTTATTTTG
6925 TTTTGA-T
1 TTTTGATT
6932 TTTTGAATT
1 TTTTG-ATT
6941 TTTTGAATTT
1 TTTTG-A-TT
6951 TTTTGATT
1 TTTTGATT
6959 TTTTGATT
1 TTTTGATT
6967 TTTTGATT
1 TTTTGATT
6975 TTTTGATT
1 TTTTGATT
6983 TTTTGATT
1 TTTTGATT
6991 TTTTGATT
1 TTTTGATT
6999 TTTTGATT
1 TTTTGATT
7007 TTTTGATT
1 TTTTGATT
7015 TTTTGATT
1 TTTTGATT
*
7023 TTTTTA-T
1 TTTTGATT
7030 TTTTGATT
1 TTTTGATT
7038 TTTTGA--
1 TTTTGATT
7044 TTTTGATT
1 TTTTGATT
7052 TTTT
1 TTTT
7056 TTTTCTTTTT
Statistics
Matches: 116, Mismatches: 2, Indels: 11
0.90 0.02 0.09
Matches are distributed among these distances:
6 6 0.05
7 11 0.09
8 83 0.72
9 9 0.08
10 7 0.06
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.75
Consensus pattern (8 bp):
TTTTGATT
Found at i:7462 original size:8 final size:8
Alignment explanation
Indices: 7445--7483 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
7435 AGTGCCTTTA
*
7445 TTTTCCTT
1 TTTTCATT
7453 TTTTCA-T
1 TTTTCATT
*
7460 TTTTCCTT
1 TTTTCATT
7468 TTTTCATT
1 TTTTCATT
7476 TTTTCATT
1 TTTTCATT
7484 CATTCTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTCATT
Found at i:7463 original size:15 final size:15
Alignment explanation
Indices: 7445--7478 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
7435 AGTGCCTTTA
7445 TTTTCCTTTTTTCAT
1 TTTTCCTTTTTTCAT
7460 TTTTCCTTTTTTCAT
1 TTTTCCTTTTTTCAT
7475 TTTT
1 TTTT
7479 TCATTCATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTCCTTTTTTCAT
Found at i:7487 original size:12 final size:12
Alignment explanation
Indices: 7465--7505 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
7455 TTCATTTTTC
7465 CTTTT-TTCATT
1 CTTTTCTTCATT
7476 -TTTTCATTCATT
1 CTTTTC-TTCATT
7488 CTTTTCTTCATT
1 CTTTTCTTCATT
7500 CATTTT
1 C-TTTT
7506 TTTTAATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 4 0.15
12 13 0.50
13 9 0.35
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.68
Consensus pattern (12 bp):
CTTTTCTTCATT
Found at i:7497 original size:16 final size:14
Alignment explanation
Indices: 7474--7520 Score: 60
Period size: 16 Copynumber: 3.3 Consensus size: 14
7464 CCTTTTTTCA
7474 TTTTTTCATTCATT
1 TTTTTTCATTCATT
7488 CTTTTCTTCATTCATT
1 -TTTT-TTCATTCATT
*
7504 TTTTTTAATT-ATT
1 TTTTTTCATTCATT
7517 TTTT
1 TTTT
7521 ATGGGAAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 7 0.23
14 5 0.17
15 8 0.27
16 10 0.33
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTTTCATTCATT
Done.