Multiple sequence alignment - TraesCS5D01G343500

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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 TraesCS5D01G343500 chr5D 100.000 4463 0 0 1 4463 431602563 431607025 0.000000e+00 8242.0
1 TraesCS5D01G343500 chr5D 87.427 684 73 9 3658 4330 431613219 431613900 0.000000e+00 774.0
2 TraesCS5D01G343500 chr5D 87.712 236 27 2 3422 3657 431612943 431613176 1.580000e-69 274.0
3 TraesCS5D01G343500 chr5D 89.610 77 3 4 1 76 452200786 452200858 4.750000e-15 93.5
4 TraesCS5D01G343500 chr5A 93.680 4367 209 29 115 4463 546691508 546695825 0.000000e+00 6473.0
5 TraesCS5D01G343500 chr5A 93.421 4423 198 35 53 4463 546976035 546971694 0.000000e+00 6469.0
6 TraesCS5D01G343500 chr5A 85.337 832 89 20 3661 4462 546897786 546896958 0.000000e+00 830.0
7 TraesCS5D01G343500 chr5A 82.709 561 60 20 3658 4206 546699162 546699697 8.740000e-127 464.0
8 TraesCS5D01G343500 chr5A 89.412 170 17 1 3492 3661 546698955 546699123 3.500000e-51 213.0
9 TraesCS5D01G343500 chr5B 95.540 3879 136 19 599 4463 521147530 521151385 0.000000e+00 6170.0
10 TraesCS5D01G343500 chr5B 87.007 685 77 8 3658 4330 521156846 521157530 0.000000e+00 761.0
11 TraesCS5D01G343500 chr5B 84.597 409 55 7 53 459 521142818 521143220 2.500000e-107 399.0
12 TraesCS5D01G343500 chr5B 87.660 235 28 1 3427 3661 521156574 521156807 5.690000e-69 272.0
13 TraesCS5D01G343500 chr3D 82.129 263 39 5 52 312 607875307 607875563 7.520000e-53 219.0
14 TraesCS5D01G343500 chr3D 100.000 50 0 0 1 50 28731186 28731235 4.750000e-15 93.5
15 TraesCS5D01G343500 chr6A 79.496 278 49 7 46 320 47896325 47896053 1.640000e-44 191.0
16 TraesCS5D01G343500 chr6D 79.026 267 49 5 48 312 383222263 383222524 4.590000e-40 176.0
17 TraesCS5D01G343500 chr6D 87.356 87 4 5 1 82 71496389 71496305 4.750000e-15 93.5
18 TraesCS5D01G343500 chr4A 78.417 278 53 6 47 320 203620225 203620499 1.650000e-39 174.0
19 TraesCS5D01G343500 chr4A 86.726 113 14 1 48 159 453680752 453680864 1.690000e-24 124.0
20 TraesCS5D01G343500 chr2D 81.095 201 38 0 47 247 516913259 516913459 1.280000e-35 161.0
21 TraesCS5D01G343500 chrUn 77.352 287 46 9 47 331 143897026 143896757 7.730000e-33 152.0
22 TraesCS5D01G343500 chr1D 79.343 213 41 3 95 305 148084511 148084300 3.600000e-31 147.0
23 TraesCS5D01G343500 chr3B 88.696 115 13 0 52 166 817415352 817415466 1.670000e-29 141.0
24 TraesCS5D01G343500 chr3B 89.474 76 4 3 1 74 47685664 47685591 4.750000e-15 93.5
25 TraesCS5D01G343500 chr3A 96.774 62 0 2 1 62 74970487 74970428 7.900000e-18 102.0
26 TraesCS5D01G343500 chr7B 86.316 95 7 6 1 89 213424404 213424310 1.020000e-16 99.0
27 TraesCS5D01G343500 chr2A 87.209 86 5 4 1 81 585022474 585022390 4.750000e-15 93.5
28 TraesCS5D01G343500 chr7A 86.364 88 7 4 1 88 273593558 273593640 1.710000e-14 91.6
29 TraesCS5D01G343500 chr7D 85.393 89 8 5 1 84 592123404 592123316 2.210000e-13 87.9


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 TraesCS5D01G343500 chr5D 431602563 431607025 4462 False 8242.000000 8242 100.000000 1 4463 1 chr5D.!!$F1 4462
1 TraesCS5D01G343500 chr5D 431612943 431613900 957 False 524.000000 774 87.569500 3422 4330 2 chr5D.!!$F3 908
2 TraesCS5D01G343500 chr5A 546971694 546976035 4341 True 6469.000000 6469 93.421000 53 4463 1 chr5A.!!$R2 4410
3 TraesCS5D01G343500 chr5A 546691508 546699697 8189 False 2383.333333 6473 88.600333 115 4463 3 chr5A.!!$F1 4348
4 TraesCS5D01G343500 chr5A 546896958 546897786 828 True 830.000000 830 85.337000 3661 4462 1 chr5A.!!$R1 801
5 TraesCS5D01G343500 chr5B 521147530 521151385 3855 False 6170.000000 6170 95.540000 599 4463 1 chr5B.!!$F2 3864
6 TraesCS5D01G343500 chr5B 521156574 521157530 956 False 516.500000 761 87.333500 3427 4330 2 chr5B.!!$F3 903

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
944 972 0.171231 GCGGCTTTCTTTCCATCCAC 59.829 55.0 0.0 0.0 0.0 4.02 F
1884 1924 0.257328 TGTTGAGGGAAGGTGTTGCA 59.743 50.0 0.0 0.0 0.0 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2456 2496 1.118838 AGCTATCTCACAGGCCTCAC 58.881 55.000 0.00 0.0 0.0 3.51 R
3822 3910 2.858745 AGTTTACGGCCAAGAACACAT 58.141 42.857 2.24 0.0 0.0 3.21 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
34 35 7.881775 AACAACTTTATTATTGCCTCTAGGG 57.118 36.000 0.00 0.00 35.18 3.53
47 48 4.982241 CCTCTAGGGCATATTTCCTTCA 57.018 45.455 0.00 0.00 34.75 3.02
48 49 4.646572 CCTCTAGGGCATATTTCCTTCAC 58.353 47.826 0.00 0.00 34.75 3.18
49 50 4.103153 CCTCTAGGGCATATTTCCTTCACA 59.897 45.833 0.00 0.00 34.75 3.58
50 51 5.296151 TCTAGGGCATATTTCCTTCACAG 57.704 43.478 0.00 0.00 34.75 3.66
51 52 4.721776 TCTAGGGCATATTTCCTTCACAGT 59.278 41.667 0.00 0.00 34.75 3.55
60 61 8.408601 GCATATTTCCTTCACAGTTATCATTGT 58.591 33.333 0.00 0.00 0.00 2.71
73 74 8.849168 ACAGTTATCATTGTGAGATAGAGAGAG 58.151 37.037 0.00 0.00 30.32 3.20
76 77 9.844790 GTTATCATTGTGAGATAGAGAGAGATG 57.155 37.037 0.00 0.00 30.32 2.90
84 85 6.262944 GTGAGATAGAGAGAGATGACATGTGT 59.737 42.308 1.15 0.00 0.00 3.72
125 126 7.398618 TGGTCATATAACATTGTCAATGGGTTT 59.601 33.333 25.59 15.18 43.21 3.27
146 147 6.456501 GTTTGACCTGATAGTAACACTGTCT 58.543 40.000 4.95 0.00 37.27 3.41
204 205 7.065085 CGATGGAATCTTTGAGTTGTCTAATGT 59.935 37.037 0.00 0.00 42.58 2.71
205 206 7.439157 TGGAATCTTTGAGTTGTCTAATGTG 57.561 36.000 0.00 0.00 0.00 3.21
207 208 7.719193 TGGAATCTTTGAGTTGTCTAATGTGAA 59.281 33.333 0.00 0.00 0.00 3.18
208 209 8.567948 GGAATCTTTGAGTTGTCTAATGTGAAA 58.432 33.333 0.00 0.00 0.00 2.69
216 217 6.373779 AGTTGTCTAATGTGAAATTTGAGCG 58.626 36.000 0.00 0.00 0.00 5.03
218 219 5.927030 TGTCTAATGTGAAATTTGAGCGAC 58.073 37.500 0.00 0.00 0.00 5.19
234 235 1.324736 GCGACCATCTCACGAAATGAC 59.675 52.381 0.00 0.00 32.37 3.06
235 236 2.881074 CGACCATCTCACGAAATGACT 58.119 47.619 0.00 0.00 32.37 3.41
250 251 9.003112 CACGAAATGACTATATTTTTGAGCAAG 57.997 33.333 0.00 0.00 30.78 4.01
271 272 8.923683 AGCAAGTATAACTTCTAACGAGAAAAC 58.076 33.333 0.00 0.00 41.23 2.43
341 343 9.833917 TTTTAAATAAAATGGTCGGGAAAAGTT 57.166 25.926 0.00 0.00 30.83 2.66
359 361 7.556635 GGAAAAGTTGTAGCCTGGTATTCTTAT 59.443 37.037 0.00 0.00 0.00 1.73
360 362 9.609346 GAAAAGTTGTAGCCTGGTATTCTTATA 57.391 33.333 0.00 0.00 0.00 0.98
361 363 9.614792 AAAAGTTGTAGCCTGGTATTCTTATAG 57.385 33.333 0.00 0.00 0.00 1.31
397 399 3.244875 TGTGGCAAGTGATGGTGTAAGAT 60.245 43.478 0.00 0.00 0.00 2.40
434 443 1.569493 CGCTTTCACAACCCAGACG 59.431 57.895 0.00 0.00 0.00 4.18
459 468 8.390354 CGCTCTTTTCATGAAGTTTGTCATATA 58.610 33.333 8.41 0.00 36.04 0.86
538 551 8.697507 AGGATAAACATTCTGATTTATGGGTC 57.302 34.615 0.75 0.00 32.42 4.46
539 552 7.445402 AGGATAAACATTCTGATTTATGGGTCG 59.555 37.037 0.75 0.00 32.42 4.79
540 553 7.444183 GGATAAACATTCTGATTTATGGGTCGA 59.556 37.037 0.75 0.00 32.42 4.20
541 554 6.436843 AAACATTCTGATTTATGGGTCGAC 57.563 37.500 7.13 7.13 0.00 4.20
542 555 5.359194 ACATTCTGATTTATGGGTCGACT 57.641 39.130 16.46 0.00 0.00 4.18
546 559 7.495934 ACATTCTGATTTATGGGTCGACTAAAG 59.504 37.037 16.46 1.80 0.00 1.85
560 573 2.424246 GACTAAAGGAGACCACCTCTCG 59.576 54.545 0.00 0.00 46.03 4.04
561 574 2.225066 ACTAAAGGAGACCACCTCTCGT 60.225 50.000 0.00 0.00 46.03 4.18
568 581 4.081586 AGGAGACCACCTCTCGTAAAATTC 60.082 45.833 0.00 0.00 46.03 2.17
569 582 4.322499 GGAGACCACCTCTCGTAAAATTCA 60.322 45.833 0.00 0.00 46.03 2.57
591 604 7.462109 TCATGACGAGTTTTCAAAAATTTGG 57.538 32.000 6.08 0.00 38.66 3.28
622 635 9.908152 AACTTTCGAAATTTTAGGGTGAAATAG 57.092 29.630 11.70 0.00 0.00 1.73
630 643 0.257039 AGGGTGAAATAGCAGGGCAG 59.743 55.000 0.00 0.00 0.00 4.85
635 648 3.370527 GGTGAAATAGCAGGGCAGACTTA 60.371 47.826 0.00 0.00 0.00 2.24
636 649 3.873952 GTGAAATAGCAGGGCAGACTTAG 59.126 47.826 0.00 0.00 0.00 2.18
652 665 3.695556 GACTTAGGGTCAGGTAGAGTGAC 59.304 52.174 0.00 0.00 43.94 3.67
653 666 3.334280 ACTTAGGGTCAGGTAGAGTGACT 59.666 47.826 3.44 0.00 43.34 3.41
656 669 2.110188 AGGGTCAGGTAGAGTGACTGAA 59.890 50.000 0.00 0.00 43.34 3.02
658 671 3.056465 GGGTCAGGTAGAGTGACTGAAAG 60.056 52.174 0.00 0.00 43.34 2.62
659 672 3.827302 GGTCAGGTAGAGTGACTGAAAGA 59.173 47.826 0.00 0.00 43.34 2.52
660 673 4.082463 GGTCAGGTAGAGTGACTGAAAGAG 60.082 50.000 0.00 0.00 43.34 2.85
710 723 2.419297 CCCAAACTCATCTCCTTCCTCG 60.419 54.545 0.00 0.00 0.00 4.63
711 724 2.419297 CCAAACTCATCTCCTTCCTCGG 60.419 54.545 0.00 0.00 0.00 4.63
717 730 4.168291 CTCCTTCCTCGGGCTGCC 62.168 72.222 11.05 11.05 0.00 4.85
941 969 0.375106 CTCGCGGCTTTCTTTCCATC 59.625 55.000 6.13 0.00 0.00 3.51
942 970 1.024579 TCGCGGCTTTCTTTCCATCC 61.025 55.000 6.13 0.00 0.00 3.51
943 971 1.305219 CGCGGCTTTCTTTCCATCCA 61.305 55.000 0.00 0.00 0.00 3.41
944 972 0.171231 GCGGCTTTCTTTCCATCCAC 59.829 55.000 0.00 0.00 0.00 4.02
945 973 0.447801 CGGCTTTCTTTCCATCCACG 59.552 55.000 0.00 0.00 0.00 4.94
946 974 1.821216 GGCTTTCTTTCCATCCACGA 58.179 50.000 0.00 0.00 0.00 4.35
947 975 2.369394 GGCTTTCTTTCCATCCACGAT 58.631 47.619 0.00 0.00 0.00 3.73
1175 1215 2.361610 CGAGGCTTGCCCCAATGT 60.362 61.111 8.17 0.00 0.00 2.71
1224 1264 2.919856 ACCGGACAGAGTGCTGCT 60.920 61.111 9.46 0.00 46.26 4.24
1476 1516 2.610479 CCACTACAATGTCGTGCTCTGT 60.610 50.000 11.93 0.00 29.59 3.41
1506 1546 4.162690 GCGAGGCGATGGGACCTT 62.163 66.667 0.00 0.00 36.05 3.50
1719 1759 1.269517 GCTGGAGAGTATGAGAAGGCG 60.270 57.143 0.00 0.00 0.00 5.52
1884 1924 0.257328 TGTTGAGGGAAGGTGTTGCA 59.743 50.000 0.00 0.00 0.00 4.08
1920 1960 6.455360 ACTTTCAACACACTGATTCATGTT 57.545 33.333 0.00 0.00 35.69 2.71
1926 1966 1.895131 ACACTGATTCATGTTTGGGGC 59.105 47.619 0.00 0.00 0.00 5.80
2097 2137 0.755686 AAGCCGAAAAATTGGTGCCA 59.244 45.000 0.00 0.00 0.00 4.92
2229 2269 0.387367 ACACGCAGTCAGCTCTAACG 60.387 55.000 0.00 0.00 41.61 3.18
2295 2335 5.935945 TGGTTTGAGAGGTTCTGTAATCAA 58.064 37.500 0.00 0.00 0.00 2.57
2456 2496 1.003580 TGGGTTAGCAGAGAAGCTTGG 59.996 52.381 2.10 0.00 43.70 3.61
2497 2537 2.731571 GGCATGGAGAGGTACGGCA 61.732 63.158 0.00 0.00 0.00 5.69
3811 3899 7.679783 TCAGTTGAGATAGAATTGGTTTGAGA 58.320 34.615 0.00 0.00 0.00 3.27
3822 3910 7.518188 AGAATTGGTTTGAGAGAGAGGTAAAA 58.482 34.615 0.00 0.00 0.00 1.52
3925 4015 5.376854 AATGACTTACTTTCGCTGCAAAT 57.623 34.783 0.00 0.00 0.00 2.32
3983 4078 4.187694 CAGAATAAGCACCTCCACTTCTC 58.812 47.826 0.00 0.00 0.00 2.87
4041 4147 8.827177 CAACTGGATTCTGTAGTTGTTAGTAA 57.173 34.615 14.90 0.00 43.75 2.24
4186 4295 4.202326 ACCACCTTCGTCTTCTGTTTACAT 60.202 41.667 0.00 0.00 0.00 2.29
4209 4318 6.441093 TGCATCAGAGGTTAAATTGCTAAG 57.559 37.500 0.00 0.00 0.00 2.18
4228 4357 7.282585 TGCTAAGGTATATTTTGCTGTCTGAT 58.717 34.615 7.48 0.00 0.00 2.90
4232 4361 7.325660 AGGTATATTTTGCTGTCTGATGTTG 57.674 36.000 0.00 0.00 0.00 3.33
4384 4517 7.715249 CCAATTTAACTACTATCCTTGCTGCTA 59.285 37.037 0.00 0.00 0.00 3.49
4413 4547 3.071479 GTGCCTTAGTTTCATCCGTCAA 58.929 45.455 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 9.574516 CCCTAGAGGCAATAATAAAGTTGTTAT 57.425 33.333 0.00 0.00 0.00 1.89
9 10 8.974060 CCCTAGAGGCAATAATAAAGTTGTTA 57.026 34.615 0.00 0.00 0.00 2.41
10 11 7.881775 CCCTAGAGGCAATAATAAAGTTGTT 57.118 36.000 0.00 0.00 0.00 2.83
26 27 4.103153 TGTGAAGGAAATATGCCCTAGAGG 59.897 45.833 0.00 0.00 39.47 3.69
27 28 5.163258 ACTGTGAAGGAAATATGCCCTAGAG 60.163 44.000 0.00 0.00 31.36 2.43
28 29 4.721776 ACTGTGAAGGAAATATGCCCTAGA 59.278 41.667 0.00 0.00 31.36 2.43
29 30 5.041191 ACTGTGAAGGAAATATGCCCTAG 57.959 43.478 0.00 0.00 31.36 3.02
30 31 5.450818 AACTGTGAAGGAAATATGCCCTA 57.549 39.130 0.00 0.00 31.36 3.53
31 32 4.322057 AACTGTGAAGGAAATATGCCCT 57.678 40.909 0.00 0.00 0.00 5.19
32 33 5.827797 TGATAACTGTGAAGGAAATATGCCC 59.172 40.000 0.00 0.00 0.00 5.36
33 34 6.942532 TGATAACTGTGAAGGAAATATGCC 57.057 37.500 0.00 0.00 0.00 4.40
34 35 8.408601 ACAATGATAACTGTGAAGGAAATATGC 58.591 33.333 0.00 0.00 0.00 3.14
35 36 9.726232 CACAATGATAACTGTGAAGGAAATATG 57.274 33.333 0.00 0.00 44.68 1.78
36 37 9.685276 TCACAATGATAACTGTGAAGGAAATAT 57.315 29.630 0.00 0.00 46.74 1.28
46 47 8.628280 TCTCTCTATCTCACAATGATAACTGTG 58.372 37.037 0.00 0.00 43.53 3.66
47 48 8.759481 TCTCTCTATCTCACAATGATAACTGT 57.241 34.615 0.00 0.00 0.00 3.55
48 49 9.065798 TCTCTCTCTATCTCACAATGATAACTG 57.934 37.037 0.00 0.00 0.00 3.16
49 50 9.812347 ATCTCTCTCTATCTCACAATGATAACT 57.188 33.333 0.00 0.00 0.00 2.24
50 51 9.844790 CATCTCTCTCTATCTCACAATGATAAC 57.155 37.037 0.00 0.00 0.00 1.89
51 52 9.804977 TCATCTCTCTCTATCTCACAATGATAA 57.195 33.333 0.00 0.00 0.00 1.75
60 61 6.262720 CACACATGTCATCTCTCTCTATCTCA 59.737 42.308 0.00 0.00 0.00 3.27
125 126 7.614192 TCATTAGACAGTGTTACTATCAGGTCA 59.386 37.037 0.00 0.00 0.00 4.02
166 167 3.956199 AGATTCCATCGTTCCGTTAGGTA 59.044 43.478 0.00 0.00 39.05 3.08
194 195 6.370593 GTCGCTCAAATTTCACATTAGACAA 58.629 36.000 0.00 0.00 0.00 3.18
204 205 3.436704 GTGAGATGGTCGCTCAAATTTCA 59.563 43.478 0.00 0.00 43.39 2.69
205 206 3.484229 CGTGAGATGGTCGCTCAAATTTC 60.484 47.826 0.00 0.00 43.39 2.17
207 208 2.002586 CGTGAGATGGTCGCTCAAATT 58.997 47.619 0.00 0.00 43.39 1.82
208 209 1.204704 TCGTGAGATGGTCGCTCAAAT 59.795 47.619 0.00 0.00 43.39 2.32
216 217 8.594881 AAATATAGTCATTTCGTGAGATGGTC 57.405 34.615 1.12 0.00 41.60 4.02
218 219 9.655769 CAAAAATATAGTCATTTCGTGAGATGG 57.344 33.333 1.12 0.00 41.60 3.51
271 272 8.678199 TGACACTAGTTGTATCTCACTATTGAG 58.322 37.037 3.74 3.74 44.24 3.02
319 321 6.822442 ACAACTTTTCCCGACCATTTTATTT 58.178 32.000 0.00 0.00 0.00 1.40
332 334 2.287977 ACCAGGCTACAACTTTTCCC 57.712 50.000 0.00 0.00 0.00 3.97
333 335 5.254115 AGAATACCAGGCTACAACTTTTCC 58.746 41.667 0.00 0.00 0.00 3.13
359 361 8.519526 CACTTGCCACAAACCTTTATTTATCTA 58.480 33.333 0.00 0.00 0.00 1.98
360 362 7.232534 TCACTTGCCACAAACCTTTATTTATCT 59.767 33.333 0.00 0.00 0.00 1.98
361 363 7.375053 TCACTTGCCACAAACCTTTATTTATC 58.625 34.615 0.00 0.00 0.00 1.75
374 376 2.647683 TACACCATCACTTGCCACAA 57.352 45.000 0.00 0.00 0.00 3.33
379 381 2.030946 GCGATCTTACACCATCACTTGC 59.969 50.000 0.00 0.00 0.00 4.01
397 399 1.679305 GGAGAGTGAGTGAGGGCGA 60.679 63.158 0.00 0.00 0.00 5.54
528 541 5.163332 GGTCTCCTTTAGTCGACCCATAAAT 60.163 44.000 13.01 0.00 39.96 1.40
529 542 4.161001 GGTCTCCTTTAGTCGACCCATAAA 59.839 45.833 13.01 9.84 39.96 1.40
530 543 3.703052 GGTCTCCTTTAGTCGACCCATAA 59.297 47.826 13.01 1.46 39.96 1.90
531 544 3.294214 GGTCTCCTTTAGTCGACCCATA 58.706 50.000 13.01 0.00 39.96 2.74
532 545 2.108970 GGTCTCCTTTAGTCGACCCAT 58.891 52.381 13.01 0.00 39.96 4.00
533 546 1.203087 TGGTCTCCTTTAGTCGACCCA 60.203 52.381 13.01 6.10 44.08 4.51
534 547 1.204231 GTGGTCTCCTTTAGTCGACCC 59.796 57.143 13.01 3.22 44.08 4.46
535 548 1.204231 GGTGGTCTCCTTTAGTCGACC 59.796 57.143 13.01 0.00 44.76 4.79
536 549 2.164017 GAGGTGGTCTCCTTTAGTCGAC 59.836 54.545 7.70 7.70 38.02 4.20
537 550 2.041350 AGAGGTGGTCTCCTTTAGTCGA 59.959 50.000 0.00 0.00 43.44 4.20
538 551 2.424246 GAGAGGTGGTCTCCTTTAGTCG 59.576 54.545 0.00 0.00 45.57 4.18
568 581 7.462109 TCCAAATTTTTGAAAACTCGTCATG 57.538 32.000 4.63 0.00 40.55 3.07
569 582 7.254421 GCTTCCAAATTTTTGAAAACTCGTCAT 60.254 33.333 4.63 0.00 40.55 3.06
591 604 6.143919 CACCCTAAAATTTCGAAAGTTGCTTC 59.856 38.462 22.65 0.00 0.00 3.86
622 635 1.222113 GACCCTAAGTCTGCCCTGC 59.778 63.158 0.00 0.00 42.69 4.85
630 643 3.695556 GTCACTCTACCTGACCCTAAGTC 59.304 52.174 0.00 0.00 46.51 3.01
635 648 1.711375 TCAGTCACTCTACCTGACCCT 59.289 52.381 0.00 0.00 39.15 4.34
636 649 2.217510 TCAGTCACTCTACCTGACCC 57.782 55.000 0.00 0.00 39.15 4.46
652 665 5.474532 TGGATGTCAAAATCACCTCTTTCAG 59.525 40.000 0.00 0.00 0.00 3.02
653 666 5.241506 GTGGATGTCAAAATCACCTCTTTCA 59.758 40.000 0.00 0.00 0.00 2.69
656 669 4.728772 TGTGGATGTCAAAATCACCTCTT 58.271 39.130 0.00 0.00 0.00 2.85
658 671 4.096984 GGATGTGGATGTCAAAATCACCTC 59.903 45.833 0.00 0.00 0.00 3.85
659 672 4.019174 GGATGTGGATGTCAAAATCACCT 58.981 43.478 0.00 0.00 0.00 4.00
660 673 3.763360 TGGATGTGGATGTCAAAATCACC 59.237 43.478 0.00 0.00 0.00 4.02
724 737 2.171209 ATTTTGGAGCGGCTTTGGGC 62.171 55.000 2.97 0.00 40.90 5.36
899 919 3.130633 TCATACCTCGAAATCAATGGCG 58.869 45.455 0.00 0.00 0.00 5.69
941 969 1.904287 TTTGGGTCCAGAAATCGTGG 58.096 50.000 0.00 0.00 36.28 4.94
942 970 3.377172 GGTATTTGGGTCCAGAAATCGTG 59.623 47.826 2.18 0.00 0.00 4.35
943 971 3.617284 GGTATTTGGGTCCAGAAATCGT 58.383 45.455 2.18 0.00 0.00 3.73
944 972 2.612212 CGGTATTTGGGTCCAGAAATCG 59.388 50.000 2.18 0.00 0.00 3.34
945 973 2.949644 CCGGTATTTGGGTCCAGAAATC 59.050 50.000 0.00 0.00 0.00 2.17
946 974 2.948600 GCCGGTATTTGGGTCCAGAAAT 60.949 50.000 1.90 0.00 0.00 2.17
947 975 1.614850 GCCGGTATTTGGGTCCAGAAA 60.615 52.381 1.90 0.00 0.00 2.52
1224 1264 4.676951 CCCTTCCCCCTTTGCGCA 62.677 66.667 5.66 5.66 0.00 6.09
1495 1535 2.511600 GGCGACAAGGTCCCATCG 60.512 66.667 3.26 3.26 37.63 3.84
1614 1654 3.329889 TCCCCGAGCCACAGCAAT 61.330 61.111 0.00 0.00 43.56 3.56
1719 1759 3.823304 ACCATCTTTGAAAGAACAGCTCC 59.177 43.478 12.10 0.00 41.63 4.70
1884 1924 5.703592 TGTGTTGAAAGTAATAATGCTCGGT 59.296 36.000 0.00 0.00 0.00 4.69
1899 1939 6.041511 CCAAACATGAATCAGTGTGTTGAAA 58.958 36.000 0.00 0.00 35.20 2.69
1920 1960 2.685106 TCTTATGGTGTTTGCCCCAA 57.315 45.000 0.00 0.00 33.66 4.12
2097 2137 2.037136 GCGGCAGCTCACAACATCT 61.037 57.895 0.00 0.00 41.01 2.90
2229 2269 4.973168 TCCCAGCATTAACATACATCCTC 58.027 43.478 0.00 0.00 0.00 3.71
2295 2335 2.039084 AGAAAAGCACTCGGAGTCCATT 59.961 45.455 7.89 0.00 0.00 3.16
2456 2496 1.118838 AGCTATCTCACAGGCCTCAC 58.881 55.000 0.00 0.00 0.00 3.51
2786 2826 5.415221 CAGCCTTTGTCACTAAACCAAAAA 58.585 37.500 0.00 0.00 0.00 1.94
3811 3899 4.762251 GCCAAGAACACATTTTACCTCTCT 59.238 41.667 0.00 0.00 0.00 3.10
3822 3910 2.858745 AGTTTACGGCCAAGAACACAT 58.141 42.857 2.24 0.00 0.00 3.21
3916 4006 4.410492 ACTACAGAGAAAATTTGCAGCG 57.590 40.909 0.00 0.00 0.00 5.18
3925 4015 9.457436 ACAAGTTAAAAGGAACTACAGAGAAAA 57.543 29.630 0.00 0.00 38.49 2.29
3983 4078 0.107214 AGGGCATATGGTCCAACGTG 60.107 55.000 4.56 0.00 46.80 4.49
4115 4222 7.040755 TGCTTAGTAAATGCTTAACTTCTTGCA 60.041 33.333 0.00 0.00 39.83 4.08
4186 4295 5.357878 CCTTAGCAATTTAACCTCTGATGCA 59.642 40.000 0.00 0.00 34.89 3.96
4209 4318 6.498304 CCAACATCAGACAGCAAAATATACC 58.502 40.000 0.00 0.00 0.00 2.73
4228 4357 9.166173 GATGATATTATAGTATTGCAGCCAACA 57.834 33.333 0.00 0.00 32.95 3.33
4232 4361 8.954950 ACTGATGATATTATAGTATTGCAGCC 57.045 34.615 0.00 0.00 0.00 4.85
4377 4509 2.517959 AGGCACTGAATTTTAGCAGCA 58.482 42.857 0.00 0.00 37.18 4.41
4384 4517 6.570378 CGGATGAAACTAAGGCACTGAATTTT 60.570 38.462 0.00 0.00 40.86 1.82


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

AutoCloner maintained by Alex Coulton.