Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011338.1 Kokia drynarioides strain JFW-HI SEQ_126318, 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: 10180
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Warning! 25 characters in sequence are not A, C, G, or T
Found at i:1100 original size:30 final size:29
Alignment explanation
Indices: 1064--1454 Score: 226
Period size: 29 Copynumber: 13.4 Consensus size: 29
1054 GTCCCTAAAC
*
1064 CTTCCAAAAATTACCATTTTACCCCTTAAA
1 CTTCCAAAAATTACCATTTTACCCC-CAAA
* * *
1094 CTTCCAAAAA-TCCCATTTTTGACCCCGAAT
1 CTTCCAAAAATTACCA-TTTT-ACCCCCAAA
* *
1124 CTTCCAAAAATTACTATTTTACCCCCGAA
1 CTTCCAAAAATTACCATTTTACCCCCAAA
* * * *
1153 CATCCAAAAA-TCCCATTTTAACCCCGAAT
1 CTTCCAAAAATTACCATTTT-ACCCCCAAA
* *
1182 CTTCTAAAAATTACTATTTTACCCCCAAA
1 CTTCCAAAAATTACCATTTTACCCCCAAA
* * * * *
1211 CTTCCAAAAA-TCCCATTTGACCTCGAAT
1 CTTCCAAAAATTACCATTTTACCCCCAAA
* * * *
1239 CTT-CTAAAATTACTATTTTACCCTCGAA
1 CTTCCAAAAATTACCATTTTACCCCCAAA
* * *
1267 CTTCTAAAAA-TCCCATTTTTAACCCCAAA
1 CTTCCAAAAATTACCA-TTTTACCCCCAAA
**
1296 CCTTCTTAAAATTACCATTTTACCCCCAAA
1 -CTTCCAAAAATTACCATTTTACCCCCAAA
* *** *
1326 CTTCCAACAA-T-CTCATTTTTTACCTTGAAT
1 CTTCCAAAAATTAC-CA--TTTTACCCCCAAA
* * * *
1356 CTTCCAAAATTTACTAATTT-CCCCTCGAA
1 CTTCCAAAAATTACCATTTTACCCC-CAAA
* * * *
1385 -TTCCCAAAAA-TCCCATTTTTAGCCTCGAAT
1 CTT-CCAAAAATTACCA-TTTTA-CCCCCAAA
* *
1415 CTTCCAAAAATTACCATTTTACCCTCGAA
1 CTTCCAAAAATTACCATTTTACCCCCAAA
1444 CTTCCAAAAAT
1 CTTCCAAAAAT
1455 CCTATTTTTG
Statistics
Matches: 263, Mismatches: 76, Indels: 45
0.68 0.20 0.12
Matches are distributed among these distances:
27 6 0.02
28 48 0.18
29 97 0.37
30 88 0.33
31 23 0.09
32 1 0.00
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (29 bp):
CTTCCAAAAATTACCATTTTACCCCCAAA
Found at i:1328 original size:59 final size:59
Alignment explanation
Indices: 1064--1463 Score: 461
Period size: 59 Copynumber: 6.8 Consensus size: 59
1054 GTCCCTAAAC
* ** *
1064 CTTCCAAAAATTACCATTTTACCCCTTAAACTTCCAAAAATCCCATTTTTGACCCCGAAT
1 CTTCCAAAAATTACTATTTTACCCC-CGAACTTCCAAAAATCCCATTTTTAACCCCGAAT
*
1124 CTTCCAAAAATTACTATTTTACCCCCGAACATCCAAAAATCCCA-TTTTAACCCCGAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCGAAT
* * * *
1182 CTTCTAAAAATTACTATTTTACCCCCAAACTTCCAAAAATCCCA--TTTGACCTCGAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCGAAT
* * * * *
1239 CTT-CTAAAATTACTATTTTACCCTCGAACTTCTAAAAATCCCATTTTTAACCCCAAAC
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCGAAT
** * * * * * **
1297 CTTCTTAAAATTACCATTTTACCCCCAAACTTCCAACAATCTCATTTTTTACCTTGAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCGAAT
* * * *
1356 CTTCCAAAATTTACTAATTT-CCCCTCGAA-TTCCCAAAAATCCCATTTTTAGCCTCGAAT
1 CTTCCAAAAATTACTATTTTACCCC-CGAACTT-CCAAAAATCCCATTTTTAACCCCGAAT
* * *
1415 CTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCTATTTTT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTT
1464 GATTCCGAAC
Statistics
Matches: 286, Mismatches: 47, Indels: 15
0.82 0.14 0.04
Matches are distributed among these distances:
56 35 0.12
57 14 0.05
58 72 0.25
59 136 0.48
60 29 0.10
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.34
Consensus pattern (59 bp):
CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCGAAT
Found at i:1463 original size:29 final size:28
Alignment explanation
Indices: 1064--1462 Score: 222
Period size: 30 Copynumber: 13.7 Consensus size: 28
1054 GTCCCTAAAC
**
1064 CTTCCAAAAATTACC-ATTTTACCCCTTAAA
1 CTTCCAAAAA-T-CCTATTTTA-CCCTCGAA
*
1094 CTTCCAAAAATCCCATTTTTGACCC-CGAA
1 CTTCCAAAAATCCTA-TTTT-ACCCTCGAA
* *
1123 TCTTCCAAAAATTACTATTTTACCCCCGAA
1 -CTTCCAAAAA-TCCTATTTTACCCTCGAA
* *
1153 CATCCAAAAATCCCATTTTAACCC-CGAA
1 CTTCCAAAAATCCTATTTT-ACCCTCGAA
* * * *
1181 TCTTCTAAAAATTACTATTTTACCCCCAAA
1 -CTTCCAAAAA-TCCTATTTTACCCTCGAA
* *
1211 CTTCCAAAAATCCCATTTGA-CCTCGAA
1 CTTCCAAAAATCCTATTTTACCCTCGAA
* * *
1238 TCTTCTAAAATTACTATTTTACCCTCGAA
1 -CTTCCAAAAATCCTATTTTACCCTCGAA
* * *
1267 CTTCTAAAAATCCCATTTTTAACCC-CAAA
1 CTTCCAAAAATCCTA-TTTT-ACCCTCGAA
* * * *
1296 CCTTCTTAAAATTACC-ATTTTACCCCCAAA
1 -CTTC-CAAAAAT-CCTATTTTACCCTCGAA
* * *
1326 CTTCCAACAATCTCATTTTTTA-CCTTGAA
1 CTTCCAAAAATC-C-TATTTTACCCTCGAA
* * * *
1355 TCTTCCAAAATTTACTAATTTCCCCTCGAA
1 -CTTCCAAAA-ATCCTATTTTACCCTCGAA
* *
1385 -TTCCCAAAAATCCCATTTTTAGCCTCGAA
1 CTT-CCAAAAATCCTA-TTTTACCCTCGAA
1414 TCTTCCAAAAATTACC-ATTTTACCCTCGAA
1 -CTTCCAAAAA-T-CCTATTTTACCCTCGAA
1444 CTTCCAAAAATCCTATTTT
1 CTTCCAAAAATCCTATTTT
1463 TGATTCCGAA
Statistics
Matches: 289, Mismatches: 49, Indels: 64
0.72 0.12 0.16
Matches are distributed among these distances:
27 8 0.03
28 63 0.22
29 98 0.34
30 100 0.35
31 16 0.06
32 4 0.01
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.33
Consensus pattern (28 bp):
CTTCCAAAAATCCTATTTTACCCTCGAA
Done.