Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014935.1 Kokia drynarioides strain JFW-HI SEQ_129978, 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: 48604
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 6 characters in sequence are not A, C, G, or T
Found at i:1127 original size:20 final size:21
Alignment explanation
Indices: 1094--1132 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1084 TTACAAAGTT
*
1094 AAAAATAAATAATTTTATTAA
1 AAAAATAAACAATTTTATTAA
1115 AAAAAT-AACAATTTTATT
1 AAAAATAAACAATTTTATT
1133 TATTGAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAAATAAACAATTTTATTAA
Found at i:1441 original size:19 final size:22
Alignment explanation
Indices: 1407--1448 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1397 AAAATAAATC
1407 AAAAAATATAATAACA-TATAA
1 AAAAAATATAATAACACTATAA
1428 AAAAAATAT-A-AACACTATAA
1 AAAAAATATAATAACACTATAA
1448 A
1 A
1449 CAAACACACT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 7 0.35
21 9 0.45
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.21
Consensus pattern (22 bp):
AAAAAATATAATAACACTATAA
Found at i:2320 original size:24 final size:26
Alignment explanation
Indices: 2288--2336 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
2278 GGCTACATTC
* *
2288 AAATGGTAAG-GAAAT-TTGCAAGTG
1 AAATAGTAAGTGAAATGTTACAAGTG
2312 AAATAGTAAGTGAAATGTTACAAGT
1 AAATAGTAAGTGAAATGTTACAAGT
2337 AACTATGCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
25 5 0.24
26 7 0.33
ACGTcount: A:0.45, C:0.04, G:0.24, T:0.27
Consensus pattern (26 bp):
AAATAGTAAGTGAAATGTTACAAGTG
Found at i:3366 original size:20 final size:19
Alignment explanation
Indices: 3322--3366 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
3312 GTTAATCATC
*
3322 ATTTTATTTAGTTAATTAA
1 ATTTAATTTAGTTAATTAA
3341 AGTTTAATTTAGTTAATTAA
1 A-TTTAATTTAGTTAATTAA
3361 TATTTA
1 -ATTTA
3367 TTAATTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (19 bp):
ATTTAATTTAGTTAATTAA
Found at i:10558 original size:31 final size:31
Alignment explanation
Indices: 10490--10557 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 31
10480 ATATTCGGGG
10490 TAAAAAATTATCAAAATTATATATAAATAAA
1 TAAAAAATTATCAAAATTATATATAAATAAA
* *
10521 TAAAAAATTATTAAAA-TATCAT-TAAATAAT
1 TAAAAAATTATCAAAATTAT-ATATAAATAAA
10551 TAAAAAA
1 TAAAAAA
10558 AAATCTACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 17 0.50
31 17 0.50
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (31 bp):
TAAAAAATTATCAAAATTATATATAAATAAA
Found at i:12472 original size:28 final size:24
Alignment explanation
Indices: 12415--12461 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
12405 AAAAATAATC
*
12415 TTTCAGTTAAACTTTGTTTATTTG
1 TTTCAATTAAACTTTGTTTATTTG
12439 TTTCAATTAAACTTTGTTTATTT
1 TTTCAATTAAACTTTGTTTATTT
12462 ATTTGAGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.60
Consensus pattern (24 bp):
TTTCAATTAAACTTTGTTTATTTG
Found at i:12474 original size:24 final size:24
Alignment explanation
Indices: 12423--12475 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
12413 TCTTTCAGTT
* *
12423 AAACTTTGTTTATTTGTTTCAATT
1 AAACTTTGTTTATTTATTTCAATC
* *
12447 AAACTTTGTTTATTTATTTGAGTC
1 AAACTTTGTTTATTTATTTCAATC
12471 AAACT
1 AAACT
12476 CTTATTAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.53
Consensus pattern (24 bp):
AAACTTTGTTTATTTATTTCAATC
Found at i:14427 original size:24 final size:24
Alignment explanation
Indices: 14399--14448 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
14389 AGAAATAATC
14399 TTCAATTAAACTCTATTTATTTGT
1 TTCAATTAAACTCTATTTATTTGT
* * *
14423 TTCAATTAAGCTTTGTTTATTTGT
1 TTCAATTAAACTCTATTTATTTGT
14447 TT
1 TT
14449 GAGTCAAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.24, C:0.10, G:0.08, T:0.58
Consensus pattern (24 bp):
TTCAATTAAACTCTATTTATTTGT
Found at i:17198 original size:13 final size:13
Alignment explanation
Indices: 17180--17214 Score: 56
Period size: 11 Copynumber: 2.8 Consensus size: 13
17170 TGATTTTTTT
17180 CAAAAAAATACGA
1 CAAAAAAATACGA
17193 C--AAAAATACGA
1 CAAAAAAATACGA
17204 CAAAAAAATAC
1 CAAAAAAATAC
17215 CTGACATCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 11 0.55
13 9 0.45
ACGTcount: A:0.69, C:0.17, G:0.06, T:0.09
Consensus pattern (13 bp):
CAAAAAAATACGA
Found at i:19103 original size:11 final size:11
Alignment explanation
Indices: 19087--19116 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
19077 GATTATGTGT
19087 TAAGTTTGGAG
1 TAAGTTTGGAG
19098 TAAGTTTGGAG
1 TAAGTTTGGAG
19109 TAGAGTTT
1 TA-AGTTT
19117 TGTCGGAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.27, C:0.00, G:0.33, T:0.40
Consensus pattern (11 bp):
TAAGTTTGGAG
Found at i:30388 original size:30 final size:31
Alignment explanation
Indices: 30301--30388 Score: 101
Period size: 31 Copynumber: 2.8 Consensus size: 31
30291 GTATCAAATT
* *
30301 TTTTTATTCAATTCGGTATTTAAACTTGACAC
1 TTTTTCTT-AATTCGGTACTTAAACTTGACAC
*
30333 TTTTTCTTAATTCGGTACCTAAACTTGACGA-
1 TTTTTCTTAATTCGGTACTTAAACTTGAC-AC
30364 TTTTT-TTAAGTTC-GTACTTAAACTT
1 TTTTTCTTAA-TTCGGTACTTAAACTT
30389 TTTAGGATCC
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
30 15 0.30
31 27 0.54
32 8 0.16
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.48
Consensus pattern (31 bp):
TTTTTCTTAATTCGGTACTTAAACTTGACAC
Found at i:31767 original size:20 final size:20
Alignment explanation
Indices: 31729--31767 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
31719 GACATAACTA
*
31729 CAAAATGCATAACTTCTTTT
1 CAAAATGCATAACTGCTTTT
* *
31749 CAAAATGTATATCTGCTTT
1 CAAAATGCATAACTGCTTT
31768 ATACAGGAGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (20 bp):
CAAAATGCATAACTGCTTTT
Found at i:33843 original size:39 final size:39
Alignment explanation
Indices: 33789--33864 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
33779 TCATTAATTA
33789 TTTATAGTATAGAAATTTACATCTTCATTTTGTGTATTG
1 TTTATAGTATAGAAATTTACATCTTCATTTTGTGTATTG
*
33828 TTTATAGTTTAGAAATTTACATCTTCATTTTGTGTAT
1 TTTATAGTATAGAAATTTACATCTTCATTTTGTGTAT
33865 ATACTAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.28, C:0.08, G:0.12, T:0.53
Consensus pattern (39 bp):
TTTATAGTATAGAAATTTACATCTTCATTTTGTGTATTG
Found at i:45135 original size:31 final size:30
Alignment explanation
Indices: 45100--45161 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 30
45090 TTAGCAACTA
45100 ATTTGTCACTTTTCGATAACGTT-AGTGACTG
1 ATTTGTCACTTTTCGA-AA-GTTGAGTGACTG
* * *
45131 ATTTGTTATTTTTTGAAAGTTGAGTGACTG
1 ATTTGTCACTTTTCGAAAGTTGAGTGACTG
45161 A
1 A
45162 ATTGAAACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 3 0.11
30 11 0.41
31 13 0.48
ACGTcount: A:0.24, C:0.10, G:0.21, T:0.45
Consensus pattern (30 bp):
ATTTGTCACTTTTCGAAAGTTGAGTGACTG
Found at i:45649 original size:16 final size:17
Alignment explanation
Indices: 45630--45666 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
45620 TAATCCTTTA
45630 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
45646 AAAA-TATTAAAATAAT
1 AAAATTATAAAAATAAT
45662 AAAAT
1 AAAAT
45667 AATATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Done.