Multiple sequence alignment - TraesCS1A01G300100

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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 TraesCS1A01G300100 chr1A 100.000 3325 0 0 1 3325 495128469 495131793 0.000000e+00 6141.0
1 TraesCS1A01G300100 chr1A 93.000 200 10 4 499 696 420572834 420573031 4.200000e-74 289.0
2 TraesCS1A01G300100 chr1B 93.359 1852 96 7 701 2541 533088351 533090186 0.000000e+00 2713.0
3 TraesCS1A01G300100 chr1B 90.712 646 40 12 2662 3300 533090524 533091156 0.000000e+00 843.0
4 TraesCS1A01G300100 chr1B 89.474 57 5 1 2605 2661 533090310 533090365 1.650000e-08 71.3
5 TraesCS1A01G300100 chr1D 92.519 1925 80 23 701 2594 397629913 397631804 0.000000e+00 2699.0
6 TraesCS1A01G300100 chr1D 92.222 450 24 6 2858 3300 397632561 397633006 7.830000e-176 627.0
7 TraesCS1A01G300100 chr1D 91.968 249 18 2 1 248 397629518 397629765 6.830000e-92 348.0
8 TraesCS1A01G300100 chr1D 88.554 166 16 2 2659 2824 397632128 397632290 7.280000e-47 198.0
9 TraesCS1A01G300100 chr1D 100.000 33 0 0 2605 2637 397631865 397631897 9.960000e-06 62.1
10 TraesCS1A01G300100 chr5D 95.283 212 9 1 1025 1236 386867622 386867412 5.320000e-88 335.0
11 TraesCS1A01G300100 chr5D 92.381 210 15 1 500 708 66765010 66765219 6.970000e-77 298.0
12 TraesCS1A01G300100 chr5D 86.909 275 20 8 1271 1532 386867428 386867157 9.020000e-76 294.0
13 TraesCS1A01G300100 chr5D 91.981 212 9 6 507 712 488352311 488352520 1.170000e-74 291.0
14 TraesCS1A01G300100 chr5D 93.789 161 7 3 355 513 245718265 245718424 4.290000e-59 239.0
15 TraesCS1A01G300100 chr5D 83.784 74 7 3 1266 1339 564235448 564235380 7.700000e-07 65.8
16 TraesCS1A01G300100 chr2A 95.361 194 5 2 515 705 196517965 196518157 4.170000e-79 305.0
17 TraesCS1A01G300100 chr2A 91.228 228 14 4 501 723 278996243 278996469 4.170000e-79 305.0
18 TraesCS1A01G300100 chr2A 91.441 222 13 6 489 707 195349911 195350129 1.940000e-77 300.0
19 TraesCS1A01G300100 chr3A 92.647 204 11 4 505 705 716806722 716806520 1.170000e-74 291.0
20 TraesCS1A01G300100 chr3A 92.233 206 13 2 508 713 741158326 741158124 4.200000e-74 289.0
21 TraesCS1A01G300100 chr3A 89.035 228 19 5 497 720 641468878 641469103 9.090000e-71 278.0
22 TraesCS1A01G300100 chr3A 96.094 128 5 0 1263 1390 503028560 503028687 3.360000e-50 209.0
23 TraesCS1A01G300100 chr3A 82.500 200 30 5 1967 2164 594590693 594590497 1.590000e-38 171.0
24 TraesCS1A01G300100 chr5B 87.059 255 21 5 1290 1532 464895915 464895661 9.090000e-71 278.0
25 TraesCS1A01G300100 chr5B 94.964 139 6 1 1050 1187 464896090 464895952 2.010000e-52 217.0
26 TraesCS1A01G300100 chr5B 92.857 126 8 1 1263 1387 60909930 60910055 7.330000e-42 182.0
27 TraesCS1A01G300100 chr4D 94.969 159 7 1 356 513 93338033 93338191 7.120000e-62 248.0
28 TraesCS1A01G300100 chr7A 94.937 158 7 1 357 513 320981345 320981188 2.560000e-61 246.0
29 TraesCS1A01G300100 chr3D 95.455 154 6 1 361 513 360695824 360695977 9.210000e-61 244.0
30 TraesCS1A01G300100 chr3D 81.500 200 32 5 1967 2164 452240248 452240052 3.430000e-35 159.0
31 TraesCS1A01G300100 chr3D 93.548 62 4 0 1049 1110 452241128 452241067 3.530000e-15 93.5
32 TraesCS1A01G300100 chr3D 94.286 35 2 0 1263 1297 329686691 329686657 2.000000e-03 54.7
33 TraesCS1A01G300100 chr7D 94.340 159 8 1 356 513 384149012 384148854 3.310000e-60 243.0
34 TraesCS1A01G300100 chr7D 91.489 47 4 0 1485 1531 194453861 194453907 7.700000e-07 65.8
35 TraesCS1A01G300100 chr6D 94.872 156 6 2 359 513 392896970 392897124 3.310000e-60 243.0
36 TraesCS1A01G300100 chr5A 94.304 158 7 2 357 513 687682578 687682734 1.190000e-59 241.0
37 TraesCS1A01G300100 chr5A 94.667 75 3 1 1267 1341 413187107 413187034 7.540000e-22 115.0
38 TraesCS1A01G300100 chr2D 92.857 168 8 4 350 513 475088520 475088353 1.190000e-59 241.0
39 TraesCS1A01G300100 chr3B 91.061 179 9 6 339 513 571752499 571752674 5.550000e-58 235.0
40 TraesCS1A01G300100 chr3B 81.481 189 32 3 1967 2154 593921604 593921418 5.750000e-33 152.0
41 TraesCS1A01G300100 chr3B 93.548 62 4 0 1049 1110 593922469 593922408 3.530000e-15 93.5
42 TraesCS1A01G300100 chr4A 97.143 35 0 1 1314 1348 690085946 690085979 1.290000e-04 58.4


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 TraesCS1A01G300100 chr1A 495128469 495131793 3324 False 6141.00 6141 100.000000 1 3325 1 chr1A.!!$F2 3324
1 TraesCS1A01G300100 chr1B 533088351 533091156 2805 False 1209.10 2713 91.181667 701 3300 3 chr1B.!!$F1 2599
2 TraesCS1A01G300100 chr1D 397629518 397633006 3488 False 786.82 2699 93.052600 1 3300 5 chr1D.!!$F1 3299

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
300 302 0.320771 CCTGCGTGTGGTAGAAGCTT 60.321 55.0 0.00 0.00 0.0 3.74 F
301 303 1.071605 CTGCGTGTGGTAGAAGCTTC 58.928 55.0 19.11 19.11 0.0 3.86 F
1270 1294 0.038526 AGGTAAGCAACGACGTCCAG 60.039 55.0 10.58 0.00 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1244 1268 0.320374 TCGTTGCTTACCTCCCTGTG 59.68 55.0 0.00 0.0 0.0 3.66 R
1736 1781 0.610232 GCTTGGGTGACATCCTGCTT 60.61 55.0 6.25 0.0 0.0 3.91 R
2491 2536 0.250252 TGTGGCGCTCAAGACATTGA 60.25 50.0 7.64 0.0 43.2 2.57 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 2.939460 TTCGCCGGTACTTAGGTTAC 57.061 50.000 1.90 0.00 0.00 2.50
56 57 7.924541 ACTTAGGTTACATTTTGGGATACAGA 58.075 34.615 0.00 0.00 39.74 3.41
58 59 8.801882 TTAGGTTACATTTTGGGATACAGAAG 57.198 34.615 0.00 0.00 39.74 2.85
62 63 4.261801 ACATTTTGGGATACAGAAGGTCG 58.738 43.478 0.00 0.00 33.61 4.79
76 77 0.678950 AGGTCGCCATTTTGGTTTGG 59.321 50.000 0.00 0.00 40.46 3.28
95 96 6.264518 GGTTTGGGAGTTTCAACTGATTTAGA 59.735 38.462 0.00 0.00 39.88 2.10
103 104 3.942829 TCAACTGATTTAGACTGGCTGG 58.057 45.455 0.00 0.00 0.00 4.85
126 127 1.248486 TGGATCTTCCCGCTATCGAG 58.752 55.000 0.00 0.00 35.03 4.04
148 149 1.131126 CAATAACTTGGCGAGGTGCTG 59.869 52.381 1.45 0.00 45.43 4.41
150 151 0.613260 TAACTTGGCGAGGTGCTGAT 59.387 50.000 1.45 0.00 45.43 2.90
165 166 2.119495 GCTGATAAAGGAGGGAGGTCA 58.881 52.381 0.00 0.00 0.00 4.02
181 182 3.496331 AGGTCAACTTGGTACCATTTGG 58.504 45.455 25.70 15.79 42.17 3.28
182 183 2.560981 GGTCAACTTGGTACCATTTGGG 59.439 50.000 25.70 13.20 44.81 4.12
193 194 2.519013 ACCATTTGGGAGAAGTCTTGC 58.481 47.619 0.96 0.00 41.15 4.01
230 232 2.437651 GGGAATGAAGAGAGGAGAAGGG 59.562 54.545 0.00 0.00 0.00 3.95
240 242 1.228510 GGAGAAGGGCCAATGAGGG 59.771 63.158 6.18 0.00 38.09 4.30
260 262 4.129148 GGGGGAGGGATGGTGCAC 62.129 72.222 8.80 8.80 0.00 4.57
261 263 4.129148 GGGGAGGGATGGTGCACC 62.129 72.222 29.67 29.67 0.00 5.01
263 265 3.717294 GGAGGGATGGTGCACCGT 61.717 66.667 30.75 30.75 39.43 4.83
269 271 3.049674 ATGGTGCACCGTCAAGCG 61.050 61.111 30.07 0.00 39.43 4.68
300 302 0.320771 CCTGCGTGTGGTAGAAGCTT 60.321 55.000 0.00 0.00 0.00 3.74
301 303 1.071605 CTGCGTGTGGTAGAAGCTTC 58.928 55.000 19.11 19.11 0.00 3.86
305 318 2.159085 GCGTGTGGTAGAAGCTTCCTAT 60.159 50.000 22.81 7.39 0.00 2.57
309 322 6.281405 CGTGTGGTAGAAGCTTCCTATTAAT 58.719 40.000 22.81 5.11 0.00 1.40
315 328 8.764558 TGGTAGAAGCTTCCTATTAATTGTACA 58.235 33.333 22.81 0.00 0.00 2.90
319 332 9.740710 AGAAGCTTCCTATTAATTGTACAACTT 57.259 29.630 22.81 9.12 0.00 2.66
342 355 9.838339 ACTTTAGTTAGTATATGATGCAGCTTT 57.162 29.630 2.53 0.00 0.00 3.51
374 387 9.859152 AACTTTAGTTAGTATATACTCCCTCGT 57.141 33.333 18.68 10.46 37.73 4.18
377 390 8.854614 TTAGTTAGTATATACTCCCTCGTTCC 57.145 38.462 18.68 0.00 37.73 3.62
378 391 7.089106 AGTTAGTATATACTCCCTCGTTCCT 57.911 40.000 18.68 1.22 37.73 3.36
379 392 8.212259 AGTTAGTATATACTCCCTCGTTCCTA 57.788 38.462 18.68 0.00 37.73 2.94
380 393 8.664079 AGTTAGTATATACTCCCTCGTTCCTAA 58.336 37.037 18.68 0.89 37.73 2.69
381 394 9.289782 GTTAGTATATACTCCCTCGTTCCTAAA 57.710 37.037 18.68 0.70 37.73 1.85
388 401 6.309389 ACTCCCTCGTTCCTAAATATTTGT 57.691 37.500 11.05 0.00 0.00 2.83
389 402 6.346896 ACTCCCTCGTTCCTAAATATTTGTC 58.653 40.000 11.05 0.00 0.00 3.18
390 403 6.156429 ACTCCCTCGTTCCTAAATATTTGTCT 59.844 38.462 11.05 0.00 0.00 3.41
391 404 6.954232 TCCCTCGTTCCTAAATATTTGTCTT 58.046 36.000 11.05 0.00 0.00 3.01
392 405 7.399634 TCCCTCGTTCCTAAATATTTGTCTTT 58.600 34.615 11.05 0.00 0.00 2.52
393 406 7.551617 TCCCTCGTTCCTAAATATTTGTCTTTC 59.448 37.037 11.05 0.00 0.00 2.62
394 407 7.553044 CCCTCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
395 408 9.595823 CCTCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
410 423 9.793259 TTTGTCTTTCTAGATATTTCAACCAGT 57.207 29.630 0.00 0.00 31.86 4.00
411 424 8.777865 TGTCTTTCTAGATATTTCAACCAGTG 57.222 34.615 0.00 0.00 31.86 3.66
412 425 8.593679 TGTCTTTCTAGATATTTCAACCAGTGA 58.406 33.333 0.00 0.00 31.86 3.41
413 426 8.874816 GTCTTTCTAGATATTTCAACCAGTGAC 58.125 37.037 0.00 0.00 31.82 3.67
414 427 8.816894 TCTTTCTAGATATTTCAACCAGTGACT 58.183 33.333 0.00 0.00 35.39 3.41
416 429 9.871238 TTTCTAGATATTTCAACCAGTGACTAC 57.129 33.333 0.00 0.00 35.39 2.73
417 430 8.589701 TCTAGATATTTCAACCAGTGACTACA 57.410 34.615 0.00 0.00 35.39 2.74
418 431 9.201989 TCTAGATATTTCAACCAGTGACTACAT 57.798 33.333 0.00 0.00 35.39 2.29
421 434 7.921214 AGATATTTCAACCAGTGACTACATACG 59.079 37.037 0.00 0.00 35.39 3.06
422 435 3.861276 TCAACCAGTGACTACATACGG 57.139 47.619 0.00 0.00 0.00 4.02
423 436 3.423749 TCAACCAGTGACTACATACGGA 58.576 45.455 0.00 0.00 0.00 4.69
424 437 3.442625 TCAACCAGTGACTACATACGGAG 59.557 47.826 0.00 0.00 0.00 4.63
425 438 1.749634 ACCAGTGACTACATACGGAGC 59.250 52.381 0.00 0.00 0.00 4.70
426 439 1.749063 CCAGTGACTACATACGGAGCA 59.251 52.381 0.00 0.00 0.00 4.26
427 440 2.165641 CCAGTGACTACATACGGAGCAA 59.834 50.000 0.00 0.00 0.00 3.91
428 441 3.368013 CCAGTGACTACATACGGAGCAAA 60.368 47.826 0.00 0.00 0.00 3.68
429 442 4.242475 CAGTGACTACATACGGAGCAAAA 58.758 43.478 0.00 0.00 0.00 2.44
430 443 4.870426 CAGTGACTACATACGGAGCAAAAT 59.130 41.667 0.00 0.00 0.00 1.82
431 444 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
432 445 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
433 446 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
434 447 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
435 448 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
436 449 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
437 450 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
438 451 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
439 452 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
440 453 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
441 454 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
442 455 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
443 456 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
444 457 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
477 490 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
479 492 8.502105 TGTCTATATACATCCGTATGTGGTAG 57.498 38.462 3.56 3.93 45.99 3.18
480 493 8.105197 TGTCTATATACATCCGTATGTGGTAGT 58.895 37.037 3.56 0.00 45.99 2.73
481 494 8.610896 GTCTATATACATCCGTATGTGGTAGTC 58.389 40.741 3.56 0.00 45.99 2.59
482 495 6.770746 ATATACATCCGTATGTGGTAGTCC 57.229 41.667 3.56 0.00 45.99 3.85
483 496 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
484 497 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
485 498 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
486 499 4.163458 ACATCCGTATGTGGTAGTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
487 500 4.131649 TCCGTATGTGGTAGTCCATTTG 57.868 45.455 0.00 0.00 46.20 2.32
488 501 3.770388 TCCGTATGTGGTAGTCCATTTGA 59.230 43.478 0.00 0.00 46.20 2.69
489 502 4.223255 TCCGTATGTGGTAGTCCATTTGAA 59.777 41.667 0.00 0.00 46.20 2.69
490 503 4.938832 CCGTATGTGGTAGTCCATTTGAAA 59.061 41.667 0.00 0.00 46.20 2.69
491 504 5.588648 CCGTATGTGGTAGTCCATTTGAAAT 59.411 40.000 0.00 0.00 46.20 2.17
492 505 6.238374 CCGTATGTGGTAGTCCATTTGAAATC 60.238 42.308 0.00 0.00 46.20 2.17
493 506 6.538742 CGTATGTGGTAGTCCATTTGAAATCT 59.461 38.462 0.00 0.00 46.20 2.40
494 507 7.709182 CGTATGTGGTAGTCCATTTGAAATCTA 59.291 37.037 0.00 0.00 46.20 1.98
495 508 9.561069 GTATGTGGTAGTCCATTTGAAATCTAT 57.439 33.333 0.00 0.00 46.20 1.98
498 511 9.967451 TGTGGTAGTCCATTTGAAATCTATAAA 57.033 29.630 0.00 0.00 46.20 1.40
529 542 7.504926 AATATTTAAGGGTGTGTCTAGGTCA 57.495 36.000 0.00 0.00 0.00 4.02
530 543 4.612264 TTTAAGGGTGTGTCTAGGTCAC 57.388 45.455 10.54 10.54 36.48 3.67
531 544 2.097110 AAGGGTGTGTCTAGGTCACA 57.903 50.000 14.43 14.43 42.41 3.58
532 545 2.327325 AGGGTGTGTCTAGGTCACAT 57.673 50.000 18.98 6.43 45.43 3.21
533 546 2.180276 AGGGTGTGTCTAGGTCACATC 58.820 52.381 18.98 18.33 45.43 3.06
534 547 2.180276 GGGTGTGTCTAGGTCACATCT 58.820 52.381 21.95 0.00 45.43 2.90
535 548 3.011369 AGGGTGTGTCTAGGTCACATCTA 59.989 47.826 21.95 3.73 45.43 1.98
536 549 3.381908 GGGTGTGTCTAGGTCACATCTAG 59.618 52.174 21.95 0.00 45.43 2.43
537 550 4.270834 GGTGTGTCTAGGTCACATCTAGA 58.729 47.826 18.98 0.00 45.43 2.43
538 551 4.890581 GGTGTGTCTAGGTCACATCTAGAT 59.109 45.833 18.98 0.00 45.43 1.98
539 552 5.221145 GGTGTGTCTAGGTCACATCTAGATG 60.221 48.000 27.63 27.63 45.43 2.90
564 577 6.878317 TGCTCTAGTTATTGCACATCTAAGT 58.122 36.000 0.00 0.00 0.00 2.24
565 578 6.758416 TGCTCTAGTTATTGCACATCTAAGTG 59.242 38.462 0.00 0.00 42.37 3.16
566 579 6.980978 GCTCTAGTTATTGCACATCTAAGTGA 59.019 38.462 0.00 0.00 42.05 3.41
567 580 7.168972 GCTCTAGTTATTGCACATCTAAGTGAG 59.831 40.741 0.00 0.00 42.05 3.51
568 581 8.067751 TCTAGTTATTGCACATCTAAGTGAGT 57.932 34.615 0.00 0.00 42.05 3.41
569 582 6.974932 AGTTATTGCACATCTAAGTGAGTG 57.025 37.500 0.00 0.00 42.05 3.51
570 583 6.701340 AGTTATTGCACATCTAAGTGAGTGA 58.299 36.000 0.00 0.00 42.05 3.41
571 584 7.161404 AGTTATTGCACATCTAAGTGAGTGAA 58.839 34.615 0.00 0.00 42.05 3.18
572 585 7.826252 AGTTATTGCACATCTAAGTGAGTGAAT 59.174 33.333 0.00 0.00 42.05 2.57
573 586 6.674694 ATTGCACATCTAAGTGAGTGAATC 57.325 37.500 0.00 0.00 42.05 2.52
574 587 5.151297 TGCACATCTAAGTGAGTGAATCA 57.849 39.130 0.00 0.00 42.05 2.57
575 588 5.550290 TGCACATCTAAGTGAGTGAATCAA 58.450 37.500 0.00 0.00 42.05 2.57
576 589 5.640783 TGCACATCTAAGTGAGTGAATCAAG 59.359 40.000 0.00 0.00 42.05 3.02
577 590 5.447010 GCACATCTAAGTGAGTGAATCAAGC 60.447 44.000 0.00 0.00 42.05 4.01
578 591 5.640783 CACATCTAAGTGAGTGAATCAAGCA 59.359 40.000 0.00 0.00 42.05 3.91
579 592 6.315642 CACATCTAAGTGAGTGAATCAAGCAT 59.684 38.462 0.00 0.00 42.05 3.79
580 593 7.493645 CACATCTAAGTGAGTGAATCAAGCATA 59.506 37.037 0.00 0.00 42.05 3.14
581 594 8.043113 ACATCTAAGTGAGTGAATCAAGCATAA 58.957 33.333 0.00 0.00 40.43 1.90
582 595 8.886719 CATCTAAGTGAGTGAATCAAGCATAAA 58.113 33.333 0.00 0.00 40.43 1.40
583 596 8.484641 TCTAAGTGAGTGAATCAAGCATAAAG 57.515 34.615 0.00 0.00 40.43 1.85
584 597 8.314021 TCTAAGTGAGTGAATCAAGCATAAAGA 58.686 33.333 0.00 0.00 40.43 2.52
585 598 6.981762 AGTGAGTGAATCAAGCATAAAGAG 57.018 37.500 0.00 0.00 40.43 2.85
586 599 6.705302 AGTGAGTGAATCAAGCATAAAGAGA 58.295 36.000 0.00 0.00 40.43 3.10
587 600 7.164122 AGTGAGTGAATCAAGCATAAAGAGAA 58.836 34.615 0.00 0.00 40.43 2.87
588 601 7.663081 AGTGAGTGAATCAAGCATAAAGAGAAA 59.337 33.333 0.00 0.00 40.43 2.52
589 602 8.292448 GTGAGTGAATCAAGCATAAAGAGAAAA 58.708 33.333 0.00 0.00 40.43 2.29
590 603 8.849168 TGAGTGAATCAAGCATAAAGAGAAAAA 58.151 29.630 0.00 0.00 34.02 1.94
626 639 9.388506 AGAAAATATTCAGACGAATCTCAATGT 57.611 29.630 0.00 0.00 41.09 2.71
632 645 7.993821 TTCAGACGAATCTCAATGTAAGATC 57.006 36.000 0.00 0.00 32.29 2.75
633 646 7.100458 TCAGACGAATCTCAATGTAAGATCA 57.900 36.000 0.00 0.00 32.29 2.92
634 647 7.547227 TCAGACGAATCTCAATGTAAGATCAA 58.453 34.615 0.00 0.00 32.29 2.57
635 648 8.200120 TCAGACGAATCTCAATGTAAGATCAAT 58.800 33.333 0.00 0.00 32.29 2.57
636 649 8.274248 CAGACGAATCTCAATGTAAGATCAATG 58.726 37.037 0.00 0.00 32.29 2.82
637 650 8.200120 AGACGAATCTCAATGTAAGATCAATGA 58.800 33.333 0.00 0.00 32.29 2.57
638 651 8.136057 ACGAATCTCAATGTAAGATCAATGAC 57.864 34.615 0.00 0.00 32.29 3.06
639 652 7.765819 ACGAATCTCAATGTAAGATCAATGACA 59.234 33.333 0.00 0.00 32.29 3.58
640 653 8.771766 CGAATCTCAATGTAAGATCAATGACAT 58.228 33.333 0.00 0.00 32.29 3.06
644 657 9.498176 TCTCAATGTAAGATCAATGACATATGG 57.502 33.333 7.80 0.00 32.31 2.74
645 658 8.102800 TCAATGTAAGATCAATGACATATGGC 57.897 34.615 7.80 4.20 32.31 4.40
646 659 7.940688 TCAATGTAAGATCAATGACATATGGCT 59.059 33.333 10.60 0.00 32.31 4.75
647 660 8.573885 CAATGTAAGATCAATGACATATGGCTT 58.426 33.333 10.60 0.00 32.31 4.35
648 661 9.797642 AATGTAAGATCAATGACATATGGCTTA 57.202 29.630 10.60 0.00 32.31 3.09
649 662 8.837788 TGTAAGATCAATGACATATGGCTTAG 57.162 34.615 10.60 0.00 0.00 2.18
650 663 8.650490 TGTAAGATCAATGACATATGGCTTAGA 58.350 33.333 10.60 5.04 0.00 2.10
651 664 9.664332 GTAAGATCAATGACATATGGCTTAGAT 57.336 33.333 10.60 9.70 0.00 1.98
652 665 8.563123 AAGATCAATGACATATGGCTTAGATG 57.437 34.615 10.60 0.00 34.19 2.90
653 666 7.687388 AGATCAATGACATATGGCTTAGATGT 58.313 34.615 10.60 5.90 43.56 3.06
654 667 7.606839 AGATCAATGACATATGGCTTAGATGTG 59.393 37.037 10.60 0.00 41.09 3.21
655 668 5.471116 TCAATGACATATGGCTTAGATGTGC 59.529 40.000 10.60 0.00 41.09 4.57
656 669 4.420522 TGACATATGGCTTAGATGTGCA 57.579 40.909 10.60 0.00 41.09 4.57
657 670 4.779696 TGACATATGGCTTAGATGTGCAA 58.220 39.130 10.60 0.00 41.09 4.08
658 671 5.379187 TGACATATGGCTTAGATGTGCAAT 58.621 37.500 10.60 0.00 41.09 3.56
659 672 6.532826 TGACATATGGCTTAGATGTGCAATA 58.467 36.000 10.60 0.00 41.09 1.90
660 673 6.427853 TGACATATGGCTTAGATGTGCAATAC 59.572 38.462 10.60 0.00 41.09 1.89
661 674 6.537355 ACATATGGCTTAGATGTGCAATACT 58.463 36.000 7.80 0.00 39.63 2.12
662 675 7.000472 ACATATGGCTTAGATGTGCAATACTT 59.000 34.615 7.80 0.00 39.63 2.24
663 676 8.156820 ACATATGGCTTAGATGTGCAATACTTA 58.843 33.333 7.80 0.00 39.63 2.24
664 677 9.170734 CATATGGCTTAGATGTGCAATACTTAT 57.829 33.333 0.00 0.00 29.08 1.73
665 678 6.866010 TGGCTTAGATGTGCAATACTTATG 57.134 37.500 0.00 0.00 0.00 1.90
666 679 5.764686 TGGCTTAGATGTGCAATACTTATGG 59.235 40.000 0.00 0.00 0.00 2.74
667 680 5.335191 GGCTTAGATGTGCAATACTTATGGC 60.335 44.000 0.00 0.00 33.16 4.40
668 681 5.239306 GCTTAGATGTGCAATACTTATGGCA 59.761 40.000 0.00 0.00 40.19 4.92
750 763 7.568267 AGAGTAACGTATCATGCATAAATCG 57.432 36.000 0.00 5.46 0.00 3.34
807 820 1.352017 TGATGCCCACACTTCACAGAT 59.648 47.619 0.00 0.00 0.00 2.90
941 955 5.024555 GCTCGTGCTCAACTATTTTTCATC 58.975 41.667 1.41 0.00 36.03 2.92
1150 1174 1.227674 GGTGCATCATCGGTCCTCC 60.228 63.158 0.00 0.00 0.00 4.30
1156 1180 3.917760 CATCGGTCCTCCTCGGCC 61.918 72.222 0.00 0.00 0.00 6.13
1265 1289 0.736325 CAGGGAGGTAAGCAACGACG 60.736 60.000 0.00 0.00 0.00 5.12
1266 1290 1.183676 AGGGAGGTAAGCAACGACGT 61.184 55.000 0.00 0.00 0.00 4.34
1267 1291 0.735287 GGGAGGTAAGCAACGACGTC 60.735 60.000 5.18 5.18 0.00 4.34
1268 1292 0.735287 GGAGGTAAGCAACGACGTCC 60.735 60.000 10.58 0.00 41.80 4.79
1269 1293 0.038892 GAGGTAAGCAACGACGTCCA 60.039 55.000 10.58 0.00 0.00 4.02
1270 1294 0.038526 AGGTAAGCAACGACGTCCAG 60.039 55.000 10.58 0.00 0.00 3.86
1271 1295 1.623973 GGTAAGCAACGACGTCCAGC 61.624 60.000 10.58 11.49 0.00 4.85
1272 1296 0.942410 GTAAGCAACGACGTCCAGCA 60.942 55.000 19.44 2.03 0.00 4.41
1273 1297 0.666274 TAAGCAACGACGTCCAGCAG 60.666 55.000 19.44 5.28 0.00 4.24
1274 1298 4.077188 GCAACGACGTCCAGCAGC 62.077 66.667 10.58 3.72 0.00 5.25
1275 1299 3.414700 CAACGACGTCCAGCAGCC 61.415 66.667 10.58 0.00 0.00 4.85
1279 1303 4.803426 GACGTCCAGCAGCCGGAG 62.803 72.222 5.05 0.00 31.65 4.63
1490 1535 1.448013 GAAGAAAGAGGACCCGCCG 60.448 63.158 0.00 0.00 43.43 6.46
1545 1590 4.634133 TGGTCGGCGTCGTGACAC 62.634 66.667 10.18 0.00 36.83 3.67
1657 1702 3.491267 GGAACGAAATCATCATCGACCTC 59.509 47.826 1.84 0.00 41.43 3.85
1659 1704 2.695666 ACGAAATCATCATCGACCTCCT 59.304 45.455 1.84 0.00 41.43 3.69
1662 1707 1.346062 ATCATCATCGACCTCCTGGG 58.654 55.000 0.00 0.00 41.89 4.45
1707 1752 2.700773 GGCCAATCGTGACCAAGCC 61.701 63.158 0.00 0.00 0.00 4.35
1708 1753 1.971167 GCCAATCGTGACCAAGCCA 60.971 57.895 0.00 0.00 0.00 4.75
1709 1754 1.926511 GCCAATCGTGACCAAGCCAG 61.927 60.000 0.00 0.00 0.00 4.85
1736 1781 4.329545 GACAGCCTGGGCCGAACA 62.330 66.667 8.11 0.00 43.17 3.18
1746 1791 1.675641 GGCCGAACAAGCAGGATGT 60.676 57.895 0.00 0.00 39.31 3.06
1749 1794 0.798776 CCGAACAAGCAGGATGTCAC 59.201 55.000 0.00 0.00 39.31 3.67
1761 1806 2.463589 GATGTCACCCAAGCCGACCA 62.464 60.000 0.00 0.00 0.00 4.02
1882 1927 3.804193 CTTTCCAAGAGCCCGCGC 61.804 66.667 0.00 0.00 0.00 6.86
2044 2089 1.372748 GGAGGAGATGATCAGCGCG 60.373 63.158 8.62 0.00 0.00 6.86
2186 2231 1.743252 GCCAGGCCGTGAAAGAGAG 60.743 63.158 0.00 0.00 0.00 3.20
2233 2278 0.757935 ATGCAGCAATGGTGGATCCC 60.758 55.000 13.54 0.00 37.53 3.85
2256 2301 2.979678 TCCTATCCTTACCATTGCTCCC 59.020 50.000 0.00 0.00 0.00 4.30
2360 2405 0.610232 GCAACCCTCCTGCACTGATT 60.610 55.000 0.00 0.00 39.69 2.57
2489 2534 1.333931 GATGATGGTGTGATGCTGCTG 59.666 52.381 0.00 0.00 0.00 4.41
2490 2535 1.310216 TGATGGTGTGATGCTGCTGC 61.310 55.000 8.89 8.89 40.20 5.25
2491 2536 1.001269 ATGGTGTGATGCTGCTGCT 60.001 52.632 17.00 2.26 40.48 4.24
2601 2695 0.034337 GTAACCGTCACTGGAAGCCA 59.966 55.000 0.00 0.00 37.60 4.75
2657 2772 5.106436 TGCATGCAGTGAACTAATTGAAGAG 60.106 40.000 18.46 0.00 0.00 2.85
2689 3017 3.060363 CCATTTCTACTGTTGTACGCGAC 59.940 47.826 15.93 7.50 0.00 5.19
2690 3018 1.954437 TTCTACTGTTGTACGCGACG 58.046 50.000 15.93 0.00 0.00 5.12
2692 3020 1.400990 CTACTGTTGTACGCGACGGC 61.401 60.000 15.93 4.40 38.64 5.68
2712 3040 1.458020 TACCCCATCCATACGGCGT 60.458 57.895 19.64 19.64 0.00 5.68
2755 3083 2.180017 GCGACGGCGGTCTCTTTA 59.820 61.111 15.06 0.00 41.16 1.85
2757 3085 0.804933 GCGACGGCGGTCTCTTTATT 60.805 55.000 15.06 0.00 41.16 1.40
2758 3086 0.921347 CGACGGCGGTCTCTTTATTG 59.079 55.000 20.54 0.70 41.16 1.90
2760 3088 1.659098 GACGGCGGTCTCTTTATTGTG 59.341 52.381 16.52 0.00 40.15 3.33
2763 3091 2.093783 CGGCGGTCTCTTTATTGTGTTC 59.906 50.000 0.00 0.00 0.00 3.18
2764 3092 2.418976 GGCGGTCTCTTTATTGTGTTCC 59.581 50.000 0.00 0.00 0.00 3.62
2855 3183 2.992689 TTGGTAGGCCGAGACGCA 60.993 61.111 0.00 0.00 37.67 5.24
2856 3184 3.001902 TTGGTAGGCCGAGACGCAG 62.002 63.158 0.00 0.00 37.67 5.18
3167 3739 1.005294 GATGCTGTTTGCCGCTGTTG 61.005 55.000 0.00 0.00 42.00 3.33
3217 3789 4.057432 CAACTGAATTTGGCCGTGATTTT 58.943 39.130 0.00 0.00 0.00 1.82
3226 3798 1.268539 GGCCGTGATTTTATTCCTGCG 60.269 52.381 0.00 0.00 0.00 5.18
3242 3814 2.673368 CCTGCGAGGAAGAACACATTAC 59.327 50.000 0.00 0.00 37.67 1.89
3243 3815 2.673368 CTGCGAGGAAGAACACATTACC 59.327 50.000 0.00 0.00 0.00 2.85
3251 3823 3.928727 AGAACACATTACCGAGAACGA 57.071 42.857 0.00 0.00 42.66 3.85
3259 3831 2.427232 TACCGAGAACGAAACACAGG 57.573 50.000 0.00 0.00 42.66 4.00
3291 3863 1.227147 GGTACAGCTTATCGCCGCA 60.227 57.895 0.00 0.00 40.39 5.69
3303 3875 4.980903 GCCGCACCGCACACTTTG 62.981 66.667 0.00 0.00 0.00 2.77
3311 3883 2.804856 GCACACTTTGCCCACGTT 59.195 55.556 0.00 0.00 46.63 3.99
3312 3884 1.299089 GCACACTTTGCCCACGTTC 60.299 57.895 0.00 0.00 46.63 3.95
3313 3885 1.999071 GCACACTTTGCCCACGTTCA 61.999 55.000 0.00 0.00 46.63 3.18
3314 3886 0.248458 CACACTTTGCCCACGTTCAC 60.248 55.000 0.00 0.00 0.00 3.18
3315 3887 1.010125 CACTTTGCCCACGTTCACG 60.010 57.895 0.00 0.00 46.33 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 3.065371 GCGACCTTCTGTATCCCAAAATG 59.935 47.826 0.00 0.00 0.00 2.32
56 57 1.069978 CCAAACCAAAATGGCGACCTT 59.930 47.619 0.00 0.00 42.67 3.50
58 59 0.320334 CCCAAACCAAAATGGCGACC 60.320 55.000 0.00 0.00 42.67 4.79
62 63 2.928801 AACTCCCAAACCAAAATGGC 57.071 45.000 0.00 0.00 42.67 4.40
76 77 5.106515 GCCAGTCTAAATCAGTTGAAACTCC 60.107 44.000 0.00 0.00 37.08 3.85
95 96 0.333993 AAGATCCATTGCCAGCCAGT 59.666 50.000 0.00 0.00 0.00 4.00
103 104 2.079925 GATAGCGGGAAGATCCATTGC 58.920 52.381 0.00 0.00 38.64 3.56
126 127 1.130561 GCACCTCGCCAAGTTATTGAC 59.869 52.381 0.00 0.00 38.83 3.18
148 149 4.518249 CAAGTTGACCTCCCTCCTTTATC 58.482 47.826 0.00 0.00 0.00 1.75
150 151 2.642807 CCAAGTTGACCTCCCTCCTTTA 59.357 50.000 3.87 0.00 0.00 1.85
165 166 4.141018 ACTTCTCCCAAATGGTACCAAGTT 60.141 41.667 20.76 13.42 34.77 2.66
181 182 3.126831 CCATCATACGCAAGACTTCTCC 58.873 50.000 0.00 0.00 43.62 3.71
182 183 4.046938 TCCATCATACGCAAGACTTCTC 57.953 45.455 0.00 0.00 43.62 2.87
193 194 1.179174 TCCCGGCTCTCCATCATACG 61.179 60.000 0.00 0.00 0.00 3.06
243 245 4.129148 GTGCACCATCCCTCCCCC 62.129 72.222 5.22 0.00 0.00 5.40
248 250 2.469465 CTTGACGGTGCACCATCCCT 62.469 60.000 34.16 11.43 35.14 4.20
249 251 2.033448 TTGACGGTGCACCATCCC 59.967 61.111 34.16 19.41 35.14 3.85
250 252 2.690778 GCTTGACGGTGCACCATCC 61.691 63.158 34.16 21.79 35.14 3.51
273 275 2.549282 CACACGCAGGTACGTTGC 59.451 61.111 10.10 10.10 45.75 4.17
274 276 0.318869 TACCACACGCAGGTACGTTG 60.319 55.000 0.00 0.00 45.75 4.10
275 277 0.038892 CTACCACACGCAGGTACGTT 60.039 55.000 0.00 0.00 45.75 3.99
278 280 1.992170 CTTCTACCACACGCAGGTAC 58.008 55.000 0.00 0.00 40.54 3.34
281 283 0.320771 AAGCTTCTACCACACGCAGG 60.321 55.000 0.00 0.00 0.00 4.85
282 284 1.071605 GAAGCTTCTACCACACGCAG 58.928 55.000 19.44 0.00 0.00 5.18
283 285 0.320421 GGAAGCTTCTACCACACGCA 60.320 55.000 25.05 0.00 0.00 5.24
284 286 0.037232 AGGAAGCTTCTACCACACGC 60.037 55.000 25.05 5.98 0.00 5.34
289 291 8.764558 TGTACAATTAATAGGAAGCTTCTACCA 58.235 33.333 25.05 9.01 0.00 3.25
315 328 9.838339 AAGCTGCATCATATACTAACTAAAGTT 57.162 29.630 1.02 0.39 41.73 2.66
325 338 9.784531 AGTTGTATTAAAGCTGCATCATATACT 57.215 29.630 1.02 0.00 0.00 2.12
366 379 6.583562 AGACAAATATTTAGGAACGAGGGAG 58.416 40.000 0.00 0.00 0.00 4.30
367 380 6.555463 AGACAAATATTTAGGAACGAGGGA 57.445 37.500 0.00 0.00 0.00 4.20
368 381 7.553044 AGAAAGACAAATATTTAGGAACGAGGG 59.447 37.037 0.00 0.00 0.00 4.30
369 382 8.494016 AGAAAGACAAATATTTAGGAACGAGG 57.506 34.615 0.00 0.00 0.00 4.63
384 397 9.793259 ACTGGTTGAAATATCTAGAAAGACAAA 57.207 29.630 0.00 0.00 33.57 2.83
386 399 8.593679 TCACTGGTTGAAATATCTAGAAAGACA 58.406 33.333 0.00 0.00 33.57 3.41
387 400 8.874816 GTCACTGGTTGAAATATCTAGAAAGAC 58.125 37.037 0.00 0.00 35.39 3.01
388 401 8.816894 AGTCACTGGTTGAAATATCTAGAAAGA 58.183 33.333 0.00 0.00 35.39 2.52
390 403 9.871238 GTAGTCACTGGTTGAAATATCTAGAAA 57.129 33.333 0.00 0.00 35.39 2.52
391 404 9.031537 TGTAGTCACTGGTTGAAATATCTAGAA 57.968 33.333 0.00 0.00 35.39 2.10
392 405 8.589701 TGTAGTCACTGGTTGAAATATCTAGA 57.410 34.615 0.00 0.00 35.39 2.43
395 408 7.921214 CGTATGTAGTCACTGGTTGAAATATCT 59.079 37.037 0.00 0.00 35.39 1.98
396 409 7.169308 CCGTATGTAGTCACTGGTTGAAATATC 59.831 40.741 0.00 0.00 35.39 1.63
397 410 6.984474 CCGTATGTAGTCACTGGTTGAAATAT 59.016 38.462 0.00 0.00 35.39 1.28
398 411 6.153170 TCCGTATGTAGTCACTGGTTGAAATA 59.847 38.462 0.00 0.00 35.39 1.40
399 412 5.046878 TCCGTATGTAGTCACTGGTTGAAAT 60.047 40.000 0.00 0.00 35.39 2.17
400 413 4.281435 TCCGTATGTAGTCACTGGTTGAAA 59.719 41.667 0.00 0.00 35.39 2.69
401 414 3.827876 TCCGTATGTAGTCACTGGTTGAA 59.172 43.478 0.00 0.00 35.39 2.69
402 415 3.423749 TCCGTATGTAGTCACTGGTTGA 58.576 45.455 0.00 0.00 0.00 3.18
403 416 3.770666 CTCCGTATGTAGTCACTGGTTG 58.229 50.000 0.00 0.00 0.00 3.77
404 417 2.165845 GCTCCGTATGTAGTCACTGGTT 59.834 50.000 0.00 0.00 0.00 3.67
405 418 1.749634 GCTCCGTATGTAGTCACTGGT 59.250 52.381 0.00 0.00 0.00 4.00
406 419 1.749063 TGCTCCGTATGTAGTCACTGG 59.251 52.381 0.00 0.00 0.00 4.00
407 420 3.503827 TTGCTCCGTATGTAGTCACTG 57.496 47.619 0.00 0.00 0.00 3.66
408 421 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
409 422 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
410 423 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
411 424 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
412 425 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
413 426 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
414 427 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
415 428 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
416 429 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
417 430 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
418 431 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
419 432 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
420 433 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
421 434 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
422 435 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
423 436 7.516198 AAAGTGTAGATTCACTCATTTTGCT 57.484 32.000 0.00 0.00 46.25 3.91
424 437 9.677567 TTTAAAGTGTAGATTCACTCATTTTGC 57.322 29.630 0.00 0.00 46.25 3.68
451 464 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
453 466 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
454 467 8.105197 ACTACCACATACGGATGTATATAGACA 58.895 37.037 22.62 2.07 44.82 3.41
455 468 8.503458 ACTACCACATACGGATGTATATAGAC 57.497 38.462 22.62 0.00 44.82 2.59
456 469 7.772292 GGACTACCACATACGGATGTATATAGA 59.228 40.741 22.62 5.04 44.82 1.98
457 470 7.555195 TGGACTACCACATACGGATGTATATAG 59.445 40.741 14.23 16.35 44.82 1.31
458 471 7.404481 TGGACTACCACATACGGATGTATATA 58.596 38.462 14.23 5.36 44.82 0.86
459 472 6.250711 TGGACTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
460 473 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
461 474 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
462 475 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
503 516 9.049050 TGACCTAGACACACCCTTAAATATTTA 57.951 33.333 3.71 3.71 0.00 1.40
504 517 7.827729 GTGACCTAGACACACCCTTAAATATTT 59.172 37.037 5.89 5.89 38.05 1.40
505 518 7.037873 TGTGACCTAGACACACCCTTAAATATT 60.038 37.037 15.22 0.00 42.20 1.28
506 519 6.442564 TGTGACCTAGACACACCCTTAAATAT 59.557 38.462 15.22 0.00 42.20 1.28
507 520 5.781306 TGTGACCTAGACACACCCTTAAATA 59.219 40.000 15.22 0.00 42.20 1.40
508 521 4.595781 TGTGACCTAGACACACCCTTAAAT 59.404 41.667 15.22 0.00 42.20 1.40
509 522 3.968649 TGTGACCTAGACACACCCTTAAA 59.031 43.478 15.22 0.00 42.20 1.52
510 523 3.578978 TGTGACCTAGACACACCCTTAA 58.421 45.455 15.22 0.00 42.20 1.85
511 524 3.247948 TGTGACCTAGACACACCCTTA 57.752 47.619 15.22 0.00 42.20 2.69
512 525 2.097110 TGTGACCTAGACACACCCTT 57.903 50.000 15.22 0.00 42.20 3.95
513 526 3.863120 TGTGACCTAGACACACCCT 57.137 52.632 15.22 0.00 42.20 4.34
540 553 6.758416 CACTTAGATGTGCAATAACTAGAGCA 59.242 38.462 0.00 0.00 34.10 4.26
541 554 6.980978 TCACTTAGATGTGCAATAACTAGAGC 59.019 38.462 0.00 0.00 37.81 4.09
542 555 8.194104 ACTCACTTAGATGTGCAATAACTAGAG 58.806 37.037 0.00 0.00 37.81 2.43
543 556 7.976175 CACTCACTTAGATGTGCAATAACTAGA 59.024 37.037 0.00 0.00 37.81 2.43
544 557 7.976175 TCACTCACTTAGATGTGCAATAACTAG 59.024 37.037 0.00 0.00 37.81 2.57
545 558 7.836842 TCACTCACTTAGATGTGCAATAACTA 58.163 34.615 0.00 0.00 37.81 2.24
546 559 6.701340 TCACTCACTTAGATGTGCAATAACT 58.299 36.000 0.00 0.00 37.81 2.24
547 560 6.968131 TCACTCACTTAGATGTGCAATAAC 57.032 37.500 0.00 0.00 37.81 1.89
548 561 7.823799 TGATTCACTCACTTAGATGTGCAATAA 59.176 33.333 0.00 0.00 37.81 1.40
549 562 7.330262 TGATTCACTCACTTAGATGTGCAATA 58.670 34.615 0.00 0.00 37.81 1.90
550 563 6.175471 TGATTCACTCACTTAGATGTGCAAT 58.825 36.000 0.00 0.00 37.81 3.56
551 564 5.550290 TGATTCACTCACTTAGATGTGCAA 58.450 37.500 0.00 0.00 37.81 4.08
552 565 5.151297 TGATTCACTCACTTAGATGTGCA 57.849 39.130 0.00 0.00 37.81 4.57
553 566 5.447010 GCTTGATTCACTCACTTAGATGTGC 60.447 44.000 0.00 0.00 37.81 4.57
554 567 5.640783 TGCTTGATTCACTCACTTAGATGTG 59.359 40.000 0.00 0.00 39.15 3.21
555 568 5.798132 TGCTTGATTCACTCACTTAGATGT 58.202 37.500 0.00 0.00 32.17 3.06
556 569 6.922247 ATGCTTGATTCACTCACTTAGATG 57.078 37.500 0.00 0.00 32.17 2.90
557 570 9.107177 CTTTATGCTTGATTCACTCACTTAGAT 57.893 33.333 0.00 0.00 32.17 1.98
558 571 8.314021 TCTTTATGCTTGATTCACTCACTTAGA 58.686 33.333 0.00 0.00 32.17 2.10
559 572 8.484641 TCTTTATGCTTGATTCACTCACTTAG 57.515 34.615 0.00 0.00 32.17 2.18
560 573 8.314021 TCTCTTTATGCTTGATTCACTCACTTA 58.686 33.333 0.00 0.00 32.17 2.24
561 574 7.164122 TCTCTTTATGCTTGATTCACTCACTT 58.836 34.615 0.00 0.00 32.17 3.16
562 575 6.705302 TCTCTTTATGCTTGATTCACTCACT 58.295 36.000 0.00 0.00 32.17 3.41
563 576 6.974932 TCTCTTTATGCTTGATTCACTCAC 57.025 37.500 0.00 0.00 32.17 3.51
564 577 7.984422 TTTCTCTTTATGCTTGATTCACTCA 57.016 32.000 0.00 0.00 0.00 3.41
600 613 9.388506 ACATTGAGATTCGTCTGAATATTTTCT 57.611 29.630 0.00 0.00 44.79 2.52
606 619 9.684448 GATCTTACATTGAGATTCGTCTGAATA 57.316 33.333 0.00 0.00 44.79 1.75
608 621 7.547227 TGATCTTACATTGAGATTCGTCTGAA 58.453 34.615 0.00 0.00 38.76 3.02
609 622 7.100458 TGATCTTACATTGAGATTCGTCTGA 57.900 36.000 0.00 0.00 34.13 3.27
610 623 7.761651 TTGATCTTACATTGAGATTCGTCTG 57.238 36.000 0.00 0.00 34.13 3.51
611 624 8.200120 TCATTGATCTTACATTGAGATTCGTCT 58.800 33.333 0.00 0.00 34.13 4.18
612 625 8.272176 GTCATTGATCTTACATTGAGATTCGTC 58.728 37.037 0.00 0.00 34.13 4.20
613 626 7.765819 TGTCATTGATCTTACATTGAGATTCGT 59.234 33.333 0.00 0.00 34.13 3.85
614 627 8.134905 TGTCATTGATCTTACATTGAGATTCG 57.865 34.615 0.00 0.00 34.13 3.34
618 631 9.498176 CCATATGTCATTGATCTTACATTGAGA 57.502 33.333 1.24 0.00 34.54 3.27
619 632 8.235226 GCCATATGTCATTGATCTTACATTGAG 58.765 37.037 1.24 0.00 34.54 3.02
620 633 7.940688 AGCCATATGTCATTGATCTTACATTGA 59.059 33.333 1.24 0.00 34.54 2.57
621 634 8.107399 AGCCATATGTCATTGATCTTACATTG 57.893 34.615 1.24 0.00 34.54 2.82
622 635 8.701908 AAGCCATATGTCATTGATCTTACATT 57.298 30.769 1.24 0.00 34.54 2.71
623 636 9.445878 CTAAGCCATATGTCATTGATCTTACAT 57.554 33.333 1.24 1.62 36.56 2.29
624 637 8.650490 TCTAAGCCATATGTCATTGATCTTACA 58.350 33.333 1.24 0.00 0.00 2.41
625 638 9.664332 ATCTAAGCCATATGTCATTGATCTTAC 57.336 33.333 1.24 0.00 0.00 2.34
626 639 9.662947 CATCTAAGCCATATGTCATTGATCTTA 57.337 33.333 1.24 1.82 0.00 2.10
627 640 8.162085 ACATCTAAGCCATATGTCATTGATCTT 58.838 33.333 1.24 0.89 0.00 2.40
628 641 7.606839 CACATCTAAGCCATATGTCATTGATCT 59.393 37.037 1.24 0.00 31.60 2.75
629 642 7.625817 GCACATCTAAGCCATATGTCATTGATC 60.626 40.741 1.24 0.00 31.60 2.92
630 643 6.150641 GCACATCTAAGCCATATGTCATTGAT 59.849 38.462 1.24 0.00 31.60 2.57
631 644 5.471116 GCACATCTAAGCCATATGTCATTGA 59.529 40.000 1.24 0.00 31.60 2.57
632 645 5.239963 TGCACATCTAAGCCATATGTCATTG 59.760 40.000 1.24 0.00 31.60 2.82
633 646 5.379187 TGCACATCTAAGCCATATGTCATT 58.621 37.500 1.24 0.00 31.60 2.57
634 647 4.976864 TGCACATCTAAGCCATATGTCAT 58.023 39.130 1.24 0.00 31.60 3.06
635 648 4.420522 TGCACATCTAAGCCATATGTCA 57.579 40.909 1.24 0.00 31.60 3.58
636 649 5.954296 ATTGCACATCTAAGCCATATGTC 57.046 39.130 1.24 0.00 31.60 3.06
637 650 6.537355 AGTATTGCACATCTAAGCCATATGT 58.463 36.000 1.24 0.00 34.22 2.29
638 651 7.444629 AAGTATTGCACATCTAAGCCATATG 57.555 36.000 0.00 0.00 0.00 1.78
639 652 9.170734 CATAAGTATTGCACATCTAAGCCATAT 57.829 33.333 0.00 0.00 0.00 1.78
640 653 7.607607 CCATAAGTATTGCACATCTAAGCCATA 59.392 37.037 0.00 0.00 0.00 2.74
641 654 6.432162 CCATAAGTATTGCACATCTAAGCCAT 59.568 38.462 0.00 0.00 0.00 4.40
642 655 5.764686 CCATAAGTATTGCACATCTAAGCCA 59.235 40.000 0.00 0.00 0.00 4.75
643 656 5.335191 GCCATAAGTATTGCACATCTAAGCC 60.335 44.000 0.00 0.00 0.00 4.35
644 657 5.239306 TGCCATAAGTATTGCACATCTAAGC 59.761 40.000 0.00 0.00 30.49 3.09
645 658 6.866010 TGCCATAAGTATTGCACATCTAAG 57.134 37.500 0.00 0.00 30.49 2.18
653 666 6.173427 TCTAGATGTGCCATAAGTATTGCA 57.827 37.500 0.00 0.00 32.69 4.08
654 667 7.069852 CATCTAGATGTGCCATAAGTATTGC 57.930 40.000 22.42 0.00 34.23 3.56
721 734 8.710835 TTATGCATGATACGTTACTCTTTTCA 57.289 30.769 10.16 0.00 0.00 2.69
734 747 5.615544 GCCACACTCGATTTATGCATGATAC 60.616 44.000 10.16 0.00 0.00 2.24
750 763 4.626081 ACACCTGGCGCCACACTC 62.626 66.667 29.03 0.00 0.00 3.51
807 820 2.705658 TGAGGCTCCTTTTGTCTCTTCA 59.294 45.455 12.86 0.00 0.00 3.02
919 933 6.414408 AGATGAAAAATAGTTGAGCACGAG 57.586 37.500 0.00 0.00 0.00 4.18
941 955 0.547712 TGGACCAGGGAGGAAAGGAG 60.548 60.000 0.00 0.00 41.22 3.69
1244 1268 0.320374 TCGTTGCTTACCTCCCTGTG 59.680 55.000 0.00 0.00 0.00 3.66
1299 1344 3.934391 GACTCCTTGGTCGGCGTGG 62.934 68.421 6.85 3.14 0.00 4.94
1545 1590 1.959899 GCCGTCACTCTTGATGCACG 61.960 60.000 0.00 0.00 37.43 5.34
1635 1680 3.458189 AGGTCGATGATGATTTCGTTCC 58.542 45.455 0.00 0.00 36.74 3.62
1736 1781 0.610232 GCTTGGGTGACATCCTGCTT 60.610 55.000 6.25 0.00 0.00 3.91
1746 1791 4.308458 CGTGGTCGGCTTGGGTGA 62.308 66.667 0.00 0.00 0.00 4.02
2044 2089 3.567797 GCGTCCTGGATGCGCTTC 61.568 66.667 23.93 14.55 46.55 3.86
2215 2260 1.380246 GGGATCCACCATTGCTGCA 60.380 57.895 15.23 0.00 41.20 4.41
2216 2261 1.380246 TGGGATCCACCATTGCTGC 60.380 57.895 15.23 0.00 41.20 5.25
2233 2278 4.566488 GGGAGCAATGGTAAGGATAGGATG 60.566 50.000 0.00 0.00 0.00 3.51
2340 2385 2.809861 ATCAGTGCAGGAGGGTTGCG 62.810 60.000 0.00 0.00 44.40 4.85
2360 2405 0.804364 GAGATCACCAACGCATGCAA 59.196 50.000 19.57 0.00 0.00 4.08
2368 2413 7.668052 ACTCTACTCTATATGGAGATCACCAAC 59.332 40.741 21.71 0.00 43.47 3.77
2436 2481 1.593196 TCCAGCAAAGAAGAACCACG 58.407 50.000 0.00 0.00 0.00 4.94
2491 2536 0.250252 TGTGGCGCTCAAGACATTGA 60.250 50.000 7.64 0.00 43.20 2.57
2561 2618 7.437748 GTTACTATCTTACTGGCATGATCACT 58.562 38.462 0.00 0.00 0.00 3.41
2601 2695 3.769739 TTCATGCCAGTAACAGTGACT 57.230 42.857 0.00 0.00 0.00 3.41
2637 2752 4.645535 AGCTCTTCAATTAGTTCACTGCA 58.354 39.130 0.00 0.00 0.00 4.41
2638 2753 5.180117 TCAAGCTCTTCAATTAGTTCACTGC 59.820 40.000 0.00 0.00 0.00 4.40
2639 2754 6.620303 GCTCAAGCTCTTCAATTAGTTCACTG 60.620 42.308 0.00 0.00 38.21 3.66
2641 2756 5.391416 GGCTCAAGCTCTTCAATTAGTTCAC 60.391 44.000 1.46 0.00 41.70 3.18
2642 2757 4.697352 GGCTCAAGCTCTTCAATTAGTTCA 59.303 41.667 1.46 0.00 41.70 3.18
2643 2758 4.940654 AGGCTCAAGCTCTTCAATTAGTTC 59.059 41.667 1.46 0.00 41.70 3.01
2652 2767 2.416680 AATGGAGGCTCAAGCTCTTC 57.583 50.000 17.69 0.00 41.70 2.87
2657 2772 2.941720 CAGTAGAAATGGAGGCTCAAGC 59.058 50.000 17.69 0.00 41.14 4.01
2689 3017 1.005394 GTATGGATGGGGTACGCCG 60.005 63.158 22.64 0.00 42.25 6.46
2690 3018 1.005394 CGTATGGATGGGGTACGCC 60.005 63.158 21.62 21.62 42.25 5.68
2692 3020 1.005394 GCCGTATGGATGGGGTACG 60.005 63.158 4.73 0.00 40.47 3.67
2697 3025 0.950555 CATGACGCCGTATGGATGGG 60.951 60.000 4.73 0.00 37.49 4.00
2712 3040 1.137675 CTCTCCGCCTTCATGTCATGA 59.862 52.381 11.62 11.62 37.55 3.07
2743 3071 2.418976 GGAACACAATAAAGAGACCGCC 59.581 50.000 0.00 0.00 0.00 6.13
2746 3074 3.353557 GGGGGAACACAATAAAGAGACC 58.646 50.000 0.00 0.00 0.00 3.85
2764 3092 0.967380 GAGCATTCAACACCAGGGGG 60.967 60.000 0.00 0.00 41.29 5.40
2841 3169 4.874977 GCCTGCGTCTCGGCCTAC 62.875 72.222 0.00 0.00 40.43 3.18
2879 3444 0.603975 AGAAGCTTTCCTCGTGTGCC 60.604 55.000 0.00 0.00 0.00 5.01
2884 3449 3.489229 GCAAAACAAGAAGCTTTCCTCGT 60.489 43.478 0.00 0.00 0.00 4.18
2885 3450 3.045688 GCAAAACAAGAAGCTTTCCTCG 58.954 45.455 0.00 0.00 0.00 4.63
3045 3610 6.371809 TCTGTTGTGTTGTGTTCTTATTCC 57.628 37.500 0.00 0.00 0.00 3.01
3104 3674 3.591835 AAACACGGGCGGTTGCTG 61.592 61.111 0.00 0.00 42.25 4.41
3167 3739 2.615447 TGATGAATCGCATGCTCCTTTC 59.385 45.455 17.13 12.82 37.34 2.62
3226 3798 4.451629 TCTCGGTAATGTGTTCTTCCTC 57.548 45.455 0.00 0.00 0.00 3.71
3242 3814 0.600255 AGCCTGTGTTTCGTTCTCGG 60.600 55.000 0.00 0.00 37.69 4.63
3243 3815 1.070577 CAAGCCTGTGTTTCGTTCTCG 60.071 52.381 0.00 0.00 38.55 4.04
3251 3823 2.427095 GACCTTTGTCAAGCCTGTGTTT 59.573 45.455 0.00 0.00 41.37 2.83
3259 3831 1.798813 CTGTACCGACCTTTGTCAAGC 59.201 52.381 0.00 0.00 41.85 4.01
3296 3868 1.711060 CGTGAACGTGGGCAAAGTGT 61.711 55.000 0.00 0.00 34.11 3.55


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

AutoCloner maintained by Alex Coulton.