Multiple sequence alignment - TraesCS4A01G113400

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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 TraesCS4A01G113400 chr4A 100.000 3418 0 0 1 3418 137539492 137542909 0.000000e+00 6312.0
1 TraesCS4A01G113400 chr4A 99.459 185 1 0 2799 2983 673448029 673447845 1.520000e-88 337.0
2 TraesCS4A01G113400 chr4B 92.786 2828 150 25 4 2802 413449795 413446993 0.000000e+00 4043.0
3 TraesCS4A01G113400 chr4B 91.406 384 21 8 2984 3367 413447011 413446640 1.820000e-142 516.0
4 TraesCS4A01G113400 chr4D 91.527 1428 88 12 4 1417 335336718 335335310 0.000000e+00 1936.0
5 TraesCS4A01G113400 chr4D 96.048 1164 41 5 1637 2798 335335132 335333972 0.000000e+00 1890.0
6 TraesCS4A01G113400 chr4D 94.378 249 14 0 3119 3367 335315743 335315495 1.920000e-102 383.0
7 TraesCS4A01G113400 chr4D 97.656 128 2 1 2996 3123 335315948 335315822 5.740000e-53 219.0
8 TraesCS4A01G113400 chr4D 90.647 139 13 0 1425 1563 335335270 335335132 5.820000e-43 185.0
9 TraesCS4A01G113400 chr4D 100.000 52 0 0 3367 3418 289620303 289620252 2.810000e-16 97.1
10 TraesCS4A01G113400 chr7B 87.569 724 69 13 1 717 124326559 124327268 0.000000e+00 819.0
11 TraesCS4A01G113400 chr7B 98.936 188 2 0 2796 2983 108539287 108539474 1.520000e-88 337.0
12 TraesCS4A01G113400 chr7B 98.421 190 3 0 2796 2985 34675629 34675818 5.470000e-88 335.0
13 TraesCS4A01G113400 chr7B 96.985 199 4 2 2789 2986 690699398 690699595 1.970000e-87 333.0
14 TraesCS4A01G113400 chr7B 94.634 205 7 4 2799 3002 358498316 358498517 7.120000e-82 315.0
15 TraesCS4A01G113400 chr7A 87.483 727 69 11 1 720 722260973 722261684 0.000000e+00 819.0
16 TraesCS4A01G113400 chr6A 86.933 727 73 12 1 720 140030693 140031404 0.000000e+00 797.0
17 TraesCS4A01G113400 chr6A 86.657 727 75 12 1 720 140052835 140053546 0.000000e+00 785.0
18 TraesCS4A01G113400 chr6A 96.923 195 5 1 2799 2993 397526000 397526193 3.290000e-85 326.0
19 TraesCS4A01G113400 chr6A 93.427 213 8 4 2786 2996 115320261 115320469 9.210000e-81 311.0
20 TraesCS4A01G113400 chr6A 100.000 52 0 0 3367 3418 381109339 381109288 2.810000e-16 97.1
21 TraesCS4A01G113400 chr6A 100.000 52 0 0 3367 3418 384031940 384031889 2.810000e-16 97.1
22 TraesCS4A01G113400 chr1D 85.560 741 102 5 1768 2507 203536261 203535525 0.000000e+00 771.0
23 TraesCS4A01G113400 chr1D 82.701 422 51 9 854 1263 203537085 203536674 4.200000e-94 355.0
24 TraesCS4A01G113400 chr1D 100.000 52 0 0 3367 3418 253205712 253205661 2.810000e-16 97.1
25 TraesCS4A01G113400 chr1A 85.460 729 103 3 1768 2495 258180765 258180039 0.000000e+00 756.0
26 TraesCS4A01G113400 chr1A 86.196 326 35 9 941 1263 258181447 258181129 9.080000e-91 344.0
27 TraesCS4A01G113400 chr1A 95.876 194 7 1 2799 2991 162803527 162803334 2.560000e-81 313.0
28 TraesCS4A01G113400 chr1B 85.198 581 76 6 1768 2346 297477528 297476956 3.800000e-164 588.0
29 TraesCS4A01G113400 chr1B 99.474 190 1 0 2799 2988 225811791 225811980 2.520000e-91 346.0
30 TraesCS4A01G113400 chr1B 93.269 208 11 3 2789 2995 374010345 374010140 1.540000e-78 303.0
31 TraesCS4A01G113400 chr1B 74.434 442 82 25 1085 1504 297480467 297480035 9.820000e-36 161.0
32 TraesCS4A01G113400 chr2A 83.735 498 62 8 228 720 766044615 766045098 1.450000e-123 453.0
33 TraesCS4A01G113400 chr5B 99.465 187 1 0 2798 2984 573807749 573807563 1.170000e-89 340.0
34 TraesCS4A01G113400 chr5B 98.947 190 2 0 2799 2988 654755921 654755732 1.170000e-89 340.0
35 TraesCS4A01G113400 chr5B 97.436 195 4 1 2799 2992 163080749 163080555 7.070000e-87 331.0
36 TraesCS4A01G113400 chr5B 94.554 202 7 4 2799 2996 225116293 225116494 3.310000e-80 309.0
37 TraesCS4A01G113400 chr5B 100.000 52 0 0 3367 3418 711721791 711721740 2.810000e-16 97.1
38 TraesCS4A01G113400 chr3B 98.947 190 2 0 2798 2987 473396910 473397099 1.170000e-89 340.0
39 TraesCS4A01G113400 chr6B 93.023 215 10 4 2783 2996 641288434 641288644 3.310000e-80 309.0
40 TraesCS4A01G113400 chr3D 100.000 52 0 0 3367 3418 123309702 123309753 2.810000e-16 97.1
41 TraesCS4A01G113400 chr2B 98.214 56 0 1 3364 3418 291606003 291606058 2.810000e-16 97.1
42 TraesCS4A01G113400 chr7D 93.548 62 2 1 3354 3415 503617482 503617541 1.310000e-14 91.6
43 TraesCS4A01G113400 chr3A 90.909 66 6 0 3353 3418 659016334 659016399 4.700000e-14 89.8


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 TraesCS4A01G113400 chr4A 137539492 137542909 3417 False 6312.0 6312 100.000000 1 3418 1 chr4A.!!$F1 3417
1 TraesCS4A01G113400 chr4B 413446640 413449795 3155 True 2279.5 4043 92.096000 4 3367 2 chr4B.!!$R1 3363
2 TraesCS4A01G113400 chr4D 335333972 335336718 2746 True 1337.0 1936 92.740667 4 2798 3 chr4D.!!$R3 2794
3 TraesCS4A01G113400 chr7B 124326559 124327268 709 False 819.0 819 87.569000 1 717 1 chr7B.!!$F3 716
4 TraesCS4A01G113400 chr7A 722260973 722261684 711 False 819.0 819 87.483000 1 720 1 chr7A.!!$F1 719
5 TraesCS4A01G113400 chr6A 140030693 140031404 711 False 797.0 797 86.933000 1 720 1 chr6A.!!$F2 719
6 TraesCS4A01G113400 chr6A 140052835 140053546 711 False 785.0 785 86.657000 1 720 1 chr6A.!!$F3 719
7 TraesCS4A01G113400 chr1D 203535525 203537085 1560 True 563.0 771 84.130500 854 2507 2 chr1D.!!$R2 1653
8 TraesCS4A01G113400 chr1A 258180039 258181447 1408 True 550.0 756 85.828000 941 2495 2 chr1A.!!$R2 1554
9 TraesCS4A01G113400 chr1B 297476956 297480467 3511 True 374.5 588 79.816000 1085 2346 2 chr1B.!!$R2 1261

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
706 714 0.036164 CTTCACCAACCCGGATGTGA 59.964 55.0 0.73 7.14 38.63 3.58 F
1417 1486 0.242017 AAGCTGCTCGGTCATTTTGC 59.758 50.0 1.00 0.00 0.00 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1706 4180 1.159285 CACCGATTGATGCACACAGT 58.841 50.0 0.0 0.0 0.00 3.55 R
2829 5309 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.0 0.0 0.0 44.78 4.85 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
44 45 3.192633 GTCGTATGCACAAGGGGAAATTT 59.807 43.478 0.00 0.00 0.00 1.82
47 48 4.321601 CGTATGCACAAGGGGAAATTTCAA 60.322 41.667 19.49 0.00 0.00 2.69
55 56 3.663025 AGGGGAAATTTCAAATGTTGCG 58.337 40.909 19.49 0.00 0.00 4.85
120 121 1.740332 GCGGCTAGGGAAGGAGACTC 61.740 65.000 0.00 0.00 42.68 3.36
132 133 5.131142 GGGAAGGAGACTCTGATAAAATCCA 59.869 44.000 1.74 0.00 42.68 3.41
136 137 5.309282 AGGAGACTCTGATAAAATCCATCCC 59.691 44.000 1.74 0.00 32.90 3.85
140 141 4.136796 CTCTGATAAAATCCATCCCGCAA 58.863 43.478 0.00 0.00 0.00 4.85
151 152 0.397535 ATCCCGCAAGCAATTCCCAT 60.398 50.000 0.00 0.00 0.00 4.00
186 187 3.312973 AGTGTTTAAATTGCCGTGTTCGA 59.687 39.130 0.00 0.00 39.71 3.71
195 196 0.237235 GCCGTGTTCGATTTGCAAGA 59.763 50.000 0.00 0.00 39.71 3.02
212 213 3.859627 GCAAGAACCTCACACGCTTAGTA 60.860 47.826 0.00 0.00 0.00 1.82
240 242 1.187087 TTTTGGGGTTCAAAGCACGT 58.813 45.000 0.00 0.00 45.00 4.49
258 260 2.755836 GTGCAACGAAAGACACACAT 57.244 45.000 0.00 0.00 34.69 3.21
264 266 1.269569 ACGAAAGACACACATGCGAGA 60.270 47.619 0.00 0.00 0.00 4.04
275 278 2.749076 CACATGCGAGAATGGGAGAAAA 59.251 45.455 0.00 0.00 32.30 2.29
276 279 3.379372 CACATGCGAGAATGGGAGAAAAT 59.621 43.478 0.00 0.00 32.30 1.82
277 280 4.576053 CACATGCGAGAATGGGAGAAAATA 59.424 41.667 0.00 0.00 32.30 1.40
297 300 2.549064 AATTGAACCAAAGGGCAAGC 57.451 45.000 0.00 0.00 37.90 4.01
303 306 2.362889 CAAAGGGCAAGCGGGGAT 60.363 61.111 0.00 0.00 0.00 3.85
341 344 1.678728 CGCATCTTCAACCAGGCCTTA 60.679 52.381 0.00 0.00 0.00 2.69
349 352 0.618458 AACCAGGCCTTATTCGCTCA 59.382 50.000 0.00 0.00 0.00 4.26
394 397 2.630580 GACCGGATTCCTTATGCTCTCT 59.369 50.000 9.46 0.00 0.00 3.10
395 398 3.041946 ACCGGATTCCTTATGCTCTCTT 58.958 45.455 9.46 0.00 0.00 2.85
396 399 3.181461 ACCGGATTCCTTATGCTCTCTTG 60.181 47.826 9.46 0.00 0.00 3.02
397 400 2.805099 CGGATTCCTTATGCTCTCTTGC 59.195 50.000 0.30 0.00 0.00 4.01
398 401 3.145286 GGATTCCTTATGCTCTCTTGCC 58.855 50.000 0.00 0.00 0.00 4.52
399 402 3.181446 GGATTCCTTATGCTCTCTTGCCT 60.181 47.826 0.00 0.00 0.00 4.75
400 403 3.550437 TTCCTTATGCTCTCTTGCCTC 57.450 47.619 0.00 0.00 0.00 4.70
401 404 2.756907 TCCTTATGCTCTCTTGCCTCT 58.243 47.619 0.00 0.00 0.00 3.69
402 405 2.697751 TCCTTATGCTCTCTTGCCTCTC 59.302 50.000 0.00 0.00 0.00 3.20
403 406 2.699846 CCTTATGCTCTCTTGCCTCTCT 59.300 50.000 0.00 0.00 0.00 3.10
415 418 2.991250 TGCCTCTCTGGTATTGAAAGC 58.009 47.619 0.00 0.00 38.35 3.51
442 445 4.692523 AATTATCCAAACAGGTCCCCTT 57.307 40.909 0.00 0.00 39.02 3.95
452 455 0.338814 AGGTCCCCTTGAGGATACGT 59.661 55.000 0.00 0.00 46.39 3.57
453 456 1.201424 GGTCCCCTTGAGGATACGTT 58.799 55.000 0.00 0.00 46.39 3.99
482 485 1.153784 CAATGCGTCCCCAACATGC 60.154 57.895 0.00 0.00 0.00 4.06
487 490 2.282180 GTCCCCAACATGCCACGT 60.282 61.111 0.00 0.00 0.00 4.49
491 494 0.393673 CCCCAACATGCCACGTGATA 60.394 55.000 19.30 5.56 0.00 2.15
585 593 4.815973 ACCCCTGGCCCTCGCATA 62.816 66.667 0.00 0.00 36.38 3.14
706 714 0.036164 CTTCACCAACCCGGATGTGA 59.964 55.000 0.73 7.14 38.63 3.58
774 782 4.458989 AGAGCAAACCGAAAAATAGCATGA 59.541 37.500 0.00 0.00 0.00 3.07
795 803 0.940833 TACACCACATTGCACACACG 59.059 50.000 0.00 0.00 0.00 4.49
1118 1134 2.535331 CTTCGCTCCTCTTTCTGCTAC 58.465 52.381 0.00 0.00 0.00 3.58
1138 1156 1.143183 CCGTGTGGACTAATCCCCG 59.857 63.158 0.00 0.00 45.59 5.73
1235 1253 0.468226 TCCCCATCGTGTAAGCATCC 59.532 55.000 0.00 0.00 0.00 3.51
1280 1341 2.930826 TTAAATGGGGATCTCCTCGC 57.069 50.000 14.22 0.00 40.19 5.03
1410 1479 0.809241 CAGATGGAAGCTGCTCGGTC 60.809 60.000 1.00 0.00 46.61 4.79
1417 1486 0.242017 AAGCTGCTCGGTCATTTTGC 59.758 50.000 1.00 0.00 0.00 3.68
1418 1487 0.890542 AGCTGCTCGGTCATTTTGCA 60.891 50.000 0.00 0.00 0.00 4.08
1419 1488 3.689224 CTGCTCGGTCATTTTGCAG 57.311 52.632 0.00 0.00 43.71 4.41
1420 1489 0.877071 CTGCTCGGTCATTTTGCAGT 59.123 50.000 0.00 0.00 44.04 4.40
1421 1490 2.076100 CTGCTCGGTCATTTTGCAGTA 58.924 47.619 0.00 0.00 44.04 2.74
1422 1491 2.076100 TGCTCGGTCATTTTGCAGTAG 58.924 47.619 0.00 0.00 0.00 2.57
1423 1492 2.076863 GCTCGGTCATTTTGCAGTAGT 58.923 47.619 0.00 0.00 0.00 2.73
1492 1607 6.017109 GCACCGTATATTGGTTGATGAATTCT 60.017 38.462 7.05 0.00 37.72 2.40
1513 3981 7.636259 TTCTGCAAATGTTGTAGTTTAATGC 57.364 32.000 6.07 0.00 42.93 3.56
1535 4003 6.539173 TGCCGTTATTATTTCCATCCATAGT 58.461 36.000 0.00 0.00 0.00 2.12
1536 4004 6.653320 TGCCGTTATTATTTCCATCCATAGTC 59.347 38.462 0.00 0.00 0.00 2.59
1555 4029 2.351726 GTCACCGCAAGATACATTGGAC 59.648 50.000 0.00 0.00 43.02 4.02
1631 4105 4.648762 AGATGTGACCGAGATCTCAGATTT 59.351 41.667 22.31 0.82 28.25 2.17
1675 4149 6.741992 TCATTAAGATGCACGAATGTTCTT 57.258 33.333 0.00 0.00 35.71 2.52
1730 4204 1.299321 TGCATCAATCGGTGCAGGA 59.701 52.632 0.00 0.00 45.60 3.86
1741 4215 2.203983 TGCAGGAGCTGGGGAGAA 60.204 61.111 0.00 0.00 42.74 2.87
1887 4362 5.049680 TCTGCAACCGTTCATTAACTTCTTC 60.050 40.000 0.00 0.00 33.15 2.87
1968 4443 6.177610 TCCCGCATTATGAGTCTAAACTTTT 58.822 36.000 0.00 0.00 35.28 2.27
2152 4627 6.889198 AGTTATGCAGATTGGAGCTTACTTA 58.111 36.000 0.00 0.00 0.00 2.24
2240 4716 9.490083 TTCCTCTTAAGCCTTCTTTAGTATACT 57.510 33.333 10.87 10.87 32.44 2.12
2243 4719 9.752961 CTCTTAAGCCTTCTTTAGTATACTTCC 57.247 37.037 11.40 0.00 32.44 3.46
2555 5031 9.751542 ATTTAAGATCAGTTTCTACGTATCCAG 57.248 33.333 0.00 0.00 0.00 3.86
2567 5043 5.865552 TCTACGTATCCAGTTGTTTGCTTAC 59.134 40.000 0.00 0.00 0.00 2.34
2582 5058 6.201806 TGTTTGCTTACATTTTGGGAATTTCG 59.798 34.615 0.00 0.00 0.00 3.46
2798 5278 5.660629 TTGTTGTAGTACCATGTTTGACG 57.339 39.130 0.00 0.00 0.00 4.35
2799 5279 4.946445 TGTTGTAGTACCATGTTTGACGA 58.054 39.130 0.00 0.00 0.00 4.20
2800 5280 5.358090 TGTTGTAGTACCATGTTTGACGAA 58.642 37.500 0.00 0.00 0.00 3.85
2801 5281 5.464057 TGTTGTAGTACCATGTTTGACGAAG 59.536 40.000 0.00 0.00 0.00 3.79
2802 5282 4.562082 TGTAGTACCATGTTTGACGAAGG 58.438 43.478 0.00 0.00 0.00 3.46
2803 5283 3.053831 AGTACCATGTTTGACGAAGGG 57.946 47.619 0.00 0.00 0.00 3.95
2804 5284 2.081462 GTACCATGTTTGACGAAGGGG 58.919 52.381 0.00 0.00 0.00 4.79
2805 5285 0.768622 ACCATGTTTGACGAAGGGGA 59.231 50.000 0.00 0.00 0.00 4.81
2806 5286 1.271379 ACCATGTTTGACGAAGGGGAG 60.271 52.381 0.00 0.00 0.00 4.30
2807 5287 0.804989 CATGTTTGACGAAGGGGAGC 59.195 55.000 0.00 0.00 0.00 4.70
2808 5288 0.322546 ATGTTTGACGAAGGGGAGCC 60.323 55.000 0.00 0.00 0.00 4.70
2809 5289 1.375326 GTTTGACGAAGGGGAGCCT 59.625 57.895 0.00 0.00 0.00 4.58
2810 5290 0.250770 GTTTGACGAAGGGGAGCCTT 60.251 55.000 0.00 0.00 0.00 4.35
2811 5291 0.250727 TTTGACGAAGGGGAGCCTTG 60.251 55.000 0.00 0.00 0.00 3.61
2812 5292 2.124507 TTGACGAAGGGGAGCCTTGG 62.125 60.000 0.00 0.00 0.00 3.61
2813 5293 3.978571 GACGAAGGGGAGCCTTGGC 62.979 68.421 2.97 2.97 0.00 4.52
2819 5299 3.830192 GGGAGCCTTGGCGCAATG 61.830 66.667 16.55 0.00 0.00 2.82
2820 5300 3.830192 GGAGCCTTGGCGCAATGG 61.830 66.667 12.38 12.38 0.00 3.16
2821 5301 3.064324 GAGCCTTGGCGCAATGGT 61.064 61.111 17.44 8.55 0.00 3.55
2822 5302 1.748879 GAGCCTTGGCGCAATGGTA 60.749 57.895 17.44 0.00 0.00 3.25
2823 5303 1.304052 AGCCTTGGCGCAATGGTAA 60.304 52.632 17.44 0.00 0.00 2.85
2824 5304 0.897863 AGCCTTGGCGCAATGGTAAA 60.898 50.000 17.44 0.00 0.00 2.01
2825 5305 0.458370 GCCTTGGCGCAATGGTAAAG 60.458 55.000 17.44 5.26 0.00 1.85
2826 5306 0.458370 CCTTGGCGCAATGGTAAAGC 60.458 55.000 10.83 0.00 0.00 3.51
2827 5307 0.527565 CTTGGCGCAATGGTAAAGCT 59.472 50.000 10.83 0.00 0.00 3.74
2828 5308 0.243365 TTGGCGCAATGGTAAAGCTG 59.757 50.000 10.83 0.00 0.00 4.24
2829 5309 1.517039 GGCGCAATGGTAAAGCTGC 60.517 57.895 10.83 0.00 0.00 5.25
2830 5310 1.508088 GCGCAATGGTAAAGCTGCT 59.492 52.632 0.30 0.00 32.52 4.24
2831 5311 0.799534 GCGCAATGGTAAAGCTGCTG 60.800 55.000 1.35 0.00 32.52 4.41
2832 5312 0.799534 CGCAATGGTAAAGCTGCTGC 60.800 55.000 1.35 7.62 40.05 5.25
2833 5313 0.459063 GCAATGGTAAAGCTGCTGCC 60.459 55.000 12.44 7.07 40.80 4.85
2834 5314 1.180029 CAATGGTAAAGCTGCTGCCT 58.820 50.000 12.44 2.45 40.80 4.75
2835 5315 1.547372 CAATGGTAAAGCTGCTGCCTT 59.453 47.619 12.44 8.34 40.80 4.35
2836 5316 1.180029 ATGGTAAAGCTGCTGCCTTG 58.820 50.000 12.44 0.00 40.80 3.61
2837 5317 0.178992 TGGTAAAGCTGCTGCCTTGT 60.179 50.000 12.44 0.00 40.80 3.16
2838 5318 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.000 12.44 0.00 40.80 3.33
2839 5319 1.238439 GTAAAGCTGCTGCCTTGTGA 58.762 50.000 12.44 0.00 40.80 3.58
2840 5320 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.00 40.80 3.67
2841 5321 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
2842 5322 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
2843 5323 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
2844 5324 1.880894 CTGCTGCCTTGTGACCATG 59.119 57.895 0.00 0.00 0.00 3.66
2845 5325 0.607217 CTGCTGCCTTGTGACCATGA 60.607 55.000 0.00 0.00 0.00 3.07
2846 5326 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
2847 5327 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
2857 5337 4.617875 CCATGAGGTCACGGGTTC 57.382 61.111 0.00 0.00 0.00 3.62
2858 5338 1.676968 CCATGAGGTCACGGGTTCA 59.323 57.895 0.00 0.00 0.00 3.18
2859 5339 0.036164 CCATGAGGTCACGGGTTCAA 59.964 55.000 0.00 0.00 0.00 2.69
2860 5340 1.442769 CATGAGGTCACGGGTTCAAG 58.557 55.000 0.00 0.00 0.00 3.02
2861 5341 1.056660 ATGAGGTCACGGGTTCAAGT 58.943 50.000 0.00 0.00 0.00 3.16
2862 5342 0.391597 TGAGGTCACGGGTTCAAGTC 59.608 55.000 0.00 0.00 0.00 3.01
2863 5343 0.320508 GAGGTCACGGGTTCAAGTCC 60.321 60.000 0.00 0.00 0.00 3.85
2864 5344 0.763223 AGGTCACGGGTTCAAGTCCT 60.763 55.000 0.00 0.00 0.00 3.85
2865 5345 0.602905 GGTCACGGGTTCAAGTCCTG 60.603 60.000 0.00 0.00 37.36 3.86
2866 5346 0.602905 GTCACGGGTTCAAGTCCTGG 60.603 60.000 0.00 0.00 35.79 4.45
2867 5347 0.761323 TCACGGGTTCAAGTCCTGGA 60.761 55.000 0.00 0.00 35.79 3.86
2868 5348 0.107831 CACGGGTTCAAGTCCTGGAA 59.892 55.000 0.00 0.00 35.79 3.53
2869 5349 0.841289 ACGGGTTCAAGTCCTGGAAA 59.159 50.000 0.00 0.00 35.79 3.13
2870 5350 1.235724 CGGGTTCAAGTCCTGGAAAC 58.764 55.000 0.00 0.00 0.00 2.78
2871 5351 1.476110 CGGGTTCAAGTCCTGGAAACA 60.476 52.381 0.00 0.00 32.36 2.83
2885 5365 4.431416 TGGAAACAGCCTCTTACAGAAA 57.569 40.909 0.00 0.00 35.01 2.52
2886 5366 4.985538 TGGAAACAGCCTCTTACAGAAAT 58.014 39.130 0.00 0.00 35.01 2.17
2887 5367 4.761739 TGGAAACAGCCTCTTACAGAAATG 59.238 41.667 0.00 0.00 35.01 2.32
2888 5368 4.762251 GGAAACAGCCTCTTACAGAAATGT 59.238 41.667 0.00 0.00 0.00 2.71
2889 5369 5.938125 GGAAACAGCCTCTTACAGAAATGTA 59.062 40.000 0.00 0.00 0.00 2.29
2890 5370 6.092807 GGAAACAGCCTCTTACAGAAATGTAG 59.907 42.308 0.00 0.00 0.00 2.74
2891 5371 5.091261 ACAGCCTCTTACAGAAATGTAGG 57.909 43.478 0.00 0.00 0.00 3.18
2892 5372 4.080863 ACAGCCTCTTACAGAAATGTAGGG 60.081 45.833 0.00 0.66 0.00 3.53
2893 5373 4.162320 CAGCCTCTTACAGAAATGTAGGGA 59.838 45.833 0.00 0.00 0.00 4.20
2894 5374 4.783227 AGCCTCTTACAGAAATGTAGGGAA 59.217 41.667 0.00 0.00 0.00 3.97
2895 5375 5.250774 AGCCTCTTACAGAAATGTAGGGAAA 59.749 40.000 0.00 0.00 0.00 3.13
2896 5376 5.586643 GCCTCTTACAGAAATGTAGGGAAAG 59.413 44.000 0.00 0.00 0.00 2.62
2897 5377 6.116126 CCTCTTACAGAAATGTAGGGAAAGG 58.884 44.000 0.00 0.00 0.00 3.11
2898 5378 5.497474 TCTTACAGAAATGTAGGGAAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
2899 5379 5.250774 TCTTACAGAAATGTAGGGAAAGGCT 59.749 40.000 0.00 0.00 0.00 4.58
2900 5380 3.690460 ACAGAAATGTAGGGAAAGGCTG 58.310 45.455 0.00 0.00 0.00 4.85
2901 5381 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
2902 5382 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
2903 5383 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
2904 5384 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
2905 5385 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
2906 5386 0.535797 GTAGGGAAAGGCTGCGTACT 59.464 55.000 0.00 0.00 34.81 2.73
2907 5387 1.753073 GTAGGGAAAGGCTGCGTACTA 59.247 52.381 0.00 0.00 34.81 1.82
2908 5388 1.497161 AGGGAAAGGCTGCGTACTAT 58.503 50.000 0.00 0.00 0.00 2.12
2909 5389 2.674420 AGGGAAAGGCTGCGTACTATA 58.326 47.619 0.00 0.00 0.00 1.31
2910 5390 2.628657 AGGGAAAGGCTGCGTACTATAG 59.371 50.000 0.00 0.00 0.00 1.31
2911 5391 2.626743 GGGAAAGGCTGCGTACTATAGA 59.373 50.000 6.78 0.00 0.00 1.98
2912 5392 3.552478 GGGAAAGGCTGCGTACTATAGAC 60.552 52.174 6.78 0.00 0.00 2.59
2913 5393 3.552478 GGAAAGGCTGCGTACTATAGACC 60.552 52.174 6.78 0.00 0.00 3.85
2914 5394 1.618487 AGGCTGCGTACTATAGACCC 58.382 55.000 6.78 0.00 0.00 4.46
2915 5395 1.133575 AGGCTGCGTACTATAGACCCA 60.134 52.381 6.78 0.00 0.00 4.51
2916 5396 1.684983 GGCTGCGTACTATAGACCCAA 59.315 52.381 6.78 0.00 0.00 4.12
2917 5397 2.101917 GGCTGCGTACTATAGACCCAAA 59.898 50.000 6.78 0.00 0.00 3.28
2918 5398 3.381949 GCTGCGTACTATAGACCCAAAG 58.618 50.000 6.78 0.00 0.00 2.77
2919 5399 3.181478 GCTGCGTACTATAGACCCAAAGT 60.181 47.826 6.78 0.00 0.00 2.66
2920 5400 4.360563 CTGCGTACTATAGACCCAAAGTG 58.639 47.826 6.78 0.00 0.00 3.16
2921 5401 3.131577 TGCGTACTATAGACCCAAAGTGG 59.868 47.826 6.78 0.00 37.25 4.00
2922 5402 3.131755 GCGTACTATAGACCCAAAGTGGT 59.868 47.826 6.78 0.00 42.79 4.16
2927 5407 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
2928 5408 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
2929 5409 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
2930 5410 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
2931 5411 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
2932 5412 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
2933 5413 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
2934 5414 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
2935 5415 3.714001 GTGGTCGGACCCTTCCCC 61.714 72.222 23.81 0.00 38.99 4.81
2941 5421 4.735599 GGACCCTTCCCCGACCCT 62.736 72.222 0.00 0.00 35.57 4.34
2942 5422 3.400054 GACCCTTCCCCGACCCTG 61.400 72.222 0.00 0.00 0.00 4.45
2968 5448 2.203070 GGAGCTACATGCACCGGG 60.203 66.667 6.32 0.00 42.21 5.73
2969 5449 2.897350 GAGCTACATGCACCGGGC 60.897 66.667 6.32 7.25 45.94 6.13
2970 5450 3.391665 GAGCTACATGCACCGGGCT 62.392 63.158 6.32 0.81 45.94 5.19
2971 5451 3.204827 GCTACATGCACCGGGCTG 61.205 66.667 6.32 9.21 45.15 4.85
2972 5452 3.204827 CTACATGCACCGGGCTGC 61.205 66.667 6.32 8.50 45.15 5.25
2973 5453 4.794648 TACATGCACCGGGCTGCC 62.795 66.667 11.05 11.05 45.15 4.85
2979 5459 2.917227 CACCGGGCTGCCCTTTTT 60.917 61.111 33.39 13.23 42.67 1.94
3023 5503 3.314635 GCAATTCCCTGCTGACTAAGATG 59.685 47.826 0.00 0.00 39.34 2.90
3087 5567 7.659652 ATCTGTTTGACTTGCTTTACTCTAC 57.340 36.000 0.00 0.00 0.00 2.59
3096 5576 7.913821 TGACTTGCTTTACTCTACGTATGTATG 59.086 37.037 0.00 1.52 0.00 2.39
3146 5626 4.456566 TCTTACGGTTCCTTAAATGTTGCC 59.543 41.667 0.00 0.00 0.00 4.52
3155 5635 3.738791 CCTTAAATGTTGCCGTTTTGGAC 59.261 43.478 0.00 0.00 42.00 4.02
3159 5639 1.393603 TGTTGCCGTTTTGGACATCA 58.606 45.000 0.00 0.00 42.00 3.07
3168 5648 5.393027 GCCGTTTTGGACATCAACATAGATT 60.393 40.000 0.00 0.00 42.00 2.40
3227 5707 6.948309 ACATATAGAGAAAGCCCAACAAAACT 59.052 34.615 0.00 0.00 0.00 2.66
3249 5729 7.974730 ACTATATATTGTAGGGAGTTAGGGC 57.025 40.000 0.00 0.00 0.00 5.19
3258 5738 1.840635 GGGAGTTAGGGCTGATTCACT 59.159 52.381 0.00 0.00 0.00 3.41
3262 5742 0.107703 TTAGGGCTGATTCACTGGCG 60.108 55.000 0.00 0.00 42.23 5.69
3285 5765 2.756829 CGAGAGCATTGATCATGAGCT 58.243 47.619 12.92 14.55 38.43 4.09
3288 5768 1.799403 GAGCATTGATCATGAGCTCCG 59.201 52.381 23.50 2.17 44.37 4.63
3289 5769 1.140452 AGCATTGATCATGAGCTCCGT 59.860 47.619 12.92 0.00 34.31 4.69
3290 5770 1.263484 GCATTGATCATGAGCTCCGTG 59.737 52.381 12.92 10.49 34.31 4.94
3291 5771 2.830104 CATTGATCATGAGCTCCGTGA 58.170 47.619 17.90 17.90 44.24 4.35
3324 5804 6.627087 TGAGAAGGGTCAACAAGAGATTAT 57.373 37.500 0.00 0.00 0.00 1.28
3325 5805 7.020827 TGAGAAGGGTCAACAAGAGATTATT 57.979 36.000 0.00 0.00 0.00 1.40
3356 5836 2.051334 TATCAATTGGAGCGTTGGGG 57.949 50.000 5.42 0.00 0.00 4.96
3367 5847 3.257375 GGAGCGTTGGGGTTTATTTCTTT 59.743 43.478 0.00 0.00 0.00 2.52
3368 5848 4.234574 GAGCGTTGGGGTTTATTTCTTTG 58.765 43.478 0.00 0.00 0.00 2.77
3369 5849 3.639561 AGCGTTGGGGTTTATTTCTTTGT 59.360 39.130 0.00 0.00 0.00 2.83
3370 5850 4.100344 AGCGTTGGGGTTTATTTCTTTGTT 59.900 37.500 0.00 0.00 0.00 2.83
3371 5851 5.302313 AGCGTTGGGGTTTATTTCTTTGTTA 59.698 36.000 0.00 0.00 0.00 2.41
3372 5852 5.631929 GCGTTGGGGTTTATTTCTTTGTTAG 59.368 40.000 0.00 0.00 0.00 2.34
3373 5853 6.515365 GCGTTGGGGTTTATTTCTTTGTTAGA 60.515 38.462 0.00 0.00 0.00 2.10
3374 5854 7.081976 CGTTGGGGTTTATTTCTTTGTTAGAG 58.918 38.462 0.00 0.00 33.51 2.43
3375 5855 7.255346 CGTTGGGGTTTATTTCTTTGTTAGAGT 60.255 37.037 0.00 0.00 33.51 3.24
3376 5856 9.070179 GTTGGGGTTTATTTCTTTGTTAGAGTA 57.930 33.333 0.00 0.00 33.51 2.59
3377 5857 8.625786 TGGGGTTTATTTCTTTGTTAGAGTAC 57.374 34.615 0.00 0.00 33.51 2.73
3378 5858 7.388500 TGGGGTTTATTTCTTTGTTAGAGTACG 59.612 37.037 0.00 0.00 33.51 3.67
3379 5859 7.388776 GGGGTTTATTTCTTTGTTAGAGTACGT 59.611 37.037 0.00 0.00 33.51 3.57
3380 5860 9.423061 GGGTTTATTTCTTTGTTAGAGTACGTA 57.577 33.333 0.00 0.00 33.51 3.57
3385 5865 7.894376 TTTCTTTGTTAGAGTACGTAATGGG 57.106 36.000 0.00 0.00 33.51 4.00
3386 5866 5.413499 TCTTTGTTAGAGTACGTAATGGGC 58.587 41.667 0.00 0.00 0.00 5.36
3387 5867 3.806625 TGTTAGAGTACGTAATGGGCC 57.193 47.619 0.00 0.00 0.00 5.80
3388 5868 3.368248 TGTTAGAGTACGTAATGGGCCT 58.632 45.455 4.53 0.00 0.00 5.19
3389 5869 4.535781 TGTTAGAGTACGTAATGGGCCTA 58.464 43.478 4.53 0.00 0.00 3.93
3390 5870 4.955450 TGTTAGAGTACGTAATGGGCCTAA 59.045 41.667 4.53 0.00 0.00 2.69
3391 5871 5.599656 TGTTAGAGTACGTAATGGGCCTAAT 59.400 40.000 4.53 0.00 0.00 1.73
3392 5872 4.602340 AGAGTACGTAATGGGCCTAATG 57.398 45.455 4.53 0.00 0.00 1.90
3393 5873 3.323979 AGAGTACGTAATGGGCCTAATGG 59.676 47.826 4.53 0.00 0.00 3.16
3403 5883 2.196776 CCTAATGGCCTGGGCTGG 59.803 66.667 21.72 13.52 41.60 4.85
3410 5890 3.556306 GCCTGGGCTGGCGGTATA 61.556 66.667 4.12 0.00 43.74 1.47
3411 5891 2.743718 CCTGGGCTGGCGGTATAG 59.256 66.667 0.00 0.00 0.00 1.31
3412 5892 2.031163 CTGGGCTGGCGGTATAGC 59.969 66.667 0.00 0.00 39.17 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 1.169661 AACTCGCCCGCAACATTTGA 61.170 50.000 0.00 0.00 0.00 2.69
47 48 1.169661 TCAAACTCGCCCGCAACATT 61.170 50.000 0.00 0.00 0.00 2.71
55 56 1.314730 TCTTTTGGTCAAACTCGCCC 58.685 50.000 0.00 0.00 0.00 6.13
95 96 2.833582 TTCCCTAGCCGCGAGAGG 60.834 66.667 8.23 10.97 0.00 3.69
103 104 1.063567 TCAGAGTCTCCTTCCCTAGCC 60.064 57.143 0.00 0.00 0.00 3.93
120 121 3.304928 GCTTGCGGGATGGATTTTATCAG 60.305 47.826 0.00 0.00 0.00 2.90
132 133 0.397535 ATGGGAATTGCTTGCGGGAT 60.398 50.000 0.00 0.00 0.00 3.85
136 137 7.276218 CCATAATATAAATGGGAATTGCTTGCG 59.724 37.037 8.53 0.00 40.27 4.85
170 171 3.238441 GCAAATCGAACACGGCAATTTA 58.762 40.909 0.00 0.00 0.00 1.40
186 187 1.001378 GCGTGTGAGGTTCTTGCAAAT 60.001 47.619 0.00 0.00 0.00 2.32
195 196 2.895404 TCCTTACTAAGCGTGTGAGGTT 59.105 45.455 13.85 0.00 40.65 3.50
223 224 2.010582 GCACGTGCTTTGAACCCCAA 62.011 55.000 32.55 0.00 38.21 4.12
240 242 1.268488 GCATGTGTGTCTTTCGTTGCA 60.268 47.619 0.00 0.00 0.00 4.08
257 259 6.966534 ATTTATTTTCTCCCATTCTCGCAT 57.033 33.333 0.00 0.00 0.00 4.73
258 260 6.376864 TCAATTTATTTTCTCCCATTCTCGCA 59.623 34.615 0.00 0.00 0.00 5.10
264 266 9.506018 CTTTGGTTCAATTTATTTTCTCCCATT 57.494 29.630 0.00 0.00 0.00 3.16
275 278 4.578871 GCTTGCCCTTTGGTTCAATTTAT 58.421 39.130 0.00 0.00 0.00 1.40
276 279 3.553922 CGCTTGCCCTTTGGTTCAATTTA 60.554 43.478 0.00 0.00 0.00 1.40
277 280 2.806382 CGCTTGCCCTTTGGTTCAATTT 60.806 45.455 0.00 0.00 0.00 1.82
297 300 2.045340 ACGGAAGCCAAATCCCCG 60.045 61.111 0.00 0.00 45.09 5.73
303 306 0.882927 CGGAAGTCACGGAAGCCAAA 60.883 55.000 0.00 0.00 0.00 3.28
394 397 3.244875 TGCTTTCAATACCAGAGAGGCAA 60.245 43.478 0.00 0.00 43.14 4.52
395 398 2.305635 TGCTTTCAATACCAGAGAGGCA 59.694 45.455 0.00 0.00 43.14 4.75
396 399 2.991250 TGCTTTCAATACCAGAGAGGC 58.009 47.619 0.00 0.00 43.14 4.70
397 400 5.964958 TTTTGCTTTCAATACCAGAGAGG 57.035 39.130 0.00 0.00 36.22 3.69
487 490 1.473257 GCTCGAGGCCATGTTGTATCA 60.473 52.381 15.58 0.00 34.27 2.15
491 494 1.376424 CAGCTCGAGGCCATGTTGT 60.376 57.895 15.58 0.00 43.05 3.32
576 579 1.689273 GGCCTATAGGATATGCGAGGG 59.311 57.143 23.61 5.33 37.39 4.30
577 580 2.388735 TGGCCTATAGGATATGCGAGG 58.611 52.381 23.61 8.04 37.39 4.63
585 593 2.303022 CACCGTGATTGGCCTATAGGAT 59.697 50.000 23.61 7.08 37.39 3.24
670 678 6.070656 TGGTGAAGAATTGTTGAAGGAGATT 58.929 36.000 0.00 0.00 0.00 2.40
733 741 5.759059 TGCTCTTTCCTTGATAATGGATGT 58.241 37.500 0.00 0.00 31.76 3.06
739 747 5.253330 TCGGTTTGCTCTTTCCTTGATAAT 58.747 37.500 0.00 0.00 0.00 1.28
744 752 3.708563 TTTCGGTTTGCTCTTTCCTTG 57.291 42.857 0.00 0.00 0.00 3.61
745 753 4.729227 TTTTTCGGTTTGCTCTTTCCTT 57.271 36.364 0.00 0.00 0.00 3.36
774 782 1.946768 GTGTGTGCAATGTGGTGTACT 59.053 47.619 0.00 0.00 35.39 2.73
1235 1253 1.470979 CGAGTTATCGTGGTTGGGGAG 60.471 57.143 0.00 0.00 44.09 4.30
1280 1341 3.553828 ATGGGTAACGGTGGTTATGAG 57.446 47.619 0.00 0.00 40.53 2.90
1410 1479 8.717821 TGCTAACTAACTAACTACTGCAAAATG 58.282 33.333 0.00 0.00 0.00 2.32
1417 1486 5.638783 AGCGTGCTAACTAACTAACTACTG 58.361 41.667 0.00 0.00 0.00 2.74
1418 1487 5.893897 AGCGTGCTAACTAACTAACTACT 57.106 39.130 0.00 0.00 0.00 2.57
1419 1488 6.546395 TGTAGCGTGCTAACTAACTAACTAC 58.454 40.000 2.62 0.00 0.00 2.73
1420 1489 6.741992 TGTAGCGTGCTAACTAACTAACTA 57.258 37.500 2.62 0.00 0.00 2.24
1421 1490 5.633830 TGTAGCGTGCTAACTAACTAACT 57.366 39.130 2.62 0.00 0.00 2.24
1422 1491 6.020837 GTCATGTAGCGTGCTAACTAACTAAC 60.021 42.308 2.62 0.00 0.00 2.34
1423 1492 6.032094 GTCATGTAGCGTGCTAACTAACTAA 58.968 40.000 2.62 0.00 0.00 2.24
1492 1607 4.920340 CGGCATTAAACTACAACATTTGCA 59.080 37.500 0.00 0.00 0.00 4.08
1513 3981 7.119262 GGTGACTATGGATGGAAATAATAACGG 59.881 40.741 0.00 0.00 0.00 4.44
1535 4003 2.027653 TGTCCAATGTATCTTGCGGTGA 60.028 45.455 0.00 0.00 0.00 4.02
1536 4004 2.355197 TGTCCAATGTATCTTGCGGTG 58.645 47.619 0.00 0.00 0.00 4.94
1706 4180 1.159285 CACCGATTGATGCACACAGT 58.841 50.000 0.00 0.00 0.00 3.55
1887 4362 2.354259 GTCTGCAGATTGTTCCTCCTG 58.646 52.381 21.47 0.00 0.00 3.86
1968 4443 9.268268 GGTCAAATTATCCGTACATAAATGAGA 57.732 33.333 0.00 0.00 0.00 3.27
2152 4627 6.787170 TGGGGATACGTACATAGAGACTAAT 58.213 40.000 0.00 0.00 37.60 1.73
2240 4716 9.753674 ATTAAATTAATTCTGACAGTCCAGGAA 57.246 29.630 0.10 1.00 34.99 3.36
2555 5031 6.859420 ATTCCCAAAATGTAAGCAAACAAC 57.141 33.333 0.00 0.00 32.02 3.32
2567 5043 7.090173 AGTTCATACACGAAATTCCCAAAATG 58.910 34.615 0.00 0.00 0.00 2.32
2582 5058 6.128795 GCTCAACTAGTGTGAAGTTCATACAC 60.129 42.308 27.93 21.69 40.39 2.90
2802 5282 3.830192 CATTGCGCCAAGGCTCCC 61.830 66.667 4.18 0.00 39.32 4.30
2803 5283 3.830192 CCATTGCGCCAAGGCTCC 61.830 66.667 4.18 0.71 39.32 4.70
2804 5284 1.312371 TTACCATTGCGCCAAGGCTC 61.312 55.000 4.18 1.20 39.32 4.70
2805 5285 0.897863 TTTACCATTGCGCCAAGGCT 60.898 50.000 4.18 0.00 39.32 4.58
2806 5286 0.458370 CTTTACCATTGCGCCAAGGC 60.458 55.000 4.18 0.00 37.85 4.35
2807 5287 0.458370 GCTTTACCATTGCGCCAAGG 60.458 55.000 4.18 2.13 0.00 3.61
2808 5288 0.527565 AGCTTTACCATTGCGCCAAG 59.472 50.000 4.18 0.00 0.00 3.61
2809 5289 0.243365 CAGCTTTACCATTGCGCCAA 59.757 50.000 4.18 0.00 0.00 4.52
2810 5290 1.882311 CAGCTTTACCATTGCGCCA 59.118 52.632 4.18 0.00 0.00 5.69
2811 5291 1.517039 GCAGCTTTACCATTGCGCC 60.517 57.895 4.18 0.00 0.00 6.53
2812 5292 0.799534 CAGCAGCTTTACCATTGCGC 60.800 55.000 0.00 0.00 41.27 6.09
2813 5293 0.799534 GCAGCAGCTTTACCATTGCG 60.800 55.000 0.00 0.00 41.27 4.85
2814 5294 0.459063 GGCAGCAGCTTTACCATTGC 60.459 55.000 0.00 0.00 41.70 3.56
2815 5295 1.180029 AGGCAGCAGCTTTACCATTG 58.820 50.000 0.00 0.00 41.70 2.82
2816 5296 1.547372 CAAGGCAGCAGCTTTACCATT 59.453 47.619 0.00 0.00 38.07 3.16
2817 5297 1.180029 CAAGGCAGCAGCTTTACCAT 58.820 50.000 0.00 0.00 38.07 3.55
2818 5298 0.178992 ACAAGGCAGCAGCTTTACCA 60.179 50.000 0.00 0.00 38.07 3.25
2819 5299 0.242017 CACAAGGCAGCAGCTTTACC 59.758 55.000 0.00 0.00 38.07 2.85
2820 5300 1.068954 GTCACAAGGCAGCAGCTTTAC 60.069 52.381 0.00 0.00 38.07 2.01
2821 5301 1.238439 GTCACAAGGCAGCAGCTTTA 58.762 50.000 0.00 0.00 38.07 1.85
2822 5302 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
2823 5303 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
2824 5304 2.282040 GGTCACAAGGCAGCAGCT 60.282 61.111 0.00 0.00 41.70 4.24
2825 5305 1.975407 ATGGTCACAAGGCAGCAGC 60.975 57.895 0.00 0.00 41.10 5.25
2826 5306 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
2827 5307 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
2828 5308 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
2829 5309 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
2830 5310 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
2841 5321 1.270839 ACTTGAACCCGTGACCTCATG 60.271 52.381 0.00 0.00 0.00 3.07
2842 5322 1.002087 GACTTGAACCCGTGACCTCAT 59.998 52.381 0.00 0.00 0.00 2.90
2843 5323 0.391597 GACTTGAACCCGTGACCTCA 59.608 55.000 0.00 0.00 0.00 3.86
2844 5324 0.320508 GGACTTGAACCCGTGACCTC 60.321 60.000 0.00 0.00 0.00 3.85
2845 5325 0.763223 AGGACTTGAACCCGTGACCT 60.763 55.000 0.00 0.00 0.00 3.85
2846 5326 0.602905 CAGGACTTGAACCCGTGACC 60.603 60.000 0.00 0.00 0.00 4.02
2847 5327 0.602905 CCAGGACTTGAACCCGTGAC 60.603 60.000 0.00 0.00 0.00 3.67
2848 5328 0.761323 TCCAGGACTTGAACCCGTGA 60.761 55.000 0.00 0.00 0.00 4.35
2849 5329 0.107831 TTCCAGGACTTGAACCCGTG 59.892 55.000 0.00 0.00 0.00 4.94
2850 5330 0.841289 TTTCCAGGACTTGAACCCGT 59.159 50.000 0.00 0.00 0.00 5.28
2851 5331 1.235724 GTTTCCAGGACTTGAACCCG 58.764 55.000 0.00 0.00 0.00 5.28
2852 5332 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
2853 5333 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
2854 5334 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
2855 5335 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
2856 5336 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
2857 5337 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
2858 5338 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
2859 5339 1.439543 AAGAGGCTGTTTCCAGGACT 58.560 50.000 0.00 0.00 39.22 3.85
2860 5340 2.038557 TGTAAGAGGCTGTTTCCAGGAC 59.961 50.000 0.90 0.00 39.22 3.85
2861 5341 2.303022 CTGTAAGAGGCTGTTTCCAGGA 59.697 50.000 0.90 0.00 35.89 3.86
2862 5342 2.303022 TCTGTAAGAGGCTGTTTCCAGG 59.697 50.000 17.71 5.83 38.67 4.45
2863 5343 3.685139 TCTGTAAGAGGCTGTTTCCAG 57.315 47.619 0.90 9.48 38.67 3.86
2875 5355 5.250774 AGCCTTTCCCTACATTTCTGTAAGA 59.749 40.000 0.00 0.00 44.68 2.10
2876 5356 5.355350 CAGCCTTTCCCTACATTTCTGTAAG 59.645 44.000 0.00 0.00 37.41 2.34
2877 5357 5.253330 CAGCCTTTCCCTACATTTCTGTAA 58.747 41.667 0.00 0.00 37.41 2.41
2878 5358 4.843728 CAGCCTTTCCCTACATTTCTGTA 58.156 43.478 0.00 0.00 36.79 2.74
2879 5359 3.690460 CAGCCTTTCCCTACATTTCTGT 58.310 45.455 0.00 0.00 39.49 3.41
2880 5360 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
2881 5361 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
2882 5362 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
2883 5363 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
2884 5364 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
2885 5365 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
2886 5366 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
2887 5367 0.535797 AGTACGCAGCCTTTCCCTAC 59.464 55.000 0.00 0.00 0.00 3.18
2888 5368 2.148446 TAGTACGCAGCCTTTCCCTA 57.852 50.000 0.00 0.00 0.00 3.53
2889 5369 1.497161 ATAGTACGCAGCCTTTCCCT 58.503 50.000 0.00 0.00 0.00 4.20
2890 5370 2.626743 TCTATAGTACGCAGCCTTTCCC 59.373 50.000 0.00 0.00 0.00 3.97
2891 5371 3.552478 GGTCTATAGTACGCAGCCTTTCC 60.552 52.174 0.00 0.00 0.00 3.13
2892 5372 3.552478 GGGTCTATAGTACGCAGCCTTTC 60.552 52.174 0.00 0.00 0.00 2.62
2893 5373 2.364647 GGGTCTATAGTACGCAGCCTTT 59.635 50.000 0.00 0.00 0.00 3.11
2894 5374 1.962100 GGGTCTATAGTACGCAGCCTT 59.038 52.381 0.00 0.00 0.00 4.35
2895 5375 1.133575 TGGGTCTATAGTACGCAGCCT 60.134 52.381 13.98 0.00 35.18 4.58
2896 5376 1.325355 TGGGTCTATAGTACGCAGCC 58.675 55.000 13.98 8.23 35.18 4.85
2897 5377 3.181478 ACTTTGGGTCTATAGTACGCAGC 60.181 47.826 16.00 2.07 40.36 5.25
2898 5378 4.360563 CACTTTGGGTCTATAGTACGCAG 58.639 47.826 16.00 11.29 40.36 5.18
2899 5379 3.131577 CCACTTTGGGTCTATAGTACGCA 59.868 47.826 13.98 13.98 37.94 5.24
2900 5380 3.131755 ACCACTTTGGGTCTATAGTACGC 59.868 47.826 0.00 6.13 43.37 4.42
2901 5381 4.996788 ACCACTTTGGGTCTATAGTACG 57.003 45.455 0.00 0.00 43.37 3.67
2911 5391 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
2912 5392 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
2913 5393 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
2914 5394 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
2915 5395 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
2916 5396 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
2917 5397 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
2918 5398 3.714001 GGGGAAGGGTCCGACCAC 61.714 72.222 19.43 8.70 46.04 4.16
2924 5404 4.735599 AGGGTCGGGGAAGGGTCC 62.736 72.222 0.00 0.00 44.10 4.46
2925 5405 3.400054 CAGGGTCGGGGAAGGGTC 61.400 72.222 0.00 0.00 0.00 4.46
2940 5420 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
2943 5423 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
2944 5424 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
2945 5425 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
2946 5426 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
2952 5432 2.897350 GCCCGGTGCATGTAGCTC 60.897 66.667 11.25 0.00 45.94 4.09
2953 5433 3.402681 AGCCCGGTGCATGTAGCT 61.403 61.111 15.92 4.82 45.94 3.32
2954 5434 3.204827 CAGCCCGGTGCATGTAGC 61.205 66.667 15.92 2.56 44.83 3.58
2955 5435 3.204827 GCAGCCCGGTGCATGTAG 61.205 66.667 13.70 0.91 43.41 2.74
2956 5436 4.794648 GGCAGCCCGGTGCATGTA 62.795 66.667 19.47 0.00 45.93 2.29
2979 5459 7.101652 TGCTTGTCAAACATGGTACTAAAAA 57.898 32.000 0.00 0.00 0.00 1.94
2980 5460 6.701145 TGCTTGTCAAACATGGTACTAAAA 57.299 33.333 0.00 0.00 0.00 1.52
2981 5461 6.701145 TTGCTTGTCAAACATGGTACTAAA 57.299 33.333 0.00 0.00 0.00 1.85
2982 5462 6.892658 ATTGCTTGTCAAACATGGTACTAA 57.107 33.333 0.00 0.00 38.34 2.24
2983 5463 6.072175 GGAATTGCTTGTCAAACATGGTACTA 60.072 38.462 0.00 0.00 38.34 1.82
2984 5464 5.278957 GGAATTGCTTGTCAAACATGGTACT 60.279 40.000 0.00 0.00 38.34 2.73
2985 5465 4.923281 GGAATTGCTTGTCAAACATGGTAC 59.077 41.667 0.00 0.00 38.34 3.34
2986 5466 4.021544 GGGAATTGCTTGTCAAACATGGTA 60.022 41.667 0.00 0.00 38.34 3.25
2987 5467 3.244181 GGGAATTGCTTGTCAAACATGGT 60.244 43.478 0.00 0.00 38.34 3.55
2988 5468 3.007182 AGGGAATTGCTTGTCAAACATGG 59.993 43.478 0.00 0.00 38.34 3.66
2989 5469 3.991773 CAGGGAATTGCTTGTCAAACATG 59.008 43.478 0.57 0.00 38.34 3.21
2990 5470 3.555586 GCAGGGAATTGCTTGTCAAACAT 60.556 43.478 10.68 0.00 40.89 2.71
2991 5471 2.224018 GCAGGGAATTGCTTGTCAAACA 60.224 45.455 10.68 0.00 40.89 2.83
2992 5472 2.407090 GCAGGGAATTGCTTGTCAAAC 58.593 47.619 10.68 0.00 40.89 2.93
3065 5545 5.462398 ACGTAGAGTAAAGCAAGTCAAACAG 59.538 40.000 0.00 0.00 0.00 3.16
3068 5548 7.149973 ACATACGTAGAGTAAAGCAAGTCAAA 58.850 34.615 0.08 0.00 39.04 2.69
3106 5586 7.263496 ACCGTAAGAAGTACAATGGTATCTTC 58.737 38.462 11.62 11.62 37.60 2.87
3109 5589 6.478016 GGAACCGTAAGAAGTACAATGGTATC 59.522 42.308 0.00 0.00 43.02 2.24
3146 5626 6.841119 TGAATCTATGTTGATGTCCAAAACG 58.159 36.000 0.00 0.00 36.36 3.60
3209 5689 9.736023 CAATATATAGTTTTGTTGGGCTTTCTC 57.264 33.333 0.00 0.00 0.00 2.87
3227 5707 7.715482 TCAGCCCTAACTCCCTACAATATATA 58.285 38.462 0.00 0.00 0.00 0.86
3245 5725 2.270205 CGCCAGTGAATCAGCCCT 59.730 61.111 0.00 0.00 0.00 5.19
3249 5729 3.197790 CGCCCGCCAGTGAATCAG 61.198 66.667 0.00 0.00 0.00 2.90
3262 5742 0.873054 CATGATCAATGCTCTCGCCC 59.127 55.000 0.00 0.00 34.43 6.13
3276 5756 1.487976 ACCAATCACGGAGCTCATGAT 59.512 47.619 21.23 21.23 34.52 2.45
3277 5757 0.904649 ACCAATCACGGAGCTCATGA 59.095 50.000 18.99 18.99 0.00 3.07
3278 5758 2.602257 TACCAATCACGGAGCTCATG 57.398 50.000 17.19 13.27 0.00 3.07
3283 5763 3.938963 TCTCAATTTACCAATCACGGAGC 59.061 43.478 0.00 0.00 0.00 4.70
3284 5764 5.065218 CCTTCTCAATTTACCAATCACGGAG 59.935 44.000 0.00 0.00 0.00 4.63
3285 5765 4.941263 CCTTCTCAATTTACCAATCACGGA 59.059 41.667 0.00 0.00 0.00 4.69
3286 5766 4.096382 CCCTTCTCAATTTACCAATCACGG 59.904 45.833 0.00 0.00 0.00 4.94
3287 5767 4.700213 ACCCTTCTCAATTTACCAATCACG 59.300 41.667 0.00 0.00 0.00 4.35
3288 5768 5.710099 TGACCCTTCTCAATTTACCAATCAC 59.290 40.000 0.00 0.00 0.00 3.06
3289 5769 5.886609 TGACCCTTCTCAATTTACCAATCA 58.113 37.500 0.00 0.00 0.00 2.57
3290 5770 6.208599 TGTTGACCCTTCTCAATTTACCAATC 59.791 38.462 0.00 0.00 32.78 2.67
3291 5771 6.074648 TGTTGACCCTTCTCAATTTACCAAT 58.925 36.000 0.00 0.00 32.78 3.16
3292 5772 5.450453 TGTTGACCCTTCTCAATTTACCAA 58.550 37.500 0.00 0.00 32.78 3.67
3293 5773 5.055265 TGTTGACCCTTCTCAATTTACCA 57.945 39.130 0.00 0.00 32.78 3.25
3324 5804 6.348478 TCCAATTGATAATTCCTACCCCAA 57.652 37.500 7.12 0.00 0.00 4.12
3325 5805 5.692781 GCTCCAATTGATAATTCCTACCCCA 60.693 44.000 7.12 0.00 0.00 4.96
3367 5847 3.368248 AGGCCCATTACGTACTCTAACA 58.632 45.455 0.00 0.00 0.00 2.41
3368 5848 5.520376 TTAGGCCCATTACGTACTCTAAC 57.480 43.478 0.00 0.00 0.00 2.34
3369 5849 5.011329 CCATTAGGCCCATTACGTACTCTAA 59.989 44.000 0.00 0.00 0.00 2.10
3370 5850 4.525487 CCATTAGGCCCATTACGTACTCTA 59.475 45.833 0.00 0.00 0.00 2.43
3371 5851 3.323979 CCATTAGGCCCATTACGTACTCT 59.676 47.826 0.00 0.00 0.00 3.24
3372 5852 3.660865 CCATTAGGCCCATTACGTACTC 58.339 50.000 0.00 0.00 0.00 2.59
3373 5853 3.764237 CCATTAGGCCCATTACGTACT 57.236 47.619 0.00 0.00 0.00 2.73
3386 5866 2.196776 CCAGCCCAGGCCATTAGG 59.803 66.667 5.01 0.00 43.17 2.69
3394 5874 2.743718 CTATACCGCCAGCCCAGG 59.256 66.667 0.00 0.00 0.00 4.45
3395 5875 2.031163 GCTATACCGCCAGCCCAG 59.969 66.667 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.