Multiple sequence alignment - TraesCS4B01G342400

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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 TraesCS4B01G342400 chr4B 100.000 3536 0 0 1 3536 635866746 635870281 0.000000e+00 6530.0
1 TraesCS4B01G342400 chr4B 76.027 1314 277 34 1206 2494 634981470 634982770 0.000000e+00 647.0
2 TraesCS4B01G342400 chr4B 76.300 1308 245 56 1218 2496 634765089 634766360 3.850000e-179 638.0
3 TraesCS4B01G342400 chr4B 75.857 1313 278 33 1209 2494 634460638 634459338 1.790000e-177 632.0
4 TraesCS4B01G342400 chr4B 76.070 1308 251 53 1218 2499 634727481 634726210 3.000000e-175 625.0
5 TraesCS4B01G342400 chr4B 96.407 167 5 1 2665 2831 94949686 94949851 1.250000e-69 274.0
6 TraesCS4B01G342400 chr4B 96.364 165 5 1 2667 2831 529358011 529358174 1.620000e-68 270.0
7 TraesCS4B01G342400 chr4B 93.421 76 4 1 3461 3536 570191912 570191838 1.040000e-20 111.0
8 TraesCS4B01G342400 chr4D 95.304 2023 46 13 685 2667 495978535 495980548 0.000000e+00 3164.0
9 TraesCS4B01G342400 chr4D 91.379 580 21 12 2825 3385 495980564 495981133 0.000000e+00 767.0
10 TraesCS4B01G342400 chr4D 76.336 1310 284 23 1203 2496 494877376 494878675 0.000000e+00 678.0
11 TraesCS4B01G342400 chr4D 76.439 1303 255 48 1218 2496 494850792 494852066 0.000000e+00 658.0
12 TraesCS4B01G342400 chr4D 87.977 524 35 15 76 589 495977713 495978218 8.450000e-166 593.0
13 TraesCS4B01G342400 chr4D 84.211 114 5 6 1 102 495976981 495977093 8.080000e-17 99.0
14 TraesCS4B01G342400 chr4D 97.561 41 1 0 643 683 495978330 495978370 1.760000e-08 71.3
15 TraesCS4B01G342400 chrUn 95.752 1389 53 4 1274 2658 64849541 64850927 0.000000e+00 2233.0
16 TraesCS4B01G342400 chr5A 76.159 1359 288 30 1156 2496 674576371 674577711 0.000000e+00 682.0
17 TraesCS4B01G342400 chr5A 76.398 1305 249 48 1218 2496 674371642 674372913 0.000000e+00 649.0
18 TraesCS4B01G342400 chr5A 91.332 473 26 7 2913 3385 675479760 675480217 1.790000e-177 632.0
19 TraesCS4B01G342400 chr3A 74.846 1296 249 59 1218 2476 711115623 711116878 1.880000e-142 516.0
20 TraesCS4B01G342400 chr3A 74.351 1310 274 52 1218 2495 711253588 711252309 5.270000e-138 501.0
21 TraesCS4B01G342400 chr3A 94.350 177 8 2 2656 2831 623797076 623797251 1.620000e-68 270.0
22 TraesCS4B01G342400 chr3B 74.054 1322 282 52 1211 2499 766636487 766635194 5.310000e-133 484.0
23 TraesCS4B01G342400 chr3B 95.322 171 7 1 2661 2831 816483133 816483302 1.620000e-68 270.0
24 TraesCS4B01G342400 chr3D 73.957 1175 232 56 1342 2476 575631709 575632849 1.180000e-109 407.0
25 TraesCS4B01G342400 chr3D 73.333 975 222 33 1547 2499 575733615 575732657 3.400000e-85 326.0
26 TraesCS4B01G342400 chr4A 95.376 173 5 2 2661 2831 323290699 323290528 4.500000e-69 272.0
27 TraesCS4B01G342400 chr4A 95.349 172 6 2 2661 2831 487887270 487887440 4.500000e-69 272.0
28 TraesCS4B01G342400 chr4A 80.180 111 20 2 2648 2758 708653155 708653263 8.140000e-12 82.4
29 TraesCS4B01G342400 chr6B 97.484 159 3 1 2673 2831 23231965 23231808 1.620000e-68 270.0
30 TraesCS4B01G342400 chr6B 97.484 159 3 1 2673 2831 26081804 26081647 1.620000e-68 270.0
31 TraesCS4B01G342400 chr6B 94.805 77 3 1 3460 3536 525106233 525106308 6.200000e-23 119.0
32 TraesCS4B01G342400 chr6B 95.890 73 2 1 3464 3536 217420748 217420819 2.230000e-22 117.0
33 TraesCS4B01G342400 chr7B 95.294 170 6 2 2660 2829 135043967 135044134 5.820000e-68 268.0
34 TraesCS4B01G342400 chr2B 85.915 142 17 3 2650 2789 693439144 693439284 7.910000e-32 148.0
35 TraesCS4B01G342400 chr2B 98.529 68 1 0 3464 3531 36413735 36413802 1.720000e-23 121.0
36 TraesCS4B01G342400 chr2B 95.890 73 2 1 3464 3536 763446832 763446761 2.230000e-22 117.0
37 TraesCS4B01G342400 chr2B 95.890 73 2 1 3464 3536 765570154 765570083 2.230000e-22 117.0
38 TraesCS4B01G342400 chr5B 95.890 73 2 1 3464 3536 346616160 346616231 2.230000e-22 117.0
39 TraesCS4B01G342400 chr5B 95.833 72 1 2 3465 3536 461580118 461580049 8.020000e-22 115.0
40 TraesCS4B01G342400 chr2A 95.890 73 2 1 3464 3536 762933459 762933530 2.230000e-22 117.0


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 TraesCS4B01G342400 chr4B 635866746 635870281 3535 False 6530.00 6530 100.0000 1 3536 1 chr4B.!!$F5 3535
1 TraesCS4B01G342400 chr4B 634981470 634982770 1300 False 647.00 647 76.0270 1206 2494 1 chr4B.!!$F4 1288
2 TraesCS4B01G342400 chr4B 634765089 634766360 1271 False 638.00 638 76.3000 1218 2496 1 chr4B.!!$F3 1278
3 TraesCS4B01G342400 chr4B 634459338 634460638 1300 True 632.00 632 75.8570 1209 2494 1 chr4B.!!$R2 1285
4 TraesCS4B01G342400 chr4B 634726210 634727481 1271 True 625.00 625 76.0700 1218 2499 1 chr4B.!!$R3 1281
5 TraesCS4B01G342400 chr4D 495976981 495981133 4152 False 938.86 3164 91.2864 1 3385 5 chr4D.!!$F3 3384
6 TraesCS4B01G342400 chr4D 494877376 494878675 1299 False 678.00 678 76.3360 1203 2496 1 chr4D.!!$F2 1293
7 TraesCS4B01G342400 chr4D 494850792 494852066 1274 False 658.00 658 76.4390 1218 2496 1 chr4D.!!$F1 1278
8 TraesCS4B01G342400 chrUn 64849541 64850927 1386 False 2233.00 2233 95.7520 1274 2658 1 chrUn.!!$F1 1384
9 TraesCS4B01G342400 chr5A 674576371 674577711 1340 False 682.00 682 76.1590 1156 2496 1 chr5A.!!$F2 1340
10 TraesCS4B01G342400 chr5A 674371642 674372913 1271 False 649.00 649 76.3980 1218 2496 1 chr5A.!!$F1 1278
11 TraesCS4B01G342400 chr3A 711115623 711116878 1255 False 516.00 516 74.8460 1218 2476 1 chr3A.!!$F2 1258
12 TraesCS4B01G342400 chr3A 711252309 711253588 1279 True 501.00 501 74.3510 1218 2495 1 chr3A.!!$R1 1277
13 TraesCS4B01G342400 chr3B 766635194 766636487 1293 True 484.00 484 74.0540 1211 2499 1 chr3B.!!$R1 1288
14 TraesCS4B01G342400 chr3D 575631709 575632849 1140 False 407.00 407 73.9570 1342 2476 1 chr3D.!!$F1 1134
15 TraesCS4B01G342400 chr3D 575732657 575733615 958 True 326.00 326 73.3330 1547 2499 1 chr3D.!!$R1 952

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
204 864 0.320374 TACTCGGTGCACCTTCCTTG 59.680 55.0 32.28 16.48 0.00 3.61 F
738 1625 0.391661 CTTGGTGACCACATCCCTCG 60.392 60.0 2.46 0.00 30.78 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2007 2949 1.526686 GTTGGGTCCGACGGGTTTT 60.527 57.895 15.25 0.0 33.83 2.43 R
2622 3589 0.107831 TTACTGGACACCTGCACACC 59.892 55.000 0.00 0.0 0.00 4.16 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
37 38 2.332654 GGGTGCGTTGTGGTGGATC 61.333 63.158 0.00 0.00 0.00 3.36
43 55 4.127171 GTGCGTTGTGGTGGATCTATTAT 58.873 43.478 0.00 0.00 0.00 1.28
67 79 5.419471 TGGTTTTCTTAATGTAAATCGGGGG 59.581 40.000 0.00 0.00 0.00 5.40
130 787 6.484540 TCGATCTAAACGTCTTATGTCTGAC 58.515 40.000 0.00 0.00 0.00 3.51
154 814 7.047891 ACATTTCTTTGCCTCGACATATTCTA 58.952 34.615 0.00 0.00 0.00 2.10
161 821 4.221482 TGCCTCGACATATTCTAGATGCAT 59.779 41.667 0.00 0.00 29.99 3.96
195 855 1.550130 CCCCCTTCTTACTCGGTGCA 61.550 60.000 0.00 0.00 0.00 4.57
196 856 0.391263 CCCCTTCTTACTCGGTGCAC 60.391 60.000 8.80 8.80 0.00 4.57
198 858 0.608640 CCTTCTTACTCGGTGCACCT 59.391 55.000 32.28 17.44 0.00 4.00
199 859 1.002087 CCTTCTTACTCGGTGCACCTT 59.998 52.381 32.28 18.90 0.00 3.50
201 861 0.606604 TCTTACTCGGTGCACCTTCC 59.393 55.000 32.28 7.73 0.00 3.46
202 862 0.608640 CTTACTCGGTGCACCTTCCT 59.391 55.000 32.28 14.76 0.00 3.36
203 863 1.002087 CTTACTCGGTGCACCTTCCTT 59.998 52.381 32.28 14.73 0.00 3.36
204 864 0.320374 TACTCGGTGCACCTTCCTTG 59.680 55.000 32.28 16.48 0.00 3.61
205 865 1.672356 CTCGGTGCACCTTCCTTGG 60.672 63.158 32.28 15.74 0.00 3.61
206 866 2.113139 CGGTGCACCTTCCTTGGT 59.887 61.111 32.28 0.00 41.77 3.67
212 872 3.341270 ACCTTCCTTGGTGTGCCA 58.659 55.556 0.00 0.00 44.38 4.92
213 873 1.152756 ACCTTCCTTGGTGTGCCAC 60.153 57.895 0.00 0.00 46.01 5.01
292 957 1.472026 GCCATTTCATGCTCGCCATTT 60.472 47.619 0.00 0.00 29.71 2.32
293 958 2.466846 CCATTTCATGCTCGCCATTTC 58.533 47.619 0.00 0.00 29.71 2.17
298 963 2.123428 ATGCTCGCCATTTCCAGCC 61.123 57.895 0.00 0.00 0.00 4.85
299 964 3.880846 GCTCGCCATTTCCAGCCG 61.881 66.667 0.00 0.00 0.00 5.52
313 978 0.673437 CAGCCGGTGGACATTTTTGT 59.327 50.000 1.90 0.00 0.00 2.83
317 982 2.288763 GCCGGTGGACATTTTTGTTCAT 60.289 45.455 1.90 0.00 28.94 2.57
321 986 3.578282 GGTGGACATTTTTGTTCATCCCT 59.422 43.478 0.00 0.00 28.94 4.20
328 993 4.335400 TTTTTGTTCATCCCTCAAAGCC 57.665 40.909 0.00 0.00 33.61 4.35
329 994 1.923356 TTGTTCATCCCTCAAAGCCC 58.077 50.000 0.00 0.00 0.00 5.19
336 1001 4.682563 TCATCCCTCAAAGCCCATAAAAA 58.317 39.130 0.00 0.00 0.00 1.94
345 1010 7.060383 TCAAAGCCCATAAAAACAAGATTCA 57.940 32.000 0.00 0.00 0.00 2.57
347 1012 7.656948 TCAAAGCCCATAAAAACAAGATTCAAG 59.343 33.333 0.00 0.00 0.00 3.02
349 1014 6.458210 AGCCCATAAAAACAAGATTCAAGTG 58.542 36.000 0.00 0.00 0.00 3.16
357 1022 5.695851 AACAAGATTCAAGTGACCACATC 57.304 39.130 2.78 0.00 0.00 3.06
384 1049 6.015918 ACCACTTTGAACATCCAATCCATAA 58.984 36.000 0.00 0.00 0.00 1.90
385 1050 6.071391 ACCACTTTGAACATCCAATCCATAAC 60.071 38.462 0.00 0.00 0.00 1.89
386 1051 6.029607 CACTTTGAACATCCAATCCATAACG 58.970 40.000 0.00 0.00 0.00 3.18
395 1060 4.735369 TCCAATCCATAACGGGCAAATAT 58.265 39.130 0.00 0.00 34.36 1.28
467 1132 7.769044 GCAAGAGAAATAATAACAGTGTCCCTA 59.231 37.037 0.00 0.00 0.00 3.53
548 1213 2.741092 TGGGACACGTCAGAAGGC 59.259 61.111 0.00 0.00 0.00 4.35
550 1215 1.296715 GGGACACGTCAGAAGGCAT 59.703 57.895 0.00 0.00 0.00 4.40
584 1250 4.082895 CCTCATATCATTGCAGCCTTAAGC 60.083 45.833 0.00 0.00 44.25 3.09
595 1279 1.934220 GCCTTAAGCGAGCAAACCCC 61.934 60.000 0.00 0.00 0.00 4.95
607 1291 2.044353 AGCAAACCCCATTCCCATTACT 59.956 45.455 0.00 0.00 0.00 2.24
610 1294 4.867086 CAAACCCCATTCCCATTACTAGT 58.133 43.478 0.00 0.00 0.00 2.57
683 1407 5.056480 TGTGCACATACCAGATATGCTAAC 58.944 41.667 17.42 0.00 44.12 2.34
686 1410 6.929049 GTGCACATACCAGATATGCTAACTAA 59.071 38.462 13.17 0.00 44.12 2.24
701 1588 7.938140 TGCTAACTAATTAATGGCTGTCTTT 57.062 32.000 7.49 0.00 0.00 2.52
712 1599 9.700831 ATTAATGGCTGTCTTTAACTAATTCCT 57.299 29.630 2.91 0.00 30.90 3.36
730 1617 1.338020 CCTTTTGCTCTTGGTGACCAC 59.662 52.381 2.46 0.00 30.78 4.16
733 1620 1.896220 TTGCTCTTGGTGACCACATC 58.104 50.000 2.46 0.00 30.78 3.06
737 1624 0.984230 TCTTGGTGACCACATCCCTC 59.016 55.000 2.46 0.00 30.78 4.30
738 1625 0.391661 CTTGGTGACCACATCCCTCG 60.392 60.000 2.46 0.00 30.78 4.63
768 1657 1.275471 CGTCGCGTATGCATTCCGAT 61.275 55.000 19.03 0.00 42.97 4.18
818 1707 1.762708 ATTAATTGGCCAGGGACGTG 58.237 50.000 5.11 0.00 0.00 4.49
856 1756 0.921166 ACCACCATGCATCTCCATGA 59.079 50.000 0.00 0.00 44.12 3.07
884 1784 2.787680 CGTACGATTTACTGCTAGCCAC 59.212 50.000 10.44 0.00 0.00 5.01
944 1846 0.670546 GCACGCATGTCTAGTGGTGT 60.671 55.000 12.21 0.00 36.48 4.16
945 1847 1.070821 CACGCATGTCTAGTGGTGTG 58.929 55.000 0.00 0.00 35.72 3.82
975 1889 2.123164 ATGGGCATGGGCATGGAC 60.123 61.111 0.00 0.00 43.71 4.02
976 1890 3.761690 ATGGGCATGGGCATGGACC 62.762 63.158 0.00 0.00 43.71 4.46
1010 1924 3.567797 GCTTCTCATGTCGGCCGC 61.568 66.667 23.51 16.75 0.00 6.53
1467 2381 4.373116 GTGCTCCCGTTCCTCGCA 62.373 66.667 0.00 0.00 38.35 5.10
1782 2711 1.002134 AGCCGCCTACAACAAGCAT 60.002 52.632 0.00 0.00 0.00 3.79
1783 2712 1.026718 AGCCGCCTACAACAAGCATC 61.027 55.000 0.00 0.00 0.00 3.91
2023 2977 2.426887 GAAAACCCGTCGGACCCA 59.573 61.111 14.39 0.00 0.00 4.51
2071 3025 2.534990 AGCTGAAGAACCTGCTCTACT 58.465 47.619 0.00 0.00 36.79 2.57
2507 3461 2.764572 GGGTCAAGAGAAGATCGGGTAA 59.235 50.000 0.00 0.00 0.00 2.85
2530 3484 2.719979 CCATGATCGGCAAGCAGC 59.280 61.111 0.00 0.00 44.65 5.25
2622 3589 4.787381 TTATTCGGCATATGTGTTGTCG 57.213 40.909 4.29 0.00 43.25 4.35
2645 3612 3.623060 GTGTGCAGGTGTCCAGTAATATG 59.377 47.826 0.00 0.00 0.00 1.78
2648 3615 5.126067 GTGCAGGTGTCCAGTAATATGATT 58.874 41.667 0.00 0.00 0.00 2.57
2677 3644 9.909644 GTACACTGTAAATCATATTATCTCCGT 57.090 33.333 0.00 0.00 0.00 4.69
2679 3646 8.088981 ACACTGTAAATCATATTATCTCCGTCC 58.911 37.037 0.00 0.00 0.00 4.79
2680 3647 7.545965 CACTGTAAATCATATTATCTCCGTCCC 59.454 40.741 0.00 0.00 0.00 4.46
2681 3648 6.627243 TGTAAATCATATTATCTCCGTCCCG 58.373 40.000 0.00 0.00 0.00 5.14
2692 3659 3.953201 CCGTCCCGGTGTATAAGTC 57.047 57.895 0.00 0.00 42.73 3.01
2693 3660 1.105457 CCGTCCCGGTGTATAAGTCA 58.895 55.000 0.00 0.00 42.73 3.41
2694 3661 1.684983 CCGTCCCGGTGTATAAGTCAT 59.315 52.381 0.00 0.00 42.73 3.06
2695 3662 2.101917 CCGTCCCGGTGTATAAGTCATT 59.898 50.000 0.00 0.00 42.73 2.57
2696 3663 3.378339 CGTCCCGGTGTATAAGTCATTC 58.622 50.000 0.00 0.00 0.00 2.67
2697 3664 3.378339 GTCCCGGTGTATAAGTCATTCG 58.622 50.000 0.00 0.00 0.00 3.34
2698 3665 2.132762 CCCGGTGTATAAGTCATTCGC 58.867 52.381 0.00 0.00 0.00 4.70
2699 3666 1.784856 CCGGTGTATAAGTCATTCGCG 59.215 52.381 0.00 0.00 0.00 5.87
2700 3667 2.456989 CGGTGTATAAGTCATTCGCGT 58.543 47.619 5.77 0.00 0.00 6.01
2701 3668 3.548616 CCGGTGTATAAGTCATTCGCGTA 60.549 47.826 5.77 0.00 0.00 4.42
2702 3669 3.662645 CGGTGTATAAGTCATTCGCGTAG 59.337 47.826 5.77 0.00 0.00 3.51
2703 3670 4.604976 GGTGTATAAGTCATTCGCGTAGT 58.395 43.478 5.77 0.00 0.00 2.73
2704 3671 5.039333 GGTGTATAAGTCATTCGCGTAGTT 58.961 41.667 5.77 2.59 0.00 2.24
2705 3672 5.172771 GGTGTATAAGTCATTCGCGTAGTTC 59.827 44.000 5.77 0.00 0.00 3.01
2706 3673 5.970023 GTGTATAAGTCATTCGCGTAGTTCT 59.030 40.000 5.77 0.00 0.00 3.01
2707 3674 7.128331 GTGTATAAGTCATTCGCGTAGTTCTA 58.872 38.462 5.77 0.00 0.00 2.10
2708 3675 7.320797 GTGTATAAGTCATTCGCGTAGTTCTAG 59.679 40.741 5.77 0.00 0.00 2.43
2709 3676 3.694535 AGTCATTCGCGTAGTTCTAGG 57.305 47.619 5.77 0.00 0.00 3.02
2710 3677 3.015327 AGTCATTCGCGTAGTTCTAGGT 58.985 45.455 5.77 0.00 0.00 3.08
2711 3678 3.065095 AGTCATTCGCGTAGTTCTAGGTC 59.935 47.826 5.77 0.00 0.00 3.85
2712 3679 3.011818 TCATTCGCGTAGTTCTAGGTCA 58.988 45.455 5.77 0.00 0.00 4.02
2713 3680 3.441222 TCATTCGCGTAGTTCTAGGTCAA 59.559 43.478 5.77 0.00 0.00 3.18
2714 3681 4.097437 TCATTCGCGTAGTTCTAGGTCAAT 59.903 41.667 5.77 0.00 0.00 2.57
2715 3682 5.297527 TCATTCGCGTAGTTCTAGGTCAATA 59.702 40.000 5.77 0.00 0.00 1.90
2716 3683 5.565592 TTCGCGTAGTTCTAGGTCAATAA 57.434 39.130 5.77 0.00 0.00 1.40
2717 3684 5.762825 TCGCGTAGTTCTAGGTCAATAAT 57.237 39.130 5.77 0.00 0.00 1.28
2718 3685 6.140303 TCGCGTAGTTCTAGGTCAATAATT 57.860 37.500 5.77 0.00 0.00 1.40
2719 3686 6.567050 TCGCGTAGTTCTAGGTCAATAATTT 58.433 36.000 5.77 0.00 0.00 1.82
2720 3687 7.706159 TCGCGTAGTTCTAGGTCAATAATTTA 58.294 34.615 5.77 0.00 0.00 1.40
2721 3688 8.190122 TCGCGTAGTTCTAGGTCAATAATTTAA 58.810 33.333 5.77 0.00 0.00 1.52
2722 3689 8.264632 CGCGTAGTTCTAGGTCAATAATTTAAC 58.735 37.037 0.00 0.00 0.00 2.01
2723 3690 9.310716 GCGTAGTTCTAGGTCAATAATTTAACT 57.689 33.333 0.00 0.00 0.00 2.24
2790 3757 2.762535 CACCCGTGTGGAAATCTAGT 57.237 50.000 0.00 0.00 38.90 2.57
2791 3758 2.346803 CACCCGTGTGGAAATCTAGTG 58.653 52.381 0.00 0.00 38.90 2.74
2792 3759 1.278127 ACCCGTGTGGAAATCTAGTGG 59.722 52.381 0.00 0.00 37.49 4.00
2793 3760 1.278127 CCCGTGTGGAAATCTAGTGGT 59.722 52.381 0.00 0.00 37.49 4.16
2794 3761 2.498481 CCCGTGTGGAAATCTAGTGGTA 59.502 50.000 0.00 0.00 37.49 3.25
2795 3762 3.134081 CCCGTGTGGAAATCTAGTGGTAT 59.866 47.826 0.00 0.00 37.49 2.73
2796 3763 4.342951 CCCGTGTGGAAATCTAGTGGTATA 59.657 45.833 0.00 0.00 37.49 1.47
2797 3764 5.287226 CCGTGTGGAAATCTAGTGGTATAC 58.713 45.833 0.00 0.00 37.49 1.47
2798 3765 5.068723 CCGTGTGGAAATCTAGTGGTATACT 59.931 44.000 2.25 0.00 39.66 2.12
2799 3766 6.406624 CCGTGTGGAAATCTAGTGGTATACTT 60.407 42.308 2.25 0.00 37.99 2.24
2800 3767 7.039882 CGTGTGGAAATCTAGTGGTATACTTT 58.960 38.462 2.25 0.00 40.89 2.66
2801 3768 7.548075 CGTGTGGAAATCTAGTGGTATACTTTT 59.452 37.037 2.25 0.00 40.89 2.27
2802 3769 8.880750 GTGTGGAAATCTAGTGGTATACTTTTC 58.119 37.037 2.25 0.00 40.89 2.29
2803 3770 8.598916 TGTGGAAATCTAGTGGTATACTTTTCA 58.401 33.333 2.25 0.00 40.89 2.69
2804 3771 9.614792 GTGGAAATCTAGTGGTATACTTTTCAT 57.385 33.333 2.25 0.00 40.89 2.57
2805 3772 9.613428 TGGAAATCTAGTGGTATACTTTTCATG 57.387 33.333 2.25 0.00 40.89 3.07
2806 3773 9.832445 GGAAATCTAGTGGTATACTTTTCATGA 57.168 33.333 2.25 0.00 40.89 3.07
2881 3848 7.923878 TCGTTGATTGATCCGAAGACATATTTA 59.076 33.333 0.00 0.00 0.00 1.40
2893 3860 8.823818 CCGAAGACATATTTATACCGAAACTTT 58.176 33.333 0.00 0.00 0.00 2.66
2959 3932 4.922206 TGGTTTCCAATCTCAGCTAACAT 58.078 39.130 0.00 0.00 0.00 2.71
2966 3939 4.331992 CCAATCTCAGCTAACATGACTGTG 59.668 45.833 0.00 2.95 35.22 3.66
3091 4064 2.249844 TGCTGTCATGCATGATCGAT 57.750 45.000 30.89 0.00 39.30 3.59
3093 4066 3.731089 TGCTGTCATGCATGATCGATTA 58.269 40.909 30.89 13.58 39.30 1.75
3094 4067 4.320870 TGCTGTCATGCATGATCGATTAT 58.679 39.130 30.89 0.00 39.30 1.28
3123 4098 3.669536 TGCCATGTTCGTTCATTCTGTA 58.330 40.909 0.00 0.00 0.00 2.74
3186 4161 1.264045 TGCCCATCATCACCGACTGA 61.264 55.000 0.00 0.00 0.00 3.41
3210 4185 3.502595 CGATCCCTTTCGCATCTAGTCTA 59.497 47.826 0.00 0.00 31.60 2.59
3227 4202 9.934784 ATCTAGTCTAGTATCATGCAGGAATAT 57.065 33.333 4.62 0.00 0.00 1.28
3230 4205 8.427902 AGTCTAGTATCATGCAGGAATATCAA 57.572 34.615 4.62 0.00 0.00 2.57
3240 4215 6.741992 TGCAGGAATATCAAAGTTAGTGTG 57.258 37.500 0.00 0.00 0.00 3.82
3247 4222 3.696281 TCAAAGTTAGTGTGACGACGA 57.304 42.857 0.00 0.00 0.00 4.20
3248 4223 3.365832 TCAAAGTTAGTGTGACGACGAC 58.634 45.455 0.00 0.00 0.00 4.34
3249 4224 2.028287 AAGTTAGTGTGACGACGACG 57.972 50.000 5.58 5.58 45.75 5.12
3275 4250 1.086696 CGTACGTCCCCTTCGTCTTA 58.913 55.000 7.22 0.00 41.72 2.10
3311 4286 1.207329 ACACGGCTTCCCTGAATCTAC 59.793 52.381 0.00 0.00 0.00 2.59
3317 4292 2.158885 GCTTCCCTGAATCTACACTCCC 60.159 54.545 0.00 0.00 0.00 4.30
3318 4293 3.379452 CTTCCCTGAATCTACACTCCCT 58.621 50.000 0.00 0.00 0.00 4.20
3320 4295 2.587777 TCCCTGAATCTACACTCCCTCT 59.412 50.000 0.00 0.00 0.00 3.69
3321 4296 3.792114 TCCCTGAATCTACACTCCCTCTA 59.208 47.826 0.00 0.00 0.00 2.43
3322 4297 4.420552 TCCCTGAATCTACACTCCCTCTAT 59.579 45.833 0.00 0.00 0.00 1.98
3377 4359 9.167311 AGTGGTATTTTCACAGAAATACAGATC 57.833 33.333 17.33 0.00 46.73 2.75
3385 4367 7.232118 TCACAGAAATACAGATCTGAGAACA 57.768 36.000 29.27 8.68 44.64 3.18
3386 4368 7.670364 TCACAGAAATACAGATCTGAGAACAA 58.330 34.615 29.27 7.31 44.64 2.83
3387 4369 7.600375 TCACAGAAATACAGATCTGAGAACAAC 59.400 37.037 29.27 12.82 44.64 3.32
3388 4370 7.601886 CACAGAAATACAGATCTGAGAACAACT 59.398 37.037 29.27 14.62 44.64 3.16
3389 4371 8.153550 ACAGAAATACAGATCTGAGAACAACTT 58.846 33.333 29.27 5.84 44.64 2.66
3390 4372 9.645059 CAGAAATACAGATCTGAGAACAACTTA 57.355 33.333 29.27 7.97 44.64 2.24
3393 4375 9.950496 AAATACAGATCTGAGAACAACTTATGT 57.050 29.630 29.27 5.49 46.82 2.29
3396 4378 8.994429 ACAGATCTGAGAACAACTTATGTAAG 57.006 34.615 29.27 0.00 42.99 2.34
3428 4410 7.490962 TTGTGATATAAATTCATCGACCACC 57.509 36.000 0.00 0.00 0.00 4.61
3429 4411 5.995282 TGTGATATAAATTCATCGACCACCC 59.005 40.000 0.00 0.00 0.00 4.61
3430 4412 5.411669 GTGATATAAATTCATCGACCACCCC 59.588 44.000 0.00 0.00 0.00 4.95
3431 4413 2.319136 TAAATTCATCGACCACCCCG 57.681 50.000 0.00 0.00 0.00 5.73
3432 4414 0.326927 AAATTCATCGACCACCCCGT 59.673 50.000 0.00 0.00 0.00 5.28
3433 4415 0.326927 AATTCATCGACCACCCCGTT 59.673 50.000 0.00 0.00 0.00 4.44
3434 4416 0.392461 ATTCATCGACCACCCCGTTG 60.392 55.000 0.00 0.00 0.00 4.10
3435 4417 2.435938 CATCGACCACCCCGTTGG 60.436 66.667 0.00 0.00 43.04 3.77
3452 4434 2.727123 TGGTGACAAAAGCTTCCTCA 57.273 45.000 0.00 0.00 37.44 3.86
3453 4435 2.297701 TGGTGACAAAAGCTTCCTCAC 58.702 47.619 17.06 17.06 37.44 3.51
3454 4436 1.609072 GGTGACAAAAGCTTCCTCACC 59.391 52.381 23.88 23.88 43.08 4.02
3455 4437 2.297701 GTGACAAAAGCTTCCTCACCA 58.702 47.619 15.45 2.33 0.00 4.17
3456 4438 2.033424 GTGACAAAAGCTTCCTCACCAC 59.967 50.000 15.45 9.22 0.00 4.16
3457 4439 2.297701 GACAAAAGCTTCCTCACCACA 58.702 47.619 0.00 0.00 0.00 4.17
3458 4440 2.687935 GACAAAAGCTTCCTCACCACAA 59.312 45.455 0.00 0.00 0.00 3.33
3459 4441 3.299503 ACAAAAGCTTCCTCACCACAAT 58.700 40.909 0.00 0.00 0.00 2.71
3460 4442 3.706086 ACAAAAGCTTCCTCACCACAATT 59.294 39.130 0.00 0.00 0.00 2.32
3461 4443 4.162131 ACAAAAGCTTCCTCACCACAATTT 59.838 37.500 0.00 0.00 0.00 1.82
3462 4444 4.590850 AAAGCTTCCTCACCACAATTTC 57.409 40.909 0.00 0.00 0.00 2.17
3463 4445 3.228188 AGCTTCCTCACCACAATTTCA 57.772 42.857 0.00 0.00 0.00 2.69
3464 4446 3.565307 AGCTTCCTCACCACAATTTCAA 58.435 40.909 0.00 0.00 0.00 2.69
3465 4447 3.960102 AGCTTCCTCACCACAATTTCAAA 59.040 39.130 0.00 0.00 0.00 2.69
3466 4448 4.405358 AGCTTCCTCACCACAATTTCAAAA 59.595 37.500 0.00 0.00 0.00 2.44
3467 4449 5.104982 AGCTTCCTCACCACAATTTCAAAAA 60.105 36.000 0.00 0.00 0.00 1.94
3468 4450 5.234972 GCTTCCTCACCACAATTTCAAAAAG 59.765 40.000 0.00 0.00 0.00 2.27
3469 4451 5.275067 TCCTCACCACAATTTCAAAAAGG 57.725 39.130 0.00 0.00 0.00 3.11
3470 4452 4.100808 TCCTCACCACAATTTCAAAAAGGG 59.899 41.667 0.00 0.00 0.00 3.95
3471 4453 4.100808 CCTCACCACAATTTCAAAAAGGGA 59.899 41.667 0.00 0.00 0.00 4.20
3472 4454 5.275067 TCACCACAATTTCAAAAAGGGAG 57.725 39.130 0.00 0.00 0.00 4.30
3473 4455 4.714308 TCACCACAATTTCAAAAAGGGAGT 59.286 37.500 0.00 0.00 0.00 3.85
3474 4456 5.894393 TCACCACAATTTCAAAAAGGGAGTA 59.106 36.000 0.00 0.00 0.00 2.59
3475 4457 5.983118 CACCACAATTTCAAAAAGGGAGTAC 59.017 40.000 0.00 0.00 0.00 2.73
3476 4458 5.069914 ACCACAATTTCAAAAAGGGAGTACC 59.930 40.000 0.00 0.00 40.67 3.34
3490 4472 5.024785 GGGAGTACCTAGAACTCATTTGG 57.975 47.826 20.28 0.00 44.25 3.28
3491 4473 4.715297 GGGAGTACCTAGAACTCATTTGGA 59.285 45.833 20.28 0.00 44.25 3.53
3492 4474 5.367060 GGGAGTACCTAGAACTCATTTGGAT 59.633 44.000 20.28 0.00 44.25 3.41
3493 4475 6.284459 GGAGTACCTAGAACTCATTTGGATG 58.716 44.000 20.28 0.00 44.25 3.51
3494 4476 6.098409 GGAGTACCTAGAACTCATTTGGATGA 59.902 42.308 20.28 0.00 44.25 2.92
3525 4507 8.424274 AATTTGGTCTCATTCACTTTGAAAAC 57.576 30.769 0.00 0.00 40.12 2.43
3526 4508 6.522625 TTGGTCTCATTCACTTTGAAAACA 57.477 33.333 0.00 0.00 40.12 2.83
3527 4509 6.522625 TGGTCTCATTCACTTTGAAAACAA 57.477 33.333 0.00 0.00 40.12 2.83
3528 4510 6.563422 TGGTCTCATTCACTTTGAAAACAAG 58.437 36.000 0.00 0.00 40.12 3.16
3529 4511 6.376864 TGGTCTCATTCACTTTGAAAACAAGA 59.623 34.615 0.00 0.00 40.12 3.02
3530 4512 7.093988 TGGTCTCATTCACTTTGAAAACAAGAA 60.094 33.333 0.00 0.00 40.12 2.52
3531 4513 7.759433 GGTCTCATTCACTTTGAAAACAAGAAA 59.241 33.333 0.00 0.00 40.12 2.52
3532 4514 8.587111 GTCTCATTCACTTTGAAAACAAGAAAC 58.413 33.333 0.00 0.00 40.12 2.78
3533 4515 8.303156 TCTCATTCACTTTGAAAACAAGAAACA 58.697 29.630 0.00 0.00 40.12 2.83
3534 4516 8.464770 TCATTCACTTTGAAAACAAGAAACAG 57.535 30.769 0.00 0.00 40.12 3.16
3535 4517 8.303156 TCATTCACTTTGAAAACAAGAAACAGA 58.697 29.630 0.00 0.00 40.12 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 55 5.419471 CCCCCGATTTACATTAAGAAAACCA 59.581 40.000 0.00 0.00 0.00 3.67
93 750 6.858993 ACGTTTAGATCGAGATCAAATAGAGC 59.141 38.462 14.64 0.00 40.22 4.09
108 765 8.635877 AATGTCAGACATAAGACGTTTAGATC 57.364 34.615 16.71 0.00 40.12 2.75
130 787 6.369059 AGAATATGTCGAGGCAAAGAAATG 57.631 37.500 0.00 0.00 0.00 2.32
154 814 1.751544 ACCGCACATGCATGCATCT 60.752 52.632 30.07 16.91 46.47 2.90
184 844 1.053424 AAGGAAGGTGCACCGAGTAA 58.947 50.000 29.68 0.00 42.08 2.24
195 855 3.341270 TGGCACACCAAGGAAGGT 58.659 55.556 0.00 0.00 45.37 3.50
205 865 4.778446 CAAGCTCATTGTGGTGGCACAC 62.778 54.545 20.82 15.44 45.92 3.82
206 866 0.467844 AAGCTCATTGTGGTGGCACA 60.468 50.000 20.82 2.61 0.00 4.57
207 867 0.038892 CAAGCTCATTGTGGTGGCAC 60.039 55.000 9.70 9.70 33.95 5.01
208 868 0.178995 TCAAGCTCATTGTGGTGGCA 60.179 50.000 0.00 0.00 40.05 4.92
209 869 0.242017 GTCAAGCTCATTGTGGTGGC 59.758 55.000 0.00 0.00 40.05 5.01
210 870 0.883833 GGTCAAGCTCATTGTGGTGG 59.116 55.000 0.00 0.00 40.05 4.61
211 871 1.267806 GTGGTCAAGCTCATTGTGGTG 59.732 52.381 0.00 0.00 40.05 4.17
212 872 1.609208 GTGGTCAAGCTCATTGTGGT 58.391 50.000 0.00 0.00 40.05 4.16
213 873 0.883833 GGTGGTCAAGCTCATTGTGG 59.116 55.000 0.00 0.00 40.05 4.17
214 874 1.608055 TGGTGGTCAAGCTCATTGTG 58.392 50.000 0.00 0.00 40.05 3.33
215 875 2.165167 CATGGTGGTCAAGCTCATTGT 58.835 47.619 0.00 0.00 40.05 2.71
278 943 1.378882 GCTGGAAATGGCGAGCATGA 61.379 55.000 0.00 0.00 39.14 3.07
280 945 2.123428 GGCTGGAAATGGCGAGCAT 61.123 57.895 0.00 0.00 40.81 3.79
293 958 0.038343 CAAAAATGTCCACCGGCTGG 60.038 55.000 11.02 11.02 42.29 4.85
298 963 3.574614 GGATGAACAAAAATGTCCACCG 58.425 45.455 0.00 0.00 0.00 4.94
299 964 3.578282 AGGGATGAACAAAAATGTCCACC 59.422 43.478 0.00 0.00 0.00 4.61
313 978 4.329638 TTTATGGGCTTTGAGGGATGAA 57.670 40.909 0.00 0.00 0.00 2.57
317 982 3.850752 TGTTTTTATGGGCTTTGAGGGA 58.149 40.909 0.00 0.00 0.00 4.20
321 986 7.060383 TGAATCTTGTTTTTATGGGCTTTGA 57.940 32.000 0.00 0.00 0.00 2.69
328 993 7.382218 GTGGTCACTTGAATCTTGTTTTTATGG 59.618 37.037 0.00 0.00 0.00 2.74
329 994 7.920151 TGTGGTCACTTGAATCTTGTTTTTATG 59.080 33.333 2.66 0.00 0.00 1.90
336 1001 4.978099 AGATGTGGTCACTTGAATCTTGT 58.022 39.130 2.66 0.00 0.00 3.16
345 1010 4.706842 AAGTGGTAAGATGTGGTCACTT 57.293 40.909 0.00 0.00 39.63 3.16
347 1012 4.385825 TCAAAGTGGTAAGATGTGGTCAC 58.614 43.478 0.00 0.00 0.00 3.67
349 1014 4.819630 TGTTCAAAGTGGTAAGATGTGGTC 59.180 41.667 0.00 0.00 0.00 4.02
357 1022 5.476599 TGGATTGGATGTTCAAAGTGGTAAG 59.523 40.000 0.00 0.00 0.00 2.34
384 1049 2.368875 CTGAGGGTCTATATTTGCCCGT 59.631 50.000 0.00 0.00 45.48 5.28
385 1050 2.289694 CCTGAGGGTCTATATTTGCCCG 60.290 54.545 0.00 0.00 45.48 6.13
386 1051 2.553247 GCCTGAGGGTCTATATTTGCCC 60.553 54.545 0.00 0.00 41.36 5.36
395 1060 2.363795 CGGTGGCCTGAGGGTCTA 60.364 66.667 3.32 0.00 38.23 2.59
491 1156 8.970020 TGGGCATTTATATGATGGATCAAATAC 58.030 33.333 0.00 0.00 40.69 1.89
492 1157 9.717994 ATGGGCATTTATATGATGGATCAAATA 57.282 29.630 0.00 0.00 40.69 1.40
495 1160 6.127281 GCATGGGCATTTATATGATGGATCAA 60.127 38.462 0.00 0.00 39.16 2.57
508 1173 7.310547 CCCATTTATTATCAGCATGGGCATTTA 60.311 37.037 2.59 0.00 45.98 1.40
510 1175 5.046159 CCCATTTATTATCAGCATGGGCATT 60.046 40.000 2.59 0.00 45.98 3.56
543 1208 3.391296 TGAGGGTAATGTAGGATGCCTTC 59.609 47.826 0.00 0.00 34.61 3.46
548 1213 7.281774 GCAATGATATGAGGGTAATGTAGGATG 59.718 40.741 0.00 0.00 0.00 3.51
550 1215 6.272090 TGCAATGATATGAGGGTAATGTAGGA 59.728 38.462 0.00 0.00 0.00 2.94
584 1250 0.684153 ATGGGAATGGGGTTTGCTCG 60.684 55.000 0.00 0.00 0.00 5.03
595 1279 7.613551 ACCCTAGTAACTAGTAATGGGAATG 57.386 40.000 19.55 3.38 30.34 2.67
607 1291 8.542926 GTTTTATCCCAAGAACCCTAGTAACTA 58.457 37.037 0.00 0.00 0.00 2.24
610 1294 6.724351 GGTTTTATCCCAAGAACCCTAGTAA 58.276 40.000 0.00 0.00 36.41 2.24
686 1410 9.700831 AGGAATTAGTTAAAGACAGCCATTAAT 57.299 29.630 0.00 0.00 0.00 1.40
701 1588 7.001674 TCACCAAGAGCAAAAGGAATTAGTTA 58.998 34.615 0.00 0.00 0.00 2.24
730 1617 1.884464 CCATGACACGCGAGGGATG 60.884 63.158 15.93 11.47 38.45 3.51
754 1641 3.928992 AGCTATCAATCGGAATGCATACG 59.071 43.478 15.29 15.29 32.45 3.06
755 1642 5.006165 GCTAGCTATCAATCGGAATGCATAC 59.994 44.000 7.70 0.00 32.45 2.39
768 1657 5.129320 TCCATTCTCAACAGCTAGCTATCAA 59.871 40.000 18.86 5.13 0.00 2.57
825 1714 3.758023 TGCATGGTGGTGCTTATATATGC 59.242 43.478 12.51 12.51 45.27 3.14
827 1716 6.070951 AGATGCATGGTGGTGCTTATATAT 57.929 37.500 2.46 0.00 45.27 0.86
856 1756 2.858344 GCAGTAAATCGTACGTGCTGAT 59.142 45.455 21.01 3.94 0.00 2.90
975 1889 2.048222 TGCAAGACGAAGAGCCGG 60.048 61.111 0.00 0.00 0.00 6.13
976 1890 2.734673 GCTGCAAGACGAAGAGCCG 61.735 63.158 0.00 0.00 34.07 5.52
1010 1924 2.055042 AGTAGCACGAGGAGGCAGG 61.055 63.158 0.00 0.00 0.00 4.85
1111 2025 3.917760 GGAGACGATGGCCGGGAG 61.918 72.222 2.18 0.00 43.93 4.30
1669 2589 2.507944 GTCCAGCCTCCGCATCAT 59.492 61.111 0.00 0.00 37.52 2.45
2007 2949 1.526686 GTTGGGTCCGACGGGTTTT 60.527 57.895 15.25 0.00 33.83 2.43
2530 3484 5.039333 GGTACAAGTACGCATAGGTTACTG 58.961 45.833 4.45 0.00 36.94 2.74
2532 3486 4.037690 CGGTACAAGTACGCATAGGTTAC 58.962 47.826 4.45 0.00 36.94 2.50
2533 3487 3.694072 ACGGTACAAGTACGCATAGGTTA 59.306 43.478 4.45 0.00 36.94 2.85
2534 3488 2.493278 ACGGTACAAGTACGCATAGGTT 59.507 45.455 4.45 0.00 36.94 3.50
2535 3489 2.094675 ACGGTACAAGTACGCATAGGT 58.905 47.619 4.45 0.00 36.94 3.08
2536 3490 2.855963 CAACGGTACAAGTACGCATAGG 59.144 50.000 4.45 0.00 36.94 2.57
2537 3491 2.280708 GCAACGGTACAAGTACGCATAG 59.719 50.000 4.45 0.00 36.94 2.23
2622 3589 0.107831 TTACTGGACACCTGCACACC 59.892 55.000 0.00 0.00 0.00 4.16
2676 3643 3.378339 CGAATGACTTATACACCGGGAC 58.622 50.000 6.32 0.00 0.00 4.46
2677 3644 2.223876 GCGAATGACTTATACACCGGGA 60.224 50.000 6.32 0.00 0.00 5.14
2678 3645 2.132762 GCGAATGACTTATACACCGGG 58.867 52.381 6.32 0.00 0.00 5.73
2679 3646 1.784856 CGCGAATGACTTATACACCGG 59.215 52.381 0.00 0.00 0.00 5.28
2680 3647 2.456989 ACGCGAATGACTTATACACCG 58.543 47.619 15.93 0.00 0.00 4.94
2681 3648 4.604976 ACTACGCGAATGACTTATACACC 58.395 43.478 15.93 0.00 0.00 4.16
2684 3651 6.796072 CCTAGAACTACGCGAATGACTTATAC 59.204 42.308 15.93 0.00 0.00 1.47
2686 3653 5.298777 ACCTAGAACTACGCGAATGACTTAT 59.701 40.000 15.93 0.00 0.00 1.73
2687 3654 4.637534 ACCTAGAACTACGCGAATGACTTA 59.362 41.667 15.93 0.00 0.00 2.24
2688 3655 3.442977 ACCTAGAACTACGCGAATGACTT 59.557 43.478 15.93 0.00 0.00 3.01
2690 3657 3.181503 TGACCTAGAACTACGCGAATGAC 60.182 47.826 15.93 0.66 0.00 3.06
2692 3659 3.416119 TGACCTAGAACTACGCGAATG 57.584 47.619 15.93 4.47 0.00 2.67
2693 3660 4.650754 ATTGACCTAGAACTACGCGAAT 57.349 40.909 15.93 0.00 0.00 3.34
2694 3661 5.565592 TTATTGACCTAGAACTACGCGAA 57.434 39.130 15.93 0.00 0.00 4.70
2695 3662 5.762825 ATTATTGACCTAGAACTACGCGA 57.237 39.130 15.93 0.00 0.00 5.87
2696 3663 6.823678 AAATTATTGACCTAGAACTACGCG 57.176 37.500 3.53 3.53 0.00 6.01
2697 3664 9.310716 AGTTAAATTATTGACCTAGAACTACGC 57.689 33.333 0.00 0.00 0.00 4.42
2754 3721 9.970395 CACACGGGTGTAGTTTCTAAATATATA 57.030 33.333 10.41 0.00 42.83 0.86
2755 3722 7.929785 CCACACGGGTGTAGTTTCTAAATATAT 59.070 37.037 18.16 0.00 42.83 0.86
2756 3723 7.123997 TCCACACGGGTGTAGTTTCTAAATATA 59.876 37.037 18.16 0.00 42.83 0.86
2757 3724 6.070653 TCCACACGGGTGTAGTTTCTAAATAT 60.071 38.462 18.16 0.00 42.83 1.28
2758 3725 5.245751 TCCACACGGGTGTAGTTTCTAAATA 59.754 40.000 18.16 0.00 42.83 1.40
2759 3726 4.040706 TCCACACGGGTGTAGTTTCTAAAT 59.959 41.667 18.16 0.00 42.83 1.40
2760 3727 3.387374 TCCACACGGGTGTAGTTTCTAAA 59.613 43.478 18.16 0.00 42.83 1.85
2761 3728 2.964464 TCCACACGGGTGTAGTTTCTAA 59.036 45.455 18.16 0.00 42.83 2.10
2762 3729 2.596346 TCCACACGGGTGTAGTTTCTA 58.404 47.619 18.16 0.00 42.83 2.10
2763 3730 1.416243 TCCACACGGGTGTAGTTTCT 58.584 50.000 18.16 0.00 42.83 2.52
2764 3731 2.243602 TTCCACACGGGTGTAGTTTC 57.756 50.000 18.16 0.00 42.83 2.78
2765 3732 2.713863 TTTCCACACGGGTGTAGTTT 57.286 45.000 18.16 0.00 42.83 2.66
2766 3733 2.370849 AGATTTCCACACGGGTGTAGTT 59.629 45.455 18.16 0.00 42.83 2.24
2767 3734 1.975680 AGATTTCCACACGGGTGTAGT 59.024 47.619 18.16 0.53 42.83 2.73
2768 3735 2.762535 AGATTTCCACACGGGTGTAG 57.237 50.000 18.16 1.84 42.83 2.74
2769 3736 3.056393 CACTAGATTTCCACACGGGTGTA 60.056 47.826 18.16 0.00 42.83 2.90
2770 3737 1.975680 ACTAGATTTCCACACGGGTGT 59.024 47.619 18.16 0.00 46.17 4.16
2771 3738 2.346803 CACTAGATTTCCACACGGGTG 58.653 52.381 11.92 11.92 44.85 4.61
2772 3739 1.278127 CCACTAGATTTCCACACGGGT 59.722 52.381 0.00 0.00 38.11 5.28
2773 3740 1.278127 ACCACTAGATTTCCACACGGG 59.722 52.381 0.00 0.00 38.37 5.28
2774 3741 2.762535 ACCACTAGATTTCCACACGG 57.237 50.000 0.00 0.00 0.00 4.94
2775 3742 6.145338 AGTATACCACTAGATTTCCACACG 57.855 41.667 0.00 0.00 34.98 4.49
2776 3743 8.788325 AAAAGTATACCACTAGATTTCCACAC 57.212 34.615 0.00 0.00 36.04 3.82
2777 3744 8.598916 TGAAAAGTATACCACTAGATTTCCACA 58.401 33.333 0.00 0.00 36.04 4.17
2778 3745 9.614792 ATGAAAAGTATACCACTAGATTTCCAC 57.385 33.333 0.00 0.00 36.04 4.02
2779 3746 9.613428 CATGAAAAGTATACCACTAGATTTCCA 57.387 33.333 0.00 0.00 36.04 3.53
2780 3747 9.832445 TCATGAAAAGTATACCACTAGATTTCC 57.168 33.333 0.00 0.00 36.04 3.13
2823 3790 9.407380 TGATACATGCAATTAATGTAGGAAACT 57.593 29.630 14.87 2.39 42.24 2.66
2826 3793 9.571816 TGATGATACATGCAATTAATGTAGGAA 57.428 29.630 14.87 6.94 42.24 3.36
2827 3794 9.571816 TTGATGATACATGCAATTAATGTAGGA 57.428 29.630 14.87 7.48 42.24 2.94
2828 3795 9.616634 GTTGATGATACATGCAATTAATGTAGG 57.383 33.333 14.87 0.00 42.24 3.18
2831 3798 8.071967 CGAGTTGATGATACATGCAATTAATGT 58.928 33.333 10.01 10.01 41.14 2.71
2856 3823 6.530913 AATATGTCTTCGGATCAATCAACG 57.469 37.500 0.00 0.00 0.00 4.10
2867 3834 7.941795 AGTTTCGGTATAAATATGTCTTCGG 57.058 36.000 0.00 0.00 0.00 4.30
2898 3865 3.882326 CAGCCCAGCCCGATCCAT 61.882 66.667 0.00 0.00 0.00 3.41
2909 3879 1.454295 CACTATGCATGCCAGCCCA 60.454 57.895 16.68 0.00 0.00 5.36
2959 3932 4.562757 GCATTGTCCCTACTTACACAGTCA 60.563 45.833 0.00 0.00 36.88 3.41
2966 3939 1.949465 CCGGCATTGTCCCTACTTAC 58.051 55.000 0.00 0.00 0.00 2.34
3091 4064 3.380954 ACGAACATGGCATGCATCAATAA 59.619 39.130 26.70 0.00 0.00 1.40
3093 4066 1.752498 ACGAACATGGCATGCATCAAT 59.248 42.857 26.70 13.08 0.00 2.57
3094 4067 1.175654 ACGAACATGGCATGCATCAA 58.824 45.000 26.70 1.71 0.00 2.57
3123 4098 0.589223 CCCGTTGCACGTACAAACAT 59.411 50.000 2.00 0.00 40.58 2.71
3193 4168 6.561737 TGATACTAGACTAGATGCGAAAGG 57.438 41.667 16.55 0.00 0.00 3.11
3210 4185 9.499479 CTAACTTTGATATTCCTGCATGATACT 57.501 33.333 0.00 0.00 0.00 2.12
3227 4202 3.365832 GTCGTCGTCACACTAACTTTGA 58.634 45.455 0.00 0.00 0.00 2.69
3230 4205 2.028287 CGTCGTCGTCACACTAACTT 57.972 50.000 0.00 0.00 0.00 2.66
3249 4224 2.126189 GGGGACGTACGTGAGCAC 60.126 66.667 28.16 12.76 0.00 4.40
3250 4225 1.870055 GAAGGGGACGTACGTGAGCA 61.870 60.000 28.16 0.00 0.00 4.26
3251 4226 1.153881 GAAGGGGACGTACGTGAGC 60.154 63.158 28.16 11.58 0.00 4.26
3252 4227 1.136147 CGAAGGGGACGTACGTGAG 59.864 63.158 28.16 4.88 0.00 3.51
3253 4228 1.577328 GACGAAGGGGACGTACGTGA 61.577 60.000 28.16 0.00 43.97 4.35
3254 4229 1.154150 GACGAAGGGGACGTACGTG 60.154 63.158 28.16 11.94 43.97 4.49
3275 4250 2.484770 CCGTGTCCGTCCATCCATTAAT 60.485 50.000 0.00 0.00 0.00 1.40
3311 4286 0.467384 CTGGTGGCATAGAGGGAGTG 59.533 60.000 0.00 0.00 0.00 3.51
3317 4292 3.234353 TCTCCATACTGGTGGCATAGAG 58.766 50.000 8.46 0.00 39.03 2.43
3318 4293 3.328535 TCTCCATACTGGTGGCATAGA 57.671 47.619 8.46 0.00 39.03 1.98
3320 4295 3.118038 GGTTTCTCCATACTGGTGGCATA 60.118 47.826 0.00 0.00 39.03 3.14
3321 4296 2.357154 GGTTTCTCCATACTGGTGGCAT 60.357 50.000 0.00 0.00 39.03 4.40
3322 4297 1.004277 GGTTTCTCCATACTGGTGGCA 59.996 52.381 0.00 0.00 39.03 4.92
3402 4384 8.567948 GGTGGTCGATGAATTTATATCACAAAT 58.432 33.333 0.00 0.00 0.00 2.32
3403 4385 7.012894 GGGTGGTCGATGAATTTATATCACAAA 59.987 37.037 0.00 0.00 0.00 2.83
3404 4386 6.485313 GGGTGGTCGATGAATTTATATCACAA 59.515 38.462 0.00 0.00 0.00 3.33
3405 4387 5.995282 GGGTGGTCGATGAATTTATATCACA 59.005 40.000 0.00 0.00 0.00 3.58
3406 4388 5.411669 GGGGTGGTCGATGAATTTATATCAC 59.588 44.000 0.00 0.00 0.00 3.06
3407 4389 5.556915 GGGGTGGTCGATGAATTTATATCA 58.443 41.667 0.00 0.00 0.00 2.15
3408 4390 4.630069 CGGGGTGGTCGATGAATTTATATC 59.370 45.833 0.00 0.00 0.00 1.63
3409 4391 4.041198 ACGGGGTGGTCGATGAATTTATAT 59.959 41.667 0.00 0.00 0.00 0.86
3410 4392 3.388676 ACGGGGTGGTCGATGAATTTATA 59.611 43.478 0.00 0.00 0.00 0.98
3411 4393 2.171870 ACGGGGTGGTCGATGAATTTAT 59.828 45.455 0.00 0.00 0.00 1.40
3412 4394 1.555992 ACGGGGTGGTCGATGAATTTA 59.444 47.619 0.00 0.00 0.00 1.40
3413 4395 0.326927 ACGGGGTGGTCGATGAATTT 59.673 50.000 0.00 0.00 0.00 1.82
3414 4396 0.326927 AACGGGGTGGTCGATGAATT 59.673 50.000 0.00 0.00 0.00 2.17
3415 4397 0.392461 CAACGGGGTGGTCGATGAAT 60.392 55.000 0.00 0.00 33.27 2.57
3416 4398 1.004320 CAACGGGGTGGTCGATGAA 60.004 57.895 0.00 0.00 33.27 2.57
3417 4399 2.660206 CAACGGGGTGGTCGATGA 59.340 61.111 0.00 0.00 33.27 2.92
3418 4400 2.435938 CCAACGGGGTGGTCGATG 60.436 66.667 0.00 0.00 33.63 3.84
3427 4409 1.106944 AGCTTTTGTCACCAACGGGG 61.107 55.000 0.00 0.00 44.81 5.73
3428 4410 0.744281 AAGCTTTTGTCACCAACGGG 59.256 50.000 0.00 0.00 41.29 5.28
3429 4411 1.269051 GGAAGCTTTTGTCACCAACGG 60.269 52.381 0.00 0.00 0.00 4.44
3430 4412 1.676006 AGGAAGCTTTTGTCACCAACG 59.324 47.619 0.00 0.00 0.00 4.10
3431 4413 2.687935 TGAGGAAGCTTTTGTCACCAAC 59.312 45.455 0.00 0.00 0.00 3.77
3432 4414 2.687935 GTGAGGAAGCTTTTGTCACCAA 59.312 45.455 18.93 0.14 32.95 3.67
3433 4415 2.297701 GTGAGGAAGCTTTTGTCACCA 58.702 47.619 18.93 3.22 32.95 4.17
3435 4417 2.033424 GTGGTGAGGAAGCTTTTGTCAC 59.967 50.000 20.43 20.43 37.41 3.67
3436 4418 2.297701 GTGGTGAGGAAGCTTTTGTCA 58.702 47.619 0.00 1.06 0.00 3.58
3437 4419 2.297701 TGTGGTGAGGAAGCTTTTGTC 58.702 47.619 0.00 0.00 0.00 3.18
3438 4420 2.435372 TGTGGTGAGGAAGCTTTTGT 57.565 45.000 0.00 0.00 0.00 2.83
3439 4421 4.326504 AATTGTGGTGAGGAAGCTTTTG 57.673 40.909 0.00 0.00 0.00 2.44
3440 4422 4.405358 TGAAATTGTGGTGAGGAAGCTTTT 59.595 37.500 0.00 0.00 0.00 2.27
3441 4423 3.960102 TGAAATTGTGGTGAGGAAGCTTT 59.040 39.130 0.00 0.00 0.00 3.51
3442 4424 3.565307 TGAAATTGTGGTGAGGAAGCTT 58.435 40.909 0.00 0.00 0.00 3.74
3443 4425 3.228188 TGAAATTGTGGTGAGGAAGCT 57.772 42.857 0.00 0.00 0.00 3.74
3444 4426 4.320608 TTTGAAATTGTGGTGAGGAAGC 57.679 40.909 0.00 0.00 0.00 3.86
3445 4427 5.754890 CCTTTTTGAAATTGTGGTGAGGAAG 59.245 40.000 0.00 0.00 0.00 3.46
3446 4428 5.396213 CCCTTTTTGAAATTGTGGTGAGGAA 60.396 40.000 0.00 0.00 0.00 3.36
3447 4429 4.100808 CCCTTTTTGAAATTGTGGTGAGGA 59.899 41.667 0.00 0.00 0.00 3.71
3448 4430 4.100808 TCCCTTTTTGAAATTGTGGTGAGG 59.899 41.667 0.00 0.00 0.00 3.86
3449 4431 5.163416 ACTCCCTTTTTGAAATTGTGGTGAG 60.163 40.000 0.00 0.00 0.00 3.51
3450 4432 4.714308 ACTCCCTTTTTGAAATTGTGGTGA 59.286 37.500 0.00 0.00 0.00 4.02
3451 4433 5.022282 ACTCCCTTTTTGAAATTGTGGTG 57.978 39.130 0.00 0.00 0.00 4.17
3452 4434 5.069914 GGTACTCCCTTTTTGAAATTGTGGT 59.930 40.000 0.00 0.00 0.00 4.16
3453 4435 5.304357 AGGTACTCCCTTTTTGAAATTGTGG 59.696 40.000 0.00 0.00 42.73 4.17
3454 4436 6.405278 AGGTACTCCCTTTTTGAAATTGTG 57.595 37.500 0.00 0.00 42.73 3.33
3455 4437 7.523415 TCTAGGTACTCCCTTTTTGAAATTGT 58.477 34.615 0.00 0.00 42.73 2.71
3456 4438 7.996098 TCTAGGTACTCCCTTTTTGAAATTG 57.004 36.000 0.00 0.00 42.73 2.32
3457 4439 8.225416 AGTTCTAGGTACTCCCTTTTTGAAATT 58.775 33.333 0.00 0.00 42.73 1.82
3458 4440 7.756614 AGTTCTAGGTACTCCCTTTTTGAAAT 58.243 34.615 0.00 0.00 42.73 2.17
3459 4441 7.145474 AGTTCTAGGTACTCCCTTTTTGAAA 57.855 36.000 0.00 0.00 42.73 2.69
3460 4442 6.328148 TGAGTTCTAGGTACTCCCTTTTTGAA 59.672 38.462 17.72 0.00 42.73 2.69
3461 4443 5.842328 TGAGTTCTAGGTACTCCCTTTTTGA 59.158 40.000 17.72 1.16 42.73 2.69
3462 4444 6.110411 TGAGTTCTAGGTACTCCCTTTTTG 57.890 41.667 17.72 0.00 42.73 2.44
3463 4445 6.954352 ATGAGTTCTAGGTACTCCCTTTTT 57.046 37.500 17.72 1.12 42.73 1.94
3464 4446 6.954352 AATGAGTTCTAGGTACTCCCTTTT 57.046 37.500 17.72 8.13 42.73 2.27
3465 4447 6.296489 CCAAATGAGTTCTAGGTACTCCCTTT 60.296 42.308 17.72 14.83 42.73 3.11
3466 4448 5.189934 CCAAATGAGTTCTAGGTACTCCCTT 59.810 44.000 17.72 11.36 42.73 3.95
3467 4449 8.784553 CATCCAAATGAGTTCTAGGTACTCCCT 61.785 44.444 17.72 7.45 41.02 4.20
3468 4450 4.715297 TCCAAATGAGTTCTAGGTACTCCC 59.285 45.833 17.72 2.30 41.02 4.30
3469 4451 5.934402 TCCAAATGAGTTCTAGGTACTCC 57.066 43.478 17.72 6.18 41.02 3.85
3470 4452 7.113658 TCATCCAAATGAGTTCTAGGTACTC 57.886 40.000 15.11 15.11 41.86 2.59
3499 4481 9.528018 GTTTTCAAAGTGAATGAGACCAAATTA 57.472 29.630 0.00 0.00 36.11 1.40
3500 4482 8.040132 TGTTTTCAAAGTGAATGAGACCAAATT 58.960 29.630 0.00 0.00 36.11 1.82
3501 4483 7.555087 TGTTTTCAAAGTGAATGAGACCAAAT 58.445 30.769 0.00 0.00 36.11 2.32
3502 4484 6.929625 TGTTTTCAAAGTGAATGAGACCAAA 58.070 32.000 0.00 0.00 36.11 3.28
3503 4485 6.522625 TGTTTTCAAAGTGAATGAGACCAA 57.477 33.333 0.00 0.00 36.11 3.67
3504 4486 6.376864 TCTTGTTTTCAAAGTGAATGAGACCA 59.623 34.615 0.00 0.00 39.47 4.02
3505 4487 6.795399 TCTTGTTTTCAAAGTGAATGAGACC 58.205 36.000 0.00 0.00 39.47 3.85
3506 4488 8.587111 GTTTCTTGTTTTCAAAGTGAATGAGAC 58.413 33.333 0.00 0.00 39.47 3.36
3507 4489 8.303156 TGTTTCTTGTTTTCAAAGTGAATGAGA 58.697 29.630 0.00 0.00 39.47 3.27
3508 4490 8.464770 TGTTTCTTGTTTTCAAAGTGAATGAG 57.535 30.769 0.00 0.00 39.47 2.90
3509 4491 8.303156 TCTGTTTCTTGTTTTCAAAGTGAATGA 58.697 29.630 0.00 0.00 39.47 2.57
3510 4492 8.464770 TCTGTTTCTTGTTTTCAAAGTGAATG 57.535 30.769 0.00 0.00 39.47 2.67


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

AutoCloner maintained by Alex Coulton.