Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011587.1 Kokia drynarioides strain JFW-HI SEQ_126577, 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: 15339
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.27
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:534 original size:22 final size:22
Alignment explanation
Indices: 503--547 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
493 GATAAGTTTT
503 TTAAAAAAAAGGGAAAAGAGAAG
1 TTAAAAAAAA-GGAAAAGAGAAG
526 TTAAAAAAAAGGAAAAGAGAAG
1 TTAAAAAAAAGGAAAAGAGAAG
548 GTTTTTACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.09
Consensus pattern (22 bp):
TTAAAAAAAAGGAAAAGAGAAG
Found at i:1375 original size:30 final size:30
Alignment explanation
Indices: 1249--1389 Score: 155
Period size: 30 Copynumber: 4.8 Consensus size: 30
1239 AGGTCCTTTG
1249 AACTTTCAAAAA-TTCCATTTTTGACCCCAA
1 AACTTTCAAAAATTTCCA-TTTTGACCCCAA
* * * *
1279 AACTTAC-ATAATTTCCATTTTCACCCCTA
1 AACTTTCAAAAATTTCCATTTTGACCCCAA
*
1308 AACTTCCAAAAA-TTCCATTTTTGACCCCAA
1 AACTTTCAAAAATTTCCA-TTTTGACCCCAA
* * *
1338 AAC-TTCAAAAATTTCCATTTTAACCTCGA
1 AACTTTCAAAAATTTCCATTTTGACCCCAA
*
1367 AACTTTCAAAAATTACCATTTTG
1 AACTTTCAAAAATTTCCATTTTG
1390 CCTTCGGATG
Statistics
Matches: 92, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
29 43 0.47
30 49 0.53
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (30 bp):
AACTTTCAAAAATTTCCATTTTGACCCCAA
Found at i:1389 original size:59 final size:59
Alignment explanation
Indices: 1249--1388 Score: 210
Period size: 59 Copynumber: 2.4 Consensus size: 59
1239 AGGTCCTTTG
* * *
1249 AACTTTCAAAAATTCCATTTTTGACCCCAAAACTTACATAATTTCCATTTTCACCCCTA
1 AACTTTCAAAAATTCCATTTTTGACCCCAAAACTTACAAAATTTCCATTTTAACCCCGA
* *
1308 AACTTCCAAAAATTCCATTTTTGACCCCAAAACTT-CAAAAATTTCCATTTTAACCTCGA
1 AACTTTCAAAAATTCCATTTTTGACCCCAAAACTTAC-AAAATTTCCATTTTAACCCCGA
1367 AACTTTCAAAAATTACCATTTT
1 AACTTTCAAAAATT-CCATTTT
1389 GCCTTCGGAT
Statistics
Matches: 73, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
58 1 0.01
59 65 0.89
60 7 0.10
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.35
Consensus pattern (59 bp):
AACTTTCAAAAATTCCATTTTTGACCCCAAAACTTACAAAATTTCCATTTTAACCCCGA
Found at i:14048 original size:204 final size:205
Alignment explanation
Indices: 13437--14239 Score: 1058
Period size: 205 Copynumber: 3.9 Consensus size: 205
13427 CCAACTCAGG
* ** *
13437 GCTCGATATGAGC-GATCTTCGAACCCCCGCTTCTTAATGAGACACTAAGAAGCA-GTCGAAGCA
1 GCTCGATATGAGCAAATCTTCGAACCCCAACTTCCTAATGAGACACTAAGAAGCAGGTCGAAGCA
*
13500 ATCAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATAC
66 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATAC
* * *
13565 AGAGAGGTGAATTGAAACAAACGACGCGGTCATC-TCCTTGATAAGATATTGAGAAGAAGACCAA
131 AGAGAAGTGAATTGAAACAAACGACGCGGTCATCTTCC-TGATAAGATACTGAGAAGAAGACAAA
13629 ATCAAACCCAC
195 ATCAAACCCAC
* * * * *
13640 ACTCGATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGACACTGAGAAGCAGGTCAAAGCA
1 GCTCGATATGAGCAAATCTTCGAACCCCAACTTCCTAATGAGACACTAAGAAGCAGGTCGAAGCA
*
13705 ATAAAAGGTTAGCATCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATAC
66 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATAC
* * * * * *
13770 AGAGAGGTGAATTGAAACAAACGACTCGGTCATCTCCCTGATAAGTTACTGAAAAGAAGACTAAA
131 AGAGAAGTGAATTGAAACAAACGACGCGGTCATCTTCCTGATAAGATACTGAGAAGAAGACAAAA
**
13835 TTGAACCCAC
196 TCAAACCCAC
* * * *
13845 GCTCGATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGACACCT-AGAAGCAGATCTAAGC
1 GCTCGATATGAGCAAATCTTCGAACCCCAACTTCCTAATGAGACA-CTAAGAAGCAGGTCGAAGC
* * * * *
13909 AATAAAAGGTTAGC-TCCTGACGAGATATTGAGAAGTGGACCAAATTTGTCTTCCTGATGAGGTA
65 AATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATA
* * *
13973 CAGAGAAGTGGATTGAAACAAACGACACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACAAA
130 CAGAGAAGTGAATTGAAACAAACGACGCGGTCATCTTCCTGATAAGATACTGAGAAGAAGACAAA
14038 ATCAAACCCAC
195 ATCAAACCCAC
* * * * *
14049 GCTCGATATGAACAAATCTTCGAACCCCAGCTTCCTAATGAGATACTCAGAAGCAGGTCGAAGTA
1 GCTCGATATGAGCAAATCTTCGAACCCCAACTTCCTAATGAGACACTAAGAAGCAGGTCGAAGCA
* * * * * *
14114 ATAAAAATGGTTAGCTTCCTGATGAGATACAGAGAAGTGAATCAAATCCGTCTTTCTGATGAAAC
66 AT-AAAA-GGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGAT
* ** ** * * *
14179 ACAGAGAAGTGGATCAAAACAAGTGATGCGGTCACCTTCCTGATGAGATACTGAGAAGAAG
129 ACAGAGAAGTGAATTGAAACAAACGACGCGGTCATCTTCCTGATAAGATACTGAGAAGAAG
14240 GCCAAGTCAA
Statistics
Matches: 529, Mismatches: 63, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
203 13 0.02
204 202 0.38
205 211 0.40
206 11 0.02
207 92 0.17
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.22
Consensus pattern (205 bp):
GCTCGATATGAGCAAATCTTCGAACCCCAACTTCCTAATGAGACACTAAGAAGCAGGTCGAAGCA
ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATAC
AGAGAAGTGAATTGAAACAAACGACGCGGTCATCTTCCTGATAAGATACTGAGAAGAAGACAAAA
TCAAACCCAC
Found at i:14590 original size:17 final size:17
Alignment explanation
Indices: 14562--14641 Score: 115
Period size: 17 Copynumber: 4.7 Consensus size: 17
14552 GGCCCAGCAG
14562 AATTTAAATTTATTTTA
1 AATTTAAATTTATTTTA
* *
14579 AAATTAAGTTTATTTTA
1 AATTTAAATTTATTTTA
* *
14596 AATTTATATTTATTTGA
1 AATTTAAATTTATTTTA
*
14613 AATTTAAATTTATTATA
1 AATTTAAATTTATTTTA
14630 AATTTAAATTTA
1 AATTTAAATTTA
14642 AATTTATTTA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 54 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:14617 original size:7 final size:6
Alignment explanation
Indices: 14562--14647 Score: 67
Period size: 6 Copynumber: 15.0 Consensus size: 6
14552 GGCCCAGCAG
* * * * *
14562 AATTTA AATTT- ATTTTA AAATTA AGTTT- ATTTTA AATTTA TATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
14607 -ATTTGA AATTTA AATTT- -ATTATA AATTTA AATTTA AATTTA
1 AATTT-A AATTTA AATTTA AATT-TA AATTTA AATTTA AATTTA
14648 TTTAAATAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
4 7 0.11
5 9 0.14
6 41 0.64
7 7 0.11
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (6 bp):
AATTTA
Found at i:14618 original size:23 final size:22
Alignment explanation
Indices: 14592--14654 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 22
14582 TTAAGTTTAT
**
14592 TTTAAATTTATATTTATTTGAAA
1 TTTAAATTTATATAAATTT-AAA
14615 TTTAAATTTATTATAAATTTAAA
1 TTTAAATTTA-TATAAATTTAAA
*
14638 TTTAAATTTATTTAAAT
1 TTTAAATTTATATAAAT
14655 AATGTCTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
22 6 0.17
23 23 0.64
24 7 0.19
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTAAATTTATATAAATTTAAA
Done.