Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012796.1 Kokia drynarioides strain JFW-HI SEQ_127809, 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: 12479
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.34
Warning! 206 characters in sequence are not A, C, G, or T
Found at i:1107 original size:30 final size:30
Alignment explanation
Indices: 1071--1303 Score: 262
Period size: 29 Copynumber: 7.9 Consensus size: 30
1061 GCCCTGAAGA
1071 CCTCGAAACTTCCAAAAATTCCATTTTTAC
1 CCTCGAAACTTCCAAAAATTCCATTTTTAC
*
1101 CCTCG-AACTTCCAAAAATTCCATTTTTAA
1 CCTCGAAACTTCCAAAAATTCCATTTTTAC
* * *
1130 CCTCAAAATTTCTAAAAATTCCATTTTTAC
1 CCTCGAAACTTCCAAAAATTCCATTTTTAC
*
1160 CCCCG-AACTTCCAAAAATTCCATTTTTAC
1 CCTCGAAACTTCCAAAAATTCCATTTTTAC
*
1189 CCACG-AACTTCCAAAAATTCCATTTTTGAC
1 CCTCGAAACTTCCAAAAATTCCATTTTT-AC
* *
1219 CC-CAAAACTTCAAAAAATTCCATTTTTTAC
1 CCTCGAAACTTCCAAAAATTCCA-TTTTTAC
* * * *
1249 CCCCAAAAC-TCCAAAATTTCAATTTTTGA-
1 CCTCGAAACTTCCAAAAATTCCATTTTT-AC
** *
1278 CCTCGAAACTTTTAAAAATTACATTT
1 CCTCGAAACTTCCAAAAATTCCATTT
1304 GGCTCCTGGA
Statistics
Matches: 174, Mismatches: 22, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
29 88 0.51
30 75 0.43
31 11 0.06
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (30 bp):
CCTCGAAACTTCCAAAAATTCCATTTTTAC
Found at i:1167 original size:59 final size:58
Alignment explanation
Indices: 1070--1275 Score: 254
Period size: 59 Copynumber: 3.5 Consensus size: 58
1060 TGCCCTGAAG
* *
1070 ACCTCGAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTT
1 ACCTCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTT
* *
1128 AACCTCAAAATTTCTAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTT
1 -ACCTCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTT
* ** *
1187 ACC-CACGAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCAAAAAATTCCATTTTTT
1 ACCTCA-AAACTTCCAAAAATTCCATTTTT-ACCCCCGAACTTCCAAAAATTCCA-TTTTT
* * *
1247 ACCCCCAAAAC-TCCAAAATTTCAATTTTT
1 A-CCTCAAAACTTCCAAAAATTCCATTTTT
1276 GACCTCGAAA
Statistics
Matches: 129, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
57 2 0.02
58 23 0.18
59 75 0.58
60 22 0.17
61 5 0.04
62 2 0.02
ACGTcount: A:0.35, C:0.29, G:0.02, T:0.33
Consensus pattern (58 bp):
ACCTCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTT
Found at i:1235 original size:88 final size:90
Alignment explanation
Indices: 1076--1275 Score: 307
Period size: 88 Copynumber: 2.3 Consensus size: 90
1066 GAAGACCTCG
* * *
1076 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCTCAAAATTT
1 AAACTTCCAAAAATTCCATTTTTACCCACGAACTTCCAAAAATTCCATTTTTAACCCCAAAACTT
*
1141 CTAAAAATTCCA-TTTTTACCCCC-
66 CAAAAAATTCCATTTTTTACCCCCA
* *
1164 GAACTTCCAAAAATTCCATTTTTACCCACGAACTTCCAAAAATTCCATTTTTGACCCCAAAACTT
1 AAACTTCCAAAAATTCCATTTTTACCCACGAACTTCCAAAAATTCCATTTTTAACCCCAAAACTT
1229 CAAAAAATTCCATTTTTTACCCCCA
66 CAAAAAATTCCATTTTTTACCCCCA
* *
1254 AAAC-TCCAAAATTTCAATTTTT
1 AAACTTCCAAAAATTCCATTTTT
1276 GACCTCGAAA
Statistics
Matches: 101, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
88 71 0.70
89 27 0.27
90 3 0.03
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.34
Consensus pattern (90 bp):
AAACTTCCAAAAATTCCATTTTTACCCACGAACTTCCAAAAATTCCATTTTTAACCCCAAAACTT
CAAAAAATTCCATTTTTTACCCCCA
Found at i:5091 original size:21 final size:20
Alignment explanation
Indices: 5045--5092 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
5035 TTAACACATG
* *
5045 TTTAATTATTTATATTTAATA
1 TTTAATTA-TTATACTAAATA
*
5066 ATTAATTATTATACTAAATTA
1 TTTAATTATTATACTAAA-TA
5087 TTTAAT
1 TTTAAT
5093 ATTTTACTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTAATTATTATACTAAATA
Found at i:9109 original size:27 final size:27
Alignment explanation
Indices: 9079--9131 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
9069 AGAAGCTTAG
9079 TACCTATGGATGTGTTGATAAAAACAA
1 TACCTATGGATGTGTTGATAAAAACAA
9106 TACCTATGGATGTGTTGATAAAAACA
1 TACCTATGGATGTGTTGATAAAAACA
9132 TCACCCCTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (27 bp):
TACCTATGGATGTGTTGATAAAAACAA
Found at i:12450 original size:2 final size:2
Alignment explanation
Indices: 12443--12479 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
12433 CCTGAACCAA
12443 AT AT AT AT AT AT AT 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
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.