Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018462.1 Corchorus olitorius cultivar O-4 contig18495, 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: 67514
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:13962 original size:2 final size:2
Alignment explanation
Indices: 13955--13983 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13945 TTAATGGTAT
13955 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13984 TGGTGGGTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24453 original size:5 final size:5
Alignment explanation
Indices: 24443--24470 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
24433 AGAACTGTCT
24443 CATAA CATAA CATAA CATAA CATAA CAT
1 CATAA CATAA CATAA CATAA CATAA CAT
24471 GAATTAATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.21, G:0.00, T:0.21
Consensus pattern (5 bp):
CATAA
Found at i:26878 original size:14 final size:14
Alignment explanation
Indices: 26859--26891 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
26849 TGAGAAAGAA
26859 AGAAAGCCCGGGTC
1 AGAAAGCCCGGGTC
26873 AGAAAGCCCGGGTC
1 AGAAAGCCCGGGTC
26887 AGAAA
1 AGAAA
26892 TCCGGACCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.36, C:0.24, G:0.33, T:0.06
Consensus pattern (14 bp):
AGAAAGCCCGGGTC
Found at i:41754 original size:2 final size:2
Alignment explanation
Indices: 41749--41777 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
41739 AATAGGCACA
41749 AT 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 AT A
41778 GCTAAGTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42598 original size:138 final size:138
Alignment explanation
Indices: 42350--42627 Score: 547
Period size: 138 Copynumber: 2.0 Consensus size: 138
42340 TCAAGAGGTC
42350 TTAGGTTCAACTCTCACGGAATGTGAGTTTGTTTGTAATTTGTTTGTTTATTTGGTAGGTATGTA
1 TTAGGTTCAACTCTCACGGAATGTGAGTTTGTTTGTAATTTGTTTGTTTATTTGGTAGGTATGTA
*
42415 GTTGATTTATGGTATAGTTTCTAGTTTGGGTTGAATTCTCATTTAGATGTTTGGGTATAGAGATT
66 GTTGATTTATGGTATAGTTTCTAGTTTGGGTTGAATTCTCATTTAGATGTCTGGGTATAGAGATT
42480 TATTTGAA
131 TATTTGAA
42488 TTAGGTTCAACTCTCACGGAATGTGAGTTTGTTTGTAATTTGTTTGTTTATTTGGTAGGTATGTA
1 TTAGGTTCAACTCTCACGGAATGTGAGTTTGTTTGTAATTTGTTTGTTTATTTGGTAGGTATGTA
42553 GTTGATTTATGGTATAGTTTCTAGTTTGGGTTGAATTCTCATTTAGATGTCTGGGTATAGAGATT
66 GTTGATTTATGGTATAGTTTCTAGTTTGGGTTGAATTCTCATTTAGATGTCTGGGTATAGAGATT
42618 TATTTGAA
131 TATTTGAA
42626 TT
1 TT
42628 GTAATGAGAT
Statistics
Matches: 139, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 139 1.00
ACGTcount: A:0.22, C:0.06, G:0.24, T:0.48
Consensus pattern (138 bp):
TTAGGTTCAACTCTCACGGAATGTGAGTTTGTTTGTAATTTGTTTGTTTATTTGGTAGGTATGTA
GTTGATTTATGGTATAGTTTCTAGTTTGGGTTGAATTCTCATTTAGATGTCTGGGTATAGAGATT
TATTTGAA
Found at i:42712 original size:40 final size:40
Alignment explanation
Indices: 42657--42736 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
42647 TTTGTTTGTT
42657 GGGGAAGGAGTTTGTTGGCTCATAGATTATCATTTCGGTA
1 GGGGAAGGAGTTTGTTGGCTCATAGATTATCATTTCGGTA
*
42697 GGGGAAGGAGTTTGTTGGCTCATAGATTATCATTTTGGTA
1 GGGGAAGGAGTTTGTTGGCTCATAGATTATCATTTCGGTA
42737 TTGTAGCTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.23, C:0.09, G:0.33, T:0.36
Consensus pattern (40 bp):
GGGGAAGGAGTTTGTTGGCTCATAGATTATCATTTCGGTA
Found at i:42948 original size:15 final size:15
Alignment explanation
Indices: 42928--42957 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42918 ACCGAAAAAA
42928 TCTTTTTTTCCTATT
1 TCTTTTTTTCCTATT
*
42943 TCTTTTTTTGCTATT
1 TCTTTTTTTCCTATT
42958 CAATGAATGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.17, G:0.03, T:0.73
Consensus pattern (15 bp):
TCTTTTTTTCCTATT
Found at i:45238 original size:208 final size:208
Alignment explanation
Indices: 44833--45386 Score: 686
Period size: 211 Copynumber: 2.6 Consensus size: 208
44823 CACGACTTTT
* ** *
44833 TTTTCCTCTTTTGAATTAATACCTCTTTTGGTATATAATAAAGAATATAAATTACTAAATCATAT
1 TTTTCCTCTTTTCAAACAATACCTCTTTTGGCATATAATAAAG---AT-AA--ACTAAATC--AT
* * *
44898 ACAAACTTAAAATGAAAACACTTGTTCATTATGCGCCGTTATTTTTTGTTTTATAACAACTCATT
58 ACAAACTTAAAATGAAAACACATGTTCATTATGCGCCGTCATTTTTTGTTTTATAACAACTAATT
* *
44963 TTTGTCGTATTTTCTGAGACAATTCCTCATTTTAATTTGATACATACTATATTAAAAATATAACT
123 TTTGTCGTATTTTCTGAGACAATTCCTCATTTTAATTCGATACATA-TATATTAAAAATAAAACT
*
45028 AAG-AAGCCATTACGCGCCGTC
187 AAGAAAGCCATTACGCGCCGCC
*
45049 TTTTCCTCTTTTCAAACAATACCTCTTTTGACATATAATAAAGATAAACTAAATCATACAAACTT
1 TTTTCCTCTTTTCAAACAATACCTCTTTTGGCATATAATAAAGATAAACTAAATCATACAAACTT
*
45114 AAAATGAAAACACGTGTTCATTATGCGCCGTCATTTTTTGTTTCT-TAACAAAACTAATTTTTGT
66 AAAATGAAAACACATGTTCATTATGCGCCGTCATTTTTTGTTT-TATAAC--AACTAATTTTTGT
*
45178 CGTATTTTCTGAGACAATTCCTCA-TTTAATTCGATACAT-TATATTAAAGATAAAAACTAAGAA
128 CGTATTTTCTGAGACAATTCCTCATTTTAATTCGATACATATATATTAAAAAT-AAAACTAAG-A
*
45241 CAAGCCATTATGCGCCGCC
191 -AAGCCATTACGCGCCGCC
* * * *
45260 TTTTCCTCCTTTCAAACAGTACCTCTTTTGGCATATAATAAAGATAAATTAAATCATGCAAACTT
1 TTTTCCTCTTTTCAAACAATACCTCTTTTGGCATATAATAAAGATAAACTAAATCATACAAACTT
* * * * * * * *
45325 GAACTGAGAACATATGTTCATTATGCGCCGCCATTTATTTCTCTTTCTAA-AACTCATTTTTG
66 AAAATGAAAACACATGTTCATTATGCGCCGTCATTT-TTTGT-TTTATAACAACTAATTTTTG
45387 CCGCCGTTTT
Statistics
Matches: 302, Mismatches: 26, Indels: 26
0.85 0.07 0.07
Matches are distributed among these distances:
207 11 0.04
208 63 0.21
209 15 0.05
210 55 0.18
211 106 0.35
212 7 0.02
213 7 0.02
216 38 0.13
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (208 bp):
TTTTCCTCTTTTCAAACAATACCTCTTTTGGCATATAATAAAGATAAACTAAATCATACAAACTT
AAAATGAAAACACATGTTCATTATGCGCCGTCATTTTTTGTTTTATAACAACTAATTTTTGTCGT
ATTTTCTGAGACAATTCCTCATTTTAATTCGATACATATATATTAAAAATAAAACTAAGAAAGCC
ATTACGCGCCGCC
Found at i:45707 original size:62 final size:63
Alignment explanation
Indices: 45605--45731 Score: 202
Period size: 62 Copynumber: 2.0 Consensus size: 63
45595 AATCTTGAAA
* * *
45605 TGGGCGGGTGAGATATTATGTTCAACCAATGGTTATACTTAATCTTAATTTATAACTA-TGTT
1 TGGGCGGGTGAGATACTATGCTCAACCAATAGTTATACTTAATCTTAATTTATAACTATTGTT
* *
45667 TGGGTGGGTGAGATACTATGCTCAACCTATAGTTATACTTAATCTTAATTTATAACTATTGTT
1 TGGGCGGGTGAGATACTATGCTCAACCAATAGTTATACTTAATCTTAATTTATAACTATTGTT
45730 TG
1 TG
45732 TAATCCAGAT
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
62 53 0.90
63 6 0.10
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (63 bp):
TGGGCGGGTGAGATACTATGCTCAACCAATAGTTATACTTAATCTTAATTTATAACTATTGTT
Found at i:49350 original size:12 final size:12
Alignment explanation
Indices: 49333--49366 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
49323 AGTCAGTCAT
49333 TAGGAATATATA
1 TAGGAATATATA
49345 TAGGAATAT-TA
1 TAGGAATATATA
49356 TA-GAATATATA
1 TAGGAATATATA
49367 GGTAGAGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.29
11 6 0.29
12 9 0.43
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (12 bp):
TAGGAATATATA
Found at i:52504 original size:76 final size:76
Alignment explanation
Indices: 52378--52529 Score: 295
Period size: 76 Copynumber: 2.0 Consensus size: 76
52368 AATCAAGACG
52378 TCGTGACATATTTGCAATCATAAATTCATTTTTGTTTCCAACTCATGAACATGATATTTAAATTA
1 TCGTGACATATTTGCAATCATAAATTCATTTTTGTTTCCAACTCATGAACATGATATTTAAATTA
*
52443 GCAACATAACA
66 ACAACATAACA
52454 TCGTGACATATTTGCAATCATAAATTCATTTTTGTTTCCAACTCATGAACATGATATTTAAATTA
1 TCGTGACATATTTGCAATCATAAATTCATTTTTGTTTCCAACTCATGAACATGATATTTAAATTA
52519 ACAACATAACA
66 ACAACATAACA
52530 GGAGTCACCC
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.37
Consensus pattern (76 bp):
TCGTGACATATTTGCAATCATAAATTCATTTTTGTTTCCAACTCATGAACATGATATTTAAATTA
ACAACATAACA
Found at i:52804 original size:47 final size:47
Alignment explanation
Indices: 52735--52833 Score: 198
Period size: 47 Copynumber: 2.1 Consensus size: 47
52725 AAGCTCTACT
52735 TCCATGCATAAGAAAACAGGAATTATTAATTATAGTACCTAGTTTAA
1 TCCATGCATAAGAAAACAGGAATTATTAATTATAGTACCTAGTTTAA
52782 TCCATGCATAAGAAAACAGGAATTATTAATTATAGTACCTAGTTTAA
1 TCCATGCATAAGAAAACAGGAATTATTAATTATAGTACCTAGTTTAA
52829 TCCAT
1 TCCAT
52834 ACAGGCAAGC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.32
Consensus pattern (47 bp):
TCCATGCATAAGAAAACAGGAATTATTAATTATAGTACCTAGTTTAA
Found at i:66947 original size:20 final size:20
Alignment explanation
Indices: 66922--66961 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
66912 CATTCAACGG
66922 ACGTGATAATTACGTCTGAT
1 ACGTGATAATTACGTCTGAT
66942 ACGTGATAATTACGTCTGAT
1 ACGTGATAATTACGTCTGAT
66962 TCCAAGGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (20 bp):
ACGTGATAATTACGTCTGAT
Found at i:67281 original size:31 final size:30
Alignment explanation
Indices: 67243--67343 Score: 105
Period size: 31 Copynumber: 3.3 Consensus size: 30
67233 AAGTACCTAA
*
67243 TTAGTCCCTGTACTATAGAAAAAAGATCAAT
1 TTAGTCCCTCTACTAT-GAAAAAAGATCAAT
* * * ***
67274 TTAGTCCCTCCATTATCAAATCTG-TCAAT
1 TTAGTCCCTCTACTATGAAAAAAGATCAAT
*
67303 TTAGTCCCTCTACTATTGAAAAGAGATCAAT
1 TTAGTCCCTCTACTA-TGAAAAAAGATCAAT
67334 TTAGTCCCTC
1 TTAGTCCCTC
67344 CGTGAAATGG
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
29 18 0.33
30 9 0.16
31 28 0.51
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.34
Consensus pattern (30 bp):
TTAGTCCCTCTACTATGAAAAAAGATCAAT
Done.