Multiple sequence alignment - TraesCS2B01G440400

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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 TraesCS2B01G440400 chr2B 100.000 7002 0 0 1 7002 632410874 632403873 0.000000e+00 12931.0
1 TraesCS2B01G440400 chr2B 79.588 534 88 11 6467 7000 526777375 526776863 5.160000e-96 363.0
2 TraesCS2B01G440400 chr2A 95.255 2824 92 21 1675 4482 676990409 676987612 0.000000e+00 4434.0
3 TraesCS2B01G440400 chr2A 96.743 1136 35 2 4481 5615 676987568 676986434 0.000000e+00 1892.0
4 TraesCS2B01G440400 chr2A 92.238 889 33 8 6119 7002 676985821 676984964 0.000000e+00 1227.0
5 TraesCS2B01G440400 chr2A 92.240 799 35 13 713 1494 676991310 676990522 0.000000e+00 1107.0
6 TraesCS2B01G440400 chr2A 92.143 700 24 8 5612 6281 676986357 676985659 0.000000e+00 959.0
7 TraesCS2B01G440400 chr2A 79.626 535 86 13 6467 7000 591279140 591278628 5.160000e-96 363.0
8 TraesCS2B01G440400 chr2A 79.930 284 52 4 6721 7000 592092285 592092003 3.310000e-48 204.0
9 TraesCS2B01G440400 chr2A 88.298 94 10 1 543 635 676993060 676992967 2.060000e-20 111.0
10 TraesCS2B01G440400 chr2D 96.112 2212 71 7 2272 4482 532431386 532429189 0.000000e+00 3594.0
11 TraesCS2B01G440400 chr2D 94.505 1092 51 6 4481 5566 532429147 532428059 0.000000e+00 1676.0
12 TraesCS2B01G440400 chr2D 88.197 1398 78 22 5659 7000 532427742 532426376 0.000000e+00 1587.0
13 TraesCS2B01G440400 chr2D 91.150 1130 64 20 540 1647 532433030 532431915 0.000000e+00 1500.0
14 TraesCS2B01G440400 chr2D 95.064 547 20 4 1668 2207 532431929 532431383 0.000000e+00 854.0
15 TraesCS2B01G440400 chr2D 92.778 360 10 8 67 416 532434709 532434356 2.250000e-139 507.0
16 TraesCS2B01G440400 chr2D 78.868 530 91 11 6471 7000 446943165 446942657 8.700000e-89 339.0
17 TraesCS2B01G440400 chr2D 77.852 298 63 2 6706 7000 447322301 447322004 1.550000e-41 182.0
18 TraesCS2B01G440400 chr1A 86.667 1050 91 26 1720 2743 354537903 354536877 0.000000e+00 1118.0
19 TraesCS2B01G440400 chr1A 87.627 493 44 8 2052 2535 68840290 68839806 2.210000e-154 556.0
20 TraesCS2B01G440400 chr1A 95.385 65 3 0 1 65 571781688 571781752 3.450000e-18 104.0
21 TraesCS2B01G440400 chr5A 86.013 1051 85 36 1720 2743 565722047 565721032 0.000000e+00 1070.0
22 TraesCS2B01G440400 chr5A 85.269 577 56 17 2052 2624 437060892 437061443 1.020000e-157 568.0
23 TraesCS2B01G440400 chr5A 87.830 493 42 9 2052 2535 137465581 137465098 4.740000e-156 562.0
24 TraesCS2B01G440400 chr5A 79.588 534 86 15 6468 7000 582982073 582981562 1.860000e-95 361.0
25 TraesCS2B01G440400 chr5A 100.000 28 0 0 520 547 129721444 129721417 1.300000e-02 52.8
26 TraesCS2B01G440400 chr4D 88.235 493 40 9 2052 2535 342544040 342543557 2.190000e-159 573.0
27 TraesCS2B01G440400 chr4A 88.032 493 41 9 2052 2535 623443239 623442756 1.020000e-157 568.0
28 TraesCS2B01G440400 chr4A 85.095 577 58 16 2052 2624 625983243 625982691 1.320000e-156 564.0
29 TraesCS2B01G440400 chr4A 94.286 70 4 0 1 70 631641330 631641399 2.670000e-19 108.0
30 TraesCS2B01G440400 chr5D 87.625 501 44 9 1720 2202 496309545 496310045 3.670000e-157 566.0
31 TraesCS2B01G440400 chr5D 79.478 536 85 18 6467 7000 463088580 463088068 2.400000e-94 357.0
32 TraesCS2B01G440400 chr5D 100.000 28 0 0 519 546 312115156 312115129 1.300000e-02 52.8
33 TraesCS2B01G440400 chr4B 85.396 493 54 8 2052 2535 255356140 255356623 4.880000e-136 496.0
34 TraesCS2B01G440400 chr3A 87.244 439 40 7 2052 2481 410099222 410098791 2.940000e-133 486.0
35 TraesCS2B01G440400 chr5B 78.026 537 91 19 6467 7000 569826669 569826157 5.270000e-81 313.0
36 TraesCS2B01G440400 chr7A 80.851 282 45 8 3913 4191 487710604 487710879 5.500000e-51 213.0
37 TraesCS2B01G440400 chr7A 85.321 109 16 0 2569 2677 546576853 546576961 5.740000e-21 113.0
38 TraesCS2B01G440400 chr1B 89.764 127 11 2 2557 2681 632026978 632027104 2.020000e-35 161.0
39 TraesCS2B01G440400 chr1B 84.375 64 7 2 489 550 561754427 561754365 7.580000e-05 60.2
40 TraesCS2B01G440400 chr7B 85.321 109 16 0 2569 2677 467532754 467532646 5.740000e-21 113.0
41 TraesCS2B01G440400 chr7B 95.455 66 3 0 1 66 147573617 147573552 9.610000e-19 106.0
42 TraesCS2B01G440400 chr7B 100.000 28 0 0 521 548 131378687 131378660 1.300000e-02 52.8
43 TraesCS2B01G440400 chr6A 96.923 65 2 0 1 65 115017530 115017594 7.430000e-20 110.0
44 TraesCS2B01G440400 chr6B 96.875 64 2 0 2 65 10037114 10037177 2.670000e-19 108.0
45 TraesCS2B01G440400 chr6B 94.366 71 3 1 1 71 711511009 711511078 2.670000e-19 108.0
46 TraesCS2B01G440400 chr6B 94.203 69 4 0 1 69 89204373 89204305 9.610000e-19 106.0
47 TraesCS2B01G440400 chr6B 89.091 55 5 1 494 547 405058561 405058507 4.530000e-07 67.6
48 TraesCS2B01G440400 chr3B 95.588 68 2 1 1 68 821157119 821157185 2.670000e-19 108.0
49 TraesCS2B01G440400 chr3B 93.333 60 3 1 489 547 809139461 809139520 3.480000e-13 87.9
50 TraesCS2B01G440400 chr7D 96.774 62 2 0 2 63 27230249 27230310 3.450000e-18 104.0
51 TraesCS2B01G440400 chr7D 90.000 60 5 1 489 547 109147211 109147152 7.530000e-10 76.8
52 TraesCS2B01G440400 chr1D 86.667 60 7 1 489 547 455075337 455075278 1.630000e-06 65.8


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 TraesCS2B01G440400 chr2B 632403873 632410874 7001 True 12931.000000 12931 100.000000 1 7002 1 chr2B.!!$R2 7001
1 TraesCS2B01G440400 chr2B 526776863 526777375 512 True 363.000000 363 79.588000 6467 7000 1 chr2B.!!$R1 533
2 TraesCS2B01G440400 chr2A 676984964 676993060 8096 True 1621.666667 4434 92.819500 543 7002 6 chr2A.!!$R3 6459
3 TraesCS2B01G440400 chr2A 591278628 591279140 512 True 363.000000 363 79.626000 6467 7000 1 chr2A.!!$R1 533
4 TraesCS2B01G440400 chr2D 532426376 532434709 8333 True 1619.666667 3594 92.967667 67 7000 6 chr2D.!!$R3 6933
5 TraesCS2B01G440400 chr2D 446942657 446943165 508 True 339.000000 339 78.868000 6471 7000 1 chr2D.!!$R1 529
6 TraesCS2B01G440400 chr1A 354536877 354537903 1026 True 1118.000000 1118 86.667000 1720 2743 1 chr1A.!!$R2 1023
7 TraesCS2B01G440400 chr5A 565721032 565722047 1015 True 1070.000000 1070 86.013000 1720 2743 1 chr5A.!!$R3 1023
8 TraesCS2B01G440400 chr5A 437060892 437061443 551 False 568.000000 568 85.269000 2052 2624 1 chr5A.!!$F1 572
9 TraesCS2B01G440400 chr5A 582981562 582982073 511 True 361.000000 361 79.588000 6468 7000 1 chr5A.!!$R4 532
10 TraesCS2B01G440400 chr4A 625982691 625983243 552 True 564.000000 564 85.095000 2052 2624 1 chr4A.!!$R2 572
11 TraesCS2B01G440400 chr5D 496309545 496310045 500 False 566.000000 566 87.625000 1720 2202 1 chr5D.!!$F1 482
12 TraesCS2B01G440400 chr5D 463088068 463088580 512 True 357.000000 357 79.478000 6467 7000 1 chr5D.!!$R2 533
13 TraesCS2B01G440400 chr5B 569826157 569826669 512 True 313.000000 313 78.026000 6467 7000 1 chr5B.!!$R1 533

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
496 507 0.104120 CGGCAGGATCATACGGTCAA 59.896 55.000 0.00 0.00 0.00 3.18 F
965 3786 0.107606 TCTCTCCTCTCCGACGGAAG 60.108 60.000 18.93 16.62 0.00 3.46 F
1654 4505 0.036105 AGACATCCAGATTGTGCGCA 60.036 50.000 5.66 5.66 0.00 6.09 F
1879 4730 0.453390 GCTTACAAGGGCATGCAGAC 59.547 55.000 21.36 9.13 0.00 3.51 F
2034 4905 1.920734 ATCCACTGGGGCGTATGCAA 61.921 55.000 9.59 0.00 45.35 4.08 F
3725 6699 3.662247 ACAGAGGTACTTTGAGTTCCG 57.338 47.619 0.00 0.00 43.96 4.30 F
4909 7932 1.332889 ATCCGATGTCAGCTGAGCCA 61.333 55.000 18.89 13.39 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1563 4413 1.614850 GGAATGTTTTGACCCCGCCTA 60.615 52.381 0.00 0.00 0.00 3.93 R
2017 4888 2.045438 TTGCATACGCCCCAGTGG 60.045 61.111 0.63 0.63 37.32 4.00 R
2998 5971 1.756538 TCTCTGTAGATGCGAATGCCA 59.243 47.619 0.00 0.00 41.78 4.92 R
3845 6820 2.736347 ACTAGGTGGTAGGTACTGCTG 58.264 52.381 0.00 0.00 42.03 4.41 R
3847 6822 3.895998 AGTACTAGGTGGTAGGTACTGC 58.104 50.000 0.00 0.00 41.52 4.40 R
4927 7950 0.601558 TACGCAGACGAAAGAGCCTT 59.398 50.000 0.00 0.00 43.93 4.35 R
6026 9315 0.104304 AGACCATCGGCCGACATTAC 59.896 55.000 33.75 20.15 0.00 1.89 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
29 30 4.295381 AAAAACGGACAAAGCGCG 57.705 50.000 0.00 0.00 0.00 6.86
30 31 1.942223 AAAAACGGACAAAGCGCGC 60.942 52.632 26.66 26.66 0.00 6.86
31 32 4.659874 AAACGGACAAAGCGCGCG 62.660 61.111 28.44 28.44 0.00 6.86
38 39 4.659874 CAAAGCGCGCGTCCGTTT 62.660 61.111 32.35 21.22 36.67 3.60
39 40 4.659874 AAAGCGCGCGTCCGTTTG 62.660 61.111 32.35 0.04 36.67 2.93
47 48 3.110178 CGTCCGTTTGGGTCGCTC 61.110 66.667 0.00 0.00 40.30 5.03
48 49 2.741211 GTCCGTTTGGGTCGCTCC 60.741 66.667 0.00 0.00 37.00 4.70
49 50 4.367023 TCCGTTTGGGTCGCTCCG 62.367 66.667 0.00 0.00 37.00 4.63
50 51 4.675029 CCGTTTGGGTCGCTCCGT 62.675 66.667 0.00 0.00 37.00 4.69
51 52 2.663852 CGTTTGGGTCGCTCCGTT 60.664 61.111 0.00 0.00 37.00 4.44
52 53 2.943653 GTTTGGGTCGCTCCGTTG 59.056 61.111 0.00 0.00 37.00 4.10
53 54 1.595929 GTTTGGGTCGCTCCGTTGA 60.596 57.895 0.00 0.00 37.00 3.18
54 55 1.146485 TTTGGGTCGCTCCGTTGAA 59.854 52.632 0.00 0.00 37.00 2.69
55 56 0.882927 TTTGGGTCGCTCCGTTGAAG 60.883 55.000 0.00 0.00 37.00 3.02
56 57 2.035237 TTGGGTCGCTCCGTTGAAGT 62.035 55.000 0.00 0.00 37.00 3.01
57 58 1.301479 GGGTCGCTCCGTTGAAGTT 60.301 57.895 0.00 0.00 37.00 2.66
58 59 1.566018 GGGTCGCTCCGTTGAAGTTG 61.566 60.000 0.00 0.00 37.00 3.16
59 60 1.204312 GTCGCTCCGTTGAAGTTGC 59.796 57.895 0.00 0.00 0.00 4.17
60 61 1.069090 TCGCTCCGTTGAAGTTGCT 59.931 52.632 0.00 0.00 0.00 3.91
61 62 0.944311 TCGCTCCGTTGAAGTTGCTC 60.944 55.000 0.00 0.00 0.00 4.26
62 63 0.946221 CGCTCCGTTGAAGTTGCTCT 60.946 55.000 0.00 0.00 0.00 4.09
63 64 1.230324 GCTCCGTTGAAGTTGCTCTT 58.770 50.000 0.00 0.00 39.32 2.85
64 65 2.413837 GCTCCGTTGAAGTTGCTCTTA 58.586 47.619 0.00 0.00 36.40 2.10
65 66 3.003480 GCTCCGTTGAAGTTGCTCTTAT 58.997 45.455 0.00 0.00 36.40 1.73
83 84 0.241749 ATGTGCTGACGTGCAATTGG 59.758 50.000 7.72 0.00 45.12 3.16
106 107 1.065551 GTTGCAGCCGTGACTCTTTTT 59.934 47.619 0.00 0.00 0.00 1.94
156 157 2.434884 CGCTGTTGTCCCATCGCT 60.435 61.111 0.00 0.00 0.00 4.93
157 158 2.743752 CGCTGTTGTCCCATCGCTG 61.744 63.158 0.00 0.00 0.00 5.18
158 159 2.401766 GCTGTTGTCCCATCGCTGG 61.402 63.158 0.00 0.00 42.73 4.85
159 160 1.296392 CTGTTGTCCCATCGCTGGA 59.704 57.895 6.92 0.00 46.37 3.86
169 170 2.283529 ATCGCTGGACCTGGACGTT 61.284 57.895 0.00 0.00 0.00 3.99
231 236 3.072915 TCAGAAAGCTCTCCCACAAATGA 59.927 43.478 0.00 0.00 0.00 2.57
241 246 0.958091 CCACAAATGAGGGCAAACGA 59.042 50.000 0.00 0.00 0.00 3.85
256 261 4.000988 GCAAACGACCTCTGGATTAAAGA 58.999 43.478 0.00 0.00 0.00 2.52
263 268 6.155827 CGACCTCTGGATTAAAGATCTCATC 58.844 44.000 0.00 0.00 0.00 2.92
295 300 6.112734 ACCTACTAATGCAATTGAATCGACA 58.887 36.000 10.34 0.00 36.99 4.35
399 404 3.984838 CCAGAGCAGGCAGAGTATC 57.015 57.895 0.00 0.00 0.00 2.24
417 428 7.784470 GAGTATCTACTACCCTCCATTTCAT 57.216 40.000 0.00 0.00 36.50 2.57
418 429 8.880991 GAGTATCTACTACCCTCCATTTCATA 57.119 38.462 0.00 0.00 36.50 2.15
419 430 9.310449 GAGTATCTACTACCCTCCATTTCATAA 57.690 37.037 0.00 0.00 36.50 1.90
420 431 9.091220 AGTATCTACTACCCTCCATTTCATAAC 57.909 37.037 0.00 0.00 34.13 1.89
421 432 6.401047 TCTACTACCCTCCATTTCATAACG 57.599 41.667 0.00 0.00 0.00 3.18
422 433 5.895534 TCTACTACCCTCCATTTCATAACGT 59.104 40.000 0.00 0.00 0.00 3.99
424 435 6.549433 ACTACCCTCCATTTCATAACGTAA 57.451 37.500 0.00 0.00 0.00 3.18
426 437 6.990349 ACTACCCTCCATTTCATAACGTAATG 59.010 38.462 0.00 0.00 33.42 1.90
427 438 4.578928 ACCCTCCATTTCATAACGTAATGC 59.421 41.667 3.00 0.00 32.56 3.56
437 448 2.773480 CGTAATGCGTCCGCGTTT 59.227 55.556 22.31 13.29 46.84 3.60
438 449 1.131016 CGTAATGCGTCCGCGTTTT 59.869 52.632 22.31 11.04 46.84 2.43
478 489 8.839947 TGATCATAAATTTAACAATGTGAGCG 57.160 30.769 1.21 0.00 0.00 5.03
479 490 7.914871 TGATCATAAATTTAACAATGTGAGCGG 59.085 33.333 1.21 0.00 0.00 5.52
480 491 6.033341 TCATAAATTTAACAATGTGAGCGGC 58.967 36.000 1.21 0.00 0.00 6.53
482 493 2.987413 TTTAACAATGTGAGCGGCAG 57.013 45.000 1.45 0.00 0.00 4.85
483 494 1.164411 TTAACAATGTGAGCGGCAGG 58.836 50.000 1.45 0.00 0.00 4.85
484 495 0.323302 TAACAATGTGAGCGGCAGGA 59.677 50.000 1.45 0.00 0.00 3.86
485 496 0.322816 AACAATGTGAGCGGCAGGAT 60.323 50.000 1.45 0.00 0.00 3.24
486 497 0.745845 ACAATGTGAGCGGCAGGATC 60.746 55.000 1.45 0.00 0.00 3.36
487 498 0.745486 CAATGTGAGCGGCAGGATCA 60.745 55.000 1.45 0.00 39.09 2.92
489 500 1.051008 ATGTGAGCGGCAGGATCATA 58.949 50.000 1.45 0.00 44.00 2.15
490 501 0.104855 TGTGAGCGGCAGGATCATAC 59.895 55.000 1.45 0.00 44.00 2.39
491 502 0.941463 GTGAGCGGCAGGATCATACG 60.941 60.000 1.45 0.00 44.00 3.06
492 503 1.373497 GAGCGGCAGGATCATACGG 60.373 63.158 1.45 0.00 0.00 4.02
493 504 2.088674 GAGCGGCAGGATCATACGGT 62.089 60.000 1.45 7.84 38.03 4.83
494 505 1.664965 GCGGCAGGATCATACGGTC 60.665 63.158 0.00 0.00 0.00 4.79
495 506 1.739667 CGGCAGGATCATACGGTCA 59.260 57.895 0.00 0.00 0.00 4.02
496 507 0.104120 CGGCAGGATCATACGGTCAA 59.896 55.000 0.00 0.00 0.00 3.18
497 508 1.472552 CGGCAGGATCATACGGTCAAA 60.473 52.381 0.00 0.00 0.00 2.69
498 509 1.940613 GGCAGGATCATACGGTCAAAC 59.059 52.381 0.00 0.00 0.00 2.93
499 510 2.420129 GGCAGGATCATACGGTCAAACT 60.420 50.000 0.00 0.00 0.00 2.66
500 511 3.270877 GCAGGATCATACGGTCAAACTT 58.729 45.455 0.00 0.00 0.00 2.66
501 512 4.439057 GCAGGATCATACGGTCAAACTTA 58.561 43.478 0.00 0.00 0.00 2.24
502 513 4.873827 GCAGGATCATACGGTCAAACTTAA 59.126 41.667 0.00 0.00 0.00 1.85
504 515 6.038271 GCAGGATCATACGGTCAAACTTAAAT 59.962 38.462 0.00 0.00 0.00 1.40
505 516 7.630924 CAGGATCATACGGTCAAACTTAAATC 58.369 38.462 0.00 0.00 0.00 2.17
506 517 7.495934 CAGGATCATACGGTCAAACTTAAATCT 59.504 37.037 0.00 0.00 0.00 2.40
507 518 8.047310 AGGATCATACGGTCAAACTTAAATCTT 58.953 33.333 0.00 0.00 0.00 2.40
510 521 8.610248 TCATACGGTCAAACTTAAATCTTGAA 57.390 30.769 0.00 0.00 31.21 2.69
512 523 9.672086 CATACGGTCAAACTTAAATCTTGAAAA 57.328 29.630 0.00 0.00 31.21 2.29
516 527 8.837059 CGGTCAAACTTAAATCTTGAAAATACG 58.163 33.333 0.00 0.00 31.21 3.06
517 528 9.887406 GGTCAAACTTAAATCTTGAAAATACGA 57.113 29.630 0.00 0.00 31.21 3.43
522 533 7.577979 ACTTAAATCTTGAAAATACGAACGCA 58.422 30.769 0.00 0.00 0.00 5.24
523 534 7.532884 ACTTAAATCTTGAAAATACGAACGCAC 59.467 33.333 0.00 0.00 0.00 5.34
524 535 5.607119 AATCTTGAAAATACGAACGCACT 57.393 34.783 0.00 0.00 0.00 4.40
525 536 6.715344 AATCTTGAAAATACGAACGCACTA 57.285 33.333 0.00 0.00 0.00 2.74
527 538 7.997107 ATCTTGAAAATACGAACGCACTATA 57.003 32.000 0.00 0.00 0.00 1.31
529 540 8.415192 TCTTGAAAATACGAACGCACTATATT 57.585 30.769 0.00 0.00 0.00 1.28
530 541 9.518906 TCTTGAAAATACGAACGCACTATATTA 57.481 29.630 0.00 0.00 0.00 0.98
533 544 9.465985 TGAAAATACGAACGCACTATATTATGA 57.534 29.630 0.00 0.00 0.00 2.15
539 550 6.926826 ACGAACGCACTATATTATGAAATGGA 59.073 34.615 0.00 0.00 0.00 3.41
540 551 7.116376 ACGAACGCACTATATTATGAAATGGAG 59.884 37.037 0.00 0.00 0.00 3.86
541 552 7.411912 CGAACGCACTATATTATGAAATGGAGG 60.412 40.741 0.00 0.00 0.00 4.30
570 1783 1.742831 GTATTTCAGAATGGCCGCACA 59.257 47.619 0.00 0.00 36.16 4.57
574 1787 1.138036 CAGAATGGCCGCACATGTG 59.862 57.895 21.83 21.83 0.00 3.21
638 1852 6.359964 GCGTGTTAGCGAGATTATTAGTAC 57.640 41.667 0.00 0.00 0.00 2.73
639 1853 5.057767 GCGTGTTAGCGAGATTATTAGTACG 59.942 44.000 0.00 0.00 0.00 3.67
640 1854 6.132056 CGTGTTAGCGAGATTATTAGTACGT 58.868 40.000 0.00 0.00 0.00 3.57
641 1855 7.283633 CGTGTTAGCGAGATTATTAGTACGTA 58.716 38.462 0.00 0.00 0.00 3.57
707 3522 3.479489 ACACACACATGACACATCACAT 58.521 40.909 0.00 0.00 37.79 3.21
748 3563 3.305398 AAAGATGCGAGAAGAAGACGT 57.695 42.857 0.00 0.00 0.00 4.34
802 3619 0.867753 GTGTGTCTGCGCTCGGATAG 60.868 60.000 9.73 0.00 0.00 2.08
923 3744 4.026300 CGCAGGTCTCTCTCCCTT 57.974 61.111 0.00 0.00 0.00 3.95
924 3745 3.192799 CGCAGGTCTCTCTCCCTTA 57.807 57.895 0.00 0.00 0.00 2.69
965 3786 0.107606 TCTCTCCTCTCCGACGGAAG 60.108 60.000 18.93 16.62 0.00 3.46
974 3795 3.257561 CGACGGAAGCAGCCATCG 61.258 66.667 0.00 0.00 0.00 3.84
1096 3923 2.301738 CCCTCCCCTTTCTTCCGCT 61.302 63.158 0.00 0.00 0.00 5.52
1347 4192 2.969628 ATTTGTTCTCGATCCGCTCT 57.030 45.000 0.00 0.00 0.00 4.09
1348 4193 2.279582 TTTGTTCTCGATCCGCTCTC 57.720 50.000 0.00 0.00 0.00 3.20
1359 4204 3.842923 CGCTCTCCGGTGATGGCT 61.843 66.667 6.68 0.00 0.00 4.75
1417 4262 7.141758 TGGAATCTACCTTTATGCTTCTGAT 57.858 36.000 0.00 0.00 0.00 2.90
1420 4265 7.387397 GGAATCTACCTTTATGCTTCTGATGAG 59.613 40.741 0.00 0.00 0.00 2.90
1525 4375 2.749280 TCTGTGCACCAGATGTACTG 57.251 50.000 15.69 0.00 45.34 2.74
1563 4413 5.053978 AGTTGGGAATCACTCTGTTCTTT 57.946 39.130 0.00 0.00 0.00 2.52
1574 4424 0.323629 CTGTTCTTTAGGCGGGGTCA 59.676 55.000 0.00 0.00 0.00 4.02
1643 4494 7.572814 TGGTTATGATCAATGTTAGACATCCA 58.427 34.615 0.00 0.00 37.97 3.41
1644 4495 7.716560 TGGTTATGATCAATGTTAGACATCCAG 59.283 37.037 0.00 0.00 37.97 3.86
1645 4496 7.933577 GGTTATGATCAATGTTAGACATCCAGA 59.066 37.037 0.00 0.00 37.97 3.86
1646 4497 9.499479 GTTATGATCAATGTTAGACATCCAGAT 57.501 33.333 0.00 0.00 37.97 2.90
1648 4499 7.797038 TGATCAATGTTAGACATCCAGATTG 57.203 36.000 0.00 0.00 37.97 2.67
1649 4500 7.341030 TGATCAATGTTAGACATCCAGATTGT 58.659 34.615 0.00 0.00 37.97 2.71
1650 4501 6.990341 TCAATGTTAGACATCCAGATTGTG 57.010 37.500 0.00 0.00 37.97 3.33
1651 4502 5.355071 TCAATGTTAGACATCCAGATTGTGC 59.645 40.000 0.00 0.00 37.97 4.57
1652 4503 3.261580 TGTTAGACATCCAGATTGTGCG 58.738 45.455 0.00 0.00 0.00 5.34
1653 4504 1.939974 TAGACATCCAGATTGTGCGC 58.060 50.000 0.00 0.00 0.00 6.09
1654 4505 0.036105 AGACATCCAGATTGTGCGCA 60.036 50.000 5.66 5.66 0.00 6.09
1655 4506 0.804364 GACATCCAGATTGTGCGCAA 59.196 50.000 14.00 16.21 39.16 4.85
1656 4507 1.199789 GACATCCAGATTGTGCGCAAA 59.800 47.619 17.92 2.45 38.21 3.68
1657 4508 1.612950 ACATCCAGATTGTGCGCAAAA 59.387 42.857 16.81 16.81 38.21 2.44
1658 4509 2.035704 ACATCCAGATTGTGCGCAAAAA 59.964 40.909 18.56 13.26 38.21 1.94
1714 4565 6.992063 ATGACATGATTGTTCCACTACTTC 57.008 37.500 0.00 0.00 35.79 3.01
1726 4577 2.126228 TACTTCCGCAGCCGTTCG 60.126 61.111 0.00 0.00 0.00 3.95
1879 4730 0.453390 GCTTACAAGGGCATGCAGAC 59.547 55.000 21.36 9.13 0.00 3.51
1957 4808 6.017440 CGAACTCAACTGAAGAAAATGGGTAA 60.017 38.462 0.00 0.00 0.00 2.85
2034 4905 1.920734 ATCCACTGGGGCGTATGCAA 61.921 55.000 9.59 0.00 45.35 4.08
2239 5192 8.334632 GTTTACTTTGCTTGCAATGTAACATTT 58.665 29.630 29.45 11.95 35.70 2.32
2240 5193 6.289745 ACTTTGCTTGCAATGTAACATTTG 57.710 33.333 20.28 0.00 0.00 2.32
2246 5199 8.599055 TGCTTGCAATGTAACATTTGATTTTA 57.401 26.923 0.00 0.00 0.00 1.52
2259 5212 9.783081 AACATTTGATTTTAGAAATGGAAGCTT 57.217 25.926 0.00 0.00 41.78 3.74
2498 5460 6.655078 AATACCCTGCATCACCATTTTATC 57.345 37.500 0.00 0.00 0.00 1.75
2894 5867 7.870027 ACTACTGACCATTTCCTACTCTACTA 58.130 38.462 0.00 0.00 0.00 1.82
2998 5971 8.559536 CAATATATGTTGCTCTTACCGTCATTT 58.440 33.333 0.00 0.00 0.00 2.32
3683 6657 5.250543 TCACTTCAATATTCTTGGGGTCTCA 59.749 40.000 0.00 0.00 0.00 3.27
3725 6699 3.662247 ACAGAGGTACTTTGAGTTCCG 57.338 47.619 0.00 0.00 43.96 4.30
3845 6820 8.519799 TCCTTGTTATGTGGATATTTCTTTCC 57.480 34.615 0.00 0.00 0.00 3.13
3847 6822 8.408601 CCTTGTTATGTGGATATTTCTTTCCAG 58.591 37.037 0.00 0.00 42.55 3.86
3858 6833 3.975168 TTCTTTCCAGCAGTACCTACC 57.025 47.619 0.00 0.00 0.00 3.18
4024 6999 1.821332 CTGGCGCTTCCATCTTCCC 60.821 63.158 7.64 0.00 45.50 3.97
4139 7114 4.660789 AGAATTTGCAACAAGACTTGCT 57.339 36.364 15.24 0.00 45.79 3.91
4186 7161 5.104277 TCAAGGAAGGACCAGAAACAGTAAA 60.104 40.000 0.00 0.00 42.04 2.01
4198 7173 6.687105 CCAGAAACAGTAAAGTTTTCTTGTCG 59.313 38.462 0.00 0.00 41.48 4.35
4211 7186 7.305474 AGTTTTCTTGTCGCCAAACTTATATG 58.695 34.615 0.00 0.00 36.29 1.78
4230 7205 2.930950 TGTATGCAATAGGTCCCAAGC 58.069 47.619 0.00 0.00 0.00 4.01
4245 7220 3.130516 TCCCAAGCATACTACTTGACTCG 59.869 47.826 5.12 0.00 45.99 4.18
4327 7302 2.192263 GTCATCCCTCCTCCAAAGACT 58.808 52.381 0.00 0.00 0.00 3.24
4446 7421 6.431234 ACTGTTAAATTCCAGTGAAGCTAAGG 59.569 38.462 0.00 0.00 40.30 2.69
4455 7430 4.691216 CCAGTGAAGCTAAGGTTACACTTC 59.309 45.833 0.00 0.00 37.77 3.01
4458 7433 4.638304 TGAAGCTAAGGTTACACTTCACC 58.362 43.478 0.00 0.00 41.20 4.02
4472 7447 4.452455 ACACTTCACCGAGCTTTCTAAATG 59.548 41.667 0.00 0.00 0.00 2.32
4476 7451 3.436704 TCACCGAGCTTTCTAAATGCTTG 59.563 43.478 7.50 7.50 37.16 4.01
4477 7452 2.162408 ACCGAGCTTTCTAAATGCTTGC 59.838 45.455 8.55 0.00 37.01 4.01
4479 7454 3.119708 CCGAGCTTTCTAAATGCTTGCTT 60.120 43.478 8.55 0.00 37.01 3.91
4495 7514 4.082354 GCTTGCTTCAGAATCCACAGAAAT 60.082 41.667 0.00 0.00 0.00 2.17
4496 7515 5.381174 TTGCTTCAGAATCCACAGAAATG 57.619 39.130 0.00 0.00 0.00 2.32
4505 7524 1.686052 TCCACAGAAATGTTGTTGCCC 59.314 47.619 0.00 0.00 0.00 5.36
4526 7545 4.100498 CCCGATGAACCCTTAAAGCTAGTA 59.900 45.833 0.00 0.00 0.00 1.82
4752 7775 6.750501 TCTGTATGCAGTCGTTATTAACTGAC 59.249 38.462 10.80 16.71 44.54 3.51
4909 7932 1.332889 ATCCGATGTCAGCTGAGCCA 61.333 55.000 18.89 13.39 0.00 4.75
4914 7937 3.200593 GTCAGCTGAGCCATGCCG 61.201 66.667 18.89 0.00 0.00 5.69
4927 7950 3.055963 AGCCATGCCGATTTCATGAAAAA 60.056 39.130 23.91 3.45 42.84 1.94
5189 8213 2.277591 TGGCCATCCAGTTGCTTGC 61.278 57.895 0.00 0.00 37.47 4.01
5610 8691 5.023533 TCTCACTGGAGCATTGTTATACC 57.976 43.478 0.00 0.00 41.13 2.73
5667 8936 3.637229 CTGGTCGTGTTCCAGGATATACT 59.363 47.826 4.27 0.00 46.03 2.12
5674 8943 6.038356 CGTGTTCCAGGATATACTTACGTTT 58.962 40.000 0.00 0.00 0.00 3.60
5738 9008 5.063204 GCATATTCAGGTGTTGGTGCTATA 58.937 41.667 0.00 0.00 0.00 1.31
5810 9080 1.141657 AGCATTATGATGTCACCGCCT 59.858 47.619 0.00 0.00 35.63 5.52
5825 9095 1.595093 CGCCTTTGACAATGACCCCC 61.595 60.000 2.74 0.00 0.00 5.40
5861 9134 8.954950 ATGAGGTAAGATCAGAAATAACAGTG 57.045 34.615 0.00 0.00 0.00 3.66
5872 9145 5.018809 AGAAATAACAGTGGCACCATCATT 58.981 37.500 15.27 6.66 0.00 2.57
5902 9191 1.033574 CTCCGGATACCACTGGACTC 58.966 60.000 3.57 0.00 40.00 3.36
5957 9246 5.105554 AGCATATACGGAGAAGCTATGAAGG 60.106 44.000 0.00 0.00 0.00 3.46
5959 9248 1.195115 ACGGAGAAGCTATGAAGGCA 58.805 50.000 0.00 0.00 0.00 4.75
6026 9315 0.736636 ATGCAGCACAACGATGATGG 59.263 50.000 0.00 0.00 36.48 3.51
6035 9324 3.001228 CACAACGATGATGGTAATGTCGG 59.999 47.826 0.00 0.00 36.68 4.79
6064 9358 5.041940 GGTCTCGGATGTGTACAGAATAAC 58.958 45.833 0.00 0.00 0.00 1.89
6065 9359 5.041940 GTCTCGGATGTGTACAGAATAACC 58.958 45.833 0.00 0.00 0.00 2.85
6116 9410 2.910688 ACGGACACTGTTCTTGATGT 57.089 45.000 0.00 0.00 0.00 3.06
6145 9468 4.952262 ATGGTGATTGACGACTTGATTG 57.048 40.909 0.00 0.00 0.00 2.67
6215 9539 6.019881 GCCAAATAAAGCCGTTTATAAGCTTG 60.020 38.462 9.86 0.00 45.77 4.01
6216 9540 6.019881 CCAAATAAAGCCGTTTATAAGCTTGC 60.020 38.462 9.86 1.40 45.77 4.01
6243 9567 7.819415 CCACTTTGATAATCTCTTGTACTGACA 59.181 37.037 0.00 0.00 0.00 3.58
6244 9568 8.651588 CACTTTGATAATCTCTTGTACTGACAC 58.348 37.037 0.00 0.00 34.48 3.67
6245 9569 8.367911 ACTTTGATAATCTCTTGTACTGACACA 58.632 33.333 0.00 0.00 34.48 3.72
6246 9570 9.208022 CTTTGATAATCTCTTGTACTGACACAA 57.792 33.333 0.00 0.00 34.48 3.33
6247 9571 9.725019 TTTGATAATCTCTTGTACTGACACAAT 57.275 29.630 0.00 0.00 37.75 2.71
6248 9572 9.725019 TTGATAATCTCTTGTACTGACACAATT 57.275 29.630 0.00 0.00 37.75 2.32
6249 9573 9.725019 TGATAATCTCTTGTACTGACACAATTT 57.275 29.630 0.00 0.00 37.75 1.82
6250 9574 9.979270 GATAATCTCTTGTACTGACACAATTTG 57.021 33.333 0.00 0.00 37.75 2.32
6251 9575 9.725019 ATAATCTCTTGTACTGACACAATTTGA 57.275 29.630 2.79 0.00 37.75 2.69
6252 9576 8.450578 AATCTCTTGTACTGACACAATTTGAA 57.549 30.769 2.79 0.00 37.75 2.69
6284 9618 8.218338 TGAAAGAATTCCTTTGAGATCTATGC 57.782 34.615 0.65 0.00 44.63 3.14
6292 9626 1.040646 TGAGATCTATGCGTCCCCAC 58.959 55.000 0.00 0.00 0.00 4.61
6295 9629 1.689273 AGATCTATGCGTCCCCACTTC 59.311 52.381 0.00 0.00 0.00 3.01
6296 9630 0.759346 ATCTATGCGTCCCCACTTCC 59.241 55.000 0.00 0.00 0.00 3.46
6297 9631 0.616395 TCTATGCGTCCCCACTTCCA 60.616 55.000 0.00 0.00 0.00 3.53
6298 9632 0.469917 CTATGCGTCCCCACTTCCAT 59.530 55.000 0.00 0.00 0.00 3.41
6299 9633 0.180171 TATGCGTCCCCACTTCCATG 59.820 55.000 0.00 0.00 0.00 3.66
6300 9634 1.561769 ATGCGTCCCCACTTCCATGA 61.562 55.000 0.00 0.00 0.00 3.07
6301 9635 1.450312 GCGTCCCCACTTCCATGAG 60.450 63.158 0.00 0.00 0.00 2.90
6302 9636 1.899437 GCGTCCCCACTTCCATGAGA 61.899 60.000 0.00 0.00 0.00 3.27
6303 9637 0.108138 CGTCCCCACTTCCATGAGAC 60.108 60.000 0.00 0.00 0.00 3.36
6304 9638 1.280457 GTCCCCACTTCCATGAGACT 58.720 55.000 0.00 0.00 0.00 3.24
6305 9639 1.065854 GTCCCCACTTCCATGAGACTG 60.066 57.143 0.00 0.00 0.00 3.51
6306 9640 0.393537 CCCCACTTCCATGAGACTGC 60.394 60.000 0.00 0.00 0.00 4.40
6307 9641 0.325933 CCCACTTCCATGAGACTGCA 59.674 55.000 0.00 0.00 0.00 4.41
6308 9642 1.678123 CCCACTTCCATGAGACTGCAG 60.678 57.143 13.48 13.48 0.00 4.41
6309 9643 1.678123 CCACTTCCATGAGACTGCAGG 60.678 57.143 19.93 0.00 0.00 4.85
6310 9644 0.617413 ACTTCCATGAGACTGCAGGG 59.383 55.000 19.93 8.44 40.92 4.45
6311 9645 0.107312 CTTCCATGAGACTGCAGGGG 60.107 60.000 19.93 9.31 40.03 4.79
6312 9646 0.547471 TTCCATGAGACTGCAGGGGA 60.547 55.000 19.93 11.47 40.03 4.81
6313 9647 1.222936 CCATGAGACTGCAGGGGAC 59.777 63.158 19.93 7.06 36.14 4.46
6314 9648 1.153489 CATGAGACTGCAGGGGACG 60.153 63.158 19.93 0.00 0.00 4.79
6315 9649 2.362369 ATGAGACTGCAGGGGACGG 61.362 63.158 19.93 0.00 0.00 4.79
6318 9652 4.083862 GACTGCAGGGGACGGACC 62.084 72.222 19.93 0.00 38.08 4.46
6346 9680 7.915397 ACCTATGTATGAATCGTTCAAAATTGC 59.085 33.333 4.87 0.00 43.95 3.56
6354 9710 6.700960 TGAATCGTTCAAAATTGCTGATGTTT 59.299 30.769 0.00 0.00 36.59 2.83
6358 9714 5.164254 CGTTCAAAATTGCTGATGTTTCTCG 60.164 40.000 0.00 0.00 0.00 4.04
6381 9737 5.163943 CGGAAGAGAAGGAACGAAAGAAATC 60.164 44.000 0.00 0.00 0.00 2.17
6430 9806 4.704833 ATGGCTGCCTGACGCGTT 62.705 61.111 21.03 0.00 42.08 4.84
6431 9807 3.309436 ATGGCTGCCTGACGCGTTA 62.309 57.895 21.03 8.86 42.08 3.18
6432 9808 3.188786 GGCTGCCTGACGCGTTAG 61.189 66.667 22.91 22.91 42.08 2.34
6433 9809 3.854459 GCTGCCTGACGCGTTAGC 61.854 66.667 24.26 21.12 42.08 3.09
6536 9912 0.038067 CGTCGGACATGGTGTGGTAA 60.038 55.000 9.10 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.942223 GCGCGCTTTGTCCGTTTTT 60.942 52.632 26.67 0.00 0.00 1.94
13 14 2.353030 GCGCGCTTTGTCCGTTTT 60.353 55.556 26.67 0.00 0.00 2.43
14 15 4.659874 CGCGCGCTTTGTCCGTTT 62.660 61.111 30.48 0.00 0.00 3.60
21 22 4.659874 AAACGGACGCGCGCTTTG 62.660 61.111 32.58 19.69 0.00 2.77
22 23 4.659874 CAAACGGACGCGCGCTTT 62.660 61.111 32.58 19.12 0.00 3.51
31 32 2.741211 GGAGCGACCCAAACGGAC 60.741 66.667 0.00 0.00 34.64 4.79
32 33 4.367023 CGGAGCGACCCAAACGGA 62.367 66.667 0.00 0.00 34.64 4.69
33 34 4.675029 ACGGAGCGACCCAAACGG 62.675 66.667 0.00 0.00 34.64 4.44
34 35 2.663852 AACGGAGCGACCCAAACG 60.664 61.111 0.00 0.00 34.64 3.60
35 36 1.161563 TTCAACGGAGCGACCCAAAC 61.162 55.000 0.00 0.00 34.64 2.93
36 37 0.882927 CTTCAACGGAGCGACCCAAA 60.883 55.000 0.00 0.00 34.64 3.28
37 38 1.301401 CTTCAACGGAGCGACCCAA 60.301 57.895 0.00 0.00 34.64 4.12
38 39 2.035237 AACTTCAACGGAGCGACCCA 62.035 55.000 0.00 0.00 34.64 4.51
39 40 1.301479 AACTTCAACGGAGCGACCC 60.301 57.895 0.00 0.00 34.64 4.46
40 41 1.860078 CAACTTCAACGGAGCGACC 59.140 57.895 0.00 0.00 0.00 4.79
41 42 1.204312 GCAACTTCAACGGAGCGAC 59.796 57.895 0.00 0.00 0.00 5.19
42 43 0.944311 GAGCAACTTCAACGGAGCGA 60.944 55.000 0.00 0.00 0.00 4.93
43 44 0.946221 AGAGCAACTTCAACGGAGCG 60.946 55.000 0.00 0.00 0.00 5.03
44 45 1.230324 AAGAGCAACTTCAACGGAGC 58.770 50.000 0.00 0.00 32.91 4.70
45 46 3.997021 ACATAAGAGCAACTTCAACGGAG 59.003 43.478 0.00 0.00 39.72 4.63
46 47 3.745975 CACATAAGAGCAACTTCAACGGA 59.254 43.478 0.00 0.00 39.72 4.69
47 48 3.667960 GCACATAAGAGCAACTTCAACGG 60.668 47.826 0.00 0.00 39.72 4.44
48 49 3.187227 AGCACATAAGAGCAACTTCAACG 59.813 43.478 0.00 0.00 39.72 4.10
49 50 4.214119 TCAGCACATAAGAGCAACTTCAAC 59.786 41.667 0.00 0.00 39.72 3.18
50 51 4.214119 GTCAGCACATAAGAGCAACTTCAA 59.786 41.667 0.00 0.00 39.72 2.69
51 52 3.748048 GTCAGCACATAAGAGCAACTTCA 59.252 43.478 0.00 0.00 39.72 3.02
52 53 3.181526 CGTCAGCACATAAGAGCAACTTC 60.182 47.826 0.00 0.00 39.72 3.01
53 54 2.738846 CGTCAGCACATAAGAGCAACTT 59.261 45.455 2.10 2.10 42.04 2.66
54 55 2.289072 ACGTCAGCACATAAGAGCAACT 60.289 45.455 0.00 0.00 33.43 3.16
55 56 2.069273 ACGTCAGCACATAAGAGCAAC 58.931 47.619 0.00 0.00 33.43 4.17
56 57 2.068519 CACGTCAGCACATAAGAGCAA 58.931 47.619 0.00 0.00 33.43 3.91
57 58 1.713597 CACGTCAGCACATAAGAGCA 58.286 50.000 0.00 0.00 33.43 4.26
58 59 0.371645 GCACGTCAGCACATAAGAGC 59.628 55.000 0.00 0.00 0.00 4.09
59 60 1.713597 TGCACGTCAGCACATAAGAG 58.286 50.000 0.00 0.00 40.11 2.85
60 61 2.162319 TTGCACGTCAGCACATAAGA 57.838 45.000 0.00 0.00 45.61 2.10
61 62 3.165890 CAATTGCACGTCAGCACATAAG 58.834 45.455 0.00 0.00 45.61 1.73
62 63 2.095314 CCAATTGCACGTCAGCACATAA 60.095 45.455 0.00 0.00 45.61 1.90
63 64 1.468127 CCAATTGCACGTCAGCACATA 59.532 47.619 0.00 0.00 45.61 2.29
64 65 0.241749 CCAATTGCACGTCAGCACAT 59.758 50.000 0.00 0.00 45.61 3.21
65 66 1.653667 CCAATTGCACGTCAGCACA 59.346 52.632 0.00 0.00 45.61 4.57
83 84 2.959357 GAGTCACGGCTGCAACTGC 61.959 63.158 0.50 0.00 42.50 4.40
106 107 2.525629 TGGTTCCACCTCCAGCGA 60.526 61.111 0.00 0.00 39.58 4.93
156 157 3.948719 GGCCAACGTCCAGGTCCA 61.949 66.667 0.00 0.00 0.00 4.02
157 158 3.637273 AGGCCAACGTCCAGGTCC 61.637 66.667 5.01 5.24 0.00 4.46
158 159 2.358737 CAGGCCAACGTCCAGGTC 60.359 66.667 5.01 0.00 0.00 3.85
159 160 4.643387 GCAGGCCAACGTCCAGGT 62.643 66.667 5.01 0.00 0.00 4.00
160 161 4.641645 TGCAGGCCAACGTCCAGG 62.642 66.667 5.01 0.00 0.00 4.45
161 162 1.926511 GATTGCAGGCCAACGTCCAG 61.927 60.000 5.01 0.00 35.99 3.86
162 163 1.971167 GATTGCAGGCCAACGTCCA 60.971 57.895 5.01 0.00 35.99 4.02
225 230 1.200020 GAGGTCGTTTGCCCTCATTTG 59.800 52.381 0.00 0.00 45.47 2.32
231 236 1.201429 ATCCAGAGGTCGTTTGCCCT 61.201 55.000 0.00 0.00 0.00 5.19
256 261 9.196139 GCATTAGTAGGTAGGATAAGATGAGAT 57.804 37.037 0.00 0.00 0.00 2.75
263 268 9.778741 TTCAATTGCATTAGTAGGTAGGATAAG 57.221 33.333 0.00 0.00 0.00 1.73
399 404 6.158023 ACGTTATGAAATGGAGGGTAGTAG 57.842 41.667 0.00 0.00 0.00 2.57
404 409 4.578928 GCATTACGTTATGAAATGGAGGGT 59.421 41.667 18.15 0.00 32.44 4.34
421 432 3.371359 AAAAACGCGGACGCATTAC 57.629 47.368 17.35 0.00 45.53 1.89
454 465 7.096477 GCCGCTCACATTGTTAAATTTATGATC 60.096 37.037 0.00 0.00 0.00 2.92
458 469 5.960113 TGCCGCTCACATTGTTAAATTTAT 58.040 33.333 0.00 0.00 0.00 1.40
459 470 5.378292 TGCCGCTCACATTGTTAAATTTA 57.622 34.783 0.00 0.00 0.00 1.40
460 471 4.236935 CTGCCGCTCACATTGTTAAATTT 58.763 39.130 0.00 0.00 0.00 1.82
461 472 3.367292 CCTGCCGCTCACATTGTTAAATT 60.367 43.478 0.00 0.00 0.00 1.82
462 473 2.164219 CCTGCCGCTCACATTGTTAAAT 59.836 45.455 0.00 0.00 0.00 1.40
463 474 1.539388 CCTGCCGCTCACATTGTTAAA 59.461 47.619 0.00 0.00 0.00 1.52
464 475 1.164411 CCTGCCGCTCACATTGTTAA 58.836 50.000 0.00 0.00 0.00 2.01
465 476 0.323302 TCCTGCCGCTCACATTGTTA 59.677 50.000 0.00 0.00 0.00 2.41
466 477 0.322816 ATCCTGCCGCTCACATTGTT 60.323 50.000 0.00 0.00 0.00 2.83
467 478 0.745845 GATCCTGCCGCTCACATTGT 60.746 55.000 0.00 0.00 0.00 2.71
468 479 0.745486 TGATCCTGCCGCTCACATTG 60.745 55.000 0.00 0.00 0.00 2.82
469 480 0.182061 ATGATCCTGCCGCTCACATT 59.818 50.000 0.00 0.00 0.00 2.71
470 481 1.051008 TATGATCCTGCCGCTCACAT 58.949 50.000 0.00 0.00 0.00 3.21
471 482 0.104855 GTATGATCCTGCCGCTCACA 59.895 55.000 0.00 0.00 0.00 3.58
473 484 1.363807 CGTATGATCCTGCCGCTCA 59.636 57.895 0.00 0.00 0.00 4.26
474 485 1.373497 CCGTATGATCCTGCCGCTC 60.373 63.158 0.00 0.00 0.00 5.03
475 486 2.088674 GACCGTATGATCCTGCCGCT 62.089 60.000 0.00 0.00 0.00 5.52
476 487 1.664965 GACCGTATGATCCTGCCGC 60.665 63.158 0.00 0.00 0.00 6.53
478 489 1.940613 GTTTGACCGTATGATCCTGCC 59.059 52.381 0.00 0.00 0.00 4.85
479 490 2.906354 AGTTTGACCGTATGATCCTGC 58.094 47.619 0.00 0.00 0.00 4.85
480 491 6.978343 TTTAAGTTTGACCGTATGATCCTG 57.022 37.500 0.00 0.00 0.00 3.86
482 493 7.787725 AGATTTAAGTTTGACCGTATGATCC 57.212 36.000 0.00 0.00 0.00 3.36
483 494 8.879759 TCAAGATTTAAGTTTGACCGTATGATC 58.120 33.333 0.00 0.00 0.00 2.92
484 495 8.786826 TCAAGATTTAAGTTTGACCGTATGAT 57.213 30.769 0.00 0.00 0.00 2.45
485 496 8.610248 TTCAAGATTTAAGTTTGACCGTATGA 57.390 30.769 0.00 0.00 31.11 2.15
486 497 9.672086 TTTTCAAGATTTAAGTTTGACCGTATG 57.328 29.630 0.00 0.00 31.11 2.39
489 500 9.673454 GTATTTTCAAGATTTAAGTTTGACCGT 57.327 29.630 0.00 0.00 31.11 4.83
490 501 8.837059 CGTATTTTCAAGATTTAAGTTTGACCG 58.163 33.333 0.00 0.00 31.11 4.79
491 502 9.887406 TCGTATTTTCAAGATTTAAGTTTGACC 57.113 29.630 0.00 0.00 31.11 4.02
495 506 8.898792 GCGTTCGTATTTTCAAGATTTAAGTTT 58.101 29.630 0.00 0.00 0.00 2.66
496 507 8.071368 TGCGTTCGTATTTTCAAGATTTAAGTT 58.929 29.630 0.00 0.00 0.00 2.66
497 508 7.532884 GTGCGTTCGTATTTTCAAGATTTAAGT 59.467 33.333 0.00 0.00 0.00 2.24
498 509 7.744715 AGTGCGTTCGTATTTTCAAGATTTAAG 59.255 33.333 0.00 0.00 0.00 1.85
499 510 7.577979 AGTGCGTTCGTATTTTCAAGATTTAA 58.422 30.769 0.00 0.00 0.00 1.52
500 511 7.124347 AGTGCGTTCGTATTTTCAAGATTTA 57.876 32.000 0.00 0.00 0.00 1.40
501 512 5.997385 AGTGCGTTCGTATTTTCAAGATTT 58.003 33.333 0.00 0.00 0.00 2.17
502 513 5.607119 AGTGCGTTCGTATTTTCAAGATT 57.393 34.783 0.00 0.00 0.00 2.40
504 515 7.997107 ATATAGTGCGTTCGTATTTTCAAGA 57.003 32.000 0.00 0.00 0.00 3.02
507 518 9.465985 TCATAATATAGTGCGTTCGTATTTTCA 57.534 29.630 0.00 0.00 0.00 2.69
512 523 8.869897 CCATTTCATAATATAGTGCGTTCGTAT 58.130 33.333 0.00 0.00 0.00 3.06
513 524 8.083462 TCCATTTCATAATATAGTGCGTTCGTA 58.917 33.333 0.00 0.00 0.00 3.43
516 527 7.148407 CCCTCCATTTCATAATATAGTGCGTTC 60.148 40.741 0.00 0.00 0.00 3.95
517 528 6.655003 CCCTCCATTTCATAATATAGTGCGTT 59.345 38.462 0.00 0.00 0.00 4.84
518 529 6.013725 TCCCTCCATTTCATAATATAGTGCGT 60.014 38.462 0.00 0.00 0.00 5.24
522 533 9.845214 ACTACTCCCTCCATTTCATAATATAGT 57.155 33.333 0.00 0.00 0.00 2.12
525 536 9.845214 ACTACTACTCCCTCCATTTCATAATAT 57.155 33.333 0.00 0.00 0.00 1.28
527 538 9.845214 ATACTACTACTCCCTCCATTTCATAAT 57.155 33.333 0.00 0.00 0.00 1.28
529 540 9.670442 AAATACTACTACTCCCTCCATTTCATA 57.330 33.333 0.00 0.00 0.00 2.15
530 541 8.568617 AAATACTACTACTCCCTCCATTTCAT 57.431 34.615 0.00 0.00 0.00 2.57
531 542 7.622081 TGAAATACTACTACTCCCTCCATTTCA 59.378 37.037 0.00 0.00 37.47 2.69
532 543 8.019656 TGAAATACTACTACTCCCTCCATTTC 57.980 38.462 0.00 0.00 32.91 2.17
533 544 7.844779 TCTGAAATACTACTACTCCCTCCATTT 59.155 37.037 0.00 0.00 0.00 2.32
534 545 7.363031 TCTGAAATACTACTACTCCCTCCATT 58.637 38.462 0.00 0.00 0.00 3.16
536 547 6.337185 TCTGAAATACTACTACTCCCTCCA 57.663 41.667 0.00 0.00 0.00 3.86
537 548 7.256012 CCATTCTGAAATACTACTACTCCCTCC 60.256 44.444 0.00 0.00 0.00 4.30
539 550 6.042208 GCCATTCTGAAATACTACTACTCCCT 59.958 42.308 0.00 0.00 0.00 4.20
540 551 6.224584 GCCATTCTGAAATACTACTACTCCC 58.775 44.000 0.00 0.00 0.00 4.30
541 552 6.224584 GGCCATTCTGAAATACTACTACTCC 58.775 44.000 0.00 0.00 0.00 3.85
550 561 1.742831 TGTGCGGCCATTCTGAAATAC 59.257 47.619 2.24 0.00 0.00 1.89
707 3522 7.156000 TCTTTTGATTTGTCGACATACCACTA 58.844 34.615 20.80 0.00 0.00 2.74
748 3563 4.267503 TGTACGTGCCGTGTGCGA 62.268 61.111 10.01 0.00 45.60 5.10
974 3795 1.451028 GCCACACAGGAGGATCAGC 60.451 63.158 0.00 0.00 41.22 4.26
1096 3923 0.961019 ACGGTTGTTGTACCTAGCGA 59.039 50.000 10.77 0.00 35.97 4.93
1260 4102 2.715046 TGAATAAGAGGCTGCCAAGTG 58.285 47.619 22.65 0.00 0.00 3.16
1263 4105 4.142403 CGAATTTGAATAAGAGGCTGCCAA 60.142 41.667 22.65 2.89 0.00 4.52
1264 4106 3.378112 CGAATTTGAATAAGAGGCTGCCA 59.622 43.478 22.65 0.00 0.00 4.92
1265 4107 3.243201 CCGAATTTGAATAAGAGGCTGCC 60.243 47.826 11.65 11.65 0.00 4.85
1266 4108 3.243201 CCCGAATTTGAATAAGAGGCTGC 60.243 47.826 0.00 0.00 0.00 5.25
1417 4262 2.289274 CCGTGCACAACAACAATACTCA 59.711 45.455 18.64 0.00 0.00 3.41
1420 4265 2.766970 ACCGTGCACAACAACAATAC 57.233 45.000 18.64 0.00 0.00 1.89
1525 4375 3.629398 CCCAACTCTCCAACTATTCATGC 59.371 47.826 0.00 0.00 0.00 4.06
1563 4413 1.614850 GGAATGTTTTGACCCCGCCTA 60.615 52.381 0.00 0.00 0.00 3.93
1610 4461 6.455360 ACATTGATCATAACCATCACAACC 57.545 37.500 0.00 0.00 29.70 3.77
1726 4577 2.027192 TGGCAGGTAAGATGTGAAGTCC 60.027 50.000 0.00 0.00 0.00 3.85
1819 4670 3.248266 CTTCACTAATTTGCTTGCCTGC 58.752 45.455 0.00 0.00 0.00 4.85
1879 4730 2.352034 GACTGATGCATCTGACAAGCTG 59.648 50.000 32.64 10.90 0.00 4.24
2017 4888 2.045438 TTGCATACGCCCCAGTGG 60.045 61.111 0.63 0.63 37.32 4.00
2209 5162 9.139174 GTTACATTGCAAGCAAAGTAAACATAT 57.861 29.630 26.92 4.59 45.34 1.78
2221 5174 7.493743 AAAATCAAATGTTACATTGCAAGCA 57.506 28.000 11.60 0.00 0.00 3.91
2222 5175 8.924691 TCTAAAATCAAATGTTACATTGCAAGC 58.075 29.630 11.60 0.00 0.00 4.01
2246 5199 7.951347 ATGAACATCTTAAGCTTCCATTTCT 57.049 32.000 0.00 0.00 0.00 2.52
2254 5207 8.616076 GCATACAGTAATGAACATCTTAAGCTT 58.384 33.333 3.48 3.48 0.00 3.74
2259 5212 9.710900 CCATAGCATACAGTAATGAACATCTTA 57.289 33.333 0.00 0.00 0.00 2.10
2268 5221 6.293081 GCTCACAACCATAGCATACAGTAATG 60.293 42.308 0.00 0.00 36.26 1.90
2435 5388 6.939730 ACAATTCTGTGGTACATAATCACACA 59.060 34.615 0.00 0.00 44.52 3.72
2967 5940 9.204570 ACGGTAAGAGCAACATATATTGTATTC 57.795 33.333 0.00 0.00 37.68 1.75
2968 5941 9.204570 GACGGTAAGAGCAACATATATTGTATT 57.795 33.333 0.00 0.00 37.68 1.89
2998 5971 1.756538 TCTCTGTAGATGCGAATGCCA 59.243 47.619 0.00 0.00 41.78 4.92
3042 6015 7.160726 TCATGTCACTTTCTCATACATGACAA 58.839 34.615 11.31 0.00 46.90 3.18
3046 6019 5.816258 AGCTCATGTCACTTTCTCATACATG 59.184 40.000 7.29 7.29 45.55 3.21
3114 6088 4.254492 GAGAAAAGGTTCCTAGCGATGTT 58.746 43.478 0.00 0.00 33.92 2.71
3845 6820 2.736347 ACTAGGTGGTAGGTACTGCTG 58.264 52.381 0.00 0.00 42.03 4.41
3847 6822 3.895998 AGTACTAGGTGGTAGGTACTGC 58.104 50.000 0.00 0.00 41.52 4.40
3858 6833 7.086230 ACTAGATTCGTCAAAGTACTAGGTG 57.914 40.000 0.00 0.00 32.82 4.00
3920 6895 6.634805 CAGGAAGACTAAAGATACAGAAGCA 58.365 40.000 0.00 0.00 0.00 3.91
4024 6999 6.303733 ACGAAATTTTGAAATAAAGCGTACCG 59.696 34.615 12.54 0.00 0.00 4.02
4047 7022 3.763097 TGCTGCATTGATCCTAAAACG 57.237 42.857 0.00 0.00 0.00 3.60
4054 7029 5.870978 AGTAACAAAAATGCTGCATTGATCC 59.129 36.000 26.87 12.06 34.04 3.36
4093 7068 1.136891 CTGTCTCACCTGTCACACACA 59.863 52.381 0.00 0.00 0.00 3.72
4099 7074 3.566351 TCTTCTTCTGTCTCACCTGTCA 58.434 45.455 0.00 0.00 0.00 3.58
4198 7173 8.110860 ACCTATTGCATACATATAAGTTTGGC 57.889 34.615 0.00 0.00 0.00 4.52
4211 7186 2.930950 TGCTTGGGACCTATTGCATAC 58.069 47.619 2.65 0.00 0.00 2.39
4230 7205 9.355215 AGAAAAATACACGAGTCAAGTAGTATG 57.645 33.333 0.00 0.00 0.00 2.39
4245 7220 7.965107 CAGCAATCTAACAGGAGAAAAATACAC 59.035 37.037 0.00 0.00 0.00 2.90
4352 7327 6.586344 TCTATCAAAAGATGTAGCTCAAGGG 58.414 40.000 0.00 0.00 0.00 3.95
4446 7421 3.391049 AGAAAGCTCGGTGAAGTGTAAC 58.609 45.455 0.00 0.00 0.00 2.50
4455 7430 3.751621 CAAGCATTTAGAAAGCTCGGTG 58.248 45.455 0.00 0.00 37.70 4.94
4458 7433 3.754188 AGCAAGCATTTAGAAAGCTCG 57.246 42.857 0.00 0.00 37.70 5.03
4472 7447 2.430465 TCTGTGGATTCTGAAGCAAGC 58.570 47.619 8.03 0.00 0.00 4.01
4476 7451 5.159209 CAACATTTCTGTGGATTCTGAAGC 58.841 41.667 0.00 0.00 35.22 3.86
4477 7452 6.323203 ACAACATTTCTGTGGATTCTGAAG 57.677 37.500 0.00 0.00 35.22 3.02
4479 7454 5.507817 GCAACAACATTTCTGTGGATTCTGA 60.508 40.000 0.00 0.00 35.22 3.27
4495 7514 1.175983 GGGTTCATCGGGCAACAACA 61.176 55.000 0.00 0.00 39.74 3.33
4496 7515 0.893727 AGGGTTCATCGGGCAACAAC 60.894 55.000 0.00 0.00 39.74 3.32
4668 7687 4.614555 TGTGTTTGACTTCACATGTGAC 57.385 40.909 27.88 16.94 39.66 3.67
4752 7775 3.062099 CGGTAATGACCTGAAACACATCG 59.938 47.826 0.00 0.00 44.46 3.84
4903 7926 1.026584 CATGAAATCGGCATGGCTCA 58.973 50.000 18.09 14.04 39.48 4.26
4927 7950 0.601558 TACGCAGACGAAAGAGCCTT 59.398 50.000 0.00 0.00 43.93 4.35
5051 8074 6.756074 GCTAGAGACATGCCAATACAGATATC 59.244 42.308 0.00 0.00 0.00 1.63
5108 8132 2.470362 GCAGCTCAGCGCACATCAT 61.470 57.895 11.47 0.00 42.61 2.45
5440 8466 6.602179 TGTCGATTATGCTTTTGAACAAGAG 58.398 36.000 0.00 1.52 0.00 2.85
5610 8691 8.970859 ATTTCTGGGATGATAAACTTCTACTG 57.029 34.615 0.00 0.00 0.00 2.74
5660 8929 9.793252 TTCTGGTTCAGTAAACGTAAGTATATC 57.207 33.333 0.00 0.00 40.76 1.63
5667 8936 7.599998 GGATACTTTCTGGTTCAGTAAACGTAA 59.400 37.037 0.00 0.00 38.87 3.18
5738 9008 0.904865 TCTGGCACTCCTGTCCGAAT 60.905 55.000 0.00 0.00 33.50 3.34
5810 9080 1.605165 GCCGGGGGTCATTGTCAAA 60.605 57.895 2.18 0.00 0.00 2.69
5825 9095 1.927174 CTTACCTCATCAACTTCGCCG 59.073 52.381 0.00 0.00 0.00 6.46
5861 9134 6.272822 AGAAAAGTAAAGAATGATGGTGCC 57.727 37.500 0.00 0.00 0.00 5.01
5872 9145 5.482878 AGTGGTATCCGGAGAAAAGTAAAGA 59.517 40.000 11.34 0.00 0.00 2.52
5902 9191 5.586339 TGATAAGAGTTTCAGAGCGAGATG 58.414 41.667 0.00 0.00 0.00 2.90
5957 9246 1.216710 CCACTCTCTCCTCCGTTGC 59.783 63.158 0.00 0.00 0.00 4.17
5959 9248 2.344203 CGCCACTCTCTCCTCCGTT 61.344 63.158 0.00 0.00 0.00 4.44
6026 9315 0.104304 AGACCATCGGCCGACATTAC 59.896 55.000 33.75 20.15 0.00 1.89
6064 9358 4.087892 CCACCTGACAGCGAGGGG 62.088 72.222 0.00 0.00 34.56 4.79
6065 9359 1.541310 TTACCACCTGACAGCGAGGG 61.541 60.000 0.00 0.00 34.56 4.30
6103 9397 1.151668 GCTCGCACATCAAGAACAGT 58.848 50.000 0.00 0.00 0.00 3.55
6116 9410 0.804364 GTCAATCACCATTGCTCGCA 59.196 50.000 0.00 0.00 39.56 5.10
6145 9468 7.497249 AGAATGTACCAAATCTATCTTGTCTGC 59.503 37.037 0.00 0.00 0.00 4.26
6215 9539 6.037610 CAGTACAAGAGATTATCAAAGTGGGC 59.962 42.308 0.00 0.00 0.00 5.36
6216 9540 7.278868 GTCAGTACAAGAGATTATCAAAGTGGG 59.721 40.741 0.00 0.00 0.00 4.61
6249 9573 9.664332 TCAAAGGAATTCTTTCAAATTGTTTCA 57.336 25.926 2.96 0.00 43.32 2.69
6251 9575 9.889128 TCTCAAAGGAATTCTTTCAAATTGTTT 57.111 25.926 2.96 0.00 43.32 2.83
6284 9618 0.108138 GTCTCATGGAAGTGGGGACG 60.108 60.000 0.00 0.00 0.00 4.79
6292 9626 0.107312 CCCCTGCAGTCTCATGGAAG 60.107 60.000 13.81 0.00 0.00 3.46
6295 9629 1.222936 GTCCCCTGCAGTCTCATGG 59.777 63.158 13.81 5.16 0.00 3.66
6296 9630 1.153489 CGTCCCCTGCAGTCTCATG 60.153 63.158 13.81 0.00 0.00 3.07
6297 9631 2.362369 CCGTCCCCTGCAGTCTCAT 61.362 63.158 13.81 0.00 0.00 2.90
6298 9632 2.997315 CCGTCCCCTGCAGTCTCA 60.997 66.667 13.81 0.00 0.00 3.27
6299 9633 2.680352 TCCGTCCCCTGCAGTCTC 60.680 66.667 13.81 0.00 0.00 3.36
6300 9634 2.997897 GTCCGTCCCCTGCAGTCT 60.998 66.667 13.81 0.00 0.00 3.24
6301 9635 4.083862 GGTCCGTCCCCTGCAGTC 62.084 72.222 13.81 0.00 0.00 3.51
6306 9640 2.923634 ATAGGTCGGTCCGTCCCCTG 62.924 65.000 21.92 0.00 41.99 4.45
6307 9641 2.698075 ATAGGTCGGTCCGTCCCCT 61.698 63.158 21.92 20.25 41.99 4.79
6308 9642 2.123554 ATAGGTCGGTCCGTCCCC 60.124 66.667 21.92 14.88 41.99 4.81
6309 9643 0.466189 TACATAGGTCGGTCCGTCCC 60.466 60.000 21.92 17.18 41.99 4.46
6310 9644 1.268899 CATACATAGGTCGGTCCGTCC 59.731 57.143 18.62 18.62 41.99 4.79
6311 9645 2.224606 TCATACATAGGTCGGTCCGTC 58.775 52.381 11.88 5.43 41.99 4.79
6312 9646 2.353357 TCATACATAGGTCGGTCCGT 57.647 50.000 11.88 0.00 41.99 4.69
6313 9647 3.669824 CGATTCATACATAGGTCGGTCCG 60.670 52.174 4.39 4.39 41.99 4.79
6314 9648 3.255149 ACGATTCATACATAGGTCGGTCC 59.745 47.826 0.00 0.00 33.75 4.46
6315 9649 4.500603 ACGATTCATACATAGGTCGGTC 57.499 45.455 0.00 0.00 33.75 4.79
6318 9652 6.822073 TTTGAACGATTCATACATAGGTCG 57.178 37.500 0.00 0.00 39.84 4.79
6354 9710 2.195741 TCGTTCCTTCTCTTCCGAGA 57.804 50.000 0.00 0.00 44.32 4.04
6358 9714 5.935206 AGATTTCTTTCGTTCCTTCTCTTCC 59.065 40.000 0.00 0.00 0.00 3.46
6368 9724 5.343325 GCACCATTTCAGATTTCTTTCGTTC 59.657 40.000 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.