Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017885.1 Corchorus olitorius cultivar O-4 contig17918, 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: 27522
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1248 original size:11 final size:11
Alignment explanation
Indices: 1232--1256 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1222 AGAAAATTGT
1232 TTGTTTTTGGA
1 TTGTTTTTGGA
1243 TTGTTTTTGGA
1 TTGTTTTTGGA
1254 TTG
1 TTG
1257 ATTATTCCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.28, T:0.64
Consensus pattern (11 bp):
TTGTTTTTGGA
Found at i:7258 original size:21 final size:21
Alignment explanation
Indices: 7205--7259 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
7195 AATTTTGTCT
* *
7205 TTATATATATATATATATATA
1 TTATATATAAAAATATATATA
*
7226 TTATTTCA-AAAAATATATATA
1 TTATAT-ATAAAAATATATATA
7247 TTATATATAAAAA
1 TTATATATAAAAA
7260 GAATAATAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TTATATATAAAAATATATATA
Found at i:7259 original size:23 final size:22
Alignment explanation
Indices: 7217--7264 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 22
7207 ATATATATAT
*
7217 ATATATATATTATTTCAAAA-A
1 ATATATATATTATTTAAAAAGA
7238 ATATATATATTATATATAAAAAGA
1 ATATATATATTAT-T-TAAAAAGA
7262 ATA
1 ATA
7265 ATAGTATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 13 0.57
22 1 0.04
23 5 0.22
24 4 0.17
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
ATATATATATTATTTAAAAAGA
Found at i:12437 original size:15 final size:15
Alignment explanation
Indices: 12417--12445 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12407 CATATTTCAA
12417 TCATGAATTGAATCG
1 TCATGAATTGAATCG
12432 TCATGAATTGAATC
1 TCATGAATTGAATC
12446 ATCACCAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (15 bp):
TCATGAATTGAATCG
Found at i:14782 original size:23 final size:22
Alignment explanation
Indices: 14750--14793 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
14740 TGATGTAAAG
* *
14750 GAAAAGGAAAATGAAACAAAGAA
1 GAAAAAGAAAAGGAAA-AAAGAA
14773 GAAAAAGAAAAGGAAAAAAGA
1 GAAAAAGAAAAGGAAAAAAGA
14794 GCAACCCCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.73, C:0.02, G:0.23, T:0.02
Consensus pattern (22 bp):
GAAAAAGAAAAGGAAAAAAGAA
Found at i:15961 original size:5 final size:5
Alignment explanation
Indices: 15951--15978 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
15941 TATATATATT
15951 ATTAA ATTAA ATTAA ATTAA ATTAA ATT
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATT
15979 TATATATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
ATTAA
Found at i:16017 original size:21 final size:19
Alignment explanation
Indices: 15976--16022 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 19
15966 ATTAAATTAA
15976 ATTTATATATATTATTATT
1 ATTTATATATATTATTATT
15995 ATTTATATATATATATATATT
1 ATTTATATATAT-TAT-TATT
16016 ATTTATA
1 ATTTATA
16023 AATTTAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 12 0.46
20 3 0.12
21 11 0.42
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTATATATATTATTATT
Found at i:16671 original size:41 final size:41
Alignment explanation
Indices: 16614--16705 Score: 141
Period size: 41 Copynumber: 2.2 Consensus size: 41
16604 AATTTGATCA
* * *
16614 GGGTTGTGCATCTAGGTTTACTGGATGAGTCACCCAATAGG
1 GGGTTGTGCACCTAGGTTTACTAGATGAGTCACCCAACAGG
16655 GGGTTGTGCACCTAGGTTTACTAGATGAGTCACCCAACAGG
1 GGGTTGTGCACCTAGGTTTACTAGATGAGTCACCCAACAGG
16696 GGCGTT-TGCA
1 GG-GTTGTGCA
16706 TACACAAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
41 44 0.94
42 3 0.06
ACGTcount: A:0.22, C:0.20, G:0.32, T:0.27
Consensus pattern (41 bp):
GGGTTGTGCACCTAGGTTTACTAGATGAGTCACCCAACAGG
Found at i:18000 original size:7 final size:8
Alignment explanation
Indices: 17974--17999 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
17964 CAATGTTAGA
17974 TTTCGAAT
1 TTTCGAAT
17982 TTTCGAAT
1 TTTCGAAT
17990 TTTCGAAT
1 TTTCGAAT
17998 TT
1 TT
18000 CTAGCTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.54
Consensus pattern (8 bp):
TTTCGAAT
Found at i:18155 original size:29 final size:29
Alignment explanation
Indices: 18113--18170 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
18103 ATTAAGAGCG
18113 GGACCAATTAGCCTGGAAGTATTAGGCTA
1 GGACCAATTAGCCTGGAAGTATTAGGCTA
18142 GGACCAATTAGCCTGGAAGTATTAGGCTA
1 GGACCAATTAGCCTGGAAGTATTAGGCTA
18171 CCCATTCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (29 bp):
GGACCAATTAGCCTGGAAGTATTAGGCTA
Found at i:20110 original size:11 final size:11
Alignment explanation
Indices: 20094--20122 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
20084 AAATTAAGAA
20094 GGTCAAAAAAC
1 GGTCAAAAAAC
20105 GGTCAAAAAAC
1 GGTCAAAAAAC
20116 GGTCAAA
1 GGTCAAA
20123 GTACCTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.52, C:0.17, G:0.21, T:0.10
Consensus pattern (11 bp):
GGTCAAAAAAC
Found at i:20170 original size:31 final size:30
Alignment explanation
Indices: 20132--20231 Score: 105
Period size: 31 Copynumber: 3.3 Consensus size: 30
20122 AGTACCTAAA
*
20132 TAGTCCCTGTACTATTGGAAAAAGATCAATT
1 TAGTCCCTCTACTATT-GAAAAAGATCAATT
* * **
20163 TAGTCCCTCCATTA-TGAAATCTG-TCAATT
1 TAGTCCCTCTACTATTGAAA-AAGATCAATT
*
20192 TAGTTCCTCTACTATTGAAAAACGATCAATT
1 TAGTCCCTCTACTATTGAAAAA-GATCAATT
20223 TAGTCCCTC
1 TAGTCCCTC
20232 CGTGAAATGG
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
29 21 0.39
30 8 0.15
31 25 0.46
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (30 bp):
TAGTCCCTCTACTATTGAAAAAGATCAATT
Found at i:20947 original size:22 final size:23
Alignment explanation
Indices: 20905--20947 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
20895 AGGTTTTTGC
*
20905 TGAAATTTGATTTATGTAATATG
1 TGAAATTTGATTGATGTAATATG
20928 TGAAA-TTGATGTGATG-AATA
1 TGAAATTTGAT-TGATGTAATA
20948 ATGGTACTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.37, C:0.00, G:0.21, T:0.42
Consensus pattern (23 bp):
TGAAATTTGATTGATGTAATATG
Found at i:21595 original size:29 final size:31
Alignment explanation
Indices: 21513--21600 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 31
21503 CTCATTTCAC
* * *
21513 GGAGGGATTAAATTGATCGTTTTTCAATAGT
1 GGAGGGACTAAATTGATCATTTTTCAATAAT
* **
21544 AGAGGGAC-AAATTGA-CAGATTTC-ATAAT
1 GGAGGGACTAAATTGATCATTTTTCAATAAT
21572 GGAGGGACTAAATTGATC-TTTTTCCAATA
1 GGAGGGACTAAATTGATCATTTTT-CAATA
21601 GTATAGGGAC
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
28 11 0.25
29 15 0.34
30 9 0.20
31 9 0.20
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.33
Consensus pattern (31 bp):
GGAGGGACTAAATTGATCATTTTTCAATAAT
Found at i:21612 original size:31 final size:31
Alignment explanation
Indices: 21514--21612 Score: 98
Period size: 31 Copynumber: 3.3 Consensus size: 31
21504 TCATTTCACG
* *
21514 GAGGGATTAAATTGATCGTTTTTCAATAGTA
1 GAGGGACTAAATTGATCATTTTTCAATAGTA
** * *
21545 GAGGGAC-AAATTGA-CAGATTTC-ATAATG
1 GAGGGACTAAATTGATCATTTTTCAATAGTA
21573 GAGGGACTAAATTGATC-TTTTTCCAATAGTA
1 GAGGGACTAAATTGATCATTTTT-CAATAGTA
*
21604 TAGGGACTA
1 GAGGGACTA
21613 TTTAGGTACT
Statistics
Matches: 53, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
28 11 0.21
29 15 0.28
30 9 0.17
31 18 0.34
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.32
Consensus pattern (31 bp):
GAGGGACTAAATTGATCATTTTTCAATAGTA
Found at i:22421 original size:21 final size:21
Alignment explanation
Indices: 22397--22456 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
22387 AACCCTTTCA
22397 ATTACCCATACCATATTTGAT
1 ATTACCCATACCATATTTGAT
* *
22418 ATTA--GA-A-CAT-CTT--T
1 ATTACCCATACCATATTTGAT
22432 ATTACCCATACCATATTTGAT
1 ATTACCCATACCATATTTGAT
22453 ATTA
1 ATTA
22457 GAACATCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 14
0.61 0.09 0.30
Matches are distributed among these distances:
14 5 0.18
16 3 0.11
17 4 0.14
18 4 0.14
19 3 0.11
21 9 0.32
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.40
Consensus pattern (21 bp):
ATTACCCATACCATATTTGAT
Found at i:22443 original size:35 final size:35
Alignment explanation
Indices: 22397--22467 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
22387 AACCCTTTCA
22397 ATTACCCATACCATATTTGATATTAGAACATCTTT
1 ATTACCCATACCATATTTGATATTAGAACATCTTT
22432 ATTACCCATACCATATTTGATATTAGAACATCTTT
1 ATTACCCATACCATATTTGATATTAGAACATCTTT
22467 A
1 A
22468 ATAGTATGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.39
Consensus pattern (35 bp):
ATTACCCATACCATATTTGATATTAGAACATCTTT
Found at i:24865 original size:31 final size:31
Alignment explanation
Indices: 24828--24975 Score: 145
Period size: 31 Copynumber: 4.8 Consensus size: 31
24818 ATGGTGTCTG
*
24828 ACGTGGCATGCCACGTGTACAAAAAAGTGAC
1 ACGTGGCATGCCATGTGTACAAAAAAGTGAC
* * * *
24859 ATGTGGCACGCCATGTGTACCAAAAGGTGAC
1 ACGTGGCATGCCATGTGTACAAAAAAGTGAC
** * ** *
24890 ACGTATCACGCCATGTGTACCCAAATGTGAC
1 ACGTGGCATGCCATGTGTACAAAAAAGTGAC
** *
24921 ACGTGGCATGATATGTGTTTC-AAAAAGTGAC
1 ACGTGGCATGCCATGTG-TACAAAAAAGTGAC
*
24952 ACGTGGCATGCCACGTGTACAAAA
1 ACGTGGCATGCCATGTGTACAAAA
24976 GGATACGTGC
Statistics
Matches: 93, Mismatches: 22, Indels: 4
0.78 0.18 0.03
Matches are distributed among these distances:
30 2 0.02
31 89 0.96
32 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.21
Consensus pattern (31 bp):
ACGTGGCATGCCATGTGTACAAAAAAGTGAC
Found at i:24970 original size:62 final size:62
Alignment explanation
Indices: 24828--24975 Score: 170
Period size: 62 Copynumber: 2.4 Consensus size: 62
24818 ATGGTGTCTG
* * *
24828 ACGTGGCATGCCACGTGTACAAAAAAGTGACATGTGGCACGCCATGTGTACCAAAAGGTGAC
1 ACGTGGCATGCCACGTGTACAAAAAAGTGACACGTGGCACGACATGTGTACCAAAAAGTGAC
** * * ** * * * **
24890 ACGTATCACGCCATGTGTACCCAAATGTGACACGTGGCATGATATGTGTTTCAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACAAAAAAGTGACACGTGGCACGACATGTGTACCAAAAAGTGAC
24952 ACGTGGCATGCCACGTGTACAAAA
1 ACGTGGCATGCCACGTGTACAAAA
24976 GGATACGTGC
Statistics
Matches: 66, Mismatches: 20, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
62 66 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.21
Consensus pattern (62 bp):
ACGTGGCATGCCACGTGTACAAAAAAGTGACACGTGGCACGACATGTGTACCAAAAAGTGAC
Done.