Multiple sequence alignment - TraesCS3A01G481400

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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 TraesCS3A01G481400 chr3A 100.000 5290 0 0 1 5290 712451676 712456965 0.000000e+00 9769.0
1 TraesCS3A01G481400 chr3A 85.923 1300 100 27 2362 3627 712380413 712381663 0.000000e+00 1310.0
2 TraesCS3A01G481400 chr3A 96.561 727 24 1 4564 5290 125056370 125057095 0.000000e+00 1203.0
3 TraesCS3A01G481400 chr3A 93.154 818 47 5 3297 4107 712324235 712325050 0.000000e+00 1192.0
4 TraesCS3A01G481400 chr3A 79.720 1642 182 87 2416 4014 711382293 711380760 0.000000e+00 1048.0
5 TraesCS3A01G481400 chr3A 85.681 852 63 28 2460 3303 712323370 712324170 0.000000e+00 843.0
6 TraesCS3A01G481400 chr3A 84.531 640 46 22 1039 1639 712322101 712322726 7.630000e-163 584.0
7 TraesCS3A01G481400 chr3A 79.726 804 81 36 880 1639 712378908 712379673 1.700000e-139 507.0
8 TraesCS3A01G481400 chr3A 81.620 642 75 27 2325 2952 711384665 711384053 4.760000e-135 492.0
9 TraesCS3A01G481400 chr3A 78.637 543 61 34 2779 3279 712307765 712308294 5.150000e-80 309.0
10 TraesCS3A01G481400 chr3A 87.963 216 26 0 1128 1343 711385633 711385418 6.800000e-64 255.0
11 TraesCS3A01G481400 chr3A 88.321 137 12 4 1800 1935 712379814 712379947 1.520000e-35 161.0
12 TraesCS3A01G481400 chr3A 83.696 184 9 7 2225 2408 712323210 712323372 2.550000e-33 154.0
13 TraesCS3A01G481400 chr3A 89.655 116 12 0 1960 2075 712307193 712307308 1.190000e-31 148.0
14 TraesCS3A01G481400 chr3A 86.765 136 13 4 1800 1931 712322867 712323001 4.270000e-31 147.0
15 TraesCS3A01G481400 chr3A 91.111 90 6 2 4104 4192 712325003 712325091 2.590000e-23 121.0
16 TraesCS3A01G481400 chr3D 91.772 3488 138 50 851 4270 577176711 577180117 0.000000e+00 4713.0
17 TraesCS3A01G481400 chr3D 88.612 1686 103 46 2460 4107 577024690 577023056 0.000000e+00 1967.0
18 TraesCS3A01G481400 chr3D 83.416 1206 103 38 2404 3558 576854672 576853513 0.000000e+00 1029.0
19 TraesCS3A01G481400 chr3D 80.528 1022 118 39 3085 4065 575837332 575836351 0.000000e+00 710.0
20 TraesCS3A01G481400 chr3D 83.140 688 63 22 990 1639 577025997 577025325 3.550000e-161 579.0
21 TraesCS3A01G481400 chr3D 79.120 886 80 42 844 1670 576856431 576855592 1.020000e-141 514.0
22 TraesCS3A01G481400 chr3D 84.288 541 55 14 3345 3874 577153749 577153228 7.910000e-138 501.0
23 TraesCS3A01G481400 chr3D 83.273 550 62 22 304 839 596270950 596271483 3.710000e-131 479.0
24 TraesCS3A01G481400 chr3D 83.871 496 60 13 3595 4072 576853509 576853016 6.250000e-124 455.0
25 TraesCS3A01G481400 chr3D 84.696 477 43 12 3423 3874 577144386 577143915 2.910000e-122 449.0
26 TraesCS3A01G481400 chr3D 79.772 613 87 27 2361 2952 575839358 575838762 1.370000e-110 411.0
27 TraesCS3A01G481400 chr3D 81.043 422 59 17 2330 2741 577155761 577155351 3.070000e-82 316.0
28 TraesCS3A01G481400 chr3D 87.745 204 25 0 1128 1331 575766503 575766300 6.850000e-59 239.0
29 TraesCS3A01G481400 chr3D 83.500 200 23 6 1945 2141 575839674 575839482 1.510000e-40 178.0
30 TraesCS3A01G481400 chr3D 88.235 153 13 2 1939 2086 577156077 577155925 1.510000e-40 178.0
31 TraesCS3A01G481400 chr3D 86.335 161 18 1 1930 2086 575765956 575765796 7.040000e-39 172.0
32 TraesCS3A01G481400 chr3D 85.326 184 6 7 2225 2408 577024850 577024688 2.530000e-38 171.0
33 TraesCS3A01G481400 chr3D 89.922 129 12 1 1959 2086 577025072 577024944 1.180000e-36 165.0
34 TraesCS3A01G481400 chr3D 87.681 138 15 2 1803 1938 576855521 576855384 5.480000e-35 159.0
35 TraesCS3A01G481400 chr3D 96.341 82 3 0 2216 2297 576854979 576854898 9.240000e-28 135.0
36 TraesCS3A01G481400 chr3D 81.879 149 13 6 1800 1944 577025184 577025046 4.330000e-21 113.0
37 TraesCS3A01G481400 chr3D 96.970 33 1 0 4528 4560 577180119 577180151 7.400000e-04 56.5
38 TraesCS3A01G481400 chr3B 92.992 2640 105 27 1662 4272 768724186 768726774 0.000000e+00 3777.0
39 TraesCS3A01G481400 chr3B 94.327 617 31 4 4560 5174 729912411 729913025 0.000000e+00 942.0
40 TraesCS3A01G481400 chr3B 86.293 839 61 25 844 1639 768723301 768724128 0.000000e+00 863.0
41 TraesCS3A01G481400 chr3B 85.868 743 75 16 3338 4071 768672208 768672929 0.000000e+00 763.0
42 TraesCS3A01G481400 chr3B 83.560 809 68 27 2528 3298 768671346 768672127 0.000000e+00 697.0
43 TraesCS3A01G481400 chr3B 83.495 721 79 22 3358 4062 768264591 768265287 2.080000e-178 636.0
44 TraesCS3A01G481400 chr3B 79.195 870 95 51 2457 3279 768511690 768512520 4.690000e-145 525.0
45 TraesCS3A01G481400 chr3B 82.085 614 67 27 2322 2920 768262381 768262966 7.970000e-133 484.0
46 TraesCS3A01G481400 chr3B 77.724 826 104 42 1130 1929 768670230 768671001 2.930000e-117 433.0
47 TraesCS3A01G481400 chr3B 79.542 655 90 21 932 1558 768572449 768573087 1.360000e-115 427.0
48 TraesCS3A01G481400 chr3B 95.420 262 9 2 4271 4529 811005626 811005365 1.060000e-111 414.0
49 TraesCS3A01G481400 chr3B 87.615 218 27 0 1128 1345 768261418 768261635 2.450000e-63 254.0
50 TraesCS3A01G481400 chr3B 88.832 197 22 0 1135 1331 766792341 766792145 5.290000e-60 243.0
51 TraesCS3A01G481400 chr3B 84.951 206 25 3 3085 3284 768264320 768264525 2.500000e-48 204.0
52 TraesCS3A01G481400 chr3B 87.417 151 14 2 1941 2086 768511276 768511426 9.110000e-38 169.0
53 TraesCS3A01G481400 chr3B 87.671 146 14 1 1945 2086 768262085 768262230 3.280000e-37 167.0
54 TraesCS3A01G481400 chr3B 91.057 123 10 1 2176 2297 768671144 768671266 1.180000e-36 165.0
55 TraesCS3A01G481400 chr3B 98.701 77 1 0 2215 2291 768671272 768671348 2.570000e-28 137.0
56 TraesCS3A01G481400 chr3B 100.000 34 0 0 4527 4560 768726773 768726806 4.420000e-06 63.9
57 TraesCS3A01G481400 chr3B 86.207 58 3 5 4092 4146 768672907 768672962 2.060000e-04 58.4
58 TraesCS3A01G481400 chr1A 97.674 731 16 1 4561 5290 24152045 24152775 0.000000e+00 1254.0
59 TraesCS3A01G481400 chr1A 95.057 263 12 1 4270 4531 454739060 454738798 3.810000e-111 412.0
60 TraesCS3A01G481400 chr2B 94.840 717 37 0 3356 4072 657053178 657052462 0.000000e+00 1120.0
61 TraesCS3A01G481400 chr2B 81.001 879 107 38 3 844 411881435 411880580 1.240000e-180 643.0
62 TraesCS3A01G481400 chr2B 80.559 823 70 33 890 1639 657055277 657054472 7.740000e-153 551.0
63 TraesCS3A01G481400 chr2B 81.890 635 47 31 2225 2857 657053926 657053358 1.720000e-129 473.0
64 TraesCS3A01G481400 chr2B 90.698 129 11 1 1959 2086 657054143 657054015 2.530000e-38 171.0
65 TraesCS3A01G481400 chr2B 86.014 143 11 8 4092 4231 657052485 657052349 1.540000e-30 145.0
66 TraesCS3A01G481400 chr2B 85.333 75 11 0 5080 5154 470394260 470394186 1.580000e-10 78.7
67 TraesCS3A01G481400 chr2B 80.645 93 12 5 5056 5145 26382764 26382853 3.420000e-07 67.6
68 TraesCS3A01G481400 chr2A 97.205 644 18 0 4560 5203 561935347 561934704 0.000000e+00 1090.0
69 TraesCS3A01G481400 chr2A 81.644 730 121 11 4564 5288 86062535 86063256 1.270000e-165 593.0
70 TraesCS3A01G481400 chr2A 80.759 764 108 27 85 832 643022476 643023216 1.290000e-155 560.0
71 TraesCS3A01G481400 chr2A 95.785 261 8 2 4271 4528 103588123 103588383 8.190000e-113 418.0
72 TraesCS3A01G481400 chr2A 95.131 267 9 3 4269 4531 528661696 528661962 8.190000e-113 418.0
73 TraesCS3A01G481400 chr2A 95.094 265 10 3 4267 4528 511648508 511648244 1.060000e-111 414.0
74 TraesCS3A01G481400 chr4B 88.260 724 81 2 4563 5286 302600247 302600966 0.000000e+00 863.0
75 TraesCS3A01G481400 chr4B 79.863 879 111 42 3 827 624515621 624516487 2.750000e-162 582.0
76 TraesCS3A01G481400 chr1B 86.483 725 97 1 4564 5288 46264740 46265463 0.000000e+00 795.0
77 TraesCS3A01G481400 chr6B 85.124 726 97 8 4564 5288 166230848 166231563 0.000000e+00 732.0
78 TraesCS3A01G481400 chr1D 82.060 864 98 32 3 844 84564287 84565115 0.000000e+00 684.0
79 TraesCS3A01G481400 chr1D 82.388 670 66 34 205 844 342115216 342114569 2.170000e-148 536.0
80 TraesCS3A01G481400 chr1D 78.245 832 123 36 47 844 394398103 394398910 1.030000e-131 481.0
81 TraesCS3A01G481400 chr7A 81.141 859 114 32 1 844 512260424 512259599 0.000000e+00 645.0
82 TraesCS3A01G481400 chr7A 95.019 261 11 2 4270 4528 19414572 19414832 4.930000e-110 409.0
83 TraesCS3A01G481400 chr5D 80.502 877 111 42 4 844 367230607 367231459 7.530000e-173 617.0
84 TraesCS3A01G481400 chr5D 95.019 261 10 2 4271 4528 209854928 209854668 1.770000e-109 407.0
85 TraesCS3A01G481400 chr5A 82.055 730 124 7 4563 5290 573320783 573320059 2.710000e-172 616.0
86 TraesCS3A01G481400 chr2D 81.643 779 108 25 71 832 498323647 498324407 9.740000e-172 614.0
87 TraesCS3A01G481400 chr7D 81.925 769 81 41 110 846 596307833 596308575 9.810000e-167 597.0
88 TraesCS3A01G481400 chr4A 86.228 501 48 15 311 802 311019672 311019184 1.690000e-144 523.0
89 TraesCS3A01G481400 chr4A 95.785 261 8 2 4271 4528 104373054 104373314 8.190000e-113 418.0
90 TraesCS3A01G481400 chr5B 84.337 498 43 21 375 844 477955744 477956234 6.250000e-124 455.0
91 TraesCS3A01G481400 chr6A 95.402 261 9 2 4271 4528 115182298 115182558 3.810000e-111 412.0


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 TraesCS3A01G481400 chr3A 712451676 712456965 5289 False 9769.000000 9769 100.000000 1 5290 1 chr3A.!!$F2 5289
1 TraesCS3A01G481400 chr3A 125056370 125057095 725 False 1203.000000 1203 96.561000 4564 5290 1 chr3A.!!$F1 726
2 TraesCS3A01G481400 chr3A 712378908 712381663 2755 False 659.333333 1310 84.656667 880 3627 3 chr3A.!!$F5 2747
3 TraesCS3A01G481400 chr3A 711380760 711385633 4873 True 598.333333 1048 83.101000 1128 4014 3 chr3A.!!$R1 2886
4 TraesCS3A01G481400 chr3A 712322101 712325091 2990 False 506.833333 1192 87.489667 1039 4192 6 chr3A.!!$F4 3153
5 TraesCS3A01G481400 chr3A 712307193 712308294 1101 False 228.500000 309 84.146000 1960 3279 2 chr3A.!!$F3 1319
6 TraesCS3A01G481400 chr3D 577176711 577180151 3440 False 2384.750000 4713 94.371000 851 4560 2 chr3D.!!$F2 3709
7 TraesCS3A01G481400 chr3D 577023056 577025997 2941 True 599.000000 1967 85.775800 990 4107 5 chr3D.!!$R5 3117
8 TraesCS3A01G481400 chr3D 596270950 596271483 533 False 479.000000 479 83.273000 304 839 1 chr3D.!!$F1 535
9 TraesCS3A01G481400 chr3D 576853016 576856431 3415 True 458.400000 1029 86.085800 844 4072 5 chr3D.!!$R4 3228
10 TraesCS3A01G481400 chr3D 575836351 575839674 3323 True 433.000000 710 81.266667 1945 4065 3 chr3D.!!$R3 2120
11 TraesCS3A01G481400 chr3D 577153228 577156077 2849 True 331.666667 501 84.522000 1939 3874 3 chr3D.!!$R6 1935
12 TraesCS3A01G481400 chr3D 575765796 575766503 707 True 205.500000 239 87.040000 1128 2086 2 chr3D.!!$R2 958
13 TraesCS3A01G481400 chr3B 768723301 768726806 3505 False 1567.966667 3777 93.095000 844 4560 3 chr3B.!!$F6 3716
14 TraesCS3A01G481400 chr3B 729912411 729913025 614 False 942.000000 942 94.327000 4560 5174 1 chr3B.!!$F1 614
15 TraesCS3A01G481400 chr3B 768572449 768573087 638 False 427.000000 427 79.542000 932 1558 1 chr3B.!!$F2 626
16 TraesCS3A01G481400 chr3B 768670230 768672962 2732 False 375.566667 763 87.186167 1130 4146 6 chr3B.!!$F5 3016
17 TraesCS3A01G481400 chr3B 768261418 768265287 3869 False 349.000000 636 85.163400 1128 4062 5 chr3B.!!$F3 2934
18 TraesCS3A01G481400 chr3B 768511276 768512520 1244 False 347.000000 525 83.306000 1941 3279 2 chr3B.!!$F4 1338
19 TraesCS3A01G481400 chr1A 24152045 24152775 730 False 1254.000000 1254 97.674000 4561 5290 1 chr1A.!!$F1 729
20 TraesCS3A01G481400 chr2B 411880580 411881435 855 True 643.000000 643 81.001000 3 844 1 chr2B.!!$R1 841
21 TraesCS3A01G481400 chr2B 657052349 657055277 2928 True 492.000000 1120 86.800200 890 4231 5 chr2B.!!$R3 3341
22 TraesCS3A01G481400 chr2A 561934704 561935347 643 True 1090.000000 1090 97.205000 4560 5203 1 chr2A.!!$R2 643
23 TraesCS3A01G481400 chr2A 86062535 86063256 721 False 593.000000 593 81.644000 4564 5288 1 chr2A.!!$F1 724
24 TraesCS3A01G481400 chr2A 643022476 643023216 740 False 560.000000 560 80.759000 85 832 1 chr2A.!!$F4 747
25 TraesCS3A01G481400 chr4B 302600247 302600966 719 False 863.000000 863 88.260000 4563 5286 1 chr4B.!!$F1 723
26 TraesCS3A01G481400 chr4B 624515621 624516487 866 False 582.000000 582 79.863000 3 827 1 chr4B.!!$F2 824
27 TraesCS3A01G481400 chr1B 46264740 46265463 723 False 795.000000 795 86.483000 4564 5288 1 chr1B.!!$F1 724
28 TraesCS3A01G481400 chr6B 166230848 166231563 715 False 732.000000 732 85.124000 4564 5288 1 chr6B.!!$F1 724
29 TraesCS3A01G481400 chr1D 84564287 84565115 828 False 684.000000 684 82.060000 3 844 1 chr1D.!!$F1 841
30 TraesCS3A01G481400 chr1D 342114569 342115216 647 True 536.000000 536 82.388000 205 844 1 chr1D.!!$R1 639
31 TraesCS3A01G481400 chr1D 394398103 394398910 807 False 481.000000 481 78.245000 47 844 1 chr1D.!!$F2 797
32 TraesCS3A01G481400 chr7A 512259599 512260424 825 True 645.000000 645 81.141000 1 844 1 chr7A.!!$R1 843
33 TraesCS3A01G481400 chr5D 367230607 367231459 852 False 617.000000 617 80.502000 4 844 1 chr5D.!!$F1 840
34 TraesCS3A01G481400 chr5A 573320059 573320783 724 True 616.000000 616 82.055000 4563 5290 1 chr5A.!!$R1 727
35 TraesCS3A01G481400 chr2D 498323647 498324407 760 False 614.000000 614 81.643000 71 832 1 chr2D.!!$F1 761
36 TraesCS3A01G481400 chr7D 596307833 596308575 742 False 597.000000 597 81.925000 110 846 1 chr7D.!!$F1 736

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
842 967 0.946221 CGCACGGACTCTCTTTTGCT 60.946 55.000 0.00 0.0 0.00 3.91 F
1313 1571 0.103208 CATCCTCGTCTTCCCCTTCG 59.897 60.000 0.00 0.0 0.00 3.79 F
2339 4466 0.389817 GTGCTAGTCACCATGTGCGA 60.390 55.000 6.14 0.0 39.79 5.10 F
2621 5018 2.523015 CTGGCTTTGCTATTTTCAGCG 58.477 47.619 0.00 0.0 44.88 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2764 6785 0.461693 AGATCAAAGAGCAGCTCGGC 60.462 55.000 16.99 4.25 35.36 5.54 R
2765 6786 1.134877 TCAGATCAAAGAGCAGCTCGG 60.135 52.381 16.99 10.68 35.36 4.63 R
4181 9376 1.120530 AACAATATCGCCCTCGTCCT 58.879 50.000 0.00 0.00 36.96 3.85 R
4512 9707 1.007963 TCATTTACTCCCTCCGGTCCT 59.992 52.381 0.00 0.00 0.00 3.85 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
83 84 8.690840 CGGGATTTTTCTAAAAATATTCGCATC 58.309 33.333 12.18 0.95 45.70 3.91
101 104 6.088173 TCGCATCTTCAAAGAAATGTTCATG 58.912 36.000 0.00 0.00 38.77 3.07
107 110 8.732413 TCTTCAAAGAAATGTTCATGATTTCG 57.268 30.769 12.39 2.55 42.33 3.46
108 111 7.809331 TCTTCAAAGAAATGTTCATGATTTCGG 59.191 33.333 12.39 8.16 42.33 4.30
402 440 7.901002 TCAAAAGAAAATGCTTAAAAACCGTC 58.099 30.769 0.00 0.00 0.00 4.79
524 611 7.426929 AGTTAAACAGTAATGCTTCTGAGTG 57.573 36.000 0.00 0.00 35.84 3.51
557 645 1.535462 ACCCGCGTGAATTTTGAAGAG 59.465 47.619 4.92 0.00 0.00 2.85
592 698 7.226720 CGGGTGGATTGGAATATTATAGTATGC 59.773 40.741 0.00 0.00 0.00 3.14
754 873 5.177142 TGTGAACAAATTTCCAAATCATGCG 59.823 36.000 0.00 0.00 0.00 4.73
755 874 5.404968 GTGAACAAATTTCCAAATCATGCGA 59.595 36.000 0.00 0.00 0.00 5.10
756 875 6.091169 GTGAACAAATTTCCAAATCATGCGAT 59.909 34.615 0.00 0.00 0.00 4.58
772 891 3.192466 TGCGATGATGAGATGTGAACAG 58.808 45.455 0.00 0.00 0.00 3.16
776 895 5.693555 GCGATGATGAGATGTGAACAGAATA 59.306 40.000 0.00 0.00 0.00 1.75
798 917 4.823790 TGATCATCGCCATTGAAGATTG 57.176 40.909 0.00 0.00 0.00 2.67
835 960 1.954146 TTGCAACGCACGGACTCTC 60.954 57.895 0.00 0.00 38.71 3.20
838 963 1.222115 GCAACGCACGGACTCTCTTT 61.222 55.000 0.00 0.00 0.00 2.52
839 964 1.217882 CAACGCACGGACTCTCTTTT 58.782 50.000 0.00 0.00 0.00 2.27
840 965 1.070577 CAACGCACGGACTCTCTTTTG 60.071 52.381 0.00 0.00 0.00 2.44
841 966 1.222115 ACGCACGGACTCTCTTTTGC 61.222 55.000 0.00 0.00 0.00 3.68
842 967 0.946221 CGCACGGACTCTCTTTTGCT 60.946 55.000 0.00 0.00 0.00 3.91
843 968 1.668919 CGCACGGACTCTCTTTTGCTA 60.669 52.381 0.00 0.00 0.00 3.49
844 969 2.413837 GCACGGACTCTCTTTTGCTAA 58.586 47.619 0.00 0.00 0.00 3.09
845 970 3.003480 GCACGGACTCTCTTTTGCTAAT 58.997 45.455 0.00 0.00 0.00 1.73
846 971 3.062774 GCACGGACTCTCTTTTGCTAATC 59.937 47.826 0.00 0.00 0.00 1.75
847 972 4.245660 CACGGACTCTCTTTTGCTAATCA 58.754 43.478 0.00 0.00 0.00 2.57
848 973 4.872691 CACGGACTCTCTTTTGCTAATCAT 59.127 41.667 0.00 0.00 0.00 2.45
849 974 5.006165 CACGGACTCTCTTTTGCTAATCATC 59.994 44.000 0.00 0.00 0.00 2.92
855 980 8.211116 ACTCTCTTTTGCTAATCATCAATCAG 57.789 34.615 0.00 0.00 0.00 2.90
882 1007 6.448207 AGAAAAAGATAGCATCTGCCTTTC 57.552 37.500 0.00 13.51 43.38 2.62
884 1009 6.318396 AGAAAAAGATAGCATCTGCCTTTCTC 59.682 38.462 15.71 0.00 38.20 2.87
1014 1170 1.667830 TTCGCTTTGCTCCGTCCTG 60.668 57.895 0.00 0.00 0.00 3.86
1198 1438 2.436292 GTCCTCTGCCTGCAGCTG 60.436 66.667 10.11 10.11 43.31 4.24
1313 1571 0.103208 CATCCTCGTCTTCCCCTTCG 59.897 60.000 0.00 0.00 0.00 3.79
1412 1707 9.431887 TGGTAAAAGAAACAGAGTATGTATGTC 57.568 33.333 0.00 0.00 43.00 3.06
1413 1708 9.431887 GGTAAAAGAAACAGAGTATGTATGTCA 57.568 33.333 0.00 0.00 43.00 3.58
1416 1711 8.553459 AAAGAAACAGAGTATGTATGTCAAGG 57.447 34.615 0.00 0.00 43.00 3.61
1417 1712 6.109359 AGAAACAGAGTATGTATGTCAAGGC 58.891 40.000 0.00 0.00 43.00 4.35
1418 1713 4.408182 ACAGAGTATGTATGTCAAGGCC 57.592 45.455 0.00 0.00 41.60 5.19
1419 1714 4.033709 ACAGAGTATGTATGTCAAGGCCT 58.966 43.478 0.00 0.00 41.60 5.19
1441 1740 5.357032 CCTACAGGGGCTGTACAAAATTAAG 59.643 44.000 0.00 0.00 43.46 1.85
1462 1761 3.427528 AGTTACGACATACAACAAGTGCG 59.572 43.478 0.00 0.00 0.00 5.34
1470 1769 6.343616 CGACATACAACAAGTGCGTTTTAAAC 60.344 38.462 0.00 0.00 0.00 2.01
1652 2032 1.602323 TCGTTGCTTCCGGGCATTT 60.602 52.632 6.20 0.00 42.09 2.32
1741 2140 1.546029 GATTTTGAGGGCCTTGGTCAC 59.454 52.381 7.89 0.00 0.00 3.67
1839 2385 5.125417 GTCCCATGCACTCTTAATTTTGCTA 59.875 40.000 0.00 0.00 35.91 3.49
2133 3014 2.363680 AGTCGCTCTGCTGCTTATGTAT 59.636 45.455 0.00 0.00 0.00 2.29
2311 4396 8.915057 ACTATTAGCTTCCTACTGTTATCGTA 57.085 34.615 0.00 0.00 0.00 3.43
2339 4466 0.389817 GTGCTAGTCACCATGTGCGA 60.390 55.000 6.14 0.00 39.79 5.10
2600 4997 7.225734 GCTAGCAGGATTACCTTTTTAGAAGAG 59.774 40.741 10.63 0.00 45.36 2.85
2603 5000 6.183360 GCAGGATTACCTTTTTAGAAGAGCTG 60.183 42.308 0.00 0.00 45.36 4.24
2621 5018 2.523015 CTGGCTTTGCTATTTTCAGCG 58.477 47.619 0.00 0.00 44.88 5.18
2727 6748 5.163499 TGTTTCTTCCGGCAACTATTTGTTT 60.163 36.000 0.00 0.00 36.63 2.83
2765 6786 9.979270 GTGTTATGATAGCAATAATATGTCAGC 57.021 33.333 0.00 0.00 0.00 4.26
2766 6787 9.166173 TGTTATGATAGCAATAATATGTCAGCC 57.834 33.333 0.00 0.00 0.00 4.85
2767 6788 6.915544 ATGATAGCAATAATATGTCAGCCG 57.084 37.500 0.00 0.00 0.00 5.52
2768 6789 6.036577 TGATAGCAATAATATGTCAGCCGA 57.963 37.500 0.00 0.00 0.00 5.54
2769 6790 6.101997 TGATAGCAATAATATGTCAGCCGAG 58.898 40.000 0.00 0.00 0.00 4.63
2770 6791 3.070018 AGCAATAATATGTCAGCCGAGC 58.930 45.455 0.00 0.00 0.00 5.03
2771 6792 3.070018 GCAATAATATGTCAGCCGAGCT 58.930 45.455 0.00 0.00 40.77 4.09
2843 6864 3.181476 GCTCAAGTTGACATGGTTTTGGT 60.181 43.478 0.08 0.00 0.00 3.67
2860 6881 3.255969 TGGTAAGGACGTGATTTAGGC 57.744 47.619 0.00 0.00 0.00 3.93
3255 8229 6.648310 AGTTCATTTAGAGATGTATGCGATGG 59.352 38.462 0.00 0.00 0.00 3.51
3328 8397 6.525280 GTGTGTGTTTTGTACTTTGTTGGTAG 59.475 38.462 0.00 0.00 0.00 3.18
3687 8862 3.006644 GCTCTCTCACATGATCTATGGCA 59.993 47.826 0.00 0.00 41.25 4.92
3730 8905 5.129320 TCAGTGGCTACATTGTCTATGACAT 59.871 40.000 2.02 0.00 42.40 3.06
3920 9100 5.129485 ACGAATTTGGTATCCTGATGAGTCT 59.871 40.000 0.00 0.00 0.00 3.24
4030 9225 2.742954 AACGTAAGAAAACCGTGTGC 57.257 45.000 0.00 0.00 43.62 4.57
4066 9261 2.684881 GGATGGTGGATGTGATGTTGTC 59.315 50.000 0.00 0.00 0.00 3.18
4073 9268 5.882557 GGTGGATGTGATGTTGTCTTTAGAT 59.117 40.000 0.00 0.00 0.00 1.98
4181 9376 0.534873 TATGTAGCTGCGTGGCTTCA 59.465 50.000 6.80 10.57 42.11 3.02
4192 9387 4.821589 GGCTTCAGGACGAGGGCG 62.822 72.222 0.00 0.00 44.79 6.13
4249 9444 2.231529 CCCGTTTTGTGGATGGTGTTA 58.768 47.619 0.00 0.00 0.00 2.41
4270 9465 9.909644 GTGTTACTCGTGGACTATATATGAAAT 57.090 33.333 0.00 0.00 0.00 2.17
4275 9470 8.958506 ACTCGTGGACTATATATGAAATACTCC 58.041 37.037 0.00 0.00 0.00 3.85
4276 9471 8.289939 TCGTGGACTATATATGAAATACTCCC 57.710 38.462 0.00 0.00 0.00 4.30
4277 9472 8.114102 TCGTGGACTATATATGAAATACTCCCT 58.886 37.037 0.00 0.00 0.00 4.20
4278 9473 8.407064 CGTGGACTATATATGAAATACTCCCTC 58.593 40.741 0.00 0.00 0.00 4.30
4279 9474 8.697292 GTGGACTATATATGAAATACTCCCTCC 58.303 40.741 0.00 0.00 0.00 4.30
4280 9475 7.560262 TGGACTATATATGAAATACTCCCTCCG 59.440 40.741 0.00 0.00 0.00 4.63
4281 9476 7.014422 GGACTATATATGAAATACTCCCTCCGG 59.986 44.444 0.00 0.00 0.00 5.14
4282 9477 7.420029 ACTATATATGAAATACTCCCTCCGGT 58.580 38.462 0.00 0.00 0.00 5.28
4283 9478 6.793505 ATATATGAAATACTCCCTCCGGTC 57.206 41.667 0.00 0.00 0.00 4.79
4284 9479 1.492764 TGAAATACTCCCTCCGGTCC 58.507 55.000 0.00 0.00 0.00 4.46
4285 9480 1.007963 TGAAATACTCCCTCCGGTCCT 59.992 52.381 0.00 0.00 0.00 3.85
4286 9481 2.117051 GAAATACTCCCTCCGGTCCTT 58.883 52.381 0.00 0.00 0.00 3.36
4287 9482 2.265526 AATACTCCCTCCGGTCCTTT 57.734 50.000 0.00 0.00 0.00 3.11
4288 9483 2.265526 ATACTCCCTCCGGTCCTTTT 57.734 50.000 0.00 0.00 0.00 2.27
4289 9484 2.034436 TACTCCCTCCGGTCCTTTTT 57.966 50.000 0.00 0.00 0.00 1.94
4290 9485 2.034436 ACTCCCTCCGGTCCTTTTTA 57.966 50.000 0.00 0.00 0.00 1.52
4291 9486 2.558974 ACTCCCTCCGGTCCTTTTTAT 58.441 47.619 0.00 0.00 0.00 1.40
4292 9487 2.917600 ACTCCCTCCGGTCCTTTTTATT 59.082 45.455 0.00 0.00 0.00 1.40
4293 9488 3.054582 ACTCCCTCCGGTCCTTTTTATTC 60.055 47.826 0.00 0.00 0.00 1.75
4294 9489 3.187112 TCCCTCCGGTCCTTTTTATTCT 58.813 45.455 0.00 0.00 0.00 2.40
4295 9490 3.054655 TCCCTCCGGTCCTTTTTATTCTG 60.055 47.826 0.00 0.00 0.00 3.02
4296 9491 2.683362 CCTCCGGTCCTTTTTATTCTGC 59.317 50.000 0.00 0.00 0.00 4.26
4297 9492 3.343617 CTCCGGTCCTTTTTATTCTGCA 58.656 45.455 0.00 0.00 0.00 4.41
4298 9493 3.947834 CTCCGGTCCTTTTTATTCTGCAT 59.052 43.478 0.00 0.00 0.00 3.96
4299 9494 5.105567 TCCGGTCCTTTTTATTCTGCATA 57.894 39.130 0.00 0.00 0.00 3.14
4300 9495 5.690865 TCCGGTCCTTTTTATTCTGCATAT 58.309 37.500 0.00 0.00 0.00 1.78
4301 9496 6.833041 TCCGGTCCTTTTTATTCTGCATATA 58.167 36.000 0.00 0.00 0.00 0.86
4302 9497 7.284074 TCCGGTCCTTTTTATTCTGCATATAA 58.716 34.615 0.00 0.00 0.00 0.98
4303 9498 7.444183 TCCGGTCCTTTTTATTCTGCATATAAG 59.556 37.037 0.00 0.00 0.00 1.73
4304 9499 7.444183 CCGGTCCTTTTTATTCTGCATATAAGA 59.556 37.037 0.00 0.00 0.00 2.10
4305 9500 8.836413 CGGTCCTTTTTATTCTGCATATAAGAA 58.164 33.333 0.00 3.25 38.01 2.52
4318 9513 9.230122 TCTGCATATAAGAATTGTTTGAAGTCA 57.770 29.630 0.00 0.00 28.54 3.41
4319 9514 9.844790 CTGCATATAAGAATTGTTTGAAGTCAA 57.155 29.630 0.00 0.00 0.00 3.18
4408 9603 5.940192 ATGAAACTTTAAGTCATGACGCA 57.060 34.783 19.85 9.13 36.20 5.24
4409 9604 5.940192 TGAAACTTTAAGTCATGACGCAT 57.060 34.783 19.85 12.70 36.20 4.73
4410 9605 5.927030 TGAAACTTTAAGTCATGACGCATC 58.073 37.500 19.85 11.06 36.20 3.91
4411 9606 5.700832 TGAAACTTTAAGTCATGACGCATCT 59.299 36.000 19.85 6.46 36.20 2.90
4412 9607 6.871492 TGAAACTTTAAGTCATGACGCATCTA 59.129 34.615 19.85 5.55 36.20 1.98
4413 9608 6.648725 AACTTTAAGTCATGACGCATCTAC 57.351 37.500 19.85 0.00 36.20 2.59
4414 9609 5.967088 ACTTTAAGTCATGACGCATCTACT 58.033 37.500 19.85 0.00 36.20 2.57
4415 9610 7.096884 ACTTTAAGTCATGACGCATCTACTA 57.903 36.000 19.85 1.06 36.20 1.82
4416 9611 7.197017 ACTTTAAGTCATGACGCATCTACTAG 58.803 38.462 19.85 10.86 36.20 2.57
4417 9612 6.694877 TTAAGTCATGACGCATCTACTAGT 57.305 37.500 19.85 0.00 36.20 2.57
4418 9613 7.797038 TTAAGTCATGACGCATCTACTAGTA 57.203 36.000 19.85 1.89 36.20 1.82
4419 9614 6.885952 AAGTCATGACGCATCTACTAGTAT 57.114 37.500 19.85 0.00 36.20 2.12
4420 9615 6.885952 AGTCATGACGCATCTACTAGTATT 57.114 37.500 19.85 0.00 36.20 1.89
4421 9616 6.673106 AGTCATGACGCATCTACTAGTATTG 58.327 40.000 19.85 5.91 36.20 1.90
4422 9617 6.486993 AGTCATGACGCATCTACTAGTATTGA 59.513 38.462 19.85 5.90 36.20 2.57
4423 9618 7.175816 AGTCATGACGCATCTACTAGTATTGAT 59.824 37.037 19.85 7.69 36.20 2.57
4424 9619 7.810282 GTCATGACGCATCTACTAGTATTGATT 59.190 37.037 10.69 3.20 0.00 2.57
4425 9620 8.360390 TCATGACGCATCTACTAGTATTGATTT 58.640 33.333 14.18 0.00 0.00 2.17
4426 9621 8.642885 CATGACGCATCTACTAGTATTGATTTC 58.357 37.037 14.18 7.31 0.00 2.17
4427 9622 7.712797 TGACGCATCTACTAGTATTGATTTCA 58.287 34.615 14.18 9.09 0.00 2.69
4428 9623 7.648112 TGACGCATCTACTAGTATTGATTTCAC 59.352 37.037 14.18 4.39 0.00 3.18
4429 9624 7.489160 ACGCATCTACTAGTATTGATTTCACA 58.511 34.615 14.18 0.00 0.00 3.58
4430 9625 8.144478 ACGCATCTACTAGTATTGATTTCACAT 58.856 33.333 14.18 0.00 0.00 3.21
4431 9626 8.982685 CGCATCTACTAGTATTGATTTCACATT 58.017 33.333 14.18 0.00 0.00 2.71
4477 9672 2.390938 GTTGGGCAAACTTTACGAAGC 58.609 47.619 0.00 0.00 36.29 3.86
4478 9673 1.975660 TGGGCAAACTTTACGAAGCT 58.024 45.000 0.00 0.00 36.29 3.74
4479 9674 2.303175 TGGGCAAACTTTACGAAGCTT 58.697 42.857 0.00 0.00 36.29 3.74
4480 9675 2.034053 TGGGCAAACTTTACGAAGCTTG 59.966 45.455 2.10 0.00 40.34 4.01
4481 9676 2.292292 GGGCAAACTTTACGAAGCTTGA 59.708 45.455 2.10 0.00 39.98 3.02
4482 9677 3.297472 GGCAAACTTTACGAAGCTTGAC 58.703 45.455 2.10 0.45 39.98 3.18
4483 9678 3.003378 GGCAAACTTTACGAAGCTTGACT 59.997 43.478 2.10 0.00 41.61 3.41
4484 9679 4.497507 GGCAAACTTTACGAAGCTTGACTT 60.498 41.667 2.10 0.00 41.61 3.01
4502 9697 8.801913 GCTTGACTTCAGACAAATTTAATATGC 58.198 33.333 0.00 0.00 30.22 3.14
4503 9698 8.894409 TTGACTTCAGACAAATTTAATATGCG 57.106 30.769 0.00 0.00 0.00 4.73
4504 9699 8.262715 TGACTTCAGACAAATTTAATATGCGA 57.737 30.769 0.00 0.00 0.00 5.10
4505 9700 8.726068 TGACTTCAGACAAATTTAATATGCGAA 58.274 29.630 0.00 0.00 0.00 4.70
4506 9701 8.895932 ACTTCAGACAAATTTAATATGCGAAC 57.104 30.769 0.00 0.00 0.00 3.95
4507 9702 8.730680 ACTTCAGACAAATTTAATATGCGAACT 58.269 29.630 0.00 0.00 0.00 3.01
4517 9712 9.797556 AATTTAATATGCGAACTAAAAAGGACC 57.202 29.630 0.00 0.00 0.00 4.46
4518 9713 5.479716 AATATGCGAACTAAAAAGGACCG 57.520 39.130 0.00 0.00 0.00 4.79
4519 9714 1.515081 TGCGAACTAAAAAGGACCGG 58.485 50.000 0.00 0.00 0.00 5.28
4520 9715 1.070445 TGCGAACTAAAAAGGACCGGA 59.930 47.619 9.46 0.00 0.00 5.14
4521 9716 1.730612 GCGAACTAAAAAGGACCGGAG 59.269 52.381 9.46 0.00 0.00 4.63
4752 9947 0.179936 GCTCTAGGCATGTTGCTCCT 59.820 55.000 0.00 0.00 44.28 3.69
4761 9956 1.822990 CATGTTGCTCCTGCCATTCTT 59.177 47.619 0.00 0.00 38.71 2.52
4859 10055 4.841813 TTCTCTCCTTCCATATCTCCCT 57.158 45.455 0.00 0.00 0.00 4.20
5103 10299 1.228337 GTAACCGTTTGGCCACCCT 60.228 57.895 3.88 0.00 39.70 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 5.975693 AGAAAAATCCCGAGCATGTTTTA 57.024 34.783 0.00 0.00 0.00 1.52
51 52 9.533253 AATATTTTTAGAAAAATCCCGAGCATG 57.467 29.630 14.59 0.00 43.12 4.06
83 84 7.809331 TCCGAAATCATGAACATTTCTTTGAAG 59.191 33.333 15.00 2.80 37.88 3.02
90 91 8.711457 ACATTTTTCCGAAATCATGAACATTTC 58.289 29.630 15.65 4.84 37.04 2.17
358 396 3.857052 TGAATCGGCGAACAATTCTAGT 58.143 40.909 15.93 0.00 31.99 2.57
473 557 4.903638 TTCGATCATTCGTGAACACTTC 57.096 40.909 3.51 0.00 45.65 3.01
497 584 7.328737 ACTCAGAAGCATTACTGTTTAACTACG 59.671 37.037 0.00 0.00 35.84 3.51
557 645 0.808755 CAATCCACCCGGCAGTTAAC 59.191 55.000 0.00 0.00 0.00 2.01
748 867 3.738830 TCACATCTCATCATCGCATGA 57.261 42.857 0.00 2.05 44.55 3.07
749 868 3.558418 TGTTCACATCTCATCATCGCATG 59.442 43.478 0.00 0.00 0.00 4.06
750 869 3.800531 TGTTCACATCTCATCATCGCAT 58.199 40.909 0.00 0.00 0.00 4.73
751 870 3.119029 TCTGTTCACATCTCATCATCGCA 60.119 43.478 0.00 0.00 0.00 5.10
752 871 3.451526 TCTGTTCACATCTCATCATCGC 58.548 45.455 0.00 0.00 0.00 4.58
754 873 8.828688 TCATATTCTGTTCACATCTCATCATC 57.171 34.615 0.00 0.00 0.00 2.92
755 874 9.438228 GATCATATTCTGTTCACATCTCATCAT 57.562 33.333 0.00 0.00 0.00 2.45
756 875 8.426489 TGATCATATTCTGTTCACATCTCATCA 58.574 33.333 0.00 0.00 30.36 3.07
772 891 6.732531 TCTTCAATGGCGATGATCATATTC 57.267 37.500 8.54 1.62 0.00 1.75
776 895 4.825634 ACAATCTTCAATGGCGATGATCAT 59.174 37.500 8.25 8.25 30.75 2.45
835 960 9.850628 TCTTTTCTGATTGATGATTAGCAAAAG 57.149 29.630 0.00 0.00 35.59 2.27
846 971 9.850628 TGCTATCTTTTTCTTTTCTGATTGATG 57.149 29.630 0.00 0.00 0.00 3.07
855 980 6.861144 AGGCAGATGCTATCTTTTTCTTTTC 58.139 36.000 4.59 0.00 37.58 2.29
882 1007 1.266989 GCGGTTTCTTCTTGTTGGGAG 59.733 52.381 0.00 0.00 0.00 4.30
884 1009 0.040425 CGCGGTTTCTTCTTGTTGGG 60.040 55.000 0.00 0.00 0.00 4.12
1070 1229 2.436646 CTTCATCTTGCCCGGCGT 60.437 61.111 6.01 0.00 0.00 5.68
1251 1491 2.731654 GCGTAGGAGGAGACGAAGAAAC 60.732 54.545 0.00 0.00 41.60 2.78
1289 1541 1.137282 GGGGAAGACGAGGATGAAGAC 59.863 57.143 0.00 0.00 0.00 3.01
1313 1571 1.671379 GGTTTGAGGCCTCACCGAC 60.671 63.158 35.26 28.88 46.52 4.79
1417 1712 2.871096 TTTTGTACAGCCCCTGTAGG 57.129 50.000 5.40 0.00 45.88 3.18
1418 1713 5.944007 ACTTAATTTTGTACAGCCCCTGTAG 59.056 40.000 5.40 0.00 45.88 2.74
1419 1714 5.883180 ACTTAATTTTGTACAGCCCCTGTA 58.117 37.500 0.00 1.18 43.46 2.74
1441 1740 3.182972 ACGCACTTGTTGTATGTCGTAAC 59.817 43.478 0.00 0.00 0.00 2.50
1462 1761 8.117370 ACATATTTGTTTTGTGGCGTTTAAAAC 58.883 29.630 0.00 0.00 41.96 2.43
1470 1769 3.492383 TGCAACATATTTGTTTTGTGGCG 59.508 39.130 0.00 0.00 43.57 5.69
1652 2032 1.059979 GCACGCATACAAATTCGTCGA 59.940 47.619 0.00 0.00 32.49 4.20
1741 2140 2.907042 AGGGAAAGTTAGTCCTGTCCTG 59.093 50.000 0.00 0.00 38.69 3.86
1839 2385 4.583489 CCACGTCCCAATCTACAGTAGTAT 59.417 45.833 7.50 0.00 0.00 2.12
1920 2470 1.675310 TGGCACAGCACTGCATACC 60.675 57.895 3.30 0.00 39.08 2.73
2600 4997 2.265683 GCTGAAAATAGCAAAGCCAGC 58.734 47.619 0.00 0.00 43.17 4.85
2603 5000 1.202348 ACCGCTGAAAATAGCAAAGCC 59.798 47.619 0.00 0.00 43.87 4.35
2621 5018 7.923878 TGCCAATTTCTTAGTGAAAAAGTAACC 59.076 33.333 0.00 0.00 46.32 2.85
2764 6785 0.461693 AGATCAAAGAGCAGCTCGGC 60.462 55.000 16.99 4.25 35.36 5.54
2765 6786 1.134877 TCAGATCAAAGAGCAGCTCGG 60.135 52.381 16.99 10.68 35.36 4.63
2766 6787 2.290531 TCAGATCAAAGAGCAGCTCG 57.709 50.000 16.99 3.05 35.36 5.03
2767 6788 2.937799 CCTTCAGATCAAAGAGCAGCTC 59.062 50.000 15.25 15.25 0.00 4.09
2768 6789 2.355920 CCCTTCAGATCAAAGAGCAGCT 60.356 50.000 0.00 0.00 0.00 4.24
2769 6790 2.015587 CCCTTCAGATCAAAGAGCAGC 58.984 52.381 8.91 0.00 0.00 5.25
2770 6791 2.015587 GCCCTTCAGATCAAAGAGCAG 58.984 52.381 8.77 0.00 28.87 4.24
2771 6792 1.340405 GGCCCTTCAGATCAAAGAGCA 60.340 52.381 13.69 0.00 29.84 4.26
2772 6793 1.387539 GGCCCTTCAGATCAAAGAGC 58.612 55.000 8.91 7.42 0.00 4.09
2773 6794 1.208052 TCGGCCCTTCAGATCAAAGAG 59.792 52.381 0.00 0.00 0.00 2.85
2774 6795 1.275666 TCGGCCCTTCAGATCAAAGA 58.724 50.000 0.00 0.00 0.00 2.52
2843 6864 2.235155 TGCAGCCTAAATCACGTCCTTA 59.765 45.455 0.00 0.00 0.00 2.69
2860 6881 5.948992 AAAAGTTTAAGCTAGTCCTGCAG 57.051 39.130 6.78 6.78 0.00 4.41
2926 6952 7.508134 CATGAAGCATCTATTGTCTTATCACG 58.492 38.462 0.00 0.00 0.00 4.35
3145 8097 5.798934 GTGATGCATTGAAGAAGCAAACTAG 59.201 40.000 0.00 0.00 42.15 2.57
3730 8905 2.116533 CGCTTGATGATGCTGCCCA 61.117 57.895 0.00 0.00 0.00 5.36
3920 9100 9.166173 CCAGACTATACAATTCTTCATGTCAAA 57.834 33.333 0.00 0.00 0.00 2.69
4030 9225 3.055819 CACCATCCATAGGATAGAACCGG 60.056 52.174 0.00 0.00 40.98 5.28
4066 9261 3.310774 CGACCAATCCAGCACATCTAAAG 59.689 47.826 0.00 0.00 0.00 1.85
4073 9268 1.452110 CAATCGACCAATCCAGCACA 58.548 50.000 0.00 0.00 0.00 4.57
4181 9376 1.120530 AACAATATCGCCCTCGTCCT 58.879 50.000 0.00 0.00 36.96 3.85
4249 9444 8.958506 GGAGTATTTCATATATAGTCCACGAGT 58.041 37.037 10.97 0.00 43.25 4.18
4276 9471 3.343617 TGCAGAATAAAAAGGACCGGAG 58.656 45.455 9.46 0.00 0.00 4.63
4277 9472 3.426787 TGCAGAATAAAAAGGACCGGA 57.573 42.857 9.46 0.00 0.00 5.14
4278 9473 7.444183 TCTTATATGCAGAATAAAAAGGACCGG 59.556 37.037 0.00 0.00 0.00 5.28
4279 9474 8.378172 TCTTATATGCAGAATAAAAAGGACCG 57.622 34.615 0.00 0.00 0.00 4.79
4292 9487 9.230122 TGACTTCAAACAATTCTTATATGCAGA 57.770 29.630 0.00 0.00 0.00 4.26
4293 9488 9.844790 TTGACTTCAAACAATTCTTATATGCAG 57.155 29.630 0.00 0.00 32.11 4.41
4380 9575 8.279800 CGTCATGACTTAAAGTTTCATGTTGTA 58.720 33.333 22.95 0.00 44.66 2.41
4381 9576 7.132213 CGTCATGACTTAAAGTTTCATGTTGT 58.868 34.615 22.95 0.00 44.66 3.32
4382 9577 6.086765 GCGTCATGACTTAAAGTTTCATGTTG 59.913 38.462 22.95 3.02 44.66 3.33
4383 9578 6.142817 GCGTCATGACTTAAAGTTTCATGTT 58.857 36.000 22.95 0.00 44.66 2.71
4384 9579 5.238432 TGCGTCATGACTTAAAGTTTCATGT 59.762 36.000 22.95 2.53 44.66 3.21
4385 9580 5.688823 TGCGTCATGACTTAAAGTTTCATG 58.311 37.500 22.95 8.41 45.39 3.07
4386 9581 5.940192 TGCGTCATGACTTAAAGTTTCAT 57.060 34.783 22.95 0.00 0.00 2.57
4387 9582 5.700832 AGATGCGTCATGACTTAAAGTTTCA 59.299 36.000 22.95 7.45 0.00 2.69
4388 9583 6.170675 AGATGCGTCATGACTTAAAGTTTC 57.829 37.500 22.95 8.71 0.00 2.78
4389 9584 6.874134 AGTAGATGCGTCATGACTTAAAGTTT 59.126 34.615 22.95 4.61 0.00 2.66
4390 9585 6.398918 AGTAGATGCGTCATGACTTAAAGTT 58.601 36.000 22.95 5.95 0.00 2.66
4391 9586 5.967088 AGTAGATGCGTCATGACTTAAAGT 58.033 37.500 22.95 6.51 0.00 2.66
4392 9587 7.197017 ACTAGTAGATGCGTCATGACTTAAAG 58.803 38.462 22.95 8.65 0.00 1.85
4393 9588 7.096884 ACTAGTAGATGCGTCATGACTTAAA 57.903 36.000 22.95 6.68 0.00 1.52
4394 9589 6.694877 ACTAGTAGATGCGTCATGACTTAA 57.305 37.500 22.95 9.11 0.00 1.85
4395 9590 7.981102 ATACTAGTAGATGCGTCATGACTTA 57.019 36.000 22.95 12.20 0.00 2.24
4396 9591 6.885952 ATACTAGTAGATGCGTCATGACTT 57.114 37.500 22.95 8.27 0.00 3.01
4397 9592 6.486993 TCAATACTAGTAGATGCGTCATGACT 59.513 38.462 22.95 10.51 0.00 3.41
4398 9593 6.669278 TCAATACTAGTAGATGCGTCATGAC 58.331 40.000 16.21 16.21 0.00 3.06
4399 9594 6.877611 TCAATACTAGTAGATGCGTCATGA 57.122 37.500 8.99 0.00 0.00 3.07
4400 9595 8.526218 AAATCAATACTAGTAGATGCGTCATG 57.474 34.615 8.99 0.00 0.00 3.07
4401 9596 8.360390 TGAAATCAATACTAGTAGATGCGTCAT 58.640 33.333 8.99 0.00 0.00 3.06
4402 9597 7.648112 GTGAAATCAATACTAGTAGATGCGTCA 59.352 37.037 8.99 10.17 0.00 4.35
4403 9598 7.648112 TGTGAAATCAATACTAGTAGATGCGTC 59.352 37.037 8.85 0.00 0.00 5.19
4404 9599 7.489160 TGTGAAATCAATACTAGTAGATGCGT 58.511 34.615 8.85 0.83 0.00 5.24
4405 9600 7.930513 TGTGAAATCAATACTAGTAGATGCG 57.069 36.000 8.85 0.00 0.00 4.73
4457 9652 2.034179 AGCTTCGTAAAGTTTGCCCAAC 59.966 45.455 0.00 0.00 34.79 3.77
4458 9653 2.303175 AGCTTCGTAAAGTTTGCCCAA 58.697 42.857 0.00 0.00 34.79 4.12
4459 9654 1.975660 AGCTTCGTAAAGTTTGCCCA 58.024 45.000 0.00 0.00 34.79 5.36
4460 9655 2.661594 CAAGCTTCGTAAAGTTTGCCC 58.338 47.619 0.00 0.00 43.66 5.36
4476 9671 8.801913 GCATATTAAATTTGTCTGAAGTCAAGC 58.198 33.333 0.00 0.00 0.00 4.01
4477 9672 9.003112 CGCATATTAAATTTGTCTGAAGTCAAG 57.997 33.333 0.00 0.00 0.00 3.02
4478 9673 8.726068 TCGCATATTAAATTTGTCTGAAGTCAA 58.274 29.630 0.00 0.00 0.00 3.18
4479 9674 8.262715 TCGCATATTAAATTTGTCTGAAGTCA 57.737 30.769 0.00 0.00 0.00 3.41
4480 9675 9.000018 GTTCGCATATTAAATTTGTCTGAAGTC 58.000 33.333 0.00 0.00 0.00 3.01
4481 9676 8.730680 AGTTCGCATATTAAATTTGTCTGAAGT 58.269 29.630 0.00 0.00 0.00 3.01
4491 9686 9.797556 GGTCCTTTTTAGTTCGCATATTAAATT 57.202 29.630 0.00 0.00 0.00 1.82
4492 9687 8.126700 CGGTCCTTTTTAGTTCGCATATTAAAT 58.873 33.333 0.00 0.00 0.00 1.40
4493 9688 7.414319 CCGGTCCTTTTTAGTTCGCATATTAAA 60.414 37.037 0.00 0.00 0.00 1.52
4494 9689 6.037391 CCGGTCCTTTTTAGTTCGCATATTAA 59.963 38.462 0.00 0.00 0.00 1.40
4495 9690 5.524646 CCGGTCCTTTTTAGTTCGCATATTA 59.475 40.000 0.00 0.00 0.00 0.98
4496 9691 4.334481 CCGGTCCTTTTTAGTTCGCATATT 59.666 41.667 0.00 0.00 0.00 1.28
4497 9692 3.875134 CCGGTCCTTTTTAGTTCGCATAT 59.125 43.478 0.00 0.00 0.00 1.78
4498 9693 3.055963 TCCGGTCCTTTTTAGTTCGCATA 60.056 43.478 0.00 0.00 0.00 3.14
4499 9694 2.081462 CCGGTCCTTTTTAGTTCGCAT 58.919 47.619 0.00 0.00 0.00 4.73
4500 9695 1.070445 TCCGGTCCTTTTTAGTTCGCA 59.930 47.619 0.00 0.00 0.00 5.10
4501 9696 1.730612 CTCCGGTCCTTTTTAGTTCGC 59.269 52.381 0.00 0.00 0.00 4.70
4502 9697 2.344025 CCTCCGGTCCTTTTTAGTTCG 58.656 52.381 0.00 0.00 0.00 3.95
4503 9698 2.303890 TCCCTCCGGTCCTTTTTAGTTC 59.696 50.000 0.00 0.00 0.00 3.01
4504 9699 2.305052 CTCCCTCCGGTCCTTTTTAGTT 59.695 50.000 0.00 0.00 0.00 2.24
4505 9700 1.907255 CTCCCTCCGGTCCTTTTTAGT 59.093 52.381 0.00 0.00 0.00 2.24
4506 9701 1.907255 ACTCCCTCCGGTCCTTTTTAG 59.093 52.381 0.00 0.00 0.00 1.85
4507 9702 2.034436 ACTCCCTCCGGTCCTTTTTA 57.966 50.000 0.00 0.00 0.00 1.52
4508 9703 2.034436 TACTCCCTCCGGTCCTTTTT 57.966 50.000 0.00 0.00 0.00 1.94
4509 9704 2.034436 TTACTCCCTCCGGTCCTTTT 57.966 50.000 0.00 0.00 0.00 2.27
4510 9705 2.034436 TTTACTCCCTCCGGTCCTTT 57.966 50.000 0.00 0.00 0.00 3.11
4511 9706 1.838077 CATTTACTCCCTCCGGTCCTT 59.162 52.381 0.00 0.00 0.00 3.36
4512 9707 1.007963 TCATTTACTCCCTCCGGTCCT 59.992 52.381 0.00 0.00 0.00 3.85
4513 9708 1.492764 TCATTTACTCCCTCCGGTCC 58.507 55.000 0.00 0.00 0.00 4.46
4514 9709 2.235402 TGTTCATTTACTCCCTCCGGTC 59.765 50.000 0.00 0.00 0.00 4.79
4515 9710 2.262637 TGTTCATTTACTCCCTCCGGT 58.737 47.619 0.00 0.00 0.00 5.28
4516 9711 3.343941 TTGTTCATTTACTCCCTCCGG 57.656 47.619 0.00 0.00 0.00 5.14
4517 9712 4.513442 TGATTGTTCATTTACTCCCTCCG 58.487 43.478 0.00 0.00 0.00 4.63
4518 9713 5.586643 GTCTGATTGTTCATTTACTCCCTCC 59.413 44.000 0.00 0.00 0.00 4.30
4519 9714 5.586643 GGTCTGATTGTTCATTTACTCCCTC 59.413 44.000 0.00 0.00 0.00 4.30
4520 9715 5.251700 AGGTCTGATTGTTCATTTACTCCCT 59.748 40.000 0.00 0.00 0.00 4.20
4521 9716 5.501156 AGGTCTGATTGTTCATTTACTCCC 58.499 41.667 0.00 0.00 0.00 4.30
4522 9717 8.738645 AATAGGTCTGATTGTTCATTTACTCC 57.261 34.615 0.00 0.00 0.00 3.85
4523 9718 9.606631 AGAATAGGTCTGATTGTTCATTTACTC 57.393 33.333 5.09 0.00 34.29 2.59
4752 9947 3.657634 GATCGAGCTATGAAGAATGGCA 58.342 45.455 0.00 0.00 44.89 4.92
4761 9956 2.033424 CAGGAACACGATCGAGCTATGA 59.967 50.000 24.34 0.00 0.00 2.15
4859 10055 2.301009 ACGATGATGATGCTGATAGCCA 59.699 45.455 0.00 0.00 41.51 4.75
5039 10235 3.106672 CTCGAATGTTCTACGCACCTAC 58.893 50.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.