Multiple sequence alignment - TraesCS5D01G181100

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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 TraesCS5D01G181100 chr5D 100.000 3327 0 0 3195 6521 281217380 281214054 0.000000e+00 6144.0
1 TraesCS5D01G181100 chr5D 100.000 2802 0 0 1 2802 281220574 281217773 0.000000e+00 5175.0
2 TraesCS5D01G181100 chr5D 81.695 590 62 34 3205 3750 410875089 410875676 3.590000e-122 449.0
3 TraesCS5D01G181100 chr5D 91.958 286 19 2 3204 3485 388792569 388792284 1.320000e-106 398.0
4 TraesCS5D01G181100 chr5D 85.062 241 32 2 3832 4068 410875715 410875955 6.530000e-60 243.0
5 TraesCS5D01G181100 chr5A 92.922 2091 92 18 4138 6202 367790078 367788018 0.000000e+00 2990.0
6 TraesCS5D01G181100 chr5A 92.438 1296 72 9 451 1737 367799567 367798289 0.000000e+00 1827.0
7 TraesCS5D01G181100 chr5A 93.878 392 18 3 1766 2155 367790634 367790247 2.620000e-163 586.0
8 TraesCS5D01G181100 chr5A 83.392 572 64 22 3195 3744 491745116 491745678 9.760000e-138 501.0
9 TraesCS5D01G181100 chr5A 86.825 463 32 13 1 439 367800101 367799644 2.110000e-134 490.0
10 TraesCS5D01G181100 chr5A 84.010 394 59 4 2405 2796 668353913 668354304 6.170000e-100 375.0
11 TraesCS5D01G181100 chr5A 82.738 336 41 6 6200 6521 367787851 367787519 3.850000e-72 283.0
12 TraesCS5D01G181100 chr5B 90.210 2186 147 31 1 2155 319338817 319336668 0.000000e+00 2789.0
13 TraesCS5D01G181100 chr5B 88.505 2140 142 37 4130 6220 319336670 319334586 0.000000e+00 2494.0
14 TraesCS5D01G181100 chr5B 75.584 942 137 46 3248 4123 492442444 492443358 4.770000e-101 379.0
15 TraesCS5D01G181100 chr5B 88.889 207 21 2 6310 6515 319334391 319334186 3.020000e-63 254.0
16 TraesCS5D01G181100 chr5B 100.000 33 0 0 6489 6521 319334193 319334161 1.960000e-05 62.1
17 TraesCS5D01G181100 chr7A 80.103 975 125 32 3208 4130 690921276 690922233 0.000000e+00 662.0
18 TraesCS5D01G181100 chr2B 81.463 793 86 31 3247 3985 158003164 158002379 1.570000e-165 593.0
19 TraesCS5D01G181100 chr2B 79.646 791 82 39 3204 3932 436259456 436260229 4.540000e-136 496.0
20 TraesCS5D01G181100 chr2B 82.634 524 68 13 2155 2660 82093811 82093293 6.000000e-120 442.0
21 TraesCS5D01G181100 chr2B 78.885 592 74 27 3560 4136 321916434 321915879 2.890000e-93 353.0
22 TraesCS5D01G181100 chr2B 78.221 551 87 20 3575 4111 82081173 82080642 8.160000e-84 322.0
23 TraesCS5D01G181100 chr2B 83.529 255 37 5 3878 4130 429149728 429149477 3.930000e-57 233.0
24 TraesCS5D01G181100 chr2B 75.158 475 88 24 3557 4018 620851434 620850977 5.160000e-46 196.0
25 TraesCS5D01G181100 chr2B 79.348 92 10 6 6435 6521 291661255 291661342 1.000000e-03 56.5
26 TraesCS5D01G181100 chr7B 79.402 937 107 39 3267 4130 205775543 205776466 3.390000e-162 582.0
27 TraesCS5D01G181100 chr7B 78.269 566 62 28 3248 3758 438886581 438887140 2.280000e-79 307.0
28 TraesCS5D01G181100 chr7B 91.045 67 4 2 2355 2421 447452357 447452421 9.010000e-14 89.8
29 TraesCS5D01G181100 chr2D 82.982 664 81 18 2155 2796 52584761 52584108 7.340000e-159 571.0
30 TraesCS5D01G181100 chr2D 86.339 366 44 5 2439 2800 314561152 314560789 1.700000e-105 394.0
31 TraesCS5D01G181100 chr2D 75.547 822 109 41 3369 4132 52583919 52583132 2.930000e-83 320.0
32 TraesCS5D01G181100 chr2D 76.134 595 92 31 3563 4132 603408508 603407939 3.880000e-67 267.0
33 TraesCS5D01G181100 chr7D 85.265 509 58 13 3549 4044 575139140 575139644 5.830000e-140 508.0
34 TraesCS5D01G181100 chr7D 81.109 577 84 13 2155 2718 126509736 126510300 7.760000e-119 438.0
35 TraesCS5D01G181100 chr7D 79.624 638 102 20 2178 2796 422661874 422661246 3.610000e-117 433.0
36 TraesCS5D01G181100 chr7D 82.405 449 54 14 2364 2796 575083343 575083782 1.030000e-97 368.0
37 TraesCS5D01G181100 chr7D 76.754 499 58 29 2155 2621 422346609 422347081 6.580000e-55 226.0
38 TraesCS5D01G181100 chr7D 76.613 496 59 27 2153 2621 605537742 605537277 3.060000e-53 220.0
39 TraesCS5D01G181100 chr7D 89.404 151 16 0 2151 2301 383392053 383391903 2.400000e-44 191.0
40 TraesCS5D01G181100 chr3D 78.072 830 118 34 3358 4132 109323207 109324027 3.560000e-127 466.0
41 TraesCS5D01G181100 chr1B 81.185 574 82 14 2151 2711 400886339 400885779 7.760000e-119 438.0
42 TraesCS5D01G181100 chr1B 80.339 590 95 14 3558 4130 400826141 400825556 1.680000e-115 427.0
43 TraesCS5D01G181100 chr1B 81.360 456 58 17 2355 2800 303247431 303247869 4.840000e-91 346.0
44 TraesCS5D01G181100 chr2A 80.160 625 74 24 3208 3790 104381190 104380574 7.820000e-114 422.0
45 TraesCS5D01G181100 chr2A 78.255 768 86 43 3213 3915 53987708 53986957 1.010000e-112 418.0
46 TraesCS5D01G181100 chr2A 89.961 259 21 1 2153 2411 758260793 758261046 4.870000e-86 329.0
47 TraesCS5D01G181100 chr2A 76.183 613 94 35 3557 4133 93997964 93997368 6.440000e-70 276.0
48 TraesCS5D01G181100 chr2A 76.119 603 101 29 3557 4130 755109336 755108748 6.440000e-70 276.0
49 TraesCS5D01G181100 chr6D 82.046 479 64 15 2283 2743 431179167 431179641 7.930000e-104 388.0
50 TraesCS5D01G181100 chr6D 80.510 431 51 24 3195 3609 206566639 206567052 3.820000e-77 300.0
51 TraesCS5D01G181100 chr6D 77.030 505 63 29 2152 2621 144603253 144603739 2.350000e-59 241.0
52 TraesCS5D01G181100 chr3B 78.116 658 107 15 2153 2795 735006461 735007096 3.690000e-102 383.0
53 TraesCS5D01G181100 chr3B 75.885 452 66 23 3557 3984 471787932 471788364 2.400000e-44 191.0
54 TraesCS5D01G181100 chr3B 84.043 94 11 3 6431 6520 203874151 203874244 3.240000e-13 87.9
55 TraesCS5D01G181100 chr1A 86.093 302 29 3 3197 3485 563117832 563118133 4.910000e-81 313.0
56 TraesCS5D01G181100 chr1A 84.892 278 34 8 3210 3485 377574757 377574486 2.320000e-69 274.0
57 TraesCS5D01G181100 chr1A 81.155 329 45 14 2155 2477 300117649 300117332 1.400000e-61 248.0
58 TraesCS5D01G181100 chr3A 83.287 359 38 10 2199 2547 22242091 22241745 1.770000e-80 311.0
59 TraesCS5D01G181100 chr4A 84.328 268 39 3 3864 4130 430179131 430179396 6.490000e-65 259.0
60 TraesCS5D01G181100 chr6A 79.452 292 35 16 2141 2427 1429909 1429638 4.020000e-42 183.0


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 TraesCS5D01G181100 chr5D 281214054 281220574 6520 True 5659.500000 6144 100.0000 1 6521 2 chr5D.!!$R2 6520
1 TraesCS5D01G181100 chr5D 410875089 410875955 866 False 346.000000 449 83.3785 3205 4068 2 chr5D.!!$F1 863
2 TraesCS5D01G181100 chr5A 367787519 367790634 3115 True 1286.333333 2990 89.8460 1766 6521 3 chr5A.!!$R1 4755
3 TraesCS5D01G181100 chr5A 367798289 367800101 1812 True 1158.500000 1827 89.6315 1 1737 2 chr5A.!!$R2 1736
4 TraesCS5D01G181100 chr5A 491745116 491745678 562 False 501.000000 501 83.3920 3195 3744 1 chr5A.!!$F1 549
5 TraesCS5D01G181100 chr5B 319334161 319338817 4656 True 1399.775000 2789 91.9010 1 6521 4 chr5B.!!$R1 6520
6 TraesCS5D01G181100 chr5B 492442444 492443358 914 False 379.000000 379 75.5840 3248 4123 1 chr5B.!!$F1 875
7 TraesCS5D01G181100 chr7A 690921276 690922233 957 False 662.000000 662 80.1030 3208 4130 1 chr7A.!!$F1 922
8 TraesCS5D01G181100 chr2B 158002379 158003164 785 True 593.000000 593 81.4630 3247 3985 1 chr2B.!!$R3 738
9 TraesCS5D01G181100 chr2B 436259456 436260229 773 False 496.000000 496 79.6460 3204 3932 1 chr2B.!!$F2 728
10 TraesCS5D01G181100 chr2B 82093293 82093811 518 True 442.000000 442 82.6340 2155 2660 1 chr2B.!!$R2 505
11 TraesCS5D01G181100 chr2B 321915879 321916434 555 True 353.000000 353 78.8850 3560 4136 1 chr2B.!!$R4 576
12 TraesCS5D01G181100 chr2B 82080642 82081173 531 True 322.000000 322 78.2210 3575 4111 1 chr2B.!!$R1 536
13 TraesCS5D01G181100 chr7B 205775543 205776466 923 False 582.000000 582 79.4020 3267 4130 1 chr7B.!!$F1 863
14 TraesCS5D01G181100 chr7B 438886581 438887140 559 False 307.000000 307 78.2690 3248 3758 1 chr7B.!!$F2 510
15 TraesCS5D01G181100 chr2D 52583132 52584761 1629 True 445.500000 571 79.2645 2155 4132 2 chr2D.!!$R3 1977
16 TraesCS5D01G181100 chr2D 603407939 603408508 569 True 267.000000 267 76.1340 3563 4132 1 chr2D.!!$R2 569
17 TraesCS5D01G181100 chr7D 575139140 575139644 504 False 508.000000 508 85.2650 3549 4044 1 chr7D.!!$F4 495
18 TraesCS5D01G181100 chr7D 126509736 126510300 564 False 438.000000 438 81.1090 2155 2718 1 chr7D.!!$F1 563
19 TraesCS5D01G181100 chr7D 422661246 422661874 628 True 433.000000 433 79.6240 2178 2796 1 chr7D.!!$R2 618
20 TraesCS5D01G181100 chr3D 109323207 109324027 820 False 466.000000 466 78.0720 3358 4132 1 chr3D.!!$F1 774
21 TraesCS5D01G181100 chr1B 400885779 400886339 560 True 438.000000 438 81.1850 2151 2711 1 chr1B.!!$R2 560
22 TraesCS5D01G181100 chr1B 400825556 400826141 585 True 427.000000 427 80.3390 3558 4130 1 chr1B.!!$R1 572
23 TraesCS5D01G181100 chr2A 104380574 104381190 616 True 422.000000 422 80.1600 3208 3790 1 chr2A.!!$R3 582
24 TraesCS5D01G181100 chr2A 53986957 53987708 751 True 418.000000 418 78.2550 3213 3915 1 chr2A.!!$R1 702
25 TraesCS5D01G181100 chr2A 93997368 93997964 596 True 276.000000 276 76.1830 3557 4133 1 chr2A.!!$R2 576
26 TraesCS5D01G181100 chr2A 755108748 755109336 588 True 276.000000 276 76.1190 3557 4130 1 chr2A.!!$R4 573
27 TraesCS5D01G181100 chr3B 735006461 735007096 635 False 383.000000 383 78.1160 2153 2795 1 chr3B.!!$F3 642

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
416 443 0.036022 GCTGGTTCTCTCCAACAGCT 59.964 55.0 7.63 0.00 37.01 4.24 F
1116 1234 0.036010 CCAATGTCCTTCGCCAGACT 60.036 55.0 0.00 0.00 34.02 3.24 F
1427 1545 0.468648 TCGGTAGCAGAGGATCGAGA 59.531 55.0 0.00 0.00 42.67 4.04 F
2301 2448 0.038618 GACCCAAATTTGCCCACGTC 60.039 55.0 12.92 8.32 0.00 4.34 F
2698 2872 0.249073 CCTCCAATGCTCGAGGTACG 60.249 60.0 15.58 0.00 40.77 3.67 F
3544 3787 0.664767 GATACGCTGTGGATCGAGGC 60.665 60.0 0.00 0.00 0.00 4.70 F
4640 5207 0.454600 ACGCTGTGTCGTATACTGGG 59.545 55.0 0.56 0.00 41.36 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 1898 0.238289 GTGCCAACGGAGTGTTCATG 59.762 55.000 0.00 0.0 45.0 3.07 R
2281 2428 0.469144 ACGTGGGCAAATTTGGGTCT 60.469 50.000 19.47 0.0 0.0 3.85 R
3360 3572 1.523711 CAGCACCACCACGTCAACT 60.524 57.895 0.00 0.0 0.0 3.16 R
3405 3621 1.671742 GTCTGGTTTGCCCTCGAGA 59.328 57.895 15.71 0.0 0.0 4.04 R
4534 5095 0.767998 TGTGGGTTGTCACTGCCATA 59.232 50.000 0.00 0.0 38.4 2.74 R
4873 5455 1.727511 AACTTCGTCACACCCGTCGA 61.728 55.000 0.00 0.0 0.0 4.20 R
6020 6620 0.321671 TCAAAGAAGGCGGGAGAGTG 59.678 55.000 0.00 0.0 0.0 3.51 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
110 111 4.338795 TCTCACAAACCCTATCTCCTCT 57.661 45.455 0.00 0.00 0.00 3.69
143 144 0.828022 CCGTAGCCACCATACTCCAA 59.172 55.000 0.00 0.00 0.00 3.53
148 149 1.223487 CCACCATACTCCAACCCCG 59.777 63.158 0.00 0.00 0.00 5.73
251 254 3.570638 CATCTGCTTGGCTCGCCG 61.571 66.667 3.14 0.00 39.42 6.46
416 443 0.036022 GCTGGTTCTCTCCAACAGCT 59.964 55.000 7.63 0.00 37.01 4.24
449 476 3.534554 CTGCTTCATACTGTACATGGCA 58.465 45.455 0.00 0.00 0.00 4.92
486 583 3.113260 AGGAGTCGGTTCTTTCTTGTG 57.887 47.619 0.00 0.00 0.00 3.33
487 584 2.434702 AGGAGTCGGTTCTTTCTTGTGT 59.565 45.455 0.00 0.00 0.00 3.72
488 585 2.801111 GGAGTCGGTTCTTTCTTGTGTC 59.199 50.000 0.00 0.00 0.00 3.67
489 586 3.454375 GAGTCGGTTCTTTCTTGTGTCA 58.546 45.455 0.00 0.00 0.00 3.58
490 587 3.458189 AGTCGGTTCTTTCTTGTGTCAG 58.542 45.455 0.00 0.00 0.00 3.51
491 588 3.118738 AGTCGGTTCTTTCTTGTGTCAGT 60.119 43.478 0.00 0.00 0.00 3.41
492 589 3.621715 GTCGGTTCTTTCTTGTGTCAGTT 59.378 43.478 0.00 0.00 0.00 3.16
493 590 4.094442 GTCGGTTCTTTCTTGTGTCAGTTT 59.906 41.667 0.00 0.00 0.00 2.66
494 591 4.331717 TCGGTTCTTTCTTGTGTCAGTTTC 59.668 41.667 0.00 0.00 0.00 2.78
541 647 6.208988 TCGTGTAGAAATAGATGCTCAGTT 57.791 37.500 0.00 0.00 0.00 3.16
547 653 9.534565 TGTAGAAATAGATGCTCAGTTGTATTC 57.465 33.333 0.00 0.00 0.00 1.75
822 931 3.502920 CTGTTCGTACGCTCTTGATCTT 58.497 45.455 11.24 0.00 0.00 2.40
855 970 3.406595 CTCCCCCAACATCCTCCGC 62.407 68.421 0.00 0.00 0.00 5.54
874 989 4.361971 TCGGTCCAGTCCTCGCCT 62.362 66.667 0.00 0.00 0.00 5.52
909 1025 4.988598 ACCAGCACCGTCTTGCCG 62.989 66.667 0.00 0.00 44.14 5.69
922 1040 1.344942 CTTGCCGTCTGTCGCACTAC 61.345 60.000 0.00 0.00 38.35 2.73
923 1041 1.802337 TTGCCGTCTGTCGCACTACT 61.802 55.000 0.00 0.00 38.35 2.57
924 1042 1.514443 GCCGTCTGTCGCACTACTC 60.514 63.158 0.00 0.00 38.35 2.59
937 1055 2.888414 GCACTACTCCTCCTCCTCATAC 59.112 54.545 0.00 0.00 0.00 2.39
964 1082 1.878656 CTTCCACCGCTCTCTTCCGT 61.879 60.000 0.00 0.00 0.00 4.69
1059 1177 3.007920 CCAGCAGGAGGCCTCTGT 61.008 66.667 31.36 16.97 46.50 3.41
1116 1234 0.036010 CCAATGTCCTTCGCCAGACT 60.036 55.000 0.00 0.00 34.02 3.24
1134 1252 2.467946 CTTGCTTCTTGTGGGCTGCG 62.468 60.000 0.00 0.00 0.00 5.18
1143 1261 3.303135 TGGGCTGCGAAGACGAGT 61.303 61.111 0.00 0.00 42.66 4.18
1174 1292 3.398318 TCAGGTTAGCTCTCCATACCA 57.602 47.619 9.32 0.00 0.00 3.25
1237 1355 7.461182 TTTGTTTGTTGCCTAGCTGTAATAT 57.539 32.000 0.00 0.00 0.00 1.28
1244 1362 6.427853 TGTTGCCTAGCTGTAATATGCTTATG 59.572 38.462 0.00 0.00 40.35 1.90
1288 1406 7.010923 GTCCAAAGTAGATTCATAGTGCTTGAG 59.989 40.741 0.00 0.00 0.00 3.02
1308 1426 3.290710 AGATATGTGTTTGGTGGCATCC 58.709 45.455 0.00 0.00 0.00 3.51
1405 1523 7.386299 CACTTTGACTATGTGCTTAAGTCTCTT 59.614 37.037 4.02 0.00 40.25 2.85
1406 1524 7.934120 ACTTTGACTATGTGCTTAAGTCTCTTT 59.066 33.333 4.02 0.00 40.25 2.52
1427 1545 0.468648 TCGGTAGCAGAGGATCGAGA 59.531 55.000 0.00 0.00 42.67 4.04
1439 1557 5.523188 CAGAGGATCGAGAATTTCCTTCTTG 59.477 44.000 6.00 2.86 44.42 3.02
1451 1569 4.706842 TTCCTTCTTGCCTACAACTCTT 57.293 40.909 0.00 0.00 0.00 2.85
1579 1706 6.015940 GTCATATTGCTATTTTGGGGGAAGAG 60.016 42.308 0.00 0.00 0.00 2.85
1585 1712 4.339530 GCTATTTTGGGGGAAGAGAATGTC 59.660 45.833 0.00 0.00 0.00 3.06
1598 1726 0.681243 GAATGTCCCCTTCACTGCCC 60.681 60.000 0.00 0.00 0.00 5.36
1599 1727 2.484287 AATGTCCCCTTCACTGCCCG 62.484 60.000 0.00 0.00 0.00 6.13
1615 1743 1.066573 GCCCGGACTCCTGATGATATG 60.067 57.143 0.73 0.00 0.00 1.78
1710 1847 1.531602 AACTTTGCCCCTCCACTGC 60.532 57.895 0.00 0.00 0.00 4.40
1747 1884 1.074775 TGGCCTGACACCCATGTTC 59.925 57.895 3.32 0.00 39.95 3.18
1761 1898 2.838386 ATGTTCGACATGCATCAAGC 57.162 45.000 0.00 0.00 37.45 4.01
1818 1955 3.481453 GCCTTCTTGGTTCTCTCAAGTT 58.519 45.455 0.00 0.00 41.52 2.66
1847 1991 2.233676 TGGCAGTGTCGTGTCTATGATT 59.766 45.455 0.00 0.00 0.00 2.57
1889 2034 4.861210 AGTGTGTTAGAGAAAGTCTGTCG 58.139 43.478 0.00 0.00 36.64 4.35
1998 2144 5.696724 CCTTGTTTTCTGTTGTCTATCGACT 59.303 40.000 0.00 0.00 40.86 4.18
2018 2164 2.725221 ATTCCTGCCATCTCACTTCC 57.275 50.000 0.00 0.00 0.00 3.46
2087 2233 2.909965 GTGTTGGCCCCTTTGCGA 60.910 61.111 0.00 0.00 0.00 5.10
2091 2237 2.199652 TTGGCCCCTTTGCGACTTG 61.200 57.895 0.00 0.00 0.00 3.16
2134 2280 1.027792 AAGTTTGTTCCACGCCACGT 61.028 50.000 0.00 0.00 42.36 4.49
2257 2404 2.432510 TGTCCGCTTTTTCATTTGGGTT 59.567 40.909 0.00 0.00 0.00 4.11
2258 2405 3.118592 TGTCCGCTTTTTCATTTGGGTTT 60.119 39.130 0.00 0.00 0.00 3.27
2301 2448 0.038618 GACCCAAATTTGCCCACGTC 60.039 55.000 12.92 8.32 0.00 4.34
2304 2458 0.390860 CCAAATTTGCCCACGTCCAA 59.609 50.000 12.92 0.00 0.00 3.53
2305 2459 1.202580 CCAAATTTGCCCACGTCCAAA 60.203 47.619 12.92 7.69 35.64 3.28
2306 2460 2.555199 CAAATTTGCCCACGTCCAAAA 58.445 42.857 5.01 0.00 34.93 2.44
2307 2461 2.524569 AATTTGCCCACGTCCAAAAG 57.475 45.000 8.92 0.00 34.93 2.27
2341 2495 2.139917 TGATAAACACGTGGCACAGAC 58.860 47.619 21.57 5.59 41.80 3.51
2345 2499 1.388547 AACACGTGGCACAGACAAAT 58.611 45.000 21.57 0.00 41.80 2.32
2384 2538 0.690762 ACATAAGTGGCCGGTCAACT 59.309 50.000 12.16 7.97 0.00 3.16
2397 2551 2.192861 TCAACTGCCGGCCAAAGTG 61.193 57.895 26.77 14.79 0.00 3.16
2482 2648 3.741476 CCTTGCCCTTGCTGTCGC 61.741 66.667 0.00 0.00 38.71 5.19
2698 2872 0.249073 CCTCCAATGCTCGAGGTACG 60.249 60.000 15.58 0.00 40.77 3.67
2699 2873 0.872021 CTCCAATGCTCGAGGTACGC 60.872 60.000 15.58 0.00 42.26 4.42
2759 2939 4.008933 GCTGACCCACTCCGCACT 62.009 66.667 0.00 0.00 0.00 4.40
2779 2959 2.181021 GCCGGTCCAGACGTACTG 59.819 66.667 1.90 7.72 45.36 2.74
3356 3565 1.993653 CTTGATGACTGGGGAGGCA 59.006 57.895 0.00 0.00 0.00 4.75
3360 3572 3.273071 ATGACTGGGGAGGCAGGGA 62.273 63.158 0.00 0.00 0.00 4.20
3405 3621 2.639327 GCCGCCATTGCTCCTTGTT 61.639 57.895 0.00 0.00 34.43 2.83
3544 3787 0.664767 GATACGCTGTGGATCGAGGC 60.665 60.000 0.00 0.00 0.00 4.70
3554 3818 4.457496 ATCGAGGCGCCAGTGGTG 62.457 66.667 31.54 18.84 36.10 4.17
3657 3961 1.452289 CGGAGGAGGAAGAGAGCGA 60.452 63.158 0.00 0.00 0.00 4.93
3876 4246 2.880879 CGGTGTCGGTGATCGCTG 60.881 66.667 8.91 8.91 39.05 5.18
4068 4458 1.299850 GTGTTGGGCTGGCGTTTTC 60.300 57.895 0.00 0.00 0.00 2.29
4198 4755 8.863086 ACTCTGTAATACTGTAACTTTACCACA 58.137 33.333 7.13 0.00 32.72 4.17
4199 4756 9.701098 CTCTGTAATACTGTAACTTTACCACAA 57.299 33.333 7.13 0.00 32.72 3.33
4228 4786 1.392589 ATATGAACCTTTGCTGCCCG 58.607 50.000 0.00 0.00 0.00 6.13
4260 4818 5.233689 ACACGAGTTACTTCAAAAGCTACAC 59.766 40.000 0.00 0.00 0.00 2.90
4278 4837 3.466836 ACACAAATCAGCAAGACGAAGA 58.533 40.909 0.00 0.00 0.00 2.87
4469 5030 7.910683 GGTTGCTAAAACTTAATAGTGATCAGC 59.089 37.037 0.00 0.00 34.01 4.26
4471 5032 6.257849 TGCTAAAACTTAATAGTGATCAGCCG 59.742 38.462 0.00 0.00 34.01 5.52
4525 5086 2.988010 TATTGAGGTTCATCGCAGCT 57.012 45.000 0.00 0.00 0.00 4.24
4534 5095 3.812053 GGTTCATCGCAGCTTTAGATCAT 59.188 43.478 0.00 0.00 0.00 2.45
4640 5207 0.454600 ACGCTGTGTCGTATACTGGG 59.545 55.000 0.56 0.00 41.36 4.45
4746 5328 8.754230 AATGTATGTAAGACATCATCGATCTG 57.246 34.615 0.00 0.00 39.88 2.90
4831 5413 4.705337 ACGTAGAGATTGGAGAACTCAC 57.295 45.455 4.23 0.00 33.69 3.51
4836 5418 2.169561 GAGATTGGAGAACTCACCCCTC 59.830 54.545 4.23 0.00 0.00 4.30
4873 5455 2.285743 GAGGAGGGGCTGGGAGTT 60.286 66.667 0.00 0.00 0.00 3.01
4966 5549 9.028284 ACTTTTATATGGAAGCATATGGGAATG 57.972 33.333 4.56 0.00 0.00 2.67
4975 5558 2.812591 GCATATGGGAATGTCTGCAGAG 59.187 50.000 18.89 1.39 0.00 3.35
5053 5644 3.253432 CCTTTGTGAAGCTTAGGAACCAC 59.747 47.826 6.38 6.57 0.00 4.16
5539 6130 4.252073 CTGAGTTCTCTGGATTCACCTTG 58.748 47.826 1.53 0.00 39.86 3.61
5640 6231 3.426695 CGCTCATGGATCAAGTTTTGGTC 60.427 47.826 0.00 0.00 40.09 4.02
5673 6264 1.326852 CAAGTGCTTGCAGAGATAGCG 59.673 52.381 3.06 0.00 37.73 4.26
5693 6284 4.910456 AGCGTATACGTGATCGATTTCTTC 59.090 41.667 25.04 4.61 42.22 2.87
5694 6285 4.088213 GCGTATACGTGATCGATTTCTTCC 59.912 45.833 25.04 0.31 42.22 3.46
5696 6287 5.913514 CGTATACGTGATCGATTTCTTCCTT 59.086 40.000 17.16 0.00 40.62 3.36
5697 6288 6.129431 CGTATACGTGATCGATTTCTTCCTTG 60.129 42.308 17.16 0.00 40.62 3.61
5699 6290 4.315803 ACGTGATCGATTTCTTCCTTGTT 58.684 39.130 0.00 0.00 40.62 2.83
5700 6291 4.389077 ACGTGATCGATTTCTTCCTTGTTC 59.611 41.667 0.00 0.00 40.62 3.18
5701 6292 4.388773 CGTGATCGATTTCTTCCTTGTTCA 59.611 41.667 0.00 0.00 39.71 3.18
5702 6293 5.063944 CGTGATCGATTTCTTCCTTGTTCAT 59.936 40.000 0.00 0.00 39.71 2.57
5703 6294 6.253746 GTGATCGATTTCTTCCTTGTTCATG 58.746 40.000 0.00 0.00 0.00 3.07
5749 6340 1.002502 GGGGTGGTGTACTCTTGGC 60.003 63.158 0.00 0.00 0.00 4.52
5798 6397 0.038435 AGCATCATCTCGCCTCATCG 60.038 55.000 0.00 0.00 0.00 3.84
5845 6444 9.956640 ATTGTTGAGTTTCTCTTAGAATCTGAT 57.043 29.630 5.25 0.00 35.16 2.90
5860 6459 5.129980 AGAATCTGATGCTGTGATGGAACTA 59.870 40.000 0.00 0.00 0.00 2.24
5866 6465 7.287696 TCTGATGCTGTGATGGAACTATTAGTA 59.712 37.037 0.00 0.00 0.00 1.82
5907 6506 3.378112 CGCAAGGAAATAATCAAGGCTGA 59.622 43.478 0.00 0.00 35.56 4.26
5914 6513 8.000780 AGGAAATAATCAAGGCTGAATTGTAC 57.999 34.615 0.00 0.00 34.49 2.90
5915 6514 7.836183 AGGAAATAATCAAGGCTGAATTGTACT 59.164 33.333 0.00 0.00 34.49 2.73
5916 6515 7.917505 GGAAATAATCAAGGCTGAATTGTACTG 59.082 37.037 0.00 0.00 34.49 2.74
5917 6516 7.944729 AATAATCAAGGCTGAATTGTACTGT 57.055 32.000 0.00 0.00 34.49 3.55
5918 6517 9.461312 AAATAATCAAGGCTGAATTGTACTGTA 57.539 29.630 0.00 0.00 34.49 2.74
5919 6518 9.461312 AATAATCAAGGCTGAATTGTACTGTAA 57.539 29.630 0.00 0.00 34.49 2.41
5920 6519 7.759489 AATCAAGGCTGAATTGTACTGTAAA 57.241 32.000 0.00 0.00 34.49 2.01
5921 6520 7.759489 ATCAAGGCTGAATTGTACTGTAAAA 57.241 32.000 0.00 0.00 34.49 1.52
5922 6521 7.202016 TCAAGGCTGAATTGTACTGTAAAAG 57.798 36.000 0.00 0.00 0.00 2.27
5923 6522 5.629079 AGGCTGAATTGTACTGTAAAAGC 57.371 39.130 0.00 0.00 0.00 3.51
5924 6523 5.316987 AGGCTGAATTGTACTGTAAAAGCT 58.683 37.500 0.00 0.00 0.00 3.74
5925 6524 5.770162 AGGCTGAATTGTACTGTAAAAGCTT 59.230 36.000 0.00 0.00 0.00 3.74
5926 6525 6.940298 AGGCTGAATTGTACTGTAAAAGCTTA 59.060 34.615 0.00 0.00 0.00 3.09
5927 6526 7.021790 GGCTGAATTGTACTGTAAAAGCTTAC 58.978 38.462 0.00 0.00 38.34 2.34
5928 6527 7.094762 GGCTGAATTGTACTGTAAAAGCTTACT 60.095 37.037 0.00 0.00 38.61 2.24
6006 6606 8.770438 TGTTCTTTCTTTGTAATTTGCTTTGT 57.230 26.923 0.00 0.00 0.00 2.83
6020 6620 4.164822 TGCTTTGTATTTCTTGCTCAGC 57.835 40.909 0.00 0.00 0.00 4.26
6023 6623 4.320788 GCTTTGTATTTCTTGCTCAGCACT 60.321 41.667 0.00 0.00 38.71 4.40
6029 6629 1.447489 CTTGCTCAGCACTCTCCCG 60.447 63.158 0.00 0.00 38.71 5.14
6048 6648 2.497273 CCGCCTTCTTTGAAATGGGAAT 59.503 45.455 0.00 0.00 0.00 3.01
6049 6649 3.429410 CCGCCTTCTTTGAAATGGGAATC 60.429 47.826 0.00 0.00 0.00 2.52
6050 6650 3.445096 CGCCTTCTTTGAAATGGGAATCT 59.555 43.478 0.00 0.00 0.00 2.40
6051 6651 4.082026 CGCCTTCTTTGAAATGGGAATCTT 60.082 41.667 0.00 0.00 0.00 2.40
6052 6652 5.567423 CGCCTTCTTTGAAATGGGAATCTTT 60.567 40.000 0.00 0.00 0.00 2.52
6053 6653 6.233434 GCCTTCTTTGAAATGGGAATCTTTT 58.767 36.000 0.00 0.00 0.00 2.27
6150 6760 2.456073 TCCCTGTAGGCCTTAGAGAC 57.544 55.000 12.58 2.24 34.51 3.36
6158 6768 0.828677 GGCCTTAGAGACGCCCTAAA 59.171 55.000 0.00 0.00 36.63 1.85
6171 6781 1.026718 CCCTAAAGCTGACGCCCAAG 61.027 60.000 0.00 0.00 36.60 3.61
6176 6786 2.738213 AAGCTGACGCCCAAGACAGG 62.738 60.000 0.00 0.00 35.15 4.00
6186 6796 1.492176 CCCAAGACAGGCATGGTATCT 59.508 52.381 2.31 0.00 33.49 1.98
6189 6881 3.614092 CAAGACAGGCATGGTATCTGTT 58.386 45.455 2.31 0.00 41.24 3.16
6193 6885 3.812053 GACAGGCATGGTATCTGTTCATC 59.188 47.826 2.31 0.00 41.24 2.92
6203 6895 1.627864 TCTGTTCATCGACTGGTCCA 58.372 50.000 0.00 0.00 0.00 4.02
6230 6924 3.733337 GTCTGCGGATATGGATGAAAGT 58.267 45.455 0.00 0.00 0.00 2.66
6243 6937 3.600388 GATGAAAGTCGGTCATCCAACT 58.400 45.455 3.51 0.00 43.73 3.16
6260 6974 6.839124 TCCAACTGTATTCCTAAACGTCTA 57.161 37.500 0.00 0.00 0.00 2.59
6262 6976 7.486647 TCCAACTGTATTCCTAAACGTCTATC 58.513 38.462 0.00 0.00 0.00 2.08
6268 6982 8.388484 TGTATTCCTAAACGTCTATCTAGGTC 57.612 38.462 0.00 0.00 33.87 3.85
6287 7001 4.020839 AGGTCTGGCCAATTTGAAATTCAG 60.021 41.667 7.01 5.93 40.61 3.02
6289 7003 5.299949 GTCTGGCCAATTTGAAATTCAGTT 58.700 37.500 7.01 0.00 0.00 3.16
6291 7005 3.814283 TGGCCAATTTGAAATTCAGTTGC 59.186 39.130 0.61 10.68 0.00 4.17
6292 7006 3.814283 GGCCAATTTGAAATTCAGTTGCA 59.186 39.130 13.96 0.00 0.00 4.08
6293 7007 4.456566 GGCCAATTTGAAATTCAGTTGCAT 59.543 37.500 13.96 0.00 0.00 3.96
6294 7008 5.642919 GGCCAATTTGAAATTCAGTTGCATA 59.357 36.000 13.96 0.00 0.00 3.14
6295 7009 6.183360 GGCCAATTTGAAATTCAGTTGCATAG 60.183 38.462 13.96 5.73 0.00 2.23
6297 7011 6.454583 CCAATTTGAAATTCAGTTGCATAGCG 60.455 38.462 13.96 0.00 0.00 4.26
6308 7140 2.797156 GTTGCATAGCGAGTTCGATCAT 59.203 45.455 5.60 0.00 43.02 2.45
6320 7152 6.470160 CGAGTTCGATCATAACCAAAAAGAG 58.530 40.000 0.00 0.00 43.02 2.85
6321 7153 6.455646 CGAGTTCGATCATAACCAAAAAGAGG 60.456 42.308 0.00 0.00 43.02 3.69
6322 7154 5.648092 AGTTCGATCATAACCAAAAAGAGGG 59.352 40.000 4.70 0.00 0.00 4.30
6328 7171 4.949856 TCATAACCAAAAAGAGGGAGATGC 59.050 41.667 0.00 0.00 0.00 3.91
6376 7219 5.812642 ACAAAAGTATCATAGTCCGCAAGAG 59.187 40.000 0.00 0.00 43.02 2.85
6392 7235 4.625028 GCAAGAGAATGAACTTTTTGCCT 58.375 39.130 0.00 0.00 36.12 4.75
6403 7246 0.753479 TTTTTGCCTTGCTGGACCGA 60.753 50.000 0.49 0.00 38.35 4.69
6408 7251 0.530870 GCCTTGCTGGACCGACTATC 60.531 60.000 0.49 0.00 38.35 2.08
6412 7255 1.359475 GCTGGACCGACTATCCGAC 59.641 63.158 0.00 0.00 39.30 4.79
6413 7256 2.031360 CTGGACCGACTATCCGACC 58.969 63.158 0.00 0.00 39.30 4.79
6438 7281 1.446272 GCTAAACTCTGTCGCCGCT 60.446 57.895 0.00 0.00 0.00 5.52
6465 7308 2.970639 CCGTCCGCTTCCTTCTCA 59.029 61.111 0.00 0.00 0.00 3.27
6468 7311 0.457851 CGTCCGCTTCCTTCTCATCT 59.542 55.000 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 111 1.209621 CTACGGGATGGGGAAAGGAA 58.790 55.000 0.00 0.00 0.00 3.36
143 144 3.382832 CGGAGAAGAGCACGGGGT 61.383 66.667 0.00 0.00 0.00 4.95
148 149 4.821589 CCGGCCGGAGAAGAGCAC 62.822 72.222 41.82 0.00 37.50 4.40
251 254 2.825836 CTGCCCGCTGGATCCAAC 60.826 66.667 17.00 10.86 0.00 3.77
439 466 5.983118 CGTATCAATCTAAGTGCCATGTACA 59.017 40.000 0.00 0.00 0.00 2.90
440 467 5.405571 CCGTATCAATCTAAGTGCCATGTAC 59.594 44.000 0.00 0.00 0.00 2.90
441 468 5.069914 ACCGTATCAATCTAAGTGCCATGTA 59.930 40.000 0.00 0.00 0.00 2.29
442 469 4.141711 ACCGTATCAATCTAAGTGCCATGT 60.142 41.667 0.00 0.00 0.00 3.21
443 470 4.380531 ACCGTATCAATCTAAGTGCCATG 58.619 43.478 0.00 0.00 0.00 3.66
449 476 5.469421 CGACTCCTACCGTATCAATCTAAGT 59.531 44.000 0.00 0.00 0.00 2.24
486 583 5.907197 TTCGAATCAACTCTGAAACTGAC 57.093 39.130 0.00 0.00 34.49 3.51
487 584 6.146184 GTCATTCGAATCAACTCTGAAACTGA 59.854 38.462 7.92 0.00 34.49 3.41
488 585 6.073602 TGTCATTCGAATCAACTCTGAAACTG 60.074 38.462 7.92 0.00 34.49 3.16
489 586 5.991606 TGTCATTCGAATCAACTCTGAAACT 59.008 36.000 7.92 0.00 34.49 2.66
490 587 6.074005 GTGTCATTCGAATCAACTCTGAAAC 58.926 40.000 7.92 4.00 34.49 2.78
491 588 5.757808 TGTGTCATTCGAATCAACTCTGAAA 59.242 36.000 7.92 0.00 34.49 2.69
492 589 5.296748 TGTGTCATTCGAATCAACTCTGAA 58.703 37.500 7.92 0.00 34.49 3.02
493 590 4.881920 TGTGTCATTCGAATCAACTCTGA 58.118 39.130 7.92 0.00 35.56 3.27
494 591 5.791367 ATGTGTCATTCGAATCAACTCTG 57.209 39.130 7.92 0.00 0.00 3.35
541 647 6.114767 TCAGCAGCATAAATGAGTGAATACA 58.885 36.000 0.00 0.00 0.00 2.29
547 653 6.588756 ACAAATTTCAGCAGCATAAATGAGTG 59.411 34.615 0.00 3.12 0.00 3.51
697 805 6.892658 ACTTCACTGTTGCCAAATGTATTA 57.107 33.333 0.00 0.00 0.00 0.98
822 931 3.371063 GAGGGACGACGGCAGACA 61.371 66.667 1.63 0.00 0.00 3.41
855 970 4.477975 GCGAGGACTGGACCGACG 62.478 72.222 0.00 0.00 37.53 5.12
879 995 2.707849 GCTGGTTGCAGGGCTGATG 61.708 63.158 0.00 0.00 42.31 3.07
880 996 2.362120 GCTGGTTGCAGGGCTGAT 60.362 61.111 0.00 0.00 42.31 2.90
904 1020 1.372499 GTAGTGCGACAGACGGCAA 60.372 57.895 0.00 0.00 42.83 4.52
909 1025 0.452585 GGAGGAGTAGTGCGACAGAC 59.547 60.000 0.00 0.00 0.00 3.51
922 1040 0.863956 AGGGGTATGAGGAGGAGGAG 59.136 60.000 0.00 0.00 0.00 3.69
923 1041 0.861155 GAGGGGTATGAGGAGGAGGA 59.139 60.000 0.00 0.00 0.00 3.71
924 1042 0.178918 GGAGGGGTATGAGGAGGAGG 60.179 65.000 0.00 0.00 0.00 4.30
979 1097 4.162690 CTGGTGAGCGGGGGCTAC 62.163 72.222 0.00 0.00 0.00 3.58
1094 1212 2.361104 GGCGAAGGACATTGGGCA 60.361 61.111 3.60 0.00 41.16 5.36
1116 1234 2.554636 CGCAGCCCACAAGAAGCAA 61.555 57.895 0.00 0.00 0.00 3.91
1134 1252 0.603569 TTGCTCCTCCACTCGTCTTC 59.396 55.000 0.00 0.00 0.00 2.87
1143 1261 1.210478 GCTAACCTGATTGCTCCTCCA 59.790 52.381 0.00 0.00 0.00 3.86
1174 1292 0.398696 TGGGTGTGGCGTAAATCAGT 59.601 50.000 0.00 0.00 0.00 3.41
1237 1355 4.603131 AGGCTTGAAAGAATCCATAAGCA 58.397 39.130 0.00 0.00 41.54 3.91
1244 1362 4.589908 TGGACTTAGGCTTGAAAGAATCC 58.410 43.478 2.62 1.37 0.00 3.01
1288 1406 3.290710 AGGATGCCACCAAACACATATC 58.709 45.455 0.00 0.00 0.00 1.63
1314 1432 4.793028 GCAAGTTTTTAACTGGAGGCAGAC 60.793 45.833 0.00 0.00 41.91 3.51
1405 1523 3.075148 CTCGATCCTCTGCTACCGATAA 58.925 50.000 0.00 0.00 0.00 1.75
1406 1524 2.302157 TCTCGATCCTCTGCTACCGATA 59.698 50.000 0.00 0.00 0.00 2.92
1427 1545 5.635120 AGAGTTGTAGGCAAGAAGGAAATT 58.365 37.500 0.00 0.00 34.94 1.82
1439 1557 1.000506 TGACGGTGAAGAGTTGTAGGC 59.999 52.381 0.00 0.00 0.00 3.93
1451 1569 5.163395 TGGCACATTAAGTATATGACGGTGA 60.163 40.000 0.00 0.00 0.00 4.02
1579 1706 0.681243 GGGCAGTGAAGGGGACATTC 60.681 60.000 0.00 0.00 0.00 2.67
1585 1712 4.410400 GTCCGGGCAGTGAAGGGG 62.410 72.222 0.00 0.00 0.00 4.79
1598 1726 1.066573 GGGCATATCATCAGGAGTCCG 60.067 57.143 2.76 0.00 0.00 4.79
1599 1727 1.980765 TGGGCATATCATCAGGAGTCC 59.019 52.381 0.00 0.00 0.00 3.85
1615 1743 3.016736 ACATGCAAGTATGTTAGTGGGC 58.983 45.455 0.00 0.00 38.05 5.36
1649 1786 7.011576 AGTCTCAAGCGTATATATCATCCTACG 59.988 40.741 0.00 0.00 39.81 3.51
1710 1847 3.181503 GCCACTGAGCAGAAATATGTGTG 60.182 47.826 4.21 0.00 0.00 3.82
1754 1891 2.079158 ACGGAGTGTTCATGCTTGATG 58.921 47.619 2.75 0.00 42.51 3.07
1761 1898 0.238289 GTGCCAACGGAGTGTTCATG 59.762 55.000 0.00 0.00 45.00 3.07
1762 1899 0.889186 GGTGCCAACGGAGTGTTCAT 60.889 55.000 0.00 0.00 45.00 2.57
1818 1955 0.394938 ACGACACTGCCACATTGGTA 59.605 50.000 0.00 0.00 40.46 3.25
1847 1991 4.273235 CACTATGTGAGCATAAAATCGCCA 59.727 41.667 0.00 0.00 37.16 5.69
1884 2028 1.676006 AGAAACCAAACAAGGCGACAG 59.324 47.619 0.00 0.00 0.00 3.51
1885 2029 1.757682 AGAAACCAAACAAGGCGACA 58.242 45.000 0.00 0.00 0.00 4.35
1889 2034 4.021981 AGCTGATAAGAAACCAAACAAGGC 60.022 41.667 0.00 0.00 0.00 4.35
1937 2083 5.663106 AGCAGATGTCATCCTTCCTAGTTTA 59.337 40.000 9.29 0.00 0.00 2.01
1948 2094 2.490903 ACAAGCAAAGCAGATGTCATCC 59.509 45.455 9.29 0.00 0.00 3.51
1998 2144 2.103094 CGGAAGTGAGATGGCAGGAATA 59.897 50.000 0.00 0.00 0.00 1.75
2018 2164 0.469917 AATCCAGTAGTGCATCCCCG 59.530 55.000 0.00 0.00 0.00 5.73
2087 2233 4.202357 TGCAGATGTACCAGAAGTTCAAGT 60.202 41.667 5.50 4.42 28.71 3.16
2091 2237 3.681897 CAGTGCAGATGTACCAGAAGTTC 59.318 47.826 0.00 0.00 0.00 3.01
2134 2280 8.504812 TGCTCTAACATTAGATTGTTAATGCA 57.495 30.769 14.33 14.33 42.23 3.96
2281 2428 0.469144 ACGTGGGCAAATTTGGGTCT 60.469 50.000 19.47 0.00 0.00 3.85
2314 2468 4.742659 GTGCCACGTGTTTATCATTTTTGT 59.257 37.500 15.65 0.00 0.00 2.83
2384 2538 2.967507 TAAGTGCACTTTGGCCGGCA 62.968 55.000 35.20 13.63 37.40 5.69
2417 2571 5.006358 GTGCGGACACGAATATCTTTTATGT 59.994 40.000 0.63 0.00 44.60 2.29
2418 2572 5.432157 GTGCGGACACGAATATCTTTTATG 58.568 41.667 0.63 0.00 44.60 1.90
2419 2573 5.652744 GTGCGGACACGAATATCTTTTAT 57.347 39.130 0.63 0.00 44.60 1.40
2502 2668 2.584608 CCGCCTCCCGTCTTCATT 59.415 61.111 0.00 0.00 34.38 2.57
2672 2846 4.845580 AGCATTGGAGGGAGCGCG 62.846 66.667 0.00 0.00 0.00 6.86
2771 2951 4.849329 CCGGCCGAGCAGTACGTC 62.849 72.222 30.73 0.00 0.00 4.34
3200 3380 2.274760 GCCCTCTCTGCAGCCAAT 59.725 61.111 9.47 0.00 0.00 3.16
3356 3565 1.764854 ACCACCACGTCAACTCCCT 60.765 57.895 0.00 0.00 0.00 4.20
3360 3572 1.523711 CAGCACCACCACGTCAACT 60.524 57.895 0.00 0.00 0.00 3.16
3405 3621 1.671742 GTCTGGTTTGCCCTCGAGA 59.328 57.895 15.71 0.00 0.00 4.04
3485 3704 1.913262 TCACATGCCGAGGAGGTGT 60.913 57.895 9.23 0.00 43.70 4.16
3528 3771 4.498520 CGCCTCGATCCACAGCGT 62.499 66.667 6.05 0.00 41.78 5.07
3657 3961 2.685380 CCCGGCACTTCCTCCTCT 60.685 66.667 0.00 0.00 0.00 3.69
3790 4133 2.825836 GGCGGCCTCATCCAGTTG 60.826 66.667 12.87 0.00 0.00 3.16
4072 4462 4.668118 TCCGTTTGGGTCGCCGAC 62.668 66.667 9.15 9.15 37.00 4.79
4198 4755 8.776470 CAGCAAAGGTTCATATTTTGACATTTT 58.224 29.630 1.79 0.00 34.55 1.82
4199 4756 7.095102 GCAGCAAAGGTTCATATTTTGACATTT 60.095 33.333 1.79 0.00 34.55 2.32
4228 4786 3.243301 TGAAGTAACTCGTGTCTGTGACC 60.243 47.826 0.00 0.00 0.00 4.02
4260 4818 6.841443 ATATCTCTTCGTCTTGCTGATTTG 57.159 37.500 0.00 0.00 0.00 2.32
4456 5017 5.730550 AGTTTCAACGGCTGATCACTATTA 58.269 37.500 0.00 0.00 32.78 0.98
4525 5086 5.822519 GGTTGTCACTGCCATATGATCTAAA 59.177 40.000 3.65 0.00 0.00 1.85
4534 5095 0.767998 TGTGGGTTGTCACTGCCATA 59.232 50.000 0.00 0.00 38.40 2.74
4631 5192 3.389983 TGCCTCCATACAACCCAGTATAC 59.610 47.826 0.00 0.00 33.12 1.47
4632 5193 3.659841 TGCCTCCATACAACCCAGTATA 58.340 45.455 0.00 0.00 33.12 1.47
4633 5194 2.487775 TGCCTCCATACAACCCAGTAT 58.512 47.619 0.00 0.00 35.14 2.12
4640 5207 3.895232 TCTCTCTTGCCTCCATACAAC 57.105 47.619 0.00 0.00 0.00 3.32
4720 5302 9.846248 CAGATCGATGATGTCTTACATACATTA 57.154 33.333 0.54 0.00 39.27 1.90
4727 5309 7.936950 GAAATCAGATCGATGATGTCTTACA 57.063 36.000 0.54 0.00 39.77 2.41
4732 5314 7.359097 GCAAGTAGAAATCAGATCGATGATGTC 60.359 40.741 0.54 6.87 42.17 3.06
4746 5328 4.579869 TGGTCCTCAAGCAAGTAGAAATC 58.420 43.478 0.00 0.00 30.91 2.17
4802 5384 8.212312 AGTTCTCCAATCTCTACGTTAGATAGA 58.788 37.037 12.05 9.35 33.32 1.98
4836 5418 3.138128 GCCCCAACCCCGATTTCG 61.138 66.667 0.00 0.00 39.44 3.46
4873 5455 1.727511 AACTTCGTCACACCCGTCGA 61.728 55.000 0.00 0.00 0.00 4.20
4941 5523 9.028284 ACATTCCCATATGCTTCCATATAAAAG 57.972 33.333 0.00 0.00 41.55 2.27
4946 5528 6.185511 CAGACATTCCCATATGCTTCCATAT 58.814 40.000 0.00 0.00 43.68 1.78
4966 5549 6.202516 ACTCTTGTATCTAACTCTGCAGAC 57.797 41.667 13.74 1.19 0.00 3.51
5539 6130 5.003214 CGCAGTACTGATACGTAAACAAGAC 59.997 44.000 27.08 1.69 36.33 3.01
5640 6231 1.364901 CACTTGGGCCAACTGCAAG 59.635 57.895 16.66 14.88 43.89 4.01
5673 6264 6.696148 ACAAGGAAGAAATCGATCACGTATAC 59.304 38.462 0.00 0.00 40.69 1.47
5693 6284 3.192001 CCACAACATCTCCATGAACAAGG 59.808 47.826 0.00 0.00 33.72 3.61
5694 6285 4.074259 TCCACAACATCTCCATGAACAAG 58.926 43.478 0.00 0.00 33.72 3.16
5696 6287 3.786368 TCCACAACATCTCCATGAACA 57.214 42.857 0.00 0.00 33.72 3.18
5697 6288 5.649782 AATTCCACAACATCTCCATGAAC 57.350 39.130 0.00 0.00 33.72 3.18
5699 6290 5.882000 CACTAATTCCACAACATCTCCATGA 59.118 40.000 0.00 0.00 33.72 3.07
5700 6291 5.649395 ACACTAATTCCACAACATCTCCATG 59.351 40.000 0.00 0.00 35.92 3.66
5701 6292 5.819991 ACACTAATTCCACAACATCTCCAT 58.180 37.500 0.00 0.00 0.00 3.41
5702 6293 5.241403 ACACTAATTCCACAACATCTCCA 57.759 39.130 0.00 0.00 0.00 3.86
5703 6294 5.940470 AGAACACTAATTCCACAACATCTCC 59.060 40.000 0.00 0.00 0.00 3.71
5749 6340 4.023107 ACATTGGTATACGATCAGTCCTCG 60.023 45.833 0.00 0.00 41.77 4.63
5798 6397 6.040842 ACAATCATATGTACATTTTCAGGCCC 59.959 38.462 14.77 0.00 0.00 5.80
5801 6400 9.726232 CTCAACAATCATATGTACATTTTCAGG 57.274 33.333 14.77 0.00 32.02 3.86
5845 6444 5.897250 TCCTACTAATAGTTCCATCACAGCA 59.103 40.000 0.00 0.00 0.00 4.41
5860 6459 7.547227 GGCACAAAAATGAACATCCTACTAAT 58.453 34.615 0.00 0.00 0.00 1.73
5866 6465 2.610232 GCGGCACAAAAATGAACATCCT 60.610 45.455 0.00 0.00 0.00 3.24
5907 6506 7.958053 ACGAGTAAGCTTTTACAGTACAATT 57.042 32.000 3.20 0.00 0.00 2.32
5914 6513 5.577164 ACATGCTACGAGTAAGCTTTTACAG 59.423 40.000 3.20 0.00 0.00 2.74
5915 6514 5.347635 CACATGCTACGAGTAAGCTTTTACA 59.652 40.000 3.20 0.00 0.00 2.41
5916 6515 5.575606 TCACATGCTACGAGTAAGCTTTTAC 59.424 40.000 3.20 0.00 0.00 2.01
5917 6516 5.716094 TCACATGCTACGAGTAAGCTTTTA 58.284 37.500 3.20 0.00 0.00 1.52
5918 6517 4.566004 TCACATGCTACGAGTAAGCTTTT 58.434 39.130 3.20 0.00 0.00 2.27
5919 6518 4.188247 TCACATGCTACGAGTAAGCTTT 57.812 40.909 3.20 0.00 0.00 3.51
5920 6519 3.868757 TCACATGCTACGAGTAAGCTT 57.131 42.857 3.48 3.48 0.00 3.74
5921 6520 3.381590 TCATCACATGCTACGAGTAAGCT 59.618 43.478 0.00 0.00 0.00 3.74
5922 6521 3.706698 TCATCACATGCTACGAGTAAGC 58.293 45.455 0.00 0.00 0.00 3.09
5923 6522 3.733224 GCTCATCACATGCTACGAGTAAG 59.267 47.826 0.00 0.00 0.00 2.34
5924 6523 3.381590 AGCTCATCACATGCTACGAGTAA 59.618 43.478 0.00 0.00 35.05 2.24
5925 6524 2.952310 AGCTCATCACATGCTACGAGTA 59.048 45.455 0.00 0.00 35.05 2.59
5926 6525 1.753649 AGCTCATCACATGCTACGAGT 59.246 47.619 0.00 0.00 35.05 4.18
5927 6526 2.125685 CAGCTCATCACATGCTACGAG 58.874 52.381 0.00 0.00 35.05 4.18
5928 6527 1.202452 CCAGCTCATCACATGCTACGA 60.202 52.381 0.00 0.00 35.05 3.43
5975 6574 8.664798 GCAAATTACAAAGAAAGAACAACCTTT 58.335 29.630 0.00 0.00 38.92 3.11
6006 6606 3.369892 GGGAGAGTGCTGAGCAAGAAATA 60.370 47.826 9.51 0.00 41.47 1.40
6020 6620 0.321671 TCAAAGAAGGCGGGAGAGTG 59.678 55.000 0.00 0.00 0.00 3.51
6023 6623 2.436417 CATTTCAAAGAAGGCGGGAGA 58.564 47.619 0.00 0.00 0.00 3.71
6029 6629 5.411831 AAGATTCCCATTTCAAAGAAGGC 57.588 39.130 0.00 0.00 0.00 4.35
6051 6651 7.883391 AGATAGACTCGGTCTCATAGAAAAA 57.117 36.000 9.44 0.00 42.40 1.94
6052 6652 7.776030 AGAAGATAGACTCGGTCTCATAGAAAA 59.224 37.037 9.44 0.00 42.40 2.29
6053 6653 7.284074 AGAAGATAGACTCGGTCTCATAGAAA 58.716 38.462 9.44 0.00 42.40 2.52
6150 6760 3.195698 GGCGTCAGCTTTAGGGCG 61.196 66.667 0.00 0.00 44.37 6.13
6158 6768 2.345244 CTGTCTTGGGCGTCAGCT 59.655 61.111 0.00 0.00 44.37 4.24
6171 6781 3.266510 TGAACAGATACCATGCCTGTC 57.733 47.619 0.00 0.00 39.93 3.51
6176 6786 3.492383 CAGTCGATGAACAGATACCATGC 59.508 47.826 0.00 0.00 0.00 4.06
6181 6791 3.130516 TGGACCAGTCGATGAACAGATAC 59.869 47.826 0.00 0.00 0.00 2.24
6186 6796 1.272490 GTCTGGACCAGTCGATGAACA 59.728 52.381 21.06 0.00 32.61 3.18
6208 6900 2.438868 TTCATCCATATCCGCAGACG 57.561 50.000 0.00 0.00 39.67 4.18
6212 6904 2.547855 CCGACTTTCATCCATATCCGCA 60.548 50.000 0.00 0.00 0.00 5.69
6214 6906 3.243737 TGACCGACTTTCATCCATATCCG 60.244 47.826 0.00 0.00 0.00 4.18
6230 6924 3.104512 AGGAATACAGTTGGATGACCGA 58.895 45.455 0.00 0.00 39.42 4.69
6242 6936 8.393671 ACCTAGATAGACGTTTAGGAATACAG 57.606 38.462 14.08 0.00 36.88 2.74
6243 6937 8.216423 AGACCTAGATAGACGTTTAGGAATACA 58.784 37.037 14.08 0.00 36.88 2.29
6260 6974 4.591321 TTCAAATTGGCCAGACCTAGAT 57.409 40.909 5.11 0.00 40.22 1.98
6262 6976 5.185635 TGAATTTCAAATTGGCCAGACCTAG 59.814 40.000 5.11 0.00 40.22 3.02
6268 6982 4.083696 GCAACTGAATTTCAAATTGGCCAG 60.084 41.667 5.11 4.45 0.00 4.85
6287 7001 2.193447 TGATCGAACTCGCTATGCAAC 58.807 47.619 0.00 0.00 39.60 4.17
6289 7003 2.800881 ATGATCGAACTCGCTATGCA 57.199 45.000 0.00 0.00 39.60 3.96
6291 7005 4.546570 TGGTTATGATCGAACTCGCTATG 58.453 43.478 9.45 0.00 39.60 2.23
6292 7006 4.848562 TGGTTATGATCGAACTCGCTAT 57.151 40.909 9.45 0.00 39.60 2.97
6293 7007 4.642445 TTGGTTATGATCGAACTCGCTA 57.358 40.909 9.45 0.00 39.60 4.26
6294 7008 3.520290 TTGGTTATGATCGAACTCGCT 57.480 42.857 9.45 0.00 39.60 4.93
6295 7009 4.593597 TTTTGGTTATGATCGAACTCGC 57.406 40.909 9.45 0.00 39.60 5.03
6297 7011 6.183360 CCCTCTTTTTGGTTATGATCGAACTC 60.183 42.308 9.45 0.00 0.00 3.01
6308 7140 4.042809 TGAGCATCTCCCTCTTTTTGGTTA 59.957 41.667 0.00 0.00 34.92 2.85
6320 7152 6.543831 ACATGTAAAAACTATGAGCATCTCCC 59.456 38.462 0.00 0.00 34.92 4.30
6321 7153 7.559590 ACATGTAAAAACTATGAGCATCTCC 57.440 36.000 0.00 0.00 34.92 3.71
6362 7205 4.437239 AGTTCATTCTCTTGCGGACTATG 58.563 43.478 0.00 0.00 0.00 2.23
6376 7219 3.495753 CCAGCAAGGCAAAAAGTTCATTC 59.504 43.478 0.00 0.00 0.00 2.67
6392 7235 0.681887 TCGGATAGTCGGTCCAGCAA 60.682 55.000 0.00 0.00 35.41 3.91
6403 7246 1.794714 AGCATGAAGGGTCGGATAGT 58.205 50.000 0.00 0.00 0.00 2.12
6408 7251 2.093447 AGAGTTTAGCATGAAGGGTCGG 60.093 50.000 0.00 0.00 0.00 4.79
6412 7255 2.932614 CGACAGAGTTTAGCATGAAGGG 59.067 50.000 0.00 0.00 0.00 3.95
6413 7256 2.349886 GCGACAGAGTTTAGCATGAAGG 59.650 50.000 0.00 0.00 0.00 3.46
6450 7293 1.933247 CAGATGAGAAGGAAGCGGAC 58.067 55.000 0.00 0.00 0.00 4.79
6465 7308 2.688666 TGCGGAGAAGGGGCAGAT 60.689 61.111 0.00 0.00 32.07 2.90
6468 7311 3.706373 GACTGCGGAGAAGGGGCA 61.706 66.667 12.26 0.00 35.07 5.36


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

AutoCloner maintained by Alex Coulton.