Multiple sequence alignment - TraesCS3A01G402100

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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 TraesCS3A01G402100 chr3A 100.000 4485 0 0 1 4485 647610588 647615072 0.000000e+00 8283.0
1 TraesCS3A01G402100 chr3B 92.996 1642 90 10 2055 3683 673171324 673169695 0.000000e+00 2372.0
2 TraesCS3A01G402100 chr3B 86.166 1930 145 51 201 2082 673173283 673171428 0.000000e+00 1973.0
3 TraesCS3A01G402100 chr3B 93.916 526 22 5 3850 4373 673282801 673283318 0.000000e+00 785.0
4 TraesCS3A01G402100 chr3B 79.622 952 81 50 3 859 673273534 673272601 3.010000e-161 579.0
5 TraesCS3A01G402100 chr3B 93.141 277 19 0 917 1193 673271732 673271456 1.500000e-109 407.0
6 TraesCS3A01G402100 chr3B 89.212 241 24 2 3174 3414 673280328 673280566 2.620000e-77 300.0
7 TraesCS3A01G402100 chr3B 88.679 159 10 3 3491 3641 673280566 673280724 2.130000e-43 187.0
8 TraesCS3A01G402100 chr3B 77.536 138 23 6 2691 2824 30683305 30683438 4.810000e-10 76.8
9 TraesCS3A01G402100 chr3D 95.419 1397 55 3 2091 3487 511535081 511536468 0.000000e+00 2217.0
10 TraesCS3A01G402100 chr3D 90.271 1069 76 11 1020 2082 511533921 511534967 0.000000e+00 1373.0
11 TraesCS3A01G402100 chr3D 81.004 837 52 29 200 956 511533087 511533896 2.340000e-157 566.0
12 TraesCS3A01G402100 chr3D 79.143 350 31 15 1960 2301 511179777 511179462 2.120000e-48 204.0
13 TraesCS3A01G402100 chr3D 94.030 67 3 1 3699 3764 593235010 593235076 2.850000e-17 100.0
14 TraesCS3A01G402100 chr1A 81.555 656 96 17 2528 3178 453074160 453074795 6.650000e-143 518.0
15 TraesCS3A01G402100 chr1A 88.312 77 7 2 3689 3764 571578897 571578972 1.720000e-14 91.6
16 TraesCS3A01G402100 chr1A 89.362 47 5 0 1141 1187 8327266 8327312 4.850000e-05 60.2
17 TraesCS3A01G402100 chr1B 80.704 653 101 18 2531 3178 474835516 474834884 6.750000e-133 484.0
18 TraesCS3A01G402100 chr1B 92.000 75 4 2 3691 3764 510811011 510811084 2.210000e-18 104.0
19 TraesCS3A01G402100 chr1B 89.362 47 5 0 1141 1187 9175498 9175544 4.850000e-05 60.2
20 TraesCS3A01G402100 chr4A 78.964 618 109 18 2559 3170 61616516 61615914 6.990000e-108 401.0
21 TraesCS3A01G402100 chr4D 78.583 621 112 20 2559 3170 404111900 404111292 1.510000e-104 390.0
22 TraesCS3A01G402100 chr4D 88.750 80 6 3 3692 3769 112721810 112721888 1.330000e-15 95.3
23 TraesCS3A01G402100 chr4B 78.641 618 111 18 2559 3170 500869321 500868719 1.510000e-104 390.0
24 TraesCS3A01G402100 chr7A 77.099 524 88 24 2636 3149 652288062 652288563 1.590000e-69 274.0
25 TraesCS3A01G402100 chr7D 76.970 495 83 24 2663 3149 566015626 566016097 2.070000e-63 254.0
26 TraesCS3A01G402100 chr7D 74.847 489 96 22 2667 3149 565645297 565645764 3.540000e-46 196.0
27 TraesCS3A01G402100 chr7D 90.667 75 5 2 3692 3765 117242047 117242120 1.030000e-16 99.0
28 TraesCS3A01G402100 chr7B 72.429 885 163 58 2553 3392 616821753 616820905 1.640000e-49 207.0
29 TraesCS3A01G402100 chr5D 93.151 73 3 2 3694 3765 462454807 462454736 6.140000e-19 106.0
30 TraesCS3A01G402100 chr2D 92.000 75 4 2 3696 3769 451292391 451292464 2.210000e-18 104.0
31 TraesCS3A01G402100 chr2D 93.182 44 1 2 1146 1187 8348805 8348762 3.750000e-06 63.9
32 TraesCS3A01G402100 chr2B 95.385 65 2 1 3702 3765 71316826 71316762 7.940000e-18 102.0
33 TraesCS3A01G402100 chr2B 91.667 48 2 2 1141 1187 4754174 4754128 1.040000e-06 65.8
34 TraesCS3A01G402100 chr6B 93.939 66 3 1 3701 3765 610952833 610952768 1.030000e-16 99.0
35 TraesCS3A01G402100 chr2A 84.848 66 7 3 2759 2822 2390159 2390223 3.750000e-06 63.9
36 TraesCS3A01G402100 chr2A 83.582 67 8 3 2759 2823 2938114 2938179 4.850000e-05 60.2
37 TraesCS3A01G402100 chr1D 89.362 47 5 0 1141 1187 6898575 6898621 4.850000e-05 60.2
38 TraesCS3A01G402100 chr1D 100.000 30 0 0 1156 1185 6721457 6721428 6.270000e-04 56.5


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 TraesCS3A01G402100 chr3A 647610588 647615072 4484 False 8283.000000 8283 100.000000 1 4485 1 chr3A.!!$F1 4484
1 TraesCS3A01G402100 chr3B 673169695 673173283 3588 True 2172.500000 2372 89.581000 201 3683 2 chr3B.!!$R1 3482
2 TraesCS3A01G402100 chr3B 673271456 673273534 2078 True 493.000000 579 86.381500 3 1193 2 chr3B.!!$R2 1190
3 TraesCS3A01G402100 chr3B 673280328 673283318 2990 False 424.000000 785 90.602333 3174 4373 3 chr3B.!!$F2 1199
4 TraesCS3A01G402100 chr3D 511533087 511536468 3381 False 1385.333333 2217 88.898000 200 3487 3 chr3D.!!$F2 3287
5 TraesCS3A01G402100 chr1A 453074160 453074795 635 False 518.000000 518 81.555000 2528 3178 1 chr1A.!!$F2 650
6 TraesCS3A01G402100 chr1B 474834884 474835516 632 True 484.000000 484 80.704000 2531 3178 1 chr1B.!!$R1 647
7 TraesCS3A01G402100 chr4A 61615914 61616516 602 True 401.000000 401 78.964000 2559 3170 1 chr4A.!!$R1 611
8 TraesCS3A01G402100 chr4D 404111292 404111900 608 True 390.000000 390 78.583000 2559 3170 1 chr4D.!!$R1 611
9 TraesCS3A01G402100 chr4B 500868719 500869321 602 True 390.000000 390 78.641000 2559 3170 1 chr4B.!!$R1 611
10 TraesCS3A01G402100 chr7A 652288062 652288563 501 False 274.000000 274 77.099000 2636 3149 1 chr7A.!!$F1 513
11 TraesCS3A01G402100 chr7B 616820905 616821753 848 True 207.000000 207 72.429000 2553 3392 1 chr7B.!!$R1 839

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
31 32 0.321346 CCAACATTCCAACAAGGGCC 59.679 55.0 0.0 0.0 38.24 5.80 F
888 1882 0.464554 CTCCTTTTCGCCCTCCATCC 60.465 60.0 0.0 0.0 0.00 3.51 F
2302 3439 0.036952 ACCTCCAAGACATGAGCACG 60.037 55.0 0.0 0.0 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1207 2206 0.033405 TAAGGAGAGTCGGAGGGGTG 60.033 60.0 0.0 0.0 0.0 4.61 R
2800 3943 0.178921 AGAAGAGGTGCCTGTCCAGA 60.179 55.0 0.0 0.0 0.0 3.86 R
3698 6710 0.178903 TGAGACCTAGCCACACCCTT 60.179 55.0 0.0 0.0 0.0 3.95 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
21 22 3.080300 TGGGACATGTACCAACATTCC 57.920 47.619 28.29 6.61 44.07 3.01
23 24 3.181428 TGGGACATGTACCAACATTCCAA 60.181 43.478 28.29 0.00 44.07 3.53
26 27 4.279671 GGACATGTACCAACATTCCAACAA 59.720 41.667 0.00 0.00 44.07 2.83
29 30 3.226777 TGTACCAACATTCCAACAAGGG 58.773 45.455 0.00 0.00 38.24 3.95
31 32 0.321346 CCAACATTCCAACAAGGGCC 59.679 55.000 0.00 0.00 38.24 5.80
59 60 2.512515 GCGAGGCTGGCTAGTTGG 60.513 66.667 14.72 0.00 0.00 3.77
65 66 0.548510 GGCTGGCTAGTTGGGAGATT 59.451 55.000 0.00 0.00 0.00 2.40
66 67 1.673168 GCTGGCTAGTTGGGAGATTG 58.327 55.000 0.00 0.00 0.00 2.67
67 68 1.065126 GCTGGCTAGTTGGGAGATTGT 60.065 52.381 0.00 0.00 0.00 2.71
68 69 2.911484 CTGGCTAGTTGGGAGATTGTC 58.089 52.381 0.00 0.00 0.00 3.18
69 70 2.237143 CTGGCTAGTTGGGAGATTGTCA 59.763 50.000 0.00 0.00 0.00 3.58
70 71 2.642311 TGGCTAGTTGGGAGATTGTCAA 59.358 45.455 0.00 0.00 0.00 3.18
71 72 3.266772 TGGCTAGTTGGGAGATTGTCAAT 59.733 43.478 0.00 0.00 0.00 2.57
78 79 5.709164 AGTTGGGAGATTGTCAATCAAGAAG 59.291 40.000 24.13 0.00 40.42 2.85
89 90 7.345422 TGTCAATCAAGAAGACAAAAATGGA 57.655 32.000 6.34 0.00 39.15 3.41
90 91 7.954835 TGTCAATCAAGAAGACAAAAATGGAT 58.045 30.769 6.34 0.00 39.15 3.41
101 126 8.856490 AAGACAAAAATGGATATATTTCGTGC 57.144 30.769 0.00 0.00 30.33 5.34
193 218 3.198489 GCGCTAAGCTGGCCTCAC 61.198 66.667 3.32 0.00 44.04 3.51
315 357 2.076100 GATCAATGCGACACCAACTCA 58.924 47.619 0.00 0.00 0.00 3.41
316 358 1.960417 TCAATGCGACACCAACTCAA 58.040 45.000 0.00 0.00 0.00 3.02
317 359 1.601903 TCAATGCGACACCAACTCAAC 59.398 47.619 0.00 0.00 0.00 3.18
318 360 1.603802 CAATGCGACACCAACTCAACT 59.396 47.619 0.00 0.00 0.00 3.16
319 361 1.512926 ATGCGACACCAACTCAACTC 58.487 50.000 0.00 0.00 0.00 3.01
341 383 0.958091 CCTGGATTTGCGTGGTTTGA 59.042 50.000 0.00 0.00 0.00 2.69
380 436 3.981308 CGATGCCCGTGTCCTTTT 58.019 55.556 0.00 0.00 0.00 2.27
462 540 2.654404 GCTCCGTGCGTCCGATAC 60.654 66.667 0.00 0.00 0.00 2.24
463 541 2.025727 CTCCGTGCGTCCGATACC 59.974 66.667 0.00 0.00 0.00 2.73
464 542 3.480225 CTCCGTGCGTCCGATACCC 62.480 68.421 0.00 0.00 0.00 3.69
465 543 3.524606 CCGTGCGTCCGATACCCT 61.525 66.667 0.00 0.00 0.00 4.34
466 544 2.025727 CGTGCGTCCGATACCCTC 59.974 66.667 0.00 0.00 0.00 4.30
540 640 3.069016 ACCCGCATCGTCATAACTCATAA 59.931 43.478 0.00 0.00 0.00 1.90
541 641 3.428870 CCCGCATCGTCATAACTCATAAC 59.571 47.826 0.00 0.00 0.00 1.89
542 642 3.428870 CCGCATCGTCATAACTCATAACC 59.571 47.826 0.00 0.00 0.00 2.85
543 643 3.119628 CGCATCGTCATAACTCATAACCG 59.880 47.826 0.00 0.00 0.00 4.44
569 669 1.982938 GGGCCGGGTATATCGAGCT 60.983 63.158 2.18 0.00 0.00 4.09
572 672 1.134560 GGCCGGGTATATCGAGCTAAG 59.865 57.143 2.18 0.00 0.00 2.18
574 674 1.749634 CCGGGTATATCGAGCTAAGGG 59.250 57.143 0.00 0.00 0.00 3.95
587 697 0.741221 CTAAGGGAGAACAGTGCGCC 60.741 60.000 4.18 0.00 0.00 6.53
588 698 1.476845 TAAGGGAGAACAGTGCGCCA 61.477 55.000 4.18 0.00 0.00 5.69
609 719 1.299850 GCACCCAAAAGTTCACCGC 60.300 57.895 0.00 0.00 0.00 5.68
657 767 4.794439 TCCATGTGGAGCGTCGCG 62.794 66.667 12.30 0.00 39.78 5.87
800 947 2.798009 CATTTAAGCCGGGCGTGG 59.202 61.111 18.00 0.87 0.00 4.94
801 948 1.747367 CATTTAAGCCGGGCGTGGA 60.747 57.895 18.00 6.15 0.00 4.02
803 950 3.905437 TTTAAGCCGGGCGTGGACC 62.905 63.158 18.00 0.00 0.00 4.46
811 958 2.671963 GGCGTGGACCACCTTTCC 60.672 66.667 19.11 10.94 37.04 3.13
812 959 3.047877 GCGTGGACCACCTTTCCG 61.048 66.667 19.11 7.29 35.70 4.30
813 960 3.047877 CGTGGACCACCTTTCCGC 61.048 66.667 19.11 0.00 39.84 5.54
814 961 2.430367 GTGGACCACCTTTCCGCT 59.570 61.111 14.16 0.00 40.06 5.52
823 986 1.377333 CCTTTCCGCTGTTCCTCCC 60.377 63.158 0.00 0.00 0.00 4.30
844 1007 2.158959 GTGAACGATCGGCCAGTCG 61.159 63.158 20.98 21.31 43.13 4.18
884 1878 1.222113 CCTCTCCTTTTCGCCCTCC 59.778 63.158 0.00 0.00 0.00 4.30
885 1879 1.553690 CCTCTCCTTTTCGCCCTCCA 61.554 60.000 0.00 0.00 0.00 3.86
886 1880 0.543749 CTCTCCTTTTCGCCCTCCAT 59.456 55.000 0.00 0.00 0.00 3.41
887 1881 0.541863 TCTCCTTTTCGCCCTCCATC 59.458 55.000 0.00 0.00 0.00 3.51
888 1882 0.464554 CTCCTTTTCGCCCTCCATCC 60.465 60.000 0.00 0.00 0.00 3.51
889 1883 1.819632 CCTTTTCGCCCTCCATCCG 60.820 63.158 0.00 0.00 0.00 4.18
890 1884 1.078426 CTTTTCGCCCTCCATCCGT 60.078 57.895 0.00 0.00 0.00 4.69
891 1885 1.369091 CTTTTCGCCCTCCATCCGTG 61.369 60.000 0.00 0.00 0.00 4.94
904 1898 2.332104 CATCCGTGTCTTCACTGTCAG 58.668 52.381 0.00 0.00 41.89 3.51
905 1899 1.399714 TCCGTGTCTTCACTGTCAGT 58.600 50.000 0.00 0.00 41.89 3.41
906 1900 2.578786 TCCGTGTCTTCACTGTCAGTA 58.421 47.619 4.85 0.00 41.89 2.74
907 1901 2.953648 TCCGTGTCTTCACTGTCAGTAA 59.046 45.455 4.85 0.00 41.89 2.24
908 1902 3.572682 TCCGTGTCTTCACTGTCAGTAAT 59.427 43.478 4.85 0.00 41.89 1.89
909 1903 4.038763 TCCGTGTCTTCACTGTCAGTAATT 59.961 41.667 4.85 0.00 41.89 1.40
910 1904 4.386049 CCGTGTCTTCACTGTCAGTAATTC 59.614 45.833 4.85 0.00 41.89 2.17
911 1905 4.982295 CGTGTCTTCACTGTCAGTAATTCA 59.018 41.667 4.85 0.00 41.89 2.57
912 1906 5.117745 CGTGTCTTCACTGTCAGTAATTCAG 59.882 44.000 4.85 0.00 41.89 3.02
927 1921 7.819415 TCAGTAATTCAGGTATCTGTTGTCTTG 59.181 37.037 2.20 0.00 41.59 3.02
1056 2055 2.348998 CTGCCTTTGCTCCTCGGT 59.651 61.111 0.00 0.00 38.71 4.69
1199 2198 0.988832 CAGCCTGGTAAACCCACCTA 59.011 55.000 0.00 0.00 38.72 3.08
1207 2206 2.507484 GTAAACCCACCTACAACACCC 58.493 52.381 0.00 0.00 0.00 4.61
1230 2234 1.028905 CCTCCGACTCTCCTTAGCTG 58.971 60.000 0.00 0.00 0.00 4.24
1248 2252 0.817634 TGTTCTTGTGGTCTTGCGGG 60.818 55.000 0.00 0.00 0.00 6.13
1262 2266 2.602257 TGCGGGTGATACAGATTCTG 57.398 50.000 12.17 12.17 37.52 3.02
1263 2267 2.107366 TGCGGGTGATACAGATTCTGA 58.893 47.619 20.33 4.65 35.18 3.27
1267 2271 4.060900 CGGGTGATACAGATTCTGAATGG 58.939 47.826 20.33 2.56 35.18 3.16
1272 2276 6.481644 GGTGATACAGATTCTGAATGGTTCTC 59.518 42.308 20.33 7.17 35.18 2.87
1305 2312 1.402968 GTGACATCCATTTCGCATGCT 59.597 47.619 17.13 0.00 0.00 3.79
1306 2313 2.093890 TGACATCCATTTCGCATGCTT 58.906 42.857 17.13 0.00 0.00 3.91
1321 2328 1.211743 TGCTTAGCAGAATCATCGCG 58.788 50.000 1.39 0.00 33.32 5.87
1323 2330 0.510359 CTTAGCAGAATCATCGCGGC 59.490 55.000 6.13 0.00 32.69 6.53
1496 2503 4.394712 CCGGCACTCTGGTCCACC 62.395 72.222 0.00 0.00 33.91 4.61
1586 2593 2.028484 GACGCGTCCAACACCTCA 59.972 61.111 28.61 0.00 0.00 3.86
1595 2602 1.224069 CCAACACCTCAGTCGTGCTG 61.224 60.000 3.92 3.92 46.34 4.41
1877 2884 1.208535 TCCCCGATGTCCATGTACAAC 59.791 52.381 0.00 0.00 32.02 3.32
1908 2915 3.991536 GACGGCAAGGACGAGAGCC 62.992 68.421 0.00 0.00 43.61 4.70
1958 2965 2.737376 GTGACGCGGTTCCTGGTC 60.737 66.667 12.47 0.00 0.00 4.02
2021 3028 1.604378 CGGCCAGTGGATCCTCTTT 59.396 57.895 15.20 0.00 0.00 2.52
2028 3035 1.279271 AGTGGATCCTCTTTTGGACGG 59.721 52.381 14.23 0.00 39.17 4.79
2064 3071 3.662623 GACGTCTACGCGCTCTGCA 62.663 63.158 5.73 0.00 46.97 4.41
2066 3073 2.179517 GTCTACGCGCTCTGCAGT 59.820 61.111 14.67 0.00 46.97 4.40
2143 3280 1.609208 GTTTCTATGCCATGCCCGAT 58.391 50.000 0.00 0.00 0.00 4.18
2295 3432 1.276421 CCTCGTCAACCTCCAAGACAT 59.724 52.381 0.00 0.00 32.68 3.06
2297 3434 1.967779 TCGTCAACCTCCAAGACATGA 59.032 47.619 0.00 0.00 32.68 3.07
2298 3435 2.029020 TCGTCAACCTCCAAGACATGAG 60.029 50.000 0.00 0.00 32.68 2.90
2299 3436 2.079925 GTCAACCTCCAAGACATGAGC 58.920 52.381 0.00 0.00 32.68 4.26
2300 3437 1.699083 TCAACCTCCAAGACATGAGCA 59.301 47.619 0.00 0.00 0.00 4.26
2301 3438 1.808945 CAACCTCCAAGACATGAGCAC 59.191 52.381 0.00 0.00 0.00 4.40
2302 3439 0.036952 ACCTCCAAGACATGAGCACG 60.037 55.000 0.00 0.00 0.00 5.34
2303 3440 0.247460 CCTCCAAGACATGAGCACGA 59.753 55.000 0.00 0.00 0.00 4.35
2304 3441 1.638133 CTCCAAGACATGAGCACGAG 58.362 55.000 0.00 0.00 0.00 4.18
2305 3442 0.390340 TCCAAGACATGAGCACGAGC 60.390 55.000 0.00 0.00 42.56 5.03
2395 3532 0.396435 CAGGGCACACCAAGACACTA 59.604 55.000 0.00 0.00 43.89 2.74
2416 3553 2.357034 ATTGCACTCGTCGCCGTT 60.357 55.556 0.00 0.00 35.01 4.44
2450 3587 2.830285 GCAGTCACCGTTGCCGTTT 61.830 57.895 0.00 0.00 34.28 3.60
2479 3616 1.474879 GTCTTCGTTCTGAGGAGGAGG 59.525 57.143 0.00 0.00 32.69 4.30
2483 3620 1.671901 CGTTCTGAGGAGGAGGAGGC 61.672 65.000 0.00 0.00 0.00 4.70
2515 3652 0.109226 GGAGAGTCGTGGAAGGTTCG 60.109 60.000 0.00 0.00 0.00 3.95
2522 3659 1.796796 GTGGAAGGTTCGCTGATGC 59.203 57.895 0.00 0.00 0.00 3.91
2819 3963 0.178921 TCTGGACAGGCACCTCTTCT 60.179 55.000 0.00 0.00 0.00 2.85
2820 3964 0.248843 CTGGACAGGCACCTCTTCTC 59.751 60.000 0.00 0.00 0.00 2.87
2992 4154 2.431260 GCGTTCGCCGTGAAGGTA 60.431 61.111 14.12 0.00 42.92 3.08
3212 4401 1.080025 GTGGACTTCTTCCCGTCGG 60.080 63.158 3.60 3.60 45.17 4.79
3398 4587 3.471244 GAGGGGCTCGTCGATGTCG 62.471 68.421 4.21 0.00 41.45 4.35
3599 4800 4.508124 GTCTTCTTCAACTGTAGTGGTGTG 59.492 45.833 0.00 0.00 0.00 3.82
3609 4810 2.157738 GTAGTGGTGTGTCCTAGTCGT 58.842 52.381 0.00 0.00 37.07 4.34
3610 4811 2.574006 AGTGGTGTGTCCTAGTCGTA 57.426 50.000 0.00 0.00 37.07 3.43
3707 6719 5.888982 AGGACATATAAGTAAGGGTGTGG 57.111 43.478 0.00 0.00 0.00 4.17
3708 6720 4.102681 AGGACATATAAGTAAGGGTGTGGC 59.897 45.833 0.00 0.00 0.00 5.01
3709 6721 4.102681 GGACATATAAGTAAGGGTGTGGCT 59.897 45.833 0.00 0.00 0.00 4.75
3710 6722 5.306160 GGACATATAAGTAAGGGTGTGGCTA 59.694 44.000 0.00 0.00 0.00 3.93
3712 6724 5.307196 ACATATAAGTAAGGGTGTGGCTAGG 59.693 44.000 0.00 0.00 0.00 3.02
3713 6725 2.040342 AAGTAAGGGTGTGGCTAGGT 57.960 50.000 0.00 0.00 0.00 3.08
3714 6726 1.569653 AGTAAGGGTGTGGCTAGGTC 58.430 55.000 0.00 0.00 0.00 3.85
3715 6727 1.078989 AGTAAGGGTGTGGCTAGGTCT 59.921 52.381 0.00 0.00 0.00 3.85
3717 6729 0.178903 AAGGGTGTGGCTAGGTCTCA 60.179 55.000 0.00 0.00 0.00 3.27
3718 6730 0.616111 AGGGTGTGGCTAGGTCTCAG 60.616 60.000 0.00 0.00 0.00 3.35
3719 6731 0.905337 GGGTGTGGCTAGGTCTCAGT 60.905 60.000 0.00 0.00 0.00 3.41
3720 6732 0.533032 GGTGTGGCTAGGTCTCAGTC 59.467 60.000 0.00 0.00 0.00 3.51
3721 6733 0.171455 GTGTGGCTAGGTCTCAGTCG 59.829 60.000 0.00 0.00 0.00 4.18
3722 6734 0.037734 TGTGGCTAGGTCTCAGTCGA 59.962 55.000 0.00 0.00 0.00 4.20
3724 6736 0.328592 TGGCTAGGTCTCAGTCGACT 59.671 55.000 13.58 13.58 34.38 4.18
3725 6737 0.736053 GGCTAGGTCTCAGTCGACTG 59.264 60.000 34.76 34.76 45.08 3.51
3739 6751 5.230942 CAGTCGACTGAGATTTAACCAAGT 58.769 41.667 36.73 0.00 46.59 3.16
3741 6753 5.244178 AGTCGACTGAGATTTAACCAAGTCT 59.756 40.000 19.30 0.00 33.74 3.24
3743 6755 5.477291 TCGACTGAGATTTAACCAAGTCTCT 59.523 40.000 10.14 0.00 44.05 3.10
3745 6757 6.426646 ACTGAGATTTAACCAAGTCTCTGT 57.573 37.500 13.10 13.10 45.95 3.41
3746 6758 6.459923 ACTGAGATTTAACCAAGTCTCTGTC 58.540 40.000 13.10 0.00 46.90 3.51
3749 6761 6.931281 TGAGATTTAACCAAGTCTCTGTCAAG 59.069 38.462 10.14 0.00 44.05 3.02
3752 6764 5.607939 TTAACCAAGTCTCTGTCAAGTGA 57.392 39.130 0.00 0.00 0.00 3.41
3753 6765 3.460857 ACCAAGTCTCTGTCAAGTGAC 57.539 47.619 4.43 4.43 43.98 3.67
3755 6767 2.223829 CCAAGTCTCTGTCAAGTGACGT 60.224 50.000 6.94 0.00 46.74 4.34
3757 6769 3.900388 AGTCTCTGTCAAGTGACGTAC 57.100 47.619 6.94 2.92 46.74 3.67
3758 6770 3.211865 AGTCTCTGTCAAGTGACGTACA 58.788 45.455 6.94 0.00 46.74 2.90
3759 6771 3.821600 AGTCTCTGTCAAGTGACGTACAT 59.178 43.478 6.94 0.00 46.74 2.29
3760 6772 4.320567 AGTCTCTGTCAAGTGACGTACATG 60.321 45.833 6.94 0.00 46.74 3.21
3761 6773 7.775860 AGTCTCTGTCAAGTGACGTACATGC 62.776 48.000 6.94 0.00 46.74 4.06
3764 6776 3.439932 GTCAAGTGACGTACATGCAAG 57.560 47.619 0.00 0.00 35.12 4.01
3766 6778 1.530720 CAAGTGACGTACATGCAAGCA 59.469 47.619 0.00 0.00 0.00 3.91
3768 6780 2.217750 AGTGACGTACATGCAAGCAAA 58.782 42.857 0.00 0.00 0.00 3.68
3769 6781 2.616376 AGTGACGTACATGCAAGCAAAA 59.384 40.909 0.00 0.00 0.00 2.44
3770 6782 3.253188 AGTGACGTACATGCAAGCAAAAT 59.747 39.130 0.00 0.00 0.00 1.82
3772 6784 2.840176 GACGTACATGCAAGCAAAATCG 59.160 45.455 0.00 5.33 0.00 3.34
3773 6785 2.176369 CGTACATGCAAGCAAAATCGG 58.824 47.619 0.00 0.00 0.00 4.18
3775 6787 2.818130 ACATGCAAGCAAAATCGGTT 57.182 40.000 0.00 0.00 0.00 4.44
3777 6789 4.454728 ACATGCAAGCAAAATCGGTTAT 57.545 36.364 0.00 0.00 0.00 1.89
3778 6790 4.819769 ACATGCAAGCAAAATCGGTTATT 58.180 34.783 0.00 0.00 0.00 1.40
3779 6791 5.960113 ACATGCAAGCAAAATCGGTTATTA 58.040 33.333 0.00 0.00 0.00 0.98
3780 6792 6.035843 ACATGCAAGCAAAATCGGTTATTAG 58.964 36.000 0.00 0.00 0.00 1.73
3781 6793 4.420168 TGCAAGCAAAATCGGTTATTAGC 58.580 39.130 0.00 0.00 0.00 3.09
3782 6794 4.082517 TGCAAGCAAAATCGGTTATTAGCA 60.083 37.500 0.00 0.00 33.43 3.49
3783 6795 4.265320 GCAAGCAAAATCGGTTATTAGCAC 59.735 41.667 0.00 0.00 33.43 4.40
3784 6796 5.640732 CAAGCAAAATCGGTTATTAGCACT 58.359 37.500 0.00 0.00 33.43 4.40
3785 6797 5.235305 AGCAAAATCGGTTATTAGCACTG 57.765 39.130 0.00 0.00 33.43 3.66
3786 6798 4.941263 AGCAAAATCGGTTATTAGCACTGA 59.059 37.500 0.00 0.00 33.43 3.41
3787 6799 5.065218 AGCAAAATCGGTTATTAGCACTGAG 59.935 40.000 0.00 0.00 32.96 3.35
3788 6800 5.730568 GCAAAATCGGTTATTAGCACTGAGG 60.731 44.000 0.00 0.00 32.96 3.86
3789 6801 3.753294 ATCGGTTATTAGCACTGAGGG 57.247 47.619 0.00 0.00 32.96 4.30
3791 6803 1.485066 CGGTTATTAGCACTGAGGGGT 59.515 52.381 0.00 0.00 0.00 4.95
3792 6804 2.093128 CGGTTATTAGCACTGAGGGGTT 60.093 50.000 0.00 0.00 0.00 4.11
3793 6805 3.621461 CGGTTATTAGCACTGAGGGGTTT 60.621 47.826 0.00 0.00 0.00 3.27
3794 6806 4.383335 CGGTTATTAGCACTGAGGGGTTTA 60.383 45.833 0.00 0.00 0.00 2.01
3796 6808 5.356190 GGTTATTAGCACTGAGGGGTTTAAC 59.644 44.000 0.00 1.37 0.00 2.01
3797 6809 3.428413 TTAGCACTGAGGGGTTTAACC 57.572 47.619 5.40 5.40 37.60 2.85
3875 6947 5.580691 TGAACAATCATGAATACCTGTCGTC 59.419 40.000 0.00 0.00 0.00 4.20
3889 6961 5.230942 ACCTGTCGTCAAACTCTTATCTTG 58.769 41.667 0.00 0.00 0.00 3.02
3892 6964 6.308282 CCTGTCGTCAAACTCTTATCTTGTAC 59.692 42.308 0.00 0.00 0.00 2.90
3894 6966 5.855395 GTCGTCAAACTCTTATCTTGTACGT 59.145 40.000 0.00 0.00 31.57 3.57
3972 7044 6.097356 TGTACCGTGCAAAAACAAATGTAAA 58.903 32.000 0.00 0.00 0.00 2.01
4088 7160 6.257630 ACAAGATTGCAAACATTAAACACACC 59.742 34.615 1.71 0.00 0.00 4.16
4092 7164 3.128764 TGCAAACATTAAACACACCGTCA 59.871 39.130 0.00 0.00 0.00 4.35
4096 7168 6.431278 CAAACATTAAACACACCGTCACATA 58.569 36.000 0.00 0.00 0.00 2.29
4355 7428 9.781834 TCTTGTTATACTTTGTGTTCAAACAAG 57.218 29.630 15.07 15.07 43.40 3.16
4356 7429 8.918961 TTGTTATACTTTGTGTTCAAACAAGG 57.081 30.769 0.00 0.00 40.93 3.61
4386 7459 7.566858 AAAAGAATTATGTCATGAAACGCAC 57.433 32.000 0.00 0.00 0.00 5.34
4387 7460 5.878332 AGAATTATGTCATGAAACGCACA 57.122 34.783 0.00 0.00 0.00 4.57
4388 7461 5.631026 AGAATTATGTCATGAAACGCACAC 58.369 37.500 0.00 0.00 0.00 3.82
4389 7462 5.181056 AGAATTATGTCATGAAACGCACACA 59.819 36.000 0.00 0.00 0.00 3.72
4390 7463 4.820284 TTATGTCATGAAACGCACACAA 57.180 36.364 0.00 0.00 0.00 3.33
4391 7464 2.466870 TGTCATGAAACGCACACAAC 57.533 45.000 0.00 0.00 0.00 3.32
4392 7465 1.740025 TGTCATGAAACGCACACAACA 59.260 42.857 0.00 0.00 0.00 3.33
4393 7466 2.108700 GTCATGAAACGCACACAACAC 58.891 47.619 0.00 0.00 0.00 3.32
4394 7467 1.740025 TCATGAAACGCACACAACACA 59.260 42.857 0.00 0.00 0.00 3.72
4395 7468 2.110990 CATGAAACGCACACAACACAG 58.889 47.619 0.00 0.00 0.00 3.66
4396 7469 0.449786 TGAAACGCACACAACACAGG 59.550 50.000 0.00 0.00 0.00 4.00
4397 7470 0.865639 GAAACGCACACAACACAGGC 60.866 55.000 0.00 0.00 0.00 4.85
4398 7471 1.590610 AAACGCACACAACACAGGCA 61.591 50.000 0.00 0.00 0.00 4.75
4399 7472 2.024588 CGCACACAACACAGGCAC 59.975 61.111 0.00 0.00 0.00 5.01
4400 7473 2.759123 CGCACACAACACAGGCACA 61.759 57.895 0.00 0.00 0.00 4.57
4401 7474 1.226660 GCACACAACACAGGCACAC 60.227 57.895 0.00 0.00 0.00 3.82
4402 7475 1.932011 GCACACAACACAGGCACACA 61.932 55.000 0.00 0.00 0.00 3.72
4403 7476 0.179166 CACACAACACAGGCACACAC 60.179 55.000 0.00 0.00 0.00 3.82
4404 7477 0.607762 ACACAACACAGGCACACACA 60.608 50.000 0.00 0.00 0.00 3.72
4405 7478 0.179166 CACAACACAGGCACACACAC 60.179 55.000 0.00 0.00 0.00 3.82
4406 7479 0.607762 ACAACACAGGCACACACACA 60.608 50.000 0.00 0.00 0.00 3.72
4407 7480 0.740149 CAACACAGGCACACACACAT 59.260 50.000 0.00 0.00 0.00 3.21
4408 7481 1.134753 CAACACAGGCACACACACATT 59.865 47.619 0.00 0.00 0.00 2.71
4409 7482 1.024271 ACACAGGCACACACACATTC 58.976 50.000 0.00 0.00 0.00 2.67
4410 7483 1.023502 CACAGGCACACACACATTCA 58.976 50.000 0.00 0.00 0.00 2.57
4411 7484 1.610038 CACAGGCACACACACATTCAT 59.390 47.619 0.00 0.00 0.00 2.57
4412 7485 1.881973 ACAGGCACACACACATTCATC 59.118 47.619 0.00 0.00 0.00 2.92
4413 7486 1.200716 CAGGCACACACACATTCATCC 59.799 52.381 0.00 0.00 0.00 3.51
4414 7487 1.202915 AGGCACACACACATTCATCCA 60.203 47.619 0.00 0.00 0.00 3.41
4415 7488 1.068333 GGCACACACACATTCATCCAC 60.068 52.381 0.00 0.00 0.00 4.02
4416 7489 1.400113 GCACACACACATTCATCCACG 60.400 52.381 0.00 0.00 0.00 4.94
4417 7490 0.874390 ACACACACATTCATCCACGC 59.126 50.000 0.00 0.00 0.00 5.34
4418 7491 0.873721 CACACACATTCATCCACGCA 59.126 50.000 0.00 0.00 0.00 5.24
4419 7492 1.266446 CACACACATTCATCCACGCAA 59.734 47.619 0.00 0.00 0.00 4.85
4421 7494 0.523072 ACACATTCATCCACGCAAGC 59.477 50.000 0.00 0.00 45.62 4.01
4422 7495 0.521867 CACATTCATCCACGCAAGCG 60.522 55.000 13.50 13.50 46.03 4.68
4423 7496 1.584483 CATTCATCCACGCAAGCGC 60.584 57.895 15.09 0.00 44.19 5.92
4424 7497 2.039974 ATTCATCCACGCAAGCGCA 61.040 52.632 15.09 0.00 44.19 6.09
4425 7498 2.257286 ATTCATCCACGCAAGCGCAC 62.257 55.000 15.09 0.00 44.19 5.34
4426 7499 3.725459 CATCCACGCAAGCGCACA 61.725 61.111 15.09 0.00 44.19 4.57
4427 7500 2.747460 ATCCACGCAAGCGCACAT 60.747 55.556 15.09 0.58 44.19 3.21
4428 7501 3.042842 ATCCACGCAAGCGCACATG 62.043 57.895 15.09 6.85 44.19 3.21
4429 7502 4.029186 CCACGCAAGCGCACATGT 62.029 61.111 15.09 0.00 44.19 3.21
4430 7503 2.500369 CACGCAAGCGCACATGTC 60.500 61.111 15.09 1.54 44.19 3.06
4431 7504 3.726517 ACGCAAGCGCACATGTCC 61.727 61.111 15.09 0.00 44.19 4.02
4432 7505 3.725459 CGCAAGCGCACATGTCCA 61.725 61.111 11.47 0.00 38.40 4.02
4433 7506 2.126734 GCAAGCGCACATGTCCAC 60.127 61.111 11.47 0.00 38.36 4.02
4434 7507 2.174107 CAAGCGCACATGTCCACG 59.826 61.111 11.47 1.24 0.00 4.94
4439 7512 2.703409 GCACATGTCCACGCGATC 59.297 61.111 15.93 0.00 0.00 3.69
4440 7513 2.813179 GCACATGTCCACGCGATCC 61.813 63.158 15.93 0.00 0.00 3.36
4441 7514 2.202743 ACATGTCCACGCGATCCG 60.203 61.111 15.93 0.00 44.21 4.18
4457 7530 5.079397 CGATCCGCTTTCTTTTATACACC 57.921 43.478 0.00 0.00 0.00 4.16
4458 7531 4.025145 CGATCCGCTTTCTTTTATACACCC 60.025 45.833 0.00 0.00 0.00 4.61
4459 7532 4.563140 TCCGCTTTCTTTTATACACCCT 57.437 40.909 0.00 0.00 0.00 4.34
4460 7533 4.258543 TCCGCTTTCTTTTATACACCCTG 58.741 43.478 0.00 0.00 0.00 4.45
4461 7534 4.007659 CCGCTTTCTTTTATACACCCTGT 58.992 43.478 0.00 0.00 0.00 4.00
4462 7535 5.046448 TCCGCTTTCTTTTATACACCCTGTA 60.046 40.000 0.00 0.00 37.24 2.74
4463 7536 5.820947 CCGCTTTCTTTTATACACCCTGTAT 59.179 40.000 0.79 0.79 44.89 2.29
4464 7537 6.987992 CCGCTTTCTTTTATACACCCTGTATA 59.012 38.462 0.00 0.00 41.41 1.47
4479 7552 9.623000 ACACCCTGTATAAACAAATATAAGACC 57.377 33.333 0.00 0.00 34.49 3.85
4480 7553 9.621629 CACCCTGTATAAACAAATATAAGACCA 57.378 33.333 0.00 0.00 34.49 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.752903 GGAATGTTGGTACATGTCCCAC 59.247 50.000 10.09 10.01 44.14 4.61
1 2 2.376855 TGGAATGTTGGTACATGTCCCA 59.623 45.455 5.96 5.96 44.14 4.37
5 6 4.280677 CCTTGTTGGAATGTTGGTACATGT 59.719 41.667 2.69 2.69 44.14 3.21
9 10 2.029380 GCCCTTGTTGGAATGTTGGTAC 60.029 50.000 0.00 0.00 38.35 3.34
18 19 1.912763 GCCATGGCCCTTGTTGGAA 60.913 57.895 27.24 0.00 38.35 3.53
21 22 2.676121 TCGCCATGGCCCTTGTTG 60.676 61.111 30.79 14.90 37.98 3.33
23 24 4.740822 GGTCGCCATGGCCCTTGT 62.741 66.667 30.79 0.00 37.98 3.16
59 60 6.808008 TTGTCTTCTTGATTGACAATCTCC 57.192 37.500 24.80 4.35 43.15 3.71
65 66 7.345422 TCCATTTTTGTCTTCTTGATTGACA 57.655 32.000 0.00 0.00 38.71 3.58
78 79 8.693504 CATGCACGAAATATATCCATTTTTGTC 58.306 33.333 0.00 0.00 0.00 3.18
86 87 6.238621 GGAACAACATGCACGAAATATATCCA 60.239 38.462 0.00 0.00 0.00 3.41
87 88 6.142817 GGAACAACATGCACGAAATATATCC 58.857 40.000 0.00 0.00 0.00 2.59
89 90 6.238731 CCTGGAACAACATGCACGAAATATAT 60.239 38.462 0.00 0.00 38.70 0.86
90 91 5.065859 CCTGGAACAACATGCACGAAATATA 59.934 40.000 0.00 0.00 38.70 0.86
92 93 3.190327 CCTGGAACAACATGCACGAAATA 59.810 43.478 0.00 0.00 38.70 1.40
93 94 2.030007 CCTGGAACAACATGCACGAAAT 60.030 45.455 0.00 0.00 38.70 2.17
101 126 2.496899 AGGCTACCTGGAACAACATG 57.503 50.000 0.00 0.00 38.70 3.21
164 189 1.153449 TTAGCGCCAGTGGGAATCG 60.153 57.895 12.15 6.93 35.59 3.34
168 193 3.003173 AGCTTAGCGCCAGTGGGA 61.003 61.111 12.15 0.00 40.39 4.37
188 213 0.597637 GGTGTCACAGTCACGTGAGG 60.598 60.000 20.73 16.70 46.23 3.86
193 218 1.660575 GGTCGGTGTCACAGTCACG 60.661 63.158 5.12 0.00 36.76 4.35
319 361 2.755469 CCACGCAAATCCAGGGGG 60.755 66.667 0.00 0.00 0.00 5.40
341 383 1.586028 GTCAACATGCAACCGCCAT 59.414 52.632 0.00 0.00 37.32 4.40
378 434 8.958119 AGTAATCAAGTGTTAACTCACTCAAA 57.042 30.769 7.22 0.00 46.25 2.69
379 435 7.656137 GGAGTAATCAAGTGTTAACTCACTCAA 59.344 37.037 17.84 5.17 46.25 3.02
380 436 7.152645 GGAGTAATCAAGTGTTAACTCACTCA 58.847 38.462 17.84 4.24 46.25 3.41
455 533 2.519441 CGAGGGGAGGGTATCGGA 59.481 66.667 0.00 0.00 0.00 4.55
553 653 1.134560 CCTTAGCTCGATATACCCGGC 59.865 57.143 0.00 0.00 0.00 6.13
555 655 2.683867 CTCCCTTAGCTCGATATACCCG 59.316 54.545 0.00 0.00 0.00 5.28
556 656 3.965694 TCTCCCTTAGCTCGATATACCC 58.034 50.000 0.00 0.00 0.00 3.69
569 669 1.295423 GGCGCACTGTTCTCCCTTA 59.705 57.895 10.83 0.00 0.00 2.69
572 672 3.050275 GTGGCGCACTGTTCTCCC 61.050 66.667 10.83 0.00 0.00 4.30
587 697 1.202405 GGTGAACTTTTGGGTGCAGTG 60.202 52.381 0.00 0.00 0.00 3.66
588 698 1.111277 GGTGAACTTTTGGGTGCAGT 58.889 50.000 0.00 0.00 0.00 4.40
634 744 2.125106 GCTCCACATGGACGGACC 60.125 66.667 0.00 0.00 39.78 4.46
657 767 0.038892 TTTCGCCAGACAGTCGTACC 60.039 55.000 0.00 0.00 0.00 3.34
667 799 3.345808 GCGTGCTGTTTCGCCAGA 61.346 61.111 0.00 0.00 45.54 3.86
729 870 2.368875 ACTTTGGTTCATCTCACCTCGT 59.631 45.455 0.00 0.00 35.07 4.18
800 947 4.475527 AACAGCGGAAAGGTGGTC 57.524 55.556 0.00 0.00 46.85 4.02
804 951 1.375326 GGAGGAACAGCGGAAAGGT 59.625 57.895 0.00 0.00 0.00 3.50
805 952 1.377333 GGGAGGAACAGCGGAAAGG 60.377 63.158 0.00 0.00 0.00 3.11
807 954 1.846124 AGGGGAGGAACAGCGGAAA 60.846 57.895 0.00 0.00 0.00 3.13
808 955 2.203938 AGGGGAGGAACAGCGGAA 60.204 61.111 0.00 0.00 0.00 4.30
811 958 2.046892 CACAGGGGAGGAACAGCG 60.047 66.667 0.00 0.00 0.00 5.18
812 959 0.606673 GTTCACAGGGGAGGAACAGC 60.607 60.000 0.00 0.00 40.39 4.40
813 960 0.320771 CGTTCACAGGGGAGGAACAG 60.321 60.000 0.00 0.00 40.62 3.16
814 961 0.761323 TCGTTCACAGGGGAGGAACA 60.761 55.000 0.00 0.00 40.62 3.18
823 986 1.811266 CTGGCCGATCGTTCACAGG 60.811 63.158 15.09 0.00 0.00 4.00
863 1857 2.272471 GGCGAAAAGGAGAGGGGG 59.728 66.667 0.00 0.00 0.00 5.40
889 1883 5.406780 CCTGAATTACTGACAGTGAAGACAC 59.593 44.000 18.58 4.15 46.24 3.67
890 1884 5.070446 ACCTGAATTACTGACAGTGAAGACA 59.930 40.000 18.58 10.37 0.00 3.41
891 1885 5.542779 ACCTGAATTACTGACAGTGAAGAC 58.457 41.667 18.58 6.61 0.00 3.01
904 1898 7.907214 ACAAGACAACAGATACCTGAATTAC 57.093 36.000 0.00 0.00 43.02 1.89
905 1899 7.094805 GCAACAAGACAACAGATACCTGAATTA 60.095 37.037 0.00 0.00 43.02 1.40
906 1900 6.294176 GCAACAAGACAACAGATACCTGAATT 60.294 38.462 0.00 0.00 43.02 2.17
907 1901 5.182001 GCAACAAGACAACAGATACCTGAAT 59.818 40.000 0.00 0.00 43.02 2.57
908 1902 4.515191 GCAACAAGACAACAGATACCTGAA 59.485 41.667 0.00 0.00 43.02 3.02
909 1903 4.065088 GCAACAAGACAACAGATACCTGA 58.935 43.478 0.00 0.00 43.02 3.86
910 1904 3.189287 GGCAACAAGACAACAGATACCTG 59.811 47.826 0.00 0.00 45.76 4.00
911 1905 3.412386 GGCAACAAGACAACAGATACCT 58.588 45.455 0.00 0.00 0.00 3.08
912 1906 2.159627 CGGCAACAAGACAACAGATACC 59.840 50.000 0.00 0.00 0.00 2.73
956 1950 2.262915 GACTGAGTGGCCTGGACG 59.737 66.667 3.32 0.00 0.00 4.79
959 1953 4.087892 CCGGACTGAGTGGCCTGG 62.088 72.222 3.32 0.00 43.44 4.45
1013 2012 2.125912 CGGAGAAGCACGGTCCAG 60.126 66.667 0.00 0.00 0.00 3.86
1056 2055 0.036952 CTCCTCGCAGAAGCAGGAAA 60.037 55.000 8.99 0.00 43.00 3.13
1092 2091 2.830264 GGCGACGGTGTTTGTATCA 58.170 52.632 0.00 0.00 0.00 2.15
1135 2134 1.004440 GCTTGGACACGAGCCTCTT 60.004 57.895 0.00 0.00 46.50 2.85
1199 2198 3.566210 CGGAGGGGTGGGTGTTGT 61.566 66.667 0.00 0.00 0.00 3.32
1207 2206 0.033405 TAAGGAGAGTCGGAGGGGTG 60.033 60.000 0.00 0.00 0.00 4.61
1230 2234 0.818040 ACCCGCAAGACCACAAGAAC 60.818 55.000 0.00 0.00 43.02 3.01
1248 2252 7.044181 TGAGAACCATTCAGAATCTGTATCAC 58.956 38.462 10.36 0.00 32.61 3.06
1262 2266 5.106555 ACACGACAATCATTGAGAACCATTC 60.107 40.000 3.79 0.00 0.00 2.67
1263 2267 4.761739 ACACGACAATCATTGAGAACCATT 59.238 37.500 3.79 0.00 0.00 3.16
1267 2271 4.702392 GTCACACGACAATCATTGAGAAC 58.298 43.478 3.79 0.00 42.13 3.01
1292 2299 1.672363 TCTGCTAAGCATGCGAAATGG 59.328 47.619 13.01 3.54 38.13 3.16
1305 2312 0.179086 TGCCGCGATGATTCTGCTAA 60.179 50.000 8.23 0.00 0.00 3.09
1306 2313 0.875908 GTGCCGCGATGATTCTGCTA 60.876 55.000 8.23 0.00 0.00 3.49
1321 2328 2.536997 AATGCCGAGGTACCAGTGCC 62.537 60.000 15.94 0.00 35.42 5.01
1323 2330 1.086696 CAAATGCCGAGGTACCAGTG 58.913 55.000 15.94 2.68 0.00 3.66
1409 2416 1.388065 TAGAGAGCTGCGAGGAAGCC 61.388 60.000 0.00 0.00 41.82 4.35
1506 2513 2.362120 GCTGCTGGGTGGAATGCT 60.362 61.111 0.00 0.00 0.00 3.79
1511 2518 3.640407 GTGGAGCTGCTGGGTGGA 61.640 66.667 7.01 0.00 0.00 4.02
1586 2593 2.341543 CTCTGCCACAGCACGACT 59.658 61.111 0.00 0.00 46.52 4.18
1595 2602 2.029844 GTGGTCGAAGCTCTGCCAC 61.030 63.158 11.96 11.96 42.03 5.01
1682 2689 2.098831 GTAGCCCTTCCACGCGAAC 61.099 63.158 15.93 0.00 0.00 3.95
1727 2734 3.068691 TTCGGGTCGAGCTCCAGG 61.069 66.667 15.18 0.00 37.14 4.45
1730 2737 4.493747 CCGTTCGGGTCGAGCTCC 62.494 72.222 15.18 0.00 37.14 4.70
1839 2846 2.224402 GGGAGTTGCTATAGGCCTTCAG 60.224 54.545 12.58 10.03 40.92 3.02
1877 2884 2.277120 CCGTCGACGTAGCCGAAG 60.277 66.667 33.49 14.06 37.81 3.79
1908 2915 3.058432 TCCTTGACGTCGTAGAAGAAGTG 60.058 47.826 16.49 5.71 38.59 3.16
1958 2965 4.129737 ATCTGGCCCGTCACGTCG 62.130 66.667 0.00 0.00 0.00 5.12
2021 3028 4.344865 GCCTTGGGCTCCGTCCAA 62.345 66.667 0.00 0.00 45.69 3.53
2279 3416 2.079925 GCTCATGTCTTGGAGGTTGAC 58.920 52.381 0.00 0.00 0.00 3.18
2295 3432 4.303993 TGCTGCTGCTCGTGCTCA 62.304 61.111 17.00 7.75 40.48 4.26
2297 3434 4.311445 AGTGCTGCTGCTCGTGCT 62.311 61.111 17.00 4.60 40.48 4.40
2298 3435 4.086178 CAGTGCTGCTGCTCGTGC 62.086 66.667 17.00 1.71 38.52 5.34
2299 3436 3.420606 CCAGTGCTGCTGCTCGTG 61.421 66.667 17.00 10.54 43.71 4.35
2302 3439 3.735029 GTGCCAGTGCTGCTGCTC 61.735 66.667 17.00 13.08 43.71 4.26
2382 3519 4.216257 GTGCAATGATTAGTGTCTTGGTGT 59.784 41.667 0.00 0.00 0.00 4.16
2395 3532 2.089854 GGCGACGAGTGCAATGATT 58.910 52.632 0.00 0.00 0.00 2.57
2450 3587 2.356695 TCAGAACGAAGACTGACACGAA 59.643 45.455 0.00 0.00 38.72 3.85
2479 3616 2.694760 CCTTTGCGCCTTCAGCCTC 61.695 63.158 4.18 0.00 38.78 4.70
2483 3620 0.321122 ACTCTCCTTTGCGCCTTCAG 60.321 55.000 4.18 0.00 0.00 3.02
2515 3652 1.693083 GGTACGTGAACGGCATCAGC 61.693 60.000 7.86 0.00 44.95 4.26
2800 3943 0.178921 AGAAGAGGTGCCTGTCCAGA 60.179 55.000 0.00 0.00 0.00 3.86
3280 4469 2.203788 TCCACCTCGCCAACCTCT 60.204 61.111 0.00 0.00 0.00 3.69
3599 4800 7.011763 TCAGTACAACACATATACGACTAGGAC 59.988 40.741 0.00 0.00 0.00 3.85
3609 4810 7.412853 TGCCTAGTTCAGTACAACACATATA 57.587 36.000 0.00 0.00 0.00 0.86
3610 4811 6.294361 TGCCTAGTTCAGTACAACACATAT 57.706 37.500 0.00 0.00 0.00 1.78
3683 6695 6.013639 GCCACACCCTTACTTATATGTCCTAT 60.014 42.308 0.00 0.00 0.00 2.57
3684 6696 5.306160 GCCACACCCTTACTTATATGTCCTA 59.694 44.000 0.00 0.00 0.00 2.94
3685 6697 4.102681 GCCACACCCTTACTTATATGTCCT 59.897 45.833 0.00 0.00 0.00 3.85
3686 6698 4.102681 AGCCACACCCTTACTTATATGTCC 59.897 45.833 0.00 0.00 0.00 4.02
3687 6699 5.291905 AGCCACACCCTTACTTATATGTC 57.708 43.478 0.00 0.00 0.00 3.06
3688 6700 5.307196 CCTAGCCACACCCTTACTTATATGT 59.693 44.000 0.00 0.00 0.00 2.29
3689 6701 5.307196 ACCTAGCCACACCCTTACTTATATG 59.693 44.000 0.00 0.00 0.00 1.78
3690 6702 5.474199 ACCTAGCCACACCCTTACTTATAT 58.526 41.667 0.00 0.00 0.00 0.86
3691 6703 4.887367 ACCTAGCCACACCCTTACTTATA 58.113 43.478 0.00 0.00 0.00 0.98
3692 6704 3.710165 GACCTAGCCACACCCTTACTTAT 59.290 47.826 0.00 0.00 0.00 1.73
3693 6705 3.102204 GACCTAGCCACACCCTTACTTA 58.898 50.000 0.00 0.00 0.00 2.24
3694 6706 1.907255 GACCTAGCCACACCCTTACTT 59.093 52.381 0.00 0.00 0.00 2.24
3695 6707 1.078989 AGACCTAGCCACACCCTTACT 59.921 52.381 0.00 0.00 0.00 2.24
3696 6708 1.481363 GAGACCTAGCCACACCCTTAC 59.519 57.143 0.00 0.00 0.00 2.34
3697 6709 1.078159 TGAGACCTAGCCACACCCTTA 59.922 52.381 0.00 0.00 0.00 2.69
3698 6710 0.178903 TGAGACCTAGCCACACCCTT 60.179 55.000 0.00 0.00 0.00 3.95
3699 6711 0.616111 CTGAGACCTAGCCACACCCT 60.616 60.000 0.00 0.00 0.00 4.34
3700 6712 0.905337 ACTGAGACCTAGCCACACCC 60.905 60.000 0.00 0.00 0.00 4.61
3701 6713 0.533032 GACTGAGACCTAGCCACACC 59.467 60.000 0.00 0.00 0.00 4.16
3704 6716 0.452585 GTCGACTGAGACCTAGCCAC 59.547 60.000 8.70 0.00 35.22 5.01
3717 6729 5.244178 AGACTTGGTTAAATCTCAGTCGACT 59.756 40.000 13.58 13.58 0.00 4.18
3718 6730 5.471257 AGACTTGGTTAAATCTCAGTCGAC 58.529 41.667 7.70 7.70 0.00 4.20
3719 6731 5.477291 AGAGACTTGGTTAAATCTCAGTCGA 59.523 40.000 3.18 0.00 40.10 4.20
3720 6732 5.574830 CAGAGACTTGGTTAAATCTCAGTCG 59.425 44.000 3.18 0.00 40.10 4.18
3721 6733 6.459923 ACAGAGACTTGGTTAAATCTCAGTC 58.540 40.000 3.18 0.00 40.10 3.51
3722 6734 6.042093 TGACAGAGACTTGGTTAAATCTCAGT 59.958 38.462 3.18 0.88 39.70 3.41
3724 6736 6.419484 TGACAGAGACTTGGTTAAATCTCA 57.581 37.500 3.18 0.00 40.10 3.27
3725 6737 6.931840 ACTTGACAGAGACTTGGTTAAATCTC 59.068 38.462 0.00 0.00 38.30 2.75
3726 6738 6.708054 CACTTGACAGAGACTTGGTTAAATCT 59.292 38.462 0.00 0.00 0.00 2.40
3727 6739 6.706270 TCACTTGACAGAGACTTGGTTAAATC 59.294 38.462 0.00 0.00 0.00 2.17
3728 6740 6.483640 GTCACTTGACAGAGACTTGGTTAAAT 59.516 38.462 4.43 0.00 44.18 1.40
3729 6741 5.815740 GTCACTTGACAGAGACTTGGTTAAA 59.184 40.000 4.43 0.00 44.18 1.52
3731 6743 4.499188 CGTCACTTGACAGAGACTTGGTTA 60.499 45.833 9.94 0.00 44.99 2.85
3732 6744 3.738281 CGTCACTTGACAGAGACTTGGTT 60.738 47.826 9.94 0.00 44.99 3.67
3734 6746 2.223829 ACGTCACTTGACAGAGACTTGG 60.224 50.000 9.94 0.00 44.99 3.61
3735 6747 3.085443 ACGTCACTTGACAGAGACTTG 57.915 47.619 9.94 0.00 44.99 3.16
3736 6748 3.630769 TGTACGTCACTTGACAGAGACTT 59.369 43.478 9.94 0.00 44.99 3.01
3737 6749 3.211865 TGTACGTCACTTGACAGAGACT 58.788 45.455 9.94 0.00 44.99 3.24
3739 6751 3.611766 GCATGTACGTCACTTGACAGAGA 60.612 47.826 9.94 0.00 44.99 3.10
3741 6753 2.035321 TGCATGTACGTCACTTGACAGA 59.965 45.455 9.94 0.00 44.99 3.41
3743 6755 2.517650 TGCATGTACGTCACTTGACA 57.482 45.000 9.94 0.00 44.99 3.58
3745 6757 1.798223 GCTTGCATGTACGTCACTTGA 59.202 47.619 0.00 0.00 34.91 3.02
3746 6758 1.530720 TGCTTGCATGTACGTCACTTG 59.469 47.619 0.00 0.00 35.82 3.16
3749 6761 2.679355 TTTGCTTGCATGTACGTCAC 57.321 45.000 0.00 0.00 0.00 3.67
3752 6764 2.414029 CCGATTTTGCTTGCATGTACGT 60.414 45.455 0.00 0.00 0.00 3.57
3753 6765 2.176369 CCGATTTTGCTTGCATGTACG 58.824 47.619 1.14 1.67 0.00 3.67
3755 6767 3.932545 AACCGATTTTGCTTGCATGTA 57.067 38.095 1.14 0.00 0.00 2.29
3757 6769 5.051508 GCTAATAACCGATTTTGCTTGCATG 60.052 40.000 0.00 0.00 0.00 4.06
3758 6770 5.043248 GCTAATAACCGATTTTGCTTGCAT 58.957 37.500 0.00 0.00 0.00 3.96
3759 6771 4.082517 TGCTAATAACCGATTTTGCTTGCA 60.083 37.500 0.00 0.00 31.21 4.08
3760 6772 4.265320 GTGCTAATAACCGATTTTGCTTGC 59.735 41.667 0.00 0.00 31.21 4.01
3761 6773 5.512788 CAGTGCTAATAACCGATTTTGCTTG 59.487 40.000 0.00 0.00 31.21 4.01
3762 6774 5.414454 TCAGTGCTAATAACCGATTTTGCTT 59.586 36.000 0.00 0.00 31.21 3.91
3764 6776 5.229921 TCAGTGCTAATAACCGATTTTGC 57.770 39.130 0.00 0.00 0.00 3.68
3766 6778 4.881850 CCCTCAGTGCTAATAACCGATTTT 59.118 41.667 0.00 0.00 0.00 1.82
3768 6780 3.181454 CCCCTCAGTGCTAATAACCGATT 60.181 47.826 0.00 0.00 0.00 3.34
3769 6781 2.368875 CCCCTCAGTGCTAATAACCGAT 59.631 50.000 0.00 0.00 0.00 4.18
3770 6782 1.760613 CCCCTCAGTGCTAATAACCGA 59.239 52.381 0.00 0.00 0.00 4.69
3772 6784 3.646736 AACCCCTCAGTGCTAATAACC 57.353 47.619 0.00 0.00 0.00 2.85
3773 6785 5.356190 GGTTAAACCCCTCAGTGCTAATAAC 59.644 44.000 0.00 0.00 30.04 1.89
3775 6787 5.106876 GGTTAAACCCCTCAGTGCTAATA 57.893 43.478 0.00 0.00 30.04 0.98
3777 6789 3.428413 GGTTAAACCCCTCAGTGCTAA 57.572 47.619 0.00 0.00 30.04 3.09
3853 6925 5.487433 TGACGACAGGTATTCATGATTGTT 58.513 37.500 0.00 0.00 0.00 2.83
3892 6964 7.061789 GCCAATTTTAGTTGTTCCAATTCTACG 59.938 37.037 0.00 0.00 0.00 3.51
3894 6966 7.870445 GTGCCAATTTTAGTTGTTCCAATTCTA 59.130 33.333 0.00 0.00 0.00 2.10
3908 6980 6.215121 TGAGTGATTTGTGTGCCAATTTTAG 58.785 36.000 0.00 0.00 31.81 1.85
4046 7118 8.375465 GCAATCTTGTGACACTATTAATTTTGC 58.625 33.333 7.20 7.22 0.00 3.68
4047 7119 9.409312 TGCAATCTTGTGACACTATTAATTTTG 57.591 29.630 7.20 0.00 0.00 2.44
4049 7121 9.979578 TTTGCAATCTTGTGACACTATTAATTT 57.020 25.926 7.20 0.00 0.00 1.82
4050 7122 9.410556 GTTTGCAATCTTGTGACACTATTAATT 57.589 29.630 7.20 0.00 0.00 1.40
4051 7123 8.575589 TGTTTGCAATCTTGTGACACTATTAAT 58.424 29.630 7.20 0.00 0.00 1.40
4052 7124 7.935520 TGTTTGCAATCTTGTGACACTATTAA 58.064 30.769 7.20 0.00 0.00 1.40
4053 7125 7.503521 TGTTTGCAATCTTGTGACACTATTA 57.496 32.000 7.20 0.00 0.00 0.98
4125 7197 8.753497 ATCTTAGTTATGTCCATTCCCTTTTC 57.247 34.615 0.00 0.00 0.00 2.29
4238 7311 9.783081 ATCATTTGCTTTTATGTTTTTCCTTCT 57.217 25.926 0.00 0.00 0.00 2.85
4339 7412 6.777526 TTTTGTCCTTGTTTGAACACAAAG 57.222 33.333 0.00 0.00 38.92 2.77
4365 7438 5.181056 TGTGTGCGTTTCATGACATAATTCT 59.819 36.000 0.00 0.00 0.00 2.40
4373 7446 2.108700 GTGTTGTGTGCGTTTCATGAC 58.891 47.619 0.00 0.00 0.00 3.06
4374 7447 1.740025 TGTGTTGTGTGCGTTTCATGA 59.260 42.857 0.00 0.00 0.00 3.07
4375 7448 2.110990 CTGTGTTGTGTGCGTTTCATG 58.889 47.619 0.00 0.00 0.00 3.07
4376 7449 1.065401 CCTGTGTTGTGTGCGTTTCAT 59.935 47.619 0.00 0.00 0.00 2.57
4377 7450 0.449786 CCTGTGTTGTGTGCGTTTCA 59.550 50.000 0.00 0.00 0.00 2.69
4378 7451 0.865639 GCCTGTGTTGTGTGCGTTTC 60.866 55.000 0.00 0.00 0.00 2.78
4379 7452 1.138671 GCCTGTGTTGTGTGCGTTT 59.861 52.632 0.00 0.00 0.00 3.60
4380 7453 2.043405 TGCCTGTGTTGTGTGCGTT 61.043 52.632 0.00 0.00 0.00 4.84
4381 7454 2.437537 TGCCTGTGTTGTGTGCGT 60.438 55.556 0.00 0.00 0.00 5.24
4382 7455 2.024588 GTGCCTGTGTTGTGTGCG 59.975 61.111 0.00 0.00 0.00 5.34
4383 7456 1.226660 GTGTGCCTGTGTTGTGTGC 60.227 57.895 0.00 0.00 0.00 4.57
4384 7457 0.179166 GTGTGTGCCTGTGTTGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
4385 7458 0.607762 TGTGTGTGCCTGTGTTGTGT 60.608 50.000 0.00 0.00 0.00 3.72
4386 7459 0.179166 GTGTGTGTGCCTGTGTTGTG 60.179 55.000 0.00 0.00 0.00 3.33
4387 7460 0.607762 TGTGTGTGTGCCTGTGTTGT 60.608 50.000 0.00 0.00 0.00 3.32
4388 7461 0.740149 ATGTGTGTGTGCCTGTGTTG 59.260 50.000 0.00 0.00 0.00 3.33
4389 7462 1.405105 GAATGTGTGTGTGCCTGTGTT 59.595 47.619 0.00 0.00 0.00 3.32
4390 7463 1.024271 GAATGTGTGTGTGCCTGTGT 58.976 50.000 0.00 0.00 0.00 3.72
4391 7464 1.023502 TGAATGTGTGTGTGCCTGTG 58.976 50.000 0.00 0.00 0.00 3.66
4392 7465 1.881973 GATGAATGTGTGTGTGCCTGT 59.118 47.619 0.00 0.00 0.00 4.00
4393 7466 1.200716 GGATGAATGTGTGTGTGCCTG 59.799 52.381 0.00 0.00 0.00 4.85
4394 7467 1.202915 TGGATGAATGTGTGTGTGCCT 60.203 47.619 0.00 0.00 0.00 4.75
4395 7468 1.068333 GTGGATGAATGTGTGTGTGCC 60.068 52.381 0.00 0.00 0.00 5.01
4396 7469 1.400113 CGTGGATGAATGTGTGTGTGC 60.400 52.381 0.00 0.00 0.00 4.57
4397 7470 1.400113 GCGTGGATGAATGTGTGTGTG 60.400 52.381 0.00 0.00 0.00 3.82
4398 7471 0.874390 GCGTGGATGAATGTGTGTGT 59.126 50.000 0.00 0.00 0.00 3.72
4399 7472 0.873721 TGCGTGGATGAATGTGTGTG 59.126 50.000 0.00 0.00 0.00 3.82
4400 7473 1.536766 CTTGCGTGGATGAATGTGTGT 59.463 47.619 0.00 0.00 0.00 3.72
4401 7474 1.730121 GCTTGCGTGGATGAATGTGTG 60.730 52.381 0.00 0.00 0.00 3.82
4402 7475 0.523072 GCTTGCGTGGATGAATGTGT 59.477 50.000 0.00 0.00 0.00 3.72
4403 7476 0.521867 CGCTTGCGTGGATGAATGTG 60.522 55.000 6.86 0.00 0.00 3.21
4404 7477 1.796151 CGCTTGCGTGGATGAATGT 59.204 52.632 6.86 0.00 0.00 2.71
4405 7478 1.584483 GCGCTTGCGTGGATGAATG 60.584 57.895 16.38 0.00 0.00 2.67
4406 7479 2.039974 TGCGCTTGCGTGGATGAAT 61.040 52.632 16.38 0.00 43.34 2.57
4407 7480 2.667874 TGCGCTTGCGTGGATGAA 60.668 55.556 16.38 0.00 43.34 2.57
4408 7481 3.422303 GTGCGCTTGCGTGGATGA 61.422 61.111 16.38 0.00 43.34 2.92
4409 7482 3.042842 ATGTGCGCTTGCGTGGATG 62.043 57.895 16.38 0.00 43.34 3.51
4410 7483 2.747460 ATGTGCGCTTGCGTGGAT 60.747 55.556 16.38 3.36 43.34 3.41
4411 7484 3.725459 CATGTGCGCTTGCGTGGA 61.725 61.111 16.38 1.11 43.34 4.02
4412 7485 3.933900 GACATGTGCGCTTGCGTGG 62.934 63.158 16.38 4.78 43.34 4.94
4413 7486 2.500369 GACATGTGCGCTTGCGTG 60.500 61.111 16.38 12.85 43.34 5.34
4414 7487 3.726517 GGACATGTGCGCTTGCGT 61.727 61.111 16.38 0.03 43.34 5.24
4415 7488 3.725459 TGGACATGTGCGCTTGCG 61.725 61.111 13.03 10.90 43.34 4.85
4416 7489 2.126734 GTGGACATGTGCGCTTGC 60.127 61.111 22.04 6.14 39.78 4.01
4417 7490 2.174107 CGTGGACATGTGCGCTTG 59.826 61.111 25.46 11.29 0.00 4.01
4418 7491 3.726517 GCGTGGACATGTGCGCTT 61.727 61.111 25.46 0.00 45.48 4.68
4422 7495 2.703409 GATCGCGTGGACATGTGC 59.297 61.111 10.90 10.90 0.00 4.57
4423 7496 2.516589 CGGATCGCGTGGACATGTG 61.517 63.158 1.15 0.00 0.00 3.21
4424 7497 2.202743 CGGATCGCGTGGACATGT 60.203 61.111 5.77 0.00 0.00 3.21
4425 7498 3.630148 GCGGATCGCGTGGACATG 61.630 66.667 5.77 0.00 44.55 3.21
4435 7508 4.025145 GGGTGTATAAAAGAAAGCGGATCG 60.025 45.833 0.00 0.00 0.00 3.69
4436 7509 5.007724 CAGGGTGTATAAAAGAAAGCGGATC 59.992 44.000 0.00 0.00 0.00 3.36
4437 7510 4.881850 CAGGGTGTATAAAAGAAAGCGGAT 59.118 41.667 0.00 0.00 0.00 4.18
4438 7511 4.258543 CAGGGTGTATAAAAGAAAGCGGA 58.741 43.478 0.00 0.00 0.00 5.54
4439 7512 4.007659 ACAGGGTGTATAAAAGAAAGCGG 58.992 43.478 0.00 0.00 0.00 5.52
4440 7513 6.920569 ATACAGGGTGTATAAAAGAAAGCG 57.079 37.500 0.00 0.00 41.41 4.68
4453 7526 9.623000 GGTCTTATATTTGTTTATACAGGGTGT 57.377 33.333 0.00 0.00 35.28 4.16
4454 7527 9.621629 TGGTCTTATATTTGTTTATACAGGGTG 57.378 33.333 0.00 0.00 35.28 4.61


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

AutoCloner maintained by Alex Coulton.