Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013572.1 Kokia drynarioides strain JFW-HI SEQ_128598, 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: 65649
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Warning! 123 characters in sequence are not A, C, G, or T
Found at i:1306 original size:17 final size:17
Alignment explanation
Indices: 1284--1322 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1274 AAAAAATTCG
1284 ATTAAAAATTT-AATAA
1 ATTAAAAATTTAAATAA
*
1300 TATTAAATATTTAAATAA
1 -ATTAAAAATTTAAATAA
1318 ATTAA
1 ATTAA
1323 TAACATTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTAAAAATTTAAATAA
Found at i:1947 original size:20 final size:21
Alignment explanation
Indices: 1922--1961 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1912 ATCTCTTTGT
1922 ATCCAAAAG-AAAAATGTTTA
1 ATCCAAAAGTAAAAATGTTTA
*
1942 ATCCAAAAGTAAAACTGTTT
1 ATCCAAAAGTAAAAATGTTT
1962 GAATATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (21 bp):
ATCCAAAAGTAAAAATGTTTA
Found at i:9193 original size:25 final size:28
Alignment explanation
Indices: 9136--9194 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
9126 AATTTGAAGG
*
9136 AATAAAAAGTTAGAATGATGAAAAACAT
1 AATAAAAAATTAGAATGATGAAAAACAT
*
9164 AATAAAAAATTAGAATGATAAAAAACAT
1 AATAAAAAATTAGAATGATGAAAAACAT
9192 AAT
1 AAT
9195 TTTTCTTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.64, C:0.03, G:0.10, T:0.22
Consensus pattern (28 bp):
AATAAAAAATTAGAATGATGAAAAACAT
Found at i:9884 original size:18 final size:19
Alignment explanation
Indices: 9854--9891 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
9844 AATATATTTA
*
9854 TTAAAAGTTAATATAAAAT
1 TTAAAAGTTAATAAAAAAT
9873 TTAAAA-TTAATAAAAAAT
1 TTAAAAGTTAATAAAAAAT
9891 T
1 T
9892 AATTATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (19 bp):
TTAAAAGTTAATAAAAAAT
Found at i:10616 original size:189 final size:192
Alignment explanation
Indices: 10293--10676 Score: 666
Period size: 189 Copynumber: 2.0 Consensus size: 192
10283 TTCGTGAAAT
*
10293 AACTTTGGACGTCATAAATATATGTGAATCAAAACCCAAAACAACTTATTTCTCACATTAAATCA
1 AACTTTGGACGTCATAAATATATGTGAATCAAAACCCAAAACAACTTATTTCTCACATTAAATAA
*
10358 ATTTAGATCTAAAATATATTTTTCTACTCAGTAATAGATATTGATCTATCATATCAATCATTAAA
66 ATTTAGATCTAAAATATATTTTTCTACTCAGTAATAGATATTGATCTATCATACCAATCATTAAA
*
10423 TTGTCACTTGAAGCTAGCTAATAAAACGTTTAAAAAATTTAACAATCTAAAGATTTAAATAA
131 TTGTCACTTGAAACTAGCTAATAAAACGTTTAAAAAATTTAACAATCTAAAGATTTAAATAA
*
10485 AACTTTGGACGTCAT-AA-ATATGTGAATCAAAACCC-AAACAATTTATTTCTCACATTAAATAA
1 AACTTTGGACGTCATAAATATATGTGAATCAAAACCCAAAACAACTTATTTCTCACATTAAATAA
* * * *
10547 ATTTGGATCTAAATTATATTTTTCTACTCATTAATAGATATTGATCTATCGTACCAATCATTAAA
66 ATTTAGATCTAAAATATATTTTTCTACTCAGTAATAGATATTGATCTATCATACCAATCATTAAA
*
10612 TTGTCACTTGAAACTAGCTGATAAAACGTTTAAAAAATTTAACAATCTAAAGATTTAAATAA
131 TTGTCACTTGAAACTAGCTAATAAAACGTTTAAAAAATTTAACAATCTAAAGATTTAAATAA
10674 AAC
1 AAC
10677 ATTTAAATAG
Statistics
Matches: 183, Mismatches: 9, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
189 148 0.81
190 18 0.10
191 2 0.01
192 15 0.08
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.35
Consensus pattern (192 bp):
AACTTTGGACGTCATAAATATATGTGAATCAAAACCCAAAACAACTTATTTCTCACATTAAATAA
ATTTAGATCTAAAATATATTTTTCTACTCAGTAATAGATATTGATCTATCATACCAATCATTAAA
TTGTCACTTGAAACTAGCTAATAAAACGTTTAAAAAATTTAACAATCTAAAGATTTAAATAA
Found at i:23463 original size:13 final size:13
Alignment explanation
Indices: 23445--23469 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23435 GTTTTTTAGA
23445 GGAAAATCAATGT
1 GGAAAATCAATGT
23458 GGAAAATCAATG
1 GGAAAATCAATG
23470 GCACAAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.24, T:0.20
Consensus pattern (13 bp):
GGAAAATCAATGT
Found at i:25375 original size:53 final size:53
Alignment explanation
Indices: 25313--25417 Score: 167
Period size: 53 Copynumber: 2.0 Consensus size: 53
25303 AACTAATAAG
*
25313 AGTGATTAAAGTT-ACTAATAATTGGATTAAGATTTACAAACCTATAAAAATGA
1 AGTGATTAAA-TTCACTAATAATTGGATTAAGATATACAAACCTATAAAAATGA
* *
25366 AGTGATTAAATTCACTAATGATTGGATTAAGATATACAAAGCTATAAAAATG
1 AGTGATTAAATTCACTAATAATTGGATTAAGATATACAAACCTATAAAAATG
25418 CATGGACTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
52 2 0.04
53 46 0.96
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (53 bp):
AGTGATTAAATTCACTAATAATTGGATTAAGATATACAAACCTATAAAAATGA
Found at i:25429 original size:53 final size:53
Alignment explanation
Indices: 25313--25436 Score: 153
Period size: 53 Copynumber: 2.3 Consensus size: 53
25303 AACTAATAAG
* *
25313 AGTGATTAAAGTT-ACTAATAATTGGATTAAGATTTACAAACCTATAAAAATGA
1 AGTGACTAAA-TTCACTAATAATTGGATTAAGATATACAAACCTATAAAAATGA
* * * *
25366 AGTGATTAAATTCACTAATGATTGGATTAAGATATACAAAGCTATAAAAATGC
1 AGTGACTAAATTCACTAATAATTGGATTAAGATATACAAACCTATAAAAATGA
*
25419 A-TGGACTAAATTTACTAA
1 AGT-GACTAAATTCACTAA
25437 AGAAAATGTG
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
52 3 0.05
53 60 0.95
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.31
Consensus pattern (53 bp):
AGTGACTAAATTCACTAATAATTGGATTAAGATATACAAACCTATAAAAATGA
Found at i:29084 original size:27 final size:27
Alignment explanation
Indices: 29054--29116 Score: 92
Period size: 27 Copynumber: 2.3 Consensus size: 27
29044 CCCAGCTGTG
29054 GTGCCTGGAGAAAAGCTCATG-GTTGTA
1 GTGCCTGGAGAAAAGCTCA-GAGTTGTA
*
29081 GTGCCTGGAGAAAAGCTCAGAGTTGTT
1 GTGCCTGGAGAAAAGCTCAGAGTTGTA
*
29108 GAGCCTGGA
1 GTGCCTGGA
29117 ATAAGGCTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 1 0.03
27 32 0.97
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (27 bp):
GTGCCTGGAGAAAAGCTCAGAGTTGTA
Found at i:40841 original size:39 final size:39
Alignment explanation
Indices: 40787--40862 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
40777 TTTTCTTCTT
40787 AATCCTCGTGGGTTAGGTGATGTCTCATGATAGCTTCGA
1 AATCCTCGTGGGTTAGGTGATGTCTCATGATAGCTTCGA
40826 AATCCTCGTGGGTTAGGTGATGTCTCATGATAGCTTC
1 AATCCTCGTGGGTTAGGTGATGTCTCATGATAGCTTC
40863 AACTTACATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (39 bp):
AATCCTCGTGGGTTAGGTGATGTCTCATGATAGCTTCGA
Found at i:42799 original size:7 final size:7
Alignment explanation
Indices: 42787--42823 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
42777 CTGAAGAATA
42787 AAAATCT
1 AAAATCT
42794 AAAATCT
1 AAAATCT
42801 AAAATCT
1 AAAATCT
*
42808 AATATCT
1 AAAATCT
*
42815 AATATCT
1 AAAATCT
42822 AA
1 AA
42824 TCCTAGCAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (7 bp):
AAAATCT
Found at i:42906 original size:20 final size:20
Alignment explanation
Indices: 42867--42907 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
42857 GCATCTGCAT
*
42867 TTTCTCCTTCTTCTTCTTCA
1 TTTCTCCTTCTTATTCTTCA
* *
42887 TTTCTTCTTCTTATTTTTCA
1 TTTCTCCTTCTTATTCTTCA
42907 T
1 T
42908 GTCATTGTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTCTCCTTCTTATTCTTCA
Found at i:43282 original size:21 final size:21
Alignment explanation
Indices: 43258--43297 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
43248 AATCCATGTG
43258 ATTTAATGTTTAAATATTTTT
1 ATTTAATGTTTAAATATTTTT
* *
43279 ATTTTATTTTTAAATATTT
1 ATTTAATGTTTAAATATTT
43298 ACTTGTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (21 bp):
ATTTAATGTTTAAATATTTTT
Found at i:52437 original size:43 final size:45
Alignment explanation
Indices: 52349--52439 Score: 121
Period size: 44 Copynumber: 2.0 Consensus size: 45
52339 TAAATTGTTT
* * *
52349 AATAAAAAATTATTATATGCTTTAATTTGTTTTATAAAATTTAAA
1 AATAAAAAATTATGATATGCTTTAATTTGATTGATAAAATTTAAA
* * *
52394 AATAAAATATT-TGATATGTTTTAATTTGATTGATAAAATTAAAA
1 AATAAAAAATTATGATATGCTTTAATTTGATTGATAAAATTTAAA
52438 AA
1 AA
52440 CTCCATCATT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 30 0.75
45 10 0.25
ACGTcount: A:0.48, C:0.01, G:0.07, T:0.44
Consensus pattern (45 bp):
AATAAAAAATTATGATATGCTTTAATTTGATTGATAAAATTTAAA
Done.