Multiple sequence alignment - TraesCS1D01G233300

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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 TraesCS1D01G233300 chr1D 100.000 2459 0 0 1 2459 321711601 321709143 0.000000e+00 4542.0
1 TraesCS1D01G233300 chr1D 85.875 800 67 20 718 1516 321322167 321322921 0.000000e+00 809.0
2 TraesCS1D01G233300 chr1D 95.676 185 7 1 698 881 321324834 321325018 1.850000e-76 296.0
3 TraesCS1D01G233300 chr1D 76.239 686 80 42 12 677 321323996 321324618 1.110000e-73 287.0
4 TraesCS1D01G233300 chr1D 81.058 359 58 8 1907 2258 271836740 271836385 6.700000e-71 278.0
5 TraesCS1D01G233300 chr1D 100.000 34 0 0 280 313 192630241 192630208 2.040000e-06 63.9
6 TraesCS1D01G233300 chr1A 91.267 1271 63 25 674 1900 400955242 400956508 0.000000e+00 1688.0
7 TraesCS1D01G233300 chr1A 91.892 777 48 11 698 1471 401227612 401226848 0.000000e+00 1072.0
8 TraesCS1D01G233300 chr1A 88.064 687 50 21 784 1462 344189985 344189323 0.000000e+00 785.0
9 TraesCS1D01G233300 chr1A 91.259 572 40 9 1892 2459 400956780 400957345 0.000000e+00 771.0
10 TraesCS1D01G233300 chr1A 85.345 580 63 19 104 677 400954259 400954822 4.560000e-162 580.0
11 TraesCS1D01G233300 chr1A 87.879 264 25 4 4 265 400954083 400954341 1.100000e-78 303.0
12 TraesCS1D01G233300 chr1A 80.791 354 62 5 1907 2258 344188958 344188609 3.120000e-69 272.0
13 TraesCS1D01G233300 chr1B 88.941 1275 82 29 698 1928 434430044 434428785 0.000000e+00 1519.0
14 TraesCS1D01G233300 chr1B 93.067 750 22 15 714 1462 434335136 434335856 0.000000e+00 1070.0
15 TraesCS1D01G233300 chr1B 90.190 683 50 14 3 677 434430917 434430244 0.000000e+00 874.0
16 TraesCS1D01G233300 chr1B 95.257 506 23 1 1954 2459 434428786 434428282 0.000000e+00 800.0
17 TraesCS1D01G233300 chr1B 96.610 472 13 1 994 1462 344375645 344375174 0.000000e+00 780.0
18 TraesCS1D01G233300 chr1B 85.938 128 17 1 2314 2441 344374347 344374221 4.270000e-28 135.0
19 TraesCS1D01G233300 chr2D 87.707 724 59 20 747 1464 399347392 399348091 0.000000e+00 817.0
20 TraesCS1D01G233300 chr2B 86.860 723 67 18 747 1464 473299688 473300387 0.000000e+00 784.0
21 TraesCS1D01G233300 chr4D 96.603 471 9 3 1003 1467 444173942 444174411 0.000000e+00 774.0
22 TraesCS1D01G233300 chr5D 81.081 222 26 7 2078 2285 58684917 58684698 1.960000e-36 163.0
23 TraesCS1D01G233300 chr5B 83.019 159 24 2 2089 2245 63849883 63849726 9.170000e-30 141.0
24 TraesCS1D01G233300 chr5B 86.792 53 6 1 260 311 62970145 62970197 9.500000e-05 58.4
25 TraesCS1D01G233300 chr5B 100.000 28 0 0 286 313 369456779 369456752 4.000000e-03 52.8
26 TraesCS1D01G233300 chr7D 85.227 88 13 0 2171 2258 58207067 58206980 9.360000e-15 91.6
27 TraesCS1D01G233300 chr7D 87.879 66 8 0 612 677 411018994 411018929 7.290000e-11 78.7
28 TraesCS1D01G233300 chr7D 82.353 68 8 4 248 312 432741523 432741589 3.420000e-04 56.5
29 TraesCS1D01G233300 chr7B 91.837 49 3 1 612 659 424534523 424534571 1.580000e-07 67.6
30 TraesCS1D01G233300 chr3A 89.091 55 5 1 268 321 617427609 617427555 1.580000e-07 67.6
31 TraesCS1D01G233300 chr6D 100.000 31 0 0 280 310 393413221 393413251 9.500000e-05 58.4
32 TraesCS1D01G233300 chr7A 96.970 33 1 0 280 312 698683857 698683825 3.420000e-04 56.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G233300 chr1D 321709143 321711601 2458 True 4542.000000 4542 100.000000 1 2459 1 chr1D.!!$R3 2458
1 TraesCS1D01G233300 chr1D 321322167 321325018 2851 False 464.000000 809 85.930000 12 1516 3 chr1D.!!$F1 1504
2 TraesCS1D01G233300 chr1A 401226848 401227612 764 True 1072.000000 1072 91.892000 698 1471 1 chr1A.!!$R1 773
3 TraesCS1D01G233300 chr1A 400954083 400957345 3262 False 835.500000 1688 88.937500 4 2459 4 chr1A.!!$F1 2455
4 TraesCS1D01G233300 chr1A 344188609 344189985 1376 True 528.500000 785 84.427500 784 2258 2 chr1A.!!$R2 1474
5 TraesCS1D01G233300 chr1B 434335136 434335856 720 False 1070.000000 1070 93.067000 714 1462 1 chr1B.!!$F1 748
6 TraesCS1D01G233300 chr1B 434428282 434430917 2635 True 1064.333333 1519 91.462667 3 2459 3 chr1B.!!$R2 2456
7 TraesCS1D01G233300 chr1B 344374221 344375645 1424 True 457.500000 780 91.274000 994 2441 2 chr1B.!!$R1 1447
8 TraesCS1D01G233300 chr2D 399347392 399348091 699 False 817.000000 817 87.707000 747 1464 1 chr2D.!!$F1 717
9 TraesCS1D01G233300 chr2B 473299688 473300387 699 False 784.000000 784 86.860000 747 1464 1 chr2B.!!$F1 717

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
889 1419 0.693092 ATAAACCTAGCCCTCCCGCA 60.693 55.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 3744 1.827789 GTGCCAACCACCAAGAGCA 60.828 57.895 0.0 0.0 38.55 4.26 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
39 40 9.817809 TTCAACGTTATTTATCTTGATAGCTCT 57.182 29.630 0.00 0.00 0.00 4.09
54 55 9.862371 CTTGATAGCTCTAGAACAGAAAACTTA 57.138 33.333 0.00 0.00 31.12 2.24
62 63 8.703604 TCTAGAACAGAAAACTTATTCGATGG 57.296 34.615 0.00 0.00 34.46 3.51
68 69 7.642669 ACAGAAAACTTATTCGATGGCATATG 58.357 34.615 0.00 0.00 34.46 1.78
69 70 7.080099 CAGAAAACTTATTCGATGGCATATGG 58.920 38.462 0.00 0.00 34.46 2.74
71 72 3.347216 ACTTATTCGATGGCATATGGGC 58.653 45.455 0.00 0.00 43.73 5.36
95 96 1.277557 CCCATTTGGAAATTGCGGGAA 59.722 47.619 0.00 0.00 33.24 3.97
97 98 3.608796 CCATTTGGAAATTGCGGGAAAT 58.391 40.909 0.00 0.00 37.39 2.17
98 99 4.009002 CCATTTGGAAATTGCGGGAAATT 58.991 39.130 0.00 0.00 37.39 1.82
100 101 5.392286 CATTTGGAAATTGCGGGAAATTTG 58.608 37.500 2.12 0.00 39.31 2.32
101 102 4.342862 TTGGAAATTGCGGGAAATTTGA 57.657 36.364 2.12 0.00 39.31 2.69
102 103 4.342862 TGGAAATTGCGGGAAATTTGAA 57.657 36.364 2.12 0.00 39.31 2.69
106 107 6.264067 TGGAAATTGCGGGAAATTTGAAAAAT 59.736 30.769 2.12 0.00 39.31 1.82
108 109 7.962373 GGAAATTGCGGGAAATTTGAAAAATAG 59.038 33.333 2.12 0.00 39.31 1.73
109 110 7.977789 AATTGCGGGAAATTTGAAAAATAGT 57.022 28.000 0.00 0.00 0.00 2.12
110 111 7.977789 ATTGCGGGAAATTTGAAAAATAGTT 57.022 28.000 0.00 0.00 0.00 2.24
111 112 9.495572 AATTGCGGGAAATTTGAAAAATAGTTA 57.504 25.926 0.00 0.00 0.00 2.24
112 113 8.888579 TTGCGGGAAATTTGAAAAATAGTTAA 57.111 26.923 0.00 0.00 0.00 2.01
113 114 8.300495 TGCGGGAAATTTGAAAAATAGTTAAC 57.700 30.769 0.00 0.00 0.00 2.01
114 115 7.385478 TGCGGGAAATTTGAAAAATAGTTAACC 59.615 33.333 0.88 0.00 0.00 2.85
115 116 7.385478 GCGGGAAATTTGAAAAATAGTTAACCA 59.615 33.333 0.88 0.00 0.00 3.67
116 117 9.430623 CGGGAAATTTGAAAAATAGTTAACCAT 57.569 29.630 0.88 0.00 0.00 3.55
133 134 9.612066 AGTTAACCATTTCAATTTTGTGAACAT 57.388 25.926 0.88 0.00 37.24 2.71
278 279 9.601971 TGAATTAGTGAACTGTTTAAAATACGC 57.398 29.630 0.00 0.00 0.00 4.42
279 280 8.649810 AATTAGTGAACTGTTTAAAATACGCG 57.350 30.769 3.53 3.53 0.00 6.01
280 281 5.910637 AGTGAACTGTTTAAAATACGCGA 57.089 34.783 15.93 0.00 0.00 5.87
281 282 6.289745 AGTGAACTGTTTAAAATACGCGAA 57.710 33.333 15.93 0.00 0.00 4.70
282 283 6.131389 AGTGAACTGTTTAAAATACGCGAAC 58.869 36.000 15.93 5.22 0.00 3.95
283 284 5.902981 GTGAACTGTTTAAAATACGCGAACA 59.097 36.000 15.93 10.29 0.00 3.18
284 285 6.575942 GTGAACTGTTTAAAATACGCGAACAT 59.424 34.615 15.93 0.00 30.73 2.71
289 290 9.448294 ACTGTTTAAAATACGCGAACATTTTTA 57.552 25.926 24.37 17.55 36.18 1.52
297 298 8.508800 AATACGCGAACATTTTTAAATTCACA 57.491 26.923 15.93 0.00 0.00 3.58
299 300 7.223058 ACGCGAACATTTTTAAATTCACAAA 57.777 28.000 15.93 0.00 0.00 2.83
300 301 7.114289 ACGCGAACATTTTTAAATTCACAAAC 58.886 30.769 15.93 0.00 0.00 2.93
302 303 7.791590 CGCGAACATTTTTAAATTCACAAACAT 59.208 29.630 0.00 0.00 0.00 2.71
303 304 9.432077 GCGAACATTTTTAAATTCACAAACATT 57.568 25.926 0.00 0.00 0.00 2.71
334 335 2.493997 CGAACAGCAGATTCGTGAAC 57.506 50.000 8.38 0.00 43.08 3.18
335 336 1.792367 CGAACAGCAGATTCGTGAACA 59.208 47.619 8.38 0.00 43.08 3.18
336 337 2.413112 CGAACAGCAGATTCGTGAACAT 59.587 45.455 8.38 0.00 43.08 2.71
337 338 3.120546 CGAACAGCAGATTCGTGAACATT 60.121 43.478 8.38 0.00 43.08 2.71
339 340 4.836125 ACAGCAGATTCGTGAACATTTT 57.164 36.364 0.00 0.00 0.00 1.82
340 341 5.186996 ACAGCAGATTCGTGAACATTTTT 57.813 34.783 0.00 0.00 0.00 1.94
392 393 3.760580 TTTTTGAATCCACGGGCATTT 57.239 38.095 0.00 0.00 0.00 2.32
393 394 3.760580 TTTTGAATCCACGGGCATTTT 57.239 38.095 0.00 0.00 0.00 1.82
394 395 3.760580 TTTGAATCCACGGGCATTTTT 57.239 38.095 0.00 0.00 0.00 1.94
415 416 6.862944 TTTTCTACTTTGCGTGAACTTTTG 57.137 33.333 0.00 0.00 0.00 2.44
433 434 7.614124 ACTTTTGTTCAAATTTGTCAGCATT 57.386 28.000 17.47 3.47 0.00 3.56
437 438 8.892887 TTTGTTCAAATTTGTCAGCATTTTTC 57.107 26.923 17.47 0.00 0.00 2.29
438 439 7.606858 TGTTCAAATTTGTCAGCATTTTTCA 57.393 28.000 17.47 0.00 0.00 2.69
439 440 8.037382 TGTTCAAATTTGTCAGCATTTTTCAA 57.963 26.923 17.47 0.00 0.00 2.69
441 442 9.505995 GTTCAAATTTGTCAGCATTTTTCAAAT 57.494 25.926 17.47 0.00 39.38 2.32
447 448 7.697352 TTGTCAGCATTTTTCAAATGTACAG 57.303 32.000 0.33 0.00 0.00 2.74
448 449 7.036996 TGTCAGCATTTTTCAAATGTACAGA 57.963 32.000 0.33 0.00 0.00 3.41
449 450 6.917477 TGTCAGCATTTTTCAAATGTACAGAC 59.083 34.615 0.33 11.83 0.00 3.51
450 451 6.917477 GTCAGCATTTTTCAAATGTACAGACA 59.083 34.615 0.33 0.00 40.72 3.41
467 468 9.944663 TGTACAGACATTTTAGAATTTGTGAAC 57.055 29.630 0.00 0.00 0.00 3.18
468 469 9.944663 GTACAGACATTTTAGAATTTGTGAACA 57.055 29.630 0.00 0.00 0.00 3.18
494 495 3.740044 TCAATCCGCGAACATCTTTTC 57.260 42.857 8.23 0.00 0.00 2.29
496 497 4.500127 TCAATCCGCGAACATCTTTTCTA 58.500 39.130 8.23 0.00 0.00 2.10
498 499 5.584649 TCAATCCGCGAACATCTTTTCTATT 59.415 36.000 8.23 0.00 0.00 1.73
499 500 6.093495 TCAATCCGCGAACATCTTTTCTATTT 59.907 34.615 8.23 0.00 0.00 1.40
500 501 5.873179 TCCGCGAACATCTTTTCTATTTT 57.127 34.783 8.23 0.00 0.00 1.82
501 502 5.627172 TCCGCGAACATCTTTTCTATTTTG 58.373 37.500 8.23 0.00 0.00 2.44
502 503 4.262976 CCGCGAACATCTTTTCTATTTTGC 59.737 41.667 8.23 0.00 0.00 3.68
503 504 4.851014 CGCGAACATCTTTTCTATTTTGCA 59.149 37.500 0.00 0.00 0.00 4.08
506 507 6.527722 GCGAACATCTTTTCTATTTTGCATGA 59.472 34.615 0.00 0.00 0.00 3.07
507 508 7.062138 GCGAACATCTTTTCTATTTTGCATGAA 59.938 33.333 0.00 0.00 0.00 2.57
508 509 8.368126 CGAACATCTTTTCTATTTTGCATGAAC 58.632 33.333 0.00 0.00 0.00 3.18
509 510 9.415544 GAACATCTTTTCTATTTTGCATGAACT 57.584 29.630 0.00 0.00 0.00 3.01
510 511 9.768662 AACATCTTTTCTATTTTGCATGAACTT 57.231 25.926 0.00 0.00 0.00 2.66
511 512 9.768662 ACATCTTTTCTATTTTGCATGAACTTT 57.231 25.926 0.00 0.00 0.00 2.66
555 556 5.811399 AGTTCACAGACATTTTGTTTCGA 57.189 34.783 0.00 0.00 0.00 3.71
556 557 5.810525 AGTTCACAGACATTTTGTTTCGAG 58.189 37.500 0.00 0.00 0.00 4.04
557 558 5.354234 AGTTCACAGACATTTTGTTTCGAGT 59.646 36.000 0.00 0.00 0.00 4.18
558 559 5.811399 TCACAGACATTTTGTTTCGAGTT 57.189 34.783 0.00 0.00 0.00 3.01
560 561 6.027131 TCACAGACATTTTGTTTCGAGTTTG 58.973 36.000 0.00 0.00 0.00 2.93
562 563 4.797868 CAGACATTTTGTTTCGAGTTTGCA 59.202 37.500 0.00 0.00 0.00 4.08
563 564 5.459762 CAGACATTTTGTTTCGAGTTTGCAT 59.540 36.000 0.00 0.00 0.00 3.96
564 565 6.019640 CAGACATTTTGTTTCGAGTTTGCATT 60.020 34.615 0.00 0.00 0.00 3.56
565 566 6.534793 AGACATTTTGTTTCGAGTTTGCATTT 59.465 30.769 0.00 0.00 0.00 2.32
566 567 7.064490 AGACATTTTGTTTCGAGTTTGCATTTT 59.936 29.630 0.00 0.00 0.00 1.82
568 569 6.959671 TTTTGTTTCGAGTTTGCATTTTCT 57.040 29.167 0.00 0.00 0.00 2.52
569 570 6.567769 TTTGTTTCGAGTTTGCATTTTCTC 57.432 33.333 0.00 0.00 0.00 2.87
576 577 5.046910 GAGTTTGCATTTTCTCGAATCCA 57.953 39.130 0.00 0.00 0.00 3.41
577 578 4.798574 AGTTTGCATTTTCTCGAATCCAC 58.201 39.130 0.00 0.00 0.00 4.02
578 579 3.469899 TTGCATTTTCTCGAATCCACG 57.530 42.857 0.00 0.00 0.00 4.94
579 580 2.694213 TGCATTTTCTCGAATCCACGA 58.306 42.857 0.00 0.00 40.00 4.35
580 581 3.070748 TGCATTTTCTCGAATCCACGAA 58.929 40.909 0.00 0.00 41.67 3.85
582 583 4.873259 TGCATTTTCTCGAATCCACGAATA 59.127 37.500 0.00 0.00 41.67 1.75
583 584 5.527214 TGCATTTTCTCGAATCCACGAATAT 59.473 36.000 0.00 0.00 41.67 1.28
584 585 6.038161 TGCATTTTCTCGAATCCACGAATATT 59.962 34.615 0.00 0.00 41.67 1.28
586 587 7.432252 GCATTTTCTCGAATCCACGAATATTTT 59.568 33.333 0.00 0.00 41.67 1.82
587 588 9.289303 CATTTTCTCGAATCCACGAATATTTTT 57.711 29.630 0.00 0.00 41.67 1.94
588 589 8.667987 TTTTCTCGAATCCACGAATATTTTTG 57.332 30.769 0.00 0.00 41.67 2.44
589 590 7.603963 TTCTCGAATCCACGAATATTTTTGA 57.396 32.000 0.00 0.00 41.67 2.69
593 594 8.835467 TCGAATCCACGAATATTTTTGAATTC 57.165 30.769 0.00 0.00 39.34 2.17
600 601 6.533192 CGAATATTTTTGAATTCGCGAACA 57.467 33.333 26.00 16.09 45.33 3.18
601 602 7.136954 CGAATATTTTTGAATTCGCGAACAT 57.863 32.000 26.00 16.47 45.33 2.71
603 604 7.778471 CGAATATTTTTGAATTCGCGAACATTC 59.222 33.333 26.00 23.74 45.33 2.67
604 605 8.687824 AATATTTTTGAATTCGCGAACATTCT 57.312 26.923 26.00 10.80 31.64 2.40
605 606 8.687824 ATATTTTTGAATTCGCGAACATTCTT 57.312 26.923 26.00 14.34 31.64 2.52
606 607 9.781834 ATATTTTTGAATTCGCGAACATTCTTA 57.218 25.926 26.00 13.66 31.64 2.10
607 608 6.904954 TTTTGAATTCGCGAACATTCTTAC 57.095 33.333 26.00 9.61 31.64 2.34
608 609 4.239505 TGAATTCGCGAACATTCTTACG 57.760 40.909 26.00 0.00 31.64 3.18
609 610 2.713927 ATTCGCGAACATTCTTACGC 57.286 45.000 26.00 0.00 46.08 4.42
618 619 7.260722 GCGAACATTCTTACGCTTTTTAATT 57.739 32.000 0.00 0.00 46.06 1.40
619 620 7.373521 GCGAACATTCTTACGCTTTTTAATTC 58.626 34.615 0.00 0.00 46.06 2.17
620 621 7.060174 GCGAACATTCTTACGCTTTTTAATTCA 59.940 33.333 0.00 0.00 46.06 2.57
622 623 9.989394 GAACATTCTTACGCTTTTTAATTCAAC 57.011 29.630 0.00 0.00 0.00 3.18
623 624 8.515473 ACATTCTTACGCTTTTTAATTCAACC 57.485 30.769 0.00 0.00 0.00 3.77
624 625 7.325097 ACATTCTTACGCTTTTTAATTCAACCG 59.675 33.333 0.00 0.00 0.00 4.44
625 626 5.691815 TCTTACGCTTTTTAATTCAACCGG 58.308 37.500 0.00 0.00 0.00 5.28
627 628 6.426328 TCTTACGCTTTTTAATTCAACCGGTA 59.574 34.615 8.00 0.00 0.00 4.02
628 629 5.435820 ACGCTTTTTAATTCAACCGGTAA 57.564 34.783 8.00 0.00 0.00 2.85
630 631 6.271566 ACGCTTTTTAATTCAACCGGTAAAA 58.728 32.000 8.00 7.10 0.00 1.52
631 632 6.198778 ACGCTTTTTAATTCAACCGGTAAAAC 59.801 34.615 8.00 3.70 0.00 2.43
632 633 6.345961 CGCTTTTTAATTCAACCGGTAAAACC 60.346 38.462 8.00 0.00 34.05 3.27
633 634 6.479331 GCTTTTTAATTCAACCGGTAAAACCA 59.521 34.615 8.00 0.00 38.47 3.67
635 636 7.948278 TTTTAATTCAACCGGTAAAACCATG 57.052 32.000 8.00 0.00 38.47 3.66
638 639 3.773418 TCAACCGGTAAAACCATGAGA 57.227 42.857 8.00 0.00 38.47 3.27
639 640 3.670625 TCAACCGGTAAAACCATGAGAG 58.329 45.455 8.00 0.00 38.47 3.20
640 641 2.747446 CAACCGGTAAAACCATGAGAGG 59.253 50.000 8.00 0.00 38.47 3.69
641 642 2.262637 ACCGGTAAAACCATGAGAGGA 58.737 47.619 4.49 0.00 38.47 3.71
642 643 2.640826 ACCGGTAAAACCATGAGAGGAA 59.359 45.455 4.49 0.00 38.47 3.36
643 644 3.073356 ACCGGTAAAACCATGAGAGGAAA 59.927 43.478 4.49 0.00 38.47 3.13
644 645 3.439129 CCGGTAAAACCATGAGAGGAAAC 59.561 47.826 0.00 0.00 38.47 2.78
645 646 3.439129 CGGTAAAACCATGAGAGGAAACC 59.561 47.826 0.00 0.00 38.47 3.27
646 647 4.403734 GGTAAAACCATGAGAGGAAACCA 58.596 43.478 0.00 0.00 38.42 3.67
647 648 4.459337 GGTAAAACCATGAGAGGAAACCAG 59.541 45.833 0.00 0.00 38.42 4.00
648 649 2.887151 AACCATGAGAGGAAACCAGG 57.113 50.000 0.00 0.00 0.00 4.45
649 650 2.044793 ACCATGAGAGGAAACCAGGA 57.955 50.000 0.00 0.00 0.00 3.86
650 651 2.348472 ACCATGAGAGGAAACCAGGAA 58.652 47.619 0.00 0.00 0.00 3.36
651 652 2.716424 ACCATGAGAGGAAACCAGGAAA 59.284 45.455 0.00 0.00 0.00 3.13
652 653 3.140144 ACCATGAGAGGAAACCAGGAAAA 59.860 43.478 0.00 0.00 0.00 2.29
654 655 4.219288 CCATGAGAGGAAACCAGGAAAAAG 59.781 45.833 0.00 0.00 0.00 2.27
655 656 4.788925 TGAGAGGAAACCAGGAAAAAGA 57.211 40.909 0.00 0.00 0.00 2.52
656 657 5.124036 TGAGAGGAAACCAGGAAAAAGAA 57.876 39.130 0.00 0.00 0.00 2.52
657 658 5.515106 TGAGAGGAAACCAGGAAAAAGAAA 58.485 37.500 0.00 0.00 0.00 2.52
659 660 6.096846 TGAGAGGAAACCAGGAAAAAGAAAAG 59.903 38.462 0.00 0.00 0.00 2.27
660 661 6.194967 AGAGGAAACCAGGAAAAAGAAAAGA 58.805 36.000 0.00 0.00 0.00 2.52
661 662 6.841229 AGAGGAAACCAGGAAAAAGAAAAGAT 59.159 34.615 0.00 0.00 0.00 2.40
663 664 8.183104 AGGAAACCAGGAAAAAGAAAAGATAG 57.817 34.615 0.00 0.00 0.00 2.08
665 666 8.300286 GGAAACCAGGAAAAAGAAAAGATAGAG 58.700 37.037 0.00 0.00 0.00 2.43
667 668 7.751768 ACCAGGAAAAAGAAAAGATAGAGTG 57.248 36.000 0.00 0.00 0.00 3.51
668 669 6.717084 ACCAGGAAAAAGAAAAGATAGAGTGG 59.283 38.462 0.00 0.00 0.00 4.00
673 674 8.630037 GGAAAAAGAAAAGATAGAGTGGTGAAA 58.370 33.333 0.00 0.00 0.00 2.69
674 675 9.670719 GAAAAAGAAAAGATAGAGTGGTGAAAG 57.329 33.333 0.00 0.00 0.00 2.62
675 676 8.980481 AAAAGAAAAGATAGAGTGGTGAAAGA 57.020 30.769 0.00 0.00 0.00 2.52
677 678 8.980481 AAGAAAAGATAGAGTGGTGAAAGAAA 57.020 30.769 0.00 0.00 0.00 2.52
678 679 9.579932 AAGAAAAGATAGAGTGGTGAAAGAAAT 57.420 29.630 0.00 0.00 0.00 2.17
679 680 9.225436 AGAAAAGATAGAGTGGTGAAAGAAATC 57.775 33.333 0.00 0.00 0.00 2.17
680 681 7.929941 AAAGATAGAGTGGTGAAAGAAATCC 57.070 36.000 0.00 0.00 0.00 3.01
681 682 6.627087 AGATAGAGTGGTGAAAGAAATCCA 57.373 37.500 0.00 0.00 0.00 3.41
683 684 7.461749 AGATAGAGTGGTGAAAGAAATCCAAA 58.538 34.615 0.00 0.00 0.00 3.28
684 685 5.774498 AGAGTGGTGAAAGAAATCCAAAC 57.226 39.130 0.00 0.00 0.00 2.93
685 686 4.584743 AGAGTGGTGAAAGAAATCCAAACC 59.415 41.667 0.00 0.00 0.00 3.27
686 687 4.285863 AGTGGTGAAAGAAATCCAAACCA 58.714 39.130 0.00 0.00 33.95 3.67
689 690 5.696270 GTGGTGAAAGAAATCCAAACCATTC 59.304 40.000 0.00 0.00 38.41 2.67
691 692 6.159293 GGTGAAAGAAATCCAAACCATTCTC 58.841 40.000 0.00 0.00 31.20 2.87
692 693 5.858581 GTGAAAGAAATCCAAACCATTCTCG 59.141 40.000 0.00 0.00 31.20 4.04
693 694 4.440839 AAGAAATCCAAACCATTCTCGC 57.559 40.909 0.00 0.00 31.20 5.03
694 695 2.420022 AGAAATCCAAACCATTCTCGCG 59.580 45.455 0.00 0.00 0.00 5.87
695 696 1.094785 AATCCAAACCATTCTCGCGG 58.905 50.000 6.13 0.00 0.00 6.46
698 699 1.419922 CAAACCATTCTCGCGGTCG 59.580 57.895 6.13 0.00 33.17 4.79
699 700 2.388232 AAACCATTCTCGCGGTCGC 61.388 57.895 6.13 5.16 33.17 5.19
877 1407 2.321296 ACCTCCCCCTCTGTATAAACCT 59.679 50.000 0.00 0.00 0.00 3.50
881 1411 2.638363 CCCCCTCTGTATAAACCTAGCC 59.362 54.545 0.00 0.00 0.00 3.93
883 1413 3.588569 CCCTCTGTATAAACCTAGCCCT 58.411 50.000 0.00 0.00 0.00 5.19
889 1419 0.693092 ATAAACCTAGCCCTCCCGCA 60.693 55.000 0.00 0.00 0.00 5.69
890 1420 1.335132 TAAACCTAGCCCTCCCGCAG 61.335 60.000 0.00 0.00 0.00 5.18
893 1423 3.474570 CTAGCCCTCCCGCAGCTT 61.475 66.667 0.00 0.00 38.06 3.74
899 1430 3.121030 CTCCCGCAGCTTGTTCCG 61.121 66.667 0.00 0.00 0.00 4.30
928 1473 3.840078 CTCCTTCCAAACAAATTCCCCAT 59.160 43.478 0.00 0.00 0.00 4.00
948 1494 1.151668 CTTCTTCCAGTTCCAGCACG 58.848 55.000 0.00 0.00 0.00 5.34
1473 2024 3.488047 CCTCTTAGATTGCCATGTTTGCG 60.488 47.826 0.00 0.00 0.00 4.85
1512 2063 2.351726 GGCTGCCGTGTATCTAAAACTG 59.648 50.000 1.35 0.00 0.00 3.16
1516 2067 2.676342 GCCGTGTATCTAAAACTGGTGG 59.324 50.000 0.00 0.00 0.00 4.61
1517 2068 3.618019 GCCGTGTATCTAAAACTGGTGGA 60.618 47.826 0.00 0.00 0.00 4.02
1518 2069 4.571919 CCGTGTATCTAAAACTGGTGGAA 58.428 43.478 0.00 0.00 0.00 3.53
1520 2071 5.064707 CCGTGTATCTAAAACTGGTGGAATG 59.935 44.000 0.00 0.00 0.00 2.67
1521 2072 5.447279 CGTGTATCTAAAACTGGTGGAATGC 60.447 44.000 0.00 0.00 0.00 3.56
1523 2270 5.647658 TGTATCTAAAACTGGTGGAATGCTG 59.352 40.000 0.00 0.00 0.00 4.41
1534 2281 4.141528 TGGTGGAATGCTGATTTTTGGTTT 60.142 37.500 0.00 0.00 0.00 3.27
1586 2580 6.695713 CCGATCTGAAATAGTAAACGATGTGA 59.304 38.462 0.00 0.00 0.00 3.58
1588 2582 9.394477 CGATCTGAAATAGTAAACGATGTGATA 57.606 33.333 0.00 0.00 0.00 2.15
1626 2630 5.866207 ACCCTCGTTTCTGATTTCTTAACT 58.134 37.500 0.00 0.00 0.00 2.24
1670 2680 0.235926 GCTTTCTGACCGAACTGTGC 59.764 55.000 0.00 0.00 0.00 4.57
1675 2929 1.002366 CTGACCGAACTGTGCTATGC 58.998 55.000 0.00 0.00 0.00 3.14
1766 3676 1.818674 GATCGGCTGTCCCATTTGTTT 59.181 47.619 0.00 0.00 0.00 2.83
1824 3744 5.680619 TCAATTGAGGTTCTGTACACTGTT 58.319 37.500 3.38 0.00 0.00 3.16
1862 3782 1.208614 CGCTTCTCTTGCAGGTTGC 59.791 57.895 0.00 0.00 45.29 4.17
1895 3816 7.175104 ACAAGTACCTGATGAATTTGTACCAT 58.825 34.615 0.00 0.00 33.87 3.55
2142 4347 4.338400 ACTGGCTGGTTAGTTCTTTGTTTC 59.662 41.667 0.00 0.00 0.00 2.78
2150 4356 5.129815 GGTTAGTTCTTTGTTTCCCCCTTTT 59.870 40.000 0.00 0.00 0.00 2.27
2182 4388 6.604795 CCTTCTTGATTTTGGTGGTCTGATAT 59.395 38.462 0.00 0.00 0.00 1.63
2240 4447 0.606401 CAAGAAGAAAGCCCGGCTCA 60.606 55.000 13.72 0.00 38.25 4.26
2258 4465 4.156008 GGCTCATGTTTCCAATCGTTTACT 59.844 41.667 0.00 0.00 0.00 2.24
2288 4495 4.697352 CAGTTTAAGTTCATCTGTGGGAGG 59.303 45.833 0.00 0.00 0.00 4.30
2405 4701 4.972751 TTATCATACTGCACCTGCCATA 57.027 40.909 0.00 0.00 41.18 2.74
2437 4733 7.448469 GGATGCTAATACCCTGTATTGACATTT 59.552 37.037 9.21 0.00 34.24 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 6.876789 TGCCATCGAATAAGTTTTCTGTTCTA 59.123 34.615 0.00 0.00 0.00 2.10
74 75 0.901124 CCCGCAATTTCCAAATGGGA 59.099 50.000 0.00 0.00 46.61 4.37
75 76 0.901124 TCCCGCAATTTCCAAATGGG 59.099 50.000 0.00 1.12 32.91 4.00
76 77 2.758736 TTCCCGCAATTTCCAAATGG 57.241 45.000 0.00 0.00 0.00 3.16
78 79 5.312079 TCAAATTTCCCGCAATTTCCAAAT 58.688 33.333 0.00 0.00 34.70 2.32
79 80 4.708177 TCAAATTTCCCGCAATTTCCAAA 58.292 34.783 0.00 0.00 34.70 3.28
80 81 4.342862 TCAAATTTCCCGCAATTTCCAA 57.657 36.364 0.00 0.00 34.70 3.53
82 83 5.681337 TTTTCAAATTTCCCGCAATTTCC 57.319 34.783 0.00 0.00 34.70 3.13
83 84 8.503196 ACTATTTTTCAAATTTCCCGCAATTTC 58.497 29.630 0.00 0.00 34.70 2.17
84 85 8.389779 ACTATTTTTCAAATTTCCCGCAATTT 57.610 26.923 0.00 0.00 36.90 1.82
87 88 8.766151 GTTAACTATTTTTCAAATTTCCCGCAA 58.234 29.630 0.00 0.00 0.00 4.85
88 89 7.385478 GGTTAACTATTTTTCAAATTTCCCGCA 59.615 33.333 5.42 0.00 0.00 5.69
89 90 7.385478 TGGTTAACTATTTTTCAAATTTCCCGC 59.615 33.333 5.42 0.00 0.00 6.13
90 91 8.819643 TGGTTAACTATTTTTCAAATTTCCCG 57.180 30.769 5.42 0.00 0.00 5.14
252 253 9.601971 GCGTATTTTAAACAGTTCACTAATTCA 57.398 29.630 0.00 0.00 0.00 2.57
253 254 8.773136 CGCGTATTTTAAACAGTTCACTAATTC 58.227 33.333 0.00 0.00 0.00 2.17
254 255 8.497554 TCGCGTATTTTAAACAGTTCACTAATT 58.502 29.630 5.77 0.00 0.00 1.40
255 256 8.020861 TCGCGTATTTTAAACAGTTCACTAAT 57.979 30.769 5.77 0.00 0.00 1.73
258 259 5.910637 TCGCGTATTTTAAACAGTTCACT 57.089 34.783 5.77 0.00 0.00 3.41
260 261 6.045698 TGTTCGCGTATTTTAAACAGTTCA 57.954 33.333 5.77 0.00 0.00 3.18
261 262 7.543127 AATGTTCGCGTATTTTAAACAGTTC 57.457 32.000 5.77 0.00 33.74 3.01
262 263 7.917720 AAATGTTCGCGTATTTTAAACAGTT 57.082 28.000 12.49 12.49 34.47 3.16
270 271 9.786224 GTGAATTTAAAAATGTTCGCGTATTTT 57.214 25.926 18.44 18.44 37.92 1.82
272 273 8.508800 TGTGAATTTAAAAATGTTCGCGTATT 57.491 26.923 5.77 2.99 0.00 1.89
273 274 8.508800 TTGTGAATTTAAAAATGTTCGCGTAT 57.491 26.923 5.77 0.00 0.00 3.06
275 276 6.814076 TTGTGAATTTAAAAATGTTCGCGT 57.186 29.167 5.77 0.00 0.00 6.01
276 277 7.113658 TGTTTGTGAATTTAAAAATGTTCGCG 58.886 30.769 0.00 0.00 0.00 5.87
277 278 8.986039 ATGTTTGTGAATTTAAAAATGTTCGC 57.014 26.923 6.06 6.06 0.00 4.70
303 304 3.122297 CTGCTGTTCGCCAATTCAAAAA 58.878 40.909 0.00 0.00 38.05 1.94
304 305 2.360483 TCTGCTGTTCGCCAATTCAAAA 59.640 40.909 0.00 0.00 38.05 2.44
308 309 2.789092 CGAATCTGCTGTTCGCCAATTC 60.789 50.000 12.51 3.35 41.43 2.17
309 310 1.131126 CGAATCTGCTGTTCGCCAATT 59.869 47.619 12.51 0.00 41.43 2.32
310 311 0.729116 CGAATCTGCTGTTCGCCAAT 59.271 50.000 12.51 0.00 41.43 3.16
311 312 2.161831 CGAATCTGCTGTTCGCCAA 58.838 52.632 12.51 0.00 41.43 4.52
316 317 4.410492 AATGTTCACGAATCTGCTGTTC 57.590 40.909 0.00 0.00 0.00 3.18
317 318 4.836125 AAATGTTCACGAATCTGCTGTT 57.164 36.364 0.00 0.00 0.00 3.16
318 319 4.836125 AAAATGTTCACGAATCTGCTGT 57.164 36.364 0.00 0.00 0.00 4.40
373 374 3.760580 AAAATGCCCGTGGATTCAAAA 57.239 38.095 0.00 0.00 0.00 2.44
374 375 3.760580 AAAAATGCCCGTGGATTCAAA 57.239 38.095 0.00 0.00 0.00 2.69
392 393 6.383415 ACAAAAGTTCACGCAAAGTAGAAAA 58.617 32.000 0.00 0.00 0.00 2.29
393 394 5.945155 ACAAAAGTTCACGCAAAGTAGAAA 58.055 33.333 0.00 0.00 0.00 2.52
394 395 5.554822 ACAAAAGTTCACGCAAAGTAGAA 57.445 34.783 0.00 0.00 0.00 2.10
395 396 5.122554 TGAACAAAAGTTCACGCAAAGTAGA 59.877 36.000 6.94 0.00 38.30 2.59
396 397 5.328691 TGAACAAAAGTTCACGCAAAGTAG 58.671 37.500 6.94 0.00 38.30 2.57
397 398 5.298197 TGAACAAAAGTTCACGCAAAGTA 57.702 34.783 6.94 0.00 38.30 2.24
398 399 4.167554 TGAACAAAAGTTCACGCAAAGT 57.832 36.364 6.94 0.00 38.30 2.66
399 400 5.508124 TTTGAACAAAAGTTCACGCAAAG 57.492 34.783 10.28 0.00 42.29 2.77
401 402 6.073548 ACAAATTTGAACAAAAGTTCACGCAA 60.074 30.769 24.64 3.97 42.29 4.85
402 403 5.406780 ACAAATTTGAACAAAAGTTCACGCA 59.593 32.000 24.64 0.00 42.29 5.24
404 405 7.043454 TGACAAATTTGAACAAAAGTTCACG 57.957 32.000 24.64 1.41 42.29 4.35
405 406 6.955407 GCTGACAAATTTGAACAAAAGTTCAC 59.045 34.615 24.64 6.02 42.29 3.18
407 408 7.059448 TGCTGACAAATTTGAACAAAAGTTC 57.941 32.000 24.64 8.68 33.96 3.01
409 410 7.614124 AATGCTGACAAATTTGAACAAAAGT 57.386 28.000 24.64 10.56 33.56 2.66
410 411 8.898983 AAAATGCTGACAAATTTGAACAAAAG 57.101 26.923 24.64 12.06 33.56 2.27
411 412 9.339492 GAAAAATGCTGACAAATTTGAACAAAA 57.661 25.926 24.64 13.45 33.56 2.44
412 413 8.509690 TGAAAAATGCTGACAAATTTGAACAAA 58.490 25.926 24.64 13.73 34.46 2.83
414 415 7.606858 TGAAAAATGCTGACAAATTTGAACA 57.393 28.000 24.64 19.85 0.00 3.18
415 416 8.892887 TTTGAAAAATGCTGACAAATTTGAAC 57.107 26.923 24.64 16.74 0.00 3.18
418 419 8.844441 ACATTTGAAAAATGCTGACAAATTTG 57.156 26.923 16.67 16.67 38.52 2.32
419 420 9.934190 GTACATTTGAAAAATGCTGACAAATTT 57.066 25.926 11.62 0.00 38.52 1.82
420 421 9.107177 TGTACATTTGAAAAATGCTGACAAATT 57.893 25.926 11.62 0.00 38.52 1.82
421 422 8.659925 TGTACATTTGAAAAATGCTGACAAAT 57.340 26.923 11.62 0.00 40.29 2.32
422 423 7.978414 TCTGTACATTTGAAAAATGCTGACAAA 59.022 29.630 11.62 0.00 35.49 2.83
423 424 7.434897 GTCTGTACATTTGAAAAATGCTGACAA 59.565 33.333 11.62 0.00 30.36 3.18
425 426 6.917477 TGTCTGTACATTTGAAAAATGCTGAC 59.083 34.615 11.62 13.93 0.00 3.51
426 427 7.036996 TGTCTGTACATTTGAAAAATGCTGA 57.963 32.000 11.62 4.87 0.00 4.26
427 428 7.878477 ATGTCTGTACATTTGAAAAATGCTG 57.122 32.000 11.62 3.01 44.07 4.41
441 442 9.944663 GTTCACAAATTCTAAAATGTCTGTACA 57.055 29.630 0.00 0.00 40.69 2.90
476 477 6.436843 AAATAGAAAAGATGTTCGCGGATT 57.563 33.333 6.13 0.00 32.50 3.01
481 482 6.527722 TCATGCAAAATAGAAAAGATGTTCGC 59.472 34.615 0.00 0.00 32.50 4.70
482 483 8.368126 GTTCATGCAAAATAGAAAAGATGTTCG 58.632 33.333 0.00 0.00 32.50 3.95
484 485 9.768662 AAGTTCATGCAAAATAGAAAAGATGTT 57.231 25.926 0.00 0.00 0.00 2.71
485 486 9.768662 AAAGTTCATGCAAAATAGAAAAGATGT 57.231 25.926 0.00 0.00 0.00 3.06
496 497 9.672086 CATGAATTGAAAAAGTTCATGCAAAAT 57.328 25.926 12.58 0.00 46.78 1.82
528 529 8.855279 CGAAACAAAATGTCTGTGAACTTAAAA 58.145 29.630 0.00 0.00 0.00 1.52
529 530 8.237949 TCGAAACAAAATGTCTGTGAACTTAAA 58.762 29.630 0.00 0.00 0.00 1.52
530 531 7.753659 TCGAAACAAAATGTCTGTGAACTTAA 58.246 30.769 0.00 0.00 0.00 1.85
531 532 7.065324 ACTCGAAACAAAATGTCTGTGAACTTA 59.935 33.333 0.00 0.00 0.00 2.24
532 533 6.128007 ACTCGAAACAAAATGTCTGTGAACTT 60.128 34.615 0.00 0.00 0.00 2.66
533 534 5.354234 ACTCGAAACAAAATGTCTGTGAACT 59.646 36.000 0.00 0.00 0.00 3.01
534 535 5.569413 ACTCGAAACAAAATGTCTGTGAAC 58.431 37.500 0.00 0.00 0.00 3.18
537 538 5.275881 GCAAACTCGAAACAAAATGTCTGTG 60.276 40.000 0.00 0.00 0.00 3.66
539 540 4.797868 TGCAAACTCGAAACAAAATGTCTG 59.202 37.500 0.00 0.00 0.00 3.51
540 541 4.992688 TGCAAACTCGAAACAAAATGTCT 58.007 34.783 0.00 0.00 0.00 3.41
541 542 5.888412 ATGCAAACTCGAAACAAAATGTC 57.112 34.783 0.00 0.00 0.00 3.06
542 543 6.660887 AAATGCAAACTCGAAACAAAATGT 57.339 29.167 0.00 0.00 0.00 2.71
543 544 7.401080 AGAAAATGCAAACTCGAAACAAAATG 58.599 30.769 0.00 0.00 0.00 2.32
544 545 7.538303 AGAAAATGCAAACTCGAAACAAAAT 57.462 28.000 0.00 0.00 0.00 1.82
545 546 6.959671 AGAAAATGCAAACTCGAAACAAAA 57.040 29.167 0.00 0.00 0.00 2.44
546 547 6.567769 GAGAAAATGCAAACTCGAAACAAA 57.432 33.333 0.00 0.00 0.00 2.83
555 556 4.613622 CGTGGATTCGAGAAAATGCAAACT 60.614 41.667 0.00 0.00 38.48 2.66
556 557 3.603770 CGTGGATTCGAGAAAATGCAAAC 59.396 43.478 0.00 0.00 38.48 2.93
557 558 3.500299 TCGTGGATTCGAGAAAATGCAAA 59.500 39.130 0.00 0.00 38.48 3.68
558 559 3.070748 TCGTGGATTCGAGAAAATGCAA 58.929 40.909 0.00 0.00 38.48 4.08
560 561 3.740044 TTCGTGGATTCGAGAAAATGC 57.260 42.857 0.00 0.00 40.86 3.56
562 563 9.289303 CAAAAATATTCGTGGATTCGAGAAAAT 57.711 29.630 0.00 0.00 40.86 1.82
563 564 8.508062 TCAAAAATATTCGTGGATTCGAGAAAA 58.492 29.630 0.00 0.00 40.86 2.29
564 565 8.035165 TCAAAAATATTCGTGGATTCGAGAAA 57.965 30.769 0.00 0.00 40.86 2.52
565 566 7.603963 TCAAAAATATTCGTGGATTCGAGAA 57.396 32.000 0.00 0.00 40.86 2.87
566 567 7.603963 TTCAAAAATATTCGTGGATTCGAGA 57.396 32.000 0.00 0.00 40.86 4.04
568 569 7.638295 CGAATTCAAAAATATTCGTGGATTCGA 59.362 33.333 29.61 1.81 44.80 3.71
569 570 7.754625 CGAATTCAAAAATATTCGTGGATTCG 58.245 34.615 25.29 25.29 44.80 3.34
578 579 8.798153 AGAATGTTCGCGAATTCAAAAATATTC 58.202 29.630 27.69 19.98 35.63 1.75
579 580 8.687824 AGAATGTTCGCGAATTCAAAAATATT 57.312 26.923 27.69 14.11 35.63 1.28
580 581 8.687824 AAGAATGTTCGCGAATTCAAAAATAT 57.312 26.923 27.69 10.18 35.63 1.28
582 583 7.201232 CGTAAGAATGTTCGCGAATTCAAAAAT 60.201 33.333 27.69 15.25 43.02 1.82
583 584 6.085718 CGTAAGAATGTTCGCGAATTCAAAAA 59.914 34.615 27.69 13.14 43.02 1.94
584 585 5.562248 CGTAAGAATGTTCGCGAATTCAAAA 59.438 36.000 27.69 14.99 43.02 2.44
586 587 4.634000 CGTAAGAATGTTCGCGAATTCAA 58.366 39.130 27.69 17.13 43.02 2.69
587 588 3.482923 GCGTAAGAATGTTCGCGAATTCA 60.483 43.478 27.69 21.60 39.35 2.57
588 589 3.020261 GCGTAAGAATGTTCGCGAATTC 58.980 45.455 26.23 23.61 39.35 2.17
589 590 3.034406 GCGTAAGAATGTTCGCGAATT 57.966 42.857 26.23 16.34 39.35 2.17
596 597 9.989394 GTTGAATTAAAAAGCGTAAGAATGTTC 57.011 29.630 0.00 0.00 43.02 3.18
598 599 7.325097 CGGTTGAATTAAAAAGCGTAAGAATGT 59.675 33.333 9.98 0.00 41.13 2.71
599 600 7.201316 CCGGTTGAATTAAAAAGCGTAAGAATG 60.201 37.037 14.57 0.20 43.68 2.67
600 601 6.804783 CCGGTTGAATTAAAAAGCGTAAGAAT 59.195 34.615 14.57 0.00 43.68 2.40
601 602 6.144175 CCGGTTGAATTAAAAAGCGTAAGAA 58.856 36.000 14.57 0.00 43.68 2.52
603 604 5.454520 ACCGGTTGAATTAAAAAGCGTAAG 58.545 37.500 0.00 6.10 43.68 2.34
604 605 5.435820 ACCGGTTGAATTAAAAAGCGTAA 57.564 34.783 0.00 0.00 43.68 3.18
605 606 6.551385 TTACCGGTTGAATTAAAAAGCGTA 57.449 33.333 15.04 0.00 43.68 4.42
606 607 3.994204 ACCGGTTGAATTAAAAAGCGT 57.006 38.095 0.00 4.83 43.68 5.07
607 608 6.345961 GGTTTTACCGGTTGAATTAAAAAGCG 60.346 38.462 15.04 10.82 44.51 4.68
608 609 6.479331 TGGTTTTACCGGTTGAATTAAAAAGC 59.521 34.615 22.58 22.58 42.58 3.51
609 610 8.491950 CATGGTTTTACCGGTTGAATTAAAAAG 58.508 33.333 15.04 0.12 42.58 2.27
613 614 6.715718 TCTCATGGTTTTACCGGTTGAATTAA 59.284 34.615 15.04 0.00 42.58 1.40
614 615 6.239396 TCTCATGGTTTTACCGGTTGAATTA 58.761 36.000 15.04 2.03 42.58 1.40
615 616 5.074115 TCTCATGGTTTTACCGGTTGAATT 58.926 37.500 15.04 0.00 42.58 2.17
616 617 4.658063 TCTCATGGTTTTACCGGTTGAAT 58.342 39.130 15.04 0.00 42.58 2.57
618 619 3.558321 CCTCTCATGGTTTTACCGGTTGA 60.558 47.826 15.04 7.68 42.58 3.18
619 620 2.747446 CCTCTCATGGTTTTACCGGTTG 59.253 50.000 15.04 2.35 42.58 3.77
620 621 2.640826 TCCTCTCATGGTTTTACCGGTT 59.359 45.455 15.04 0.00 42.58 4.44
622 623 3.343941 TTCCTCTCATGGTTTTACCGG 57.656 47.619 0.00 0.00 42.58 5.28
623 624 3.439129 GGTTTCCTCTCATGGTTTTACCG 59.561 47.826 0.00 0.00 42.58 4.02
624 625 4.403734 TGGTTTCCTCTCATGGTTTTACC 58.596 43.478 0.00 0.00 39.22 2.85
625 626 4.459337 CCTGGTTTCCTCTCATGGTTTTAC 59.541 45.833 0.00 0.00 0.00 2.01
627 628 3.140144 TCCTGGTTTCCTCTCATGGTTTT 59.860 43.478 0.00 0.00 0.00 2.43
628 629 2.716424 TCCTGGTTTCCTCTCATGGTTT 59.284 45.455 0.00 0.00 0.00 3.27
630 631 2.044793 TCCTGGTTTCCTCTCATGGT 57.955 50.000 0.00 0.00 0.00 3.55
631 632 3.439857 TTTCCTGGTTTCCTCTCATGG 57.560 47.619 0.00 0.00 0.00 3.66
632 633 5.072741 TCTTTTTCCTGGTTTCCTCTCATG 58.927 41.667 0.00 0.00 0.00 3.07
633 634 5.324832 TCTTTTTCCTGGTTTCCTCTCAT 57.675 39.130 0.00 0.00 0.00 2.90
635 636 6.321435 TCTTTTCTTTTTCCTGGTTTCCTCTC 59.679 38.462 0.00 0.00 0.00 3.20
638 639 8.004801 TCTATCTTTTCTTTTTCCTGGTTTCCT 58.995 33.333 0.00 0.00 0.00 3.36
639 640 8.178313 TCTATCTTTTCTTTTTCCTGGTTTCC 57.822 34.615 0.00 0.00 0.00 3.13
640 641 8.851145 ACTCTATCTTTTCTTTTTCCTGGTTTC 58.149 33.333 0.00 0.00 0.00 2.78
641 642 8.633561 CACTCTATCTTTTCTTTTTCCTGGTTT 58.366 33.333 0.00 0.00 0.00 3.27
642 643 7.231519 CCACTCTATCTTTTCTTTTTCCTGGTT 59.768 37.037 0.00 0.00 0.00 3.67
643 644 6.717084 CCACTCTATCTTTTCTTTTTCCTGGT 59.283 38.462 0.00 0.00 0.00 4.00
644 645 6.717084 ACCACTCTATCTTTTCTTTTTCCTGG 59.283 38.462 0.00 0.00 0.00 4.45
645 646 7.445402 TCACCACTCTATCTTTTCTTTTTCCTG 59.555 37.037 0.00 0.00 0.00 3.86
646 647 7.518188 TCACCACTCTATCTTTTCTTTTTCCT 58.482 34.615 0.00 0.00 0.00 3.36
647 648 7.745620 TCACCACTCTATCTTTTCTTTTTCC 57.254 36.000 0.00 0.00 0.00 3.13
648 649 9.670719 CTTTCACCACTCTATCTTTTCTTTTTC 57.329 33.333 0.00 0.00 0.00 2.29
649 650 9.408648 TCTTTCACCACTCTATCTTTTCTTTTT 57.591 29.630 0.00 0.00 0.00 1.94
650 651 8.980481 TCTTTCACCACTCTATCTTTTCTTTT 57.020 30.769 0.00 0.00 0.00 2.27
651 652 8.980481 TTCTTTCACCACTCTATCTTTTCTTT 57.020 30.769 0.00 0.00 0.00 2.52
652 653 8.980481 TTTCTTTCACCACTCTATCTTTTCTT 57.020 30.769 0.00 0.00 0.00 2.52
654 655 8.454894 GGATTTCTTTCACCACTCTATCTTTTC 58.545 37.037 0.00 0.00 0.00 2.29
655 656 7.944554 TGGATTTCTTTCACCACTCTATCTTTT 59.055 33.333 0.00 0.00 0.00 2.27
656 657 7.461749 TGGATTTCTTTCACCACTCTATCTTT 58.538 34.615 0.00 0.00 0.00 2.52
657 658 7.020827 TGGATTTCTTTCACCACTCTATCTT 57.979 36.000 0.00 0.00 0.00 2.40
659 660 7.362142 GGTTTGGATTTCTTTCACCACTCTATC 60.362 40.741 0.00 0.00 31.87 2.08
660 661 6.434340 GGTTTGGATTTCTTTCACCACTCTAT 59.566 38.462 0.00 0.00 31.87 1.98
661 662 5.768164 GGTTTGGATTTCTTTCACCACTCTA 59.232 40.000 0.00 0.00 31.87 2.43
663 664 4.340950 TGGTTTGGATTTCTTTCACCACTC 59.659 41.667 0.00 0.00 31.87 3.51
665 666 4.664150 TGGTTTGGATTTCTTTCACCAC 57.336 40.909 0.00 0.00 31.87 4.16
667 668 6.101650 AGAATGGTTTGGATTTCTTTCACC 57.898 37.500 0.00 0.00 0.00 4.02
668 669 5.858581 CGAGAATGGTTTGGATTTCTTTCAC 59.141 40.000 0.00 0.00 0.00 3.18
673 674 2.420022 CGCGAGAATGGTTTGGATTTCT 59.580 45.455 0.00 0.00 0.00 2.52
674 675 2.477863 CCGCGAGAATGGTTTGGATTTC 60.478 50.000 8.23 0.00 0.00 2.17
675 676 1.472480 CCGCGAGAATGGTTTGGATTT 59.528 47.619 8.23 0.00 0.00 2.17
677 678 0.035439 ACCGCGAGAATGGTTTGGAT 60.035 50.000 8.23 0.00 33.81 3.41
678 679 0.672401 GACCGCGAGAATGGTTTGGA 60.672 55.000 8.23 0.00 38.99 3.53
679 680 1.794222 GACCGCGAGAATGGTTTGG 59.206 57.895 8.23 0.00 38.99 3.28
680 681 1.419922 CGACCGCGAGAATGGTTTG 59.580 57.895 8.23 0.00 38.99 2.93
681 682 2.388232 GCGACCGCGAGAATGGTTT 61.388 57.895 8.23 0.00 38.99 3.27
701 702 2.358737 AACGGAAAGGCCAGAGCG 60.359 61.111 5.01 0.00 41.24 5.03
703 704 1.377333 GGGAACGGAAAGGCCAGAG 60.377 63.158 5.01 0.00 35.94 3.35
837 1367 1.148273 GGGCGCTGATTGGTGGATA 59.852 57.895 7.64 0.00 0.00 2.59
838 1368 2.124151 GGGCGCTGATTGGTGGAT 60.124 61.111 7.64 0.00 0.00 3.41
877 1407 3.785859 CAAGCTGCGGGAGGGCTA 61.786 66.667 0.00 0.00 35.06 3.93
881 1411 2.747855 GGAACAAGCTGCGGGAGG 60.748 66.667 0.00 0.00 0.00 4.30
889 1419 1.160137 GAGATGTTGCGGAACAAGCT 58.840 50.000 26.45 23.96 45.23 3.74
890 1420 0.169009 GGAGATGTTGCGGAACAAGC 59.831 55.000 26.45 19.95 45.23 4.01
893 1423 1.610624 GGAAGGAGATGTTGCGGAACA 60.611 52.381 25.00 25.00 46.13 3.18
899 1430 4.320608 TTTGTTTGGAAGGAGATGTTGC 57.679 40.909 0.00 0.00 0.00 4.17
928 1473 1.270305 CGTGCTGGAACTGGAAGAAGA 60.270 52.381 0.00 0.00 37.43 2.87
979 1527 1.251251 GCTGCTGAGGTTGATTTGGT 58.749 50.000 0.00 0.00 0.00 3.67
982 1530 1.741706 CATCGCTGCTGAGGTTGATTT 59.258 47.619 0.00 0.00 0.00 2.17
983 1531 1.376543 CATCGCTGCTGAGGTTGATT 58.623 50.000 0.00 0.00 0.00 2.57
1473 2024 2.300437 AGCCAACTACAGTTCCTGAGAC 59.700 50.000 0.00 0.00 35.83 3.36
1512 2063 3.683365 ACCAAAAATCAGCATTCCACC 57.317 42.857 0.00 0.00 0.00 4.61
1516 2067 6.072893 AGCAATCAAACCAAAAATCAGCATTC 60.073 34.615 0.00 0.00 0.00 2.67
1517 2068 5.766174 AGCAATCAAACCAAAAATCAGCATT 59.234 32.000 0.00 0.00 0.00 3.56
1518 2069 5.180492 CAGCAATCAAACCAAAAATCAGCAT 59.820 36.000 0.00 0.00 0.00 3.79
1520 2071 4.751098 TCAGCAATCAAACCAAAAATCAGC 59.249 37.500 0.00 0.00 0.00 4.26
1521 2072 6.425721 ACATCAGCAATCAAACCAAAAATCAG 59.574 34.615 0.00 0.00 0.00 2.90
1523 2270 6.790285 ACATCAGCAATCAAACCAAAAATC 57.210 33.333 0.00 0.00 0.00 2.17
1534 2281 0.522626 CACGGCAACATCAGCAATCA 59.477 50.000 0.00 0.00 0.00 2.57
1586 2580 3.059097 AGGGTTCCCAAGAGATGCATAT 58.941 45.455 10.73 0.00 0.00 1.78
1588 2582 1.213926 GAGGGTTCCCAAGAGATGCAT 59.786 52.381 10.73 0.00 0.00 3.96
1626 2630 3.194861 GCCATGCATCAAACGAGTACTA 58.805 45.455 0.00 0.00 0.00 1.82
1670 2680 6.159293 ACATACATCACTTACCATCGCATAG 58.841 40.000 0.00 0.00 0.00 2.23
1675 2929 7.539712 AGAAAACATACATCACTTACCATCG 57.460 36.000 0.00 0.00 0.00 3.84
1766 3676 5.247862 TGCAGCTGATTCTAAGAAATGTCA 58.752 37.500 20.43 0.00 0.00 3.58
1824 3744 1.827789 GTGCCAACCACCAAGAGCA 60.828 57.895 0.00 0.00 38.55 4.26
1862 3782 5.152623 TCATCAGGTACTTGTCTTTGGAG 57.847 43.478 4.75 0.00 34.60 3.86
1895 3816 4.081142 TCGCTGGTTTATCTCCAAAGATCA 60.081 41.667 0.00 0.00 41.46 2.92
1942 4144 8.548025 TCATAAAGATTACCAATGTCTCCTTCA 58.452 33.333 0.00 0.00 0.00 3.02
2142 4347 4.043686 TCAAGAAGGTAACCTAAAAGGGGG 59.956 45.833 0.00 0.00 40.58 5.40
2150 4356 6.007703 CCACCAAAATCAAGAAGGTAACCTA 58.992 40.000 0.00 0.00 31.13 3.08
2240 4447 6.348540 GCTCTTCAGTAAACGATTGGAAACAT 60.349 38.462 0.00 0.00 42.32 2.71
2258 4465 6.203530 CACAGATGAACTTAAACTGCTCTTCA 59.796 38.462 0.00 0.00 32.67 3.02
2288 4495 6.205658 AGCAGTTTCTAAGAATGAAACCAGTC 59.794 38.462 13.51 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.