Multiple sequence alignment - TraesCS5A01G378200

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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 TraesCS5A01G378200 chr5A 100.000 2860 0 0 1 2860 575614395 575611536 0.000000e+00 5282.0
1 TraesCS5A01G378200 chr5A 82.456 228 22 7 1452 1679 57563479 57563688 1.750000e-42 183.0
2 TraesCS5A01G378200 chr5B 90.722 2285 78 34 1 2234 559780068 559777867 0.000000e+00 2922.0
3 TraesCS5A01G378200 chr5B 81.931 321 34 12 2553 2860 559777561 559777252 1.700000e-62 250.0
4 TraesCS5A01G378200 chr5B 78.799 283 39 13 2245 2521 559777818 559777551 1.360000e-38 171.0
5 TraesCS5A01G378200 chr5B 81.140 228 25 7 1452 1679 64419321 64419530 1.760000e-37 167.0
6 TraesCS5A01G378200 chr5B 85.333 75 10 1 1604 1678 617711878 617711805 3.060000e-10 76.8
7 TraesCS5A01G378200 chr5D 87.271 1964 83 48 1 1893 457681743 457679876 0.000000e+00 2087.0
8 TraesCS5A01G378200 chr5D 94.269 349 8 3 1912 2252 457679672 457679328 9.080000e-145 523.0
9 TraesCS5A01G378200 chr5D 78.583 635 74 30 2245 2860 457679304 457678713 2.090000e-96 363.0
10 TraesCS5A01G378200 chr5D 82.456 228 22 7 1452 1679 66668839 66668630 1.750000e-42 183.0
11 TraesCS5A01G378200 chr5D 74.009 227 44 10 1452 1678 498404342 498404131 8.500000e-11 78.7


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 TraesCS5A01G378200 chr5A 575611536 575614395 2859 True 5282.000000 5282 100.000000 1 2860 1 chr5A.!!$R1 2859
1 TraesCS5A01G378200 chr5B 559777252 559780068 2816 True 1114.333333 2922 83.817333 1 2860 3 chr5B.!!$R2 2859
2 TraesCS5A01G378200 chr5D 457678713 457681743 3030 True 991.000000 2087 86.707667 1 2860 3 chr5D.!!$R3 2859

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
231 234 0.037605 ACCTAGCCACACTTACGCAC 60.038 55.0 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1963 2240 0.108472 TCTCTGATGCACCAAGCTCG 60.108 55.0 0.0 0.0 45.94 5.03 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
84 87 1.526887 CCATACGTGCATGATTCGTCC 59.473 52.381 14.17 0.00 38.69 4.79
85 88 1.190103 CATACGTGCATGATTCGTCCG 59.810 52.381 14.17 0.00 38.69 4.79
98 101 4.222847 GTCCGTCGGCCCATCCTC 62.223 72.222 6.34 0.00 0.00 3.71
125 128 1.538382 TTACAGGGGTGCCGGGTTA 60.538 57.895 2.18 0.00 0.00 2.85
191 194 3.191539 GCCGCTCAGAAGCTTCCG 61.192 66.667 22.81 17.72 46.91 4.30
229 232 0.245539 TCACCTAGCCACACTTACGC 59.754 55.000 0.00 0.00 0.00 4.42
231 234 0.037605 ACCTAGCCACACTTACGCAC 60.038 55.000 0.00 0.00 0.00 5.34
232 235 1.076533 CCTAGCCACACTTACGCACG 61.077 60.000 0.00 0.00 0.00 5.34
233 236 0.388134 CTAGCCACACTTACGCACGT 60.388 55.000 0.00 0.00 0.00 4.49
234 237 0.880441 TAGCCACACTTACGCACGTA 59.120 50.000 0.00 0.00 0.00 3.57
235 238 0.388134 AGCCACACTTACGCACGTAG 60.388 55.000 2.87 1.37 31.71 3.51
261 264 0.316689 GAACTGAAACCCGTTGCGTG 60.317 55.000 0.00 0.00 0.00 5.34
390 393 2.417719 CACCCATCCGAATTAGCTAGC 58.582 52.381 6.62 6.62 0.00 3.42
391 394 2.037772 CACCCATCCGAATTAGCTAGCT 59.962 50.000 23.12 23.12 0.00 3.32
392 395 3.258372 CACCCATCCGAATTAGCTAGCTA 59.742 47.826 20.67 20.67 0.00 3.32
394 397 3.118956 CCCATCCGAATTAGCTAGCTAGG 60.119 52.174 23.03 20.09 0.00 3.02
395 398 3.764434 CCATCCGAATTAGCTAGCTAGGA 59.236 47.826 24.83 24.83 0.00 2.94
396 399 4.404073 CCATCCGAATTAGCTAGCTAGGAT 59.596 45.833 26.39 26.39 33.10 3.24
397 400 5.594725 CCATCCGAATTAGCTAGCTAGGATA 59.405 44.000 29.20 16.53 31.93 2.59
398 401 6.096987 CCATCCGAATTAGCTAGCTAGGATAA 59.903 42.308 29.20 17.63 31.93 1.75
399 402 7.201956 CCATCCGAATTAGCTAGCTAGGATAAT 60.202 40.741 29.20 18.81 31.93 1.28
400 403 7.336161 TCCGAATTAGCTAGCTAGGATAATC 57.664 40.000 23.03 11.03 0.00 1.75
403 406 7.489757 CCGAATTAGCTAGCTAGGATAATCAAC 59.510 40.741 23.03 10.31 0.00 3.18
410 413 6.593382 GCTAGCTAGGATAATCAACCAATCAG 59.407 42.308 22.10 0.00 0.00 2.90
423 430 1.406614 CCAATCAGTCAGTCCAGCTCC 60.407 57.143 0.00 0.00 0.00 4.70
734 802 0.713883 GATCGTTGCACCTACGTGTG 59.286 55.000 9.08 0.00 42.39 3.82
757 825 4.762825 GCCCCGCGTATGTCATTA 57.237 55.556 4.92 0.00 0.00 1.90
796 870 0.942410 TGTGCCAACTTACTCGCGAC 60.942 55.000 3.71 0.00 0.00 5.19
863 937 1.255882 CTACCATTGCCAAGCCAACA 58.744 50.000 0.00 0.00 0.00 3.33
899 974 1.745232 GTCTTCTCCTCTCAGCGAGA 58.255 55.000 7.79 7.79 42.62 4.04
1088 1165 1.021390 CCACACAAGATCACCTCGGC 61.021 60.000 0.00 0.00 0.00 5.54
1180 1257 3.359523 CCGACAGGTCCGACGACA 61.360 66.667 0.00 0.00 41.13 4.35
1181 1258 2.126965 CGACAGGTCCGACGACAC 60.127 66.667 0.00 0.00 41.13 3.67
1236 1313 2.356667 CAACCCCTTCAGCCTCCC 59.643 66.667 0.00 0.00 0.00 4.30
1262 1339 5.263968 TCGCTACCTTATTCTTCTTCCTG 57.736 43.478 0.00 0.00 0.00 3.86
1357 1447 4.087892 GAGGCGCTGCTTCCAGGA 62.088 66.667 7.64 0.00 39.54 3.86
1358 1448 3.612247 GAGGCGCTGCTTCCAGGAA 62.612 63.158 7.64 0.71 39.54 3.36
1484 1574 3.902086 GACGGAGCGCCCTACCTC 61.902 72.222 2.29 0.00 0.00 3.85
1685 1775 3.260884 TGCCCTTCGAGTAAGTCTTGATT 59.739 43.478 0.00 0.00 36.56 2.57
1691 1781 7.201565 CCCTTCGAGTAAGTCTTGATTCATTTC 60.202 40.741 0.00 0.00 36.56 2.17
1708 1798 9.719279 GATTCATTTCATCACTTCTTCATCTTC 57.281 33.333 0.00 0.00 0.00 2.87
1709 1799 7.299787 TCATTTCATCACTTCTTCATCTTCG 57.700 36.000 0.00 0.00 0.00 3.79
1710 1800 7.099120 TCATTTCATCACTTCTTCATCTTCGA 58.901 34.615 0.00 0.00 0.00 3.71
1711 1801 6.712241 TTTCATCACTTCTTCATCTTCGAC 57.288 37.500 0.00 0.00 0.00 4.20
1712 1802 5.391312 TCATCACTTCTTCATCTTCGACA 57.609 39.130 0.00 0.00 0.00 4.35
1713 1803 5.970592 TCATCACTTCTTCATCTTCGACAT 58.029 37.500 0.00 0.00 0.00 3.06
1714 1804 7.100458 TCATCACTTCTTCATCTTCGACATA 57.900 36.000 0.00 0.00 0.00 2.29
1715 1805 7.720442 TCATCACTTCTTCATCTTCGACATAT 58.280 34.615 0.00 0.00 0.00 1.78
1716 1806 8.850156 TCATCACTTCTTCATCTTCGACATATA 58.150 33.333 0.00 0.00 0.00 0.86
1717 1807 9.636879 CATCACTTCTTCATCTTCGACATATAT 57.363 33.333 0.00 0.00 0.00 0.86
1723 1813 9.914131 TTCTTCATCTTCGACATATATTAGGTG 57.086 33.333 0.00 0.00 0.00 4.00
1724 1814 9.297037 TCTTCATCTTCGACATATATTAGGTGA 57.703 33.333 0.00 0.00 0.00 4.02
1725 1815 9.347934 CTTCATCTTCGACATATATTAGGTGAC 57.652 37.037 0.00 0.00 0.00 3.67
1727 1817 8.515414 TCATCTTCGACATATATTAGGTGACTG 58.485 37.037 0.00 0.00 43.88 3.51
1728 1818 7.818997 TCTTCGACATATATTAGGTGACTGT 57.181 36.000 0.00 0.00 43.88 3.55
1729 1819 7.649057 TCTTCGACATATATTAGGTGACTGTG 58.351 38.462 0.00 0.00 43.88 3.66
1730 1820 7.501225 TCTTCGACATATATTAGGTGACTGTGA 59.499 37.037 0.00 0.00 43.88 3.58
1731 1821 7.576861 TCGACATATATTAGGTGACTGTGAA 57.423 36.000 0.00 0.00 43.88 3.18
1732 1822 7.423199 TCGACATATATTAGGTGACTGTGAAC 58.577 38.462 0.00 0.00 43.88 3.18
1733 1823 7.284716 TCGACATATATTAGGTGACTGTGAACT 59.715 37.037 0.00 0.00 43.88 3.01
1734 1824 7.379797 CGACATATATTAGGTGACTGTGAACTG 59.620 40.741 0.00 0.00 43.88 3.16
1770 1860 7.386059 TGTGAAGCAGTGACTTATGATCTTTA 58.614 34.615 0.00 0.00 0.00 1.85
1774 1864 8.443953 AAGCAGTGACTTATGATCTTTATTCC 57.556 34.615 0.00 0.00 0.00 3.01
1776 1866 8.928448 AGCAGTGACTTATGATCTTTATTCCTA 58.072 33.333 0.00 0.00 0.00 2.94
1866 1957 4.279420 GCCTGGGATCCAAATAATGAAGAC 59.721 45.833 15.23 0.00 30.80 3.01
1963 2240 1.546029 GATCACCAAGCCAAAAGGGAC 59.454 52.381 0.00 0.00 40.01 4.46
2144 2421 1.058284 ATGCATGTTTTTGCTGGGGT 58.942 45.000 0.00 0.00 43.18 4.95
2170 2447 2.426305 CTTCCGGTTTCCCCTTGGCT 62.426 60.000 0.00 0.00 0.00 4.75
2171 2448 2.014033 TTCCGGTTTCCCCTTGGCTT 62.014 55.000 0.00 0.00 0.00 4.35
2172 2449 2.275380 CCGGTTTCCCCTTGGCTTG 61.275 63.158 0.00 0.00 0.00 4.01
2173 2450 2.275380 CGGTTTCCCCTTGGCTTGG 61.275 63.158 0.00 0.00 0.00 3.61
2174 2451 2.583441 GGTTTCCCCTTGGCTTGGC 61.583 63.158 0.00 0.00 0.00 4.52
2241 2526 3.617540 TTATGTTGTTTGTGAGCACCG 57.382 42.857 0.00 0.00 0.00 4.94
2261 2608 1.472480 GCTTGTTTATGTGCGGTGGAT 59.528 47.619 0.00 0.00 0.00 3.41
2272 2619 4.403734 TGTGCGGTGGATAGTGATATCTA 58.596 43.478 3.98 0.00 0.00 1.98
2273 2620 5.016831 TGTGCGGTGGATAGTGATATCTAT 58.983 41.667 3.98 0.00 33.89 1.98
2289 2636 7.274468 GTGATATCTATGACGATCGAGCATTTT 59.726 37.037 24.34 13.61 0.00 1.82
2290 2637 8.458843 TGATATCTATGACGATCGAGCATTTTA 58.541 33.333 24.34 15.00 0.00 1.52
2293 2640 3.899835 TGACGATCGAGCATTTTAACG 57.100 42.857 24.34 0.00 0.00 3.18
2298 2645 3.596454 CGATCGAGCATTTTAACGACGTC 60.596 47.826 10.26 5.18 37.58 4.34
2299 2646 1.987770 TCGAGCATTTTAACGACGTCC 59.012 47.619 10.58 0.00 0.00 4.79
2300 2647 1.266211 CGAGCATTTTAACGACGTCCG 60.266 52.381 10.58 7.90 45.44 4.79
2304 2651 2.536130 GCATTTTAACGACGTCCGGATG 60.536 50.000 22.38 22.38 43.93 3.51
2307 2654 0.880441 TTAACGACGTCCGGATGTGA 59.120 50.000 33.52 12.99 43.93 3.58
2309 2656 0.245539 AACGACGTCCGGATGTGATT 59.754 50.000 33.52 22.43 43.93 2.57
2311 2658 0.921347 CGACGTCCGGATGTGATTTC 59.079 55.000 33.52 17.19 33.91 2.17
2313 2660 1.927174 GACGTCCGGATGTGATTTCTG 59.073 52.381 33.52 4.61 0.00 3.02
2314 2661 1.548719 ACGTCCGGATGTGATTTCTGA 59.451 47.619 28.38 0.00 0.00 3.27
2316 2663 2.417379 CGTCCGGATGTGATTTCTGAGT 60.417 50.000 15.98 0.00 0.00 3.41
2317 2664 3.181490 CGTCCGGATGTGATTTCTGAGTA 60.181 47.826 15.98 0.00 0.00 2.59
2318 2665 4.499865 CGTCCGGATGTGATTTCTGAGTAT 60.500 45.833 15.98 0.00 0.00 2.12
2319 2666 5.278315 CGTCCGGATGTGATTTCTGAGTATA 60.278 44.000 15.98 0.00 0.00 1.47
2320 2667 5.921408 GTCCGGATGTGATTTCTGAGTATAC 59.079 44.000 7.81 0.00 0.00 1.47
2321 2668 5.010719 TCCGGATGTGATTTCTGAGTATACC 59.989 44.000 0.00 0.00 0.00 2.73
2322 2669 4.917998 CGGATGTGATTTCTGAGTATACCG 59.082 45.833 0.00 0.00 0.00 4.02
2324 2671 3.702330 TGTGATTTCTGAGTATACCGCG 58.298 45.455 0.00 0.00 0.00 6.46
2325 2672 2.471743 GTGATTTCTGAGTATACCGCGC 59.528 50.000 0.00 0.00 0.00 6.86
2326 2673 2.100087 TGATTTCTGAGTATACCGCGCA 59.900 45.455 8.75 0.00 0.00 6.09
2327 2674 2.658373 TTTCTGAGTATACCGCGCAA 57.342 45.000 8.75 0.00 0.00 4.85
2328 2675 1.917273 TTCTGAGTATACCGCGCAAC 58.083 50.000 8.75 0.00 0.00 4.17
2329 2676 0.101759 TCTGAGTATACCGCGCAACC 59.898 55.000 8.75 0.00 0.00 3.77
2330 2677 0.179121 CTGAGTATACCGCGCAACCA 60.179 55.000 8.75 0.00 0.00 3.67
2371 2718 5.334414 CCACTTGTTTAGCTAAGACTGCAAG 60.334 44.000 21.41 21.41 42.29 4.01
2380 2732 3.489059 GCTAAGACTGCAAGCACAAACAA 60.489 43.478 2.44 0.00 37.60 2.83
2424 2776 3.613737 CGCAACATTTTAGGGCATCTTTG 59.386 43.478 0.00 0.00 0.00 2.77
2428 2780 6.372381 GCAACATTTTAGGGCATCTTTGAATT 59.628 34.615 0.00 0.00 0.00 2.17
2429 2781 7.548780 GCAACATTTTAGGGCATCTTTGAATTA 59.451 33.333 0.00 0.00 0.00 1.40
2432 2784 9.435688 ACATTTTAGGGCATCTTTGAATTAAAC 57.564 29.630 0.00 0.00 0.00 2.01
2433 2785 9.434420 CATTTTAGGGCATCTTTGAATTAAACA 57.566 29.630 0.00 0.00 0.00 2.83
2464 2816 9.882996 TCAAAGATATTATGCACGATTTCAATC 57.117 29.630 0.00 0.00 0.00 2.67
2471 2823 4.340894 TGCACGATTTCAATCTGCTTAC 57.659 40.909 17.40 0.00 38.83 2.34
2513 2865 5.593679 ATGATGAGAAAGCCTTTTGGATG 57.406 39.130 0.00 0.00 44.07 3.51
2515 2867 4.834496 TGATGAGAAAGCCTTTTGGATGTT 59.166 37.500 0.00 0.00 44.07 2.71
2523 2875 4.993028 AGCCTTTTGGATGTTACCTACAA 58.007 39.130 0.00 0.00 44.07 2.41
2525 2877 5.243060 AGCCTTTTGGATGTTACCTACAAAC 59.757 40.000 0.00 0.00 44.07 2.93
2547 2899 9.057089 CAAACTGATATGTAGGATTAGAAACCC 57.943 37.037 0.00 0.00 0.00 4.11
2550 2902 6.989659 TGATATGTAGGATTAGAAACCCGAC 58.010 40.000 0.00 0.00 0.00 4.79
2556 2912 2.872858 GGATTAGAAACCCGACAGATGC 59.127 50.000 0.00 0.00 0.00 3.91
2567 2923 3.319405 CCCGACAGATGCTACTTATGAGT 59.681 47.826 0.00 0.00 39.97 3.41
2574 2930 5.982516 CAGATGCTACTTATGAGTCACTTCC 59.017 44.000 0.00 0.00 37.33 3.46
2591 2947 3.716872 ACTTCCCATCCGATACCAAATCT 59.283 43.478 0.00 0.00 0.00 2.40
2597 2953 6.940298 TCCCATCCGATACCAAATCTAAATTC 59.060 38.462 0.00 0.00 0.00 2.17
2603 2959 7.230510 TCCGATACCAAATCTAAATTCCCATTG 59.769 37.037 0.00 0.00 0.00 2.82
2608 2964 7.134842 ACCAAATCTAAATTCCCATTGGAGAT 58.865 34.615 3.62 0.28 43.07 2.75
2623 2979 7.362660 CCCATTGGAGATTTCATATGCTATGTG 60.363 40.741 3.62 0.00 0.00 3.21
2624 2980 7.362660 CCATTGGAGATTTCATATGCTATGTGG 60.363 40.741 0.00 0.00 0.00 4.17
2627 2983 6.938596 TGGAGATTTCATATGCTATGTGGAAG 59.061 38.462 0.00 0.00 0.00 3.46
2630 2986 8.985315 AGATTTCATATGCTATGTGGAAGAAA 57.015 30.769 0.00 0.00 0.00 2.52
2631 2987 9.412460 AGATTTCATATGCTATGTGGAAGAAAA 57.588 29.630 0.00 0.00 0.00 2.29
2674 3035 8.694540 CCAATTCATGTATGGTTTTCAATCCTA 58.305 33.333 0.00 0.00 0.00 2.94
2695 3057 8.038862 TCCTATGAGATTGAAGAAAGCCTAAT 57.961 34.615 0.00 0.00 0.00 1.73
2708 3076 5.767168 AGAAAGCCTAATATCACATTCCTGC 59.233 40.000 0.00 0.00 0.00 4.85
2709 3077 4.026356 AGCCTAATATCACATTCCTGCC 57.974 45.455 0.00 0.00 0.00 4.85
2713 3081 5.302823 GCCTAATATCACATTCCTGCCTTTT 59.697 40.000 0.00 0.00 0.00 2.27
2714 3082 6.490040 GCCTAATATCACATTCCTGCCTTTTA 59.510 38.462 0.00 0.00 0.00 1.52
2715 3083 7.308830 GCCTAATATCACATTCCTGCCTTTTAG 60.309 40.741 0.00 0.00 0.00 1.85
2729 3097 5.428253 TGCCTTTTAGTAGAATCTTGCGAT 58.572 37.500 0.00 0.00 0.00 4.58
2731 3099 5.755861 GCCTTTTAGTAGAATCTTGCGATCT 59.244 40.000 0.00 0.00 0.00 2.75
2733 3101 6.292596 CCTTTTAGTAGAATCTTGCGATCTGC 60.293 42.308 0.00 3.07 46.70 4.26
2743 3111 2.334653 CGATCTGCGGAGGCTCTC 59.665 66.667 15.23 7.38 40.82 3.20
2746 3114 0.463620 GATCTGCGGAGGCTCTCTTT 59.536 55.000 15.23 0.00 40.82 2.52
2747 3115 0.177604 ATCTGCGGAGGCTCTCTTTG 59.822 55.000 15.23 1.93 40.82 2.77
2748 3116 1.449246 CTGCGGAGGCTCTCTTTGG 60.449 63.158 15.23 0.00 40.82 3.28
2771 3139 7.123383 TGGATCTTAGACCTAATGACACTACA 58.877 38.462 0.00 0.00 0.00 2.74
2783 3151 5.568620 ATGACACTACAAAAGGAAGGACT 57.431 39.130 0.00 0.00 0.00 3.85
2795 3163 6.954352 AAAGGAAGGACTACTAGTTCCATT 57.046 37.500 14.68 5.28 40.92 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.352814 CCGGAATGGAGCGGAATAGTAG 60.353 54.545 0.00 0.00 42.00 2.57
6 7 1.616865 CCGGAATGGAGCGGAATAGTA 59.383 52.381 0.00 0.00 42.00 1.82
7 8 0.393077 CCGGAATGGAGCGGAATAGT 59.607 55.000 0.00 0.00 42.00 2.12
96 99 2.584608 CCTGTAACCTGGCCGGAG 59.415 66.667 15.09 5.75 36.31 4.63
97 100 3.006728 CCCTGTAACCTGGCCGGA 61.007 66.667 15.09 0.00 36.31 5.14
98 101 4.109675 CCCCTGTAACCTGGCCGG 62.110 72.222 3.88 3.88 39.35 6.13
104 107 3.327404 CCGGCACCCCTGTAACCT 61.327 66.667 0.00 0.00 0.00 3.50
144 147 2.046285 GGGACTTGAACGGCATGGG 61.046 63.158 0.00 0.00 0.00 4.00
147 150 0.035439 AATCGGGACTTGAACGGCAT 60.035 50.000 0.00 0.00 0.00 4.40
148 151 0.672401 GAATCGGGACTTGAACGGCA 60.672 55.000 0.00 0.00 0.00 5.69
149 152 1.366854 GGAATCGGGACTTGAACGGC 61.367 60.000 0.00 0.00 0.00 5.68
150 153 0.743345 GGGAATCGGGACTTGAACGG 60.743 60.000 0.00 0.00 0.00 4.44
151 154 1.082117 CGGGAATCGGGACTTGAACG 61.082 60.000 0.00 0.00 34.75 3.95
152 155 0.248289 TCGGGAATCGGGACTTGAAC 59.752 55.000 0.00 0.00 39.77 3.18
153 156 1.138266 GATCGGGAATCGGGACTTGAA 59.862 52.381 0.00 0.00 39.77 2.69
154 157 0.750850 GATCGGGAATCGGGACTTGA 59.249 55.000 0.00 0.00 39.77 3.02
191 194 2.357517 CACTGGACGTGTCAGGCC 60.358 66.667 16.71 0.00 38.84 5.19
213 216 1.076533 CGTGCGTAAGTGTGGCTAGG 61.077 60.000 0.00 0.00 41.68 3.02
229 232 0.098200 TCAGTTCGATCCGCTACGTG 59.902 55.000 0.00 0.00 0.00 4.49
231 234 1.582502 GTTTCAGTTCGATCCGCTACG 59.417 52.381 0.00 0.00 0.00 3.51
232 235 1.925185 GGTTTCAGTTCGATCCGCTAC 59.075 52.381 0.00 0.00 0.00 3.58
233 236 1.134907 GGGTTTCAGTTCGATCCGCTA 60.135 52.381 0.00 0.00 0.00 4.26
234 237 0.391263 GGGTTTCAGTTCGATCCGCT 60.391 55.000 0.00 0.00 0.00 5.52
235 238 1.693083 CGGGTTTCAGTTCGATCCGC 61.693 60.000 0.00 0.00 0.00 5.54
261 264 2.125673 CGTCCCGTCCATCACACC 60.126 66.667 0.00 0.00 0.00 4.16
281 284 3.998672 TTGTCTGCCGTCCCCGTC 61.999 66.667 0.00 0.00 0.00 4.79
282 285 4.309950 GTTGTCTGCCGTCCCCGT 62.310 66.667 0.00 0.00 0.00 5.28
284 287 4.717313 GGGTTGTCTGCCGTCCCC 62.717 72.222 0.00 0.00 32.66 4.81
390 393 7.504403 ACTGACTGATTGGTTGATTATCCTAG 58.496 38.462 0.00 0.00 0.00 3.02
391 394 7.419057 GGACTGACTGATTGGTTGATTATCCTA 60.419 40.741 0.00 0.00 0.00 2.94
392 395 6.319048 ACTGACTGATTGGTTGATTATCCT 57.681 37.500 0.00 0.00 0.00 3.24
394 397 6.115446 TGGACTGACTGATTGGTTGATTATC 58.885 40.000 0.00 0.00 0.00 1.75
395 398 6.065976 TGGACTGACTGATTGGTTGATTAT 57.934 37.500 0.00 0.00 0.00 1.28
396 399 5.491070 CTGGACTGACTGATTGGTTGATTA 58.509 41.667 0.00 0.00 0.00 1.75
397 400 4.330250 CTGGACTGACTGATTGGTTGATT 58.670 43.478 0.00 0.00 0.00 2.57
398 401 3.871463 GCTGGACTGACTGATTGGTTGAT 60.871 47.826 0.00 0.00 0.00 2.57
399 402 2.550855 GCTGGACTGACTGATTGGTTGA 60.551 50.000 0.00 0.00 0.00 3.18
400 403 1.808945 GCTGGACTGACTGATTGGTTG 59.191 52.381 0.00 0.00 0.00 3.77
403 406 1.406614 GGAGCTGGACTGACTGATTGG 60.407 57.143 0.00 0.00 0.00 3.16
410 413 0.460987 CAATCGGGAGCTGGACTGAC 60.461 60.000 0.00 0.00 0.00 3.51
423 430 6.895607 ACCTAAACAAAACAAAACAATCGG 57.104 33.333 0.00 0.00 0.00 4.18
655 705 3.976490 CTAGGCTGGGGTGTCGGGA 62.976 68.421 0.00 0.00 0.00 5.14
740 808 1.076332 GATAATGACATACGCGGGGC 58.924 55.000 12.47 1.51 0.00 5.80
741 809 2.337583 CTGATAATGACATACGCGGGG 58.662 52.381 12.47 0.94 0.00 5.73
742 810 1.726791 GCTGATAATGACATACGCGGG 59.273 52.381 12.47 1.38 0.00 6.13
776 846 0.942410 TCGCGAGTAAGTTGGCACAC 60.942 55.000 3.71 0.00 39.29 3.82
778 848 1.779683 GTCGCGAGTAAGTTGGCAC 59.220 57.895 10.24 0.00 0.00 5.01
811 885 1.487558 TGTTTTATAGGCGGGGACTCC 59.512 52.381 0.00 0.00 0.00 3.85
812 886 2.994186 TGTTTTATAGGCGGGGACTC 57.006 50.000 0.00 0.00 0.00 3.36
813 887 2.158667 CCATGTTTTATAGGCGGGGACT 60.159 50.000 0.00 0.00 0.00 3.85
849 923 0.249996 GCTTGTGTTGGCTTGGCAAT 60.250 50.000 12.54 0.00 0.00 3.56
863 937 2.288666 AGACGATGTGTGTTTGCTTGT 58.711 42.857 0.00 0.00 0.00 3.16
899 974 3.814625 TGACGAGATCTGATAGCTCTGT 58.185 45.455 0.00 4.93 38.54 3.41
974 1049 2.511600 GACGTGGGAAGATGCCGG 60.512 66.667 0.00 0.00 0.00 6.13
1236 1313 2.034812 AGAAGAATAAGGTAGCGAGCCG 59.965 50.000 0.00 0.00 0.00 5.52
1242 1319 4.770795 TGCAGGAAGAAGAATAAGGTAGC 58.229 43.478 0.00 0.00 0.00 3.58
1262 1339 2.677875 CCCTGGCCTTGGAGTTGC 60.678 66.667 15.51 0.00 0.00 4.17
1357 1447 4.687215 TGCTCTTGCTCGCCGCTT 62.687 61.111 0.00 0.00 40.48 4.68
1358 1448 4.687215 TTGCTCTTGCTCGCCGCT 62.687 61.111 0.00 0.00 40.48 5.52
1484 1574 1.186200 TCCTCATGTCGACCTTCCTG 58.814 55.000 14.12 3.17 0.00 3.86
1685 1775 7.063898 GTCGAAGATGAAGAAGTGATGAAATGA 59.936 37.037 0.00 0.00 40.67 2.57
1691 1781 7.943413 ATATGTCGAAGATGAAGAAGTGATG 57.057 36.000 0.00 0.00 40.67 3.07
1708 1798 7.379797 CAGTTCACAGTCACCTAATATATGTCG 59.620 40.741 0.00 0.00 0.00 4.35
1709 1799 8.414003 TCAGTTCACAGTCACCTAATATATGTC 58.586 37.037 0.00 0.00 0.00 3.06
1710 1800 8.306313 TCAGTTCACAGTCACCTAATATATGT 57.694 34.615 0.00 0.00 0.00 2.29
1711 1801 9.254133 CTTCAGTTCACAGTCACCTAATATATG 57.746 37.037 0.00 0.00 0.00 1.78
1712 1802 9.201989 TCTTCAGTTCACAGTCACCTAATATAT 57.798 33.333 0.00 0.00 0.00 0.86
1713 1803 8.589701 TCTTCAGTTCACAGTCACCTAATATA 57.410 34.615 0.00 0.00 0.00 0.86
1714 1804 7.482169 TCTTCAGTTCACAGTCACCTAATAT 57.518 36.000 0.00 0.00 0.00 1.28
1715 1805 6.911250 TCTTCAGTTCACAGTCACCTAATA 57.089 37.500 0.00 0.00 0.00 0.98
1716 1806 5.808366 TCTTCAGTTCACAGTCACCTAAT 57.192 39.130 0.00 0.00 0.00 1.73
1717 1807 5.304357 TGATCTTCAGTTCACAGTCACCTAA 59.696 40.000 0.00 0.00 0.00 2.69
1718 1808 4.832823 TGATCTTCAGTTCACAGTCACCTA 59.167 41.667 0.00 0.00 0.00 3.08
1719 1809 3.643320 TGATCTTCAGTTCACAGTCACCT 59.357 43.478 0.00 0.00 0.00 4.00
1720 1810 3.995199 TGATCTTCAGTTCACAGTCACC 58.005 45.455 0.00 0.00 0.00 4.02
1721 1811 6.551385 AAATGATCTTCAGTTCACAGTCAC 57.449 37.500 0.00 0.00 27.15 3.67
1722 1812 6.543465 ACAAAATGATCTTCAGTTCACAGTCA 59.457 34.615 0.00 0.00 33.14 3.41
1723 1813 6.854892 CACAAAATGATCTTCAGTTCACAGTC 59.145 38.462 0.00 0.00 33.14 3.51
1724 1814 6.543465 TCACAAAATGATCTTCAGTTCACAGT 59.457 34.615 0.00 0.00 33.14 3.55
1725 1815 6.962686 TCACAAAATGATCTTCAGTTCACAG 58.037 36.000 0.00 0.00 33.14 3.66
1726 1816 6.940831 TCACAAAATGATCTTCAGTTCACA 57.059 33.333 0.00 0.00 33.14 3.58
1727 1817 6.361748 GCTTCACAAAATGATCTTCAGTTCAC 59.638 38.462 0.00 0.00 33.14 3.18
1728 1818 6.039605 TGCTTCACAAAATGATCTTCAGTTCA 59.960 34.615 0.00 0.00 33.14 3.18
1729 1819 6.441274 TGCTTCACAAAATGATCTTCAGTTC 58.559 36.000 0.00 0.00 33.14 3.01
1730 1820 6.040166 ACTGCTTCACAAAATGATCTTCAGTT 59.960 34.615 0.00 0.00 36.10 3.16
1731 1821 5.533903 ACTGCTTCACAAAATGATCTTCAGT 59.466 36.000 0.00 0.00 37.11 3.41
1732 1822 5.856986 CACTGCTTCACAAAATGATCTTCAG 59.143 40.000 0.00 0.00 37.11 3.02
1733 1823 5.532032 TCACTGCTTCACAAAATGATCTTCA 59.468 36.000 0.00 0.00 37.11 3.02
1734 1824 5.855395 GTCACTGCTTCACAAAATGATCTTC 59.145 40.000 0.00 0.00 37.11 2.87
1770 1860 5.703592 TGAACATACTGCAAAACGTAGGAAT 59.296 36.000 2.94 0.00 0.00 3.01
1774 1864 4.394795 GCTGAACATACTGCAAAACGTAG 58.605 43.478 0.00 0.00 35.40 3.51
1776 1866 2.349438 CGCTGAACATACTGCAAAACGT 60.349 45.455 0.00 0.00 35.10 3.99
1910 2007 8.440833 AGATCGAAGAACAAAAAGTATAAACCG 58.559 33.333 0.00 0.00 43.58 4.44
1963 2240 0.108472 TCTCTGATGCACCAAGCTCG 60.108 55.000 0.00 0.00 45.94 5.03
2030 2307 4.394300 CCACATCTCCTTTGTGCTTCTAAG 59.606 45.833 0.00 0.00 42.47 2.18
2114 2391 7.990541 GCAAAAACATGCATGATGATAAGTA 57.009 32.000 32.75 0.00 45.70 2.24
2170 2447 4.099266 ACTTGAATACAAAAGCACAGCCAA 59.901 37.500 0.00 0.00 35.49 4.52
2171 2448 3.636300 ACTTGAATACAAAAGCACAGCCA 59.364 39.130 0.00 0.00 35.49 4.75
2172 2449 4.243007 ACTTGAATACAAAAGCACAGCC 57.757 40.909 0.00 0.00 35.49 4.85
2173 2450 5.043248 ACAACTTGAATACAAAAGCACAGC 58.957 37.500 0.00 0.00 35.49 4.40
2174 2451 6.264832 TGACAACTTGAATACAAAAGCACAG 58.735 36.000 0.00 0.00 35.49 3.66
2241 2526 0.878416 TCCACCGCACATAAACAAGC 59.122 50.000 0.00 0.00 0.00 4.01
2261 2608 6.106673 TGCTCGATCGTCATAGATATCACTA 58.893 40.000 15.94 0.00 0.00 2.74
2272 2619 4.026804 GTCGTTAAAATGCTCGATCGTCAT 60.027 41.667 15.94 15.96 34.93 3.06
2273 2620 3.302434 GTCGTTAAAATGCTCGATCGTCA 59.698 43.478 15.94 14.38 34.93 4.35
2289 2636 1.097232 ATCACATCCGGACGTCGTTA 58.903 50.000 6.12 0.00 37.11 3.18
2290 2637 0.245539 AATCACATCCGGACGTCGTT 59.754 50.000 6.12 0.00 37.11 3.85
2293 2640 1.927174 CAGAAATCACATCCGGACGTC 59.073 52.381 6.12 7.13 0.00 4.34
2298 2645 5.230942 GGTATACTCAGAAATCACATCCGG 58.769 45.833 2.25 0.00 0.00 5.14
2299 2646 4.917998 CGGTATACTCAGAAATCACATCCG 59.082 45.833 2.25 0.00 0.00 4.18
2300 2647 4.686554 GCGGTATACTCAGAAATCACATCC 59.313 45.833 2.25 0.00 0.00 3.51
2304 2651 2.471743 GCGCGGTATACTCAGAAATCAC 59.528 50.000 8.83 0.00 0.00 3.06
2307 2654 2.864343 GTTGCGCGGTATACTCAGAAAT 59.136 45.455 8.83 0.00 0.00 2.17
2309 2656 1.470285 GGTTGCGCGGTATACTCAGAA 60.470 52.381 8.83 0.00 0.00 3.02
2311 2658 0.179121 TGGTTGCGCGGTATACTCAG 60.179 55.000 8.83 0.00 0.00 3.35
2313 2660 1.361793 TTTGGTTGCGCGGTATACTC 58.638 50.000 8.83 0.00 0.00 2.59
2314 2661 1.810959 TTTTGGTTGCGCGGTATACT 58.189 45.000 8.83 0.00 0.00 2.12
2316 2663 2.159366 CCAATTTTGGTTGCGCGGTATA 60.159 45.455 8.83 0.00 43.43 1.47
2317 2664 1.403514 CCAATTTTGGTTGCGCGGTAT 60.404 47.619 8.83 0.00 43.43 2.73
2318 2665 0.039074 CCAATTTTGGTTGCGCGGTA 60.039 50.000 8.83 0.00 43.43 4.02
2319 2666 1.300542 CCAATTTTGGTTGCGCGGT 60.301 52.632 8.83 0.00 43.43 5.68
2320 2667 3.548280 CCAATTTTGGTTGCGCGG 58.452 55.556 8.83 0.00 43.43 6.46
2324 2671 6.142067 GGAAGATCCATCCAATTTTGGTTGC 61.142 44.000 12.85 2.95 43.47 4.17
2325 2672 5.046448 TGGAAGATCCATCCAATTTTGGTTG 60.046 40.000 13.94 10.58 44.57 3.77
2326 2673 5.092968 TGGAAGATCCATCCAATTTTGGTT 58.907 37.500 13.94 0.00 44.57 3.67
2327 2674 4.686891 TGGAAGATCCATCCAATTTTGGT 58.313 39.130 13.94 0.00 44.57 3.67
2371 2718 3.177997 AGGAACCACATTTGTTTGTGC 57.822 42.857 0.00 0.00 44.53 4.57
2380 2732 4.217550 CGGTGATACAAAAGGAACCACATT 59.782 41.667 0.00 0.00 0.00 2.71
2389 2741 3.848272 ATGTTGCGGTGATACAAAAGG 57.152 42.857 0.00 0.00 0.00 3.11
2443 2795 7.524912 AGCAGATTGAAATCGTGCATAATATC 58.475 34.615 19.94 0.00 39.66 1.63
2449 2801 4.395854 TGTAAGCAGATTGAAATCGTGCAT 59.604 37.500 19.94 14.55 39.66 3.96
2452 2804 5.784750 TCTGTAAGCAGATTGAAATCGTG 57.215 39.130 0.00 0.00 45.94 4.35
2464 2816 8.429493 TCATGTCTATCAATTTCTGTAAGCAG 57.571 34.615 0.00 0.00 43.87 4.24
2485 2837 7.013942 TCCAAAAGGCTTTCTCATCATATCATG 59.986 37.037 13.76 2.88 0.00 3.07
2486 2838 7.064866 TCCAAAAGGCTTTCTCATCATATCAT 58.935 34.615 13.76 0.00 0.00 2.45
2492 2844 4.410099 ACATCCAAAAGGCTTTCTCATCA 58.590 39.130 13.76 0.00 0.00 3.07
2495 2847 4.522789 GGTAACATCCAAAAGGCTTTCTCA 59.477 41.667 13.76 0.00 0.00 3.27
2496 2848 4.767409 AGGTAACATCCAAAAGGCTTTCTC 59.233 41.667 13.76 0.00 41.41 2.87
2497 2849 4.740902 AGGTAACATCCAAAAGGCTTTCT 58.259 39.130 13.76 0.94 41.41 2.52
2498 2850 5.475564 TGTAGGTAACATCCAAAAGGCTTTC 59.524 40.000 13.76 0.00 41.41 2.62
2499 2851 5.390387 TGTAGGTAACATCCAAAAGGCTTT 58.610 37.500 6.68 6.68 41.41 3.51
2500 2852 4.993028 TGTAGGTAACATCCAAAAGGCTT 58.007 39.130 0.00 0.00 41.41 4.35
2501 2853 4.650972 TGTAGGTAACATCCAAAAGGCT 57.349 40.909 0.00 0.00 41.41 4.58
2502 2854 5.243060 AGTTTGTAGGTAACATCCAAAAGGC 59.757 40.000 0.00 0.00 38.10 4.35
2523 2875 7.289317 TCGGGTTTCTAATCCTACATATCAGTT 59.711 37.037 0.00 0.00 0.00 3.16
2525 2877 7.091443 GTCGGGTTTCTAATCCTACATATCAG 58.909 42.308 0.00 0.00 0.00 2.90
2538 2890 3.767673 AGTAGCATCTGTCGGGTTTCTAA 59.232 43.478 0.00 0.00 0.00 2.10
2547 2899 4.973051 GTGACTCATAAGTAGCATCTGTCG 59.027 45.833 0.00 0.00 35.28 4.35
2550 2902 5.982516 GGAAGTGACTCATAAGTAGCATCTG 59.017 44.000 0.00 0.00 35.28 2.90
2556 2912 5.508153 CGGATGGGAAGTGACTCATAAGTAG 60.508 48.000 0.00 0.00 35.28 2.57
2567 2923 2.168458 TGGTATCGGATGGGAAGTGA 57.832 50.000 0.00 0.00 0.00 3.41
2574 2930 6.151144 GGGAATTTAGATTTGGTATCGGATGG 59.849 42.308 0.00 0.00 0.00 3.51
2591 2947 8.587608 GCATATGAAATCTCCAATGGGAATTTA 58.412 33.333 6.97 0.94 44.38 1.40
2597 2953 6.662234 ACATAGCATATGAAATCTCCAATGGG 59.338 38.462 6.97 0.00 0.00 4.00
2603 2959 7.164122 TCTTCCACATAGCATATGAAATCTCC 58.836 38.462 6.97 0.00 0.00 3.71
2642 2998 2.760092 ACCATACATGAATTGGCACACC 59.240 45.455 0.00 0.00 39.29 4.16
2643 2999 4.454728 AACCATACATGAATTGGCACAC 57.545 40.909 0.00 0.00 39.29 3.82
2644 3000 5.011431 TGAAAACCATACATGAATTGGCACA 59.989 36.000 0.00 0.20 33.66 4.57
2655 3011 9.872684 AATCTCATAGGATTGAAAACCATACAT 57.127 29.630 0.00 0.00 34.99 2.29
2674 3035 9.282569 GTGATATTAGGCTTTCTTCAATCTCAT 57.717 33.333 0.00 0.00 0.00 2.90
2676 3038 8.668510 TGTGATATTAGGCTTTCTTCAATCTC 57.331 34.615 0.00 0.00 0.00 2.75
2682 3044 7.521261 GCAGGAATGTGATATTAGGCTTTCTTC 60.521 40.741 0.00 0.00 0.00 2.87
2687 3049 4.105377 AGGCAGGAATGTGATATTAGGCTT 59.895 41.667 0.00 0.00 0.00 4.35
2688 3050 3.654806 AGGCAGGAATGTGATATTAGGCT 59.345 43.478 0.00 0.00 0.00 4.58
2689 3051 4.026356 AGGCAGGAATGTGATATTAGGC 57.974 45.455 0.00 0.00 0.00 3.93
2690 3052 6.966534 AAAAGGCAGGAATGTGATATTAGG 57.033 37.500 0.00 0.00 0.00 2.69
2695 3057 7.432148 TCTACTAAAAGGCAGGAATGTGATA 57.568 36.000 0.00 0.00 0.00 2.15
2729 3097 1.593787 CAAAGAGAGCCTCCGCAGA 59.406 57.895 0.00 0.00 37.52 4.26
2731 3099 1.267574 ATCCAAAGAGAGCCTCCGCA 61.268 55.000 0.00 0.00 37.52 5.69
2733 3101 1.118838 AGATCCAAAGAGAGCCTCCG 58.881 55.000 0.00 0.00 0.00 4.63
2743 3111 7.560368 AGTGTCATTAGGTCTAAGATCCAAAG 58.440 38.462 0.00 0.00 0.00 2.77
2746 3114 7.123383 TGTAGTGTCATTAGGTCTAAGATCCA 58.877 38.462 0.00 0.00 0.00 3.41
2747 3115 7.584122 TGTAGTGTCATTAGGTCTAAGATCC 57.416 40.000 0.00 0.00 0.00 3.36
2748 3116 9.871238 TTTTGTAGTGTCATTAGGTCTAAGATC 57.129 33.333 0.00 0.00 0.00 2.75
2771 3139 6.954352 ATGGAACTAGTAGTCCTTCCTTTT 57.046 37.500 16.86 3.87 0.00 2.27
2783 3151 7.208080 GGCTAAAGATTCGAATGGAACTAGTA 58.792 38.462 16.96 2.32 37.50 1.82
2795 3163 3.541632 GGAACATGGGCTAAAGATTCGA 58.458 45.455 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.