Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006462.1 Kokia drynarioides strain JFW-HI SEQ_121045, 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: 58304
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3089 original size:19 final size:19
Alignment explanation
Indices: 3065--3102 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
3055 AATATTTTTT
3065 TATTTTT-TTATTTTTCTCA
1 TATTTTTCTT-TTTTTCTCA
3084 TATTTTTCTTTTTTTCTCA
1 TATTTTTCTTTTTTTCTCA
3103 ACTTTTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (19 bp):
TATTTTTCTTTTTTTCTCA
Found at i:16458 original size:23 final size:23
Alignment explanation
Indices: 16428--16473 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
16418 GTATCAGATC
16428 GTAAATATTAATTATTTAATATT
1 GTAAATATTAATTATTTAATATT
16451 GTAAATATTAATTATTTAATATT
1 GTAAATATTAATTATTTAATATT
16474 TACGAGGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (23 bp):
GTAAATATTAATTATTTAATATT
Found at i:17921 original size:195 final size:195
Alignment explanation
Indices: 17582--18026 Score: 723
Period size: 195 Copynumber: 2.3 Consensus size: 195
17572 AATTGACGCA
** *
17582 ATGGTTGAGGTACTACATATGTTGCGAGTCCTCGACAACTCGTGTGAGCAGCATCGTGAGTCGAG
1 ATGGTTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTCGAG
17647 AAATGAGAAAAGAATCCAAGAATGGATTATAGGCCTTACGATGGCTGAGATTTATGCATAAGTGC
66 AAATGAGAAAAGAATCCAAGAATGGATTATAGGCCTTACGATGGCTGAGATTTATGCATAAGTGC
* * * * *
17712 ATATTCTTGATAGCTTGTGTGAGTAGCATCGTTAGGGAACAGTTATATGCACAGATATCGCATCG
131 ATATTCTCGATAGCTCGTGTGAGCAGCATCATTAGAGAACAGTTATATGCACAGATATCGCATCG
* **
17777 ATGGTTGAGGTACCGCATATGTTGCAAGTCCTCGACAGCTTATGTGAGCAGCATCGTGAGTC-AT
1 ATGGTTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTCGA-
*
17841 GAAATGAGAAAATAATCCAAGAATGGATTATAGGCCTTACGATGGCTGAGATTTATGCATAAGTG
65 GAAATGAGAAAAGAATCCAAGAATGGATTATAGGCCTTACGATGGCTGAGATTTATGCATAAGTG
*
17906 CATATTCTCGATAGCTCGTGTGAGCAGCATCATTAGAGAACAGTTATATGCATAGATATCGCATC
130 CATATTCTCGATAGCTCGTGTGAGCAGCATCATTAGAGAACAGTTATATGCACAGATATCGCATC
17971 G
195 G
* * *
17972 ATAGTTGAGGTACCGCATATGTTG-GAGTCCTCAATAGCTCGTGTGAGCAGCATCG
1 ATGGTTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCG
18027 AGTACTGGTA
Statistics
Matches: 230, Mismatches: 19, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
194 27 0.12
195 203 0.88
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (195 bp):
ATGGTTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTCGAG
AAATGAGAAAAGAATCCAAGAATGGATTATAGGCCTTACGATGGCTGAGATTTATGCATAAGTGC
ATATTCTCGATAGCTCGTGTGAGCAGCATCATTAGAGAACAGTTATATGCACAGATATCGCATCG
Found at i:19909 original size:24 final size:25
Alignment explanation
Indices: 19875--19930 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
19865 AAAAGTGAAA
*
19875 AAAAAAAGAAA-TTTGAAAATAGTG
1 AAAAAAAGAAACTTCGAAAATAGTG
*
19899 AAAAAAGGAAACTTCGAAAATAGTG
1 AAAAAAAGAAACTTCGAAAATAGTG
19924 AAAAAAA
1 AAAAAAA
19931 AAAGAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 10 0.36
25 18 0.64
ACGTcount: A:0.64, C:0.04, G:0.16, T:0.16
Consensus pattern (25 bp):
AAAAAAAGAAACTTCGAAAATAGTG
Found at i:22453 original size:31 final size:31
Alignment explanation
Indices: 22391--22453 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
22381 TTCAGTTTAA
*
22391 TAAGTGTTTGCATCTTTAATTATATCTTGCAT
1 TAAGTGTTTGCA-CTTTAATTATATCATGCAT
22423 TAAGTGTTTTGCA-TTTAATTA-AGTCATGCAT
1 TAAGTG-TTTGCACTTTAATTATA-TCATGCAT
22454 AAAAGCATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 1 0.04
31 15 0.54
32 6 0.21
33 6 0.21
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (31 bp):
TAAGTGTTTGCACTTTAATTATATCATGCAT
Found at i:37371 original size:17 final size:17
Alignment explanation
Indices: 37327--37377 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
37317 TTAAAATGAC
*
37327 TATATAAAAAAATTAAA
1 TATATAAAAATATTAAA
*
37344 TAAATAAAAATATATAAA
1 TATATAAAAATAT-TAAA
* *
37362 AATAT-TAAATATTAAA
1 TATATAAAAATATTAAA
37378 ATAATATAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 4 0.14
17 17 0.61
18 7 0.25
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TATATAAAAATATTAAA
Found at i:37373 original size:15 final size:16
Alignment explanation
Indices: 37328--37392 Score: 54
Period size: 15 Copynumber: 4.4 Consensus size: 16
37318 TAAAATGACT
37328 ATATAAAAA-AAT-TA
1 ATATAAAAATAATATA
37342 A-ATAAATAA-AA-AT-
1 ATATAAA-AATAATATA
*
37355 ATATAAAAATATTA-A
1 ATATAAAAATAATATA
*
37370 ATATTAAAATAATATA
1 ATATAAAAATAATATA
37386 ATATAAA
1 ATATAAA
37393 TATTTTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
13 8 0.20
14 12 0.30
15 13 0.32
16 7 0.17
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
ATATAAAAATAATATA
Found at i:37388 original size:16 final size:15
Alignment explanation
Indices: 37345--37392 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
37335 AAAATTAAAT
*
37345 AAATAAAAATATATAA
1 AAATAATAA-ATATAA
* *
37361 AAATATTAAATATTA
1 AAATAATAAATATAA
37376 AAATAATATAATATAA
1 AAATAATA-AATATAA
37392 A
1 A
37393 TATTTTTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATAATAAATATAA
Found at i:38186 original size:14 final size:14
Alignment explanation
Indices: 38167--38197 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
38157 TTGTTAGATA
*
38167 AGTGATTCTTATTT
1 AGTGATTCTTATAT
38181 AGTGATTCTTATAT
1 AGTGATTCTTATAT
38195 AGT
1 AGT
38198 TTTTGGAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.16, T:0.52
Consensus pattern (14 bp):
AGTGATTCTTATAT
Found at i:42998 original size:15 final size:14
Alignment explanation
Indices: 42965--43015 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 14
42955 ATAAACATAC
42965 ACCAAACCAAACCCA-
1 ACCAAACC-AA-CCAT
42980 ACCAAACCAAGCCAT
1 ACCAAACCAA-CCAT
*
42995 ACCATACCATACCAT
1 ACCAAACCA-ACCAT
43010 ACCAAA
1 ACCAAA
43016 ATAAAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
14 5 0.16
15 25 0.81
16 1 0.03
ACGTcount: A:0.49, C:0.41, G:0.02, T:0.08
Consensus pattern (14 bp):
ACCAAACCAACCAT
Found at i:47219 original size:13 final size:13
Alignment explanation
Indices: 47201--47227 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
47191 ATATGCAAAT
47201 AATAAAAAATAAA
1 AATAAAAAATAAA
47214 AATAAAAAATAAA
1 AATAAAAAATAAA
47227 A
1 A
47228 CAAATCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AATAAAAAATAAA
Found at i:53364 original size:24 final size:24
Alignment explanation
Indices: 53331--53381 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
53321 AGAAATAATC
* *
53331 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
53355 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
53379 TTT
1 TTT
53382 GAGCCAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.08, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATTTG
Found at i:53390 original size:24 final size:24
Alignment explanation
Indices: 53339--53393 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
53329 TCTTTCAGTT
* **
53339 AAACTCTGTTTATTTGTTTCAATT
1 AAACTCTATTTATTTGTTTCAACC
* *
53363 AAACTCTATTTATTTGTTTGAGCC
1 AAACTCTATTTATTTGTTTCAACC
53387 AAACTCT
1 AAACTCT
53394 TATTAGTCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.47
Consensus pattern (24 bp):
AAACTCTATTTATTTGTTTCAACC
Done.