Multiple sequence alignment - TraesCS1D01G372700

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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 TraesCS1D01G372700 chr1D 100.000 3392 0 0 1 3392 451036705 451033314 0.000000e+00 6264.0
1 TraesCS1D01G372700 chr1D 85.829 2357 185 69 621 2901 450758024 450755741 0.000000e+00 2364.0
2 TraesCS1D01G372700 chr1D 83.323 1661 201 44 748 2348 450578930 450580574 0.000000e+00 1463.0
3 TraesCS1D01G372700 chr1D 86.182 1252 146 16 1006 2233 450739243 450740491 0.000000e+00 1328.0
4 TraesCS1D01G372700 chr1D 92.490 253 12 3 2978 3229 450610838 450610592 4.160000e-94 355.0
5 TraesCS1D01G372700 chr1D 88.789 223 20 5 2997 3217 450754509 450754290 5.580000e-68 268.0
6 TraesCS1D01G372700 chr1D 85.253 217 20 4 1 216 450758599 450758394 2.650000e-51 213.0
7 TraesCS1D01G372700 chr1D 91.379 58 4 1 2925 2981 450611166 450611109 1.010000e-10 78.7
8 TraesCS1D01G372700 chr1A 85.862 1938 184 45 476 2351 545764482 545762573 0.000000e+00 1978.0
9 TraesCS1D01G372700 chr1A 83.295 1317 152 32 748 2005 545778581 545777274 0.000000e+00 1151.0
10 TraesCS1D01G372700 chr1A 84.202 652 54 25 2403 3022 545762496 545761862 3.770000e-164 588.0
11 TraesCS1D01G372700 chr1A 84.324 185 9 7 3227 3392 554359331 554359148 2.710000e-36 163.0
12 TraesCS1D01G372700 chr1A 83.784 185 10 7 3227 3392 554341805 554341622 1.260000e-34 158.0
13 TraesCS1D01G372700 chr1B 87.929 1690 149 23 598 2247 618699338 618697664 0.000000e+00 1940.0
14 TraesCS1D01G372700 chr1B 85.485 1247 145 22 1006 2231 618543005 618544236 0.000000e+00 1267.0
15 TraesCS1D01G372700 chr1B 82.883 1443 175 41 611 2008 618908457 618907042 0.000000e+00 1230.0
16 TraesCS1D01G372700 chr1B 87.819 1059 114 11 1006 2058 618196983 618198032 0.000000e+00 1227.0
17 TraesCS1D01G372700 chr1B 86.872 1074 113 14 1006 2062 619095560 619094498 0.000000e+00 1177.0
18 TraesCS1D01G372700 chr1B 85.185 810 64 34 2449 3219 618697419 618696627 0.000000e+00 780.0
19 TraesCS1D01G372700 chr1B 81.542 428 39 17 1 413 618699779 618699377 1.960000e-82 316.0
20 TraesCS1D01G372700 chr2D 79.570 186 14 13 3229 3392 607662704 607662887 9.950000e-21 111.0
21 TraesCS1D01G372700 chr7D 78.610 187 18 9 3227 3392 11916663 11916478 1.660000e-18 104.0
22 TraesCS1D01G372700 chr7A 79.630 162 11 10 3227 3368 4707650 4707491 2.790000e-16 97.1
23 TraesCS1D01G372700 chr6B 98.113 53 1 0 3226 3278 114074554 114074606 3.600000e-15 93.5
24 TraesCS1D01G372700 chr7B 77.297 185 17 14 3227 3389 6125737 6125918 6.030000e-13 86.1
25 TraesCS1D01G372700 chr7B 94.231 52 3 0 3227 3278 65143250 65143301 2.810000e-11 80.5
26 TraesCS1D01G372700 chr2B 94.231 52 3 0 3227 3278 17069648 17069597 2.810000e-11 80.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G372700 chr1D 451033314 451036705 3391 True 6264.000000 6264 100.000000 1 3392 1 chr1D.!!$R1 3391
1 TraesCS1D01G372700 chr1D 450578930 450580574 1644 False 1463.000000 1463 83.323000 748 2348 1 chr1D.!!$F1 1600
2 TraesCS1D01G372700 chr1D 450739243 450740491 1248 False 1328.000000 1328 86.182000 1006 2233 1 chr1D.!!$F2 1227
3 TraesCS1D01G372700 chr1D 450754290 450758599 4309 True 948.333333 2364 86.623667 1 3217 3 chr1D.!!$R3 3216
4 TraesCS1D01G372700 chr1D 450610592 450611166 574 True 216.850000 355 91.934500 2925 3229 2 chr1D.!!$R2 304
5 TraesCS1D01G372700 chr1A 545761862 545764482 2620 True 1283.000000 1978 85.032000 476 3022 2 chr1A.!!$R4 2546
6 TraesCS1D01G372700 chr1A 545777274 545778581 1307 True 1151.000000 1151 83.295000 748 2005 1 chr1A.!!$R1 1257
7 TraesCS1D01G372700 chr1B 618543005 618544236 1231 False 1267.000000 1267 85.485000 1006 2231 1 chr1B.!!$F2 1225
8 TraesCS1D01G372700 chr1B 618907042 618908457 1415 True 1230.000000 1230 82.883000 611 2008 1 chr1B.!!$R1 1397
9 TraesCS1D01G372700 chr1B 618196983 618198032 1049 False 1227.000000 1227 87.819000 1006 2058 1 chr1B.!!$F1 1052
10 TraesCS1D01G372700 chr1B 619094498 619095560 1062 True 1177.000000 1177 86.872000 1006 2062 1 chr1B.!!$R2 1056
11 TraesCS1D01G372700 chr1B 618696627 618699779 3152 True 1012.000000 1940 84.885333 1 3219 3 chr1B.!!$R3 3218

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
45 46 0.107361 ATTTTTCCCTCCGGTAGGCG 60.107 55.0 12.92 7.81 45.03 5.52 F
571 625 0.236711 CGGCTGAGCTCAAAACACTG 59.763 55.0 18.85 5.15 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1833 2024 1.069765 CTCCCATAATGCCGCGTCT 59.930 57.895 4.92 0.0 0.00 4.18 R
2397 2754 0.598562 CGATCCATCGGATTCGGAGT 59.401 55.000 0.73 0.0 43.27 3.85 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
43 44 2.651455 GGAATTTTTCCCTCCGGTAGG 58.349 52.381 0.00 7.18 44.30 3.18
44 45 2.022195 GAATTTTTCCCTCCGGTAGGC 58.978 52.381 12.92 0.00 45.03 3.93
45 46 0.107361 ATTTTTCCCTCCGGTAGGCG 60.107 55.000 12.92 7.81 45.03 5.52
47 48 3.605412 TTTCCCTCCGGTAGGCGGA 62.605 63.158 12.92 0.00 45.26 5.54
65 66 4.003788 CGAGGAGCCACCCACGTT 62.004 66.667 0.00 0.00 40.05 3.99
66 67 2.047179 GAGGAGCCACCCACGTTC 60.047 66.667 0.00 0.00 40.05 3.95
67 68 2.847234 AGGAGCCACCCACGTTCA 60.847 61.111 0.00 0.00 40.05 3.18
68 69 2.112297 GGAGCCACCCACGTTCAA 59.888 61.111 0.00 0.00 0.00 2.69
69 70 1.966451 GGAGCCACCCACGTTCAAG 60.966 63.158 0.00 0.00 0.00 3.02
70 71 1.966451 GAGCCACCCACGTTCAAGG 60.966 63.158 0.00 0.00 0.00 3.61
71 72 3.670377 GCCACCCACGTTCAAGGC 61.670 66.667 3.45 3.45 34.71 4.35
72 73 2.983592 CCACCCACGTTCAAGGCC 60.984 66.667 0.00 0.00 0.00 5.19
73 74 3.353836 CACCCACGTTCAAGGCCG 61.354 66.667 0.00 0.00 0.00 6.13
74 75 3.868985 ACCCACGTTCAAGGCCGT 61.869 61.111 0.00 0.00 37.90 5.68
93 94 1.865340 GTCCACGACGAGCTTTCTTTT 59.135 47.619 0.00 0.00 0.00 2.27
98 99 1.509703 GACGAGCTTTCTTTTCCGGT 58.490 50.000 0.00 0.00 0.00 5.28
149 151 1.180029 CAGCTGTGAAATTGGAGGGG 58.820 55.000 5.25 0.00 0.00 4.79
172 175 1.002868 GCCTGTGACCAGCTGTGAT 60.003 57.895 13.81 0.00 37.38 3.06
199 202 3.075148 GCTTCGGGCTAAAGAGAAACTT 58.925 45.455 4.02 0.00 38.00 2.66
223 226 3.735181 GGGACGTCGCTTACATTCT 57.265 52.632 23.96 0.00 0.00 2.40
243 254 3.125146 TCTTTCAGAAATGATCCGCGTTG 59.875 43.478 4.92 0.00 0.00 4.10
266 277 4.189639 GGAGTATTTCCGTCAGTCTTGT 57.810 45.455 0.00 0.00 35.91 3.16
268 279 4.626172 GGAGTATTTCCGTCAGTCTTGTTC 59.374 45.833 0.00 0.00 35.91 3.18
269 280 5.470047 AGTATTTCCGTCAGTCTTGTTCT 57.530 39.130 0.00 0.00 0.00 3.01
270 281 6.349944 GGAGTATTTCCGTCAGTCTTGTTCTA 60.350 42.308 0.00 0.00 35.91 2.10
271 282 6.622549 AGTATTTCCGTCAGTCTTGTTCTAG 58.377 40.000 0.00 0.00 0.00 2.43
272 283 5.723672 ATTTCCGTCAGTCTTGTTCTAGA 57.276 39.130 0.00 0.00 0.00 2.43
273 284 5.723672 TTTCCGTCAGTCTTGTTCTAGAT 57.276 39.130 0.00 0.00 0.00 1.98
274 285 6.829229 TTTCCGTCAGTCTTGTTCTAGATA 57.171 37.500 0.00 0.00 0.00 1.98
275 286 7.406031 TTTCCGTCAGTCTTGTTCTAGATAT 57.594 36.000 0.00 0.00 0.00 1.63
277 288 5.299531 TCCGTCAGTCTTGTTCTAGATATGG 59.700 44.000 0.00 0.00 0.00 2.74
278 289 5.299531 CCGTCAGTCTTGTTCTAGATATGGA 59.700 44.000 0.00 0.00 0.00 3.41
279 290 6.015856 CCGTCAGTCTTGTTCTAGATATGGAT 60.016 42.308 0.00 0.00 0.00 3.41
280 291 6.860539 CGTCAGTCTTGTTCTAGATATGGATG 59.139 42.308 0.00 0.00 0.00 3.51
281 292 6.644592 GTCAGTCTTGTTCTAGATATGGATGC 59.355 42.308 0.00 0.00 0.00 3.91
282 293 6.552725 TCAGTCTTGTTCTAGATATGGATGCT 59.447 38.462 0.00 0.00 0.00 3.79
328 342 3.208383 TGGCGCCGCACCATAATG 61.208 61.111 23.90 0.00 30.29 1.90
331 345 2.024588 CGCCGCACCATAATGCAC 59.975 61.111 0.00 0.00 46.47 4.57
332 346 2.759123 CGCCGCACCATAATGCACA 61.759 57.895 0.00 0.00 46.47 4.57
333 347 1.064621 GCCGCACCATAATGCACAG 59.935 57.895 0.00 0.00 46.47 3.66
349 363 3.371102 CACAGTACAGTACAGTGCAGT 57.629 47.619 19.83 4.19 38.92 4.40
350 364 3.052745 CACAGTACAGTACAGTGCAGTG 58.947 50.000 19.83 20.11 38.92 3.66
351 365 2.061773 CAGTACAGTACAGTGCAGTGC 58.938 52.381 21.57 8.58 0.00 4.40
352 366 1.686587 AGTACAGTACAGTGCAGTGCA 59.313 47.619 21.57 15.37 35.60 4.57
404 421 1.826487 AGTGGCAAACGACCAACCC 60.826 57.895 0.00 0.00 39.39 4.11
424 442 1.152830 GGAGACCCAACTGGCCAAA 59.847 57.895 7.01 0.00 37.83 3.28
426 444 1.005450 GGAGACCCAACTGGCCAAATA 59.995 52.381 7.01 0.00 37.83 1.40
428 446 1.182667 GACCCAACTGGCCAAATACC 58.817 55.000 7.01 0.00 37.83 2.73
429 447 0.485099 ACCCAACTGGCCAAATACCA 59.515 50.000 7.01 0.00 37.83 3.25
430 448 1.133009 ACCCAACTGGCCAAATACCAA 60.133 47.619 7.01 0.00 36.56 3.67
434 471 1.627864 ACTGGCCAAATACCAACACC 58.372 50.000 7.01 0.00 36.56 4.16
439 476 1.818674 GCCAAATACCAACACCTCCAG 59.181 52.381 0.00 0.00 0.00 3.86
447 484 2.231380 AACACCTCCAGCCCCGATT 61.231 57.895 0.00 0.00 0.00 3.34
448 485 2.190578 CACCTCCAGCCCCGATTC 59.809 66.667 0.00 0.00 0.00 2.52
459 496 1.798283 CCCCGATTCGTTTACACACA 58.202 50.000 5.20 0.00 0.00 3.72
461 498 2.136728 CCCGATTCGTTTACACACACA 58.863 47.619 5.20 0.00 0.00 3.72
462 499 2.096614 CCCGATTCGTTTACACACACAC 60.097 50.000 5.20 0.00 0.00 3.82
465 502 3.000423 CGATTCGTTTACACACACACACA 60.000 43.478 0.00 0.00 0.00 3.72
468 505 2.412429 TCGTTTACACACACACACACAC 59.588 45.455 0.00 0.00 0.00 3.82
469 506 2.157863 CGTTTACACACACACACACACA 59.842 45.455 0.00 0.00 0.00 3.72
470 507 3.484683 GTTTACACACACACACACACAC 58.515 45.455 0.00 0.00 0.00 3.82
471 508 1.351153 TACACACACACACACACACG 58.649 50.000 0.00 0.00 0.00 4.49
472 509 1.225991 CACACACACACACACACGC 60.226 57.895 0.00 0.00 0.00 5.34
473 510 2.021243 CACACACACACACACGCG 59.979 61.111 3.53 3.53 0.00 6.01
474 511 3.192230 ACACACACACACACGCGG 61.192 61.111 12.47 1.27 0.00 6.46
484 531 3.533105 ACACGCGGACACACCTCA 61.533 61.111 12.47 0.00 36.31 3.86
491 538 1.153549 GGACACACCTCATCTCGCC 60.154 63.158 0.00 0.00 35.41 5.54
520 567 5.062308 GCGACCAAGACTTTGACAACTATAG 59.938 44.000 0.00 0.00 36.36 1.31
522 569 6.115448 ACCAAGACTTTGACAACTATAGCT 57.885 37.500 0.00 0.00 36.36 3.32
523 570 5.934625 ACCAAGACTTTGACAACTATAGCTG 59.065 40.000 0.00 0.00 36.36 4.24
534 588 6.884295 TGACAACTATAGCTGGTAGCAAATTT 59.116 34.615 7.99 0.00 45.56 1.82
571 625 0.236711 CGGCTGAGCTCAAAACACTG 59.763 55.000 18.85 5.15 0.00 3.66
588 642 3.071602 ACACTGGCGCCATTAGATAGAAT 59.928 43.478 32.87 7.04 0.00 2.40
589 643 3.681897 CACTGGCGCCATTAGATAGAATC 59.318 47.826 32.87 0.00 0.00 2.52
590 644 3.265791 CTGGCGCCATTAGATAGAATCC 58.734 50.000 32.87 0.00 0.00 3.01
591 645 2.271800 GGCGCCATTAGATAGAATCCG 58.728 52.381 24.80 0.00 0.00 4.18
592 646 2.094182 GGCGCCATTAGATAGAATCCGA 60.094 50.000 24.80 0.00 0.00 4.55
594 648 3.119459 GCGCCATTAGATAGAATCCGAGA 60.119 47.826 0.00 0.00 0.00 4.04
639 695 5.046910 AGATTTGACACGGTTTAATGCTG 57.953 39.130 0.00 0.00 0.00 4.41
644 700 1.883926 ACACGGTTTAATGCTGTTCCC 59.116 47.619 0.00 0.00 0.00 3.97
714 772 1.746615 CTTGGTCAGGTCATGCCCG 60.747 63.158 2.95 0.00 38.26 6.13
715 773 3.266686 TTGGTCAGGTCATGCCCGG 62.267 63.158 0.00 0.00 38.26 5.73
716 774 3.399181 GGTCAGGTCATGCCCGGA 61.399 66.667 0.73 0.00 38.26 5.14
717 775 2.125106 GTCAGGTCATGCCCGGAC 60.125 66.667 10.27 10.27 41.40 4.79
840 926 2.835431 CCCCCACACGCCAAACAA 60.835 61.111 0.00 0.00 0.00 2.83
899 1028 6.042638 ACAAGGCCTATATATACACAGCAG 57.957 41.667 5.16 0.00 0.00 4.24
935 1074 3.896888 AGAACCCATCAACAATTCAGCAA 59.103 39.130 0.00 0.00 0.00 3.91
938 1077 2.232941 CCCATCAACAATTCAGCAAGCT 59.767 45.455 0.00 0.00 0.00 3.74
940 1079 2.975410 TCAACAATTCAGCAAGCTCG 57.025 45.000 0.00 0.00 0.00 5.03
942 1081 2.481568 TCAACAATTCAGCAAGCTCGAG 59.518 45.455 8.45 8.45 0.00 4.04
955 1107 2.088423 AGCTCGAGAACAGAGTACCAG 58.912 52.381 18.75 0.00 37.99 4.00
966 1118 1.000955 AGAGTACCAGCAGAAACCACG 59.999 52.381 0.00 0.00 0.00 4.94
990 1147 1.729131 CCCAATTCGCAACGCACAC 60.729 57.895 0.00 0.00 0.00 3.82
1692 1868 2.034221 GCCGAGGCCAAGGACTTT 59.966 61.111 19.30 0.00 30.74 2.66
1716 1892 2.036256 GGGTGCTTGGTCAGGCAT 59.964 61.111 10.79 0.00 45.17 4.40
1833 2024 3.378602 TCGCCCAAGAGCACGCTA 61.379 61.111 0.00 0.00 0.00 4.26
1915 2118 0.182061 GAGGATCAGAGCATTGGCCA 59.818 55.000 0.00 0.00 36.12 5.36
2031 2234 0.824109 CCAAGGAGACGACTGGCATA 59.176 55.000 0.00 0.00 0.00 3.14
2062 2268 3.399330 GACGGGATCACAAGTGAAGAAA 58.601 45.455 7.02 0.00 43.58 2.52
2112 2321 2.063266 GACATTGCCGTTGACGTAGAA 58.937 47.619 2.63 0.00 37.74 2.10
2132 2344 1.302033 ACAGCAGCTTCCTCAACGG 60.302 57.895 0.00 0.00 0.00 4.44
2144 2356 2.322355 CTCAACGGAGGAGATGCATT 57.678 50.000 0.00 0.00 37.51 3.56
2148 2360 2.749076 CAACGGAGGAGATGCATTTGAA 59.251 45.455 0.00 0.00 0.00 2.69
2151 2363 2.611292 CGGAGGAGATGCATTTGAAGAC 59.389 50.000 0.00 0.00 0.00 3.01
2192 2422 5.441718 AGGCATTATCAGTCTTTGGAGAA 57.558 39.130 0.00 0.00 32.66 2.87
2210 2440 5.553290 GAGAATTTAGCTTCTCACCAACC 57.447 43.478 8.05 0.00 46.81 3.77
2211 2441 4.003648 AGAATTTAGCTTCTCACCAACCG 58.996 43.478 0.00 0.00 29.38 4.44
2212 2442 3.695830 ATTTAGCTTCTCACCAACCGA 57.304 42.857 0.00 0.00 0.00 4.69
2280 2612 7.895870 ACATAATCGATTTCGTTCTTACACAG 58.104 34.615 17.19 0.00 40.80 3.66
2281 2613 4.842139 ATCGATTTCGTTCTTACACAGC 57.158 40.909 0.00 0.00 40.80 4.40
2309 2645 2.884685 CTTCGCGCTGCTCCTCTG 60.885 66.667 5.56 0.00 0.00 3.35
2362 2698 1.411394 GCGACGTGCAGTAACTAACA 58.589 50.000 0.00 0.00 45.45 2.41
2363 2699 1.385743 GCGACGTGCAGTAACTAACAG 59.614 52.381 0.00 0.00 45.45 3.16
2365 2701 2.673833 GACGTGCAGTAACTAACAGCT 58.326 47.619 0.00 0.00 41.01 4.24
2367 2703 2.035449 ACGTGCAGTAACTAACAGCTCA 59.965 45.455 0.00 0.00 41.01 4.26
2368 2704 3.254060 CGTGCAGTAACTAACAGCTCAT 58.746 45.455 0.00 0.00 41.01 2.90
2369 2705 4.082408 ACGTGCAGTAACTAACAGCTCATA 60.082 41.667 0.00 0.00 41.01 2.15
2370 2706 4.265556 CGTGCAGTAACTAACAGCTCATAC 59.734 45.833 0.00 0.00 41.01 2.39
2371 2707 5.411781 GTGCAGTAACTAACAGCTCATACT 58.588 41.667 0.00 0.00 41.01 2.12
2372 2708 5.869888 GTGCAGTAACTAACAGCTCATACTT 59.130 40.000 0.00 0.00 41.01 2.24
2373 2709 6.035112 GTGCAGTAACTAACAGCTCATACTTC 59.965 42.308 0.00 0.00 41.01 3.01
2376 2731 7.412020 GCAGTAACTAACAGCTCATACTTCAAC 60.412 40.741 0.00 0.00 37.61 3.18
2379 2734 5.403246 ACTAACAGCTCATACTTCAACTCG 58.597 41.667 0.00 0.00 0.00 4.18
2443 2820 1.065998 TCGGGGGAAAATTAGGTCACG 60.066 52.381 0.00 0.00 0.00 4.35
2447 2824 2.099098 GGGGAAAATTAGGTCACGCATG 59.901 50.000 0.00 0.00 0.00 4.06
2656 3038 1.731093 CCGCACGGTCAAAAACCTT 59.269 52.632 0.00 0.00 46.87 3.50
2659 3041 2.263945 CGCACGGTCAAAAACCTTTTT 58.736 42.857 0.00 0.00 46.87 1.94
2660 3042 3.436496 CGCACGGTCAAAAACCTTTTTA 58.564 40.909 0.00 0.00 46.87 1.52
2661 3044 3.858238 CGCACGGTCAAAAACCTTTTTAA 59.142 39.130 0.00 0.00 46.87 1.52
2662 3045 4.027214 CGCACGGTCAAAAACCTTTTTAAG 60.027 41.667 0.00 0.00 46.87 1.85
2663 3046 4.260051 GCACGGTCAAAAACCTTTTTAAGC 60.260 41.667 0.00 0.00 46.87 3.09
2677 3060 1.927487 TTAAGCTACGTGGGTCCAGA 58.073 50.000 3.45 0.00 0.00 3.86
2678 3061 2.154567 TAAGCTACGTGGGTCCAGAT 57.845 50.000 3.45 0.00 0.00 2.90
2747 3134 2.512515 AGAGATTGCTTCGCCGGC 60.513 61.111 19.07 19.07 0.00 6.13
2880 3312 2.559840 CGCAGTCGACACGTACCT 59.440 61.111 19.50 0.00 38.10 3.08
2905 3343 2.203112 ATGCTCCGCGATGCATGT 60.203 55.556 28.33 13.54 43.53 3.21
2906 3344 1.820906 ATGCTCCGCGATGCATGTT 60.821 52.632 28.33 12.95 43.53 2.71
2907 3345 1.378882 ATGCTCCGCGATGCATGTTT 61.379 50.000 28.33 12.66 43.53 2.83
2908 3346 1.137404 GCTCCGCGATGCATGTTTT 59.863 52.632 8.23 0.00 0.00 2.43
2909 3347 0.863119 GCTCCGCGATGCATGTTTTC 60.863 55.000 8.23 0.00 0.00 2.29
2910 3348 0.729116 CTCCGCGATGCATGTTTTCT 59.271 50.000 8.23 0.00 0.00 2.52
2911 3349 1.933181 CTCCGCGATGCATGTTTTCTA 59.067 47.619 8.23 0.00 0.00 2.10
2912 3350 1.933181 TCCGCGATGCATGTTTTCTAG 59.067 47.619 8.23 0.00 0.00 2.43
2913 3351 1.933181 CCGCGATGCATGTTTTCTAGA 59.067 47.619 8.23 0.00 0.00 2.43
2914 3352 2.285834 CCGCGATGCATGTTTTCTAGAC 60.286 50.000 8.23 0.00 0.00 2.59
2915 3353 2.595188 CGCGATGCATGTTTTCTAGACG 60.595 50.000 2.46 0.00 0.00 4.18
2916 3354 2.603110 GCGATGCATGTTTTCTAGACGA 59.397 45.455 2.46 0.00 0.00 4.20
2917 3355 3.302092 GCGATGCATGTTTTCTAGACGAG 60.302 47.826 2.46 0.00 0.00 4.18
2918 3356 3.859961 CGATGCATGTTTTCTAGACGAGT 59.140 43.478 2.46 0.00 0.00 4.18
2919 3357 4.259570 CGATGCATGTTTTCTAGACGAGTG 60.260 45.833 2.46 0.00 0.00 3.51
2920 3358 4.251543 TGCATGTTTTCTAGACGAGTGA 57.748 40.909 0.00 0.00 0.00 3.41
2921 3359 3.987868 TGCATGTTTTCTAGACGAGTGAC 59.012 43.478 0.00 0.00 0.00 3.67
2922 3360 4.238514 GCATGTTTTCTAGACGAGTGACT 58.761 43.478 0.00 0.00 0.00 3.41
2923 3361 4.324936 GCATGTTTTCTAGACGAGTGACTC 59.675 45.833 1.65 1.65 0.00 3.36
2968 3406 0.373716 GCCCGTGCTTATCTGTTTCG 59.626 55.000 0.00 0.00 33.53 3.46
3120 4781 3.475774 GTACGCGCCACAGAACCG 61.476 66.667 5.73 0.00 0.00 4.44
3142 4803 0.394762 GCTCACATGGGCAGATGGAA 60.395 55.000 0.00 0.00 0.00 3.53
3249 4910 2.474816 GAGCATCTTCATCCACGTACC 58.525 52.381 0.00 0.00 0.00 3.34
3250 4911 2.101582 GAGCATCTTCATCCACGTACCT 59.898 50.000 0.00 0.00 0.00 3.08
3251 4912 2.101582 AGCATCTTCATCCACGTACCTC 59.898 50.000 0.00 0.00 0.00 3.85
3252 4913 2.101582 GCATCTTCATCCACGTACCTCT 59.898 50.000 0.00 0.00 0.00 3.69
3253 4914 3.318275 GCATCTTCATCCACGTACCTCTA 59.682 47.826 0.00 0.00 0.00 2.43
3254 4915 4.202121 GCATCTTCATCCACGTACCTCTAA 60.202 45.833 0.00 0.00 0.00 2.10
3255 4916 5.509840 GCATCTTCATCCACGTACCTCTAAT 60.510 44.000 0.00 0.00 0.00 1.73
3256 4917 6.516718 CATCTTCATCCACGTACCTCTAATT 58.483 40.000 0.00 0.00 0.00 1.40
3257 4918 6.145338 TCTTCATCCACGTACCTCTAATTC 57.855 41.667 0.00 0.00 0.00 2.17
3258 4919 4.563337 TCATCCACGTACCTCTAATTCG 57.437 45.455 0.00 0.00 0.00 3.34
3259 4920 4.201657 TCATCCACGTACCTCTAATTCGA 58.798 43.478 0.00 0.00 0.00 3.71
3260 4921 4.036027 TCATCCACGTACCTCTAATTCGAC 59.964 45.833 0.00 0.00 0.00 4.20
3261 4922 2.684881 TCCACGTACCTCTAATTCGACC 59.315 50.000 0.00 0.00 0.00 4.79
3262 4923 2.223665 CCACGTACCTCTAATTCGACCC 60.224 54.545 0.00 0.00 0.00 4.46
3263 4924 2.027385 ACGTACCTCTAATTCGACCCC 58.973 52.381 0.00 0.00 0.00 4.95
3264 4925 2.305009 CGTACCTCTAATTCGACCCCT 58.695 52.381 0.00 0.00 0.00 4.79
3265 4926 2.292845 CGTACCTCTAATTCGACCCCTC 59.707 54.545 0.00 0.00 0.00 4.30
3266 4927 2.544844 ACCTCTAATTCGACCCCTCA 57.455 50.000 0.00 0.00 0.00 3.86
3267 4928 2.829023 ACCTCTAATTCGACCCCTCAA 58.171 47.619 0.00 0.00 0.00 3.02
3268 4929 3.178865 ACCTCTAATTCGACCCCTCAAA 58.821 45.455 0.00 0.00 0.00 2.69
3269 4930 3.055312 ACCTCTAATTCGACCCCTCAAAC 60.055 47.826 0.00 0.00 0.00 2.93
3270 4931 3.187700 CTCTAATTCGACCCCTCAAACG 58.812 50.000 0.00 0.00 0.00 3.60
3271 4932 1.664151 CTAATTCGACCCCTCAAACGC 59.336 52.381 0.00 0.00 0.00 4.84
3272 4933 0.958876 AATTCGACCCCTCAAACGCC 60.959 55.000 0.00 0.00 0.00 5.68
3273 4934 2.814913 ATTCGACCCCTCAAACGCCC 62.815 60.000 0.00 0.00 0.00 6.13
3292 4953 4.305011 CGGGGCATGTCCGTTTTA 57.695 55.556 10.95 0.00 42.33 1.52
3293 4954 2.557451 CGGGGCATGTCCGTTTTAA 58.443 52.632 10.95 0.00 42.33 1.52
3294 4955 0.450184 CGGGGCATGTCCGTTTTAAG 59.550 55.000 10.95 0.00 42.33 1.85
3295 4956 0.172578 GGGGCATGTCCGTTTTAAGC 59.827 55.000 10.95 0.00 34.94 3.09
3296 4957 0.172578 GGGCATGTCCGTTTTAAGCC 59.827 55.000 0.00 0.00 39.86 4.35
3297 4958 0.172578 GGCATGTCCGTTTTAAGCCC 59.827 55.000 0.00 0.00 34.71 5.19
3298 4959 0.172578 GCATGTCCGTTTTAAGCCCC 59.827 55.000 0.00 0.00 0.00 5.80
3299 4960 1.834188 CATGTCCGTTTTAAGCCCCT 58.166 50.000 0.00 0.00 0.00 4.79
3300 4961 2.942306 GCATGTCCGTTTTAAGCCCCTA 60.942 50.000 0.00 0.00 0.00 3.53
3301 4962 3.551846 CATGTCCGTTTTAAGCCCCTAT 58.448 45.455 0.00 0.00 0.00 2.57
3302 4963 3.724732 TGTCCGTTTTAAGCCCCTATT 57.275 42.857 0.00 0.00 0.00 1.73
3303 4964 4.036941 TGTCCGTTTTAAGCCCCTATTT 57.963 40.909 0.00 0.00 0.00 1.40
3304 4965 4.409187 TGTCCGTTTTAAGCCCCTATTTT 58.591 39.130 0.00 0.00 0.00 1.82
3305 4966 4.833938 TGTCCGTTTTAAGCCCCTATTTTT 59.166 37.500 0.00 0.00 0.00 1.94
3326 4987 6.817765 TTTTCCTTCATACATCCACACTTC 57.182 37.500 0.00 0.00 0.00 3.01
3327 4988 5.762179 TTCCTTCATACATCCACACTTCT 57.238 39.130 0.00 0.00 0.00 2.85
3328 4989 5.344743 TCCTTCATACATCCACACTTCTC 57.655 43.478 0.00 0.00 0.00 2.87
3329 4990 4.777366 TCCTTCATACATCCACACTTCTCA 59.223 41.667 0.00 0.00 0.00 3.27
3330 4991 5.426509 TCCTTCATACATCCACACTTCTCAT 59.573 40.000 0.00 0.00 0.00 2.90
3331 4992 6.070021 TCCTTCATACATCCACACTTCTCATT 60.070 38.462 0.00 0.00 0.00 2.57
3332 4993 6.600822 CCTTCATACATCCACACTTCTCATTT 59.399 38.462 0.00 0.00 0.00 2.32
3333 4994 7.121759 CCTTCATACATCCACACTTCTCATTTT 59.878 37.037 0.00 0.00 0.00 1.82
3334 4995 8.408043 TTCATACATCCACACTTCTCATTTTT 57.592 30.769 0.00 0.00 0.00 1.94
3354 5015 5.414789 TTTTTCTCTCATATGTCCGGTCA 57.585 39.130 3.25 3.25 0.00 4.02
3355 5016 4.386867 TTTCTCTCATATGTCCGGTCAC 57.613 45.455 2.72 0.00 0.00 3.67
3356 5017 3.298686 TCTCTCATATGTCCGGTCACT 57.701 47.619 2.72 0.00 0.00 3.41
3357 5018 3.632333 TCTCTCATATGTCCGGTCACTT 58.368 45.455 2.72 0.00 0.00 3.16
3358 5019 4.788679 TCTCTCATATGTCCGGTCACTTA 58.211 43.478 2.72 0.00 0.00 2.24
3359 5020 4.579340 TCTCTCATATGTCCGGTCACTTAC 59.421 45.833 2.72 0.00 0.00 2.34
3360 5021 4.274978 TCTCATATGTCCGGTCACTTACA 58.725 43.478 2.72 0.00 0.00 2.41
3361 5022 4.893524 TCTCATATGTCCGGTCACTTACAT 59.106 41.667 2.72 6.49 36.56 2.29
3362 5023 4.944048 TCATATGTCCGGTCACTTACATG 58.056 43.478 13.01 8.05 34.54 3.21
3363 5024 4.404394 TCATATGTCCGGTCACTTACATGT 59.596 41.667 13.01 2.69 34.54 3.21
3364 5025 2.448926 TGTCCGGTCACTTACATGTG 57.551 50.000 9.11 0.00 39.15 3.21
3365 5026 1.964933 TGTCCGGTCACTTACATGTGA 59.035 47.619 9.11 0.00 43.72 3.58
3366 5027 2.565391 TGTCCGGTCACTTACATGTGAT 59.435 45.455 9.11 0.00 46.77 3.06
3367 5028 3.007506 TGTCCGGTCACTTACATGTGATT 59.992 43.478 9.11 0.00 46.77 2.57
3368 5029 3.370978 GTCCGGTCACTTACATGTGATTG 59.629 47.826 9.11 5.02 46.77 2.67
3369 5030 2.677836 CCGGTCACTTACATGTGATTGG 59.322 50.000 9.11 0.00 46.77 3.16
3370 5031 3.334691 CGGTCACTTACATGTGATTGGT 58.665 45.455 9.11 0.00 46.77 3.67
3371 5032 3.125146 CGGTCACTTACATGTGATTGGTG 59.875 47.826 9.11 5.41 46.77 4.17
3372 5033 3.440173 GGTCACTTACATGTGATTGGTGG 59.560 47.826 9.11 0.00 46.77 4.61
3373 5034 4.323417 GTCACTTACATGTGATTGGTGGA 58.677 43.478 9.11 0.00 46.77 4.02
3374 5035 4.393062 GTCACTTACATGTGATTGGTGGAG 59.607 45.833 9.11 0.00 46.77 3.86
3375 5036 4.285775 TCACTTACATGTGATTGGTGGAGA 59.714 41.667 9.11 0.00 41.43 3.71
3376 5037 4.633126 CACTTACATGTGATTGGTGGAGAG 59.367 45.833 9.11 0.00 40.12 3.20
3377 5038 4.532126 ACTTACATGTGATTGGTGGAGAGA 59.468 41.667 9.11 0.00 0.00 3.10
3378 5039 5.013079 ACTTACATGTGATTGGTGGAGAGAA 59.987 40.000 9.11 0.00 0.00 2.87
3379 5040 3.947868 ACATGTGATTGGTGGAGAGAAG 58.052 45.455 0.00 0.00 0.00 2.85
3380 5041 3.584406 ACATGTGATTGGTGGAGAGAAGA 59.416 43.478 0.00 0.00 0.00 2.87
3381 5042 4.042062 ACATGTGATTGGTGGAGAGAAGAA 59.958 41.667 0.00 0.00 0.00 2.52
3382 5043 4.705110 TGTGATTGGTGGAGAGAAGAAA 57.295 40.909 0.00 0.00 0.00 2.52
3383 5044 5.246981 TGTGATTGGTGGAGAGAAGAAAT 57.753 39.130 0.00 0.00 0.00 2.17
3384 5045 6.373005 TGTGATTGGTGGAGAGAAGAAATA 57.627 37.500 0.00 0.00 0.00 1.40
3385 5046 6.409704 TGTGATTGGTGGAGAGAAGAAATAG 58.590 40.000 0.00 0.00 0.00 1.73
3386 5047 6.213397 TGTGATTGGTGGAGAGAAGAAATAGA 59.787 38.462 0.00 0.00 0.00 1.98
3387 5048 7.106239 GTGATTGGTGGAGAGAAGAAATAGAA 58.894 38.462 0.00 0.00 0.00 2.10
3388 5049 7.607991 GTGATTGGTGGAGAGAAGAAATAGAAA 59.392 37.037 0.00 0.00 0.00 2.52
3389 5050 7.826252 TGATTGGTGGAGAGAAGAAATAGAAAG 59.174 37.037 0.00 0.00 0.00 2.62
3390 5051 6.935240 TGGTGGAGAGAAGAAATAGAAAGA 57.065 37.500 0.00 0.00 0.00 2.52
3391 5052 7.316393 TGGTGGAGAGAAGAAATAGAAAGAA 57.684 36.000 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 4.083862 GTGGGTGGCTCCTCGTCC 62.084 72.222 5.46 0.00 36.25 4.79
73 74 1.499049 AAAGAAAGCTCGTCGTGGAC 58.501 50.000 0.00 0.00 0.00 4.02
74 75 2.132762 GAAAAGAAAGCTCGTCGTGGA 58.867 47.619 0.00 0.00 0.00 4.02
93 94 1.117142 AGTTCCCTTTCGTCACCGGA 61.117 55.000 9.46 0.00 33.95 5.14
222 225 3.125146 TCAACGCGGATCATTTCTGAAAG 59.875 43.478 12.47 1.82 34.37 2.62
223 226 3.070748 TCAACGCGGATCATTTCTGAAA 58.929 40.909 12.47 5.15 34.37 2.69
243 254 4.082136 ACAAGACTGACGGAAATACTCCTC 60.082 45.833 0.00 0.00 42.85 3.71
259 270 6.239543 CCAGCATCCATATCTAGAACAAGACT 60.240 42.308 0.00 0.00 0.00 3.24
266 277 3.184628 CCCCCAGCATCCATATCTAGAA 58.815 50.000 0.00 0.00 0.00 2.10
268 279 1.211457 GCCCCCAGCATCCATATCTAG 59.789 57.143 0.00 0.00 42.97 2.43
269 280 1.289160 GCCCCCAGCATCCATATCTA 58.711 55.000 0.00 0.00 42.97 1.98
270 281 2.081955 GCCCCCAGCATCCATATCT 58.918 57.895 0.00 0.00 42.97 1.98
271 282 4.751431 GCCCCCAGCATCCATATC 57.249 61.111 0.00 0.00 42.97 1.63
331 345 2.061773 GCACTGCACTGTACTGTACTG 58.938 52.381 19.36 19.36 0.00 2.74
332 346 1.686587 TGCACTGCACTGTACTGTACT 59.313 47.619 17.98 0.00 31.71 2.73
333 347 2.148916 TGCACTGCACTGTACTGTAC 57.851 50.000 10.98 10.98 31.71 2.90
360 377 1.907807 TGGCATGCCAAGTCAACCC 60.908 57.895 36.95 6.63 44.12 4.11
404 421 2.067932 TTGGCCAGTTGGGTCTCCTG 62.068 60.000 5.11 0.00 43.75 3.86
424 442 1.571773 GGGGCTGGAGGTGTTGGTAT 61.572 60.000 0.00 0.00 0.00 2.73
426 444 3.580319 GGGGCTGGAGGTGTTGGT 61.580 66.667 0.00 0.00 0.00 3.67
428 446 2.484287 AATCGGGGCTGGAGGTGTTG 62.484 60.000 0.00 0.00 0.00 3.33
429 447 2.198304 GAATCGGGGCTGGAGGTGTT 62.198 60.000 0.00 0.00 0.00 3.32
430 448 2.610859 AATCGGGGCTGGAGGTGT 60.611 61.111 0.00 0.00 0.00 4.16
434 471 0.177141 TAAACGAATCGGGGCTGGAG 59.823 55.000 7.80 0.00 0.00 3.86
439 476 0.445043 GTGTGTAAACGAATCGGGGC 59.555 55.000 7.80 0.00 0.00 5.80
447 484 2.412429 GTGTGTGTGTGTGTGTAAACGA 59.588 45.455 0.00 0.00 0.00 3.85
448 485 2.157863 TGTGTGTGTGTGTGTGTAAACG 59.842 45.455 0.00 0.00 0.00 3.60
459 496 2.888534 GTCCGCGTGTGTGTGTGT 60.889 61.111 4.92 0.00 0.00 3.72
461 498 2.888534 GTGTCCGCGTGTGTGTGT 60.889 61.111 4.92 0.00 0.00 3.72
462 499 2.888051 TGTGTCCGCGTGTGTGTG 60.888 61.111 4.92 0.00 0.00 3.82
465 502 3.785189 GAGGTGTGTCCGCGTGTGT 62.785 63.158 4.92 0.00 41.99 3.72
468 505 2.048222 ATGAGGTGTGTCCGCGTG 60.048 61.111 4.92 0.00 41.99 5.34
469 506 2.214181 GAGATGAGGTGTGTCCGCGT 62.214 60.000 4.92 0.00 41.99 6.01
470 507 1.517257 GAGATGAGGTGTGTCCGCG 60.517 63.158 0.00 0.00 41.99 6.46
471 508 1.517257 CGAGATGAGGTGTGTCCGC 60.517 63.158 0.00 0.00 41.99 5.54
472 509 1.517257 GCGAGATGAGGTGTGTCCG 60.517 63.158 0.00 0.00 41.99 4.79
473 510 1.153549 GGCGAGATGAGGTGTGTCC 60.154 63.158 0.00 0.00 0.00 4.02
474 511 0.737715 GTGGCGAGATGAGGTGTGTC 60.738 60.000 0.00 0.00 0.00 3.67
491 538 0.508641 CAAAGTCTTGGTCGCTCGTG 59.491 55.000 0.00 0.00 0.00 4.35
520 567 3.367395 GGAAGGTGAAATTTGCTACCAGC 60.367 47.826 14.73 7.85 42.82 4.85
522 569 3.838565 TGGAAGGTGAAATTTGCTACCA 58.161 40.909 14.73 6.51 35.66 3.25
523 570 4.522789 TCTTGGAAGGTGAAATTTGCTACC 59.477 41.667 0.00 1.54 0.00 3.18
534 588 1.555075 CCGAGGATTCTTGGAAGGTGA 59.445 52.381 0.00 0.00 45.61 4.02
571 625 2.094182 TCGGATTCTATCTAATGGCGCC 60.094 50.000 22.73 22.73 0.00 6.53
588 642 1.378250 GGGTCGACTTCCTCTCGGA 60.378 63.158 16.46 0.00 37.60 4.55
589 643 2.762234 CGGGTCGACTTCCTCTCGG 61.762 68.421 16.46 0.00 0.00 4.63
590 644 2.762234 CCGGGTCGACTTCCTCTCG 61.762 68.421 16.46 0.00 0.00 4.04
591 645 2.416432 CCCGGGTCGACTTCCTCTC 61.416 68.421 14.18 0.00 0.00 3.20
592 646 2.226149 ATCCCGGGTCGACTTCCTCT 62.226 60.000 22.86 0.00 0.00 3.69
594 648 2.058595 CATCCCGGGTCGACTTCCT 61.059 63.158 22.86 0.00 0.00 3.36
644 700 4.386049 GCCTAATAATCTCGTGTCCGAATG 59.614 45.833 0.00 0.00 43.69 2.67
666 722 3.191539 CCTCTTCTTGCTCCGCGC 61.192 66.667 0.00 0.00 39.77 6.86
793 873 2.820197 GGAAATCCAGAAGCGAAAAGGT 59.180 45.455 0.00 0.00 35.64 3.50
840 926 6.888105 AGAAAAGTTTGGAACATGGTGAAAT 58.112 32.000 0.00 0.00 39.30 2.17
899 1028 0.596577 GGTTCTTTCTTTGGCGGGTC 59.403 55.000 0.00 0.00 0.00 4.46
935 1074 2.088423 CTGGTACTCTGTTCTCGAGCT 58.912 52.381 7.81 0.00 31.71 4.09
938 1077 1.813178 CTGCTGGTACTCTGTTCTCGA 59.187 52.381 0.00 0.00 0.00 4.04
940 1079 3.944055 TTCTGCTGGTACTCTGTTCTC 57.056 47.619 0.00 0.00 0.00 2.87
942 1081 3.067833 GGTTTCTGCTGGTACTCTGTTC 58.932 50.000 0.00 0.00 0.00 3.18
955 1107 1.652563 GGGTTGTCGTGGTTTCTGC 59.347 57.895 0.00 0.00 0.00 4.26
966 1118 0.386731 CGTTGCGAATTGGGGTTGTC 60.387 55.000 0.00 0.00 0.00 3.18
990 1147 1.660167 TGCTCGCCATCTTGATCTTG 58.340 50.000 0.00 0.00 0.00 3.02
1833 2024 1.069765 CTCCCATAATGCCGCGTCT 59.930 57.895 4.92 0.00 0.00 4.18
1881 2072 2.716017 CCTCCTCTCGGTGCTGTCC 61.716 68.421 0.00 0.00 0.00 4.02
2011 2214 1.194781 ATGCCAGTCGTCTCCTTGGT 61.195 55.000 0.00 0.00 33.21 3.67
2045 2251 6.974965 ACTGATTTTTCTTCACTTGTGATCC 58.025 36.000 4.18 0.00 0.00 3.36
2062 2268 3.181471 CCGGACTCTGCATCTACTGATTT 60.181 47.826 0.00 0.00 0.00 2.17
2112 2321 0.882042 CGTTGAGGAAGCTGCTGTGT 60.882 55.000 1.35 0.00 0.00 3.72
2132 2344 3.525537 TCGTCTTCAAATGCATCTCCTC 58.474 45.455 0.00 0.00 0.00 3.71
2144 2356 1.480954 GCCCTACTGGATCGTCTTCAA 59.519 52.381 0.00 0.00 35.39 2.69
2148 2360 1.043673 GGTGCCCTACTGGATCGTCT 61.044 60.000 0.00 0.00 35.39 4.18
2151 2363 1.105167 TACGGTGCCCTACTGGATCG 61.105 60.000 0.00 0.00 40.13 3.69
2167 2391 4.693283 TCCAAAGACTGATAATGCCTACG 58.307 43.478 0.00 0.00 0.00 3.51
2192 2422 3.695830 TCGGTTGGTGAGAAGCTAAAT 57.304 42.857 0.00 0.00 0.00 1.40
2209 2439 8.420374 ACTAGTAACAATTTACATGACATCGG 57.580 34.615 0.00 0.00 40.25 4.18
2315 2651 3.131933 GGAGCAGAAGTATGAGCTGAGAA 59.868 47.826 0.00 0.00 37.48 2.87
2320 2656 1.127343 GGGGAGCAGAAGTATGAGCT 58.873 55.000 0.00 0.00 40.60 4.09
2351 2687 7.815068 AGTTGAAGTATGAGCTGTTAGTTACTG 59.185 37.037 0.00 0.00 0.00 2.74
2352 2688 7.897864 AGTTGAAGTATGAGCTGTTAGTTACT 58.102 34.615 0.00 0.00 0.00 2.24
2353 2689 7.008447 CGAGTTGAAGTATGAGCTGTTAGTTAC 59.992 40.741 0.00 0.00 0.00 2.50
2354 2690 7.027760 CGAGTTGAAGTATGAGCTGTTAGTTA 58.972 38.462 0.00 0.00 0.00 2.24
2355 2691 5.864474 CGAGTTGAAGTATGAGCTGTTAGTT 59.136 40.000 0.00 0.00 0.00 2.24
2356 2692 5.183331 TCGAGTTGAAGTATGAGCTGTTAGT 59.817 40.000 0.00 0.00 0.00 2.24
2357 2693 5.641709 TCGAGTTGAAGTATGAGCTGTTAG 58.358 41.667 0.00 0.00 0.00 2.34
2359 2695 4.521130 TCGAGTTGAAGTATGAGCTGTT 57.479 40.909 0.00 0.00 0.00 3.16
2360 2696 4.521130 TTCGAGTTGAAGTATGAGCTGT 57.479 40.909 0.00 0.00 31.44 4.40
2369 2705 7.254795 CAACCTAATTGTTCTTCGAGTTGAAGT 60.255 37.037 17.92 2.60 42.71 3.01
2370 2706 7.072030 CAACCTAATTGTTCTTCGAGTTGAAG 58.928 38.462 13.29 13.29 43.08 3.02
2371 2707 6.954944 CAACCTAATTGTTCTTCGAGTTGAA 58.045 36.000 0.00 0.00 35.29 2.69
2372 2708 6.539649 CAACCTAATTGTTCTTCGAGTTGA 57.460 37.500 0.00 0.00 35.29 3.18
2385 2740 4.506654 CGGATTCGGAGTACAACCTAATTG 59.493 45.833 0.00 0.00 44.60 2.32
2397 2754 0.598562 CGATCCATCGGATTCGGAGT 59.401 55.000 0.73 0.00 43.27 3.85
2539 2916 1.079127 CCGCGGTGGAAGATTCAGT 60.079 57.895 19.50 0.00 42.00 3.41
2602 2984 0.946221 CGATCCATTCGGGCAGTAGC 60.946 60.000 0.00 0.00 44.28 3.58
2656 3038 2.633967 TCTGGACCCACGTAGCTTAAAA 59.366 45.455 0.00 0.00 0.00 1.52
2659 3041 1.754803 CATCTGGACCCACGTAGCTTA 59.245 52.381 0.00 0.00 0.00 3.09
2660 3042 0.537188 CATCTGGACCCACGTAGCTT 59.463 55.000 0.00 0.00 0.00 3.74
2661 3044 0.324368 TCATCTGGACCCACGTAGCT 60.324 55.000 0.00 0.00 0.00 3.32
2662 3045 0.753262 ATCATCTGGACCCACGTAGC 59.247 55.000 0.00 0.00 0.00 3.58
2663 3046 2.515926 CATCATCTGGACCCACGTAG 57.484 55.000 0.00 0.00 0.00 3.51
2677 3060 2.911143 GGCCGTCCACTCCATCAT 59.089 61.111 0.00 0.00 0.00 2.45
2678 3061 3.770040 CGGCCGTCCACTCCATCA 61.770 66.667 19.50 0.00 0.00 3.07
2905 3343 6.636562 AGAAAGAGTCACTCGTCTAGAAAA 57.363 37.500 11.29 0.00 35.36 2.29
2906 3344 7.160049 TCTAGAAAGAGTCACTCGTCTAGAAA 58.840 38.462 30.38 18.90 45.18 2.52
2907 3345 6.699366 TCTAGAAAGAGTCACTCGTCTAGAA 58.301 40.000 30.38 20.92 45.18 2.10
2908 3346 6.283544 TCTAGAAAGAGTCACTCGTCTAGA 57.716 41.667 29.59 29.59 45.50 2.43
2909 3347 6.583912 CTCTAGAAAGAGTCACTCGTCTAG 57.416 45.833 27.29 27.29 43.75 2.43
2922 3360 5.105554 GCCAGTTCTCATCACTCTAGAAAGA 60.106 44.000 0.00 0.00 31.41 2.52
2923 3361 5.108517 GCCAGTTCTCATCACTCTAGAAAG 58.891 45.833 0.00 0.00 31.41 2.62
2932 3370 1.028868 GGCCTGCCAGTTCTCATCAC 61.029 60.000 2.58 0.00 35.81 3.06
2968 3406 1.792949 CGTGTGGACTAACTCAACAGC 59.207 52.381 0.00 0.00 0.00 4.40
3026 4685 2.793933 GCATGAATCGGCTGCTCTTTTC 60.794 50.000 0.00 0.00 33.15 2.29
3120 4781 1.077212 ATCTGCCCATGTGAGCACC 60.077 57.895 0.00 0.00 34.68 5.01
3123 4784 0.394762 TTCCATCTGCCCATGTGAGC 60.395 55.000 0.00 0.00 0.00 4.26
3142 4803 5.957842 TCCAAAGAAAACAGAATATGCGT 57.042 34.783 0.00 0.00 0.00 5.24
3220 4881 6.493116 GTGGATGAAGATGCTCTAAAACATG 58.507 40.000 0.00 0.00 0.00 3.21
3221 4882 5.295292 CGTGGATGAAGATGCTCTAAAACAT 59.705 40.000 0.00 0.00 0.00 2.71
3223 4884 4.631813 ACGTGGATGAAGATGCTCTAAAAC 59.368 41.667 0.00 0.00 0.00 2.43
3226 4887 4.202121 GGTACGTGGATGAAGATGCTCTAA 60.202 45.833 0.00 0.00 0.00 2.10
3227 4888 3.318275 GGTACGTGGATGAAGATGCTCTA 59.682 47.826 0.00 0.00 0.00 2.43
3228 4889 2.101582 GGTACGTGGATGAAGATGCTCT 59.898 50.000 0.00 0.00 0.00 4.09
3229 4890 2.101582 AGGTACGTGGATGAAGATGCTC 59.898 50.000 0.00 0.00 0.00 4.26
3230 4891 2.101582 GAGGTACGTGGATGAAGATGCT 59.898 50.000 0.00 0.00 0.00 3.79
3231 4892 2.101582 AGAGGTACGTGGATGAAGATGC 59.898 50.000 0.00 0.00 0.00 3.91
3232 4893 5.515797 TTAGAGGTACGTGGATGAAGATG 57.484 43.478 0.00 0.00 0.00 2.90
3233 4894 6.515200 CGAATTAGAGGTACGTGGATGAAGAT 60.515 42.308 0.00 0.00 0.00 2.40
3234 4895 5.220989 CGAATTAGAGGTACGTGGATGAAGA 60.221 44.000 0.00 0.00 0.00 2.87
3235 4896 4.976731 CGAATTAGAGGTACGTGGATGAAG 59.023 45.833 0.00 0.00 0.00 3.02
3236 4897 4.641541 TCGAATTAGAGGTACGTGGATGAA 59.358 41.667 0.00 0.00 0.00 2.57
3237 4898 4.036027 GTCGAATTAGAGGTACGTGGATGA 59.964 45.833 0.00 0.00 0.00 2.92
3238 4899 4.288531 GTCGAATTAGAGGTACGTGGATG 58.711 47.826 0.00 0.00 0.00 3.51
3239 4900 3.317430 GGTCGAATTAGAGGTACGTGGAT 59.683 47.826 0.00 0.00 0.00 3.41
3240 4901 2.684881 GGTCGAATTAGAGGTACGTGGA 59.315 50.000 0.00 0.00 0.00 4.02
3241 4902 2.223665 GGGTCGAATTAGAGGTACGTGG 60.224 54.545 0.00 0.00 0.00 4.94
3242 4903 2.223665 GGGGTCGAATTAGAGGTACGTG 60.224 54.545 0.00 0.00 0.00 4.49
3243 4904 2.027385 GGGGTCGAATTAGAGGTACGT 58.973 52.381 0.00 0.00 0.00 3.57
3244 4905 2.292845 GAGGGGTCGAATTAGAGGTACG 59.707 54.545 0.00 0.00 0.00 3.67
3245 4906 3.294214 TGAGGGGTCGAATTAGAGGTAC 58.706 50.000 0.00 0.00 0.00 3.34
3246 4907 3.675348 TGAGGGGTCGAATTAGAGGTA 57.325 47.619 0.00 0.00 0.00 3.08
3247 4908 2.544844 TGAGGGGTCGAATTAGAGGT 57.455 50.000 0.00 0.00 0.00 3.85
3248 4909 3.532542 GTTTGAGGGGTCGAATTAGAGG 58.467 50.000 0.00 0.00 0.00 3.69
3249 4910 3.187700 CGTTTGAGGGGTCGAATTAGAG 58.812 50.000 0.00 0.00 0.00 2.43
3250 4911 2.675889 GCGTTTGAGGGGTCGAATTAGA 60.676 50.000 0.00 0.00 0.00 2.10
3251 4912 1.664151 GCGTTTGAGGGGTCGAATTAG 59.336 52.381 0.00 0.00 0.00 1.73
3252 4913 1.676615 GGCGTTTGAGGGGTCGAATTA 60.677 52.381 0.00 0.00 0.00 1.40
3253 4914 0.958876 GGCGTTTGAGGGGTCGAATT 60.959 55.000 0.00 0.00 0.00 2.17
3254 4915 1.376812 GGCGTTTGAGGGGTCGAAT 60.377 57.895 0.00 0.00 0.00 3.34
3255 4916 2.031465 GGCGTTTGAGGGGTCGAA 59.969 61.111 0.00 0.00 0.00 3.71
3256 4917 4.011517 GGGCGTTTGAGGGGTCGA 62.012 66.667 0.00 0.00 0.00 4.20
3276 4937 0.172578 GCTTAAAACGGACATGCCCC 59.827 55.000 0.00 0.00 0.00 5.80
3277 4938 0.172578 GGCTTAAAACGGACATGCCC 59.827 55.000 0.00 0.00 33.45 5.36
3278 4939 0.172578 GGGCTTAAAACGGACATGCC 59.827 55.000 0.00 0.00 38.28 4.40
3279 4940 0.172578 GGGGCTTAAAACGGACATGC 59.827 55.000 0.00 0.00 0.00 4.06
3280 4941 1.834188 AGGGGCTTAAAACGGACATG 58.166 50.000 0.00 0.00 0.00 3.21
3281 4942 3.945640 ATAGGGGCTTAAAACGGACAT 57.054 42.857 0.00 0.00 0.00 3.06
3282 4943 3.724732 AATAGGGGCTTAAAACGGACA 57.275 42.857 0.00 0.00 0.00 4.02
3283 4944 5.395682 AAAAATAGGGGCTTAAAACGGAC 57.604 39.130 0.00 0.00 0.00 4.79
3302 4963 7.004086 AGAAGTGTGGATGTATGAAGGAAAAA 58.996 34.615 0.00 0.00 0.00 1.94
3303 4964 6.542821 AGAAGTGTGGATGTATGAAGGAAAA 58.457 36.000 0.00 0.00 0.00 2.29
3304 4965 6.126863 AGAAGTGTGGATGTATGAAGGAAA 57.873 37.500 0.00 0.00 0.00 3.13
3305 4966 5.248248 TGAGAAGTGTGGATGTATGAAGGAA 59.752 40.000 0.00 0.00 0.00 3.36
3306 4967 4.777366 TGAGAAGTGTGGATGTATGAAGGA 59.223 41.667 0.00 0.00 0.00 3.36
3307 4968 5.089970 TGAGAAGTGTGGATGTATGAAGG 57.910 43.478 0.00 0.00 0.00 3.46
3308 4969 7.621428 AAATGAGAAGTGTGGATGTATGAAG 57.379 36.000 0.00 0.00 0.00 3.02
3309 4970 8.408043 AAAAATGAGAAGTGTGGATGTATGAA 57.592 30.769 0.00 0.00 0.00 2.57
3332 4993 5.046591 AGTGACCGGACATATGAGAGAAAAA 60.047 40.000 9.46 0.00 0.00 1.94
3333 4994 4.466370 AGTGACCGGACATATGAGAGAAAA 59.534 41.667 9.46 0.00 0.00 2.29
3334 4995 4.023980 AGTGACCGGACATATGAGAGAAA 58.976 43.478 9.46 0.00 0.00 2.52
3335 4996 3.632333 AGTGACCGGACATATGAGAGAA 58.368 45.455 9.46 0.00 0.00 2.87
3336 4997 3.298686 AGTGACCGGACATATGAGAGA 57.701 47.619 9.46 0.00 0.00 3.10
3337 4998 4.338400 TGTAAGTGACCGGACATATGAGAG 59.662 45.833 9.46 0.00 0.00 3.20
3338 4999 4.274978 TGTAAGTGACCGGACATATGAGA 58.725 43.478 9.46 0.00 0.00 3.27
3339 5000 4.649088 TGTAAGTGACCGGACATATGAG 57.351 45.455 9.46 0.24 0.00 2.90
3340 5001 4.404394 ACATGTAAGTGACCGGACATATGA 59.596 41.667 9.46 0.00 31.41 2.15
3341 5002 4.507756 CACATGTAAGTGACCGGACATATG 59.492 45.833 9.46 11.65 42.05 1.78
3342 5003 4.404394 TCACATGTAAGTGACCGGACATAT 59.596 41.667 9.46 3.84 43.18 1.78
3343 5004 3.764972 TCACATGTAAGTGACCGGACATA 59.235 43.478 9.46 0.00 43.18 2.29
3344 5005 2.565391 TCACATGTAAGTGACCGGACAT 59.435 45.455 9.46 2.80 43.18 3.06
3345 5006 1.964933 TCACATGTAAGTGACCGGACA 59.035 47.619 9.46 5.04 43.18 4.02
3346 5007 2.736144 TCACATGTAAGTGACCGGAC 57.264 50.000 9.46 1.07 43.18 4.79
3353 5014 4.578871 TCTCCACCAATCACATGTAAGTG 58.421 43.478 0.00 0.00 40.85 3.16
3354 5015 4.532126 TCTCTCCACCAATCACATGTAAGT 59.468 41.667 0.00 0.00 0.00 2.24
3355 5016 5.089970 TCTCTCCACCAATCACATGTAAG 57.910 43.478 0.00 0.00 0.00 2.34
3356 5017 5.248248 TCTTCTCTCCACCAATCACATGTAA 59.752 40.000 0.00 0.00 0.00 2.41
3357 5018 4.777366 TCTTCTCTCCACCAATCACATGTA 59.223 41.667 0.00 0.00 0.00 2.29
3358 5019 3.584406 TCTTCTCTCCACCAATCACATGT 59.416 43.478 0.00 0.00 0.00 3.21
3359 5020 4.212143 TCTTCTCTCCACCAATCACATG 57.788 45.455 0.00 0.00 0.00 3.21
3360 5021 4.916041 TTCTTCTCTCCACCAATCACAT 57.084 40.909 0.00 0.00 0.00 3.21
3361 5022 4.705110 TTTCTTCTCTCCACCAATCACA 57.295 40.909 0.00 0.00 0.00 3.58
3362 5023 6.644347 TCTATTTCTTCTCTCCACCAATCAC 58.356 40.000 0.00 0.00 0.00 3.06
3363 5024 6.874278 TCTATTTCTTCTCTCCACCAATCA 57.126 37.500 0.00 0.00 0.00 2.57
3364 5025 8.043710 TCTTTCTATTTCTTCTCTCCACCAATC 58.956 37.037 0.00 0.00 0.00 2.67
3365 5026 7.922382 TCTTTCTATTTCTTCTCTCCACCAAT 58.078 34.615 0.00 0.00 0.00 3.16
3366 5027 7.316393 TCTTTCTATTTCTTCTCTCCACCAA 57.684 36.000 0.00 0.00 0.00 3.67
3367 5028 6.935240 TCTTTCTATTTCTTCTCTCCACCA 57.065 37.500 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.