Multiple sequence alignment - TraesCS1A01G362100

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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 TraesCS1A01G362100 chr1A 100.000 3188 0 0 1 3188 542827549 542824362 0.000000e+00 5888
1 TraesCS1A01G362100 chr1D 87.567 2413 127 63 587 2935 446802447 446800144 0.000000e+00 2634
2 TraesCS1A01G362100 chr1D 88.850 287 10 8 1 283 446803304 446803036 1.830000e-87 333
3 TraesCS1A01G362100 chr1D 93.865 163 7 3 3012 3172 446800129 446799968 3.180000e-60 243
4 TraesCS1A01G362100 chr1B 87.213 1916 120 57 707 2574 612404888 612403050 0.000000e+00 2065
5 TraesCS1A01G362100 chr1B 85.283 530 44 15 2658 3176 612401796 612401290 1.700000e-142 516
6 TraesCS1A01G362100 chr1B 89.437 284 21 8 435 718 612411387 612411113 1.820000e-92 350
7 TraesCS1A01G362100 chr1B 97.674 43 1 0 51 93 612428605 612428563 1.230000e-09 75
8 TraesCS1A01G362100 chr5B 85.930 199 12 4 1052 1237 278893027 278893222 6.980000e-47 198
9 TraesCS1A01G362100 chr3D 91.228 114 9 1 2073 2185 352108230 352108117 1.530000e-33 154
10 TraesCS1A01G362100 chr3D 89.247 93 10 0 1280 1372 352108623 352108531 2.010000e-22 117
11 TraesCS1A01G362100 chr3B 91.818 110 8 1 2073 2181 450365010 450364901 5.510000e-33 152
12 TraesCS1A01G362100 chr3B 89.247 93 10 0 1280 1372 450365400 450365308 2.010000e-22 117
13 TraesCS1A01G362100 chr3A 91.818 110 8 1 2073 2181 469831962 469831853 5.510000e-33 152
14 TraesCS1A01G362100 chr3A 89.247 93 10 0 1280 1372 469832361 469832269 2.010000e-22 117


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 TraesCS1A01G362100 chr1A 542824362 542827549 3187 True 5888.0 5888 100.000 1 3188 1 chr1A.!!$R1 3187
1 TraesCS1A01G362100 chr1D 446799968 446803304 3336 True 1070.0 2634 90.094 1 3172 3 chr1D.!!$R1 3171
2 TraesCS1A01G362100 chr1B 612401290 612404888 3598 True 1290.5 2065 86.248 707 3176 2 chr1B.!!$R3 2469

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
614 969 0.030908 GACGACCGAGGATGATGACC 59.969 60.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2520 2968 0.035439 TCTTTCCGAGGCCATGGAAC 60.035 55.0 23.94 7.43 43.68 3.62 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
28 29 0.319083 TCACCAAATACGCGTCAGGT 59.681 50.000 18.63 16.95 0.00 4.00
29 30 1.153353 CACCAAATACGCGTCAGGTT 58.847 50.000 18.63 3.91 0.00 3.50
30 31 1.127951 CACCAAATACGCGTCAGGTTC 59.872 52.381 18.63 0.00 0.00 3.62
32 33 2.231964 ACCAAATACGCGTCAGGTTCTA 59.768 45.455 18.63 0.00 0.00 2.10
33 34 3.118884 ACCAAATACGCGTCAGGTTCTAT 60.119 43.478 18.63 0.00 0.00 1.98
34 35 3.245284 CCAAATACGCGTCAGGTTCTATG 59.755 47.826 18.63 3.19 0.00 2.23
35 36 2.135664 ATACGCGTCAGGTTCTATGC 57.864 50.000 18.63 0.00 0.00 3.14
36 37 0.812549 TACGCGTCAGGTTCTATGCA 59.187 50.000 18.63 0.00 0.00 3.96
37 38 0.175760 ACGCGTCAGGTTCTATGCAT 59.824 50.000 5.58 3.79 0.00 3.96
38 39 1.407618 ACGCGTCAGGTTCTATGCATA 59.592 47.619 5.58 6.20 0.00 3.14
39 40 2.035961 ACGCGTCAGGTTCTATGCATAT 59.964 45.455 5.58 0.00 0.00 1.78
40 41 2.409715 CGCGTCAGGTTCTATGCATATG 59.590 50.000 6.92 2.30 0.00 1.78
41 42 2.158449 GCGTCAGGTTCTATGCATATGC 59.842 50.000 21.09 21.09 42.50 3.14
82 83 2.223745 GTTTGCCGAGGAACTTAACCA 58.776 47.619 0.00 0.00 41.55 3.67
89 90 3.408634 CGAGGAACTTAACCAATGGTGT 58.591 45.455 5.34 0.00 41.55 4.16
90 91 3.435671 CGAGGAACTTAACCAATGGTGTC 59.564 47.826 5.34 0.00 41.55 3.67
91 92 4.394729 GAGGAACTTAACCAATGGTGTCA 58.605 43.478 5.34 0.00 41.55 3.58
92 93 4.398319 AGGAACTTAACCAATGGTGTCAG 58.602 43.478 5.34 4.93 30.60 3.51
93 94 4.104102 AGGAACTTAACCAATGGTGTCAGA 59.896 41.667 5.34 0.00 30.60 3.27
94 95 4.215613 GGAACTTAACCAATGGTGTCAGAC 59.784 45.833 5.34 0.00 35.34 3.51
95 96 4.706842 ACTTAACCAATGGTGTCAGACT 57.293 40.909 5.34 0.00 35.34 3.24
96 97 4.389374 ACTTAACCAATGGTGTCAGACTG 58.611 43.478 5.34 0.00 35.34 3.51
97 98 4.141482 ACTTAACCAATGGTGTCAGACTGT 60.141 41.667 5.34 0.00 35.34 3.55
152 153 1.068264 GCAGGAAGCTTGGTTAACTGC 60.068 52.381 2.10 18.57 42.27 4.40
177 178 1.500844 CCTGAGTTACGACGCGTCT 59.499 57.895 33.94 23.31 41.54 4.18
204 208 0.533755 ACTGTGCTGTCTGGTCTTGC 60.534 55.000 0.00 0.00 0.00 4.01
206 210 1.595382 GTGCTGTCTGGTCTTGCGT 60.595 57.895 0.00 0.00 0.00 5.24
254 258 4.747108 ACTTCAAGAAAGTCATCGTGAGTG 59.253 41.667 0.00 0.00 45.28 3.51
279 284 8.052748 TGAAAATATGTGCCAGGTAGATAAACT 58.947 33.333 0.00 0.00 0.00 2.66
283 288 2.678336 GTGCCAGGTAGATAAACTGTGC 59.322 50.000 0.00 0.00 0.00 4.57
285 290 1.933853 CCAGGTAGATAAACTGTGCGC 59.066 52.381 0.00 0.00 0.00 6.09
287 292 1.475280 AGGTAGATAAACTGTGCGCGA 59.525 47.619 12.10 0.00 0.00 5.87
289 294 1.852895 GTAGATAAACTGTGCGCGAGG 59.147 52.381 12.10 0.00 0.00 4.63
292 574 0.321298 ATAAACTGTGCGCGAGGGTT 60.321 50.000 12.10 5.79 0.00 4.11
307 589 2.819608 GAGGGTTGCTGAAATAGTTGCA 59.180 45.455 0.00 0.00 0.00 4.08
316 598 4.665212 CTGAAATAGTTGCATGCGATTGT 58.335 39.130 11.68 1.85 0.00 2.71
343 625 6.314784 CCGTCCAATCAATTTCTCAACTTAC 58.685 40.000 0.00 0.00 0.00 2.34
346 628 7.095229 CGTCCAATCAATTTCTCAACTTACAGA 60.095 37.037 0.00 0.00 0.00 3.41
347 629 8.233190 GTCCAATCAATTTCTCAACTTACAGAG 58.767 37.037 0.00 0.00 0.00 3.35
348 630 8.156820 TCCAATCAATTTCTCAACTTACAGAGA 58.843 33.333 0.00 0.00 39.01 3.10
349 631 8.449397 CCAATCAATTTCTCAACTTACAGAGAG 58.551 37.037 0.00 0.00 41.49 3.20
351 633 7.953158 TCAATTTCTCAACTTACAGAGAGTG 57.047 36.000 0.00 0.00 41.49 3.51
352 634 7.726216 TCAATTTCTCAACTTACAGAGAGTGA 58.274 34.615 0.00 0.00 41.49 3.41
353 635 7.653713 TCAATTTCTCAACTTACAGAGAGTGAC 59.346 37.037 0.00 0.00 41.49 3.67
354 636 5.455056 TTCTCAACTTACAGAGAGTGACC 57.545 43.478 0.00 0.00 41.49 4.02
355 637 4.470602 TCTCAACTTACAGAGAGTGACCA 58.529 43.478 0.00 0.00 36.05 4.02
356 638 4.278669 TCTCAACTTACAGAGAGTGACCAC 59.721 45.833 0.00 0.00 36.05 4.16
357 639 4.215908 TCAACTTACAGAGAGTGACCACT 58.784 43.478 1.78 1.78 45.84 4.00
358 640 4.038042 TCAACTTACAGAGAGTGACCACTG 59.962 45.833 7.47 0.00 42.66 3.66
364 719 1.539869 AGAGTGACCACTGGGCCAT 60.540 57.895 6.72 0.00 42.66 4.40
366 721 2.361610 GTGACCACTGGGCCATGG 60.362 66.667 24.61 24.61 42.13 3.66
371 726 2.677524 CACTGGGCCATGGTGGTG 60.678 66.667 14.67 12.33 40.46 4.17
382 737 1.852157 ATGGTGGTGGCGTCCATCTT 61.852 55.000 11.89 4.39 39.19 2.40
383 738 1.745489 GGTGGTGGCGTCCATCTTC 60.745 63.158 9.95 4.34 39.81 2.87
386 741 1.144057 GGTGGCGTCCATCTTCGAT 59.856 57.895 1.90 0.00 35.28 3.59
388 743 1.143838 TGGCGTCCATCTTCGATGG 59.856 57.895 15.12 15.12 40.48 3.51
389 744 2.247437 GGCGTCCATCTTCGATGGC 61.247 63.158 16.20 11.09 39.01 4.40
390 745 1.521457 GCGTCCATCTTCGATGGCA 60.521 57.895 16.20 0.00 39.01 4.92
391 746 1.766143 GCGTCCATCTTCGATGGCAC 61.766 60.000 16.20 13.66 39.01 5.01
395 750 1.640069 CATCTTCGATGGCACGCAG 59.360 57.895 0.00 0.00 0.00 5.18
396 751 1.522355 ATCTTCGATGGCACGCAGG 60.522 57.895 0.00 0.00 0.00 4.85
397 752 2.244117 ATCTTCGATGGCACGCAGGT 62.244 55.000 0.00 0.00 0.00 4.00
398 753 1.153647 CTTCGATGGCACGCAGGTA 60.154 57.895 0.00 0.00 0.00 3.08
400 755 2.572095 TTCGATGGCACGCAGGTAGG 62.572 60.000 0.00 0.00 0.00 3.18
401 756 2.897350 GATGGCACGCAGGTAGGC 60.897 66.667 0.00 0.00 0.00 3.93
417 772 4.932789 GCGGTAGCCTCATGACAA 57.067 55.556 0.00 0.00 37.42 3.18
418 773 2.384203 GCGGTAGCCTCATGACAAC 58.616 57.895 0.00 0.00 37.42 3.32
419 774 0.108138 GCGGTAGCCTCATGACAACT 60.108 55.000 0.00 0.00 37.42 3.16
420 775 1.927895 CGGTAGCCTCATGACAACTC 58.072 55.000 0.00 0.00 0.00 3.01
421 776 1.471676 CGGTAGCCTCATGACAACTCC 60.472 57.143 0.00 0.00 0.00 3.85
423 778 0.824109 TAGCCTCATGACAACTCCGG 59.176 55.000 0.00 0.00 0.00 5.14
427 782 0.898320 CTCATGACAACTCCGGGTCT 59.102 55.000 0.00 0.00 35.11 3.85
428 783 2.100197 CTCATGACAACTCCGGGTCTA 58.900 52.381 0.00 0.00 35.11 2.59
429 784 1.822990 TCATGACAACTCCGGGTCTAC 59.177 52.381 0.00 0.00 35.11 2.59
430 785 1.134788 CATGACAACTCCGGGTCTACC 60.135 57.143 0.00 0.00 35.11 3.18
432 787 0.245813 GACAACTCCGGGTCTACCAC 59.754 60.000 0.00 0.00 40.22 4.16
434 789 0.246635 CAACTCCGGGTCTACCACAG 59.753 60.000 0.00 0.00 40.22 3.66
435 790 0.178941 AACTCCGGGTCTACCACAGT 60.179 55.000 0.00 0.00 40.22 3.55
436 791 0.611340 ACTCCGGGTCTACCACAGTC 60.611 60.000 0.00 0.00 40.22 3.51
438 793 0.611062 TCCGGGTCTACCACAGTCAG 60.611 60.000 0.00 0.00 40.22 3.51
439 794 1.605058 CCGGGTCTACCACAGTCAGG 61.605 65.000 0.00 0.00 40.22 3.86
440 795 0.898789 CGGGTCTACCACAGTCAGGT 60.899 60.000 0.81 0.00 43.14 4.00
441 796 1.349067 GGGTCTACCACAGTCAGGTT 58.651 55.000 0.81 0.00 40.54 3.50
442 797 2.532843 GGGTCTACCACAGTCAGGTTA 58.467 52.381 0.81 0.00 40.54 2.85
443 798 2.496470 GGGTCTACCACAGTCAGGTTAG 59.504 54.545 0.81 0.00 40.54 2.34
445 800 2.094130 GTCTACCACAGTCAGGTTAGGC 60.094 54.545 0.00 0.00 40.54 3.93
446 801 1.899814 CTACCACAGTCAGGTTAGGCA 59.100 52.381 0.00 0.00 40.54 4.75
447 802 0.687354 ACCACAGTCAGGTTAGGCAG 59.313 55.000 0.00 0.00 35.33 4.85
448 803 0.674895 CCACAGTCAGGTTAGGCAGC 60.675 60.000 0.00 0.00 0.00 5.25
449 804 1.016130 CACAGTCAGGTTAGGCAGCG 61.016 60.000 0.00 0.00 0.00 5.18
450 805 1.448540 CAGTCAGGTTAGGCAGCGG 60.449 63.158 0.00 0.00 0.00 5.52
451 806 2.820037 GTCAGGTTAGGCAGCGGC 60.820 66.667 0.00 0.00 40.13 6.53
452 807 4.451150 TCAGGTTAGGCAGCGGCG 62.451 66.667 0.51 0.51 42.47 6.46
468 823 4.802051 CGGGGGAGCCACCATGTG 62.802 72.222 8.81 0.00 41.20 3.21
472 827 2.267642 GGAGCCACCATGTGCGTA 59.732 61.111 0.00 0.00 38.79 4.42
473 828 1.376683 GGAGCCACCATGTGCGTAA 60.377 57.895 0.00 0.00 38.79 3.18
474 829 1.644786 GGAGCCACCATGTGCGTAAC 61.645 60.000 0.00 0.00 38.79 2.50
477 832 1.015085 GCCACCATGTGCGTAACGTA 61.015 55.000 0.00 0.00 31.34 3.57
478 833 0.717224 CCACCATGTGCGTAACGTAC 59.283 55.000 0.00 0.00 42.37 3.67
496 851 1.992170 ACGCTACGAACTTGATGACC 58.008 50.000 0.00 0.00 0.00 4.02
497 852 0.914551 CGCTACGAACTTGATGACCG 59.085 55.000 0.00 0.00 0.00 4.79
498 853 1.278238 GCTACGAACTTGATGACCGG 58.722 55.000 0.00 0.00 0.00 5.28
499 854 1.278238 CTACGAACTTGATGACCGGC 58.722 55.000 0.00 0.00 0.00 6.13
500 855 0.108520 TACGAACTTGATGACCGGCC 60.109 55.000 0.00 0.00 0.00 6.13
501 856 2.452813 CGAACTTGATGACCGGCCG 61.453 63.158 21.04 21.04 0.00 6.13
502 857 2.046314 AACTTGATGACCGGCCGG 60.046 61.111 42.17 42.17 42.03 6.13
503 858 3.622060 AACTTGATGACCGGCCGGG 62.622 63.158 44.99 28.48 43.62 5.73
504 859 4.856801 CTTGATGACCGGCCGGGG 62.857 72.222 44.99 24.22 41.60 5.73
520 875 3.155167 GGAGACGAGGGGCGGAAT 61.155 66.667 0.00 0.00 46.49 3.01
521 876 2.107141 GAGACGAGGGGCGGAATG 59.893 66.667 0.00 0.00 46.49 2.67
522 877 4.162690 AGACGAGGGGCGGAATGC 62.163 66.667 0.00 0.00 46.49 3.56
531 886 2.325857 GCGGAATGCGAGCATGTC 59.674 61.111 11.64 10.57 36.68 3.06
558 913 3.635204 CGAAGCATCCAGATCGGC 58.365 61.111 0.00 0.00 33.14 5.54
559 914 1.227350 CGAAGCATCCAGATCGGCA 60.227 57.895 0.00 0.00 33.14 5.69
560 915 1.493950 CGAAGCATCCAGATCGGCAC 61.494 60.000 0.00 0.00 33.14 5.01
614 969 0.030908 GACGACCGAGGATGATGACC 59.969 60.000 0.00 0.00 0.00 4.02
629 987 2.252535 TGACCACTCATGAGATGGGA 57.747 50.000 30.88 21.23 35.40 4.37
636 994 2.366837 ATGAGATGGGACCCGGCA 60.367 61.111 5.91 1.32 0.00 5.69
639 997 1.227383 GAGATGGGACCCGGCAATT 59.773 57.895 5.91 0.00 0.00 2.32
652 1010 1.206578 GCAATTGCGTGCGTAGTGT 59.793 52.632 15.87 0.00 34.21 3.55
670 1032 0.248539 GTGAGTGAGATACCGCGTCC 60.249 60.000 4.92 0.00 0.00 4.79
839 1213 1.214325 GCCACCACCATTTAACGCC 59.786 57.895 0.00 0.00 0.00 5.68
887 1262 3.326578 CACCCCACCCCGTCATCA 61.327 66.667 0.00 0.00 0.00 3.07
925 1300 4.278513 CCTCGGCCCACCCAACAA 62.279 66.667 0.00 0.00 0.00 2.83
927 1302 3.783362 CTCGGCCCACCCAACAACA 62.783 63.158 0.00 0.00 0.00 3.33
928 1303 3.294493 CGGCCCACCCAACAACAG 61.294 66.667 0.00 0.00 0.00 3.16
929 1304 3.615709 GGCCCACCCAACAACAGC 61.616 66.667 0.00 0.00 0.00 4.40
930 1305 2.521708 GCCCACCCAACAACAGCT 60.522 61.111 0.00 0.00 0.00 4.24
938 1313 1.008538 CAACAACAGCTCCAACCGC 60.009 57.895 0.00 0.00 0.00 5.68
941 1316 4.927782 AACAGCTCCAACCGCGCA 62.928 61.111 8.75 0.00 0.00 6.09
1609 2014 2.364842 TGCTGGAGGAGGAGGAGC 60.365 66.667 0.00 0.00 0.00 4.70
1830 2235 1.856265 GCTTCAACTCCGGCAACCTG 61.856 60.000 0.00 0.00 0.00 4.00
1831 2236 0.535102 CTTCAACTCCGGCAACCTGT 60.535 55.000 0.00 0.00 0.00 4.00
1833 2238 1.966451 CAACTCCGGCAACCTGTCC 60.966 63.158 0.00 0.00 0.00 4.02
1846 2251 4.779733 TGTCCCCCGAGCTCTCCC 62.780 72.222 12.85 0.00 0.00 4.30
1905 2310 1.460359 GACGAGAAGAAGACGTCGACT 59.540 52.381 14.70 10.63 44.55 4.18
1962 2367 0.251519 AGGGCAAGAAGGGCAAGAAG 60.252 55.000 0.00 0.00 34.52 2.85
1963 2368 1.588597 GGCAAGAAGGGCAAGAAGC 59.411 57.895 0.00 0.00 44.65 3.86
2210 2621 1.816537 CCGCCGGAGAAGAAGATCA 59.183 57.895 5.05 0.00 0.00 2.92
2211 2622 0.528684 CCGCCGGAGAAGAAGATCAC 60.529 60.000 5.05 0.00 0.00 3.06
2212 2623 0.867753 CGCCGGAGAAGAAGATCACG 60.868 60.000 5.05 0.00 0.00 4.35
2217 2628 1.135083 GGAGAAGAAGATCACGCCGAA 60.135 52.381 0.00 0.00 0.00 4.30
2219 2630 1.819288 AGAAGAAGATCACGCCGAAGA 59.181 47.619 0.00 0.00 0.00 2.87
2227 2638 0.958876 TCACGCCGAAGAGCAGTAGA 60.959 55.000 0.00 0.00 0.00 2.59
2228 2639 0.101399 CACGCCGAAGAGCAGTAGAT 59.899 55.000 0.00 0.00 0.00 1.98
2230 2641 0.382158 CGCCGAAGAGCAGTAGATCA 59.618 55.000 0.00 0.00 30.99 2.92
2231 2642 1.000827 CGCCGAAGAGCAGTAGATCAT 60.001 52.381 0.00 0.00 30.99 2.45
2232 2643 2.671596 GCCGAAGAGCAGTAGATCATC 58.328 52.381 0.00 0.00 30.99 2.92
2233 2644 2.035193 GCCGAAGAGCAGTAGATCATCA 59.965 50.000 0.00 0.00 29.01 3.07
2236 2647 3.551863 CGAAGAGCAGTAGATCATCACCC 60.552 52.174 0.00 0.00 29.01 4.61
2237 2648 3.326946 AGAGCAGTAGATCATCACCCT 57.673 47.619 0.00 0.00 30.99 4.34
2238 2649 4.461450 AGAGCAGTAGATCATCACCCTA 57.539 45.455 0.00 0.00 30.99 3.53
2239 2650 4.148838 AGAGCAGTAGATCATCACCCTAC 58.851 47.826 0.00 0.00 34.52 3.18
2240 2651 3.235200 AGCAGTAGATCATCACCCTACC 58.765 50.000 0.00 0.00 34.78 3.18
2242 2653 3.850752 CAGTAGATCATCACCCTACCCT 58.149 50.000 0.00 0.00 34.78 4.34
2243 2654 3.576118 CAGTAGATCATCACCCTACCCTG 59.424 52.174 0.00 0.00 34.78 4.45
2244 2655 1.428869 AGATCATCACCCTACCCTGC 58.571 55.000 0.00 0.00 0.00 4.85
2245 2656 0.398318 GATCATCACCCTACCCTGCC 59.602 60.000 0.00 0.00 0.00 4.85
2246 2657 0.327480 ATCATCACCCTACCCTGCCA 60.327 55.000 0.00 0.00 0.00 4.92
2248 2659 0.107017 CATCACCCTACCCTGCCAAG 60.107 60.000 0.00 0.00 0.00 3.61
2249 2660 0.550147 ATCACCCTACCCTGCCAAGT 60.550 55.000 0.00 0.00 0.00 3.16
2250 2661 1.002134 CACCCTACCCTGCCAAGTG 60.002 63.158 0.00 0.00 0.00 3.16
2251 2662 2.231380 ACCCTACCCTGCCAAGTGG 61.231 63.158 0.00 0.00 38.53 4.00
2252 2663 2.231380 CCCTACCCTGCCAAGTGGT 61.231 63.158 0.00 0.00 37.57 4.16
2253 2664 1.767692 CCTACCCTGCCAAGTGGTT 59.232 57.895 0.00 0.00 37.57 3.67
2254 2665 0.322546 CCTACCCTGCCAAGTGGTTC 60.323 60.000 0.00 0.00 37.57 3.62
2255 2666 0.400213 CTACCCTGCCAAGTGGTTCA 59.600 55.000 0.00 0.00 37.57 3.18
2256 2667 1.004745 CTACCCTGCCAAGTGGTTCAT 59.995 52.381 0.00 0.00 37.57 2.57
2295 2706 8.074613 ACTACTACTACATACATTTTCCTGCA 57.925 34.615 0.00 0.00 0.00 4.41
2306 2717 6.199937 ACATTTTCCTGCATGTGATTAGAC 57.800 37.500 0.00 0.00 32.19 2.59
2312 2736 8.662781 TTTCCTGCATGTGATTAGACTAATAC 57.337 34.615 7.71 7.51 0.00 1.89
2328 2752 7.442656 AGACTAATACTGTGGCGCTAATTAAT 58.557 34.615 7.64 0.00 0.00 1.40
2335 2759 5.878116 ACTGTGGCGCTAATTAATCTGTTAA 59.122 36.000 7.64 0.00 34.50 2.01
2342 2766 7.950496 GGCGCTAATTAATCTGTTAATTACTCG 59.050 37.037 7.64 16.26 44.58 4.18
2352 2777 7.303634 TCTGTTAATTACTCGAGGATTTTGC 57.696 36.000 18.41 7.87 0.00 3.68
2358 2783 2.693069 ACTCGAGGATTTTGCTCTGTG 58.307 47.619 18.41 0.00 32.20 3.66
2384 2809 2.916052 GCATCATGCATCGCCTGGG 61.916 63.158 4.20 0.00 44.26 4.45
2386 2811 1.105167 CATCATGCATCGCCTGGGTT 61.105 55.000 0.00 0.00 0.00 4.11
2389 2814 1.452651 ATGCATCGCCTGGGTTGAG 60.453 57.895 0.00 0.00 0.00 3.02
2390 2815 1.913951 ATGCATCGCCTGGGTTGAGA 61.914 55.000 0.00 0.00 0.00 3.27
2391 2816 2.109126 GCATCGCCTGGGTTGAGAC 61.109 63.158 0.00 0.00 0.00 3.36
2392 2817 1.599047 CATCGCCTGGGTTGAGACT 59.401 57.895 0.00 0.00 0.00 3.24
2395 2820 1.118965 TCGCCTGGGTTGAGACTTGA 61.119 55.000 0.00 0.00 0.00 3.02
2396 2821 0.671781 CGCCTGGGTTGAGACTTGAG 60.672 60.000 0.00 0.00 0.00 3.02
2397 2822 0.687354 GCCTGGGTTGAGACTTGAGA 59.313 55.000 0.00 0.00 0.00 3.27
2398 2823 1.338579 GCCTGGGTTGAGACTTGAGAG 60.339 57.143 0.00 0.00 0.00 3.20
2399 2824 2.251818 CCTGGGTTGAGACTTGAGAGA 58.748 52.381 0.00 0.00 0.00 3.10
2400 2825 2.233431 CCTGGGTTGAGACTTGAGAGAG 59.767 54.545 0.00 0.00 0.00 3.20
2401 2826 2.896685 CTGGGTTGAGACTTGAGAGAGT 59.103 50.000 0.00 0.00 0.00 3.24
2402 2827 3.309296 TGGGTTGAGACTTGAGAGAGTT 58.691 45.455 0.00 0.00 0.00 3.01
2403 2828 3.070159 TGGGTTGAGACTTGAGAGAGTTG 59.930 47.826 0.00 0.00 0.00 3.16
2404 2829 3.556004 GGGTTGAGACTTGAGAGAGTTGG 60.556 52.174 0.00 0.00 0.00 3.77
2405 2830 3.556004 GGTTGAGACTTGAGAGAGTTGGG 60.556 52.174 0.00 0.00 0.00 4.12
2406 2831 3.244887 TGAGACTTGAGAGAGTTGGGA 57.755 47.619 0.00 0.00 0.00 4.37
2407 2832 3.784178 TGAGACTTGAGAGAGTTGGGAT 58.216 45.455 0.00 0.00 0.00 3.85
2408 2833 4.935578 TGAGACTTGAGAGAGTTGGGATA 58.064 43.478 0.00 0.00 0.00 2.59
2409 2834 4.952957 TGAGACTTGAGAGAGTTGGGATAG 59.047 45.833 0.00 0.00 0.00 2.08
2410 2835 5.197451 GAGACTTGAGAGAGTTGGGATAGA 58.803 45.833 0.00 0.00 0.00 1.98
2411 2836 5.776358 AGACTTGAGAGAGTTGGGATAGAT 58.224 41.667 0.00 0.00 0.00 1.98
2412 2837 5.598005 AGACTTGAGAGAGTTGGGATAGATG 59.402 44.000 0.00 0.00 0.00 2.90
2413 2838 4.653341 ACTTGAGAGAGTTGGGATAGATGG 59.347 45.833 0.00 0.00 0.00 3.51
2414 2839 2.968574 TGAGAGAGTTGGGATAGATGGC 59.031 50.000 0.00 0.00 0.00 4.40
2415 2840 2.968574 GAGAGAGTTGGGATAGATGGCA 59.031 50.000 0.00 0.00 0.00 4.92
2416 2841 2.971330 AGAGAGTTGGGATAGATGGCAG 59.029 50.000 0.00 0.00 0.00 4.85
2417 2842 2.703007 GAGAGTTGGGATAGATGGCAGT 59.297 50.000 0.00 0.00 0.00 4.40
2418 2843 3.898123 GAGAGTTGGGATAGATGGCAGTA 59.102 47.826 0.00 0.00 0.00 2.74
2459 2884 2.417933 GTGAACAGTGAGTGATGATGCC 59.582 50.000 0.00 0.00 0.00 4.40
2460 2885 1.662629 GAACAGTGAGTGATGATGCCG 59.337 52.381 0.00 0.00 0.00 5.69
2517 2965 2.028658 TCTCGATCTTTTGCTGTCTGCT 60.029 45.455 3.20 0.00 43.37 4.24
2518 2966 2.740981 CTCGATCTTTTGCTGTCTGCTT 59.259 45.455 3.20 0.00 43.37 3.91
2519 2967 2.738846 TCGATCTTTTGCTGTCTGCTTC 59.261 45.455 3.20 0.00 43.37 3.86
2520 2968 2.473540 CGATCTTTTGCTGTCTGCTTCG 60.474 50.000 3.20 0.02 43.37 3.79
2575 3023 3.131400 GGAGCGAGTTTAGGATCTCAGTT 59.869 47.826 0.00 0.00 0.00 3.16
2576 3024 4.338682 GGAGCGAGTTTAGGATCTCAGTTA 59.661 45.833 0.00 0.00 0.00 2.24
2579 3027 6.120905 AGCGAGTTTAGGATCTCAGTTACTA 58.879 40.000 0.00 0.00 0.00 1.82
2581 3029 6.183360 GCGAGTTTAGGATCTCAGTTACTACA 60.183 42.308 0.00 0.00 0.00 2.74
2582 3030 7.411274 CGAGTTTAGGATCTCAGTTACTACAG 58.589 42.308 0.00 0.00 0.00 2.74
2583 3031 7.066043 CGAGTTTAGGATCTCAGTTACTACAGT 59.934 40.741 0.00 0.00 0.00 3.55
2584 3032 8.653036 AGTTTAGGATCTCAGTTACTACAGTT 57.347 34.615 0.00 0.00 0.00 3.16
2673 4297 2.162754 GTAACCCGACGCGATGGTG 61.163 63.158 15.93 10.36 31.32 4.17
2674 4298 3.359515 TAACCCGACGCGATGGTGG 62.360 63.158 15.93 8.28 31.32 4.61
2692 4316 2.037208 CCGCCCTTTGGACCCATT 59.963 61.111 0.00 0.00 0.00 3.16
2738 4362 4.578898 TCGTGCACGCGACCTGTT 62.579 61.111 33.63 0.00 39.60 3.16
2783 4407 0.455815 GGATTGGAATTCACCACGGC 59.544 55.000 7.93 0.00 39.85 5.68
2789 4413 1.666209 GAATTCACCACGGCCCATGG 61.666 60.000 17.50 17.50 43.43 3.66
2810 4436 2.501723 GTGCCTCTTGTCCTCTTATGGA 59.498 50.000 0.00 0.00 0.00 3.41
2908 4537 3.031812 GCGTTCTCCGTATACGTACTTG 58.968 50.000 22.87 8.19 39.32 3.16
2910 4539 3.063997 CGTTCTCCGTATACGTACTTGGT 59.936 47.826 22.87 0.00 37.74 3.67
2911 4540 4.346129 GTTCTCCGTATACGTACTTGGTG 58.654 47.826 22.87 8.28 37.74 4.17
2915 4544 3.947196 TCCGTATACGTACTTGGTGACAT 59.053 43.478 22.87 0.00 37.76 3.06
2916 4545 4.398988 TCCGTATACGTACTTGGTGACATT 59.601 41.667 22.87 0.00 37.76 2.71
2962 4592 0.685131 TCGGTCGCCCTCCATCTTTA 60.685 55.000 0.00 0.00 0.00 1.85
2966 4596 2.495084 GTCGCCCTCCATCTTTAATCC 58.505 52.381 0.00 0.00 0.00 3.01
2979 4609 0.751277 TTAATCCCTGGCCGCACATG 60.751 55.000 0.00 0.00 0.00 3.21
2980 4610 1.920734 TAATCCCTGGCCGCACATGT 61.921 55.000 0.00 0.00 0.00 3.21
2981 4611 3.704231 ATCCCTGGCCGCACATGTC 62.704 63.158 0.00 0.00 0.00 3.06
2983 4613 4.720902 CCTGGCCGCACATGTCCA 62.721 66.667 0.00 0.00 0.00 4.02
2984 4614 3.129502 CTGGCCGCACATGTCCAG 61.130 66.667 14.85 14.85 39.95 3.86
2985 4615 4.720902 TGGCCGCACATGTCCAGG 62.721 66.667 0.00 0.36 0.00 4.45
2986 4616 4.722700 GGCCGCACATGTCCAGGT 62.723 66.667 0.00 0.00 0.00 4.00
2987 4617 3.127533 GCCGCACATGTCCAGGTC 61.128 66.667 0.00 0.00 0.00 3.85
3007 4637 3.480133 GCCCCTCCAGCGGTGTAT 61.480 66.667 14.40 0.00 0.00 2.29
3048 4678 0.890996 AAAGTTTGCTCCGCTCCTGG 60.891 55.000 0.00 0.00 0.00 4.45
3055 4685 1.153489 CTCCGCTCCTGGTGACATG 60.153 63.158 0.00 0.00 41.51 3.21
3056 4686 1.607801 CTCCGCTCCTGGTGACATGA 61.608 60.000 0.00 0.00 41.51 3.07
3075 4710 1.001860 GAGGAGTGCAGAGCATATCCC 59.998 57.143 17.35 7.73 43.60 3.85
3077 4712 1.270732 GGAGTGCAGAGCATATCCCAG 60.271 57.143 12.55 0.00 41.91 4.45
3139 4774 1.296392 CTGCAGTCGATGGGTCCAA 59.704 57.895 5.25 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 3.743911 ACAAACAAGCACATGCATTGATG 59.256 39.130 17.33 16.32 45.16 3.07
42 43 3.997762 ACAAACAAGCACATGCATTGAT 58.002 36.364 17.33 0.00 45.16 2.57
43 44 3.455990 ACAAACAAGCACATGCATTGA 57.544 38.095 17.33 0.00 45.16 2.57
44 45 4.275662 CAAACAAACAAGCACATGCATTG 58.724 39.130 6.64 9.91 45.16 2.82
45 46 3.242804 GCAAACAAACAAGCACATGCATT 60.243 39.130 6.64 0.00 45.16 3.56
57 58 1.757682 AGTTCCTCGGCAAACAAACA 58.242 45.000 0.00 0.00 0.00 2.83
82 83 2.224378 CCACTGACAGTCTGACACCATT 60.224 50.000 14.03 0.00 0.00 3.16
89 90 2.073252 ACTGACCACTGACAGTCTGA 57.927 50.000 14.03 0.00 42.54 3.27
90 91 2.898729 AACTGACCACTGACAGTCTG 57.101 50.000 4.74 5.91 44.80 3.51
91 92 3.833732 TCTAACTGACCACTGACAGTCT 58.166 45.455 4.74 0.00 44.80 3.24
92 93 4.792521 ATCTAACTGACCACTGACAGTC 57.207 45.455 4.74 0.00 44.80 3.51
93 94 6.437477 TGAATATCTAACTGACCACTGACAGT 59.563 38.462 1.07 1.07 46.97 3.55
94 95 6.867550 TGAATATCTAACTGACCACTGACAG 58.132 40.000 0.00 0.00 39.69 3.51
95 96 6.663523 TCTGAATATCTAACTGACCACTGACA 59.336 38.462 0.00 0.00 0.00 3.58
96 97 6.975772 GTCTGAATATCTAACTGACCACTGAC 59.024 42.308 0.00 0.00 0.00 3.51
97 98 6.183360 CGTCTGAATATCTAACTGACCACTGA 60.183 42.308 0.00 0.00 31.93 3.41
152 153 1.478137 GTCGTAACTCAGGCGCTATG 58.522 55.000 7.64 7.13 0.00 2.23
177 178 5.187772 AGACCAGACAGCACAGTAATCAATA 59.812 40.000 0.00 0.00 0.00 1.90
206 210 1.891919 GGCACAGTTGACCGCTCAA 60.892 57.895 0.00 0.00 33.76 3.02
211 215 2.111043 AGGTGGCACAGTTGACCG 59.889 61.111 20.82 0.00 41.80 4.79
232 236 4.984785 TCACTCACGATGACTTTCTTGAAG 59.015 41.667 0.00 0.00 41.32 3.02
254 258 8.345565 CAGTTTATCTACCTGGCACATATTTTC 58.654 37.037 0.00 0.00 38.20 2.29
283 288 0.652592 CTATTTCAGCAACCCTCGCG 59.347 55.000 0.00 0.00 0.00 5.87
285 290 2.159517 GCAACTATTTCAGCAACCCTCG 60.160 50.000 0.00 0.00 0.00 4.63
287 292 2.875296 TGCAACTATTTCAGCAACCCT 58.125 42.857 0.00 0.00 33.48 4.34
289 294 2.925563 GCATGCAACTATTTCAGCAACC 59.074 45.455 14.21 0.00 40.76 3.77
292 574 2.083002 TCGCATGCAACTATTTCAGCA 58.917 42.857 19.57 0.00 41.73 4.41
307 589 0.322098 TTGGACGGGAACAATCGCAT 60.322 50.000 0.00 0.00 38.36 4.73
316 598 4.027674 TGAGAAATTGATTGGACGGGAA 57.972 40.909 0.00 0.00 0.00 3.97
343 625 1.294780 GCCCAGTGGTCACTCTCTG 59.705 63.158 8.74 0.00 40.20 3.35
346 628 2.122413 TGGCCCAGTGGTCACTCT 60.122 61.111 8.74 0.00 42.76 3.24
351 633 2.361610 CACCATGGCCCAGTGGTC 60.362 66.667 18.63 0.00 45.30 4.02
354 636 2.677524 CACCACCATGGCCCAGTG 60.678 66.667 13.04 10.52 42.67 3.66
355 637 3.983420 CCACCACCATGGCCCAGT 61.983 66.667 13.04 0.64 42.67 4.00
364 719 2.463589 GAAGATGGACGCCACCACCA 62.464 60.000 0.50 0.00 43.03 4.17
366 721 2.100631 CGAAGATGGACGCCACCAC 61.101 63.158 0.50 0.00 43.03 4.16
367 722 1.613317 ATCGAAGATGGACGCCACCA 61.613 55.000 0.50 0.00 45.12 4.17
368 723 1.144057 ATCGAAGATGGACGCCACC 59.856 57.895 0.50 0.00 45.12 4.61
371 726 2.247437 GCCATCGAAGATGGACGCC 61.247 63.158 27.62 10.11 45.12 5.68
375 730 1.521457 GCGTGCCATCGAAGATGGA 60.521 57.895 27.62 13.13 45.12 3.41
377 732 1.640069 CTGCGTGCCATCGAAGATG 59.360 57.895 3.21 3.21 45.12 2.90
382 737 2.494445 CTACCTGCGTGCCATCGA 59.506 61.111 0.00 0.00 0.00 3.59
383 738 2.586079 CCTACCTGCGTGCCATCG 60.586 66.667 0.00 0.00 0.00 3.84
400 755 0.108138 AGTTGTCATGAGGCTACCGC 60.108 55.000 0.00 0.00 0.00 5.68
401 756 1.471676 GGAGTTGTCATGAGGCTACCG 60.472 57.143 0.00 0.00 0.00 4.02
403 758 1.471676 CCGGAGTTGTCATGAGGCTAC 60.472 57.143 0.00 0.00 0.00 3.58
404 759 0.824109 CCGGAGTTGTCATGAGGCTA 59.176 55.000 0.00 0.00 0.00 3.93
405 760 1.599047 CCGGAGTTGTCATGAGGCT 59.401 57.895 0.00 0.00 0.00 4.58
407 762 0.108138 GACCCGGAGTTGTCATGAGG 60.108 60.000 0.73 0.00 0.00 3.86
409 764 1.822990 GTAGACCCGGAGTTGTCATGA 59.177 52.381 0.73 0.00 33.89 3.07
411 766 1.192428 GGTAGACCCGGAGTTGTCAT 58.808 55.000 0.73 0.00 33.89 3.06
413 768 0.245813 GTGGTAGACCCGGAGTTGTC 59.754 60.000 0.73 0.70 35.15 3.18
414 769 0.470456 TGTGGTAGACCCGGAGTTGT 60.470 55.000 0.73 0.00 35.15 3.32
415 770 0.246635 CTGTGGTAGACCCGGAGTTG 59.753 60.000 0.73 0.00 35.15 3.16
416 771 0.178941 ACTGTGGTAGACCCGGAGTT 60.179 55.000 0.73 0.00 35.15 3.01
417 772 0.611340 GACTGTGGTAGACCCGGAGT 60.611 60.000 0.73 0.00 35.15 3.85
418 773 0.611062 TGACTGTGGTAGACCCGGAG 60.611 60.000 0.73 0.00 35.15 4.63
419 774 0.611062 CTGACTGTGGTAGACCCGGA 60.611 60.000 0.73 0.00 35.15 5.14
420 775 1.605058 CCTGACTGTGGTAGACCCGG 61.605 65.000 0.00 0.00 35.15 5.73
421 776 0.898789 ACCTGACTGTGGTAGACCCG 60.899 60.000 0.00 0.00 35.80 5.28
423 778 2.496470 CCTAACCTGACTGTGGTAGACC 59.504 54.545 0.00 0.00 36.69 3.85
427 782 1.899814 CTGCCTAACCTGACTGTGGTA 59.100 52.381 0.00 0.00 36.69 3.25
428 783 0.687354 CTGCCTAACCTGACTGTGGT 59.313 55.000 0.00 0.00 39.91 4.16
429 784 0.674895 GCTGCCTAACCTGACTGTGG 60.675 60.000 0.00 0.00 0.00 4.17
430 785 1.016130 CGCTGCCTAACCTGACTGTG 61.016 60.000 0.00 0.00 0.00 3.66
432 787 1.448540 CCGCTGCCTAACCTGACTG 60.449 63.158 0.00 0.00 0.00 3.51
434 789 2.820037 GCCGCTGCCTAACCTGAC 60.820 66.667 0.00 0.00 0.00 3.51
435 790 4.451150 CGCCGCTGCCTAACCTGA 62.451 66.667 0.00 0.00 0.00 3.86
451 806 4.802051 CACATGGTGGCTCCCCCG 62.802 72.222 2.66 0.00 35.87 5.73
455 810 1.376683 TTACGCACATGGTGGCTCC 60.377 57.895 0.00 0.00 33.64 4.70
456 811 1.794222 GTTACGCACATGGTGGCTC 59.206 57.895 0.00 0.00 33.64 4.70
457 812 2.032634 CGTTACGCACATGGTGGCT 61.033 57.895 0.00 0.00 33.64 4.75
458 813 1.015085 TACGTTACGCACATGGTGGC 61.015 55.000 4.09 0.00 33.64 5.01
459 814 0.717224 GTACGTTACGCACATGGTGG 59.283 55.000 4.09 0.00 33.64 4.61
461 816 2.728132 CGTACGTTACGCACATGGT 58.272 52.632 7.22 0.00 45.81 3.55
477 832 1.731424 CGGTCATCAAGTTCGTAGCGT 60.731 52.381 0.00 0.00 0.00 5.07
478 833 0.914551 CGGTCATCAAGTTCGTAGCG 59.085 55.000 0.00 0.00 0.00 4.26
479 834 1.278238 CCGGTCATCAAGTTCGTAGC 58.722 55.000 0.00 0.00 0.00 3.58
480 835 1.278238 GCCGGTCATCAAGTTCGTAG 58.722 55.000 1.90 0.00 0.00 3.51
482 837 1.375523 GGCCGGTCATCAAGTTCGT 60.376 57.895 0.00 0.00 0.00 3.85
483 838 2.452813 CGGCCGGTCATCAAGTTCG 61.453 63.158 20.10 0.00 0.00 3.95
484 839 2.106683 CCGGCCGGTCATCAAGTTC 61.107 63.158 36.64 0.00 0.00 3.01
485 840 2.046314 CCGGCCGGTCATCAAGTT 60.046 61.111 36.64 0.00 0.00 2.66
486 841 4.096003 CCCGGCCGGTCATCAAGT 62.096 66.667 40.52 0.00 0.00 3.16
503 858 3.155167 ATTCCGCCCCTCGTCTCC 61.155 66.667 0.00 0.00 36.19 3.71
504 859 2.107141 CATTCCGCCCCTCGTCTC 59.893 66.667 0.00 0.00 36.19 3.36
505 860 4.162690 GCATTCCGCCCCTCGTCT 62.163 66.667 0.00 0.00 36.19 4.18
512 867 3.957535 CATGCTCGCATTCCGCCC 61.958 66.667 0.85 0.00 37.30 6.13
513 868 3.173390 GACATGCTCGCATTCCGCC 62.173 63.158 0.85 0.00 37.30 6.13
514 869 2.325857 GACATGCTCGCATTCCGC 59.674 61.111 0.85 0.00 33.90 5.54
516 871 3.017323 CCGACATGCTCGCATTCC 58.983 61.111 0.85 0.00 41.46 3.01
517 872 2.325857 GCCGACATGCTCGCATTC 59.674 61.111 0.85 3.41 41.46 2.67
518 873 3.566853 CGCCGACATGCTCGCATT 61.567 61.111 0.85 0.00 41.46 3.56
519 874 4.512961 TCGCCGACATGCTCGCAT 62.513 61.111 10.87 0.00 41.46 4.73
534 889 4.812476 TGGATGCTTCGCCGGTCG 62.812 66.667 1.90 7.73 40.15 4.79
535 890 2.650813 ATCTGGATGCTTCGCCGGTC 62.651 60.000 1.90 0.00 32.28 4.79
536 891 2.650813 GATCTGGATGCTTCGCCGGT 62.651 60.000 1.90 0.00 32.28 5.28
537 892 1.958205 GATCTGGATGCTTCGCCGG 60.958 63.158 0.00 0.00 0.00 6.13
538 893 2.305853 CGATCTGGATGCTTCGCCG 61.306 63.158 0.00 0.00 0.00 6.46
539 894 1.958205 CCGATCTGGATGCTTCGCC 60.958 63.158 0.00 0.00 42.00 5.54
540 895 2.602322 GCCGATCTGGATGCTTCGC 61.602 63.158 7.64 0.00 42.00 4.70
541 896 1.227350 TGCCGATCTGGATGCTTCG 60.227 57.895 7.64 0.00 42.00 3.79
542 897 1.493950 CGTGCCGATCTGGATGCTTC 61.494 60.000 7.64 0.00 42.00 3.86
543 898 1.522355 CGTGCCGATCTGGATGCTT 60.522 57.895 7.64 0.00 42.00 3.91
544 899 2.107750 CGTGCCGATCTGGATGCT 59.892 61.111 7.64 0.00 42.00 3.79
545 900 2.923426 TTCCGTGCCGATCTGGATGC 62.923 60.000 7.64 0.00 42.00 3.91
546 901 0.461870 TTTCCGTGCCGATCTGGATG 60.462 55.000 7.64 0.00 42.00 3.51
547 902 0.179073 CTTTCCGTGCCGATCTGGAT 60.179 55.000 7.64 0.00 42.00 3.41
548 903 1.218047 CTTTCCGTGCCGATCTGGA 59.782 57.895 7.64 0.00 42.00 3.86
549 904 1.815421 CCTTTCCGTGCCGATCTGG 60.815 63.158 0.00 0.00 42.50 3.86
550 905 2.464459 GCCTTTCCGTGCCGATCTG 61.464 63.158 0.00 0.00 0.00 2.90
551 906 2.125106 GCCTTTCCGTGCCGATCT 60.125 61.111 0.00 0.00 0.00 2.75
552 907 3.564027 CGCCTTTCCGTGCCGATC 61.564 66.667 0.00 0.00 0.00 3.69
592 947 1.833049 ATCATCCTCGGTCGTCCCC 60.833 63.158 0.00 0.00 0.00 4.81
614 969 0.105593 CGGGTCCCATCTCATGAGTG 59.894 60.000 21.92 17.71 0.00 3.51
636 994 0.790207 CTCACACTACGCACGCAATT 59.210 50.000 0.00 0.00 0.00 2.32
639 997 1.660264 CACTCACACTACGCACGCA 60.660 57.895 0.00 0.00 0.00 5.24
647 1005 1.669265 CGCGGTATCTCACTCACACTA 59.331 52.381 0.00 0.00 0.00 2.74
652 1010 1.712018 CGGACGCGGTATCTCACTCA 61.712 60.000 12.47 0.00 0.00 3.41
881 1256 1.728490 GGGGATTGGCGCTTGATGAC 61.728 60.000 7.64 0.00 0.00 3.06
887 1262 3.978193 TGGTGGGGATTGGCGCTT 61.978 61.111 7.64 0.00 0.00 4.68
922 1297 2.972505 CGCGGTTGGAGCTGTTGT 60.973 61.111 0.00 0.00 0.00 3.32
924 1299 4.927782 TGCGCGGTTGGAGCTGTT 62.928 61.111 8.83 0.00 42.55 3.16
965 1340 0.970937 CAAGTACAGGGAGGGAGCGA 60.971 60.000 0.00 0.00 0.00 4.93
966 1341 1.517832 CAAGTACAGGGAGGGAGCG 59.482 63.158 0.00 0.00 0.00 5.03
969 1344 1.987855 CGGCAAGTACAGGGAGGGA 60.988 63.158 0.00 0.00 0.00 4.20
975 1351 2.746277 GGCACCGGCAAGTACAGG 60.746 66.667 0.00 0.00 43.71 4.00
1905 2310 2.351244 CCGGCTCCTGCTGTACTGA 61.351 63.158 3.61 0.00 43.76 3.41
1997 2402 1.134848 AGCTCGACTTGCTCATCTTCC 60.135 52.381 0.00 0.00 35.67 3.46
2190 2601 2.022240 GATCTTCTTCTCCGGCGGCT 62.022 60.000 23.83 0.00 0.00 5.52
2210 2621 0.382515 GATCTACTGCTCTTCGGCGT 59.617 55.000 6.85 0.00 34.52 5.68
2211 2622 0.382158 TGATCTACTGCTCTTCGGCG 59.618 55.000 0.00 0.00 34.52 6.46
2212 2623 2.035193 TGATGATCTACTGCTCTTCGGC 59.965 50.000 0.00 0.00 0.00 5.54
2217 2628 3.326946 AGGGTGATGATCTACTGCTCT 57.673 47.619 0.00 0.00 0.00 4.09
2219 2630 3.235200 GGTAGGGTGATGATCTACTGCT 58.765 50.000 0.00 0.00 35.15 4.24
2227 2638 0.327480 TGGCAGGGTAGGGTGATGAT 60.327 55.000 0.00 0.00 0.00 2.45
2228 2639 0.548926 TTGGCAGGGTAGGGTGATGA 60.549 55.000 0.00 0.00 0.00 2.92
2230 2641 0.550147 ACTTGGCAGGGTAGGGTGAT 60.550 55.000 0.44 0.00 0.00 3.06
2231 2642 1.151899 ACTTGGCAGGGTAGGGTGA 60.152 57.895 0.44 0.00 0.00 4.02
2232 2643 1.002134 CACTTGGCAGGGTAGGGTG 60.002 63.158 0.44 0.00 0.00 4.61
2233 2644 2.231380 CCACTTGGCAGGGTAGGGT 61.231 63.158 0.44 0.00 0.00 4.34
2236 2647 0.400213 TGAACCACTTGGCAGGGTAG 59.600 55.000 0.44 0.00 39.32 3.18
2237 2648 1.072266 ATGAACCACTTGGCAGGGTA 58.928 50.000 0.44 0.00 39.32 3.69
2238 2649 0.188342 AATGAACCACTTGGCAGGGT 59.812 50.000 0.44 1.44 39.32 4.34
2239 2650 2.094675 CTAATGAACCACTTGGCAGGG 58.905 52.381 0.44 0.75 39.32 4.45
2240 2651 1.474077 GCTAATGAACCACTTGGCAGG 59.526 52.381 0.00 0.00 39.32 4.85
2242 2653 2.161855 CTGCTAATGAACCACTTGGCA 58.838 47.619 0.00 0.00 39.32 4.92
2243 2654 2.436417 TCTGCTAATGAACCACTTGGC 58.564 47.619 0.00 0.00 39.32 4.52
2244 2655 6.949352 ATAATCTGCTAATGAACCACTTGG 57.051 37.500 0.00 0.00 42.17 3.61
2245 2656 9.722056 GTTAATAATCTGCTAATGAACCACTTG 57.278 33.333 0.00 0.00 0.00 3.16
2246 2657 9.686683 AGTTAATAATCTGCTAATGAACCACTT 57.313 29.630 0.00 0.00 0.00 3.16
2281 2692 7.776969 AGTCTAATCACATGCAGGAAAATGTAT 59.223 33.333 4.84 0.00 35.28 2.29
2282 2693 7.112122 AGTCTAATCACATGCAGGAAAATGTA 58.888 34.615 4.84 0.00 35.28 2.29
2283 2694 5.948162 AGTCTAATCACATGCAGGAAAATGT 59.052 36.000 4.84 0.00 37.50 2.71
2295 2706 6.216569 CGCCACAGTATTAGTCTAATCACAT 58.783 40.000 8.41 0.00 0.00 3.21
2306 2717 7.385205 ACAGATTAATTAGCGCCACAGTATTAG 59.615 37.037 2.29 0.00 0.00 1.73
2312 2736 4.882671 AACAGATTAATTAGCGCCACAG 57.117 40.909 2.29 0.00 0.00 3.66
2328 2752 7.103641 AGCAAAATCCTCGAGTAATTAACAGA 58.896 34.615 12.31 0.00 0.00 3.41
2335 2759 4.872691 CACAGAGCAAAATCCTCGAGTAAT 59.127 41.667 12.31 1.47 34.56 1.89
2342 2766 3.149196 TGTTCCACAGAGCAAAATCCTC 58.851 45.455 0.00 0.00 29.24 3.71
2352 2777 2.118313 TGATGCCATGTTCCACAGAG 57.882 50.000 0.00 0.00 0.00 3.35
2382 2807 3.556004 CCAACTCTCTCAAGTCTCAACCC 60.556 52.174 0.00 0.00 0.00 4.11
2384 2809 3.322254 TCCCAACTCTCTCAAGTCTCAAC 59.678 47.826 0.00 0.00 0.00 3.18
2386 2811 3.244887 TCCCAACTCTCTCAAGTCTCA 57.755 47.619 0.00 0.00 0.00 3.27
2389 2814 5.221422 CCATCTATCCCAACTCTCTCAAGTC 60.221 48.000 0.00 0.00 0.00 3.01
2390 2815 4.653341 CCATCTATCCCAACTCTCTCAAGT 59.347 45.833 0.00 0.00 0.00 3.16
2391 2816 4.502950 GCCATCTATCCCAACTCTCTCAAG 60.503 50.000 0.00 0.00 0.00 3.02
2392 2817 3.389329 GCCATCTATCCCAACTCTCTCAA 59.611 47.826 0.00 0.00 0.00 3.02
2395 2820 2.971330 CTGCCATCTATCCCAACTCTCT 59.029 50.000 0.00 0.00 0.00 3.10
2396 2821 2.703007 ACTGCCATCTATCCCAACTCTC 59.297 50.000 0.00 0.00 0.00 3.20
2397 2822 2.769209 ACTGCCATCTATCCCAACTCT 58.231 47.619 0.00 0.00 0.00 3.24
2398 2823 3.556004 GCTACTGCCATCTATCCCAACTC 60.556 52.174 0.00 0.00 0.00 3.01
2399 2824 2.370189 GCTACTGCCATCTATCCCAACT 59.630 50.000 0.00 0.00 0.00 3.16
2400 2825 2.772287 GCTACTGCCATCTATCCCAAC 58.228 52.381 0.00 0.00 0.00 3.77
2431 2856 4.248691 TCACTCACTGTTCACTCATCAG 57.751 45.455 0.00 0.00 35.60 2.90
2459 2884 2.590575 AGACGCACAAACCACCCG 60.591 61.111 0.00 0.00 0.00 5.28
2460 2885 2.604174 CGAGACGCACAAACCACCC 61.604 63.158 0.00 0.00 0.00 4.61
2517 2965 1.832719 TTCCGAGGCCATGGAACGAA 61.833 55.000 21.23 6.02 39.29 3.85
2518 2966 1.832719 TTTCCGAGGCCATGGAACGA 61.833 55.000 23.94 11.23 43.68 3.85
2519 2967 1.369091 CTTTCCGAGGCCATGGAACG 61.369 60.000 23.94 19.38 43.68 3.95
2520 2968 0.035439 TCTTTCCGAGGCCATGGAAC 60.035 55.000 23.94 7.43 43.68 3.62
2575 3023 4.219944 CCTGCCTGACAACTAACTGTAGTA 59.780 45.833 0.00 0.00 39.79 1.82
2576 3024 3.006967 CCTGCCTGACAACTAACTGTAGT 59.993 47.826 0.00 0.00 42.66 2.73
2579 3027 2.047061 TCCTGCCTGACAACTAACTGT 58.953 47.619 0.00 0.00 0.00 3.55
2581 3029 2.026822 CCATCCTGCCTGACAACTAACT 60.027 50.000 0.00 0.00 0.00 2.24
2582 3030 2.359900 CCATCCTGCCTGACAACTAAC 58.640 52.381 0.00 0.00 0.00 2.34
2583 3031 1.340017 GCCATCCTGCCTGACAACTAA 60.340 52.381 0.00 0.00 0.00 2.24
2584 3032 0.253044 GCCATCCTGCCTGACAACTA 59.747 55.000 0.00 0.00 0.00 2.24
2628 3379 0.179181 CACAGGCGACGTACGTACAT 60.179 55.000 22.87 10.69 44.60 2.29
2654 3405 2.952783 CCATCGCGTCGGGTTACG 60.953 66.667 5.77 0.00 45.58 3.18
2674 4298 4.759205 ATGGGTCCAAAGGGCGGC 62.759 66.667 0.00 0.00 0.00 6.53
2675 4299 2.037208 AATGGGTCCAAAGGGCGG 59.963 61.111 0.00 0.00 0.00 6.13
2676 4300 2.406616 CGAATGGGTCCAAAGGGCG 61.407 63.158 0.00 0.00 0.00 6.13
2677 4301 1.304134 ACGAATGGGTCCAAAGGGC 60.304 57.895 0.00 0.00 0.00 5.19
2738 4362 8.331022 CGTTACTGCTTTCTAGTAGTACGATTA 58.669 37.037 13.94 0.00 45.47 1.75
2783 4407 1.379044 GGACAAGAGGCACCATGGG 60.379 63.158 18.09 6.26 0.00 4.00
2789 4413 2.501723 TCCATAAGAGGACAAGAGGCAC 59.498 50.000 0.00 0.00 31.23 5.01
2908 4537 3.366374 GGAGCAGCAGTAAAAATGTCACC 60.366 47.826 0.00 0.00 0.00 4.02
2910 4539 2.483877 CGGAGCAGCAGTAAAAATGTCA 59.516 45.455 0.00 0.00 0.00 3.58
2911 4540 2.159517 CCGGAGCAGCAGTAAAAATGTC 60.160 50.000 0.00 0.00 0.00 3.06
2915 4544 1.202710 TGACCGGAGCAGCAGTAAAAA 60.203 47.619 9.46 0.00 0.00 1.94
2916 4545 0.394938 TGACCGGAGCAGCAGTAAAA 59.605 50.000 9.46 0.00 0.00 1.52
2962 4592 2.440796 CATGTGCGGCCAGGGATT 60.441 61.111 2.24 0.00 0.00 3.01
2966 4596 4.720902 TGGACATGTGCGGCCAGG 62.721 66.667 13.03 0.00 0.00 4.45
2979 4609 4.083862 GAGGGGCACGACCTGGAC 62.084 72.222 0.00 0.00 38.79 4.02
2982 4612 4.087892 CTGGAGGGGCACGACCTG 62.088 72.222 7.45 3.56 38.79 4.00
3003 4633 1.520564 CGCGGCTTGGCAGTATACA 60.521 57.895 5.50 0.00 0.00 2.29
3004 4634 1.227147 TCGCGGCTTGGCAGTATAC 60.227 57.895 6.13 0.00 0.00 1.47
3048 4678 2.006056 GCTCTGCACTCCTCATGTCAC 61.006 57.143 0.00 0.00 0.00 3.67
3055 4685 1.001860 GGGATATGCTCTGCACTCCTC 59.998 57.143 17.03 8.31 43.04 3.71
3056 4686 1.055040 GGGATATGCTCTGCACTCCT 58.945 55.000 17.03 0.00 43.04 3.69


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

AutoCloner maintained by Alex Coulton.