Multiple sequence alignment - TraesCS5A01G389700

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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 TraesCS5A01G389700 chr5A 100.000 3564 0 0 1 3564 585431469 585427906 0.000000e+00 6582.0
1 TraesCS5A01G389700 chr5A 81.098 492 77 13 1063 1551 585417226 585416748 2.600000e-101 379.0
2 TraesCS5A01G389700 chr5A 96.040 101 4 0 2466 2566 585416648 585416548 7.920000e-37 165.0
3 TraesCS5A01G389700 chr5A 85.417 144 16 4 2438 2579 585421057 585420917 1.030000e-30 145.0
4 TraesCS5A01G389700 chr5B 83.304 2276 215 90 829 2989 572391042 572388817 0.000000e+00 1945.0
5 TraesCS5A01G389700 chr5B 86.443 863 50 37 1 826 572391908 572391076 0.000000e+00 883.0
6 TraesCS5A01G389700 chr5B 85.072 556 70 8 3013 3562 572381290 572380742 4.020000e-154 555.0
7 TraesCS5A01G389700 chr5B 83.495 515 58 19 1045 1551 572364512 572364017 4.190000e-124 455.0
8 TraesCS5A01G389700 chr5B 89.686 223 23 0 1329 1551 572379150 572378928 5.820000e-73 285.0
9 TraesCS5A01G389700 chr5B 94.059 101 6 0 2466 2566 572363924 572363824 1.710000e-33 154.0
10 TraesCS5A01G389700 chr5B 85.833 120 16 1 2450 2569 572378856 572378738 3.740000e-25 126.0
11 TraesCS5A01G389700 chr5D 84.323 1027 70 41 679 1651 465032134 465031145 0.000000e+00 920.0
12 TraesCS5A01G389700 chr5D 87.336 608 44 18 1 603 465034671 465034092 0.000000e+00 665.0
13 TraesCS5A01G389700 chr5D 81.657 845 75 42 2187 2990 465030512 465029707 2.340000e-176 628.0
14 TraesCS5A01G389700 chr5D 84.587 545 71 8 3024 3562 465024346 465023809 2.440000e-146 529.0
15 TraesCS5A01G389700 chr5D 85.433 508 51 14 1652 2137 465031111 465030605 1.140000e-139 507.0
16 TraesCS5A01G389700 chr5D 89.686 223 23 0 1329 1551 465012453 465012231 5.820000e-73 285.0
17 TraesCS5A01G389700 chr5D 87.892 223 27 0 1329 1551 465022232 465022010 2.730000e-66 263.0
18 TraesCS5A01G389700 chr5D 92.361 144 10 1 1055 1197 465012708 465012565 1.680000e-48 204.0
19 TraesCS5A01G389700 chr5D 91.156 147 13 0 1057 1203 465022497 465022351 2.170000e-47 200.0
20 TraesCS5A01G389700 chr5D 96.000 100 4 0 2466 2565 465012133 465012034 2.850000e-36 163.0
21 TraesCS5A01G389700 chr1A 78.680 591 112 11 2978 3562 499637697 499638279 7.220000e-102 381.0
22 TraesCS5A01G389700 chr7A 82.707 399 56 10 1713 2098 533600591 533600989 3.410000e-90 342.0
23 TraesCS5A01G389700 chr7A 86.780 295 37 2 1728 2021 533585084 533585377 9.540000e-86 327.0
24 TraesCS5A01G389700 chr7A 84.839 310 45 2 1713 2021 533597520 533597828 9.610000e-81 311.0
25 TraesCS5A01G389700 chr7D 81.373 408 51 20 1712 2099 467041414 467041012 3.460000e-80 309.0
26 TraesCS5A01G389700 chr7D 85.714 56 8 0 3210 3265 598622570 598622515 3.840000e-05 60.2
27 TraesCS5A01G389700 chr6A 84.488 303 44 3 1716 2017 18743605 18743305 2.690000e-76 296.0
28 TraesCS5A01G389700 chr6A 83.498 303 47 3 1716 2017 18738459 18738159 2.710000e-71 279.0
29 TraesCS5A01G389700 chr6B 86.957 253 31 2 1721 1971 159131077 159131329 2.090000e-72 283.0
30 TraesCS5A01G389700 chr1D 92.683 41 1 1 2977 3015 196002452 196002492 1.380000e-04 58.4
31 TraesCS5A01G389700 chr1B 92.683 41 1 1 2977 3015 269293814 269293774 1.380000e-04 58.4


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 TraesCS5A01G389700 chr5A 585427906 585431469 3563 True 6582.000000 6582 100.000000 1 3564 1 chr5A.!!$R1 3563
1 TraesCS5A01G389700 chr5A 585416548 585421057 4509 True 229.666667 379 87.518333 1063 2579 3 chr5A.!!$R2 1516
2 TraesCS5A01G389700 chr5B 572388817 572391908 3091 True 1414.000000 1945 84.873500 1 2989 2 chr5B.!!$R3 2988
3 TraesCS5A01G389700 chr5B 572378738 572381290 2552 True 322.000000 555 86.863667 1329 3562 3 chr5B.!!$R2 2233
4 TraesCS5A01G389700 chr5B 572363824 572364512 688 True 304.500000 455 88.777000 1045 2566 2 chr5B.!!$R1 1521
5 TraesCS5A01G389700 chr5D 465029707 465034671 4964 True 680.000000 920 84.687250 1 2990 4 chr5D.!!$R3 2989
6 TraesCS5A01G389700 chr5D 465022010 465024346 2336 True 330.666667 529 87.878333 1057 3562 3 chr5D.!!$R2 2505
7 TraesCS5A01G389700 chr5D 465012034 465012708 674 True 217.333333 285 92.682333 1055 2565 3 chr5D.!!$R1 1510
8 TraesCS5A01G389700 chr1A 499637697 499638279 582 False 381.000000 381 78.680000 2978 3562 1 chr1A.!!$F1 584
9 TraesCS5A01G389700 chr7A 533597520 533600989 3469 False 326.500000 342 83.773000 1713 2098 2 chr7A.!!$F2 385

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
718 2626 0.307760 GTGCGTTGGGACTTGACTTG 59.692 55.0 0.0 0.0 0.0 3.16 F
720 2628 0.534203 GCGTTGGGACTTGACTTGGA 60.534 55.0 0.0 0.0 0.0 3.53 F
2197 7509 0.112412 TCCCTTTGTGCCTTCCCTTC 59.888 55.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1754 6979 0.250295 GTGTTGCACTACTGCCTGGA 60.250 55.0 0.00 0.0 43.51 3.86 R
2418 7748 0.749454 AAGGCGTGGCTTGATGATCC 60.749 55.0 7.97 0.0 0.00 3.36 R
3389 8774 0.034896 TCAAGTGCCGAGAAACCCTC 59.965 55.0 0.00 0.0 38.55 4.30 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
38 39 0.389391 AAGACTACATCATCCCGGCG 59.611 55.000 0.00 0.00 0.00 6.46
73 75 6.347402 CCGTTCTTCAACCTGTGTATACTTTG 60.347 42.308 4.17 0.89 0.00 2.77
122 127 2.813754 TGTTCAGCGCAAATAAGAGCTT 59.186 40.909 11.47 0.00 42.08 3.74
175 180 1.834188 TTCAAGGAAATCCGCCTTCC 58.166 50.000 0.00 1.29 43.68 3.46
243 252 4.857588 CGTGTAGTAGTTCAGTTCACCATC 59.142 45.833 0.00 0.00 0.00 3.51
271 283 2.683475 GCCAAGGGTGCTATGGGT 59.317 61.111 0.00 0.00 34.71 4.51
304 321 1.831580 AGAGGAAGCTGGCAATTGTC 58.168 50.000 2.20 2.20 0.00 3.18
308 325 2.901839 AGGAAGCTGGCAATTGTCAATT 59.098 40.909 14.69 11.65 0.00 2.32
423 440 1.341383 GGTTGGTTGATGGCTCAGGAT 60.341 52.381 0.00 0.00 31.68 3.24
430 447 1.098050 GATGGCTCAGGATTGCGTTT 58.902 50.000 0.00 0.00 0.00 3.60
478 495 7.636259 TGCAACTTTTCATGTGTATTTTAGC 57.364 32.000 0.00 0.00 0.00 3.09
513 530 4.387598 TGAACTTTTTGGGATTTGGCATG 58.612 39.130 0.00 0.00 0.00 4.06
539 561 1.630369 ACTTGCTTCTCTGTATGCCCA 59.370 47.619 0.00 0.00 0.00 5.36
543 565 2.284190 GCTTCTCTGTATGCCCAGAAC 58.716 52.381 0.00 0.00 40.78 3.01
555 577 3.411446 TGCCCAGAACAGTACTGATTTG 58.589 45.455 29.30 21.14 37.54 2.32
578 600 6.264832 TGGATGCGATTATGTTGTTCAATTC 58.735 36.000 0.00 0.00 0.00 2.17
613 635 7.758076 GGCATGATTTAACTTTTTGGTACTACC 59.242 37.037 0.00 0.00 39.22 3.18
615 637 9.840427 CATGATTTAACTTTTTGGTACTACCTG 57.160 33.333 6.79 0.00 39.58 4.00
616 638 8.983702 TGATTTAACTTTTTGGTACTACCTGT 57.016 30.769 6.79 0.00 39.58 4.00
617 639 8.842280 TGATTTAACTTTTTGGTACTACCTGTG 58.158 33.333 6.79 0.00 39.58 3.66
673 2572 2.827800 ATCAGTATCACGCCATCCAG 57.172 50.000 0.00 0.00 0.00 3.86
715 2623 1.507141 CTGGTGCGTTGGGACTTGAC 61.507 60.000 0.00 0.00 34.50 3.18
718 2626 0.307760 GTGCGTTGGGACTTGACTTG 59.692 55.000 0.00 0.00 0.00 3.16
719 2627 0.817634 TGCGTTGGGACTTGACTTGG 60.818 55.000 0.00 0.00 0.00 3.61
720 2628 0.534203 GCGTTGGGACTTGACTTGGA 60.534 55.000 0.00 0.00 0.00 3.53
721 2629 1.512926 CGTTGGGACTTGACTTGGAG 58.487 55.000 0.00 0.00 0.00 3.86
838 2785 5.473846 ACAAGATGTCTAGAGAGTCGAAACA 59.526 40.000 0.00 0.00 0.00 2.83
888 2835 1.371635 CAAGAAAGCCAAACGCCGG 60.372 57.895 0.00 0.00 38.78 6.13
889 2836 1.826487 AAGAAAGCCAAACGCCGGT 60.826 52.632 1.90 0.00 38.78 5.28
925 2872 5.957798 CGTAGGTGCGGATATTTATAGGAA 58.042 41.667 0.00 0.00 0.00 3.36
937 2884 7.816031 GGATATTTATAGGAACCAACGATCGAA 59.184 37.037 24.34 0.30 0.00 3.71
972 2929 2.608261 GCTGTGTCAGAGTGTCAGTACC 60.608 54.545 0.00 0.00 32.44 3.34
1077 4308 1.745489 GACGATGAAGGTGGTGGCC 60.745 63.158 0.00 0.00 0.00 5.36
1263 4494 0.597377 CTAGCTCACACGCACACACA 60.597 55.000 0.00 0.00 0.00 3.72
1270 4501 2.102749 ACGCACACACACGTACGT 59.897 55.556 16.72 16.72 41.48 3.57
1282 4531 1.926886 CGTACGTACGCTCACGCTC 60.927 63.158 32.36 0.00 45.77 5.03
1289 4538 2.508755 TACGCTCACGCTCACTGACG 62.509 60.000 0.00 0.00 45.53 4.35
1292 4541 1.285950 CTCACGCTCACTGACGGAA 59.714 57.895 0.00 0.00 0.00 4.30
1296 4545 1.797933 CGCTCACTGACGGAACTCG 60.798 63.158 0.00 0.00 45.88 4.18
1428 4681 2.282040 GTGCAGGCAGAAGCAGGT 60.282 61.111 0.00 0.00 42.14 4.00
1551 4804 1.221414 GGCATGATCAAGAGGTACGC 58.779 55.000 0.00 0.00 0.00 4.42
1607 4867 6.758416 TCTTCGATAACAGATTGTGATTCTGG 59.242 38.462 5.75 0.00 43.95 3.86
1614 4874 2.040813 AGATTGTGATTCTGGGTGCAGT 59.959 45.455 0.00 0.00 0.00 4.40
1615 4875 2.363306 TTGTGATTCTGGGTGCAGTT 57.637 45.000 0.00 0.00 0.00 3.16
1616 4876 1.896220 TGTGATTCTGGGTGCAGTTC 58.104 50.000 0.00 0.00 0.00 3.01
1617 4877 0.798776 GTGATTCTGGGTGCAGTTCG 59.201 55.000 0.00 0.00 0.00 3.95
1635 4895 1.813178 TCGACTACTTCACTGGCAGAG 59.187 52.381 23.66 14.39 0.00 3.35
1670 4965 3.072944 AGCACAGCTTAGCTTTCTTCAG 58.927 45.455 3.00 0.00 38.01 3.02
1680 4977 2.289002 AGCTTTCTTCAGTGTTCAAGCG 59.711 45.455 11.02 0.00 41.25 4.68
1686 4983 2.595124 TCAGTGTTCAAGCGACTTGA 57.405 45.000 15.33 15.33 46.93 3.02
1695 4992 3.371168 TCAAGCGACTTGAATTGCAAAC 58.629 40.909 16.49 1.21 45.84 2.93
1696 4993 3.114809 CAAGCGACTTGAATTGCAAACA 58.885 40.909 1.71 4.25 43.42 2.83
1697 4994 3.648339 AGCGACTTGAATTGCAAACAT 57.352 38.095 1.71 0.00 35.74 2.71
1698 4995 4.764679 AGCGACTTGAATTGCAAACATA 57.235 36.364 1.71 0.00 35.74 2.29
1699 4996 5.314923 AGCGACTTGAATTGCAAACATAT 57.685 34.783 1.71 0.00 35.74 1.78
1700 4997 5.097529 AGCGACTTGAATTGCAAACATATG 58.902 37.500 1.71 0.00 35.74 1.78
1701 4998 4.266029 GCGACTTGAATTGCAAACATATGG 59.734 41.667 1.71 1.76 35.74 2.74
1702 4999 5.639757 CGACTTGAATTGCAAACATATGGA 58.360 37.500 1.71 0.00 35.74 3.41
1709 5006 7.622713 TGAATTGCAAACATATGGAAATCCTT 58.377 30.769 1.71 0.00 34.21 3.36
1746 6971 1.799933 TGCTTGATTTGGTTGGGGTT 58.200 45.000 0.00 0.00 0.00 4.11
1747 6972 2.122768 TGCTTGATTTGGTTGGGGTTT 58.877 42.857 0.00 0.00 0.00 3.27
1754 6979 2.123033 GGTTGGGGTTTGCCAGGT 60.123 61.111 0.00 0.00 36.17 4.00
1795 7020 1.608717 GGACGACACATGAGAGCCCT 61.609 60.000 0.00 0.00 0.00 5.19
1942 7167 2.280628 GCCGAGAAAGGTATGAGTTGG 58.719 52.381 0.00 0.00 0.00 3.77
1946 7171 4.562757 CCGAGAAAGGTATGAGTTGGAACA 60.563 45.833 0.00 0.00 0.00 3.18
1961 7186 1.363744 GAACATTGAGCTGGGTCTCG 58.636 55.000 0.00 0.00 35.90 4.04
1975 7200 3.709653 TGGGTCTCGTTTTATAGCCATCT 59.290 43.478 0.00 0.00 34.72 2.90
1980 7205 5.236695 GTCTCGTTTTATAGCCATCTTTCCC 59.763 44.000 0.00 0.00 0.00 3.97
1982 7207 4.080243 TCGTTTTATAGCCATCTTTCCCCA 60.080 41.667 0.00 0.00 0.00 4.96
1984 7209 4.453480 TTTATAGCCATCTTTCCCCAGG 57.547 45.455 0.00 0.00 0.00 4.45
1986 7211 0.253630 TAGCCATCTTTCCCCAGGGT 60.254 55.000 4.22 0.00 36.47 4.34
1988 7213 0.252239 GCCATCTTTCCCCAGGGTTT 60.252 55.000 4.22 0.00 36.47 3.27
2028 7257 2.419713 GGTACTAAACCTGCTACTGCCC 60.420 54.545 0.00 0.00 45.75 5.36
2038 7267 3.230134 CTGCTACTGCCCTCTCTTCTAT 58.770 50.000 0.00 0.00 38.71 1.98
2039 7268 2.961741 TGCTACTGCCCTCTCTTCTATG 59.038 50.000 0.00 0.00 38.71 2.23
2040 7269 2.288763 GCTACTGCCCTCTCTTCTATGC 60.289 54.545 0.00 0.00 0.00 3.14
2044 7273 0.316841 GCCCTCTCTTCTATGCTCCG 59.683 60.000 0.00 0.00 0.00 4.63
2063 7321 3.818787 CAATGCCACCCGCTGCTC 61.819 66.667 0.00 0.00 38.78 4.26
2078 7336 2.989253 CTCGGTTGGGCCCAAACC 60.989 66.667 40.66 35.23 40.28 3.27
2139 7405 5.419542 GCTTTTCTGTTCCTGTTCCTTTTT 58.580 37.500 0.00 0.00 0.00 1.94
2141 7407 5.592104 TTTCTGTTCCTGTTCCTTTTTCC 57.408 39.130 0.00 0.00 0.00 3.13
2142 7408 4.243793 TCTGTTCCTGTTCCTTTTTCCA 57.756 40.909 0.00 0.00 0.00 3.53
2146 7412 5.208121 TGTTCCTGTTCCTTTTTCCATTCT 58.792 37.500 0.00 0.00 0.00 2.40
2148 7414 5.324832 TCCTGTTCCTTTTTCCATTCTCT 57.675 39.130 0.00 0.00 0.00 3.10
2149 7415 5.316987 TCCTGTTCCTTTTTCCATTCTCTC 58.683 41.667 0.00 0.00 0.00 3.20
2150 7416 5.073691 TCCTGTTCCTTTTTCCATTCTCTCT 59.926 40.000 0.00 0.00 0.00 3.10
2175 7441 1.002868 GCTTGCCTCCTCTTCTGCA 60.003 57.895 0.00 0.00 0.00 4.41
2180 7446 1.340405 TGCCTCCTCTTCTGCATTTCC 60.340 52.381 0.00 0.00 0.00 3.13
2186 7452 3.160269 CCTCTTCTGCATTTCCCTTTGT 58.840 45.455 0.00 0.00 0.00 2.83
2197 7509 0.112412 TCCCTTTGTGCCTTCCCTTC 59.888 55.000 0.00 0.00 0.00 3.46
2236 7548 2.429250 TGAAATGCATGGCTGGAAGATG 59.571 45.455 0.00 0.00 34.07 2.90
2245 7557 1.336125 GGCTGGAAGATGTGCAATAGC 59.664 52.381 0.00 0.00 37.45 2.97
2248 7560 3.497640 GCTGGAAGATGTGCAATAGCTAG 59.502 47.826 0.00 0.00 37.77 3.42
2250 7562 5.102953 TGGAAGATGTGCAATAGCTAGTT 57.897 39.130 0.00 0.00 42.74 2.24
2254 7566 6.763610 GGAAGATGTGCAATAGCTAGTTAACT 59.236 38.462 13.68 13.68 42.74 2.24
2263 7575 5.959583 ATAGCTAGTTAACTTGCCTCCTT 57.040 39.130 30.08 18.11 43.95 3.36
2264 7576 7.272978 CAATAGCTAGTTAACTTGCCTCCTTA 58.727 38.462 30.08 19.37 43.95 2.69
2274 7586 6.429521 AACTTGCCTCCTTAAACAGTAGTA 57.570 37.500 0.00 0.00 0.00 1.82
2276 7588 5.306160 ACTTGCCTCCTTAAACAGTAGTACA 59.694 40.000 2.52 0.00 0.00 2.90
2280 7592 7.909518 TGCCTCCTTAAACAGTAGTACATTTA 58.090 34.615 2.52 4.62 0.00 1.40
2281 7593 8.377034 TGCCTCCTTAAACAGTAGTACATTTAA 58.623 33.333 15.94 15.94 0.00 1.52
2300 7612 9.657419 ACATTTAAGAAAATCCAATGGCTAAAG 57.343 29.630 0.00 0.00 32.87 1.85
2358 7681 8.614469 ATTTACTATGAGAGCAAGCCTTTATC 57.386 34.615 0.00 0.00 0.00 1.75
2361 7684 2.991250 TGAGAGCAAGCCTTTATCACC 58.009 47.619 0.00 0.00 0.00 4.02
2387 7710 6.968131 GACAATAGTCATGTTGCTTACAGA 57.032 37.500 0.00 0.00 44.34 3.41
2388 7711 6.974932 ACAATAGTCATGTTGCTTACAGAG 57.025 37.500 0.00 0.00 40.83 3.35
2389 7712 6.467677 ACAATAGTCATGTTGCTTACAGAGT 58.532 36.000 0.00 3.04 40.83 3.24
2390 7713 6.936900 ACAATAGTCATGTTGCTTACAGAGTT 59.063 34.615 0.00 0.00 40.83 3.01
2391 7714 8.094548 ACAATAGTCATGTTGCTTACAGAGTTA 58.905 33.333 0.00 0.00 40.83 2.24
2392 7715 8.383619 CAATAGTCATGTTGCTTACAGAGTTAC 58.616 37.037 0.00 0.00 40.83 2.50
2418 7748 9.135843 CAAGCATATGCATAATAAAACTCCATG 57.864 33.333 28.62 1.96 45.16 3.66
2441 7771 2.281484 TCAAGCCACGCCTTGACC 60.281 61.111 9.00 0.00 44.49 4.02
2443 7773 3.570212 AAGCCACGCCTTGACCCT 61.570 61.111 0.00 0.00 0.00 4.34
2582 7925 2.033141 GCTCCAACTCTGCTGCCA 59.967 61.111 0.00 0.00 0.00 4.92
2583 7926 2.331132 GCTCCAACTCTGCTGCCAC 61.331 63.158 0.00 0.00 0.00 5.01
2584 7927 1.374190 CTCCAACTCTGCTGCCACT 59.626 57.895 0.00 0.00 0.00 4.00
2586 7929 1.228063 CCAACTCTGCTGCCACTGT 60.228 57.895 0.00 0.00 0.00 3.55
2588 7931 1.301244 AACTCTGCTGCCACTGTCG 60.301 57.895 0.00 0.00 0.00 4.35
2601 7966 2.245942 CACTGTCGACTGAATGTCTCG 58.754 52.381 26.71 3.34 43.25 4.04
2656 8021 3.956848 AGCTCATGTGCAGTACTCTATGA 59.043 43.478 20.92 0.41 34.99 2.15
2661 8026 6.276091 TCATGTGCAGTACTCTATGAACATC 58.724 40.000 3.94 0.00 0.00 3.06
2668 8033 7.507277 TGCAGTACTCTATGAACATCCTAGAAT 59.493 37.037 0.00 0.00 0.00 2.40
2688 8062 9.449719 CTAGAATGTAGGGAATAAACTGTTGTT 57.550 33.333 0.00 0.00 38.16 2.83
2697 8071 0.247736 AAACTGTTGTTTGGCCGCAA 59.752 45.000 0.00 0.00 43.90 4.85
2725 8099 8.829612 CACTTGCTGAAATTTTTAATCTTGGTT 58.170 29.630 0.00 0.00 0.00 3.67
2733 8109 9.476202 GAAATTTTTAATCTTGGTTAGTGCAGT 57.524 29.630 0.00 0.00 0.00 4.40
2747 8123 1.246649 TGCAGTTGTTCCGATGCATT 58.753 45.000 0.00 0.00 43.34 3.56
2748 8124 2.431454 TGCAGTTGTTCCGATGCATTA 58.569 42.857 0.00 0.00 43.34 1.90
2749 8125 2.161410 TGCAGTTGTTCCGATGCATTAC 59.839 45.455 0.00 0.00 43.34 1.89
2750 8126 2.161410 GCAGTTGTTCCGATGCATTACA 59.839 45.455 0.00 0.65 38.54 2.41
2764 8147 2.616376 GCATTACATTGCCATGGACGTA 59.384 45.455 18.40 7.40 36.60 3.57
2765 8148 3.303990 GCATTACATTGCCATGGACGTAG 60.304 47.826 18.40 2.83 36.60 3.51
2771 8154 6.613028 ACATTGCCATGGACGTAGTGTTCT 62.613 45.833 18.40 0.00 35.37 3.01
2796 8179 1.272490 TCCTTGAAGTACAGAGTGCGG 59.728 52.381 0.00 0.00 0.00 5.69
2825 8208 2.666619 GCTGAAAAACAGGCACATCTCG 60.667 50.000 0.00 0.00 45.82 4.04
2842 8225 4.667420 GAAGAGTTCGGTTCGCCA 57.333 55.556 0.00 0.00 37.00 5.69
2845 8228 0.942252 AAGAGTTCGGTTCGCCAAAC 59.058 50.000 0.00 0.00 37.00 2.93
2849 8232 0.309612 GTTCGGTTCGCCAAACACAT 59.690 50.000 0.00 0.00 39.81 3.21
2851 8234 0.533085 TCGGTTCGCCAAACACATGA 60.533 50.000 0.00 0.00 39.81 3.07
2855 8238 0.950836 TTCGCCAAACACATGACCAG 59.049 50.000 0.00 0.00 0.00 4.00
2863 8246 4.024048 CCAAACACATGACCAGTACAAGAC 60.024 45.833 0.00 0.00 0.00 3.01
2871 8254 6.156949 ACATGACCAGTACAAGACCTATTGAT 59.843 38.462 0.00 0.00 34.20 2.57
2872 8255 6.222038 TGACCAGTACAAGACCTATTGATC 57.778 41.667 0.00 0.00 34.20 2.92
2885 8268 8.038862 AGACCTATTGATCACAAATACTCCAT 57.961 34.615 0.00 0.00 39.54 3.41
2952 8336 1.358877 CATGAATGACCGTCGAAGCA 58.641 50.000 0.00 0.00 0.00 3.91
2953 8337 1.935873 CATGAATGACCGTCGAAGCAT 59.064 47.619 0.00 0.00 0.00 3.79
2954 8338 1.358877 TGAATGACCGTCGAAGCATG 58.641 50.000 0.00 0.00 0.00 4.06
2955 8339 1.337728 TGAATGACCGTCGAAGCATGT 60.338 47.619 0.00 0.00 0.00 3.21
2956 8340 1.732259 GAATGACCGTCGAAGCATGTT 59.268 47.619 0.00 0.00 0.00 2.71
2957 8341 1.359848 ATGACCGTCGAAGCATGTTC 58.640 50.000 0.00 0.00 0.00 3.18
2958 8342 0.317160 TGACCGTCGAAGCATGTTCT 59.683 50.000 0.00 0.00 0.00 3.01
2962 8346 1.531149 CCGTCGAAGCATGTTCTGTTT 59.469 47.619 0.00 0.00 0.00 2.83
3000 8384 6.912051 GCTTTTGTTTTAAAATGGAGGCAAAG 59.088 34.615 3.52 6.51 0.00 2.77
3001 8385 6.934048 TTTGTTTTAAAATGGAGGCAAAGG 57.066 33.333 3.52 0.00 0.00 3.11
3002 8386 5.622346 TGTTTTAAAATGGAGGCAAAGGT 57.378 34.783 3.52 0.00 0.00 3.50
3022 8406 6.436843 AGGTTTTGCCTCGTCTATTTAATG 57.563 37.500 0.00 0.00 46.96 1.90
3032 8416 7.938563 CTCGTCTATTTAATGAAGAAGAGGG 57.061 40.000 10.67 0.00 40.20 4.30
3055 8439 4.124851 AGAGTTCTGTATTACAAGGCCG 57.875 45.455 0.00 0.00 0.00 6.13
3075 8459 1.379309 GAGGCCCACCCGCAATAAA 60.379 57.895 0.00 0.00 39.21 1.40
3080 8464 0.459489 CCCACCCGCAATAAACATGG 59.541 55.000 0.00 0.00 0.00 3.66
3083 8467 2.430332 CCACCCGCAATAAACATGGAAT 59.570 45.455 0.00 0.00 0.00 3.01
3088 8472 5.067283 ACCCGCAATAAACATGGAATTACTC 59.933 40.000 0.00 0.00 0.00 2.59
3089 8473 5.299279 CCCGCAATAAACATGGAATTACTCT 59.701 40.000 0.00 0.00 0.00 3.24
3091 8475 6.430451 CGCAATAAACATGGAATTACTCTCC 58.570 40.000 0.00 0.00 0.00 3.71
3092 8476 6.260936 CGCAATAAACATGGAATTACTCTCCT 59.739 38.462 0.00 0.00 33.77 3.69
3094 8478 7.283127 GCAATAAACATGGAATTACTCTCCTGA 59.717 37.037 0.00 0.00 33.77 3.86
3102 8486 7.921041 TGGAATTACTCTCCTGATAGAATGT 57.079 36.000 0.00 0.00 33.77 2.71
3103 8487 8.324191 TGGAATTACTCTCCTGATAGAATGTT 57.676 34.615 0.00 0.00 33.77 2.71
3110 8494 6.012508 ACTCTCCTGATAGAATGTTTCCCAAA 60.013 38.462 0.00 0.00 0.00 3.28
3111 8495 6.789268 TCTCCTGATAGAATGTTTCCCAAAA 58.211 36.000 0.00 0.00 0.00 2.44
3113 8497 8.556589 TCTCCTGATAGAATGTTTCCCAAAATA 58.443 33.333 0.00 0.00 0.00 1.40
3114 8498 9.189156 CTCCTGATAGAATGTTTCCCAAAATAA 57.811 33.333 0.00 0.00 0.00 1.40
3115 8499 8.966868 TCCTGATAGAATGTTTCCCAAAATAAC 58.033 33.333 0.00 0.00 0.00 1.89
3116 8500 8.748412 CCTGATAGAATGTTTCCCAAAATAACA 58.252 33.333 0.00 0.00 36.35 2.41
3125 8509 8.230472 TGTTTCCCAAAATAACAAAATTGCAT 57.770 26.923 0.00 0.00 0.00 3.96
3127 8511 8.567104 GTTTCCCAAAATAACAAAATTGCATCT 58.433 29.630 0.00 0.00 0.00 2.90
3131 8515 6.072618 CCAAAATAACAAAATTGCATCTGCCA 60.073 34.615 0.00 0.00 41.18 4.92
3141 8525 0.529378 GCATCTGCCAAGACCCAAAG 59.471 55.000 0.00 0.00 34.48 2.77
3179 8563 0.034670 GGCCTTGAGCAAGATGGTCT 60.035 55.000 11.61 0.00 44.58 3.85
3180 8564 1.615384 GGCCTTGAGCAAGATGGTCTT 60.615 52.381 11.61 0.00 44.58 3.01
3181 8565 1.742268 GCCTTGAGCAAGATGGTCTTC 59.258 52.381 11.61 0.00 44.58 2.87
3192 8576 1.137086 GATGGTCTTCGGCTTGCTCTA 59.863 52.381 0.00 0.00 0.00 2.43
3195 8579 2.205911 GGTCTTCGGCTTGCTCTATTC 58.794 52.381 0.00 0.00 0.00 1.75
3196 8580 2.159028 GGTCTTCGGCTTGCTCTATTCT 60.159 50.000 0.00 0.00 0.00 2.40
3199 8583 1.389555 TCGGCTTGCTCTATTCTCGA 58.610 50.000 0.00 0.00 0.00 4.04
3201 8585 2.165641 TCGGCTTGCTCTATTCTCGAAA 59.834 45.455 0.00 0.00 0.00 3.46
3204 8588 3.062774 GGCTTGCTCTATTCTCGAAACAC 59.937 47.826 0.00 0.00 0.00 3.32
3205 8589 3.679980 GCTTGCTCTATTCTCGAAACACA 59.320 43.478 0.00 0.00 0.00 3.72
3206 8590 4.434857 GCTTGCTCTATTCTCGAAACACAC 60.435 45.833 0.00 0.00 0.00 3.82
3208 8592 2.599082 GCTCTATTCTCGAAACACACGG 59.401 50.000 0.00 0.00 0.00 4.94
3210 8594 1.659098 CTATTCTCGAAACACACGGGC 59.341 52.381 0.00 0.00 0.00 6.13
3215 8599 0.589223 TCGAAACACACGGGCATTTC 59.411 50.000 4.52 4.52 0.00 2.17
3219 8603 1.523758 AACACACGGGCATTTCTCTC 58.476 50.000 0.00 0.00 0.00 3.20
3223 8607 1.156736 CACGGGCATTTCTCTCGTTT 58.843 50.000 0.00 0.00 31.35 3.60
3250 8634 5.172687 TGGTCCAACTAATGAGCATTGTA 57.827 39.130 5.99 0.00 32.50 2.41
3256 8640 5.258622 CAACTAATGAGCATTGTAAGCGAC 58.741 41.667 5.99 0.00 37.01 5.19
3270 8654 0.953471 AGCGACGCCATTGCTTTACA 60.953 50.000 17.79 0.00 46.98 2.41
3271 8655 0.521242 GCGACGCCATTGCTTTACAG 60.521 55.000 9.14 0.00 34.45 2.74
3275 8659 2.225491 GACGCCATTGCTTTACAGTTGA 59.775 45.455 0.00 0.00 34.43 3.18
3276 8660 2.031157 ACGCCATTGCTTTACAGTTGAC 60.031 45.455 0.00 0.00 34.43 3.18
3277 8661 2.668279 CGCCATTGCTTTACAGTTGACC 60.668 50.000 0.00 0.00 34.43 4.02
3279 8663 3.005791 GCCATTGCTTTACAGTTGACCTT 59.994 43.478 0.00 0.00 33.53 3.50
3280 8664 4.549458 CCATTGCTTTACAGTTGACCTTG 58.451 43.478 0.00 0.00 0.00 3.61
3282 8666 5.451798 CCATTGCTTTACAGTTGACCTTGTT 60.452 40.000 0.00 0.00 0.00 2.83
3283 8667 4.630894 TGCTTTACAGTTGACCTTGTTG 57.369 40.909 0.00 0.00 0.00 3.33
3285 8669 4.461081 TGCTTTACAGTTGACCTTGTTGTT 59.539 37.500 0.00 0.00 0.00 2.83
3286 8670 4.798387 GCTTTACAGTTGACCTTGTTGTTG 59.202 41.667 0.00 0.00 0.00 3.33
3288 8672 1.132262 ACAGTTGACCTTGTTGTTGCG 59.868 47.619 0.00 0.00 0.00 4.85
3294 8678 1.673920 GACCTTGTTGTTGCGGAAAGA 59.326 47.619 0.00 0.00 0.00 2.52
3300 8684 2.034053 TGTTGTTGCGGAAAGATTGACC 59.966 45.455 0.00 0.00 0.00 4.02
3323 8707 2.250924 CCAATCTTTGTTGGGGCTCTT 58.749 47.619 0.00 0.00 43.94 2.85
3324 8708 3.430453 CCAATCTTTGTTGGGGCTCTTA 58.570 45.455 0.00 0.00 43.94 2.10
3347 8731 0.250295 CGCCAAGAGGAGGTGTCAAA 60.250 55.000 0.00 0.00 36.89 2.69
3354 8738 4.779993 AGAGGAGGTGTCAAAGTTTTCT 57.220 40.909 0.00 0.00 0.00 2.52
3360 8744 5.589050 GGAGGTGTCAAAGTTTTCTAAGTGT 59.411 40.000 0.00 0.00 0.00 3.55
3361 8745 6.764560 GGAGGTGTCAAAGTTTTCTAAGTGTA 59.235 38.462 0.00 0.00 0.00 2.90
3364 8749 6.127403 GTGTCAAAGTTTTCTAAGTGTAGCG 58.873 40.000 0.00 0.00 0.00 4.26
3365 8750 5.813672 TGTCAAAGTTTTCTAAGTGTAGCGT 59.186 36.000 0.00 0.00 0.00 5.07
3368 8753 5.571778 AAGTTTTCTAAGTGTAGCGTTCG 57.428 39.130 0.00 0.00 0.00 3.95
3374 8759 1.706443 AAGTGTAGCGTTCGTTAGCC 58.294 50.000 0.00 0.00 0.00 3.93
3376 8761 1.000060 AGTGTAGCGTTCGTTAGCCAA 60.000 47.619 0.00 0.00 0.00 4.52
3385 8770 3.120786 CGTTCGTTAGCCAAGTTCGAAAT 60.121 43.478 0.00 0.00 41.01 2.17
3387 8772 5.220340 CGTTCGTTAGCCAAGTTCGAAATAT 60.220 40.000 0.00 0.00 41.01 1.28
3388 8773 6.020440 CGTTCGTTAGCCAAGTTCGAAATATA 60.020 38.462 0.00 0.00 41.01 0.86
3389 8774 7.335491 GTTCGTTAGCCAAGTTCGAAATATAG 58.665 38.462 0.00 0.00 41.01 1.31
3395 8780 5.104485 AGCCAAGTTCGAAATATAGAGGGTT 60.104 40.000 0.00 0.00 0.00 4.11
3396 8781 5.589050 GCCAAGTTCGAAATATAGAGGGTTT 59.411 40.000 0.00 0.00 0.00 3.27
3397 8782 6.238402 GCCAAGTTCGAAATATAGAGGGTTTC 60.238 42.308 0.00 0.00 0.00 2.78
3398 8783 7.048512 CCAAGTTCGAAATATAGAGGGTTTCT 58.951 38.462 0.00 0.00 40.06 2.52
3401 8786 5.449107 TCGAAATATAGAGGGTTTCTCGG 57.551 43.478 0.00 0.00 46.82 4.63
3404 8789 4.338379 AATATAGAGGGTTTCTCGGCAC 57.662 45.455 0.00 0.00 46.82 5.01
3420 8805 1.876156 GGCACTTGAAGAAGAGGTGTG 59.124 52.381 0.00 0.00 32.98 3.82
3422 8807 2.545946 GCACTTGAAGAAGAGGTGTGTC 59.454 50.000 0.00 0.00 32.98 3.67
3424 8809 2.224066 ACTTGAAGAAGAGGTGTGTCCG 60.224 50.000 0.00 0.00 35.49 4.79
3425 8810 0.679505 TGAAGAAGAGGTGTGTCCGG 59.320 55.000 0.00 0.00 41.99 5.14
3427 8812 0.763223 AAGAAGAGGTGTGTCCGGGT 60.763 55.000 0.00 0.00 41.99 5.28
3428 8813 0.763223 AGAAGAGGTGTGTCCGGGTT 60.763 55.000 0.00 0.00 41.99 4.11
3434 8819 0.179040 GGTGTGTCCGGGTTTCTTGA 60.179 55.000 0.00 0.00 0.00 3.02
3436 8821 2.227194 GTGTGTCCGGGTTTCTTGATT 58.773 47.619 0.00 0.00 0.00 2.57
3443 8828 4.072131 TCCGGGTTTCTTGATTTCTCTTG 58.928 43.478 0.00 0.00 0.00 3.02
3448 8833 5.463392 GGGTTTCTTGATTTCTCTTGCAAAC 59.537 40.000 0.00 0.00 0.00 2.93
3452 8837 5.132502 TCTTGATTTCTCTTGCAAACAGGA 58.867 37.500 0.00 0.00 0.00 3.86
3476 8861 1.988834 GACCGCAATTTGGCTACCCG 61.989 60.000 0.00 0.00 0.00 5.28
3482 8869 1.604147 AATTTGGCTACCCGCTTGGC 61.604 55.000 0.00 0.00 37.83 4.52
3486 8873 2.440247 GCTACCCGCTTGGCCAAT 60.440 61.111 20.85 6.15 37.83 3.16
3488 8875 0.750182 GCTACCCGCTTGGCCAATTA 60.750 55.000 20.85 0.00 37.83 1.40
3491 8878 0.251608 ACCCGCTTGGCCAATTAGTT 60.252 50.000 20.85 0.44 37.83 2.24
3493 8880 0.887933 CCGCTTGGCCAATTAGTTGT 59.112 50.000 20.85 0.00 33.36 3.32
3495 8882 1.812571 CGCTTGGCCAATTAGTTGTCT 59.187 47.619 20.85 0.00 33.36 3.41
3496 8883 3.006940 CGCTTGGCCAATTAGTTGTCTA 58.993 45.455 20.85 0.00 33.36 2.59
3499 8886 4.884164 GCTTGGCCAATTAGTTGTCTATCT 59.116 41.667 20.85 0.00 33.36 1.98
3502 8889 7.229506 GCTTGGCCAATTAGTTGTCTATCTAAT 59.770 37.037 20.85 0.00 38.14 1.73
3505 8892 9.474313 TGGCCAATTAGTTGTCTATCTAATTTT 57.526 29.630 0.61 0.00 41.73 1.82
3530 8918 3.071312 TCTTGATGGCCAACAAAGCAAAT 59.929 39.130 26.29 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 0.971386 TGAAGAACGGACCAGGTACC 59.029 55.000 2.73 2.73 0.00 3.34
122 127 2.016318 CTGCACGCAGGAATTAATGGA 58.984 47.619 11.29 0.00 40.17 3.41
175 180 1.470098 CCCAGCCTTGAACTTCGAATG 59.530 52.381 0.00 0.00 0.00 2.67
243 252 1.204113 ACCCTTGGCCTCTTCCAGAG 61.204 60.000 3.32 0.00 41.96 3.35
271 283 6.013898 CCAGCTTCCTCTTTCCTGATCATATA 60.014 42.308 0.00 0.00 0.00 0.86
304 321 3.469008 TCTAGGACCATACGGCAATTG 57.531 47.619 0.00 0.00 34.57 2.32
308 325 1.342674 ACCTTCTAGGACCATACGGCA 60.343 52.381 0.00 0.00 37.67 5.69
380 397 2.024414 GCAGTGGTTGGAAGAACTTGT 58.976 47.619 0.00 0.00 0.00 3.16
384 401 2.781945 CAAGCAGTGGTTGGAAGAAC 57.218 50.000 24.25 0.00 37.38 3.01
423 440 2.353803 GCTTCTCCCTCTAGAAACGCAA 60.354 50.000 0.00 0.00 35.14 4.85
430 447 1.005569 TCGGTTGCTTCTCCCTCTAGA 59.994 52.381 0.00 0.00 0.00 2.43
478 495 1.901591 AAGTTCAGTCATGCCCACTG 58.098 50.000 6.68 6.68 42.40 3.66
513 530 4.509600 GCATACAGAGAAGCAAGTATGACC 59.490 45.833 13.74 0.00 43.94 4.02
539 561 3.935203 CGCATCCAAATCAGTACTGTTCT 59.065 43.478 21.99 6.19 0.00 3.01
543 565 6.203530 ACATAATCGCATCCAAATCAGTACTG 59.796 38.462 17.17 17.17 0.00 2.74
555 577 6.498304 AGAATTGAACAACATAATCGCATCC 58.502 36.000 0.00 0.00 0.00 3.51
578 600 6.515272 AAGTTAAATCATGCCCACAACTAG 57.485 37.500 0.00 0.00 0.00 2.57
673 2572 0.823460 CTCCTCTCTCTTCTGTGGGC 59.177 60.000 0.00 0.00 0.00 5.36
715 2623 4.785453 GCGTCCCCCAGCTCCAAG 62.785 72.222 0.00 0.00 0.00 3.61
781 2689 2.815211 CAGTCATGTCCACGGCGG 60.815 66.667 13.24 0.00 0.00 6.13
782 2690 3.490759 GCAGTCATGTCCACGGCG 61.491 66.667 4.80 4.80 0.00 6.46
826 2742 1.371389 ACGGCGTGTTTCGACTCTC 60.371 57.895 13.76 0.00 46.75 3.20
827 2743 1.660575 CACGGCGTGTTTCGACTCT 60.661 57.895 30.56 0.00 46.75 3.24
838 2785 0.672342 GTATGGGATAGACACGGCGT 59.328 55.000 6.77 6.77 0.00 5.68
888 2835 2.609002 CACCTACGGGCGGTAATAAAAC 59.391 50.000 6.38 0.00 35.63 2.43
889 2836 2.903798 CACCTACGGGCGGTAATAAAA 58.096 47.619 6.38 0.00 35.63 1.52
925 2872 1.805945 GAGCGCTTCGATCGTTGGT 60.806 57.895 13.26 8.84 31.50 3.67
1052 3013 4.514577 CCTTCATCGTCGCGCCCT 62.515 66.667 0.00 0.00 0.00 5.19
1053 3014 4.814294 ACCTTCATCGTCGCGCCC 62.814 66.667 0.00 0.00 0.00 6.13
1060 3021 2.351276 GGCCACCACCTTCATCGT 59.649 61.111 0.00 0.00 0.00 3.73
1061 3022 2.819595 CGGCCACCACCTTCATCG 60.820 66.667 2.24 0.00 0.00 3.84
1062 3023 3.134127 GCGGCCACCACCTTCATC 61.134 66.667 2.24 0.00 0.00 2.92
1278 4527 1.797933 CGAGTTCCGTCAGTGAGCG 60.798 63.158 0.00 0.33 0.00 5.03
1289 4538 1.368850 GCACACGCAAACGAGTTCC 60.369 57.895 0.00 0.00 41.31 3.62
1300 4549 3.564027 GCCTCCGTATGCACACGC 61.564 66.667 13.07 0.00 40.59 5.34
1301 4550 2.125713 TGCCTCCGTATGCACACG 60.126 61.111 11.33 11.33 41.59 4.49
1310 4559 2.509931 TACTGTAGGCCTGCCTCCGT 62.510 60.000 17.99 12.24 44.43 4.69
1315 4564 1.141234 GACGTACTGTAGGCCTGCC 59.859 63.158 17.99 6.39 0.00 4.85
1551 4804 0.309922 GGTGATCTCATTGGCATGCG 59.690 55.000 12.44 0.00 0.00 4.73
1591 4850 2.224843 TGCACCCAGAATCACAATCTGT 60.225 45.455 3.18 0.00 42.19 3.41
1607 4867 2.059541 GTGAAGTAGTCGAACTGCACC 58.940 52.381 15.05 1.06 46.44 5.01
1614 4874 2.229062 CTCTGCCAGTGAAGTAGTCGAA 59.771 50.000 0.00 0.00 0.00 3.71
1615 4875 1.813178 CTCTGCCAGTGAAGTAGTCGA 59.187 52.381 0.00 0.00 0.00 4.20
1616 4876 1.734047 GCTCTGCCAGTGAAGTAGTCG 60.734 57.143 0.00 0.00 0.00 4.18
1617 4877 2.003196 GCTCTGCCAGTGAAGTAGTC 57.997 55.000 0.00 0.00 0.00 2.59
1635 4895 3.691609 AGCTGTGCTTTAGTATCTTTGGC 59.308 43.478 0.00 0.00 33.89 4.52
1680 4977 7.887996 TTTCCATATGTTTGCAATTCAAGTC 57.112 32.000 0.00 0.00 35.84 3.01
1686 4983 9.956640 TTTAAGGATTTCCATATGTTTGCAATT 57.043 25.926 0.00 0.00 38.89 2.32
1754 6979 0.250295 GTGTTGCACTACTGCCTGGA 60.250 55.000 0.00 0.00 43.51 3.86
1778 7003 1.593787 CAGGGCTCTCATGTGTCGT 59.406 57.895 0.00 0.00 0.00 4.34
1795 7020 2.358615 CACGGTAGCTTGCTGCCA 60.359 61.111 24.92 0.00 44.23 4.92
1942 7167 1.338200 ACGAGACCCAGCTCAATGTTC 60.338 52.381 0.00 0.00 34.56 3.18
1946 7171 2.568623 AAAACGAGACCCAGCTCAAT 57.431 45.000 0.00 0.00 34.56 2.57
1961 7186 4.584743 CCTGGGGAAAGATGGCTATAAAAC 59.415 45.833 0.00 0.00 0.00 2.43
1975 7200 1.073098 GAGGAGAAACCCTGGGGAAA 58.927 55.000 18.88 0.00 40.05 3.13
1980 7205 1.597461 GACGGAGGAGAAACCCTGG 59.403 63.158 0.00 0.00 40.05 4.45
1982 7207 1.982938 CGGACGGAGGAGAAACCCT 60.983 63.158 0.00 0.00 40.05 4.34
1984 7209 2.125633 GCGGACGGAGGAGAAACC 60.126 66.667 0.00 0.00 39.35 3.27
1986 7211 2.050350 ATCGCGGACGGAGGAGAAA 61.050 57.895 6.13 0.00 40.63 2.52
1988 7213 3.209812 CATCGCGGACGGAGGAGA 61.210 66.667 6.13 0.00 40.63 3.71
2022 7248 2.038659 GAGCATAGAAGAGAGGGCAGT 58.961 52.381 0.00 0.00 0.00 4.40
2023 7249 1.344114 GGAGCATAGAAGAGAGGGCAG 59.656 57.143 0.00 0.00 0.00 4.85
2024 7250 1.418334 GGAGCATAGAAGAGAGGGCA 58.582 55.000 0.00 0.00 0.00 5.36
2028 7257 1.035923 TGCCGGAGCATAGAAGAGAG 58.964 55.000 5.05 0.00 46.52 3.20
2063 7321 4.958897 TCGGTTTGGGCCCAACCG 62.959 66.667 42.42 42.42 44.18 4.44
2065 7323 1.971695 CTCTCGGTTTGGGCCCAAC 60.972 63.158 37.33 28.29 35.46 3.77
2139 7405 2.186243 AGCTGCAAGAGAGAGAATGGA 58.814 47.619 1.02 0.00 34.07 3.41
2141 7407 2.096174 GCAAGCTGCAAGAGAGAGAATG 59.904 50.000 1.02 0.00 44.26 2.67
2142 7408 2.358015 GCAAGCTGCAAGAGAGAGAAT 58.642 47.619 1.02 0.00 44.26 2.40
2175 7441 1.149923 AGGGAAGGCACAAAGGGAAAT 59.850 47.619 0.00 0.00 0.00 2.17
2180 7446 2.001076 AAGAAGGGAAGGCACAAAGG 57.999 50.000 0.00 0.00 0.00 3.11
2186 7452 1.846439 CCAGGATAAGAAGGGAAGGCA 59.154 52.381 0.00 0.00 0.00 4.75
2197 7509 7.533426 GCATTTCAATATGCTACCAGGATAAG 58.467 38.462 0.00 0.00 45.80 1.73
2230 7542 7.778470 AGTTAACTAGCTATTGCACATCTTC 57.222 36.000 6.26 0.00 42.74 2.87
2236 7548 4.636206 AGGCAAGTTAACTAGCTATTGCAC 59.364 41.667 22.55 14.70 43.61 4.57
2245 7557 6.935208 ACTGTTTAAGGAGGCAAGTTAACTAG 59.065 38.462 8.92 0.00 0.00 2.57
2248 7560 6.709397 ACTACTGTTTAAGGAGGCAAGTTAAC 59.291 38.462 0.00 0.00 41.85 2.01
2250 7562 6.429521 ACTACTGTTTAAGGAGGCAAGTTA 57.570 37.500 0.00 0.00 41.85 2.24
2254 7566 5.811796 TGTACTACTGTTTAAGGAGGCAA 57.188 39.130 0.00 0.00 41.85 4.52
2274 7586 9.657419 CTTTAGCCATTGGATTTTCTTAAATGT 57.343 29.630 6.95 0.00 34.16 2.71
2280 7592 8.210265 TGTTTTCTTTAGCCATTGGATTTTCTT 58.790 29.630 6.95 0.00 0.00 2.52
2281 7593 7.657354 GTGTTTTCTTTAGCCATTGGATTTTCT 59.343 33.333 6.95 0.00 0.00 2.52
2333 7656 8.213679 TGATAAAGGCTTGCTCTCATAGTAAAT 58.786 33.333 0.00 0.00 28.61 1.40
2350 7673 4.694339 ACTATTGTCTCGGTGATAAAGGC 58.306 43.478 0.00 0.00 29.78 4.35
2358 7681 3.062639 GCAACATGACTATTGTCTCGGTG 59.937 47.826 8.74 8.97 43.29 4.94
2361 7684 5.576774 TGTAAGCAACATGACTATTGTCTCG 59.423 40.000 8.74 2.53 37.35 4.04
2390 7713 9.348476 TGGAGTTTTATTATGCATATGCTTGTA 57.652 29.630 27.13 14.82 42.66 2.41
2391 7714 8.236585 TGGAGTTTTATTATGCATATGCTTGT 57.763 30.769 27.13 15.75 42.66 3.16
2392 7715 9.135843 CATGGAGTTTTATTATGCATATGCTTG 57.864 33.333 27.13 1.31 42.66 4.01
2418 7748 0.749454 AAGGCGTGGCTTGATGATCC 60.749 55.000 7.97 0.00 0.00 3.36
2441 7771 2.558286 CCACCAGCACAAGCACAGG 61.558 63.158 0.00 0.00 45.49 4.00
2443 7773 2.120282 CACCACCAGCACAAGCACA 61.120 57.895 0.00 0.00 45.49 4.57
2656 8021 9.004231 AGTTTATTCCCTACATTCTAGGATGTT 57.996 33.333 21.80 5.54 40.54 2.71
2661 8026 8.047310 ACAACAGTTTATTCCCTACATTCTAGG 58.953 37.037 0.00 0.00 34.52 3.02
2668 8033 5.010213 GCCAAACAACAGTTTATTCCCTACA 59.990 40.000 0.00 0.00 33.90 2.74
2705 8079 9.474920 TGCACTAACCAAGATTAAAAATTTCAG 57.525 29.630 0.00 0.00 0.00 3.02
2711 8085 7.777095 ACAACTGCACTAACCAAGATTAAAAA 58.223 30.769 0.00 0.00 0.00 1.94
2712 8086 7.341445 ACAACTGCACTAACCAAGATTAAAA 57.659 32.000 0.00 0.00 0.00 1.52
2725 8099 1.270571 TGCATCGGAACAACTGCACTA 60.271 47.619 0.00 0.00 39.54 2.74
2733 8109 3.768406 GCAATGTAATGCATCGGAACAA 58.232 40.909 0.00 0.00 45.70 2.83
2747 8123 2.235155 ACACTACGTCCATGGCAATGTA 59.765 45.455 6.96 6.11 31.27 2.29
2748 8124 1.003118 ACACTACGTCCATGGCAATGT 59.997 47.619 6.96 5.13 31.27 2.71
2749 8125 1.737838 ACACTACGTCCATGGCAATG 58.262 50.000 6.96 0.00 0.00 2.82
2750 8126 2.027192 AGAACACTACGTCCATGGCAAT 60.027 45.455 6.96 0.00 0.00 3.56
2764 8147 6.650120 TGTACTTCAAGGAAGAAAGAACACT 58.350 36.000 12.56 0.00 41.71 3.55
2765 8148 6.761714 TCTGTACTTCAAGGAAGAAAGAACAC 59.238 38.462 12.56 0.91 41.71 3.32
2771 8154 5.057149 GCACTCTGTACTTCAAGGAAGAAA 58.943 41.667 12.56 0.00 41.71 2.52
2773 8156 3.305403 CGCACTCTGTACTTCAAGGAAGA 60.305 47.826 12.56 0.00 41.71 2.87
2774 8157 2.989840 CGCACTCTGTACTTCAAGGAAG 59.010 50.000 4.51 4.51 44.37 3.46
2775 8158 2.288825 CCGCACTCTGTACTTCAAGGAA 60.289 50.000 0.00 0.00 0.00 3.36
2776 8159 1.272490 CCGCACTCTGTACTTCAAGGA 59.728 52.381 0.00 0.00 0.00 3.36
2777 8160 1.000955 ACCGCACTCTGTACTTCAAGG 59.999 52.381 0.00 0.00 0.00 3.61
2778 8161 2.061773 CACCGCACTCTGTACTTCAAG 58.938 52.381 0.00 0.00 0.00 3.02
2779 8162 1.684450 TCACCGCACTCTGTACTTCAA 59.316 47.619 0.00 0.00 0.00 2.69
2796 8179 2.669364 CCTGTTTTTCAGCAGCATCAC 58.331 47.619 0.00 0.00 42.38 3.06
2809 8192 3.070018 CTCTTCGAGATGTGCCTGTTTT 58.930 45.455 0.00 0.00 0.00 2.43
2825 8208 1.223187 TTTGGCGAACCGAACTCTTC 58.777 50.000 0.00 0.00 39.70 2.87
2842 8225 4.134563 GGTCTTGTACTGGTCATGTGTTT 58.865 43.478 0.00 0.00 0.00 2.83
2845 8228 3.685139 AGGTCTTGTACTGGTCATGTG 57.315 47.619 0.00 0.00 0.00 3.21
2849 8232 5.719563 TGATCAATAGGTCTTGTACTGGTCA 59.280 40.000 0.00 0.00 0.00 4.02
2851 8234 5.483937 TGTGATCAATAGGTCTTGTACTGGT 59.516 40.000 0.00 0.00 0.00 4.00
2855 8238 9.601217 AGTATTTGTGATCAATAGGTCTTGTAC 57.399 33.333 0.00 0.00 33.32 2.90
2871 8254 6.582636 AGAGCGAATTATGGAGTATTTGTGA 58.417 36.000 0.00 0.00 0.00 3.58
2872 8255 6.851222 AGAGCGAATTATGGAGTATTTGTG 57.149 37.500 0.00 0.00 0.00 3.33
2952 8336 5.706916 CATGCTTGCTTAGAAACAGAACAT 58.293 37.500 0.00 0.00 0.00 2.71
2953 8337 4.557296 GCATGCTTGCTTAGAAACAGAACA 60.557 41.667 16.80 0.00 45.77 3.18
2954 8338 3.916776 GCATGCTTGCTTAGAAACAGAAC 59.083 43.478 16.80 0.00 45.77 3.01
2955 8339 4.164822 GCATGCTTGCTTAGAAACAGAA 57.835 40.909 16.80 0.00 45.77 3.02
2956 8340 3.837213 GCATGCTTGCTTAGAAACAGA 57.163 42.857 16.80 0.00 45.77 3.41
2981 8365 6.935741 AAACCTTTGCCTCCATTTTAAAAC 57.064 33.333 1.97 0.00 0.00 2.43
3000 8384 6.431198 TCATTAAATAGACGAGGCAAAACC 57.569 37.500 0.00 0.00 39.61 3.27
3001 8385 7.748847 TCTTCATTAAATAGACGAGGCAAAAC 58.251 34.615 0.00 0.00 0.00 2.43
3002 8386 7.915293 TCTTCATTAAATAGACGAGGCAAAA 57.085 32.000 0.00 0.00 0.00 2.44
3011 8395 9.974980 CTCTACCCTCTTCTTCATTAAATAGAC 57.025 37.037 0.00 0.00 0.00 2.59
3017 8401 7.455008 ACAGAACTCTACCCTCTTCTTCATTAA 59.545 37.037 0.00 0.00 0.00 1.40
3022 8406 7.412853 AATACAGAACTCTACCCTCTTCTTC 57.587 40.000 0.00 0.00 0.00 2.87
3031 8415 5.358090 GGCCTTGTAATACAGAACTCTACC 58.642 45.833 0.00 0.00 0.00 3.18
3032 8416 5.041940 CGGCCTTGTAATACAGAACTCTAC 58.958 45.833 0.00 0.00 0.00 2.59
3040 8424 1.209128 CTCGCGGCCTTGTAATACAG 58.791 55.000 6.13 0.00 0.00 2.74
3064 8448 4.953579 AGTAATTCCATGTTTATTGCGGGT 59.046 37.500 0.00 0.00 0.00 5.28
3067 8451 6.260936 AGGAGAGTAATTCCATGTTTATTGCG 59.739 38.462 0.00 0.00 37.18 4.85
3068 8452 7.283127 TCAGGAGAGTAATTCCATGTTTATTGC 59.717 37.037 0.00 0.00 37.18 3.56
3075 8459 7.921041 TTCTATCAGGAGAGTAATTCCATGT 57.079 36.000 0.00 0.00 37.18 3.21
3080 8464 9.267084 GGAAACATTCTATCAGGAGAGTAATTC 57.733 37.037 0.00 0.00 0.00 2.17
3083 8467 6.672218 TGGGAAACATTCTATCAGGAGAGTAA 59.328 38.462 0.00 0.00 0.00 2.24
3088 8472 7.651027 ATTTTGGGAAACATTCTATCAGGAG 57.349 36.000 0.00 0.00 0.00 3.69
3089 8473 8.966868 GTTATTTTGGGAAACATTCTATCAGGA 58.033 33.333 0.00 0.00 0.00 3.86
3097 8481 9.179552 GCAATTTTGTTATTTTGGGAAACATTC 57.820 29.630 0.00 0.00 33.44 2.67
3102 8486 8.566260 CAGATGCAATTTTGTTATTTTGGGAAA 58.434 29.630 0.00 0.00 0.00 3.13
3103 8487 7.308469 GCAGATGCAATTTTGTTATTTTGGGAA 60.308 33.333 0.00 0.00 41.59 3.97
3110 8494 6.369615 GTCTTGGCAGATGCAATTTTGTTATT 59.630 34.615 7.19 0.00 44.36 1.40
3111 8495 5.870978 GTCTTGGCAGATGCAATTTTGTTAT 59.129 36.000 7.19 0.00 44.36 1.89
3113 8497 4.060205 GTCTTGGCAGATGCAATTTTGTT 58.940 39.130 7.19 0.00 44.36 2.83
3114 8498 3.555586 GGTCTTGGCAGATGCAATTTTGT 60.556 43.478 7.19 0.00 44.36 2.83
3115 8499 2.997986 GGTCTTGGCAGATGCAATTTTG 59.002 45.455 7.19 0.00 44.36 2.44
3116 8500 2.027837 GGGTCTTGGCAGATGCAATTTT 60.028 45.455 7.19 0.00 44.36 1.82
3117 8501 1.551883 GGGTCTTGGCAGATGCAATTT 59.448 47.619 7.19 0.00 44.36 1.82
3118 8502 1.188863 GGGTCTTGGCAGATGCAATT 58.811 50.000 7.19 0.00 44.36 2.32
3119 8503 0.040058 TGGGTCTTGGCAGATGCAAT 59.960 50.000 7.19 0.00 44.36 3.56
3125 8509 0.185901 AAGCTTTGGGTCTTGGCAGA 59.814 50.000 0.00 0.00 0.00 4.26
3127 8511 2.428834 CAAGCTTTGGGTCTTGGCA 58.571 52.632 0.00 0.00 36.83 4.92
3141 8525 2.680339 GCCATCAAAGACTAGACCAAGC 59.320 50.000 0.00 0.00 0.00 4.01
3150 8534 1.074405 TGCTCAAGGCCATCAAAGACT 59.926 47.619 5.01 0.00 40.92 3.24
3179 8563 1.749063 TCGAGAATAGAGCAAGCCGAA 59.251 47.619 0.00 0.00 0.00 4.30
3180 8564 1.389555 TCGAGAATAGAGCAAGCCGA 58.610 50.000 0.00 0.00 0.00 5.54
3181 8565 2.209838 TTCGAGAATAGAGCAAGCCG 57.790 50.000 0.00 0.00 0.00 5.52
3192 8576 0.250124 TGCCCGTGTGTTTCGAGAAT 60.250 50.000 0.00 0.00 0.00 2.40
3195 8579 0.591170 AAATGCCCGTGTGTTTCGAG 59.409 50.000 0.00 0.00 0.00 4.04
3196 8580 0.589223 GAAATGCCCGTGTGTTTCGA 59.411 50.000 0.00 0.00 0.00 3.71
3199 8583 1.880027 GAGAGAAATGCCCGTGTGTTT 59.120 47.619 0.00 0.00 0.00 2.83
3201 8585 0.670546 CGAGAGAAATGCCCGTGTGT 60.671 55.000 0.00 0.00 0.00 3.72
3204 8588 1.128692 GAAACGAGAGAAATGCCCGTG 59.871 52.381 0.00 0.00 33.48 4.94
3205 8589 1.270625 TGAAACGAGAGAAATGCCCGT 60.271 47.619 0.00 0.00 34.74 5.28
3206 8590 1.438651 TGAAACGAGAGAAATGCCCG 58.561 50.000 0.00 0.00 0.00 6.13
3208 8592 4.168760 CCATTTGAAACGAGAGAAATGCC 58.831 43.478 0.00 0.00 35.41 4.40
3210 8594 5.048782 TGGACCATTTGAAACGAGAGAAATG 60.049 40.000 0.00 0.00 36.14 2.32
3215 8599 3.815401 AGTTGGACCATTTGAAACGAGAG 59.185 43.478 0.00 0.00 0.00 3.20
3219 8603 6.007936 TCATTAGTTGGACCATTTGAAACG 57.992 37.500 0.00 0.00 0.00 3.60
3223 8607 4.661222 TGCTCATTAGTTGGACCATTTGA 58.339 39.130 0.00 0.00 0.00 2.69
3270 8654 0.738389 CCGCAACAACAAGGTCAACT 59.262 50.000 0.00 0.00 0.00 3.16
3271 8655 0.736053 TCCGCAACAACAAGGTCAAC 59.264 50.000 0.00 0.00 0.00 3.18
3275 8659 1.757682 TCTTTCCGCAACAACAAGGT 58.242 45.000 0.00 0.00 0.00 3.50
3276 8660 3.052036 CAATCTTTCCGCAACAACAAGG 58.948 45.455 0.00 0.00 0.00 3.61
3277 8661 3.730715 GTCAATCTTTCCGCAACAACAAG 59.269 43.478 0.00 0.00 0.00 3.16
3279 8663 2.034053 GGTCAATCTTTCCGCAACAACA 59.966 45.455 0.00 0.00 0.00 3.33
3280 8664 2.607038 GGGTCAATCTTTCCGCAACAAC 60.607 50.000 0.00 0.00 0.00 3.32
3282 8666 1.243902 GGGTCAATCTTTCCGCAACA 58.756 50.000 0.00 0.00 0.00 3.33
3283 8667 1.068541 GTGGGTCAATCTTTCCGCAAC 60.069 52.381 0.00 0.00 0.00 4.17
3285 8669 0.608035 GGTGGGTCAATCTTTCCGCA 60.608 55.000 0.00 0.00 0.00 5.69
3286 8670 0.608035 TGGTGGGTCAATCTTTCCGC 60.608 55.000 0.00 0.00 0.00 5.54
3294 8678 4.605640 CAACAAAGATTGGTGGGTCAAT 57.394 40.909 0.16 0.00 44.55 2.57
3313 8697 2.045340 GCGCCTTAAGAGCCCCAA 60.045 61.111 3.36 0.00 0.00 4.12
3323 8707 1.612442 ACCTCCTCTTGGCGCCTTA 60.612 57.895 29.70 14.91 0.00 2.69
3324 8708 2.930562 ACCTCCTCTTGGCGCCTT 60.931 61.111 29.70 0.00 0.00 4.35
3328 8712 0.250295 TTTGACACCTCCTCTTGGCG 60.250 55.000 0.00 0.00 0.00 5.69
3347 8731 4.614946 ACGAACGCTACACTTAGAAAACT 58.385 39.130 0.00 0.00 0.00 2.66
3354 8738 2.228582 TGGCTAACGAACGCTACACTTA 59.771 45.455 0.00 0.00 0.00 2.24
3360 8744 2.331194 GAACTTGGCTAACGAACGCTA 58.669 47.619 0.00 0.00 0.00 4.26
3361 8745 1.145803 GAACTTGGCTAACGAACGCT 58.854 50.000 0.00 0.00 0.00 5.07
3364 8749 3.865224 TTTCGAACTTGGCTAACGAAC 57.135 42.857 0.00 0.00 41.39 3.95
3365 8750 7.259882 TCTATATTTCGAACTTGGCTAACGAA 58.740 34.615 0.00 3.19 40.30 3.85
3368 8753 6.424207 CCCTCTATATTTCGAACTTGGCTAAC 59.576 42.308 0.00 0.00 0.00 2.34
3374 8759 7.043325 CGAGAAACCCTCTATATTTCGAACTTG 60.043 40.741 0.00 0.00 39.78 3.16
3376 8761 6.461231 CCGAGAAACCCTCTATATTTCGAACT 60.461 42.308 0.00 0.00 39.78 3.01
3385 8770 3.028094 AGTGCCGAGAAACCCTCTATA 57.972 47.619 0.00 0.00 39.78 1.31
3387 8772 1.275291 CAAGTGCCGAGAAACCCTCTA 59.725 52.381 0.00 0.00 39.78 2.43
3388 8773 0.035458 CAAGTGCCGAGAAACCCTCT 59.965 55.000 0.00 0.00 39.78 3.69
3389 8774 0.034896 TCAAGTGCCGAGAAACCCTC 59.965 55.000 0.00 0.00 38.55 4.30
3395 8780 2.289072 CCTCTTCTTCAAGTGCCGAGAA 60.289 50.000 0.00 0.00 0.00 2.87
3396 8781 1.273606 CCTCTTCTTCAAGTGCCGAGA 59.726 52.381 0.00 0.00 0.00 4.04
3397 8782 1.001406 ACCTCTTCTTCAAGTGCCGAG 59.999 52.381 0.00 0.00 0.00 4.63
3398 8783 1.048601 ACCTCTTCTTCAAGTGCCGA 58.951 50.000 0.00 0.00 0.00 5.54
3401 8786 2.545946 GACACACCTCTTCTTCAAGTGC 59.454 50.000 0.00 0.00 31.58 4.40
3404 8789 2.408050 CGGACACACCTCTTCTTCAAG 58.592 52.381 0.00 0.00 36.31 3.02
3420 8805 3.676093 AGAGAAATCAAGAAACCCGGAC 58.324 45.455 0.73 0.00 0.00 4.79
3422 8807 3.366374 GCAAGAGAAATCAAGAAACCCGG 60.366 47.826 0.00 0.00 0.00 5.73
3424 8809 4.853924 TGCAAGAGAAATCAAGAAACCC 57.146 40.909 0.00 0.00 0.00 4.11
3425 8810 6.042143 TGTTTGCAAGAGAAATCAAGAAACC 58.958 36.000 0.00 0.00 0.00 3.27
3427 8812 6.096705 TCCTGTTTGCAAGAGAAATCAAGAAA 59.903 34.615 0.00 0.00 0.00 2.52
3428 8813 5.593909 TCCTGTTTGCAAGAGAAATCAAGAA 59.406 36.000 0.00 0.00 0.00 2.52
3436 8821 4.576463 GTCTTTCTCCTGTTTGCAAGAGAA 59.424 41.667 19.43 19.43 45.36 2.87
3443 8828 0.238553 GCGGTCTTTCTCCTGTTTGC 59.761 55.000 0.00 0.00 0.00 3.68
3448 8833 2.095059 CCAAATTGCGGTCTTTCTCCTG 60.095 50.000 0.00 0.00 0.00 3.86
3452 8837 1.620822 AGCCAAATTGCGGTCTTTCT 58.379 45.000 0.00 0.00 36.02 2.52
3453 8838 2.415491 GGTAGCCAAATTGCGGTCTTTC 60.415 50.000 0.00 0.00 36.02 2.62
3458 8843 2.043980 CGGGTAGCCAAATTGCGGT 61.044 57.895 12.31 0.00 36.02 5.68
3476 8861 4.884164 AGATAGACAACTAATTGGCCAAGC 59.116 41.667 24.94 0.00 46.11 4.01
3505 8892 3.118482 TGCTTTGTTGGCCATCAAGAAAA 60.118 39.130 24.47 12.41 44.44 2.29
3507 8894 2.037901 TGCTTTGTTGGCCATCAAGAA 58.962 42.857 24.47 13.34 36.93 2.52
3522 8910 5.179182 CGCCCAAAGTCAAATTATTTGCTTT 59.821 36.000 22.05 22.05 42.27 3.51
3530 8918 1.816224 GCTCCGCCCAAAGTCAAATTA 59.184 47.619 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.