Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000451.1 Kokia drynarioides strain JFW-HI SEQ_111305, 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: 21847
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Found at i:1263 original size:16 final size:16
Alignment explanation
Indices: 1239--1276 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
1229 AAATTTTTAT
1239 TTTTAATTTAAT-TTAAA
1 TTTT-ATTTAATGTT-AA
1256 TTTTATTTAATGTTAA
1 TTTTATTTAATGTTAA
1272 TTTTA
1 TTTTA
1277 AATATTTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (16 bp):
TTTTATTTAATGTTAA
Found at i:2074 original size:59 final size:61
Alignment explanation
Indices: 1979--2105 Score: 168
Period size: 59 Copynumber: 2.1 Consensus size: 61
1969 TTAATATAAA
* * * * * *
1979 AATAATTATATTAAGAATGTTATTAAATTATATATTATTATTTTTATTAAGTTATATTTAAT
1 AATAA-TATATTAAGAATATGATTAAATTATATATTATGATTTTTATTAAATTACACTTAAT
*
2041 AATAATATATTAA-AATATGATT-AATTATTTATTATGATTTTTATTAAATTACACTTAAT
1 AATAATATATTAAGAATATGATTAAATTATATATTATGATTTTTATTAAATTACACTTAAT
2100 AATAAT
1 AATAAT
2106 CCTATTATAT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
59 38 0.66
60 7 0.12
61 8 0.14
62 5 0.09
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (61 bp):
AATAATATATTAAGAATATGATTAAATTATATATTATGATTTTTATTAAATTACACTTAAT
Found at i:4107 original size:23 final size:23
Alignment explanation
Indices: 4064--4112 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
4054 AATATTTATT
*
4064 ATTTTTAATTTGTGTTTTTTAAGA
1 ATTTTAAATTTGTGTTTTTTAA-A
4088 ATTTTAAATTT-T-TTTATTTAAA
1 ATTTTAAATTTGTGTTT-TTTAAA
4110 ATT
1 ATT
4113 ATGTGTGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 7 0.30
23 6 0.26
24 10 0.43
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (23 bp):
ATTTTAAATTTGTGTTTTTTAAA
Found at i:4187 original size:23 final size:23
Alignment explanation
Indices: 4161--4219 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
4151 TTTATTTAAT
*
4161 TTAATCGAACATGTTAATGAATA
1 TTAATCGAACATGTTAATGAACA
* *
4184 TTAAACGAACATGTTCATGAACA
1 TTAATCGAACATGTTAATGAACA
*
4207 TATAATTGAACAT
1 T-TAATCGAACAT
4220 ATGCACGAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 21 0.70
24 9 0.30
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (23 bp):
TTAATCGAACATGTTAATGAACA
Found at i:8477 original size:20 final size:21
Alignment explanation
Indices: 8450--8505 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
8440 GAGTGAGTTA
8450 GACAAAAAGAGAAGCAACTTG
1 GACAAAAAGAGAAGCAACTTG
8471 GACAAAAAGAGAAGCAACTTG
1 GACAAAAAGAGAAGCAACTTG
*
8492 GACAAAAAAAGAAG
1 GACAAAAAGAGAAG
8506 AAGTGATTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.57, C:0.12, G:0.23, T:0.07
Consensus pattern (21 bp):
GACAAAAAGAGAAGCAACTTG
Found at i:10355 original size:15 final size:17
Alignment explanation
Indices: 10312--10355 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
10302 TGTTTTTTTT
10312 TTTTAAATTTTTATAAAC
1 TTTT-AATTTTTATAAAC
*
10330 TTTT-ATTTTT-TAAAA
1 TTTTAATTTTTATAAAC
10345 TTTTAATTTTT
1 TTTTAATTTTT
10356 CTTAATTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 8 0.33
16 12 0.50
18 4 0.17
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTAATTTTTATAAAC
Found at i:11041 original size:17 final size:17
Alignment explanation
Indices: 11015--11049 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
11005 CAATTTTAAT
*
11015 TCAAAATAAAATAAAAA
1 TCAAAATAAAAAAAAAA
*
11032 TCAAATTAAAAAAAAAA
1 TCAAAATAAAAAAAAAA
11049 T
1 T
11050 TTAAACAAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.20
Consensus pattern (17 bp):
TCAAAATAAAAAAAAAA
Found at i:13217 original size:10 final size:10
Alignment explanation
Indices: 13202--13226 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
13192 AGTTATATGA
13202 AGAAAAGAAG
1 AGAAAAGAAG
13212 AGAAAAGAAG
1 AGAAAAGAAG
13222 AGAAA
1 AGAAA
13227 TTATATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (10 bp):
AGAAAAGAAG
Found at i:13694 original size:6 final size:6
Alignment explanation
Indices: 13683--13707 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
13673 TCAAACACAG
13683 TTGAGA TTGAGA TTGAGA TTGAGA T
1 TTGAGA TTGAGA TTGAGA TTGAGA T
13708 CAAATCAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (6 bp):
TTGAGA
Found at i:17232 original size:28 final size:29
Alignment explanation
Indices: 17194--17250 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 29
17184 GGTGGGATGG
17194 GAGGAGAATAAAAGTTTTAAGGGAAAATA
1 GAGGAGAATAAAAGTTTTAAGGGAAAATA
*
17223 GAGGA-AATAAAAGTTTTGAGGGAAAATA
1 GAGGAGAATAAAAGTTTTAAGGGAAAATA
17251 AAAAGTTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.28, T:0.21
Consensus pattern (29 bp):
GAGGAGAATAAAAGTTTTAAGGGAAAATA
Found at i:17251 original size:19 final size:20
Alignment explanation
Indices: 17227--17264 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
17217 AAAATAGAGG
17227 AAAT-AAAAGTTTTGAGGGA
1 AAATAAAAAGTTTTGAGGGA
17246 AAATAAAAAGTTTTGAGGG
1 AAATAAAAAGTTTTGAGGG
17265 TTTTTAGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.26
Consensus pattern (20 bp):
AAATAAAAAGTTTTGAGGGA
Found at i:17390 original size:30 final size:30
Alignment explanation
Indices: 17354--17412 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
17344 AGATGAGGGG
*
17354 GTAAAAG-TTTTGGGAGAAAAGTAAGAAGGA
1 GTAAAAGTTTTTGGG-GAAAAGTAAAAAGGA
17384 GTAAAAGTTTTTGGGGAAAAGTAAAAAGG
1 GTAAAAGTTTTTGGGGAAAAGTAAAAAGG
17413 TTTGGGGCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 20 0.74
31 7 0.26
ACGTcount: A:0.46, C:0.00, G:0.32, T:0.22
Consensus pattern (30 bp):
GTAAAAGTTTTTGGGGAAAAGTAAAAAGGA
Found at i:17477 original size:18 final size:18
Alignment explanation
Indices: 17454--17490 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
17444 TATTGTTTGA
* *
17454 TATTCGATTTATTCGAAT
1 TATTCGAGTTATTCAAAT
17472 TATTCGAGTTATTCAAAT
1 TATTCGAGTTATTCAAAT
17490 T
1 T
17491 CGAAAACTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.49
Consensus pattern (18 bp):
TATTCGAGTTATTCAAAT
Found at i:18448 original size:20 final size:21
Alignment explanation
Indices: 18423--18466 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
18413 CCCAGCCTAG
*
18423 GTGGCT-CTCCACATGGTCGT
1 GTGGCTACTCCACATGCTCGT
*
18443 GTGGCTACTTCACATGCTCGT
1 GTGGCTACTCCACATGCTCGT
18464 GTG
1 GTG
18467 TCCACCCGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.11, C:0.27, G:0.30, T:0.32
Consensus pattern (21 bp):
GTGGCTACTCCACATGCTCGT
Found at i:19485 original size:34 final size:34
Alignment explanation
Indices: 19405--19488 Score: 105
Period size: 34 Copynumber: 2.5 Consensus size: 34
19395 ATACGGTTAA
*
19405 CCATCCAACACACCAGATGCTCATATGAGCCAAT
1 CCATCCAACACACCAAATGCTCATATGAGCCAAT
* * * * * *
19439 CTATCTAGCACACCAAATGCTCGTATGAGCTAGT
1 CCATCCAACACACCAAATGCTCATATGAGCCAAT
19473 CCATCCAACACACCAA
1 CCATCCAACACACCAA
19489 TAATACTATA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.35, C:0.35, G:0.12, T:0.19
Consensus pattern (34 bp):
CCATCCAACACACCAAATGCTCATATGAGCCAAT
Found at i:21014 original size:3 final size:3
Alignment explanation
Indices: 21006--21048 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
20996 CTTTGGTGGG
*
21006 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
21049 TATTTATTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Done.