Multiple sequence alignment - TraesCS5A01G446600

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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 TraesCS5A01G446600 chr5A 100.000 3320 0 0 1 3320 626258437 626261756 0.000000e+00 6131.0
1 TraesCS5A01G446600 chr7D 93.316 1122 74 1 2199 3320 528006200 528007320 0.000000e+00 1655.0
2 TraesCS5A01G446600 chr7D 92.982 456 32 0 1603 2058 527995025 527995480 0.000000e+00 665.0
3 TraesCS5A01G446600 chr7D 84.581 454 48 9 1129 1582 527994320 527994751 6.580000e-117 431.0
4 TraesCS5A01G446600 chr7D 91.700 253 18 1 897 1146 527994054 527994306 6.820000e-92 348.0
5 TraesCS5A01G446600 chr7D 95.862 145 6 0 2056 2200 528003566 528003710 5.540000e-58 235.0
6 TraesCS5A01G446600 chr7A 91.273 1123 95 3 2199 3320 494992932 494991812 0.000000e+00 1528.0
7 TraesCS5A01G446600 chr7A 84.858 1334 180 15 884 2200 465769062 465767734 0.000000e+00 1325.0
8 TraesCS5A01G446600 chr7A 87.979 1123 129 6 2199 3319 299589608 299590726 0.000000e+00 1321.0
9 TraesCS5A01G446600 chr7A 89.452 493 50 2 1709 2200 299586662 299587153 3.640000e-174 621.0
10 TraesCS5A01G446600 chr7A 89.431 492 52 0 1709 2200 482724628 482725119 3.640000e-174 621.0
11 TraesCS5A01G446600 chr7A 81.884 690 79 24 874 1526 299585627 299586307 1.050000e-149 540.0
12 TraesCS5A01G446600 chr7A 86.290 248 32 2 1288 1534 482724355 482724601 5.460000e-68 268.0
13 TraesCS5A01G446600 chr3B 91.324 1118 95 2 2203 3319 478085284 478084168 0.000000e+00 1526.0
14 TraesCS5A01G446600 chr3B 90.455 1121 102 4 2203 3320 740490023 740491141 0.000000e+00 1472.0
15 TraesCS5A01G446600 chr1D 90.404 1115 104 3 2204 3317 236271105 236272217 0.000000e+00 1463.0
16 TraesCS5A01G446600 chr1A 89.785 1116 112 2 2203 3317 242007795 242008909 0.000000e+00 1428.0
17 TraesCS5A01G446600 chr1B 87.611 1130 136 4 2193 3320 390341825 390342952 0.000000e+00 1308.0
18 TraesCS5A01G446600 chr1B 87.216 485 49 10 1725 2197 390317773 390318256 1.050000e-149 540.0
19 TraesCS5A01G446600 chr6A 87.578 1119 138 1 2199 3317 14768187 14769304 0.000000e+00 1295.0
20 TraesCS5A01G446600 chr6A 84.679 1325 172 15 902 2200 14741668 14742987 0.000000e+00 1293.0
21 TraesCS5A01G446600 chr6A 85.776 232 24 6 894 1117 15317078 15317308 1.540000e-58 237.0
22 TraesCS5A01G446600 chr2B 86.294 788 93 7 888 1663 326341406 326340622 0.000000e+00 843.0
23 TraesCS5A01G446600 chr2B 85.159 566 72 1 1635 2200 767935379 767935932 1.340000e-158 569.0
24 TraesCS5A01G446600 chr2B 90.145 345 34 0 1856 2200 326340618 326340274 1.820000e-122 449.0
25 TraesCS5A01G446600 chr2B 81.404 570 77 9 1010 1550 767934598 767935167 3.930000e-119 438.0
26 TraesCS5A01G446600 chr2B 90.278 72 7 0 885 956 767934222 767934293 9.810000e-16 95.3
27 TraesCS5A01G446600 chr7B 89.021 674 69 3 1528 2200 615173846 615173177 0.000000e+00 830.0
28 TraesCS5A01G446600 chr7B 80.851 705 89 20 895 1562 615174540 615173845 2.280000e-141 512.0
29 TraesCS5A01G446600 chr5D 74.953 1058 204 50 1166 2200 448356684 448357703 2.370000e-116 429.0
30 TraesCS5A01G446600 chr5D 84.491 432 32 11 7 437 501053610 501053213 8.630000e-106 394.0
31 TraesCS5A01G446600 chr5D 86.705 346 31 5 436 771 501053183 501052843 1.450000e-98 370.0
32 TraesCS5A01G446600 chr3A 79.496 278 49 6 1175 1448 83248646 83248373 1.220000e-44 191.0
33 TraesCS5A01G446600 chr3D 77.188 320 63 10 1134 1448 319850448 319850134 9.460000e-41 178.0


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 TraesCS5A01G446600 chr5A 626258437 626261756 3319 False 6131.000000 6131 100.000000 1 3320 1 chr5A.!!$F1 3319
1 TraesCS5A01G446600 chr7D 528003566 528007320 3754 False 945.000000 1655 94.589000 2056 3320 2 chr7D.!!$F2 1264
2 TraesCS5A01G446600 chr7D 527994054 527995480 1426 False 481.333333 665 89.754333 897 2058 3 chr7D.!!$F1 1161
3 TraesCS5A01G446600 chr7A 494991812 494992932 1120 True 1528.000000 1528 91.273000 2199 3320 1 chr7A.!!$R2 1121
4 TraesCS5A01G446600 chr7A 465767734 465769062 1328 True 1325.000000 1325 84.858000 884 2200 1 chr7A.!!$R1 1316
5 TraesCS5A01G446600 chr7A 299585627 299590726 5099 False 827.333333 1321 86.438333 874 3319 3 chr7A.!!$F1 2445
6 TraesCS5A01G446600 chr7A 482724355 482725119 764 False 444.500000 621 87.860500 1288 2200 2 chr7A.!!$F2 912
7 TraesCS5A01G446600 chr3B 478084168 478085284 1116 True 1526.000000 1526 91.324000 2203 3319 1 chr3B.!!$R1 1116
8 TraesCS5A01G446600 chr3B 740490023 740491141 1118 False 1472.000000 1472 90.455000 2203 3320 1 chr3B.!!$F1 1117
9 TraesCS5A01G446600 chr1D 236271105 236272217 1112 False 1463.000000 1463 90.404000 2204 3317 1 chr1D.!!$F1 1113
10 TraesCS5A01G446600 chr1A 242007795 242008909 1114 False 1428.000000 1428 89.785000 2203 3317 1 chr1A.!!$F1 1114
11 TraesCS5A01G446600 chr1B 390341825 390342952 1127 False 1308.000000 1308 87.611000 2193 3320 1 chr1B.!!$F2 1127
12 TraesCS5A01G446600 chr6A 14768187 14769304 1117 False 1295.000000 1295 87.578000 2199 3317 1 chr6A.!!$F2 1118
13 TraesCS5A01G446600 chr6A 14741668 14742987 1319 False 1293.000000 1293 84.679000 902 2200 1 chr6A.!!$F1 1298
14 TraesCS5A01G446600 chr2B 326340274 326341406 1132 True 646.000000 843 88.219500 888 2200 2 chr2B.!!$R1 1312
15 TraesCS5A01G446600 chr2B 767934222 767935932 1710 False 367.433333 569 85.613667 885 2200 3 chr2B.!!$F1 1315
16 TraesCS5A01G446600 chr7B 615173177 615174540 1363 True 671.000000 830 84.936000 895 2200 2 chr7B.!!$R1 1305
17 TraesCS5A01G446600 chr5D 448356684 448357703 1019 False 429.000000 429 74.953000 1166 2200 1 chr5D.!!$F1 1034
18 TraesCS5A01G446600 chr5D 501052843 501053610 767 True 382.000000 394 85.598000 7 771 2 chr5D.!!$R1 764

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
391 392 0.179094 TTGATGGTATCCACGGCGAC 60.179 55.0 16.62 0.0 35.8 5.19 F
716 758 0.250166 ACGAAGCGGCAGTTAACCTT 60.250 50.0 1.45 0.0 0.0 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1362 1715 0.67964 GAACCCAATGACGATGGCCA 60.680 55.0 8.56 8.56 36.58 5.36 R
2711 6037 0.03467 GGAGCAATGTCAAGAGGGCT 60.035 55.0 0.00 0.00 0.00 5.19 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
25 26 7.881775 ATATAAAACTCCATTCTGTCCAACC 57.118 36.000 0.00 0.00 0.00 3.77
37 38 3.142174 CTGTCCAACCAAGAACTCCTTC 58.858 50.000 0.00 0.00 31.42 3.46
39 40 3.202151 TGTCCAACCAAGAACTCCTTCTT 59.798 43.478 0.00 0.00 46.01 2.52
103 104 1.941812 GTGGTGCCACGAGTTTCTG 59.058 57.895 5.53 0.00 37.19 3.02
104 105 1.227823 TGGTGCCACGAGTTTCTGG 60.228 57.895 0.00 0.00 0.00 3.86
117 118 4.865365 CGAGTTTCTGGTAGATTCCACTTC 59.135 45.833 0.00 0.00 33.55 3.01
128 129 7.037586 TGGTAGATTCCACTTCTTCATACCTTT 60.038 37.037 0.00 0.00 31.96 3.11
148 149 2.018542 TTGGTTAGGTACGCAGATGC 57.981 50.000 0.00 0.00 37.78 3.91
170 171 3.744530 CGACCTCCAAACCAAAGAACTCT 60.745 47.826 0.00 0.00 0.00 3.24
171 172 3.555966 ACCTCCAAACCAAAGAACTCTG 58.444 45.455 0.00 0.00 0.00 3.35
172 173 3.053619 ACCTCCAAACCAAAGAACTCTGT 60.054 43.478 0.00 0.00 0.00 3.41
182 183 0.759346 AGAACTCTGTGGCCGTCTTT 59.241 50.000 0.00 0.00 0.00 2.52
186 187 1.151668 CTCTGTGGCCGTCTTTTGAG 58.848 55.000 0.00 0.00 0.00 3.02
196 197 1.740025 CGTCTTTTGAGAATCCAGGGC 59.260 52.381 0.00 0.00 0.00 5.19
200 201 2.795231 TTTGAGAATCCAGGGCTCTG 57.205 50.000 6.61 6.61 40.59 3.35
261 262 8.146053 TCTTTATTCAAGTGGGTCTAATCTCA 57.854 34.615 0.00 0.00 33.66 3.27
267 268 6.601332 TCAAGTGGGTCTAATCTCAAAGTTT 58.399 36.000 0.00 0.00 0.00 2.66
275 276 6.456181 GGTCTAATCTCAAAGTTTGCGAGATG 60.456 42.308 16.45 8.51 43.92 2.90
277 278 3.401033 TCTCAAAGTTTGCGAGATGGA 57.599 42.857 10.90 0.00 30.94 3.41
278 279 3.067106 TCTCAAAGTTTGCGAGATGGAC 58.933 45.455 10.90 0.00 30.94 4.02
293 294 4.204012 AGATGGACACTACTGACTAGCTC 58.796 47.826 0.00 0.00 0.00 4.09
299 300 2.288458 CACTACTGACTAGCTCTACGCC 59.712 54.545 0.00 0.00 40.39 5.68
330 331 3.610911 GAAGCCTTAATGTAGCACTGGT 58.389 45.455 0.00 0.00 0.00 4.00
331 332 3.721087 AGCCTTAATGTAGCACTGGTT 57.279 42.857 0.00 0.00 0.00 3.67
332 333 3.347216 AGCCTTAATGTAGCACTGGTTG 58.653 45.455 0.00 0.00 0.00 3.77
342 343 3.277652 CACTGGTTGCTTTGCTTGG 57.722 52.632 0.00 0.00 0.00 3.61
343 344 0.461135 CACTGGTTGCTTTGCTTGGT 59.539 50.000 0.00 0.00 0.00 3.67
344 345 0.746659 ACTGGTTGCTTTGCTTGGTC 59.253 50.000 0.00 0.00 0.00 4.02
345 346 0.746063 CTGGTTGCTTTGCTTGGTCA 59.254 50.000 0.00 0.00 0.00 4.02
346 347 1.136695 CTGGTTGCTTTGCTTGGTCAA 59.863 47.619 0.00 0.00 0.00 3.18
347 348 1.136695 TGGTTGCTTTGCTTGGTCAAG 59.863 47.619 6.36 6.36 41.24 3.02
348 349 1.538849 GGTTGCTTTGCTTGGTCAAGG 60.539 52.381 12.02 0.00 38.80 3.61
349 350 1.136891 GTTGCTTTGCTTGGTCAAGGT 59.863 47.619 12.02 0.00 38.80 3.50
350 351 2.356665 TGCTTTGCTTGGTCAAGGTA 57.643 45.000 12.02 0.00 38.80 3.08
351 352 2.875296 TGCTTTGCTTGGTCAAGGTAT 58.125 42.857 12.02 0.00 38.80 2.73
352 353 4.027674 TGCTTTGCTTGGTCAAGGTATA 57.972 40.909 12.02 0.00 38.80 1.47
353 354 4.009675 TGCTTTGCTTGGTCAAGGTATAG 58.990 43.478 12.02 0.75 38.80 1.31
354 355 3.181496 GCTTTGCTTGGTCAAGGTATAGC 60.181 47.826 12.02 0.00 38.80 2.97
371 372 1.751927 GCAGGGACATGGCTTCCTG 60.752 63.158 17.25 17.25 46.93 3.86
372 373 1.687612 CAGGGACATGGCTTCCTGT 59.312 57.895 14.16 0.00 41.21 4.00
391 392 0.179094 TTGATGGTATCCACGGCGAC 60.179 55.000 16.62 0.00 35.80 5.19
392 393 1.324005 TGATGGTATCCACGGCGACA 61.324 55.000 16.62 0.00 35.80 4.35
395 396 1.112950 TGGTATCCACGGCGACATTA 58.887 50.000 16.62 0.00 0.00 1.90
414 415 7.604164 CGACATTAGCCTTATCAAGATGGTAAT 59.396 37.037 0.00 0.00 0.00 1.89
443 475 4.504864 CCAAAGTCATAGTGGTCAAGTCCA 60.505 45.833 0.00 0.00 34.85 4.02
451 483 0.325933 TGGTCAAGTCCATCTGGCAG 59.674 55.000 8.58 8.58 34.44 4.85
454 486 2.354259 GTCAAGTCCATCTGGCAGAAG 58.646 52.381 22.84 17.42 34.44 2.85
469 501 3.744426 GGCAGAAGACAAACGTAAAGCTA 59.256 43.478 0.00 0.00 0.00 3.32
475 507 5.880054 AGACAAACGTAAAGCTATTGCAT 57.120 34.783 1.12 0.00 42.74 3.96
488 520 4.039730 AGCTATTGCATTCCGTGTAGATCT 59.960 41.667 0.00 0.00 42.74 2.75
512 544 9.702253 TCTTGAAGAGATTACCTATGAAGTACT 57.298 33.333 0.00 0.00 0.00 2.73
533 565 5.688807 ACTAATGCCATGTCTTAAGAGCAT 58.311 37.500 19.05 19.05 42.44 3.79
551 583 3.067461 AGCATGCACTACTGCTACTAGAC 59.933 47.826 21.98 0.00 46.49 2.59
577 609 7.341769 CCCAAATCATTGTTAGGGTAATTCTCA 59.658 37.037 0.00 0.00 34.60 3.27
587 619 5.559148 AGGGTAATTCTCATCATGAGGAC 57.441 43.478 14.96 7.86 44.39 3.85
589 621 4.039245 GGGTAATTCTCATCATGAGGACGA 59.961 45.833 14.96 5.77 44.39 4.20
590 622 5.279708 GGGTAATTCTCATCATGAGGACGAT 60.280 44.000 14.96 0.57 44.39 3.73
621 653 5.247084 TGATAGATAGGCTACGACTCTTCC 58.753 45.833 0.00 0.00 0.00 3.46
622 654 3.868619 AGATAGGCTACGACTCTTCCT 57.131 47.619 0.00 0.00 0.00 3.36
623 655 4.173290 AGATAGGCTACGACTCTTCCTT 57.827 45.455 0.00 0.00 0.00 3.36
624 656 4.139038 AGATAGGCTACGACTCTTCCTTC 58.861 47.826 0.00 0.00 0.00 3.46
627 659 3.965694 AGGCTACGACTCTTCCTTCTTA 58.034 45.455 0.00 0.00 0.00 2.10
638 670 7.067496 ACTCTTCCTTCTTACATCAAGACAA 57.933 36.000 0.00 0.00 43.09 3.18
641 673 8.746052 TCTTCCTTCTTACATCAAGACAAAAA 57.254 30.769 0.00 0.00 43.09 1.94
643 675 8.746052 TTCCTTCTTACATCAAGACAAAAAGA 57.254 30.769 0.00 0.00 43.09 2.52
682 714 4.023963 GCCTCACAGTAACTTCAAAACTCC 60.024 45.833 0.00 0.00 0.00 3.85
683 715 4.211374 CCTCACAGTAACTTCAAAACTCCG 59.789 45.833 0.00 0.00 0.00 4.63
684 716 4.124238 TCACAGTAACTTCAAAACTCCGG 58.876 43.478 0.00 0.00 0.00 5.14
685 717 2.876550 ACAGTAACTTCAAAACTCCGGC 59.123 45.455 0.00 0.00 0.00 6.13
694 736 3.600898 AAACTCCGGCGGTGGCTAC 62.601 63.158 29.03 0.00 39.81 3.58
702 744 2.442188 GCGGTGGCTACGAACGAAG 61.442 63.158 0.14 0.00 35.83 3.79
705 747 2.126228 TGGCTACGAACGAAGCGG 60.126 61.111 0.14 0.00 39.71 5.52
706 748 3.551915 GGCTACGAACGAAGCGGC 61.552 66.667 0.14 0.00 39.71 6.53
707 749 2.807895 GCTACGAACGAAGCGGCA 60.808 61.111 1.45 0.00 0.00 5.69
716 758 0.250166 ACGAAGCGGCAGTTAACCTT 60.250 50.000 1.45 0.00 0.00 3.50
725 767 4.287720 CGGCAGTTAACCTTTTCTTGAAC 58.712 43.478 0.88 0.00 0.00 3.18
753 795 1.000283 AGCTCTCTTGACACTTGGACG 60.000 52.381 0.00 0.00 0.00 4.79
771 813 4.753107 TGGACGTCCATTCAAACTTCTTAC 59.247 41.667 33.23 1.21 42.01 2.34
772 814 4.995487 GGACGTCCATTCAAACTTCTTACT 59.005 41.667 29.75 0.00 35.64 2.24
773 815 5.120363 GGACGTCCATTCAAACTTCTTACTC 59.880 44.000 29.75 0.00 35.64 2.59
774 816 4.995487 ACGTCCATTCAAACTTCTTACTCC 59.005 41.667 0.00 0.00 0.00 3.85
775 817 4.392138 CGTCCATTCAAACTTCTTACTCCC 59.608 45.833 0.00 0.00 0.00 4.30
776 818 5.561679 GTCCATTCAAACTTCTTACTCCCT 58.438 41.667 0.00 0.00 0.00 4.20
777 819 6.004574 GTCCATTCAAACTTCTTACTCCCTT 58.995 40.000 0.00 0.00 0.00 3.95
778 820 7.166167 GTCCATTCAAACTTCTTACTCCCTTA 58.834 38.462 0.00 0.00 0.00 2.69
779 821 7.334671 GTCCATTCAAACTTCTTACTCCCTTAG 59.665 40.741 0.00 0.00 0.00 2.18
780 822 7.017254 TCCATTCAAACTTCTTACTCCCTTAGT 59.983 37.037 0.00 0.00 42.62 2.24
781 823 7.665974 CCATTCAAACTTCTTACTCCCTTAGTT 59.334 37.037 0.00 0.00 39.80 2.24
782 824 8.722394 CATTCAAACTTCTTACTCCCTTAGTTC 58.278 37.037 0.00 0.00 39.80 3.01
783 825 6.766429 TCAAACTTCTTACTCCCTTAGTTCC 58.234 40.000 0.00 0.00 39.80 3.62
784 826 6.328148 TCAAACTTCTTACTCCCTTAGTTCCA 59.672 38.462 0.00 0.00 39.80 3.53
785 827 6.954352 AACTTCTTACTCCCTTAGTTCCAT 57.046 37.500 0.00 0.00 39.80 3.41
786 828 8.319146 CAAACTTCTTACTCCCTTAGTTCCATA 58.681 37.037 0.00 0.00 39.80 2.74
787 829 8.445361 AACTTCTTACTCCCTTAGTTCCATAA 57.555 34.615 0.00 0.00 39.80 1.90
788 830 8.625467 ACTTCTTACTCCCTTAGTTCCATAAT 57.375 34.615 0.00 0.00 39.80 1.28
789 831 8.487028 ACTTCTTACTCCCTTAGTTCCATAATG 58.513 37.037 0.00 0.00 39.80 1.90
790 832 7.989947 TCTTACTCCCTTAGTTCCATAATGT 57.010 36.000 0.00 0.00 39.80 2.71
791 833 9.496710 TTCTTACTCCCTTAGTTCCATAATGTA 57.503 33.333 0.00 0.00 39.80 2.29
792 834 9.144298 TCTTACTCCCTTAGTTCCATAATGTAG 57.856 37.037 0.00 0.00 39.80 2.74
793 835 8.849543 TTACTCCCTTAGTTCCATAATGTAGT 57.150 34.615 0.00 0.00 39.80 2.73
794 836 7.125792 ACTCCCTTAGTTCCATAATGTAGTG 57.874 40.000 0.00 0.00 33.35 2.74
795 837 5.925509 TCCCTTAGTTCCATAATGTAGTGC 58.074 41.667 0.00 0.00 0.00 4.40
796 838 4.750098 CCCTTAGTTCCATAATGTAGTGCG 59.250 45.833 0.00 0.00 0.00 5.34
797 839 5.357257 CCTTAGTTCCATAATGTAGTGCGT 58.643 41.667 0.00 0.00 0.00 5.24
798 840 6.461927 CCCTTAGTTCCATAATGTAGTGCGTA 60.462 42.308 0.00 0.00 0.00 4.42
799 841 7.152645 CCTTAGTTCCATAATGTAGTGCGTAT 58.847 38.462 0.00 0.00 0.00 3.06
800 842 8.301720 CCTTAGTTCCATAATGTAGTGCGTATA 58.698 37.037 0.00 0.00 0.00 1.47
801 843 9.343103 CTTAGTTCCATAATGTAGTGCGTATAG 57.657 37.037 0.00 0.00 0.00 1.31
802 844 7.520451 AGTTCCATAATGTAGTGCGTATAGA 57.480 36.000 0.00 0.00 0.00 1.98
803 845 8.123639 AGTTCCATAATGTAGTGCGTATAGAT 57.876 34.615 0.00 0.00 0.00 1.98
804 846 8.585881 AGTTCCATAATGTAGTGCGTATAGATT 58.414 33.333 0.00 0.00 0.00 2.40
805 847 9.204570 GTTCCATAATGTAGTGCGTATAGATTT 57.795 33.333 0.00 0.00 0.00 2.17
806 848 9.772973 TTCCATAATGTAGTGCGTATAGATTTT 57.227 29.630 0.00 0.00 0.00 1.82
807 849 9.772973 TCCATAATGTAGTGCGTATAGATTTTT 57.227 29.630 0.00 0.00 0.00 1.94
837 879 7.586714 AAGTCAAAACTTTGCAAAAGAAGAG 57.413 32.000 13.84 2.51 43.28 2.85
838 880 5.578336 AGTCAAAACTTTGCAAAAGAAGAGC 59.422 36.000 13.84 2.48 38.05 4.09
839 881 4.869861 TCAAAACTTTGCAAAAGAAGAGCC 59.130 37.500 13.84 0.00 38.05 4.70
840 882 4.470334 AAACTTTGCAAAAGAAGAGCCA 57.530 36.364 13.84 0.00 0.00 4.75
841 883 3.722728 ACTTTGCAAAAGAAGAGCCAG 57.277 42.857 13.84 0.00 0.00 4.85
842 884 2.363359 ACTTTGCAAAAGAAGAGCCAGG 59.637 45.455 13.84 0.00 0.00 4.45
843 885 2.071778 TTGCAAAAGAAGAGCCAGGT 57.928 45.000 0.00 0.00 0.00 4.00
844 886 2.071778 TGCAAAAGAAGAGCCAGGTT 57.928 45.000 0.00 0.00 0.00 3.50
845 887 2.387757 TGCAAAAGAAGAGCCAGGTTT 58.612 42.857 0.00 0.00 0.00 3.27
846 888 2.101249 TGCAAAAGAAGAGCCAGGTTTG 59.899 45.455 0.00 0.00 0.00 2.93
848 890 2.695147 CAAAAGAAGAGCCAGGTTTGGT 59.305 45.455 0.00 0.00 46.80 3.67
849 891 1.986882 AAGAAGAGCCAGGTTTGGTG 58.013 50.000 0.00 0.00 46.80 4.17
850 892 0.846693 AGAAGAGCCAGGTTTGGTGT 59.153 50.000 0.00 0.00 46.80 4.16
851 893 1.215423 AGAAGAGCCAGGTTTGGTGTT 59.785 47.619 0.00 0.00 46.80 3.32
852 894 2.031870 GAAGAGCCAGGTTTGGTGTTT 58.968 47.619 0.00 0.00 46.80 2.83
853 895 3.117663 AGAAGAGCCAGGTTTGGTGTTTA 60.118 43.478 0.00 0.00 46.80 2.01
854 896 2.583143 AGAGCCAGGTTTGGTGTTTAC 58.417 47.619 0.00 0.00 46.80 2.01
855 897 2.092103 AGAGCCAGGTTTGGTGTTTACA 60.092 45.455 0.00 0.00 46.80 2.41
856 898 2.293399 GAGCCAGGTTTGGTGTTTACAG 59.707 50.000 0.00 0.00 46.80 2.74
857 899 1.339929 GCCAGGTTTGGTGTTTACAGG 59.660 52.381 0.00 0.00 46.80 4.00
858 900 2.938838 CCAGGTTTGGTGTTTACAGGA 58.061 47.619 0.00 0.00 39.79 3.86
859 901 2.621526 CCAGGTTTGGTGTTTACAGGAC 59.378 50.000 0.00 0.00 39.79 3.85
860 902 2.289547 CAGGTTTGGTGTTTACAGGACG 59.710 50.000 0.00 0.00 0.00 4.79
861 903 2.171027 AGGTTTGGTGTTTACAGGACGA 59.829 45.455 0.00 0.00 0.00 4.20
862 904 2.288729 GGTTTGGTGTTTACAGGACGAC 59.711 50.000 0.00 0.00 0.00 4.34
863 905 1.855513 TTGGTGTTTACAGGACGACG 58.144 50.000 0.00 0.00 0.00 5.12
864 906 0.746063 TGGTGTTTACAGGACGACGT 59.254 50.000 0.00 0.00 0.00 4.34
865 907 1.134226 GGTGTTTACAGGACGACGTG 58.866 55.000 4.58 6.05 37.82 4.49
866 908 1.536709 GGTGTTTACAGGACGACGTGT 60.537 52.381 16.59 16.59 45.19 4.49
867 909 1.519758 GTGTTTACAGGACGACGTGTG 59.480 52.381 20.46 5.21 43.48 3.82
868 910 1.134226 GTTTACAGGACGACGTGTGG 58.866 55.000 20.46 0.00 43.48 4.17
869 911 1.031235 TTTACAGGACGACGTGTGGA 58.969 50.000 20.46 8.52 43.48 4.02
870 912 0.594602 TTACAGGACGACGTGTGGAG 59.405 55.000 20.46 0.00 43.48 3.86
871 913 1.859427 TACAGGACGACGTGTGGAGC 61.859 60.000 20.46 0.00 43.48 4.70
872 914 2.597805 AGGACGACGTGTGGAGCT 60.598 61.111 4.58 0.00 0.00 4.09
935 977 3.089874 TCTAGCCCGGCTGCCATT 61.090 61.111 22.95 3.01 40.10 3.16
942 984 1.454479 CCGGCTGCCATTGAATCCT 60.454 57.895 20.29 0.00 0.00 3.24
1088 1381 2.108157 TGGCAGCGTGTTCGACTT 59.892 55.556 0.00 0.00 39.71 3.01
1099 1392 1.073768 GTTCGACTTGGAGAGCGAGC 61.074 60.000 0.00 0.00 36.07 5.03
1120 1413 2.048597 CGCCACGTTCCTACAGCA 60.049 61.111 0.00 0.00 0.00 4.41
1221 1553 4.754667 GTCTCCGGCGGGGTTCAC 62.755 72.222 27.52 13.55 37.00 3.18
1230 1562 2.264794 GGGGTTCACGTCGATGCT 59.735 61.111 4.06 0.00 0.00 3.79
1333 1686 4.166888 GCAGCCCATCGCCAGAGA 62.167 66.667 0.00 0.00 38.78 3.10
1362 1715 2.046507 CTCTGCTTCCGCTGCCTT 60.047 61.111 0.00 0.00 36.97 4.35
1364 1717 3.437795 CTGCTTCCGCTGCCTTGG 61.438 66.667 0.00 0.00 36.97 3.61
1375 1728 1.001020 TGCCTTGGCCATCGTCATT 60.001 52.632 6.09 0.00 0.00 2.57
1390 1743 2.046285 CATTGGGTTCGGGACTGCC 61.046 63.158 0.00 0.00 0.00 4.85
1585 1992 4.832608 CCGCCCTAGTCGTTGCCC 62.833 72.222 0.00 0.00 0.00 5.36
1656 2488 1.826054 CGTCGAGATGGAGGAGGCT 60.826 63.158 0.00 0.00 0.00 4.58
1676 2508 3.145551 GGAGGTCCTAAGCCGCGA 61.146 66.667 8.23 0.00 0.00 5.87
1785 2617 1.947146 CGACTTCACCGTGCACGAA 60.947 57.895 39.10 24.12 43.02 3.85
1865 2697 2.037772 ACGGAGAGCACTTCATCAACTT 59.962 45.455 0.00 0.00 0.00 2.66
1890 2722 0.681564 GGTTCTCGCTCTCCCTCAGA 60.682 60.000 0.00 0.00 0.00 3.27
1937 2769 0.393402 TCCGGCGAGCTTGAGTACTA 60.393 55.000 9.30 0.00 0.00 1.82
1988 2820 2.674380 GGCTTGGCACCTGTCCAG 60.674 66.667 0.00 0.00 34.66 3.86
2044 2876 3.083997 GCCTCCATCCCAGGACGT 61.084 66.667 0.00 0.00 33.19 4.34
2111 2943 0.035534 CACCCCGACAACATCCATCA 60.036 55.000 0.00 0.00 0.00 3.07
2200 3032 1.524863 CCTCACCTACCCTATCGCCG 61.525 65.000 0.00 0.00 0.00 6.46
2253 5576 1.490490 CATACTTGGGGCTGGCTTCTA 59.510 52.381 0.00 0.00 0.00 2.10
2330 5655 3.055094 ACGCTAACATGACCTTCTTCCAT 60.055 43.478 0.00 0.00 0.00 3.41
2382 5707 2.111384 ACATATTCAGCCTCGTGGTCT 58.889 47.619 5.26 0.13 35.27 3.85
2499 5824 3.149981 CTGGACCTATCGTAGCTCATCA 58.850 50.000 0.00 0.00 0.00 3.07
2571 5896 4.087892 ATGCCGTCAAGCGCCTCT 62.088 61.111 2.29 0.00 39.71 3.69
2612 5938 1.450669 GGATGGCTTTACCGCGGAA 60.451 57.895 35.90 19.01 43.94 4.30
2618 5944 1.473788 GGCTTTACCGCGGAATTCCTA 60.474 52.381 35.90 9.91 0.00 2.94
2652 5978 5.147162 GGAGCATTGTTAAACAAGACTTCG 58.853 41.667 0.00 0.00 41.94 3.79
2660 5986 2.199291 AACAAGACTTCGTCGACGTT 57.801 45.000 34.40 19.94 40.80 3.99
2831 6157 3.966104 CTATCGCTCCGCCTCGCA 61.966 66.667 0.00 0.00 0.00 5.10
2905 6231 1.658409 GCCTGCACGACAACTTTGC 60.658 57.895 0.00 0.00 36.76 3.68
2950 6276 1.270907 CTGCACCAACTAGGAGTCCT 58.729 55.000 17.78 17.78 41.22 3.85
2969 6295 2.354906 CCTGAGAGTGATGCTCAAGCTT 60.355 50.000 3.32 0.00 46.47 3.74
3027 6353 1.160137 CCTCTTTGAGGTTCTTGGCG 58.840 55.000 5.50 0.00 44.25 5.69
3056 6382 0.541998 TCAGACCTCGCTTCAGGGAA 60.542 55.000 0.00 0.00 37.96 3.97
3091 6417 2.624838 TGCTATCATCATCGAGCACTCA 59.375 45.455 0.00 0.00 39.93 3.41
3092 6418 3.068590 TGCTATCATCATCGAGCACTCAA 59.931 43.478 0.00 0.00 39.93 3.02
3236 6562 4.201679 CACGACGCCGGCATCCTA 62.202 66.667 28.98 0.00 40.78 2.94
3237 6563 3.900892 ACGACGCCGGCATCCTAG 61.901 66.667 28.98 11.05 40.78 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.553153 TGGTTGGACAGAATGGAGTTTTATATA 58.447 33.333 0.00 0.00 43.62 0.86
2 3 6.785076 TGGTTGGACAGAATGGAGTTTTATA 58.215 36.000 0.00 0.00 43.62 0.98
3 4 5.640147 TGGTTGGACAGAATGGAGTTTTAT 58.360 37.500 0.00 0.00 43.62 1.40
4 5 5.055265 TGGTTGGACAGAATGGAGTTTTA 57.945 39.130 0.00 0.00 43.62 1.52
17 18 2.777692 AGAAGGAGTTCTTGGTTGGACA 59.222 45.455 0.00 0.00 40.35 4.02
18 19 3.493767 AGAAGGAGTTCTTGGTTGGAC 57.506 47.619 0.00 0.00 40.35 4.02
37 38 4.384208 CCCAAGTTATACCAGGACCTCAAG 60.384 50.000 0.00 0.00 0.00 3.02
39 40 3.112263 CCCAAGTTATACCAGGACCTCA 58.888 50.000 0.00 0.00 0.00 3.86
40 41 3.113043 ACCCAAGTTATACCAGGACCTC 58.887 50.000 0.00 0.00 0.00 3.85
41 42 3.216230 ACCCAAGTTATACCAGGACCT 57.784 47.619 0.00 0.00 0.00 3.85
70 71 3.088532 GCACCACTTTATTCCATCCACA 58.911 45.455 0.00 0.00 0.00 4.17
103 104 6.487299 AGGTATGAAGAAGTGGAATCTACC 57.513 41.667 0.00 0.00 0.00 3.18
104 105 8.794335 AAAAGGTATGAAGAAGTGGAATCTAC 57.206 34.615 0.00 0.00 0.00 2.59
128 129 2.352388 GCATCTGCGTACCTAACCAAA 58.648 47.619 0.00 0.00 0.00 3.28
141 142 1.648467 GGTTTGGAGGTCGCATCTGC 61.648 60.000 0.00 0.00 37.78 4.26
148 149 2.548480 GAGTTCTTTGGTTTGGAGGTCG 59.452 50.000 0.00 0.00 0.00 4.79
153 154 3.287222 CCACAGAGTTCTTTGGTTTGGA 58.713 45.455 6.22 0.00 38.63 3.53
170 171 2.151202 GATTCTCAAAAGACGGCCACA 58.849 47.619 2.24 0.00 0.00 4.17
171 172 1.468914 GGATTCTCAAAAGACGGCCAC 59.531 52.381 2.24 0.00 0.00 5.01
172 173 1.073125 TGGATTCTCAAAAGACGGCCA 59.927 47.619 2.24 0.00 0.00 5.36
174 175 1.740025 CCTGGATTCTCAAAAGACGGC 59.260 52.381 0.00 0.00 0.00 5.68
175 176 2.359900 CCCTGGATTCTCAAAAGACGG 58.640 52.381 0.00 0.00 0.00 4.79
182 183 0.254178 GCAGAGCCCTGGATTCTCAA 59.746 55.000 0.00 0.00 40.72 3.02
196 197 6.998968 AGAAAATGATCAAGTAAGGCAGAG 57.001 37.500 0.00 0.00 0.00 3.35
200 201 8.992835 AAATCAAGAAAATGATCAAGTAAGGC 57.007 30.769 0.00 0.00 39.08 4.35
233 234 8.826765 AGATTAGACCCACTTGAATAAAGAAGA 58.173 33.333 0.00 0.00 39.38 2.87
240 241 7.918076 ACTTTGAGATTAGACCCACTTGAATA 58.082 34.615 0.00 0.00 0.00 1.75
244 245 6.672147 CAAACTTTGAGATTAGACCCACTTG 58.328 40.000 0.00 0.00 0.00 3.16
261 262 2.851195 AGTGTCCATCTCGCAAACTTT 58.149 42.857 0.00 0.00 0.00 2.66
267 268 1.472878 GTCAGTAGTGTCCATCTCGCA 59.527 52.381 0.00 0.00 0.00 5.10
275 276 3.556775 CGTAGAGCTAGTCAGTAGTGTCC 59.443 52.174 0.00 0.00 0.00 4.02
277 278 2.937799 GCGTAGAGCTAGTCAGTAGTGT 59.062 50.000 0.00 0.00 44.04 3.55
278 279 3.595709 GCGTAGAGCTAGTCAGTAGTG 57.404 52.381 0.00 0.00 44.04 2.74
293 294 2.223044 GGCTTCGAGAAATTTGGCGTAG 60.223 50.000 0.00 3.69 0.00 3.51
299 300 6.688813 GCTACATTAAGGCTTCGAGAAATTTG 59.311 38.462 1.30 0.00 0.00 2.32
330 331 1.484038 ACCTTGACCAAGCAAAGCAA 58.516 45.000 4.31 0.00 37.11 3.91
331 332 2.356665 TACCTTGACCAAGCAAAGCA 57.643 45.000 4.31 0.00 37.11 3.91
332 333 3.181496 GCTATACCTTGACCAAGCAAAGC 60.181 47.826 4.31 6.56 37.11 3.51
333 334 4.009675 TGCTATACCTTGACCAAGCAAAG 58.990 43.478 4.31 1.20 37.05 2.77
334 335 4.009675 CTGCTATACCTTGACCAAGCAAA 58.990 43.478 4.31 0.00 39.29 3.68
335 336 3.609853 CTGCTATACCTTGACCAAGCAA 58.390 45.455 4.31 0.00 39.29 3.91
336 337 2.092968 CCTGCTATACCTTGACCAAGCA 60.093 50.000 4.31 0.00 37.62 3.91
337 338 2.565841 CCTGCTATACCTTGACCAAGC 58.434 52.381 4.31 0.00 37.11 4.01
338 339 2.771943 TCCCTGCTATACCTTGACCAAG 59.228 50.000 2.89 2.89 38.14 3.61
339 340 2.504175 GTCCCTGCTATACCTTGACCAA 59.496 50.000 0.00 0.00 0.00 3.67
340 341 2.116238 GTCCCTGCTATACCTTGACCA 58.884 52.381 0.00 0.00 0.00 4.02
341 342 2.116238 TGTCCCTGCTATACCTTGACC 58.884 52.381 0.00 0.00 0.00 4.02
342 343 3.495100 CCATGTCCCTGCTATACCTTGAC 60.495 52.174 0.00 0.00 0.00 3.18
343 344 2.705658 CCATGTCCCTGCTATACCTTGA 59.294 50.000 0.00 0.00 0.00 3.02
344 345 2.811873 GCCATGTCCCTGCTATACCTTG 60.812 54.545 0.00 0.00 0.00 3.61
345 346 1.421646 GCCATGTCCCTGCTATACCTT 59.578 52.381 0.00 0.00 0.00 3.50
346 347 1.059913 GCCATGTCCCTGCTATACCT 58.940 55.000 0.00 0.00 0.00 3.08
347 348 1.059913 AGCCATGTCCCTGCTATACC 58.940 55.000 0.00 0.00 32.56 2.73
348 349 2.551071 GGAAGCCATGTCCCTGCTATAC 60.551 54.545 0.00 0.00 34.29 1.47
349 350 1.699634 GGAAGCCATGTCCCTGCTATA 59.300 52.381 0.00 0.00 34.29 1.31
350 351 0.475906 GGAAGCCATGTCCCTGCTAT 59.524 55.000 0.00 0.00 34.29 2.97
351 352 0.621571 AGGAAGCCATGTCCCTGCTA 60.622 55.000 0.00 0.00 35.59 3.49
352 353 1.927527 AGGAAGCCATGTCCCTGCT 60.928 57.895 0.00 0.00 35.59 4.24
353 354 1.751927 CAGGAAGCCATGTCCCTGC 60.752 63.158 0.00 0.00 39.59 4.85
354 355 4.651867 CAGGAAGCCATGTCCCTG 57.348 61.111 0.00 0.00 40.01 4.45
371 372 0.179094 TCGCCGTGGATACCATCAAC 60.179 55.000 0.00 0.00 35.28 3.18
372 373 0.179094 GTCGCCGTGGATACCATCAA 60.179 55.000 0.00 0.00 35.28 2.57
414 415 7.399191 ACTTGACCACTATGACTTTGGTATCTA 59.601 37.037 0.00 0.00 43.94 1.98
443 475 2.550830 ACGTTTGTCTTCTGCCAGAT 57.449 45.000 0.00 0.00 0.00 2.90
451 483 5.685841 TGCAATAGCTTTACGTTTGTCTTC 58.314 37.500 0.00 0.00 42.74 2.87
454 486 5.511729 GGAATGCAATAGCTTTACGTTTGTC 59.488 40.000 0.00 0.00 42.74 3.18
469 501 4.769688 TCAAGATCTACACGGAATGCAAT 58.230 39.130 0.00 0.00 0.00 3.56
475 507 6.531503 AATCTCTTCAAGATCTACACGGAA 57.468 37.500 0.00 0.00 44.26 4.30
511 543 5.562307 GCATGCTCTTAAGACATGGCATTAG 60.562 44.000 29.13 19.97 41.17 1.73
512 544 4.276678 GCATGCTCTTAAGACATGGCATTA 59.723 41.667 29.13 10.65 41.17 1.90
513 545 3.067742 GCATGCTCTTAAGACATGGCATT 59.932 43.478 29.13 15.45 41.17 3.56
517 549 3.276857 AGTGCATGCTCTTAAGACATGG 58.723 45.455 29.13 19.51 41.17 3.66
545 577 5.755849 CCCTAACAATGATTTGGGTCTAGT 58.244 41.667 6.82 0.00 39.15 2.57
551 583 7.341769 TGAGAATTACCCTAACAATGATTTGGG 59.658 37.037 11.20 11.20 46.61 4.12
577 609 1.487976 AGGCAACATCGTCCTCATGAT 59.512 47.619 0.00 0.00 41.41 2.45
612 644 5.802956 GTCTTGATGTAAGAAGGAAGAGTCG 59.197 44.000 0.00 0.00 46.48 4.18
621 653 9.657121 GACTTCTTTTTGTCTTGATGTAAGAAG 57.343 33.333 16.03 16.03 46.48 2.85
622 654 8.621286 GGACTTCTTTTTGTCTTGATGTAAGAA 58.379 33.333 0.00 0.00 46.48 2.52
623 655 7.773224 TGGACTTCTTTTTGTCTTGATGTAAGA 59.227 33.333 0.00 0.00 43.01 2.10
624 656 7.930217 TGGACTTCTTTTTGTCTTGATGTAAG 58.070 34.615 0.00 0.00 37.76 2.34
627 659 6.736794 GCATGGACTTCTTTTTGTCTTGATGT 60.737 38.462 0.00 0.00 34.01 3.06
638 670 4.400567 GGCATCTAAGCATGGACTTCTTTT 59.599 41.667 0.00 0.00 35.83 2.27
641 673 2.776536 AGGCATCTAAGCATGGACTTCT 59.223 45.455 0.00 0.00 35.83 2.85
643 675 2.507058 TGAGGCATCTAAGCATGGACTT 59.493 45.455 0.00 0.00 35.83 3.01
683 715 3.919973 TTCGTTCGTAGCCACCGCC 62.920 63.158 0.00 0.00 34.57 6.13
684 716 2.431260 TTCGTTCGTAGCCACCGC 60.431 61.111 0.00 0.00 0.00 5.68
685 717 2.442188 GCTTCGTTCGTAGCCACCG 61.442 63.158 11.60 0.00 0.00 4.94
694 736 0.179258 GTTAACTGCCGCTTCGTTCG 60.179 55.000 0.00 0.00 0.00 3.95
702 744 2.292292 TCAAGAAAAGGTTAACTGCCGC 59.708 45.455 5.42 0.00 0.00 6.53
705 747 6.378710 AGAGTTCAAGAAAAGGTTAACTGC 57.621 37.500 5.42 0.00 0.00 4.40
706 748 6.479001 TCGAGAGTTCAAGAAAAGGTTAACTG 59.521 38.462 5.42 0.00 0.00 3.16
707 749 6.579865 TCGAGAGTTCAAGAAAAGGTTAACT 58.420 36.000 5.42 0.00 0.00 2.24
716 758 4.950050 AGAGCTTTCGAGAGTTCAAGAAA 58.050 39.130 19.53 0.00 30.23 2.52
725 767 3.057596 AGTGTCAAGAGAGCTTTCGAGAG 60.058 47.826 0.00 0.00 30.14 3.20
753 795 5.561679 AGGGAGTAAGAAGTTTGAATGGAC 58.438 41.667 0.00 0.00 0.00 4.02
771 813 5.992217 GCACTACATTATGGAACTAAGGGAG 59.008 44.000 0.00 0.00 31.21 4.30
772 814 5.452776 CGCACTACATTATGGAACTAAGGGA 60.453 44.000 0.00 0.00 0.00 4.20
773 815 4.750098 CGCACTACATTATGGAACTAAGGG 59.250 45.833 0.00 0.00 0.00 3.95
774 816 5.357257 ACGCACTACATTATGGAACTAAGG 58.643 41.667 0.00 0.00 0.00 2.69
775 817 9.343103 CTATACGCACTACATTATGGAACTAAG 57.657 37.037 0.00 0.00 0.00 2.18
776 818 9.070179 TCTATACGCACTACATTATGGAACTAA 57.930 33.333 0.00 0.00 0.00 2.24
777 819 8.625786 TCTATACGCACTACATTATGGAACTA 57.374 34.615 0.00 0.00 0.00 2.24
778 820 7.520451 TCTATACGCACTACATTATGGAACT 57.480 36.000 0.00 0.00 0.00 3.01
779 821 8.758633 AATCTATACGCACTACATTATGGAAC 57.241 34.615 0.00 0.00 0.00 3.62
780 822 9.772973 AAAATCTATACGCACTACATTATGGAA 57.227 29.630 0.00 0.00 0.00 3.53
781 823 9.772973 AAAAATCTATACGCACTACATTATGGA 57.227 29.630 0.00 0.00 0.00 3.41
805 847 9.573133 TTTTGCAAAGTTTTGACTTTTGAAAAA 57.427 22.222 12.41 9.74 40.55 1.94
806 848 9.230932 CTTTTGCAAAGTTTTGACTTTTGAAAA 57.769 25.926 12.41 6.74 40.55 2.29
807 849 8.616076 TCTTTTGCAAAGTTTTGACTTTTGAAA 58.384 25.926 12.41 0.00 40.55 2.69
808 850 8.147642 TCTTTTGCAAAGTTTTGACTTTTGAA 57.852 26.923 12.41 0.00 40.55 2.69
809 851 7.721286 TCTTTTGCAAAGTTTTGACTTTTGA 57.279 28.000 12.41 0.00 40.55 2.69
810 852 8.281893 TCTTCTTTTGCAAAGTTTTGACTTTTG 58.718 29.630 12.41 0.00 40.55 2.44
811 853 8.376889 TCTTCTTTTGCAAAGTTTTGACTTTT 57.623 26.923 12.41 0.00 40.55 2.27
812 854 7.360353 GCTCTTCTTTTGCAAAGTTTTGACTTT 60.360 33.333 12.41 0.00 40.55 2.66
813 855 6.091305 GCTCTTCTTTTGCAAAGTTTTGACTT 59.909 34.615 12.41 0.00 40.55 3.01
814 856 5.578336 GCTCTTCTTTTGCAAAGTTTTGACT 59.422 36.000 12.41 0.00 40.55 3.41
815 857 5.220472 GGCTCTTCTTTTGCAAAGTTTTGAC 60.220 40.000 12.41 1.50 40.55 3.18
816 858 4.869861 GGCTCTTCTTTTGCAAAGTTTTGA 59.130 37.500 12.41 7.67 40.55 2.69
817 859 4.630940 TGGCTCTTCTTTTGCAAAGTTTTG 59.369 37.500 12.41 3.81 41.03 2.44
818 860 4.831107 TGGCTCTTCTTTTGCAAAGTTTT 58.169 34.783 12.41 0.00 0.00 2.43
819 861 4.436332 CTGGCTCTTCTTTTGCAAAGTTT 58.564 39.130 12.41 0.00 0.00 2.66
820 862 3.181472 CCTGGCTCTTCTTTTGCAAAGTT 60.181 43.478 12.41 0.00 0.00 2.66
821 863 2.363359 CCTGGCTCTTCTTTTGCAAAGT 59.637 45.455 12.41 0.00 0.00 2.66
822 864 2.363359 ACCTGGCTCTTCTTTTGCAAAG 59.637 45.455 12.41 7.09 0.00 2.77
823 865 2.387757 ACCTGGCTCTTCTTTTGCAAA 58.612 42.857 8.05 8.05 0.00 3.68
824 866 2.071778 ACCTGGCTCTTCTTTTGCAA 57.928 45.000 0.00 0.00 0.00 4.08
825 867 2.071778 AACCTGGCTCTTCTTTTGCA 57.928 45.000 0.00 0.00 0.00 4.08
826 868 2.546584 CCAAACCTGGCTCTTCTTTTGC 60.547 50.000 0.00 0.00 35.39 3.68
827 869 3.375782 CCAAACCTGGCTCTTCTTTTG 57.624 47.619 0.00 0.00 35.39 2.44
839 881 2.289547 CGTCCTGTAAACACCAAACCTG 59.710 50.000 0.00 0.00 0.00 4.00
840 882 2.171027 TCGTCCTGTAAACACCAAACCT 59.829 45.455 0.00 0.00 0.00 3.50
841 883 2.288729 GTCGTCCTGTAAACACCAAACC 59.711 50.000 0.00 0.00 0.00 3.27
842 884 2.033492 CGTCGTCCTGTAAACACCAAAC 60.033 50.000 0.00 0.00 0.00 2.93
843 885 2.203401 CGTCGTCCTGTAAACACCAAA 58.797 47.619 0.00 0.00 0.00 3.28
844 886 1.136695 ACGTCGTCCTGTAAACACCAA 59.863 47.619 0.00 0.00 0.00 3.67
845 887 0.746063 ACGTCGTCCTGTAAACACCA 59.254 50.000 0.00 0.00 0.00 4.17
846 888 1.134226 CACGTCGTCCTGTAAACACC 58.866 55.000 0.00 0.00 0.00 4.16
847 889 1.519758 CACACGTCGTCCTGTAAACAC 59.480 52.381 0.00 0.00 0.00 3.32
848 890 1.536496 CCACACGTCGTCCTGTAAACA 60.536 52.381 0.00 0.00 0.00 2.83
849 891 1.134226 CCACACGTCGTCCTGTAAAC 58.866 55.000 0.00 0.00 0.00 2.01
850 892 1.001048 CTCCACACGTCGTCCTGTAAA 60.001 52.381 0.00 0.00 0.00 2.01
851 893 0.594602 CTCCACACGTCGTCCTGTAA 59.405 55.000 0.00 0.00 0.00 2.41
852 894 1.859427 GCTCCACACGTCGTCCTGTA 61.859 60.000 0.00 0.00 0.00 2.74
853 895 3.039988 CTCCACACGTCGTCCTGT 58.960 61.111 0.00 0.00 0.00 4.00
854 896 2.421877 AAGCTCCACACGTCGTCCTG 62.422 60.000 0.00 0.00 0.00 3.86
855 897 2.201022 AAGCTCCACACGTCGTCCT 61.201 57.895 0.00 0.00 0.00 3.85
856 898 2.022129 CAAGCTCCACACGTCGTCC 61.022 63.158 0.00 0.00 0.00 4.79
857 899 2.022129 CCAAGCTCCACACGTCGTC 61.022 63.158 0.00 0.00 0.00 4.20
858 900 2.029073 CCAAGCTCCACACGTCGT 59.971 61.111 0.00 0.00 0.00 4.34
859 901 2.029073 ACCAAGCTCCACACGTCG 59.971 61.111 0.00 0.00 0.00 5.12
860 902 0.946221 CTCACCAAGCTCCACACGTC 60.946 60.000 0.00 0.00 0.00 4.34
861 903 1.069765 CTCACCAAGCTCCACACGT 59.930 57.895 0.00 0.00 0.00 4.49
862 904 3.957260 CTCACCAAGCTCCACACG 58.043 61.111 0.00 0.00 0.00 4.49
871 913 3.494378 CGGAGCATGCTCACCAAG 58.506 61.111 40.37 24.60 44.40 3.61
933 975 1.227263 CCGCCGACGAGGATTCAAT 60.227 57.895 0.00 0.00 45.00 2.57
935 977 4.508128 GCCGCCGACGAGGATTCA 62.508 66.667 12.49 0.00 45.00 2.57
1099 1392 2.183555 GTAGGAACGTGGCGAGGG 59.816 66.667 0.00 0.00 0.00 4.30
1362 1715 0.679640 GAACCCAATGACGATGGCCA 60.680 55.000 8.56 8.56 36.58 5.36
1364 1717 1.714899 CCGAACCCAATGACGATGGC 61.715 60.000 0.00 0.00 36.58 4.40
1615 2275 1.825191 GTGCCATGATCACCCGCAT 60.825 57.895 14.26 0.00 0.00 4.73
1656 2488 2.058595 GCGGCTTAGGACCTCCTCA 61.059 63.158 0.00 0.00 44.77 3.86
1785 2617 1.584724 AGAAATCCTCGGGATGGTGT 58.415 50.000 6.24 0.00 42.27 4.16
1843 2675 2.037772 AGTTGATGAAGTGCTCTCCGTT 59.962 45.455 0.00 0.00 0.00 4.44
1890 2722 1.522569 GGCGAGCTTACTCCATGGT 59.477 57.895 12.58 0.00 40.03 3.55
2044 2876 1.000521 CAAGATTGGCCCTGGAGCA 60.001 57.895 0.00 0.00 0.00 4.26
2200 3032 3.149196 TGTTTTCACAGCCAATCCTCTC 58.851 45.455 0.00 0.00 0.00 3.20
2214 5537 6.705302 AGTATGAGATCTTGAGCTGTTTTCA 58.295 36.000 0.00 0.00 0.00 2.69
2330 5655 2.472059 GCGGAATGAGCATTGCCGA 61.472 57.895 24.61 0.00 40.53 5.54
2382 5707 1.135489 GTCAGTGATCGCGTGTCCTTA 60.135 52.381 5.77 0.00 0.00 2.69
2431 5756 2.135139 CAAGTAGCTCGTCAAAGTGCA 58.865 47.619 0.00 0.00 33.52 4.57
2475 5800 1.001158 GAGCTACGATAGGTCCAGTGC 60.001 57.143 11.00 0.00 45.14 4.40
2499 5824 2.045926 GGTCAGGTCATGCGGCTT 60.046 61.111 0.00 0.00 0.00 4.35
2588 5913 1.912971 GGTAAAGCCATCCGGTCCT 59.087 57.895 0.00 0.00 37.17 3.85
2652 5978 0.935196 AGTTGCTGGAAAACGTCGAC 59.065 50.000 5.18 5.18 32.65 4.20
2711 6037 0.034670 GGAGCAATGTCAAGAGGGCT 60.035 55.000 0.00 0.00 0.00 5.19
2905 6231 0.933097 CATCGATTGCTTGACGAGGG 59.067 55.000 0.00 0.00 39.31 4.30
2969 6295 1.214589 GAAGGCTCGCGTTAGGTCA 59.785 57.895 5.77 0.00 0.00 4.02
3027 6353 1.268640 GCGAGGTCTGAATCCGTACTC 60.269 57.143 0.00 0.00 0.00 2.59
3056 6382 2.149578 GATAGCAAGATCGCAAGCCAT 58.850 47.619 0.00 0.00 37.18 4.40
3091 6417 3.317149 CGGCTCACCATTGATCATGATTT 59.683 43.478 10.14 0.00 34.31 2.17
3092 6418 2.882761 CGGCTCACCATTGATCATGATT 59.117 45.455 10.14 0.00 34.31 2.57
3156 6482 1.001268 GAAGAGCTGCGATGATACGGA 60.001 52.381 0.00 0.00 0.00 4.69


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

AutoCloner maintained by Alex Coulton.