Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017936.1 Corchorus olitorius cultivar O-4 contig17969, 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: 18382
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:429 original size:27 final size:27
Alignment explanation
Indices: 381--441 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
371 ATTACCAAAA
* * *
381 TACCCGTGATGGACAAATTTACTATGT
1 TACCCCTGATGGACAAAATTACGATGT
* * *
408 TACCCCTGATTGATAAAATTACGATTT
1 TACCCCTGATGGACAAAATTACGATGT
435 TACCCCT
1 TACCCCT
442 ATAATGAGGG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (27 bp):
TACCCCTGATGGACAAAATTACGATGT
Found at i:3917 original size:53 final size:52
Alignment explanation
Indices: 3847--3996 Score: 264
Period size: 53 Copynumber: 2.9 Consensus size: 52
3837 AAAATGTTGT
*
3847 TTGAACGCTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAA
1 TTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAA
3899 TTGAACACTTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAA
1 TTGAACAC-TTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAA
* *
3952 TCGAACACTTTGAAAACTTGTTGGGAACTTTCCCACTTTGAAAAG
1 TTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAG
3997 TGATAAGTGT
Statistics
Matches: 94, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
52 43 0.46
53 51 0.54
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (52 bp):
TTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAA
Found at i:5421 original size:53 final size:52
Alignment explanation
Indices: 5339--5441 Score: 125
Period size: 53 Copynumber: 2.0 Consensus size: 52
5329 TATTGTGAGG
** * **
5339 CCTAAATCGAACAAATTGAAAACTTGATGGGAACTTTTCTTACTTTGAAAATA
1 CCTAAATCGAACAAATTGAAAACCAGATGGAAAC-TTTCCCACTTTGAAAATA
* **
5392 CCTAAATTGAACACTTTGAAAACCAGATGGAAACTTTCCCACTTTGAAAA
1 CCTAAATCGAACAAATTGAAAACCAGATGGAAACTTTCCCACTTTGAAAA
5442 CTTTAAAGGA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
52 14 0.33
53 28 0.67
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (52 bp):
CCTAAATCGAACAAATTGAAAACCAGATGGAAACTTTCCCACTTTGAAAATA
Found at i:5499 original size:7 final size:7
Alignment explanation
Indices: 5465--5489 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5455 TCTTTTTAAT
5465 TTTTGAA
1 TTTTGAA
5472 TTTTGAA
1 TTTTGAA
5479 TTTTGAA
1 TTTTGAA
5486 TTTT
1 TTTT
5490 TTGGATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (7 bp):
TTTTGAA
Found at i:10937 original size:15 final size:16
Alignment explanation
Indices: 10881--10937 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
10871 TCCGAACCGT
10881 ATGACCCGAAACCGAAA
1 ATGACCCG-AACCGAAA
*
10898 ATGACCC-AACCTAAA
1 ATGACCCGAACCGAAA
* *
10913 ATTTACCCGAACC-CAA
1 A-TGACCCGAACCGAAA
10929 ATGACCCGA
1 ATGACCCGA
10938 TATTTGAACG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 15 0.44
16 8 0.24
17 11 0.32
ACGTcount: A:0.42, C:0.33, G:0.12, T:0.12
Consensus pattern (16 bp):
ATGACCCGAACCGAAA
Found at i:11697 original size:52 final size:52
Alignment explanation
Indices: 11629--11740 Score: 152
Period size: 52 Copynumber: 2.2 Consensus size: 52
11619 TGAAATAAAC
* * * *
11629 TGAAGAACGACCACCCCCGATCGTTCCGAACTAAATTGAAACATTGAATAAT
1 TGAAGAAAGACCACCCCCGATCATTCCGAAATAAATTGAAACATTGAAGAAT
* * **
11681 TGAAGAAAGACCACCCCCGATTATTCTGAAATAAATTGAAGTATTGAAGAAT
1 TGAAGAAAGACCACCCCCGATCATTCCGAAATAAATTGAAACATTGAAGAAT
11733 TGAAGAAA
1 TGAAGAAA
11741 AAGATCAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (52 bp):
TGAAGAAAGACCACCCCCGATCATTCCGAAATAAATTGAAACATTGAAGAAT
Found at i:11860 original size:8 final size:8
Alignment explanation
Indices: 11835--11882 Score: 62
Period size: 8 Copynumber: 5.9 Consensus size: 8
11825 AATCATTCTA
11835 GAATAAATT
1 GAAT-AATT
11844 GAA-ACATT
1 GAATA-ATT
11852 GAATAATT
1 GAATAATT
11860 GAATAATT
1 GAATAATT
*
11868 GAAGAATT
1 GAATAATT
11876 GAATAAT
1 GAATAAT
11883 AGAAAAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
7 1 0.03
8 30 0.86
9 4 0.11
ACGTcount: A:0.52, C:0.02, G:0.15, T:0.31
Consensus pattern (8 bp):
GAATAATT
Found at i:11869 original size:24 final size:24
Alignment explanation
Indices: 11833--11897 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
11823 CCAATCATTC
11833 TAGAATAAATTGAA-ACATTGAATAA
1 TAGAAT-AATTGAAGA-ATTGAATAA
*
11858 TTGAATAATTGAAGAATTGAATAA
1 TAGAATAATTGAAGAATTGAATAA
* *
11882 TAGAAAAATTAAAGAA
1 TAGAATAATTGAAGAA
11898 ATACGACCCC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 29 0.83
25 6 0.17
ACGTcount: A:0.57, C:0.02, G:0.14, T:0.28
Consensus pattern (24 bp):
TAGAATAATTGAAGAATTGAATAA
Found at i:11891 original size:16 final size:16
Alignment explanation
Indices: 11833--11891 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
11823 CCAATCATTC
11833 TAGAATAAATTGAA-ACA
1 TAGAA-AAATTGAATA-A
* *
11850 TTGAATAATTGAATAA
1 TAGAAAAATTGAATAA
* *
11866 TTGAAGAATTGAATAA
1 TAGAAAAATTGAATAA
11882 TAGAAAAATT
1 TAGAAAAATT
11892 AAAGAAATAC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
16 31 0.86
17 5 0.14
ACGTcount: A:0.54, C:0.02, G:0.14, T:0.31
Consensus pattern (16 bp):
TAGAAAAATTGAATAA
Found at i:11948 original size:22 final size:22
Alignment explanation
Indices: 11923--12029 Score: 150
Period size: 22 Copynumber: 4.9 Consensus size: 22
11913 ATTCTGAAAT
*
11923 AAATTGAGGCATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
11945 AAATTGAAGCATCT-AA-ATATTG
1 AAATTGAAGCAT-TGAAGA-ATTG
11967 -AATTGAAGCATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
11988 AAATTGAAGCATTGAA-ATATTG
1 AAATTGAAGCATTGAAGA-ATTG
12010 AAATTGAAGCATTGAAGAAT
1 AAATTGAAGCATTGAAGAAT
12030 CTCCACGGTT
Statistics
Matches: 77, Mismatches: 1, Indels: 14
0.84 0.01 0.15
Matches are distributed among these distances:
20 1 0.01
21 19 0.25
22 55 0.71
23 2 0.03
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.29
Consensus pattern (22 bp):
AAATTGAAGCATTGAAGAATTG
Found at i:11971 original size:43 final size:44
Alignment explanation
Indices: 11923--12029 Score: 182
Period size: 43 Copynumber: 2.5 Consensus size: 44
11913 ATTCTGAAAT
*
11923 AAATTGAGGCATTGAAGAATTGAAATTGAAGCATCT-AAATATTG
1 AAATTGAAGCATTGAAGAATTGAAATTGAAGCAT-TGAAATATTG
11967 -AATTGAAGCATTGAAGAATTGAAATTGAAGCATTGAAATATTG
1 AAATTGAAGCATTGAAGAATTGAAATTGAAGCATTGAAATATTG
12010 AAATTGAAGCATTGAAGAAT
1 AAATTGAAGCATTGAAGAAT
12030 CTCCACGGTT
Statistics
Matches: 60, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
42 1 0.02
43 40 0.67
44 19 0.32
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.29
Consensus pattern (44 bp):
AAATTGAAGCATTGAAGAATTGAAATTGAAGCATTGAAATATTG
Found at i:11981 original size:8 final size:8
Alignment explanation
Indices: 11968--12026 Score: 63
Period size: 8 Copynumber: 7.9 Consensus size: 8
11958 TAAATATTGA
11968 ATTGAAGC
1 ATTGAAGC
*
11976 ATTGAAGA
1 ATTGAAGC
11984 ATTGAA--
1 ATTGAAGC
11990 ATTGAAGC
1 ATTGAAGC
**
11998 ATTGAAAT
1 ATTGAAGC
12006 ATTGAA--
1 ATTGAAGC
12012 ATTGAAGC
1 ATTGAAGC
12020 ATTGAAG
1 ATTGAAG
12027 AATCTCCACG
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
6 12 0.27
8 32 0.73
ACGTcount: A:0.44, C:0.05, G:0.22, T:0.29
Consensus pattern (8 bp):
ATTGAAGC
Found at i:12025 original size:14 final size:14
Alignment explanation
Indices: 11933--12005 Score: 62
Period size: 14 Copynumber: 5.1 Consensus size: 14
11923 AAATTGAGGC
11933 ATTGAAGAATTGAA
1 ATTGAAGAATTGAA
*
11947 ATTGAAGCATCT-AA
1 ATTGAAGAAT-TGAA
*
11961 A-T-ATTGAATTGAA
1 ATTGA-AGAATTGAA
11974 GCATTGAAGAATTGAA
1 --ATTGAAGAATTGAA
*
11990 ATTGAAGCATTGAA
1 ATTGAAGAATTGAA
12004 AT
1 AT
12006 ATTGAAATTG
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
12 2 0.04
13 6 0.13
14 27 0.57
15 2 0.04
16 9 0.19
17 1 0.02
ACGTcount: A:0.45, C:0.05, G:0.19, T:0.30
Consensus pattern (14 bp):
ATTGAAGAATTGAA
Found at i:13847 original size:20 final size:20
Alignment explanation
Indices: 13822--13861 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
13812 AAAAACAAAG
13822 ACAAAA-GATAATAGTAAAAA
1 ACAAAAGGA-AATAGTAAAAA
13842 ACAAAAGGAAATAGTAAAAA
1 ACAAAAGGAAATAGTAAAAA
13862 GCATCAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.70, C:0.05, G:0.12, T:0.12
Consensus pattern (20 bp):
ACAAAAGGAAATAGTAAAAA
Found at i:14394 original size:40 final size:46
Alignment explanation
Indices: 14327--14409 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 46
14317 ATATATATTA
*
14327 TTATTTATTTATTTTGAACTCATTATATA-T-TATCTAAAATATAT
1 TTATTTATTTATTTTGAACTCAATATATATTATATCTAAAATATAT
14371 TTATTTATTTA-TTT-AA-T-AATATATATTATATCTAAAATA
1 TTATTTATTTATTTTGAACTCAATATATATTATATCTAAAATA
14410 GTAAAGCTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
40 7 0.19
41 2 0.06
42 13 0.36
43 3 0.08
44 11 0.31
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.54
Consensus pattern (46 bp):
TTATTTATTTATTTTGAACTCAATATATATTATATCTAAAATATAT
Found at i:16628 original size:22 final size:22
Alignment explanation
Indices: 16597--16639 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
16587 TACTTGTTAA
* *
16597 AATTGTAAAATAAATTAGCAAT
1 AATTGAAAAATAAAATAGCAAT
16619 AATTGAAAAATAAAATAGCAA
1 AATTGAAAAATAAAATAGCAA
16640 AAATACATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.60, C:0.05, G:0.09, T:0.26
Consensus pattern (22 bp):
AATTGAAAAATAAAATAGCAAT
Found at i:18157 original size:16 final size:16
Alignment explanation
Indices: 18136--18166 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18126 TTGAAAAATA
18136 TTACTAAATATTTATT
1 TTACTAAATATTTATT
*
18152 TTACTAAATCTTTAT
1 TTACTAAATATTTAT
18167 AATATTTAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (16 bp):
TTACTAAATATTTATT
Done.