Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015252.1 Kokia drynarioides strain JFW-HI SEQ_130297, 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: 344124
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 305 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:290748 original size:16 final size:17
Alignment explanation
Indices: 290721--290760 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
290711 AAAAAATTTG
*
290721 AATATATTTTATCT-AAT
1 AATAT-TTTTATCTCAAA
290738 AATATTTTTATCTCAAA
1 AATATTTTTATCTCAAA
290755 AATATT
1 AATATT
290761 ATTTTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (17 bp):
AATATTTTTATCTCAAA
Found at i:290767 original size:19 final size:17
Alignment explanation
Indices: 290721--290777 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 17
290711 AAAAAATTTG
*
290721 AATATATTTTATCTAAT
1 AATATATTTTATCTAAA
290738 AATAT-TTTTATCTCAAA
1 AATATATTTTATCT-AAA
*
290755 AATATTATTTTATTTTAAA
1 AATA-TATTTTA-TCTAAA
290774 AATA
1 AATA
290778 CTTCTAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 8 0.24
17 11 0.32
18 1 0.03
19 12 0.35
20 2 0.06
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (17 bp):
AATATATTTTATCTAAA
Found at i:303192 original size:31 final size:32
Alignment explanation
Indices: 303129--303198 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
303119 TTATAAATGA
*
303129 ATTAAAACCATTAAATTTTATAAAAATAATTT
1 ATTAAAACCATTAAAATTTATAAAAATAATTT
*
303161 ATTAAAACCCA-TAAAATTTA-AAAAATCATTT
1 ATTAAAA-CCATTAAAATTTATAAAAATAATTT
*
303192 ATAAAAA
1 ATTAAAA
303199 TTGTTATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 16 0.47
32 15 0.44
33 3 0.09
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (32 bp):
ATTAAAACCATTAAAATTTATAAAAATAATTT
Found at i:303265 original size:55 final size:51
Alignment explanation
Indices: 303156--303266 Score: 125
Period size: 55 Copynumber: 2.1 Consensus size: 51
303146 TTATAAAAAT
* * *
303156 AATTTATTAAAACCCATAAAATTTAAAAAATCATTTATAAAAATTGTTATA
1 AATTAATTAAAAACCATAAAATTTAAAAAATCATTTATAAAAATTGTTAAA
* *
303207 AATTAATTAAAAACCATAAAATTTTATTAAAAATGTATTTATAAAGATT-TATAAA
1 AATTAATTAAAAACCATAAAA-TTTA--AAAAAT-CATTTATAAAAATTGT-TAAA
303262 AATTA
1 AATTA
303267 TTTCTATTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
51 19 0.38
52 4 0.08
54 7 0.14
55 20 0.40
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (51 bp):
AATTAATTAAAAACCATAAAATTTAAAAAATCATTTATAAAAATTGTTAAA
Found at i:303499 original size:27 final size:28
Alignment explanation
Indices: 303469--303534 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 28
303459 AAAATAAATT
303469 ATTTTATAAAATAAATTATTTTATAA-A
1 ATTTTATAAAATAAATTATTTTATAATA
* ** * *
303496 ATTTTATTATTTTAATTATTTTCTAATA
1 ATTTTATAAAATAAATTATTTTATAATA
303524 ATTTTTATAAA
1 A-TTTTATAAA
303535 TCATATTTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
27 21 0.70
28 2 0.07
29 7 0.23
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (28 bp):
ATTTTATAAAATAAATTATTTTATAATA
Found at i:303509 original size:18 final size:17
Alignment explanation
Indices: 303452--303497 Score: 92
Period size: 17 Copynumber: 2.7 Consensus size: 17
303442 TTCTAATAAA
303452 ATTTTATAAAATAAATT
1 ATTTTATAAAATAAATT
303469 ATTTTATAAAATAAATT
1 ATTTTATAAAATAAATT
303486 ATTTTATAAAAT
1 ATTTTATAAAAT
303498 TTTATTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTTTATAAAATAAATT
Found at i:308902 original size:88 final size:89
Alignment explanation
Indices: 308748--308930 Score: 341
Period size: 88 Copynumber: 2.1 Consensus size: 89
308738 CAAAAAATTA
308748 TATTATTTATAAGAAATGTTATGAAAGTTTGGACAATTTATAAAACTTGATATATTTTATATTTT
1 TATTATTTATAAGAAATGTTATGAAAGTTTGGACAATTTATAAAACTTGATATATTTTATATTTT
* *
308813 ATATTATTTTTTATTTATTTTACG
66 ATATTACTTTTTATTTAATTTACG
308837 TATT-TTTATAAGAAATGTTATGAAAGTTTGGACAATTTATAAAACTTGATATATTTTATATTTT
1 TATTATTTATAAGAAATGTTATGAAAGTTTGGACAATTTATAAAACTTGATATATTTTATATTTT
308901 ATATTACTTTTTATTTAATTTACG
66 ATATTACTTTTTATTTAATTTACG
308925 TATTAT
1 TATTAT
308931 AAAAAGTTAT
Statistics
Matches: 91, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
88 86 0.95
89 5 0.05
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.52
Consensus pattern (89 bp):
TATTATTTATAAGAAATGTTATGAAAGTTTGGACAATTTATAAAACTTGATATATTTTATATTTT
ATATTACTTTTTATTTAATTTACG
Found at i:312174 original size:26 final size:26
Alignment explanation
Indices: 312119--312189 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
312109 ATCGTTTTTT
* * *
312119 CTTAAAACTATAAA-ATTCAAAGATA
1 CTTAAAATTTTAAACATTCAAAAATA
* *
312144 ATTAAAATTTTAAACATTCAAAAATC
1 CTTAAAATTTTAAACATTCAAAAATA
*
312170 CTTAAAATTATAAAACATTC
1 CTTAAAATT-TTAAACATTC
312190 CCAAAAAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
25 11 0.30
26 17 0.46
27 9 0.24
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (26 bp):
CTTAAAATTTTAAACATTCAAAAATA
Found at i:314243 original size:211 final size:210
Alignment explanation
Indices: 313872--314313 Score: 796
Period size: 211 Copynumber: 2.1 Consensus size: 210
313862 TTATTTAAAA
* *
313872 AATATAATAATATAAATTATTAGAATAATAAAATCACATTTTTATTATGATAAAAATATACAATT
1 AATA-AATAATATAATTTATTAGAATAATAAAATCACATTTTTATTATAATAAAAATATACAATT
313937 TAATTTTAACCTCTCTTAAAAATTTTATGATTTCGTCCTCACCTCCCACTTCATTAAAATCAGTT
65 TAATTTTAACCTCTCTTAAAAATTTTATGATTTCGTCCTCACCTCCCACTTCATTAAAATCAGTT
314002 AACAGAAAATGACTAAAAATATTATTAATGATTATTTTTAATTTTATTTTTATAAGTCAATGAGT
130 AACAGAAAATGACTAAAAATATTATTAATGATTATTTTTAATTTTATTTTTATAAGTCAATGAGT
*
314067 AAGAGAAAGTCTTTCT
195 AACAGAAAGTCTTTCT
*
314083 AATAAATTAATATAATTTATTAGAATAATAAAATCATATTTTTATTATAATAAAAATATACAATT
1 AATAAA-TAATATAATTTATTAGAATAATAAAATCACATTTTTATTATAATAAAAATATACAATT
* *
314148 TAATTTTAATCTCTCTTAAAAATTTTATGATTTCGTCCTTACCTCCCACTTCATTAAAATCAGTT
65 TAATTTTAACCTCTCTTAAAAATTTTATGATTTCGTCCTCACCTCCCACTTCATTAAAATCAGTT
314213 AACAGAAAATGACTAAAAATATTATTAATGATTATTTTTAATTTTATTTTTATAAGTCAATGAGT
130 AACAGAAAATGACTAAAAATATTATTAATGATTATTTTTAATTTTATTTTTATAAGTCAATGAGT
314278 AACAGAAAGTCTTTCT
195 AACAGAAAGTCTTTCT
*
314294 AATAAATGA-ATAATTTATTA
1 AATAAATAATATAATTTATTA
314314 TAAAAAAAAT
Statistics
Matches: 223, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
209 11 0.05
210 4 0.02
211 208 0.93
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.41
Consensus pattern (210 bp):
AATAAATAATATAATTTATTAGAATAATAAAATCACATTTTTATTATAATAAAAATATACAATTT
AATTTTAACCTCTCTTAAAAATTTTATGATTTCGTCCTCACCTCCCACTTCATTAAAATCAGTTA
ACAGAAAATGACTAAAAATATTATTAATGATTATTTTTAATTTTATTTTTATAAGTCAATGAGTA
ACAGAAAGTCTTTCT
Found at i:317584 original size:23 final size:23
Alignment explanation
Indices: 317554--317601 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
317544 TTATTGAAAC
317554 CTAGAGACTTTTCCATGTTCTAA
1 CTAGAGACTTTTCCATGTTCTAA
317577 CTAGAGACTTTTCCATGTTCTAA
1 CTAGAGACTTTTCCATGTTCTAA
317600 CT
1 CT
317602 TCTACGTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (23 bp):
CTAGAGACTTTTCCATGTTCTAA
Found at i:327313 original size:2 final size:2
Alignment explanation
Indices: 327306--327339 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
327296 TATTATGTCG
327306 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
327340 GGTGTTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:328107 original size:24 final size:24
Alignment explanation
Indices: 328080--328129 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
328070 ATGACACAAT
*
328080 AATCTACTACAGGAGTATAGATTG
1 AATCTACTACAAGAGTATAGATTG
328104 AATCTACTACAAGAGTATAGATTG
1 AATCTACTACAAGAGTATAGATTG
328128 AA
1 AA
328130 GATGAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (24 bp):
AATCTACTACAAGAGTATAGATTG
Found at i:331531 original size:8 final size:8
Alignment explanation
Indices: 331518--331560 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
331508 AACAAAAAAA
*
331518 ATACATAC
1 ATACATAT
331526 ATACATAT
1 ATACATAT
*
331534 ATATATAT
1 ATACATAT
*
331542 ATATATAT
1 ATACATAT
331550 ATACATAT
1 ATACATAT
331558 ATA
1 ATA
331561 TATTATTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (8 bp):
ATACATAT
Found at i:331535 original size:2 final size:2
Alignment explanation
Indices: 331530--331563 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
331520 ACATACATAC
*
331530 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
331564 TATTTTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:335655 original size:60 final size:60
Alignment explanation
Indices: 335571--335720 Score: 151
Period size: 60 Copynumber: 2.5 Consensus size: 60
335561 TTGTTATAAT
* * * *
335571 AACAAATTTAATCCTTTAATATTTACACATTCTATCAATTTGA-TCCTAAGTATAAAAAAATC
1 AACAAACTTAATCC-TCAATATTTACAAATT-TATC-ATTTGAGTCCAAAGTATAAAAAAATC
* * * *
335633 AACAAA-TTAATCCTCAATATTTACAAAATTTATCATTTTAGTTCAAATTCTAAAAAAATC
1 AACAAACTTAATCCTCAATATTTAC-AAATTTATCATTTGAGTCCAAAGTATAAAAAAATC
* * *
335693 AACAAACTTATTACTCAACATTTACAAA
1 AACAAACTTAATCCTCAATATTTACAAA
335721 AAAGACAAAA
Statistics
Matches: 75, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
59 5 0.07
60 38 0.51
61 26 0.35
62 6 0.08
ACGTcount: A:0.46, C:0.17, G:0.02, T:0.35
Consensus pattern (60 bp):
AACAAACTTAATCCTCAATATTTACAAATTTATCATTTGAGTCCAAAGTATAAAAAAATC
Found at i:340634 original size:24 final size:24
Alignment explanation
Indices: 340589--340634 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
340579 GAAAAATAAT
*
340589 TTTTAAAAAATAAAATTCTAAAAG
1 TTTTAAAAAATAAAATTATAAAAG
*
340613 TTTTAAAATATATAAA-TATAAA
1 TTTTAAAAAATA-AAATTATAAA
340635 TATTCAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (24 bp):
TTTTAAAAAATAAAATTATAAAAG
Found at i:340644 original size:32 final size:33
Alignment explanation
Indices: 340598--340661 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
340588 TTTTTAAAAA
**
340598 ATAAAATTCTAAAAGTTTTAA-AATATATAAAT
1 ATAAAATTCTAAAAGTCATAATAATATATAAAT
340630 ATAAATATTC-AAAAGTCATAATAATATATAAA
1 ATAAA-ATTCTAAAAGTCATAATAATATATAAA
340662 AATTGAACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (33 bp):
ATAAAATTCTAAAAGTCATAATAATATATAAAT
Found at i:341833 original size:21 final size:20
Alignment explanation
Indices: 341796--341835 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
341786 AAAAAATTAC
* *
341796 ATTTTTAAAGTTTTTTTTTA
1 ATTTTAAAAGTTATTTTTTA
341816 ATTTTAAAGAGTTATTTTTT
1 ATTTTAAA-AGTTATTTTTT
341836 GTTGACGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (20 bp):
ATTTTAAAAGTTATTTTTTA
Found at i:342640 original size:43 final size:43
Alignment explanation
Indices: 342579--342660 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
342569 AAAATAAAAG
*
342579 TATAGAGACTAGTTTTAACAAACGGAAAACATAAAAAAAACTA
1 TATAGAGACTAGTTTTAACAAACGAAAAACATAAAAAAAACTA
* *
342622 TATAGAGATTAGTTTTAACAAATGAAAAACATAAAAAAA
1 TATAGAGACTAGTTTTAACAAACGAAAAACATAAAAAAA
342661 TTATGTTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.57, C:0.09, G:0.11, T:0.23
Consensus pattern (43 bp):
TATAGAGACTAGTTTTAACAAACGAAAAACATAAAAAAAACTA
Done.