Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020433.1 Corchorus olitorius cultivar O-4 contig20466, 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: 24769
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Found at i:1532 original size:19 final size:19
Alignment explanation
Indices: 1508--1545 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1498 TGGGATTTTT
1508 AATAATAATTATTCAATAA
1 AATAATAATTATTCAATAA
* *
1527 AATAATTATTATTTAATAA
1 AATAATAATTATTCAATAA
1546 TTAATTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
AATAATAATTATTCAATAA
Found at i:3053 original size:19 final size:19
Alignment explanation
Indices: 3024--3063 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
3014 AAGGAACTTT
*
3024 TAAAAG-AAAAATTATTAA
1 TAAAAGAAAAAATTATAAA
3042 TAAAAGGAAAAAATTATAAA
1 TAAAA-GAAAAAATTATAAA
3062 TA
1 TA
3064 CATAAAGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 1 0.05
20 13 0.68
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (19 bp):
TAAAAGAAAAAATTATAAA
Found at i:4852 original size:24 final size:24
Alignment explanation
Indices: 4825--4876 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
4815 ACGTTAGAGA
*
4825 TAATGGACAGACGATTTGAAACAT
1 TAATGGACACACGATTTGAAACAT
** * *
4849 TAATTTAGACATGATTTGAAACAT
1 TAATGGACACACGATTTGAAACAT
4873 TAAT
1 TAAT
4877 TTAGACATGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (24 bp):
TAATGGACACACGATTTGAAACAT
Found at i:4877 original size:24 final size:24
Alignment explanation
Indices: 4837--4886 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
4827 ATGGACAGAC
4837 GATTTGAAACATTAATTTAGACAT
1 GATTTGAAACATTAATTTAGACAT
4861 GATTTGAAACATTAATTTAGACAT
1 GATTTGAAACATTAATTTAGACAT
4885 GA
1 GA
4887 AGGATTAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (24 bp):
GATTTGAAACATTAATTTAGACAT
Found at i:7274 original size:30 final size:30
Alignment explanation
Indices: 7238--7325 Score: 149
Period size: 30 Copynumber: 2.9 Consensus size: 30
7228 TTGTTGCCCA
7238 AACATGCCACCCCAACCATGAATTTCAATG
1 AACATGCCACCCCAACCATGAATTTCAATG
*
7268 AACATGCCACCCCAACCATTAATTTCAATG
1 AACATGCCACCCCAACCATGAATTTCAATG
* *
7298 AACATGCCACCCCAAGCATGAACTTCAA
1 AACATGCCACCCCAACCATGAATTTCAA
7326 GAATCTCAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.38, C:0.34, G:0.09, T:0.19
Consensus pattern (30 bp):
AACATGCCACCCCAACCATGAATTTCAATG
Found at i:7862 original size:18 final size:18
Alignment explanation
Indices: 7839--7985 Score: 114
Period size: 18 Copynumber: 8.2 Consensus size: 18
7829 AAACTAAAAG
*
7839 TAACCATAACAATAATCA
1 TAACCATAACAATAATAA
*
7857 TAACCATAATAATAATAA
1 TAACCATAACAATAATAA
** *
7875 TAATAATAATAATAATAA
1 TAACCATAACAATAATAA
** *
7893 TAATAATAATAATAATAA
1 TAACCATAACAATAATAA
** *
7911 TAATAATAATAATAATAA
1 TAACCATAACAATAATAA
** *
7929 TAATAATAATAATAATAA
1 TAACCATAACAATAATAA
** *
7947 TAATAATAATAATAATAA
1 TAACCATAACAATAATAA
** *
7965 TAATAATAATAATAATAA
1 TAACCATAACAATAATAA
7983 TAA
1 TAA
7986 TATAATAATA
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 125 1.00
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (18 bp):
TAACCATAACAATAATAA
Found at i:7865 original size:12 final size:12
Alignment explanation
Indices: 7843--7995 Score: 101
Period size: 12 Copynumber: 12.8 Consensus size: 12
7833 TAAAAGTAAC
7843 CATAACAATAAT
1 CATAACAATAAT
*
7855 CATAACCATAAT
1 CATAACAATAAT
* *
7867 AATAATAATAAT
1 CATAACAATAAT
* *
7879 AATAATAATAAT
1 CATAACAATAAT
* *
7891 AATAATAATAAT
1 CATAACAATAAT
* *
7903 AATAATAATAAT
1 CATAACAATAAT
* *
7915 AATAATAATAAT
1 CATAACAATAAT
* *
7927 AATAATAATAAT
1 CATAACAATAAT
* *
7939 AATAATAATAAT
1 CATAACAATAAT
* *
7951 AATAATAATAAT
1 CATAACAATAAT
* *
7963 AATAATAATAAT
1 CATAACAATAAT
* *
7975 AATAATAATAAT
1 CATAACAATAAT
*
7987 -ATAATAATA
1 CATAACAATA
7996 TGAAAGGAAA
Statistics
Matches: 137, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
11 9 0.07
12 128 0.93
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (12 bp):
CATAACAATAAT
Found at i:7870 original size:3 final size:3
Alignment explanation
Indices: 7862--7995 Score: 261
Period size: 3 Copynumber: 45.0 Consensus size: 3
7852 AATCATAACC
7862 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
7910 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
7958 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
7996 TGAAAGGAAA
Statistics
Matches: 130, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 128 0.98
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:11175 original size:96 final size:94
Alignment explanation
Indices: 10998--11191 Score: 352
Period size: 96 Copynumber: 2.0 Consensus size: 94
10988 GGTGCGTGAA
*
10998 AATATCCATTGAATTTGTCCACGATAAACCCCAAAAGCCCATCCTTTTTTCTTGTTCCAGCACAA
1 AATACCCATTGAATTTGTCCACGATAAACCCCAAAAGCCCATCCTTTTTTCTTGTTCCAGCACAA
11063 AAAAACACCGAAGAAATCTTGAAAAGAAT
66 AAAAACACCGAAGAAATCTTGAAAAGAAT
*
11092 AATACCCATTGAATTTGTCCACGATAAACCCCCAAAAGCCCATCCTTTTTTTCTTGTTCCAGCTC
1 AATACCCATTGAATTTGTCCACGATAAA-CCCCAAAAGCCCATCC-TTTTTTCTTGTTCCAGCAC
11157 AAAAAAACACCGAAGAAATCTTGAAAAGAAT
64 AAAAAAACACCGAAGAAATCTTGAAAAGAAT
11188 AATA
1 AATA
11192 AAAGGAGATT
Statistics
Matches: 96, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
94 27 0.28
95 16 0.17
96 53 0.55
ACGTcount: A:0.39, C:0.25, G:0.10, T:0.26
Consensus pattern (94 bp):
AATACCCATTGAATTTGTCCACGATAAACCCCAAAAGCCCATCCTTTTTTCTTGTTCCAGCACAA
AAAAACACCGAAGAAATCTTGAAAAGAAT
Found at i:16359 original size:64 final size:64
Alignment explanation
Indices: 16253--16381 Score: 222
Period size: 64 Copynumber: 2.0 Consensus size: 64
16243 CCTTATTAGG
* * *
16253 AGAGGTAAGAGTTTTACCTCATAGTGGGCCGACCCGACTCGAACAAGAATTAATTTATAAATAT
1 AGAGCTAAGAGTTTTACCTCATAGTGGACCAACCCGACTCGAACAAGAATTAATTTATAAATAT
*
16317 AGAGCTAAGAGTTTTACCTCATAGTGGACCAACCCGACTCGAACAAGAATTAATTTGTAAATAT
1 AGAGCTAAGAGTTTTACCTCATAGTGGACCAACCCGACTCGAACAAGAATTAATTTATAAATAT
16381 A
1 A
16382 TAAAAAAATA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (64 bp):
AGAGCTAAGAGTTTTACCTCATAGTGGACCAACCCGACTCGAACAAGAATTAATTTATAAATAT
Found at i:16629 original size:21 final size:21
Alignment explanation
Indices: 16594--16645 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
16584 AATTAGAGGT
*
16594 GTTCGTGGCCGGGCCGGG-TCGG
1 GTTCG-GGCCAGGCCGGGCT-GG
16616 GTTCGGGCCAGGCCGGGCTGG
1 GTTCGGGCCAGGCCGGGCTGG
*
16637 ATTCGGGCC
1 GTTCGGGCC
16646 GGGTCCAAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 21 0.78
22 6 0.22
ACGTcount: A:0.04, C:0.29, G:0.50, T:0.17
Consensus pattern (21 bp):
GTTCGGGCCAGGCCGGGCTGG
Found at i:16844 original size:22 final size:23
Alignment explanation
Indices: 16786--16855 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 23
16776 CGTTTAGTAA
16786 TTAAA-TATATATTATTTATTTATT
1 TTAAACTATAT-TTATTTATTTA-T
* *
16810 TTGAACT-CA-TTATTTA-TTAT
1 TTAAACTATATTTATTTATTTAT
16830 TTAAACTATATTTA-TTATTTAT
1 TTAAACTATATTTATTTATTTAT
16852 TTAA
1 TTAA
16856 TAATATATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
20 7 0.18
21 7 0.18
22 18 0.47
24 5 0.13
25 1 0.03
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (23 bp):
TTAAACTATATTTATTTATTTAT
Found at i:18271 original size:76 final size:76
Alignment explanation
Indices: 18179--18328 Score: 273
Period size: 76 Copynumber: 2.0 Consensus size: 76
18169 TTCCCTAACA
*
18179 TTTCTCTGAATTGGTTTCACATGGACTATGTTCTGTTTCCTAAAATTTCCAAGTGGACGTTGATG
1 TTTCTCTGAATTGGTTTCACATGGACTATGTTCTGTTTCCTAAAATTTCCAAGTGGACGTTGATA
18244 AGATCCTTCTT
66 AGATCCTTCTT
* *
18255 TTTCTCTGAATTGGTTTCACATGGACTCTGTTCTGTTTCCTAAAATTTCCAGGTGGACGTTGATA
1 TTTCTCTGAATTGGTTTCACATGGACTATGTTCTGTTTCCTAAAATTTCCAAGTGGACGTTGATA
18320 AGATCCTTC
66 AGATCCTTC
18329 CATTTAATTT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 71 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (76 bp):
TTTCTCTGAATTGGTTTCACATGGACTATGTTCTGTTTCCTAAAATTTCCAAGTGGACGTTGATA
AGATCCTTCTT
Found at i:19107 original size:18 final size:18
Alignment explanation
Indices: 19084--19119 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
19074 GCCCTGCTTG
19084 TAAAAGATTAAGAATAAA
1 TAAAAGATTAAGAATAAA
19102 TAAAAGATTAAGAATAAA
1 TAAAAGATTAAGAATAAA
19120 AAATCATAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (18 bp):
TAAAAGATTAAGAATAAA
Found at i:20596 original size:20 final size:21
Alignment explanation
Indices: 20573--20612 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20563 ATCTGCTTTA
* *
20573 CTTT-CCTTATTATTGTTTTT
1 CTTTCCCTTAATATTATTTTT
20593 CTTTCCCTTAATATTATTTT
1 CTTTCCCTTAATATTATTTT
20613 CATGCTAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.15, C:0.17, G:0.03, T:0.65
Consensus pattern (21 bp):
CTTTCCCTTAATATTATTTTT
Done.