Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012589.1 Kokia drynarioides strain JFW-HI SEQ_127598, 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: 2476
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Found at i:253 original size:30 final size:30
Alignment explanation
Indices: 210--311 Score: 84
Period size: 30 Copynumber: 3.5 Consensus size: 30
200 TAAACTGTCC
** * *
210 AAAAATTCCATTTTTGATCCTAAAATTTTT
1 AAAAATTATATTTTTGACCCTAAAATTTTA
** * *
240 AAAAATTATA-TTTT-ACCCTCGAACTTTC
1 AAAAATTATATTTTTGACCCTAAAATTTTA
* * *
268 AAAAATTCTATTTTTGACCCCAAAATTTCA
1 AAAAATTATATTTTTGACCCTAAAATTTTA
298 AAAAATTAT-TTTTT
1 AAAAATTATATTTTT
312 AGCCCCAAAC
Statistics
Matches: 55, Mismatches: 15, Indels: 5
0.73 0.20 0.07
Matches are distributed among these distances:
28 18 0.33
29 13 0.24
30 24 0.44
ACGTcount: A:0.38, C:0.16, G:0.03, T:0.43
Consensus pattern (30 bp):
AAAAATTATATTTTTGACCCTAAAATTTTA
Found at i:273 original size:58 final size:57
Alignment explanation
Indices: 202--458 Score: 257
Period size: 58 Copynumber: 4.4 Consensus size: 57
192 GAGGTCCCTA
* * **
202 AACTGTCCAAAAATTCCATTTTTGATCCTAAAATTTTTAAAAATTATATTTTACCCTCG
1 AACT-TCCAAAAATTCCATTTTTGACCCCAAAATTTCAAAAAATTATATTTTACCC-CG
* * * *
261 AACTTTCAAAAATTCTATTTTTGACCCCAAAATTTCAAAAAATTATTTTTTAGCCCCA
1 AACTTCCAAAAATTCCATTTTTGACCCCAAAATTTCAAAAAATTATATTTTA-CCCCG
* * * * *
319 AACTTCCAAAAATTCTATTTTTAACCCCGAAATTTCCAAAAATTACATTTTTACCCACG
1 AACTTCCAAAAATTCCATTTTTGACCCCAAAATTTCAAAAAATTATA-TTTTACCC-CG
* *** *
378 AACTTCCAAAATTTCCATTTTTGACCCCGAAGCCTTC-AAAAATTACCATTTTACCCCTG
1 AACTTCCAAAAATTCCATTTTTGACCCC-AAAATTTCAAAAAATTA-TATTTTACCCC-G
437 AA-TGTCCAAAAATTCCATTTTT
1 AACT-TCCAAAAATTCCATTTTT
459 TATCTCGATT
Statistics
Matches: 168, Mismatches: 23, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
58 88 0.52
59 74 0.44
60 6 0.04
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.37
Consensus pattern (57 bp):
AACTTCCAAAAATTCCATTTTTGACCCCAAAATTTCAAAAAATTATATTTTACCCCG
Found at i:296 original size:29 final size:29
Alignment explanation
Indices: 209--405 Score: 143
Period size: 29 Copynumber: 6.8 Consensus size: 29
199 CTAAACTGTC
* * *
209 CAAAAATTCCATTTTTGATCCTAAAATTTT
1 CAAAAATTCTATTTTTGACCCCAAAA-TTT
* * * *
239 TAAAAATTATA-TTTT-ACCCTCGAACTTT
1 CAAAAATTCTATTTTTGACCC-CAAAATTT
267 CAAAAATTCTATTTTTGACCCCAAAATTT
1 CAAAAATTCTATTTTTGACCCCAAAATTT
* * * *
296 CAAAAAAT-TATTTTTTAGCCCCAAACTTC
1 CAAAAATTCTATTTTTGA-CCCCAAAATTT
* *
325 CAAAAATTCTATTTTTAACCCCGAAATTT
1 CAAAAATTCTATTTTTGACCCCAAAATTT
* * *
354 CCAAAAATTAC-ATTTTT-ACCCACGAACTTC
1 -CAAAAATT-CTATTTTTGACCC-CAAAATTT
* *
384 CAAAATTTCCATTTTTGACCCC
1 CAAAAATTCTATTTTTGACCCC
406 GAAGCCTTCA
Statistics
Matches: 134, Mismatches: 23, Indels: 21
0.75 0.13 0.12
Matches are distributed among these distances:
28 24 0.18
29 65 0.49
30 44 0.33
31 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.38
Consensus pattern (29 bp):
CAAAAATTCTATTTTTGACCCCAAAATTT
Found at i:388 original size:59 final size:57
Alignment explanation
Indices: 202--517 Score: 262
Period size: 59 Copynumber: 5.4 Consensus size: 57
192 GAGGTCCCTA
* * ** *
202 AACTGTCCAAAAATTCCATTTTTGATCCTAAAATTTTTAAAAATTATATTTTACCCTCG
1 AACT-TCCAAAAATTCCATTTTTGACCCCAAAATTTCCAAAAATTACATTTTACCC-CG
* * * ** *
261 AACTTTCAAAAATTCTATTTTTGACCCCAAAATTTCAAAAAATTATTTTTTAGCCCCA
1 AACTTCCAAAAATTCCATTTTTGACCCCAAAATTTCCAAAAATTACATTTTA-CCCCG
* * *
319 AACTTCCAAAAATTCTATTTTTAACCCCGAAATTTCCAAAAATTACATTTTTACCCACG
1 AACTTCCAAAAATTCCATTTTTGACCCCAAAATTTCCAAAAATTACA-TTTTACCC-CG
* ***
378 AACTTCCAAAATTTCCATTTTTGACCCCGAAGCCTT-CAAAAATTACCATTTTACCCCTG
1 AACTTCCAAAAATTCCATTTTTGACCCC-AAAATTTCCAAAAATTA-CATTTTACCCC-G
* * * * *
437 AA-TGTCCAAAAATTCCATTTTTTATCTC-GATTTTCCTAAAAATTACCATTTTATCCCCG
1 AACT-TCCAAAAATTCCATTTTTGACCCCAAAATTTCC-AAAAATTA-CATTTTA-CCCCG
* *
496 GA-TGTCCAAAAATTCCGTTTTT
1 AACT-TCCAAAAATTCCATTTTT
518 TATCCCGATT
Statistics
Matches: 215, Mismatches: 32, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
57 2 0.01
58 89 0.41
59 115 0.53
60 9 0.04
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.37
Consensus pattern (57 bp):
AACTTCCAAAAATTCCATTTTTGACCCCAAAATTTCCAAAAATTACATTTTACCCCG
Found at i:408 original size:29 final size:28
Alignment explanation
Indices: 250--517 Score: 172
Period size: 29 Copynumber: 9.1 Consensus size: 28
240 AAAAATTATA
* *
250 TTTTACCCTCGAACTTTCAAAAATTCTAT
1 TTTTACCC-CGAACTTCCAAAAATTCCAT
* * *
279 TTTTGACCCCAAAATTTCAAAAAATT--ATT
1 TTTT-ACCCC-GAACTTCCAAAAATTCCA-T
* *
308 TTTTAGCCCCAAACTTCCAAAAATTCTAT
1 TTTTA-CCCCGAACTTCCAAAAATTCCAT
* *
337 TTTTAACCCCGAAATTTCCAAAAATTACAT
1 TTTT-ACCCCG-AACTTCCAAAAATTCCAT
*
367 TTTTACCCACGAACTTCCAAAATTTCCAT
1 TTTTACCC-CGAACTTCCAAAAATTCCAT
396 TTTTGACCCCGAAGCCTT-CAAAAATTACCA-
1 TTTT-ACCCCGAA--CTTCCAAAAATT-CCAT
426 TTTTACCCCTGAA-TGTCCAAAAATTCCATT
1 TTTTACCCC-GAACT-TCCAAAAATTCCA-T
* * **
456 TTTTATCTCGATTTTCCTAAAAATTACCA-
1 TTTTACCCCGAACTTCC-AAAAATT-CCAT
* *
485 TTTTATCCCCGGA-TGTCCAAAAATTCCGT
1 TTTTA-CCCCGAACT-TCCAAAAATTCCAT
514 TTTT
1 TTTT
518 TATCCCGATT
Statistics
Matches: 193, Mismatches: 22, Indels: 48
0.73 0.08 0.18
Matches are distributed among these distances:
27 1 0.01
28 21 0.11
29 85 0.44
30 77 0.40
31 9 0.05
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (28 bp):
TTTTACCCCGAACTTCCAAAAATTCCAT
Found at i:504 original size:118 final size:119
Alignment explanation
Indices: 205--607 Score: 335
Period size: 118 Copynumber: 3.4 Consensus size: 119
195 GTCCCTAAAC
* * ** * * *
205 TGTCCAAAAATTCCATTTTTGATCCT-AAAATTTTTAAAAATTA-TA-TTTTACCCTCGAACTTT
1 TGTCCAAAAATTCCATTTTT-AACCTCGAAATTTCCAAAAATTACCATTTTTACCCACGAACTTC
* *** ** *
267 CAAAAATTCTATTTTTGACCCC-AAAATTTCAAAAAATTA-TTTTTTAGCCCC-AAA
65 CAAAAATTCCATTTTTGACCCCGAAGCCTTC-AAAAATTACCATTTTA-CCCCTGAA
* *
321 CT-TCCAAAAATTCTATTTTTAACCCCGAAATTTCCAAAAATTA-CATTTTTACCCACGAACTTC
1 -TGTCCAAAAATTCCATTTTTAACCTCGAAATTTCCAAAAATTACCATTTTTACCCACGAACTTC
*
384 CAAAATTTCCATTTTTGACCCCGAAGCCTTCAAAAATTACCATTTTACCCCTGAA
65 CAAAAATTCCATTTTTGACCCCGAAGCCTTCAAAAATTACCATTTTACCCCTGAA
* * * *
439 TGTCCAAAAATTCCATTTTTTATCTCG-ATTTTCCTAAAAATTACCA-TTTTATCCC-CGGA-TG
1 TGTCCAAAAATTCCATTTTTAACCTCGAAATTTCC-AAAAATTACCATTTTTA-CCCACGAACT-
* * * **** * * * *
500 TCCAAAAATTCCGTTTTTTATCCCGATTTTTTTAAAAGTTACCGTTTTACCCCTGAG
63 TCCAAAAATTCCATTTTTGACCCCGAAGCCTTCAAAAATTACCATTTTACCCCTGAA
* * * *
557 TGTCTATAAATTCCATTTTTAACCTCGAACTTTCCCAAAATTACCATTTTT
1 TGTCCAAAAATTCCATTTTTAACCTCGAAATTTCCAAAAATTACCATTTTT
608 CCTCAAAGTC
Statistics
Matches: 233, Mismatches: 41, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
115 3 0.01
116 32 0.14
117 56 0.24
118 127 0.55
119 15 0.06
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (119 bp):
TGTCCAAAAATTCCATTTTTAACCTCGAAATTTCCAAAAATTACCATTTTTACCCACGAACTTCC
AAAAATTCCATTTTTGACCCCGAAGCCTTCAAAAATTACCATTTTACCCCTGAA
Found at i:518 original size:59 final size:58
Alignment explanation
Indices: 415--606 Score: 215
Period size: 59 Copynumber: 3.3 Consensus size: 58
405 CGAAGCCTTC
*
415 AAAAATTACCATTTTACCCCTGAATGTCCAAAAATTCCATTTTTTATCTCGATTTTCCT
1 AAAAATTACCATTTTACCCC-GGATGTCCAAAAATTCCATTTTTTATCTCGATTTTCCT
* * **
474 AAAAATTACCATTTTATCCCCGGATGTCCAAAAATTCCGTTTTTTATCCCGATTTTTTT
1 AAAAATTACCATTTTA-CCCCGGATGTCCAAAAATTCCATTTTTTATCTCGATTTTCCT
* * * * * * * *
533 AAAAGTTACCGTTTTACCCCTGAGTGTCTATAAATTCCATTTTTAACCTCGAACTTTCC-
1 AAAAATTACCATTTTACCCCGGA-TGTCCAAAAATTCCATTTTTTATCTCG-ATTTTCCT
*
592 CAAAATTACCATTTT
1 AAAAATTACCATTTT
607 TCCTCAAAGT
Statistics
Matches: 110, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
58 6 0.05
59 96 0.87
60 8 0.07
ACGTcount: A:0.29, C:0.23, G:0.07, T:0.40
Consensus pattern (58 bp):
AAAAATTACCATTTTACCCCGGATGTCCAAAAATTCCATTTTTTATCTCGATTTTCCT
Done.