Multiple sequence alignment - TraesCS5A01G138300

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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 TraesCS5A01G138300 chr5A 100.000 4209 0 0 1 4209 310876109 310871901 0.000000e+00 7773.0
1 TraesCS5A01G138300 chr5A 82.500 160 16 7 498 645 531536562 531536721 3.420000e-26 130.0
2 TraesCS5A01G138300 chr5D 93.119 4258 203 51 2 4206 242355589 242359809 0.000000e+00 6157.0
3 TraesCS5A01G138300 chr5D 82.278 158 15 7 501 645 517846845 517846688 1.590000e-24 124.0
4 TraesCS5A01G138300 chr5D 81.169 154 25 3 6 155 432691729 432691882 2.060000e-23 121.0
5 TraesCS5A01G138300 chr5D 87.654 81 6 2 2759 2839 541806257 541806181 1.610000e-14 91.6
6 TraesCS5A01G138300 chr5B 93.471 2466 110 27 319 2750 259537370 259539818 0.000000e+00 3615.0
7 TraesCS5A01G138300 chr5B 92.241 1495 79 17 2737 4209 259539832 259541311 0.000000e+00 2084.0
8 TraesCS5A01G138300 chr5B 88.798 366 38 3 2 365 259537022 259537386 2.990000e-121 446.0
9 TraesCS5A01G138300 chr5B 87.500 88 8 3 431 516 391460581 391460495 9.630000e-17 99.0
10 TraesCS5A01G138300 chr4D 88.186 838 90 6 1189 2022 109911952 109911120 0.000000e+00 990.0
11 TraesCS5A01G138300 chr4D 94.667 75 3 1 435 508 416060712 416060786 9.560000e-22 115.0
12 TraesCS5A01G138300 chr4A 87.814 837 95 6 1189 2022 466926025 466926857 0.000000e+00 974.0
13 TraesCS5A01G138300 chr4A 94.667 75 3 1 435 508 47751185 47751111 9.560000e-22 115.0
14 TraesCS5A01G138300 chr4B 86.754 838 102 5 1189 2022 171028540 171027708 0.000000e+00 924.0
15 TraesCS5A01G138300 chr4B 91.250 80 5 2 433 510 141541189 141541110 1.600000e-19 108.0
16 TraesCS5A01G138300 chr1A 77.564 1297 231 46 1189 2457 500343352 500342088 0.000000e+00 728.0
17 TraesCS5A01G138300 chr1D 81.312 808 139 12 1217 2018 404970783 404969982 0.000000e+00 645.0
18 TraesCS5A01G138300 chr1D 84.800 125 17 2 6 128 943588 943712 1.590000e-24 124.0
19 TraesCS5A01G138300 chr1D 85.870 92 5 7 2749 2839 298568557 298568641 1.610000e-14 91.6
20 TraesCS5A01G138300 chr3A 82.674 531 88 4 1189 1717 579552998 579553526 6.370000e-128 468.0
21 TraesCS5A01G138300 chr3A 82.609 161 15 8 498 645 566874471 566874631 3.420000e-26 130.0
22 TraesCS5A01G138300 chr3A 90.000 60 5 1 2342 2401 467018983 467019041 4.510000e-10 76.8
23 TraesCS5A01G138300 chr3D 82.298 531 90 4 1189 1717 439838745 439839273 1.380000e-124 457.0
24 TraesCS5A01G138300 chr3D 92.308 78 6 0 431 508 579587104 579587027 1.240000e-20 111.0
25 TraesCS5A01G138300 chr3D 90.476 84 8 0 425 508 590409470 590409553 1.240000e-20 111.0
26 TraesCS5A01G138300 chr3D 92.188 64 5 0 501 564 402801776 402801713 1.610000e-14 91.6
27 TraesCS5A01G138300 chr6B 79.667 300 53 6 1674 1969 717076324 717076029 4.260000e-50 209.0
28 TraesCS5A01G138300 chr6B 88.043 92 5 4 2749 2839 278674611 278674697 2.070000e-18 104.0
29 TraesCS5A01G138300 chr6A 78.333 300 57 6 1674 1969 617657602 617657897 2.000000e-43 187.0
30 TraesCS5A01G138300 chr6A 88.043 92 5 4 2749 2839 209391339 209391425 2.070000e-18 104.0
31 TraesCS5A01G138300 chr6A 87.059 85 5 6 2756 2839 14351067 14350988 1.610000e-14 91.6
32 TraesCS5A01G138300 chr1B 79.167 216 37 7 437 645 273658247 273658033 4.390000e-30 143.0
33 TraesCS5A01G138300 chr3B 81.875 160 16 7 501 648 550653001 550652843 5.710000e-24 122.0
34 TraesCS5A01G138300 chr3B 79.012 162 19 8 498 645 604770103 604770263 3.460000e-16 97.1
35 TraesCS5A01G138300 chr2B 82.443 131 21 2 2 130 699830703 699830833 3.440000e-21 113.0
36 TraesCS5A01G138300 chr2B 84.444 90 10 2 2750 2839 52408856 52408771 7.500000e-13 86.1
37 TraesCS5A01G138300 chr6D 88.043 92 5 5 2749 2839 155601959 155602045 2.070000e-18 104.0
38 TraesCS5A01G138300 chr7D 90.909 55 5 0 2342 2396 622401682 622401628 1.620000e-09 75.0


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 TraesCS5A01G138300 chr5A 310871901 310876109 4208 True 7773.000000 7773 100.000000 1 4209 1 chr5A.!!$R1 4208
1 TraesCS5A01G138300 chr5D 242355589 242359809 4220 False 6157.000000 6157 93.119000 2 4206 1 chr5D.!!$F1 4204
2 TraesCS5A01G138300 chr5B 259537022 259541311 4289 False 2048.333333 3615 91.503333 2 4209 3 chr5B.!!$F1 4207
3 TraesCS5A01G138300 chr4D 109911120 109911952 832 True 990.000000 990 88.186000 1189 2022 1 chr4D.!!$R1 833
4 TraesCS5A01G138300 chr4A 466926025 466926857 832 False 974.000000 974 87.814000 1189 2022 1 chr4A.!!$F1 833
5 TraesCS5A01G138300 chr4B 171027708 171028540 832 True 924.000000 924 86.754000 1189 2022 1 chr4B.!!$R2 833
6 TraesCS5A01G138300 chr1A 500342088 500343352 1264 True 728.000000 728 77.564000 1189 2457 1 chr1A.!!$R1 1268
7 TraesCS5A01G138300 chr1D 404969982 404970783 801 True 645.000000 645 81.312000 1217 2018 1 chr1D.!!$R1 801
8 TraesCS5A01G138300 chr3A 579552998 579553526 528 False 468.000000 468 82.674000 1189 1717 1 chr3A.!!$F3 528
9 TraesCS5A01G138300 chr3D 439838745 439839273 528 False 457.000000 457 82.298000 1189 1717 1 chr3D.!!$F1 528

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
709 775 0.665298 CTCATCGACGAGATCAGGCA 59.335 55.0 1.34 0.0 37.52 4.75 F
860 930 0.674895 CTCCCAACCTTCCAAGCTCG 60.675 60.0 0.00 0.0 0.00 5.03 F
2320 2392 0.869880 AACTTTGCGGCGAACTTTGC 60.870 50.0 12.98 0.0 0.00 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2515 2591 1.329292 CACGTCGTTGATTGGTTGTGT 59.671 47.619 0.00 0.0 0.0 3.72 R
2516 2592 1.333702 CCACGTCGTTGATTGGTTGTG 60.334 52.381 0.00 0.0 0.0 3.33 R
3622 3741 0.522626 TGTGCATGCATTCCTGTTCG 59.477 50.000 25.64 0.0 0.0 3.95 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
35 37 5.786401 AATGAGCTTAACAAACGAGCTAG 57.214 39.130 0.00 0.00 35.83 3.42
73 75 6.237595 GCAGCTCATTAAACTCGTTAGTACAG 60.238 42.308 0.00 0.00 33.75 2.74
120 122 5.736951 TGGCAACATTTTTATAGCACCTT 57.263 34.783 0.00 0.00 46.17 3.50
121 123 5.477510 TGGCAACATTTTTATAGCACCTTG 58.522 37.500 0.00 0.00 46.17 3.61
130 132 4.623932 TTATAGCACCTTGCCCATCTAG 57.376 45.455 0.00 0.00 46.52 2.43
142 144 1.428869 CCATCTAGCCAACCTAGCCT 58.571 55.000 0.00 0.00 42.73 4.58
174 176 7.953752 GGCAACTAGTACACCTTCTTCTATAT 58.046 38.462 0.00 0.00 0.00 0.86
207 209 5.345702 TCCTCCGTAAAAATCACATCTACG 58.654 41.667 0.00 0.00 36.10 3.51
231 233 2.103094 CACATCCCATAGACCGTGACAT 59.897 50.000 0.00 0.00 34.53 3.06
234 236 2.184533 TCCCATAGACCGTGACATGTT 58.815 47.619 0.00 0.00 0.00 2.71
258 260 3.846360 AGTCTATTAACGAGCGCTTGTT 58.154 40.909 37.67 37.67 40.16 2.83
259 261 4.990257 AGTCTATTAACGAGCGCTTGTTA 58.010 39.130 35.73 35.73 38.16 2.41
301 303 3.726557 TCCAAATGAACAGAGCCATCT 57.273 42.857 0.00 0.00 35.63 2.90
314 316 4.751098 CAGAGCCATCTAGATTTTCTGCTC 59.249 45.833 19.99 19.99 43.19 4.26
361 394 3.423539 TGAGCACAAGCCTTAATGAGT 57.576 42.857 0.00 0.00 43.56 3.41
365 398 4.338879 AGCACAAGCCTTAATGAGTTGAT 58.661 39.130 0.00 0.00 43.56 2.57
371 404 6.317391 ACAAGCCTTAATGAGTTGATTAGCTC 59.683 38.462 0.00 0.00 35.01 4.09
384 417 3.008157 TGATTAGCTCGTTAAACCACCCA 59.992 43.478 0.00 0.00 0.00 4.51
389 422 2.481568 GCTCGTTAAACCACCCACTTAC 59.518 50.000 0.00 0.00 0.00 2.34
395 428 5.563592 GTTAAACCACCCACTTACATAGGT 58.436 41.667 0.00 0.00 0.00 3.08
396 429 6.574073 CGTTAAACCACCCACTTACATAGGTA 60.574 42.308 0.00 0.00 0.00 3.08
400 433 5.592795 ACCACCCACTTACATAGGTAGTTA 58.407 41.667 0.00 0.00 0.00 2.24
414 447 9.270707 ACATAGGTAGTTAATTACCCACTACAA 57.729 33.333 20.32 12.10 43.20 2.41
422 455 8.102676 AGTTAATTACCCACTACAACGGTTAAT 58.897 33.333 0.00 0.00 0.00 1.40
430 463 5.390145 CCACTACAACGGTTAATGTACTTGC 60.390 44.000 0.00 0.00 0.00 4.01
478 512 6.556212 TCGATTTTTGTGCAAGTCAAACTTA 58.444 32.000 0.78 0.00 36.03 2.24
652 717 5.484715 TGGAACGGAAGGAGTAAATAACAG 58.515 41.667 0.00 0.00 0.00 3.16
659 724 7.985752 ACGGAAGGAGTAAATAACAGGAATAAG 59.014 37.037 0.00 0.00 0.00 1.73
694 760 1.207791 AAAGGGATCTGACGGCTCAT 58.792 50.000 0.00 0.00 0.00 2.90
709 775 0.665298 CTCATCGACGAGATCAGGCA 59.335 55.000 1.34 0.00 37.52 4.75
752 818 2.701073 CCGATCGAAACGGTATAGCT 57.299 50.000 18.66 0.00 44.57 3.32
860 930 0.674895 CTCCCAACCTTCCAAGCTCG 60.675 60.000 0.00 0.00 0.00 5.03
927 997 3.706802 TTGGTTTGTGCATGTGTGTAG 57.293 42.857 0.00 0.00 0.00 2.74
2076 2146 2.797491 GCTTCGTGCACACTTCTTTTT 58.203 42.857 18.64 0.00 42.31 1.94
2250 2322 2.103143 CCGCACTGAGAGTAGGCG 59.897 66.667 0.00 0.00 46.61 5.52
2311 2383 5.880341 ACTAATCTTTGATAACTTTGCGGC 58.120 37.500 0.00 0.00 0.00 6.53
2320 2392 0.869880 AACTTTGCGGCGAACTTTGC 60.870 50.000 12.98 0.00 0.00 3.68
2504 2580 5.426689 TGATGGAAGCAGTGAGTCTTATT 57.573 39.130 0.00 0.00 0.00 1.40
2515 2591 8.481314 AGCAGTGAGTCTTATTAATTCAGATGA 58.519 33.333 0.00 0.00 0.00 2.92
2516 2592 8.547069 GCAGTGAGTCTTATTAATTCAGATGAC 58.453 37.037 0.00 0.00 0.00 3.06
2546 2622 3.567530 TCAACGACGTGGTGTTACATAG 58.432 45.455 3.24 0.00 0.00 2.23
2563 2640 9.083080 TGTTACATAGAGTATTTGACATGAACG 57.917 33.333 0.00 0.00 31.53 3.95
2569 2646 7.687941 AGAGTATTTGACATGAACGGAAATT 57.312 32.000 0.00 0.00 0.00 1.82
2866 2971 6.096846 TCCTGGAAAAAGAAAAGAAACAGAGG 59.903 38.462 0.00 0.00 0.00 3.69
2882 2987 2.625790 CAGAGGTAGTACATCTCAGGCC 59.374 54.545 14.37 0.00 37.10 5.19
2919 3024 9.660180 GGATTTTTGGATACTCATATACCTCTC 57.340 37.037 0.00 0.00 37.61 3.20
3031 3136 2.597305 CCGATTCCGACAACGTAAGAAG 59.403 50.000 0.00 0.00 38.51 2.85
3045 3150 8.013378 ACAACGTAAGAAGGAAAAATACATTCG 58.987 33.333 0.00 0.00 43.62 3.34
3066 3174 6.043327 TCGAAACAATAGATGGTAAATGCG 57.957 37.500 0.00 0.00 0.00 4.73
3100 3208 3.927758 TGAAACTGTTTTCTTGACGACGA 59.072 39.130 7.28 0.00 41.64 4.20
3254 3362 3.321968 TGTATGTCAACAGAGTGCAGAGT 59.678 43.478 0.00 0.00 0.00 3.24
3258 3366 2.286294 GTCAACAGAGTGCAGAGTTGTG 59.714 50.000 15.65 2.89 41.43 3.33
3407 3515 1.519234 GCATCCGACATGACGAGCA 60.519 57.895 19.00 2.97 35.09 4.26
3612 3731 4.952262 AGAAACATCAATCGGACATGTG 57.048 40.909 1.15 0.00 31.00 3.21
3618 3737 3.490800 TCAATCGGACATGTGCAAATG 57.509 42.857 15.63 15.63 0.00 2.32
3619 3738 2.819019 TCAATCGGACATGTGCAAATGT 59.181 40.909 22.68 22.68 43.47 2.71
3620 3739 4.006319 TCAATCGGACATGTGCAAATGTA 58.994 39.130 22.54 7.96 40.87 2.29
3621 3740 4.457257 TCAATCGGACATGTGCAAATGTAA 59.543 37.500 22.54 11.50 40.87 2.41
3622 3741 3.822594 TCGGACATGTGCAAATGTAAC 57.177 42.857 22.54 16.55 40.87 2.50
3623 3742 2.158645 TCGGACATGTGCAAATGTAACG 59.841 45.455 27.87 27.87 40.87 3.18
3624 3743 2.158645 CGGACATGTGCAAATGTAACGA 59.841 45.455 29.02 0.00 40.87 3.85
3625 3744 3.364465 CGGACATGTGCAAATGTAACGAA 60.364 43.478 29.02 0.00 40.87 3.85
3626 3745 3.911964 GGACATGTGCAAATGTAACGAAC 59.088 43.478 22.54 8.87 40.87 3.95
3627 3746 4.532276 GACATGTGCAAATGTAACGAACA 58.468 39.130 22.54 0.00 40.87 3.18
3628 3747 4.536065 ACATGTGCAAATGTAACGAACAG 58.464 39.130 21.25 0.00 42.70 3.16
3649 3779 2.353903 GGAATGCATGCACACATCCAAA 60.354 45.455 25.37 0.00 32.87 3.28
3658 3788 7.149973 GCATGCACACATCCAAATTAGATTAT 58.850 34.615 14.21 0.00 32.87 1.28
3777 3910 4.160439 ACCTCATCACGATCTTCAAAGCTA 59.840 41.667 0.00 0.00 0.00 3.32
3778 3911 4.505922 CCTCATCACGATCTTCAAAGCTAC 59.494 45.833 0.00 0.00 0.00 3.58
3779 3912 5.330455 TCATCACGATCTTCAAAGCTACT 57.670 39.130 0.00 0.00 0.00 2.57
3780 3913 5.344066 TCATCACGATCTTCAAAGCTACTC 58.656 41.667 0.00 0.00 0.00 2.59
3781 3914 5.126222 TCATCACGATCTTCAAAGCTACTCT 59.874 40.000 0.00 0.00 0.00 3.24
3797 3930 7.847711 AGCTACTCTAGATCCAAATGTACAT 57.152 36.000 1.41 1.41 0.00 2.29
3822 3955 4.297510 TGCAATGAATGTTTTCACGAAGG 58.702 39.130 0.00 0.00 44.36 3.46
3863 3996 6.428385 AGCAAGTTTGTACTATGAATCTGC 57.572 37.500 0.00 0.00 33.17 4.26
3880 4013 3.884895 TCTGCTTTTCTCTCACAAACCA 58.115 40.909 0.00 0.00 0.00 3.67
3881 4014 4.269183 TCTGCTTTTCTCTCACAAACCAA 58.731 39.130 0.00 0.00 0.00 3.67
3978 4111 9.754382 ATCATATGTACAATTTTCAGAAATGCC 57.246 29.630 0.00 0.00 35.69 4.40
4037 4172 5.566016 CGAAAAGAAAACGAGTGTGACAAAA 59.434 36.000 0.00 0.00 0.00 2.44
4043 4178 4.370364 AACGAGTGTGACAAAAAGCAAT 57.630 36.364 0.00 0.00 0.00 3.56
4066 4201 4.614555 TGTAATAAAGATTGTGGCGCAG 57.385 40.909 10.83 0.00 0.00 5.18
4103 4238 5.619220 ACACAATGGCATGTTTTGGTTTAT 58.381 33.333 0.00 0.00 0.00 1.40
4104 4239 6.763355 ACACAATGGCATGTTTTGGTTTATA 58.237 32.000 0.00 0.00 0.00 0.98
4105 4240 6.873076 ACACAATGGCATGTTTTGGTTTATAG 59.127 34.615 0.00 0.00 0.00 1.31
4106 4241 5.874261 ACAATGGCATGTTTTGGTTTATAGC 59.126 36.000 0.00 0.00 0.00 2.97
4108 4243 5.474578 TGGCATGTTTTGGTTTATAGCAA 57.525 34.783 0.00 0.00 39.82 3.91
4163 4305 3.415212 CGGATATGATGAATTGCACCCT 58.585 45.455 0.00 0.00 0.00 4.34
4179 4321 5.732633 TGCACCCTTAATTGATTTTGATGG 58.267 37.500 0.00 0.00 0.00 3.51
4183 4325 7.361116 GCACCCTTAATTGATTTTGATGGTTTG 60.361 37.037 0.00 0.00 0.00 2.93
4195 4339 8.816640 ATTTTGATGGTTTGTGACAACTATTC 57.183 30.769 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 37 1.895280 GAGCTGCTTGTGACACTCGC 61.895 60.000 2.53 9.60 0.00 5.03
111 113 1.072965 GCTAGATGGGCAAGGTGCTAT 59.927 52.381 0.00 0.00 44.28 2.97
120 122 1.131638 CTAGGTTGGCTAGATGGGCA 58.868 55.000 0.00 0.00 39.99 5.36
121 123 0.250510 GCTAGGTTGGCTAGATGGGC 60.251 60.000 0.00 0.00 0.00 5.36
130 132 1.903183 CCTCCTATAGGCTAGGTTGGC 59.097 57.143 14.50 0.00 38.97 4.52
142 144 5.399052 AGGTGTACTAGTTGCCTCCTATA 57.601 43.478 0.00 0.00 0.00 1.31
174 176 8.026607 GTGATTTTTACGGAGGAAAATGATGAA 58.973 33.333 0.00 0.00 37.44 2.57
197 199 1.409064 GGGATGTGAGCGTAGATGTGA 59.591 52.381 0.00 0.00 0.00 3.58
207 209 0.753262 ACGGTCTATGGGATGTGAGC 59.247 55.000 0.00 0.00 0.00 4.26
231 233 4.100529 GCGCTCGTTAATAGACTACAACA 58.899 43.478 0.00 0.00 0.00 3.33
234 236 4.142534 ACAAGCGCTCGTTAATAGACTACA 60.143 41.667 12.06 0.00 0.00 2.74
314 316 3.368236 GCCTCAACTCACTAAGCTTAACG 59.632 47.826 7.74 1.64 0.00 3.18
361 394 4.004982 GGGTGGTTTAACGAGCTAATCAA 58.995 43.478 8.96 0.00 0.00 2.57
365 398 2.369532 AGTGGGTGGTTTAACGAGCTAA 59.630 45.455 8.96 0.00 0.00 3.09
371 404 4.632688 CCTATGTAAGTGGGTGGTTTAACG 59.367 45.833 0.00 0.00 0.00 3.18
384 417 9.498039 AGTGGGTAATTAACTACCTATGTAAGT 57.502 33.333 12.92 0.00 41.12 2.24
389 422 9.538508 GTTGTAGTGGGTAATTAACTACCTATG 57.461 37.037 12.92 0.00 43.63 2.23
395 428 6.603940 ACCGTTGTAGTGGGTAATTAACTA 57.396 37.500 0.00 0.00 30.76 2.24
396 429 5.488262 ACCGTTGTAGTGGGTAATTAACT 57.512 39.130 0.00 0.00 30.76 2.24
400 433 6.240145 ACATTAACCGTTGTAGTGGGTAATT 58.760 36.000 0.00 0.00 43.88 1.40
414 447 2.570302 AGGGAGCAAGTACATTAACCGT 59.430 45.455 0.00 0.00 0.00 4.83
422 455 4.640771 ATTCTGAAAGGGAGCAAGTACA 57.359 40.909 0.00 0.00 0.00 2.90
430 463 7.815068 CGATACACCTTATATTCTGAAAGGGAG 59.185 40.741 9.90 5.38 43.41 4.30
462 496 6.875948 ACATACATAAGTTTGACTTGCACA 57.124 33.333 3.70 0.00 39.11 4.57
622 687 6.995511 TTACTCCTTCCGTTCCAAAATATG 57.004 37.500 0.00 0.00 0.00 1.78
652 717 8.652810 TTTAACCGTTATAGAGTGCTTATTCC 57.347 34.615 0.00 0.00 0.00 3.01
659 724 5.014808 TCCCTTTAACCGTTATAGAGTGC 57.985 43.478 9.58 0.00 0.00 4.40
694 760 0.679960 TCCTTGCCTGATCTCGTCGA 60.680 55.000 0.00 0.00 0.00 4.20
709 775 1.414181 CTACGGATCACATGGCTCCTT 59.586 52.381 0.00 0.00 0.00 3.36
723 789 1.605710 GTTTCGATCGGATCCTACGGA 59.394 52.381 16.41 4.62 35.55 4.69
739 805 6.921857 TGTAGCATTTCTAGCTATACCGTTTC 59.078 38.462 0.00 0.00 45.38 2.78
742 808 5.770417 GTGTAGCATTTCTAGCTATACCGT 58.230 41.667 9.91 0.00 45.34 4.83
749 815 5.422331 TCAGTTAGGTGTAGCATTTCTAGCT 59.578 40.000 0.00 0.00 45.77 3.32
752 818 7.476540 TCTTCAGTTAGGTGTAGCATTTCTA 57.523 36.000 0.00 0.00 0.00 2.10
783 853 1.876156 CACAACCTGAACCTGAAGCTC 59.124 52.381 0.00 0.00 0.00 4.09
927 997 2.327343 TGCATGAAGAGCACGCACC 61.327 57.895 0.00 0.00 41.33 5.01
1284 1354 3.056458 CACAGGTAGGTCACGCCA 58.944 61.111 0.00 0.00 40.61 5.69
2074 2144 4.462508 TTGTCTTGGTCATGCACAAAAA 57.537 36.364 0.00 0.00 0.00 1.94
2076 2146 3.304592 CGATTGTCTTGGTCATGCACAAA 60.305 43.478 0.00 0.00 31.04 2.83
2077 2147 2.226200 CGATTGTCTTGGTCATGCACAA 59.774 45.455 0.00 0.00 0.00 3.33
2081 2151 2.540361 GCATCGATTGTCTTGGTCATGC 60.540 50.000 0.00 0.00 0.00 4.06
2088 2158 2.028420 TCAGGGCATCGATTGTCTTG 57.972 50.000 0.00 0.11 38.32 3.02
2250 2322 4.692625 AGTGTTGTCAATGTCAGTCTATGC 59.307 41.667 0.00 0.00 0.00 3.14
2311 2383 2.724839 GCAATGACCTACGCAAAGTTCG 60.725 50.000 0.00 0.00 0.00 3.95
2320 2392 1.813753 CACCCGGCAATGACCTACG 60.814 63.158 0.00 0.00 0.00 3.51
2502 2578 8.352137 TGATTGGTTGTGTCATCTGAATTAAT 57.648 30.769 0.00 0.00 0.00 1.40
2503 2579 7.757941 TGATTGGTTGTGTCATCTGAATTAA 57.242 32.000 0.00 0.00 0.00 1.40
2504 2580 7.572910 CGTTGATTGGTTGTGTCATCTGAATTA 60.573 37.037 0.00 0.00 0.00 1.40
2515 2591 1.329292 CACGTCGTTGATTGGTTGTGT 59.671 47.619 0.00 0.00 0.00 3.72
2516 2592 1.333702 CCACGTCGTTGATTGGTTGTG 60.334 52.381 0.00 0.00 0.00 3.33
2563 2640 7.759433 TGGAAATCGAAGCAGAAAATAATTTCC 59.241 33.333 13.84 13.84 44.96 3.13
2569 2646 4.096382 GCCTGGAAATCGAAGCAGAAAATA 59.904 41.667 0.00 0.00 0.00 1.40
2866 2971 1.689273 CAGGGGCCTGAGATGTACTAC 59.311 57.143 0.84 0.00 46.30 2.73
2919 3024 3.745975 TCTTCTTTTGTGATGTACCTGCG 59.254 43.478 0.00 0.00 0.00 5.18
3045 3150 5.901884 CGACGCATTTACCATCTATTGTTTC 59.098 40.000 0.00 0.00 0.00 2.78
3066 3174 4.877323 AACAGTTTCAGTTCCTTTCGAC 57.123 40.909 0.00 0.00 0.00 4.20
3100 3208 2.641815 GTCTATCCTCCCATCCTGCATT 59.358 50.000 0.00 0.00 0.00 3.56
3227 3335 6.036577 TGCACTCTGTTGACATACATAAGA 57.963 37.500 0.00 0.00 0.00 2.10
3228 3336 6.101997 TCTGCACTCTGTTGACATACATAAG 58.898 40.000 0.00 0.00 0.00 1.73
3229 3337 6.036577 TCTGCACTCTGTTGACATACATAA 57.963 37.500 0.00 0.00 0.00 1.90
3230 3338 5.185828 ACTCTGCACTCTGTTGACATACATA 59.814 40.000 0.00 0.00 0.00 2.29
3231 3339 4.020751 ACTCTGCACTCTGTTGACATACAT 60.021 41.667 0.00 0.00 0.00 2.29
3254 3362 3.058085 CAGCATGCACATTACAGTCACAA 60.058 43.478 21.98 0.00 0.00 3.33
3355 3463 6.212955 TCATTTCGGAACACAAATTCCTTTC 58.787 36.000 3.22 0.00 45.27 2.62
3407 3515 4.200874 TCAACCACACGAACCAGTAATTT 58.799 39.130 0.00 0.00 0.00 1.82
3448 3566 3.880047 CCGTAGTGGTAGATTTGGACA 57.120 47.619 0.00 0.00 0.00 4.02
3498 3617 6.343716 TGTACACATCCATTTGAATTTGCT 57.656 33.333 0.00 0.00 0.00 3.91
3612 3731 3.608073 GCATTCCTGTTCGTTACATTTGC 59.392 43.478 0.00 0.00 35.85 3.68
3618 3737 2.161410 TGCATGCATTCCTGTTCGTTAC 59.839 45.455 18.46 0.00 0.00 2.50
3619 3738 2.161410 GTGCATGCATTCCTGTTCGTTA 59.839 45.455 25.64 0.00 0.00 3.18
3620 3739 1.068333 GTGCATGCATTCCTGTTCGTT 60.068 47.619 25.64 0.00 0.00 3.85
3621 3740 0.523072 GTGCATGCATTCCTGTTCGT 59.477 50.000 25.64 0.00 0.00 3.85
3622 3741 0.522626 TGTGCATGCATTCCTGTTCG 59.477 50.000 25.64 0.00 0.00 3.95
3623 3742 1.270274 TGTGTGCATGCATTCCTGTTC 59.730 47.619 25.64 8.75 0.00 3.18
3624 3743 1.330234 TGTGTGCATGCATTCCTGTT 58.670 45.000 25.64 0.00 0.00 3.16
3625 3744 1.475280 GATGTGTGCATGCATTCCTGT 59.525 47.619 25.64 8.28 35.07 4.00
3626 3745 1.202371 GGATGTGTGCATGCATTCCTG 60.202 52.381 25.64 0.00 42.14 3.86
3627 3746 1.108776 GGATGTGTGCATGCATTCCT 58.891 50.000 25.64 12.56 42.14 3.36
3628 3747 0.818938 TGGATGTGTGCATGCATTCC 59.181 50.000 25.64 24.56 46.20 3.01
3697 3827 4.072131 ACGTCTTGAACACCTTGCATAAT 58.928 39.130 0.00 0.00 0.00 1.28
3706 3836 0.575390 CGACACACGTCTTGAACACC 59.425 55.000 0.65 0.00 40.23 4.16
3712 3842 3.110358 TGTAGTTTCGACACACGTCTTG 58.890 45.455 4.26 0.00 40.23 3.02
3753 3884 3.308323 GCTTTGAAGATCGTGATGAGGTC 59.692 47.826 0.00 0.00 0.00 3.85
3754 3885 3.055530 AGCTTTGAAGATCGTGATGAGGT 60.056 43.478 0.00 0.00 0.00 3.85
3777 3910 6.540189 GCAACATGTACATTTGGATCTAGAGT 59.460 38.462 21.63 6.93 0.00 3.24
3778 3911 6.539826 TGCAACATGTACATTTGGATCTAGAG 59.460 38.462 21.63 6.44 0.00 2.43
3779 3912 6.413892 TGCAACATGTACATTTGGATCTAGA 58.586 36.000 21.63 0.00 0.00 2.43
3780 3913 6.682423 TGCAACATGTACATTTGGATCTAG 57.318 37.500 21.63 7.38 0.00 2.43
3781 3914 7.338957 TCATTGCAACATGTACATTTGGATCTA 59.661 33.333 21.63 11.73 0.00 1.98
3797 3930 4.676546 TCGTGAAAACATTCATTGCAACA 58.323 34.783 0.00 0.00 33.02 3.33
3861 3994 4.016444 ACTTGGTTTGTGAGAGAAAAGCA 58.984 39.130 0.00 0.00 40.81 3.91
3863 3996 7.264373 ACATACTTGGTTTGTGAGAGAAAAG 57.736 36.000 0.00 0.00 0.00 2.27
3978 4111 9.914923 GGTGCAAACTCTTAAAATTTTGTAAAG 57.085 29.630 13.76 9.26 32.57 1.85
4025 4160 7.518731 TTACAAATTGCTTTTTGTCACACTC 57.481 32.000 17.15 0.00 44.39 3.51
4037 4172 7.063308 CGCCACAATCTTTATTACAAATTGCTT 59.937 33.333 0.00 0.00 31.96 3.91
4043 4178 5.048364 ACTGCGCCACAATCTTTATTACAAA 60.048 36.000 4.18 0.00 0.00 2.83
4066 4201 3.440173 CCATTGTGTACACTGGGATTGAC 59.560 47.826 25.60 0.00 41.40 3.18
4103 4238 5.637810 CGATGAACCTTACTTGAGTTTGCTA 59.362 40.000 0.00 0.00 0.00 3.49
4104 4239 4.452455 CGATGAACCTTACTTGAGTTTGCT 59.548 41.667 0.00 0.00 0.00 3.91
4105 4240 4.213482 ACGATGAACCTTACTTGAGTTTGC 59.787 41.667 0.00 0.00 0.00 3.68
4106 4241 5.924475 ACGATGAACCTTACTTGAGTTTG 57.076 39.130 0.00 0.00 0.00 2.93
4108 4243 6.987992 TGTTTACGATGAACCTTACTTGAGTT 59.012 34.615 0.00 0.00 0.00 3.01
4163 4305 9.605275 TTGTCACAAACCATCAAAATCAATTAA 57.395 25.926 0.00 0.00 0.00 1.40
4179 4321 5.118817 GTCCTCTCGAATAGTTGTCACAAAC 59.881 44.000 0.00 0.00 0.00 2.93
4183 4325 3.192844 TGGTCCTCTCGAATAGTTGTCAC 59.807 47.826 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.