Multiple sequence alignment - TraesCS5B01G529700

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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 TraesCS5B01G529700 chr5B 100.000 3300 0 0 1 3300 688490745 688487446 0.000000e+00 6095.0
1 TraesCS5B01G529700 chr5B 100.000 310 0 0 3425 3734 688487321 688487012 1.160000e-159 573.0
2 TraesCS5B01G529700 chr5B 100.000 40 0 0 2684 2723 688487962 688487923 1.440000e-09 75.0
3 TraesCS5B01G529700 chr5B 100.000 40 0 0 2784 2823 688488062 688488023 1.440000e-09 75.0
4 TraesCS5B01G529700 chrUn 99.755 2451 6 0 816 3266 340111766 340114216 0.000000e+00 4494.0
5 TraesCS5B01G529700 chrUn 96.000 125 4 1 3610 3734 360414937 360414814 6.320000e-48 202.0
6 TraesCS5B01G529700 chrUn 97.872 47 1 0 2997 3043 15366810 15366764 8.600000e-12 82.4
7 TraesCS5B01G529700 chrUn 97.674 43 1 0 2781 2823 340113631 340113673 1.440000e-09 75.0
8 TraesCS5B01G529700 chrUn 97.674 43 1 0 2681 2723 340113731 340113773 1.440000e-09 75.0
9 TraesCS5B01G529700 chrUn 100.000 32 0 0 3269 3300 15366202 15366171 4.030000e-05 60.2
10 TraesCS5B01G529700 chr5D 92.420 752 48 4 799 1541 545633217 545632466 0.000000e+00 1064.0
11 TraesCS5B01G529700 chr5D 88.929 551 44 6 1 543 545640476 545639935 0.000000e+00 664.0
12 TraesCS5B01G529700 chr5D 92.717 357 23 1 2392 2748 545631847 545631494 2.570000e-141 512.0
13 TraesCS5B01G529700 chr5D 92.675 314 23 0 1851 2164 545632178 545631865 1.580000e-123 453.0
14 TraesCS5B01G529700 chr5D 92.337 261 18 2 1532 1791 545632447 545632188 1.640000e-98 370.0
15 TraesCS5B01G529700 chr4B 94.586 314 6 1 2998 3300 647393434 647393747 3.370000e-130 475.0
16 TraesCS5B01G529700 chr4B 95.506 267 10 2 3034 3300 122658739 122658475 3.450000e-115 425.0
17 TraesCS5B01G529700 chr4B 96.380 221 8 0 2170 2390 530233917 530234137 7.620000e-97 364.0
18 TraesCS5B01G529700 chr4B 98.095 210 2 2 3425 3632 647393781 647393990 7.620000e-97 364.0
19 TraesCS5B01G529700 chr4B 99.123 114 1 0 3621 3734 101950148 101950035 4.890000e-49 206.0
20 TraesCS5B01G529700 chr4B 75.000 284 44 16 2997 3278 146554514 146554256 5.100000e-19 106.0
21 TraesCS5B01G529700 chr1B 97.378 267 7 0 3034 3300 570506336 570506070 4.400000e-124 455.0
22 TraesCS5B01G529700 chr1B 96.255 267 10 0 3034 3300 635115992 635115726 4.430000e-119 438.0
23 TraesCS5B01G529700 chr1B 97.143 210 4 2 3425 3632 570506035 570505826 1.650000e-93 353.0
24 TraesCS5B01G529700 chr1B 99.123 114 1 0 3621 3734 570505794 570505681 4.890000e-49 206.0
25 TraesCS5B01G529700 chr1B 99.123 114 1 0 3621 3734 678832631 678832744 4.890000e-49 206.0
26 TraesCS5B01G529700 chr6B 95.880 267 11 0 3034 3300 18430951 18430685 2.060000e-117 433.0
27 TraesCS5B01G529700 chr6B 95.131 267 12 1 3034 3300 256332477 256332212 1.600000e-113 420.0
28 TraesCS5B01G529700 chr6B 97.630 211 2 3 3425 3632 256332177 256331967 3.550000e-95 359.0
29 TraesCS5B01G529700 chr6B 93.333 240 12 4 2167 2405 598447472 598447708 5.930000e-93 351.0
30 TraesCS5B01G529700 chr6B 99.123 114 1 0 3621 3734 256331935 256331822 4.890000e-49 206.0
31 TraesCS5B01G529700 chr6B 99.123 114 1 0 3621 3734 691626079 691625966 4.890000e-49 206.0
32 TraesCS5B01G529700 chr6B 77.982 218 33 11 2997 3213 644400845 644401048 5.060000e-24 122.0
33 TraesCS5B01G529700 chr6B 97.872 47 1 0 2997 3043 18431028 18430982 8.600000e-12 82.4
34 TraesCS5B01G529700 chr6B 97.872 47 1 0 2997 3043 91856254 91856300 8.600000e-12 82.4
35 TraesCS5B01G529700 chr2B 96.875 256 7 1 3044 3299 62171429 62171683 9.580000e-116 427.0
36 TraesCS5B01G529700 chr2B 96.729 214 6 1 3425 3637 59244706 59244493 4.590000e-94 355.0
37 TraesCS5B01G529700 chr2B 90.272 257 23 2 2146 2401 800481047 800480792 5.980000e-88 335.0
38 TraesCS5B01G529700 chr2B 80.814 172 33 0 2470 2641 725390332 725390503 6.510000e-28 135.0
39 TraesCS5B01G529700 chr4A 95.817 263 11 0 3034 3296 693409658 693409396 3.450000e-115 425.0
40 TraesCS5B01G529700 chr4A 97.143 210 4 2 3425 3632 694392941 694393150 1.650000e-93 353.0
41 TraesCS5B01G529700 chr4A 99.123 114 1 0 3621 3734 686539470 686539583 4.890000e-49 206.0
42 TraesCS5B01G529700 chr4A 87.013 77 9 1 392 468 26766583 26766658 6.640000e-13 86.1
43 TraesCS5B01G529700 chr3B 94.553 257 13 1 3044 3300 828731207 828730952 2.700000e-106 396.0
44 TraesCS5B01G529700 chr3B 95.946 222 9 0 2170 2391 757951496 757951717 9.860000e-96 361.0
45 TraesCS5B01G529700 chr3B 97.619 210 3 2 3425 3632 828451267 828451476 3.550000e-95 359.0
46 TraesCS5B01G529700 chr3B 80.000 120 19 5 399 517 547128519 547128634 2.390000e-12 84.2
47 TraesCS5B01G529700 chr3B 97.917 48 1 0 2996 3043 828450951 828450998 2.390000e-12 84.2
48 TraesCS5B01G529700 chr7B 98.571 210 1 2 3425 3632 552838873 552838664 1.640000e-98 370.0
49 TraesCS5B01G529700 chr7B 95.928 221 9 0 2168 2388 388177179 388176959 3.550000e-95 359.0
50 TraesCS5B01G529700 chr7B 86.667 60 3 3 435 489 125726652 125726593 1.120000e-05 62.1
51 TraesCS5B01G529700 chr3A 96.364 220 8 0 2170 2389 535225523 535225742 2.740000e-96 363.0
52 TraesCS5B01G529700 chr3A 84.615 78 9 3 399 474 530940839 530940763 1.440000e-09 75.0
53 TraesCS5B01G529700 chr2A 96.347 219 8 0 2170 2388 258346965 258346747 9.860000e-96 361.0
54 TraesCS5B01G529700 chr7A 97.630 211 2 3 3425 3632 734141677 734141887 3.550000e-95 359.0
55 TraesCS5B01G529700 chr7A 96.744 215 5 2 3425 3637 732711322 732711536 1.280000e-94 357.0
56 TraesCS5B01G529700 chr1D 92.683 246 14 4 2153 2397 271285326 271285568 5.930000e-93 351.0
57 TraesCS5B01G529700 chr4D 89.474 209 18 4 563 769 488242642 488242436 1.030000e-65 261.0
58 TraesCS5B01G529700 chr4D 100.000 31 0 0 763 793 488242455 488242425 1.450000e-04 58.4
59 TraesCS5B01G529700 chr6A 83.772 228 32 5 3075 3299 50426608 50426383 1.050000e-50 211.0
60 TraesCS5B01G529700 chr6A 99.123 114 1 0 3621 3734 46719989 46720102 4.890000e-49 206.0
61 TraesCS5B01G529700 chr6A 92.500 40 2 1 434 472 591953302 591953263 5.210000e-04 56.5
62 TraesCS5B01G529700 chr5A 96.000 125 4 1 3610 3734 3636112 3635989 6.320000e-48 202.0
63 TraesCS5B01G529700 chr5A 79.412 102 4 17 2360 2450 694177760 694177665 5.210000e-04 56.5
64 TraesCS5B01G529700 chr2D 86.364 110 11 3 399 508 317878760 317878655 2.360000e-22 117.0
65 TraesCS5B01G529700 chr2D 79.348 92 14 5 392 480 401446782 401446693 4.030000e-05 60.2


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 TraesCS5B01G529700 chr5B 688487012 688490745 3733 True 1704.500000 6095 100.000000 1 3734 4 chr5B.!!$R1 3733
1 TraesCS5B01G529700 chrUn 340111766 340114216 2450 False 1548.000000 4494 98.367667 816 3266 3 chrUn.!!$F1 2450
2 TraesCS5B01G529700 chr5D 545639935 545640476 541 True 664.000000 664 88.929000 1 543 1 chr5D.!!$R1 542
3 TraesCS5B01G529700 chr5D 545631494 545633217 1723 True 599.750000 1064 92.537250 799 2748 4 chr5D.!!$R2 1949
4 TraesCS5B01G529700 chr4B 647393434 647393990 556 False 419.500000 475 96.340500 2998 3632 2 chr4B.!!$F2 634
5 TraesCS5B01G529700 chr1B 570505681 570506336 655 True 338.000000 455 97.881333 3034 3734 3 chr1B.!!$R2 700
6 TraesCS5B01G529700 chr6B 256331822 256332477 655 True 328.333333 420 97.294667 3034 3734 3 chr6B.!!$R3 700
7 TraesCS5B01G529700 chr3B 828450951 828451476 525 False 221.600000 359 97.768000 2996 3632 2 chr3B.!!$F3 636

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
653 662 0.031817 CAAAGGGGAAGGATGGGCAT 60.032 55.0 0.0 0.0 0.0 4.40 F
748 757 0.393808 ATGTACACCGTTGGATGGCC 60.394 55.0 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2355 2408 4.976731 CGTCTAGGTGAATAAGTCATTCGG 59.023 45.833 0.0 0.0 45.25 4.30 R
2854 2907 1.139095 CAAGACGCCCGAGGAGTAC 59.861 63.158 0.0 0.0 35.49 2.73 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
37 38 2.331893 CGCCATTCTTGGGAACGCA 61.332 57.895 0.00 0.00 43.84 5.24
49 50 0.949105 GGAACGCATCGGTGTGACTT 60.949 55.000 17.69 0.00 37.91 3.01
54 55 0.391130 GCATCGGTGTGACTTGCCTA 60.391 55.000 0.00 0.00 0.00 3.93
55 56 1.359848 CATCGGTGTGACTTGCCTAC 58.640 55.000 0.00 0.00 0.00 3.18
83 84 2.610438 AGAAGTCCATGGGCAACATT 57.390 45.000 20.74 3.24 37.84 2.71
89 90 2.684881 GTCCATGGGCAACATTGTAGAG 59.315 50.000 12.68 0.00 37.84 2.43
103 104 5.010719 ACATTGTAGAGAAGAAGGACGACAA 59.989 40.000 0.00 0.00 0.00 3.18
107 108 3.983741 AGAGAAGAAGGACGACAACTTG 58.016 45.455 0.00 0.00 0.00 3.16
113 114 2.617274 GGACGACAACTTGCAGCCC 61.617 63.158 0.00 0.00 0.00 5.19
117 118 0.605319 CGACAACTTGCAGCCCCTTA 60.605 55.000 0.00 0.00 0.00 2.69
119 120 0.478507 ACAACTTGCAGCCCCTTACT 59.521 50.000 0.00 0.00 0.00 2.24
145 146 4.045104 GTGATTCACGACATACTAGGCTG 58.955 47.826 0.13 0.00 0.00 4.85
155 156 3.118738 ACATACTAGGCTGGAGGAAAACG 60.119 47.826 4.33 0.00 0.00 3.60
167 168 1.166531 GGAAAACGAGTGGCTGTGCT 61.167 55.000 0.00 0.00 0.00 4.40
176 177 2.168521 GAGTGGCTGTGCTAGGTGATAA 59.831 50.000 0.00 0.00 0.00 1.75
186 187 5.483937 TGTGCTAGGTGATAAGGAAGAAGAA 59.516 40.000 0.00 0.00 0.00 2.52
190 191 3.783082 AGGTGATAAGGAAGAAGAAGGGG 59.217 47.826 0.00 0.00 0.00 4.79
193 194 2.053747 TAAGGAAGAAGAAGGGGGCA 57.946 50.000 0.00 0.00 0.00 5.36
205 206 3.068064 GGGGCAATTGGTGGACCG 61.068 66.667 7.72 0.00 39.43 4.79
217 218 1.152860 TGGACCGCCACAACACATT 60.153 52.632 0.00 0.00 39.92 2.71
237 238 4.056125 TGTGCGAGAGGGAGCGTG 62.056 66.667 0.00 0.00 35.87 5.34
238 239 3.749064 GTGCGAGAGGGAGCGTGA 61.749 66.667 0.00 0.00 35.87 4.35
239 240 2.989253 TGCGAGAGGGAGCGTGAA 60.989 61.111 0.00 0.00 35.87 3.18
242 243 0.102481 GCGAGAGGGAGCGTGAAATA 59.898 55.000 0.00 0.00 0.00 1.40
271 272 4.323843 AACGTCTCGCGCGTGACT 62.324 61.111 42.77 32.44 46.11 3.41
306 307 2.769621 ATCGGCCTGCTGGGATCA 60.770 61.111 12.06 0.00 37.23 2.92
330 331 8.519526 TCATTTACCTTAGCAATTGGTGTAAAG 58.480 33.333 24.05 18.22 35.48 1.85
333 334 8.921353 TTACCTTAGCAATTGGTGTAAAGTTA 57.079 30.769 20.13 6.16 35.48 2.24
382 383 9.421399 ACTTATCTTTTCCTTTTTCTTCTTGGA 57.579 29.630 0.00 0.00 0.00 3.53
412 421 1.670811 CTTTTATGGCGGCAGTAGTGG 59.329 52.381 19.29 2.05 0.00 4.00
413 422 0.616371 TTTATGGCGGCAGTAGTGGT 59.384 50.000 19.29 0.22 0.00 4.16
414 423 0.177141 TTATGGCGGCAGTAGTGGTC 59.823 55.000 19.29 0.00 0.00 4.02
415 424 0.973496 TATGGCGGCAGTAGTGGTCA 60.973 55.000 19.29 0.00 0.00 4.02
416 425 1.626356 ATGGCGGCAGTAGTGGTCAT 61.626 55.000 19.29 0.00 0.00 3.06
429 438 2.009774 GTGGTCATTCGATGGTCTTGG 58.990 52.381 0.00 0.00 0.00 3.61
435 444 4.878397 GTCATTCGATGGTCTTGGAATCTT 59.122 41.667 0.00 0.00 0.00 2.40
477 486 7.030165 TGTTTGAGTTGCTTTGTATTTTCGAA 58.970 30.769 0.00 0.00 0.00 3.71
532 541 6.208599 TCCCTAAAAATAGTGCTTTCTTGGTG 59.791 38.462 0.00 0.00 0.00 4.17
549 558 4.729227 TGGTGAAAACCAAAAACTCTCC 57.271 40.909 0.00 0.00 36.74 3.71
550 559 4.090090 TGGTGAAAACCAAAAACTCTCCA 58.910 39.130 0.00 0.00 36.74 3.86
551 560 4.528596 TGGTGAAAACCAAAAACTCTCCAA 59.471 37.500 0.00 0.00 36.74 3.53
552 561 5.012148 TGGTGAAAACCAAAAACTCTCCAAA 59.988 36.000 0.00 0.00 36.74 3.28
553 562 5.935206 GGTGAAAACCAAAAACTCTCCAAAA 59.065 36.000 0.00 0.00 0.00 2.44
554 563 6.092122 GGTGAAAACCAAAAACTCTCCAAAAG 59.908 38.462 0.00 0.00 0.00 2.27
555 564 6.871492 GTGAAAACCAAAAACTCTCCAAAAGA 59.129 34.615 0.00 0.00 0.00 2.52
556 565 7.549134 GTGAAAACCAAAAACTCTCCAAAAGAT 59.451 33.333 0.00 0.00 32.19 2.40
557 566 8.100164 TGAAAACCAAAAACTCTCCAAAAGATT 58.900 29.630 0.00 0.00 32.19 2.40
558 567 9.594478 GAAAACCAAAAACTCTCCAAAAGATTA 57.406 29.630 0.00 0.00 32.19 1.75
559 568 9.952030 AAAACCAAAAACTCTCCAAAAGATTAA 57.048 25.926 0.00 0.00 32.19 1.40
560 569 9.599866 AAACCAAAAACTCTCCAAAAGATTAAG 57.400 29.630 0.00 0.00 32.19 1.85
561 570 7.726216 ACCAAAAACTCTCCAAAAGATTAAGG 58.274 34.615 0.00 0.00 32.19 2.69
562 571 6.646653 CCAAAAACTCTCCAAAAGATTAAGGC 59.353 38.462 0.00 0.00 32.19 4.35
563 572 5.629079 AAACTCTCCAAAAGATTAAGGCG 57.371 39.130 0.00 0.00 32.19 5.52
564 573 4.553330 ACTCTCCAAAAGATTAAGGCGA 57.447 40.909 0.00 0.00 32.19 5.54
565 574 4.254492 ACTCTCCAAAAGATTAAGGCGAC 58.746 43.478 0.00 0.00 32.19 5.19
566 575 3.259064 TCTCCAAAAGATTAAGGCGACG 58.741 45.455 0.00 0.00 0.00 5.12
567 576 2.351726 CTCCAAAAGATTAAGGCGACGG 59.648 50.000 0.00 0.00 0.00 4.79
568 577 2.027929 TCCAAAAGATTAAGGCGACGGA 60.028 45.455 0.00 0.00 0.00 4.69
569 578 2.095372 CCAAAAGATTAAGGCGACGGAC 59.905 50.000 0.00 0.00 0.00 4.79
570 579 1.636988 AAAGATTAAGGCGACGGACG 58.363 50.000 0.00 0.00 45.66 4.79
571 580 0.179119 AAGATTAAGGCGACGGACGG 60.179 55.000 1.66 0.00 42.83 4.79
572 581 1.140375 GATTAAGGCGACGGACGGT 59.860 57.895 1.66 0.00 42.83 4.83
573 582 0.381801 GATTAAGGCGACGGACGGTA 59.618 55.000 1.66 0.00 42.83 4.02
574 583 0.383231 ATTAAGGCGACGGACGGTAG 59.617 55.000 1.66 0.00 42.83 3.18
575 584 2.270297 TTAAGGCGACGGACGGTAGC 62.270 60.000 9.32 9.32 45.38 3.58
578 587 4.849329 GCGACGGACGGTAGCCAG 62.849 72.222 6.95 0.00 40.91 4.85
579 588 3.437795 CGACGGACGGTAGCCAGT 61.438 66.667 0.00 0.00 38.46 4.00
580 589 2.968206 GACGGACGGTAGCCAGTT 59.032 61.111 0.00 0.00 0.00 3.16
581 590 1.153881 GACGGACGGTAGCCAGTTC 60.154 63.158 0.00 0.00 0.00 3.01
582 591 1.870055 GACGGACGGTAGCCAGTTCA 61.870 60.000 0.00 0.00 0.00 3.18
583 592 1.255667 ACGGACGGTAGCCAGTTCAT 61.256 55.000 0.00 0.00 0.00 2.57
584 593 0.742505 CGGACGGTAGCCAGTTCATA 59.257 55.000 0.00 0.00 0.00 2.15
585 594 1.269102 CGGACGGTAGCCAGTTCATAG 60.269 57.143 0.00 0.00 0.00 2.23
586 595 1.068741 GGACGGTAGCCAGTTCATAGG 59.931 57.143 0.00 0.00 0.00 2.57
596 605 4.799564 CCAGTTCATAGGCTATCTCTCC 57.200 50.000 3.47 0.00 0.00 3.71
597 606 3.513515 CCAGTTCATAGGCTATCTCTCCC 59.486 52.174 3.47 0.00 0.00 4.30
598 607 3.192422 CAGTTCATAGGCTATCTCTCCCG 59.808 52.174 3.47 0.00 0.00 5.14
599 608 3.074687 AGTTCATAGGCTATCTCTCCCGA 59.925 47.826 3.47 0.00 0.00 5.14
600 609 3.358111 TCATAGGCTATCTCTCCCGAG 57.642 52.381 3.47 0.00 38.67 4.63
601 610 2.025793 TCATAGGCTATCTCTCCCGAGG 60.026 54.545 3.47 0.00 37.86 4.63
602 611 1.447099 TAGGCTATCTCTCCCGAGGT 58.553 55.000 0.00 0.00 37.86 3.85
603 612 0.111639 AGGCTATCTCTCCCGAGGTC 59.888 60.000 0.00 0.00 37.86 3.85
604 613 1.238625 GGCTATCTCTCCCGAGGTCG 61.239 65.000 0.00 0.00 37.86 4.79
605 614 0.250381 GCTATCTCTCCCGAGGTCGA 60.250 60.000 0.00 0.00 43.02 4.20
606 615 1.803334 CTATCTCTCCCGAGGTCGAG 58.197 60.000 0.00 0.00 43.02 4.04
607 616 0.397187 TATCTCTCCCGAGGTCGAGG 59.603 60.000 0.00 0.88 43.02 4.63
619 628 3.809423 TCGAGGGACGATCGACTG 58.191 61.111 24.34 10.99 46.45 3.51
620 629 2.024871 CGAGGGACGATCGACTGC 59.975 66.667 24.34 5.27 45.77 4.40
621 630 2.761195 CGAGGGACGATCGACTGCA 61.761 63.158 24.34 0.00 45.77 4.41
622 631 1.064946 GAGGGACGATCGACTGCAG 59.935 63.158 24.34 13.48 0.00 4.41
623 632 1.377366 GAGGGACGATCGACTGCAGA 61.377 60.000 24.34 0.00 0.00 4.26
624 633 0.965866 AGGGACGATCGACTGCAGAA 60.966 55.000 24.34 5.64 0.00 3.02
625 634 0.108804 GGGACGATCGACTGCAGAAA 60.109 55.000 24.34 5.23 0.00 2.52
626 635 1.272781 GGACGATCGACTGCAGAAAG 58.727 55.000 24.34 11.01 0.00 2.62
627 636 1.135373 GGACGATCGACTGCAGAAAGA 60.135 52.381 24.34 16.13 0.00 2.52
628 637 2.181205 GACGATCGACTGCAGAAAGAG 58.819 52.381 24.34 9.34 0.00 2.85
629 638 1.813178 ACGATCGACTGCAGAAAGAGA 59.187 47.619 24.34 11.78 0.00 3.10
630 639 2.229062 ACGATCGACTGCAGAAAGAGAA 59.771 45.455 24.34 0.00 0.00 2.87
631 640 3.245797 CGATCGACTGCAGAAAGAGAAA 58.754 45.455 23.35 0.00 0.00 2.52
632 641 3.862267 CGATCGACTGCAGAAAGAGAAAT 59.138 43.478 23.35 1.26 0.00 2.17
633 642 4.026968 CGATCGACTGCAGAAAGAGAAATC 60.027 45.833 23.35 9.34 0.00 2.17
634 643 3.589988 TCGACTGCAGAAAGAGAAATCC 58.410 45.455 23.35 0.00 0.00 3.01
635 644 3.006859 TCGACTGCAGAAAGAGAAATCCA 59.993 43.478 23.35 0.00 0.00 3.41
636 645 3.748048 CGACTGCAGAAAGAGAAATCCAA 59.252 43.478 23.35 0.00 0.00 3.53
637 646 4.214119 CGACTGCAGAAAGAGAAATCCAAA 59.786 41.667 23.35 0.00 0.00 3.28
638 647 5.616424 CGACTGCAGAAAGAGAAATCCAAAG 60.616 44.000 23.35 0.00 0.00 2.77
639 648 4.522022 ACTGCAGAAAGAGAAATCCAAAGG 59.478 41.667 23.35 0.00 0.00 3.11
640 649 3.828451 TGCAGAAAGAGAAATCCAAAGGG 59.172 43.478 0.00 0.00 0.00 3.95
641 650 3.194329 GCAGAAAGAGAAATCCAAAGGGG 59.806 47.826 0.00 0.00 38.37 4.79
650 659 2.408920 TCCAAAGGGGAAGGATGGG 58.591 57.895 0.00 0.00 44.80 4.00
651 660 1.381735 CCAAAGGGGAAGGATGGGC 60.382 63.158 0.00 0.00 40.01 5.36
652 661 1.387737 CAAAGGGGAAGGATGGGCA 59.612 57.895 0.00 0.00 0.00 5.36
653 662 0.031817 CAAAGGGGAAGGATGGGCAT 60.032 55.000 0.00 0.00 0.00 4.40
654 663 1.217689 CAAAGGGGAAGGATGGGCATA 59.782 52.381 0.00 0.00 0.00 3.14
655 664 0.853530 AAGGGGAAGGATGGGCATAC 59.146 55.000 0.00 0.00 0.00 2.39
656 665 1.073199 GGGGAAGGATGGGCATACG 59.927 63.158 0.00 0.00 0.00 3.06
657 666 1.705997 GGGGAAGGATGGGCATACGT 61.706 60.000 0.00 0.00 0.00 3.57
658 667 1.053424 GGGAAGGATGGGCATACGTA 58.947 55.000 0.00 0.00 0.00 3.57
659 668 1.628846 GGGAAGGATGGGCATACGTAT 59.371 52.381 1.14 1.14 0.00 3.06
660 669 2.615493 GGGAAGGATGGGCATACGTATG 60.615 54.545 27.59 27.59 36.78 2.39
661 670 2.615493 GGAAGGATGGGCATACGTATGG 60.615 54.545 31.14 16.47 34.32 2.74
662 671 0.984230 AGGATGGGCATACGTATGGG 59.016 55.000 31.14 12.35 34.32 4.00
663 672 0.981183 GGATGGGCATACGTATGGGA 59.019 55.000 31.14 0.00 34.32 4.37
664 673 1.349688 GGATGGGCATACGTATGGGAA 59.650 52.381 31.14 0.00 34.32 3.97
665 674 2.615493 GGATGGGCATACGTATGGGAAG 60.615 54.545 31.14 10.98 34.32 3.46
666 675 1.796017 TGGGCATACGTATGGGAAGA 58.204 50.000 31.14 0.00 34.32 2.87
667 676 2.120312 TGGGCATACGTATGGGAAGAA 58.880 47.619 31.14 0.00 34.32 2.52
668 677 2.506231 TGGGCATACGTATGGGAAGAAA 59.494 45.455 31.14 0.00 34.32 2.52
669 678 2.876550 GGGCATACGTATGGGAAGAAAC 59.123 50.000 31.14 15.12 34.32 2.78
670 679 2.542595 GGCATACGTATGGGAAGAAACG 59.457 50.000 31.14 7.62 40.99 3.60
671 680 2.542595 GCATACGTATGGGAAGAAACGG 59.457 50.000 31.14 7.14 39.57 4.44
672 681 2.965572 TACGTATGGGAAGAAACGGG 57.034 50.000 0.00 0.00 39.57 5.28
673 682 1.269012 ACGTATGGGAAGAAACGGGA 58.731 50.000 0.00 0.00 39.57 5.14
674 683 1.624813 ACGTATGGGAAGAAACGGGAA 59.375 47.619 0.00 0.00 39.57 3.97
675 684 2.237893 ACGTATGGGAAGAAACGGGAAT 59.762 45.455 0.00 0.00 39.57 3.01
676 685 3.451902 ACGTATGGGAAGAAACGGGAATA 59.548 43.478 0.00 0.00 39.57 1.75
677 686 3.805971 CGTATGGGAAGAAACGGGAATAC 59.194 47.826 0.00 0.00 0.00 1.89
678 687 2.389962 TGGGAAGAAACGGGAATACG 57.610 50.000 0.00 0.00 40.31 3.06
679 688 1.065998 TGGGAAGAAACGGGAATACGG 60.066 52.381 0.00 0.00 38.39 4.02
680 689 1.207811 GGGAAGAAACGGGAATACGGA 59.792 52.381 0.00 0.00 38.39 4.69
681 690 2.547826 GGAAGAAACGGGAATACGGAG 58.452 52.381 0.00 0.00 38.39 4.63
682 691 1.931841 GAAGAAACGGGAATACGGAGC 59.068 52.381 0.00 0.00 38.39 4.70
683 692 1.192428 AGAAACGGGAATACGGAGCT 58.808 50.000 0.00 0.00 38.39 4.09
684 693 1.134788 AGAAACGGGAATACGGAGCTG 60.135 52.381 0.00 0.00 38.39 4.24
685 694 0.743345 AAACGGGAATACGGAGCTGC 60.743 55.000 0.00 0.00 38.39 5.25
686 695 2.658593 CGGGAATACGGAGCTGCG 60.659 66.667 26.95 26.95 0.00 5.18
687 696 2.967615 GGGAATACGGAGCTGCGC 60.968 66.667 28.46 11.08 0.00 6.09
688 697 3.330853 GGAATACGGAGCTGCGCG 61.331 66.667 28.46 0.00 0.00 6.86
689 698 3.330853 GAATACGGAGCTGCGCGG 61.331 66.667 28.46 13.18 0.00 6.46
690 699 4.891727 AATACGGAGCTGCGCGGG 62.892 66.667 28.46 7.13 0.00 6.13
697 706 4.643387 AGCTGCGCGGGTTCCTTT 62.643 61.111 16.70 0.00 0.00 3.11
698 707 4.103103 GCTGCGCGGGTTCCTTTC 62.103 66.667 19.75 0.00 0.00 2.62
699 708 3.431725 CTGCGCGGGTTCCTTTCC 61.432 66.667 8.83 0.00 0.00 3.13
704 713 2.746277 CGGGTTCCTTTCCGCCAG 60.746 66.667 0.00 0.00 39.78 4.85
705 714 2.754375 GGGTTCCTTTCCGCCAGA 59.246 61.111 0.00 0.00 0.00 3.86
706 715 1.074248 GGGTTCCTTTCCGCCAGAA 59.926 57.895 0.00 0.00 0.00 3.02
707 716 0.538746 GGGTTCCTTTCCGCCAGAAA 60.539 55.000 0.00 0.00 42.28 2.52
708 717 1.324383 GGTTCCTTTCCGCCAGAAAA 58.676 50.000 0.00 0.00 43.84 2.29
709 718 1.684450 GGTTCCTTTCCGCCAGAAAAA 59.316 47.619 0.00 0.00 43.84 1.94
710 719 2.299013 GGTTCCTTTCCGCCAGAAAAAT 59.701 45.455 0.00 0.00 43.84 1.82
711 720 3.508402 GGTTCCTTTCCGCCAGAAAAATA 59.492 43.478 0.00 0.00 43.84 1.40
712 721 4.159693 GGTTCCTTTCCGCCAGAAAAATAT 59.840 41.667 0.00 0.00 43.84 1.28
713 722 4.981806 TCCTTTCCGCCAGAAAAATATG 57.018 40.909 0.00 0.00 43.84 1.78
714 723 4.340617 TCCTTTCCGCCAGAAAAATATGT 58.659 39.130 0.00 0.00 43.84 2.29
715 724 4.157656 TCCTTTCCGCCAGAAAAATATGTG 59.842 41.667 0.00 0.00 43.84 3.21
716 725 4.082245 CCTTTCCGCCAGAAAAATATGTGT 60.082 41.667 0.00 0.00 43.84 3.72
717 726 4.695217 TTCCGCCAGAAAAATATGTGTC 57.305 40.909 0.00 0.00 0.00 3.67
718 727 3.950397 TCCGCCAGAAAAATATGTGTCT 58.050 40.909 0.00 0.00 0.00 3.41
719 728 3.689161 TCCGCCAGAAAAATATGTGTCTG 59.311 43.478 6.13 6.13 37.77 3.51
720 729 3.689161 CCGCCAGAAAAATATGTGTCTGA 59.311 43.478 13.99 0.00 39.94 3.27
721 730 4.201851 CCGCCAGAAAAATATGTGTCTGAG 60.202 45.833 13.99 7.80 39.94 3.35
722 731 4.201851 CGCCAGAAAAATATGTGTCTGAGG 60.202 45.833 13.99 0.36 39.94 3.86
723 732 4.943705 GCCAGAAAAATATGTGTCTGAGGA 59.056 41.667 13.99 0.00 39.94 3.71
724 733 5.415701 GCCAGAAAAATATGTGTCTGAGGAA 59.584 40.000 13.99 0.00 39.94 3.36
725 734 6.071952 GCCAGAAAAATATGTGTCTGAGGAAA 60.072 38.462 13.99 0.00 39.94 3.13
726 735 7.523709 GCCAGAAAAATATGTGTCTGAGGAAAA 60.524 37.037 13.99 0.00 39.94 2.29
727 736 8.359642 CCAGAAAAATATGTGTCTGAGGAAAAA 58.640 33.333 13.99 0.00 39.94 1.94
728 737 9.403110 CAGAAAAATATGTGTCTGAGGAAAAAG 57.597 33.333 7.25 0.00 39.94 2.27
729 738 9.354673 AGAAAAATATGTGTCTGAGGAAAAAGA 57.645 29.630 0.00 0.00 0.00 2.52
731 740 9.918630 AAAAATATGTGTCTGAGGAAAAAGATG 57.081 29.630 0.00 0.00 0.00 2.90
732 741 8.641498 AAATATGTGTCTGAGGAAAAAGATGT 57.359 30.769 0.00 0.00 0.00 3.06
733 742 9.739276 AAATATGTGTCTGAGGAAAAAGATGTA 57.261 29.630 0.00 0.00 0.00 2.29
734 743 8.723942 ATATGTGTCTGAGGAAAAAGATGTAC 57.276 34.615 0.00 0.00 0.00 2.90
735 744 5.924356 TGTGTCTGAGGAAAAAGATGTACA 58.076 37.500 0.00 0.00 0.00 2.90
736 745 5.758296 TGTGTCTGAGGAAAAAGATGTACAC 59.242 40.000 0.00 0.00 0.00 2.90
737 746 5.179555 GTGTCTGAGGAAAAAGATGTACACC 59.820 44.000 0.00 0.00 0.00 4.16
738 747 4.389077 GTCTGAGGAAAAAGATGTACACCG 59.611 45.833 0.00 0.00 0.00 4.94
739 748 4.039973 TCTGAGGAAAAAGATGTACACCGT 59.960 41.667 0.00 0.00 0.00 4.83
740 749 4.710324 TGAGGAAAAAGATGTACACCGTT 58.290 39.130 0.00 0.00 0.00 4.44
741 750 4.513692 TGAGGAAAAAGATGTACACCGTTG 59.486 41.667 0.00 0.00 0.00 4.10
742 751 3.818773 AGGAAAAAGATGTACACCGTTGG 59.181 43.478 0.00 0.00 0.00 3.77
743 752 3.816523 GGAAAAAGATGTACACCGTTGGA 59.183 43.478 0.00 0.00 0.00 3.53
744 753 4.457949 GGAAAAAGATGTACACCGTTGGAT 59.542 41.667 0.00 0.00 0.00 3.41
745 754 5.371115 AAAAAGATGTACACCGTTGGATG 57.629 39.130 0.00 0.00 0.00 3.51
746 755 2.691409 AGATGTACACCGTTGGATGG 57.309 50.000 0.00 0.00 0.00 3.51
747 756 1.014352 GATGTACACCGTTGGATGGC 58.986 55.000 0.00 0.00 0.00 4.40
748 757 0.393808 ATGTACACCGTTGGATGGCC 60.394 55.000 0.00 0.00 0.00 5.36
749 758 2.104253 GTACACCGTTGGATGGCCG 61.104 63.158 0.00 0.00 36.79 6.13
750 759 3.318006 TACACCGTTGGATGGCCGG 62.318 63.158 0.00 0.00 46.93 6.13
753 762 4.418328 CCGTTGGATGGCCGGGAA 62.418 66.667 2.18 0.00 38.09 3.97
754 763 2.824041 CGTTGGATGGCCGGGAAG 60.824 66.667 2.18 0.00 36.79 3.46
755 764 3.140814 GTTGGATGGCCGGGAAGC 61.141 66.667 2.18 0.00 36.79 3.86
756 765 3.656280 TTGGATGGCCGGGAAGCA 61.656 61.111 2.18 0.00 36.79 3.91
757 766 3.936772 TTGGATGGCCGGGAAGCAC 62.937 63.158 2.18 0.00 36.79 4.40
765 774 3.781307 CGGGAAGCACGGATGGGA 61.781 66.667 0.00 0.00 0.00 4.37
766 775 2.190578 GGGAAGCACGGATGGGAG 59.809 66.667 0.00 0.00 0.00 4.30
767 776 2.514824 GGAAGCACGGATGGGAGC 60.515 66.667 0.00 0.00 0.00 4.70
768 777 2.268920 GAAGCACGGATGGGAGCA 59.731 61.111 0.00 0.00 0.00 4.26
769 778 2.045926 AAGCACGGATGGGAGCAC 60.046 61.111 0.00 0.00 0.00 4.40
770 779 2.527951 GAAGCACGGATGGGAGCACT 62.528 60.000 0.00 0.00 0.00 4.40
771 780 2.809861 AAGCACGGATGGGAGCACTG 62.810 60.000 0.00 0.00 0.00 3.66
772 781 2.981302 CACGGATGGGAGCACTGA 59.019 61.111 0.00 0.00 0.00 3.41
773 782 1.153489 CACGGATGGGAGCACTGAG 60.153 63.158 0.00 0.00 0.00 3.35
774 783 1.305297 ACGGATGGGAGCACTGAGA 60.305 57.895 0.00 0.00 0.00 3.27
775 784 1.326213 ACGGATGGGAGCACTGAGAG 61.326 60.000 0.00 0.00 0.00 3.20
776 785 1.828768 GGATGGGAGCACTGAGAGG 59.171 63.158 0.00 0.00 0.00 3.69
777 786 1.694133 GGATGGGAGCACTGAGAGGG 61.694 65.000 0.00 0.00 0.00 4.30
778 787 0.689080 GATGGGAGCACTGAGAGGGA 60.689 60.000 0.00 0.00 0.00 4.20
779 788 0.690411 ATGGGAGCACTGAGAGGGAG 60.690 60.000 0.00 0.00 0.00 4.30
780 789 2.730524 GGGAGCACTGAGAGGGAGC 61.731 68.421 0.00 0.00 0.00 4.70
781 790 1.986757 GGAGCACTGAGAGGGAGCA 60.987 63.158 0.00 0.00 0.00 4.26
782 791 1.516892 GAGCACTGAGAGGGAGCAG 59.483 63.158 0.00 0.00 38.10 4.24
783 792 1.958902 GAGCACTGAGAGGGAGCAGG 61.959 65.000 0.00 0.00 36.47 4.85
784 793 2.583520 CACTGAGAGGGAGCAGGC 59.416 66.667 0.00 0.00 36.47 4.85
785 794 2.121385 ACTGAGAGGGAGCAGGCA 59.879 61.111 0.00 0.00 36.47 4.75
786 795 1.537397 ACTGAGAGGGAGCAGGCAA 60.537 57.895 0.00 0.00 36.47 4.52
787 796 1.221293 CTGAGAGGGAGCAGGCAAG 59.779 63.158 0.00 0.00 0.00 4.01
788 797 2.124778 GAGAGGGAGCAGGCAAGC 60.125 66.667 0.00 0.00 0.00 4.01
789 798 3.695747 GAGAGGGAGCAGGCAAGCC 62.696 68.421 2.02 2.02 34.23 4.35
790 799 4.811364 GAGGGAGCAGGCAAGCCC 62.811 72.222 7.62 8.32 41.00 5.19
793 802 4.453892 GGAGCAGGCAAGCCCCAT 62.454 66.667 7.62 0.00 36.58 4.00
794 803 2.832201 GAGCAGGCAAGCCCCATC 60.832 66.667 7.62 0.00 36.58 3.51
795 804 4.453892 AGCAGGCAAGCCCCATCC 62.454 66.667 7.62 0.00 36.58 3.51
814 823 4.181010 CCCCTGCGTCCCCATGAG 62.181 72.222 0.00 0.00 0.00 2.90
2355 2408 6.145338 TCAAATCGATGACCTAGAACTACC 57.855 41.667 0.00 0.00 0.00 3.18
2854 2907 6.265196 ACCAATACATATGCACCCATACAAAG 59.735 38.462 1.58 0.00 36.79 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.484417 CCAAGAATGGCGAGCTATGAGT 60.484 50.000 0.00 0.00 40.58 3.41
37 38 0.108804 CGTAGGCAAGTCACACCGAT 60.109 55.000 0.00 0.00 0.00 4.18
54 55 1.478510 CATGGACTTCTACCTCTGCGT 59.521 52.381 0.00 0.00 0.00 5.24
55 56 1.202463 CCATGGACTTCTACCTCTGCG 60.202 57.143 5.56 0.00 0.00 5.18
66 67 2.014010 ACAATGTTGCCCATGGACTT 57.986 45.000 15.22 0.00 32.82 3.01
83 84 4.142790 AGTTGTCGTCCTTCTTCTCTACA 58.857 43.478 0.00 0.00 0.00 2.74
89 90 2.210116 TGCAAGTTGTCGTCCTTCTTC 58.790 47.619 4.48 0.00 0.00 2.87
103 104 1.282157 CCTTAGTAAGGGGCTGCAAGT 59.718 52.381 19.81 0.00 45.27 3.16
117 118 5.916661 AGTATGTCGTGAATCACCTTAGT 57.083 39.130 7.91 0.00 0.00 2.24
119 120 5.221185 GCCTAGTATGTCGTGAATCACCTTA 60.221 44.000 7.91 0.00 0.00 2.69
131 132 1.982660 TCCTCCAGCCTAGTATGTCG 58.017 55.000 0.00 0.00 0.00 4.35
145 146 0.250338 ACAGCCACTCGTTTTCCTCC 60.250 55.000 0.00 0.00 0.00 4.30
155 156 0.539051 ATCACCTAGCACAGCCACTC 59.461 55.000 0.00 0.00 0.00 3.51
167 168 4.969359 CCCCTTCTTCTTCCTTATCACCTA 59.031 45.833 0.00 0.00 0.00 3.08
176 177 1.387119 ATTGCCCCCTTCTTCTTCCT 58.613 50.000 0.00 0.00 0.00 3.36
186 187 2.445155 GTCCACCAATTGCCCCCT 59.555 61.111 0.00 0.00 0.00 4.79
190 191 3.758931 GGCGGTCCACCAATTGCC 61.759 66.667 0.00 0.00 35.14 4.52
217 218 2.343758 GCTCCCTCTCGCACACAA 59.656 61.111 0.00 0.00 0.00 3.33
237 238 4.508124 AGACGTTCCATCAAGCGATATTTC 59.492 41.667 0.00 0.00 0.00 2.17
238 239 4.442706 AGACGTTCCATCAAGCGATATTT 58.557 39.130 0.00 0.00 0.00 1.40
239 240 4.051922 GAGACGTTCCATCAAGCGATATT 58.948 43.478 0.00 0.00 0.00 1.28
242 243 1.799181 CGAGACGTTCCATCAAGCGAT 60.799 52.381 0.00 0.00 0.00 4.58
247 248 2.092291 GCGCGAGACGTTCCATCAA 61.092 57.895 12.10 0.00 46.11 2.57
271 272 0.106569 ATCGGCCAAGAATCATGCCA 60.107 50.000 2.24 0.00 44.22 4.92
300 301 5.598417 ACCAATTGCTAAGGTAAATGATCCC 59.402 40.000 0.00 0.00 32.92 3.85
301 302 6.096846 ACACCAATTGCTAAGGTAAATGATCC 59.903 38.462 0.00 0.00 33.49 3.36
306 307 8.417273 ACTTTACACCAATTGCTAAGGTAAAT 57.583 30.769 0.00 0.00 33.49 1.40
397 406 1.626356 ATGACCACTACTGCCGCCAT 61.626 55.000 0.00 0.00 0.00 4.40
412 421 4.446371 AGATTCCAAGACCATCGAATGAC 58.554 43.478 0.00 0.00 0.00 3.06
413 422 4.760530 AGATTCCAAGACCATCGAATGA 57.239 40.909 0.00 0.00 0.00 2.57
414 423 4.877823 TCAAGATTCCAAGACCATCGAATG 59.122 41.667 0.00 0.00 0.00 2.67
415 424 5.102953 TCAAGATTCCAAGACCATCGAAT 57.897 39.130 0.00 0.00 0.00 3.34
416 425 4.551702 TCAAGATTCCAAGACCATCGAA 57.448 40.909 0.00 0.00 0.00 3.71
455 464 7.022055 TCTTCGAAAATACAAAGCAACTCAA 57.978 32.000 0.00 0.00 0.00 3.02
532 541 8.492673 AATCTTTTGGAGAGTTTTTGGTTTTC 57.507 30.769 0.00 0.00 37.93 2.29
543 552 4.254492 GTCGCCTTAATCTTTTGGAGAGT 58.746 43.478 0.00 0.00 37.93 3.24
544 553 3.307242 CGTCGCCTTAATCTTTTGGAGAG 59.693 47.826 0.00 0.00 37.93 3.20
545 554 3.259064 CGTCGCCTTAATCTTTTGGAGA 58.741 45.455 0.00 0.00 39.13 3.71
546 555 2.351726 CCGTCGCCTTAATCTTTTGGAG 59.648 50.000 0.00 0.00 0.00 3.86
547 556 2.027929 TCCGTCGCCTTAATCTTTTGGA 60.028 45.455 0.00 0.00 0.00 3.53
548 557 2.095372 GTCCGTCGCCTTAATCTTTTGG 59.905 50.000 0.00 0.00 0.00 3.28
549 558 2.222729 CGTCCGTCGCCTTAATCTTTTG 60.223 50.000 0.00 0.00 0.00 2.44
550 559 1.997606 CGTCCGTCGCCTTAATCTTTT 59.002 47.619 0.00 0.00 0.00 2.27
551 560 1.636988 CGTCCGTCGCCTTAATCTTT 58.363 50.000 0.00 0.00 0.00 2.52
552 561 0.179119 CCGTCCGTCGCCTTAATCTT 60.179 55.000 0.00 0.00 38.35 2.40
553 562 1.318158 ACCGTCCGTCGCCTTAATCT 61.318 55.000 0.00 0.00 38.35 2.40
554 563 0.381801 TACCGTCCGTCGCCTTAATC 59.618 55.000 0.00 0.00 38.35 1.75
555 564 0.383231 CTACCGTCCGTCGCCTTAAT 59.617 55.000 0.00 0.00 38.35 1.40
556 565 1.802636 CTACCGTCCGTCGCCTTAA 59.197 57.895 0.00 0.00 38.35 1.85
557 566 2.764314 GCTACCGTCCGTCGCCTTA 61.764 63.158 0.00 0.00 38.35 2.69
558 567 4.125695 GCTACCGTCCGTCGCCTT 62.126 66.667 0.00 0.00 38.35 4.35
561 570 4.849329 CTGGCTACCGTCCGTCGC 62.849 72.222 0.00 0.00 38.35 5.19
562 571 2.862347 GAACTGGCTACCGTCCGTCG 62.862 65.000 0.00 0.00 39.52 5.12
563 572 1.153881 GAACTGGCTACCGTCCGTC 60.154 63.158 0.00 0.00 0.00 4.79
564 573 1.255667 ATGAACTGGCTACCGTCCGT 61.256 55.000 0.00 0.00 0.00 4.69
565 574 0.742505 TATGAACTGGCTACCGTCCG 59.257 55.000 0.00 0.00 0.00 4.79
566 575 1.068741 CCTATGAACTGGCTACCGTCC 59.931 57.143 0.00 0.00 0.00 4.79
567 576 1.538419 GCCTATGAACTGGCTACCGTC 60.538 57.143 0.00 0.00 45.26 4.79
568 577 0.464452 GCCTATGAACTGGCTACCGT 59.536 55.000 0.00 0.00 45.26 4.83
569 578 3.290776 GCCTATGAACTGGCTACCG 57.709 57.895 0.00 0.00 45.26 4.02
575 584 3.513515 GGGAGAGATAGCCTATGAACTGG 59.486 52.174 0.00 0.00 0.00 4.00
576 585 3.192422 CGGGAGAGATAGCCTATGAACTG 59.808 52.174 0.00 0.00 0.00 3.16
577 586 3.074687 TCGGGAGAGATAGCCTATGAACT 59.925 47.826 0.00 0.00 0.00 3.01
578 587 3.422796 TCGGGAGAGATAGCCTATGAAC 58.577 50.000 0.00 0.00 0.00 3.18
579 588 3.808834 TCGGGAGAGATAGCCTATGAA 57.191 47.619 0.00 0.00 0.00 2.57
592 601 3.013327 TCCCTCGACCTCGGGAGA 61.013 66.667 6.07 0.00 44.42 3.71
595 604 4.790962 TCGTCCCTCGACCTCGGG 62.791 72.222 0.93 0.93 44.01 5.14
603 612 2.024871 GCAGTCGATCGTCCCTCG 59.975 66.667 15.94 6.25 41.41 4.63
604 613 1.064946 CTGCAGTCGATCGTCCCTC 59.935 63.158 15.94 2.40 0.00 4.30
605 614 0.965866 TTCTGCAGTCGATCGTCCCT 60.966 55.000 15.94 6.93 0.00 4.20
606 615 0.108804 TTTCTGCAGTCGATCGTCCC 60.109 55.000 15.94 4.59 0.00 4.46
607 616 1.135373 TCTTTCTGCAGTCGATCGTCC 60.135 52.381 15.94 7.21 0.00 4.79
608 617 2.159503 TCTCTTTCTGCAGTCGATCGTC 60.160 50.000 15.94 9.91 0.00 4.20
609 618 1.813178 TCTCTTTCTGCAGTCGATCGT 59.187 47.619 15.94 0.00 0.00 3.73
610 619 2.551355 TCTCTTTCTGCAGTCGATCG 57.449 50.000 14.67 9.36 0.00 3.69
611 620 4.269844 GGATTTCTCTTTCTGCAGTCGATC 59.730 45.833 14.67 7.18 0.00 3.69
612 621 4.187694 GGATTTCTCTTTCTGCAGTCGAT 58.812 43.478 14.67 0.00 0.00 3.59
613 622 3.006859 TGGATTTCTCTTTCTGCAGTCGA 59.993 43.478 14.67 7.79 0.00 4.20
614 623 3.329386 TGGATTTCTCTTTCTGCAGTCG 58.671 45.455 14.67 3.49 0.00 4.18
615 624 5.335504 CCTTTGGATTTCTCTTTCTGCAGTC 60.336 44.000 14.67 0.00 0.00 3.51
616 625 4.522022 CCTTTGGATTTCTCTTTCTGCAGT 59.478 41.667 14.67 0.00 0.00 4.40
617 626 4.082354 CCCTTTGGATTTCTCTTTCTGCAG 60.082 45.833 7.63 7.63 0.00 4.41
618 627 3.828451 CCCTTTGGATTTCTCTTTCTGCA 59.172 43.478 0.00 0.00 0.00 4.41
619 628 3.194329 CCCCTTTGGATTTCTCTTTCTGC 59.806 47.826 0.00 0.00 35.39 4.26
620 629 4.666512 TCCCCTTTGGATTTCTCTTTCTG 58.333 43.478 0.00 0.00 38.61 3.02
621 630 5.328565 CTTCCCCTTTGGATTTCTCTTTCT 58.671 41.667 0.00 0.00 44.66 2.52
622 631 4.464244 CCTTCCCCTTTGGATTTCTCTTTC 59.536 45.833 0.00 0.00 44.66 2.62
623 632 4.107961 TCCTTCCCCTTTGGATTTCTCTTT 59.892 41.667 0.00 0.00 44.66 2.52
624 633 3.662642 TCCTTCCCCTTTGGATTTCTCTT 59.337 43.478 0.00 0.00 44.66 2.85
625 634 3.269034 TCCTTCCCCTTTGGATTTCTCT 58.731 45.455 0.00 0.00 44.66 3.10
626 635 3.739401 TCCTTCCCCTTTGGATTTCTC 57.261 47.619 0.00 0.00 44.66 2.87
627 636 3.310141 CCATCCTTCCCCTTTGGATTTCT 60.310 47.826 0.00 0.00 44.66 2.52
628 637 3.033909 CCATCCTTCCCCTTTGGATTTC 58.966 50.000 0.00 0.00 44.66 2.17
629 638 2.293118 CCCATCCTTCCCCTTTGGATTT 60.293 50.000 0.00 0.00 44.66 2.17
630 639 1.291939 CCCATCCTTCCCCTTTGGATT 59.708 52.381 0.00 0.00 44.66 3.01
631 640 0.936691 CCCATCCTTCCCCTTTGGAT 59.063 55.000 0.00 0.00 44.66 3.41
632 641 1.874299 GCCCATCCTTCCCCTTTGGA 61.874 60.000 0.00 0.00 43.18 3.53
633 642 1.381735 GCCCATCCTTCCCCTTTGG 60.382 63.158 0.00 0.00 0.00 3.28
634 643 0.031817 ATGCCCATCCTTCCCCTTTG 60.032 55.000 0.00 0.00 0.00 2.77
635 644 1.217942 GTATGCCCATCCTTCCCCTTT 59.782 52.381 0.00 0.00 0.00 3.11
636 645 0.853530 GTATGCCCATCCTTCCCCTT 59.146 55.000 0.00 0.00 0.00 3.95
637 646 1.418908 CGTATGCCCATCCTTCCCCT 61.419 60.000 0.00 0.00 0.00 4.79
638 647 1.073199 CGTATGCCCATCCTTCCCC 59.927 63.158 0.00 0.00 0.00 4.81
639 648 1.053424 TACGTATGCCCATCCTTCCC 58.947 55.000 0.00 0.00 0.00 3.97
640 649 2.615493 CCATACGTATGCCCATCCTTCC 60.615 54.545 26.79 0.00 32.40 3.46
641 650 2.615493 CCCATACGTATGCCCATCCTTC 60.615 54.545 26.79 0.00 32.40 3.46
642 651 1.351017 CCCATACGTATGCCCATCCTT 59.649 52.381 26.79 0.00 32.40 3.36
643 652 0.984230 CCCATACGTATGCCCATCCT 59.016 55.000 26.79 0.00 32.40 3.24
644 653 0.981183 TCCCATACGTATGCCCATCC 59.019 55.000 26.79 0.00 32.40 3.51
645 654 2.301870 TCTTCCCATACGTATGCCCATC 59.698 50.000 26.79 0.00 32.40 3.51
646 655 2.334977 TCTTCCCATACGTATGCCCAT 58.665 47.619 26.79 0.00 32.40 4.00
647 656 1.796017 TCTTCCCATACGTATGCCCA 58.204 50.000 26.79 11.67 32.40 5.36
648 657 2.876550 GTTTCTTCCCATACGTATGCCC 59.123 50.000 26.79 6.64 32.40 5.36
649 658 2.542595 CGTTTCTTCCCATACGTATGCC 59.457 50.000 26.79 7.91 32.40 4.40
650 659 2.542595 CCGTTTCTTCCCATACGTATGC 59.457 50.000 26.79 11.68 32.40 3.14
651 660 3.128349 CCCGTTTCTTCCCATACGTATG 58.872 50.000 25.55 25.55 32.45 2.39
652 661 3.033184 TCCCGTTTCTTCCCATACGTAT 58.967 45.455 1.14 1.14 32.45 3.06
653 662 2.455557 TCCCGTTTCTTCCCATACGTA 58.544 47.619 0.00 0.00 32.45 3.57
654 663 1.269012 TCCCGTTTCTTCCCATACGT 58.731 50.000 0.00 0.00 32.45 3.57
655 664 2.389962 TTCCCGTTTCTTCCCATACG 57.610 50.000 0.00 0.00 0.00 3.06
656 665 3.805971 CGTATTCCCGTTTCTTCCCATAC 59.194 47.826 0.00 0.00 0.00 2.39
657 666 3.181463 CCGTATTCCCGTTTCTTCCCATA 60.181 47.826 0.00 0.00 0.00 2.74
658 667 2.420967 CCGTATTCCCGTTTCTTCCCAT 60.421 50.000 0.00 0.00 0.00 4.00
659 668 1.065998 CCGTATTCCCGTTTCTTCCCA 60.066 52.381 0.00 0.00 0.00 4.37
660 669 1.207811 TCCGTATTCCCGTTTCTTCCC 59.792 52.381 0.00 0.00 0.00 3.97
661 670 2.547826 CTCCGTATTCCCGTTTCTTCC 58.452 52.381 0.00 0.00 0.00 3.46
662 671 1.931841 GCTCCGTATTCCCGTTTCTTC 59.068 52.381 0.00 0.00 0.00 2.87
663 672 1.553704 AGCTCCGTATTCCCGTTTCTT 59.446 47.619 0.00 0.00 0.00 2.52
664 673 1.134788 CAGCTCCGTATTCCCGTTTCT 60.135 52.381 0.00 0.00 0.00 2.52
665 674 1.287425 CAGCTCCGTATTCCCGTTTC 58.713 55.000 0.00 0.00 0.00 2.78
666 675 0.743345 GCAGCTCCGTATTCCCGTTT 60.743 55.000 0.00 0.00 0.00 3.60
667 676 1.153429 GCAGCTCCGTATTCCCGTT 60.153 57.895 0.00 0.00 0.00 4.44
668 677 2.499685 GCAGCTCCGTATTCCCGT 59.500 61.111 0.00 0.00 0.00 5.28
669 678 2.658593 CGCAGCTCCGTATTCCCG 60.659 66.667 0.00 0.00 0.00 5.14
682 691 3.431725 GGAAAGGAACCCGCGCAG 61.432 66.667 8.75 0.00 0.00 5.18
688 697 0.538746 TTTCTGGCGGAAAGGAACCC 60.539 55.000 17.30 0.00 38.81 4.11
689 698 1.324383 TTTTCTGGCGGAAAGGAACC 58.676 50.000 19.93 0.00 43.68 3.62
690 699 3.660501 ATTTTTCTGGCGGAAAGGAAC 57.339 42.857 19.93 0.00 43.68 3.62
691 700 4.770010 ACATATTTTTCTGGCGGAAAGGAA 59.230 37.500 19.93 13.71 43.68 3.36
692 701 4.157656 CACATATTTTTCTGGCGGAAAGGA 59.842 41.667 19.93 13.85 43.68 3.36
693 702 4.082245 ACACATATTTTTCTGGCGGAAAGG 60.082 41.667 19.93 11.63 43.68 3.11
694 703 5.059404 ACACATATTTTTCTGGCGGAAAG 57.941 39.130 19.93 11.59 43.68 2.62
695 704 4.764823 AGACACATATTTTTCTGGCGGAAA 59.235 37.500 17.30 17.30 41.58 3.13
696 705 4.155826 CAGACACATATTTTTCTGGCGGAA 59.844 41.667 4.22 4.22 33.25 4.30
697 706 3.689161 CAGACACATATTTTTCTGGCGGA 59.311 43.478 0.00 0.00 33.25 5.54
698 707 3.689161 TCAGACACATATTTTTCTGGCGG 59.311 43.478 5.43 0.00 36.84 6.13
699 708 4.201851 CCTCAGACACATATTTTTCTGGCG 60.202 45.833 5.43 0.00 36.84 5.69
700 709 4.943705 TCCTCAGACACATATTTTTCTGGC 59.056 41.667 5.43 0.00 36.84 4.85
701 710 7.452880 TTTCCTCAGACACATATTTTTCTGG 57.547 36.000 5.43 0.00 36.84 3.86
702 711 9.403110 CTTTTTCCTCAGACACATATTTTTCTG 57.597 33.333 0.00 0.00 37.43 3.02
703 712 9.354673 TCTTTTTCCTCAGACACATATTTTTCT 57.645 29.630 0.00 0.00 0.00 2.52
705 714 9.918630 CATCTTTTTCCTCAGACACATATTTTT 57.081 29.630 0.00 0.00 0.00 1.94
706 715 9.082313 ACATCTTTTTCCTCAGACACATATTTT 57.918 29.630 0.00 0.00 0.00 1.82
707 716 8.641498 ACATCTTTTTCCTCAGACACATATTT 57.359 30.769 0.00 0.00 0.00 1.40
708 717 9.167311 GTACATCTTTTTCCTCAGACACATATT 57.833 33.333 0.00 0.00 0.00 1.28
709 718 8.321353 TGTACATCTTTTTCCTCAGACACATAT 58.679 33.333 0.00 0.00 0.00 1.78
710 719 7.602644 GTGTACATCTTTTTCCTCAGACACATA 59.397 37.037 0.00 0.00 34.89 2.29
711 720 6.428159 GTGTACATCTTTTTCCTCAGACACAT 59.572 38.462 0.00 0.00 34.89 3.21
712 721 5.758296 GTGTACATCTTTTTCCTCAGACACA 59.242 40.000 0.00 0.00 34.89 3.72
713 722 5.179555 GGTGTACATCTTTTTCCTCAGACAC 59.820 44.000 0.00 0.00 34.20 3.67
714 723 5.305585 GGTGTACATCTTTTTCCTCAGACA 58.694 41.667 0.00 0.00 0.00 3.41
715 724 4.389077 CGGTGTACATCTTTTTCCTCAGAC 59.611 45.833 4.28 0.00 0.00 3.51
716 725 4.039973 ACGGTGTACATCTTTTTCCTCAGA 59.960 41.667 4.28 0.00 0.00 3.27
717 726 4.315803 ACGGTGTACATCTTTTTCCTCAG 58.684 43.478 4.28 0.00 0.00 3.35
718 727 4.345859 ACGGTGTACATCTTTTTCCTCA 57.654 40.909 4.28 0.00 0.00 3.86
719 728 4.083484 CCAACGGTGTACATCTTTTTCCTC 60.083 45.833 4.28 0.00 0.00 3.71
720 729 3.818773 CCAACGGTGTACATCTTTTTCCT 59.181 43.478 4.28 0.00 0.00 3.36
721 730 3.816523 TCCAACGGTGTACATCTTTTTCC 59.183 43.478 4.28 0.00 0.00 3.13
722 731 5.390613 CATCCAACGGTGTACATCTTTTTC 58.609 41.667 4.28 0.00 0.00 2.29
723 732 4.217550 CCATCCAACGGTGTACATCTTTTT 59.782 41.667 4.28 0.00 0.00 1.94
724 733 3.756434 CCATCCAACGGTGTACATCTTTT 59.244 43.478 4.28 0.00 0.00 2.27
725 734 3.343617 CCATCCAACGGTGTACATCTTT 58.656 45.455 4.28 0.00 0.00 2.52
726 735 2.939640 GCCATCCAACGGTGTACATCTT 60.940 50.000 4.28 0.00 0.00 2.40
727 736 1.406887 GCCATCCAACGGTGTACATCT 60.407 52.381 4.28 0.00 0.00 2.90
728 737 1.014352 GCCATCCAACGGTGTACATC 58.986 55.000 0.00 0.00 0.00 3.06
729 738 0.393808 GGCCATCCAACGGTGTACAT 60.394 55.000 0.00 0.00 0.00 2.29
730 739 1.003112 GGCCATCCAACGGTGTACA 60.003 57.895 0.00 0.00 0.00 2.90
731 740 2.104253 CGGCCATCCAACGGTGTAC 61.104 63.158 2.24 0.00 0.00 2.90
732 741 2.266372 CGGCCATCCAACGGTGTA 59.734 61.111 2.24 0.00 0.00 2.90
733 742 4.715523 CCGGCCATCCAACGGTGT 62.716 66.667 2.24 0.00 42.53 4.16
736 745 4.418328 TTCCCGGCCATCCAACGG 62.418 66.667 2.24 0.00 46.79 4.44
737 746 2.824041 CTTCCCGGCCATCCAACG 60.824 66.667 2.24 0.00 0.00 4.10
738 747 3.140814 GCTTCCCGGCCATCCAAC 61.141 66.667 2.24 0.00 0.00 3.77
739 748 3.656280 TGCTTCCCGGCCATCCAA 61.656 61.111 2.24 0.00 0.00 3.53
740 749 4.424711 GTGCTTCCCGGCCATCCA 62.425 66.667 2.24 0.00 0.00 3.41
747 756 4.856801 CCCATCCGTGCTTCCCGG 62.857 72.222 0.00 0.00 46.83 5.73
748 757 3.740128 CTCCCATCCGTGCTTCCCG 62.740 68.421 0.00 0.00 0.00 5.14
749 758 2.190578 CTCCCATCCGTGCTTCCC 59.809 66.667 0.00 0.00 0.00 3.97
750 759 2.514824 GCTCCCATCCGTGCTTCC 60.515 66.667 0.00 0.00 0.00 3.46
751 760 2.109126 GTGCTCCCATCCGTGCTTC 61.109 63.158 0.00 0.00 0.00 3.86
752 761 2.045926 GTGCTCCCATCCGTGCTT 60.046 61.111 0.00 0.00 0.00 3.91
753 762 3.005539 AGTGCTCCCATCCGTGCT 61.006 61.111 0.00 0.00 0.00 4.40
754 763 2.821366 CAGTGCTCCCATCCGTGC 60.821 66.667 0.00 0.00 0.00 5.34
755 764 1.153489 CTCAGTGCTCCCATCCGTG 60.153 63.158 0.00 0.00 0.00 4.94
756 765 1.305297 TCTCAGTGCTCCCATCCGT 60.305 57.895 0.00 0.00 0.00 4.69
757 766 1.440893 CTCTCAGTGCTCCCATCCG 59.559 63.158 0.00 0.00 0.00 4.18
758 767 1.694133 CCCTCTCAGTGCTCCCATCC 61.694 65.000 0.00 0.00 0.00 3.51
759 768 0.689080 TCCCTCTCAGTGCTCCCATC 60.689 60.000 0.00 0.00 0.00 3.51
760 769 0.690411 CTCCCTCTCAGTGCTCCCAT 60.690 60.000 0.00 0.00 0.00 4.00
761 770 1.305633 CTCCCTCTCAGTGCTCCCA 60.306 63.158 0.00 0.00 0.00 4.37
762 771 2.730524 GCTCCCTCTCAGTGCTCCC 61.731 68.421 0.00 0.00 0.00 4.30
763 772 1.958902 CTGCTCCCTCTCAGTGCTCC 61.959 65.000 0.00 0.00 0.00 4.70
764 773 1.516892 CTGCTCCCTCTCAGTGCTC 59.483 63.158 0.00 0.00 0.00 4.26
765 774 1.988956 CCTGCTCCCTCTCAGTGCT 60.989 63.158 0.00 0.00 0.00 4.40
766 775 2.583520 CCTGCTCCCTCTCAGTGC 59.416 66.667 0.00 0.00 0.00 4.40
767 776 1.834856 TTGCCTGCTCCCTCTCAGTG 61.835 60.000 0.00 0.00 0.00 3.66
768 777 1.537397 TTGCCTGCTCCCTCTCAGT 60.537 57.895 0.00 0.00 0.00 3.41
769 778 1.221293 CTTGCCTGCTCCCTCTCAG 59.779 63.158 0.00 0.00 0.00 3.35
770 779 2.964310 GCTTGCCTGCTCCCTCTCA 61.964 63.158 0.00 0.00 0.00 3.27
771 780 2.124778 GCTTGCCTGCTCCCTCTC 60.125 66.667 0.00 0.00 0.00 3.20
772 781 3.726144 GGCTTGCCTGCTCCCTCT 61.726 66.667 4.11 0.00 0.00 3.69
773 782 4.811364 GGGCTTGCCTGCTCCCTC 62.811 72.222 11.71 0.00 35.87 4.30
777 786 2.832201 GATGGGGCTTGCCTGCTC 60.832 66.667 11.71 2.43 0.00 4.26
778 787 4.453892 GGATGGGGCTTGCCTGCT 62.454 66.667 11.71 0.00 0.00 4.24
797 806 4.181010 CTCATGGGGACGCAGGGG 62.181 72.222 1.32 0.00 0.00 4.79
2355 2408 4.976731 CGTCTAGGTGAATAAGTCATTCGG 59.023 45.833 0.00 0.00 45.25 4.30
2854 2907 1.139095 CAAGACGCCCGAGGAGTAC 59.861 63.158 0.00 0.00 35.49 2.73
3213 3307 1.153549 CCTGAGCCGCCAGTAGTTC 60.154 63.158 7.73 0.00 32.43 3.01


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

AutoCloner maintained by Alex Coulton.