Multiple sequence alignment - TraesCS2D01G465300

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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 TraesCS2D01G465300 chr2D 100.000 7263 0 0 1 7263 571193838 571201100 0.000000e+00 13413
1 TraesCS2D01G465300 chr2D 85.695 2901 377 22 1533 4423 571209185 571212057 0.000000e+00 3024
2 TraesCS2D01G465300 chr2D 84.028 2905 410 36 1543 4420 571443443 571446320 0.000000e+00 2745
3 TraesCS2D01G465300 chr2D 83.075 2647 368 50 711 3318 571526376 571528981 0.000000e+00 2333
4 TraesCS2D01G465300 chr2D 79.898 2746 435 64 4423 7087 571212084 571214793 0.000000e+00 1905
5 TraesCS2D01G465300 chr2D 80.655 2259 367 51 4442 6650 571530171 571532409 0.000000e+00 1687
6 TraesCS2D01G465300 chr2D 84.327 587 81 9 113 694 645479955 645479375 1.370000e-156 564
7 TraesCS2D01G465300 chr2D 86.432 398 54 0 4443 4840 571446370 571446767 3.110000e-118 436
8 TraesCS2D01G465300 chr2B 92.289 5758 396 31 1529 7263 683043164 683048896 0.000000e+00 8130
9 TraesCS2D01G465300 chr2B 83.929 5034 716 58 1564 6543 683067906 683072900 0.000000e+00 4728
10 TraesCS2D01G465300 chr2B 83.437 2904 424 36 1543 4420 683159759 683162631 0.000000e+00 2645
11 TraesCS2D01G465300 chr2B 83.278 2422 367 23 911 3318 683127777 683130174 0.000000e+00 2194
12 TraesCS2D01G465300 chr2B 88.187 1456 160 9 3347 4797 683056128 683057576 0.000000e+00 1725
13 TraesCS2D01G465300 chr2B 81.814 2040 308 40 4557 6553 794691214 794689195 0.000000e+00 1653
14 TraesCS2D01G465300 chr2B 81.814 2040 308 40 4557 6553 794800115 794798096 0.000000e+00 1653
15 TraesCS2D01G465300 chr2B 83.018 1743 262 22 4825 6543 683057571 683059303 0.000000e+00 1548
16 TraesCS2D01G465300 chr2B 83.058 1694 259 24 4876 6550 683132069 683133753 0.000000e+00 1513
17 TraesCS2D01G465300 chr2B 85.663 1381 145 33 12 1356 683041695 683043058 0.000000e+00 1404
18 TraesCS2D01G465300 chr2B 86.988 1099 134 5 3328 4420 683130214 683131309 0.000000e+00 1229
19 TraesCS2D01G465300 chr2B 87.585 733 87 4 4423 5153 683131339 683132069 0.000000e+00 846
20 TraesCS2D01G465300 chr2B 90.611 458 39 3 911 1364 683067316 683067773 8.060000e-169 604
21 TraesCS2D01G465300 chr2B 87.745 408 49 1 951 1358 683053771 683054177 6.590000e-130 475
22 TraesCS2D01G465300 chr2B 83.507 479 71 6 884 1359 794696863 794696390 2.410000e-119 440
23 TraesCS2D01G465300 chr2B 83.193 119 20 0 6306 6424 683074161 683074279 7.700000e-20 110
24 TraesCS2D01G465300 chr2A 95.411 3334 113 22 3960 7263 709858411 709861734 0.000000e+00 5273
25 TraesCS2D01G465300 chr2A 85.706 4883 597 55 1529 6357 710093251 710098086 0.000000e+00 5057
26 TraesCS2D01G465300 chr2A 85.665 2902 376 24 1533 4423 710036399 710039271 0.000000e+00 3018
27 TraesCS2D01G465300 chr2A 85.784 2448 305 24 1529 3965 709850452 709852867 0.000000e+00 2553
28 TraesCS2D01G465300 chr2A 82.867 1967 322 10 4423 6379 710039298 710041259 0.000000e+00 1751
29 TraesCS2D01G465300 chr2A 87.525 1475 172 9 3328 4797 710189963 710191430 0.000000e+00 1694
30 TraesCS2D01G465300 chr2A 87.721 1360 123 14 12 1356 710091815 710093145 0.000000e+00 1546
31 TraesCS2D01G465300 chr2A 86.763 1390 127 24 10 1356 709849009 709850384 0.000000e+00 1495
32 TraesCS2D01G465300 chr2A 82.814 1059 168 10 5332 6379 710041877 710042932 0.000000e+00 935
33 TraesCS2D01G465300 chr2A 88.480 408 47 0 951 1358 710035892 710036299 1.820000e-135 494
34 TraesCS2D01G465300 chr2A 80.504 595 90 19 813 1393 710187179 710187761 4.020000e-117 433
35 TraesCS2D01G465300 chr6B 85.381 643 92 2 4938 5579 717745534 717744893 0.000000e+00 665
36 TraesCS2D01G465300 chr6B 84.407 590 81 9 110 694 149349730 149350313 2.940000e-158 569
37 TraesCS2D01G465300 chr6B 81.818 319 48 8 4423 4736 717745848 717745535 7.230000e-65 259
38 TraesCS2D01G465300 chr7A 84.497 587 80 9 113 694 476374037 476373457 2.940000e-158 569
39 TraesCS2D01G465300 chr7A 83.729 590 85 10 110 694 67885238 67885821 1.380000e-151 547
40 TraesCS2D01G465300 chr6A 84.512 594 72 10 110 694 402590040 402590622 2.940000e-158 569
41 TraesCS2D01G465300 chr6A 84.157 587 82 9 113 694 69497795 69497215 6.360000e-155 558
42 TraesCS2D01G465300 chr7D 83.108 592 84 13 110 694 271124871 271125453 6.450000e-145 525
43 TraesCS2D01G465300 chrUn 83.613 476 70 6 884 1356 332504351 332504821 2.410000e-119 440
44 TraesCS2D01G465300 chr7B 85.258 407 52 6 292 694 648997957 648997555 5.240000e-111 412
45 TraesCS2D01G465300 chr3B 84.521 407 55 6 292 694 644366988 644367390 5.280000e-106 396
46 TraesCS2D01G465300 chr4A 82.609 414 64 7 113 524 700680510 700680103 6.930000e-95 359


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 TraesCS2D01G465300 chr2D 571193838 571201100 7262 False 13413.000000 13413 100.000000 1 7263 1 chr2D.!!$F1 7262
1 TraesCS2D01G465300 chr2D 571209185 571214793 5608 False 2464.500000 3024 82.796500 1533 7087 2 chr2D.!!$F2 5554
2 TraesCS2D01G465300 chr2D 571526376 571532409 6033 False 2010.000000 2333 81.865000 711 6650 2 chr2D.!!$F4 5939
3 TraesCS2D01G465300 chr2D 571443443 571446767 3324 False 1590.500000 2745 85.230000 1543 4840 2 chr2D.!!$F3 3297
4 TraesCS2D01G465300 chr2D 645479375 645479955 580 True 564.000000 564 84.327000 113 694 1 chr2D.!!$R1 581
5 TraesCS2D01G465300 chr2B 683041695 683048896 7201 False 4767.000000 8130 88.976000 12 7263 2 chr2B.!!$F2 7251
6 TraesCS2D01G465300 chr2B 683159759 683162631 2872 False 2645.000000 2645 83.437000 1543 4420 1 chr2B.!!$F1 2877
7 TraesCS2D01G465300 chr2B 683067316 683074279 6963 False 1814.000000 4728 85.911000 911 6543 3 chr2B.!!$F4 5632
8 TraesCS2D01G465300 chr2B 794689195 794691214 2019 True 1653.000000 1653 81.814000 4557 6553 1 chr2B.!!$R1 1996
9 TraesCS2D01G465300 chr2B 794798096 794800115 2019 True 1653.000000 1653 81.814000 4557 6553 1 chr2B.!!$R3 1996
10 TraesCS2D01G465300 chr2B 683127777 683133753 5976 False 1445.500000 2194 85.227250 911 6550 4 chr2B.!!$F5 5639
11 TraesCS2D01G465300 chr2B 683053771 683059303 5532 False 1249.333333 1725 86.316667 951 6543 3 chr2B.!!$F3 5592
12 TraesCS2D01G465300 chr2A 709858411 709861734 3323 False 5273.000000 5273 95.411000 3960 7263 1 chr2A.!!$F1 3303
13 TraesCS2D01G465300 chr2A 710091815 710098086 6271 False 3301.500000 5057 86.713500 12 6357 2 chr2A.!!$F4 6345
14 TraesCS2D01G465300 chr2A 709849009 709852867 3858 False 2024.000000 2553 86.273500 10 3965 2 chr2A.!!$F2 3955
15 TraesCS2D01G465300 chr2A 710035892 710042932 7040 False 1549.500000 3018 84.956500 951 6379 4 chr2A.!!$F3 5428
16 TraesCS2D01G465300 chr2A 710187179 710191430 4251 False 1063.500000 1694 84.014500 813 4797 2 chr2A.!!$F5 3984
17 TraesCS2D01G465300 chr6B 149349730 149350313 583 False 569.000000 569 84.407000 110 694 1 chr6B.!!$F1 584
18 TraesCS2D01G465300 chr6B 717744893 717745848 955 True 462.000000 665 83.599500 4423 5579 2 chr6B.!!$R1 1156
19 TraesCS2D01G465300 chr7A 476373457 476374037 580 True 569.000000 569 84.497000 113 694 1 chr7A.!!$R1 581
20 TraesCS2D01G465300 chr7A 67885238 67885821 583 False 547.000000 547 83.729000 110 694 1 chr7A.!!$F1 584
21 TraesCS2D01G465300 chr6A 402590040 402590622 582 False 569.000000 569 84.512000 110 694 1 chr6A.!!$F1 584
22 TraesCS2D01G465300 chr6A 69497215 69497795 580 True 558.000000 558 84.157000 113 694 1 chr6A.!!$R1 581
23 TraesCS2D01G465300 chr7D 271124871 271125453 582 False 525.000000 525 83.108000 110 694 1 chr7D.!!$F1 584

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
851 905 0.030101 TTAGCTGCGTTTTGGTGCAC 59.970 50.0 8.80 8.8 35.90 4.57 F
856 910 0.179150 TGCGTTTTGGTGCACTGTTC 60.179 50.0 17.98 0.0 35.90 3.18 F
2390 2794 0.250727 TCCTGGCTCCGTTGAAAAGG 60.251 55.0 0.00 0.0 0.00 3.11 F
2930 3338 0.110486 TGGACTTGGGCTTCTTCCAC 59.890 55.0 0.00 0.0 33.43 4.02 F
3060 3468 0.238289 AAGCGTTCGCCATTTGTCAG 59.762 50.0 13.54 0.0 0.00 3.51 F
3829 4282 0.477597 TCCCCAACCTGGTTCTCCAT 60.478 55.0 9.62 0.0 43.43 3.41 F
4521 5008 0.523519 CCTTTTCCGCCTTCTGCTTC 59.476 55.0 0.00 0.0 38.05 3.86 F
5189 5962 1.064003 TTGCCCCAAGCTACTCTCAA 58.936 50.0 0.00 0.0 44.23 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2468 2873 1.201647 TCGAGACCATTCACTTCGACC 59.798 52.381 0.00 0.0 0.00 4.79 R
2786 3194 2.196595 TCAAATGGGTAGTCCTCTGGG 58.803 52.381 0.00 0.0 36.20 4.45 R
3809 4262 0.477597 TGGAGAACCAGGTTGGGGAT 60.478 55.000 10.47 0.0 43.37 3.85 R
3871 4324 0.614812 AATTTGCCATTCCCTGCACC 59.385 50.000 0.00 0.0 37.18 5.01 R
4965 5732 3.007614 CCCTTCCGTTTCTCTAGGTTGAA 59.992 47.826 0.00 0.0 0.00 2.69 R
5703 6479 1.879380 CGCAGTCTCCAATTTCCAACA 59.121 47.619 0.00 0.0 0.00 3.33 R
6161 6953 2.576191 TGCAATAGGCTACCTCAAGGTT 59.424 45.455 7.07 0.0 45.08 3.50 R
6610 7475 8.398665 CCACTAACAAAGCTAATCAGGATAAAC 58.601 37.037 0.00 0.0 0.00 2.01 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
60 61 2.579873 CAGATTACCCATTCCTGCAGG 58.420 52.381 27.87 27.87 0.00 4.85
145 177 4.767409 GGTTCCTACTGCCTTCAGAATTTT 59.233 41.667 0.00 0.00 42.95 1.82
149 181 4.397417 CCTACTGCCTTCAGAATTTTGGAG 59.603 45.833 0.00 0.00 42.95 3.86
192 224 0.179084 TTTGGGAATCTCTAGGCGCG 60.179 55.000 0.00 0.00 0.00 6.86
210 242 1.356624 GCCGCATTCAAGGAATCGG 59.643 57.895 17.58 17.58 41.20 4.18
290 323 2.292103 TTTTGTTGACAGGCACAAGC 57.708 45.000 0.00 0.00 41.10 4.01
312 345 6.006449 AGCTTGTGTAGAAACCATCAAGATT 58.994 36.000 0.00 0.00 33.57 2.40
344 378 2.723124 AATTTGTCGATGGGTGCAAC 57.277 45.000 0.00 0.00 0.00 4.17
364 398 0.453793 CGTGCAAGGTTGTGGAAACA 59.546 50.000 0.00 0.00 38.70 2.83
367 401 2.865551 GTGCAAGGTTGTGGAAACAATG 59.134 45.455 0.00 0.00 46.06 2.82
376 415 2.562298 TGTGGAAACAATGGAAGCATCC 59.438 45.455 0.00 0.00 46.06 3.51
391 430 1.537202 GCATCCCATTAGATTGTCGCC 59.463 52.381 0.00 0.00 0.00 5.54
400 439 1.112113 AGATTGTCGCCAGGTACGAT 58.888 50.000 0.00 0.00 42.26 3.73
405 444 0.108992 GTCGCCAGGTACGATGTTGA 60.109 55.000 0.00 0.00 42.26 3.18
437 476 1.880027 AGGAACCATCAACGTCAAAGC 59.120 47.619 0.00 0.00 0.00 3.51
443 482 3.684788 ACCATCAACGTCAAAGCATCTAC 59.315 43.478 0.00 0.00 0.00 2.59
444 483 3.063997 CCATCAACGTCAAAGCATCTACC 59.936 47.826 0.00 0.00 0.00 3.18
466 505 5.130477 ACCGAGGATTCAATTTAAGCCTAGA 59.870 40.000 15.71 0.00 45.10 2.43
474 513 8.845413 ATTCAATTTAAGCCTAGAGATAGCAG 57.155 34.615 0.00 0.00 0.00 4.24
478 517 3.320610 AAGCCTAGAGATAGCAGGACA 57.679 47.619 0.00 0.00 0.00 4.02
510 549 4.202524 TGTTTTGTCCCCTACTGCTTGTAT 60.203 41.667 0.00 0.00 0.00 2.29
546 585 2.808202 GCATATGCGTCCACAGATTCCT 60.808 50.000 12.82 0.00 0.00 3.36
610 650 2.945668 GGCTCAGCTTCCACGAAAATAT 59.054 45.455 0.00 0.00 0.00 1.28
616 659 6.148948 TCAGCTTCCACGAAAATATTTTGTG 58.851 36.000 17.98 21.14 33.27 3.33
617 660 5.345741 CAGCTTCCACGAAAATATTTTGTGG 59.654 40.000 31.44 31.44 43.16 4.17
619 662 5.118510 GCTTCCACGAAAATATTTTGTGGTG 59.881 40.000 33.08 29.25 42.81 4.17
629 672 9.482627 GAAAATATTTTGTGGTGGTCATGTAAA 57.517 29.630 17.98 0.00 0.00 2.01
651 694 7.396540 AAAATCATAAGCTCGTCTTTTCCAT 57.603 32.000 0.00 0.00 36.25 3.41
701 744 8.602472 ATCAGTAAAGAGGAGTCTATTTCAGT 57.398 34.615 0.00 0.00 36.10 3.41
702 745 8.057536 TCAGTAAAGAGGAGTCTATTTCAGTC 57.942 38.462 0.00 0.00 36.10 3.51
703 746 7.670140 TCAGTAAAGAGGAGTCTATTTCAGTCA 59.330 37.037 0.00 0.00 36.10 3.41
708 751 7.962995 AGAGGAGTCTATTTCAGTCATACAA 57.037 36.000 0.00 0.00 0.00 2.41
709 752 8.546083 AGAGGAGTCTATTTCAGTCATACAAT 57.454 34.615 0.00 0.00 0.00 2.71
730 784 1.490490 ACTGTGGAGCCAAGACTTGAA 59.510 47.619 16.99 0.00 0.00 2.69
839 893 4.153655 GTGTTACCTGGTAAAGTTAGCTGC 59.846 45.833 20.28 6.06 29.42 5.25
851 905 0.030101 TTAGCTGCGTTTTGGTGCAC 59.970 50.000 8.80 8.80 35.90 4.57
856 910 0.179150 TGCGTTTTGGTGCACTGTTC 60.179 50.000 17.98 0.00 35.90 3.18
870 943 3.366422 GCACTGTTCGACTCTTCTCATTC 59.634 47.826 0.00 0.00 0.00 2.67
913 996 3.567397 TGGTTCACTATAGCTCTCTCCC 58.433 50.000 0.00 0.00 0.00 4.30
939 1023 3.138283 AGTCCATCTGTTTGGTTTCTCCA 59.862 43.478 0.00 0.00 45.60 3.86
954 1038 2.203394 CCACTGTGCAAGGCCTGT 60.203 61.111 5.69 0.00 0.00 4.00
978 1062 1.078143 CTCCTGCTGTTACTGGGCC 60.078 63.158 0.00 0.00 0.00 5.80
993 1081 4.715523 GCCGCCTTAGGTGTGCCA 62.716 66.667 11.18 0.00 37.19 4.92
1038 1126 1.340889 ACGGTTGTTGATGCAGCAATT 59.659 42.857 21.76 0.00 36.98 2.32
1102 1190 2.029623 GTATGGAAGCCTGGACTCGTA 58.970 52.381 0.00 0.00 0.00 3.43
1330 1418 3.914312 TCATTCGTCTCTCTTGTTCCAC 58.086 45.455 0.00 0.00 0.00 4.02
1363 1720 8.748412 TGCTTTCAGCTTATTTTATATTGGTGT 58.252 29.630 0.00 0.00 42.97 4.16
1364 1721 9.023967 GCTTTCAGCTTATTTTATATTGGTGTG 57.976 33.333 0.00 0.00 38.45 3.82
1367 1724 9.461312 TTCAGCTTATTTTATATTGGTGTGACT 57.539 29.630 0.00 0.00 0.00 3.41
1368 1725 8.892723 TCAGCTTATTTTATATTGGTGTGACTG 58.107 33.333 0.00 0.00 0.00 3.51
1369 1726 8.677300 CAGCTTATTTTATATTGGTGTGACTGT 58.323 33.333 0.00 0.00 0.00 3.55
1370 1727 8.677300 AGCTTATTTTATATTGGTGTGACTGTG 58.323 33.333 0.00 0.00 0.00 3.66
1371 1728 8.673711 GCTTATTTTATATTGGTGTGACTGTGA 58.326 33.333 0.00 0.00 0.00 3.58
1373 1730 6.494893 TTTTATATTGGTGTGACTGTGAGC 57.505 37.500 0.00 0.00 0.00 4.26
1374 1731 2.078849 TATTGGTGTGACTGTGAGCG 57.921 50.000 0.00 0.00 0.00 5.03
1375 1732 1.230635 ATTGGTGTGACTGTGAGCGC 61.231 55.000 0.00 0.00 0.00 5.92
1376 1733 2.029666 GGTGTGACTGTGAGCGCT 59.970 61.111 11.27 11.27 0.00 5.92
1377 1734 2.313172 GGTGTGACTGTGAGCGCTG 61.313 63.158 18.48 1.67 0.00 5.18
1378 1735 2.662857 TGTGACTGTGAGCGCTGC 60.663 61.111 18.48 8.36 0.00 5.25
1379 1736 2.356793 GTGACTGTGAGCGCTGCT 60.357 61.111 18.48 2.68 43.88 4.24
1380 1737 1.958205 GTGACTGTGAGCGCTGCTT 60.958 57.895 18.48 0.00 39.88 3.91
1381 1738 1.957695 TGACTGTGAGCGCTGCTTG 60.958 57.895 18.48 4.93 39.88 4.01
1382 1739 2.667536 ACTGTGAGCGCTGCTTGG 60.668 61.111 18.48 3.28 39.88 3.61
1383 1740 2.357881 CTGTGAGCGCTGCTTGGA 60.358 61.111 18.48 0.00 39.88 3.53
1384 1741 2.357881 TGTGAGCGCTGCTTGGAG 60.358 61.111 18.48 0.00 39.88 3.86
1385 1742 2.358003 GTGAGCGCTGCTTGGAGT 60.358 61.111 18.48 0.00 39.88 3.85
1386 1743 1.079819 GTGAGCGCTGCTTGGAGTA 60.080 57.895 18.48 0.00 39.88 2.59
1387 1744 0.460987 GTGAGCGCTGCTTGGAGTAT 60.461 55.000 18.48 0.00 39.88 2.12
1388 1745 1.111277 TGAGCGCTGCTTGGAGTATA 58.889 50.000 18.48 0.00 39.88 1.47
1389 1746 1.067669 TGAGCGCTGCTTGGAGTATAG 59.932 52.381 18.48 0.00 39.88 1.31
1390 1747 1.067821 GAGCGCTGCTTGGAGTATAGT 59.932 52.381 18.48 0.00 39.88 2.12
1391 1748 1.482593 AGCGCTGCTTGGAGTATAGTT 59.517 47.619 10.39 0.00 33.89 2.24
1399 1756 7.522374 GCTGCTTGGAGTATAGTTTAATATGC 58.478 38.462 0.00 0.00 0.00 3.14
1414 1799 4.644103 AATATGCAACCATGAACAGCTC 57.356 40.909 0.00 0.00 32.85 4.09
1429 1814 5.704053 TGAACAGCTCAATATCATAGGCATG 59.296 40.000 0.00 0.00 0.00 4.06
1514 1902 1.400737 TCCTAGGCGAAAGGTAGAGC 58.599 55.000 2.96 0.00 35.48 4.09
1515 1903 1.063867 TCCTAGGCGAAAGGTAGAGCT 60.064 52.381 2.96 0.00 35.48 4.09
1538 1926 6.633500 TGTCTTTACCTCATGGAACTTTTG 57.367 37.500 0.00 0.00 37.04 2.44
1587 1975 8.424274 AATAATATTTGCCTTTGCTTAAGTGC 57.576 30.769 4.02 0.86 38.71 4.40
1602 1990 5.333568 GCTTAAGTGCTTTTCATTTGCTTGG 60.334 40.000 4.02 0.00 0.00 3.61
1604 1992 2.103601 AGTGCTTTTCATTTGCTTGGCT 59.896 40.909 0.00 0.00 0.00 4.75
1609 2000 4.565564 GCTTTTCATTTGCTTGGCTCATAG 59.434 41.667 0.00 0.00 0.00 2.23
1684 2081 3.054802 CCTGAGGGAAGCTATGTGTTCTT 60.055 47.826 0.00 0.00 33.58 2.52
1725 2122 3.314080 TGTTAAATTAGTATGCAGCGCCC 59.686 43.478 2.29 0.00 0.00 6.13
1793 2190 3.791586 GAGGAGGGGCCAGCTCAC 61.792 72.222 4.39 0.00 40.02 3.51
1872 2269 8.894768 AATAGTGATTCTTCTATGCAGTAACC 57.105 34.615 0.00 0.00 0.00 2.85
1939 2336 4.623932 TGGCAACATCAAGTAAGAGTCT 57.376 40.909 0.00 0.00 46.17 3.24
1940 2337 4.569943 TGGCAACATCAAGTAAGAGTCTC 58.430 43.478 0.00 0.00 46.17 3.36
1954 2351 5.379706 AAGAGTCTCAATATTTCCAGGGG 57.620 43.478 1.94 0.00 0.00 4.79
1989 2386 5.180117 ACAACTTCTGTTCCGATTGAATCTG 59.820 40.000 3.43 0.00 32.99 2.90
2021 2418 4.081752 GGAAGAGATGCAGAGAGAGACAAA 60.082 45.833 0.00 0.00 0.00 2.83
2045 2442 2.165357 TAGAGCTGCTGAGGAATGGA 57.835 50.000 7.01 0.00 0.00 3.41
2197 2594 4.141733 TGTGTCCACTGACTTCAATGAAGA 60.142 41.667 27.63 7.08 41.71 2.87
2297 2701 5.009410 ACTGCAGAACATCCTTTTGAAGAAG 59.991 40.000 23.35 0.00 0.00 2.85
2336 2740 6.459670 TTTCTGCTTGTACTGGACGATATA 57.540 37.500 0.00 0.00 0.00 0.86
2347 2751 4.524714 ACTGGACGATATATGGGAAGACAG 59.475 45.833 0.00 0.00 0.00 3.51
2360 2764 1.548269 GAAGACAGAGACAGGAGTGGG 59.452 57.143 0.00 0.00 0.00 4.61
2390 2794 0.250727 TCCTGGCTCCGTTGAAAAGG 60.251 55.000 0.00 0.00 0.00 3.11
2401 2806 3.735746 CCGTTGAAAAGGAATCAAGCAAC 59.264 43.478 0.00 0.00 37.46 4.17
2464 2869 6.357579 TGCAAAAATGATAGGAACAATGGT 57.642 33.333 0.00 0.00 0.00 3.55
2468 2873 7.063780 GCAAAAATGATAGGAACAATGGTTGAG 59.936 37.037 0.00 0.00 37.36 3.02
2472 2877 2.185004 AGGAACAATGGTTGAGGTCG 57.815 50.000 0.00 0.00 37.36 4.79
2492 2897 3.381590 TCGAAGTGAATGGTCTCGATGAT 59.618 43.478 0.00 0.00 0.00 2.45
2495 2900 5.923114 CGAAGTGAATGGTCTCGATGATAAT 59.077 40.000 0.00 0.00 0.00 1.28
2497 2902 6.166984 AGTGAATGGTCTCGATGATAATGT 57.833 37.500 0.00 0.00 0.00 2.71
2508 2913 4.811024 TCGATGATAATGTGTTCTGGCTTC 59.189 41.667 0.00 0.00 0.00 3.86
2640 3045 2.612212 AGTGTTGGTGCACTTCTAAACG 59.388 45.455 17.98 0.00 46.45 3.60
2771 3179 0.394565 ACCTTCAGCGCTGTTTCTCT 59.605 50.000 34.70 12.50 0.00 3.10
2786 3194 6.604735 TGTTTCTCTTACTGCTCTTTGTTC 57.395 37.500 0.00 0.00 0.00 3.18
2880 3288 2.367567 GGCCGTACCATAAGATTGGAGA 59.632 50.000 0.00 0.00 39.25 3.71
2894 3302 0.250901 TGGAGAAAACAGGGCAGAGC 60.251 55.000 0.00 0.00 0.00 4.09
2915 3323 7.011857 CAGAGCTATTTGGAAAGATTAGTGGAC 59.988 40.741 0.00 0.00 0.00 4.02
2930 3338 0.110486 TGGACTTGGGCTTCTTCCAC 59.890 55.000 0.00 0.00 33.43 4.02
2978 3386 3.221771 TGACCTAATGCATGTATTGGCC 58.778 45.455 18.10 10.65 0.00 5.36
2979 3387 3.221771 GACCTAATGCATGTATTGGCCA 58.778 45.455 18.10 0.00 0.00 5.36
2995 3403 2.892852 TGGCCAGGAAAGTTTCATCAAG 59.107 45.455 17.16 3.00 0.00 3.02
3027 3435 7.600752 GTGCTACTATAGATGGATTGAAACCTC 59.399 40.741 6.78 0.00 0.00 3.85
3032 3440 2.027385 GATGGATTGAAACCTCAGGCC 58.973 52.381 0.00 0.00 31.69 5.19
3044 3452 0.529378 CTCAGGCCATTCAACCAAGC 59.471 55.000 5.01 0.00 0.00 4.01
3060 3468 0.238289 AAGCGTTCGCCATTTGTCAG 59.762 50.000 13.54 0.00 0.00 3.51
3128 3536 8.311836 CCTAGTGAGAAGTTTGACCAAATACTA 58.688 37.037 0.00 0.00 32.36 1.82
3132 3540 6.934645 TGAGAAGTTTGACCAAATACTACAGG 59.065 38.462 0.00 0.00 32.36 4.00
3134 3542 7.514721 AGAAGTTTGACCAAATACTACAGGAA 58.485 34.615 0.00 0.00 32.36 3.36
3141 3549 6.499350 TGACCAAATACTACAGGAAGTTAGGT 59.501 38.462 0.00 0.00 0.00 3.08
3142 3550 6.944096 ACCAAATACTACAGGAAGTTAGGTC 58.056 40.000 0.00 0.00 0.00 3.85
3161 3569 4.338118 AGGTCGTCTTTGCAAAAATTGAGA 59.662 37.500 13.84 2.56 0.00 3.27
3197 3605 1.676006 GGGCGAAGGACCATACATTTG 59.324 52.381 0.00 0.00 42.95 2.32
3256 3664 9.815936 AAAATGTTTACGGTTACTAAGAATTCG 57.184 29.630 0.00 0.00 0.00 3.34
3562 4015 6.345298 AGGTTCAAAATGTTGGTAGTTTTGG 58.655 36.000 9.18 0.00 41.05 3.28
3636 4089 9.787532 CTCAACTTGAAAATGTGAAGACTAAAA 57.212 29.630 0.00 0.00 0.00 1.52
3734 4187 1.676967 CTTCCAACCTGAGGCTGCC 60.677 63.158 11.65 11.65 0.00 4.85
3809 4262 2.477245 ACTGGATATGGTGGTGCTACA 58.523 47.619 0.00 0.00 0.00 2.74
3822 4275 0.844661 TGCTACATCCCCAACCTGGT 60.845 55.000 0.00 0.00 35.17 4.00
3824 4277 1.682087 GCTACATCCCCAACCTGGTTC 60.682 57.143 9.62 0.00 35.17 3.62
3829 4282 0.477597 TCCCCAACCTGGTTCTCCAT 60.478 55.000 9.62 0.00 43.43 3.41
3832 4285 1.203050 CCCAACCTGGTTCTCCATTGT 60.203 52.381 9.62 0.00 43.43 2.71
3848 4301 4.010349 CCATTGTTTCCTCAGTTACCTCC 58.990 47.826 0.00 0.00 0.00 4.30
3871 4324 3.300388 TGCAGGTACTTCATCTAGAGGG 58.700 50.000 4.28 0.00 34.60 4.30
3898 4351 5.221581 GCAGGGAATGGCAAATTCTATCAAT 60.222 40.000 10.23 0.00 0.00 2.57
3901 4354 5.922544 GGGAATGGCAAATTCTATCAATTCG 59.077 40.000 10.23 0.00 0.00 3.34
4034 4490 8.810990 AAAAATGTACCGGTTCTTATGGAATA 57.189 30.769 15.04 0.00 36.24 1.75
4078 4534 4.161333 GTTTTGATGATCAAGAACTGCCG 58.839 43.478 17.78 0.00 37.70 5.69
4080 4536 2.349590 TGATGATCAAGAACTGCCGTG 58.650 47.619 0.00 0.00 0.00 4.94
4181 4637 1.379044 CTCCATTGGGCAGTGTCCC 60.379 63.158 12.24 13.23 46.73 4.46
4346 4803 3.245518 TGATGGACCTACATGTTGTCG 57.754 47.619 2.30 0.00 0.00 4.35
4445 4932 3.373438 CCAAGGAGATCAAATGGGATGGT 60.373 47.826 0.00 0.00 0.00 3.55
4505 4992 5.707298 CCTTGTTTGATAGTGTCACATCCTT 59.293 40.000 5.62 0.00 36.32 3.36
4521 5008 0.523519 CCTTTTCCGCCTTCTGCTTC 59.476 55.000 0.00 0.00 38.05 3.86
4602 5089 9.790389 CCATAGATGGTTAACTATCGAATCTAC 57.210 37.037 21.85 1.52 43.05 2.59
4961 5728 6.042777 TGTCCGCAGATAAAGTTTCTATCAG 58.957 40.000 0.00 0.00 0.00 2.90
4965 5732 6.703607 CCGCAGATAAAGTTTCTATCAGTCAT 59.296 38.462 0.00 0.00 0.00 3.06
5189 5962 1.064003 TTGCCCCAAGCTACTCTCAA 58.936 50.000 0.00 0.00 44.23 3.02
5191 5964 1.635487 TGCCCCAAGCTACTCTCAATT 59.365 47.619 0.00 0.00 44.23 2.32
5227 6000 5.195940 ACAAAAGATGATGGTACCATGGAG 58.804 41.667 32.07 13.93 36.70 3.86
5594 6370 2.214181 GATCACGGCTGTCACGGACT 62.214 60.000 0.00 0.00 33.15 3.85
5801 6577 1.829138 ATTTAACTCCCCCGGCCTAT 58.171 50.000 0.00 0.00 0.00 2.57
6161 6953 1.795768 CTTTGCACCTTCGCTCAGTA 58.204 50.000 0.00 0.00 0.00 2.74
6610 7475 8.554528 CATGGTATGCTTCTTTGTACTTCTATG 58.445 37.037 0.00 0.00 0.00 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 0.245539 CTGGCCAAGGAAGCAACATG 59.754 55.000 7.01 0.00 0.00 3.21
60 61 2.146073 AAACAGCACATCCGCTTGGC 62.146 55.000 0.00 0.00 41.38 4.52
145 177 1.615116 CCTGTGTAGGGTACGTCTCCA 60.615 57.143 11.01 0.00 40.63 3.86
149 181 2.292845 GCTATCCTGTGTAGGGTACGTC 59.707 54.545 0.00 0.00 44.70 4.34
192 224 1.095228 TCCGATTCCTTGAATGCGGC 61.095 55.000 16.14 0.00 39.77 6.53
290 323 7.965107 GCTTAATCTTGATGGTTTCTACACAAG 59.035 37.037 0.00 0.00 35.18 3.16
312 345 7.041167 CCCATCGACAAATTAATGAGATGCTTA 60.041 37.037 0.00 0.00 37.50 3.09
344 378 0.248866 GTTTCCACAACCTTGCACGG 60.249 55.000 7.87 7.87 0.00 4.94
345 379 0.453793 TGTTTCCACAACCTTGCACG 59.546 50.000 0.00 0.00 0.00 5.34
346 380 2.663826 TTGTTTCCACAACCTTGCAC 57.336 45.000 0.00 0.00 38.03 4.57
347 381 2.158986 CCATTGTTTCCACAACCTTGCA 60.159 45.455 0.00 0.00 45.88 4.08
348 382 2.102252 TCCATTGTTTCCACAACCTTGC 59.898 45.455 0.00 0.00 45.88 4.01
349 383 4.370917 CTTCCATTGTTTCCACAACCTTG 58.629 43.478 0.00 0.00 45.88 3.61
350 384 3.181466 GCTTCCATTGTTTCCACAACCTT 60.181 43.478 0.00 0.00 45.88 3.50
351 385 2.365293 GCTTCCATTGTTTCCACAACCT 59.635 45.455 0.00 0.00 45.88 3.50
367 401 3.499918 CGACAATCTAATGGGATGCTTCC 59.500 47.826 10.18 10.18 41.77 3.46
376 415 2.332063 ACCTGGCGACAATCTAATGG 57.668 50.000 0.00 0.00 42.06 3.16
382 421 1.209128 CATCGTACCTGGCGACAATC 58.791 55.000 0.00 0.00 42.06 2.67
383 422 0.535335 ACATCGTACCTGGCGACAAT 59.465 50.000 0.00 0.00 42.06 2.71
391 430 4.046938 AGTATGCTCAACATCGTACCTG 57.953 45.455 0.00 0.00 40.38 4.00
400 439 5.045942 TGGTTCCTGATAAGTATGCTCAACA 60.046 40.000 0.00 0.00 0.00 3.33
405 444 5.894298 TGATGGTTCCTGATAAGTATGCT 57.106 39.130 0.00 0.00 0.00 3.79
437 476 6.073003 GGCTTAAATTGAATCCTCGGTAGATG 60.073 42.308 0.00 0.00 0.00 2.90
443 482 5.611374 TCTAGGCTTAAATTGAATCCTCGG 58.389 41.667 0.90 0.00 0.00 4.63
444 483 6.516718 TCTCTAGGCTTAAATTGAATCCTCG 58.483 40.000 0.90 0.00 0.00 4.63
466 505 4.080695 ACATCACAATGTGTCCTGCTATCT 60.081 41.667 13.55 0.00 44.51 1.98
474 513 4.298332 GGACAAAACATCACAATGTGTCC 58.702 43.478 13.55 6.47 45.48 4.02
510 549 5.296531 ACGCATATGCATACTGAACAAATGA 59.703 36.000 26.52 0.00 42.21 2.57
546 585 0.969149 CAGTGGTCCTGTAGCAGACA 59.031 55.000 0.00 0.00 35.94 3.41
548 587 0.542938 AGCAGTGGTCCTGTAGCAGA 60.543 55.000 0.00 0.00 43.55 4.26
555 594 3.356529 AAAGGATAAGCAGTGGTCCTG 57.643 47.619 2.09 0.00 40.10 3.86
610 650 6.471233 TGATTTTACATGACCACCACAAAA 57.529 33.333 0.00 0.00 0.00 2.44
616 659 6.511767 CGAGCTTATGATTTTACATGACCACC 60.512 42.308 0.00 0.00 0.00 4.61
617 660 6.037172 ACGAGCTTATGATTTTACATGACCAC 59.963 38.462 0.00 0.00 0.00 4.16
619 662 6.480320 AGACGAGCTTATGATTTTACATGACC 59.520 38.462 0.00 0.00 0.00 4.02
629 672 7.173907 CCATATGGAAAAGACGAGCTTATGATT 59.826 37.037 17.49 0.00 34.38 2.57
700 743 4.137116 TGGCTCCACAGTATTGTATGAC 57.863 45.455 0.00 0.00 35.25 3.06
701 744 4.469586 TCTTGGCTCCACAGTATTGTATGA 59.530 41.667 0.00 0.00 35.25 2.15
702 745 4.572389 GTCTTGGCTCCACAGTATTGTATG 59.428 45.833 0.00 0.00 35.25 2.39
703 746 4.471386 AGTCTTGGCTCCACAGTATTGTAT 59.529 41.667 0.00 0.00 35.25 2.29
708 751 2.906389 TCAAGTCTTGGCTCCACAGTAT 59.094 45.455 12.66 0.00 0.00 2.12
709 752 2.325484 TCAAGTCTTGGCTCCACAGTA 58.675 47.619 12.66 0.00 0.00 2.74
730 784 4.383118 CGTGGAACTATGGAAGTCCTTGAT 60.383 45.833 0.00 0.00 37.50 2.57
768 822 2.806856 CTCATGGCAAGCTCGACGC 61.807 63.158 0.00 0.00 39.57 5.19
770 824 1.817099 CCCTCATGGCAAGCTCGAC 60.817 63.158 0.00 0.00 0.00 4.20
791 845 4.082125 GGATCCCTTCAACTGAAACACAT 58.918 43.478 0.00 0.00 33.07 3.21
797 851 4.168101 ACACTAGGATCCCTTCAACTGAA 58.832 43.478 8.55 0.00 34.61 3.02
839 893 0.375454 TCGAACAGTGCACCAAAACG 59.625 50.000 14.63 13.24 0.00 3.60
851 905 2.596419 GCGAATGAGAAGAGTCGAACAG 59.404 50.000 0.00 0.00 35.51 3.16
856 910 2.551355 TCAGCGAATGAGAAGAGTCG 57.449 50.000 0.00 0.00 36.55 4.18
870 943 2.202570 GCAGGCAGCAATTCAGCG 60.203 61.111 0.00 0.00 44.79 5.18
913 996 2.867109 ACCAAACAGATGGACTCAGG 57.133 50.000 0.00 0.00 43.54 3.86
939 1023 1.194218 AAAAACAGGCCTTGCACAGT 58.806 45.000 0.00 0.00 0.00 3.55
959 1043 1.553690 GGCCCAGTAACAGCAGGAGA 61.554 60.000 0.00 0.00 0.00 3.71
978 1062 2.436646 CCTGGCACACCTAAGGCG 60.437 66.667 0.00 0.00 36.63 5.52
993 1081 1.617947 GCAACCCCGACATCTCTCCT 61.618 60.000 0.00 0.00 0.00 3.69
1038 1126 2.277591 GCTTTGCACCAGCCATCCA 61.278 57.895 5.86 0.00 41.13 3.41
1102 1190 1.909700 TCTTCAGCAAGCCCGATTTT 58.090 45.000 0.00 0.00 0.00 1.82
1363 1720 1.957695 CAAGCAGCGCTCACAGTCA 60.958 57.895 7.13 0.00 38.25 3.41
1364 1721 2.675056 CCAAGCAGCGCTCACAGTC 61.675 63.158 7.13 0.00 38.25 3.51
1365 1722 2.667536 CCAAGCAGCGCTCACAGT 60.668 61.111 7.13 0.00 38.25 3.55
1366 1723 2.357881 TCCAAGCAGCGCTCACAG 60.358 61.111 7.13 0.00 38.25 3.66
1367 1724 1.815817 TACTCCAAGCAGCGCTCACA 61.816 55.000 7.13 0.00 38.25 3.58
1368 1725 0.460987 ATACTCCAAGCAGCGCTCAC 60.461 55.000 7.13 1.95 38.25 3.51
1369 1726 1.067669 CTATACTCCAAGCAGCGCTCA 59.932 52.381 7.13 0.00 38.25 4.26
1370 1727 1.067821 ACTATACTCCAAGCAGCGCTC 59.932 52.381 7.13 2.24 38.25 5.03
1371 1728 1.115467 ACTATACTCCAAGCAGCGCT 58.885 50.000 2.64 2.64 42.56 5.92
1372 1729 1.941325 AACTATACTCCAAGCAGCGC 58.059 50.000 0.00 0.00 0.00 5.92
1373 1730 7.622256 GCATATTAAACTATACTCCAAGCAGCG 60.622 40.741 0.00 0.00 0.00 5.18
1374 1731 7.173218 TGCATATTAAACTATACTCCAAGCAGC 59.827 37.037 0.00 0.00 0.00 5.25
1375 1732 8.607441 TGCATATTAAACTATACTCCAAGCAG 57.393 34.615 0.00 0.00 0.00 4.24
1376 1733 8.836413 GTTGCATATTAAACTATACTCCAAGCA 58.164 33.333 0.00 0.00 0.00 3.91
1377 1734 8.290325 GGTTGCATATTAAACTATACTCCAAGC 58.710 37.037 0.00 0.00 0.00 4.01
1378 1735 9.337396 TGGTTGCATATTAAACTATACTCCAAG 57.663 33.333 0.00 0.00 0.00 3.61
1379 1736 9.860650 ATGGTTGCATATTAAACTATACTCCAA 57.139 29.630 0.00 0.00 0.00 3.53
1380 1737 9.283768 CATGGTTGCATATTAAACTATACTCCA 57.716 33.333 0.00 0.00 0.00 3.86
1381 1738 9.502091 TCATGGTTGCATATTAAACTATACTCC 57.498 33.333 0.00 0.00 0.00 3.85
1386 1743 8.137437 GCTGTTCATGGTTGCATATTAAACTAT 58.863 33.333 0.00 0.00 0.00 2.12
1387 1744 7.339212 AGCTGTTCATGGTTGCATATTAAACTA 59.661 33.333 0.00 0.00 0.00 2.24
1388 1745 6.153340 AGCTGTTCATGGTTGCATATTAAACT 59.847 34.615 0.00 0.00 0.00 2.66
1389 1746 6.332630 AGCTGTTCATGGTTGCATATTAAAC 58.667 36.000 0.00 0.00 0.00 2.01
1390 1747 6.152492 TGAGCTGTTCATGGTTGCATATTAAA 59.848 34.615 0.00 0.00 0.00 1.52
1391 1748 5.651576 TGAGCTGTTCATGGTTGCATATTAA 59.348 36.000 0.00 0.00 0.00 1.40
1399 1756 5.823209 TGATATTGAGCTGTTCATGGTTG 57.177 39.130 0.00 0.00 35.27 3.77
1429 1814 5.743636 AGCAAGAGATAATCTGAGGGATC 57.256 43.478 0.00 0.00 38.67 3.36
1431 1816 6.613271 AGTTAAGCAAGAGATAATCTGAGGGA 59.387 38.462 0.00 0.00 38.67 4.20
1487 1875 5.892160 ACCTTTCGCCTAGGAAAAATAAC 57.108 39.130 14.75 0.00 35.64 1.89
1489 1877 6.549433 TCTACCTTTCGCCTAGGAAAAATA 57.451 37.500 14.75 6.72 35.64 1.40
1514 1902 6.263168 ACAAAAGTTCCATGAGGTAAAGACAG 59.737 38.462 0.00 0.00 35.89 3.51
1515 1903 6.126409 ACAAAAGTTCCATGAGGTAAAGACA 58.874 36.000 0.00 0.00 35.89 3.41
1526 1914 8.140677 TGCTGAAAATTAACAAAAGTTCCATG 57.859 30.769 0.00 0.00 0.00 3.66
1561 1949 9.528018 GCACTTAAGCAAAGGCAAATATTATTA 57.472 29.630 1.29 0.00 44.61 0.98
1562 1950 8.260114 AGCACTTAAGCAAAGGCAAATATTATT 58.740 29.630 1.29 0.00 44.61 1.40
1574 1962 6.018507 AGCAAATGAAAAGCACTTAAGCAAAG 60.019 34.615 1.29 0.00 41.33 2.77
1587 1975 4.565564 GCTATGAGCCAAGCAAATGAAAAG 59.434 41.667 0.00 0.00 38.63 2.27
1616 2007 6.883744 ACAAACTTTCCCTGCATAAGAAAAA 58.116 32.000 7.19 0.00 0.00 1.94
1725 2122 3.897239 TCCAACCAGTTATATGGCTTGG 58.103 45.455 15.26 15.26 44.80 3.61
1733 2130 4.500205 CCGCGTAAGATCCAACCAGTTATA 60.500 45.833 4.92 0.00 43.02 0.98
1793 2190 3.503363 TCTCAAAAGGCAGCATGTTACAG 59.497 43.478 0.00 0.00 39.31 2.74
1855 2252 3.603158 TGCGGTTACTGCATAGAAGAA 57.397 42.857 15.54 0.00 37.44 2.52
1871 2268 2.703798 CCCCTGCACAGAATTGCGG 61.704 63.158 0.00 0.00 46.20 5.69
1872 2269 2.703798 CCCCCTGCACAGAATTGCG 61.704 63.158 0.00 0.00 46.20 4.85
1939 2336 3.747388 GCGATGACCCCTGGAAATATTGA 60.747 47.826 0.00 0.00 0.00 2.57
1940 2337 2.554032 GCGATGACCCCTGGAAATATTG 59.446 50.000 0.00 0.00 0.00 1.90
1989 2386 1.476891 TGCATCTCTTCCGTACACCTC 59.523 52.381 0.00 0.00 0.00 3.85
2021 2418 5.309020 TCCATTCCTCAGCAGCTCTATTATT 59.691 40.000 0.00 0.00 0.00 1.40
2045 2442 8.031277 GGCAAAACATTCAGATCACTAGATTTT 58.969 33.333 0.00 0.00 33.72 1.82
2161 2558 2.028130 TGGACACACAAACCCACATTC 58.972 47.619 0.00 0.00 0.00 2.67
2197 2594 1.751924 GGATCTCACGTGTTAGCCTCT 59.248 52.381 16.51 0.00 0.00 3.69
2325 2729 4.767409 TCTGTCTTCCCATATATCGTCCAG 59.233 45.833 0.00 0.00 0.00 3.86
2336 2740 2.225496 ACTCCTGTCTCTGTCTTCCCAT 60.225 50.000 0.00 0.00 0.00 4.00
2347 2751 1.280457 AATCCACCCACTCCTGTCTC 58.720 55.000 0.00 0.00 0.00 3.36
2360 2764 2.618709 CGGAGCCAGGAAATTAATCCAC 59.381 50.000 0.00 0.00 42.27 4.02
2401 2806 2.937469 TGCTAAAATCATGCAACCGG 57.063 45.000 0.00 0.00 33.48 5.28
2464 2869 2.632996 AGACCATTCACTTCGACCTCAA 59.367 45.455 0.00 0.00 0.00 3.02
2468 2873 1.201647 TCGAGACCATTCACTTCGACC 59.798 52.381 0.00 0.00 0.00 4.79
2472 2877 6.703607 ACATTATCATCGAGACCATTCACTTC 59.296 38.462 0.00 0.00 0.00 3.01
2492 2897 5.012046 TCTGAAGAGAAGCCAGAACACATTA 59.988 40.000 0.00 0.00 34.38 1.90
2495 2900 2.700371 TCTGAAGAGAAGCCAGAACACA 59.300 45.455 0.00 0.00 34.38 3.72
2497 2902 2.289320 GCTCTGAAGAGAAGCCAGAACA 60.289 50.000 11.56 0.00 44.74 3.18
2508 2913 3.427638 CCAAATGCACATGCTCTGAAGAG 60.428 47.826 5.31 2.81 44.75 2.85
2640 3045 4.083431 CCAATGCTGATAGCTAACATCTGC 60.083 45.833 15.99 15.99 42.97 4.26
2771 3179 3.244561 CCTCTGGGAACAAAGAGCAGTAA 60.245 47.826 0.00 0.00 42.06 2.24
2786 3194 2.196595 TCAAATGGGTAGTCCTCTGGG 58.803 52.381 0.00 0.00 36.20 4.45
2880 3288 2.827921 CCAAATAGCTCTGCCCTGTTTT 59.172 45.455 0.00 0.00 0.00 2.43
2894 3302 7.067494 CCCAAGTCCACTAATCTTTCCAAATAG 59.933 40.741 0.00 0.00 0.00 1.73
2915 3323 1.202927 TCCTTGTGGAAGAAGCCCAAG 60.203 52.381 0.00 0.00 39.87 3.61
2930 3338 3.272574 ACATAGTGTGAGCCATCCTTG 57.727 47.619 0.00 0.00 0.00 3.61
2978 3386 5.297776 ACACTCACTTGATGAAACTTTCCTG 59.702 40.000 0.00 0.00 36.69 3.86
2979 3387 5.297776 CACACTCACTTGATGAAACTTTCCT 59.702 40.000 0.00 0.00 36.69 3.36
2995 3403 6.582677 ATCCATCTATAGTAGCACACTCAC 57.417 41.667 0.00 0.00 38.80 3.51
3027 3435 1.213537 CGCTTGGTTGAATGGCCTG 59.786 57.895 3.32 0.00 0.00 4.85
3032 3440 0.729140 GGCGAACGCTTGGTTGAATG 60.729 55.000 18.14 0.00 39.50 2.67
3044 3452 0.865111 TGACTGACAAATGGCGAACG 59.135 50.000 0.00 0.00 0.00 3.95
3079 3487 5.920840 GGAAAACTGCCTTGTTCATCTTTAC 59.079 40.000 0.00 0.00 0.00 2.01
3092 3500 3.648545 ACTTCTCACTAGGAAAACTGCCT 59.351 43.478 0.00 0.00 39.56 4.75
3128 3536 3.802675 GCAAAGACGACCTAACTTCCTGT 60.803 47.826 0.00 0.00 0.00 4.00
3132 3540 4.806342 TTTGCAAAGACGACCTAACTTC 57.194 40.909 8.05 0.00 0.00 3.01
3134 3542 5.767816 ATTTTTGCAAAGACGACCTAACT 57.232 34.783 12.41 0.00 0.00 2.24
3141 3549 5.040635 GGTTCTCAATTTTTGCAAAGACGA 58.959 37.500 12.41 7.60 0.00 4.20
3142 3550 5.043248 AGGTTCTCAATTTTTGCAAAGACG 58.957 37.500 12.41 3.48 0.00 4.18
3496 3949 2.548057 GAGGTCATTTTGCTGACACGAA 59.452 45.455 6.21 0.00 45.95 3.85
3498 3951 2.146342 AGAGGTCATTTTGCTGACACG 58.854 47.619 6.21 0.00 45.95 4.49
3655 4108 8.988546 TTCTAGATACTCTTTGTCTATCAGCT 57.011 34.615 0.00 0.00 0.00 4.24
3717 4170 2.005606 TTGGCAGCCTCAGGTTGGAA 62.006 55.000 14.15 0.00 34.44 3.53
3719 4172 1.975407 CTTGGCAGCCTCAGGTTGG 60.975 63.158 14.15 0.00 34.44 3.77
3734 4187 2.787994 AGACCTTCAAGCACATCCTTG 58.212 47.619 0.00 0.00 42.73 3.61
3809 4262 0.477597 TGGAGAACCAGGTTGGGGAT 60.478 55.000 10.47 0.00 43.37 3.85
3822 4275 5.313712 GGTAACTGAGGAAACAATGGAGAA 58.686 41.667 0.00 0.00 0.00 2.87
3848 4301 4.202202 CCCTCTAGATGAAGTACCTGCAAG 60.202 50.000 0.00 0.00 0.00 4.01
3871 4324 0.614812 AATTTGCCATTCCCTGCACC 59.385 50.000 0.00 0.00 37.18 5.01
3898 4351 3.694072 CCTAAGGGAATGCATTTCACGAA 59.306 43.478 19.43 1.11 42.96 3.85
4034 4490 8.721133 AAACCCTTAAATGGTAAGTCAATTCT 57.279 30.769 0.00 0.00 34.15 2.40
4346 4803 3.325135 TCCAGAGAAGGAACTGAAACTCC 59.675 47.826 0.00 0.00 40.86 3.85
4445 4932 4.202121 GGTAAGTCTACGCAGATTGGATGA 60.202 45.833 0.00 0.00 32.09 2.92
4450 4937 4.051922 GGATGGTAAGTCTACGCAGATTG 58.948 47.826 0.00 0.00 32.09 2.67
4521 5008 3.055591 CTGATGGACATCTCGGAAATCG 58.944 50.000 12.97 0.00 38.60 3.34
4588 5075 7.121463 ACACTCAACTCAGTAGATTCGATAGTT 59.879 37.037 0.00 0.00 37.40 2.24
4602 5089 4.172505 GTCATCTAGCACACTCAACTCAG 58.827 47.826 0.00 0.00 0.00 3.35
4961 5728 4.817517 TCCGTTTCTCTAGGTTGAATGAC 58.182 43.478 0.00 0.00 0.00 3.06
4965 5732 3.007614 CCCTTCCGTTTCTCTAGGTTGAA 59.992 47.826 0.00 0.00 0.00 2.69
5189 5962 5.428184 TCTTTTGTTTCACCCACCAAAAT 57.572 34.783 0.00 0.00 36.52 1.82
5191 5964 4.467795 TCATCTTTTGTTTCACCCACCAAA 59.532 37.500 0.00 0.00 0.00 3.28
5703 6479 1.879380 CGCAGTCTCCAATTTCCAACA 59.121 47.619 0.00 0.00 0.00 3.33
6161 6953 2.576191 TGCAATAGGCTACCTCAAGGTT 59.424 45.455 7.07 0.00 45.08 3.50
6610 7475 8.398665 CCACTAACAAAGCTAATCAGGATAAAC 58.601 37.037 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.