Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010587.1 Corchorus olitorius cultivar O-4 contig10619, 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: 4827
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Found at i:746 original size:42 final size:42
Alignment explanation
Indices: 648--783 Score: 220
Period size: 42 Copynumber: 3.2 Consensus size: 42
638 AGCAACAATT
648 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGAT---GGAGTAG
* *
693 AATATTGGCTTTATTTTGATGAATTACCTAGAGATGGAGTAT
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
735 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
777 AAT-TTAG
1 AATATTAG
784 GTAATACACT
Statistics
Matches: 87, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
41 4 0.05
42 49 0.56
45 34 0.39
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.38
Consensus pattern (42 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
Found at i:2417 original size:2 final size:2
Alignment explanation
Indices: 2399--2436 Score: 51
Period size: 2 Copynumber: 18.5 Consensus size: 2
2389 TTTTTGAAGA
2399 AT AT AT -T AT GAT GAT 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 AT AT AT AT A
2437 CACTAGTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 28 0.82
3 5 0.15
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2916 original size:21 final size:22
Alignment explanation
Indices: 2833--3220 Score: 120
Period size: 22 Copynumber: 17.5 Consensus size: 22
2823 TTGCTATATT
* *
2833 ATTTTGATAACCTCTCTAAGAA
1 ATTTTGATAACCTCACTATGAA
* * *
2855 ATTGTGATAACCTCCCTGTGAA
1 ATTTTGATAACCTCACTATGAA
* * *
2877 ACTTTGATGACCACACTATGAA
1 ATTTTGATAACCTCACTATGAA
*
2899 ATTTTGAT-ACCATC-CTATAAA
1 ATTTTGATAACC-TCACTATGAA
* *
2920 ATTTTGATAACCACACTATAAA
1 ATTTTGATAACCTCACTATGAA
* *
2942 ACTGTGATAACCTCTA-TATGAA
1 ATTTTGATAACCTC-ACTATGAA
* * * * *
2964 ATTTTTTTTGATGACTTTAATATAAA
1 A----TTTTGATAACCTCACTATGAA
*
2990 ATTTTGA-ATCC-CACATTAATTGCAAA
1 ATTTTGATAACCTCAC--T-A-TG--AA
** ****
3016 AGGTTGATTTGGTACACTATGAA
1 ATTTTGATAACCT-CACTATGAA
*
3039 ATTTGGATAACCAT-ACTATGAA
1 ATTTTGATAACC-TCACTATGAA
*
3061 ATTTTGATAACCTCCCTAT-AGA
1 ATTTTGATAACCTCACTATGA-A
* * * *
3083 ATGTTAATAACTTCCCTAT-AGA
1 ATTTTGATAACCTCACTATGA-A
*** * *
3105 ATTTCCTTAATCTCACTATTAA
1 ATTTTGATAACCTCACTATGAA
* *
3127 ATTTTGATTAGCT---T-TGAA
1 ATTTTGATAACCTCACTATGAA
* *
3145 ATTTTTG-TAACCACATTATGAA
1 A-TTTTGATAACCTCACTATGAA
* * *
3167 ATTTTGACAACCACATTATGAA
1 ATTTTGATAACCTCACTATGAA
*
3189 ATTTTGAT-AGCTACACTATGAA
1 ATTTTGATAACCT-CACTATGAA
3211 ATTTTGATAA
1 ATTTTGATAA
3221 TCTGCAAAGT
Statistics
Matches: 268, Mismatches: 68, Indels: 59
0.68 0.17 0.15
Matches are distributed among these distances:
18 7 0.03
19 6 0.02
20 1 0.00
21 29 0.11
22 182 0.68
23 11 0.04
24 2 0.01
25 3 0.01
26 22 0.08
27 2 0.01
29 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (22 bp):
ATTTTGATAACCTCACTATGAA
Found at i:2933 original size:43 final size:44
Alignment explanation
Indices: 2833--2955 Score: 133
Period size: 43 Copynumber: 2.8 Consensus size: 44
2823 TTGCTATATT
* * * * *
2833 ATTTTGATAACCTCTCTAAGAAATTGTGATAACCTCCCTGTGAA
1 ATTTTGATAACCACACTATGAAATTGTGATAACCTCCCTATAAA
* * *
2877 ACTTTGATGACCACACTATGAAATTTTGAT-ACCAT-CCTATAAA
1 ATTTTGATAACCACACTATGAAATTGTGATAACC-TCCCTATAAA
* *
2920 ATTTTGATAACCACACTATAAAACTGTGATAACCTC
1 ATTTTGATAACCACACTATGAAATTGTGATAACCTC
2956 TATATGAAAT
Statistics
Matches: 63, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
43 35 0.56
44 28 0.44
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.33
Consensus pattern (44 bp):
ATTTTGATAACCACACTATGAAATTGTGATAACCTCCCTATAAA
Found at i:3979 original size:428 final size:428
Alignment explanation
Indices: 3182--4040 Score: 1610
Period size: 428 Copynumber: 2.0 Consensus size: 428
3172 GACAACCACA
* *
3182 TTATGAAATTTTGATAGCTACACTATGAAATTTTGATAATCTGCAAAGTTCATCTTATTCTATAG
1 TTATGAAATTTTGATAGCTACACTATGAAATTTCGATAATCTGCAAAGTTCAACTTATTCTATAG
* *
3247 GGTAGAGAGTAATTTATTATCCTTTGGTTAGGACTTATAGACTTATAGTTCAAATCCTATTTTGT
66 GGTAGAGAGTAATTTATTATCCTTTGGTTAGGACTTATAGACATATAGTTCAAATCCTACTTTGT
* * *
3312 AATTGAAAAATCTAGCGTGAGAGAAGTGGTAAAAATTGAAAATTTATAAATAATTTTTTTTTAAG
131 AATTGAAAAATCTAGCATGAGAGAAGTGGCAAAAATTGAAAATTTATAAATAATGTTTTTTTAAG
3377 TATTATATAGTATTTATTATCCTTTAAGCGGTATTTAGGAGTTATTATACCTCAAATCCTAGTAT
196 TATTATATAGTATTTATTATCCTTTAAGCGGTATTTAGGAGTTATTATACCTCAAATCCTAGTAT
* *
3442 GTAGGGTATAAAAACTAATTCAAATCTAGCATAAGCAAAGTCCGGTTAGACTTTAAATTTTATAA
261 GTAGGGTATAAAAACTAATTCAAATCTAACATAAGCAAAGTCCGGTCAGACTTTAAATTTTATAA
3507 TTAATTTTTTAAATGAAATTCTATTTTGTAGAAAATAAAATTATAGTATTTTATAAAAAATTAAA
326 TTAATTTTTTAAATGAAATTCTATTTTGTAGAAAATAAAATTATAGTATTTTATAAAAAATTAAA
*
3572 TTGGGCATAGTAAATATATAAAATCTAAAATTAATTTT
391 TTGGGCATAGTAAATATATAAAATCTAAAATTAAATTT
3610 TTATGAAATTTTGATAGCTACACTATGAAATTTCGATAATCTGCAAAGTTCAACTTATTCTATAG
1 TTATGAAATTTTGATAGCTACACTATGAAATTTCGATAATCTGCAAAGTTCAACTTATTCTATAG
3675 GGTAGAGAGTAATTTATTATCCTTTGGTTAGGACTTATAGACATATAGTTCAAATCCTACTTTGT
66 GGTAGAGAGTAATTTATTATCCTTTGGTTAGGACTTATAGACATATAGTTCAAATCCTACTTTGT
* *
3740 AATTGAAAAATCTAGCATGAGAGAAGTGGCAAAAATTGAAATTTTATAATTAATGTTTTTTTAAG
131 AATTGAAAAATCTAGCATGAGAGAAGTGGCAAAAATTGAAAATTTATAAATAATGTTTTTTTAAG
3805 TATTATATAGTATTTATTATCCTTTAAGCGGTATTTAGGAGTTATTATACCTCAAATCCTAGTAT
196 TATTATATAGTATTTATTATCCTTTAAGCGGTATTTAGGAGTTATTATACCTCAAATCCTAGTAT
3870 GTAGGGTATAAAAACTAATTCAAATCTAACATAAGCAAAGTCCGGTCAGACTTTAAATTTTATAA
261 GTAGGGTATAAAAACTAATTCAAATCTAACATAAGCAAAGTCCGGTCAGACTTTAAATTTTATAA
3935 TTAATTTTTTAAATGAAATTCTATTTTGTAGAAAATAAAATTATAGTATTTTATAAAAAATTAAA
326 TTAATTTTTTAAATGAAATTCTATTTTGTAGAAAATAAAATTATAGTATTTTATAAAAAATTAAA
4000 TTGGGCATAGTAAATATATAAAATCTAAAATTAAATTT
391 TTGGGCATAGTAAATATATAAAATCTAAAATTAAATTT
4038 TTA
1 TTA
4041 ATAACAGAAT
Statistics
Matches: 419, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
428 419 1.00
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (428 bp):
TTATGAAATTTTGATAGCTACACTATGAAATTTCGATAATCTGCAAAGTTCAACTTATTCTATAG
GGTAGAGAGTAATTTATTATCCTTTGGTTAGGACTTATAGACATATAGTTCAAATCCTACTTTGT
AATTGAAAAATCTAGCATGAGAGAAGTGGCAAAAATTGAAAATTTATAAATAATGTTTTTTTAAG
TATTATATAGTATTTATTATCCTTTAAGCGGTATTTAGGAGTTATTATACCTCAAATCCTAGTAT
GTAGGGTATAAAAACTAATTCAAATCTAACATAAGCAAAGTCCGGTCAGACTTTAAATTTTATAA
TTAATTTTTTAAATGAAATTCTATTTTGTAGAAAATAAAATTATAGTATTTTATAAAAAATTAAA
TTGGGCATAGTAAATATATAAAATCTAAAATTAAATTT
Found at i:4121 original size:129 final size:129
Alignment explanation
Indices: 3916--4171 Score: 485
Period size: 129 Copynumber: 2.0 Consensus size: 129
3906 AAAGTCCGGT
*
3916 CAGACTTTAAATTTTATAATTAATTTTTTAAATGAAATTCTATTTTGTAGAAAATAAAATTATAG
1 CAGAATTTAAATTTTATAATTAATTTTTTAAATGAAATTCTATTTTGTAGAAAATAAAATTATAG
*
3981 TATTTTATAAAAAATTAAATTGGGCATAGTAAATATATAAAATCTAAAATTAAATTTTTAATAA
66 TATTTTATAAAAAATTAAATTGGGCATAGCAAATATATAAAATCTAAAATTAAATTTTTAATAA
4045 CAGAATTTAAATTTTATAATTAATTTTTTAAATGAAATTCTATTTTGTAGAAAATAAAATTATAG
1 CAGAATTTAAATTTTATAATTAATTTTTTAAATGAAATTCTATTTTGTAGAAAATAAAATTATAG
*
4110 TATTTTATAAAAAATTAAATTGGGCATAGCAAATATATACAATCTAAAATTAAATTTTTAAT
66 TATTTTATAAAAAATTAAATTGGGCATAGCAAATATATAAAATCTAAAATTAAATTTTTAAT
4172 GATGGCAATT
Statistics
Matches: 124, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 124 1.00
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (129 bp):
CAGAATTTAAATTTTATAATTAATTTTTTAAATGAAATTCTATTTTGTAGAAAATAAAATTATAG
TATTTTATAAAAAATTAAATTGGGCATAGCAAATATATAAAATCTAAAATTAAATTTTTAATAA
Done.