Multiple sequence alignment - TraesCS2A01G019800

Loading Multiple Alignment...

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 TraesCS2A01G019800 chr2A 100.000 3053 0 0 1 3053 9122620 9119568 0.000000e+00 5638.0
1 TraesCS2A01G019800 chr2A 86.166 1771 215 18 497 2242 9394999 9396764 0.000000e+00 1886.0
2 TraesCS2A01G019800 chr2A 86.020 1774 215 17 497 2242 9847476 9849244 0.000000e+00 1871.0
3 TraesCS2A01G019800 chr2A 90.331 393 37 1 523 915 7515095 7514704 5.840000e-142 514.0
4 TraesCS2A01G019800 chr2A 100.000 35 0 0 321 355 9122196 9122162 7.070000e-07 65.8
5 TraesCS2A01G019800 chr2A 100.000 35 0 0 425 459 9122300 9122266 7.070000e-07 65.8
6 TraesCS2A01G019800 chr2B 93.199 1882 99 18 1 1873 13181495 13179634 0.000000e+00 2739.0
7 TraesCS2A01G019800 chr2B 93.814 1180 62 7 701 1873 13315024 13313849 0.000000e+00 1764.0
8 TraesCS2A01G019800 chr2B 82.756 1531 244 11 624 2138 768807004 768805478 0.000000e+00 1347.0
9 TraesCS2A01G019800 chr2B 81.555 1659 249 27 490 2138 11226560 11224949 0.000000e+00 1315.0
10 TraesCS2A01G019800 chr2B 81.842 1531 257 12 624 2138 768929424 768927899 0.000000e+00 1267.0
11 TraesCS2A01G019800 chr2B 81.938 1135 169 18 490 1616 11173154 11172048 0.000000e+00 928.0
12 TraesCS2A01G019800 chr2B 93.414 577 27 3 2481 3050 13144726 13144154 0.000000e+00 845.0
13 TraesCS2A01G019800 chr2B 89.065 567 30 12 1 550 13315572 13315021 0.000000e+00 675.0
14 TraesCS2A01G019800 chr2B 86.697 218 28 1 2651 2868 13083019 13082803 1.090000e-59 241.0
15 TraesCS2A01G019800 chr2D 85.408 1775 219 19 497 2242 9879890 9878127 0.000000e+00 1807.0
16 TraesCS2A01G019800 chr2D 82.169 1531 251 13 624 2139 19587012 19588535 0.000000e+00 1295.0
17 TraesCS2A01G019800 chr2D 82.036 1503 214 30 500 1991 8479463 8478006 0.000000e+00 1229.0
18 TraesCS2A01G019800 chr2D 90.811 370 30 4 458 826 9791366 9791000 2.740000e-135 492.0
19 TraesCS2A01G019800 chr2D 86.928 153 16 1 5 157 9792180 9792032 5.240000e-38 169.0
20 TraesCS2A01G019800 chrUn 82.315 1227 204 11 920 2138 3529245 3528024 0.000000e+00 1051.0


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 TraesCS2A01G019800 chr2A 9119568 9122620 3052 True 1923.2 5638 100.0000 1 3053 3 chr2A.!!$R2 3052
1 TraesCS2A01G019800 chr2A 9394999 9396764 1765 False 1886.0 1886 86.1660 497 2242 1 chr2A.!!$F1 1745
2 TraesCS2A01G019800 chr2A 9847476 9849244 1768 False 1871.0 1871 86.0200 497 2242 1 chr2A.!!$F2 1745
3 TraesCS2A01G019800 chr2B 13179634 13181495 1861 True 2739.0 2739 93.1990 1 1873 1 chr2B.!!$R5 1872
4 TraesCS2A01G019800 chr2B 768805478 768807004 1526 True 1347.0 1347 82.7560 624 2138 1 chr2B.!!$R6 1514
5 TraesCS2A01G019800 chr2B 11224949 11226560 1611 True 1315.0 1315 81.5550 490 2138 1 chr2B.!!$R2 1648
6 TraesCS2A01G019800 chr2B 768927899 768929424 1525 True 1267.0 1267 81.8420 624 2138 1 chr2B.!!$R7 1514
7 TraesCS2A01G019800 chr2B 13313849 13315572 1723 True 1219.5 1764 91.4395 1 1873 2 chr2B.!!$R8 1872
8 TraesCS2A01G019800 chr2B 11172048 11173154 1106 True 928.0 928 81.9380 490 1616 1 chr2B.!!$R1 1126
9 TraesCS2A01G019800 chr2B 13144154 13144726 572 True 845.0 845 93.4140 2481 3050 1 chr2B.!!$R4 569
10 TraesCS2A01G019800 chr2D 9878127 9879890 1763 True 1807.0 1807 85.4080 497 2242 1 chr2D.!!$R2 1745
11 TraesCS2A01G019800 chr2D 19587012 19588535 1523 False 1295.0 1295 82.1690 624 2139 1 chr2D.!!$F1 1515
12 TraesCS2A01G019800 chr2D 8478006 8479463 1457 True 1229.0 1229 82.0360 500 1991 1 chr2D.!!$R1 1491
13 TraesCS2A01G019800 chr2D 9791000 9792180 1180 True 330.5 492 88.8695 5 826 2 chr2D.!!$R3 821
14 TraesCS2A01G019800 chrUn 3528024 3529245 1221 True 1051.0 1051 82.3150 920 2138 1 chrUn.!!$R1 1218

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
19 20 1.106944 CCGGTTGGACTGTTGGCTTT 61.107 55.000 0.0 0.0 37.49 3.51 F
286 417 1.465387 ACGAACGTGCAACAGTTTTCA 59.535 42.857 0.0 0.0 34.66 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1809 2282 2.133281 CCACATGATGGCCTTCTTCA 57.867 50.0 18.67 9.92 43.24 3.02 R
2056 2529 1.852157 TTCGCTTCCTCCCTGGCAAT 61.852 55.0 0.00 0.00 35.26 3.56 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
19 20 1.106944 CCGGTTGGACTGTTGGCTTT 61.107 55.000 0.00 0.00 37.49 3.51
77 78 6.799926 TTGTGTGTACAGTATAGACACGTA 57.200 37.500 6.79 0.00 45.18 3.57
270 401 7.441890 TCCTAAACTATCAAAAATGCACGAA 57.558 32.000 0.00 0.00 0.00 3.85
272 403 6.248420 CCTAAACTATCAAAAATGCACGAACG 59.752 38.462 0.00 0.00 0.00 3.95
286 417 1.465387 ACGAACGTGCAACAGTTTTCA 59.535 42.857 0.00 0.00 34.66 2.69
289 420 3.177643 CGAACGTGCAACAGTTTTCAATC 59.822 43.478 0.00 0.00 34.66 2.67
303 434 9.434420 ACAGTTTTCAATCAAAGATTGAACAAA 57.566 25.926 26.12 18.83 44.67 2.83
341 491 4.286032 AGCAAACTGGTTACATGTCCTCTA 59.714 41.667 0.00 0.00 0.00 2.43
400 840 8.500773 CAATGACAGAAAAATGCAAAGCTAATT 58.499 29.630 0.00 0.00 0.00 1.40
426 866 7.072263 ACAATAATCAATTTTGACCCACCAA 57.928 32.000 0.00 0.00 40.49 3.67
427 867 7.512992 ACAATAATCAATTTTGACCCACCAAA 58.487 30.769 0.00 0.00 40.49 3.28
428 868 7.443879 ACAATAATCAATTTTGACCCACCAAAC 59.556 33.333 0.00 0.00 40.49 2.93
429 869 5.628797 AATCAATTTTGACCCACCAAACT 57.371 34.783 0.00 0.00 40.49 2.66
430 870 4.399004 TCAATTTTGACCCACCAAACTG 57.601 40.909 0.00 0.00 35.95 3.16
431 871 3.133721 TCAATTTTGACCCACCAAACTGG 59.866 43.478 0.00 0.00 36.45 4.00
432 872 5.364664 TCAATTTTGACCCACCAAACTGGT 61.365 41.667 0.00 0.00 41.32 4.00
435 875 9.460748 TCAATTTTGACCCACCAAACTGGTTAC 62.461 40.741 0.00 0.00 39.66 2.50
444 884 4.021102 CCAAACTGGTTACATGTCCTCT 57.979 45.455 0.00 0.00 31.35 3.69
445 885 5.160607 CCAAACTGGTTACATGTCCTCTA 57.839 43.478 0.00 0.00 31.35 2.43
446 886 5.178797 CCAAACTGGTTACATGTCCTCTAG 58.821 45.833 0.00 4.24 31.35 2.43
447 887 5.046591 CCAAACTGGTTACATGTCCTCTAGA 60.047 44.000 0.00 0.00 31.35 2.43
448 888 6.464222 CAAACTGGTTACATGTCCTCTAGAA 58.536 40.000 0.00 0.00 0.00 2.10
449 889 5.923733 ACTGGTTACATGTCCTCTAGAAG 57.076 43.478 0.00 0.00 0.00 2.85
450 890 5.580998 ACTGGTTACATGTCCTCTAGAAGA 58.419 41.667 0.00 0.00 0.00 2.87
451 891 6.198639 ACTGGTTACATGTCCTCTAGAAGAT 58.801 40.000 0.00 0.00 0.00 2.40
452 892 6.670027 ACTGGTTACATGTCCTCTAGAAGATT 59.330 38.462 0.00 0.00 0.00 2.40
453 893 7.839705 ACTGGTTACATGTCCTCTAGAAGATTA 59.160 37.037 0.00 0.00 0.00 1.75
454 894 8.008513 TGGTTACATGTCCTCTAGAAGATTAC 57.991 38.462 0.00 0.00 0.00 1.89
455 895 7.839705 TGGTTACATGTCCTCTAGAAGATTACT 59.160 37.037 0.00 0.00 0.00 2.24
478 918 6.491403 ACTCATTTTCCATGCTTCTTGTACTT 59.509 34.615 0.00 0.00 0.00 2.24
621 1071 4.574674 AACAGCTTACCTCATCAATCCA 57.425 40.909 0.00 0.00 0.00 3.41
899 1355 1.707989 TGAGGTATTGTGCCCTCCAAA 59.292 47.619 3.41 0.00 45.56 3.28
932 1395 3.503827 TCGTAGCATCAATGACTCGTT 57.496 42.857 0.00 0.00 0.00 3.85
968 1434 4.448732 GCAATTCATTCCTTTCAAGCGTTT 59.551 37.500 0.00 0.00 0.00 3.60
1042 1508 5.511373 GGTGCCTTGGAAAGCTTAGAAATTT 60.511 40.000 0.00 0.00 44.44 1.82
1118 1584 1.864711 CCGTAGGCCGTATGACATTTG 59.135 52.381 0.00 0.00 46.14 2.32
1171 1637 1.605710 GCACTGAGAAGCAAAAGCTCA 59.394 47.619 0.00 0.00 37.17 4.26
1239 1707 6.095860 CACTTGCAATTCTTCCAATCATAGGA 59.904 38.462 0.00 0.00 0.00 2.94
1311 1779 1.666011 GGTCCACTCACGCTTCTCA 59.334 57.895 0.00 0.00 0.00 3.27
1398 1867 6.181190 TGGGACGATGTTGGTAATTATTGAA 58.819 36.000 0.00 0.00 0.00 2.69
1584 2053 4.455877 AGATACCTTTTCAAGAAACTGGCG 59.544 41.667 11.39 0.00 31.45 5.69
1716 2188 3.815401 CGGATGTGTTGAGAAAGAACCTT 59.185 43.478 0.00 0.00 0.00 3.50
1775 2247 7.383300 GGTGATAAGATATGCCAAAAGAAATGC 59.617 37.037 0.00 0.00 0.00 3.56
1785 2257 4.747810 CCAAAAGAAATGCCTCCACATAC 58.252 43.478 0.00 0.00 0.00 2.39
1786 2258 4.414852 CAAAAGAAATGCCTCCACATACG 58.585 43.478 0.00 0.00 0.00 3.06
1809 2282 2.287769 GTGCACCCAAACATGCTTTTT 58.712 42.857 5.22 0.00 42.55 1.94
1865 2338 1.725641 CTGCATCCACTTAGCGTGAA 58.274 50.000 0.00 0.00 46.81 3.18
1920 2393 2.732289 ACCAAGTGTGACAATGGGC 58.268 52.632 19.12 0.00 37.26 5.36
1951 2424 3.055530 AGCAGATCCAAGTGTTAGACCAG 60.056 47.826 0.00 0.00 0.00 4.00
2003 2476 5.304686 TCAAGGATACCGCCTCATAATTT 57.695 39.130 0.00 0.00 37.26 1.82
2005 2478 6.464222 TCAAGGATACCGCCTCATAATTTAG 58.536 40.000 0.00 0.00 37.26 1.85
2009 2482 6.042781 AGGATACCGCCTCATAATTTAGTTCA 59.957 38.462 0.00 0.00 30.76 3.18
2029 2502 6.537301 AGTTCATCTTTTTGTCACAAGTCGTA 59.463 34.615 0.00 0.00 0.00 3.43
2049 2522 1.909302 ACTCAGGGTACACATGAAGGG 59.091 52.381 0.00 0.00 0.00 3.95
2050 2523 1.909302 CTCAGGGTACACATGAAGGGT 59.091 52.381 0.00 0.00 37.77 4.34
2056 2529 0.899019 TACACATGAAGGGTAGCGCA 59.101 50.000 11.47 0.00 34.16 6.09
2245 2732 9.334947 ACTGGAGATCTATCATAAAATTGTGTG 57.665 33.333 0.00 0.00 0.00 3.82
2246 2733 9.334947 CTGGAGATCTATCATAAAATTGTGTGT 57.665 33.333 0.00 0.00 0.00 3.72
2247 2734 9.685276 TGGAGATCTATCATAAAATTGTGTGTT 57.315 29.630 0.00 0.00 0.00 3.32
2258 2745 9.941664 CATAAAATTGTGTGTTCTATCAGATCC 57.058 33.333 0.00 0.00 0.00 3.36
2259 2746 9.911788 ATAAAATTGTGTGTTCTATCAGATCCT 57.088 29.630 0.00 0.00 0.00 3.24
2261 2748 8.723942 AAATTGTGTGTTCTATCAGATCCTAC 57.276 34.615 0.00 0.00 0.00 3.18
2262 2749 6.850752 TTGTGTGTTCTATCAGATCCTACA 57.149 37.500 0.00 0.00 0.00 2.74
2263 2750 6.208988 TGTGTGTTCTATCAGATCCTACAC 57.791 41.667 11.96 11.96 34.50 2.90
2264 2751 5.952347 TGTGTGTTCTATCAGATCCTACACT 59.048 40.000 16.63 0.00 34.81 3.55
2265 2752 6.437477 TGTGTGTTCTATCAGATCCTACACTT 59.563 38.462 16.63 0.00 34.81 3.16
2266 2753 7.039011 TGTGTGTTCTATCAGATCCTACACTTT 60.039 37.037 16.63 0.00 34.81 2.66
2267 2754 7.819900 GTGTGTTCTATCAGATCCTACACTTTT 59.180 37.037 16.63 0.00 34.81 2.27
2268 2755 8.375506 TGTGTTCTATCAGATCCTACACTTTTT 58.624 33.333 16.63 0.00 34.81 1.94
2301 2788 9.232473 GGGATAAGTATATTTTCATCCCTCAAC 57.768 37.037 16.38 0.00 45.49 3.18
2313 2800 9.753674 TTTTCATCCCTCAACTATTTTGATAGT 57.246 29.630 0.00 0.00 38.90 2.12
2330 2817 9.542462 TTTTGATAGTATAGAAATTGTCCCTCG 57.458 33.333 0.00 0.00 0.00 4.63
2331 2818 8.473358 TTGATAGTATAGAAATTGTCCCTCGA 57.527 34.615 0.00 0.00 0.00 4.04
2332 2819 7.883217 TGATAGTATAGAAATTGTCCCTCGAC 58.117 38.462 0.00 0.00 39.66 4.20
2333 2820 7.724506 TGATAGTATAGAAATTGTCCCTCGACT 59.275 37.037 0.00 0.00 39.94 4.18
2334 2821 6.394025 AGTATAGAAATTGTCCCTCGACTC 57.606 41.667 0.00 0.00 39.94 3.36
2335 2822 4.674281 ATAGAAATTGTCCCTCGACTCC 57.326 45.455 0.00 0.00 39.94 3.85
2336 2823 2.257207 AGAAATTGTCCCTCGACTCCA 58.743 47.619 0.00 0.00 39.94 3.86
2337 2824 2.637872 AGAAATTGTCCCTCGACTCCAA 59.362 45.455 0.00 0.00 39.94 3.53
2338 2825 3.072476 AGAAATTGTCCCTCGACTCCAAA 59.928 43.478 0.00 0.00 39.94 3.28
2339 2826 3.502123 AATTGTCCCTCGACTCCAAAA 57.498 42.857 0.00 0.00 39.94 2.44
2340 2827 2.249844 TTGTCCCTCGACTCCAAAAC 57.750 50.000 0.00 0.00 39.94 2.43
2341 2828 0.395312 TGTCCCTCGACTCCAAAACC 59.605 55.000 0.00 0.00 39.94 3.27
2342 2829 0.395312 GTCCCTCGACTCCAAAACCA 59.605 55.000 0.00 0.00 35.99 3.67
2343 2830 1.133363 TCCCTCGACTCCAAAACCAA 58.867 50.000 0.00 0.00 0.00 3.67
2344 2831 1.202722 TCCCTCGACTCCAAAACCAAC 60.203 52.381 0.00 0.00 0.00 3.77
2345 2832 1.476110 CCCTCGACTCCAAAACCAACA 60.476 52.381 0.00 0.00 0.00 3.33
2346 2833 2.294074 CCTCGACTCCAAAACCAACAA 58.706 47.619 0.00 0.00 0.00 2.83
2347 2834 2.685897 CCTCGACTCCAAAACCAACAAA 59.314 45.455 0.00 0.00 0.00 2.83
2348 2835 3.317993 CCTCGACTCCAAAACCAACAAAT 59.682 43.478 0.00 0.00 0.00 2.32
2349 2836 4.537015 CTCGACTCCAAAACCAACAAATC 58.463 43.478 0.00 0.00 0.00 2.17
2350 2837 4.204012 TCGACTCCAAAACCAACAAATCT 58.796 39.130 0.00 0.00 0.00 2.40
2351 2838 4.642885 TCGACTCCAAAACCAACAAATCTT 59.357 37.500 0.00 0.00 0.00 2.40
2352 2839 4.739716 CGACTCCAAAACCAACAAATCTTG 59.260 41.667 0.00 0.00 0.00 3.02
2353 2840 5.022282 ACTCCAAAACCAACAAATCTTGG 57.978 39.130 0.00 0.00 45.62 3.61
2360 2847 3.942130 CCAACAAATCTTGGTTCCTCC 57.058 47.619 0.00 0.00 36.65 4.30
2361 2848 3.230134 CCAACAAATCTTGGTTCCTCCA 58.770 45.455 0.00 0.00 45.60 3.86
2372 2859 3.028130 TGGTTCCTCCACTTTCAAAACC 58.972 45.455 0.00 0.00 41.93 3.27
2373 2860 2.034179 GGTTCCTCCACTTTCAAAACCG 59.966 50.000 0.00 0.00 35.97 4.44
2374 2861 1.975660 TCCTCCACTTTCAAAACCGG 58.024 50.000 0.00 0.00 0.00 5.28
2375 2862 1.491332 TCCTCCACTTTCAAAACCGGA 59.509 47.619 9.46 0.00 0.00 5.14
2376 2863 2.107552 TCCTCCACTTTCAAAACCGGAT 59.892 45.455 9.46 0.00 0.00 4.18
2377 2864 3.328343 TCCTCCACTTTCAAAACCGGATA 59.672 43.478 9.46 0.00 0.00 2.59
2378 2865 4.076394 CCTCCACTTTCAAAACCGGATAA 58.924 43.478 9.46 0.00 0.00 1.75
2379 2866 4.156008 CCTCCACTTTCAAAACCGGATAAG 59.844 45.833 9.46 0.00 0.00 1.73
2380 2867 3.504520 TCCACTTTCAAAACCGGATAAGC 59.495 43.478 9.46 0.00 0.00 3.09
2381 2868 3.506067 CCACTTTCAAAACCGGATAAGCT 59.494 43.478 9.46 0.00 0.00 3.74
2382 2869 4.022329 CCACTTTCAAAACCGGATAAGCTT 60.022 41.667 9.46 3.48 0.00 3.74
2383 2870 5.182380 CCACTTTCAAAACCGGATAAGCTTA 59.818 40.000 9.46 8.99 0.00 3.09
2384 2871 6.314784 CACTTTCAAAACCGGATAAGCTTAG 58.685 40.000 9.46 0.59 0.00 2.18
2385 2872 6.002082 ACTTTCAAAACCGGATAAGCTTAGT 58.998 36.000 9.46 1.25 0.00 2.24
2386 2873 6.148976 ACTTTCAAAACCGGATAAGCTTAGTC 59.851 38.462 9.46 9.32 0.00 2.59
2387 2874 4.510571 TCAAAACCGGATAAGCTTAGTCC 58.489 43.478 9.46 15.95 0.00 3.85
2388 2875 4.020039 TCAAAACCGGATAAGCTTAGTCCA 60.020 41.667 23.33 2.79 32.23 4.02
2389 2876 4.772886 AAACCGGATAAGCTTAGTCCAT 57.227 40.909 23.33 14.15 32.23 3.41
2390 2877 4.338379 AACCGGATAAGCTTAGTCCATC 57.662 45.455 23.33 13.69 32.23 3.51
2391 2878 2.296471 ACCGGATAAGCTTAGTCCATCG 59.704 50.000 23.33 16.23 32.23 3.84
2392 2879 2.296471 CCGGATAAGCTTAGTCCATCGT 59.704 50.000 23.33 4.33 32.23 3.73
2393 2880 3.504906 CCGGATAAGCTTAGTCCATCGTA 59.495 47.826 23.33 0.00 32.23 3.43
2394 2881 4.158025 CCGGATAAGCTTAGTCCATCGTAT 59.842 45.833 23.33 3.97 32.23 3.06
2395 2882 5.333513 CGGATAAGCTTAGTCCATCGTATC 58.666 45.833 23.33 10.96 32.23 2.24
2396 2883 5.106277 CGGATAAGCTTAGTCCATCGTATCA 60.106 44.000 23.33 0.00 32.23 2.15
2397 2884 6.094061 GGATAAGCTTAGTCCATCGTATCAC 58.906 44.000 20.90 2.60 32.23 3.06
2398 2885 6.294564 GGATAAGCTTAGTCCATCGTATCACA 60.295 42.308 20.90 0.00 32.23 3.58
2399 2886 5.339008 AAGCTTAGTCCATCGTATCACAA 57.661 39.130 0.00 0.00 0.00 3.33
2400 2887 4.938080 AGCTTAGTCCATCGTATCACAAG 58.062 43.478 0.00 0.00 0.00 3.16
2401 2888 3.491267 GCTTAGTCCATCGTATCACAAGC 59.509 47.826 0.00 0.00 0.00 4.01
2402 2889 4.737946 GCTTAGTCCATCGTATCACAAGCT 60.738 45.833 0.00 0.00 34.49 3.74
2403 2890 3.444703 AGTCCATCGTATCACAAGCTC 57.555 47.619 0.00 0.00 0.00 4.09
2404 2891 3.027412 AGTCCATCGTATCACAAGCTCT 58.973 45.455 0.00 0.00 0.00 4.09
2405 2892 3.067461 AGTCCATCGTATCACAAGCTCTC 59.933 47.826 0.00 0.00 0.00 3.20
2406 2893 2.362397 TCCATCGTATCACAAGCTCTCC 59.638 50.000 0.00 0.00 0.00 3.71
2407 2894 2.546795 CCATCGTATCACAAGCTCTCCC 60.547 54.545 0.00 0.00 0.00 4.30
2408 2895 2.145397 TCGTATCACAAGCTCTCCCT 57.855 50.000 0.00 0.00 0.00 4.20
2409 2896 2.025155 TCGTATCACAAGCTCTCCCTC 58.975 52.381 0.00 0.00 0.00 4.30
2410 2897 1.751351 CGTATCACAAGCTCTCCCTCA 59.249 52.381 0.00 0.00 0.00 3.86
2411 2898 2.363680 CGTATCACAAGCTCTCCCTCAT 59.636 50.000 0.00 0.00 0.00 2.90
2412 2899 3.726607 GTATCACAAGCTCTCCCTCATG 58.273 50.000 0.00 0.00 0.00 3.07
2413 2900 0.251354 TCACAAGCTCTCCCTCATGC 59.749 55.000 0.00 0.00 0.00 4.06
2414 2901 1.088340 CACAAGCTCTCCCTCATGCG 61.088 60.000 0.00 0.00 0.00 4.73
2415 2902 2.178890 CAAGCTCTCCCTCATGCGC 61.179 63.158 0.00 0.00 0.00 6.09
2416 2903 2.365586 AAGCTCTCCCTCATGCGCT 61.366 57.895 9.73 0.00 0.00 5.92
2417 2904 1.908340 AAGCTCTCCCTCATGCGCTT 61.908 55.000 9.73 0.00 33.32 4.68
2418 2905 1.886777 GCTCTCCCTCATGCGCTTC 60.887 63.158 9.73 0.00 0.00 3.86
2419 2906 1.821936 CTCTCCCTCATGCGCTTCT 59.178 57.895 9.73 0.00 0.00 2.85
2420 2907 1.035923 CTCTCCCTCATGCGCTTCTA 58.964 55.000 9.73 0.00 0.00 2.10
2421 2908 1.000385 CTCTCCCTCATGCGCTTCTAG 60.000 57.143 9.73 1.95 0.00 2.43
2422 2909 0.599728 CTCCCTCATGCGCTTCTAGC 60.600 60.000 9.73 0.00 38.02 3.42
2423 2910 1.596477 CCCTCATGCGCTTCTAGCC 60.596 63.158 9.73 0.00 38.18 3.93
2424 2911 1.953138 CCTCATGCGCTTCTAGCCG 60.953 63.158 9.73 0.00 38.18 5.52
2425 2912 1.953138 CTCATGCGCTTCTAGCCGG 60.953 63.158 9.73 0.00 38.18 6.13
2426 2913 2.202932 CATGCGCTTCTAGCCGGT 60.203 61.111 9.73 0.00 38.18 5.28
2427 2914 2.202932 ATGCGCTTCTAGCCGGTG 60.203 61.111 9.73 0.00 38.18 4.94
2430 2917 4.796231 CGCTTCTAGCCGGTGCGT 62.796 66.667 1.90 0.00 44.33 5.24
2431 2918 2.434359 GCTTCTAGCCGGTGCGTT 60.434 61.111 1.90 0.00 44.33 4.84
2432 2919 1.153706 GCTTCTAGCCGGTGCGTTA 60.154 57.895 1.90 0.00 44.33 3.18
2433 2920 1.146358 GCTTCTAGCCGGTGCGTTAG 61.146 60.000 1.90 0.00 44.33 2.34
2434 2921 0.527817 CTTCTAGCCGGTGCGTTAGG 60.528 60.000 1.90 0.00 44.33 2.69
2440 2927 4.690719 CGGTGCGTTAGGCCACCA 62.691 66.667 5.01 0.00 40.61 4.17
2441 2928 2.281900 GGTGCGTTAGGCCACCAA 60.282 61.111 5.01 0.00 42.61 3.67
2442 2929 2.332654 GGTGCGTTAGGCCACCAAG 61.333 63.158 5.01 0.00 42.61 3.61
2443 2930 2.033448 TGCGTTAGGCCACCAAGG 59.967 61.111 5.01 2.66 42.61 3.61
2444 2931 2.349755 GCGTTAGGCCACCAAGGA 59.650 61.111 5.01 0.00 41.22 3.36
2445 2932 1.302993 GCGTTAGGCCACCAAGGAA 60.303 57.895 5.01 0.00 41.22 3.36
2446 2933 0.679960 GCGTTAGGCCACCAAGGAAT 60.680 55.000 5.01 0.00 41.22 3.01
2447 2934 1.379527 CGTTAGGCCACCAAGGAATC 58.620 55.000 5.01 0.00 41.22 2.52
2448 2935 1.339631 CGTTAGGCCACCAAGGAATCA 60.340 52.381 5.01 0.00 41.22 2.57
2449 2936 2.802719 GTTAGGCCACCAAGGAATCAA 58.197 47.619 5.01 0.00 41.22 2.57
2450 2937 2.492088 GTTAGGCCACCAAGGAATCAAC 59.508 50.000 5.01 0.00 41.22 3.18
2451 2938 0.779997 AGGCCACCAAGGAATCAACT 59.220 50.000 5.01 0.00 41.22 3.16
2452 2939 1.992557 AGGCCACCAAGGAATCAACTA 59.007 47.619 5.01 0.00 41.22 2.24
2453 2940 2.025887 AGGCCACCAAGGAATCAACTAG 60.026 50.000 5.01 0.00 41.22 2.57
2454 2941 2.026262 GGCCACCAAGGAATCAACTAGA 60.026 50.000 0.00 0.00 41.22 2.43
2455 2942 3.561313 GGCCACCAAGGAATCAACTAGAA 60.561 47.826 0.00 0.00 41.22 2.10
2456 2943 3.440522 GCCACCAAGGAATCAACTAGAAC 59.559 47.826 0.00 0.00 41.22 3.01
2457 2944 4.651778 CCACCAAGGAATCAACTAGAACA 58.348 43.478 0.00 0.00 41.22 3.18
2458 2945 5.070001 CCACCAAGGAATCAACTAGAACAA 58.930 41.667 0.00 0.00 41.22 2.83
2459 2946 5.711976 CCACCAAGGAATCAACTAGAACAAT 59.288 40.000 0.00 0.00 41.22 2.71
2460 2947 6.209391 CCACCAAGGAATCAACTAGAACAATT 59.791 38.462 0.00 0.00 41.22 2.32
2461 2948 7.393234 CCACCAAGGAATCAACTAGAACAATTA 59.607 37.037 0.00 0.00 41.22 1.40
2462 2949 8.792633 CACCAAGGAATCAACTAGAACAATTAA 58.207 33.333 0.00 0.00 0.00 1.40
2463 2950 8.793592 ACCAAGGAATCAACTAGAACAATTAAC 58.206 33.333 0.00 0.00 0.00 2.01
2464 2951 9.014297 CCAAGGAATCAACTAGAACAATTAACT 57.986 33.333 0.00 0.00 0.00 2.24
2499 2986 6.548321 AGCTAACTCTGCTAGTATACCAGAT 58.452 40.000 9.79 1.62 37.50 2.90
2501 2988 7.040062 AGCTAACTCTGCTAGTATACCAGATTG 60.040 40.741 9.79 4.06 37.50 2.67
2518 3005 4.846137 CAGATTGCTTTGCTTTACGTGTAC 59.154 41.667 0.00 0.00 0.00 2.90
2635 3129 5.164620 ACATCATCTCACACCATTGTACA 57.835 39.130 0.00 0.00 33.30 2.90
2658 3152 4.851639 ATCCTGATCCATATACCAAGGC 57.148 45.455 0.00 0.00 0.00 4.35
2700 3194 9.914131 AAATAAGAAAAGATTGTTTACTGGAGC 57.086 29.630 0.00 0.00 0.00 4.70
2714 3208 8.730680 TGTTTACTGGAGCTCTAAATTTGAATC 58.269 33.333 14.64 0.00 0.00 2.52
2727 3221 8.477256 TCTAAATTTGAATCTGGGCAAAATAGG 58.523 33.333 0.00 0.00 37.52 2.57
2729 3223 5.920193 TTTGAATCTGGGCAAAATAGGAG 57.080 39.130 0.00 0.00 31.64 3.69
2739 3233 3.190535 GGCAAAATAGGAGAAAAGCGTCA 59.809 43.478 0.00 0.00 0.00 4.35
2743 3237 6.611381 CAAAATAGGAGAAAAGCGTCATTCA 58.389 36.000 0.00 0.00 0.00 2.57
2750 3244 3.251004 AGAAAAGCGTCATTCACTTCACC 59.749 43.478 0.00 0.00 0.00 4.02
2831 3325 7.664318 ACTCGTTTACCATTTCCTTCTTGTATT 59.336 33.333 0.00 0.00 0.00 1.89
2839 3333 8.957466 ACCATTTCCTTCTTGTATTTAGTTAGC 58.043 33.333 0.00 0.00 0.00 3.09
2885 3379 5.070847 TCATCATTGCATAGTTCTGGCTAGA 59.929 40.000 0.00 0.00 0.00 2.43
2903 3397 7.796054 TGGCTAGAATTTTACTAGAGCTGATT 58.204 34.615 0.00 0.00 39.48 2.57
2937 3431 2.486966 GCTTGCAATCGACCAGCC 59.513 61.111 0.00 0.00 0.00 4.85
2944 3438 1.656652 CAATCGACCAGCCGAAATCT 58.343 50.000 0.00 0.00 42.22 2.40
2954 3448 5.602628 ACCAGCCGAAATCTCTATTTCTAC 58.397 41.667 8.69 2.11 45.92 2.59
3013 3507 4.082408 CGAACTAGTTACATGTCCACTGGA 60.082 45.833 21.48 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.686052 GTCCAAACATGTGGCAAGGAA 59.314 47.619 0.00 0.00 38.68 3.36
67 68 1.567649 TCTCCAGGGGTACGTGTCTAT 59.432 52.381 0.00 0.00 0.00 1.98
77 78 0.771755 GTGGAAAAGTCTCCAGGGGT 59.228 55.000 0.00 0.00 46.29 4.95
110 127 4.756642 CACTGCCAAACAAGTCTCAGATAA 59.243 41.667 0.00 0.00 0.00 1.75
270 401 3.773860 TGATTGAAAACTGTTGCACGT 57.226 38.095 0.00 0.00 0.00 4.49
272 403 6.833342 ATCTTTGATTGAAAACTGTTGCAC 57.167 33.333 0.00 0.00 0.00 4.57
286 417 6.409524 TGCTCCTTTGTTCAATCTTTGATT 57.590 33.333 0.00 0.00 39.84 2.57
289 420 6.480981 ACATTTGCTCCTTTGTTCAATCTTTG 59.519 34.615 0.00 0.00 0.00 2.77
303 434 3.891366 AGTTTGCTTGTACATTTGCTCCT 59.109 39.130 14.23 7.00 0.00 3.69
357 796 5.465390 TGTCATTGGACTCTTTTTACACGAG 59.535 40.000 0.00 0.00 44.61 4.18
400 840 8.195165 TGGTGGGTCAAAATTGATTATTGTTA 57.805 30.769 0.00 0.00 39.73 2.41
410 850 3.465871 CCAGTTTGGTGGGTCAAAATTG 58.534 45.455 0.00 0.00 38.21 2.32
426 866 6.017192 TCTTCTAGAGGACATGTAACCAGTT 58.983 40.000 0.00 0.00 0.00 3.16
427 867 5.580998 TCTTCTAGAGGACATGTAACCAGT 58.419 41.667 0.00 0.00 0.00 4.00
428 868 6.723298 ATCTTCTAGAGGACATGTAACCAG 57.277 41.667 6.72 0.00 0.00 4.00
429 869 7.839705 AGTAATCTTCTAGAGGACATGTAACCA 59.160 37.037 6.72 0.00 0.00 3.67
430 870 8.240267 AGTAATCTTCTAGAGGACATGTAACC 57.760 38.462 6.72 0.00 0.00 2.85
431 871 8.904834 TGAGTAATCTTCTAGAGGACATGTAAC 58.095 37.037 6.72 0.00 0.00 2.50
432 872 9.647918 ATGAGTAATCTTCTAGAGGACATGTAA 57.352 33.333 6.72 0.00 0.00 2.41
435 875 9.829507 AAAATGAGTAATCTTCTAGAGGACATG 57.170 33.333 6.72 0.00 0.00 3.21
438 878 8.478877 TGGAAAATGAGTAATCTTCTAGAGGAC 58.521 37.037 6.72 0.00 0.00 3.85
439 879 8.609617 TGGAAAATGAGTAATCTTCTAGAGGA 57.390 34.615 7.06 7.06 0.00 3.71
440 880 9.270640 CATGGAAAATGAGTAATCTTCTAGAGG 57.729 37.037 0.00 0.00 0.00 3.69
441 881 8.772705 GCATGGAAAATGAGTAATCTTCTAGAG 58.227 37.037 0.00 0.00 0.00 2.43
442 882 8.489489 AGCATGGAAAATGAGTAATCTTCTAGA 58.511 33.333 0.00 0.00 0.00 2.43
443 883 8.674263 AGCATGGAAAATGAGTAATCTTCTAG 57.326 34.615 0.00 0.00 0.00 2.43
444 884 9.113838 GAAGCATGGAAAATGAGTAATCTTCTA 57.886 33.333 0.00 0.00 0.00 2.10
445 885 7.833183 AGAAGCATGGAAAATGAGTAATCTTCT 59.167 33.333 0.00 0.00 32.96 2.85
446 886 7.994194 AGAAGCATGGAAAATGAGTAATCTTC 58.006 34.615 0.00 0.00 0.00 2.87
447 887 7.951347 AGAAGCATGGAAAATGAGTAATCTT 57.049 32.000 0.00 0.00 0.00 2.40
448 888 7.395489 ACAAGAAGCATGGAAAATGAGTAATCT 59.605 33.333 0.00 0.00 0.00 2.40
449 889 7.542025 ACAAGAAGCATGGAAAATGAGTAATC 58.458 34.615 0.00 0.00 0.00 1.75
450 890 7.472334 ACAAGAAGCATGGAAAATGAGTAAT 57.528 32.000 0.00 0.00 0.00 1.89
451 891 6.899393 ACAAGAAGCATGGAAAATGAGTAA 57.101 33.333 0.00 0.00 0.00 2.24
452 892 7.168219 AGTACAAGAAGCATGGAAAATGAGTA 58.832 34.615 0.00 0.00 0.00 2.59
453 893 6.006449 AGTACAAGAAGCATGGAAAATGAGT 58.994 36.000 0.00 0.00 0.00 3.41
454 894 6.506500 AGTACAAGAAGCATGGAAAATGAG 57.493 37.500 0.00 0.00 0.00 2.90
455 895 6.489700 TGAAGTACAAGAAGCATGGAAAATGA 59.510 34.615 0.00 0.00 0.00 2.57
478 918 4.282496 ACAAGTGGGTGGTTAAAACATGA 58.718 39.130 0.00 0.00 0.00 3.07
621 1071 1.216064 TATGGCAGTCTCCATGGCTT 58.784 50.000 6.96 0.00 45.84 4.35
693 1143 2.875672 GCATGGCTCAAGGAGTTGTACA 60.876 50.000 0.00 0.00 34.98 2.90
899 1355 0.951040 GCTACGAAGCCTGCACTGTT 60.951 55.000 0.00 0.00 43.40 3.16
968 1434 4.079980 TCCTTCTTGGATGTTGTTCGAA 57.920 40.909 0.00 0.00 40.56 3.71
1015 1481 2.603075 AAGCTTTCCAAGGCACCATA 57.397 45.000 0.00 0.00 0.00 2.74
1118 1584 7.321271 CGAACATGAAATTGTCAGTGTAAAGAC 59.679 37.037 0.00 0.00 40.43 3.01
1171 1637 4.090761 TGTTCTCCAACAAGAAGCTCAT 57.909 40.909 0.00 0.00 39.69 2.90
1199 1665 2.439409 CAAGTGCATGATCACCAGGAA 58.561 47.619 0.00 0.00 37.68 3.36
1222 1690 5.983333 ACACCTCCTATGATTGGAAGAAT 57.017 39.130 0.00 0.00 32.61 2.40
1239 1707 2.380064 TCTTTCCAATGCCAACACCT 57.620 45.000 0.00 0.00 0.00 4.00
1311 1779 6.209192 TGTGTCCATTCAAGTGCAAAATAGAT 59.791 34.615 0.00 0.00 0.00 1.98
1398 1867 2.939103 GTCGCCTACATCAGAAGCAAAT 59.061 45.455 0.00 0.00 0.00 2.32
1716 2188 2.227865 GCAGAGCCAAAACCGAACATTA 59.772 45.455 0.00 0.00 0.00 1.90
1809 2282 2.133281 CCACATGATGGCCTTCTTCA 57.867 50.000 18.67 9.92 43.24 3.02
1861 2334 9.388346 TGAAACATCAATTGTATAACGTTTCAC 57.612 29.630 21.36 5.53 43.40 3.18
1890 2363 2.972348 ACACTTGGTGACTCCTCCTTA 58.028 47.619 4.62 0.00 36.96 2.69
1920 2393 3.862267 CACTTGGATCTGCTAGAAGTTCG 59.138 47.826 0.00 0.00 0.00 3.95
1951 2424 6.500684 TGCAATTAGAATGAAGTCACCTTC 57.499 37.500 0.00 0.00 46.09 3.46
1956 2429 5.508567 TCCCATGCAATTAGAATGAAGTCA 58.491 37.500 0.00 0.00 34.97 3.41
2003 2476 6.537301 ACGACTTGTGACAAAAAGATGAACTA 59.463 34.615 0.00 0.00 0.00 2.24
2005 2478 5.569413 ACGACTTGTGACAAAAAGATGAAC 58.431 37.500 0.00 0.00 0.00 3.18
2009 2482 6.046593 TGAGTACGACTTGTGACAAAAAGAT 58.953 36.000 0.00 0.00 0.00 2.40
2019 2492 3.213249 GTACCCTGAGTACGACTTGTG 57.787 52.381 0.00 0.00 41.94 3.33
2029 2502 1.909302 CCCTTCATGTGTACCCTGAGT 59.091 52.381 0.00 0.00 0.00 3.41
2049 2522 2.124736 TCCCTGGCAATGCGCTAC 60.125 61.111 9.73 0.00 41.91 3.58
2050 2523 2.190313 CTCCCTGGCAATGCGCTA 59.810 61.111 9.73 0.00 41.91 4.26
2053 2526 2.045045 TTCCTCCCTGGCAATGCG 60.045 61.111 0.00 0.00 35.26 4.73
2056 2529 1.852157 TTCGCTTCCTCCCTGGCAAT 61.852 55.000 0.00 0.00 35.26 3.56
2142 2626 3.924073 CGTGAACACATCCGTTTCAGATA 59.076 43.478 5.80 0.00 0.00 1.98
2145 2629 1.864711 ACGTGAACACATCCGTTTCAG 59.135 47.619 5.80 0.00 33.14 3.02
2232 2719 9.941664 GGATCTGATAGAACACACAATTTTATG 57.058 33.333 0.00 0.00 0.00 1.90
2237 2724 7.766278 GTGTAGGATCTGATAGAACACACAATT 59.234 37.037 17.25 0.00 34.23 2.32
2242 2729 7.482169 AAAGTGTAGGATCTGATAGAACACA 57.518 36.000 21.17 8.07 35.68 3.72
2243 2730 8.779354 AAAAAGTGTAGGATCTGATAGAACAC 57.221 34.615 15.57 15.57 34.25 3.32
2287 2774 9.753674 ACTATCAAAATAGTTGAGGGATGAAAA 57.246 29.630 0.00 0.00 44.62 2.29
2304 2791 9.542462 CGAGGGACAATTTCTATACTATCAAAA 57.458 33.333 0.00 0.00 0.00 2.44
2305 2792 8.920174 TCGAGGGACAATTTCTATACTATCAAA 58.080 33.333 0.00 0.00 0.00 2.69
2306 2793 8.358148 GTCGAGGGACAATTTCTATACTATCAA 58.642 37.037 0.00 0.00 42.91 2.57
2307 2794 7.724506 AGTCGAGGGACAATTTCTATACTATCA 59.275 37.037 0.00 0.00 45.92 2.15
2308 2795 8.113173 AGTCGAGGGACAATTTCTATACTATC 57.887 38.462 0.00 0.00 45.92 2.08
2309 2796 7.177041 GGAGTCGAGGGACAATTTCTATACTAT 59.823 40.741 0.00 0.00 45.92 2.12
2310 2797 6.489361 GGAGTCGAGGGACAATTTCTATACTA 59.511 42.308 0.00 0.00 45.92 1.82
2311 2798 5.302313 GGAGTCGAGGGACAATTTCTATACT 59.698 44.000 0.00 0.00 45.92 2.12
2312 2799 5.068723 TGGAGTCGAGGGACAATTTCTATAC 59.931 44.000 0.00 0.00 45.92 1.47
2313 2800 5.205821 TGGAGTCGAGGGACAATTTCTATA 58.794 41.667 0.00 0.00 45.92 1.31
2314 2801 4.030913 TGGAGTCGAGGGACAATTTCTAT 58.969 43.478 0.00 0.00 45.92 1.98
2315 2802 3.437213 TGGAGTCGAGGGACAATTTCTA 58.563 45.455 0.00 0.00 45.92 2.10
2316 2803 2.257207 TGGAGTCGAGGGACAATTTCT 58.743 47.619 0.00 0.00 45.92 2.52
2317 2804 2.762535 TGGAGTCGAGGGACAATTTC 57.237 50.000 0.00 0.00 45.92 2.17
2318 2805 3.502123 TTTGGAGTCGAGGGACAATTT 57.498 42.857 0.00 0.00 45.92 1.82
2319 2806 3.146847 GTTTTGGAGTCGAGGGACAATT 58.853 45.455 0.00 0.00 45.92 2.32
2320 2807 2.552373 GGTTTTGGAGTCGAGGGACAAT 60.552 50.000 0.00 0.00 45.92 2.71
2321 2808 1.202722 GGTTTTGGAGTCGAGGGACAA 60.203 52.381 0.00 0.00 45.92 3.18
2322 2809 0.395312 GGTTTTGGAGTCGAGGGACA 59.605 55.000 0.00 0.00 45.92 4.02
2323 2810 0.395312 TGGTTTTGGAGTCGAGGGAC 59.605 55.000 0.00 0.00 43.76 4.46
2324 2811 1.133363 TTGGTTTTGGAGTCGAGGGA 58.867 50.000 0.00 0.00 0.00 4.20
2325 2812 1.235724 GTTGGTTTTGGAGTCGAGGG 58.764 55.000 0.00 0.00 0.00 4.30
2326 2813 1.961793 TGTTGGTTTTGGAGTCGAGG 58.038 50.000 0.00 0.00 0.00 4.63
2327 2814 4.275936 AGATTTGTTGGTTTTGGAGTCGAG 59.724 41.667 0.00 0.00 0.00 4.04
2328 2815 4.204012 AGATTTGTTGGTTTTGGAGTCGA 58.796 39.130 0.00 0.00 0.00 4.20
2329 2816 4.568152 AGATTTGTTGGTTTTGGAGTCG 57.432 40.909 0.00 0.00 0.00 4.18
2330 2817 5.049828 CCAAGATTTGTTGGTTTTGGAGTC 58.950 41.667 0.00 0.00 41.96 3.36
2331 2818 5.022282 CCAAGATTTGTTGGTTTTGGAGT 57.978 39.130 0.00 0.00 41.96 3.85
2352 2839 2.034179 CGGTTTTGAAAGTGGAGGAACC 59.966 50.000 0.00 0.00 39.54 3.62
2353 2840 2.034179 CCGGTTTTGAAAGTGGAGGAAC 59.966 50.000 0.00 0.00 0.00 3.62
2354 2841 2.092321 TCCGGTTTTGAAAGTGGAGGAA 60.092 45.455 0.00 0.00 0.00 3.36
2355 2842 1.491332 TCCGGTTTTGAAAGTGGAGGA 59.509 47.619 0.00 0.00 0.00 3.71
2356 2843 1.975660 TCCGGTTTTGAAAGTGGAGG 58.024 50.000 0.00 0.00 0.00 4.30
2357 2844 4.379499 GCTTATCCGGTTTTGAAAGTGGAG 60.379 45.833 0.00 0.00 0.00 3.86
2358 2845 3.504520 GCTTATCCGGTTTTGAAAGTGGA 59.495 43.478 0.00 0.00 0.00 4.02
2359 2846 3.506067 AGCTTATCCGGTTTTGAAAGTGG 59.494 43.478 0.00 0.00 0.00 4.00
2360 2847 4.766404 AGCTTATCCGGTTTTGAAAGTG 57.234 40.909 0.00 0.00 0.00 3.16
2361 2848 6.002082 ACTAAGCTTATCCGGTTTTGAAAGT 58.998 36.000 6.64 0.00 0.00 2.66
2362 2849 6.403309 GGACTAAGCTTATCCGGTTTTGAAAG 60.403 42.308 6.64 0.00 0.00 2.62
2363 2850 5.413523 GGACTAAGCTTATCCGGTTTTGAAA 59.586 40.000 6.64 0.00 0.00 2.69
2364 2851 4.939439 GGACTAAGCTTATCCGGTTTTGAA 59.061 41.667 6.64 0.00 0.00 2.69
2365 2852 4.020039 TGGACTAAGCTTATCCGGTTTTGA 60.020 41.667 20.58 7.25 35.06 2.69
2366 2853 4.258543 TGGACTAAGCTTATCCGGTTTTG 58.741 43.478 20.58 6.35 35.06 2.44
2367 2854 4.563140 TGGACTAAGCTTATCCGGTTTT 57.437 40.909 20.58 0.00 35.06 2.43
2368 2855 4.704965 GATGGACTAAGCTTATCCGGTTT 58.295 43.478 20.58 11.40 35.06 3.27
2369 2856 3.243771 CGATGGACTAAGCTTATCCGGTT 60.244 47.826 20.58 12.99 35.06 4.44
2370 2857 2.296471 CGATGGACTAAGCTTATCCGGT 59.704 50.000 20.58 11.37 35.06 5.28
2371 2858 2.296471 ACGATGGACTAAGCTTATCCGG 59.704 50.000 20.58 16.57 35.06 5.14
2372 2859 3.644884 ACGATGGACTAAGCTTATCCG 57.355 47.619 20.58 14.81 35.06 4.18
2373 2860 6.094061 GTGATACGATGGACTAAGCTTATCC 58.906 44.000 19.82 19.82 0.00 2.59
2374 2861 6.678878 TGTGATACGATGGACTAAGCTTATC 58.321 40.000 6.64 6.95 0.00 1.75
2375 2862 6.650427 TGTGATACGATGGACTAAGCTTAT 57.350 37.500 6.64 0.00 0.00 1.73
2376 2863 6.459670 TTGTGATACGATGGACTAAGCTTA 57.540 37.500 5.94 5.94 0.00 3.09
2377 2864 5.339008 TTGTGATACGATGGACTAAGCTT 57.661 39.130 3.48 3.48 0.00 3.74
2378 2865 4.737946 GCTTGTGATACGATGGACTAAGCT 60.738 45.833 0.00 0.00 36.15 3.74
2379 2866 3.491267 GCTTGTGATACGATGGACTAAGC 59.509 47.826 0.00 0.00 0.00 3.09
2380 2867 4.938080 AGCTTGTGATACGATGGACTAAG 58.062 43.478 0.00 0.00 0.00 2.18
2381 2868 4.645136 AGAGCTTGTGATACGATGGACTAA 59.355 41.667 0.00 0.00 0.00 2.24
2382 2869 4.207955 AGAGCTTGTGATACGATGGACTA 58.792 43.478 0.00 0.00 0.00 2.59
2383 2870 3.027412 AGAGCTTGTGATACGATGGACT 58.973 45.455 0.00 0.00 0.00 3.85
2384 2871 3.376540 GAGAGCTTGTGATACGATGGAC 58.623 50.000 0.00 0.00 0.00 4.02
2385 2872 2.362397 GGAGAGCTTGTGATACGATGGA 59.638 50.000 0.00 0.00 0.00 3.41
2386 2873 2.546795 GGGAGAGCTTGTGATACGATGG 60.547 54.545 0.00 0.00 0.00 3.51
2387 2874 2.363680 AGGGAGAGCTTGTGATACGATG 59.636 50.000 0.00 0.00 0.00 3.84
2388 2875 2.625790 GAGGGAGAGCTTGTGATACGAT 59.374 50.000 0.00 0.00 0.00 3.73
2389 2876 2.025155 GAGGGAGAGCTTGTGATACGA 58.975 52.381 0.00 0.00 0.00 3.43
2390 2877 1.751351 TGAGGGAGAGCTTGTGATACG 59.249 52.381 0.00 0.00 0.00 3.06
2391 2878 3.726607 CATGAGGGAGAGCTTGTGATAC 58.273 50.000 0.00 0.00 0.00 2.24
2392 2879 2.103771 GCATGAGGGAGAGCTTGTGATA 59.896 50.000 0.00 0.00 0.00 2.15
2393 2880 1.134159 GCATGAGGGAGAGCTTGTGAT 60.134 52.381 0.00 0.00 0.00 3.06
2394 2881 0.251354 GCATGAGGGAGAGCTTGTGA 59.749 55.000 0.00 0.00 0.00 3.58
2395 2882 1.088340 CGCATGAGGGAGAGCTTGTG 61.088 60.000 0.00 0.00 0.00 3.33
2396 2883 1.220206 CGCATGAGGGAGAGCTTGT 59.780 57.895 0.00 0.00 0.00 3.16
2397 2884 2.178890 GCGCATGAGGGAGAGCTTG 61.179 63.158 0.30 0.00 0.00 4.01
2398 2885 1.908340 AAGCGCATGAGGGAGAGCTT 61.908 55.000 11.47 0.00 44.23 3.74
2399 2886 2.308968 GAAGCGCATGAGGGAGAGCT 62.309 60.000 11.47 0.00 42.74 4.09
2400 2887 1.886777 GAAGCGCATGAGGGAGAGC 60.887 63.158 11.47 0.00 0.00 4.09
2401 2888 1.000385 CTAGAAGCGCATGAGGGAGAG 60.000 57.143 11.47 0.00 0.00 3.20
2402 2889 1.035923 CTAGAAGCGCATGAGGGAGA 58.964 55.000 11.47 0.00 0.00 3.71
2403 2890 0.599728 GCTAGAAGCGCATGAGGGAG 60.600 60.000 11.47 0.00 0.00 4.30
2404 2891 1.443407 GCTAGAAGCGCATGAGGGA 59.557 57.895 11.47 0.00 0.00 4.20
2405 2892 1.596477 GGCTAGAAGCGCATGAGGG 60.596 63.158 11.47 0.00 43.62 4.30
2406 2893 1.953138 CGGCTAGAAGCGCATGAGG 60.953 63.158 11.47 0.00 43.62 3.86
2407 2894 1.953138 CCGGCTAGAAGCGCATGAG 60.953 63.158 11.47 1.76 43.62 2.90
2408 2895 2.106938 CCGGCTAGAAGCGCATGA 59.893 61.111 11.47 0.00 43.62 3.07
2409 2896 2.202932 ACCGGCTAGAAGCGCATG 60.203 61.111 11.47 0.00 43.62 4.06
2410 2897 2.202932 CACCGGCTAGAAGCGCAT 60.203 61.111 11.47 0.00 43.62 4.73
2414 2901 1.146358 CTAACGCACCGGCTAGAAGC 61.146 60.000 0.00 0.00 41.46 3.86
2415 2902 0.527817 CCTAACGCACCGGCTAGAAG 60.528 60.000 0.00 0.00 38.10 2.85
2416 2903 1.514087 CCTAACGCACCGGCTAGAA 59.486 57.895 0.00 0.00 38.10 2.10
2417 2904 3.072486 GCCTAACGCACCGGCTAGA 62.072 63.158 0.00 0.00 40.62 2.43
2418 2905 2.585247 GCCTAACGCACCGGCTAG 60.585 66.667 0.00 0.00 40.62 3.42
2419 2906 4.151582 GGCCTAACGCACCGGCTA 62.152 66.667 0.00 0.00 43.29 3.93
2423 2910 4.690719 TGGTGGCCTAACGCACCG 62.691 66.667 3.32 0.00 39.90 4.94
2424 2911 2.281900 TTGGTGGCCTAACGCACC 60.282 61.111 3.32 1.76 40.31 5.01
2425 2912 2.332654 CCTTGGTGGCCTAACGCAC 61.333 63.158 3.32 0.00 40.31 5.34
2426 2913 2.033448 CCTTGGTGGCCTAACGCA 59.967 61.111 3.32 0.00 40.31 5.24
2427 2914 0.679960 ATTCCTTGGTGGCCTAACGC 60.680 55.000 3.32 0.00 35.26 4.84
2428 2915 1.339631 TGATTCCTTGGTGGCCTAACG 60.340 52.381 3.32 0.00 35.26 3.18
2429 2916 2.492088 GTTGATTCCTTGGTGGCCTAAC 59.508 50.000 3.32 0.00 35.26 2.34
2430 2917 2.378547 AGTTGATTCCTTGGTGGCCTAA 59.621 45.455 3.32 0.00 35.26 2.69
2431 2918 1.992557 AGTTGATTCCTTGGTGGCCTA 59.007 47.619 3.32 0.00 35.26 3.93
2432 2919 0.779997 AGTTGATTCCTTGGTGGCCT 59.220 50.000 3.32 0.00 35.26 5.19
2433 2920 2.026262 TCTAGTTGATTCCTTGGTGGCC 60.026 50.000 0.00 0.00 35.26 5.36
2434 2921 3.350219 TCTAGTTGATTCCTTGGTGGC 57.650 47.619 0.00 0.00 35.26 5.01
2435 2922 4.651778 TGTTCTAGTTGATTCCTTGGTGG 58.348 43.478 0.00 0.00 37.10 4.61
2436 2923 6.824305 ATTGTTCTAGTTGATTCCTTGGTG 57.176 37.500 0.00 0.00 0.00 4.17
2437 2924 8.793592 GTTAATTGTTCTAGTTGATTCCTTGGT 58.206 33.333 0.00 0.00 0.00 3.67
2438 2925 9.014297 AGTTAATTGTTCTAGTTGATTCCTTGG 57.986 33.333 0.00 0.00 0.00 3.61
2456 2943 8.721478 AGTTAGCTCACATACACAAGTTAATTG 58.279 33.333 0.03 0.00 45.01 2.32
2457 2944 8.848474 AGTTAGCTCACATACACAAGTTAATT 57.152 30.769 0.03 0.00 0.00 1.40
2458 2945 8.314751 AGAGTTAGCTCACATACACAAGTTAAT 58.685 33.333 9.43 0.00 44.00 1.40
2459 2946 7.598869 CAGAGTTAGCTCACATACACAAGTTAA 59.401 37.037 9.43 0.00 44.00 2.01
2460 2947 7.090808 CAGAGTTAGCTCACATACACAAGTTA 58.909 38.462 9.43 0.00 44.00 2.24
2461 2948 5.928839 CAGAGTTAGCTCACATACACAAGTT 59.071 40.000 9.43 0.00 44.00 2.66
2462 2949 5.473931 CAGAGTTAGCTCACATACACAAGT 58.526 41.667 9.43 0.00 44.00 3.16
2463 2950 4.328440 GCAGAGTTAGCTCACATACACAAG 59.672 45.833 9.43 0.00 44.00 3.16
2464 2951 4.021104 AGCAGAGTTAGCTCACATACACAA 60.021 41.667 9.43 0.00 44.00 3.33
2465 2952 3.511540 AGCAGAGTTAGCTCACATACACA 59.488 43.478 9.43 0.00 44.00 3.72
2466 2953 4.116747 AGCAGAGTTAGCTCACATACAC 57.883 45.455 9.43 0.00 44.00 2.90
2467 2954 4.950475 ACTAGCAGAGTTAGCTCACATACA 59.050 41.667 9.43 0.00 44.00 2.29
2468 2955 5.508200 ACTAGCAGAGTTAGCTCACATAC 57.492 43.478 9.43 0.00 44.00 2.39
2469 2956 7.390996 GGTATACTAGCAGAGTTAGCTCACATA 59.609 40.741 9.43 0.00 44.00 2.29
2470 2957 6.207810 GGTATACTAGCAGAGTTAGCTCACAT 59.792 42.308 9.43 0.00 44.00 3.21
2471 2958 5.531659 GGTATACTAGCAGAGTTAGCTCACA 59.468 44.000 9.43 0.00 44.00 3.58
2472 2959 5.531659 TGGTATACTAGCAGAGTTAGCTCAC 59.468 44.000 9.43 0.63 44.00 3.51
2473 2960 5.691896 TGGTATACTAGCAGAGTTAGCTCA 58.308 41.667 9.43 0.00 44.00 4.26
2499 2986 2.032722 CCGTACACGTAAAGCAAAGCAA 60.033 45.455 0.58 0.00 37.74 3.91
2501 2988 1.528161 ACCGTACACGTAAAGCAAAGC 59.472 47.619 0.58 0.00 37.74 3.51
2562 3056 8.950007 ATATTTTTGTCCCTCTACCTTTTTGA 57.050 30.769 0.00 0.00 0.00 2.69
2603 3097 4.456911 GTGTGAGATGATGTTGTTGGTCAT 59.543 41.667 0.00 0.00 35.42 3.06
2605 3099 3.189287 GGTGTGAGATGATGTTGTTGGTC 59.811 47.826 0.00 0.00 0.00 4.02
2635 3129 5.574188 GCCTTGGTATATGGATCAGGATTT 58.426 41.667 0.00 0.00 0.00 2.17
2658 3152 9.716507 TTTTCTTATTTCAGTTCAGTTTTCTCG 57.283 29.630 0.00 0.00 0.00 4.04
2700 3194 9.525409 CTATTTTGCCCAGATTCAAATTTAGAG 57.475 33.333 0.00 0.00 32.92 2.43
2714 3208 3.428045 CGCTTTTCTCCTATTTTGCCCAG 60.428 47.826 0.00 0.00 0.00 4.45
2739 3233 1.072331 AGTGAAGGCGGTGAAGTGAAT 59.928 47.619 0.00 0.00 0.00 2.57
2743 3237 0.468226 TTGAGTGAAGGCGGTGAAGT 59.532 50.000 0.00 0.00 0.00 3.01
2750 3244 1.018226 CCTGAGCTTGAGTGAAGGCG 61.018 60.000 0.00 0.00 31.56 5.52
2865 3359 6.630444 AATTCTAGCCAGAACTATGCAATG 57.370 37.500 0.00 0.00 43.50 2.82
2866 3360 7.651027 AAAATTCTAGCCAGAACTATGCAAT 57.349 32.000 0.00 0.00 43.50 3.56
2867 3361 7.829211 AGTAAAATTCTAGCCAGAACTATGCAA 59.171 33.333 0.00 0.00 43.50 4.08
2877 3371 6.810911 TCAGCTCTAGTAAAATTCTAGCCAG 58.189 40.000 0.00 0.00 36.00 4.85
2885 3379 9.512588 CCATATGGAATCAGCTCTAGTAAAATT 57.487 33.333 17.49 0.00 37.39 1.82
2903 3397 0.620030 AGCGCATATGCCCATATGGA 59.380 50.000 24.00 4.24 46.62 3.41
2908 3402 1.829096 TGCAAGCGCATATGCCCAT 60.829 52.632 21.77 2.90 45.36 4.00
2944 3438 6.384015 TGAAGAAGCCCATCTGTAGAAATAGA 59.616 38.462 0.00 0.00 0.00 1.98
2954 3448 2.027377 AGAGTGTGAAGAAGCCCATCTG 60.027 50.000 0.00 0.00 0.00 2.90
3013 3507 6.388619 ACTACATAGTTGGGTGGAAATCTT 57.611 37.500 0.00 0.00 31.13 2.40


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

AutoCloner maintained by Alex Coulton.