Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013582.1 Kokia drynarioides strain JFW-HI SEQ_128608, 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: 12679
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.25
Warning! 402 characters in sequence are not A, C, G, or T
Found at i:11919 original size:200 final size:192
Alignment explanation
Indices: 11628--12113 Score: 670
Period size: 200 Copynumber: 2.5 Consensus size: 192
11618 TTTTGAATCA
*
11628 CAGCTTCCTGATGAGATATTGAGAACAAGGGCGAAGCAACAAAAA-GTTAGCTTCCTGATGAGAT
1 CAGCTTCCTGATGAGATATTGAGAAC-AGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGAT
* *
11692 ACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGACTGAAACAAGTAAGG
65 ACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAACTGAAACAAGTAAGG
* * * *
11757 CGGTCATCTTCCAGATGGGAGACAGGGAAGAATACCAACTCGAGGCTTAATGCGAGCAAATCTTC
130 CGGTCATCTTCCAGATGAGAGACAGAGAAGAATACCAACT-----C--AATGCAAACAAATCTTC
11822 GACCC
188 GACCC
* ** *
11827 CAGCTTCCTGATGAGACATTGAGAAGCAGAACGAAGCAATAAAAAGGTCAGCTTCCTGATGAGAT
1 CAGCTTCCTGATGAGATATTGAGAA-CAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGAT
* * *
11892 ACTGAGAAGTGGACCAAATTTGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAGTGAGG
65 ACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAACTGAAACAAGTAAGG
* * *
11957 CGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCAAACAAATCTTCGACCC
130 CGGTCATCTTCCAGATGAGAGACAGAGAAGAATACCAACTCAATGCAAACAAATCTTCGACCC
12020 CAGCTTCCTGATGAGATACTGTGA-AACAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGA
1 CAGCTTCCTGATGAGATA-T-TGAGAACAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGA
* * * *
12084 TACGGAGAAGTGAACCAAATCCATCTTCCT
64 TACTGAGAAGTGGACCAAATTCGTCTTCCT
12114 AAGGAAACAC
Statistics
Matches: 257, Mismatches: 26, Indels: 14
0.87 0.09 0.05
Matches are distributed among these distances:
193 97 0.38
194 3 0.01
195 4 0.02
199 39 0.15
200 114 0.44
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.21
Consensus pattern (192 bp):
CAGCTTCCTGATGAGATATTGAGAACAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGATA
CTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAACTGAAACAAGTAAGGC
GGTCATCTTCCAGATGAGAGACAGAGAAGAATACCAACTCAATGCAAACAAATCTTCGACCC
Found at i:12113 original size:193 final size:194
Alignment explanation
Indices: 11628--12181 Score: 688
Period size: 193 Copynumber: 2.8 Consensus size: 194
11618 TTTTGAATCA
*
11628 CAGCTTCCTGATGAGATAT-TGAGAACAAGGGCGAAGCAACAAAAA-GTTAGCTTCCTGATGAGA
1 CAGCTTCCTGATGAGATATGTGA-AAC-AGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGA
* * *
11691 TACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGACTGAAACAAGTAAG
64 TACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGAG
* * * * * *
11756 GCGGTCATCTTCCAGATGGGAGACAGGGAAGAATACCAACTCGAGGCTTAATGCGAGCAAATCTT
129 GCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACT----GC-TAATGCAAACAAATCTT
11821 CGACCC
189 CGACCC
* ** *
11827 CAGCTTCCTGATGAGACAT-TGAGAAGCAGAACGAAGCAATAAAAAGGTCAGCTTCCTGATGAGA
1 CAGCTTCCTGATGAGATATGTGA-AA-CAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGA
* *
11891 TACTGAGAAGTGGACCAAATTTGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAGTGAG
64 TACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGAG
*
11956 GCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACT-C-AATGCAAACAAATCTTCGACC
129 GCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTGCTAATGCAAACAAATCTTCGACC
12019 C
194 C
12020 CAGCTTCCTGATGAGATACTGTGAAACAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGAT
1 CAGCTTCCTGATGAGATA-TGTGAAACAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGAT
* * * * * * * * * ** * *
12085 ACGGAGAAGTGAACCAAATCCATCTTCCTAAGGAAACACAGAGAAGTGGATCAAAACAAGCGA-T
65 ACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGAGG
*
12149 CTGGTCATCTTCCTGATGAGATACTGAGAAGAA
130 C-GGTCATCTTCCTGATGAGATACAGAGAAGAA
12182 GGCTAAGTCA
Statistics
Matches: 312, Mismatches: 38, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
192 1 0.00
193 151 0.48
194 3 0.01
195 4 0.01
199 39 0.12
200 114 0.37
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.20
Consensus pattern (194 bp):
CAGCTTCCTGATGAGATATGTGAAACAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGATA
CTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGAGGC
GGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTGCTAATGCAAACAAATCTTCGACCC
Found at i:12544 original size:17 final size:17
Alignment explanation
Indices: 12505--12616 Score: 79
Period size: 17 Copynumber: 6.5 Consensus size: 17
12495 TTAAACCCAT
*
12505 TTTAAGATTTATTTTAAGA
1 TTTAA-ATTGATTTTAA-A
*
12524 -TTAAATTGATTTTGAA
1 TTTAAATTGATTTTAAA
*
12540 TTTAAATTTATTTTAAA
1 TTTAAATTGATTTTAAA
12557 TTTAAATTTG-TTTTAAAA
1 TTTAAA-TTGATTTT-AAA
* *
12575 TTT-AATTTAATTTAAA
1 TTTAAATTGATTTTAAA
* *
12591 TTTAGATTTAGA-TTTATA
1 TTTA-AATT-GATTTTAAA
12609 TTTAAATT
1 TTTAAATT
12617 TAAAACTTAT
Statistics
Matches: 75, Mismatches: 11, Indels: 16
0.74 0.11 0.16
Matches are distributed among these distances:
16 9 0.12
17 41 0.55
18 24 0.32
19 1 0.01
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.55
Consensus pattern (17 bp):
TTTAAATTGATTTTAAA
Found at i:12547 original size:6 final size:6
Alignment explanation
Indices: 12538--12620 Score: 75
Period size: 6 Copynumber: 14.3 Consensus size: 6
12528 ATTGATTTTG
* **
12538 AATTTA AATTT- ATTTTA AATTTA AATTT- GTTTTAA AATTT- AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A AATTTA AATTTA
* * *
12583 AATTTA AATTTA GATTTA GATTTA TATTTA AATTTA AA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AA
12621 ACTTATTATA
Statistics
Matches: 64, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
5 17 0.27
6 44 0.69
7 3 0.05
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (6 bp):
AATTTA
Done.