Multiple sequence alignment - TraesCS1A01G360300

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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 TraesCS1A01G360300 chr1A 100.000 6966 0 0 1 6966 541474354 541467389 0.000000e+00 12864.0
1 TraesCS1A01G360300 chr1A 93.537 5029 283 21 1588 6588 265021402 265026416 0.000000e+00 7448.0
2 TraesCS1A01G360300 chr1A 100.000 2156 0 0 7278 9433 541467077 541464922 0.000000e+00 3982.0
3 TraesCS1A01G360300 chr1A 89.846 975 98 1 8460 9433 61255471 61254497 0.000000e+00 1251.0
4 TraesCS1A01G360300 chr1A 94.099 322 15 4 7278 7599 541834370 541834687 3.960000e-133 486.0
5 TraesCS1A01G360300 chr1A 83.042 401 49 10 7855 8245 265028763 265029154 7.010000e-91 346.0
6 TraesCS1A01G360300 chr1A 84.800 125 16 3 1415 1538 342435650 342435528 1.290000e-23 122.0
7 TraesCS1A01G360300 chr1B 96.358 5766 157 25 850 6588 608471812 608466073 0.000000e+00 9435.0
8 TraesCS1A01G360300 chr1B 93.810 5024 275 17 1588 6588 302205849 302210859 0.000000e+00 7522.0
9 TraesCS1A01G360300 chr1B 89.641 975 100 1 8460 9433 286317227 286318201 0.000000e+00 1240.0
10 TraesCS1A01G360300 chr1B 93.673 648 30 5 7593 8230 608466085 608465439 0.000000e+00 959.0
11 TraesCS1A01G360300 chr1B 82.883 222 21 7 8037 8245 302211515 302211732 5.820000e-42 183.0
12 TraesCS1A01G360300 chr1B 81.657 169 19 6 1418 1575 640059496 640059663 7.690000e-26 130.0
13 TraesCS1A01G360300 chr1B 90.526 95 8 1 7855 7948 302211349 302211443 3.580000e-24 124.0
14 TraesCS1A01G360300 chr1B 80.571 175 10 7 8289 8460 608465439 608465286 7.740000e-21 113.0
15 TraesCS1A01G360300 chr1D 96.380 5552 163 16 1057 6588 445395816 445390283 0.000000e+00 9105.0
16 TraesCS1A01G360300 chr1D 93.895 5012 268 18 1588 6588 206494738 206499722 0.000000e+00 7526.0
17 TraesCS1A01G360300 chr1D 89.314 889 48 14 7593 8456 445390295 445389429 0.000000e+00 1072.0
18 TraesCS1A01G360300 chr1D 85.287 401 39 12 7855 8245 206500183 206500573 6.860000e-106 396.0
19 TraesCS1A01G360300 chr1D 90.800 250 9 5 850 1096 445396043 445395805 1.180000e-83 322.0
20 TraesCS1A01G360300 chr1D 85.926 135 15 4 7593 7726 206499710 206499841 3.550000e-29 141.0
21 TraesCS1A01G360300 chr2A 87.219 4311 530 19 2174 6475 486212171 486207873 0.000000e+00 4889.0
22 TraesCS1A01G360300 chr2D 87.330 4262 526 13 2227 6481 361258880 361254626 0.000000e+00 4867.0
23 TraesCS1A01G360300 chr2D 85.662 823 84 20 2 805 608381551 608382358 0.000000e+00 835.0
24 TraesCS1A01G360300 chr2D 85.337 832 78 25 2 805 489573896 489573081 0.000000e+00 821.0
25 TraesCS1A01G360300 chr2D 84.672 822 91 20 2 804 576459371 576460176 0.000000e+00 787.0
26 TraesCS1A01G360300 chr2D 84.531 821 89 27 6 805 35977589 35978392 0.000000e+00 778.0
27 TraesCS1A01G360300 chr2D 82.249 169 24 3 1359 1525 212933417 212933581 3.550000e-29 141.0
28 TraesCS1A01G360300 chr2B 86.940 4265 540 15 2227 6481 429490127 429485870 0.000000e+00 4774.0
29 TraesCS1A01G360300 chr2B 96.970 990 26 3 5599 6588 161023907 161024892 0.000000e+00 1659.0
30 TraesCS1A01G360300 chr2B 89.298 598 34 15 7593 8168 161024880 161025469 0.000000e+00 723.0
31 TraesCS1A01G360300 chr6D 93.756 977 59 2 8458 9433 414119336 414118361 0.000000e+00 1465.0
32 TraesCS1A01G360300 chr6D 89.746 985 99 2 8450 9433 471321956 471320973 0.000000e+00 1258.0
33 TraesCS1A01G360300 chr6D 84.672 822 90 19 2 805 457327192 457326389 0.000000e+00 787.0
34 TraesCS1A01G360300 chr7A 92.331 978 72 3 8458 9433 251597736 251596760 0.000000e+00 1387.0
35 TraesCS1A01G360300 chr7A 89.641 975 99 2 8460 9433 666428589 666429562 0.000000e+00 1240.0
36 TraesCS1A01G360300 chr7A 96.960 329 7 3 6586 6912 620291989 620291662 4.980000e-152 549.0
37 TraesCS1A01G360300 chr5A 90.154 975 95 1 8460 9433 494400877 494399903 0.000000e+00 1267.0
38 TraesCS1A01G360300 chr5A 96.842 380 9 2 6588 6966 354537681 354538058 4.810000e-177 632.0
39 TraesCS1A01G360300 chr5A 98.754 321 1 3 7278 7596 354538133 354538452 1.370000e-157 568.0
40 TraesCS1A01G360300 chr5A 92.690 342 15 7 6620 6961 590383466 590383797 1.420000e-132 484.0
41 TraesCS1A01G360300 chr5B 89.846 975 98 1 8460 9433 493604391 493603417 0.000000e+00 1251.0
42 TraesCS1A01G360300 chr5B 89.538 975 101 1 8460 9433 531693242 531694216 0.000000e+00 1234.0
43 TraesCS1A01G360300 chr5D 86.425 744 74 18 79 809 454030236 454029507 0.000000e+00 789.0
44 TraesCS1A01G360300 chr5D 82.941 170 17 4 1418 1576 326123809 326123977 9.870000e-30 143.0
45 TraesCS1A01G360300 chr4A 84.364 825 96 21 1 805 109191216 109190405 0.000000e+00 778.0
46 TraesCS1A01G360300 chr4A 95.298 319 13 2 7279 7596 475420068 475419751 1.090000e-138 505.0
47 TraesCS1A01G360300 chr4A 89.351 385 27 10 6580 6961 683260364 683259991 1.110000e-128 472.0
48 TraesCS1A01G360300 chr4A 89.182 379 28 8 6586 6961 679188554 679188186 2.400000e-125 460.0
49 TraesCS1A01G360300 chr4A 81.373 102 19 0 1479 1580 311725333 311725434 6.070000e-12 84.2
50 TraesCS1A01G360300 chr3D 84.466 824 89 26 2 805 441369748 441370552 0.000000e+00 776.0
51 TraesCS1A01G360300 chr3D 83.575 828 106 21 2 810 111978303 111979119 0.000000e+00 749.0
52 TraesCS1A01G360300 chr6A 95.789 380 10 4 6589 6966 87056780 87056405 8.100000e-170 608.0
53 TraesCS1A01G360300 chr6A 98.125 320 5 1 7278 7597 87056332 87056014 2.980000e-154 556.0
54 TraesCS1A01G360300 chr6A 90.186 377 25 8 6587 6961 82102594 82102228 1.840000e-131 481.0
55 TraesCS1A01G360300 chr6A 93.691 317 17 3 7279 7595 171799193 171798880 1.110000e-128 472.0
56 TraesCS1A01G360300 chr6A 88.630 387 26 13 6579 6961 66644691 66644319 1.120000e-123 455.0
57 TraesCS1A01G360300 chr3A 98.428 318 4 1 7278 7595 482064708 482065024 8.270000e-155 558.0
58 TraesCS1A01G360300 chr3A 94.940 336 12 3 6633 6966 482064301 482064633 1.090000e-143 521.0
59 TraesCS1A01G360300 chr3A 94.512 328 12 6 7278 7604 391252750 391253072 1.410000e-137 501.0
60 TraesCS1A01G360300 chr3A 94.495 327 13 5 7278 7604 391275391 391275712 5.090000e-137 499.0
61 TraesCS1A01G360300 chr3A 94.207 328 15 4 7278 7604 391297422 391297746 1.830000e-136 497.0
62 TraesCS1A01G360300 chr3A 86.740 181 13 5 1 170 7121973 7122153 3.480000e-44 191.0
63 TraesCS1A01G360300 chr3A 78.319 226 31 9 1359 1576 142694436 142694221 7.690000e-26 130.0
64 TraesCS1A01G360300 chr3A 86.607 112 11 2 1418 1526 617256654 617256764 4.630000e-23 121.0
65 TraesCS1A01G360300 chr3B 81.176 170 20 7 1418 1576 508714401 508714233 9.940000e-25 126.0
66 TraesCS1A01G360300 chr7B 83.529 85 14 0 1492 1576 246959334 246959250 7.850000e-11 80.5


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 TraesCS1A01G360300 chr1A 541464922 541474354 9432 True 8423.000000 12864 100.000000 1 9433 2 chr1A.!!$R3 9432
1 TraesCS1A01G360300 chr1A 265021402 265029154 7752 False 3897.000000 7448 88.289500 1588 8245 2 chr1A.!!$F2 6657
2 TraesCS1A01G360300 chr1A 61254497 61255471 974 True 1251.000000 1251 89.846000 8460 9433 1 chr1A.!!$R1 973
3 TraesCS1A01G360300 chr1B 608465286 608471812 6526 True 3502.333333 9435 90.200667 850 8460 3 chr1B.!!$R1 7610
4 TraesCS1A01G360300 chr1B 302205849 302211732 5883 False 2609.666667 7522 89.073000 1588 8245 3 chr1B.!!$F3 6657
5 TraesCS1A01G360300 chr1B 286317227 286318201 974 False 1240.000000 1240 89.641000 8460 9433 1 chr1B.!!$F1 973
6 TraesCS1A01G360300 chr1D 445389429 445396043 6614 True 3499.666667 9105 92.164667 850 8456 3 chr1D.!!$R1 7606
7 TraesCS1A01G360300 chr1D 206494738 206500573 5835 False 2687.666667 7526 88.369333 1588 8245 3 chr1D.!!$F1 6657
8 TraesCS1A01G360300 chr2A 486207873 486212171 4298 True 4889.000000 4889 87.219000 2174 6475 1 chr2A.!!$R1 4301
9 TraesCS1A01G360300 chr2D 361254626 361258880 4254 True 4867.000000 4867 87.330000 2227 6481 1 chr2D.!!$R1 4254
10 TraesCS1A01G360300 chr2D 608381551 608382358 807 False 835.000000 835 85.662000 2 805 1 chr2D.!!$F4 803
11 TraesCS1A01G360300 chr2D 489573081 489573896 815 True 821.000000 821 85.337000 2 805 1 chr2D.!!$R2 803
12 TraesCS1A01G360300 chr2D 576459371 576460176 805 False 787.000000 787 84.672000 2 804 1 chr2D.!!$F3 802
13 TraesCS1A01G360300 chr2D 35977589 35978392 803 False 778.000000 778 84.531000 6 805 1 chr2D.!!$F1 799
14 TraesCS1A01G360300 chr2B 429485870 429490127 4257 True 4774.000000 4774 86.940000 2227 6481 1 chr2B.!!$R1 4254
15 TraesCS1A01G360300 chr2B 161023907 161025469 1562 False 1191.000000 1659 93.134000 5599 8168 2 chr2B.!!$F1 2569
16 TraesCS1A01G360300 chr6D 414118361 414119336 975 True 1465.000000 1465 93.756000 8458 9433 1 chr6D.!!$R1 975
17 TraesCS1A01G360300 chr6D 471320973 471321956 983 True 1258.000000 1258 89.746000 8450 9433 1 chr6D.!!$R3 983
18 TraesCS1A01G360300 chr6D 457326389 457327192 803 True 787.000000 787 84.672000 2 805 1 chr6D.!!$R2 803
19 TraesCS1A01G360300 chr7A 251596760 251597736 976 True 1387.000000 1387 92.331000 8458 9433 1 chr7A.!!$R1 975
20 TraesCS1A01G360300 chr7A 666428589 666429562 973 False 1240.000000 1240 89.641000 8460 9433 1 chr7A.!!$F1 973
21 TraesCS1A01G360300 chr5A 494399903 494400877 974 True 1267.000000 1267 90.154000 8460 9433 1 chr5A.!!$R1 973
22 TraesCS1A01G360300 chr5A 354537681 354538452 771 False 600.000000 632 97.798000 6588 7596 2 chr5A.!!$F2 1008
23 TraesCS1A01G360300 chr5B 493603417 493604391 974 True 1251.000000 1251 89.846000 8460 9433 1 chr5B.!!$R1 973
24 TraesCS1A01G360300 chr5B 531693242 531694216 974 False 1234.000000 1234 89.538000 8460 9433 1 chr5B.!!$F1 973
25 TraesCS1A01G360300 chr5D 454029507 454030236 729 True 789.000000 789 86.425000 79 809 1 chr5D.!!$R1 730
26 TraesCS1A01G360300 chr4A 109190405 109191216 811 True 778.000000 778 84.364000 1 805 1 chr4A.!!$R1 804
27 TraesCS1A01G360300 chr3D 441369748 441370552 804 False 776.000000 776 84.466000 2 805 1 chr3D.!!$F2 803
28 TraesCS1A01G360300 chr3D 111978303 111979119 816 False 749.000000 749 83.575000 2 810 1 chr3D.!!$F1 808
29 TraesCS1A01G360300 chr6A 87056014 87056780 766 True 582.000000 608 96.957000 6589 7597 2 chr6A.!!$R4 1008
30 TraesCS1A01G360300 chr3A 482064301 482065024 723 False 539.500000 558 96.684000 6633 7595 2 chr3A.!!$F6 962

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
725 770 0.030638 ATTATGACAAATGGCGCGCC 59.969 50.000 42.35 42.35 0.00 6.53 F
907 952 0.170339 GATACAACCAACCAAGCGGC 59.830 55.000 0.00 0.00 34.57 6.53 F
1284 1381 0.655733 GTACTTGTGTGCGTGCTTGT 59.344 50.000 0.00 0.00 0.00 3.16 F
1881 2003 2.030946 GTCTTGAAGTGTGTCTGTGTGC 59.969 50.000 0.00 0.00 0.00 4.57 F
3341 3477 1.053424 AGGTTCCACTTCACCGCTAA 58.947 50.000 0.00 0.00 38.21 3.09 F
4549 4685 1.228429 GGTTGGCCCACTGCAACTA 60.228 57.895 6.95 0.00 43.89 2.24 F
5297 5433 1.134965 CGGAGGAGCTTGGTCTTGTAG 60.135 57.143 0.00 0.00 0.00 2.74 F
6334 6470 2.223340 GCGTTCCTTTATGATGTGGCAG 60.223 50.000 0.00 0.00 0.00 4.85 F
6584 6728 2.027745 ACATCTGAACCGCTCATTCTGT 60.028 45.455 0.00 0.00 32.14 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1546 1643 1.003704 TGGGGACATGGGATACGGT 59.996 57.895 0.00 0.00 33.40 4.83 R
2599 2735 1.331756 CACTGAAGTGTTGCGAGCTTT 59.668 47.619 2.14 0.00 40.96 3.51 R
2651 2787 3.077359 CCAGAAAGCTCCCTGTTTGTAG 58.923 50.000 12.52 0.00 0.00 2.74 R
3743 3879 0.174162 GCATGGTCAATCTGCCCAAC 59.826 55.000 0.00 0.00 0.00 3.77 R
4719 4855 0.593128 GCCACTTGCTTTGACGTCAT 59.407 50.000 20.80 0.00 36.87 3.06 R
5405 5541 0.884259 CGCACCTCACCATCAACACA 60.884 55.000 0.00 0.00 0.00 3.72 R
6524 6668 2.366266 TGTGTTCAGTTAACGGGCTAGT 59.634 45.455 5.89 0.00 41.30 2.57 R
8014 10483 0.456482 CTGAGAGCTGCTGTCAGTCG 60.456 60.000 35.56 20.08 43.84 4.18 R
8519 11037 0.183492 TGGAAGTTGTTGCAGAGGCT 59.817 50.000 0.00 0.00 41.91 4.58 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
75 76 0.736325 CGGTCGTGCCTCTCGAAAAT 60.736 55.000 0.00 0.00 39.01 1.82
166 178 2.653702 GAGAGTCACGGCTGTGCT 59.346 61.111 21.33 19.76 46.01 4.40
229 252 2.601979 CGCGAGTCACATTTTTGCTTCA 60.602 45.455 0.00 0.00 0.00 3.02
255 278 2.712539 CACGGTTGTGCTTTGCGA 59.287 55.556 0.00 0.00 39.67 5.10
257 280 1.522806 ACGGTTGTGCTTTGCGAGA 60.523 52.632 0.00 0.00 0.00 4.04
258 281 1.205064 CGGTTGTGCTTTGCGAGAG 59.795 57.895 0.00 0.00 0.00 3.20
260 283 1.081840 GTTGTGCTTTGCGAGAGGC 60.082 57.895 0.00 0.00 43.96 4.70
365 392 4.307908 ACGGTTGTGCTTTCGCGC 62.308 61.111 0.00 0.00 46.63 6.86
377 404 3.776659 TTCGCGCAAGTCACGGTCA 62.777 57.895 8.75 0.00 41.68 4.02
393 420 1.559682 GGTCATGCCTCCTAGGAAACA 59.440 52.381 13.77 14.00 37.67 2.83
483 516 1.344438 TGTGATTTCGTGAGAGGCACT 59.656 47.619 0.00 0.00 45.49 4.40
544 582 2.416701 GGTTCGGTTATTTCGTCCGGTA 60.417 50.000 0.00 0.00 43.75 4.02
555 594 2.598589 TCGTCCGGTATTTTTCGTGAG 58.401 47.619 0.00 0.00 0.00 3.51
605 644 9.484806 AACATGGGATCTAATTTTGAAGATCTT 57.515 29.630 7.95 7.95 44.94 2.40
619 658 1.751351 AGATCTTGACGCGAGGAATCA 59.249 47.619 15.93 1.67 0.00 2.57
623 662 2.069273 CTTGACGCGAGGAATCAAACT 58.931 47.619 15.93 0.00 32.19 2.66
633 672 3.214328 AGGAATCAAACTGTGAAAGCGT 58.786 40.909 0.00 0.00 40.50 5.07
725 770 0.030638 ATTATGACAAATGGCGCGCC 59.969 50.000 42.35 42.35 0.00 6.53
743 788 0.602562 CCGCATGTGGGTCATTTGTT 59.397 50.000 18.06 0.00 34.09 2.83
749 794 0.388659 GTGGGTCATTTGTTGCAGCA 59.611 50.000 0.00 0.00 0.00 4.41
787 832 2.029290 TCTTTGCAACGAGTACTCCTCC 60.029 50.000 17.23 4.20 36.82 4.30
788 833 0.606604 TTGCAACGAGTACTCCTCCC 59.393 55.000 17.23 4.55 36.82 4.30
789 834 0.251653 TGCAACGAGTACTCCTCCCT 60.252 55.000 17.23 0.00 36.82 4.20
790 835 0.456628 GCAACGAGTACTCCTCCCTC 59.543 60.000 17.23 0.00 36.82 4.30
805 850 3.195825 CCTCCCTCAACTAGTGATTTCGT 59.804 47.826 0.00 0.00 35.07 3.85
808 853 3.262420 CCTCAACTAGTGATTTCGTGGG 58.738 50.000 0.00 0.00 35.07 4.61
809 854 3.056107 CCTCAACTAGTGATTTCGTGGGA 60.056 47.826 0.00 0.00 35.07 4.37
810 855 4.562757 CCTCAACTAGTGATTTCGTGGGAA 60.563 45.833 0.00 0.00 35.07 3.97
811 856 5.160607 TCAACTAGTGATTTCGTGGGAAT 57.839 39.130 0.00 0.00 30.88 3.01
812 857 5.175859 TCAACTAGTGATTTCGTGGGAATC 58.824 41.667 0.00 0.00 30.88 2.52
813 858 4.138487 ACTAGTGATTTCGTGGGAATCC 57.862 45.455 0.00 0.00 30.88 3.01
814 859 3.517901 ACTAGTGATTTCGTGGGAATCCA 59.482 43.478 0.09 0.00 41.58 3.41
815 860 3.652057 AGTGATTTCGTGGGAATCCAT 57.348 42.857 0.09 0.00 46.09 3.41
816 861 3.545703 AGTGATTTCGTGGGAATCCATC 58.454 45.455 0.09 0.00 46.09 3.51
817 862 3.054434 AGTGATTTCGTGGGAATCCATCA 60.054 43.478 0.09 0.00 46.09 3.07
818 863 3.694072 GTGATTTCGTGGGAATCCATCAA 59.306 43.478 0.09 0.00 46.09 2.57
819 864 4.339247 GTGATTTCGTGGGAATCCATCAAT 59.661 41.667 0.09 0.00 46.09 2.57
820 865 4.580167 TGATTTCGTGGGAATCCATCAATC 59.420 41.667 0.09 2.28 46.09 2.67
821 866 2.638480 TCGTGGGAATCCATCAATCC 57.362 50.000 0.09 0.00 46.09 3.01
822 867 1.202639 TCGTGGGAATCCATCAATCCG 60.203 52.381 0.09 0.00 46.09 4.18
823 868 1.609208 GTGGGAATCCATCAATCCGG 58.391 55.000 0.09 0.00 46.09 5.14
824 869 1.142870 GTGGGAATCCATCAATCCGGA 59.857 52.381 6.61 6.61 46.09 5.14
825 870 2.065007 TGGGAATCCATCAATCCGGAT 58.935 47.619 12.38 12.38 44.09 4.18
834 879 7.703058 ATCCATCAATCCGGATTTTATTACC 57.297 36.000 27.21 0.00 38.99 2.85
835 880 6.007703 TCCATCAATCCGGATTTTATTACCC 58.992 40.000 27.21 0.00 0.00 3.69
836 881 5.106317 CCATCAATCCGGATTTTATTACCCG 60.106 44.000 27.21 12.48 41.47 5.28
837 882 5.038651 TCAATCCGGATTTTATTACCCGT 57.961 39.130 27.21 0.00 40.30 5.28
838 883 4.817464 TCAATCCGGATTTTATTACCCGTG 59.183 41.667 27.21 12.12 40.30 4.94
839 884 3.910568 TCCGGATTTTATTACCCGTGT 57.089 42.857 0.00 0.00 40.30 4.49
840 885 3.533547 TCCGGATTTTATTACCCGTGTG 58.466 45.455 0.00 0.00 40.30 3.82
841 886 2.614983 CCGGATTTTATTACCCGTGTGG 59.385 50.000 0.00 0.00 40.30 4.17
851 896 3.616284 CCCGTGTGGTGTACAATGA 57.384 52.632 0.00 0.00 41.89 2.57
852 897 2.107950 CCCGTGTGGTGTACAATGAT 57.892 50.000 0.00 0.00 41.89 2.45
853 898 3.254470 CCCGTGTGGTGTACAATGATA 57.746 47.619 0.00 0.00 41.89 2.15
854 899 2.933906 CCCGTGTGGTGTACAATGATAC 59.066 50.000 0.00 0.00 41.89 2.24
855 900 3.591023 CCGTGTGGTGTACAATGATACA 58.409 45.455 0.00 0.00 41.89 2.29
856 901 3.616821 CCGTGTGGTGTACAATGATACAG 59.383 47.826 0.00 0.00 41.89 2.74
857 902 4.242475 CGTGTGGTGTACAATGATACAGT 58.758 43.478 0.00 0.00 41.89 3.55
858 903 4.091365 CGTGTGGTGTACAATGATACAGTG 59.909 45.833 0.00 0.00 41.89 3.66
859 904 4.994852 GTGTGGTGTACAATGATACAGTGT 59.005 41.667 9.55 9.55 44.74 3.55
860 905 5.468746 GTGTGGTGTACAATGATACAGTGTT 59.531 40.000 9.86 0.00 39.70 3.32
890 935 1.402720 CGATTTGGGCTGCAAAACGAT 60.403 47.619 11.46 0.00 39.18 3.73
893 938 1.610363 TTGGGCTGCAAAACGATACA 58.390 45.000 0.50 0.00 0.00 2.29
905 950 1.153353 ACGATACAACCAACCAAGCG 58.847 50.000 0.00 0.00 0.00 4.68
906 951 0.446222 CGATACAACCAACCAAGCGG 59.554 55.000 0.00 0.00 38.77 5.52
907 952 0.170339 GATACAACCAACCAAGCGGC 59.830 55.000 0.00 0.00 34.57 6.53
908 953 1.248101 ATACAACCAACCAAGCGGCC 61.248 55.000 0.00 0.00 34.57 6.13
909 954 4.341502 CAACCAACCAAGCGGCCG 62.342 66.667 24.05 24.05 34.57 6.13
910 955 4.887190 AACCAACCAAGCGGCCGT 62.887 61.111 28.70 11.01 34.57 5.68
911 956 3.479127 AACCAACCAAGCGGCCGTA 62.479 57.895 28.70 0.00 34.57 4.02
1157 1240 1.216710 CTGCTCTTCTCCGGTGGTC 59.783 63.158 0.00 0.00 0.00 4.02
1158 1241 2.232298 CTGCTCTTCTCCGGTGGTCC 62.232 65.000 0.00 0.00 0.00 4.46
1159 1242 1.985116 GCTCTTCTCCGGTGGTCCT 60.985 63.158 0.00 0.00 0.00 3.85
1161 1244 1.305046 TCTTCTCCGGTGGTCCTCC 60.305 63.158 0.00 0.00 0.00 4.30
1162 1245 2.284405 TTCTCCGGTGGTCCTCCC 60.284 66.667 0.00 0.00 0.00 4.30
1163 1246 4.753662 TCTCCGGTGGTCCTCCCG 62.754 72.222 0.00 12.17 43.82 5.14
1180 1272 1.299620 CGCACTTGCTTGCTTGCTT 60.300 52.632 0.00 0.00 40.62 3.91
1260 1357 2.280119 TGTCTGTGTGCGTGCTCC 60.280 61.111 0.00 0.00 0.00 4.70
1284 1381 0.655733 GTACTTGTGTGCGTGCTTGT 59.344 50.000 0.00 0.00 0.00 3.16
1387 1484 7.358765 CGAGGATTGAGTAAATTGACGATCATC 60.359 40.741 9.65 9.65 0.00 2.92
1546 1643 7.018826 CGCCGAATTGTAGTTTTTAGAAATCA 58.981 34.615 0.00 0.00 0.00 2.57
1556 1653 6.478129 AGTTTTTAGAAATCACCGTATCCCA 58.522 36.000 0.00 0.00 0.00 4.37
1722 1826 4.770795 AGTATGTGAATGCTGGAACTACC 58.229 43.478 0.00 0.00 39.54 3.18
1791 1896 3.562609 GGGTGCACAATCTAAGGGGTTTA 60.563 47.826 20.43 0.00 0.00 2.01
1820 1942 7.117236 GTCCACTCTGTATTTTCATTCAACGTA 59.883 37.037 0.00 0.00 0.00 3.57
1881 2003 2.030946 GTCTTGAAGTGTGTCTGTGTGC 59.969 50.000 0.00 0.00 0.00 4.57
1953 2077 8.358895 TCTGAATTCAACATTTGCTAATGACAA 58.641 29.630 24.57 14.36 43.12 3.18
2063 2196 5.187967 ACAGGTTCTTGGAGTATCTTAGGTG 59.812 44.000 0.00 0.00 33.73 4.00
2065 2198 5.422650 AGGTTCTTGGAGTATCTTAGGTGTC 59.577 44.000 0.00 0.00 33.73 3.67
2068 2201 4.639310 TCTTGGAGTATCTTAGGTGTCGTC 59.361 45.833 0.00 0.00 33.73 4.20
2149 2282 7.956328 TCCTAGTAATATGGTATGCACCTAG 57.044 40.000 0.00 0.00 45.98 3.02
2150 2283 7.476153 TCCTAGTAATATGGTATGCACCTAGT 58.524 38.462 0.00 0.00 45.98 2.57
2151 2284 7.954056 TCCTAGTAATATGGTATGCACCTAGTT 59.046 37.037 0.00 0.00 45.98 2.24
2152 2285 8.251721 CCTAGTAATATGGTATGCACCTAGTTC 58.748 40.741 0.00 0.00 45.98 3.01
2153 2286 7.857404 AGTAATATGGTATGCACCTAGTTCT 57.143 36.000 0.00 0.00 45.98 3.01
2154 2287 8.951614 AGTAATATGGTATGCACCTAGTTCTA 57.048 34.615 0.00 0.00 45.98 2.10
2599 2735 3.031736 GGAGGATGCACTAGGTTCTACA 58.968 50.000 0.00 0.00 0.00 2.74
2651 2787 5.562890 GCAGAAACTTATGAACCTGACAACC 60.563 44.000 0.00 0.00 0.00 3.77
2693 2829 3.371034 GAGGAGGAAGTTTCTAGGAGCT 58.629 50.000 0.00 0.00 0.00 4.09
3099 3235 3.557577 TGACATCAAACGCAATCCAAG 57.442 42.857 0.00 0.00 0.00 3.61
3106 3242 1.886886 AACGCAATCCAAGTACCGTT 58.113 45.000 0.00 0.00 34.54 4.44
3203 3339 2.159028 GGAGAGACCATGCCAAGTACTC 60.159 54.545 0.00 0.00 38.79 2.59
3341 3477 1.053424 AGGTTCCACTTCACCGCTAA 58.947 50.000 0.00 0.00 38.21 3.09
3563 3699 4.159135 CACCTTGGGAGGATTCATCTTTTG 59.841 45.833 0.00 0.00 46.74 2.44
3584 3720 4.199310 TGCATACCCATCAAACTTAGCTC 58.801 43.478 0.00 0.00 0.00 4.09
3589 3725 2.555199 CCATCAAACTTAGCTCCTCCG 58.445 52.381 0.00 0.00 0.00 4.63
3743 3879 3.480470 CCTATAATGTTCAGTGGGGCAG 58.520 50.000 0.00 0.00 0.00 4.85
3790 3926 3.560636 TCGAAAGGGGATCCAGAAATC 57.439 47.619 15.23 4.02 34.83 2.17
4180 4316 1.949525 GAGAGCAGAAACCTGTTGCAA 59.050 47.619 0.00 0.00 40.22 4.08
4540 4676 4.641645 CAGCAGACGGTTGGCCCA 62.642 66.667 0.00 0.00 0.00 5.36
4549 4685 1.228429 GGTTGGCCCACTGCAACTA 60.228 57.895 6.95 0.00 43.89 2.24
4573 4709 3.070018 ACTTGCTGATGTTGCTGTAGTC 58.930 45.455 0.00 0.00 0.00 2.59
4600 4736 5.046529 CAGACATACACAGATCTTACTGGC 58.953 45.833 0.00 0.00 41.59 4.85
4719 4855 5.755409 TGGGCTAAAGTTACATCTCTTGA 57.245 39.130 0.00 0.00 0.00 3.02
5297 5433 1.134965 CGGAGGAGCTTGGTCTTGTAG 60.135 57.143 0.00 0.00 0.00 2.74
5375 5511 5.437060 GGGTTTCTGCTAATGTGATAGGAA 58.563 41.667 0.00 0.00 0.00 3.36
5405 5541 2.983229 CAGCACCAGAAATAGAGCTGT 58.017 47.619 0.00 0.00 43.16 4.40
5406 5542 2.676839 CAGCACCAGAAATAGAGCTGTG 59.323 50.000 0.00 0.00 43.16 3.66
5446 5582 6.183360 TGCGTTTGAAAGAAAGAACTTCAGAT 60.183 34.615 0.00 0.00 36.40 2.90
5584 5720 3.231160 GTCTTTTACGCCCAAATTCACG 58.769 45.455 0.00 0.00 0.00 4.35
6334 6470 2.223340 GCGTTCCTTTATGATGTGGCAG 60.223 50.000 0.00 0.00 0.00 4.85
6415 6551 3.181499 GCATGTTCCAGAATGCAAGAGAG 60.181 47.826 0.00 0.00 46.75 3.20
6524 6668 9.756571 GGTTCCCTATATAGTTAAGATCTCTGA 57.243 37.037 8.92 0.00 0.00 3.27
6539 6683 2.753452 TCTCTGACTAGCCCGTTAACTG 59.247 50.000 3.71 0.00 0.00 3.16
6540 6684 2.753452 CTCTGACTAGCCCGTTAACTGA 59.247 50.000 3.71 0.00 0.00 3.41
6581 6725 3.799420 GTCTACATCTGAACCGCTCATTC 59.201 47.826 0.00 0.00 32.14 2.67
6582 6726 3.701542 TCTACATCTGAACCGCTCATTCT 59.298 43.478 0.00 0.00 32.14 2.40
6583 6727 2.625737 ACATCTGAACCGCTCATTCTG 58.374 47.619 0.00 0.00 32.14 3.02
6584 6728 2.027745 ACATCTGAACCGCTCATTCTGT 60.028 45.455 0.00 0.00 32.14 3.41
6585 6729 3.195610 ACATCTGAACCGCTCATTCTGTA 59.804 43.478 0.00 0.00 32.14 2.74
6586 6730 3.953712 TCTGAACCGCTCATTCTGTAA 57.046 42.857 0.00 0.00 32.14 2.41
7738 7921 6.656693 GCAGTGATAATTATTAGGCATCCAGT 59.343 38.462 0.00 0.00 0.00 4.00
7754 7937 5.453057 GCATCCAGTGTCTCTCATGTTCTAT 60.453 44.000 0.00 0.00 0.00 1.98
7756 7939 4.646945 TCCAGTGTCTCTCATGTTCTATCC 59.353 45.833 0.00 0.00 0.00 2.59
7783 7966 6.026513 GTGCTTCACTGCAATAGAAAGAATC 58.973 40.000 0.00 0.00 45.12 2.52
7789 7974 8.801715 TCACTGCAATAGAAAGAATCAAAAAC 57.198 30.769 0.00 0.00 0.00 2.43
7820 8005 7.029563 GCTAGGGATTGTATTTTGTTGTTCTG 58.970 38.462 0.00 0.00 0.00 3.02
7853 8047 4.868171 TCTCGTACAATACTGCCATGAAAC 59.132 41.667 0.00 0.00 0.00 2.78
7859 10115 6.254281 ACAATACTGCCATGAAACAACTAC 57.746 37.500 0.00 0.00 0.00 2.73
8014 10483 0.110644 CGCGTTGGAAGAACTCAAGC 60.111 55.000 0.00 0.00 0.00 4.01
8018 10487 2.484889 GTTGGAAGAACTCAAGCGACT 58.515 47.619 0.00 0.00 0.00 4.18
8195 10700 2.128771 AGCTGTCCGGCAACATAAAT 57.871 45.000 0.00 0.00 34.17 1.40
8196 10701 3.275617 AGCTGTCCGGCAACATAAATA 57.724 42.857 0.00 0.00 34.17 1.40
8230 10735 6.600822 TCAGCTTTCTTTCTGCTAAGCATATT 59.399 34.615 0.00 0.00 44.08 1.28
8231 10736 7.770433 TCAGCTTTCTTTCTGCTAAGCATATTA 59.230 33.333 0.00 0.00 44.08 0.98
8232 10737 8.566260 CAGCTTTCTTTCTGCTAAGCATATTAT 58.434 33.333 0.00 0.00 44.08 1.28
8269 10776 0.180406 AGGAATGTACCATGTCGCCC 59.820 55.000 0.00 0.00 0.00 6.13
8343 10850 1.971357 ACACTTAGACAGGGTGGACAG 59.029 52.381 0.00 0.00 37.95 3.51
8344 10851 0.977395 ACTTAGACAGGGTGGACAGC 59.023 55.000 0.00 0.00 0.00 4.40
8347 10854 0.114364 TAGACAGGGTGGACAGCAGA 59.886 55.000 3.77 0.00 0.00 4.26
8348 10855 0.546267 AGACAGGGTGGACAGCAGAT 60.546 55.000 3.77 0.00 0.00 2.90
8349 10856 0.326264 GACAGGGTGGACAGCAGATT 59.674 55.000 3.77 0.00 0.00 2.40
8350 10857 0.773644 ACAGGGTGGACAGCAGATTT 59.226 50.000 3.77 0.00 0.00 2.17
8351 10858 1.145738 ACAGGGTGGACAGCAGATTTT 59.854 47.619 3.77 0.00 0.00 1.82
8352 10859 2.242043 CAGGGTGGACAGCAGATTTTT 58.758 47.619 3.77 0.00 0.00 1.94
8397 10904 5.443283 CTGGATTCATGGAATTGAGGAAGA 58.557 41.667 0.00 0.00 31.89 2.87
8398 10905 5.829986 TGGATTCATGGAATTGAGGAAGAA 58.170 37.500 0.00 0.00 31.89 2.52
8399 10906 5.889853 TGGATTCATGGAATTGAGGAAGAAG 59.110 40.000 0.00 0.00 31.89 2.85
8421 10936 8.107095 AGAAGGTCTTAAACAAGCCACAATATA 58.893 33.333 0.00 0.00 0.00 0.86
8423 10938 6.318900 AGGTCTTAAACAAGCCACAATATAGC 59.681 38.462 0.00 0.00 0.00 2.97
8425 10940 7.189512 GTCTTAAACAAGCCACAATATAGCTG 58.810 38.462 0.00 0.00 36.84 4.24
8440 10958 1.853963 AGCTGGTTCCAGACTCGTAT 58.146 50.000 21.32 0.00 36.24 3.06
8452 10970 8.879759 GTTCCAGACTCGTATCATTTGATTTTA 58.120 33.333 0.00 0.00 36.05 1.52
8470 10988 6.718912 TGATTTTATGAACACCCATCAAGACA 59.281 34.615 0.00 0.00 0.00 3.41
8510 11028 4.662278 TGCTATCTTACAAGGCTTTGGTT 58.338 39.130 13.65 0.00 38.66 3.67
8519 11037 0.390124 AGGCTTTGGTTACGTGACGA 59.610 50.000 13.70 0.00 0.00 4.20
8529 11047 1.520600 TACGTGACGAGCCTCTGCAA 61.521 55.000 13.70 0.00 41.13 4.08
8624 11142 2.061182 GACGATCCGCGCTACCTTCT 62.061 60.000 5.56 0.00 46.04 2.85
8625 11143 1.065928 CGATCCGCGCTACCTTCTT 59.934 57.895 5.56 0.00 0.00 2.52
8652 11170 8.975295 GGTGAAATACCTAGACTTACCTCTTTA 58.025 37.037 0.00 0.00 46.51 1.85
8694 11212 4.085357 TGGATTTCCAATATCTGGTCGG 57.915 45.455 0.00 0.00 46.51 4.79
8715 11233 1.535462 CAAGGCGGCCGGATAATTAAG 59.465 52.381 29.38 0.00 0.00 1.85
8782 11300 2.096248 GTCAAGTCGGTCATCTCCTCT 58.904 52.381 0.00 0.00 0.00 3.69
8839 11357 2.224305 GCCGGGCATTCTAGATACACTT 60.224 50.000 15.62 0.00 0.00 3.16
8842 11360 5.794894 CCGGGCATTCTAGATACACTTAAT 58.205 41.667 0.00 0.00 0.00 1.40
8861 11379 6.388394 ACTTAATAAGATTGAGAGGGCCTTCT 59.612 38.462 18.85 18.85 0.00 2.85
9004 11522 1.680338 GGCTTGGTTGGCTATGGTAG 58.320 55.000 0.00 0.00 0.00 3.18
9012 11530 3.496870 GGTTGGCTATGGTAGGAATGGAG 60.497 52.174 0.00 0.00 0.00 3.86
9131 11650 3.288092 GTCAAACACCTTTCTGGGACTT 58.712 45.455 0.00 0.00 41.11 3.01
9134 11653 1.821088 ACACCTTTCTGGGACTTCCT 58.179 50.000 0.00 0.00 41.11 3.36
9169 11688 0.899720 CAAGCCCAAGGACATTGCAT 59.100 50.000 0.00 0.00 37.60 3.96
9185 11704 3.599730 TGCATCGCTAATCTATGAGGG 57.400 47.619 0.00 0.00 0.00 4.30
9188 11707 3.618507 GCATCGCTAATCTATGAGGGCTT 60.619 47.826 0.00 0.00 0.00 4.35
9209 11728 0.735471 GCGAGGAAGAATTGGAAGGC 59.265 55.000 0.00 0.00 0.00 4.35
9225 11744 2.690778 GGCGCGTGAGGCTTTGAAT 61.691 57.895 8.43 0.00 40.44 2.57
9233 11752 1.073125 TGAGGCTTTGAATGGGAACGA 59.927 47.619 0.00 0.00 0.00 3.85
9244 11763 0.464036 TGGGAACGATTGGATCCTCG 59.536 55.000 18.95 18.95 40.62 4.63
9376 11895 2.051804 GAAGCATGCGAACGATGGGG 62.052 60.000 13.01 0.00 0.00 4.96
9381 11900 2.761559 CATGCGAACGATGGGGTATAA 58.238 47.619 0.00 0.00 0.00 0.98
9424 11943 0.984230 TCAATTTCTCGGCCTGACCT 59.016 50.000 0.00 0.00 35.61 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
218 241 1.200948 GCCTCTCGCTGAAGCAAAAAT 59.799 47.619 2.79 0.00 42.21 1.82
229 252 3.616721 ACAACCGTGCCTCTCGCT 61.617 61.111 0.00 0.00 38.78 4.93
299 325 4.833126 TCTCGCGAAAGAAAGAAAAACAG 58.167 39.130 11.33 0.00 0.00 3.16
301 327 4.834234 ACTCTCGCGAAAGAAAGAAAAAC 58.166 39.130 17.91 0.00 0.00 2.43
365 392 1.021390 GGAGGCATGACCGTGACTTG 61.021 60.000 0.00 0.00 46.52 3.16
532 569 3.995705 TCACGAAAAATACCGGACGAAAT 59.004 39.130 9.46 0.00 0.00 2.17
605 644 1.270094 ACAGTTTGATTCCTCGCGTCA 60.270 47.619 5.77 0.00 0.00 4.35
643 687 8.928733 CAAAACATTTTATCTCTCAAACCATGG 58.071 33.333 11.19 11.19 0.00 3.66
705 750 1.535860 GGCGCGCCATTTGTCATAATT 60.536 47.619 43.55 0.00 35.81 1.40
706 751 0.030638 GGCGCGCCATTTGTCATAAT 59.969 50.000 43.55 0.00 35.81 1.28
709 754 4.178214 CGGCGCGCCATTTGTCAT 62.178 61.111 45.26 0.00 35.37 3.06
725 770 1.700523 CAACAAATGACCCACATGCG 58.299 50.000 0.00 0.00 39.39 4.73
733 778 1.673626 CCCATGCTGCAACAAATGACC 60.674 52.381 6.36 0.00 0.00 4.02
738 783 1.412079 ACTTCCCATGCTGCAACAAA 58.588 45.000 6.36 0.00 0.00 2.83
743 788 0.609957 CTCCAACTTCCCATGCTGCA 60.610 55.000 4.13 4.13 0.00 4.41
749 794 4.338879 CAAAGATCACTCCAACTTCCCAT 58.661 43.478 0.00 0.00 0.00 4.00
787 832 3.056107 TCCCACGAAATCACTAGTTGAGG 60.056 47.826 0.00 0.00 37.77 3.86
788 833 4.188247 TCCCACGAAATCACTAGTTGAG 57.812 45.455 0.00 0.00 37.77 3.02
789 834 4.610605 TTCCCACGAAATCACTAGTTGA 57.389 40.909 0.00 0.00 39.11 3.18
790 835 4.332819 GGATTCCCACGAAATCACTAGTTG 59.667 45.833 0.00 0.00 35.30 3.16
805 850 2.065007 ATCCGGATTGATGGATTCCCA 58.935 47.619 12.38 0.00 42.31 4.37
810 855 6.663523 GGGTAATAAAATCCGGATTGATGGAT 59.336 38.462 29.84 15.24 46.89 3.41
811 856 6.007703 GGGTAATAAAATCCGGATTGATGGA 58.992 40.000 29.84 13.10 38.95 3.41
812 857 5.106317 CGGGTAATAAAATCCGGATTGATGG 60.106 44.000 29.84 9.11 38.93 3.51
813 858 5.472137 ACGGGTAATAAAATCCGGATTGATG 59.528 40.000 29.84 15.14 45.97 3.07
814 859 5.472137 CACGGGTAATAAAATCCGGATTGAT 59.528 40.000 29.84 21.89 45.97 2.57
815 860 4.817464 CACGGGTAATAAAATCCGGATTGA 59.183 41.667 29.84 20.66 45.97 2.57
816 861 4.577283 ACACGGGTAATAAAATCCGGATTG 59.423 41.667 29.84 15.63 45.97 2.67
817 862 4.577283 CACACGGGTAATAAAATCCGGATT 59.423 41.667 24.27 24.27 45.97 3.01
818 863 4.131596 CACACGGGTAATAAAATCCGGAT 58.868 43.478 12.38 12.38 45.97 4.18
819 864 3.533547 CACACGGGTAATAAAATCCGGA 58.466 45.455 6.61 6.61 45.97 5.14
820 865 2.614983 CCACACGGGTAATAAAATCCGG 59.385 50.000 0.00 0.00 45.97 5.14
821 866 3.955771 CCACACGGGTAATAAAATCCG 57.044 47.619 0.00 0.00 46.95 4.18
833 878 2.107950 ATCATTGTACACCACACGGG 57.892 50.000 0.00 0.00 44.81 5.28
834 879 3.591023 TGTATCATTGTACACCACACGG 58.409 45.455 0.00 0.00 36.69 4.94
835 880 4.091365 CACTGTATCATTGTACACCACACG 59.909 45.833 0.00 0.00 36.69 4.49
836 881 4.994852 ACACTGTATCATTGTACACCACAC 59.005 41.667 0.00 0.00 36.69 3.82
837 882 5.222079 ACACTGTATCATTGTACACCACA 57.778 39.130 0.00 0.00 34.51 4.17
838 883 6.554334 AAACACTGTATCATTGTACACCAC 57.446 37.500 0.00 0.00 31.64 4.16
839 884 7.575414 AAAAACACTGTATCATTGTACACCA 57.425 32.000 0.00 0.00 31.64 4.17
860 905 2.029470 CAGCCCAAATCGCCTGTAAAAA 60.029 45.455 0.00 0.00 0.00 1.94
870 915 2.433637 CGTTTTGCAGCCCAAATCG 58.566 52.632 13.15 13.15 44.89 3.34
872 917 2.560542 TGTATCGTTTTGCAGCCCAAAT 59.439 40.909 1.52 0.00 42.63 2.32
890 935 1.899534 GGCCGCTTGGTTGGTTGTA 60.900 57.895 0.00 0.00 34.16 2.41
893 938 3.479127 TACGGCCGCTTGGTTGGTT 62.479 57.895 28.58 3.48 34.16 3.67
908 953 2.183555 GCTTCCCGTGTCCCTACG 59.816 66.667 0.00 0.00 43.35 3.51
909 954 2.582978 GGCTTCCCGTGTCCCTAC 59.417 66.667 0.00 0.00 0.00 3.18
910 955 2.686106 GGGCTTCCCGTGTCCCTA 60.686 66.667 0.00 0.00 35.87 3.53
1163 1246 0.031721 AGAAGCAAGCAAGCAAGTGC 59.968 50.000 3.19 0.00 45.28 4.40
1165 1248 0.672342 CCAGAAGCAAGCAAGCAAGT 59.328 50.000 3.19 0.00 36.85 3.16
1260 1357 1.594518 GCACGCACACAAGTACACAAG 60.595 52.381 0.00 0.00 0.00 3.16
1312 1409 1.148310 CCTCGTGGTACTTGCACAAG 58.852 55.000 8.82 8.82 43.79 3.16
1387 1484 1.680522 CCCATCTCCTCGGTGACTGG 61.681 65.000 0.00 8.35 0.00 4.00
1440 1537 9.656323 TGTGAGACTATATCAAAATACTACCCT 57.344 33.333 0.00 0.00 0.00 4.34
1532 1629 6.478129 TGGGATACGGTGATTTCTAAAAACT 58.522 36.000 0.00 0.00 37.60 2.66
1546 1643 1.003704 TGGGGACATGGGATACGGT 59.996 57.895 0.00 0.00 33.40 4.83
1791 1896 8.299570 GTTGAATGAAAATACAGAGTGGACATT 58.700 33.333 0.00 0.00 0.00 2.71
1820 1942 3.355378 TCATTGTTCCGGATTGCAGATT 58.645 40.909 4.15 0.00 0.00 2.40
1881 2003 6.468956 ACGATGTAAGCAAAAAGATAAATGCG 59.531 34.615 0.00 0.00 43.39 4.73
1926 2049 8.024865 TGTCATTAGCAAATGTTGAATTCAGAG 58.975 33.333 8.41 0.00 42.66 3.35
2063 2196 4.658713 CATGAGATGCCATATTGACGAC 57.341 45.455 0.00 0.00 0.00 4.34
2599 2735 1.331756 CACTGAAGTGTTGCGAGCTTT 59.668 47.619 2.14 0.00 40.96 3.51
2651 2787 3.077359 CCAGAAAGCTCCCTGTTTGTAG 58.923 50.000 12.52 0.00 0.00 2.74
3099 3235 5.849604 GCTATGTCAAAAAGTTCAACGGTAC 59.150 40.000 0.00 0.00 0.00 3.34
3106 3242 4.560136 TTGCGCTATGTCAAAAAGTTCA 57.440 36.364 9.73 0.00 0.00 3.18
3203 3339 4.695928 GGGGCTCTTTACTAACTGAAACAG 59.304 45.833 0.00 0.00 37.52 3.16
3341 3477 0.615331 AGTTCACGCATCATCAGGGT 59.385 50.000 0.00 0.00 0.00 4.34
3385 3521 4.108699 CACGGCACATGGAAAATTATGT 57.891 40.909 0.00 0.00 37.99 2.29
3563 3699 3.565902 GGAGCTAAGTTTGATGGGTATGC 59.434 47.826 0.00 0.00 0.00 3.14
3584 3720 4.191544 TCAATAAGAATCTGCAACGGAGG 58.808 43.478 0.00 0.00 0.00 4.30
3589 3725 6.141462 GCTAGCATCAATAAGAATCTGCAAC 58.859 40.000 10.63 0.00 32.18 4.17
3743 3879 0.174162 GCATGGTCAATCTGCCCAAC 59.826 55.000 0.00 0.00 0.00 3.77
3790 3926 1.725641 TCTTCACAACTAGCATGCCG 58.274 50.000 15.66 8.67 0.00 5.69
3931 4067 4.307432 CCCTGATCACGCGATATAACTTT 58.693 43.478 15.93 0.00 29.66 2.66
3934 4070 1.993370 GCCCTGATCACGCGATATAAC 59.007 52.381 15.93 0.00 29.66 1.89
4393 4529 1.120530 CGGGTGCTATGTCTAAGGGT 58.879 55.000 0.00 0.00 0.00 4.34
4549 4685 0.956633 CAGCAACATCAGCAAGTGGT 59.043 50.000 0.00 0.00 0.00 4.16
4573 4709 3.156511 AGATCTGTGTATGTCTGTGCG 57.843 47.619 0.00 0.00 0.00 5.34
4719 4855 0.593128 GCCACTTGCTTTGACGTCAT 59.407 50.000 20.80 0.00 36.87 3.06
5297 5433 3.256631 AGGTCATCCAAATGCACTTCAAC 59.743 43.478 0.00 0.00 35.89 3.18
5375 5511 2.638480 TCTGGTGCTGCAGTTACTTT 57.362 45.000 16.64 0.00 0.00 2.66
5405 5541 0.884259 CGCACCTCACCATCAACACA 60.884 55.000 0.00 0.00 0.00 3.72
5406 5542 0.884704 ACGCACCTCACCATCAACAC 60.885 55.000 0.00 0.00 0.00 3.32
5446 5582 3.190383 TCCTCCCACAAATCTCTGAGA 57.810 47.619 10.23 10.23 0.00 3.27
5584 5720 3.728845 TGCAGACAGTAGTTTCTTGTCC 58.271 45.455 0.64 0.00 0.00 4.02
5947 6083 1.202687 CCAAGCGAGCCTCCAATATCA 60.203 52.381 0.00 0.00 0.00 2.15
6415 6551 7.103641 TGATTTACCTTCTCTATGAACACCAC 58.896 38.462 0.00 0.00 0.00 4.16
6510 6654 3.886505 CGGGCTAGTCAGAGATCTTAACT 59.113 47.826 0.00 3.85 0.00 2.24
6524 6668 2.366266 TGTGTTCAGTTAACGGGCTAGT 59.634 45.455 5.89 0.00 41.30 2.57
6581 6725 7.642669 TGAAAAATGCACTTCTCTCTTTACAG 58.357 34.615 0.00 0.00 0.00 2.74
6582 6726 7.566760 TGAAAAATGCACTTCTCTCTTTACA 57.433 32.000 0.00 0.00 0.00 2.41
6583 6727 7.379797 GGTTGAAAAATGCACTTCTCTCTTTAC 59.620 37.037 0.00 0.00 0.00 2.01
6584 6728 7.425606 GGTTGAAAAATGCACTTCTCTCTTTA 58.574 34.615 0.00 0.00 0.00 1.85
6585 6729 6.276091 GGTTGAAAAATGCACTTCTCTCTTT 58.724 36.000 0.00 0.00 0.00 2.52
6586 6730 5.221322 GGGTTGAAAAATGCACTTCTCTCTT 60.221 40.000 0.00 0.00 0.00 2.85
6748 6892 2.550855 GCTGATTGGACCTGTTGACTGA 60.551 50.000 0.00 0.00 0.00 3.41
7738 7921 4.403752 CACTGGGATAGAACATGAGAGACA 59.596 45.833 0.00 0.00 0.00 3.41
7783 7966 6.515272 ACAATCCCTAGCACTATGTTTTTG 57.485 37.500 0.00 0.00 0.00 2.44
7789 7974 7.807977 ACAAAATACAATCCCTAGCACTATG 57.192 36.000 0.00 0.00 0.00 2.23
7820 8005 5.744345 CAGTATTGTACGAGACCTCATGAAC 59.256 44.000 4.20 0.00 0.00 3.18
7853 8047 4.287766 AGGAAGGGTAAGCAAGTAGTTG 57.712 45.455 5.89 5.89 36.67 3.16
7859 10115 3.084786 CAGGAAAGGAAGGGTAAGCAAG 58.915 50.000 0.00 0.00 0.00 4.01
7895 10356 4.188462 CAGACATACGAGCCACCAATTTA 58.812 43.478 0.00 0.00 0.00 1.40
8014 10483 0.456482 CTGAGAGCTGCTGTCAGTCG 60.456 60.000 35.56 20.08 43.84 4.18
8018 10487 1.336131 AGAACTGAGAGCTGCTGTCA 58.664 50.000 25.39 25.39 32.85 3.58
8195 10700 6.540189 GCAGAAAGAAAGCTGACAGGATATTA 59.460 38.462 4.26 0.00 34.06 0.98
8196 10701 5.356470 GCAGAAAGAAAGCTGACAGGATATT 59.644 40.000 4.26 0.00 34.06 1.28
8230 10735 9.173021 CATTCCTGTGTAACTACAAAATGGATA 57.827 33.333 0.00 0.00 38.04 2.59
8231 10736 7.669722 ACATTCCTGTGTAACTACAAAATGGAT 59.330 33.333 13.52 0.00 37.71 3.41
8232 10737 7.001674 ACATTCCTGTGTAACTACAAAATGGA 58.998 34.615 13.52 7.97 37.71 3.41
8269 10776 8.552865 TGAAAATACAATCCCGAATATGTAACG 58.447 33.333 0.00 0.00 32.53 3.18
8360 10867 4.293494 TGAATCCAGGAGTTCTATCTGCT 58.707 43.478 0.00 0.00 36.59 4.24
8361 10868 4.679373 TGAATCCAGGAGTTCTATCTGC 57.321 45.455 0.00 0.00 0.00 4.26
8362 10869 5.306419 TCCATGAATCCAGGAGTTCTATCTG 59.694 44.000 0.00 0.00 0.00 2.90
8363 10870 5.471424 TCCATGAATCCAGGAGTTCTATCT 58.529 41.667 0.00 0.00 0.00 1.98
8364 10871 5.815233 TCCATGAATCCAGGAGTTCTATC 57.185 43.478 0.00 0.00 0.00 2.08
8365 10872 6.776887 ATTCCATGAATCCAGGAGTTCTAT 57.223 37.500 0.00 0.00 32.11 1.98
8397 10904 7.148069 GCTATATTGTGGCTTGTTTAAGACCTT 60.148 37.037 0.00 0.00 41.51 3.50
8398 10905 6.318900 GCTATATTGTGGCTTGTTTAAGACCT 59.681 38.462 0.00 0.00 41.51 3.85
8399 10906 6.318900 AGCTATATTGTGGCTTGTTTAAGACC 59.681 38.462 0.00 0.00 42.71 3.85
8421 10936 1.751924 GATACGAGTCTGGAACCAGCT 59.248 52.381 15.20 14.63 43.31 4.24
8423 10938 4.392921 AATGATACGAGTCTGGAACCAG 57.607 45.455 14.01 14.01 44.86 4.00
8425 10940 4.755411 TCAAATGATACGAGTCTGGAACC 58.245 43.478 0.00 0.00 0.00 3.62
8440 10958 8.131847 TGATGGGTGTTCATAAAATCAAATGA 57.868 30.769 0.00 0.00 0.00 2.57
8452 10970 3.072915 TGTCTGTCTTGATGGGTGTTCAT 59.927 43.478 0.00 0.00 0.00 2.57
8470 10988 2.304180 AGCAGCTAGGTTGTCAATGTCT 59.696 45.455 0.00 0.00 0.00 3.41
8510 11028 1.520600 TTGCAGAGGCTCGTCACGTA 61.521 55.000 9.22 0.00 41.91 3.57
8519 11037 0.183492 TGGAAGTTGTTGCAGAGGCT 59.817 50.000 0.00 0.00 41.91 4.58
8652 11170 1.523758 CGTCTTTAGCTGCCAAACCT 58.476 50.000 0.00 0.00 0.00 3.50
8694 11212 0.887387 TAATTATCCGGCCGCCTTGC 60.887 55.000 22.85 0.00 0.00 4.01
8708 11226 3.295973 GCCCATCCCAAGTGCTTAATTA 58.704 45.455 0.00 0.00 0.00 1.40
8715 11233 0.320683 GTTTTGCCCATCCCAAGTGC 60.321 55.000 0.00 0.00 0.00 4.40
8782 11300 2.097629 CGTGATAGAGAAGACCGCTTGA 59.902 50.000 0.00 0.00 33.61 3.02
8839 11357 6.831664 AAGAAGGCCCTCTCAATCTTATTA 57.168 37.500 3.79 0.00 0.00 0.98
8842 11360 5.256474 CAAAAGAAGGCCCTCTCAATCTTA 58.744 41.667 3.79 0.00 0.00 2.10
8861 11379 1.035932 TTTTCCGCACCCGACCAAAA 61.036 50.000 0.00 0.00 36.29 2.44
8990 11508 2.441750 TCCATTCCTACCATAGCCAACC 59.558 50.000 0.00 0.00 0.00 3.77
9004 11522 3.878667 CGGGGCTCCCTCCATTCC 61.879 72.222 0.00 0.00 42.67 3.01
9012 11530 1.186267 CCATAGTCTACGGGGCTCCC 61.186 65.000 0.00 0.00 41.09 4.30
9111 11629 3.551846 GAAGTCCCAGAAAGGTGTTTGA 58.448 45.455 0.00 0.00 34.66 2.69
9131 11650 3.661648 GCCCCAGGAGCCAAAGGA 61.662 66.667 0.00 0.00 0.00 3.36
9169 11688 2.300152 CCAAGCCCTCATAGATTAGCGA 59.700 50.000 0.00 0.00 0.00 4.93
9185 11704 0.453390 CCAATTCTTCCTCGCCAAGC 59.547 55.000 0.00 0.00 0.00 4.01
9188 11707 1.340017 CCTTCCAATTCTTCCTCGCCA 60.340 52.381 0.00 0.00 0.00 5.69
9209 11728 1.135315 CCATTCAAAGCCTCACGCG 59.865 57.895 3.53 3.53 44.76 6.01
9225 11744 0.464036 CGAGGATCCAATCGTTCCCA 59.536 55.000 15.82 0.00 34.30 4.37
9233 11752 3.889815 TGCTTGATTTCGAGGATCCAAT 58.110 40.909 15.82 4.48 0.00 3.16
9244 11763 1.468054 GGCGGTGTCATGCTTGATTTC 60.468 52.381 5.49 0.30 33.56 2.17
9376 11895 0.300789 GCAGTGCTCGCCGTTTATAC 59.699 55.000 8.18 0.00 0.00 1.47


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

AutoCloner maintained by Alex Coulton.