Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017445.1 Corchorus olitorius cultivar O-4 contig17478, 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: 4052
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.35
Found at i:532 original size:30 final size:30
Alignment explanation
Indices: 496--1331 Score: 921
Period size: 30 Copynumber: 27.7 Consensus size: 30
486 ATTCAATTCC
*
496 AATCCTGTTTGAGGATCATTGCTTCATTTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTT
* * *
526 AATCCTGGTTGAGGATCGTTACTTTATTTTT
1 AATCCTGTTTGAGGATCATTGCTTTA-TTTT
* * *
557 AATCCTGGTTGAGGATCGTTACTTTATTTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTT
* * *
587 AATCCTGGTTGAGGAT-ATTTGCATCATTTT
1 AATCCTGTTTGAGGATCA-TTGCTTTATTTT
* * *
617 AATCCTGTTCGAGGACCATTGCTCTATTTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTT
* *
647 AATCATGTTTGAGGATCATTGTTTTATTTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTT
* *
677 AATCCTGTTTGAGGATCTTTGCTTTGTTTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTT
*
707 AATCCTGATTGAGGATC---G--TTATTTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTT
* *
732 AATCCTGTTTGAGGATCGTTGCTTTTTTTTT
1 AATCCTGTTTGAGGATCATTGC-TTTATTTT
* * *
763 AATCCTGGTTGAGGATCTTTGCTTTCTTTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTT
793 AATCCTGTTTGAGGATCATTGCTTTATTTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTT
* *
823 AATCCTGATTT-AAGATCATCG-TATTGA-TTT
1 AATCCTG-TTTGAGGATCATTGCT-TT-ATTTT
*
853 AATCCTGGTTGAGGATCATTGCTTTATTTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTT
*
883 AATCCTGATTT-AGGATCATTGCTTTGTTTT
1 AATCCTG-TTTGAGGATCATTGCTTTATTTT
* * *
913 AATTCTGGTTGAGGATCATTGTTTTATTTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTT
943 AATCCTGATTT-AGGATCATTGCTTTATTTT
1 AATCCTG-TTTGAGGATCATTGCTTTATTTT
973 AATCCTGGTTT-AGGATCATTGCTTTATTTT
1 AATCCT-GTTTGAGGATCATTGCTTTATTTT
*
1003 AATCCTGGTTGAGGATCATTGCTTTATTGCTTTGATTT
1 AATCCTGTTTGAGGATCATTGCTTTA------T--TTT
*
1041 AATCCTGTTTGAGGATCATTGCTCTATTTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTT
* * * *
1071 TATCCTGGTTGAGGAT-ATTTGCTATATGTT
1 AATCCTGTTTGAGGATCA-TTGCTTTATTTT
1101 AATCCTGGTTT-AGGATCATTGCTTTATTTT
1 AATCCT-GTTTGAGGATCATTGCTTTATTTT
* *
1131 AATCCTGTTTGAGGATCATTGATTTCTTTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTT
* *
1161 AATCCTGTTTGAGGATCATTGCTTCATCTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTT
* *
1191 AATCCTGGTTGAGGATCATTGCTTCATTTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTT
* *
1221 AATCATGTTTGAGGATCATTGCTTCATTTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTT
* **
1251 AATCCTGGTTGAGGATCATTGCTCCATTTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTT
*
1281 AATCCTGGTTGAGGATCATTG-TGTTATTTT
1 AATCCTGTTTGAGGATCATTGCT-TTATTTT
* *
1311 CATCTTGGTTT-AGGATCATTG
1 AATCCT-GTTTGAGGATCATTG
1332 TTTCATCAGT
Statistics
Matches: 696, Mismatches: 76, Indels: 68
0.83 0.09 0.08
Matches are distributed among these distances:
25 22 0.03
27 1 0.00
28 1 0.00
29 15 0.02
30 554 0.80
31 74 0.11
32 1 0.00
36 1 0.00
38 27 0.04
ACGTcount: A:0.20, C:0.14, G:0.19, T:0.47
Consensus pattern (30 bp):
AATCCTGTTTGAGGATCATTGCTTTATTTT
Found at i:1042 original size:38 final size:38
Alignment explanation
Indices: 990--1068 Score: 124
Period size: 38 Copynumber: 2.1 Consensus size: 38
980 GTTTAGGATC
*
990 ATTGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTT
1 ATTGCTTTATTTTAATCCTGGTTGAGGATCATTGCTCT
*
1028 ATTGCTTTGA-TTTAATCCTGTTTGAGGATCATTGCTCT
1 ATTGCTTT-ATTTTAATCCTGGTTGAGGATCATTGCTCT
1066 ATT
1 ATT
1069 TTTATCCTGG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 37 0.97
39 1 0.03
ACGTcount: A:0.19, C:0.14, G:0.18, T:0.49
Consensus pattern (38 bp):
ATTGCTTTATTTTAATCCTGGTTGAGGATCATTGCTCT
Found at i:1874 original size:28 final size:29
Alignment explanation
Indices: 1839--1911 Score: 93
Period size: 27 Copynumber: 2.7 Consensus size: 29
1829 GGTCATCTAG
1839 GGGCATTTTGAGTCATTTTTGCA-TTCAA
1 GGGCATTTTGAGTCATTTTTGCATTTCAA
*
1867 GGGCATTTTG-GTCA--TTTGCATTTTCAG
1 GGGCATTTTGAGTCATTTTTGCA-TTTCAA
1894 GGGCATTTT-AGTCATTTT
1 GGGCATTTTGAGTCATTTT
1912 AATCTCACTT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
25 6 0.15
27 21 0.54
28 10 0.26
29 2 0.05
ACGTcount: A:0.18, C:0.14, G:0.23, T:0.45
Consensus pattern (29 bp):
GGGCATTTTGAGTCATTTTTGCATTTCAA
Done.