Multiple sequence alignment - TraesCS2D01G318100

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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 TraesCS2D01G318100 chr2D 100.000 9275 0 0 1 9275 407960521 407969795 0.000000e+00 17128.0
1 TraesCS2D01G318100 chr2D 93.196 485 31 2 19 502 561904579 561905062 0.000000e+00 712.0
2 TraesCS2D01G318100 chr2D 90.000 50 3 2 7235 7282 394522374 394522325 7.780000e-06 63.9
3 TraesCS2D01G318100 chr2A 95.230 3606 110 18 528 4105 575598454 575602025 0.000000e+00 5650.0
4 TraesCS2D01G318100 chr2A 94.750 3257 77 21 4102 7302 575602127 575605345 0.000000e+00 4981.0
5 TraesCS2D01G318100 chr2A 93.887 1047 48 11 7739 8776 575605982 575607021 0.000000e+00 1565.0
6 TraesCS2D01G318100 chr2A 95.465 419 15 3 8859 9275 575607047 575607463 0.000000e+00 665.0
7 TraesCS2D01G318100 chr2A 95.420 262 9 3 7481 7740 575605560 575605820 1.860000e-111 414.0
8 TraesCS2D01G318100 chr2B 94.716 3615 112 30 531 4105 483449381 483452956 0.000000e+00 5544.0
9 TraesCS2D01G318100 chr2B 95.685 1854 59 7 5432 7282 483454456 483456291 0.000000e+00 2961.0
10 TraesCS2D01G318100 chr2B 92.742 1557 70 22 7284 8824 483456454 483457983 0.000000e+00 2209.0
11 TraesCS2D01G318100 chr2B 95.585 1359 31 6 4102 5436 483453036 483454389 0.000000e+00 2150.0
12 TraesCS2D01G318100 chr2B 92.365 406 20 5 8872 9275 483458083 483458479 1.350000e-157 568.0
13 TraesCS2D01G318100 chr2B 98.438 64 1 0 8795 8858 779340575 779340638 7.610000e-21 113.0
14 TraesCS2D01G318100 chr2B 85.870 92 5 5 7415 7498 749227916 749228007 3.570000e-14 91.6
15 TraesCS2D01G318100 chr5D 93.529 510 23 5 1 502 170318397 170318904 0.000000e+00 750.0
16 TraesCS2D01G318100 chr6D 93.267 505 27 6 1 502 448624942 448625442 0.000000e+00 737.0
17 TraesCS2D01G318100 chr6D 93.210 486 27 6 20 502 40537513 40537031 0.000000e+00 710.0
18 TraesCS2D01G318100 chr6D 92.110 507 32 6 1 501 422220745 422221249 0.000000e+00 708.0
19 TraesCS2D01G318100 chr5A 92.172 511 30 5 1 502 296306508 296307017 0.000000e+00 713.0
20 TraesCS2D01G318100 chr5A 82.474 97 14 3 7003 7098 703316124 703316030 2.150000e-11 82.4
21 TraesCS2D01G318100 chrUn 93.388 484 25 4 19 502 97635749 97635273 0.000000e+00 710.0
22 TraesCS2D01G318100 chr6A 92.369 498 32 3 9 500 578542202 578541705 0.000000e+00 704.0
23 TraesCS2D01G318100 chr6A 81.102 254 31 14 7237 7480 448048378 448048624 4.420000e-43 187.0
24 TraesCS2D01G318100 chr3A 91.881 505 35 5 1 501 585062152 585062654 0.000000e+00 701.0
25 TraesCS2D01G318100 chr6B 81.347 193 25 7 7258 7444 515211325 515211138 7.510000e-31 147.0
26 TraesCS2D01G318100 chr6B 97.143 35 0 1 7235 7269 670981442 670981475 3.620000e-04 58.4
27 TraesCS2D01G318100 chr4B 80.645 186 22 7 7349 7523 432819333 432819151 2.100000e-26 132.0
28 TraesCS2D01G318100 chr4B 94.118 68 4 0 8791 8858 404127558 404127625 4.580000e-18 104.0
29 TraesCS2D01G318100 chr4B 79.646 113 17 5 7229 7338 72662270 72662379 9.990000e-10 76.8
30 TraesCS2D01G318100 chr4D 83.553 152 12 9 7382 7520 479313332 479313181 7.560000e-26 130.0
31 TraesCS2D01G318100 chr4D 77.523 218 32 15 6926 7138 506932247 506932042 2.120000e-21 115.0
32 TraesCS2D01G318100 chr4A 78.495 186 27 6 7349 7523 115285398 115285581 9.850000e-20 110.0
33 TraesCS2D01G318100 chr4A 89.189 74 7 1 7449 7521 1071696 1071623 3.570000e-14 91.6
34 TraesCS2D01G318100 chr1D 98.387 62 1 0 8797 8858 205490290 205490351 9.850000e-20 110.0
35 TraesCS2D01G318100 chr5B 98.361 61 1 0 8798 8858 460658924 460658984 3.540000e-19 108.0
36 TraesCS2D01G318100 chr5B 78.788 99 20 1 7236 7333 366497225 366497323 2.160000e-06 65.8
37 TraesCS2D01G318100 chr3B 98.361 61 1 0 8798 8858 127932637 127932697 3.540000e-19 108.0
38 TraesCS2D01G318100 chr3B 73.899 318 44 19 7237 7515 83913066 83913383 3.570000e-14 91.6
39 TraesCS2D01G318100 chr3B 76.374 182 28 11 6926 7102 800710295 800710124 5.970000e-12 84.2
40 TraesCS2D01G318100 chr7B 96.774 62 2 0 8797 8858 511462093 511462154 4.580000e-18 104.0
41 TraesCS2D01G318100 chr7B 96.774 62 2 0 8797 8858 648913927 648913866 4.580000e-18 104.0
42 TraesCS2D01G318100 chr1A 96.825 63 1 1 8797 8858 463825451 463825389 4.580000e-18 104.0
43 TraesCS2D01G318100 chr3D 96.721 61 2 0 8798 8858 107672334 107672274 1.650000e-17 102.0
44 TraesCS2D01G318100 chr3D 86.517 89 7 4 7415 7498 606934785 606934873 9.920000e-15 93.5
45 TraesCS2D01G318100 chr7A 80.488 123 13 8 7409 7521 692498417 692498296 5.970000e-12 84.2


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 TraesCS2D01G318100 chr2D 407960521 407969795 9274 False 17128.0 17128 100.0000 1 9275 1 chr2D.!!$F1 9274
1 TraesCS2D01G318100 chr2A 575598454 575607463 9009 False 2655.0 5650 94.9504 528 9275 5 chr2A.!!$F1 8747
2 TraesCS2D01G318100 chr2B 483449381 483458479 9098 False 2686.4 5544 94.2186 531 9275 5 chr2B.!!$F3 8744
3 TraesCS2D01G318100 chr5D 170318397 170318904 507 False 750.0 750 93.5290 1 502 1 chr5D.!!$F1 501
4 TraesCS2D01G318100 chr6D 448624942 448625442 500 False 737.0 737 93.2670 1 502 1 chr6D.!!$F2 501
5 TraesCS2D01G318100 chr6D 422220745 422221249 504 False 708.0 708 92.1100 1 501 1 chr6D.!!$F1 500
6 TraesCS2D01G318100 chr5A 296306508 296307017 509 False 713.0 713 92.1720 1 502 1 chr5A.!!$F1 501
7 TraesCS2D01G318100 chr3A 585062152 585062654 502 False 701.0 701 91.8810 1 501 1 chr3A.!!$F1 500

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
507 520 0.037232 AAGTGGAGTGTTCTAGGCGC 60.037 55.000 0.00 0.00 0.00 6.53 F
1312 1363 0.036022 AGCAGGCTTCAGTGAAGTCC 59.964 55.000 29.34 27.57 44.36 3.85 F
1593 1644 1.714794 ACTCTGCTCGCATAACACAC 58.285 50.000 0.00 0.00 0.00 3.82 F
1914 1973 2.898181 TGCATGTTATGTGAAGCACG 57.102 45.000 0.00 0.00 37.14 5.34 F
2927 2986 1.482593 GCTGCATATCGGCTAGGGTAT 59.517 52.381 0.00 0.00 43.74 2.73 F
3693 3755 2.076100 TCAATGTCAAGTCATGTCGCC 58.924 47.619 0.00 0.00 0.00 5.54 F
4509 4676 1.964552 CCCAGATCCAAGCATCACTC 58.035 55.000 0.00 0.00 0.00 3.51 F
5201 5385 2.545526 CACGTTGCTCACTGTTGAAGAT 59.454 45.455 0.00 0.00 0.00 2.40 F
5944 6212 3.198635 TGAATTGAGGGAGGTCAGTCATC 59.801 47.826 0.00 0.00 0.00 2.92 F
7265 7536 0.108774 TACCCCACATGTTGTTGCGA 59.891 50.000 0.00 0.00 0.00 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1778 1833 0.251922 AACACATGCAGCCCCAGAAT 60.252 50.000 0.00 0.00 0.00 2.40 R
2726 2785 0.549902 TCTTCCCAAGCATCCCCTCA 60.550 55.000 0.00 0.00 0.00 3.86 R
2907 2966 0.895530 TACCCTAGCCGATATGCAGC 59.104 55.000 0.00 0.00 0.00 5.25 R
3506 3568 3.706086 ACATGCAAGGTTTTCTTTCAGGT 59.294 39.130 0.00 0.00 38.42 4.00 R
4251 4418 0.532115 TAGCAATCTCGCTGTGCAGA 59.468 50.000 3.02 0.00 43.68 4.26 R
4868 5039 2.620585 GTGCTCCATTTCCCTTATGAGC 59.379 50.000 0.00 0.00 35.27 4.26 R
5711 5979 0.318955 GGCTGACACCATGCAAACAC 60.319 55.000 0.00 0.00 0.00 3.32 R
6064 6332 3.005554 CTGACAATCTTCTTCATGCCGT 58.994 45.455 0.00 0.00 0.00 5.68 R
7444 7876 1.491754 TGCTACCTCATCATGCATGGT 59.508 47.619 25.97 17.67 32.64 3.55 R
8603 9243 2.163412 GTGCCATGGCGAAAATAAGTCA 59.837 45.455 30.87 6.56 45.51 3.41 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
328 341 9.177608 CTATCAACATGGGATCTAGTTTTGAAA 57.822 33.333 5.52 0.00 0.00 2.69
339 352 4.986034 TCTAGTTTTGAAAATCTCGACGCA 59.014 37.500 0.00 0.00 0.00 5.24
352 365 1.066502 TCGACGCAAGGAATCCAATGA 60.067 47.619 0.61 0.00 46.39 2.57
367 380 5.720371 TCCAATGATGAAAACGGTTCAAT 57.280 34.783 7.74 0.00 31.55 2.57
381 394 2.417239 GGTTCAATATTTGGACGCACGA 59.583 45.455 0.00 0.00 40.19 4.35
502 515 3.714798 ACCTGGAAAAGTGGAGTGTTCTA 59.285 43.478 0.00 0.00 0.00 2.10
503 516 4.202367 ACCTGGAAAAGTGGAGTGTTCTAG 60.202 45.833 0.00 0.00 0.00 2.43
504 517 4.319177 CTGGAAAAGTGGAGTGTTCTAGG 58.681 47.826 0.00 0.00 0.00 3.02
505 518 3.075148 GGAAAAGTGGAGTGTTCTAGGC 58.925 50.000 0.00 0.00 0.00 3.93
506 519 2.457366 AAAGTGGAGTGTTCTAGGCG 57.543 50.000 0.00 0.00 0.00 5.52
507 520 0.037232 AAGTGGAGTGTTCTAGGCGC 60.037 55.000 0.00 0.00 0.00 6.53
508 521 1.448013 GTGGAGTGTTCTAGGCGCC 60.448 63.158 21.89 21.89 0.00 6.53
509 522 2.202756 GGAGTGTTCTAGGCGCCG 60.203 66.667 23.20 8.11 0.00 6.46
510 523 2.572284 GAGTGTTCTAGGCGCCGT 59.428 61.111 23.20 12.38 0.00 5.68
511 524 1.080025 GAGTGTTCTAGGCGCCGTT 60.080 57.895 23.20 7.21 0.00 4.44
512 525 0.669625 GAGTGTTCTAGGCGCCGTTT 60.670 55.000 23.20 6.30 0.00 3.60
513 526 0.604578 AGTGTTCTAGGCGCCGTTTA 59.395 50.000 23.20 7.32 0.00 2.01
514 527 0.997196 GTGTTCTAGGCGCCGTTTAG 59.003 55.000 23.20 17.66 0.00 1.85
515 528 0.108520 TGTTCTAGGCGCCGTTTAGG 60.109 55.000 23.20 8.80 44.97 2.69
516 529 0.174162 GTTCTAGGCGCCGTTTAGGA 59.826 55.000 23.20 9.68 45.00 2.94
517 530 0.896923 TTCTAGGCGCCGTTTAGGAA 59.103 50.000 23.20 16.18 45.00 3.36
518 531 1.117150 TCTAGGCGCCGTTTAGGAAT 58.883 50.000 23.20 1.83 45.00 3.01
519 532 1.483415 TCTAGGCGCCGTTTAGGAATT 59.517 47.619 23.20 0.95 45.00 2.17
520 533 1.597663 CTAGGCGCCGTTTAGGAATTG 59.402 52.381 23.20 0.00 45.00 2.32
521 534 1.226575 GGCGCCGTTTAGGAATTGC 60.227 57.895 12.58 0.00 45.00 3.56
522 535 1.226575 GCGCCGTTTAGGAATTGCC 60.227 57.895 0.00 0.00 45.00 4.52
523 536 1.431845 CGCCGTTTAGGAATTGCCC 59.568 57.895 0.00 0.00 45.00 5.36
524 537 1.029947 CGCCGTTTAGGAATTGCCCT 61.030 55.000 0.00 0.00 45.00 5.19
525 538 1.182667 GCCGTTTAGGAATTGCCCTT 58.817 50.000 0.00 0.00 45.00 3.95
526 539 1.548719 GCCGTTTAGGAATTGCCCTTT 59.451 47.619 0.00 0.00 45.00 3.11
527 540 2.028476 GCCGTTTAGGAATTGCCCTTTT 60.028 45.455 0.00 0.00 45.00 2.27
528 541 3.193903 GCCGTTTAGGAATTGCCCTTTTA 59.806 43.478 0.00 0.00 45.00 1.52
529 542 4.676986 GCCGTTTAGGAATTGCCCTTTTAG 60.677 45.833 0.00 0.00 45.00 1.85
738 755 1.226859 GCCGTGACGTAGCATAGCA 60.227 57.895 3.64 0.00 0.00 3.49
921 972 2.107552 TCCACCGACCTCCAGAAATTTT 59.892 45.455 0.00 0.00 0.00 1.82
1155 1206 2.716217 GCCAACCTTAAGATCACAGCT 58.284 47.619 3.36 0.00 0.00 4.24
1312 1363 0.036022 AGCAGGCTTCAGTGAAGTCC 59.964 55.000 29.34 27.57 44.36 3.85
1345 1396 6.959639 ATGGCGGTATATTTCTGAACATTT 57.040 33.333 0.00 0.00 0.00 2.32
1593 1644 1.714794 ACTCTGCTCGCATAACACAC 58.285 50.000 0.00 0.00 0.00 3.82
1613 1665 4.124238 CACGGGTAGTTTTCTGTTTCTCA 58.876 43.478 0.00 0.00 0.00 3.27
1671 1724 3.840890 TGTGCAAAACAGACGAACTTT 57.159 38.095 0.00 0.00 33.78 2.66
1686 1739 9.367444 CAGACGAACTTTAGTATCCTTGTTAAT 57.633 33.333 0.00 0.00 0.00 1.40
1761 1816 3.126879 GCGGCAGCACAGCATACA 61.127 61.111 3.18 0.00 44.35 2.29
1778 1833 8.575589 ACAGCATACAAATGTGAAACTTTATCA 58.424 29.630 0.00 0.00 38.04 2.15
1905 1964 4.024133 TGCGCTAAACCTATGCATGTTATG 60.024 41.667 10.16 3.97 0.00 1.90
1914 1973 2.898181 TGCATGTTATGTGAAGCACG 57.102 45.000 0.00 0.00 37.14 5.34
1941 2000 5.699458 CGGTGTTTGTTTCTCTGGTAGTATT 59.301 40.000 0.00 0.00 0.00 1.89
1942 2001 6.204108 CGGTGTTTGTTTCTCTGGTAGTATTT 59.796 38.462 0.00 0.00 0.00 1.40
1943 2002 7.360361 GGTGTTTGTTTCTCTGGTAGTATTTG 58.640 38.462 0.00 0.00 0.00 2.32
1944 2003 7.227910 GGTGTTTGTTTCTCTGGTAGTATTTGA 59.772 37.037 0.00 0.00 0.00 2.69
1945 2004 8.784043 GTGTTTGTTTCTCTGGTAGTATTTGAT 58.216 33.333 0.00 0.00 0.00 2.57
1946 2005 9.349713 TGTTTGTTTCTCTGGTAGTATTTGATT 57.650 29.630 0.00 0.00 0.00 2.57
1991 2050 6.876257 ACTATTTTTGTGAAGGAGCTCTGTAG 59.124 38.462 14.64 3.06 0.00 2.74
2142 2201 7.412672 GGCTAGTCCTGAACTTATTTAAACACG 60.413 40.741 0.00 0.00 39.55 4.49
2175 2234 5.456548 TTAGAATCACTACCGTGTCACAA 57.543 39.130 3.42 0.00 41.89 3.33
2176 2235 4.537135 AGAATCACTACCGTGTCACAAT 57.463 40.909 3.42 0.00 41.89 2.71
2177 2236 5.654603 AGAATCACTACCGTGTCACAATA 57.345 39.130 3.42 0.00 41.89 1.90
2178 2237 5.408356 AGAATCACTACCGTGTCACAATAC 58.592 41.667 3.42 0.00 41.89 1.89
2406 2465 7.874528 CAGAATATCCTATTACTGATGCACACA 59.125 37.037 0.00 0.00 0.00 3.72
2413 2472 4.919677 TTACTGATGCACACACGTTATG 57.080 40.909 0.00 0.00 0.00 1.90
2512 2571 7.115378 GTCAATGAAAACATGAAGCTTAAGGTG 59.885 37.037 8.16 0.39 0.00 4.00
2778 2837 6.208204 AGCTTTAGATGAATTGAACTGCTTGT 59.792 34.615 0.00 0.00 0.00 3.16
2822 2881 3.069872 TGGAATGTGCAGAACAAAGCATT 59.930 39.130 0.00 0.00 43.61 3.56
2853 2912 4.753516 TGGTTTGTCTCTTCTCACTTCA 57.246 40.909 0.00 0.00 0.00 3.02
2907 2966 7.533426 ACAACTAGTTAACTCACCACTATACG 58.467 38.462 12.39 0.00 0.00 3.06
2927 2986 1.482593 GCTGCATATCGGCTAGGGTAT 59.517 52.381 0.00 0.00 43.74 2.73
2945 3007 4.342665 GGGTATCCCTATCTGCTATACTGC 59.657 50.000 0.00 0.00 41.34 4.40
3121 3183 2.128771 TTTGCTGACCCCTCAATAGC 57.871 50.000 0.00 0.00 35.06 2.97
3126 3188 2.555199 CTGACCCCTCAATAGCGAAAG 58.445 52.381 0.00 0.00 0.00 2.62
3176 3238 5.470098 GTGTGATAACATTGTCAACTGTCCT 59.530 40.000 0.00 0.00 29.97 3.85
3184 3246 8.691661 AACATTGTCAACTGTCCTATTTACTT 57.308 30.769 0.00 0.00 0.00 2.24
3327 3389 9.042450 TCTGTACCAATTTACTGAGGAGATAAA 57.958 33.333 0.00 0.00 0.00 1.40
3351 3413 4.217767 TCATATTAGCGAGCGGTAGTGATT 59.782 41.667 7.26 0.00 0.00 2.57
3377 3439 4.431661 GCATTAAGCTGTCTTTGCTCTT 57.568 40.909 0.00 0.00 40.22 2.85
3378 3440 4.410448 GCATTAAGCTGTCTTTGCTCTTC 58.590 43.478 0.00 0.00 40.22 2.87
3495 3557 7.418408 AGCAAGAGTTAAAGCTAAAACAAGAC 58.582 34.615 12.23 3.17 35.19 3.01
3527 3589 4.326504 ACCTGAAAGAAAACCTTGCATG 57.673 40.909 0.00 0.00 39.63 4.06
3693 3755 2.076100 TCAATGTCAAGTCATGTCGCC 58.924 47.619 0.00 0.00 0.00 5.54
3831 3893 5.192927 ACATCAGAAAACAGTGGTCTCAAA 58.807 37.500 0.00 0.00 0.00 2.69
4083 4145 2.882137 GGTTTGCAACTAGCTGGTTACA 59.118 45.455 15.73 13.50 45.94 2.41
4251 4418 9.906660 GATGAGAAATCTAACGATACAGAATCT 57.093 33.333 0.00 0.00 31.87 2.40
4440 4607 8.459911 TCTTGCAATCTCATGATGTAATGATT 57.540 30.769 0.00 0.00 36.03 2.57
4441 4608 9.563748 TCTTGCAATCTCATGATGTAATGATTA 57.436 29.630 0.00 0.00 36.03 1.75
4443 4610 9.563748 TTGCAATCTCATGATGTAATGATTAGA 57.436 29.630 0.00 0.00 36.03 2.10
4509 4676 1.964552 CCCAGATCCAAGCATCACTC 58.035 55.000 0.00 0.00 0.00 3.51
4851 5022 9.616156 CTACTCTCTGTTTATCCTACTGTTCTA 57.384 37.037 0.00 0.00 0.00 2.10
4987 5158 3.067040 GCAGTGGTAGGTAGAGCTAGTTC 59.933 52.174 0.00 0.00 0.00 3.01
5201 5385 2.545526 CACGTTGCTCACTGTTGAAGAT 59.454 45.455 0.00 0.00 0.00 2.40
5208 5392 5.005740 TGCTCACTGTTGAAGATGCTTTAT 58.994 37.500 0.00 0.00 0.00 1.40
5253 5437 6.662414 TTCTTGGTATCTTGTATTCTTGCG 57.338 37.500 0.00 0.00 0.00 4.85
5529 5797 9.573133 GGAAAATGTATCAGAAACCACTTTATG 57.427 33.333 0.00 0.00 30.99 1.90
5540 5808 9.268268 CAGAAACCACTTTATGTAGTTGTCTAA 57.732 33.333 0.00 0.00 31.24 2.10
5559 5827 7.372714 TGTCTAACAATAGAGCTTTGACGTTA 58.627 34.615 3.66 2.07 38.82 3.18
5599 5867 9.868277 GCAGTTCAGAGATGCTATTTAGTATAT 57.132 33.333 2.41 0.00 37.00 0.86
5619 5887 9.119418 AGTATATGTACAGATAGAGCTATGCTG 57.881 37.037 10.42 10.38 34.27 4.41
5711 5979 6.147821 CACCAGTATACACTTGTCCAAAAGAG 59.852 42.308 5.50 0.00 28.46 2.85
5775 6043 8.465273 TGCATACTATAGTGAAGATGTACAGT 57.535 34.615 15.90 0.00 0.00 3.55
5782 6050 9.713713 CTATAGTGAAGATGTACAGTAGAGCTA 57.286 37.037 0.33 0.99 29.11 3.32
5805 6073 6.633500 ATTTTTCTCCTGAAATGACAACGA 57.367 33.333 0.00 0.00 41.24 3.85
5944 6212 3.198635 TGAATTGAGGGAGGTCAGTCATC 59.801 47.826 0.00 0.00 0.00 2.92
5969 6237 4.933505 TGAACCAGATGTTTTGATTGCA 57.066 36.364 0.00 0.00 37.29 4.08
5974 6242 4.525487 ACCAGATGTTTTGATTGCATCAGT 59.475 37.500 0.00 0.00 40.94 3.41
5976 6244 5.575606 CCAGATGTTTTGATTGCATCAGTTC 59.424 40.000 0.00 0.00 40.94 3.01
6064 6332 9.677567 GAAGCTCAAATAAAAACAGTGAACATA 57.322 29.630 0.00 0.00 0.00 2.29
6308 6577 3.306780 GCTCTTGTCAAGCCTGGTAACTA 60.307 47.826 7.78 0.00 33.53 2.24
6364 6633 9.646427 TGTGGTATCTATTTAATTTTTGTTGCC 57.354 29.630 0.00 0.00 0.00 4.52
6395 6664 7.878477 CAAAGCATGCTAAGAATTCAAGAAA 57.122 32.000 23.00 0.00 0.00 2.52
6429 6698 5.677091 GCCGCATATGTTCTCACTTGAAAAT 60.677 40.000 4.29 0.00 0.00 1.82
6484 6753 5.046950 AGGATCACTTAGTTTCTCAGTCCAC 60.047 44.000 0.00 0.00 0.00 4.02
6687 6956 2.612221 CCTGAGACCAAACGGAAGGTAC 60.612 54.545 0.00 0.00 38.50 3.34
6772 7042 6.545666 TGTTCTATGTTGTGTTTCAGGATGTT 59.454 34.615 0.00 0.00 37.40 2.71
6904 7174 8.033626 AGATTCTTTCTTTCATCCATTTTGAGC 58.966 33.333 0.00 0.00 0.00 4.26
6923 7194 4.022068 TGAGCATGAACCAGGTTTCATTTC 60.022 41.667 6.21 11.01 42.45 2.17
6944 7215 5.885230 TCCAGTTAGTCTGAAAATGCATG 57.115 39.130 0.00 0.00 46.27 4.06
7084 7355 2.228822 CTGTCATGTTTGGGGTACAAGC 59.771 50.000 0.00 0.00 40.82 4.01
7255 7526 5.975988 ACAAACTAGATGATACCCCACAT 57.024 39.130 0.00 0.00 0.00 3.21
7265 7536 0.108774 TACCCCACATGTTGTTGCGA 59.891 50.000 0.00 0.00 0.00 5.10
7461 7901 5.132502 CCTTTTACCATGCATGATGAGGTA 58.867 41.667 28.31 17.47 33.31 3.08
7565 8034 9.423061 CCCAGTATTGATTTTCAAAGGTTTAAG 57.577 33.333 0.00 0.00 40.12 1.85
7616 8085 6.127535 CCTGTTTAATGTTTGCTCAGATGGAT 60.128 38.462 0.00 0.00 0.00 3.41
7620 8089 2.089201 TGTTTGCTCAGATGGATGCTG 58.911 47.619 0.00 0.00 34.71 4.41
7766 8398 1.774110 TGGCACATTGAACACCACTT 58.226 45.000 0.00 0.00 0.00 3.16
7862 8496 7.876936 AGTCAGCTATCATTCAAAATGTGAT 57.123 32.000 0.00 0.00 35.70 3.06
7876 8510 8.945481 TCAAAATGTGATGAAAATGTTGTTCT 57.055 26.923 0.00 0.00 0.00 3.01
7944 8580 4.994852 TGTTTCCTTGTTATTCTCTCGTGG 59.005 41.667 0.00 0.00 0.00 4.94
7953 8589 2.202797 CTCTCGTGGCATCACCGG 60.203 66.667 0.00 0.00 43.94 5.28
7994 8630 5.045578 ACCCACTGTATCTAGCAATGTTCTT 60.046 40.000 0.00 0.00 0.00 2.52
7995 8631 5.295292 CCCACTGTATCTAGCAATGTTCTTG 59.705 44.000 0.00 0.00 0.00 3.02
8006 8642 3.253188 GCAATGTTCTTGGAGTAAGCACA 59.747 43.478 0.00 0.00 44.56 4.57
8061 8697 6.456718 GCTCTGCTTTTCTACAGTGATTGATC 60.457 42.308 0.00 0.00 35.37 2.92
8133 8771 6.312180 GCATGATGATTCTCTGCGTGATATAA 59.688 38.462 0.00 0.00 0.00 0.98
8160 8798 9.410556 GTTCTGCATTACTTTTGACATTTATGT 57.589 29.630 0.00 0.00 45.16 2.29
8205 8843 3.721172 ATCCCGTCCCCATCCTGCT 62.721 63.158 0.00 0.00 0.00 4.24
8341 8979 5.466058 TCGTTTTTGGAGAACAGCGTTATAA 59.534 36.000 0.00 0.00 0.00 0.98
8368 9006 2.557924 TCACACCCAACATTTGCATCTC 59.442 45.455 0.00 0.00 0.00 2.75
8410 9048 5.520288 CACTTGGATCAATAGTGTAAGTCCG 59.480 44.000 11.04 0.00 35.65 4.79
8432 9070 7.012421 GTCCGATCAGGCTTAGAATTTTGTAAT 59.988 37.037 0.00 0.00 40.77 1.89
8615 9255 3.241678 CGACCGCTCTTGACTTATTTTCG 60.242 47.826 0.00 0.00 0.00 3.46
8641 9281 2.754552 GGCACCATGATTAGTTTGCAGA 59.245 45.455 0.00 0.00 0.00 4.26
8652 9292 3.525800 AGTTTGCAGATTGGGGTTACT 57.474 42.857 0.00 0.00 0.00 2.24
8661 9301 5.475564 GCAGATTGGGGTTACTAACTTTTCA 59.524 40.000 0.00 0.00 0.00 2.69
8692 9332 3.554934 ACTGCCAACAACTGATCAGAAA 58.445 40.909 29.27 4.37 32.83 2.52
8776 9416 8.873186 TGACCATCGATGTAGAGGTATATTTA 57.127 34.615 23.27 0.00 31.57 1.40
8811 9451 0.106116 GGTGATACTCCCTCCGTCCT 60.106 60.000 0.00 0.00 0.00 3.85
8824 9464 3.179830 CTCCGTCCTGAATTACTTGTCG 58.820 50.000 0.00 0.00 0.00 4.35
8827 9467 2.345641 CGTCCTGAATTACTTGTCGCAG 59.654 50.000 0.00 0.00 0.00 5.18
8828 9468 3.585862 GTCCTGAATTACTTGTCGCAGA 58.414 45.455 0.00 0.00 0.00 4.26
8829 9469 3.994392 GTCCTGAATTACTTGTCGCAGAA 59.006 43.478 0.00 0.00 39.69 3.02
8830 9470 4.451096 GTCCTGAATTACTTGTCGCAGAAA 59.549 41.667 0.00 0.00 39.69 2.52
8831 9471 5.122396 GTCCTGAATTACTTGTCGCAGAAAT 59.878 40.000 0.00 0.00 39.69 2.17
8832 9472 5.122239 TCCTGAATTACTTGTCGCAGAAATG 59.878 40.000 0.00 0.00 39.69 2.32
8833 9473 5.295431 TGAATTACTTGTCGCAGAAATGG 57.705 39.130 0.00 0.00 39.69 3.16
8834 9474 5.000591 TGAATTACTTGTCGCAGAAATGGA 58.999 37.500 0.00 0.00 39.69 3.41
8835 9475 5.647658 TGAATTACTTGTCGCAGAAATGGAT 59.352 36.000 0.00 0.00 39.69 3.41
8836 9476 6.821160 TGAATTACTTGTCGCAGAAATGGATA 59.179 34.615 0.00 0.00 39.69 2.59
8837 9477 6.851222 ATTACTTGTCGCAGAAATGGATAG 57.149 37.500 0.00 0.00 39.69 2.08
8838 9478 4.471904 ACTTGTCGCAGAAATGGATAGA 57.528 40.909 0.00 0.00 39.69 1.98
8839 9479 4.832248 ACTTGTCGCAGAAATGGATAGAA 58.168 39.130 0.00 0.00 39.69 2.10
8840 9480 5.245531 ACTTGTCGCAGAAATGGATAGAAA 58.754 37.500 0.00 0.00 39.69 2.52
8841 9481 5.882557 ACTTGTCGCAGAAATGGATAGAAAT 59.117 36.000 0.00 0.00 39.69 2.17
8842 9482 5.739752 TGTCGCAGAAATGGATAGAAATG 57.260 39.130 0.00 0.00 39.69 2.32
8843 9483 4.576053 TGTCGCAGAAATGGATAGAAATGG 59.424 41.667 0.00 0.00 39.69 3.16
8844 9484 4.816385 GTCGCAGAAATGGATAGAAATGGA 59.184 41.667 0.00 0.00 39.69 3.41
8845 9485 5.471456 GTCGCAGAAATGGATAGAAATGGAT 59.529 40.000 0.00 0.00 39.69 3.41
8846 9486 5.471116 TCGCAGAAATGGATAGAAATGGATG 59.529 40.000 0.00 0.00 0.00 3.51
8847 9487 5.240183 CGCAGAAATGGATAGAAATGGATGT 59.760 40.000 0.00 0.00 0.00 3.06
8848 9488 6.427853 CGCAGAAATGGATAGAAATGGATGTA 59.572 38.462 0.00 0.00 0.00 2.29
8849 9489 7.120285 CGCAGAAATGGATAGAAATGGATGTAT 59.880 37.037 0.00 0.00 0.00 2.29
8850 9490 8.457261 GCAGAAATGGATAGAAATGGATGTATC 58.543 37.037 0.00 0.00 0.00 2.24
8851 9491 9.736414 CAGAAATGGATAGAAATGGATGTATCT 57.264 33.333 0.00 0.00 0.00 1.98
8936 9658 4.332819 CCTATGGGCTTTCTTTAGAACACG 59.667 45.833 0.00 0.00 33.13 4.49
8940 9662 3.059120 GGGCTTTCTTTAGAACACGTGTC 60.059 47.826 23.61 15.17 33.13 3.67
8941 9663 3.059120 GGCTTTCTTTAGAACACGTGTCC 60.059 47.826 23.61 9.96 33.13 4.02
8942 9664 3.808174 GCTTTCTTTAGAACACGTGTCCT 59.192 43.478 23.61 18.48 33.13 3.85
8992 9714 6.120220 GGTGTAATTGCCTTCCATAGTTACT 58.880 40.000 0.00 0.00 0.00 2.24
8994 9716 7.415206 GGTGTAATTGCCTTCCATAGTTACTTG 60.415 40.741 0.00 0.00 0.00 3.16
9015 9737 5.070770 TGTGTTTTTCAGCACAAGAATGT 57.929 34.783 0.00 0.00 41.89 2.71
9049 9771 8.814235 GCTGACTATTTGATCCATTTTCATTTG 58.186 33.333 0.00 0.00 0.00 2.32
9060 9782 5.774690 TCCATTTTCATTTGTAAGAGCTGGT 59.225 36.000 0.00 0.00 0.00 4.00
9124 9846 6.152379 CCAGAAAAATTAACTGCTCCTGAAC 58.848 40.000 0.00 0.00 0.00 3.18
9128 9850 5.948992 AAATTAACTGCTCCTGAACTGAC 57.051 39.130 0.00 0.00 0.00 3.51
9154 9876 1.812571 ACCTAATTTTGCAGCTCACGG 59.187 47.619 0.00 0.00 0.00 4.94
9254 9976 3.754586 TTTGCTGCCTGCCCTGGTT 62.755 57.895 0.00 0.00 42.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
328 341 1.207089 TGGATTCCTTGCGTCGAGATT 59.793 47.619 3.95 0.00 0.00 2.40
339 352 4.772100 ACCGTTTTCATCATTGGATTCCTT 59.228 37.500 3.95 0.00 0.00 3.36
352 365 6.090129 CGTCCAAATATTGAACCGTTTTCAT 58.910 36.000 0.00 0.00 0.00 2.57
367 380 5.412640 TCTCTTAAATCGTGCGTCCAAATA 58.587 37.500 0.00 0.00 0.00 1.40
427 440 2.088423 TGTCGCAACCTGTGAGTTTTT 58.912 42.857 0.00 0.00 37.59 1.94
435 448 2.186826 GCCACTTGTCGCAACCTGT 61.187 57.895 0.00 0.00 0.00 4.00
502 515 1.654023 GCAATTCCTAAACGGCGCCT 61.654 55.000 26.68 8.66 0.00 5.52
503 516 1.226575 GCAATTCCTAAACGGCGCC 60.227 57.895 19.07 19.07 0.00 6.53
504 517 1.226575 GGCAATTCCTAAACGGCGC 60.227 57.895 6.90 0.00 0.00 6.53
505 518 1.029947 AGGGCAATTCCTAAACGGCG 61.030 55.000 4.80 4.80 34.92 6.46
506 519 1.182667 AAGGGCAATTCCTAAACGGC 58.817 50.000 0.00 0.00 35.80 5.68
507 520 3.953712 AAAAGGGCAATTCCTAAACGG 57.046 42.857 0.00 0.00 35.80 4.44
508 521 5.392703 GGACTAAAAGGGCAATTCCTAAACG 60.393 44.000 0.00 0.00 35.80 3.60
509 522 5.392703 CGGACTAAAAGGGCAATTCCTAAAC 60.393 44.000 0.00 0.00 35.80 2.01
510 523 4.703093 CGGACTAAAAGGGCAATTCCTAAA 59.297 41.667 0.00 0.00 35.80 1.85
511 524 4.019141 TCGGACTAAAAGGGCAATTCCTAA 60.019 41.667 0.00 0.00 35.80 2.69
512 525 3.520317 TCGGACTAAAAGGGCAATTCCTA 59.480 43.478 0.00 0.00 35.80 2.94
513 526 2.307686 TCGGACTAAAAGGGCAATTCCT 59.692 45.455 0.00 0.00 39.17 3.36
514 527 2.718563 TCGGACTAAAAGGGCAATTCC 58.281 47.619 0.00 0.00 0.00 3.01
515 528 4.457949 TCTTTCGGACTAAAAGGGCAATTC 59.542 41.667 0.00 0.00 35.03 2.17
516 529 4.403734 TCTTTCGGACTAAAAGGGCAATT 58.596 39.130 0.00 0.00 35.03 2.32
517 530 4.028993 TCTTTCGGACTAAAAGGGCAAT 57.971 40.909 0.00 0.00 35.03 3.56
518 531 3.495434 TCTTTCGGACTAAAAGGGCAA 57.505 42.857 0.00 0.00 35.03 4.52
519 532 3.408634 CTTCTTTCGGACTAAAAGGGCA 58.591 45.455 0.00 0.00 35.03 5.36
520 533 2.161808 GCTTCTTTCGGACTAAAAGGGC 59.838 50.000 0.00 0.00 35.03 5.19
521 534 2.747989 GGCTTCTTTCGGACTAAAAGGG 59.252 50.000 0.00 0.00 35.03 3.95
522 535 2.747989 GGGCTTCTTTCGGACTAAAAGG 59.252 50.000 0.00 0.00 35.03 3.11
523 536 3.188667 GTGGGCTTCTTTCGGACTAAAAG 59.811 47.826 0.00 0.00 35.49 2.27
524 537 3.143728 GTGGGCTTCTTTCGGACTAAAA 58.856 45.455 0.00 0.00 0.00 1.52
525 538 2.105134 TGTGGGCTTCTTTCGGACTAAA 59.895 45.455 0.00 0.00 0.00 1.85
526 539 1.695242 TGTGGGCTTCTTTCGGACTAA 59.305 47.619 0.00 0.00 0.00 2.24
527 540 1.344065 TGTGGGCTTCTTTCGGACTA 58.656 50.000 0.00 0.00 0.00 2.59
528 541 0.472471 TTGTGGGCTTCTTTCGGACT 59.528 50.000 0.00 0.00 0.00 3.85
529 542 0.875059 CTTGTGGGCTTCTTTCGGAC 59.125 55.000 0.00 0.00 0.00 4.79
762 803 1.684734 GTGAGAGGCGGAGGGGTTA 60.685 63.158 0.00 0.00 0.00 2.85
921 972 2.022035 AGGATCTAGATGGTTCACCCCA 60.022 50.000 10.74 0.00 39.27 4.96
1312 1363 7.009631 CAGAAATATACCGCCATTTCTAGATCG 59.990 40.741 8.73 0.00 45.33 3.69
1345 1396 3.243035 CGACAGATGACCAAAAACTGCAA 60.243 43.478 0.00 0.00 32.67 4.08
1593 1644 5.941948 AATGAGAAACAGAAAACTACCCG 57.058 39.130 0.00 0.00 0.00 5.28
1613 1665 5.327732 ACATCACAGGATCCAAGACAAAAT 58.672 37.500 15.82 0.00 0.00 1.82
1686 1739 6.317391 TGTTGCATACATGATTAAACGATGGA 59.683 34.615 0.00 0.00 0.00 3.41
1720 1773 5.691754 CCTTTTTGGTCTAACATTTCACTGC 59.308 40.000 0.00 0.00 0.00 4.40
1761 1816 7.614494 CCCCAGAATGATAAAGTTTCACATTT 58.386 34.615 16.05 8.07 39.69 2.32
1778 1833 0.251922 AACACATGCAGCCCCAGAAT 60.252 50.000 0.00 0.00 0.00 2.40
1820 1875 2.811431 CACCACAGAAGGACGCATAAAA 59.189 45.455 0.00 0.00 0.00 1.52
1884 1942 5.236263 TCACATAACATGCATAGGTTTAGCG 59.764 40.000 7.62 0.00 32.39 4.26
1914 1973 1.264288 CCAGAGAAACAAACACCGAGC 59.736 52.381 0.00 0.00 0.00 5.03
1991 2050 5.529060 CCCTATACTTTCCAAGTGAGCAATC 59.471 44.000 0.00 0.00 42.84 2.67
2015 2074 5.163884 GCAGAACCTAAAGACGGAAACATAC 60.164 44.000 0.00 0.00 0.00 2.39
2142 2201 3.956744 AGTGATTCTAAAGGACAAGCCC 58.043 45.455 0.00 0.00 37.37 5.19
2406 2465 7.201582 GCTTGGTATGCTAAAGTTACATAACGT 60.202 37.037 0.00 0.00 40.96 3.99
2413 2472 6.106673 TCTCAGCTTGGTATGCTAAAGTTAC 58.893 40.000 0.00 0.00 38.92 2.50
2512 2571 2.949451 TCGAATCCTCAGTCTGCTTC 57.051 50.000 0.00 0.00 0.00 3.86
2617 2676 3.356529 ACATTACCTCTTTCTGCCTGG 57.643 47.619 0.00 0.00 0.00 4.45
2726 2785 0.549902 TCTTCCCAAGCATCCCCTCA 60.550 55.000 0.00 0.00 0.00 3.86
2778 2837 1.473677 CTTTGCCGAGGAATCATGCAA 59.526 47.619 0.00 0.00 39.92 4.08
2822 2881 4.974645 AGAGACAAACCAACCTGACATA 57.025 40.909 0.00 0.00 0.00 2.29
2853 2912 9.726438 ACATTCTAAAAGATTAGCACTAACTGT 57.274 29.630 0.00 0.00 38.73 3.55
2890 2949 3.193903 TGCAGCGTATAGTGGTGAGTTAA 59.806 43.478 7.98 0.00 36.99 2.01
2907 2966 0.895530 TACCCTAGCCGATATGCAGC 59.104 55.000 0.00 0.00 0.00 5.25
2927 2986 4.119556 ACAGCAGTATAGCAGATAGGGA 57.880 45.455 0.00 0.00 36.85 4.20
2945 3007 8.206325 ACATCAGAGTTTAGATGCATAAACAG 57.794 34.615 21.41 13.35 44.51 3.16
3078 3140 6.560253 AAACAGACCTGATGTGTTATCAAC 57.440 37.500 3.76 0.00 43.73 3.18
3121 3183 5.567138 AAATATTCCTGCTGAACCTTTCG 57.433 39.130 0.00 0.00 35.31 3.46
3152 3214 5.470098 AGGACAGTTGACAATGTTATCACAC 59.530 40.000 0.00 0.00 35.03 3.82
3184 3246 4.020039 TCCGCAAAATCTCCTGTTTACCTA 60.020 41.667 0.00 0.00 0.00 3.08
3327 3389 3.756963 TCACTACCGCTCGCTAATATGAT 59.243 43.478 0.00 0.00 0.00 2.45
3495 3557 6.292114 GGTTTTCTTTCAGGTAAATGCAAACG 60.292 38.462 0.00 0.00 0.00 3.60
3506 3568 3.706086 ACATGCAAGGTTTTCTTTCAGGT 59.294 39.130 0.00 0.00 38.42 4.00
3831 3893 4.546674 ACTTCAGTTCCCCAATTTCACTT 58.453 39.130 0.00 0.00 0.00 3.16
4125 4292 6.091713 CCTGCAAAATTCCAATTTCATGAGTC 59.908 38.462 0.00 0.00 37.62 3.36
4251 4418 0.532115 TAGCAATCTCGCTGTGCAGA 59.468 50.000 3.02 0.00 43.68 4.26
4440 4607 8.631480 TGTCTACAGTGAAGTTCTACATTCTA 57.369 34.615 4.17 0.00 0.00 2.10
4441 4608 7.526142 TGTCTACAGTGAAGTTCTACATTCT 57.474 36.000 4.17 0.00 0.00 2.40
4443 4610 7.497595 TGTTGTCTACAGTGAAGTTCTACATT 58.502 34.615 4.17 0.00 31.68 2.71
4445 4612 6.459670 TGTTGTCTACAGTGAAGTTCTACA 57.540 37.500 4.17 0.00 31.68 2.74
4448 4615 9.640963 GTTATATGTTGTCTACAGTGAAGTTCT 57.359 33.333 4.17 0.00 40.83 3.01
4450 4617 8.594550 AGGTTATATGTTGTCTACAGTGAAGTT 58.405 33.333 0.00 0.00 40.83 2.66
4452 4619 9.436957 AAAGGTTATATGTTGTCTACAGTGAAG 57.563 33.333 0.00 0.00 40.83 3.02
4453 4620 9.787435 AAAAGGTTATATGTTGTCTACAGTGAA 57.213 29.630 0.00 0.00 40.83 3.18
4454 4621 9.431887 GAAAAGGTTATATGTTGTCTACAGTGA 57.568 33.333 0.00 0.00 40.83 3.41
4455 4622 9.214957 TGAAAAGGTTATATGTTGTCTACAGTG 57.785 33.333 0.00 0.00 40.83 3.66
4509 4676 3.970721 TGACATTCTGTGGCAGCG 58.029 55.556 0.00 0.00 42.26 5.18
4655 4822 7.166851 AGACTGTCATTTGTGATTCAGAAGAT 58.833 34.615 10.88 0.00 0.00 2.40
4821 4992 6.975772 CAGTAGGATAAACAGAGAGTAGCAAC 59.024 42.308 0.00 0.00 0.00 4.17
4851 5022 4.942761 TGAGCTTTTCTGCCTGAAATTT 57.057 36.364 0.00 0.00 43.34 1.82
4868 5039 2.620585 GTGCTCCATTTCCCTTATGAGC 59.379 50.000 0.00 0.00 35.27 4.26
4987 5158 6.436843 AATGTAGCCTTTATTGAGAAACCG 57.563 37.500 0.00 0.00 0.00 4.44
5222 5406 9.220767 GAATACAAGATACCAAGAAAACTCTGT 57.779 33.333 0.00 0.00 0.00 3.41
5253 5437 8.934507 ACTCTTACATGTCAAGTCTAATTAGC 57.065 34.615 0.00 3.49 0.00 3.09
5294 5488 9.950496 ATACTTTGAACTCATTTAGATGTCAGT 57.050 29.630 0.00 0.00 34.77 3.41
5321 5515 4.968259 TGTTACTCTAAAGCAGCTTGGAA 58.032 39.130 8.88 0.00 0.00 3.53
5323 5517 5.886960 AATGTTACTCTAAAGCAGCTTGG 57.113 39.130 8.88 5.23 0.00 3.61
5378 5575 5.666969 TCGAACTTTTCACCAGTATGTTG 57.333 39.130 0.00 0.00 0.00 3.33
5498 5766 7.287696 AGTGGTTTCTGATACATTTTCCACTTT 59.712 33.333 7.13 0.00 46.97 2.66
5529 5797 8.648968 GTCAAAGCTCTATTGTTAGACAACTAC 58.351 37.037 0.00 0.00 41.40 2.73
5540 5808 7.041372 ACAAATGTAACGTCAAAGCTCTATTGT 60.041 33.333 0.00 0.00 0.00 2.71
5548 5816 4.439776 GTGGAACAAATGTAACGTCAAAGC 59.560 41.667 0.00 0.00 44.16 3.51
5599 5867 6.715347 TTTCAGCATAGCTCTATCTGTACA 57.285 37.500 0.00 0.00 36.40 2.90
5619 5887 5.713025 TCCAAGATTAACAGCAGCATTTTC 58.287 37.500 0.00 0.00 0.00 2.29
5711 5979 0.318955 GGCTGACACCATGCAAACAC 60.319 55.000 0.00 0.00 0.00 3.32
5775 6043 8.321353 TGTCATTTCAGGAGAAAAATAGCTCTA 58.679 33.333 0.00 0.00 46.06 2.43
5782 6050 6.633500 TCGTTGTCATTTCAGGAGAAAAAT 57.367 33.333 0.00 0.00 46.06 1.82
5944 6212 5.176223 GCAATCAAAACATCTGGTTCAACTG 59.824 40.000 0.00 0.00 39.29 3.16
6064 6332 3.005554 CTGACAATCTTCTTCATGCCGT 58.994 45.455 0.00 0.00 0.00 5.68
6339 6608 9.869757 AGGCAACAAAAATTAAATAGATACCAC 57.130 29.630 0.00 0.00 41.41 4.16
6441 6710 3.262915 TCCTGCCCCAAAATAACCAAATG 59.737 43.478 0.00 0.00 0.00 2.32
6484 6753 9.520515 ACATTATAATAGTAAAAGGGCAGGATG 57.479 33.333 0.00 0.00 40.87 3.51
6600 6869 4.964897 TGGCTCTCTCCTCTTTATCAATGA 59.035 41.667 0.00 0.00 0.00 2.57
6620 6889 6.500684 TGACTTTCTTTTCTGACATATGGC 57.499 37.500 7.80 4.20 0.00 4.40
6901 7171 4.488879 GAAATGAAACCTGGTTCATGCTC 58.511 43.478 13.36 6.89 45.42 4.26
6902 7172 3.259123 GGAAATGAAACCTGGTTCATGCT 59.741 43.478 13.36 8.90 45.42 3.79
6904 7174 4.281688 ACTGGAAATGAAACCTGGTTCATG 59.718 41.667 13.36 8.16 45.42 3.07
6923 7194 5.633830 ACATGCATTTTCAGACTAACTGG 57.366 39.130 0.00 0.00 45.76 4.00
7255 7526 2.098934 ACAAGCAATTCTCGCAACAACA 59.901 40.909 0.00 0.00 0.00 3.33
7303 7735 8.700722 TTGTTAATGCAAATATCCATGTTCAC 57.299 30.769 0.00 0.00 0.00 3.18
7421 7853 1.907807 GGCCCACCTCAACATGCAA 60.908 57.895 0.00 0.00 0.00 4.08
7422 7854 2.283101 GGCCCACCTCAACATGCA 60.283 61.111 0.00 0.00 0.00 3.96
7423 7855 2.036256 AGGCCCACCTCAACATGC 59.964 61.111 0.00 0.00 46.34 4.06
7444 7876 1.491754 TGCTACCTCATCATGCATGGT 59.508 47.619 25.97 17.67 32.64 3.55
7526 7995 7.923414 ATCAATACTGGGAAGTTGAAAGTAC 57.077 36.000 0.00 0.00 34.62 2.73
7527 7996 8.934023 AAATCAATACTGGGAAGTTGAAAGTA 57.066 30.769 0.00 0.00 34.62 2.24
7528 7997 7.839680 AAATCAATACTGGGAAGTTGAAAGT 57.160 32.000 0.00 0.00 34.62 2.66
7529 7998 8.359642 TGAAAATCAATACTGGGAAGTTGAAAG 58.640 33.333 0.00 0.00 34.62 2.62
7530 7999 8.243961 TGAAAATCAATACTGGGAAGTTGAAA 57.756 30.769 0.00 0.00 34.62 2.69
7593 8062 6.623486 CATCCATCTGAGCAAACATTAAACA 58.377 36.000 0.00 0.00 0.00 2.83
7743 8375 2.164219 GTGGTGTTCAATGTGCCATAGG 59.836 50.000 0.00 0.00 0.00 2.57
7766 8398 6.663953 AGGCTTACAGTCTAAACTCTACATGA 59.336 38.462 0.00 0.00 31.71 3.07
7862 8496 9.575783 GGTAAAAACACTAGAACAACATTTTCA 57.424 29.630 0.00 0.00 0.00 2.69
7876 8510 7.364149 TGGAGACTAACTGGTAAAAACACTA 57.636 36.000 0.00 0.00 0.00 2.74
7994 8630 5.906113 TGTTTTCTTTTGTGCTTACTCCA 57.094 34.783 0.00 0.00 0.00 3.86
7995 8631 7.770801 AATTGTTTTCTTTTGTGCTTACTCC 57.229 32.000 0.00 0.00 0.00 3.85
8032 8668 3.999001 CACTGTAGAAAAGCAGAGCATGA 59.001 43.478 0.00 0.00 36.62 3.07
8133 8771 9.630098 CATAAATGTCAAAAGTAATGCAGAACT 57.370 29.630 0.00 0.00 0.00 3.01
8205 8843 9.502091 CCCTCAGAAAATAATTCACCGATATTA 57.498 33.333 0.00 0.00 0.00 0.98
8306 8944 2.356382 TCCAAAAACGACGAACTGCAAT 59.644 40.909 0.00 0.00 0.00 3.56
8341 8979 3.243839 GCAAATGTTGGGTGTGAGATTGT 60.244 43.478 0.00 0.00 0.00 2.71
8410 9048 9.860898 ACAAATTACAAAATTCTAAGCCTGATC 57.139 29.630 0.00 0.00 34.12 2.92
8511 9151 8.483218 CAGAGCATGATTACAGTTTATAGTTCG 58.517 37.037 0.00 0.00 0.00 3.95
8603 9243 2.163412 GTGCCATGGCGAAAATAAGTCA 59.837 45.455 30.87 6.56 45.51 3.41
8629 9269 5.580022 AGTAACCCCAATCTGCAAACTAAT 58.420 37.500 0.00 0.00 0.00 1.73
8641 9281 6.496911 AGCATTGAAAAGTTAGTAACCCCAAT 59.503 34.615 9.46 10.46 0.00 3.16
8652 9292 5.460646 GCAGTAAGCAGCATTGAAAAGTTA 58.539 37.500 0.00 0.00 44.79 2.24
8692 9332 2.704065 ACTATAATGCACTAACGGGCCT 59.296 45.455 0.84 0.00 0.00 5.19
8776 9416 8.643324 GGAGTATCACCTATCATTAGAAACAGT 58.357 37.037 0.00 0.00 36.25 3.55
8811 9451 5.000591 TCCATTTCTGCGACAAGTAATTCA 58.999 37.500 0.00 0.00 0.00 2.57
8824 9464 6.645790 ACATCCATTTCTATCCATTTCTGC 57.354 37.500 0.00 0.00 0.00 4.26
8831 9471 9.607333 AGTTCTAGATACATCCATTTCTATCCA 57.393 33.333 0.00 0.00 0.00 3.41
8832 9472 9.868277 CAGTTCTAGATACATCCATTTCTATCC 57.132 37.037 0.00 0.00 0.00 2.59
8833 9473 9.868277 CCAGTTCTAGATACATCCATTTCTATC 57.132 37.037 0.00 0.00 0.00 2.08
8834 9474 8.820831 CCCAGTTCTAGATACATCCATTTCTAT 58.179 37.037 0.00 0.00 0.00 1.98
8835 9475 8.010697 TCCCAGTTCTAGATACATCCATTTCTA 58.989 37.037 0.00 0.00 0.00 2.10
8836 9476 6.846505 TCCCAGTTCTAGATACATCCATTTCT 59.153 38.462 0.00 0.00 0.00 2.52
8837 9477 7.067496 TCCCAGTTCTAGATACATCCATTTC 57.933 40.000 0.00 0.00 0.00 2.17
8838 9478 6.617371 ACTCCCAGTTCTAGATACATCCATTT 59.383 38.462 0.00 0.00 0.00 2.32
8839 9479 6.146760 ACTCCCAGTTCTAGATACATCCATT 58.853 40.000 0.00 0.00 0.00 3.16
8840 9480 5.721225 ACTCCCAGTTCTAGATACATCCAT 58.279 41.667 0.00 0.00 0.00 3.41
8841 9481 5.144159 ACTCCCAGTTCTAGATACATCCA 57.856 43.478 0.00 0.00 0.00 3.41
8842 9482 6.308566 ACTACTCCCAGTTCTAGATACATCC 58.691 44.000 0.00 0.00 0.00 3.51
8843 9483 9.523168 AATACTACTCCCAGTTCTAGATACATC 57.477 37.037 0.00 0.00 0.00 3.06
8844 9484 9.884814 AAATACTACTCCCAGTTCTAGATACAT 57.115 33.333 0.00 0.00 0.00 2.29
8845 9485 9.710818 AAAATACTACTCCCAGTTCTAGATACA 57.289 33.333 0.00 0.00 0.00 2.29
8848 9488 9.939424 ACTAAAATACTACTCCCAGTTCTAGAT 57.061 33.333 0.00 0.00 0.00 1.98
8849 9489 9.765295 AACTAAAATACTACTCCCAGTTCTAGA 57.235 33.333 0.00 0.00 0.00 2.43
8851 9491 9.537852 TGAACTAAAATACTACTCCCAGTTCTA 57.462 33.333 11.19 0.00 40.64 2.10
8852 9492 8.431910 TGAACTAAAATACTACTCCCAGTTCT 57.568 34.615 11.19 0.00 40.64 3.01
8853 9493 8.312564 ACTGAACTAAAATACTACTCCCAGTTC 58.687 37.037 0.00 0.00 40.50 3.01
8854 9494 8.203681 ACTGAACTAAAATACTACTCCCAGTT 57.796 34.615 0.00 0.00 0.00 3.16
8855 9495 7.793948 ACTGAACTAAAATACTACTCCCAGT 57.206 36.000 0.00 0.00 0.00 4.00
8856 9496 8.968969 ACTACTGAACTAAAATACTACTCCCAG 58.031 37.037 0.00 0.00 0.00 4.45
8894 9616 7.351454 CCCATAGGATACCCTCTATAGAGTACT 59.649 44.444 24.80 15.98 43.14 2.73
8962 9684 4.523083 TGGAAGGCAATTACACCATCTAC 58.477 43.478 0.00 0.00 0.00 2.59
8994 9716 5.576384 TGAACATTCTTGTGCTGAAAAACAC 59.424 36.000 0.00 0.00 35.83 3.32
9015 9737 7.465353 TGGATCAAATAGTCAGCAAATTGAA 57.535 32.000 0.00 0.00 31.37 2.69
9049 9771 5.123820 TGCATATGAAACAACCAGCTCTTAC 59.876 40.000 6.97 0.00 0.00 2.34
9060 9782 7.884257 TCAAACTTGAGATGCATATGAAACAA 58.116 30.769 6.97 4.28 32.50 2.83
9105 9827 5.827797 TGTCAGTTCAGGAGCAGTTAATTTT 59.172 36.000 0.00 0.00 0.00 1.82
9124 9846 5.617751 GCTGCAAAATTAGGTGTAGTGTCAG 60.618 44.000 0.00 0.00 30.92 3.51
9128 9850 4.455533 TGAGCTGCAAAATTAGGTGTAGTG 59.544 41.667 1.02 0.00 30.92 2.74
9154 9876 5.277731 GCTTCTTAAGATCAGCACCAATAGC 60.278 44.000 19.75 11.50 30.43 2.97


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

AutoCloner maintained by Alex Coulton.