Multiple sequence alignment - TraesCS4A01G224500

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 TraesCS4A01G224500 chr4A 100.000 3038 0 0 1 3038 532215853 532218890 0.000000e+00 5611.0
1 TraesCS4A01G224500 chr4A 85.450 2378 288 28 4 2327 531679883 531677510 0.000000e+00 2422.0
2 TraesCS4A01G224500 chr4A 80.620 2389 375 56 4 2330 531385964 531383602 0.000000e+00 1766.0
3 TraesCS4A01G224500 chr4A 81.048 496 84 10 379 867 626299911 626299419 1.320000e-103 387.0
4 TraesCS4A01G224500 chr4D 85.636 2381 284 30 1 2327 64538654 64541030 0.000000e+00 2449.0
5 TraesCS4A01G224500 chr4D 84.896 1920 189 41 802 2649 64349333 64347443 0.000000e+00 1845.0
6 TraesCS4A01G224500 chr4D 94.314 299 17 0 2740 3038 64340098 64339800 2.760000e-125 459.0
7 TraesCS4A01G224500 chr4D 97.222 108 3 0 2646 2753 64347363 64347256 1.860000e-42 183.0
8 TraesCS4A01G224500 chr4B 84.910 2379 287 35 1 2327 95069888 95072246 0.000000e+00 2338.0
9 TraesCS4A01G224500 chr4B 82.909 2475 344 41 4 2424 94790935 94788486 0.000000e+00 2154.0
10 TraesCS4A01G224500 chr2D 81.659 2170 334 29 1 2130 580192756 580194901 0.000000e+00 1744.0
11 TraesCS4A01G224500 chr2D 76.846 799 150 22 402 1175 7413152 7413940 4.680000e-113 418.0
12 TraesCS4A01G224500 chr2B 80.910 2263 355 34 1 2214 699108401 699110635 0.000000e+00 1714.0
13 TraesCS4A01G224500 chr2B 89.189 74 8 0 2744 2817 699111148 699111221 3.230000e-15 93.5
14 TraesCS4A01G224500 chr2A 82.656 1649 242 23 458 2085 718119199 718120824 0.000000e+00 1421.0
15 TraesCS4A01G224500 chr3A 78.531 1784 331 35 342 2090 687593896 687595662 0.000000e+00 1125.0
16 TraesCS4A01G224500 chr3B 77.809 1789 338 41 342 2090 730284398 730286167 0.000000e+00 1050.0
17 TraesCS4A01G224500 chr3B 77.621 1564 302 33 537 2067 730310685 730312233 0.000000e+00 905.0
18 TraesCS4A01G224500 chr3D 77.740 1788 341 40 342 2090 550661200 550662969 0.000000e+00 1044.0


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 TraesCS4A01G224500 chr4A 532215853 532218890 3037 False 5611.00 5611 100.0000 1 3038 1 chr4A.!!$F1 3037
1 TraesCS4A01G224500 chr4A 531677510 531679883 2373 True 2422.00 2422 85.4500 4 2327 1 chr4A.!!$R2 2323
2 TraesCS4A01G224500 chr4A 531383602 531385964 2362 True 1766.00 1766 80.6200 4 2330 1 chr4A.!!$R1 2326
3 TraesCS4A01G224500 chr4D 64538654 64541030 2376 False 2449.00 2449 85.6360 1 2327 1 chr4D.!!$F1 2326
4 TraesCS4A01G224500 chr4D 64347256 64349333 2077 True 1014.00 1845 91.0590 802 2753 2 chr4D.!!$R2 1951
5 TraesCS4A01G224500 chr4B 95069888 95072246 2358 False 2338.00 2338 84.9100 1 2327 1 chr4B.!!$F1 2326
6 TraesCS4A01G224500 chr4B 94788486 94790935 2449 True 2154.00 2154 82.9090 4 2424 1 chr4B.!!$R1 2420
7 TraesCS4A01G224500 chr2D 580192756 580194901 2145 False 1744.00 1744 81.6590 1 2130 1 chr2D.!!$F2 2129
8 TraesCS4A01G224500 chr2D 7413152 7413940 788 False 418.00 418 76.8460 402 1175 1 chr2D.!!$F1 773
9 TraesCS4A01G224500 chr2B 699108401 699111221 2820 False 903.75 1714 85.0495 1 2817 2 chr2B.!!$F1 2816
10 TraesCS4A01G224500 chr2A 718119199 718120824 1625 False 1421.00 1421 82.6560 458 2085 1 chr2A.!!$F1 1627
11 TraesCS4A01G224500 chr3A 687593896 687595662 1766 False 1125.00 1125 78.5310 342 2090 1 chr3A.!!$F1 1748
12 TraesCS4A01G224500 chr3B 730284398 730286167 1769 False 1050.00 1050 77.8090 342 2090 1 chr3B.!!$F1 1748
13 TraesCS4A01G224500 chr3B 730310685 730312233 1548 False 905.00 905 77.6210 537 2067 1 chr3B.!!$F2 1530
14 TraesCS4A01G224500 chr3D 550661200 550662969 1769 False 1044.00 1044 77.7400 342 2090 1 chr3D.!!$F1 1748

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
655 676 0.10212 CCATGTCACGAGAGAGCCTC 59.898 60.0 0.00 0.0 38.55 4.70 F
1130 1171 0.03582 ATCGGGTTACAACGCACCAT 60.036 50.0 9.46 0.0 41.43 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1467 1508 0.375106 GAAGCGGCATAGTTGACAGC 59.625 55.0 1.45 0.0 32.69 4.40 R
2805 3110 0.107831 AGTGCGCCCTTGTTGAACTA 59.892 50.0 4.18 0.0 0.00 2.24 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
29 30 3.994204 GCACATGCATGGATCAATGTA 57.006 42.857 29.41 7.66 41.59 2.29
44 45 6.038271 GGATCAATGTATCACAGGTTTACACC 59.962 42.308 0.00 0.00 44.67 4.16
53 54 3.668641 GGTTTACACCGTTGATGCG 57.331 52.632 0.00 0.00 31.60 4.73
56 57 1.727880 GTTTACACCGTTGATGCGCTA 59.272 47.619 9.73 0.00 0.00 4.26
68 83 4.818534 TGATGCGCTATTGAGGAAATTC 57.181 40.909 9.73 0.00 0.00 2.17
74 89 4.433022 GCGCTATTGAGGAAATTCGATACG 60.433 45.833 0.00 0.00 0.00 3.06
93 108 1.234821 GCCGAAACACCATTGTCAGA 58.765 50.000 0.00 0.00 33.55 3.27
108 123 2.618241 TGTCAGAAGGCATTGACACAAC 59.382 45.455 12.66 0.00 46.27 3.32
109 124 2.618241 GTCAGAAGGCATTGACACAACA 59.382 45.455 10.04 0.00 42.47 3.33
115 130 2.816087 AGGCATTGACACAACAGATGTC 59.184 45.455 0.00 0.00 45.58 3.06
120 135 2.781923 TGACACAACAGATGTCCATGG 58.218 47.619 4.97 4.97 44.91 3.66
133 148 3.509442 TGTCCATGGCTTGAAAAAGGAT 58.491 40.909 6.96 0.00 0.00 3.24
139 154 6.894654 TCCATGGCTTGAAAAAGGATATACAA 59.105 34.615 6.96 0.00 0.00 2.41
186 201 5.539582 TTAATTGTACTGGATGACGTTGC 57.460 39.130 0.00 0.00 0.00 4.17
190 205 0.821517 TACTGGATGACGTTGCGGAT 59.178 50.000 0.00 0.00 0.00 4.18
191 206 0.740868 ACTGGATGACGTTGCGGATG 60.741 55.000 0.00 0.00 0.00 3.51
195 210 1.359848 GATGACGTTGCGGATGAAGT 58.640 50.000 0.00 0.00 0.00 3.01
223 238 9.669353 GTATACTTCCAAATACATGATGCTTTG 57.331 33.333 0.00 11.83 0.00 2.77
242 257 3.795688 TGCAGAATCTCCAAGGAAGTT 57.204 42.857 0.00 0.00 0.00 2.66
257 272 4.708177 AGGAAGTTGGATCATCATTACGG 58.292 43.478 0.00 0.00 0.00 4.02
273 288 2.877691 GGCACGGAAGGAACATGC 59.122 61.111 0.00 0.00 35.51 4.06
275 290 1.971167 GCACGGAAGGAACATGCCA 60.971 57.895 0.00 0.00 0.00 4.92
327 342 1.407989 GCTCCAGCCATTGAGTAAGCT 60.408 52.381 0.00 0.00 35.52 3.74
335 350 3.488721 GCCATTGAGTAAGCTTGATGCAG 60.489 47.826 9.86 0.00 45.94 4.41
336 351 3.943381 CCATTGAGTAAGCTTGATGCAGA 59.057 43.478 9.86 0.00 45.94 4.26
338 353 5.277876 CCATTGAGTAAGCTTGATGCAGATC 60.278 44.000 9.86 0.00 45.94 2.75
339 354 3.451526 TGAGTAAGCTTGATGCAGATCG 58.548 45.455 9.86 0.00 45.94 3.69
401 416 1.210478 TGTGCCCTAAGGATCTTGAGC 59.790 52.381 0.00 0.00 33.47 4.26
439 454 3.876300 GACAGGTGTCATGGCGTC 58.124 61.111 5.21 0.00 44.18 5.19
456 471 2.004017 CGTCCCGCTAGCAATTGTTAA 58.996 47.619 16.45 0.00 0.00 2.01
477 492 0.968405 ATTGGCGGCATGTTGTCTTT 59.032 45.000 14.32 0.00 0.00 2.52
495 510 6.207864 GTCTTTAAGACAACGGTTAGACAC 57.792 41.667 19.00 0.00 44.45 3.67
521 539 4.923281 GGACGCAAAAATACAATCAGCTTT 59.077 37.500 0.00 0.00 0.00 3.51
527 548 4.361451 AAATACAATCAGCTTTGCGAGG 57.639 40.909 0.00 0.00 0.00 4.63
529 550 2.472695 ACAATCAGCTTTGCGAGGTA 57.527 45.000 0.00 0.00 33.99 3.08
534 555 2.346803 TCAGCTTTGCGAGGTATCAAC 58.653 47.619 0.00 0.00 33.99 3.18
549 570 6.607970 AGGTATCAACCAATGATCATGTCAT 58.392 36.000 9.46 3.01 45.91 3.06
552 573 4.857679 TCAACCAATGATCATGTCATGGA 58.142 39.130 24.61 10.45 46.80 3.41
553 574 4.641541 TCAACCAATGATCATGTCATGGAC 59.358 41.667 24.61 7.86 46.80 4.02
604 625 2.038295 AGGAGACCTCAGAAACTGCTTG 59.962 50.000 0.00 0.00 0.00 4.01
605 626 2.421619 GAGACCTCAGAAACTGCTTGG 58.578 52.381 0.00 0.00 0.00 3.61
620 641 2.029020 TGCTTGGTGTACTGCAGTCTAG 60.029 50.000 25.56 15.62 0.00 2.43
630 651 1.480137 CTGCAGTCTAGTCCCTGAAGG 59.520 57.143 5.25 0.00 31.68 3.46
646 667 0.907704 AAGGCTACCCCATGTCACGA 60.908 55.000 0.00 0.00 35.39 4.35
655 676 0.102120 CCATGTCACGAGAGAGCCTC 59.898 60.000 0.00 0.00 38.55 4.70
662 683 4.536316 GAGAGAGCCTCGTACGGA 57.464 61.111 16.52 1.19 35.36 4.69
736 757 5.237048 GTGATAGCTGAGGGAAATCTCATC 58.763 45.833 0.00 0.00 42.19 2.92
784 805 3.871485 AGTTGTGGAGAATGATGAGCTC 58.129 45.455 6.82 6.82 0.00 4.09
804 825 0.824759 GGTAGGGTCAGCACCTGTAG 59.175 60.000 0.00 0.00 43.22 2.74
811 832 0.983467 TCAGCACCTGTAGGATGCAA 59.017 50.000 20.01 10.21 41.46 4.08
815 836 2.240667 AGCACCTGTAGGATGCAAGATT 59.759 45.455 20.01 4.40 41.46 2.40
824 845 3.081061 AGGATGCAAGATTTTGTGCGTA 58.919 40.909 0.00 0.00 43.93 4.42
841 862 5.575606 TGTGCGTAAACTAGCTATTTCTGTC 59.424 40.000 0.00 0.00 0.00 3.51
867 888 6.371271 GCTAAAGAAGAGAGATTTGCTTCAGT 59.629 38.462 0.00 0.00 40.26 3.41
868 889 6.557291 AAAGAAGAGAGATTTGCTTCAGTG 57.443 37.500 0.00 0.00 40.26 3.66
873 894 1.815003 GAGATTTGCTTCAGTGGGTGG 59.185 52.381 0.00 0.00 0.00 4.61
894 915 5.048364 GTGGTTACAGCACAATTACATTGGA 60.048 40.000 1.23 0.00 45.26 3.53
900 921 3.056607 AGCACAATTACATTGGAACAGCC 60.057 43.478 1.72 0.00 44.42 4.85
913 934 2.224402 GGAACAGCCAGATGAGGATACC 60.224 54.545 0.00 0.00 36.34 2.73
929 950 3.549625 GGATACCCGTCGTCTGTCATTAC 60.550 52.174 0.00 0.00 0.00 1.89
930 951 1.542492 ACCCGTCGTCTGTCATTACT 58.458 50.000 0.00 0.00 0.00 2.24
939 960 4.405680 TCGTCTGTCATTACTTGGATGGAT 59.594 41.667 0.00 0.00 0.00 3.41
940 961 5.104941 TCGTCTGTCATTACTTGGATGGATT 60.105 40.000 0.00 0.00 0.00 3.01
946 967 5.235186 GTCATTACTTGGATGGATTGACGAG 59.765 44.000 0.00 0.00 0.00 4.18
986 1007 5.407407 ACTTCCACATCTTCGAACAGTAT 57.593 39.130 0.00 0.00 0.00 2.12
988 1009 6.931838 ACTTCCACATCTTCGAACAGTATTA 58.068 36.000 0.00 0.00 0.00 0.98
991 1012 6.513180 TCCACATCTTCGAACAGTATTATCC 58.487 40.000 0.00 0.00 0.00 2.59
1012 1052 6.078456 TCCCTTGGAACATGTTATCTTCAT 57.922 37.500 11.95 0.00 39.30 2.57
1016 1056 7.546667 CCCTTGGAACATGTTATCTTCATTTTG 59.453 37.037 11.95 0.00 39.30 2.44
1121 1162 5.125257 TCAATCTACGTTACATCGGGTTACA 59.875 40.000 0.00 0.00 34.94 2.41
1130 1171 0.035820 ATCGGGTTACAACGCACCAT 60.036 50.000 9.46 0.00 41.43 3.55
1182 1223 4.652679 TCTGTCTAACCTCCACACTCTA 57.347 45.455 0.00 0.00 0.00 2.43
1185 1226 5.044772 TCTGTCTAACCTCCACACTCTAGAT 60.045 44.000 0.00 0.00 0.00 1.98
1199 1240 6.257411 CACACTCTAGATATCAAGCAAACCAG 59.743 42.308 5.32 0.00 0.00 4.00
1204 1245 9.202273 CTCTAGATATCAAGCAAACCAGAATAC 57.798 37.037 5.32 0.00 0.00 1.89
1205 1246 6.851222 AGATATCAAGCAAACCAGAATACG 57.149 37.500 5.32 0.00 0.00 3.06
1233 1274 4.847990 ACCACGGGGAATTGTTAAGATA 57.152 40.909 12.96 0.00 38.05 1.98
1314 1355 3.181510 GGTACTTTATTGGAGTGCAAGCG 60.182 47.826 2.75 0.00 32.25 4.68
1353 1394 3.629398 ACTTGGAAGAACTGCAAACTCTG 59.371 43.478 0.00 0.00 34.60 3.35
1389 1430 0.670162 GCTTTGACTTGGCTGAGCAA 59.330 50.000 6.82 0.00 0.00 3.91
1392 1433 1.597742 TTGACTTGGCTGAGCAACTC 58.402 50.000 6.82 0.00 0.00 3.01
1444 1485 5.528690 TGGATTGATAACATTAGTGCTGCTC 59.471 40.000 0.00 0.00 0.00 4.26
1462 1503 4.695396 TGCTCATTGTGCAAATCTGTTTT 58.305 34.783 10.76 0.00 37.51 2.43
1467 1508 6.142139 TCATTGTGCAAATCTGTTTTCTACG 58.858 36.000 0.00 0.00 0.00 3.51
1493 1534 1.641577 ACTATGCCGCTTCTTTCGAC 58.358 50.000 0.00 0.00 0.00 4.20
1634 1675 0.942962 CCGATCTTTCTCAGCCATGC 59.057 55.000 0.00 0.00 0.00 4.06
1654 1695 7.099764 CCATGCGAAATACCTCAAGTATCTAT 58.900 38.462 0.00 0.00 40.98 1.98
1677 1718 1.347707 CTAAGCTGGTGTCACCTTGGA 59.652 52.381 22.56 1.50 39.58 3.53
1744 1797 6.815142 CACATATCTGAGACTCAACAACATGA 59.185 38.462 6.61 0.00 0.00 3.07
1885 1938 7.812191 GCATTGAAGGTTTGTATATTGTGTCAA 59.188 33.333 0.00 0.00 0.00 3.18
1999 2052 3.561960 TCAATGGGACACTGAAGGAATGG 60.562 47.826 0.00 0.00 43.43 3.16
2050 2103 1.075542 TGTTTAGATGCGGCAAGTCG 58.924 50.000 6.82 0.00 0.00 4.18
2078 2134 0.809385 CTGCAGTGCCATTCTTGGAG 59.191 55.000 13.72 0.00 46.92 3.86
2101 2176 0.745845 ATCCAGTCCAACTGCATCGC 60.746 55.000 1.49 0.00 44.63 4.58
2135 2210 7.610865 TCATTCCAATAAGTTTGTGAAATCCC 58.389 34.615 0.00 0.00 0.00 3.85
2136 2211 5.637006 TCCAATAAGTTTGTGAAATCCCG 57.363 39.130 0.00 0.00 0.00 5.14
2137 2212 4.461081 TCCAATAAGTTTGTGAAATCCCGG 59.539 41.667 0.00 0.00 0.00 5.73
2138 2213 4.173256 CAATAAGTTTGTGAAATCCCGGC 58.827 43.478 0.00 0.00 0.00 6.13
2139 2214 1.698506 AAGTTTGTGAAATCCCGGCA 58.301 45.000 0.00 0.00 0.00 5.69
2152 2236 2.560861 CGGCACATTTGGTCGGTG 59.439 61.111 0.00 0.00 35.68 4.94
2166 2250 3.630769 TGGTCGGTGCTTCTATACTGTAG 59.369 47.826 0.00 0.00 0.00 2.74
2199 2292 2.226330 TCAAAGATTGGTTGGTGTCCG 58.774 47.619 0.00 0.00 0.00 4.79
2236 2329 3.554524 CTCTGTGCCGTATGTGTTTTTG 58.445 45.455 0.00 0.00 0.00 2.44
2283 2381 7.748031 TGTGTTGTTTAAGTTACATGCTTTG 57.252 32.000 0.00 0.00 0.00 2.77
2285 2383 5.751028 TGTTGTTTAAGTTACATGCTTTGGC 59.249 36.000 0.00 0.00 39.26 4.52
2300 2398 4.082625 TGCTTTGGCACTCATTTCATGTAG 60.083 41.667 0.00 0.00 44.28 2.74
2331 2481 8.942669 TGTATTGTTTGTATCGAACATTTCAC 57.057 30.769 0.00 2.04 37.55 3.18
2412 2562 6.569226 GCCAAGAGTTATCATTCATACATGGC 60.569 42.308 0.00 0.00 40.08 4.40
2424 2574 5.011090 TCATACATGGCTACACTGTCTTC 57.989 43.478 0.00 0.00 0.00 2.87
2527 2711 5.163612 GGGGATTTTCAATAGCACTTCTGTC 60.164 44.000 0.00 0.00 0.00 3.51
2561 2745 4.331968 CAGGTGTTTAGGTCTGCCAATTA 58.668 43.478 0.00 0.00 37.19 1.40
2614 2802 3.181520 GGTTCGTCTGATATGTTGTGTGC 60.182 47.826 0.00 0.00 0.00 4.57
2649 2920 4.957759 AGGAACGCAAATTACATGTACC 57.042 40.909 4.68 0.05 0.00 3.34
2812 3117 2.622942 CCAAAGCTTGGCAGTAGTTCAA 59.377 45.455 0.00 0.00 45.17 2.69
2817 3122 2.030805 GCTTGGCAGTAGTTCAACAAGG 60.031 50.000 0.00 0.00 36.67 3.61
2818 3123 2.270352 TGGCAGTAGTTCAACAAGGG 57.730 50.000 0.00 0.00 0.00 3.95
2819 3124 0.881796 GGCAGTAGTTCAACAAGGGC 59.118 55.000 0.00 0.00 0.00 5.19
2820 3125 0.517316 GCAGTAGTTCAACAAGGGCG 59.483 55.000 0.00 0.00 0.00 6.13
2821 3126 0.517316 CAGTAGTTCAACAAGGGCGC 59.483 55.000 0.00 0.00 0.00 6.53
2822 3127 0.107831 AGTAGTTCAACAAGGGCGCA 59.892 50.000 10.83 0.00 0.00 6.09
2823 3128 0.237498 GTAGTTCAACAAGGGCGCAC 59.763 55.000 10.83 5.15 0.00 5.34
2824 3129 0.107831 TAGTTCAACAAGGGCGCACT 59.892 50.000 6.19 6.19 0.00 4.40
2825 3130 0.751643 AGTTCAACAAGGGCGCACTT 60.752 50.000 21.73 21.73 0.00 3.16
2826 3131 0.102300 GTTCAACAAGGGCGCACTTT 59.898 50.000 25.25 11.81 0.00 2.66
2827 3132 0.102120 TTCAACAAGGGCGCACTTTG 59.898 50.000 25.25 20.12 0.00 2.77
2828 3133 1.950630 CAACAAGGGCGCACTTTGC 60.951 57.895 25.25 0.00 40.69 3.68
2829 3134 2.127232 AACAAGGGCGCACTTTGCT 61.127 52.632 25.25 7.03 42.25 3.91
2830 3135 0.821711 AACAAGGGCGCACTTTGCTA 60.822 50.000 25.25 0.00 42.25 3.49
2831 3136 1.237285 ACAAGGGCGCACTTTGCTAG 61.237 55.000 25.25 14.02 42.25 3.42
2832 3137 0.955428 CAAGGGCGCACTTTGCTAGA 60.955 55.000 25.25 0.00 42.25 2.43
2833 3138 0.035056 AAGGGCGCACTTTGCTAGAT 60.035 50.000 21.73 0.00 42.25 1.98
2834 3139 0.745845 AGGGCGCACTTTGCTAGATG 60.746 55.000 6.19 0.00 42.25 2.90
2835 3140 0.744414 GGGCGCACTTTGCTAGATGA 60.744 55.000 10.83 0.00 42.25 2.92
2836 3141 1.303309 GGCGCACTTTGCTAGATGAT 58.697 50.000 10.83 0.00 42.25 2.45
2837 3142 2.483876 GGCGCACTTTGCTAGATGATA 58.516 47.619 10.83 0.00 42.25 2.15
2838 3143 2.221981 GGCGCACTTTGCTAGATGATAC 59.778 50.000 10.83 0.00 42.25 2.24
2839 3144 2.866156 GCGCACTTTGCTAGATGATACA 59.134 45.455 0.30 0.00 42.25 2.29
2840 3145 3.309682 GCGCACTTTGCTAGATGATACAA 59.690 43.478 0.30 0.00 42.25 2.41
2841 3146 4.024556 GCGCACTTTGCTAGATGATACAAT 60.025 41.667 0.30 0.00 42.25 2.71
2842 3147 5.504665 GCGCACTTTGCTAGATGATACAATT 60.505 40.000 0.30 0.00 42.25 2.32
2843 3148 6.292865 GCGCACTTTGCTAGATGATACAATTA 60.293 38.462 0.30 0.00 42.25 1.40
2844 3149 7.571983 GCGCACTTTGCTAGATGATACAATTAT 60.572 37.037 0.30 0.00 42.25 1.28
2845 3150 7.954248 CGCACTTTGCTAGATGATACAATTATC 59.046 37.037 0.00 0.00 42.25 1.75
2846 3151 7.954248 GCACTTTGCTAGATGATACAATTATCG 59.046 37.037 0.00 0.00 40.96 2.92
2847 3152 9.196552 CACTTTGCTAGATGATACAATTATCGA 57.803 33.333 0.00 0.00 37.51 3.59
2848 3153 9.935241 ACTTTGCTAGATGATACAATTATCGAT 57.065 29.630 2.16 2.16 37.51 3.59
2850 3155 9.927668 TTTGCTAGATGATACAATTATCGATCA 57.072 29.630 0.00 0.00 37.51 2.92
2862 3167 8.970859 ACAATTATCGATCATCTTTTCCTCTT 57.029 30.769 0.00 0.00 0.00 2.85
2869 3174 8.256611 TCGATCATCTTTTCCTCTTAGTTTTG 57.743 34.615 0.00 0.00 0.00 2.44
2870 3175 8.094548 TCGATCATCTTTTCCTCTTAGTTTTGA 58.905 33.333 0.00 0.00 0.00 2.69
2871 3176 8.171840 CGATCATCTTTTCCTCTTAGTTTTGAC 58.828 37.037 0.00 0.00 0.00 3.18
2872 3177 8.924511 ATCATCTTTTCCTCTTAGTTTTGACA 57.075 30.769 0.00 0.00 0.00 3.58
2873 3178 8.154649 TCATCTTTTCCTCTTAGTTTTGACAC 57.845 34.615 0.00 0.00 0.00 3.67
2874 3179 7.993183 TCATCTTTTCCTCTTAGTTTTGACACT 59.007 33.333 0.00 0.00 0.00 3.55
2875 3180 9.273016 CATCTTTTCCTCTTAGTTTTGACACTA 57.727 33.333 0.00 0.00 0.00 2.74
2876 3181 9.847224 ATCTTTTCCTCTTAGTTTTGACACTAA 57.153 29.630 0.00 0.00 36.99 2.24
2877 3182 9.675464 TCTTTTCCTCTTAGTTTTGACACTAAA 57.325 29.630 0.00 0.00 38.50 1.85
2880 3185 7.492352 TCCTCTTAGTTTTGACACTAAAAGC 57.508 36.000 0.00 0.00 38.50 3.51
2881 3186 7.280356 TCCTCTTAGTTTTGACACTAAAAGCT 58.720 34.615 0.00 0.00 38.50 3.74
2882 3187 7.773690 TCCTCTTAGTTTTGACACTAAAAGCTT 59.226 33.333 0.00 0.00 38.50 3.74
2883 3188 8.406297 CCTCTTAGTTTTGACACTAAAAGCTTT 58.594 33.333 5.69 5.69 38.50 3.51
2884 3189 9.439537 CTCTTAGTTTTGACACTAAAAGCTTTC 57.560 33.333 13.10 0.00 38.50 2.62
2885 3190 9.174166 TCTTAGTTTTGACACTAAAAGCTTTCT 57.826 29.630 13.10 5.69 38.50 2.52
2886 3191 9.788960 CTTAGTTTTGACACTAAAAGCTTTCTT 57.211 29.630 13.10 0.00 38.50 2.52
2888 3193 8.466086 AGTTTTGACACTAAAAGCTTTCTTTG 57.534 30.769 13.10 11.62 41.40 2.77
2889 3194 7.545615 AGTTTTGACACTAAAAGCTTTCTTTGG 59.454 33.333 13.10 1.45 41.40 3.28
2890 3195 4.932146 TGACACTAAAAGCTTTCTTTGGC 58.068 39.130 13.10 11.91 41.40 4.52
2891 3196 4.400884 TGACACTAAAAGCTTTCTTTGGCA 59.599 37.500 13.10 14.34 41.40 4.92
2892 3197 4.936891 ACACTAAAAGCTTTCTTTGGCAG 58.063 39.130 13.10 4.24 41.40 4.85
2893 3198 3.737774 CACTAAAAGCTTTCTTTGGCAGC 59.262 43.478 13.10 0.00 41.40 5.25
2894 3199 2.985957 AAAAGCTTTCTTTGGCAGCA 57.014 40.000 13.10 0.00 41.40 4.41
2895 3200 2.985957 AAAGCTTTCTTTGGCAGCAA 57.014 40.000 5.69 0.00 40.77 3.91
2896 3201 3.480505 AAAGCTTTCTTTGGCAGCAAT 57.519 38.095 5.69 0.00 40.77 3.56
2897 3202 4.605640 AAAGCTTTCTTTGGCAGCAATA 57.394 36.364 5.69 0.00 40.77 1.90
2898 3203 4.813750 AAGCTTTCTTTGGCAGCAATAT 57.186 36.364 0.00 0.00 35.88 1.28
2899 3204 5.920193 AAGCTTTCTTTGGCAGCAATATA 57.080 34.783 0.00 0.00 35.88 0.86
2900 3205 6.475596 AAGCTTTCTTTGGCAGCAATATAT 57.524 33.333 0.00 0.00 35.88 0.86
2901 3206 6.475596 AGCTTTCTTTGGCAGCAATATATT 57.524 33.333 0.00 0.00 35.88 1.28
2902 3207 6.881570 AGCTTTCTTTGGCAGCAATATATTT 58.118 32.000 0.00 0.00 35.88 1.40
2903 3208 7.333323 AGCTTTCTTTGGCAGCAATATATTTT 58.667 30.769 0.00 0.00 35.88 1.82
2904 3209 7.825761 AGCTTTCTTTGGCAGCAATATATTTTT 59.174 29.630 0.00 0.00 35.88 1.94
2937 3242 8.293114 TGAAAAAGAAATCGATTACAAAAGGC 57.707 30.769 11.83 0.00 0.00 4.35
2938 3243 7.923344 TGAAAAAGAAATCGATTACAAAAGGCA 59.077 29.630 11.83 1.89 0.00 4.75
2939 3244 8.655651 AAAAAGAAATCGATTACAAAAGGCAA 57.344 26.923 11.83 0.00 0.00 4.52
2940 3245 8.831715 AAAAGAAATCGATTACAAAAGGCAAT 57.168 26.923 11.83 0.00 0.00 3.56
2941 3246 9.921637 AAAAGAAATCGATTACAAAAGGCAATA 57.078 25.926 11.83 0.00 0.00 1.90
2947 3252 9.463443 AATCGATTACAAAAGGCAATATTTAGC 57.537 29.630 9.39 0.00 0.00 3.09
2948 3253 8.220755 TCGATTACAAAAGGCAATATTTAGCT 57.779 30.769 0.00 0.00 0.00 3.32
2949 3254 8.128582 TCGATTACAAAAGGCAATATTTAGCTG 58.871 33.333 0.00 0.00 0.00 4.24
2950 3255 7.379529 CGATTACAAAAGGCAATATTTAGCTGG 59.620 37.037 0.00 0.00 0.00 4.85
2951 3256 7.710676 TTACAAAAGGCAATATTTAGCTGGA 57.289 32.000 0.00 0.00 0.00 3.86
2952 3257 6.796785 ACAAAAGGCAATATTTAGCTGGAT 57.203 33.333 0.00 0.00 0.00 3.41
2953 3258 7.896383 ACAAAAGGCAATATTTAGCTGGATA 57.104 32.000 0.00 0.00 0.00 2.59
2954 3259 8.482852 ACAAAAGGCAATATTTAGCTGGATAT 57.517 30.769 0.00 0.00 0.00 1.63
2955 3260 8.579863 ACAAAAGGCAATATTTAGCTGGATATC 58.420 33.333 0.00 0.00 0.00 1.63
2956 3261 8.579006 CAAAAGGCAATATTTAGCTGGATATCA 58.421 33.333 4.83 0.00 0.00 2.15
2957 3262 7.693969 AAGGCAATATTTAGCTGGATATCAC 57.306 36.000 4.83 0.00 0.00 3.06
2958 3263 6.183347 AGGCAATATTTAGCTGGATATCACC 58.817 40.000 4.83 5.59 0.00 4.02
2959 3264 5.945784 GGCAATATTTAGCTGGATATCACCA 59.054 40.000 4.83 0.00 38.33 4.17
2971 3276 6.566079 TGGATATCACCAGAATTCAGAACT 57.434 37.500 8.44 0.00 34.77 3.01
2972 3277 6.586344 TGGATATCACCAGAATTCAGAACTC 58.414 40.000 8.44 0.00 34.77 3.01
2973 3278 6.156775 TGGATATCACCAGAATTCAGAACTCA 59.843 38.462 8.44 0.00 34.77 3.41
2974 3279 6.705381 GGATATCACCAGAATTCAGAACTCAG 59.295 42.308 8.44 0.00 0.00 3.35
2975 3280 5.752036 ATCACCAGAATTCAGAACTCAGA 57.248 39.130 8.44 0.00 0.00 3.27
2976 3281 5.551305 TCACCAGAATTCAGAACTCAGAA 57.449 39.130 8.44 0.00 0.00 3.02
2977 3282 5.300752 TCACCAGAATTCAGAACTCAGAAC 58.699 41.667 8.44 0.00 0.00 3.01
2978 3283 5.059161 CACCAGAATTCAGAACTCAGAACA 58.941 41.667 8.44 0.00 0.00 3.18
2979 3284 5.704515 CACCAGAATTCAGAACTCAGAACAT 59.295 40.000 8.44 0.00 0.00 2.71
2980 3285 5.936956 ACCAGAATTCAGAACTCAGAACATC 59.063 40.000 8.44 0.00 0.00 3.06
2981 3286 6.171921 CCAGAATTCAGAACTCAGAACATCT 58.828 40.000 8.44 0.00 0.00 2.90
2982 3287 6.654161 CCAGAATTCAGAACTCAGAACATCTT 59.346 38.462 8.44 0.00 0.00 2.40
2983 3288 7.148440 CCAGAATTCAGAACTCAGAACATCTTC 60.148 40.741 8.44 0.00 0.00 2.87
2984 3289 7.387122 CAGAATTCAGAACTCAGAACATCTTCA 59.613 37.037 8.44 0.00 0.00 3.02
2985 3290 7.603404 AGAATTCAGAACTCAGAACATCTTCAG 59.397 37.037 8.44 0.00 0.00 3.02
2986 3291 6.410942 TTCAGAACTCAGAACATCTTCAGA 57.589 37.500 0.00 0.00 0.00 3.27
2987 3292 6.602410 TCAGAACTCAGAACATCTTCAGAT 57.398 37.500 0.00 0.00 34.56 2.90
2997 3302 3.965292 CATCTTCAGATGTCCACATGC 57.035 47.619 8.45 0.00 45.10 4.06
2998 3303 3.275999 CATCTTCAGATGTCCACATGCA 58.724 45.455 8.45 0.00 45.10 3.96
2999 3304 3.421919 TCTTCAGATGTCCACATGCAA 57.578 42.857 0.00 0.00 36.57 4.08
3000 3305 3.076621 TCTTCAGATGTCCACATGCAAC 58.923 45.455 0.00 0.00 36.57 4.17
3001 3306 2.865119 TCAGATGTCCACATGCAACT 57.135 45.000 0.00 0.00 36.57 3.16
3002 3307 2.429478 TCAGATGTCCACATGCAACTG 58.571 47.619 0.00 0.00 36.57 3.16
3003 3308 1.135489 CAGATGTCCACATGCAACTGC 60.135 52.381 0.00 0.00 36.57 4.40
3033 3338 2.573920 GGAGACCTCGAGTTCAGCT 58.426 57.895 12.87 1.38 0.00 4.24
3034 3339 0.892063 GGAGACCTCGAGTTCAGCTT 59.108 55.000 12.87 0.00 0.00 3.74
3035 3340 1.135228 GGAGACCTCGAGTTCAGCTTC 60.135 57.143 12.87 0.74 0.00 3.86
3036 3341 1.542030 GAGACCTCGAGTTCAGCTTCA 59.458 52.381 12.87 0.00 0.00 3.02
3037 3342 2.165437 GAGACCTCGAGTTCAGCTTCAT 59.835 50.000 12.87 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 4.901868 ACGGTGTAAACCTGTGATACATT 58.098 39.130 0.00 0.00 32.65 2.71
25 26 4.546829 ACGGTGTAAACCTGTGATACAT 57.453 40.909 0.00 0.00 32.65 2.29
29 30 3.478857 TCAACGGTGTAAACCTGTGAT 57.521 42.857 0.00 0.00 0.00 3.06
44 45 1.570813 TCCTCAATAGCGCATCAACG 58.429 50.000 11.47 0.00 0.00 4.10
53 54 4.143094 GGCGTATCGAATTTCCTCAATAGC 60.143 45.833 0.00 0.00 0.00 2.97
56 57 2.800544 CGGCGTATCGAATTTCCTCAAT 59.199 45.455 0.00 0.00 0.00 2.57
68 83 1.003851 AATGGTGTTTCGGCGTATCG 58.996 50.000 6.85 0.00 0.00 2.92
74 89 1.234821 TCTGACAATGGTGTTTCGGC 58.765 50.000 0.00 0.00 38.41 5.54
81 96 2.821378 TCAATGCCTTCTGACAATGGTG 59.179 45.455 0.00 0.00 0.00 4.17
93 108 3.225104 ACATCTGTTGTGTCAATGCCTT 58.775 40.909 0.00 0.00 37.11 4.35
105 120 2.439409 TCAAGCCATGGACATCTGTTG 58.561 47.619 18.40 7.26 0.00 3.33
108 123 4.491676 CTTTTTCAAGCCATGGACATCTG 58.508 43.478 18.40 4.28 0.00 2.90
109 124 3.512724 CCTTTTTCAAGCCATGGACATCT 59.487 43.478 18.40 0.00 0.00 2.90
115 130 6.713762 TGTATATCCTTTTTCAAGCCATGG 57.286 37.500 7.63 7.63 0.00 3.66
120 135 8.178313 GTCTCTGTTGTATATCCTTTTTCAAGC 58.822 37.037 0.00 0.00 0.00 4.01
166 181 2.415168 CGCAACGTCATCCAGTACAATT 59.585 45.455 0.00 0.00 0.00 2.32
181 196 3.863424 AGTATACAACTTCATCCGCAACG 59.137 43.478 5.50 0.00 33.35 4.10
195 210 8.978874 AGCATCATGTATTTGGAAGTATACAA 57.021 30.769 5.50 0.00 39.78 2.41
242 257 1.540146 CCGTGCCGTAATGATGATCCA 60.540 52.381 0.00 0.00 0.00 3.41
257 272 1.971167 TGGCATGTTCCTTCCGTGC 60.971 57.895 0.00 0.00 42.73 5.34
268 283 1.818674 GAAGAAATTCCGGTGGCATGT 59.181 47.619 0.00 0.00 0.00 3.21
273 288 1.004277 TGGGAGAAGAAATTCCGGTGG 59.996 52.381 0.00 0.00 34.17 4.61
275 290 1.004394 GGTGGGAGAAGAAATTCCGGT 59.996 52.381 0.00 0.00 34.17 5.28
335 350 3.748863 TTCTGCAGAAGAGGCGATC 57.251 52.632 25.16 0.00 35.91 3.69
361 376 1.072266 TGTGGCCCTTCTGGTTGTAT 58.928 50.000 0.00 0.00 36.04 2.29
401 416 7.201591 CCTGTCAACAATAGAAGTAGCAATCTG 60.202 40.741 0.00 0.00 0.00 2.90
437 452 2.745281 TGTTAACAATTGCTAGCGGGAC 59.255 45.455 10.77 1.07 0.00 4.46
439 454 4.104776 CAATGTTAACAATTGCTAGCGGG 58.895 43.478 13.23 1.67 0.00 6.13
456 471 0.895100 AGACAACATGCCGCCAATGT 60.895 50.000 0.00 0.00 0.00 2.71
477 492 4.341806 TCCAAGTGTCTAACCGTTGTCTTA 59.658 41.667 0.00 0.00 0.00 2.10
495 510 4.324402 GCTGATTGTATTTTTGCGTCCAAG 59.676 41.667 0.00 0.00 31.52 3.61
521 539 3.118445 TGATCATTGGTTGATACCTCGCA 60.118 43.478 0.00 0.00 45.29 5.10
527 548 6.487668 TCCATGACATGATCATTGGTTGATAC 59.512 38.462 17.24 1.10 46.54 2.24
529 550 5.301045 GTCCATGACATGATCATTGGTTGAT 59.699 40.000 17.24 5.39 46.54 2.57
549 570 6.007076 TGGTAGCTCAAATTTACAATGTCCA 58.993 36.000 0.00 0.00 0.00 4.02
552 573 7.362920 GGTCATGGTAGCTCAAATTTACAATGT 60.363 37.037 0.00 0.00 32.81 2.71
553 574 6.974622 GGTCATGGTAGCTCAAATTTACAATG 59.025 38.462 0.00 0.00 32.43 2.82
557 578 7.715249 TGATAGGTCATGGTAGCTCAAATTTAC 59.285 37.037 0.00 0.00 0.00 2.01
563 584 3.643320 CCTGATAGGTCATGGTAGCTCAA 59.357 47.826 0.00 0.00 32.98 3.02
604 625 1.477295 GGGACTAGACTGCAGTACACC 59.523 57.143 21.73 17.50 0.00 4.16
605 626 2.164624 CAGGGACTAGACTGCAGTACAC 59.835 54.545 21.73 7.74 36.02 2.90
620 641 0.988678 ATGGGGTAGCCTTCAGGGAC 60.989 60.000 11.48 0.00 37.23 4.46
630 651 0.103208 CTCTCGTGACATGGGGTAGC 59.897 60.000 0.00 0.00 0.00 3.58
646 667 0.107116 ACATCCGTACGAGGCTCTCT 60.107 55.000 18.76 0.00 0.00 3.10
655 676 1.079405 AGCAACCCACATCCGTACG 60.079 57.895 8.69 8.69 0.00 3.67
658 679 0.606401 CTTCAGCAACCCACATCCGT 60.606 55.000 0.00 0.00 0.00 4.69
662 683 4.102113 GCCTTCAGCAACCCACAT 57.898 55.556 0.00 0.00 42.97 3.21
716 737 4.155709 TCGATGAGATTTCCCTCAGCTAT 58.844 43.478 7.43 0.00 44.75 2.97
736 757 1.934589 TATTGCGGTGGATCAGTTCG 58.065 50.000 0.00 0.00 0.00 3.95
784 805 0.968901 TACAGGTGCTGACCCTACCG 60.969 60.000 0.00 0.00 44.40 4.02
804 825 2.352503 ACGCACAAAATCTTGCATCC 57.647 45.000 0.00 0.00 38.76 3.51
811 832 7.611213 AATAGCTAGTTTACGCACAAAATCT 57.389 32.000 0.00 0.00 0.00 2.40
815 836 6.425721 ACAGAAATAGCTAGTTTACGCACAAA 59.574 34.615 8.00 0.00 0.00 2.83
824 845 7.321153 TCTTTAGCGACAGAAATAGCTAGTTT 58.679 34.615 8.00 4.58 42.24 2.66
841 862 5.349817 TGAAGCAAATCTCTCTTCTTTAGCG 59.650 40.000 0.00 0.00 37.63 4.26
867 888 2.373335 AATTGTGCTGTAACCACCCA 57.627 45.000 0.00 0.00 32.30 4.51
868 889 3.150767 TGTAATTGTGCTGTAACCACCC 58.849 45.455 0.00 0.00 32.30 4.61
888 909 2.022195 CCTCATCTGGCTGTTCCAATG 58.978 52.381 0.00 0.00 46.01 2.82
894 915 1.771255 GGGTATCCTCATCTGGCTGTT 59.229 52.381 0.00 0.00 0.00 3.16
900 921 1.267261 GACGACGGGTATCCTCATCTG 59.733 57.143 0.00 0.00 0.00 2.90
901 922 1.143277 AGACGACGGGTATCCTCATCT 59.857 52.381 0.00 0.00 0.00 2.90
905 926 0.662085 GACAGACGACGGGTATCCTC 59.338 60.000 0.00 0.00 0.00 3.71
913 934 2.094906 TCCAAGTAATGACAGACGACGG 60.095 50.000 0.00 0.00 0.00 4.79
929 950 3.193263 CAGTCTCGTCAATCCATCCAAG 58.807 50.000 0.00 0.00 0.00 3.61
930 951 2.677902 GCAGTCTCGTCAATCCATCCAA 60.678 50.000 0.00 0.00 0.00 3.53
939 960 2.159099 ACTTTCAGTGCAGTCTCGTCAA 60.159 45.455 0.00 0.00 0.00 3.18
940 961 1.409064 ACTTTCAGTGCAGTCTCGTCA 59.591 47.619 0.00 0.00 0.00 4.35
946 967 4.496507 GGAAGTTCAACTTTCAGTGCAGTC 60.497 45.833 3.76 0.00 38.80 3.51
986 1007 7.638444 TGAAGATAACATGTTCCAAGGGATAA 58.362 34.615 15.85 0.00 32.04 1.75
988 1009 6.078456 TGAAGATAACATGTTCCAAGGGAT 57.922 37.500 15.85 0.33 32.04 3.85
991 1012 7.546667 CCAAAATGAAGATAACATGTTCCAAGG 59.453 37.037 15.85 0.03 32.04 3.61
1012 1052 8.877195 AGTAAGGTAGTTAGATTCAGACCAAAA 58.123 33.333 0.00 0.00 0.00 2.44
1016 1056 7.407393 ACAGTAAGGTAGTTAGATTCAGACC 57.593 40.000 0.00 0.00 0.00 3.85
1121 1162 1.302511 GACCTGACCATGGTGCGTT 60.303 57.895 25.52 3.39 38.03 4.84
1130 1171 1.152419 TCGGGAAGTGACCTGACCA 60.152 57.895 0.00 0.00 40.00 4.02
1182 1223 5.760253 CCGTATTCTGGTTTGCTTGATATCT 59.240 40.000 3.98 0.00 0.00 1.98
1185 1226 5.092554 TCCGTATTCTGGTTTGCTTGATA 57.907 39.130 0.00 0.00 0.00 2.15
1199 1240 1.537562 CCCGTGGTAGCTTCCGTATTC 60.538 57.143 4.78 0.00 0.00 1.75
1204 1245 1.968050 ATTCCCCGTGGTAGCTTCCG 61.968 60.000 4.78 0.00 0.00 4.30
1205 1246 0.255033 AATTCCCCGTGGTAGCTTCC 59.745 55.000 1.68 1.68 0.00 3.46
1233 1274 2.113986 AGGTGCCGCAGCTTCTTT 59.886 55.556 19.30 0.00 39.27 2.52
1314 1355 2.481289 AGTTGGACAGCTCTTTAGGC 57.519 50.000 0.00 0.00 0.00 3.93
1389 1430 6.291377 TCTTAGTTGCATCAGTTTCTTGAGT 58.709 36.000 0.00 0.00 0.00 3.41
1392 1433 6.854892 CACTTCTTAGTTGCATCAGTTTCTTG 59.145 38.462 0.00 0.00 30.26 3.02
1444 1485 5.164158 GCGTAGAAAACAGATTTGCACAATG 60.164 40.000 0.00 0.00 0.00 2.82
1462 1503 1.202256 CGGCATAGTTGACAGCGTAGA 60.202 52.381 0.00 0.00 0.00 2.59
1467 1508 0.375106 GAAGCGGCATAGTTGACAGC 59.625 55.000 1.45 0.00 32.69 4.40
1606 1647 4.096382 GCTGAGAAAGATCGGGCAATTTAA 59.904 41.667 0.00 0.00 0.00 1.52
1712 1759 5.264395 TGAGTCTCAGATATGTGAGGTTCA 58.736 41.667 25.09 23.30 43.69 3.18
1744 1797 3.055891 AGAACCAAAGTTTTTGCACTGCT 60.056 39.130 1.98 0.00 35.94 4.24
1951 2004 6.647334 TCTGAAATCCTTGTGCAAATACAA 57.353 33.333 0.00 0.00 38.17 2.41
1956 2009 4.644234 TGAGTTCTGAAATCCTTGTGCAAA 59.356 37.500 14.45 0.00 0.00 3.68
1999 2052 3.743396 GGAACATGTAGCATCTTCGGATC 59.257 47.826 0.00 0.00 31.35 3.36
2050 2103 0.823356 TGGCACTGCAGAAAGAACCC 60.823 55.000 23.35 9.51 0.00 4.11
2078 2134 0.890542 TGCAGTTGGACTGGATGCAC 60.891 55.000 9.85 0.00 46.01 4.57
2130 2205 1.312371 CGACCAAATGTGCCGGGATT 61.312 55.000 2.18 0.00 0.00 3.01
2131 2206 1.748879 CGACCAAATGTGCCGGGAT 60.749 57.895 2.18 0.00 0.00 3.85
2132 2207 2.359354 CGACCAAATGTGCCGGGA 60.359 61.111 2.18 0.00 0.00 5.14
2133 2208 3.439540 CCGACCAAATGTGCCGGG 61.440 66.667 2.18 0.00 36.43 5.73
2135 2210 2.560861 CACCGACCAAATGTGCCG 59.439 61.111 0.00 0.00 0.00 5.69
2138 2213 1.238439 AGAAGCACCGACCAAATGTG 58.762 50.000 0.00 0.00 0.00 3.21
2139 2214 2.851263 TAGAAGCACCGACCAAATGT 57.149 45.000 0.00 0.00 0.00 2.71
2166 2250 8.445493 CAACCAATCTTTGAGGAATAAATTTGC 58.555 33.333 0.00 0.00 0.00 3.68
2221 2314 3.047093 GTCAACCAAAAACACATACGGC 58.953 45.455 0.00 0.00 0.00 5.68
2236 2329 0.669625 GGTACAGAGCACGGTCAACC 60.670 60.000 0.00 0.14 0.00 3.77
2300 2398 5.893512 TCGATACAAACAATACATACCGC 57.106 39.130 0.00 0.00 0.00 5.68
2412 2562 3.099905 TGGGGATCAGAAGACAGTGTAG 58.900 50.000 0.00 0.00 0.00 2.74
2424 2574 6.726490 ATTGATCTGAAATTTGGGGATCAG 57.274 37.500 18.31 10.22 42.05 2.90
2471 2655 5.723295 AGTGCTGCTGAAAAGAAAAAGAAA 58.277 33.333 0.00 0.00 0.00 2.52
2474 2658 6.413018 AAAAGTGCTGCTGAAAAGAAAAAG 57.587 33.333 0.00 0.00 0.00 2.27
2475 2659 6.799926 AAAAAGTGCTGCTGAAAAGAAAAA 57.200 29.167 0.00 0.00 0.00 1.94
2527 2711 3.354089 AAACACCTGCGAAATTCACAG 57.646 42.857 4.15 4.15 0.00 3.66
2561 2745 4.604156 ACTACTACTAGTTTAGCCCCGTT 58.396 43.478 0.00 0.00 27.62 4.44
2614 2802 4.312443 TGCGTTCCTTTTTCCTAGTGTAG 58.688 43.478 0.00 0.00 0.00 2.74
2649 2920 9.619316 TGAACGGAAAACACATATTCATAAAAG 57.381 29.630 0.00 0.00 0.00 2.27
2754 3059 2.814097 GCAGGGACTTTAACTGGAGCAA 60.814 50.000 0.00 0.00 34.60 3.91
2758 3063 2.708861 TGAAGCAGGGACTTTAACTGGA 59.291 45.455 0.00 0.00 34.60 3.86
2794 3099 2.930950 TGTTGAACTACTGCCAAGCTT 58.069 42.857 0.00 0.00 0.00 3.74
2802 3107 0.517316 GCGCCCTTGTTGAACTACTG 59.483 55.000 0.00 0.00 0.00 2.74
2805 3110 0.107831 AGTGCGCCCTTGTTGAACTA 59.892 50.000 4.18 0.00 0.00 2.24
2819 3124 7.954248 GATAATTGTATCATCTAGCAAAGTGCG 59.046 37.037 0.00 0.00 41.12 5.34
2820 3125 7.954248 CGATAATTGTATCATCTAGCAAAGTGC 59.046 37.037 0.00 0.00 38.92 4.40
2821 3126 9.196552 TCGATAATTGTATCATCTAGCAAAGTG 57.803 33.333 0.00 0.00 36.65 3.16
2822 3127 9.935241 ATCGATAATTGTATCATCTAGCAAAGT 57.065 29.630 0.00 0.00 36.65 2.66
2824 3129 9.927668 TGATCGATAATTGTATCATCTAGCAAA 57.072 29.630 0.00 0.00 36.65 3.68
2826 3131 9.741647 GATGATCGATAATTGTATCATCTAGCA 57.258 33.333 15.48 1.98 45.80 3.49
2837 3142 8.970859 AAGAGGAAAAGATGATCGATAATTGT 57.029 30.769 0.00 0.00 0.00 2.71
2843 3148 8.887717 CAAAACTAAGAGGAAAAGATGATCGAT 58.112 33.333 0.00 0.00 0.00 3.59
2844 3149 8.094548 TCAAAACTAAGAGGAAAAGATGATCGA 58.905 33.333 0.00 0.00 0.00 3.59
2845 3150 8.171840 GTCAAAACTAAGAGGAAAAGATGATCG 58.828 37.037 0.00 0.00 0.00 3.69
2846 3151 9.003658 TGTCAAAACTAAGAGGAAAAGATGATC 57.996 33.333 0.00 0.00 0.00 2.92
2847 3152 8.787852 GTGTCAAAACTAAGAGGAAAAGATGAT 58.212 33.333 0.00 0.00 0.00 2.45
2848 3153 7.993183 AGTGTCAAAACTAAGAGGAAAAGATGA 59.007 33.333 0.00 0.00 0.00 2.92
2849 3154 8.159344 AGTGTCAAAACTAAGAGGAAAAGATG 57.841 34.615 0.00 0.00 0.00 2.90
2850 3155 9.847224 TTAGTGTCAAAACTAAGAGGAAAAGAT 57.153 29.630 0.00 0.00 37.65 2.40
2851 3156 9.675464 TTTAGTGTCAAAACTAAGAGGAAAAGA 57.325 29.630 0.00 0.00 42.15 2.52
2854 3159 8.403236 GCTTTTAGTGTCAAAACTAAGAGGAAA 58.597 33.333 13.39 0.00 41.65 3.13
2855 3160 7.773690 AGCTTTTAGTGTCAAAACTAAGAGGAA 59.226 33.333 13.39 0.25 41.65 3.36
2856 3161 7.280356 AGCTTTTAGTGTCAAAACTAAGAGGA 58.720 34.615 13.39 0.00 41.65 3.71
2857 3162 7.497925 AGCTTTTAGTGTCAAAACTAAGAGG 57.502 36.000 13.39 4.05 41.65 3.69
2858 3163 9.439537 GAAAGCTTTTAGTGTCAAAACTAAGAG 57.560 33.333 14.05 9.22 43.06 2.85
2859 3164 9.174166 AGAAAGCTTTTAGTGTCAAAACTAAGA 57.826 29.630 14.05 0.00 42.15 2.10
2860 3165 9.788960 AAGAAAGCTTTTAGTGTCAAAACTAAG 57.211 29.630 14.05 0.00 42.15 2.18
2862 3167 9.567848 CAAAGAAAGCTTTTAGTGTCAAAACTA 57.432 29.630 14.05 0.00 42.27 2.24
2863 3168 7.545615 CCAAAGAAAGCTTTTAGTGTCAAAACT 59.454 33.333 14.05 0.00 42.27 2.66
2864 3169 7.674008 GCCAAAGAAAGCTTTTAGTGTCAAAAC 60.674 37.037 14.05 0.00 42.27 2.43
2865 3170 6.312672 GCCAAAGAAAGCTTTTAGTGTCAAAA 59.687 34.615 14.05 0.00 42.27 2.44
2866 3171 5.810074 GCCAAAGAAAGCTTTTAGTGTCAAA 59.190 36.000 14.05 0.00 42.27 2.69
2867 3172 5.105554 TGCCAAAGAAAGCTTTTAGTGTCAA 60.106 36.000 14.05 0.00 42.27 3.18
2868 3173 4.400884 TGCCAAAGAAAGCTTTTAGTGTCA 59.599 37.500 14.05 4.99 42.27 3.58
2869 3174 4.932146 TGCCAAAGAAAGCTTTTAGTGTC 58.068 39.130 14.05 0.00 42.27 3.67
2870 3175 4.737649 GCTGCCAAAGAAAGCTTTTAGTGT 60.738 41.667 14.05 0.00 42.27 3.55
2871 3176 3.737774 GCTGCCAAAGAAAGCTTTTAGTG 59.262 43.478 14.05 10.94 42.27 2.74
2872 3177 3.384467 TGCTGCCAAAGAAAGCTTTTAGT 59.616 39.130 14.05 0.00 42.27 2.24
2873 3178 3.981211 TGCTGCCAAAGAAAGCTTTTAG 58.019 40.909 14.05 3.86 42.27 1.85
2874 3179 4.399004 TTGCTGCCAAAGAAAGCTTTTA 57.601 36.364 14.05 0.00 42.27 1.52
2875 3180 2.985957 TGCTGCCAAAGAAAGCTTTT 57.014 40.000 14.05 0.54 42.27 2.27
2876 3181 2.985957 TTGCTGCCAAAGAAAGCTTT 57.014 40.000 12.53 12.53 44.93 3.51
2877 3182 4.813750 ATATTGCTGCCAAAGAAAGCTT 57.186 36.364 0.00 0.00 37.82 3.74
2878 3183 6.475596 AATATATTGCTGCCAAAGAAAGCT 57.524 33.333 0.00 0.00 37.82 3.74
2879 3184 7.543947 AAAATATATTGCTGCCAAAGAAAGC 57.456 32.000 0.00 0.00 34.05 3.51
2911 3216 8.925700 GCCTTTTGTAATCGATTTCTTTTTCAT 58.074 29.630 17.19 0.00 0.00 2.57
2912 3217 7.923344 TGCCTTTTGTAATCGATTTCTTTTTCA 59.077 29.630 17.19 3.85 0.00 2.69
2913 3218 8.293114 TGCCTTTTGTAATCGATTTCTTTTTC 57.707 30.769 17.19 1.32 0.00 2.29
2914 3219 8.655651 TTGCCTTTTGTAATCGATTTCTTTTT 57.344 26.923 17.19 0.00 0.00 1.94
2915 3220 8.831715 ATTGCCTTTTGTAATCGATTTCTTTT 57.168 26.923 17.19 0.00 0.00 2.27
2921 3226 9.463443 GCTAAATATTGCCTTTTGTAATCGATT 57.537 29.630 16.15 16.15 31.27 3.34
2922 3227 8.850156 AGCTAAATATTGCCTTTTGTAATCGAT 58.150 29.630 0.00 0.00 31.27 3.59
2923 3228 8.128582 CAGCTAAATATTGCCTTTTGTAATCGA 58.871 33.333 0.00 0.00 31.27 3.59
2924 3229 7.379529 CCAGCTAAATATTGCCTTTTGTAATCG 59.620 37.037 0.00 0.00 31.27 3.34
2925 3230 8.413229 TCCAGCTAAATATTGCCTTTTGTAATC 58.587 33.333 0.00 0.00 31.27 1.75
2926 3231 8.305046 TCCAGCTAAATATTGCCTTTTGTAAT 57.695 30.769 0.00 0.00 33.53 1.89
2927 3232 7.710676 TCCAGCTAAATATTGCCTTTTGTAA 57.289 32.000 0.00 0.00 0.00 2.41
2928 3233 7.896383 ATCCAGCTAAATATTGCCTTTTGTA 57.104 32.000 0.00 0.00 0.00 2.41
2929 3234 6.796785 ATCCAGCTAAATATTGCCTTTTGT 57.203 33.333 0.00 0.00 0.00 2.83
2930 3235 8.579006 TGATATCCAGCTAAATATTGCCTTTTG 58.421 33.333 0.00 0.00 0.00 2.44
2931 3236 8.579863 GTGATATCCAGCTAAATATTGCCTTTT 58.420 33.333 0.00 0.00 0.00 2.27
2932 3237 7.177392 GGTGATATCCAGCTAAATATTGCCTTT 59.823 37.037 0.00 0.00 40.01 3.11
2933 3238 6.660949 GGTGATATCCAGCTAAATATTGCCTT 59.339 38.462 0.00 0.00 40.01 4.35
2934 3239 6.183347 GGTGATATCCAGCTAAATATTGCCT 58.817 40.000 0.00 0.00 40.01 4.75
2935 3240 5.945784 TGGTGATATCCAGCTAAATATTGCC 59.054 40.000 0.00 0.97 43.38 4.52
2936 3241 7.081526 CTGGTGATATCCAGCTAAATATTGC 57.918 40.000 0.00 0.00 46.53 3.56
2948 3253 6.156775 TGAGTTCTGAATTCTGGTGATATCCA 59.843 38.462 13.11 0.00 36.00 3.41
2949 3254 6.586344 TGAGTTCTGAATTCTGGTGATATCC 58.414 40.000 13.11 0.00 0.00 2.59
2950 3255 7.495901 TCTGAGTTCTGAATTCTGGTGATATC 58.504 38.462 15.98 0.00 0.00 1.63
2951 3256 7.429374 TCTGAGTTCTGAATTCTGGTGATAT 57.571 36.000 15.98 0.00 0.00 1.63
2952 3257 6.857437 TCTGAGTTCTGAATTCTGGTGATA 57.143 37.500 15.98 0.00 0.00 2.15
2953 3258 5.752036 TCTGAGTTCTGAATTCTGGTGAT 57.248 39.130 15.98 0.00 0.00 3.06
2954 3259 5.163311 TGTTCTGAGTTCTGAATTCTGGTGA 60.163 40.000 15.98 6.99 36.46 4.02
2955 3260 5.059161 TGTTCTGAGTTCTGAATTCTGGTG 58.941 41.667 15.98 5.29 36.46 4.17
2956 3261 5.296151 TGTTCTGAGTTCTGAATTCTGGT 57.704 39.130 15.98 0.00 36.46 4.00
2957 3262 6.171921 AGATGTTCTGAGTTCTGAATTCTGG 58.828 40.000 15.98 8.99 36.46 3.86
2958 3263 7.387122 TGAAGATGTTCTGAGTTCTGAATTCTG 59.613 37.037 13.11 12.40 36.46 3.02
2959 3264 7.448420 TGAAGATGTTCTGAGTTCTGAATTCT 58.552 34.615 13.11 7.60 36.46 2.40
2960 3265 7.601886 TCTGAAGATGTTCTGAGTTCTGAATTC 59.398 37.037 7.93 6.01 36.14 2.17
2961 3266 7.448420 TCTGAAGATGTTCTGAGTTCTGAATT 58.552 34.615 7.93 0.00 36.14 2.17
2962 3267 7.002250 TCTGAAGATGTTCTGAGTTCTGAAT 57.998 36.000 7.93 0.00 36.14 2.57
2963 3268 6.410942 TCTGAAGATGTTCTGAGTTCTGAA 57.589 37.500 7.93 0.00 36.14 3.02
2964 3269 6.396450 CATCTGAAGATGTTCTGAGTTCTGA 58.604 40.000 15.67 0.00 45.10 3.27
2965 3270 6.650239 CATCTGAAGATGTTCTGAGTTCTG 57.350 41.667 15.67 7.19 45.10 3.02
2978 3283 3.639672 TGCATGTGGACATCTGAAGAT 57.360 42.857 0.00 0.00 33.61 2.40
2979 3284 3.076621 GTTGCATGTGGACATCTGAAGA 58.923 45.455 0.00 0.00 33.61 2.87
2980 3285 3.079578 AGTTGCATGTGGACATCTGAAG 58.920 45.455 0.00 0.00 33.61 3.02
2981 3286 2.815503 CAGTTGCATGTGGACATCTGAA 59.184 45.455 0.00 0.00 36.25 3.02
2982 3287 2.429478 CAGTTGCATGTGGACATCTGA 58.571 47.619 0.00 0.00 36.25 3.27
2983 3288 1.135489 GCAGTTGCATGTGGACATCTG 60.135 52.381 0.00 0.05 41.59 2.90
2984 3289 1.171308 GCAGTTGCATGTGGACATCT 58.829 50.000 0.00 0.00 41.59 2.90
2985 3290 3.708195 GCAGTTGCATGTGGACATC 57.292 52.632 0.00 0.00 41.59 3.06
2996 3301 1.285023 CTTCAGTGCCTGCAGTTGC 59.715 57.895 13.81 10.56 42.50 4.17
2997 3302 1.521450 CCCTTCAGTGCCTGCAGTTG 61.521 60.000 13.81 5.75 0.00 3.16
2998 3303 1.228367 CCCTTCAGTGCCTGCAGTT 60.228 57.895 13.81 0.00 0.00 3.16
2999 3304 2.121992 CTCCCTTCAGTGCCTGCAGT 62.122 60.000 13.81 0.00 0.00 4.40
3000 3305 1.376942 CTCCCTTCAGTGCCTGCAG 60.377 63.158 6.78 6.78 0.00 4.41
3001 3306 1.842920 TCTCCCTTCAGTGCCTGCA 60.843 57.895 0.00 0.00 0.00 4.41
3002 3307 1.376553 GTCTCCCTTCAGTGCCTGC 60.377 63.158 0.00 0.00 0.00 4.85
3003 3308 1.197430 AGGTCTCCCTTCAGTGCCTG 61.197 60.000 0.00 0.00 38.13 4.85
3004 3309 0.907230 GAGGTCTCCCTTCAGTGCCT 60.907 60.000 0.00 0.00 42.86 4.75
3005 3310 1.599576 GAGGTCTCCCTTCAGTGCC 59.400 63.158 0.00 0.00 42.86 5.01
3006 3311 1.216710 CGAGGTCTCCCTTCAGTGC 59.783 63.158 0.00 0.00 42.86 4.40
3007 3312 0.814457 CTCGAGGTCTCCCTTCAGTG 59.186 60.000 3.91 0.00 42.86 3.66
3008 3313 0.406361 ACTCGAGGTCTCCCTTCAGT 59.594 55.000 18.41 0.00 42.86 3.41
3009 3314 1.474879 GAACTCGAGGTCTCCCTTCAG 59.525 57.143 23.36 0.00 42.86 3.02
3010 3315 1.203013 TGAACTCGAGGTCTCCCTTCA 60.203 52.381 29.54 18.11 42.86 3.02
3011 3316 1.474879 CTGAACTCGAGGTCTCCCTTC 59.525 57.143 29.54 15.84 42.86 3.46
3012 3317 1.551452 CTGAACTCGAGGTCTCCCTT 58.449 55.000 29.54 6.97 42.86 3.95
3013 3318 0.968393 GCTGAACTCGAGGTCTCCCT 60.968 60.000 29.54 0.00 46.66 4.20
3014 3319 0.968393 AGCTGAACTCGAGGTCTCCC 60.968 60.000 29.54 17.50 0.00 4.30
3015 3320 0.892063 AAGCTGAACTCGAGGTCTCC 59.108 55.000 29.54 19.82 0.00 3.71
3016 3321 1.542030 TGAAGCTGAACTCGAGGTCTC 59.458 52.381 29.54 19.25 0.00 3.36
3017 3322 1.621992 TGAAGCTGAACTCGAGGTCT 58.378 50.000 29.54 10.93 0.00 3.85
3018 3323 2.663826 ATGAAGCTGAACTCGAGGTC 57.336 50.000 23.85 23.85 0.00 3.85


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

AutoCloner maintained by Alex Coulton.