Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010805.1 Kokia drynarioides strain JFW-HI SEQ_125772, 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: 1919
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1267 original size:29 final size:29
Alignment explanation
Indices: 1174--1580 Score: 444
Period size: 29 Copynumber: 13.8 Consensus size: 29
1164 AGAGGTCCCG
*
1174 AAACTGTCCAAAAATTCCATTTTCACCACT-
1 AAACT-TCCAAAAATTCCATTTTTACC-CTC
*
1204 AAACTTCCAAAAAATTCCATTTTTAACCTC
1 AAACTTCC-AAAAATTCCATTTTTACCCTC
* *
1234 GAAACTTCTAAAAATTCCATTTTTACCCTT
1 -AAACTTCCAAAAATTCCATTTTTACCCTC
*** *
1264 AAACTTTTGAAAATCCCATTTTTGACCC-C
1 AAACTTCCAAAAATTCCATTTTT-ACCCTC
* * *
1293 AAAACTTCCAAAAATTCCATTTTCACCATG
1 -AAACTTCCAAAAATTCCATTTTTACCCTC
* *
1323 AAACTTCCAAAAATTCCATTTTTACCATG
1 AAACTTCCAAAAATTCCATTTTTACCCTC
1352 AAACTTCCAAAAATTCCATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCTC
* *
1381 GAACTTCCAAAAA-TCTCATTTTTAACCTC
1 AAACTTCCAAAAATTC-CATTTTTACCCTC
1410 GAAACTTCCAAAAATTCCATTTTTACCCTC
1 -AAACTTCCAAAAATTCCATTTTTACCCTC
* * *
1440 AAACATCCAAAAATCCCATTTTTGACCCTA
1 AAACTTCCAAAAATTCCATTTTT-ACCCTC
* * *
1470 AAACTTCTAAAAAATACATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCTC
* *
1499 AAACTTCCAAAAATCCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCTC
* *
1528 AAACTTCTAAAAATCCCATTTTTAACCC-C
1 AAACTTCCAAAAATTCCATTTTT-ACCCTC
*
1557 AAAACTTCTAAAAATTACCATTTT
1 -AAACTTCCAAAAATT-CCATTTT
1581 GCCCCCGGAT
Statistics
Matches: 325, Mismatches: 39, Indels: 25
0.84 0.10 0.06
Matches are distributed among these distances:
28 2 0.01
29 180 0.55
30 127 0.39
31 16 0.05
ACGTcount: A:0.37, C:0.28, G:0.02, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCTC
Found at i:1306 original size:59 final size:58
Alignment explanation
Indices: 1170--1580 Score: 457
Period size: 59 Copynumber: 6.9 Consensus size: 58
1160 CCCTAGAGGT
* *
1170 CCCGAAACTGTCCAAAAATTCCATTTTCACCACT-AAACTTCCAAAAAATTCCATTTTTAAC
1 CCCGAAACT-TCCAAAAATTCCATTTTTACC-CTCAAACTTCC-AAAAATCCCATTTTT-AC
* * * ***
1231 CTCGAAACTTCTAAAAATTCCATTTTTACCCTTAAACTTTTGAAAATCCCATTTTTGAC
1 CCCGAAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTT-AC
* * * * *
1290 CCCAAAACTTCCAAAAATTCCATTTTCACCATGAAACTTCCAAAAATTCCATTTTTAC
1 CCCGAAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAC
** * *
1348 CATGAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCTCATTTTTAAC
1 CCCGAAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTT-AC
* *
1407 CTCGAAACTTCCAAAAATTCCATTTTTACCCTCAAACATCCAAAAATCCCATTTTTGAC
1 CCCGAAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTT-AC
** * * *
1466 CCTAAAACTTCTAAAAAATACATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAC
1 CCCGAAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAC
* * * * *
1524 CCCCAAACTTCTAAAAATCCCATTTTTAACCC-CAAAACTTCTAAAAATTACCATTTT
1 CCCGAAACTTCCAAAAATTCCATTTTT-ACCCTC-AAACTTCCAAAAA-TCCCATTTT
1581 GCCCCCGGAT
Statistics
Matches: 298, Mismatches: 47, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
58 74 0.25
59 183 0.61
60 33 0.11
61 8 0.03
ACGTcount: A:0.37, C:0.28, G:0.02, T:0.33
Consensus pattern (58 bp):
CCCGAAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAC
Found at i:1609 original size:88 final size:89
Alignment explanation
Indices: 1174--1580 Score: 484
Period size: 88 Copynumber: 4.6 Consensus size: 89
1164 AGAGGTCCCG
* * * * *
1174 AAACTGTCCAAAAATTCCA-TTTTCACCACTAAACTTCCAAAAAATTCCATTTTTAACCTCGAAA
1 AAACT-TCCAAAAATCCCATTTTTGACCCCAAAACTTCC-AAAAATTCCATTTTTACCCTCGAAA
* *
1238 CTTCTAAAAATTCCATTTTTACCCTT
64 CTTCCAAAAATTCCATTTTTACCCTC
*** * *
1264 AAACTTTTGAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTCACCAT-GAAACT
1 AAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCGAAACT
* *
1328 TCCAAAAATTCCATTTTTACCATG
66 TCCAAAAATTCCATTTTTACCCTC
* * *
1352 AAACTTCCAAAAATTCCATTTTT-ACCCTC-GAACTTCCAAAAA-TCTCATTTTTAACCTCGAAA
1 AAACTTCCAAAAATCCCATTTTTGACCC-CAAAACTTCCAAAAATTC-CATTTTTACCCTCGAAA
1414 CTTCCAAAAATTCCATTTTTACCCTC
64 CTTCCAAAAATTCCATTTTTACCCTC
* * * * *
1440 AAACATCCAAAAATCCCATTTTTGACCCTAAAACTTCTAAAAAATACATTTTTACCCTC-AAACT
1 AAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCGAAACT
* *
1504 TCCAAAAATCCCATTTTTACCCCC
66 TCCAAAAATTCCATTTTTACCCTC
* * *
1528 AAACTTCTAAAAATCCCATTTTTAACCCCAAAACTTCTAAAAATTACCATTTT
1 AAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATT-CCATTTT
1581 GCCCCCGGAT
Statistics
Matches: 271, Mismatches: 38, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
86 2 0.01
87 25 0.09
88 163 0.60
89 59 0.22
90 22 0.08
ACGTcount: A:0.37, C:0.28, G:0.02, T:0.33
Consensus pattern (89 bp):
AAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCGAAACT
TCCAAAAATTCCATTTTTACCCTC
Done.