Multiple sequence alignment - TraesCS6D01G015200

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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 TraesCS6D01G015200 chr6D 100.000 3807 0 0 1 3807 6318420 6322226 0.000000e+00 7031.0
1 TraesCS6D01G015200 chr6D 89.036 830 71 9 1996 2806 6328091 6328919 0.000000e+00 1011.0
2 TraesCS6D01G015200 chr6D 95.858 169 7 0 790 958 243033054 243032886 1.350000e-69 274.0
3 TraesCS6D01G015200 chr6D 95.783 166 7 0 790 955 293177240 293177405 6.270000e-68 268.0
4 TraesCS6D01G015200 chr6D 91.327 196 16 1 3612 3807 431064566 431064372 2.250000e-67 267.0
5 TraesCS6D01G015200 chr6D 90.500 200 17 2 3606 3805 33250565 33250762 2.920000e-66 263.0
6 TraesCS6D01G015200 chr6A 94.964 1509 70 4 953 2456 5861525 5863032 0.000000e+00 2361.0
7 TraesCS6D01G015200 chr6A 95.748 1176 46 3 2443 3615 5863053 5864227 0.000000e+00 1892.0
8 TraesCS6D01G015200 chr6A 95.694 627 26 1 1 626 5651575 5652201 0.000000e+00 1007.0
9 TraesCS6D01G015200 chr6A 95.694 627 26 1 1 626 5859198 5859824 0.000000e+00 1007.0
10 TraesCS6D01G015200 chr6A 95.375 627 28 1 1 626 5753994 5754620 0.000000e+00 996.0
11 TraesCS6D01G015200 chr6A 92.350 183 11 3 781 961 153669885 153669704 1.360000e-64 257.0
12 TraesCS6D01G015200 chr6A 80.000 120 7 4 686 791 5861410 5861526 5.280000e-09 73.1
13 TraesCS6D01G015200 chr6B 88.591 1455 121 23 2107 3551 11577402 11578821 0.000000e+00 1725.0
14 TraesCS6D01G015200 chr6B 93.076 1011 62 5 953 1956 11574656 11575665 0.000000e+00 1472.0
15 TraesCS6D01G015200 chr7D 88.260 937 94 9 1000 1931 522504194 522503269 0.000000e+00 1107.0
16 TraesCS6D01G015200 chr7D 87.519 657 73 4 2159 2806 522503176 522502520 0.000000e+00 750.0
17 TraesCS6D01G015200 chr7D 94.286 175 9 1 789 962 525720963 525721137 2.250000e-67 267.0
18 TraesCS6D01G015200 chr7D 91.327 196 16 1 3612 3807 632827762 632827568 2.250000e-67 267.0
19 TraesCS6D01G015200 chr7B 87.128 940 105 11 1000 1931 556458519 556457588 0.000000e+00 1051.0
20 TraesCS6D01G015200 chr7B 88.280 657 68 4 2159 2806 556457064 556456408 0.000000e+00 778.0
21 TraesCS6D01G015200 chr7B 95.783 166 7 0 789 954 595442059 595441894 6.270000e-68 268.0
22 TraesCS6D01G015200 chr7A 87.128 940 105 11 1000 1931 602806353 602805422 0.000000e+00 1051.0
23 TraesCS6D01G015200 chr7A 87.215 657 75 4 2159 2806 602805325 602804669 0.000000e+00 739.0
24 TraesCS6D01G015200 chr1D 99.479 192 1 0 3616 3807 30277784 30277593 2.180000e-92 350.0
25 TraesCS6D01G015200 chr1D 77.932 503 105 6 2186 2684 492534871 492534371 3.690000e-80 309.0
26 TraesCS6D01G015200 chr4D 98.462 195 3 0 3613 3807 426900977 426901171 1.010000e-90 344.0
27 TraesCS6D01G015200 chrUn 97.959 196 4 0 3612 3807 96940801 96940996 1.310000e-89 340.0
28 TraesCS6D01G015200 chr5A 95.833 168 7 0 787 954 458199045 458198878 4.850000e-69 272.0
29 TraesCS6D01G015200 chr2A 91.795 195 16 0 3613 3807 1195057 1195251 4.850000e-69 272.0
30 TraesCS6D01G015200 chr2A 94.828 174 9 0 790 963 275929233 275929406 4.850000e-69 272.0
31 TraesCS6D01G015200 chr2A 95.122 41 0 1 3004 3042 213090225 213090185 3.170000e-06 63.9
32 TraesCS6D01G015200 chr3D 91.327 196 16 1 3612 3807 17649909 17649715 2.250000e-67 267.0
33 TraesCS6D01G015200 chr5D 90.452 199 19 0 3609 3807 505431249 505431447 2.920000e-66 263.0
34 TraesCS6D01G015200 chr5D 92.737 179 13 0 776 954 520165298 520165120 3.770000e-65 259.0
35 TraesCS6D01G015200 chr4A 91.146 192 15 2 767 957 665604099 665604289 3.770000e-65 259.0
36 TraesCS6D01G015200 chr4A 100.000 33 0 0 3013 3045 684529781 684529749 1.140000e-05 62.1
37 TraesCS6D01G015200 chr2B 97.500 40 1 0 2998 3037 793322657 793322696 6.820000e-08 69.4


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 TraesCS6D01G015200 chr6D 6318420 6322226 3806 False 7031.000 7031 100.0000 1 3807 1 chr6D.!!$F1 3806
1 TraesCS6D01G015200 chr6D 6328091 6328919 828 False 1011.000 1011 89.0360 1996 2806 1 chr6D.!!$F2 810
2 TraesCS6D01G015200 chr6A 5859198 5864227 5029 False 1333.275 2361 91.6015 1 3615 4 chr6A.!!$F3 3614
3 TraesCS6D01G015200 chr6A 5651575 5652201 626 False 1007.000 1007 95.6940 1 626 1 chr6A.!!$F1 625
4 TraesCS6D01G015200 chr6A 5753994 5754620 626 False 996.000 996 95.3750 1 626 1 chr6A.!!$F2 625
5 TraesCS6D01G015200 chr6B 11574656 11578821 4165 False 1598.500 1725 90.8335 953 3551 2 chr6B.!!$F1 2598
6 TraesCS6D01G015200 chr7D 522502520 522504194 1674 True 928.500 1107 87.8895 1000 2806 2 chr7D.!!$R2 1806
7 TraesCS6D01G015200 chr7B 556456408 556458519 2111 True 914.500 1051 87.7040 1000 2806 2 chr7B.!!$R2 1806
8 TraesCS6D01G015200 chr7A 602804669 602806353 1684 True 895.000 1051 87.1715 1000 2806 2 chr7A.!!$R1 1806
9 TraesCS6D01G015200 chr1D 492534371 492534871 500 True 309.000 309 77.9320 2186 2684 1 chr1D.!!$R2 498

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
412 414 0.961019 ACAATTGTGTGCGATTGGCT 59.039 45.0 11.07 0.0 46.06 4.75 F
1183 2737 1.081892 CAAGACCTTGCACGAGATGG 58.918 55.0 0.00 0.0 33.45 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1401 2955 1.289066 CGCGGAGAAGAGGTTCACA 59.711 57.895 0.0 0.0 34.82 3.58 R
3042 6708 1.014564 GTGCCGGTGCTCAGTCTTAC 61.015 60.000 1.9 0.0 38.71 2.34 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
33 34 5.304101 TCCAATAAGCTTCATGTTTGTGGTT 59.696 36.000 0.00 0.00 31.81 3.67
68 69 8.087750 TCATTCAGCTGGTTTAAATTTACCTTG 58.912 33.333 15.13 7.31 35.41 3.61
103 104 4.634443 ACGGCTAAACATATGGTCAAGAAC 59.366 41.667 7.80 0.00 0.00 3.01
142 143 4.357918 ACACATTTTGCAGGACTACTCT 57.642 40.909 0.00 0.00 0.00 3.24
236 238 0.965439 CGAACCCTGAAAATGCCCAA 59.035 50.000 0.00 0.00 0.00 4.12
238 240 2.757868 CGAACCCTGAAAATGCCCAATA 59.242 45.455 0.00 0.00 0.00 1.90
333 335 5.455392 GTTTCACCTTCAATCATCACACAG 58.545 41.667 0.00 0.00 0.00 3.66
340 342 5.704515 CCTTCAATCATCACACAGTCTCTTT 59.295 40.000 0.00 0.00 0.00 2.52
378 380 5.901413 TCCTATGAGATGCTTTGGATTCT 57.099 39.130 0.00 0.00 0.00 2.40
411 413 3.495124 ACAATTGTGTGCGATTGGC 57.505 47.368 11.07 0.00 46.06 4.52
412 414 0.961019 ACAATTGTGTGCGATTGGCT 59.039 45.000 11.07 0.00 46.06 4.75
473 475 4.261801 ACCATGTCAAGCCTATTGTACAC 58.738 43.478 0.00 0.00 0.00 2.90
496 498 9.989869 ACACGAGTCATAAAGATATATGATACG 57.010 33.333 16.42 16.42 42.54 3.06
499 501 7.591795 CGAGTCATAAAGATATATGATACGGCC 59.408 40.741 0.00 0.00 42.54 6.13
573 575 7.974675 TGTTGCTAGCTATGACTAACAAATTC 58.025 34.615 17.23 0.00 31.84 2.17
619 621 3.961182 TGCATACGCTTACTAGTAGTGC 58.039 45.455 13.29 15.67 39.64 4.40
620 622 3.630769 TGCATACGCTTACTAGTAGTGCT 59.369 43.478 13.29 13.25 39.64 4.40
621 623 4.818005 TGCATACGCTTACTAGTAGTGCTA 59.182 41.667 13.29 14.38 39.64 3.49
622 624 5.049612 TGCATACGCTTACTAGTAGTGCTAG 60.050 44.000 13.29 13.18 44.77 3.42
623 625 5.178996 GCATACGCTTACTAGTAGTGCTAGA 59.821 44.000 20.64 3.29 41.45 2.43
624 626 6.128227 GCATACGCTTACTAGTAGTGCTAGAT 60.128 42.308 20.64 8.49 41.45 1.98
639 641 7.483580 AGTGCTAGATATAGATAAACACCCC 57.516 40.000 0.00 0.00 0.00 4.95
706 2240 7.479150 AGTAGTGGTAGATAAGCGAAAGTTAC 58.521 38.462 0.00 0.00 0.00 2.50
713 2247 2.943843 AAGCGAAAGTTACAAGCGAC 57.056 45.000 0.00 0.00 0.00 5.19
717 2251 1.193874 CGAAAGTTACAAGCGACCCAC 59.806 52.381 0.00 0.00 0.00 4.61
731 2265 3.123804 CGACCCACATTATAGTCAGTGC 58.876 50.000 0.00 0.00 0.00 4.40
751 2295 3.405823 CTAGCCGAGCTACCTAGTACT 57.594 52.381 0.00 0.00 40.44 2.73
752 2296 2.259266 AGCCGAGCTACCTAGTACTC 57.741 55.000 0.00 0.00 36.99 2.59
753 2297 1.770061 AGCCGAGCTACCTAGTACTCT 59.230 52.381 0.00 0.00 36.99 3.24
755 2299 2.769893 CCGAGCTACCTAGTACTCTCC 58.230 57.143 0.00 0.00 0.00 3.71
757 2301 3.555586 CCGAGCTACCTAGTACTCTCCTC 60.556 56.522 0.00 0.00 0.00 3.71
758 2302 3.322828 CGAGCTACCTAGTACTCTCCTCT 59.677 52.174 0.00 0.00 0.00 3.69
759 2303 4.202284 CGAGCTACCTAGTACTCTCCTCTT 60.202 50.000 0.00 0.00 0.00 2.85
760 2304 5.010922 CGAGCTACCTAGTACTCTCCTCTTA 59.989 48.000 0.00 0.00 0.00 2.10
794 2339 8.557592 TCATTGAATCTCATGCATTATACTCC 57.442 34.615 0.00 0.00 0.00 3.85
795 2340 8.158789 TCATTGAATCTCATGCATTATACTCCA 58.841 33.333 0.00 0.00 0.00 3.86
796 2341 8.957466 CATTGAATCTCATGCATTATACTCCAT 58.043 33.333 0.00 0.00 0.00 3.41
797 2342 8.557592 TTGAATCTCATGCATTATACTCCATC 57.442 34.615 0.00 0.00 0.00 3.51
798 2343 7.108194 TGAATCTCATGCATTATACTCCATCC 58.892 38.462 0.00 0.00 0.00 3.51
799 2344 5.077134 TCTCATGCATTATACTCCATCCG 57.923 43.478 0.00 0.00 0.00 4.18
800 2345 4.528206 TCTCATGCATTATACTCCATCCGT 59.472 41.667 0.00 0.00 0.00 4.69
801 2346 5.012046 TCTCATGCATTATACTCCATCCGTT 59.988 40.000 0.00 0.00 0.00 4.44
802 2347 5.237815 TCATGCATTATACTCCATCCGTTC 58.762 41.667 0.00 0.00 0.00 3.95
803 2348 4.002906 TGCATTATACTCCATCCGTTCC 57.997 45.455 0.00 0.00 0.00 3.62
804 2349 3.646162 TGCATTATACTCCATCCGTTCCT 59.354 43.478 0.00 0.00 0.00 3.36
805 2350 4.836175 TGCATTATACTCCATCCGTTCCTA 59.164 41.667 0.00 0.00 0.00 2.94
806 2351 5.305902 TGCATTATACTCCATCCGTTCCTAA 59.694 40.000 0.00 0.00 0.00 2.69
807 2352 6.183361 TGCATTATACTCCATCCGTTCCTAAA 60.183 38.462 0.00 0.00 0.00 1.85
808 2353 6.879458 GCATTATACTCCATCCGTTCCTAAAT 59.121 38.462 0.00 0.00 0.00 1.40
809 2354 8.038944 GCATTATACTCCATCCGTTCCTAAATA 58.961 37.037 0.00 0.00 0.00 1.40
814 2359 7.613551 ACTCCATCCGTTCCTAAATATAAGT 57.386 36.000 0.00 0.00 0.00 2.24
815 2360 7.668492 ACTCCATCCGTTCCTAAATATAAGTC 58.332 38.462 0.00 0.00 0.00 3.01
816 2361 7.509659 ACTCCATCCGTTCCTAAATATAAGTCT 59.490 37.037 0.00 0.00 0.00 3.24
817 2362 8.258850 TCCATCCGTTCCTAAATATAAGTCTT 57.741 34.615 0.00 0.00 0.00 3.01
818 2363 8.711170 TCCATCCGTTCCTAAATATAAGTCTTT 58.289 33.333 0.00 0.00 0.00 2.52
819 2364 9.338622 CCATCCGTTCCTAAATATAAGTCTTTT 57.661 33.333 0.00 0.00 0.00 2.27
849 2394 9.273016 AGATTTCAAATGAACTACCATATACGG 57.727 33.333 0.00 0.00 33.13 4.02
850 2395 9.268268 GATTTCAAATGAACTACCATATACGGA 57.732 33.333 0.00 0.00 33.13 4.69
851 2396 9.793259 ATTTCAAATGAACTACCATATACGGAT 57.207 29.630 0.00 0.00 33.13 4.18
852 2397 8.601845 TTCAAATGAACTACCATATACGGATG 57.398 34.615 0.00 0.00 0.00 3.51
853 2398 7.732025 TCAAATGAACTACCATATACGGATGT 58.268 34.615 0.00 0.00 0.00 3.06
854 2399 8.862085 TCAAATGAACTACCATATACGGATGTA 58.138 33.333 0.00 0.00 34.45 2.29
855 2400 9.653287 CAAATGAACTACCATATACGGATGTAT 57.347 33.333 0.00 0.00 43.62 2.29
893 2438 7.934855 AGATTGTAGATTCACTCATTTTGCT 57.065 32.000 0.00 0.00 0.00 3.91
894 2439 7.983307 AGATTGTAGATTCACTCATTTTGCTC 58.017 34.615 0.00 0.00 0.00 4.26
895 2440 6.500684 TTGTAGATTCACTCATTTTGCTCC 57.499 37.500 0.00 0.00 0.00 4.70
896 2441 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
897 2442 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
898 2443 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
899 2444 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
900 2445 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
901 2446 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
902 2447 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
903 2448 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
904 2449 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
905 2450 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
906 2451 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
907 2452 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
908 2453 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
909 2454 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
910 2455 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
911 2456 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
912 2457 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
913 2458 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
914 2459 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
915 2460 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
916 2461 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
917 2462 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
918 2463 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
919 2464 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
920 2465 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
921 2466 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
922 2467 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
923 2468 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
924 2469 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
925 2470 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
926 2471 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
927 2472 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
928 2473 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
929 2474 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
930 2475 7.657761 TCACTTGTTGAAATCTCTAGAAAGACC 59.342 37.037 0.00 0.00 0.00 3.85
931 2476 7.659390 CACTTGTTGAAATCTCTAGAAAGACCT 59.341 37.037 0.00 0.00 0.00 3.85
932 2477 8.871125 ACTTGTTGAAATCTCTAGAAAGACCTA 58.129 33.333 0.00 0.00 0.00 3.08
933 2478 9.883142 CTTGTTGAAATCTCTAGAAAGACCTAT 57.117 33.333 0.00 0.00 0.00 2.57
966 2511 4.209911 CGGATGTAGTACATGCATGAACAG 59.790 45.833 32.75 14.03 45.68 3.16
984 2529 2.034432 ACAGTCGAACATTTGCATGCAA 59.966 40.909 28.80 28.80 33.05 4.08
1085 2639 2.509336 CTTCTTCCGCGCCGACAT 60.509 61.111 0.00 0.00 0.00 3.06
1161 2715 4.749310 CAGCTCGGCGGCAAGACT 62.749 66.667 19.61 0.00 34.17 3.24
1165 2719 3.573772 CTCGGCGGCAAGACTCACA 62.574 63.158 10.53 0.00 0.00 3.58
1183 2737 1.081892 CAAGACCTTGCACGAGATGG 58.918 55.000 0.00 0.00 33.45 3.51
1242 2796 4.954118 TCCCTCGTGGTGGTGGCT 62.954 66.667 2.33 0.00 34.77 4.75
1359 2913 1.821759 CCAGGACGTGGTGTTTGCA 60.822 57.895 6.00 0.00 42.17 4.08
1665 3221 2.355115 GTGGGCGGGGTTCTGAAT 59.645 61.111 0.00 0.00 0.00 2.57
1807 3363 2.265182 GCTTTTGCTACCACGGCCA 61.265 57.895 2.24 0.00 43.35 5.36
1831 3390 2.448383 AGGGCGGTAAGGACCTGA 59.552 61.111 0.00 0.00 46.32 3.86
1908 3470 5.282055 AGAACAAGATCACAGACACAGAA 57.718 39.130 0.00 0.00 0.00 3.02
1991 5038 1.550065 AATAGCGCGCTATAGCATCG 58.450 50.000 43.81 23.94 42.21 3.84
2038 5132 0.529773 ATCAGTGCACAACGTGTCGT 60.530 50.000 21.04 0.00 43.97 4.34
2097 5206 4.527564 GGCGCTATTTTGTTGTAGCATAG 58.472 43.478 7.64 0.00 42.62 2.23
2098 5207 3.968724 GCGCTATTTTGTTGTAGCATAGC 59.031 43.478 0.00 0.00 42.62 2.97
2100 5209 5.200454 CGCTATTTTGTTGTAGCATAGCAG 58.800 41.667 9.49 0.57 41.60 4.24
2132 5280 3.577848 TGGTAGCTCAACATGGCAAATTT 59.422 39.130 0.00 0.00 0.00 1.82
2139 5287 5.523552 GCTCAACATGGCAAATTTATAACCC 59.476 40.000 0.00 0.00 0.00 4.11
2402 6005 1.153765 CTCTCGCTGCCACGAATGA 60.154 57.895 0.00 0.00 42.39 2.57
2479 6116 3.599285 GAACGTGTGGGGGATCGCA 62.599 63.158 12.32 0.00 0.00 5.10
2721 6379 2.818132 GCCGGACATGGAGGAGAG 59.182 66.667 5.05 0.00 0.00 3.20
2779 6437 3.717294 CACCCGGTGCCTAGGCTT 61.717 66.667 33.07 8.81 42.51 4.35
2992 6658 9.233232 GCTTGTGTTTTTAACATATATAGTGCC 57.767 33.333 0.00 0.00 44.35 5.01
3014 6680 2.162319 TGCAGACGCTCATACAAACA 57.838 45.000 0.00 0.00 39.64 2.83
3042 6708 5.201713 ACACTCATCCCTATGAATACACG 57.798 43.478 0.00 0.00 41.57 4.49
3043 6709 4.649674 ACACTCATCCCTATGAATACACGT 59.350 41.667 0.00 0.00 41.57 4.49
3059 6725 1.805945 CGTAAGACTGAGCACCGGC 60.806 63.158 0.00 0.00 43.02 6.13
3064 6730 1.672356 GACTGAGCACCGGCACATT 60.672 57.895 0.00 0.00 44.61 2.71
3129 6795 0.666577 GGAACGTCTCCCACTGAACG 60.667 60.000 0.00 0.00 38.44 3.95
3163 6829 0.321653 GTGAGAATGACCAACGGGCT 60.322 55.000 0.00 0.00 37.90 5.19
3170 6836 2.279935 TGACCAACGGGCTAATTTGT 57.720 45.000 0.00 0.00 37.90 2.83
3219 6885 5.689383 ACAAAGTGTCTCGCATACAAATT 57.311 34.783 0.00 0.00 0.00 1.82
3274 6940 3.214328 ACGAGCTTCACCACAAGATTTT 58.786 40.909 0.00 0.00 0.00 1.82
3472 7139 9.297586 CGCATAAACTCTCTTACACTAATTGTA 57.702 33.333 0.00 0.00 39.91 2.41
3558 7225 5.835257 ACAAACACAATGGAAGAACTCATG 58.165 37.500 0.00 0.00 0.00 3.07
3613 7280 8.637196 ATTCATGTATCTTCGACTAGTATCCA 57.363 34.615 0.00 0.00 0.00 3.41
3614 7281 8.637196 TTCATGTATCTTCGACTAGTATCCAT 57.363 34.615 0.00 0.00 0.00 3.41
3615 7282 9.734984 TTCATGTATCTTCGACTAGTATCCATA 57.265 33.333 0.00 0.00 0.00 2.74
3616 7283 9.384764 TCATGTATCTTCGACTAGTATCCATAG 57.615 37.037 0.00 0.00 0.00 2.23
3617 7284 9.384764 CATGTATCTTCGACTAGTATCCATAGA 57.615 37.037 0.00 0.00 0.00 1.98
3619 7286 9.961264 TGTATCTTCGACTAGTATCCATAGATT 57.039 33.333 0.00 0.00 33.67 2.40
3630 7297 9.751542 CTAGTATCCATAGATTAAAATAGCCCG 57.248 37.037 0.00 0.00 33.67 6.13
3631 7298 7.048512 AGTATCCATAGATTAAAATAGCCCGC 58.951 38.462 0.00 0.00 33.67 6.13
3632 7299 4.250464 TCCATAGATTAAAATAGCCCGCG 58.750 43.478 0.00 0.00 0.00 6.46
3633 7300 4.020928 TCCATAGATTAAAATAGCCCGCGA 60.021 41.667 8.23 0.00 0.00 5.87
3634 7301 4.693566 CCATAGATTAAAATAGCCCGCGAA 59.306 41.667 8.23 0.00 0.00 4.70
3635 7302 5.180492 CCATAGATTAAAATAGCCCGCGAAA 59.820 40.000 8.23 0.00 0.00 3.46
3636 7303 6.128007 CCATAGATTAAAATAGCCCGCGAAAT 60.128 38.462 8.23 0.00 0.00 2.17
3637 7304 7.065324 CCATAGATTAAAATAGCCCGCGAAATA 59.935 37.037 8.23 0.00 0.00 1.40
3638 7305 6.481954 AGATTAAAATAGCCCGCGAAATAG 57.518 37.500 8.23 0.00 0.00 1.73
3639 7306 4.477302 TTAAAATAGCCCGCGAAATAGC 57.523 40.909 8.23 1.83 0.00 2.97
3640 7307 1.235724 AAATAGCCCGCGAAATAGCC 58.764 50.000 8.23 0.00 0.00 3.93
3641 7308 0.949105 AATAGCCCGCGAAATAGCCG 60.949 55.000 8.23 0.00 0.00 5.52
3665 7332 2.423018 CTGCGCTATAGCTGCCCA 59.577 61.111 27.09 16.58 38.89 5.36
3666 7333 1.667191 CTGCGCTATAGCTGCCCAG 60.667 63.158 27.09 20.34 38.89 4.45
3667 7334 2.358003 GCGCTATAGCTGCCCAGG 60.358 66.667 21.98 6.20 39.32 4.45
3668 7335 2.872388 GCGCTATAGCTGCCCAGGA 61.872 63.158 21.98 0.00 39.32 3.86
3669 7336 1.291588 CGCTATAGCTGCCCAGGAG 59.708 63.158 21.98 0.00 39.32 3.69
3670 7337 1.003959 GCTATAGCTGCCCAGGAGC 60.004 63.158 17.75 0.00 38.21 4.70
3671 7338 1.676384 CTATAGCTGCCCAGGAGCC 59.324 63.158 4.35 0.00 37.12 4.70
3672 7339 0.835543 CTATAGCTGCCCAGGAGCCT 60.836 60.000 4.35 0.00 37.12 4.58
3673 7340 0.400525 TATAGCTGCCCAGGAGCCTT 60.401 55.000 4.35 0.00 37.12 4.35
3674 7341 1.992519 ATAGCTGCCCAGGAGCCTTG 61.993 60.000 4.35 0.00 37.12 3.61
3680 7347 3.785859 CCAGGAGCCTTGCCGCTA 61.786 66.667 0.00 0.00 39.87 4.26
3681 7348 2.512515 CAGGAGCCTTGCCGCTAC 60.513 66.667 0.00 0.00 39.87 3.58
3682 7349 4.148825 AGGAGCCTTGCCGCTACG 62.149 66.667 0.00 0.00 45.09 3.51
3684 7351 4.821589 GAGCCTTGCCGCTACGCT 62.822 66.667 0.00 0.00 39.87 5.07
3685 7352 3.426117 GAGCCTTGCCGCTACGCTA 62.426 63.158 0.00 0.00 39.87 4.26
3686 7353 2.280186 GCCTTGCCGCTACGCTAT 60.280 61.111 0.00 0.00 0.00 2.97
3687 7354 2.598632 GCCTTGCCGCTACGCTATG 61.599 63.158 0.00 0.00 0.00 2.23
3688 7355 1.956170 CCTTGCCGCTACGCTATGG 60.956 63.158 0.00 0.00 0.00 2.74
3691 7358 3.038417 GCCGCTACGCTATGGCTG 61.038 66.667 0.00 0.00 44.16 4.85
3692 7359 3.038417 CCGCTACGCTATGGCTGC 61.038 66.667 0.00 0.08 36.09 5.25
3693 7360 2.028190 CGCTACGCTATGGCTGCT 59.972 61.111 0.00 0.00 36.09 4.24
3694 7361 2.305853 CGCTACGCTATGGCTGCTG 61.306 63.158 0.00 0.00 36.09 4.41
3695 7362 2.602322 GCTACGCTATGGCTGCTGC 61.602 63.158 7.10 7.10 36.09 5.25
3705 7372 4.543084 GCTGCTGCCGCGAAATCC 62.543 66.667 8.23 0.00 39.65 3.01
3706 7373 2.821366 CTGCTGCCGCGAAATCCT 60.821 61.111 8.23 0.00 39.65 3.24
3707 7374 2.817423 CTGCTGCCGCGAAATCCTC 61.817 63.158 8.23 0.00 39.65 3.71
3708 7375 3.577313 GCTGCCGCGAAATCCTCC 61.577 66.667 8.23 0.00 0.00 4.30
3709 7376 3.264897 CTGCCGCGAAATCCTCCG 61.265 66.667 8.23 0.00 0.00 4.63
3716 7383 2.384203 CGAAATCCTCCGCAACTCC 58.616 57.895 0.00 0.00 0.00 3.85
3717 7384 1.090052 CGAAATCCTCCGCAACTCCC 61.090 60.000 0.00 0.00 0.00 4.30
3718 7385 0.253327 GAAATCCTCCGCAACTCCCT 59.747 55.000 0.00 0.00 0.00 4.20
3719 7386 0.035056 AAATCCTCCGCAACTCCCTG 60.035 55.000 0.00 0.00 0.00 4.45
3720 7387 1.201429 AATCCTCCGCAACTCCCTGT 61.201 55.000 0.00 0.00 0.00 4.00
3721 7388 0.325296 ATCCTCCGCAACTCCCTGTA 60.325 55.000 0.00 0.00 0.00 2.74
3722 7389 0.543410 TCCTCCGCAACTCCCTGTAA 60.543 55.000 0.00 0.00 0.00 2.41
3723 7390 0.323629 CCTCCGCAACTCCCTGTAAA 59.676 55.000 0.00 0.00 0.00 2.01
3724 7391 1.065418 CCTCCGCAACTCCCTGTAAAT 60.065 52.381 0.00 0.00 0.00 1.40
3725 7392 2.009774 CTCCGCAACTCCCTGTAAATG 58.990 52.381 0.00 0.00 0.00 2.32
3726 7393 1.094785 CCGCAACTCCCTGTAAATGG 58.905 55.000 0.00 0.00 0.00 3.16
3727 7394 1.613255 CCGCAACTCCCTGTAAATGGT 60.613 52.381 0.00 0.00 0.00 3.55
3728 7395 2.159382 CGCAACTCCCTGTAAATGGTT 58.841 47.619 0.00 0.00 0.00 3.67
3729 7396 2.161609 CGCAACTCCCTGTAAATGGTTC 59.838 50.000 0.00 0.00 0.00 3.62
3730 7397 3.153919 GCAACTCCCTGTAAATGGTTCA 58.846 45.455 0.00 0.00 0.00 3.18
3731 7398 3.191371 GCAACTCCCTGTAAATGGTTCAG 59.809 47.826 0.00 0.00 0.00 3.02
3732 7399 3.073274 ACTCCCTGTAAATGGTTCAGC 57.927 47.619 0.00 0.00 0.00 4.26
3733 7400 2.375174 ACTCCCTGTAAATGGTTCAGCA 59.625 45.455 0.00 0.00 0.00 4.41
3734 7401 3.181434 ACTCCCTGTAAATGGTTCAGCAA 60.181 43.478 0.00 0.00 0.00 3.91
3735 7402 4.019174 CTCCCTGTAAATGGTTCAGCAAT 58.981 43.478 0.00 0.00 0.00 3.56
3736 7403 3.763360 TCCCTGTAAATGGTTCAGCAATG 59.237 43.478 0.00 0.00 0.00 2.82
3737 7404 3.763360 CCCTGTAAATGGTTCAGCAATGA 59.237 43.478 0.00 0.00 0.00 2.57
3738 7405 4.142315 CCCTGTAAATGGTTCAGCAATGAG 60.142 45.833 0.00 0.00 0.00 2.90
3739 7406 4.418392 CTGTAAATGGTTCAGCAATGAGC 58.582 43.478 0.00 0.00 46.19 4.26
3746 7413 2.867647 GGTTCAGCAATGAGCAAAACCC 60.868 50.000 10.64 0.00 46.28 4.11
3747 7414 5.122354 GGTTCAGCAATGAGCAAAACCCT 62.122 47.826 10.64 0.00 46.28 4.34
3748 7415 6.870169 GGTTCAGCAATGAGCAAAACCCTC 62.870 50.000 10.64 0.00 46.28 4.30
3749 7416 3.820595 GCAATGAGCAAAACCCTCC 57.179 52.632 0.00 0.00 44.79 4.30
3750 7417 0.109132 GCAATGAGCAAAACCCTCCG 60.109 55.000 0.00 0.00 44.79 4.63
3751 7418 0.527565 CAATGAGCAAAACCCTCCGG 59.472 55.000 0.00 0.00 0.00 5.14
3752 7419 0.404040 AATGAGCAAAACCCTCCGGA 59.596 50.000 2.93 2.93 0.00 5.14
3753 7420 0.404040 ATGAGCAAAACCCTCCGGAA 59.596 50.000 5.23 0.00 0.00 4.30
3754 7421 0.183971 TGAGCAAAACCCTCCGGAAA 59.816 50.000 5.23 0.00 0.00 3.13
3755 7422 1.203001 TGAGCAAAACCCTCCGGAAAT 60.203 47.619 5.23 0.00 0.00 2.17
3756 7423 1.472878 GAGCAAAACCCTCCGGAAATC 59.527 52.381 5.23 0.00 0.00 2.17
3757 7424 1.203001 AGCAAAACCCTCCGGAAATCA 60.203 47.619 5.23 0.00 0.00 2.57
3758 7425 1.824852 GCAAAACCCTCCGGAAATCAT 59.175 47.619 5.23 0.00 0.00 2.45
3759 7426 2.159240 GCAAAACCCTCCGGAAATCATC 60.159 50.000 5.23 0.00 0.00 2.92
3760 7427 3.356290 CAAAACCCTCCGGAAATCATCT 58.644 45.455 5.23 0.00 0.00 2.90
3761 7428 3.283259 AAACCCTCCGGAAATCATCTC 57.717 47.619 5.23 0.00 0.00 2.75
3762 7429 2.182516 ACCCTCCGGAAATCATCTCT 57.817 50.000 5.23 0.00 0.00 3.10
3763 7430 2.043227 ACCCTCCGGAAATCATCTCTC 58.957 52.381 5.23 0.00 0.00 3.20
3764 7431 1.346068 CCCTCCGGAAATCATCTCTCC 59.654 57.143 5.23 0.00 0.00 3.71
3765 7432 1.346068 CCTCCGGAAATCATCTCTCCC 59.654 57.143 5.23 0.00 0.00 4.30
3766 7433 1.000283 CTCCGGAAATCATCTCTCCCG 60.000 57.143 5.23 0.00 36.98 5.14
3767 7434 0.753262 CCGGAAATCATCTCTCCCGT 59.247 55.000 0.00 0.00 35.61 5.28
3768 7435 1.269831 CCGGAAATCATCTCTCCCGTC 60.270 57.143 0.00 0.00 35.61 4.79
3769 7436 1.409064 CGGAAATCATCTCTCCCGTCA 59.591 52.381 0.00 0.00 33.02 4.35
3770 7437 2.544694 CGGAAATCATCTCTCCCGTCAG 60.545 54.545 0.00 0.00 33.02 3.51
3771 7438 2.695666 GGAAATCATCTCTCCCGTCAGA 59.304 50.000 0.00 0.00 0.00 3.27
3772 7439 3.133003 GGAAATCATCTCTCCCGTCAGAA 59.867 47.826 0.00 0.00 0.00 3.02
3773 7440 4.383118 GGAAATCATCTCTCCCGTCAGAAA 60.383 45.833 0.00 0.00 0.00 2.52
3774 7441 4.826274 AATCATCTCTCCCGTCAGAAAA 57.174 40.909 0.00 0.00 0.00 2.29
3775 7442 4.826274 ATCATCTCTCCCGTCAGAAAAA 57.174 40.909 0.00 0.00 0.00 1.94
3776 7443 4.826274 TCATCTCTCCCGTCAGAAAAAT 57.174 40.909 0.00 0.00 0.00 1.82
3777 7444 5.165961 TCATCTCTCCCGTCAGAAAAATT 57.834 39.130 0.00 0.00 0.00 1.82
3778 7445 5.560724 TCATCTCTCCCGTCAGAAAAATTT 58.439 37.500 0.00 0.00 0.00 1.82
3779 7446 5.643777 TCATCTCTCCCGTCAGAAAAATTTC 59.356 40.000 0.00 0.00 37.45 2.17
3780 7447 4.324267 TCTCTCCCGTCAGAAAAATTTCC 58.676 43.478 2.37 0.00 37.92 3.13
3781 7448 3.071479 TCTCCCGTCAGAAAAATTTCCG 58.929 45.455 2.37 0.23 37.92 4.30
3782 7449 1.538075 TCCCGTCAGAAAAATTTCCGC 59.462 47.619 2.37 0.00 37.92 5.54
3783 7450 1.539827 CCCGTCAGAAAAATTTCCGCT 59.460 47.619 2.37 0.00 37.92 5.52
3784 7451 2.745281 CCCGTCAGAAAAATTTCCGCTA 59.255 45.455 2.37 0.00 37.92 4.26
3785 7452 3.377172 CCCGTCAGAAAAATTTCCGCTAT 59.623 43.478 2.37 0.00 37.92 2.97
3786 7453 4.142469 CCCGTCAGAAAAATTTCCGCTATT 60.142 41.667 2.37 0.00 37.92 1.73
3787 7454 5.399013 CCGTCAGAAAAATTTCCGCTATTT 58.601 37.500 2.37 0.00 37.92 1.40
3788 7455 5.286082 CCGTCAGAAAAATTTCCGCTATTTG 59.714 40.000 2.37 0.00 37.92 2.32
3789 7456 5.220024 CGTCAGAAAAATTTCCGCTATTTGC 60.220 40.000 2.37 0.00 37.92 3.68
3790 7457 5.062183 GTCAGAAAAATTTCCGCTATTTGCC 59.938 40.000 2.37 0.00 37.92 4.52
3791 7458 4.031652 CAGAAAAATTTCCGCTATTTGCCG 59.968 41.667 2.37 0.00 37.92 5.69
3792 7459 1.921243 AAATTTCCGCTATTTGCCGC 58.079 45.000 0.00 0.00 38.78 6.53
3798 7465 3.907893 GCTATTTGCCGCGATTGC 58.092 55.556 8.23 2.45 35.15 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 4.634004 TGTTCTTGACCATATGTTTAGCCG 59.366 41.667 1.24 0.00 0.00 5.52
88 89 9.803507 ATCATATTGATGTTCTTGACCATATGT 57.196 29.630 1.24 0.00 35.43 2.29
142 143 6.655078 AGAAACTTGAACCGTAAGTACCTA 57.345 37.500 0.00 0.00 37.39 3.08
212 213 2.315901 GCATTTTCAGGGTTCGTTTCG 58.684 47.619 0.00 0.00 0.00 3.46
267 269 8.740123 TTGACCTTCAAAACATTTCTACACTA 57.260 30.769 0.00 0.00 32.71 2.74
333 335 4.936891 ACAAGCATGGTTTTCAAAGAGAC 58.063 39.130 7.57 0.00 0.00 3.36
340 342 5.076182 TCATAGGAACAAGCATGGTTTTCA 58.924 37.500 22.31 11.52 0.00 2.69
378 380 5.941733 CACAATTGTGCTGTAAGATGCTTA 58.058 37.500 24.69 0.00 39.39 3.09
411 413 6.746822 TCAATATGTTGTCGCTAAAATTGCAG 59.253 34.615 1.86 0.00 36.69 4.41
412 414 6.616017 TCAATATGTTGTCGCTAAAATTGCA 58.384 32.000 1.86 0.00 36.69 4.08
473 475 7.591795 GGCCGTATCATATATCTTTATGACTCG 59.408 40.741 0.00 5.24 40.44 4.18
573 575 1.265905 AGGGCGCTCGTTTACTTTTTG 59.734 47.619 7.64 0.00 0.00 2.44
669 671 4.909088 TCTACCACTACTTCCCCTCAAAAA 59.091 41.667 0.00 0.00 0.00 1.94
670 672 4.495565 TCTACCACTACTTCCCCTCAAAA 58.504 43.478 0.00 0.00 0.00 2.44
671 673 4.136341 TCTACCACTACTTCCCCTCAAA 57.864 45.455 0.00 0.00 0.00 2.69
672 674 3.839323 TCTACCACTACTTCCCCTCAA 57.161 47.619 0.00 0.00 0.00 3.02
675 677 4.224762 GCTTATCTACCACTACTTCCCCT 58.775 47.826 0.00 0.00 0.00 4.79
676 678 3.005578 CGCTTATCTACCACTACTTCCCC 59.994 52.174 0.00 0.00 0.00 4.81
677 679 3.887716 TCGCTTATCTACCACTACTTCCC 59.112 47.826 0.00 0.00 0.00 3.97
678 680 5.511234 TTCGCTTATCTACCACTACTTCC 57.489 43.478 0.00 0.00 0.00 3.46
679 681 6.562518 ACTTTCGCTTATCTACCACTACTTC 58.437 40.000 0.00 0.00 0.00 3.01
680 682 6.527057 ACTTTCGCTTATCTACCACTACTT 57.473 37.500 0.00 0.00 0.00 2.24
681 683 6.527057 AACTTTCGCTTATCTACCACTACT 57.473 37.500 0.00 0.00 0.00 2.57
682 684 7.253422 TGTAACTTTCGCTTATCTACCACTAC 58.747 38.462 0.00 0.00 0.00 2.73
683 685 7.395190 TGTAACTTTCGCTTATCTACCACTA 57.605 36.000 0.00 0.00 0.00 2.74
685 687 6.455246 GCTTGTAACTTTCGCTTATCTACCAC 60.455 42.308 0.00 0.00 0.00 4.16
687 689 5.276254 CGCTTGTAACTTTCGCTTATCTACC 60.276 44.000 0.00 0.00 0.00 3.18
706 2240 3.792401 TGACTATAATGTGGGTCGCTTG 58.208 45.455 0.00 0.00 0.00 4.01
713 2247 4.310769 GCTAGCACTGACTATAATGTGGG 58.689 47.826 10.63 0.00 0.00 4.61
717 2251 4.480541 CTCGGCTAGCACTGACTATAATG 58.519 47.826 18.24 0.00 0.00 1.90
731 2265 3.007182 AGAGTACTAGGTAGCTCGGCTAG 59.993 52.174 0.00 0.00 42.11 3.42
791 2336 7.897864 AGACTTATATTTAGGAACGGATGGAG 58.102 38.462 0.00 0.00 0.00 3.86
792 2337 7.850935 AGACTTATATTTAGGAACGGATGGA 57.149 36.000 0.00 0.00 0.00 3.41
793 2338 8.904099 AAAGACTTATATTTAGGAACGGATGG 57.096 34.615 0.00 0.00 0.00 3.51
823 2368 9.273016 CCGTATATGGTAGTTCATTTGAAATCT 57.727 33.333 2.46 0.00 35.58 2.40
824 2369 9.268268 TCCGTATATGGTAGTTCATTTGAAATC 57.732 33.333 10.85 0.00 35.58 2.17
825 2370 9.793259 ATCCGTATATGGTAGTTCATTTGAAAT 57.207 29.630 10.85 0.00 35.58 2.17
826 2371 9.051679 CATCCGTATATGGTAGTTCATTTGAAA 57.948 33.333 10.85 0.00 35.58 2.69
827 2372 8.208224 ACATCCGTATATGGTAGTTCATTTGAA 58.792 33.333 10.85 0.00 0.00 2.69
828 2373 7.732025 ACATCCGTATATGGTAGTTCATTTGA 58.268 34.615 10.85 0.00 0.00 2.69
829 2374 7.962964 ACATCCGTATATGGTAGTTCATTTG 57.037 36.000 10.85 0.34 0.00 2.32
867 2412 9.453572 AGCAAAATGAGTGAATCTACAATCTAA 57.546 29.630 0.00 0.00 36.14 2.10
868 2413 9.102757 GAGCAAAATGAGTGAATCTACAATCTA 57.897 33.333 0.00 0.00 36.14 1.98
869 2414 7.066766 GGAGCAAAATGAGTGAATCTACAATCT 59.933 37.037 0.00 0.00 36.14 2.40
870 2415 7.192232 GGAGCAAAATGAGTGAATCTACAATC 58.808 38.462 0.00 0.00 35.78 2.67
871 2416 6.183360 CGGAGCAAAATGAGTGAATCTACAAT 60.183 38.462 0.00 0.00 0.00 2.71
872 2417 5.122239 CGGAGCAAAATGAGTGAATCTACAA 59.878 40.000 0.00 0.00 0.00 2.41
873 2418 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
874 2419 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
875 2420 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
876 2421 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
877 2422 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
878 2423 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
879 2424 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
880 2425 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
881 2426 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
882 2427 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
883 2428 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
884 2429 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
885 2430 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
886 2431 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
887 2432 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
888 2433 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
889 2434 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
890 2435 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
891 2436 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
892 2437 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
893 2438 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
894 2439 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
895 2440 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
896 2441 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
898 2443 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
899 2444 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
900 2445 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
901 2446 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
902 2447 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
903 2448 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
904 2449 7.657761 GGTCTTTCTAGAGATTTCAACAAGTGA 59.342 37.037 0.00 0.00 0.00 3.41
905 2450 7.659390 AGGTCTTTCTAGAGATTTCAACAAGTG 59.341 37.037 0.00 0.00 0.00 3.16
906 2451 7.740805 AGGTCTTTCTAGAGATTTCAACAAGT 58.259 34.615 0.00 0.00 0.00 3.16
907 2452 9.883142 ATAGGTCTTTCTAGAGATTTCAACAAG 57.117 33.333 0.00 0.00 0.00 3.16
932 2477 7.817962 GCATGTACTACATCCGTTCCTAAATAT 59.182 37.037 0.00 0.00 36.53 1.28
933 2478 7.149973 GCATGTACTACATCCGTTCCTAAATA 58.850 38.462 0.00 0.00 36.53 1.40
934 2479 5.989777 GCATGTACTACATCCGTTCCTAAAT 59.010 40.000 0.00 0.00 36.53 1.40
935 2480 5.105269 TGCATGTACTACATCCGTTCCTAAA 60.105 40.000 0.00 0.00 36.53 1.85
936 2481 4.403113 TGCATGTACTACATCCGTTCCTAA 59.597 41.667 0.00 0.00 36.53 2.69
937 2482 3.955551 TGCATGTACTACATCCGTTCCTA 59.044 43.478 0.00 0.00 36.53 2.94
938 2483 2.764010 TGCATGTACTACATCCGTTCCT 59.236 45.455 0.00 0.00 36.53 3.36
939 2484 3.173668 TGCATGTACTACATCCGTTCC 57.826 47.619 0.00 0.00 36.53 3.62
940 2485 4.368315 TCATGCATGTACTACATCCGTTC 58.632 43.478 25.43 0.00 36.53 3.95
941 2486 4.400529 TCATGCATGTACTACATCCGTT 57.599 40.909 25.43 0.00 36.53 4.44
942 2487 4.119862 GTTCATGCATGTACTACATCCGT 58.880 43.478 25.43 0.00 36.53 4.69
943 2488 4.119136 TGTTCATGCATGTACTACATCCG 58.881 43.478 29.25 2.40 36.53 4.18
944 2489 5.118990 ACTGTTCATGCATGTACTACATCC 58.881 41.667 29.25 8.88 36.53 3.51
945 2490 5.051441 CGACTGTTCATGCATGTACTACATC 60.051 44.000 29.25 20.79 36.53 3.06
946 2491 4.805719 CGACTGTTCATGCATGTACTACAT 59.194 41.667 29.25 16.18 39.91 2.29
947 2492 4.082463 TCGACTGTTCATGCATGTACTACA 60.082 41.667 29.25 23.24 0.00 2.74
948 2493 4.421058 TCGACTGTTCATGCATGTACTAC 58.579 43.478 29.25 20.79 0.00 2.73
949 2494 4.712122 TCGACTGTTCATGCATGTACTA 57.288 40.909 29.25 18.10 0.00 1.82
950 2495 3.592898 TCGACTGTTCATGCATGTACT 57.407 42.857 29.25 15.65 0.00 2.73
951 2496 3.431912 TGTTCGACTGTTCATGCATGTAC 59.568 43.478 24.78 24.78 0.00 2.90
952 2497 3.658709 TGTTCGACTGTTCATGCATGTA 58.341 40.909 25.43 14.44 0.00 2.29
953 2498 2.493035 TGTTCGACTGTTCATGCATGT 58.507 42.857 25.43 6.51 0.00 3.21
954 2499 3.752412 ATGTTCGACTGTTCATGCATG 57.248 42.857 21.07 21.07 0.00 4.06
966 2511 1.387756 GCTTGCATGCAAATGTTCGAC 59.612 47.619 31.37 12.51 35.33 4.20
984 2529 1.665916 CATGCCGCTACGCTATGCT 60.666 57.895 0.00 0.00 0.00 3.79
1161 2715 0.750249 TCTCGTGCAAGGTCTTGTGA 59.250 50.000 11.71 7.21 42.31 3.58
1165 2719 0.674895 GCCATCTCGTGCAAGGTCTT 60.675 55.000 0.00 0.00 0.00 3.01
1183 2737 3.428282 CGGGCCGTACAACCTTGC 61.428 66.667 19.97 0.00 0.00 4.01
1260 2814 2.035442 GGTGCGGAGGAACAGCTTC 61.035 63.158 0.00 0.00 40.20 3.86
1265 2819 4.308458 CGTGGGTGCGGAGGAACA 62.308 66.667 0.00 0.00 37.19 3.18
1401 2955 1.289066 CGCGGAGAAGAGGTTCACA 59.711 57.895 0.00 0.00 34.82 3.58
1611 3167 3.804873 GCACGATCTCATTAAACTCCTCC 59.195 47.826 0.00 0.00 0.00 4.30
1665 3221 3.998672 GGCACGAAGTCCCCGACA 61.999 66.667 0.00 0.00 41.61 4.35
1807 3363 3.148279 CTTACCGCCCTCCTCGCT 61.148 66.667 0.00 0.00 0.00 4.93
1908 3470 1.831736 ACCAGTATAAGCGCCTTGACT 59.168 47.619 2.29 0.00 0.00 3.41
1991 5038 8.601243 ATTTAGCGATGCAATTATTAATACGC 57.399 30.769 13.46 13.46 43.00 4.42
2067 5176 1.377987 AAAATAGCGCCGGCCTCAA 60.378 52.632 23.46 4.08 41.24 3.02
2097 5206 2.680339 GAGCTACCATCAAGGAAACTGC 59.320 50.000 0.00 0.00 42.68 4.40
2098 5207 3.942829 TGAGCTACCATCAAGGAAACTG 58.057 45.455 0.00 0.00 42.68 3.16
2100 5209 4.072131 TGTTGAGCTACCATCAAGGAAAC 58.928 43.478 0.00 0.00 41.22 2.78
2132 5280 5.071250 AGTGCATTAGACGAATGGGGTTATA 59.929 40.000 9.90 0.00 44.53 0.98
2139 5287 2.286294 GCAGAGTGCATTAGACGAATGG 59.714 50.000 9.90 0.00 44.53 3.16
2302 5905 1.674651 CAGGTCCGACTCCGAGACA 60.675 63.158 1.33 0.00 37.56 3.41
2398 6001 1.296715 GCACTCCTCGGTGGTCATT 59.703 57.895 0.00 0.00 37.65 2.57
2402 6005 3.374402 CTCGCACTCCTCGGTGGT 61.374 66.667 0.00 0.00 37.65 4.16
2479 6116 4.082523 CACAGGGCCGGATCACGT 62.083 66.667 11.67 0.00 42.24 4.49
2500 6137 1.980052 CCTAAACTCCAGCGGGTCA 59.020 57.895 1.81 0.00 34.93 4.02
2779 6437 1.208706 TTTGGTATGCCGATGGGAGA 58.791 50.000 0.00 0.00 37.67 3.71
2992 6658 1.559831 TTGTATGAGCGTCTGCATCG 58.440 50.000 7.00 7.00 46.23 3.84
3014 6680 6.753913 ATTCATAGGGATGAGTGTATGTGT 57.246 37.500 0.00 0.00 43.03 3.72
3042 6708 1.014564 GTGCCGGTGCTCAGTCTTAC 61.015 60.000 1.90 0.00 38.71 2.34
3043 6709 1.292223 GTGCCGGTGCTCAGTCTTA 59.708 57.895 1.90 0.00 38.71 2.10
3129 6795 9.303537 GGTCATTCTCACTAAGTTCTAATGTAC 57.696 37.037 0.00 0.00 0.00 2.90
3170 6836 1.304254 CGTGTGTGATGTTTGGGTCA 58.696 50.000 0.00 0.00 0.00 4.02
3219 6885 0.390492 CATGAGACTGGCCGATGCTA 59.610 55.000 0.00 0.00 37.74 3.49
3274 6940 7.374272 TGTGCCGATTGAATTTAAGATGAAAA 58.626 30.769 0.00 0.00 0.00 2.29
3361 7027 4.283467 GTGGAATTTCCTAGCCTGGTTTTT 59.717 41.667 16.25 0.00 37.46 1.94
3558 7225 5.063180 TGATGTGATTGTGGCAGAAAATC 57.937 39.130 0.00 5.91 0.00 2.17
3612 7279 5.856126 TTCGCGGGCTATTTTAATCTATG 57.144 39.130 6.13 0.00 0.00 2.23
3613 7280 7.201617 GCTATTTCGCGGGCTATTTTAATCTAT 60.202 37.037 6.13 0.00 0.00 1.98
3614 7281 6.091713 GCTATTTCGCGGGCTATTTTAATCTA 59.908 38.462 6.13 0.00 0.00 1.98
3615 7282 5.106673 GCTATTTCGCGGGCTATTTTAATCT 60.107 40.000 6.13 0.00 0.00 2.40
3616 7283 5.086727 GCTATTTCGCGGGCTATTTTAATC 58.913 41.667 6.13 0.00 0.00 1.75
3617 7284 4.082949 GGCTATTTCGCGGGCTATTTTAAT 60.083 41.667 6.13 0.00 0.00 1.40
3618 7285 3.251487 GGCTATTTCGCGGGCTATTTTAA 59.749 43.478 6.13 0.00 0.00 1.52
3619 7286 2.809696 GGCTATTTCGCGGGCTATTTTA 59.190 45.455 6.13 0.00 0.00 1.52
3620 7287 1.607148 GGCTATTTCGCGGGCTATTTT 59.393 47.619 6.13 0.00 0.00 1.82
3621 7288 1.235724 GGCTATTTCGCGGGCTATTT 58.764 50.000 6.13 0.00 0.00 1.40
3622 7289 0.949105 CGGCTATTTCGCGGGCTATT 60.949 55.000 6.13 0.00 0.00 1.73
3623 7290 1.374252 CGGCTATTTCGCGGGCTAT 60.374 57.895 6.13 0.00 0.00 2.97
3624 7291 2.028484 CGGCTATTTCGCGGGCTA 59.972 61.111 6.13 0.00 0.00 3.93
3631 7298 0.710567 CAGCTATCGCGGCTATTTCG 59.289 55.000 6.13 0.00 42.32 3.46
3652 7319 1.003959 GCTCCTGGGCAGCTATAGC 60.004 63.158 17.33 17.33 42.49 2.97
3653 7320 0.835543 AGGCTCCTGGGCAGCTATAG 60.836 60.000 7.26 0.00 43.56 1.31
3654 7321 0.400525 AAGGCTCCTGGGCAGCTATA 60.401 55.000 7.26 0.00 43.56 1.31
3655 7322 1.695597 AAGGCTCCTGGGCAGCTAT 60.696 57.895 7.26 0.00 43.56 2.97
3656 7323 2.285668 AAGGCTCCTGGGCAGCTA 60.286 61.111 7.26 0.00 43.56 3.32
3657 7324 4.044439 CAAGGCTCCTGGGCAGCT 62.044 66.667 7.26 0.00 43.56 4.24
3663 7330 3.785859 TAGCGGCAAGGCTCCTGG 61.786 66.667 1.45 0.00 43.54 4.45
3664 7331 2.512515 GTAGCGGCAAGGCTCCTG 60.513 66.667 1.45 0.00 43.54 3.86
3665 7332 4.148825 CGTAGCGGCAAGGCTCCT 62.149 66.667 1.45 0.00 43.54 3.69
3677 7344 2.602322 GCAGCAGCCATAGCGTAGC 61.602 63.158 0.00 0.00 46.32 3.58
3678 7345 3.635204 GCAGCAGCCATAGCGTAG 58.365 61.111 0.00 0.00 46.67 3.51
3688 7355 4.543084 GGATTTCGCGGCAGCAGC 62.543 66.667 10.08 7.57 45.49 5.25
3689 7356 2.817423 GAGGATTTCGCGGCAGCAG 61.817 63.158 10.08 1.86 45.49 4.24
3690 7357 2.819595 GAGGATTTCGCGGCAGCA 60.820 61.111 10.08 0.00 45.49 4.41
3691 7358 3.577313 GGAGGATTTCGCGGCAGC 61.577 66.667 6.13 0.00 40.74 5.25
3692 7359 3.264897 CGGAGGATTTCGCGGCAG 61.265 66.667 6.13 0.00 0.00 4.85
3698 7365 1.090052 GGGAGTTGCGGAGGATTTCG 61.090 60.000 0.00 0.00 0.00 3.46
3699 7366 0.253327 AGGGAGTTGCGGAGGATTTC 59.747 55.000 0.00 0.00 0.00 2.17
3700 7367 0.035056 CAGGGAGTTGCGGAGGATTT 60.035 55.000 0.00 0.00 0.00 2.17
3701 7368 1.201429 ACAGGGAGTTGCGGAGGATT 61.201 55.000 0.00 0.00 0.00 3.01
3702 7369 0.325296 TACAGGGAGTTGCGGAGGAT 60.325 55.000 0.00 0.00 0.00 3.24
3703 7370 0.543410 TTACAGGGAGTTGCGGAGGA 60.543 55.000 0.00 0.00 0.00 3.71
3704 7371 0.323629 TTTACAGGGAGTTGCGGAGG 59.676 55.000 0.00 0.00 0.00 4.30
3705 7372 2.009774 CATTTACAGGGAGTTGCGGAG 58.990 52.381 0.00 0.00 0.00 4.63
3706 7373 1.339631 CCATTTACAGGGAGTTGCGGA 60.340 52.381 0.00 0.00 0.00 5.54
3707 7374 1.094785 CCATTTACAGGGAGTTGCGG 58.905 55.000 0.00 0.00 0.00 5.69
3708 7375 1.821216 ACCATTTACAGGGAGTTGCG 58.179 50.000 0.00 0.00 0.00 4.85
3709 7376 3.153919 TGAACCATTTACAGGGAGTTGC 58.846 45.455 0.00 0.00 0.00 4.17
3710 7377 3.191371 GCTGAACCATTTACAGGGAGTTG 59.809 47.826 0.00 0.00 33.00 3.16
3711 7378 3.181434 TGCTGAACCATTTACAGGGAGTT 60.181 43.478 0.00 0.00 33.00 3.01
3712 7379 2.375174 TGCTGAACCATTTACAGGGAGT 59.625 45.455 0.00 0.00 33.00 3.85
3713 7380 3.071874 TGCTGAACCATTTACAGGGAG 57.928 47.619 0.00 0.00 33.00 4.30
3714 7381 3.517296 TTGCTGAACCATTTACAGGGA 57.483 42.857 0.00 0.00 33.00 4.20
3715 7382 3.763360 TCATTGCTGAACCATTTACAGGG 59.237 43.478 0.00 0.00 33.00 4.45
3716 7383 4.676196 GCTCATTGCTGAACCATTTACAGG 60.676 45.833 0.00 0.00 38.95 4.00
3717 7384 4.082625 TGCTCATTGCTGAACCATTTACAG 60.083 41.667 0.00 0.00 43.37 2.74
3718 7385 3.825585 TGCTCATTGCTGAACCATTTACA 59.174 39.130 0.00 0.00 43.37 2.41
3719 7386 4.439305 TGCTCATTGCTGAACCATTTAC 57.561 40.909 0.00 0.00 43.37 2.01
3720 7387 5.465532 TTTGCTCATTGCTGAACCATTTA 57.534 34.783 0.00 0.00 43.37 1.40
3721 7388 4.339872 TTTGCTCATTGCTGAACCATTT 57.660 36.364 0.00 0.00 43.37 2.32
3722 7389 4.060205 GTTTTGCTCATTGCTGAACCATT 58.940 39.130 0.00 0.00 43.37 3.16
3723 7390 3.555586 GGTTTTGCTCATTGCTGAACCAT 60.556 43.478 15.32 0.00 46.50 3.55
3724 7391 2.224018 GGTTTTGCTCATTGCTGAACCA 60.224 45.455 15.32 0.00 46.50 3.67
3725 7392 2.407090 GGTTTTGCTCATTGCTGAACC 58.593 47.619 8.86 8.86 43.87 3.62
3726 7393 2.036346 AGGGTTTTGCTCATTGCTGAAC 59.964 45.455 0.00 0.00 43.37 3.18
3727 7394 2.297033 GAGGGTTTTGCTCATTGCTGAA 59.703 45.455 0.00 0.00 43.37 3.02
3728 7395 1.888512 GAGGGTTTTGCTCATTGCTGA 59.111 47.619 0.00 0.00 43.37 4.26
3729 7396 1.067354 GGAGGGTTTTGCTCATTGCTG 60.067 52.381 0.00 0.00 43.37 4.41
3730 7397 1.260544 GGAGGGTTTTGCTCATTGCT 58.739 50.000 0.00 0.00 43.37 3.91
3731 7398 0.109132 CGGAGGGTTTTGCTCATTGC 60.109 55.000 0.00 0.00 43.25 3.56
3746 7413 1.000283 CGGGAGAGATGATTTCCGGAG 60.000 57.143 3.34 0.00 34.32 4.63
3747 7414 1.040646 CGGGAGAGATGATTTCCGGA 58.959 55.000 0.00 0.00 34.32 5.14
3748 7415 0.753262 ACGGGAGAGATGATTTCCGG 59.247 55.000 0.00 0.00 41.49 5.14
3749 7416 1.409064 TGACGGGAGAGATGATTTCCG 59.591 52.381 0.00 0.00 42.69 4.30
3750 7417 2.695666 TCTGACGGGAGAGATGATTTCC 59.304 50.000 0.00 0.00 0.00 3.13
3751 7418 4.392921 TTCTGACGGGAGAGATGATTTC 57.607 45.455 0.00 0.00 0.00 2.17
3752 7419 4.826274 TTTCTGACGGGAGAGATGATTT 57.174 40.909 0.00 0.00 0.00 2.17
3753 7420 4.826274 TTTTCTGACGGGAGAGATGATT 57.174 40.909 0.00 0.00 0.00 2.57
3754 7421 4.826274 TTTTTCTGACGGGAGAGATGAT 57.174 40.909 0.00 0.00 0.00 2.45
3755 7422 4.826274 ATTTTTCTGACGGGAGAGATGA 57.174 40.909 0.00 0.00 0.00 2.92
3756 7423 5.163713 GGAAATTTTTCTGACGGGAGAGATG 60.164 44.000 3.28 0.00 37.35 2.90
3757 7424 4.944317 GGAAATTTTTCTGACGGGAGAGAT 59.056 41.667 3.28 0.00 37.35 2.75
3758 7425 4.324267 GGAAATTTTTCTGACGGGAGAGA 58.676 43.478 3.28 0.00 37.35 3.10
3759 7426 3.125316 CGGAAATTTTTCTGACGGGAGAG 59.875 47.826 6.06 0.00 44.44 3.20
3760 7427 3.071479 CGGAAATTTTTCTGACGGGAGA 58.929 45.455 6.06 0.00 44.44 3.71
3761 7428 2.414161 GCGGAAATTTTTCTGACGGGAG 60.414 50.000 14.54 0.00 44.44 4.30
3762 7429 1.538075 GCGGAAATTTTTCTGACGGGA 59.462 47.619 14.54 0.00 44.44 5.14
3763 7430 1.539827 AGCGGAAATTTTTCTGACGGG 59.460 47.619 14.54 0.00 44.44 5.28
3764 7431 2.989422 AGCGGAAATTTTTCTGACGG 57.011 45.000 14.54 0.00 44.44 4.79
3765 7432 5.220024 GCAAATAGCGGAAATTTTTCTGACG 60.220 40.000 14.54 6.07 44.44 4.35
3766 7433 5.062183 GGCAAATAGCGGAAATTTTTCTGAC 59.938 40.000 14.54 7.00 44.44 3.51
3767 7434 5.167845 GGCAAATAGCGGAAATTTTTCTGA 58.832 37.500 14.54 0.00 44.44 3.27
3781 7448 3.907893 GCAATCGCGGCAAATAGC 58.092 55.556 6.13 0.00 44.65 2.97


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

AutoCloner maintained by Alex Coulton.