Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001011.1 Kokia drynarioides strain JFW-HI SEQ_112220, 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, 834
Length: 1391
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:857 original size:58 final size:59
Alignment explanation
Indices: 739--1236 Score: 638
Period size: 59 Copynumber: 8.5 Consensus size: 59
729 AAGGTTCCTA
* * *
739 AACCTTTCAAAAATTATCATTTTACCC-CGAACTTCCAAAAATCCCATTTTTGA-CCCG
1 AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCG
*
796 AACCTTCCAAAAATTACCATTTTACCCTTGAACTTCC-AAAATCCCATTTTTAACCCCG
1 AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCG
* * * *
854 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCACA
1 AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCG
* *
913 AACCTTCCAAAAATTACCATTTTACCC-CTAAACTTCCAAAAATCCCATTTTTAACCACG
1 AACCTTCCAAAAATTACCATTTTACCCTC-GAACTTCCAAAAATCCCATTTTTAACCCCG
* *
972 AACCTTCC-AAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTAAACCTCG
1 AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCG
* * * *
1030 AACCTTCC-AAAATTACTATTTTACCCCCAAACTTCC-AAAATCCTATTTTTAACCCCG
1 AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCG
* * * *
1087 AACCTTCCAAAAATTACCATTTTATTCC-CGGACTTCCAAAAATCCCATTTTTGACCTCG
1 AACCTTCCAAAAATTACCATTTTA-CCCTCGAACTTCCAAAAATCCCATTTTTAACCCCG
* * * * ** *
1146 AACCTTCCAAAAATTTCCATTTCACCTTCAAACTTCCAAAAATCCCATTTTCGACCTCG
1 AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCG
*
1205 AAAC-TCTC-AAAATTACCATTTTTACCCTCGAA
1 AACCTTC-CAAAAATTACCA-TTTTACCCTCGAA
1237 TGTTTTAAGT
Statistics
Matches: 390, Mismatches: 40, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
57 66 0.17
58 159 0.41
59 165 0.42
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.30
Consensus pattern (59 bp):
AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCG
Found at i:1080 original size:233 final size:233
Alignment explanation
Indices: 739--1236 Score: 734
Period size: 233 Copynumber: 2.1 Consensus size: 233
729 AAGGTTCCTA
* * **
739 AACCTTTCAAAAATTATCATTTTACCC-CGAACTTCCAAAAATCCCATTTTTGACCCGAACCTTC
1 AACC-TTCCAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTAAACCCGAACCTTC
***
803 CAAAAATTACCATTTTACCCTTGAACTTCCAAAATCCCATTTTTAACCCCGAACCTTCCAAAAAT
65 CAAAAATTACCATTTTACCCCCAAACTTCCAAAATCCCATTTTTAACCCCGAACCTTCCAAAAAT
868 TACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCACAAACCTTCCAAAAATTACCAT
130 TACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCACAAACCTTCCAAAAATTACCAT
* *
933 TTTACCC-CTAAACTTCCAAAAATCCCATTTTTAACCACG
195 TTCACCCTC-AAACTTCCAAAAATCCCATTTTCAACCACG
972 AACCTTCCAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTAAACCTCGAACCTTC
1 AACCTTCCAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTAAACC-CGAACCTTC
* *
1037 C-AAAATTACTATTTTACCCCCAAACTTCCAAAATCCTATTTTTAACCCCGAACCTTCCAAAAAT
65 CAAAAATTACCATTTTACCCCCAAACTTCCAAAATCCCATTTTTAACCCCGAACCTTCCAAAAAT
** * * * *
1101 TACCATTTTATTCCCGGACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCCAAAAATTTCCAT
130 TACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCACAAACCTTCCAAAAATTACCAT
* * *
1166 TTCACCTTCAAACTTCCAAAAATCCCATTTTCGACCTCG
195 TTCACCCTCAAACTTCCAAAAATCCCATTTTCAACCACG
*
1205 AAAC-TCTCAAAATTACCATTTTTACCCTCGAA
1 AACCTTC-CAAAATTACCA-TTTTACCCTCGAA
1237 TGTTTTAAGT
Statistics
Matches: 239, Mismatches: 21, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
232 22 0.09
233 193 0.81
234 24 0.10
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.30
Consensus pattern (233 bp):
AACCTTCCAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTAAACCCGAACCTTCC
AAAAATTACCATTTTACCCCCAAACTTCCAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATT
ACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCACAAACCTTCCAAAAATTACCATT
TCACCCTCAAACTTCCAAAAATCCCATTTTCAACCACG
Found at i:1216 original size:30 final size:30
Alignment explanation
Indices: 768--1226 Score: 262
Period size: 30 Copynumber: 15.7 Consensus size: 30
758 TTTTACCCCG
*
768 AACTTCCAAAAATCCCATTTTTGACC-CGA
1 AACTTCCAAAAATCCCATTTTCGACCTCGA
* * *
797 ACCTTCCAAAAATTACCATTTT--ACCCTTG-
1 AACTTCCAAAAA-TCCCATTTTCGA-CCTCGA
** *
826 AACTTCC-AAAATCCCATTTTTAACCCCGA
1 AACTTCCAAAAATCCCATTTTCGACCTCGA
* * *
855 ACCTTCCAAAAATTACCATTTT--ACCCCCG-
1 AACTTCCAAAAA-TCCCATTTTCGA-CCTCGA
* *
884 AACTTCCAAAAATCCCATTTTTGACCAC-A
1 AACTTCCAAAAATCCCATTTTCGACCTCGA
* * *
913 AACCTTCCAAAAATTACCATTTT--ACCCCTA
1 AA-CTTCCAAAAA-TCCCATTTTCGACCTCGA
** *
943 AACTTCCAAAAATCCCATTTTTAACCACGA
1 AACTTCCAAAAATCCCATTTTCGACCTCGA
* * *
973 ACCTTCCAAAATTACCATTTT--ACCCTCG-
1 AACTTCCAAAAATCCCATTTTCGA-CCTCGA
**
1001 AACTTCCAAAAATCCCATTTTAAACCTCGA
1 AACTTCCAAAAATCCCATTTTCGACCTCGA
* * * * * *
1031 ACCTTCCAAAATTACTATTTT--ACCCCCA
1 AACTTCCAAAAATCCCATTTTCGACCTCGA
* ** *
1059 AACTTCC-AAAATCCTATTTTTAACCCCGA
1 AACTTCCAAAAATCCCATTTTCGACCTCGA
* * ***
1088 ACCTTCCAAAAATTACCATTTTATTCC-CG-
1 AACTTCCAAAAA-TCCCATTTTCGACCTCGA
* *
1117 GACTTCCAAAAATCCCATTTTTGACCTCGA
1 AACTTCCAAAAATCCCATTTTCGACCTCGA
* *
1147 ACCTTCCAAAAATTTCCA-TTTC-ACCTTC-A
1 AACTTCCAAAAA-TCCCATTTTCGACC-TCGA
1176 AACTTCCAAAAATCCCATTTTCGACCTCGA
1 AACTTCCAAAAATCCCATTTTCGACCTCGA
* *
1206 AAC-TCTCAAAATTACCATTTT
1 AACTTC-CAAAAATCCCATTTT
1227 TACCCTCGAA
Statistics
Matches: 343, Mismatches: 54, Indels: 65
0.74 0.12 0.14
Matches are distributed among these distances:
27 19 0.06
28 68 0.20
29 113 0.33
30 114 0.33
31 29 0.08
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.30
Consensus pattern (30 bp):
AACTTCCAAAAATCCCATTTTCGACCTCGA
Done.