Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018392.1 Corchorus olitorius cultivar O-4 contig18425, 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: 66081
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:20224 original size:12 final size:12
Alignment explanation
Indices: 20207--20232 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20197 AACTATTTAG
20207 CTGATGATGAAA
1 CTGATGATGAAA
20219 CTGATGATGAAA
1 CTGATGATGAAA
20231 CT
1 CT
20233 TATGCGAGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (12 bp):
CTGATGATGAAA
Found at i:26482 original size:214 final size:214
Alignment explanation
Indices: 26113--26501 Score: 735
Period size: 214 Copynumber: 1.8 Consensus size: 214
26103 GGCATCATTA
26113 ATTGGCTGTTTGAGGGGGACGATAGCTATTCCATAGTAATGGATAGTAATGAATGCAAATAGATA
1 ATTGGCTGTTTGAGGGGGACGATAGCTATTCCATAGTAATGGATAGTAATGAATGCAAATAGATA
* * *
26178 CAGCGTGGGACTGGGCCTAAATGGTAATGTGGGCTTTGGGTAAAAGGAAAAAAAACAATGTTAGG
66 CAGCGTGGAACTGGGCCTAAATGGTAATGTGGGCTTTGGGTAAAAGCAAAAAAAAAAATGTTAGG
26243 TATTGTAATGGGTTGGCTTTATGTCTATTATTTAGTTGACATTAACAACTTGAAATAGCTATTCC
131 TATTGTAATGGGTTGGCTTTATGTCTATTATTTAGTTGACATTAACAACTTGAAATAGCTATTCC
26308 ATAGTAATGGATAGTAATG
196 ATAGTAATGGATAGTAATG
26327 ATTGGCTGTTTGAGGGGGACGATAGCTATTCCATAGTAATGGATAGTAATGAATGCAAATAGATA
1 ATTGGCTGTTTGAGGGGGACGATAGCTATTCCATAGTAATGGATAGTAATGAATGCAAATAGATA
26392 CAGCGTGGAACTGGGCCTAAATGGTAATGTGGGCTTTGGGTAAAAGCAAAAAAAAAAATGTTAGG
66 CAGCGTGGAACTGGGCCTAAATGGTAATGTGGGCTTTGGGTAAAAGCAAAAAAAAAAATGTTAGG
26457 TATTGTAATGGGTTGGGC-TTATGTCTATTATTTAGTTGACATTAA
131 TATTGTAATGGGTT-GGCTTTATGTCTATTATTTAGTTGACATTAA
26502 ACAAAAATTA
Statistics
Matches: 171, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
214 168 0.98
215 3 0.02
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.31
Consensus pattern (214 bp):
ATTGGCTGTTTGAGGGGGACGATAGCTATTCCATAGTAATGGATAGTAATGAATGCAAATAGATA
CAGCGTGGAACTGGGCCTAAATGGTAATGTGGGCTTTGGGTAAAAGCAAAAAAAAAAATGTTAGG
TATTGTAATGGGTTGGCTTTATGTCTATTATTTAGTTGACATTAACAACTTGAAATAGCTATTCC
ATAGTAATGGATAGTAATG
Found at i:41081 original size:517 final size:517
Alignment explanation
Indices: 40102--41087 Score: 1846
Period size: 517 Copynumber: 1.9 Consensus size: 517
40092 TTGGAAGTTT
*
40102 CAGATCGTTTTTCATATTGTAACATATGTTCAAATACGAACTTGTCTGGGAAAAAAGGGATTTTA
1 CAGATCGTTTTTCATATTGTAACATATGTTCAAATACGAACTTGTCTAGGAAAAAAGGGATTTTA
*
40167 AATAGGTACAAAGAGTCTAAAACCTACATAAGAATCTATAATATCTGGAGGTCAAAAGTATAAAA
66 AATAGGTACAAAGAGACTAAAACCTACATAAGAATCTATAATATCTGGAGGTCAAAAGTATAAAA
40232 AAATAAAGCAATTTGGACTAAAAAGAAAGGCTAGAAAAAATTGTTTGATTTTTAAATAACGAAAA
131 AAATAAAGCAATTTGGACTAAAAAGAAAGGCTAGAAAAAATTGTTTGATTTTTAAATAACGAAAA
40297 AAGAAAGGCTAGAAACAACTTTAGCAGATCTTTCCATTCAGGAGATACTATAAGGATTCCATTAA
196 AAGAAAGGCTAGAAACAACTTTAGCAGATCTTTCCATTCAGGAGATACTATAAGGATTCCATTAA
*
40362 AGACCACTTTAGCCTTATGGTTTAGCAAGGAGATAGACAACCAGTTACCTTTGAAAGGACTGTTT
261 AGACCACTTTAGCCTTAGGGTTTAGCAAGGAGATAGACAACCAGTTACCTTTGAAAGGACTGTTT
40427 GCCCCCTGACCCTTTGGCCAAACCAAAGTTAGGTTAAGGTAAGAGATATCTGGGTTAAAAAAAAA
326 GCCCCCTGACCCTTTGGCCAAACCAAAGTTAGGTTAAGGTAAGAGATATCTGGGTTAAAAAAAAA
* *
40492 AGGAATTTACATAAGGACTAAGAGAACAATCCCTGCCTAACTAATGGGATTATTATCGTGGTACC
391 AAGAATTTACATAAGGACTAAGAGAACAAACCCTGCCTAACTAATGGGATTATTATCGTGGTACC
40557 TACCAGGGTAGTCCATTGATTGCAAATATATTGAACGACATGTGTAAAGTGGGAAATATATG
456 TACCAGGGTAGTCCATTGATTGCAAATATATTGAACGACATGTGTAAAGTGGGAAATATATG
*
40619 CAGATTGTTTTTCATATTGTAACATATGTTCAAATACGAACTTGTCTAGGAAAAAAGGGATTTTA
1 CAGATCGTTTTTCATATTGTAACATATGTTCAAATACGAACTTGTCTAGGAAAAAAGGGATTTTA
* * * *
40684 AATAGGTACAAAGAGAGTAAAACCTCCATAAGAATCTATAATATTTGGAGGTCAAAGGTATAAAA
66 AATAGGTACAAAGAGACTAAAACCTACATAAGAATCTATAATATCTGGAGGTCAAAAGTATAAAA
* *
40749 AAATAAAGCAATTTGGACTAAATAGAAAGGCTGGAAAAAATTGTTTGATTTTTAAATAACGAAAA
131 AAATAAAGCAATTTGGACTAAAAAGAAAGGCTAGAAAAAATTGTTTGATTTTTAAATAACGAAAA
* *
40814 AAGAAAGGCTAGAAACAGCTTTAGCAGATCTTTCCATTCAGGAGATGCTATAAGGATTCCATTAA
196 AAGAAAGGCTAGAAACAACTTTAGCAGATCTTTCCATTCAGGAGATACTATAAGGATTCCATTAA
40879 AGACCACTTTAGCCTTAGGGTTTAGCAAGGAGATAGACAACCAGTTACCTTTGAAAGGACTGTTT
261 AGACCACTTTAGCCTTAGGGTTTAGCAAGGAGATAGACAACCAGTTACCTTTGAAAGGACTGTTT
40944 GCCCCCTGACCCTTTGGCCAAACCAAAGTTAGGTTAAGGTAAGAGATATCTGGGTTAAAAAAAAA
326 GCCCCCTGACCCTTTGGCCAAACCAAAGTTAGGTTAAGGTAAGAGATATCTGGGTTAAAAAAAAA
41009 AAGAATTTACATAAGGACTAAGAGAACAAACCCTGCCTAACTAATGGGATTATTATCGTGGTACC
391 AAGAATTTACATAAGGACTAAGAGAACAAACCCTGCCTAACTAATGGGATTATTATCGTGGTACC
41074 TACCAGGGTAGTCC
456 TACCAGGGTAGTCC
41088 CACTTGTCTG
Statistics
Matches: 455, Mismatches: 14, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
517 455 1.00
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (517 bp):
CAGATCGTTTTTCATATTGTAACATATGTTCAAATACGAACTTGTCTAGGAAAAAAGGGATTTTA
AATAGGTACAAAGAGACTAAAACCTACATAAGAATCTATAATATCTGGAGGTCAAAAGTATAAAA
AAATAAAGCAATTTGGACTAAAAAGAAAGGCTAGAAAAAATTGTTTGATTTTTAAATAACGAAAA
AAGAAAGGCTAGAAACAACTTTAGCAGATCTTTCCATTCAGGAGATACTATAAGGATTCCATTAA
AGACCACTTTAGCCTTAGGGTTTAGCAAGGAGATAGACAACCAGTTACCTTTGAAAGGACTGTTT
GCCCCCTGACCCTTTGGCCAAACCAAAGTTAGGTTAAGGTAAGAGATATCTGGGTTAAAAAAAAA
AAGAATTTACATAAGGACTAAGAGAACAAACCCTGCCTAACTAATGGGATTATTATCGTGGTACC
TACCAGGGTAGTCCATTGATTGCAAATATATTGAACGACATGTGTAAAGTGGGAAATATATG
Found at i:42673 original size:167 final size:165
Alignment explanation
Indices: 42397--42730 Score: 582
Period size: 167 Copynumber: 2.0 Consensus size: 165
42387 CTGAACTGAG
42397 TTTGGGGCTTGAGGCTAGACCGATGTTCTTGCAGCTGATGGAAGCCAAACCTTGGAATGATTTAG
1 TTTGGGGCTTGAGGCTAGACCGATGTTCTTGCAGCTGATGGAAGCCAAACCTTGGAATGATTTAG
* *
42462 ATTTAGATAGGACTGATTGCTGCAAGGTGTTGGGTCTAAGATCACCGGCTGAATTGAGGATAATA
66 ATTTAGATAGGACTGATTGCTGCAAGGTGTTGGGTCGAAGATCACCGGCTGAATTGAGGATAACA
*
42527 GATTGATAGAGAGAGAGAGAAAAAAAAAGGAACATAT
131 GATTGAT--AGAGAGAGAGAAAAAAAAAGGAACAGAT
*
42564 TTTGGGGCTTG-GTGCTAGACCGATGTTTTTGCAGCTGATGGAAGCCAAACCTTGGAATGATTTA
1 TTTGGGGCTTGAG-GCTAGACCGATGTTCTTGCAGCTGATGGAAGCCAAACCTTGGAATGATTTA
42628 GATTTCA-ATAGGACTGATTGCTGCAAGGTGTTGGGTCGAAGATCACCGGCTGAATTGAGGATAA
65 GATTT-AGATAGGACTGATTGCTGCAAGGTGTTGGGTCGAAGATCACCGGCTGAATTGAGGATAA
42692 CAGATTGATAGAGAGAGAGAAAAAAAAAGGAACAGAT
129 CAGATTGATAGAGAGAGAGAAAAAAAAAGGAACAGAT
42729 TT
1 TT
42731 CGTTTAGAGA
Statistics
Matches: 161, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
165 29 0.18
166 1 0.01
167 130 0.81
168 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.26
Consensus pattern (165 bp):
TTTGGGGCTTGAGGCTAGACCGATGTTCTTGCAGCTGATGGAAGCCAAACCTTGGAATGATTTAG
ATTTAGATAGGACTGATTGCTGCAAGGTGTTGGGTCGAAGATCACCGGCTGAATTGAGGATAACA
GATTGATAGAGAGAGAGAAAAAAAAAGGAACAGAT
Found at i:43828 original size:22 final size:22
Alignment explanation
Indices: 43803--43877 Score: 96
Period size: 22 Copynumber: 3.3 Consensus size: 22
43793 TCATTTGTCC
43803 TTTAAATTTATGTAAATTTAAA
1 TTTAAATTTATGTAAATTTAAA
* *
43825 TTTAAATTTATGTAAATCTAAT
1 TTTAAATTTATGTAAATTTAAA
* *
43847 TTTAAATTTAAATCTAATTTTAAA
1 TTTAAATTT--ATGTAAATTTAAA
43871 TTTAAAT
1 TTTAAAT
43878 CTAATTTTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
22 29 0.64
24 16 0.36
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (22 bp):
TTTAAATTTATGTAAATTTAAA
Found at i:43860 original size:18 final size:18
Alignment explanation
Indices: 43815--43893 Score: 117
Period size: 18 Copynumber: 4.5 Consensus size: 18
43805 TAAATTTATG
* *
43815 TAAATTTAAATTTAAATT
1 TAAATTTAAATCTAATTT
*
43833 T--ATGTAAATCTAATTT
1 TAAATTTAAATCTAATTT
43849 TAAATTTAAATCTAATTT
1 TAAATTTAAATCTAATTT
43867 TAAATTTAAATCTAATTT
1 TAAATTTAAATCTAATTT
43885 TAAATTTAA
1 TAAATTTAA
43894 TAGATTTCAT
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
16 13 0.24
18 42 0.76
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (18 bp):
TAAATTTAAATCTAATTT
Found at i:43917 original size:6 final size:6
Alignment explanation
Indices: 43803--43893 Score: 82
Period size: 6 Copynumber: 15.8 Consensus size: 6
43793 TCATTTGTCC
* * * *
43803 TTTAAA TTT--A TGTAAA TTTAAA TTTAAA TTT--A TGTAAA TCTAAT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
43847 TTTAAA TTTAAA TCTAAT TTTAAA TTTAAA TCTAAT TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
43894 TAGATTTCAT
Statistics
Matches: 66, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
4 6 0.09
6 60 0.91
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:49214 original size:2 final size:2
Alignment explanation
Indices: 49202--49242 Score: 52
Period size: 2 Copynumber: 21.5 Consensus size: 2
49192 CGACCCCGAA
49202 AT AT AT A- AT AT AT -T CAT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
49242 A
1 A
49243 CACACACTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
1 3 0.09
2 31 0.89
3 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:49344 original size:29 final size:29
Alignment explanation
Indices: 49302--49365 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
49292 AGAAGTGCAA
*
49302 GATGATAATTATTTCATAAATTTTATTTG
1 GATGATAATTATTTCATAAATTTTATTGG
*
49331 GATGATAATTATTTCATGAATTTTATTGG
1 GATGATAATTATTTCATAAATTTTATTGG
49360 GATGAT
1 GATGAT
49366 GGATTTGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.33, C:0.03, G:0.16, T:0.48
Consensus pattern (29 bp):
GATGATAATTATTTCATAAATTTTATTGG
Found at i:49452 original size:29 final size:29
Alignment explanation
Indices: 49410--49465 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
49400 CCTTGCACGG
*
49410 TGTTGAAAGCTTGTAATTGTGGTGTTGAT
1 TGTTGAAAACTTGTAATTGTGGTGTTGAT
49439 TGTTGAAAACTTGTAATTGTGGTGTTG
1 TGTTGAAAACTTGTAATTGTGGTGTTG
49466 TAAACTTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.04, G:0.30, T:0.45
Consensus pattern (29 bp):
TGTTGAAAACTTGTAATTGTGGTGTTGAT
Found at i:50539 original size:19 final size:19
Alignment explanation
Indices: 50528--50564 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
50518 AATTTTTAAG
50528 TAAAAATTTAATATATAAA
1 TAAAAATTTAATATATAAA
50547 TAAAAATTTAATAT-TAAA
1 TAAAAATTTAATATATAAA
50565 ACAATGAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAAATTTAATATATAAA
Found at i:57727 original size:12 final size:11
Alignment explanation
Indices: 57705--57735 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
57695 CCTTAATGCC
57705 AAAAAAGAAAA
1 AAAAAAGAAAA
57716 AAAAAAGAAAA
1 AAAAAAGAAAA
57727 AAAAAAGAA
1 AAAAAAGAA
57736 CTGCTATTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:62392 original size:13 final size:13
Alignment explanation
Indices: 62360--62393 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
62350 AAATCTTTTC
62360 CTTTCTTTTCTTT
1 CTTTCTTTTCTTT
62373 -TTCTCTTTTCTTT
1 CTT-TCTTTTCTTT
62386 CTTTCTTT
1 CTTTCTTT
62394 GCTTCATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.11
13 15 0.79
14 2 0.11
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
CTTTCTTTTCTTT
Found at i:65754 original size:78 final size:78
Alignment explanation
Indices: 65665--65825 Score: 286
Period size: 78 Copynumber: 2.1 Consensus size: 78
65655 AGATTTATAG
* * *
65665 TTTTACTCAACTAAAAATTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTTATTT
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTCAGTT
65730 TACCATTTTACTA
66 TACCATTTTACTA
*
65743 TTTTACTCAACTAAAAACTCTATTTTTATTTGATTAAATCTAATATCTTTATAACTATTTCAGTT
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTCAGTT
65808 TACCATTTTACTA
66 TACCATTTTACTA
65821 TTTTA
1 TTTTA
65826 AGTAGAAAAC
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.34, C:0.14, G:0.01, T:0.52
Consensus pattern (78 bp):
TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTCAGTT
TACCATTTTACTA
Done.