Multiple sequence alignment - TraesCS1A01G164400

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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 TraesCS1A01G164400 chr1A 100.000 5116 0 0 1 5116 296216426 296211311 0.000000e+00 9448.0
1 TraesCS1A01G164400 chr1A 85.027 187 18 9 4771 4952 456937653 456937834 1.130000e-41 182.0
2 TraesCS1A01G164400 chr1A 75.455 330 77 4 93 420 539498388 539498715 1.910000e-34 158.0
3 TraesCS1A01G164400 chr1A 75.455 330 77 4 93 420 539539732 539540059 1.910000e-34 158.0
4 TraesCS1A01G164400 chr1B 90.089 2482 133 40 2708 5116 327843723 327841282 0.000000e+00 3116.0
5 TraesCS1A01G164400 chr1B 91.073 1221 57 12 1414 2627 327844898 327843723 0.000000e+00 1604.0
6 TraesCS1A01G164400 chr1B 95.954 519 20 1 860 1377 327845415 327844897 0.000000e+00 841.0
7 TraesCS1A01G164400 chr1B 87.730 163 17 3 4791 4952 673751896 673751736 2.430000e-43 187.0
8 TraesCS1A01G164400 chr1B 90.385 52 4 1 675 725 327900349 327900298 3.310000e-07 67.6
9 TraesCS1A01G164400 chr1D 90.537 2177 103 27 2708 4812 208821740 208823885 0.000000e+00 2784.0
10 TraesCS1A01G164400 chr1D 94.328 1675 60 10 2708 4354 228303087 228301420 0.000000e+00 2534.0
11 TraesCS1A01G164400 chr1D 93.725 1243 57 6 1392 2627 208820512 208821740 0.000000e+00 1844.0
12 TraesCS1A01G164400 chr1D 94.190 1222 49 7 1414 2627 228304294 228303087 0.000000e+00 1844.0
13 TraesCS1A01G164400 chr1D 95.652 506 21 1 873 1377 228304798 228304293 0.000000e+00 811.0
14 TraesCS1A01G164400 chr1D 86.047 731 95 6 1 727 208817489 208818216 0.000000e+00 778.0
15 TraesCS1A01G164400 chr1D 87.860 659 54 11 4470 5116 228301344 228300700 0.000000e+00 750.0
16 TraesCS1A01G164400 chr1D 96.316 380 13 1 1013 1392 208820107 208820485 1.560000e-174 623.0
17 TraesCS1A01G164400 chr1D 83.745 689 69 21 1 649 228305781 228305096 3.390000e-171 612.0
18 TraesCS1A01G164400 chr1D 94.318 264 7 5 762 1024 208818214 208818470 1.030000e-106 398.0
19 TraesCS1A01G164400 chr1D 85.166 391 39 7 4726 5116 208823897 208824268 2.890000e-102 383.0
20 TraesCS1A01G164400 chr1D 87.879 165 17 3 4791 4953 483524068 483523905 1.880000e-44 191.0
21 TraesCS1A01G164400 chr1D 90.580 138 6 6 752 887 228304951 228304819 5.260000e-40 176.0
22 TraesCS1A01G164400 chr1D 92.308 104 4 3 2609 2711 402722623 402722723 1.480000e-30 145.0
23 TraesCS1A01G164400 chr1D 100.000 29 0 0 4306 4334 113600727 113600699 3.000000e-03 54.7
24 TraesCS1A01G164400 chr5A 90.123 162 14 2 4793 4953 526384584 526384744 5.190000e-50 209.0
25 TraesCS1A01G164400 chr5A 92.381 105 6 2 2625 2728 670270015 670269912 1.150000e-31 148.0
26 TraesCS1A01G164400 chr4A 84.158 202 24 8 4791 4988 577540895 577541092 6.760000e-44 189.0
27 TraesCS1A01G164400 chr4A 84.158 202 21 10 4791 4987 622182322 622182127 8.750000e-43 185.0
28 TraesCS1A01G164400 chr4A 84.158 202 21 11 4791 4987 622198055 622197860 8.750000e-43 185.0
29 TraesCS1A01G164400 chr4B 97.778 90 2 0 2626 2715 218581615 218581704 6.860000e-34 156.0
30 TraesCS1A01G164400 chr5B 94.845 97 4 1 2621 2716 271112898 271112802 3.190000e-32 150.0
31 TraesCS1A01G164400 chr7B 93.939 99 4 2 2624 2721 440325690 440325593 1.150000e-31 148.0
32 TraesCS1A01G164400 chr7B 91.743 109 5 3 2611 2717 708066815 708066921 1.150000e-31 148.0
33 TraesCS1A01G164400 chr7D 93.939 99 3 3 2616 2714 540863758 540863663 4.130000e-31 147.0
34 TraesCS1A01G164400 chr3D 90.826 109 8 2 2622 2729 587947468 587947361 1.480000e-30 145.0
35 TraesCS1A01G164400 chr2A 87.603 121 9 5 2602 2721 261173653 261173768 8.940000e-28 135.0


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 TraesCS1A01G164400 chr1A 296211311 296216426 5115 True 9448.000000 9448 100.000000 1 5116 1 chr1A.!!$R1 5115
1 TraesCS1A01G164400 chr1B 327841282 327845415 4133 True 1853.666667 3116 92.372000 860 5116 3 chr1B.!!$R3 4256
2 TraesCS1A01G164400 chr1D 208817489 208824268 6779 False 1135.000000 2784 91.018167 1 5116 6 chr1D.!!$F2 5115
3 TraesCS1A01G164400 chr1D 228300700 228305781 5081 True 1121.166667 2534 91.059167 1 5116 6 chr1D.!!$R3 5115

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
202 204 0.677842 ACTGTTAAGAACTCCCGCGT 59.322 50.0 4.92 0.0 0.00 6.01 F
1232 3036 1.022451 TTACAAACTCCGCCATCGCC 61.022 55.0 0.00 0.0 0.00 5.54 F
1344 3148 0.038159 CCGCCTCGTATGGAATCCTC 60.038 60.0 0.00 0.0 0.00 3.71 F
2713 4563 0.338814 ATGGGACGGAGGGAGTAGTT 59.661 55.0 0.00 0.0 0.00 2.24 F
3446 5297 0.955919 CTCCACTTCGCCAAGAACCC 60.956 60.0 0.00 0.0 34.66 4.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1344 3148 0.468771 GGGGGAAGATGCTGGGATTG 60.469 60.0 0.00 0.0 0.00 2.67 R
2694 4544 0.338814 AACTACTCCCTCCGTCCCAT 59.661 55.0 0.00 0.0 0.00 4.00 R
3248 5099 0.896940 TGGACTGGTGGTACCGAGAC 60.897 60.0 7.57 0.0 42.58 3.36 R
3619 5470 0.041535 TTGCATCTGGAAAGGGGCAT 59.958 50.0 0.00 0.0 0.00 4.40 R
4443 6353 0.174845 AACGTAGCCTTGCGCAGATA 59.825 50.0 11.31 0.0 41.38 1.98 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 5.351465 TCGTCTTTCATCTGCATTAACCTTC 59.649 40.000 0.00 0.00 0.00 3.46
30 31 7.867403 TCTTTCATCTGCATTAACCTTCAAAAC 59.133 33.333 0.00 0.00 0.00 2.43
32 33 5.538053 TCATCTGCATTAACCTTCAAAACCA 59.462 36.000 0.00 0.00 0.00 3.67
66 67 2.299993 ACATGTGTCAGTATGGAGCG 57.700 50.000 0.00 0.00 36.16 5.03
67 68 1.550524 ACATGTGTCAGTATGGAGCGT 59.449 47.619 0.00 0.00 36.16 5.07
71 72 1.067142 GTGTCAGTATGGAGCGTTGGA 60.067 52.381 0.00 0.00 36.16 3.53
94 95 6.254804 GGAAAAACGCCAACCATATATTGTTC 59.745 38.462 0.00 0.00 0.00 3.18
150 152 4.470334 TCGAGAATGTGTTGATCCATCA 57.530 40.909 0.00 0.00 34.44 3.07
164 166 3.541242 TCCATCATGGAACCCAAACTT 57.459 42.857 2.95 0.00 45.00 2.66
179 181 5.658190 ACCCAAACTTGATGATAGGGATTTG 59.342 40.000 0.00 0.00 38.21 2.32
191 193 6.115446 TGATAGGGATTTGAGCACTGTTAAG 58.885 40.000 0.00 0.00 0.00 1.85
202 204 0.677842 ACTGTTAAGAACTCCCGCGT 59.322 50.000 4.92 0.00 0.00 6.01
211 213 4.435436 CTCCCGCGTGCAGCTACA 62.435 66.667 4.92 0.00 45.59 2.74
214 216 2.398554 CCCGCGTGCAGCTACAATT 61.399 57.895 4.92 0.00 45.59 2.32
231 233 8.142994 GCTACAATTGCTTAGCTTTGATAGTA 57.857 34.615 20.92 8.51 38.16 1.82
253 265 1.961793 TTGTGCTTTAGCTTGGTCGT 58.038 45.000 0.00 0.00 42.66 4.34
262 274 5.657474 CTTTAGCTTGGTCGTTATGGACTA 58.343 41.667 0.00 0.00 37.12 2.59
290 302 2.951229 AAACTTGTCACCGAGGGAAT 57.049 45.000 0.00 0.00 0.00 3.01
308 320 4.817517 GGAATCATTTCATCCCATCATGC 58.182 43.478 0.00 0.00 33.23 4.06
401 413 1.363744 CGGCAGACATCCTTCTCAAC 58.636 55.000 0.00 0.00 0.00 3.18
428 467 3.998099 CATCTTCATGCTCCTCGTAGA 57.002 47.619 0.00 0.00 0.00 2.59
437 476 2.231478 TGCTCCTCGTAGAAACTCTTGG 59.769 50.000 0.00 0.00 34.09 3.61
444 483 3.006537 TCGTAGAAACTCTTGGGTTGGAG 59.993 47.826 0.00 0.00 35.86 3.86
451 490 1.902508 CTCTTGGGTTGGAGCTAGTCA 59.097 52.381 0.00 0.00 0.00 3.41
452 491 2.303022 CTCTTGGGTTGGAGCTAGTCAA 59.697 50.000 0.00 0.00 0.00 3.18
464 503 4.381718 GGAGCTAGTCAAACCGTAGTGATT 60.382 45.833 0.00 0.00 0.00 2.57
468 507 5.390567 GCTAGTCAAACCGTAGTGATTTTGG 60.391 44.000 0.00 0.00 31.20 3.28
470 509 3.003897 GTCAAACCGTAGTGATTTTGGCA 59.996 43.478 0.00 0.00 34.42 4.92
471 510 3.823873 TCAAACCGTAGTGATTTTGGCAT 59.176 39.130 0.00 0.00 31.20 4.40
479 518 7.032580 CCGTAGTGATTTTGGCATTCATTTTA 58.967 34.615 0.00 0.00 0.00 1.52
486 525 6.791887 TTTTGGCATTCATTTTAAATCGCA 57.208 29.167 0.00 0.00 0.00 5.10
508 547 8.908903 TCGCAATATGTATCCCTGTTTATTTTT 58.091 29.630 0.00 0.00 0.00 1.94
518 557 4.423732 CCTGTTTATTTTTCTCGCATGGG 58.576 43.478 2.76 2.76 0.00 4.00
533 572 3.186817 CGCATGGGTGTAAGAACGTAAAA 59.813 43.478 0.68 0.00 0.00 1.52
589 628 4.650972 TTTAAGCTGGTATCCCTTGTGT 57.349 40.909 0.00 0.00 0.00 3.72
631 672 7.274686 CCAAATAAAAACAGTTGTGTCGTCTTT 59.725 33.333 0.00 0.00 35.08 2.52
650 765 9.491675 TCGTCTTTAATACACTTTATCAAACCA 57.508 29.630 0.00 0.00 0.00 3.67
671 786 5.594317 ACCAGTTTACAAAGCACATCTTCTT 59.406 36.000 0.00 0.00 32.88 2.52
673 788 7.448469 ACCAGTTTACAAAGCACATCTTCTTAT 59.552 33.333 0.00 0.00 32.88 1.73
712 827 6.594937 CACATTGTAAATGAGAATTTTGGGGG 59.405 38.462 6.96 0.00 0.00 5.40
715 830 6.353404 TGTAAATGAGAATTTTGGGGGTTC 57.647 37.500 0.00 0.00 0.00 3.62
716 831 5.841237 TGTAAATGAGAATTTTGGGGGTTCA 59.159 36.000 0.00 0.00 0.00 3.18
717 832 5.488262 AAATGAGAATTTTGGGGGTTCAG 57.512 39.130 0.00 0.00 0.00 3.02
721 836 5.459505 TGAGAATTTTGGGGGTTCAGTTTA 58.540 37.500 0.00 0.00 0.00 2.01
722 837 5.303333 TGAGAATTTTGGGGGTTCAGTTTAC 59.697 40.000 0.00 0.00 0.00 2.01
723 838 5.212745 AGAATTTTGGGGGTTCAGTTTACA 58.787 37.500 0.00 0.00 0.00 2.41
724 839 5.663556 AGAATTTTGGGGGTTCAGTTTACAA 59.336 36.000 0.00 0.00 0.00 2.41
725 840 5.959583 ATTTTGGGGGTTCAGTTTACAAA 57.040 34.783 0.00 0.00 0.00 2.83
726 841 5.346181 TTTTGGGGGTTCAGTTTACAAAG 57.654 39.130 0.00 0.00 0.00 2.77
727 842 2.312390 TGGGGGTTCAGTTTACAAAGC 58.688 47.619 0.00 0.00 0.00 3.51
728 843 2.312390 GGGGGTTCAGTTTACAAAGCA 58.688 47.619 0.00 0.00 0.00 3.91
729 844 2.696187 GGGGGTTCAGTTTACAAAGCAA 59.304 45.455 0.00 0.00 0.00 3.91
730 845 3.243737 GGGGGTTCAGTTTACAAAGCAAG 60.244 47.826 0.00 0.00 0.00 4.01
731 846 3.383505 GGGGTTCAGTTTACAAAGCAAGT 59.616 43.478 0.00 0.00 0.00 3.16
732 847 4.142026 GGGGTTCAGTTTACAAAGCAAGTT 60.142 41.667 0.00 0.00 0.00 2.66
733 848 5.416083 GGGTTCAGTTTACAAAGCAAGTTT 58.584 37.500 0.00 0.00 0.00 2.66
734 849 5.518847 GGGTTCAGTTTACAAAGCAAGTTTC 59.481 40.000 0.00 0.00 0.00 2.78
735 850 5.229260 GGTTCAGTTTACAAAGCAAGTTTCG 59.771 40.000 0.00 0.00 0.00 3.46
736 851 4.347813 TCAGTTTACAAAGCAAGTTTCGC 58.652 39.130 0.00 0.00 0.00 4.70
737 852 4.101942 CAGTTTACAAAGCAAGTTTCGCA 58.898 39.130 0.00 0.00 0.00 5.10
738 853 4.560819 CAGTTTACAAAGCAAGTTTCGCAA 59.439 37.500 0.00 0.00 0.00 4.85
739 854 4.561213 AGTTTACAAAGCAAGTTTCGCAAC 59.439 37.500 0.00 0.00 0.00 4.17
740 855 2.645730 ACAAAGCAAGTTTCGCAACA 57.354 40.000 0.00 0.00 35.05 3.33
741 856 2.953020 ACAAAGCAAGTTTCGCAACAA 58.047 38.095 0.00 0.00 35.05 2.83
742 857 3.321497 ACAAAGCAAGTTTCGCAACAAA 58.679 36.364 0.00 0.00 35.05 2.83
743 858 3.743396 ACAAAGCAAGTTTCGCAACAAAA 59.257 34.783 0.00 0.00 35.05 2.44
744 859 4.212214 ACAAAGCAAGTTTCGCAACAAAAA 59.788 33.333 0.00 0.00 35.05 1.94
769 884 4.766404 AAGTTTACAAAGCAAGGATCCG 57.234 40.909 5.98 0.00 0.00 4.18
813 928 9.586435 ACTTCACCAAAGAAAAAGAAAATGTAG 57.414 29.630 0.00 0.00 38.44 2.74
826 941 6.851222 AGAAAATGTAGTCTTGCATATCCG 57.149 37.500 0.00 0.00 0.00 4.18
914 1069 1.743995 GTACGTTCAAGCGGGCCAT 60.744 57.895 4.39 0.00 35.98 4.40
1055 2859 2.124653 ATCGGCTCGTCGGACTCT 60.125 61.111 6.57 0.00 0.00 3.24
1232 3036 1.022451 TTACAAACTCCGCCATCGCC 61.022 55.000 0.00 0.00 0.00 5.54
1344 3148 0.038159 CCGCCTCGTATGGAATCCTC 60.038 60.000 0.00 0.00 0.00 3.71
1363 3167 0.468771 CAATCCCAGCATCTTCCCCC 60.469 60.000 0.00 0.00 0.00 5.40
1502 3333 2.338577 ATAGTCAAGTGCATCAGGCC 57.661 50.000 0.00 0.00 43.89 5.19
1520 3351 2.682856 GGCCGATGTAGAATTTCTGCAA 59.317 45.455 19.04 5.46 42.19 4.08
1526 3357 4.340894 TGTAGAATTTCTGCAATGTCGC 57.659 40.909 13.88 0.00 36.18 5.19
1529 3360 5.641636 TGTAGAATTTCTGCAATGTCGCTAA 59.358 36.000 13.88 0.00 36.18 3.09
1530 3361 5.824904 AGAATTTCTGCAATGTCGCTAAT 57.175 34.783 0.00 0.00 0.00 1.73
1534 3365 2.463876 TCTGCAATGTCGCTAATCTCG 58.536 47.619 0.00 0.00 0.00 4.04
1553 3384 5.801380 TCTCGCTGTTTAAGGATTTTAGGT 58.199 37.500 0.00 0.00 0.00 3.08
1706 3537 6.976934 ATCCTTCTGTTTGTGGTACATTTT 57.023 33.333 0.00 0.00 44.52 1.82
2074 3923 2.602878 GAAACCACTGATTGCATGCAG 58.397 47.619 21.50 11.84 38.10 4.41
2181 4030 4.982916 CAGTTACCGGTCTGAACTATATGC 59.017 45.833 18.51 0.00 32.22 3.14
2267 4116 6.321181 TCTTTAACTTTGTGCAGATTCCTTGT 59.679 34.615 0.00 0.00 0.00 3.16
2309 4158 3.144506 CTGTGCAAGAAGTGATTCCAGT 58.855 45.455 0.00 0.00 0.00 4.00
2312 4161 3.316308 GTGCAAGAAGTGATTCCAGTTGT 59.684 43.478 0.00 0.00 36.15 3.32
2350 4199 3.562557 TCCTGAACTTTTCGTAACTTGGC 59.437 43.478 0.00 0.00 0.00 4.52
2354 4203 5.956642 TGAACTTTTCGTAACTTGGCTTTT 58.043 33.333 0.00 0.00 0.00 2.27
2355 4204 5.802956 TGAACTTTTCGTAACTTGGCTTTTG 59.197 36.000 0.00 0.00 0.00 2.44
2464 4314 7.478322 CATGATACTTGCTGAAATAAGCTTGT 58.522 34.615 9.86 0.00 43.90 3.16
2495 4345 7.343057 TGACATCTAAGTATCCACTGATTGAGT 59.657 37.037 0.00 0.00 34.36 3.41
2548 4398 7.758613 TGTTAGCATGCATGTATTTTCAATG 57.241 32.000 26.79 0.00 0.00 2.82
2555 4405 4.689812 TGCATGTATTTTCAATGTTGTGGC 59.310 37.500 0.00 0.00 0.00 5.01
2623 4473 9.744468 GTTTCAGCTTGTTTCCTTTTATCTTTA 57.256 29.630 0.00 0.00 0.00 1.85
2627 4477 9.827411 CAGCTTGTTTCCTTTTATCTTTACTAC 57.173 33.333 0.00 0.00 0.00 2.73
2631 4481 9.511272 TTGTTTCCTTTTATCTTTACTACTCCC 57.489 33.333 0.00 0.00 0.00 4.30
2633 4483 9.381033 GTTTCCTTTTATCTTTACTACTCCCTC 57.619 37.037 0.00 0.00 0.00 4.30
2635 4485 6.323225 TCCTTTTATCTTTACTACTCCCTCCG 59.677 42.308 0.00 0.00 0.00 4.63
2636 4486 6.097981 CCTTTTATCTTTACTACTCCCTCCGT 59.902 42.308 0.00 0.00 0.00 4.69
2637 4487 6.705863 TTTATCTTTACTACTCCCTCCGTC 57.294 41.667 0.00 0.00 0.00 4.79
2638 4488 3.010200 TCTTTACTACTCCCTCCGTCC 57.990 52.381 0.00 0.00 0.00 4.79
2639 4489 2.030371 CTTTACTACTCCCTCCGTCCC 58.970 57.143 0.00 0.00 0.00 4.46
2640 4490 1.002069 TTACTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
2641 4491 1.229131 TACTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
2642 4492 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
2643 4493 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
2644 4494 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
2645 4495 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
2646 4496 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
2647 4497 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
2648 4498 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
2649 4499 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
2650 4500 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
2651 4501 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
2653 4503 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
2654 4504 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
2655 4505 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
2656 4506 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
2657 4507 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
2703 4553 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
2704 4554 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
2705 4555 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
2706 4556 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
2707 4557 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
2708 4558 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
2709 4559 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
2710 4560 2.090943 ACATTATGGGACGGAGGGAGTA 60.091 50.000 0.00 0.00 0.00 2.59
2711 4561 2.376695 TTATGGGACGGAGGGAGTAG 57.623 55.000 0.00 0.00 0.00 2.57
2712 4562 1.229131 TATGGGACGGAGGGAGTAGT 58.771 55.000 0.00 0.00 0.00 2.73
2713 4563 0.338814 ATGGGACGGAGGGAGTAGTT 59.661 55.000 0.00 0.00 0.00 2.24
2714 4564 1.002069 TGGGACGGAGGGAGTAGTTA 58.998 55.000 0.00 0.00 0.00 2.24
2715 4565 1.572415 TGGGACGGAGGGAGTAGTTAT 59.428 52.381 0.00 0.00 0.00 1.89
2763 4613 8.883731 ACATTAGTTAAGCAGTGATGTACATTC 58.116 33.333 10.30 6.83 34.10 2.67
2987 4838 9.671279 GTGAAAATGATGGAAGGGATTTTTATT 57.329 29.630 0.00 0.00 30.11 1.40
3155 5006 1.666054 GAGGAGATGCTCAAAGGCAG 58.334 55.000 0.00 0.00 45.75 4.85
3248 5099 2.383527 GCAAGAGCGTGAAGACCGG 61.384 63.158 0.00 0.00 0.00 5.28
3359 5210 2.043115 TCCACCAGGTGATACTCAGTCT 59.957 50.000 22.37 0.00 35.23 3.24
3446 5297 0.955919 CTCCACTTCGCCAAGAACCC 60.956 60.000 0.00 0.00 34.66 4.11
3619 5470 1.626321 TGGGAATCCGCAGTACTTCAA 59.374 47.619 0.00 0.00 35.24 2.69
3623 5474 1.668419 ATCCGCAGTACTTCAATGCC 58.332 50.000 0.00 0.00 36.60 4.40
3670 5521 2.169352 CCGGATCAGATCAAGGTTCAGT 59.831 50.000 12.66 0.00 0.00 3.41
3674 5525 4.323028 GGATCAGATCAAGGTTCAGTGTCA 60.323 45.833 12.66 0.00 0.00 3.58
3680 5531 0.179018 AAGGTTCAGTGTCAGTGCCC 60.179 55.000 2.50 5.59 0.00 5.36
3779 5630 0.107017 CTGGTTTCGGGATGATGCCT 60.107 55.000 0.42 0.00 0.00 4.75
3839 5690 4.643387 GGCCAAGCTGACCGTGGT 62.643 66.667 0.00 0.00 43.98 4.16
3928 5779 1.295423 CTACACAACCCCCGTCTGG 59.705 63.158 0.00 0.00 0.00 3.86
3929 5780 2.798148 CTACACAACCCCCGTCTGGC 62.798 65.000 0.00 0.00 0.00 4.85
4006 5857 1.466360 GCTGCCAAAATCGTGCTGTAG 60.466 52.381 0.00 0.00 0.00 2.74
4103 5954 8.859156 GCTAAAAACGATGCAATTTAATCTGAA 58.141 29.630 0.00 0.00 0.00 3.02
4136 6012 5.236047 TGCTATTTGTGAATTGTTTTGGTGC 59.764 36.000 0.00 0.00 0.00 5.01
4138 6014 6.018016 GCTATTTGTGAATTGTTTTGGTGCTT 60.018 34.615 0.00 0.00 0.00 3.91
4147 6023 2.606725 TGTTTTGGTGCTTCAAAATGCG 59.393 40.909 16.46 0.00 44.90 4.73
4149 6025 3.717400 TTTGGTGCTTCAAAATGCGTA 57.283 38.095 3.24 0.00 34.17 4.42
4151 6027 2.226330 TGGTGCTTCAAAATGCGTACT 58.774 42.857 0.00 0.00 0.00 2.73
4157 6033 1.832883 TCAAAATGCGTACTGCCCAT 58.167 45.000 7.13 0.00 45.60 4.00
4172 6048 1.984817 CCATTGTTGGGCTGCCAAT 59.015 52.632 22.05 8.60 39.56 3.16
4290 6167 5.767816 ACACCCAAAATAAGTGTCTCAAC 57.232 39.130 0.00 0.00 40.65 3.18
4293 6170 6.039382 ACACCCAAAATAAGTGTCTCAACTTC 59.961 38.462 0.00 0.00 40.65 3.01
4296 6173 6.486657 CCCAAAATAAGTGTCTCAACTTCAGA 59.513 38.462 0.00 0.00 40.77 3.27
4326 6203 4.232820 ACACTTATTTTGGGATGGAGGGAT 59.767 41.667 0.00 0.00 0.00 3.85
4334 6211 4.015617 TGGGATGGAGGGATTACAAGTA 57.984 45.455 0.00 0.00 0.00 2.24
4429 6339 9.796120 AAAGTAGAGAAGAGAGTTCATATTTCG 57.204 33.333 0.00 0.00 0.00 3.46
4430 6340 8.740123 AGTAGAGAAGAGAGTTCATATTTCGA 57.260 34.615 0.00 0.00 0.00 3.71
4431 6341 9.349713 AGTAGAGAAGAGAGTTCATATTTCGAT 57.650 33.333 0.00 0.00 0.00 3.59
4432 6342 9.959749 GTAGAGAAGAGAGTTCATATTTCGATT 57.040 33.333 0.00 0.00 0.00 3.34
4433 6343 8.870160 AGAGAAGAGAGTTCATATTTCGATTG 57.130 34.615 0.00 0.00 0.00 2.67
4434 6344 7.437862 AGAGAAGAGAGTTCATATTTCGATTGC 59.562 37.037 0.00 0.00 0.00 3.56
4435 6345 7.271511 AGAAGAGAGTTCATATTTCGATTGCT 58.728 34.615 0.00 0.00 0.00 3.91
4443 6353 7.281774 AGTTCATATTTCGATTGCTGATGTTCT 59.718 33.333 0.00 0.00 0.00 3.01
4450 6360 3.121092 CGATTGCTGATGTTCTATCTGCG 60.121 47.826 12.09 0.00 43.17 5.18
4459 6369 1.861575 GTTCTATCTGCGCAAGGCTAC 59.138 52.381 13.05 1.83 44.05 3.58
4476 6386 3.482786 GCTACGTTCGTCGAGTAAGAAA 58.517 45.455 0.00 0.00 42.86 2.52
4486 6396 8.592998 GTTCGTCGAGTAAGAAATTATGAATGT 58.407 33.333 0.00 0.00 0.00 2.71
4529 6439 2.560542 ACAGTGGCCGAAATGCAAAATA 59.439 40.909 0.00 0.00 0.00 1.40
4534 6455 3.181477 TGGCCGAAATGCAAAATATCTGG 60.181 43.478 0.00 0.00 0.00 3.86
4540 6461 6.979817 CCGAAATGCAAAATATCTGGAATGAA 59.020 34.615 0.00 0.00 0.00 2.57
4570 6494 4.498345 CCTCTGAGGTTCTATCTGCGTAAC 60.498 50.000 15.76 0.00 0.00 2.50
4576 6500 6.016527 TGAGGTTCTATCTGCGTAACGATATT 60.017 38.462 0.00 0.00 0.00 1.28
4582 6506 4.330944 TCTGCGTAACGATATTCCCATT 57.669 40.909 0.00 0.00 0.00 3.16
4583 6507 4.055360 TCTGCGTAACGATATTCCCATTG 58.945 43.478 0.00 0.00 0.00 2.82
4639 6563 2.158813 ACAGTACAGGGGTGAAAGTGTG 60.159 50.000 0.00 0.00 0.00 3.82
4667 6591 1.269012 CAAACATGAAGGGGCCACAT 58.731 50.000 8.31 0.00 0.00 3.21
4676 6600 1.003112 GGGGCCACATACACAACGA 60.003 57.895 4.39 0.00 0.00 3.85
4677 6601 0.606944 GGGGCCACATACACAACGAA 60.607 55.000 4.39 0.00 0.00 3.85
4683 6607 3.063452 GCCACATACACAACGAATACAGG 59.937 47.826 0.00 0.00 0.00 4.00
4707 6631 4.451096 AGTGAAAGCGCTAAATCTCGAAAA 59.549 37.500 12.05 0.00 31.91 2.29
4708 6632 5.049680 AGTGAAAGCGCTAAATCTCGAAAAA 60.050 36.000 12.05 0.00 31.91 1.94
4710 6634 3.369835 AGCGCTAAATCTCGAAAAACG 57.630 42.857 8.99 0.00 44.09 3.60
4711 6635 2.735134 AGCGCTAAATCTCGAAAAACGT 59.265 40.909 8.99 0.00 43.13 3.99
4712 6636 3.185797 AGCGCTAAATCTCGAAAAACGTT 59.814 39.130 8.99 0.00 43.13 3.99
4713 6637 4.386652 AGCGCTAAATCTCGAAAAACGTTA 59.613 37.500 8.99 0.00 43.13 3.18
4714 6638 5.074791 GCGCTAAATCTCGAAAAACGTTAA 58.925 37.500 0.00 0.00 43.13 2.01
4715 6639 5.222488 GCGCTAAATCTCGAAAAACGTTAAG 59.778 40.000 0.00 0.00 43.13 1.85
4716 6640 5.726679 CGCTAAATCTCGAAAAACGTTAAGG 59.273 40.000 0.00 0.00 43.13 2.69
4717 6641 6.019762 GCTAAATCTCGAAAAACGTTAAGGG 58.980 40.000 0.00 0.00 43.13 3.95
4718 6642 6.347969 GCTAAATCTCGAAAAACGTTAAGGGT 60.348 38.462 0.00 0.00 43.13 4.34
4719 6643 5.602458 AATCTCGAAAAACGTTAAGGGTC 57.398 39.130 0.00 0.00 43.13 4.46
4720 6644 3.392882 TCTCGAAAAACGTTAAGGGTCC 58.607 45.455 0.00 0.00 43.13 4.46
4721 6645 3.132925 CTCGAAAAACGTTAAGGGTCCA 58.867 45.455 0.00 0.00 43.13 4.02
4722 6646 3.539604 TCGAAAAACGTTAAGGGTCCAA 58.460 40.909 0.00 0.00 43.13 3.53
4723 6647 3.944015 TCGAAAAACGTTAAGGGTCCAAA 59.056 39.130 0.00 0.00 43.13 3.28
4724 6648 4.037021 CGAAAAACGTTAAGGGTCCAAAC 58.963 43.478 0.00 0.00 37.22 2.93
4775 6797 3.329814 AGTCTCGGAAAACATAAAGGGGT 59.670 43.478 0.00 0.00 0.00 4.95
4780 6802 4.076394 CGGAAAACATAAAGGGGTCAAGA 58.924 43.478 0.00 0.00 0.00 3.02
4795 6817 4.202430 GGGTCAAGAAGAAAAGTACAGGGA 60.202 45.833 0.00 0.00 0.00 4.20
4796 6818 4.755629 GGTCAAGAAGAAAAGTACAGGGAC 59.244 45.833 0.00 0.00 0.00 4.46
4805 6827 1.302192 GTACAGGGACCAAAGCGCA 60.302 57.895 11.47 0.00 0.00 6.09
4806 6828 0.887387 GTACAGGGACCAAAGCGCAA 60.887 55.000 11.47 0.00 0.00 4.85
4807 6829 0.179015 TACAGGGACCAAAGCGCAAA 60.179 50.000 11.47 0.00 0.00 3.68
4808 6830 1.040339 ACAGGGACCAAAGCGCAAAA 61.040 50.000 11.47 0.00 0.00 2.44
4809 6831 0.318120 CAGGGACCAAAGCGCAAAAT 59.682 50.000 11.47 0.00 0.00 1.82
4810 6832 0.603065 AGGGACCAAAGCGCAAAATC 59.397 50.000 11.47 0.00 0.00 2.17
4811 6833 0.603065 GGGACCAAAGCGCAAAATCT 59.397 50.000 11.47 0.00 0.00 2.40
4812 6834 1.000843 GGGACCAAAGCGCAAAATCTT 59.999 47.619 11.47 0.00 0.00 2.40
4813 6835 2.061028 GGACCAAAGCGCAAAATCTTG 58.939 47.619 11.47 2.84 35.49 3.02
4814 6836 2.288152 GGACCAAAGCGCAAAATCTTGA 60.288 45.455 11.47 0.00 34.14 3.02
4815 6837 3.380142 GACCAAAGCGCAAAATCTTGAA 58.620 40.909 11.47 0.00 34.14 2.69
4842 6875 9.942850 AAAATTTGGACCATTTCTCGATTTATT 57.057 25.926 0.00 0.00 0.00 1.40
4881 6914 4.282957 CAGGAGCCATGCTAATCTTCTCTA 59.717 45.833 0.00 0.00 39.88 2.43
4932 6965 1.357420 AGGGAGAAGAGAGCTCTCACA 59.643 52.381 38.20 0.00 45.21 3.58
4934 6967 1.132262 GGAGAAGAGAGCTCTCACACG 59.868 57.143 38.20 0.00 45.21 4.49
5037 7070 1.451207 TGGGCCGTCCGATTCAATG 60.451 57.895 0.00 0.00 38.76 2.82
5103 7138 0.404040 TTTTGCGGGGGATCTTCTGT 59.596 50.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 5.538053 TGGTTTTGAAGGTTAATGCAGATGA 59.462 36.000 0.00 0.00 0.00 2.92
30 31 2.358125 TTGCGTGGACCGTGATGG 60.358 61.111 0.00 0.00 46.41 3.51
32 33 1.003839 ATGTTGCGTGGACCGTGAT 60.004 52.632 0.00 0.00 39.32 3.06
42 43 2.076100 CCATACTGACACATGTTGCGT 58.924 47.619 0.00 0.00 0.00 5.24
43 44 2.345876 TCCATACTGACACATGTTGCG 58.654 47.619 0.00 0.00 0.00 4.85
67 68 5.923733 ATATATGGTTGGCGTTTTTCCAA 57.076 34.783 0.00 0.00 40.98 3.53
71 72 6.103330 GGAACAATATATGGTTGGCGTTTTT 58.897 36.000 10.33 0.00 0.00 1.94
150 152 5.203528 CCTATCATCAAGTTTGGGTTCCAT 58.796 41.667 0.00 0.00 31.53 3.41
156 158 5.893255 TCAAATCCCTATCATCAAGTTTGGG 59.107 40.000 0.00 0.00 34.44 4.12
164 166 4.164796 ACAGTGCTCAAATCCCTATCATCA 59.835 41.667 0.00 0.00 0.00 3.07
179 181 2.338500 CGGGAGTTCTTAACAGTGCTC 58.662 52.381 0.00 0.00 0.00 4.26
191 193 3.642778 TAGCTGCACGCGGGAGTTC 62.643 63.158 15.48 0.00 45.59 3.01
214 216 7.121168 AGCACAAAATACTATCAAAGCTAAGCA 59.879 33.333 0.00 0.00 0.00 3.91
229 231 4.851558 CGACCAAGCTAAAGCACAAAATAC 59.148 41.667 4.54 0.00 45.16 1.89
231 233 3.317993 ACGACCAAGCTAAAGCACAAAAT 59.682 39.130 4.54 0.00 45.16 1.82
262 274 6.106673 CCTCGGTGACAAGTTTATTATGACT 58.893 40.000 0.00 0.00 0.00 3.41
277 289 2.985896 TGAAATGATTCCCTCGGTGAC 58.014 47.619 0.00 0.00 34.49 3.67
290 302 5.698104 AGTTAGCATGATGGGATGAAATGA 58.302 37.500 0.00 0.00 0.00 2.57
339 351 4.811969 TCCTTAAAGGACGTCATTGCTA 57.188 40.909 17.13 3.12 40.06 3.49
347 359 4.463891 TCCTTCGTATTCCTTAAAGGACGT 59.536 41.667 0.00 0.00 45.78 4.34
354 366 7.042321 CGCATAACAATCCTTCGTATTCCTTAA 60.042 37.037 0.00 0.00 0.00 1.85
361 373 2.806244 GCCGCATAACAATCCTTCGTAT 59.194 45.455 0.00 0.00 0.00 3.06
364 376 0.042188 CGCCGCATAACAATCCTTCG 60.042 55.000 0.00 0.00 0.00 3.79
371 383 2.046796 TCTGCCGCCGCATAACAA 60.047 55.556 0.00 0.00 46.11 2.83
421 433 3.006537 TCCAACCCAAGAGTTTCTACGAG 59.993 47.826 0.00 0.00 0.00 4.18
428 467 2.711547 ACTAGCTCCAACCCAAGAGTTT 59.288 45.455 0.00 0.00 32.47 2.66
437 476 1.270678 ACGGTTTGACTAGCTCCAACC 60.271 52.381 13.64 13.64 40.10 3.77
444 483 5.390567 CCAAAATCACTACGGTTTGACTAGC 60.391 44.000 0.00 0.00 33.70 3.42
451 490 4.279671 TGAATGCCAAAATCACTACGGTTT 59.720 37.500 0.00 0.00 0.00 3.27
452 491 3.823873 TGAATGCCAAAATCACTACGGTT 59.176 39.130 0.00 0.00 0.00 4.44
464 503 6.791887 TTGCGATTTAAAATGAATGCCAAA 57.208 29.167 0.00 0.00 0.00 3.28
471 510 9.906660 GGGATACATATTGCGATTTAAAATGAA 57.093 29.630 0.00 0.00 39.74 2.57
479 518 6.959639 AAACAGGGATACATATTGCGATTT 57.040 33.333 0.00 0.00 39.74 2.17
508 547 1.403647 CGTTCTTACACCCATGCGAGA 60.404 52.381 0.00 0.00 0.00 4.04
518 557 5.366829 AGCCCAATTTTACGTTCTTACAC 57.633 39.130 0.00 0.00 0.00 2.90
601 642 6.020201 CGACACAACTGTTTTTATTTGGGAAC 60.020 38.462 0.00 0.00 0.00 3.62
617 658 7.781548 AAAGTGTATTAAAGACGACACAACT 57.218 32.000 6.76 0.00 43.72 3.16
650 765 8.396272 ACATAAGAAGATGTGCTTTGTAAACT 57.604 30.769 0.00 0.00 38.64 2.66
671 786 4.878971 ACAATGTGGCGTGCTATTAACATA 59.121 37.500 0.00 0.00 0.00 2.29
673 788 3.078097 ACAATGTGGCGTGCTATTAACA 58.922 40.909 0.00 0.00 0.00 2.41
677 792 4.397730 TCATTTACAATGTGGCGTGCTATT 59.602 37.500 0.00 0.00 0.00 1.73
712 827 5.275741 GCGAAACTTGCTTTGTAAACTGAAC 60.276 40.000 0.00 0.00 0.00 3.18
715 830 4.101942 TGCGAAACTTGCTTTGTAAACTG 58.898 39.130 0.00 0.00 0.00 3.16
716 831 4.364415 TGCGAAACTTGCTTTGTAAACT 57.636 36.364 0.00 0.00 0.00 2.66
717 832 4.324936 TGTTGCGAAACTTGCTTTGTAAAC 59.675 37.500 8.00 0.00 0.00 2.01
721 836 2.645730 TGTTGCGAAACTTGCTTTGT 57.354 40.000 8.00 0.00 0.00 2.83
722 837 3.987807 TTTGTTGCGAAACTTGCTTTG 57.012 38.095 8.00 0.00 0.00 2.77
723 838 4.999751 TTTTTGTTGCGAAACTTGCTTT 57.000 31.818 8.00 0.00 0.00 3.51
745 860 5.983118 CGGATCCTTGCTTTGTAAACTTTTT 59.017 36.000 10.75 0.00 0.00 1.94
746 861 5.068591 ACGGATCCTTGCTTTGTAAACTTTT 59.931 36.000 10.75 0.00 0.00 2.27
747 862 4.583073 ACGGATCCTTGCTTTGTAAACTTT 59.417 37.500 10.75 0.00 0.00 2.66
748 863 4.142038 ACGGATCCTTGCTTTGTAAACTT 58.858 39.130 10.75 0.00 0.00 2.66
749 864 3.751518 ACGGATCCTTGCTTTGTAAACT 58.248 40.909 10.75 0.00 0.00 2.66
750 865 3.751698 AGACGGATCCTTGCTTTGTAAAC 59.248 43.478 10.75 0.00 0.00 2.01
751 866 3.751175 CAGACGGATCCTTGCTTTGTAAA 59.249 43.478 10.75 0.00 0.00 2.01
752 867 3.334691 CAGACGGATCCTTGCTTTGTAA 58.665 45.455 10.75 0.00 0.00 2.41
753 868 2.935238 GCAGACGGATCCTTGCTTTGTA 60.935 50.000 19.59 0.00 0.00 2.41
754 869 1.813513 CAGACGGATCCTTGCTTTGT 58.186 50.000 10.75 0.00 0.00 2.83
755 870 0.449388 GCAGACGGATCCTTGCTTTG 59.551 55.000 19.59 7.88 0.00 2.77
756 871 1.021390 CGCAGACGGATCCTTGCTTT 61.021 55.000 22.40 0.00 34.97 3.51
895 1050 3.484547 GGCCCGCTTGAACGTACG 61.485 66.667 15.01 15.01 0.00 3.67
896 1051 1.743995 ATGGCCCGCTTGAACGTAC 60.744 57.895 0.00 0.00 0.00 3.67
897 1052 1.743623 CATGGCCCGCTTGAACGTA 60.744 57.895 0.00 0.00 0.00 3.57
898 1053 3.055719 CATGGCCCGCTTGAACGT 61.056 61.111 0.00 0.00 0.00 3.99
899 1054 4.481112 GCATGGCCCGCTTGAACG 62.481 66.667 0.00 0.00 0.00 3.95
914 1069 0.030638 GCAGCTTCGGTTTTTCAGCA 59.969 50.000 0.00 0.00 34.49 4.41
1214 3018 1.448893 GGCGATGGCGGAGTTTGTA 60.449 57.895 0.00 0.00 41.24 2.41
1277 3081 2.125912 GAGCAGATGTGGACGCGT 60.126 61.111 13.85 13.85 0.00 6.01
1344 3148 0.468771 GGGGGAAGATGCTGGGATTG 60.469 60.000 0.00 0.00 0.00 2.67
1363 3167 4.106197 GTGAAGTAGTGAAGGCATAGACG 58.894 47.826 0.00 0.00 0.00 4.18
1502 3333 5.193216 CGACATTGCAGAAATTCTACATCG 58.807 41.667 0.00 0.00 0.00 3.84
1520 3351 2.586258 AACAGCGAGATTAGCGACAT 57.414 45.000 0.00 0.00 40.04 3.06
1526 3357 8.552034 CCTAAAATCCTTAAACAGCGAGATTAG 58.448 37.037 0.00 0.00 0.00 1.73
1529 3360 6.316390 CACCTAAAATCCTTAAACAGCGAGAT 59.684 38.462 0.00 0.00 0.00 2.75
1530 3361 5.642063 CACCTAAAATCCTTAAACAGCGAGA 59.358 40.000 0.00 0.00 0.00 4.04
1534 3365 6.430000 TCAGACACCTAAAATCCTTAAACAGC 59.570 38.462 0.00 0.00 0.00 4.40
1553 3384 3.072476 GCCTTGGGCTCTCAGACA 58.928 61.111 0.80 0.00 46.69 3.41
1706 3537 4.080638 ACCAACATCCTTTTTCTGGCAAAA 60.081 37.500 0.00 0.00 0.00 2.44
1726 3557 5.624344 TCGACACTTAAACAAAACAACCA 57.376 34.783 0.00 0.00 0.00 3.67
1926 3769 1.066002 GAACATCCCATGCCGTCAATG 59.934 52.381 0.00 0.00 0.00 2.82
1987 3830 4.200092 AGCCGGAATACTTTCAGAAATCC 58.800 43.478 5.05 0.00 33.23 3.01
2074 3923 6.925610 TGCCTAGATGATTGTGAAATGTAC 57.074 37.500 0.00 0.00 0.00 2.90
2168 4017 6.894339 TGAATAGACCGCATATAGTTCAGA 57.106 37.500 0.00 0.00 0.00 3.27
2181 4030 9.573133 AGCAAAAGAATTAAAATGAATAGACCG 57.427 29.630 0.00 0.00 0.00 4.79
2267 4116 4.022935 CAGGCTAAACAGAAAGCATGTTCA 60.023 41.667 1.14 0.00 43.54 3.18
2309 4158 6.946340 TCAGGAGAATGCTTACAGATAACAA 58.054 36.000 0.00 0.00 29.87 2.83
2312 4161 7.187824 AGTTCAGGAGAATGCTTACAGATAA 57.812 36.000 0.00 0.00 29.87 1.75
2355 4204 2.496470 ACTACGAAGGTGAGAATGGGAC 59.504 50.000 0.00 0.00 0.00 4.46
2398 4248 9.499479 CAGAGTTATGCAAGTTATCCTATCATT 57.501 33.333 0.00 0.00 0.00 2.57
2464 4314 8.533569 TCAGTGGATACTTAGATGTCACATAA 57.466 34.615 0.00 0.00 34.07 1.90
2548 4398 1.383456 TTCCACTGCACTGCCACAAC 61.383 55.000 0.00 0.00 0.00 3.32
2555 4405 5.105310 AGGTTACTATAGTTCCACTGCACTG 60.105 44.000 21.08 0.00 0.00 3.66
2623 4473 1.229131 TATGGGACGGAGGGAGTAGT 58.771 55.000 0.00 0.00 0.00 2.73
2627 4477 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
2629 4479 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
2630 4480 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
2631 4481 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
2678 4528 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
2679 4529 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
2680 4530 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
2681 4531 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
2682 4532 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
2684 4534 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
2685 4535 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
2686 4536 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
2687 4537 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
2688 4538 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
2689 4539 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
2690 4540 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
2691 4541 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
2692 4542 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
2693 4543 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
2694 4544 0.338814 AACTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
2695 4545 1.002069 TAACTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
2696 4546 2.364647 CAATAACTACTCCCTCCGTCCC 59.635 54.545 0.00 0.00 0.00 4.46
2697 4547 3.029570 ACAATAACTACTCCCTCCGTCC 58.970 50.000 0.00 0.00 0.00 4.79
2698 4548 4.732672 AACAATAACTACTCCCTCCGTC 57.267 45.455 0.00 0.00 0.00 4.79
2699 4549 4.099113 GCTAACAATAACTACTCCCTCCGT 59.901 45.833 0.00 0.00 0.00 4.69
2700 4550 4.098960 TGCTAACAATAACTACTCCCTCCG 59.901 45.833 0.00 0.00 0.00 4.63
2701 4551 5.609533 TGCTAACAATAACTACTCCCTCC 57.390 43.478 0.00 0.00 0.00 4.30
2702 4552 6.817184 TGATGCTAACAATAACTACTCCCTC 58.183 40.000 0.00 0.00 0.00 4.30
2703 4553 6.808321 TGATGCTAACAATAACTACTCCCT 57.192 37.500 0.00 0.00 0.00 4.20
2704 4554 9.209175 CTATTGATGCTAACAATAACTACTCCC 57.791 37.037 0.00 0.00 38.93 4.30
2705 4555 8.713271 GCTATTGATGCTAACAATAACTACTCC 58.287 37.037 0.00 0.00 38.93 3.85
2706 4556 9.482627 AGCTATTGATGCTAACAATAACTACTC 57.517 33.333 0.00 0.00 38.93 2.59
2707 4557 9.265901 CAGCTATTGATGCTAACAATAACTACT 57.734 33.333 0.00 0.00 38.93 2.57
2923 4774 2.743752 CGCTCATCACAACTGCGGG 61.744 63.158 0.00 0.00 42.46 6.13
2987 4838 3.577229 CACATAGGTGCAGCGCAA 58.423 55.556 11.47 0.32 41.47 4.85
3215 5066 3.439476 GCTCTTGCATGTGAGAACTTGAT 59.561 43.478 13.73 0.00 39.41 2.57
3248 5099 0.896940 TGGACTGGTGGTACCGAGAC 60.897 60.000 7.57 0.00 42.58 3.36
3257 5108 1.992277 CCTCTCCCTGGACTGGTGG 60.992 68.421 0.00 0.00 0.00 4.61
3359 5210 3.691575 TCCTTGAGGTGTGTTGTTTTCA 58.308 40.909 0.00 0.00 36.34 2.69
3446 5297 3.254060 CTTGTCTTGAGTACCATGGTCG 58.746 50.000 23.76 4.34 0.00 4.79
3619 5470 0.041535 TTGCATCTGGAAAGGGGCAT 59.958 50.000 0.00 0.00 0.00 4.40
3623 5474 0.529378 GCAGTTGCATCTGGAAAGGG 59.471 55.000 22.92 0.09 41.59 3.95
3759 5610 0.107214 GGCATCATCCCGAAACCAGA 60.107 55.000 0.00 0.00 0.00 3.86
3779 5630 1.137675 CCTGGATTCATCGAGCTGTCA 59.862 52.381 0.00 0.00 32.12 3.58
3928 5779 0.235926 GTTGAAAGACTGCTGTCCGC 59.764 55.000 18.96 9.92 43.91 5.54
3929 5780 1.528586 CTGTTGAAAGACTGCTGTCCG 59.471 52.381 18.96 0.00 43.91 4.79
4006 5857 1.794512 ATTGCAATTTCCCAACGCAC 58.205 45.000 5.99 0.00 31.10 5.34
4033 5884 3.273434 GCTCATCAGTTACATGCCAAGA 58.727 45.455 0.00 0.00 0.00 3.02
4116 5967 5.879223 TGAAGCACCAAAACAATTCACAAAT 59.121 32.000 0.00 0.00 0.00 2.32
4136 6012 1.539388 TGGGCAGTACGCATTTTGAAG 59.461 47.619 10.92 0.00 45.17 3.02
4138 6014 3.331002 TGGGCAGTACGCATTTTGA 57.669 47.368 10.92 0.00 45.17 2.69
4232 6108 7.033185 GGTTCATAACAAAAACAAGACACACT 58.967 34.615 0.00 0.00 0.00 3.55
4233 6109 6.809196 TGGTTCATAACAAAAACAAGACACAC 59.191 34.615 0.00 0.00 0.00 3.82
4234 6110 6.925211 TGGTTCATAACAAAAACAAGACACA 58.075 32.000 0.00 0.00 0.00 3.72
4236 6112 7.397892 TCTGGTTCATAACAAAAACAAGACA 57.602 32.000 0.00 0.00 29.95 3.41
4237 6113 7.973944 AGTTCTGGTTCATAACAAAAACAAGAC 59.026 33.333 0.00 0.00 33.71 3.01
4238 6114 8.062065 AGTTCTGGTTCATAACAAAAACAAGA 57.938 30.769 0.00 0.00 32.44 3.02
4239 6115 9.233232 GTAGTTCTGGTTCATAACAAAAACAAG 57.767 33.333 0.00 0.00 0.00 3.16
4240 6116 8.962679 AGTAGTTCTGGTTCATAACAAAAACAA 58.037 29.630 0.00 0.00 0.00 2.83
4290 6167 8.883731 CCCAAAATAAGTGTAGTACATCTGAAG 58.116 37.037 6.21 0.00 0.00 3.02
4293 6170 8.830580 CATCCCAAAATAAGTGTAGTACATCTG 58.169 37.037 6.21 0.00 0.00 2.90
4296 6173 7.867921 TCCATCCCAAAATAAGTGTAGTACAT 58.132 34.615 6.21 0.00 0.00 2.29
4334 6211 9.912634 AATCACATTCGTATTCAGTTTTCATTT 57.087 25.926 0.00 0.00 0.00 2.32
4420 6330 8.837788 ATAGAACATCAGCAATCGAAATATGA 57.162 30.769 0.00 0.00 0.00 2.15
4421 6331 8.933807 AGATAGAACATCAGCAATCGAAATATG 58.066 33.333 0.00 0.00 0.00 1.78
4422 6332 8.933807 CAGATAGAACATCAGCAATCGAAATAT 58.066 33.333 0.00 0.00 0.00 1.28
4423 6333 7.095481 GCAGATAGAACATCAGCAATCGAAATA 60.095 37.037 0.00 0.00 31.91 1.40
4424 6334 6.293298 GCAGATAGAACATCAGCAATCGAAAT 60.293 38.462 0.00 0.00 31.91 2.17
4425 6335 5.007039 GCAGATAGAACATCAGCAATCGAAA 59.993 40.000 0.00 0.00 31.91 3.46
4426 6336 4.509230 GCAGATAGAACATCAGCAATCGAA 59.491 41.667 0.00 0.00 31.91 3.71
4427 6337 4.053983 GCAGATAGAACATCAGCAATCGA 58.946 43.478 0.00 0.00 31.91 3.59
4428 6338 3.121092 CGCAGATAGAACATCAGCAATCG 60.121 47.826 3.13 0.00 31.91 3.34
4429 6339 3.363772 GCGCAGATAGAACATCAGCAATC 60.364 47.826 0.30 0.00 31.91 2.67
4430 6340 2.547211 GCGCAGATAGAACATCAGCAAT 59.453 45.455 0.30 0.00 31.91 3.56
4431 6341 1.935873 GCGCAGATAGAACATCAGCAA 59.064 47.619 0.30 0.00 31.91 3.91
4432 6342 1.134729 TGCGCAGATAGAACATCAGCA 60.135 47.619 5.66 1.61 31.91 4.41
4433 6343 1.575244 TGCGCAGATAGAACATCAGC 58.425 50.000 5.66 0.00 0.00 4.26
4434 6344 2.543012 CCTTGCGCAGATAGAACATCAG 59.457 50.000 11.31 0.00 0.00 2.90
4435 6345 2.554142 CCTTGCGCAGATAGAACATCA 58.446 47.619 11.31 0.00 0.00 3.07
4443 6353 0.174845 AACGTAGCCTTGCGCAGATA 59.825 50.000 11.31 0.00 41.38 1.98
4450 6360 1.403972 CTCGACGAACGTAGCCTTGC 61.404 60.000 0.00 0.00 43.13 4.01
4459 6369 6.785633 TCATAATTTCTTACTCGACGAACG 57.214 37.500 0.00 0.00 44.09 3.95
4476 6386 8.532977 GTGTTTTGCACCTTTACATTCATAAT 57.467 30.769 0.00 0.00 42.10 1.28
4506 6416 0.749649 TTGCATTTCGGCCACTGTTT 59.250 45.000 2.24 0.00 0.00 2.83
4540 6461 7.068103 CGCAGATAGAACCTCAGAGGAATATAT 59.932 40.741 24.45 16.62 37.67 0.86
4546 6467 2.302260 CGCAGATAGAACCTCAGAGGA 58.698 52.381 24.45 0.00 37.67 3.71
4570 6494 5.483685 TCCCTTACTCAATGGGAATATCG 57.516 43.478 0.00 0.00 46.06 2.92
4595 6519 6.879993 TGTTTGGCTCCTTTACGTTCATAATA 59.120 34.615 0.00 0.00 0.00 0.98
4639 6563 4.619160 GCCCCTTCATGTTTGTGAGATTTC 60.619 45.833 0.00 0.00 0.00 2.17
4648 6572 1.269012 ATGTGGCCCCTTCATGTTTG 58.731 50.000 0.00 0.00 0.00 2.93
4667 6591 5.456548 TTCACTCCTGTATTCGTTGTGTA 57.543 39.130 0.00 0.00 0.00 2.90
4676 6600 2.770164 AGCGCTTTCACTCCTGTATT 57.230 45.000 2.64 0.00 0.00 1.89
4677 6601 3.887621 TTAGCGCTTTCACTCCTGTAT 57.112 42.857 18.68 0.00 0.00 2.29
4683 6607 3.179830 TCGAGATTTAGCGCTTTCACTC 58.820 45.455 18.68 18.11 0.00 3.51
4707 6631 2.684374 GTGTGTTTGGACCCTTAACGTT 59.316 45.455 5.88 5.88 0.00 3.99
4708 6632 2.291365 GTGTGTTTGGACCCTTAACGT 58.709 47.619 0.00 0.00 0.00 3.99
4710 6634 1.605232 CCGTGTGTTTGGACCCTTAAC 59.395 52.381 0.00 0.00 0.00 2.01
4711 6635 1.212441 ACCGTGTGTTTGGACCCTTAA 59.788 47.619 0.00 0.00 0.00 1.85
4712 6636 0.838608 ACCGTGTGTTTGGACCCTTA 59.161 50.000 0.00 0.00 0.00 2.69
4713 6637 0.838608 TACCGTGTGTTTGGACCCTT 59.161 50.000 0.00 0.00 0.00 3.95
4714 6638 0.395312 CTACCGTGTGTTTGGACCCT 59.605 55.000 0.00 0.00 0.00 4.34
4715 6639 1.232621 GCTACCGTGTGTTTGGACCC 61.233 60.000 0.00 0.00 0.00 4.46
4716 6640 0.533308 TGCTACCGTGTGTTTGGACC 60.533 55.000 0.00 0.00 0.00 4.46
4717 6641 0.584876 GTGCTACCGTGTGTTTGGAC 59.415 55.000 0.00 0.00 0.00 4.02
4718 6642 0.178301 TGTGCTACCGTGTGTTTGGA 59.822 50.000 0.00 0.00 0.00 3.53
4719 6643 0.586319 CTGTGCTACCGTGTGTTTGG 59.414 55.000 0.00 0.00 0.00 3.28
4720 6644 0.586319 CCTGTGCTACCGTGTGTTTG 59.414 55.000 0.00 0.00 0.00 2.93
4721 6645 0.534203 CCCTGTGCTACCGTGTGTTT 60.534 55.000 0.00 0.00 0.00 2.83
4722 6646 1.070786 CCCTGTGCTACCGTGTGTT 59.929 57.895 0.00 0.00 0.00 3.32
4723 6647 2.095978 GACCCTGTGCTACCGTGTGT 62.096 60.000 0.00 0.00 0.00 3.72
4724 6648 1.374252 GACCCTGTGCTACCGTGTG 60.374 63.158 0.00 0.00 0.00 3.82
4775 6797 4.410883 TGGTCCCTGTACTTTTCTTCTTGA 59.589 41.667 0.00 0.00 0.00 3.02
4780 6802 3.889538 GCTTTGGTCCCTGTACTTTTCTT 59.110 43.478 0.00 0.00 0.00 2.52
4795 6817 3.451141 TTCAAGATTTTGCGCTTTGGT 57.549 38.095 9.73 0.00 34.21 3.67
4796 6818 4.792528 TTTTCAAGATTTTGCGCTTTGG 57.207 36.364 9.73 0.00 34.21 3.28
4815 6837 9.942850 ATAAATCGAGAAATGGTCCAAATTTTT 57.057 25.926 0.00 0.00 0.00 1.94
4840 6873 0.673333 TGCGCAAGGATGACACGAAT 60.673 50.000 8.16 0.00 38.28 3.34
4842 6875 1.737735 CTGCGCAAGGATGACACGA 60.738 57.895 13.05 0.00 36.74 4.35
4862 6895 6.379703 ACGATATAGAGAAGATTAGCATGGCT 59.620 38.462 0.00 0.00 43.41 4.75
4881 6914 7.119262 GGACATCCGATAAAATTGGAACGATAT 59.881 37.037 0.00 0.00 45.74 1.63
4917 6950 1.465020 CGACGTGTGAGAGCTCTCTTC 60.465 57.143 36.78 29.19 43.25 2.87
4918 6951 0.519519 CGACGTGTGAGAGCTCTCTT 59.480 55.000 36.78 19.79 43.25 2.85
4932 6965 2.494870 AGACCAGTTTATAAGCCGACGT 59.505 45.455 0.00 0.00 0.00 4.34
4934 6967 2.608090 GCAGACCAGTTTATAAGCCGAC 59.392 50.000 0.00 0.00 0.00 4.79
4972 7005 1.086696 CCAGCGTTTAGTCCCACATG 58.913 55.000 0.00 0.00 0.00 3.21
5018 7051 1.451387 ATTGAATCGGACGGCCCAC 60.451 57.895 0.00 0.00 34.14 4.61
5090 7125 1.225704 CAGCCACAGAAGATCCCCC 59.774 63.158 0.00 0.00 0.00 5.40


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

AutoCloner maintained by Alex Coulton.