Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006144.1 Kokia drynarioides strain JFW-HI SEQ_120678, 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: 3803
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Found at i:879 original size:84 final size:81
Alignment explanation
Indices: 615--1202 Score: 472
Period size: 84 Copynumber: 7.0 Consensus size: 81
605 AATTCTGAAA
* * * * * * * *
615 CAAAATCAAAATCAATTCTGTTGAATGGCAGGATTAAATCTTGAAACAGAATTATTTAATTATTT
1 CAAAATC-AAATCAAATCTGTTAAACGACA-GAATAAATCTCGAAACAGAATTATTCAATTAATT
*
680 CTTGTTTTGAAACAAAAT
64 CTTGTTTGGAAACAAAAT
*
698 CAAAATCAAATCAAATCTGTTAAACGACGAGAATAAATCTCGAAACATAATTATTCAATTAATTC
1 CAAAATCAAATCAAATCTGTTAAACGAC-AGAATAAATCTCGAAACAGAATTATTCAATTAATTC
* *
763 TTATTTGGAAGCAAAAT
65 TTGTTTGGAAACAAAAT
* * * * *
780 CAAAATCAAATCAAATCTATTTAACAACATAAATAAAT-TCCGAAACAAAATTATTCAATTTTAA
1 CAAAATCAAATCAAATCTGTTAAACGACA-GAATAAATCT-CGAAACAGAATTATTCAA--TTAA
*
844 TTCTTGTTTGGAATCAAAAT
62 TTCTTGTTTGGAAACAAAAT
* * * * * *
864 CAAAATCTAATCAAATTTGTTGAACGGCGGGAATAAATCTCGAATA-AGAATTATTTAATTTTAA
1 CAAAATCAAATCAAATCTGTTAAACGAC-AGAATAAATCTCGAA-ACAGAATTATTCAA--TTAA
*
928 TTCTTGTTTGAAAACAAAAT
62 TTCTTGTTTGGAAACAAAAT
** * * * *
948 CAAAATCAAATCAAATAAGTTGAACGGCGGGAATAAATC-CTGAAAACAGAATTATTTAATTTTA
1 CAAAATCAAATCAAATCTGTTAAACGAC-AGAATAAATCTC-G-AAACAGAATTATTCAA--TTA
* *
1012 ATTCCTCTTTGGAAACAAAAT
61 ATTCTTGTTTGGAAACAAAAT
* * * * * *
1033 AAAAAAT-AGAATAAAATCTGTTGAACGGCGGGAATAAATC-CTGAAACAGATTTATTCAACTT-
1 -CAAAATCA-AATCAAATCTGTTAAACGAC-AGAATAAATCTC-GAAACAGAATTATTCAA-TTA
*
1095 ATTCTTATTTTGGAAACAAAAT
61 ATTCTT-GTTTGGAAACAAAAT
* ** * * *
1117 TAAAAAAATAATAAAATCTGTTAAACGACAGGAATAAATC-CTGAAACAAAATTATTCACTTAAT
1 CAAAATCA-AATCAAATCTGTTAAACGACA-GAATAAATCTC-GAAACAGAATTATTCAATTAAT
*
1181 TCTTGGTTGGAAAC-AAAT
63 TCTTGTTTGGAAACAAAAT
1199 CAAA
1 CAAA
1203 GTATTTGTTA
Statistics
Matches: 430, Mismatches: 58, Indels: 35
0.82 0.11 0.07
Matches are distributed among these distances:
81 2 0.00
82 117 0.27
83 28 0.07
84 193 0.45
85 54 0.13
86 36 0.08
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.31
Consensus pattern (81 bp):
CAAAATCAAATCAAATCTGTTAAACGACAGAATAAATCTCGAAACAGAATTATTCAATTAATTCT
TGTTTGGAAACAAAAT
Found at i:1158 original size:170 final size:165
Alignment explanation
Indices: 615--1202 Score: 591
Period size: 170 Copynumber: 3.5 Consensus size: 165
605 AATTCTGAAA
* * * * * * * *
615 CAAAATCAAAATCAATTCTGTTGAATGGCAGGATTAAATCTTGAAACAGAATTATTTAA--TTAT
1 CAAAATC-AAATCAAATCTGTTAAACGACAGGAATAAATCCTGAAACAAAATTATTTAATTTTAA
* * * *
678 TTCTTGTTTTGAAACAAAATCAAAATCAAATCAAATCTGTTAAACGACGAGAATAAATCTCGAAA
65 TTCTTGTTTGGAAACAAAATCAAAAT-AAATCAAATCTGTTGAACGGCGGGAATAAATCTCGAAA
* *
743 CATAATTATTCAATTAATTCTTATTTGGAAGCAAAAT
129 CAGAATTATTCAATTAATTCTTATTTGGAAACAAAAT
* * * ** *
780 CAAAATCAAATCAAATCTATTTAACAACATAAATAAATTCC-GAAACAAAATTATTCAATTTTAA
1 CAAAATCAAATCAAATCTGTTAAACGACAGGAATAAA-TCCTGAAACAAAATTATTTAATTTTAA
* * *
844 TTCTTGTTTGGAATCAAAATCAAAATCTAATCAAATTTGTTGAACGGCGGGAATAAATCTCGAAT
65 TTCTTGTTTGGAAACAAAATCAAAAT-AAATCAAATCTGTTGAACGGCGGGAATAAATCTCGAA-
* * *
909 A-AGAATTATTTAATTTTAATTCTTGTTTGAAAACAAAAT
128 ACAGAATTATTCAA--TTAATTCTTATTTGGAAACAAAAT
** * * * *
948 CAAAATCAAATCAAATAAGTTGAACGGCGGGAATAAATCCTGAAAACAGAATTATTTAATTTTAA
1 CAAAATCAAATCAAATCTGTTAAACGACAGGAATAAATCCTG-AAACAAAATTATTTAATTTTAA
* * * *
1013 TTCCTCTTTGGAAACAAAATAAAAAATAGAATAAAATCTGTTGAACGGCGGGAATAAATC-CTGA
65 TTCTTGTTTGGAAACAAAAT-CAAAATA-AATCAAATCTGTTGAACGGCGGGAATAAATCTC-GA
*
1077 AACAGATTTATTCAACTT-ATTCTTATTTTGGAAACAAAAT
127 AACAGAATTATTCAA-TTAATTCTTA-TTTGGAAACAAAAT
* ** * * *
1117 TAAAAAAATAATAAAATCTGTTAAACGACAGGAATAAATCCTGAAACAAAATTA-TTCA-CTTAA
1 CAAAATCA-AATCAAATCTGTTAAACGACAGGAATAAATCCTGAAACAAAATTATTTAATTTTAA
*
1180 TTCTTGGTTGGAAAC-AAATCAAA
65 TTCTTGTTTGGAAACAAAATCAAA
1203 GTATTTGTTA
Statistics
Matches: 345, Mismatches: 64, Indels: 28
0.79 0.15 0.06
Matches are distributed among these distances:
164 36 0.10
165 12 0.03
166 74 0.21
167 20 0.06
168 59 0.17
169 69 0.20
170 75 0.22
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.31
Consensus pattern (165 bp):
CAAAATCAAATCAAATCTGTTAAACGACAGGAATAAATCCTGAAACAAAATTATTTAATTTTAAT
TCTTGTTTGGAAACAAAATCAAAATAAATCAAATCTGTTGAACGGCGGGAATAAATCTCGAAACA
GAATTATTCAATTAATTCTTATTTGGAAACAAAAT
Found at i:1554 original size:50 final size:52
Alignment explanation
Indices: 1444--1611 Score: 180
Period size: 50 Copynumber: 3.2 Consensus size: 52
1434 CAAAATAATA
* * * * * *
1444 TAAACAAACATTTATGTTTATGTAAAAACACTAGATCTTAAACAAAAACAAGT
1 TAAATAAATATTTATATTTAT-TTAAAACATTAGATCTTAAACAAAAACAAAT
1497 TAAATAAATATTTATATTTATTTAAAACATTAGAT-TTAAAC-AAAACAAAT
1 TAAATAAATATTTATATTTATTTAAAACATTAGATCTTAAACAAAAACAAAT
* * * * * *
1547 TAAATAAATGTTTATATTTATTTAAAACATCATATCTAAAAAAATAAATAAAT
1 TAAATAAATATTTATATTTATTTAAAACATTAGATCTTAAACAA-AAACAAAT
*
1600 TAAA-CAATATTT
1 TAAATAAATATTT
1612 GAAACCATAA
Statistics
Matches: 98, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
50 40 0.41
51 10 0.10
52 19 0.19
53 29 0.30
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (52 bp):
TAAATAAATATTTATATTTATTTAAAACATTAGATCTTAAACAAAAACAAAT
Done.