Multiple sequence alignment - TraesCS3A01G516500

Loading Multiple Alignment...

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 TraesCS3A01G516500 chr3A 100.000 1733 0 0 1 1733 734005201 734003469 0.000000e+00 3201
1 TraesCS3A01G516500 chr3A 100.000 568 0 0 2113 2680 734003089 734002522 0.000000e+00 1050
2 TraesCS3A01G516500 chr3D 90.820 1732 72 33 1 1680 604364337 604362641 0.000000e+00 2237
3 TraesCS3A01G516500 chr3D 80.645 465 67 10 2193 2646 604362442 604361990 3.300000e-89 339
4 TraesCS3A01G516500 chrUn 87.847 1835 89 58 1 1716 42189815 42191634 0.000000e+00 2030
5 TraesCS3A01G516500 chr5A 87.739 261 29 2 5 265 231068757 231069014 4.340000e-78 302
6 TraesCS3A01G516500 chr5A 90.066 151 14 1 303 453 231091759 231091908 7.570000e-46 195
7 TraesCS3A01G516500 chr7A 83.146 267 38 3 5 271 594570755 594570496 1.240000e-58 237
8 TraesCS3A01G516500 chr4D 76.829 410 65 21 83 469 306379987 306379585 1.260000e-48 204


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 TraesCS3A01G516500 chr3A 734002522 734005201 2679 True 2125.5 3201 100.0000 1 2680 2 chr3A.!!$R1 2679
1 TraesCS3A01G516500 chr3D 604361990 604364337 2347 True 1288.0 2237 85.7325 1 2646 2 chr3D.!!$R1 2645
2 TraesCS3A01G516500 chrUn 42189815 42191634 1819 False 2030.0 2030 87.8470 1 1716 1 chrUn.!!$F1 1715

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
300 330 0.473501 GCTCATCAGGAGGGGGAGAT 60.474 60.0 0.0 0.0 44.22 2.75 F
623 655 0.582005 CTAAATACAAGCGGGCGAGC 59.418 55.0 0.0 0.0 37.41 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1149 1236 0.038709 AGAAGCAGCGTGTGAGAGAC 60.039 55.0 0.0 0.0 0.0 3.36 R
2494 2637 0.170116 GACATTTGCCGCCGAAATCA 59.830 50.0 0.0 0.0 0.0 2.57 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
251 252 1.599797 GGACCCTGACAAACCACCG 60.600 63.158 0.00 0.00 0.00 4.94
290 320 1.885359 GCACCATATGGGCTCATCAGG 60.885 57.143 25.55 9.21 42.05 3.86
294 324 1.281287 CATATGGGCTCATCAGGAGGG 59.719 57.143 0.00 0.00 44.22 4.30
297 327 2.040464 GGCTCATCAGGAGGGGGA 60.040 66.667 0.00 0.00 44.22 4.81
298 328 2.146061 GGCTCATCAGGAGGGGGAG 61.146 68.421 0.00 0.00 44.22 4.30
299 329 1.074926 GCTCATCAGGAGGGGGAGA 60.075 63.158 0.00 0.00 44.22 3.71
300 330 0.473501 GCTCATCAGGAGGGGGAGAT 60.474 60.000 0.00 0.00 44.22 2.75
561 591 1.342082 GCTTCGCACAGCTGCAATTG 61.342 55.000 15.27 5.57 44.50 2.32
616 646 1.593006 CAGGGCGACTAAATACAAGCG 59.407 52.381 0.00 0.00 0.00 4.68
623 655 0.582005 CTAAATACAAGCGGGCGAGC 59.418 55.000 0.00 0.00 37.41 5.03
787 844 3.710722 CTCGGTCTGCTGGGCCTT 61.711 66.667 4.53 0.00 0.00 4.35
844 901 3.371063 GCCGTCGTCCACTGGAGA 61.371 66.667 0.00 0.00 29.39 3.71
866 923 1.209504 CCGGTAGAATGAGCCCAAGAA 59.790 52.381 0.00 0.00 0.00 2.52
973 1031 2.684843 CGCTGTTGCTGCTTCCCTC 61.685 63.158 0.00 0.00 36.97 4.30
1030 1090 3.240134 ATGCTCAAGCCGTCGGTGT 62.240 57.895 13.94 0.00 41.18 4.16
1035 1095 1.666553 CAAGCCGTCGGTGTTGCTA 60.667 57.895 13.94 0.00 32.82 3.49
1036 1096 1.019278 CAAGCCGTCGGTGTTGCTAT 61.019 55.000 13.94 0.00 32.82 2.97
1124 1211 3.626930 TGGTTCTTGGTTGCTTACTGTT 58.373 40.909 0.00 0.00 0.00 3.16
1149 1236 1.372748 GAGCGAGCTCCATCCATCG 60.373 63.158 13.73 0.00 37.11 3.84
1188 1276 7.986320 TGCTTCTTTTTCATTTCTTTCCAATCA 59.014 29.630 0.00 0.00 0.00 2.57
1670 1809 0.411452 TCCTCTCCCAGCAAGTCTCT 59.589 55.000 0.00 0.00 0.00 3.10
1680 1819 1.004979 AGCAAGTCTCTCCCTCGTAGT 59.995 52.381 0.00 0.00 0.00 2.73
1681 1820 2.239150 AGCAAGTCTCTCCCTCGTAGTA 59.761 50.000 0.00 0.00 0.00 1.82
1684 1823 4.710324 CAAGTCTCTCCCTCGTAGTATCT 58.290 47.826 0.00 0.00 0.00 1.98
1696 1835 6.293735 CCCTCGTAGTATCTTCTTCAGCTTAG 60.294 46.154 0.00 0.00 0.00 2.18
1705 1844 6.017400 TCTTCTTCAGCTTAGCCAAAAATG 57.983 37.500 0.00 0.00 0.00 2.32
1707 1846 3.828451 TCTTCAGCTTAGCCAAAAATGCT 59.172 39.130 0.00 0.00 42.81 3.79
1709 1848 4.178545 TCAGCTTAGCCAAAAATGCTTC 57.821 40.909 0.00 0.00 40.23 3.86
1710 1849 3.828451 TCAGCTTAGCCAAAAATGCTTCT 59.172 39.130 0.00 0.00 40.23 2.85
1712 1851 5.476599 TCAGCTTAGCCAAAAATGCTTCTTA 59.523 36.000 0.00 0.00 40.23 2.10
1713 1852 6.153340 TCAGCTTAGCCAAAAATGCTTCTTAT 59.847 34.615 0.00 0.00 40.23 1.73
1717 1856 8.171196 GCTTAGCCAAAAATGCTTCTTATTTTC 58.829 33.333 0.00 0.00 40.23 2.29
1719 1858 7.662604 AGCCAAAAATGCTTCTTATTTTCTG 57.337 32.000 0.00 0.00 36.89 3.02
2136 2275 4.705337 ACAGAAGATACAAGTCGAGTCC 57.295 45.455 0.00 0.00 0.00 3.85
2137 2276 4.079970 ACAGAAGATACAAGTCGAGTCCA 58.920 43.478 0.00 0.00 0.00 4.02
2138 2277 4.156922 ACAGAAGATACAAGTCGAGTCCAG 59.843 45.833 0.00 0.00 0.00 3.86
2139 2278 4.396478 CAGAAGATACAAGTCGAGTCCAGA 59.604 45.833 0.00 0.00 0.00 3.86
2140 2279 4.396790 AGAAGATACAAGTCGAGTCCAGAC 59.603 45.833 0.00 0.00 38.81 3.51
2141 2280 2.678836 AGATACAAGTCGAGTCCAGACG 59.321 50.000 0.00 0.00 42.97 4.18
2142 2281 1.888215 TACAAGTCGAGTCCAGACGT 58.112 50.000 0.00 0.00 42.97 4.34
2143 2282 3.093566 CAAGTCGAGTCCAGACGTG 57.906 57.895 0.00 1.15 42.97 4.49
2144 2283 0.387367 CAAGTCGAGTCCAGACGTGG 60.387 60.000 0.00 0.00 46.63 4.94
2163 2302 4.640201 CGTGGAAACCAAGTCCATATTCAT 59.360 41.667 0.00 0.00 46.67 2.57
2172 2311 8.319057 ACCAAGTCCATATTCATACTCAACTA 57.681 34.615 0.00 0.00 0.00 2.24
2173 2312 8.938883 ACCAAGTCCATATTCATACTCAACTAT 58.061 33.333 0.00 0.00 0.00 2.12
2184 2323 8.941995 TTCATACTCAACTATACTATCTGCCT 57.058 34.615 0.00 0.00 0.00 4.75
2185 2324 8.941995 TCATACTCAACTATACTATCTGCCTT 57.058 34.615 0.00 0.00 0.00 4.35
2186 2325 9.368416 TCATACTCAACTATACTATCTGCCTTT 57.632 33.333 0.00 0.00 0.00 3.11
2187 2326 9.632807 CATACTCAACTATACTATCTGCCTTTC 57.367 37.037 0.00 0.00 0.00 2.62
2188 2327 7.056844 ACTCAACTATACTATCTGCCTTTCC 57.943 40.000 0.00 0.00 0.00 3.13
2189 2328 6.085555 TCAACTATACTATCTGCCTTTCCG 57.914 41.667 0.00 0.00 0.00 4.30
2190 2329 5.010719 TCAACTATACTATCTGCCTTTCCGG 59.989 44.000 0.00 0.00 0.00 5.14
2200 2339 2.571548 CCTTTCCGGCAATGAAGCT 58.428 52.632 0.00 0.00 34.17 3.74
2203 2342 2.289010 CCTTTCCGGCAATGAAGCTTTT 60.289 45.455 0.00 0.00 34.17 2.27
2246 2385 3.519579 CACAGGTTGCAACAATTTGACA 58.480 40.909 29.55 0.00 34.24 3.58
2247 2386 3.552699 CACAGGTTGCAACAATTTGACAG 59.447 43.478 29.55 10.65 34.24 3.51
2248 2387 3.195396 ACAGGTTGCAACAATTTGACAGT 59.805 39.130 29.55 11.26 34.24 3.55
2249 2388 4.400884 ACAGGTTGCAACAATTTGACAGTA 59.599 37.500 29.55 0.00 34.24 2.74
2250 2389 4.739716 CAGGTTGCAACAATTTGACAGTAC 59.260 41.667 29.55 8.54 34.24 2.73
2253 2392 6.320164 AGGTTGCAACAATTTGACAGTACTAA 59.680 34.615 29.55 0.00 34.24 2.24
2258 2397 7.075741 GCAACAATTTGACAGTACTAAACGAT 58.924 34.615 2.79 0.00 34.24 3.73
2262 2401 8.999431 ACAATTTGACAGTACTAAACGATGAAT 58.001 29.630 2.79 0.00 0.00 2.57
2265 2404 7.956420 TTGACAGTACTAAACGATGAATTGT 57.044 32.000 0.00 0.00 0.00 2.71
2277 2416 4.097714 CGATGAATTGTGAAACCATTCCG 58.902 43.478 2.77 0.00 45.48 4.30
2300 2439 6.093495 CCGAATTTGCTTTAGGTATGAACTCA 59.907 38.462 0.00 0.00 0.00 3.41
2301 2440 7.201732 CCGAATTTGCTTTAGGTATGAACTCAT 60.202 37.037 0.00 0.00 40.22 2.90
2313 2452 7.050377 AGGTATGAACTCATCACAAAATCGAT 58.950 34.615 0.00 0.00 41.93 3.59
2315 2454 6.748333 ATGAACTCATCACAAAATCGATGT 57.252 33.333 0.00 0.00 41.93 3.06
2317 2456 4.952262 ACTCATCACAAAATCGATGTGG 57.048 40.909 15.62 3.07 46.37 4.17
2319 2458 3.080319 TCATCACAAAATCGATGTGGCA 58.920 40.909 15.62 0.62 46.37 4.92
2320 2459 3.505293 TCATCACAAAATCGATGTGGCAA 59.495 39.130 15.62 0.00 46.37 4.52
2321 2460 3.281341 TCACAAAATCGATGTGGCAAC 57.719 42.857 15.62 0.00 46.37 4.17
2322 2461 2.620585 TCACAAAATCGATGTGGCAACA 59.379 40.909 15.62 0.00 46.37 3.33
2341 2481 2.040412 ACACCCCAAACAGAAGAGATCC 59.960 50.000 0.00 0.00 0.00 3.36
2342 2482 1.636003 ACCCCAAACAGAAGAGATCCC 59.364 52.381 0.00 0.00 0.00 3.85
2343 2483 1.918957 CCCCAAACAGAAGAGATCCCT 59.081 52.381 0.00 0.00 0.00 4.20
2350 2490 6.126940 CCAAACAGAAGAGATCCCTAATCAGA 60.127 42.308 0.00 0.00 36.79 3.27
2360 2500 1.269309 CCCTAATCAGAAGGCGACTCG 60.269 57.143 0.00 0.00 42.68 4.18
2379 2519 1.385743 CGGTCGACGCAGAACTAAAAG 59.614 52.381 9.92 0.00 34.82 2.27
2384 2524 2.410262 CGACGCAGAACTAAAAGCACAG 60.410 50.000 0.00 0.00 0.00 3.66
2399 2539 0.740149 CACAGTGCAAGACAAAGGCA 59.260 50.000 0.00 0.00 34.70 4.75
2400 2540 1.338973 CACAGTGCAAGACAAAGGCAT 59.661 47.619 0.00 0.00 40.05 4.40
2412 2552 4.079901 AGACAAAGGCATCATCAGGAAGAT 60.080 41.667 0.00 0.00 37.48 2.40
2429 2570 5.649831 AGGAAGATGGATTTGAACTAGTTGC 59.350 40.000 14.14 5.53 0.00 4.17
2430 2571 5.163612 GGAAGATGGATTTGAACTAGTTGCC 60.164 44.000 14.14 6.94 0.00 4.52
2439 2580 7.542130 GGATTTGAACTAGTTGCCATTTACAAG 59.458 37.037 14.14 0.00 0.00 3.16
2443 2584 1.937191 AGTTGCCATTTACAAGGGGG 58.063 50.000 0.00 0.00 31.67 5.40
2444 2585 0.249120 GTTGCCATTTACAAGGGGGC 59.751 55.000 0.00 0.00 44.82 5.80
2445 2586 4.451544 GCCATTTACAAGGGGGCA 57.548 55.556 0.00 0.00 44.01 5.36
2446 2587 1.897423 GCCATTTACAAGGGGGCAC 59.103 57.895 0.00 0.00 44.01 5.01
2475 2617 4.907582 GCGCCCGTGTTTATACAAATAATC 59.092 41.667 0.00 0.00 35.69 1.75
2477 2619 5.276963 CGCCCGTGTTTATACAAATAATCGT 60.277 40.000 0.00 0.00 35.69 3.73
2482 2624 9.412390 CCGTGTTTATACAAATAATCGTTACAC 57.588 33.333 0.00 0.00 35.69 2.90
2483 2625 9.412390 CGTGTTTATACAAATAATCGTTACACC 57.588 33.333 0.00 0.00 34.09 4.16
2485 2628 9.445878 TGTTTATACAAATAATCGTTACACCCA 57.554 29.630 0.00 0.00 0.00 4.51
2488 2631 4.653868 ACAAATAATCGTTACACCCACCA 58.346 39.130 0.00 0.00 0.00 4.17
2493 2636 0.322322 TCGTTACACCCACCACCATC 59.678 55.000 0.00 0.00 0.00 3.51
2494 2637 0.323629 CGTTACACCCACCACCATCT 59.676 55.000 0.00 0.00 0.00 2.90
2499 2642 1.428912 ACACCCACCACCATCTGATTT 59.571 47.619 0.00 0.00 0.00 2.17
2501 2644 1.340017 ACCCACCACCATCTGATTTCG 60.340 52.381 0.00 0.00 0.00 3.46
2511 2654 0.451383 TCTGATTTCGGCGGCAAATG 59.549 50.000 18.87 9.54 0.00 2.32
2513 2656 0.170116 TGATTTCGGCGGCAAATGTC 59.830 50.000 18.87 10.46 0.00 3.06
2519 2662 1.353103 GGCGGCAAATGTCATCTCG 59.647 57.895 3.07 0.00 0.00 4.04
2604 2753 2.354328 ACATTTCCCTCCTACAACCCA 58.646 47.619 0.00 0.00 0.00 4.51
2605 2754 2.926329 ACATTTCCCTCCTACAACCCAT 59.074 45.455 0.00 0.00 0.00 4.00
2606 2755 3.290710 CATTTCCCTCCTACAACCCATG 58.709 50.000 0.00 0.00 0.00 3.66
2607 2756 2.053747 TTCCCTCCTACAACCCATGT 57.946 50.000 0.00 0.00 46.36 3.21
2608 2757 2.953093 TCCCTCCTACAACCCATGTA 57.047 50.000 0.00 0.00 43.63 2.29
2623 2772 8.271458 ACAACCCATGTATGTATATTGTTCTGA 58.729 33.333 0.00 0.00 41.63 3.27
2639 2788 5.933617 TGTTCTGATCTATCTCCAATTGGG 58.066 41.667 24.29 14.71 35.41 4.12
2646 2795 0.040058 ATCTCCAATTGGGTGCTGCA 59.960 50.000 24.29 0.00 38.11 4.41
2647 2796 0.040058 TCTCCAATTGGGTGCTGCAT 59.960 50.000 24.29 0.00 38.11 3.96
2648 2797 0.174845 CTCCAATTGGGTGCTGCATG 59.825 55.000 24.29 0.00 38.11 4.06
2649 2798 1.448893 CCAATTGGGTGCTGCATGC 60.449 57.895 17.36 11.82 43.25 4.06
2650 2799 1.448893 CAATTGGGTGCTGCATGCC 60.449 57.895 16.68 2.72 42.00 4.40
2651 2800 1.611261 AATTGGGTGCTGCATGCCT 60.611 52.632 16.68 0.00 42.00 4.75
2652 2801 1.610554 AATTGGGTGCTGCATGCCTC 61.611 55.000 16.68 7.31 42.00 4.70
2653 2802 4.746309 TGGGTGCTGCATGCCTCC 62.746 66.667 16.68 10.67 42.00 4.30
2655 2804 4.437587 GGTGCTGCATGCCTCCCT 62.438 66.667 16.68 0.00 42.00 4.20
2656 2805 3.138798 GTGCTGCATGCCTCCCTG 61.139 66.667 16.68 0.00 42.00 4.45
2657 2806 4.435970 TGCTGCATGCCTCCCTGG 62.436 66.667 16.68 0.00 42.00 4.45
2674 2823 4.530581 GCTTCTACAGGCAGCCTC 57.469 61.111 12.53 0.00 0.00 4.70
2675 2824 1.904032 GCTTCTACAGGCAGCCTCT 59.096 57.895 12.53 1.55 0.00 3.69
2676 2825 0.461693 GCTTCTACAGGCAGCCTCTG 60.462 60.000 12.53 4.80 38.16 3.35
2677 2826 0.901124 CTTCTACAGGCAGCCTCTGT 59.099 55.000 12.53 11.59 46.02 3.41
2678 2827 1.277557 CTTCTACAGGCAGCCTCTGTT 59.722 52.381 12.53 0.00 42.17 3.16
2679 2828 1.352083 TCTACAGGCAGCCTCTGTTT 58.648 50.000 12.53 0.00 42.17 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
290 320 2.122189 CTCCCCCATCTCCCCCTC 60.122 72.222 0.00 0.00 0.00 4.30
294 324 2.774351 CCACCTCCCCCATCTCCC 60.774 72.222 0.00 0.00 0.00 4.30
297 327 2.286425 CACCCACCTCCCCCATCT 60.286 66.667 0.00 0.00 0.00 2.90
298 328 2.850851 TACCACCCACCTCCCCCATC 62.851 65.000 0.00 0.00 0.00 3.51
299 329 2.900040 TACCACCCACCTCCCCCAT 61.900 63.158 0.00 0.00 0.00 4.00
300 330 3.543626 TACCACCCACCTCCCCCA 61.544 66.667 0.00 0.00 0.00 4.96
503 533 2.035442 GCGAGGTCCAAAGAGTGCC 61.035 63.158 0.00 0.00 0.00 5.01
504 534 2.035442 GGCGAGGTCCAAAGAGTGC 61.035 63.158 0.00 0.00 0.00 4.40
505 535 1.738099 CGGCGAGGTCCAAAGAGTG 60.738 63.158 0.00 0.00 0.00 3.51
561 591 1.401905 GTTTCTGGGATGGATTGCGTC 59.598 52.381 0.00 0.00 0.00 5.19
721 772 2.284258 ACGGCAGCTTCTCCTCCT 60.284 61.111 0.00 0.00 0.00 3.69
844 901 0.912487 TTGGGCTCATTCTACCGGGT 60.912 55.000 6.32 4.46 0.00 5.28
866 923 3.009714 GGAAGGGCCGGGAACTCT 61.010 66.667 2.18 0.00 0.00 3.24
973 1031 3.333804 GCAGAGAAAAACAGAGGAGAGG 58.666 50.000 0.00 0.00 0.00 3.69
1102 1189 3.214328 ACAGTAAGCAACCAAGAACCAG 58.786 45.455 0.00 0.00 0.00 4.00
1149 1236 0.038709 AGAAGCAGCGTGTGAGAGAC 60.039 55.000 0.00 0.00 0.00 3.36
1188 1276 1.202582 CCGTGTCTCGAGGTTCTGATT 59.797 52.381 13.56 0.00 42.86 2.57
1190 1278 1.863662 GCCGTGTCTCGAGGTTCTGA 61.864 60.000 13.56 0.00 42.86 3.27
1670 1809 3.884091 GCTGAAGAAGATACTACGAGGGA 59.116 47.826 0.00 0.00 0.00 4.20
1680 1819 7.629222 GCATTTTTGGCTAAGCTGAAGAAGATA 60.629 37.037 0.56 0.00 0.00 1.98
1681 1820 6.628185 CATTTTTGGCTAAGCTGAAGAAGAT 58.372 36.000 0.56 0.00 0.00 2.40
1684 1823 4.281688 AGCATTTTTGGCTAAGCTGAAGAA 59.718 37.500 0.56 0.00 40.47 2.52
1696 1835 7.386025 ACTCAGAAAATAAGAAGCATTTTTGGC 59.614 33.333 0.00 0.00 36.09 4.52
2112 2251 5.927115 GGACTCGACTTGTATCTTCTGTTTT 59.073 40.000 0.00 0.00 0.00 2.43
2113 2252 5.010719 TGGACTCGACTTGTATCTTCTGTTT 59.989 40.000 0.00 0.00 0.00 2.83
2114 2253 4.523173 TGGACTCGACTTGTATCTTCTGTT 59.477 41.667 0.00 0.00 0.00 3.16
2115 2254 4.079970 TGGACTCGACTTGTATCTTCTGT 58.920 43.478 0.00 0.00 0.00 3.41
2116 2255 4.396478 TCTGGACTCGACTTGTATCTTCTG 59.604 45.833 0.00 0.00 0.00 3.02
2117 2256 4.396790 GTCTGGACTCGACTTGTATCTTCT 59.603 45.833 0.00 0.00 0.00 2.85
2118 2257 4.664188 GTCTGGACTCGACTTGTATCTTC 58.336 47.826 0.00 0.00 0.00 2.87
2119 2258 3.127203 CGTCTGGACTCGACTTGTATCTT 59.873 47.826 0.00 0.00 0.00 2.40
2120 2259 2.678836 CGTCTGGACTCGACTTGTATCT 59.321 50.000 0.00 0.00 0.00 1.98
2121 2260 2.419324 ACGTCTGGACTCGACTTGTATC 59.581 50.000 0.00 0.00 0.00 2.24
2122 2261 2.161808 CACGTCTGGACTCGACTTGTAT 59.838 50.000 0.00 0.00 0.00 2.29
2123 2262 1.534163 CACGTCTGGACTCGACTTGTA 59.466 52.381 0.00 0.00 0.00 2.41
2124 2263 0.311165 CACGTCTGGACTCGACTTGT 59.689 55.000 0.00 0.00 0.00 3.16
2125 2264 0.387367 CCACGTCTGGACTCGACTTG 60.387 60.000 0.00 0.00 40.55 3.16
2126 2265 0.536687 TCCACGTCTGGACTCGACTT 60.537 55.000 0.00 0.00 42.15 3.01
2127 2266 1.072678 TCCACGTCTGGACTCGACT 59.927 57.895 0.00 0.00 42.15 4.18
2128 2267 3.664495 TCCACGTCTGGACTCGAC 58.336 61.111 0.00 0.00 42.15 4.20
2134 2273 0.834612 ACTTGGTTTCCACGTCTGGA 59.165 50.000 0.00 0.00 45.68 3.86
2135 2274 1.226746 GACTTGGTTTCCACGTCTGG 58.773 55.000 15.08 0.00 45.49 3.86
2139 2278 3.713826 ATATGGACTTGGTTTCCACGT 57.286 42.857 0.00 0.00 46.09 4.49
2140 2279 4.006989 TGAATATGGACTTGGTTTCCACG 58.993 43.478 0.00 0.00 46.09 4.94
2141 2280 6.828785 AGTATGAATATGGACTTGGTTTCCAC 59.171 38.462 0.00 0.00 46.09 4.02
2143 2282 7.054124 TGAGTATGAATATGGACTTGGTTTCC 58.946 38.462 0.00 0.00 0.00 3.13
2144 2283 8.398665 GTTGAGTATGAATATGGACTTGGTTTC 58.601 37.037 0.00 0.00 0.00 2.78
2145 2284 8.109634 AGTTGAGTATGAATATGGACTTGGTTT 58.890 33.333 0.00 0.00 0.00 3.27
2146 2285 7.633789 AGTTGAGTATGAATATGGACTTGGTT 58.366 34.615 0.00 0.00 0.00 3.67
2147 2286 7.200434 AGTTGAGTATGAATATGGACTTGGT 57.800 36.000 0.00 0.00 0.00 3.67
2163 2302 7.040617 CGGAAAGGCAGATAGTATAGTTGAGTA 60.041 40.741 0.00 0.00 0.00 2.59
2182 2321 0.890683 AAGCTTCATTGCCGGAAAGG 59.109 50.000 5.05 1.45 44.97 3.11
2183 2322 2.730550 AAAGCTTCATTGCCGGAAAG 57.269 45.000 5.05 0.83 0.00 2.62
2184 2323 2.606795 CGAAAAGCTTCATTGCCGGAAA 60.607 45.455 5.05 0.00 0.00 3.13
2185 2324 1.068610 CGAAAAGCTTCATTGCCGGAA 60.069 47.619 5.05 0.00 0.00 4.30
2186 2325 0.521291 CGAAAAGCTTCATTGCCGGA 59.479 50.000 5.05 0.00 0.00 5.14
2187 2326 1.072666 GCGAAAAGCTTCATTGCCGG 61.073 55.000 0.00 0.00 44.04 6.13
2188 2327 2.352814 GCGAAAAGCTTCATTGCCG 58.647 52.632 0.00 0.00 44.04 5.69
2200 2339 1.686355 TTCTCCTTTGGCAGCGAAAA 58.314 45.000 3.99 0.00 0.00 2.29
2203 2342 0.396435 TCTTTCTCCTTTGGCAGCGA 59.604 50.000 0.00 0.00 0.00 4.93
2210 2349 3.152341 ACCTGTGCATCTTTCTCCTTTG 58.848 45.455 0.00 0.00 0.00 2.77
2212 2351 3.152341 CAACCTGTGCATCTTTCTCCTT 58.848 45.455 0.00 0.00 0.00 3.36
2213 2352 2.787994 CAACCTGTGCATCTTTCTCCT 58.212 47.619 0.00 0.00 0.00 3.69
2241 2380 7.654116 TCACAATTCATCGTTTAGTACTGTCAA 59.346 33.333 5.39 0.00 0.00 3.18
2242 2381 7.149307 TCACAATTCATCGTTTAGTACTGTCA 58.851 34.615 5.39 0.00 0.00 3.58
2243 2382 7.576750 TCACAATTCATCGTTTAGTACTGTC 57.423 36.000 5.39 0.00 0.00 3.51
2244 2383 7.956420 TTCACAATTCATCGTTTAGTACTGT 57.044 32.000 5.39 0.00 0.00 3.55
2246 2385 7.442969 TGGTTTCACAATTCATCGTTTAGTACT 59.557 33.333 0.00 0.00 0.00 2.73
2247 2386 7.577979 TGGTTTCACAATTCATCGTTTAGTAC 58.422 34.615 0.00 0.00 0.00 2.73
2248 2387 7.731882 TGGTTTCACAATTCATCGTTTAGTA 57.268 32.000 0.00 0.00 0.00 1.82
2249 2388 6.627395 TGGTTTCACAATTCATCGTTTAGT 57.373 33.333 0.00 0.00 0.00 2.24
2250 2389 7.273381 GGAATGGTTTCACAATTCATCGTTTAG 59.727 37.037 6.38 0.00 33.23 1.85
2253 2392 5.469479 GGAATGGTTTCACAATTCATCGTT 58.531 37.500 6.38 0.00 33.23 3.85
2258 2397 5.720371 ATTCGGAATGGTTTCACAATTCA 57.280 34.783 1.68 0.00 33.23 2.57
2262 2401 4.054671 GCAAATTCGGAATGGTTTCACAA 58.945 39.130 3.59 0.00 33.23 3.33
2265 2404 4.599047 AAGCAAATTCGGAATGGTTTCA 57.401 36.364 3.59 0.00 31.27 2.69
2277 2416 8.677300 TGATGAGTTCATACCTAAAGCAAATTC 58.323 33.333 0.00 0.00 36.57 2.17
2300 2439 3.255395 TGTTGCCACATCGATTTTGTGAT 59.745 39.130 17.16 0.00 45.83 3.06
2301 2440 2.620585 TGTTGCCACATCGATTTTGTGA 59.379 40.909 17.16 0.00 45.83 3.58
2315 2454 0.324738 TTCTGTTTGGGGTGTTGCCA 60.325 50.000 0.00 0.00 39.65 4.92
2316 2455 0.389025 CTTCTGTTTGGGGTGTTGCC 59.611 55.000 0.00 0.00 0.00 4.52
2317 2456 1.338020 CTCTTCTGTTTGGGGTGTTGC 59.662 52.381 0.00 0.00 0.00 4.17
2319 2458 3.498661 GGATCTCTTCTGTTTGGGGTGTT 60.499 47.826 0.00 0.00 0.00 3.32
2320 2459 2.040412 GGATCTCTTCTGTTTGGGGTGT 59.960 50.000 0.00 0.00 0.00 4.16
2321 2460 2.619074 GGGATCTCTTCTGTTTGGGGTG 60.619 54.545 0.00 0.00 0.00 4.61
2322 2461 1.636003 GGGATCTCTTCTGTTTGGGGT 59.364 52.381 0.00 0.00 0.00 4.95
2323 2462 1.918957 AGGGATCTCTTCTGTTTGGGG 59.081 52.381 0.00 0.00 0.00 4.96
2326 2465 6.882656 TCTGATTAGGGATCTCTTCTGTTTG 58.117 40.000 0.00 0.00 35.69 2.93
2327 2466 7.365473 CCTTCTGATTAGGGATCTCTTCTGTTT 60.365 40.741 0.00 0.00 35.69 2.83
2341 2481 1.269309 CCGAGTCGCCTTCTGATTAGG 60.269 57.143 7.12 0.00 35.80 2.69
2342 2482 1.405821 ACCGAGTCGCCTTCTGATTAG 59.594 52.381 7.12 0.00 0.00 1.73
2343 2483 1.404391 GACCGAGTCGCCTTCTGATTA 59.596 52.381 7.12 0.00 0.00 1.75
2360 2500 1.126296 GCTTTTAGTTCTGCGTCGACC 59.874 52.381 10.58 3.43 0.00 4.79
2367 2507 2.033299 TGCACTGTGCTTTTAGTTCTGC 59.967 45.455 30.43 2.86 45.31 4.26
2379 2519 0.595825 GCCTTTGTCTTGCACTGTGC 60.596 55.000 25.15 25.15 45.29 4.57
2384 2524 2.229543 TGATGATGCCTTTGTCTTGCAC 59.770 45.455 0.00 0.00 37.92 4.57
2412 2552 6.491745 TGTAAATGGCAACTAGTTCAAATCCA 59.508 34.615 4.77 8.55 37.61 3.41
2414 2554 7.542130 CCTTGTAAATGGCAACTAGTTCAAATC 59.458 37.037 4.77 0.00 37.61 2.17
2429 2570 1.944234 GCGTGCCCCCTTGTAAATGG 61.944 60.000 0.00 0.00 0.00 3.16
2430 2571 0.965363 AGCGTGCCCCCTTGTAAATG 60.965 55.000 0.00 0.00 0.00 2.32
2454 2596 6.051646 ACGATTATTTGTATAAACACGGGC 57.948 37.500 0.00 0.00 34.61 6.13
2457 2599 9.412390 GGTGTAACGATTATTTGTATAAACACG 57.588 33.333 0.00 0.00 35.62 4.49
2475 2617 0.323629 AGATGGTGGTGGGTGTAACG 59.676 55.000 0.00 0.00 38.12 3.18
2477 2619 1.735926 TCAGATGGTGGTGGGTGTAA 58.264 50.000 0.00 0.00 0.00 2.41
2482 2624 1.382522 CGAAATCAGATGGTGGTGGG 58.617 55.000 0.00 0.00 0.00 4.61
2483 2625 1.382522 CCGAAATCAGATGGTGGTGG 58.617 55.000 0.00 0.00 0.00 4.61
2485 2628 0.744414 CGCCGAAATCAGATGGTGGT 60.744 55.000 0.00 0.00 0.00 4.16
2488 2631 1.819632 GCCGCCGAAATCAGATGGT 60.820 57.895 0.00 0.00 0.00 3.55
2493 2636 0.171007 ACATTTGCCGCCGAAATCAG 59.829 50.000 0.00 0.00 0.00 2.90
2494 2637 0.170116 GACATTTGCCGCCGAAATCA 59.830 50.000 0.00 0.00 0.00 2.57
2499 2642 1.078497 AGATGACATTTGCCGCCGA 60.078 52.632 0.00 0.00 0.00 5.54
2501 2644 1.353103 CGAGATGACATTTGCCGCC 59.647 57.895 0.00 0.00 0.00 6.13
2511 2654 3.775202 ACAGAATACACAGCGAGATGAC 58.225 45.455 0.00 0.00 0.00 3.06
2513 2656 5.523369 TCATACAGAATACACAGCGAGATG 58.477 41.667 0.00 0.00 0.00 2.90
2519 2662 6.813649 TCTTGTTCTCATACAGAATACACAGC 59.186 38.462 0.00 0.00 43.33 4.40
2580 2729 4.591498 GGGTTGTAGGAGGGAAATGTTTTT 59.409 41.667 0.00 0.00 0.00 1.94
2581 2730 4.157246 GGGTTGTAGGAGGGAAATGTTTT 58.843 43.478 0.00 0.00 0.00 2.43
2582 2731 3.141272 TGGGTTGTAGGAGGGAAATGTTT 59.859 43.478 0.00 0.00 0.00 2.83
2583 2732 2.719705 TGGGTTGTAGGAGGGAAATGTT 59.280 45.455 0.00 0.00 0.00 2.71
2584 2733 2.354328 TGGGTTGTAGGAGGGAAATGT 58.646 47.619 0.00 0.00 0.00 2.71
2585 2734 3.290710 CATGGGTTGTAGGAGGGAAATG 58.709 50.000 0.00 0.00 0.00 2.32
2594 2743 8.918202 AACAATATACATACATGGGTTGTAGG 57.082 34.615 0.00 0.00 45.77 3.18
2623 2772 3.749954 GCAGCACCCAATTGGAGATAGAT 60.750 47.826 26.60 6.31 37.39 1.98
2649 2798 2.216148 CCTGTAGAAGCCAGGGAGG 58.784 63.158 0.00 0.00 44.77 4.30
2654 2803 4.215349 GCTGCCTGTAGAAGCCAG 57.785 61.111 0.00 0.00 0.00 4.85
2657 2806 0.461693 CAGAGGCTGCCTGTAGAAGC 60.462 60.000 28.82 9.73 31.76 3.86
2658 2807 0.901124 ACAGAGGCTGCCTGTAGAAG 59.099 55.000 28.82 12.67 42.51 2.85
2659 2808 1.352083 AACAGAGGCTGCCTGTAGAA 58.648 50.000 28.82 0.00 43.42 2.10
2660 2809 1.352083 AAACAGAGGCTGCCTGTAGA 58.648 50.000 28.82 0.00 43.42 2.59
2661 2810 3.944476 AAACAGAGGCTGCCTGTAG 57.056 52.632 28.82 18.30 43.42 2.74


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

AutoCloner maintained by Alex Coulton.