Multiple sequence alignment - TraesCS2D01G310400

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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 TraesCS2D01G310400 chr2D 100.000 5033 0 0 1 5033 398671677 398666645 0.000000e+00 9295.0
1 TraesCS2D01G310400 chr2D 93.056 432 27 3 192 621 577534780 577534350 3.310000e-176 628.0
2 TraesCS2D01G310400 chr2D 89.640 444 29 5 191 631 424682557 424682128 2.650000e-152 549.0
3 TraesCS2D01G310400 chr2D 97.222 36 1 0 1359 1394 35002968 35002933 1.510000e-05 62.1
4 TraesCS2D01G310400 chr2D 97.222 36 1 0 1359 1394 35025453 35025418 1.510000e-05 62.1
5 TraesCS2D01G310400 chr2A 90.058 1710 89 36 915 2590 535839102 535837440 0.000000e+00 2141.0
6 TraesCS2D01G310400 chr2A 96.125 542 16 1 3112 3648 535836948 535836407 0.000000e+00 880.0
7 TraesCS2D01G310400 chr2A 94.690 452 19 2 3639 4089 535836380 535835933 0.000000e+00 697.0
8 TraesCS2D01G310400 chr2A 90.227 440 40 3 191 627 475780665 475781104 5.650000e-159 571.0
9 TraesCS2D01G310400 chr2A 97.717 219 5 0 2838 3056 535837152 535836934 1.320000e-100 377.0
10 TraesCS2D01G310400 chr2A 93.264 193 12 1 1 193 722111710 722111901 2.970000e-72 283.0
11 TraesCS2D01G310400 chr2A 91.878 197 8 5 2625 2813 535837442 535837246 8.310000e-68 268.0
12 TraesCS2D01G310400 chr2A 84.677 248 22 6 656 903 535840221 535839990 3.030000e-57 233.0
13 TraesCS2D01G310400 chr2A 97.222 36 1 0 1359 1394 38324554 38324519 1.510000e-05 62.1
14 TraesCS2D01G310400 chr2A 97.222 36 1 0 1359 1394 38332457 38332422 1.510000e-05 62.1
15 TraesCS2D01G310400 chr2B 91.704 904 36 16 3158 4032 471322164 471323057 0.000000e+00 1218.0
16 TraesCS2D01G310400 chr2B 86.644 891 57 29 1309 2181 471320385 471321231 0.000000e+00 929.0
17 TraesCS2D01G310400 chr2B 93.365 633 28 5 653 1276 471319682 471320309 0.000000e+00 924.0
18 TraesCS2D01G310400 chr2B 91.573 534 22 7 2271 2795 471321274 471321793 0.000000e+00 715.0
19 TraesCS2D01G310400 chr2B 87.415 294 22 12 2835 3119 471321925 471322212 1.750000e-84 324.0
20 TraesCS2D01G310400 chr2B 90.385 52 5 0 4501 4552 644128081 644128030 9.040000e-08 69.4
21 TraesCS2D01G310400 chr2B 97.222 36 1 0 1359 1394 57682365 57682330 1.510000e-05 62.1
22 TraesCS2D01G310400 chr5B 87.730 978 63 26 4111 5033 65099206 65100181 0.000000e+00 1088.0
23 TraesCS2D01G310400 chr5B 82.759 203 24 5 4563 4757 16875251 16875450 2.410000e-38 171.0
24 TraesCS2D01G310400 chr5B 81.773 203 26 5 4563 4757 16923181 16923380 5.220000e-35 159.0
25 TraesCS2D01G310400 chr1A 95.980 597 23 1 4438 5033 493588979 493589575 0.000000e+00 968.0
26 TraesCS2D01G310400 chr1A 88.810 563 40 7 4485 5033 563790378 563789825 0.000000e+00 669.0
27 TraesCS2D01G310400 chr1A 85.393 178 13 10 4304 4478 563790600 563790433 6.700000e-39 172.0
28 TraesCS2D01G310400 chr7B 95.018 542 21 2 4498 5033 9798749 9799290 0.000000e+00 846.0
29 TraesCS2D01G310400 chr7B 85.577 416 20 24 4086 4467 9798340 9798749 2.820000e-107 399.0
30 TraesCS2D01G310400 chr7B 94.388 196 11 0 1 196 456498583 456498388 8.190000e-78 302.0
31 TraesCS2D01G310400 chr6B 91.451 503 34 7 4538 5033 611901125 611900625 0.000000e+00 682.0
32 TraesCS2D01G310400 chr6B 96.087 230 8 1 4314 4542 611906041 611905812 1.710000e-99 374.0
33 TraesCS2D01G310400 chr6B 94.416 197 9 1 4111 4305 611906276 611906080 8.190000e-78 302.0
34 TraesCS2D01G310400 chr5A 88.277 563 43 7 4485 5033 400489636 400490189 0.000000e+00 652.0
35 TraesCS2D01G310400 chr5A 88.099 563 44 7 4485 5033 400423978 400423425 0.000000e+00 647.0
36 TraesCS2D01G310400 chr5A 84.127 378 37 14 4111 4478 400424397 400424033 1.340000e-90 344.0
37 TraesCS2D01G310400 chr5A 83.598 378 39 14 4111 4478 400489217 400489581 2.900000e-87 333.0
38 TraesCS2D01G310400 chr7D 93.056 432 28 2 191 620 209584359 209584790 9.200000e-177 630.0
39 TraesCS2D01G310400 chr7D 92.807 431 24 7 191 617 110218165 110218592 7.160000e-173 617.0
40 TraesCS2D01G310400 chr7D 94.388 196 11 0 1 196 511120589 511120784 8.190000e-78 302.0
41 TraesCS2D01G310400 chr7D 94.301 193 11 0 1 193 209584126 209584318 3.810000e-76 296.0
42 TraesCS2D01G310400 chr7D 92.857 42 3 0 1353 1394 13454218 13454259 1.510000e-05 62.1
43 TraesCS2D01G310400 chr6D 92.841 433 29 2 192 622 465425273 465425705 1.190000e-175 627.0
44 TraesCS2D01G310400 chr6D 90.000 380 30 4 4485 4863 76128110 76127738 7.580000e-133 484.0
45 TraesCS2D01G310400 chr6D 93.367 196 11 2 1 196 471150579 471150772 6.380000e-74 289.0
46 TraesCS2D01G310400 chr6D 90.355 197 15 2 4111 4305 76128528 76128334 6.470000e-64 255.0
47 TraesCS2D01G310400 chr6D 87.500 192 20 2 4116 4305 76128772 76128583 8.480000e-53 219.0
48 TraesCS2D01G310400 chr6D 91.379 58 5 0 4421 4478 76128245 76128188 4.180000e-11 80.5
49 TraesCS2D01G310400 chr4A 91.954 435 33 2 191 623 618921953 618921519 4.310000e-170 608.0
50 TraesCS2D01G310400 chr4A 91.762 437 34 2 191 625 2567143 2566707 1.550000e-169 606.0
51 TraesCS2D01G310400 chr4A 91.224 433 35 3 191 621 621469805 621470236 2.020000e-163 586.0
52 TraesCS2D01G310400 chr4A 92.308 195 15 0 2 196 665661741 665661547 1.380000e-70 278.0
53 TraesCS2D01G310400 chr3D 91.898 432 33 2 191 620 45344724 45344293 2.000000e-168 603.0
54 TraesCS2D01G310400 chr3D 87.963 432 27 7 4485 4908 19019562 19019148 2.110000e-133 486.0
55 TraesCS2D01G310400 chr3D 81.910 398 39 18 4111 4479 19020316 19019923 6.330000e-79 305.0
56 TraesCS2D01G310400 chr3D 92.857 196 13 1 1 196 123643196 123643002 2.970000e-72 283.0
57 TraesCS2D01G310400 chr3D 92.347 196 15 0 1 196 91370923 91370728 3.840000e-71 279.0
58 TraesCS2D01G310400 chr3D 79.101 378 56 16 4111 4467 28377934 28377559 6.510000e-59 239.0
59 TraesCS2D01G310400 chr3D 78.610 374 58 15 4115 4467 28370970 28370598 1.410000e-55 228.0
60 TraesCS2D01G310400 chr3D 74.477 239 54 6 3202 3439 512676082 512675850 4.150000e-16 97.1
61 TraesCS2D01G310400 chr1D 91.724 435 33 3 191 623 472353698 472353265 7.210000e-168 601.0
62 TraesCS2D01G310400 chr1D 78.378 111 24 0 3327 3437 355470610 355470500 6.990000e-09 73.1
63 TraesCS2D01G310400 chr3B 85.766 555 50 10 4485 5030 784584565 784585099 1.220000e-155 560.0
64 TraesCS2D01G310400 chr3B 91.878 197 16 0 1 197 40769616 40769812 4.960000e-70 276.0
65 TraesCS2D01G310400 chr3B 84.831 178 14 10 4304 4478 784584343 784584510 3.120000e-37 167.0
66 TraesCS2D01G310400 chr3B 75.234 214 48 4 3214 3426 675040629 675040838 4.150000e-16 97.1
67 TraesCS2D01G310400 chr1B 85.820 543 41 10 1927 2465 22639820 22640330 1.230000e-150 544.0
68 TraesCS2D01G310400 chr1B 96.970 66 2 0 2505 2570 22642548 22642483 1.480000e-20 111.0
69 TraesCS2D01G310400 chr3A 91.460 363 29 2 4532 4893 26503340 26502979 9.730000e-137 497.0
70 TraesCS2D01G310400 chr3A 90.400 125 8 1 4909 5033 26500787 26500667 1.450000e-35 161.0
71 TraesCS2D01G310400 chr3A 74.059 239 55 6 3202 3439 648263607 648263375 1.930000e-14 91.6


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 TraesCS2D01G310400 chr2D 398666645 398671677 5032 True 9295.000 9295 100.000000 1 5033 1 chr2D.!!$R3 5032
1 TraesCS2D01G310400 chr2A 535835933 535840221 4288 True 766.000 2141 92.524167 656 4089 6 chr2A.!!$R3 3433
2 TraesCS2D01G310400 chr2B 471319682 471323057 3375 False 822.000 1218 90.140200 653 4032 5 chr2B.!!$F1 3379
3 TraesCS2D01G310400 chr5B 65099206 65100181 975 False 1088.000 1088 87.730000 4111 5033 1 chr5B.!!$F3 922
4 TraesCS2D01G310400 chr1A 493588979 493589575 596 False 968.000 968 95.980000 4438 5033 1 chr1A.!!$F1 595
5 TraesCS2D01G310400 chr1A 563789825 563790600 775 True 420.500 669 87.101500 4304 5033 2 chr1A.!!$R1 729
6 TraesCS2D01G310400 chr7B 9798340 9799290 950 False 622.500 846 90.297500 4086 5033 2 chr7B.!!$F1 947
7 TraesCS2D01G310400 chr6B 611900625 611901125 500 True 682.000 682 91.451000 4538 5033 1 chr6B.!!$R1 495
8 TraesCS2D01G310400 chr5A 400423425 400424397 972 True 495.500 647 86.113000 4111 5033 2 chr5A.!!$R1 922
9 TraesCS2D01G310400 chr5A 400489217 400490189 972 False 492.500 652 85.937500 4111 5033 2 chr5A.!!$F1 922
10 TraesCS2D01G310400 chr7D 209584126 209584790 664 False 463.000 630 93.678500 1 620 2 chr7D.!!$F4 619
11 TraesCS2D01G310400 chr6D 76127738 76128772 1034 True 259.625 484 89.808500 4111 4863 4 chr6D.!!$R1 752
12 TraesCS2D01G310400 chr3D 19019148 19020316 1168 True 395.500 486 84.936500 4111 4908 2 chr3D.!!$R7 797
13 TraesCS2D01G310400 chr3B 784584343 784585099 756 False 363.500 560 85.298500 4304 5030 2 chr3B.!!$F3 726
14 TraesCS2D01G310400 chr1B 22639820 22640330 510 False 544.000 544 85.820000 1927 2465 1 chr1B.!!$F1 538
15 TraesCS2D01G310400 chr3A 26500667 26503340 2673 True 329.000 497 90.930000 4532 5033 2 chr3A.!!$R2 501

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
638 684 0.322906 GGAGAGTCCAGCCCCAAAAG 60.323 60.0 0.00 0.0 36.28 2.27 F
1446 2422 0.466372 ATCGACGAGAGCCTCATGGA 60.466 55.0 3.01 0.0 34.57 3.41 F
2638 3666 0.615850 TCATGCGTGTGGATTGGGTA 59.384 50.0 5.68 0.0 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2490 3513 1.134788 CGCTGGAAAGGAAGATACCGT 60.135 52.381 0.00 0.00 34.73 4.83 R
3088 4308 0.179217 CACGCACGTGTGAATGATGG 60.179 55.000 34.03 10.86 42.55 3.51 R
4152 5435 0.584876 GGTTGTTCTGTGTACGTGCC 59.415 55.000 0.00 0.00 0.00 5.01 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
25 26 1.707427 AGTGGCCTTGAACTTCTCCAT 59.293 47.619 3.32 0.00 0.00 3.41
88 89 2.818274 CCGGCCTTAACAGACGCC 60.818 66.667 0.00 0.00 38.07 5.68
134 135 1.103803 TCGAAGGGATCCAACTCTCG 58.896 55.000 15.23 13.02 0.00 4.04
135 136 0.528684 CGAAGGGATCCAACTCTCGC 60.529 60.000 15.23 0.00 0.00 5.03
252 296 4.662961 CGCGCACAGAGACCACCA 62.663 66.667 8.75 0.00 0.00 4.17
257 301 2.842462 ACAGAGACCACCACCGCA 60.842 61.111 0.00 0.00 0.00 5.69
264 308 3.740397 CCACCACCGCATGCACAG 61.740 66.667 19.57 8.19 0.00 3.66
442 486 4.690719 AACAACCGCCGCGATCCA 62.691 61.111 15.93 0.00 0.00 3.41
465 509 2.895680 GCCAGATCCAGCGAGTCA 59.104 61.111 0.00 0.00 0.00 3.41
470 514 1.070445 GATCCAGCGAGTCATGGGG 59.930 63.158 10.66 0.00 37.19 4.96
478 522 1.418334 CGAGTCATGGGGGAAGAGAT 58.582 55.000 0.00 0.00 0.00 2.75
624 670 2.517402 CGGGAGGAGTCGGGAGAG 60.517 72.222 0.00 0.00 41.26 3.20
631 677 2.363147 AGTCGGGAGAGTCCAGCC 60.363 66.667 0.00 0.00 38.35 4.85
632 678 3.462678 GTCGGGAGAGTCCAGCCC 61.463 72.222 3.74 3.74 38.64 5.19
633 679 4.779733 TCGGGAGAGTCCAGCCCC 62.780 72.222 7.53 0.00 38.64 5.80
635 681 2.610859 GGGAGAGTCCAGCCCCAA 60.611 66.667 2.59 0.00 38.64 4.12
636 682 2.231380 GGGAGAGTCCAGCCCCAAA 61.231 63.158 2.59 0.00 38.64 3.28
637 683 1.767692 GGAGAGTCCAGCCCCAAAA 59.232 57.895 0.00 0.00 36.28 2.44
638 684 0.322906 GGAGAGTCCAGCCCCAAAAG 60.323 60.000 0.00 0.00 36.28 2.27
639 685 0.962855 GAGAGTCCAGCCCCAAAAGC 60.963 60.000 0.00 0.00 0.00 3.51
640 686 1.075659 GAGTCCAGCCCCAAAAGCT 59.924 57.895 0.00 0.00 42.70 3.74
641 687 0.540597 GAGTCCAGCCCCAAAAGCTT 60.541 55.000 0.00 0.00 38.95 3.74
642 688 0.829182 AGTCCAGCCCCAAAAGCTTG 60.829 55.000 0.00 0.00 38.95 4.01
643 689 1.115326 GTCCAGCCCCAAAAGCTTGT 61.115 55.000 0.00 0.00 38.95 3.16
644 690 0.480690 TCCAGCCCCAAAAGCTTGTA 59.519 50.000 0.00 0.00 38.95 2.41
645 691 0.603065 CCAGCCCCAAAAGCTTGTAC 59.397 55.000 0.00 0.00 38.95 2.90
646 692 1.620822 CAGCCCCAAAAGCTTGTACT 58.379 50.000 0.00 0.00 38.95 2.73
647 693 1.270550 CAGCCCCAAAAGCTTGTACTG 59.729 52.381 0.00 0.00 38.95 2.74
648 694 1.133482 AGCCCCAAAAGCTTGTACTGT 60.133 47.619 0.00 0.00 37.24 3.55
649 695 1.686587 GCCCCAAAAGCTTGTACTGTT 59.313 47.619 0.00 0.00 0.00 3.16
650 696 2.288213 GCCCCAAAAGCTTGTACTGTTC 60.288 50.000 0.00 0.00 0.00 3.18
651 697 2.955660 CCCCAAAAGCTTGTACTGTTCA 59.044 45.455 0.00 0.00 0.00 3.18
667 713 6.645790 ACTGTTCATGAAGCTTTTGAATCT 57.354 33.333 21.50 9.83 32.48 2.40
879 925 2.910319 TCTACAAGGCCCTGAAAAGCTA 59.090 45.455 8.77 0.00 0.00 3.32
883 929 2.489722 CAAGGCCCTGAAAAGCTAAGTC 59.510 50.000 0.00 0.00 0.00 3.01
902 987 2.993899 GTCCTCCGTGTGACAATACTTG 59.006 50.000 0.00 0.00 0.00 3.16
1087 2014 1.882623 TCATCGTCCTCATCTCCATCG 59.117 52.381 0.00 0.00 0.00 3.84
1131 2058 2.029918 TCTCGGCAAGGTGATCATATCG 60.030 50.000 0.00 0.00 0.00 2.92
1141 2068 5.844004 AGGTGATCATATCGACAACCTTAC 58.156 41.667 0.00 0.00 38.93 2.34
1142 2069 5.362717 AGGTGATCATATCGACAACCTTACA 59.637 40.000 0.00 0.00 38.93 2.41
1143 2070 5.692204 GGTGATCATATCGACAACCTTACAG 59.308 44.000 0.00 0.00 32.10 2.74
1144 2071 5.175856 GTGATCATATCGACAACCTTACAGC 59.824 44.000 0.00 0.00 0.00 4.40
1185 2113 1.740585 TGTCGCAAATTATGTTCCCCG 59.259 47.619 0.00 0.00 0.00 5.73
1189 2117 1.822371 GCAAATTATGTTCCCCGGTGT 59.178 47.619 0.00 0.00 0.00 4.16
1230 2163 4.373116 GCGCTGGTTCACCGGAGA 62.373 66.667 9.46 1.33 45.36 3.71
1304 2247 0.523072 CCATTGGCCTTCGTTCACTG 59.477 55.000 3.32 0.00 0.00 3.66
1316 2292 1.002576 CGTTCACTGATGTTGCTTGCA 60.003 47.619 0.00 0.00 0.00 4.08
1402 2378 1.079543 GCTGATGCTCGTGGTGTCT 60.080 57.895 0.00 0.00 36.03 3.41
1446 2422 0.466372 ATCGACGAGAGCCTCATGGA 60.466 55.000 3.01 0.00 34.57 3.41
1567 2549 3.724624 CTCAAGGGAGAGCAGGCT 58.275 61.111 0.00 0.00 44.26 4.58
1586 2568 4.015406 CAGCCACGGGGTACTGCA 62.015 66.667 5.12 0.00 36.17 4.41
1618 2600 9.869757 AAGCAGGTTTGAAAATGTTATTATACC 57.130 29.630 0.00 0.00 0.00 2.73
1619 2601 9.030452 AGCAGGTTTGAAAATGTTATTATACCA 57.970 29.630 0.00 0.00 0.00 3.25
1621 2603 9.801873 CAGGTTTGAAAATGTTATTATACCAGG 57.198 33.333 0.00 0.00 0.00 4.45
1623 2605 8.201464 GGTTTGAAAATGTTATTATACCAGGGG 58.799 37.037 0.00 0.00 0.00 4.79
1624 2606 8.973182 GTTTGAAAATGTTATTATACCAGGGGA 58.027 33.333 0.00 0.00 0.00 4.81
1625 2607 9.548631 TTTGAAAATGTTATTATACCAGGGGAA 57.451 29.630 0.00 0.00 0.00 3.97
1626 2608 9.722317 TTGAAAATGTTATTATACCAGGGGAAT 57.278 29.630 0.00 0.00 0.00 3.01
1628 2610 7.996098 AAATGTTATTATACCAGGGGAATCG 57.004 36.000 0.00 0.00 0.00 3.34
1629 2611 6.945636 ATGTTATTATACCAGGGGAATCGA 57.054 37.500 0.00 0.00 0.00 3.59
1630 2612 6.945636 TGTTATTATACCAGGGGAATCGAT 57.054 37.500 0.00 0.00 0.00 3.59
1631 2613 6.942976 TGTTATTATACCAGGGGAATCGATC 58.057 40.000 0.00 0.00 0.00 3.69
1632 2614 4.737855 ATTATACCAGGGGAATCGATCG 57.262 45.455 9.36 9.36 0.00 3.69
1652 2637 1.285641 GCCGGTTTGGACATGTGTG 59.714 57.895 1.15 0.00 42.00 3.82
1664 2649 3.971453 ATGTGTGAGAGTCGGCGCG 62.971 63.158 0.00 0.00 0.00 6.86
1865 2861 8.302047 CAGTGTACTTACTGTAACGCATCGTTA 61.302 40.741 7.61 7.61 43.85 3.18
1890 2888 7.630082 ACATCTGCCTACTTGGATTTTAGTAA 58.370 34.615 0.00 0.00 38.35 2.24
2043 3044 1.123928 CCTGGGGCTTCTACAGGTAG 58.876 60.000 0.00 0.00 45.21 3.18
2044 3045 1.622725 CCTGGGGCTTCTACAGGTAGT 60.623 57.143 6.37 0.00 45.21 2.73
2045 3046 2.358932 CCTGGGGCTTCTACAGGTAGTA 60.359 54.545 6.37 0.00 45.21 1.82
2080 3086 1.009829 CTGGTCCGTGCTTAGCATTC 58.990 55.000 11.03 0.00 41.91 2.67
2258 3272 2.355007 GGAAAATTGGCAACTGATGGGG 60.355 50.000 0.00 0.00 37.61 4.96
2267 3281 6.019656 TGGCAACTGATGGGGTAATTAATA 57.980 37.500 0.00 0.00 37.61 0.98
2268 3282 5.830991 TGGCAACTGATGGGGTAATTAATAC 59.169 40.000 0.00 0.00 37.61 1.89
2269 3283 6.068670 GGCAACTGATGGGGTAATTAATACT 58.931 40.000 0.00 0.00 34.74 2.12
2350 3364 0.679002 AGCAGCGCAAGTTCATCCAT 60.679 50.000 11.47 0.00 41.68 3.41
2409 3423 0.930310 CTGTGGATGGTACGCAATCG 59.070 55.000 0.00 0.00 42.43 3.34
2467 3484 4.315803 ACTACTTGCTGTATGTGTGAACC 58.684 43.478 0.00 0.00 0.00 3.62
2502 3525 2.963782 GACCCACATACGGTATCTTCCT 59.036 50.000 0.00 0.00 32.27 3.36
2587 3610 2.378547 AGGCTTGGTTTCCTGATGGTAA 59.621 45.455 0.00 0.00 34.23 2.85
2588 3611 2.755103 GGCTTGGTTTCCTGATGGTAAG 59.245 50.000 0.00 0.00 34.23 2.34
2634 3657 1.552226 GCATTCATGCGTGTGGATTG 58.448 50.000 5.68 0.00 44.67 2.67
2638 3666 0.615850 TCATGCGTGTGGATTGGGTA 59.384 50.000 5.68 0.00 0.00 3.69
2660 3688 6.863126 GGTATTGTTGTTTCTGATTTCTGGTG 59.137 38.462 0.00 0.00 0.00 4.17
2662 3690 4.277476 TGTTGTTTCTGATTTCTGGTGGT 58.723 39.130 0.00 0.00 0.00 4.16
2666 3694 5.659463 TGTTTCTGATTTCTGGTGGTTTTG 58.341 37.500 0.00 0.00 0.00 2.44
2667 3695 4.320608 TTCTGATTTCTGGTGGTTTTGC 57.679 40.909 0.00 0.00 0.00 3.68
2668 3696 3.295093 TCTGATTTCTGGTGGTTTTGCA 58.705 40.909 0.00 0.00 0.00 4.08
2669 3697 3.068024 TCTGATTTCTGGTGGTTTTGCAC 59.932 43.478 0.00 0.00 0.00 4.57
2688 3724 4.941263 TGCACCACAATACTATTTCTGGTC 59.059 41.667 5.42 3.45 29.23 4.02
2692 3728 4.809426 CCACAATACTATTTCTGGTCGACC 59.191 45.833 28.17 28.17 0.00 4.79
2814 3954 5.297029 AGTTCCTTCTTCTTTTTCGAACCAG 59.703 40.000 0.00 0.00 30.80 4.00
2821 3961 7.576861 TCTTCTTTTTCGAACCAGGTATTTT 57.423 32.000 0.00 0.00 0.00 1.82
2850 4059 9.166126 GTTGTTGTACTAATAACTTGAGTTTGC 57.834 33.333 1.20 0.00 39.31 3.68
2929 4138 5.006746 CACCGGTATGCTTCATTTCTCTTAC 59.993 44.000 6.87 0.00 0.00 2.34
2930 4139 4.511826 CCGGTATGCTTCATTTCTCTTACC 59.488 45.833 0.00 0.00 0.00 2.85
2984 4204 4.843147 TGCGTAACAAAGTTGACAATGAG 58.157 39.130 0.00 0.00 0.00 2.90
3066 4286 3.257393 CTGTAAGTGCCTGTGATCTGAC 58.743 50.000 0.00 0.00 0.00 3.51
3067 4287 2.899900 TGTAAGTGCCTGTGATCTGACT 59.100 45.455 0.00 0.00 0.00 3.41
3086 4306 7.671302 TCTGACTCTCTAATTGCTTTACTGTT 58.329 34.615 0.00 0.00 0.00 3.16
3087 4307 7.600375 TCTGACTCTCTAATTGCTTTACTGTTG 59.400 37.037 0.00 0.00 0.00 3.33
3088 4308 6.147821 TGACTCTCTAATTGCTTTACTGTTGC 59.852 38.462 0.00 0.00 0.00 4.17
3098 4319 4.168760 GCTTTACTGTTGCCATCATTCAC 58.831 43.478 0.00 0.00 0.00 3.18
3115 4336 2.053116 CACGTGCGTGTGCTTGAC 60.053 61.111 15.60 0.00 43.34 3.18
3116 4337 2.202878 ACGTGCGTGTGCTTGACT 60.203 55.556 0.00 0.00 43.34 3.41
3117 4338 2.246397 CGTGCGTGTGCTTGACTG 59.754 61.111 0.00 0.00 43.34 3.51
3118 4339 2.525248 CGTGCGTGTGCTTGACTGT 61.525 57.895 0.00 0.00 43.34 3.55
3119 4340 1.212455 CGTGCGTGTGCTTGACTGTA 61.212 55.000 0.00 0.00 43.34 2.74
3120 4341 0.934496 GTGCGTGTGCTTGACTGTAA 59.066 50.000 0.00 0.00 43.34 2.41
3121 4342 1.070577 GTGCGTGTGCTTGACTGTAAG 60.071 52.381 0.00 0.00 43.34 2.34
3122 4343 1.217882 GCGTGTGCTTGACTGTAAGT 58.782 50.000 0.00 0.00 45.60 2.24
3123 4344 1.070577 GCGTGTGCTTGACTGTAAGTG 60.071 52.381 0.00 0.00 43.58 3.16
3124 4345 4.788897 GCGTGTGCTTGACTGTAAGTGC 62.789 54.545 0.00 0.00 43.58 4.40
3182 4403 8.892723 CCTAATTGCTTTACTGTTGTCATCATA 58.107 33.333 0.00 0.00 0.00 2.15
3281 4502 0.172803 GATGGCGTACGAGGTGAACT 59.827 55.000 21.65 0.00 0.00 3.01
3349 4570 0.826672 ACGACCTCTTCTGGTTCCGT 60.827 55.000 0.00 0.00 41.00 4.69
3517 4738 3.052082 CTCTTGTGGGTGCAGGCG 61.052 66.667 0.00 0.00 0.00 5.52
3550 4771 0.107312 ACTCCTGCATCATGGACAGC 60.107 55.000 0.00 0.00 0.00 4.40
3568 4789 2.005960 GCCTCGGATACAGCGTGTCT 62.006 60.000 5.70 0.00 0.00 3.41
3637 4861 4.457810 GAATCACACATGTTTGTCTGTCG 58.542 43.478 11.59 0.00 32.34 4.35
3747 5022 1.850377 CCATCGTCTCTCATGTGAGC 58.150 55.000 18.01 12.60 41.80 4.26
3808 5091 3.340814 ACAGAGCCTTGACAAATCGAT 57.659 42.857 0.00 0.00 0.00 3.59
3809 5092 4.471904 ACAGAGCCTTGACAAATCGATA 57.528 40.909 0.00 0.00 0.00 2.92
3810 5093 4.832248 ACAGAGCCTTGACAAATCGATAA 58.168 39.130 0.00 0.00 0.00 1.75
3811 5094 5.245531 ACAGAGCCTTGACAAATCGATAAA 58.754 37.500 0.00 0.00 0.00 1.40
4008 5291 1.606531 GCAGGACAAGGCAGAGGAT 59.393 57.895 0.00 0.00 0.00 3.24
4075 5358 8.664211 ATTTTTATTTTGTAAAACGGAGGCAA 57.336 26.923 0.00 0.00 0.00 4.52
4078 5361 8.488651 TTTATTTTGTAAAACGGAGGCAAAAA 57.511 26.923 0.00 1.23 40.73 1.94
4079 5362 8.664211 TTATTTTGTAAAACGGAGGCAAAAAT 57.336 26.923 0.00 7.07 40.73 1.82
4082 5365 8.488651 TTTTGTAAAACGGAGGCAAAAATTTA 57.511 26.923 0.00 0.00 36.50 1.40
4083 5366 7.466193 TTGTAAAACGGAGGCAAAAATTTAC 57.534 32.000 0.00 0.00 34.19 2.01
4085 5368 4.948341 AAACGGAGGCAAAAATTTACCT 57.052 36.364 6.97 6.97 36.64 3.08
4087 5370 6.408107 AAACGGAGGCAAAAATTTACCTTA 57.592 33.333 8.32 0.00 34.10 2.69
4088 5371 6.599356 AACGGAGGCAAAAATTTACCTTAT 57.401 33.333 8.32 0.00 34.10 1.73
4089 5372 6.203808 ACGGAGGCAAAAATTTACCTTATC 57.796 37.500 8.32 2.98 34.10 1.75
4090 5373 5.949952 ACGGAGGCAAAAATTTACCTTATCT 59.050 36.000 8.32 0.00 34.10 1.98
4091 5374 6.095021 ACGGAGGCAAAAATTTACCTTATCTC 59.905 38.462 8.32 3.06 34.10 2.75
4092 5375 6.318900 CGGAGGCAAAAATTTACCTTATCTCT 59.681 38.462 8.32 0.00 34.10 3.10
4093 5376 7.497909 CGGAGGCAAAAATTTACCTTATCTCTA 59.502 37.037 8.32 0.00 34.10 2.43
4094 5377 8.622157 GGAGGCAAAAATTTACCTTATCTCTAC 58.378 37.037 8.32 0.00 34.10 2.59
4095 5378 9.397280 GAGGCAAAAATTTACCTTATCTCTACT 57.603 33.333 8.32 0.00 34.10 2.57
4096 5379 9.755122 AGGCAAAAATTTACCTTATCTCTACTT 57.245 29.630 0.00 0.00 29.56 2.24
4152 5435 1.200020 CTTTCCTAAGCGCACCCAAAG 59.800 52.381 11.47 7.30 0.00 2.77
4467 5850 3.231736 GCCGGATCCGCTCCCTTA 61.232 66.667 29.12 0.00 41.49 2.69
4708 6480 3.315142 GATGGAGGGCGTGTGCAGA 62.315 63.158 0.00 0.00 45.35 4.26
4928 8878 5.402630 TCAGGTATGTTCTCTGCCCATATA 58.597 41.667 0.00 0.00 0.00 0.86
4945 8896 7.050377 GCCCATATATGTATTGTATGTCAGCT 58.950 38.462 11.73 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.089920 CGCCATGGAGAAGTTCAAGG 58.910 55.000 18.40 0.63 0.00 3.61
88 89 1.001378 CTGGGTGAAAACTTGCCTTCG 60.001 52.381 0.00 0.00 0.00 3.79
146 147 1.338769 GGTTCTGCCTGGTGATAACGT 60.339 52.381 0.00 0.00 0.00 3.99
167 168 2.268920 GATCTGCCGGTGCTCCAA 59.731 61.111 1.90 0.00 38.71 3.53
212 256 2.752238 CGGCTCCGTCTCTGACCT 60.752 66.667 0.00 0.00 34.35 3.85
244 288 3.952508 TGCATGCGGTGGTGGTCT 61.953 61.111 14.09 0.00 0.00 3.85
343 387 2.513895 CGGTTTCCCCTGGTGTGT 59.486 61.111 0.00 0.00 0.00 3.72
442 486 4.521062 GCTGGATCTGGCGCGAGT 62.521 66.667 19.32 6.76 0.00 4.18
470 514 4.610714 GGCGGCGGGATCTCTTCC 62.611 72.222 9.78 0.00 44.62 3.46
539 583 3.756783 CCCTCCCCCGACCTCTCT 61.757 72.222 0.00 0.00 0.00 3.10
606 650 4.124943 TCTCCCGACTCCTCCCGG 62.125 72.222 0.00 0.00 44.94 5.73
620 666 0.962855 GCTTTTGGGGCTGGACTCTC 60.963 60.000 0.00 0.00 0.00 3.20
621 667 1.075659 GCTTTTGGGGCTGGACTCT 59.924 57.895 0.00 0.00 0.00 3.24
622 668 0.540597 AAGCTTTTGGGGCTGGACTC 60.541 55.000 0.00 0.00 40.19 3.36
623 669 0.829182 CAAGCTTTTGGGGCTGGACT 60.829 55.000 0.00 0.00 40.19 3.85
624 670 1.115326 ACAAGCTTTTGGGGCTGGAC 61.115 55.000 0.00 0.00 40.19 4.02
625 671 0.480690 TACAAGCTTTTGGGGCTGGA 59.519 50.000 0.00 0.00 40.19 3.86
626 672 0.603065 GTACAAGCTTTTGGGGCTGG 59.397 55.000 0.00 0.00 40.19 4.85
627 673 1.270550 CAGTACAAGCTTTTGGGGCTG 59.729 52.381 0.00 0.00 40.19 4.85
628 674 1.133482 ACAGTACAAGCTTTTGGGGCT 60.133 47.619 0.00 0.00 42.31 5.19
629 675 1.328279 ACAGTACAAGCTTTTGGGGC 58.672 50.000 0.00 0.00 0.00 5.80
630 676 2.955660 TGAACAGTACAAGCTTTTGGGG 59.044 45.455 0.00 0.00 0.00 4.96
631 677 4.278170 TCATGAACAGTACAAGCTTTTGGG 59.722 41.667 0.00 0.00 0.00 4.12
632 678 5.437289 TCATGAACAGTACAAGCTTTTGG 57.563 39.130 0.00 0.00 0.00 3.28
633 679 5.400485 GCTTCATGAACAGTACAAGCTTTTG 59.600 40.000 3.38 0.00 0.00 2.44
634 680 5.300286 AGCTTCATGAACAGTACAAGCTTTT 59.700 36.000 3.38 0.00 39.05 2.27
635 681 4.823989 AGCTTCATGAACAGTACAAGCTTT 59.176 37.500 3.38 0.00 39.05 3.51
636 682 4.392940 AGCTTCATGAACAGTACAAGCTT 58.607 39.130 3.38 0.00 39.05 3.74
637 683 4.013267 AGCTTCATGAACAGTACAAGCT 57.987 40.909 3.38 6.24 37.52 3.74
638 684 4.756084 AAGCTTCATGAACAGTACAAGC 57.244 40.909 3.38 3.75 0.00 4.01
639 685 6.728200 TCAAAAGCTTCATGAACAGTACAAG 58.272 36.000 3.38 0.00 0.00 3.16
640 686 6.691754 TCAAAAGCTTCATGAACAGTACAA 57.308 33.333 3.38 0.00 0.00 2.41
641 687 6.691754 TTCAAAAGCTTCATGAACAGTACA 57.308 33.333 18.58 1.55 0.00 2.90
642 688 7.588512 AGATTCAAAAGCTTCATGAACAGTAC 58.411 34.615 22.63 14.40 36.03 2.73
643 689 7.750229 AGATTCAAAAGCTTCATGAACAGTA 57.250 32.000 22.63 7.55 36.03 2.74
644 690 6.645790 AGATTCAAAAGCTTCATGAACAGT 57.354 33.333 22.63 12.16 36.03 3.55
645 691 7.149015 CGAAAGATTCAAAAGCTTCATGAACAG 60.149 37.037 22.63 0.00 35.82 3.16
646 692 6.638063 CGAAAGATTCAAAAGCTTCATGAACA 59.362 34.615 22.63 8.69 35.82 3.18
647 693 6.399354 GCGAAAGATTCAAAAGCTTCATGAAC 60.399 38.462 22.63 17.48 35.82 3.18
648 694 5.630680 GCGAAAGATTCAAAAGCTTCATGAA 59.369 36.000 22.49 22.49 35.82 2.57
649 695 5.156355 GCGAAAGATTCAAAAGCTTCATGA 58.844 37.500 0.00 5.02 35.82 3.07
650 696 4.029861 CGCGAAAGATTCAAAAGCTTCATG 59.970 41.667 0.00 2.30 35.82 3.07
651 697 4.161333 CGCGAAAGATTCAAAAGCTTCAT 58.839 39.130 0.00 0.00 35.82 2.57
667 713 4.033817 CCGTATGGTATTTTAACCGCGAAA 59.966 41.667 8.23 0.00 42.91 3.46
752 798 0.965363 TCCCAAAGGCCAAAGCGATC 60.965 55.000 5.01 0.00 41.24 3.69
879 925 2.897969 AGTATTGTCACACGGAGGACTT 59.102 45.455 0.00 0.00 35.11 3.01
929 1852 1.978542 CACCGTACTCTTCGTCCTTG 58.021 55.000 0.00 0.00 0.00 3.61
992 1919 2.046988 CGCCAGCCATCACTGACA 60.047 61.111 0.00 0.00 40.25 3.58
1087 2014 2.202676 CAGGGAGCGCTCGAAGAC 60.203 66.667 29.81 16.04 0.00 3.01
1131 2058 0.250727 TGGCTGGCTGTAAGGTTGTC 60.251 55.000 2.00 0.00 0.00 3.18
1141 2068 1.699656 CGAACGAATCTGGCTGGCTG 61.700 60.000 2.00 1.75 0.00 4.85
1142 2069 1.448540 CGAACGAATCTGGCTGGCT 60.449 57.895 2.00 0.00 0.00 4.75
1143 2070 0.811616 ATCGAACGAATCTGGCTGGC 60.812 55.000 0.12 0.00 0.00 4.85
1144 2071 1.202463 AGATCGAACGAATCTGGCTGG 60.202 52.381 0.12 0.00 0.00 4.85
1185 2113 1.673033 CCCTCGTGAATCAGTGACACC 60.673 57.143 0.84 0.00 0.00 4.16
1189 2117 1.546029 CACTCCCTCGTGAATCAGTGA 59.454 52.381 0.00 0.00 37.06 3.41
1230 2163 1.749638 CGCCTCGTACAGGGTCTCT 60.750 63.158 11.72 0.00 43.70 3.10
1304 2247 2.227149 TCAGTGACATGCAAGCAACATC 59.773 45.455 0.00 0.00 0.00 3.06
1316 2292 0.531974 AAACCACGCGTCAGTGACAT 60.532 50.000 22.66 5.03 44.43 3.06
1402 2378 5.163468 GCAGATCTTCTGTATCAGGTCTTGA 60.163 44.000 6.40 0.00 45.94 3.02
1537 2513 3.306595 CTTGAGCAGCCTCCTCGCA 62.307 63.158 0.00 0.00 37.29 5.10
1567 2549 4.015406 CAGTACCCCGTGGCTGCA 62.015 66.667 0.50 0.00 33.59 4.41
1586 2568 1.388547 TTTCAAACCTGCTTGCTCGT 58.611 45.000 0.00 0.00 0.00 4.18
1594 2576 9.301153 CTGGTATAATAACATTTTCAAACCTGC 57.699 33.333 0.00 0.00 0.00 4.85
1618 2600 2.031163 GCCCGATCGATTCCCCTG 59.969 66.667 18.66 0.00 0.00 4.45
1619 2601 3.242291 GGCCCGATCGATTCCCCT 61.242 66.667 18.66 0.00 0.00 4.79
1621 2603 4.681978 CCGGCCCGATCGATTCCC 62.682 72.222 18.66 9.72 0.00 3.97
1623 2605 1.523032 AAACCGGCCCGATCGATTC 60.523 57.895 18.66 4.66 0.00 2.52
1624 2606 1.817941 CAAACCGGCCCGATCGATT 60.818 57.895 18.66 0.00 0.00 3.34
1625 2607 2.203015 CAAACCGGCCCGATCGAT 60.203 61.111 18.66 0.00 0.00 3.59
1626 2608 4.460683 CCAAACCGGCCCGATCGA 62.461 66.667 18.66 0.00 0.00 3.59
1628 2610 2.822701 GTCCAAACCGGCCCGATC 60.823 66.667 3.71 0.00 33.14 3.69
1629 2611 2.978946 ATGTCCAAACCGGCCCGAT 61.979 57.895 3.71 0.00 33.14 4.18
1630 2612 3.642503 ATGTCCAAACCGGCCCGA 61.643 61.111 3.71 0.00 33.14 5.14
1631 2613 3.439540 CATGTCCAAACCGGCCCG 61.440 66.667 0.00 0.00 33.14 6.13
1632 2614 2.282887 ACATGTCCAAACCGGCCC 60.283 61.111 0.00 0.00 33.14 5.80
1652 2637 4.456253 TTCGACGCGCCGACTCTC 62.456 66.667 19.25 0.00 38.39 3.20
1664 2649 3.492011 TCGCAGTTTTCTAAACCTTCGAC 59.508 43.478 0.00 0.00 0.00 4.20
1668 2653 6.228258 TGTCTATCGCAGTTTTCTAAACCTT 58.772 36.000 0.00 0.00 0.00 3.50
1686 2671 3.687125 TGGACAGAGTCGACTTGTCTAT 58.313 45.455 34.03 17.67 32.65 1.98
1837 2830 9.875729 ACGATGCGTTACAGTAAGTACACTGAG 62.876 44.444 17.63 8.56 42.18 3.35
1865 2861 6.067217 ACTAAAATCCAAGTAGGCAGATGT 57.933 37.500 0.00 0.00 37.29 3.06
1890 2888 4.081087 ACGTATACAAGATGGGCTCAAAGT 60.081 41.667 3.32 0.00 0.00 2.66
2043 3044 5.402997 ACCAGCAGTAGTTTAGGAGTTAC 57.597 43.478 0.00 0.00 0.00 2.50
2044 3045 4.465305 GGACCAGCAGTAGTTTAGGAGTTA 59.535 45.833 0.00 0.00 0.00 2.24
2045 3046 3.261137 GGACCAGCAGTAGTTTAGGAGTT 59.739 47.826 0.00 0.00 0.00 3.01
2080 3086 1.602377 GGTCAACGTTGGAAGTTCAGG 59.398 52.381 27.02 0.00 0.00 3.86
2258 3272 8.813643 AGCACACCTCGATTAGTATTAATTAC 57.186 34.615 0.00 0.00 29.67 1.89
2267 3281 1.276421 AGCAAGCACACCTCGATTAGT 59.724 47.619 0.00 0.00 0.00 2.24
2268 3282 2.015736 AGCAAGCACACCTCGATTAG 57.984 50.000 0.00 0.00 0.00 1.73
2269 3283 2.076100 CAAGCAAGCACACCTCGATTA 58.924 47.619 0.00 0.00 0.00 1.75
2350 3364 1.250154 CGTACCCCTTGTACCGGTCA 61.250 60.000 12.40 6.49 45.89 4.02
2467 3484 3.633361 GGGTCACCCAAGTTCAGAG 57.367 57.895 8.52 0.00 44.65 3.35
2488 3511 3.243771 CGCTGGAAAGGAAGATACCGTAT 60.244 47.826 0.00 0.00 34.73 3.06
2490 3513 1.134788 CGCTGGAAAGGAAGATACCGT 60.135 52.381 0.00 0.00 34.73 4.83
2502 3525 3.243068 GCTTGAAGAAAGAACGCTGGAAA 60.243 43.478 0.00 0.00 38.24 3.13
2587 3610 8.810990 AGTAAGTACAGTAAGAAGCATCTACT 57.189 34.615 0.00 0.00 33.77 2.57
2588 3611 9.291664 CAAGTAAGTACAGTAAGAAGCATCTAC 57.708 37.037 0.00 0.00 33.77 2.59
2634 3657 6.015434 ACCAGAAATCAGAAACAACAATACCC 60.015 38.462 0.00 0.00 0.00 3.69
2638 3666 5.363580 ACCACCAGAAATCAGAAACAACAAT 59.636 36.000 0.00 0.00 0.00 2.71
2662 3690 6.686630 CCAGAAATAGTATTGTGGTGCAAAA 58.313 36.000 13.25 0.00 40.91 2.44
2669 3697 4.809426 GGTCGACCAGAAATAGTATTGTGG 59.191 45.833 29.75 17.50 46.34 4.17
2671 3699 5.934402 AGGTCGACCAGAAATAGTATTGT 57.066 39.130 35.00 7.40 38.89 2.71
2672 3700 6.802608 TGTAGGTCGACCAGAAATAGTATTG 58.197 40.000 35.00 0.00 38.89 1.90
2673 3701 6.040616 CCTGTAGGTCGACCAGAAATAGTATT 59.959 42.308 35.00 13.18 38.89 1.89
2674 3702 5.535406 CCTGTAGGTCGACCAGAAATAGTAT 59.465 44.000 35.00 13.71 38.89 2.12
2675 3703 4.885907 CCTGTAGGTCGACCAGAAATAGTA 59.114 45.833 35.00 14.13 38.89 1.82
2676 3704 3.700038 CCTGTAGGTCGACCAGAAATAGT 59.300 47.826 35.00 15.20 38.89 2.12
2677 3705 3.952323 TCCTGTAGGTCGACCAGAAATAG 59.048 47.826 35.00 22.03 38.89 1.73
2688 3724 0.888619 TGAAGTGCTCCTGTAGGTCG 59.111 55.000 0.00 0.00 36.34 4.79
2692 3728 0.539051 CCCCTGAAGTGCTCCTGTAG 59.461 60.000 0.00 0.00 0.00 2.74
2824 3964 9.166126 GCAAACTCAAGTTATTAGTACAACAAC 57.834 33.333 0.00 0.00 37.25 3.32
2825 3965 9.116067 AGCAAACTCAAGTTATTAGTACAACAA 57.884 29.630 0.00 0.00 37.25 2.83
2826 3966 8.671384 AGCAAACTCAAGTTATTAGTACAACA 57.329 30.769 0.00 0.00 37.25 3.33
2929 4138 3.880047 TGGACAAGTATACCGAAGTGG 57.120 47.619 0.00 0.00 46.41 4.00
2930 4139 4.804139 GTCATGGACAAGTATACCGAAGTG 59.196 45.833 0.00 0.00 32.09 3.16
2984 4204 2.143122 TGCATCACGAGTTTTCAGTCC 58.857 47.619 0.00 0.00 0.00 3.85
3061 4281 7.233389 ACAGTAAAGCAATTAGAGAGTCAGA 57.767 36.000 0.00 0.00 0.00 3.27
3066 4286 5.412594 TGGCAACAGTAAAGCAATTAGAGAG 59.587 40.000 0.00 0.00 46.17 3.20
3067 4287 5.312895 TGGCAACAGTAAAGCAATTAGAGA 58.687 37.500 0.00 0.00 46.17 3.10
3086 4306 1.875262 GCACGTGTGAATGATGGCA 59.125 52.632 18.38 0.00 0.00 4.92
3087 4307 1.226101 CGCACGTGTGAATGATGGC 60.226 57.895 24.50 0.00 0.00 4.40
3088 4308 0.179217 CACGCACGTGTGAATGATGG 60.179 55.000 34.03 10.86 42.55 3.51
3111 4332 3.834813 AGATGAGAGGCACTTACAGTCAA 59.165 43.478 0.00 0.00 41.55 3.18
3114 4335 3.435275 TCAGATGAGAGGCACTTACAGT 58.565 45.455 0.00 0.00 41.55 3.55
3115 4336 4.341806 AGATCAGATGAGAGGCACTTACAG 59.658 45.833 0.00 0.00 41.55 2.74
3116 4337 4.099113 CAGATCAGATGAGAGGCACTTACA 59.901 45.833 0.00 0.00 41.55 2.41
3117 4338 4.340666 TCAGATCAGATGAGAGGCACTTAC 59.659 45.833 0.00 0.00 41.55 2.34
3118 4339 4.540715 TCAGATCAGATGAGAGGCACTTA 58.459 43.478 0.00 0.00 41.55 2.24
3119 4340 3.372897 TCAGATCAGATGAGAGGCACTT 58.627 45.455 0.00 0.00 41.55 3.16
3121 4342 3.306225 GGATCAGATCAGATGAGAGGCAC 60.306 52.174 12.66 0.00 0.00 5.01
3122 4343 2.898612 GGATCAGATCAGATGAGAGGCA 59.101 50.000 12.66 0.00 0.00 4.75
3123 4344 2.898612 TGGATCAGATCAGATGAGAGGC 59.101 50.000 12.66 0.00 0.00 4.70
3124 4345 3.057386 CGTGGATCAGATCAGATGAGAGG 60.057 52.174 12.66 0.00 0.00 3.69
3125 4346 3.819902 TCGTGGATCAGATCAGATGAGAG 59.180 47.826 12.66 0.00 0.00 3.20
3129 4350 3.317430 TGACTCGTGGATCAGATCAGATG 59.683 47.826 12.66 3.99 0.00 2.90
3182 4403 0.885196 ACACCAAAGCACACGTTTGT 59.115 45.000 3.29 0.00 33.75 2.83
3349 4570 2.041922 AGCAGCATCCGGGGACTA 60.042 61.111 0.00 0.00 0.00 2.59
3517 4738 1.734465 CAGGAGTTGAAGCCGAACATC 59.266 52.381 0.00 0.00 0.00 3.06
3550 4771 1.264557 CTAGACACGCTGTATCCGAGG 59.735 57.143 0.00 0.00 0.00 4.63
3588 4809 1.221293 CAAGAGGGGAGAGCAGCTG 59.779 63.158 10.11 10.11 0.00 4.24
3637 4861 4.440880 GGTCAGCTATGCATCTATCATCC 58.559 47.826 0.19 0.00 0.00 3.51
3747 5022 0.888619 TCTGGTTCCTGACTACTGCG 59.111 55.000 0.00 0.00 0.00 5.18
3808 5091 8.369424 CCCCATCTGCATCAATGAATTTATTTA 58.631 33.333 5.66 0.00 0.00 1.40
3809 5092 7.071447 TCCCCATCTGCATCAATGAATTTATTT 59.929 33.333 5.66 0.00 0.00 1.40
3810 5093 6.555738 TCCCCATCTGCATCAATGAATTTATT 59.444 34.615 5.66 0.00 0.00 1.40
3811 5094 6.079336 TCCCCATCTGCATCAATGAATTTAT 58.921 36.000 5.66 0.00 0.00 1.40
4008 5291 2.224597 TGATGAAAGTTGAGCAGCTGGA 60.225 45.455 17.12 0.00 0.00 3.86
4060 5343 5.984323 GGTAAATTTTTGCCTCCGTTTTACA 59.016 36.000 0.00 0.00 39.49 2.41
4061 5344 6.456447 GGTAAATTTTTGCCTCCGTTTTAC 57.544 37.500 0.00 0.00 39.49 2.01
4120 5403 6.596106 TGCGCTTAGGAAAGAATATGTTTACA 59.404 34.615 9.73 0.00 34.37 2.41
4152 5435 0.584876 GGTTGTTCTGTGTACGTGCC 59.415 55.000 0.00 0.00 0.00 5.01
4467 5850 1.216710 CTTCGCCTTCGGAGAGCTT 59.783 57.895 0.00 0.00 44.02 3.74
4928 8878 7.826252 ACTTCTTGAAGCTGACATACAATACAT 59.174 33.333 9.98 0.00 0.00 2.29
4945 8896 3.971305 TGAGAGTTGGGGTACTTCTTGAA 59.029 43.478 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.