Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003617.1 Kokia drynarioides strain JFW-HI SEQ_116509, 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: 4480
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Found at i:2334 original size:38 final size:38
Alignment explanation
Indices: 2262--2339 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 38
2252 TATTCGATCT
2262 TTTACCCCTAACTCAAGAGGGGCAAATTGAAGCCAGTCA
1 TTTACCCCTAACTCAAGAGGGGCAAATTGAAGCCA-TCA
* * * *
2301 TTTACCCC-AAGTCAATAGGGGCAGATTGCAGCCATCA
1 TTTACCCCTAACTCAAGAGGGGCAAATTGAAGCCATCA
2338 TT
1 TT
2340 CAATCATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 5 0.14
38 22 0.63
39 8 0.23
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.23
Consensus pattern (38 bp):
TTTACCCCTAACTCAAGAGGGGCAAATTGAAGCCATCA
Found at i:2420 original size:46 final size:45
Alignment explanation
Indices: 2301--2455 Score: 140
Period size: 45 Copynumber: 3.5 Consensus size: 45
2291 AAGCCAGTCA
* * * * *
2301 TTTACCCC-AAGTCAATAGGGGCAGATTGCAGCCATCA-TTCAATCA
1 TTTACCCCTAAGTCAAGA-AGGCAGATTGAAACCA-CATTTCAATCT
*
2346 TTTA-CCCTAAGTCAAGAGAGGCAGATTGAAACCGCATTTCAATCT
1 TTTACCCCTAAGTCAAGA-AGGCAGATTGAAACCACATTTCAATCT
* * * **
2391 TTTACCCCTAAGTCAAGAAGGCCATATTGAAGCTACATTTTGATCT
1 TTTACCCCTAAGTCAAGAAGG-CAGATTGAAACCACATTTCAATCT
2437 TTTACCCCT-AGTCAA-AAGG
1 TTTACCCCTAAGTCAAGAAGG
2456 GGCAGATCAA
Statistics
Matches: 94, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
44 9 0.10
45 45 0.48
46 40 0.43
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.28
Consensus pattern (45 bp):
TTTACCCCTAAGTCAAGAAGGCAGATTGAAACCACATTTCAATCT
Found at i:2572 original size:85 final size:85
Alignment explanation
Indices: 2463--2639 Score: 228
Period size: 85 Copynumber: 2.1 Consensus size: 85
2453 AGGGGCAGAT
* * ** *
2463 CAAACTCCATCTTCTTGATAAGATACAGAGAAGTGGGTCAAAGCAATAAAATGGTCATCTTTCTG
1 CAAA-TCCATCTTCTTGATAAGATACAAAGAAGTGGATCAAAGCAATAAAACAGTCATCTTCCTG
2528 ATGAGATACAGAGAAGTAAAC
65 ATGAGATACAGAGAAGTAAAC
* * * * * **
2549 TAAATCCATCTTCTTGATGAGATACAAAGAAGTGGATTAAATCAATGAGGCAGTCATCTTCCTGA
1 CAAATCCATCTTCTTGATAAGATACAAAGAAGTGGATCAAAGCAATAAAACAGTCATCTTCCTGA
*
2614 TGAGATACAGAGAAGTAGAC
66 TGAGATACAGAGAAGTAAAC
2634 CAAATC
1 CAAATC
2640 AATGAAGCAA
Statistics
Matches: 77, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
85 74 0.96
86 3 0.04
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (85 bp):
CAAATCCATCTTCTTGATAAGATACAAAGAAGTGGATCAAAGCAATAAAACAGTCATCTTCCTGA
TGAGATACAGAGAAGTAAAC
Found at i:2985 original size:209 final size:207
Alignment explanation
Indices: 2464--3255 Score: 1047
Period size: 209 Copynumber: 3.8 Consensus size: 207
2454 GGGGCAGATC
* * *
2464 AAACTCCATCTTCTTGATAAGATACAGAGAAGTGGGTCAAAGCAATAAAATGGTCATCTTTCTGA
1 AAAC-CCATCTTCTTGATAAGATACAGAGAAGTGGGTCAAAGCAATAAAACGGTCACCTTCCTGA
* * * * *
2529 TGAGATACAGAGAAGTAAACTAAATCCATCTTCTTGATGAGATACAAAGAAGTGGATTAAATCAA
65 TGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAA
2594 TGAGGCAGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATG
130 TGAGGCAGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATG
2659 TGAGTGAAACTTA
195 TGAGTGAAACTTA
* * * ** *
2672 AAACACCATCTTCTTGATGAGATACAGAGAAATGGGTCGAAGCAATAAAGTGGTAACCTTCCTGA
1 AAAC-CCATCTTCTTGATAAGATACAGAGAAGTGGGTCAAAGCAATAAAACGGTCACCTTCCTGA
* *
2737 TGAGATGCAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGATATAGAGAAGTGGATTAAAAT-A
65 TGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGATACAGAGAAGTGGATT-AAATCA
* * * * * * *
2801 ATGAGGC-GATCATCTTCCTGATGGGATACTGAGAATTAGACCAAATCGATGAAACAAAACTCGA
129 ATGAGGCAG-TCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAA
* *
2865 TATGAGTGAAACTTT
193 TGTGAGTGAAACTTA
*
2880 AAACCCTTATCTT-TCTGATAAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGGTCACCTTCCT
1 AAACCC--ATCTTCT-TGATAAGATACAGAGAAGTGGGTCAAAGCAATAAAACGGTCACCTTCCT
*
2944 GATGAGATACAGAGAAGT-AGACCAAATCTGTCTTCCTGATGAGATACAGAGAAGTGGATTAAAT
63 GATGAGATACAGAGAAGTGA-ACCAAATCCGTCTTCCTGATGAGATACAGAGAAGTGGATTAAAT
* * * * * *
3008 CAATGAGACATTGATCTTCCTAATGAGATACAAATAAGTAGACCAAATCAATGAAGCAAAGCTCA
127 CAATGAGGCAGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAGCTCA
3073 ATGTGAGTGAAACTTCA
192 ATGTGAGTGAAACTT-A
* * * * *
3090 AACCCCCATCTTCTTGATGAGATATAGAGAAGTGGGTTAAAGCAATAAAACGGTTACCTTCCTGA
1 AA-ACCCATCTTCTTGATAAGATACAGAGAAGTGGGTCAAAGCAATAAAACGGTCACCTTCCTGA
* * *
3155 TGAGATACAAAGAAGTGAACCAAATCCGTCTT-CTTACTGAGATACAGAGAAGTGGATTAAAACA
65 TGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGA-TGAGATACAGAGAAGTGGATTAAATCA
* *
3219 ATGAGG-TGATCATCTTCCTGATGAGATATAGAGAAGT
129 ATGAGGCAG-TCATCTTCCTGATGAGATACAGAGAAGT
3256 GGGTCAAAGC
Statistics
Matches: 505, Mismatches: 65, Indels: 27
0.85 0.11 0.05
Matches are distributed among these distances:
207 3 0.01
208 190 0.38
209 305 0.60
210 4 0.01
211 3 0.01
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.24
Consensus pattern (207 bp):
AAACCCATCTTCTTGATAAGATACAGAGAAGTGGGTCAAAGCAATAAAACGGTCACCTTCCTGAT
GAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAAT
GAGGCAGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATGT
GAGTGAAACTTA
Found at i:3254 original size:48 final size:48
Alignment explanation
Indices: 3192--3388 Score: 141
Period size: 48 Copynumber: 4.3 Consensus size: 48
3182 GTCTTCTTAC
*
3192 TGAGATACAGAGAAGTGGATTAAAACAATGAGGTGATCATCTTCCTGA
1 TGAGATATAGAGAAGTGGATTAAAACAATGAGGTGATCATCTTCCTGA
* * * * * * * *
3240 TGAGATATAGAGAAGTGGGTCAAAGCAATAAAG-CAGTCACCTTCTTGA
1 TGAGATATAGAGAAGTGGATTAAAACAATGAGGTGA-TCATCTTCCTGA
* * *
3288 TGAGATACAGAGAAGT-G----AACCAA--A--T--CCATCTTCCTGA
1 TGAGATATAGAGAAGTGGATTAAAACAATGAGGTGATCATCTTCCTGA
* * * *
3325 TGAGAAATAGAGAAGTGGATTAAAATAATGAGGCGGTCATCTTCCTGA
1 TGAGATATAGAGAAGTGGATTAAAACAATGAGGTGATCATCTTCCTGA
3373 TGAGATACT-GAGAAGT
1 TGAGATA-TAGAGAAGT
3389 AAACCAAATT
Statistics
Matches: 114, Mismatches: 21, Indels: 28
0.70 0.13 0.17
Matches are distributed among these distances:
37 23 0.20
38 1 0.01
41 1 0.01
42 4 0.04
43 5 0.04
44 1 0.01
47 2 0.02
48 76 0.67
49 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.24
Consensus pattern (48 bp):
TGAGATATAGAGAAGTGGATTAAAACAATGAGGTGATCATCTTCCTGA
Found at i:3281 original size:342 final size:342
Alignment explanation
Indices: 2888--3515 Score: 972
Period size: 342 Copynumber: 1.8 Consensus size: 342
2878 TTAAACCCTT
* *
2888 ATCTTTCTGATAAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGGTCACCTTCCTGATGAGATA
1 ATCTTCCTGATAAGATACAGAGAAGTGGGTCAAAGCAATAAAGCAGTCACCTTCCTGATGAGATA
** *
2953 CAGAGAAGT-AGACCAAATCTGTCTTCCTGATGAGATACAGAGAAGTGGATT-AAATCAATGAGA
66 CAGAGAAGTGA-ACCAAATCCATCTTCCTGATGAGAAACAGAGAAGTGGATTAAAAT-AATGAGA
* * * * *
3016 CATTGATCTTCCTAATGAGATACAAATAAGTAGACCAAATCAATGAAGCAAAGCTCAATGTGAGT
129 CAGTCATCTTCCTAATGAGATACAAAGAAGTAAACCAAATCAATGAAGCAAAACTCAATGTGAGT
* * * *
3081 GAAACTTCAAACCCCCATCTTCTTGATGAGATATAGAGAAGTGGGTTAAAGCAATAAAACGGTTA
194 GAAACTTCAAACCCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAACGGTCA
3146 CCTTCCTGATGAGATACAAAGAAGTGAACCAAATCCGTCTTCTTACTGAGATACAGAGAAGTGGA
259 CCTTCCTGATGAGATACAAAGAAGTGAACCAAATCCGTCTTCTTACTGAGATACAGAGAAGTGGA
3211 TTAAAACAATGAGGTGATC
324 TTAAAACAATGAGGTGATC
* * *
3230 ATCTTCCTGATGAGATATAGAGAAGTGGGTCAAAGCAATAAAGCAGTCACCTTCTTGATGAGATA
1 ATCTTCCTGATAAGATACAGAGAAGTGGGTCAAAGCAATAAAGCAGTCACCTTCCTGATGAGATA
* * *
3295 CAGAGAAGTGAACCAAATCCATCTTCCTGATGAGAAATAGAGAAGTGGATTAAAATAATGAGGCG
66 CAGAGAAGTGAACCAAATCCATCTTCCTGATGAGAAACAGAGAAGTGGATTAAAATAATGAGACA
* ** **
3360 GTCATCTTCCTGATGAGATACTGAGAAGTAAACCAAATTGATGAAGCAAAACTCAATGTGAGTGA
131 GTCATCTTCCTAATGAGATACAAAGAAGTAAACCAAATCAATGAAGCAAAACTCAATGTGAGTGA
* *
3425 AACTTCAAACCCCTATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGGTCACC
196 AACTTCAAACCCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAACGGTCACC
*
3490 TTCCTGATGAGATACAGAGAAGTGAA
261 TTCCTGATGAGATACAAAGAAGTGAA
3516 TTAAAACAAT
Statistics
Matches: 256, Mismatches: 28, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
342 251 0.98
343 5 0.02
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (342 bp):
ATCTTCCTGATAAGATACAGAGAAGTGGGTCAAAGCAATAAAGCAGTCACCTTCCTGATGAGATA
CAGAGAAGTGAACCAAATCCATCTTCCTGATGAGAAACAGAGAAGTGGATTAAAATAATGAGACA
GTCATCTTCCTAATGAGATACAAAGAAGTAAACCAAATCAATGAAGCAAAACTCAATGTGAGTGA
AACTTCAAACCCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAACGGTCACC
TTCCTGATGAGATACAAAGAAGTGAACCAAATCCGTCTTCTTACTGAGATACAGAGAAGTGGATT
AAAACAATGAGGTGATC
Found at i:3322 original size:85 final size:85
Alignment explanation
Indices: 3229--3397 Score: 230
Period size: 85 Copynumber: 2.0 Consensus size: 85
3219 ATGAGGTGAT
* * * *
3229 CATCTTCCTGATGAGATATAGAGAAGTGGGTCAAAGCAATAAAGCAGTCACCTTCTTGATGAGAT
1 CATCTTCCTGATGAGAAATAGAGAAGTGGATCAAAACAATAAAGCAGTCACCTTCCTGATGAGAT
*
3294 ACAGAGAAGTGAACCAAATC
66 ACAGAGAAGTAAACCAAATC
* * * * * *
3314 CATCTTCCTGATGAGAAATAGAGAAGTGGATTAAAATAATGAGGCGGTCATCTTCCTGATGAGAT
1 CATCTTCCTGATGAGAAATAGAGAAGTGGATCAAAACAATAAAGCAGTCACCTTCCTGATGAGAT
*
3379 ACTGAGAAGTAAACCAAAT
66 ACAGAGAAGTAAACCAAAT
3398 TGATGAAGCA
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
85 72 1.00
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (85 bp):
CATCTTCCTGATGAGAAATAGAGAAGTGGATCAAAACAATAAAGCAGTCACCTTCCTGATGAGAT
ACAGAGAAGTAAACCAAATC
Found at i:3337 original size:133 final size:133
Alignment explanation
Indices: 3096--3388 Score: 428
Period size: 133 Copynumber: 2.2 Consensus size: 133
3086 TTCAAACCCC
* * * *
3096 CATCTTCTTGATGAGATATAGAGAAGTGGGTTAAAGCAATAAAACGGTTACCTTCCTGATGAGAT
1 CATCTTCCTGATGAGATATAGAGAAGTGGGTCAAAGCAATAAAACAGTCACCTTCCTGATGAGAT
* * * *
3161 ACAAAGAAGTGAACCAAATCCGTCTTCTTACTGAGATACAGAGAAGTGGATTAAAACAATGAGGT
66 ACAAAGAAGTGAACCAAATCCATCTTCTGACTGAGAAACAGAGAAGTGGATTAAAACAATGAGGC
3226 GAT
131 GAT
* *
3229 CATCTTCCTGATGAGATATAGAGAAGTGGGTCAAAGCAATAAAGCAGTCACCTTCTTGATGAGAT
1 CATCTTCCTGATGAGATATAGAGAAGTGGGTCAAAGCAATAAAACAGTCACCTTCCTGATGAGAT
* * *
3294 ACAGAGAAGTGAACCAAATCCATCTTCCTGA-TGAGAAATAGAGAAGTGGATTAAAATAATGAGG
66 ACAAAGAAGTGAACCAAATCCATCTT-CTGACTGAGAAACAGAGAAGTGGATTAAAACAATGAGG
*
3358 CGGT
130 CGAT
3362 CATCTTCCTGATGAGATACT-GAGAAGT
1 CATCTTCCTGATGAGATA-TAGAGAAGT
3389 AAACCAAATT
Statistics
Matches: 144, Mismatches: 14, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
133 140 0.97
134 4 0.03
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (133 bp):
CATCTTCCTGATGAGATATAGAGAAGTGGGTCAAAGCAATAAAACAGTCACCTTCCTGATGAGAT
ACAAAGAAGTGAACCAAATCCATCTTCTGACTGAGAAACAGAGAAGTGGATTAAAACAATGAGGC
GAT
Found at i:3496 original size:48 final size:48
Alignment explanation
Indices: 3441--3560 Score: 159
Period size: 48 Copynumber: 2.5 Consensus size: 48
3431 AAACCCCTAT
** * *
3441 CTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGGTCAC
1 CTTCCTGATGAGATACAGAGAAGTGAATCAAAACAATAAAGCGATCAC
* * * *
3489 CTTCCTGATGAGATACAGAGAAGTGAATTAAAACAATGAGGCGATCAT
1 CTTCCTGATGAGATACAGAGAAGTGAATCAAAACAATAAAGCGATCAC
*
3537 CTTCCTGATGAGATTCAGAGAAGT
1 CTTCCTGATGAGATACAGAGAAGT
3561 AGACCAAATC
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 63 1.00
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (48 bp):
CTTCCTGATGAGATACAGAGAAGTGAATCAAAACAATAAAGCGATCAC
Found at i:3529 original size:172 final size:172
Alignment explanation
Indices: 3317--3684 Score: 495
Period size: 172 Copynumber: 2.1 Consensus size: 172
3307 CCAAATCCAT
* * * * * *
3317 CTTCCTGATGAGAAATAGAGAAGTGGATTAAAATAATGAGGCGGTCATCTTCCTGATGAGATACT
1 CTTCCTGATGAGATACAGAGAAGTGAATTAAAACAATGAGGCGATCATCTTCCTGATGAGATACA
* * *
3382 GAGAAGTAAACCAAATTGATGAAGCAAAACTCAATGTGAGTGAAACTTCAAACCCCTATCTTCCT
66 GAGAAGTAAACCAAATCGATGAAGCAAAACTCAATGTAAGCGAAACTTCAAACCCCTATCTTCCT
** *
3447 GATGAGAT-ACAGAGAAGTGGGTCAAAGCAATAAAGCGGTCAC
131 GATGAGATAACAGAGAAACGGGTCAAA-CAATAAAGCGATCAC
*
3489 CTTCCTGATGAGATACAGAGAAGTGAATTAAAACAATGAGGCGATCATCTTCCTGATGAGATTCA
1 CTTCCTGATGAGATACAGAGAAGTGAATTAAAACAATGAGGCGATCATCTTCCTGATGAGATACA
* * * * * * *
3554 GAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGTAAGCGGAACTTTAAACCCTTATTTTCCT
66 GAGAAGTAAACCAAATCGATGAAGCAAAACTCAATGTAAGCGAAACTTCAAACCCCTATCTTCCT
* * *
3619 GATGAGATAATAGAGAAACGGGTTAAACAATAAAGCGATCAT
131 GATGAGATAACAGAGAAACGGGTCAAACAATAAAGCGATCAC
* *
3661 CTTCCTGGTAAGATACAGAGAAGT
1 CTTCCTGATGAGATACAGAGAAGT
3685 TGACCAAATC
Statistics
Matches: 170, Mismatches: 25, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
172 156 0.92
173 14 0.08
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (172 bp):
CTTCCTGATGAGATACAGAGAAGTGAATTAAAACAATGAGGCGATCATCTTCCTGATGAGATACA
GAGAAGTAAACCAAATCGATGAAGCAAAACTCAATGTAAGCGAAACTTCAAACCCCTATCTTCCT
GATGAGATAACAGAGAAACGGGTCAAACAATAAAGCGATCAC
Done.