Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005680.1 Kokia drynarioides strain JFW-HI SEQ_119870, 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: 10081
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.38
Found at i:1432 original size:108 final size:108
Alignment explanation
Indices: 1240--1436 Score: 252
Period size: 108 Copynumber: 1.8 Consensus size: 108
1230 ATGTGGTAGC
* * * * *
1240 ATTCCATCAAATATTTTTAATTCAACTATGCTCGAAAAAATAGATCTGTTTGACAACAGTTTAGA
1 ATTCCATCAAATATTTTTAATTCAAATATGCTCGAAAAAATAAATCTATATGACAACAATTTAGA
* *
1305 ATATATGTTTTTCACTTTAATTTTCGACTATGTTGCAGGTCAA
66 AGATATATTTTTCACTTTAATTTTCGACTATGTTGCAGGTCAA
* * ** *
1348 ATTCCATCAAGTATTTTTAATTCAAATGTGCTTC-AAGGAATAAATCTATATGGCAACAATTTAG
1 ATTCCATCAAATATTTTTAATTCAAATATGC-TCGAAAAAATAAATCTATATGACAACAATTTAG
* *
1412 AAGGTATATTTTTCATTTTAATTTT
65 AAGATATATTTTTCACTTTAATTTT
1437 TCCAAACTCC
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
108 72 0.97
109 2 0.03
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (108 bp):
ATTCCATCAAATATTTTTAATTCAAATATGCTCGAAAAAATAAATCTATATGACAACAATTTAGA
AGATATATTTTTCACTTTAATTTTCGACTATGTTGCAGGTCAA
Found at i:2334 original size:102 final size:102
Alignment explanation
Indices: 2153--2364 Score: 415
Period size: 102 Copynumber: 2.1 Consensus size: 102
2143 TAAAATAGAT
*
2153 TAAATCATATAAATATATTATTTATATCTGAAAAGTAATGAAGATTTCAACGCAAGGCTATAGCT
1 TAAAACATATAAATATATTATTTATATCTGAAAAGTAATGAAGATTTCAACGCAAGGCTATAGCT
2218 AAGAATAGTTTGGAGTACACAATATATATACACACAC
66 AAGAATAGTTTGGAGTACACAATATATATACACACAC
2255 TAAAACATATAAATATATTATTTATATCTGAAAAGTAATGAAGATTTCAACGCAAGGCTATAGCT
1 TAAAACATATAAATATATTATTTATATCTGAAAAGTAATGAAGATTTCAACGCAAGGCTATAGCT
2320 AAGAATAGTTTGGAGTACACAATATATATACACACAC
66 AAGAATAGTTTGGAGTACACAATATATATACACACAC
2357 TAAAACAT
1 TAAAACAT
2365 GCAATTTTTG
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 109 1.00
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (102 bp):
TAAAACATATAAATATATTATTTATATCTGAAAAGTAATGAAGATTTCAACGCAAGGCTATAGCT
AAGAATAGTTTGGAGTACACAATATATATACACACAC
Found at i:2512 original size:22 final size:21
Alignment explanation
Indices: 2480--2529 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 21
2470 TTATTTTTAA
2480 TTTA-TTTAAAGTTTTACAATT
1 TTTATTTTAAAGTTTTA-AATT
2501 TTTATTTTAAAGTTTTAAATT
1 TTTATTTTAAAGTTTTAAATT
2522 TTCTATTT
1 TT-TATTT
2530 GAAACTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (21 bp):
TTTATTTTAAAGTTTTAAATT
Found at i:3254 original size:19 final size:19
Alignment explanation
Indices: 3223--3260 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
3213 TACATATGAT
3223 AAATTTTATAAATAACAAA
1 AAATTTTATAAATAACAAA
3242 AAATATTTA-AAATAACAAA
1 AAAT-TTTATAAATAACAAA
3261 TTTAGTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (19 bp):
AAATTTTATAAATAACAAA
Found at i:4259 original size:31 final size:31
Alignment explanation
Indices: 4224--4284 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
4214 ATGCGTATGA
* *
4224 TTAAATCAAAATTAAAGTTTCAAGTATATAT
1 TTAAACCAAAATTAAAATTTCAAGTATATAT
* *
4255 TTAAACCACAATTAAAATTTCAGGTATATA
1 TTAAACCAAAATTAAAATTTCAAGTATATA
4285 ATTGCACCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.36
Consensus pattern (31 bp):
TTAAACCAAAATTAAAATTTCAAGTATATAT
Found at i:4305 original size:29 final size:29
Alignment explanation
Indices: 4232--4320 Score: 81
Period size: 31 Copynumber: 3.0 Consensus size: 29
4222 GATTAAATCA
* **
4232 AAATTAAAGTTTCAAGTATATATTTAAACC
1 AAATTAAAG-TTCAAGTATATAATTGCACC
* *
4262 ACAATTAAAATTTCAGGTATATAATTGCACC
1 A-AATT-AAAGTTCAAGTATATAATTGCACC
*
4293 AAATTAAAGTTCATA-TATACAATTGCAC
1 AAATTAAAGTTCA-AGTATATAATTGCAC
4321 ATTAAATCAA
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
29 19 0.40
30 5 0.10
31 21 0.44
32 3 0.06
ACGTcount: A:0.45, C:0.13, G:0.08, T:0.34
Consensus pattern (29 bp):
AAATTAAAGTTCAAGTATATAATTGCACC
Found at i:4345 original size:29 final size:27
Alignment explanation
Indices: 4279--4345 Score: 71
Period size: 31 Copynumber: 2.3 Consensus size: 27
4269 AAATTTCAGG
*
4279 TATATAATTGCACCAAATTAAAGTTCA
1 TATATAATTGCACCAAATCAAAGTTCA
*
4306 TATATACAATTGCACATTAAATCAAAGTTCA
1 TATAT--AATTGCAC--CAAATCAAAGTTCA
*
4337 TGTATAATT
1 TATATAATT
4346 TTGAGATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 5 0.15
29 12 0.36
31 16 0.48
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.36
Consensus pattern (27 bp):
TATATAATTGCACCAAATCAAAGTTCA
Found at i:4832 original size:23 final size:26
Alignment explanation
Indices: 4812--4861 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
4802 TAAATATAAT
4812 ATATTATTTAAA-AAATTTATAAATGA
1 ATATTATTTAAACAAATTTATAAAT-A
* *
4838 ATATTTTTTAAACAAATTTTTAAA
1 ATATTATTTAAACAAATTTATAAA
4862 AGAATAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.52
27 10 0.48
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (26 bp):
ATATTATTTAAACAAATTTATAAATA
Found at i:4848 original size:26 final size:27
Alignment explanation
Indices: 4812--4867 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
4802 TAAATATAAT
*
4812 ATATTATTTAAA-AAATTTATAAATGA
1 ATATTATTTAAACAAATTTATAAAAGA
* *
4838 ATATTTTTTAAACAAATTTTTAAAAGA
1 ATATTATTTAAACAAATTTATAAAAGA
4865 ATA
1 ATA
4868 AAAAAAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.43
Consensus pattern (27 bp):
ATATTATTTAAACAAATTTATAAAAGA
Done.