Multiple sequence alignment - TraesCS5A01G305100

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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 TraesCS5A01G305100 chr5A 100.000 3523 0 0 1 3523 514002177 514005699 0.000000e+00 6506.0
1 TraesCS5A01G305100 chr5A 85.320 688 94 6 1775 2457 513869855 513869170 0.000000e+00 704.0
2 TraesCS5A01G305100 chr5A 84.507 142 18 3 718 855 566367118 566366977 1.710000e-28 137.0
3 TraesCS5A01G305100 chr5A 83.673 147 20 4 715 857 640619613 640619759 6.130000e-28 135.0
4 TraesCS5A01G305100 chr5A 92.941 85 6 0 304 388 601705453 601705537 1.330000e-24 124.0
5 TraesCS5A01G305100 chr5D 91.935 1773 126 14 885 2655 408218904 408220661 0.000000e+00 2466.0
6 TraesCS5A01G305100 chr5D 85.735 687 93 4 1775 2457 407988379 407987694 0.000000e+00 721.0
7 TraesCS5A01G305100 chr5D 86.350 652 80 8 2875 3521 61933187 61933834 0.000000e+00 702.0
8 TraesCS5A01G305100 chr5D 89.935 308 24 7 1 306 408217721 408218023 1.190000e-104 390.0
9 TraesCS5A01G305100 chr5D 90.377 239 17 3 2638 2875 408220676 408220909 3.420000e-80 309.0
10 TraesCS5A01G305100 chr5D 93.130 131 7 2 387 517 408218021 408218149 1.290000e-44 191.0
11 TraesCS5A01G305100 chr5B 91.198 1670 116 21 884 2539 489522644 489524296 0.000000e+00 2241.0
12 TraesCS5A01G305100 chr5B 95.023 864 35 4 1775 2638 489575137 489575992 0.000000e+00 1351.0
13 TraesCS5A01G305100 chr5B 89.487 818 64 6 882 1678 489574267 489575083 0.000000e+00 1014.0
14 TraesCS5A01G305100 chr5B 85.153 687 97 4 1775 2457 489313170 489312485 0.000000e+00 699.0
15 TraesCS5A01G305100 chr5B 82.200 691 70 28 2879 3523 209281267 209281950 2.390000e-151 545.0
16 TraesCS5A01G305100 chr5B 92.063 189 11 4 2688 2875 489576228 489576413 2.700000e-66 263.0
17 TraesCS5A01G305100 chr5B 94.286 35 1 1 138 172 683397737 683397704 6.000000e-03 52.8
18 TraesCS5A01G305100 chr2B 87.152 646 72 10 2881 3523 355527278 355526641 0.000000e+00 723.0
19 TraesCS5A01G305100 chr2B 88.095 126 12 3 387 510 134369452 134369328 2.830000e-31 147.0
20 TraesCS5A01G305100 chr2B 88.172 93 11 0 296 388 743188056 743188148 1.030000e-20 111.0
21 TraesCS5A01G305100 chr2D 87.346 648 58 20 2879 3521 202987926 202988554 0.000000e+00 721.0
22 TraesCS5A01G305100 chr2D 89.516 124 12 1 387 510 627516580 627516458 4.710000e-34 156.0
23 TraesCS5A01G305100 chr2D 88.298 94 9 2 296 388 609151971 609152063 1.030000e-20 111.0
24 TraesCS5A01G305100 chr2A 84.074 653 83 16 2880 3521 286815848 286815206 8.360000e-171 610.0
25 TraesCS5A01G305100 chr2A 75.651 653 123 27 2880 3521 407244803 407244176 3.440000e-75 292.0
26 TraesCS5A01G305100 chr2A 84.028 144 19 3 718 857 752008423 752008280 6.130000e-28 135.0
27 TraesCS5A01G305100 chr2A 82.468 154 23 3 709 858 189816462 189816615 7.940000e-27 132.0
28 TraesCS5A01G305100 chr2A 100.000 29 0 0 141 169 546744681 546744709 2.000000e-03 54.7
29 TraesCS5A01G305100 chr4B 83.742 652 75 26 2880 3521 283389022 283389652 3.920000e-164 588.0
30 TraesCS5A01G305100 chr4B 81.040 654 96 23 2879 3521 150488534 150487898 2.440000e-136 496.0
31 TraesCS5A01G305100 chr4B 85.315 143 15 5 712 849 603515154 603515013 3.670000e-30 143.0
32 TraesCS5A01G305100 chr4B 88.000 100 11 1 299 397 641175913 641176012 2.220000e-22 117.0
33 TraesCS5A01G305100 chr3D 81.692 650 84 27 2880 3521 262004274 262003652 3.140000e-140 508.0
34 TraesCS5A01G305100 chr4A 83.943 492 70 7 3038 3523 156223878 156224366 2.480000e-126 462.0
35 TraesCS5A01G305100 chr4D 80.693 606 82 29 2878 3475 193167618 193168196 4.180000e-119 438.0
36 TraesCS5A01G305100 chr7A 74.804 639 129 28 2878 3503 235574397 235575016 3.490000e-65 259.0
37 TraesCS5A01G305100 chr7A 85.915 142 19 1 368 509 136772188 136772328 2.190000e-32 150.0
38 TraesCS5A01G305100 chr7A 87.903 124 14 1 387 510 566034481 566034359 1.020000e-30 145.0
39 TraesCS5A01G305100 chr7A 88.660 97 8 2 304 399 66692201 66692295 7.990000e-22 115.0
40 TraesCS5A01G305100 chr7A 76.113 247 44 14 2140 2377 543596762 543596522 7.990000e-22 115.0
41 TraesCS5A01G305100 chr7B 75.634 513 98 23 2879 3384 209923701 209923209 2.740000e-56 230.0
42 TraesCS5A01G305100 chr6D 89.600 125 12 1 387 511 402325183 402325306 1.310000e-34 158.0
43 TraesCS5A01G305100 chr6A 89.147 129 11 3 387 513 146478964 146478837 1.310000e-34 158.0
44 TraesCS5A01G305100 chr6A 85.417 144 17 3 718 857 78486817 78486674 2.830000e-31 147.0
45 TraesCS5A01G305100 chr1A 85.906 149 17 4 713 857 9542534 9542682 4.710000e-34 156.0
46 TraesCS5A01G305100 chr1A 84.677 124 15 4 2148 2269 551156450 551156329 1.720000e-23 121.0
47 TraesCS5A01G305100 chr3B 85.906 149 14 6 714 858 370941256 370941111 6.090000e-33 152.0
48 TraesCS5A01G305100 chr3B 92.473 93 5 2 300 391 338994418 338994327 7.940000e-27 132.0
49 TraesCS5A01G305100 chr1D 87.786 131 14 2 387 517 313566835 313566707 6.090000e-33 152.0
50 TraesCS5A01G305100 chr1B 87.023 131 15 2 714 842 681030464 681030594 2.830000e-31 147.0
51 TraesCS5A01G305100 chr1B 92.045 88 6 1 303 389 200123207 200123120 4.780000e-24 122.0
52 TraesCS5A01G305100 chr1B 90.323 93 6 3 299 388 612728330 612728422 6.180000e-23 119.0
53 TraesCS5A01G305100 chr3A 87.903 124 14 1 387 510 561134494 561134372 1.020000e-30 145.0
54 TraesCS5A01G305100 chr3A 91.011 89 8 0 304 392 649834830 649834918 1.720000e-23 121.0
55 TraesCS5A01G305100 chr7D 78.333 180 31 8 2131 2307 454379317 454379491 3.720000e-20 110.0


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 TraesCS5A01G305100 chr5A 514002177 514005699 3522 False 6506 6506 100.00000 1 3523 1 chr5A.!!$F1 3522
1 TraesCS5A01G305100 chr5A 513869170 513869855 685 True 704 704 85.32000 1775 2457 1 chr5A.!!$R1 682
2 TraesCS5A01G305100 chr5D 408217721 408220909 3188 False 839 2466 91.34425 1 2875 4 chr5D.!!$F2 2874
3 TraesCS5A01G305100 chr5D 407987694 407988379 685 True 721 721 85.73500 1775 2457 1 chr5D.!!$R1 682
4 TraesCS5A01G305100 chr5D 61933187 61933834 647 False 702 702 86.35000 2875 3521 1 chr5D.!!$F1 646
5 TraesCS5A01G305100 chr5B 489522644 489524296 1652 False 2241 2241 91.19800 884 2539 1 chr5B.!!$F2 1655
6 TraesCS5A01G305100 chr5B 489574267 489576413 2146 False 876 1351 92.19100 882 2875 3 chr5B.!!$F3 1993
7 TraesCS5A01G305100 chr5B 489312485 489313170 685 True 699 699 85.15300 1775 2457 1 chr5B.!!$R1 682
8 TraesCS5A01G305100 chr5B 209281267 209281950 683 False 545 545 82.20000 2879 3523 1 chr5B.!!$F1 644
9 TraesCS5A01G305100 chr2B 355526641 355527278 637 True 723 723 87.15200 2881 3523 1 chr2B.!!$R2 642
10 TraesCS5A01G305100 chr2D 202987926 202988554 628 False 721 721 87.34600 2879 3521 1 chr2D.!!$F1 642
11 TraesCS5A01G305100 chr2A 286815206 286815848 642 True 610 610 84.07400 2880 3521 1 chr2A.!!$R1 641
12 TraesCS5A01G305100 chr2A 407244176 407244803 627 True 292 292 75.65100 2880 3521 1 chr2A.!!$R2 641
13 TraesCS5A01G305100 chr4B 283389022 283389652 630 False 588 588 83.74200 2880 3521 1 chr4B.!!$F1 641
14 TraesCS5A01G305100 chr4B 150487898 150488534 636 True 496 496 81.04000 2879 3521 1 chr4B.!!$R1 642
15 TraesCS5A01G305100 chr3D 262003652 262004274 622 True 508 508 81.69200 2880 3521 1 chr3D.!!$R1 641
16 TraesCS5A01G305100 chr4D 193167618 193168196 578 False 438 438 80.69300 2878 3475 1 chr4D.!!$F1 597
17 TraesCS5A01G305100 chr7A 235574397 235575016 619 False 259 259 74.80400 2878 3503 1 chr7A.!!$F3 625

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
29 30 2.816087 CTCCCTCCATTTCATAATGCGG 59.184 50.000 0.0 0.0 39.87 5.69 F
1620 2115 1.004918 GGTGAGACAGTTCGTGGGG 60.005 63.158 0.0 0.0 0.00 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1641 2136 0.388649 CGTGGAAGGAGTTGACGAGG 60.389 60.0 0.0 0.0 31.71 4.63 R
2661 3208 0.164002 GTTTCTCCACGCTTCGCTTC 59.836 55.0 0.0 0.0 0.00 3.86 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
29 30 2.816087 CTCCCTCCATTTCATAATGCGG 59.184 50.000 0.00 0.00 39.87 5.69
35 36 3.761218 TCCATTTCATAATGCGGTTGTGT 59.239 39.130 0.00 0.00 39.87 3.72
48 49 4.397730 TGCGGTTGTGTTGCATATAGATTT 59.602 37.500 0.00 0.00 32.86 2.17
49 50 5.586643 TGCGGTTGTGTTGCATATAGATTTA 59.413 36.000 0.00 0.00 32.86 1.40
50 51 6.262049 TGCGGTTGTGTTGCATATAGATTTAT 59.738 34.615 0.00 0.00 32.86 1.40
91 92 6.975197 TGTAAGCTTTGATCGAGTTCATAGAG 59.025 38.462 3.20 2.04 29.29 2.43
106 107 9.174166 GAGTTCATAGAGAAAACTACTCTCTCT 57.826 37.037 5.66 6.14 45.24 3.10
120 121 8.958119 ACTACTCTCTCTGTCTTCTAATGTAG 57.042 38.462 0.00 0.00 0.00 2.74
121 122 8.545472 ACTACTCTCTCTGTCTTCTAATGTAGT 58.455 37.037 0.00 0.00 33.35 2.73
124 125 9.337396 ACTCTCTCTGTCTTCTAATGTAGTATG 57.663 37.037 0.00 0.00 0.00 2.39
200 201 4.838904 AGTAATGTACTCCCTTTGGTCC 57.161 45.455 0.00 0.00 32.47 4.46
201 202 3.522343 AGTAATGTACTCCCTTTGGTCCC 59.478 47.826 0.00 0.00 32.47 4.46
211 212 3.464080 TCCCTTTGGTCCCTTTTACTTCA 59.536 43.478 0.00 0.00 0.00 3.02
230 231 5.583061 ACTTCACGTGTTAGATTTGTGTCAA 59.417 36.000 16.51 0.00 32.55 3.18
233 234 5.583061 TCACGTGTTAGATTTGTGTCAAGTT 59.417 36.000 16.51 0.00 32.55 2.66
319 320 8.579682 GTTGTAAACTACTTCCTTCGTTCTAA 57.420 34.615 0.00 0.00 45.32 2.10
320 321 9.034544 GTTGTAAACTACTTCCTTCGTTCTAAA 57.965 33.333 0.00 0.00 45.32 1.85
321 322 9.598517 TTGTAAACTACTTCCTTCGTTCTAAAA 57.401 29.630 0.00 0.00 0.00 1.52
322 323 9.768662 TGTAAACTACTTCCTTCGTTCTAAAAT 57.231 29.630 0.00 0.00 0.00 1.82
327 328 9.804758 ACTACTTCCTTCGTTCTAAAATAGATG 57.195 33.333 0.00 0.00 34.22 2.90
329 330 8.705048 ACTTCCTTCGTTCTAAAATAGATGAC 57.295 34.615 0.00 0.00 34.22 3.06
330 331 8.532819 ACTTCCTTCGTTCTAAAATAGATGACT 58.467 33.333 0.00 0.00 34.22 3.41
331 332 8.928270 TTCCTTCGTTCTAAAATAGATGACTC 57.072 34.615 0.00 0.00 34.22 3.36
332 333 8.063200 TCCTTCGTTCTAAAATAGATGACTCA 57.937 34.615 0.00 0.00 34.22 3.41
333 334 8.528643 TCCTTCGTTCTAAAATAGATGACTCAA 58.471 33.333 0.00 0.00 34.22 3.02
334 335 8.596380 CCTTCGTTCTAAAATAGATGACTCAAC 58.404 37.037 0.00 0.00 34.22 3.18
335 336 9.360093 CTTCGTTCTAAAATAGATGACTCAACT 57.640 33.333 0.00 0.00 34.22 3.16
336 337 9.706691 TTCGTTCTAAAATAGATGACTCAACTT 57.293 29.630 0.00 0.00 34.22 2.66
337 338 9.706691 TCGTTCTAAAATAGATGACTCAACTTT 57.293 29.630 0.00 0.00 34.22 2.66
375 376 7.921786 ACAAAATTGAGTCATCTATTTCGGA 57.078 32.000 0.00 0.00 39.11 4.55
376 377 8.335532 ACAAAATTGAGTCATCTATTTCGGAA 57.664 30.769 0.00 0.00 39.11 4.30
377 378 8.237267 ACAAAATTGAGTCATCTATTTCGGAAC 58.763 33.333 0.00 0.00 39.11 3.62
378 379 7.005062 AAATTGAGTCATCTATTTCGGAACG 57.995 36.000 0.00 0.00 40.60 3.95
379 380 6.037172 AAATTGAGTCATCTATTTCGGAACGG 59.963 38.462 0.00 0.00 40.08 4.44
380 381 8.061237 AAATTGAGTCATCTATTTCGGAACGGA 61.061 37.037 0.00 0.00 40.08 4.69
521 522 9.842775 ATGCAGACTATAAAGATCATGAAAAGA 57.157 29.630 0.00 0.00 0.00 2.52
522 523 9.842775 TGCAGACTATAAAGATCATGAAAAGAT 57.157 29.630 0.00 0.00 0.00 2.40
549 550 8.807667 ATTTGACTTTGTAAGCTTTGATCAAG 57.192 30.769 3.20 4.57 35.29 3.02
550 551 6.942532 TGACTTTGTAAGCTTTGATCAAGT 57.057 33.333 3.20 6.59 34.56 3.16
551 552 7.333528 TGACTTTGTAAGCTTTGATCAAGTT 57.666 32.000 3.20 6.62 34.56 2.66
552 553 7.417612 TGACTTTGTAAGCTTTGATCAAGTTC 58.582 34.615 3.20 2.24 34.56 3.01
553 554 7.066887 TGACTTTGTAAGCTTTGATCAAGTTCA 59.933 33.333 3.20 8.85 34.56 3.18
554 555 7.945134 ACTTTGTAAGCTTTGATCAAGTTCAT 58.055 30.769 3.20 0.00 34.56 2.57
555 556 9.066892 ACTTTGTAAGCTTTGATCAAGTTCATA 57.933 29.630 3.20 0.00 34.56 2.15
556 557 9.552114 CTTTGTAAGCTTTGATCAAGTTCATAG 57.448 33.333 3.20 3.30 34.56 2.23
557 558 8.846943 TTGTAAGCTTTGATCAAGTTCATAGA 57.153 30.769 3.20 0.00 34.56 1.98
558 559 8.484641 TGTAAGCTTTGATCAAGTTCATAGAG 57.515 34.615 3.20 1.83 34.56 2.43
559 560 8.314021 TGTAAGCTTTGATCAAGTTCATAGAGA 58.686 33.333 3.20 0.00 34.56 3.10
560 561 9.155975 GTAAGCTTTGATCAAGTTCATAGAGAA 57.844 33.333 3.20 0.00 34.56 2.87
561 562 8.627208 AAGCTTTGATCAAGTTCATAGAGAAA 57.373 30.769 8.41 0.00 38.13 2.52
562 563 8.627208 AGCTTTGATCAAGTTCATAGAGAAAA 57.373 30.769 8.41 0.00 38.13 2.29
563 564 8.510505 AGCTTTGATCAAGTTCATAGAGAAAAC 58.489 33.333 8.41 0.00 38.13 2.43
564 565 8.510505 GCTTTGATCAAGTTCATAGAGAAAACT 58.489 33.333 8.41 0.00 38.13 2.66
571 572 9.832445 TCAAGTTCATAGAGAAAACTACTTTGT 57.168 29.630 0.00 0.00 38.13 2.83
574 575 9.057089 AGTTCATAGAGAAAACTACTTTGTTGG 57.943 33.333 0.00 0.00 38.13 3.77
575 576 8.837389 GTTCATAGAGAAAACTACTTTGTTGGT 58.163 33.333 0.00 0.00 38.13 3.67
576 577 8.603242 TCATAGAGAAAACTACTTTGTTGGTC 57.397 34.615 0.00 0.00 0.00 4.02
577 578 8.429641 TCATAGAGAAAACTACTTTGTTGGTCT 58.570 33.333 0.00 0.00 31.77 3.85
578 579 9.057089 CATAGAGAAAACTACTTTGTTGGTCTT 57.943 33.333 0.00 0.00 30.29 3.01
579 580 7.939784 AGAGAAAACTACTTTGTTGGTCTTT 57.060 32.000 0.00 0.00 30.29 2.52
580 581 8.349568 AGAGAAAACTACTTTGTTGGTCTTTT 57.650 30.769 0.00 0.00 30.29 2.27
581 582 9.457436 AGAGAAAACTACTTTGTTGGTCTTTTA 57.543 29.630 0.00 0.00 30.29 1.52
614 615 7.519032 TTTTTGATACCTCGGAAAACATCTT 57.481 32.000 0.00 0.00 0.00 2.40
615 616 8.624367 TTTTTGATACCTCGGAAAACATCTTA 57.376 30.769 0.00 0.00 0.00 2.10
616 617 8.624367 TTTTGATACCTCGGAAAACATCTTAA 57.376 30.769 0.00 0.00 0.00 1.85
617 618 7.843490 TTGATACCTCGGAAAACATCTTAAG 57.157 36.000 0.00 0.00 0.00 1.85
618 619 7.177832 TGATACCTCGGAAAACATCTTAAGA 57.822 36.000 7.82 7.82 0.00 2.10
619 620 7.039882 TGATACCTCGGAAAACATCTTAAGAC 58.960 38.462 7.48 0.00 0.00 3.01
620 621 4.243270 ACCTCGGAAAACATCTTAAGACG 58.757 43.478 7.48 1.23 0.00 4.18
621 622 3.617263 CCTCGGAAAACATCTTAAGACGG 59.383 47.826 7.48 5.88 0.00 4.79
622 623 4.491676 CTCGGAAAACATCTTAAGACGGA 58.508 43.478 7.48 3.31 0.00 4.69
623 624 5.080969 TCGGAAAACATCTTAAGACGGAT 57.919 39.130 7.48 0.00 0.00 4.18
624 625 4.868171 TCGGAAAACATCTTAAGACGGATG 59.132 41.667 7.48 4.77 43.30 3.51
625 626 4.034048 CGGAAAACATCTTAAGACGGATGG 59.966 45.833 7.48 0.00 42.34 3.51
626 627 5.183228 GGAAAACATCTTAAGACGGATGGA 58.817 41.667 7.48 0.00 42.34 3.41
627 628 5.294552 GGAAAACATCTTAAGACGGATGGAG 59.705 44.000 7.48 0.00 42.34 3.86
628 629 5.422214 AAACATCTTAAGACGGATGGAGT 57.578 39.130 7.48 0.00 42.34 3.85
631 632 6.732896 ACATCTTAAGACGGATGGAGTATT 57.267 37.500 7.48 0.00 42.34 1.89
632 633 7.125792 ACATCTTAAGACGGATGGAGTATTT 57.874 36.000 7.48 0.00 42.34 1.40
634 635 8.871125 ACATCTTAAGACGGATGGAGTATTTAT 58.129 33.333 7.48 0.00 42.34 1.40
637 638 9.803507 TCTTAAGACGGATGGAGTATTTATAGA 57.196 33.333 0.00 0.00 0.00 1.98
639 640 9.584008 TTAAGACGGATGGAGTATTTATAGAGT 57.416 33.333 0.00 0.00 0.00 3.24
640 641 8.480133 AAGACGGATGGAGTATTTATAGAGTT 57.520 34.615 0.00 0.00 0.00 3.01
642 643 9.756571 AGACGGATGGAGTATTTATAGAGTTAT 57.243 33.333 0.00 0.00 0.00 1.89
657 658 4.304537 GAGTTATGTACTCCCTCCGTTC 57.695 50.000 0.00 0.00 46.30 3.95
658 659 3.952967 GAGTTATGTACTCCCTCCGTTCT 59.047 47.826 0.00 0.00 46.30 3.01
659 660 4.351127 AGTTATGTACTCCCTCCGTTCTT 58.649 43.478 0.00 0.00 28.23 2.52
660 661 4.776308 AGTTATGTACTCCCTCCGTTCTTT 59.224 41.667 0.00 0.00 28.23 2.52
661 662 5.247792 AGTTATGTACTCCCTCCGTTCTTTT 59.752 40.000 0.00 0.00 28.23 2.27
662 663 4.635699 ATGTACTCCCTCCGTTCTTTTT 57.364 40.909 0.00 0.00 0.00 1.94
689 690 5.720202 ACTCTGCGTATTAGATTTGTGTCA 58.280 37.500 0.00 0.00 0.00 3.58
690 691 6.341316 ACTCTGCGTATTAGATTTGTGTCAT 58.659 36.000 0.00 0.00 0.00 3.06
691 692 6.256539 ACTCTGCGTATTAGATTTGTGTCATG 59.743 38.462 0.00 0.00 0.00 3.07
692 693 6.106003 TCTGCGTATTAGATTTGTGTCATGT 58.894 36.000 0.00 0.00 0.00 3.21
694 695 7.762159 TCTGCGTATTAGATTTGTGTCATGTTA 59.238 33.333 0.00 0.00 0.00 2.41
695 696 8.257830 TGCGTATTAGATTTGTGTCATGTTAA 57.742 30.769 0.00 0.00 0.00 2.01
696 697 8.722394 TGCGTATTAGATTTGTGTCATGTTAAA 58.278 29.630 0.00 0.00 0.00 1.52
697 698 8.995906 GCGTATTAGATTTGTGTCATGTTAAAC 58.004 33.333 0.00 0.00 0.00 2.01
702 703 7.698836 AGATTTGTGTCATGTTAAACTTTGC 57.301 32.000 0.00 0.00 0.00 3.68
703 704 7.264221 AGATTTGTGTCATGTTAAACTTTGCA 58.736 30.769 0.00 0.00 0.00 4.08
704 705 7.763528 AGATTTGTGTCATGTTAAACTTTGCAA 59.236 29.630 0.00 0.00 0.00 4.08
705 706 7.658179 TTTGTGTCATGTTAAACTTTGCAAA 57.342 28.000 12.14 12.14 0.00 3.68
706 707 6.884096 TGTGTCATGTTAAACTTTGCAAAG 57.116 33.333 32.53 32.53 41.73 2.77
833 834 7.972832 ATTTCGGACAAAACTTATGTACAGA 57.027 32.000 0.33 0.00 30.67 3.41
834 835 6.774354 TTCGGACAAAACTTATGTACAGAC 57.226 37.500 0.33 0.00 30.67 3.51
836 837 7.218228 TCGGACAAAACTTATGTACAGACTA 57.782 36.000 0.33 0.00 30.67 2.59
837 838 7.660112 TCGGACAAAACTTATGTACAGACTAA 58.340 34.615 0.33 0.00 30.67 2.24
838 839 8.143193 TCGGACAAAACTTATGTACAGACTAAA 58.857 33.333 0.33 0.00 30.67 1.85
839 840 8.767085 CGGACAAAACTTATGTACAGACTAAAA 58.233 33.333 0.33 0.00 30.67 1.52
907 1376 4.009675 TCATCGGCCATTCTATAAATGCC 58.990 43.478 2.24 0.00 0.00 4.40
920 1389 7.643569 TCTATAAATGCCACATTTCACATGT 57.356 32.000 8.72 0.00 0.00 3.21
928 1397 4.637534 GCCACATTTCACATGTCATCTAGT 59.362 41.667 0.00 0.00 0.00 2.57
1570 2058 1.953017 CCGTCGTTCATGGCCAAAA 59.047 52.632 10.96 4.32 0.00 2.44
1620 2115 1.004918 GGTGAGACAGTTCGTGGGG 60.005 63.158 0.00 0.00 0.00 4.96
1673 2168 4.994471 CCACGAGCTGCAGCCACA 62.994 66.667 34.39 0.00 43.38 4.17
1678 2173 2.348998 AGCTGCAGCCACAGGTAC 59.651 61.111 34.39 4.46 46.10 3.34
1680 2175 3.121030 CTGCAGCCACAGGTACGC 61.121 66.667 0.00 0.00 33.85 4.42
1682 2177 3.423154 GCAGCCACAGGTACGCAC 61.423 66.667 0.00 0.00 0.00 5.34
1683 2178 2.030412 CAGCCACAGGTACGCACA 59.970 61.111 0.00 0.00 0.00 4.57
1684 2179 2.030562 AGCCACAGGTACGCACAC 59.969 61.111 0.00 0.00 0.00 3.82
1685 2180 2.280524 GCCACAGGTACGCACACA 60.281 61.111 0.00 0.00 0.00 3.72
1686 2181 1.890041 GCCACAGGTACGCACACAA 60.890 57.895 0.00 0.00 0.00 3.33
1687 2182 1.841663 GCCACAGGTACGCACACAAG 61.842 60.000 0.00 0.00 0.00 3.16
1688 2183 1.569493 CACAGGTACGCACACAAGC 59.431 57.895 0.00 0.00 0.00 4.01
1689 2184 0.880278 CACAGGTACGCACACAAGCT 60.880 55.000 0.00 0.00 0.00 3.74
1690 2185 0.600255 ACAGGTACGCACACAAGCTC 60.600 55.000 0.00 0.00 0.00 4.09
1691 2186 1.372997 AGGTACGCACACAAGCTCG 60.373 57.895 0.00 0.00 0.00 5.03
1694 2206 1.728074 TACGCACACAAGCTCGTCG 60.728 57.895 0.00 0.00 36.50 5.12
1705 2217 1.210413 GCTCGTCGCTCTCACTCAA 59.790 57.895 0.00 0.00 35.14 3.02
1707 2219 1.543614 CTCGTCGCTCTCACTCAATG 58.456 55.000 0.00 0.00 0.00 2.82
1710 2222 1.667177 CGTCGCTCTCACTCAATGTGT 60.667 52.381 0.00 0.00 46.27 3.72
1711 2223 1.989165 GTCGCTCTCACTCAATGTGTC 59.011 52.381 0.00 0.00 46.27 3.67
1712 2224 1.613437 TCGCTCTCACTCAATGTGTCA 59.387 47.619 0.00 0.00 46.27 3.58
1715 2227 2.992543 GCTCTCACTCAATGTGTCACTC 59.007 50.000 4.27 0.00 46.27 3.51
1717 2229 4.236147 CTCTCACTCAATGTGTCACTCTG 58.764 47.826 4.27 1.79 46.27 3.35
1718 2230 3.638627 TCTCACTCAATGTGTCACTCTGT 59.361 43.478 4.27 0.00 46.27 3.41
1719 2231 4.100035 TCTCACTCAATGTGTCACTCTGTT 59.900 41.667 4.27 0.00 46.27 3.16
1720 2232 4.371786 TCACTCAATGTGTCACTCTGTTC 58.628 43.478 4.27 0.00 46.27 3.18
1723 2235 4.141846 ACTCAATGTGTCACTCTGTTCACT 60.142 41.667 4.27 0.00 0.00 3.41
1725 2237 2.492019 TGTGTCACTCTGTTCACTCG 57.508 50.000 4.27 0.00 0.00 4.18
1726 2238 1.132588 GTGTCACTCTGTTCACTCGC 58.867 55.000 0.00 0.00 0.00 5.03
1727 2239 1.032794 TGTCACTCTGTTCACTCGCT 58.967 50.000 0.00 0.00 0.00 4.93
1728 2240 2.031069 GTGTCACTCTGTTCACTCGCTA 60.031 50.000 0.00 0.00 0.00 4.26
1729 2241 2.820197 TGTCACTCTGTTCACTCGCTAT 59.180 45.455 0.00 0.00 0.00 2.97
1730 2242 4.007659 TGTCACTCTGTTCACTCGCTATA 58.992 43.478 0.00 0.00 0.00 1.31
1732 2244 4.333095 GTCACTCTGTTCACTCGCTATAGA 59.667 45.833 3.21 0.00 0.00 1.98
1738 2250 0.661552 TCACTCGCTATAGACGGCAC 59.338 55.000 3.21 0.00 0.00 5.01
1740 2252 1.871676 CACTCGCTATAGACGGCACTA 59.128 52.381 3.21 0.00 0.00 2.74
1741 2253 2.096169 CACTCGCTATAGACGGCACTAG 60.096 54.545 3.21 2.94 0.00 2.57
1742 2254 1.465387 CTCGCTATAGACGGCACTAGG 59.535 57.143 3.21 0.00 0.00 3.02
1744 2256 2.037641 TCGCTATAGACGGCACTAGGTA 59.962 50.000 3.21 0.00 0.00 3.08
1745 2257 2.159234 CGCTATAGACGGCACTAGGTAC 59.841 54.545 3.21 0.00 0.00 3.34
1746 2258 3.410508 GCTATAGACGGCACTAGGTACT 58.589 50.000 3.21 0.00 46.37 2.73
1747 2259 3.188873 GCTATAGACGGCACTAGGTACTG 59.811 52.174 3.21 0.00 41.52 2.74
1748 2260 3.572632 ATAGACGGCACTAGGTACTGA 57.427 47.619 0.00 0.00 41.52 3.41
1749 2261 2.211250 AGACGGCACTAGGTACTGAA 57.789 50.000 0.00 0.00 41.52 3.02
1750 2262 2.522185 AGACGGCACTAGGTACTGAAA 58.478 47.619 0.00 0.00 41.52 2.69
1751 2263 2.230750 AGACGGCACTAGGTACTGAAAC 59.769 50.000 0.00 0.00 41.52 2.78
1752 2264 1.965643 ACGGCACTAGGTACTGAAACA 59.034 47.619 0.00 0.00 41.52 2.83
1753 2265 2.288640 ACGGCACTAGGTACTGAAACAC 60.289 50.000 0.00 0.00 41.52 3.32
1754 2266 2.029290 CGGCACTAGGTACTGAAACACT 60.029 50.000 0.00 0.00 41.52 3.55
1755 2267 3.192001 CGGCACTAGGTACTGAAACACTA 59.808 47.826 0.00 0.00 41.52 2.74
1756 2268 4.492611 GGCACTAGGTACTGAAACACTAC 58.507 47.826 0.00 0.00 41.52 2.73
1757 2269 4.220163 GGCACTAGGTACTGAAACACTACT 59.780 45.833 0.00 0.00 41.52 2.57
1758 2270 5.416952 GGCACTAGGTACTGAAACACTACTA 59.583 44.000 0.00 0.00 41.52 1.82
1759 2271 6.096564 GGCACTAGGTACTGAAACACTACTAT 59.903 42.308 0.00 0.00 41.52 2.12
1760 2272 7.363617 GGCACTAGGTACTGAAACACTACTATT 60.364 40.741 0.00 0.00 41.52 1.73
1761 2273 7.488471 GCACTAGGTACTGAAACACTACTATTG 59.512 40.741 0.00 0.00 41.52 1.90
1762 2274 8.521176 CACTAGGTACTGAAACACTACTATTGT 58.479 37.037 0.00 0.00 41.52 2.71
1763 2275 8.738106 ACTAGGTACTGAAACACTACTATTGTC 58.262 37.037 0.00 0.00 41.52 3.18
1764 2276 7.534723 AGGTACTGAAACACTACTATTGTCA 57.465 36.000 0.00 0.00 37.18 3.58
1765 2277 7.959175 AGGTACTGAAACACTACTATTGTCAA 58.041 34.615 0.00 0.00 37.18 3.18
1766 2278 8.426489 AGGTACTGAAACACTACTATTGTCAAA 58.574 33.333 0.00 0.00 37.18 2.69
1767 2279 9.048446 GGTACTGAAACACTACTATTGTCAAAA 57.952 33.333 0.00 0.00 0.00 2.44
1772 2284 9.743057 TGAAACACTACTATTGTCAAAATTTGG 57.257 29.630 5.83 0.00 0.00 3.28
1886 2398 1.885163 CGTCCTACGGCTTCCACCTT 61.885 60.000 0.00 0.00 38.08 3.50
1898 2410 3.041940 CACCTTCACACGCCGACC 61.042 66.667 0.00 0.00 0.00 4.79
2029 2541 1.067250 GCCTTTTCAACAGCGGCAA 59.933 52.632 1.45 0.00 40.41 4.52
2561 3076 1.429463 GAAAATCTGCTGTCCGTCGT 58.571 50.000 0.00 0.00 0.00 4.34
2576 3091 1.460267 CGTCGTTTTGATGTCTCGTGC 60.460 52.381 0.00 0.00 0.00 5.34
2601 3116 2.327081 TTCTCTGACAAGTACGCGTC 57.673 50.000 18.63 7.94 0.00 5.19
2650 3197 7.176690 TGAATTTCTCTGAATAAAACCCAGTCC 59.823 37.037 0.00 0.00 0.00 3.85
2657 3204 4.140900 TGAATAAAACCCAGTCCCCTTGAA 60.141 41.667 0.00 0.00 0.00 2.69
2661 3208 0.405585 ACCCAGTCCCCTTGAATGTG 59.594 55.000 0.00 0.00 37.36 3.21
2662 3209 0.698238 CCCAGTCCCCTTGAATGTGA 59.302 55.000 0.00 0.00 37.36 3.58
2668 3215 1.073125 TCCCCTTGAATGTGAAGCGAA 59.927 47.619 0.00 0.00 0.00 4.70
2764 3498 2.036862 ACGGTTTAGTCACACTTCCCTC 59.963 50.000 0.00 0.00 0.00 4.30
2919 3654 0.677288 GGTAAAACCCCACTGCAACC 59.323 55.000 0.00 0.00 30.04 3.77
2934 3671 7.277760 CCCACTGCAACCTTTATTAAATAAAGC 59.722 37.037 0.00 0.00 46.49 3.51
2994 3737 7.841222 AGATAAGCCCCAAGAAATACAAAGAAT 59.159 33.333 0.00 0.00 0.00 2.40
3118 3937 2.552743 GGACTCCAACCAAGCAGTAAAC 59.447 50.000 0.00 0.00 0.00 2.01
3183 4002 4.716794 AGCTCCTCCATGAAGATGAATTC 58.283 43.478 0.00 0.00 0.00 2.17
3194 4013 3.010200 AGATGAATTCCCAGCCTTGAC 57.990 47.619 2.27 0.00 0.00 3.18
3200 4019 0.478072 TTCCCAGCCTTGACATGTGT 59.522 50.000 1.15 0.00 0.00 3.72
3245 4064 8.821686 TTTATTGTTTCTGGATATCCACATGT 57.178 30.769 20.98 10.87 42.01 3.21
3246 4065 8.821686 TTATTGTTTCTGGATATCCACATGTT 57.178 30.769 20.98 7.81 42.01 2.71
3386 4206 3.453353 AGCATTGAATAGCAAAAGGGCAT 59.547 39.130 0.00 0.00 40.48 4.40
3446 4266 4.679373 ATCCCTCACTGCACAGTTATAG 57.321 45.455 0.00 0.00 40.20 1.31
3513 4333 7.862873 TGTTTACTCTATCATGTAAGAGCATCG 59.137 37.037 20.12 5.03 42.50 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.925913 GCAACACAACCGCATTATGAAAT 59.074 39.130 0.00 0.00 0.00 2.17
55 56 7.803189 TCGATCAAAGCTTACAAAGTTTGATTC 59.197 33.333 22.23 7.94 42.43 2.52
91 92 9.567848 CATTAGAAGACAGAGAGAGTAGTTTTC 57.432 37.037 0.00 0.00 0.00 2.29
189 190 3.464080 TGAAGTAAAAGGGACCAAAGGGA 59.536 43.478 0.00 0.00 38.05 4.20
195 196 2.171027 ACACGTGAAGTAAAAGGGACCA 59.829 45.455 25.01 0.00 0.00 4.02
200 201 7.586300 CACAAATCTAACACGTGAAGTAAAAGG 59.414 37.037 25.01 6.95 0.00 3.11
201 202 8.120465 ACACAAATCTAACACGTGAAGTAAAAG 58.880 33.333 25.01 8.71 0.00 2.27
211 212 7.542534 TTAACTTGACACAAATCTAACACGT 57.457 32.000 0.00 0.00 0.00 4.49
295 296 9.598517 TTTTAGAACGAAGGAAGTAGTTTACAA 57.401 29.630 0.00 0.00 0.00 2.41
303 304 9.798994 GTCATCTATTTTAGAACGAAGGAAGTA 57.201 33.333 0.00 0.00 38.50 2.24
304 305 8.532819 AGTCATCTATTTTAGAACGAAGGAAGT 58.467 33.333 0.00 0.00 38.50 3.01
305 306 8.934507 AGTCATCTATTTTAGAACGAAGGAAG 57.065 34.615 0.00 0.00 38.50 3.46
306 307 8.528643 TGAGTCATCTATTTTAGAACGAAGGAA 58.471 33.333 0.00 0.00 38.50 3.36
307 308 8.063200 TGAGTCATCTATTTTAGAACGAAGGA 57.937 34.615 0.00 0.00 38.50 3.36
308 309 8.596380 GTTGAGTCATCTATTTTAGAACGAAGG 58.404 37.037 0.00 0.00 38.50 3.46
309 310 9.360093 AGTTGAGTCATCTATTTTAGAACGAAG 57.640 33.333 1.70 0.00 38.50 3.79
310 311 9.706691 AAGTTGAGTCATCTATTTTAGAACGAA 57.293 29.630 4.14 0.00 38.50 3.85
311 312 9.706691 AAAGTTGAGTCATCTATTTTAGAACGA 57.293 29.630 4.14 0.00 38.50 3.85
349 350 9.613428 TCCGAAATAGATGACTCAATTTTGTAT 57.387 29.630 0.00 0.00 0.00 2.29
350 351 9.443323 TTCCGAAATAGATGACTCAATTTTGTA 57.557 29.630 0.00 0.00 0.00 2.41
351 352 7.921786 TCCGAAATAGATGACTCAATTTTGT 57.078 32.000 0.00 0.00 0.00 2.83
352 353 7.426456 CGTTCCGAAATAGATGACTCAATTTTG 59.574 37.037 0.00 0.00 0.00 2.44
353 354 7.414098 CCGTTCCGAAATAGATGACTCAATTTT 60.414 37.037 0.00 0.00 0.00 1.82
354 355 6.037172 CCGTTCCGAAATAGATGACTCAATTT 59.963 38.462 0.00 0.00 0.00 1.82
355 356 5.523916 CCGTTCCGAAATAGATGACTCAATT 59.476 40.000 0.00 0.00 0.00 2.32
356 357 5.050490 CCGTTCCGAAATAGATGACTCAAT 58.950 41.667 0.00 0.00 0.00 2.57
357 358 4.158949 TCCGTTCCGAAATAGATGACTCAA 59.841 41.667 0.00 0.00 0.00 3.02
358 359 3.697542 TCCGTTCCGAAATAGATGACTCA 59.302 43.478 0.00 0.00 0.00 3.41
359 360 4.291783 CTCCGTTCCGAAATAGATGACTC 58.708 47.826 0.00 0.00 0.00 3.36
360 361 3.068307 CCTCCGTTCCGAAATAGATGACT 59.932 47.826 0.00 0.00 0.00 3.41
361 362 3.381949 CCTCCGTTCCGAAATAGATGAC 58.618 50.000 0.00 0.00 0.00 3.06
362 363 2.364324 CCCTCCGTTCCGAAATAGATGA 59.636 50.000 0.00 0.00 0.00 2.92
363 364 2.364324 TCCCTCCGTTCCGAAATAGATG 59.636 50.000 0.00 0.00 0.00 2.90
364 365 2.628657 CTCCCTCCGTTCCGAAATAGAT 59.371 50.000 0.00 0.00 0.00 1.98
365 366 2.029623 CTCCCTCCGTTCCGAAATAGA 58.970 52.381 0.00 0.00 0.00 1.98
366 367 1.755380 ACTCCCTCCGTTCCGAAATAG 59.245 52.381 0.00 0.00 0.00 1.73
367 368 1.856629 ACTCCCTCCGTTCCGAAATA 58.143 50.000 0.00 0.00 0.00 1.40
368 369 1.479730 GTACTCCCTCCGTTCCGAAAT 59.520 52.381 0.00 0.00 0.00 2.17
369 370 0.890683 GTACTCCCTCCGTTCCGAAA 59.109 55.000 0.00 0.00 0.00 3.46
370 371 0.251297 TGTACTCCCTCCGTTCCGAA 60.251 55.000 0.00 0.00 0.00 4.30
371 372 0.033796 ATGTACTCCCTCCGTTCCGA 60.034 55.000 0.00 0.00 0.00 4.55
372 373 0.822164 AATGTACTCCCTCCGTTCCG 59.178 55.000 0.00 0.00 0.00 4.30
373 374 2.235402 TGAAATGTACTCCCTCCGTTCC 59.765 50.000 0.00 0.00 0.00 3.62
374 375 3.604875 TGAAATGTACTCCCTCCGTTC 57.395 47.619 0.00 0.00 0.00 3.95
375 376 5.687166 TTATGAAATGTACTCCCTCCGTT 57.313 39.130 0.00 0.00 0.00 4.44
376 377 5.365605 TCATTATGAAATGTACTCCCTCCGT 59.634 40.000 0.00 0.00 42.66 4.69
377 378 5.853936 TCATTATGAAATGTACTCCCTCCG 58.146 41.667 0.00 0.00 42.66 4.63
378 379 8.160106 AGATTCATTATGAAATGTACTCCCTCC 58.840 37.037 11.88 0.00 40.12 4.30
523 524 9.252962 CTTGATCAAAGCTTACAAAGTCAAATT 57.747 29.630 9.88 0.00 0.00 1.82
524 525 8.416329 ACTTGATCAAAGCTTACAAAGTCAAAT 58.584 29.630 9.88 0.00 39.76 2.32
525 526 7.771183 ACTTGATCAAAGCTTACAAAGTCAAA 58.229 30.769 9.88 0.00 39.76 2.69
526 527 7.333528 ACTTGATCAAAGCTTACAAAGTCAA 57.666 32.000 9.88 4.66 39.76 3.18
527 528 6.942532 ACTTGATCAAAGCTTACAAAGTCA 57.057 33.333 9.88 0.00 39.76 3.41
528 529 7.417612 TGAACTTGATCAAAGCTTACAAAGTC 58.582 34.615 9.88 5.60 39.76 3.01
529 530 7.333528 TGAACTTGATCAAAGCTTACAAAGT 57.666 32.000 9.88 3.39 39.76 2.66
530 531 9.552114 CTATGAACTTGATCAAAGCTTACAAAG 57.448 33.333 9.88 2.75 39.76 2.77
531 532 9.283768 TCTATGAACTTGATCAAAGCTTACAAA 57.716 29.630 9.88 0.00 39.76 2.83
532 533 8.846943 TCTATGAACTTGATCAAAGCTTACAA 57.153 30.769 9.88 3.95 39.76 2.41
533 534 8.314021 TCTCTATGAACTTGATCAAAGCTTACA 58.686 33.333 9.88 5.02 39.76 2.41
534 535 8.709386 TCTCTATGAACTTGATCAAAGCTTAC 57.291 34.615 9.88 0.00 39.76 2.34
535 536 9.725019 TTTCTCTATGAACTTGATCAAAGCTTA 57.275 29.630 9.88 4.06 39.76 3.09
536 537 8.627208 TTTCTCTATGAACTTGATCAAAGCTT 57.373 30.769 9.88 0.00 39.76 3.74
537 538 8.510505 GTTTTCTCTATGAACTTGATCAAAGCT 58.489 33.333 9.88 0.00 39.76 3.74
538 539 8.510505 AGTTTTCTCTATGAACTTGATCAAAGC 58.489 33.333 9.88 2.53 39.76 3.51
545 546 9.832445 ACAAAGTAGTTTTCTCTATGAACTTGA 57.168 29.630 0.00 0.00 35.43 3.02
548 549 9.057089 CCAACAAAGTAGTTTTCTCTATGAACT 57.943 33.333 0.00 0.00 37.40 3.01
549 550 8.837389 ACCAACAAAGTAGTTTTCTCTATGAAC 58.163 33.333 0.00 0.00 33.88 3.18
550 551 8.974060 ACCAACAAAGTAGTTTTCTCTATGAA 57.026 30.769 0.00 0.00 0.00 2.57
551 552 8.429641 AGACCAACAAAGTAGTTTTCTCTATGA 58.570 33.333 0.00 0.00 0.00 2.15
552 553 8.608844 AGACCAACAAAGTAGTTTTCTCTATG 57.391 34.615 0.00 0.00 0.00 2.23
553 554 9.628500 AAAGACCAACAAAGTAGTTTTCTCTAT 57.372 29.630 0.00 0.00 0.00 1.98
554 555 9.457436 AAAAGACCAACAAAGTAGTTTTCTCTA 57.543 29.630 0.00 0.00 0.00 2.43
555 556 7.939784 AAAGACCAACAAAGTAGTTTTCTCT 57.060 32.000 0.00 0.00 0.00 3.10
599 600 3.617263 CCGTCTTAAGATGTTTTCCGAGG 59.383 47.826 20.65 1.60 0.00 4.63
600 601 4.491676 TCCGTCTTAAGATGTTTTCCGAG 58.508 43.478 20.65 5.67 0.00 4.63
601 602 4.524316 TCCGTCTTAAGATGTTTTCCGA 57.476 40.909 20.65 8.90 0.00 4.55
602 603 4.034048 CCATCCGTCTTAAGATGTTTTCCG 59.966 45.833 20.65 11.94 38.57 4.30
603 604 5.183228 TCCATCCGTCTTAAGATGTTTTCC 58.817 41.667 20.65 1.06 38.57 3.13
606 607 5.422214 ACTCCATCCGTCTTAAGATGTTT 57.578 39.130 20.65 7.24 38.57 2.83
607 608 6.732896 ATACTCCATCCGTCTTAAGATGTT 57.267 37.500 20.65 7.56 38.57 2.71
608 609 6.732896 AATACTCCATCCGTCTTAAGATGT 57.267 37.500 20.65 3.32 38.57 3.06
611 612 9.803507 TCTATAAATACTCCATCCGTCTTAAGA 57.196 33.333 0.00 0.00 0.00 2.10
614 615 9.584008 AACTCTATAAATACTCCATCCGTCTTA 57.416 33.333 0.00 0.00 0.00 2.10
615 616 8.480133 AACTCTATAAATACTCCATCCGTCTT 57.520 34.615 0.00 0.00 0.00 3.01
616 617 9.756571 ATAACTCTATAAATACTCCATCCGTCT 57.243 33.333 0.00 0.00 0.00 4.18
617 618 9.790389 CATAACTCTATAAATACTCCATCCGTC 57.210 37.037 0.00 0.00 0.00 4.79
618 619 9.310449 ACATAACTCTATAAATACTCCATCCGT 57.690 33.333 0.00 0.00 0.00 4.69
637 638 3.978610 AGAACGGAGGGAGTACATAACT 58.021 45.455 0.00 0.00 42.80 2.24
638 639 4.732672 AAGAACGGAGGGAGTACATAAC 57.267 45.455 0.00 0.00 0.00 1.89
639 640 5.750352 AAAAGAACGGAGGGAGTACATAA 57.250 39.130 0.00 0.00 0.00 1.90
640 641 5.750352 AAAAAGAACGGAGGGAGTACATA 57.250 39.130 0.00 0.00 0.00 2.29
661 662 8.995220 ACACAAATCTAATACGCAGAGTAAAAA 58.005 29.630 0.00 0.00 39.04 1.94
662 663 8.542497 ACACAAATCTAATACGCAGAGTAAAA 57.458 30.769 0.00 0.00 39.04 1.52
665 666 6.859017 TGACACAAATCTAATACGCAGAGTA 58.141 36.000 0.00 0.00 40.03 2.59
667 668 6.256539 ACATGACACAAATCTAATACGCAGAG 59.743 38.462 0.00 0.00 0.00 3.35
668 669 6.106003 ACATGACACAAATCTAATACGCAGA 58.894 36.000 0.00 0.00 0.00 4.26
670 671 6.735678 AACATGACACAAATCTAATACGCA 57.264 33.333 0.00 0.00 0.00 5.24
671 672 8.995906 GTTTAACATGACACAAATCTAATACGC 58.004 33.333 0.00 0.00 0.00 4.42
676 677 9.243637 GCAAAGTTTAACATGACACAAATCTAA 57.756 29.630 0.00 0.00 0.00 2.10
677 678 8.409371 TGCAAAGTTTAACATGACACAAATCTA 58.591 29.630 0.00 0.00 0.00 1.98
678 679 7.264221 TGCAAAGTTTAACATGACACAAATCT 58.736 30.769 0.00 0.00 0.00 2.40
679 680 7.462109 TGCAAAGTTTAACATGACACAAATC 57.538 32.000 0.00 0.00 0.00 2.17
681 682 7.386299 ACTTTGCAAAGTTTAACATGACACAAA 59.614 29.630 33.85 0.00 46.52 2.83
682 683 6.870965 ACTTTGCAAAGTTTAACATGACACAA 59.129 30.769 33.85 0.00 46.52 3.33
807 808 9.491675 TCTGTACATAAGTTTTGTCCGAAATTA 57.508 29.630 1.96 0.00 0.00 1.40
809 810 7.660208 AGTCTGTACATAAGTTTTGTCCGAAAT 59.340 33.333 1.96 0.00 0.00 2.17
810 811 6.987992 AGTCTGTACATAAGTTTTGTCCGAAA 59.012 34.615 1.96 0.00 0.00 3.46
811 812 6.518493 AGTCTGTACATAAGTTTTGTCCGAA 58.482 36.000 1.96 0.00 0.00 4.30
812 813 6.092955 AGTCTGTACATAAGTTTTGTCCGA 57.907 37.500 1.96 0.00 0.00 4.55
813 814 7.878477 TTAGTCTGTACATAAGTTTTGTCCG 57.122 36.000 1.96 0.00 0.00 4.79
870 1339 5.221621 TGGCCGATGATCAACATAAGATGTA 60.222 40.000 0.00 0.00 44.07 2.29
872 1341 4.067192 TGGCCGATGATCAACATAAGATG 58.933 43.478 0.00 0.00 39.56 2.90
873 1342 4.356405 TGGCCGATGATCAACATAAGAT 57.644 40.909 0.00 0.00 39.56 2.40
874 1343 3.836365 TGGCCGATGATCAACATAAGA 57.164 42.857 0.00 0.00 39.56 2.10
875 1344 4.758674 AGAATGGCCGATGATCAACATAAG 59.241 41.667 0.00 0.00 39.56 1.73
876 1345 4.717877 AGAATGGCCGATGATCAACATAA 58.282 39.130 0.00 0.00 39.56 1.90
877 1346 4.356405 AGAATGGCCGATGATCAACATA 57.644 40.909 0.00 0.00 39.56 2.29
878 1347 3.219176 AGAATGGCCGATGATCAACAT 57.781 42.857 0.00 0.00 42.47 2.71
879 1348 2.715749 AGAATGGCCGATGATCAACA 57.284 45.000 0.00 0.00 0.00 3.33
880 1349 6.801539 TTTATAGAATGGCCGATGATCAAC 57.198 37.500 0.00 0.00 0.00 3.18
881 1350 6.127925 GCATTTATAGAATGGCCGATGATCAA 60.128 38.462 0.00 0.00 0.00 2.57
882 1351 5.355071 GCATTTATAGAATGGCCGATGATCA 59.645 40.000 0.00 0.00 0.00 2.92
907 1376 8.546244 GTGATACTAGATGACATGTGAAATGTG 58.454 37.037 1.15 0.00 31.52 3.21
920 1389 6.322201 TGATTGCAGTGAGTGATACTAGATGA 59.678 38.462 0.00 0.00 0.00 2.92
928 1397 4.541973 ACTGTGATTGCAGTGAGTGATA 57.458 40.909 0.00 0.00 46.72 2.15
1138 1626 2.409651 GAGGAGGTAGCGCGTGAG 59.590 66.667 8.43 0.00 0.00 3.51
1561 2049 1.072505 ACTCGTCGGTTTTGGCCAT 59.927 52.632 6.09 0.00 0.00 4.40
1641 2136 0.388649 CGTGGAAGGAGTTGACGAGG 60.389 60.000 0.00 0.00 31.71 4.63
1673 2168 1.372997 CGAGCTTGTGTGCGTACCT 60.373 57.895 0.00 0.00 38.13 3.08
1678 2173 4.415501 GCGACGAGCTTGTGTGCG 62.416 66.667 12.53 10.33 44.04 5.34
1688 2183 1.135546 ACATTGAGTGAGAGCGACGAG 60.136 52.381 0.00 0.00 0.00 4.18
1689 2184 0.881796 ACATTGAGTGAGAGCGACGA 59.118 50.000 0.00 0.00 0.00 4.20
1690 2185 3.408389 ACATTGAGTGAGAGCGACG 57.592 52.632 0.00 0.00 0.00 5.12
1705 2217 2.864097 GCGAGTGAACAGAGTGACACAT 60.864 50.000 8.59 0.00 33.58 3.21
1707 2219 1.132588 GCGAGTGAACAGAGTGACAC 58.867 55.000 0.00 0.00 0.00 3.67
1709 2221 2.991434 TAGCGAGTGAACAGAGTGAC 57.009 50.000 0.00 0.00 0.00 3.67
1710 2222 4.333095 GTCTATAGCGAGTGAACAGAGTGA 59.667 45.833 0.00 0.00 0.00 3.41
1711 2223 4.593157 GTCTATAGCGAGTGAACAGAGTG 58.407 47.826 0.00 0.00 0.00 3.51
1712 2224 3.310227 CGTCTATAGCGAGTGAACAGAGT 59.690 47.826 9.97 0.00 0.00 3.24
1715 2227 2.855187 GCCGTCTATAGCGAGTGAACAG 60.855 54.545 15.26 1.45 0.00 3.16
1717 2229 1.065102 TGCCGTCTATAGCGAGTGAAC 59.935 52.381 15.26 0.00 0.00 3.18
1718 2230 1.065102 GTGCCGTCTATAGCGAGTGAA 59.935 52.381 15.26 0.00 0.00 3.18
1719 2231 0.661552 GTGCCGTCTATAGCGAGTGA 59.338 55.000 15.26 0.00 0.00 3.41
1720 2232 0.663688 AGTGCCGTCTATAGCGAGTG 59.336 55.000 15.26 3.64 0.00 3.51
1723 2235 1.202734 ACCTAGTGCCGTCTATAGCGA 60.203 52.381 15.26 0.00 0.00 4.93
1725 2237 3.188873 CAGTACCTAGTGCCGTCTATAGC 59.811 52.174 0.00 0.00 0.00 2.97
1726 2238 4.639334 TCAGTACCTAGTGCCGTCTATAG 58.361 47.826 0.00 0.00 0.00 1.31
1727 2239 4.694760 TCAGTACCTAGTGCCGTCTATA 57.305 45.455 0.00 0.00 0.00 1.31
1728 2240 3.572632 TCAGTACCTAGTGCCGTCTAT 57.427 47.619 0.00 0.00 0.00 1.98
1729 2241 3.354948 TTCAGTACCTAGTGCCGTCTA 57.645 47.619 0.00 0.00 0.00 2.59
1730 2242 2.211250 TTCAGTACCTAGTGCCGTCT 57.789 50.000 0.00 0.00 0.00 4.18
1732 2244 1.965643 TGTTTCAGTACCTAGTGCCGT 59.034 47.619 0.00 0.00 0.00 5.68
1738 2250 8.737175 TGACAATAGTAGTGTTTCAGTACCTAG 58.263 37.037 4.51 0.00 40.11 3.02
1740 2252 7.534723 TGACAATAGTAGTGTTTCAGTACCT 57.465 36.000 4.51 3.09 40.11 3.08
1741 2253 8.597662 TTTGACAATAGTAGTGTTTCAGTACC 57.402 34.615 4.51 0.00 40.11 3.34
1746 2258 9.743057 CCAAATTTTGACAATAGTAGTGTTTCA 57.257 29.630 10.72 0.00 0.00 2.69
1747 2259 9.959749 TCCAAATTTTGACAATAGTAGTGTTTC 57.040 29.630 10.72 0.00 0.00 2.78
1749 2261 9.965824 CTTCCAAATTTTGACAATAGTAGTGTT 57.034 29.630 10.72 0.00 0.00 3.32
1750 2262 8.576442 CCTTCCAAATTTTGACAATAGTAGTGT 58.424 33.333 10.72 2.26 0.00 3.55
1751 2263 8.792633 TCCTTCCAAATTTTGACAATAGTAGTG 58.207 33.333 10.72 0.00 0.00 2.74
1752 2264 8.934023 TCCTTCCAAATTTTGACAATAGTAGT 57.066 30.769 10.72 0.00 0.00 2.73
1755 2267 8.028938 CGATTCCTTCCAAATTTTGACAATAGT 58.971 33.333 10.72 0.00 0.00 2.12
1756 2268 7.489113 CCGATTCCTTCCAAATTTTGACAATAG 59.511 37.037 10.72 1.17 0.00 1.73
1757 2269 7.177568 TCCGATTCCTTCCAAATTTTGACAATA 59.822 33.333 10.72 0.00 0.00 1.90
1758 2270 6.014669 TCCGATTCCTTCCAAATTTTGACAAT 60.015 34.615 10.72 1.81 0.00 2.71
1759 2271 5.303078 TCCGATTCCTTCCAAATTTTGACAA 59.697 36.000 10.72 2.66 0.00 3.18
1760 2272 4.830046 TCCGATTCCTTCCAAATTTTGACA 59.170 37.500 10.72 0.00 0.00 3.58
1761 2273 5.048013 ACTCCGATTCCTTCCAAATTTTGAC 60.048 40.000 10.72 0.00 0.00 3.18
1762 2274 5.076873 ACTCCGATTCCTTCCAAATTTTGA 58.923 37.500 10.72 0.00 0.00 2.69
1763 2275 5.391312 ACTCCGATTCCTTCCAAATTTTG 57.609 39.130 1.99 1.99 0.00 2.44
1764 2276 6.007703 TGTACTCCGATTCCTTCCAAATTTT 58.992 36.000 0.00 0.00 0.00 1.82
1765 2277 5.566469 TGTACTCCGATTCCTTCCAAATTT 58.434 37.500 0.00 0.00 0.00 1.82
1766 2278 5.174037 TGTACTCCGATTCCTTCCAAATT 57.826 39.130 0.00 0.00 0.00 1.82
1767 2279 4.837093 TGTACTCCGATTCCTTCCAAAT 57.163 40.909 0.00 0.00 0.00 2.32
1768 2280 4.513442 CATGTACTCCGATTCCTTCCAAA 58.487 43.478 0.00 0.00 0.00 3.28
1772 2284 2.484889 GCCATGTACTCCGATTCCTTC 58.515 52.381 0.00 0.00 0.00 3.46
1832 2344 1.081242 GTTGTCGAGGTACGCCGAA 60.081 57.895 9.32 0.07 39.49 4.30
2029 2541 2.142292 GACCACCCACAGGAATGGCT 62.142 60.000 6.30 0.00 38.55 4.75
2397 2912 1.535896 CTTCGTCTTCTCACTCCACGA 59.464 52.381 0.00 0.00 37.69 4.35
2398 2913 1.401670 CCTTCGTCTTCTCACTCCACG 60.402 57.143 0.00 0.00 0.00 4.94
2444 2959 3.425162 AACTCCAAGATGTTCCTGTCC 57.575 47.619 0.00 0.00 0.00 4.02
2561 3076 4.582701 AAAATGGCACGAGACATCAAAA 57.417 36.364 0.29 0.00 44.76 2.44
2576 3091 4.666655 CGCGTACTTGTCAGAGAAAAATGG 60.667 45.833 0.00 0.00 0.00 3.16
2622 3137 7.725844 ACTGGGTTTTATTCAGAGAAATTCAGT 59.274 33.333 0.00 0.00 33.19 3.41
2623 3138 8.115490 ACTGGGTTTTATTCAGAGAAATTCAG 57.885 34.615 0.00 0.00 33.19 3.02
2650 3197 1.135575 GCTTCGCTTCACATTCAAGGG 60.136 52.381 0.00 0.00 35.62 3.95
2657 3204 1.005037 TCCACGCTTCGCTTCACAT 60.005 52.632 0.00 0.00 0.00 3.21
2661 3208 0.164002 GTTTCTCCACGCTTCGCTTC 59.836 55.000 0.00 0.00 0.00 3.86
2662 3209 0.249911 AGTTTCTCCACGCTTCGCTT 60.250 50.000 0.00 0.00 0.00 4.68
2668 3215 1.141053 ACCAGAAAGTTTCTCCACGCT 59.859 47.619 15.35 0.00 38.11 5.07
2764 3498 5.261209 TGGACTTGTCCAAATTGTTTCTG 57.739 39.130 18.98 0.00 36.74 3.02
2833 3567 6.299141 AGTGCTCCTAAAAAGAATTGACTGA 58.701 36.000 0.00 0.00 0.00 3.41
2843 3577 4.828072 AGGACCTAGTGCTCCTAAAAAG 57.172 45.455 0.00 0.00 34.93 2.27
3183 4002 1.246056 CCACACATGTCAAGGCTGGG 61.246 60.000 0.00 0.00 0.00 4.45
3194 4013 5.882000 TCTTTGAGAATATCACCCACACATG 59.118 40.000 0.00 0.00 37.77 3.21
3241 4060 9.682465 ATCATTATCTTAGGATCATGGAACATG 57.318 33.333 8.63 2.91 36.87 3.21
3245 4064 8.766476 GGAGATCATTATCTTAGGATCATGGAA 58.234 37.037 8.63 0.00 42.73 3.53
3246 4065 7.902941 TGGAGATCATTATCTTAGGATCATGGA 59.097 37.037 8.63 0.00 42.73 3.41
3281 4101 3.391296 TCAAGGACAAGCTCAACTACCTT 59.609 43.478 0.00 0.00 37.16 3.50
3282 4102 2.972713 TCAAGGACAAGCTCAACTACCT 59.027 45.455 0.00 0.00 0.00 3.08
3386 4206 5.527385 ACATTACATCATCCATTTTGGGGA 58.473 37.500 0.00 0.00 38.32 4.81
3396 4216 6.971184 CAGCAAGAAGAAACATTACATCATCC 59.029 38.462 0.00 0.00 0.00 3.51
3446 4266 7.708322 AGAAGAAAAAGCTTTGAATTGGAAGTC 59.292 33.333 13.54 0.43 0.00 3.01
3481 4301 8.258007 TCTTACATGATAGAGTAAACACAAGGG 58.742 37.037 0.00 0.00 30.57 3.95


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

AutoCloner maintained by Alex Coulton.