Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019318.1 Corchorus olitorius cultivar O-4 contig19351, 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: 13390
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Found at i:43 original size:29 final size:29
Alignment explanation
Indices: 1--96 Score: 138
Period size: 30 Copynumber: 3.2 Consensus size: 29
*
1 ATGCCCCTAGATATGCAGAAATTATCATA
1 ATGCCCCTAGATATGCAAAAATTATCATA
30 ATGCCCCTAGATATGCAAAAAATTATCATA
1 ATGCCCCTAGATATGC-AAAAATTATCATA
* * *
60 ATGCCCCTGGATATGCAAAAATGACCATA
1 ATGCCCCTAGATATGCAAAAATTATCATA
89 ATGTCCCC
1 ATG-CCCC
97 GGATCTGTAA
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
29 30 0.49
30 31 0.51
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.25
Consensus pattern (29 bp):
ATGCCCCTAGATATGCAAAAATTATCATA
Found at i:114 original size:29 final size:29
Alignment explanation
Indices: 1--275 Score: 142
Period size: 29 Copynumber: 9.4 Consensus size: 29
* * ** *
1 ATGCCCCTAGATATGCAGAAATTATCATA
1 ATGCCCCTGGATATGCAAAAACGACCATA
* ** *
30 ATGCCCCTAGATATGCAAAAAATTATCATA
1 ATGCCCCTGGATATGC-AAAAACGACCATA
*
60 ATGCCCCTGGATATGCAAAAATGACCATA
1 ATGCCCCTGGATATGCAAAAACGACCATA
* * *
89 ATGTCCCC-GGATCTGTAAACACGACCA-A
1 ATG-CCCCTGGATATGCAAAAACGACCATA
* ** * * *
117 ATTG-CCTTCGGACGTGCAAAAACAAACAAA
1 A-TGCCCCT-GGATATGCAAAAACGACCATA
* * * * *
147 ATGCCCCTGAATTGTGCAAACATGACCAAA
1 ATGCCCCTGGA-TATGCAAAAACGACCATA
* * * * *
177 ATGCCCTTGGATGTGCCAAAATGACCAAA
1 ATGCCCCTGGATATGCAAAAACGACCATA
* * *
206 ATGCCCTTGGATATGCGAAAATGACCATA
1 ATGCCCCTGGATATGCAAAAACGACCATA
* * ** * *
235 ATGCCCTTGGATTTGCGTAAATGACCAAA
1 ATGCCCCTGGATATGCAAAAACGACCATA
264 ATGCCCCTGGAT
1 ATGCCCCTGGAT
276 TCACAAAAGG
Statistics
Matches: 205, Mismatches: 33, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
27 2 0.01
28 2 0.01
29 143 0.70
30 58 0.28
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (29 bp):
ATGCCCCTGGATATGCAAAAACGACCATA
Found at i:276 original size:29 final size:29
Alignment explanation
Indices: 143--276 Score: 171
Period size: 29 Copynumber: 4.6 Consensus size: 29
133 CAAAAACAAA
* *
143 CAAAATGCCCCTGAATTGTGC-AAACATGAC
1 CAAAATGCCCTTGGATT-TGCGAAA-ATGAC
* *
173 CAAAATGCCCTTGGATGTGCCAAAATGAC
1 CAAAATGCCCTTGGATTTGCGAAAATGAC
*
202 CAAAATGCCCTTGGATATGCGAAAATGAC
1 CAAAATGCCCTTGGATTTGCGAAAATGAC
* *
231 CATAATGCCCTTGGATTTGCGTAAATGAC
1 CAAAATGCCCTTGGATTTGCGAAAATGAC
*
260 CAAAATGCCCCTGGATT
1 CAAAATGCCCTTGGATT
277 CACAAAAGGT
Statistics
Matches: 93, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
29 76 0.82
30 17 0.18
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (29 bp):
CAAAATGCCCTTGGATTTGCGAAAATGAC
Found at i:663 original size:58 final size:58
Alignment explanation
Indices: 534--1123 Score: 765
Period size: 58 Copynumber: 10.1 Consensus size: 58
524 CCAAAATAAG
* * ** * *
534 ATTGAAAATTCTCTAACGGAGACCTCGAACAGGATTTCAAAAACAAGATAAAATTTTAA
1 ATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTT-TGAAACAAGATAAGATTTTGA
* * * * * * *
593 ATTGAAAACTCTCTAGCCGAGACCTTGAGCAGGATTTTAAAACAAGATAAGTTTTTCA
1 ATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACAAGATAAGATTTTGA
* * *
651 ATTGAAAGCTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTATGA
1 ATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACAAGATAAGATTTTGA
** * *
709 ACCGAAAACTCTCTAACAGAGACCTCAAACAGGATTTT-AAATCAAG--AAGCTACTTTGA
1 ATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTGAAA-CAAGATAAG--ATTTTGA
* * * *
767 ATTGGAAACTCCCTAACAGAGACCTTGAACAGGATTTTGAAACAAGATGAA-ATTTTAA
1 ATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACAAGAT-AAGATTTTGA
* * * *
825 ATTGAACACTCTCTAACCGAGACCTCGAACAGGATTTTGAAACGAGATAAGGTTTTGA
1 ATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACAAGATAAGATTTTGA
* *
883 ATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACGAGATAAGGTTTTGA
1 ATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACAAGATAAGATTTTGA
* *
941 ATTGAAAAACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACGAGATAAGGTTTTGA
1 ATTG-AAAACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACAAGATAAGATTTTGA
* *
1000 ATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACGAGATAAGGTTTTGA
1 ATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACAAGATAAGATTTTGA
* *
1058 ATTGAAAAACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACGAGATAAGATTTTAA
1 ATTG-AAAACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACAAGATAAGATTTTGA
1117 ATTGAAA
1 ATTGAAA
1124 CTCAAACAAG
Statistics
Matches: 478, Mismatches: 43, Indels: 21
0.88 0.08 0.04
Matches are distributed among these distances:
56 3 0.01
57 5 0.01
58 319 0.67
59 149 0.31
61 2 0.00
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (58 bp):
ATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACAAGATAAGATTTTGA
Found at i:1001 original size:117 final size:116
Alignment explanation
Indices: 534--1123 Score: 783
Period size: 117 Copynumber: 5.1 Consensus size: 116
524 CCAAAATAAG
* * ** * *
534 ATTGAAAATTCTCTAACGGAGACCTCGAACAGGATTTCAAAAACAAGATAAAATTTTAAATTGAA
1 ATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTT-TGAAACAAGATAAGATTTTGAATTGAA
* * * * * * * *
599 AACTCTCTAGCCGAGACCTTGAGCAGGATTTTAAAACAAGATAAGTTTTTCA
65 AACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACGAGATAAGGTTTTGA
* * * **
651 ATTGAAAGCTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTATGAACCGAAA
1 ATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACAAGATAAGATTTTGAATTGAAA
* * *
716 ACTCTCTAACAGAGACCTCAAACAGGATTTT-AAATC-A-AGAAGCTACTTTGA
66 ACTCTCTAACAGAGACCTCGAACAGGATTTTGAAA-CGAGATAAGGT--TTTGA
* * * *
767 ATTGGAAACTCCCTAACAGAGACCTTGAACAGGATTTTGAAACAAGATGAA-ATTTTAAATTGAA
1 ATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACAAGAT-AAGATTTTGAATTGAA
* *
831 CACTCTCTAACCGAGACCTCGAACAGGATTTTGAAACGAGATAAGGTTTTGA
65 AACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACGAGATAAGGTTTTGA
* *
883 ATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACGAGATAAGGTTTTGAATTGAAA
1 ATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACAAGATAAGATTTTGAATTG-AA
948 AACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACGAGATAAGGTTTTGA
65 AACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACGAGATAAGGTTTTGA
* *
1000 ATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACGAGATAAGGTTTTGAATTGAAA
1 ATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACAAGATAAGATTTTGAATTG-AA
* *
1065 AACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACGAGATAAGATTTTAA
65 AACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACGAGATAAGGTTTTGA
1117 ATTGAAA
1 ATTGAAA
1124 CTCAAACAAG
Statistics
Matches: 423, Mismatches: 41, Indels: 18
0.88 0.09 0.04
Matches are distributed among these distances:
114 5 0.01
115 6 0.01
116 193 0.46
117 214 0.51
118 5 0.01
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (116 bp):
ATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACAAGATAAGATTTTGAATTGAAA
ACTCTCTAACAGAGACCTCGAACAGGATTTTGAAACGAGATAAGGTTTTGA
Done.