Multiple sequence alignment - TraesCS4A01G052200

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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 TraesCS4A01G052200 chr4A 100.000 6135 0 0 1 6135 43236846 43230712 0.000000e+00 11330.0
1 TraesCS4A01G052200 chr4A 94.897 823 37 5 5316 6135 596799414 596798594 0.000000e+00 1282.0
2 TraesCS4A01G052200 chr4A 94.897 823 37 5 5316 6135 596807325 596806505 0.000000e+00 1282.0
3 TraesCS4A01G052200 chr4A 83.687 1367 203 15 3781 5137 593356264 593354908 0.000000e+00 1271.0
4 TraesCS4A01G052200 chr4A 79.544 1359 246 21 3784 5129 550482508 550481169 0.000000e+00 941.0
5 TraesCS4A01G052200 chr4A 84.229 558 88 0 3120 3677 593356830 593356273 1.500000e-150 544.0
6 TraesCS4A01G052200 chr4A 85.161 465 66 2 3121 3582 550483260 550482796 2.000000e-129 473.0
7 TraesCS4A01G052200 chr4A 88.660 291 30 3 1136 1425 593357385 593357097 9.780000e-93 351.0
8 TraesCS4A01G052200 chr4A 83.228 316 47 6 1119 1430 550487281 550486968 1.010000e-72 285.0
9 TraesCS4A01G052200 chr4D 93.768 2744 103 28 2604 5317 420941680 420944385 0.000000e+00 4058.0
10 TraesCS4A01G052200 chr4D 89.858 2120 90 47 3 2051 420938973 420941038 0.000000e+00 2608.0
11 TraesCS4A01G052200 chr4D 84.314 1377 193 16 3771 5136 10250855 10252219 0.000000e+00 1325.0
12 TraesCS4A01G052200 chr4D 80.427 1359 234 23 3784 5129 47535711 47534372 0.000000e+00 1007.0
13 TraesCS4A01G052200 chr4D 85.099 557 81 2 3122 3677 10250300 10250855 8.920000e-158 568.0
14 TraesCS4A01G052200 chr4D 88.989 445 26 13 2054 2479 420941086 420941526 4.210000e-146 529.0
15 TraesCS4A01G052200 chr4D 85.591 465 64 2 3121 3582 47536520 47536056 9.250000e-133 484.0
16 TraesCS4A01G052200 chr4D 89.062 256 26 2 1162 1416 10249590 10249844 3.570000e-82 316.0
17 TraesCS4A01G052200 chr4B 93.699 2714 97 29 2629 5317 518097017 518099681 0.000000e+00 3997.0
18 TraesCS4A01G052200 chr4B 89.622 1850 86 34 5 1781 518094259 518096075 0.000000e+00 2255.0
19 TraesCS4A01G052200 chr4B 84.103 1365 195 16 3775 5128 19736659 19738012 0.000000e+00 1299.0
20 TraesCS4A01G052200 chr4B 79.778 1350 241 23 3769 5105 69378921 69380251 0.000000e+00 952.0
21 TraesCS4A01G052200 chr4B 85.252 556 82 0 3122 3677 19736101 19736656 1.920000e-159 573.0
22 TraesCS4A01G052200 chr4B 85.806 465 63 2 3121 3582 69378047 69378511 1.990000e-134 490.0
23 TraesCS4A01G052200 chr4B 88.144 388 32 7 2055 2432 518096389 518096772 3.370000e-122 449.0
24 TraesCS4A01G052200 chr4B 81.658 398 58 13 1025 1416 19735508 19735896 3.570000e-82 316.0
25 TraesCS4A01G052200 chr4B 84.768 302 42 4 1115 1414 69375913 69376212 3.590000e-77 300.0
26 TraesCS4A01G052200 chr2A 96.078 816 32 0 5320 6135 533857640 533858455 0.000000e+00 1330.0
27 TraesCS4A01G052200 chr3A 95.844 818 32 2 5319 6135 250356168 250355352 0.000000e+00 1321.0
28 TraesCS4A01G052200 chr3A 95.349 817 35 3 5320 6135 522452437 522453251 0.000000e+00 1295.0
29 TraesCS4A01G052200 chr3A 95.238 819 36 3 5316 6133 522460300 522461116 0.000000e+00 1293.0
30 TraesCS4A01G052200 chr1A 95.588 816 33 3 5320 6135 153689977 153690789 0.000000e+00 1304.0
31 TraesCS4A01G052200 chr1A 95.221 816 37 2 5320 6135 229884554 229885367 0.000000e+00 1290.0
32 TraesCS4A01G052200 chr7A 95.122 820 38 2 5316 6135 257342240 257343057 0.000000e+00 1291.0
33 TraesCS4A01G052200 chr6D 76.214 597 116 21 4540 5126 389370151 389370731 6.010000e-75 292.0
34 TraesCS4A01G052200 chr6D 92.683 41 1 2 2455 2493 290327938 290327898 2.390000e-04 58.4
35 TraesCS4A01G052200 chr3B 83.505 194 24 3 4004 4190 104157461 104157653 2.270000e-39 174.0
36 TraesCS4A01G052200 chr2B 84.884 172 19 5 3135 3304 748723219 748723385 3.800000e-37 167.0
37 TraesCS4A01G052200 chr2B 96.774 31 1 0 2461 2491 45045383 45045413 1.100000e-02 52.8
38 TraesCS4A01G052200 chr3D 83.333 174 29 0 3408 3581 578422038 578421865 1.770000e-35 161.0
39 TraesCS4A01G052200 chr6B 92.308 39 1 2 2455 2491 450913205 450913167 3.000000e-03 54.7


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 TraesCS4A01G052200 chr4A 43230712 43236846 6134 True 11330.000000 11330 100.000000 1 6135 1 chr4A.!!$R1 6134
1 TraesCS4A01G052200 chr4A 596798594 596799414 820 True 1282.000000 1282 94.897000 5316 6135 1 chr4A.!!$R2 819
2 TraesCS4A01G052200 chr4A 596806505 596807325 820 True 1282.000000 1282 94.897000 5316 6135 1 chr4A.!!$R3 819
3 TraesCS4A01G052200 chr4A 593354908 593357385 2477 True 722.000000 1271 85.525333 1136 5137 3 chr4A.!!$R5 4001
4 TraesCS4A01G052200 chr4A 550481169 550487281 6112 True 566.333333 941 82.644333 1119 5129 3 chr4A.!!$R4 4010
5 TraesCS4A01G052200 chr4D 420938973 420944385 5412 False 2398.333333 4058 90.871667 3 5317 3 chr4D.!!$F2 5314
6 TraesCS4A01G052200 chr4D 47534372 47536520 2148 True 745.500000 1007 83.009000 3121 5129 2 chr4D.!!$R1 2008
7 TraesCS4A01G052200 chr4D 10249590 10252219 2629 False 736.333333 1325 86.158333 1162 5136 3 chr4D.!!$F1 3974
8 TraesCS4A01G052200 chr4B 518094259 518099681 5422 False 2233.666667 3997 90.488333 5 5317 3 chr4B.!!$F3 5312
9 TraesCS4A01G052200 chr4B 19735508 19738012 2504 False 729.333333 1299 83.671000 1025 5128 3 chr4B.!!$F1 4103
10 TraesCS4A01G052200 chr4B 69375913 69380251 4338 False 580.666667 952 83.450667 1115 5105 3 chr4B.!!$F2 3990
11 TraesCS4A01G052200 chr2A 533857640 533858455 815 False 1330.000000 1330 96.078000 5320 6135 1 chr2A.!!$F1 815
12 TraesCS4A01G052200 chr3A 250355352 250356168 816 True 1321.000000 1321 95.844000 5319 6135 1 chr3A.!!$R1 816
13 TraesCS4A01G052200 chr3A 522452437 522453251 814 False 1295.000000 1295 95.349000 5320 6135 1 chr3A.!!$F1 815
14 TraesCS4A01G052200 chr3A 522460300 522461116 816 False 1293.000000 1293 95.238000 5316 6133 1 chr3A.!!$F2 817
15 TraesCS4A01G052200 chr1A 153689977 153690789 812 False 1304.000000 1304 95.588000 5320 6135 1 chr1A.!!$F1 815
16 TraesCS4A01G052200 chr1A 229884554 229885367 813 False 1290.000000 1290 95.221000 5320 6135 1 chr1A.!!$F2 815
17 TraesCS4A01G052200 chr7A 257342240 257343057 817 False 1291.000000 1291 95.122000 5316 6135 1 chr7A.!!$F1 819
18 TraesCS4A01G052200 chr6D 389370151 389370731 580 False 292.000000 292 76.214000 4540 5126 1 chr6D.!!$F1 586

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
93 109 0.108585 AACGTGAAGCCAGACACCAT 59.891 50.0 0.00 0.0 34.05 3.55 F
315 335 0.248215 CCGCTCAAAATCGATGGCAC 60.248 55.0 0.00 0.0 0.00 5.01 F
1785 1969 0.094730 GATCGGTTCGGACGCAAAAG 59.905 55.0 0.00 0.0 0.00 2.27 F
2105 5423 0.815734 TACTAGCTCCACTTCCGTGC 59.184 55.0 0.00 0.0 39.86 5.34 F
3022 6511 0.176680 CCGCAAGCATCTGTCCTACT 59.823 55.0 0.00 0.0 0.00 2.57 F
4274 8125 0.514255 CTCGTCGGACTACGTGTTCA 59.486 55.0 6.57 0.0 43.31 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1499 1676 1.153353 TCCAAAACGCTGGATTCGAC 58.847 50.000 0.00 0.00 40.71 4.20 R
2245 5571 0.545646 TGTAGGCCTACATGCATGCA 59.454 50.000 36.63 25.04 40.77 3.96 R
2736 6224 1.067199 CGCCAATTGCTCACGCTTTC 61.067 55.000 0.00 0.00 38.05 2.62 R
3118 6610 1.514087 GTCCCGATCGCCTACACAA 59.486 57.895 10.32 0.00 0.00 3.33 R
4444 8295 0.608035 TTGCACCGATCTTGGGGTTC 60.608 55.000 0.00 0.00 33.77 3.62 R
5927 9815 0.028902 GAAGTGAACACGGTGTTGGC 59.971 55.000 29.46 20.24 41.28 4.52 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
49 50 1.527034 CACCACCAGATGAACACAGG 58.473 55.000 0.00 0.00 0.00 4.00
59 60 4.329545 AACACAGGCGCCATCGGT 62.330 61.111 31.54 18.01 35.95 4.69
93 109 0.108585 AACGTGAAGCCAGACACCAT 59.891 50.000 0.00 0.00 34.05 3.55
112 128 1.105167 TCACCGACGAGAACACAGGT 61.105 55.000 0.00 0.00 0.00 4.00
146 162 8.621532 ATGTCATTCTATGTAAACACAACTGT 57.378 30.769 0.00 0.00 0.00 3.55
246 266 6.778069 CCATCCTACAAGTCTATCTTCCACTA 59.222 42.308 0.00 0.00 33.63 2.74
315 335 0.248215 CCGCTCAAAATCGATGGCAC 60.248 55.000 0.00 0.00 0.00 5.01
360 380 1.149401 TGCCACACCGATCAAACCA 59.851 52.632 0.00 0.00 0.00 3.67
364 384 1.671054 ACACCGATCAAACCAGGCG 60.671 57.895 0.00 0.00 0.00 5.52
367 387 2.106683 CCGATCAAACCAGGCGGAC 61.107 63.158 0.00 0.00 44.43 4.79
397 418 5.105228 CGTTTATCTACTCAGGGGTGGTTAA 60.105 44.000 0.00 0.00 0.00 2.01
446 467 0.316196 GCAAAGCACGGACGATATGC 60.316 55.000 0.00 0.00 39.74 3.14
477 498 1.136141 GTTGCTGTCGTCTTGCATGAG 60.136 52.381 1.91 0.00 36.55 2.90
481 502 2.030213 GCTGTCGTCTTGCATGAGAATC 59.970 50.000 1.91 0.00 0.00 2.52
512 533 3.272334 GGCTAACGGCGCCTCATG 61.272 66.667 26.68 11.62 44.17 3.07
513 534 3.941836 GCTAACGGCGCCTCATGC 61.942 66.667 26.68 19.14 0.00 4.06
514 535 2.511373 CTAACGGCGCCTCATGCA 60.511 61.111 26.68 2.25 41.33 3.96
515 536 1.889105 CTAACGGCGCCTCATGCAT 60.889 57.895 26.68 0.00 41.33 3.96
516 537 2.109538 CTAACGGCGCCTCATGCATG 62.110 60.000 26.68 21.07 41.33 4.06
593 616 2.502510 CAACCGTACGTCCGTCCG 60.503 66.667 15.21 0.00 0.00 4.79
594 617 2.978010 AACCGTACGTCCGTCCGT 60.978 61.111 15.21 0.00 44.50 4.69
595 618 2.966309 AACCGTACGTCCGTCCGTC 61.966 63.158 15.21 0.00 42.00 4.79
596 619 4.166011 CCGTACGTCCGTCCGTCC 62.166 72.222 15.21 0.00 42.00 4.79
625 652 2.280628 CCCATCGTTCTTTACTGGAGC 58.719 52.381 0.00 0.00 0.00 4.70
656 683 1.133792 CCGACCAGGGGCTTTATTCAT 60.134 52.381 0.00 0.00 35.97 2.57
740 771 1.668419 GAGCCTACATTGAACGGCAT 58.332 50.000 14.55 4.09 44.85 4.40
741 772 1.331756 GAGCCTACATTGAACGGCATG 59.668 52.381 14.55 0.00 44.85 4.06
818 849 3.437049 GCCGAATCTTATTACCATCTGGC 59.563 47.826 0.00 0.00 39.32 4.85
842 873 2.363795 TCCGAATGGAGCCCGACT 60.364 61.111 0.00 0.00 40.17 4.18
961 998 1.169577 GAGCTTCTCTCACGTCCTCA 58.830 55.000 0.00 0.00 41.51 3.86
979 1016 1.193323 CACCTCCTGTCTGCTCTCAT 58.807 55.000 0.00 0.00 0.00 2.90
989 1026 2.027745 GTCTGCTCTCATCCTCCACAAA 60.028 50.000 0.00 0.00 0.00 2.83
990 1027 2.027745 TCTGCTCTCATCCTCCACAAAC 60.028 50.000 0.00 0.00 0.00 2.93
991 1028 1.699083 TGCTCTCATCCTCCACAAACA 59.301 47.619 0.00 0.00 0.00 2.83
992 1029 2.079925 GCTCTCATCCTCCACAAACAC 58.920 52.381 0.00 0.00 0.00 3.32
993 1030 2.289945 GCTCTCATCCTCCACAAACACT 60.290 50.000 0.00 0.00 0.00 3.55
995 1032 3.242867 TCTCATCCTCCACAAACACTCT 58.757 45.455 0.00 0.00 0.00 3.24
997 1034 2.972021 TCATCCTCCACAAACACTCTCA 59.028 45.455 0.00 0.00 0.00 3.27
998 1035 3.390967 TCATCCTCCACAAACACTCTCAA 59.609 43.478 0.00 0.00 0.00 3.02
999 1036 3.924114 TCCTCCACAAACACTCTCAAA 57.076 42.857 0.00 0.00 0.00 2.69
1003 1040 4.580167 CCTCCACAAACACTCTCAAAATGA 59.420 41.667 0.00 0.00 0.00 2.57
1546 1728 2.276493 CCAGTCGTCGAGCGTACG 60.276 66.667 11.84 11.84 42.13 3.67
1561 1743 3.299304 TACGTCGTGGTCGTGCTCG 62.299 63.158 8.47 0.81 41.62 5.03
1612 1794 3.127533 GGCCAGCAGTTTCGCGAT 61.128 61.111 10.88 0.00 36.85 4.58
1688 1870 0.885596 CGTTTGGTTAAGCCGGACCA 60.886 55.000 5.05 7.26 43.87 4.02
1691 1873 3.823369 TGGTTAAGCCGGACCAAAA 57.177 47.368 5.05 0.00 42.68 2.44
1692 1874 2.068834 TGGTTAAGCCGGACCAAAAA 57.931 45.000 5.05 0.00 42.68 1.94
1693 1875 1.682323 TGGTTAAGCCGGACCAAAAAC 59.318 47.619 5.05 0.00 42.68 2.43
1694 1876 1.682323 GGTTAAGCCGGACCAAAAACA 59.318 47.619 5.05 0.00 35.95 2.83
1695 1877 2.101082 GGTTAAGCCGGACCAAAAACAA 59.899 45.455 5.05 0.00 35.95 2.83
1696 1878 3.430513 GGTTAAGCCGGACCAAAAACAAA 60.431 43.478 5.05 0.00 35.95 2.83
1697 1879 4.182339 GTTAAGCCGGACCAAAAACAAAA 58.818 39.130 5.05 0.00 0.00 2.44
1698 1880 3.336138 AAGCCGGACCAAAAACAAAAA 57.664 38.095 5.05 0.00 0.00 1.94
1785 1969 0.094730 GATCGGTTCGGACGCAAAAG 59.905 55.000 0.00 0.00 0.00 2.27
1797 1981 4.287720 GGACGCAAAAGAAAACCAGTAAG 58.712 43.478 0.00 0.00 0.00 2.34
1831 2078 1.887242 CATGTGTATGGCCGGGTCG 60.887 63.158 2.18 0.00 0.00 4.79
1876 3752 8.992835 ATTAAAGTGAAAAGGTAGTACGTAGG 57.007 34.615 0.00 0.00 0.00 3.18
1878 3754 5.893897 AGTGAAAAGGTAGTACGTAGGAG 57.106 43.478 0.00 0.00 0.00 3.69
1880 3756 6.476378 AGTGAAAAGGTAGTACGTAGGAGTA 58.524 40.000 0.00 0.00 0.00 2.59
1881 3757 6.942576 AGTGAAAAGGTAGTACGTAGGAGTAA 59.057 38.462 0.00 0.00 0.00 2.24
1882 3758 7.613411 AGTGAAAAGGTAGTACGTAGGAGTAAT 59.387 37.037 0.00 0.00 0.00 1.89
2051 5286 9.554395 TGATTATATCTTGATTTCGCAAGGTAA 57.446 29.630 0.00 0.00 42.77 2.85
2058 5293 7.045416 TCTTGATTTCGCAAGGTAATTAGCTA 58.955 34.615 17.14 1.54 44.14 3.32
2094 5412 6.769512 TCCATCAATTAACCCATACTAGCTC 58.230 40.000 0.00 0.00 0.00 4.09
2104 5422 2.223829 CCATACTAGCTCCACTTCCGTG 60.224 54.545 0.00 0.00 40.89 4.94
2105 5423 0.815734 TACTAGCTCCACTTCCGTGC 59.184 55.000 0.00 0.00 39.86 5.34
2107 5425 1.103803 CTAGCTCCACTTCCGTGCTA 58.896 55.000 0.00 0.00 39.86 3.49
2108 5426 1.476891 CTAGCTCCACTTCCGTGCTAA 59.523 52.381 0.00 0.00 39.86 3.09
2233 5551 3.959293 TGGGATCGCTACCTATCGATAA 58.041 45.455 11.46 0.00 44.35 1.75
2235 5553 3.243134 GGGATCGCTACCTATCGATAAGC 60.243 52.174 14.85 14.85 44.35 3.09
2339 5670 1.578897 TGGCCATGGCTAGAGTGTAA 58.421 50.000 34.70 7.92 41.60 2.41
2351 5682 3.876309 AGAGTGTAACCACCACCAAAT 57.124 42.857 0.00 0.00 42.88 2.32
2352 5683 4.986054 AGAGTGTAACCACCACCAAATA 57.014 40.909 0.00 0.00 42.88 1.40
2354 5685 3.404899 AGTGTAACCACCACCAAATACG 58.595 45.455 0.00 0.00 42.88 3.06
2355 5686 3.140623 GTGTAACCACCACCAAATACGT 58.859 45.455 0.00 0.00 35.44 3.57
2356 5687 4.040217 AGTGTAACCACCACCAAATACGTA 59.960 41.667 0.00 0.00 42.88 3.57
2384 5715 1.183549 CGTCCTTGGTGGTAGCTAGT 58.816 55.000 0.00 0.00 37.07 2.57
2387 5723 1.078159 TCCTTGGTGGTAGCTAGTGGA 59.922 52.381 0.00 0.00 37.07 4.02
2459 5810 8.616076 GCTACTACTTAATTAGTACGAGGTTGA 58.384 37.037 8.26 0.00 38.33 3.18
2479 5830 7.339721 AGGTTGATAAATCTCAGTCGACTAAGA 59.660 37.037 20.63 20.63 0.00 2.10
2525 5876 7.276878 AGGTTTTATACAATAACAAAATGCGGC 59.723 33.333 0.00 0.00 0.00 6.53
2527 5878 1.989430 ACAATAACAAAATGCGGCCG 58.011 45.000 24.05 24.05 0.00 6.13
2529 5880 1.653114 CAATAACAAAATGCGGCCGTG 59.347 47.619 28.70 19.09 0.00 4.94
2535 5886 0.963355 AAAATGCGGCCGTGGTATGT 60.963 50.000 28.70 8.78 0.00 2.29
2538 5889 1.653094 ATGCGGCCGTGGTATGTTTG 61.653 55.000 28.70 0.00 0.00 2.93
2540 5891 1.499949 CGGCCGTGGTATGTTTGTG 59.500 57.895 19.50 0.00 0.00 3.33
2541 5892 0.951525 CGGCCGTGGTATGTTTGTGA 60.952 55.000 19.50 0.00 0.00 3.58
2544 5895 2.159435 GGCCGTGGTATGTTTGTGATTC 60.159 50.000 0.00 0.00 0.00 2.52
2546 5897 2.095213 CCGTGGTATGTTTGTGATTCGG 59.905 50.000 0.00 0.00 0.00 4.30
2548 5899 3.927758 CGTGGTATGTTTGTGATTCGGTA 59.072 43.478 0.00 0.00 0.00 4.02
2551 5902 6.566187 CGTGGTATGTTTGTGATTCGGTAAAA 60.566 38.462 0.00 0.00 0.00 1.52
2572 5923 6.625873 AAAAAGAAAAGAGATCGAGCTTGT 57.374 33.333 3.92 0.00 0.00 3.16
2573 5924 5.604010 AAAGAAAAGAGATCGAGCTTGTG 57.396 39.130 3.92 0.00 0.00 3.33
2574 5925 3.594134 AGAAAAGAGATCGAGCTTGTGG 58.406 45.455 3.92 0.00 0.00 4.17
2575 5926 3.007398 AGAAAAGAGATCGAGCTTGTGGT 59.993 43.478 3.92 0.00 0.00 4.16
2577 5928 4.744795 AAAGAGATCGAGCTTGTGGTAT 57.255 40.909 3.92 0.00 0.00 2.73
2579 5930 2.363680 AGAGATCGAGCTTGTGGTATGG 59.636 50.000 3.92 0.00 0.00 2.74
2580 5931 2.101582 GAGATCGAGCTTGTGGTATGGT 59.898 50.000 3.92 0.00 0.00 3.55
2583 5934 3.965379 TCGAGCTTGTGGTATGGTAAA 57.035 42.857 0.00 0.00 0.00 2.01
2585 5936 3.512329 TCGAGCTTGTGGTATGGTAAAGA 59.488 43.478 0.00 0.00 0.00 2.52
2590 5941 5.830991 AGCTTGTGGTATGGTAAAGAAACAA 59.169 36.000 0.00 0.00 0.00 2.83
2591 5942 6.322712 AGCTTGTGGTATGGTAAAGAAACAAA 59.677 34.615 0.00 0.00 0.00 2.83
2594 5945 9.541143 CTTGTGGTATGGTAAAGAAACAAAATT 57.459 29.630 0.00 0.00 0.00 1.82
2599 5950 7.442666 GGTATGGTAAAGAAACAAAATTGGCAA 59.557 33.333 0.68 0.68 0.00 4.52
2602 5953 5.295540 GGTAAAGAAACAAAATTGGCAAGCA 59.704 36.000 5.96 0.00 0.00 3.91
2617 6093 4.142403 TGGCAAGCAAGCAATATAGACAAC 60.142 41.667 2.78 0.00 35.83 3.32
2625 6101 6.073873 GCAAGCAATATAGACAACTGCTCTAG 60.074 42.308 0.00 0.00 42.36 2.43
2649 6129 4.602340 TTTCTCCTTGTAGACACAGTCC 57.398 45.455 0.00 0.00 35.67 3.85
2662 6142 3.093057 ACACAGTCCAGAGACCATAGAC 58.907 50.000 0.00 0.00 44.72 2.59
2724 6212 2.430694 AGAACCACTTTTGACTTTGCCC 59.569 45.455 0.00 0.00 0.00 5.36
2736 6224 1.714899 CTTTGCCCGGGATACGCAAG 61.715 60.000 29.31 11.78 40.66 4.01
2784 6272 3.751175 ACACAATCATTGTCCTGGTTACG 59.249 43.478 0.00 0.00 43.23 3.18
2810 6298 7.200434 AGTGATGATCCATAAGTGTAAACCT 57.800 36.000 0.00 0.00 0.00 3.50
2871 6359 2.124768 TGTGGCCTCCCTCCATGA 59.875 61.111 3.32 0.00 35.81 3.07
2874 6362 1.771746 TGGCCTCCCTCCATGATCC 60.772 63.158 3.32 0.00 0.00 3.36
2875 6363 2.533463 GGCCTCCCTCCATGATCCC 61.533 68.421 0.00 0.00 0.00 3.85
2896 6385 6.695429 TCCCTTGATCTCATCGATTGATTAG 58.305 40.000 10.78 10.77 32.72 1.73
2897 6386 5.350914 CCCTTGATCTCATCGATTGATTAGC 59.649 44.000 10.78 2.01 32.72 3.09
2898 6387 6.164876 CCTTGATCTCATCGATTGATTAGCT 58.835 40.000 10.78 0.00 32.72 3.32
2899 6388 7.318893 CCTTGATCTCATCGATTGATTAGCTA 58.681 38.462 10.78 0.00 32.72 3.32
2900 6389 7.816513 CCTTGATCTCATCGATTGATTAGCTAA 59.183 37.037 8.99 8.99 32.72 3.09
2901 6390 9.201127 CTTGATCTCATCGATTGATTAGCTAAA 57.799 33.333 10.85 0.00 32.72 1.85
2902 6391 8.754230 TGATCTCATCGATTGATTAGCTAAAG 57.246 34.615 10.85 0.00 32.72 1.85
2903 6392 8.363390 TGATCTCATCGATTGATTAGCTAAAGT 58.637 33.333 10.85 0.00 32.72 2.66
2904 6393 7.936950 TCTCATCGATTGATTAGCTAAAGTG 57.063 36.000 10.85 1.68 32.72 3.16
2905 6394 7.716612 TCTCATCGATTGATTAGCTAAAGTGA 58.283 34.615 10.85 3.77 32.72 3.41
2906 6395 8.197439 TCTCATCGATTGATTAGCTAAAGTGAA 58.803 33.333 10.85 0.00 32.72 3.18
2907 6396 8.131455 TCATCGATTGATTAGCTAAAGTGAAC 57.869 34.615 10.85 0.71 30.49 3.18
2908 6397 7.763985 TCATCGATTGATTAGCTAAAGTGAACA 59.236 33.333 10.85 2.13 30.49 3.18
2909 6398 7.525688 TCGATTGATTAGCTAAAGTGAACAG 57.474 36.000 10.85 0.00 0.00 3.16
2910 6399 7.097192 TCGATTGATTAGCTAAAGTGAACAGT 58.903 34.615 10.85 1.91 0.00 3.55
2911 6400 8.248253 TCGATTGATTAGCTAAAGTGAACAGTA 58.752 33.333 10.85 0.00 0.00 2.74
2912 6401 8.535592 CGATTGATTAGCTAAAGTGAACAGTAG 58.464 37.037 10.85 0.00 0.00 2.57
2915 6404 9.856488 TTGATTAGCTAAAGTGAACAGTAGTAG 57.144 33.333 10.85 0.00 0.00 2.57
2928 6417 8.701540 GTGAACAGTAGTAGAGCTCTTTTTAAC 58.298 37.037 23.84 13.62 0.00 2.01
2950 6439 2.641321 GGGGTTGGTACTTTGTACTCCT 59.359 50.000 7.64 0.00 0.00 3.69
2951 6440 3.558533 GGGGTTGGTACTTTGTACTCCTG 60.559 52.174 7.64 0.00 0.00 3.86
2978 6467 1.065854 GTGATCCCACTACTGCAAGCT 60.066 52.381 0.00 0.00 40.10 3.74
2979 6468 1.065926 TGATCCCACTACTGCAAGCTG 60.066 52.381 0.00 0.00 37.60 4.24
2989 6478 2.505557 GCAAGCTGCGCATGAACC 60.506 61.111 12.24 0.00 31.71 3.62
2990 6479 2.956194 CAAGCTGCGCATGAACCA 59.044 55.556 12.24 0.00 27.85 3.67
2991 6480 1.286570 CAAGCTGCGCATGAACCAA 59.713 52.632 12.24 0.00 27.85 3.67
2992 6481 0.318869 CAAGCTGCGCATGAACCAAA 60.319 50.000 12.24 0.00 27.85 3.28
2993 6482 0.318955 AAGCTGCGCATGAACCAAAC 60.319 50.000 12.24 0.00 0.00 2.93
3020 6509 1.136305 GTACCGCAAGCATCTGTCCTA 59.864 52.381 0.00 0.00 0.00 2.94
3022 6511 0.176680 CCGCAAGCATCTGTCCTACT 59.823 55.000 0.00 0.00 0.00 2.57
3023 6512 1.565305 CGCAAGCATCTGTCCTACTC 58.435 55.000 0.00 0.00 0.00 2.59
3069 6558 5.622914 GCCATGTGAATGAAATGCAGTACTT 60.623 40.000 0.00 0.00 27.29 2.24
3118 6610 3.128589 CGATCGATGGGTGAAAAATGGTT 59.871 43.478 10.26 0.00 0.00 3.67
3502 6997 0.744414 GTCATGTGCGCCTACACCAT 60.744 55.000 4.18 0.00 39.93 3.55
4198 8049 3.319198 GTCAGGTTCCTGGCCGGA 61.319 66.667 15.09 13.06 41.06 5.14
4274 8125 0.514255 CTCGTCGGACTACGTGTTCA 59.486 55.000 6.57 0.00 43.31 3.18
4285 8136 2.270352 ACGTGTTCATGTTCATGGGT 57.730 45.000 12.02 2.21 0.00 4.51
4444 8295 2.241722 GACGTGACATTCGCCAAATTG 58.758 47.619 0.00 0.00 0.00 2.32
4731 8582 2.028748 GCCAACTAGTTGTCTCCGGTAA 60.029 50.000 29.05 0.00 38.85 2.85
4732 8583 3.369157 GCCAACTAGTTGTCTCCGGTAAT 60.369 47.826 29.05 0.00 38.85 1.89
4963 8832 2.513204 CCGGTGAGCCAGCTGATG 60.513 66.667 17.39 0.00 34.09 3.07
5179 9057 2.890808 AGAAGACGAACTGCAGTGAA 57.109 45.000 22.49 0.00 0.00 3.18
5248 9131 9.937175 GTTATAATTCAGTTGCCTCAGAAATAC 57.063 33.333 0.00 0.00 0.00 1.89
5249 9132 9.679661 TTATAATTCAGTTGCCTCAGAAATACA 57.320 29.630 0.00 0.00 0.00 2.29
5250 9133 6.506500 AATTCAGTTGCCTCAGAAATACAG 57.493 37.500 0.00 0.00 0.00 2.74
5251 9134 4.623932 TCAGTTGCCTCAGAAATACAGT 57.376 40.909 0.00 0.00 0.00 3.55
5252 9135 5.738619 TCAGTTGCCTCAGAAATACAGTA 57.261 39.130 0.00 0.00 0.00 2.74
5326 9209 4.525912 AATACTCCCGAACTTGTAACGT 57.474 40.909 0.00 0.00 0.00 3.99
5337 9220 0.522626 TTGTAACGTCCTCGATGCGA 59.477 50.000 9.74 0.00 40.62 5.10
5362 9245 1.079819 CTCCCACGTGTCGAAGCAT 60.080 57.895 15.65 0.00 0.00 3.79
5432 9316 9.120538 GTAATCTTCACACAACCCATGTAATAT 57.879 33.333 0.00 0.00 41.46 1.28
5535 9419 4.181578 CAATCAAGGTCCGACTACGAAAT 58.818 43.478 0.00 0.00 42.66 2.17
5564 9448 5.712152 AAAAGAAGAACTCCAAATGCGAT 57.288 34.783 0.00 0.00 0.00 4.58
5581 9466 1.544691 CGATAAAGGTCCCCGATCGAT 59.455 52.381 18.66 0.00 37.54 3.59
5787 9674 8.838649 ATTTAAGCTCATGGGTAAGGTAAAAT 57.161 30.769 0.00 0.00 0.00 1.82
5920 9808 6.643770 GTGATCTTAGAACAACCTACGTCAAA 59.356 38.462 0.00 0.00 0.00 2.69
5927 9815 4.977741 ACAACCTACGTCAAACATTACG 57.022 40.909 0.00 0.00 44.47 3.18
5956 9844 0.761323 TGTTCACTTCCCGGACTCCA 60.761 55.000 0.73 0.00 0.00 3.86
6010 9898 6.312672 GCGGTTGATGCATTTTAATTAAGGTT 59.687 34.615 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.171308 GTCTCGCACCAGTGTAGGTA 58.829 55.000 0.00 0.00 40.77 3.08
1 2 0.826256 TGTCTCGCACCAGTGTAGGT 60.826 55.000 0.00 0.00 44.48 3.08
28 29 0.537143 TGTGTTCATCTGGTGGTGGC 60.537 55.000 0.00 0.00 0.00 5.01
70 71 2.027625 GTCTGGCTTCACGTTCCCG 61.028 63.158 0.00 0.00 40.83 5.14
93 109 1.105167 ACCTGTGTTCTCGTCGGTGA 61.105 55.000 0.00 0.00 0.00 4.02
112 128 9.502091 GTTTACATAGAATGACATATTGGCCTA 57.498 33.333 3.32 0.00 0.00 3.93
146 162 4.688879 CCACGTGTCTTGCTTATCTGTTTA 59.311 41.667 15.65 0.00 0.00 2.01
176 196 2.135933 GCTATACACGTGGAATGAGGC 58.864 52.381 21.57 13.89 0.00 4.70
188 208 0.250081 GAGCTGGGCTGGCTATACAC 60.250 60.000 0.00 0.00 39.88 2.90
246 266 5.242838 TGCCATCAGTTTTATCGTTTTTCCT 59.757 36.000 0.00 0.00 0.00 3.36
315 335 1.872952 TGCACACAACAAAGGAGATCG 59.127 47.619 0.00 0.00 0.00 3.69
367 387 3.309388 CCTGAGTAGATAAACGATGCCG 58.691 50.000 0.00 0.00 42.50 5.69
397 418 1.684869 CCCGTGCCATTAAATCCACCT 60.685 52.381 0.00 0.00 0.00 4.00
446 467 0.238289 GACAGCAACATTGACGGTGG 59.762 55.000 11.78 0.00 32.53 4.61
477 498 7.095187 CCGTTAGCCTATTATTCCACTTGATTC 60.095 40.741 0.00 0.00 0.00 2.52
481 502 4.213482 GCCGTTAGCCTATTATTCCACTTG 59.787 45.833 0.00 0.00 34.35 3.16
485 506 2.868839 GCGCCGTTAGCCTATTATTCCA 60.869 50.000 0.00 0.00 38.78 3.53
593 616 1.123928 ACGATGGGGATCAAGAGGAC 58.876 55.000 0.00 0.00 0.00 3.85
594 617 1.762957 GAACGATGGGGATCAAGAGGA 59.237 52.381 0.00 0.00 0.00 3.71
595 618 1.765314 AGAACGATGGGGATCAAGAGG 59.235 52.381 0.00 0.00 0.00 3.69
596 619 3.550437 AAGAACGATGGGGATCAAGAG 57.450 47.619 0.00 0.00 0.00 2.85
625 652 1.522355 CTGGTCGGCATGCCTAGTG 60.522 63.158 33.07 18.40 0.00 2.74
636 663 0.254747 TGAATAAAGCCCCTGGTCGG 59.745 55.000 0.00 0.00 0.00 4.79
656 683 1.000843 CATTCGGGCCATGACTATCGA 59.999 52.381 4.39 0.00 0.00 3.59
740 771 0.179078 ACGTACTTTCCGTTGCCACA 60.179 50.000 0.00 0.00 34.28 4.17
741 772 1.782044 TACGTACTTTCCGTTGCCAC 58.218 50.000 0.00 0.00 39.60 5.01
818 849 2.158959 GCTCCATTCGGACGACACG 61.159 63.158 0.00 0.00 35.91 4.49
961 998 1.484038 GATGAGAGCAGACAGGAGGT 58.516 55.000 0.00 0.00 0.00 3.85
979 1016 3.924114 TTTGAGAGTGTTTGTGGAGGA 57.076 42.857 0.00 0.00 0.00 3.71
995 1032 1.995542 AGGAGAAGGCCCTCATTTTGA 59.004 47.619 3.68 0.00 34.94 2.69
997 1034 2.242452 GGTAGGAGAAGGCCCTCATTTT 59.758 50.000 3.68 0.00 35.30 1.82
998 1035 1.847088 GGTAGGAGAAGGCCCTCATTT 59.153 52.381 3.68 0.00 35.30 2.32
999 1036 1.274416 TGGTAGGAGAAGGCCCTCATT 60.274 52.381 3.68 0.00 35.30 2.57
1003 1040 1.686110 CGTGGTAGGAGAAGGCCCT 60.686 63.158 0.00 0.00 37.80 5.19
1027 1064 3.490759 CGTGAGCGCCACCATGAC 61.491 66.667 19.09 0.00 42.76 3.06
1492 1669 2.104331 CTGGATTCGACCGGACCG 59.896 66.667 9.46 11.95 38.49 4.79
1494 1671 2.582498 CGCTGGATTCGACCGGAC 60.582 66.667 9.46 0.00 38.49 4.79
1499 1676 1.153353 TCCAAAACGCTGGATTCGAC 58.847 50.000 0.00 0.00 40.71 4.20
1561 1743 1.448013 GGTAGACCACGAAGCAGGC 60.448 63.158 0.00 0.00 35.64 4.85
1596 1778 1.911293 TTCATCGCGAAACTGCTGGC 61.911 55.000 15.24 0.00 0.00 4.85
1608 1790 2.200067 CATCAGAGTGTCCTTCATCGC 58.800 52.381 0.00 0.00 0.00 4.58
1610 1792 3.196469 TCACCATCAGAGTGTCCTTCATC 59.804 47.826 0.00 0.00 36.58 2.92
1611 1793 3.055530 GTCACCATCAGAGTGTCCTTCAT 60.056 47.826 0.00 0.00 36.58 2.57
1612 1794 2.300152 GTCACCATCAGAGTGTCCTTCA 59.700 50.000 0.00 0.00 36.58 3.02
1697 1879 1.301165 ACCGCTACGCCGAGTTTTT 60.301 52.632 0.00 0.00 0.00 1.94
1698 1880 2.025418 CACCGCTACGCCGAGTTTT 61.025 57.895 0.00 0.00 0.00 2.43
1699 1881 2.431942 CACCGCTACGCCGAGTTT 60.432 61.111 0.00 0.00 0.00 2.66
1785 1969 4.295857 TGCGGTTTTCTTACTGGTTTTC 57.704 40.909 0.00 0.00 0.00 2.29
1817 2001 1.615165 TAAAGCGACCCGGCCATACA 61.615 55.000 2.24 0.00 0.00 2.29
1902 3778 1.995376 AACAGTTTGCCTCCCGAATT 58.005 45.000 0.00 0.00 0.00 2.17
1955 3858 8.934023 TTAGACTGAATTTCACATTTTACCCT 57.066 30.769 0.00 0.00 0.00 4.34
2010 4422 8.783833 AGATATAATCACATGCATGAGGTAAC 57.216 34.615 32.75 13.74 30.46 2.50
2013 4426 7.455891 TCAAGATATAATCACATGCATGAGGT 58.544 34.615 32.75 19.21 30.46 3.85
2014 4427 7.916914 TCAAGATATAATCACATGCATGAGG 57.083 36.000 32.75 22.40 30.46 3.86
2042 5080 7.381678 CCTTAAGTACTAGCTAATTACCTTGCG 59.618 40.741 0.00 0.00 0.00 4.85
2051 5286 6.782988 TGATGGAGCCTTAAGTACTAGCTAAT 59.217 38.462 8.97 6.92 32.97 1.73
2054 5289 4.547671 TGATGGAGCCTTAAGTACTAGCT 58.452 43.478 8.80 8.80 36.25 3.32
2055 5290 4.939052 TGATGGAGCCTTAAGTACTAGC 57.061 45.455 0.00 0.00 0.00 3.42
2058 5293 7.054751 GGTTAATTGATGGAGCCTTAAGTACT 58.945 38.462 0.97 0.00 0.00 2.73
2104 5422 2.067013 GTCCGTTTCTGTCCTGTTAGC 58.933 52.381 0.00 0.00 0.00 3.09
2105 5423 3.380479 TGTCCGTTTCTGTCCTGTTAG 57.620 47.619 0.00 0.00 0.00 2.34
2107 5425 2.093128 AGTTGTCCGTTTCTGTCCTGTT 60.093 45.455 0.00 0.00 0.00 3.16
2108 5426 1.485066 AGTTGTCCGTTTCTGTCCTGT 59.515 47.619 0.00 0.00 0.00 4.00
2245 5571 0.545646 TGTAGGCCTACATGCATGCA 59.454 50.000 36.63 25.04 40.77 3.96
2246 5572 0.947244 GTGTAGGCCTACATGCATGC 59.053 55.000 40.65 26.11 46.36 4.06
2339 5670 4.023726 ACAATACGTATTTGGTGGTGGT 57.976 40.909 18.06 7.81 0.00 4.16
2351 5682 3.427909 CCAAGGACGCTGTACAATACGTA 60.428 47.826 15.61 0.00 39.16 3.57
2352 5683 2.602878 CAAGGACGCTGTACAATACGT 58.397 47.619 15.58 15.58 42.27 3.57
2354 5685 2.671396 CACCAAGGACGCTGTACAATAC 59.329 50.000 0.00 0.00 0.00 1.89
2355 5686 2.354303 CCACCAAGGACGCTGTACAATA 60.354 50.000 0.00 0.00 41.22 1.90
2356 5687 1.610624 CCACCAAGGACGCTGTACAAT 60.611 52.381 0.00 0.00 41.22 2.71
2384 5715 1.832167 GCCCAAACCAGCAACTCCA 60.832 57.895 0.00 0.00 0.00 3.86
2387 5723 2.912025 CGGCCCAAACCAGCAACT 60.912 61.111 0.00 0.00 0.00 3.16
2446 5797 7.254692 CGACTGAGATTTATCAACCTCGTACTA 60.255 40.741 0.00 0.00 0.00 1.82
2450 5801 4.398358 TCGACTGAGATTTATCAACCTCGT 59.602 41.667 0.00 0.00 0.00 4.18
2451 5802 4.735822 GTCGACTGAGATTTATCAACCTCG 59.264 45.833 8.70 0.00 0.00 4.63
2498 5849 9.145865 CCGCATTTTGTTATTGTATAAAACCTT 57.854 29.630 0.00 0.00 0.00 3.50
2499 5850 7.276878 GCCGCATTTTGTTATTGTATAAAACCT 59.723 33.333 0.00 0.00 0.00 3.50
2504 5855 5.163642 ACGGCCGCATTTTGTTATTGTATAA 60.164 36.000 28.58 0.00 0.00 0.98
2509 5860 1.653114 CACGGCCGCATTTTGTTATTG 59.347 47.619 28.58 7.40 0.00 1.90
2513 5864 1.173444 TACCACGGCCGCATTTTGTT 61.173 50.000 28.58 6.51 0.00 2.83
2515 5866 0.525242 CATACCACGGCCGCATTTTG 60.525 55.000 28.58 15.97 0.00 2.44
2518 5869 0.963355 AAACATACCACGGCCGCATT 60.963 50.000 28.58 12.06 0.00 3.56
2525 5876 2.095213 CCGAATCACAAACATACCACGG 59.905 50.000 0.00 0.00 0.00 4.94
2527 5878 5.866335 TTACCGAATCACAAACATACCAC 57.134 39.130 0.00 0.00 0.00 4.16
2551 5902 4.453819 CCACAAGCTCGATCTCTTTTCTTT 59.546 41.667 0.00 0.00 0.00 2.52
2553 5904 3.007398 ACCACAAGCTCGATCTCTTTTCT 59.993 43.478 0.00 0.00 0.00 2.52
2555 5906 3.409026 ACCACAAGCTCGATCTCTTTT 57.591 42.857 0.00 0.00 0.00 2.27
2556 5907 4.437239 CATACCACAAGCTCGATCTCTTT 58.563 43.478 0.00 0.00 0.00 2.52
2557 5908 3.181471 CCATACCACAAGCTCGATCTCTT 60.181 47.826 0.00 0.00 0.00 2.85
2558 5909 2.363680 CCATACCACAAGCTCGATCTCT 59.636 50.000 0.00 0.00 0.00 3.10
2559 5910 2.101582 ACCATACCACAAGCTCGATCTC 59.898 50.000 0.00 0.00 0.00 2.75
2560 5911 2.111384 ACCATACCACAAGCTCGATCT 58.889 47.619 0.00 0.00 0.00 2.75
2561 5912 2.604046 ACCATACCACAAGCTCGATC 57.396 50.000 0.00 0.00 0.00 3.69
2564 5915 3.857052 TCTTTACCATACCACAAGCTCG 58.143 45.455 0.00 0.00 0.00 5.03
2565 5916 5.472137 TGTTTCTTTACCATACCACAAGCTC 59.528 40.000 0.00 0.00 0.00 4.09
2568 5919 9.541143 AATTTTGTTTCTTTACCATACCACAAG 57.459 29.630 0.00 0.00 0.00 3.16
2571 5922 7.095397 GCCAATTTTGTTTCTTTACCATACCAC 60.095 37.037 0.00 0.00 0.00 4.16
2572 5923 6.931840 GCCAATTTTGTTTCTTTACCATACCA 59.068 34.615 0.00 0.00 0.00 3.25
2573 5924 6.931840 TGCCAATTTTGTTTCTTTACCATACC 59.068 34.615 0.00 0.00 0.00 2.73
2574 5925 7.954788 TGCCAATTTTGTTTCTTTACCATAC 57.045 32.000 0.00 0.00 0.00 2.39
2575 5926 7.172361 GCTTGCCAATTTTGTTTCTTTACCATA 59.828 33.333 0.00 0.00 0.00 2.74
2577 5928 5.295540 GCTTGCCAATTTTGTTTCTTTACCA 59.704 36.000 0.00 0.00 0.00 3.25
2579 5930 6.356757 TGCTTGCCAATTTTGTTTCTTTAC 57.643 33.333 0.00 0.00 0.00 2.01
2580 5931 6.458070 GCTTGCTTGCCAATTTTGTTTCTTTA 60.458 34.615 0.00 0.00 31.91 1.85
2583 5934 3.313249 GCTTGCTTGCCAATTTTGTTTCT 59.687 39.130 0.00 0.00 31.91 2.52
2585 5936 3.015327 TGCTTGCTTGCCAATTTTGTTT 58.985 36.364 0.00 0.00 31.91 2.83
2590 5941 6.044682 GTCTATATTGCTTGCTTGCCAATTT 58.955 36.000 2.10 0.00 31.91 1.82
2591 5942 5.127519 TGTCTATATTGCTTGCTTGCCAATT 59.872 36.000 2.10 0.00 31.91 2.32
2594 5945 3.619419 TGTCTATATTGCTTGCTTGCCA 58.381 40.909 0.00 0.00 0.00 4.92
2599 5950 4.521146 AGCAGTTGTCTATATTGCTTGCT 58.479 39.130 0.00 0.00 42.01 3.91
2602 5953 6.098982 ACCTAGAGCAGTTGTCTATATTGCTT 59.901 38.462 0.00 0.00 44.46 3.91
2617 6093 4.278975 ACAAGGAGAAAACCTAGAGCAG 57.721 45.455 0.00 0.00 39.62 4.24
2625 6101 4.704965 ACTGTGTCTACAAGGAGAAAACC 58.295 43.478 0.00 0.00 36.14 3.27
2649 6129 3.975670 GCGAATTACGTCTATGGTCTCTG 59.024 47.826 0.00 0.00 44.60 3.35
2662 6142 1.722464 TGTCGAACCTTGCGAATTACG 59.278 47.619 0.00 0.00 45.66 3.18
2736 6224 1.067199 CGCCAATTGCTCACGCTTTC 61.067 55.000 0.00 0.00 38.05 2.62
2784 6272 6.483640 GGTTTACACTTATGGATCATCACTCC 59.516 42.308 0.00 0.00 0.00 3.85
2810 6298 1.805943 CACGTGTGGCATGAATGAGAA 59.194 47.619 7.58 0.00 0.00 2.87
2871 6359 5.758790 ATCAATCGATGAGATCAAGGGAT 57.241 39.130 0.00 0.00 42.53 3.85
2874 6362 6.164876 AGCTAATCAATCGATGAGATCAAGG 58.835 40.000 12.43 6.30 42.53 3.61
2875 6363 8.754230 TTAGCTAATCAATCGATGAGATCAAG 57.246 34.615 12.43 13.08 42.53 3.02
2896 6385 5.956642 AGCTCTACTACTGTTCACTTTAGC 58.043 41.667 0.00 0.00 0.00 3.09
2897 6386 7.385778 AGAGCTCTACTACTGTTCACTTTAG 57.614 40.000 16.50 0.00 0.00 1.85
2898 6387 7.762588 AAGAGCTCTACTACTGTTCACTTTA 57.237 36.000 18.59 0.00 0.00 1.85
2899 6388 6.658188 AAGAGCTCTACTACTGTTCACTTT 57.342 37.500 18.59 0.00 0.00 2.66
2900 6389 6.658188 AAAGAGCTCTACTACTGTTCACTT 57.342 37.500 18.59 0.00 0.00 3.16
2901 6390 6.658188 AAAAGAGCTCTACTACTGTTCACT 57.342 37.500 18.59 0.00 0.00 3.41
2902 6391 8.701540 GTTAAAAAGAGCTCTACTACTGTTCAC 58.298 37.037 18.59 0.28 0.00 3.18
2903 6392 7.594015 CGTTAAAAAGAGCTCTACTACTGTTCA 59.406 37.037 18.59 0.00 0.00 3.18
2904 6393 7.062022 CCGTTAAAAAGAGCTCTACTACTGTTC 59.938 40.741 18.59 2.07 0.00 3.18
2905 6394 6.867293 CCGTTAAAAAGAGCTCTACTACTGTT 59.133 38.462 18.59 4.78 0.00 3.16
2906 6395 6.388278 CCGTTAAAAAGAGCTCTACTACTGT 58.612 40.000 18.59 0.00 0.00 3.55
2907 6396 5.805994 CCCGTTAAAAAGAGCTCTACTACTG 59.194 44.000 18.59 7.57 0.00 2.74
2908 6397 5.105432 CCCCGTTAAAAAGAGCTCTACTACT 60.105 44.000 18.59 0.00 0.00 2.57
2909 6398 5.107824 CCCCGTTAAAAAGAGCTCTACTAC 58.892 45.833 18.59 10.04 0.00 2.73
2910 6399 4.774200 ACCCCGTTAAAAAGAGCTCTACTA 59.226 41.667 18.59 5.97 0.00 1.82
2911 6400 3.581770 ACCCCGTTAAAAAGAGCTCTACT 59.418 43.478 18.59 4.34 0.00 2.57
2912 6401 3.935315 ACCCCGTTAAAAAGAGCTCTAC 58.065 45.455 18.59 10.16 0.00 2.59
2915 6404 2.228103 CCAACCCCGTTAAAAAGAGCTC 59.772 50.000 5.27 5.27 0.00 4.09
2928 6417 2.613725 GGAGTACAAAGTACCAACCCCG 60.614 54.545 3.85 0.00 0.00 5.73
2978 6467 2.050533 GCGTTTGGTTCATGCGCA 60.051 55.556 14.96 14.96 46.23 6.09
2979 6468 3.165318 CGCGTTTGGTTCATGCGC 61.165 61.111 0.00 0.00 42.42 6.09
2982 6471 2.074353 CACGCGCGTTTGGTTCATG 61.074 57.895 35.90 15.25 0.00 3.07
2984 6473 1.881709 TACACGCGCGTTTGGTTCA 60.882 52.632 35.90 11.57 0.00 3.18
2986 6475 2.627555 GTACACGCGCGTTTGGTT 59.372 55.556 35.90 17.19 0.00 3.67
2987 6476 3.340253 GGTACACGCGCGTTTGGT 61.340 61.111 35.90 29.26 0.00 3.67
2988 6477 4.418470 CGGTACACGCGCGTTTGG 62.418 66.667 35.90 24.89 34.82 3.28
3006 6495 5.021033 AGATTGAGTAGGACAGATGCTTG 57.979 43.478 0.00 0.00 0.00 4.01
3022 6511 5.188434 CAGGCAATTTGGACTCTAGATTGA 58.812 41.667 9.17 0.00 31.15 2.57
3023 6512 4.201990 GCAGGCAATTTGGACTCTAGATTG 60.202 45.833 0.00 2.29 0.00 2.67
3118 6610 1.514087 GTCCCGATCGCCTACACAA 59.486 57.895 10.32 0.00 0.00 3.33
3170 6662 2.503061 CAGATGGTGAGCCCCTCG 59.497 66.667 0.00 0.00 32.35 4.63
3709 7355 8.201554 TCTCACAATATTAACTGCAACAGATC 57.798 34.615 0.78 0.00 35.18 2.75
3712 7358 9.630098 AATTTCTCACAATATTAACTGCAACAG 57.370 29.630 0.00 0.00 37.52 3.16
3745 7391 5.187480 GCAAACAGTTCGCAACATTTTTAC 58.813 37.500 0.00 0.00 0.00 2.01
3761 7408 4.524316 TCAAATCCAATCCTGCAAACAG 57.476 40.909 0.00 0.00 44.05 3.16
4274 8125 0.994247 TGGCTCAGACCCATGAACAT 59.006 50.000 0.00 0.00 0.00 2.71
4387 8238 2.607750 AGCACCAGGATCACCGGT 60.608 61.111 0.00 0.00 41.24 5.28
4444 8295 0.608035 TTGCACCGATCTTGGGGTTC 60.608 55.000 0.00 0.00 33.77 3.62
4731 8582 2.292292 GTGTTCGGTGCTTTGTTACCAT 59.708 45.455 0.00 0.00 36.76 3.55
4732 8583 1.671845 GTGTTCGGTGCTTTGTTACCA 59.328 47.619 0.00 0.00 36.76 3.25
4982 8851 2.187946 CTTCTCGCCGGCCTTGAT 59.812 61.111 23.46 0.00 0.00 2.57
5156 9034 1.068472 ACTGCAGTTCGTCTTCTACCG 60.068 52.381 15.25 0.00 0.00 4.02
5326 9209 3.632604 GGGAGATATAATCGCATCGAGGA 59.367 47.826 0.00 0.00 39.91 3.71
5337 9220 4.558898 GCTTCGACACGTGGGAGATATAAT 60.559 45.833 21.57 0.00 0.00 1.28
5389 9273 2.831685 TACCTCACTTGCGACATTGT 57.168 45.000 0.00 0.00 0.00 2.71
5432 9316 9.569122 GCCAACTATGTATCTTTTTCCCTTATA 57.431 33.333 0.00 0.00 0.00 0.98
5535 9419 9.260002 GCATTTGGAGTTCTTCTTTTATTTTGA 57.740 29.630 0.00 0.00 0.00 2.69
5553 9437 2.650322 GGGACCTTTATCGCATTTGGA 58.350 47.619 0.00 0.00 0.00 3.53
5787 9674 0.538584 CTGCAGCTCCACCTCATACA 59.461 55.000 0.00 0.00 0.00 2.29
5901 9788 7.096106 CGTAATGTTTGACGTAGGTTGTTCTAA 60.096 37.037 0.00 0.00 34.39 2.10
5920 9808 0.533308 ACACGGTGTTGGCGTAATGT 60.533 50.000 8.21 0.00 0.00 2.71
5927 9815 0.028902 GAAGTGAACACGGTGTTGGC 59.971 55.000 29.46 20.24 41.28 4.52
5956 9844 0.246635 CGTGATGGTCTCTTTCCGGT 59.753 55.000 0.00 0.00 0.00 5.28
6010 9898 5.058490 CCGGTTGTAGAAAACCTGAAGTTA 58.942 41.667 0.00 0.00 46.31 2.24


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

AutoCloner maintained by Alex Coulton.