Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010771.1 Kokia drynarioides strain JFW-HI SEQ_125733, 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: 1987
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.34
Warning! 102 characters in sequence are not A, C, G, or T
Found at i:981 original size:30 final size:29
Alignment explanation
Indices: 937--1350 Score: 281
Period size: 29 Copynumber: 14.1 Consensus size: 29
927 CCTTGAAAGT
937 CCCTAAACTGTCCAAAAATTCCATTTTTGAC
1 CCCTAAACT-TCCAAAAATTCCATTTTT-AC
* *
968 TCCGAAACTTCCAAAAATTCCATTTTTGA-
1 CCCTAAACTTCCAAAAATTCCATTTTT-AC
* * *
997 CCCTACAATTTTCAAAAATTCTATTTTTA-
1 CCCTA-AACTTCCAAAAATTCCATTTTTAC
*
1026 CCCTCAAACTTCC-AAAATTCCATTTTGAC
1 CCCT-AAACTTCCAAAAATTCCATTTTTAC
* * ** **
1055 CCCAAAACTTTCAAAAATTATATACTTA-
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
* *
1083 CCCTCGAACTTTCAAAAATTCCATTTTTAGC
1 CCCT-AAACTTCCAAAAATTCCATTTTTA-C
* *
1114 CCCAAAACTTCCAAAAATTACATTTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
* * *
1143 CCCTAAACTTCCAAGAATTTTC-TTTATAAC
1 CCCTAAACTTCCAA-AAATTCCATTT-TTAC
* *
1173 CCCTAAACTTCTAAAAATTACATTTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
* * * *
1202 TCTCGAATC-TCCAAAAATTCCATTTTGAC
1 -CCCTAAACTTCCAAAAATTCCATTTTTAC
* * *
1231 CCCTAGACTTCTAAAAATTACA-TTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
** * *
1259 CCCCGAA-TATCCAAAAACTCCATTTTTGAT
1 CCCTAAACT-TCCAAAAATTCCATTTTT-AC
* * * *
1289 CCCAAAAC-TCTAAAAAATTACAATTTTA-
1 CCCTAAACTTC-CAAAAATTCCATTTTTAC
* *
1317 CCCTCAAATTTCCAAAAAATCCATTTTTTAC
1 CCCT-AAACTTCCAAAAATTCCA-TTTTTAC
1348 CCC
1 CCC
1351 GAATTTAAAC
Statistics
Matches: 294, Mismatches: 68, Indels: 42
0.73 0.17 0.10
Matches are distributed among these distances:
27 1 0.00
28 49 0.17
29 116 0.39
30 115 0.39
31 13 0.04
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTCCATTTTTAC
Found at i:1028 original size:29 final size:29
Alignment explanation
Indices: 949--1349 Score: 170
Period size: 30 Copynumber: 13.7 Consensus size: 29
939 CTAAACTGTC
* *
949 CAAAAATTCCATTTTTGACTCCGA-AACTTC
1 CAAAAATTCCATTTTT-AC-CCTACAACTTT
*
979 CAAAAATTCCATTTTTGACCCTACAATTTT
1 CAAAAATTCCATTTTT-ACCCTACAACTTT
*
1009 CAAAAATTCTATTTTTACCCT-CAAAC-TT
1 CAAAAATTCCATTTTTACCCTAC-AACTTT
* * * *
1037 CCAAAATTCCATTTTGACCCCAAAACTTT
1 CAAAAATTCCATTTTTACCCTACAACTTT
** **
1066 CAAAAATTATATACTTACCCT-CGAACTTT
1 CAAAAATTCCATTTTTACCCTAC-AACTTT
* * *
1095 CAAAAATTCCATTTTTAGCCCCAAAACTTC
1 CAAAAATTCCATTTTTA-CCCTACAACTTT
* *
1125 CAAAAATTACATTTTTACCCCTA-AACTTC
1 CAAAAATTCCATTTTTA-CCCTACAACTTT
* * *
1154 CAAGAATTTTC-TTTATAACCCCTA-AAC-TT
1 CAA-AAATTCCATTT-TTA-CCCTACAACTTT
* * *
1183 CTAAAAATTACATTTTTACTCT-CGAA-TCTC
1 C-AAAAATTCCATTTTTACCCTAC-AACT-TT
* *
1213 CAAAAATTCCATTTTGACCCCTA-GAC-TT
1 CAAAAATTCCATTTTTA-CCCTACAACTTT
* * *
1241 CTAAAAATTACA-TTTTACCC-CCGAA-TATC
1 C-AAAAATTCCATTTTTACCCTAC-AACT-TT
* * *
1270 CAAAAACTCCATTTTTGATCCC-AAAACTCT
1 CAAAAATTCCATTTTT-A-CCCTACAACTTT
* * * *
1300 AAAAAATTACAATTTTACCCT-CAAATTT
1 CAAAAATTCCATTTTTACCCTACAACTTT
*
1328 CCAAAAAATCCATTTTTTACCC
1 -CAAAAATTCCA-TTTTTACCC
1350 CGAATTTAAA
Statistics
Matches: 277, Mismatches: 64, Indels: 60
0.69 0.16 0.15
Matches are distributed among these distances:
27 3 0.01
28 48 0.17
29 107 0.39
30 115 0.42
31 4 0.01
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.34
Consensus pattern (29 bp):
CAAAAATTCCATTTTTACCCTACAACTTT
Found at i:1131 original size:59 final size:59
Alignment explanation
Indices: 941--1344 Score: 321
Period size: 59 Copynumber: 6.9 Consensus size: 59
931 GAAAGTCCCT
* * *
941 AAACTGTCCAAAAATTCCATTTTTGACTC-CGAAACTTCCAAAAATTCCATTTTT-GACCCTA
1 AAACT-TCCAAAAATTACATTTTT-ACCCTCG-AACTTCCAAAAATTCCATTTTTAG-CCCCA
* * * * *
1002 CAATTTTCAAAAATT-CTATTTTTACCCTCAAACTTCC-AAAATTCCATTTTGA-CCCCA
1 AAACTTCCAAAAATTAC-ATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAGCCCCA
* * ** *
1059 AAACTTTCAAAAATTATATACTTACCCTCGAACTTTCAAAAATTCCATTTTTAGCCCCA
1 AAACTTCCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAGCCCCA
* * * * * *
1118 AAACTTCCAAAAATTACATTTTTACCC-CTAAACTTCCAAGAATTTTC-TTTATAACCCCT
1 AAACTTCCAAAAATTACATTTTTACCCTC-GAACTTCCAA-AAATTCCATTTTTAGCCCCA
* * * *
1177 AAACTTCTAAAAATTACATTTTTACTCTCGAA-TCTCCAAAAATTCCATTTTGA-CCCCT
1 AAACTTCCAAAAATTACATTTTTACCCTCGAACT-TCCAAAAATTCCATTTTTAGCCCCA
* * * * *
1235 AGACTTCTAAAAATTACA-TTTTACCCCCGAA-TATCCAAAAACTCCATTTTT-GATCCCA
1 AAACTTCCAAAAATTACATTTTTACCCTCGAACT-TCCAAAAATTCCATTTTTAG-CCCCA
* * * * *
1293 AAAC-TCTAAAAAATTACAATTTTACCCTCAAATTTCCAAAAAATCCATTTTT
1 AAACTTC-CAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTT
1345 TACCCCGAAT
Statistics
Matches: 281, Mismatches: 46, Indels: 34
0.78 0.13 0.09
Matches are distributed among these distances:
57 63 0.22
58 72 0.26
59 120 0.43
60 23 0.08
61 3 0.01
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.34
Consensus pattern (59 bp):
AAACTTCCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAGCCCCA
Done.