Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008241.1 Kokia drynarioides strain JFW-HI SEQ_122905, 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: 2338
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Found at i:315 original size:3 final size:3
Alignment explanation
Indices: 307--351 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
297 TTAAATGAAT
* * **
307 TAA TAA TAA TAA TAA TTA TAT TTT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
352 ACCGAAAGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:1522 original size:29 final size:29
Alignment explanation
Indices: 1479--1888 Score: 311
Period size: 30 Copynumber: 13.8 Consensus size: 29
1469 AAAGGTCCTT
*
1479 AAACTATCCGAAAATTCCATTTTTACCCTC
1 AAACT-TCCAAAAATTCCATTTTTACCCTC
*
1509 AAACTTCCAAAAA-TCCTATTTTTAACCTC
1 AAACTTCCAAAAATTCC-ATTTTTACCCTC
1538 GAAACTTCCAAAAATTCCATTTTTAACCC-C
1 -AAACTTCCAAAAATTCCATTTTT-ACCCTC
*
1568 AAAACTTCCAAAAATTTCATTTTTAACCC-C
1 -AAACTTCCAAAAATTCCATTTTT-ACCCTC
* * * * *
1598 GAACTTCCAAAAATCCCATTTTTGATCTTG
1 AAACTTCCAAAAATTCCATTTTT-ACCCTC
* *
1628 AAACTTTCAAAAATTTCATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCTC
* *
1657 GAACTTCCAAAAATCCCATTTTTAACCC-C
1 AAACTTCCAAAAATTCCATTTTT-ACCCTC
*
1686 GAAACATT-CAAAAATTTCATTTTTACCC-C
1 -AAAC-TTCCAAAAATTCCATTTTTACCCTC
* *
1715 TAAAGTTCCAAAAATTCCATTTTTAACCTC
1 -AAACTTCCAAAAATTCCATTTTTACCCTC
1745 AAAACTTCC-AAAATT-CAGTTTTTACTCCCCTC
1 -AAACTTCCAAAAATTCCA-TTTTTA---CCCTC
* **
1777 GAACTTTTAAAAATTCCATTTTTGA-CCTC
1 AAACTTCCAAAAATTCCATTTTT-ACCCTC
* * *
1806 AAAACTTCTAAAAATTCTATTTTTACCCCTG
1 -AAACTTCCAAAAATTCCATTTTTA-CCCTC
* * * *
1837 AATC-TCTAAAATTTCCATTTTTAACACC-G
1 AAACTTCCAAAAATTCCATTTTT-AC-CCTC
*
1866 AAACTTTCAAAAATTACCATTTT
1 AAACTTCCAAAAATT-CCATTTT
1889 GCCTCTCGAG
Statistics
Matches: 309, Mismatches: 47, Indels: 47
0.77 0.12 0.12
Matches are distributed among these distances:
28 7 0.02
29 127 0.41
30 134 0.43
31 23 0.07
32 15 0.05
33 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCTC
Found at i:1603 original size:59 final size:58
Alignment explanation
Indices: 1480--1880 Score: 368
Period size: 59 Copynumber: 6.8 Consensus size: 58
1470 AAGGTCCTTA
* * *
1480 AACTATCCGAAAATTCCATTTTT-ACCCTC-AAACTTCCAAAAA-TCCTATTTTTAACCTCG
1 AACT-TCCAAAAATTCCATTTTTAACCC-CAAAACTTCCAAAAATTTC-ATTTTT-ACCCCG
1539 AAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTTCATTTTTAACCCCG
1 -AACTTCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTTCATTTTT-ACCCCG
* * * *** *
1599 AACTTCCAAAAATCCCATTTTTGATCTTGAAACTTTCAAAAATTTCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTTCATTTTTACCC-CG
* * *
1658 AACTTCCAAAAATCCCATTTTTAACCCCGAAACATT-CAAAAATTTCATTTTTACCCCTA
1 AACTTCCAAAAATTCCATTTTTAACCCCAAAAC-TTCCAAAAATTTCATTTTTACCCC-G
* *
1717 AAGTTCCAAAAATTCCATTTTTAACCTCAAAACTTCC-AAAA-TTCAGTTTTTACTCCCCTCG
1 AACTTCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTTCA-TTTTTA---CCC-CG
** * * *
1778 AACTTTTAAAAATTCCATTTTTGACCTCAAAACTTCTAAAAA-TTCTATTTTTACCCCTG
1 AACTTCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTTC-ATTTTTACCCC-G
* * * * *
1837 AA-TCTCTAAAATTTCCATTTTTAACACCGAAACTTTCAAAAATT
1 AACT-TCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATT
1881 ACCATTTTGC
Statistics
Matches: 291, Mismatches: 33, Indels: 34
0.81 0.09 0.09
Matches are distributed among these distances:
57 4 0.01
58 19 0.07
59 180 0.62
60 36 0.12
61 37 0.13
62 14 0.05
63 1 0.00
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.35
Consensus pattern (58 bp):
AACTTCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTTCATTTTTACCCCG
Done.