Multiple sequence alignment - TraesCS7D01G184500

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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 TraesCS7D01G184500 chr7D 100.000 3167 0 0 1 3167 138040121 138036955 0.000000e+00 5849.0
1 TraesCS7D01G184500 chr7D 94.749 1352 54 11 992 2337 138086854 138085514 0.000000e+00 2087.0
2 TraesCS7D01G184500 chr7D 83.395 271 16 12 316 583 2047138 2047382 1.140000e-54 224.0
3 TraesCS7D01G184500 chr7A 92.352 2079 95 28 578 2621 138013041 138010992 0.000000e+00 2900.0
4 TraesCS7D01G184500 chr7A 88.421 570 40 5 1 554 91624053 91624612 0.000000e+00 664.0
5 TraesCS7D01G184500 chr7A 87.372 586 47 7 1 569 696016527 696017102 0.000000e+00 647.0
6 TraesCS7D01G184500 chr7A 86.018 565 49 20 1 563 118334235 118334771 2.120000e-161 579.0
7 TraesCS7D01G184500 chr7A 90.520 327 27 4 1 326 74137398 74137721 2.260000e-116 429.0
8 TraesCS7D01G184500 chr7A 90.476 147 13 1 408 554 80566547 80566402 3.220000e-45 193.0
9 TraesCS7D01G184500 chr5D 82.339 872 144 8 1290 2153 319138339 319137470 0.000000e+00 749.0
10 TraesCS7D01G184500 chr5D 87.209 516 66 0 1290 1805 318933840 318933325 3.520000e-164 588.0
11 TraesCS7D01G184500 chr5D 86.434 516 70 0 1290 1805 326904106 326904621 1.650000e-157 566.0
12 TraesCS7D01G184500 chr5D 84.375 576 57 16 1 552 438335989 438336555 4.650000e-148 534.0
13 TraesCS7D01G184500 chr5D 87.466 367 42 2 1803 2167 318933235 318932871 1.360000e-113 420.0
14 TraesCS7D01G184500 chr5D 84.483 348 52 2 1800 2146 326904727 326905073 3.020000e-90 342.0
15 TraesCS7D01G184500 chr5D 87.023 131 9 4 2338 2465 451008163 451008288 1.180000e-29 141.0
16 TraesCS7D01G184500 chr5D 86.765 68 9 0 1018 1085 326903743 326903810 3.390000e-10 76.8
17 TraesCS7D01G184500 chr5B 80.941 871 158 7 1290 2153 369154200 369153331 0.000000e+00 682.0
18 TraesCS7D01G184500 chr5B 87.984 516 62 0 1290 1805 368786738 368786223 7.510000e-171 610.0
19 TraesCS7D01G184500 chr5B 86.649 367 45 2 1803 2167 368786131 368785767 1.370000e-108 403.0
20 TraesCS7D01G184500 chr5B 84.438 347 54 0 1800 2146 379597886 379598232 3.020000e-90 342.0
21 TraesCS7D01G184500 chr5B 87.023 131 9 4 2338 2465 551227465 551227590 1.180000e-29 141.0
22 TraesCS7D01G184500 chr5B 90.000 60 6 0 1026 1085 379596902 379596961 9.420000e-11 78.7
23 TraesCS7D01G184500 chr7B 83.796 685 70 19 2251 2904 103509496 103508822 2.090000e-171 612.0
24 TraesCS7D01G184500 chr7B 90.741 54 1 4 2322 2373 606730424 606730475 5.670000e-08 69.4
25 TraesCS7D01G184500 chr5A 87.403 516 65 0 1290 1805 415430856 415431371 7.560000e-166 593.0
26 TraesCS7D01G184500 chr5A 86.628 516 69 0 1290 1805 429656739 429656224 3.540000e-159 571.0
27 TraesCS7D01G184500 chr5A 88.081 344 41 0 1803 2146 415431441 415431784 2.940000e-110 409.0
28 TraesCS7D01G184500 chr5A 88.172 93 9 2 395 487 677165983 677166073 3.340000e-20 110.0
29 TraesCS7D01G184500 chr5A 86.441 59 8 0 1027 1085 429657096 429657038 7.330000e-07 65.8
30 TraesCS7D01G184500 chrUn 86.225 559 56 11 1 554 95314186 95314728 1.270000e-163 586.0
31 TraesCS7D01G184500 chrUn 87.597 129 7 7 2341 2465 328115666 328115543 1.180000e-29 141.0
32 TraesCS7D01G184500 chr3D 84.500 600 39 22 1 554 501792164 501791573 7.730000e-151 544.0
33 TraesCS7D01G184500 chr4A 83.705 583 55 22 1 554 259778540 259779111 6.060000e-142 514.0
34 TraesCS7D01G184500 chr4A 87.586 145 13 2 408 552 32097072 32096933 2.530000e-36 163.0
35 TraesCS7D01G184500 chr6A 83.779 561 67 14 1 553 26733052 26733596 7.840000e-141 510.0
36 TraesCS7D01G184500 chr6A 89.116 147 16 0 408 554 360611343 360611489 1.940000e-42 183.0
37 TraesCS7D01G184500 chr2A 93.060 317 22 0 1 317 59719941 59720257 6.190000e-127 464.0
38 TraesCS7D01G184500 chr2D 88.718 390 27 11 1 381 375356573 375356192 8.000000e-126 460.0
39 TraesCS7D01G184500 chr2D 84.211 76 9 3 2326 2399 20186026 20185952 1.580000e-08 71.3
40 TraesCS7D01G184500 chr1D 88.974 390 20 12 1 381 468133254 468133629 8.000000e-126 460.0
41 TraesCS7D01G184500 chr1D 88.387 155 12 3 409 563 405279564 405279416 6.980000e-42 182.0
42 TraesCS7D01G184500 chr1D 84.298 121 11 4 2348 2465 52325825 52325710 9.290000e-21 111.0
43 TraesCS7D01G184500 chr3A 88.542 384 33 7 1 381 670553865 670554240 3.720000e-124 455.0
44 TraesCS7D01G184500 chr3A 83.568 213 26 7 359 568 26047628 26047834 1.160000e-44 191.0
45 TraesCS7D01G184500 chr3A 86.364 66 6 3 2326 2390 706444700 706444637 5.670000e-08 69.4
46 TraesCS7D01G184500 chr1B 84.167 120 10 5 2350 2465 77624660 77624546 1.200000e-19 108.0
47 TraesCS7D01G184500 chr1B 83.333 78 11 2 2355 2430 390382394 390382317 1.580000e-08 71.3
48 TraesCS7D01G184500 chr1B 100.000 32 0 0 2434 2465 112339561 112339530 3.410000e-05 60.2
49 TraesCS7D01G184500 chr4B 79.012 162 16 13 2320 2466 546251703 546251861 9.350000e-16 95.3
50 TraesCS7D01G184500 chr6B 87.671 73 3 4 2394 2465 655866229 655866296 2.620000e-11 80.5
51 TraesCS7D01G184500 chr3B 86.364 66 6 3 2326 2390 367052717 367052654 5.670000e-08 69.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G184500 chr7D 138036955 138040121 3166 True 5849.000000 5849 100.0000 1 3167 1 chr7D.!!$R1 3166
1 TraesCS7D01G184500 chr7D 138085514 138086854 1340 True 2087.000000 2087 94.7490 992 2337 1 chr7D.!!$R2 1345
2 TraesCS7D01G184500 chr7A 138010992 138013041 2049 True 2900.000000 2900 92.3520 578 2621 1 chr7A.!!$R2 2043
3 TraesCS7D01G184500 chr7A 91624053 91624612 559 False 664.000000 664 88.4210 1 554 1 chr7A.!!$F2 553
4 TraesCS7D01G184500 chr7A 696016527 696017102 575 False 647.000000 647 87.3720 1 569 1 chr7A.!!$F4 568
5 TraesCS7D01G184500 chr7A 118334235 118334771 536 False 579.000000 579 86.0180 1 563 1 chr7A.!!$F3 562
6 TraesCS7D01G184500 chr5D 319137470 319138339 869 True 749.000000 749 82.3390 1290 2153 1 chr5D.!!$R1 863
7 TraesCS7D01G184500 chr5D 438335989 438336555 566 False 534.000000 534 84.3750 1 552 1 chr5D.!!$F1 551
8 TraesCS7D01G184500 chr5D 318932871 318933840 969 True 504.000000 588 87.3375 1290 2167 2 chr5D.!!$R2 877
9 TraesCS7D01G184500 chr5D 326903743 326905073 1330 False 328.266667 566 85.8940 1018 2146 3 chr5D.!!$F3 1128
10 TraesCS7D01G184500 chr5B 369153331 369154200 869 True 682.000000 682 80.9410 1290 2153 1 chr5B.!!$R1 863
11 TraesCS7D01G184500 chr5B 368785767 368786738 971 True 506.500000 610 87.3165 1290 2167 2 chr5B.!!$R2 877
12 TraesCS7D01G184500 chr5B 379596902 379598232 1330 False 210.350000 342 87.2190 1026 2146 2 chr5B.!!$F2 1120
13 TraesCS7D01G184500 chr7B 103508822 103509496 674 True 612.000000 612 83.7960 2251 2904 1 chr7B.!!$R1 653
14 TraesCS7D01G184500 chr5A 415430856 415431784 928 False 501.000000 593 87.7420 1290 2146 2 chr5A.!!$F2 856
15 TraesCS7D01G184500 chr5A 429656224 429657096 872 True 318.400000 571 86.5345 1027 1805 2 chr5A.!!$R1 778
16 TraesCS7D01G184500 chrUn 95314186 95314728 542 False 586.000000 586 86.2250 1 554 1 chrUn.!!$F1 553
17 TraesCS7D01G184500 chr3D 501791573 501792164 591 True 544.000000 544 84.5000 1 554 1 chr3D.!!$R1 553
18 TraesCS7D01G184500 chr4A 259778540 259779111 571 False 514.000000 514 83.7050 1 554 1 chr4A.!!$F1 553
19 TraesCS7D01G184500 chr6A 26733052 26733596 544 False 510.000000 510 83.7790 1 553 1 chr6A.!!$F1 552

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
239 244 0.037605 CGGTTCCTTGACGCCTACTT 60.038 55.0 0.00 0.00 0.00 2.24 F
563 585 0.179163 GATTTTTAGCTTGCGCGGCT 60.179 50.0 26.09 26.09 42.32 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2049 2443 0.526211 CCATCTTGACGACCTCGACA 59.474 55.000 0.78 0.0 43.02 4.35 R
2203 2597 1.802508 CGTGCCGATGACTGCTTCATA 60.803 52.381 1.82 0.0 45.67 2.15 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
182 187 2.855963 CGGTCGCTAAATACAACATCGT 59.144 45.455 0.00 0.00 0.00 3.73
238 243 1.590147 CGGTTCCTTGACGCCTACT 59.410 57.895 0.00 0.00 0.00 2.57
239 244 0.037605 CGGTTCCTTGACGCCTACTT 60.038 55.000 0.00 0.00 0.00 2.24
246 251 2.230508 CCTTGACGCCTACTTACAGACA 59.769 50.000 0.00 0.00 0.00 3.41
268 273 1.433879 GACGAGGACATCACCGAGG 59.566 63.158 0.00 0.00 34.73 4.63
280 285 4.200283 CCGAGGCAGAGTCCGAGC 62.200 72.222 0.00 0.00 0.00 5.03
297 302 2.479656 CGAGCCGGATGAGTAGTACTAC 59.520 54.545 23.03 23.03 36.35 2.73
303 308 5.747675 GCCGGATGAGTAGTACTACTTTTTC 59.252 44.000 31.14 25.29 45.63 2.29
342 363 1.882989 AAGCAGGCAGAGTCCGAGTC 61.883 60.000 0.00 0.00 0.00 3.36
343 364 2.640302 GCAGGCAGAGTCCGAGTCA 61.640 63.158 6.01 0.00 0.00 3.41
364 386 8.911918 AGTCAGACGAACTATGAACTATCTAT 57.088 34.615 0.00 0.00 0.00 1.98
366 388 8.775527 GTCAGACGAACTATGAACTATCTATCA 58.224 37.037 0.00 0.00 0.00 2.15
449 471 4.663636 AACAGATAAAATATAGCGCGCC 57.336 40.909 30.33 10.31 0.00 6.53
452 474 2.673368 AGATAAAATATAGCGCGCCTGC 59.327 45.455 30.33 0.00 37.91 4.85
466 488 4.463879 CTGCTGGAGTGGCTCGGG 62.464 72.222 0.00 0.00 0.00 5.14
523 545 2.175811 GCCGTGCGTAAAAGCTGG 59.824 61.111 0.00 0.00 38.13 4.85
524 546 2.175811 CCGTGCGTAAAAGCTGGC 59.824 61.111 0.00 0.00 38.13 4.85
525 547 2.325082 CCGTGCGTAAAAGCTGGCT 61.325 57.895 0.00 0.00 38.13 4.75
526 548 1.017177 CCGTGCGTAAAAGCTGGCTA 61.017 55.000 0.00 0.00 38.13 3.93
527 549 0.793861 CGTGCGTAAAAGCTGGCTAA 59.206 50.000 0.00 0.00 38.13 3.09
528 550 1.396996 CGTGCGTAAAAGCTGGCTAAT 59.603 47.619 0.00 0.00 38.13 1.73
529 551 2.536928 CGTGCGTAAAAGCTGGCTAATC 60.537 50.000 0.00 0.00 38.13 1.75
530 552 2.014128 TGCGTAAAAGCTGGCTAATCC 58.986 47.619 0.00 0.00 38.13 3.01
531 553 1.003866 GCGTAAAAGCTGGCTAATCCG 60.004 52.381 0.00 0.00 37.80 4.18
532 554 1.597663 CGTAAAAGCTGGCTAATCCGG 59.402 52.381 0.00 0.00 44.43 5.14
537 559 2.969238 CTGGCTAATCCGGCGCTG 60.969 66.667 9.96 9.96 37.80 5.18
538 560 3.740128 CTGGCTAATCCGGCGCTGT 62.740 63.158 16.49 0.00 37.80 4.40
539 561 2.363711 CTGGCTAATCCGGCGCTGTA 62.364 60.000 16.49 0.00 37.80 2.74
540 562 1.004918 GGCTAATCCGGCGCTGTAT 60.005 57.895 16.49 0.76 0.00 2.29
541 563 0.602905 GGCTAATCCGGCGCTGTATT 60.603 55.000 16.49 14.07 0.00 1.89
542 564 0.790814 GCTAATCCGGCGCTGTATTC 59.209 55.000 16.49 0.00 0.00 1.75
543 565 1.605712 GCTAATCCGGCGCTGTATTCT 60.606 52.381 16.49 0.00 0.00 2.40
544 566 2.061773 CTAATCCGGCGCTGTATTCTG 58.938 52.381 16.49 4.42 0.00 3.02
545 567 0.464036 AATCCGGCGCTGTATTCTGA 59.536 50.000 16.49 4.12 0.00 3.27
546 568 0.681733 ATCCGGCGCTGTATTCTGAT 59.318 50.000 16.49 6.53 0.00 2.90
547 569 0.464036 TCCGGCGCTGTATTCTGATT 59.536 50.000 16.49 0.00 0.00 2.57
548 570 1.134521 TCCGGCGCTGTATTCTGATTT 60.135 47.619 16.49 0.00 0.00 2.17
549 571 1.670811 CCGGCGCTGTATTCTGATTTT 59.329 47.619 16.49 0.00 0.00 1.82
550 572 2.097466 CCGGCGCTGTATTCTGATTTTT 59.903 45.455 16.49 0.00 0.00 1.94
551 573 3.311322 CCGGCGCTGTATTCTGATTTTTA 59.689 43.478 16.49 0.00 0.00 1.52
552 574 4.518217 CGGCGCTGTATTCTGATTTTTAG 58.482 43.478 8.45 0.00 0.00 1.85
553 575 4.282873 GGCGCTGTATTCTGATTTTTAGC 58.717 43.478 7.64 0.00 0.00 3.09
554 576 4.035675 GGCGCTGTATTCTGATTTTTAGCT 59.964 41.667 7.64 0.00 0.00 3.32
555 577 5.449177 GGCGCTGTATTCTGATTTTTAGCTT 60.449 40.000 7.64 0.00 0.00 3.74
556 578 5.453587 GCGCTGTATTCTGATTTTTAGCTTG 59.546 40.000 0.00 0.00 0.00 4.01
557 579 5.453587 CGCTGTATTCTGATTTTTAGCTTGC 59.546 40.000 0.00 0.00 0.00 4.01
558 580 5.453587 GCTGTATTCTGATTTTTAGCTTGCG 59.546 40.000 0.00 0.00 0.00 4.85
559 581 5.331902 TGTATTCTGATTTTTAGCTTGCGC 58.668 37.500 0.00 0.00 0.00 6.09
560 582 2.525750 TCTGATTTTTAGCTTGCGCG 57.474 45.000 0.00 0.00 42.32 6.86
561 583 1.130373 TCTGATTTTTAGCTTGCGCGG 59.870 47.619 8.83 0.00 42.32 6.46
562 584 0.455972 TGATTTTTAGCTTGCGCGGC 60.456 50.000 8.83 15.77 42.32 6.53
563 585 0.179163 GATTTTTAGCTTGCGCGGCT 60.179 50.000 26.09 26.09 42.32 5.52
564 586 0.456653 ATTTTTAGCTTGCGCGGCTG 60.457 50.000 29.30 10.46 42.32 4.85
565 587 1.791103 TTTTTAGCTTGCGCGGCTGT 61.791 50.000 29.30 13.17 42.32 4.40
566 588 1.791103 TTTTAGCTTGCGCGGCTGTT 61.791 50.000 29.30 12.57 42.32 3.16
567 589 2.456594 TTTAGCTTGCGCGGCTGTTG 62.457 55.000 29.30 5.95 42.32 3.33
570 592 4.093952 CTTGCGCGGCTGTTGGAG 62.094 66.667 8.83 0.00 0.00 3.86
571 593 4.617520 TTGCGCGGCTGTTGGAGA 62.618 61.111 8.83 0.00 0.00 3.71
572 594 3.899981 TTGCGCGGCTGTTGGAGAT 62.900 57.895 8.83 0.00 0.00 2.75
573 595 2.202878 GCGCGGCTGTTGGAGATA 60.203 61.111 8.83 0.00 0.00 1.98
574 596 1.595382 GCGCGGCTGTTGGAGATAT 60.595 57.895 8.83 0.00 0.00 1.63
575 597 1.160329 GCGCGGCTGTTGGAGATATT 61.160 55.000 8.83 0.00 0.00 1.28
576 598 0.861837 CGCGGCTGTTGGAGATATTC 59.138 55.000 0.00 0.00 0.00 1.75
621 643 1.727880 TGAAATAAGTACGCGTGCCAC 59.272 47.619 24.59 12.81 0.00 5.01
638 660 2.439409 CCACTGCATGAGATGGTTTGA 58.561 47.619 0.00 0.00 0.00 2.69
751 776 2.815647 GGCCTACAGCACTGCGTC 60.816 66.667 0.00 0.00 46.50 5.19
761 786 2.480037 CAGCACTGCGTCTGTTAAATCA 59.520 45.455 0.00 0.00 0.00 2.57
775 800 8.500773 GTCTGTTAAATCATTCTTCACGGTTTA 58.499 33.333 0.00 0.00 0.00 2.01
776 801 9.058174 TCTGTTAAATCATTCTTCACGGTTTAA 57.942 29.630 0.00 0.00 0.00 1.52
810 835 1.140852 CAAGTCGCCCCATATCCTTCA 59.859 52.381 0.00 0.00 0.00 3.02
832 857 5.538053 TCAGCCATTTCCATTTGAGTGTTTA 59.462 36.000 0.00 0.00 0.00 2.01
1205 1239 1.268794 GGAGGACGATGTGACGATCAG 60.269 57.143 0.00 0.00 37.03 2.90
1355 1488 3.121030 CTTCAAGGCCGGCGACAG 61.121 66.667 22.54 10.51 0.00 3.51
1463 1602 3.716006 CTGCAACGGCGTGGACTG 61.716 66.667 20.56 12.12 45.35 3.51
1698 1838 3.291383 TTCGGCAAGGCGTTTGGG 61.291 61.111 15.62 0.00 37.26 4.12
1782 1922 0.679505 CCGACAACTTCCTGGTCAGA 59.320 55.000 0.00 0.00 0.00 3.27
1794 1934 2.050714 GTCAGACACGACGCCGAA 60.051 61.111 0.00 0.00 39.50 4.30
1806 2059 4.941609 GCCGAAGAGATGAAGGCA 57.058 55.556 0.00 0.00 46.48 4.75
2203 2597 0.037232 GCTTGGCTCGGTTACTCACT 60.037 55.000 0.00 0.00 0.00 3.41
2219 2613 3.181482 ACTCACTATGAAGCAGTCATCGG 60.181 47.826 6.21 4.58 44.01 4.18
2376 2782 6.658816 ACCTTATTTATCTCAACATGCACACA 59.341 34.615 0.00 0.00 0.00 3.72
2392 2798 4.154556 TGCACACATGTCACATTATCACTG 59.845 41.667 0.00 0.00 0.00 3.66
2405 2812 2.398252 ATCACTGTGCCACTCATCAG 57.602 50.000 2.12 0.00 33.21 2.90
2428 2835 7.891183 TCAGCCCCACTACATTTATTTCTTTTA 59.109 33.333 0.00 0.00 0.00 1.52
2429 2836 8.527810 CAGCCCCACTACATTTATTTCTTTTAA 58.472 33.333 0.00 0.00 0.00 1.52
2430 2837 9.267071 AGCCCCACTACATTTATTTCTTTTAAT 57.733 29.630 0.00 0.00 0.00 1.40
2480 2893 7.428020 ACCTATACTAGAGTCGCTATATCTCG 58.572 42.308 0.00 0.00 33.96 4.04
2491 2904 4.579340 TCGCTATATCTCGGTTGACTCTTT 59.421 41.667 0.00 0.00 0.00 2.52
2584 3011 7.445096 TCTTTCTTTCTTGCATGTTATGTCTGA 59.555 33.333 0.00 0.00 0.00 3.27
2616 3043 1.206610 TCGACTGAGACCTAGCTACGT 59.793 52.381 0.00 0.00 0.00 3.57
2621 3048 3.199508 ACTGAGACCTAGCTACGTCCTAA 59.800 47.826 16.39 5.00 0.00 2.69
2622 3049 3.806380 TGAGACCTAGCTACGTCCTAAG 58.194 50.000 16.39 0.00 0.00 2.18
2623 3050 3.140623 GAGACCTAGCTACGTCCTAAGG 58.859 54.545 16.39 6.34 0.00 2.69
2624 3051 2.158638 AGACCTAGCTACGTCCTAAGGG 60.159 54.545 16.39 4.19 0.00 3.95
2626 3053 1.955080 CCTAGCTACGTCCTAAGGGTG 59.045 57.143 0.00 0.00 0.00 4.61
2627 3054 2.652590 CTAGCTACGTCCTAAGGGTGT 58.347 52.381 0.00 0.00 0.00 4.16
2628 3055 1.472188 AGCTACGTCCTAAGGGTGTC 58.528 55.000 0.00 0.00 0.00 3.67
2629 3056 0.100146 GCTACGTCCTAAGGGTGTCG 59.900 60.000 0.00 0.00 0.00 4.35
2630 3057 1.457346 CTACGTCCTAAGGGTGTCGT 58.543 55.000 0.00 0.00 38.27 4.34
2631 3058 2.632377 CTACGTCCTAAGGGTGTCGTA 58.368 52.381 0.00 0.00 37.05 3.43
2632 3059 2.134789 ACGTCCTAAGGGTGTCGTAT 57.865 50.000 0.00 0.00 35.45 3.06
2633 3060 3.281727 ACGTCCTAAGGGTGTCGTATA 57.718 47.619 0.00 0.00 35.45 1.47
2635 3062 3.118261 ACGTCCTAAGGGTGTCGTATAGA 60.118 47.826 0.00 0.00 35.45 1.98
2649 3088 4.023021 GTCGTATAGAAGGCTAGGTCAAGG 60.023 50.000 0.00 0.00 0.00 3.61
2667 3106 6.597672 GGTCAAGGGAACAAAAGAAACAAAAT 59.402 34.615 0.00 0.00 0.00 1.82
2671 3110 5.942826 AGGGAACAAAAGAAACAAAATTGCA 59.057 32.000 0.00 0.00 0.00 4.08
2698 3137 7.976734 AGTTAGCTGGCGATATATAGTTTGATC 59.023 37.037 0.00 0.00 0.00 2.92
2699 3138 6.537453 AGCTGGCGATATATAGTTTGATCT 57.463 37.500 0.00 0.00 0.00 2.75
2712 3151 7.876936 ATAGTTTGATCTCATTCACAAGCAT 57.123 32.000 0.00 0.00 0.00 3.79
2713 3152 5.950883 AGTTTGATCTCATTCACAAGCATG 58.049 37.500 0.00 0.00 0.00 4.06
2714 3153 4.976224 TTGATCTCATTCACAAGCATGG 57.024 40.909 0.00 0.00 0.00 3.66
2723 3162 1.304381 ACAAGCATGGCCGTTGGAT 60.304 52.632 0.00 0.00 0.00 3.41
2725 3164 2.114670 AAGCATGGCCGTTGGATCG 61.115 57.895 0.00 0.00 0.00 3.69
2740 3179 0.731514 GATCGAAACTCACGCCGTGA 60.732 55.000 20.04 20.04 40.50 4.35
2763 3202 1.069022 CATGTTGTGGCCTCAAGAACG 60.069 52.381 20.22 11.01 0.00 3.95
2776 3215 0.165079 AAGAACGTTTGTATGCGGCG 59.835 50.000 0.46 0.51 0.00 6.46
2798 3237 3.194062 CATGTTGGCCTGTTTTCGTTTT 58.806 40.909 3.32 0.00 0.00 2.43
2800 3239 1.849829 GTTGGCCTGTTTTCGTTTTCG 59.150 47.619 3.32 0.00 45.64 3.46
2824 3263 1.675641 AGCGCATGTTTCAGGGTCC 60.676 57.895 11.47 0.00 0.00 4.46
2827 3266 1.361668 CGCATGTTTCAGGGTCCGAG 61.362 60.000 0.00 0.00 0.00 4.63
2830 3269 1.550524 CATGTTTCAGGGTCCGAGAGA 59.449 52.381 0.00 0.00 0.00 3.10
2866 3305 3.483922 CAGCGAGACTAGCTTTTGTATCG 59.516 47.826 19.52 19.52 46.43 2.92
2868 3307 2.789893 CGAGACTAGCTTTTGTATCGCC 59.210 50.000 14.66 0.00 40.16 5.54
2873 3312 4.770795 ACTAGCTTTTGTATCGCCTGAAT 58.229 39.130 0.00 0.00 0.00 2.57
2874 3313 5.186198 ACTAGCTTTTGTATCGCCTGAATT 58.814 37.500 0.00 0.00 0.00 2.17
2904 3343 4.575236 TGCATTCTCTACAGTACTAGACCG 59.425 45.833 0.00 0.00 0.00 4.79
2905 3344 4.815308 GCATTCTCTACAGTACTAGACCGA 59.185 45.833 0.00 0.00 0.00 4.69
2906 3345 5.277442 GCATTCTCTACAGTACTAGACCGAC 60.277 48.000 0.00 0.00 0.00 4.79
2907 3346 5.674052 TTCTCTACAGTACTAGACCGACT 57.326 43.478 0.00 0.00 0.00 4.18
2908 3347 6.782082 TTCTCTACAGTACTAGACCGACTA 57.218 41.667 0.00 0.00 0.00 2.59
2918 3357 4.816786 CTAGACCGACTAGTTTCCTAGC 57.183 50.000 0.00 0.00 43.87 3.42
2919 3358 2.377073 AGACCGACTAGTTTCCTAGCC 58.623 52.381 0.00 0.00 43.87 3.93
2920 3359 1.408340 GACCGACTAGTTTCCTAGCCC 59.592 57.143 0.00 0.00 43.87 5.19
2921 3360 1.006878 ACCGACTAGTTTCCTAGCCCT 59.993 52.381 0.00 0.00 43.87 5.19
2922 3361 2.108970 CCGACTAGTTTCCTAGCCCTT 58.891 52.381 0.00 0.00 43.87 3.95
2923 3362 2.159085 CCGACTAGTTTCCTAGCCCTTG 60.159 54.545 0.00 0.00 43.87 3.61
2924 3363 2.738964 CGACTAGTTTCCTAGCCCTTGC 60.739 54.545 0.00 0.00 43.87 4.01
2934 3373 4.303257 GCCCTTGCTAGTTCGCTT 57.697 55.556 0.00 0.00 33.53 4.68
2935 3374 1.796796 GCCCTTGCTAGTTCGCTTG 59.203 57.895 0.00 0.00 33.53 4.01
2936 3375 1.796796 CCCTTGCTAGTTCGCTTGC 59.203 57.895 0.00 0.00 44.31 4.01
2937 3376 0.674895 CCCTTGCTAGTTCGCTTGCT 60.675 55.000 0.00 0.00 44.35 3.91
2938 3377 0.723981 CCTTGCTAGTTCGCTTGCTC 59.276 55.000 0.00 0.00 44.35 4.26
2939 3378 1.432514 CTTGCTAGTTCGCTTGCTCA 58.567 50.000 0.00 0.00 44.35 4.26
2940 3379 1.127582 CTTGCTAGTTCGCTTGCTCAC 59.872 52.381 0.00 0.00 44.35 3.51
2941 3380 0.033366 TGCTAGTTCGCTTGCTCACA 59.967 50.000 0.00 0.00 44.35 3.58
2942 3381 0.718343 GCTAGTTCGCTTGCTCACAG 59.282 55.000 0.00 0.00 41.58 3.66
2943 3382 1.354040 CTAGTTCGCTTGCTCACAGG 58.646 55.000 0.00 0.00 0.00 4.00
2944 3383 0.679505 TAGTTCGCTTGCTCACAGGT 59.320 50.000 0.00 0.00 0.00 4.00
2945 3384 0.679505 AGTTCGCTTGCTCACAGGTA 59.320 50.000 0.00 0.00 0.00 3.08
2946 3385 1.071605 GTTCGCTTGCTCACAGGTAG 58.928 55.000 0.00 0.00 0.00 3.18
2947 3386 0.670546 TTCGCTTGCTCACAGGTAGC 60.671 55.000 0.00 0.00 40.50 3.58
2963 3402 4.357018 GGTAGCATTACCTGTCTTTTGC 57.643 45.455 0.00 0.00 45.01 3.68
2964 3403 4.010349 GGTAGCATTACCTGTCTTTTGCT 58.990 43.478 0.00 0.00 45.01 3.91
2965 3404 4.459337 GGTAGCATTACCTGTCTTTTGCTT 59.541 41.667 0.13 0.00 45.01 3.91
2966 3405 4.773323 AGCATTACCTGTCTTTTGCTTC 57.227 40.909 0.00 0.00 37.12 3.86
2967 3406 4.401925 AGCATTACCTGTCTTTTGCTTCT 58.598 39.130 0.00 0.00 37.12 2.85
2968 3407 4.829492 AGCATTACCTGTCTTTTGCTTCTT 59.171 37.500 0.00 0.00 37.12 2.52
2969 3408 5.048434 AGCATTACCTGTCTTTTGCTTCTTC 60.048 40.000 0.00 0.00 37.12 2.87
2970 3409 5.048434 GCATTACCTGTCTTTTGCTTCTTCT 60.048 40.000 0.00 0.00 0.00 2.85
2971 3410 6.515696 GCATTACCTGTCTTTTGCTTCTTCTT 60.516 38.462 0.00 0.00 0.00 2.52
2972 3411 7.428826 CATTACCTGTCTTTTGCTTCTTCTTT 58.571 34.615 0.00 0.00 0.00 2.52
2973 3412 5.921962 ACCTGTCTTTTGCTTCTTCTTTT 57.078 34.783 0.00 0.00 0.00 2.27
2974 3413 6.286240 ACCTGTCTTTTGCTTCTTCTTTTT 57.714 33.333 0.00 0.00 0.00 1.94
2995 3434 7.749539 TTTTTCGTTTCATTTTGTTCTCTCC 57.250 32.000 0.00 0.00 0.00 3.71
2996 3435 4.725556 TCGTTTCATTTTGTTCTCTCCG 57.274 40.909 0.00 0.00 0.00 4.63
2997 3436 3.496884 TCGTTTCATTTTGTTCTCTCCGG 59.503 43.478 0.00 0.00 0.00 5.14
2998 3437 3.250040 CGTTTCATTTTGTTCTCTCCGGT 59.750 43.478 0.00 0.00 0.00 5.28
2999 3438 4.261031 CGTTTCATTTTGTTCTCTCCGGTT 60.261 41.667 0.00 0.00 0.00 4.44
3000 3439 5.588240 GTTTCATTTTGTTCTCTCCGGTTT 58.412 37.500 0.00 0.00 0.00 3.27
3001 3440 5.845391 TTCATTTTGTTCTCTCCGGTTTT 57.155 34.783 0.00 0.00 0.00 2.43
3002 3441 5.845391 TCATTTTGTTCTCTCCGGTTTTT 57.155 34.783 0.00 0.00 0.00 1.94
3026 3465 9.927668 TTTTTGTTTCTTCATGAGTTTCTTCTT 57.072 25.926 0.00 0.00 0.00 2.52
3027 3466 9.927668 TTTTGTTTCTTCATGAGTTTCTTCTTT 57.072 25.926 0.00 0.00 0.00 2.52
3028 3467 9.927668 TTTGTTTCTTCATGAGTTTCTTCTTTT 57.072 25.926 0.00 0.00 0.00 2.27
3029 3468 9.573133 TTGTTTCTTCATGAGTTTCTTCTTTTC 57.427 29.630 0.00 0.00 0.00 2.29
3030 3469 8.960591 TGTTTCTTCATGAGTTTCTTCTTTTCT 58.039 29.630 0.00 0.00 0.00 2.52
3031 3470 9.230932 GTTTCTTCATGAGTTTCTTCTTTTCTG 57.769 33.333 0.00 0.00 0.00 3.02
3032 3471 8.511604 TTCTTCATGAGTTTCTTCTTTTCTGT 57.488 30.769 0.00 0.00 0.00 3.41
3033 3472 8.511604 TCTTCATGAGTTTCTTCTTTTCTGTT 57.488 30.769 0.00 0.00 0.00 3.16
3034 3473 8.960591 TCTTCATGAGTTTCTTCTTTTCTGTTT 58.039 29.630 0.00 0.00 0.00 2.83
3035 3474 9.578439 CTTCATGAGTTTCTTCTTTTCTGTTTT 57.422 29.630 0.00 0.00 0.00 2.43
3036 3475 9.927668 TTCATGAGTTTCTTCTTTTCTGTTTTT 57.072 25.926 0.00 0.00 0.00 1.94
3044 3483 9.990360 TTTCTTCTTTTCTGTTTTTACAAAGGT 57.010 25.926 0.00 0.00 0.00 3.50
3045 3484 9.990360 TTCTTCTTTTCTGTTTTTACAAAGGTT 57.010 25.926 0.00 0.00 0.00 3.50
3046 3485 9.990360 TCTTCTTTTCTGTTTTTACAAAGGTTT 57.010 25.926 0.00 0.00 0.00 3.27
3073 3512 8.716646 TTTTCTCTTTTGTTTCCTTTTCCATC 57.283 30.769 0.00 0.00 0.00 3.51
3074 3513 7.660030 TTCTCTTTTGTTTCCTTTTCCATCT 57.340 32.000 0.00 0.00 0.00 2.90
3075 3514 7.660030 TCTCTTTTGTTTCCTTTTCCATCTT 57.340 32.000 0.00 0.00 0.00 2.40
3076 3515 7.716612 TCTCTTTTGTTTCCTTTTCCATCTTC 58.283 34.615 0.00 0.00 0.00 2.87
3077 3516 7.341769 TCTCTTTTGTTTCCTTTTCCATCTTCA 59.658 33.333 0.00 0.00 0.00 3.02
3078 3517 8.021898 TCTTTTGTTTCCTTTTCCATCTTCAT 57.978 30.769 0.00 0.00 0.00 2.57
3079 3518 8.485392 TCTTTTGTTTCCTTTTCCATCTTCATT 58.515 29.630 0.00 0.00 0.00 2.57
3080 3519 8.436046 TTTTGTTTCCTTTTCCATCTTCATTG 57.564 30.769 0.00 0.00 0.00 2.82
3081 3520 6.100404 TGTTTCCTTTTCCATCTTCATTGG 57.900 37.500 0.00 0.00 35.45 3.16
3082 3521 5.602145 TGTTTCCTTTTCCATCTTCATTGGT 59.398 36.000 0.00 0.00 35.64 3.67
3083 3522 5.726980 TTCCTTTTCCATCTTCATTGGTG 57.273 39.130 0.00 0.00 35.64 4.17
3084 3523 4.739793 TCCTTTTCCATCTTCATTGGTGT 58.260 39.130 0.00 0.00 35.64 4.16
3085 3524 5.147032 TCCTTTTCCATCTTCATTGGTGTT 58.853 37.500 0.00 0.00 35.64 3.32
3086 3525 5.602145 TCCTTTTCCATCTTCATTGGTGTTT 59.398 36.000 0.00 0.00 35.64 2.83
3087 3526 6.099557 TCCTTTTCCATCTTCATTGGTGTTTT 59.900 34.615 0.00 0.00 35.64 2.43
3088 3527 6.424812 CCTTTTCCATCTTCATTGGTGTTTTC 59.575 38.462 0.00 0.00 35.64 2.29
3089 3528 6.729690 TTTCCATCTTCATTGGTGTTTTCT 57.270 33.333 0.00 0.00 35.64 2.52
3090 3529 6.729690 TTCCATCTTCATTGGTGTTTTCTT 57.270 33.333 0.00 0.00 35.64 2.52
3091 3530 6.729690 TCCATCTTCATTGGTGTTTTCTTT 57.270 33.333 0.00 0.00 35.64 2.52
3092 3531 7.123355 TCCATCTTCATTGGTGTTTTCTTTT 57.877 32.000 0.00 0.00 35.64 2.27
3093 3532 7.209475 TCCATCTTCATTGGTGTTTTCTTTTC 58.791 34.615 0.00 0.00 35.64 2.29
3094 3533 7.069826 TCCATCTTCATTGGTGTTTTCTTTTCT 59.930 33.333 0.00 0.00 35.64 2.52
3095 3534 8.359642 CCATCTTCATTGGTGTTTTCTTTTCTA 58.640 33.333 0.00 0.00 0.00 2.10
3096 3535 9.403110 CATCTTCATTGGTGTTTTCTTTTCTAG 57.597 33.333 0.00 0.00 0.00 2.43
3097 3536 8.519799 TCTTCATTGGTGTTTTCTTTTCTAGT 57.480 30.769 0.00 0.00 0.00 2.57
3098 3537 8.621286 TCTTCATTGGTGTTTTCTTTTCTAGTC 58.379 33.333 0.00 0.00 0.00 2.59
3099 3538 8.519799 TTCATTGGTGTTTTCTTTTCTAGTCT 57.480 30.769 0.00 0.00 0.00 3.24
3100 3539 9.621629 TTCATTGGTGTTTTCTTTTCTAGTCTA 57.378 29.630 0.00 0.00 0.00 2.59
3101 3540 9.793259 TCATTGGTGTTTTCTTTTCTAGTCTAT 57.207 29.630 0.00 0.00 0.00 1.98
3103 3542 8.617290 TTGGTGTTTTCTTTTCTAGTCTATCC 57.383 34.615 0.00 0.00 0.00 2.59
3104 3543 7.974504 TGGTGTTTTCTTTTCTAGTCTATCCT 58.025 34.615 0.00 0.00 0.00 3.24
3105 3544 9.096823 TGGTGTTTTCTTTTCTAGTCTATCCTA 57.903 33.333 0.00 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 91 2.131067 CCTCTTCGCCCTCCTCTCC 61.131 68.421 0.00 0.00 0.00 3.71
182 187 1.109920 GGAGGACGCATCTCCTAGCA 61.110 60.000 10.81 0.00 45.46 3.49
238 243 1.741706 GTCCTCGTCCGATGTCTGTAA 59.258 52.381 0.00 0.00 0.00 2.41
239 244 1.339342 TGTCCTCGTCCGATGTCTGTA 60.339 52.381 0.00 0.00 0.00 2.74
246 251 1.725557 CGGTGATGTCCTCGTCCGAT 61.726 60.000 0.00 0.00 42.61 4.18
280 285 5.970023 CGAAAAAGTAGTACTACTCATCCGG 59.030 44.000 30.81 17.03 44.96 5.14
282 287 8.754230 AAACGAAAAAGTAGTACTACTCATCC 57.246 34.615 30.81 20.04 44.96 3.51
303 308 7.634817 CCTGCTTCTACGATACAAAATAAAACG 59.365 37.037 0.00 0.00 0.00 3.60
391 413 9.908152 ACGATTCGATAATTGATAGTTGATACA 57.092 29.630 13.95 0.00 31.74 2.29
398 420 9.445878 TCCTACTACGATTCGATAATTGATAGT 57.554 33.333 13.95 9.55 33.13 2.12
435 457 0.588252 CAGCAGGCGCGCTATATTTT 59.412 50.000 32.29 7.58 45.49 1.82
449 471 4.463879 CCCGAGCCACTCCAGCAG 62.464 72.222 0.00 0.00 0.00 4.24
510 532 2.014128 GGATTAGCCAGCTTTTACGCA 58.986 47.619 0.00 0.00 36.34 5.24
511 533 1.003866 CGGATTAGCCAGCTTTTACGC 60.004 52.381 0.00 0.00 35.94 4.42
512 534 1.597663 CCGGATTAGCCAGCTTTTACG 59.402 52.381 0.00 0.00 35.94 3.18
513 535 1.333931 GCCGGATTAGCCAGCTTTTAC 59.666 52.381 5.05 0.00 37.09 2.01
514 536 1.675552 GCCGGATTAGCCAGCTTTTA 58.324 50.000 5.05 0.00 37.09 1.52
515 537 1.376609 CGCCGGATTAGCCAGCTTTT 61.377 55.000 5.05 0.00 37.96 2.27
516 538 1.819632 CGCCGGATTAGCCAGCTTT 60.820 57.895 5.05 0.00 37.96 3.51
517 539 2.203070 CGCCGGATTAGCCAGCTT 60.203 61.111 5.05 0.00 37.96 3.74
518 540 4.918201 GCGCCGGATTAGCCAGCT 62.918 66.667 5.05 0.00 37.96 4.24
519 541 4.918201 AGCGCCGGATTAGCCAGC 62.918 66.667 5.05 0.00 36.68 4.85
520 542 2.363711 TACAGCGCCGGATTAGCCAG 62.364 60.000 5.05 3.00 35.94 4.85
521 543 1.754380 ATACAGCGCCGGATTAGCCA 61.754 55.000 5.05 0.00 35.94 4.75
522 544 0.602905 AATACAGCGCCGGATTAGCC 60.603 55.000 5.05 0.00 0.00 3.93
523 545 0.790814 GAATACAGCGCCGGATTAGC 59.209 55.000 5.05 4.30 0.00 3.09
524 546 2.061773 CAGAATACAGCGCCGGATTAG 58.938 52.381 5.05 0.00 0.00 1.73
525 547 1.684450 TCAGAATACAGCGCCGGATTA 59.316 47.619 5.05 0.00 0.00 1.75
526 548 0.464036 TCAGAATACAGCGCCGGATT 59.536 50.000 5.05 0.61 0.00 3.01
527 549 0.681733 ATCAGAATACAGCGCCGGAT 59.318 50.000 5.05 0.00 0.00 4.18
528 550 0.464036 AATCAGAATACAGCGCCGGA 59.536 50.000 5.05 0.00 0.00 5.14
529 551 1.299541 AAATCAGAATACAGCGCCGG 58.700 50.000 2.29 0.00 0.00 6.13
530 552 3.405170 AAAAATCAGAATACAGCGCCG 57.595 42.857 2.29 0.00 0.00 6.46
531 553 4.035675 AGCTAAAAATCAGAATACAGCGCC 59.964 41.667 2.29 0.00 33.10 6.53
532 554 5.162000 AGCTAAAAATCAGAATACAGCGC 57.838 39.130 0.00 0.00 33.10 5.92
533 555 5.453587 GCAAGCTAAAAATCAGAATACAGCG 59.546 40.000 0.00 0.00 33.10 5.18
534 556 5.453587 CGCAAGCTAAAAATCAGAATACAGC 59.546 40.000 0.00 0.00 0.00 4.40
553 575 4.093952 CTCCAACAGCCGCGCAAG 62.094 66.667 8.75 0.00 43.44 4.01
554 576 2.514510 TATCTCCAACAGCCGCGCAA 62.515 55.000 8.75 0.00 0.00 4.85
555 577 2.310327 ATATCTCCAACAGCCGCGCA 62.310 55.000 8.75 0.00 0.00 6.09
556 578 1.160329 AATATCTCCAACAGCCGCGC 61.160 55.000 0.00 0.00 0.00 6.86
557 579 0.861837 GAATATCTCCAACAGCCGCG 59.138 55.000 0.00 0.00 0.00 6.46
558 580 2.246719 AGAATATCTCCAACAGCCGC 57.753 50.000 0.00 0.00 0.00 6.53
559 581 6.102663 CCTATTAGAATATCTCCAACAGCCG 58.897 44.000 0.00 0.00 0.00 5.52
560 582 6.410540 CCCTATTAGAATATCTCCAACAGCC 58.589 44.000 0.00 0.00 0.00 4.85
561 583 6.013293 ACCCCTATTAGAATATCTCCAACAGC 60.013 42.308 0.00 0.00 0.00 4.40
562 584 7.560796 ACCCCTATTAGAATATCTCCAACAG 57.439 40.000 0.00 0.00 0.00 3.16
563 585 8.014263 TGTACCCCTATTAGAATATCTCCAACA 58.986 37.037 0.00 0.00 0.00 3.33
564 586 8.431910 TGTACCCCTATTAGAATATCTCCAAC 57.568 38.462 0.00 0.00 0.00 3.77
565 587 9.629649 AATGTACCCCTATTAGAATATCTCCAA 57.370 33.333 0.00 0.00 0.00 3.53
566 588 9.629649 AAATGTACCCCTATTAGAATATCTCCA 57.370 33.333 0.00 0.00 0.00 3.86
567 589 9.892130 CAAATGTACCCCTATTAGAATATCTCC 57.108 37.037 0.00 0.00 0.00 3.71
568 590 9.892130 CCAAATGTACCCCTATTAGAATATCTC 57.108 37.037 0.00 0.00 0.00 2.75
569 591 9.406662 ACCAAATGTACCCCTATTAGAATATCT 57.593 33.333 0.00 0.00 0.00 1.98
573 595 8.445588 CCTTACCAAATGTACCCCTATTAGAAT 58.554 37.037 0.00 0.00 0.00 2.40
574 596 7.638638 GCCTTACCAAATGTACCCCTATTAGAA 60.639 40.741 0.00 0.00 0.00 2.10
575 597 6.183361 GCCTTACCAAATGTACCCCTATTAGA 60.183 42.308 0.00 0.00 0.00 2.10
576 598 6.002082 GCCTTACCAAATGTACCCCTATTAG 58.998 44.000 0.00 0.00 0.00 1.73
621 643 3.242641 CGTCATCAAACCATCTCATGCAG 60.243 47.826 0.00 0.00 0.00 4.41
638 660 0.673644 CCTTCCGACCAAAGCGTCAT 60.674 55.000 0.00 0.00 32.74 3.06
710 735 2.100989 GTAGTGGAGTGGGTAGGTGAG 58.899 57.143 0.00 0.00 0.00 3.51
751 776 9.672086 TTTAAACCGTGAAGAATGATTTAACAG 57.328 29.630 0.00 0.00 0.00 3.16
794 819 1.754745 GCTGAAGGATATGGGGCGA 59.245 57.895 0.00 0.00 0.00 5.54
810 835 4.961438 AAACACTCAAATGGAAATGGCT 57.039 36.364 0.00 0.00 0.00 4.75
832 857 6.381133 TGGGCATGGGTTTTAATTTTGTTTTT 59.619 30.769 0.00 0.00 0.00 1.94
1159 1193 2.240493 ACCCTGAAGTGAAACGACAG 57.760 50.000 0.00 0.00 45.86 3.51
1205 1239 2.932130 GATCCCGCAGAAGAGCACCC 62.932 65.000 0.00 0.00 0.00 4.61
1406 1539 2.036733 CAGTTGTTCTCGTACCCCTTGA 59.963 50.000 0.00 0.00 0.00 3.02
1768 1908 1.068741 GTCGTGTCTGACCAGGAAGTT 59.931 52.381 5.17 0.00 31.68 2.66
1782 1922 1.154016 CATCTCTTCGGCGTCGTGT 60.154 57.895 10.18 0.00 37.69 4.49
1794 1934 2.188994 GCCGCTGCCTTCATCTCT 59.811 61.111 0.00 0.00 0.00 3.10
2010 2404 2.436646 CCCGCGAAGTCCAGCATT 60.437 61.111 8.23 0.00 0.00 3.56
2049 2443 0.526211 CCATCTTGACGACCTCGACA 59.474 55.000 0.78 0.00 43.02 4.35
2176 2570 3.425713 CGAGCCAAGCGCACATGT 61.426 61.111 11.47 0.00 41.38 3.21
2203 2597 1.802508 CGTGCCGATGACTGCTTCATA 60.803 52.381 1.82 0.00 45.67 2.15
2219 2613 3.119849 AGCCAAATTATGACTTCACGTGC 60.120 43.478 11.67 0.00 0.00 5.34
2286 2684 2.687935 GCAGGGCATTATCCGAAGAAAA 59.312 45.455 0.00 0.00 0.00 2.29
2287 2685 2.297701 GCAGGGCATTATCCGAAGAAA 58.702 47.619 0.00 0.00 0.00 2.52
2294 2692 1.889170 GCTAAAGGCAGGGCATTATCC 59.111 52.381 0.00 0.00 41.35 2.59
2328 2726 6.325804 GGTAGTGGGGTGAACTTGTATATAGT 59.674 42.308 0.00 0.00 0.00 2.12
2380 2786 3.337358 TGAGTGGCACAGTGATAATGTG 58.663 45.455 21.41 5.16 45.14 3.21
2385 2791 2.419159 GCTGATGAGTGGCACAGTGATA 60.419 50.000 21.41 0.43 45.14 2.15
2392 2798 2.439156 GGGGCTGATGAGTGGCAC 60.439 66.667 10.29 10.29 0.00 5.01
2465 2875 3.499157 AGTCAACCGAGATATAGCGACTC 59.501 47.826 0.00 0.00 0.00 3.36
2547 2960 8.579682 TGCAAGAAAGAAAGAAAAGAATAAGC 57.420 30.769 0.00 0.00 0.00 3.09
2551 2964 8.953368 AACATGCAAGAAAGAAAGAAAAGAAT 57.047 26.923 0.00 0.00 0.00 2.40
2553 2966 9.467258 CATAACATGCAAGAAAGAAAGAAAAGA 57.533 29.630 0.00 0.00 0.00 2.52
2554 2967 9.252962 ACATAACATGCAAGAAAGAAAGAAAAG 57.747 29.630 0.00 0.00 0.00 2.27
2616 3043 4.467769 CCTTCTATACGACACCCTTAGGA 58.532 47.826 0.00 0.00 36.73 2.94
2621 3048 2.456073 AGCCTTCTATACGACACCCT 57.544 50.000 0.00 0.00 0.00 4.34
2622 3049 2.557490 CCTAGCCTTCTATACGACACCC 59.443 54.545 0.00 0.00 0.00 4.61
2623 3050 3.220940 ACCTAGCCTTCTATACGACACC 58.779 50.000 0.00 0.00 0.00 4.16
2624 3051 3.881688 TGACCTAGCCTTCTATACGACAC 59.118 47.826 0.00 0.00 0.00 3.67
2626 3053 4.023021 CCTTGACCTAGCCTTCTATACGAC 60.023 50.000 0.00 0.00 0.00 4.34
2627 3054 4.142790 CCTTGACCTAGCCTTCTATACGA 58.857 47.826 0.00 0.00 0.00 3.43
2628 3055 3.256136 CCCTTGACCTAGCCTTCTATACG 59.744 52.174 0.00 0.00 0.00 3.06
2629 3056 4.481072 TCCCTTGACCTAGCCTTCTATAC 58.519 47.826 0.00 0.00 0.00 1.47
2630 3057 4.827036 TCCCTTGACCTAGCCTTCTATA 57.173 45.455 0.00 0.00 0.00 1.31
2631 3058 3.708236 TCCCTTGACCTAGCCTTCTAT 57.292 47.619 0.00 0.00 0.00 1.98
2632 3059 3.105283 GTTCCCTTGACCTAGCCTTCTA 58.895 50.000 0.00 0.00 0.00 2.10
2633 3060 1.909986 GTTCCCTTGACCTAGCCTTCT 59.090 52.381 0.00 0.00 0.00 2.85
2635 3062 1.742308 TGTTCCCTTGACCTAGCCTT 58.258 50.000 0.00 0.00 0.00 4.35
2649 3088 7.304735 ACTTGCAATTTTGTTTCTTTTGTTCC 58.695 30.769 0.00 0.00 0.00 3.62
2667 3106 2.394930 TATCGCCAGCTAACTTGCAA 57.605 45.000 0.00 0.00 34.23 4.08
2671 3110 7.667557 TCAAACTATATATCGCCAGCTAACTT 58.332 34.615 0.00 0.00 0.00 2.66
2698 3137 0.099968 CGGCCATGCTTGTGAATGAG 59.900 55.000 2.24 0.00 30.62 2.90
2699 3138 0.608856 ACGGCCATGCTTGTGAATGA 60.609 50.000 2.24 0.00 30.62 2.57
2712 3151 0.672401 GAGTTTCGATCCAACGGCCA 60.672 55.000 2.24 0.00 0.00 5.36
2713 3152 0.672401 TGAGTTTCGATCCAACGGCC 60.672 55.000 0.00 0.00 0.00 6.13
2714 3153 0.442699 GTGAGTTTCGATCCAACGGC 59.557 55.000 0.00 0.00 0.00 5.68
2723 3162 0.319211 AATCACGGCGTGAGTTTCGA 60.319 50.000 40.31 21.46 46.04 3.71
2725 3164 1.144969 TGAATCACGGCGTGAGTTTC 58.855 50.000 40.31 36.32 46.04 2.78
2740 3179 3.159213 TCTTGAGGCCACAACATGAAT 57.841 42.857 11.97 0.00 0.00 2.57
2776 3215 0.031994 ACGAAAACAGGCCAACATGC 59.968 50.000 5.01 0.00 0.00 4.06
2786 3225 3.535860 CTGAGAGCGAAAACGAAAACAG 58.464 45.455 0.00 0.00 0.00 3.16
2800 3239 0.096628 CTGAAACATGCGCTGAGAGC 59.903 55.000 9.73 0.00 38.02 4.09
2809 3248 0.036388 TCTCGGACCCTGAAACATGC 60.036 55.000 0.00 0.00 0.00 4.06
2839 3278 0.814457 AAGCTAGTCTCGCTGTGAGG 59.186 55.000 17.44 3.43 45.32 3.86
2842 3281 2.408050 ACAAAAGCTAGTCTCGCTGTG 58.592 47.619 0.00 4.50 37.87 3.66
2844 3283 3.483922 CGATACAAAAGCTAGTCTCGCTG 59.516 47.826 0.00 0.00 37.87 5.18
2917 3356 1.796796 CAAGCGAACTAGCAAGGGC 59.203 57.895 0.00 0.00 40.15 5.19
2918 3357 0.674895 AGCAAGCGAACTAGCAAGGG 60.675 55.000 0.00 0.00 40.15 3.95
2919 3358 0.723981 GAGCAAGCGAACTAGCAAGG 59.276 55.000 0.00 0.00 40.15 3.61
2920 3359 1.127582 GTGAGCAAGCGAACTAGCAAG 59.872 52.381 0.00 0.00 40.15 4.01
2921 3360 1.148310 GTGAGCAAGCGAACTAGCAA 58.852 50.000 0.00 0.00 40.15 3.91
2922 3361 0.033366 TGTGAGCAAGCGAACTAGCA 59.967 50.000 0.00 0.00 40.15 3.49
2923 3362 0.718343 CTGTGAGCAAGCGAACTAGC 59.282 55.000 0.00 0.00 37.41 3.42
2924 3363 1.337260 ACCTGTGAGCAAGCGAACTAG 60.337 52.381 0.00 0.00 0.00 2.57
2925 3364 0.679505 ACCTGTGAGCAAGCGAACTA 59.320 50.000 0.00 0.00 0.00 2.24
2926 3365 0.679505 TACCTGTGAGCAAGCGAACT 59.320 50.000 0.00 0.00 0.00 3.01
2927 3366 1.071605 CTACCTGTGAGCAAGCGAAC 58.928 55.000 0.00 0.00 0.00 3.95
2928 3367 0.670546 GCTACCTGTGAGCAAGCGAA 60.671 55.000 0.00 0.00 39.84 4.70
2929 3368 1.079819 GCTACCTGTGAGCAAGCGA 60.080 57.895 0.00 0.00 39.84 4.93
2930 3369 1.374631 TGCTACCTGTGAGCAAGCG 60.375 57.895 0.00 0.00 46.71 4.68
2931 3370 4.701663 TGCTACCTGTGAGCAAGC 57.298 55.556 0.00 0.00 46.71 4.01
2943 3382 5.412904 AGAAGCAAAAGACAGGTAATGCTAC 59.587 40.000 0.00 0.00 42.82 3.58
2944 3383 5.560724 AGAAGCAAAAGACAGGTAATGCTA 58.439 37.500 0.00 0.00 42.82 3.49
2945 3384 4.401925 AGAAGCAAAAGACAGGTAATGCT 58.598 39.130 0.00 0.00 45.32 3.79
2946 3385 4.773323 AGAAGCAAAAGACAGGTAATGC 57.227 40.909 0.00 0.00 0.00 3.56
2947 3386 6.566197 AGAAGAAGCAAAAGACAGGTAATG 57.434 37.500 0.00 0.00 0.00 1.90
2948 3387 7.588497 AAAGAAGAAGCAAAAGACAGGTAAT 57.412 32.000 0.00 0.00 0.00 1.89
2949 3388 7.404671 AAAAGAAGAAGCAAAAGACAGGTAA 57.595 32.000 0.00 0.00 0.00 2.85
2950 3389 7.404671 AAAAAGAAGAAGCAAAAGACAGGTA 57.595 32.000 0.00 0.00 0.00 3.08
2951 3390 5.921962 AAAAGAAGAAGCAAAAGACAGGT 57.078 34.783 0.00 0.00 0.00 4.00
2971 3410 6.470877 CGGAGAGAACAAAATGAAACGAAAAA 59.529 34.615 0.00 0.00 0.00 1.94
2972 3411 5.968848 CGGAGAGAACAAAATGAAACGAAAA 59.031 36.000 0.00 0.00 0.00 2.29
2973 3412 5.504994 CCGGAGAGAACAAAATGAAACGAAA 60.505 40.000 0.00 0.00 0.00 3.46
2974 3413 4.024387 CCGGAGAGAACAAAATGAAACGAA 60.024 41.667 0.00 0.00 0.00 3.85
2975 3414 3.496884 CCGGAGAGAACAAAATGAAACGA 59.503 43.478 0.00 0.00 0.00 3.85
2976 3415 3.250040 ACCGGAGAGAACAAAATGAAACG 59.750 43.478 9.46 0.00 0.00 3.60
2977 3416 4.830826 ACCGGAGAGAACAAAATGAAAC 57.169 40.909 9.46 0.00 0.00 2.78
2978 3417 5.845391 AAACCGGAGAGAACAAAATGAAA 57.155 34.783 9.46 0.00 0.00 2.69
2979 3418 5.845391 AAAACCGGAGAGAACAAAATGAA 57.155 34.783 9.46 0.00 0.00 2.57
2980 3419 5.845391 AAAAACCGGAGAGAACAAAATGA 57.155 34.783 9.46 0.00 0.00 2.57
3000 3439 9.927668 AAGAAGAAACTCATGAAGAAACAAAAA 57.072 25.926 0.00 0.00 0.00 1.94
3001 3440 9.927668 AAAGAAGAAACTCATGAAGAAACAAAA 57.072 25.926 0.00 0.00 0.00 2.44
3002 3441 9.927668 AAAAGAAGAAACTCATGAAGAAACAAA 57.072 25.926 0.00 0.00 0.00 2.83
3003 3442 9.573133 GAAAAGAAGAAACTCATGAAGAAACAA 57.427 29.630 0.00 0.00 0.00 2.83
3004 3443 8.960591 AGAAAAGAAGAAACTCATGAAGAAACA 58.039 29.630 0.00 0.00 0.00 2.83
3005 3444 9.230932 CAGAAAAGAAGAAACTCATGAAGAAAC 57.769 33.333 0.00 0.00 0.00 2.78
3006 3445 8.960591 ACAGAAAAGAAGAAACTCATGAAGAAA 58.039 29.630 0.00 0.00 0.00 2.52
3007 3446 8.511604 ACAGAAAAGAAGAAACTCATGAAGAA 57.488 30.769 0.00 0.00 0.00 2.52
3008 3447 8.511604 AACAGAAAAGAAGAAACTCATGAAGA 57.488 30.769 0.00 0.00 0.00 2.87
3009 3448 9.578439 AAAACAGAAAAGAAGAAACTCATGAAG 57.422 29.630 0.00 0.00 0.00 3.02
3010 3449 9.927668 AAAAACAGAAAAGAAGAAACTCATGAA 57.072 25.926 0.00 0.00 0.00 2.57
3018 3457 9.990360 ACCTTTGTAAAAACAGAAAAGAAGAAA 57.010 25.926 0.00 0.00 31.01 2.52
3019 3458 9.990360 AACCTTTGTAAAAACAGAAAAGAAGAA 57.010 25.926 0.00 0.00 31.01 2.52
3020 3459 9.990360 AAACCTTTGTAAAAACAGAAAAGAAGA 57.010 25.926 0.00 0.00 31.01 2.87
3047 3486 9.161629 GATGGAAAAGGAAACAAAAGAGAAAAA 57.838 29.630 0.00 0.00 0.00 1.94
3048 3487 8.539544 AGATGGAAAAGGAAACAAAAGAGAAAA 58.460 29.630 0.00 0.00 0.00 2.29
3049 3488 8.078060 AGATGGAAAAGGAAACAAAAGAGAAA 57.922 30.769 0.00 0.00 0.00 2.52
3050 3489 7.660030 AGATGGAAAAGGAAACAAAAGAGAA 57.340 32.000 0.00 0.00 0.00 2.87
3051 3490 7.341769 TGAAGATGGAAAAGGAAACAAAAGAGA 59.658 33.333 0.00 0.00 0.00 3.10
3052 3491 7.491682 TGAAGATGGAAAAGGAAACAAAAGAG 58.508 34.615 0.00 0.00 0.00 2.85
3053 3492 7.416964 TGAAGATGGAAAAGGAAACAAAAGA 57.583 32.000 0.00 0.00 0.00 2.52
3054 3493 8.553696 CAATGAAGATGGAAAAGGAAACAAAAG 58.446 33.333 0.00 0.00 0.00 2.27
3055 3494 7.498570 CCAATGAAGATGGAAAAGGAAACAAAA 59.501 33.333 0.00 0.00 40.56 2.44
3056 3495 6.991531 CCAATGAAGATGGAAAAGGAAACAAA 59.008 34.615 0.00 0.00 40.56 2.83
3057 3496 6.099557 ACCAATGAAGATGGAAAAGGAAACAA 59.900 34.615 0.00 0.00 40.56 2.83
3058 3497 5.602145 ACCAATGAAGATGGAAAAGGAAACA 59.398 36.000 0.00 0.00 40.56 2.83
3059 3498 5.928264 CACCAATGAAGATGGAAAAGGAAAC 59.072 40.000 0.00 0.00 40.56 2.78
3060 3499 5.602145 ACACCAATGAAGATGGAAAAGGAAA 59.398 36.000 0.00 0.00 40.56 3.13
3061 3500 5.147032 ACACCAATGAAGATGGAAAAGGAA 58.853 37.500 0.00 0.00 40.56 3.36
3062 3501 4.739793 ACACCAATGAAGATGGAAAAGGA 58.260 39.130 0.00 0.00 40.56 3.36
3063 3502 5.473066 AACACCAATGAAGATGGAAAAGG 57.527 39.130 0.00 0.00 40.56 3.11
3064 3503 7.212274 AGAAAACACCAATGAAGATGGAAAAG 58.788 34.615 0.00 0.00 40.56 2.27
3065 3504 7.123355 AGAAAACACCAATGAAGATGGAAAA 57.877 32.000 0.00 0.00 40.56 2.29
3066 3505 6.729690 AGAAAACACCAATGAAGATGGAAA 57.270 33.333 0.00 0.00 40.56 3.13
3067 3506 6.729690 AAGAAAACACCAATGAAGATGGAA 57.270 33.333 0.00 0.00 40.56 3.53
3068 3507 6.729690 AAAGAAAACACCAATGAAGATGGA 57.270 33.333 0.00 0.00 40.56 3.41
3069 3508 7.212274 AGAAAAGAAAACACCAATGAAGATGG 58.788 34.615 0.00 0.00 43.84 3.51
3070 3509 9.403110 CTAGAAAAGAAAACACCAATGAAGATG 57.597 33.333 0.00 0.00 0.00 2.90
3071 3510 9.136323 ACTAGAAAAGAAAACACCAATGAAGAT 57.864 29.630 0.00 0.00 0.00 2.40
3072 3511 8.519799 ACTAGAAAAGAAAACACCAATGAAGA 57.480 30.769 0.00 0.00 0.00 2.87
3073 3512 8.624776 AGACTAGAAAAGAAAACACCAATGAAG 58.375 33.333 0.00 0.00 0.00 3.02
3074 3513 8.519799 AGACTAGAAAAGAAAACACCAATGAA 57.480 30.769 0.00 0.00 0.00 2.57
3075 3514 9.793259 ATAGACTAGAAAAGAAAACACCAATGA 57.207 29.630 0.00 0.00 0.00 2.57
3077 3516 9.232473 GGATAGACTAGAAAAGAAAACACCAAT 57.768 33.333 0.00 0.00 0.00 3.16
3078 3517 8.437575 AGGATAGACTAGAAAAGAAAACACCAA 58.562 33.333 0.00 0.00 0.00 3.67
3079 3518 7.974504 AGGATAGACTAGAAAAGAAAACACCA 58.025 34.615 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.