Multiple sequence alignment - TraesCS3A01G224700

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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 TraesCS3A01G224700 chr3A 100.000 9159 0 0 1 9159 420751892 420742734 0.000000e+00 16914.0
1 TraesCS3A01G224700 chr3D 96.378 6294 131 26 241 6467 311656103 311662366 0.000000e+00 10270.0
2 TraesCS3A01G224700 chr3D 95.143 1400 28 9 7241 8632 311663358 311664725 0.000000e+00 2172.0
3 TraesCS3A01G224700 chr3D 94.330 776 23 6 6472 7244 311662490 311663247 0.000000e+00 1170.0
4 TraesCS3A01G224700 chr3D 94.611 167 7 2 8922 9087 311665438 311665603 3.280000e-64 257.0
5 TraesCS3A01G224700 chr3D 93.878 147 4 2 8631 8777 311665153 311665294 5.570000e-52 217.0
6 TraesCS3A01G224700 chr3D 95.935 123 4 1 8791 8913 311665279 311665400 2.020000e-46 198.0
7 TraesCS3A01G224700 chr3D 83.182 220 15 14 43 243 311655459 311655675 2.030000e-41 182.0
8 TraesCS3A01G224700 chr3B 97.236 3292 66 2 2218 5484 409607218 409603927 0.000000e+00 5552.0
9 TraesCS3A01G224700 chr3B 91.719 2222 81 42 64 2219 409609484 409607300 0.000000e+00 2988.0
10 TraesCS3A01G224700 chr3B 96.645 1669 31 4 5483 7129 409603765 409602100 0.000000e+00 2748.0
11 TraesCS3A01G224700 chr3B 93.672 1280 28 12 7165 8405 409602122 409600857 0.000000e+00 1866.0
12 TraesCS3A01G224700 chr3B 94.253 174 10 0 8453 8626 409547268 409547095 5.450000e-67 267.0
13 TraesCS3A01G224700 chr3B 84.034 119 18 1 6552 6670 69673126 69673009 7.520000e-21 113.0
14 TraesCS3A01G224700 chr3B 84.034 119 17 1 6552 6670 680249114 680249230 7.520000e-21 113.0
15 TraesCS3A01G224700 chr5B 83.125 160 20 6 2348 2502 550433398 550433241 1.240000e-28 139.0
16 TraesCS3A01G224700 chr5A 100.000 74 0 0 9086 9159 574780262 574780189 4.460000e-28 137.0
17 TraesCS3A01G224700 chr7B 89.189 111 8 4 6565 6673 509514136 509514028 1.600000e-27 135.0
18 TraesCS3A01G224700 chr7B 87.037 108 11 3 6564 6670 397594963 397594858 1.620000e-22 119.0
19 TraesCS3A01G224700 chr2A 94.253 87 5 0 6584 6670 65084814 65084900 5.770000e-27 134.0
20 TraesCS3A01G224700 chr2A 96.154 78 3 0 9082 9159 75116546 75116469 2.680000e-25 128.0
21 TraesCS3A01G224700 chr2A 94.118 85 3 2 9076 9159 717816426 717816509 2.680000e-25 128.0
22 TraesCS3A01G224700 chr6A 98.649 74 1 0 9086 9159 13437284 13437211 2.080000e-26 132.0
23 TraesCS3A01G224700 chr7D 95.122 82 4 0 9078 9159 251359475 251359556 7.460000e-26 130.0
24 TraesCS3A01G224700 chr4D 89.423 104 9 2 6572 6674 64347346 64347448 7.460000e-26 130.0
25 TraesCS3A01G224700 chr4D 95.062 81 3 1 9079 9159 80470029 80469950 9.650000e-25 126.0
26 TraesCS3A01G224700 chr7A 94.118 85 3 2 9077 9159 27059580 27059496 2.680000e-25 128.0
27 TraesCS3A01G224700 chr4A 96.203 79 2 1 9082 9159 368568495 368568573 2.680000e-25 128.0
28 TraesCS3A01G224700 chr4A 98.592 71 1 0 9089 9159 315236456 315236386 9.650000e-25 126.0
29 TraesCS3A01G224700 chr5D 86.916 107 13 1 6586 6692 452219481 452219376 1.620000e-22 119.0
30 TraesCS3A01G224700 chr2D 81.022 137 22 4 2367 2502 580242341 580242474 1.260000e-18 106.0
31 TraesCS3A01G224700 chr2D 98.182 55 1 0 7671 7725 139503110 139503056 7.570000e-16 97.1


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 TraesCS3A01G224700 chr3A 420742734 420751892 9158 True 16914.000000 16914 100.000 1 9159 1 chr3A.!!$R1 9158
1 TraesCS3A01G224700 chr3D 311655459 311665603 10144 False 2066.571429 10270 93.351 43 9087 7 chr3D.!!$F1 9044
2 TraesCS3A01G224700 chr3B 409600857 409609484 8627 True 3288.500000 5552 94.818 64 8405 4 chr3B.!!$R3 8341

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
382 835 0.037975 GCCCAGACTTTACGGTCGAA 60.038 55.000 0.00 0.00 40.76 3.71 F
456 909 0.238289 CCTGCGTGCTTTCGTTCATT 59.762 50.000 0.00 0.00 0.00 2.57 F
754 1215 0.300789 GTCCGATCAAAATCCGACGC 59.699 55.000 0.00 0.00 32.84 5.19 F
922 1390 0.324285 CCAGCTCTCCTCAACTGCTT 59.676 55.000 0.00 0.00 0.00 3.91 F
1497 1970 0.535780 TGAGTTGTTGAGCTGGGCTG 60.536 55.000 0.00 0.00 39.88 4.85 F
1498 1971 1.228367 AGTTGTTGAGCTGGGCTGG 60.228 57.895 0.00 0.00 39.88 4.85 F
1620 2095 2.013483 GATGATCAGCGTCGCCTCG 61.013 63.158 14.86 2.82 0.00 4.63 F
3420 4012 1.586422 TGTGTCTTGCTGCAGTCTTC 58.414 50.000 16.64 0.00 0.00 2.87 F
4255 4847 0.181114 TGATGAGCAATCCTTCCCCG 59.819 55.000 0.00 0.00 34.00 5.73 F
4661 5253 1.796459 CGAAACACTGACCCCGTTAAG 59.204 52.381 0.00 0.00 0.00 1.85 F
5282 5874 2.226962 AATGGTCAGCCTGAATGCTT 57.773 45.000 0.00 0.00 40.32 3.91 F
6913 7830 2.368548 TCTGCCACGTATGCCTAATGAT 59.631 45.455 6.77 0.00 0.00 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1496 1969 0.817634 CAGAACTCAAACACCGCCCA 60.818 55.000 0.00 0.00 0.00 5.36 R
1497 1970 0.818040 ACAGAACTCAAACACCGCCC 60.818 55.000 0.00 0.00 0.00 6.13 R
2492 3080 0.190815 AAGGCCCCACTTGGATTGTT 59.809 50.000 0.00 0.00 37.39 2.83 R
2699 3291 1.393539 CTCGACTAATTGTGCAACCCG 59.606 52.381 0.00 0.00 34.36 5.28 R
3186 3778 0.031716 TAGGATGTGAGGCTGAGGCT 60.032 55.000 8.79 8.79 42.48 4.58 R
3420 4012 1.475682 GGATTTGAAAGGCTCCTGCAG 59.524 52.381 6.78 6.78 41.91 4.41 R
3639 4231 4.420214 AGGCTGGGGGATCTACATAAAAAT 59.580 41.667 0.00 0.00 0.00 1.82 R
4488 5080 1.072331 ACCACTTGCAGTAGGACTTGG 59.928 52.381 7.31 0.29 29.70 3.61 R
6260 7036 5.199982 TGCTTAGGAAATGGGATGGTAAA 57.800 39.130 0.00 0.00 0.00 2.01 R
6491 7408 9.424319 TGTTAAAACTAGAACATTTGCAAAACA 57.576 25.926 17.19 7.66 30.72 2.83 R
7293 8327 1.367346 TGGACCTTAGCCCAATGTCA 58.633 50.000 0.00 0.00 34.46 3.58 R
8431 9500 0.034756 AATGCACAGTACGGTCAGCA 59.965 50.000 12.26 12.26 36.34 4.41 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
24 25 6.985117 TGATATTTTCAATTGCTCTATGGGC 58.015 36.000 0.00 0.00 0.00 5.36
25 26 6.550481 TGATATTTTCAATTGCTCTATGGGCA 59.450 34.615 0.00 0.00 37.97 5.36
26 27 4.724074 TTTTCAATTGCTCTATGGGCAG 57.276 40.909 0.00 0.00 40.90 4.85
27 28 3.650281 TTCAATTGCTCTATGGGCAGA 57.350 42.857 0.00 0.00 40.90 4.26
28 29 2.923121 TCAATTGCTCTATGGGCAGAC 58.077 47.619 0.00 0.00 40.90 3.51
29 30 1.600957 CAATTGCTCTATGGGCAGACG 59.399 52.381 0.00 0.00 40.90 4.18
30 31 0.833287 ATTGCTCTATGGGCAGACGT 59.167 50.000 0.00 0.00 40.90 4.34
31 32 0.108186 TTGCTCTATGGGCAGACGTG 60.108 55.000 0.00 0.00 40.90 4.49
32 33 1.257750 TGCTCTATGGGCAGACGTGT 61.258 55.000 0.00 0.00 34.56 4.49
33 34 0.744874 GCTCTATGGGCAGACGTGTA 59.255 55.000 0.00 0.00 0.00 2.90
34 35 1.269309 GCTCTATGGGCAGACGTGTAG 60.269 57.143 0.00 0.00 0.00 2.74
35 36 0.744874 TCTATGGGCAGACGTGTAGC 59.255 55.000 0.00 0.00 0.00 3.58
94 96 3.613910 GCCTTATGTTTTTGATGCGGTGT 60.614 43.478 0.00 0.00 0.00 4.16
149 151 4.850859 TTTTGCGTTCCACTCGTATATG 57.149 40.909 0.00 0.00 0.00 1.78
154 156 3.549423 GCGTTCCACTCGTATATGTAGCA 60.549 47.826 0.00 0.00 0.00 3.49
166 185 6.035542 TCGTATATGTAGCAACACAACACATG 59.964 38.462 0.00 0.00 38.78 3.21
180 199 1.146930 ACATGTCCCAGCCGCATAG 59.853 57.895 0.00 0.00 0.00 2.23
207 226 3.121030 ATTGCGTCAGCCGTCAGC 61.121 61.111 0.00 0.00 44.33 4.26
379 832 1.012486 CGTGCCCAGACTTTACGGTC 61.012 60.000 0.00 0.00 36.56 4.79
380 833 1.012486 GTGCCCAGACTTTACGGTCG 61.012 60.000 0.00 0.00 40.76 4.79
381 834 1.180456 TGCCCAGACTTTACGGTCGA 61.180 55.000 0.00 0.00 40.76 4.20
382 835 0.037975 GCCCAGACTTTACGGTCGAA 60.038 55.000 0.00 0.00 40.76 3.71
383 836 1.706443 CCCAGACTTTACGGTCGAAC 58.294 55.000 0.00 0.00 40.76 3.95
384 837 1.334054 CCAGACTTTACGGTCGAACG 58.666 55.000 23.55 23.55 40.76 3.95
385 838 1.069022 CCAGACTTTACGGTCGAACGA 60.069 52.381 32.41 10.65 40.76 3.85
386 839 1.974680 CAGACTTTACGGTCGAACGAC 59.025 52.381 32.41 17.33 43.87 4.34
387 840 0.970606 GACTTTACGGTCGAACGACG 59.029 55.000 32.41 15.99 45.41 5.12
415 868 1.934956 CGACGAATCACCGCTCTCG 60.935 63.158 0.00 0.00 37.33 4.04
456 909 0.238289 CCTGCGTGCTTTCGTTCATT 59.762 50.000 0.00 0.00 0.00 2.57
467 920 7.271223 CGTGCTTTCGTTCATTTTCTGATTAAT 59.729 33.333 0.00 0.00 32.72 1.40
468 921 8.915654 GTGCTTTCGTTCATTTTCTGATTAATT 58.084 29.630 0.00 0.00 32.72 1.40
556 1017 3.858247 ACAGATACCTTGTAAACGGCTC 58.142 45.455 0.00 0.00 0.00 4.70
592 1053 2.345991 CGGGCCCGAAAGAAGTCA 59.654 61.111 41.82 0.00 42.83 3.41
593 1054 1.741770 CGGGCCCGAAAGAAGTCAG 60.742 63.158 41.82 3.97 42.83 3.51
606 1067 1.555075 GAAGTCAGCCCACCTGTCATA 59.445 52.381 0.00 0.00 42.38 2.15
610 1071 2.001269 AGCCCACCTGTCATACCCC 61.001 63.158 0.00 0.00 0.00 4.95
611 1072 2.305607 GCCCACCTGTCATACCCCA 61.306 63.158 0.00 0.00 0.00 4.96
745 1206 4.460683 CCCCGCCGTCCGATCAAA 62.461 66.667 0.00 0.00 40.02 2.69
754 1215 0.300789 GTCCGATCAAAATCCGACGC 59.699 55.000 0.00 0.00 32.84 5.19
757 1218 1.772063 CGATCAAAATCCGACGCCCC 61.772 60.000 0.00 0.00 0.00 5.80
758 1219 0.746563 GATCAAAATCCGACGCCCCA 60.747 55.000 0.00 0.00 0.00 4.96
759 1220 0.748005 ATCAAAATCCGACGCCCCAG 60.748 55.000 0.00 0.00 0.00 4.45
851 1319 0.379316 ACCAAACGAACGAAACAGGC 59.621 50.000 0.14 0.00 0.00 4.85
853 1321 0.656205 CAAACGAACGAAACAGGCGG 60.656 55.000 0.14 0.00 0.00 6.13
922 1390 0.324285 CCAGCTCTCCTCAACTGCTT 59.676 55.000 0.00 0.00 0.00 3.91
934 1402 2.923655 TCAACTGCTTCGCTTCTAATCG 59.076 45.455 0.00 0.00 0.00 3.34
935 1403 1.281899 ACTGCTTCGCTTCTAATCGC 58.718 50.000 0.00 0.00 0.00 4.58
936 1404 1.134965 ACTGCTTCGCTTCTAATCGCT 60.135 47.619 0.00 0.00 0.00 4.93
937 1405 1.520590 CTGCTTCGCTTCTAATCGCTC 59.479 52.381 0.00 0.00 0.00 5.03
942 1410 1.272114 CGCTTCTAATCGCTCGCTCC 61.272 60.000 0.00 0.00 0.00 4.70
1178 1646 3.309436 TTCAGTGGATCGGCACCGG 62.309 63.158 9.58 0.00 40.25 5.28
1231 1699 3.930012 CCTTCCTCCCCGGATCGC 61.930 72.222 0.73 0.00 42.70 4.58
1496 1969 0.536006 GTGAGTTGTTGAGCTGGGCT 60.536 55.000 0.00 0.00 43.88 5.19
1497 1970 0.535780 TGAGTTGTTGAGCTGGGCTG 60.536 55.000 0.00 0.00 39.88 4.85
1498 1971 1.228367 AGTTGTTGAGCTGGGCTGG 60.228 57.895 0.00 0.00 39.88 4.85
1499 1972 2.115910 TTGTTGAGCTGGGCTGGG 59.884 61.111 0.00 0.00 39.88 4.45
1500 1973 4.666253 TGTTGAGCTGGGCTGGGC 62.666 66.667 0.00 0.00 39.88 5.36
1620 2095 2.013483 GATGATCAGCGTCGCCTCG 61.013 63.158 14.86 2.82 0.00 4.63
1735 2210 4.522789 TCCTTCATTAGTTGGTTTGCTTCC 59.477 41.667 0.00 0.00 0.00 3.46
2098 2603 9.630098 TCTTTCAGCAAGTTTGATATTTTGATC 57.370 29.630 0.00 0.00 33.66 2.92
2122 2627 4.118410 CTGCTAGTTCATGAGCACTTAGG 58.882 47.826 12.41 2.39 43.64 2.69
2262 2850 5.175859 GTGCATAGGTTCTAAAGTGCTGTA 58.824 41.667 0.00 0.00 33.95 2.74
2492 3080 2.445525 GGGGGTATTTAGGAGCCAATCA 59.554 50.000 0.00 0.00 36.11 2.57
2699 3291 6.861055 GTCTAACATGAGCTCAGTCTTATAGC 59.139 42.308 22.96 10.09 36.48 2.97
2762 3354 3.489785 GTCACGTCTAGTCAACAAGTTGG 59.510 47.826 12.54 0.00 40.78 3.77
2813 3405 3.079578 GTCTAGCCAAAACCCAAGTACC 58.920 50.000 0.00 0.00 0.00 3.34
2865 3457 6.073327 TCATCGTGTGTATCTATGGTCTTC 57.927 41.667 0.00 0.00 0.00 2.87
2950 3542 2.770164 ACTCCCTGTCTGTATGTTGC 57.230 50.000 0.00 0.00 0.00 4.17
3313 3905 6.934645 TCAAGGTAGTTATGAAACAAGGACTG 59.065 38.462 0.00 0.00 38.12 3.51
3375 3967 6.783708 AAGTCAGGTGTTTAATTTTGACCA 57.216 33.333 0.00 0.00 36.49 4.02
3420 4012 1.586422 TGTGTCTTGCTGCAGTCTTC 58.414 50.000 16.64 0.00 0.00 2.87
4013 4605 6.043706 ACCAAACTGATAAGCATAGGATAGCT 59.956 38.462 0.00 0.00 44.31 3.32
4118 4710 8.018537 TCTAACTGCTTGGTATTGCTCTAATA 57.981 34.615 0.00 0.00 0.00 0.98
4255 4847 0.181114 TGATGAGCAATCCTTCCCCG 59.819 55.000 0.00 0.00 34.00 5.73
4417 5009 9.672673 ACATCTTATCATAAGCTAACACTGTTT 57.327 29.630 0.00 0.00 0.00 2.83
4488 5080 6.305693 AGAAAGAATATCGCCATGTTAAGC 57.694 37.500 0.00 0.00 0.00 3.09
4591 5183 4.521146 GAAGGATCTGATGGCTTCTGAAA 58.479 43.478 12.71 0.00 36.11 2.69
4661 5253 1.796459 CGAAACACTGACCCCGTTAAG 59.204 52.381 0.00 0.00 0.00 1.85
4680 5272 3.130734 AGTGCTGGGGAGATACCTTTA 57.869 47.619 0.00 0.00 38.98 1.85
4726 5318 5.104402 TGGCATCTATTTGAGGATGTGAAGA 60.104 40.000 0.00 0.00 40.76 2.87
4806 5398 2.485814 GCACAGGAACAGAAAGGATGAC 59.514 50.000 0.00 0.00 0.00 3.06
4878 5470 3.829026 GGAAGGAAGAAAGAGCAAATGGT 59.171 43.478 0.00 0.00 0.00 3.55
5239 5831 3.406764 AGCTGTTTTCACCTCTTAGCAG 58.593 45.455 0.00 0.00 32.42 4.24
5250 5842 5.541101 TCACCTCTTAGCAGTAACCAAGTTA 59.459 40.000 0.00 0.00 0.00 2.24
5282 5874 2.226962 AATGGTCAGCCTGAATGCTT 57.773 45.000 0.00 0.00 40.32 3.91
5352 5965 5.007385 TCTAAAATCTGTAGCCGACCTTC 57.993 43.478 0.00 0.00 0.00 3.46
5537 6313 5.591472 CCATTGAGTCAGATTTGGATTGCTA 59.409 40.000 7.39 0.00 0.00 3.49
5616 6392 4.345547 TGTGGTGACTGGTGACTTTACATA 59.654 41.667 0.00 0.00 0.00 2.29
6232 7008 7.147567 TGCAATGTAGATTAGTTATCCAGGTCA 60.148 37.037 0.00 0.00 33.45 4.02
6251 7027 5.242393 AGGTCATGCATAATTGTTAGCATCC 59.758 40.000 0.00 0.00 45.14 3.51
6499 7416 2.671888 CACTGTTGCATGTTGTTTTGCA 59.328 40.909 0.00 0.00 46.51 4.08
6612 7529 5.482878 TCCCTCCGTAAAGAAACATAAGAGT 59.517 40.000 0.00 0.00 0.00 3.24
6625 7542 9.107177 AGAAACATAAGAGTGCTTAGATCATTG 57.893 33.333 0.00 0.00 39.79 2.82
6859 7776 5.600484 TGTTTTGGAGGCTTTTCAAAGGATA 59.400 36.000 1.55 0.00 36.53 2.59
6913 7830 2.368548 TCTGCCACGTATGCCTAATGAT 59.631 45.455 6.77 0.00 0.00 2.45
7038 7955 6.749036 AGCCAAACCATATAGCTAGTACTT 57.251 37.500 0.00 0.00 30.46 2.24
7125 8045 5.562506 TTCAAGTGATCTACTACCGTGAG 57.437 43.478 0.00 0.00 39.18 3.51
7160 8080 3.751479 CCTGCATATACACAGGCTGTA 57.249 47.619 21.59 6.14 46.50 2.74
7293 8327 0.249573 GCCTTGTTGTTGCATGTGCT 60.250 50.000 6.55 0.00 42.66 4.40
7451 8485 3.186909 GCACAGATGTACGACAAGCATA 58.813 45.455 0.00 0.00 0.00 3.14
7504 8538 1.676678 GGGTGAGCGCCTCTATCACA 61.677 60.000 23.06 2.48 44.08 3.58
7505 8539 0.249238 GGTGAGCGCCTCTATCACAG 60.249 60.000 23.06 0.00 44.08 3.66
7506 8540 0.457851 GTGAGCGCCTCTATCACAGT 59.542 55.000 18.59 0.00 42.30 3.55
7507 8541 1.676529 GTGAGCGCCTCTATCACAGTA 59.323 52.381 18.59 0.00 42.30 2.74
7509 8543 2.959030 TGAGCGCCTCTATCACAGTATT 59.041 45.455 2.29 0.00 0.00 1.89
7510 8544 4.023107 GTGAGCGCCTCTATCACAGTATTA 60.023 45.833 18.59 0.00 42.30 0.98
7713 8769 5.525012 TGCTCTCTTGTTGATATGTACATGC 59.475 40.000 18.81 10.65 0.00 4.06
8029 9085 3.011635 GCAGCAGGAGAAGGAGCGA 62.012 63.158 0.00 0.00 0.00 4.93
8154 9210 0.391597 AACGACACAAGGACGGACAT 59.608 50.000 0.00 0.00 0.00 3.06
8187 9243 2.870411 GCGCTTAACCACATACTTAGGG 59.130 50.000 0.00 0.00 0.00 3.53
8364 9428 0.329596 ATGGAGCTTCTGTTGACCCC 59.670 55.000 0.00 0.00 0.00 4.95
8421 9490 4.569943 TCTCTTGGAACATTGTACTGAGC 58.430 43.478 0.00 0.00 39.30 4.26
8422 9491 3.325870 TCTTGGAACATTGTACTGAGCG 58.674 45.455 0.00 0.00 39.30 5.03
8423 9492 2.831685 TGGAACATTGTACTGAGCGT 57.168 45.000 0.00 0.00 0.00 5.07
8424 9493 2.683968 TGGAACATTGTACTGAGCGTC 58.316 47.619 0.00 0.00 0.00 5.19
8425 9494 2.299013 TGGAACATTGTACTGAGCGTCT 59.701 45.455 0.00 0.00 0.00 4.18
8426 9495 3.244078 TGGAACATTGTACTGAGCGTCTT 60.244 43.478 0.00 0.00 0.00 3.01
8427 9496 3.368236 GGAACATTGTACTGAGCGTCTTC 59.632 47.826 0.00 0.00 0.00 2.87
8428 9497 2.960819 ACATTGTACTGAGCGTCTTCC 58.039 47.619 0.00 0.00 0.00 3.46
8429 9498 2.563179 ACATTGTACTGAGCGTCTTCCT 59.437 45.455 0.00 0.00 0.00 3.36
8430 9499 3.762288 ACATTGTACTGAGCGTCTTCCTA 59.238 43.478 0.00 0.00 0.00 2.94
8431 9500 4.402793 ACATTGTACTGAGCGTCTTCCTAT 59.597 41.667 0.00 0.00 0.00 2.57
8432 9501 4.371855 TTGTACTGAGCGTCTTCCTATG 57.628 45.455 0.00 0.00 0.00 2.23
8433 9502 2.099263 TGTACTGAGCGTCTTCCTATGC 59.901 50.000 0.00 0.00 0.00 3.14
8434 9503 1.479709 ACTGAGCGTCTTCCTATGCT 58.520 50.000 0.00 0.00 44.38 3.79
8435 9504 1.135915 ACTGAGCGTCTTCCTATGCTG 59.864 52.381 0.00 0.00 41.78 4.41
8436 9505 1.406898 CTGAGCGTCTTCCTATGCTGA 59.593 52.381 0.00 0.00 41.78 4.26
8437 9506 1.135139 TGAGCGTCTTCCTATGCTGAC 59.865 52.381 0.00 0.00 41.78 3.51
8477 9546 7.281100 GCCTTTACTCTTGAGTTAACTGCATAT 59.719 37.037 14.14 0.00 0.00 1.78
8493 9562 5.826737 ACTGCATATCATCTCCTTTTCCTTG 59.173 40.000 0.00 0.00 0.00 3.61
8523 9592 2.483583 TTCATGTTGCGTGTTGGTTC 57.516 45.000 0.00 0.00 0.00 3.62
8540 9609 1.967319 TTCAGGAAGAACCAGTGCAC 58.033 50.000 9.40 9.40 42.04 4.57
8541 9610 1.131638 TCAGGAAGAACCAGTGCACT 58.868 50.000 15.25 15.25 42.04 4.40
8542 9611 2.325484 TCAGGAAGAACCAGTGCACTA 58.675 47.619 21.20 0.00 42.04 2.74
8543 9612 2.300152 TCAGGAAGAACCAGTGCACTAG 59.700 50.000 21.20 15.81 42.04 2.57
8544 9613 2.300152 CAGGAAGAACCAGTGCACTAGA 59.700 50.000 21.20 0.00 42.04 2.43
8545 9614 2.564947 AGGAAGAACCAGTGCACTAGAG 59.435 50.000 21.20 13.82 42.04 2.43
8546 9615 2.354203 GGAAGAACCAGTGCACTAGAGG 60.354 54.545 21.20 19.20 38.79 3.69
8547 9616 2.016905 AGAACCAGTGCACTAGAGGT 57.983 50.000 21.20 19.91 0.00 3.85
8548 9617 2.330216 AGAACCAGTGCACTAGAGGTT 58.670 47.619 30.13 30.13 44.69 3.50
8549 9618 2.706190 AGAACCAGTGCACTAGAGGTTT 59.294 45.455 30.20 20.68 42.26 3.27
8632 9701 0.676782 GATTCCCAGGGTCGTTGGTG 60.677 60.000 5.01 0.00 33.73 4.17
8634 9703 1.637724 TTCCCAGGGTCGTTGGTGTT 61.638 55.000 5.01 0.00 33.73 3.32
8637 9706 0.321298 CCAGGGTCGTTGGTGTTAGG 60.321 60.000 0.00 0.00 0.00 2.69
8656 10154 4.388577 AGGCTCAAACATCTAACCCTTT 57.611 40.909 0.00 0.00 0.00 3.11
8658 10156 3.367395 GGCTCAAACATCTAACCCTTTGC 60.367 47.826 0.00 0.00 0.00 3.68
8722 10220 4.228666 TGTAACATTTGGTACCCTGGCTAT 59.771 41.667 10.07 0.00 37.41 2.97
8723 10221 3.577805 ACATTTGGTACCCTGGCTATC 57.422 47.619 10.07 0.00 0.00 2.08
8724 10222 3.123273 ACATTTGGTACCCTGGCTATCT 58.877 45.455 10.07 0.00 0.00 1.98
8725 10223 3.527665 ACATTTGGTACCCTGGCTATCTT 59.472 43.478 10.07 0.00 0.00 2.40
8766 10264 0.615331 TGGAACCTGCCTCACATCTC 59.385 55.000 0.00 0.00 0.00 2.75
8767 10265 0.908198 GGAACCTGCCTCACATCTCT 59.092 55.000 0.00 0.00 0.00 3.10
8768 10266 1.280421 GGAACCTGCCTCACATCTCTT 59.720 52.381 0.00 0.00 0.00 2.85
8769 10267 2.626840 GAACCTGCCTCACATCTCTTC 58.373 52.381 0.00 0.00 0.00 2.87
8770 10268 1.949799 ACCTGCCTCACATCTCTTCT 58.050 50.000 0.00 0.00 0.00 2.85
8771 10269 2.264455 ACCTGCCTCACATCTCTTCTT 58.736 47.619 0.00 0.00 0.00 2.52
8772 10270 2.641815 ACCTGCCTCACATCTCTTCTTT 59.358 45.455 0.00 0.00 0.00 2.52
8773 10271 3.269178 CCTGCCTCACATCTCTTCTTTC 58.731 50.000 0.00 0.00 0.00 2.62
8774 10272 3.055240 CCTGCCTCACATCTCTTCTTTCT 60.055 47.826 0.00 0.00 0.00 2.52
8775 10273 4.565236 CCTGCCTCACATCTCTTCTTTCTT 60.565 45.833 0.00 0.00 0.00 2.52
8776 10274 4.978099 TGCCTCACATCTCTTCTTTCTTT 58.022 39.130 0.00 0.00 0.00 2.52
8777 10275 5.380043 TGCCTCACATCTCTTCTTTCTTTT 58.620 37.500 0.00 0.00 0.00 2.27
8778 10276 5.829924 TGCCTCACATCTCTTCTTTCTTTTT 59.170 36.000 0.00 0.00 0.00 1.94
8864 10362 1.702022 TTTACATAGCCCGGGCCTCC 61.702 60.000 41.72 15.57 43.17 4.30
8868 10366 2.313427 ATAGCCCGGGCCTCCAAAA 61.313 57.895 41.72 18.45 43.17 2.44
8891 10389 0.756903 ATACATGGCGGTCTGGTACC 59.243 55.000 4.43 4.43 45.77 3.34
8946 10473 4.201990 GGGCATCAACATTCATCTCTTGAC 60.202 45.833 0.00 0.00 32.84 3.18
9075 10603 1.953686 GGCACACAAGTTTGCTAGGAA 59.046 47.619 10.71 0.00 38.85 3.36
9087 10615 8.348507 CAAGTTTGCTAGGAATTCCTATGATTC 58.651 37.037 30.13 20.48 46.71 2.52
9088 10616 7.810260 AGTTTGCTAGGAATTCCTATGATTCT 58.190 34.615 30.13 21.95 46.71 2.40
9089 10617 8.938883 AGTTTGCTAGGAATTCCTATGATTCTA 58.061 33.333 30.13 11.32 46.71 2.10
9090 10618 8.994170 GTTTGCTAGGAATTCCTATGATTCTAC 58.006 37.037 30.13 18.38 46.71 2.59
9091 10619 8.497910 TTGCTAGGAATTCCTATGATTCTACT 57.502 34.615 30.13 7.13 46.71 2.57
9092 10620 8.128322 TGCTAGGAATTCCTATGATTCTACTC 57.872 38.462 30.13 11.92 46.71 2.59
9093 10621 7.179338 TGCTAGGAATTCCTATGATTCTACTCC 59.821 40.741 30.13 11.39 46.71 3.85
9094 10622 6.943899 AGGAATTCCTATGATTCTACTCCC 57.056 41.667 25.99 0.00 46.48 4.30
9095 10623 6.638953 AGGAATTCCTATGATTCTACTCCCT 58.361 40.000 25.99 0.00 46.48 4.20
9096 10624 6.728632 AGGAATTCCTATGATTCTACTCCCTC 59.271 42.308 25.99 0.00 46.48 4.30
9097 10625 6.728632 GGAATTCCTATGATTCTACTCCCTCT 59.271 42.308 17.73 0.00 0.00 3.69
9098 10626 7.310361 GGAATTCCTATGATTCTACTCCCTCTG 60.310 44.444 17.73 0.00 0.00 3.35
9099 10627 5.671463 TCCTATGATTCTACTCCCTCTGT 57.329 43.478 0.00 0.00 0.00 3.41
9100 10628 6.031964 TCCTATGATTCTACTCCCTCTGTT 57.968 41.667 0.00 0.00 0.00 3.16
9101 10629 6.444704 TCCTATGATTCTACTCCCTCTGTTT 58.555 40.000 0.00 0.00 0.00 2.83
9102 10630 6.551601 TCCTATGATTCTACTCCCTCTGTTTC 59.448 42.308 0.00 0.00 0.00 2.78
9103 10631 4.720649 TGATTCTACTCCCTCTGTTTCG 57.279 45.455 0.00 0.00 0.00 3.46
9104 10632 4.341487 TGATTCTACTCCCTCTGTTTCGA 58.659 43.478 0.00 0.00 0.00 3.71
9105 10633 4.770531 TGATTCTACTCCCTCTGTTTCGAA 59.229 41.667 0.00 0.00 0.00 3.71
9106 10634 5.422331 TGATTCTACTCCCTCTGTTTCGAAT 59.578 40.000 0.00 0.00 0.00 3.34
9107 10635 5.740290 TTCTACTCCCTCTGTTTCGAATT 57.260 39.130 0.00 0.00 0.00 2.17
9108 10636 6.845758 TTCTACTCCCTCTGTTTCGAATTA 57.154 37.500 0.00 0.00 0.00 1.40
9109 10637 6.205101 TCTACTCCCTCTGTTTCGAATTAC 57.795 41.667 0.00 0.00 0.00 1.89
9110 10638 5.950549 TCTACTCCCTCTGTTTCGAATTACT 59.049 40.000 0.00 0.00 0.00 2.24
9111 10639 5.485209 ACTCCCTCTGTTTCGAATTACTT 57.515 39.130 0.00 0.00 0.00 2.24
9112 10640 5.238583 ACTCCCTCTGTTTCGAATTACTTG 58.761 41.667 0.00 0.00 0.00 3.16
9113 10641 5.221661 ACTCCCTCTGTTTCGAATTACTTGT 60.222 40.000 0.00 0.00 0.00 3.16
9114 10642 5.235516 TCCCTCTGTTTCGAATTACTTGTC 58.764 41.667 0.00 0.00 0.00 3.18
9115 10643 4.091509 CCCTCTGTTTCGAATTACTTGTCG 59.908 45.833 0.00 0.00 38.62 4.35
9116 10644 4.434330 CCTCTGTTTCGAATTACTTGTCGC 60.434 45.833 0.00 0.00 37.19 5.19
9117 10645 4.052608 TCTGTTTCGAATTACTTGTCGCA 58.947 39.130 0.00 0.00 37.19 5.10
9118 10646 4.149922 TCTGTTTCGAATTACTTGTCGCAG 59.850 41.667 0.00 0.00 37.19 5.18
9119 10647 3.185594 TGTTTCGAATTACTTGTCGCAGG 59.814 43.478 0.00 0.00 37.19 4.85
9120 10648 2.736144 TCGAATTACTTGTCGCAGGT 57.264 45.000 0.00 0.91 37.19 4.00
9121 10649 3.853831 TCGAATTACTTGTCGCAGGTA 57.146 42.857 0.00 0.00 37.19 3.08
9122 10650 4.380841 TCGAATTACTTGTCGCAGGTAT 57.619 40.909 3.46 0.00 37.19 2.73
9123 10651 4.109766 TCGAATTACTTGTCGCAGGTATG 58.890 43.478 3.46 0.00 37.19 2.39
9124 10652 3.245284 CGAATTACTTGTCGCAGGTATGG 59.755 47.826 3.46 0.00 0.00 2.74
9125 10653 4.439057 GAATTACTTGTCGCAGGTATGGA 58.561 43.478 3.46 0.00 0.00 3.41
9126 10654 4.689612 ATTACTTGTCGCAGGTATGGAT 57.310 40.909 3.46 0.00 0.00 3.41
9127 10655 2.315925 ACTTGTCGCAGGTATGGATG 57.684 50.000 0.00 0.00 0.00 3.51
9128 10656 1.555075 ACTTGTCGCAGGTATGGATGT 59.445 47.619 0.00 0.00 0.00 3.06
9129 10657 2.764010 ACTTGTCGCAGGTATGGATGTA 59.236 45.455 0.00 0.00 0.00 2.29
9130 10658 3.388024 ACTTGTCGCAGGTATGGATGTAT 59.612 43.478 0.00 0.00 0.00 2.29
9131 10659 3.660501 TGTCGCAGGTATGGATGTATC 57.339 47.619 0.00 0.00 0.00 2.24
9132 10660 3.230976 TGTCGCAGGTATGGATGTATCT 58.769 45.455 0.00 0.00 0.00 1.98
9133 10661 4.403734 TGTCGCAGGTATGGATGTATCTA 58.596 43.478 0.00 0.00 0.00 1.98
9134 10662 4.459337 TGTCGCAGGTATGGATGTATCTAG 59.541 45.833 0.00 0.00 0.00 2.43
9135 10663 4.700692 GTCGCAGGTATGGATGTATCTAGA 59.299 45.833 0.00 0.00 0.00 2.43
9136 10664 5.358442 GTCGCAGGTATGGATGTATCTAGAT 59.642 44.000 10.73 10.73 0.00 1.98
9137 10665 5.358160 TCGCAGGTATGGATGTATCTAGATG 59.642 44.000 15.79 0.00 0.00 2.90
9138 10666 5.126222 CGCAGGTATGGATGTATCTAGATGT 59.874 44.000 15.79 1.25 0.00 3.06
9139 10667 6.318900 CGCAGGTATGGATGTATCTAGATGTA 59.681 42.308 15.79 4.44 0.00 2.29
9140 10668 7.013750 CGCAGGTATGGATGTATCTAGATGTAT 59.986 40.741 15.79 9.11 0.00 2.29
9141 10669 8.700051 GCAGGTATGGATGTATCTAGATGTATT 58.300 37.037 15.79 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.550481 TGCCCATAGAGCAATTGAAAATATCA 59.450 34.615 10.34 0.00 37.28 2.15
1 2 6.985117 TGCCCATAGAGCAATTGAAAATATC 58.015 36.000 10.34 0.00 37.28 1.63
2 3 6.779049 TCTGCCCATAGAGCAATTGAAAATAT 59.221 34.615 10.34 0.00 40.35 1.28
3 4 6.039717 GTCTGCCCATAGAGCAATTGAAAATA 59.960 38.462 10.34 0.00 40.35 1.40
4 5 4.957954 TCTGCCCATAGAGCAATTGAAAAT 59.042 37.500 10.34 0.00 40.35 1.82
5 6 4.158394 GTCTGCCCATAGAGCAATTGAAAA 59.842 41.667 10.34 0.00 40.35 2.29
6 7 3.696051 GTCTGCCCATAGAGCAATTGAAA 59.304 43.478 10.34 0.00 40.35 2.69
7 8 3.282021 GTCTGCCCATAGAGCAATTGAA 58.718 45.455 10.34 0.00 40.35 2.69
8 9 2.742856 CGTCTGCCCATAGAGCAATTGA 60.743 50.000 10.34 0.00 40.35 2.57
9 10 1.600957 CGTCTGCCCATAGAGCAATTG 59.399 52.381 0.00 0.00 40.35 2.32
10 11 1.210478 ACGTCTGCCCATAGAGCAATT 59.790 47.619 0.00 0.00 40.35 2.32
11 12 0.833287 ACGTCTGCCCATAGAGCAAT 59.167 50.000 0.00 0.00 40.35 3.56
12 13 0.108186 CACGTCTGCCCATAGAGCAA 60.108 55.000 0.00 0.00 40.35 3.91
13 14 1.257750 ACACGTCTGCCCATAGAGCA 61.258 55.000 0.00 0.00 38.82 4.26
14 15 0.744874 TACACGTCTGCCCATAGAGC 59.255 55.000 0.00 0.00 0.00 4.09
15 16 1.269309 GCTACACGTCTGCCCATAGAG 60.269 57.143 0.00 0.00 0.00 2.43
16 17 0.744874 GCTACACGTCTGCCCATAGA 59.255 55.000 0.00 0.00 0.00 1.98
17 18 0.595053 CGCTACACGTCTGCCCATAG 60.595 60.000 0.00 0.00 36.87 2.23
18 19 1.435925 CGCTACACGTCTGCCCATA 59.564 57.895 0.00 0.00 36.87 2.74
19 20 2.184322 CGCTACACGTCTGCCCAT 59.816 61.111 0.00 0.00 36.87 4.00
134 136 5.231568 GTGTTGCTACATATACGAGTGGAAC 59.768 44.000 3.85 0.00 36.50 3.62
149 151 2.031157 GGGACATGTGTTGTGTTGCTAC 60.031 50.000 1.15 0.00 39.18 3.58
154 156 1.032014 GCTGGGACATGTGTTGTGTT 58.968 50.000 1.15 0.00 39.18 3.32
166 185 2.279517 CGTCTATGCGGCTGGGAC 60.280 66.667 0.00 5.72 0.00 4.46
207 226 3.832237 AAGATATGCCGCCCCGCTG 62.832 63.158 0.00 0.00 0.00 5.18
211 231 1.003233 GGAGAAGATATGCCGCCCC 60.003 63.158 0.00 0.00 0.00 5.80
273 723 4.388499 GGCTCCGTGGCCGAAAGA 62.388 66.667 0.00 0.00 42.82 2.52
379 832 1.401044 GTTCGTCGTTCGTCGTTCG 59.599 57.895 10.78 0.00 40.80 3.95
380 833 0.986874 TCGTTCGTCGTTCGTCGTTC 60.987 55.000 10.78 5.72 40.80 3.95
381 834 1.011242 TCGTTCGTCGTTCGTCGTT 60.011 52.632 10.78 0.00 40.80 3.85
382 835 1.719085 GTCGTTCGTCGTTCGTCGT 60.719 57.895 10.78 0.00 40.80 4.34
383 836 2.738475 CGTCGTTCGTCGTTCGTCG 61.738 63.158 13.27 13.27 40.80 5.12
384 837 0.986874 TTCGTCGTTCGTCGTTCGTC 60.987 55.000 10.78 5.72 40.80 4.20
385 838 0.384725 ATTCGTCGTTCGTCGTTCGT 60.385 50.000 10.78 0.00 40.80 3.85
386 839 0.287143 GATTCGTCGTTCGTCGTTCG 59.713 55.000 10.78 0.00 40.80 3.95
387 840 1.055476 GTGATTCGTCGTTCGTCGTTC 59.945 52.381 10.78 9.75 40.80 3.95
388 841 1.047739 GTGATTCGTCGTTCGTCGTT 58.952 50.000 10.78 2.02 40.80 3.85
389 842 0.727122 GGTGATTCGTCGTTCGTCGT 60.727 55.000 10.78 0.00 40.80 4.34
390 843 1.717555 CGGTGATTCGTCGTTCGTCG 61.718 60.000 5.63 5.63 40.80 5.12
391 844 1.978697 CGGTGATTCGTCGTTCGTC 59.021 57.895 0.00 0.00 40.80 4.20
392 845 2.084681 GCGGTGATTCGTCGTTCGT 61.085 57.895 0.00 0.00 40.80 3.85
415 868 0.318441 GGAAAGTGGCAGGGAAAAGC 59.682 55.000 0.00 0.00 0.00 3.51
456 909 9.026121 TGGGACGGAAATAAAATTAATCAGAAA 57.974 29.630 0.00 0.00 0.00 2.52
467 920 2.588464 TGCCTGGGACGGAAATAAAA 57.412 45.000 0.00 0.00 36.31 1.52
468 921 2.224917 ACTTGCCTGGGACGGAAATAAA 60.225 45.455 0.00 0.00 36.31 1.40
542 995 0.036306 AGGGTGAGCCGTTTACAAGG 59.964 55.000 0.00 0.00 34.97 3.61
543 996 1.439679 GAGGGTGAGCCGTTTACAAG 58.560 55.000 0.00 0.00 34.97 3.16
545 998 1.180456 TCGAGGGTGAGCCGTTTACA 61.180 55.000 0.00 0.00 34.97 2.41
592 1053 2.001269 GGGGTATGACAGGTGGGCT 61.001 63.158 0.00 0.00 0.00 5.19
593 1054 1.645402 ATGGGGTATGACAGGTGGGC 61.645 60.000 0.00 0.00 0.00 5.36
606 1067 0.107214 CGTCATGGCTGTTATGGGGT 60.107 55.000 0.00 0.00 0.00 4.95
743 1204 2.750237 GCTGGGGCGTCGGATTTT 60.750 61.111 0.00 0.00 0.00 1.82
922 1390 0.317103 GAGCGAGCGATTAGAAGCGA 60.317 55.000 3.77 0.00 40.84 4.93
942 1410 4.218578 AGAGCATGGCGAGCGAGG 62.219 66.667 0.00 0.00 37.01 4.63
1178 1646 3.854459 CGAAGAAGAAGGCGGCGC 61.854 66.667 26.17 26.17 0.00 6.53
1179 1647 2.432628 ACGAAGAAGAAGGCGGCG 60.433 61.111 0.51 0.51 0.00 6.46
1496 1969 0.817634 CAGAACTCAAACACCGCCCA 60.818 55.000 0.00 0.00 0.00 5.36
1497 1970 0.818040 ACAGAACTCAAACACCGCCC 60.818 55.000 0.00 0.00 0.00 6.13
1498 1971 1.021968 AACAGAACTCAAACACCGCC 58.978 50.000 0.00 0.00 0.00 6.13
1499 1972 2.844122 AAACAGAACTCAAACACCGC 57.156 45.000 0.00 0.00 0.00 5.68
1500 1973 4.588278 GAGAAAACAGAACTCAAACACCG 58.412 43.478 0.00 0.00 0.00 4.94
1620 2095 4.864334 CCCATCGCCTCCAGCACC 62.864 72.222 0.00 0.00 44.04 5.01
1692 2167 4.023193 AGGAAACAATAAAGACACGGCAAG 60.023 41.667 0.00 0.00 0.00 4.01
1735 2210 8.993121 GTATACCATCAAGGAATATCACTTGTG 58.007 37.037 15.10 12.81 43.40 3.33
1831 2307 5.163642 ACTGCTATACTAGGAAGTGTGAACG 60.164 44.000 0.00 0.00 36.36 3.95
1925 2401 6.092670 TCACTAAGACTTGCACTGCATAAATC 59.907 38.462 4.10 0.83 38.76 2.17
1977 2453 8.139989 GGGATAATTAGGATACATATACGCGTT 58.860 37.037 20.78 8.23 41.41 4.84
2000 2476 3.556213 GCATACCATAACGCACATAGGGA 60.556 47.826 0.00 0.00 0.00 4.20
2262 2850 5.112129 ACTCTTCGGCCCATAAACTTAAT 57.888 39.130 0.00 0.00 0.00 1.40
2288 2876 3.431725 GCACCCCGGCGAAAAGAG 61.432 66.667 9.30 0.00 0.00 2.85
2492 3080 0.190815 AAGGCCCCACTTGGATTGTT 59.809 50.000 0.00 0.00 37.39 2.83
2699 3291 1.393539 CTCGACTAATTGTGCAACCCG 59.606 52.381 0.00 0.00 34.36 5.28
2762 3354 7.964604 AACTTGAATAGTTGGACTAGACAAC 57.035 36.000 20.05 20.05 45.33 3.32
2813 3405 6.219473 AGTGATTCAAGTAATCTATGCCTCG 58.781 40.000 0.00 0.00 43.83 4.63
2865 3457 2.599973 GTGCAGTTCAAGTTTTGTGCAG 59.400 45.455 6.00 0.00 39.72 4.41
2950 3542 8.183830 TGAAAATTTGCAAAGCGGATTAATAG 57.816 30.769 18.19 0.00 0.00 1.73
3186 3778 0.031716 TAGGATGTGAGGCTGAGGCT 60.032 55.000 8.79 8.79 42.48 4.58
3420 4012 1.475682 GGATTTGAAAGGCTCCTGCAG 59.524 52.381 6.78 6.78 41.91 4.41
3639 4231 4.420214 AGGCTGGGGGATCTACATAAAAAT 59.580 41.667 0.00 0.00 0.00 1.82
4013 4605 4.841813 TGGTTGTACATCCTAACCTCAAGA 59.158 41.667 20.93 0.00 43.28 3.02
4118 4710 7.128234 ACATTTAAAGCAATGGCCTATGATT 57.872 32.000 3.32 5.03 42.56 2.57
4255 4847 3.861840 TCATAGCTTCAACTAGCACACC 58.138 45.455 0.00 0.00 43.68 4.16
4417 5009 6.489022 CCATCATCAATCTAAGCCATCAAGAA 59.511 38.462 0.00 0.00 0.00 2.52
4488 5080 1.072331 ACCACTTGCAGTAGGACTTGG 59.928 52.381 7.31 0.29 29.70 3.61
4591 5183 2.814805 ACAGCATAGCCTTCAATGGT 57.185 45.000 0.00 0.00 34.29 3.55
4661 5253 2.158798 GGTAAAGGTATCTCCCCAGCAC 60.159 54.545 0.00 0.00 36.75 4.40
4680 5272 5.163416 CCATTTCCACTCTTGTTTCAAAGGT 60.163 40.000 0.00 0.00 0.00 3.50
4806 5398 5.160607 TCTTTGGTGTAATACTGTGAGGG 57.839 43.478 0.00 0.00 0.00 4.30
4878 5470 6.700960 CCAATTTCATTTTGGCGCTCATAATA 59.299 34.615 7.64 0.00 37.42 0.98
5250 5842 5.954150 AGGCTGACCATTTAACATTCTGAAT 59.046 36.000 0.00 0.00 39.06 2.57
5537 6313 9.432982 AGATATCTCCTCAAGTGACTAAATCTT 57.567 33.333 0.00 0.00 0.00 2.40
5710 6486 8.504005 CCAACATCCGTTCCATTAGTATTAATC 58.496 37.037 0.00 0.00 31.13 1.75
6057 6833 8.586744 TCAGTGGTACCCCAAAATAAAAATAAC 58.413 33.333 10.07 0.00 44.15 1.89
6260 7036 5.199982 TGCTTAGGAAATGGGATGGTAAA 57.800 39.130 0.00 0.00 0.00 2.01
6491 7408 9.424319 TGTTAAAACTAGAACATTTGCAAAACA 57.576 25.926 17.19 7.66 30.72 2.83
7047 7964 4.411869 TGCACCAGGATTTCCATATCTACA 59.588 41.667 0.00 0.00 38.89 2.74
7048 7965 4.757149 GTGCACCAGGATTTCCATATCTAC 59.243 45.833 5.22 0.00 38.89 2.59
7293 8327 1.367346 TGGACCTTAGCCCAATGTCA 58.633 50.000 0.00 0.00 34.46 3.58
7376 8410 4.516698 CAGCATCTCTGTAAAACACCAACT 59.483 41.667 0.00 0.00 38.02 3.16
7451 8485 2.835764 AGATGCAATGCCCAGTTTGATT 59.164 40.909 1.53 0.00 0.00 2.57
7713 8769 1.151668 GTAGCAGTGCTTGTCCTGTG 58.848 55.000 25.23 0.00 40.44 3.66
7936 8992 1.079543 CCAGAGCCACCTTCTGTCG 60.080 63.158 2.05 0.00 40.32 4.35
8029 9085 2.952310 GTCTTTGGTCTGTTGCTTCCTT 59.048 45.455 0.00 0.00 0.00 3.36
8154 9210 4.153475 GTGGTTAAGCGCTACTCAATCAAA 59.847 41.667 12.05 0.00 0.00 2.69
8187 9243 8.992835 AAATTTCCTGAAGAATGAATAACTGC 57.007 30.769 0.00 0.00 33.44 4.40
8364 9428 2.240040 CTACGAAGGAGAACGTGAACG 58.760 52.381 0.40 0.40 42.61 3.95
8421 9490 0.456221 ACGGTCAGCATAGGAAGACG 59.544 55.000 0.00 0.00 31.93 4.18
8422 9491 2.688958 AGTACGGTCAGCATAGGAAGAC 59.311 50.000 0.00 0.00 0.00 3.01
8423 9492 2.688446 CAGTACGGTCAGCATAGGAAGA 59.312 50.000 0.00 0.00 0.00 2.87
8424 9493 2.427453 ACAGTACGGTCAGCATAGGAAG 59.573 50.000 0.00 0.00 0.00 3.46
8425 9494 2.165641 CACAGTACGGTCAGCATAGGAA 59.834 50.000 0.00 0.00 0.00 3.36
8426 9495 1.749063 CACAGTACGGTCAGCATAGGA 59.251 52.381 0.00 0.00 0.00 2.94
8427 9496 1.802880 GCACAGTACGGTCAGCATAGG 60.803 57.143 0.00 0.00 0.00 2.57
8428 9497 1.135112 TGCACAGTACGGTCAGCATAG 60.135 52.381 6.99 0.00 0.00 2.23
8429 9498 0.892063 TGCACAGTACGGTCAGCATA 59.108 50.000 6.99 0.00 0.00 3.14
8430 9499 0.250234 ATGCACAGTACGGTCAGCAT 59.750 50.000 15.11 15.11 37.83 3.79
8431 9500 0.034756 AATGCACAGTACGGTCAGCA 59.965 50.000 12.26 12.26 36.34 4.41
8432 9501 0.443869 CAATGCACAGTACGGTCAGC 59.556 55.000 0.00 0.00 0.00 4.26
8433 9502 0.443869 GCAATGCACAGTACGGTCAG 59.556 55.000 0.00 0.00 0.00 3.51
8434 9503 0.953471 GGCAATGCACAGTACGGTCA 60.953 55.000 7.79 0.00 0.00 4.02
8435 9504 0.673644 AGGCAATGCACAGTACGGTC 60.674 55.000 7.79 0.00 0.00 4.79
8436 9505 0.250727 AAGGCAATGCACAGTACGGT 60.251 50.000 7.79 0.00 0.00 4.83
8437 9506 0.881118 AAAGGCAATGCACAGTACGG 59.119 50.000 7.79 0.00 0.00 4.02
8477 9546 2.027192 CCCGACAAGGAAAAGGAGATGA 60.027 50.000 0.00 0.00 45.00 2.92
8493 9562 1.334869 GCAACATGAATGATCCCCGAC 59.665 52.381 0.00 0.00 0.00 4.79
8523 9592 2.300152 TCTAGTGCACTGGTTCTTCCTG 59.700 50.000 29.57 6.32 40.38 3.86
8537 9606 3.059800 GTGTCAAACGAAACCTCTAGTGC 60.060 47.826 0.00 0.00 0.00 4.40
8538 9607 4.209288 CAGTGTCAAACGAAACCTCTAGTG 59.791 45.833 0.00 0.00 0.00 2.74
8539 9608 4.369182 CAGTGTCAAACGAAACCTCTAGT 58.631 43.478 0.00 0.00 0.00 2.57
8540 9609 3.741344 CCAGTGTCAAACGAAACCTCTAG 59.259 47.826 0.00 0.00 0.00 2.43
8541 9610 3.133362 ACCAGTGTCAAACGAAACCTCTA 59.867 43.478 0.00 0.00 0.00 2.43
8542 9611 2.093128 ACCAGTGTCAAACGAAACCTCT 60.093 45.455 0.00 0.00 0.00 3.69
8543 9612 2.031683 CACCAGTGTCAAACGAAACCTC 59.968 50.000 0.00 0.00 0.00 3.85
8544 9613 2.014128 CACCAGTGTCAAACGAAACCT 58.986 47.619 0.00 0.00 0.00 3.50
8545 9614 1.533129 GCACCAGTGTCAAACGAAACC 60.533 52.381 0.00 0.00 0.00 3.27
8546 9615 1.131504 TGCACCAGTGTCAAACGAAAC 59.868 47.619 0.00 0.00 0.00 2.78
8547 9616 1.400142 CTGCACCAGTGTCAAACGAAA 59.600 47.619 0.00 0.00 0.00 3.46
8548 9617 1.013596 CTGCACCAGTGTCAAACGAA 58.986 50.000 0.00 0.00 0.00 3.85
8549 9618 0.813610 CCTGCACCAGTGTCAAACGA 60.814 55.000 0.00 0.00 0.00 3.85
8632 9701 4.844884 AGGGTTAGATGTTTGAGCCTAAC 58.155 43.478 0.00 0.00 38.17 2.34
8634 9703 5.253330 CAAAGGGTTAGATGTTTGAGCCTA 58.747 41.667 0.00 0.00 38.95 3.93
8637 9706 3.255642 TGCAAAGGGTTAGATGTTTGAGC 59.744 43.478 0.00 0.00 32.65 4.26
8656 10154 5.067936 GCTAGAGTTAGACTTGGAGTATGCA 59.932 44.000 0.00 0.00 30.91 3.96
8658 10156 5.010213 GGGCTAGAGTTAGACTTGGAGTATG 59.990 48.000 0.00 0.00 35.11 2.39
8722 10220 2.600164 TTGTGGCCAGGCACAAGA 59.400 55.556 29.31 13.93 36.52 3.02
8724 10222 3.225798 GCTTGTGGCCAGGCACAA 61.226 61.111 30.34 30.34 42.83 3.33
8725 10223 3.736996 AAGCTTGTGGCCAGGCACA 62.737 57.895 21.64 21.64 45.54 4.57
8733 10231 1.228552 TTCCAGGGAAGCTTGTGGC 60.229 57.895 2.10 0.00 42.19 5.01
8775 10273 7.775120 AGAAGAGATGTTGCTTCAAAGAAAAA 58.225 30.769 0.00 0.00 42.21 1.94
8776 10274 7.338800 AGAAGAGATGTTGCTTCAAAGAAAA 57.661 32.000 0.00 0.00 42.21 2.29
8777 10275 6.949352 AGAAGAGATGTTGCTTCAAAGAAA 57.051 33.333 0.00 0.00 42.21 2.52
8778 10276 6.949352 AAGAAGAGATGTTGCTTCAAAGAA 57.051 33.333 0.00 0.00 42.21 2.52
8779 10277 6.949352 AAAGAAGAGATGTTGCTTCAAAGA 57.051 33.333 0.00 0.00 42.21 2.52
8780 10278 7.998753 AAAAAGAAGAGATGTTGCTTCAAAG 57.001 32.000 0.00 0.00 42.21 2.77
8810 10308 4.843728 TGATCAATAAAGCTCGGGAGTTT 58.156 39.130 0.00 0.00 33.15 2.66
8850 10348 2.284515 CTTTTGGAGGCCCGGGCTAT 62.285 60.000 42.70 31.94 38.98 2.97
8913 10411 7.836479 TGAATGTTGATGCCCATATATCAAA 57.164 32.000 0.00 0.00 42.86 2.69
8914 10412 7.891712 AGATGAATGTTGATGCCCATATATCAA 59.108 33.333 0.00 0.00 40.06 2.57
8915 10413 7.407729 AGATGAATGTTGATGCCCATATATCA 58.592 34.615 0.00 0.00 0.00 2.15
8916 10414 7.774157 AGAGATGAATGTTGATGCCCATATATC 59.226 37.037 0.00 0.00 0.00 1.63
8917 10415 7.640313 AGAGATGAATGTTGATGCCCATATAT 58.360 34.615 0.00 0.00 0.00 0.86
8919 10417 5.888901 AGAGATGAATGTTGATGCCCATAT 58.111 37.500 0.00 0.00 0.00 1.78
8946 10473 8.928270 AAACTCTAGATTTAGTACCATGAACG 57.072 34.615 0.00 0.00 0.00 3.95
8976 10503 9.915629 AACACTTGTTCAGAGTAGTAGAATAAG 57.084 33.333 14.74 14.74 42.50 1.73
9023 10551 3.583086 CCCTAAGTGAGAGGAAAAGGACA 59.417 47.826 0.00 0.00 35.99 4.02
9025 10553 3.181399 TCCCCTAAGTGAGAGGAAAAGGA 60.181 47.826 0.00 0.00 35.99 3.36
9026 10554 3.182152 TCCCCTAAGTGAGAGGAAAAGG 58.818 50.000 0.00 0.00 35.99 3.11
9027 10555 4.041691 TGTTCCCCTAAGTGAGAGGAAAAG 59.958 45.833 0.00 0.00 38.30 2.27
9075 10603 6.629156 ACAGAGGGAGTAGAATCATAGGAAT 58.371 40.000 0.00 0.00 0.00 3.01
9087 10615 6.210287 AGTAATTCGAAACAGAGGGAGTAG 57.790 41.667 0.00 0.00 0.00 2.57
9088 10616 6.014840 ACAAGTAATTCGAAACAGAGGGAGTA 60.015 38.462 0.00 0.00 0.00 2.59
9089 10617 5.221661 ACAAGTAATTCGAAACAGAGGGAGT 60.222 40.000 0.00 0.00 0.00 3.85
9090 10618 5.238583 ACAAGTAATTCGAAACAGAGGGAG 58.761 41.667 0.00 0.00 0.00 4.30
9091 10619 5.223449 ACAAGTAATTCGAAACAGAGGGA 57.777 39.130 0.00 0.00 0.00 4.20
9092 10620 4.091509 CGACAAGTAATTCGAAACAGAGGG 59.908 45.833 0.00 0.00 37.43 4.30
9093 10621 4.434330 GCGACAAGTAATTCGAAACAGAGG 60.434 45.833 0.00 0.00 37.43 3.69
9094 10622 4.149922 TGCGACAAGTAATTCGAAACAGAG 59.850 41.667 0.00 0.00 37.43 3.35
9095 10623 4.052608 TGCGACAAGTAATTCGAAACAGA 58.947 39.130 0.00 0.00 37.43 3.41
9096 10624 4.383774 TGCGACAAGTAATTCGAAACAG 57.616 40.909 0.00 0.00 37.43 3.16
9097 10625 3.185594 CCTGCGACAAGTAATTCGAAACA 59.814 43.478 0.00 0.00 37.43 2.83
9098 10626 3.185797 ACCTGCGACAAGTAATTCGAAAC 59.814 43.478 0.00 0.00 37.43 2.78
9099 10627 3.395639 ACCTGCGACAAGTAATTCGAAA 58.604 40.909 0.00 0.00 37.43 3.46
9100 10628 3.034721 ACCTGCGACAAGTAATTCGAA 57.965 42.857 0.00 0.00 37.43 3.71
9101 10629 2.736144 ACCTGCGACAAGTAATTCGA 57.264 45.000 0.00 0.00 37.43 3.71
9102 10630 3.245284 CCATACCTGCGACAAGTAATTCG 59.755 47.826 0.00 0.00 38.31 3.34
9103 10631 4.439057 TCCATACCTGCGACAAGTAATTC 58.561 43.478 0.00 0.00 0.00 2.17
9104 10632 4.481368 TCCATACCTGCGACAAGTAATT 57.519 40.909 0.00 0.00 0.00 1.40
9105 10633 4.141711 ACATCCATACCTGCGACAAGTAAT 60.142 41.667 0.00 0.00 0.00 1.89
9106 10634 3.196901 ACATCCATACCTGCGACAAGTAA 59.803 43.478 0.00 0.00 0.00 2.24
9107 10635 2.764010 ACATCCATACCTGCGACAAGTA 59.236 45.455 0.00 0.00 0.00 2.24
9108 10636 1.555075 ACATCCATACCTGCGACAAGT 59.445 47.619 0.00 0.00 0.00 3.16
9109 10637 2.315925 ACATCCATACCTGCGACAAG 57.684 50.000 0.00 0.00 0.00 3.16
9110 10638 3.641436 AGATACATCCATACCTGCGACAA 59.359 43.478 0.00 0.00 0.00 3.18
9111 10639 3.230976 AGATACATCCATACCTGCGACA 58.769 45.455 0.00 0.00 0.00 4.35
9112 10640 3.944055 AGATACATCCATACCTGCGAC 57.056 47.619 0.00 0.00 0.00 5.19
9113 10641 4.918588 TCTAGATACATCCATACCTGCGA 58.081 43.478 0.00 0.00 0.00 5.10
9114 10642 5.126222 ACATCTAGATACATCCATACCTGCG 59.874 44.000 4.54 0.00 0.00 5.18
9115 10643 6.537453 ACATCTAGATACATCCATACCTGC 57.463 41.667 4.54 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.