Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012003.1 Kokia drynarioides strain JFW-HI SEQ_127001, 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: 291786
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 113 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:254168 original size:34 final size:34
Alignment explanation
Indices: 254130--254250 Score: 127
Period size: 34 Copynumber: 3.4 Consensus size: 34
254120 ATTAAATATT
254130 TAATTAAATAATTAAATATTTGGATTGTTTTTAA
1 TAATTAAATAATTAAATATTTGGATTGTTTTTAA
* * * * *
254164 TAATTAATTAATTAATTAATTAATTGGGTTGATTTAAA
1 TAATT-A--AA-TAATTAAATATTTGGATTGTTTTTAA
*
254202 TAATTAAATAATTAAGTATTT-GAGTTGTTTTTAA
1 TAATTAAATAATTAAATATTTGGA-TTGTTTTTAA
*
254236 TAATTAAATATTTAA
1 TAATTAAATAATTAA
254251 TTAAATAATT
Statistics
Matches: 71, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
33 1 0.01
34 38 0.54
35 3 0.04
37 3 0.04
38 26 0.37
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (34 bp):
TAATTAAATAATTAAATATTTGGATTGTTTTTAA
Found at i:254169 original size:26 final size:26
Alignment explanation
Indices: 254090--254170 Score: 84
Period size: 26 Copynumber: 3.3 Consensus size: 26
254080 TAAATAATTA
* *
254090 AATAATTAATTATTTGGGTTGTTTTT
1 AATAATTAAATATTTGGATTGTTTTT
* *
254116 AATAATTAAATATTT--A----ATTA
1 AATAATTAAATATTTGGATTGTTTTT
254136 AATAATTAAATATTTGGATTGTTTTT
1 AATAATTAAATATTTGGATTGTTTTT
254162 AATAATTAA
1 AATAATTAA
254171 TTAATTAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
20 17 0.40
22 1 0.02
26 25 0.58
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.51
Consensus pattern (26 bp):
AATAATTAAATATTTGGATTGTTTTT
Found at i:254173 original size:4 final size:4
Alignment explanation
Indices: 254160--254188 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
254150 TGGATTGTTT
254160 TTAA -TAA TTAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
254189 GGGTTGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:254237 original size:26 final size:26
Alignment explanation
Indices: 254205--254317 Score: 103
Period size: 26 Copynumber: 4.6 Consensus size: 26
254195 ATTTAAATAA
*
254205 TTAAATAATTAAGTATTTGAGTTGTT
1 TTAAATAATTAAATATTTGAGTTGTT
* *
254231 TTTAATAATTAAATATTT-A-----A
1 TTAAATAATTAAATATTTGAGTTGTT
*
254251 TTAAATAATTAAATATTTGAATTGTT
1 TTAAATAATTAAATATTTGAGTTGTT
* * * * *
254277 TTTAATAATTAATTAATTGGGTTATT
1 TTAAATAATTAAATATTTGAGTTGTT
254303 TTAAATAATTAAATA
1 TTAAATAATTAAATA
254318 ATTAAATAGA
Statistics
Matches: 68, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
20 17 0.25
21 1 0.01
25 1 0.01
26 49 0.72
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (26 bp):
TTAAATAATTAAATATTTGAGTTGTT
Found at i:254259 original size:20 final size:21
Alignment explanation
Indices: 254234--254273 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
254224 AGTTGTTTTT
254234 AATAATTAAATATTT-AATTA
1 AATAATTAAATATTTGAATTA
254254 AATAATTAAATATTTGAATT
1 AATAATTAAATATTTGAATT
254274 GTTTTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (21 bp):
AATAATTAAATATTTGAATTA
Found at i:254318 original size:34 final size:35
Alignment explanation
Indices: 254130--254322 Score: 115
Period size: 34 Copynumber: 5.4 Consensus size: 35
254120 ATTAAATATT
* * * **
254130 TAATTAAATAATTAAATATTTGGATTGTTTTTAATAA
1 TAATTAAATAATTAATTAATTGGGTTAATTTT-A-AA
* *
254167 TTAATTAATTAATTAATTAATTGGGTTGA-TTTAAA
1 -TAATTAAATAATTAATTAATTGGGTTAATTTTAAA
* * * * *
254202 TAATTAAATAATTAAGTATTTGAGTT-GTTTTTAA
1 TAATTAAATAATTAATTAATTGGGTTAATTTTAAA
* * ** *
254236 TAATTAAATATTTAATTAAAT-AATTAAATATTTGAAT
1 TAATTAAATAATTAATTAATTGGGTT-AAT-TTT-AAA
** *
254273 TGTTTTTAATAATTAATTAATTGGGTT-ATTTTAAA
1 T-AATTAAATAATTAATTAATTGGGTTAATTTTAAA
254308 TAATTAAATAATTAA
1 TAATTAAATAATTAA
254323 ATAGAAAAAA
Statistics
Matches: 118, Mismatches: 30, Indels: 18
0.71 0.18 0.11
Matches are distributed among these distances:
33 3 0.03
34 55 0.47
35 6 0.05
36 7 0.06
37 7 0.06
38 38 0.32
39 2 0.02
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (35 bp):
TAATTAAATAATTAATTAATTGGGTTAATTTTAAA
Found at i:256436 original size:41 final size:41
Alignment explanation
Indices: 256391--256691 Score: 295
Period size: 41 Copynumber: 7.3 Consensus size: 41
256381 TGTTTTTCCA
* *
256391 ATAAACGTCGCTAATGCT-TAGACATTTAGCGGCGCTTCCTC
1 ATAAACGCCGCTAATGCTCT-GACCTTTAGCGGCGCTTCCTC
* *
256432 ATAAACGCCGCTAATGCTCTGACCTTTAGCGGTGCTTTCTC
1 ATAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTCCTC
* * * * *
256473 ATAAACGCCGCTAATGCTCTAATCTTTAGCGGCGTTTTCTT
1 ATAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTCCTC
* * * * ** * **
256514 ATAAATGCCGTTAATGCTCTAACTTTTAGTAGTG-TTTTTCC
1 ATAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTCCT-C
* *
256555 ATAAACGCCGCTAATTCTCTGACCTTTAGCGGTGCTTTCC-C
1 ATAAACGCCGCTAATGCTCTGACCTTTAGCGGCGC-TTCCTC
***
256596 ATAAACGCCGCTAATGCTCTGACCTTTTAGCGGCGCTTGGAC
1 ATAAACGCCGCTAATGCTCTGACC-TTTAGCGGCGCTTCCTC
* * *
256638 ATAAAAGCCGCTAATGCTCCGACCTTTAGCGGCGCTTTCAT-
1 ATAAACGCCGCTAATGCTCTGACCTTTAGCGGCGC-TTCCTC
256679 ATAAACGCCGCTA
1 ATAAACGCCGCTA
256692 TGAAAAACGC
Statistics
Matches: 216, Mismatches: 37, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
40 4 0.02
41 174 0.81
42 36 0.17
43 2 0.01
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.32
Consensus pattern (41 bp):
ATAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTCCTC
Found at i:256477 original size:82 final size:84
Alignment explanation
Indices: 256352--256691 Score: 358
Period size: 82 Copynumber: 4.1 Consensus size: 84
256342 ATTTTTGAGA
* * * *
256352 AAACACCGCTATTGCTC-AACCTTTAGCGGTGTTTTTCCAATAAACGTCGCTAATGCT-TAGACA
1 AAACGCCGCTAATGCTCTAACCTTTAGCGGTGTTTTTCC-ATAAACGCCGCTAATGCTCTAGACC
256415 TTTAGCGGCGC-TTCCTCAT
65 TTTAGCGGCGCTTTCCTCAT
* * *
256434 AAACGCCGCTAATGCTCTGACCTTTAGCGGTG-CTTTCTCATAAACGCCGCTAATGCTCTA-ATC
1 AAACGCCGCTAATGCTCTAACCTTTAGCGGTGTTTTTC-CATAAACGCCGCTAATGCTCTAGACC
* *
256497 TTTAGCGGCG-TTTTCTTAT
65 TTTAGCGGCGCTTTCCTCAT
* * * ** *
256516 AAATGCCGTTAATGCTCTAACTTTTAGTAGTGTTTTTCCATAAACGCCGCTAATTCTCT-GACCT
1 AAACGCCGCTAATGCTCTAACCTTTAGCGGTGTTTTTCCATAAACGCCGCTAATGCTCTAGACCT
*
256580 TTAGCGGTGCTTTCC-CAT
66 TTAGCGGCGCTTTCCTCAT
* * * *** * *
256598 AAACGCCGCTAATGCTCTGACCTTTTAGCGGCGCTTGGACATAAAAGCCGCTAATGCTC-CGACC
1 AAACGCCGCTAATGCTCTAACC-TTTAGCGGTGTTTTTCCATAAACGCCGCTAATGCTCTAGACC
*
256662 TTTAGCGGCGCTTTCAT-AT
65 TTTAGCGGCGCTTTCCTCAT
256681 AAACGCCGCTA
1 AAACGCCGCTA
256692 TGAAAAACGC
Statistics
Matches: 212, Mismatches: 36, Indels: 19
0.79 0.13 0.07
Matches are distributed among these distances:
82 130 0.61
83 82 0.39
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (84 bp):
AAACGCCGCTAATGCTCTAACCTTTAGCGGTGTTTTTCCATAAACGCCGCTAATGCTCTAGACCT
TTAGCGGCGCTTTCCTCAT
Found at i:258906 original size:41 final size:41
Alignment explanation
Indices: 258850--259177 Score: 337
Period size: 41 Copynumber: 8.4 Consensus size: 41
258840 TTAGCGACGC
258850 CTATTGCT-T-ACCTTTAGCGGCGCTTTCCCATAAGCGTCG
1 CTATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGTCG
* * * *
258889 TTATTGCTCTGACCTTTAGCAGCACTTTCCCATAAGCGCCG
1 CTATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGTCG
* *
258930 CTATTGCTCTGACCTTTAGCGGCACTTGCCCATAAGCGTCG
1 CTATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGTCG
* *
258971 CTATTGCTCTGACCTTTAGCGGCGCTTTCACATAAGCGACG
1 CTATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGTCG
* * **
259012 CTATTGCTTTGACCTTTAGCGACGCTTTAACATAAGCGTCG
1 CTATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGTCG
* *
259053 CTATTGCTCTGTCTTTTAGCGGCGC-TT---AT----G--G
1 CTATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGTCG
** ** *
259084 --ATTGCTCTGACCTTTAGCGAAGCTTTCCTGTAAGCGCCG
1 CTATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGTCG
* * *
259123 CTATTGCTCTGACCTTTAGCGGTGCTTTCCCGTAAGCG-CTA
1 CTATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGTC-G
259164 CTATTGCTCT-ACCT
1 CTATTGCTCTGACCT
259178 GTTGCAGCGT
Statistics
Matches: 245, Mismatches: 29, Indels: 29
0.81 0.10 0.10
Matches are distributed among these distances:
29 19 0.08
30 2 0.01
31 1 0.00
33 2 0.01
37 3 0.01
39 8 0.03
40 8 0.03
41 202 0.82
ACGTcount: A:0.17, C:0.29, G:0.21, T:0.33
Consensus pattern (41 bp):
CTATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGTCG
Found at i:259127 original size:70 final size:70
Alignment explanation
Indices: 259014--259149 Score: 184
Period size: 70 Copynumber: 1.9 Consensus size: 70
259004 AAGCGACGCT
* * * * *
259014 ATTGCTTTGACCTTTAGCGACGCTTTAACATAAGCGTCGCTATTGCTCTGTCTTTTAGCGGCGCT
1 ATTGCTCTGACCTTTAGCGAAGCTTTAACATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCT
259079 TATGG
66 TATGG
* * *
259084 ATTGCTCTGACCTTTAGCGAAGCTTT-CCTGTAAGCGCCGCTATTGCTCTGACCTTTAGCGGTGC
1 ATTGCTCTGACCTTTAGCGAAGCTTTAAC-ATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGC
259148 TT
65 TT
259150 TCCCGTAAGC
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
69 1 0.02
70 56 0.98
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (70 bp):
ATTGCTCTGACCTTTAGCGAAGCTTTAACATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCT
TATGG
Found at i:266577 original size:71 final size:71
Alignment explanation
Indices: 266501--266640 Score: 235
Period size: 71 Copynumber: 2.0 Consensus size: 71
266491 TATCCTTTTT
* *
266501 CTTTTTAAGAATTTTATAACTCTTTTAGATTTAATTTTGTTTTCAATAAATTAACATAGCACATT
1 CTTTTTAAGAATTTTAAAACTCTTTTAAATTTAATTTTGTTTTCAATAAATTAACATAGCACATT
266566 TTTTAA
66 TTTTAA
* * *
266572 CTTTTTAAGAATTTTAAAACTCTTTTAAATTTAATTTTGTTTTCAATAAATTAACTTATCATATT
1 CTTTTTAAGAATTTTAAAACTCTTTTAAATTTAATTTTGTTTTCAATAAATTAACATAGCACATT
266637 TTTT
66 TTTT
266641 TACCTATTTA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 64 1.00
ACGTcount: A:0.34, C:0.09, G:0.04, T:0.53
Consensus pattern (71 bp):
CTTTTTAAGAATTTTAAAACTCTTTTAAATTTAATTTTGTTTTCAATAAATTAACATAGCACATT
TTTTAA
Found at i:266854 original size:2 final size:2
Alignment explanation
Indices: 266849--266873 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
266839 TTTTTAACCT
266849 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
266874 TACTCTACGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:278011 original size:40 final size:40
Alignment explanation
Indices: 277960--278047 Score: 119
Period size: 40 Copynumber: 2.2 Consensus size: 40
277950 ATTAGCAAAC
*
277960 TAATAAA-TATTATTTTGA-G-TATTTAAGTTTTTTATATTT
1 TAATAAATTATTATTTTAAGGATATTT-A-TTTTTTATATTT
*
277999 TGATAAATTATTATTTTAAGGATATTTATTTTTTATATTT
1 TAATAAATTATTATTTTAAGGATATTTATTTTTTATATTT
278039 TAATAAATT
1 TAATAAATT
278048 TTAAAAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
39 6 0.14
40 30 0.70
41 2 0.05
42 5 0.12
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (40 bp):
TAATAAATTATTATTTTAAGGATATTTATTTTTTATATTT
Found at i:287225 original size:22 final size:22
Alignment explanation
Indices: 287197--287244 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
287187 AAATTTAGTG
* *
287197 AGCAGGTTCGCAGGTAATGGCT
1 AGCAGGTTCGCAGGCAATGCCT
287219 AGCAGGTTCGCAGGCAATGCCT
1 AGCAGGTTCGCAGGCAATGCCT
287241 AGCA
1 AGCA
287245 ATGAGCGGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.25, C:0.23, G:0.33, T:0.19
Consensus pattern (22 bp):
AGCAGGTTCGCAGGCAATGCCT
Found at i:287535 original size:22 final size:23
Alignment explanation
Indices: 287494--287536 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
287484 CCCGTTCATA
287494 TTATTATTTTTTAAATATTTATT
1 TTATTATTTTTTAAATATTTATT
287517 TTATT-TTATTTT-AATATTTA
1 TTATTATT-TTTTAAATATTTA
287537 ATAATTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TTATTATTTTTTAAATATTTATT
Found at i:289045 original size:4 final size:4
Alignment explanation
Indices: 289025--289088 Score: 69
Period size: 4 Copynumber: 15.8 Consensus size: 4
289015 GGAAAAAAAA
* *
289025 AAAG AAA- AAAG AGAG AAAG AAAG AAAG AAAG AAAG AAAG -AAG AAGGG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AA-AG
289072 AAAG AAGGAG AAAG AAA
1 AAAG AA--AG AAAG AAA
289089 AAAAAAAGGT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
3 6 0.12
4 38 0.75
5 3 0.06
6 4 0.08
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:289475 original size:20 final size:21
Alignment explanation
Indices: 289434--289476 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
289424 TAATTTACTT
289434 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
* *
289455 TAATTTTATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
289475 TA
1 TA
289477 GTAGTAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Found at i:289999 original size:16 final size:16
Alignment explanation
Indices: 289954--290003 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
289944 TAAACCTAGC
*
289954 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
289970 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
289984 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
290000 TAAT
1 TAAT
290004 ATCCCCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Done.