Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013270.1 Corchorus olitorius cultivar O-4 contig13303, 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: 15732
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:906 original size:59 final size:60
Alignment explanation
Indices: 838--970 Score: 223
Period size: 59 Copynumber: 2.2 Consensus size: 60
828 AATTAACATA
*
838 TAGAATTGAATAGTTAATAAATTTGAATATAACGTTAATAACGTCAAC-AATTAAAGTTG
1 TAGAATTGAATAGTTAATAAAATTGAATATAACGTTAATAACGTCAACAAATTAAAGTTG
* *
897 TAGAATTGAATAGTTAATAAAATTGAATATAACGTTAATAATGTTAACAAATTAAAGTTG
1 TAGAATTGAATAGTTAATAAAATTGAATATAACGTTAATAACGTCAACAAATTAAAGTTG
*
957 TATAATTGAATAGT
1 TAGAATTGAATAGT
971 ATACTCTATA
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
59 45 0.65
60 24 0.35
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.35
Consensus pattern (60 bp):
TAGAATTGAATAGTTAATAAAATTGAATATAACGTTAATAACGTCAACAAATTAAAGTTG
Found at i:1244 original size:25 final size:25
Alignment explanation
Indices: 1201--1251 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 25
1191 TGATAAATTT
1201 TTATATATAGTTATGATTTCTTAAAAA
1 TTATATATAGTTATGA-TT-TTAAAAA
*
1228 TTATATGTA-TTAT-ATTTTAAAAA
1 TTATATATAGTTATGATTTTAAAAA
1251 T
1 T
1252 AATGTGGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 8 0.35
24 2 0.09
25 1 0.04
26 4 0.17
27 8 0.35
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (25 bp):
TTATATATAGTTATGATTTTAAAAA
Found at i:2712 original size:2 final size:2
Alignment explanation
Indices: 2705--2739 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2695 TCAAGAATAC
* *
2705 AT AT AT AT AT AT AT AG AT AA AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2740 CTAGCAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (2 bp):
AT
Found at i:2861 original size:25 final size:25
Alignment explanation
Indices: 2818--2868 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 25
2808 ATGATAATTT
2818 TTATATATAGTTATGATTTCTTAAAAA
1 TTATATATAGTTATGA-TT-TTAAAAA
*
2845 TTATATGTA-TTAT-ATTTTAAAAA
1 TTATATATAGTTATGATTTTAAAAA
2868 T
1 T
2869 AATGTGGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 8 0.35
24 2 0.09
25 1 0.04
26 4 0.17
27 8 0.35
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (25 bp):
TTATATATAGTTATGATTTTAAAAA
Found at i:4232 original size:12 final size:12
Alignment explanation
Indices: 4215--4250 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
4205 TAAGACATTG
4215 AAATAGTATTAA
1 AAATAGTATTAA
4227 AAATAGTAATTAA
1 AAATAGT-ATTAA
*
4240 TAATAGTATTA
1 AAATAGTATTA
4251 TTACTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (12 bp):
AAATAGTATTAA
Found at i:4238 original size:13 final size:13
Alignment explanation
Indices: 4215--4247 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
4205 TAAGACATTG
4215 AAATAGT-ATTAA
1 AAATAGTAATTAA
4227 AAATAGTAATTAA
1 AAATAGTAATTAA
*
4240 TAATAGTA
1 AAATAGTA
4248 TTATTACTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (13 bp):
AAATAGTAATTAA
Found at i:4390 original size:2 final size:2
Alignment explanation
Indices: 4383--4409 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4373 CCAAGAATAC
4383 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4410 AACATATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8881 original size:19 final size:19
Alignment explanation
Indices: 8857--8894 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
8847 TCAATGTGTA
8857 AGTTAATAAAAAACCAATT
1 AGTTAATAAAAAACCAATT
*
8876 AGTTAATCAAAAACCAATT
1 AGTTAATAAAAAACCAATT
8895 TTTCAAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.13, G:0.05, T:0.26
Consensus pattern (19 bp):
AGTTAATAAAAAACCAATT
Found at i:9941 original size:20 final size:21
Alignment explanation
Indices: 9903--9945 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
9893 CTATCATATG
*
9903 ACTCAATTATTCAAGCAATAA
1 ACTCAATTATTCAAACAATAA
9924 ACTCAATTA-TCAAACAATAA
1 ACTCAATTATTCAAACAATAA
9944 AC
1 AC
9946 CTATCAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.51, C:0.21, G:0.02, T:0.26
Consensus pattern (21 bp):
ACTCAATTATTCAAACAATAA
Found at i:11810 original size:54 final size:55
Alignment explanation
Indices: 11683--11810 Score: 154
Period size: 54 Copynumber: 2.3 Consensus size: 55
11673 GGCTCGGACA
* *
11683 TGTCCGAGTCATGGCCTGCTGCTGGCCGGTGCCTGGCCTCGGCATGGCTCGGTGC
1 TGTCCGAGCCATGGCCTGGTGCTGGCCGGTGCCTGGCCTCGGCATGGCTCGGTGC
* * * *
11738 T-TGCCGAGCTATGCCCTGGTG-TGGCTGGTGCGC-GGCTTCGGCATGGCTCGGTGC
1 TGT-CCGAGCCATGGCCTGGTGCTGGCCGGTGC-CTGGCCTCGGCATGGCTCGGTGC
*
11792 TGTCCGGGCCATGGCCTGG
1 TGTCCGAGCCATGGCCTGG
11811 CCATGTCCGG
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
54 44 0.72
55 17 0.28
ACGTcount: A:0.05, C:0.30, G:0.40, T:0.24
Consensus pattern (55 bp):
TGTCCGAGCCATGGCCTGGTGCTGGCCGGTGCCTGGCCTCGGCATGGCTCGGTGC
Found at i:11827 original size:11 final size:11
Alignment explanation
Indices: 11792--11828 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
11782 GGCTCGGTGC
11792 TGTCCGGGCCA
1 TGTCCGGGCCA
* *
11803 TGGCCTGGCCA
1 TGTCCGGGCCA
11814 TGTCCGGGCCA
1 TGTCCGGGCCA
11825 TGTC
1 TGTC
11829 ATGGTGCCAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.08, C:0.35, G:0.35, T:0.22
Consensus pattern (11 bp):
TGTCCGGGCCA
Found at i:12809 original size:21 final size:21
Alignment explanation
Indices: 12759--12803 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
12749 GGGACACTGC
* *
12759 CCACCTGGGTTCTCAAGCAAA
1 CCACATGGGTGCTCAAGCAAA
*
12780 CCACATGGGTGCTCAAGGAAA
1 CCACATGGGTGCTCAAGCAAA
12801 CCA
1 CCA
12804 TGTGGGCGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16
Consensus pattern (21 bp):
CCACATGGGTGCTCAAGCAAA
Found at i:14856 original size:180 final size:178
Alignment explanation
Indices: 14520--14877 Score: 698
Period size: 180 Copynumber: 2.0 Consensus size: 178
14510 TACTCGAAAG
14520 AATCTTGAAAGATTCTAGGCCAATAAAATCCACAATCTAAGATTTTTCTTGCTGTCTTCTTGTGT
1 AATCTTGAAAGATTCTAGGCCAATAAAATCCACAATCTAAGATTTTTCTTGCTGTCTTCTTGTGT
14585 CCAAAGTGGCCTCCTCTCATCATTGTGGCAGAACTTCAGAACTGATTGAATTTCATTATCACGGA
66 CCAAAGTGGCCTCCTCTCATCATTGTGGCAGAACTTCAGAACTGATTGAATTTCATTATCACGGA
14650 TGCATCTCCTCATAACTTGATCAGAACCTTGTCTCCATAAGTATGGGT
131 TGCATCTCCTCATAACTTGATCAGAACCTTGTCTCCATAAGTATGGGT
14698 AATCTTGAAAGATTCTAGGCCAATAAAATCCACAATCTAAGATTTTTCTTGCTGTCTTCTTGTGT
1 AATCTTGAAAGATTCTAGGCCAATAAAATCCACAATCTAAGATTTTTCTTGCTGTCTTCTTGTGT
14763 CCAAAGTGGCCTCCGCTCTCATCATTGTGGCAGAACTTCAGAACTGATTGAATTTCATTATCACG
66 CCAAAGTGGCCT-C-CTCTCATCATTGTGGCAGAACTTCAGAACTGATTGAATTTCATTATCACG
14828 GATGCATCTCCTCATAACTTGATCAGAACCTTGTCTCCATAAGTATGGGT
129 GATGCATCTCCTCATAACTTGATCAGAACCTTGTCTCCATAAGTATGGGT
14878 CATCCCAAAG
Statistics
Matches: 178, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
178 77 0.43
179 1 0.01
180 100 0.56
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (178 bp):
AATCTTGAAAGATTCTAGGCCAATAAAATCCACAATCTAAGATTTTTCTTGCTGTCTTCTTGTGT
CCAAAGTGGCCTCCTCTCATCATTGTGGCAGAACTTCAGAACTGATTGAATTTCATTATCACGGA
TGCATCTCCTCATAACTTGATCAGAACCTTGTCTCCATAAGTATGGGT
Done.