Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013078.1 Kokia drynarioides strain JFW-HI SEQ_128096, 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: 40475
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:304 original size:30 final size:30
Alignment explanation
Indices: 270--694 Score: 254
Period size: 30 Copynumber: 14.5 Consensus size: 30
260 GAAATTTCTG
270 AAAATCCCATTTTTAACCTCGAACCTTCCA
1 AAAATCCCATTTTTAACCTCGAACCTTCCA
** * *
300 AAAATTGC-TATTTTACCCTCGAA-CTTCTAA
1 AAAATCCCAT-TTTTAACCTCGAACCTTC-CA
* * *
330 AAAATCTCATTTTTGATCC-CGAACCTTCTA
1 AAAATCCCATTTTT-AACCTCGAACCTTCCA
* * *
360 AAAATTACCA-TTTTACCCCCGAA-CTTCCA
1 AAAA-TCCCATTTTTAACCTCGAACCTTCCA
* *
389 AAAATCCCATTTTTGACCCCGAACCTTCCA
1 AAAATCCCATTTTTAACCTCGAACCTTCCA
* * * * *
419 AAATTACCA-TTTT-ACCCCCAAACTTCCA
1 AAAATCCCATTTTTAACCTCGAACCTTCCA
* *
447 AAAATCCCATTTTAAACC-CTAAACCTTCCA
1 AAAATCCCATTTTTAACCTC-GAACCTTCCA
* * * *
477 AAATTACCA-ATTTACCCTCGAA-CTTCCA
1 AAAATCCCATTTTTAACCTCGAACCTTCCA
* * * *
505 AAAATCTCATTTTTAACCCCAAACTTTCCA
1 AAAATCCCATTTTTAACCTCGAACCTTCCA
* * * *
535 AAAATTACCA-TTTTACCCTC-AAACTTCTA
1 AAAA-TCCCATTTTTAACCTCGAACCTTCCA
* * *
564 AAAATCCCATTTTTGACCTCAAACCTTCTA
1 AAAATCCCATTTTTAACCTCGAACCTTCCA
* * * * *
594 AAAATTACC-GTTTCATCCTC-AAACTTCCA
1 AAAA-TCCCATTTTTAACCTCGAACCTTCCA
* *
623 AAAATCCCATTTTTGACC-CTGAACTTTCCA
1 AAAATCCCATTTTTAACCTC-GAACCTTCCA
* * *
653 AAATTACCA-TTTTACCCTCGAA-CTTCCA
1 AAAATCCCATTTTTAACCTCGAACCTTCCA
*
681 AAAATCCAATTTTT
1 AAAATCCCATTTTT
695 GATTACGAAT
Statistics
Matches: 300, Mismatches: 71, Indels: 49
0.71 0.17 0.12
Matches are distributed among these distances:
28 55 0.18
29 99 0.33
30 129 0.43
31 17 0.06
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32
Consensus pattern (30 bp):
AAAATCCCATTTTTAACCTCGAACCTTCCA
Found at i:550 original size:59 final size:59
Alignment explanation
Indices: 270--696 Score: 536
Period size: 58 Copynumber: 7.3 Consensus size: 59
260 GAAATTTCTG
* * * * *
270 AAAATCCCATTTTTAACCTCGAACCTTCCAAAAATTGCTATTTTACCCTCGAACTTCTAA
1 AAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTC-CA
* * * *
330 AAAATCTCATTTTTGATCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCA
1 AAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCA
* *
389 AAAATCCCATTTTTGACCCCGAACCTTCC-AAAATTACCATTTTACCCCCAAACTTCCA
1 AAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCA
** ** *
447 AAAATCCCATTTTAAACCCTAAACCTTCC-AAAATTACCAATTTACCCTCGAACTTCCA
1 AAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCA
* * * * * *
505 AAAATCTCATTTTTAACCCCAAACTTTCCAAAAATTACCATTTTACCCTCAAACTTCTA
1 AAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCA
* * * * * * *
564 AAAATCCCATTTTTGACCTCAAACCTTCTAAAAATTACCGTTTCATCCTCAAACTTCCA
1 AAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCA
* *
623 AAAATCCCATTTTTGACCCTGAACTTTCC-AAAATTACCATTTTACCCTCGAACTTCCA
1 AAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCA
*
681 AAAATCCAATTTTTGA
1 AAAATCCCATTTTTGA
697 TTACGAATAT
Statistics
Matches: 320, Mismatches: 46, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
58 144 0.45
59 127 0.40
60 49 0.15
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (59 bp):
AAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCA
Found at i:1090 original size:96 final size:96
Alignment explanation
Indices: 962--1152 Score: 255
Period size: 96 Copynumber: 2.0 Consensus size: 96
952 AAACTTTAAT
**
962 ATCGAGGCAATATTCGTTTATTTCGAGTTCCGAAA-ATTTGCGCCTTAACTCACTAGGTGCAATT
1 ATCGAGGCAATATTCGTTTATTTCGAGTTCCGAAATA-TTGCGCCTTAACTCACTAGGTGCAACC
*
1026 TTTCTTCAAATCGA-AGTAATCGAATACCCTTA
65 TTTCTTCAAATCGAGA-TAATCAAATACCCTTA
* * *
1058 ATCGAGGCAATGTT-TTCTTATCTTCGA-TTCCGAAATATTGCGCCTTAACTTACTAGGTGCAAC
1 ATCGAGGCAATATTCGT-TTAT-TTCGAGTTCCGAAATATTGCGCCTTAACTCACTAGGTGCAAC
*
1121 CTTTCTTCAAATCGAGATAATCAAATATCCTT
64 CTTTCTTCAAATCGAGATAATCAAATACCCTT
1153 CTCGCAAAAG
Statistics
Matches: 84, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
95 1 0.01
96 76 0.90
97 7 0.08
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (96 bp):
ATCGAGGCAATATTCGTTTATTTCGAGTTCCGAAATATTGCGCCTTAACTCACTAGGTGCAACCT
TTCTTCAAATCGAGATAATCAAATACCCTTA
Found at i:12449 original size:50 final size:49
Alignment explanation
Indices: 12371--12470 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 49
12361 CATTATCTTT
*
12371 GTTTTCGTTTCAGTTCCCACCTGCACTATTGCTCTTCCCTGGGTGTCTG
1 GTTTTCGTTTCAGTTCCCACCTGAACTATTGCTCTTCCCTGGGTGTCTG
12420 NGTTTTCGTTTCAGTTCCCACCTGAACTATTGCTCTTCCCTGGGTGTCTG
1 -GTTTTCGTTTCAGTTCCCACCTGAACTATTGCTCTTCCCTGGGTGTCTG
12470 G
1 G
12471 CATTCTGTAG
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 1 0.02
50 48 0.98
ACGTcount: A:0.09, C:0.29, G:0.21, T:0.40
Consensus pattern (49 bp):
GTTTTCGTTTCAGTTCCCACCTGAACTATTGCTCTTCCCTGGGTGTCTG
Found at i:14115 original size:30 final size:30
Alignment explanation
Indices: 14081--14140 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
14071 GATACAAGTG
14081 AGATTTCTA-CTGATACTTATCATGCTTCTA
1 AGATTTCTATC-GATACTTATCATGCTTCTA
*
14111 AGATTTCTATCGATACTTATCCTGCTTCTA
1 AGATTTCTATCGATACTTATCATGCTTCTA
14141 CTGATACTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.25, C:0.22, G:0.10, T:0.43
Consensus pattern (30 bp):
AGATTTCTATCGATACTTATCATGCTTCTA
Found at i:16197 original size:20 final size:20
Alignment explanation
Indices: 16161--16210 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
16151 TCATTAAGCT
*
16161 TTAATTAACCACTTTTA-ATC
1 TTAATTAAACACTTTTACA-C
16181 TTAATTAAAC-CTATTTACAC
1 TTAATTAAACACT-TTTACAC
16201 TTAATATAAA
1 TTAAT-TAAA
16211 TCATGTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 19 0.73
21 5 0.19
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAATTAAACACTTTTACAC
Found at i:17091 original size:19 final size:19
Alignment explanation
Indices: 17049--17088 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
17039 ACAACTAAGT
* *
17049 AAACTACTGATACTTTATG
1 AAACTACCGATACTTGATG
17068 AAACTACCGATACTTGA-G
1 AAACTACCGATACTTGATG
17086 AAA
1 AAA
17089 ACTTTTACTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.28
Consensus pattern (19 bp):
AAACTACCGATACTTGATG
Found at i:18027 original size:158 final size:158
Alignment explanation
Indices: 17739--18046 Score: 400
Period size: 158 Copynumber: 1.9 Consensus size: 158
17729 TCATGTATTA
*
17739 CTCACACGAGCTGTGAAATAGGCCTGCTCACACGAGCTATAGGTCGAAATGTTAGACTATACGAT
1 CTCACACGAGCTGTGAAATAGGCCTGCTCACACGAGCTATAGGTCGAAATGTTAGACTACACGAT
* ** * * * *
17804 ACTTCTCACTTGAGCTATGGAAAATCCGTAATAAATGTCGGATCTCAGCCATCAGTAGGACATCT
66 ACTGCTCACACGAGCTATGGAAAATCCGCAATAAATGCCAGATCTCAGCCATCAATAGGACATCT
*
17869 AAGACCAGCACCTATATAACGTGTAATG
131 AAGACCAGCACCCATATAACGTGTAATG
* * * * * * * * * *
17897 CTCACATGAGCTGTGAAGTGGGCCTGCTCATATGAGCTGTGGGTTGAGATGTTAGGCTACACGAT
1 CTCACACGAGCTGTGAAATAGGCCTGCTCACACGAGCTATAGGTCGAAATGTTAGACTACACGAT
* * * *
17962 GCTGCTCACACGAGCTGTGGAGAATCCGCATTAAATGCCAGATCTCAGCCATCAATAGGACATCT
66 ACTGCTCACACGAGCTATGGAAAATCCGCAATAAATGCCAGATCTCAGCCATCAATAGGACATCT
*
18027 AAGACTAGCACCCATATAAC
131 AAGACCAGCACCCATATAAC
18047 CTATAAATTC
Statistics
Matches: 126, Mismatches: 24, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
158 126 1.00
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.24
Consensus pattern (158 bp):
CTCACACGAGCTGTGAAATAGGCCTGCTCACACGAGCTATAGGTCGAAATGTTAGACTACACGAT
ACTGCTCACACGAGCTATGGAAAATCCGCAATAAATGCCAGATCTCAGCCATCAATAGGACATCT
AAGACCAGCACCCATATAACGTGTAATG
Found at i:26064 original size:191 final size:196
Alignment explanation
Indices: 25712--26148 Score: 548
Period size: 195 Copynumber: 2.2 Consensus size: 196
25702 CGATGATTGT
* * * *
25712 GGTACCGCATGTGTTGCGAGTCCTCGCTAGCTCGTGTGAGCAGCATCGTGAGTCGAAAAAAGAGA
1 GGTACCGCATATGTTGCGAGTCCTCGATAGCTCGTGTGAGCAGCATCATGACTCGAAAAAAGAGA
* * ** *
25777 TATGGATCCTAGAATGGATTACAGGCCCTAGGATGGCTGAGATTTATGTATAAATGCATATTCTC
66 TATGGACCCTAGAATGGATTACAGACCCTACAATGGCTGAGATCTATGTATAAATGCATATTCTC
* * *
25842 GATAGCTCGTGTGAGCAGCATCGTAAAGGAAC-AGTTATATGCACAGAT-ACCGTATCGATGGCT
131 GATAGCTCGTATGAGCAGCATCGTAAAGGAACAATTTATA-GCACAGATGACCGTACCGATGGCT
25905 -G
195 AG
* **
25906 AGGTACCGCATATGTTGCGAGTCCTCGATAGCTCGTGTGAGTAGCATCATGACTCG-GGAAAGAG
1 -GGTACCGCATATGTTGCGAGTCCTCGATAGCTCGTGTGAGCAGCATCATGACTCGAAAAAAGAG
* *
25970 ATATGGACCCTA-AATGGATTACAGACCCTACAATGGCTGGGA-CTATGCT-T-ATTGCATATTC
65 ATATGGACCCTAGAATGGATTACAGACCCTACAATGGCTGAGATCTATG-TATAAATGCATATTC
* *
26031 TCGATAGCTCGTATGAGCAGCATCGTTAAGGAACAATTTATAGTACAGATAGGCACCGTACCGAT
129 TCGATAGCTCGTATGAGCAGCATCGTAAAGGAACAATTTATAGCACAGAT--G-ACCGTACCGAT
26096 GGCTAG
191 GGCTAG
* * * * *
26102 GGTACCGCATACGTTACGAGTCCTCAACAGCTCGTGTGGGCAGCATC
1 GGTACCGCATATGTTGCGAGTCCTCGATAGCTCGTGTGAGCAGCATC
26149 GAGTACTGGT
Statistics
Matches: 210, Mismatches: 25, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
191 49 0.23
192 11 0.05
193 27 0.13
194 17 0.08
195 105 0.50
196 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (196 bp):
GGTACCGCATATGTTGCGAGTCCTCGATAGCTCGTGTGAGCAGCATCATGACTCGAAAAAAGAGA
TATGGACCCTAGAATGGATTACAGACCCTACAATGGCTGAGATCTATGTATAAATGCATATTCTC
GATAGCTCGTATGAGCAGCATCGTAAAGGAACAATTTATAGCACAGATGACCGTACCGATGGCTA
G
Found at i:26953 original size:21 final size:21
Alignment explanation
Indices: 26902--26953 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
26892 AGAGTTTTTA
26902 GTATCGGTAGAAGCATTACAT
1 GTATCGGTAGAAGCATTACAT
* * *
26923 GTTTCAGTAGAAGTCA-TACTT
1 GTATCGGTAGAAG-CATTACAT
26944 GTATCGGTAG
1 GTATCGGTAG
26954 TATTGTCTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (21 bp):
GTATCGGTAGAAGCATTACAT
Found at i:29493 original size:9 final size:9
Alignment explanation
Indices: 29475--29540 Score: 55
Period size: 9 Copynumber: 7.1 Consensus size: 9
29465 TACATACATG
29475 AATAAAATA
1 AATAAAATA
29484 AA-ATAAATA
1 AATA-AAATA
*
29493 AATACAATTA
1 AATA-AAATA
*
29503 AATAAAATT
1 AATAAAATA
*
29512 AATAACATA
1 AATAAAATA
29521 AATAATAAT-
1 AATAA-AATA
29530 AATAATAATA
1 AATAA-AATA
29540 A
1 A
29541 TAATAGTGAT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
8 1 0.02
9 33 0.72
10 12 0.26
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (9 bp):
AATAAAATA
Found at i:29529 original size:3 final size:3
Alignment explanation
Indices: 29521--29545 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
29511 TAATAACATA
29521 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
29546 GTGATAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:29986 original size:11 final size:11
Alignment explanation
Indices: 29970--29996 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
29960 AGACCCGAAA
29970 AAACCTTTTTT
1 AAACCTTTTTT
29981 AAACCTTTTTT
1 AAACCTTTTTT
29992 AAACC
1 AAACC
29997 CTAAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (11 bp):
AAACCTTTTTT
Found at i:34608 original size:38 final size:38
Alignment explanation
Indices: 34557--34632 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
34547 ATTATGCCTT
34557 TTTTATAAAAATGATGGACTAATTGGATAATTTTTATA
1 TTTTATAAAAATGATGGACTAATTGGATAATTTTTATA
34595 TTTTATAAAAATGATGGACTAATTGGATAATTTTTATA
1 TTTTATAAAAATGATGGACTAATTGGATAATTTTTATA
34633 ATTGTCTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.39, C:0.03, G:0.13, T:0.45
Consensus pattern (38 bp):
TTTTATAAAAATGATGGACTAATTGGATAATTTTTATA
Found at i:36003 original size:25 final size:23
Alignment explanation
Indices: 35963--36008 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
35953 CTAATTAGGG
35963 AATTATTATTTAAATTTAATTCT
1 AATTATTATTTAAATTTAATTCT
*
35986 AATTATCTTTTTACAATTTAATT
1 AATTAT-TATTTA-AATTTAATT
36009 TGGGTCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 5 0.25
25 9 0.45
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (23 bp):
AATTATTATTTAAATTTAATTCT
Done.