Multiple sequence alignment - TraesCS6D01G348800

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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 TraesCS6D01G348800 chr6D 100.000 2508 0 0 1 2508 446622722 446620215 0.000000e+00 4632.0
1 TraesCS6D01G348800 chr6D 100.000 1482 0 0 2841 4322 446619882 446618401 0.000000e+00 2737.0
2 TraesCS6D01G348800 chr6D 82.000 550 62 25 3550 4087 78818527 78818003 2.390000e-117 433.0
3 TraesCS6D01G348800 chr6D 98.039 51 1 0 3441 3491 135102248 135102298 5.950000e-14 89.8
4 TraesCS6D01G348800 chr6A 93.999 1483 61 10 1 1466 593439280 593437809 0.000000e+00 2220.0
5 TraesCS6D01G348800 chr6A 97.133 872 25 0 1610 2481 593437654 593436783 0.000000e+00 1472.0
6 TraesCS6D01G348800 chr6A 95.661 484 19 2 2957 3440 593436685 593436204 0.000000e+00 776.0
7 TraesCS6D01G348800 chr6A 93.243 148 10 0 2841 2988 495353539 495353686 7.280000e-53 219.0
8 TraesCS6D01G348800 chr6A 97.647 85 2 0 1475 1559 593437735 593437651 3.480000e-31 147.0
9 TraesCS6D01G348800 chr6B 91.296 1080 66 11 1440 2506 675449841 675448777 0.000000e+00 1448.0
10 TraesCS6D01G348800 chr6B 94.222 450 24 2 1 449 675451225 675450777 0.000000e+00 686.0
11 TraesCS6D01G348800 chr6B 90.176 397 39 0 498 894 675450767 675450371 6.410000e-143 518.0
12 TraesCS6D01G348800 chr6B 93.146 321 22 0 3064 3384 675443434 675443114 5.060000e-129 472.0
13 TraesCS6D01G348800 chr6B 88.395 405 25 7 956 1348 675450372 675449978 6.540000e-128 468.0
14 TraesCS6D01G348800 chr6B 96.774 93 0 3 2981 3072 675448730 675448640 7.490000e-33 152.0
15 TraesCS6D01G348800 chr6B 80.000 110 22 0 150 259 698975804 698975913 9.960000e-12 82.4
16 TraesCS6D01G348800 chr1D 93.064 793 38 3 3531 4322 46325839 46326615 0.000000e+00 1144.0
17 TraesCS6D01G348800 chr1D 90.945 762 43 11 3570 4322 342451524 342450780 0.000000e+00 1002.0
18 TraesCS6D01G348800 chr4D 93.047 791 36 6 3533 4322 204710231 204709459 0.000000e+00 1138.0
19 TraesCS6D01G348800 chr4D 89.882 425 26 6 3525 3948 455752815 455752407 8.230000e-147 531.0
20 TraesCS6D01G348800 chr4D 86.911 191 25 0 3537 3727 172016764 172016954 9.410000e-52 215.0
21 TraesCS6D01G348800 chr2B 91.058 794 51 5 3530 4322 253706628 253707402 0.000000e+00 1055.0
22 TraesCS6D01G348800 chr2B 84.756 820 116 7 1683 2498 756637094 756637908 0.000000e+00 813.0
23 TraesCS6D01G348800 chr2B 83.768 844 115 17 1675 2502 707621306 707620469 0.000000e+00 780.0
24 TraesCS6D01G348800 chr2B 83.597 823 120 13 1683 2498 756969118 756969932 0.000000e+00 758.0
25 TraesCS6D01G348800 chr2B 83.055 838 118 16 1672 2495 707656927 707656100 0.000000e+00 739.0
26 TraesCS6D01G348800 chr2B 78.517 526 88 22 812 1327 707960786 707960276 5.390000e-84 322.0
27 TraesCS6D01G348800 chr2B 77.122 542 93 25 708 1239 707531270 707530750 7.070000e-73 285.0
28 TraesCS6D01G348800 chr2B 76.225 551 111 16 708 1251 707658036 707657499 1.530000e-69 274.0
29 TraesCS6D01G348800 chr2B 95.035 141 7 0 2841 2981 124626295 124626435 5.630000e-54 222.0
30 TraesCS6D01G348800 chr2B 92.715 151 10 1 2841 2990 659017192 659017042 2.620000e-52 217.0
31 TraesCS6D01G348800 chr2B 76.440 382 86 3 3 382 707464208 707463829 2.040000e-48 204.0
32 TraesCS6D01G348800 chr3A 89.788 803 57 10 3525 4319 735721374 735722159 0.000000e+00 1005.0
33 TraesCS6D01G348800 chr3B 88.917 803 69 12 3527 4322 599097878 599097089 0.000000e+00 972.0
34 TraesCS6D01G348800 chr3B 88.312 77 8 1 3410 3486 302359207 302359132 1.660000e-14 91.6
35 TraesCS6D01G348800 chrUn 86.332 856 107 8 1641 2492 74781442 74782291 0.000000e+00 924.0
36 TraesCS6D01G348800 chrUn 85.427 398 55 3 1 395 74778473 74778870 1.120000e-110 411.0
37 TraesCS6D01G348800 chr1B 87.909 794 72 13 3536 4322 486495744 486494968 0.000000e+00 913.0
38 TraesCS6D01G348800 chr1B 87.588 427 35 7 3523 3948 630552042 630551633 3.020000e-131 479.0
39 TraesCS6D01G348800 chr1B 81.047 554 69 20 3549 4087 486493941 486493409 4.020000e-110 409.0
40 TraesCS6D01G348800 chr1B 95.775 142 6 0 2841 2982 643449107 643448966 3.360000e-56 230.0
41 TraesCS6D01G348800 chr2D 85.226 819 111 7 1683 2497 619147428 619148240 0.000000e+00 833.0
42 TraesCS6D01G348800 chr2D 82.598 839 121 17 1671 2495 586294006 586293179 0.000000e+00 717.0
43 TraesCS6D01G348800 chr2D 76.799 556 105 15 693 1237 619146726 619147268 1.520000e-74 291.0
44 TraesCS6D01G348800 chr2D 76.425 386 87 3 3 386 585914552 585914935 5.670000e-49 206.0
45 TraesCS6D01G348800 chr2A 84.502 813 116 10 1689 2497 750208857 750208051 0.000000e+00 795.0
46 TraesCS6D01G348800 chr2A 88.138 666 56 15 3676 4322 89597648 89598309 0.000000e+00 771.0
47 TraesCS6D01G348800 chr2A 83.294 838 116 17 1672 2495 720574897 720574070 0.000000e+00 750.0
48 TraesCS6D01G348800 chr2A 77.586 522 100 12 812 1327 721065740 721065230 2.530000e-77 300.0
49 TraesCS6D01G348800 chr2A 76.122 557 115 12 693 1240 750209568 750209021 4.260000e-70 276.0
50 TraesCS6D01G348800 chr2A 76.326 528 100 21 827 1348 720575919 720575411 4.290000e-65 259.0
51 TraesCS6D01G348800 chr2A 75.648 386 90 4 3 386 720520556 720520173 5.710000e-44 189.0
52 TraesCS6D01G348800 chr2A 92.537 67 5 0 3441 3507 289360913 289360847 3.560000e-16 97.1
53 TraesCS6D01G348800 chr5D 88.456 667 52 15 3676 4322 548630694 548631355 0.000000e+00 782.0
54 TraesCS6D01G348800 chr5D 94.406 143 8 0 2841 2983 537178208 537178350 2.020000e-53 220.0
55 TraesCS6D01G348800 chr5D 100.000 32 0 0 3500 3531 545166773 545166742 4.670000e-05 60.2
56 TraesCS6D01G348800 chr3D 83.189 809 87 24 3531 4311 562522874 562522087 0.000000e+00 695.0
57 TraesCS6D01G348800 chr3D 95.070 142 7 0 2841 2982 238999555 238999414 1.560000e-54 224.0
58 TraesCS6D01G348800 chr3D 89.610 77 7 1 3410 3486 254743083 254743008 3.560000e-16 97.1
59 TraesCS6D01G348800 chr5B 94.483 145 8 0 2841 2985 539322742 539322886 1.560000e-54 224.0
60 TraesCS6D01G348800 chr5B 98.039 51 1 0 3441 3491 291064236 291064286 5.950000e-14 89.8
61 TraesCS6D01G348800 chr4B 95.070 142 6 1 2841 2982 659160844 659160704 5.630000e-54 222.0
62 TraesCS6D01G348800 chr5A 94.444 144 7 1 2841 2984 150983514 150983372 2.020000e-53 220.0
63 TraesCS6D01G348800 chr7A 90.541 74 7 0 3441 3514 94787542 94787469 9.890000e-17 99.0
64 TraesCS6D01G348800 chr7A 88.462 78 5 3 3441 3514 326987445 326987368 1.660000e-14 91.6
65 TraesCS6D01G348800 chr1A 91.429 70 6 0 3441 3510 299627973 299628042 3.560000e-16 97.1
66 TraesCS6D01G348800 chr1A 85.714 91 6 6 3437 3526 426259177 426259093 5.950000e-14 89.8


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 TraesCS6D01G348800 chr6D 446618401 446622722 4321 True 3684.50 4632 100.0000 1 4322 2 chr6D.!!$R2 4321
1 TraesCS6D01G348800 chr6D 78818003 78818527 524 True 433.00 433 82.0000 3550 4087 1 chr6D.!!$R1 537
2 TraesCS6D01G348800 chr6A 593436204 593439280 3076 True 1153.75 2220 96.1100 1 3440 4 chr6A.!!$R1 3439
3 TraesCS6D01G348800 chr6B 675448640 675451225 2585 True 654.40 1448 92.1726 1 3072 5 chr6B.!!$R2 3071
4 TraesCS6D01G348800 chr1D 46325839 46326615 776 False 1144.00 1144 93.0640 3531 4322 1 chr1D.!!$F1 791
5 TraesCS6D01G348800 chr1D 342450780 342451524 744 True 1002.00 1002 90.9450 3570 4322 1 chr1D.!!$R1 752
6 TraesCS6D01G348800 chr4D 204709459 204710231 772 True 1138.00 1138 93.0470 3533 4322 1 chr4D.!!$R1 789
7 TraesCS6D01G348800 chr2B 253706628 253707402 774 False 1055.00 1055 91.0580 3530 4322 1 chr2B.!!$F2 792
8 TraesCS6D01G348800 chr2B 756637094 756637908 814 False 813.00 813 84.7560 1683 2498 1 chr2B.!!$F3 815
9 TraesCS6D01G348800 chr2B 707620469 707621306 837 True 780.00 780 83.7680 1675 2502 1 chr2B.!!$R4 827
10 TraesCS6D01G348800 chr2B 756969118 756969932 814 False 758.00 758 83.5970 1683 2498 1 chr2B.!!$F4 815
11 TraesCS6D01G348800 chr2B 707656100 707658036 1936 True 506.50 739 79.6400 708 2495 2 chr2B.!!$R6 1787
12 TraesCS6D01G348800 chr2B 707960276 707960786 510 True 322.00 322 78.5170 812 1327 1 chr2B.!!$R5 515
13 TraesCS6D01G348800 chr2B 707530750 707531270 520 True 285.00 285 77.1220 708 1239 1 chr2B.!!$R3 531
14 TraesCS6D01G348800 chr3A 735721374 735722159 785 False 1005.00 1005 89.7880 3525 4319 1 chr3A.!!$F1 794
15 TraesCS6D01G348800 chr3B 599097089 599097878 789 True 972.00 972 88.9170 3527 4322 1 chr3B.!!$R2 795
16 TraesCS6D01G348800 chrUn 74778473 74782291 3818 False 667.50 924 85.8795 1 2492 2 chrUn.!!$F1 2491
17 TraesCS6D01G348800 chr1B 486493409 486495744 2335 True 661.00 913 84.4780 3536 4322 2 chr1B.!!$R3 786
18 TraesCS6D01G348800 chr2D 586293179 586294006 827 True 717.00 717 82.5980 1671 2495 1 chr2D.!!$R1 824
19 TraesCS6D01G348800 chr2D 619146726 619148240 1514 False 562.00 833 81.0125 693 2497 2 chr2D.!!$F2 1804
20 TraesCS6D01G348800 chr2A 89597648 89598309 661 False 771.00 771 88.1380 3676 4322 1 chr2A.!!$F1 646
21 TraesCS6D01G348800 chr2A 750208051 750209568 1517 True 535.50 795 80.3120 693 2497 2 chr2A.!!$R5 1804
22 TraesCS6D01G348800 chr2A 720574070 720575919 1849 True 504.50 750 79.8100 827 2495 2 chr2A.!!$R4 1668
23 TraesCS6D01G348800 chr2A 721065230 721065740 510 True 300.00 300 77.5860 812 1327 1 chr2A.!!$R3 515
24 TraesCS6D01G348800 chr5D 548630694 548631355 661 False 782.00 782 88.4560 3676 4322 1 chr5D.!!$F2 646
25 TraesCS6D01G348800 chr3D 562522087 562522874 787 True 695.00 695 83.1890 3531 4311 1 chr3D.!!$R3 780

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
301 305 0.738389 CGACAAGGTGCTTGGTTTGT 59.262 50.0 0.00 0.00 44.81 2.83 F
350 354 1.040646 AACTGACTCTGGCGAGAACA 58.959 50.0 12.16 2.81 39.74 3.18 F
1810 3591 1.027357 AACTGCAGCACAAGAACCTG 58.973 50.0 15.27 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1810 3591 2.154462 CAACACCCATGAAGTCTGACC 58.846 52.381 3.76 0.0 0.00 4.02 R
1988 3780 5.008118 TGTGTTTTCGTGCAACATCTTGATA 59.992 36.000 0.00 0.0 36.54 2.15 R
3626 5437 0.179067 TTCCTCGCGAACAGGTTGTT 60.179 50.000 11.33 0.0 44.37 2.83 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
23 24 1.134995 TCAGCTATTGCGACCTCACTG 60.135 52.381 0.00 0.00 45.42 3.66
50 51 1.519898 CCGGCATGCAAATGCTTCC 60.520 57.895 21.36 0.00 46.22 3.46
67 68 0.776810 TCCATGGGTTTGAGCCTGAA 59.223 50.000 13.02 0.00 36.53 3.02
69 70 1.969923 CCATGGGTTTGAGCCTGAAAA 59.030 47.619 2.85 0.00 36.53 2.29
142 146 7.138736 GCAAGCAAAGTCAGTTCATAACTTTA 58.861 34.615 0.00 0.00 40.32 1.85
178 182 5.181433 GGTCCCTGACAAGTTCTTACATTTC 59.819 44.000 0.00 0.00 33.68 2.17
259 263 3.063452 CGTATGCTTACGCCAATTTGAGT 59.937 43.478 17.74 0.70 44.11 3.41
301 305 0.738389 CGACAAGGTGCTTGGTTTGT 59.262 50.000 0.00 0.00 44.81 2.83
350 354 1.040646 AACTGACTCTGGCGAGAACA 58.959 50.000 12.16 2.81 39.74 3.18
461 1919 4.904154 GTCATATATTTGCGAACCGAAAGC 59.096 41.667 0.00 0.00 0.00 3.51
519 1994 8.792830 TCCTTCCTTTTAACATCATCTTACAG 57.207 34.615 0.00 0.00 0.00 2.74
667 2145 1.452110 TCTCACATTGACAATGGCCG 58.548 50.000 27.46 17.15 43.21 6.13
759 2241 4.959560 TTACCACAAGCACTGGTAGTTA 57.040 40.909 7.12 0.00 43.64 2.24
775 2259 6.775708 TGGTAGTTAAGGCACTCAAATTACT 58.224 36.000 0.00 0.00 38.49 2.24
776 2260 6.653320 TGGTAGTTAAGGCACTCAAATTACTG 59.347 38.462 0.00 0.00 38.49 2.74
778 2262 6.560253 AGTTAAGGCACTCAAATTACTGTG 57.440 37.500 0.00 0.00 38.49 3.66
876 2368 5.368145 TGCATTTCTACAGTTGACAAGAGT 58.632 37.500 0.00 0.00 0.00 3.24
900 2392 8.937835 AGTAGTTTACTAAAGGTTTTACTCCCA 58.062 33.333 0.00 0.00 37.23 4.37
967 2459 7.234782 TCTGGACTTACAAATTCAGAGGTAGAA 59.765 37.037 0.00 0.00 0.00 2.10
1080 2583 3.315470 GCGAAAGAAGGAAAACCAGAAGT 59.685 43.478 0.00 0.00 0.00 3.01
1285 2799 9.844257 ATCTTTTGGGTTAAAAATGAAACATGA 57.156 25.926 0.00 0.00 37.78 3.07
1413 2987 5.270853 ACGCATTTAGTTGTTGTTGTTCTC 58.729 37.500 0.00 0.00 0.00 2.87
1425 2999 3.206150 TGTTGTTCTCACTGAAGCCTTC 58.794 45.455 0.00 0.00 35.01 3.46
1427 3001 4.100963 TGTTGTTCTCACTGAAGCCTTCTA 59.899 41.667 5.96 0.00 35.01 2.10
1522 3232 1.340088 ATGAGTTGCCCATTTGCACA 58.660 45.000 0.00 0.00 41.88 4.57
1664 3444 6.387041 AAAAGTTAGCTTCCAAGTGTTACC 57.613 37.500 0.00 0.00 33.01 2.85
1735 3516 2.608016 GGTTGCTGTCAAAAGGCTTAGC 60.608 50.000 11.17 11.17 33.37 3.09
1810 3591 1.027357 AACTGCAGCACAAGAACCTG 58.973 50.000 15.27 0.00 0.00 4.00
2452 4252 2.235898 GCCTGAAGATCAGTTCACCTCT 59.764 50.000 6.62 0.00 42.80 3.69
2506 4306 7.515643 ACTTATGTAAGTATTGTTGAACGTGC 58.484 34.615 3.69 0.00 44.18 5.34
2868 4668 9.647918 AAGTCTTTGTAGAGATATCACTATGGA 57.352 33.333 12.27 6.68 0.00 3.41
2869 4669 9.073475 AGTCTTTGTAGAGATATCACTATGGAC 57.927 37.037 12.27 15.07 0.00 4.02
2870 4670 9.073475 GTCTTTGTAGAGATATCACTATGGACT 57.927 37.037 12.27 0.00 0.00 3.85
2884 4684 6.379988 TCACTATGGACTACATACAGAGCAAA 59.620 38.462 0.00 0.00 41.03 3.68
2885 4685 7.041721 CACTATGGACTACATACAGAGCAAAA 58.958 38.462 0.00 0.00 41.03 2.44
2886 4686 7.712639 CACTATGGACTACATACAGAGCAAAAT 59.287 37.037 0.00 0.00 41.03 1.82
2887 4687 8.924303 ACTATGGACTACATACAGAGCAAAATA 58.076 33.333 0.00 0.00 41.03 1.40
2888 4688 9.764363 CTATGGACTACATACAGAGCAAAATAA 57.236 33.333 0.00 0.00 41.03 1.40
2889 4689 8.668510 ATGGACTACATACAGAGCAAAATAAG 57.331 34.615 0.00 0.00 38.26 1.73
2890 4690 7.620880 TGGACTACATACAGAGCAAAATAAGT 58.379 34.615 0.00 0.00 0.00 2.24
2891 4691 7.549134 TGGACTACATACAGAGCAAAATAAGTG 59.451 37.037 0.00 0.00 0.00 3.16
2893 4693 9.151471 GACTACATACAGAGCAAAATAAGTGAA 57.849 33.333 0.00 0.00 0.00 3.18
2895 4695 7.145932 ACATACAGAGCAAAATAAGTGAACC 57.854 36.000 0.00 0.00 0.00 3.62
2896 4696 6.942576 ACATACAGAGCAAAATAAGTGAACCT 59.057 34.615 0.00 0.00 0.00 3.50
2898 4698 6.803154 ACAGAGCAAAATAAGTGAACCTAC 57.197 37.500 0.00 0.00 0.00 3.18
2900 4700 6.204882 ACAGAGCAAAATAAGTGAACCTACAC 59.795 38.462 0.00 0.00 40.60 2.90
2911 4711 5.865085 AGTGAACCTACACTCTAAAATGCA 58.135 37.500 0.00 0.00 46.36 3.96
2912 4712 6.476378 AGTGAACCTACACTCTAAAATGCAT 58.524 36.000 0.00 0.00 46.36 3.96
2913 4713 6.595716 AGTGAACCTACACTCTAAAATGCATC 59.404 38.462 0.00 0.00 46.36 3.91
2914 4714 6.595716 GTGAACCTACACTCTAAAATGCATCT 59.404 38.462 0.00 0.00 37.73 2.90
2915 4715 7.764443 GTGAACCTACACTCTAAAATGCATCTA 59.236 37.037 0.00 0.00 37.73 1.98
2916 4716 7.764443 TGAACCTACACTCTAAAATGCATCTAC 59.236 37.037 0.00 0.00 0.00 2.59
2917 4717 7.182817 ACCTACACTCTAAAATGCATCTACA 57.817 36.000 0.00 0.00 0.00 2.74
2918 4718 7.796054 ACCTACACTCTAAAATGCATCTACAT 58.204 34.615 0.00 0.00 0.00 2.29
2919 4719 8.924303 ACCTACACTCTAAAATGCATCTACATA 58.076 33.333 0.00 0.00 0.00 2.29
2923 4723 9.618890 ACACTCTAAAATGCATCTACATACATT 57.381 29.630 0.00 0.00 34.30 2.71
2925 4725 8.982685 ACTCTAAAATGCATCTACATACATTCG 58.017 33.333 0.00 0.00 31.75 3.34
2926 4726 8.887036 TCTAAAATGCATCTACATACATTCGT 57.113 30.769 0.00 0.00 31.75 3.85
2929 4729 6.690704 AATGCATCTACATACATTCGTACG 57.309 37.500 9.53 9.53 0.00 3.67
2930 4730 5.177725 TGCATCTACATACATTCGTACGT 57.822 39.130 16.05 0.00 0.00 3.57
2931 4731 4.973663 TGCATCTACATACATTCGTACGTG 59.026 41.667 16.05 9.78 0.00 4.49
2932 4732 4.381863 GCATCTACATACATTCGTACGTGG 59.618 45.833 16.05 8.47 0.00 4.94
2933 4733 5.516996 CATCTACATACATTCGTACGTGGT 58.483 41.667 16.05 13.75 0.00 4.16
2934 4734 5.160699 TCTACATACATTCGTACGTGGTC 57.839 43.478 16.05 0.00 0.00 4.02
2935 4735 3.155093 ACATACATTCGTACGTGGTCC 57.845 47.619 16.05 0.00 0.00 4.46
2936 4736 2.492881 ACATACATTCGTACGTGGTCCA 59.507 45.455 16.05 0.00 0.00 4.02
2937 4737 3.131577 ACATACATTCGTACGTGGTCCAT 59.868 43.478 16.05 0.51 0.00 3.41
2938 4738 4.338964 ACATACATTCGTACGTGGTCCATA 59.661 41.667 16.05 0.97 0.00 2.74
2939 4739 3.431922 ACATTCGTACGTGGTCCATAG 57.568 47.619 16.05 0.00 0.00 2.23
2941 4741 2.925578 TTCGTACGTGGTCCATAGTG 57.074 50.000 16.05 0.00 0.00 2.74
2942 4742 2.112380 TCGTACGTGGTCCATAGTGA 57.888 50.000 16.05 1.30 0.00 3.41
2943 4743 2.435422 TCGTACGTGGTCCATAGTGAA 58.565 47.619 16.05 0.00 0.00 3.18
2944 4744 2.819019 TCGTACGTGGTCCATAGTGAAA 59.181 45.455 16.05 0.00 0.00 2.69
2946 4746 3.795101 CGTACGTGGTCCATAGTGAAATC 59.205 47.826 7.22 0.00 0.00 2.17
2947 4747 4.439700 CGTACGTGGTCCATAGTGAAATCT 60.440 45.833 7.22 0.00 0.00 2.40
2948 4748 4.124851 ACGTGGTCCATAGTGAAATCTC 57.875 45.455 0.00 0.00 0.00 2.75
2949 4749 3.769844 ACGTGGTCCATAGTGAAATCTCT 59.230 43.478 0.00 0.00 0.00 3.10
2950 4750 4.954202 ACGTGGTCCATAGTGAAATCTCTA 59.046 41.667 0.00 0.00 0.00 2.43
2951 4751 5.163540 ACGTGGTCCATAGTGAAATCTCTAC 60.164 44.000 0.00 0.00 0.00 2.59
2952 4752 5.163550 CGTGGTCCATAGTGAAATCTCTACA 60.164 44.000 0.00 0.00 0.00 2.74
2953 4753 6.627287 CGTGGTCCATAGTGAAATCTCTACAA 60.627 42.308 0.00 0.00 0.00 2.41
2954 4754 7.103641 GTGGTCCATAGTGAAATCTCTACAAA 58.896 38.462 0.00 0.00 0.00 2.83
2955 4755 7.278868 GTGGTCCATAGTGAAATCTCTACAAAG 59.721 40.741 0.00 0.00 0.00 2.77
2956 4756 7.180229 TGGTCCATAGTGAAATCTCTACAAAGA 59.820 37.037 0.00 0.00 0.00 2.52
2957 4757 7.492994 GGTCCATAGTGAAATCTCTACAAAGAC 59.507 40.741 0.00 0.00 0.00 3.01
2958 4758 8.254508 GTCCATAGTGAAATCTCTACAAAGACT 58.745 37.037 0.00 0.00 0.00 3.24
2959 4759 8.816894 TCCATAGTGAAATCTCTACAAAGACTT 58.183 33.333 0.00 0.00 0.00 3.01
3070 4871 5.226396 CAACTGAACTAGTGGACTCTTCTG 58.774 45.833 0.00 0.00 40.26 3.02
3077 4878 1.140816 GTGGACTCTTCTGTTGTCGC 58.859 55.000 0.00 0.00 0.00 5.19
3078 4879 0.318699 TGGACTCTTCTGTTGTCGCG 60.319 55.000 0.00 0.00 0.00 5.87
3115 4916 4.055360 TGAAGTTCTACGGTGTGTTCATG 58.945 43.478 4.17 0.00 0.00 3.07
3156 4957 1.301716 CCATCCCAACGATAGGCCG 60.302 63.158 0.00 0.00 43.77 6.13
3175 4976 3.390135 CCGCTAATGTCATCGGTTATGT 58.610 45.455 3.79 0.00 37.33 2.29
3181 4982 7.307160 CGCTAATGTCATCGGTTATGTTTATGT 60.307 37.037 0.00 0.00 36.89 2.29
3273 5074 6.711277 AGGTCAAGAAGCAACAGATAACATA 58.289 36.000 0.00 0.00 0.00 2.29
3282 5083 6.578023 AGCAACAGATAACATAGAGAACTCC 58.422 40.000 0.00 0.00 0.00 3.85
3284 5085 6.256757 GCAACAGATAACATAGAGAACTCCAC 59.743 42.308 0.00 0.00 0.00 4.02
3338 5139 7.271868 GGGTCGTTAAATGTTGTATAACTTTGC 59.728 37.037 3.89 0.00 37.68 3.68
3363 5164 6.092396 CGTGTGCGGATATTAGTATACTCTCT 59.908 42.308 9.12 0.00 0.00 3.10
3385 5186 9.066892 TCTCTTTGTGAACTAAACTTTGCATAT 57.933 29.630 0.00 0.00 0.00 1.78
3397 5198 1.252175 TTGCATATGCCGGTTGTGTT 58.748 45.000 24.54 0.00 41.18 3.32
3453 5254 3.434940 CTTTGTAAGCCTACCCCAACT 57.565 47.619 0.00 0.00 0.00 3.16
3454 5255 3.763057 CTTTGTAAGCCTACCCCAACTT 58.237 45.455 0.00 0.00 0.00 2.66
3455 5256 2.871096 TGTAAGCCTACCCCAACTTG 57.129 50.000 0.00 0.00 0.00 3.16
3456 5257 2.059490 TGTAAGCCTACCCCAACTTGT 58.941 47.619 0.00 0.00 0.00 3.16
3457 5258 2.444010 TGTAAGCCTACCCCAACTTGTT 59.556 45.455 0.00 0.00 0.00 2.83
3458 5259 2.767644 AAGCCTACCCCAACTTGTTT 57.232 45.000 0.00 0.00 0.00 2.83
3459 5260 1.995376 AGCCTACCCCAACTTGTTTG 58.005 50.000 0.00 0.00 34.63 2.93
3470 5271 3.977427 CAACTTGTTTGGGACTAAAGGC 58.023 45.455 0.00 0.00 0.00 4.35
3471 5272 3.595190 ACTTGTTTGGGACTAAAGGCT 57.405 42.857 0.00 0.00 0.00 4.58
3472 5273 3.910989 ACTTGTTTGGGACTAAAGGCTT 58.089 40.909 0.00 0.00 0.00 4.35
3473 5274 4.286707 ACTTGTTTGGGACTAAAGGCTTT 58.713 39.130 17.76 17.76 0.00 3.51
3474 5275 4.714802 ACTTGTTTGGGACTAAAGGCTTTT 59.285 37.500 18.93 0.00 0.00 2.27
3475 5276 5.188948 ACTTGTTTGGGACTAAAGGCTTTTT 59.811 36.000 18.93 5.62 0.00 1.94
3497 5298 8.993852 TTTTTGTTGTTGTTGTTGTATTTGTG 57.006 26.923 0.00 0.00 0.00 3.33
3498 5299 6.712241 TTGTTGTTGTTGTTGTATTTGTGG 57.288 33.333 0.00 0.00 0.00 4.17
3499 5300 5.784177 TGTTGTTGTTGTTGTATTTGTGGT 58.216 33.333 0.00 0.00 0.00 4.16
3500 5301 5.635280 TGTTGTTGTTGTTGTATTTGTGGTG 59.365 36.000 0.00 0.00 0.00 4.17
3501 5302 4.177026 TGTTGTTGTTGTATTTGTGGTGC 58.823 39.130 0.00 0.00 0.00 5.01
3502 5303 4.081972 TGTTGTTGTTGTATTTGTGGTGCT 60.082 37.500 0.00 0.00 0.00 4.40
3503 5304 4.727507 TGTTGTTGTATTTGTGGTGCTT 57.272 36.364 0.00 0.00 0.00 3.91
3504 5305 5.078411 TGTTGTTGTATTTGTGGTGCTTT 57.922 34.783 0.00 0.00 0.00 3.51
3505 5306 4.867047 TGTTGTTGTATTTGTGGTGCTTTG 59.133 37.500 0.00 0.00 0.00 2.77
3506 5307 4.727507 TGTTGTATTTGTGGTGCTTTGT 57.272 36.364 0.00 0.00 0.00 2.83
3507 5308 5.836821 TGTTGTATTTGTGGTGCTTTGTA 57.163 34.783 0.00 0.00 0.00 2.41
3508 5309 5.583495 TGTTGTATTTGTGGTGCTTTGTAC 58.417 37.500 0.00 0.00 0.00 2.90
3509 5310 5.358442 TGTTGTATTTGTGGTGCTTTGTACT 59.642 36.000 0.00 0.00 0.00 2.73
3510 5311 6.127591 TGTTGTATTTGTGGTGCTTTGTACTT 60.128 34.615 0.00 0.00 0.00 2.24
3511 5312 6.067263 TGTATTTGTGGTGCTTTGTACTTC 57.933 37.500 0.00 0.00 0.00 3.01
3512 5313 5.825679 TGTATTTGTGGTGCTTTGTACTTCT 59.174 36.000 0.00 0.00 0.00 2.85
3513 5314 5.852282 ATTTGTGGTGCTTTGTACTTCTT 57.148 34.783 0.00 0.00 0.00 2.52
3514 5315 6.952773 ATTTGTGGTGCTTTGTACTTCTTA 57.047 33.333 0.00 0.00 0.00 2.10
3515 5316 6.952773 TTTGTGGTGCTTTGTACTTCTTAT 57.047 33.333 0.00 0.00 0.00 1.73
3516 5317 5.940192 TGTGGTGCTTTGTACTTCTTATG 57.060 39.130 0.00 0.00 0.00 1.90
3517 5318 5.616270 TGTGGTGCTTTGTACTTCTTATGA 58.384 37.500 0.00 0.00 0.00 2.15
3518 5319 6.058833 TGTGGTGCTTTGTACTTCTTATGAA 58.941 36.000 0.00 0.00 0.00 2.57
3519 5320 6.017440 TGTGGTGCTTTGTACTTCTTATGAAC 60.017 38.462 0.00 0.00 0.00 3.18
3520 5321 5.472137 TGGTGCTTTGTACTTCTTATGAACC 59.528 40.000 0.00 0.00 0.00 3.62
3521 5322 5.705905 GGTGCTTTGTACTTCTTATGAACCT 59.294 40.000 0.00 0.00 0.00 3.50
3522 5323 6.206829 GGTGCTTTGTACTTCTTATGAACCTT 59.793 38.462 0.00 0.00 0.00 3.50
3523 5324 7.255486 GGTGCTTTGTACTTCTTATGAACCTTT 60.255 37.037 0.00 0.00 0.00 3.11
3524 5325 8.780249 GTGCTTTGTACTTCTTATGAACCTTTA 58.220 33.333 0.00 0.00 0.00 1.85
3525 5326 9.344772 TGCTTTGTACTTCTTATGAACCTTTAA 57.655 29.630 0.00 0.00 0.00 1.52
3547 5348 4.724074 AATAGGACGTCGATAACAACCA 57.276 40.909 9.92 0.00 0.00 3.67
3616 5427 3.431207 GGAAGGGGTATCGATCGAACAAA 60.431 47.826 23.50 5.31 0.00 2.83
3645 5456 0.179067 AACAACCTGTTCGCGAGGAA 60.179 50.000 18.70 3.74 35.27 3.36
3971 5831 4.142381 GCCATGAAGTGATAGGGTGAAAAC 60.142 45.833 0.00 0.00 0.00 2.43
4101 5968 6.434018 TCAAAACTTTTTGCCATGGAAAAG 57.566 33.333 25.98 25.98 45.35 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.513897 GCATGCCGGGACAGTACC 60.514 66.667 6.36 0.00 0.00 3.34
50 51 3.512724 AGATTTTCAGGCTCAAACCCATG 59.487 43.478 0.00 0.00 0.00 3.66
178 182 3.993081 ACTCATCGAAGCTTCTGTTCTTG 59.007 43.478 23.50 11.52 0.00 3.02
219 223 1.425428 GCCGTACATGAGCAGTTGC 59.575 57.895 0.00 0.00 42.49 4.17
259 263 2.094390 GTCATCGTTAGCACCACCACTA 60.094 50.000 0.00 0.00 0.00 2.74
301 305 2.029623 GTGTCGATAAGCTCCCCTGTA 58.970 52.381 0.00 0.00 0.00 2.74
350 354 0.613260 TCAGCAAGGCGAAGGTACAT 59.387 50.000 0.00 0.00 0.00 2.29
445 1855 0.165944 CTCGCTTTCGGTTCGCAAAT 59.834 50.000 0.00 0.00 36.13 2.32
647 2125 1.811965 CGGCCATTGTCAATGTGAGAA 59.188 47.619 21.32 0.00 37.18 2.87
652 2130 4.016444 AGTTAATCGGCCATTGTCAATGT 58.984 39.130 21.32 6.99 37.18 2.71
759 2241 3.832527 ACCACAGTAATTTGAGTGCCTT 58.167 40.909 0.00 0.00 0.00 4.35
775 2259 8.685427 TCAAGCTAATTAAGTACGTATACCACA 58.315 33.333 0.00 0.00 30.88 4.17
776 2260 8.962111 GTCAAGCTAATTAAGTACGTATACCAC 58.038 37.037 0.00 0.00 30.88 4.16
778 2262 9.178427 CTGTCAAGCTAATTAAGTACGTATACC 57.822 37.037 0.00 0.00 30.88 2.73
1080 2583 7.977293 TGTGCTAAAGTATTCTCGCATTAGTTA 59.023 33.333 0.00 0.00 0.00 2.24
1285 2799 7.287810 AGACAACAGTTGAAGGGTAAATTAGT 58.712 34.615 20.56 0.00 0.00 2.24
1413 2987 2.355209 GGGGAAGTAGAAGGCTTCAGTG 60.355 54.545 27.70 0.00 42.88 3.66
1425 2999 7.565680 AGATGTATTAACAACTGGGGAAGTAG 58.434 38.462 0.00 0.00 38.56 2.57
1427 3001 6.388619 AGATGTATTAACAACTGGGGAAGT 57.611 37.500 0.00 0.00 42.60 3.01
1578 3288 4.346478 ACCCCTTTTAATTGTAGCCCAT 57.654 40.909 0.00 0.00 0.00 4.00
1586 3297 6.989759 AGTGCACTTTTAACCCCTTTTAATTG 59.010 34.615 15.25 0.00 0.00 2.32
1681 3462 4.141390 CCTTCCATTGTGCCCTATAAGAGT 60.141 45.833 0.00 0.00 0.00 3.24
1810 3591 2.154462 CAACACCCATGAAGTCTGACC 58.846 52.381 3.76 0.00 0.00 4.02
1988 3780 5.008118 TGTGTTTTCGTGCAACATCTTGATA 59.992 36.000 0.00 0.00 36.54 2.15
2141 3939 9.631257 AAAATCTGAAATTTTGGGAGTCATTTT 57.369 25.926 0.00 0.00 30.84 1.82
2452 4252 4.438472 GGCTGCAAAAATTTGTTTTGAGCA 60.438 37.500 22.51 16.65 40.73 4.26
2842 4642 9.647918 TCCATAGTGATATCTCTACAAAGACTT 57.352 33.333 15.01 0.00 0.00 3.01
2843 4643 9.073475 GTCCATAGTGATATCTCTACAAAGACT 57.927 37.037 15.01 4.61 0.00 3.24
2844 4644 9.073475 AGTCCATAGTGATATCTCTACAAAGAC 57.927 37.037 15.01 16.45 0.00 3.01
2847 4647 9.862149 TGTAGTCCATAGTGATATCTCTACAAA 57.138 33.333 15.01 3.19 34.46 2.83
2852 4652 9.679661 CTGTATGTAGTCCATAGTGATATCTCT 57.320 37.037 11.77 11.77 36.71 3.10
2853 4653 9.674068 TCTGTATGTAGTCCATAGTGATATCTC 57.326 37.037 3.98 0.00 36.71 2.75
2854 4654 9.679661 CTCTGTATGTAGTCCATAGTGATATCT 57.320 37.037 3.98 0.00 36.71 1.98
2855 4655 8.402472 GCTCTGTATGTAGTCCATAGTGATATC 58.598 40.741 0.00 0.00 36.71 1.63
2856 4656 7.890655 TGCTCTGTATGTAGTCCATAGTGATAT 59.109 37.037 0.00 0.00 36.71 1.63
2857 4657 7.231467 TGCTCTGTATGTAGTCCATAGTGATA 58.769 38.462 0.00 0.00 36.71 2.15
2858 4658 6.071320 TGCTCTGTATGTAGTCCATAGTGAT 58.929 40.000 0.00 0.00 36.71 3.06
2859 4659 5.445964 TGCTCTGTATGTAGTCCATAGTGA 58.554 41.667 0.00 0.00 36.71 3.41
2860 4660 5.774498 TGCTCTGTATGTAGTCCATAGTG 57.226 43.478 0.00 0.00 36.71 2.74
2861 4661 6.791867 TTTGCTCTGTATGTAGTCCATAGT 57.208 37.500 0.00 0.00 36.71 2.12
2862 4662 9.764363 TTATTTTGCTCTGTATGTAGTCCATAG 57.236 33.333 0.00 0.00 36.71 2.23
2863 4663 9.764363 CTTATTTTGCTCTGTATGTAGTCCATA 57.236 33.333 0.00 0.00 34.86 2.74
2864 4664 8.267894 ACTTATTTTGCTCTGTATGTAGTCCAT 58.732 33.333 0.00 0.00 37.58 3.41
2865 4665 7.549134 CACTTATTTTGCTCTGTATGTAGTCCA 59.451 37.037 0.00 0.00 0.00 4.02
2866 4666 7.764443 TCACTTATTTTGCTCTGTATGTAGTCC 59.236 37.037 0.00 0.00 0.00 3.85
2867 4667 8.703604 TCACTTATTTTGCTCTGTATGTAGTC 57.296 34.615 0.00 0.00 0.00 2.59
2868 4668 8.936864 GTTCACTTATTTTGCTCTGTATGTAGT 58.063 33.333 0.00 0.00 0.00 2.73
2869 4669 8.391106 GGTTCACTTATTTTGCTCTGTATGTAG 58.609 37.037 0.00 0.00 0.00 2.74
2870 4670 8.100791 AGGTTCACTTATTTTGCTCTGTATGTA 58.899 33.333 0.00 0.00 0.00 2.29
2874 4674 7.386848 GTGTAGGTTCACTTATTTTGCTCTGTA 59.613 37.037 0.00 0.00 35.68 2.74
2884 4684 8.947115 GCATTTTAGAGTGTAGGTTCACTTATT 58.053 33.333 0.98 0.00 46.81 1.40
2885 4685 8.100791 TGCATTTTAGAGTGTAGGTTCACTTAT 58.899 33.333 0.98 0.00 46.81 1.73
2886 4686 7.446769 TGCATTTTAGAGTGTAGGTTCACTTA 58.553 34.615 0.98 0.00 46.81 2.24
2887 4687 6.296026 TGCATTTTAGAGTGTAGGTTCACTT 58.704 36.000 0.98 0.00 46.81 3.16
2889 4689 6.595716 AGATGCATTTTAGAGTGTAGGTTCAC 59.404 38.462 0.00 0.00 38.46 3.18
2890 4690 6.711277 AGATGCATTTTAGAGTGTAGGTTCA 58.289 36.000 0.00 0.00 0.00 3.18
2891 4691 7.764443 TGTAGATGCATTTTAGAGTGTAGGTTC 59.236 37.037 0.00 0.00 0.00 3.62
2893 4693 7.182817 TGTAGATGCATTTTAGAGTGTAGGT 57.817 36.000 0.00 0.00 0.00 3.08
2895 4695 9.750125 TGTATGTAGATGCATTTTAGAGTGTAG 57.250 33.333 0.00 0.00 0.00 2.74
2900 4700 8.982685 ACGAATGTATGTAGATGCATTTTAGAG 58.017 33.333 15.62 8.96 42.85 2.43
2901 4701 8.887036 ACGAATGTATGTAGATGCATTTTAGA 57.113 30.769 15.62 0.00 42.85 2.10
2905 4705 6.700081 ACGTACGAATGTATGTAGATGCATTT 59.300 34.615 24.41 0.00 46.45 2.32
2906 4706 6.143919 CACGTACGAATGTATGTAGATGCATT 59.856 38.462 24.41 14.65 46.55 3.56
2908 4708 4.973663 CACGTACGAATGTATGTAGATGCA 59.026 41.667 24.41 0.00 46.55 3.96
2909 4709 4.381863 CCACGTACGAATGTATGTAGATGC 59.618 45.833 24.41 0.00 46.55 3.91
2911 4711 5.278169 GGACCACGTACGAATGTATGTAGAT 60.278 44.000 24.41 0.00 46.55 1.98
2912 4712 4.035558 GGACCACGTACGAATGTATGTAGA 59.964 45.833 24.41 0.00 46.55 2.59
2913 4713 4.201940 TGGACCACGTACGAATGTATGTAG 60.202 45.833 24.41 0.00 46.55 2.74
2914 4714 3.693578 TGGACCACGTACGAATGTATGTA 59.306 43.478 24.41 0.00 46.55 2.29
2916 4716 3.153676 TGGACCACGTACGAATGTATG 57.846 47.619 24.41 8.36 42.24 2.39
2917 4717 4.581824 ACTATGGACCACGTACGAATGTAT 59.418 41.667 24.41 10.94 32.11 2.29
2918 4718 3.947196 ACTATGGACCACGTACGAATGTA 59.053 43.478 24.41 3.83 0.00 2.29
2919 4719 2.756760 ACTATGGACCACGTACGAATGT 59.243 45.455 24.41 15.05 0.00 2.71
2922 4722 2.435422 TCACTATGGACCACGTACGAA 58.565 47.619 24.41 0.13 0.00 3.85
2923 4723 2.112380 TCACTATGGACCACGTACGA 57.888 50.000 24.41 0.00 0.00 3.43
2924 4724 2.925578 TTCACTATGGACCACGTACG 57.074 50.000 15.01 15.01 0.00 3.67
2925 4725 5.007385 AGATTTCACTATGGACCACGTAC 57.993 43.478 0.00 0.00 0.00 3.67
2926 4726 4.954202 AGAGATTTCACTATGGACCACGTA 59.046 41.667 0.00 0.00 0.00 3.57
2928 4728 4.392921 AGAGATTTCACTATGGACCACG 57.607 45.455 0.00 0.00 0.00 4.94
2929 4729 6.222038 TGTAGAGATTTCACTATGGACCAC 57.778 41.667 0.00 0.00 0.00 4.16
2930 4730 6.867519 TTGTAGAGATTTCACTATGGACCA 57.132 37.500 0.00 0.00 0.00 4.02
2931 4731 7.492994 GTCTTTGTAGAGATTTCACTATGGACC 59.507 40.741 0.00 0.00 0.00 4.46
2932 4732 8.254508 AGTCTTTGTAGAGATTTCACTATGGAC 58.745 37.037 0.00 0.00 0.00 4.02
2933 4733 8.367660 AGTCTTTGTAGAGATTTCACTATGGA 57.632 34.615 0.00 0.00 0.00 3.41
2950 4750 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
2951 4751 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
2952 4752 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
2953 4753 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
2954 4754 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
2955 4755 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
2956 4756 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2957 4757 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2958 4758 7.300658 AGTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
2959 4759 6.856757 AGTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
2960 4760 5.713807 AGTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
2961 4761 5.134725 AGTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2962 4762 3.991683 AGTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2963 4763 3.463048 AGTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2964 4764 3.094572 CAAGTACTCCCTCCGTTCCTAA 58.905 50.000 0.00 0.00 0.00 2.69
2965 4765 2.042162 ACAAGTACTCCCTCCGTTCCTA 59.958 50.000 0.00 0.00 0.00 2.94
2966 4766 1.203149 ACAAGTACTCCCTCCGTTCCT 60.203 52.381 0.00 0.00 0.00 3.36
2967 4767 1.264295 ACAAGTACTCCCTCCGTTCC 58.736 55.000 0.00 0.00 0.00 3.62
2968 4768 4.021632 AGTTAACAAGTACTCCCTCCGTTC 60.022 45.833 8.61 0.00 0.00 3.95
2969 4769 3.899980 AGTTAACAAGTACTCCCTCCGTT 59.100 43.478 8.61 0.00 0.00 4.44
2970 4770 3.504375 AGTTAACAAGTACTCCCTCCGT 58.496 45.455 8.61 0.00 0.00 4.69
2971 4771 4.021719 TGAAGTTAACAAGTACTCCCTCCG 60.022 45.833 8.61 0.00 0.00 4.63
3115 4916 2.218953 TGAACACACAAGAGTCCGAC 57.781 50.000 0.00 0.00 0.00 4.79
3156 4957 7.861630 ACATAAACATAACCGATGACATTAGC 58.138 34.615 0.00 0.00 39.06 3.09
3175 4976 5.918011 GCGTGTTTTCATTCTCCAACATAAA 59.082 36.000 0.00 0.00 32.00 1.40
3181 4982 3.882888 AGAAGCGTGTTTTCATTCTCCAA 59.117 39.130 0.00 0.00 0.00 3.53
3228 5029 5.869888 ACCTTCACGATTACTTAGAGCAAAG 59.130 40.000 0.00 0.00 0.00 2.77
3273 5074 5.105997 GCTAATTGCATTTGTGGAGTTCTCT 60.106 40.000 4.11 0.00 42.31 3.10
3338 5139 6.092396 AGAGAGTATACTAATATCCGCACACG 59.908 42.308 5.09 0.00 39.67 4.49
3363 5164 6.644592 GGCATATGCAAAGTTTAGTTCACAAA 59.355 34.615 28.07 0.00 44.36 2.83
3385 5186 2.147958 GAGTATTCAACACAACCGGCA 58.852 47.619 0.00 0.00 0.00 5.69
3440 5241 1.995376 CAAACAAGTTGGGGTAGGCT 58.005 50.000 7.96 0.00 33.18 4.58
3449 5250 3.636764 AGCCTTTAGTCCCAAACAAGTTG 59.363 43.478 0.00 0.00 36.94 3.16
3450 5251 3.910989 AGCCTTTAGTCCCAAACAAGTT 58.089 40.909 0.00 0.00 0.00 2.66
3451 5252 3.595190 AGCCTTTAGTCCCAAACAAGT 57.405 42.857 0.00 0.00 0.00 3.16
3452 5253 4.937201 AAAGCCTTTAGTCCCAAACAAG 57.063 40.909 0.00 0.00 0.00 3.16
3453 5254 5.685520 AAAAAGCCTTTAGTCCCAAACAA 57.314 34.783 0.00 0.00 0.00 2.83
3472 5273 8.070171 CCACAAATACAACAACAACAACAAAAA 58.930 29.630 0.00 0.00 0.00 1.94
3473 5274 7.226720 ACCACAAATACAACAACAACAACAAAA 59.773 29.630 0.00 0.00 0.00 2.44
3474 5275 6.706270 ACCACAAATACAACAACAACAACAAA 59.294 30.769 0.00 0.00 0.00 2.83
3475 5276 6.146184 CACCACAAATACAACAACAACAACAA 59.854 34.615 0.00 0.00 0.00 2.83
3476 5277 5.635280 CACCACAAATACAACAACAACAACA 59.365 36.000 0.00 0.00 0.00 3.33
3477 5278 5.445275 GCACCACAAATACAACAACAACAAC 60.445 40.000 0.00 0.00 0.00 3.32
3478 5279 4.627467 GCACCACAAATACAACAACAACAA 59.373 37.500 0.00 0.00 0.00 2.83
3479 5280 4.081972 AGCACCACAAATACAACAACAACA 60.082 37.500 0.00 0.00 0.00 3.33
3480 5281 4.429108 AGCACCACAAATACAACAACAAC 58.571 39.130 0.00 0.00 0.00 3.32
3481 5282 4.727507 AGCACCACAAATACAACAACAA 57.272 36.364 0.00 0.00 0.00 2.83
3482 5283 4.727507 AAGCACCACAAATACAACAACA 57.272 36.364 0.00 0.00 0.00 3.33
3483 5284 4.867608 ACAAAGCACCACAAATACAACAAC 59.132 37.500 0.00 0.00 0.00 3.32
3484 5285 5.078411 ACAAAGCACCACAAATACAACAA 57.922 34.783 0.00 0.00 0.00 2.83
3485 5286 4.727507 ACAAAGCACCACAAATACAACA 57.272 36.364 0.00 0.00 0.00 3.33
3486 5287 5.827666 AGTACAAAGCACCACAAATACAAC 58.172 37.500 0.00 0.00 0.00 3.32
3487 5288 6.320164 AGAAGTACAAAGCACCACAAATACAA 59.680 34.615 0.00 0.00 0.00 2.41
3488 5289 5.825679 AGAAGTACAAAGCACCACAAATACA 59.174 36.000 0.00 0.00 0.00 2.29
3489 5290 6.313744 AGAAGTACAAAGCACCACAAATAC 57.686 37.500 0.00 0.00 0.00 1.89
3490 5291 6.952773 AAGAAGTACAAAGCACCACAAATA 57.047 33.333 0.00 0.00 0.00 1.40
3491 5292 5.852282 AAGAAGTACAAAGCACCACAAAT 57.148 34.783 0.00 0.00 0.00 2.32
3492 5293 6.544197 TCATAAGAAGTACAAAGCACCACAAA 59.456 34.615 0.00 0.00 0.00 2.83
3493 5294 6.058833 TCATAAGAAGTACAAAGCACCACAA 58.941 36.000 0.00 0.00 0.00 3.33
3494 5295 5.616270 TCATAAGAAGTACAAAGCACCACA 58.384 37.500 0.00 0.00 0.00 4.17
3495 5296 6.371389 GTTCATAAGAAGTACAAAGCACCAC 58.629 40.000 0.00 0.00 33.63 4.16
3496 5297 5.472137 GGTTCATAAGAAGTACAAAGCACCA 59.528 40.000 0.00 0.00 33.63 4.17
3497 5298 5.705905 AGGTTCATAAGAAGTACAAAGCACC 59.294 40.000 0.00 0.00 33.63 5.01
3498 5299 6.803154 AGGTTCATAAGAAGTACAAAGCAC 57.197 37.500 0.00 0.00 33.63 4.40
3499 5300 7.817418 AAAGGTTCATAAGAAGTACAAAGCA 57.183 32.000 0.00 0.00 33.63 3.91
3509 5310 9.729281 ACGTCCTATTTTAAAGGTTCATAAGAA 57.271 29.630 0.00 0.00 35.48 2.52
3510 5311 9.374838 GACGTCCTATTTTAAAGGTTCATAAGA 57.625 33.333 3.51 0.00 35.48 2.10
3511 5312 8.325997 CGACGTCCTATTTTAAAGGTTCATAAG 58.674 37.037 10.58 0.00 35.48 1.73
3512 5313 8.034215 TCGACGTCCTATTTTAAAGGTTCATAA 58.966 33.333 10.58 0.00 35.48 1.90
3513 5314 7.546358 TCGACGTCCTATTTTAAAGGTTCATA 58.454 34.615 10.58 0.00 35.48 2.15
3514 5315 6.400568 TCGACGTCCTATTTTAAAGGTTCAT 58.599 36.000 10.58 0.00 35.48 2.57
3515 5316 5.782047 TCGACGTCCTATTTTAAAGGTTCA 58.218 37.500 10.58 0.00 35.48 3.18
3516 5317 6.898912 ATCGACGTCCTATTTTAAAGGTTC 57.101 37.500 10.58 0.00 35.48 3.62
3517 5318 7.818930 TGTTATCGACGTCCTATTTTAAAGGTT 59.181 33.333 10.58 0.00 35.48 3.50
3518 5319 7.322664 TGTTATCGACGTCCTATTTTAAAGGT 58.677 34.615 10.58 0.00 35.48 3.50
3519 5320 7.760131 TGTTATCGACGTCCTATTTTAAAGG 57.240 36.000 10.58 0.00 35.26 3.11
3520 5321 8.112449 GGTTGTTATCGACGTCCTATTTTAAAG 58.888 37.037 10.58 0.00 0.00 1.85
3521 5322 7.601886 TGGTTGTTATCGACGTCCTATTTTAAA 59.398 33.333 10.58 0.00 0.00 1.52
3522 5323 7.095910 TGGTTGTTATCGACGTCCTATTTTAA 58.904 34.615 10.58 0.00 0.00 1.52
3523 5324 6.629128 TGGTTGTTATCGACGTCCTATTTTA 58.371 36.000 10.58 0.00 0.00 1.52
3524 5325 5.481105 TGGTTGTTATCGACGTCCTATTTT 58.519 37.500 10.58 0.00 0.00 1.82
3525 5326 5.075858 TGGTTGTTATCGACGTCCTATTT 57.924 39.130 10.58 0.00 0.00 1.40
3526 5327 4.724074 TGGTTGTTATCGACGTCCTATT 57.276 40.909 10.58 0.00 0.00 1.73
3527 5328 4.427312 GTTGGTTGTTATCGACGTCCTAT 58.573 43.478 10.58 6.63 0.00 2.57
3528 5329 3.367292 GGTTGGTTGTTATCGACGTCCTA 60.367 47.826 10.58 0.00 0.00 2.94
3626 5437 0.179067 TTCCTCGCGAACAGGTTGTT 60.179 50.000 11.33 0.00 44.37 2.83
3627 5438 0.179067 TTTCCTCGCGAACAGGTTGT 60.179 50.000 11.33 0.00 32.20 3.32
3628 5439 0.941542 TTTTCCTCGCGAACAGGTTG 59.058 50.000 11.33 0.00 32.20 3.77
3629 5440 0.942252 GTTTTCCTCGCGAACAGGTT 59.058 50.000 11.33 0.00 32.20 3.50
3630 5441 1.219522 CGTTTTCCTCGCGAACAGGT 61.220 55.000 11.33 0.00 32.20 4.00
3631 5442 1.491563 CGTTTTCCTCGCGAACAGG 59.508 57.895 11.33 8.62 0.00 4.00
3632 5443 1.154654 GCGTTTTCCTCGCGAACAG 60.155 57.895 11.33 1.66 43.94 3.16
3756 5611 7.654520 TGCAAAAGACTAGTGTTTATTAGTCGT 59.345 33.333 17.48 0.00 45.59 4.34


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

AutoCloner maintained by Alex Coulton.