Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019120.1 Corchorus olitorius cultivar O-4 contig19153, 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: 49677
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3231 original size:19 final size:20
Alignment explanation
Indices: 3171--3232 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 20
3161 CATTTTTTAT
*
3171 AAATCATTTTTAAATCATAG-
1 AAATCATTTTTATAT-ATAGC
* * *
3191 AAATCATTTTTCTGTA-ATC
1 AAATCATTTTTATATATAGC
3210 AAATCATTTTT-TATATAGC
1 AAATCATTTTTATATATAGC
3229 AAAT
1 AAAT
3233 TAATTGTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
18 4 0.12
19 18 0.53
20 12 0.35
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (20 bp):
AAATCATTTTTATATATAGC
Found at i:5061 original size:41 final size:41
Alignment explanation
Indices: 5016--5099 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
5006 CATATATATC
*
5016 TTGCTTTGTTAGAATCGAAGCATAATCACTGGAATTAAGAG
1 TTGCTTTGTTAGAATCGAAGCATAATCACTGAAATTAAGAG
5057 TTGCTTTGTTAGAATCGAAGCATAATCACTGAAATTAAGAG
1 TTGCTTTGTTAGAATCGAAGCATAATCACTGAAATTAAGAG
5098 TT
1 TT
5100 CAGTACTCTA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (41 bp):
TTGCTTTGTTAGAATCGAAGCATAATCACTGAAATTAAGAG
Found at i:6639 original size:28 final size:30
Alignment explanation
Indices: 6573--6646 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 30
6563 ACTCAAAACT
*
6573 AAATTACTAAT-CGATCTTTGTGCCAAAAA
1 AAATTACTAATACGATCTTTGTACCAAAAA
*
6602 AAATTACTAATACGATC-TTGTACCCAAAA
1 AAATTACTAATACGATCTTTGTACCAAAAA
6631 AAA-TACTAATACGATC
1 AAATTACTAATACGATC
6647 ATTCATACAA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
28 13 0.31
29 24 0.57
30 5 0.12
ACGTcount: A:0.45, C:0.19, G:0.08, T:0.28
Consensus pattern (30 bp):
AAATTACTAATACGATCTTTGTACCAAAAA
Found at i:23892 original size:3 final size:3
Alignment explanation
Indices: 23884--23947 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
23874 AACTATGTAT
*
23884 TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
23932 TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T
23948 ATATGTGTGT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:27310 original size:25 final size:26
Alignment explanation
Indices: 27282--27343 Score: 110
Period size: 25 Copynumber: 2.5 Consensus size: 26
27272 ATTTATTAAT
27282 AAACTAAACAAACAAG-CCAAAAAAA
1 AAACTAAACAAACAAGCCCAAAAAAA
27307 AAACTAAACAAACAAGCCCAAAAAAA
1 AAACTAAACAAACAAGCCCAAAAAAA
27333 AAAC-AAACAAA
1 AAACTAAACAAA
27344 AATAGCTCAG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 23 0.64
26 13 0.36
ACGTcount: A:0.73, C:0.21, G:0.03, T:0.03
Consensus pattern (26 bp):
AAACTAAACAAACAAGCCCAAAAAAA
Found at i:29743 original size:11 final size:11
Alignment explanation
Indices: 29700--29737 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
29690 TTCCTATATA
*
29700 AAATAAATTAT
1 AAATTAATTAT
29711 CAAA-TAATTAT
1 -AAATTAATTAT
29722 AAATTAATTAT
1 AAATTAATTAT
29733 AAATT
1 AAATT
29738 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:30116 original size:28 final size:31
Alignment explanation
Indices: 30059--30119 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
30049 CAATATTTAT
* *
30059 TTTTTTGTGTATTATTAGTATGTAACATTAA
1 TTTTTTGTGTATTATTAATATATAACATTAA
30090 TTTTTTGTGTATTA-TAATA-ATAA-ATTAA
1 TTTTTTGTGTATTATTAATATATAACATTAA
30118 TT
1 TT
30120 ATAGTTTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.25
29 3 0.11
30 4 0.14
31 14 0.50
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.56
Consensus pattern (31 bp):
TTTTTTGTGTATTATTAATATATAACATTAA
Found at i:30641 original size:107 final size:104
Alignment explanation
Indices: 30478--30686 Score: 294
Period size: 107 Copynumber: 2.0 Consensus size: 104
30468 TTCCAATTAT
** *
30478 AAATATGTTTTATTTTTTTAAGGATAAACCTTAAATTTTAAGACCCATTATTTTAGGATTTTAGA
1 AAATATGTTTTATTTTTTTAAGGAT--A-CTTAAATGGTAAGACCCATTATCTTAGGATTTTAGA
* *
30543 AAAATACTAATTTTGAACACTTTTAAATAAGTTTTAGCCCAACTA
63 AAAATA--AA-TTTGAACACTTATAAATAAGGTTTAGCCCAACTA
*
30588 AAATATGTTTTATTTTTTTAAGTGAT-CTTAAATGGTAAGACCCATTATCTTAGGGTTTTAGAAA
1 AAATATGTTTTATTTTTTTAAG-GATACTTAAATGGTAAGACCCATTATCTTAGGATTTTAGAAA
30652 AATAAATTTGAACACTTATAAATAAGGTTTAGCCC
65 AATAAATTTGAACACTTATAAATAAGGTTTAGCCC
30687 CATTATAAAG
Statistics
Matches: 92, Mismatches: 6, Indels: 8
0.87 0.06 0.08
Matches are distributed among these distances:
104 27 0.29
105 2 0.02
107 38 0.41
110 22 0.24
111 3 0.03
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (104 bp):
AAATATGTTTTATTTTTTTAAGGATACTTAAATGGTAAGACCCATTATCTTAGGATTTTAGAAAA
ATAAATTTGAACACTTATAAATAAGGTTTAGCCCAACTA
Found at i:34680 original size:14 final size:14
Alignment explanation
Indices: 34623--34704 Score: 59
Period size: 12 Copynumber: 6.0 Consensus size: 14
34613 ATCGTTTAGT
*
34623 AATATTTATAATTA
1 AATATATATAATTA
34637 AATATATATTATATATA
1 AATATATA-TA-AT-TA
*
34654 AA-AAATA-ATATTA
1 AATATATATA-ATTA
34667 AATATATATAATT-
1 AATATATATAATTA
*
34680 -ACATATATAA-T-
1 AATATATATAATTA
34691 AATATATATAATTA
1 AATATATATAATTA
34705 TTAAACGGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
11 1 0.02
12 18 0.33
13 5 0.09
14 18 0.33
15 3 0.05
16 6 0.11
17 4 0.07
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (14 bp):
AATATATATAATTA
Found at i:42431 original size:7 final size:7
Alignment explanation
Indices: 42419--42450 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
42409 TGGCCCCTTC
42419 TTTTTGT
1 TTTTTGT
42426 TTTTTGT
1 TTTTTGT
42433 TTTTTGT
1 TTTTTGT
42440 TTTTT-T
1 TTTTTGT
42446 TTTTT
1 TTTTT
42451 CCCTTATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (7 bp):
TTTTTGT
Found at i:44503 original size:31 final size:31
Alignment explanation
Indices: 44465--44540 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 31
44455 CTAAAAAAAT
44465 GATCAATTTAGTCCCTCTACTTGTAAGATTG
1 GATCAATTTAGTCCCTCTACTTGTAAGATTG
* *
44496 GATCAATTTAGTCCCTCTTCTTGTCAGATTG
1 GATCAATTTAGTCCCTCTACTTGTAAGATTG
*
44527 GATCAATTAAGTCC
1 GATCAATTTAGTCC
44541 AATTAATAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (31 bp):
GATCAATTTAGTCCCTCTACTTGTAAGATTG
Found at i:44616 original size:12 final size:12
Alignment explanation
Indices: 44599--44628 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
44589 CGTTAAGTAA
44599 TGACACGTCAGC
1 TGACACGTCAGC
44611 TGACACGTCAGC
1 TGACACGTCAGC
44623 TGACAC
1 TGACAC
44629 ATGTAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.27, C:0.33, G:0.23, T:0.17
Consensus pattern (12 bp):
TGACACGTCAGC
Found at i:45942 original size:28 final size:31
Alignment explanation
Indices: 45898--45969 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 31
45888 CCAATCTCAC
*
45898 AAGTAGAGGGACTAAATTGATATTTTT-T-T
1 AAGTAGAGGGACCAAATTGATATTTTTGTGT
*
45927 -AGTAGAGGGACCAAATTGATTTTTTTGTGT
1 AAGTAGAGGGACCAAATTGATATTTTTGTGT
45957 AAGTAGAGGGACC
1 AAGTAGAGGGACC
45970 TCCCGGGTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 24 0.63
29 1 0.03
30 1 0.03
31 12 0.32
ACGTcount: A:0.32, C:0.07, G:0.26, T:0.35
Consensus pattern (31 bp):
AAGTAGAGGGACCAAATTGATATTTTTGTGT
Found at i:46574 original size:20 final size:20
Alignment explanation
Indices: 46549--46587 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
46539 CTGCTGTTAC
46549 TGAGAGTTTGAGACCCTCAA
1 TGAGAGTTTGAGACCCTCAA
46569 TGAGAGTTTGAGACCCTCA
1 TGAGAGTTTGAGACCCTCA
46588 CAGCTTATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (20 bp):
TGAGAGTTTGAGACCCTCAA
Done.