Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012190.1 Corchorus olitorius cultivar O-4 contig12223, 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: 24043
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:147 original size:33 final size:32
Alignment explanation
Indices: 105--174 Score: 122
Period size: 33 Copynumber: 2.2 Consensus size: 32
95 ACTATTGAAA
105 ACCATATTTACCCTTGCCAATTTAACATAGAAC
1 ACCATATTTACCCTTGCCAATTT-ACATAGAAC
*
138 ACCATATTTACCCTTGCCAATTTACATGGAAC
1 ACCATATTTACCCTTGCCAATTTACATAGAAC
170 ACCAT
1 ACCAT
175 TACCCTTGCA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 13 0.36
33 23 0.64
ACGTcount: A:0.34, C:0.29, G:0.07, T:0.30
Consensus pattern (32 bp):
ACCATATTTACCCTTGCCAATTTACATAGAAC
Found at i:736 original size:29 final size:29
Alignment explanation
Indices: 700--758 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
690 GTCTCAATTG
700 TCCCACTAAAATTATCTCATAAACAATCA
1 TCCCACTAAAATTATCTCATAAACAATCA
729 TCCCACTAAAATTATCTCATAAACAATCA
1 TCCCACTAAAATTATCTCATAAACAATCA
758 T
1 T
759 TTGAGTACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (29 bp):
TCCCACTAAAATTATCTCATAAACAATCA
Found at i:918 original size:15 final size:15
Alignment explanation
Indices: 900--930 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
890 AATATAGGAT
900 AAATTAGTAAGACAA
1 AAATTAGTAAGACAA
915 AAATTAGTAAGACAA
1 AAATTAGTAAGACAA
930 A
1 A
931 TAAGTATACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.13, T:0.19
Consensus pattern (15 bp):
AAATTAGTAAGACAA
Found at i:1030 original size:31 final size:31
Alignment explanation
Indices: 979--1047 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
969 TTTTGTTGAT
* *
979 TAAGTCCCAAACGTTGCAAAATCGGCTCAAA
1 TAAGTCCCAAACATTACAAAATCGGCTCAAA
* *
1010 TCAGTCCCTAACATTACAAAATCGGCTCAAA
1 TAAGTCCCAAACATTACAAAATCGGCTCAAA
1041 TAAGTCC
1 TAAGTCC
1048 ATAGATTCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.38, C:0.28, G:0.13, T:0.22
Consensus pattern (31 bp):
TAAGTCCCAAACATTACAAAATCGGCTCAAA
Found at i:1458 original size:20 final size:20
Alignment explanation
Indices: 1433--1475 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1423 GTGTAAATTA
1433 ATTTTTTATTAAAAAATCTG
1 ATTTTTTATTAAAAAATCTG
* * *
1453 ATTTTTTTTTCAAAATTCTG
1 ATTTTTTATTAAAAAATCTG
1473 ATT
1 ATT
1476 CTTAATTCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.56
Consensus pattern (20 bp):
ATTTTTTATTAAAAAATCTG
Found at i:2108 original size:5 final size:5
Alignment explanation
Indices: 2094--2133 Score: 71
Period size: 5 Copynumber: 8.0 Consensus size: 5
2084 TCAAGTAACT
*
2094 AAAGG AAAGG GAAGG AAAGG AAAGG AAAGG AAAGG AAAGG
1 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG
2134 GGAGGGAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.57, C:0.00, G:0.42, T:0.00
Consensus pattern (5 bp):
AAAGG
Found at i:2392 original size:20 final size:21
Alignment explanation
Indices: 2359--2405 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
2349 AAAAAAAACG
* *
2359 AAAAAATTAGAAATTTTCAAC
1 AAAAAAATAGAAATCTTCAAC
2380 AAAAAAATA-AAATCTTC-AC
1 AAAAAAATAGAAATCTTCAAC
*
2399 AAGAAAA
1 AAAAAAA
2406 GAAATGAGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 8 0.35
20 7 0.30
21 8 0.35
ACGTcount: A:0.64, C:0.11, G:0.04, T:0.21
Consensus pattern (21 bp):
AAAAAAATAGAAATCTTCAAC
Found at i:4983 original size:178 final size:177
Alignment explanation
Indices: 4671--5001 Score: 540
Period size: 178 Copynumber: 1.9 Consensus size: 177
4661 TTGTAATATT
* * * *
4671 TTAAGTAGACCGTCTATTTCCGTTAACCGAAACAACTAATTTTTTGGAAGCATTTTTTATACCTT
1 TTAAGTAGACCGTCTATTCCCGTTAACCAAAACAACAAATTTTTTGGAAGCATTTTTTATAACTT
4736 GAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGAAACAACTTTTCAAGAG
66 GAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGAAACAACTTTT-AAGAG
* *
4801 ACACTTGAATCATCTCAATCAGACATCTAGAGCAAAAGTTATATAATA
130 ACACTTAAATCACCTCAATCAGACATCTAGAGCAAAAGTTATATAATA
*
4849 TTAAGTGGACCGTCTATTCCCGTTAACCAAAACAACAAATTTTTTGGAAGCATTTTTTA-AACTT
1 TTAAGTAGACCGTCTATTCCCGTTAACCAAAACAACAAATTTTTTGGAAGCATTTTTTATAACTT
4913 GAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGAAACAATCTTTT-AGT
66 G-AACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGAAACAA-CTTTTAAG-
*
4977 AGACACTTAAATCACCTTAATCAGA
128 AGACACTTAAATCACCTCAATCAGA
5002 TAACCGGAGA
Statistics
Matches: 142, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
177 7 0.05
178 130 0.92
179 5 0.04
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.34
Consensus pattern (177 bp):
TTAAGTAGACCGTCTATTCCCGTTAACCAAAACAACAAATTTTTTGGAAGCATTTTTTATAACTT
GAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGAAACAACTTTTAAGAGA
CACTTAAATCACCTCAATCAGACATCTAGAGCAAAAGTTATATAATA
Found at i:5743 original size:13 final size:13
Alignment explanation
Indices: 5720--5760 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
5710 TTGAAATTTG
5720 AATTGAAACCCCAA
1 AATT-AAACCCCAA
5734 AATTAAACCCCAA
1 AATTAAACCCCAA
*
5747 AAAT-AACCCCAA
1 AATTAAACCCCAA
5759 AA
1 AA
5761 GCAACCTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 10 0.38
13 12 0.46
14 4 0.15
ACGTcount: A:0.56, C:0.29, G:0.02, T:0.12
Consensus pattern (13 bp):
AATTAAACCCCAA
Found at i:8898 original size:45 final size:45
Alignment explanation
Indices: 8849--9072 Score: 288
Period size: 45 Copynumber: 4.9 Consensus size: 45
8839 AGATCTTTTC
*
8849 TTTGTTTGTAAAGGAGAAGATTCTGATTTTGTTCTTGATGAAGGA
1 TTTGTTTGTGAAGGAGAAGATTCTGATTTTGTTCTTGATGAAGGA
* *
8894 TTTGTTTGTGAAGGAGAAGATTATGATTTTGTTCTTGATTAAGGA
1 TTTGTTTGTGAAGGAGAAGATTCTGATTTTGTTCTTGATGAAGGA
* * * * *
8939 TTTGATTGATTATAAAGGACAAGATTATGATTTTGTTCTTGATGAAGGG
1 TTTG--T--TTGTGAAGGAGAAGATTCTGATTTTGTTCTTGATGAAGGA
8988 TTTGTTTGTGAAGGAGAAGATTCTGATTTTGTTCTTGATGAAGGA
1 TTTGTTTGTGAAGGAGAAGATTCTGATTTTGTTCTTGATGAAGGA
* * * *
9033 TTTGTTTGTGAGGGAGAGGAGTCTGAGTTT-TTCATTGATG
1 TTTGTTTGTGAAGGAGAAGATTCTGATTTTGTTC-TTGATG
9073 GAAAAAGATT
Statistics
Matches: 157, Mismatches: 17, Indels: 10
0.85 0.09 0.05
Matches are distributed among these distances:
44 3 0.02
45 113 0.72
47 2 0.01
49 39 0.25
ACGTcount: A:0.25, C:0.04, G:0.28, T:0.42
Consensus pattern (45 bp):
TTTGTTTGTGAAGGAGAAGATTCTGATTTTGTTCTTGATGAAGGA
Found at i:8970 original size:94 final size:94
Alignment explanation
Indices: 8857--9036 Score: 315
Period size: 94 Copynumber: 1.9 Consensus size: 94
8847 TCTTTGTTTG
* *
8857 TAAAGGAGAAGATTCTGATTTTGTTCTTGATGAAGGATTTGTTTGTGAAGGAGAAGATTATGATT
1 TAAAGGACAAGATTATGATTTTGTTCTTGATGAAGGATTTGTTTGTGAAGGAGAAGATTATGATT
*
8922 TTGTTCTTGATTAAGGATTTGATTGATTA
66 TTGTTCTTGATGAAGGATTTGATTGATTA
* *
8951 TAAAGGACAAGATTATGATTTTGTTCTTGATGAAGGGTTTGTTTGTGAAGGAGAAGATTCTGATT
1 TAAAGGACAAGATTATGATTTTGTTCTTGATGAAGGATTTGTTTGTGAAGGAGAAGATTATGATT
9016 TTGTTCTTGATGAAGGATTTG
66 TTGTTCTTGATGAAGGATTTG
9037 TTTGTGAGGG
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
94 81 1.00
ACGTcount: A:0.28, C:0.04, G:0.27, T:0.42
Consensus pattern (94 bp):
TAAAGGACAAGATTATGATTTTGTTCTTGATGAAGGATTTGTTTGTGAAGGAGAAGATTATGATT
TTGTTCTTGATGAAGGATTTGATTGATTA
Found at i:9484 original size:24 final size:21
Alignment explanation
Indices: 9434--9485 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
9424 ATGATGCAGC
*
9434 TACTTTAATTATTTATGTCTT
1 TACTTTAATTAATTATGTCTT
9455 TA-TTTAATTAATTATGAGTCTTT
1 TACTTTAATTAATTAT--GTC-TT
9478 TACTTTAA
1 TACTTTAA
9486 CCTTAAGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 12 0.46
21 2 0.08
22 3 0.12
23 4 0.15
24 5 0.19
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.58
Consensus pattern (21 bp):
TACTTTAATTAATTATGTCTT
Found at i:12459 original size:70 final size:70
Alignment explanation
Indices: 12371--12508 Score: 267
Period size: 70 Copynumber: 2.0 Consensus size: 70
12361 AACACAAGAA
12371 TTGATTTTTGGGAACATATTTCCTACGTGTGCAGGCCTAGTTTCAATTTTAAAGGAAAGAAAGAA
1 TTGATTTTTGGGAACATATTTCCTACGTGTGCAGGCCTAGTTTCAATTTTAAAGGAAAGAAAGAA
12436 ACTTC
66 ACTTC
*
12441 TTGATTTTTGGGAACATATTTCCTATGTGTGCAGGCCTAGTTTCAATTTTAAAGGAAAGAAAGAA
1 TTGATTTTTGGGAACATATTTCCTACGTGTGCAGGCCTAGTTTCAATTTTAAAGGAAAGAAAGAA
12506 ACT
66 ACT
12509 AGTTTCAATT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (70 bp):
TTGATTTTTGGGAACATATTTCCTACGTGTGCAGGCCTAGTTTCAATTTTAAAGGAAAGAAAGAA
ACTTC
Found at i:12511 original size:30 final size:30
Alignment explanation
Indices: 12477--12539 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
12467 GTGTGCAGGC
12477 CTAGTTTCAATTTTAAAGGAAAGAAAGAAA
1 CTAGTTTCAATTTTAAAGGAAAGAAAGAAA
*
12507 CTAGTTTCAATTTTAAAGGAAAGTAAGAAA
1 CTAGTTTCAATTTTAAAGGAAAGAAAGAAA
12537 CTA
1 CTA
12540 AAAAAGATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.29
Consensus pattern (30 bp):
CTAGTTTCAATTTTAAAGGAAAGAAAGAAA
Found at i:22859 original size:6 final size:6
Alignment explanation
Indices: 22848--22887 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
22838 GTATCCATCA
22848 TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTC
1 TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTC
22888 TTTGTAATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTCAT
Done.