Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013826.1 Corchorus olitorius cultivar O-4 contig13859, 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: 6191
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:11 original size:2 final size:2
Alignment explanation
Indices: 5--30 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1 TTAG
5 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
31 ATGTTCCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:192 original size:6 final size:6
Alignment explanation
Indices: 183--216 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
173 TTTATTTATT
*
183 TATCTA TATCTA TATGTA TATCTA TACTCTA TAT
1 TATCTA TATCTA TATCTA TATCTA TA-TCTA TAT
217 ATAAAAGCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.32, C:0.15, G:0.03, T:0.50
Consensus pattern (6 bp):
TATCTA
Found at i:817 original size:44 final size:44
Alignment explanation
Indices: 764--866 Score: 116
Period size: 44 Copynumber: 2.3 Consensus size: 44
754 TACGGCTTAT
* * *
764 CAAAATTTTATAGTGTTGTGACCAAAATTTCATAGGGAGGATAA
1 CAAAATTTTATAGTGTGGTGACCAAAATTTAATAGAGAGGATAA
* *** * * *
808 CAAAATTTTAAAGTGTGGTTTTCAAATTTTAATAGAGAGGTTAT
1 CAAAATTTTATAGTGTGGTGACCAAAATTTAATAGAGAGGATAA
852 CAAAATTTTATAGTG
1 CAAAATTTTATAGTG
867 AGTTTATTTA
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.37
Consensus pattern (44 bp):
CAAAATTTTATAGTGTGGTGACCAAAATTTAATAGAGAGGATAA
Found at i:833 original size:22 final size:22
Alignment explanation
Indices: 691--873 Score: 84
Period size: 22 Copynumber: 8.3 Consensus size: 22
681 TTATGTGTGT
* * **
691 GGTTATCAAAATTTCACAGTTT
1 GGTTATCAAAATTTTAAAGTGA
* * *
713 GGATATCAATATTTCATAA-TGA
1 GGTTATCAAAATTTTA-AAGTGA
* * *
735 GGTTATCACAATTTCATAGT-A
1 GGTTATCAAAATTTTAAAGTGA
* *
756 CGGCTTATCAAAATTTTATAGTGT
1 -GG-TTATCAAAATTTTAAAGTGA
* * * * * *
780 TGTGACCAAAATTTCATAGGGA
1 GGTTATCAAAATTTTAAAGTGA
* * *
802 GGATAACAAAATTTTAAAGTGT
1 GGTTATCAAAATTTTAAAGTGA
* *
824 GGTTTTC-AAATTTTAATAGAGA
1 GGTTATCAAAATTTTAA-AGTGA
*
846 GGTTATCAAAATTTTATAGTGA
1 GGTTATCAAAATTTTAAAGTGA
*
868 GTTTAT
1 GGTTAT
874 TTAACTTCCA
Statistics
Matches: 119, Mismatches: 35, Indels: 14
0.71 0.21 0.08
Matches are distributed among these distances:
21 11 0.09
22 82 0.69
23 26 0.22
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GGTTATCAAAATTTTAAAGTGA
Found at i:1036 original size:44 final size:44
Alignment explanation
Indices: 960--1087 Score: 143
Period size: 44 Copynumber: 2.9 Consensus size: 44
950 TAGGGATCAA
* * *
960 GTTATTAAAATTTCATCGGAAGATTATAAAAATTTCATTGTGTG
1 GTTATCAAAATTTCATCGGAAGATTATAAAAATTTCATAGTGAG
* *
1004 GTTATCAAAATTTCATTGGAA-ATTTATCAAAATTTCATAGTGAG
1 GTTATCAAAATTTCATCGGAAGA-TTATAAAAATTTCATAGTGAG
* * * *
1048 GTTATCAAAATTTTATAGCGAAG-TTATCAGAATTTCATAG
1 GTTATCAAAATTTCATCG-GAAGATTATAAAAATTTCATAG
1088 ATTTGTAGAT
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
43 1 0.01
44 69 0.95
45 3 0.04
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.39
Consensus pattern (44 bp):
GTTATCAAAATTTCATCGGAAGATTATAAAAATTTCATAGTGAG
Found at i:1087 original size:22 final size:21
Alignment explanation
Indices: 958--1087 Score: 116
Period size: 22 Copynumber: 6.0 Consensus size: 21
948 TATAGGGATC
* *
958 AAGTTATTAAAATTTCATCGG
1 AAGTTATCAAAATTTCATAGG
* *
979 AAGATTATAAAAATTTCATTGTG
1 AAG-TTATCAAAATTTCATAG-G
** *
1002 TGGTTATCAAAATTTCATTGG
1 AAGTTATCAAAATTTCATAGG
*
1023 AAATTTATCAAAATTTCATAGTG
1 -AAGTTATCAAAATTTCATAG-G
* *
1046 AGGTTATCAAAATTTTATAGCG
1 AAGTTATCAAAATTTCATAG-G
*
1068 AAGTTATCAGAATTTCATAG
1 AAGTTATCAAAATTTCATAG
1088 ATTTGTAGAT
Statistics
Matches: 89, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
21 4 0.04
22 82 0.92
23 3 0.03
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (21 bp):
AAGTTATCAAAATTTCATAGG
Found at i:1583 original size:2 final size:2
Alignment explanation
Indices: 1578--1602 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1568 ACTTAAAAAC
1578 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 T
1603 GTATGTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1607 original size:4 final size:4
Alignment explanation
Indices: 1600--1626 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1590 TATATATATA
1600 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
1627 ATAACATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Done.