Multiple sequence alignment - TraesCS5B01G241400

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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 TraesCS5B01G241400 chr5B 100.000 5376 0 0 1 5376 421446233 421451608 0.000000e+00 9928.0
1 TraesCS5B01G241400 chr5D 93.563 5313 209 49 1 5244 356618778 356624026 0.000000e+00 7793.0
2 TraesCS5B01G241400 chr5D 83.266 741 88 14 3260 3992 539778930 539778218 0.000000e+00 649.0
3 TraesCS5B01G241400 chr5D 83.311 737 88 13 3260 3988 35483908 35483199 0.000000e+00 647.0
4 TraesCS5B01G241400 chr5D 90.930 441 28 8 2263 2695 35484339 35483903 2.790000e-162 582.0
5 TraesCS5B01G241400 chr5D 91.096 438 27 8 2266 2695 539779358 539778925 2.790000e-162 582.0
6 TraesCS5B01G241400 chr5A 93.866 4532 172 41 355 4815 458102010 458106506 0.000000e+00 6732.0
7 TraesCS5B01G241400 chr5A 88.469 503 32 7 29 520 458003044 458003531 7.760000e-163 584.0
8 TraesCS5B01G241400 chr5A 91.968 249 10 4 1 241 458101677 458101923 1.850000e-89 340.0
9 TraesCS5B01G241400 chr5A 88.462 130 13 1 4812 4941 458109630 458109757 7.210000e-34 156.0
10 TraesCS5B01G241400 chr1B 83.671 741 87 17 3260 3992 252373683 252374397 0.000000e+00 667.0
11 TraesCS5B01G241400 chr1B 83.880 732 84 14 3265 3988 653970113 653970818 0.000000e+00 667.0
12 TraesCS5B01G241400 chr1B 85.932 263 22 3 2216 2466 252373237 252373496 3.190000e-67 267.0
13 TraesCS5B01G241400 chr1B 91.000 200 12 5 2502 2695 252373489 252373688 1.150000e-66 265.0
14 TraesCS5B01G241400 chr1B 79.012 324 54 9 5034 5347 150170418 150170099 5.460000e-50 209.0
15 TraesCS5B01G241400 chr6D 82.838 740 92 16 3260 3992 231080972 231080261 9.830000e-177 630.0
16 TraesCS5B01G241400 chr6D 90.787 445 26 9 2263 2695 231081408 231080967 1.000000e-161 580.0
17 TraesCS5B01G241400 chr7D 90.930 441 29 7 2263 2695 598731684 598732121 2.790000e-162 582.0
18 TraesCS5B01G241400 chr7D 84.397 564 71 10 3260 3817 598732116 598732668 6.130000e-149 538.0
19 TraesCS5B01G241400 chr7D 80.840 381 46 9 4995 5350 110886580 110886202 1.910000e-69 274.0
20 TraesCS5B01G241400 chr7A 87.854 494 27 11 1664 2129 665439470 665439958 2.830000e-152 549.0
21 TraesCS5B01G241400 chr7B 86.785 507 37 13 2216 2695 82146999 82147502 6.130000e-149 538.0
22 TraesCS5B01G241400 chr1A 87.273 495 29 11 1664 2129 466349109 466349598 7.930000e-148 534.0
23 TraesCS5B01G241400 chr3D 83.422 374 50 3 4989 5350 611071492 611071119 2.400000e-88 337.0
24 TraesCS5B01G241400 chr6B 83.146 356 38 7 4991 5326 32996059 32995706 6.760000e-79 305.0
25 TraesCS5B01G241400 chr6B 80.260 385 50 8 4990 5348 22461145 22460761 3.190000e-67 267.0
26 TraesCS5B01G241400 chr6B 84.739 249 25 3 2216 2452 304153962 304154209 2.500000e-58 237.0
27 TraesCS5B01G241400 chr6A 82.031 384 42 12 4990 5350 617188583 617188204 8.750000e-78 302.0
28 TraesCS5B01G241400 chr6A 79.224 361 50 9 4988 5326 562680342 562680699 1.510000e-55 228.0
29 TraesCS5B01G241400 chr2A 86.692 263 25 4 4991 5244 194465108 194465369 3.170000e-72 283.0
30 TraesCS5B01G241400 chr2A 92.135 89 7 0 1037 1125 543120696 543120784 5.650000e-25 126.0
31 TraesCS5B01G241400 chr2A 78.400 125 27 0 3750 3874 543123076 543123200 1.240000e-11 82.4
32 TraesCS5B01G241400 chrUn 80.475 379 48 7 4990 5342 371021482 371021860 3.190000e-67 267.0
33 TraesCS5B01G241400 chr3A 84.528 265 31 6 4990 5244 690684602 690684866 2.490000e-63 254.0
34 TraesCS5B01G241400 chr1D 84.411 263 31 2 4992 5244 3895262 3895000 3.210000e-62 250.0
35 TraesCS5B01G241400 chr4D 84.091 264 32 6 4991 5244 32419111 32419374 4.160000e-61 246.0
36 TraesCS5B01G241400 chr4B 83.019 265 35 5 4990 5244 631636327 631636591 1.160000e-56 231.0
37 TraesCS5B01G241400 chr2B 79.282 362 50 8 5012 5350 710327739 710327380 4.190000e-56 230.0
38 TraesCS5B01G241400 chr2B 90.625 160 15 0 4990 5149 627835110 627834951 4.220000e-51 213.0
39 TraesCS5B01G241400 chr2D 76.413 407 66 16 4991 5367 606206156 606206562 5.490000e-45 193.0
40 TraesCS5B01G241400 chr2D 92.135 89 7 0 1037 1125 405062396 405062484 5.650000e-25 126.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G241400 chr5B 421446233 421451608 5375 False 9928.000000 9928 100.000000 1 5376 1 chr5B.!!$F1 5375
1 TraesCS5B01G241400 chr5D 356618778 356624026 5248 False 7793.000000 7793 93.563000 1 5244 1 chr5D.!!$F1 5243
2 TraesCS5B01G241400 chr5D 539778218 539779358 1140 True 615.500000 649 87.181000 2266 3992 2 chr5D.!!$R2 1726
3 TraesCS5B01G241400 chr5D 35483199 35484339 1140 True 614.500000 647 87.120500 2263 3988 2 chr5D.!!$R1 1725
4 TraesCS5B01G241400 chr5A 458101677 458109757 8080 False 2409.333333 6732 91.432000 1 4941 3 chr5A.!!$F2 4940
5 TraesCS5B01G241400 chr1B 653970113 653970818 705 False 667.000000 667 83.880000 3265 3988 1 chr1B.!!$F1 723
6 TraesCS5B01G241400 chr1B 252373237 252374397 1160 False 399.666667 667 86.867667 2216 3992 3 chr1B.!!$F2 1776
7 TraesCS5B01G241400 chr6D 231080261 231081408 1147 True 605.000000 630 86.812500 2263 3992 2 chr6D.!!$R1 1729
8 TraesCS5B01G241400 chr7D 598731684 598732668 984 False 560.000000 582 87.663500 2263 3817 2 chr7D.!!$F1 1554
9 TraesCS5B01G241400 chr7B 82146999 82147502 503 False 538.000000 538 86.785000 2216 2695 1 chr7B.!!$F1 479

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
673 701 0.255033 ACCCCTCGCCTCCAAATTAC 59.745 55.000 0.0 0.0 0.00 1.89 F
1511 1557 0.171231 GTGCGGAAAGAGGAAATGGC 59.829 55.000 0.0 0.0 0.00 4.40 F
1715 1762 0.319083 TGGCCGTACATCTGTTTCGT 59.681 50.000 0.0 0.0 0.00 3.85 F
1926 2008 0.404040 AGGGTTTCCGCTTGAATGGA 59.596 50.000 0.0 0.0 38.33 3.41 F
2054 2136 1.881973 TGTCTTTGCTGCACTTCCATC 59.118 47.619 0.0 0.0 0.00 3.51 F
3973 4116 1.351076 TGCCTCTGTCACCTTGATGA 58.649 50.000 0.0 0.0 0.00 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1715 1762 0.178947 AAAAACGGGCCAATGAGGGA 60.179 50.000 4.39 0.0 38.09 4.20 R
3397 3523 2.178912 TCCAAAAAGGTAGTGCGGAG 57.821 50.000 0.00 0.0 39.02 4.63 R
3546 3673 7.661027 AGCTATGCAAACAACATTAAATGGTTT 59.339 29.630 0.00 0.0 32.33 3.27 R
3918 4060 0.182775 ATTGTATGCGGGGAGGAACC 59.817 55.000 0.00 0.0 38.08 3.62 R
4046 4189 2.046285 CCCAATGGTGCTCCCGTTC 61.046 63.158 1.59 0.0 40.66 3.95 R
5346 8643 0.660300 CGGCTCGGTTTGTTTGAAGC 60.660 55.000 0.00 0.0 0.00 3.86 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 31 3.170717 AGGTTAAACTGATCACCGGAGA 58.829 45.455 9.46 6.11 34.19 3.71
52 54 7.862675 AGAAGGCTAAATTATGTGGAGTAACT 58.137 34.615 0.00 0.00 0.00 2.24
169 179 1.208614 GCAGCTCAGCCGTGAAAAG 59.791 57.895 0.00 0.00 30.14 2.27
222 232 8.710749 AAAGCTATATTTAGGATCCATGCAAA 57.289 30.769 15.82 8.73 0.00 3.68
244 254 1.863155 TTTGACCAGCCAGGATCCCC 61.863 60.000 8.55 0.00 41.22 4.81
253 263 1.583784 CCAGGATCCCCCACATTGGT 61.584 60.000 8.55 0.00 35.17 3.67
271 281 6.879458 ACATTGGTTCTGGTTCACTAGAATAC 59.121 38.462 8.78 6.45 43.64 1.89
276 286 5.916661 TCTGGTTCACTAGAATACCAGAC 57.083 43.478 26.18 5.41 45.11 3.51
292 302 0.824759 AGACCAGGATTACTGCGGAC 59.175 55.000 0.00 0.00 46.14 4.79
309 319 3.917985 GCGGACGCAAATAAAAGTGAAAT 59.082 39.130 12.31 0.00 41.49 2.17
310 320 4.384547 GCGGACGCAAATAAAAGTGAAATT 59.615 37.500 12.31 0.00 41.49 1.82
589 611 3.011257 TGCTTTATTTAGCCACCTCCCTT 59.989 43.478 0.00 0.00 40.49 3.95
614 636 4.504916 CCGCGAGCTGCTACTGCT 62.505 66.667 8.23 0.00 43.27 4.24
615 637 2.953824 CGCGAGCTGCTACTGCTC 60.954 66.667 0.00 14.35 46.84 4.26
649 677 0.689412 CTCCTCCACCTCTTCCCTCC 60.689 65.000 0.00 0.00 0.00 4.30
650 678 1.690985 CCTCCACCTCTTCCCTCCC 60.691 68.421 0.00 0.00 0.00 4.30
651 679 1.690985 CTCCACCTCTTCCCTCCCC 60.691 68.421 0.00 0.00 0.00 4.81
652 680 2.184631 TCCACCTCTTCCCTCCCCT 61.185 63.158 0.00 0.00 0.00 4.79
653 681 1.997874 CCACCTCTTCCCTCCCCTG 60.998 68.421 0.00 0.00 0.00 4.45
654 682 1.081092 CACCTCTTCCCTCCCCTGA 59.919 63.158 0.00 0.00 0.00 3.86
655 683 1.081277 ACCTCTTCCCTCCCCTGAC 59.919 63.158 0.00 0.00 0.00 3.51
673 701 0.255033 ACCCCTCGCCTCCAAATTAC 59.745 55.000 0.00 0.00 0.00 1.89
674 702 0.546598 CCCCTCGCCTCCAAATTACT 59.453 55.000 0.00 0.00 0.00 2.24
675 703 1.766496 CCCCTCGCCTCCAAATTACTA 59.234 52.381 0.00 0.00 0.00 1.82
1294 1330 3.454375 CCCGCGAGATACACTAAATGTT 58.546 45.455 8.23 0.00 43.19 2.71
1345 1381 1.301716 GCGACAGGTTTCAGAGGCA 60.302 57.895 0.00 0.00 0.00 4.75
1391 1437 0.622154 TCGGGGGAGAGAGAGAGAGT 60.622 60.000 0.00 0.00 0.00 3.24
1420 1466 5.740290 TCTTAACAAAGACTGGGTAGAGG 57.260 43.478 0.00 0.00 0.00 3.69
1511 1557 0.171231 GTGCGGAAAGAGGAAATGGC 59.829 55.000 0.00 0.00 0.00 4.40
1578 1624 2.046217 GGAAACTCGCAGTCCCCC 60.046 66.667 0.00 0.00 0.00 5.40
1606 1652 3.925453 TGAGGCAACGCAAGATACA 57.075 47.368 0.00 0.00 46.20 2.29
1609 1655 0.324943 AGGCAACGCAAGATACACCT 59.675 50.000 0.00 0.00 46.39 4.00
1610 1656 1.553248 AGGCAACGCAAGATACACCTA 59.447 47.619 0.00 0.00 46.39 3.08
1611 1657 2.170607 AGGCAACGCAAGATACACCTAT 59.829 45.455 0.00 0.00 46.39 2.57
1715 1762 0.319083 TGGCCGTACATCTGTTTCGT 59.681 50.000 0.00 0.00 0.00 3.85
1740 1787 4.502431 CCTCATTGGCCCGTTTTTAGTTTT 60.502 41.667 0.00 0.00 0.00 2.43
1746 1793 3.191669 GCCCGTTTTTAGTTTTGCAGTT 58.808 40.909 0.00 0.00 0.00 3.16
1778 1829 3.433598 GGGATGTGCTGATTAGGTGCTTA 60.434 47.826 0.00 0.00 0.00 3.09
1819 1890 8.303876 GGCAGAAAAGGAGAACATTTACATTAA 58.696 33.333 0.00 0.00 29.78 1.40
1844 1915 6.746745 TTTCTCAAACTACGTTCAAAACCT 57.253 33.333 0.00 0.00 0.00 3.50
1862 1944 4.017177 ACCTGTTAGGGCTTTACACTTC 57.983 45.455 0.00 0.00 40.58 3.01
1888 1970 7.794041 AGAAGAACTGAGCTCTGAATATTCAT 58.206 34.615 25.49 12.13 36.46 2.57
1926 2008 0.404040 AGGGTTTCCGCTTGAATGGA 59.596 50.000 0.00 0.00 38.33 3.41
1929 2011 2.159382 GGTTTCCGCTTGAATGGAAGA 58.841 47.619 0.35 0.00 44.58 2.87
1961 2043 4.415596 TGCTATTCCCTTTTTGTGTCCAT 58.584 39.130 0.00 0.00 0.00 3.41
2054 2136 1.881973 TGTCTTTGCTGCACTTCCATC 59.118 47.619 0.00 0.00 0.00 3.51
2102 2184 2.045926 GCGGCATTGTCACCTCCT 60.046 61.111 0.00 0.00 0.00 3.69
2127 2210 6.429078 TGAACAATGGAGAAAGACTTGATCAG 59.571 38.462 0.00 0.00 29.13 2.90
2149 2232 4.975147 AGACATGGGGTTTATATGAGGACA 59.025 41.667 0.00 0.00 0.00 4.02
2230 2314 4.441356 GGCCTGTGTCTTGACAATTGAAAA 60.441 41.667 13.59 4.99 0.00 2.29
2261 2355 4.346709 TGTCCAGTCAGTTGAGGAACATAA 59.653 41.667 0.00 0.00 34.17 1.90
2312 2425 9.290988 TGCAATTTACAGTTCTTACTATCCAAA 57.709 29.630 0.00 0.00 31.96 3.28
2531 2648 2.124507 TTAGCATGGGGGATAGGCGC 62.125 60.000 0.00 0.00 0.00 6.53
2732 2855 2.224281 TGAGAAGACAAACGCCATGACT 60.224 45.455 0.00 0.00 0.00 3.41
2968 3092 8.911018 ACCCTCTACCTATATGCAAACATATA 57.089 34.615 0.00 5.82 45.67 0.86
3188 3314 7.454260 ACAATTCATAGAAGTTCTGGTTTCC 57.546 36.000 15.90 0.00 0.00 3.13
3252 3378 6.795399 TCTCTTTGCCACTTTAACTTGAAAG 58.205 36.000 0.00 0.00 41.38 2.62
3276 3402 7.916552 AGTTTCACTTGTACTTAATCACACAC 58.083 34.615 0.00 0.00 0.00 3.82
3427 3553 6.097129 CACTACCTTTTTGGAAAGTGGGTTTA 59.903 38.462 11.32 0.00 43.24 2.01
3440 3566 8.410912 GGAAAGTGGGTTTATATTGGTGATAAC 58.589 37.037 0.00 0.00 0.00 1.89
3821 3962 7.842447 TAAGCAAACCTTCTCCCAGTATGGC 62.842 48.000 0.00 0.00 44.66 4.40
3899 4041 5.419155 TCTTCAGAGGTATGGATATTAGCCG 59.581 44.000 0.00 0.00 0.00 5.52
3916 4058 7.852971 ATTAGCCGTGCACTTTTATACTTTA 57.147 32.000 16.19 0.00 0.00 1.85
3918 4060 4.092383 AGCCGTGCACTTTTATACTTTACG 59.908 41.667 16.19 0.00 0.00 3.18
3967 4110 3.181434 TGGTTAAATTGCCTCTGTCACCT 60.181 43.478 0.00 0.00 0.00 4.00
3973 4116 1.351076 TGCCTCTGTCACCTTGATGA 58.649 50.000 0.00 0.00 0.00 2.92
3981 4124 3.334691 TGTCACCTTGATGAAATCCGAC 58.665 45.455 0.00 0.00 44.73 4.79
3991 4134 4.754618 TGATGAAATCCGACCGATTAATGG 59.245 41.667 0.00 0.00 44.73 3.16
4046 4189 0.535335 AAGATGCATTGCAAGGGCTG 59.465 50.000 16.46 9.88 43.62 4.85
4061 4204 1.675641 GCTGAACGGGAGCACCATT 60.676 57.895 1.58 0.00 40.22 3.16
4129 4272 3.246301 AGCAGGTACCATCATATGCTCT 58.754 45.455 15.94 0.00 39.72 4.09
4131 4274 3.999663 GCAGGTACCATCATATGCTCTTC 59.000 47.826 15.94 0.00 0.00 2.87
4135 4278 5.367937 AGGTACCATCATATGCTCTTCTTGT 59.632 40.000 15.94 0.00 0.00 3.16
4137 4280 5.363562 ACCATCATATGCTCTTCTTGTCA 57.636 39.130 0.00 0.00 0.00 3.58
4139 4282 7.071069 ACCATCATATGCTCTTCTTGTCATA 57.929 36.000 0.00 0.00 0.00 2.15
4146 4289 2.158885 GCTCTTCTTGTCATACCTCCCC 60.159 54.545 0.00 0.00 0.00 4.81
4178 4326 0.527565 GTGCAGCCAACATAACCCAG 59.472 55.000 0.00 0.00 0.00 4.45
4345 4493 2.359975 GCCTATGGCGCATACCCC 60.360 66.667 10.83 0.00 39.62 4.95
4380 4528 1.736681 GCAACAGGTCAGCTGAAGATC 59.263 52.381 20.19 5.66 0.00 2.75
4386 4534 1.107114 GTCAGCTGAAGATCGGAGGA 58.893 55.000 20.19 0.00 0.00 3.71
4401 4549 2.016393 GAGGATCACACGCCCATCGA 62.016 60.000 0.00 0.00 36.94 3.59
4402 4550 1.069765 GGATCACACGCCCATCGAT 59.930 57.895 0.00 0.00 41.67 3.59
4403 4551 0.946221 GGATCACACGCCCATCGATC 60.946 60.000 0.00 0.00 41.67 3.69
4404 4552 0.946221 GATCACACGCCCATCGATCC 60.946 60.000 0.00 0.00 41.67 3.36
4405 4553 2.383245 ATCACACGCCCATCGATCCC 62.383 60.000 0.00 0.00 41.67 3.85
4406 4554 2.764128 ACACGCCCATCGATCCCT 60.764 61.111 0.00 0.00 41.67 4.20
4407 4555 2.029666 CACGCCCATCGATCCCTC 59.970 66.667 0.00 0.00 41.67 4.30
4408 4556 3.606662 ACGCCCATCGATCCCTCG 61.607 66.667 0.00 0.00 46.41 4.63
4418 4566 3.154589 GATCCCTCGACAACAACCC 57.845 57.895 0.00 0.00 0.00 4.11
4470 4618 5.194432 TGCTAGAGAAAGAAGGTAGACGAT 58.806 41.667 0.00 0.00 0.00 3.73
4550 4701 3.056749 ACGAAGAACTAGCACCACTAAGG 60.057 47.826 0.00 0.00 45.67 2.69
4568 4719 2.973945 AGGCACCTAAAATGACTCGAC 58.026 47.619 0.00 0.00 24.00 4.20
4688 4840 1.737236 CGGTTTCTGATCGATTTGGCA 59.263 47.619 0.00 0.00 0.00 4.92
4696 4848 3.260740 TGATCGATTTGGCATTTTTGGC 58.739 40.909 0.00 0.00 0.00 4.52
4733 4885 3.007290 TGATGTTGAGCTGAGCAAGTAGT 59.993 43.478 7.39 0.00 0.00 2.73
4751 4903 8.291888 CAAGTAGTGCTAGCTGTTAGAATATG 57.708 38.462 17.23 0.00 0.00 1.78
4776 4928 3.493176 GCAAACAATCAATAGCCCATCCC 60.493 47.826 0.00 0.00 0.00 3.85
4849 8128 2.943036 TAGTTTTGGCCTCGGAAAGT 57.057 45.000 3.32 5.75 0.00 2.66
4866 8145 5.119588 CGGAAAGTCAGCTGAACGTATTTTA 59.880 40.000 20.19 0.00 0.00 1.52
4879 8158 9.395707 CTGAACGTATTTTATAGCTAGTTCGAT 57.604 33.333 0.00 0.00 39.42 3.59
4880 8159 9.177304 TGAACGTATTTTATAGCTAGTTCGATG 57.823 33.333 0.00 0.00 39.42 3.84
4897 8185 4.433615 TCGATGAGATTTCCTTTTCCTCG 58.566 43.478 0.00 0.00 0.00 4.63
4898 8186 4.081642 TCGATGAGATTTCCTTTTCCTCGT 60.082 41.667 0.00 0.00 32.19 4.18
4899 8187 4.033358 CGATGAGATTTCCTTTTCCTCGTG 59.967 45.833 0.00 0.00 0.00 4.35
4900 8188 4.351874 TGAGATTTCCTTTTCCTCGTGT 57.648 40.909 0.00 0.00 0.00 4.49
4901 8189 4.714632 TGAGATTTCCTTTTCCTCGTGTT 58.285 39.130 0.00 0.00 0.00 3.32
4902 8190 4.515191 TGAGATTTCCTTTTCCTCGTGTTG 59.485 41.667 0.00 0.00 0.00 3.33
4903 8191 4.461198 AGATTTCCTTTTCCTCGTGTTGT 58.539 39.130 0.00 0.00 0.00 3.32
4904 8192 4.275936 AGATTTCCTTTTCCTCGTGTTGTG 59.724 41.667 0.00 0.00 0.00 3.33
4905 8193 1.305201 TCCTTTTCCTCGTGTTGTGC 58.695 50.000 0.00 0.00 0.00 4.57
4906 8194 1.134220 TCCTTTTCCTCGTGTTGTGCT 60.134 47.619 0.00 0.00 0.00 4.40
4907 8195 2.103432 TCCTTTTCCTCGTGTTGTGCTA 59.897 45.455 0.00 0.00 0.00 3.49
4919 8207 6.541969 TCGTGTTGTGCTATGTCAAATATTG 58.458 36.000 0.00 0.00 0.00 1.90
4949 8237 9.494271 CAACTATTATGAAGCTAATAAGGAGCA 57.506 33.333 7.58 0.00 42.69 4.26
4957 8245 6.658816 TGAAGCTAATAAGGAGCATCAAACAA 59.341 34.615 0.46 0.00 42.78 2.83
4962 8250 8.125448 GCTAATAAGGAGCATCAAACAAAGTAG 58.875 37.037 0.00 0.00 39.84 2.57
5010 8298 0.771127 AGGGCTGTACCAAAAGCTCA 59.229 50.000 5.67 0.00 42.68 4.26
5044 8332 1.759994 AATGAGCGCTCGATAGTTCG 58.240 50.000 30.75 0.00 46.87 3.95
5048 8336 1.164662 AGCGCTCGATAGTTCGGCTA 61.165 55.000 2.64 0.00 45.53 3.93
5053 8341 3.120269 CGCTCGATAGTTCGGCTAGTTAT 60.120 47.826 0.00 0.00 45.53 1.89
5057 8345 4.277672 TCGATAGTTCGGCTAGTTATGCTT 59.722 41.667 0.00 0.00 45.53 3.91
5069 8357 1.200020 GTTATGCTTGTGGCTCGCTTT 59.800 47.619 0.00 0.00 42.39 3.51
5083 8371 4.982295 GGCTCGCTTTTTAATGAACAAAGT 59.018 37.500 0.00 0.00 31.29 2.66
5102 8390 9.768662 AACAAAGTTAATCATCAATTTCAGCTT 57.231 25.926 0.00 0.00 0.00 3.74
5135 8432 8.597662 TTAACAAACTAGCTAACGAGTTTCAT 57.402 30.769 8.99 4.84 45.19 2.57
5146 8443 1.849219 CGAGTTTCATGAGTAGCTCGC 59.151 52.381 17.12 0.00 39.12 5.03
5214 8511 2.338577 ATTGATGTAGCACCTCAGCC 57.661 50.000 0.00 0.00 34.23 4.85
5246 8543 8.657387 TTCAATCTAATCTAGATAGGAGGGTG 57.343 38.462 5.46 7.39 44.44 4.61
5247 8544 6.665680 TCAATCTAATCTAGATAGGAGGGTGC 59.334 42.308 5.46 0.00 44.44 5.01
5248 8545 5.600669 TCTAATCTAGATAGGAGGGTGCA 57.399 43.478 5.46 0.00 0.00 4.57
5249 8546 6.159172 TCTAATCTAGATAGGAGGGTGCAT 57.841 41.667 5.46 0.00 0.00 3.96
5250 8547 6.565974 TCTAATCTAGATAGGAGGGTGCATT 58.434 40.000 5.46 0.00 0.00 3.56
5251 8548 7.019388 TCTAATCTAGATAGGAGGGTGCATTT 58.981 38.462 5.46 0.00 0.00 2.32
5252 8549 5.753721 ATCTAGATAGGAGGGTGCATTTC 57.246 43.478 2.53 0.00 0.00 2.17
5253 8550 3.904339 TCTAGATAGGAGGGTGCATTTCC 59.096 47.826 6.10 6.10 0.00 3.13
5254 8551 2.781667 AGATAGGAGGGTGCATTTCCT 58.218 47.619 17.34 17.34 43.53 3.36
5255 8552 3.126453 AGATAGGAGGGTGCATTTCCTT 58.874 45.455 18.11 0.00 41.46 3.36
5256 8553 3.529319 AGATAGGAGGGTGCATTTCCTTT 59.471 43.478 18.11 12.33 41.46 3.11
5257 8554 2.702270 AGGAGGGTGCATTTCCTTTT 57.298 45.000 9.95 0.01 38.13 2.27
5258 8555 2.250924 AGGAGGGTGCATTTCCTTTTG 58.749 47.619 9.95 0.00 38.13 2.44
5259 8556 1.970640 GGAGGGTGCATTTCCTTTTGT 59.029 47.619 7.49 0.00 32.74 2.83
5260 8557 3.161866 GGAGGGTGCATTTCCTTTTGTA 58.838 45.455 7.49 0.00 32.74 2.41
5261 8558 3.193479 GGAGGGTGCATTTCCTTTTGTAG 59.807 47.826 7.49 0.00 32.74 2.74
5262 8559 3.826729 GAGGGTGCATTTCCTTTTGTAGT 59.173 43.478 7.49 0.00 32.74 2.73
5263 8560 3.826729 AGGGTGCATTTCCTTTTGTAGTC 59.173 43.478 0.00 0.00 0.00 2.59
5264 8561 3.572255 GGGTGCATTTCCTTTTGTAGTCA 59.428 43.478 0.00 0.00 0.00 3.41
5265 8562 4.220602 GGGTGCATTTCCTTTTGTAGTCAT 59.779 41.667 0.00 0.00 0.00 3.06
5266 8563 5.402398 GGTGCATTTCCTTTTGTAGTCATC 58.598 41.667 0.00 0.00 0.00 2.92
5267 8564 5.048083 GGTGCATTTCCTTTTGTAGTCATCA 60.048 40.000 0.00 0.00 0.00 3.07
5268 8565 6.350445 GGTGCATTTCCTTTTGTAGTCATCAT 60.350 38.462 0.00 0.00 0.00 2.45
5269 8566 6.749118 GTGCATTTCCTTTTGTAGTCATCATC 59.251 38.462 0.00 0.00 0.00 2.92
5270 8567 6.127647 TGCATTTCCTTTTGTAGTCATCATCC 60.128 38.462 0.00 0.00 0.00 3.51
5271 8568 6.096001 GCATTTCCTTTTGTAGTCATCATCCT 59.904 38.462 0.00 0.00 0.00 3.24
5272 8569 7.363268 GCATTTCCTTTTGTAGTCATCATCCTT 60.363 37.037 0.00 0.00 0.00 3.36
5273 8570 8.526147 CATTTCCTTTTGTAGTCATCATCCTTT 58.474 33.333 0.00 0.00 0.00 3.11
5274 8571 8.477419 TTTCCTTTTGTAGTCATCATCCTTTT 57.523 30.769 0.00 0.00 0.00 2.27
5275 8572 9.581289 TTTCCTTTTGTAGTCATCATCCTTTTA 57.419 29.630 0.00 0.00 0.00 1.52
5276 8573 9.581289 TTCCTTTTGTAGTCATCATCCTTTTAA 57.419 29.630 0.00 0.00 0.00 1.52
5277 8574 9.581289 TCCTTTTGTAGTCATCATCCTTTTAAA 57.419 29.630 0.00 0.00 0.00 1.52
5301 8598 6.500684 AAAAATCACATCTACGCACTCATT 57.499 33.333 0.00 0.00 0.00 2.57
5302 8599 7.609760 AAAAATCACATCTACGCACTCATTA 57.390 32.000 0.00 0.00 0.00 1.90
5303 8600 7.792374 AAAATCACATCTACGCACTCATTAT 57.208 32.000 0.00 0.00 0.00 1.28
5304 8601 6.775939 AATCACATCTACGCACTCATTATG 57.224 37.500 0.00 0.00 0.00 1.90
5305 8602 5.262588 TCACATCTACGCACTCATTATGT 57.737 39.130 0.00 0.00 0.00 2.29
5306 8603 6.385649 TCACATCTACGCACTCATTATGTA 57.614 37.500 0.00 0.00 0.00 2.29
5307 8604 6.438763 TCACATCTACGCACTCATTATGTAG 58.561 40.000 0.00 0.00 35.09 2.74
5308 8605 6.262273 TCACATCTACGCACTCATTATGTAGA 59.738 38.462 3.21 3.21 43.83 2.59
5310 8607 7.596621 CACATCTACGCACTCATTATGTAGATT 59.403 37.037 9.74 1.80 45.68 2.40
5311 8608 7.596621 ACATCTACGCACTCATTATGTAGATTG 59.403 37.037 9.74 8.58 45.68 2.67
5312 8609 7.039313 TCTACGCACTCATTATGTAGATTGT 57.961 36.000 0.00 0.00 37.27 2.71
5313 8610 8.161699 TCTACGCACTCATTATGTAGATTGTA 57.838 34.615 0.00 0.00 37.27 2.41
5314 8611 8.626526 TCTACGCACTCATTATGTAGATTGTAA 58.373 33.333 0.00 0.00 37.27 2.41
5315 8612 7.464830 ACGCACTCATTATGTAGATTGTAAC 57.535 36.000 0.00 0.00 0.00 2.50
5316 8613 7.039270 ACGCACTCATTATGTAGATTGTAACA 58.961 34.615 0.00 0.00 0.00 2.41
5317 8614 7.222805 ACGCACTCATTATGTAGATTGTAACAG 59.777 37.037 0.00 0.00 0.00 3.16
5318 8615 7.435192 CGCACTCATTATGTAGATTGTAACAGA 59.565 37.037 0.00 0.00 0.00 3.41
5319 8616 9.265901 GCACTCATTATGTAGATTGTAACAGAT 57.734 33.333 0.00 0.00 0.00 2.90
5339 8636 7.928103 ACAGATCAGAATTCATTAATGAGTGC 58.072 34.615 17.28 13.72 38.19 4.40
5340 8637 7.774157 ACAGATCAGAATTCATTAATGAGTGCT 59.226 33.333 17.28 15.71 38.19 4.40
5341 8638 8.283992 CAGATCAGAATTCATTAATGAGTGCTC 58.716 37.037 16.58 10.47 38.19 4.26
5342 8639 7.991460 AGATCAGAATTCATTAATGAGTGCTCA 59.009 33.333 16.58 6.73 44.59 4.26
5343 8640 7.312657 TCAGAATTCATTAATGAGTGCTCAC 57.687 36.000 16.58 7.34 43.11 3.51
5344 8641 6.036408 TCAGAATTCATTAATGAGTGCTCACG 59.964 38.462 16.58 8.06 43.11 4.35
5345 8642 6.036408 CAGAATTCATTAATGAGTGCTCACGA 59.964 38.462 16.58 1.41 43.11 4.35
5346 8643 5.980698 ATTCATTAATGAGTGCTCACGAG 57.019 39.130 17.28 0.00 43.11 4.18
5347 8644 3.190079 TCATTAATGAGTGCTCACGAGC 58.810 45.455 14.23 12.17 43.11 5.03
5348 8645 3.118992 TCATTAATGAGTGCTCACGAGCT 60.119 43.478 19.17 0.44 43.11 4.09
5349 8646 4.621510 TCATTAATGAGTGCTCACGAGCTT 60.622 41.667 19.17 8.25 43.11 3.74
5350 8647 6.414966 TCATTAATGAGTGCTCACGAGCTTC 61.415 44.000 19.17 16.01 43.11 3.86
5351 8648 8.727889 TCATTAATGAGTGCTCACGAGCTTCA 62.728 42.308 19.17 20.20 45.37 3.02
5359 8656 2.987046 CTCACGAGCTTCAAACAAACC 58.013 47.619 0.00 0.00 0.00 3.27
5360 8657 1.329292 TCACGAGCTTCAAACAAACCG 59.671 47.619 0.00 0.00 0.00 4.44
5361 8658 1.329292 CACGAGCTTCAAACAAACCGA 59.671 47.619 0.00 0.00 0.00 4.69
5362 8659 1.597663 ACGAGCTTCAAACAAACCGAG 59.402 47.619 0.00 0.00 0.00 4.63
5363 8660 1.660333 CGAGCTTCAAACAAACCGAGC 60.660 52.381 0.00 0.00 0.00 5.03
5364 8661 0.668535 AGCTTCAAACAAACCGAGCC 59.331 50.000 0.00 0.00 0.00 4.70
5365 8662 0.660300 GCTTCAAACAAACCGAGCCG 60.660 55.000 0.00 0.00 0.00 5.52
5366 8663 0.941542 CTTCAAACAAACCGAGCCGA 59.058 50.000 0.00 0.00 0.00 5.54
5367 8664 1.332375 CTTCAAACAAACCGAGCCGAA 59.668 47.619 0.00 0.00 0.00 4.30
5368 8665 1.600023 TCAAACAAACCGAGCCGAAT 58.400 45.000 0.00 0.00 0.00 3.34
5369 8666 1.533731 TCAAACAAACCGAGCCGAATC 59.466 47.619 0.00 0.00 0.00 2.52
5370 8667 1.535462 CAAACAAACCGAGCCGAATCT 59.465 47.619 0.00 0.00 0.00 2.40
5371 8668 1.892209 AACAAACCGAGCCGAATCTT 58.108 45.000 0.00 0.00 0.00 2.40
5372 8669 2.754946 ACAAACCGAGCCGAATCTTA 57.245 45.000 0.00 0.00 0.00 2.10
5373 8670 2.344025 ACAAACCGAGCCGAATCTTAC 58.656 47.619 0.00 0.00 0.00 2.34
5374 8671 1.664151 CAAACCGAGCCGAATCTTACC 59.336 52.381 0.00 0.00 0.00 2.85
5375 8672 1.192428 AACCGAGCCGAATCTTACCT 58.808 50.000 0.00 0.00 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.194968 TCTCCGGTGATCAGTTTAACCTC 59.805 47.826 0.00 0.00 0.00 3.85
29 31 8.769359 ACTAGTTACTCCACATAATTTAGCCTT 58.231 33.333 0.00 0.00 0.00 4.35
52 54 8.880991 ACTAAAATAGACAGTCTCTGGAACTA 57.119 34.615 6.27 0.00 35.51 2.24
169 179 3.192001 GGGAGGTTTAATTTCACGGTTCC 59.808 47.826 0.00 0.00 0.00 3.62
222 232 1.341383 GGATCCTGGCTGGTCAAACAT 60.341 52.381 3.84 0.00 37.07 2.71
271 281 0.179073 CCGCAGTAATCCTGGTCTGG 60.179 60.000 0.00 0.00 41.81 3.86
276 286 1.883084 GCGTCCGCAGTAATCCTGG 60.883 63.158 6.82 0.00 41.81 4.45
287 297 2.604969 TCACTTTTATTTGCGTCCGC 57.395 45.000 4.42 4.42 42.35 5.54
292 302 6.139672 AGCGAAATTTCACTTTTATTTGCG 57.860 33.333 17.99 1.30 0.00 4.85
347 358 2.159448 TGAACTGAAAAACACTGGCACG 60.159 45.455 0.00 0.00 0.00 5.34
348 359 3.502191 TGAACTGAAAAACACTGGCAC 57.498 42.857 0.00 0.00 0.00 5.01
349 360 4.734398 AATGAACTGAAAAACACTGGCA 57.266 36.364 0.00 0.00 0.00 4.92
350 361 7.713764 AATAAATGAACTGAAAAACACTGGC 57.286 32.000 0.00 0.00 0.00 4.85
613 635 2.018086 AGGAGGGAGGAGGGAGGAG 61.018 68.421 0.00 0.00 0.00 3.69
614 636 2.015726 GAGGAGGGAGGAGGGAGGA 61.016 68.421 0.00 0.00 0.00 3.71
615 637 2.612251 GAGGAGGGAGGAGGGAGG 59.388 72.222 0.00 0.00 0.00 4.30
651 679 1.915078 ATTTGGAGGCGAGGGGTCAG 61.915 60.000 0.00 0.00 0.00 3.51
652 680 1.497309 AATTTGGAGGCGAGGGGTCA 61.497 55.000 0.00 0.00 0.00 4.02
653 681 0.544697 TAATTTGGAGGCGAGGGGTC 59.455 55.000 0.00 0.00 0.00 4.46
654 682 0.255033 GTAATTTGGAGGCGAGGGGT 59.745 55.000 0.00 0.00 0.00 4.95
655 683 0.546598 AGTAATTTGGAGGCGAGGGG 59.453 55.000 0.00 0.00 0.00 4.79
673 701 1.009900 GTGCGTCCGACGGAGATAG 60.010 63.158 18.98 10.34 44.00 2.08
674 702 2.816360 CGTGCGTCCGACGGAGATA 61.816 63.158 18.98 3.08 44.00 1.98
675 703 4.175489 CGTGCGTCCGACGGAGAT 62.175 66.667 18.98 0.00 44.00 2.75
705 741 1.134936 GTCACCGCAAAACCAAACCTT 60.135 47.619 0.00 0.00 0.00 3.50
1143 1179 2.204244 GGGTTGGGGGAGGAAGGA 60.204 66.667 0.00 0.00 0.00 3.36
1294 1330 2.223803 ATGGGGCGTGATTTAACCAA 57.776 45.000 0.00 0.00 0.00 3.67
1345 1381 1.703438 CGACCCGAGAGACGAATCGT 61.703 60.000 8.47 8.47 45.77 3.73
1391 1437 3.334691 CAGTCTTTGTTAAGATCCGCCA 58.665 45.455 0.00 0.00 42.14 5.69
1578 1624 1.293924 CGTTGCCTCAGCCAATCTAG 58.706 55.000 0.00 0.00 38.69 2.43
1606 1652 1.003051 AGCACGGGAAGGGATAGGT 59.997 57.895 0.00 0.00 0.00 3.08
1609 1655 1.306654 ACCAGCACGGGAAGGGATA 60.307 57.895 0.00 0.00 40.22 2.59
1610 1656 2.610859 ACCAGCACGGGAAGGGAT 60.611 61.111 0.00 0.00 40.22 3.85
1611 1657 3.319198 GACCAGCACGGGAAGGGA 61.319 66.667 0.00 0.00 40.22 4.20
1715 1762 0.178947 AAAAACGGGCCAATGAGGGA 60.179 50.000 4.39 0.00 38.09 4.20
1740 1787 0.189574 TCCCAATCCCCAAAACTGCA 59.810 50.000 0.00 0.00 0.00 4.41
1746 1793 0.413037 AGCACATCCCAATCCCCAAA 59.587 50.000 0.00 0.00 0.00 3.28
1778 1829 5.344743 TTTCTGCCAAGAAGTAGATCGAT 57.655 39.130 0.00 0.00 43.27 3.59
1844 1915 4.967084 TCTGAAGTGTAAAGCCCTAACA 57.033 40.909 0.00 0.00 0.00 2.41
1862 1944 7.040494 TGAATATTCAGAGCTCAGTTCTTCTG 58.960 38.462 17.77 2.52 37.79 3.02
1894 1976 6.184789 AGCGGAAACCCTCATTTCTTATAAA 58.815 36.000 0.00 0.00 38.43 1.40
1896 1978 5.367945 AGCGGAAACCCTCATTTCTTATA 57.632 39.130 0.00 0.00 38.43 0.98
1900 1982 2.162681 CAAGCGGAAACCCTCATTTCT 58.837 47.619 0.00 0.00 38.43 2.52
1901 1983 2.159382 TCAAGCGGAAACCCTCATTTC 58.841 47.619 0.00 0.00 37.78 2.17
1915 1997 1.135575 GGTGCTTCTTCCATTCAAGCG 60.136 52.381 0.00 0.00 44.66 4.68
1943 2025 6.739331 TGTTAATGGACACAAAAAGGGAAT 57.261 33.333 0.00 0.00 0.00 3.01
1953 2035 9.508642 TGACATTTTACTATGTTAATGGACACA 57.491 29.630 0.00 0.00 38.80 3.72
2054 2136 7.007725 CGTTTTAGCTGCTACAAAATGATGAAG 59.992 37.037 18.47 3.01 32.41 3.02
2102 2184 6.298361 TGATCAAGTCTTTCTCCATTGTTCA 58.702 36.000 0.00 0.00 30.93 3.18
2127 2210 5.304686 TGTCCTCATATAAACCCCATGTC 57.695 43.478 0.00 0.00 0.00 3.06
2261 2355 3.319972 AGAAGACACATTGCAATGCAGTT 59.680 39.130 33.94 22.95 40.61 3.16
2338 2455 5.423886 TGATTGCGACAACCTACATCATAA 58.576 37.500 0.00 0.00 0.00 1.90
2531 2648 2.897436 TGATCTGAAGCAATGTCCGAG 58.103 47.619 0.00 0.00 0.00 4.63
2732 2855 5.104817 TGAGCAATACACTCCATTCATCTCA 60.105 40.000 0.00 0.00 32.98 3.27
2968 3092 3.009033 TCAGTAATACAACAGCCAGGCTT 59.991 43.478 12.86 0.00 36.40 4.35
3188 3314 6.356186 ACTAACTAAAAGTAGTCCCACCTG 57.644 41.667 0.00 0.00 39.79 4.00
3252 3378 7.012044 AGGTGTGTGATTAAGTACAAGTGAAAC 59.988 37.037 0.00 0.00 0.00 2.78
3267 3393 3.297134 AACAAGTCCAGGTGTGTGATT 57.703 42.857 0.00 0.00 0.00 2.57
3276 3402 3.820467 TGCTGAATGTAAACAAGTCCAGG 59.180 43.478 0.00 0.00 0.00 4.45
3355 3481 5.125417 TGCAGAGCAAAAACAGTTTTCTACT 59.875 36.000 11.77 9.30 34.64 2.57
3397 3523 2.178912 TCCAAAAAGGTAGTGCGGAG 57.821 50.000 0.00 0.00 39.02 4.63
3427 3553 9.778741 ATGAACTTATGTCGTTATCACCAATAT 57.221 29.630 0.00 0.00 0.00 1.28
3546 3673 7.661027 AGCTATGCAAACAACATTAAATGGTTT 59.339 29.630 0.00 0.00 32.33 3.27
3821 3962 4.808364 GGAATCTTCACAGAGGAAATCTCG 59.192 45.833 0.00 0.00 46.82 4.04
3899 4041 6.148315 AGGAACCGTAAAGTATAAAAGTGCAC 59.852 38.462 9.40 9.40 0.00 4.57
3918 4060 0.182775 ATTGTATGCGGGGAGGAACC 59.817 55.000 0.00 0.00 38.08 3.62
3967 4110 5.238432 CCATTAATCGGTCGGATTTCATCAA 59.762 40.000 10.53 0.47 42.77 2.57
3973 4116 3.875134 GACACCATTAATCGGTCGGATTT 59.125 43.478 10.53 0.00 42.77 2.17
4005 4148 5.233083 TCTGCATTCTTTCTGAGAAAGGA 57.767 39.130 28.78 23.73 46.90 3.36
4046 4189 2.046285 CCCAATGGTGCTCCCGTTC 61.046 63.158 1.59 0.00 40.66 3.95
4061 4204 2.280524 CGCACGGTCTGTTTCCCA 60.281 61.111 0.00 0.00 0.00 4.37
4129 4272 2.983192 TGTTGGGGAGGTATGACAAGAA 59.017 45.455 0.00 0.00 0.00 2.52
4131 4274 2.305927 ACTGTTGGGGAGGTATGACAAG 59.694 50.000 0.00 0.00 0.00 3.16
4135 4278 5.789574 ATTTTACTGTTGGGGAGGTATGA 57.210 39.130 0.00 0.00 0.00 2.15
4137 4280 5.714806 CACAATTTTACTGTTGGGGAGGTAT 59.285 40.000 0.00 0.00 0.00 2.73
4139 4282 3.895041 CACAATTTTACTGTTGGGGAGGT 59.105 43.478 0.00 0.00 0.00 3.85
4146 4289 3.715495 TGGCTGCACAATTTTACTGTTG 58.285 40.909 0.50 0.00 0.00 3.33
4178 4326 0.108138 ATGCAGTAGCGTCAGGTTCC 60.108 55.000 0.00 0.00 46.23 3.62
4267 4415 0.529378 AGCCGTACCCGTTGTAGAAG 59.471 55.000 0.00 0.00 0.00 2.85
4345 4493 1.012486 GTTGCTGGTTCCCGTAGACG 61.012 60.000 0.00 0.00 39.44 4.18
4380 4528 2.978452 GATGGGCGTGTGATCCTCCG 62.978 65.000 0.00 0.00 0.00 4.63
4386 4534 1.069765 GGATCGATGGGCGTGTGAT 59.930 57.895 0.54 0.00 41.80 3.06
4388 4536 2.588877 GGGATCGATGGGCGTGTG 60.589 66.667 0.54 0.00 41.80 3.82
4401 4549 1.189524 TCGGGTTGTTGTCGAGGGAT 61.190 55.000 0.00 0.00 0.00 3.85
4402 4550 1.812686 CTCGGGTTGTTGTCGAGGGA 61.813 60.000 0.00 0.00 44.40 4.20
4403 4551 1.374252 CTCGGGTTGTTGTCGAGGG 60.374 63.158 0.00 0.00 44.40 4.30
4404 4552 4.261888 CTCGGGTTGTTGTCGAGG 57.738 61.111 0.00 0.00 44.40 4.63
4405 4553 2.027625 GCCTCGGGTTGTTGTCGAG 61.028 63.158 0.00 0.00 46.73 4.04
4406 4554 2.029964 GCCTCGGGTTGTTGTCGA 59.970 61.111 0.00 0.00 0.00 4.20
4407 4555 3.411351 CGCCTCGGGTTGTTGTCG 61.411 66.667 0.00 0.00 0.00 4.35
4408 4556 3.723348 GCGCCTCGGGTTGTTGTC 61.723 66.667 0.00 0.00 0.00 3.18
4470 4618 0.246635 GCTCACCTAAGAAGCCGTCA 59.753 55.000 0.00 0.00 0.00 4.35
4550 4701 1.659098 CGGTCGAGTCATTTTAGGTGC 59.341 52.381 0.00 0.00 0.00 5.01
4607 4758 2.892852 TGCAGCTCTATGCCAAAACTTT 59.107 40.909 0.00 0.00 45.91 2.66
4618 4769 8.195165 TGTTCTACCTTATATTGCAGCTCTAT 57.805 34.615 0.00 0.00 0.00 1.98
4688 4840 6.705381 TCAGTTCGAAATCAAATGCCAAAAAT 59.295 30.769 0.00 0.00 0.00 1.82
4696 4848 6.033196 GCTCAACATCAGTTCGAAATCAAATG 59.967 38.462 0.00 5.09 35.28 2.32
4733 4885 5.427378 TGCAACATATTCTAACAGCTAGCA 58.573 37.500 18.83 0.00 0.00 3.49
4751 4903 3.924144 TGGGCTATTGATTGTTTGCAAC 58.076 40.909 0.00 0.00 37.44 4.17
4770 4922 1.605710 CGAAATTGCTAGCTGGGATGG 59.394 52.381 17.23 0.00 0.00 3.51
4776 4928 5.469373 TTATGTGACGAAATTGCTAGCTG 57.531 39.130 17.23 1.48 0.00 4.24
4816 8095 2.734606 CAAAACTATCGTCAAGCGTCCA 59.265 45.455 0.00 0.00 42.13 4.02
4818 8097 2.474032 GCCAAAACTATCGTCAAGCGTC 60.474 50.000 0.00 0.00 42.13 5.19
4849 8128 7.713750 ACTAGCTATAAAATACGTTCAGCTGA 58.286 34.615 13.74 13.74 38.30 4.26
4866 8145 6.909550 AGGAAATCTCATCGAACTAGCTAT 57.090 37.500 0.00 0.00 0.00 2.97
4879 8158 4.351874 ACACGAGGAAAAGGAAATCTCA 57.648 40.909 0.00 0.00 0.00 3.27
4880 8159 4.515567 ACAACACGAGGAAAAGGAAATCTC 59.484 41.667 0.00 0.00 0.00 2.75
4897 8185 6.620678 ACCAATATTTGACATAGCACAACAC 58.379 36.000 0.00 0.00 0.00 3.32
4898 8186 6.832520 ACCAATATTTGACATAGCACAACA 57.167 33.333 0.00 0.00 0.00 3.33
4899 8187 7.757526 TGTACCAATATTTGACATAGCACAAC 58.242 34.615 0.00 0.00 0.00 3.32
4900 8188 7.929941 TGTACCAATATTTGACATAGCACAA 57.070 32.000 0.00 0.00 0.00 3.33
4901 8189 7.609918 AGTTGTACCAATATTTGACATAGCACA 59.390 33.333 0.00 0.00 0.00 4.57
4902 8190 7.985476 AGTTGTACCAATATTTGACATAGCAC 58.015 34.615 0.00 0.00 0.00 4.40
4903 8191 9.845740 ATAGTTGTACCAATATTTGACATAGCA 57.154 29.630 0.00 0.00 0.00 3.49
4926 8214 9.881649 TGATGCTCCTTATTAGCTTCATAATAG 57.118 33.333 8.94 0.00 44.49 1.73
4943 8231 5.352569 CGATTCTACTTTGTTTGATGCTCCT 59.647 40.000 0.00 0.00 0.00 3.69
4957 8245 8.351461 GGCTACTACTAAATGTCGATTCTACTT 58.649 37.037 0.00 0.00 0.00 2.24
4962 8250 4.916249 CGGGCTACTACTAAATGTCGATTC 59.084 45.833 0.00 0.00 0.00 2.52
5057 8345 3.316588 TGTTCATTAAAAAGCGAGCCACA 59.683 39.130 0.00 0.00 0.00 4.17
5115 8412 6.456501 ACTCATGAAACTCGTTAGCTAGTTT 58.543 36.000 11.28 11.28 45.99 2.66
5119 8416 5.357314 AGCTACTCATGAAACTCGTTAGCTA 59.643 40.000 0.00 0.00 35.69 3.32
5146 8443 9.434559 GTGTTGTCTTTTTACTAACAAGCTTAG 57.565 33.333 0.00 0.00 33.59 2.18
5165 8462 9.708222 GTCATGTAAGATGAAATATGTGTTGTC 57.292 33.333 0.00 0.00 0.00 3.18
5186 8483 5.957798 AGGTGCTACATCAATTTTGTCATG 58.042 37.500 0.00 0.00 0.00 3.07
5194 8491 2.240667 AGGCTGAGGTGCTACATCAATT 59.759 45.455 5.43 0.00 38.52 2.32
5199 8496 2.969628 AGATAGGCTGAGGTGCTACAT 58.030 47.619 0.00 0.00 0.00 2.29
5235 8532 3.584733 AAGGAAATGCACCCTCCTATC 57.415 47.619 12.27 0.00 38.69 2.08
5239 8536 1.970640 ACAAAAGGAAATGCACCCTCC 59.029 47.619 4.80 3.84 31.17 4.30
5244 8541 6.012658 TGATGACTACAAAAGGAAATGCAC 57.987 37.500 0.00 0.00 0.00 4.57
5245 8542 6.127647 GGATGATGACTACAAAAGGAAATGCA 60.128 38.462 0.00 0.00 0.00 3.96
5246 8543 6.096001 AGGATGATGACTACAAAAGGAAATGC 59.904 38.462 0.00 0.00 0.00 3.56
5247 8544 7.636150 AGGATGATGACTACAAAAGGAAATG 57.364 36.000 0.00 0.00 0.00 2.32
5248 8545 8.655935 AAAGGATGATGACTACAAAAGGAAAT 57.344 30.769 0.00 0.00 0.00 2.17
5249 8546 8.477419 AAAAGGATGATGACTACAAAAGGAAA 57.523 30.769 0.00 0.00 0.00 3.13
5250 8547 9.581289 TTAAAAGGATGATGACTACAAAAGGAA 57.419 29.630 0.00 0.00 0.00 3.36
5251 8548 9.581289 TTTAAAAGGATGATGACTACAAAAGGA 57.419 29.630 0.00 0.00 0.00 3.36
5278 8575 6.500684 AATGAGTGCGTAGATGTGATTTTT 57.499 33.333 0.00 0.00 0.00 1.94
5279 8576 7.280876 ACATAATGAGTGCGTAGATGTGATTTT 59.719 33.333 0.00 0.00 0.00 1.82
5280 8577 6.763135 ACATAATGAGTGCGTAGATGTGATTT 59.237 34.615 0.00 0.00 0.00 2.17
5281 8578 6.283694 ACATAATGAGTGCGTAGATGTGATT 58.716 36.000 0.00 0.00 0.00 2.57
5282 8579 5.847304 ACATAATGAGTGCGTAGATGTGAT 58.153 37.500 0.00 0.00 0.00 3.06
5283 8580 5.262588 ACATAATGAGTGCGTAGATGTGA 57.737 39.130 0.00 0.00 0.00 3.58
5284 8581 6.438763 TCTACATAATGAGTGCGTAGATGTG 58.561 40.000 0.00 0.00 34.98 3.21
5285 8582 6.635030 TCTACATAATGAGTGCGTAGATGT 57.365 37.500 0.00 0.00 34.98 3.06
5286 8583 7.596621 ACAATCTACATAATGAGTGCGTAGATG 59.403 37.037 10.26 7.86 44.91 2.90
5287 8584 7.661968 ACAATCTACATAATGAGTGCGTAGAT 58.338 34.615 0.00 0.00 46.65 1.98
5288 8585 7.039313 ACAATCTACATAATGAGTGCGTAGA 57.961 36.000 0.00 0.00 41.87 2.59
5289 8586 8.691727 GTTACAATCTACATAATGAGTGCGTAG 58.308 37.037 0.00 0.00 32.37 3.51
5290 8587 8.192110 TGTTACAATCTACATAATGAGTGCGTA 58.808 33.333 0.00 0.00 32.37 4.42
5291 8588 7.039270 TGTTACAATCTACATAATGAGTGCGT 58.961 34.615 0.00 0.00 32.37 5.24
5292 8589 7.435192 TCTGTTACAATCTACATAATGAGTGCG 59.565 37.037 0.00 0.00 32.37 5.34
5293 8590 8.648557 TCTGTTACAATCTACATAATGAGTGC 57.351 34.615 0.00 0.00 32.37 4.40
5313 8610 8.404000 GCACTCATTAATGAATTCTGATCTGTT 58.596 33.333 18.47 0.00 36.18 3.16
5314 8611 7.774157 AGCACTCATTAATGAATTCTGATCTGT 59.226 33.333 18.47 6.70 36.18 3.41
5315 8612 8.155821 AGCACTCATTAATGAATTCTGATCTG 57.844 34.615 18.47 6.12 36.18 2.90
5316 8613 7.991460 TGAGCACTCATTAATGAATTCTGATCT 59.009 33.333 18.47 9.01 36.18 2.75
5317 8614 8.068977 GTGAGCACTCATTAATGAATTCTGATC 58.931 37.037 18.47 17.06 42.18 2.92
5318 8615 7.254692 CGTGAGCACTCATTAATGAATTCTGAT 60.255 37.037 18.47 10.19 42.18 2.90
5319 8616 6.036408 CGTGAGCACTCATTAATGAATTCTGA 59.964 38.462 18.47 0.60 42.18 3.27
5320 8617 6.036408 TCGTGAGCACTCATTAATGAATTCTG 59.964 38.462 18.47 9.41 42.18 3.02
5321 8618 6.108687 TCGTGAGCACTCATTAATGAATTCT 58.891 36.000 18.47 9.11 42.18 2.40
5322 8619 6.349973 TCGTGAGCACTCATTAATGAATTC 57.650 37.500 18.47 13.15 42.18 2.17
5323 8620 6.355397 CTCGTGAGCACTCATTAATGAATT 57.645 37.500 18.47 6.52 42.18 2.17
5324 8621 5.980698 CTCGTGAGCACTCATTAATGAAT 57.019 39.130 18.47 6.60 42.18 2.57
5339 8636 2.599848 CGGTTTGTTTGAAGCTCGTGAG 60.600 50.000 0.00 0.00 0.00 3.51
5340 8637 1.329292 CGGTTTGTTTGAAGCTCGTGA 59.671 47.619 0.00 0.00 0.00 4.35
5341 8638 1.329292 TCGGTTTGTTTGAAGCTCGTG 59.671 47.619 0.00 0.00 0.00 4.35
5342 8639 1.597663 CTCGGTTTGTTTGAAGCTCGT 59.402 47.619 0.00 0.00 0.00 4.18
5343 8640 1.660333 GCTCGGTTTGTTTGAAGCTCG 60.660 52.381 0.00 0.00 0.00 5.03
5344 8641 1.335051 GGCTCGGTTTGTTTGAAGCTC 60.335 52.381 0.00 0.00 0.00 4.09
5345 8642 0.668535 GGCTCGGTTTGTTTGAAGCT 59.331 50.000 0.00 0.00 0.00 3.74
5346 8643 0.660300 CGGCTCGGTTTGTTTGAAGC 60.660 55.000 0.00 0.00 0.00 3.86
5347 8644 0.941542 TCGGCTCGGTTTGTTTGAAG 59.058 50.000 0.00 0.00 0.00 3.02
5348 8645 1.380524 TTCGGCTCGGTTTGTTTGAA 58.619 45.000 0.00 0.00 0.00 2.69
5349 8646 1.533731 GATTCGGCTCGGTTTGTTTGA 59.466 47.619 0.00 0.00 0.00 2.69
5350 8647 1.535462 AGATTCGGCTCGGTTTGTTTG 59.465 47.619 0.00 0.00 0.00 2.93
5351 8648 1.892209 AGATTCGGCTCGGTTTGTTT 58.108 45.000 0.00 0.00 0.00 2.83
5352 8649 1.892209 AAGATTCGGCTCGGTTTGTT 58.108 45.000 0.00 0.00 0.00 2.83
5353 8650 2.344025 GTAAGATTCGGCTCGGTTTGT 58.656 47.619 0.00 0.00 0.00 2.83
5354 8651 1.664151 GGTAAGATTCGGCTCGGTTTG 59.336 52.381 0.00 0.00 0.00 2.93
5355 8652 1.553704 AGGTAAGATTCGGCTCGGTTT 59.446 47.619 0.00 0.00 0.00 3.27
5356 8653 1.192428 AGGTAAGATTCGGCTCGGTT 58.808 50.000 0.00 0.00 0.00 4.44
5357 8654 2.897699 AGGTAAGATTCGGCTCGGT 58.102 52.632 0.00 0.00 0.00 4.69


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

AutoCloner maintained by Alex Coulton.