Multiple sequence alignment - TraesCS4D01G248700

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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 TraesCS4D01G248700 chr4D 100.000 5945 0 0 1 5945 417806362 417812306 0.000000e+00 10979.0
1 TraesCS4D01G248700 chr4D 92.857 1834 82 25 830 2655 401366519 401368311 0.000000e+00 2615.0
2 TraesCS4D01G248700 chr4D 92.429 1651 69 26 3709 5337 401369524 401371140 0.000000e+00 2305.0
3 TraesCS4D01G248700 chr4D 94.427 933 36 5 2796 3713 401368547 401369478 0.000000e+00 1421.0
4 TraesCS4D01G248700 chr4D 83.713 571 74 16 12 575 633700 633142 6.830000e-144 521.0
5 TraesCS4D01G248700 chr4D 91.304 184 11 3 5429 5607 401371137 401371320 4.600000e-61 246.0
6 TraesCS4D01G248700 chr4D 94.783 115 4 2 579 693 401351553 401351441 1.700000e-40 178.0
7 TraesCS4D01G248700 chr4D 93.277 119 7 1 717 834 401361127 401361245 2.200000e-39 174.0
8 TraesCS4D01G248700 chr4D 90.083 121 11 1 2677 2797 401368303 401368422 7.980000e-34 156.0
9 TraesCS4D01G248700 chr4B 92.948 2113 78 22 581 2661 496421190 496423263 0.000000e+00 3011.0
10 TraesCS4D01G248700 chr4B 91.898 1259 58 17 4108 5337 496424443 496425686 0.000000e+00 1720.0
11 TraesCS4D01G248700 chr4B 88.120 766 49 19 2803 3541 496423433 496424183 0.000000e+00 872.0
12 TraesCS4D01G248700 chr4B 96.525 518 16 2 5429 5945 496425683 496426199 0.000000e+00 856.0
13 TraesCS4D01G248700 chr4B 82.851 449 53 17 1 441 624751174 624750742 1.210000e-101 381.0
14 TraesCS4D01G248700 chr4B 98.347 121 2 0 2677 2797 496423249 496423369 4.670000e-51 213.0
15 TraesCS4D01G248700 chr4B 91.429 70 6 0 2588 2657 589783482 589783551 4.900000e-16 97.1
16 TraesCS4D01G248700 chr4A 95.105 1716 55 18 579 2285 59230417 59232112 0.000000e+00 2676.0
17 TraesCS4D01G248700 chr4A 85.970 1283 92 39 2677 3888 59232570 59233835 0.000000e+00 1291.0
18 TraesCS4D01G248700 chr4A 92.720 783 46 7 3878 4655 59233861 59234637 0.000000e+00 1120.0
19 TraesCS4D01G248700 chr4A 89.618 655 43 13 4694 5327 59234642 59235292 0.000000e+00 809.0
20 TraesCS4D01G248700 chr4A 87.578 322 30 7 5605 5919 59242552 59242870 1.220000e-96 364.0
21 TraesCS4D01G248700 chr4A 95.531 179 8 0 5429 5607 59240943 59241121 2.710000e-73 287.0
22 TraesCS4D01G248700 chr4A 77.540 374 34 19 2288 2661 59232261 59232584 4.730000e-41 180.0
23 TraesCS4D01G248700 chr4A 100.000 29 0 0 5896 5924 712852295 712852267 3.000000e-03 54.7
24 TraesCS4D01G248700 chr5B 85.930 1059 73 30 2715 3713 687363630 687362588 0.000000e+00 1061.0
25 TraesCS4D01G248700 chr5B 85.458 1059 78 26 2715 3713 683038466 683039508 0.000000e+00 1033.0
26 TraesCS4D01G248700 chr5B 94.530 457 25 0 4108 4564 687362255 687361799 0.000000e+00 706.0
27 TraesCS4D01G248700 chr5B 93.231 458 29 2 4108 4564 683039859 683040315 0.000000e+00 673.0
28 TraesCS4D01G248700 chr5B 81.431 587 87 17 1 575 660239677 660240253 1.510000e-125 460.0
29 TraesCS4D01G248700 chr5B 83.077 325 38 14 256 576 484882376 484882687 4.540000e-71 279.0
30 TraesCS4D01G248700 chr5B 91.549 71 6 0 2588 2658 521744067 521743997 1.360000e-16 99.0
31 TraesCS4D01G248700 chr5B 93.220 59 3 1 2699 2757 25485259 25485316 1.060000e-12 86.1
32 TraesCS4D01G248700 chr2B 84.528 963 85 25 2803 3716 240186220 240185273 0.000000e+00 894.0
33 TraesCS4D01G248700 chr2B 92.779 457 33 0 4108 4564 240184727 240184271 0.000000e+00 662.0
34 TraesCS4D01G248700 chr2B 85.172 580 72 11 1 575 784849618 784849048 3.090000e-162 582.0
35 TraesCS4D01G248700 chr2B 82.526 578 79 13 7 574 693436799 693437364 6.920000e-134 488.0
36 TraesCS4D01G248700 chr2B 82.343 589 72 25 1 577 773656931 773656363 3.220000e-132 483.0
37 TraesCS4D01G248700 chr2B 97.590 83 2 0 2715 2797 240186402 240186320 6.210000e-30 143.0
38 TraesCS4D01G248700 chr7D 85.969 784 56 34 1875 2657 157760285 157761015 0.000000e+00 789.0
39 TraesCS4D01G248700 chr7D 87.692 65 5 3 2373 2434 157760671 157760735 8.260000e-09 73.1
40 TraesCS4D01G248700 chr6B 89.819 609 43 7 2715 3305 566644282 566643675 0.000000e+00 763.0
41 TraesCS4D01G248700 chr6B 89.267 382 33 2 1788 2169 279014173 279013800 6.970000e-129 472.0
42 TraesCS4D01G248700 chr6B 90.032 311 24 5 1 310 637139055 637138751 4.320000e-106 396.0
43 TraesCS4D01G248700 chr6B 93.220 59 3 1 2699 2757 76225437 76225380 1.060000e-12 86.1
44 TraesCS4D01G248700 chr5D 88.428 579 59 5 1 575 444069988 444069414 0.000000e+00 691.0
45 TraesCS4D01G248700 chr5D 84.615 117 12 5 461 575 564840294 564840182 1.750000e-20 111.0
46 TraesCS4D01G248700 chr5D 91.667 72 6 0 2586 2657 438349193 438349264 3.790000e-17 100.0
47 TraesCS4D01G248700 chr5D 91.429 70 6 0 2588 2657 75598449 75598380 4.900000e-16 97.1
48 TraesCS4D01G248700 chr5D 91.429 70 6 0 2588 2657 123297119 123297050 4.900000e-16 97.1
49 TraesCS4D01G248700 chr7B 92.779 457 33 0 4108 4564 604516483 604516939 0.000000e+00 662.0
50 TraesCS4D01G248700 chr7B 82.391 778 73 27 2984 3713 604515372 604516133 2.350000e-173 619.0
51 TraesCS4D01G248700 chr7B 86.058 416 42 5 1657 2071 612843297 612843697 3.290000e-117 433.0
52 TraesCS4D01G248700 chr7B 92.364 275 9 2 2715 2977 604509868 604510142 1.210000e-101 381.0
53 TraesCS4D01G248700 chr5A 79.585 578 83 27 13 574 658620992 658620434 1.210000e-101 381.0
54 TraesCS4D01G248700 chr5A 79.322 590 87 26 1 574 692876156 692875586 1.210000e-101 381.0
55 TraesCS4D01G248700 chr1A 79.357 591 80 32 2 574 586930607 586931173 1.560000e-100 377.0
56 TraesCS4D01G248700 chr1A 100.000 31 0 0 5352 5382 445548037 445548067 2.310000e-04 58.4
57 TraesCS4D01G248700 chr3D 88.088 319 32 5 1 318 584438781 584438468 2.020000e-99 374.0
58 TraesCS4D01G248700 chr7A 86.957 322 31 8 5605 5919 499447851 499447534 9.480000e-93 351.0
59 TraesCS4D01G248700 chr2D 77.759 580 89 29 7 575 36072361 36071811 2.670000e-83 320.0
60 TraesCS4D01G248700 chr6A 91.429 70 6 0 2588 2657 413093673 413093742 4.900000e-16 97.1
61 TraesCS4D01G248700 chr2A 100.000 29 0 0 5390 5418 659281156 659281128 3.000000e-03 54.7


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 TraesCS4D01G248700 chr4D 417806362 417812306 5944 False 10979.000000 10979 100.000000 1 5945 1 chr4D.!!$F2 5944
1 TraesCS4D01G248700 chr4D 401366519 401371320 4801 False 1348.600000 2615 92.220000 830 5607 5 chr4D.!!$F3 4777
2 TraesCS4D01G248700 chr4D 633142 633700 558 True 521.000000 521 83.713000 12 575 1 chr4D.!!$R1 563
3 TraesCS4D01G248700 chr4B 496421190 496426199 5009 False 1334.400000 3011 93.567600 581 5945 5 chr4B.!!$F2 5364
4 TraesCS4D01G248700 chr4A 59230417 59235292 4875 False 1215.200000 2676 88.190600 579 5327 5 chr4A.!!$F1 4748
5 TraesCS4D01G248700 chr4A 59240943 59242870 1927 False 325.500000 364 91.554500 5429 5919 2 chr4A.!!$F2 490
6 TraesCS4D01G248700 chr5B 687361799 687363630 1831 True 883.500000 1061 90.230000 2715 4564 2 chr5B.!!$R2 1849
7 TraesCS4D01G248700 chr5B 683038466 683040315 1849 False 853.000000 1033 89.344500 2715 4564 2 chr5B.!!$F4 1849
8 TraesCS4D01G248700 chr5B 660239677 660240253 576 False 460.000000 460 81.431000 1 575 1 chr5B.!!$F3 574
9 TraesCS4D01G248700 chr2B 784849048 784849618 570 True 582.000000 582 85.172000 1 575 1 chr2B.!!$R2 574
10 TraesCS4D01G248700 chr2B 240184271 240186402 2131 True 566.333333 894 91.632333 2715 4564 3 chr2B.!!$R3 1849
11 TraesCS4D01G248700 chr2B 693436799 693437364 565 False 488.000000 488 82.526000 7 574 1 chr2B.!!$F1 567
12 TraesCS4D01G248700 chr2B 773656363 773656931 568 True 483.000000 483 82.343000 1 577 1 chr2B.!!$R1 576
13 TraesCS4D01G248700 chr7D 157760285 157761015 730 False 431.050000 789 86.830500 1875 2657 2 chr7D.!!$F1 782
14 TraesCS4D01G248700 chr6B 566643675 566644282 607 True 763.000000 763 89.819000 2715 3305 1 chr6B.!!$R3 590
15 TraesCS4D01G248700 chr5D 444069414 444069988 574 True 691.000000 691 88.428000 1 575 1 chr5D.!!$R3 574
16 TraesCS4D01G248700 chr7B 604515372 604516939 1567 False 640.500000 662 87.585000 2984 4564 2 chr7B.!!$F3 1580
17 TraesCS4D01G248700 chr5A 658620434 658620992 558 True 381.000000 381 79.585000 13 574 1 chr5A.!!$R1 561
18 TraesCS4D01G248700 chr5A 692875586 692876156 570 True 381.000000 381 79.322000 1 574 1 chr5A.!!$R2 573
19 TraesCS4D01G248700 chr1A 586930607 586931173 566 False 377.000000 377 79.357000 2 574 1 chr1A.!!$F2 572
20 TraesCS4D01G248700 chr2D 36071811 36072361 550 True 320.000000 320 77.759000 7 575 1 chr2D.!!$R1 568

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
213 231 0.447801 GTCCGTTGCTGCGATGAAAT 59.552 50.000 10.71 0.0 0.00 2.17 F
471 517 1.032114 GTGACAGTTGCATAGGGGGC 61.032 60.000 0.00 0.0 0.00 5.80 F
2195 2287 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.0 0.00 3.82 F
2235 2327 0.108207 AGCAGATCCAGCTATGCACC 59.892 55.000 8.39 0.0 41.32 5.01 F
2771 3013 1.010125 CTGTCGGCACCGTGTTTTG 60.010 57.895 9.23 0.0 40.74 2.44 F
3664 4117 1.144565 CTGCAATCAGGTCGCTCTCG 61.145 60.000 0.00 0.0 36.68 4.04 F
4688 5455 1.027357 TCCGTAAGACCTACCGATGC 58.973 55.000 0.00 0.0 43.02 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2185 2277 0.096281 CCGAACACACACACACACAC 59.904 55.000 0.00 0.00 0.00 3.82 R
2211 2303 1.138568 ATAGCTGGATCTGCTGCCTT 58.861 50.000 19.04 4.12 38.96 4.35 R
3234 3642 0.251474 TTGCAGGGATGCTTGAAGCT 60.251 50.000 18.94 3.75 42.97 3.74 R
4126 4891 1.680207 GAATGGAGGCAAAGATGAGGC 59.320 52.381 0.00 0.00 0.00 4.70 R
4652 5419 1.189446 CGGAAGTTCTGAACGTGAACG 59.811 52.381 13.57 10.92 45.84 3.95 R
4824 5595 0.179073 AGTTTCTGCACGCTGTCAGT 60.179 50.000 0.93 0.00 0.00 3.41 R
5622 7863 1.547675 GCTGGATCAGGTGGTGGAAAA 60.548 52.381 0.00 0.00 31.21 2.29 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
80 81 3.432186 CCCCGCAAGAAGTAAGATGATGA 60.432 47.826 0.00 0.00 43.02 2.92
213 231 0.447801 GTCCGTTGCTGCGATGAAAT 59.552 50.000 10.71 0.00 0.00 2.17
214 232 1.663643 GTCCGTTGCTGCGATGAAATA 59.336 47.619 10.71 0.00 0.00 1.40
230 251 6.313905 CGATGAAATAAACTGCTTCCACTACT 59.686 38.462 0.00 0.00 0.00 2.57
249 271 4.489679 ACTTTTTAGCTTGCTTCCTTCG 57.510 40.909 0.00 0.00 0.00 3.79
250 272 3.883489 ACTTTTTAGCTTGCTTCCTTCGT 59.117 39.130 0.00 0.00 0.00 3.85
269 292 3.767673 TCGTTTCCTCAGTTAGCCTATGT 59.232 43.478 0.00 0.00 0.00 2.29
283 310 5.883685 AGCCTATGTTCTTCTGATGATGA 57.116 39.130 0.00 0.00 0.00 2.92
284 311 6.436738 AGCCTATGTTCTTCTGATGATGAT 57.563 37.500 0.00 0.00 0.00 2.45
293 320 9.376075 TGTTCTTCTGATGATGATAAAAGACTC 57.624 33.333 0.00 0.00 0.00 3.36
316 346 8.575589 ACTCTAATCATGATGTATGTCTCTGTC 58.424 37.037 9.46 0.00 38.01 3.51
318 348 8.574737 TCTAATCATGATGTATGTCTCTGTCTG 58.425 37.037 9.46 0.00 38.01 3.51
444 486 2.354328 TGGCTTTCCTTCCCTCCTTAA 58.646 47.619 0.00 0.00 0.00 1.85
463 505 5.338056 CCTTAATAGGGTAGTGACAGTTGCA 60.338 44.000 0.00 0.00 37.94 4.08
471 517 1.032114 GTGACAGTTGCATAGGGGGC 61.032 60.000 0.00 0.00 0.00 5.80
495 543 5.739161 CGGAGTTTTATGTTGCATCTTTAGC 59.261 40.000 0.00 0.00 0.00 3.09
509 561 5.292101 GCATCTTTAGCTTCTTCTCGCTTTA 59.708 40.000 0.00 0.00 37.68 1.85
511 563 7.563270 CATCTTTAGCTTCTTCTCGCTTTATC 58.437 38.462 0.00 0.00 37.68 1.75
671 731 2.595238 ACAGTTCTAGAACGTGGGTCT 58.405 47.619 25.92 7.60 45.50 3.85
709 770 2.256117 AAAAGAACGTGGGTCCTCTG 57.744 50.000 0.00 0.00 0.00 3.35
715 776 3.695606 GTGGGTCCTCTGCTGCGA 61.696 66.667 0.00 0.00 0.00 5.10
732 793 1.686110 GAGGGGTCCACGGATCTGT 60.686 63.158 0.00 0.00 0.00 3.41
750 811 4.416738 GCTGACAGGAGGTGGGGC 62.417 72.222 4.26 0.00 0.00 5.80
752 813 4.590553 TGACAGGAGGTGGGGCCA 62.591 66.667 4.39 0.00 40.61 5.36
753 814 3.017581 GACAGGAGGTGGGGCCAT 61.018 66.667 4.39 0.00 40.61 4.40
754 815 1.692749 GACAGGAGGTGGGGCCATA 60.693 63.158 4.39 0.00 40.61 2.74
1187 1272 4.033776 CTCCACCACCACCGCCAT 62.034 66.667 0.00 0.00 0.00 4.40
1499 1590 1.203523 CTGCACTGACTACTCCCTCAC 59.796 57.143 0.00 0.00 0.00 3.51
1942 2034 4.074970 GTTCTGTCATGGTGAACTGGATT 58.925 43.478 14.56 0.00 37.62 3.01
1997 2089 3.364023 GCATTCTACATGTATACCGCGAC 59.636 47.826 8.23 0.00 0.00 5.19
2083 2175 8.104566 AGTTGGTATTGTGCTGGTAATTTACTA 58.895 33.333 6.52 0.00 0.00 1.82
2173 2265 1.531149 GTGGTTGTGTGGTTGATCTCG 59.469 52.381 0.00 0.00 0.00 4.04
2174 2266 1.140052 TGGTTGTGTGGTTGATCTCGT 59.860 47.619 0.00 0.00 0.00 4.18
2175 2267 1.531149 GGTTGTGTGGTTGATCTCGTG 59.469 52.381 0.00 0.00 0.00 4.35
2176 2268 2.210116 GTTGTGTGGTTGATCTCGTGT 58.790 47.619 0.00 0.00 0.00 4.49
2177 2269 1.864565 TGTGTGGTTGATCTCGTGTG 58.135 50.000 0.00 0.00 0.00 3.82
2178 2270 1.138069 TGTGTGGTTGATCTCGTGTGT 59.862 47.619 0.00 0.00 0.00 3.72
2179 2271 1.526887 GTGTGGTTGATCTCGTGTGTG 59.473 52.381 0.00 0.00 0.00 3.82
2180 2272 1.138069 TGTGGTTGATCTCGTGTGTGT 59.862 47.619 0.00 0.00 0.00 3.72
2181 2273 1.526887 GTGGTTGATCTCGTGTGTGTG 59.473 52.381 0.00 0.00 0.00 3.82
2182 2274 1.138069 TGGTTGATCTCGTGTGTGTGT 59.862 47.619 0.00 0.00 0.00 3.72
2183 2275 1.526887 GGTTGATCTCGTGTGTGTGTG 59.473 52.381 0.00 0.00 0.00 3.82
2184 2276 2.201732 GTTGATCTCGTGTGTGTGTGT 58.798 47.619 0.00 0.00 0.00 3.72
2185 2277 1.851658 TGATCTCGTGTGTGTGTGTG 58.148 50.000 0.00 0.00 0.00 3.82
2186 2278 1.136110 TGATCTCGTGTGTGTGTGTGT 59.864 47.619 0.00 0.00 0.00 3.72
2195 2287 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2211 2303 1.952133 GTGTGTGTTCGGCGTGCTA 60.952 57.895 6.85 0.00 0.00 3.49
2235 2327 0.108207 AGCAGATCCAGCTATGCACC 59.892 55.000 8.39 0.00 41.32 5.01
2465 2703 6.907206 AACATTTTGACATTCAGTGTTTGG 57.093 33.333 0.00 0.00 42.36 3.28
2501 2743 7.452880 TCTTCAGTTATGCTGCAAAGTTATT 57.547 32.000 6.36 0.00 44.66 1.40
2541 2783 8.840321 GCTATTTGATTAGCTTATGGTCTTCAA 58.160 33.333 0.00 0.00 41.15 2.69
2545 2787 7.187824 TGATTAGCTTATGGTCTTCAACTCT 57.812 36.000 0.00 0.00 0.00 3.24
2546 2788 7.624549 TGATTAGCTTATGGTCTTCAACTCTT 58.375 34.615 0.00 0.00 0.00 2.85
2547 2789 7.766278 TGATTAGCTTATGGTCTTCAACTCTTC 59.234 37.037 0.00 0.00 0.00 2.87
2548 2790 5.489792 AGCTTATGGTCTTCAACTCTTCA 57.510 39.130 0.00 0.00 0.00 3.02
2549 2791 6.059787 AGCTTATGGTCTTCAACTCTTCAT 57.940 37.500 0.00 0.00 0.00 2.57
2550 2792 5.879223 AGCTTATGGTCTTCAACTCTTCATG 59.121 40.000 0.00 0.00 0.00 3.07
2551 2793 5.448360 GCTTATGGTCTTCAACTCTTCATGC 60.448 44.000 0.00 0.00 0.00 4.06
2552 2794 2.783135 TGGTCTTCAACTCTTCATGCC 58.217 47.619 0.00 0.00 0.00 4.40
2553 2795 2.373169 TGGTCTTCAACTCTTCATGCCT 59.627 45.455 0.00 0.00 0.00 4.75
2554 2796 3.582647 TGGTCTTCAACTCTTCATGCCTA 59.417 43.478 0.00 0.00 0.00 3.93
2555 2797 4.187694 GGTCTTCAACTCTTCATGCCTAG 58.812 47.826 0.00 0.00 0.00 3.02
2556 2798 4.187694 GTCTTCAACTCTTCATGCCTAGG 58.812 47.826 3.67 3.67 0.00 3.02
2557 2799 4.081420 GTCTTCAACTCTTCATGCCTAGGA 60.081 45.833 14.75 0.00 0.00 2.94
2645 2887 2.922740 TTGTCCGTATATGCCCCTTC 57.077 50.000 0.00 0.00 0.00 3.46
2646 2888 2.097110 TGTCCGTATATGCCCCTTCT 57.903 50.000 0.00 0.00 0.00 2.85
2647 2889 3.247948 TGTCCGTATATGCCCCTTCTA 57.752 47.619 0.00 0.00 0.00 2.10
2648 2890 3.786553 TGTCCGTATATGCCCCTTCTAT 58.213 45.455 0.00 0.00 0.00 1.98
2649 2891 4.938028 TGTCCGTATATGCCCCTTCTATA 58.062 43.478 0.00 0.00 0.00 1.31
2650 2892 4.708421 TGTCCGTATATGCCCCTTCTATAC 59.292 45.833 0.00 0.00 0.00 1.47
2651 2893 4.099113 GTCCGTATATGCCCCTTCTATACC 59.901 50.000 0.00 0.00 0.00 2.73
2652 2894 4.028131 CCGTATATGCCCCTTCTATACCA 58.972 47.826 0.00 0.00 0.00 3.25
2653 2895 4.654262 CCGTATATGCCCCTTCTATACCAT 59.346 45.833 0.00 0.00 0.00 3.55
2654 2896 5.130477 CCGTATATGCCCCTTCTATACCATT 59.870 44.000 0.00 0.00 0.00 3.16
2655 2897 6.281405 CGTATATGCCCCTTCTATACCATTC 58.719 44.000 0.00 0.00 0.00 2.67
2656 2898 5.717119 ATATGCCCCTTCTATACCATTCC 57.283 43.478 0.00 0.00 0.00 3.01
2657 2899 2.782922 TGCCCCTTCTATACCATTCCA 58.217 47.619 0.00 0.00 0.00 3.53
2658 2900 3.335748 TGCCCCTTCTATACCATTCCAT 58.664 45.455 0.00 0.00 0.00 3.41
2659 2901 3.726859 TGCCCCTTCTATACCATTCCATT 59.273 43.478 0.00 0.00 0.00 3.16
2660 2902 4.202567 TGCCCCTTCTATACCATTCCATTC 60.203 45.833 0.00 0.00 0.00 2.67
2661 2903 4.043435 GCCCCTTCTATACCATTCCATTCT 59.957 45.833 0.00 0.00 0.00 2.40
2662 2904 5.458215 GCCCCTTCTATACCATTCCATTCTT 60.458 44.000 0.00 0.00 0.00 2.52
2663 2905 6.614657 CCCCTTCTATACCATTCCATTCTTT 58.385 40.000 0.00 0.00 0.00 2.52
2664 2906 7.069344 CCCCTTCTATACCATTCCATTCTTTT 58.931 38.462 0.00 0.00 0.00 2.27
2665 2907 7.565029 CCCCTTCTATACCATTCCATTCTTTTT 59.435 37.037 0.00 0.00 0.00 1.94
2771 3013 1.010125 CTGTCGGCACCGTGTTTTG 60.010 57.895 9.23 0.00 40.74 2.44
2968 3348 1.284785 GGGAATTGGACTGATGGACCA 59.715 52.381 0.00 0.00 0.00 4.02
2991 3371 4.082354 ACTTCTTGACACGTGGATACCTAC 60.082 45.833 21.57 1.47 0.00 3.18
3050 3430 3.480133 ACCCTAGCCACCCGCATC 61.480 66.667 0.00 0.00 41.38 3.91
3089 3469 5.717119 ACAATAGGTATTGAGCTCCCTTT 57.283 39.130 12.15 2.58 44.40 3.11
3223 3631 7.209475 GGTTTATACCATGTTATGCATTGCTT 58.791 34.615 3.54 6.23 44.36 3.91
3234 3642 8.049655 TGTTATGCATTGCTTACTGAAATACA 57.950 30.769 3.54 4.85 0.00 2.29
3584 4016 6.128336 GGCTTATCTCTGCATGCTATTACTTG 60.128 42.308 20.33 5.17 0.00 3.16
3585 4017 6.128336 GCTTATCTCTGCATGCTATTACTTGG 60.128 42.308 20.33 3.81 0.00 3.61
3588 4020 4.063689 CTCTGCATGCTATTACTTGGGAG 58.936 47.826 20.33 2.98 0.00 4.30
3643 4096 9.173939 GCATAATTGACTTTCCTAATTCATTCG 57.826 33.333 0.00 0.00 0.00 3.34
3664 4117 1.144565 CTGCAATCAGGTCGCTCTCG 61.145 60.000 0.00 0.00 36.68 4.04
3688 4141 4.631813 CCAACCACTTGAGCATAGTAGTTC 59.368 45.833 0.00 0.00 27.36 3.01
3689 4142 5.482908 CAACCACTTGAGCATAGTAGTTCT 58.517 41.667 0.00 0.00 27.36 3.01
3736 4239 7.805083 AGTGATGCTACCATAAGATCCTAAT 57.195 36.000 0.00 0.00 0.00 1.73
3759 4262 7.582667 ATTTTAGTTTGTACTTCAGGCAGTT 57.417 32.000 0.00 0.00 35.78 3.16
3764 4267 4.634012 TTGTACTTCAGGCAGTTACCAT 57.366 40.909 0.00 0.00 0.00 3.55
3769 4272 7.172342 TGTACTTCAGGCAGTTACCATTATTT 58.828 34.615 0.00 0.00 0.00 1.40
3774 4277 5.588648 TCAGGCAGTTACCATTATTTAGTGC 59.411 40.000 0.00 0.00 35.08 4.40
3812 4412 2.173569 AGACAGTCCTTGGCAGAGTTTT 59.826 45.455 0.00 0.00 37.23 2.43
3889 4527 8.015087 CGTGATTACATAACTTGCAAGAGAAAA 58.985 33.333 32.50 17.19 0.00 2.29
3929 4567 5.411361 GGTTTTGTTGAAGTTTTTGAGCCTT 59.589 36.000 0.00 0.00 0.00 4.35
3935 4573 7.781056 TGTTGAAGTTTTTGAGCCTTAATTCT 58.219 30.769 0.00 0.00 0.00 2.40
4138 4903 2.268298 CATTTGCTGCCTCATCTTTGC 58.732 47.619 0.00 0.00 0.00 3.68
4149 4914 2.358267 CTCATCTTTGCCTCCATTCAGC 59.642 50.000 0.00 0.00 0.00 4.26
4174 4939 6.423604 CACAATGTAATCTCACTGTGTGTGTA 59.576 38.462 7.79 0.30 46.27 2.90
4560 5326 3.688159 CTTGCCTGCCTTGCCACC 61.688 66.667 0.00 0.00 0.00 4.61
4650 5417 8.646004 AGCTATGCATTTCTCTTATGTCTTCTA 58.354 33.333 3.54 0.00 0.00 2.10
4653 5420 7.936950 TGCATTTCTCTTATGTCTTCTATCG 57.063 36.000 0.00 0.00 0.00 2.92
4654 5421 7.492524 TGCATTTCTCTTATGTCTTCTATCGT 58.507 34.615 0.00 0.00 0.00 3.73
4655 5422 7.981789 TGCATTTCTCTTATGTCTTCTATCGTT 59.018 33.333 0.00 0.00 0.00 3.85
4656 5423 8.484008 GCATTTCTCTTATGTCTTCTATCGTTC 58.516 37.037 0.00 0.00 0.00 3.95
4657 5424 9.521503 CATTTCTCTTATGTCTTCTATCGTTCA 57.478 33.333 0.00 0.00 0.00 3.18
4671 5438 2.466846 TCGTTCACGTTCAGAACTTCC 58.533 47.619 11.60 0.00 42.37 3.46
4672 5439 1.189446 CGTTCACGTTCAGAACTTCCG 59.811 52.381 11.60 0.67 42.37 4.30
4679 5446 2.985139 CGTTCAGAACTTCCGTAAGACC 59.015 50.000 11.60 0.00 43.02 3.85
4683 5450 3.760684 TCAGAACTTCCGTAAGACCTACC 59.239 47.826 0.00 0.00 43.02 3.18
4686 5453 3.010200 ACTTCCGTAAGACCTACCGAT 57.990 47.619 0.00 0.00 43.02 4.18
4687 5454 2.686915 ACTTCCGTAAGACCTACCGATG 59.313 50.000 0.00 0.00 43.02 3.84
4688 5455 1.027357 TCCGTAAGACCTACCGATGC 58.973 55.000 0.00 0.00 43.02 3.91
4689 5456 1.030457 CCGTAAGACCTACCGATGCT 58.970 55.000 0.00 0.00 43.02 3.79
4690 5457 2.158769 TCCGTAAGACCTACCGATGCTA 60.159 50.000 0.00 0.00 43.02 3.49
4691 5458 2.620115 CCGTAAGACCTACCGATGCTAA 59.380 50.000 0.00 0.00 43.02 3.09
4692 5459 3.549625 CCGTAAGACCTACCGATGCTAAC 60.550 52.174 0.00 0.00 43.02 2.34
4714 5481 1.629043 AGACTAGAAACGCCTGACCA 58.371 50.000 0.00 0.00 0.00 4.02
4814 5585 1.339055 CCTCGCATCCTTGTTCTTGGA 60.339 52.381 0.00 0.00 36.72 3.53
4820 5591 3.119352 GCATCCTTGTTCTTGGAACCATC 60.119 47.826 7.77 0.00 35.81 3.51
4821 5592 4.338879 CATCCTTGTTCTTGGAACCATCT 58.661 43.478 7.77 0.00 35.81 2.90
4822 5593 3.754965 TCCTTGTTCTTGGAACCATCTG 58.245 45.455 7.77 0.00 0.00 2.90
4823 5594 3.394274 TCCTTGTTCTTGGAACCATCTGA 59.606 43.478 7.77 0.00 0.00 3.27
4824 5595 4.141274 TCCTTGTTCTTGGAACCATCTGAA 60.141 41.667 7.77 0.00 0.00 3.02
4825 5596 4.022849 CCTTGTTCTTGGAACCATCTGAAC 60.023 45.833 18.39 18.39 34.67 3.18
4832 5623 2.079925 GGAACCATCTGAACTGACAGC 58.920 52.381 1.25 0.00 37.75 4.40
4850 5641 4.062293 ACAGCGTGCAGAAACTTATGTAA 58.938 39.130 0.00 0.00 0.00 2.41
4872 5667 0.316841 GAATTTTTGGGCTGCCACGA 59.683 50.000 22.05 7.00 0.00 4.35
4907 5702 1.069022 TCTGCTGTGCAATCTTTTCGC 60.069 47.619 0.00 0.00 38.41 4.70
5027 5822 2.676076 CACAGCCATTTAGCAACAACC 58.324 47.619 0.00 0.00 34.23 3.77
5037 5832 0.532862 AGCAACAACCGGAGAGTGTG 60.533 55.000 9.46 6.07 0.00 3.82
5070 5865 4.644685 AGTTTGCACAGCGGGATAAAATAT 59.355 37.500 0.00 0.00 0.00 1.28
5083 5878 6.573680 CGGGATAAAATATATGAGGACACGGT 60.574 42.308 0.00 0.00 0.00 4.83
5097 5892 4.082081 AGGACACGGTAACATGTTTATCGA 60.082 41.667 17.78 0.00 0.00 3.59
5101 5896 5.062934 ACACGGTAACATGTTTATCGATGTG 59.937 40.000 17.78 16.41 33.03 3.21
5102 5897 5.062934 CACGGTAACATGTTTATCGATGTGT 59.937 40.000 17.78 2.56 33.03 3.72
5107 5903 2.411628 TGTTTATCGATGTGTGGGGG 57.588 50.000 8.54 0.00 0.00 5.40
5333 6136 7.826744 TCTTGTTTAATGGCAGTGTACATATGA 59.173 33.333 10.38 0.00 0.00 2.15
5334 6137 8.518430 TTGTTTAATGGCAGTGTACATATGAT 57.482 30.769 10.38 0.00 0.00 2.45
5335 6138 9.620259 TTGTTTAATGGCAGTGTACATATGATA 57.380 29.630 10.38 0.00 0.00 2.15
5336 6139 9.051679 TGTTTAATGGCAGTGTACATATGATAC 57.948 33.333 10.38 8.81 0.00 2.24
5337 6140 8.504005 GTTTAATGGCAGTGTACATATGATACC 58.496 37.037 10.38 7.06 0.00 2.73
5338 6141 4.617253 TGGCAGTGTACATATGATACCC 57.383 45.455 10.38 5.83 0.00 3.69
5339 6142 4.231273 TGGCAGTGTACATATGATACCCT 58.769 43.478 10.38 2.60 0.00 4.34
5340 6143 4.283467 TGGCAGTGTACATATGATACCCTC 59.717 45.833 10.38 3.08 0.00 4.30
5341 6144 4.322801 GGCAGTGTACATATGATACCCTCC 60.323 50.000 10.38 5.58 0.00 4.30
5342 6145 4.618460 GCAGTGTACATATGATACCCTCCG 60.618 50.000 10.38 0.00 0.00 4.63
5343 6146 4.523173 CAGTGTACATATGATACCCTCCGT 59.477 45.833 10.38 0.00 0.00 4.69
5344 6147 4.765856 AGTGTACATATGATACCCTCCGTC 59.234 45.833 10.38 0.00 0.00 4.79
5345 6148 4.765856 GTGTACATATGATACCCTCCGTCT 59.234 45.833 10.38 0.00 0.00 4.18
5346 6149 4.765339 TGTACATATGATACCCTCCGTCTG 59.235 45.833 10.38 0.00 0.00 3.51
5347 6150 4.114015 ACATATGATACCCTCCGTCTGA 57.886 45.455 10.38 0.00 0.00 3.27
5348 6151 4.678256 ACATATGATACCCTCCGTCTGAT 58.322 43.478 10.38 0.00 0.00 2.90
5349 6152 5.827756 ACATATGATACCCTCCGTCTGATA 58.172 41.667 10.38 0.00 0.00 2.15
5350 6153 6.253758 ACATATGATACCCTCCGTCTGATAA 58.746 40.000 10.38 0.00 0.00 1.75
5351 6154 6.724441 ACATATGATACCCTCCGTCTGATAAA 59.276 38.462 10.38 0.00 0.00 1.40
5352 6155 7.234782 ACATATGATACCCTCCGTCTGATAAAA 59.765 37.037 10.38 0.00 0.00 1.52
5353 6156 5.531122 TGATACCCTCCGTCTGATAAAAG 57.469 43.478 0.00 0.00 0.00 2.27
5354 6157 2.693267 ACCCTCCGTCTGATAAAAGC 57.307 50.000 0.00 0.00 0.00 3.51
5355 6158 2.188817 ACCCTCCGTCTGATAAAAGCT 58.811 47.619 0.00 0.00 0.00 3.74
5356 6159 2.572104 ACCCTCCGTCTGATAAAAGCTT 59.428 45.455 0.00 0.00 0.00 3.74
5357 6160 2.939103 CCCTCCGTCTGATAAAAGCTTG 59.061 50.000 0.00 0.00 0.00 4.01
5358 6161 3.600388 CCTCCGTCTGATAAAAGCTTGT 58.400 45.455 0.00 0.00 0.00 3.16
5359 6162 3.619038 CCTCCGTCTGATAAAAGCTTGTC 59.381 47.826 0.00 0.00 0.00 3.18
5360 6163 3.596214 TCCGTCTGATAAAAGCTTGTCC 58.404 45.455 0.00 0.00 0.00 4.02
5361 6164 2.678336 CCGTCTGATAAAAGCTTGTCCC 59.322 50.000 0.00 0.00 0.00 4.46
5362 6165 3.600388 CGTCTGATAAAAGCTTGTCCCT 58.400 45.455 0.00 0.00 0.00 4.20
5363 6166 3.619038 CGTCTGATAAAAGCTTGTCCCTC 59.381 47.826 0.00 0.00 0.00 4.30
5364 6167 4.579869 GTCTGATAAAAGCTTGTCCCTCA 58.420 43.478 0.00 0.00 0.00 3.86
5365 6168 4.393371 GTCTGATAAAAGCTTGTCCCTCAC 59.607 45.833 0.00 0.00 0.00 3.51
5366 6169 4.041567 TCTGATAAAAGCTTGTCCCTCACA 59.958 41.667 0.00 0.00 0.00 3.58
5367 6170 4.922206 TGATAAAAGCTTGTCCCTCACAT 58.078 39.130 0.00 0.00 33.90 3.21
5368 6171 4.701651 TGATAAAAGCTTGTCCCTCACATG 59.298 41.667 0.00 0.00 33.90 3.21
5369 6172 1.915141 AAAGCTTGTCCCTCACATGG 58.085 50.000 0.00 0.00 33.90 3.66
5370 6173 1.067295 AAGCTTGTCCCTCACATGGA 58.933 50.000 0.00 0.00 33.90 3.41
5371 6174 1.293062 AGCTTGTCCCTCACATGGAT 58.707 50.000 0.00 0.00 33.90 3.41
5372 6175 1.064906 AGCTTGTCCCTCACATGGATG 60.065 52.381 0.00 0.00 33.90 3.51
5373 6176 1.340405 GCTTGTCCCTCACATGGATGT 60.340 52.381 0.00 0.00 42.84 3.06
5374 6177 2.092968 GCTTGTCCCTCACATGGATGTA 60.093 50.000 0.00 0.00 39.39 2.29
5375 6178 3.434167 GCTTGTCCCTCACATGGATGTAT 60.434 47.826 0.00 0.00 39.39 2.29
5376 6179 4.384056 CTTGTCCCTCACATGGATGTATC 58.616 47.826 0.00 0.00 39.39 2.24
5377 6180 3.657610 TGTCCCTCACATGGATGTATCT 58.342 45.455 0.00 0.00 39.39 1.98
5378 6181 4.814967 TGTCCCTCACATGGATGTATCTA 58.185 43.478 0.00 0.00 39.39 1.98
5379 6182 4.835056 TGTCCCTCACATGGATGTATCTAG 59.165 45.833 0.00 0.00 39.39 2.43
5380 6183 3.834813 TCCCTCACATGGATGTATCTAGC 59.165 47.826 0.00 0.00 39.39 3.42
5381 6184 3.580022 CCCTCACATGGATGTATCTAGCA 59.420 47.826 0.00 0.00 39.39 3.49
5382 6185 4.224594 CCCTCACATGGATGTATCTAGCAT 59.775 45.833 0.00 0.00 39.39 3.79
5383 6186 5.417811 CCTCACATGGATGTATCTAGCATC 58.582 45.833 0.00 1.37 39.39 3.91
5384 6187 5.046807 CCTCACATGGATGTATCTAGCATCA 60.047 44.000 9.99 0.00 43.17 3.07
5385 6188 6.423776 TCACATGGATGTATCTAGCATCAA 57.576 37.500 9.99 0.98 43.17 2.57
5386 6189 6.461640 TCACATGGATGTATCTAGCATCAAG 58.538 40.000 9.99 3.44 43.17 3.02
5387 6190 6.042437 TCACATGGATGTATCTAGCATCAAGT 59.958 38.462 9.99 3.90 43.17 3.16
5388 6191 6.147328 CACATGGATGTATCTAGCATCAAGTG 59.853 42.308 9.99 10.13 43.17 3.16
5389 6192 7.239620 ACATGGATGTATCTAGCATCAAGTGC 61.240 42.308 9.99 0.00 46.30 4.40
5403 6206 6.688637 CATCAAGTGCATCCATTTAAGAGA 57.311 37.500 0.00 0.00 0.00 3.10
5404 6207 7.273320 CATCAAGTGCATCCATTTAAGAGAT 57.727 36.000 0.00 0.00 0.00 2.75
5405 6208 8.387190 CATCAAGTGCATCCATTTAAGAGATA 57.613 34.615 0.00 0.00 0.00 1.98
5406 6209 8.843262 CATCAAGTGCATCCATTTAAGAGATAA 58.157 33.333 0.00 0.00 0.00 1.75
5407 6210 8.442632 TCAAGTGCATCCATTTAAGAGATAAG 57.557 34.615 0.00 0.00 0.00 1.73
5408 6211 6.874288 AGTGCATCCATTTAAGAGATAAGC 57.126 37.500 0.00 0.00 0.00 3.09
5409 6212 6.599445 AGTGCATCCATTTAAGAGATAAGCT 58.401 36.000 0.00 0.00 0.00 3.74
5410 6213 7.059156 AGTGCATCCATTTAAGAGATAAGCTT 58.941 34.615 3.48 3.48 0.00 3.74
5411 6214 7.013083 AGTGCATCCATTTAAGAGATAAGCTTG 59.987 37.037 9.86 0.00 0.00 4.01
5412 6215 6.263842 TGCATCCATTTAAGAGATAAGCTTGG 59.736 38.462 9.86 0.00 0.00 3.61
5413 6216 6.294397 GCATCCATTTAAGAGATAAGCTTGGG 60.294 42.308 9.86 0.00 0.00 4.12
5414 6217 6.575244 TCCATTTAAGAGATAAGCTTGGGA 57.425 37.500 9.86 0.00 0.00 4.37
5415 6218 6.357367 TCCATTTAAGAGATAAGCTTGGGAC 58.643 40.000 9.86 0.00 0.00 4.46
5416 6219 6.069673 TCCATTTAAGAGATAAGCTTGGGACA 60.070 38.462 9.86 0.00 0.00 4.02
5544 6352 8.043113 TCAAGCAGATGTGTATGTCTTAAGATT 58.957 33.333 8.75 2.40 0.00 2.40
5579 6387 0.108804 TTGTCCTGAAGATCGCCGAC 60.109 55.000 0.00 0.00 0.00 4.79
5711 7957 1.179152 TCATCAAGCAACCATGGCAG 58.821 50.000 13.04 5.55 0.00 4.85
5874 8121 0.304705 ACAAAGAAGCGACAACTGCG 59.695 50.000 0.00 0.00 37.44 5.18
5919 8166 3.053095 AGACCATCTCCAAAATGATGCCT 60.053 43.478 0.00 0.00 38.84 4.75
5924 8171 3.359033 TCTCCAAAATGATGCCTCCAAG 58.641 45.455 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 0.475906 ACTTGCTTCACTCCAGCCTT 59.524 50.000 0.00 0.00 36.33 4.35
213 231 6.996282 AGCTAAAAAGTAGTGGAAGCAGTTTA 59.004 34.615 0.00 0.00 0.00 2.01
214 232 5.828328 AGCTAAAAAGTAGTGGAAGCAGTTT 59.172 36.000 0.00 0.00 0.00 2.66
230 251 4.911514 AACGAAGGAAGCAAGCTAAAAA 57.088 36.364 0.00 0.00 0.00 1.94
249 271 5.735766 AGAACATAGGCTAACTGAGGAAAC 58.264 41.667 0.00 0.00 0.00 2.78
250 272 6.213600 AGAAGAACATAGGCTAACTGAGGAAA 59.786 38.462 0.00 0.00 0.00 3.13
293 320 8.574737 TCAGACAGAGACATACATCATGATTAG 58.425 37.037 5.16 0.00 38.10 1.73
341 374 0.031616 AAACAAGAACCCAGCCCCAA 60.032 50.000 0.00 0.00 0.00 4.12
342 375 0.031616 AAAACAAGAACCCAGCCCCA 60.032 50.000 0.00 0.00 0.00 4.96
444 486 4.345257 CCTATGCAACTGTCACTACCCTAT 59.655 45.833 0.00 0.00 0.00 2.57
463 505 2.132686 ACATAAAACTCCGCCCCCTAT 58.867 47.619 0.00 0.00 0.00 2.57
471 517 5.739161 GCTAAAGATGCAACATAAAACTCCG 59.261 40.000 0.00 0.00 0.00 4.63
495 543 6.028368 TGTCTTACGATAAAGCGAGAAGAAG 58.972 40.000 9.89 0.54 37.96 2.85
529 582 7.122650 AGCATTCTCTCCGATTTCCATTAAAAA 59.877 33.333 0.00 0.00 0.00 1.94
577 630 1.005394 GTCCGTGGGAATGTCGTGT 60.005 57.895 0.00 0.00 31.38 4.49
715 776 1.990060 CACAGATCCGTGGACCCCT 60.990 63.158 0.76 0.00 33.05 4.79
732 793 2.930019 CCCCACCTCCTGTCAGCA 60.930 66.667 0.00 0.00 0.00 4.41
741 802 2.750350 CCGATATGGCCCCACCTC 59.250 66.667 0.00 0.00 40.22 3.85
750 811 2.032528 ATGCACCGCCCGATATGG 59.967 61.111 0.00 0.00 37.55 2.74
752 813 1.597854 CACATGCACCGCCCGATAT 60.598 57.895 0.00 0.00 0.00 1.63
753 814 2.203001 CACATGCACCGCCCGATA 60.203 61.111 0.00 0.00 0.00 2.92
811 872 2.774439 TTGAACTTCCGAAGCTTTGC 57.226 45.000 8.32 0.00 0.00 3.68
1485 1576 1.390926 GGGGGTGAGGGAGTAGTCA 59.609 63.158 0.00 0.00 0.00 3.41
1942 2034 3.014623 CTGGTGTACACTGACCTCGATA 58.985 50.000 24.55 0.00 32.98 2.92
1997 2089 6.521151 AATTGGAATTGAGCTAAAGTGGAG 57.479 37.500 0.00 0.00 0.00 3.86
2083 2175 4.898320 TCTGCAGTACAATGTGACTTCAT 58.102 39.130 14.67 0.00 0.00 2.57
2173 2265 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2174 2266 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2175 2267 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2176 2268 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2177 2269 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2178 2270 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2179 2271 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2180 2272 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2181 2273 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2182 2274 1.533299 GAACACACACACACACACACA 59.467 47.619 0.00 0.00 0.00 3.72
2183 2275 1.463363 CGAACACACACACACACACAC 60.463 52.381 0.00 0.00 0.00 3.82
2184 2276 0.793250 CGAACACACACACACACACA 59.207 50.000 0.00 0.00 0.00 3.72
2185 2277 0.096281 CCGAACACACACACACACAC 59.904 55.000 0.00 0.00 0.00 3.82
2186 2278 1.640210 GCCGAACACACACACACACA 61.640 55.000 0.00 0.00 0.00 3.72
2195 2287 1.491563 CTTAGCACGCCGAACACAC 59.508 57.895 0.00 0.00 0.00 3.82
2211 2303 1.138568 ATAGCTGGATCTGCTGCCTT 58.861 50.000 19.04 4.12 38.96 4.35
2235 2327 7.410120 ACTATCCCCTGCAAAATTTAAGAAG 57.590 36.000 0.00 0.00 0.00 2.85
2465 2703 8.457238 AGCATAACTGAAGATATTTCCCTTTC 57.543 34.615 0.00 0.00 0.00 2.62
2541 2783 4.415596 CTCCTATCCTAGGCATGAAGAGT 58.584 47.826 2.96 0.00 45.82 3.24
2542 2784 3.768757 CCTCCTATCCTAGGCATGAAGAG 59.231 52.174 2.96 5.26 45.82 2.85
2552 2794 4.322349 GCTACAATGTGCCTCCTATCCTAG 60.322 50.000 0.00 0.00 0.00 3.02
2553 2795 3.578716 GCTACAATGTGCCTCCTATCCTA 59.421 47.826 0.00 0.00 0.00 2.94
2554 2796 2.370189 GCTACAATGTGCCTCCTATCCT 59.630 50.000 0.00 0.00 0.00 3.24
2555 2797 2.104792 TGCTACAATGTGCCTCCTATCC 59.895 50.000 0.00 0.00 0.00 2.59
2556 2798 3.475566 TGCTACAATGTGCCTCCTATC 57.524 47.619 0.00 0.00 0.00 2.08
2557 2799 3.931907 TTGCTACAATGTGCCTCCTAT 57.068 42.857 0.00 0.00 0.00 2.57
2664 2906 2.445682 ATGGTATAGCCCCGCAAAAA 57.554 45.000 0.00 0.00 36.04 1.94
2665 2907 2.303175 GAATGGTATAGCCCCGCAAAA 58.697 47.619 0.00 0.00 36.04 2.44
2666 2908 1.477923 GGAATGGTATAGCCCCGCAAA 60.478 52.381 0.00 0.00 36.04 3.68
2667 2909 0.109723 GGAATGGTATAGCCCCGCAA 59.890 55.000 0.00 0.00 36.04 4.85
2668 2910 1.057275 TGGAATGGTATAGCCCCGCA 61.057 55.000 0.00 0.00 36.04 5.69
2669 2911 0.328258 ATGGAATGGTATAGCCCCGC 59.672 55.000 0.00 0.00 36.04 6.13
2670 2912 2.039746 TGAATGGAATGGTATAGCCCCG 59.960 50.000 0.00 0.00 36.04 5.73
2671 2913 3.806949 TGAATGGAATGGTATAGCCCC 57.193 47.619 0.00 0.00 36.04 5.80
2672 2914 6.012745 AGATTTGAATGGAATGGTATAGCCC 58.987 40.000 0.00 0.00 36.04 5.19
2673 2915 8.635765 TTAGATTTGAATGGAATGGTATAGCC 57.364 34.615 0.00 0.00 37.90 3.93
2674 2916 8.239998 GCTTAGATTTGAATGGAATGGTATAGC 58.760 37.037 0.00 0.00 0.00 2.97
2675 2917 9.512588 AGCTTAGATTTGAATGGAATGGTATAG 57.487 33.333 0.00 0.00 0.00 1.31
2771 3013 5.122396 AGTTGCGTATCAAAATCTTCAGGTC 59.878 40.000 0.00 0.00 36.26 3.85
2968 3348 2.897969 AGGTATCCACGTGTCAAGAAGT 59.102 45.455 15.65 0.00 0.00 3.01
2991 3371 0.543277 TGCACATTCCTAGAGCCCTG 59.457 55.000 0.00 0.00 0.00 4.45
3050 3430 2.672961 TGTATGGCTGGTTCTCTTCG 57.327 50.000 0.00 0.00 0.00 3.79
3223 3631 5.586243 GGATGCTTGAAGCTGTATTTCAGTA 59.414 40.000 18.94 0.00 45.23 2.74
3234 3642 0.251474 TTGCAGGGATGCTTGAAGCT 60.251 50.000 18.94 3.75 42.97 3.74
3358 3768 9.265901 GAAAATGCATCATAGAAGAGCTTAGTA 57.734 33.333 0.00 0.00 0.00 1.82
3545 3973 8.628280 GCAGAGATAAGCCTTTAATGAGAAAAT 58.372 33.333 0.00 0.00 0.00 1.82
3664 4117 1.826385 ACTATGCTCAAGTGGTTGGC 58.174 50.000 0.00 0.00 34.09 4.52
3688 4141 8.454106 ACTTTTATGTTCCAAATCGAAGATGAG 58.546 33.333 0.00 0.00 45.12 2.90
3689 4142 8.236586 CACTTTTATGTTCCAAATCGAAGATGA 58.763 33.333 0.00 0.00 45.12 2.92
3736 4239 7.012610 GGTAACTGCCTGAAGTACAAACTAAAA 59.987 37.037 0.00 0.00 33.75 1.52
3747 4250 7.336931 CACTAAATAATGGTAACTGCCTGAAGT 59.663 37.037 0.00 0.00 37.61 3.01
3759 4262 7.617723 AGTCAAAATGGGCACTAAATAATGGTA 59.382 33.333 0.00 0.00 0.00 3.25
3764 4267 6.268847 ACCAAGTCAAAATGGGCACTAAATAA 59.731 34.615 0.00 0.00 41.17 1.40
3769 4272 3.237268 ACCAAGTCAAAATGGGCACTA 57.763 42.857 0.00 0.00 41.17 2.74
3774 4277 4.827284 ACTGTCTAACCAAGTCAAAATGGG 59.173 41.667 0.00 0.00 41.17 4.00
3889 4527 2.159179 AACCACAAAAAGGGCTCTGT 57.841 45.000 0.00 0.00 0.00 3.41
3935 4573 8.956426 GTGGTCAAGAATAAGAAAATATCACCA 58.044 33.333 0.00 0.00 0.00 4.17
4017 4741 5.296283 AGAATATGTCATGCTGTTCTGAAGC 59.704 40.000 0.00 0.00 41.22 3.86
4126 4891 1.680207 GAATGGAGGCAAAGATGAGGC 59.320 52.381 0.00 0.00 0.00 4.70
4138 4903 4.885907 AGATTACATTGTGCTGAATGGAGG 59.114 41.667 11.45 0.00 37.60 4.30
4174 4939 4.524053 TCTGCATGATGCTGAAAGAGATT 58.476 39.130 22.10 0.00 46.01 2.40
4560 5326 1.444553 GCACGAGGACTCCTTGTCG 60.445 63.158 14.48 9.02 44.34 4.35
4650 5417 3.057734 GGAAGTTCTGAACGTGAACGAT 58.942 45.455 13.57 0.00 45.84 3.73
4652 5419 1.189446 CGGAAGTTCTGAACGTGAACG 59.811 52.381 13.57 10.92 45.84 3.95
4653 5420 2.199236 ACGGAAGTTCTGAACGTGAAC 58.801 47.619 18.72 8.74 46.40 3.18
4654 5421 2.589798 ACGGAAGTTCTGAACGTGAA 57.410 45.000 18.72 0.00 46.40 3.18
4655 5422 3.316029 TCTTACGGAAGTTCTGAACGTGA 59.684 43.478 18.72 7.56 46.40 4.35
4656 5423 3.424529 GTCTTACGGAAGTTCTGAACGTG 59.575 47.826 18.72 7.98 46.40 4.49
4657 5424 3.551659 GGTCTTACGGAAGTTCTGAACGT 60.552 47.826 18.72 13.45 46.40 3.99
4671 5438 3.625938 GTTAGCATCGGTAGGTCTTACG 58.374 50.000 0.00 0.00 32.79 3.18
4672 5439 3.313526 TCGTTAGCATCGGTAGGTCTTAC 59.686 47.826 0.00 0.00 0.00 2.34
4679 5446 3.694535 AGTCTTCGTTAGCATCGGTAG 57.305 47.619 0.00 0.00 0.00 3.18
4683 5450 4.202558 CGTTTCTAGTCTTCGTTAGCATCG 59.797 45.833 0.00 0.00 0.00 3.84
4686 5453 3.240069 GCGTTTCTAGTCTTCGTTAGCA 58.760 45.455 0.00 0.00 0.00 3.49
4687 5454 2.597748 GGCGTTTCTAGTCTTCGTTAGC 59.402 50.000 0.00 0.00 0.00 3.09
4688 5455 3.852536 CAGGCGTTTCTAGTCTTCGTTAG 59.147 47.826 0.00 0.00 0.00 2.34
4689 5456 3.503363 TCAGGCGTTTCTAGTCTTCGTTA 59.497 43.478 0.00 0.00 0.00 3.18
4690 5457 2.295349 TCAGGCGTTTCTAGTCTTCGTT 59.705 45.455 0.00 0.00 0.00 3.85
4691 5458 1.884579 TCAGGCGTTTCTAGTCTTCGT 59.115 47.619 0.00 0.00 0.00 3.85
4692 5459 2.251893 GTCAGGCGTTTCTAGTCTTCG 58.748 52.381 0.00 0.00 0.00 3.79
4757 5524 2.768253 AACATTCAGGCAGATCGTCA 57.232 45.000 0.00 0.00 0.00 4.35
4814 5585 1.070758 ACGCTGTCAGTTCAGATGGTT 59.929 47.619 0.93 0.00 37.61 3.67
4820 5591 0.598419 TCTGCACGCTGTCAGTTCAG 60.598 55.000 0.93 4.47 34.88 3.02
4821 5592 0.179086 TTCTGCACGCTGTCAGTTCA 60.179 50.000 0.93 0.00 0.00 3.18
4822 5593 0.937304 TTTCTGCACGCTGTCAGTTC 59.063 50.000 0.93 0.00 0.00 3.01
4823 5594 0.657840 GTTTCTGCACGCTGTCAGTT 59.342 50.000 0.93 0.00 0.00 3.16
4824 5595 0.179073 AGTTTCTGCACGCTGTCAGT 60.179 50.000 0.93 0.00 0.00 3.41
4825 5596 0.940126 AAGTTTCTGCACGCTGTCAG 59.060 50.000 0.00 0.00 0.00 3.51
4832 5623 5.839262 TCAGTTACATAAGTTTCTGCACG 57.161 39.130 0.00 0.00 31.76 5.34
4850 5641 1.070601 GTGGCAGCCCAAAAATTCAGT 59.929 47.619 9.64 0.00 44.33 3.41
4861 5655 3.291101 TTAGTCGTCGTGGCAGCCC 62.291 63.158 9.64 0.00 0.00 5.19
4872 5667 3.006967 ACAGCAGAAGGAATGTTAGTCGT 59.993 43.478 0.00 0.00 0.00 4.34
4907 5702 2.125753 GCCACTCCAGACTCTGCG 60.126 66.667 0.00 0.00 0.00 5.18
5027 5822 1.028330 AATGGCATGCACACTCTCCG 61.028 55.000 21.36 0.00 0.00 4.63
5037 5832 2.264813 CTGTGCAAACTAATGGCATGC 58.735 47.619 9.90 9.90 40.05 4.06
5070 5865 4.811969 AACATGTTACCGTGTCCTCATA 57.188 40.909 9.97 0.00 39.93 2.15
5083 5878 4.878971 CCCCACACATCGATAAACATGTTA 59.121 41.667 12.39 0.87 30.48 2.41
5097 5892 1.485066 GTTACGATCTCCCCCACACAT 59.515 52.381 0.00 0.00 0.00 3.21
5101 5896 0.179081 GCAGTTACGATCTCCCCCAC 60.179 60.000 0.00 0.00 0.00 4.61
5102 5897 0.616395 TGCAGTTACGATCTCCCCCA 60.616 55.000 0.00 0.00 0.00 4.96
5107 5903 4.563184 ACGAAATTCTGCAGTTACGATCTC 59.437 41.667 14.67 0.63 0.00 2.75
5333 6136 3.967987 AGCTTTTATCAGACGGAGGGTAT 59.032 43.478 0.00 0.00 0.00 2.73
5334 6137 3.371965 AGCTTTTATCAGACGGAGGGTA 58.628 45.455 0.00 0.00 0.00 3.69
5335 6138 2.188817 AGCTTTTATCAGACGGAGGGT 58.811 47.619 0.00 0.00 0.00 4.34
5336 6139 2.939103 CAAGCTTTTATCAGACGGAGGG 59.061 50.000 0.00 0.00 0.00 4.30
5337 6140 3.600388 ACAAGCTTTTATCAGACGGAGG 58.400 45.455 0.00 0.00 0.00 4.30
5338 6141 3.619038 GGACAAGCTTTTATCAGACGGAG 59.381 47.826 0.00 0.00 0.00 4.63
5339 6142 3.596214 GGACAAGCTTTTATCAGACGGA 58.404 45.455 0.00 0.00 0.00 4.69
5340 6143 2.678336 GGGACAAGCTTTTATCAGACGG 59.322 50.000 0.00 0.00 0.00 4.79
5341 6144 3.600388 AGGGACAAGCTTTTATCAGACG 58.400 45.455 0.00 0.00 0.00 4.18
5342 6145 4.393371 GTGAGGGACAAGCTTTTATCAGAC 59.607 45.833 0.00 0.00 0.00 3.51
5343 6146 4.041567 TGTGAGGGACAAGCTTTTATCAGA 59.958 41.667 0.00 0.00 0.00 3.27
5344 6147 4.326826 TGTGAGGGACAAGCTTTTATCAG 58.673 43.478 0.00 0.00 0.00 2.90
5345 6148 4.365514 TGTGAGGGACAAGCTTTTATCA 57.634 40.909 0.00 0.00 0.00 2.15
5346 6149 4.096984 CCATGTGAGGGACAAGCTTTTATC 59.903 45.833 0.00 0.00 38.36 1.75
5347 6150 4.019174 CCATGTGAGGGACAAGCTTTTAT 58.981 43.478 0.00 0.00 38.36 1.40
5348 6151 3.073798 TCCATGTGAGGGACAAGCTTTTA 59.926 43.478 0.00 0.00 38.36 1.52
5349 6152 2.158475 TCCATGTGAGGGACAAGCTTTT 60.158 45.455 0.00 0.00 38.36 2.27
5350 6153 1.425066 TCCATGTGAGGGACAAGCTTT 59.575 47.619 0.00 0.00 38.36 3.51
5351 6154 1.067295 TCCATGTGAGGGACAAGCTT 58.933 50.000 0.00 0.00 38.36 3.74
5352 6155 1.064906 CATCCATGTGAGGGACAAGCT 60.065 52.381 0.00 0.00 38.36 3.74
5353 6156 1.340405 ACATCCATGTGAGGGACAAGC 60.340 52.381 0.00 0.00 40.03 4.01
5354 6157 2.795231 ACATCCATGTGAGGGACAAG 57.205 50.000 0.00 0.00 40.03 3.16
5355 6158 4.040047 AGATACATCCATGTGAGGGACAA 58.960 43.478 2.26 0.00 41.89 3.18
5356 6159 3.657610 AGATACATCCATGTGAGGGACA 58.342 45.455 2.26 0.00 41.89 4.02
5357 6160 4.322349 GCTAGATACATCCATGTGAGGGAC 60.322 50.000 2.26 0.00 41.89 4.46
5358 6161 3.834813 GCTAGATACATCCATGTGAGGGA 59.165 47.826 2.26 0.00 41.89 4.20
5359 6162 3.580022 TGCTAGATACATCCATGTGAGGG 59.420 47.826 2.26 0.00 41.89 4.30
5360 6163 4.879197 TGCTAGATACATCCATGTGAGG 57.121 45.455 2.26 0.00 41.89 3.86
5361 6164 6.034161 TGATGCTAGATACATCCATGTGAG 57.966 41.667 2.26 0.00 42.68 3.51
5362 6165 6.042437 ACTTGATGCTAGATACATCCATGTGA 59.958 38.462 2.26 0.00 42.68 3.58
5363 6166 6.147328 CACTTGATGCTAGATACATCCATGTG 59.853 42.308 2.26 3.45 42.68 3.21
5364 6167 6.228995 CACTTGATGCTAGATACATCCATGT 58.771 40.000 0.00 0.00 42.68 3.21
5365 6168 6.723131 CACTTGATGCTAGATACATCCATG 57.277 41.667 0.00 0.00 42.68 3.66
5380 6183 6.688637 TCTCTTAAATGGATGCACTTGATG 57.311 37.500 0.00 0.00 0.00 3.07
5381 6184 8.985315 TTATCTCTTAAATGGATGCACTTGAT 57.015 30.769 0.00 0.00 0.00 2.57
5382 6185 7.012704 GCTTATCTCTTAAATGGATGCACTTGA 59.987 37.037 0.00 0.00 0.00 3.02
5383 6186 7.013083 AGCTTATCTCTTAAATGGATGCACTTG 59.987 37.037 0.00 0.00 0.00 3.16
5384 6187 7.059156 AGCTTATCTCTTAAATGGATGCACTT 58.941 34.615 0.00 0.00 0.00 3.16
5385 6188 6.599445 AGCTTATCTCTTAAATGGATGCACT 58.401 36.000 0.00 0.00 0.00 4.40
5386 6189 6.874288 AGCTTATCTCTTAAATGGATGCAC 57.126 37.500 0.00 0.00 0.00 4.57
5387 6190 6.263842 CCAAGCTTATCTCTTAAATGGATGCA 59.736 38.462 0.00 0.00 0.00 3.96
5388 6191 6.294397 CCCAAGCTTATCTCTTAAATGGATGC 60.294 42.308 0.00 0.00 0.00 3.91
5389 6192 7.000472 TCCCAAGCTTATCTCTTAAATGGATG 59.000 38.462 0.00 0.00 0.00 3.51
5390 6193 7.001073 GTCCCAAGCTTATCTCTTAAATGGAT 58.999 38.462 0.00 0.00 0.00 3.41
5391 6194 6.069673 TGTCCCAAGCTTATCTCTTAAATGGA 60.070 38.462 0.00 0.00 0.00 3.41
5392 6195 6.122277 TGTCCCAAGCTTATCTCTTAAATGG 58.878 40.000 0.00 0.00 0.00 3.16
5393 6196 7.554118 TCTTGTCCCAAGCTTATCTCTTAAATG 59.446 37.037 0.00 0.00 0.00 2.32
5394 6197 7.554476 GTCTTGTCCCAAGCTTATCTCTTAAAT 59.446 37.037 0.00 0.00 0.00 1.40
5395 6198 6.879458 GTCTTGTCCCAAGCTTATCTCTTAAA 59.121 38.462 0.00 0.00 0.00 1.52
5396 6199 6.213600 AGTCTTGTCCCAAGCTTATCTCTTAA 59.786 38.462 0.00 0.00 0.00 1.85
5397 6200 5.721960 AGTCTTGTCCCAAGCTTATCTCTTA 59.278 40.000 0.00 0.00 0.00 2.10
5398 6201 4.534103 AGTCTTGTCCCAAGCTTATCTCTT 59.466 41.667 0.00 0.00 0.00 2.85
5399 6202 4.081198 CAGTCTTGTCCCAAGCTTATCTCT 60.081 45.833 0.00 0.00 0.00 3.10
5400 6203 4.081420 TCAGTCTTGTCCCAAGCTTATCTC 60.081 45.833 0.00 0.00 0.00 2.75
5401 6204 3.840666 TCAGTCTTGTCCCAAGCTTATCT 59.159 43.478 0.00 0.00 0.00 1.98
5402 6205 4.187694 CTCAGTCTTGTCCCAAGCTTATC 58.812 47.826 0.00 0.00 0.00 1.75
5403 6206 3.054802 CCTCAGTCTTGTCCCAAGCTTAT 60.055 47.826 0.00 0.00 0.00 1.73
5404 6207 2.303022 CCTCAGTCTTGTCCCAAGCTTA 59.697 50.000 0.00 0.00 0.00 3.09
5405 6208 1.072965 CCTCAGTCTTGTCCCAAGCTT 59.927 52.381 0.00 0.00 0.00 3.74
5406 6209 0.689623 CCTCAGTCTTGTCCCAAGCT 59.310 55.000 0.00 0.00 0.00 3.74
5407 6210 0.322008 CCCTCAGTCTTGTCCCAAGC 60.322 60.000 0.00 0.00 0.00 4.01
5408 6211 1.277557 CTCCCTCAGTCTTGTCCCAAG 59.722 57.143 0.00 0.00 0.00 3.61
5409 6212 1.352083 CTCCCTCAGTCTTGTCCCAA 58.648 55.000 0.00 0.00 0.00 4.12
5410 6213 0.191064 ACTCCCTCAGTCTTGTCCCA 59.809 55.000 0.00 0.00 0.00 4.37
5411 6214 1.826096 GTACTCCCTCAGTCTTGTCCC 59.174 57.143 0.00 0.00 36.43 4.46
5412 6215 2.810164 AGTACTCCCTCAGTCTTGTCC 58.190 52.381 0.00 0.00 36.43 4.02
5413 6216 4.875561 AAAGTACTCCCTCAGTCTTGTC 57.124 45.455 0.00 0.00 36.43 3.18
5414 6217 5.632034 AAAAAGTACTCCCTCAGTCTTGT 57.368 39.130 0.00 0.00 36.43 3.16
5473 6278 4.826274 AATCTGAAATCCGAGACCTTCA 57.174 40.909 0.00 0.00 0.00 3.02
5544 6352 3.776969 AGGACAAGCACATCTCCTTATCA 59.223 43.478 0.00 0.00 27.83 2.15
5579 6387 4.270808 GTCAAACTGGGCATTTTCTTTGTG 59.729 41.667 0.00 0.00 0.00 3.33
5618 7859 1.804748 GATCAGGTGGTGGAAAACGAC 59.195 52.381 0.00 0.00 36.81 4.34
5622 7863 1.547675 GCTGGATCAGGTGGTGGAAAA 60.548 52.381 0.00 0.00 31.21 2.29
5711 7957 3.030291 TGGCAAATGGTGTGAATATCCC 58.970 45.455 0.00 0.00 0.00 3.85
5874 8121 1.668101 CTGGAGGGAGCCGTAGTGTC 61.668 65.000 0.00 0.00 0.00 3.67
5919 8166 3.766691 GCCGCGTACCCTCTTGGA 61.767 66.667 4.92 0.00 38.00 3.53
5924 8171 2.890474 CATGTGCCGCGTACCCTC 60.890 66.667 4.92 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.