Multiple sequence alignment - TraesCS2A01G185900

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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 TraesCS2A01G185900 chr2A 100.000 6236 0 0 1 6236 147472994 147479229 0.000000e+00 11516
1 TraesCS2A01G185900 chr2A 93.529 510 32 1 1 509 192108049 192107540 0.000000e+00 758
2 TraesCS2A01G185900 chr2A 93.663 505 32 0 1 505 729246621 729247125 0.000000e+00 756
3 TraesCS2A01G185900 chr2A 97.101 69 2 0 3708 3776 148162183 148162115 3.950000e-22 117
4 TraesCS2A01G185900 chr2D 98.224 1689 24 2 1685 3373 153795181 153793499 0.000000e+00 2948
5 TraesCS2A01G185900 chr2D 98.102 1370 25 1 3319 4687 153793505 153792136 0.000000e+00 2385
6 TraesCS2A01G185900 chr2D 90.647 1422 48 20 598 1947 153801983 153800575 0.000000e+00 1810
7 TraesCS2A01G185900 chr2D 92.960 767 31 12 4784 5544 153792134 153791385 0.000000e+00 1096
8 TraesCS2A01G185900 chr2D 96.265 589 20 2 5649 6236 153790331 153789744 0.000000e+00 965
9 TraesCS2A01G185900 chr2D 95.283 106 4 1 5552 5656 153791344 153791239 3.870000e-37 167
10 TraesCS2A01G185900 chr2B 93.415 1959 88 22 2759 4692 211213035 211211093 0.000000e+00 2865
11 TraesCS2A01G185900 chr2B 93.509 1294 68 10 1419 2704 211214320 211213035 0.000000e+00 1910
12 TraesCS2A01G185900 chr2B 92.248 774 37 9 4783 5544 211211097 211210335 0.000000e+00 1075
13 TraesCS2A01G185900 chr2B 89.877 731 32 19 598 1298 211215149 211214431 0.000000e+00 902
14 TraesCS2A01G185900 chr2B 97.080 274 4 1 5667 5936 211194517 211194244 5.700000e-125 459
15 TraesCS2A01G185900 chr2B 90.857 175 12 3 1705 1876 76912299 76912126 1.350000e-56 231
16 TraesCS2A01G185900 chr2B 94.574 129 6 1 6109 6236 211194248 211194120 1.370000e-46 198
17 TraesCS2A01G185900 chr2B 95.000 80 2 2 5465 5543 211210185 211210107 2.360000e-24 124
18 TraesCS2A01G185900 chr3A 94.622 502 27 0 4 505 716109203 716108702 0.000000e+00 778
19 TraesCS2A01G185900 chr3A 94.269 506 27 2 1 505 571188529 571189033 0.000000e+00 773
20 TraesCS2A01G185900 chr3A 92.308 169 8 4 1703 1868 726769130 726768964 1.050000e-57 235
21 TraesCS2A01G185900 chr3A 90.090 111 10 1 4676 4786 624721730 624721621 6.520000e-30 143
22 TraesCS2A01G185900 chr1B 94.071 506 30 0 1 506 324343678 324343173 0.000000e+00 769
23 TraesCS2A01G185900 chr7A 94.059 505 30 0 1 505 25908964 25908460 0.000000e+00 767
24 TraesCS2A01G185900 chr5B 93.372 513 32 2 1 512 166675054 166675565 0.000000e+00 758
25 TraesCS2A01G185900 chr5B 92.157 102 8 0 4686 4787 418470879 418470980 1.810000e-30 145
26 TraesCS2A01G185900 chr5B 84.354 147 18 4 725 871 669479611 669479752 8.430000e-29 139
27 TraesCS2A01G185900 chr6B 93.663 505 32 0 1 505 484006349 484006853 0.000000e+00 756
28 TraesCS2A01G185900 chr6B 94.792 96 5 0 4690 4785 343781181 343781276 3.890000e-32 150
29 TraesCS2A01G185900 chr3D 93.663 505 32 0 1 505 54371744 54371240 0.000000e+00 756
30 TraesCS2A01G185900 chr3D 94.845 97 5 0 4690 4786 108210741 108210837 1.080000e-32 152
31 TraesCS2A01G185900 chr6A 93.827 162 7 2 1705 1863 442395716 442395555 2.250000e-59 241
32 TraesCS2A01G185900 chr6A 93.069 101 6 1 4690 4790 8173802 8173703 5.040000e-31 147
33 TraesCS2A01G185900 chr6D 91.813 171 9 4 1696 1863 90112231 90112399 3.760000e-57 233
34 TraesCS2A01G185900 chr6D 91.667 168 11 2 1705 1869 90134890 90135057 4.860000e-56 230
35 TraesCS2A01G185900 chr6D 94.792 96 5 0 4690 4785 374820208 374820303 3.890000e-32 150
36 TraesCS2A01G185900 chr6D 92.784 97 7 0 4690 4786 808206 808302 2.340000e-29 141
37 TraesCS2A01G185900 chr6D 92.784 97 3 3 4690 4785 422327412 422327505 3.030000e-28 137
38 TraesCS2A01G185900 chr6D 91.919 99 6 2 4690 4787 465968866 465968963 3.030000e-28 137
39 TraesCS2A01G185900 chr6D 91.000 100 7 2 4690 4788 98100062 98099964 3.920000e-27 134
40 TraesCS2A01G185900 chr3B 90.857 175 13 2 1698 1869 552226400 552226574 1.350000e-56 231
41 TraesCS2A01G185900 chr3B 91.892 74 6 0 798 871 405225689 405225616 3.070000e-18 104
42 TraesCS2A01G185900 chr5A 94.059 101 6 0 4685 4785 641586664 641586564 3.010000e-33 154
43 TraesCS2A01G185900 chr7B 93.204 103 7 0 4690 4792 134634216 134634114 1.080000e-32 152
44 TraesCS2A01G185900 chr7B 90.179 112 8 3 4678 4786 501308906 501308795 6.520000e-30 143
45 TraesCS2A01G185900 chr7D 93.939 99 6 0 4690 4788 168580014 168579916 3.890000e-32 150
46 TraesCS2A01G185900 chr1A 93.069 101 7 0 4690 4790 474641678 474641778 1.400000e-31 148
47 TraesCS2A01G185900 chr4B 92.233 103 8 0 4690 4792 103270512 103270614 5.040000e-31 147
48 TraesCS2A01G185900 chr4D 93.750 96 6 0 4690 4785 13198377 13198282 1.810000e-30 145
49 TraesCS2A01G185900 chr4D 92.784 97 5 2 4690 4785 31822001 31822096 8.430000e-29 139
50 TraesCS2A01G185900 chr4D 90.291 103 10 0 4690 4792 503153846 503153948 1.090000e-27 135
51 TraesCS2A01G185900 chr1D 91.262 103 9 0 4690 4792 225936947 225936845 2.340000e-29 141
52 TraesCS2A01G185900 chr1D 91.262 103 9 0 4690 4792 225944037 225943935 2.340000e-29 141
53 TraesCS2A01G185900 chr1D 90.654 107 9 1 4690 4796 272547555 272547660 2.340000e-29 141
54 TraesCS2A01G185900 chrUn 89.908 109 10 1 4690 4797 2713992 2713884 8.430000e-29 139
55 TraesCS2A01G185900 chrUn 89.908 109 10 1 4690 4797 2717594 2717486 8.430000e-29 139
56 TraesCS2A01G185900 chrUn 89.908 109 10 1 4690 4797 2780472 2780364 8.430000e-29 139
57 TraesCS2A01G185900 chrUn 89.091 110 9 3 4679 4787 8484448 8484341 3.920000e-27 134
58 TraesCS2A01G185900 chrUn 90.625 96 9 0 4690 4785 79951900 79951805 1.820000e-25 128
59 TraesCS2A01G185900 chrUn 91.398 93 8 0 4690 4782 89396768 89396860 1.820000e-25 128
60 TraesCS2A01G185900 chrUn 90.722 97 7 2 4690 4785 479972394 479972489 1.820000e-25 128
61 TraesCS2A01G185900 chrUn 89.899 99 8 2 4690 4787 341053843 341053746 6.560000e-25 126
62 TraesCS2A01G185900 chrUn 89.899 99 8 2 4690 4787 462783201 462783298 6.560000e-25 126


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 TraesCS2A01G185900 chr2A 147472994 147479229 6235 False 11516.0 11516 100.0000 1 6236 1 chr2A.!!$F1 6235
1 TraesCS2A01G185900 chr2A 192107540 192108049 509 True 758.0 758 93.5290 1 509 1 chr2A.!!$R2 508
2 TraesCS2A01G185900 chr2A 729246621 729247125 504 False 756.0 756 93.6630 1 505 1 chr2A.!!$F2 504
3 TraesCS2A01G185900 chr2D 153800575 153801983 1408 True 1810.0 1810 90.6470 598 1947 1 chr2D.!!$R1 1349
4 TraesCS2A01G185900 chr2D 153789744 153795181 5437 True 1512.2 2948 96.1668 1685 6236 5 chr2D.!!$R2 4551
5 TraesCS2A01G185900 chr2B 211210107 211215149 5042 True 1375.2 2865 92.8098 598 5544 5 chr2B.!!$R3 4946
6 TraesCS2A01G185900 chr3A 716108702 716109203 501 True 778.0 778 94.6220 4 505 1 chr3A.!!$R2 501
7 TraesCS2A01G185900 chr3A 571188529 571189033 504 False 773.0 773 94.2690 1 505 1 chr3A.!!$F1 504
8 TraesCS2A01G185900 chr1B 324343173 324343678 505 True 769.0 769 94.0710 1 506 1 chr1B.!!$R1 505
9 TraesCS2A01G185900 chr7A 25908460 25908964 504 True 767.0 767 94.0590 1 505 1 chr7A.!!$R1 504
10 TraesCS2A01G185900 chr5B 166675054 166675565 511 False 758.0 758 93.3720 1 512 1 chr5B.!!$F1 511
11 TraesCS2A01G185900 chr6B 484006349 484006853 504 False 756.0 756 93.6630 1 505 1 chr6B.!!$F2 504
12 TraesCS2A01G185900 chr3D 54371240 54371744 504 True 756.0 756 93.6630 1 505 1 chr3D.!!$R1 504

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
573 574 0.182299 GATTGAGGGCTGGAAGAGGG 59.818 60.0 0.0 0.0 34.07 4.30 F
574 575 0.253347 ATTGAGGGCTGGAAGAGGGA 60.253 55.0 0.0 0.0 34.07 4.20 F
579 580 0.322906 GGGCTGGAAGAGGGAACTTG 60.323 60.0 0.0 0.0 44.43 3.16 F
1235 1280 0.537653 GCCACCCTGTCTCTCTTACC 59.462 60.0 0.0 0.0 0.00 2.85 F
1281 1349 2.497675 AGTCATGTGGTGCTAGGTAGTG 59.502 50.0 0.0 0.0 0.00 2.74 F
3182 3292 0.107703 TGCTAGGGTGATTTCGCAGG 60.108 55.0 0.0 0.0 0.00 4.85 F
4007 4176 0.178950 TCTCTGTGCTGGGACTCTGT 60.179 55.0 0.0 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2509 2609 0.591236 CAACCGCAAACTGACCGTTG 60.591 55.000 0.00 0.00 35.61 4.10 R
2704 2804 8.458843 GCTTTTCATTAGGTATTTCTGTAGCAA 58.541 33.333 0.00 0.00 0.00 3.91 R
2717 2817 6.715347 ACTTTCTTGTGCTTTTCATTAGGT 57.285 33.333 0.00 0.00 0.00 3.08 R
2751 2851 0.458197 GCACACAAGCTGCACACAAA 60.458 50.000 1.02 0.00 34.56 2.83 R
3384 3547 3.165071 CATGACCTAGGCCAAAAAGGTT 58.835 45.455 17.18 3.56 43.69 3.50 R
4688 4860 0.328258 ATTTTGGGACGGAGGGAGTG 59.672 55.000 0.00 0.00 0.00 3.51 R
5772 6975 0.592754 GATCCTACACGCGTCTCTGC 60.593 60.000 9.86 0.00 0.00 4.26 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
90 91 0.673644 GCCGCCAAGCAAGTCTTCTA 60.674 55.000 0.00 0.00 31.27 2.10
159 160 4.271816 CCCGCCTCTCGTGATCCG 62.272 72.222 0.00 0.00 36.19 4.18
186 187 1.202348 GAAAGGGGCGATCAGGTTTTG 59.798 52.381 0.00 0.00 0.00 2.44
370 371 8.258007 AGATCGTGGTAGAATTCATGTTTCTAA 58.742 33.333 16.92 7.00 37.41 2.10
515 516 9.426837 ACTCATATTTCCAACACAATCAAATTG 57.573 29.630 0.00 0.00 45.59 2.32
516 517 8.774890 TCATATTTCCAACACAATCAAATTGG 57.225 30.769 4.82 0.00 44.42 3.16
517 518 8.591940 TCATATTTCCAACACAATCAAATTGGA 58.408 29.630 0.42 0.42 46.92 3.53
522 523 6.339730 TCCAACACAATCAAATTGGATATGC 58.660 36.000 0.00 0.00 44.43 3.14
523 524 6.070938 TCCAACACAATCAAATTGGATATGCA 60.071 34.615 0.00 0.00 44.43 3.96
524 525 6.256975 CCAACACAATCAAATTGGATATGCAG 59.743 38.462 0.00 0.00 43.66 4.41
525 526 6.778834 ACACAATCAAATTGGATATGCAGA 57.221 33.333 0.00 0.00 44.42 4.26
526 527 7.172868 ACACAATCAAATTGGATATGCAGAA 57.827 32.000 0.00 0.00 44.42 3.02
527 528 7.262772 ACACAATCAAATTGGATATGCAGAAG 58.737 34.615 0.00 0.00 44.42 2.85
528 529 6.200286 CACAATCAAATTGGATATGCAGAAGC 59.800 38.462 0.00 0.00 44.42 3.86
529 530 6.097839 ACAATCAAATTGGATATGCAGAAGCT 59.902 34.615 0.00 0.00 44.42 3.74
530 531 6.726490 ATCAAATTGGATATGCAGAAGCTT 57.274 33.333 0.00 0.00 42.74 3.74
531 532 5.898174 TCAAATTGGATATGCAGAAGCTTG 58.102 37.500 2.10 0.00 42.74 4.01
532 533 5.419788 TCAAATTGGATATGCAGAAGCTTGT 59.580 36.000 2.10 0.00 42.74 3.16
533 534 5.927281 AATTGGATATGCAGAAGCTTGTT 57.073 34.783 2.10 0.00 42.74 2.83
534 535 5.927281 ATTGGATATGCAGAAGCTTGTTT 57.073 34.783 2.10 0.00 42.74 2.83
535 536 4.970662 TGGATATGCAGAAGCTTGTTTC 57.029 40.909 2.10 0.00 42.74 2.78
536 537 4.334552 TGGATATGCAGAAGCTTGTTTCA 58.665 39.130 2.10 0.05 42.74 2.69
537 538 4.951715 TGGATATGCAGAAGCTTGTTTCAT 59.048 37.500 2.10 8.45 42.74 2.57
538 539 6.121590 TGGATATGCAGAAGCTTGTTTCATA 58.878 36.000 2.10 10.44 42.74 2.15
539 540 6.261603 TGGATATGCAGAAGCTTGTTTCATAG 59.738 38.462 2.10 0.00 42.74 2.23
540 541 3.837213 TGCAGAAGCTTGTTTCATAGC 57.163 42.857 2.10 0.00 42.74 2.97
548 549 5.126396 AGCTTGTTTCATAGCTTTTCACC 57.874 39.130 0.00 0.00 45.03 4.02
549 550 4.584325 AGCTTGTTTCATAGCTTTTCACCA 59.416 37.500 0.00 0.00 45.03 4.17
550 551 5.244626 AGCTTGTTTCATAGCTTTTCACCAT 59.755 36.000 0.00 0.00 45.03 3.55
551 552 6.434028 AGCTTGTTTCATAGCTTTTCACCATA 59.566 34.615 0.00 0.00 45.03 2.74
552 553 7.039784 AGCTTGTTTCATAGCTTTTCACCATAA 60.040 33.333 0.00 0.00 45.03 1.90
553 554 7.761249 GCTTGTTTCATAGCTTTTCACCATAAT 59.239 33.333 0.00 0.00 34.57 1.28
554 555 8.984891 TTGTTTCATAGCTTTTCACCATAATG 57.015 30.769 0.00 0.00 0.00 1.90
555 556 8.347004 TGTTTCATAGCTTTTCACCATAATGA 57.653 30.769 0.00 0.00 0.00 2.57
556 557 8.970020 TGTTTCATAGCTTTTCACCATAATGAT 58.030 29.630 0.00 0.00 0.00 2.45
557 558 9.807649 GTTTCATAGCTTTTCACCATAATGATT 57.192 29.630 0.00 0.00 0.00 2.57
558 559 9.806203 TTTCATAGCTTTTCACCATAATGATTG 57.194 29.630 0.00 0.00 0.00 2.67
559 560 8.750515 TCATAGCTTTTCACCATAATGATTGA 57.249 30.769 0.00 0.00 0.00 2.57
560 561 8.843262 TCATAGCTTTTCACCATAATGATTGAG 58.157 33.333 0.00 0.00 0.00 3.02
561 562 6.461110 AGCTTTTCACCATAATGATTGAGG 57.539 37.500 0.00 0.00 0.00 3.86
562 563 5.361857 AGCTTTTCACCATAATGATTGAGGG 59.638 40.000 3.38 0.00 0.00 4.30
563 564 5.594926 CTTTTCACCATAATGATTGAGGGC 58.405 41.667 3.38 0.00 0.00 5.19
564 565 4.524802 TTCACCATAATGATTGAGGGCT 57.475 40.909 3.38 0.00 0.00 5.19
565 566 3.824133 TCACCATAATGATTGAGGGCTG 58.176 45.455 3.38 0.00 0.00 4.85
566 567 2.889045 CACCATAATGATTGAGGGCTGG 59.111 50.000 3.38 0.00 0.00 4.85
567 568 2.785269 ACCATAATGATTGAGGGCTGGA 59.215 45.455 0.00 0.00 0.00 3.86
568 569 3.205056 ACCATAATGATTGAGGGCTGGAA 59.795 43.478 0.00 0.00 0.00 3.53
569 570 3.825014 CCATAATGATTGAGGGCTGGAAG 59.175 47.826 0.00 0.00 0.00 3.46
570 571 4.446745 CCATAATGATTGAGGGCTGGAAGA 60.447 45.833 0.00 0.00 34.07 2.87
571 572 3.294038 AATGATTGAGGGCTGGAAGAG 57.706 47.619 0.00 0.00 34.07 2.85
572 573 0.914644 TGATTGAGGGCTGGAAGAGG 59.085 55.000 0.00 0.00 34.07 3.69
573 574 0.182299 GATTGAGGGCTGGAAGAGGG 59.818 60.000 0.00 0.00 34.07 4.30
574 575 0.253347 ATTGAGGGCTGGAAGAGGGA 60.253 55.000 0.00 0.00 34.07 4.20
575 576 0.475632 TTGAGGGCTGGAAGAGGGAA 60.476 55.000 0.00 0.00 34.07 3.97
576 577 1.201429 TGAGGGCTGGAAGAGGGAAC 61.201 60.000 0.00 0.00 34.07 3.62
578 579 0.476611 AGGGCTGGAAGAGGGAACTT 60.477 55.000 0.00 0.00 44.43 2.66
579 580 0.322906 GGGCTGGAAGAGGGAACTTG 60.323 60.000 0.00 0.00 44.43 3.16
580 581 0.693049 GGCTGGAAGAGGGAACTTGA 59.307 55.000 0.00 0.00 44.43 3.02
581 582 1.339535 GGCTGGAAGAGGGAACTTGAG 60.340 57.143 0.00 0.00 44.43 3.02
582 583 1.625818 GCTGGAAGAGGGAACTTGAGA 59.374 52.381 0.00 0.00 44.43 3.27
583 584 2.238395 GCTGGAAGAGGGAACTTGAGAT 59.762 50.000 0.00 0.00 44.43 2.75
584 585 3.871485 CTGGAAGAGGGAACTTGAGATG 58.129 50.000 0.00 0.00 44.43 2.90
585 586 3.251484 TGGAAGAGGGAACTTGAGATGT 58.749 45.455 0.00 0.00 44.43 3.06
586 587 3.008375 TGGAAGAGGGAACTTGAGATGTG 59.992 47.826 0.00 0.00 44.43 3.21
587 588 3.261897 GGAAGAGGGAACTTGAGATGTGA 59.738 47.826 0.00 0.00 44.43 3.58
588 589 3.971245 AGAGGGAACTTGAGATGTGAC 57.029 47.619 0.00 0.00 44.43 3.67
589 590 3.515562 AGAGGGAACTTGAGATGTGACT 58.484 45.455 0.00 0.00 44.43 3.41
590 591 4.678256 AGAGGGAACTTGAGATGTGACTA 58.322 43.478 0.00 0.00 44.43 2.59
591 592 4.709397 AGAGGGAACTTGAGATGTGACTAG 59.291 45.833 0.00 0.00 44.43 2.57
592 593 4.678256 AGGGAACTTGAGATGTGACTAGA 58.322 43.478 0.00 0.00 37.44 2.43
593 594 5.276440 AGGGAACTTGAGATGTGACTAGAT 58.724 41.667 0.00 0.00 37.44 1.98
594 595 5.362430 AGGGAACTTGAGATGTGACTAGATC 59.638 44.000 0.00 0.00 37.44 2.75
595 596 5.362430 GGGAACTTGAGATGTGACTAGATCT 59.638 44.000 0.00 0.00 39.43 2.75
723 724 1.296001 CGCTACGACGAGTCACGAG 60.296 63.158 0.00 7.42 45.77 4.18
797 806 1.583404 CGGCAAAGCAAATATTCGCAC 59.417 47.619 0.42 0.00 0.00 5.34
873 887 2.283388 ACAATGCAGGCCCACCAG 60.283 61.111 0.00 0.00 39.06 4.00
925 951 3.617735 TACACTCCGGCGCACCAA 61.618 61.111 10.83 0.00 34.57 3.67
1211 1255 1.271163 CGCCTTCCACCTCCTTGTAAA 60.271 52.381 0.00 0.00 0.00 2.01
1235 1280 0.537653 GCCACCCTGTCTCTCTTACC 59.462 60.000 0.00 0.00 0.00 2.85
1259 1304 8.432805 ACCATCTAATTTCAGTATACCTTGAGG 58.567 37.037 0.00 0.00 42.17 3.86
1260 1305 8.651389 CCATCTAATTTCAGTATACCTTGAGGA 58.349 37.037 3.59 0.00 38.94 3.71
1281 1349 2.497675 AGTCATGTGGTGCTAGGTAGTG 59.502 50.000 0.00 0.00 0.00 2.74
1405 1473 6.785488 TTCGGATTAACACATGATAGATGC 57.215 37.500 0.00 0.00 0.00 3.91
1406 1474 4.923281 TCGGATTAACACATGATAGATGCG 59.077 41.667 0.00 4.23 0.00 4.73
1508 1586 3.082698 TGTTGACTTTGTGCATTGAGC 57.917 42.857 0.00 0.00 45.96 4.26
1765 1857 5.758784 TCTCAGTACGGACTACATACAGATG 59.241 44.000 0.00 0.00 34.61 2.90
1884 1982 5.532025 AGCTTTTAGATTTTCGGTTCGAG 57.468 39.130 0.00 0.00 37.14 4.04
1902 2000 6.183360 GGTTCGAGATATTGAGCATGACAAAA 60.183 38.462 0.00 0.00 0.00 2.44
1979 2078 5.275067 ACTTGCTATCATGGACTTCTCTC 57.725 43.478 0.00 0.00 0.00 3.20
2104 2203 7.068348 TGGTGCTACTTTATGGTTGTTTTTACA 59.932 33.333 0.00 0.00 0.00 2.41
2141 2240 3.152341 CCTGAAAACTGGAGACATGCTT 58.848 45.455 0.00 0.00 41.51 3.91
2468 2568 2.969950 CCGGATTATGGTCCCTGAACTA 59.030 50.000 0.00 0.00 34.67 2.24
2509 2609 7.492352 AGTACTGGTGTTACTTTCAATGAAC 57.508 36.000 0.00 0.00 0.00 3.18
2704 2804 4.315803 CACGAAAGGGTGATCTGTAAAGT 58.684 43.478 0.00 0.00 40.38 2.66
2775 2875 1.067000 TGTGCAGCTTGTGTGCTTTTT 60.067 42.857 0.00 0.00 41.98 1.94
3182 3292 0.107703 TGCTAGGGTGATTTCGCAGG 60.108 55.000 0.00 0.00 0.00 4.85
3218 3328 6.666113 TGTTGTGGGATATACTAGTTCTGTCA 59.334 38.462 0.00 0.00 0.00 3.58
3442 3607 6.913170 TGCCAATTGCTAGTTTTTCTAGAAG 58.087 36.000 5.12 0.00 46.53 2.85
3601 3766 6.266168 TGTTTCCATTTTGTAGCCACATAG 57.734 37.500 0.00 0.00 33.76 2.23
3817 3983 8.761689 ACCAGAATTTGCATATTTAGGATTGTT 58.238 29.630 20.38 3.63 0.00 2.83
3838 4004 6.472016 TGTTGGACTTGCTCATCTGTATTTA 58.528 36.000 0.00 0.00 0.00 1.40
3870 4036 5.298347 ACTGTAGGTAGCAAGAAAAGACAC 58.702 41.667 0.00 0.00 0.00 3.67
4007 4176 0.178950 TCTCTGTGCTGGGACTCTGT 60.179 55.000 0.00 0.00 0.00 3.41
4083 4252 5.381757 TCATAAGGGCACAAACAAACTACT 58.618 37.500 0.00 0.00 0.00 2.57
4144 4314 8.198109 TGTCTTCTTGCTACACTTCCTATAATC 58.802 37.037 0.00 0.00 0.00 1.75
4538 4710 5.195001 TGTGAATACTTTTGGTTTCCTGC 57.805 39.130 0.00 0.00 0.00 4.85
4667 4839 7.816640 ACATCACACACCTGTTCAAATAATAC 58.183 34.615 0.00 0.00 0.00 1.89
4687 4859 7.750229 AATACCATGTAGCTCATTACATTGG 57.250 36.000 0.00 2.09 41.17 3.16
4688 4860 3.885297 ACCATGTAGCTCATTACATTGGC 59.115 43.478 12.16 0.00 41.17 4.52
4689 4861 3.884693 CCATGTAGCTCATTACATTGGCA 59.115 43.478 0.00 0.00 41.17 4.92
4690 4862 4.261322 CCATGTAGCTCATTACATTGGCAC 60.261 45.833 0.00 0.00 41.17 5.01
4691 4863 4.220693 TGTAGCTCATTACATTGGCACT 57.779 40.909 0.00 0.00 0.00 4.40
4692 4864 4.191544 TGTAGCTCATTACATTGGCACTC 58.808 43.478 0.00 0.00 0.00 3.51
4693 4865 2.648059 AGCTCATTACATTGGCACTCC 58.352 47.619 0.00 0.00 0.00 3.85
4694 4866 1.678101 GCTCATTACATTGGCACTCCC 59.322 52.381 0.00 0.00 0.00 4.30
4695 4867 2.684927 GCTCATTACATTGGCACTCCCT 60.685 50.000 0.00 0.00 0.00 4.20
4696 4868 3.209410 CTCATTACATTGGCACTCCCTC 58.791 50.000 0.00 0.00 0.00 4.30
4697 4869 2.092429 TCATTACATTGGCACTCCCTCC 60.092 50.000 0.00 0.00 0.00 4.30
4698 4870 0.251916 TTACATTGGCACTCCCTCCG 59.748 55.000 0.00 0.00 0.00 4.63
4699 4871 0.907704 TACATTGGCACTCCCTCCGT 60.908 55.000 0.00 0.00 0.00 4.69
4700 4872 1.450312 CATTGGCACTCCCTCCGTC 60.450 63.158 0.00 0.00 0.00 4.79
4701 4873 2.670148 ATTGGCACTCCCTCCGTCC 61.670 63.158 0.00 0.00 0.00 4.79
4704 4876 3.319198 GCACTCCCTCCGTCCCAA 61.319 66.667 0.00 0.00 0.00 4.12
4705 4877 2.890766 GCACTCCCTCCGTCCCAAA 61.891 63.158 0.00 0.00 0.00 3.28
4706 4878 1.758592 CACTCCCTCCGTCCCAAAA 59.241 57.895 0.00 0.00 0.00 2.44
4707 4879 0.328258 CACTCCCTCCGTCCCAAAAT 59.672 55.000 0.00 0.00 0.00 1.82
4708 4880 1.557832 CACTCCCTCCGTCCCAAAATA 59.442 52.381 0.00 0.00 0.00 1.40
4709 4881 2.026636 CACTCCCTCCGTCCCAAAATAA 60.027 50.000 0.00 0.00 0.00 1.40
4710 4882 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
4711 4883 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
4712 4884 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
4713 4885 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
4714 4886 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
4715 4887 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
4716 4888 4.324267 CTCCGTCCCAAAATAAGTGTCTT 58.676 43.478 0.00 0.00 0.00 3.01
4717 4889 5.484715 CTCCGTCCCAAAATAAGTGTCTTA 58.515 41.667 0.00 0.00 0.00 2.10
4718 4890 5.867330 TCCGTCCCAAAATAAGTGTCTTAA 58.133 37.500 0.00 0.00 0.00 1.85
4719 4891 5.702209 TCCGTCCCAAAATAAGTGTCTTAAC 59.298 40.000 0.00 0.00 0.00 2.01
4720 4892 5.704053 CCGTCCCAAAATAAGTGTCTTAACT 59.296 40.000 0.00 0.00 0.00 2.24
4721 4893 6.206048 CCGTCCCAAAATAAGTGTCTTAACTT 59.794 38.462 0.00 0.00 42.89 2.66
4722 4894 7.295930 CGTCCCAAAATAAGTGTCTTAACTTC 58.704 38.462 0.00 0.00 40.77 3.01
4723 4895 7.041644 CGTCCCAAAATAAGTGTCTTAACTTCA 60.042 37.037 0.00 0.00 40.77 3.02
4724 4896 8.290325 GTCCCAAAATAAGTGTCTTAACTTCAG 58.710 37.037 0.00 0.00 40.77 3.02
4725 4897 7.996644 TCCCAAAATAAGTGTCTTAACTTCAGT 59.003 33.333 0.00 0.00 40.77 3.41
4726 4898 9.280174 CCCAAAATAAGTGTCTTAACTTCAGTA 57.720 33.333 0.00 0.00 40.77 2.74
4733 4905 8.788325 AAGTGTCTTAACTTCAGTACAACTTT 57.212 30.769 0.00 0.00 35.44 2.66
4734 4906 8.197988 AGTGTCTTAACTTCAGTACAACTTTG 57.802 34.615 0.00 0.00 0.00 2.77
4735 4907 6.905609 GTGTCTTAACTTCAGTACAACTTTGC 59.094 38.462 0.00 0.00 0.00 3.68
4736 4908 6.596106 TGTCTTAACTTCAGTACAACTTTGCA 59.404 34.615 0.00 0.00 0.00 4.08
4737 4909 6.905609 GTCTTAACTTCAGTACAACTTTGCAC 59.094 38.462 0.00 0.00 0.00 4.57
4738 4910 6.821665 TCTTAACTTCAGTACAACTTTGCACT 59.178 34.615 0.00 0.00 35.22 4.40
4739 4911 7.982919 TCTTAACTTCAGTACAACTTTGCACTA 59.017 33.333 0.00 0.00 33.18 2.74
4740 4912 6.995511 AACTTCAGTACAACTTTGCACTAA 57.004 33.333 0.00 0.00 33.18 2.24
4741 4913 6.995511 ACTTCAGTACAACTTTGCACTAAA 57.004 33.333 0.00 0.00 33.18 1.85
4760 4932 7.247929 ACTAAAGTTAGTGCAAAGTTGAGAC 57.752 36.000 9.27 0.00 42.13 3.36
4761 4933 6.821665 ACTAAAGTTAGTGCAAAGTTGAGACA 59.178 34.615 9.27 0.00 42.13 3.41
4762 4934 5.485662 AAGTTAGTGCAAAGTTGAGACAC 57.514 39.130 0.00 0.00 0.00 3.67
4763 4935 4.770795 AGTTAGTGCAAAGTTGAGACACT 58.229 39.130 0.00 0.00 43.60 3.55
4764 4936 5.186198 AGTTAGTGCAAAGTTGAGACACTT 58.814 37.500 7.72 0.00 41.56 3.16
4765 4937 6.346096 AGTTAGTGCAAAGTTGAGACACTTA 58.654 36.000 7.72 0.00 41.56 2.24
4766 4938 6.992715 AGTTAGTGCAAAGTTGAGACACTTAT 59.007 34.615 7.72 0.00 41.56 1.73
4767 4939 7.499232 AGTTAGTGCAAAGTTGAGACACTTATT 59.501 33.333 7.72 0.00 41.56 1.40
4768 4940 6.699575 AGTGCAAAGTTGAGACACTTATTT 57.300 33.333 0.00 0.00 38.38 1.40
4769 4941 7.100458 AGTGCAAAGTTGAGACACTTATTTT 57.900 32.000 0.00 0.00 38.38 1.82
4770 4942 6.974622 AGTGCAAAGTTGAGACACTTATTTTG 59.025 34.615 0.00 0.00 38.38 2.44
4771 4943 6.972328 GTGCAAAGTTGAGACACTTATTTTGA 59.028 34.615 0.00 0.00 35.87 2.69
4772 4944 7.166473 GTGCAAAGTTGAGACACTTATTTTGAG 59.834 37.037 0.00 0.00 35.87 3.02
4773 4945 7.066887 TGCAAAGTTGAGACACTTATTTTGAGA 59.933 33.333 0.00 0.00 35.87 3.27
4774 4946 7.377131 GCAAAGTTGAGACACTTATTTTGAGAC 59.623 37.037 0.00 0.00 35.87 3.36
4775 4947 6.771188 AGTTGAGACACTTATTTTGAGACG 57.229 37.500 0.00 0.00 0.00 4.18
4776 4948 5.696724 AGTTGAGACACTTATTTTGAGACGG 59.303 40.000 0.00 0.00 0.00 4.79
4777 4949 5.462530 TGAGACACTTATTTTGAGACGGA 57.537 39.130 0.00 0.00 0.00 4.69
4778 4950 5.470368 TGAGACACTTATTTTGAGACGGAG 58.530 41.667 0.00 0.00 0.00 4.63
4779 4951 4.822026 AGACACTTATTTTGAGACGGAGG 58.178 43.478 0.00 0.00 0.00 4.30
4780 4952 3.933332 GACACTTATTTTGAGACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
4781 4953 3.581332 ACACTTATTTTGAGACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
4800 4972 7.065504 GGAGGGAGTACTTGATAACCTAGTAA 58.934 42.308 0.00 0.00 35.47 2.24
4895 5071 8.308931 TCAGCTTGAATTTCTTGCAAGAATAAT 58.691 29.630 35.66 26.03 43.92 1.28
4911 5087 9.076596 GCAAGAATAATGAGATTTTGGTTGTAC 57.923 33.333 0.00 0.00 0.00 2.90
4948 5124 1.345089 TGGCATGCCCAAATGATATGC 59.655 47.619 33.44 4.48 41.82 3.14
5074 5250 1.011968 TGCATTTCCGTTCGTCCGAG 61.012 55.000 0.00 0.00 0.00 4.63
5185 5361 2.489329 ACCGAGGATCTGCAAAACATTG 59.511 45.455 0.00 0.00 0.00 2.82
5235 5411 1.657594 CGTTCTGATGCAGTGCTGTAG 59.342 52.381 17.60 11.20 32.61 2.74
5250 5426 2.225491 GCTGTAGTTGCGATTTGGTTGA 59.775 45.455 0.00 0.00 0.00 3.18
5307 5483 8.524870 TCACTTTGTAGATTAAACCGTCTTAC 57.475 34.615 0.00 0.00 0.00 2.34
5317 5493 8.529476 AGATTAAACCGTCTTACTTCTGTACAT 58.471 33.333 0.00 0.00 0.00 2.29
5324 5500 8.136165 ACCGTCTTACTTCTGTACATAATCATC 58.864 37.037 0.00 0.00 0.00 2.92
5416 5592 3.127548 GCAAATGTATGGACTGGACAGTG 59.872 47.826 10.08 0.00 42.66 3.66
5421 5597 4.017126 TGTATGGACTGGACAGTGTAGAG 58.983 47.826 10.08 0.00 42.66 2.43
5438 5614 6.617371 AGTGTAGAGATTTAAGGGTCATCCAT 59.383 38.462 0.00 0.00 38.24 3.41
5495 5680 7.939039 TGAAATCTCACAAACTAGGATCAAACT 59.061 33.333 0.00 0.00 0.00 2.66
5544 5729 1.003355 CAGACAATGCGGACCACCT 60.003 57.895 0.00 0.00 0.00 4.00
5545 5730 1.003355 AGACAATGCGGACCACCTG 60.003 57.895 0.00 0.00 0.00 4.00
5577 5864 3.557595 GTGAGGTATTATGTGTGCTCAGC 59.442 47.826 0.00 0.00 0.00 4.26
5592 5879 2.880890 GCTCAGCGGATTATCATGGTTT 59.119 45.455 0.00 0.00 0.00 3.27
5672 6875 4.331968 ACATATCTTTTGCCTCGGTTTCA 58.668 39.130 0.00 0.00 0.00 2.69
5679 6882 6.754193 TCTTTTGCCTCGGTTTCAAATAAAT 58.246 32.000 0.00 0.00 30.89 1.40
5775 6978 5.987777 TGGTGATTGAAAATTTGTTGCAG 57.012 34.783 0.00 0.00 0.00 4.41
5861 7064 4.319766 CGTCCCAAATCAGTGAAAGACTTG 60.320 45.833 0.00 0.00 29.75 3.16
5966 7169 0.468226 TGGCTTCCACGTCAAACTCT 59.532 50.000 0.00 0.00 0.00 3.24
5976 7179 1.363744 GTCAAACTCTGCAGATCCCG 58.636 55.000 18.63 8.09 0.00 5.14
5977 7180 1.066858 GTCAAACTCTGCAGATCCCGA 60.067 52.381 18.63 9.29 0.00 5.14
5978 7181 1.066858 TCAAACTCTGCAGATCCCGAC 60.067 52.381 18.63 0.00 0.00 4.79
6016 7219 2.650116 GCTTCCTCTGGCTGTCCGA 61.650 63.158 0.00 0.00 34.14 4.55
6171 7374 0.944386 GTGGCTGAAGCAGTTTTCGA 59.056 50.000 4.43 0.00 44.36 3.71
6198 7401 0.249741 ACCTTTGTTCTCGACGTGGG 60.250 55.000 0.00 0.00 0.00 4.61
6203 7406 0.250858 TGTTCTCGACGTGGGGAGTA 60.251 55.000 0.00 0.00 0.00 2.59
6211 7414 2.685100 GACGTGGGGAGTAAAGTTGAG 58.315 52.381 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
159 160 2.655526 GATCGCCCCTTTCCCGTACC 62.656 65.000 0.00 0.00 0.00 3.34
168 169 0.611896 CCAAAACCTGATCGCCCCTT 60.612 55.000 0.00 0.00 0.00 3.95
370 371 6.154203 ACAGATCACATCGAAGACACATAT 57.846 37.500 0.00 0.00 42.51 1.78
379 380 3.867493 GCAGATGAACAGATCACATCGAA 59.133 43.478 0.00 0.00 41.93 3.71
381 382 3.455327 AGCAGATGAACAGATCACATCG 58.545 45.455 0.00 3.52 41.93 3.84
489 490 9.426837 CAATTTGATTGTGTTGGAAATATGAGT 57.573 29.630 0.00 0.00 35.57 3.41
506 507 6.726490 AGCTTCTGCATATCCAATTTGATT 57.274 33.333 0.00 0.00 42.74 2.57
508 509 5.419788 ACAAGCTTCTGCATATCCAATTTGA 59.580 36.000 0.00 0.00 42.74 2.69
512 513 5.419788 TGAAACAAGCTTCTGCATATCCAAT 59.580 36.000 0.00 0.00 42.74 3.16
513 514 4.766373 TGAAACAAGCTTCTGCATATCCAA 59.234 37.500 0.00 0.00 42.74 3.53
514 515 4.334552 TGAAACAAGCTTCTGCATATCCA 58.665 39.130 0.00 0.00 42.74 3.41
515 516 4.970662 TGAAACAAGCTTCTGCATATCC 57.029 40.909 0.00 0.00 42.74 2.59
516 517 6.017275 AGCTATGAAACAAGCTTCTGCATATC 60.017 38.462 0.00 0.00 46.82 1.63
517 518 5.826737 AGCTATGAAACAAGCTTCTGCATAT 59.173 36.000 0.00 0.00 46.82 1.78
518 519 5.188434 AGCTATGAAACAAGCTTCTGCATA 58.812 37.500 0.00 0.75 46.82 3.14
519 520 4.015084 AGCTATGAAACAAGCTTCTGCAT 58.985 39.130 0.00 0.00 46.82 3.96
520 521 3.415212 AGCTATGAAACAAGCTTCTGCA 58.585 40.909 0.00 0.00 46.82 4.41
527 528 4.870363 TGGTGAAAAGCTATGAAACAAGC 58.130 39.130 0.00 0.00 39.08 4.01
528 529 9.079833 CATTATGGTGAAAAGCTATGAAACAAG 57.920 33.333 0.00 0.00 0.00 3.16
529 530 8.801299 TCATTATGGTGAAAAGCTATGAAACAA 58.199 29.630 0.00 0.00 0.00 2.83
530 531 8.347004 TCATTATGGTGAAAAGCTATGAAACA 57.653 30.769 0.00 0.00 0.00 2.83
531 532 9.807649 AATCATTATGGTGAAAAGCTATGAAAC 57.192 29.630 0.00 0.00 0.00 2.78
532 533 9.806203 CAATCATTATGGTGAAAAGCTATGAAA 57.194 29.630 0.00 0.00 0.00 2.69
533 534 9.187996 TCAATCATTATGGTGAAAAGCTATGAA 57.812 29.630 0.00 0.00 0.00 2.57
534 535 8.750515 TCAATCATTATGGTGAAAAGCTATGA 57.249 30.769 0.00 0.00 0.00 2.15
535 536 8.080417 CCTCAATCATTATGGTGAAAAGCTATG 58.920 37.037 0.00 0.00 0.00 2.23
536 537 7.232127 CCCTCAATCATTATGGTGAAAAGCTAT 59.768 37.037 0.00 0.00 0.00 2.97
537 538 6.547141 CCCTCAATCATTATGGTGAAAAGCTA 59.453 38.462 0.00 0.00 0.00 3.32
538 539 5.361857 CCCTCAATCATTATGGTGAAAAGCT 59.638 40.000 0.00 0.00 0.00 3.74
539 540 5.594926 CCCTCAATCATTATGGTGAAAAGC 58.405 41.667 0.00 0.00 0.00 3.51
540 541 5.361857 AGCCCTCAATCATTATGGTGAAAAG 59.638 40.000 0.00 0.00 0.00 2.27
541 542 5.127519 CAGCCCTCAATCATTATGGTGAAAA 59.872 40.000 0.00 0.00 0.00 2.29
542 543 4.646040 CAGCCCTCAATCATTATGGTGAAA 59.354 41.667 0.00 0.00 0.00 2.69
543 544 4.209538 CAGCCCTCAATCATTATGGTGAA 58.790 43.478 0.00 0.00 0.00 3.18
544 545 3.435457 CCAGCCCTCAATCATTATGGTGA 60.435 47.826 0.00 0.00 0.00 4.02
545 546 2.889045 CCAGCCCTCAATCATTATGGTG 59.111 50.000 0.00 0.00 0.00 4.17
546 547 2.785269 TCCAGCCCTCAATCATTATGGT 59.215 45.455 0.00 0.00 0.00 3.55
547 548 3.513909 TCCAGCCCTCAATCATTATGG 57.486 47.619 0.00 0.00 0.00 2.74
548 549 4.722220 TCTTCCAGCCCTCAATCATTATG 58.278 43.478 0.00 0.00 0.00 1.90
549 550 4.202545 CCTCTTCCAGCCCTCAATCATTAT 60.203 45.833 0.00 0.00 0.00 1.28
550 551 3.137176 CCTCTTCCAGCCCTCAATCATTA 59.863 47.826 0.00 0.00 0.00 1.90
551 552 2.091994 CCTCTTCCAGCCCTCAATCATT 60.092 50.000 0.00 0.00 0.00 2.57
552 553 1.493871 CCTCTTCCAGCCCTCAATCAT 59.506 52.381 0.00 0.00 0.00 2.45
553 554 0.914644 CCTCTTCCAGCCCTCAATCA 59.085 55.000 0.00 0.00 0.00 2.57
554 555 0.182299 CCCTCTTCCAGCCCTCAATC 59.818 60.000 0.00 0.00 0.00 2.67
555 556 0.253347 TCCCTCTTCCAGCCCTCAAT 60.253 55.000 0.00 0.00 0.00 2.57
556 557 0.475632 TTCCCTCTTCCAGCCCTCAA 60.476 55.000 0.00 0.00 0.00 3.02
557 558 1.160870 TTCCCTCTTCCAGCCCTCA 59.839 57.895 0.00 0.00 0.00 3.86
558 559 0.912006 AGTTCCCTCTTCCAGCCCTC 60.912 60.000 0.00 0.00 0.00 4.30
559 560 0.476611 AAGTTCCCTCTTCCAGCCCT 60.477 55.000 0.00 0.00 0.00 5.19
560 561 0.322906 CAAGTTCCCTCTTCCAGCCC 60.323 60.000 0.00 0.00 0.00 5.19
561 562 0.693049 TCAAGTTCCCTCTTCCAGCC 59.307 55.000 0.00 0.00 0.00 4.85
562 563 1.625818 TCTCAAGTTCCCTCTTCCAGC 59.374 52.381 0.00 0.00 0.00 4.85
563 564 3.262915 ACATCTCAAGTTCCCTCTTCCAG 59.737 47.826 0.00 0.00 0.00 3.86
564 565 3.008375 CACATCTCAAGTTCCCTCTTCCA 59.992 47.826 0.00 0.00 0.00 3.53
565 566 3.261897 TCACATCTCAAGTTCCCTCTTCC 59.738 47.826 0.00 0.00 0.00 3.46
566 567 4.020662 AGTCACATCTCAAGTTCCCTCTTC 60.021 45.833 0.00 0.00 0.00 2.87
567 568 3.906846 AGTCACATCTCAAGTTCCCTCTT 59.093 43.478 0.00 0.00 0.00 2.85
568 569 3.515562 AGTCACATCTCAAGTTCCCTCT 58.484 45.455 0.00 0.00 0.00 3.69
569 570 3.971245 AGTCACATCTCAAGTTCCCTC 57.029 47.619 0.00 0.00 0.00 4.30
570 571 4.678256 TCTAGTCACATCTCAAGTTCCCT 58.322 43.478 0.00 0.00 0.00 4.20
571 572 5.362430 AGATCTAGTCACATCTCAAGTTCCC 59.638 44.000 0.00 0.00 0.00 3.97
572 573 6.460953 GGAGATCTAGTCACATCTCAAGTTCC 60.461 46.154 16.73 1.28 44.81 3.62
573 574 6.503524 GGAGATCTAGTCACATCTCAAGTTC 58.496 44.000 16.73 1.22 44.81 3.01
574 575 5.067153 CGGAGATCTAGTCACATCTCAAGTT 59.933 44.000 16.73 0.00 44.81 2.66
575 576 4.578516 CGGAGATCTAGTCACATCTCAAGT 59.421 45.833 16.73 0.00 44.81 3.16
576 577 4.023279 CCGGAGATCTAGTCACATCTCAAG 60.023 50.000 16.73 11.46 44.81 3.02
577 578 3.885901 CCGGAGATCTAGTCACATCTCAA 59.114 47.826 16.73 0.00 44.81 3.02
578 579 3.136626 TCCGGAGATCTAGTCACATCTCA 59.863 47.826 16.73 0.00 44.81 3.27
579 580 3.745799 TCCGGAGATCTAGTCACATCTC 58.254 50.000 0.00 9.62 43.04 2.75
580 581 3.866703 TCCGGAGATCTAGTCACATCT 57.133 47.619 0.00 0.00 31.70 2.90
581 582 3.305064 GCTTCCGGAGATCTAGTCACATC 60.305 52.174 3.34 0.00 0.00 3.06
582 583 2.625790 GCTTCCGGAGATCTAGTCACAT 59.374 50.000 3.34 0.00 0.00 3.21
583 584 2.025155 GCTTCCGGAGATCTAGTCACA 58.975 52.381 3.34 0.00 0.00 3.58
584 585 2.025155 TGCTTCCGGAGATCTAGTCAC 58.975 52.381 3.34 0.00 0.00 3.67
585 586 2.437085 TGCTTCCGGAGATCTAGTCA 57.563 50.000 3.34 0.00 0.00 3.41
586 587 3.491792 CCTTTGCTTCCGGAGATCTAGTC 60.492 52.174 3.34 0.00 0.00 2.59
587 588 2.432510 CCTTTGCTTCCGGAGATCTAGT 59.567 50.000 3.34 0.00 0.00 2.57
588 589 2.804933 GCCTTTGCTTCCGGAGATCTAG 60.805 54.545 3.34 0.00 33.53 2.43
589 590 1.139058 GCCTTTGCTTCCGGAGATCTA 59.861 52.381 3.34 0.00 33.53 1.98
590 591 0.107459 GCCTTTGCTTCCGGAGATCT 60.107 55.000 3.34 0.00 33.53 2.75
591 592 2.398803 GCCTTTGCTTCCGGAGATC 58.601 57.895 3.34 0.00 33.53 2.75
592 593 4.645809 GCCTTTGCTTCCGGAGAT 57.354 55.556 3.34 0.00 33.53 2.75
797 806 2.801162 CTCGACGTGCCGTGACTG 60.801 66.667 4.94 0.00 41.37 3.51
896 910 0.321122 GGAGTGTACTGCAAGCTGCT 60.321 55.000 0.00 0.00 45.31 4.24
907 923 3.869473 TTGGTGCGCCGGAGTGTAC 62.869 63.158 12.58 3.20 38.27 2.90
1235 1280 9.703892 CTCCTCAAGGTATACTGAAATTAGATG 57.296 37.037 2.25 0.00 36.34 2.90
1250 1295 2.567169 CACCACATGACTCCTCAAGGTA 59.433 50.000 0.00 0.00 32.08 3.08
1252 1297 1.947678 GCACCACATGACTCCTCAAGG 60.948 57.143 0.00 0.00 0.00 3.61
1253 1298 1.002888 AGCACCACATGACTCCTCAAG 59.997 52.381 0.00 0.00 0.00 3.02
1256 1301 1.137872 CCTAGCACCACATGACTCCTC 59.862 57.143 0.00 0.00 0.00 3.71
1257 1302 1.198713 CCTAGCACCACATGACTCCT 58.801 55.000 0.00 0.00 0.00 3.69
1258 1303 0.905357 ACCTAGCACCACATGACTCC 59.095 55.000 0.00 0.00 0.00 3.85
1259 1304 2.761208 ACTACCTAGCACCACATGACTC 59.239 50.000 0.00 0.00 0.00 3.36
1260 1305 2.497675 CACTACCTAGCACCACATGACT 59.502 50.000 0.00 0.00 0.00 3.41
1281 1349 2.959030 AGTTGAAGGAAAAACAGAGGCC 59.041 45.455 0.00 0.00 0.00 5.19
1467 1545 7.071321 TCAACAATAAGAAAGGGCCCTTAAAAA 59.929 33.333 37.33 22.63 34.84 1.94
1472 1550 3.832490 GTCAACAATAAGAAAGGGCCCTT 59.168 43.478 32.48 32.48 37.98 3.95
1534 1612 9.625747 TTGAATAAGAGTATAACCATTGCATGA 57.374 29.630 0.00 0.00 0.00 3.07
1602 1680 9.190858 GATCTATATGCTACTGACTTGTTTGAG 57.809 37.037 0.00 0.00 0.00 3.02
1884 1982 7.478322 ACACATCTTTTGTCATGCTCAATATC 58.522 34.615 4.51 0.00 36.00 1.63
1979 2078 7.605449 TGGCCTGATTTTCTCATTTAAAGAAG 58.395 34.615 3.32 0.00 34.42 2.85
2104 2203 2.551270 TCAGGTACAGCTCCAGGATTT 58.449 47.619 0.00 0.00 0.00 2.17
2141 2240 4.021981 CGCATACATACCATCCTCTTCAGA 60.022 45.833 0.00 0.00 0.00 3.27
2346 2445 2.365293 GTTTGAAACAGTGGCATTCCCT 59.635 45.455 2.68 0.00 0.00 4.20
2347 2446 2.547855 GGTTTGAAACAGTGGCATTCCC 60.548 50.000 10.53 0.00 0.00 3.97
2348 2447 2.102252 TGGTTTGAAACAGTGGCATTCC 59.898 45.455 10.53 0.00 0.00 3.01
2349 2448 3.451141 TGGTTTGAAACAGTGGCATTC 57.549 42.857 10.53 0.00 0.00 2.67
2350 2449 3.530535 GTTGGTTTGAAACAGTGGCATT 58.469 40.909 10.53 0.00 0.00 3.56
2468 2568 5.882557 CCAGTACTAAAGCCACATTCAATCT 59.117 40.000 0.00 0.00 0.00 2.40
2509 2609 0.591236 CAACCGCAAACTGACCGTTG 60.591 55.000 0.00 0.00 35.61 4.10
2704 2804 8.458843 GCTTTTCATTAGGTATTTCTGTAGCAA 58.541 33.333 0.00 0.00 0.00 3.91
2717 2817 6.715347 ACTTTCTTGTGCTTTTCATTAGGT 57.285 33.333 0.00 0.00 0.00 3.08
2751 2851 0.458197 GCACACAAGCTGCACACAAA 60.458 50.000 1.02 0.00 34.56 2.83
3218 3328 6.119536 TCTAAAATCTGTTCCGTTATGGCAT 58.880 36.000 4.88 4.88 37.80 4.40
3352 3467 5.914898 AGCCCATAAAATAGTTCAACCAC 57.085 39.130 0.00 0.00 0.00 4.16
3384 3547 3.165071 CATGACCTAGGCCAAAAAGGTT 58.835 45.455 17.18 3.56 43.69 3.50
3582 3747 5.321102 ACAACTATGTGGCTACAAAATGGA 58.679 37.500 7.10 0.00 40.84 3.41
3817 3983 8.579850 AAAATAAATACAGATGAGCAAGTCCA 57.420 30.769 0.00 0.00 0.00 4.02
3838 4004 7.817418 TCTTGCTACCTACAGTTTGAAAAAT 57.183 32.000 0.00 0.00 0.00 1.82
4538 4710 4.997395 AGTGTACTTATGAACAGTGGCAAG 59.003 41.667 0.00 0.00 0.00 4.01
4667 4839 3.884693 TGCCAATGTAATGAGCTACATGG 59.115 43.478 0.64 6.17 40.79 3.66
4682 4854 1.450312 GACGGAGGGAGTGCCAATG 60.450 63.158 2.50 0.00 35.15 2.82
4687 4859 2.406002 TTTTGGGACGGAGGGAGTGC 62.406 60.000 0.00 0.00 0.00 4.40
4688 4860 0.328258 ATTTTGGGACGGAGGGAGTG 59.672 55.000 0.00 0.00 0.00 3.51
4689 4861 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
4690 4862 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
4691 4863 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
4692 4864 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
4693 4865 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
4694 4866 3.939066 AGACACTTATTTTGGGACGGAG 58.061 45.455 0.00 0.00 0.00 4.63
4695 4867 4.360951 AAGACACTTATTTTGGGACGGA 57.639 40.909 0.00 0.00 0.00 4.69
4696 4868 5.704053 AGTTAAGACACTTATTTTGGGACGG 59.296 40.000 0.00 0.00 0.00 4.79
4697 4869 6.796705 AGTTAAGACACTTATTTTGGGACG 57.203 37.500 0.00 0.00 0.00 4.79
4698 4870 8.161699 TGAAGTTAAGACACTTATTTTGGGAC 57.838 34.615 0.00 0.00 37.11 4.46
4699 4871 7.996644 ACTGAAGTTAAGACACTTATTTTGGGA 59.003 33.333 0.00 0.00 37.11 4.37
4700 4872 8.166422 ACTGAAGTTAAGACACTTATTTTGGG 57.834 34.615 0.00 0.00 37.11 4.12
4707 4879 9.880157 AAAGTTGTACTGAAGTTAAGACACTTA 57.120 29.630 0.00 0.00 37.11 2.24
4708 4880 8.665685 CAAAGTTGTACTGAAGTTAAGACACTT 58.334 33.333 0.00 0.00 39.84 3.16
4709 4881 7.201617 GCAAAGTTGTACTGAAGTTAAGACACT 60.202 37.037 0.00 0.00 0.00 3.55
4710 4882 6.905609 GCAAAGTTGTACTGAAGTTAAGACAC 59.094 38.462 0.00 0.00 0.00 3.67
4711 4883 6.596106 TGCAAAGTTGTACTGAAGTTAAGACA 59.404 34.615 0.00 0.00 0.00 3.41
4712 4884 6.905609 GTGCAAAGTTGTACTGAAGTTAAGAC 59.094 38.462 5.17 0.00 40.10 3.01
4713 4885 7.011828 GTGCAAAGTTGTACTGAAGTTAAGA 57.988 36.000 5.17 0.00 40.10 2.10
4736 4908 6.821665 TGTCTCAACTTTGCACTAACTTTAGT 59.178 34.615 0.00 0.00 44.42 2.24
4737 4909 7.011482 AGTGTCTCAACTTTGCACTAACTTTAG 59.989 37.037 0.00 0.00 38.46 1.85
4738 4910 6.821665 AGTGTCTCAACTTTGCACTAACTTTA 59.178 34.615 0.00 0.00 38.46 1.85
4739 4911 5.648092 AGTGTCTCAACTTTGCACTAACTTT 59.352 36.000 0.00 0.00 38.46 2.66
4740 4912 5.186198 AGTGTCTCAACTTTGCACTAACTT 58.814 37.500 0.00 0.00 38.46 2.66
4741 4913 4.770795 AGTGTCTCAACTTTGCACTAACT 58.229 39.130 0.00 0.00 38.46 2.24
4742 4914 5.485662 AAGTGTCTCAACTTTGCACTAAC 57.514 39.130 0.00 0.00 37.05 2.34
4743 4915 7.801716 AATAAGTGTCTCAACTTTGCACTAA 57.198 32.000 0.00 0.00 40.77 2.24
4744 4916 7.801716 AAATAAGTGTCTCAACTTTGCACTA 57.198 32.000 0.00 0.00 40.77 2.74
4745 4917 6.699575 AAATAAGTGTCTCAACTTTGCACT 57.300 33.333 0.00 0.00 40.77 4.40
4746 4918 6.972328 TCAAAATAAGTGTCTCAACTTTGCAC 59.028 34.615 0.00 0.00 40.77 4.57
4747 4919 7.066887 TCTCAAAATAAGTGTCTCAACTTTGCA 59.933 33.333 0.00 0.00 40.77 4.08
4748 4920 7.377131 GTCTCAAAATAAGTGTCTCAACTTTGC 59.623 37.037 0.00 0.00 40.77 3.68
4749 4921 7.584123 CGTCTCAAAATAAGTGTCTCAACTTTG 59.416 37.037 0.00 0.00 40.77 2.77
4750 4922 7.254795 CCGTCTCAAAATAAGTGTCTCAACTTT 60.255 37.037 0.00 0.00 40.77 2.66
4751 4923 6.202954 CCGTCTCAAAATAAGTGTCTCAACTT 59.797 38.462 0.00 0.00 42.89 2.66
4752 4924 5.696724 CCGTCTCAAAATAAGTGTCTCAACT 59.303 40.000 0.00 0.00 0.00 3.16
4753 4925 5.694910 TCCGTCTCAAAATAAGTGTCTCAAC 59.305 40.000 0.00 0.00 0.00 3.18
4754 4926 5.849510 TCCGTCTCAAAATAAGTGTCTCAA 58.150 37.500 0.00 0.00 0.00 3.02
4755 4927 5.462530 TCCGTCTCAAAATAAGTGTCTCA 57.537 39.130 0.00 0.00 0.00 3.27
4756 4928 4.865365 CCTCCGTCTCAAAATAAGTGTCTC 59.135 45.833 0.00 0.00 0.00 3.36
4757 4929 4.322801 CCCTCCGTCTCAAAATAAGTGTCT 60.323 45.833 0.00 0.00 0.00 3.41
4758 4930 3.933332 CCCTCCGTCTCAAAATAAGTGTC 59.067 47.826 0.00 0.00 0.00 3.67
4759 4931 3.581332 TCCCTCCGTCTCAAAATAAGTGT 59.419 43.478 0.00 0.00 0.00 3.55
4760 4932 4.184629 CTCCCTCCGTCTCAAAATAAGTG 58.815 47.826 0.00 0.00 0.00 3.16
4761 4933 3.838903 ACTCCCTCCGTCTCAAAATAAGT 59.161 43.478 0.00 0.00 0.00 2.24
4762 4934 4.473477 ACTCCCTCCGTCTCAAAATAAG 57.527 45.455 0.00 0.00 0.00 1.73
4763 4935 5.021458 AGTACTCCCTCCGTCTCAAAATAA 58.979 41.667 0.00 0.00 0.00 1.40
4764 4936 4.607239 AGTACTCCCTCCGTCTCAAAATA 58.393 43.478 0.00 0.00 0.00 1.40
4765 4937 3.442076 AGTACTCCCTCCGTCTCAAAAT 58.558 45.455 0.00 0.00 0.00 1.82
4766 4938 2.885616 AGTACTCCCTCCGTCTCAAAA 58.114 47.619 0.00 0.00 0.00 2.44
4767 4939 2.561419 CAAGTACTCCCTCCGTCTCAAA 59.439 50.000 0.00 0.00 0.00 2.69
4768 4940 2.168496 CAAGTACTCCCTCCGTCTCAA 58.832 52.381 0.00 0.00 0.00 3.02
4769 4941 1.353358 TCAAGTACTCCCTCCGTCTCA 59.647 52.381 0.00 0.00 0.00 3.27
4770 4942 2.125773 TCAAGTACTCCCTCCGTCTC 57.874 55.000 0.00 0.00 0.00 3.36
4771 4943 2.830651 ATCAAGTACTCCCTCCGTCT 57.169 50.000 0.00 0.00 0.00 4.18
4772 4944 3.067883 GGTTATCAAGTACTCCCTCCGTC 59.932 52.174 0.00 0.00 0.00 4.79
4773 4945 3.029570 GGTTATCAAGTACTCCCTCCGT 58.970 50.000 0.00 0.00 0.00 4.69
4774 4946 3.297736 AGGTTATCAAGTACTCCCTCCG 58.702 50.000 0.00 0.00 0.00 4.63
4775 4947 5.456779 ACTAGGTTATCAAGTACTCCCTCC 58.543 45.833 0.00 0.00 0.00 4.30
4776 4948 8.709272 ATTACTAGGTTATCAAGTACTCCCTC 57.291 38.462 0.00 0.00 0.00 4.30
4777 4949 9.145442 GAATTACTAGGTTATCAAGTACTCCCT 57.855 37.037 0.00 0.00 0.00 4.20
4778 4950 8.921205 TGAATTACTAGGTTATCAAGTACTCCC 58.079 37.037 0.00 0.00 0.00 4.30
4829 5001 5.708230 TGTACTGTTGAACCAGTGAGTTTTT 59.292 36.000 9.58 0.00 45.08 1.94
4830 5002 5.250200 TGTACTGTTGAACCAGTGAGTTTT 58.750 37.500 9.58 0.00 45.08 2.43
4843 5015 8.514330 AACCTAGATTGTTTTTGTACTGTTGA 57.486 30.769 0.00 0.00 0.00 3.18
4855 5030 6.959639 TTCAAGCTGAAACCTAGATTGTTT 57.040 33.333 0.00 0.00 41.10 2.83
4895 5071 5.680619 AGTCACTGTACAACCAAAATCTCA 58.319 37.500 0.00 0.00 0.00 3.27
4911 5087 1.574925 CAGCAGCAGCAAGTCACTG 59.425 57.895 3.17 0.00 45.49 3.66
4965 5141 7.105588 TCGCTCGTATACCTGGAATTAGTATA 58.894 38.462 0.00 0.00 0.00 1.47
4966 5142 5.942236 TCGCTCGTATACCTGGAATTAGTAT 59.058 40.000 0.00 0.00 0.00 2.12
4967 5143 5.308014 TCGCTCGTATACCTGGAATTAGTA 58.692 41.667 0.00 0.00 0.00 1.82
5074 5250 4.704965 AGGTTCGTATGGAATTAAGGAGC 58.295 43.478 0.00 0.00 36.92 4.70
5235 5411 2.774439 ACTGTCAACCAAATCGCAAC 57.226 45.000 0.00 0.00 0.00 4.17
5250 5426 7.602644 CCGTATGGCATAACAAGAATATACTGT 59.397 37.037 9.14 0.00 0.00 3.55
5273 5449 1.899814 TCTACAAAGTGAGATGGCCGT 59.100 47.619 0.00 0.00 0.00 5.68
5286 5462 9.199982 CAGAAGTAAGACGGTTTAATCTACAAA 57.800 33.333 0.00 0.00 0.00 2.83
5324 5500 9.334693 GATGAAGTAGCTTTGTACAGAAAAATG 57.665 33.333 0.00 0.00 0.00 2.32
5416 5592 7.509546 TCAATGGATGACCCTTAAATCTCTAC 58.490 38.462 0.00 0.00 35.38 2.59
5438 5614 2.359531 GGACAAATTTGGTGACGGTCAA 59.640 45.455 21.74 0.00 0.00 3.18
5443 5619 1.069500 GTCCGGACAAATTTGGTGACG 60.069 52.381 29.75 17.67 0.00 4.35
5495 5680 1.070105 CAAACGTTCGGACTCCCCA 59.930 57.895 0.00 0.00 34.14 4.96
5544 5729 2.024176 ATACCTCACACACACCTCCA 57.976 50.000 0.00 0.00 0.00 3.86
5545 5730 4.081087 ACATAATACCTCACACACACCTCC 60.081 45.833 0.00 0.00 0.00 4.30
5577 5864 5.592688 ACCAGGTAAAAACCATGATAATCCG 59.407 40.000 0.00 0.00 0.00 4.18
5592 5879 9.118300 TCAGTTAATTAACGAAAACCAGGTAAA 57.882 29.630 19.92 0.00 40.96 2.01
5672 6875 7.334858 ACTGTTGTGTTTGGTCCAATTTATTT 58.665 30.769 4.80 0.00 0.00 1.40
5679 6882 5.394663 CCATTAACTGTTGTGTTTGGTCCAA 60.395 40.000 0.00 0.00 0.00 3.53
5772 6975 0.592754 GATCCTACACGCGTCTCTGC 60.593 60.000 9.86 0.00 0.00 4.26
5775 6978 1.009900 CCGATCCTACACGCGTCTC 60.010 63.158 9.86 0.00 0.00 3.36
5861 7064 2.796651 CAGCAGCCTTCGGATTGC 59.203 61.111 0.00 0.00 35.86 3.56
5894 7097 1.009675 CGTGCTGTGGTGCAAACTC 60.010 57.895 0.00 0.00 45.12 3.01
6107 7310 1.084370 GCGTTGTCATCGGAGAAGGG 61.084 60.000 5.51 0.00 43.58 3.95
6171 7374 3.128068 GTCGAGAACAAAGGTTTGGTGTT 59.872 43.478 7.35 0.00 38.41 3.32
6198 7401 1.359459 CCGGCGCTCAACTTTACTCC 61.359 60.000 7.64 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.