Multiple sequence alignment - TraesCS4D01G097900

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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 TraesCS4D01G097900 chr4D 100.000 6659 0 0 1 6659 74375710 74369052 0.000000e+00 12297
1 TraesCS4D01G097900 chr4B 94.965 4131 125 26 2582 6659 106858328 106854228 0.000000e+00 6399
2 TraesCS4D01G097900 chr4B 93.050 1856 90 25 1 1848 106860926 106859102 0.000000e+00 2676
3 TraesCS4D01G097900 chr4B 94.371 302 16 1 1988 2288 106858886 106858585 4.700000e-126 462
4 TraesCS4D01G097900 chr4B 96.324 136 4 1 2287 2421 106858461 106858326 8.690000e-54 222
5 TraesCS4D01G097900 chr4B 90.789 76 7 0 3213 3288 637342429 637342504 1.180000e-17 102
6 TraesCS4D01G097900 chr4A 92.096 3277 157 45 3199 6423 513290539 513293765 0.000000e+00 4523
7 TraesCS4D01G097900 chr4A 94.819 1795 60 15 1 1786 513287348 513289118 0.000000e+00 2769
8 TraesCS4D01G097900 chr4A 90.077 1552 99 23 3399 4922 644494487 644492963 0.000000e+00 1962
9 TraesCS4D01G097900 chr4A 89.418 567 48 6 2582 3142 513289838 513290398 0.000000e+00 704
10 TraesCS4D01G097900 chr4A 85.819 684 45 23 1789 2421 513289158 513289840 0.000000e+00 678
11 TraesCS4D01G097900 chr4A 96.111 180 6 1 2418 2597 582529976 582530154 6.530000e-75 292
12 TraesCS4D01G097900 chr7A 90.374 696 35 10 3399 4074 685860774 685860091 0.000000e+00 885
13 TraesCS4D01G097900 chr7A 92.647 204 14 1 4115 4318 685854918 685854716 6.530000e-75 292
14 TraesCS4D01G097900 chr7A 95.187 187 3 3 2398 2583 320981156 320981337 2.350000e-74 291
15 TraesCS4D01G097900 chr7A 92.462 199 8 3 4903 5094 685854715 685854517 1.830000e-70 278
16 TraesCS4D01G097900 chr7A 85.321 109 16 0 3088 3196 734625410 734625302 5.460000e-21 113
17 TraesCS4D01G097900 chr7A 89.655 87 9 0 1041 1127 708668687 708668601 1.960000e-20 111
18 TraesCS4D01G097900 chr7D 84.862 436 44 14 4315 4746 188348306 188348723 2.870000e-113 420
19 TraesCS4D01G097900 chr7D 94.792 192 7 3 2400 2589 459391905 459392095 5.050000e-76 296
20 TraesCS4D01G097900 chr7D 85.833 120 15 2 1041 1159 615907052 615906934 7.010000e-25 126
21 TraesCS4D01G097900 chr1B 89.933 298 25 4 3247 3543 119574441 119574148 4.870000e-101 379
22 TraesCS4D01G097900 chr2D 98.810 168 2 0 2416 2583 426427798 426427965 3.900000e-77 300
23 TraesCS4D01G097900 chr2D 97.076 171 5 0 2416 2586 192752401 192752571 8.450000e-74 289
24 TraesCS4D01G097900 chr2D 88.172 93 9 2 3198 3288 620318414 620318506 7.060000e-20 110
25 TraesCS4D01G097900 chr2A 98.225 169 3 0 2419 2587 746757154 746756986 5.050000e-76 296
26 TraesCS4D01G097900 chr5A 97.126 174 4 1 2410 2583 290391869 290391697 6.530000e-75 292
27 TraesCS4D01G097900 chr7B 93.229 192 10 3 2400 2589 481302172 481302362 5.080000e-71 279
28 TraesCS4D01G097900 chr7B 84.167 120 17 2 1041 1159 708955029 708954911 1.520000e-21 115
29 TraesCS4D01G097900 chr7B 88.172 93 9 2 3198 3288 681743975 681743883 7.060000e-20 110
30 TraesCS4D01G097900 chr3A 93.194 191 11 2 2393 2583 334179795 334179983 5.080000e-71 279
31 TraesCS4D01G097900 chr1A 83.019 318 38 12 6291 6598 339904878 339904567 2.370000e-69 274
32 TraesCS4D01G097900 chr6D 86.809 235 27 3 3198 3430 433116432 433116664 6.620000e-65 259
33 TraesCS4D01G097900 chr3D 85.345 116 17 0 5276 5391 516879587 516879472 3.260000e-23 121
34 TraesCS4D01G097900 chr3D 85.321 109 16 0 3088 3196 35687821 35687713 5.460000e-21 113
35 TraesCS4D01G097900 chr3D 85.321 109 16 0 3088 3196 35701221 35701329 5.460000e-21 113
36 TraesCS4D01G097900 chr5D 87.629 97 11 1 3198 3293 503800082 503800178 1.960000e-20 111
37 TraesCS4D01G097900 chr3B 88.172 93 9 2 3198 3288 299743955 299744047 7.060000e-20 110


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 TraesCS4D01G097900 chr4D 74369052 74375710 6658 True 12297.00 12297 100.0000 1 6659 1 chr4D.!!$R1 6658
1 TraesCS4D01G097900 chr4B 106854228 106860926 6698 True 2439.75 6399 94.6775 1 6659 4 chr4B.!!$R1 6658
2 TraesCS4D01G097900 chr4A 513287348 513293765 6417 False 2168.50 4523 90.5380 1 6423 4 chr4A.!!$F2 6422
3 TraesCS4D01G097900 chr4A 644492963 644494487 1524 True 1962.00 1962 90.0770 3399 4922 1 chr4A.!!$R1 1523
4 TraesCS4D01G097900 chr7A 685860091 685860774 683 True 885.00 885 90.3740 3399 4074 1 chr7A.!!$R1 675

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
212 213 3.137176 CCCATTCAATTCAGGAGCCTAGA 59.863 47.826 0.00 0.00 0.00 2.43 F
1512 1526 1.048601 TTTCTTGCTCTCGTGGGTCT 58.951 50.000 0.00 0.00 0.00 3.85 F
1652 1667 0.237235 TCGCATCTTTCCGTTGCAAC 59.763 50.000 19.89 19.89 38.05 4.17 F
1941 2076 0.457035 TATCGGTGGCTCGTTGGTAC 59.543 55.000 1.40 0.00 0.00 3.34 F
2944 3259 0.376152 GCAGACACGCATGGAGATTG 59.624 55.000 0.00 0.00 0.00 2.67 F
2952 3267 1.987770 CGCATGGAGATTGTTTTGTGC 59.012 47.619 0.00 0.00 0.00 4.57 F
3864 4288 2.288518 GGATCTCTCACCGTATGCCTTC 60.289 54.545 0.00 0.00 0.00 3.46 F
5410 5907 0.322456 TCCCGAGTCTGGCCATTTTG 60.322 55.000 5.51 0.00 0.00 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1522 1536 0.179234 TTTCCAGCGTCAACTCCACA 59.821 50.000 0.00 0.0 0.00 4.17 R
2519 2832 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.0 0.00 4.26 R
2933 3248 3.308438 AGCACAAAACAATCTCCATGC 57.692 42.857 0.00 0.0 0.00 4.06 R
3907 4372 3.956199 TCAGATGGAAAATGGGATTCAGC 59.044 43.478 0.00 0.0 0.00 4.26 R
4908 5387 1.222936 CCAGGCCACTTAGGAGCAG 59.777 63.158 5.01 0.0 41.22 4.24 R
5194 5686 7.876936 ATGAGAAGTAACAGCATCAATGAAT 57.123 32.000 0.00 0.0 0.00 2.57 R
5517 6014 0.248215 GAACCTCGATGGCAAATGCG 60.248 55.000 0.00 0.0 43.26 4.73 R
6546 7067 1.135083 AGCCACAGCACGTACTCATAC 60.135 52.381 0.00 0.0 43.56 2.39 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
147 148 5.054390 TCCGTGACATTCCAATAAAAAGC 57.946 39.130 0.00 0.00 0.00 3.51
200 201 5.321927 AGTACGGAAAAGACCCATTCAATT 58.678 37.500 0.00 0.00 0.00 2.32
212 213 3.137176 CCCATTCAATTCAGGAGCCTAGA 59.863 47.826 0.00 0.00 0.00 2.43
283 284 7.279313 AGCCAAATTTCATGATATTGAAAGTGC 59.721 33.333 11.51 8.26 45.83 4.40
558 560 3.264104 CTCCCGATGTTTTAACCGCTTA 58.736 45.455 0.00 0.00 0.00 3.09
681 685 5.989168 TCCTATGAACGTTTGCACCATATAG 59.011 40.000 0.46 0.85 0.00 1.31
723 727 5.519566 TGCACAAAACAATCTTAGCACAAAG 59.480 36.000 0.00 0.00 0.00 2.77
754 762 8.517878 CAACAATAATGACAAGAGGAATCAAGT 58.482 33.333 0.00 0.00 0.00 3.16
760 769 6.918067 TGACAAGAGGAATCAAGTTCTCTA 57.082 37.500 0.00 0.00 37.01 2.43
761 770 7.487822 TGACAAGAGGAATCAAGTTCTCTAT 57.512 36.000 0.00 0.00 37.01 1.98
764 773 9.877178 GACAAGAGGAATCAAGTTCTCTATAAA 57.123 33.333 0.00 0.00 37.01 1.40
1309 1323 1.359459 GCGGAATCGAGCGGAGTTTT 61.359 55.000 0.00 0.00 39.00 2.43
1364 1378 3.391296 GAGGGATCTGCCTGTGGTAATAA 59.609 47.826 0.00 0.00 36.66 1.40
1365 1379 3.785887 AGGGATCTGCCTGTGGTAATAAA 59.214 43.478 0.00 0.00 36.66 1.40
1366 1380 4.416848 AGGGATCTGCCTGTGGTAATAAAT 59.583 41.667 0.00 0.00 36.66 1.40
1367 1381 5.610982 AGGGATCTGCCTGTGGTAATAAATA 59.389 40.000 0.00 0.00 36.66 1.40
1368 1382 6.102615 AGGGATCTGCCTGTGGTAATAAATAA 59.897 38.462 0.00 0.00 36.66 1.40
1512 1526 1.048601 TTTCTTGCTCTCGTGGGTCT 58.951 50.000 0.00 0.00 0.00 3.85
1522 1536 0.469331 TCGTGGGTCTGAACAGAGGT 60.469 55.000 4.67 0.00 38.27 3.85
1539 1553 1.069090 GTGTGGAGTTGACGCTGGA 59.931 57.895 0.00 0.00 0.00 3.86
1544 1558 1.946768 TGGAGTTGACGCTGGAAAAAG 59.053 47.619 0.00 0.00 0.00 2.27
1545 1559 1.266989 GGAGTTGACGCTGGAAAAAGG 59.733 52.381 0.00 0.00 0.00 3.11
1597 1612 1.448893 GGTAGATTTGGCCGCGTGA 60.449 57.895 4.92 0.00 0.00 4.35
1652 1667 0.237235 TCGCATCTTTCCGTTGCAAC 59.763 50.000 19.89 19.89 38.05 4.17
1679 1694 5.495926 TGGCTTGATTCTCTTCTCTTTCT 57.504 39.130 0.00 0.00 0.00 2.52
1688 1703 1.151668 CTTCTCTTTCTGCGGTGTGG 58.848 55.000 0.00 0.00 0.00 4.17
1759 1774 1.819288 TGTGCTGTTTTGGTCCGAAAA 59.181 42.857 5.81 1.04 0.00 2.29
1801 1853 4.974275 CCATGATCTCGCATTTGTTTCATC 59.026 41.667 0.00 0.00 0.00 2.92
1814 1866 7.650903 GCATTTGTTTCATCTCTTGAGTTTCTT 59.349 33.333 0.00 0.00 35.27 2.52
1834 1886 3.959535 TTTGTTGGAATTGGGATGAGC 57.040 42.857 0.00 0.00 0.00 4.26
1851 1903 2.651361 CGAGTCTGCGGAAGTGGT 59.349 61.111 0.00 0.00 0.00 4.16
1880 1938 3.106986 GCTAGGATGGCCTTCCGCA 62.107 63.158 27.28 19.45 43.90 5.69
1883 1941 1.271840 TAGGATGGCCTTCCGCAGTT 61.272 55.000 27.28 14.99 43.90 3.16
1885 1943 3.056313 GATGGCCTTCCGCAGTTGC 62.056 63.158 3.32 0.00 40.31 4.17
1890 1948 1.600636 CCTTCCGCAGTTGCCTTCA 60.601 57.895 0.00 0.00 37.91 3.02
1893 1951 2.083774 CTTCCGCAGTTGCCTTCAATA 58.916 47.619 0.00 0.00 37.91 1.90
1900 1958 4.415735 GCAGTTGCCTTCAATAGCTAAAC 58.584 43.478 0.00 0.00 34.29 2.01
1901 1959 4.651994 CAGTTGCCTTCAATAGCTAAACG 58.348 43.478 0.00 0.00 34.29 3.60
1916 2051 2.128771 AAACGTGCTTATGGATGGCT 57.871 45.000 0.00 0.00 0.00 4.75
1938 2073 0.937304 CATTATCGGTGGCTCGTTGG 59.063 55.000 1.40 0.00 0.00 3.77
1939 2074 0.539986 ATTATCGGTGGCTCGTTGGT 59.460 50.000 1.40 0.00 0.00 3.67
1941 2076 0.457035 TATCGGTGGCTCGTTGGTAC 59.543 55.000 1.40 0.00 0.00 3.34
2004 2172 1.281867 TGCCACTGATCTTTACCTGGG 59.718 52.381 0.00 0.00 0.00 4.45
2007 2175 3.610911 CCACTGATCTTTACCTGGGTTC 58.389 50.000 0.00 0.00 0.00 3.62
2155 2327 8.731275 TCTGTTAAAGAGACAATGACTCAAAA 57.269 30.769 14.42 3.59 36.91 2.44
2228 2407 8.771920 TGTGTTTTATATCGTCTTGTTGATCT 57.228 30.769 0.00 0.00 0.00 2.75
2259 2438 5.959618 ATTTAGTTTGTTGGGTACTCAGC 57.040 39.130 2.03 2.03 0.00 4.26
2384 2697 4.408182 AGTCTGACCAATGCACCTATAC 57.592 45.455 3.76 0.00 0.00 1.47
2428 2741 5.793030 AATCATACTTTCTACTCCCTCCG 57.207 43.478 0.00 0.00 0.00 4.63
2429 2742 4.246712 TCATACTTTCTACTCCCTCCGT 57.753 45.455 0.00 0.00 0.00 4.69
2430 2743 4.607239 TCATACTTTCTACTCCCTCCGTT 58.393 43.478 0.00 0.00 0.00 4.44
2431 2744 4.643784 TCATACTTTCTACTCCCTCCGTTC 59.356 45.833 0.00 0.00 0.00 3.95
2432 2745 2.177734 ACTTTCTACTCCCTCCGTTCC 58.822 52.381 0.00 0.00 0.00 3.62
2433 2746 2.225318 ACTTTCTACTCCCTCCGTTCCT 60.225 50.000 0.00 0.00 0.00 3.36
2434 2747 3.011032 ACTTTCTACTCCCTCCGTTCCTA 59.989 47.826 0.00 0.00 0.00 2.94
2435 2748 3.744940 TTCTACTCCCTCCGTTCCTAA 57.255 47.619 0.00 0.00 0.00 2.69
2436 2749 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
2437 2750 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
2438 2751 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
2439 2752 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
2440 2753 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
2441 2754 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2442 2755 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2443 2756 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2444 2757 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2445 2758 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2446 2759 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2447 2760 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2448 2761 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
2449 2762 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
2477 2790 8.873215 AGATTTCAAATAGACTACCACATACG 57.127 34.615 0.00 0.00 0.00 3.06
2478 2791 7.926555 AGATTTCAAATAGACTACCACATACGG 59.073 37.037 0.00 0.00 0.00 4.02
2479 2792 6.778834 TTCAAATAGACTACCACATACGGA 57.221 37.500 0.00 0.00 0.00 4.69
2480 2793 6.971726 TCAAATAGACTACCACATACGGAT 57.028 37.500 0.00 0.00 0.00 4.18
2481 2794 6.745116 TCAAATAGACTACCACATACGGATG 58.255 40.000 5.94 5.94 39.16 3.51
2483 2796 7.503230 TCAAATAGACTACCACATACGGATGTA 59.497 37.037 14.23 0.00 44.82 2.29
2484 2797 8.304596 CAAATAGACTACCACATACGGATGTAT 58.695 37.037 14.23 7.46 44.82 2.29
2485 2798 9.524496 AAATAGACTACCACATACGGATGTATA 57.476 33.333 14.23 8.27 44.82 1.47
2486 2799 9.696572 AATAGACTACCACATACGGATGTATAT 57.303 33.333 14.23 4.37 44.82 0.86
2488 2801 8.734218 AGACTACCACATACGGATGTATATAG 57.266 38.462 14.23 16.35 44.82 1.31
2489 2802 8.546322 AGACTACCACATACGGATGTATATAGA 58.454 37.037 22.62 5.04 44.82 1.98
2490 2803 8.503458 ACTACCACATACGGATGTATATAGAC 57.497 38.462 22.62 0.00 44.82 2.59
2491 2804 8.105197 ACTACCACATACGGATGTATATAGACA 58.895 37.037 22.62 2.07 44.82 3.41
2492 2805 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
2494 2807 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
2523 2836 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
2524 2837 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
2525 2838 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
2526 2839 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
2527 2840 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
2528 2841 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
2529 2842 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2530 2843 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2531 2844 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2532 2845 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
2533 2846 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
2534 2847 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
2535 2848 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
2536 2849 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
2537 2850 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
2538 2851 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
2539 2852 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
2540 2853 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
2541 2854 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
2542 2855 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
2543 2856 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
2544 2857 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
2545 2858 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
2546 2859 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
2547 2860 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
2548 2861 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
2549 2862 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
2550 2863 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
2551 2864 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
2552 2865 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
2553 2866 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
2554 2867 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
2555 2868 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
2556 2869 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
2557 2870 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
2558 2871 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
2559 2872 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
2560 2873 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
2561 2874 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
2577 2890 9.454859 AGAAAGACAAATATTTAGGAACAGAGG 57.545 33.333 0.00 0.00 0.00 3.69
2578 2891 9.449719 GAAAGACAAATATTTAGGAACAGAGGA 57.550 33.333 0.00 0.00 0.00 3.71
2579 2892 9.807921 AAAGACAAATATTTAGGAACAGAGGAA 57.192 29.630 0.00 0.00 0.00 3.36
2580 2893 9.454859 AAGACAAATATTTAGGAACAGAGGAAG 57.545 33.333 0.00 0.00 0.00 3.46
2581 2894 8.606830 AGACAAATATTTAGGAACAGAGGAAGT 58.393 33.333 0.00 0.00 0.00 3.01
2582 2895 9.886132 GACAAATATTTAGGAACAGAGGAAGTA 57.114 33.333 0.00 0.00 0.00 2.24
2583 2896 9.668497 ACAAATATTTAGGAACAGAGGAAGTAC 57.332 33.333 0.00 0.00 0.00 2.73
2696 3009 5.854010 AGGCATGATTTCTAGTAAGTCGA 57.146 39.130 0.00 0.00 0.00 4.20
2908 3223 0.729116 CCTCACATTGGTCGTGATGC 59.271 55.000 0.00 0.00 42.27 3.91
2917 3232 1.384222 GGTCGTGATGCCCATTTCCC 61.384 60.000 0.00 0.00 0.00 3.97
2933 3248 4.742201 CCCAGGGACGCAGACACG 62.742 72.222 0.00 0.00 39.50 4.49
2936 3251 3.695606 AGGGACGCAGACACGCAT 61.696 61.111 0.00 0.00 36.19 4.73
2938 3253 3.490759 GGACGCAGACACGCATGG 61.491 66.667 0.00 0.00 36.19 3.66
2944 3259 0.376152 GCAGACACGCATGGAGATTG 59.624 55.000 0.00 0.00 0.00 2.67
2952 3267 1.987770 CGCATGGAGATTGTTTTGTGC 59.012 47.619 0.00 0.00 0.00 4.57
3035 3350 4.943705 GTCAGATGATAGTGCAGGGAAAAA 59.056 41.667 0.00 0.00 0.00 1.94
3036 3351 5.065731 GTCAGATGATAGTGCAGGGAAAAAG 59.934 44.000 0.00 0.00 0.00 2.27
3185 3505 6.173339 TGTTTGCTGTTCTTAGGGAATAGAG 58.827 40.000 6.36 0.00 43.10 2.43
3640 4064 5.242795 ACTGAGCCAGGTATTTACAACTT 57.757 39.130 7.06 0.00 35.51 2.66
3864 4288 2.288518 GGATCTCTCACCGTATGCCTTC 60.289 54.545 0.00 0.00 0.00 3.46
3907 4372 8.677300 TCTTGAGATTTCTTTATGGGATTTTCG 58.323 33.333 0.00 0.00 0.00 3.46
3964 4429 3.951663 ACAGGTTATGAGTGTAAAGGCC 58.048 45.455 0.00 0.00 0.00 5.19
4106 4573 9.965824 ACAAGGTAAATATTTCAGTTTCTGTTG 57.034 29.630 3.39 0.78 32.61 3.33
4119 4586 5.630680 CAGTTTCTGTTGTTATTGATGCCAC 59.369 40.000 0.00 0.00 0.00 5.01
4120 4587 5.536161 AGTTTCTGTTGTTATTGATGCCACT 59.464 36.000 0.00 0.00 0.00 4.00
4243 4711 8.956446 TCACATCACCCAAGAGAATATAGATA 57.044 34.615 0.00 0.00 0.00 1.98
4407 4883 9.591792 TCTCTCTCATTATGTTGATTTACAGTG 57.408 33.333 0.00 0.00 0.00 3.66
4410 4886 8.722480 TCTCATTATGTTGATTTACAGTGGAG 57.278 34.615 0.00 0.00 0.00 3.86
4419 4895 7.710907 TGTTGATTTACAGTGGAGTAGCATATC 59.289 37.037 0.00 0.00 0.00 1.63
4431 4907 8.521170 TGGAGTAGCATATCCACTATATGTAC 57.479 38.462 6.81 7.67 46.35 2.90
4451 4927 2.821969 ACTAGCATTTGGTCCTTGCAAG 59.178 45.455 19.93 19.93 38.84 4.01
4835 5313 5.710099 CCTTATTGCCAACTGAACTTCCTTA 59.290 40.000 0.00 0.00 0.00 2.69
4908 5387 9.928236 CTTTTATGTCTTGCTCTTCTTATTAGC 57.072 33.333 0.00 0.00 36.77 3.09
4972 5451 3.977427 TCACGAATCACGATGATAAGGG 58.023 45.455 0.00 0.00 45.77 3.95
5221 5713 7.785033 TCATTGATGCTGTTACTTCTCATAGA 58.215 34.615 0.00 0.00 0.00 1.98
5222 5714 8.260114 TCATTGATGCTGTTACTTCTCATAGAA 58.740 33.333 0.00 0.00 32.50 2.10
5224 5716 8.484641 TTGATGCTGTTACTTCTCATAGAAAG 57.515 34.615 0.00 0.00 33.19 2.62
5226 5718 8.481314 TGATGCTGTTACTTCTCATAGAAAGAT 58.519 33.333 0.00 0.00 33.19 2.40
5228 5720 9.979578 ATGCTGTTACTTCTCATAGAAAGATAG 57.020 33.333 0.00 0.00 33.19 2.08
5229 5721 7.923344 TGCTGTTACTTCTCATAGAAAGATAGC 59.077 37.037 0.00 0.00 33.19 2.97
5230 5722 8.141268 GCTGTTACTTCTCATAGAAAGATAGCT 58.859 37.037 0.00 0.00 33.19 3.32
5410 5907 0.322456 TCCCGAGTCTGGCCATTTTG 60.322 55.000 5.51 0.00 0.00 2.44
5418 5915 0.526954 CTGGCCATTTTGCGCATCTC 60.527 55.000 12.75 0.00 0.00 2.75
5420 5917 0.526954 GGCCATTTTGCGCATCTCTG 60.527 55.000 12.75 6.86 0.00 3.35
5430 5927 3.398406 TGCGCATCTCTGTTAGAAACAA 58.602 40.909 5.66 0.00 41.61 2.83
5517 6014 2.935201 CTCAAAGCATGCTAGTCAGACC 59.065 50.000 23.00 0.00 0.00 3.85
5663 6160 5.950023 AGACTTGAATATTGCCTGATGGAT 58.050 37.500 0.00 0.00 34.57 3.41
5673 6170 3.836146 TGCCTGATGGATATTCCTTTGG 58.164 45.455 0.00 0.00 37.46 3.28
5675 6172 3.753193 GCCTGATGGATATTCCTTTGGCT 60.753 47.826 14.41 0.00 38.86 4.75
5683 6180 4.520492 GGATATTCCTTTGGCTACATGTGG 59.480 45.833 9.11 6.75 32.53 4.17
5827 6324 8.894768 ACAAGTTGATAGTATTATCCTTGCTC 57.105 34.615 10.54 0.57 38.16 4.26
5828 6325 7.934120 ACAAGTTGATAGTATTATCCTTGCTCC 59.066 37.037 10.54 0.00 38.16 4.70
5829 6326 7.863901 AGTTGATAGTATTATCCTTGCTCCT 57.136 36.000 3.06 0.00 35.76 3.69
5830 6327 8.268878 AGTTGATAGTATTATCCTTGCTCCTT 57.731 34.615 3.06 0.00 35.76 3.36
5831 6328 8.371699 AGTTGATAGTATTATCCTTGCTCCTTC 58.628 37.037 3.06 0.00 35.76 3.46
5832 6329 7.246171 TGATAGTATTATCCTTGCTCCTTCC 57.754 40.000 3.06 0.00 35.76 3.46
5833 6330 7.019388 TGATAGTATTATCCTTGCTCCTTCCT 58.981 38.462 3.06 0.00 35.76 3.36
5834 6331 5.559148 AGTATTATCCTTGCTCCTTCCTG 57.441 43.478 0.00 0.00 0.00 3.86
5835 6332 3.872459 ATTATCCTTGCTCCTTCCTGG 57.128 47.619 0.00 0.00 37.10 4.45
5836 6333 2.568546 TATCCTTGCTCCTTCCTGGA 57.431 50.000 0.00 0.00 43.86 3.86
5917 6429 3.870559 AGGGATGGTTACTCGGGAATAT 58.129 45.455 0.00 0.00 0.00 1.28
6015 6534 8.140628 TCATTTTTAGACAGTAAATGCTGCAAA 58.859 29.630 6.36 0.00 39.96 3.68
6228 6747 4.851558 GGTCACTGCGTTATGACATTTTTC 59.148 41.667 14.27 0.00 45.83 2.29
6277 6798 7.687005 TTCAGTTAATTTGGTTAAAGCAACG 57.313 32.000 0.00 0.00 38.09 4.10
6289 6810 2.177531 GCAACGAGCTGTGCATGG 59.822 61.111 8.40 0.00 41.15 3.66
6361 6882 8.761575 AAATCAATGTTTTTACAGCAGGTATG 57.238 30.769 0.00 0.00 0.00 2.39
6456 6977 5.438761 AGAAGTGTGATGTTACAAAAGGC 57.561 39.130 0.00 0.00 31.36 4.35
6524 7045 9.444600 AACAACAGAATTTATGTATCGTTAGGT 57.555 29.630 0.00 0.00 0.00 3.08
6546 7067 3.866651 ACTGATGCAGCAGTAGGTAAAG 58.133 45.455 34.69 8.20 46.67 1.85
6555 7076 5.978322 GCAGCAGTAGGTAAAGTATGAGTAC 59.022 44.000 0.00 0.00 0.00 2.73
6557 7078 5.884792 AGCAGTAGGTAAAGTATGAGTACGT 59.115 40.000 0.00 0.00 35.92 3.57
6648 7169 9.703892 AGTGAGCATATTGAATAATGAGTAGTC 57.296 33.333 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 6.209391 GCTATATATGGCAATTTGGTTGAGGT 59.791 38.462 15.56 0.00 40.37 3.85
128 129 7.656707 AACATGCTTTTTATTGGAATGTCAC 57.343 32.000 0.00 0.00 29.81 3.67
283 284 9.810545 TTTTTAAATGTTTAGGTTCCTCAACAG 57.189 29.630 19.00 0.00 34.84 3.16
531 533 4.334481 CGGTTAAAACATCGGGAGCTAATT 59.666 41.667 0.00 0.00 0.00 1.40
532 534 3.875134 CGGTTAAAACATCGGGAGCTAAT 59.125 43.478 0.00 0.00 0.00 1.73
533 535 3.264104 CGGTTAAAACATCGGGAGCTAA 58.736 45.455 0.00 0.00 0.00 3.09
558 560 7.572523 ATCATTATGGATTTGATTGACACGT 57.427 32.000 0.00 0.00 0.00 4.49
673 677 8.157476 AGTTTTGAGTGTTGAGAACTATATGGT 58.843 33.333 0.00 0.00 0.00 3.55
681 685 4.098416 GTGCAGTTTTGAGTGTTGAGAAC 58.902 43.478 0.00 0.00 0.00 3.01
723 727 6.173339 TCCTCTTGTCATTATTGTTGGAGTC 58.827 40.000 0.00 0.00 0.00 3.36
761 770 9.268282 AGTTAGGAGTCCTAATCAGTTGATTTA 57.732 33.333 29.94 4.75 46.16 1.40
764 773 8.840200 TTAGTTAGGAGTCCTAATCAGTTGAT 57.160 34.615 29.94 13.58 46.16 2.57
769 778 9.720769 TTTTGTTTAGTTAGGAGTCCTAATCAG 57.279 33.333 29.94 0.00 46.16 2.90
1155 1169 3.050275 GAGTGGCGCAACTCACCC 61.050 66.667 34.89 12.63 44.98 4.61
1309 1323 2.999355 GCAAAGAACAGCAACCAAAACA 59.001 40.909 0.00 0.00 0.00 2.83
1374 1388 2.802414 CGCGCTGCTCCTTTTTGC 60.802 61.111 5.56 0.00 0.00 3.68
1512 1526 2.115427 TCAACTCCACACCTCTGTTCA 58.885 47.619 0.00 0.00 0.00 3.18
1522 1536 0.179234 TTTCCAGCGTCAACTCCACA 59.821 50.000 0.00 0.00 0.00 4.17
1539 1553 4.224762 TGTCCGAATTTTACCCCCTTTTT 58.775 39.130 0.00 0.00 0.00 1.94
1544 1558 1.683938 CCCTGTCCGAATTTTACCCCC 60.684 57.143 0.00 0.00 0.00 5.40
1545 1559 1.683938 CCCCTGTCCGAATTTTACCCC 60.684 57.143 0.00 0.00 0.00 4.95
1597 1612 1.148027 TCTGGACTCAACTGGACTCCT 59.852 52.381 0.00 0.00 31.71 3.69
1652 1667 4.128643 GAGAAGAGAATCAAGCCATCCAG 58.871 47.826 0.00 0.00 37.82 3.86
1679 1694 1.444119 GCAGTCTTTTCCACACCGCA 61.444 55.000 0.00 0.00 0.00 5.69
1688 1703 6.346040 CGAAACCAAATGATTGCAGTCTTTTC 60.346 38.462 16.88 11.11 35.10 2.29
1759 1774 4.387026 TGGACTGGATTTTCATGGAAGT 57.613 40.909 0.00 0.00 0.00 3.01
1801 1853 7.223387 CCAATTCCAACAAAAGAAACTCAAGAG 59.777 37.037 0.00 0.00 0.00 2.85
1814 1866 2.230992 CGCTCATCCCAATTCCAACAAA 59.769 45.455 0.00 0.00 0.00 2.83
1834 1886 0.600255 AAACCACTTCCGCAGACTCG 60.600 55.000 0.00 0.00 0.00 4.18
1883 1941 2.418628 GCACGTTTAGCTATTGAAGGCA 59.581 45.455 0.00 0.00 0.00 4.75
1885 1943 4.946784 AAGCACGTTTAGCTATTGAAGG 57.053 40.909 0.00 0.00 42.53 3.46
1890 1948 5.470098 CCATCCATAAGCACGTTTAGCTATT 59.530 40.000 0.00 0.00 42.53 1.73
1893 1951 3.206150 CCATCCATAAGCACGTTTAGCT 58.794 45.455 0.00 0.00 45.97 3.32
1916 2051 0.828022 ACGAGCCACCGATAATGGAA 59.172 50.000 0.00 0.00 39.87 3.53
2004 2172 6.279882 TGAATCAATCCAACAAAACAGGAAC 58.720 36.000 0.00 0.00 34.62 3.62
2007 2175 7.441760 TGATTTGAATCAATCCAACAAAACAGG 59.558 33.333 4.02 0.00 42.11 4.00
2155 2327 7.169158 TCCTTATCATTTTCGAAAAGGCATT 57.831 32.000 25.97 16.68 34.72 3.56
2228 2407 4.279671 CCCAACAAACTAAATAGCCACACA 59.720 41.667 0.00 0.00 0.00 3.72
2259 2438 9.305925 GTAAGCTGGGAAATTGATCATTTTAAG 57.694 33.333 13.97 12.65 35.02 1.85
2313 2618 4.142600 GCAGACTTCGTTGCAAGGAATAAT 60.143 41.667 28.93 19.49 40.02 1.28
2416 2729 3.744940 TTTAGGAACGGAGGGAGTAGA 57.255 47.619 0.00 0.00 0.00 2.59
2421 2734 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2422 2735 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2423 2736 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
2451 2764 8.969267 CGTATGTGGTAGTCTATTTGAAATCTC 58.031 37.037 0.00 0.00 0.00 2.75
2452 2765 7.926555 CCGTATGTGGTAGTCTATTTGAAATCT 59.073 37.037 0.00 0.00 0.00 2.40
2453 2766 7.924412 TCCGTATGTGGTAGTCTATTTGAAATC 59.076 37.037 0.00 0.00 0.00 2.17
2454 2767 7.788026 TCCGTATGTGGTAGTCTATTTGAAAT 58.212 34.615 0.00 0.00 0.00 2.17
2455 2768 7.172868 TCCGTATGTGGTAGTCTATTTGAAA 57.827 36.000 0.00 0.00 0.00 2.69
2456 2769 6.778834 TCCGTATGTGGTAGTCTATTTGAA 57.221 37.500 0.00 0.00 0.00 2.69
2457 2770 6.322969 ACATCCGTATGTGGTAGTCTATTTGA 59.677 38.462 0.00 0.00 44.79 2.69
2458 2771 6.513180 ACATCCGTATGTGGTAGTCTATTTG 58.487 40.000 0.00 0.00 44.79 2.32
2459 2772 6.726490 ACATCCGTATGTGGTAGTCTATTT 57.274 37.500 0.00 0.00 44.79 1.40
2460 2773 9.696572 ATATACATCCGTATGTGGTAGTCTATT 57.303 33.333 3.56 0.00 45.99 1.73
2462 2775 9.828039 CTATATACATCCGTATGTGGTAGTCTA 57.172 37.037 3.56 0.00 45.99 2.59
2463 2776 8.546322 TCTATATACATCCGTATGTGGTAGTCT 58.454 37.037 3.56 0.00 45.99 3.24
2464 2777 8.610896 GTCTATATACATCCGTATGTGGTAGTC 58.389 40.741 3.56 0.00 45.99 2.59
2465 2778 8.105197 TGTCTATATACATCCGTATGTGGTAGT 58.895 37.037 3.56 0.00 45.99 2.73
2466 2779 8.502105 TGTCTATATACATCCGTATGTGGTAG 57.498 38.462 3.56 3.93 45.99 3.18
2468 2781 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
2501 2814 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
2502 2815 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
2503 2816 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
2504 2817 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
2505 2818 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2506 2819 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
2507 2820 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
2508 2821 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
2509 2822 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
2510 2823 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
2511 2824 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
2512 2825 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
2513 2826 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
2514 2827 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
2515 2828 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
2516 2829 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
2517 2830 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
2518 2831 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
2519 2832 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
2520 2833 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
2521 2834 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
2522 2835 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
2523 2836 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
2524 2837 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
2525 2838 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
2527 2840 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
2528 2841 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
2529 2842 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
2530 2843 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
2531 2844 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
2532 2845 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
2533 2846 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
2534 2847 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
2535 2848 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
2551 2864 9.454859 CCTCTGTTCCTAAATATTTGTCTTTCT 57.545 33.333 11.05 0.00 0.00 2.52
2552 2865 9.449719 TCCTCTGTTCCTAAATATTTGTCTTTC 57.550 33.333 11.05 0.00 0.00 2.62
2553 2866 9.807921 TTCCTCTGTTCCTAAATATTTGTCTTT 57.192 29.630 11.05 0.00 0.00 2.52
2554 2867 9.454859 CTTCCTCTGTTCCTAAATATTTGTCTT 57.545 33.333 11.05 0.00 0.00 3.01
2555 2868 8.606830 ACTTCCTCTGTTCCTAAATATTTGTCT 58.393 33.333 11.05 0.00 0.00 3.41
2556 2869 8.794335 ACTTCCTCTGTTCCTAAATATTTGTC 57.206 34.615 11.05 0.00 0.00 3.18
2557 2870 9.668497 GTACTTCCTCTGTTCCTAAATATTTGT 57.332 33.333 11.05 0.00 0.00 2.83
2558 2871 9.667107 TGTACTTCCTCTGTTCCTAAATATTTG 57.333 33.333 11.05 1.40 0.00 2.32
2563 2876 9.588096 AAATTTGTACTTCCTCTGTTCCTAAAT 57.412 29.630 0.00 0.00 0.00 1.40
2564 2877 8.990163 AAATTTGTACTTCCTCTGTTCCTAAA 57.010 30.769 0.00 0.00 0.00 1.85
2565 2878 8.990163 AAAATTTGTACTTCCTCTGTTCCTAA 57.010 30.769 0.00 0.00 0.00 2.69
2566 2879 9.720769 CTAAAATTTGTACTTCCTCTGTTCCTA 57.279 33.333 0.00 0.00 0.00 2.94
2567 2880 8.218488 ACTAAAATTTGTACTTCCTCTGTTCCT 58.782 33.333 0.00 0.00 0.00 3.36
2568 2881 8.290325 CACTAAAATTTGTACTTCCTCTGTTCC 58.710 37.037 0.00 0.00 0.00 3.62
2569 2882 7.803659 GCACTAAAATTTGTACTTCCTCTGTTC 59.196 37.037 0.00 0.00 0.00 3.18
2570 2883 7.502561 AGCACTAAAATTTGTACTTCCTCTGTT 59.497 33.333 0.00 0.00 0.00 3.16
2571 2884 6.998673 AGCACTAAAATTTGTACTTCCTCTGT 59.001 34.615 0.00 0.00 0.00 3.41
2572 2885 7.173218 TCAGCACTAAAATTTGTACTTCCTCTG 59.827 37.037 0.00 0.00 0.00 3.35
2573 2886 7.224297 TCAGCACTAAAATTTGTACTTCCTCT 58.776 34.615 0.00 0.00 0.00 3.69
2574 2887 7.435068 TCAGCACTAAAATTTGTACTTCCTC 57.565 36.000 0.00 0.00 0.00 3.71
2575 2888 7.817418 TTCAGCACTAAAATTTGTACTTCCT 57.183 32.000 0.00 0.00 0.00 3.36
2696 3009 7.196331 GCATAGCGTTTAGAAAGAATGGAAAT 58.804 34.615 0.00 0.00 0.00 2.17
2755 3070 8.109634 ACACTGATCCCAAATAAGTGATAAAGT 58.890 33.333 12.54 0.00 40.54 2.66
2765 3080 5.074115 ACGGAAAACACTGATCCCAAATAA 58.926 37.500 0.00 0.00 0.00 1.40
2841 3156 6.000246 TCATCATGGTCAGGCATTTACTTA 58.000 37.500 0.00 0.00 0.00 2.24
2842 3157 4.858850 TCATCATGGTCAGGCATTTACTT 58.141 39.130 0.00 0.00 0.00 2.24
2843 3158 4.164796 TCTCATCATGGTCAGGCATTTACT 59.835 41.667 0.00 0.00 0.00 2.24
2844 3159 4.454678 TCTCATCATGGTCAGGCATTTAC 58.545 43.478 0.00 0.00 0.00 2.01
2933 3248 3.308438 AGCACAAAACAATCTCCATGC 57.692 42.857 0.00 0.00 0.00 4.06
2936 3251 5.827797 ACTCTTAAGCACAAAACAATCTCCA 59.172 36.000 0.00 0.00 0.00 3.86
2938 3253 7.417612 TCAACTCTTAAGCACAAAACAATCTC 58.582 34.615 0.00 0.00 0.00 2.75
2944 3259 7.417612 TCAATCTCAACTCTTAAGCACAAAAC 58.582 34.615 0.00 0.00 0.00 2.43
3082 3398 5.106317 GCTCTCTAGCCACTATCATGAGTAC 60.106 48.000 0.09 0.00 43.40 2.73
3572 3996 4.813161 ACAGAATCAATATCACGCTCTTGG 59.187 41.667 0.00 0.00 0.00 3.61
3640 4064 7.643569 AATGGCATTGTCATCACTATGTTTA 57.356 32.000 12.82 0.00 37.86 2.01
3864 4288 4.592942 TCAAGATGAATCTGTTTGGGGAG 58.407 43.478 0.00 0.00 37.19 4.30
3907 4372 3.956199 TCAGATGGAAAATGGGATTCAGC 59.044 43.478 0.00 0.00 0.00 4.26
3964 4429 3.855689 AACTTCAATGCAATTCCGAGG 57.144 42.857 0.00 0.00 31.22 4.63
4106 4573 4.726416 CACAACTCAGTGGCATCAATAAC 58.274 43.478 0.00 0.00 35.88 1.89
4243 4711 5.183904 GTGTGGAGAAATGCCAGAAATAGTT 59.816 40.000 0.00 0.00 35.77 2.24
4379 4853 9.814899 CTGTAAATCAACATAATGAGAGAGAGT 57.185 33.333 0.00 0.00 31.76 3.24
4419 4895 6.874134 GGACCAAATGCTAGTACATATAGTGG 59.126 42.308 0.00 0.00 0.00 4.00
4431 4907 3.498927 CTTGCAAGGACCAAATGCTAG 57.501 47.619 19.14 13.42 40.66 3.42
4550 5028 4.659088 CAGCATGCATTAGAGAGTTGTTG 58.341 43.478 21.98 0.00 0.00 3.33
4663 5141 7.948137 TGCAATTTACAGACGAAATAAAATGC 58.052 30.769 13.93 13.93 41.71 3.56
4835 5313 7.010091 GCAGCAATGTTTACAACAGTTTACTTT 59.990 33.333 0.00 0.00 45.95 2.66
4908 5387 1.222936 CCAGGCCACTTAGGAGCAG 59.777 63.158 5.01 0.00 41.22 4.24
5194 5686 7.876936 ATGAGAAGTAACAGCATCAATGAAT 57.123 32.000 0.00 0.00 0.00 2.57
5221 5713 7.886629 TTCTGGCATAATGAAAGCTATCTTT 57.113 32.000 0.00 0.00 44.67 2.52
5222 5714 8.474710 AATTCTGGCATAATGAAAGCTATCTT 57.525 30.769 0.00 0.00 0.00 2.40
5224 5716 9.189723 GAAAATTCTGGCATAATGAAAGCTATC 57.810 33.333 0.00 0.00 0.00 2.08
5226 5718 8.297470 AGAAAATTCTGGCATAATGAAAGCTA 57.703 30.769 0.00 0.00 35.89 3.32
5228 5720 6.478016 GGAGAAAATTCTGGCATAATGAAAGC 59.522 38.462 0.00 0.00 37.73 3.51
5229 5721 7.779073 AGGAGAAAATTCTGGCATAATGAAAG 58.221 34.615 0.00 0.00 37.73 2.62
5230 5722 7.396907 TGAGGAGAAAATTCTGGCATAATGAAA 59.603 33.333 0.00 0.00 37.73 2.69
5393 5890 1.508088 GCAAAATGGCCAGACTCGG 59.492 57.895 13.05 0.00 0.00 4.63
5399 5896 0.526954 GAGATGCGCAAAATGGCCAG 60.527 55.000 17.11 0.00 0.00 4.85
5401 5898 0.526954 CAGAGATGCGCAAAATGGCC 60.527 55.000 17.11 0.00 0.00 5.36
5410 5907 4.404507 TTTGTTTCTAACAGAGATGCGC 57.595 40.909 0.00 0.00 43.27 6.09
5517 6014 0.248215 GAACCTCGATGGCAAATGCG 60.248 55.000 0.00 0.00 43.26 4.73
5663 6160 4.584638 ACCACATGTAGCCAAAGGAATA 57.415 40.909 0.00 0.00 0.00 1.75
5683 6180 6.242508 CAAACTTTGCTAAGAGGTTCCTAC 57.757 41.667 14.98 0.00 35.30 3.18
5827 6324 3.445096 GGTGAAATTGTCATCCAGGAAGG 59.555 47.826 0.00 0.00 38.90 3.46
5828 6325 4.338879 AGGTGAAATTGTCATCCAGGAAG 58.661 43.478 0.00 0.00 38.23 3.46
5829 6326 4.387026 AGGTGAAATTGTCATCCAGGAA 57.613 40.909 0.00 0.00 38.23 3.36
5830 6327 4.387026 AAGGTGAAATTGTCATCCAGGA 57.613 40.909 0.00 0.00 38.23 3.86
5831 6328 5.473066 AAAAGGTGAAATTGTCATCCAGG 57.527 39.130 0.00 0.00 38.23 4.45
5832 6329 9.793252 CTTATAAAAGGTGAAATTGTCATCCAG 57.207 33.333 0.00 0.00 38.23 3.86
5833 6330 8.748412 CCTTATAAAAGGTGAAATTGTCATCCA 58.252 33.333 0.00 0.00 46.34 3.41
6004 6516 2.572209 AAGCCCAATTTGCAGCATTT 57.428 40.000 0.00 0.00 0.00 2.32
6015 6534 6.770286 TCCTAGAAATCAGATAAGCCCAAT 57.230 37.500 0.00 0.00 0.00 3.16
6277 6798 1.538047 TTTTCTCCCATGCACAGCTC 58.462 50.000 0.00 0.00 0.00 4.09
6361 6882 7.706179 GGACTATAATCTCAATGATAGAGCAGC 59.294 40.741 0.00 0.00 32.45 5.25
6510 7031 6.569801 GCTGCATCAGTACCTAACGATACATA 60.570 42.308 0.00 0.00 33.43 2.29
6524 7045 4.466370 ACTTTACCTACTGCTGCATCAGTA 59.534 41.667 24.67 24.67 44.77 2.74
6544 7065 2.674177 GCCACAGCACGTACTCATACTT 60.674 50.000 0.00 0.00 39.53 2.24
6546 7067 1.135083 AGCCACAGCACGTACTCATAC 60.135 52.381 0.00 0.00 43.56 2.39
6555 7076 2.162208 ACATATTTCAAGCCACAGCACG 59.838 45.455 0.00 0.00 43.56 5.34
6557 7078 5.192176 TCATACATATTTCAAGCCACAGCA 58.808 37.500 0.00 0.00 43.56 4.41
6616 7137 9.264719 TCATTATTCAATATGCTCACTGTACTG 57.735 33.333 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.