Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010604.1 Kokia drynarioides strain JFW-HI SEQ_125536, 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: 51076
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:26719 original size:24 final size:24
Alignment explanation
Indices: 26685--26731 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
26675 ATTCATCTTT
*
26685 TATTAATTTGCTCTGACA-TTTTA
1 TATTAATTTGCACTGACAGTTTTA
26708 TATTACATTTGCACTGACAGTTTT
1 TATTA-ATTTGCACTGACAGTTTT
26732 TACTCTTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 12 0.57
25 4 0.19
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.49
Consensus pattern (24 bp):
TATTAATTTGCACTGACAGTTTTA
Found at i:27093 original size:26 final size:26
Alignment explanation
Indices: 27064--27115 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
27054 TTATACTAAT
27064 TACTTCTTTTCTTTGTAGGGATAAAA
1 TACTTCTTTTCTTTGTAGGGATAAAA
27090 TACTTCTTTTCTTTGTAGGGATAAAA
1 TACTTCTTTTCTTTGTAGGGATAAAA
27116 ACCACTATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (26 bp):
TACTTCTTTTCTTTGTAGGGATAAAA
Found at i:37332 original size:21 final size:21
Alignment explanation
Indices: 37308--37348 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
37298 AAGAAAAAGA
37308 AAAAGAATGAAAGG-AGGAAGG
1 AAAAGAA-GAAAGGAAGGAAGG
*
37329 AAAAGAAGGAAGGAAGGAAG
1 AAAAGAAGAAAGGAAGGAAG
37349 AACCTACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.59, C:0.00, G:0.39, T:0.02
Consensus pattern (21 bp):
AAAAGAAGAAAGGAAGGAAGG
Found at i:37663 original size:3 final size:3
Alignment explanation
Indices: 37657--37697 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
37647 GGAGGAACGC
*
37657 AAG AAG AAG AAG AAG AAG AAG GAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
37698 AACCCATGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:38457 original size:16 final size:16
Alignment explanation
Indices: 38427--38457 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38417 AGTCACATAA
*
38427 AAAAAGAATAAAAAAG
1 AAAAAGAAAAAAAAAG
38443 AAAAAGAAAAAAAAA
1 AAAAAGAAAAAAAAA
38458 TGTATATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (16 bp):
AAAAAGAAAAAAAAAG
Found at i:40675 original size:17 final size:17
Alignment explanation
Indices: 40653--40686 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40643 TTTAATGACA
40653 CAAATCTAAACACTATG
1 CAAATCTAAACACTATG
*
40670 CAAATCTAAACATTATG
1 CAAATCTAAACACTATG
40687 AACCTGCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.21, G:0.06, T:0.26
Consensus pattern (17 bp):
CAAATCTAAACACTATG
Found at i:41132 original size:8 final size:8
Alignment explanation
Indices: 41119--41151 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
41109 AAAAAGGGAT
*
41119 TGAGAGGA
1 TGAGAGAA
41127 TGAGAGAA
1 TGAGAGAA
41135 TGAGAGAA
1 TGAGAGAA
41143 TGA-AGAA
1 TGAGAGAA
41150 TG
1 TG
41152 TTGAGTGATG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
7 6 0.25
8 18 0.75
ACGTcount: A:0.45, C:0.00, G:0.39, T:0.15
Consensus pattern (8 bp):
TGAGAGAA
Found at i:41140 original size:16 final size:16
Alignment explanation
Indices: 41119--41166 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
41109 AAAAAGGGAT
41119 TGAGAGGATGAGAGAA
1 TGAGAGGATGAGAGAA
*
41135 TGAGAGAATGA-AGAA
1 TGAGAGGATGAGAGAA
*
41150 TGTTGAGTGATGAGAGA
1 TG-AGAG-GATGAGAGA
41167 TGATTTGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 6 0.23
16 13 0.50
17 4 0.15
18 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.40, T:0.19
Consensus pattern (16 bp):
TGAGAGGATGAGAGAA
Found at i:42176 original size:39 final size:39
Alignment explanation
Indices: 42122--42200 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
42112 TAAACCTCAT
* *
42122 AGTTTTGGCTGAGTATAAAACATATATTAAGTATATGAG
1 AGTTTTGGCTGAGTATAAAACACATATCAAGTATATGAG
* *
42161 AGTTTTGGCTGAGTATAAAAGACATATCAAGTATCTGAG
1 AGTTTTGGCTGAGTATAAAACACATATCAAGTATATGAG
42200 A
1 A
42201 AAGTTGTAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.33
Consensus pattern (39 bp):
AGTTTTGGCTGAGTATAAAACACATATCAAGTATATGAG
Found at i:43387 original size:23 final size:23
Alignment explanation
Indices: 43338--43429 Score: 94
Period size: 23 Copynumber: 4.0 Consensus size: 23
43328 TGGAATTTTG
* * *
43338 TGATGCCTTTTTGGTGCATTATG
1 TGATGCCTTTTTGGCGCATTCTA
43361 TGATGCCTTTTTGGCGCATTCTA
1 TGATGCCTTTTTGGCGCATTCTA
* ** *
43384 TGATTCCTTAATGGCACATTCTA
1 TGATGCCTTTTTGGCGCATTCTA
* * *
43407 TGTTGCCTTTGTGGCGTATTCTA
1 TGATGCCTTTTTGGCGCATTCTA
43430 ATATCCACCT
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.15, C:0.18, G:0.22, T:0.45
Consensus pattern (23 bp):
TGATGCCTTTTTGGCGCATTCTA
Found at i:49677 original size:13 final size:14
Alignment explanation
Indices: 49643--49681 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
49633 TATCTCTTTT
49643 TCTTTCTTTTCATC
1 TCTTTCTTTTCATC
*
49657 TTTTTCTTTTC-TC
1 TCTTTCTTTTCATC
49670 TCTTTCTTTTCA
1 TCTTTCTTTTCA
49682 CTTTCTTTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.69
Consensus pattern (14 bp):
TCTTTCTTTTCATC
Found at i:49700 original size:31 final size:28
Alignment explanation
Indices: 49643--49722 Score: 73
Period size: 27 Copynumber: 2.9 Consensus size: 28
49633 TATCTCTTTT
49643 TCTTTCTTTTCA-TCTT-TTTCTTTTCTC
1 TCTTTCTTTTCACT-TTCTTTCTTTTCTC
49670 TCTTTCTTTTCACTTTCTTTGCTCTGTTCTC
1 TCTTTCTTTTCACTTTCTTT-CT-T-TTCTC
*
49701 TC-AT-TTTTC-CTTTCTTT-TTTTC
1 TCTTTCTTTTCACTTTCTTTCTTTTC
49723 AATTTTCTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
24 3 0.06
25 1 0.02
26 1 0.02
27 14 0.30
28 12 0.26
29 7 0.15
30 2 0.04
31 7 0.15
ACGTcount: A:0.04, C:0.26, G:0.03, T:0.68
Consensus pattern (28 bp):
TCTTTCTTTTCACTTTCTTTCTTTTCTC
Done.