Multiple sequence alignment - TraesCS2B01G060500

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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 TraesCS2B01G060500 chr2B 100.000 2673 0 0 1 2673 29045744 29048416 0.000000e+00 4937
1 TraesCS2B01G060500 chr2B 87.439 1839 183 24 3 1812 29992446 29990627 0.000000e+00 2073
2 TraesCS2B01G060500 chr2B 85.481 1226 113 27 1082 2284 28921253 28922436 0.000000e+00 1218
3 TraesCS2B01G060500 chr2B 86.654 547 59 4 1804 2349 29990609 29990076 6.370000e-166 593
4 TraesCS2B01G060500 chr2B 85.204 392 34 9 84 456 28920445 28920831 5.400000e-102 381
5 TraesCS2B01G060500 chr2B 78.947 323 57 6 2350 2671 28923732 28924044 2.700000e-50 209
6 TraesCS2B01G060500 chr2A 90.488 2029 142 23 3 1993 18585773 18587788 0.000000e+00 2630
7 TraesCS2B01G060500 chr2A 87.525 2012 173 44 3 1957 18635352 18637342 0.000000e+00 2254
8 TraesCS2B01G060500 chr2A 82.215 298 51 2 2374 2669 18638077 18638374 3.410000e-64 255
9 TraesCS2B01G060500 chr2D 88.101 1933 175 35 9 1908 17311706 17313616 0.000000e+00 2244
10 TraesCS2B01G060500 chr2D 87.882 1048 92 17 943 1957 17169522 17170567 0.000000e+00 1199
11 TraesCS2B01G060500 chr2D 86.674 893 80 15 9 877 17168645 17169522 0.000000e+00 953
12 TraesCS2B01G060500 chr2D 81.062 565 81 16 1566 2106 17208646 17209208 6.840000e-116 427
13 TraesCS2B01G060500 chr2D 89.641 251 24 2 1320 1569 17208272 17208521 4.290000e-83 318
14 TraesCS2B01G060500 chr2D 82.043 323 56 2 2348 2669 17171827 17172148 9.430000e-70 274
15 TraesCS2B01G060500 chr2D 82.231 242 39 2 2429 2669 17316255 17316493 3.490000e-49 206


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 TraesCS2B01G060500 chr2B 29045744 29048416 2672 False 4937.000000 4937 100.000000 1 2673 1 chr2B.!!$F1 2672
1 TraesCS2B01G060500 chr2B 29990076 29992446 2370 True 1333.000000 2073 87.046500 3 2349 2 chr2B.!!$R1 2346
2 TraesCS2B01G060500 chr2B 28920445 28924044 3599 False 602.666667 1218 83.210667 84 2671 3 chr2B.!!$F2 2587
3 TraesCS2B01G060500 chr2A 18585773 18587788 2015 False 2630.000000 2630 90.488000 3 1993 1 chr2A.!!$F1 1990
4 TraesCS2B01G060500 chr2A 18635352 18638374 3022 False 1254.500000 2254 84.870000 3 2669 2 chr2A.!!$F2 2666
5 TraesCS2B01G060500 chr2D 17311706 17316493 4787 False 1225.000000 2244 85.166000 9 2669 2 chr2D.!!$F3 2660
6 TraesCS2B01G060500 chr2D 17168645 17172148 3503 False 808.666667 1199 85.533000 9 2669 3 chr2D.!!$F1 2660
7 TraesCS2B01G060500 chr2D 17208272 17209208 936 False 372.500000 427 85.351500 1320 2106 2 chr2D.!!$F2 786

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
859 1089 0.243365 TGGCTGCCATTTTTGCTACG 59.757 50.0 19.3 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2527 5517 0.17668 ACTGACATGGTGAGCGGATC 59.823 55.0 0.0 0.0 0.0 3.36 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
114 130 6.245115 TCATATGACGATGCAATTCCATTC 57.755 37.500 0.00 0.00 0.00 2.67
176 194 7.606456 ACATGGGTTTTAAGTCATAGTGTACAG 59.394 37.037 0.00 0.00 0.00 2.74
207 231 6.874134 GCCGTGTGGATATTAGAATAATGAGT 59.126 38.462 0.00 0.00 37.49 3.41
218 242 8.738645 ATTAGAATAATGAGTTGTTGTCCTCC 57.261 34.615 0.00 0.00 0.00 4.30
227 251 0.391597 TGTTGTCCTCCGGTTCAGTC 59.608 55.000 0.00 0.00 0.00 3.51
238 262 2.857748 CCGGTTCAGTCTTTTTGCAAAC 59.142 45.455 12.39 0.37 0.00 2.93
242 266 3.163630 TCAGTCTTTTTGCAAACTGCC 57.836 42.857 19.65 6.96 44.23 4.85
352 376 4.496183 CGCTAACTAGCTAGAAAGACGTTG 59.504 45.833 27.45 6.37 46.85 4.10
374 398 9.416794 CGTTGTCTTATCTGATATATTCTGCTT 57.583 33.333 0.00 0.00 0.00 3.91
509 738 5.112129 AGAAACCCACTGTGTTTAAGAGT 57.888 39.130 7.08 0.00 36.13 3.24
534 763 7.660030 TCAATGACTCCACTAATATCTGTCA 57.340 36.000 0.00 0.00 37.37 3.58
541 770 7.877003 ACTCCACTAATATCTGTCATTCTACG 58.123 38.462 0.00 0.00 0.00 3.51
599 828 1.439679 CTAACTGAAGCGGTTGGGTC 58.560 55.000 3.70 0.00 34.54 4.46
612 841 3.243907 CGGTTGGGTCAAAATTTAGGCAA 60.244 43.478 0.00 0.00 0.00 4.52
627 856 1.992557 AGGCAAGGTTATTCTCCACCA 59.007 47.619 0.00 0.00 35.25 4.17
671 900 7.329962 TCATCGTCACGTTGTCATAATAAAAGT 59.670 33.333 8.09 0.00 0.00 2.66
723 953 9.733556 ACTATTGGTAGTGTTTGATGATTTACA 57.266 29.630 0.00 0.00 39.66 2.41
765 995 5.630121 TGACAGTGATTGGACCAAGTAATT 58.370 37.500 13.43 0.00 0.00 1.40
790 1020 7.814264 ACCATAATCTTCAGAATTGGTGATC 57.186 36.000 7.53 0.00 35.05 2.92
854 1084 3.666274 TCTGATTTGGCTGCCATTTTTG 58.334 40.909 24.03 12.97 31.53 2.44
859 1089 0.243365 TGGCTGCCATTTTTGCTACG 59.757 50.000 19.30 0.00 0.00 3.51
1073 1311 5.175126 CGCGTAGAATATCCAAACTTCGATT 59.825 40.000 0.00 0.00 0.00 3.34
1079 1317 8.737168 AGAATATCCAAACTTCGATTGAATCA 57.263 30.769 5.95 0.00 32.61 2.57
1111 1349 6.394345 AGATTTCCCAGGTATGACTCTTTT 57.606 37.500 0.00 0.00 0.00 2.27
1144 1382 7.440556 GCTAGTTTCTTCTTGCTCATGATCATA 59.559 37.037 8.15 0.00 34.44 2.15
1196 1434 4.558226 TTCCTATGCATGTGTCTCTGTT 57.442 40.909 10.16 0.00 0.00 3.16
1205 1443 7.364522 TGCATGTGTCTCTGTTAAGTTAATC 57.635 36.000 0.00 0.00 0.00 1.75
1233 1471 4.276678 CACCATGAAAGAGCAACTGAAAGA 59.723 41.667 0.00 0.00 37.43 2.52
1252 1490 9.388506 CTGAAAGAAAGCAGGATTAAGATCTTA 57.611 33.333 11.24 11.24 34.07 2.10
1256 1494 8.256356 AGAAAGCAGGATTAAGATCTTAGCTA 57.744 34.615 20.38 7.10 34.77 3.32
1282 1520 1.818674 CTGGTCTTTGCCATGGTTACC 59.181 52.381 14.67 13.68 37.96 2.85
1283 1521 0.808755 GGTCTTTGCCATGGTTACCG 59.191 55.000 14.67 0.00 0.00 4.02
1306 1544 0.447801 GCTTGGCGATTCGTGTCAAT 59.552 50.000 8.03 0.00 0.00 2.57
1338 1576 0.253044 AATGACATCACCGGTGAGGG 59.747 55.000 42.09 34.88 44.76 4.30
1360 1598 1.110442 TCAGCACAAAAACCACCCTG 58.890 50.000 0.00 0.00 0.00 4.45
1446 1684 1.862242 TGGAGGAGAGGATGGATCAGA 59.138 52.381 0.00 0.00 0.00 3.27
1504 1742 5.510349 CCATTCTCTGAGACTGTTCTGTTCA 60.510 44.000 19.62 0.00 29.47 3.18
1513 1751 4.058817 GACTGTTCTGTTCACCGAAGATT 58.941 43.478 0.00 0.00 0.00 2.40
1522 1762 9.667107 TTCTGTTCACCGAAGATTTATATTCTT 57.333 29.630 0.00 0.00 36.16 2.52
1572 1941 5.122396 GCCAGCAGCGCTATAATTATTACTT 59.878 40.000 10.99 0.00 36.40 2.24
1598 1967 2.698274 TGCCTACATGAGAATAAGCCGA 59.302 45.455 0.00 0.00 0.00 5.54
1614 1983 2.168728 AGCCGATGAAGGGAAGAGTAAC 59.831 50.000 0.00 0.00 0.00 2.50
1642 2018 8.699130 TCGAAGATAATATGCATACATCCTCAT 58.301 33.333 19.46 9.25 37.74 2.90
1746 2131 5.995282 AGGAAACTTTCATGATGTTACACGA 59.005 36.000 12.89 0.00 37.44 4.35
1758 2143 2.741517 TGTTACACGACAGCCATCAATG 59.258 45.455 0.00 0.00 0.00 2.82
1764 2149 4.022068 ACACGACAGCCATCAATGAAATTT 60.022 37.500 0.00 0.00 31.22 1.82
1767 2152 6.753279 CACGACAGCCATCAATGAAATTTATT 59.247 34.615 0.00 0.00 31.22 1.40
1808 2193 6.097554 TCAGGAAAGAACCAAATTAACTGCAA 59.902 34.615 0.00 0.00 0.00 4.08
1814 2199 6.447162 AGAACCAAATTAACTGCAAGCTTAC 58.553 36.000 0.00 0.00 37.60 2.34
1817 2228 4.165779 CAAATTAACTGCAAGCTTACGGG 58.834 43.478 10.30 0.00 37.60 5.28
1855 2266 8.496707 AATCATGGTTTTATGCTTCAATTTCC 57.503 30.769 0.00 0.00 0.00 3.13
1893 2304 3.990369 TGTCCTACATGTACTAAGGGCT 58.010 45.455 16.09 0.00 34.72 5.19
1910 2321 1.066787 GGCTACTCTAATCGATGCCCC 60.067 57.143 9.01 0.00 33.45 5.80
1912 2323 2.234908 GCTACTCTAATCGATGCCCCAT 59.765 50.000 0.00 0.00 0.00 4.00
1932 2357 2.586648 ACTCCATCCCCAAAACTGAC 57.413 50.000 0.00 0.00 0.00 3.51
1940 2365 2.962421 TCCCCAAAACTGACATCCAAAC 59.038 45.455 0.00 0.00 0.00 2.93
2003 2428 7.896496 TGCCTAGAACTTAATCCCCAAAAATAA 59.104 33.333 0.00 0.00 0.00 1.40
2119 2545 9.776158 TTATAATTAAACACAATGCCAACTACG 57.224 29.630 0.00 0.00 0.00 3.51
2310 5260 3.922375 CCTTACTCTCCTCCTCTTCCAT 58.078 50.000 0.00 0.00 0.00 3.41
2320 5270 1.227089 CTCTTCCATCTCCACGGCG 60.227 63.158 4.80 4.80 0.00 6.46
2323 5273 2.907897 CTTCCATCTCCACGGCGTCC 62.908 65.000 10.85 0.00 0.00 4.79
2328 5278 1.899437 ATCTCCACGGCGTCCATGTT 61.899 55.000 10.85 0.00 0.00 2.71
2340 5290 3.074412 CGTCCATGTTTTCCTGTAGCTT 58.926 45.455 0.00 0.00 0.00 3.74
2344 5294 5.880332 GTCCATGTTTTCCTGTAGCTTGATA 59.120 40.000 0.00 0.00 0.00 2.15
2349 5299 6.303839 TGTTTTCCTGTAGCTTGATAAAGGT 58.696 36.000 0.00 0.00 32.61 3.50
2350 5300 6.206634 TGTTTTCCTGTAGCTTGATAAAGGTG 59.793 38.462 4.66 0.00 32.61 4.00
2351 5301 3.873910 TCCTGTAGCTTGATAAAGGTGC 58.126 45.455 4.66 3.94 32.61 5.01
2352 5302 3.519510 TCCTGTAGCTTGATAAAGGTGCT 59.480 43.478 10.92 0.00 32.61 4.40
2354 5304 4.507710 CTGTAGCTTGATAAAGGTGCTCA 58.492 43.478 10.92 4.55 34.65 4.26
2360 5350 2.368439 TGATAAAGGTGCTCATGGTGC 58.632 47.619 0.00 0.00 0.00 5.01
2366 5356 1.709147 GGTGCTCATGGTGCGTGATC 61.709 60.000 0.00 0.00 0.00 2.92
2368 5358 0.460811 TGCTCATGGTGCGTGATCTC 60.461 55.000 0.00 0.00 0.00 2.75
2378 5368 1.587350 CGTGATCTCAGCGCGACAT 60.587 57.895 12.10 0.00 41.39 3.06
2386 5376 4.166888 AGCGCGACATGAGGCCAT 62.167 61.111 12.10 0.00 0.00 4.40
2387 5377 3.204827 GCGCGACATGAGGCCATT 61.205 61.111 12.10 0.00 0.00 3.16
2390 5380 1.368345 CGCGACATGAGGCCATTGAA 61.368 55.000 5.01 0.00 0.00 2.69
2407 5397 5.163519 CCATTGAAGCCTCGATTTATTGGTT 60.164 40.000 0.00 0.00 0.00 3.67
2409 5399 3.945285 TGAAGCCTCGATTTATTGGTTCC 59.055 43.478 0.00 0.00 0.00 3.62
2427 5417 1.564622 CCGTCAATAGCGCATTCCG 59.435 57.895 11.47 11.17 40.75 4.30
2448 5438 0.663153 GTGAGTGGTGAACTTGGCAC 59.337 55.000 0.00 0.00 40.07 5.01
2449 5439 0.254462 TGAGTGGTGAACTTGGCACA 59.746 50.000 0.00 0.00 40.07 4.57
2463 5453 2.122783 GGCACAGTACAAGGCCATAA 57.877 50.000 5.01 0.00 45.70 1.90
2464 5454 2.442413 GGCACAGTACAAGGCCATAAA 58.558 47.619 5.01 0.00 45.70 1.40
2466 5456 3.081804 GCACAGTACAAGGCCATAAAGT 58.918 45.455 5.01 0.00 0.00 2.66
2472 5462 3.933861 ACAAGGCCATAAAGTCCTAGG 57.066 47.619 5.01 0.82 0.00 3.02
2483 5473 3.697619 AAGTCCTAGGTTGTTAGGTGC 57.302 47.619 9.08 0.00 40.91 5.01
2489 5479 2.388232 GGTTGTTAGGTGCTCCGCG 61.388 63.158 0.00 0.00 39.05 6.46
2493 5483 1.141019 GTTAGGTGCTCCGCGATGA 59.859 57.895 8.23 0.00 39.05 2.92
2497 5487 1.741770 GGTGCTCCGCGATGAACTT 60.742 57.895 8.23 0.00 0.00 2.66
2513 5503 3.262420 GAACTTATCGCCTTCTTGCTCA 58.738 45.455 0.00 0.00 0.00 4.26
2515 5505 3.674997 ACTTATCGCCTTCTTGCTCAAA 58.325 40.909 0.00 0.00 0.00 2.69
2516 5506 3.437049 ACTTATCGCCTTCTTGCTCAAAC 59.563 43.478 0.00 0.00 0.00 2.93
2518 5508 1.512926 TCGCCTTCTTGCTCAAACTC 58.487 50.000 0.00 0.00 0.00 3.01
2519 5509 1.202639 TCGCCTTCTTGCTCAAACTCA 60.203 47.619 0.00 0.00 0.00 3.41
2521 5511 2.413765 CGCCTTCTTGCTCAAACTCATG 60.414 50.000 0.00 0.00 0.00 3.07
2522 5512 2.670509 GCCTTCTTGCTCAAACTCATGC 60.671 50.000 0.00 0.00 0.00 4.06
2524 5514 3.119919 CCTTCTTGCTCAAACTCATGCTC 60.120 47.826 0.00 0.00 0.00 4.26
2525 5515 3.130280 TCTTGCTCAAACTCATGCTCA 57.870 42.857 0.00 0.00 0.00 4.26
2527 5517 3.501062 TCTTGCTCAAACTCATGCTCAAG 59.499 43.478 0.00 0.00 34.06 3.02
2528 5518 3.130280 TGCTCAAACTCATGCTCAAGA 57.870 42.857 0.00 0.00 0.00 3.02
2529 5519 3.682696 TGCTCAAACTCATGCTCAAGAT 58.317 40.909 0.00 0.00 0.00 2.40
2530 5520 3.688185 TGCTCAAACTCATGCTCAAGATC 59.312 43.478 0.00 0.00 0.00 2.75
2532 5522 3.264947 TCAAACTCATGCTCAAGATCCG 58.735 45.455 0.00 0.00 0.00 4.18
2533 5523 1.661341 AACTCATGCTCAAGATCCGC 58.339 50.000 0.00 0.00 0.00 5.54
2534 5524 0.829333 ACTCATGCTCAAGATCCGCT 59.171 50.000 0.00 0.00 0.00 5.52
2535 5525 1.202510 ACTCATGCTCAAGATCCGCTC 60.203 52.381 0.00 0.00 0.00 5.03
2536 5526 0.826062 TCATGCTCAAGATCCGCTCA 59.174 50.000 0.00 0.00 0.00 4.26
2537 5527 0.935898 CATGCTCAAGATCCGCTCAC 59.064 55.000 0.00 0.00 0.00 3.51
2538 5528 0.179062 ATGCTCAAGATCCGCTCACC 60.179 55.000 0.00 0.00 0.00 4.02
2539 5529 1.219124 GCTCAAGATCCGCTCACCA 59.781 57.895 0.00 0.00 0.00 4.17
2540 5530 0.179062 GCTCAAGATCCGCTCACCAT 60.179 55.000 0.00 0.00 0.00 3.55
2541 5531 1.579698 CTCAAGATCCGCTCACCATG 58.420 55.000 0.00 0.00 0.00 3.66
2542 5532 0.904649 TCAAGATCCGCTCACCATGT 59.095 50.000 0.00 0.00 0.00 3.21
2550 5549 1.300971 CGCTCACCATGTCAGTTGGG 61.301 60.000 0.00 0.00 38.64 4.12
2555 5554 1.820519 CACCATGTCAGTTGGGGATTG 59.179 52.381 0.00 0.00 40.29 2.67
2556 5555 1.272648 ACCATGTCAGTTGGGGATTGG 60.273 52.381 0.00 0.00 38.64 3.16
2559 5558 1.144691 TGTCAGTTGGGGATTGGACA 58.855 50.000 0.00 0.00 0.00 4.02
2576 5575 3.054434 TGGACACAATGGAGGATTTCGAT 60.054 43.478 0.00 0.00 0.00 3.59
2584 5583 1.876156 GGAGGATTTCGATGCCATCAC 59.124 52.381 5.40 0.00 0.00 3.06
2593 5592 1.399440 CGATGCCATCACCAAGTCTTG 59.601 52.381 5.40 5.53 0.00 3.02
2633 5632 6.833933 AGAGAGGGAAAGTTGTACAAAAACAT 59.166 34.615 10.51 0.00 0.00 2.71
2637 5636 8.706322 AGGGAAAGTTGTACAAAAACATAGAT 57.294 30.769 10.51 0.00 0.00 1.98
2639 5638 7.812669 GGGAAAGTTGTACAAAAACATAGATGG 59.187 37.037 10.51 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 108 6.004408 TGAATGGAATTGCATCGTCATATG 57.996 37.500 13.26 0.00 36.07 1.78
93 109 6.638096 TTGAATGGAATTGCATCGTCATAT 57.362 33.333 13.26 0.00 36.07 1.78
94 110 6.448207 TTTGAATGGAATTGCATCGTCATA 57.552 33.333 13.26 6.77 36.07 2.15
95 111 4.987408 TTGAATGGAATTGCATCGTCAT 57.013 36.364 13.26 0.00 36.07 3.06
96 112 4.780275 TTTGAATGGAATTGCATCGTCA 57.220 36.364 13.26 11.13 36.07 4.35
97 113 7.489113 AGTTATTTTGAATGGAATTGCATCGTC 59.511 33.333 13.26 8.62 36.07 4.20
98 114 7.322664 AGTTATTTTGAATGGAATTGCATCGT 58.677 30.769 13.26 0.00 36.07 3.73
99 115 7.760131 AGTTATTTTGAATGGAATTGCATCG 57.240 32.000 13.26 0.00 36.07 3.84
176 194 3.750373 ATATCCACACGGCGGCACC 62.750 63.158 13.24 0.00 0.00 5.01
217 241 2.857748 GTTTGCAAAAAGACTGAACCGG 59.142 45.455 14.67 0.00 0.00 5.28
218 242 3.547468 CAGTTTGCAAAAAGACTGAACCG 59.453 43.478 19.73 0.00 41.46 4.44
238 262 6.372659 ACAGTTACAAGAATGATAGTTGGCAG 59.627 38.462 0.00 0.00 0.00 4.85
374 398 7.928307 AAGTTCTCTTGCAGATTAAATGCTA 57.072 32.000 14.82 8.27 44.17 3.49
383 407 4.395542 GCAGATGAAAGTTCTCTTGCAGAT 59.604 41.667 0.00 0.00 41.88 2.90
509 738 8.078060 TGACAGATATTAGTGGAGTCATTGAA 57.922 34.615 0.00 0.00 30.43 2.69
599 828 7.545615 GTGGAGAATAACCTTGCCTAAATTTTG 59.454 37.037 0.00 0.00 0.00 2.44
612 841 8.485578 TTTTATTTGTTGGTGGAGAATAACCT 57.514 30.769 0.00 0.00 37.36 3.50
765 995 8.717717 AGATCACCAATTCTGAAGATTATGGTA 58.282 33.333 11.61 5.07 37.59 3.25
790 1020 8.981647 GGCCAGTGATATAAATTATTTGCAAAG 58.018 33.333 18.19 0.00 0.00 2.77
854 1084 1.340568 GGACCAGTAGAATCCCGTAGC 59.659 57.143 0.00 0.00 0.00 3.58
1073 1311 4.335416 GGAAATCTCCACCTTGTGATTCA 58.665 43.478 0.00 0.00 41.96 2.57
1079 1317 1.355720 CCTGGGAAATCTCCACCTTGT 59.644 52.381 0.00 0.00 44.51 3.16
1111 1349 5.126067 AGCAAGAAGAAACTAGCTTGAACA 58.874 37.500 1.04 0.00 39.97 3.18
1144 1382 8.477419 TGAAGTTAATGGTCAAAGAAGGAAAT 57.523 30.769 0.00 0.00 0.00 2.17
1196 1434 7.685481 TCTTTCATGGTGTCTGGATTAACTTA 58.315 34.615 0.00 0.00 0.00 2.24
1205 1443 2.189594 TGCTCTTTCATGGTGTCTGG 57.810 50.000 0.00 0.00 0.00 3.86
1233 1471 7.071824 AGGTAGCTAAGATCTTAATCCTGCTTT 59.928 37.037 23.42 12.16 35.38 3.51
1282 1520 2.100631 ACGAATCGCCAAGCCTTCG 61.101 57.895 1.15 13.95 42.11 3.79
1283 1521 1.298859 ACACGAATCGCCAAGCCTTC 61.299 55.000 1.15 0.00 0.00 3.46
1306 1544 0.834261 TGTCATTCCTCACCGTCCCA 60.834 55.000 0.00 0.00 0.00 4.37
1446 1684 1.289160 AGTATCACCACCACTGCCAT 58.711 50.000 0.00 0.00 0.00 4.40
1588 1957 4.061596 CTCTTCCCTTCATCGGCTTATTC 58.938 47.826 0.00 0.00 0.00 1.75
1596 1965 3.436496 GACGTTACTCTTCCCTTCATCG 58.564 50.000 0.00 0.00 0.00 3.84
1598 1967 3.087031 TCGACGTTACTCTTCCCTTCAT 58.913 45.455 0.00 0.00 0.00 2.57
1614 1983 6.975197 AGGATGTATGCATATTATCTTCGACG 59.025 38.462 22.58 0.00 35.07 5.12
1705 2086 5.767665 AGTTTCCTTACACACACATGCATAA 59.232 36.000 0.00 0.00 0.00 1.90
1711 2096 6.545666 TCATGAAAGTTTCCTTACACACACAT 59.454 34.615 13.01 0.00 0.00 3.21
1746 2131 7.427989 AGGAATAAATTTCATTGATGGCTGT 57.572 32.000 0.00 0.00 0.00 4.40
1808 2193 2.211250 TCAGTACTCACCCGTAAGCT 57.789 50.000 0.00 0.00 0.00 3.74
1814 2199 4.991056 CCATGATTAATCAGTACTCACCCG 59.009 45.833 21.97 2.51 40.64 5.28
1865 2276 8.701895 CCCTTAGTACATGTAGGACAAATCTTA 58.298 37.037 13.09 0.00 0.00 2.10
1893 2304 4.673968 AGTATGGGGCATCGATTAGAGTA 58.326 43.478 0.00 0.00 0.00 2.59
1910 2321 3.947834 GTCAGTTTTGGGGATGGAGTATG 59.052 47.826 0.00 0.00 0.00 2.39
1912 2323 2.983192 TGTCAGTTTTGGGGATGGAGTA 59.017 45.455 0.00 0.00 0.00 2.59
1932 2357 5.920193 ATACCCAGAATGTTGTTTGGATG 57.080 39.130 0.00 0.00 32.34 3.51
1940 2365 3.290710 CCTCCCAATACCCAGAATGTTG 58.709 50.000 0.00 0.00 0.00 3.33
2009 2434 7.145323 GCACAAAGCTGGAGAATTTAGTTAAA 58.855 34.615 0.00 0.00 41.15 1.52
2010 2435 6.264292 TGCACAAAGCTGGAGAATTTAGTTAA 59.736 34.615 0.00 0.00 45.94 2.01
2011 2436 5.767665 TGCACAAAGCTGGAGAATTTAGTTA 59.232 36.000 0.00 0.00 45.94 2.24
2224 2650 5.094387 TCCTCCTCTGACAAGGACTAAAAT 58.906 41.667 3.16 0.00 40.60 1.82
2239 2665 2.534042 TCATTTCCTCGTCCTCCTCT 57.466 50.000 0.00 0.00 0.00 3.69
2248 2674 4.595116 GCAACTTCATCATCATTTCCTCG 58.405 43.478 0.00 0.00 0.00 4.63
2310 5260 2.107041 AAACATGGACGCCGTGGAGA 62.107 55.000 18.31 0.00 44.23 3.71
2320 5270 4.072131 TCAAGCTACAGGAAAACATGGAC 58.928 43.478 0.00 0.00 0.00 4.02
2323 5273 7.094205 ACCTTTATCAAGCTACAGGAAAACATG 60.094 37.037 0.00 0.00 0.00 3.21
2328 5278 4.700213 GCACCTTTATCAAGCTACAGGAAA 59.300 41.667 0.00 0.00 0.00 3.13
2340 5290 2.368439 GCACCATGAGCACCTTTATCA 58.632 47.619 0.00 0.00 0.00 2.15
2344 5294 1.228245 ACGCACCATGAGCACCTTT 60.228 52.632 10.12 0.00 0.00 3.11
2349 5299 0.460811 GAGATCACGCACCATGAGCA 60.461 55.000 10.12 0.00 34.89 4.26
2350 5300 0.460811 TGAGATCACGCACCATGAGC 60.461 55.000 0.00 0.00 32.56 4.26
2351 5301 1.568606 CTGAGATCACGCACCATGAG 58.431 55.000 0.00 0.00 0.00 2.90
2352 5302 0.460811 GCTGAGATCACGCACCATGA 60.461 55.000 0.00 0.00 0.00 3.07
2354 5304 1.520120 CGCTGAGATCACGCACCAT 60.520 57.895 0.00 0.00 0.00 3.55
2360 5350 1.587350 ATGTCGCGCTGAGATCACG 60.587 57.895 5.56 0.00 0.00 4.35
2366 5356 3.260483 GCCTCATGTCGCGCTGAG 61.260 66.667 19.75 19.75 38.88 3.35
2386 5376 4.398044 GGAACCAATAAATCGAGGCTTCAA 59.602 41.667 0.00 0.00 0.00 2.69
2387 5377 3.945285 GGAACCAATAAATCGAGGCTTCA 59.055 43.478 0.00 0.00 0.00 3.02
2407 5397 0.531974 GGAATGCGCTATTGACGGGA 60.532 55.000 9.73 0.00 0.00 5.14
2409 5399 1.564622 CGGAATGCGCTATTGACGG 59.435 57.895 9.73 0.00 0.00 4.79
2427 5417 1.941812 CCAAGTTCACCACTCACGC 59.058 57.895 0.00 0.00 32.94 5.34
2463 5453 3.248888 AGCACCTAACAACCTAGGACTT 58.751 45.455 17.98 5.70 41.02 3.01
2464 5454 2.832733 GAGCACCTAACAACCTAGGACT 59.167 50.000 17.98 0.00 41.02 3.85
2466 5456 2.185387 GGAGCACCTAACAACCTAGGA 58.815 52.381 17.98 0.00 41.02 2.94
2489 5479 3.873952 AGCAAGAAGGCGATAAGTTCATC 59.126 43.478 0.00 0.00 39.27 2.92
2493 5483 3.334583 TGAGCAAGAAGGCGATAAGTT 57.665 42.857 0.00 0.00 39.27 2.66
2497 5487 3.262420 GAGTTTGAGCAAGAAGGCGATA 58.738 45.455 0.00 0.00 39.27 2.92
2504 5494 3.479489 TGAGCATGAGTTTGAGCAAGAA 58.521 40.909 0.00 0.00 0.00 2.52
2507 5497 3.479489 TCTTGAGCATGAGTTTGAGCAA 58.521 40.909 0.00 0.00 0.00 3.91
2513 5503 2.012673 GCGGATCTTGAGCATGAGTTT 58.987 47.619 0.00 0.00 0.00 2.66
2515 5505 0.829333 AGCGGATCTTGAGCATGAGT 59.171 50.000 0.00 0.00 0.00 3.41
2516 5506 1.202498 TGAGCGGATCTTGAGCATGAG 60.202 52.381 0.00 0.00 0.00 2.90
2518 5508 0.935898 GTGAGCGGATCTTGAGCATG 59.064 55.000 0.00 0.00 0.00 4.06
2519 5509 0.179062 GGTGAGCGGATCTTGAGCAT 60.179 55.000 0.00 0.00 0.00 3.79
2521 5511 0.179062 ATGGTGAGCGGATCTTGAGC 60.179 55.000 0.00 0.00 0.00 4.26
2522 5512 1.134580 ACATGGTGAGCGGATCTTGAG 60.135 52.381 0.00 0.00 0.00 3.02
2524 5514 1.293924 GACATGGTGAGCGGATCTTG 58.706 55.000 0.00 0.00 0.00 3.02
2525 5515 0.904649 TGACATGGTGAGCGGATCTT 59.095 50.000 0.00 0.00 0.00 2.40
2527 5517 0.176680 ACTGACATGGTGAGCGGATC 59.823 55.000 0.00 0.00 0.00 3.36
2528 5518 0.615331 AACTGACATGGTGAGCGGAT 59.385 50.000 0.00 0.00 0.00 4.18
2529 5519 0.320683 CAACTGACATGGTGAGCGGA 60.321 55.000 0.00 0.00 0.00 5.54
2530 5520 1.300971 CCAACTGACATGGTGAGCGG 61.301 60.000 0.00 0.00 33.08 5.52
2532 5522 0.962356 CCCCAACTGACATGGTGAGC 60.962 60.000 0.00 0.00 36.14 4.26
2533 5523 0.692476 TCCCCAACTGACATGGTGAG 59.308 55.000 0.00 0.00 36.14 3.51
2534 5524 1.371467 ATCCCCAACTGACATGGTGA 58.629 50.000 0.00 0.00 36.14 4.02
2535 5525 1.820519 CAATCCCCAACTGACATGGTG 59.179 52.381 0.00 0.00 36.14 4.17
2536 5526 1.272648 CCAATCCCCAACTGACATGGT 60.273 52.381 0.00 0.00 36.14 3.55
2537 5527 1.005805 TCCAATCCCCAACTGACATGG 59.994 52.381 0.00 0.00 37.71 3.66
2538 5528 2.094675 GTCCAATCCCCAACTGACATG 58.905 52.381 0.00 0.00 0.00 3.21
2539 5529 1.710244 TGTCCAATCCCCAACTGACAT 59.290 47.619 0.00 0.00 0.00 3.06
2540 5530 1.144691 TGTCCAATCCCCAACTGACA 58.855 50.000 0.00 0.00 0.00 3.58
2541 5531 1.202879 TGTGTCCAATCCCCAACTGAC 60.203 52.381 0.00 0.00 0.00 3.51
2542 5532 1.144691 TGTGTCCAATCCCCAACTGA 58.855 50.000 0.00 0.00 0.00 3.41
2550 5549 2.806945 TCCTCCATTGTGTCCAATCC 57.193 50.000 0.00 0.00 39.28 3.01
2555 5554 2.985896 TCGAAATCCTCCATTGTGTCC 58.014 47.619 0.00 0.00 0.00 4.02
2556 5555 3.242870 GCATCGAAATCCTCCATTGTGTC 60.243 47.826 0.00 0.00 0.00 3.67
2559 5558 2.301346 GGCATCGAAATCCTCCATTGT 58.699 47.619 0.00 0.00 0.00 2.71
2576 5575 3.344703 CCAAGACTTGGTGATGGCA 57.655 52.632 23.92 0.00 45.93 4.92
2633 5632 5.012561 CCCACAAATTCCAAAAACCCATCTA 59.987 40.000 0.00 0.00 0.00 1.98
2637 5636 2.422093 GCCCACAAATTCCAAAAACCCA 60.422 45.455 0.00 0.00 0.00 4.51
2639 5638 1.870402 CGCCCACAAATTCCAAAAACC 59.130 47.619 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.