Multiple sequence alignment - TraesCS3A01G127600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3A01G127600 chr3A 100.000 2573 0 0 1 2573 102793069 102795641 0.000000e+00 4752.0
1 TraesCS3A01G127600 chr3A 98.102 2107 37 3 468 2573 730380801 730378697 0.000000e+00 3666.0
2 TraesCS3A01G127600 chr3A 96.632 2108 37 7 468 2573 696644096 696646171 0.000000e+00 3469.0
3 TraesCS3A01G127600 chr3A 95.026 382 17 1 89 470 514223253 514222874 1.320000e-167 599.0
4 TraesCS3A01G127600 chr3A 96.143 363 11 1 108 470 641659687 641659328 7.930000e-165 590.0
5 TraesCS3A01G127600 chr3A 80.139 287 36 14 468 738 748243407 748243688 7.260000e-46 195.0
6 TraesCS3A01G127600 chr3A 98.980 98 1 0 1 98 102824263 102824360 2.630000e-40 176.0
7 TraesCS3A01G127600 chr2A 90.180 499 18 7 1 470 685082470 685082966 2.810000e-174 621.0
8 TraesCS3A01G127600 chr2A 95.676 370 12 2 108 476 182826486 182826852 2.200000e-165 592.0
9 TraesCS3A01G127600 chr2A 96.122 361 10 2 108 467 255231378 255231735 1.030000e-163 586.0
10 TraesCS3A01G127600 chr2A 90.909 121 7 2 1 119 182826936 182826818 2.650000e-35 159.0
11 TraesCS3A01G127600 chr7A 96.143 363 11 1 108 470 18386363 18386722 7.930000e-165 590.0
12 TraesCS3A01G127600 chr7A 95.868 363 13 1 108 470 368481729 368481369 1.030000e-163 586.0
13 TraesCS3A01G127600 chr7A 94.241 382 19 1 89 470 480317685 480318063 4.770000e-162 580.0
14 TraesCS3A01G127600 chr7A 98.980 98 1 0 1 98 493204395 493204492 2.630000e-40 176.0
15 TraesCS3A01G127600 chr5A 95.868 363 13 1 108 470 202891800 202892160 1.030000e-163 586.0
16 TraesCS3A01G127600 chr5A 98.980 98 1 0 1 98 321504389 321504486 2.630000e-40 176.0
17 TraesCS3A01G127600 chr4A 95.868 363 13 1 108 470 452251809 452251449 1.030000e-163 586.0
18 TraesCS3A01G127600 chr6A 82.267 344 59 1 127 470 403302424 403302765 1.940000e-76 296.0
19 TraesCS3A01G127600 chr6A 98.980 98 1 0 1 98 431895668 431895571 2.630000e-40 176.0
20 TraesCS3A01G127600 chr2B 79.225 284 40 14 468 736 623335615 623335894 2.030000e-41 180.0
21 TraesCS3A01G127600 chr1A 98.980 98 1 0 1 98 396180663 396180760 2.630000e-40 176.0
22 TraesCS3A01G127600 chr1A 98.980 98 1 0 1 98 502698804 502698901 2.630000e-40 176.0
23 TraesCS3A01G127600 chr1A 92.982 114 7 1 1 113 177655806 177655919 5.700000e-37 165.0
24 TraesCS3A01G127600 chr1B 90.541 74 7 0 468 541 511481196 511481269 5.860000e-17 99.0
25 TraesCS3A01G127600 chr7D 94.643 56 2 1 462 516 296636678 296636623 4.560000e-13 86.1
26 TraesCS3A01G127600 chr3B 97.917 48 1 0 468 515 171295999 171296046 1.640000e-12 84.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G127600 chr3A 102793069 102795641 2572 False 4752 4752 100.000 1 2573 1 chr3A.!!$F1 2572
1 TraesCS3A01G127600 chr3A 730378697 730380801 2104 True 3666 3666 98.102 468 2573 1 chr3A.!!$R3 2105
2 TraesCS3A01G127600 chr3A 696644096 696646171 2075 False 3469 3469 96.632 468 2573 1 chr3A.!!$F3 2105

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
116 117 0.179108 AGGGTCGCGCTATTCTTCAC 60.179 55.0 5.56 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1802 1805 0.459585 GTGCGGCCGATTACTCTGAA 60.46 55.0 33.48 0.0 0.0 3.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 9.506018 TCAATGAAGTTTCTGATTCATACTTGA 57.494 29.630 11.42 4.86 43.56 3.02
51 52 9.903682 AGTTTCTGATTCATACTTGAAATTGTG 57.096 29.630 2.54 0.00 44.70 3.33
52 53 9.897744 GTTTCTGATTCATACTTGAAATTGTGA 57.102 29.630 2.54 0.00 44.70 3.58
71 72 9.979578 AATTGTGAATGAATTGTTACTTTAGCA 57.020 25.926 0.00 0.00 0.00 3.49
106 107 5.936686 TGACTATATATATAGGGTCGCGC 57.063 43.478 26.36 0.00 39.91 6.86
107 108 5.618236 TGACTATATATATAGGGTCGCGCT 58.382 41.667 26.36 9.07 39.91 5.92
108 109 6.762333 TGACTATATATATAGGGTCGCGCTA 58.238 40.000 26.36 0.00 39.91 4.26
109 110 7.392418 TGACTATATATATAGGGTCGCGCTAT 58.608 38.462 26.36 16.35 41.39 2.97
110 111 7.881751 TGACTATATATATAGGGTCGCGCTATT 59.118 37.037 26.36 7.48 39.65 1.73
111 112 8.266392 ACTATATATATAGGGTCGCGCTATTC 57.734 38.462 26.36 0.00 39.65 1.75
112 113 8.102047 ACTATATATATAGGGTCGCGCTATTCT 58.898 37.037 26.36 0.31 39.65 2.40
113 114 7.762588 ATATATATAGGGTCGCGCTATTCTT 57.237 36.000 17.00 8.91 39.65 2.52
114 115 2.726832 ATAGGGTCGCGCTATTCTTC 57.273 50.000 5.56 0.00 36.44 2.87
115 116 1.395635 TAGGGTCGCGCTATTCTTCA 58.604 50.000 5.56 0.00 0.00 3.02
116 117 0.179108 AGGGTCGCGCTATTCTTCAC 60.179 55.000 5.56 0.00 0.00 3.18
117 118 1.152383 GGGTCGCGCTATTCTTCACC 61.152 60.000 5.56 0.00 0.00 4.02
118 119 1.152383 GGTCGCGCTATTCTTCACCC 61.152 60.000 5.56 0.00 0.00 4.61
119 120 1.143183 TCGCGCTATTCTTCACCCC 59.857 57.895 5.56 0.00 0.00 4.95
120 121 1.887707 CGCGCTATTCTTCACCCCC 60.888 63.158 5.56 0.00 0.00 5.40
143 144 4.524328 CCCCCTCTATTTTACCATCAATGC 59.476 45.833 0.00 0.00 0.00 3.56
144 145 5.139727 CCCCTCTATTTTACCATCAATGCA 58.860 41.667 0.00 0.00 0.00 3.96
145 146 5.010012 CCCCTCTATTTTACCATCAATGCAC 59.990 44.000 0.00 0.00 0.00 4.57
146 147 5.010012 CCCTCTATTTTACCATCAATGCACC 59.990 44.000 0.00 0.00 0.00 5.01
147 148 5.277974 CCTCTATTTTACCATCAATGCACCG 60.278 44.000 0.00 0.00 0.00 4.94
148 149 5.189928 TCTATTTTACCATCAATGCACCGT 58.810 37.500 0.00 0.00 0.00 4.83
149 150 6.350103 TCTATTTTACCATCAATGCACCGTA 58.650 36.000 0.00 0.00 0.00 4.02
150 151 5.906113 ATTTTACCATCAATGCACCGTAA 57.094 34.783 0.00 0.00 0.00 3.18
151 152 5.906113 TTTTACCATCAATGCACCGTAAT 57.094 34.783 0.00 0.00 0.00 1.89
152 153 5.906113 TTTACCATCAATGCACCGTAATT 57.094 34.783 0.00 0.00 0.00 1.40
153 154 5.906113 TTACCATCAATGCACCGTAATTT 57.094 34.783 0.00 0.00 0.00 1.82
154 155 4.799564 ACCATCAATGCACCGTAATTTT 57.200 36.364 0.00 0.00 0.00 1.82
155 156 5.906113 ACCATCAATGCACCGTAATTTTA 57.094 34.783 0.00 0.00 0.00 1.52
156 157 5.646606 ACCATCAATGCACCGTAATTTTAC 58.353 37.500 0.00 0.00 0.00 2.01
180 181 8.718047 ACGTTCCGTAAATTTTGTCTTATTTC 57.282 30.769 0.00 0.00 38.73 2.17
181 182 7.804600 ACGTTCCGTAAATTTTGTCTTATTTCC 59.195 33.333 0.00 0.00 38.73 3.13
182 183 7.006742 CGTTCCGTAAATTTTGTCTTATTTCCG 59.993 37.037 0.00 0.00 0.00 4.30
183 184 7.670009 TCCGTAAATTTTGTCTTATTTCCGA 57.330 32.000 0.00 0.00 28.37 4.55
184 185 8.271312 TCCGTAAATTTTGTCTTATTTCCGAT 57.729 30.769 0.00 0.00 28.37 4.18
185 186 8.178964 TCCGTAAATTTTGTCTTATTTCCGATG 58.821 33.333 0.00 0.00 28.37 3.84
186 187 7.044314 CCGTAAATTTTGTCTTATTTCCGATGC 60.044 37.037 0.00 0.00 28.37 3.91
187 188 7.483375 CGTAAATTTTGTCTTATTTCCGATGCA 59.517 33.333 0.00 0.00 28.37 3.96
188 189 9.134734 GTAAATTTTGTCTTATTTCCGATGCAA 57.865 29.630 0.00 0.00 0.00 4.08
189 190 8.600449 AAATTTTGTCTTATTTCCGATGCAAA 57.400 26.923 0.00 0.00 0.00 3.68
190 191 8.600449 AATTTTGTCTTATTTCCGATGCAAAA 57.400 26.923 0.00 0.00 38.40 2.44
191 192 8.600449 ATTTTGTCTTATTTCCGATGCAAAAA 57.400 26.923 0.00 0.00 37.85 1.94
192 193 7.636259 TTTGTCTTATTTCCGATGCAAAAAG 57.364 32.000 0.00 0.00 0.00 2.27
193 194 6.567687 TGTCTTATTTCCGATGCAAAAAGA 57.432 33.333 0.00 0.00 0.00 2.52
194 195 6.611381 TGTCTTATTTCCGATGCAAAAAGAG 58.389 36.000 0.00 0.00 0.00 2.85
195 196 6.429692 TGTCTTATTTCCGATGCAAAAAGAGA 59.570 34.615 0.00 0.00 0.00 3.10
196 197 6.743172 GTCTTATTTCCGATGCAAAAAGAGAC 59.257 38.462 0.00 1.64 0.00 3.36
197 198 3.915437 TTTCCGATGCAAAAAGAGACC 57.085 42.857 0.00 0.00 0.00 3.85
198 199 1.438651 TCCGATGCAAAAAGAGACCG 58.561 50.000 0.00 0.00 0.00 4.79
199 200 1.156736 CCGATGCAAAAAGAGACCGT 58.843 50.000 0.00 0.00 0.00 4.83
200 201 2.028839 TCCGATGCAAAAAGAGACCGTA 60.029 45.455 0.00 0.00 0.00 4.02
201 202 2.739913 CCGATGCAAAAAGAGACCGTAA 59.260 45.455 0.00 0.00 0.00 3.18
202 203 3.181520 CCGATGCAAAAAGAGACCGTAAG 60.182 47.826 0.00 0.00 0.00 2.34
203 204 3.678072 CGATGCAAAAAGAGACCGTAAGA 59.322 43.478 0.00 0.00 43.02 2.10
204 205 4.151689 CGATGCAAAAAGAGACCGTAAGAA 59.848 41.667 0.00 0.00 43.02 2.52
205 206 5.333798 CGATGCAAAAAGAGACCGTAAGAAA 60.334 40.000 0.00 0.00 43.02 2.52
206 207 5.821516 TGCAAAAAGAGACCGTAAGAAAA 57.178 34.783 0.00 0.00 43.02 2.29
207 208 6.385649 TGCAAAAAGAGACCGTAAGAAAAT 57.614 33.333 0.00 0.00 43.02 1.82
208 209 7.499321 TGCAAAAAGAGACCGTAAGAAAATA 57.501 32.000 0.00 0.00 43.02 1.40
209 210 8.106247 TGCAAAAAGAGACCGTAAGAAAATAT 57.894 30.769 0.00 0.00 43.02 1.28
210 211 9.221933 TGCAAAAAGAGACCGTAAGAAAATATA 57.778 29.630 0.00 0.00 43.02 0.86
217 218 9.570488 AGAGACCGTAAGAAAATATATAATCGC 57.430 33.333 0.00 0.00 43.02 4.58
218 219 8.699283 AGACCGTAAGAAAATATATAATCGCC 57.301 34.615 0.00 0.00 43.02 5.54
219 220 7.487189 AGACCGTAAGAAAATATATAATCGCCG 59.513 37.037 0.00 0.00 43.02 6.46
220 221 7.092716 ACCGTAAGAAAATATATAATCGCCGT 58.907 34.615 0.00 0.00 43.02 5.68
221 222 8.243426 ACCGTAAGAAAATATATAATCGCCGTA 58.757 33.333 0.00 0.00 43.02 4.02
222 223 9.075519 CCGTAAGAAAATATATAATCGCCGTAA 57.924 33.333 0.00 0.00 43.02 3.18
308 309 9.574516 ACTACAAATTTTCTTGTCTTATGACCT 57.425 29.630 6.32 0.00 42.28 3.85
344 345 9.583530 TTTTCGTATGTCAAATTTTACGTAGTG 57.416 29.630 15.87 8.11 45.73 2.74
345 346 8.518151 TTCGTATGTCAAATTTTACGTAGTGA 57.482 30.769 15.87 9.74 45.73 3.41
346 347 8.518151 TCGTATGTCAAATTTTACGTAGTGAA 57.482 30.769 15.87 0.00 45.73 3.18
347 348 9.142515 TCGTATGTCAAATTTTACGTAGTGAAT 57.857 29.630 15.87 0.00 45.73 2.57
348 349 9.405083 CGTATGTCAAATTTTACGTAGTGAATC 57.595 33.333 10.57 0.00 45.73 2.52
359 360 9.715121 TTTTACGTAGTGAATCAATAGAAAGGT 57.285 29.630 0.00 0.00 45.73 3.50
362 363 8.699283 ACGTAGTGAATCAATAGAAAGGTAAC 57.301 34.615 0.00 0.00 42.51 2.50
419 420 3.003394 TCGTAAGATTACCTCGGGTGA 57.997 47.619 5.90 0.00 45.01 4.02
420 421 3.355378 TCGTAAGATTACCTCGGGTGAA 58.645 45.455 5.90 0.00 45.01 3.18
421 422 3.379372 TCGTAAGATTACCTCGGGTGAAG 59.621 47.826 5.90 0.00 45.01 3.02
422 423 3.379372 CGTAAGATTACCTCGGGTGAAGA 59.621 47.826 5.90 0.00 36.23 2.87
423 424 4.142315 CGTAAGATTACCTCGGGTGAAGAA 60.142 45.833 5.90 0.00 36.23 2.52
424 425 5.451520 CGTAAGATTACCTCGGGTGAAGAAT 60.452 44.000 5.90 0.00 36.23 2.40
425 426 6.238842 CGTAAGATTACCTCGGGTGAAGAATA 60.239 42.308 5.90 0.00 36.23 1.75
426 427 6.555463 AAGATTACCTCGGGTGAAGAATAA 57.445 37.500 5.90 0.00 36.19 1.40
427 428 5.915175 AGATTACCTCGGGTGAAGAATAAC 58.085 41.667 5.90 0.00 36.19 1.89
428 429 5.661759 AGATTACCTCGGGTGAAGAATAACT 59.338 40.000 5.90 0.00 36.19 2.24
429 430 5.750352 TTACCTCGGGTGAAGAATAACTT 57.250 39.130 5.90 0.00 38.14 2.66
430 431 6.855763 TTACCTCGGGTGAAGAATAACTTA 57.144 37.500 5.90 0.00 36.67 2.24
431 432 5.952347 ACCTCGGGTGAAGAATAACTTAT 57.048 39.130 0.00 0.00 39.13 1.73
432 433 6.309389 ACCTCGGGTGAAGAATAACTTATT 57.691 37.500 0.00 0.00 39.13 1.40
433 434 6.346896 ACCTCGGGTGAAGAATAACTTATTC 58.653 40.000 12.07 12.07 38.76 1.75
434 435 6.156429 ACCTCGGGTGAAGAATAACTTATTCT 59.844 38.462 15.62 15.62 44.74 2.40
435 436 7.848201 ACCTCGGGTGAAGAATAACTTATTCTG 60.848 40.741 20.22 10.00 43.39 3.02
443 444 5.757850 GAATAACTTATTCTGCACCCTGG 57.242 43.478 12.55 0.00 41.00 4.45
444 445 2.514458 AACTTATTCTGCACCCTGGG 57.486 50.000 12.28 12.28 0.00 4.45
445 446 1.372501 ACTTATTCTGCACCCTGGGT 58.627 50.000 14.05 14.05 35.62 4.51
446 447 7.850027 GAATAACTTATTCTGCACCCTGGGTG 61.850 46.154 36.31 36.31 46.08 4.61
447 448 9.907723 GAATAACTTATTCTGCACCCTGGGTGA 62.908 44.444 42.58 27.49 46.15 4.02
458 459 4.772886 ACCCTGGGTGATGAATAGTAAC 57.227 45.455 19.82 0.00 32.98 2.50
459 460 4.108570 ACCCTGGGTGATGAATAGTAACA 58.891 43.478 19.82 0.00 32.98 2.41
460 461 4.080526 ACCCTGGGTGATGAATAGTAACAC 60.081 45.833 19.82 0.00 32.98 3.32
461 462 4.164221 CCCTGGGTGATGAATAGTAACACT 59.836 45.833 3.97 0.00 0.00 3.55
462 463 5.365605 CCCTGGGTGATGAATAGTAACACTA 59.634 44.000 3.97 0.00 34.82 2.74
463 464 6.043243 CCCTGGGTGATGAATAGTAACACTAT 59.957 42.308 3.97 0.00 42.86 2.12
464 465 7.234782 CCCTGGGTGATGAATAGTAACACTATA 59.765 40.741 3.97 0.00 40.32 1.31
465 466 8.816894 CCTGGGTGATGAATAGTAACACTATAT 58.183 37.037 0.00 0.00 40.32 0.86
669 670 5.874897 AGTAATATTACGGCCTACACCAA 57.125 39.130 17.77 0.00 38.65 3.67
799 800 7.824779 CCTGACTTTGTAGTAGGATAAAAGCTT 59.175 37.037 0.00 0.00 33.84 3.74
800 801 9.220767 CTGACTTTGTAGTAGGATAAAAGCTTT 57.779 33.333 5.69 5.69 33.84 3.51
1081 1082 0.824595 TCGTGGTCTTCCGTTCTCCA 60.825 55.000 0.00 0.00 36.30 3.86
1318 1319 3.798889 GCGTGGATCGAAATACATCCTCA 60.799 47.826 2.40 0.00 39.62 3.86
1478 1479 7.632898 GCCAAGATGTACAATAGGTCAGTTCTA 60.633 40.741 0.00 0.00 0.00 2.10
1802 1805 8.320396 TGATTAGAGAGTATTATTACGCGACT 57.680 34.615 15.93 2.84 33.79 4.18
2313 2317 0.546122 TGCCTTGGCATCGAGGTAAT 59.454 50.000 10.65 0.00 44.75 1.89
2439 2443 0.949105 GTCTCCACGGCGAACAACAT 60.949 55.000 16.62 0.00 0.00 2.71
2455 2459 0.537143 ACATGAAGTGAAAGGCGGCA 60.537 50.000 13.08 0.00 0.00 5.69
2522 2526 3.576982 TCGTTGTGAGTGTTTATCTCCCT 59.423 43.478 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 9.506018 TCAAGTATGAATCAGAAACTTCATTGA 57.494 29.630 3.57 1.11 41.22 2.57
25 26 9.903682 CACAATTTCAAGTATGAATCAGAAACT 57.096 29.630 0.00 0.00 44.70 2.66
26 27 9.897744 TCACAATTTCAAGTATGAATCAGAAAC 57.102 29.630 0.00 0.00 44.70 2.78
45 46 9.979578 TGCTAAAGTAACAATTCATTCACAATT 57.020 25.926 0.00 0.00 0.00 2.32
80 81 8.675504 GCGCGACCCTATATATATAGTCATATT 58.324 37.037 22.60 5.72 35.09 1.28
81 82 8.047911 AGCGCGACCCTATATATATAGTCATAT 58.952 37.037 22.60 8.03 35.09 1.78
82 83 7.392418 AGCGCGACCCTATATATATAGTCATA 58.608 38.462 22.60 0.00 35.09 2.15
83 84 6.239396 AGCGCGACCCTATATATATAGTCAT 58.761 40.000 22.60 11.37 35.09 3.06
84 85 5.618236 AGCGCGACCCTATATATATAGTCA 58.382 41.667 22.60 0.00 35.09 3.41
85 86 7.846644 ATAGCGCGACCCTATATATATAGTC 57.153 40.000 22.60 16.16 35.09 2.59
86 87 8.102047 AGAATAGCGCGACCCTATATATATAGT 58.898 37.037 22.60 10.54 35.09 2.12
87 88 8.495361 AGAATAGCGCGACCCTATATATATAG 57.505 38.462 19.15 19.15 36.32 1.31
88 89 8.859236 AAGAATAGCGCGACCCTATATATATA 57.141 34.615 12.10 2.49 0.00 0.86
89 90 7.447545 TGAAGAATAGCGCGACCCTATATATAT 59.552 37.037 12.10 0.00 0.00 0.86
90 91 6.769341 TGAAGAATAGCGCGACCCTATATATA 59.231 38.462 12.10 0.00 0.00 0.86
91 92 5.593095 TGAAGAATAGCGCGACCCTATATAT 59.407 40.000 12.10 0.00 0.00 0.86
92 93 4.945543 TGAAGAATAGCGCGACCCTATATA 59.054 41.667 12.10 0.00 0.00 0.86
93 94 3.762288 TGAAGAATAGCGCGACCCTATAT 59.238 43.478 12.10 0.00 0.00 0.86
94 95 3.057736 GTGAAGAATAGCGCGACCCTATA 60.058 47.826 12.10 0.00 0.00 1.31
95 96 1.961394 TGAAGAATAGCGCGACCCTAT 59.039 47.619 12.10 4.35 0.00 2.57
96 97 1.066605 GTGAAGAATAGCGCGACCCTA 59.933 52.381 12.10 1.47 0.00 3.53
97 98 0.179108 GTGAAGAATAGCGCGACCCT 60.179 55.000 12.10 0.00 0.00 4.34
98 99 1.152383 GGTGAAGAATAGCGCGACCC 61.152 60.000 12.10 0.00 0.00 4.46
99 100 1.152383 GGGTGAAGAATAGCGCGACC 61.152 60.000 12.10 4.48 0.00 4.79
100 101 1.152383 GGGGTGAAGAATAGCGCGAC 61.152 60.000 12.10 0.04 0.00 5.19
101 102 1.143183 GGGGTGAAGAATAGCGCGA 59.857 57.895 12.10 0.00 0.00 5.87
102 103 1.887707 GGGGGTGAAGAATAGCGCG 60.888 63.158 0.00 0.00 0.00 6.86
103 104 4.142780 GGGGGTGAAGAATAGCGC 57.857 61.111 0.00 0.00 0.00 5.92
120 121 4.524328 GCATTGATGGTAAAATAGAGGGGG 59.476 45.833 0.00 0.00 0.00 5.40
121 122 5.010012 GTGCATTGATGGTAAAATAGAGGGG 59.990 44.000 0.00 0.00 0.00 4.79
122 123 5.010012 GGTGCATTGATGGTAAAATAGAGGG 59.990 44.000 0.00 0.00 0.00 4.30
123 124 5.277974 CGGTGCATTGATGGTAAAATAGAGG 60.278 44.000 0.00 0.00 0.00 3.69
124 125 5.296780 ACGGTGCATTGATGGTAAAATAGAG 59.703 40.000 0.00 0.00 0.00 2.43
125 126 5.189928 ACGGTGCATTGATGGTAAAATAGA 58.810 37.500 0.00 0.00 0.00 1.98
126 127 5.499139 ACGGTGCATTGATGGTAAAATAG 57.501 39.130 0.00 0.00 0.00 1.73
127 128 7.575414 ATTACGGTGCATTGATGGTAAAATA 57.425 32.000 0.00 0.00 0.00 1.40
128 129 5.906113 TTACGGTGCATTGATGGTAAAAT 57.094 34.783 0.00 0.00 0.00 1.82
129 130 5.906113 ATTACGGTGCATTGATGGTAAAA 57.094 34.783 0.00 0.00 0.00 1.52
130 131 5.906113 AATTACGGTGCATTGATGGTAAA 57.094 34.783 0.00 0.00 0.00 2.01
131 132 5.906113 AAATTACGGTGCATTGATGGTAA 57.094 34.783 0.00 0.00 0.00 2.85
132 133 5.906113 AAAATTACGGTGCATTGATGGTA 57.094 34.783 0.00 0.00 0.00 3.25
133 134 4.799564 AAAATTACGGTGCATTGATGGT 57.200 36.364 0.00 0.00 0.00 3.55
157 158 8.016801 TCGGAAATAAGACAAAATTTACGGAAC 58.983 33.333 11.29 0.00 45.31 3.62
158 159 8.097078 TCGGAAATAAGACAAAATTTACGGAA 57.903 30.769 11.29 0.00 45.31 4.30
159 160 7.670009 TCGGAAATAAGACAAAATTTACGGA 57.330 32.000 11.29 0.00 45.31 4.69
160 161 7.044314 GCATCGGAAATAAGACAAAATTTACGG 60.044 37.037 11.29 0.22 45.31 4.02
161 162 7.483375 TGCATCGGAAATAAGACAAAATTTACG 59.517 33.333 6.15 6.15 46.17 3.18
162 163 8.682128 TGCATCGGAAATAAGACAAAATTTAC 57.318 30.769 0.00 0.00 0.00 2.01
163 164 9.698309 TTTGCATCGGAAATAAGACAAAATTTA 57.302 25.926 0.00 0.00 0.00 1.40
164 165 8.600449 TTTGCATCGGAAATAAGACAAAATTT 57.400 26.923 0.00 0.00 0.00 1.82
165 166 8.600449 TTTTGCATCGGAAATAAGACAAAATT 57.400 26.923 0.00 0.00 32.55 1.82
166 167 8.600449 TTTTTGCATCGGAAATAAGACAAAAT 57.400 26.923 0.00 0.00 36.14 1.82
167 168 7.923344 TCTTTTTGCATCGGAAATAAGACAAAA 59.077 29.630 0.00 0.00 34.86 2.44
168 169 7.429633 TCTTTTTGCATCGGAAATAAGACAAA 58.570 30.769 0.00 0.00 0.00 2.83
169 170 6.976088 TCTTTTTGCATCGGAAATAAGACAA 58.024 32.000 0.00 0.00 0.00 3.18
170 171 6.429692 TCTCTTTTTGCATCGGAAATAAGACA 59.570 34.615 0.00 0.00 0.00 3.41
171 172 6.743172 GTCTCTTTTTGCATCGGAAATAAGAC 59.257 38.462 0.00 0.00 0.00 3.01
172 173 6.128007 GGTCTCTTTTTGCATCGGAAATAAGA 60.128 38.462 0.00 0.00 0.00 2.10
173 174 6.030228 GGTCTCTTTTTGCATCGGAAATAAG 58.970 40.000 0.00 0.00 0.00 1.73
174 175 5.391523 CGGTCTCTTTTTGCATCGGAAATAA 60.392 40.000 0.00 0.00 0.00 1.40
175 176 4.094294 CGGTCTCTTTTTGCATCGGAAATA 59.906 41.667 0.00 0.00 0.00 1.40
176 177 3.119849 CGGTCTCTTTTTGCATCGGAAAT 60.120 43.478 0.00 0.00 0.00 2.17
177 178 2.225491 CGGTCTCTTTTTGCATCGGAAA 59.775 45.455 0.00 0.00 0.00 3.13
178 179 1.804151 CGGTCTCTTTTTGCATCGGAA 59.196 47.619 0.00 0.00 0.00 4.30
179 180 1.270625 ACGGTCTCTTTTTGCATCGGA 60.271 47.619 0.00 0.00 0.00 4.55
180 181 1.156736 ACGGTCTCTTTTTGCATCGG 58.843 50.000 0.00 0.00 0.00 4.18
181 182 3.678072 TCTTACGGTCTCTTTTTGCATCG 59.322 43.478 0.00 0.00 0.00 3.84
182 183 5.607119 TTCTTACGGTCTCTTTTTGCATC 57.393 39.130 0.00 0.00 0.00 3.91
183 184 6.385649 TTTTCTTACGGTCTCTTTTTGCAT 57.614 33.333 0.00 0.00 0.00 3.96
184 185 5.821516 TTTTCTTACGGTCTCTTTTTGCA 57.178 34.783 0.00 0.00 0.00 4.08
191 192 9.570488 GCGATTATATATTTTCTTACGGTCTCT 57.430 33.333 0.00 0.00 0.00 3.10
192 193 8.805688 GGCGATTATATATTTTCTTACGGTCTC 58.194 37.037 0.00 0.00 0.00 3.36
193 194 7.487189 CGGCGATTATATATTTTCTTACGGTCT 59.513 37.037 0.00 0.00 0.00 3.85
194 195 7.274250 ACGGCGATTATATATTTTCTTACGGTC 59.726 37.037 16.62 0.00 0.00 4.79
195 196 7.092716 ACGGCGATTATATATTTTCTTACGGT 58.907 34.615 16.62 0.00 0.00 4.83
196 197 7.515957 ACGGCGATTATATATTTTCTTACGG 57.484 36.000 16.62 0.00 0.00 4.02
282 283 9.574516 AGGTCATAAGACAAGAAAATTTGTAGT 57.425 29.630 0.00 0.00 46.80 2.73
318 319 9.583530 CACTACGTAAAATTTGACATACGAAAA 57.416 29.630 21.02 9.32 42.66 2.29
319 320 8.976471 TCACTACGTAAAATTTGACATACGAAA 58.024 29.630 21.02 11.08 42.66 3.46
320 321 8.518151 TCACTACGTAAAATTTGACATACGAA 57.482 30.769 21.02 4.56 42.66 3.85
321 322 8.518151 TTCACTACGTAAAATTTGACATACGA 57.482 30.769 21.02 8.61 42.66 3.43
322 323 9.405083 GATTCACTACGTAAAATTTGACATACG 57.595 33.333 15.23 15.23 44.82 3.06
333 334 9.715121 ACCTTTCTATTGATTCACTACGTAAAA 57.285 29.630 0.00 0.00 0.00 1.52
336 337 9.793252 GTTACCTTTCTATTGATTCACTACGTA 57.207 33.333 0.00 0.00 0.00 3.57
337 338 8.529476 AGTTACCTTTCTATTGATTCACTACGT 58.471 33.333 0.00 0.00 0.00 3.57
338 339 8.928270 AGTTACCTTTCTATTGATTCACTACG 57.072 34.615 0.00 0.00 0.00 3.51
353 354 9.124807 CGTTTGGAATTCAAATAGTTACCTTTC 57.875 33.333 7.93 0.00 45.79 2.62
354 355 8.635328 ACGTTTGGAATTCAAATAGTTACCTTT 58.365 29.630 7.93 0.00 45.79 3.11
355 356 8.173542 ACGTTTGGAATTCAAATAGTTACCTT 57.826 30.769 7.93 0.00 45.79 3.50
356 357 7.754851 ACGTTTGGAATTCAAATAGTTACCT 57.245 32.000 7.93 0.00 45.79 3.08
388 389 9.406828 CGAGGTAATCTTACGATCATTTCATAA 57.593 33.333 0.00 0.00 34.50 1.90
389 390 8.027189 CCGAGGTAATCTTACGATCATTTCATA 58.973 37.037 0.00 0.00 34.50 2.15
390 391 6.868864 CCGAGGTAATCTTACGATCATTTCAT 59.131 38.462 0.00 0.00 34.50 2.57
391 392 6.213677 CCGAGGTAATCTTACGATCATTTCA 58.786 40.000 0.00 0.00 34.50 2.69
392 393 5.634020 CCCGAGGTAATCTTACGATCATTTC 59.366 44.000 0.00 0.00 34.50 2.17
393 394 5.070047 ACCCGAGGTAATCTTACGATCATTT 59.930 40.000 0.00 0.00 32.11 2.32
394 395 4.587684 ACCCGAGGTAATCTTACGATCATT 59.412 41.667 0.00 0.00 32.11 2.57
395 396 4.022242 CACCCGAGGTAATCTTACGATCAT 60.022 45.833 0.00 0.00 32.11 2.45
396 397 3.317149 CACCCGAGGTAATCTTACGATCA 59.683 47.826 0.00 0.00 32.11 2.92
397 398 3.567164 TCACCCGAGGTAATCTTACGATC 59.433 47.826 0.00 0.00 32.11 3.69
398 399 3.559069 TCACCCGAGGTAATCTTACGAT 58.441 45.455 0.00 0.00 32.11 3.73
399 400 3.003394 TCACCCGAGGTAATCTTACGA 57.997 47.619 0.00 0.00 32.11 3.43
400 401 3.379372 TCTTCACCCGAGGTAATCTTACG 59.621 47.826 0.00 0.00 32.11 3.18
401 402 4.996788 TCTTCACCCGAGGTAATCTTAC 57.003 45.455 0.00 0.00 32.11 2.34
402 403 7.343833 AGTTATTCTTCACCCGAGGTAATCTTA 59.656 37.037 0.00 0.00 32.11 2.10
403 404 6.156429 AGTTATTCTTCACCCGAGGTAATCTT 59.844 38.462 0.00 0.00 32.11 2.40
404 405 5.661759 AGTTATTCTTCACCCGAGGTAATCT 59.338 40.000 0.00 0.00 32.11 2.40
405 406 5.915175 AGTTATTCTTCACCCGAGGTAATC 58.085 41.667 0.00 0.00 32.11 1.75
406 407 5.952347 AGTTATTCTTCACCCGAGGTAAT 57.048 39.130 0.00 0.00 32.11 1.89
407 408 5.750352 AAGTTATTCTTCACCCGAGGTAA 57.250 39.130 0.00 0.00 32.11 2.85
408 409 7.427989 AATAAGTTATTCTTCACCCGAGGTA 57.572 36.000 2.10 0.00 37.56 3.08
409 410 5.952347 ATAAGTTATTCTTCACCCGAGGT 57.048 39.130 0.00 0.00 37.56 3.85
410 411 6.846325 GAATAAGTTATTCTTCACCCGAGG 57.154 41.667 22.93 0.00 41.00 4.63
419 420 9.397480 ACCCAGGGTGCAGAATAAGTTATTCTT 62.397 40.741 28.07 14.74 42.47 2.52
420 421 8.008283 ACCCAGGGTGCAGAATAAGTTATTCT 62.008 42.308 25.91 25.91 44.21 2.40
421 422 4.580580 CCCAGGGTGCAGAATAAGTTATTC 59.419 45.833 22.80 22.80 43.77 1.75
422 423 4.017499 ACCCAGGGTGCAGAATAAGTTATT 60.017 41.667 11.70 7.87 32.98 1.40
423 424 3.527665 ACCCAGGGTGCAGAATAAGTTAT 59.472 43.478 11.70 0.00 32.98 1.89
424 425 2.916934 ACCCAGGGTGCAGAATAAGTTA 59.083 45.455 11.70 0.00 32.98 2.24
425 426 1.710809 ACCCAGGGTGCAGAATAAGTT 59.289 47.619 11.70 0.00 32.98 2.66
426 427 1.372501 ACCCAGGGTGCAGAATAAGT 58.627 50.000 11.70 0.00 32.98 2.24
437 438 4.080526 GTGTTACTATTCATCACCCAGGGT 60.081 45.833 4.76 4.76 35.62 4.34
438 439 4.164221 AGTGTTACTATTCATCACCCAGGG 59.836 45.833 2.85 2.85 0.00 4.45
439 440 5.359194 AGTGTTACTATTCATCACCCAGG 57.641 43.478 0.00 0.00 0.00 4.45
453 454 9.524496 TGGGTGACGAATATATATAGTGTTACT 57.476 33.333 0.00 0.00 0.00 2.24
454 455 9.784680 CTGGGTGACGAATATATATAGTGTTAC 57.215 37.037 0.00 3.51 0.00 2.50
455 456 8.963725 CCTGGGTGACGAATATATATAGTGTTA 58.036 37.037 0.00 0.00 0.00 2.41
456 457 7.093465 CCCTGGGTGACGAATATATATAGTGTT 60.093 40.741 3.97 0.00 0.00 3.32
457 458 6.380274 CCCTGGGTGACGAATATATATAGTGT 59.620 42.308 3.97 0.00 0.00 3.55
458 459 6.380274 ACCCTGGGTGACGAATATATATAGTG 59.620 42.308 19.82 0.00 32.98 2.74
459 460 6.500336 ACCCTGGGTGACGAATATATATAGT 58.500 40.000 19.82 0.00 32.98 2.12
669 670 1.939980 ACGGGGCTACTTCTCTCTTT 58.060 50.000 0.00 0.00 0.00 2.52
893 894 4.034975 CGGACATGCAAAACAAACCAAAAT 59.965 37.500 0.00 0.00 0.00 1.82
1081 1082 5.805994 GTCTCGGTACTCTGATCGAAAATTT 59.194 40.000 0.00 0.00 0.00 1.82
1318 1319 1.584724 AACATCTCCCATTCTCCGGT 58.415 50.000 0.00 0.00 0.00 5.28
1688 1690 5.876357 ACAAACTCCCTAATTCAACTGCTA 58.124 37.500 0.00 0.00 0.00 3.49
1802 1805 0.459585 GTGCGGCCGATTACTCTGAA 60.460 55.000 33.48 0.00 0.00 3.02
1997 2000 4.155826 CACTTCTAGAGATAGGGCATCGAG 59.844 50.000 0.00 0.00 38.81 4.04
2351 2355 3.189080 CAGATCAGAAAATCACGGCAACA 59.811 43.478 0.00 0.00 0.00 3.33
2439 2443 1.243342 CCATGCCGCCTTTCACTTCA 61.243 55.000 0.00 0.00 0.00 3.02


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.