Multiple sequence alignment - TraesCS7B01G397700

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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 TraesCS7B01G397700 chr7B 100.000 3437 0 0 1 3437 663752167 663748731 0.000000e+00 6348.0
1 TraesCS7B01G397700 chr7B 94.174 2489 127 11 32 2509 663842339 663844820 0.000000e+00 3777.0
2 TraesCS7B01G397700 chr7B 87.698 569 42 15 2706 3253 663846247 663846808 3.740000e-179 638.0
3 TraesCS7B01G397700 chr7B 93.151 146 10 0 2576 2721 663844848 663844993 7.470000e-52 215.0
4 TraesCS7B01G397700 chr7A 94.359 2588 109 20 548 3107 680681156 680678578 0.000000e+00 3936.0
5 TraesCS7B01G397700 chr7A 91.053 570 45 4 1 564 680682013 680681444 0.000000e+00 765.0
6 TraesCS7B01G397700 chr7A 89.873 158 12 3 3100 3253 680677658 680677501 2.090000e-47 200.0
7 TraesCS7B01G397700 chr7A 83.626 171 13 5 3282 3437 680665615 680665445 2.760000e-31 147.0
8 TraesCS7B01G397700 chr7D 92.644 2746 134 32 563 3253 589391688 589388956 0.000000e+00 3890.0
9 TraesCS7B01G397700 chr7D 89.362 188 12 3 3258 3437 589341762 589341575 2.670000e-56 230.0
10 TraesCS7B01G397700 chr2D 80.733 1993 298 48 511 2442 19586527 19588494 0.000000e+00 1474.0
11 TraesCS7B01G397700 chr2D 81.381 1767 246 48 638 2342 9604386 9606131 0.000000e+00 1363.0
12 TraesCS7B01G397700 chr2D 82.385 1635 208 43 901 2480 9665345 9663736 0.000000e+00 1351.0
13 TraesCS7B01G397700 chr2D 81.588 1423 232 12 1000 2392 8659797 8661219 0.000000e+00 1149.0
14 TraesCS7B01G397700 chr2B 81.221 1752 254 43 650 2343 12421964 12423698 0.000000e+00 1343.0
15 TraesCS7B01G397700 chr2B 82.193 1623 205 40 916 2480 12996047 12994451 0.000000e+00 1319.0
16 TraesCS7B01G397700 chr2B 81.774 1635 217 41 901 2480 11445348 11446956 0.000000e+00 1293.0
17 TraesCS7B01G397700 chr2B 80.482 1701 268 34 928 2581 768929492 768927809 0.000000e+00 1243.0
18 TraesCS7B01G397700 chr2B 76.296 135 19 5 2527 2656 13066996 13066870 3.700000e-05 60.2
19 TraesCS7B01G397700 chr2A 81.131 1415 235 15 1000 2383 7727400 7728813 0.000000e+00 1105.0
20 TraesCS7B01G397700 chr2A 76.296 135 19 5 2527 2656 9092976 9092850 3.700000e-05 60.2
21 TraesCS7B01G397700 chrUn 83.292 1197 179 13 1280 2461 334662455 334663645 0.000000e+00 1083.0
22 TraesCS7B01G397700 chrUn 83.208 1197 180 13 1280 2461 3529239 3528049 0.000000e+00 1077.0
23 TraesCS7B01G397700 chr3D 84.177 158 25 0 2278 2435 563992751 563992594 1.650000e-33 154.0
24 TraesCS7B01G397700 chr1D 94.444 54 1 2 293 345 253346896 253346844 7.910000e-12 82.4
25 TraesCS7B01G397700 chr1D 97.674 43 1 0 293 335 37884688 37884646 1.320000e-09 75.0
26 TraesCS7B01G397700 chr5D 100.000 43 0 0 293 335 542700737 542700695 2.840000e-11 80.5
27 TraesCS7B01G397700 chr1A 100.000 42 0 0 293 334 363698915 363698956 1.020000e-10 78.7
28 TraesCS7B01G397700 chr3B 90.909 55 4 1 288 341 76489612 76489558 4.760000e-09 73.1
29 TraesCS7B01G397700 chr5A 92.157 51 2 2 288 337 661177479 661177430 1.710000e-08 71.3
30 TraesCS7B01G397700 chr6A 88.136 59 6 1 292 349 604571360 604571302 6.150000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G397700 chr7B 663748731 663752167 3436 True 6348.000000 6348 100.000000 1 3437 1 chr7B.!!$R1 3436
1 TraesCS7B01G397700 chr7B 663842339 663846808 4469 False 1543.333333 3777 91.674333 32 3253 3 chr7B.!!$F1 3221
2 TraesCS7B01G397700 chr7A 680677501 680682013 4512 True 1633.666667 3936 91.761667 1 3253 3 chr7A.!!$R2 3252
3 TraesCS7B01G397700 chr7D 589388956 589391688 2732 True 3890.000000 3890 92.644000 563 3253 1 chr7D.!!$R2 2690
4 TraesCS7B01G397700 chr2D 19586527 19588494 1967 False 1474.000000 1474 80.733000 511 2442 1 chr2D.!!$F3 1931
5 TraesCS7B01G397700 chr2D 9604386 9606131 1745 False 1363.000000 1363 81.381000 638 2342 1 chr2D.!!$F2 1704
6 TraesCS7B01G397700 chr2D 9663736 9665345 1609 True 1351.000000 1351 82.385000 901 2480 1 chr2D.!!$R1 1579
7 TraesCS7B01G397700 chr2D 8659797 8661219 1422 False 1149.000000 1149 81.588000 1000 2392 1 chr2D.!!$F1 1392
8 TraesCS7B01G397700 chr2B 12421964 12423698 1734 False 1343.000000 1343 81.221000 650 2343 1 chr2B.!!$F2 1693
9 TraesCS7B01G397700 chr2B 12994451 12996047 1596 True 1319.000000 1319 82.193000 916 2480 1 chr2B.!!$R1 1564
10 TraesCS7B01G397700 chr2B 11445348 11446956 1608 False 1293.000000 1293 81.774000 901 2480 1 chr2B.!!$F1 1579
11 TraesCS7B01G397700 chr2B 768927809 768929492 1683 True 1243.000000 1243 80.482000 928 2581 1 chr2B.!!$R3 1653
12 TraesCS7B01G397700 chr2A 7727400 7728813 1413 False 1105.000000 1105 81.131000 1000 2383 1 chr2A.!!$F1 1383
13 TraesCS7B01G397700 chrUn 334662455 334663645 1190 False 1083.000000 1083 83.292000 1280 2461 1 chrUn.!!$F1 1181
14 TraesCS7B01G397700 chrUn 3528049 3529239 1190 True 1077.000000 1077 83.208000 1280 2461 1 chrUn.!!$R1 1181

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
351 357 0.322816 TAGGTCGTAGCACCTCCGTT 60.323 55.0 0.0 0.0 44.08 4.44 F
1125 1499 0.983467 TGGACAGATTGCAGCACCTA 59.017 50.0 0.0 0.0 0.00 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2284 2717 0.883833 TCTCGTTCCGGTCTAACACC 59.116 55.0 0.00 0.00 42.69 4.16 R
2906 4639 0.041312 GCACAACAGCTGGTACAACG 60.041 55.0 19.93 0.86 38.70 4.10 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
41 42 7.890515 AGGATTCAAATTTCTCTCAGGAAAAC 58.109 34.615 0.00 0.00 38.46 2.43
54 55 3.042887 CAGGAAAACGGAAAAAGAAGCG 58.957 45.455 0.00 0.00 0.00 4.68
80 81 5.242838 CCCACTGCCTAAAACTTGAAACATA 59.757 40.000 0.00 0.00 0.00 2.29
81 82 6.071391 CCCACTGCCTAAAACTTGAAACATAT 60.071 38.462 0.00 0.00 0.00 1.78
118 119 0.951558 CACCTACACACAAGGCAACC 59.048 55.000 0.00 0.00 37.67 3.77
218 220 5.221722 TGCTACATTTTTCTCCACTCTCTGT 60.222 40.000 0.00 0.00 0.00 3.41
238 240 2.739379 GTCTGACCTGTCTTTTGCTAGC 59.261 50.000 8.10 8.10 0.00 3.42
259 262 1.405821 AGGACGACCGAAGATGATGAC 59.594 52.381 0.00 0.00 41.83 3.06
260 263 1.134367 GGACGACCGAAGATGATGACA 59.866 52.381 0.00 0.00 0.00 3.58
277 283 4.085357 TGACAATAAGGACAACACAGCT 57.915 40.909 0.00 0.00 0.00 4.24
278 284 3.814842 TGACAATAAGGACAACACAGCTG 59.185 43.478 13.48 13.48 0.00 4.24
297 303 6.082338 CAGCTGTGATGAATTGTACTTGAAC 58.918 40.000 5.25 0.00 0.00 3.18
323 329 6.399639 AAACCACGACACTTATTTTGGATT 57.600 33.333 0.00 0.00 0.00 3.01
339 345 1.688627 GGATTGGAGGGAGTAGGTCGT 60.689 57.143 0.00 0.00 0.00 4.34
351 357 0.322816 TAGGTCGTAGCACCTCCGTT 60.323 55.000 0.00 0.00 44.08 4.44
367 376 1.821061 CGTTGCCACCTCCTCTCACT 61.821 60.000 0.00 0.00 0.00 3.41
376 385 1.834856 CTCCTCTCACTTGGCCAGCA 61.835 60.000 5.11 0.00 0.00 4.41
396 406 2.727798 CAGCTTGTTTGCGAGATTTTGG 59.272 45.455 0.00 0.00 38.13 3.28
448 458 8.943909 ATTACAGTACTAAAGTATGGAGTTGC 57.056 34.615 0.00 0.00 32.54 4.17
467 477 3.451526 TGCGATTCTCATCATCACTGAC 58.548 45.455 0.00 0.00 33.22 3.51
476 486 7.340122 TCTCATCATCACTGACTAAGGTAAG 57.660 40.000 0.00 0.00 33.22 2.34
487 497 4.404715 TGACTAAGGTAAGAGGGTGCATAC 59.595 45.833 0.00 0.00 0.00 2.39
488 498 4.621769 ACTAAGGTAAGAGGGTGCATACT 58.378 43.478 0.00 0.00 0.00 2.12
524 534 8.500773 CCAATGAATTTTGTTCATCTGGAAAAG 58.499 33.333 17.46 0.00 38.11 2.27
546 556 4.949856 AGCTCAAATAATTTCCACCGTCAT 59.050 37.500 0.00 0.00 0.00 3.06
608 922 8.788806 TGTGTGAAATATAAAACGAGTCCAATT 58.211 29.630 0.00 0.00 0.00 2.32
647 961 7.469260 AGAATAATTACACCGTACATGTTTGC 58.531 34.615 2.30 0.00 0.00 3.68
726 1063 5.643379 ACAAGTCACTGTTTTCATGTTGT 57.357 34.783 0.00 0.00 0.00 3.32
789 1128 3.245229 TGCAACTTCTGTATTCCATGGGT 60.245 43.478 13.02 3.69 0.00 4.51
1063 1428 3.118629 TCGTTTCATCTCCTTCCTGATGG 60.119 47.826 0.00 0.00 40.13 3.51
1125 1499 0.983467 TGGACAGATTGCAGCACCTA 59.017 50.000 0.00 0.00 0.00 3.08
1207 1581 4.760715 GGATGATATTGCAGCTCAAGATGT 59.239 41.667 9.69 1.46 36.80 3.06
1331 1729 1.275291 TCCTTCCAAGCGTTCTCGAAT 59.725 47.619 0.00 0.00 39.71 3.34
1974 2383 1.077501 CCCTGCCGAACATCCACAT 60.078 57.895 0.00 0.00 0.00 3.21
2127 2536 7.223584 ACAAGGGAATGAAAATGGTTAAAAGG 58.776 34.615 0.00 0.00 0.00 3.11
2235 2668 5.447818 GCTTAGCTTGCTACCTTACACAATG 60.448 44.000 1.37 0.00 0.00 2.82
2392 2825 2.604914 CGTGCTCAGGATGTACATGAAC 59.395 50.000 14.43 2.03 38.83 3.18
2408 2847 3.714487 AACGTGGTGCCTTGCCAGT 62.714 57.895 0.00 0.00 36.57 4.00
2430 2869 4.421479 AAGCGACGAGGACTGCCG 62.421 66.667 0.00 0.00 39.96 5.69
2446 2885 4.130118 ACTGCCGATCTGATTATGTTTCC 58.870 43.478 0.00 0.00 0.00 3.13
2463 2902 6.476243 TGTTTCCGAACTCTTTGTAATAGC 57.524 37.500 0.00 0.00 36.70 2.97
2608 3051 9.899661 AGCATACCTTGAACTTGTATGTTTATA 57.100 29.630 9.75 0.00 42.32 0.98
2677 3123 2.232696 TCGTTTGATGTGGCAGTAGCTA 59.767 45.455 0.00 0.00 41.70 3.32
2725 4443 7.922505 TGTTAATGAAACAGAAATTGAACCG 57.077 32.000 0.00 0.00 43.22 4.44
2759 4491 7.389884 AGAGGTATACACATCATCATTGCATTC 59.610 37.037 5.01 0.00 37.94 2.67
2761 4493 8.377799 AGGTATACACATCATCATTGCATTCTA 58.622 33.333 5.01 0.00 0.00 2.10
2779 4511 5.738619 TTCTACAGCTGATACCAAAGTCA 57.261 39.130 23.35 0.00 0.00 3.41
2783 4515 4.910195 ACAGCTGATACCAAAGTCAATCA 58.090 39.130 23.35 0.00 0.00 2.57
2815 4547 6.780457 AGTATAAGCTTGCAATCAACCAAT 57.220 33.333 9.86 0.00 0.00 3.16
2847 4580 4.344679 CCATATATGTGCAACCCATGGTTT 59.655 41.667 11.73 0.00 44.33 3.27
2873 4606 3.756434 CCATTCCAACCAATCAGTAACGT 59.244 43.478 0.00 0.00 0.00 3.99
2897 4630 7.519008 CGTCATACATAAAGGAAAGATGAAGCC 60.519 40.741 0.00 0.00 0.00 4.35
2906 4639 0.674895 AAGATGAAGCCCTGTGACGC 60.675 55.000 0.00 0.00 0.00 5.19
2934 4667 0.956633 AGCTGTTGTGCTGATGTTGG 59.043 50.000 0.00 0.00 42.33 3.77
2940 4673 0.754587 TGTGCTGATGTTGGTGCCAA 60.755 50.000 0.00 0.00 0.00 4.52
2946 4679 3.740764 GCTGATGTTGGTGCCAAGAAAAA 60.741 43.478 3.57 0.00 36.52 1.94
2960 4693 8.411683 GTGCCAAGAAAAATTAGATCTGATCAT 58.588 33.333 19.12 7.47 0.00 2.45
3079 4824 5.163302 TCAAAACACGTGTGAATTCGATT 57.837 34.783 24.16 7.09 0.00 3.34
3127 5801 2.611292 GCTCGTAGTCGGTTTAGCTAGA 59.389 50.000 0.00 0.00 37.69 2.43
3144 5818 3.005539 ACGCCTCCCTCTGTGCAT 61.006 61.111 0.00 0.00 0.00 3.96
3159 5833 1.605710 GTGCATGCACTTGAAGTCTGT 59.394 47.619 37.48 0.00 43.12 3.41
3170 5844 1.002430 TGAAGTCTGTGACCTCCATGC 59.998 52.381 0.00 0.00 32.18 4.06
3173 5847 1.229625 TCTGTGACCTCCATGCCCT 60.230 57.895 0.00 0.00 0.00 5.19
3254 5930 4.416738 GGAGGAGCCTGGTGGTGC 62.417 72.222 0.00 0.00 35.27 5.01
3255 5931 3.325753 GAGGAGCCTGGTGGTGCT 61.326 66.667 0.00 0.00 46.65 4.40
3258 5934 4.008933 GAGCCTGGTGGTGCTCGT 62.009 66.667 0.00 0.00 43.94 4.18
3259 5935 2.603473 AGCCTGGTGGTGCTCGTA 60.603 61.111 0.00 0.00 30.33 3.43
3260 5936 2.125512 GCCTGGTGGTGCTCGTAG 60.126 66.667 0.00 0.00 35.27 3.51
3261 5937 2.943978 GCCTGGTGGTGCTCGTAGT 61.944 63.158 0.00 0.00 35.27 2.73
3262 5938 1.671742 CCTGGTGGTGCTCGTAGTT 59.328 57.895 0.00 0.00 0.00 2.24
3263 5939 0.389948 CCTGGTGGTGCTCGTAGTTC 60.390 60.000 0.00 0.00 0.00 3.01
3264 5940 0.317160 CTGGTGGTGCTCGTAGTTCA 59.683 55.000 0.00 0.00 0.00 3.18
3265 5941 0.753867 TGGTGGTGCTCGTAGTTCAA 59.246 50.000 0.00 0.00 0.00 2.69
3266 5942 1.145803 GGTGGTGCTCGTAGTTCAAC 58.854 55.000 0.00 0.00 0.00 3.18
3267 5943 1.539496 GGTGGTGCTCGTAGTTCAACA 60.539 52.381 0.00 0.00 0.00 3.33
3268 5944 2.206750 GTGGTGCTCGTAGTTCAACAA 58.793 47.619 0.00 0.00 31.03 2.83
3269 5945 2.806244 GTGGTGCTCGTAGTTCAACAAT 59.194 45.455 0.00 0.00 31.03 2.71
3270 5946 2.805671 TGGTGCTCGTAGTTCAACAATG 59.194 45.455 0.00 0.00 0.00 2.82
3271 5947 3.064207 GGTGCTCGTAGTTCAACAATGA 58.936 45.455 0.00 0.00 0.00 2.57
3272 5948 3.496884 GGTGCTCGTAGTTCAACAATGAA 59.503 43.478 0.00 0.00 43.18 2.57
3273 5949 4.024387 GGTGCTCGTAGTTCAACAATGAAA 60.024 41.667 0.00 0.00 46.66 2.69
3274 5950 5.334879 GGTGCTCGTAGTTCAACAATGAAAT 60.335 40.000 0.00 0.00 46.66 2.17
3275 5951 5.790495 GTGCTCGTAGTTCAACAATGAAATC 59.210 40.000 0.00 0.00 46.66 2.17
3276 5952 5.106712 TGCTCGTAGTTCAACAATGAAATCC 60.107 40.000 0.00 0.00 46.66 3.01
3277 5953 5.106712 GCTCGTAGTTCAACAATGAAATCCA 60.107 40.000 0.00 0.00 46.66 3.41
3278 5954 6.403636 GCTCGTAGTTCAACAATGAAATCCAT 60.404 38.462 0.00 0.00 46.66 3.41
3279 5955 7.072177 TCGTAGTTCAACAATGAAATCCATC 57.928 36.000 0.00 0.00 46.66 3.51
3280 5956 6.878923 TCGTAGTTCAACAATGAAATCCATCT 59.121 34.615 0.00 0.00 46.66 2.90
3281 5957 7.390440 TCGTAGTTCAACAATGAAATCCATCTT 59.610 33.333 0.00 0.00 46.66 2.40
3282 5958 7.693951 CGTAGTTCAACAATGAAATCCATCTTC 59.306 37.037 0.00 0.00 46.66 2.87
3283 5959 7.528996 AGTTCAACAATGAAATCCATCTTCA 57.471 32.000 0.00 0.00 46.66 3.02
3284 5960 7.954835 AGTTCAACAATGAAATCCATCTTCAA 58.045 30.769 0.00 0.00 46.66 2.69
3285 5961 7.869429 AGTTCAACAATGAAATCCATCTTCAAC 59.131 33.333 0.00 0.00 46.66 3.18
3286 5962 7.528996 TCAACAATGAAATCCATCTTCAACT 57.471 32.000 0.00 0.00 36.43 3.16
3287 5963 7.596494 TCAACAATGAAATCCATCTTCAACTC 58.404 34.615 0.00 0.00 36.43 3.01
3288 5964 7.449395 TCAACAATGAAATCCATCTTCAACTCT 59.551 33.333 0.00 0.00 36.43 3.24
3289 5965 7.771927 ACAATGAAATCCATCTTCAACTCTT 57.228 32.000 0.00 0.00 36.43 2.85
3290 5966 7.824672 ACAATGAAATCCATCTTCAACTCTTC 58.175 34.615 0.00 0.00 36.43 2.87
3291 5967 7.449395 ACAATGAAATCCATCTTCAACTCTTCA 59.551 33.333 0.00 0.00 36.43 3.02
3292 5968 8.467598 CAATGAAATCCATCTTCAACTCTTCAT 58.532 33.333 0.00 0.00 36.43 2.57
3293 5969 7.387119 TGAAATCCATCTTCAACTCTTCATG 57.613 36.000 0.00 0.00 29.93 3.07
3294 5970 7.170277 TGAAATCCATCTTCAACTCTTCATGA 58.830 34.615 0.00 0.00 29.93 3.07
3296 5972 4.511527 TCCATCTTCAACTCTTCATGAGC 58.488 43.478 0.00 0.00 46.41 4.26
3297 5973 4.019950 TCCATCTTCAACTCTTCATGAGCA 60.020 41.667 0.00 0.00 46.41 4.26
3298 5974 4.333095 CCATCTTCAACTCTTCATGAGCAG 59.667 45.833 0.00 0.00 46.41 4.24
3299 5975 3.935315 TCTTCAACTCTTCATGAGCAGG 58.065 45.455 0.00 0.00 46.41 4.85
3300 5976 3.580022 TCTTCAACTCTTCATGAGCAGGA 59.420 43.478 0.00 0.00 46.41 3.86
3301 5977 3.325293 TCAACTCTTCATGAGCAGGAC 57.675 47.619 0.00 0.00 46.41 3.85
3302 5978 2.027745 TCAACTCTTCATGAGCAGGACC 60.028 50.000 0.00 0.00 46.41 4.46
3303 5979 1.649321 ACTCTTCATGAGCAGGACCA 58.351 50.000 0.00 0.00 46.41 4.02
3304 5980 2.194859 ACTCTTCATGAGCAGGACCAT 58.805 47.619 0.00 0.00 46.41 3.55
3305 5981 3.378512 ACTCTTCATGAGCAGGACCATA 58.621 45.455 0.00 0.00 46.41 2.74
3306 5982 3.133721 ACTCTTCATGAGCAGGACCATAC 59.866 47.826 0.00 0.00 46.41 2.39
3307 5983 3.106827 TCTTCATGAGCAGGACCATACA 58.893 45.455 0.00 0.00 0.00 2.29
3308 5984 2.988010 TCATGAGCAGGACCATACAC 57.012 50.000 0.00 0.00 0.00 2.90
3309 5985 2.187100 TCATGAGCAGGACCATACACA 58.813 47.619 0.00 0.00 0.00 3.72
3310 5986 2.571202 TCATGAGCAGGACCATACACAA 59.429 45.455 0.00 0.00 0.00 3.33
3311 5987 2.472695 TGAGCAGGACCATACACAAC 57.527 50.000 0.00 0.00 0.00 3.32
3312 5988 1.977854 TGAGCAGGACCATACACAACT 59.022 47.619 0.00 0.00 0.00 3.16
3313 5989 3.169908 TGAGCAGGACCATACACAACTA 58.830 45.455 0.00 0.00 0.00 2.24
3314 5990 3.195610 TGAGCAGGACCATACACAACTAG 59.804 47.826 0.00 0.00 0.00 2.57
3315 5991 3.441101 AGCAGGACCATACACAACTAGA 58.559 45.455 0.00 0.00 0.00 2.43
3316 5992 3.838317 AGCAGGACCATACACAACTAGAA 59.162 43.478 0.00 0.00 0.00 2.10
3317 5993 4.286032 AGCAGGACCATACACAACTAGAAA 59.714 41.667 0.00 0.00 0.00 2.52
3318 5994 5.045578 AGCAGGACCATACACAACTAGAAAT 60.046 40.000 0.00 0.00 0.00 2.17
3319 5995 5.065218 GCAGGACCATACACAACTAGAAATG 59.935 44.000 0.00 0.00 0.00 2.32
3320 5996 6.173339 CAGGACCATACACAACTAGAAATGT 58.827 40.000 0.00 0.00 0.00 2.71
3321 5997 6.313905 CAGGACCATACACAACTAGAAATGTC 59.686 42.308 0.00 0.00 0.00 3.06
3322 5998 6.013725 AGGACCATACACAACTAGAAATGTCA 60.014 38.462 0.00 0.00 0.00 3.58
3323 5999 6.092259 GGACCATACACAACTAGAAATGTCAC 59.908 42.308 0.00 0.00 0.00 3.67
3324 6000 6.769512 ACCATACACAACTAGAAATGTCACT 58.230 36.000 0.00 0.00 0.00 3.41
3325 6001 6.874134 ACCATACACAACTAGAAATGTCACTC 59.126 38.462 0.00 0.00 0.00 3.51
3326 6002 7.099764 CCATACACAACTAGAAATGTCACTCT 58.900 38.462 0.00 0.00 0.00 3.24
3327 6003 7.604164 CCATACACAACTAGAAATGTCACTCTT 59.396 37.037 0.00 0.00 0.00 2.85
3328 6004 9.639601 CATACACAACTAGAAATGTCACTCTTA 57.360 33.333 0.00 0.00 0.00 2.10
3330 6006 8.594881 ACACAACTAGAAATGTCACTCTTAAG 57.405 34.615 0.00 0.00 0.00 1.85
3331 6007 7.657761 ACACAACTAGAAATGTCACTCTTAAGG 59.342 37.037 1.85 0.00 0.00 2.69
3332 6008 7.657761 CACAACTAGAAATGTCACTCTTAAGGT 59.342 37.037 1.85 0.00 0.00 3.50
3333 6009 7.873505 ACAACTAGAAATGTCACTCTTAAGGTC 59.126 37.037 1.85 0.00 0.00 3.85
3334 6010 7.784470 ACTAGAAATGTCACTCTTAAGGTCT 57.216 36.000 1.85 0.00 0.00 3.85
3335 6011 8.196378 ACTAGAAATGTCACTCTTAAGGTCTT 57.804 34.615 1.85 0.00 0.00 3.01
3336 6012 8.652290 ACTAGAAATGTCACTCTTAAGGTCTTT 58.348 33.333 1.85 0.00 0.00 2.52
3337 6013 7.736447 AGAAATGTCACTCTTAAGGTCTTTG 57.264 36.000 1.85 0.00 0.00 2.77
3338 6014 7.283329 AGAAATGTCACTCTTAAGGTCTTTGT 58.717 34.615 1.85 0.00 0.00 2.83
3339 6015 6.867662 AATGTCACTCTTAAGGTCTTTGTG 57.132 37.500 1.85 3.60 0.00 3.33
3340 6016 4.703897 TGTCACTCTTAAGGTCTTTGTGG 58.296 43.478 1.85 0.00 0.00 4.17
3341 6017 4.163458 TGTCACTCTTAAGGTCTTTGTGGT 59.837 41.667 1.85 0.00 0.00 4.16
3342 6018 4.511826 GTCACTCTTAAGGTCTTTGTGGTG 59.488 45.833 1.85 0.00 0.00 4.17
3343 6019 4.407621 TCACTCTTAAGGTCTTTGTGGTGA 59.592 41.667 1.85 0.00 0.00 4.02
3344 6020 5.104693 TCACTCTTAAGGTCTTTGTGGTGAA 60.105 40.000 1.85 0.00 0.00 3.18
3345 6021 5.237344 CACTCTTAAGGTCTTTGTGGTGAAG 59.763 44.000 1.85 0.00 0.00 3.02
3346 6022 5.130477 ACTCTTAAGGTCTTTGTGGTGAAGA 59.870 40.000 1.85 0.00 0.00 2.87
3347 6023 6.183361 ACTCTTAAGGTCTTTGTGGTGAAGAT 60.183 38.462 1.85 0.00 35.74 2.40
3348 6024 5.997746 TCTTAAGGTCTTTGTGGTGAAGATG 59.002 40.000 1.85 0.00 35.74 2.90
3349 6025 3.146104 AGGTCTTTGTGGTGAAGATGG 57.854 47.619 0.00 0.00 35.74 3.51
3350 6026 2.711009 AGGTCTTTGTGGTGAAGATGGA 59.289 45.455 0.00 0.00 35.74 3.41
3351 6027 3.331889 AGGTCTTTGTGGTGAAGATGGAT 59.668 43.478 0.00 0.00 35.74 3.41
3352 6028 4.082125 GGTCTTTGTGGTGAAGATGGATT 58.918 43.478 0.00 0.00 35.74 3.01
3353 6029 5.014123 AGGTCTTTGTGGTGAAGATGGATTA 59.986 40.000 0.00 0.00 35.74 1.75
3354 6030 5.710099 GGTCTTTGTGGTGAAGATGGATTAA 59.290 40.000 0.00 0.00 35.74 1.40
3355 6031 6.208599 GGTCTTTGTGGTGAAGATGGATTAAA 59.791 38.462 0.00 0.00 35.74 1.52
3356 6032 7.255801 GGTCTTTGTGGTGAAGATGGATTAAAA 60.256 37.037 0.00 0.00 35.74 1.52
3357 6033 8.141268 GTCTTTGTGGTGAAGATGGATTAAAAA 58.859 33.333 0.00 0.00 35.74 1.94
3375 6051 2.323999 AAAATGCCTCCCACATTCCA 57.676 45.000 0.00 0.00 36.74 3.53
3376 6052 1.560505 AAATGCCTCCCACATTCCAC 58.439 50.000 0.00 0.00 36.74 4.02
3377 6053 0.324645 AATGCCTCCCACATTCCACC 60.325 55.000 0.00 0.00 32.28 4.61
3378 6054 1.508667 ATGCCTCCCACATTCCACCA 61.509 55.000 0.00 0.00 0.00 4.17
3379 6055 1.076549 GCCTCCCACATTCCACCAA 59.923 57.895 0.00 0.00 0.00 3.67
3380 6056 0.541764 GCCTCCCACATTCCACCAAA 60.542 55.000 0.00 0.00 0.00 3.28
3381 6057 1.549203 CCTCCCACATTCCACCAAAG 58.451 55.000 0.00 0.00 0.00 2.77
3382 6058 1.075374 CCTCCCACATTCCACCAAAGA 59.925 52.381 0.00 0.00 0.00 2.52
3383 6059 2.162681 CTCCCACATTCCACCAAAGAC 58.837 52.381 0.00 0.00 0.00 3.01
3384 6060 1.496857 TCCCACATTCCACCAAAGACA 59.503 47.619 0.00 0.00 0.00 3.41
3385 6061 2.109834 TCCCACATTCCACCAAAGACAT 59.890 45.455 0.00 0.00 0.00 3.06
3386 6062 2.493278 CCCACATTCCACCAAAGACATC 59.507 50.000 0.00 0.00 0.00 3.06
3387 6063 3.156293 CCACATTCCACCAAAGACATCA 58.844 45.455 0.00 0.00 0.00 3.07
3388 6064 3.573538 CCACATTCCACCAAAGACATCAA 59.426 43.478 0.00 0.00 0.00 2.57
3389 6065 4.039004 CCACATTCCACCAAAGACATCAAA 59.961 41.667 0.00 0.00 0.00 2.69
3390 6066 5.453057 CCACATTCCACCAAAGACATCAAAA 60.453 40.000 0.00 0.00 0.00 2.44
3391 6067 5.693104 CACATTCCACCAAAGACATCAAAAG 59.307 40.000 0.00 0.00 0.00 2.27
3392 6068 5.363580 ACATTCCACCAAAGACATCAAAAGT 59.636 36.000 0.00 0.00 0.00 2.66
3393 6069 6.549364 ACATTCCACCAAAGACATCAAAAGTA 59.451 34.615 0.00 0.00 0.00 2.24
3394 6070 6.633500 TTCCACCAAAGACATCAAAAGTAG 57.367 37.500 0.00 0.00 0.00 2.57
3395 6071 5.935945 TCCACCAAAGACATCAAAAGTAGA 58.064 37.500 0.00 0.00 0.00 2.59
3396 6072 5.997746 TCCACCAAAGACATCAAAAGTAGAG 59.002 40.000 0.00 0.00 0.00 2.43
3397 6073 5.335191 CCACCAAAGACATCAAAAGTAGAGC 60.335 44.000 0.00 0.00 0.00 4.09
3398 6074 5.239306 CACCAAAGACATCAAAAGTAGAGCA 59.761 40.000 0.00 0.00 0.00 4.26
3399 6075 5.827797 ACCAAAGACATCAAAAGTAGAGCAA 59.172 36.000 0.00 0.00 0.00 3.91
3400 6076 6.145535 CCAAAGACATCAAAAGTAGAGCAAC 58.854 40.000 0.00 0.00 0.00 4.17
3401 6077 6.016777 CCAAAGACATCAAAAGTAGAGCAACT 60.017 38.462 0.00 0.00 0.00 3.16
3402 6078 7.173218 CCAAAGACATCAAAAGTAGAGCAACTA 59.827 37.037 0.00 0.00 0.00 2.24
3403 6079 7.897575 AAGACATCAAAAGTAGAGCAACTAG 57.102 36.000 0.00 0.00 0.00 2.57
3404 6080 5.872070 AGACATCAAAAGTAGAGCAACTAGC 59.128 40.000 0.00 0.00 46.19 3.42
3413 6089 2.772189 GCAACTAGCGCGACACAG 59.228 61.111 12.10 2.30 0.00 3.66
3414 6090 2.730672 GCAACTAGCGCGACACAGG 61.731 63.158 12.10 0.00 0.00 4.00
3415 6091 1.080772 CAACTAGCGCGACACAGGA 60.081 57.895 12.10 0.00 0.00 3.86
3416 6092 0.458543 CAACTAGCGCGACACAGGAT 60.459 55.000 12.10 0.00 0.00 3.24
3417 6093 1.100510 AACTAGCGCGACACAGGATA 58.899 50.000 12.10 0.00 0.00 2.59
3418 6094 0.381089 ACTAGCGCGACACAGGATAC 59.619 55.000 12.10 0.00 0.00 2.24
3419 6095 0.317938 CTAGCGCGACACAGGATACC 60.318 60.000 12.10 0.00 37.17 2.73
3420 6096 1.033202 TAGCGCGACACAGGATACCA 61.033 55.000 12.10 0.00 37.17 3.25
3421 6097 2.165301 GCGCGACACAGGATACCAC 61.165 63.158 12.10 0.00 37.17 4.16
3422 6098 1.518572 CGCGACACAGGATACCACC 60.519 63.158 0.00 0.00 37.17 4.61
3423 6099 1.898154 GCGACACAGGATACCACCT 59.102 57.895 0.00 0.00 41.43 4.00
3424 6100 1.108776 GCGACACAGGATACCACCTA 58.891 55.000 0.00 0.00 38.32 3.08
3425 6101 1.479323 GCGACACAGGATACCACCTAA 59.521 52.381 0.00 0.00 38.32 2.69
3426 6102 2.102588 GCGACACAGGATACCACCTAAT 59.897 50.000 0.00 0.00 38.32 1.73
3427 6103 3.431766 GCGACACAGGATACCACCTAATT 60.432 47.826 0.00 0.00 38.32 1.40
3428 6104 4.766375 CGACACAGGATACCACCTAATTT 58.234 43.478 0.00 0.00 38.32 1.82
3429 6105 5.682990 GCGACACAGGATACCACCTAATTTA 60.683 44.000 0.00 0.00 38.32 1.40
3430 6106 5.751990 CGACACAGGATACCACCTAATTTAC 59.248 44.000 0.00 0.00 38.32 2.01
3431 6107 5.997843 ACACAGGATACCACCTAATTTACC 58.002 41.667 0.00 0.00 38.32 2.85
3432 6108 5.489637 ACACAGGATACCACCTAATTTACCA 59.510 40.000 0.00 0.00 38.32 3.25
3433 6109 6.012333 ACACAGGATACCACCTAATTTACCAA 60.012 38.462 0.00 0.00 38.32 3.67
3434 6110 7.060421 CACAGGATACCACCTAATTTACCAAT 58.940 38.462 0.00 0.00 38.32 3.16
3435 6111 8.215050 CACAGGATACCACCTAATTTACCAATA 58.785 37.037 0.00 0.00 38.32 1.90
3436 6112 8.437575 ACAGGATACCACCTAATTTACCAATAG 58.562 37.037 0.00 0.00 38.32 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 5.883673 TCTTTTTCCGTTTTCCTGAGAGAAA 59.116 36.000 0.00 0.00 33.98 2.52
41 42 2.265182 TGGGGCGCTTCTTTTTCCG 61.265 57.895 7.64 0.00 0.00 4.30
54 55 0.603065 CAAGTTTTAGGCAGTGGGGC 59.397 55.000 0.00 0.00 43.80 5.80
80 81 4.018050 AGGTGCTTTGTTATCAGGGAAGAT 60.018 41.667 0.00 0.00 0.00 2.40
81 82 3.330701 AGGTGCTTTGTTATCAGGGAAGA 59.669 43.478 0.00 0.00 0.00 2.87
118 119 4.772434 CGAATGCGGGTTATCAAGTTATG 58.228 43.478 0.00 0.00 0.00 1.90
218 220 2.368548 TGCTAGCAAAAGACAGGTCAGA 59.631 45.455 16.84 0.00 0.00 3.27
238 240 1.405463 TCATCATCTTCGGTCGTCCTG 59.595 52.381 0.00 0.00 0.00 3.86
259 262 3.814842 TCACAGCTGTGTTGTCCTTATTG 59.185 43.478 38.41 15.05 45.76 1.90
260 263 4.085357 TCACAGCTGTGTTGTCCTTATT 57.915 40.909 38.41 2.65 45.76 1.40
277 283 9.944663 GTTTTAGTTCAAGTACAATTCATCACA 57.055 29.630 0.00 0.00 0.00 3.58
278 284 9.394477 GGTTTTAGTTCAAGTACAATTCATCAC 57.606 33.333 0.00 0.00 0.00 3.06
297 303 6.961576 TCCAAAATAAGTGTCGTGGTTTTAG 58.038 36.000 0.00 0.00 0.00 1.85
323 329 0.106819 GCTACGACCTACTCCCTCCA 60.107 60.000 0.00 0.00 0.00 3.86
339 345 2.345991 GTGGCAACGGAGGTGCTA 59.654 61.111 10.02 0.43 42.51 3.49
351 357 1.483595 CCAAGTGAGAGGAGGTGGCA 61.484 60.000 0.00 0.00 0.00 4.92
367 376 1.442567 CAAACAAGCTGCTGGCCAA 59.557 52.632 7.01 0.00 43.05 4.52
376 385 2.863704 GCCAAAATCTCGCAAACAAGCT 60.864 45.455 0.00 0.00 0.00 3.74
396 406 0.108585 TTTCAGAGGACACTGTGGGC 59.891 55.000 13.09 3.62 38.46 5.36
448 458 5.919707 CCTTAGTCAGTGATGATGAGAATCG 59.080 44.000 0.00 0.00 38.61 3.34
467 477 4.406003 ACAGTATGCACCCTCTTACCTTAG 59.594 45.833 0.00 0.00 42.53 2.18
476 486 3.499918 GCATGATAACAGTATGCACCCTC 59.500 47.826 0.00 0.00 44.88 4.30
487 497 7.837202 ACAAAATTCATTGGCATGATAACAG 57.163 32.000 0.00 0.00 39.28 3.16
488 498 7.876582 TGAACAAAATTCATTGGCATGATAACA 59.123 29.630 0.00 0.00 39.28 2.41
524 534 4.695217 TGACGGTGGAAATTATTTGAGC 57.305 40.909 0.00 0.00 0.00 4.26
546 556 2.367241 TGCACTCTGCTGTACCAAAGTA 59.633 45.455 0.00 0.00 45.31 2.24
614 928 8.516234 TGTACGGTGTAATTATTCTTGCATTTT 58.484 29.630 0.00 0.00 0.00 1.82
726 1063 0.878523 CGACAAGCCAACTGTCCGAA 60.879 55.000 0.00 0.00 0.00 4.30
1063 1428 2.613223 GGCTCAAGGAGTGGTACTTGTC 60.613 54.545 0.00 0.00 43.40 3.18
1125 1499 2.098614 ACGATGCTGACTCTCATCAGT 58.901 47.619 4.80 7.49 46.65 3.41
1207 1581 3.133542 CCTCTGTACATGGCATCTGAGAA 59.866 47.826 17.53 0.00 0.00 2.87
1331 1729 6.071952 GGCCTTGTCATCAATCTCAGTTTTTA 60.072 38.462 0.00 0.00 32.82 1.52
2001 2410 1.754803 CGGACACTATGCAACTCCCTA 59.245 52.381 0.00 0.00 0.00 3.53
2127 2536 3.366374 GCAAACCATAGCTTGACAGGTTC 60.366 47.826 0.00 0.00 41.43 3.62
2235 2668 3.425162 ACACTTGGTGAATCCTCCTTC 57.575 47.619 4.62 0.00 36.96 3.46
2284 2717 0.883833 TCTCGTTCCGGTCTAACACC 59.116 55.000 0.00 0.00 42.69 4.16
2299 2732 4.269603 CCATGCAATTAGAGTGAAGTCTCG 59.730 45.833 0.00 0.00 39.21 4.04
2368 2801 0.530744 TGTACATCCTGAGCACGACC 59.469 55.000 0.00 0.00 0.00 4.79
2392 2825 3.663176 CACTGGCAAGGCACCACG 61.663 66.667 0.00 0.00 32.49 4.94
2408 2847 1.303398 AGTCCTCGTCGCTTCCTCA 60.303 57.895 0.00 0.00 0.00 3.86
2430 2869 7.778470 AAGAGTTCGGAAACATAATCAGATC 57.222 36.000 0.00 0.00 37.88 2.75
2446 2885 6.556212 TGAGAGAGCTATTACAAAGAGTTCG 58.444 40.000 0.00 0.00 0.00 3.95
2485 2926 4.761739 ACACACCCATCTGTCATGTTTTAG 59.238 41.667 0.00 0.00 0.00 1.85
2608 3051 8.906867 CAGGTGGATTGTTGTATCTGATAAAAT 58.093 33.333 3.70 1.03 0.00 1.82
2677 3123 3.622455 GCCACCTTACTGAAACCAGCTAT 60.622 47.826 0.00 0.00 35.09 2.97
2689 3135 5.830991 TGTTTCATTAACAAGCCACCTTACT 59.169 36.000 0.00 0.00 43.58 2.24
2725 4443 7.981789 TGATGATGTGTATACCTCTTTCTTGTC 59.018 37.037 0.00 0.00 0.00 3.18
2759 4491 6.108687 TGATTGACTTTGGTATCAGCTGTAG 58.891 40.000 14.67 3.90 0.00 2.74
2761 4493 4.910195 TGATTGACTTTGGTATCAGCTGT 58.090 39.130 14.67 3.75 0.00 4.40
2804 4536 5.199024 TGGAGTTGTTGATTGGTTGATTG 57.801 39.130 0.00 0.00 0.00 2.67
2815 4547 5.356751 GGTTGCACATATATGGAGTTGTTGA 59.643 40.000 16.96 0.00 0.00 3.18
2847 4580 3.843422 ACTGATTGGTTGGAATGGTTCA 58.157 40.909 0.00 0.00 0.00 3.18
2859 4592 7.494625 CCTTTATGTATGACGTTACTGATTGGT 59.505 37.037 0.00 0.00 0.00 3.67
2873 4606 6.772716 GGGCTTCATCTTTCCTTTATGTATGA 59.227 38.462 0.00 0.00 0.00 2.15
2897 4630 1.282248 CTGGTACAACGCGTCACAGG 61.282 60.000 14.44 2.49 38.70 4.00
2906 4639 0.041312 GCACAACAGCTGGTACAACG 60.041 55.000 19.93 0.86 38.70 4.10
2932 4665 6.009589 TCAGATCTAATTTTTCTTGGCACCA 58.990 36.000 0.00 0.00 0.00 4.17
2934 4667 7.765307 TGATCAGATCTAATTTTTCTTGGCAC 58.235 34.615 11.83 0.00 0.00 5.01
2946 4679 8.864087 TGCAACTGTAGTATGATCAGATCTAAT 58.136 33.333 11.83 0.59 33.93 1.73
2960 4693 4.095932 CGTATCCTGACTGCAACTGTAGTA 59.904 45.833 0.08 0.00 41.05 1.82
3048 4793 6.612247 TCACACGTGTTTTGATGTAAGAAT 57.388 33.333 20.79 0.00 0.00 2.40
3079 4824 3.078837 GCCAAAACCGATTCCTCAGTAA 58.921 45.455 0.00 0.00 0.00 2.24
3127 5801 3.005539 ATGCACAGAGGGAGGCGT 61.006 61.111 0.00 0.00 0.00 5.68
3144 5818 1.486310 AGGTCACAGACTTCAAGTGCA 59.514 47.619 0.00 0.00 33.44 4.57
3159 5833 2.934932 TGCAGGGCATGGAGGTCA 60.935 61.111 0.00 0.00 31.71 4.02
3253 5929 5.106712 TGGATTTCATTGTTGAACTACGAGC 60.107 40.000 0.00 0.00 41.50 5.03
3254 5930 6.480524 TGGATTTCATTGTTGAACTACGAG 57.519 37.500 0.00 0.00 41.50 4.18
3255 5931 6.878923 AGATGGATTTCATTGTTGAACTACGA 59.121 34.615 0.00 0.00 41.50 3.43
3256 5932 7.076842 AGATGGATTTCATTGTTGAACTACG 57.923 36.000 0.00 0.00 41.50 3.51
3257 5933 8.514594 TGAAGATGGATTTCATTGTTGAACTAC 58.485 33.333 0.00 0.00 41.50 2.73
3258 5934 8.634335 TGAAGATGGATTTCATTGTTGAACTA 57.366 30.769 0.00 0.00 41.50 2.24
3259 5935 7.528996 TGAAGATGGATTTCATTGTTGAACT 57.471 32.000 0.00 0.00 41.50 3.01
3260 5936 7.869429 AGTTGAAGATGGATTTCATTGTTGAAC 59.131 33.333 0.00 0.00 41.50 3.18
3261 5937 7.954835 AGTTGAAGATGGATTTCATTGTTGAA 58.045 30.769 0.00 0.00 40.09 2.69
3262 5938 7.449395 AGAGTTGAAGATGGATTTCATTGTTGA 59.551 33.333 0.00 0.00 35.97 3.18
3263 5939 7.600065 AGAGTTGAAGATGGATTTCATTGTTG 58.400 34.615 0.00 0.00 35.97 3.33
3264 5940 7.771927 AGAGTTGAAGATGGATTTCATTGTT 57.228 32.000 0.00 0.00 35.97 2.83
3265 5941 7.449395 TGAAGAGTTGAAGATGGATTTCATTGT 59.551 33.333 0.00 0.00 35.97 2.71
3266 5942 7.823665 TGAAGAGTTGAAGATGGATTTCATTG 58.176 34.615 0.00 0.00 35.97 2.82
3267 5943 8.467598 CATGAAGAGTTGAAGATGGATTTCATT 58.532 33.333 0.00 0.00 35.97 2.57
3268 5944 7.832685 TCATGAAGAGTTGAAGATGGATTTCAT 59.167 33.333 0.00 0.00 39.13 2.57
3269 5945 7.170277 TCATGAAGAGTTGAAGATGGATTTCA 58.830 34.615 0.00 0.00 33.00 2.69
3270 5946 7.621428 TCATGAAGAGTTGAAGATGGATTTC 57.379 36.000 0.00 0.00 0.00 2.17
3271 5947 6.095160 GCTCATGAAGAGTTGAAGATGGATTT 59.905 38.462 0.00 0.00 46.47 2.17
3272 5948 5.589452 GCTCATGAAGAGTTGAAGATGGATT 59.411 40.000 0.00 0.00 46.47 3.01
3273 5949 5.124645 GCTCATGAAGAGTTGAAGATGGAT 58.875 41.667 0.00 0.00 46.47 3.41
3274 5950 4.019950 TGCTCATGAAGAGTTGAAGATGGA 60.020 41.667 0.00 0.00 46.47 3.41
3275 5951 4.259356 TGCTCATGAAGAGTTGAAGATGG 58.741 43.478 0.00 0.00 46.47 3.51
3276 5952 4.333095 CCTGCTCATGAAGAGTTGAAGATG 59.667 45.833 0.00 0.00 46.47 2.90
3277 5953 4.224594 TCCTGCTCATGAAGAGTTGAAGAT 59.775 41.667 0.00 0.00 46.47 2.40
3278 5954 3.580022 TCCTGCTCATGAAGAGTTGAAGA 59.420 43.478 0.00 0.00 46.47 2.87
3279 5955 3.683822 GTCCTGCTCATGAAGAGTTGAAG 59.316 47.826 0.00 0.00 46.47 3.02
3280 5956 3.557898 GGTCCTGCTCATGAAGAGTTGAA 60.558 47.826 0.00 0.00 46.47 2.69
3281 5957 2.027745 GGTCCTGCTCATGAAGAGTTGA 60.028 50.000 0.00 0.00 46.47 3.18
3282 5958 2.289882 TGGTCCTGCTCATGAAGAGTTG 60.290 50.000 0.00 0.00 46.47 3.16
3283 5959 1.980765 TGGTCCTGCTCATGAAGAGTT 59.019 47.619 0.00 0.00 46.47 3.01
3284 5960 1.649321 TGGTCCTGCTCATGAAGAGT 58.351 50.000 0.00 0.00 46.47 3.24
3286 5962 3.106827 TGTATGGTCCTGCTCATGAAGA 58.893 45.455 0.00 0.00 0.00 2.87
3287 5963 3.201290 GTGTATGGTCCTGCTCATGAAG 58.799 50.000 0.00 0.00 0.00 3.02
3288 5964 2.571202 TGTGTATGGTCCTGCTCATGAA 59.429 45.455 0.00 0.00 0.00 2.57
3289 5965 2.187100 TGTGTATGGTCCTGCTCATGA 58.813 47.619 0.00 0.00 0.00 3.07
3290 5966 2.679837 GTTGTGTATGGTCCTGCTCATG 59.320 50.000 0.00 0.00 0.00 3.07
3291 5967 2.573462 AGTTGTGTATGGTCCTGCTCAT 59.427 45.455 0.00 0.00 0.00 2.90
3292 5968 1.977854 AGTTGTGTATGGTCCTGCTCA 59.022 47.619 0.00 0.00 0.00 4.26
3293 5969 2.770164 AGTTGTGTATGGTCCTGCTC 57.230 50.000 0.00 0.00 0.00 4.26
3294 5970 3.441101 TCTAGTTGTGTATGGTCCTGCT 58.559 45.455 0.00 0.00 0.00 4.24
3295 5971 3.887621 TCTAGTTGTGTATGGTCCTGC 57.112 47.619 0.00 0.00 0.00 4.85
3296 5972 6.173339 ACATTTCTAGTTGTGTATGGTCCTG 58.827 40.000 0.00 0.00 0.00 3.86
3297 5973 6.013725 TGACATTTCTAGTTGTGTATGGTCCT 60.014 38.462 0.00 0.00 0.00 3.85
3298 5974 6.092259 GTGACATTTCTAGTTGTGTATGGTCC 59.908 42.308 0.00 0.00 0.00 4.46
3299 5975 6.874134 AGTGACATTTCTAGTTGTGTATGGTC 59.126 38.462 0.00 0.00 0.00 4.02
3300 5976 6.769512 AGTGACATTTCTAGTTGTGTATGGT 58.230 36.000 0.00 0.00 0.00 3.55
3301 5977 7.099764 AGAGTGACATTTCTAGTTGTGTATGG 58.900 38.462 0.00 0.00 0.00 2.74
3302 5978 8.539770 AAGAGTGACATTTCTAGTTGTGTATG 57.460 34.615 0.00 0.00 0.00 2.39
3304 5980 9.692749 CTTAAGAGTGACATTTCTAGTTGTGTA 57.307 33.333 0.00 0.00 0.00 2.90
3305 5981 7.657761 CCTTAAGAGTGACATTTCTAGTTGTGT 59.342 37.037 3.36 0.00 0.00 3.72
3306 5982 7.657761 ACCTTAAGAGTGACATTTCTAGTTGTG 59.342 37.037 3.36 0.00 0.00 3.33
3307 5983 7.736893 ACCTTAAGAGTGACATTTCTAGTTGT 58.263 34.615 3.36 0.00 0.00 3.32
3308 5984 8.091449 AGACCTTAAGAGTGACATTTCTAGTTG 58.909 37.037 3.36 0.00 0.00 3.16
3309 5985 8.196378 AGACCTTAAGAGTGACATTTCTAGTT 57.804 34.615 3.36 0.00 0.00 2.24
3310 5986 7.784470 AGACCTTAAGAGTGACATTTCTAGT 57.216 36.000 3.36 0.00 0.00 2.57
3311 5987 8.930760 CAAAGACCTTAAGAGTGACATTTCTAG 58.069 37.037 3.36 0.00 0.00 2.43
3312 5988 8.429641 ACAAAGACCTTAAGAGTGACATTTCTA 58.570 33.333 3.36 0.00 0.00 2.10
3313 5989 7.227512 CACAAAGACCTTAAGAGTGACATTTCT 59.772 37.037 3.36 0.00 0.00 2.52
3314 5990 7.355778 CACAAAGACCTTAAGAGTGACATTTC 58.644 38.462 3.36 0.00 0.00 2.17
3315 5991 6.263168 CCACAAAGACCTTAAGAGTGACATTT 59.737 38.462 3.36 0.00 0.00 2.32
3316 5992 5.765182 CCACAAAGACCTTAAGAGTGACATT 59.235 40.000 3.36 0.00 0.00 2.71
3317 5993 5.163195 ACCACAAAGACCTTAAGAGTGACAT 60.163 40.000 3.36 0.00 0.00 3.06
3318 5994 4.163458 ACCACAAAGACCTTAAGAGTGACA 59.837 41.667 3.36 0.00 0.00 3.58
3319 5995 4.511826 CACCACAAAGACCTTAAGAGTGAC 59.488 45.833 3.36 0.00 0.00 3.67
3320 5996 4.407621 TCACCACAAAGACCTTAAGAGTGA 59.592 41.667 3.36 0.00 0.00 3.41
3321 5997 4.703897 TCACCACAAAGACCTTAAGAGTG 58.296 43.478 3.36 3.15 0.00 3.51
3322 5998 5.130477 TCTTCACCACAAAGACCTTAAGAGT 59.870 40.000 3.36 0.00 0.00 3.24
3323 5999 5.611374 TCTTCACCACAAAGACCTTAAGAG 58.389 41.667 3.36 0.00 0.00 2.85
3324 6000 5.623956 TCTTCACCACAAAGACCTTAAGA 57.376 39.130 3.36 0.00 0.00 2.10
3325 6001 5.182001 CCATCTTCACCACAAAGACCTTAAG 59.818 44.000 0.00 0.00 35.68 1.85
3326 6002 5.070001 CCATCTTCACCACAAAGACCTTAA 58.930 41.667 0.00 0.00 35.68 1.85
3327 6003 4.349636 TCCATCTTCACCACAAAGACCTTA 59.650 41.667 0.00 0.00 35.68 2.69
3328 6004 3.138283 TCCATCTTCACCACAAAGACCTT 59.862 43.478 0.00 0.00 35.68 3.50
3329 6005 2.711009 TCCATCTTCACCACAAAGACCT 59.289 45.455 0.00 0.00 35.68 3.85
3330 6006 3.140325 TCCATCTTCACCACAAAGACC 57.860 47.619 0.00 0.00 35.68 3.85
3331 6007 6.817765 TTAATCCATCTTCACCACAAAGAC 57.182 37.500 0.00 0.00 35.68 3.01
3332 6008 7.831691 TTTTAATCCATCTTCACCACAAAGA 57.168 32.000 0.00 0.00 37.18 2.52
3355 6031 2.302733 GTGGAATGTGGGAGGCATTTTT 59.697 45.455 0.00 0.00 36.77 1.94
3356 6032 1.901833 GTGGAATGTGGGAGGCATTTT 59.098 47.619 0.00 0.00 36.77 1.82
3357 6033 1.560505 GTGGAATGTGGGAGGCATTT 58.439 50.000 0.00 0.00 36.77 2.32
3358 6034 0.324645 GGTGGAATGTGGGAGGCATT 60.325 55.000 0.00 0.00 39.04 3.56
3359 6035 1.307647 GGTGGAATGTGGGAGGCAT 59.692 57.895 0.00 0.00 0.00 4.40
3360 6036 1.724148 TTGGTGGAATGTGGGAGGCA 61.724 55.000 0.00 0.00 0.00 4.75
3361 6037 0.541764 TTTGGTGGAATGTGGGAGGC 60.542 55.000 0.00 0.00 0.00 4.70
3362 6038 1.075374 TCTTTGGTGGAATGTGGGAGG 59.925 52.381 0.00 0.00 0.00 4.30
3363 6039 2.162681 GTCTTTGGTGGAATGTGGGAG 58.837 52.381 0.00 0.00 0.00 4.30
3364 6040 1.496857 TGTCTTTGGTGGAATGTGGGA 59.503 47.619 0.00 0.00 0.00 4.37
3365 6041 1.993956 TGTCTTTGGTGGAATGTGGG 58.006 50.000 0.00 0.00 0.00 4.61
3366 6042 3.156293 TGATGTCTTTGGTGGAATGTGG 58.844 45.455 0.00 0.00 0.00 4.17
3367 6043 4.852134 TTGATGTCTTTGGTGGAATGTG 57.148 40.909 0.00 0.00 0.00 3.21
3368 6044 5.363580 ACTTTTGATGTCTTTGGTGGAATGT 59.636 36.000 0.00 0.00 0.00 2.71
3369 6045 5.846203 ACTTTTGATGTCTTTGGTGGAATG 58.154 37.500 0.00 0.00 0.00 2.67
3370 6046 7.004086 TCTACTTTTGATGTCTTTGGTGGAAT 58.996 34.615 0.00 0.00 0.00 3.01
3371 6047 6.361433 TCTACTTTTGATGTCTTTGGTGGAA 58.639 36.000 0.00 0.00 0.00 3.53
3372 6048 5.935945 TCTACTTTTGATGTCTTTGGTGGA 58.064 37.500 0.00 0.00 0.00 4.02
3373 6049 5.335191 GCTCTACTTTTGATGTCTTTGGTGG 60.335 44.000 0.00 0.00 0.00 4.61
3374 6050 5.239306 TGCTCTACTTTTGATGTCTTTGGTG 59.761 40.000 0.00 0.00 0.00 4.17
3375 6051 5.376625 TGCTCTACTTTTGATGTCTTTGGT 58.623 37.500 0.00 0.00 0.00 3.67
3376 6052 5.947228 TGCTCTACTTTTGATGTCTTTGG 57.053 39.130 0.00 0.00 0.00 3.28
3377 6053 6.963796 AGTTGCTCTACTTTTGATGTCTTTG 58.036 36.000 0.00 0.00 0.00 2.77
3378 6054 7.095017 GCTAGTTGCTCTACTTTTGATGTCTTT 60.095 37.037 0.00 0.00 38.95 2.52
3379 6055 6.370166 GCTAGTTGCTCTACTTTTGATGTCTT 59.630 38.462 0.00 0.00 38.95 3.01
3380 6056 5.872070 GCTAGTTGCTCTACTTTTGATGTCT 59.128 40.000 0.00 0.00 38.95 3.41
3381 6057 5.220303 CGCTAGTTGCTCTACTTTTGATGTC 60.220 44.000 0.00 0.00 40.11 3.06
3382 6058 4.627467 CGCTAGTTGCTCTACTTTTGATGT 59.373 41.667 0.00 0.00 40.11 3.06
3383 6059 4.493220 GCGCTAGTTGCTCTACTTTTGATG 60.493 45.833 0.00 0.00 40.11 3.07
3384 6060 3.619038 GCGCTAGTTGCTCTACTTTTGAT 59.381 43.478 0.00 0.00 40.11 2.57
3385 6061 2.993899 GCGCTAGTTGCTCTACTTTTGA 59.006 45.455 0.00 0.00 40.11 2.69
3386 6062 2.222596 CGCGCTAGTTGCTCTACTTTTG 60.223 50.000 5.56 0.00 40.11 2.44
3387 6063 1.993370 CGCGCTAGTTGCTCTACTTTT 59.007 47.619 5.56 0.00 40.11 2.27
3388 6064 1.201647 TCGCGCTAGTTGCTCTACTTT 59.798 47.619 5.56 0.00 40.11 2.66
3389 6065 0.809385 TCGCGCTAGTTGCTCTACTT 59.191 50.000 5.56 0.00 40.11 2.24
3390 6066 0.099082 GTCGCGCTAGTTGCTCTACT 59.901 55.000 5.56 0.00 40.11 2.57
3391 6067 0.179171 TGTCGCGCTAGTTGCTCTAC 60.179 55.000 5.56 0.00 40.11 2.59
3392 6068 0.179171 GTGTCGCGCTAGTTGCTCTA 60.179 55.000 5.56 0.00 40.11 2.43
3393 6069 1.444553 GTGTCGCGCTAGTTGCTCT 60.445 57.895 5.56 0.00 40.11 4.09
3394 6070 1.678269 CTGTGTCGCGCTAGTTGCTC 61.678 60.000 5.56 2.32 40.11 4.26
3395 6071 1.734477 CTGTGTCGCGCTAGTTGCT 60.734 57.895 5.56 0.00 40.11 3.91
3396 6072 2.730672 CCTGTGTCGCGCTAGTTGC 61.731 63.158 5.56 0.00 38.57 4.17
3397 6073 0.458543 ATCCTGTGTCGCGCTAGTTG 60.459 55.000 5.56 0.00 0.00 3.16
3398 6074 1.100510 TATCCTGTGTCGCGCTAGTT 58.899 50.000 5.56 0.00 0.00 2.24
3399 6075 0.381089 GTATCCTGTGTCGCGCTAGT 59.619 55.000 5.56 0.00 0.00 2.57
3400 6076 0.317938 GGTATCCTGTGTCGCGCTAG 60.318 60.000 5.56 0.00 0.00 3.42
3401 6077 1.033202 TGGTATCCTGTGTCGCGCTA 61.033 55.000 5.56 0.00 0.00 4.26
3402 6078 2.348104 TGGTATCCTGTGTCGCGCT 61.348 57.895 5.56 0.00 0.00 5.92
3403 6079 2.165301 GTGGTATCCTGTGTCGCGC 61.165 63.158 0.00 0.00 0.00 6.86
3404 6080 1.518572 GGTGGTATCCTGTGTCGCG 60.519 63.158 0.00 0.00 0.00 5.87
3405 6081 1.108776 TAGGTGGTATCCTGTGTCGC 58.891 55.000 0.00 0.00 38.41 5.19
3406 6082 4.402056 AATTAGGTGGTATCCTGTGTCG 57.598 45.455 0.00 0.00 38.41 4.35
3407 6083 6.053650 GGTAAATTAGGTGGTATCCTGTGTC 58.946 44.000 0.00 0.00 38.41 3.67
3408 6084 5.489637 TGGTAAATTAGGTGGTATCCTGTGT 59.510 40.000 0.00 0.00 38.41 3.72
3409 6085 5.996644 TGGTAAATTAGGTGGTATCCTGTG 58.003 41.667 0.00 0.00 38.41 3.66
3410 6086 6.645884 TTGGTAAATTAGGTGGTATCCTGT 57.354 37.500 0.00 0.00 38.41 4.00
3411 6087 8.848474 CTATTGGTAAATTAGGTGGTATCCTG 57.152 38.462 0.00 0.00 38.41 3.86


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

AutoCloner maintained by Alex Coulton.