Multiple sequence alignment - TraesCS2A01G203500

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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 TraesCS2A01G203500 chr2A 100.000 3452 0 0 1 3452 179346738 179350189 0.000000e+00 6375.0
1 TraesCS2A01G203500 chr2A 74.543 1422 283 58 1012 2403 722062179 722060807 6.510000e-152 547.0
2 TraesCS2A01G203500 chr2A 80.556 144 24 4 2017 2158 604749061 604748920 1.310000e-19 108.0
3 TraesCS2A01G203500 chr2D 94.141 2048 87 11 607 2645 170481155 170479132 0.000000e+00 3086.0
4 TraesCS2A01G203500 chr2D 87.102 566 43 8 26 580 170481686 170481140 6.330000e-172 614.0
5 TraesCS2A01G203500 chr2D 82.353 731 106 12 2718 3431 461799619 461800343 6.330000e-172 614.0
6 TraesCS2A01G203500 chr2D 80.435 92 17 1 2714 2804 35258731 35258640 6.180000e-08 69.4
7 TraesCS2A01G203500 chr2B 94.899 1882 76 12 608 2474 226729438 226731314 0.000000e+00 2926.0
8 TraesCS2A01G203500 chr2B 74.474 1426 277 66 1012 2403 708994409 708993037 1.410000e-148 536.0
9 TraesCS2A01G203500 chr2B 80.565 566 52 24 1 549 226728903 226729427 1.940000e-102 383.0
10 TraesCS2A01G203500 chr2B 85.625 160 12 3 2490 2645 226731508 226731660 1.280000e-34 158.0
11 TraesCS2A01G203500 chr2B 100.000 31 0 0 2720 2750 736888324 736888354 1.340000e-04 58.4
12 TraesCS2A01G203500 chr1A 76.836 1416 268 54 1013 2404 441032373 441033752 0.000000e+00 743.0
13 TraesCS2A01G203500 chr1A 75.169 1329 277 43 1097 2404 533155810 533154514 8.310000e-161 577.0
14 TraesCS2A01G203500 chr1A 74.419 1032 209 46 1336 2332 526757875 526758886 3.230000e-105 392.0
15 TraesCS2A01G203500 chr1D 82.167 729 113 6 2718 3434 288939669 288940392 8.190000e-171 610.0
16 TraesCS2A01G203500 chr1D 83.664 655 98 7 2801 3450 274475318 274475968 2.950000e-170 608.0
17 TraesCS2A01G203500 chr1D 74.903 1032 204 46 1336 2332 429025517 429026528 1.480000e-113 420.0
18 TraesCS2A01G203500 chr1D 80.000 85 15 2 2721 2804 203573760 203573677 1.030000e-05 62.1
19 TraesCS2A01G203500 chr3D 83.725 639 94 9 2806 3440 48819212 48818580 2.290000e-166 595.0
20 TraesCS2A01G203500 chr3D 81.873 662 105 11 2802 3452 559132827 559133484 8.430000e-151 544.0
21 TraesCS2A01G203500 chr3D 76.568 303 48 9 2718 3007 170078152 170077860 9.990000e-31 145.0
22 TraesCS2A01G203500 chr3A 81.150 748 118 14 2720 3452 69265014 69264275 2.310000e-161 579.0
23 TraesCS2A01G203500 chr3A 77.748 755 136 20 2718 3450 80694151 80693407 5.290000e-118 435.0
24 TraesCS2A01G203500 chr3B 80.585 752 115 19 2718 3451 818995025 818995763 5.040000e-153 551.0
25 TraesCS2A01G203500 chr6D 81.126 657 113 8 2800 3449 395504784 395505436 1.840000e-142 516.0
26 TraesCS2A01G203500 chr7B 74.740 1152 233 51 1276 2404 45176683 45175567 2.430000e-126 462.0
27 TraesCS2A01G203500 chr5D 73.717 1442 268 77 1030 2404 431970299 431971696 8.730000e-126 460.0
28 TraesCS2A01G203500 chr7D 74.550 1167 227 54 1276 2404 92762747 92763881 2.440000e-121 446.0
29 TraesCS2A01G203500 chr5A 73.458 1443 270 81 1030 2404 547060466 547061863 4.090000e-119 438.0
30 TraesCS2A01G203500 chr1B 72.985 1340 282 68 1036 2332 580537649 580538951 2.500000e-106 396.0
31 TraesCS2A01G203500 chr1B 75.598 209 33 14 323 514 133163481 133163274 1.710000e-13 87.9
32 TraesCS2A01G203500 chr7A 75.238 210 48 4 1962 2169 51091534 51091741 2.840000e-16 97.1
33 TraesCS2A01G203500 chr6B 86.885 61 8 0 2716 2776 694448989 694448929 6.180000e-08 69.4
34 TraesCS2A01G203500 chr4A 81.176 85 16 0 2720 2804 689650566 689650650 6.180000e-08 69.4


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 TraesCS2A01G203500 chr2A 179346738 179350189 3451 False 6375.000000 6375 100.000000 1 3452 1 chr2A.!!$F1 3451
1 TraesCS2A01G203500 chr2A 722060807 722062179 1372 True 547.000000 547 74.543000 1012 2403 1 chr2A.!!$R2 1391
2 TraesCS2A01G203500 chr2D 170479132 170481686 2554 True 1850.000000 3086 90.621500 26 2645 2 chr2D.!!$R2 2619
3 TraesCS2A01G203500 chr2D 461799619 461800343 724 False 614.000000 614 82.353000 2718 3431 1 chr2D.!!$F1 713
4 TraesCS2A01G203500 chr2B 226728903 226731660 2757 False 1155.666667 2926 87.029667 1 2645 3 chr2B.!!$F2 2644
5 TraesCS2A01G203500 chr2B 708993037 708994409 1372 True 536.000000 536 74.474000 1012 2403 1 chr2B.!!$R1 1391
6 TraesCS2A01G203500 chr1A 441032373 441033752 1379 False 743.000000 743 76.836000 1013 2404 1 chr1A.!!$F1 1391
7 TraesCS2A01G203500 chr1A 533154514 533155810 1296 True 577.000000 577 75.169000 1097 2404 1 chr1A.!!$R1 1307
8 TraesCS2A01G203500 chr1A 526757875 526758886 1011 False 392.000000 392 74.419000 1336 2332 1 chr1A.!!$F2 996
9 TraesCS2A01G203500 chr1D 288939669 288940392 723 False 610.000000 610 82.167000 2718 3434 1 chr1D.!!$F2 716
10 TraesCS2A01G203500 chr1D 274475318 274475968 650 False 608.000000 608 83.664000 2801 3450 1 chr1D.!!$F1 649
11 TraesCS2A01G203500 chr1D 429025517 429026528 1011 False 420.000000 420 74.903000 1336 2332 1 chr1D.!!$F3 996
12 TraesCS2A01G203500 chr3D 48818580 48819212 632 True 595.000000 595 83.725000 2806 3440 1 chr3D.!!$R1 634
13 TraesCS2A01G203500 chr3D 559132827 559133484 657 False 544.000000 544 81.873000 2802 3452 1 chr3D.!!$F1 650
14 TraesCS2A01G203500 chr3A 69264275 69265014 739 True 579.000000 579 81.150000 2720 3452 1 chr3A.!!$R1 732
15 TraesCS2A01G203500 chr3A 80693407 80694151 744 True 435.000000 435 77.748000 2718 3450 1 chr3A.!!$R2 732
16 TraesCS2A01G203500 chr3B 818995025 818995763 738 False 551.000000 551 80.585000 2718 3451 1 chr3B.!!$F1 733
17 TraesCS2A01G203500 chr6D 395504784 395505436 652 False 516.000000 516 81.126000 2800 3449 1 chr6D.!!$F1 649
18 TraesCS2A01G203500 chr7B 45175567 45176683 1116 True 462.000000 462 74.740000 1276 2404 1 chr7B.!!$R1 1128
19 TraesCS2A01G203500 chr5D 431970299 431971696 1397 False 460.000000 460 73.717000 1030 2404 1 chr5D.!!$F1 1374
20 TraesCS2A01G203500 chr7D 92762747 92763881 1134 False 446.000000 446 74.550000 1276 2404 1 chr7D.!!$F1 1128
21 TraesCS2A01G203500 chr5A 547060466 547061863 1397 False 438.000000 438 73.458000 1030 2404 1 chr5A.!!$F1 1374
22 TraesCS2A01G203500 chr1B 580537649 580538951 1302 False 396.000000 396 72.985000 1036 2332 1 chr1B.!!$F1 1296

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
23 24 0.192566 ACCCACCCACCTCACTTAGA 59.807 55.0 0.0 0.0 0.00 2.10 F
990 1026 0.250901 AGTGCCATTGTGTCCACTCC 60.251 55.0 0.0 0.0 33.57 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1641 1689 0.315568 GCTCGACTGAGGTGTTCACT 59.684 55.0 2.98 0.0 42.79 3.41 R
2706 3043 0.174845 TGGCTTCCGTGATAAGTCGG 59.825 55.0 0.00 0.0 46.93 4.79 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
18 19 3.966543 CCCACCCACCCACCTCAC 61.967 72.222 0.00 0.00 0.00 3.51
19 20 2.854032 CCACCCACCCACCTCACT 60.854 66.667 0.00 0.00 0.00 3.41
20 21 2.460853 CCACCCACCCACCTCACTT 61.461 63.158 0.00 0.00 0.00 3.16
21 22 1.131303 CCACCCACCCACCTCACTTA 61.131 60.000 0.00 0.00 0.00 2.24
23 24 0.192566 ACCCACCCACCTCACTTAGA 59.807 55.000 0.00 0.00 0.00 2.10
24 25 1.358152 CCCACCCACCTCACTTAGAA 58.642 55.000 0.00 0.00 0.00 2.10
29 30 3.056465 CACCCACCTCACTTAGAAGAGAC 60.056 52.174 7.72 0.00 33.74 3.36
35 36 4.525100 ACCTCACTTAGAAGAGACAAGGAC 59.475 45.833 7.72 0.00 33.74 3.85
40 41 4.591072 ACTTAGAAGAGACAAGGACTTGCT 59.409 41.667 11.73 9.71 44.03 3.91
59 62 0.257328 TGGAGTTGGTTTGTGGCTCA 59.743 50.000 0.00 0.00 0.00 4.26
68 71 4.661222 TGGTTTGTGGCTCAGAATAATGA 58.339 39.130 0.00 0.00 0.00 2.57
74 77 7.792374 TTGTGGCTCAGAATAATGATAGAAC 57.208 36.000 0.00 0.00 0.00 3.01
93 96 2.790433 ACACATGTAAGATTTGCCCGT 58.210 42.857 0.00 0.00 0.00 5.28
94 97 3.945346 ACACATGTAAGATTTGCCCGTA 58.055 40.909 0.00 0.00 0.00 4.02
95 98 4.328536 ACACATGTAAGATTTGCCCGTAA 58.671 39.130 0.00 0.00 0.00 3.18
96 99 4.762765 ACACATGTAAGATTTGCCCGTAAA 59.237 37.500 0.00 0.00 0.00 2.01
97 100 5.106317 ACACATGTAAGATTTGCCCGTAAAG 60.106 40.000 0.00 0.00 0.00 1.85
98 101 4.142469 ACATGTAAGATTTGCCCGTAAAGC 60.142 41.667 0.00 0.00 0.00 3.51
99 102 2.750712 TGTAAGATTTGCCCGTAAAGCC 59.249 45.455 0.00 0.00 0.00 4.35
100 103 1.182667 AAGATTTGCCCGTAAAGCCC 58.817 50.000 0.00 0.00 0.00 5.19
101 104 1.029947 AGATTTGCCCGTAAAGCCCG 61.030 55.000 0.00 0.00 0.00 6.13
102 105 1.303806 ATTTGCCCGTAAAGCCCGT 60.304 52.632 0.00 0.00 0.00 5.28
143 146 1.289830 ACCCTTAAATAGCCAACCCCC 59.710 52.381 0.00 0.00 0.00 5.40
153 156 0.320374 GCCAACCCCCAAAAGTTAGC 59.680 55.000 0.00 0.00 0.00 3.09
176 179 2.933906 GTTGGACTCAAACGACACTTCA 59.066 45.455 0.00 0.00 34.28 3.02
256 259 7.201767 GCATGAGGATAAGCTCATTTAAACACT 60.202 37.037 0.00 0.00 34.48 3.55
291 294 3.444742 TGCGGAGAACGTTAATCCTTCTA 59.555 43.478 22.81 9.13 46.52 2.10
292 295 4.043073 GCGGAGAACGTTAATCCTTCTAG 58.957 47.826 22.81 12.32 46.52 2.43
377 381 2.031768 GCTGCCAGATCCCGATCC 59.968 66.667 0.00 0.00 38.58 3.36
399 403 3.558931 ACGGATGACCATTATTCTGCA 57.441 42.857 0.00 0.00 35.59 4.41
423 428 3.749609 AGCTTTGCAATTTTCTGCCAATC 59.250 39.130 0.00 0.00 41.90 2.67
506 521 1.031235 TCACATGGCAATTATGGGCG 58.969 50.000 0.00 0.00 0.00 6.13
531 549 3.564225 CGCTGGGAGATGTAAAAATACCC 59.436 47.826 0.00 0.00 36.72 3.69
575 593 7.548196 AAAATCTAACGTCAGTTCTTTGACA 57.452 32.000 6.91 0.00 46.11 3.58
576 594 7.730364 AAATCTAACGTCAGTTCTTTGACAT 57.270 32.000 6.91 0.00 46.11 3.06
577 595 6.952935 ATCTAACGTCAGTTCTTTGACATC 57.047 37.500 6.91 0.00 46.11 3.06
578 596 6.085555 TCTAACGTCAGTTCTTTGACATCT 57.914 37.500 6.91 0.00 46.11 2.90
579 597 6.513180 TCTAACGTCAGTTCTTTGACATCTT 58.487 36.000 6.91 0.00 46.11 2.40
580 598 5.659048 AACGTCAGTTCTTTGACATCTTC 57.341 39.130 6.91 0.00 46.11 2.87
581 599 4.950050 ACGTCAGTTCTTTGACATCTTCT 58.050 39.130 6.91 0.00 46.11 2.85
582 600 5.360591 ACGTCAGTTCTTTGACATCTTCTT 58.639 37.500 6.91 0.00 46.11 2.52
583 601 5.463724 ACGTCAGTTCTTTGACATCTTCTTC 59.536 40.000 6.91 0.00 46.11 2.87
584 602 5.694006 CGTCAGTTCTTTGACATCTTCTTCT 59.306 40.000 6.91 0.00 46.11 2.85
585 603 6.201806 CGTCAGTTCTTTGACATCTTCTTCTT 59.798 38.462 6.91 0.00 46.11 2.52
586 604 7.568497 CGTCAGTTCTTTGACATCTTCTTCTTC 60.568 40.741 6.91 0.00 46.11 2.87
587 605 7.440856 GTCAGTTCTTTGACATCTTCTTCTTCT 59.559 37.037 1.54 0.00 45.32 2.85
588 606 7.989741 TCAGTTCTTTGACATCTTCTTCTTCTT 59.010 33.333 0.00 0.00 0.00 2.52
589 607 8.281893 CAGTTCTTTGACATCTTCTTCTTCTTC 58.718 37.037 0.00 0.00 0.00 2.87
590 608 8.210265 AGTTCTTTGACATCTTCTTCTTCTTCT 58.790 33.333 0.00 0.00 0.00 2.85
591 609 8.495148 GTTCTTTGACATCTTCTTCTTCTTCTC 58.505 37.037 0.00 0.00 0.00 2.87
592 610 7.961351 TCTTTGACATCTTCTTCTTCTTCTCT 58.039 34.615 0.00 0.00 0.00 3.10
593 611 8.428063 TCTTTGACATCTTCTTCTTCTTCTCTT 58.572 33.333 0.00 0.00 0.00 2.85
594 612 8.970859 TTTGACATCTTCTTCTTCTTCTCTTT 57.029 30.769 0.00 0.00 0.00 2.52
595 613 8.970859 TTGACATCTTCTTCTTCTTCTCTTTT 57.029 30.769 0.00 0.00 0.00 2.27
596 614 8.970859 TGACATCTTCTTCTTCTTCTCTTTTT 57.029 30.769 0.00 0.00 0.00 1.94
623 641 7.509546 TGAGTGGAAGTTCTTTAACATCTTCT 58.490 34.615 2.25 0.00 38.12 2.85
721 741 4.448060 TCATACTAGTACGATGACAGCGAG 59.552 45.833 21.46 9.04 0.00 5.03
868 894 0.618458 CCAAAGCCAGGGTAGCACTA 59.382 55.000 0.00 0.00 0.00 2.74
872 906 1.153349 GCCAGGGTAGCACTAGCAC 60.153 63.158 8.95 0.00 45.49 4.40
878 912 0.546598 GGTAGCACTAGCACCCCAAT 59.453 55.000 2.08 0.00 45.49 3.16
890 924 2.874849 CACCCCAATTTGTCGCATAAC 58.125 47.619 0.00 0.00 0.00 1.89
990 1026 0.250901 AGTGCCATTGTGTCCACTCC 60.251 55.000 0.00 0.00 33.57 3.85
1011 1047 1.135139 AGTCCATCAATGACGTCTCGG 59.865 52.381 17.92 7.96 0.00 4.63
1758 1806 4.636435 CCGGTTGCCTGGTTCGGT 62.636 66.667 0.00 0.00 36.38 4.69
2155 2275 4.221422 CGATGATCCCGTGGCCGT 62.221 66.667 0.00 0.00 0.00 5.68
2232 2352 3.838271 GCGCTGGAGATGGACCGA 61.838 66.667 0.00 0.00 0.00 4.69
2316 2466 1.305887 GTCGGAGGAGGGGAGGAAA 60.306 63.158 0.00 0.00 0.00 3.13
2423 2573 1.327507 GTGCGCGAGATTTTGGTTTC 58.672 50.000 12.10 0.00 0.00 2.78
2464 2614 0.994263 CCGCTAAATTTGCAGCAAGC 59.006 50.000 8.12 6.94 45.96 4.01
2475 2625 4.704833 AGCAAGCGCCGTGGTGAT 62.705 61.111 12.11 0.00 39.83 3.06
2476 2626 4.465512 GCAAGCGCCGTGGTGATG 62.466 66.667 2.29 2.69 0.00 3.07
2477 2627 4.465512 CAAGCGCCGTGGTGATGC 62.466 66.667 2.29 0.00 0.00 3.91
2481 2631 3.792047 CGCCGTGGTGATGCACTG 61.792 66.667 0.00 0.00 34.40 3.66
2484 2634 1.985447 GCCGTGGTGATGCACTGATG 61.985 60.000 0.00 0.00 34.40 3.07
2485 2635 1.371337 CCGTGGTGATGCACTGATGG 61.371 60.000 0.00 0.00 34.40 3.51
2486 2636 1.371337 CGTGGTGATGCACTGATGGG 61.371 60.000 0.00 0.00 34.40 4.00
2497 2825 3.295734 CTGATGGGCAGTGTATCCG 57.704 57.895 0.00 0.00 39.85 4.18
2507 2835 0.179134 AGTGTATCCGTTCTGCGAGC 60.179 55.000 0.00 0.00 44.77 5.03
2508 2836 0.457853 GTGTATCCGTTCTGCGAGCA 60.458 55.000 0.00 0.00 44.77 4.26
2522 2850 1.671261 GCGAGCAGCTTTCTTCTCTGA 60.671 52.381 0.00 0.00 44.04 3.27
2545 2873 1.613630 ATCAGTGTTCGGCTCCCCT 60.614 57.895 0.00 0.00 0.00 4.79
2547 2875 2.526873 AGTGTTCGGCTCCCCTGT 60.527 61.111 0.00 0.00 0.00 4.00
2561 2889 2.580322 TCCCCTGTTCCATTTGCATAGA 59.420 45.455 0.00 0.00 0.00 1.98
2564 2892 4.381932 CCCCTGTTCCATTTGCATAGAAAC 60.382 45.833 0.00 0.00 0.00 2.78
2565 2893 4.381932 CCCTGTTCCATTTGCATAGAAACC 60.382 45.833 0.00 0.00 0.00 3.27
2567 2895 5.105228 CCTGTTCCATTTGCATAGAAACCAT 60.105 40.000 0.00 0.00 0.00 3.55
2568 2896 5.722263 TGTTCCATTTGCATAGAAACCATG 58.278 37.500 0.00 0.00 0.00 3.66
2569 2897 5.479724 TGTTCCATTTGCATAGAAACCATGA 59.520 36.000 0.00 0.00 0.00 3.07
2570 2898 6.154877 TGTTCCATTTGCATAGAAACCATGAT 59.845 34.615 0.00 0.00 0.00 2.45
2596 2928 3.068732 CAGATAAGATTCAGACCAGCCGA 59.931 47.826 0.00 0.00 0.00 5.54
2609 2941 3.059386 GCCGACGGCCAAATCCAA 61.059 61.111 28.74 0.00 44.06 3.53
2610 2942 2.631580 GCCGACGGCCAAATCCAAA 61.632 57.895 28.74 0.00 44.06 3.28
2611 2943 1.211709 CCGACGGCCAAATCCAAAC 59.788 57.895 2.24 0.00 0.00 2.93
2612 2944 1.211709 CGACGGCCAAATCCAAACC 59.788 57.895 2.24 0.00 0.00 3.27
2646 2983 7.321745 AGAAACATGCTATACAAACCTAAGC 57.678 36.000 0.00 0.00 0.00 3.09
2647 2984 6.884295 AGAAACATGCTATACAAACCTAAGCA 59.116 34.615 0.00 0.00 46.30 3.91
2648 2985 7.393234 AGAAACATGCTATACAAACCTAAGCAA 59.607 33.333 0.00 0.00 45.47 3.91
2649 2986 7.645058 AACATGCTATACAAACCTAAGCAAT 57.355 32.000 0.00 0.00 45.47 3.56
2650 2987 7.264373 ACATGCTATACAAACCTAAGCAATC 57.736 36.000 0.00 0.00 45.47 2.67
2651 2988 6.263168 ACATGCTATACAAACCTAAGCAATCC 59.737 38.462 0.00 0.00 45.47 3.01
2652 2989 5.750524 TGCTATACAAACCTAAGCAATCCA 58.249 37.500 0.00 0.00 40.05 3.41
2653 2990 5.588648 TGCTATACAAACCTAAGCAATCCAC 59.411 40.000 0.00 0.00 40.05 4.02
2654 2991 5.588648 GCTATACAAACCTAAGCAATCCACA 59.411 40.000 0.00 0.00 33.38 4.17
2655 2992 6.238484 GCTATACAAACCTAAGCAATCCACAG 60.238 42.308 0.00 0.00 33.38 3.66
2656 2993 4.098914 ACAAACCTAAGCAATCCACAGA 57.901 40.909 0.00 0.00 0.00 3.41
2657 2994 4.074970 ACAAACCTAAGCAATCCACAGAG 58.925 43.478 0.00 0.00 0.00 3.35
2658 2995 4.202461 ACAAACCTAAGCAATCCACAGAGA 60.202 41.667 0.00 0.00 0.00 3.10
2659 2996 4.640771 AACCTAAGCAATCCACAGAGAA 57.359 40.909 0.00 0.00 0.00 2.87
2660 2997 3.944087 ACCTAAGCAATCCACAGAGAAC 58.056 45.455 0.00 0.00 0.00 3.01
2661 2998 3.327757 ACCTAAGCAATCCACAGAGAACA 59.672 43.478 0.00 0.00 0.00 3.18
2662 2999 3.686726 CCTAAGCAATCCACAGAGAACAC 59.313 47.826 0.00 0.00 0.00 3.32
2663 3000 2.191128 AGCAATCCACAGAGAACACC 57.809 50.000 0.00 0.00 0.00 4.16
2664 3001 1.421268 AGCAATCCACAGAGAACACCA 59.579 47.619 0.00 0.00 0.00 4.17
2665 3002 2.158623 AGCAATCCACAGAGAACACCAA 60.159 45.455 0.00 0.00 0.00 3.67
2666 3003 2.622942 GCAATCCACAGAGAACACCAAA 59.377 45.455 0.00 0.00 0.00 3.28
2667 3004 3.550842 GCAATCCACAGAGAACACCAAAC 60.551 47.826 0.00 0.00 0.00 2.93
2668 3005 3.576078 ATCCACAGAGAACACCAAACA 57.424 42.857 0.00 0.00 0.00 2.83
2669 3006 3.358111 TCCACAGAGAACACCAAACAA 57.642 42.857 0.00 0.00 0.00 2.83
2670 3007 3.278574 TCCACAGAGAACACCAAACAAG 58.721 45.455 0.00 0.00 0.00 3.16
2671 3008 3.016736 CCACAGAGAACACCAAACAAGT 58.983 45.455 0.00 0.00 0.00 3.16
2672 3009 3.443681 CCACAGAGAACACCAAACAAGTT 59.556 43.478 0.00 0.00 0.00 2.66
2673 3010 4.438744 CCACAGAGAACACCAAACAAGTTC 60.439 45.833 0.00 0.00 41.37 3.01
2674 3011 4.155826 CACAGAGAACACCAAACAAGTTCA 59.844 41.667 0.00 0.00 43.00 3.18
2675 3012 4.396166 ACAGAGAACACCAAACAAGTTCAG 59.604 41.667 0.00 0.00 43.00 3.02
2676 3013 4.396166 CAGAGAACACCAAACAAGTTCAGT 59.604 41.667 0.00 0.00 43.00 3.41
2677 3014 4.636206 AGAGAACACCAAACAAGTTCAGTC 59.364 41.667 0.00 0.00 43.00 3.51
2678 3015 3.694566 AGAACACCAAACAAGTTCAGTCC 59.305 43.478 0.00 0.00 43.00 3.85
2679 3016 2.375146 ACACCAAACAAGTTCAGTCCC 58.625 47.619 0.00 0.00 0.00 4.46
2680 3017 1.681264 CACCAAACAAGTTCAGTCCCC 59.319 52.381 0.00 0.00 0.00 4.81
2681 3018 1.328279 CCAAACAAGTTCAGTCCCCC 58.672 55.000 0.00 0.00 0.00 5.40
2706 3043 2.486796 GCAAGGGCATCTCCAAGAC 58.513 57.895 0.00 0.00 40.72 3.01
2707 3044 1.034292 GCAAGGGCATCTCCAAGACC 61.034 60.000 0.00 0.00 40.72 3.85
2708 3045 0.745845 CAAGGGCATCTCCAAGACCG 60.746 60.000 0.00 0.00 36.21 4.79
2709 3046 0.909610 AAGGGCATCTCCAAGACCGA 60.910 55.000 0.00 0.00 36.21 4.69
2710 3047 1.153349 GGGCATCTCCAAGACCGAC 60.153 63.158 0.00 0.00 36.21 4.79
2711 3048 1.617947 GGGCATCTCCAAGACCGACT 61.618 60.000 0.00 0.00 36.21 4.18
2712 3049 0.250513 GGCATCTCCAAGACCGACTT 59.749 55.000 0.00 0.00 39.70 3.01
2713 3050 1.480954 GGCATCTCCAAGACCGACTTA 59.519 52.381 0.00 0.00 37.03 2.24
2714 3051 2.103263 GGCATCTCCAAGACCGACTTAT 59.897 50.000 0.00 0.00 37.03 1.73
2715 3052 3.385577 GCATCTCCAAGACCGACTTATC 58.614 50.000 0.00 0.00 37.03 1.75
2716 3053 3.181475 GCATCTCCAAGACCGACTTATCA 60.181 47.826 0.00 0.00 37.03 2.15
2776 3113 2.094854 ACGGTCTAGACGCGATTTCTTT 60.095 45.455 28.78 10.93 34.00 2.52
2778 3115 2.858941 GGTCTAGACGCGATTTCTTTCC 59.141 50.000 15.93 5.30 0.00 3.13
2798 3146 2.228822 CCCAAATCGAGGACAAAAGTGG 59.771 50.000 0.00 0.00 0.00 4.00
2804 3152 0.609406 GAGGACAAAAGTGGGGGAGC 60.609 60.000 0.00 0.00 0.00 4.70
2825 3173 3.782443 GACCGCTCCCAATCCCGT 61.782 66.667 0.00 0.00 0.00 5.28
2832 3181 1.408822 GCTCCCAATCCCGTTTCTGAT 60.409 52.381 0.00 0.00 0.00 2.90
2904 3261 2.707849 GCCAGCTGCCCACATTCAG 61.708 63.158 8.66 0.00 0.00 3.02
2915 3272 1.610624 CCACATTCAGGCCGTTGTAGT 60.611 52.381 0.00 0.00 0.00 2.73
2946 3303 2.047274 CATTGACGACCGCCCAGT 60.047 61.111 0.00 0.00 0.00 4.00
2971 3328 2.487428 CGACCTCTCACTGCCTCG 59.513 66.667 0.00 0.00 0.00 4.63
2983 3340 2.751436 GCCTCGGCCATTGAAGCA 60.751 61.111 2.24 0.00 34.56 3.91
3047 3408 1.600957 CTCCTTGCCGCATTCATACAG 59.399 52.381 0.00 0.00 0.00 2.74
3050 3411 2.283298 CTTGCCGCATTCATACAGTCT 58.717 47.619 0.00 0.00 0.00 3.24
3085 3450 2.177734 GGAACCCGAGAAACCTACTCT 58.822 52.381 0.00 0.00 32.87 3.24
3089 3454 1.204941 CCCGAGAAACCTACTCTGGTG 59.795 57.143 0.00 0.00 40.73 4.17
3106 3471 1.862201 GGTGACACGTTCGTTCATGAA 59.138 47.619 3.38 3.38 0.00 2.57
3107 3472 2.478894 GGTGACACGTTCGTTCATGAAT 59.521 45.455 12.12 0.00 0.00 2.57
3133 3498 0.238817 GCATTAAACACAACGCCGGA 59.761 50.000 5.05 0.00 0.00 5.14
3164 3529 6.497259 TCCTATCGTCTGCCCTCTATTTAAAT 59.503 38.462 5.89 5.89 0.00 1.40
3223 3590 1.227383 CCCCCAATTTCCTCCTCCG 59.773 63.158 0.00 0.00 0.00 4.63
3252 3619 1.167851 CGATGGCTTCCAAAGAGCAA 58.832 50.000 0.00 0.00 41.89 3.91
3258 3625 2.821969 GGCTTCCAAAGAGCAATTCTCA 59.178 45.455 7.39 0.00 44.35 3.27
3331 3699 3.916438 TTCGCTGCCCCACCTCCTA 62.916 63.158 0.00 0.00 0.00 2.94
3412 3780 1.109920 TCTAGGCCCACTCGATGAGC 61.110 60.000 0.00 0.00 32.04 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.166679 GTCTCTTCTAAGTGAGGTGGGT 58.833 50.000 0.00 0.00 0.00 4.51
15 16 5.509840 GCAAGTCCTTGTCTCTTCTAAGTGA 60.510 44.000 8.69 0.00 42.31 3.41
17 18 4.591072 AGCAAGTCCTTGTCTCTTCTAAGT 59.409 41.667 8.69 0.00 42.31 2.24
18 19 4.928615 CAGCAAGTCCTTGTCTCTTCTAAG 59.071 45.833 8.69 0.00 42.31 2.18
19 20 4.262635 CCAGCAAGTCCTTGTCTCTTCTAA 60.263 45.833 8.69 0.00 42.31 2.10
20 21 3.259374 CCAGCAAGTCCTTGTCTCTTCTA 59.741 47.826 8.69 0.00 42.31 2.10
21 22 2.038295 CCAGCAAGTCCTTGTCTCTTCT 59.962 50.000 8.69 0.00 42.31 2.85
23 24 2.038295 CTCCAGCAAGTCCTTGTCTCTT 59.962 50.000 8.69 0.00 42.31 2.85
24 25 1.622811 CTCCAGCAAGTCCTTGTCTCT 59.377 52.381 8.69 0.00 42.31 3.10
29 30 1.242076 CCAACTCCAGCAAGTCCTTG 58.758 55.000 2.63 2.63 43.14 3.61
35 36 1.067516 CCACAAACCAACTCCAGCAAG 59.932 52.381 0.00 0.00 0.00 4.01
40 41 0.257328 TGAGCCACAAACCAACTCCA 59.743 50.000 0.00 0.00 0.00 3.86
68 71 5.296780 CGGGCAAATCTTACATGTGTTCTAT 59.703 40.000 9.11 0.00 0.00 1.98
74 77 4.955925 TTACGGGCAAATCTTACATGTG 57.044 40.909 9.11 0.00 0.00 3.21
93 96 1.070038 CGTCGCTTTTACGGGCTTTA 58.930 50.000 0.00 0.00 36.71 1.85
94 97 0.881600 ACGTCGCTTTTACGGGCTTT 60.882 50.000 0.00 0.00 44.48 3.51
95 98 1.301165 ACGTCGCTTTTACGGGCTT 60.301 52.632 0.00 0.00 44.48 4.35
96 99 2.025418 CACGTCGCTTTTACGGGCT 61.025 57.895 0.00 0.00 44.48 5.19
97 100 2.472934 CACGTCGCTTTTACGGGC 59.527 61.111 0.00 0.00 44.48 6.13
98 101 0.945265 TTCCACGTCGCTTTTACGGG 60.945 55.000 0.00 0.00 44.48 5.28
99 102 0.437295 CTTCCACGTCGCTTTTACGG 59.563 55.000 0.00 0.00 44.48 4.02
100 103 1.411394 TCTTCCACGTCGCTTTTACG 58.589 50.000 0.00 0.00 45.64 3.18
101 104 3.430895 TCATTCTTCCACGTCGCTTTTAC 59.569 43.478 0.00 0.00 0.00 2.01
102 105 3.430895 GTCATTCTTCCACGTCGCTTTTA 59.569 43.478 0.00 0.00 0.00 1.52
143 146 5.499139 TTGAGTCCAACAGCTAACTTTTG 57.501 39.130 0.00 0.00 34.07 2.44
153 156 2.550978 AGTGTCGTTTGAGTCCAACAG 58.449 47.619 7.76 1.40 30.88 3.16
176 179 1.762460 CCATGGGAGGGCGTCTAGT 60.762 63.158 2.85 0.00 0.00 2.57
256 259 6.567050 ACGTTCTCCGCAGTTTTATCTTATA 58.433 36.000 0.00 0.00 41.42 0.98
258 261 4.813027 ACGTTCTCCGCAGTTTTATCTTA 58.187 39.130 0.00 0.00 41.42 2.10
259 262 3.660865 ACGTTCTCCGCAGTTTTATCTT 58.339 40.909 0.00 0.00 41.42 2.40
260 263 3.314541 ACGTTCTCCGCAGTTTTATCT 57.685 42.857 0.00 0.00 41.42 1.98
292 295 9.399403 GGTTAGTGATGTCTTTTTCTTTTCATC 57.601 33.333 0.00 0.00 34.28 2.92
377 381 3.627123 TGCAGAATAATGGTCATCCGTTG 59.373 43.478 2.43 0.00 42.29 4.10
382 386 3.881688 AGCTGTGCAGAATAATGGTCATC 59.118 43.478 3.02 0.00 0.00 2.92
399 403 2.158928 TGGCAGAAAATTGCAAAGCTGT 60.159 40.909 1.71 0.00 45.86 4.40
423 428 9.825972 AAACGAAAATTGACATATAGTGTGAAG 57.174 29.630 0.00 0.00 42.36 3.02
506 521 4.965119 ATTTTTACATCTCCCAGCGAAC 57.035 40.909 0.00 0.00 0.00 3.95
561 579 7.440856 AGAAGAAGAAGATGTCAAAGAACTGAC 59.559 37.037 0.00 0.00 45.01 3.51
562 580 7.504403 AGAAGAAGAAGATGTCAAAGAACTGA 58.496 34.615 0.00 0.00 0.00 3.41
563 581 7.727331 AGAAGAAGAAGATGTCAAAGAACTG 57.273 36.000 0.00 0.00 0.00 3.16
564 582 8.210265 AGAAGAAGAAGAAGATGTCAAAGAACT 58.790 33.333 0.00 0.00 0.00 3.01
565 583 8.376889 AGAAGAAGAAGAAGATGTCAAAGAAC 57.623 34.615 0.00 0.00 0.00 3.01
566 584 8.428063 AGAGAAGAAGAAGAAGATGTCAAAGAA 58.572 33.333 0.00 0.00 0.00 2.52
567 585 7.961351 AGAGAAGAAGAAGAAGATGTCAAAGA 58.039 34.615 0.00 0.00 0.00 2.52
568 586 8.606040 AAGAGAAGAAGAAGAAGATGTCAAAG 57.394 34.615 0.00 0.00 0.00 2.77
569 587 8.970859 AAAGAGAAGAAGAAGAAGATGTCAAA 57.029 30.769 0.00 0.00 0.00 2.69
570 588 8.970859 AAAAGAGAAGAAGAAGAAGATGTCAA 57.029 30.769 0.00 0.00 0.00 3.18
571 589 8.970859 AAAAAGAGAAGAAGAAGAAGATGTCA 57.029 30.769 0.00 0.00 0.00 3.58
594 612 8.966868 AGATGTTAAAGAACTTCCACTCAAAAA 58.033 29.630 0.00 0.00 39.45 1.94
595 613 8.519799 AGATGTTAAAGAACTTCCACTCAAAA 57.480 30.769 0.00 0.00 39.45 2.44
596 614 8.519799 AAGATGTTAAAGAACTTCCACTCAAA 57.480 30.769 0.00 0.00 39.45 2.69
597 615 7.993183 AGAAGATGTTAAAGAACTTCCACTCAA 59.007 33.333 0.00 0.00 39.45 3.02
598 616 7.509546 AGAAGATGTTAAAGAACTTCCACTCA 58.490 34.615 0.00 0.00 39.45 3.41
599 617 7.971183 AGAAGATGTTAAAGAACTTCCACTC 57.029 36.000 0.00 0.00 39.45 3.51
600 618 9.847224 TTTAGAAGATGTTAAAGAACTTCCACT 57.153 29.630 0.00 4.39 39.45 4.00
602 620 9.284968 CCTTTAGAAGATGTTAAAGAACTTCCA 57.715 33.333 0.00 0.00 39.45 3.53
603 621 8.731605 CCCTTTAGAAGATGTTAAAGAACTTCC 58.268 37.037 0.00 0.00 39.45 3.46
604 622 9.503399 TCCCTTTAGAAGATGTTAAAGAACTTC 57.497 33.333 0.00 0.00 38.53 3.01
605 623 9.862149 TTCCCTTTAGAAGATGTTAAAGAACTT 57.138 29.630 5.76 0.00 38.53 2.66
619 637 6.363357 CGCTTCAAAACATTTCCCTTTAGAAG 59.637 38.462 0.00 0.00 33.73 2.85
623 641 4.342665 ACCGCTTCAAAACATTTCCCTTTA 59.657 37.500 0.00 0.00 0.00 1.85
721 741 6.765915 AGCAAAACTAAGGATTCTCCATTC 57.234 37.500 0.00 0.00 39.61 2.67
735 756 8.931775 CAACGCCATATGTATATAGCAAAACTA 58.068 33.333 1.24 0.00 34.64 2.24
736 757 7.573096 GCAACGCCATATGTATATAGCAAAACT 60.573 37.037 1.24 0.00 29.55 2.66
737 758 6.523201 GCAACGCCATATGTATATAGCAAAAC 59.477 38.462 1.24 0.00 29.55 2.43
738 759 6.607689 GCAACGCCATATGTATATAGCAAAA 58.392 36.000 1.24 0.00 29.55 2.44
741 762 3.862845 CGCAACGCCATATGTATATAGCA 59.137 43.478 1.24 0.00 29.55 3.49
742 763 3.863424 ACGCAACGCCATATGTATATAGC 59.137 43.478 1.24 0.00 0.00 2.97
743 764 6.345803 GCATACGCAACGCCATATGTATATAG 60.346 42.308 1.24 0.00 38.36 1.31
744 765 5.460748 GCATACGCAACGCCATATGTATATA 59.539 40.000 1.24 0.00 38.36 0.86
745 766 4.270084 GCATACGCAACGCCATATGTATAT 59.730 41.667 1.24 0.00 38.36 0.86
746 767 3.615056 GCATACGCAACGCCATATGTATA 59.385 43.478 1.24 0.00 38.36 1.47
747 768 2.415168 GCATACGCAACGCCATATGTAT 59.585 45.455 1.24 0.00 38.36 2.29
868 894 0.899717 ATGCGACAAATTGGGGTGCT 60.900 50.000 0.00 0.00 0.00 4.40
872 906 3.799281 ATGTTATGCGACAAATTGGGG 57.201 42.857 0.00 0.00 32.47 4.96
878 912 2.092646 AGGCCCTATGTTATGCGACAAA 60.093 45.455 0.00 0.00 32.47 2.83
890 924 1.302033 GATCACGCCAGGCCCTATG 60.302 63.158 5.63 0.00 0.00 2.23
920 956 1.876416 CGTTGGACAAGTTGGACGGAT 60.876 52.381 7.96 0.00 0.00 4.18
990 1026 2.188524 CGAGACGTCATTGATGGACTG 58.811 52.381 19.50 2.32 33.11 3.51
1641 1689 0.315568 GCTCGACTGAGGTGTTCACT 59.684 55.000 2.98 0.00 42.79 3.41
1748 1796 2.431942 CCGTCGAACCGAACCAGG 60.432 66.667 0.00 0.00 37.72 4.45
2155 2275 2.345991 GTGCTGCTCCCCGTACAA 59.654 61.111 0.00 0.00 0.00 2.41
2232 2352 2.237392 CTCCACGAAGAATCCCTTCCTT 59.763 50.000 0.00 0.00 46.65 3.36
2407 2557 2.625488 GCGAAACCAAAATCTCGCG 58.375 52.632 0.00 0.00 46.00 5.87
2451 2601 2.431260 CGGCGCTTGCTGCAAATT 60.431 55.556 16.74 0.00 43.06 1.82
2464 2614 3.792047 CAGTGCATCACCACGGCG 61.792 66.667 4.80 4.80 40.59 6.46
2480 2630 0.908910 AACGGATACACTGCCCATCA 59.091 50.000 0.00 0.00 0.00 3.07
2481 2631 1.139058 AGAACGGATACACTGCCCATC 59.861 52.381 0.00 0.00 0.00 3.51
2484 2634 1.090052 GCAGAACGGATACACTGCCC 61.090 60.000 0.00 0.00 45.53 5.36
2485 2635 2.384203 GCAGAACGGATACACTGCC 58.616 57.895 0.00 0.00 45.53 4.85
2486 2636 0.457853 TCGCAGAACGGATACACTGC 60.458 55.000 0.00 0.00 46.74 4.40
2497 2825 0.871057 AAGAAAGCTGCTCGCAGAAC 59.129 50.000 22.09 5.81 46.30 3.01
2522 2850 1.523758 GAGCCGAACACTGATGGTTT 58.476 50.000 0.00 0.00 0.00 3.27
2531 2859 1.671379 GAACAGGGGAGCCGAACAC 60.671 63.158 0.00 0.00 0.00 3.32
2532 2860 2.747686 GAACAGGGGAGCCGAACA 59.252 61.111 0.00 0.00 0.00 3.18
2533 2861 2.046217 GGAACAGGGGAGCCGAAC 60.046 66.667 0.00 0.00 0.00 3.95
2547 2875 6.154877 ACATCATGGTTTCTATGCAAATGGAA 59.845 34.615 0.00 0.00 0.00 3.53
2561 2889 8.812513 TGAATCTTATCTGAACATCATGGTTT 57.187 30.769 0.00 0.00 0.00 3.27
2564 2892 7.172875 GGTCTGAATCTTATCTGAACATCATGG 59.827 40.741 0.00 0.00 35.67 3.66
2565 2893 7.713942 TGGTCTGAATCTTATCTGAACATCATG 59.286 37.037 0.00 0.00 39.25 3.07
2567 2895 7.186570 TGGTCTGAATCTTATCTGAACATCA 57.813 36.000 0.00 0.00 39.25 3.07
2568 2896 6.202570 GCTGGTCTGAATCTTATCTGAACATC 59.797 42.308 2.99 0.00 41.98 3.06
2569 2897 6.054295 GCTGGTCTGAATCTTATCTGAACAT 58.946 40.000 2.99 0.00 41.98 2.71
2570 2898 5.423015 GCTGGTCTGAATCTTATCTGAACA 58.577 41.667 2.65 2.65 41.07 3.18
2596 2928 0.678950 CTTGGTTTGGATTTGGCCGT 59.321 50.000 0.00 0.00 0.00 5.68
2605 2937 7.441017 CATGTTTCTATTTTCCTTGGTTTGGA 58.559 34.615 0.00 0.00 0.00 3.53
2609 2941 6.670695 AGCATGTTTCTATTTTCCTTGGTT 57.329 33.333 0.00 0.00 0.00 3.67
2610 2942 7.961326 ATAGCATGTTTCTATTTTCCTTGGT 57.039 32.000 0.00 0.00 0.00 3.67
2611 2943 8.902806 TGTATAGCATGTTTCTATTTTCCTTGG 58.097 33.333 0.00 0.00 0.00 3.61
2645 2982 1.896220 TGGTGTTCTCTGTGGATTGC 58.104 50.000 0.00 0.00 0.00 3.56
2646 2983 3.631686 TGTTTGGTGTTCTCTGTGGATTG 59.368 43.478 0.00 0.00 0.00 2.67
2647 2984 3.897239 TGTTTGGTGTTCTCTGTGGATT 58.103 40.909 0.00 0.00 0.00 3.01
2648 2985 3.576078 TGTTTGGTGTTCTCTGTGGAT 57.424 42.857 0.00 0.00 0.00 3.41
2649 2986 3.278574 CTTGTTTGGTGTTCTCTGTGGA 58.721 45.455 0.00 0.00 0.00 4.02
2650 2987 3.016736 ACTTGTTTGGTGTTCTCTGTGG 58.983 45.455 0.00 0.00 0.00 4.17
2651 2988 4.155826 TGAACTTGTTTGGTGTTCTCTGTG 59.844 41.667 0.00 0.00 40.27 3.66
2652 2989 4.331968 TGAACTTGTTTGGTGTTCTCTGT 58.668 39.130 0.00 0.00 40.27 3.41
2653 2990 4.396166 ACTGAACTTGTTTGGTGTTCTCTG 59.604 41.667 0.00 0.00 40.27 3.35
2654 2991 4.589908 ACTGAACTTGTTTGGTGTTCTCT 58.410 39.130 0.00 0.00 40.27 3.10
2655 2992 4.201920 GGACTGAACTTGTTTGGTGTTCTC 60.202 45.833 0.00 0.00 40.27 2.87
2656 2993 3.694566 GGACTGAACTTGTTTGGTGTTCT 59.305 43.478 0.00 0.00 40.27 3.01
2657 2994 3.181490 GGGACTGAACTTGTTTGGTGTTC 60.181 47.826 0.00 0.00 40.09 3.18
2658 2995 2.758423 GGGACTGAACTTGTTTGGTGTT 59.242 45.455 0.00 0.00 0.00 3.32
2659 2996 2.375146 GGGACTGAACTTGTTTGGTGT 58.625 47.619 0.00 0.00 0.00 4.16
2660 2997 1.681264 GGGGACTGAACTTGTTTGGTG 59.319 52.381 0.00 0.00 0.00 4.17
2661 2998 1.411074 GGGGGACTGAACTTGTTTGGT 60.411 52.381 0.00 0.00 0.00 3.67
2662 2999 1.328279 GGGGGACTGAACTTGTTTGG 58.672 55.000 0.00 0.00 0.00 3.28
2688 3025 1.034292 GGTCTTGGAGATGCCCTTGC 61.034 60.000 0.00 0.00 34.97 4.01
2689 3026 0.745845 CGGTCTTGGAGATGCCCTTG 60.746 60.000 0.00 0.00 34.97 3.61
2690 3027 0.909610 TCGGTCTTGGAGATGCCCTT 60.910 55.000 0.00 0.00 34.97 3.95
2691 3028 1.306141 TCGGTCTTGGAGATGCCCT 60.306 57.895 0.00 0.00 34.97 5.19
2692 3029 1.153349 GTCGGTCTTGGAGATGCCC 60.153 63.158 0.00 0.00 34.97 5.36
2693 3030 0.250513 AAGTCGGTCTTGGAGATGCC 59.749 55.000 0.00 0.00 34.77 4.40
2694 3031 2.961526 TAAGTCGGTCTTGGAGATGC 57.038 50.000 0.00 0.00 37.56 3.91
2695 3032 4.363999 GTGATAAGTCGGTCTTGGAGATG 58.636 47.826 0.00 0.00 37.56 2.90
2696 3033 3.066900 CGTGATAAGTCGGTCTTGGAGAT 59.933 47.826 0.00 0.00 37.56 2.75
2697 3034 2.422479 CGTGATAAGTCGGTCTTGGAGA 59.578 50.000 0.00 0.00 37.56 3.71
2698 3035 2.479730 CCGTGATAAGTCGGTCTTGGAG 60.480 54.545 0.00 0.00 41.58 3.86
2699 3036 1.475280 CCGTGATAAGTCGGTCTTGGA 59.525 52.381 0.00 0.00 41.58 3.53
2700 3037 1.475280 TCCGTGATAAGTCGGTCTTGG 59.525 52.381 3.64 0.00 45.88 3.61
2701 3038 2.933495 TCCGTGATAAGTCGGTCTTG 57.067 50.000 3.64 0.00 45.88 3.02
2702 3039 2.416972 GCTTCCGTGATAAGTCGGTCTT 60.417 50.000 3.64 0.00 45.88 3.01
2703 3040 1.134560 GCTTCCGTGATAAGTCGGTCT 59.865 52.381 3.64 0.00 45.88 3.85
2704 3041 1.557651 GCTTCCGTGATAAGTCGGTC 58.442 55.000 3.64 0.00 45.88 4.79
2705 3042 0.175073 GGCTTCCGTGATAAGTCGGT 59.825 55.000 3.64 0.00 45.88 4.69
2706 3043 0.174845 TGGCTTCCGTGATAAGTCGG 59.825 55.000 0.00 0.00 46.93 4.79
2707 3044 2.128035 GATGGCTTCCGTGATAAGTCG 58.872 52.381 0.00 0.00 31.05 4.18
2708 3045 2.484889 GGATGGCTTCCGTGATAAGTC 58.515 52.381 3.39 0.00 33.93 3.01
2709 3046 2.622064 GGATGGCTTCCGTGATAAGT 57.378 50.000 3.39 0.00 33.93 2.24
2748 3085 1.466866 CGCGTCTAGACCGTTTCATGA 60.467 52.381 17.23 0.00 0.00 3.07
2753 3090 2.094854 AGAAATCGCGTCTAGACCGTTT 60.095 45.455 23.88 21.84 0.00 3.60
2776 3113 3.146066 CACTTTTGTCCTCGATTTGGGA 58.854 45.455 0.00 0.00 0.00 4.37
2778 3115 2.228822 CCCACTTTTGTCCTCGATTTGG 59.771 50.000 0.00 0.00 0.00 3.28
2786 3123 1.460699 GCTCCCCCACTTTTGTCCT 59.539 57.895 0.00 0.00 0.00 3.85
2787 3124 1.606601 GGCTCCCCCACTTTTGTCC 60.607 63.158 0.00 0.00 0.00 4.02
2804 3152 4.547367 GATTGGGAGCGGTCCGGG 62.547 72.222 26.31 0.00 45.05 5.73
2820 3168 1.987855 AGGGCGATCAGAAACGGGA 60.988 57.895 0.00 0.00 0.00 5.14
2825 3173 1.198094 TGGGTCAGGGCGATCAGAAA 61.198 55.000 0.00 0.00 0.00 2.52
2832 3181 2.285889 TTTTTGGTGGGTCAGGGCGA 62.286 55.000 0.00 0.00 0.00 5.54
2897 3254 1.808411 CACTACAACGGCCTGAATGT 58.192 50.000 0.00 8.30 0.00 2.71
2946 3303 4.710167 TGAGAGGTCGCGTCCGGA 62.710 66.667 16.59 0.00 34.56 5.14
2971 3328 2.180017 CACGCTGCTTCAATGGCC 59.820 61.111 0.00 0.00 0.00 5.36
3017 3378 1.033746 CGGCAAGGAGGCATGTTCAT 61.034 55.000 0.00 0.00 44.47 2.57
3047 3408 1.087771 CCACGCGGGGTTAATGAGAC 61.088 60.000 22.33 0.00 0.00 3.36
3050 3411 0.674269 GTTCCACGCGGGGTTAATGA 60.674 55.000 29.71 2.91 37.22 2.57
3085 3450 1.202428 TCATGAACGAACGTGTCACCA 60.202 47.619 0.00 0.00 0.00 4.17
3089 3454 2.159707 CCCATTCATGAACGAACGTGTC 60.160 50.000 11.07 2.27 0.00 3.67
3106 3471 0.613292 TGTGTTTAATGCCGGCCCAT 60.613 50.000 26.77 9.10 0.00 4.00
3107 3472 0.827925 TTGTGTTTAATGCCGGCCCA 60.828 50.000 26.77 6.41 0.00 5.36
3331 3699 3.023949 GCTCCGTCAGGTGAGGCAT 62.024 63.158 0.00 0.00 39.05 4.40
3412 3780 2.031012 TCGAGCAACTGGCCACTG 59.969 61.111 0.00 3.00 46.50 3.66


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

AutoCloner maintained by Alex Coulton.