Multiple sequence alignment - TraesCS1B01G145400

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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 TraesCS1B01G145400 chr1B 100.000 2711 0 0 1 2711 198758282 198760992 0.000000e+00 5007.0
1 TraesCS1B01G145400 chr1B 79.743 311 55 5 6 310 133169512 133169204 4.540000e-53 219.0
2 TraesCS1B01G145400 chr1A 95.696 1301 41 7 791 2082 151351421 151352715 0.000000e+00 2078.0
3 TraesCS1B01G145400 chr1A 97.997 749 15 0 1 749 307055736 307054988 0.000000e+00 1301.0
4 TraesCS1B01G145400 chr1A 100.000 39 0 0 769 807 151351385 151351423 3.740000e-09 73.1
5 TraesCS1B01G145400 chr1D 95.101 1286 33 11 769 2039 139905929 139904659 0.000000e+00 1999.0
6 TraesCS1B01G145400 chr2B 98.686 761 9 1 1 760 73628373 73627613 0.000000e+00 1349.0
7 TraesCS1B01G145400 chr2B 89.164 766 69 6 1 760 470516870 470517627 0.000000e+00 942.0
8 TraesCS1B01G145400 chr2A 98.808 755 8 1 7 760 279506368 279507122 0.000000e+00 1343.0
9 TraesCS1B01G145400 chr2A 98.054 771 13 2 1 769 261674893 261675663 0.000000e+00 1339.0
10 TraesCS1B01G145400 chr4A 97.240 761 20 1 1 760 323791200 323790440 0.000000e+00 1288.0
11 TraesCS1B01G145400 chr4A 74.341 417 77 18 2282 2683 43371138 43370737 1.680000e-32 150.0
12 TraesCS1B01G145400 chr7A 96.757 771 14 2 1 760 690367865 690368635 0.000000e+00 1275.0
13 TraesCS1B01G145400 chr4B 86.728 761 76 13 1 757 607042347 607041608 0.000000e+00 822.0
14 TraesCS1B01G145400 chr4B 83.908 87 10 2 675 760 458319780 458319863 2.240000e-11 80.5
15 TraesCS1B01G145400 chr4B 88.525 61 7 0 2624 2684 617399124 617399184 1.040000e-09 75.0
16 TraesCS1B01G145400 chr4D 89.695 262 27 0 352 613 469156379 469156640 4.330000e-88 335.0
17 TraesCS1B01G145400 chr7D 73.613 739 136 39 1998 2711 138283651 138282947 2.100000e-56 230.0
18 TraesCS1B01G145400 chr5B 79.474 190 21 11 2058 2244 255969339 255969513 4.740000e-23 119.0
19 TraesCS1B01G145400 chr5D 86.517 89 7 4 675 760 23678572 23678486 2.870000e-15 93.5


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 TraesCS1B01G145400 chr1B 198758282 198760992 2710 False 5007.00 5007 100.000 1 2711 1 chr1B.!!$F1 2710
1 TraesCS1B01G145400 chr1A 307054988 307055736 748 True 1301.00 1301 97.997 1 749 1 chr1A.!!$R1 748
2 TraesCS1B01G145400 chr1A 151351385 151352715 1330 False 1075.55 2078 97.848 769 2082 2 chr1A.!!$F1 1313
3 TraesCS1B01G145400 chr1D 139904659 139905929 1270 True 1999.00 1999 95.101 769 2039 1 chr1D.!!$R1 1270
4 TraesCS1B01G145400 chr2B 73627613 73628373 760 True 1349.00 1349 98.686 1 760 1 chr2B.!!$R1 759
5 TraesCS1B01G145400 chr2B 470516870 470517627 757 False 942.00 942 89.164 1 760 1 chr2B.!!$F1 759
6 TraesCS1B01G145400 chr2A 279506368 279507122 754 False 1343.00 1343 98.808 7 760 1 chr2A.!!$F2 753
7 TraesCS1B01G145400 chr2A 261674893 261675663 770 False 1339.00 1339 98.054 1 769 1 chr2A.!!$F1 768
8 TraesCS1B01G145400 chr4A 323790440 323791200 760 True 1288.00 1288 97.240 1 760 1 chr4A.!!$R2 759
9 TraesCS1B01G145400 chr7A 690367865 690368635 770 False 1275.00 1275 96.757 1 760 1 chr7A.!!$F1 759
10 TraesCS1B01G145400 chr4B 607041608 607042347 739 True 822.00 822 86.728 1 757 1 chr4B.!!$R1 756
11 TraesCS1B01G145400 chr7D 138282947 138283651 704 True 230.00 230 73.613 1998 2711 1 chr7D.!!$R1 713

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
757 774 1.295792 ACGCACGGGCATATTTACTG 58.704 50.0 11.77 0.0 41.24 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2212 2263 0.179004 AATGAAGTGGCGGTTGGACA 60.179 50.0 0.0 0.0 0.0 4.02 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
540 554 1.909287 GGGCTCGGATCCTCTACCC 60.909 68.421 10.75 11.39 0.00 3.69
573 587 2.631580 GGCCAAAAATCGCCGGACA 61.632 57.895 5.05 0.00 34.94 4.02
656 673 5.181622 GGACAAATTTATGTGTGTCGGGTAA 59.818 40.000 0.00 0.00 41.05 2.85
757 774 1.295792 ACGCACGGGCATATTTACTG 58.704 50.000 11.77 0.00 41.24 2.74
758 775 1.295792 CGCACGGGCATATTTACTGT 58.704 50.000 11.77 0.00 41.24 3.55
759 776 2.159071 ACGCACGGGCATATTTACTGTA 60.159 45.455 11.77 0.00 41.24 2.74
760 777 2.220133 CGCACGGGCATATTTACTGTAC 59.780 50.000 11.77 0.00 41.24 2.90
761 778 3.199677 GCACGGGCATATTTACTGTACA 58.800 45.455 3.77 0.00 40.72 2.90
762 779 3.001939 GCACGGGCATATTTACTGTACAC 59.998 47.826 3.77 0.00 40.72 2.90
763 780 4.439057 CACGGGCATATTTACTGTACACT 58.561 43.478 0.00 0.00 0.00 3.55
764 781 5.593968 CACGGGCATATTTACTGTACACTA 58.406 41.667 0.00 0.00 0.00 2.74
765 782 6.044046 CACGGGCATATTTACTGTACACTAA 58.956 40.000 0.00 0.00 0.00 2.24
766 783 6.535865 CACGGGCATATTTACTGTACACTAAA 59.464 38.462 9.29 9.29 0.00 1.85
767 784 7.064847 CACGGGCATATTTACTGTACACTAAAA 59.935 37.037 10.50 4.10 0.00 1.52
1249 1280 0.678395 CCTCGCCATACTGCTCATCT 59.322 55.000 0.00 0.00 0.00 2.90
1623 1663 4.257654 TGCGCCGGGAAGGAACAA 62.258 61.111 4.18 0.00 45.00 2.83
1714 1754 2.283604 TGGAGGCGCAGTAGGACA 60.284 61.111 10.83 0.00 0.00 4.02
1841 1882 5.493250 TGAGTAGTATTTGGGGGTGGTTATT 59.507 40.000 0.00 0.00 0.00 1.40
1852 1893 3.451526 GGGTGGTTATTGCGAGTAGTAC 58.548 50.000 0.00 0.00 0.00 2.73
1854 1895 4.382362 GGGTGGTTATTGCGAGTAGTACTT 60.382 45.833 0.00 0.00 0.00 2.24
1911 1953 7.482654 GCTGTAGCATTGTGTATTATGAGAA 57.517 36.000 0.00 0.00 41.59 2.87
1912 1954 8.092521 GCTGTAGCATTGTGTATTATGAGAAT 57.907 34.615 0.00 0.00 41.59 2.40
1963 2005 7.389053 GGACATTAAAGTTCTCACTCAGATGTT 59.611 37.037 0.00 0.00 32.70 2.71
1990 2033 8.637986 ACATTTTGTTTTATAGGACATGTGTGT 58.362 29.630 1.15 0.00 42.49 3.72
2020 2065 8.589335 TTAGAGCGTCTCCAATAAATAATGAC 57.411 34.615 3.66 0.00 0.00 3.06
2066 2111 4.864704 TTACATCTTGGAGGCCAAAAAC 57.135 40.909 5.01 0.00 43.44 2.43
2085 2136 8.415553 CCAAAAACAATGCTCCAATAGATGATA 58.584 33.333 0.00 0.00 0.00 2.15
2086 2137 9.976511 CAAAAACAATGCTCCAATAGATGATAT 57.023 29.630 0.00 0.00 0.00 1.63
2128 2179 3.981071 TTACATCACCTCCTCCAAGTG 57.019 47.619 0.00 0.00 0.00 3.16
2132 2183 2.030027 TCACCTCCTCCAAGTGATGT 57.970 50.000 0.00 0.00 35.67 3.06
2133 2184 1.625315 TCACCTCCTCCAAGTGATGTG 59.375 52.381 0.00 0.00 35.67 3.21
2134 2185 0.326264 ACCTCCTCCAAGTGATGTGC 59.674 55.000 0.00 0.00 0.00 4.57
2144 2195 6.403636 CCTCCAAGTGATGTGCTGTAAAATAC 60.404 42.308 0.00 0.00 0.00 1.89
2158 2209 4.938832 TGTAAAATACAACACCCGGAGATG 59.061 41.667 0.73 2.39 35.38 2.90
2165 2216 1.176527 ACACCCGGAGATGCAAATTG 58.823 50.000 0.73 0.00 0.00 2.32
2177 2228 2.250031 TGCAAATTGGCATCTTCACCT 58.750 42.857 2.48 0.00 39.25 4.00
2178 2229 2.231964 TGCAAATTGGCATCTTCACCTC 59.768 45.455 2.48 0.00 39.25 3.85
2195 2246 3.433306 CCTCCCTGGTGATGTAAAACA 57.567 47.619 0.00 0.00 0.00 2.83
2196 2247 3.347216 CCTCCCTGGTGATGTAAAACAG 58.653 50.000 0.00 0.00 0.00 3.16
2197 2248 3.244911 CCTCCCTGGTGATGTAAAACAGT 60.245 47.826 0.00 0.00 0.00 3.55
2207 2258 1.595655 TAAAACAGTCAGCCGCGCA 60.596 52.632 8.75 0.00 0.00 6.09
2208 2259 1.837538 TAAAACAGTCAGCCGCGCAC 61.838 55.000 8.75 0.00 0.00 5.34
2212 2263 4.742201 AGTCAGCCGCGCACGAAT 62.742 61.111 8.75 0.00 43.93 3.34
2213 2264 4.505217 GTCAGCCGCGCACGAATG 62.505 66.667 8.75 0.00 43.93 2.67
2224 2275 1.963855 CACGAATGTCCAACCGCCA 60.964 57.895 0.00 0.00 0.00 5.69
2225 2276 1.964373 ACGAATGTCCAACCGCCAC 60.964 57.895 0.00 0.00 0.00 5.01
2226 2277 1.671054 CGAATGTCCAACCGCCACT 60.671 57.895 0.00 0.00 0.00 4.00
2229 2280 0.179004 AATGTCCAACCGCCACTTCA 60.179 50.000 0.00 0.00 0.00 3.02
2230 2281 0.038166 ATGTCCAACCGCCACTTCAT 59.962 50.000 0.00 0.00 0.00 2.57
2231 2282 0.179004 TGTCCAACCGCCACTTCATT 60.179 50.000 0.00 0.00 0.00 2.57
2232 2283 0.958822 GTCCAACCGCCACTTCATTT 59.041 50.000 0.00 0.00 0.00 2.32
2233 2284 1.068541 GTCCAACCGCCACTTCATTTC 60.069 52.381 0.00 0.00 0.00 2.17
2234 2285 0.958091 CCAACCGCCACTTCATTTCA 59.042 50.000 0.00 0.00 0.00 2.69
2235 2286 1.339610 CCAACCGCCACTTCATTTCAA 59.660 47.619 0.00 0.00 0.00 2.69
2240 2294 2.230992 CCGCCACTTCATTTCAATTCCA 59.769 45.455 0.00 0.00 0.00 3.53
2250 2304 1.839148 TTCAATTCCACCCGCCCGTA 61.839 55.000 0.00 0.00 0.00 4.02
2252 2306 1.153046 AATTCCACCCGCCCGTATG 60.153 57.895 0.00 0.00 0.00 2.39
2264 2318 2.717044 CCGTATGCCCGTCACTGGA 61.717 63.158 0.00 0.00 0.00 3.86
2266 2320 1.153429 GTATGCCCGTCACTGGACC 60.153 63.158 0.00 0.00 41.13 4.46
2267 2321 1.610967 TATGCCCGTCACTGGACCA 60.611 57.895 0.00 0.00 41.13 4.02
2268 2322 0.980754 TATGCCCGTCACTGGACCAT 60.981 55.000 0.00 0.00 41.13 3.55
2269 2323 2.436646 GCCCGTCACTGGACCATG 60.437 66.667 0.00 0.00 41.13 3.66
2270 2324 3.068881 CCCGTCACTGGACCATGT 58.931 61.111 0.00 0.00 41.13 3.21
2271 2325 1.374947 CCCGTCACTGGACCATGTT 59.625 57.895 0.00 0.00 41.13 2.71
2272 2326 0.673644 CCCGTCACTGGACCATGTTC 60.674 60.000 0.00 0.00 41.13 3.18
2273 2327 0.673644 CCGTCACTGGACCATGTTCC 60.674 60.000 1.52 1.52 41.13 3.62
2274 2328 1.014044 CGTCACTGGACCATGTTCCG 61.014 60.000 4.66 2.48 41.13 4.30
2276 2330 2.040544 CACTGGACCATGTTCCGCC 61.041 63.158 4.66 0.00 38.69 6.13
2277 2331 2.819595 CTGGACCATGTTCCGCCG 60.820 66.667 4.66 0.00 38.69 6.46
2278 2332 4.402528 TGGACCATGTTCCGCCGG 62.403 66.667 4.66 0.00 38.69 6.13
2280 2334 2.818274 GACCATGTTCCGCCGGTC 60.818 66.667 1.63 0.00 41.08 4.79
2281 2335 4.752879 ACCATGTTCCGCCGGTCG 62.753 66.667 1.63 7.37 38.08 4.79
2312 2366 3.900892 CCGACTCCGATGACCCCG 61.901 72.222 0.00 0.00 38.22 5.73
2314 2368 3.148279 GACTCCGATGACCCCGCT 61.148 66.667 0.00 0.00 0.00 5.52
2315 2369 1.826921 GACTCCGATGACCCCGCTA 60.827 63.158 0.00 0.00 0.00 4.26
2318 2372 4.280494 CCGATGACCCCGCTACCG 62.280 72.222 0.00 0.00 0.00 4.02
2319 2373 4.944372 CGATGACCCCGCTACCGC 62.944 72.222 0.00 0.00 0.00 5.68
2320 2374 4.603946 GATGACCCCGCTACCGCC 62.604 72.222 0.00 0.00 0.00 6.13
2322 2376 3.744003 ATGACCCCGCTACCGCCTA 62.744 63.158 0.00 0.00 0.00 3.93
2323 2377 3.909285 GACCCCGCTACCGCCTAC 61.909 72.222 0.00 0.00 0.00 3.18
2345 2404 2.217038 GCTGGTCTGACCCACCTCA 61.217 63.158 23.42 3.30 37.50 3.86
2346 2405 1.978473 CTGGTCTGACCCACCTCAG 59.022 63.158 23.42 9.56 37.50 3.35
2348 2407 2.262915 GTCTGACCCACCTCAGCG 59.737 66.667 0.00 0.00 38.07 5.18
2377 2436 2.594592 GGCGCAACCACCTTCACT 60.595 61.111 10.83 0.00 38.86 3.41
2383 2442 0.474184 CAACCACCTTCACTGACCCT 59.526 55.000 0.00 0.00 0.00 4.34
2390 2449 1.461268 TTCACTGACCCTGCCTCCA 60.461 57.895 0.00 0.00 0.00 3.86
2426 2485 2.111878 CATCTCGCCACCCCCATC 59.888 66.667 0.00 0.00 0.00 3.51
2427 2486 3.171388 ATCTCGCCACCCCCATCC 61.171 66.667 0.00 0.00 0.00 3.51
2480 2545 2.357517 CACCCGCGAAGAAGCTGT 60.358 61.111 8.23 0.00 34.40 4.40
2495 2560 4.572571 TGTCGGCGGCCAAAACCT 62.573 61.111 20.71 0.00 0.00 3.50
2496 2561 4.038080 GTCGGCGGCCAAAACCTG 62.038 66.667 20.71 0.11 0.00 4.00
2506 2571 0.106217 CCAAAACCTGTGGTGGAGGT 60.106 55.000 0.00 0.00 46.36 3.85
2508 2573 0.629058 AAAACCTGTGGTGGAGGTGT 59.371 50.000 0.00 0.00 43.42 4.16
2514 2579 1.148273 GTGGTGGAGGTGTGAAGCA 59.852 57.895 0.00 0.00 0.00 3.91
2515 2580 1.148273 TGGTGGAGGTGTGAAGCAC 59.852 57.895 0.00 0.00 46.97 4.40
2523 2588 1.961277 GTGTGAAGCACCCGACAGG 60.961 63.158 0.00 0.00 42.10 4.00
2541 2606 2.644992 GCAAAACCCTGCGGTGAG 59.355 61.111 0.00 0.00 43.71 3.51
2544 2609 1.228154 AAAACCCTGCGGTGAGTCC 60.228 57.895 0.00 0.00 43.71 3.85
2549 2614 1.599047 CCTGCGGTGAGTCCATCTT 59.401 57.895 0.00 0.00 35.57 2.40
2553 2618 1.086634 GCGGTGAGTCCATCTTGAGC 61.087 60.000 0.00 0.00 35.57 4.26
2556 2621 1.086634 GTGAGTCCATCTTGAGCGGC 61.087 60.000 0.00 0.00 0.00 6.53
2557 2622 1.522580 GAGTCCATCTTGAGCGGCC 60.523 63.158 0.00 0.00 0.00 6.13
2565 2630 0.320771 TCTTGAGCGGCCAAGAAGAC 60.321 55.000 22.88 0.00 46.59 3.01
2566 2631 1.630244 CTTGAGCGGCCAAGAAGACG 61.630 60.000 19.87 0.00 44.66 4.18
2573 2638 2.391389 GCCAAGAAGACGAAGGCGG 61.391 63.158 0.00 0.00 43.17 6.13
2574 2639 1.004918 CCAAGAAGACGAAGGCGGT 60.005 57.895 0.00 0.00 43.17 5.68
2575 2640 1.014564 CCAAGAAGACGAAGGCGGTC 61.015 60.000 0.00 0.00 43.17 4.79
2576 2641 0.319555 CAAGAAGACGAAGGCGGTCA 60.320 55.000 8.63 0.00 43.17 4.02
2577 2642 0.608640 AAGAAGACGAAGGCGGTCAT 59.391 50.000 8.63 0.00 43.17 3.06
2587 2652 2.747460 GCGGTCATGGCTGCTTCA 60.747 61.111 23.90 0.00 37.74 3.02
2597 2662 2.866028 CTGCTTCAGCCAGTTCGC 59.134 61.111 0.00 0.00 41.18 4.70
2635 2700 2.894257 AACTGCCGCTGGTCATGGA 61.894 57.895 2.06 0.00 0.00 3.41
2684 2749 0.460987 GCCTGTCATGGAGGAAGACG 60.461 60.000 14.13 0.00 35.09 4.18
2685 2750 0.898320 CCTGTCATGGAGGAAGACGT 59.102 55.000 5.93 0.00 35.09 4.34
2689 2754 1.191489 TCATGGAGGAAGACGTGGCA 61.191 55.000 0.00 0.00 0.00 4.92
2702 2767 3.798511 TGGCAACACCCACGACCA 61.799 61.111 0.00 0.00 46.17 4.02
2703 2768 2.282180 GGCAACACCCACGACCAT 60.282 61.111 0.00 0.00 0.00 3.55
2704 2769 2.332654 GGCAACACCCACGACCATC 61.333 63.158 0.00 0.00 0.00 3.51
2705 2770 2.677003 GCAACACCCACGACCATCG 61.677 63.158 0.00 0.00 46.93 3.84
2707 2772 3.894547 AACACCCACGACCATCGCC 62.895 63.158 0.00 0.00 45.12 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
573 587 1.129058 ACTTCGTCACCCAAACTCCT 58.871 50.000 0.00 0.00 0.00 3.69
757 774 7.270579 GCCAATCTTCGTGAATTTTTAGTGTAC 59.729 37.037 0.00 0.00 0.00 2.90
758 775 7.302524 GCCAATCTTCGTGAATTTTTAGTGTA 58.697 34.615 0.00 0.00 0.00 2.90
759 776 6.149633 GCCAATCTTCGTGAATTTTTAGTGT 58.850 36.000 0.00 0.00 0.00 3.55
760 777 5.572896 GGCCAATCTTCGTGAATTTTTAGTG 59.427 40.000 0.00 0.00 0.00 2.74
761 778 5.619086 CGGCCAATCTTCGTGAATTTTTAGT 60.619 40.000 2.24 0.00 0.00 2.24
762 779 4.793216 CGGCCAATCTTCGTGAATTTTTAG 59.207 41.667 2.24 0.00 0.00 1.85
763 780 4.456222 TCGGCCAATCTTCGTGAATTTTTA 59.544 37.500 2.24 0.00 0.00 1.52
764 781 3.254657 TCGGCCAATCTTCGTGAATTTTT 59.745 39.130 2.24 0.00 0.00 1.94
765 782 2.817258 TCGGCCAATCTTCGTGAATTTT 59.183 40.909 2.24 0.00 0.00 1.82
766 783 2.420022 CTCGGCCAATCTTCGTGAATTT 59.580 45.455 2.24 0.00 0.00 1.82
767 784 2.009774 CTCGGCCAATCTTCGTGAATT 58.990 47.619 2.24 0.00 0.00 2.17
1249 1280 1.049402 TACCACCGGATCACACACAA 58.951 50.000 9.46 0.00 0.00 3.33
1623 1663 4.969196 CGTGACGTGCTGCCCACT 62.969 66.667 0.00 0.00 42.42 4.00
1762 1803 1.332180 GCTACGACGCGCGCATATAA 61.332 55.000 32.58 12.08 46.04 0.98
1763 1804 1.794785 GCTACGACGCGCGCATATA 60.795 57.895 32.58 16.11 46.04 0.86
1841 1882 2.211250 ACTCCCAAGTACTACTCGCA 57.789 50.000 0.00 0.00 32.59 5.10
1906 1948 7.031226 GCATTGCCATTCTAGTTTATTCTCA 57.969 36.000 0.00 0.00 0.00 3.27
1976 2018 0.250234 AGCGCACACACATGTCCTAT 59.750 50.000 11.47 0.00 36.72 2.57
2054 2099 1.338105 GGAGCATTGTTTTTGGCCTCC 60.338 52.381 3.32 0.00 0.00 4.30
2055 2100 1.344114 TGGAGCATTGTTTTTGGCCTC 59.656 47.619 3.32 0.00 0.00 4.70
2098 2149 7.893302 TGGAGGAGGTGATGTAATTTATTTGTT 59.107 33.333 0.00 0.00 0.00 2.83
2099 2150 7.410174 TGGAGGAGGTGATGTAATTTATTTGT 58.590 34.615 0.00 0.00 0.00 2.83
2100 2151 7.880160 TGGAGGAGGTGATGTAATTTATTTG 57.120 36.000 0.00 0.00 0.00 2.32
2101 2152 8.116026 ACTTGGAGGAGGTGATGTAATTTATTT 58.884 33.333 0.00 0.00 0.00 1.40
2102 2153 7.557719 CACTTGGAGGAGGTGATGTAATTTATT 59.442 37.037 0.00 0.00 33.32 1.40
2103 2154 7.056635 CACTTGGAGGAGGTGATGTAATTTAT 58.943 38.462 0.00 0.00 33.32 1.40
2104 2155 6.214615 TCACTTGGAGGAGGTGATGTAATTTA 59.785 38.462 0.00 0.00 35.44 1.40
2105 2156 5.014123 TCACTTGGAGGAGGTGATGTAATTT 59.986 40.000 0.00 0.00 35.44 1.82
2106 2157 4.536090 TCACTTGGAGGAGGTGATGTAATT 59.464 41.667 0.00 0.00 35.44 1.40
2107 2158 4.104086 TCACTTGGAGGAGGTGATGTAAT 58.896 43.478 0.00 0.00 35.44 1.89
2119 2170 2.768253 TACAGCACATCACTTGGAGG 57.232 50.000 0.00 0.00 0.00 4.30
2121 2172 6.000840 TGTATTTTACAGCACATCACTTGGA 58.999 36.000 0.00 0.00 34.06 3.53
2132 2183 2.814919 CCGGGTGTTGTATTTTACAGCA 59.185 45.455 0.00 0.79 45.60 4.41
2133 2184 3.075884 TCCGGGTGTTGTATTTTACAGC 58.924 45.455 0.00 0.00 40.24 4.40
2134 2185 4.571919 TCTCCGGGTGTTGTATTTTACAG 58.428 43.478 0.00 0.00 40.24 2.74
2144 2195 1.176527 ATTTGCATCTCCGGGTGTTG 58.823 50.000 0.00 1.82 0.00 3.33
2150 2201 2.191680 TGCCAATTTGCATCTCCGG 58.808 52.632 0.00 0.00 36.04 5.14
2158 2209 2.417787 GGAGGTGAAGATGCCAATTTGC 60.418 50.000 0.00 0.00 0.00 3.68
2165 2216 1.225704 CCAGGGAGGTGAAGATGCC 59.774 63.158 0.00 0.00 0.00 4.40
2175 2226 3.244911 ACTGTTTTACATCACCAGGGAGG 60.245 47.826 0.00 0.00 45.67 4.30
2177 2228 3.392947 TGACTGTTTTACATCACCAGGGA 59.607 43.478 0.00 0.00 0.00 4.20
2178 2229 3.750371 TGACTGTTTTACATCACCAGGG 58.250 45.455 0.00 0.00 0.00 4.45
2195 2246 4.742201 ATTCGTGCGCGGCTGACT 62.742 61.111 21.04 0.00 38.89 3.41
2196 2247 4.505217 CATTCGTGCGCGGCTGAC 62.505 66.667 21.04 0.00 38.89 3.51
2207 2258 1.964373 GTGGCGGTTGGACATTCGT 60.964 57.895 0.00 0.00 34.91 3.85
2208 2259 1.234615 AAGTGGCGGTTGGACATTCG 61.235 55.000 0.00 0.00 34.91 3.34
2212 2263 0.179004 AATGAAGTGGCGGTTGGACA 60.179 50.000 0.00 0.00 0.00 4.02
2213 2264 0.958822 AAATGAAGTGGCGGTTGGAC 59.041 50.000 0.00 0.00 0.00 4.02
2214 2265 1.243902 GAAATGAAGTGGCGGTTGGA 58.756 50.000 0.00 0.00 0.00 3.53
2224 2275 2.231235 GCGGGTGGAATTGAAATGAAGT 59.769 45.455 0.00 0.00 0.00 3.01
2225 2276 2.417243 GGCGGGTGGAATTGAAATGAAG 60.417 50.000 0.00 0.00 0.00 3.02
2226 2277 1.548269 GGCGGGTGGAATTGAAATGAA 59.452 47.619 0.00 0.00 0.00 2.57
2229 2280 1.319614 CGGGCGGGTGGAATTGAAAT 61.320 55.000 0.00 0.00 0.00 2.17
2230 2281 1.974343 CGGGCGGGTGGAATTGAAA 60.974 57.895 0.00 0.00 0.00 2.69
2231 2282 1.839148 TACGGGCGGGTGGAATTGAA 61.839 55.000 0.00 0.00 0.00 2.69
2232 2283 1.628238 ATACGGGCGGGTGGAATTGA 61.628 55.000 0.00 0.00 0.00 2.57
2233 2284 1.153046 ATACGGGCGGGTGGAATTG 60.153 57.895 0.00 0.00 0.00 2.32
2234 2285 1.153046 CATACGGGCGGGTGGAATT 60.153 57.895 0.00 0.00 0.00 2.17
2235 2286 2.508928 CATACGGGCGGGTGGAAT 59.491 61.111 0.00 0.00 0.00 3.01
2250 2304 2.300967 ATGGTCCAGTGACGGGCAT 61.301 57.895 0.00 0.00 42.73 4.40
2252 2306 2.436646 CATGGTCCAGTGACGGGC 60.437 66.667 0.00 0.00 42.73 6.13
2255 2309 1.014044 CGGAACATGGTCCAGTGACG 61.014 60.000 29.00 10.40 42.73 4.35
2256 2310 1.298859 GCGGAACATGGTCCAGTGAC 61.299 60.000 29.00 9.09 37.56 3.67
2257 2311 1.003839 GCGGAACATGGTCCAGTGA 60.004 57.895 29.00 0.00 37.56 3.41
2259 2313 2.351276 GGCGGAACATGGTCCAGT 59.649 61.111 29.00 0.00 37.56 4.00
2264 2318 4.752879 CGACCGGCGGAACATGGT 62.753 66.667 35.78 8.07 37.44 3.55
2300 2354 2.836360 GGTAGCGGGGTCATCGGA 60.836 66.667 0.00 0.00 0.00 4.55
2319 2373 3.449227 TCAGACCAGCGGCGTAGG 61.449 66.667 16.27 16.27 0.00 3.18
2320 2374 2.202623 GTCAGACCAGCGGCGTAG 60.203 66.667 9.37 0.55 0.00 3.51
2321 2375 3.755628 GGTCAGACCAGCGGCGTA 61.756 66.667 15.43 0.00 38.42 4.42
2359 2418 2.594592 GTGAAGGTGGTTGCGCCT 60.595 61.111 4.18 0.00 38.35 5.52
2360 2419 2.594592 AGTGAAGGTGGTTGCGCC 60.595 61.111 4.18 0.00 37.90 6.53
2367 2426 1.302832 GCAGGGTCAGTGAAGGTGG 60.303 63.158 0.00 0.00 0.00 4.61
2443 2508 2.813908 GCACCTGTTCCCGTAGCG 60.814 66.667 0.00 0.00 0.00 4.26
2446 2511 4.382320 GGCGCACCTGTTCCCGTA 62.382 66.667 10.83 0.00 0.00 4.02
2464 2529 2.048127 GACAGCTTCTTCGCGGGT 60.048 61.111 6.13 0.00 34.40 5.28
2467 2532 3.843240 GCCGACAGCTTCTTCGCG 61.843 66.667 0.00 0.00 38.99 5.87
2469 2534 3.181967 CCGCCGACAGCTTCTTCG 61.182 66.667 2.74 2.74 40.39 3.79
2478 2543 4.572571 AGGTTTTGGCCGCCGACA 62.573 61.111 4.58 0.00 0.00 4.35
2480 2545 4.572571 ACAGGTTTTGGCCGCCGA 62.573 61.111 4.58 0.00 0.00 5.54
2488 2553 1.032014 CACCTCCACCACAGGTTTTG 58.968 55.000 0.00 0.00 41.95 2.44
2492 2557 0.986019 TTCACACCTCCACCACAGGT 60.986 55.000 0.00 0.00 45.89 4.00
2495 2560 1.148273 GCTTCACACCTCCACCACA 59.852 57.895 0.00 0.00 0.00 4.17
2496 2561 1.148273 TGCTTCACACCTCCACCAC 59.852 57.895 0.00 0.00 0.00 4.16
2506 2571 2.425592 CCTGTCGGGTGCTTCACA 59.574 61.111 0.00 0.00 35.86 3.58
2533 2598 0.247460 CTCAAGATGGACTCACCGCA 59.753 55.000 0.00 0.00 42.61 5.69
2536 2601 0.460987 CCGCTCAAGATGGACTCACC 60.461 60.000 0.00 0.00 39.54 4.02
2537 2602 1.086634 GCCGCTCAAGATGGACTCAC 61.087 60.000 0.00 0.00 0.00 3.51
2538 2603 1.219124 GCCGCTCAAGATGGACTCA 59.781 57.895 0.00 0.00 0.00 3.41
2541 2606 1.372087 CTTGGCCGCTCAAGATGGAC 61.372 60.000 13.41 0.00 44.98 4.02
2544 2609 4.623814 TCTTGGCCGCTCAAGATG 57.376 55.556 16.00 0.00 45.53 2.90
2549 2614 2.048222 CGTCTTCTTGGCCGCTCA 60.048 61.111 0.00 0.00 0.00 4.26
2553 2618 2.391389 GCCTTCGTCTTCTTGGCCG 61.391 63.158 0.00 0.00 37.81 6.13
2556 2621 1.004918 ACCGCCTTCGTCTTCTTGG 60.005 57.895 0.00 0.00 0.00 3.61
2557 2622 0.319555 TGACCGCCTTCGTCTTCTTG 60.320 55.000 0.00 0.00 0.00 3.02
2562 2627 2.579201 CCATGACCGCCTTCGTCT 59.421 61.111 0.00 0.00 0.00 4.18
2565 2630 3.197790 CAGCCATGACCGCCTTCG 61.198 66.667 0.00 0.00 0.00 3.79
2566 2631 3.512516 GCAGCCATGACCGCCTTC 61.513 66.667 0.00 0.00 0.00 3.46
2635 2700 1.913762 CGGTGGTGGAGGAGAAGGT 60.914 63.158 0.00 0.00 0.00 3.50
2637 2702 2.111999 TTGCGGTGGTGGAGGAGAAG 62.112 60.000 0.00 0.00 0.00 2.85
2638 2703 2.111999 CTTGCGGTGGTGGAGGAGAA 62.112 60.000 0.00 0.00 0.00 2.87
2639 2704 2.525629 TTGCGGTGGTGGAGGAGA 60.526 61.111 0.00 0.00 0.00 3.71
2668 2733 0.608130 CCACGTCTTCCTCCATGACA 59.392 55.000 0.00 0.00 0.00 3.58
2669 2734 0.741221 GCCACGTCTTCCTCCATGAC 60.741 60.000 0.00 0.00 0.00 3.06
2670 2735 1.191489 TGCCACGTCTTCCTCCATGA 61.191 55.000 0.00 0.00 0.00 3.07
2684 2749 3.284449 GGTCGTGGGTGTTGCCAC 61.284 66.667 0.00 0.00 41.06 5.01
2685 2750 3.126703 ATGGTCGTGGGTGTTGCCA 62.127 57.895 0.00 0.00 39.65 4.92
2689 2754 2.358247 GCGATGGTCGTGGGTGTT 60.358 61.111 1.11 0.00 42.81 3.32


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

AutoCloner maintained by Alex Coulton.