Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014349.1 Kokia drynarioides strain JFW-HI SEQ_129386, 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: 49111
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Warning! 80 characters in sequence are not A, C, G, or T
Found at i:15112 original size:21 final size:19
Alignment explanation
Indices: 15073--15135 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
15063 TAAAATTAAA
* *
15073 AAAATTAAAAATACT-TAT
1 AAAATTAAAAAAAATATAT
15091 AAAATTACAAAAAAAATATAT
1 AAAATT--AAAAAAAATATAT
*
15112 AAAAGTTTAAAAAAATA-AT
1 AAAA-TTAAAAAAAATATAT
15131 AAAAT
1 AAAAT
15136 ATATATGGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 7 0.18
19 6 0.16
20 16 0.42
21 7 0.18
22 2 0.05
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAATTAAAAAAAATATAT
Found at i:31340 original size:31 final size:29
Alignment explanation
Indices: 31305--31364 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
31295 GTGATCATTT
31305 CATAACAAAACAATAACATAAGTGACTAAAA
1 CATAACAAAACAAT--CATAAGTGACTAAAA
***
31336 CATAACATTTCAATCATAAGTGACTAAAA
1 CATAACAAAACAATCATAAGTGACTAAAA
31365 TGAAATTTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 15 0.58
31 11 0.42
ACGTcount: A:0.55, C:0.17, G:0.07, T:0.22
Consensus pattern (29 bp):
CATAACAAAACAATCATAAGTGACTAAAA
Found at i:35487 original size:82 final size:82
Alignment explanation
Indices: 35360--35526 Score: 244
Period size: 82 Copynumber: 2.0 Consensus size: 82
35350 GTTAGGTGAA
* ** * *
35360 TAGATTTAACCTAAAGGGATCATGAATATTCAATGAGGGTAACACACATATGACAAGTTCATTGG
1 TAGATTTAACCGAAACAGATCATAAATATCCAATGAGGGTAACACACATATGACAAGTTCATTGG
35425 ATAAAAGTTTAATTAAG
66 ATAAAAGTTTAATTAAG
* * * *
35442 TAGATTTAACCGAAACAGATCATAAATATCCTATGAGGGTAACACATATATTACAAGTTTATTGG
1 TAGATTTAACCGAAACAGATCATAAATATCCAATGAGGGTAACACACATATGACAAGTTCATTGG
*
35507 ATAAAATTTTAATTAAG
66 ATAAAAGTTTAATTAAG
35524 TAG
1 TAG
35527 CTTCTGTCAA
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
82 75 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (82 bp):
TAGATTTAACCGAAACAGATCATAAATATCCAATGAGGGTAACACACATATGACAAGTTCATTGG
ATAAAAGTTTAATTAAG
Found at i:35746 original size:28 final size:28
Alignment explanation
Indices: 35711--35767 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
35701 AAGATTAATT
35711 ATAATTAGAATATGATTAGTTAAAGCTA
1 ATAATTAGAATATGATTAGTTAAAGCTA
35739 ATAATTAGAATATGATTAGTTAAAGCTA
1 ATAATTAGAATATGATTAGTTAAAGCTA
35767 A
1 A
35768 ATTAATCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.47, C:0.04, G:0.14, T:0.35
Consensus pattern (28 bp):
ATAATTAGAATATGATTAGTTAAAGCTA
Found at i:40343 original size:187 final size:188
Alignment explanation
Indices: 40014--40379 Score: 698
Period size: 187 Copynumber: 2.0 Consensus size: 188
40004 AACAAAAAAG
40014 GATAAGGTTTTGGATTTTCTTATTATATTTTATTTTAATTAGAATTTTTAAATTTATAAAAATTT
1 GATAAGGTTTTGGATTTTCTTATTATATTTTATTTTAATTAGAATTTTTAAATTTATAAAAATTT
*
40079 GAGATTTTTTTTTTAATAATGACATGGCAACGTTCGGTGTGAAGTGACATGTTTCCCATGTGGAA
66 GAGATTTTTTTTTTAATAATGACATGACAACGTTCGGTGTGAAGTGACATGTTTCCCATGTGGAA
40144 GAAAAACATTGCCATACATTGCATTCTTACAAGCTTATCTTTTAACATAAAAATTTGA
131 GAAAAACATTGCCATACATTGCATTCTTACAAGCTTATCTTTTAACATAAAAATTTGA
* *
40202 GATATGGTTTTGGATTTTTTTATTATATTTTATTTTAATTAGAATTTTTAAATTTATAAAAATTT
1 GATAAGGTTTTGGATTTTCTTATTATATTTTATTTTAATTAGAATTTTTAAATTTATAAAAATTT
40267 GAGA-TTTTTTTTTAATAATGACATGACAACGTTCGGTGTGAAGTGACATGTTTCCCATGTGGAA
66 GAGATTTTTTTTTTAATAATGACATGACAACGTTCGGTGTGAAGTGACATGTTTCCCATGTGGAA
40331 GAAAAACATTGCCATACATTGCATTCTTACAAGCTTATCTTTTAACATA
131 GAAAAACATTGCCATACATTGCATTCTTACAAGCTTATCTTTTAACATA
40380 GGTTTAAGGT
Statistics
Matches: 175, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
187 108 0.62
188 67 0.38
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (188 bp):
GATAAGGTTTTGGATTTTCTTATTATATTTTATTTTAATTAGAATTTTTAAATTTATAAAAATTT
GAGATTTTTTTTTTAATAATGACATGACAACGTTCGGTGTGAAGTGACATGTTTCCCATGTGGAA
GAAAAACATTGCCATACATTGCATTCTTACAAGCTTATCTTTTAACATAAAAATTTGA
Found at i:41497 original size:12 final size:12
Alignment explanation
Indices: 41457--41489 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
41447 TCATCATGCC
41457 TTATTGTTACTT
1 TTATTGTTACTT
41469 TTATTGTTACTT
1 TTATTGTTACTT
41481 TTATTGTTA
1 TTATTGTTA
41490 TTATTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.18, C:0.06, G:0.09, T:0.67
Consensus pattern (12 bp):
TTATTGTTACTT
Found at i:42204 original size:3 final size:3
Alignment explanation
Indices: 42149--42188 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
42139 AATATCAACC
*
42149 AAG AAG AGG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
42189 GATAAATCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:45648 original size:81 final size:80
Alignment explanation
Indices: 45537--45778 Score: 322
Period size: 81 Copynumber: 3.0 Consensus size: 80
45527 AGATCAGCAC
* * **
45537 CTGCTCTGTTTGCTAAAGGTTCTGGTGAAGGTGTGTCATTCTGAACCCTCCATTTCCTTTGAGGA
1 CTGCTCGGTTTACTAAAGGTTCTGGTGAAGGTGTGTCATTCT-AACCCTCCATTTCCTAGGAGGA
45602 GATAAATCAGTACCAT
65 GATAAATCAGTACCAT
* * * *
45618 CTGTTCGGTTTACTACAGGTTCTGGTGAAGGTGTGTCATTCCAAACCCTACATTTCCTAGGAGGA
1 CTGCTCGGTTTACTAAAGGTTCTGGTGAAGGTGTGTCATT-CTAACCCTCCATTTCCTAGGAGGA
45683 GATAAATCAGTACCAT
65 GATAAATCAGTACCAT
* * * * ** *
45699 CTGCTCTGTTTACTAAAGGTTCTGATGAGGGTGTGCCATTCCTAACCCTCCGCTTCCGAGGAGGA
1 CTGCTCGGTTTACTAAAGGTTCTGGTGAAGGTGTGTCATT-CTAACCCTCCATTTCCTAGGAGGA
45764 GATAAATCAGTACCA
65 GATAAATCAGTACCA
45779 CCTCTAGAAG
Statistics
Matches: 141, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
81 140 0.99
82 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (80 bp):
CTGCTCGGTTTACTAAAGGTTCTGGTGAAGGTGTGTCATTCTAACCCTCCATTTCCTAGGAGGAG
ATAAATCAGTACCAT
Found at i:46453 original size:17 final size:15
Alignment explanation
Indices: 46419--46457 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
46409 GATTTGGTTT
*
46419 TCTTCTTTTTCTTCC
1 TCTTCTTATTCTTCC
46434 TCTTCTTATTCTGCTCC
1 TCTTCTTATTCT--TCC
46451 TCTTCTT
1 TCTTCTT
46458 CGTTTTTGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.52
17 10 0.48
ACGTcount: A:0.03, C:0.33, G:0.03, T:0.62
Consensus pattern (15 bp):
TCTTCTTATTCTTCC
Done.