Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011869.1 Kokia drynarioides strain JFW-HI SEQ_126866, 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: 8848
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.24
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:7740 original size:37 final size:38
Alignment explanation
Indices: 7651--7748 Score: 121
Period size: 37 Copynumber: 2.6 Consensus size: 38
7641 AAACGGTTAG
*
7651 CTTCCTGATGAGATACTGAGAAGTTGATCAAAATTCGT
1 CTTCCTGATGAGATACTGAGAAGTTGAACAAAATTCGT
* * *
7689 CTT-CTAGATAAGATACTGAGGAG-TGAACCAAATTCGT
1 CTTCCT-GATGAGATACTGAGAAGTTGAACAAAATTCGT
7726 CTTCCTGATGAGATA-TAGAGAAG
1 CTTCCTGATGAGATACT-GAGAAG
7749 CGGATTGAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
36 1 0.02
37 30 0.59
38 20 0.39
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (38 bp):
CTTCCTGATGAGATACTGAGAAGTTGAACAAAATTCGT
Found at i:8122 original size:206 final size:205
Alignment explanation
Indices: 7718--8426 Score: 1032
Period size: 206 Copynumber: 3.5 Consensus size: 205
7708 GGAGTGAACC
* * * * * *
7718 AAATTCGTCTTCCTGATGAGATATAGAGAAGCGGATTGAAACAAGCGATGCGGTCATCTTCCTGA
1 AAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGACGCAGTCATCTTCC-CA
* * * * * * * *
7783 A-GAGATACTGAGAAGAAGGCCAAACCAAACCCACGCACGA--TGAATAAACCTTCGAACCCCAA
65 ATGAGATACTGAGAAGAAGACCAAATCAAACTCGCGC-CGATGTGAGTAAATCTTCGAA-CACAG
* * *
7845 CTTCTTGATAAGATATTGAGAAGCAAGTCGAAGTAATAAACCGGTTAGCTTCCTGATGAGATACG
128 CTTCTTGATAAGATATTGAGAAGCAGGTCGAAGTAATAAAACGGTTAGCTTCCTGATGAGATACA
7910 GAGAAGTTGATCA
193 GAGAAGTTGATCA
*
7923 AAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACTACGCAGTCATCTTCCCAA
1 AAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGACGCAGTCATCTTCCCAA
*
7988 TGAGATACTGAGAAGAAGACTAAATCAAACTCGCGTCCGATGTGAGTAAATCTTCGAACACAGCT
66 TGAGATACTGAGAAGAAGACCAAATCAAACTCGCG-CCGATGTGAGTAAATCTTCGAACACAGCT
8053 TCTTGATAAGATATTGAGAAGCAGGTCGAAGTAATAAAACGGTTAGCTTCCTGATGAGATACAGA
130 TCTTGATAAGATATTGAGAAGCAGGTCGAAGTAATAAAACGGTTAGCTTCCTGATGAGATACAGA
8118 GAAGTTGATCA
195 GAAGTTGATCA
*
8129 AAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACTACGCAGTCATCTTCCCAA
1 AAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGACGCAGTCATCTTCCCAA
*
8194 TAAGATACTGAGAAGAAGACCAAATCAAACTCGCGCCCGATGTGAGTAAATCTTCGAACACAGCT
66 TGAGATACTGAGAAGAAGACCAAATCAAACTCGCG-CCGATGTGAGTAAATCTTCGAACACAGCT
* * * * * * * *
8259 TCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTAATGAGATACTGA
130 TCTTGATAAGATATTGAGAAGCAGGTCGAAGTAATAAAACGGTTAGCTTCCTGATGAGATACAGA
8324 GAAG-TGAATC-
195 GAAGTTG-ATCA
*
8334 AAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGACGCAGTCATCTTCCCGA
1 AAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGACGCAGTCATCTTCCCAA
* * *
8399 TGAGATACTGGGAAGAAGGCCAAGTCAA
66 TGAGATACTGAGAAGAAGACCAAATCAA
8427 TGAAACCAGA
Statistics
Matches: 463, Mismatches: 36, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
204 2 0.00
205 177 0.38
206 270 0.58
207 14 0.03
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (205 bp):
AAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGACGCAGTCATCTTCCCAA
TGAGATACTGAGAAGAAGACCAAATCAAACTCGCGCCGATGTGAGTAAATCTTCGAACACAGCTT
CTTGATAAGATATTGAGAAGCAGGTCGAAGTAATAAAACGGTTAGCTTCCTGATGAGATACAGAG
AAGTTGATCA
Found at i:8795 original size:18 final size:18
Alignment explanation
Indices: 8756--8840 Score: 95
Period size: 17 Copynumber: 4.8 Consensus size: 18
8746 CCAAACTCCC
*
8756 TTTAAATTTTTTTAAAAA
1 TTTAAATTTATTTAAAAA
*
8774 -TTAAATTTGTTTAAAAA
1 TTTAAATTTATTTAAAAA
*
8791 TTTAAATTTATTT-TAAA
1 TTTAAATTTATTTAAAAA
**
8808 TTTAAATTTATTT-TGAA
1 TTTAAATTTATTTAAAAA
8825 TTTAAATTTAATTTAA
1 TTTAAATTT-ATTTAA
8841 GTTTAAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
17 44 0.75
18 15 0.25
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
TTTAAATTTATTTAAAAA
Found at i:8799 original size:6 final size:6
Alignment explanation
Indices: 8788--8848 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
8778 ATTTGTTTAA
* * *
8788 AAATTT AAATTT -ATTTT AAATTT AAATTT -ATTTT GAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
*
8834 -AATTT AAGTTT AAAT
1 AAATTT AAATTT AAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
5 13 0.29
6 32 0.71
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (6 bp):
AAATTT
Found at i:8827 original size:34 final size:35
Alignment explanation
Indices: 8756--8848 Score: 109
Period size: 34 Copynumber: 2.7 Consensus size: 35
8746 CCAAACTCCC
* *
8756 TTTAAATTT-TTTTAAAAATTAAATTTGTTTAAAAA
1 TTTAAATTTATTTT-AAATTTAAATTTATTTAAAAA
**
8791 TTTAAATTTATTTTAAATTTAAATTTATTT-TGAA
1 TTTAAATTTATTTTAAATTTAAATTTATTTAAAAA
* *
8825 TTTAAATTTAATTTAAGTTTAAAT
1 TTTAAATTTATTTTAAATTTAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
34 24 0.47
35 23 0.45
36 4 0.08
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (35 bp):
TTTAAATTTATTTTAAATTTAAATTTATTTAAAAA
Found at i:8837 original size:11 final size:11
Alignment explanation
Indices: 8789--8846 Score: 64
Period size: 11 Copynumber: 5.2 Consensus size: 11
8779 TTTGTTTAAA
8789 AATTTAAATTT
1 AATTTAAATTT
*
8800 ATTTTAAATTT
1 AATTTAAATTT
*
8811 AAATTT-ATTTT
1 -AATTTAAATTT
8822 GAATTTAAATTT
1 -AATTTAAATTT
*
8834 AATTTAAGTTT
1 AATTTAAATTT
8845 AA
1 AA
8847 AT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
11 31 0.79
12 8 0.21
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:8845 original size:17 final size:16
Alignment explanation
Indices: 8789--8848 Score: 84
Period size: 17 Copynumber: 3.6 Consensus size: 16
8779 TTTGTTTAAA
8789 AATTTAAATTTATTTT
1 AATTTAAATTTATTTT
8805 AAATTTAAATTTATTTT
1 -AATTTAAATTTATTTT
*
8822 GAATTTAAATTTAATTT
1 -AATTTAAATTTATTTT
8839 AAGTTTAAAT
1 AA-TTTAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
16 2 0.05
17 38 0.95
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
AATTTAAATTTATTTT
Done.