Multiple sequence alignment - TraesCS1D01G201900

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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 TraesCS1D01G201900 chr1D 100.000 2501 0 0 1 2501 285048615 285046115 0.000000e+00 4619.0
1 TraesCS1D01G201900 chr1A 88.692 1017 58 18 808 1803 356465533 356464553 0.000000e+00 1188.0
2 TraesCS1D01G201900 chr1A 90.463 713 41 15 1811 2501 356464577 356463870 0.000000e+00 915.0
3 TraesCS1D01G201900 chr1A 86.982 507 62 3 8 510 356466100 356465594 3.610000e-158 568.0
4 TraesCS1D01G201900 chr1B 94.928 414 18 2 2091 2501 387290433 387290020 0.000000e+00 645.0
5 TraesCS1D01G201900 chr1B 91.386 267 17 4 1817 2081 387291086 387290824 6.580000e-96 361.0
6 TraesCS1D01G201900 chr1B 89.200 250 21 4 1448 1693 387291469 387291222 8.690000e-80 307.0
7 TraesCS1D01G201900 chr1B 89.744 117 8 3 553 665 494234814 494234930 2.000000e-31 147.0
8 TraesCS1D01G201900 chr1B 92.857 70 5 0 662 731 494235280 494235349 4.400000e-18 102.0
9 TraesCS1D01G201900 chr3B 85.763 583 62 11 1000 1572 61528311 61527740 4.600000e-167 597.0
10 TraesCS1D01G201900 chr3B 87.912 182 18 3 557 736 256728203 256728024 7.010000e-51 211.0
11 TraesCS1D01G201900 chr3D 84.459 592 68 15 914 1491 38509497 38510078 1.680000e-156 562.0
12 TraesCS1D01G201900 chr3D 87.209 86 6 4 550 630 134958175 134958260 2.650000e-15 93.5
13 TraesCS1D01G201900 chr6A 87.770 278 22 6 1822 2090 423316058 423315784 5.190000e-82 315.0
14 TraesCS1D01G201900 chr6A 84.932 73 9 1 550 620 575490490 575490418 3.450000e-09 73.1
15 TraesCS1D01G201900 chr4A 86.195 297 25 12 1808 2090 182121586 182121880 8.690000e-80 307.0
16 TraesCS1D01G201900 chr4A 93.103 58 2 1 550 605 161260594 161260651 1.590000e-12 84.2
17 TraesCS1D01G201900 chr6D 86.833 281 23 10 1822 2090 255024851 255024573 4.040000e-78 302.0
18 TraesCS1D01G201900 chr6D 86.282 277 27 6 1822 2090 296691962 296691689 8.750000e-75 291.0
19 TraesCS1D01G201900 chr3A 86.833 281 22 6 1822 2090 584256128 584256405 1.450000e-77 300.0
20 TraesCS1D01G201900 chr7A 86.477 281 24 9 1822 2090 19077901 19078179 1.880000e-76 296.0
21 TraesCS1D01G201900 chr7A 86.081 273 30 4 1822 2090 731956353 731956085 1.130000e-73 287.0
22 TraesCS1D01G201900 chr7A 96.296 54 2 0 684 737 46053800 46053853 3.430000e-14 89.8
23 TraesCS1D01G201900 chr7A 92.727 55 3 1 684 737 136859267 136859321 7.420000e-11 78.7
24 TraesCS1D01G201900 chr6B 89.604 202 16 3 544 741 124384275 124384075 4.130000e-63 252.0
25 TraesCS1D01G201900 chr2D 87.895 190 16 6 553 737 52224353 52224540 1.510000e-52 217.0
26 TraesCS1D01G201900 chr4B 85.638 188 21 4 554 737 466057657 466057472 2.540000e-45 193.0
27 TraesCS1D01G201900 chr2B 76.049 405 59 28 1686 2089 653261423 653261056 2.560000e-40 176.0
28 TraesCS1D01G201900 chr2B 88.281 128 8 4 633 754 774840176 774840050 2.000000e-31 147.0
29 TraesCS1D01G201900 chr5A 79.558 181 37 0 1031 1211 671484121 671484301 2.020000e-26 130.0
30 TraesCS1D01G201900 chr4D 80.769 156 30 0 1031 1186 490138736 490138891 3.380000e-24 122.0
31 TraesCS1D01G201900 chr7D 90.323 62 4 1 552 611 66408570 66408509 2.060000e-11 80.5
32 TraesCS1D01G201900 chr5D 92.593 54 4 0 684 737 348496228 348496175 7.420000e-11 78.7
33 TraesCS1D01G201900 chr5B 76.642 137 27 4 2255 2389 697861639 697861772 1.240000e-08 71.3


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G201900 chr1D 285046115 285048615 2500 True 4619.000000 4619 100.000000 1 2501 1 chr1D.!!$R1 2500
1 TraesCS1D01G201900 chr1A 356463870 356466100 2230 True 890.333333 1188 88.712333 8 2501 3 chr1A.!!$R1 2493
2 TraesCS1D01G201900 chr1B 387290020 387291469 1449 True 437.666667 645 91.838000 1448 2501 3 chr1B.!!$R1 1053
3 TraesCS1D01G201900 chr3B 61527740 61528311 571 True 597.000000 597 85.763000 1000 1572 1 chr3B.!!$R1 572
4 TraesCS1D01G201900 chr3D 38509497 38510078 581 False 562.000000 562 84.459000 914 1491 1 chr3D.!!$F1 577

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
449 454 0.394216 TTTGGATCAGGGCCGTCATG 60.394 55.0 0.0 0.0 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1707 1806 0.590682 TACTGCCGCAACAACATGTG 59.409 50.0 0.0 0.0 0.0 3.21 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
44 46 9.179552 TCTTTGTCGATTTGTTTTAATGACATG 57.820 29.630 0.00 0.00 35.12 3.21
48 50 8.015087 TGTCGATTTGTTTTAATGACATGAGAC 58.985 33.333 0.00 0.00 30.61 3.36
53 55 8.877864 TTTGTTTTAATGACATGAGACCCTAT 57.122 30.769 0.00 0.00 0.00 2.57
67 69 6.595682 TGAGACCCTATTCATGAAGGATTTC 58.404 40.000 16.81 5.49 34.58 2.17
76 79 0.550914 TGAAGGATTTCCCCCATCCG 59.449 55.000 0.00 0.00 44.57 4.18
78 81 0.551396 AAGGATTTCCCCCATCCGTC 59.449 55.000 0.00 0.00 44.57 4.79
84 87 2.438434 CCCCCATCCGTCTGCAAC 60.438 66.667 0.00 0.00 0.00 4.17
85 88 2.438434 CCCCATCCGTCTGCAACC 60.438 66.667 0.00 0.00 0.00 3.77
95 98 1.965930 TCTGCAACCGCGCAAAGAT 60.966 52.632 8.75 0.00 42.45 2.40
111 114 4.681483 GCAAAGATCAACTACAGCCAAAAC 59.319 41.667 0.00 0.00 0.00 2.43
113 116 4.002906 AGATCAACTACAGCCAAAACGA 57.997 40.909 0.00 0.00 0.00 3.85
121 124 3.680786 GCCAAAACGACTGGGGCC 61.681 66.667 0.00 0.00 38.70 5.80
125 128 2.763645 AAAACGACTGGGGCCACCT 61.764 57.895 0.20 0.00 41.11 4.00
129 132 4.083862 GACTGGGGCCACCTCGTC 62.084 72.222 0.20 9.62 41.11 4.20
152 155 3.842126 CGTGTGCGTCGCCTCATG 61.842 66.667 15.88 14.81 0.00 3.07
153 156 2.738521 GTGTGCGTCGCCTCATGT 60.739 61.111 15.88 0.00 0.00 3.21
165 168 1.586154 CCTCATGTGTTGTTCCGCCC 61.586 60.000 0.00 0.00 0.00 6.13
167 170 3.361977 ATGTGTTGTTCCGCCCGC 61.362 61.111 0.00 0.00 0.00 6.13
182 185 4.249020 CGCGTGCCTGTTTGTGCA 62.249 61.111 0.00 0.00 34.54 4.57
188 191 1.373748 GCCTGTTTGTGCATGGCTG 60.374 57.895 0.00 0.00 40.36 4.85
190 193 1.466025 CCTGTTTGTGCATGGCTGGT 61.466 55.000 0.00 0.00 0.00 4.00
194 197 0.467844 TTTGTGCATGGCTGGTCTGT 60.468 50.000 0.00 0.00 0.00 3.41
199 202 3.402681 ATGGCTGGTCTGTCCGGG 61.403 66.667 0.00 0.00 42.62 5.73
213 216 4.404098 CGGGCGTGTAGGGGCTTT 62.404 66.667 0.00 0.00 0.00 3.51
220 223 0.960861 GTGTAGGGGCTTTGACTGGC 60.961 60.000 0.00 0.00 0.00 4.85
259 262 4.878397 CGGGAAGCTCTTTCATTGTCTAAT 59.122 41.667 0.00 0.00 37.54 1.73
276 279 9.675464 ATTGTCTAATGATTTACTTAACCGGAA 57.325 29.630 9.46 0.00 0.00 4.30
282 285 6.827586 TGATTTACTTAACCGGAAATTGCT 57.172 33.333 9.46 0.00 0.00 3.91
306 309 1.072331 GTGTTGAGGCAAGGAGAGGAA 59.928 52.381 0.00 0.00 0.00 3.36
312 315 2.771372 GAGGCAAGGAGAGGAAGAAGAT 59.229 50.000 0.00 0.00 0.00 2.40
314 317 3.966665 AGGCAAGGAGAGGAAGAAGATAG 59.033 47.826 0.00 0.00 0.00 2.08
327 330 9.855021 GAGGAAGAAGATAGTGAAGCTATTATC 57.145 37.037 0.00 0.00 40.30 1.75
341 346 9.499479 TGAAGCTATTATCAGAGATCAATTTCC 57.501 33.333 0.00 0.00 0.00 3.13
342 347 8.545229 AAGCTATTATCAGAGATCAATTTCCG 57.455 34.615 0.00 0.00 0.00 4.30
359 364 5.740290 TTTCCGGAGATCATCTTATACCC 57.260 43.478 3.34 0.00 0.00 3.69
402 407 9.445786 TGAATTTCAAAGTTCGAACTATGAAAC 57.554 29.630 29.91 16.94 38.57 2.78
445 450 1.507140 TATCTTTGGATCAGGGCCGT 58.493 50.000 0.00 0.00 33.71 5.68
449 454 0.394216 TTTGGATCAGGGCCGTCATG 60.394 55.000 0.00 0.00 0.00 3.07
454 459 1.976132 ATCAGGGCCGTCATGTCTGG 61.976 60.000 0.00 0.00 0.00 3.86
465 470 1.002134 ATGTCTGGCCGGGTCAAAG 60.002 57.895 12.87 0.00 0.00 2.77
474 479 1.318576 CCGGGTCAAAGCCATAATCC 58.681 55.000 0.00 0.00 34.89 3.01
480 485 5.048713 CGGGTCAAAGCCATAATCCTATTTC 60.049 44.000 0.00 0.00 34.89 2.17
500 505 9.305555 CTATTTCTATCCCCATGTTGATTGATT 57.694 33.333 6.66 2.75 0.00 2.57
510 515 9.492973 CCCCATGTTGATTGATTAATAAAATCC 57.507 33.333 15.65 6.71 30.75 3.01
514 519 8.854979 TGTTGATTGATTAATAAAATCCAGCG 57.145 30.769 15.65 0.00 30.75 5.18
515 520 8.681806 TGTTGATTGATTAATAAAATCCAGCGA 58.318 29.630 15.65 1.16 30.75 4.93
516 521 9.683069 GTTGATTGATTAATAAAATCCAGCGAT 57.317 29.630 15.65 0.00 30.75 4.58
527 532 9.956720 AATAAAATCCAGCGATTATTCTTGAAG 57.043 29.630 0.00 0.00 37.76 3.02
528 533 7.630242 AAAATCCAGCGATTATTCTTGAAGA 57.370 32.000 0.00 0.00 37.76 2.87
532 537 7.076842 TCCAGCGATTATTCTTGAAGAAAAG 57.923 36.000 12.10 3.42 37.82 2.27
533 538 6.878923 TCCAGCGATTATTCTTGAAGAAAAGA 59.121 34.615 12.10 1.53 37.82 2.52
534 539 6.963805 CCAGCGATTATTCTTGAAGAAAAGAC 59.036 38.462 12.10 4.04 37.82 3.01
535 540 7.361201 CCAGCGATTATTCTTGAAGAAAAGACA 60.361 37.037 12.10 0.00 37.82 3.41
536 541 8.180267 CAGCGATTATTCTTGAAGAAAAGACAT 58.820 33.333 12.10 0.00 37.82 3.06
537 542 8.180267 AGCGATTATTCTTGAAGAAAAGACATG 58.820 33.333 12.10 0.00 37.82 3.21
538 543 7.965107 GCGATTATTCTTGAAGAAAAGACATGT 59.035 33.333 12.10 0.00 37.82 3.21
539 544 9.270576 CGATTATTCTTGAAGAAAAGACATGTG 57.729 33.333 12.10 0.00 37.82 3.21
540 545 8.976986 ATTATTCTTGAAGAAAAGACATGTGC 57.023 30.769 12.10 0.00 37.82 4.57
541 546 4.836125 TCTTGAAGAAAAGACATGTGCC 57.164 40.909 1.15 0.00 31.19 5.01
542 547 4.464008 TCTTGAAGAAAAGACATGTGCCT 58.536 39.130 1.15 0.00 31.19 4.75
543 548 4.889409 TCTTGAAGAAAAGACATGTGCCTT 59.111 37.500 1.15 0.00 31.19 4.35
544 549 6.061441 TCTTGAAGAAAAGACATGTGCCTTA 58.939 36.000 1.15 0.00 31.19 2.69
545 550 6.716628 TCTTGAAGAAAAGACATGTGCCTTAT 59.283 34.615 1.15 0.00 31.19 1.73
546 551 6.899393 TGAAGAAAAGACATGTGCCTTATT 57.101 33.333 1.15 0.00 0.00 1.40
547 552 7.288810 TGAAGAAAAGACATGTGCCTTATTT 57.711 32.000 1.15 0.00 0.00 1.40
548 553 7.147312 TGAAGAAAAGACATGTGCCTTATTTG 58.853 34.615 1.15 0.00 0.00 2.32
549 554 6.899393 AGAAAAGACATGTGCCTTATTTGA 57.101 33.333 1.15 0.00 0.00 2.69
550 555 7.288810 AGAAAAGACATGTGCCTTATTTGAA 57.711 32.000 1.15 0.00 0.00 2.69
551 556 7.725251 AGAAAAGACATGTGCCTTATTTGAAA 58.275 30.769 1.15 0.00 0.00 2.69
552 557 7.869429 AGAAAAGACATGTGCCTTATTTGAAAG 59.131 33.333 1.15 0.00 0.00 2.62
554 559 4.463891 AGACATGTGCCTTATTTGAAAGGG 59.536 41.667 1.15 0.00 45.31 3.95
555 560 4.159557 ACATGTGCCTTATTTGAAAGGGT 58.840 39.130 0.00 0.00 45.31 4.34
556 561 4.021192 ACATGTGCCTTATTTGAAAGGGTG 60.021 41.667 0.00 0.00 45.31 4.61
557 562 3.571590 TGTGCCTTATTTGAAAGGGTGT 58.428 40.909 4.89 0.00 45.31 4.16
558 563 3.320541 TGTGCCTTATTTGAAAGGGTGTG 59.679 43.478 4.89 0.00 45.31 3.82
559 564 2.896685 TGCCTTATTTGAAAGGGTGTGG 59.103 45.455 4.89 0.00 45.31 4.17
560 565 2.353704 GCCTTATTTGAAAGGGTGTGGC 60.354 50.000 4.89 0.00 45.31 5.01
561 566 3.165071 CCTTATTTGAAAGGGTGTGGCT 58.835 45.455 0.00 0.00 42.08 4.75
562 567 4.340617 CCTTATTTGAAAGGGTGTGGCTA 58.659 43.478 0.00 0.00 42.08 3.93
563 568 4.399303 CCTTATTTGAAAGGGTGTGGCTAG 59.601 45.833 0.00 0.00 42.08 3.42
564 569 2.286365 TTTGAAAGGGTGTGGCTAGG 57.714 50.000 0.00 0.00 0.00 3.02
565 570 1.440618 TTGAAAGGGTGTGGCTAGGA 58.559 50.000 0.00 0.00 0.00 2.94
566 571 1.668826 TGAAAGGGTGTGGCTAGGAT 58.331 50.000 0.00 0.00 0.00 3.24
567 572 1.992557 TGAAAGGGTGTGGCTAGGATT 59.007 47.619 0.00 0.00 0.00 3.01
568 573 2.026262 TGAAAGGGTGTGGCTAGGATTC 60.026 50.000 0.00 0.00 0.00 2.52
569 574 1.668826 AAGGGTGTGGCTAGGATTCA 58.331 50.000 0.00 0.00 0.00 2.57
570 575 1.898863 AGGGTGTGGCTAGGATTCAT 58.101 50.000 0.00 0.00 0.00 2.57
571 576 1.771255 AGGGTGTGGCTAGGATTCATC 59.229 52.381 0.00 0.00 0.00 2.92
572 577 1.771255 GGGTGTGGCTAGGATTCATCT 59.229 52.381 0.00 0.00 0.00 2.90
573 578 2.972713 GGGTGTGGCTAGGATTCATCTA 59.027 50.000 0.00 0.00 0.00 1.98
574 579 3.584848 GGGTGTGGCTAGGATTCATCTAT 59.415 47.826 0.00 0.00 0.00 1.98
575 580 4.564406 GGGTGTGGCTAGGATTCATCTATG 60.564 50.000 0.00 0.00 0.00 2.23
576 581 4.040952 GGTGTGGCTAGGATTCATCTATGT 59.959 45.833 0.00 0.00 0.00 2.29
577 582 4.993584 GTGTGGCTAGGATTCATCTATGTG 59.006 45.833 0.00 0.00 0.00 3.21
578 583 4.901250 TGTGGCTAGGATTCATCTATGTGA 59.099 41.667 0.00 0.00 0.00 3.58
579 584 5.221521 TGTGGCTAGGATTCATCTATGTGAC 60.222 44.000 0.00 0.00 0.00 3.67
580 585 4.901250 TGGCTAGGATTCATCTATGTGACA 59.099 41.667 0.00 0.00 0.00 3.58
581 586 5.545335 TGGCTAGGATTCATCTATGTGACAT 59.455 40.000 2.65 2.65 0.00 3.06
582 587 6.725834 TGGCTAGGATTCATCTATGTGACATA 59.274 38.462 5.05 5.05 0.00 2.29
583 588 7.235399 TGGCTAGGATTCATCTATGTGACATAA 59.765 37.037 6.75 0.00 0.00 1.90
584 589 7.547370 GGCTAGGATTCATCTATGTGACATAAC 59.453 40.741 6.75 0.00 0.00 1.89
585 590 8.310382 GCTAGGATTCATCTATGTGACATAACT 58.690 37.037 6.75 0.00 0.00 2.24
608 613 9.973450 AACTATGTCACATCTAAGTATGATGTC 57.027 33.333 0.00 0.00 0.00 3.06
609 614 9.136323 ACTATGTCACATCTAAGTATGATGTCA 57.864 33.333 0.00 4.17 0.00 3.58
610 615 9.404348 CTATGTCACATCTAAGTATGATGTCAC 57.596 37.037 0.00 5.36 0.00 3.67
611 616 7.169158 TGTCACATCTAAGTATGATGTCACA 57.831 36.000 8.95 8.95 0.00 3.58
612 617 7.610865 TGTCACATCTAAGTATGATGTCACAA 58.389 34.615 10.25 0.00 0.00 3.33
613 618 8.093927 TGTCACATCTAAGTATGATGTCACAAA 58.906 33.333 10.25 0.00 0.00 2.83
614 619 8.935844 GTCACATCTAAGTATGATGTCACAAAA 58.064 33.333 6.42 0.00 0.00 2.44
615 620 8.935844 TCACATCTAAGTATGATGTCACAAAAC 58.064 33.333 6.42 0.00 0.00 2.43
616 621 8.720562 CACATCTAAGTATGATGTCACAAAACA 58.279 33.333 6.42 0.00 0.00 2.83
617 622 9.453572 ACATCTAAGTATGATGTCACAAAACAT 57.546 29.630 3.84 0.00 42.49 2.71
661 666 8.587952 AAACATTTTGTACAAATCTTGTAGCC 57.412 30.769 21.17 0.00 45.99 3.93
662 667 6.687604 ACATTTTGTACAAATCTTGTAGCCC 58.312 36.000 21.17 0.00 45.99 5.19
663 668 5.715434 TTTTGTACAAATCTTGTAGCCCC 57.285 39.130 21.17 0.00 45.99 5.80
664 669 4.650972 TTGTACAAATCTTGTAGCCCCT 57.349 40.909 5.64 0.00 45.99 4.79
665 670 5.765576 TTGTACAAATCTTGTAGCCCCTA 57.234 39.130 5.64 0.00 45.99 3.53
666 671 5.765576 TGTACAAATCTTGTAGCCCCTAA 57.234 39.130 0.00 0.00 45.99 2.69
667 672 6.321821 TGTACAAATCTTGTAGCCCCTAAT 57.678 37.500 0.00 0.00 45.99 1.73
668 673 6.727394 TGTACAAATCTTGTAGCCCCTAATT 58.273 36.000 0.00 0.00 45.99 1.40
669 674 7.863722 TGTACAAATCTTGTAGCCCCTAATTA 58.136 34.615 0.00 0.00 45.99 1.40
670 675 8.499406 TGTACAAATCTTGTAGCCCCTAATTAT 58.501 33.333 0.00 0.00 45.99 1.28
673 678 9.520515 ACAAATCTTGTAGCCCCTAATTATATG 57.479 33.333 0.00 0.00 43.27 1.78
674 679 8.960591 CAAATCTTGTAGCCCCTAATTATATGG 58.039 37.037 0.00 0.00 0.00 2.74
675 680 7.830848 ATCTTGTAGCCCCTAATTATATGGT 57.169 36.000 0.00 0.00 0.00 3.55
676 681 7.016153 TCTTGTAGCCCCTAATTATATGGTG 57.984 40.000 0.00 0.00 0.00 4.17
677 682 6.790461 TCTTGTAGCCCCTAATTATATGGTGA 59.210 38.462 0.00 0.00 0.00 4.02
678 683 7.293771 TCTTGTAGCCCCTAATTATATGGTGAA 59.706 37.037 0.00 0.00 0.00 3.18
679 684 6.775708 TGTAGCCCCTAATTATATGGTGAAC 58.224 40.000 0.00 0.00 0.00 3.18
680 685 6.561070 TGTAGCCCCTAATTATATGGTGAACT 59.439 38.462 0.00 0.00 0.00 3.01
681 686 7.735777 TGTAGCCCCTAATTATATGGTGAACTA 59.264 37.037 0.00 0.00 0.00 2.24
682 687 7.830848 AGCCCCTAATTATATGGTGAACTAT 57.169 36.000 0.00 0.00 0.00 2.12
683 688 8.232098 AGCCCCTAATTATATGGTGAACTATT 57.768 34.615 0.00 0.00 0.00 1.73
684 689 8.678798 AGCCCCTAATTATATGGTGAACTATTT 58.321 33.333 0.00 0.00 0.00 1.40
685 690 9.969001 GCCCCTAATTATATGGTGAACTATTTA 57.031 33.333 0.00 0.00 0.00 1.40
698 703 9.739276 TGGTGAACTATTTAGATGTGAAATTCT 57.261 29.630 0.00 0.00 0.00 2.40
790 795 3.893572 TGCCTGTGCATCACGATG 58.106 55.556 2.53 2.53 44.23 3.84
791 796 1.746239 TGCCTGTGCATCACGATGG 60.746 57.895 9.01 0.00 44.23 3.51
792 797 1.450134 GCCTGTGCATCACGATGGA 60.450 57.895 9.01 3.08 39.16 3.41
793 798 1.026182 GCCTGTGCATCACGATGGAA 61.026 55.000 9.01 0.00 40.81 3.53
794 799 1.452110 CCTGTGCATCACGATGGAAA 58.548 50.000 9.01 0.31 40.81 3.13
795 800 1.811965 CCTGTGCATCACGATGGAAAA 59.188 47.619 9.01 0.00 40.81 2.29
796 801 2.414559 CCTGTGCATCACGATGGAAAAC 60.415 50.000 9.01 0.00 40.81 2.43
797 802 1.539388 TGTGCATCACGATGGAAAACC 59.461 47.619 9.01 0.00 40.81 3.27
798 803 1.539388 GTGCATCACGATGGAAAACCA 59.461 47.619 9.01 0.00 40.81 3.67
799 804 2.164219 GTGCATCACGATGGAAAACCAT 59.836 45.455 9.01 1.14 40.81 3.55
800 805 2.164017 TGCATCACGATGGAAAACCATG 59.836 45.455 6.48 2.63 36.19 3.66
801 806 2.164219 GCATCACGATGGAAAACCATGT 59.836 45.455 6.48 3.19 39.16 3.21
802 807 3.731867 GCATCACGATGGAAAACCATGTC 60.732 47.826 6.48 0.00 39.16 3.06
803 808 3.133141 TCACGATGGAAAACCATGTCA 57.867 42.857 6.48 0.00 0.00 3.58
804 809 3.684908 TCACGATGGAAAACCATGTCAT 58.315 40.909 6.48 0.00 0.00 3.06
805 810 3.689161 TCACGATGGAAAACCATGTCATC 59.311 43.478 6.48 0.00 0.00 2.92
806 811 3.016736 ACGATGGAAAACCATGTCATCC 58.983 45.455 6.48 0.00 32.87 3.51
827 832 7.496263 TCATCCGTCAATACAAATTTCGGATTA 59.504 33.333 19.40 12.48 46.30 1.75
859 873 2.291282 TGTATTCTTCCCGCAACCCAAT 60.291 45.455 0.00 0.00 0.00 3.16
862 876 2.122783 TCTTCCCGCAACCCAATAAG 57.877 50.000 0.00 0.00 0.00 1.73
889 903 3.607310 CGCCGCCGACTCATCTATATATC 60.607 52.174 0.00 0.00 36.29 1.63
896 911 4.609559 CGACTCATCTATATATCCGAGCGC 60.610 50.000 0.00 0.00 0.00 5.92
922 937 0.616679 TCCCTTCTTACTCCCACCCG 60.617 60.000 0.00 0.00 0.00 5.28
932 954 3.766691 CCCACCCGTCGACCGATT 61.767 66.667 10.58 0.00 39.56 3.34
997 1019 1.511464 CGACACACGCGTAGGAGAC 60.511 63.158 13.44 0.00 34.51 3.36
1005 1027 2.782222 GCGTAGGAGACCGATGGCA 61.782 63.158 0.00 0.00 0.00 4.92
1007 1029 0.527817 CGTAGGAGACCGATGGCAAC 60.528 60.000 0.00 0.00 0.00 4.17
1118 1152 2.993008 GCACATGCTGGAGGAGGA 59.007 61.111 0.00 0.00 38.21 3.71
1120 1154 1.222936 CACATGCTGGAGGAGGACC 59.777 63.158 0.00 0.00 0.00 4.46
1199 1233 1.737696 CGACTACTGCAACCGCCATTA 60.738 52.381 0.00 0.00 37.32 1.90
1200 1234 1.664151 GACTACTGCAACCGCCATTAC 59.336 52.381 0.00 0.00 37.32 1.89
1201 1235 0.650512 CTACTGCAACCGCCATTACG 59.349 55.000 0.00 0.00 37.32 3.18
1202 1236 1.363145 TACTGCAACCGCCATTACGC 61.363 55.000 0.00 0.00 37.32 4.42
1203 1237 3.395470 CTGCAACCGCCATTACGCC 62.395 63.158 0.00 0.00 37.32 5.68
1204 1238 4.530325 GCAACCGCCATTACGCCG 62.530 66.667 0.00 0.00 0.00 6.46
1315 1355 1.079750 GACCAGGACACGCTCTTCC 60.080 63.158 0.00 0.00 0.00 3.46
1326 1366 0.686112 CGCTCTTCCTCCTCCTCCTT 60.686 60.000 0.00 0.00 0.00 3.36
1528 1573 5.410132 CACAAATCACTACCCAATCACGTTA 59.590 40.000 0.00 0.00 0.00 3.18
1657 1705 5.399113 ACCTATTTTCTTTACCCTTGGCAA 58.601 37.500 0.00 0.00 0.00 4.52
1674 1722 3.944650 TGGCAATTGCGTCATTATAGTGT 59.055 39.130 23.48 0.00 43.26 3.55
1675 1723 4.201901 TGGCAATTGCGTCATTATAGTGTG 60.202 41.667 23.48 0.00 43.26 3.82
1682 1730 4.982295 TGCGTCATTATAGTGTGCATAGTC 59.018 41.667 11.66 0.00 30.72 2.59
1684 1732 5.107837 GCGTCATTATAGTGTGCATAGTCAC 60.108 44.000 0.00 0.00 37.48 3.67
1722 1821 1.081242 CCTCACATGTTGTTGCGGC 60.081 57.895 0.00 0.00 0.00 6.53
1941 2046 3.822167 TCTCATGTGTGTTTGCATGATGT 59.178 39.130 0.00 0.00 46.79 3.06
1977 2083 5.416326 TCATGCATGTTTCATGATGAAGTGA 59.584 36.000 25.43 0.00 43.63 3.41
2007 2113 5.114081 TGCATGTTGAGAGACATATGACAG 58.886 41.667 10.38 0.00 38.15 3.51
2011 2117 4.772100 TGTTGAGAGACATATGACAGTGGA 59.228 41.667 10.38 0.00 0.00 4.02
2012 2118 5.245977 TGTTGAGAGACATATGACAGTGGAA 59.754 40.000 10.38 0.00 0.00 3.53
2029 2135 5.762218 CAGTGGAAGTGAGTCTTTTCTCATT 59.238 40.000 0.00 0.00 44.59 2.57
2034 2140 5.876612 AGTGAGTCTTTTCTCATTCATGC 57.123 39.130 0.00 0.00 44.59 4.06
2046 2152 3.731089 TCATTCATGCTGTGCGATGATA 58.269 40.909 0.00 0.00 30.80 2.15
2081 2187 9.372369 GCTTACATGTTGAGAGAAATAGTTAGT 57.628 33.333 2.30 0.00 0.00 2.24
2086 2192 5.783360 TGTTGAGAGAAATAGTTAGTGGGGA 59.217 40.000 0.00 0.00 0.00 4.81
2087 2193 5.934402 TGAGAGAAATAGTTAGTGGGGAC 57.066 43.478 0.00 0.00 0.00 4.46
2178 2679 5.470047 ACGACCAAGTCTATTTCTTCTGT 57.530 39.130 0.00 0.00 0.00 3.41
2202 2703 3.133362 ACCGTTCACCAAGTTGTCTCTTA 59.867 43.478 1.45 0.00 0.00 2.10
2247 2749 8.533657 AGATAGGAATCTTCAGATCTATGCTTG 58.466 37.037 0.00 0.00 39.55 4.01
2361 2864 2.165319 AGTCTGTCGTTGCTAAACCC 57.835 50.000 0.00 0.00 32.23 4.11
2401 2904 5.128919 GCCAAGAGTTTCATCCAGATACAT 58.871 41.667 0.00 0.00 31.46 2.29
2418 2921 0.957395 CATGCCTTCGCCAACACTCT 60.957 55.000 0.00 0.00 0.00 3.24
2431 2934 0.625316 ACACTCTATGCCATGGCCAA 59.375 50.000 33.44 20.04 41.09 4.52
2439 2945 1.484038 TGCCATGGCCAAAAGGTATC 58.516 50.000 33.44 2.26 41.09 2.24
2455 2961 5.906113 AGGTATCAGTAGATTGGCTATCG 57.094 43.478 3.32 0.00 38.36 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.221933 TCGACAAAGAAAACTATAGGCAATAAA 57.778 29.630 4.43 0.00 0.00 1.40
3 4 8.958119 ATCGACAAAGAAAACTATAGGCAATA 57.042 30.769 4.43 0.00 0.00 1.90
4 5 7.865706 ATCGACAAAGAAAACTATAGGCAAT 57.134 32.000 4.43 0.00 0.00 3.56
5 6 7.681939 AATCGACAAAGAAAACTATAGGCAA 57.318 32.000 4.43 0.00 0.00 4.52
6 7 7.174253 ACAAATCGACAAAGAAAACTATAGGCA 59.826 33.333 4.43 0.00 0.00 4.75
44 46 6.000840 GGAAATCCTTCATGAATAGGGTCTC 58.999 44.000 8.96 0.00 32.75 3.36
48 50 4.411013 GGGGAAATCCTTCATGAATAGGG 58.589 47.826 8.96 7.24 35.95 3.53
53 55 3.374098 GGATGGGGGAAATCCTTCATGAA 60.374 47.826 8.12 8.12 40.50 2.57
67 69 2.438434 GTTGCAGACGGATGGGGG 60.438 66.667 0.00 0.00 0.00 5.40
84 87 1.061131 CTGTAGTTGATCTTTGCGCGG 59.939 52.381 8.83 0.00 0.00 6.46
85 88 1.527793 GCTGTAGTTGATCTTTGCGCG 60.528 52.381 0.00 0.00 0.00 6.86
95 98 2.869801 CAGTCGTTTTGGCTGTAGTTGA 59.130 45.455 0.00 0.00 0.00 3.18
142 145 0.517316 GGAACAACACATGAGGCGAC 59.483 55.000 0.00 0.00 0.00 5.19
149 152 2.560861 CGGGCGGAACAACACATG 59.439 61.111 0.00 0.00 0.00 3.21
150 153 3.361977 GCGGGCGGAACAACACAT 61.362 61.111 0.00 0.00 0.00 3.21
165 168 3.541093 ATGCACAAACAGGCACGCG 62.541 57.895 3.53 3.53 43.75 6.01
167 170 1.372004 CCATGCACAAACAGGCACG 60.372 57.895 0.00 0.00 43.75 5.34
173 176 0.467844 AGACCAGCCATGCACAAACA 60.468 50.000 0.00 0.00 0.00 2.83
182 185 3.402681 CCCGGACAGACCAGCCAT 61.403 66.667 0.73 0.00 38.90 4.40
188 191 3.352338 CTACACGCCCGGACAGACC 62.352 68.421 0.73 0.00 0.00 3.85
190 193 3.066190 CCTACACGCCCGGACAGA 61.066 66.667 0.73 0.00 0.00 3.41
199 202 1.003718 AGTCAAAGCCCCTACACGC 60.004 57.895 0.00 0.00 0.00 5.34
213 216 2.668632 CTAAAGCCCGGCCAGTCA 59.331 61.111 5.55 0.00 0.00 3.41
220 223 2.106683 CCGACAAGCTAAAGCCCGG 61.107 63.158 0.00 0.00 43.38 5.73
259 262 6.827586 AGCAATTTCCGGTTAAGTAAATCA 57.172 33.333 0.00 0.00 0.00 2.57
270 273 1.981256 ACACTCAAGCAATTTCCGGT 58.019 45.000 0.00 0.00 0.00 5.28
273 276 3.858503 GCCTCAACACTCAAGCAATTTCC 60.859 47.826 0.00 0.00 0.00 3.13
276 279 2.309613 TGCCTCAACACTCAAGCAATT 58.690 42.857 0.00 0.00 0.00 2.32
282 285 1.768275 TCTCCTTGCCTCAACACTCAA 59.232 47.619 0.00 0.00 0.00 3.02
306 309 9.806448 TCTCTGATAATAGCTTCACTATCTTCT 57.194 33.333 0.00 0.00 40.90 2.85
327 330 4.953667 TGATCTCCGGAAATTGATCTCTG 58.046 43.478 24.09 3.33 37.00 3.35
333 338 7.386851 GGTATAAGATGATCTCCGGAAATTGA 58.613 38.462 5.23 0.00 0.00 2.57
341 346 6.102897 ACAAAGGGTATAAGATGATCTCCG 57.897 41.667 0.00 0.00 0.00 4.63
342 347 8.871125 TCTTACAAAGGGTATAAGATGATCTCC 58.129 37.037 0.00 0.00 31.53 3.71
374 379 9.611284 TTCATAGTTCGAACTTTGAAATTCATG 57.389 29.630 38.87 29.47 46.52 3.07
383 388 6.943981 TGTGAGTTTCATAGTTCGAACTTTG 58.056 36.000 33.82 32.26 40.37 2.77
384 389 7.280205 AGTTGTGAGTTTCATAGTTCGAACTTT 59.720 33.333 33.82 24.05 40.37 2.66
418 423 5.713861 GCCCTGATCCAAAGATAAAGCATAT 59.286 40.000 0.00 0.00 30.90 1.78
419 424 5.072741 GCCCTGATCCAAAGATAAAGCATA 58.927 41.667 0.00 0.00 30.90 3.14
429 434 0.107017 ATGACGGCCCTGATCCAAAG 60.107 55.000 0.00 0.00 0.00 2.77
445 450 1.773856 TTTGACCCGGCCAGACATGA 61.774 55.000 2.24 0.00 0.00 3.07
449 454 3.056328 GCTTTGACCCGGCCAGAC 61.056 66.667 2.24 0.00 0.00 3.51
454 459 0.668535 GATTATGGCTTTGACCCGGC 59.331 55.000 0.00 0.00 0.00 6.13
456 461 2.348411 AGGATTATGGCTTTGACCCG 57.652 50.000 0.00 0.00 0.00 5.28
465 470 6.327386 TGGGGATAGAAATAGGATTATGGC 57.673 41.667 0.00 0.00 0.00 4.40
474 479 8.874744 ATCAATCAACATGGGGATAGAAATAG 57.125 34.615 0.00 0.00 0.00 1.73
510 515 7.521529 TGTCTTTTCTTCAAGAATAATCGCTG 58.478 34.615 0.00 0.00 33.67 5.18
512 517 7.965107 ACATGTCTTTTCTTCAAGAATAATCGC 59.035 33.333 0.00 0.00 33.67 4.58
513 518 9.270576 CACATGTCTTTTCTTCAAGAATAATCG 57.729 33.333 0.00 0.00 33.67 3.34
514 519 9.070149 GCACATGTCTTTTCTTCAAGAATAATC 57.930 33.333 0.00 0.00 33.67 1.75
515 520 8.031277 GGCACATGTCTTTTCTTCAAGAATAAT 58.969 33.333 0.00 0.00 33.67 1.28
516 521 7.231317 AGGCACATGTCTTTTCTTCAAGAATAA 59.769 33.333 0.00 0.00 33.67 1.40
517 522 6.716628 AGGCACATGTCTTTTCTTCAAGAATA 59.283 34.615 0.00 0.00 33.67 1.75
518 523 5.537674 AGGCACATGTCTTTTCTTCAAGAAT 59.462 36.000 0.00 0.00 33.67 2.40
519 524 4.889409 AGGCACATGTCTTTTCTTCAAGAA 59.111 37.500 0.00 0.00 34.50 2.52
521 526 4.843220 AGGCACATGTCTTTTCTTCAAG 57.157 40.909 0.00 0.00 0.00 3.02
522 527 6.899393 ATAAGGCACATGTCTTTTCTTCAA 57.101 33.333 3.70 0.00 40.86 2.69
524 529 7.370383 TCAAATAAGGCACATGTCTTTTCTTC 58.630 34.615 3.70 0.00 40.86 2.87
525 530 7.288810 TCAAATAAGGCACATGTCTTTTCTT 57.711 32.000 3.70 3.77 40.86 2.52
526 531 6.899393 TCAAATAAGGCACATGTCTTTTCT 57.101 33.333 3.70 0.00 40.86 2.52
527 532 7.116805 CCTTTCAAATAAGGCACATGTCTTTTC 59.883 37.037 3.70 0.00 40.86 2.29
528 533 6.930722 CCTTTCAAATAAGGCACATGTCTTTT 59.069 34.615 3.70 0.00 40.86 2.27
532 537 4.220602 ACCCTTTCAAATAAGGCACATGTC 59.779 41.667 0.00 0.00 42.79 3.06
533 538 4.021192 CACCCTTTCAAATAAGGCACATGT 60.021 41.667 0.00 0.00 42.79 3.21
534 539 4.021192 ACACCCTTTCAAATAAGGCACATG 60.021 41.667 0.00 0.00 42.79 3.21
535 540 4.021192 CACACCCTTTCAAATAAGGCACAT 60.021 41.667 0.00 0.00 42.79 3.21
536 541 3.320541 CACACCCTTTCAAATAAGGCACA 59.679 43.478 0.00 0.00 42.79 4.57
537 542 3.306019 CCACACCCTTTCAAATAAGGCAC 60.306 47.826 0.00 0.00 42.79 5.01
538 543 2.896685 CCACACCCTTTCAAATAAGGCA 59.103 45.455 0.00 0.00 42.79 4.75
539 544 2.353704 GCCACACCCTTTCAAATAAGGC 60.354 50.000 0.00 0.00 42.79 4.35
540 545 3.165071 AGCCACACCCTTTCAAATAAGG 58.835 45.455 0.00 0.00 43.58 2.69
541 546 4.399303 CCTAGCCACACCCTTTCAAATAAG 59.601 45.833 0.00 0.00 0.00 1.73
542 547 4.043561 TCCTAGCCACACCCTTTCAAATAA 59.956 41.667 0.00 0.00 0.00 1.40
543 548 3.589735 TCCTAGCCACACCCTTTCAAATA 59.410 43.478 0.00 0.00 0.00 1.40
544 549 2.378547 TCCTAGCCACACCCTTTCAAAT 59.621 45.455 0.00 0.00 0.00 2.32
545 550 1.777878 TCCTAGCCACACCCTTTCAAA 59.222 47.619 0.00 0.00 0.00 2.69
546 551 1.440618 TCCTAGCCACACCCTTTCAA 58.559 50.000 0.00 0.00 0.00 2.69
547 552 1.668826 ATCCTAGCCACACCCTTTCA 58.331 50.000 0.00 0.00 0.00 2.69
548 553 2.026262 TGAATCCTAGCCACACCCTTTC 60.026 50.000 0.00 0.00 0.00 2.62
549 554 1.992557 TGAATCCTAGCCACACCCTTT 59.007 47.619 0.00 0.00 0.00 3.11
550 555 1.668826 TGAATCCTAGCCACACCCTT 58.331 50.000 0.00 0.00 0.00 3.95
551 556 1.771255 GATGAATCCTAGCCACACCCT 59.229 52.381 0.00 0.00 0.00 4.34
552 557 1.771255 AGATGAATCCTAGCCACACCC 59.229 52.381 0.00 0.00 0.00 4.61
553 558 4.040952 ACATAGATGAATCCTAGCCACACC 59.959 45.833 0.00 0.00 0.00 4.16
554 559 4.993584 CACATAGATGAATCCTAGCCACAC 59.006 45.833 0.00 0.00 0.00 3.82
555 560 4.901250 TCACATAGATGAATCCTAGCCACA 59.099 41.667 0.00 0.00 0.00 4.17
556 561 5.221521 TGTCACATAGATGAATCCTAGCCAC 60.222 44.000 0.00 0.00 0.00 5.01
557 562 4.901250 TGTCACATAGATGAATCCTAGCCA 59.099 41.667 0.00 0.00 0.00 4.75
558 563 5.474578 TGTCACATAGATGAATCCTAGCC 57.525 43.478 0.00 0.00 0.00 3.93
559 564 8.310382 AGTTATGTCACATAGATGAATCCTAGC 58.690 37.037 0.00 0.00 0.00 3.42
563 568 9.935241 ACATAGTTATGTCACATAGATGAATCC 57.065 33.333 17.20 0.00 42.96 3.01
635 640 9.040939 GGCTACAAGATTTGTACAAAATGTTTT 57.959 29.630 27.82 17.11 43.27 2.43
636 641 7.655732 GGGCTACAAGATTTGTACAAAATGTTT 59.344 33.333 27.82 17.29 43.27 2.83
637 642 7.151976 GGGCTACAAGATTTGTACAAAATGTT 58.848 34.615 27.82 18.57 43.27 2.71
638 643 6.295067 GGGGCTACAAGATTTGTACAAAATGT 60.295 38.462 26.74 26.74 43.27 2.71
639 644 6.071391 AGGGGCTACAAGATTTGTACAAAATG 60.071 38.462 23.97 22.27 43.27 2.32
640 645 6.016555 AGGGGCTACAAGATTTGTACAAAAT 58.983 36.000 23.97 13.42 43.27 1.82
641 646 5.390387 AGGGGCTACAAGATTTGTACAAAA 58.610 37.500 23.97 8.78 43.27 2.44
642 647 4.993028 AGGGGCTACAAGATTTGTACAAA 58.007 39.130 22.58 22.58 43.27 2.83
643 648 4.650972 AGGGGCTACAAGATTTGTACAA 57.349 40.909 3.59 3.59 43.27 2.41
644 649 5.765576 TTAGGGGCTACAAGATTTGTACA 57.234 39.130 0.00 0.00 43.27 2.90
645 650 8.919777 ATAATTAGGGGCTACAAGATTTGTAC 57.080 34.615 0.00 0.00 43.27 2.90
648 653 8.960591 CCATATAATTAGGGGCTACAAGATTTG 58.039 37.037 0.00 0.00 0.00 2.32
649 654 8.678798 ACCATATAATTAGGGGCTACAAGATTT 58.321 33.333 5.81 0.00 33.44 2.17
650 655 8.109634 CACCATATAATTAGGGGCTACAAGATT 58.890 37.037 5.81 0.00 33.44 2.40
651 656 7.461043 TCACCATATAATTAGGGGCTACAAGAT 59.539 37.037 5.81 0.00 33.44 2.40
652 657 6.790461 TCACCATATAATTAGGGGCTACAAGA 59.210 38.462 5.81 0.00 33.44 3.02
653 658 7.016153 TCACCATATAATTAGGGGCTACAAG 57.984 40.000 5.81 0.00 33.44 3.16
654 659 7.073215 AGTTCACCATATAATTAGGGGCTACAA 59.927 37.037 5.81 0.00 33.44 2.41
655 660 6.561070 AGTTCACCATATAATTAGGGGCTACA 59.439 38.462 5.81 0.00 33.44 2.74
656 661 7.017319 AGTTCACCATATAATTAGGGGCTAC 57.983 40.000 5.81 0.00 33.44 3.58
657 662 8.927059 ATAGTTCACCATATAATTAGGGGCTA 57.073 34.615 5.81 0.00 33.44 3.93
658 663 7.830848 ATAGTTCACCATATAATTAGGGGCT 57.169 36.000 5.81 0.00 33.44 5.19
659 664 8.879427 AAATAGTTCACCATATAATTAGGGGC 57.121 34.615 5.81 0.00 33.44 5.80
672 677 9.739276 AGAATTTCACATCTAAATAGTTCACCA 57.261 29.630 0.00 0.00 0.00 4.17
722 727 9.683069 GACATGTTTTTCAAATACAGAATGACT 57.317 29.630 0.00 0.00 39.69 3.41
723 728 9.462174 TGACATGTTTTTCAAATACAGAATGAC 57.538 29.630 0.00 0.00 39.69 3.06
775 780 1.452110 TTTCCATCGTGATGCACAGG 58.548 50.000 4.29 0.00 37.49 4.00
776 781 2.414559 GGTTTTCCATCGTGATGCACAG 60.415 50.000 4.29 0.00 40.31 3.66
777 782 1.539388 GGTTTTCCATCGTGATGCACA 59.461 47.619 4.29 0.00 40.31 4.57
778 783 1.539388 TGGTTTTCCATCGTGATGCAC 59.461 47.619 4.29 0.00 46.22 4.57
779 784 1.902938 TGGTTTTCCATCGTGATGCA 58.097 45.000 4.29 0.00 46.22 3.96
790 795 2.432444 TGACGGATGACATGGTTTTCC 58.568 47.619 0.00 0.00 41.14 3.13
791 796 4.701956 ATTGACGGATGACATGGTTTTC 57.298 40.909 0.00 0.00 0.00 2.29
792 797 5.007034 TGTATTGACGGATGACATGGTTTT 58.993 37.500 0.00 0.00 0.00 2.43
793 798 4.584874 TGTATTGACGGATGACATGGTTT 58.415 39.130 0.00 0.00 0.00 3.27
794 799 4.214986 TGTATTGACGGATGACATGGTT 57.785 40.909 0.00 0.00 0.00 3.67
795 800 3.904800 TGTATTGACGGATGACATGGT 57.095 42.857 0.00 0.00 0.00 3.55
796 801 5.756195 ATTTGTATTGACGGATGACATGG 57.244 39.130 0.00 0.00 0.00 3.66
797 802 6.411782 CGAAATTTGTATTGACGGATGACATG 59.588 38.462 0.00 0.00 0.00 3.21
798 803 6.458206 CCGAAATTTGTATTGACGGATGACAT 60.458 38.462 6.41 0.00 42.13 3.06
799 804 5.163804 CCGAAATTTGTATTGACGGATGACA 60.164 40.000 6.41 0.00 42.13 3.58
800 805 5.064198 TCCGAAATTTGTATTGACGGATGAC 59.936 40.000 9.99 0.00 42.70 3.06
801 806 5.179533 TCCGAAATTTGTATTGACGGATGA 58.820 37.500 9.99 0.00 42.70 2.92
802 807 5.478233 TCCGAAATTTGTATTGACGGATG 57.522 39.130 9.99 0.00 42.70 3.51
804 809 7.612668 TTAATCCGAAATTTGTATTGACGGA 57.387 32.000 14.82 14.82 46.74 4.69
805 810 9.938670 TTATTAATCCGAAATTTGTATTGACGG 57.061 29.630 0.00 0.15 41.54 4.79
841 846 2.818751 TATTGGGTTGCGGGAAGAAT 57.181 45.000 0.00 0.00 0.00 2.40
846 851 1.953311 GCTTCTTATTGGGTTGCGGGA 60.953 52.381 0.00 0.00 0.00 5.14
859 873 4.807039 GTCGGCGGCGGCTTCTTA 62.807 66.667 29.80 5.51 39.81 2.10
896 911 0.100861 GAGTAAGAAGGGAGACGCGG 59.899 60.000 12.47 0.00 0.00 6.46
909 924 1.509923 GTCGACGGGTGGGAGTAAG 59.490 63.158 0.00 0.00 0.00 2.34
929 944 4.330074 ACTCGGTGTTTCAATCGATCAATC 59.670 41.667 0.00 0.00 0.00 2.67
932 954 3.313012 ACTCGGTGTTTCAATCGATCA 57.687 42.857 0.00 0.00 0.00 2.92
974 996 1.059838 CTACGCGTGTGTCGATCGA 59.940 57.895 24.59 15.15 42.86 3.59
997 1019 2.528743 CGCTGCTAGTTGCCATCGG 61.529 63.158 0.00 0.00 42.00 4.18
1005 1027 2.317609 CGTGTTGCCGCTGCTAGTT 61.318 57.895 0.70 0.00 38.71 2.24
1007 1029 3.490759 CCGTGTTGCCGCTGCTAG 61.491 66.667 0.70 0.00 38.71 3.42
1137 1171 3.001406 GTCACCTGGGGTAGCGGT 61.001 66.667 0.00 0.00 32.11 5.68
1261 1301 2.029964 GGTGTCGAACCGCTCCAA 59.970 61.111 0.00 0.00 39.81 3.53
1315 1355 4.168291 GGCGGCAAGGAGGAGGAG 62.168 72.222 3.07 0.00 0.00 3.69
1326 1366 3.621805 TCGAGGTCTTTGGCGGCA 61.622 61.111 7.97 7.97 0.00 5.69
1627 1675 4.874396 GGGTAAAGAAAATAGGTCCTGACG 59.126 45.833 0.00 0.00 0.00 4.35
1657 1705 5.991606 ACTATGCACACTATAATGACGCAAT 59.008 36.000 7.03 1.25 35.95 3.56
1674 1722 9.764363 CATCTACCTAATAAAAGTGACTATGCA 57.236 33.333 0.00 0.00 0.00 3.96
1675 1723 9.982651 TCATCTACCTAATAAAAGTGACTATGC 57.017 33.333 0.00 0.00 0.00 3.14
1693 1741 5.918608 ACAACATGTGAGGTATCATCTACC 58.081 41.667 0.00 0.00 37.87 3.18
1706 1805 1.100463 ACTGCCGCAACAACATGTGA 61.100 50.000 0.00 0.00 32.55 3.58
1707 1806 0.590682 TACTGCCGCAACAACATGTG 59.409 50.000 0.00 0.00 0.00 3.21
1708 1807 0.874390 CTACTGCCGCAACAACATGT 59.126 50.000 0.00 0.00 0.00 3.21
1722 1821 7.970061 CACATTGAAATATGTCCCAAACTACTG 59.030 37.037 0.00 0.00 36.64 2.74
2011 2117 6.072618 CAGCATGAATGAGAAAAGACTCACTT 60.073 38.462 0.00 0.00 43.84 3.16
2012 2118 5.411977 CAGCATGAATGAGAAAAGACTCACT 59.588 40.000 0.00 0.00 43.84 3.41
2029 2135 2.419667 CCATATCATCGCACAGCATGA 58.580 47.619 0.00 6.59 39.69 3.07
2034 2140 3.242641 GCATATGCCATATCATCGCACAG 60.243 47.826 17.26 0.00 34.87 3.66
2046 2152 5.379187 TCTCAACATGTAAGCATATGCCAT 58.621 37.500 23.96 16.71 43.38 4.40
2178 2679 3.133362 AGAGACAACTTGGTGAACGGTTA 59.867 43.478 0.00 0.00 0.00 2.85
2266 2768 2.158682 TGGCTAGTCTTGCAACAAGGAA 60.159 45.455 8.55 0.00 0.00 3.36
2374 2877 1.820519 TGGATGAAACTCTTGGCATGC 59.179 47.619 9.90 9.90 0.00 4.06
2418 2921 2.836636 TACCTTTTGGCCATGGCATA 57.163 45.000 36.56 22.75 45.59 3.14
2431 2934 6.267928 ACGATAGCCAATCTACTGATACCTTT 59.732 38.462 0.00 0.00 42.67 3.11
2439 2945 8.594881 AAAAATCTACGATAGCCAATCTACTG 57.405 34.615 0.00 0.00 42.67 2.74


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

AutoCloner maintained by Alex Coulton.