Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002360.1 Kokia drynarioides strain JFW-HI SEQ_114430, 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: 25381
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Warning! 41 characters in sequence are not A, C, G, or T
Found at i:4624 original size:30 final size:30
Alignment explanation
Indices: 4564--4624 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
4554 CTGGCCCGTT
* *
4564 GCTTGGAAAGATGGAAGGCTTATCTACAAA
1 GCTTGGAAACATGGAAGGCTGATCTACAAA
*
4594 GCTTGGCAAACATGGAAGG-TGATCTTCAAA
1 GCTTGG-AAACATGGAAGGCTGATCTACAAA
4624 G
1 G
4625 ATTGATGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 16 0.59
31 11 0.41
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.23
Consensus pattern (30 bp):
GCTTGGAAACATGGAAGGCTGATCTACAAA
Found at i:10841 original size:20 final size:20
Alignment explanation
Indices: 10818--10857 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
10808 TACTAGAACA
10818 AAAAGAGAC-AAAATAATATT
1 AAAA-AGACGAAAATAATATT
*
10838 AAAAAGACGATAATAATATT
1 AAAAAGACGAAAATAATATT
10858 TTAATAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.23
Consensus pattern (20 bp):
AAAAAGACGAAAATAATATT
Found at i:16632 original size:23 final size:23
Alignment explanation
Indices: 16604--16649 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
16594 TTAAAAATAC
16604 TAAAATACTAATTAAATTAATTT
1 TAAAATACTAATTAAATTAATTT
* * *
16627 TAAAATATTATTTAAATTTATTT
1 TAAAATACTAATTAAATTAATTT
16650 AATTAAAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TAAAATACTAATTAAATTAATTT
Found at i:23745 original size:163 final size:161
Alignment explanation
Indices: 23471--23848 Score: 487
Period size: 163 Copynumber: 2.3 Consensus size: 161
23461 ATGACATTAC
23471 AAATATTTAAACCCTAAACTTCAAATGAGAACATAAAACTTTTAACCACTAACTCTCCTAAATTG
1 AAATATTTAAACCCTAAACTTCAAATGAGAACATAAAACTTTTAACCACTAACTCTCCTAAATTG
* * * *
23536 TTGGTTAAATTGAAATAATATTTGAATCATAAACTTCAATTGCGAACATAAAAC-TTTAACCACT
66 TTGGATAAATTCAAATAATATTTAAATCATAAACTTCAAGTGCGAACATAAAACTTTTAACCACT
*** ***
23600 AACTCTTTTGAATTGTTGGGTAAATTCAAAT
131 AACTCTTCCAAATTGTTAACTAAATTCAAAT
* * * * *
23631 AAAT-TTTAAATCCTAAACTTCAATTGCGAACATATATAAAACTTTTAACCACTAACTCT-TTCG
1 AAATATTTAAACCCTAAACTTCAAATGAGAAC----ATAAAACTTTTAACCACTAACTCTCCT-A
* *
23694 AATTGTTGGATAAATTCAAATAATTTTTAAATCCTAAACTTCAAGTGCGAACATAAAACTTTTAA
61 AATTGTTGGATAAATTCAAATAATATTTAAATCATAAACTTCAAGTGCGAACATAAAACTTTTAA
23759 CCACTAACTCTTCCAAATTGTTAACTAAATTCAAAT
126 CCACTAACTCTTCCAAATTGTTAACTAAATTCAAAT
* * *
23795 -ATTATTTAAACCCTAAACTTTAAAT-AGAAACATAAAACTTTCAACCACTAACTC
1 AAATATTTAAACCCTAAACTTCAAATGAG-AACATAAAACTTTTAACCACTAACTC
23849 CTTCTAACTT
Statistics
Matches: 187, Mismatches: 23, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
159 24 0.13
160 26 0.14
162 1 0.01
163 80 0.43
164 56 0.30
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.34
Consensus pattern (161 bp):
AAATATTTAAACCCTAAACTTCAAATGAGAACATAAAACTTTTAACCACTAACTCTCCTAAATTG
TTGGATAAATTCAAATAATATTTAAATCATAAACTTCAAGTGCGAACATAAAACTTTTAACCACT
AACTCTTCCAAATTGTTAACTAAATTCAAAT
Found at i:23794 original size:80 final size:79
Alignment explanation
Indices: 23476--23848 Score: 421
Period size: 80 Copynumber: 4.6 Consensus size: 79
23466 ATTACAAATA
* *
23476 TTTAAACCCTAAACTTCAAATGAGAACATAAAACTTTTAACCACTAACTC-TCCTAAATTGTTGG
1 TTTAAATCCTAAACTTCAAATGCGAACATAAAACTTTTAACCACTAACTCTTCC-AAATTGTT-G
* * *
23540 TTAAATTGAAATAATA
64 ATAAATTCAAATAATT
* * * *** *
23556 TTTGAATCATAAACTTCAATTGCGAACATAAAAC-TTTAACCACTAACTCTTTTGAATTGTTGGG
1 TTTAAATCCTAAACTTCAAATGCGAACATAAAACTTTTAACCACTAACTCTTCCAAATTGTT-GA
*
23620 TAAATTCAAATAAAT
65 TAAATTCAAATAATT
* * *
23635 TTTAAATCCTAAACTTCAATTGCGAACATATATAAAACTTTTAACCACTAACTCTTTCGAATTGT
1 TTTAAATCCTAAACTTCAAATGCGAAC----ATAAAACTTTTAACCACTAACTCTTCCAAATTGT
23700 TGGATAAATTCAAATAATT
62 T-GATAAATTCAAATAATT
* *
23719 TTTAAATCCTAAACTTCAAGTGCGAACATAAAACTTTTAACCACTAACTCTTCCAAATTGTTAAC
1 TTTAAATCCTAAACTTCAAATGCGAACATAAAACTTTTAACCACTAACTCTTCCAAATTGTTGA-
23784 TAAATTCAAAT-ATT
65 TAAATTCAAATAATT
* * * *
23798 ATTTAAACCCTAAACTTTAAATAG-AAACATAAAACTTTCAACCACTAACTC
1 -TTTAAATCCTAAACTTCAAAT-GCGAACATAAAACTTTTAACCACTAACTC
23849 CTTCTAACTT
Statistics
Matches: 258, Mismatches: 26, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
79 65 0.25
80 117 0.45
81 1 0.00
83 7 0.03
84 68 0.26
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (79 bp):
TTTAAATCCTAAACTTCAAATGCGAACATAAAACTTTTAACCACTAACTCTTCCAAATTGTTGAT
AAATTCAAATAATT
Found at i:24139 original size:3 final size:3
Alignment explanation
Indices: 24131--24169 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
24121 TATATTTGTA
*
24131 AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
24170 GTTATTCCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Done.