Multiple sequence alignment - TraesCS5D01G224200

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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 TraesCS5D01G224200 chr5D 100.000 6418 0 0 1 6418 332045588 332039171 0.000000e+00 11852.0
1 TraesCS5D01G224200 chr5D 81.853 259 34 8 66 312 438042644 438042387 8.430000e-49 206.0
2 TraesCS5D01G224200 chr5D 78.802 217 33 5 317 520 404258626 404258842 4.040000e-27 134.0
3 TraesCS5D01G224200 chr5D 92.135 89 7 0 3804 3892 34445605 34445517 6.760000e-25 126.0
4 TraesCS5D01G224200 chr5D 97.872 47 1 0 5317 5363 332040223 332040177 1.480000e-11 82.4
5 TraesCS5D01G224200 chr5D 97.872 47 1 0 5366 5412 332040272 332040226 1.480000e-11 82.4
6 TraesCS5D01G224200 chr5A 92.206 2720 98 44 2393 5028 432446370 432443681 0.000000e+00 3744.0
7 TraesCS5D01G224200 chr5A 95.384 1408 45 7 5026 6418 432443522 432442120 0.000000e+00 2222.0
8 TraesCS5D01G224200 chr5A 91.945 1527 67 18 855 2367 432448043 432446559 0.000000e+00 2087.0
9 TraesCS5D01G224200 chr5A 94.792 96 3 1 743 836 432448411 432448316 1.440000e-31 148.0
10 TraesCS5D01G224200 chr5A 100.000 47 0 0 5366 5412 432443236 432443190 3.190000e-13 87.9
11 TraesCS5D01G224200 chr5A 97.872 47 1 0 5317 5363 432443187 432443141 1.480000e-11 82.4
12 TraesCS5D01G224200 chr5A 95.745 47 2 0 1513 1559 432447455 432447409 6.900000e-10 76.8
13 TraesCS5D01G224200 chr5B 92.573 2612 113 37 3849 6417 387741648 387739075 0.000000e+00 3674.0
14 TraesCS5D01G224200 chr5B 94.793 1498 49 11 2364 3858 387743143 387741672 0.000000e+00 2307.0
15 TraesCS5D01G224200 chr5B 90.984 1697 90 31 716 2367 387744952 387743274 0.000000e+00 2228.0
16 TraesCS5D01G224200 chr5B 89.073 302 32 1 1 302 387747214 387746914 2.180000e-99 374.0
17 TraesCS5D01G224200 chr5B 80.569 211 33 6 317 523 485569562 485569768 8.620000e-34 156.0
18 TraesCS5D01G224200 chr5B 90.625 96 5 1 3803 3898 315928861 315928952 2.430000e-24 124.0
19 TraesCS5D01G224200 chr5B 77.489 231 28 13 317 523 293662796 293663026 4.070000e-22 117.0
20 TraesCS5D01G224200 chr5B 84.034 119 10 7 3779 3893 621464047 621464160 8.800000e-19 106.0
21 TraesCS5D01G224200 chr5B 97.872 47 1 0 5317 5363 387740140 387740094 1.480000e-11 82.4
22 TraesCS5D01G224200 chr3D 88.100 479 50 3 3163 3641 390102455 390101984 4.340000e-156 562.0
23 TraesCS5D01G224200 chr3D 89.344 366 36 3 2749 3112 390102836 390102472 2.110000e-124 457.0
24 TraesCS5D01G224200 chr4D 87.891 479 50 2 3163 3641 216320105 216320575 2.020000e-154 556.0
25 TraesCS5D01G224200 chr4D 88.798 366 38 3 2749 3112 216319724 216320088 4.570000e-121 446.0
26 TraesCS5D01G224200 chr1D 87.683 479 53 2 3163 3641 116472531 116472059 2.610000e-153 553.0
27 TraesCS5D01G224200 chr1D 77.106 546 74 33 26 521 420202418 420202962 1.060000e-67 268.0
28 TraesCS5D01G224200 chr1D 92.222 90 5 1 3804 3893 458142845 458142932 6.760000e-25 126.0
29 TraesCS5D01G224200 chrUn 86.848 479 56 3 3163 3641 83993852 83994323 4.410000e-146 529.0
30 TraesCS5D01G224200 chrUn 86.848 479 56 3 3163 3641 232032131 232032602 4.410000e-146 529.0
31 TraesCS5D01G224200 chrUn 86.848 479 56 3 3163 3641 232040338 232040809 4.410000e-146 529.0
32 TraesCS5D01G224200 chrUn 86.017 472 49 10 5665 6123 83994668 83995135 2.080000e-134 490.0
33 TraesCS5D01G224200 chrUn 86.017 472 49 10 5665 6123 232032947 232033414 2.080000e-134 490.0
34 TraesCS5D01G224200 chrUn 86.017 472 49 10 5665 6123 232041154 232041621 2.080000e-134 490.0
35 TraesCS5D01G224200 chrUn 88.493 365 38 3 2749 3112 83993474 83993835 7.640000e-119 438.0
36 TraesCS5D01G224200 chrUn 88.493 365 38 3 2749 3112 232031753 232032114 7.640000e-119 438.0
37 TraesCS5D01G224200 chrUn 88.493 365 38 3 2749 3112 232039960 232040321 7.640000e-119 438.0
38 TraesCS5D01G224200 chr7B 86.848 479 56 3 3163 3641 2314390 2314861 4.410000e-146 529.0
39 TraesCS5D01G224200 chr7B 86.017 472 49 10 5665 6123 2315206 2315673 2.080000e-134 490.0
40 TraesCS5D01G224200 chr7B 88.493 365 38 3 2749 3112 2314012 2314373 7.640000e-119 438.0
41 TraesCS5D01G224200 chr4A 85.714 469 53 9 5665 6123 731998887 731999351 3.480000e-132 483.0
42 TraesCS5D01G224200 chr4A 79.060 234 40 5 3937 4166 63103141 63103369 1.110000e-32 152.0
43 TraesCS5D01G224200 chr4A 93.258 89 2 1 3809 3893 590661840 590661752 1.880000e-25 128.0
44 TraesCS5D01G224200 chr2D 89.344 366 36 3 2749 3112 592578739 592579103 2.110000e-124 457.0
45 TraesCS5D01G224200 chr2D 80.645 217 26 6 312 527 2004722 2004521 3.100000e-33 154.0
46 TraesCS5D01G224200 chr1B 79.102 579 69 24 1 528 403615648 403615071 1.020000e-92 351.0
47 TraesCS5D01G224200 chr1B 83.801 321 43 6 1 312 458013297 458013617 4.870000e-76 296.0
48 TraesCS5D01G224200 chr1A 85.220 318 38 6 1 310 74319229 74318913 1.040000e-82 318.0
49 TraesCS5D01G224200 chr1A 76.190 294 56 11 9 293 248361839 248361551 6.710000e-30 143.0
50 TraesCS5D01G224200 chr1A 89.691 97 8 2 3805 3900 344442506 344442411 8.740000e-24 122.0
51 TraesCS5D01G224200 chr2A 85.256 312 37 7 1 304 518346 518656 4.830000e-81 313.0
52 TraesCS5D01G224200 chr2A 77.682 233 29 10 317 528 778289474 778289244 3.140000e-23 121.0
53 TraesCS5D01G224200 chr6A 83.974 312 41 6 1 304 483474 483784 2.260000e-74 291.0
54 TraesCS5D01G224200 chr6B 82.468 308 45 6 1 303 680995939 680996242 1.770000e-65 261.0
55 TraesCS5D01G224200 chr2B 81.979 283 40 8 1 274 790685248 790684968 5.010000e-56 230.0
56 TraesCS5D01G224200 chr3B 78.947 228 30 9 319 528 786722205 786721978 8.680000e-29 139.0
57 TraesCS5D01G224200 chr3B 83.459 133 21 1 391 523 31255620 31255751 8.740000e-24 122.0


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 TraesCS5D01G224200 chr5D 332039171 332045588 6417 True 11852.000000 11852 100.000000 1 6418 1 chr5D.!!$R2 6417
1 TraesCS5D01G224200 chr5A 432442120 432448411 6291 True 1206.871429 3744 95.420571 743 6418 7 chr5A.!!$R1 5675
2 TraesCS5D01G224200 chr5B 387739075 387747214 8139 True 1733.080000 3674 93.059000 1 6417 5 chr5B.!!$R1 6416
3 TraesCS5D01G224200 chr3D 390101984 390102836 852 True 509.500000 562 88.722000 2749 3641 2 chr3D.!!$R1 892
4 TraesCS5D01G224200 chr4D 216319724 216320575 851 False 501.000000 556 88.344500 2749 3641 2 chr4D.!!$F1 892
5 TraesCS5D01G224200 chr1D 420202418 420202962 544 False 268.000000 268 77.106000 26 521 1 chr1D.!!$F1 495
6 TraesCS5D01G224200 chrUn 83993474 83995135 1661 False 485.666667 529 87.119333 2749 6123 3 chrUn.!!$F1 3374
7 TraesCS5D01G224200 chrUn 232031753 232033414 1661 False 485.666667 529 87.119333 2749 6123 3 chrUn.!!$F2 3374
8 TraesCS5D01G224200 chrUn 232039960 232041621 1661 False 485.666667 529 87.119333 2749 6123 3 chrUn.!!$F3 3374
9 TraesCS5D01G224200 chr7B 2314012 2315673 1661 False 485.666667 529 87.119333 2749 6123 3 chr7B.!!$F1 3374
10 TraesCS5D01G224200 chr1B 403615071 403615648 577 True 351.000000 351 79.102000 1 528 1 chr1B.!!$R1 527

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
525 565 0.035056 GAGGCCAGGTGTGTGCTTAT 60.035 55.000 5.01 0.0 0.00 1.73 F
528 568 0.109132 GCCAGGTGTGTGCTTATTGC 60.109 55.000 0.00 0.0 43.25 3.56 F
529 569 0.168788 CCAGGTGTGTGCTTATTGCG 59.831 55.000 0.00 0.0 46.63 4.85 F
530 570 0.168788 CAGGTGTGTGCTTATTGCGG 59.831 55.000 0.00 0.0 46.63 5.69 F
770 2350 0.177141 TGAAGCGCCATACTACCACC 59.823 55.000 2.29 0.0 0.00 4.61 F
2430 4530 0.449786 TTCTGCACCACGTTGTTGTG 59.550 50.000 0.00 0.0 39.60 3.33 F
2438 4538 1.330521 CCACGTTGTTGTGAACTCCTG 59.669 52.381 0.00 0.0 42.55 3.86 F
3991 6254 0.038744 AACTCCCAGTGAATGCCCTG 59.961 55.000 0.00 0.0 0.00 4.45 F
4618 6906 0.324943 ACATACGCACTGCCTCCTTT 59.675 50.000 0.00 0.0 0.00 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1417 3281 0.037882 CACTGCCACTGACTGTCGAT 60.038 55.000 2.98 0.0 0.00 3.59 R
1712 3593 0.252881 TCCATCTCCTGCTCCAACCT 60.253 55.000 0.00 0.0 0.00 3.50 R
2147 4033 1.089920 ACGCATCAATGGCTGAAGAC 58.910 50.000 0.00 0.0 37.67 3.01 R
2407 4427 1.156736 ACAACGTGGTGCAGAATAGC 58.843 50.000 0.00 0.0 0.00 2.97 R
2607 4707 1.477700 GCAGCCCAATTTAGCATGTCA 59.522 47.619 0.00 0.0 0.00 3.58 R
3958 6221 0.253327 GGAGTTCCTTCCCAGCGAAT 59.747 55.000 0.00 0.0 0.00 3.34 R
4125 6388 0.685458 GCTGGGAGGATGGCATTTGT 60.685 55.000 0.00 0.0 0.00 2.83 R
5184 7662 0.249868 CTTGAGGCGCGGGATCATTA 60.250 55.000 8.83 0.0 0.00 1.90 R
5618 8105 0.884704 TGTTGTCCTTTGCTCGCTCC 60.885 55.000 0.00 0.0 0.00 4.70 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 45 0.984230 GAGGGATGGTTGTGGAGTGA 59.016 55.000 0.00 0.00 0.00 3.41
92 94 4.404654 GAAAAGCGGTGGCGGCAG 62.405 66.667 13.91 2.06 46.35 4.85
113 122 3.250744 GCACTGTTACTTCGATGTGCTA 58.749 45.455 13.80 0.00 44.80 3.49
115 124 4.234574 CACTGTTACTTCGATGTGCTACA 58.765 43.478 13.80 12.79 0.00 2.74
151 160 0.537188 CTCCGAGGCAAAAGCCTAGA 59.463 55.000 16.62 12.02 40.79 2.43
228 237 4.836175 TGTTGGAGGTATTGCTCGGATATA 59.164 41.667 0.00 0.00 0.00 0.86
304 313 2.260434 GACGGCGGCACTTGAGTA 59.740 61.111 8.47 0.00 0.00 2.59
306 315 0.739813 GACGGCGGCACTTGAGTATT 60.740 55.000 8.47 0.00 0.00 1.89
307 316 1.019278 ACGGCGGCACTTGAGTATTG 61.019 55.000 13.24 0.00 0.00 1.90
315 355 1.920574 CACTTGAGTATTGCTCCGTCG 59.079 52.381 0.00 0.00 43.48 5.12
324 364 2.094757 TTGCTCCGTCGTCCATGTGT 62.095 55.000 0.00 0.00 0.00 3.72
328 368 0.319211 TCCGTCGTCCATGTGTTGTC 60.319 55.000 0.00 0.00 0.00 3.18
336 376 3.125146 CGTCCATGTGTTGTCTATGGTTG 59.875 47.826 0.00 0.00 41.61 3.77
341 381 1.196808 GTGTTGTCTATGGTTGGTGCG 59.803 52.381 0.00 0.00 0.00 5.34
342 382 1.202710 TGTTGTCTATGGTTGGTGCGT 60.203 47.619 0.00 0.00 0.00 5.24
343 383 2.037381 TGTTGTCTATGGTTGGTGCGTA 59.963 45.455 0.00 0.00 0.00 4.42
353 393 2.124903 GTTGGTGCGTATATGGTCTCG 58.875 52.381 0.00 0.00 0.00 4.04
359 399 2.691526 TGCGTATATGGTCTCGGTTCTT 59.308 45.455 0.00 0.00 0.00 2.52
367 407 2.680841 TGGTCTCGGTTCTTGTTTGTTG 59.319 45.455 0.00 0.00 0.00 3.33
370 410 4.319549 GGTCTCGGTTCTTGTTTGTTGATC 60.320 45.833 0.00 0.00 0.00 2.92
372 412 2.032377 TCGGTTCTTGTTTGTTGATCGC 60.032 45.455 0.00 0.00 0.00 4.58
383 423 3.806625 TGTTGATCGCTGATCTGATCA 57.193 42.857 18.61 18.61 46.79 2.92
389 429 3.874392 TCGCTGATCTGATCACTTTGA 57.126 42.857 16.06 8.77 35.06 2.69
430 470 2.221169 TCGCCTATGCATAGCTTTTGG 58.779 47.619 25.60 14.39 37.32 3.28
431 471 1.949525 CGCCTATGCATAGCTTTTGGT 59.050 47.619 25.60 0.00 37.32 3.67
435 475 4.498682 GCCTATGCATAGCTTTTGGTCTTG 60.499 45.833 25.60 10.27 37.47 3.02
439 479 3.888323 TGCATAGCTTTTGGTCTTGTGAA 59.112 39.130 0.00 0.00 0.00 3.18
440 480 4.523943 TGCATAGCTTTTGGTCTTGTGAAT 59.476 37.500 0.00 0.00 0.00 2.57
451 491 4.887071 TGGTCTTGTGAATTTGCTAGTTGT 59.113 37.500 0.00 0.00 0.00 3.32
452 492 5.359576 TGGTCTTGTGAATTTGCTAGTTGTT 59.640 36.000 0.00 0.00 0.00 2.83
453 493 5.687285 GGTCTTGTGAATTTGCTAGTTGTTG 59.313 40.000 0.00 0.00 0.00 3.33
483 523 2.136298 ACATGTGTGTGTTGGGTTGA 57.864 45.000 0.00 0.00 37.14 3.18
485 525 2.622942 ACATGTGTGTGTTGGGTTGATC 59.377 45.455 0.00 0.00 37.14 2.92
492 532 0.464554 TGTTGGGTTGATCGTGTGCA 60.465 50.000 0.00 0.00 0.00 4.57
493 533 0.881118 GTTGGGTTGATCGTGTGCAT 59.119 50.000 0.00 0.00 0.00 3.96
498 538 1.131126 GGTTGATCGTGTGCATCCTTG 59.869 52.381 0.00 0.00 0.00 3.61
501 541 1.805943 TGATCGTGTGCATCCTTGTTG 59.194 47.619 0.00 0.00 0.00 3.33
504 544 0.661187 CGTGTGCATCCTTGTTGTGC 60.661 55.000 0.00 0.00 39.26 4.57
505 545 0.385029 GTGTGCATCCTTGTTGTGCA 59.615 50.000 0.00 0.00 45.69 4.57
507 547 3.418022 TGCATCCTTGTTGTGCAGA 57.582 47.368 0.00 0.00 43.30 4.26
509 549 0.524862 GCATCCTTGTTGTGCAGAGG 59.475 55.000 0.00 0.00 38.68 3.69
510 550 0.524862 CATCCTTGTTGTGCAGAGGC 59.475 55.000 0.00 0.00 41.68 4.70
511 551 0.610232 ATCCTTGTTGTGCAGAGGCC 60.610 55.000 0.00 0.00 40.13 5.19
512 552 1.529010 CCTTGTTGTGCAGAGGCCA 60.529 57.895 5.01 0.00 40.13 5.36
514 554 1.521450 CTTGTTGTGCAGAGGCCAGG 61.521 60.000 5.01 0.00 40.13 4.45
515 555 2.113986 GTTGTGCAGAGGCCAGGT 59.886 61.111 5.01 0.00 40.13 4.00
516 556 2.113774 TTGTGCAGAGGCCAGGTG 59.886 61.111 5.01 0.00 40.13 4.00
517 557 2.756042 TTGTGCAGAGGCCAGGTGT 61.756 57.895 5.01 0.00 40.13 4.16
518 558 2.670934 GTGCAGAGGCCAGGTGTG 60.671 66.667 5.01 0.00 40.13 3.82
519 559 3.170672 TGCAGAGGCCAGGTGTGT 61.171 61.111 5.01 0.00 40.13 3.72
520 560 2.670934 GCAGAGGCCAGGTGTGTG 60.671 66.667 5.01 0.00 0.00 3.82
521 561 2.670934 CAGAGGCCAGGTGTGTGC 60.671 66.667 5.01 0.00 0.00 4.57
524 564 1.127567 AGAGGCCAGGTGTGTGCTTA 61.128 55.000 5.01 0.00 0.00 3.09
525 565 0.035056 GAGGCCAGGTGTGTGCTTAT 60.035 55.000 5.01 0.00 0.00 1.73
526 566 0.405585 AGGCCAGGTGTGTGCTTATT 59.594 50.000 5.01 0.00 0.00 1.40
527 567 0.527565 GGCCAGGTGTGTGCTTATTG 59.472 55.000 0.00 0.00 0.00 1.90
528 568 0.109132 GCCAGGTGTGTGCTTATTGC 60.109 55.000 0.00 0.00 43.25 3.56
529 569 0.168788 CCAGGTGTGTGCTTATTGCG 59.831 55.000 0.00 0.00 46.63 4.85
530 570 0.168788 CAGGTGTGTGCTTATTGCGG 59.831 55.000 0.00 0.00 46.63 5.69
531 571 0.250727 AGGTGTGTGCTTATTGCGGT 60.251 50.000 0.00 0.00 46.63 5.68
532 572 1.002659 AGGTGTGTGCTTATTGCGGTA 59.997 47.619 0.00 0.00 46.63 4.02
533 573 2.014128 GGTGTGTGCTTATTGCGGTAT 58.986 47.619 0.00 0.00 46.63 2.73
534 574 2.223249 GGTGTGTGCTTATTGCGGTATG 60.223 50.000 0.00 0.00 46.63 2.39
535 575 2.418628 GTGTGTGCTTATTGCGGTATGT 59.581 45.455 0.00 0.00 46.63 2.29
536 576 3.619483 GTGTGTGCTTATTGCGGTATGTA 59.381 43.478 0.00 0.00 46.63 2.29
537 577 4.272504 GTGTGTGCTTATTGCGGTATGTAT 59.727 41.667 0.00 0.00 46.63 2.29
538 578 4.509970 TGTGTGCTTATTGCGGTATGTATC 59.490 41.667 0.00 0.00 46.63 2.24
539 579 4.062293 TGTGCTTATTGCGGTATGTATCC 58.938 43.478 0.00 0.00 46.63 2.59
540 580 4.202315 TGTGCTTATTGCGGTATGTATCCT 60.202 41.667 0.00 0.00 46.63 3.24
541 581 4.389077 GTGCTTATTGCGGTATGTATCCTC 59.611 45.833 0.00 0.00 46.63 3.71
547 587 1.965083 CGGTATGTATCCTCGCTTCG 58.035 55.000 0.00 0.00 0.00 3.79
603 643 6.486993 AGAAAAGATGTACTTTCTTGTGGGTC 59.513 38.462 10.98 6.02 46.55 4.46
604 644 3.926616 AGATGTACTTTCTTGTGGGTCG 58.073 45.455 0.00 0.00 0.00 4.79
606 646 1.071071 TGTACTTTCTTGTGGGTCGGG 59.929 52.381 0.00 0.00 0.00 5.14
607 647 1.071228 GTACTTTCTTGTGGGTCGGGT 59.929 52.381 0.00 0.00 0.00 5.28
609 649 0.605589 CTTTCTTGTGGGTCGGGTCC 60.606 60.000 0.00 0.00 0.00 4.46
611 651 3.622826 CTTGTGGGTCGGGTCCGT 61.623 66.667 9.36 0.00 40.74 4.69
612 652 2.203611 TTGTGGGTCGGGTCCGTA 60.204 61.111 9.36 0.00 40.74 4.02
613 653 2.221906 CTTGTGGGTCGGGTCCGTAG 62.222 65.000 9.36 0.00 40.74 3.51
614 654 4.139234 GTGGGTCGGGTCCGTAGC 62.139 72.222 9.36 6.01 40.74 3.58
615 655 4.682334 TGGGTCGGGTCCGTAGCA 62.682 66.667 9.36 0.00 40.74 3.49
616 656 3.152400 GGGTCGGGTCCGTAGCAT 61.152 66.667 9.36 0.00 40.74 3.79
617 657 1.829533 GGGTCGGGTCCGTAGCATA 60.830 63.158 9.36 0.00 40.74 3.14
618 658 1.658673 GGTCGGGTCCGTAGCATAG 59.341 63.158 9.36 0.00 40.74 2.23
620 660 2.050351 CGGGTCCGTAGCATAGCG 60.050 66.667 0.55 0.00 34.35 4.26
621 661 2.355956 GGGTCCGTAGCATAGCGC 60.356 66.667 0.00 0.00 42.91 5.92
622 662 2.415843 GGTCCGTAGCATAGCGCA 59.584 61.111 11.47 0.00 46.13 6.09
623 663 1.661821 GGTCCGTAGCATAGCGCAG 60.662 63.158 11.47 0.00 46.13 5.18
624 664 1.661821 GTCCGTAGCATAGCGCAGG 60.662 63.158 11.47 0.00 46.13 4.85
625 665 3.038417 CCGTAGCATAGCGCAGGC 61.038 66.667 11.47 10.32 46.13 4.85
628 668 0.388520 CGTAGCATAGCGCAGGCATA 60.389 55.000 11.47 0.00 46.13 3.14
698 740 3.925688 GTTCATACGAACGATGCATGT 57.074 42.857 2.46 0.00 42.05 3.21
699 741 3.597324 GTTCATACGAACGATGCATGTG 58.403 45.455 2.46 0.00 42.05 3.21
700 742 3.157932 TCATACGAACGATGCATGTGA 57.842 42.857 2.46 0.00 0.00 3.58
701 743 3.115554 TCATACGAACGATGCATGTGAG 58.884 45.455 2.46 3.66 0.00 3.51
702 744 2.647529 TACGAACGATGCATGTGAGT 57.352 45.000 2.46 9.04 0.00 3.41
703 745 1.795768 ACGAACGATGCATGTGAGTT 58.204 45.000 2.46 4.99 0.00 3.01
704 746 1.460743 ACGAACGATGCATGTGAGTTG 59.539 47.619 2.46 3.55 0.00 3.16
705 747 1.201954 CGAACGATGCATGTGAGTTGG 60.202 52.381 2.46 2.91 0.00 3.77
706 748 2.076100 GAACGATGCATGTGAGTTGGA 58.924 47.619 2.46 0.00 0.00 3.53
707 749 1.730501 ACGATGCATGTGAGTTGGAG 58.269 50.000 2.46 0.00 0.00 3.86
708 750 1.276138 ACGATGCATGTGAGTTGGAGA 59.724 47.619 2.46 0.00 0.00 3.71
710 752 2.676176 CGATGCATGTGAGTTGGAGACT 60.676 50.000 2.46 0.00 42.70 3.24
711 753 3.429410 CGATGCATGTGAGTTGGAGACTA 60.429 47.826 2.46 0.00 39.19 2.59
712 754 4.701765 GATGCATGTGAGTTGGAGACTAT 58.298 43.478 2.46 0.00 39.19 2.12
713 755 5.507985 CGATGCATGTGAGTTGGAGACTATA 60.508 44.000 2.46 0.00 39.19 1.31
714 756 5.268118 TGCATGTGAGTTGGAGACTATAG 57.732 43.478 0.00 0.00 39.19 1.31
715 757 4.711846 TGCATGTGAGTTGGAGACTATAGT 59.288 41.667 4.68 4.68 39.19 2.12
717 759 5.521735 GCATGTGAGTTGGAGACTATAGTTG 59.478 44.000 6.88 0.00 39.19 3.16
718 760 5.661056 TGTGAGTTGGAGACTATAGTTGG 57.339 43.478 6.88 0.00 39.19 3.77
720 762 5.047306 TGTGAGTTGGAGACTATAGTTGGTG 60.047 44.000 6.88 0.00 39.19 4.17
724 2302 4.055710 TGGAGACTATAGTTGGTGTGGA 57.944 45.455 6.88 0.00 0.00 4.02
735 2313 1.956869 TGGTGTGGATGAGTGGATCT 58.043 50.000 0.00 0.00 0.00 2.75
770 2350 0.177141 TGAAGCGCCATACTACCACC 59.823 55.000 2.29 0.00 0.00 4.61
851 2433 2.427245 GGGCAGCTCTCTCGGCTTA 61.427 63.158 0.00 0.00 38.03 3.09
852 2434 1.227118 GGCAGCTCTCTCGGCTTAC 60.227 63.158 0.00 0.00 38.03 2.34
853 2435 1.671901 GGCAGCTCTCTCGGCTTACT 61.672 60.000 0.00 0.00 38.03 2.24
959 2795 3.787001 GCCACCGCCTAAGCTCCT 61.787 66.667 0.00 0.00 36.60 3.69
995 2834 4.648626 GCTCTGCCACCCAGCACA 62.649 66.667 0.00 0.00 41.50 4.57
1078 2917 2.689034 CTCCTTCCTTCCCCGCCT 60.689 66.667 0.00 0.00 0.00 5.52
1128 2971 1.126113 GCCATGTCGTACAACAAGACG 59.874 52.381 0.00 0.00 38.36 4.18
1131 2974 0.935831 TGTCGTACAACAAGACGGCG 60.936 55.000 4.80 4.80 46.38 6.46
1162 3005 1.408266 CGGAGACCATAAACCCCAAGG 60.408 57.143 0.00 0.00 40.04 3.61
1213 3062 4.424711 TCATCCGGTGCTTGCCCC 62.425 66.667 0.00 0.00 0.00 5.80
1222 3071 1.228552 TGCTTGCCCCTTCTTCACC 60.229 57.895 0.00 0.00 0.00 4.02
1254 3108 6.581171 ACCTGATTCTCCATGTTTTTCTTC 57.419 37.500 0.00 0.00 0.00 2.87
1299 3153 3.138798 GACTACGAGCCCTGCGGA 61.139 66.667 0.00 0.00 0.00 5.54
1376 3231 3.334691 CCGTTCAACTGTCCATGTATGT 58.665 45.455 0.00 0.00 0.00 2.29
1377 3232 4.500127 CCGTTCAACTGTCCATGTATGTA 58.500 43.478 0.00 0.00 0.00 2.29
1378 3233 5.116180 CCGTTCAACTGTCCATGTATGTAT 58.884 41.667 0.00 0.00 0.00 2.29
1379 3234 5.234329 CCGTTCAACTGTCCATGTATGTATC 59.766 44.000 0.00 0.00 0.00 2.24
1380 3235 5.810074 CGTTCAACTGTCCATGTATGTATCA 59.190 40.000 0.00 0.00 0.00 2.15
1381 3236 6.019559 CGTTCAACTGTCCATGTATGTATCAG 60.020 42.308 0.00 0.00 0.00 2.90
1405 3269 2.559231 TGTATGTGTCGCAGTAGTCCAA 59.441 45.455 0.00 0.00 0.00 3.53
1416 3280 3.056536 GCAGTAGTCCAATCAGACTGTCA 60.057 47.826 10.88 0.00 46.54 3.58
1417 3281 4.561530 GCAGTAGTCCAATCAGACTGTCAA 60.562 45.833 10.88 0.00 46.54 3.18
1420 3284 3.854666 AGTCCAATCAGACTGTCAATCG 58.145 45.455 10.88 0.00 45.41 3.34
1438 3315 1.963338 GACAGTCAGTGGCAGTGGC 60.963 63.158 19.02 19.02 32.31 5.01
1472 3349 1.271656 AGTAGTACCCGAGTGCACAAC 59.728 52.381 21.04 11.64 0.00 3.32
1489 3366 7.041098 AGTGCACAACCTAACTAAAGAAATGAG 60.041 37.037 21.04 0.00 0.00 2.90
1554 3432 7.931275 AGAAATGACTTCTGTAAACTGAAACC 58.069 34.615 4.34 0.98 43.09 3.27
1564 3442 4.819630 TGTAAACTGAAACCAAGTGCTAGG 59.180 41.667 0.00 0.00 0.00 3.02
1625 3503 6.316140 TCCAACTTTGATCTTTGGTATCATCG 59.684 38.462 12.67 0.00 40.68 3.84
1635 3513 4.771114 TTGGTATCATCGGACATTCCTT 57.229 40.909 0.00 0.00 33.30 3.36
1649 3530 3.278574 CATTCCTTGCCCGTAAATCTGA 58.721 45.455 0.00 0.00 0.00 3.27
1674 3555 3.820557 AGCACTGGTTTGACTGTACAAT 58.179 40.909 0.00 0.00 0.00 2.71
1712 3593 2.690786 CCGGTTTTCGTGTTATCCAGA 58.309 47.619 0.00 0.00 37.11 3.86
1786 3667 6.821665 AGGTGCGTCTTTGTTTACATACATAT 59.178 34.615 0.00 0.00 0.00 1.78
1809 3690 7.673641 ATATATGTTCAATCCTGGCCAAAAA 57.326 32.000 7.01 0.00 0.00 1.94
1933 3814 5.944007 GGTTACAACCCATAATCACACTCTT 59.056 40.000 0.00 0.00 43.43 2.85
2053 3939 2.738643 CGCAGGGATGAAACTCGTATGT 60.739 50.000 0.00 0.00 0.00 2.29
2074 3960 4.202202 TGTTATTCAGGTTTGTTGGGCTTG 60.202 41.667 0.00 0.00 0.00 4.01
2194 4080 6.377327 TTTCAGTTCTAGCAGAAAAGTTGG 57.623 37.500 0.96 0.00 35.75 3.77
2206 4092 7.676947 AGCAGAAAAGTTGGTAGTAGTATCAA 58.323 34.615 0.00 0.00 0.00 2.57
2208 4094 7.603024 GCAGAAAAGTTGGTAGTAGTATCAAGT 59.397 37.037 3.40 4.39 34.82 3.16
2216 4102 8.351461 GTTGGTAGTAGTATCAAGTACCATCTC 58.649 40.741 3.40 2.74 46.99 2.75
2217 4103 7.813331 TGGTAGTAGTATCAAGTACCATCTCT 58.187 38.462 5.84 0.00 44.37 3.10
2230 4116 5.886474 AGTACCATCTCTCTGTGACGATTTA 59.114 40.000 0.00 0.00 0.00 1.40
2248 4134 5.164031 CGATTTAATTCGTCGAAACCTGACA 60.164 40.000 12.40 0.00 37.55 3.58
2249 4135 5.585500 TTTAATTCGTCGAAACCTGACAG 57.415 39.130 12.40 0.00 36.11 3.51
2250 4136 3.380479 AATTCGTCGAAACCTGACAGA 57.620 42.857 12.40 0.00 36.11 3.41
2407 4427 7.750458 CCGACGATGAATAATATTTTTCCCATG 59.250 37.037 13.86 6.15 0.00 3.66
2430 4530 0.449786 TTCTGCACCACGTTGTTGTG 59.550 50.000 0.00 0.00 39.60 3.33
2438 4538 1.330521 CCACGTTGTTGTGAACTCCTG 59.669 52.381 0.00 0.00 42.55 3.86
2607 4707 5.292834 CACATCAATGCACTTCGTCTATCTT 59.707 40.000 0.00 0.00 0.00 2.40
2694 4794 4.111577 TCATTAGGTCCCAAGAAGATGGT 58.888 43.478 0.00 0.00 38.91 3.55
2797 4898 3.559238 ATGAAATAATTGATCGGCGGC 57.441 42.857 7.21 0.00 0.00 6.53
2891 4994 5.982890 ATAAAGTGTAAAATGGCAGTGCT 57.017 34.783 16.11 0.00 0.00 4.40
2901 5004 2.065899 TGGCAGTGCTTGTAAAAGGT 57.934 45.000 16.11 0.00 0.00 3.50
2943 5046 5.008613 TGCAAGAAATGACCAAGTTACTGAC 59.991 40.000 0.00 0.00 0.00 3.51
3287 5450 3.500343 AGAAGGTTTGGTTATGCTTGCT 58.500 40.909 0.00 0.00 0.00 3.91
3401 5564 5.670792 ACCAAGATAACGTCTATGTGGAA 57.329 39.130 12.82 0.00 36.34 3.53
3538 5701 6.328672 AGAAACATAGTTCATAGCCTCTGGAT 59.671 38.462 0.00 0.00 0.00 3.41
3556 5719 5.247110 TCTGGATAATAAGCCTTAGAGCAGG 59.753 44.000 0.00 0.00 36.95 4.85
3658 5855 7.121382 AGATATGTGGTTTTGGAGATGATGTT 58.879 34.615 0.00 0.00 0.00 2.71
3785 5985 7.329226 CCTGCCTTTCTTGTGTTTGTTATAATG 59.671 37.037 0.00 0.00 0.00 1.90
3869 6131 9.685828 GGATGTATCTAGACAAATCTAAGACAC 57.314 37.037 1.23 0.00 36.98 3.67
3958 6221 2.676750 CGGTAATGCTAGCTGGTGAACA 60.677 50.000 17.23 0.00 0.00 3.18
3991 6254 0.038744 AACTCCCAGTGAATGCCCTG 59.961 55.000 0.00 0.00 0.00 4.45
4010 6273 2.143122 TGGCAGTCGTTTGATCAAGAC 58.857 47.619 16.31 16.31 0.00 3.01
4087 6350 2.165998 AGTCTGAAGAAATTGCTGCCC 58.834 47.619 0.00 0.00 0.00 5.36
4088 6351 1.203287 GTCTGAAGAAATTGCTGCCCC 59.797 52.381 0.00 0.00 0.00 5.80
4089 6352 0.533951 CTGAAGAAATTGCTGCCCCC 59.466 55.000 0.00 0.00 0.00 5.40
4125 6388 4.533919 AAATTGCCATGGAAATCGTTCA 57.466 36.364 18.87 0.00 35.25 3.18
4138 6401 2.198827 TCGTTCACAAATGCCATCCT 57.801 45.000 0.00 0.00 0.00 3.24
4184 6448 6.041637 TGTTGAAGTCCTTACATGACAGTACT 59.958 38.462 0.00 0.00 35.15 2.73
4190 6454 7.155328 AGTCCTTACATGACAGTACTCAAAAG 58.845 38.462 0.00 0.00 35.15 2.27
4192 6456 7.656137 GTCCTTACATGACAGTACTCAAAAGAA 59.344 37.037 0.00 0.00 32.91 2.52
4193 6457 8.375506 TCCTTACATGACAGTACTCAAAAGAAT 58.624 33.333 0.00 0.00 0.00 2.40
4368 6656 8.289618 TGAGATTTTCGTTCTGGTTTTTAGATG 58.710 33.333 0.00 0.00 0.00 2.90
4412 6700 2.430248 ATTAGTTGCCCCTTAACCCG 57.570 50.000 0.00 0.00 0.00 5.28
4447 6735 7.839680 ATTTTCTCACAAAATAGACAACCCT 57.160 32.000 0.00 0.00 0.00 4.34
4473 6761 8.150945 TCCACCTAGAAAAGAATAGATATGCAC 58.849 37.037 0.00 0.00 0.00 4.57
4605 6893 4.304048 AGGTATCCTCCTCCTACATACG 57.696 50.000 0.00 0.00 31.32 3.06
4608 6896 1.688772 TCCTCCTCCTACATACGCAC 58.311 55.000 0.00 0.00 0.00 5.34
4611 6899 0.744874 TCCTCCTACATACGCACTGC 59.255 55.000 0.00 0.00 0.00 4.40
4613 6901 0.747255 CTCCTACATACGCACTGCCT 59.253 55.000 0.00 0.00 0.00 4.75
4614 6902 0.744874 TCCTACATACGCACTGCCTC 59.255 55.000 0.00 0.00 0.00 4.70
4616 6904 0.747255 CTACATACGCACTGCCTCCT 59.253 55.000 0.00 0.00 0.00 3.69
4617 6905 1.137086 CTACATACGCACTGCCTCCTT 59.863 52.381 0.00 0.00 0.00 3.36
4618 6906 0.324943 ACATACGCACTGCCTCCTTT 59.675 50.000 0.00 0.00 0.00 3.11
4619 6907 1.271379 ACATACGCACTGCCTCCTTTT 60.271 47.619 0.00 0.00 0.00 2.27
4620 6908 1.398390 CATACGCACTGCCTCCTTTTC 59.602 52.381 0.00 0.00 0.00 2.29
4621 6909 0.394938 TACGCACTGCCTCCTTTTCA 59.605 50.000 0.00 0.00 0.00 2.69
4623 6911 0.667993 CGCACTGCCTCCTTTTCAAA 59.332 50.000 0.00 0.00 0.00 2.69
4624 6912 1.066908 CGCACTGCCTCCTTTTCAAAA 59.933 47.619 0.00 0.00 0.00 2.44
4660 6964 6.867816 GGAATGATGATATGACTCAGTGAGAC 59.132 42.308 26.86 20.45 33.32 3.36
4661 6965 5.429957 TGATGATATGACTCAGTGAGACG 57.570 43.478 26.86 1.32 33.32 4.18
4690 6996 9.953565 AGTCTTGCATACCTTGTACTAATAAAA 57.046 29.630 0.00 0.00 0.00 1.52
4734 7040 1.672356 CCTTCACAGACCTTGGCGG 60.672 63.158 0.00 0.00 39.35 6.13
4766 7072 1.566298 GCCTGGAGGGAATGACCTGT 61.566 60.000 0.00 0.00 42.10 4.00
4771 7077 2.571653 TGGAGGGAATGACCTGTAACAG 59.428 50.000 0.00 0.00 42.10 3.16
4784 7090 3.502920 CTGTAACAGAGTAGAAGGTGCG 58.497 50.000 0.00 0.00 32.44 5.34
4860 7166 1.326213 CGAGGGCATGTCTCCAGACT 61.326 60.000 8.19 0.00 44.99 3.24
4892 7198 4.421479 CGCCTTCTCGACGCCACT 62.421 66.667 0.00 0.00 0.00 4.00
4898 7204 1.541310 TTCTCGACGCCACTGGGATT 61.541 55.000 0.00 0.00 35.59 3.01
5034 7512 6.562518 TGTTTCCATGCACATGTATATGTTG 58.437 36.000 16.05 0.00 45.01 3.33
5080 7558 2.365293 GTGGTGGCCTTTGATCTTGTTT 59.635 45.455 3.32 0.00 0.00 2.83
5119 7597 0.817634 CAACAAAGGTGTCTGGGCGA 60.818 55.000 0.00 0.00 36.80 5.54
5184 7662 0.250513 GGCGAGGACAAGATCAAGGT 59.749 55.000 0.00 0.00 0.00 3.50
5185 7663 1.480954 GGCGAGGACAAGATCAAGGTA 59.519 52.381 0.00 0.00 0.00 3.08
5308 7786 4.598257 CGAAGGCGGTGTGATCTT 57.402 55.556 0.00 0.00 0.00 2.40
5309 7787 2.373938 CGAAGGCGGTGTGATCTTC 58.626 57.895 0.00 0.00 34.09 2.87
5310 7788 0.389817 CGAAGGCGGTGTGATCTTCA 60.390 55.000 0.00 0.00 36.39 3.02
5418 7896 5.167845 ACCAATAAATAAACTTTGGCAGCG 58.832 37.500 0.62 0.00 41.89 5.18
5456 7934 4.764823 CCCTGTAAATTAAGCCTGTGTTGA 59.235 41.667 0.00 0.00 0.00 3.18
5495 7973 2.134201 GCAAAGTGCAAACCTGGTAC 57.866 50.000 0.00 0.00 44.26 3.34
5587 8074 3.366679 GCACCTCAATTCACAACATCCAG 60.367 47.826 0.00 0.00 0.00 3.86
5618 8105 0.450583 TCCGAATTCCGAGACGACTG 59.549 55.000 0.00 0.00 41.76 3.51
5861 8369 0.971959 TACCCTACCACCGACGCATT 60.972 55.000 0.00 0.00 0.00 3.56
5887 8399 1.617947 AAACCTAGGGCAGAGAGGCG 61.618 60.000 14.81 0.00 45.36 5.52
5969 8481 1.873863 GCAAACCCGTTGGCTACTC 59.126 57.895 0.00 0.00 36.60 2.59
6034 8546 0.181350 GGGGGCAGATGTACTCCAAG 59.819 60.000 0.00 0.00 0.00 3.61
6049 8561 0.674581 CCAAGCCATCTGTCTTCGCA 60.675 55.000 0.00 0.00 0.00 5.10
6078 8593 2.263077 CAAGGAAGAAGACCGATCGTG 58.737 52.381 15.09 8.18 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 45 2.232941 ACATCTACAATTGGACCGTCGT 59.767 45.455 10.83 0.00 0.00 4.34
89 91 2.069273 ACATCGAAGTAACAGTGCTGC 58.931 47.619 0.00 0.00 0.00 5.25
92 94 2.510615 GCACATCGAAGTAACAGTGC 57.489 50.000 0.00 0.00 44.31 4.40
113 122 2.915659 TCGAGACGGGGTGCTTGT 60.916 61.111 0.00 0.00 0.00 3.16
115 124 4.070552 GCTCGAGACGGGGTGCTT 62.071 66.667 18.75 0.00 0.00 3.91
141 150 4.031611 ACTCGGGTCTAATCTAGGCTTTT 58.968 43.478 0.00 0.00 0.00 2.27
214 223 6.238648 TCAGTCTGAGTATATCCGAGCAATA 58.761 40.000 0.00 0.00 0.00 1.90
219 228 7.174080 TGAAGAATCAGTCTGAGTATATCCGAG 59.826 40.741 8.82 0.00 36.40 4.63
304 313 0.740868 CACATGGACGACGGAGCAAT 60.741 55.000 0.00 0.00 0.00 3.56
306 315 2.094757 AACACATGGACGACGGAGCA 62.095 55.000 0.00 0.00 0.00 4.26
307 316 1.374252 AACACATGGACGACGGAGC 60.374 57.895 0.00 0.00 0.00 4.70
315 355 3.440173 CCAACCATAGACAACACATGGAC 59.560 47.826 6.83 0.00 41.53 4.02
324 364 3.620427 ATACGCACCAACCATAGACAA 57.380 42.857 0.00 0.00 0.00 3.18
328 368 3.994392 GACCATATACGCACCAACCATAG 59.006 47.826 0.00 0.00 0.00 2.23
336 376 0.672342 ACCGAGACCATATACGCACC 59.328 55.000 0.00 0.00 0.00 5.01
341 381 5.873164 ACAAACAAGAACCGAGACCATATAC 59.127 40.000 0.00 0.00 0.00 1.47
342 382 6.045072 ACAAACAAGAACCGAGACCATATA 57.955 37.500 0.00 0.00 0.00 0.86
343 383 4.906618 ACAAACAAGAACCGAGACCATAT 58.093 39.130 0.00 0.00 0.00 1.78
353 393 3.003275 TCAGCGATCAACAAACAAGAACC 59.997 43.478 0.00 0.00 0.00 3.62
359 399 3.663025 TCAGATCAGCGATCAACAAACA 58.337 40.909 16.97 0.00 41.12 2.83
367 407 4.366586 TCAAAGTGATCAGATCAGCGATC 58.633 43.478 13.78 11.05 40.53 3.69
370 410 3.519579 ACTCAAAGTGATCAGATCAGCG 58.480 45.455 13.78 3.05 40.53 5.18
408 448 3.133691 CAAAAGCTATGCATAGGCGAGA 58.866 45.455 30.14 0.00 45.35 4.04
413 453 4.641989 ACAAGACCAAAAGCTATGCATAGG 59.358 41.667 30.14 18.24 0.00 2.57
417 457 3.485394 TCACAAGACCAAAAGCTATGCA 58.515 40.909 0.00 0.00 0.00 3.96
423 463 4.122046 AGCAAATTCACAAGACCAAAAGC 58.878 39.130 0.00 0.00 0.00 3.51
424 464 6.507023 ACTAGCAAATTCACAAGACCAAAAG 58.493 36.000 0.00 0.00 0.00 2.27
430 470 5.687285 CCAACAACTAGCAAATTCACAAGAC 59.313 40.000 0.00 0.00 0.00 3.01
431 471 5.359576 ACCAACAACTAGCAAATTCACAAGA 59.640 36.000 0.00 0.00 0.00 3.02
435 475 4.739716 CACACCAACAACTAGCAAATTCAC 59.260 41.667 0.00 0.00 0.00 3.18
439 479 5.337578 AAACACACCAACAACTAGCAAAT 57.662 34.783 0.00 0.00 0.00 2.32
440 480 4.792521 AAACACACCAACAACTAGCAAA 57.207 36.364 0.00 0.00 0.00 3.68
471 511 1.304254 CACACGATCAACCCAACACA 58.696 50.000 0.00 0.00 0.00 3.72
472 512 0.040425 GCACACGATCAACCCAACAC 60.040 55.000 0.00 0.00 0.00 3.32
473 513 0.464554 TGCACACGATCAACCCAACA 60.465 50.000 0.00 0.00 0.00 3.33
474 514 0.881118 ATGCACACGATCAACCCAAC 59.119 50.000 0.00 0.00 0.00 3.77
481 521 1.805943 CAACAAGGATGCACACGATCA 59.194 47.619 0.00 0.00 0.00 2.92
483 523 1.536766 CACAACAAGGATGCACACGAT 59.463 47.619 0.00 0.00 0.00 3.73
485 525 0.661187 GCACAACAAGGATGCACACG 60.661 55.000 0.00 0.00 39.23 4.49
492 532 0.610232 GGCCTCTGCACAACAAGGAT 60.610 55.000 0.00 0.00 40.13 3.24
493 533 1.228245 GGCCTCTGCACAACAAGGA 60.228 57.895 0.00 0.00 40.13 3.36
498 538 2.113986 ACCTGGCCTCTGCACAAC 59.886 61.111 3.32 0.00 40.13 3.32
501 541 2.670934 CACACCTGGCCTCTGCAC 60.671 66.667 3.32 0.00 40.13 4.57
504 544 2.670934 GCACACACCTGGCCTCTG 60.671 66.667 3.32 0.00 0.00 3.35
505 545 1.127567 TAAGCACACACCTGGCCTCT 61.128 55.000 3.32 0.00 0.00 3.69
507 547 0.405585 AATAAGCACACACCTGGCCT 59.594 50.000 3.32 0.00 0.00 5.19
509 549 0.109132 GCAATAAGCACACACCTGGC 60.109 55.000 0.00 0.00 44.79 4.85
510 550 0.168788 CGCAATAAGCACACACCTGG 59.831 55.000 0.00 0.00 46.13 4.45
511 551 0.168788 CCGCAATAAGCACACACCTG 59.831 55.000 0.00 0.00 46.13 4.00
512 552 0.250727 ACCGCAATAAGCACACACCT 60.251 50.000 0.00 0.00 46.13 4.00
514 554 2.418628 ACATACCGCAATAAGCACACAC 59.581 45.455 0.00 0.00 46.13 3.82
515 555 2.705730 ACATACCGCAATAAGCACACA 58.294 42.857 0.00 0.00 46.13 3.72
516 556 4.084013 GGATACATACCGCAATAAGCACAC 60.084 45.833 0.00 0.00 46.13 3.82
517 557 4.062293 GGATACATACCGCAATAAGCACA 58.938 43.478 0.00 0.00 46.13 4.57
518 558 4.315803 AGGATACATACCGCAATAAGCAC 58.684 43.478 0.00 0.00 41.84 4.40
519 559 4.566004 GAGGATACATACCGCAATAAGCA 58.434 43.478 0.00 0.00 41.84 3.91
520 560 3.612860 CGAGGATACATACCGCAATAAGC 59.387 47.826 0.00 0.00 41.41 3.09
521 561 3.612860 GCGAGGATACATACCGCAATAAG 59.387 47.826 0.00 0.00 44.55 1.73
524 564 2.080286 GCGAGGATACATACCGCAAT 57.920 50.000 0.00 0.00 44.55 3.56
525 565 3.580904 GCGAGGATACATACCGCAA 57.419 52.632 0.00 0.00 44.55 4.85
527 567 1.699343 GAAGCGAGGATACATACCGC 58.301 55.000 0.00 0.00 45.39 5.68
528 568 1.266175 ACGAAGCGAGGATACATACCG 59.734 52.381 0.00 0.00 41.41 4.02
529 569 3.366440 AACGAAGCGAGGATACATACC 57.634 47.619 0.00 0.00 41.41 2.73
530 570 6.561717 GCTTAAAACGAAGCGAGGATACATAC 60.562 42.308 0.00 0.00 42.26 2.39
531 571 5.461078 GCTTAAAACGAAGCGAGGATACATA 59.539 40.000 0.00 0.00 42.26 2.29
532 572 4.270325 GCTTAAAACGAAGCGAGGATACAT 59.730 41.667 0.00 0.00 42.26 2.29
533 573 3.615496 GCTTAAAACGAAGCGAGGATACA 59.385 43.478 0.00 0.00 42.26 2.29
534 574 4.179499 GCTTAAAACGAAGCGAGGATAC 57.821 45.455 0.00 0.00 42.26 2.24
573 613 9.390795 CACAAGAAAGTACATCTTTTCTTGATG 57.609 33.333 33.02 26.16 45.15 3.07
574 614 8.571336 CCACAAGAAAGTACATCTTTTCTTGAT 58.429 33.333 33.02 22.44 45.15 2.57
584 624 3.000727 CCGACCCACAAGAAAGTACATC 58.999 50.000 0.00 0.00 0.00 3.06
588 628 1.345415 GACCCGACCCACAAGAAAGTA 59.655 52.381 0.00 0.00 0.00 2.24
590 630 0.605589 GGACCCGACCCACAAGAAAG 60.606 60.000 0.00 0.00 0.00 2.62
603 643 2.050351 CGCTATGCTACGGACCCG 60.050 66.667 6.94 6.94 46.03 5.28
604 644 2.355956 GCGCTATGCTACGGACCC 60.356 66.667 0.00 0.00 41.73 4.46
606 646 1.661821 CCTGCGCTATGCTACGGAC 60.662 63.158 9.73 0.00 46.63 4.79
607 647 2.728180 CCTGCGCTATGCTACGGA 59.272 61.111 9.73 0.00 46.63 4.69
609 649 0.388520 TATGCCTGCGCTATGCTACG 60.389 55.000 9.73 0.00 46.63 3.51
611 651 2.542020 TTTATGCCTGCGCTATGCTA 57.458 45.000 9.73 0.34 46.63 3.49
612 652 1.679139 TTTTATGCCTGCGCTATGCT 58.321 45.000 9.73 1.77 46.63 3.79
613 653 2.490328 TTTTTATGCCTGCGCTATGC 57.510 45.000 9.73 9.29 46.70 3.14
688 730 1.276138 TCTCCAACTCACATGCATCGT 59.724 47.619 0.00 0.00 0.00 3.73
689 731 1.662629 GTCTCCAACTCACATGCATCG 59.337 52.381 0.00 0.00 0.00 3.84
690 732 2.983229 AGTCTCCAACTCACATGCATC 58.017 47.619 0.00 0.00 30.02 3.91
691 733 4.767578 ATAGTCTCCAACTCACATGCAT 57.232 40.909 0.00 0.00 39.55 3.96
692 734 4.711846 ACTATAGTCTCCAACTCACATGCA 59.288 41.667 0.00 0.00 39.55 3.96
693 735 5.269505 ACTATAGTCTCCAACTCACATGC 57.730 43.478 0.00 0.00 39.55 4.06
694 736 6.045318 CCAACTATAGTCTCCAACTCACATG 58.955 44.000 5.70 0.00 39.55 3.21
697 739 5.047235 ACACCAACTATAGTCTCCAACTCAC 60.047 44.000 5.70 0.00 39.55 3.51
698 740 5.047306 CACACCAACTATAGTCTCCAACTCA 60.047 44.000 5.70 0.00 39.55 3.41
699 741 5.411781 CACACCAACTATAGTCTCCAACTC 58.588 45.833 5.70 0.00 39.55 3.01
700 742 4.223032 CCACACCAACTATAGTCTCCAACT 59.777 45.833 5.70 0.00 42.33 3.16
701 743 4.222145 TCCACACCAACTATAGTCTCCAAC 59.778 45.833 5.70 0.00 0.00 3.77
702 744 4.422057 TCCACACCAACTATAGTCTCCAA 58.578 43.478 5.70 0.00 0.00 3.53
703 745 4.055710 TCCACACCAACTATAGTCTCCA 57.944 45.455 5.70 0.00 0.00 3.86
704 746 4.649674 TCATCCACACCAACTATAGTCTCC 59.350 45.833 5.70 0.00 0.00 3.71
705 747 5.361285 ACTCATCCACACCAACTATAGTCTC 59.639 44.000 5.70 0.00 0.00 3.36
706 748 5.127845 CACTCATCCACACCAACTATAGTCT 59.872 44.000 5.70 0.00 0.00 3.24
707 749 5.352284 CACTCATCCACACCAACTATAGTC 58.648 45.833 5.70 0.00 0.00 2.59
708 750 4.162320 CCACTCATCCACACCAACTATAGT 59.838 45.833 0.00 0.00 0.00 2.12
710 752 4.358214 TCCACTCATCCACACCAACTATA 58.642 43.478 0.00 0.00 0.00 1.31
711 753 3.181329 TCCACTCATCCACACCAACTAT 58.819 45.455 0.00 0.00 0.00 2.12
712 754 2.615391 TCCACTCATCCACACCAACTA 58.385 47.619 0.00 0.00 0.00 2.24
713 755 1.434188 TCCACTCATCCACACCAACT 58.566 50.000 0.00 0.00 0.00 3.16
714 756 2.026822 AGATCCACTCATCCACACCAAC 60.027 50.000 0.00 0.00 0.00 3.77
715 757 2.269023 AGATCCACTCATCCACACCAA 58.731 47.619 0.00 0.00 0.00 3.67
717 759 3.012518 CAAAGATCCACTCATCCACACC 58.987 50.000 0.00 0.00 0.00 4.16
718 760 2.421424 GCAAAGATCCACTCATCCACAC 59.579 50.000 0.00 0.00 0.00 3.82
720 762 2.421424 GTGCAAAGATCCACTCATCCAC 59.579 50.000 0.00 0.00 0.00 4.02
724 2302 2.816087 GTGTGTGCAAAGATCCACTCAT 59.184 45.455 7.52 0.00 37.65 2.90
735 2313 3.882013 CACGGGCGTGTGTGCAAA 61.882 61.111 0.00 0.00 40.91 3.68
851 2433 1.938861 CGGCGTGTAAAGCAACAGT 59.061 52.632 0.00 0.00 45.63 3.55
852 2434 1.440353 GCGGCGTGTAAAGCAACAG 60.440 57.895 9.37 0.00 45.63 3.16
853 2435 2.634777 GCGGCGTGTAAAGCAACA 59.365 55.556 9.37 0.00 45.63 3.33
959 2795 2.681064 CGGGTCAAGGGGTACGGA 60.681 66.667 0.00 0.00 0.00 4.69
995 2834 2.612471 GCAGAGAGTGAGTGATTGTGCT 60.612 50.000 0.00 0.00 0.00 4.40
1131 2974 2.202756 GTCTCCGCGGTGATGGAC 60.203 66.667 30.35 22.23 0.00 4.02
1143 2986 1.639108 ACCTTGGGGTTTATGGTCTCC 59.361 52.381 0.00 0.00 44.73 3.71
1213 3062 1.804748 GGTTTGGCGTAGGTGAAGAAG 59.195 52.381 0.00 0.00 0.00 2.85
1222 3071 2.280628 GGAGAATCAGGTTTGGCGTAG 58.719 52.381 0.00 0.00 36.25 3.51
1254 3108 1.079543 CACCTGTGAGCGAGGAAGG 60.080 63.158 0.00 0.00 34.37 3.46
1299 3153 4.521062 GCGTGCCTGGCGATCTCT 62.521 66.667 14.98 0.00 0.00 3.10
1376 3231 5.767816 ACTGCGACACATACATACTGATA 57.232 39.130 0.00 0.00 0.00 2.15
1377 3232 4.655762 ACTGCGACACATACATACTGAT 57.344 40.909 0.00 0.00 0.00 2.90
1378 3233 4.638865 ACTACTGCGACACATACATACTGA 59.361 41.667 0.00 0.00 0.00 3.41
1379 3234 4.921547 ACTACTGCGACACATACATACTG 58.078 43.478 0.00 0.00 0.00 2.74
1380 3235 4.036498 GGACTACTGCGACACATACATACT 59.964 45.833 0.00 0.00 0.00 2.12
1381 3236 4.201980 TGGACTACTGCGACACATACATAC 60.202 45.833 0.00 0.00 0.00 2.39
1416 3280 0.681733 ACTGCCACTGACTGTCGATT 59.318 50.000 2.98 0.00 0.00 3.34
1417 3281 0.037882 CACTGCCACTGACTGTCGAT 60.038 55.000 2.98 0.00 0.00 3.59
1420 3284 1.963338 GCCACTGCCACTGACTGTC 60.963 63.158 0.00 0.00 0.00 3.51
1438 3315 4.468713 GGTACTACTAGGTCAGGGGTAAG 58.531 52.174 0.00 0.00 0.00 2.34
1489 3366 8.274248 GCACTACTTAGTTTCAGTTTACAGAAC 58.726 37.037 0.00 0.00 33.46 3.01
1635 3513 2.887783 TGCTTTTTCAGATTTACGGGCA 59.112 40.909 0.00 0.00 0.00 5.36
1640 3521 6.978080 TCAAACCAGTGCTTTTTCAGATTTAC 59.022 34.615 0.00 0.00 0.00 2.01
1649 3530 4.461081 TGTACAGTCAAACCAGTGCTTTTT 59.539 37.500 0.00 0.00 0.00 1.94
1712 3593 0.252881 TCCATCTCCTGCTCCAACCT 60.253 55.000 0.00 0.00 0.00 3.50
1786 3667 6.438741 TGTTTTTGGCCAGGATTGAACATATA 59.561 34.615 5.11 0.00 0.00 0.86
1809 3690 5.464722 GCAACTCATCATCATCGATTAGTGT 59.535 40.000 0.00 0.00 31.72 3.55
1965 3851 7.610692 CAGATGATGATATTTGAGGCATAAGGT 59.389 37.037 0.00 0.00 0.00 3.50
1966 3852 7.415318 GCAGATGATGATATTTGAGGCATAAGG 60.415 40.741 0.00 0.00 0.00 2.69
2053 3939 4.219115 TCAAGCCCAACAAACCTGAATAA 58.781 39.130 0.00 0.00 0.00 1.40
2147 4033 1.089920 ACGCATCAATGGCTGAAGAC 58.910 50.000 0.00 0.00 37.67 3.01
2194 4080 8.995220 CAGAGAGATGGTACTTGATACTACTAC 58.005 40.741 0.00 0.00 33.87 2.73
2206 4092 3.351794 TCGTCACAGAGAGATGGTACT 57.648 47.619 0.00 0.00 0.00 2.73
2208 4094 6.769134 TTAAATCGTCACAGAGAGATGGTA 57.231 37.500 0.00 0.00 0.00 3.25
2230 4116 3.380479 TCTGTCAGGTTTCGACGAATT 57.620 42.857 11.71 0.00 36.11 2.17
2248 4134 9.113838 CTGTAATAGCAGGTTGAAACAATATCT 57.886 33.333 0.00 0.00 33.11 1.98
2390 4410 9.933723 GCAGAATAGCATGGGAAAAATATTATT 57.066 29.630 0.00 0.00 0.00 1.40
2407 4427 1.156736 ACAACGTGGTGCAGAATAGC 58.843 50.000 0.00 0.00 0.00 2.97
2438 4538 6.352516 ACTTCTGATTCCCTGATCATGTTAC 58.647 40.000 0.00 0.00 35.62 2.50
2607 4707 1.477700 GCAGCCCAATTTAGCATGTCA 59.522 47.619 0.00 0.00 0.00 3.58
2694 4794 7.286775 GGATATTCAGGTAAAGGGCATAAAACA 59.713 37.037 0.00 0.00 0.00 2.83
2797 4898 7.305474 ACAAATTAAGTACTGAAGAATTGCGG 58.695 34.615 12.55 6.74 0.00 5.69
2870 4973 5.068460 ACAAGCACTGCCATTTTACACTTTA 59.932 36.000 0.00 0.00 0.00 1.85
2885 4988 2.880890 AGCAGACCTTTTACAAGCACTG 59.119 45.455 8.12 8.12 36.04 3.66
2901 5004 7.628769 TCTTGCATGTAATAAAATGAGCAGA 57.371 32.000 0.00 0.00 31.87 4.26
3287 5450 1.955778 CACCAAGTGCAAACCTCATCA 59.044 47.619 0.00 0.00 0.00 3.07
3401 5564 9.759473 TTCTTGAAAGAATGGAATTTCCTATCT 57.241 29.630 16.25 15.07 39.95 1.98
3538 5701 4.557705 AGTCCCTGCTCTAAGGCTTATTA 58.442 43.478 7.54 0.00 35.85 0.98
3658 5855 3.270027 CACTTTGCGAATCTCACCCATA 58.730 45.455 0.00 0.00 0.00 2.74
3785 5985 8.820933 GGACGGAGGTTGTAGTAATTAAAATAC 58.179 37.037 0.00 0.00 0.00 1.89
3869 6131 1.067212 CTCCCTCCGTCCTGAATTACG 59.933 57.143 0.00 0.00 38.80 3.18
3958 6221 0.253327 GGAGTTCCTTCCCAGCGAAT 59.747 55.000 0.00 0.00 0.00 3.34
3991 6254 1.464997 GGTCTTGATCAAACGACTGCC 59.535 52.381 20.85 7.21 0.00 4.85
4034 6297 8.797438 ACAATTCCTTCCTAGAAAAGACAATTC 58.203 33.333 6.45 0.00 0.00 2.17
4040 6303 8.826765 AGTATGACAATTCCTTCCTAGAAAAGA 58.173 33.333 6.45 0.00 0.00 2.52
4125 6388 0.685458 GCTGGGAGGATGGCATTTGT 60.685 55.000 0.00 0.00 0.00 2.83
4227 6491 5.068987 ACTTGCAGCAAAAGTCAATAAGGAA 59.931 36.000 9.65 0.00 32.36 3.36
4287 6575 4.761739 AGTATGCGAATGGTGGGAATAATG 59.238 41.667 0.00 0.00 0.00 1.90
4368 6656 3.130340 TGCAAAGGACACAAAAACCTCTC 59.870 43.478 0.00 0.00 33.16 3.20
4412 6700 2.294233 TGTGAGAAAATTGAGGCAGCAC 59.706 45.455 0.00 0.00 0.00 4.40
4447 6735 8.150945 GTGCATATCTATTCTTTTCTAGGTGGA 58.849 37.037 0.00 0.00 0.00 4.02
4605 6893 2.888834 TTTTGAAAAGGAGGCAGTGC 57.111 45.000 6.55 6.55 0.00 4.40
4626 6914 9.504708 GAGTCATATCATCATTCCTCTGATTTT 57.495 33.333 0.00 0.00 33.59 1.82
4627 6915 8.657712 TGAGTCATATCATCATTCCTCTGATTT 58.342 33.333 0.00 0.00 33.59 2.17
4628 6916 8.203681 TGAGTCATATCATCATTCCTCTGATT 57.796 34.615 0.00 0.00 33.59 2.57
4645 6949 2.820197 ACTTGCGTCTCACTGAGTCATA 59.180 45.455 5.94 0.00 0.00 2.15
4690 6996 1.999634 GAGGGCCAGCCACATGGTAT 62.000 60.000 11.50 0.00 42.75 2.73
4716 7022 1.672356 CCGCCAAGGTCTGTGAAGG 60.672 63.158 0.00 0.00 34.51 3.46
4766 7072 4.270834 AGATCGCACCTTCTACTCTGTTA 58.729 43.478 0.00 0.00 0.00 2.41
4771 7077 3.256285 CGTAGATCGCACCTTCTACTC 57.744 52.381 8.09 0.00 41.31 2.59
4784 7090 1.067582 CCGTGGGAAGGCGTAGATC 59.932 63.158 0.00 0.00 0.00 2.75
4985 7291 5.010820 ACTTCAAGTACTAGACAACACCCTC 59.989 44.000 0.00 0.00 0.00 4.30
4986 7292 4.900054 ACTTCAAGTACTAGACAACACCCT 59.100 41.667 0.00 0.00 0.00 4.34
4987 7293 5.211174 ACTTCAAGTACTAGACAACACCC 57.789 43.478 0.00 0.00 0.00 4.61
5080 7558 1.790755 CGTCCATGGAAGTCGTTTGA 58.209 50.000 18.20 0.00 0.00 2.69
5119 7597 2.203437 GTCCCGGTGGCCTTGTTT 60.203 61.111 3.32 0.00 0.00 2.83
5184 7662 0.249868 CTTGAGGCGCGGGATCATTA 60.250 55.000 8.83 0.00 0.00 1.90
5185 7663 1.524621 CTTGAGGCGCGGGATCATT 60.525 57.895 8.83 0.00 0.00 2.57
5236 7714 2.815211 GCGCATCAGCTTCGGTCA 60.815 61.111 0.30 0.00 39.10 4.02
5306 7784 5.952347 ATTTACAGGGTAGGGTAGTGAAG 57.048 43.478 0.00 0.00 0.00 3.02
5307 7785 7.582048 GCTTAATTTACAGGGTAGGGTAGTGAA 60.582 40.741 0.00 0.00 0.00 3.18
5308 7786 6.126968 GCTTAATTTACAGGGTAGGGTAGTGA 60.127 42.308 0.00 0.00 0.00 3.41
5309 7787 6.053650 GCTTAATTTACAGGGTAGGGTAGTG 58.946 44.000 0.00 0.00 0.00 2.74
5310 7788 5.131642 GGCTTAATTTACAGGGTAGGGTAGT 59.868 44.000 0.00 0.00 0.00 2.73
5418 7896 0.602905 CAGGGAAGGACGAACACACC 60.603 60.000 0.00 0.00 0.00 4.16
5456 7934 4.588899 TGCAGAGCCAAAGTGTATTACAT 58.411 39.130 0.00 0.00 0.00 2.29
5495 7973 2.941064 CAATGAGACAGGCAGGTACATG 59.059 50.000 2.43 2.43 0.00 3.21
5618 8105 0.884704 TGTTGTCCTTTGCTCGCTCC 60.885 55.000 0.00 0.00 0.00 4.70
5861 8369 0.979187 CTGCCCTAGGTTTCGGGGTA 60.979 60.000 8.29 0.00 42.01 3.69
6034 8546 2.481952 GGATTATGCGAAGACAGATGGC 59.518 50.000 0.00 0.00 0.00 4.40
6049 8561 4.684485 CGGTCTTCTTCCTTGCAGGATTAT 60.684 45.833 0.00 0.00 45.34 1.28
6078 8593 3.254657 CCCTCTCCATGATAACTCGTCTC 59.745 52.174 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.