Multiple sequence alignment - TraesCS5A01G190600

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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 TraesCS5A01G190600 chr5A 100.000 6330 0 0 1 6330 395052759 395059088 0.000000e+00 11690.0
1 TraesCS5A01G190600 chr5A 89.922 129 12 1 2873 3000 415373409 415373537 1.410000e-36 165.0
2 TraesCS5A01G190600 chr5A 84.884 86 9 3 3175 3257 353844089 353844173 4.070000e-12 84.2
3 TraesCS5A01G190600 chr5D 94.356 3012 123 17 3099 6088 302885897 302882911 0.000000e+00 4577.0
4 TraesCS5A01G190600 chr5D 90.398 1937 79 29 669 2574 302891361 302889501 0.000000e+00 2447.0
5 TraesCS5A01G190600 chr5D 85.522 594 70 8 1 585 302892106 302891520 1.950000e-169 606.0
6 TraesCS5A01G190600 chr5D 86.713 429 33 10 2569 2993 302886751 302886343 7.480000e-124 455.0
7 TraesCS5A01G190600 chr5D 90.947 243 13 4 6092 6330 302882858 302882621 1.020000e-82 318.0
8 TraesCS5A01G190600 chr5D 87.097 93 5 3 595 681 302891470 302891379 1.450000e-16 99.0
9 TraesCS5A01G190600 chr5B 94.503 2747 105 18 3608 6330 347698284 347695560 0.000000e+00 4194.0
10 TraesCS5A01G190600 chr5B 87.866 1640 127 35 1392 3011 347700912 347699325 0.000000e+00 1860.0
11 TraesCS5A01G190600 chr5B 86.585 492 31 12 914 1391 347701482 347701012 1.570000e-140 510.0
12 TraesCS5A01G190600 chr5B 85.652 460 45 8 398 839 347701972 347701516 1.240000e-126 464.0
13 TraesCS5A01G190600 chr5B 87.901 405 36 7 1 401 347773062 347772667 1.240000e-126 464.0
14 TraesCS5A01G190600 chr5B 90.968 310 11 5 3113 3419 347698809 347698514 9.880000e-108 401.0
15 TraesCS5A01G190600 chr5B 91.667 96 8 0 3170 3265 300394545 300394450 3.980000e-27 134.0
16 TraesCS5A01G190600 chr5B 100.000 37 0 0 867 903 347701515 347701479 1.140000e-07 69.4
17 TraesCS5A01G190600 chr5B 100.000 29 0 0 3415 3443 347698313 347698285 3.000000e-03 54.7
18 TraesCS5A01G190600 chr4A 84.461 399 49 9 2819 3207 13761670 13761275 1.290000e-101 381.0
19 TraesCS5A01G190600 chr4A 82.161 398 56 11 2819 3207 13762945 13762554 1.700000e-85 327.0
20 TraesCS5A01G190600 chr4A 77.434 452 60 24 2820 3262 578536646 578537064 1.370000e-56 231.0
21 TraesCS5A01G190600 chr4A 80.620 258 32 14 2922 3170 13760534 13760286 3.900000e-42 183.0
22 TraesCS5A01G190600 chr4A 92.308 117 9 0 3281 3397 475905892 475905776 3.930000e-37 167.0
23 TraesCS5A01G190600 chr4A 82.667 75 9 4 2601 2673 168738552 168738480 5.300000e-06 63.9
24 TraesCS5A01G190600 chr3A 82.750 400 38 14 2873 3262 456444340 456444718 1.700000e-85 327.0
25 TraesCS5A01G190600 chr3A 93.913 115 6 1 3281 3394 466795837 466795723 8.440000e-39 172.0
26 TraesCS5A01G190600 chr3A 91.525 118 8 2 3281 3397 57281356 57281472 1.830000e-35 161.0
27 TraesCS5A01G190600 chr3D 81.818 407 38 17 2860 3262 338316064 338316438 6.160000e-80 309.0
28 TraesCS5A01G190600 chr3D 94.000 150 9 0 3113 3262 554073788 554073639 1.780000e-55 228.0
29 TraesCS5A01G190600 chr2B 82.730 359 48 10 2820 3170 743334531 743334883 2.220000e-79 307.0
30 TraesCS5A01G190600 chr2B 92.143 140 11 0 3113 3252 743334958 743335097 1.390000e-46 198.0
31 TraesCS5A01G190600 chr2B 93.043 115 7 1 3281 3394 166470784 166470898 3.930000e-37 167.0
32 TraesCS5A01G190600 chr2B 93.750 112 6 1 3283 3393 399342026 399342137 3.930000e-37 167.0
33 TraesCS5A01G190600 chr2B 79.920 249 25 16 2933 3170 505007750 505007516 6.570000e-35 159.0
34 TraesCS5A01G190600 chr2B 80.220 182 35 1 2579 2759 222055955 222056136 1.110000e-27 135.0
35 TraesCS5A01G190600 chr2D 82.329 249 28 11 2933 3170 427971181 427970938 1.080000e-47 202.0
36 TraesCS5A01G190600 chr2D 93.805 113 7 0 3282 3394 388833777 388833665 3.030000e-38 171.0
37 TraesCS5A01G190600 chr4B 91.429 140 12 0 3113 3252 566977141 566977280 6.480000e-45 193.0
38 TraesCS5A01G190600 chr7D 81.223 229 33 8 2578 2798 555049192 555048966 6.520000e-40 176.0
39 TraesCS5A01G190600 chr2A 93.043 115 6 2 3281 3394 586454814 586454927 3.930000e-37 167.0
40 TraesCS5A01G190600 chr2A 77.729 229 46 4 2579 2804 397969064 397968838 1.110000e-27 135.0
41 TraesCS5A01G190600 chr2A 79.121 182 37 1 2579 2759 399330333 399330514 2.400000e-24 124.0
42 TraesCS5A01G190600 chr6B 78.756 193 34 6 2572 2761 576014226 576014414 8.620000e-24 122.0
43 TraesCS5A01G190600 chr6B 89.333 75 8 0 2877 2951 553057987 553058061 1.880000e-15 95.3
44 TraesCS5A01G190600 chr3B 78.022 182 39 1 2579 2759 558090207 558090388 5.190000e-21 113.0
45 TraesCS5A01G190600 chr3B 85.714 70 10 0 2817 2886 818302690 818302621 2.450000e-09 75.0
46 TraesCS5A01G190600 chr1A 77.473 182 39 2 2579 2759 257769197 257769377 2.410000e-19 108.0
47 TraesCS5A01G190600 chr6D 89.333 75 8 0 2877 2951 368364500 368364426 1.880000e-15 95.3
48 TraesCS5A01G190600 chr6A 89.333 75 8 0 2877 2951 509278273 509278199 1.880000e-15 95.3


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 TraesCS5A01G190600 chr5A 395052759 395059088 6329 False 11690.000000 11690 100.000000 1 6330 1 chr5A.!!$F2 6329
1 TraesCS5A01G190600 chr5D 302882621 302892106 9485 True 1417.000000 4577 89.172167 1 6330 6 chr5D.!!$R1 6329
2 TraesCS5A01G190600 chr5B 347695560 347701972 6412 True 1079.014286 4194 92.224857 398 6330 7 chr5B.!!$R3 5932
3 TraesCS5A01G190600 chr4A 13760286 13762945 2659 True 297.000000 381 82.414000 2819 3207 3 chr4A.!!$R3 388
4 TraesCS5A01G190600 chr2B 743334531 743335097 566 False 252.500000 307 87.436500 2820 3252 2 chr2B.!!$F4 432

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
465 475 0.036875 CAAGAAGTCCCAGTGGGTCC 59.963 60.0 27.87 18.79 44.74 4.46 F
481 491 0.108329 GTCCGATGGAAAAGAGCCGA 60.108 55.0 0.00 0.00 31.38 5.54 F
1535 1741 0.320697 GGCTGGGTTGTCGACTTACT 59.679 55.0 17.92 0.00 0.00 2.24 F
2408 2635 0.107459 ATGCCCTTTCTTCCTCTCGC 60.107 55.0 0.00 0.00 0.00 5.03 F
2820 5803 0.399833 TATGAAGGCAGTGTGGTGCA 59.600 50.0 0.00 0.00 45.93 4.57 F
3570 8272 0.248866 CACCACCGTTTTTGTGAGCC 60.249 55.0 0.00 0.00 35.74 4.70 F
5092 9816 0.179029 AACACCGCCTTGTGCTAACT 60.179 50.0 0.00 0.00 39.93 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1448 1654 0.457443 GCAAAATCTAGCAGCACCCC 59.543 55.0 0.00 0.00 0.00 4.95 R
2266 2493 0.734889 GGGCTGAATGTCGTCAATGG 59.265 55.0 0.00 0.00 0.00 3.16 R
3214 7710 0.456628 GGGGTAGCGACTCTTGACTC 59.543 60.0 0.00 0.00 0.00 3.36 R
3541 8243 0.387565 AACGGTGGTGATTGGCAAAC 59.612 50.0 3.01 1.26 0.00 2.93 R
4785 9505 0.955919 GGGTAGTGCAGCACAAGACC 60.956 60.0 27.35 26.30 36.74 3.85 R
5097 9821 0.393267 TTCCTTAACGGGGCATTCGG 60.393 55.0 0.00 0.00 0.00 4.30 R
6157 10933 0.790495 CACACATCATTGTCGCACGC 60.790 55.0 0.00 0.00 32.34 5.34 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
30 31 5.931146 AGAGATTTGTGACACTCTTCATCAC 59.069 40.000 7.20 0.00 42.54 3.06
31 32 4.999950 AGATTTGTGACACTCTTCATCACC 59.000 41.667 7.20 0.00 41.71 4.02
47 48 2.291365 TCACCGAATTGATCCATGCAG 58.709 47.619 0.00 0.00 0.00 4.41
82 83 2.479566 TGGAGAGACAACCATGAAGC 57.520 50.000 0.00 0.00 0.00 3.86
84 85 3.173151 TGGAGAGACAACCATGAAGCTA 58.827 45.455 0.00 0.00 0.00 3.32
91 92 4.018960 AGACAACCATGAAGCTAACTCCAT 60.019 41.667 0.00 0.00 0.00 3.41
99 100 4.713553 TGAAGCTAACTCCATTCAACACA 58.286 39.130 0.00 0.00 0.00 3.72
145 146 0.112995 TCATGGCAAAGAAGGGCTGT 59.887 50.000 0.00 0.00 0.00 4.40
177 178 6.507771 CGTTGTTTTCTAATTGTGTGCAAAGG 60.508 38.462 0.00 0.00 38.21 3.11
210 211 9.826574 AGCAATAAGAGTATTGTCGGTAATTAA 57.173 29.630 7.96 0.00 45.75 1.40
216 217 6.641314 AGAGTATTGTCGGTAATTAATCTGCG 59.359 38.462 0.00 0.00 0.00 5.18
222 223 3.576982 TCGGTAATTAATCTGCGAGGGAT 59.423 43.478 0.00 0.00 0.00 3.85
232 233 2.094182 TCTGCGAGGGATAAACACACTC 60.094 50.000 0.00 0.00 0.00 3.51
241 242 4.389077 GGGATAAACACACTCTGAAACTCG 59.611 45.833 0.00 0.00 0.00 4.18
242 243 5.227908 GGATAAACACACTCTGAAACTCGA 58.772 41.667 0.00 0.00 0.00 4.04
253 254 5.584649 ACTCTGAAACTCGAAAATGACAACA 59.415 36.000 0.00 0.00 0.00 3.33
262 263 8.553459 ACTCGAAAATGACAACAGATAAGAAT 57.447 30.769 0.00 0.00 0.00 2.40
275 276 8.943002 CAACAGATAAGAATACCTTTAAACGGT 58.057 33.333 12.17 12.17 36.34 4.83
279 280 9.828039 AGATAAGAATACCTTTAAACGGTTAGG 57.172 33.333 12.60 0.20 36.34 2.69
282 283 6.240145 AGAATACCTTTAAACGGTTAGGCAA 58.760 36.000 12.60 0.00 35.98 4.52
284 285 6.897706 ATACCTTTAAACGGTTAGGCAAAA 57.102 33.333 12.60 0.00 35.98 2.44
285 286 4.935702 ACCTTTAAACGGTTAGGCAAAAC 58.064 39.130 1.73 0.00 0.00 2.43
297 298 2.049372 AGGCAAAACTTTGGAGGCAAT 58.951 42.857 4.45 0.00 38.57 3.56
300 301 3.631686 GGCAAAACTTTGGAGGCAATTTT 59.368 39.130 4.45 0.00 38.57 1.82
306 307 9.050601 CAAAACTTTGGAGGCAATTTTATACAA 57.949 29.630 0.00 0.00 34.59 2.41
312 313 7.238486 TGGAGGCAATTTTATACAACACATT 57.762 32.000 0.00 0.00 0.00 2.71
313 314 7.095910 TGGAGGCAATTTTATACAACACATTG 58.904 34.615 0.00 0.00 41.98 2.82
315 316 6.462500 AGGCAATTTTATACAACACATTGCA 58.538 32.000 14.67 0.00 45.42 4.08
316 317 7.104939 AGGCAATTTTATACAACACATTGCAT 58.895 30.769 14.67 6.53 45.42 3.96
328 329 5.876651 ACACATTGCATAGACTGATAGGA 57.123 39.130 0.00 0.00 0.00 2.94
331 332 4.584743 ACATTGCATAGACTGATAGGACGA 59.415 41.667 0.00 0.00 0.00 4.20
363 364 0.884704 TGCTTGGGTCTTGCGACTTC 60.885 55.000 0.00 0.00 40.10 3.01
365 366 0.319555 CTTGGGTCTTGCGACTTCGA 60.320 55.000 2.02 0.00 43.02 3.71
383 384 3.511699 TCGAGAATCAGAACAATCACCG 58.488 45.455 0.00 0.00 33.17 4.94
391 392 3.006859 TCAGAACAATCACCGAGTCACAT 59.993 43.478 0.00 0.00 0.00 3.21
402 403 3.056393 ACCGAGTCACATAAACCATTCGA 60.056 43.478 0.00 0.00 0.00 3.71
408 410 5.523916 AGTCACATAAACCATTCGACATAGC 59.476 40.000 0.00 0.00 0.00 2.97
465 475 0.036875 CAAGAAGTCCCAGTGGGTCC 59.963 60.000 27.87 18.79 44.74 4.46
467 477 1.911766 GAAGTCCCAGTGGGTCCGA 60.912 63.158 27.87 5.55 44.74 4.55
469 479 1.553690 AAGTCCCAGTGGGTCCGATG 61.554 60.000 27.87 0.03 44.74 3.84
481 491 0.108329 GTCCGATGGAAAAGAGCCGA 60.108 55.000 0.00 0.00 31.38 5.54
493 503 4.664150 AAAGAGCCGAAAAACCATTTGA 57.336 36.364 0.00 0.00 0.00 2.69
495 505 4.871933 AGAGCCGAAAAACCATTTGAAT 57.128 36.364 0.00 0.00 0.00 2.57
501 511 4.985409 CCGAAAAACCATTTGAATCGGAAA 59.015 37.500 13.78 0.00 42.18 3.13
507 517 5.782893 ACCATTTGAATCGGAAACTTTCA 57.217 34.783 3.93 0.00 0.00 2.69
559 569 3.795623 TTCCTCGTTAGTGTATGGCTC 57.204 47.619 0.00 0.00 0.00 4.70
567 577 4.688879 CGTTAGTGTATGGCTCACAAAGAA 59.311 41.667 9.67 0.00 38.16 2.52
584 594 6.905609 CACAAAGAACATCATTCATCTCATCG 59.094 38.462 0.00 0.00 0.00 3.84
612 667 4.637534 TCTTGTGAGGAATAGCATCAAAGC 59.362 41.667 0.00 0.00 39.28 3.51
737 832 2.545952 GCCGGACACATACATTCGAGAT 60.546 50.000 5.05 0.00 0.00 2.75
908 1004 3.793144 GCCAACGAAGCAGCCTCG 61.793 66.667 12.00 12.00 0.00 4.63
909 1005 3.121030 CCAACGAAGCAGCCTCGG 61.121 66.667 17.60 0.79 0.00 4.63
910 1006 3.793144 CAACGAAGCAGCCTCGGC 61.793 66.667 17.60 0.00 42.33 5.54
982 1078 4.580044 CATCGCATCGCACCGCAC 62.580 66.667 0.00 0.00 0.00 5.34
1141 1237 2.581354 CTCACTTCCTCCCGCCAG 59.419 66.667 0.00 0.00 0.00 4.85
1165 1261 2.158959 CGGCGCTTCAGGTAACGAG 61.159 63.158 7.64 0.00 46.39 4.18
1170 1266 1.351153 GCTTCAGGTAACGAGACAGC 58.649 55.000 0.00 0.00 46.39 4.40
1171 1267 1.997669 CTTCAGGTAACGAGACAGCC 58.002 55.000 0.00 0.00 46.39 4.85
1173 1269 0.892358 TCAGGTAACGAGACAGCCGT 60.892 55.000 0.00 0.00 46.39 5.68
1212 1308 1.549203 TGCTTGCCTTTTCCATCCTC 58.451 50.000 0.00 0.00 0.00 3.71
1213 1309 1.203038 TGCTTGCCTTTTCCATCCTCA 60.203 47.619 0.00 0.00 0.00 3.86
1216 1312 0.323725 TGCCTTTTCCATCCTCAGCC 60.324 55.000 0.00 0.00 0.00 4.85
1321 1430 3.050275 GACCTGCACCGTTGGAGC 61.050 66.667 0.00 0.00 39.82 4.70
1386 1496 0.750850 TAGGTTACAGGATCGGCAGC 59.249 55.000 0.00 0.00 0.00 5.25
1387 1497 1.523938 GGTTACAGGATCGGCAGCC 60.524 63.158 0.00 0.00 0.00 4.85
1448 1654 4.082125 AGATTTGGACTTTGTAGCCTTGG 58.918 43.478 0.00 0.00 0.00 3.61
1530 1736 1.816074 TTTATGGCTGGGTTGTCGAC 58.184 50.000 9.11 9.11 0.00 4.20
1535 1741 0.320697 GGCTGGGTTGTCGACTTACT 59.679 55.000 17.92 0.00 0.00 2.24
1618 1824 5.425217 TGCCTGGAATTCTAGTAGTTGATGA 59.575 40.000 16.64 0.00 0.00 2.92
1704 1919 8.541133 TCATTTACAACTTCATATCGTGAACA 57.459 30.769 0.00 0.00 41.79 3.18
1750 1965 1.800315 GCGACGCGTTCAAGCTAGA 60.800 57.895 15.53 0.00 34.40 2.43
1949 2174 2.918712 AGCCATAAGTGAGCGCTTAT 57.081 45.000 13.26 1.68 40.99 1.73
2138 2365 4.041938 ACATGGGTCATTTTCCTTGCAAAT 59.958 37.500 0.00 0.00 33.17 2.32
2263 2490 3.826754 GCAAGGGGCTTAAGCGGC 61.827 66.667 20.80 14.45 43.26 6.53
2387 2614 3.206150 ACTGTGTGCTTGGTAAGTTCTG 58.794 45.455 0.00 0.00 0.00 3.02
2408 2635 0.107459 ATGCCCTTTCTTCCTCTCGC 60.107 55.000 0.00 0.00 0.00 5.03
2549 2777 8.004215 TCCTATTCCATAATTACTGGCATGTTT 58.996 33.333 0.00 0.00 33.56 2.83
2623 5606 1.128692 GCATGCACGTGTTTCTAGGTC 59.871 52.381 18.38 0.00 0.00 3.85
2789 5772 1.002134 CCTTTGCACCCAGACGGAT 60.002 57.895 0.00 0.00 34.64 4.18
2795 5778 1.219124 CACCCAGACGGATGGAGTG 59.781 63.158 9.56 11.10 43.57 3.51
2809 5792 4.457257 GGATGGAGTGCTATTTATGAAGGC 59.543 45.833 0.00 0.00 0.00 4.35
2810 5793 4.502105 TGGAGTGCTATTTATGAAGGCA 57.498 40.909 0.00 0.00 0.00 4.75
2811 5794 4.454678 TGGAGTGCTATTTATGAAGGCAG 58.545 43.478 1.87 0.00 33.47 4.85
2812 5795 4.080356 TGGAGTGCTATTTATGAAGGCAGT 60.080 41.667 7.63 7.63 38.96 4.40
2813 5796 4.274459 GGAGTGCTATTTATGAAGGCAGTG 59.726 45.833 11.20 0.00 36.81 3.66
2814 5797 4.848357 AGTGCTATTTATGAAGGCAGTGT 58.152 39.130 7.26 0.00 35.60 3.55
2815 5798 4.637534 AGTGCTATTTATGAAGGCAGTGTG 59.362 41.667 7.26 0.00 35.60 3.82
2817 5800 3.947834 GCTATTTATGAAGGCAGTGTGGT 59.052 43.478 0.00 0.00 0.00 4.16
2818 5801 4.201950 GCTATTTATGAAGGCAGTGTGGTG 60.202 45.833 0.00 0.00 0.00 4.17
2819 5802 1.533625 TTATGAAGGCAGTGTGGTGC 58.466 50.000 0.00 0.00 43.19 5.01
2820 5803 0.399833 TATGAAGGCAGTGTGGTGCA 59.600 50.000 0.00 0.00 45.93 4.57
2821 5804 1.174712 ATGAAGGCAGTGTGGTGCAC 61.175 55.000 8.80 8.80 45.93 4.57
2853 5837 3.317150 TCGAACGACTAGTCACGACTAA 58.683 45.455 22.37 6.45 42.72 2.24
2856 5840 4.201656 CGAACGACTAGTCACGACTAATCA 60.202 45.833 22.37 0.00 42.72 2.57
2857 5841 5.502058 CGAACGACTAGTCACGACTAATCAT 60.502 44.000 22.37 4.24 42.72 2.45
2863 5847 4.966965 AGTCACGACTAATCATCGAGTT 57.033 40.909 0.00 0.00 42.25 3.01
2899 5896 3.008330 GACTCGACTAGTTGGCTGAGTA 58.992 50.000 10.33 0.00 39.07 2.59
2924 5921 2.730069 GACTCGATCGACTAGTCTCGA 58.270 52.381 26.32 26.32 46.31 4.04
2925 5922 2.462889 ACTCGATCGACTAGTCTCGAC 58.537 52.381 25.10 12.35 45.14 4.20
2926 5923 2.099592 ACTCGATCGACTAGTCTCGACT 59.900 50.000 25.10 17.04 45.14 4.18
2927 5924 3.314913 ACTCGATCGACTAGTCTCGACTA 59.685 47.826 25.10 11.63 45.14 2.59
2952 5949 1.595794 TGGTTTTTGAGTCGAACGAGC 59.404 47.619 0.00 0.00 0.00 5.03
2953 5950 1.865340 GGTTTTTGAGTCGAACGAGCT 59.135 47.619 0.00 0.00 0.00 4.09
2978 5976 1.453928 GCCCCACCTGCCATACTTC 60.454 63.158 0.00 0.00 0.00 3.01
2989 5987 6.599244 CACCTGCCATACTTCTTTCTATTTGA 59.401 38.462 0.00 0.00 0.00 2.69
3026 6024 1.209747 GGAAACCTAGATCGCCCAGTT 59.790 52.381 0.00 0.00 0.00 3.16
3028 6026 3.344515 GAAACCTAGATCGCCCAGTTTT 58.655 45.455 0.00 0.00 0.00 2.43
3057 6060 1.674057 CAAACCTCTCCTGCGACCT 59.326 57.895 0.00 0.00 0.00 3.85
3068 6071 1.831652 CTGCGACCTTCTCCCTTGGT 61.832 60.000 0.00 0.00 36.70 3.67
3071 6074 3.938109 GACCTTCTCCCTTGGTCAC 57.062 57.895 6.52 0.00 46.79 3.67
3097 6497 3.727258 CCCCACAATCCTGCCGGA 61.727 66.667 5.05 0.00 45.16 5.14
3165 7659 1.954362 CTTCTGGTCTGCTCCTCCCG 61.954 65.000 0.00 0.00 0.00 5.14
3180 7674 1.548719 CTCCCGTGGTAACTCATGTCA 59.451 52.381 0.00 0.00 37.61 3.58
3195 7691 2.363788 TGTCAACTAGTCGACCATGC 57.636 50.000 13.01 3.99 0.00 4.06
3210 7706 2.263077 CCATGCGTCTTGACTAGTCAC 58.737 52.381 25.13 13.60 39.66 3.67
3399 7896 5.590530 AGCTTTATTGTTGTTGTGTGGAA 57.409 34.783 0.00 0.00 0.00 3.53
3443 8145 7.012704 GGCTCAAGAGAAGAAATGTGCAATATA 59.987 37.037 0.32 0.00 34.83 0.86
3495 8197 4.532126 TGTGACTCCACTTCATGTTCCTAT 59.468 41.667 0.00 0.00 43.55 2.57
3511 8213 9.784531 CATGTTCCTATTACCTATTCATGAACT 57.215 33.333 11.07 3.09 34.14 3.01
3532 8234 8.172484 TGAACTGTATATTTTTCATTTCCGTCG 58.828 33.333 0.00 0.00 0.00 5.12
3541 8243 2.690786 TCATTTCCGTCGTAGGTTTGG 58.309 47.619 0.00 0.00 0.00 3.28
3558 8260 1.288752 GGTTTGCCAATCACCACCG 59.711 57.895 0.00 0.00 34.09 4.94
3570 8272 0.248866 CACCACCGTTTTTGTGAGCC 60.249 55.000 0.00 0.00 35.74 4.70
3591 8293 3.118038 CCAGTAGTCTCCTCTAGAGCACT 60.118 52.174 14.73 16.07 42.90 4.40
3707 8409 1.131883 AGCGATGTTGAAGCATCTTGC 59.868 47.619 5.73 3.13 45.46 4.01
3775 8477 4.637534 CCCAGTCCATAGAACATTGACTTG 59.362 45.833 0.00 0.00 34.21 3.16
3779 8481 5.356190 AGTCCATAGAACATTGACTTGCATG 59.644 40.000 0.00 0.00 32.61 4.06
4147 8853 3.379372 ACAGCACAATTATGGCAGACATC 59.621 43.478 0.00 0.00 41.03 3.06
4344 9064 4.641989 GTGCACATTTCAGATGGGATAGTT 59.358 41.667 13.17 0.00 0.00 2.24
4499 9219 9.227777 GGCCTCTTAGAAATTTTCAGTAACTTA 57.772 33.333 11.53 0.00 0.00 2.24
4610 9330 1.645034 CTCATTGTGATCGGAAGCGT 58.355 50.000 0.00 0.00 0.00 5.07
4618 9338 1.270625 TGATCGGAAGCGTGTCCTTTT 60.271 47.619 5.19 0.00 35.31 2.27
4827 9547 9.408648 ACCCTACCTAATATTTTTCTTCATGTG 57.591 33.333 0.00 0.00 0.00 3.21
4972 9696 5.456763 GGGATCTTATAATGGAGCAACACCT 60.457 44.000 0.00 0.00 0.00 4.00
5021 9745 1.605232 TGTCTTCTAGTCGTGTTCGCA 59.395 47.619 0.00 0.00 36.96 5.10
5035 9759 0.736053 TTCGCAAAGCTTTGTCGGTT 59.264 45.000 34.18 7.32 40.24 4.44
5092 9816 0.179029 AACACCGCCTTGTGCTAACT 60.179 50.000 0.00 0.00 39.93 2.24
5097 9821 0.512952 CGCCTTGTGCTAACTGTGAC 59.487 55.000 0.00 0.00 38.05 3.67
5098 9822 0.875059 GCCTTGTGCTAACTGTGACC 59.125 55.000 0.00 0.00 36.87 4.02
5103 9827 2.412870 TGTGCTAACTGTGACCGAATG 58.587 47.619 0.00 0.00 0.00 2.67
5105 9829 0.727398 GCTAACTGTGACCGAATGCC 59.273 55.000 0.00 0.00 0.00 4.40
5108 9832 2.819595 CTGTGACCGAATGCCCCG 60.820 66.667 0.00 0.00 0.00 5.73
5170 9894 0.034574 TTAACATGCCACCAGCCGAT 60.035 50.000 0.00 0.00 42.71 4.18
5185 9909 2.034812 AGCCGATGGATTCTACGAGAAC 59.965 50.000 0.00 0.00 37.00 3.01
5237 9961 1.037030 ATGCAGGGTGGCCATTAACG 61.037 55.000 9.72 0.00 0.00 3.18
5404 10128 5.420421 TCACCTTTTGGACAATTTTGAGTCA 59.580 36.000 0.00 0.00 44.07 3.41
5465 10189 7.780064 AGGATATATGACGGAAATGATCAGAG 58.220 38.462 0.09 0.00 0.00 3.35
5501 10225 3.544684 TCATCAAGGTTCATCAATCCGG 58.455 45.455 0.00 0.00 0.00 5.14
5509 10233 3.343617 GTTCATCAATCCGGAAGTCCAA 58.656 45.455 9.01 0.00 35.14 3.53
5520 10244 3.304659 CCGGAAGTCCAATTCACAGTTTG 60.305 47.826 0.00 0.00 35.14 2.93
5538 10262 7.337689 CACAGTTTGATGGAAAGATTATCCTGA 59.662 37.037 0.00 0.00 37.85 3.86
5634 10358 6.294508 GGCAAATAAAGAGTTTACTGGCTTCA 60.295 38.462 8.51 0.00 35.61 3.02
5683 10407 2.302445 AGAGACTCTTCTTGCAGCATGT 59.698 45.455 8.09 0.00 31.85 3.21
5723 10447 5.556915 TGTAGTCTGTACATTTTCAAGGGG 58.443 41.667 0.00 0.00 0.00 4.79
5734 10458 4.400529 TTTTCAAGGGGTTTTTCAGAGC 57.599 40.909 0.00 0.00 0.00 4.09
5854 10578 7.472543 ACGATTAAGCAGGATTTCATTACAAC 58.527 34.615 0.00 0.00 0.00 3.32
5859 10584 7.951530 AAGCAGGATTTCATTACAACAAAAG 57.048 32.000 0.00 0.00 0.00 2.27
5866 10591 8.755018 GGATTTCATTACAACAAAAGACTTGTG 58.245 33.333 3.67 3.67 32.77 3.33
5880 10605 1.348036 ACTTGTGTCTACCCAGGCTTC 59.652 52.381 0.00 0.00 0.00 3.86
6072 10799 2.812011 CAAGGGTGTAGGTGCTTGTTAC 59.188 50.000 0.00 0.00 0.00 2.50
6089 10816 4.838152 CCGTGCCATCGAGGGTGG 62.838 72.222 18.73 13.37 39.80 4.61
6133 10909 2.728007 GGCAAAGCTGAGGTTTAGGAT 58.272 47.619 9.51 0.00 31.81 3.24
6154 10930 5.237127 GGATTTGAGTTTTTCCTTGCCAAAG 59.763 40.000 0.00 0.00 0.00 2.77
6155 10931 4.817318 TTGAGTTTTTCCTTGCCAAAGT 57.183 36.364 0.00 0.00 0.00 2.66
6156 10932 5.923733 TTGAGTTTTTCCTTGCCAAAGTA 57.076 34.783 0.00 0.00 0.00 2.24
6157 10933 5.514274 TGAGTTTTTCCTTGCCAAAGTAG 57.486 39.130 0.00 0.00 0.00 2.57
6158 10934 4.202111 TGAGTTTTTCCTTGCCAAAGTAGC 60.202 41.667 0.00 0.00 0.00 3.58
6168 10944 0.796312 CCAAAGTAGCGTGCGACAAT 59.204 50.000 7.81 0.00 0.00 2.71
6327 11107 2.176369 CGTGTATGCGCAAAAGATTGG 58.824 47.619 17.11 0.00 37.02 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 5.931146 GTGATGAAGAGTGTCACAAATCTCT 59.069 40.000 5.62 0.00 41.35 3.10
9 10 4.143030 CGGTGATGAAGAGTGTCACAAATC 60.143 45.833 5.62 0.67 43.01 2.17
21 22 4.486125 TGGATCAATTCGGTGATGAAGA 57.514 40.909 0.00 0.00 38.38 2.87
23 24 3.316029 GCATGGATCAATTCGGTGATGAA 59.684 43.478 0.00 0.00 38.38 2.57
30 31 0.956633 CCCTGCATGGATCAATTCGG 59.043 55.000 0.97 0.00 38.35 4.30
31 32 0.956633 CCCCTGCATGGATCAATTCG 59.043 55.000 9.96 0.00 38.35 3.34
47 48 1.071299 CCAAGCTTGGTTTTGCCCC 59.929 57.895 33.46 0.00 43.43 5.80
65 66 4.826556 AGTTAGCTTCATGGTTGTCTCTC 58.173 43.478 0.00 0.00 0.00 3.20
82 83 5.862924 ACGATTGTGTTGAATGGAGTTAG 57.137 39.130 0.00 0.00 0.00 2.34
84 85 5.334879 GCTTACGATTGTGTTGAATGGAGTT 60.335 40.000 0.00 0.00 0.00 3.01
91 92 7.866729 TGATAAAAGCTTACGATTGTGTTGAA 58.133 30.769 0.00 0.00 0.00 2.69
99 100 9.113838 AGATTGACATGATAAAAGCTTACGATT 57.886 29.630 0.00 0.00 0.00 3.34
145 146 7.219154 CACACAATTAGAAAACAACGTGCTAAA 59.781 33.333 0.00 0.00 0.00 1.85
177 178 8.276325 CCGACAATACTCTTATTGCTTATGAAC 58.724 37.037 4.62 0.00 46.03 3.18
210 211 2.501723 AGTGTGTTTATCCCTCGCAGAT 59.498 45.455 0.00 0.00 33.89 2.90
216 217 5.552178 AGTTTCAGAGTGTGTTTATCCCTC 58.448 41.667 0.00 0.00 0.00 4.30
222 223 6.971527 TTTTCGAGTTTCAGAGTGTGTTTA 57.028 33.333 0.00 0.00 0.00 2.01
232 233 6.048073 TCTGTTGTCATTTTCGAGTTTCAG 57.952 37.500 0.00 0.00 0.00 3.02
253 254 9.828039 CCTAACCGTTTAAAGGTATTCTTATCT 57.172 33.333 2.54 0.00 41.95 1.98
262 263 5.827267 AGTTTTGCCTAACCGTTTAAAGGTA 59.173 36.000 2.54 0.00 41.95 3.08
268 269 4.643784 TCCAAAGTTTTGCCTAACCGTTTA 59.356 37.500 0.00 0.00 36.86 2.01
275 276 2.672098 TGCCTCCAAAGTTTTGCCTAA 58.328 42.857 0.00 0.00 36.86 2.69
279 280 4.898829 AAAATTGCCTCCAAAGTTTTGC 57.101 36.364 0.00 0.00 36.86 3.68
282 283 8.207545 TGTTGTATAAAATTGCCTCCAAAGTTT 58.792 29.630 0.00 0.00 34.05 2.66
284 285 7.151976 GTGTTGTATAAAATTGCCTCCAAAGT 58.848 34.615 0.00 0.00 34.05 2.66
285 286 7.151308 TGTGTTGTATAAAATTGCCTCCAAAG 58.849 34.615 0.00 0.00 34.05 2.77
297 298 9.225436 TCAGTCTATGCAATGTGTTGTATAAAA 57.775 29.630 0.00 0.00 40.72 1.52
300 301 9.696917 CTATCAGTCTATGCAATGTGTTGTATA 57.303 33.333 0.00 0.00 40.48 1.47
306 307 5.605534 GTCCTATCAGTCTATGCAATGTGT 58.394 41.667 0.00 0.00 0.00 3.72
312 313 4.645136 ACTTTCGTCCTATCAGTCTATGCA 59.355 41.667 0.00 0.00 0.00 3.96
313 314 5.189659 ACTTTCGTCCTATCAGTCTATGC 57.810 43.478 0.00 0.00 0.00 3.14
315 316 7.339721 TCAAGAACTTTCGTCCTATCAGTCTAT 59.660 37.037 0.00 0.00 0.00 1.98
316 317 6.657966 TCAAGAACTTTCGTCCTATCAGTCTA 59.342 38.462 0.00 0.00 0.00 2.59
328 329 3.065371 CCAAGCAACTCAAGAACTTTCGT 59.935 43.478 0.00 0.00 0.00 3.85
331 332 3.365472 ACCCAAGCAACTCAAGAACTTT 58.635 40.909 0.00 0.00 0.00 2.66
363 364 3.511699 TCGGTGATTGTTCTGATTCTCG 58.488 45.455 0.00 0.00 0.00 4.04
365 366 4.021104 TGACTCGGTGATTGTTCTGATTCT 60.021 41.667 0.00 0.00 0.00 2.40
383 384 6.292381 GCTATGTCGAATGGTTTATGTGACTC 60.292 42.308 0.00 0.00 0.00 3.36
391 392 4.448210 GGAAGGCTATGTCGAATGGTTTA 58.552 43.478 0.00 0.00 0.00 2.01
402 403 2.562296 TCTTGGAAGGGAAGGCTATGT 58.438 47.619 0.00 0.00 0.00 2.29
408 410 2.376855 AGGAGTTTCTTGGAAGGGAAGG 59.623 50.000 0.00 0.00 0.00 3.46
465 475 3.234386 GTTTTTCGGCTCTTTTCCATCG 58.766 45.455 0.00 0.00 0.00 3.84
467 477 2.962421 TGGTTTTTCGGCTCTTTTCCAT 59.038 40.909 0.00 0.00 0.00 3.41
469 479 3.660501 ATGGTTTTTCGGCTCTTTTCC 57.339 42.857 0.00 0.00 0.00 3.13
481 491 7.550906 TGAAAGTTTCCGATTCAAATGGTTTTT 59.449 29.630 13.01 0.00 30.60 1.94
493 503 3.288092 GGGCCTATGAAAGTTTCCGATT 58.712 45.455 13.01 0.00 0.00 3.34
495 505 1.064979 GGGGCCTATGAAAGTTTCCGA 60.065 52.381 13.01 0.17 0.00 4.55
501 511 2.492025 TCAGATGGGGCCTATGAAAGT 58.508 47.619 7.30 0.00 0.00 2.66
507 517 2.091111 CCCTTTTTCAGATGGGGCCTAT 60.091 50.000 0.25 0.25 36.15 2.57
559 569 6.905609 CGATGAGATGAATGATGTTCTTTGTG 59.094 38.462 0.00 0.00 0.00 3.33
567 577 6.531923 AGATTTCCGATGAGATGAATGATGT 58.468 36.000 0.00 0.00 0.00 3.06
584 594 5.824624 TGATGCTATTCCTCACAAGATTTCC 59.175 40.000 0.00 0.00 0.00 3.13
612 667 4.368874 TTCTCAATCTCTTGCTCTCTCG 57.631 45.455 0.00 0.00 32.11 4.04
746 842 2.032528 ATGTGTGTGTCCGGCAGG 59.967 61.111 0.00 0.00 39.46 4.85
807 903 1.755380 CTCTTAGGTTCGGGTCGGAAT 59.245 52.381 0.00 0.00 0.00 3.01
908 1004 3.667282 CCTGTGCTGTGCTGTGCC 61.667 66.667 0.00 0.00 0.00 5.01
909 1005 4.338539 GCCTGTGCTGTGCTGTGC 62.339 66.667 0.00 0.00 33.53 4.57
910 1006 4.021631 CGCCTGTGCTGTGCTGTG 62.022 66.667 0.00 0.00 34.43 3.66
938 1034 1.694696 ACTCCTGTCCTGTGTTCCTTC 59.305 52.381 0.00 0.00 0.00 3.46
1165 1261 0.955905 GAGGATAGGAGACGGCTGTC 59.044 60.000 18.39 18.39 45.86 3.51
1170 1266 1.238625 GCGGAGAGGATAGGAGACGG 61.239 65.000 0.00 0.00 0.00 4.79
1171 1267 1.570347 CGCGGAGAGGATAGGAGACG 61.570 65.000 0.00 0.00 0.00 4.18
1173 1269 1.601197 GCGCGGAGAGGATAGGAGA 60.601 63.158 8.83 0.00 0.00 3.71
1386 1496 2.042259 GGCGTTTAAAGACCCCGGG 61.042 63.158 15.80 15.80 0.00 5.73
1387 1497 0.607217 AAGGCGTTTAAAGACCCCGG 60.607 55.000 0.00 0.00 0.00 5.73
1448 1654 0.457443 GCAAAATCTAGCAGCACCCC 59.543 55.000 0.00 0.00 0.00 4.95
1499 1705 4.339247 CCCAGCCATAAATAACTGTCCAAG 59.661 45.833 0.00 0.00 0.00 3.61
1530 1736 4.445452 TGAACGTGGGTAAGCTAGTAAG 57.555 45.455 0.00 0.00 0.00 2.34
1535 1741 3.449377 TCATCATGAACGTGGGTAAGCTA 59.551 43.478 0.00 0.00 0.00 3.32
1618 1824 2.154462 CCCAACATTCTTGTTCTCGCT 58.846 47.619 0.00 0.00 44.24 4.93
1737 1952 2.431906 GCGAAAATCTAGCTTGAACGC 58.568 47.619 18.70 18.70 37.11 4.84
1750 1965 1.462731 TTGGCTGCAGTGGCGAAAAT 61.463 50.000 16.64 0.00 45.35 1.82
1870 2085 8.607441 TTAATAAGCATTTATGTCGAGAGCAT 57.393 30.769 0.00 0.00 30.00 3.79
2116 2343 3.681593 TTGCAAGGAAAATGACCCATG 57.318 42.857 0.00 0.00 0.00 3.66
2131 2358 7.973388 GGCCGAAATTATGCTATATATTTGCAA 59.027 33.333 14.29 0.00 40.24 4.08
2138 2365 5.104527 AGCCAGGCCGAAATTATGCTATATA 60.105 40.000 8.22 0.00 0.00 0.86
2263 2490 1.131126 GCTGAATGTCGTCAATGGGTG 59.869 52.381 0.00 0.00 0.00 4.61
2266 2493 0.734889 GGGCTGAATGTCGTCAATGG 59.265 55.000 0.00 0.00 0.00 3.16
2299 2526 1.542472 TGCATCGTTCAGACTAACCGA 59.458 47.619 0.00 0.00 0.00 4.69
2387 2614 2.827652 CGAGAGGAAGAAAGGGCATAC 58.172 52.381 0.00 0.00 0.00 2.39
2408 2635 8.723311 ACAGCATGATTTTGGAATTTGTTAATG 58.277 29.630 0.00 0.00 39.69 1.90
2539 2767 8.044060 TCTCAGAAATTACTAAAACATGCCAG 57.956 34.615 0.00 0.00 0.00 4.85
2549 2777 9.607988 TGAACAGTGTTTCTCAGAAATTACTAA 57.392 29.630 10.45 4.58 0.00 2.24
2560 2788 5.297547 GGAGTATGTGAACAGTGTTTCTCA 58.702 41.667 10.45 10.04 34.44 3.27
2623 5606 8.751335 GCATATATTTGGTTGGTTAAATTGACG 58.249 33.333 0.00 0.00 0.00 4.35
2652 5635 9.772973 ATCCAATGATATGATTTTGGTGAAATG 57.227 29.630 0.00 0.00 38.06 2.32
2655 5638 9.602568 CAAATCCAATGATATGATTTTGGTGAA 57.397 29.630 0.00 0.00 39.67 3.18
2742 5725 5.204833 CGTGTGTTTCTAGGTGACAATTTG 58.795 41.667 0.00 0.00 0.00 2.32
2789 5772 4.080356 ACTGCCTTCATAAATAGCACTCCA 60.080 41.667 0.00 0.00 0.00 3.86
2795 5778 3.947834 ACCACACTGCCTTCATAAATAGC 59.052 43.478 0.00 0.00 0.00 2.97
2812 5795 2.163412 GACTCAAAAACAGTGCACCACA 59.837 45.455 14.63 0.00 36.74 4.17
2813 5796 2.791158 CGACTCAAAAACAGTGCACCAC 60.791 50.000 14.63 0.00 34.10 4.16
2814 5797 1.400142 CGACTCAAAAACAGTGCACCA 59.600 47.619 14.63 0.00 0.00 4.17
2815 5798 1.668751 TCGACTCAAAAACAGTGCACC 59.331 47.619 14.63 0.00 0.00 5.01
2817 5800 2.222931 CGTTCGACTCAAAAACAGTGCA 60.223 45.455 0.00 0.00 0.00 4.57
2818 5801 2.029970 TCGTTCGACTCAAAAACAGTGC 59.970 45.455 0.00 0.00 0.00 4.40
2819 5802 3.306166 AGTCGTTCGACTCAAAAACAGTG 59.694 43.478 19.92 0.00 41.08 3.66
2820 5803 3.518590 AGTCGTTCGACTCAAAAACAGT 58.481 40.909 19.92 0.00 41.08 3.55
2821 5804 4.738740 ACTAGTCGTTCGACTCAAAAACAG 59.261 41.667 27.01 19.54 43.52 3.16
2822 5805 4.675510 ACTAGTCGTTCGACTCAAAAACA 58.324 39.130 27.01 10.46 43.52 2.83
2853 5837 1.089920 GCCAGTTGCAACTCGATGAT 58.910 50.000 28.97 4.11 40.77 2.45
2923 5920 3.424529 CGACTCAAAAACCACGACTAGTC 59.575 47.826 13.18 13.18 0.00 2.59
2924 5921 3.067180 TCGACTCAAAAACCACGACTAGT 59.933 43.478 0.00 0.00 0.00 2.57
2925 5922 3.635331 TCGACTCAAAAACCACGACTAG 58.365 45.455 0.00 0.00 0.00 2.57
2926 5923 3.713858 TCGACTCAAAAACCACGACTA 57.286 42.857 0.00 0.00 0.00 2.59
2927 5924 2.589798 TCGACTCAAAAACCACGACT 57.410 45.000 0.00 0.00 0.00 4.18
2928 5925 2.595881 CGTTCGACTCAAAAACCACGAC 60.596 50.000 0.00 0.00 0.00 4.34
2929 5926 1.589320 CGTTCGACTCAAAAACCACGA 59.411 47.619 0.00 0.00 0.00 4.35
2930 5927 1.589320 TCGTTCGACTCAAAAACCACG 59.411 47.619 0.00 0.00 0.00 4.94
2952 5949 2.201927 GCAGGTGGGGCCAATTTAG 58.798 57.895 4.39 0.00 40.61 1.85
2953 5950 4.451544 GCAGGTGGGGCCAATTTA 57.548 55.556 4.39 0.00 40.61 1.40
2975 5973 6.982724 GGATTGGGCAATCAAATAGAAAGAAG 59.017 38.462 0.00 0.00 46.77 2.85
2978 5976 5.453762 GGGGATTGGGCAATCAAATAGAAAG 60.454 44.000 0.00 0.00 46.77 2.62
3057 6060 1.761174 GGCAGTGACCAAGGGAGAA 59.239 57.895 0.00 0.00 0.00 2.87
3142 7568 0.835543 AGGAGCAGACCAGAAGCAGT 60.836 55.000 0.00 0.00 0.00 4.40
3148 7574 2.363018 CGGGAGGAGCAGACCAGA 60.363 66.667 0.00 0.00 0.00 3.86
3165 7659 4.857588 CGACTAGTTGACATGAGTTACCAC 59.142 45.833 3.81 0.00 0.00 4.16
3180 7674 3.715854 GACGCATGGTCGACTAGTT 57.284 52.632 16.46 0.00 35.61 2.24
3214 7710 0.456628 GGGGTAGCGACTCTTGACTC 59.543 60.000 0.00 0.00 0.00 3.36
3399 7896 1.949547 GCCTGCAATCTCTGAACTGCT 60.950 52.381 0.00 0.00 35.78 4.24
3511 8213 7.765360 ACCTACGACGGAAATGAAAAATATACA 59.235 33.333 0.00 0.00 0.00 2.29
3529 8231 1.310904 TGGCAAACCAAACCTACGAC 58.689 50.000 0.00 0.00 45.37 4.34
3541 8243 0.387565 AACGGTGGTGATTGGCAAAC 59.612 50.000 3.01 1.26 0.00 2.93
3558 8260 3.498777 GGAGACTACTGGCTCACAAAAAC 59.501 47.826 1.15 0.00 32.83 2.43
3570 8272 4.150897 AGTGCTCTAGAGGAGACTACTG 57.849 50.000 21.23 0.00 44.45 2.74
3591 8293 6.714356 TGAGGAACAATTCACATGATACACAA 59.286 34.615 0.00 0.00 0.00 3.33
3707 8409 7.993101 ACTCAGATCCAACATTTATCACATTG 58.007 34.615 0.00 0.00 0.00 2.82
3775 8477 9.942850 AATTATTTTTATTAGGGGTATGCATGC 57.057 29.630 11.82 11.82 0.00 4.06
3808 8510 7.011389 GGGAAATTTGCCAGATATAAAAGCAAC 59.989 37.037 22.62 0.00 42.69 4.17
4121 8827 5.418524 TGTCTGCCATAATTGTGCTGTATTT 59.581 36.000 0.00 0.00 0.00 1.40
4122 8828 4.949238 TGTCTGCCATAATTGTGCTGTATT 59.051 37.500 0.00 0.00 0.00 1.89
4147 8853 5.609483 GCAAATTTCCTTTTTAGTGTTCGCG 60.609 40.000 0.00 0.00 0.00 5.87
4234 8954 1.134965 AGGAGAGTGAAAATCGGCGAG 60.135 52.381 17.22 0.00 35.11 5.03
4344 9064 2.290197 GGCATCAAATTTTCCCAAGGCA 60.290 45.455 0.00 0.00 0.00 4.75
4610 9330 1.478654 GGAGCCCAAGACAAAAGGACA 60.479 52.381 0.00 0.00 0.00 4.02
4618 9338 4.037222 TCTACAATATGGAGCCCAAGACA 58.963 43.478 0.00 0.00 36.95 3.41
4785 9505 0.955919 GGGTAGTGCAGCACAAGACC 60.956 60.000 27.35 26.30 36.74 3.85
4788 9508 1.676014 GGTAGGGTAGTGCAGCACAAG 60.676 57.143 27.35 0.00 36.74 3.16
4827 9547 4.377431 CGAATCTGTAGTTTTCACCTGTGC 60.377 45.833 0.00 0.00 0.00 4.57
4972 9696 4.201871 CCTTTATCGCTTGAATTTACGGCA 60.202 41.667 0.00 0.00 0.00 5.69
5021 9745 1.404035 GTCACCAACCGACAAAGCTTT 59.596 47.619 5.69 5.69 33.43 3.51
5092 9816 1.828461 TAACGGGGCATTCGGTCACA 61.828 55.000 0.00 0.00 0.00 3.58
5097 9821 0.393267 TTCCTTAACGGGGCATTCGG 60.393 55.000 0.00 0.00 0.00 4.30
5098 9822 0.730840 GTTCCTTAACGGGGCATTCG 59.269 55.000 0.00 0.00 0.00 3.34
5108 9832 9.764870 GACTATAATGTTTTTCCGTTCCTTAAC 57.235 33.333 0.00 0.00 0.00 2.01
5170 9894 3.119459 GCTCACAGTTCTCGTAGAATCCA 60.119 47.826 1.55 0.00 36.50 3.41
5173 9897 4.013728 AGAGCTCACAGTTCTCGTAGAAT 58.986 43.478 17.77 0.00 36.50 2.40
5185 9909 2.630158 CCTCCATTGAAGAGCTCACAG 58.370 52.381 17.77 5.05 32.21 3.66
5237 9961 4.511617 TCTCGATATCAATGGTCTCTGC 57.488 45.455 3.12 0.00 0.00 4.26
5309 10033 5.745227 ACATCACCCAAACTCAATACCTAG 58.255 41.667 0.00 0.00 0.00 3.02
5323 10047 1.303561 GGAGCTGCAACATCACCCA 60.304 57.895 0.00 0.00 0.00 4.51
5404 10128 3.612795 AAAACTCCCACCTAAGGCTTT 57.387 42.857 4.45 0.00 0.00 3.51
5433 10157 6.935240 TTTCCGTCATATATCCTCCATCTT 57.065 37.500 0.00 0.00 0.00 2.40
5465 10189 4.999950 CCTTGATGAGGCTGAATACATACC 59.000 45.833 0.00 0.00 39.09 2.73
5501 10225 5.241506 TCCATCAAACTGTGAATTGGACTTC 59.758 40.000 0.00 0.00 39.50 3.01
5509 10233 8.689972 GGATAATCTTTCCATCAAACTGTGAAT 58.310 33.333 0.00 0.00 40.50 2.57
5520 10244 9.571816 AATCTTCTTCAGGATAATCTTTCCATC 57.428 33.333 0.00 0.00 35.59 3.51
5538 10262 5.182001 GTGTGCACCAATGTCTAATCTTCTT 59.818 40.000 15.69 0.00 0.00 2.52
5634 10358 3.377172 GGTTTCAATACATACAGCCGCTT 59.623 43.478 0.00 0.00 0.00 4.68
5683 10407 8.327271 ACAGACTACAATGTACTAGGACTAAGA 58.673 37.037 6.66 0.00 0.00 2.10
5723 10447 1.172812 ACGGGCTGGCTCTGAAAAAC 61.173 55.000 0.00 0.00 0.00 2.43
5734 10458 1.463674 AGCAATAGAAAACGGGCTGG 58.536 50.000 0.00 0.00 0.00 4.85
5782 10506 8.225603 ACAAACAAGTATCATCTTCACTGTTT 57.774 30.769 0.00 0.00 30.64 2.83
5859 10584 0.977395 AGCCTGGGTAGACACAAGTC 59.023 55.000 0.00 0.00 45.31 3.01
5866 10591 2.567615 TCTTTGAGAAGCCTGGGTAGAC 59.432 50.000 0.00 0.00 32.75 2.59
5880 10605 2.877168 AGCTGCTCACAAGTTCTTTGAG 59.123 45.455 0.00 14.33 39.21 3.02
6005 10731 3.457903 AACGCGGAAACACGGCAAC 62.458 57.895 12.47 0.00 43.51 4.17
6072 10799 4.838152 CCACCCTCGATGGCACGG 62.838 72.222 6.65 1.53 0.00 4.94
6089 10816 2.887568 CCGCATCCACAGCTCGAC 60.888 66.667 0.00 0.00 0.00 4.20
6133 10909 5.159273 ACTTTGGCAAGGAAAAACTCAAA 57.841 34.783 16.87 0.00 33.82 2.69
6154 10930 0.999406 ACATCATTGTCGCACGCTAC 59.001 50.000 0.00 0.00 0.00 3.58
6155 10931 0.998669 CACATCATTGTCGCACGCTA 59.001 50.000 0.00 0.00 32.34 4.26
6156 10932 0.950555 ACACATCATTGTCGCACGCT 60.951 50.000 0.00 0.00 32.34 5.07
6157 10933 0.790495 CACACATCATTGTCGCACGC 60.790 55.000 0.00 0.00 32.34 5.34
6158 10934 0.790495 GCACACATCATTGTCGCACG 60.790 55.000 0.00 0.00 33.45 5.34
6216 10992 1.153588 GGATGCCATTTGTTGCCGG 60.154 57.895 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.