Multiple sequence alignment - TraesCS2A01G011200

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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 TraesCS2A01G011200 chr2A 100.000 4205 0 0 1 4205 4179242 4183446 0.000000e+00 7766.0
1 TraesCS2A01G011200 chr2A 91.348 601 22 2 3634 4205 22967279 22967878 0.000000e+00 795.0
2 TraesCS2A01G011200 chr2A 91.220 410 15 3 3276 3664 22966937 22967346 4.780000e-149 538.0
3 TraesCS2A01G011200 chr2A 91.049 391 29 4 3276 3661 727701049 727700660 1.340000e-144 523.0
4 TraesCS2A01G011200 chr2A 90.306 392 32 4 3276 3662 197538928 197538538 3.750000e-140 508.0
5 TraesCS2A01G011200 chr2A 86.325 468 22 10 3235 3662 41787284 41786819 4.920000e-129 472.0
6 TraesCS2A01G011200 chr2A 85.151 431 54 8 3240 3664 202094031 202093605 2.320000e-117 433.0
7 TraesCS2A01G011200 chr2A 81.761 318 43 11 427 733 278445410 278445723 6.980000e-63 252.0
8 TraesCS2A01G011200 chr2A 95.327 107 4 1 3276 3382 14695398 14695503 7.230000e-38 169.0
9 TraesCS2A01G011200 chr2D 89.509 1954 137 38 1324 3239 5688995 5690918 0.000000e+00 2410.0
10 TraesCS2A01G011200 chr2D 94.258 1341 55 9 1 1326 5687600 5688933 0.000000e+00 2030.0
11 TraesCS2A01G011200 chr6D 83.545 1258 165 28 1324 2576 492467 491247 0.000000e+00 1138.0
12 TraesCS2A01G011200 chr6D 82.609 322 47 4 993 1314 492847 492535 4.140000e-70 276.0
13 TraesCS2A01G011200 chr6D 81.433 307 37 9 436 736 451546434 451546142 2.530000e-57 233.0
14 TraesCS2A01G011200 chrUn 86.810 978 61 20 3276 4205 349630623 349631580 0.000000e+00 1029.0
15 TraesCS2A01G011200 chrUn 78.375 1415 235 38 1326 2689 69319212 69317818 0.000000e+00 852.0
16 TraesCS2A01G011200 chrUn 89.018 601 37 8 3634 4205 146972413 146973013 0.000000e+00 717.0
17 TraesCS2A01G011200 chrUn 93.841 276 16 1 3634 3909 154153306 154153580 8.410000e-112 414.0
18 TraesCS2A01G011200 chrUn 84.375 192 21 5 432 614 156525838 156525647 3.340000e-41 180.0
19 TraesCS2A01G011200 chr7B 82.267 1094 168 20 1324 2400 745403338 745402254 0.000000e+00 922.0
20 TraesCS2A01G011200 chr7B 86.519 586 41 8 3634 4205 11839574 11840135 1.000000e-170 610.0
21 TraesCS2A01G011200 chr7B 85.781 429 52 7 3240 3662 7602013 7601588 2.980000e-121 446.0
22 TraesCS2A01G011200 chr6A 77.963 1443 243 40 1323 2714 55280023 55281441 0.000000e+00 833.0
23 TraesCS2A01G011200 chr6A 80.795 302 38 10 436 730 597351916 597352204 7.080000e-53 219.0
24 TraesCS2A01G011200 chr6B 77.847 1440 244 39 1326 2714 100953859 100952444 0.000000e+00 822.0
25 TraesCS2A01G011200 chr6B 81.457 302 34 12 437 730 685979540 685979827 1.180000e-55 228.0
26 TraesCS2A01G011200 chr7A 87.602 734 41 13 3505 4205 705078208 705078924 0.000000e+00 806.0
27 TraesCS2A01G011200 chr7A 93.548 279 15 2 3634 3912 488799847 488799572 3.030000e-111 412.0
28 TraesCS2A01G011200 chr3A 91.681 601 16 4 3634 4205 706236044 706235449 0.000000e+00 802.0
29 TraesCS2A01G011200 chr3A 90.071 564 10 2 3671 4205 11174304 11174850 0.000000e+00 689.0
30 TraesCS2A01G011200 chr3A 90.830 458 19 9 3634 4072 170253867 170254320 3.620000e-165 592.0
31 TraesCS2A01G011200 chr3A 87.786 393 40 7 3276 3662 36704271 36703881 1.780000e-123 453.0
32 TraesCS2A01G011200 chr3A 85.574 305 34 7 429 732 540962850 540962555 1.140000e-80 311.0
33 TraesCS2A01G011200 chr3A 100.000 28 0 0 76 103 749337375 749337348 8.000000e-03 52.8
34 TraesCS2A01G011200 chr4A 91.181 601 21 2 3634 4205 29884789 29885386 0.000000e+00 787.0
35 TraesCS2A01G011200 chr4A 89.679 436 30 13 3240 3662 564694171 564693738 3.700000e-150 542.0
36 TraesCS2A01G011200 chr1A 90.349 601 26 15 3634 4205 517816890 517817487 0.000000e+00 760.0
37 TraesCS2A01G011200 chr1A 90.183 601 16 3 3634 4205 499598073 499598659 0.000000e+00 743.0
38 TraesCS2A01G011200 chr1A 83.168 303 46 1 432 729 425718071 425717769 5.360000e-69 272.0
39 TraesCS2A01G011200 chr1A 82.353 306 42 6 436 732 143816899 143816597 5.400000e-64 255.0
40 TraesCS2A01G011200 chr5A 87.179 585 39 8 3635 4205 599292584 599292022 2.130000e-177 632.0
41 TraesCS2A01G011200 chr5A 94.764 382 14 3 3674 4055 502029347 502028972 1.300000e-164 590.0
42 TraesCS2A01G011200 chr5A 88.354 395 38 7 3276 3664 607407335 607406943 6.370000e-128 468.0
43 TraesCS2A01G011200 chr5A 88.265 392 39 5 3280 3665 502029807 502029417 2.960000e-126 462.0
44 TraesCS2A01G011200 chr5A 97.059 102 3 0 3239 3340 493661532 493661431 5.590000e-39 172.0
45 TraesCS2A01G011200 chr2B 83.437 483 45 14 3634 4105 655808586 655809044 2.340000e-112 416.0
46 TraesCS2A01G011200 chr1D 84.459 296 41 4 438 728 328882503 328882208 1.910000e-73 287.0
47 TraesCS2A01G011200 chr1D 79.677 310 50 11 436 732 145939663 145939354 1.180000e-50 211.0
48 TraesCS2A01G011200 chr1B 84.589 292 38 2 443 729 443470187 443469898 2.470000e-72 283.0
49 TraesCS2A01G011200 chr1B 80.000 310 49 10 436 732 194791545 194791236 2.550000e-52 217.0
50 TraesCS2A01G011200 chr3D 82.969 229 25 8 415 631 410671146 410671372 1.190000e-45 195.0
51 TraesCS2A01G011200 chr5B 85.556 180 23 3 557 735 665992591 665992768 7.180000e-43 185.0
52 TraesCS2A01G011200 chr4B 100.000 28 0 0 74 101 654268881 654268908 8.000000e-03 52.8


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 TraesCS2A01G011200 chr2A 4179242 4183446 4204 False 7766.0 7766 100.0000 1 4205 1 chr2A.!!$F1 4204
1 TraesCS2A01G011200 chr2A 22966937 22967878 941 False 666.5 795 91.2840 3276 4205 2 chr2A.!!$F4 929
2 TraesCS2A01G011200 chr2D 5687600 5690918 3318 False 2220.0 2410 91.8835 1 3239 2 chr2D.!!$F1 3238
3 TraesCS2A01G011200 chr6D 491247 492847 1600 True 707.0 1138 83.0770 993 2576 2 chr6D.!!$R2 1583
4 TraesCS2A01G011200 chrUn 349630623 349631580 957 False 1029.0 1029 86.8100 3276 4205 1 chrUn.!!$F3 929
5 TraesCS2A01G011200 chrUn 69317818 69319212 1394 True 852.0 852 78.3750 1326 2689 1 chrUn.!!$R1 1363
6 TraesCS2A01G011200 chrUn 146972413 146973013 600 False 717.0 717 89.0180 3634 4205 1 chrUn.!!$F1 571
7 TraesCS2A01G011200 chr7B 745402254 745403338 1084 True 922.0 922 82.2670 1324 2400 1 chr7B.!!$R2 1076
8 TraesCS2A01G011200 chr7B 11839574 11840135 561 False 610.0 610 86.5190 3634 4205 1 chr7B.!!$F1 571
9 TraesCS2A01G011200 chr6A 55280023 55281441 1418 False 833.0 833 77.9630 1323 2714 1 chr6A.!!$F1 1391
10 TraesCS2A01G011200 chr6B 100952444 100953859 1415 True 822.0 822 77.8470 1326 2714 1 chr6B.!!$R1 1388
11 TraesCS2A01G011200 chr7A 705078208 705078924 716 False 806.0 806 87.6020 3505 4205 1 chr7A.!!$F1 700
12 TraesCS2A01G011200 chr3A 706235449 706236044 595 True 802.0 802 91.6810 3634 4205 1 chr3A.!!$R3 571
13 TraesCS2A01G011200 chr3A 11174304 11174850 546 False 689.0 689 90.0710 3671 4205 1 chr3A.!!$F1 534
14 TraesCS2A01G011200 chr4A 29884789 29885386 597 False 787.0 787 91.1810 3634 4205 1 chr4A.!!$F1 571
15 TraesCS2A01G011200 chr1A 517816890 517817487 597 False 760.0 760 90.3490 3634 4205 1 chr1A.!!$F2 571
16 TraesCS2A01G011200 chr1A 499598073 499598659 586 False 743.0 743 90.1830 3634 4205 1 chr1A.!!$F1 571
17 TraesCS2A01G011200 chr5A 599292022 599292584 562 True 632.0 632 87.1790 3635 4205 1 chr5A.!!$R2 570
18 TraesCS2A01G011200 chr5A 502028972 502029807 835 True 526.0 590 91.5145 3280 4055 2 chr5A.!!$R4 775

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
196 209 1.182667 GGCACACATAAAACCCCTCC 58.817 55.000 0.00 0.0 0.0 4.30 F
1328 1407 0.380378 TTTCACGCCAGTTGTCTTGC 59.620 50.000 0.00 0.0 0.0 4.01 F
2420 2558 1.066143 CCACGACTCATTAGGCCTTGT 60.066 52.381 12.58 2.3 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1957 2062 0.173481 TGCTCAGCATCGACACTACC 59.827 55.0 0.00 0.00 31.71 3.18 R
2433 2571 0.033208 GGATGGATTGAGGTTGCCCA 60.033 55.0 0.00 0.00 0.00 5.36 R
3247 3418 0.040246 GTAGGCATAGACCGCGAGTC 60.040 60.0 8.23 13.88 46.71 3.36 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
29 30 7.557358 ACAGAATCCATGCATACATTGTCTAAA 59.443 33.333 0.00 0.00 32.87 1.85
30 31 8.573885 CAGAATCCATGCATACATTGTCTAAAT 58.426 33.333 0.00 0.00 32.87 1.40
91 102 3.119029 GCTAGGCATCTCATCTCATCTCC 60.119 52.174 0.00 0.00 0.00 3.71
92 103 3.263369 AGGCATCTCATCTCATCTCCT 57.737 47.619 0.00 0.00 0.00 3.69
132 145 8.776376 TGCACATATGTATATATGGTGACTTG 57.224 34.615 19.89 11.01 46.80 3.16
140 153 7.506114 TGTATATATGGTGACTTGGAGGAAAC 58.494 38.462 0.00 0.00 0.00 2.78
166 179 7.068716 CCGTTATGGTCTGGATATGATCAGATA 59.931 40.741 2.08 0.00 41.36 1.98
167 180 8.637099 CGTTATGGTCTGGATATGATCAGATAT 58.363 37.037 2.08 0.00 41.36 1.63
168 181 9.761504 GTTATGGTCTGGATATGATCAGATATG 57.238 37.037 2.08 0.00 41.36 1.78
169 182 9.719433 TTATGGTCTGGATATGATCAGATATGA 57.281 33.333 2.08 0.00 41.36 2.15
170 183 8.800515 ATGGTCTGGATATGATCAGATATGAT 57.199 34.615 1.59 1.59 41.36 2.45
196 209 1.182667 GGCACACATAAAACCCCTCC 58.817 55.000 0.00 0.00 0.00 4.30
197 210 1.182667 GCACACATAAAACCCCTCCC 58.817 55.000 0.00 0.00 0.00 4.30
201 214 3.643792 CACACATAAAACCCCTCCCAAAA 59.356 43.478 0.00 0.00 0.00 2.44
250 263 1.394618 ACTCGGAGTCAGCAGGTATC 58.605 55.000 4.45 0.00 0.00 2.24
260 273 3.388024 GTCAGCAGGTATCCCTTGATGTA 59.612 47.826 0.00 0.00 39.89 2.29
310 323 7.448748 ACCAGTTCCAGTAATTTTCACATAC 57.551 36.000 0.00 0.00 0.00 2.39
393 407 6.827762 TGCATCAACAAGGTCATAATCATACA 59.172 34.615 0.00 0.00 0.00 2.29
441 455 4.041815 CCCCTATACTTTTAGGCCCTCTTC 59.958 50.000 0.00 0.00 37.93 2.87
498 512 8.568794 GGATCCTAATCTTTAGGAATTTTTCCG 58.431 37.037 17.47 0.00 45.83 4.30
517 531 2.556189 CCGACATGGGTTGTTTGATTCA 59.444 45.455 0.00 0.00 39.18 2.57
518 532 3.193267 CCGACATGGGTTGTTTGATTCAT 59.807 43.478 0.00 0.00 39.18 2.57
527 541 7.178573 TGGGTTGTTTGATTCATAGGATTACA 58.821 34.615 0.00 0.00 0.00 2.41
621 635 4.586841 TGAAGAATCCAATGTTTTTCCGGT 59.413 37.500 0.00 0.00 0.00 5.28
647 661 7.148255 TGCACAATCAAACACTCATACTAATCC 60.148 37.037 0.00 0.00 0.00 3.01
682 696 3.827008 TGACATGCCACTCTATTCCTC 57.173 47.619 0.00 0.00 0.00 3.71
700 714 4.589908 TCCTCTGTTTTTCCTATTCCTGC 58.410 43.478 0.00 0.00 0.00 4.85
716 730 2.227865 TCCTGCGTTTTACAAATCCTGC 59.772 45.455 0.00 0.00 0.00 4.85
740 754 6.405397 GCGAATCAAAGAGGCCCTTAAATTAA 60.405 38.462 0.00 0.00 34.00 1.40
873 887 5.574815 AAACGGATTGCAAGAATTTTTCG 57.425 34.783 4.94 0.00 34.02 3.46
945 960 8.719648 GTCATGAATTAATTCTCTGCTATCCAG 58.280 37.037 24.77 2.82 37.53 3.86
1100 1115 4.785511 TCAAGCTAGAGTACTTGTGTCC 57.214 45.455 0.00 0.00 43.05 4.02
1107 1122 2.076863 GAGTACTTGTGTCCATGGCAC 58.923 52.381 24.12 24.12 37.37 5.01
1150 1165 6.207417 ACTGTTATGCAAGTATTCAGCAGTTT 59.793 34.615 0.00 0.00 42.14 2.66
1315 1330 2.100631 CGCTGGGCTACCTTTCACG 61.101 63.158 0.00 0.00 37.76 4.35
1328 1407 0.380378 TTTCACGCCAGTTGTCTTGC 59.620 50.000 0.00 0.00 0.00 4.01
1536 1618 1.940613 GTTGCCGGGATCATCAAGTAC 59.059 52.381 2.18 0.00 0.00 2.73
1568 1650 1.152830 GGGCACTCAAGTTGGGGAA 59.847 57.895 7.84 0.00 0.00 3.97
1639 1731 1.623811 TGGAAGTAGAGGGCAGTGAAC 59.376 52.381 0.00 0.00 0.00 3.18
1741 1833 3.900601 ACAGGATCTCTATGACATGGACC 59.099 47.826 0.00 0.00 0.00 4.46
1742 1834 4.158786 CAGGATCTCTATGACATGGACCT 58.841 47.826 0.00 0.84 0.00 3.85
1748 1840 3.875727 CTCTATGACATGGACCTGCAAAG 59.124 47.826 0.00 0.00 0.00 2.77
1753 1845 1.346395 ACATGGACCTGCAAAGTCGTA 59.654 47.619 9.72 3.43 34.97 3.43
1769 1861 7.955864 GCAAAGTCGTAGTAAATTTCGAGATTT 59.044 33.333 16.99 16.99 33.09 2.17
1811 1916 7.819900 GGAGTATGTACAAGACAAGTTCAAGAT 59.180 37.037 0.00 0.00 42.78 2.40
1957 2062 6.509199 GCTTTACGTCAAGATGATGATGAGTG 60.509 42.308 13.58 0.00 38.37 3.51
2046 2157 4.021719 GCTGCCATCACCTATGCATTATTT 60.022 41.667 3.54 0.00 33.92 1.40
2047 2158 5.456548 TGCCATCACCTATGCATTATTTG 57.543 39.130 3.54 0.00 33.92 2.32
2077 2209 2.148916 TTTTCTCGAAGCTTGCTCGA 57.851 45.000 2.10 6.21 42.75 4.04
2278 2413 2.149383 TCAGCTGAAGGCCACAGGT 61.149 57.895 22.68 22.68 45.03 4.00
2420 2558 1.066143 CCACGACTCATTAGGCCTTGT 60.066 52.381 12.58 2.30 0.00 3.16
2421 2559 2.167693 CCACGACTCATTAGGCCTTGTA 59.832 50.000 12.58 0.00 0.00 2.41
2422 2560 3.448686 CACGACTCATTAGGCCTTGTAG 58.551 50.000 12.58 6.56 0.00 2.74
2423 2561 3.130516 CACGACTCATTAGGCCTTGTAGA 59.869 47.826 12.58 3.41 0.00 2.59
2424 2562 3.130693 ACGACTCATTAGGCCTTGTAGAC 59.869 47.826 12.58 3.58 0.00 2.59
2425 2563 3.491104 CGACTCATTAGGCCTTGTAGACC 60.491 52.174 12.58 0.00 0.00 3.85
2426 2564 3.707102 GACTCATTAGGCCTTGTAGACCT 59.293 47.826 12.58 0.00 37.61 3.85
2429 2567 3.844211 TCATTAGGCCTTGTAGACCTTGT 59.156 43.478 12.58 0.00 34.92 3.16
2431 2569 1.435256 AGGCCTTGTAGACCTTGTGT 58.565 50.000 0.00 0.00 0.00 3.72
2433 2571 2.174854 AGGCCTTGTAGACCTTGTGTTT 59.825 45.455 0.00 0.00 0.00 2.83
2434 2572 2.293399 GGCCTTGTAGACCTTGTGTTTG 59.707 50.000 0.00 0.00 0.00 2.93
2435 2573 2.293399 GCCTTGTAGACCTTGTGTTTGG 59.707 50.000 0.00 0.00 0.00 3.28
2436 2574 2.884639 CCTTGTAGACCTTGTGTTTGGG 59.115 50.000 0.00 0.00 0.00 4.12
2437 2575 1.975660 TGTAGACCTTGTGTTTGGGC 58.024 50.000 0.00 0.00 0.00 5.36
2438 2576 1.213182 TGTAGACCTTGTGTTTGGGCA 59.787 47.619 0.00 0.00 32.68 5.36
2465 2603 1.060729 TCCATCCGTGTTCCAAGGAA 58.939 50.000 3.07 0.00 44.27 3.36
2499 2637 3.561143 ACTGTCTATCTCCTTCGAGCAT 58.439 45.455 0.00 0.00 35.94 3.79
2531 2669 1.000506 GCTACACCTTTGGACAGACGA 59.999 52.381 0.00 0.00 0.00 4.20
2576 2714 4.512944 GTCGACAATGGTGATGAATAGCAT 59.487 41.667 11.55 0.00 40.77 3.79
2686 2848 2.898840 CGCACCCTGCCATGCTAG 60.899 66.667 0.00 0.00 41.12 3.42
2687 2849 3.214845 GCACCCTGCCATGCTAGC 61.215 66.667 8.10 8.10 37.42 3.42
2688 2850 2.593978 CACCCTGCCATGCTAGCT 59.406 61.111 17.23 0.00 0.00 3.32
2689 2851 1.832219 CACCCTGCCATGCTAGCTA 59.168 57.895 17.23 2.58 0.00 3.32
2722 2884 1.589993 CGTGCAGGATCTACTGGCG 60.590 63.158 0.00 0.00 38.90 5.69
2743 2905 2.036256 GCCTCACAGTGGGCCAAT 59.964 61.111 8.40 3.05 42.30 3.16
2744 2906 2.345760 GCCTCACAGTGGGCCAATG 61.346 63.158 30.65 30.65 42.30 2.82
2768 2930 3.341823 GCATCCAGCATCGAGGATATTT 58.658 45.455 0.00 0.00 42.61 1.40
2770 2932 4.937620 GCATCCAGCATCGAGGATATTTTA 59.062 41.667 0.00 0.00 42.61 1.52
2772 2934 6.457934 GCATCCAGCATCGAGGATATTTTATG 60.458 42.308 0.00 0.00 42.61 1.90
2774 2936 7.239763 TCCAGCATCGAGGATATTTTATGTA 57.760 36.000 0.00 0.00 0.00 2.29
2776 2938 8.154203 TCCAGCATCGAGGATATTTTATGTAAA 58.846 33.333 0.00 0.00 0.00 2.01
2812 2979 6.809630 ATTTTCTTCTAGTTTCTGGCACTC 57.190 37.500 0.00 0.00 0.00 3.51
2818 2985 1.609208 AGTTTCTGGCACTCGCAAAT 58.391 45.000 0.00 0.00 41.24 2.32
2826 2994 2.676471 ACTCGCAAATGGGGTGCC 60.676 61.111 0.00 0.00 38.86 5.01
2839 3007 2.650778 GTGCCGGAAAGCCAAAGG 59.349 61.111 5.05 0.00 0.00 3.11
2893 3061 1.377725 GTGGGTGAGGATGCTGGTG 60.378 63.158 0.00 0.00 0.00 4.17
2968 3136 0.529555 GAGAGCTCATCACCTTCGCC 60.530 60.000 17.77 0.00 0.00 5.54
2979 3147 1.222936 CCTTCGCCTGGATGCTCTT 59.777 57.895 0.00 0.00 0.00 2.85
2980 3148 1.094073 CCTTCGCCTGGATGCTCTTG 61.094 60.000 0.00 0.00 0.00 3.02
2992 3160 4.161295 CTCTTGGCGCATCGGGGA 62.161 66.667 10.83 0.00 0.00 4.81
2993 3161 3.680620 CTCTTGGCGCATCGGGGAA 62.681 63.158 10.83 0.00 0.00 3.97
2995 3163 2.828095 TTGGCGCATCGGGGAATG 60.828 61.111 10.83 0.00 0.00 2.67
2996 3164 4.873810 TGGCGCATCGGGGAATGG 62.874 66.667 10.83 0.00 0.00 3.16
2998 3166 4.562425 GCGCATCGGGGAATGGGA 62.562 66.667 0.30 0.00 40.89 4.37
2999 3167 2.281070 CGCATCGGGGAATGGGAG 60.281 66.667 0.00 0.00 40.89 4.30
3000 3168 2.807107 CGCATCGGGGAATGGGAGA 61.807 63.158 0.00 0.00 40.89 3.71
3001 3169 1.227973 GCATCGGGGAATGGGAGAC 60.228 63.158 0.00 0.00 0.00 3.36
3002 3170 1.069765 CATCGGGGAATGGGAGACG 59.930 63.158 0.00 0.00 0.00 4.18
3003 3171 1.382695 ATCGGGGAATGGGAGACGT 60.383 57.895 0.00 0.00 0.00 4.34
3004 3172 1.686325 ATCGGGGAATGGGAGACGTG 61.686 60.000 0.00 0.00 0.00 4.49
3005 3173 2.124695 GGGGAATGGGAGACGTGC 60.125 66.667 0.00 0.00 0.00 5.34
3006 3174 2.668632 GGGAATGGGAGACGTGCA 59.331 61.111 0.00 0.00 0.00 4.57
3007 3175 1.450312 GGGAATGGGAGACGTGCAG 60.450 63.158 0.00 0.00 0.00 4.41
3008 3176 2.109126 GGAATGGGAGACGTGCAGC 61.109 63.158 0.00 0.00 0.00 5.25
3009 3177 1.375908 GAATGGGAGACGTGCAGCA 60.376 57.895 0.00 0.00 0.00 4.41
3013 3181 2.340078 GGAGACGTGCAGCACAGA 59.660 61.111 25.19 0.00 33.40 3.41
3068 3236 6.268387 AGGAGCAAATCTTTTGGAATTTGAGA 59.732 34.615 10.99 0.00 36.43 3.27
3099 3267 6.128336 GCAAATTAAGATGGATCGATCAGGAG 60.128 42.308 25.93 4.94 0.00 3.69
3108 3276 4.098044 TGGATCGATCAGGAGTTAGTTCAC 59.902 45.833 25.93 4.84 0.00 3.18
3113 3281 5.944599 TCGATCAGGAGTTAGTTCACTACTT 59.055 40.000 0.00 0.00 35.56 2.24
3114 3282 7.108194 TCGATCAGGAGTTAGTTCACTACTTA 58.892 38.462 0.00 0.00 35.56 2.24
3115 3283 7.065563 TCGATCAGGAGTTAGTTCACTACTTAC 59.934 40.741 0.00 0.00 35.56 2.34
3136 3307 2.866762 CTCGGCTCAATTACTTGCCTAC 59.133 50.000 0.00 0.00 42.90 3.18
3153 3324 3.304794 GCCTACTAGCCTCTGTTGTATCG 60.305 52.174 0.00 0.00 0.00 2.92
3187 3358 8.928270 ACATTTATGAGTACTACAGTTAGTGC 57.072 34.615 0.00 0.00 39.06 4.40
3202 3373 4.081309 AGTTAGTGCCGCTGTATTTCCTTA 60.081 41.667 0.00 0.00 0.00 2.69
3221 3392 4.141779 CCTTAAACAGCTAATACCGTCCCT 60.142 45.833 0.00 0.00 0.00 4.20
3222 3393 3.538634 AAACAGCTAATACCGTCCCTC 57.461 47.619 0.00 0.00 0.00 4.30
3231 3402 6.099269 AGCTAATACCGTCCCTCTTTATTTGA 59.901 38.462 0.00 0.00 0.00 2.69
3239 3410 5.927115 CGTCCCTCTTTATTTGATACCTAGC 59.073 44.000 0.00 0.00 0.00 3.42
3240 3411 6.462487 CGTCCCTCTTTATTTGATACCTAGCA 60.462 42.308 0.00 0.00 0.00 3.49
3241 3412 6.706716 GTCCCTCTTTATTTGATACCTAGCAC 59.293 42.308 0.00 0.00 0.00 4.40
3242 3413 6.615726 TCCCTCTTTATTTGATACCTAGCACT 59.384 38.462 0.00 0.00 0.00 4.40
3243 3414 7.787904 TCCCTCTTTATTTGATACCTAGCACTA 59.212 37.037 0.00 0.00 0.00 2.74
3244 3415 7.873505 CCCTCTTTATTTGATACCTAGCACTAC 59.126 40.741 0.00 0.00 0.00 2.73
3245 3416 7.873505 CCTCTTTATTTGATACCTAGCACTACC 59.126 40.741 0.00 0.00 0.00 3.18
3246 3417 7.431249 TCTTTATTTGATACCTAGCACTACCG 58.569 38.462 0.00 0.00 0.00 4.02
3247 3418 4.602340 ATTTGATACCTAGCACTACCGG 57.398 45.455 0.00 0.00 0.00 5.28
3248 3419 3.301794 TTGATACCTAGCACTACCGGA 57.698 47.619 9.46 0.00 0.00 5.14
3249 3420 2.579873 TGATACCTAGCACTACCGGAC 58.420 52.381 9.46 0.00 0.00 4.79
3250 3421 2.174210 TGATACCTAGCACTACCGGACT 59.826 50.000 9.46 0.00 0.00 3.85
3251 3422 2.338577 TACCTAGCACTACCGGACTC 57.661 55.000 9.46 0.00 0.00 3.36
3252 3423 0.747283 ACCTAGCACTACCGGACTCG 60.747 60.000 9.46 0.00 0.00 4.18
3253 3424 1.355916 CTAGCACTACCGGACTCGC 59.644 63.158 9.46 5.39 34.56 5.03
3254 3425 2.376231 CTAGCACTACCGGACTCGCG 62.376 65.000 9.46 0.00 34.56 5.87
3255 3426 4.849329 GCACTACCGGACTCGCGG 62.849 72.222 9.46 0.00 34.56 6.46
3256 3427 3.437795 CACTACCGGACTCGCGGT 61.438 66.667 9.46 9.75 41.78 5.68
3257 3428 3.130160 ACTACCGGACTCGCGGTC 61.130 66.667 9.46 16.40 43.79 4.79
3258 3429 2.823147 CTACCGGACTCGCGGTCT 60.823 66.667 21.54 9.40 43.97 3.85
3259 3430 1.522355 CTACCGGACTCGCGGTCTA 60.522 63.158 21.54 9.91 43.97 2.59
3260 3431 0.883814 CTACCGGACTCGCGGTCTAT 60.884 60.000 21.54 12.76 43.97 1.98
3261 3432 1.162181 TACCGGACTCGCGGTCTATG 61.162 60.000 21.54 14.55 43.97 2.23
3262 3433 2.353607 CGGACTCGCGGTCTATGC 60.354 66.667 21.54 8.79 43.97 3.14
3263 3434 2.027751 GGACTCGCGGTCTATGCC 59.972 66.667 21.54 7.03 43.97 4.40
3264 3435 2.491022 GGACTCGCGGTCTATGCCT 61.491 63.158 21.54 0.00 43.97 4.75
3265 3436 1.170919 GGACTCGCGGTCTATGCCTA 61.171 60.000 21.54 0.00 43.97 3.93
3266 3437 0.040246 GACTCGCGGTCTATGCCTAC 60.040 60.000 17.12 0.00 41.46 3.18
3267 3438 1.082038 CTCGCGGTCTATGCCTACG 60.082 63.158 6.13 0.00 0.00 3.51
3268 3439 2.050351 CGCGGTCTATGCCTACGG 60.050 66.667 0.00 0.00 0.00 4.02
3340 3511 1.070376 CGTCGGCGTAGATATCGTCAA 60.070 52.381 6.85 0.00 32.96 3.18
3496 3691 1.596934 CCATGTGGCAGAGGTACGT 59.403 57.895 0.00 0.00 0.00 3.57
4140 4571 1.208776 CACCATCACTCTGCCAGATCA 59.791 52.381 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 8.294311 AGGGCCTTTATTCCTTTCTCTTATAT 57.706 34.615 0.00 0.00 0.00 0.86
30 31 7.707467 AGGGCCTTTATTCCTTTCTCTTATA 57.293 36.000 0.00 0.00 0.00 0.98
122 135 1.271379 CGGTTTCCTCCAAGTCACCAT 60.271 52.381 0.00 0.00 0.00 3.55
140 153 5.185828 TCTGATCATATCCAGACCATAACGG 59.814 44.000 0.00 0.00 42.50 4.44
166 179 7.394359 GGGTTTTATGTGTGCCTATATCATCAT 59.606 37.037 0.00 0.00 0.00 2.45
167 180 6.714810 GGGTTTTATGTGTGCCTATATCATCA 59.285 38.462 0.00 0.00 0.00 3.07
168 181 6.151144 GGGGTTTTATGTGTGCCTATATCATC 59.849 42.308 0.00 0.00 0.00 2.92
169 182 6.010219 GGGGTTTTATGTGTGCCTATATCAT 58.990 40.000 0.00 0.00 0.00 2.45
170 183 5.133660 AGGGGTTTTATGTGTGCCTATATCA 59.866 40.000 0.00 0.00 0.00 2.15
204 217 1.574428 GCATGCGTTCGTGGACTTT 59.426 52.632 0.00 0.00 0.00 2.66
250 263 2.305927 ACTGGAACTGGTACATCAAGGG 59.694 50.000 0.00 0.00 38.20 3.95
326 339 0.108396 TGCTCAGCACAAACCTAGCA 59.892 50.000 0.00 0.00 37.62 3.49
441 455 9.860898 AAATTCCTTTAGAAATCCTTTGAATCG 57.139 29.630 0.00 0.00 38.21 3.34
468 482 7.954539 AATTCCTAAAGATTAGGATCCTCCA 57.045 36.000 20.22 6.80 42.74 3.86
492 506 3.024547 TCAAACAACCCATGTCGGAAAA 58.975 40.909 0.00 0.00 42.99 2.29
498 512 5.652014 TCCTATGAATCAAACAACCCATGTC 59.348 40.000 0.00 0.00 42.99 3.06
537 551 8.753497 AACTAGTTGAATCCTATGGGAAAATC 57.247 34.615 7.48 1.99 45.78 2.17
543 557 9.277783 CTATGAAAACTAGTTGAATCCTATGGG 57.722 37.037 9.34 0.00 0.00 4.00
571 585 4.492646 AGGTTGGAGTGGATGGAAATTTT 58.507 39.130 0.00 0.00 0.00 1.82
578 592 1.283029 ACATGAGGTTGGAGTGGATGG 59.717 52.381 0.00 0.00 0.00 3.51
582 596 2.038952 TCTTCACATGAGGTTGGAGTGG 59.961 50.000 0.00 0.00 0.00 4.00
621 635 7.148255 GGATTAGTATGAGTGTTTGATTGTGCA 60.148 37.037 0.00 0.00 0.00 4.57
647 661 3.986572 GCATGTCATCTTCGATCCTACAG 59.013 47.826 0.00 0.00 0.00 2.74
656 670 2.306341 AGAGTGGCATGTCATCTTCG 57.694 50.000 1.89 0.00 0.00 3.79
682 696 4.766404 AACGCAGGAATAGGAAAAACAG 57.234 40.909 0.00 0.00 0.00 3.16
700 714 4.717991 TGATTCGCAGGATTTGTAAAACG 58.282 39.130 0.00 0.00 0.00 3.60
716 730 5.582689 AATTTAAGGGCCTCTTTGATTCG 57.417 39.130 6.46 0.00 36.93 3.34
745 759 3.120108 TCTACCCCTAAATCCAAGGTGG 58.880 50.000 0.00 0.00 39.43 4.61
746 760 5.607171 ACTATCTACCCCTAAATCCAAGGTG 59.393 44.000 0.00 0.00 31.70 4.00
747 761 5.800653 ACTATCTACCCCTAAATCCAAGGT 58.199 41.667 0.00 0.00 31.70 3.50
881 895 5.421277 TGTCAAATTATACACCAGGTACCG 58.579 41.667 6.18 1.26 34.07 4.02
882 896 7.690952 TTTGTCAAATTATACACCAGGTACC 57.309 36.000 2.73 2.73 34.07 3.34
919 934 8.613060 TGGATAGCAGAGAATTAATTCATGAC 57.387 34.615 26.02 18.58 39.23 3.06
945 960 9.706846 ATTTATAACCAAGAAAATAACGTACGC 57.293 29.630 16.72 0.00 0.00 4.42
1077 1092 5.105716 TGGACACAAGTACTCTAGCTTGATC 60.106 44.000 12.93 9.88 43.29 2.92
1100 1115 1.337354 TGCATTGAAGCTTGTGCCATG 60.337 47.619 19.50 8.73 40.80 3.66
1107 1122 3.251729 ACAGTAGTGTGCATTGAAGCTTG 59.748 43.478 2.10 0.00 34.75 4.01
1150 1165 5.205821 AGAGAATCAATGCATGGATTTCCA 58.794 37.500 26.52 0.94 45.16 3.53
1315 1330 4.043200 GCCCGCAAGACAACTGGC 62.043 66.667 0.00 0.00 39.52 4.85
1328 1407 2.289565 GATAAGAAGGAAAGGTGCCCG 58.710 52.381 0.00 0.00 0.00 6.13
1536 1618 0.462759 GTGCCCAAATCCTCTCTCCG 60.463 60.000 0.00 0.00 0.00 4.63
1568 1650 1.492993 GGTCCTCAGGCCTTTCTGGT 61.493 60.000 0.00 0.00 38.35 4.00
1631 1713 3.189080 TGTCTGCACATATTGTTCACTGC 59.811 43.478 0.00 0.00 0.00 4.40
1741 1833 6.089016 TCTCGAAATTTACTACGACTTTGCAG 59.911 38.462 0.00 0.00 0.00 4.41
1742 1834 5.921976 TCTCGAAATTTACTACGACTTTGCA 59.078 36.000 0.00 0.00 0.00 4.08
1774 1866 9.026121 GTCTTGTACATACTCCATATCATACCT 57.974 37.037 0.00 0.00 0.00 3.08
1775 1867 8.803235 TGTCTTGTACATACTCCATATCATACC 58.197 37.037 0.00 0.00 31.43 2.73
1781 1873 8.758829 TGAACTTGTCTTGTACATACTCCATAT 58.241 33.333 0.00 0.00 38.10 1.78
1783 1875 7.004555 TGAACTTGTCTTGTACATACTCCAT 57.995 36.000 0.00 0.00 38.10 3.41
1789 1894 8.311109 TGCTATCTTGAACTTGTCTTGTACATA 58.689 33.333 0.00 0.00 38.10 2.29
1811 1916 9.083422 ACATTATACTAAGCTCAATCTCTGCTA 57.917 33.333 0.00 0.00 35.85 3.49
1957 2062 0.173481 TGCTCAGCATCGACACTACC 59.827 55.000 0.00 0.00 31.71 3.18
1983 2091 2.094762 AGTCGTCCTTGTATGCAACC 57.905 50.000 0.00 0.00 0.00 3.77
2278 2413 5.632190 CCATTCTGATGGTTCTATTCCACCA 60.632 44.000 0.00 0.00 46.48 4.17
2354 2492 0.613292 TTGGGTGTGCTTGGTGTTGT 60.613 50.000 0.00 0.00 0.00 3.32
2420 2558 2.303175 GTTGCCCAAACACAAGGTCTA 58.697 47.619 0.00 0.00 38.75 2.59
2421 2559 1.111277 GTTGCCCAAACACAAGGTCT 58.889 50.000 0.00 0.00 38.75 3.85
2422 2560 0.104120 GGTTGCCCAAACACAAGGTC 59.896 55.000 0.00 0.00 40.86 3.85
2423 2561 0.325203 AGGTTGCCCAAACACAAGGT 60.325 50.000 0.00 0.00 40.86 3.50
2424 2562 0.389025 GAGGTTGCCCAAACACAAGG 59.611 55.000 0.00 0.00 40.86 3.61
2425 2563 1.110442 TGAGGTTGCCCAAACACAAG 58.890 50.000 0.00 0.00 40.86 3.16
2426 2564 1.561643 TTGAGGTTGCCCAAACACAA 58.438 45.000 5.08 5.08 40.86 3.33
2429 2567 1.337118 GGATTGAGGTTGCCCAAACA 58.663 50.000 0.00 0.00 40.86 2.83
2431 2569 2.178580 GATGGATTGAGGTTGCCCAAA 58.821 47.619 0.00 0.00 0.00 3.28
2433 2571 0.033208 GGATGGATTGAGGTTGCCCA 60.033 55.000 0.00 0.00 0.00 5.36
2434 2572 1.103398 CGGATGGATTGAGGTTGCCC 61.103 60.000 0.00 0.00 0.00 5.36
2435 2573 0.394352 ACGGATGGATTGAGGTTGCC 60.394 55.000 0.00 0.00 0.00 4.52
2436 2574 0.734889 CACGGATGGATTGAGGTTGC 59.265 55.000 0.00 0.00 0.00 4.17
2437 2575 2.113860 ACACGGATGGATTGAGGTTG 57.886 50.000 0.00 0.00 0.00 3.77
2438 2576 2.618045 GGAACACGGATGGATTGAGGTT 60.618 50.000 0.00 0.00 0.00 3.50
2485 2623 0.835941 AAGGCATGCTCGAAGGAGAT 59.164 50.000 18.92 0.00 43.27 2.75
2499 2637 0.882927 GGTGTAGCGTCAACAAGGCA 60.883 55.000 0.00 0.00 41.29 4.75
2531 2669 2.982130 CCGCCTTCTGTAGCACCT 59.018 61.111 0.00 0.00 0.00 4.00
2576 2714 2.112297 GGTCTTGGGTGGTGCGAA 59.888 61.111 0.00 0.00 0.00 4.70
2686 2848 1.369091 CGTTGGTGCTGATGGGTAGC 61.369 60.000 0.00 0.00 41.49 3.58
2687 2849 0.036388 ACGTTGGTGCTGATGGGTAG 60.036 55.000 0.00 0.00 0.00 3.18
2688 2850 0.321210 CACGTTGGTGCTGATGGGTA 60.321 55.000 0.00 0.00 37.35 3.69
2689 2851 1.600636 CACGTTGGTGCTGATGGGT 60.601 57.895 0.00 0.00 37.35 4.51
2722 2884 2.360475 GCCCACTGTGAGGCCTTC 60.360 66.667 22.18 4.06 43.76 3.46
2733 2895 0.757935 GGATGCATCATTGGCCCACT 60.758 55.000 27.25 0.00 0.00 4.00
2784 2946 9.216117 GTGCCAGAAACTAGAAGAAAATACTAA 57.784 33.333 0.00 0.00 0.00 2.24
2785 2947 8.594550 AGTGCCAGAAACTAGAAGAAAATACTA 58.405 33.333 0.00 0.00 0.00 1.82
2786 2948 7.454225 AGTGCCAGAAACTAGAAGAAAATACT 58.546 34.615 0.00 0.00 0.00 2.12
2787 2949 7.412020 CGAGTGCCAGAAACTAGAAGAAAATAC 60.412 40.741 0.00 0.00 0.00 1.89
2789 2951 5.409826 CGAGTGCCAGAAACTAGAAGAAAAT 59.590 40.000 0.00 0.00 0.00 1.82
2790 2952 4.750098 CGAGTGCCAGAAACTAGAAGAAAA 59.250 41.667 0.00 0.00 0.00 2.29
2792 2954 3.861131 GCGAGTGCCAGAAACTAGAAGAA 60.861 47.826 0.00 0.00 33.98 2.52
2794 2956 1.996191 GCGAGTGCCAGAAACTAGAAG 59.004 52.381 0.00 0.00 33.98 2.85
2797 2959 1.795768 TTGCGAGTGCCAGAAACTAG 58.204 50.000 0.00 0.00 41.78 2.57
2798 2960 2.248280 TTTGCGAGTGCCAGAAACTA 57.752 45.000 0.00 0.00 41.78 2.24
2799 2961 1.267806 CATTTGCGAGTGCCAGAAACT 59.732 47.619 0.00 0.00 41.78 2.66
2800 2962 1.666888 CCATTTGCGAGTGCCAGAAAC 60.667 52.381 0.00 0.00 41.78 2.78
2826 2994 1.389555 GATACCCCTTTGGCTTTCCG 58.610 55.000 0.00 0.00 37.83 4.30
2839 3007 3.090219 AAGCTCCGCGTGGATACCC 62.090 63.158 19.93 7.53 45.33 3.69
2842 3010 1.035385 TCTCAAGCTCCGCGTGGATA 61.035 55.000 19.93 0.00 45.33 2.59
2873 3041 1.379916 CCAGCATCCTCACCCACAA 59.620 57.895 0.00 0.00 0.00 3.33
2893 3061 1.226295 GCATTTTCCGGCTGCGTAC 60.226 57.895 0.00 0.00 0.00 3.67
2917 3085 1.821332 CCTTCGGGCATGCTCTTCC 60.821 63.158 17.16 8.38 0.00 3.46
2968 3136 2.437180 TGCGCCAAGAGCATCCAG 60.437 61.111 4.18 0.00 44.04 3.86
2979 3147 4.873810 CCATTCCCCGATGCGCCA 62.874 66.667 4.18 0.00 0.00 5.69
2986 3154 2.038329 ACGTCTCCCATTCCCCGA 59.962 61.111 0.00 0.00 0.00 5.14
2988 3156 2.124695 GCACGTCTCCCATTCCCC 60.125 66.667 0.00 0.00 0.00 4.81
2990 3158 2.109126 GCTGCACGTCTCCCATTCC 61.109 63.158 0.00 0.00 0.00 3.01
2991 3159 1.375908 TGCTGCACGTCTCCCATTC 60.376 57.895 0.00 0.00 0.00 2.67
2992 3160 1.672356 GTGCTGCACGTCTCCCATT 60.672 57.895 17.93 0.00 0.00 3.16
2993 3161 2.046892 GTGCTGCACGTCTCCCAT 60.047 61.111 17.93 0.00 0.00 4.00
2995 3163 2.740055 CTGTGCTGCACGTCTCCC 60.740 66.667 25.88 2.78 37.14 4.30
2996 3164 1.735920 CTCTGTGCTGCACGTCTCC 60.736 63.158 25.88 3.52 37.14 3.71
2997 3165 1.006314 GACTCTGTGCTGCACGTCTC 61.006 60.000 25.88 14.29 37.14 3.36
2998 3166 1.006805 GACTCTGTGCTGCACGTCT 60.007 57.895 25.88 9.69 37.14 4.18
2999 3167 1.280886 CTGACTCTGTGCTGCACGTC 61.281 60.000 25.88 24.56 37.14 4.34
3000 3168 1.300465 CTGACTCTGTGCTGCACGT 60.300 57.895 25.88 18.24 37.14 4.49
3001 3169 1.280886 GACTGACTCTGTGCTGCACG 61.281 60.000 25.88 20.05 37.14 5.34
3002 3170 0.033228 AGACTGACTCTGTGCTGCAC 59.967 55.000 25.15 25.15 34.56 4.57
3003 3171 0.755079 AAGACTGACTCTGTGCTGCA 59.245 50.000 0.00 0.00 0.00 4.41
3004 3172 1.876322 AAAGACTGACTCTGTGCTGC 58.124 50.000 0.00 0.00 0.00 5.25
3005 3173 3.726607 AGAAAAGACTGACTCTGTGCTG 58.273 45.455 0.00 0.00 0.00 4.41
3006 3174 3.386078 TGAGAAAAGACTGACTCTGTGCT 59.614 43.478 0.00 0.00 0.00 4.40
3007 3175 3.722147 TGAGAAAAGACTGACTCTGTGC 58.278 45.455 0.00 0.00 0.00 4.57
3008 3176 4.038522 TCCTGAGAAAAGACTGACTCTGTG 59.961 45.833 0.00 0.00 0.00 3.66
3009 3177 4.038642 GTCCTGAGAAAAGACTGACTCTGT 59.961 45.833 0.00 0.00 0.00 3.41
3013 3181 5.119694 GTTTGTCCTGAGAAAAGACTGACT 58.880 41.667 0.00 0.00 0.00 3.41
3068 3236 6.057533 TCGATCCATCTTAATTTGCAGATGT 58.942 36.000 15.53 4.24 43.42 3.06
3099 3267 5.106396 TGAGCCGAGTAAGTAGTGAACTAAC 60.106 44.000 0.00 0.00 37.50 2.34
3108 3276 5.232414 GCAAGTAATTGAGCCGAGTAAGTAG 59.768 44.000 7.18 0.00 0.00 2.57
3113 3281 2.901249 GGCAAGTAATTGAGCCGAGTA 58.099 47.619 7.18 0.00 37.41 2.59
3114 3282 1.739067 GGCAAGTAATTGAGCCGAGT 58.261 50.000 7.18 0.00 37.41 4.18
3118 3286 7.432010 AGGCTAGTAGGCAAGTAATTGAGCC 62.432 48.000 24.23 18.25 44.19 4.70
3119 3287 3.810386 GGCTAGTAGGCAAGTAATTGAGC 59.190 47.826 18.34 5.35 40.97 4.26
3136 3307 2.355132 ACGACGATACAACAGAGGCTAG 59.645 50.000 0.00 0.00 0.00 3.42
3202 3373 3.105283 AGAGGGACGGTATTAGCTGTTT 58.895 45.455 0.00 0.00 0.00 2.83
3221 3392 7.431249 CGGTAGTGCTAGGTATCAAATAAAGA 58.569 38.462 0.00 0.00 0.00 2.52
3222 3393 6.645415 CCGGTAGTGCTAGGTATCAAATAAAG 59.355 42.308 0.00 0.00 0.00 1.85
3231 3402 2.809665 CGAGTCCGGTAGTGCTAGGTAT 60.810 54.545 0.00 0.00 0.00 2.73
3247 3418 0.040246 GTAGGCATAGACCGCGAGTC 60.040 60.000 8.23 13.88 46.71 3.36
3248 3419 1.783031 CGTAGGCATAGACCGCGAGT 61.783 60.000 8.23 3.14 35.83 4.18
3249 3420 1.082038 CGTAGGCATAGACCGCGAG 60.082 63.158 8.23 0.00 35.83 5.03
3250 3421 2.549198 CCGTAGGCATAGACCGCGA 61.549 63.158 8.23 0.00 46.14 5.87
3251 3422 2.050351 CCGTAGGCATAGACCGCG 60.050 66.667 0.00 0.00 46.14 6.46
3481 3676 1.601477 TCGACGTACCTCTGCCACA 60.601 57.895 0.00 0.00 0.00 4.17
3576 3771 3.259314 TGCCACCAGGAGCACCAT 61.259 61.111 2.07 0.00 38.94 3.55
3720 4089 5.109903 GCATATATAAGCCCAGGAGTTACG 58.890 45.833 0.00 0.00 0.00 3.18
3884 4272 9.322773 TCTTTAGATGATGATGATGAACTTGAC 57.677 33.333 0.00 0.00 0.00 3.18
4140 4571 1.972223 CGTCGACCCCAGTCACTCT 60.972 63.158 10.58 0.00 43.73 3.24


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

AutoCloner maintained by Alex Coulton.