Multiple sequence alignment - TraesCS1B01G150500

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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 TraesCS1B01G150500 chr1B 100.000 7787 0 0 1 7787 230942119 230949905 0.000000e+00 14380.0
1 TraesCS1B01G150500 chr1D 96.921 3637 84 8 4169 7786 153773191 153776818 0.000000e+00 6071.0
2 TraesCS1B01G150500 chr1D 94.904 2649 80 21 1 2627 153769105 153771720 0.000000e+00 4093.0
3 TraesCS1B01G150500 chr1D 94.678 1165 29 11 2717 3870 153771722 153772864 0.000000e+00 1777.0
4 TraesCS1B01G150500 chr1D 94.860 214 11 0 3959 4172 153772865 153773078 1.250000e-87 335.0
5 TraesCS1B01G150500 chr1A 96.799 3530 91 6 4275 7786 208212457 208208932 0.000000e+00 5873.0
6 TraesCS1B01G150500 chr1A 96.351 2220 52 5 408 2627 208216271 208214081 0.000000e+00 3624.0
7 TraesCS1B01G150500 chr1A 95.280 1462 37 5 2717 4172 208214082 208212647 0.000000e+00 2289.0
8 TraesCS1B01G150500 chr1A 95.205 855 41 0 5204 6058 207986861 207986007 0.000000e+00 1352.0
9 TraesCS1B01G150500 chr1A 95.216 439 21 0 6057 6495 207957766 207957328 0.000000e+00 695.0
10 TraesCS1B01G150500 chr1A 90.654 428 21 7 3 412 208216720 208216294 1.140000e-152 551.0
11 TraesCS1B01G150500 chr1A 95.000 80 2 1 4169 4246 208212534 208212455 2.950000e-24 124.0
12 TraesCS1B01G150500 chr4B 86.091 2502 320 21 4305 6789 203850380 203847890 0.000000e+00 2667.0
13 TraesCS1B01G150500 chr4B 78.792 712 121 24 2948 3637 203851762 203851059 1.190000e-122 451.0
14 TraesCS1B01G150500 chr4B 84.286 140 18 3 96 232 464078751 464078613 4.900000e-27 134.0
15 TraesCS1B01G150500 chr4D 86.006 2501 320 23 4307 6789 172023461 172025949 0.000000e+00 2652.0
16 TraesCS1B01G150500 chr4D 78.571 714 119 27 2948 3637 172022074 172022777 2.580000e-119 440.0
17 TraesCS1B01G150500 chr4A 85.914 2499 326 20 4307 6789 415680871 415683359 0.000000e+00 2641.0
18 TraesCS1B01G150500 chr4A 78.711 714 118 28 2948 3637 415679487 415680190 5.540000e-121 446.0
19 TraesCS1B01G150500 chr4A 94.175 103 2 1 2624 2722 573631105 573631003 3.760000e-33 154.0
20 TraesCS1B01G150500 chrUn 98.465 391 6 0 1603 1993 479833821 479833431 0.000000e+00 689.0
21 TraesCS1B01G150500 chr5D 82.423 421 58 12 4596 5014 55548073 55547667 3.460000e-93 353.0
22 TraesCS1B01G150500 chr5D 84.298 242 31 6 2925 3163 55548836 55548599 6.080000e-56 230.0
23 TraesCS1B01G150500 chr5D 83.128 243 29 11 2925 3161 55545059 55544823 2.200000e-50 211.0
24 TraesCS1B01G150500 chr5B 83.750 240 32 6 2925 3161 57977296 57977061 3.660000e-53 220.0
25 TraesCS1B01G150500 chr5A 84.513 226 24 8 2925 3147 44287269 44287052 6.120000e-51 213.0
26 TraesCS1B01G150500 chr5A 90.551 127 11 1 1459 1585 452465229 452465104 4.830000e-37 167.0
27 TraesCS1B01G150500 chr6B 92.913 127 9 0 1459 1585 538999208 538999334 1.330000e-42 185.0
28 TraesCS1B01G150500 chr6B 92.683 82 4 2 1505 1585 69881564 69881644 4.940000e-22 117.0
29 TraesCS1B01G150500 chr6B 92.593 81 6 0 1505 1585 317011227 317011307 4.940000e-22 117.0
30 TraesCS1B01G150500 chr3A 96.907 97 3 0 2626 2722 83750312 83750216 6.250000e-36 163.0
31 TraesCS1B01G150500 chr2D 95.146 103 1 1 2624 2722 532305900 532306002 8.090000e-35 159.0
32 TraesCS1B01G150500 chr7D 94.340 106 1 2 2624 2725 617181762 617181658 2.910000e-34 158.0
33 TraesCS1B01G150500 chr7D 91.379 116 3 4 2621 2729 60439590 60439705 1.350000e-32 152.0
34 TraesCS1B01G150500 chr7D 82.278 79 6 8 2582 2657 430131623 430131550 2.350000e-05 62.1
35 TraesCS1B01G150500 chr7A 95.098 102 1 1 2626 2723 629780021 629780122 2.910000e-34 158.0
36 TraesCS1B01G150500 chr7A 82.051 156 20 6 80 232 116000449 116000299 8.200000e-25 126.0
37 TraesCS1B01G150500 chr7A 92.593 81 6 0 1505 1585 565741845 565741765 4.940000e-22 117.0
38 TraesCS1B01G150500 chr3B 93.519 108 2 2 2615 2718 561029528 561029422 1.050000e-33 156.0
39 TraesCS1B01G150500 chr3B 92.593 81 6 0 1505 1585 15816199 15816119 4.940000e-22 117.0
40 TraesCS1B01G150500 chr6A 94.175 103 2 1 2624 2722 40170357 40170255 3.760000e-33 154.0
41 TraesCS1B01G150500 chr6A 94.175 103 2 1 2624 2722 557906859 557906757 3.760000e-33 154.0
42 TraesCS1B01G150500 chr6A 92.593 81 6 0 1505 1585 20530069 20530149 4.940000e-22 117.0
43 TraesCS1B01G150500 chr6A 90.141 71 7 0 1 71 379034967 379034897 8.320000e-15 93.5
44 TraesCS1B01G150500 chr6A 90.141 71 7 0 1 71 379044012 379043942 8.320000e-15 93.5
45 TraesCS1B01G150500 chr6D 85.714 91 11 2 143 232 326443394 326443483 2.310000e-15 95.3


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 TraesCS1B01G150500 chr1B 230942119 230949905 7786 False 14380.000000 14380 100.00000 1 7787 1 chr1B.!!$F1 7786
1 TraesCS1B01G150500 chr1D 153769105 153776818 7713 False 3069.000000 6071 95.34075 1 7786 4 chr1D.!!$F1 7785
2 TraesCS1B01G150500 chr1A 208208932 208216720 7788 True 2492.200000 5873 94.81680 3 7786 5 chr1A.!!$R3 7783
3 TraesCS1B01G150500 chr1A 207986007 207986861 854 True 1352.000000 1352 95.20500 5204 6058 1 chr1A.!!$R2 854
4 TraesCS1B01G150500 chr4B 203847890 203851762 3872 True 1559.000000 2667 82.44150 2948 6789 2 chr4B.!!$R2 3841
5 TraesCS1B01G150500 chr4D 172022074 172025949 3875 False 1546.000000 2652 82.28850 2948 6789 2 chr4D.!!$F1 3841
6 TraesCS1B01G150500 chr4A 415679487 415683359 3872 False 1543.500000 2641 82.31250 2948 6789 2 chr4A.!!$F1 3841
7 TraesCS1B01G150500 chr5D 55544823 55548836 4013 True 264.666667 353 83.28300 2925 5014 3 chr5D.!!$R1 2089

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
500 548 0.040067 CCTTTTCAACGAGTGCAGCC 60.040 55.000 0.00 0.00 0.00 4.85 F
502 550 0.749818 TTTTCAACGAGTGCAGCCCA 60.750 50.000 0.00 0.00 0.00 5.36 F
1917 1965 1.355066 CCGTGAAGGAAGCTTCTCGC 61.355 60.000 25.05 19.78 44.12 5.03 F
2358 2406 0.109597 GCAAGTTCTGGCACAATCCG 60.110 55.000 0.00 0.00 38.70 4.18 F
3536 3619 1.749634 AGGTACAGTCAGACGCCATAC 59.250 52.381 0.00 0.00 0.00 2.39 F
4882 5296 1.202582 AGTACCACTAACAGCAGCTCG 59.797 52.381 0.00 0.00 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1543 1591 0.106708 TCAGTGTCACCAGGTTCAGC 59.893 55.000 0.00 0.0 0.00 4.26 R
1949 1997 0.257039 ATCCCTGATGACTGGTTGGC 59.743 55.000 0.00 0.0 34.02 4.52 R
3851 4114 2.292845 TCGTGCAGTGCAAAATTCATCA 59.707 40.909 21.67 0.0 41.47 3.07 R
4124 4393 2.237143 GTCCATGAACCTCATCACAGGA 59.763 50.000 0.00 0.0 34.28 3.86 R
5470 5888 0.385390 CGTTGGCAAAACTGGCTTCT 59.615 50.000 0.00 0.0 35.21 2.85 R
6842 9734 0.776810 TCCAACCAAGCTTCATCCCA 59.223 50.000 0.00 0.0 0.00 4.37 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
103 104 4.460263 AGTTGTGTTTTCATCTAGGTGCA 58.540 39.130 0.00 0.00 0.00 4.57
104 105 5.072741 AGTTGTGTTTTCATCTAGGTGCAT 58.927 37.500 0.00 0.00 0.00 3.96
124 127 1.291132 GCACCTAGCATCGTTCCTTC 58.709 55.000 0.00 0.00 44.79 3.46
157 160 6.783708 TCAAACTCCTCTCTCCTCTTAATC 57.216 41.667 0.00 0.00 0.00 1.75
218 221 1.489560 GCCCCTGTACAAGGTGGAGT 61.490 60.000 9.67 0.00 45.78 3.85
220 223 2.478292 CCCCTGTACAAGGTGGAGTAT 58.522 52.381 9.67 0.00 45.78 2.12
275 279 5.396057 TTGAGCTATACTCTCTCCCTCTT 57.604 43.478 0.00 0.00 46.41 2.85
281 301 6.274672 AGCTATACTCTCTCCCTCTTCTACAT 59.725 42.308 0.00 0.00 0.00 2.29
297 317 9.650539 CTCTTCTACATCCATTAATGTATCCTG 57.349 37.037 14.25 6.57 40.41 3.86
310 330 4.771114 TGTATCCTGTGTTTGATAGGGG 57.229 45.455 0.00 0.00 33.65 4.79
360 380 8.063200 TGATACTAGTCTTGCTACAAGCTTTA 57.937 34.615 0.00 0.00 42.97 1.85
425 473 8.200024 ACTTCATGTTGATAGTATAGATGCCT 57.800 34.615 0.00 0.00 0.00 4.75
461 509 9.720667 CATAATGGTGTGTATGACAATGTTTAG 57.279 33.333 0.00 0.00 35.91 1.85
477 525 9.734984 ACAATGTTTAGCTTTAGGTAGTTATGT 57.265 29.630 0.00 0.00 0.00 2.29
486 534 9.803507 AGCTTTAGGTAGTTATGTAAACCTTTT 57.196 29.630 0.00 0.00 42.34 2.27
491 539 8.091385 AGGTAGTTATGTAAACCTTTTCAACG 57.909 34.615 0.00 0.00 39.32 4.10
492 540 7.933033 AGGTAGTTATGTAAACCTTTTCAACGA 59.067 33.333 0.00 0.00 39.32 3.85
493 541 8.225777 GGTAGTTATGTAAACCTTTTCAACGAG 58.774 37.037 0.00 0.00 0.00 4.18
494 542 7.797038 AGTTATGTAAACCTTTTCAACGAGT 57.203 32.000 0.00 0.00 0.00 4.18
495 543 7.636326 AGTTATGTAAACCTTTTCAACGAGTG 58.364 34.615 0.00 0.00 0.00 3.51
496 544 4.281525 TGTAAACCTTTTCAACGAGTGC 57.718 40.909 0.00 0.00 0.00 4.40
497 545 3.690139 TGTAAACCTTTTCAACGAGTGCA 59.310 39.130 0.00 0.00 0.00 4.57
498 546 3.420839 AAACCTTTTCAACGAGTGCAG 57.579 42.857 0.00 0.00 0.00 4.41
499 547 0.663153 ACCTTTTCAACGAGTGCAGC 59.337 50.000 0.00 0.00 0.00 5.25
500 548 0.040067 CCTTTTCAACGAGTGCAGCC 60.040 55.000 0.00 0.00 0.00 4.85
501 549 0.040067 CTTTTCAACGAGTGCAGCCC 60.040 55.000 0.00 0.00 0.00 5.19
502 550 0.749818 TTTTCAACGAGTGCAGCCCA 60.750 50.000 0.00 0.00 0.00 5.36
503 551 1.444119 TTTCAACGAGTGCAGCCCAC 61.444 55.000 0.00 0.00 45.01 4.61
578 626 1.415659 GTCTGGATGTGGAGATCCTGG 59.584 57.143 9.08 0.00 42.36 4.45
723 771 8.208224 TCAAGATTTGTCTTTTCTGTAGTACCA 58.792 33.333 0.00 0.00 0.00 3.25
775 823 1.696336 TCCTTGTTCAGCTCTGCTTCT 59.304 47.619 0.00 0.00 36.40 2.85
788 836 1.534595 CTGCTTCTGCCTCTTGTTGAC 59.465 52.381 0.00 0.00 38.71 3.18
796 844 1.656652 CCTCTTGTTGACGGGCTATG 58.343 55.000 0.00 0.00 0.00 2.23
804 852 3.007074 TGTTGACGGGCTATGTCAGTAAA 59.993 43.478 7.57 0.00 46.17 2.01
805 853 4.189231 GTTGACGGGCTATGTCAGTAAAT 58.811 43.478 7.57 0.00 46.17 1.40
807 855 3.449377 TGACGGGCTATGTCAGTAAATGA 59.551 43.478 4.15 0.00 41.20 2.57
846 894 2.825532 CCCCTTGAACACCCTGTTTATG 59.174 50.000 0.00 0.00 41.28 1.90
907 955 7.714377 CAGATTTCTTGCTATACAGAAGGTCAT 59.286 37.037 0.00 0.00 0.00 3.06
941 989 2.047061 CCAGTAGGTGCTATTGCCCTA 58.953 52.381 10.67 10.67 39.45 3.53
971 1019 8.650143 ATTGTTACTGAATCCACCAGTTAAAT 57.350 30.769 0.00 0.00 41.68 1.40
1231 1279 6.014584 TCAGCCTTTTGTGAGAAGTACAGATA 60.015 38.462 0.00 0.00 0.00 1.98
1242 1290 8.774586 GTGAGAAGTACAGATACACAAAATGTT 58.225 33.333 0.00 0.00 43.19 2.71
1312 1360 9.469807 CTTCTACATCTGTGGTAACTAATCATC 57.530 37.037 0.00 0.00 37.61 2.92
1482 1530 5.755375 TGCAAGTACTCAAGTGAAAAGAGAG 59.245 40.000 0.00 0.00 33.69 3.20
1514 1562 5.882557 AGAGTGGACCTGCTATTGTTAAATG 59.117 40.000 0.00 0.00 0.00 2.32
1543 1591 7.431376 GTGATGTGATTAAAGATGACATTGCTG 59.569 37.037 0.00 0.00 0.00 4.41
1626 1674 4.530161 ACAGGACTAGAGAGCATGAAAACT 59.470 41.667 0.00 0.00 0.00 2.66
1666 1714 3.156293 CAACCTGTGGATGATTTGGACA 58.844 45.455 0.00 0.00 0.00 4.02
1737 1785 3.276091 TGCACGAACAACCCTGCG 61.276 61.111 0.00 0.00 31.96 5.18
1917 1965 1.355066 CCGTGAAGGAAGCTTCTCGC 61.355 60.000 25.05 19.78 44.12 5.03
2196 2244 1.620819 GGCAGACCAGTCTCTTCTCAA 59.379 52.381 0.00 0.00 37.98 3.02
2358 2406 0.109597 GCAAGTTCTGGCACAATCCG 60.110 55.000 0.00 0.00 38.70 4.18
2415 2463 2.812011 ACATCTTTGGTTAACTGACGCC 59.188 45.455 5.42 0.00 0.00 5.68
2416 2464 1.886886 TCTTTGGTTAACTGACGCCC 58.113 50.000 5.42 0.00 0.00 6.13
2458 2506 2.290197 TGTCATGTGCTGTGAGGCAATA 60.290 45.455 0.00 0.00 44.18 1.90
2488 2536 5.046529 TGTTTATGCGCTTGTGAAATTTGT 58.953 33.333 9.73 0.00 0.00 2.83
2545 2593 2.162408 GTGACTTGCAGAACATAAGGGC 59.838 50.000 0.00 0.00 0.00 5.19
2634 2682 9.311676 AGTAAGCTTAAGTATTATACTCCCTCC 57.688 37.037 7.99 0.00 38.26 4.30
2635 2683 6.837471 AGCTTAAGTATTATACTCCCTCCG 57.163 41.667 5.26 0.00 38.26 4.63
2636 2684 6.313324 AGCTTAAGTATTATACTCCCTCCGT 58.687 40.000 5.26 0.00 38.26 4.69
2637 2685 6.781507 AGCTTAAGTATTATACTCCCTCCGTT 59.218 38.462 5.26 0.00 38.26 4.44
2638 2686 7.039853 AGCTTAAGTATTATACTCCCTCCGTTC 60.040 40.741 5.26 0.00 38.26 3.95
2639 2687 7.530426 TTAAGTATTATACTCCCTCCGTTCC 57.470 40.000 5.26 0.00 38.26 3.62
2640 2688 5.070823 AGTATTATACTCCCTCCGTTCCA 57.929 43.478 0.00 0.00 32.47 3.53
2641 2689 5.461327 AGTATTATACTCCCTCCGTTCCAA 58.539 41.667 0.00 0.00 32.47 3.53
2642 2690 5.901276 AGTATTATACTCCCTCCGTTCCAAA 59.099 40.000 0.00 0.00 32.47 3.28
2643 2691 5.703730 ATTATACTCCCTCCGTTCCAAAA 57.296 39.130 0.00 0.00 0.00 2.44
2644 2692 5.703730 TTATACTCCCTCCGTTCCAAAAT 57.296 39.130 0.00 0.00 0.00 1.82
2645 2693 6.811634 TTATACTCCCTCCGTTCCAAAATA 57.188 37.500 0.00 0.00 0.00 1.40
2646 2694 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2647 2695 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2648 2696 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2649 2697 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2650 2698 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2651 2699 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2652 2700 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
2653 2701 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
2654 2702 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
2655 2703 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
2656 2704 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
2657 2705 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
2658 2706 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
2659 2707 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
2660 2708 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
2661 2709 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
2662 2710 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
2663 2711 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
2664 2712 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
2665 2713 8.576442 CAAAATAGATGACCCAACTTTGTACTT 58.424 33.333 0.00 0.00 0.00 2.24
2666 2714 8.706322 AAATAGATGACCCAACTTTGTACTTT 57.294 30.769 0.00 0.00 0.00 2.66
2667 2715 7.687941 ATAGATGACCCAACTTTGTACTTTG 57.312 36.000 0.00 0.00 0.00 2.77
2668 2716 5.445964 AGATGACCCAACTTTGTACTTTGT 58.554 37.500 0.00 0.00 0.00 2.83
2669 2717 6.597562 AGATGACCCAACTTTGTACTTTGTA 58.402 36.000 0.00 0.00 0.00 2.41
2670 2718 6.485648 AGATGACCCAACTTTGTACTTTGTAC 59.514 38.462 0.00 1.33 0.00 2.90
2671 2719 5.747342 TGACCCAACTTTGTACTTTGTACT 58.253 37.500 8.94 0.00 0.00 2.73
2672 2720 6.887013 TGACCCAACTTTGTACTTTGTACTA 58.113 36.000 8.94 0.00 0.00 1.82
2673 2721 7.337167 TGACCCAACTTTGTACTTTGTACTAA 58.663 34.615 8.94 6.91 0.00 2.24
2674 2722 7.828223 TGACCCAACTTTGTACTTTGTACTAAA 59.172 33.333 8.94 7.13 0.00 1.85
2675 2723 8.217131 ACCCAACTTTGTACTTTGTACTAAAG 57.783 34.615 19.03 19.03 0.00 1.85
2676 2724 7.830697 ACCCAACTTTGTACTTTGTACTAAAGT 59.169 33.333 19.97 19.97 42.53 2.66
2677 2725 8.680001 CCCAACTTTGTACTTTGTACTAAAGTT 58.320 33.333 24.47 24.47 44.48 2.66
2699 2747 9.694137 AAGTTAGTACAAAGTTGAGTCATCTAC 57.306 33.333 4.14 0.00 0.00 2.59
2700 2748 9.080097 AGTTAGTACAAAGTTGAGTCATCTACT 57.920 33.333 4.14 6.82 42.32 2.57
2708 2756 5.230942 AGTTGAGTCATCTACTTTGGAACG 58.769 41.667 1.70 0.00 38.17 3.95
2709 2757 4.188247 TGAGTCATCTACTTTGGAACGG 57.812 45.455 0.00 0.00 39.07 4.44
2710 2758 3.830178 TGAGTCATCTACTTTGGAACGGA 59.170 43.478 0.00 0.00 39.07 4.69
2711 2759 4.082190 TGAGTCATCTACTTTGGAACGGAG 60.082 45.833 0.00 0.00 39.07 4.63
2712 2760 3.195825 AGTCATCTACTTTGGAACGGAGG 59.804 47.826 0.00 0.00 33.35 4.30
2713 2761 2.500098 TCATCTACTTTGGAACGGAGGG 59.500 50.000 0.00 0.00 0.00 4.30
2714 2762 2.314071 TCTACTTTGGAACGGAGGGA 57.686 50.000 0.00 0.00 0.00 4.20
2715 2763 2.176889 TCTACTTTGGAACGGAGGGAG 58.823 52.381 0.00 0.00 0.00 4.30
2716 2764 1.900486 CTACTTTGGAACGGAGGGAGT 59.100 52.381 0.00 0.00 0.00 3.85
2717 2765 2.019807 ACTTTGGAACGGAGGGAGTA 57.980 50.000 0.00 0.00 0.00 2.59
2718 2766 2.547990 ACTTTGGAACGGAGGGAGTAT 58.452 47.619 0.00 0.00 0.00 2.12
2719 2767 2.910977 ACTTTGGAACGGAGGGAGTATT 59.089 45.455 0.00 0.00 0.00 1.89
2738 2786 2.418368 TTGTCTGCCTGTGTTCTGTT 57.582 45.000 0.00 0.00 0.00 3.16
2902 2951 7.987649 ACTTGGTTTCGTTCTATTGTAAAACA 58.012 30.769 0.00 0.00 0.00 2.83
3105 3155 2.911484 CTTGAGGCTGTATCAAGGGAC 58.089 52.381 13.07 0.00 46.45 4.46
3148 3198 2.094762 AAGTGTGGATAGGCGTGAAC 57.905 50.000 0.00 0.00 0.00 3.18
3355 3433 3.134623 TGGTTCAGGTAGCCATACTGATG 59.865 47.826 0.00 0.00 32.74 3.07
3536 3619 1.749634 AGGTACAGTCAGACGCCATAC 59.250 52.381 0.00 0.00 0.00 2.39
3725 3951 8.807118 TCCCTTCATACTATATCAACAGTGATC 58.193 37.037 0.00 0.00 43.69 2.92
3764 4027 5.412594 TCTTTTAGTCACTGGCATGTGATTC 59.587 40.000 18.25 9.84 46.77 2.52
3851 4114 6.759827 GCTTTGGAATTTATCATGCTTGACAT 59.240 34.615 4.14 0.00 40.66 3.06
3940 4203 5.284861 TGTCTAACTTGTCAGTTTGCCTA 57.715 39.130 0.00 0.00 40.66 3.93
3942 4205 6.296026 TGTCTAACTTGTCAGTTTGCCTATT 58.704 36.000 0.00 0.00 40.66 1.73
3960 4223 2.243602 TTGCTTTTAAGGTCGTCGGT 57.756 45.000 0.00 0.00 0.00 4.69
4030 4293 3.909776 TCTGCTCTGCAATTTTCTGTG 57.090 42.857 0.00 0.00 38.41 3.66
4044 4307 7.572168 GCAATTTTCTGTGACTTCCTAGTTCTC 60.572 40.741 0.00 0.00 33.84 2.87
4124 4393 5.449553 GAAAATCCCCTCATCCTAACATGT 58.550 41.667 0.00 0.00 0.00 3.21
4470 4881 7.444183 TGGTTGTTATCTGTCTTTCTTGGTTAG 59.556 37.037 0.00 0.00 0.00 2.34
4482 4893 7.651704 GTCTTTCTTGGTTAGCATTTTTGCTTA 59.348 33.333 5.72 0.00 43.52 3.09
4484 4895 8.900983 TTTCTTGGTTAGCATTTTTGCTTAAT 57.099 26.923 5.72 0.00 43.52 1.40
4500 4914 8.519492 TTTGCTTAATGCTGATAAAACACTTC 57.481 30.769 0.00 0.00 43.37 3.01
4692 5106 1.214589 CTGGCACAAGCAATGGAGC 59.785 57.895 0.00 0.00 44.61 4.70
4807 5221 9.760660 GTTATTCATCTTGTTCAGTATCAACAC 57.239 33.333 0.00 0.00 33.42 3.32
4882 5296 1.202582 AGTACCACTAACAGCAGCTCG 59.797 52.381 0.00 0.00 0.00 5.03
5113 5531 4.730081 GACACACAGTCTCGTGCA 57.270 55.556 0.00 0.00 44.09 4.57
5188 5606 4.938832 CGTGATGAAGTAATTGGGTGGTTA 59.061 41.667 0.00 0.00 0.00 2.85
5287 5705 1.490490 GCTGGTAGATCCCATGGTTCA 59.510 52.381 11.73 0.00 33.00 3.18
5470 5888 6.853490 TCTGGAAGATGCTAGGTCTAATCTA 58.147 40.000 0.00 0.00 38.67 1.98
5560 5978 3.247006 TCTCGCCTTAGTCATGGTTTC 57.753 47.619 0.00 0.00 0.00 2.78
5761 8650 3.332485 AGGCTGGTTGTCCTACCATTTTA 59.668 43.478 1.12 0.00 46.63 1.52
5828 8717 5.279206 CCATCACGATACTTCTATCAAGGCT 60.279 44.000 0.00 0.00 30.53 4.58
6029 8918 7.450074 TCTTCAGAGGCTTGTGAAAGTTAATA 58.550 34.615 9.70 0.00 36.31 0.98
6588 9477 1.375326 GACTGGTGGACCAAGACCC 59.625 63.158 0.00 0.00 46.97 4.46
6702 9591 0.394352 ATTTGGATGACCTGGGACGC 60.394 55.000 0.00 0.00 37.04 5.19
6817 9709 4.260907 GCATTGCTATCTTCATCTTTGCGA 60.261 41.667 0.16 0.00 0.00 5.10
6836 9728 1.927174 GAGCGCGTAACAATGATGAGT 59.073 47.619 8.43 0.00 0.00 3.41
6842 9734 4.142902 CGCGTAACAATGATGAGTTTCCTT 60.143 41.667 0.00 0.00 0.00 3.36
6923 9815 4.321230 GGTTGTGTTAAGGAGAAGGCATTG 60.321 45.833 0.00 0.00 0.00 2.82
6924 9816 2.819608 TGTGTTAAGGAGAAGGCATTGC 59.180 45.455 0.00 0.00 0.00 3.56
6925 9817 3.084786 GTGTTAAGGAGAAGGCATTGCT 58.915 45.455 8.82 0.00 0.00 3.91
6939 9831 6.570672 AGGCATTGCTATTGACATAATGAG 57.429 37.500 8.82 0.00 32.05 2.90
6947 9839 7.971201 TGCTATTGACATAATGAGAGGATTCT 58.029 34.615 0.00 0.00 36.01 2.40
6949 9841 9.282569 GCTATTGACATAATGAGAGGATTCTTT 57.717 33.333 0.00 0.00 32.53 2.52
7080 9972 1.306141 CTGCCCCAGGTCCTCAGTA 60.306 63.158 0.00 0.00 0.00 2.74
7152 10044 2.827642 GGCTGCAGCTGGATGGTC 60.828 66.667 35.82 14.76 41.70 4.02
7463 10372 1.024271 GCTGCCTTGTTGTCTGTCAA 58.976 50.000 0.00 0.00 0.00 3.18
7478 10387 4.025979 GTCTGTCAACTGTTGTTAGTTCGG 60.026 45.833 19.12 9.57 38.78 4.30
7533 10443 8.455903 AAGATGGTATCATGTTTCAGTTATGG 57.544 34.615 0.00 0.00 33.74 2.74
7559 10469 4.032960 ACCTGATATTGCACCTTGTTGA 57.967 40.909 0.00 0.00 0.00 3.18
7633 10543 5.592688 GGTATGTGGTATAGCATGGTGTTTT 59.407 40.000 7.89 0.00 0.00 2.43
7643 10553 2.031857 GCATGGTGTTTTGTTGGCATTG 60.032 45.455 0.00 0.00 0.00 2.82
7676 10586 1.258676 TGTAAAATTCCAACCGGGGC 58.741 50.000 6.32 0.00 37.22 5.80
7716 10626 0.463620 TTTGTGGAAGCCCTGTTTGC 59.536 50.000 0.00 0.00 0.00 3.68
7786 10696 3.328505 CCAGCCCTTGTTATTTTTGCTG 58.671 45.455 0.00 0.00 43.19 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 4.829064 TGCACCTAGATGAAAACACAAC 57.171 40.909 0.00 0.00 0.00 3.32
120 123 0.804989 GTTTGATGAGCCCACGAAGG 59.195 55.000 0.00 0.00 37.03 3.46
124 127 0.036010 AGGAGTTTGATGAGCCCACG 60.036 55.000 0.00 0.00 0.00 4.94
157 160 3.947910 AAAATCTGATGTGGCAAGGTG 57.052 42.857 0.00 0.00 0.00 4.00
218 221 1.580059 ACTTCGAGGCCCTTCCAATA 58.420 50.000 0.00 0.00 37.29 1.90
220 223 0.476771 AAACTTCGAGGCCCTTCCAA 59.523 50.000 0.00 0.00 37.29 3.53
270 274 8.820831 AGGATACATTAATGGATGTAGAAGAGG 58.179 37.037 18.16 0.00 43.53 3.69
275 279 8.262601 ACACAGGATACATTAATGGATGTAGA 57.737 34.615 18.16 0.00 43.53 2.59
281 301 9.559732 CTATCAAACACAGGATACATTAATGGA 57.440 33.333 19.37 11.88 41.41 3.41
297 317 3.896854 GGGGTCCCCTATCAAACAC 57.103 57.895 21.13 0.00 41.34 3.32
310 330 6.474140 TTTCTTCCAAACTAAAAAGGGGTC 57.526 37.500 0.00 0.00 0.00 4.46
477 525 3.242936 GCTGCACTCGTTGAAAAGGTTTA 60.243 43.478 0.00 0.00 32.62 2.01
479 527 1.065551 GCTGCACTCGTTGAAAAGGTT 59.934 47.619 0.00 0.00 32.62 3.50
480 528 0.663153 GCTGCACTCGTTGAAAAGGT 59.337 50.000 0.00 0.00 32.62 3.50
481 529 0.040067 GGCTGCACTCGTTGAAAAGG 60.040 55.000 0.50 0.00 0.00 3.11
482 530 0.040067 GGGCTGCACTCGTTGAAAAG 60.040 55.000 0.50 0.00 0.00 2.27
483 531 0.749818 TGGGCTGCACTCGTTGAAAA 60.750 50.000 2.50 0.00 0.00 2.29
484 532 1.153066 TGGGCTGCACTCGTTGAAA 60.153 52.632 2.50 0.00 0.00 2.69
485 533 1.891919 GTGGGCTGCACTCGTTGAA 60.892 57.895 2.50 0.00 0.00 2.69
486 534 2.280797 GTGGGCTGCACTCGTTGA 60.281 61.111 2.50 0.00 0.00 3.18
487 535 2.281070 AGTGGGCTGCACTCGTTG 60.281 61.111 2.50 0.00 0.00 4.10
488 536 2.031163 GAGTGGGCTGCACTCGTT 59.969 61.111 2.50 0.00 39.49 3.85
491 539 0.877743 GAAAAGAGTGGGCTGCACTC 59.122 55.000 13.93 13.93 46.82 3.51
492 540 0.475906 AGAAAAGAGTGGGCTGCACT 59.524 50.000 2.50 0.00 35.30 4.40
493 541 0.595095 CAGAAAAGAGTGGGCTGCAC 59.405 55.000 0.50 0.00 0.00 4.57
494 542 3.025924 CAGAAAAGAGTGGGCTGCA 57.974 52.632 0.50 0.00 0.00 4.41
495 543 1.583477 GCAGAAAAGAGTGGGCTGC 59.417 57.895 0.00 0.00 44.11 5.25
496 544 1.268899 CAAGCAGAAAAGAGTGGGCTG 59.731 52.381 0.00 0.00 0.00 4.85
497 545 1.143684 TCAAGCAGAAAAGAGTGGGCT 59.856 47.619 0.00 0.00 0.00 5.19
498 546 1.609208 TCAAGCAGAAAAGAGTGGGC 58.391 50.000 0.00 0.00 0.00 5.36
499 547 4.946157 ACATATCAAGCAGAAAAGAGTGGG 59.054 41.667 0.00 0.00 0.00 4.61
500 548 6.404074 GGAACATATCAAGCAGAAAAGAGTGG 60.404 42.308 0.00 0.00 0.00 4.00
501 549 6.149973 TGGAACATATCAAGCAGAAAAGAGTG 59.850 38.462 0.00 0.00 0.00 3.51
502 550 6.150140 GTGGAACATATCAAGCAGAAAAGAGT 59.850 38.462 0.00 0.00 44.52 3.24
503 551 6.149973 TGTGGAACATATCAAGCAGAAAAGAG 59.850 38.462 0.00 0.00 45.67 2.85
504 552 6.003326 TGTGGAACATATCAAGCAGAAAAGA 58.997 36.000 0.00 0.00 45.67 2.52
505 553 6.258230 TGTGGAACATATCAAGCAGAAAAG 57.742 37.500 0.00 0.00 45.67 2.27
578 626 8.970859 TCTCAAGAAATTGGATTCTAGGAATC 57.029 34.615 10.69 10.69 38.69 2.52
723 771 5.045578 AGTTACAGCAGAACCCTCATTGTAT 60.046 40.000 0.00 0.00 0.00 2.29
775 823 1.476845 TAGCCCGTCAACAAGAGGCA 61.477 55.000 1.74 0.00 46.35 4.75
788 836 5.527214 TCATTTCATTTACTGACATAGCCCG 59.473 40.000 0.00 0.00 32.17 6.13
796 844 6.855836 TGGATGCTTCATTTCATTTACTGAC 58.144 36.000 1.64 0.00 32.17 3.51
804 852 2.429610 GTGCCTGGATGCTTCATTTCAT 59.570 45.455 0.00 0.00 0.00 2.57
805 853 1.820519 GTGCCTGGATGCTTCATTTCA 59.179 47.619 0.00 0.00 0.00 2.69
807 855 1.188863 GGTGCCTGGATGCTTCATTT 58.811 50.000 0.00 0.00 0.00 2.32
866 914 1.442769 ATCTGCAACAACCAGCGTAG 58.557 50.000 0.00 0.00 0.00 3.51
907 955 6.668283 AGCACCTACTGGAAGAGAACTATTAA 59.332 38.462 0.00 0.00 37.43 1.40
941 989 6.126863 TGGTGGATTCAGTAACAATCTTCT 57.873 37.500 0.00 0.00 31.82 2.85
1092 1140 5.163088 GGGATACATATTGGGAACAGGAAGT 60.163 44.000 0.00 0.00 40.00 3.01
1170 1218 5.831525 AGAAGATGCATGATTAAAGGCATGA 59.168 36.000 2.46 6.03 46.17 3.07
1276 1324 2.099921 CAGATGTAGAAGCCGCAGTAGT 59.900 50.000 0.00 0.00 0.00 2.73
1312 1360 6.214191 AGGACACACAACACTATCAGATAG 57.786 41.667 15.03 15.03 38.81 2.08
1514 1562 9.926751 CAATGTCATCTTTAATCACATCACTAC 57.073 33.333 0.00 0.00 0.00 2.73
1543 1591 0.106708 TCAGTGTCACCAGGTTCAGC 59.893 55.000 0.00 0.00 0.00 4.26
1626 1674 6.936900 CAGGTTGACTTCCTTTAGATTCAGAA 59.063 38.462 0.00 0.00 32.37 3.02
1666 1714 4.718961 ACATCCTTTGACTTAGTGCACTT 58.281 39.130 27.06 7.02 0.00 3.16
1737 1785 8.001881 TGTGATCATCTAACTTAGGTCTCTTC 57.998 38.462 0.00 0.00 0.00 2.87
1905 1953 1.668151 AACACCGCGAGAAGCTTCC 60.668 57.895 22.81 13.07 45.59 3.46
1917 1965 0.588252 CAGCTCTTTCACCAACACCG 59.412 55.000 0.00 0.00 0.00 4.94
1949 1997 0.257039 ATCCCTGATGACTGGTTGGC 59.743 55.000 0.00 0.00 34.02 4.52
2196 2244 4.141711 TGTTGTCCTGTTAGAAGTGCTCTT 60.142 41.667 0.00 0.00 35.41 2.85
2358 2406 2.418976 GACAATGCCGAAGAACTAACCC 59.581 50.000 0.00 0.00 0.00 4.11
2415 2463 7.013274 TGACAGAAGTTTCCAGATTAAACAAGG 59.987 37.037 0.00 0.00 38.92 3.61
2416 2464 7.930217 TGACAGAAGTTTCCAGATTAAACAAG 58.070 34.615 0.00 0.00 38.92 3.16
2458 2506 5.046529 TCACAAGCGCATAAACAAAATGTT 58.953 33.333 11.47 0.00 43.41 2.71
2488 2536 4.467795 AGCATTTGAGGAAGTAGCACTAGA 59.532 41.667 0.00 0.00 0.00 2.43
2613 2661 6.587206 ACGGAGGGAGTATAATACTTAAGC 57.413 41.667 1.29 0.00 39.59 3.09
2627 2675 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2629 2677 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2630 2678 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
2631 2679 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
2632 2680 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
2633 2681 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
2634 2682 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
2635 2683 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
2636 2684 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
2637 2685 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
2638 2686 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
2639 2687 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
2640 2688 8.706322 AAGTACAAAGTTGGGTCATCTATTTT 57.294 30.769 0.00 0.00 0.00 1.82
2641 2689 8.576442 CAAAGTACAAAGTTGGGTCATCTATTT 58.424 33.333 0.00 0.00 0.00 1.40
2642 2690 7.724061 ACAAAGTACAAAGTTGGGTCATCTATT 59.276 33.333 0.00 0.00 0.00 1.73
2643 2691 7.231467 ACAAAGTACAAAGTTGGGTCATCTAT 58.769 34.615 0.00 0.00 0.00 1.98
2644 2692 6.597562 ACAAAGTACAAAGTTGGGTCATCTA 58.402 36.000 0.00 0.00 0.00 1.98
2645 2693 5.445964 ACAAAGTACAAAGTTGGGTCATCT 58.554 37.500 0.00 0.00 0.00 2.90
2646 2694 5.767816 ACAAAGTACAAAGTTGGGTCATC 57.232 39.130 0.00 0.00 0.00 2.92
2647 2695 6.362248 AGTACAAAGTACAAAGTTGGGTCAT 58.638 36.000 9.68 0.00 0.00 3.06
2648 2696 5.747342 AGTACAAAGTACAAAGTTGGGTCA 58.253 37.500 9.68 0.00 0.00 4.02
2649 2697 7.790823 TTAGTACAAAGTACAAAGTTGGGTC 57.209 36.000 9.68 0.00 0.00 4.46
2650 2698 7.830697 ACTTTAGTACAAAGTACAAAGTTGGGT 59.169 33.333 19.84 8.52 38.58 4.51
2651 2699 8.217131 ACTTTAGTACAAAGTACAAAGTTGGG 57.783 34.615 19.84 8.15 38.58 4.12
2673 2721 9.694137 GTAGATGACTCAACTTTGTACTAACTT 57.306 33.333 0.00 0.00 0.00 2.66
2674 2722 9.080097 AGTAGATGACTCAACTTTGTACTAACT 57.920 33.333 0.00 0.00 29.95 2.24
2675 2723 9.694137 AAGTAGATGACTCAACTTTGTACTAAC 57.306 33.333 0.00 0.00 37.44 2.34
2677 2725 9.692749 CAAAGTAGATGACTCAACTTTGTACTA 57.307 33.333 18.71 0.00 46.99 1.82
2678 2726 8.594881 CAAAGTAGATGACTCAACTTTGTACT 57.405 34.615 18.71 5.58 46.99 2.73
2683 2731 6.202954 CGTTCCAAAGTAGATGACTCAACTTT 59.797 38.462 2.66 2.66 41.56 2.66
2684 2732 5.696724 CGTTCCAAAGTAGATGACTCAACTT 59.303 40.000 0.00 0.00 37.44 2.66
2685 2733 5.230942 CGTTCCAAAGTAGATGACTCAACT 58.769 41.667 0.00 0.00 37.44 3.16
2686 2734 4.389077 CCGTTCCAAAGTAGATGACTCAAC 59.611 45.833 0.00 0.00 37.44 3.18
2687 2735 4.282449 TCCGTTCCAAAGTAGATGACTCAA 59.718 41.667 0.00 0.00 37.44 3.02
2688 2736 3.830178 TCCGTTCCAAAGTAGATGACTCA 59.170 43.478 0.00 0.00 37.44 3.41
2689 2737 4.425520 CTCCGTTCCAAAGTAGATGACTC 58.574 47.826 0.00 0.00 37.44 3.36
2690 2738 3.195825 CCTCCGTTCCAAAGTAGATGACT 59.804 47.826 0.00 0.00 41.56 3.41
2691 2739 3.522553 CCTCCGTTCCAAAGTAGATGAC 58.477 50.000 0.00 0.00 0.00 3.06
2692 2740 2.500098 CCCTCCGTTCCAAAGTAGATGA 59.500 50.000 0.00 0.00 0.00 2.92
2693 2741 2.500098 TCCCTCCGTTCCAAAGTAGATG 59.500 50.000 0.00 0.00 0.00 2.90
2694 2742 2.766828 CTCCCTCCGTTCCAAAGTAGAT 59.233 50.000 0.00 0.00 0.00 1.98
2695 2743 2.176889 CTCCCTCCGTTCCAAAGTAGA 58.823 52.381 0.00 0.00 0.00 2.59
2696 2744 1.900486 ACTCCCTCCGTTCCAAAGTAG 59.100 52.381 0.00 0.00 0.00 2.57
2697 2745 2.019807 ACTCCCTCCGTTCCAAAGTA 57.980 50.000 0.00 0.00 0.00 2.24
2698 2746 2.019807 TACTCCCTCCGTTCCAAAGT 57.980 50.000 0.00 0.00 0.00 2.66
2699 2747 3.629142 AATACTCCCTCCGTTCCAAAG 57.371 47.619 0.00 0.00 0.00 2.77
2700 2748 3.073356 ACAAATACTCCCTCCGTTCCAAA 59.927 43.478 0.00 0.00 0.00 3.28
2701 2749 2.640826 ACAAATACTCCCTCCGTTCCAA 59.359 45.455 0.00 0.00 0.00 3.53
2702 2750 2.235402 GACAAATACTCCCTCCGTTCCA 59.765 50.000 0.00 0.00 0.00 3.53
2703 2751 2.500504 AGACAAATACTCCCTCCGTTCC 59.499 50.000 0.00 0.00 0.00 3.62
2704 2752 3.522553 CAGACAAATACTCCCTCCGTTC 58.477 50.000 0.00 0.00 0.00 3.95
2705 2753 2.354805 GCAGACAAATACTCCCTCCGTT 60.355 50.000 0.00 0.00 0.00 4.44
2706 2754 1.207329 GCAGACAAATACTCCCTCCGT 59.793 52.381 0.00 0.00 0.00 4.69
2707 2755 1.473434 GGCAGACAAATACTCCCTCCG 60.473 57.143 0.00 0.00 0.00 4.63
2708 2756 1.840635 AGGCAGACAAATACTCCCTCC 59.159 52.381 0.00 0.00 0.00 4.30
2709 2757 2.237392 ACAGGCAGACAAATACTCCCTC 59.763 50.000 0.00 0.00 0.00 4.30
2710 2758 2.026822 CACAGGCAGACAAATACTCCCT 60.027 50.000 0.00 0.00 0.00 4.20
2711 2759 2.290323 ACACAGGCAGACAAATACTCCC 60.290 50.000 0.00 0.00 0.00 4.30
2712 2760 3.059352 ACACAGGCAGACAAATACTCC 57.941 47.619 0.00 0.00 0.00 3.85
2713 2761 4.153117 CAGAACACAGGCAGACAAATACTC 59.847 45.833 0.00 0.00 0.00 2.59
2714 2762 4.067896 CAGAACACAGGCAGACAAATACT 58.932 43.478 0.00 0.00 0.00 2.12
2715 2763 3.815401 ACAGAACACAGGCAGACAAATAC 59.185 43.478 0.00 0.00 0.00 1.89
2716 2764 4.085357 ACAGAACACAGGCAGACAAATA 57.915 40.909 0.00 0.00 0.00 1.40
2717 2765 2.936202 ACAGAACACAGGCAGACAAAT 58.064 42.857 0.00 0.00 0.00 2.32
2718 2766 2.418368 ACAGAACACAGGCAGACAAA 57.582 45.000 0.00 0.00 0.00 2.83
2719 2767 2.418368 AACAGAACACAGGCAGACAA 57.582 45.000 0.00 0.00 0.00 3.18
2855 2904 9.195411 CAAGTAAACACTGACAATGCAATAATT 57.805 29.630 0.00 0.00 0.00 1.40
2856 2905 7.814107 CCAAGTAAACACTGACAATGCAATAAT 59.186 33.333 0.00 0.00 0.00 1.28
2857 2906 7.144661 CCAAGTAAACACTGACAATGCAATAA 58.855 34.615 0.00 0.00 0.00 1.40
2858 2907 6.264292 ACCAAGTAAACACTGACAATGCAATA 59.736 34.615 0.00 0.00 0.00 1.90
2859 2908 5.068987 ACCAAGTAAACACTGACAATGCAAT 59.931 36.000 0.00 0.00 0.00 3.56
2860 2909 4.400884 ACCAAGTAAACACTGACAATGCAA 59.599 37.500 0.00 0.00 0.00 4.08
2866 2915 4.255301 ACGAAACCAAGTAAACACTGACA 58.745 39.130 0.00 0.00 0.00 3.58
2877 2926 7.987649 TGTTTTACAATAGAACGAAACCAAGT 58.012 30.769 0.00 0.00 0.00 3.16
2902 2951 3.099002 TGCTCATGCACACACACTT 57.901 47.368 0.00 0.00 45.31 3.16
3303 3376 2.719046 GGACGACAAAATTGCAACTTCG 59.281 45.455 0.00 8.28 0.00 3.79
3552 3635 3.441572 GGATAATTGCTCCAATGGGATCG 59.558 47.826 0.00 0.00 43.91 3.69
3725 3951 9.595357 GTGACTAAAAGAACTAAGAAAATTCCG 57.405 33.333 0.00 0.00 0.00 4.30
3764 4027 7.915508 TCATGTGTGTGAACTGTTAAGTAAAG 58.084 34.615 0.00 0.00 34.77 1.85
3851 4114 2.292845 TCGTGCAGTGCAAAATTCATCA 59.707 40.909 21.67 0.00 41.47 3.07
3940 4203 2.774687 ACCGACGACCTTAAAAGCAAT 58.225 42.857 0.00 0.00 0.00 3.56
3942 4205 2.243602 AACCGACGACCTTAAAAGCA 57.756 45.000 0.00 0.00 0.00 3.91
3976 4239 5.570973 GTGCATGCGTAATGTTCAATGTAAA 59.429 36.000 14.09 0.00 38.65 2.01
4030 4293 5.123805 AGACAAACGAGAACTAGGAAGTC 57.876 43.478 0.00 0.00 33.75 3.01
4044 4307 3.381045 TGTTCTCAGCACTAGACAAACG 58.619 45.455 0.00 0.00 0.00 3.60
4124 4393 2.237143 GTCCATGAACCTCATCACAGGA 59.763 50.000 0.00 0.00 34.28 3.86
4406 4812 0.739462 TGCACATTAAGACGGCGGAG 60.739 55.000 13.24 0.00 0.00 4.63
4482 4893 5.716228 TGATGGGAAGTGTTTTATCAGCATT 59.284 36.000 0.00 0.00 0.00 3.56
4484 4895 4.661222 TGATGGGAAGTGTTTTATCAGCA 58.339 39.130 0.00 0.00 0.00 4.41
4495 4908 3.671433 CGTTTTGCATCTGATGGGAAGTG 60.671 47.826 18.60 0.00 0.00 3.16
4500 4914 3.334078 GCGTTTTGCATCTGATGGG 57.666 52.632 18.60 0.00 45.45 4.00
4692 5106 4.794169 CCATGGTTCTTGTTTCTTAACCG 58.206 43.478 2.57 0.00 43.53 4.44
4807 5221 5.193663 TCTTTAGCAGAGCAGCATAGTAG 57.806 43.478 0.00 0.00 36.85 2.57
4882 5296 3.752339 CCCGCAGCAAAAGCCTCC 61.752 66.667 0.00 0.00 0.00 4.30
5188 5606 1.073199 ACGGCCTTTTAGCTGCTGT 59.927 52.632 13.43 0.00 43.28 4.40
5287 5705 2.774234 CACATCAGGATCTACCCCAACT 59.226 50.000 0.00 0.00 40.05 3.16
5466 5884 3.439857 TGGCAAAACTGGCTTCTAGAT 57.560 42.857 0.00 0.00 35.21 1.98
5470 5888 0.385390 CGTTGGCAAAACTGGCTTCT 59.615 50.000 0.00 0.00 35.21 2.85
5533 5951 6.357367 ACCATGACTAAGGCGAGAAAATAAT 58.643 36.000 0.00 0.00 0.00 1.28
5560 5978 5.702670 AGCCTCATCAATAACAACCATATCG 59.297 40.000 0.00 0.00 0.00 2.92
5674 6092 5.127519 TCCAGCCGCTTTACTAATAACAGTA 59.872 40.000 0.00 0.00 0.00 2.74
5761 8650 3.251729 GCATCCGATATTGCACTGACAAT 59.748 43.478 0.00 6.09 42.73 2.71
6012 8901 5.959618 ACCACTATTAACTTTCACAAGCC 57.040 39.130 0.00 0.00 32.57 4.35
6029 8918 3.560025 CCAACAGATGCCTTCTTACCACT 60.560 47.826 0.00 0.00 29.93 4.00
6319 9208 2.228103 TGAAGTAGCAGTACAGTGGTCG 59.772 50.000 0.00 0.00 0.00 4.79
6549 9438 2.623416 CCTCAAGTTCCTTGGGTTGTTC 59.377 50.000 3.38 0.00 40.07 3.18
6702 9591 6.074648 ACTTTCCCTAGATCTATCACCAGAG 58.925 44.000 2.11 0.00 0.00 3.35
6817 9709 2.010145 ACTCATCATTGTTACGCGCT 57.990 45.000 5.73 0.00 0.00 5.92
6836 9728 2.158325 ACCAAGCTTCATCCCAAGGAAA 60.158 45.455 0.00 0.00 34.34 3.13
6842 9734 0.776810 TCCAACCAAGCTTCATCCCA 59.223 50.000 0.00 0.00 0.00 4.37
6923 9815 8.845413 AAGAATCCTCTCATTATGTCAATAGC 57.155 34.615 0.00 0.00 0.00 2.97
6939 9831 7.174080 GGCCTACTCATTTCATAAAGAATCCTC 59.826 40.741 0.00 0.00 35.83 3.71
7100 9992 4.099266 TGGTTATATCAACAGCCCAAATGC 59.901 41.667 0.00 0.00 0.00 3.56
7108 10000 6.371548 TGTTGAAGTCTGGTTATATCAACAGC 59.628 38.462 13.35 0.00 46.73 4.40
7152 10044 6.599244 TGTTAGTATTGCAATCCCAGAAAGAG 59.401 38.462 16.86 0.00 0.00 2.85
7317 10225 1.009222 GGCATATCAAGCAGCGCAC 60.009 57.895 11.47 0.00 0.00 5.34
7322 10230 2.551721 CCTACAGGGGCATATCAAGCAG 60.552 54.545 0.00 0.00 0.00 4.24
7463 10372 2.433239 ACAGTCCCGAACTAACAACAGT 59.567 45.455 0.00 0.00 36.07 3.55
7478 10387 7.867403 ACAACATAAAACATCATTCAACAGTCC 59.133 33.333 0.00 0.00 0.00 3.85
7533 10443 5.186198 ACAAGGTGCAATATCAGGTAAGAC 58.814 41.667 0.00 0.00 0.00 3.01
7633 10543 8.476447 ACATCAATCAATATAACAATGCCAACA 58.524 29.630 0.00 0.00 0.00 3.33
7676 10586 2.152699 CGGAGCAAGTACAGCGTCG 61.153 63.158 0.00 5.00 37.01 5.12
7687 10597 1.593196 CTTCCACAAACTCGGAGCAA 58.407 50.000 4.58 0.00 31.51 3.91
7745 10655 1.477014 GCTTATGCTAACAGGGGACCC 60.477 57.143 0.03 0.03 43.46 4.46


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

AutoCloner maintained by Alex Coulton.