Multiple sequence alignment - TraesCS6A01G393900

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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 TraesCS6A01G393900 chr6A 100.000 5465 0 0 1 5465 607677966 607683430 0.000000e+00 10093.0
1 TraesCS6A01G393900 chr6B 93.697 2364 124 13 2729 5089 702563792 702566133 0.000000e+00 3517.0
2 TraesCS6A01G393900 chr6B 93.409 1229 70 4 881 2106 702562039 702563259 0.000000e+00 1810.0
3 TraesCS6A01G393900 chr6B 94.976 418 17 4 2205 2620 702563258 702563673 0.000000e+00 652.0
4 TraesCS6A01G393900 chr6B 92.257 452 26 3 318 769 702561523 702561965 2.780000e-177 632.0
5 TraesCS6A01G393900 chr6B 87.029 239 25 5 1 233 702560849 702561087 1.170000e-66 265.0
6 TraesCS6A01G393900 chr6B 92.941 85 3 3 2618 2702 702563710 702563791 2.670000e-23 121.0
7 TraesCS6A01G393900 chr6D 93.492 1306 77 7 806 2106 461006734 461008036 0.000000e+00 1934.0
8 TraesCS6A01G393900 chr6D 93.628 1177 60 7 3510 4683 461009486 461010650 0.000000e+00 1744.0
9 TraesCS6A01G393900 chr6D 97.253 728 19 1 4738 5465 461010668 461011394 0.000000e+00 1232.0
10 TraesCS6A01G393900 chr6D 89.513 801 65 10 1 790 461005955 461006747 0.000000e+00 996.0
11 TraesCS6A01G393900 chr6D 85.627 327 31 9 2205 2525 461008035 461008351 4.080000e-86 329.0
12 TraesCS6A01G393900 chr6D 81.667 240 21 10 2618 2854 461008567 461008786 1.560000e-40 178.0
13 TraesCS6A01G393900 chr6D 87.156 109 10 2 2101 2208 412044531 412044636 2.670000e-23 121.0
14 TraesCS6A01G393900 chr2D 87.611 113 8 3 2099 2206 79387434 79387323 5.750000e-25 126.0
15 TraesCS6A01G393900 chr3B 84.800 125 10 5 2100 2218 636441645 636441524 3.460000e-22 117.0
16 TraesCS6A01G393900 chr3D 85.593 118 8 6 2102 2211 94644867 94644751 1.240000e-21 115.0
17 TraesCS6A01G393900 chr3D 86.607 112 6 4 2105 2207 609740913 609741024 1.240000e-21 115.0
18 TraesCS6A01G393900 chr3D 86.111 108 11 2 2104 2210 300256305 300256201 4.470000e-21 113.0
19 TraesCS6A01G393900 chr3D 85.185 108 12 2 2102 2208 8363724 8363828 2.080000e-19 108.0
20 TraesCS6A01G393900 chr3D 94.118 51 1 2 703 751 491960045 491959995 5.870000e-10 76.8
21 TraesCS6A01G393900 chr7D 91.358 81 4 3 550 630 68988181 68988258 2.080000e-19 108.0
22 TraesCS6A01G393900 chr4B 78.286 175 32 4 515 687 87537612 87537442 2.080000e-19 108.0
23 TraesCS6A01G393900 chr4B 93.023 43 3 0 563 605 495081863 495081905 4.570000e-06 63.9
24 TraesCS6A01G393900 chr3A 84.545 110 12 3 2100 2208 515726035 515725930 2.690000e-18 104.0
25 TraesCS6A01G393900 chr5D 84.762 105 11 5 2105 2206 395933878 395933980 3.480000e-17 100.0
26 TraesCS6A01G393900 chr4D 93.220 59 2 2 695 751 32419012 32419070 9.750000e-13 86.1


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 TraesCS6A01G393900 chr6A 607677966 607683430 5464 False 10093.000000 10093 100.000000 1 5465 1 chr6A.!!$F1 5464
1 TraesCS6A01G393900 chr6B 702560849 702566133 5284 False 1166.166667 3517 92.384833 1 5089 6 chr6B.!!$F1 5088
2 TraesCS6A01G393900 chr6D 461005955 461011394 5439 False 1068.833333 1934 90.196667 1 5465 6 chr6D.!!$F2 5464

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
887 1341 0.254178 AACGAGATTGAGCAGCCCAT 59.746 50.0 0.00 0.0 0.00 4.00 F
1655 2111 0.316204 GTTGCATCAACAAGCCTGCT 59.684 50.0 4.95 0.0 43.09 4.24 F
3209 3910 0.036448 TCGGGATAGCTAGGTCGAGG 59.964 60.0 0.00 0.0 0.00 4.63 F
3796 4506 0.370273 GCTGTAACATCGCGGACAAG 59.630 55.0 6.13 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2189 2648 0.338814 AACTACTCCCTCCGTCCCAT 59.661 55.0 0.00 0.0 0.00 4.00 R
3486 4195 0.109039 AAAACCACAAACGCGCAAGT 60.109 45.0 5.73 0.0 41.68 3.16 R
4096 4806 0.390472 GCCACTTCGCTCTAACTGCT 60.390 55.0 0.00 0.0 0.00 4.24 R
5299 6020 0.318360 TCAATCGTGTGTTCGTCGCT 60.318 50.0 0.00 0.0 0.00 4.93 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
245 666 2.620627 CCAAATAGGGGCTCTTTTCCGT 60.621 50.000 0.00 0.00 0.00 4.69
261 682 2.799017 TCCGTGAGTAGTTTAGCCAGA 58.201 47.619 0.00 0.00 0.00 3.86
288 709 3.245087 TGGGAAAGCTATGCACCAAACTA 60.245 43.478 0.00 0.00 0.00 2.24
314 735 4.826183 AGGCCAGAAATCTGAAATATCTGC 59.174 41.667 11.94 4.11 46.59 4.26
369 790 1.246056 CCTGGTTGAGGTGGTGCATG 61.246 60.000 0.00 0.00 37.02 4.06
403 824 3.501828 CAGACGGAAACATTGGTTGATGA 59.498 43.478 0.00 0.00 37.30 2.92
418 839 4.375272 GTTGATGACATCGAGGACATCAT 58.625 43.478 33.44 19.96 45.05 2.45
460 881 5.665916 AAAAATGGTTGGAGCTAAGATGG 57.334 39.130 0.00 0.00 0.00 3.51
506 928 3.641436 TCACTAGGACAATCACTGTGTGT 59.359 43.478 7.79 5.72 38.84 3.72
520 942 7.032377 TCACTGTGTGTTGCAACAAATATTA 57.968 32.000 32.61 14.57 41.21 0.98
561 983 9.895894 GTGATTTACGTGTATATATTTATGCCG 57.104 33.333 0.00 0.00 0.00 5.69
764 1218 5.047377 GGTGGAAAGAATGAACCTTGCATTA 60.047 40.000 0.00 0.00 36.19 1.90
790 1244 9.930693 ATTTTGTAAAGTCGTAGAGAAGAGATT 57.069 29.630 0.00 0.00 36.95 2.40
791 1245 9.760077 TTTTGTAAAGTCGTAGAGAAGAGATTT 57.240 29.630 0.00 0.00 36.95 2.17
792 1246 9.760077 TTTGTAAAGTCGTAGAGAAGAGATTTT 57.240 29.630 0.00 0.00 36.95 1.82
793 1247 9.760077 TTGTAAAGTCGTAGAGAAGAGATTTTT 57.240 29.630 0.00 0.00 36.95 1.94
863 1317 4.043561 TCAAGGACCTACATTAAAAGGCCA 59.956 41.667 5.01 0.00 36.24 5.36
864 1318 4.881157 AGGACCTACATTAAAAGGCCAT 57.119 40.909 5.01 0.00 36.24 4.40
867 1321 4.580580 GGACCTACATTAAAAGGCCATCTG 59.419 45.833 5.01 0.00 36.24 2.90
870 1324 5.652452 ACCTACATTAAAAGGCCATCTGAAC 59.348 40.000 5.01 0.00 36.24 3.18
877 1331 2.322355 AGGCCATCTGAACGAGATTG 57.678 50.000 5.01 0.00 39.64 2.67
887 1341 0.254178 AACGAGATTGAGCAGCCCAT 59.746 50.000 0.00 0.00 0.00 4.00
975 1429 0.889306 CGAGACCGAGAAGAAAGGGT 59.111 55.000 0.00 0.00 38.22 4.34
1117 1571 4.336581 CGGTGTTCGTCTTGCTGA 57.663 55.556 0.00 0.00 0.00 4.26
1303 1757 2.430332 CCAGATCTCTCTCGCCTTCTTT 59.570 50.000 0.00 0.00 0.00 2.52
1308 1762 1.391826 CTCTCTCGCCTTCTTTTTCGC 59.608 52.381 0.00 0.00 0.00 4.70
1311 1765 1.923227 CTCGCCTTCTTTTTCGCCCC 61.923 60.000 0.00 0.00 0.00 5.80
1372 1826 2.548057 TGCAGCGTCTCCAAGTTTAAAG 59.452 45.455 0.00 0.00 0.00 1.85
1404 1858 7.840931 AGAATTTTCCATAGTGAATTCAACCC 58.159 34.615 10.35 0.00 39.67 4.11
1425 1879 4.142026 CCCGACACCTAGTTCATATCACAA 60.142 45.833 0.00 0.00 0.00 3.33
1453 1907 3.005155 CAGCTATCTGTGGATCGATCACA 59.995 47.826 25.93 23.24 42.11 3.58
1479 1933 5.002464 AGCTAAATGTGAATCCATTGTGC 57.998 39.130 0.00 10.60 35.30 4.57
1601 2057 5.119279 CCTGATAAAGCTCGATATTTGGTCG 59.881 44.000 5.50 0.00 40.30 4.79
1644 2100 4.023279 GGTATTGTGACAAGTGTTGCATCA 60.023 41.667 3.74 0.00 0.00 3.07
1655 2111 0.316204 GTTGCATCAACAAGCCTGCT 59.684 50.000 4.95 0.00 43.09 4.24
1718 2174 4.957684 AATGGTAGGTGTGGCTATCTAC 57.042 45.455 4.76 4.76 33.37 2.59
1761 2217 4.595762 ATGAAGTTGTGCTGAAAATGCT 57.404 36.364 0.00 0.00 0.00 3.79
1762 2218 4.389890 TGAAGTTGTGCTGAAAATGCTT 57.610 36.364 0.00 0.00 0.00 3.91
1768 2224 2.295909 TGTGCTGAAAATGCTTGGGTAC 59.704 45.455 0.00 0.00 0.00 3.34
1822 2278 4.096382 GGATTAACAACTGTGTGGGCTATG 59.904 45.833 0.00 0.00 38.27 2.23
1909 2365 8.842280 TGGTAAGTTACTACATTGAACAAAAGG 58.158 33.333 12.65 0.00 0.00 3.11
1910 2366 7.806487 GGTAAGTTACTACATTGAACAAAAGGC 59.194 37.037 12.65 0.00 0.00 4.35
1937 2393 6.901357 GCACATTTTCAACAAACATTTCTCAC 59.099 34.615 0.00 0.00 0.00 3.51
1941 2397 2.948979 TCAACAAACATTTCTCACGGCT 59.051 40.909 0.00 0.00 0.00 5.52
1942 2398 3.380004 TCAACAAACATTTCTCACGGCTT 59.620 39.130 0.00 0.00 0.00 4.35
1943 2399 3.626028 ACAAACATTTCTCACGGCTTC 57.374 42.857 0.00 0.00 0.00 3.86
1944 2400 2.948979 ACAAACATTTCTCACGGCTTCA 59.051 40.909 0.00 0.00 0.00 3.02
2008 2466 6.754209 CGAACAGAGCATGACTTTAGTATTCT 59.246 38.462 0.00 0.00 0.00 2.40
2036 2494 6.108687 TGTGAAGATCATCCATGTAAGTGAC 58.891 40.000 0.00 0.00 0.00 3.67
2038 2496 5.426509 TGAAGATCATCCATGTAAGTGACCT 59.573 40.000 0.00 0.00 0.00 3.85
2043 2501 4.532126 TCATCCATGTAAGTGACCTTGACT 59.468 41.667 0.00 0.00 31.89 3.41
2046 2504 6.222038 TCCATGTAAGTGACCTTGACTATC 57.778 41.667 0.00 0.00 31.89 2.08
2104 2563 8.689972 CAATCTTTTCCAGCTACCTTCAATATT 58.310 33.333 0.00 0.00 0.00 1.28
2105 2564 9.920946 AATCTTTTCCAGCTACCTTCAATATTA 57.079 29.630 0.00 0.00 0.00 0.98
2106 2565 8.732746 TCTTTTCCAGCTACCTTCAATATTAC 57.267 34.615 0.00 0.00 0.00 1.89
2107 2566 8.548877 TCTTTTCCAGCTACCTTCAATATTACT 58.451 33.333 0.00 0.00 0.00 2.24
2108 2567 8.732746 TTTTCCAGCTACCTTCAATATTACTC 57.267 34.615 0.00 0.00 0.00 2.59
2109 2568 6.085555 TCCAGCTACCTTCAATATTACTCG 57.914 41.667 0.00 0.00 0.00 4.18
2110 2569 4.686554 CCAGCTACCTTCAATATTACTCGC 59.313 45.833 0.00 0.00 0.00 5.03
2111 2570 5.509840 CCAGCTACCTTCAATATTACTCGCT 60.510 44.000 0.00 0.00 0.00 4.93
2112 2571 5.631512 CAGCTACCTTCAATATTACTCGCTC 59.368 44.000 0.00 0.00 0.00 5.03
2113 2572 4.924462 GCTACCTTCAATATTACTCGCTCC 59.076 45.833 0.00 0.00 0.00 4.70
2114 2573 3.978687 ACCTTCAATATTACTCGCTCCG 58.021 45.455 0.00 0.00 0.00 4.63
2115 2574 3.383825 ACCTTCAATATTACTCGCTCCGT 59.616 43.478 0.00 0.00 0.00 4.69
2116 2575 3.982058 CCTTCAATATTACTCGCTCCGTC 59.018 47.826 0.00 0.00 0.00 4.79
2117 2576 3.637998 TCAATATTACTCGCTCCGTCC 57.362 47.619 0.00 0.00 0.00 4.79
2118 2577 2.295349 TCAATATTACTCGCTCCGTCCC 59.705 50.000 0.00 0.00 0.00 4.46
2119 2578 1.991121 ATATTACTCGCTCCGTCCCA 58.009 50.000 0.00 0.00 0.00 4.37
2120 2579 1.991121 TATTACTCGCTCCGTCCCAT 58.009 50.000 0.00 0.00 0.00 4.00
2121 2580 1.991121 ATTACTCGCTCCGTCCCATA 58.009 50.000 0.00 0.00 0.00 2.74
2122 2581 1.766494 TTACTCGCTCCGTCCCATAA 58.234 50.000 0.00 0.00 0.00 1.90
2123 2582 1.991121 TACTCGCTCCGTCCCATAAT 58.009 50.000 0.00 0.00 0.00 1.28
2124 2583 0.674534 ACTCGCTCCGTCCCATAATC 59.325 55.000 0.00 0.00 0.00 1.75
2125 2584 0.673985 CTCGCTCCGTCCCATAATCA 59.326 55.000 0.00 0.00 0.00 2.57
2126 2585 1.068588 CTCGCTCCGTCCCATAATCAA 59.931 52.381 0.00 0.00 0.00 2.57
2127 2586 1.068588 TCGCTCCGTCCCATAATCAAG 59.931 52.381 0.00 0.00 0.00 3.02
2128 2587 1.068588 CGCTCCGTCCCATAATCAAGA 59.931 52.381 0.00 0.00 0.00 3.02
2129 2588 2.484889 GCTCCGTCCCATAATCAAGAC 58.515 52.381 0.00 0.00 0.00 3.01
2130 2589 2.807108 GCTCCGTCCCATAATCAAGACC 60.807 54.545 0.00 0.00 0.00 3.85
2131 2590 1.411246 TCCGTCCCATAATCAAGACCG 59.589 52.381 0.00 0.00 0.00 4.79
2132 2591 1.138266 CCGTCCCATAATCAAGACCGT 59.862 52.381 0.00 0.00 0.00 4.83
2133 2592 2.419574 CCGTCCCATAATCAAGACCGTT 60.420 50.000 0.00 0.00 0.00 4.44
2134 2593 3.267483 CGTCCCATAATCAAGACCGTTT 58.733 45.455 0.00 0.00 0.00 3.60
2135 2594 3.687698 CGTCCCATAATCAAGACCGTTTT 59.312 43.478 0.00 0.00 0.00 2.43
2136 2595 4.155280 CGTCCCATAATCAAGACCGTTTTT 59.845 41.667 0.00 0.00 0.00 1.94
2165 2624 7.813852 CTAGTATAGTGTCAAAAACGCTCTT 57.186 36.000 0.00 0.00 45.69 2.85
2166 2625 8.906636 CTAGTATAGTGTCAAAAACGCTCTTA 57.093 34.615 0.00 0.00 45.69 2.10
2167 2626 7.813852 AGTATAGTGTCAAAAACGCTCTTAG 57.186 36.000 0.00 0.00 45.69 2.18
2168 2627 7.376615 AGTATAGTGTCAAAAACGCTCTTAGT 58.623 34.615 0.00 0.00 45.69 2.24
2169 2628 4.795970 AGTGTCAAAAACGCTCTTAGTG 57.204 40.909 0.00 0.00 45.69 2.74
2170 2629 4.189231 AGTGTCAAAAACGCTCTTAGTGT 58.811 39.130 0.00 0.00 45.69 3.55
2171 2630 4.270325 AGTGTCAAAAACGCTCTTAGTGTC 59.730 41.667 0.00 0.00 45.69 3.67
2172 2631 4.033587 GTGTCAAAAACGCTCTTAGTGTCA 59.966 41.667 0.00 0.00 38.11 3.58
2173 2632 4.632251 TGTCAAAAACGCTCTTAGTGTCAA 59.368 37.500 0.00 0.00 38.11 3.18
2174 2633 5.122554 TGTCAAAAACGCTCTTAGTGTCAAA 59.877 36.000 0.00 0.00 38.11 2.69
2175 2634 6.025280 GTCAAAAACGCTCTTAGTGTCAAAA 58.975 36.000 0.00 0.00 38.11 2.44
2176 2635 6.525280 GTCAAAAACGCTCTTAGTGTCAAAAA 59.475 34.615 0.00 0.00 38.11 1.94
2177 2636 7.220108 GTCAAAAACGCTCTTAGTGTCAAAAAT 59.780 33.333 0.00 0.00 38.11 1.82
2178 2637 7.219917 TCAAAAACGCTCTTAGTGTCAAAAATG 59.780 33.333 0.00 0.00 38.11 2.32
2179 2638 4.147219 ACGCTCTTAGTGTCAAAAATGC 57.853 40.909 0.00 0.00 32.75 3.56
2180 2639 3.815401 ACGCTCTTAGTGTCAAAAATGCT 59.185 39.130 0.00 0.00 32.75 3.79
2181 2640 4.083802 ACGCTCTTAGTGTCAAAAATGCTC 60.084 41.667 0.00 0.00 32.75 4.26
2182 2641 4.153117 CGCTCTTAGTGTCAAAAATGCTCT 59.847 41.667 0.00 0.00 0.00 4.09
2183 2642 5.334414 CGCTCTTAGTGTCAAAAATGCTCTT 60.334 40.000 0.00 0.00 0.00 2.85
2184 2643 6.128553 CGCTCTTAGTGTCAAAAATGCTCTTA 60.129 38.462 0.00 0.00 0.00 2.10
2185 2644 7.413438 CGCTCTTAGTGTCAAAAATGCTCTTAT 60.413 37.037 0.00 0.00 0.00 1.73
2186 2645 8.883731 GCTCTTAGTGTCAAAAATGCTCTTATA 58.116 33.333 0.00 0.00 0.00 0.98
2193 2652 9.683069 GTGTCAAAAATGCTCTTATATTATGGG 57.317 33.333 0.00 0.00 0.00 4.00
2194 2653 9.639563 TGTCAAAAATGCTCTTATATTATGGGA 57.360 29.630 0.00 0.00 0.00 4.37
2195 2654 9.899226 GTCAAAAATGCTCTTATATTATGGGAC 57.101 33.333 0.00 0.00 0.00 4.46
2196 2655 8.783093 TCAAAAATGCTCTTATATTATGGGACG 58.217 33.333 0.00 0.00 0.00 4.79
2197 2656 7.687941 AAAATGCTCTTATATTATGGGACGG 57.312 36.000 0.00 0.00 0.00 4.79
2198 2657 6.620877 AATGCTCTTATATTATGGGACGGA 57.379 37.500 0.00 0.00 0.00 4.69
2199 2658 5.661056 TGCTCTTATATTATGGGACGGAG 57.339 43.478 0.00 0.00 0.00 4.63
2200 2659 4.466370 TGCTCTTATATTATGGGACGGAGG 59.534 45.833 0.00 0.00 0.00 4.30
2201 2660 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
2202 2661 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
2203 2662 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2439 2901 2.876581 TGTGCTGGAAGTCTAGTCTGA 58.123 47.619 0.00 0.00 35.30 3.27
2444 2909 4.884744 TGCTGGAAGTCTAGTCTGAGATAC 59.115 45.833 0.00 0.00 35.30 2.24
2501 2966 1.745232 TTCTGAAATGCGCCCGTATT 58.255 45.000 4.18 0.00 31.98 1.89
2528 2993 6.413818 GGATACGCTTGACCATTAAAAATTCG 59.586 38.462 0.00 0.00 0.00 3.34
2586 3139 4.910195 TGATGTTGTGCTCTGTTCCTAAT 58.090 39.130 0.00 0.00 0.00 1.73
2626 3218 7.180051 CAGATTAGATAGAAATAGCAGGGAGGT 59.820 40.741 0.00 0.00 0.00 3.85
2702 3296 1.600957 CCGCAGAATACCTTGATGCTG 59.399 52.381 0.00 0.00 35.77 4.41
2703 3297 2.554142 CGCAGAATACCTTGATGCTGA 58.446 47.619 0.00 0.00 34.72 4.26
2704 3298 2.938451 CGCAGAATACCTTGATGCTGAA 59.062 45.455 0.00 0.00 34.72 3.02
2705 3299 3.242543 CGCAGAATACCTTGATGCTGAAC 60.243 47.826 0.00 0.00 34.72 3.18
2706 3300 3.065925 GCAGAATACCTTGATGCTGAACC 59.934 47.826 0.00 0.00 34.72 3.62
2707 3301 4.521146 CAGAATACCTTGATGCTGAACCT 58.479 43.478 0.00 0.00 34.72 3.50
2708 3302 4.334759 CAGAATACCTTGATGCTGAACCTG 59.665 45.833 0.00 0.00 34.72 4.00
2709 3303 4.225942 AGAATACCTTGATGCTGAACCTGA 59.774 41.667 0.00 0.00 0.00 3.86
2710 3304 2.486472 ACCTTGATGCTGAACCTGAG 57.514 50.000 0.00 0.00 0.00 3.35
2711 3305 1.004044 ACCTTGATGCTGAACCTGAGG 59.996 52.381 0.00 0.00 0.00 3.86
2712 3306 1.681166 CCTTGATGCTGAACCTGAGGG 60.681 57.143 2.38 0.00 38.88 4.30
2713 3307 0.322816 TTGATGCTGAACCTGAGGGC 60.323 55.000 2.38 0.00 35.63 5.19
2714 3308 1.300963 GATGCTGAACCTGAGGGCA 59.699 57.895 2.38 2.55 37.32 5.36
2715 3309 0.322816 GATGCTGAACCTGAGGGCAA 60.323 55.000 2.38 0.00 36.49 4.52
2716 3310 0.333993 ATGCTGAACCTGAGGGCAAT 59.666 50.000 2.38 0.00 36.49 3.56
2717 3311 0.609957 TGCTGAACCTGAGGGCAATG 60.610 55.000 2.38 0.00 35.63 2.82
2718 3312 0.322816 GCTGAACCTGAGGGCAATGA 60.323 55.000 2.38 0.00 35.63 2.57
2719 3313 1.747709 CTGAACCTGAGGGCAATGAG 58.252 55.000 2.38 0.00 35.63 2.90
2720 3314 0.329261 TGAACCTGAGGGCAATGAGG 59.671 55.000 2.38 0.00 35.63 3.86
2743 3337 3.501911 AGCCCACCACCTGCTTGT 61.502 61.111 0.00 0.00 29.17 3.16
2759 3353 1.812686 TTGTCGCCGGTGAGCTACTT 61.813 55.000 20.25 0.00 30.23 2.24
2771 3365 3.196685 GTGAGCTACTTCTTGACCCTGAT 59.803 47.826 0.00 0.00 0.00 2.90
2822 3514 0.178921 TGTTCCTGGAGCCTGAGAGT 60.179 55.000 8.14 0.00 0.00 3.24
2840 3532 2.773053 GGGAGGAGGTAAGGGGCC 60.773 72.222 0.00 0.00 0.00 5.80
2882 3583 3.894427 GTCTTCTGCTGGATCCTCAGATA 59.106 47.826 26.74 19.08 36.81 1.98
2978 3679 3.160585 CCCACCACTGGCTTCTCA 58.839 61.111 0.00 0.00 36.00 3.27
2985 3686 1.605710 CCACTGGCTTCTCACAGTTTG 59.394 52.381 0.00 0.00 45.03 2.93
2993 3694 0.250467 TCTCACAGTTTGCTGGAGCC 60.250 55.000 0.00 0.00 46.62 4.70
3033 3734 1.012841 GCAGCTATTGTGTGAGAGGC 58.987 55.000 0.00 0.00 0.00 4.70
3065 3766 0.390472 GGAGCAGGAGCACTACACAC 60.390 60.000 0.00 0.00 45.49 3.82
3163 3864 4.141914 GGTAGTGAAATGAATCGGAGAGGT 60.142 45.833 0.00 0.00 43.63 3.85
3167 3868 4.752101 GTGAAATGAATCGGAGAGGTATGG 59.248 45.833 0.00 0.00 43.63 2.74
3169 3870 0.673985 TGAATCGGAGAGGTATGGCG 59.326 55.000 0.00 0.00 43.63 5.69
3170 3871 0.667792 GAATCGGAGAGGTATGGCGC 60.668 60.000 0.00 0.00 43.63 6.53
3171 3872 1.115930 AATCGGAGAGGTATGGCGCT 61.116 55.000 7.64 0.00 43.63 5.92
3172 3873 1.810606 ATCGGAGAGGTATGGCGCTG 61.811 60.000 7.64 0.00 43.63 5.18
3173 3874 2.423446 GGAGAGGTATGGCGCTGG 59.577 66.667 7.64 0.00 0.00 4.85
3174 3875 2.134287 GGAGAGGTATGGCGCTGGA 61.134 63.158 7.64 0.00 0.00 3.86
3175 3876 1.365633 GAGAGGTATGGCGCTGGAG 59.634 63.158 7.64 0.00 0.00 3.86
3209 3910 0.036448 TCGGGATAGCTAGGTCGAGG 59.964 60.000 0.00 0.00 0.00 4.63
3217 3918 0.744874 GCTAGGTCGAGGCATACACA 59.255 55.000 0.00 0.00 0.00 3.72
3371 4078 2.229062 ACTGGTATCCGATACAGATGCG 59.771 50.000 18.23 4.42 37.48 4.73
3390 4097 2.512896 CAGCCCCAGCACCTATCC 59.487 66.667 0.00 0.00 43.56 2.59
3396 4104 0.744414 CCCAGCACCTATCCGTGTTG 60.744 60.000 0.00 0.00 42.63 3.33
3507 4216 0.992802 TTGCGCGTTTGTGGTTTTTC 59.007 45.000 8.43 0.00 0.00 2.29
3548 4258 8.863086 CATGGAAACTGATTATTAACCATGGAT 58.137 33.333 21.47 9.83 45.26 3.41
3549 4259 8.837099 TGGAAACTGATTATTAACCATGGATT 57.163 30.769 21.47 11.61 0.00 3.01
3695 4405 6.489127 TTAAAGAACATGATTGTACCACCG 57.511 37.500 0.00 0.00 34.06 4.94
3757 4467 9.472361 GACAGAGTTGTACAAGTAAGATAAACA 57.528 33.333 15.87 0.00 37.76 2.83
3796 4506 0.370273 GCTGTAACATCGCGGACAAG 59.630 55.000 6.13 0.00 0.00 3.16
3825 4535 6.528072 GTGCCACATTTGTTCTCTATTTTAGC 59.472 38.462 0.00 0.00 0.00 3.09
4075 4785 7.480760 ACCATTGTTTGATAATTTACTGCCT 57.519 32.000 0.00 0.00 0.00 4.75
4096 4806 4.339530 CCTCCTTGTCATCAGTATCGAGAA 59.660 45.833 0.00 0.00 0.00 2.87
4147 4857 1.084289 GTGGACAGAATTACCGCCAC 58.916 55.000 0.00 0.00 38.98 5.01
4159 4869 3.177600 CGCCACCGGTTTGATCAG 58.822 61.111 2.97 0.00 0.00 2.90
4206 4916 4.098960 GGTAGGGCTATATATACGCAGCAA 59.901 45.833 12.44 0.00 35.69 3.91
4240 4950 9.959749 AAAAACGCAATCAGACTTTTAATTCTA 57.040 25.926 0.00 0.00 0.00 2.10
4288 4999 3.056322 GCCTTTGAATCTGGTGCTGAAAT 60.056 43.478 0.00 0.00 0.00 2.17
4316 5027 6.006449 AGCATGGTCTACAGAGTTCAATTTT 58.994 36.000 0.00 0.00 0.00 1.82
4328 5039 9.480053 ACAGAGTTCAATTTTATTCACCATTTG 57.520 29.630 0.00 0.00 0.00 2.32
4329 5040 9.480053 CAGAGTTCAATTTTATTCACCATTTGT 57.520 29.630 0.00 0.00 0.00 2.83
4389 5100 2.024414 GTACAGATCATGGGCCCAAAC 58.976 52.381 32.58 19.63 0.00 2.93
4468 5179 5.789521 TCCAGAATACGAACAACTGATCAA 58.210 37.500 0.00 0.00 0.00 2.57
4552 5265 5.163447 CCAGATTGATCATTTCTGCCATTGT 60.163 40.000 22.10 0.00 36.41 2.71
4559 5272 5.021033 TCATTTCTGCCATTGTGTTGTTT 57.979 34.783 0.00 0.00 0.00 2.83
4597 5310 2.357517 AGCTCGGGCAGTTTCACG 60.358 61.111 11.40 0.00 41.70 4.35
4722 5435 8.597227 CAATTGCAAATGTAACCAGAATATGTG 58.403 33.333 1.71 0.00 0.00 3.21
4761 5474 4.102210 TGTGCAAAAGGGAATGGAAATTGA 59.898 37.500 0.00 0.00 0.00 2.57
4771 5484 5.221621 GGGAATGGAAATTGAAAGTGTGGAA 60.222 40.000 0.00 0.00 0.00 3.53
4772 5485 5.928264 GGAATGGAAATTGAAAGTGTGGAAG 59.072 40.000 0.00 0.00 0.00 3.46
4773 5486 6.239289 GGAATGGAAATTGAAAGTGTGGAAGA 60.239 38.462 0.00 0.00 0.00 2.87
4774 5487 6.729690 ATGGAAATTGAAAGTGTGGAAGAA 57.270 33.333 0.00 0.00 0.00 2.52
4775 5488 6.537453 TGGAAATTGAAAGTGTGGAAGAAA 57.463 33.333 0.00 0.00 0.00 2.52
4776 5489 6.572519 TGGAAATTGAAAGTGTGGAAGAAAG 58.427 36.000 0.00 0.00 0.00 2.62
4777 5490 5.985530 GGAAATTGAAAGTGTGGAAGAAAGG 59.014 40.000 0.00 0.00 0.00 3.11
4778 5491 4.590850 ATTGAAAGTGTGGAAGAAAGGC 57.409 40.909 0.00 0.00 0.00 4.35
4781 5494 1.322442 AAGTGTGGAAGAAAGGCAGC 58.678 50.000 0.00 0.00 0.00 5.25
4791 5512 1.758862 AGAAAGGCAGCAAGCTTTGTT 59.241 42.857 0.00 0.00 42.31 2.83
4885 5606 6.051717 ACTAGAGTGTATGGTGAAATGATGC 58.948 40.000 0.00 0.00 0.00 3.91
4996 5717 4.822685 TGCATATTTCCTGGCATGTTTT 57.177 36.364 0.00 0.00 0.00 2.43
5051 5772 7.775397 ATTATTGTTTTCACTTATGCATGGC 57.225 32.000 10.16 0.00 0.00 4.40
5103 5824 2.193536 AAAACACCAGCCTCCGTGC 61.194 57.895 0.00 0.00 33.09 5.34
5110 5831 2.032681 AGCCTCCGTGCTTTCCAC 59.967 61.111 0.00 0.00 38.85 4.02
5182 5903 5.516090 TCTTGAAACGAAGTGCATAAAACC 58.484 37.500 0.00 0.00 45.00 3.27
5235 5956 7.797038 TCTTTACATCATTGATGAGTGGATG 57.203 36.000 28.81 13.56 42.09 3.51
5299 6020 1.171308 CTTCTTCGGTCGTGGGAGTA 58.829 55.000 0.00 0.00 0.00 2.59
5306 6027 2.046988 TCGTGGGAGTAGCGACGA 60.047 61.111 0.00 0.00 38.45 4.20
5319 6040 0.179282 GCGACGAACACACGATTGAC 60.179 55.000 0.00 0.00 37.03 3.18
5382 6103 5.965033 ATCAGGATACCTCATCTGTGTTT 57.035 39.130 0.00 0.00 33.78 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 137 8.768957 TGCTGCTGCATGTTTTTATTTTAATA 57.231 26.923 14.93 0.00 45.31 0.98
239 660 3.575256 TCTGGCTAAACTACTCACGGAAA 59.425 43.478 0.00 0.00 0.00 3.13
242 663 3.512680 CTTCTGGCTAAACTACTCACGG 58.487 50.000 0.00 0.00 0.00 4.94
272 693 4.137543 GCCTATTAGTTTGGTGCATAGCT 58.862 43.478 0.00 0.00 0.00 3.32
288 709 7.176340 GCAGATATTTCAGATTTCTGGCCTATT 59.824 37.037 3.32 0.00 43.91 1.73
369 790 1.144936 CCGTCTGGATGGGAGCTTC 59.855 63.158 1.09 0.00 37.49 3.86
403 824 4.437239 GTCAAAGATGATGTCCTCGATGT 58.563 43.478 0.00 0.00 38.01 3.06
418 839 3.478857 TTCCTAGCAAACGGTCAAAGA 57.521 42.857 0.00 0.00 0.00 2.52
442 863 4.019174 CAAACCATCTTAGCTCCAACCAT 58.981 43.478 0.00 0.00 0.00 3.55
477 899 6.998074 ACAGTGATTGTCCTAGTGATTTGAAA 59.002 34.615 0.00 0.00 33.87 2.69
478 900 6.427853 CACAGTGATTGTCCTAGTGATTTGAA 59.572 38.462 0.00 0.00 38.16 2.69
479 901 5.934043 CACAGTGATTGTCCTAGTGATTTGA 59.066 40.000 0.00 0.00 38.16 2.69
498 920 6.800543 TGTAATATTTGTTGCAACACACAGT 58.199 32.000 31.17 16.68 38.92 3.55
506 928 9.279904 GCTAACGTAATGTAATATTTGTTGCAA 57.720 29.630 0.00 0.00 0.00 4.08
520 942 6.564854 GTAAATCACGAGCTAACGTAATGT 57.435 37.500 0.00 0.00 44.76 2.71
717 1143 0.249398 CCTTCGTCCAATCTTCCCGT 59.751 55.000 0.00 0.00 0.00 5.28
718 1144 0.462047 CCCTTCGTCCAATCTTCCCG 60.462 60.000 0.00 0.00 0.00 5.14
764 1218 9.930693 AATCTCTTCTCTACGACTTTACAAAAT 57.069 29.630 0.00 0.00 0.00 1.82
794 1248 9.355215 CTATCTCTTCTCTACGTTTGCTAAAAA 57.645 33.333 0.00 0.00 0.00 1.94
795 1249 8.737175 TCTATCTCTTCTCTACGTTTGCTAAAA 58.263 33.333 0.00 0.00 0.00 1.52
796 1250 8.277490 TCTATCTCTTCTCTACGTTTGCTAAA 57.723 34.615 0.00 0.00 0.00 1.85
797 1251 7.769507 TCTCTATCTCTTCTCTACGTTTGCTAA 59.230 37.037 0.00 0.00 0.00 3.09
798 1252 7.273712 TCTCTATCTCTTCTCTACGTTTGCTA 58.726 38.462 0.00 0.00 0.00 3.49
799 1253 6.116806 TCTCTATCTCTTCTCTACGTTTGCT 58.883 40.000 0.00 0.00 0.00 3.91
800 1254 6.366315 TCTCTATCTCTTCTCTACGTTTGC 57.634 41.667 0.00 0.00 0.00 3.68
801 1255 9.268268 ACTATCTCTATCTCTTCTCTACGTTTG 57.732 37.037 0.00 0.00 0.00 2.93
809 1263 9.383519 CCACAGATACTATCTCTATCTCTTCTC 57.616 40.741 0.00 0.00 37.58 2.87
810 1264 7.829211 GCCACAGATACTATCTCTATCTCTTCT 59.171 40.741 0.00 0.00 37.58 2.85
811 1265 7.067008 GGCCACAGATACTATCTCTATCTCTTC 59.933 44.444 0.00 0.00 37.58 2.87
812 1266 6.889722 GGCCACAGATACTATCTCTATCTCTT 59.110 42.308 0.00 0.00 37.58 2.85
813 1267 6.423182 GGCCACAGATACTATCTCTATCTCT 58.577 44.000 0.00 0.00 37.58 3.10
814 1268 5.592688 GGGCCACAGATACTATCTCTATCTC 59.407 48.000 4.39 0.00 37.58 2.75
815 1269 5.015710 TGGGCCACAGATACTATCTCTATCT 59.984 44.000 0.00 0.00 37.58 1.98
863 1317 2.548875 GCTGCTCAATCTCGTTCAGAT 58.451 47.619 0.00 0.00 44.56 2.90
864 1318 1.404717 GGCTGCTCAATCTCGTTCAGA 60.405 52.381 0.00 0.00 34.78 3.27
867 1321 0.391661 TGGGCTGCTCAATCTCGTTC 60.392 55.000 0.00 0.00 0.00 3.95
870 1324 2.141517 CTAATGGGCTGCTCAATCTCG 58.858 52.381 6.18 0.00 0.00 4.04
877 1331 3.243201 GCATAAACACTAATGGGCTGCTC 60.243 47.826 0.00 0.00 0.00 4.26
887 1341 2.307392 TGGCCTCCAGCATAAACACTAA 59.693 45.455 3.32 0.00 46.50 2.24
975 1429 3.818787 GAGGTCGGGCGCTTCGTA 61.819 66.667 19.26 7.38 0.00 3.43
1191 1645 1.338200 GCGCAGAGGAAGGAGAAGAAA 60.338 52.381 0.30 0.00 0.00 2.52
1281 1735 0.031994 GAAGGCGAGAGAGATCTGGC 59.968 60.000 0.00 3.93 40.11 4.85
1320 1774 7.118496 TCAAGCACCTAAATTCCAAGAAAAA 57.882 32.000 0.00 0.00 0.00 1.94
1324 1778 6.009589 TGAATCAAGCACCTAAATTCCAAGA 58.990 36.000 0.00 0.00 0.00 3.02
1339 1793 1.916000 GACGCTGCAATTGAATCAAGC 59.084 47.619 10.34 8.31 0.00 4.01
1372 1826 8.649973 ATTCACTATGGAAAATTCTACGTCTC 57.350 34.615 0.00 0.00 0.00 3.36
1404 1858 7.649057 TCTATTGTGATATGAACTAGGTGTCG 58.351 38.462 0.00 0.00 0.00 4.35
1425 1879 5.504853 TCGATCCACAGATAGCTGATCTAT 58.495 41.667 16.32 2.43 43.52 1.98
1453 1907 7.262772 CACAATGGATTCACATTTAGCTCAAT 58.737 34.615 0.00 0.00 38.94 2.57
1509 1964 3.247006 GGCAACAACTACTAGCAGCTA 57.753 47.619 1.13 1.13 0.00 3.32
1601 2057 2.229784 CCTTGATTTCAGTCCCTGTTGC 59.770 50.000 0.00 0.00 32.61 4.17
1644 2100 1.600916 GGGTTCGAGCAGGCTTGTT 60.601 57.895 8.31 0.00 0.00 2.83
1655 2111 1.700739 ACCTTACAATGGTGGGTTCGA 59.299 47.619 0.00 0.00 36.30 3.71
1718 2174 5.666969 TTCCACAACTAACAGAATGAACG 57.333 39.130 0.00 0.00 39.69 3.95
1761 2217 4.073549 CCTGACATTAAAACCGTACCCAA 58.926 43.478 0.00 0.00 0.00 4.12
1762 2218 3.327172 TCCTGACATTAAAACCGTACCCA 59.673 43.478 0.00 0.00 0.00 4.51
1768 2224 4.006989 TGGTGATCCTGACATTAAAACCG 58.993 43.478 0.00 0.00 34.23 4.44
1822 2278 7.254218 GCAGATGATAAAGGCTTTGTAATTTGC 60.254 37.037 24.24 24.24 0.00 3.68
1883 2339 8.842280 CCTTTTGTTCAATGTAGTAACTTACCA 58.158 33.333 0.00 0.00 0.00 3.25
1909 2365 1.929836 TGTTTGTTGAAAATGTGCCGC 59.070 42.857 0.00 0.00 0.00 6.53
1910 2366 4.792528 AATGTTTGTTGAAAATGTGCCG 57.207 36.364 0.00 0.00 0.00 5.69
1937 2393 3.488047 CCTGCAATACTTTGATGAAGCCG 60.488 47.826 0.00 0.00 39.04 5.52
1941 2397 8.523915 AATATCACCTGCAATACTTTGATGAA 57.476 30.769 0.00 0.00 34.60 2.57
1942 2398 8.407832 CAAATATCACCTGCAATACTTTGATGA 58.592 33.333 0.00 0.00 34.60 2.92
1943 2399 8.192774 ACAAATATCACCTGCAATACTTTGATG 58.807 33.333 12.71 1.49 34.60 3.07
1944 2400 8.297470 ACAAATATCACCTGCAATACTTTGAT 57.703 30.769 12.71 0.00 34.60 2.57
2008 2466 9.112725 CACTTACATGGATGATCTTCACATAAA 57.887 33.333 10.48 8.08 0.00 1.40
2036 2494 7.481798 GCTTGTAATTCAAAACGATAGTCAAGG 59.518 37.037 0.00 0.00 39.70 3.61
2038 2496 8.094798 AGCTTGTAATTCAAAACGATAGTCAA 57.905 30.769 0.00 0.00 39.70 3.18
2043 2501 7.172532 ACAGTGAGCTTGTAATTCAAAACGATA 59.827 33.333 0.00 0.00 35.48 2.92
2046 2504 5.396362 CACAGTGAGCTTGTAATTCAAAACG 59.604 40.000 0.00 0.00 35.48 3.60
2084 2542 6.984474 CGAGTAATATTGAAGGTAGCTGGAAA 59.016 38.462 0.00 0.00 0.00 3.13
2104 2563 1.884579 GATTATGGGACGGAGCGAGTA 59.115 52.381 0.00 0.00 0.00 2.59
2105 2564 0.674534 GATTATGGGACGGAGCGAGT 59.325 55.000 0.00 0.00 0.00 4.18
2106 2565 0.673985 TGATTATGGGACGGAGCGAG 59.326 55.000 0.00 0.00 0.00 5.03
2107 2566 1.068588 CTTGATTATGGGACGGAGCGA 59.931 52.381 0.00 0.00 0.00 4.93
2108 2567 1.068588 TCTTGATTATGGGACGGAGCG 59.931 52.381 0.00 0.00 0.00 5.03
2109 2568 2.484889 GTCTTGATTATGGGACGGAGC 58.515 52.381 0.00 0.00 0.00 4.70
2110 2569 2.545952 CGGTCTTGATTATGGGACGGAG 60.546 54.545 0.00 0.00 33.06 4.63
2111 2570 1.411246 CGGTCTTGATTATGGGACGGA 59.589 52.381 0.00 0.00 33.06 4.69
2112 2571 1.138266 ACGGTCTTGATTATGGGACGG 59.862 52.381 0.00 0.00 35.91 4.79
2113 2572 2.596904 ACGGTCTTGATTATGGGACG 57.403 50.000 0.00 0.00 0.00 4.79
2114 2573 5.638596 AAAAACGGTCTTGATTATGGGAC 57.361 39.130 0.00 0.00 0.00 4.46
2140 2599 6.921914 AGAGCGTTTTTGACACTATACTAGT 58.078 36.000 0.00 0.00 40.28 2.57
2141 2600 7.813852 AAGAGCGTTTTTGACACTATACTAG 57.186 36.000 0.00 0.00 0.00 2.57
2142 2601 8.517878 ACTAAGAGCGTTTTTGACACTATACTA 58.482 33.333 0.00 0.00 0.00 1.82
2143 2602 7.328737 CACTAAGAGCGTTTTTGACACTATACT 59.671 37.037 0.00 0.00 0.00 2.12
2144 2603 7.115947 ACACTAAGAGCGTTTTTGACACTATAC 59.884 37.037 0.00 0.00 0.00 1.47
2145 2604 7.149973 ACACTAAGAGCGTTTTTGACACTATA 58.850 34.615 0.00 0.00 0.00 1.31
2146 2605 5.989777 ACACTAAGAGCGTTTTTGACACTAT 59.010 36.000 0.00 0.00 0.00 2.12
2147 2606 5.353938 ACACTAAGAGCGTTTTTGACACTA 58.646 37.500 0.00 0.00 0.00 2.74
2148 2607 4.189231 ACACTAAGAGCGTTTTTGACACT 58.811 39.130 0.00 0.00 0.00 3.55
2149 2608 4.033587 TGACACTAAGAGCGTTTTTGACAC 59.966 41.667 0.00 0.00 0.00 3.67
2150 2609 4.185394 TGACACTAAGAGCGTTTTTGACA 58.815 39.130 0.00 0.00 0.00 3.58
2151 2610 4.789095 TGACACTAAGAGCGTTTTTGAC 57.211 40.909 0.00 0.00 0.00 3.18
2152 2611 5.804692 TTTGACACTAAGAGCGTTTTTGA 57.195 34.783 0.00 0.00 0.00 2.69
2153 2612 6.862944 TTTTTGACACTAAGAGCGTTTTTG 57.137 33.333 0.00 0.00 0.00 2.44
2154 2613 6.019881 GCATTTTTGACACTAAGAGCGTTTTT 60.020 34.615 0.00 0.00 0.00 1.94
2155 2614 5.458779 GCATTTTTGACACTAAGAGCGTTTT 59.541 36.000 0.00 0.00 0.00 2.43
2156 2615 4.976116 GCATTTTTGACACTAAGAGCGTTT 59.024 37.500 0.00 0.00 0.00 3.60
2157 2616 4.275936 AGCATTTTTGACACTAAGAGCGTT 59.724 37.500 0.00 0.00 0.00 4.84
2158 2617 3.815401 AGCATTTTTGACACTAAGAGCGT 59.185 39.130 0.00 0.00 0.00 5.07
2159 2618 4.153117 AGAGCATTTTTGACACTAAGAGCG 59.847 41.667 0.00 0.00 0.00 5.03
2160 2619 5.619625 AGAGCATTTTTGACACTAAGAGC 57.380 39.130 0.00 0.00 0.00 4.09
2167 2626 9.683069 CCCATAATATAAGAGCATTTTTGACAC 57.317 33.333 0.00 0.00 0.00 3.67
2168 2627 9.639563 TCCCATAATATAAGAGCATTTTTGACA 57.360 29.630 0.00 0.00 0.00 3.58
2169 2628 9.899226 GTCCCATAATATAAGAGCATTTTTGAC 57.101 33.333 0.00 0.00 0.00 3.18
2170 2629 8.783093 CGTCCCATAATATAAGAGCATTTTTGA 58.217 33.333 0.00 0.00 0.00 2.69
2171 2630 8.023128 CCGTCCCATAATATAAGAGCATTTTTG 58.977 37.037 0.00 0.00 0.00 2.44
2172 2631 7.942341 TCCGTCCCATAATATAAGAGCATTTTT 59.058 33.333 0.00 0.00 0.00 1.94
2173 2632 7.458397 TCCGTCCCATAATATAAGAGCATTTT 58.542 34.615 0.00 0.00 0.00 1.82
2174 2633 7.016153 TCCGTCCCATAATATAAGAGCATTT 57.984 36.000 0.00 0.00 0.00 2.32
2175 2634 6.352222 CCTCCGTCCCATAATATAAGAGCATT 60.352 42.308 0.00 0.00 0.00 3.56
2176 2635 5.129485 CCTCCGTCCCATAATATAAGAGCAT 59.871 44.000 0.00 0.00 0.00 3.79
2177 2636 4.466370 CCTCCGTCCCATAATATAAGAGCA 59.534 45.833 0.00 0.00 0.00 4.26
2178 2637 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
2179 2638 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
2180 2639 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2181 2640 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2182 2641 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2183 2642 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2184 2643 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2185 2644 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
2186 2645 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
2187 2646 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
2188 2647 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
2189 2648 0.338814 AACTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
2190 2649 1.002069 TAACTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
2191 2650 1.397672 GTAACTACTCCCTCCGTCCC 58.602 60.000 0.00 0.00 0.00 4.46
2192 2651 1.341383 TGGTAACTACTCCCTCCGTCC 60.341 57.143 0.00 0.00 37.61 4.79
2193 2652 2.134789 TGGTAACTACTCCCTCCGTC 57.865 55.000 0.00 0.00 37.61 4.79
2194 2653 2.385803 CATGGTAACTACTCCCTCCGT 58.614 52.381 0.00 0.00 37.61 4.69
2195 2654 1.068741 GCATGGTAACTACTCCCTCCG 59.931 57.143 0.00 0.00 37.61 4.63
2196 2655 1.416772 GGCATGGTAACTACTCCCTCC 59.583 57.143 0.00 0.00 37.61 4.30
2197 2656 2.116238 TGGCATGGTAACTACTCCCTC 58.884 52.381 0.00 0.00 37.61 4.30
2198 2657 2.263895 TGGCATGGTAACTACTCCCT 57.736 50.000 0.00 0.00 37.61 4.20
2199 2658 3.577805 AATGGCATGGTAACTACTCCC 57.422 47.619 0.00 0.00 37.61 4.30
2200 2659 5.221843 TGGATAATGGCATGGTAACTACTCC 60.222 44.000 0.00 0.00 37.61 3.85
2201 2660 5.865085 TGGATAATGGCATGGTAACTACTC 58.135 41.667 0.00 0.00 37.61 2.59
2202 2661 5.904984 TGGATAATGGCATGGTAACTACT 57.095 39.130 0.00 0.00 37.61 2.57
2203 2662 6.071952 CCAATGGATAATGGCATGGTAACTAC 60.072 42.308 0.00 0.00 37.61 2.73
2300 2760 2.885135 TGGCCTTCATGACAGAACAT 57.115 45.000 3.32 0.00 0.00 2.71
2444 2909 4.100529 CCTAATACCAATACGCGTATCCG 58.899 47.826 30.32 23.73 37.07 4.18
2501 2966 3.916359 TTAATGGTCAAGCGTATCCCA 57.084 42.857 0.00 0.00 0.00 4.37
2586 3139 2.988010 AATCTGCACCTTCGCTATGA 57.012 45.000 0.00 0.00 0.00 2.15
2626 3218 3.768215 CAGATCCTATCTATGGCAGCTCA 59.232 47.826 0.00 0.00 37.58 4.26
2685 3279 4.334759 CAGGTTCAGCATCAAGGTATTCTG 59.665 45.833 0.00 0.00 0.00 3.02
2702 3296 1.034292 GCCTCATTGCCCTCAGGTTC 61.034 60.000 0.00 0.00 34.57 3.62
2703 3297 1.000396 GCCTCATTGCCCTCAGGTT 60.000 57.895 0.00 0.00 34.57 3.50
2704 3298 2.679716 GCCTCATTGCCCTCAGGT 59.320 61.111 0.00 0.00 34.57 4.00
2705 3299 2.515523 CGCCTCATTGCCCTCAGG 60.516 66.667 0.00 0.00 0.00 3.86
2706 3300 1.523258 CTCGCCTCATTGCCCTCAG 60.523 63.158 0.00 0.00 0.00 3.35
2707 3301 2.586245 CTCGCCTCATTGCCCTCA 59.414 61.111 0.00 0.00 0.00 3.86
2708 3302 2.899339 GCTCGCCTCATTGCCCTC 60.899 66.667 0.00 0.00 0.00 4.30
2709 3303 3.694058 CTGCTCGCCTCATTGCCCT 62.694 63.158 0.00 0.00 0.00 5.19
2710 3304 3.207669 CTGCTCGCCTCATTGCCC 61.208 66.667 0.00 0.00 0.00 5.36
2711 3305 3.885521 GCTGCTCGCCTCATTGCC 61.886 66.667 0.00 0.00 0.00 4.52
2743 3337 1.248785 AAGAAGTAGCTCACCGGCGA 61.249 55.000 9.30 0.00 37.29 5.54
2771 3365 1.384502 CTCCCTGCATCCTACCCCA 60.385 63.158 0.00 0.00 0.00 4.96
2822 3514 2.042261 GCCCCTTACCTCCTCCCA 59.958 66.667 0.00 0.00 0.00 4.37
2882 3583 1.763655 TGCTCCTCGCATCATCCCT 60.764 57.895 0.00 0.00 45.47 4.20
2903 3604 4.169696 CCGGCGGCAAGATGGGTA 62.170 66.667 15.42 0.00 0.00 3.69
2927 3628 1.263342 CCCTCTCAGGCTTCAGCAGA 61.263 60.000 0.30 0.00 44.36 4.26
2967 3668 1.133976 AGCAAACTGTGAGAAGCCAGT 60.134 47.619 0.00 0.00 43.53 4.00
2975 3676 1.572085 CGGCTCCAGCAAACTGTGAG 61.572 60.000 0.03 0.00 42.81 3.51
2978 3679 2.980233 GCGGCTCCAGCAAACTGT 60.980 61.111 0.03 0.00 42.81 3.55
2993 3694 3.730761 GGCAACTCACCAGCAGCG 61.731 66.667 0.00 0.00 0.00 5.18
3020 3721 0.534412 CTCCTCGCCTCTCACACAAT 59.466 55.000 0.00 0.00 0.00 2.71
3033 3734 0.388659 CTGCTCCTCATTCCTCCTCG 59.611 60.000 0.00 0.00 0.00 4.63
3080 3781 2.280797 GCTCACTTGTCGGTGGCA 60.281 61.111 0.00 0.00 37.75 4.92
3090 3791 1.069765 CGGTGGTGTCAGCTCACTT 59.930 57.895 3.30 0.00 39.09 3.16
3142 3843 6.239317 CCATACCTCTCCGATTCATTTCACTA 60.239 42.308 0.00 0.00 0.00 2.74
3169 3870 4.106925 CCCTGTCCAGCCTCCAGC 62.107 72.222 0.00 0.00 44.25 4.85
3170 3871 2.822643 TACCCCTGTCCAGCCTCCAG 62.823 65.000 0.00 0.00 0.00 3.86
3171 3872 2.194951 ATACCCCTGTCCAGCCTCCA 62.195 60.000 0.00 0.00 0.00 3.86
3172 3873 1.384643 ATACCCCTGTCCAGCCTCC 60.385 63.158 0.00 0.00 0.00 4.30
3173 3874 1.749334 CGATACCCCTGTCCAGCCTC 61.749 65.000 0.00 0.00 0.00 4.70
3174 3875 1.762460 CGATACCCCTGTCCAGCCT 60.762 63.158 0.00 0.00 0.00 4.58
3175 3876 2.808206 CCGATACCCCTGTCCAGCC 61.808 68.421 0.00 0.00 0.00 4.85
3209 3910 2.052104 GGCCCAACCCTGTGTATGC 61.052 63.158 0.00 0.00 0.00 3.14
3231 3932 1.043116 TCTCCCAGATACCTGCACGG 61.043 60.000 1.16 1.16 39.07 4.94
3276 3982 6.403092 GCATTGGCGGTTTAAGCAATAAAAAT 60.403 34.615 0.00 0.00 35.33 1.82
3371 4078 3.781605 GATAGGTGCTGGGGCTGGC 62.782 68.421 0.00 0.00 39.59 4.85
3390 4097 1.878953 ACCTCCAGCTAAACAACACG 58.121 50.000 0.00 0.00 0.00 4.49
3396 4104 3.610911 ACAGCATAACCTCCAGCTAAAC 58.389 45.455 0.00 0.00 35.19 2.01
3486 4195 0.109039 AAAACCACAAACGCGCAAGT 60.109 45.000 5.73 0.00 41.68 3.16
3568 4278 4.826274 TCTGTCCTGCAGCTAAGTTTAT 57.174 40.909 8.66 0.00 44.66 1.40
3570 4280 3.341823 CATCTGTCCTGCAGCTAAGTTT 58.658 45.455 8.66 0.00 44.66 2.66
3726 4436 8.958119 TCTTACTTGTACAACTCTGTCATTTT 57.042 30.769 3.59 0.00 36.96 1.82
3757 4467 9.890629 TTACAGCTCAGTTAAAGAATCATACAT 57.109 29.630 0.00 0.00 0.00 2.29
3796 4506 2.029649 AGAGAACAAATGTGGCACATGC 60.030 45.455 31.99 18.49 44.52 4.06
4075 4785 4.202060 GCTTCTCGATACTGATGACAAGGA 60.202 45.833 0.00 0.00 0.00 3.36
4096 4806 0.390472 GCCACTTCGCTCTAACTGCT 60.390 55.000 0.00 0.00 0.00 4.24
4138 4848 0.674269 GATCAAACCGGTGGCGGTAA 60.674 55.000 8.52 0.00 42.06 2.85
4147 4857 2.398554 CGTGCCCTGATCAAACCGG 61.399 63.158 0.00 0.00 0.00 5.28
4159 4869 3.194005 TGAATATTCTTCCTCGTGCCC 57.806 47.619 16.24 0.00 0.00 5.36
4199 4909 2.756755 GTTTTTGTTGTTGTTGCTGCG 58.243 42.857 0.00 0.00 0.00 5.18
4206 4916 4.326009 GTCTGATTGCGTTTTTGTTGTTGT 59.674 37.500 0.00 0.00 0.00 3.32
4240 4950 6.824305 AGAAACTGAAAATTCGATGATGGT 57.176 33.333 0.00 0.00 0.00 3.55
4288 4999 6.109156 TGAACTCTGTAGACCATGCTAAAA 57.891 37.500 0.00 0.00 0.00 1.52
4328 5039 5.986135 CAGATACCTAGAGCACCAACATAAC 59.014 44.000 0.00 0.00 0.00 1.89
4329 5040 5.897250 TCAGATACCTAGAGCACCAACATAA 59.103 40.000 0.00 0.00 0.00 1.90
4389 5100 2.509845 GCAAAGCCAGCAGAAAACG 58.490 52.632 0.00 0.00 0.00 3.60
4512 5224 6.417258 TCAATCTGGTCAGCAGATAAATTCA 58.583 36.000 19.65 0.00 38.34 2.57
4552 5265 1.110442 CTGCCTGGGTGAAAACAACA 58.890 50.000 0.00 0.00 0.00 3.33
4597 5310 8.398665 GGTGAGGTTTACATGATTTACAAGATC 58.601 37.037 0.00 0.00 0.00 2.75
4689 5402 5.931146 TGGTTACATTTGCAATTGAATGACC 59.069 36.000 24.13 21.70 36.87 4.02
4722 5435 2.098934 TGCACACCTCAAATTGTGACAC 59.901 45.455 5.91 0.00 45.03 3.67
4729 5442 3.037549 TCCCTTTTGCACACCTCAAATT 58.962 40.909 0.00 0.00 33.94 1.82
4761 5474 1.683385 GCTGCCTTTCTTCCACACTTT 59.317 47.619 0.00 0.00 0.00 2.66
4771 5484 1.406903 ACAAAGCTTGCTGCCTTTCT 58.593 45.000 0.00 0.00 44.23 2.52
4772 5485 2.229675 AACAAAGCTTGCTGCCTTTC 57.770 45.000 0.00 0.00 44.23 2.62
4773 5486 2.093553 TCAAACAAAGCTTGCTGCCTTT 60.094 40.909 0.00 0.00 44.23 3.11
4774 5487 1.481772 TCAAACAAAGCTTGCTGCCTT 59.518 42.857 0.00 0.00 44.23 4.35
4775 5488 1.113788 TCAAACAAAGCTTGCTGCCT 58.886 45.000 0.00 0.00 44.23 4.75
4776 5489 2.159327 ATCAAACAAAGCTTGCTGCC 57.841 45.000 0.00 0.00 44.23 4.85
4777 5490 4.271776 AGAAAATCAAACAAAGCTTGCTGC 59.728 37.500 0.00 0.00 43.29 5.25
4778 5491 5.978934 AGAAAATCAAACAAAGCTTGCTG 57.021 34.783 0.00 0.00 0.00 4.41
4781 5494 8.823818 AGAATCAAGAAAATCAAACAAAGCTTG 58.176 29.630 0.00 0.00 34.41 4.01
4885 5606 6.942886 TTTACTGCAAAACAAACAACTGAG 57.057 33.333 0.00 0.00 0.00 3.35
4996 5717 3.854856 GCCACAGTTTCTGGGCAA 58.145 55.556 17.64 0.00 42.85 4.52
5051 5772 2.028112 TCTGTTGAGGGAATCTTGACGG 60.028 50.000 0.00 0.00 0.00 4.79
5103 5824 0.721718 GATCAACGCTCCGTGGAAAG 59.278 55.000 0.00 0.00 43.25 2.62
5110 5831 2.806856 GCTGCTGATCAACGCTCCG 61.807 63.158 8.27 0.00 0.00 4.63
5182 5903 2.178580 ACCTGAAGCTCTCTTCTCCAG 58.821 52.381 6.60 0.00 46.81 3.86
5235 5956 1.757118 TCAGGGATGTCGGTCAAGATC 59.243 52.381 0.00 0.00 0.00 2.75
5299 6020 0.318360 TCAATCGTGTGTTCGTCGCT 60.318 50.000 0.00 0.00 0.00 4.93
5306 6027 3.804036 TGAAGAAGGTCAATCGTGTGTT 58.196 40.909 0.00 0.00 0.00 3.32
5409 6130 5.472137 GGCCATACTTGTTTAGACTGTGAAA 59.528 40.000 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.