Multiple sequence alignment - TraesCS2D01G414600

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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 TraesCS2D01G414600 chr2D 100.000 2870 0 0 1 2870 528634297 528637166 0.000000e+00 5301
1 TraesCS2D01G414600 chr2B 92.145 1706 71 28 776 2469 627072884 627074538 0.000000e+00 2350
2 TraesCS2D01G414600 chr2B 86.990 515 38 14 268 771 627072331 627072827 1.160000e-153 553
3 TraesCS2D01G414600 chr2B 90.819 403 15 14 2489 2870 627074589 627074990 1.180000e-143 520
4 TraesCS2D01G414600 chr2B 86.256 211 24 3 1094 1304 17896600 17896395 1.030000e-54 224
5 TraesCS2D01G414600 chr2B 87.755 147 15 2 1 144 627072005 627072151 4.920000e-38 169
6 TraesCS2D01G414600 chr2A 87.258 2166 122 53 252 2342 673326211 673328297 0.000000e+00 2329
7 TraesCS2D01G414600 chr2A 86.571 417 21 17 2489 2870 673328422 673328838 7.350000e-116 427
8 TraesCS2D01G414600 chr2A 88.660 194 12 5 1 185 673324255 673324447 8.000000e-56 228
9 TraesCS2D01G414600 chr2A 89.071 183 9 4 295 476 673324468 673324640 1.730000e-52 217
10 TraesCS2D01G414600 chr6A 84.615 689 77 21 1095 1777 454712539 454711874 0.000000e+00 658
11 TraesCS2D01G414600 chr6A 85.632 174 23 2 1418 1590 454934518 454934690 6.320000e-42 182
12 TraesCS2D01G414600 chr6D 83.576 688 80 23 1095 1777 317106279 317105620 5.260000e-172 614
13 TraesCS2D01G414600 chr6D 85.632 174 23 2 1418 1590 317414366 317414538 6.320000e-42 182
14 TraesCS2D01G414600 chr6B 81.659 687 83 26 1095 1777 507404507 507405154 5.440000e-147 531
15 TraesCS2D01G414600 chr6B 95.312 64 3 0 1215 1278 659580540 659580603 5.060000e-18 102
16 TraesCS2D01G414600 chr1D 85.632 174 23 2 1418 1590 307420814 307420642 6.320000e-42 182
17 TraesCS2D01G414600 chr1D 86.364 154 16 5 1414 1566 409799205 409799056 2.290000e-36 163


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 TraesCS2D01G414600 chr2D 528634297 528637166 2869 False 5301.00 5301 100.00000 1 2870 1 chr2D.!!$F1 2869
1 TraesCS2D01G414600 chr2B 627072005 627074990 2985 False 898.00 2350 89.42725 1 2870 4 chr2B.!!$F1 2869
2 TraesCS2D01G414600 chr2A 673324255 673328838 4583 False 800.25 2329 87.89000 1 2870 4 chr2A.!!$F1 2869
3 TraesCS2D01G414600 chr6A 454711874 454712539 665 True 658.00 658 84.61500 1095 1777 1 chr6A.!!$R1 682
4 TraesCS2D01G414600 chr6D 317105620 317106279 659 True 614.00 614 83.57600 1095 1777 1 chr6D.!!$R1 682
5 TraesCS2D01G414600 chr6B 507404507 507405154 647 False 531.00 531 81.65900 1095 1777 1 chr6B.!!$F1 682

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
292 367 0.035317 TGCAAGCGGTCTTCAGATGT 59.965 50.0 0.0 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1913 3906 0.032403 ATTGCACTTGCGCATTGTGT 59.968 45.0 30.75 18.26 45.83 3.72 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
69 72 2.970974 GCAAGCTTGCGGTCCACTC 61.971 63.158 33.75 7.41 45.11 3.51
109 112 1.602377 CGTTTTGTCAGGGTTCAGACC 59.398 52.381 0.00 0.00 45.75 3.85
185 217 5.346822 ACGAGGACAATAAACAATCACGTAC 59.653 40.000 0.00 0.00 0.00 3.67
188 220 7.253552 CGAGGACAATAAACAATCACGTACTAC 60.254 40.741 0.00 0.00 0.00 2.73
210 242 2.428569 GTCGTGTCGAGCAAGCGA 60.429 61.111 0.00 0.00 36.23 4.93
211 243 2.126850 TCGTGTCGAGCAAGCGAG 60.127 61.111 0.00 0.00 41.49 5.03
212 244 3.832171 CGTGTCGAGCAAGCGAGC 61.832 66.667 0.00 0.00 41.49 5.03
213 245 2.734723 GTGTCGAGCAAGCGAGCA 60.735 61.111 6.21 0.00 41.49 4.26
214 246 2.431430 TGTCGAGCAAGCGAGCAG 60.431 61.111 6.21 0.29 41.49 4.24
215 247 2.126307 GTCGAGCAAGCGAGCAGA 60.126 61.111 6.21 2.52 41.49 4.26
216 248 1.518133 GTCGAGCAAGCGAGCAGAT 60.518 57.895 6.21 0.00 41.49 2.90
235 267 2.839486 TGCTGTACCAAGTCCTGAAG 57.161 50.000 0.00 0.00 0.00 3.02
236 268 2.047061 TGCTGTACCAAGTCCTGAAGT 58.953 47.619 0.00 0.00 0.00 3.01
239 271 3.318017 CTGTACCAAGTCCTGAAGTTCG 58.682 50.000 0.00 0.00 0.00 3.95
243 275 2.224066 ACCAAGTCCTGAAGTTCGTCAG 60.224 50.000 8.37 8.37 43.98 3.51
245 277 2.797156 CAAGTCCTGAAGTTCGTCAGTG 59.203 50.000 12.88 6.50 43.02 3.66
247 279 2.128035 GTCCTGAAGTTCGTCAGTGTG 58.872 52.381 12.88 1.29 43.02 3.82
248 280 1.068588 TCCTGAAGTTCGTCAGTGTGG 59.931 52.381 12.88 1.64 43.02 4.17
257 289 0.939577 CGTCAGTGTGGGAGTGAACG 60.940 60.000 0.00 0.00 35.70 3.95
258 290 0.387929 GTCAGTGTGGGAGTGAACGA 59.612 55.000 0.00 0.00 35.70 3.85
264 296 0.106149 GTGGGAGTGAACGAAGGTGT 59.894 55.000 0.00 0.00 0.00 4.16
265 297 1.342174 GTGGGAGTGAACGAAGGTGTA 59.658 52.381 0.00 0.00 0.00 2.90
266 298 1.342174 TGGGAGTGAACGAAGGTGTAC 59.658 52.381 0.00 0.00 0.00 2.90
289 364 1.301716 GGTGCAAGCGGTCTTCAGA 60.302 57.895 0.00 0.00 0.00 3.27
291 366 0.445436 GTGCAAGCGGTCTTCAGATG 59.555 55.000 0.00 0.00 0.00 2.90
292 367 0.035317 TGCAAGCGGTCTTCAGATGT 59.965 50.000 0.00 0.00 0.00 3.06
337 412 6.515272 AATTGCAGTACACAAGGGAATAAG 57.485 37.500 7.33 0.00 0.00 1.73
345 420 3.268595 ACACAAGGGAATAAGGTAAGGGG 59.731 47.826 0.00 0.00 0.00 4.79
350 426 3.530564 AGGGAATAAGGTAAGGGGTTTCC 59.469 47.826 0.00 0.00 0.00 3.13
390 466 2.292103 AGAGAAGCGATTCTGCAGAC 57.708 50.000 22.47 5.76 37.31 3.51
417 2274 4.870426 TCGACAAAACAATGATAGAGGAGC 59.130 41.667 0.00 0.00 0.00 4.70
439 2296 8.677300 GGAGCATAAAAGAACAAGTTCATCATA 58.323 33.333 14.69 3.72 41.84 2.15
522 2394 1.068753 CGAGCGATCCAGAAGGCAT 59.931 57.895 0.00 0.00 33.74 4.40
524 2396 1.505477 GAGCGATCCAGAAGGCATGC 61.505 60.000 9.90 9.90 33.74 4.06
538 2410 5.533903 AGAAGGCATGCGAATATGAAAATCT 59.466 36.000 12.44 0.00 0.00 2.40
540 2412 4.823442 AGGCATGCGAATATGAAAATCTCA 59.177 37.500 12.44 0.00 38.81 3.27
548 2435 5.332883 CGAATATGAAAATCTCAGCCTCACG 60.333 44.000 0.00 0.00 37.52 4.35
553 2440 1.107114 AATCTCAGCCTCACGATCGT 58.893 50.000 16.60 16.60 0.00 3.73
554 2441 0.383590 ATCTCAGCCTCACGATCGTG 59.616 55.000 36.47 36.47 46.64 4.35
635 2524 1.682323 GGGCTACCCAACAAAAACGAA 59.318 47.619 0.00 0.00 44.65 3.85
646 2535 5.332506 CCAACAAAAACGAAACATGATGAGC 60.333 40.000 0.00 0.00 0.00 4.26
647 2536 3.974401 ACAAAAACGAAACATGATGAGCG 59.026 39.130 0.00 2.16 0.00 5.03
648 2537 2.900122 AAACGAAACATGATGAGCGG 57.100 45.000 0.00 0.00 0.00 5.52
649 2538 1.086696 AACGAAACATGATGAGCGGG 58.913 50.000 0.00 0.00 0.00 6.13
650 2539 0.249120 ACGAAACATGATGAGCGGGA 59.751 50.000 0.00 0.00 0.00 5.14
651 2540 0.933097 CGAAACATGATGAGCGGGAG 59.067 55.000 0.00 0.00 0.00 4.30
743 2632 2.037902 GCTAAACCTATCTGGCCCTCTC 59.962 54.545 0.00 0.00 40.22 3.20
745 2634 0.760945 AACCTATCTGGCCCTCTCGG 60.761 60.000 0.00 0.00 40.22 4.63
765 2654 7.687388 TCTCGGCCTCTTCTAGATTATTACTA 58.313 38.462 0.00 0.00 0.00 1.82
766 2655 7.825270 TCTCGGCCTCTTCTAGATTATTACTAG 59.175 40.741 0.00 0.00 38.76 2.57
767 2656 7.460071 TCGGCCTCTTCTAGATTATTACTAGT 58.540 38.462 0.00 0.00 38.59 2.57
768 2657 8.600668 TCGGCCTCTTCTAGATTATTACTAGTA 58.399 37.037 0.00 0.00 38.59 1.82
769 2658 8.667463 CGGCCTCTTCTAGATTATTACTAGTAC 58.333 40.741 0.91 0.00 38.59 2.73
770 2659 9.743581 GGCCTCTTCTAGATTATTACTAGTACT 57.256 37.037 0.91 0.00 38.59 2.73
807 2747 1.102978 GGTGGATGGAAACCCATTCG 58.897 55.000 0.00 0.00 44.15 3.34
968 2910 1.697982 GAGTACAGACCCAACCCAACT 59.302 52.381 0.00 0.00 0.00 3.16
984 2926 0.969894 AACTCCGGGAGACAACAGAG 59.030 55.000 30.13 1.62 33.32 3.35
985 2927 1.216710 CTCCGGGAGACAACAGAGC 59.783 63.158 19.57 0.00 0.00 4.09
986 2928 1.533033 TCCGGGAGACAACAGAGCA 60.533 57.895 0.00 0.00 0.00 4.26
987 2929 1.079543 CCGGGAGACAACAGAGCAG 60.080 63.158 0.00 0.00 0.00 4.24
988 2930 1.536073 CCGGGAGACAACAGAGCAGA 61.536 60.000 0.00 0.00 0.00 4.26
999 2941 4.121669 GAGCAGAGCACGGCGAGA 62.122 66.667 16.62 0.00 41.73 4.04
2019 4012 0.034186 GGTGGTGATGGCAATGGAGA 60.034 55.000 0.00 0.00 0.00 3.71
2026 4019 0.536687 ATGGCAATGGAGAGCGATGG 60.537 55.000 0.00 0.00 0.00 3.51
2033 4030 4.257510 GAGAGCGATGGCGAGCGA 62.258 66.667 11.49 0.00 46.35 4.93
2099 4101 2.224523 TGGATATTTGGATGGGTCGAGC 60.225 50.000 5.93 5.93 0.00 5.03
2100 4102 2.427506 GATATTTGGATGGGTCGAGCC 58.572 52.381 26.70 26.70 0.00 4.70
2101 4103 0.105964 TATTTGGATGGGTCGAGCCG 59.894 55.000 27.33 0.00 38.44 5.52
2102 4104 1.910580 ATTTGGATGGGTCGAGCCGT 61.911 55.000 27.79 27.79 38.44 5.68
2103 4105 2.515996 TTTGGATGGGTCGAGCCGTC 62.516 60.000 36.88 36.88 38.44 4.79
2135 4139 1.192146 TAAGCTCGGAGCAACTGGGT 61.192 55.000 29.88 6.30 45.56 4.51
2175 4180 4.823364 ATGATAGTTCCTCCTCTCTCCA 57.177 45.455 0.00 0.00 0.00 3.86
2220 4225 1.401539 GGATCAAAGCGAAACTGTGCC 60.402 52.381 0.00 0.00 33.10 5.01
2229 4234 1.403647 CGAAACTGTGCCAGTATCGGA 60.404 52.381 8.07 0.00 44.62 4.55
2300 4308 5.297278 AGAGTGCGTGTGGTAAAAATTACAA 59.703 36.000 3.00 0.00 0.00 2.41
2301 4309 5.892568 AGTGCGTGTGGTAAAAATTACAAA 58.107 33.333 3.00 0.00 0.00 2.83
2304 4312 5.972382 TGCGTGTGGTAAAAATTACAAACTC 59.028 36.000 3.00 1.74 0.00 3.01
2309 4317 7.697291 GTGTGGTAAAAATTACAAACTCGTGAA 59.303 33.333 3.00 0.00 0.00 3.18
2310 4318 8.407064 TGTGGTAAAAATTACAAACTCGTGAAT 58.593 29.630 3.00 0.00 0.00 2.57
2311 4319 8.898792 GTGGTAAAAATTACAAACTCGTGAATC 58.101 33.333 3.00 0.00 0.00 2.52
2331 4339 3.381045 TCGTGATCGAGCATAATGGAAC 58.619 45.455 6.66 0.00 41.35 3.62
2380 4388 4.853007 AGAGAATTCCAGGGAGTGAATTG 58.147 43.478 0.65 0.00 40.34 2.32
2382 4390 5.003096 AGAATTCCAGGGAGTGAATTGTT 57.997 39.130 0.65 0.00 40.34 2.83
2407 4415 5.543405 ACCCCATTTGTTCTTTGATCAATGA 59.457 36.000 17.55 17.55 0.00 2.57
2410 4418 7.065324 CCCCATTTGTTCTTTGATCAATGAATG 59.935 37.037 29.02 23.64 37.01 2.67
2440 4448 2.689766 GTCACGCACGATCGAAGC 59.310 61.111 24.34 22.55 0.00 3.86
2453 4461 0.389426 TCGAAGCAGCCTAACCGAAC 60.389 55.000 0.00 0.00 0.00 3.95
2454 4462 0.669318 CGAAGCAGCCTAACCGAACA 60.669 55.000 0.00 0.00 0.00 3.18
2455 4463 0.796927 GAAGCAGCCTAACCGAACAC 59.203 55.000 0.00 0.00 0.00 3.32
2456 4464 0.107831 AAGCAGCCTAACCGAACACA 59.892 50.000 0.00 0.00 0.00 3.72
2457 4465 0.324943 AGCAGCCTAACCGAACACAT 59.675 50.000 0.00 0.00 0.00 3.21
2458 4466 0.447801 GCAGCCTAACCGAACACATG 59.552 55.000 0.00 0.00 0.00 3.21
2459 4467 1.943968 GCAGCCTAACCGAACACATGA 60.944 52.381 0.00 0.00 0.00 3.07
2460 4468 2.002586 CAGCCTAACCGAACACATGAG 58.997 52.381 0.00 0.00 0.00 2.90
2461 4469 1.623811 AGCCTAACCGAACACATGAGT 59.376 47.619 0.00 0.00 0.00 3.41
2462 4470 2.000447 GCCTAACCGAACACATGAGTC 59.000 52.381 0.00 0.00 0.00 3.36
2477 4488 3.988379 TGAGTCAAGAAACAATGGCAC 57.012 42.857 0.00 0.00 0.00 5.01
2478 4489 2.622942 TGAGTCAAGAAACAATGGCACC 59.377 45.455 0.00 0.00 0.00 5.01
2480 4491 3.233507 AGTCAAGAAACAATGGCACCAT 58.766 40.909 0.00 0.00 38.46 3.55
2482 4493 2.964464 TCAAGAAACAATGGCACCATGT 59.036 40.909 2.19 1.24 36.68 3.21
2483 4494 3.387374 TCAAGAAACAATGGCACCATGTT 59.613 39.130 2.19 7.21 36.68 2.71
2484 4495 4.586421 TCAAGAAACAATGGCACCATGTTA 59.414 37.500 13.44 0.00 36.68 2.41
2485 4496 5.069648 TCAAGAAACAATGGCACCATGTTAA 59.930 36.000 13.44 0.00 36.68 2.01
2486 4497 5.543507 AGAAACAATGGCACCATGTTAAA 57.456 34.783 13.44 0.00 36.68 1.52
2487 4498 5.296748 AGAAACAATGGCACCATGTTAAAC 58.703 37.500 13.44 9.42 36.68 2.01
2587 4643 2.592861 GCGAGGCCCCATGATGAC 60.593 66.667 0.00 0.00 0.00 3.06
2589 4645 1.224315 CGAGGCCCCATGATGACAA 59.776 57.895 0.00 0.00 0.00 3.18
2590 4646 0.179009 CGAGGCCCCATGATGACAAT 60.179 55.000 0.00 0.00 0.00 2.71
2591 4647 1.072173 CGAGGCCCCATGATGACAATA 59.928 52.381 0.00 0.00 0.00 1.90
2670 4738 0.820074 ACTAGGCTGGAGACGATCGG 60.820 60.000 20.98 0.82 0.00 4.18
2751 4835 0.301687 CGTGCTTATCCATGACGTGC 59.698 55.000 0.00 0.00 0.00 5.34
2762 4847 3.056107 TCCATGACGTGCTAAGTTAAGCT 60.056 43.478 0.00 0.00 43.19 3.74
2837 4922 2.533266 GCAAAATATCCAGCAGTGCAC 58.467 47.619 19.20 9.40 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 63 1.593006 GTATTGAATGCGAGTGGACCG 59.407 52.381 0.00 0.00 0.00 4.79
69 72 2.092681 CGATGGATCCGTATTGAATGCG 59.907 50.000 6.41 8.71 38.14 4.73
122 125 5.453762 CCTTTGCAGGAAGAAAAACCAAGAT 60.454 40.000 0.00 0.00 44.19 2.40
125 128 3.681313 GCCTTTGCAGGAAGAAAAACCAA 60.681 43.478 0.00 0.00 44.19 3.67
140 143 0.035176 TCCAAATTGCCTGCCTTTGC 59.965 50.000 8.11 0.00 38.26 3.68
193 225 2.428569 TCGCTTGCTCGACACGAC 60.429 61.111 0.00 0.00 33.02 4.34
200 232 3.004283 CATCTGCTCGCTTGCTCG 58.996 61.111 0.00 0.00 0.00 5.03
201 233 2.708255 GCATCTGCTCGCTTGCTC 59.292 61.111 0.00 0.00 38.21 4.26
211 243 1.065854 AGGACTTGGTACAGCATCTGC 60.066 52.381 0.00 0.00 42.39 4.26
212 244 2.234661 TCAGGACTTGGTACAGCATCTG 59.765 50.000 0.00 0.00 42.39 2.90
213 245 2.540383 TCAGGACTTGGTACAGCATCT 58.460 47.619 0.00 0.00 42.39 2.90
214 246 3.265791 CTTCAGGACTTGGTACAGCATC 58.734 50.000 0.00 0.00 42.39 3.91
215 247 2.639839 ACTTCAGGACTTGGTACAGCAT 59.360 45.455 0.00 0.00 42.39 3.79
216 248 2.047061 ACTTCAGGACTTGGTACAGCA 58.953 47.619 0.00 0.00 42.39 4.41
221 253 2.960384 TGACGAACTTCAGGACTTGGTA 59.040 45.455 0.00 0.00 0.00 3.25
223 255 2.224066 ACTGACGAACTTCAGGACTTGG 60.224 50.000 11.76 0.00 46.38 3.61
229 261 1.502231 CCACACTGACGAACTTCAGG 58.498 55.000 11.76 4.91 46.38 3.86
235 267 0.387929 TCACTCCCACACTGACGAAC 59.612 55.000 0.00 0.00 0.00 3.95
236 268 1.116308 TTCACTCCCACACTGACGAA 58.884 50.000 0.00 0.00 0.00 3.85
239 271 0.387929 TCGTTCACTCCCACACTGAC 59.612 55.000 0.00 0.00 0.00 3.51
243 275 0.106149 ACCTTCGTTCACTCCCACAC 59.894 55.000 0.00 0.00 0.00 3.82
245 277 0.106149 ACACCTTCGTTCACTCCCAC 59.894 55.000 0.00 0.00 0.00 4.61
247 279 1.668047 CGTACACCTTCGTTCACTCCC 60.668 57.143 0.00 0.00 0.00 4.30
248 280 1.694639 CGTACACCTTCGTTCACTCC 58.305 55.000 0.00 0.00 0.00 3.85
257 289 2.433664 CACCGGGCGTACACCTTC 60.434 66.667 6.32 0.00 0.00 3.46
258 290 4.692475 GCACCGGGCGTACACCTT 62.692 66.667 6.32 0.00 0.00 3.50
280 355 3.330267 GTCACCTTGACATCTGAAGACC 58.670 50.000 1.34 0.00 46.22 3.85
292 367 4.753516 TTCACTTCTCTTGTCACCTTGA 57.246 40.909 0.00 0.00 0.00 3.02
337 412 0.671472 CACGTCGGAAACCCCTTACC 60.671 60.000 0.00 0.00 0.00 2.85
345 420 1.263217 ACTGCATTTCACGTCGGAAAC 59.737 47.619 9.95 2.24 39.40 2.78
350 426 1.260297 TGTCAACTGCATTTCACGTCG 59.740 47.619 0.00 0.00 0.00 5.12
390 466 6.371548 TCCTCTATCATTGTTTTGTCGAAAGG 59.628 38.462 0.00 0.00 0.00 3.11
439 2296 8.274322 TGGGCATATTCTCGGATTATTATTCAT 58.726 33.333 0.00 0.00 0.00 2.57
522 2394 4.454678 AGGCTGAGATTTTCATATTCGCA 58.545 39.130 0.00 0.00 34.68 5.10
524 2396 5.332883 CGTGAGGCTGAGATTTTCATATTCG 60.333 44.000 0.00 0.00 34.68 3.34
548 2435 1.421410 CCGCTACTGTTGGCACGATC 61.421 60.000 0.00 0.00 0.00 3.69
635 2524 0.467384 CTCCTCCCGCTCATCATGTT 59.533 55.000 0.00 0.00 0.00 2.71
646 2535 2.507110 TTTTGCGCTCTCTCCTCCCG 62.507 60.000 9.73 0.00 0.00 5.14
647 2536 0.742635 CTTTTGCGCTCTCTCCTCCC 60.743 60.000 9.73 0.00 0.00 4.30
648 2537 0.742635 CCTTTTGCGCTCTCTCCTCC 60.743 60.000 9.73 0.00 0.00 4.30
649 2538 1.365368 GCCTTTTGCGCTCTCTCCTC 61.365 60.000 9.73 0.00 0.00 3.71
650 2539 1.376553 GCCTTTTGCGCTCTCTCCT 60.377 57.895 9.73 0.00 0.00 3.69
651 2540 3.182312 GCCTTTTGCGCTCTCTCC 58.818 61.111 9.73 0.00 0.00 3.71
743 2632 7.690952 ACTAGTAATAATCTAGAAGAGGCCG 57.309 40.000 0.00 0.00 38.45 6.13
770 2659 9.567776 CCATCCACCAGTAAAATAATACATACA 57.432 33.333 0.00 0.00 0.00 2.29
771 2660 9.787435 TCCATCCACCAGTAAAATAATACATAC 57.213 33.333 0.00 0.00 0.00 2.39
773 2662 9.707957 TTTCCATCCACCAGTAAAATAATACAT 57.292 29.630 0.00 0.00 0.00 2.29
774 2663 8.962679 GTTTCCATCCACCAGTAAAATAATACA 58.037 33.333 0.00 0.00 0.00 2.29
807 2747 2.125269 CCCCGGATTCACGTGACC 60.125 66.667 19.90 16.33 0.00 4.02
968 2910 1.533033 TGCTCTGTTGTCTCCCGGA 60.533 57.895 0.73 0.00 0.00 5.14
984 2926 2.510238 ATTCTCGCCGTGCTCTGC 60.510 61.111 0.00 0.00 0.00 4.26
985 2927 2.806856 GCATTCTCGCCGTGCTCTG 61.807 63.158 0.00 0.00 36.02 3.35
986 2928 2.510238 GCATTCTCGCCGTGCTCT 60.510 61.111 0.00 0.00 36.02 4.09
987 2929 2.510238 AGCATTCTCGCCGTGCTC 60.510 61.111 0.00 0.00 45.42 4.26
999 2941 3.064324 GCCGGGTTCAGCAGCATT 61.064 61.111 2.18 0.00 0.00 3.56
1347 3334 2.123897 GCCTCCTCCTCGCTCTCT 60.124 66.667 0.00 0.00 0.00 3.10
1575 3565 1.219393 GAGCGGGAAGTTGAGGAGG 59.781 63.158 0.00 0.00 0.00 4.30
1686 3676 1.454295 GGAGGAGGAGGAGGACGAC 60.454 68.421 0.00 0.00 0.00 4.34
1719 3712 3.403558 GCCTCGCCCCTCTTCCTT 61.404 66.667 0.00 0.00 0.00 3.36
1912 3905 0.870735 TTGCACTTGCGCATTGTGTG 60.871 50.000 30.75 25.98 45.83 3.82
1913 3906 0.032403 ATTGCACTTGCGCATTGTGT 59.968 45.000 30.75 18.26 45.83 3.72
1914 3907 0.436913 CATTGCACTTGCGCATTGTG 59.563 50.000 28.41 28.41 45.83 3.33
2033 4030 2.202851 CCTGATTGCTCGCTCGCT 60.203 61.111 0.00 0.00 0.00 4.93
2101 4103 2.853003 GAGCTTATCTTCCGTTGTCGAC 59.147 50.000 9.11 9.11 39.71 4.20
2102 4104 2.477357 CGAGCTTATCTTCCGTTGTCGA 60.477 50.000 0.00 0.00 39.71 4.20
2103 4105 1.846782 CGAGCTTATCTTCCGTTGTCG 59.153 52.381 0.00 0.00 0.00 4.35
2104 4106 2.159282 TCCGAGCTTATCTTCCGTTGTC 60.159 50.000 0.00 0.00 0.00 3.18
2105 4107 1.822990 TCCGAGCTTATCTTCCGTTGT 59.177 47.619 0.00 0.00 0.00 3.32
2109 4111 0.385751 TGCTCCGAGCTTATCTTCCG 59.614 55.000 20.87 0.00 42.97 4.30
2135 4139 1.120184 TTCCAGGCCAAATTGCAGCA 61.120 50.000 5.01 0.00 0.00 4.41
2220 4225 0.661552 ACCACGACGATCCGATACTG 59.338 55.000 0.00 0.00 0.00 2.74
2229 4234 1.202582 CTCAGAAGGAACCACGACGAT 59.797 52.381 0.00 0.00 0.00 3.73
2300 4308 2.913777 TCGATCACGATTCACGAGTT 57.086 45.000 0.00 0.00 43.81 3.01
2310 4318 3.068165 AGTTCCATTATGCTCGATCACGA 59.932 43.478 0.00 0.00 46.56 4.35
2311 4319 3.384668 AGTTCCATTATGCTCGATCACG 58.615 45.455 0.00 0.00 41.26 4.35
2373 4381 6.096673 AGAACAAATGGGGTAACAATTCAC 57.903 37.500 0.00 0.00 39.74 3.18
2380 4388 6.339587 TGATCAAAGAACAAATGGGGTAAC 57.660 37.500 0.00 0.00 0.00 2.50
2382 4390 6.723515 TCATTGATCAAAGAACAAATGGGGTA 59.276 34.615 13.09 0.00 28.93 3.69
2410 4418 1.209127 CGTGACGCCAATGGGAAAC 59.791 57.895 0.00 0.00 35.59 2.78
2434 4442 0.389426 GTTCGGTTAGGCTGCTTCGA 60.389 55.000 0.00 0.00 0.00 3.71
2440 4448 2.002586 CTCATGTGTTCGGTTAGGCTG 58.997 52.381 0.00 0.00 0.00 4.85
2453 4461 4.232221 GCCATTGTTTCTTGACTCATGTG 58.768 43.478 0.00 0.00 0.00 3.21
2454 4462 3.890756 TGCCATTGTTTCTTGACTCATGT 59.109 39.130 0.00 0.00 0.00 3.21
2455 4463 4.232221 GTGCCATTGTTTCTTGACTCATG 58.768 43.478 0.00 0.00 0.00 3.07
2456 4464 3.256631 GGTGCCATTGTTTCTTGACTCAT 59.743 43.478 0.00 0.00 0.00 2.90
2457 4465 2.622942 GGTGCCATTGTTTCTTGACTCA 59.377 45.455 0.00 0.00 0.00 3.41
2458 4466 2.622942 TGGTGCCATTGTTTCTTGACTC 59.377 45.455 0.00 0.00 0.00 3.36
2459 4467 2.665165 TGGTGCCATTGTTTCTTGACT 58.335 42.857 0.00 0.00 0.00 3.41
2460 4468 3.243839 ACATGGTGCCATTGTTTCTTGAC 60.244 43.478 0.13 0.00 33.90 3.18
2461 4469 2.964464 ACATGGTGCCATTGTTTCTTGA 59.036 40.909 0.13 0.00 33.90 3.02
2462 4470 3.389925 ACATGGTGCCATTGTTTCTTG 57.610 42.857 0.13 0.00 33.90 3.02
2477 4488 5.382573 CCGTGTTTGTTTGTTTAACATGG 57.617 39.130 10.10 10.10 45.72 3.66
2478 4489 4.268884 CCCCGTGTTTGTTTGTTTAACATG 59.731 41.667 0.00 0.00 45.72 3.21
2480 4491 3.508793 TCCCCGTGTTTGTTTGTTTAACA 59.491 39.130 0.00 0.00 44.81 2.41
2482 4493 5.127356 AGAATCCCCGTGTTTGTTTGTTTAA 59.873 36.000 0.00 0.00 0.00 1.52
2483 4494 4.645588 AGAATCCCCGTGTTTGTTTGTTTA 59.354 37.500 0.00 0.00 0.00 2.01
2484 4495 3.449377 AGAATCCCCGTGTTTGTTTGTTT 59.551 39.130 0.00 0.00 0.00 2.83
2485 4496 3.028130 AGAATCCCCGTGTTTGTTTGTT 58.972 40.909 0.00 0.00 0.00 2.83
2486 4497 2.661718 AGAATCCCCGTGTTTGTTTGT 58.338 42.857 0.00 0.00 0.00 2.83
2487 4498 3.726291 AAGAATCCCCGTGTTTGTTTG 57.274 42.857 0.00 0.00 0.00 2.93
2534 4576 4.265073 CCTCGAATTATGGGGGATTGATC 58.735 47.826 0.00 0.00 0.00 2.92
2587 4643 0.107703 TTGCTCCAGACGGGCTATTG 60.108 55.000 0.00 0.00 36.21 1.90
2589 4645 0.978146 ACTTGCTCCAGACGGGCTAT 60.978 55.000 0.00 0.00 36.21 2.97
2590 4646 1.609501 ACTTGCTCCAGACGGGCTA 60.610 57.895 0.00 0.00 36.21 3.93
2591 4647 2.925170 ACTTGCTCCAGACGGGCT 60.925 61.111 0.00 0.00 36.21 5.19
2655 4718 2.833582 TCCCGATCGTCTCCAGCC 60.834 66.667 15.09 0.00 0.00 4.85
2670 4738 1.079057 GCTTCCCGTTCTCACCTCC 60.079 63.158 0.00 0.00 0.00 4.30
2723 4807 3.678056 TGGATAAGCACGAGTTCAAGT 57.322 42.857 0.00 0.00 0.00 3.16
2751 4835 4.371786 TCATCCATCGCAGCTTAACTTAG 58.628 43.478 0.00 0.00 0.00 2.18
2762 4847 0.602638 GGCGGTTATCATCCATCGCA 60.603 55.000 7.76 0.00 44.14 5.10
2811 4896 2.621998 CTGCTGGATATTTTGCCTGGAG 59.378 50.000 0.00 0.00 35.83 3.86


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

AutoCloner maintained by Alex Coulton.