Multiple sequence alignment - TraesCS4D01G248500

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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 TraesCS4D01G248500 chr4D 100.000 7349 0 0 1 7349 417633053 417625705 0.000000e+00 13572.0
1 TraesCS4D01G248500 chr4D 95.419 1943 71 10 2768 4696 401088496 401086558 0.000000e+00 3079.0
2 TraesCS4D01G248500 chr4D 93.283 1459 50 20 5916 7349 401085516 401084081 0.000000e+00 2108.0
3 TraesCS4D01G248500 chr4D 93.577 1370 73 8 840 2204 401090781 401089422 0.000000e+00 2028.0
4 TraesCS4D01G248500 chr4D 92.850 1049 48 14 4785 5816 401086552 401085514 0.000000e+00 1496.0
5 TraesCS4D01G248500 chr4D 88.336 643 40 17 1 630 401094286 401093666 0.000000e+00 739.0
6 TraesCS4D01G248500 chr4D 90.184 489 29 11 2312 2785 401089165 401088681 2.910000e-173 619.0
7 TraesCS4D01G248500 chr4D 81.622 370 51 13 163 517 82742738 82743105 2.590000e-74 291.0
8 TraesCS4D01G248500 chr4D 91.707 205 14 3 628 830 401092839 401092636 1.560000e-71 281.0
9 TraesCS4D01G248500 chr4B 97.195 2389 51 7 2311 4696 495595310 495592935 0.000000e+00 4026.0
10 TraesCS4D01G248500 chr4B 92.553 1692 83 17 544 2214 495597252 495595583 0.000000e+00 2386.0
11 TraesCS4D01G248500 chr4B 94.255 1323 50 12 5821 7123 495591905 495590589 0.000000e+00 1999.0
12 TraesCS4D01G248500 chr4B 95.541 785 30 4 4785 5565 495592929 495592146 0.000000e+00 1251.0
13 TraesCS4D01G248500 chr4B 95.652 207 9 0 5546 5752 495592134 495591928 4.250000e-87 333.0
14 TraesCS4D01G248500 chr4A 94.230 2409 110 17 2311 4696 58882572 58880170 0.000000e+00 3651.0
15 TraesCS4D01G248500 chr4A 91.670 2605 119 43 4785 7347 58880164 58877616 0.000000e+00 3518.0
16 TraesCS4D01G248500 chr4A 92.746 1544 60 16 692 2204 58884350 58882828 0.000000e+00 2183.0
17 TraesCS4D01G248500 chr4A 81.471 367 53 11 164 516 503613908 503613543 3.360000e-73 287.0
18 TraesCS4D01G248500 chr4A 93.865 163 5 3 1 163 58884612 58884455 2.650000e-59 241.0
19 TraesCS4D01G248500 chr4A 88.430 121 13 1 545 664 58884462 58884342 2.140000e-30 145.0
20 TraesCS4D01G248500 chr3D 82.561 367 48 13 164 516 373599813 373599449 7.160000e-80 309.0
21 TraesCS4D01G248500 chr1A 81.793 368 51 12 163 516 508209589 508209954 2.010000e-75 294.0
22 TraesCS4D01G248500 chr5B 81.793 368 49 14 162 516 588793452 588793090 7.210000e-75 292.0
23 TraesCS4D01G248500 chr5B 80.978 368 52 14 164 515 586912590 586912955 7.260000e-70 276.0
24 TraesCS4D01G248500 chr5B 84.564 149 16 5 4637 4780 557898201 557898055 2.760000e-29 141.0
25 TraesCS4D01G248500 chr7A 81.944 360 49 14 163 507 63576658 63577016 2.590000e-74 291.0
26 TraesCS4D01G248500 chrUn 83.129 326 42 10 165 481 28336084 28335763 1.210000e-72 285.0
27 TraesCS4D01G248500 chrUn 100.000 30 0 0 5424 5453 36547635 36547664 1.000000e-03 56.5
28 TraesCS4D01G248500 chrUn 100.000 30 0 0 5424 5453 186205832 186205803 1.000000e-03 56.5
29 TraesCS4D01G248500 chrUn 100.000 30 0 0 5424 5453 434806169 434806198 1.000000e-03 56.5
30 TraesCS4D01G248500 chrUn 100.000 30 0 0 5424 5453 464745809 464745780 1.000000e-03 56.5
31 TraesCS4D01G248500 chr3B 80.488 369 54 13 164 516 662010750 662010384 4.370000e-67 267.0
32 TraesCS4D01G248500 chr2B 97.778 90 2 0 4692 4781 33495529 33495618 9.870000e-34 156.0
33 TraesCS4D01G248500 chr6B 94.000 100 6 0 4680 4779 349967748 349967649 1.280000e-32 152.0
34 TraesCS4D01G248500 chr6A 95.745 94 4 0 4686 4779 382867351 382867444 1.280000e-32 152.0
35 TraesCS4D01G248500 chr7B 94.845 97 4 1 4684 4780 167622329 167622234 4.590000e-32 150.0
36 TraesCS4D01G248500 chr7B 92.381 105 7 1 4676 4779 414571485 414571381 1.650000e-31 148.0
37 TraesCS4D01G248500 chr1D 93.137 102 6 1 4678 4779 265533241 265533141 1.650000e-31 148.0
38 TraesCS4D01G248500 chr1B 93.137 102 4 3 4687 4786 172000866 172000766 5.940000e-31 147.0
39 TraesCS4D01G248500 chr2D 91.509 106 8 1 4675 4780 37535476 37535580 2.140000e-30 145.0
40 TraesCS4D01G248500 chr6D 100.000 30 0 0 5424 5453 124520116 124520145 1.000000e-03 56.5
41 TraesCS4D01G248500 chr6D 100.000 30 0 0 5424 5453 168757692 168757721 1.000000e-03 56.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G248500 chr4D 417625705 417633053 7348 True 13572.000000 13572 100.000000 1 7349 1 chr4D.!!$R1 7348
1 TraesCS4D01G248500 chr4D 401084081 401094286 10205 True 1478.571429 3079 92.193714 1 7349 7 chr4D.!!$R2 7348
2 TraesCS4D01G248500 chr4B 495590589 495597252 6663 True 1999.000000 4026 95.039200 544 7123 5 chr4B.!!$R1 6579
3 TraesCS4D01G248500 chr4A 58877616 58884612 6996 True 1947.600000 3651 92.188200 1 7347 5 chr4A.!!$R2 7346

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
904 3599 0.321564 CATCACCAAACTCCTCGGCA 60.322 55.000 0.00 0.0 0.00 5.69 F
1900 4632 1.098050 GGTGTGATGTCTTGCCCATC 58.902 55.000 0.00 0.0 39.32 3.51 F
3141 6275 0.898320 ACTGCGCAGAAGAGGTATGT 59.102 50.000 42.03 15.2 0.00 2.29 F
4073 7209 2.158081 AGTGAGGGAGGGAGTTTCTCTT 60.158 50.000 0.00 0.0 0.00 2.85 F
4829 7986 0.740737 ATGCTATCGGTGCAAAAGGC 59.259 50.000 0.00 0.0 44.01 4.35 F
5627 8827 2.032681 GAGGAGCAGCCGGTGTTT 59.967 61.111 1.90 0.0 43.43 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2386 5306 0.598065 GGCTCATTCGGTTTGCAGTT 59.402 50.000 0.00 0.0 0.00 3.16 R
3485 6621 2.836479 TGTTGCAGATGAATGATGCG 57.164 45.000 0.00 0.0 42.92 4.73 R
4432 7568 2.092968 AGCGGAAGATAACTTGATGGCA 60.093 45.455 0.00 0.0 36.39 4.92 R
5615 8813 0.033366 AAATCCAAAACACCGGCTGC 59.967 50.000 0.00 0.0 0.00 5.25 R
5956 9177 0.808453 TTATCTACCAAGGCACGCGC 60.808 55.000 5.73 0.0 37.44 6.86 R
6906 10152 1.038681 TGCATCCGCCAAATCAGCAT 61.039 50.000 0.00 0.0 37.32 3.79 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
122 123 3.145286 GTCAGCTCTTGCCTTTTTCTCT 58.855 45.455 0.00 0.00 40.80 3.10
176 177 2.370393 GCGTCGGACGTGGAGTTTC 61.370 63.158 28.75 8.40 44.73 2.78
181 182 2.094854 GTCGGACGTGGAGTTTCTACAT 60.095 50.000 0.00 0.00 0.00 2.29
216 224 5.626142 TGCTCTTGGGTGAACAGTAAATTA 58.374 37.500 0.00 0.00 0.00 1.40
218 226 6.547880 TGCTCTTGGGTGAACAGTAAATTAAA 59.452 34.615 0.00 0.00 0.00 1.52
276 285 6.484977 GTGGCAAAATTTAAGGAATGTTTGGA 59.515 34.615 0.00 0.00 32.49 3.53
279 288 7.307930 GGCAAAATTTAAGGAATGTTTGGAGTG 60.308 37.037 0.00 0.00 32.49 3.51
280 289 7.226523 GCAAAATTTAAGGAATGTTTGGAGTGT 59.773 33.333 0.00 0.00 32.49 3.55
281 290 9.757227 CAAAATTTAAGGAATGTTTGGAGTGTA 57.243 29.630 0.00 0.00 30.58 2.90
283 292 9.927668 AAATTTAAGGAATGTTTGGAGTGTATG 57.072 29.630 0.00 0.00 0.00 2.39
284 293 6.509418 TTAAGGAATGTTTGGAGTGTATGC 57.491 37.500 0.00 0.00 0.00 3.14
287 296 4.832266 AGGAATGTTTGGAGTGTATGCAAA 59.168 37.500 0.00 0.00 45.75 3.68
312 321 2.479837 CCATCATGCAATCACATTGGC 58.520 47.619 0.00 0.00 40.57 4.52
314 323 1.461559 TCATGCAATCACATTGGCGA 58.538 45.000 0.00 0.00 40.57 5.54
368 377 7.758495 ACTCTGAAAATGTTACTTTCAAACGT 58.242 30.769 2.32 0.00 41.10 3.99
380 389 6.144078 ACTTTCAAACGTATTTTGGAGCTT 57.856 33.333 0.00 0.00 44.30 3.74
429 438 4.943093 TCACCAATGTGATTTCGTGATGAT 59.057 37.500 0.00 0.00 46.40 2.45
453 462 4.959596 TTTGCATGCACAACAAACATTT 57.040 31.818 22.58 0.00 0.00 2.32
463 472 8.401046 TGCACAACAAACATTTCTTAAAGTAC 57.599 30.769 0.00 0.00 0.00 2.73
468 477 6.797454 ACAAACATTTCTTAAAGTACGCCAA 58.203 32.000 0.00 0.00 0.00 4.52
469 478 7.259161 ACAAACATTTCTTAAAGTACGCCAAA 58.741 30.769 0.00 0.00 0.00 3.28
631 1470 7.148722 GCTGGCGTTTTGTTGCTTAAAATATTA 60.149 33.333 0.00 0.00 30.62 0.98
644 1483 7.073265 GCTTAAAATATTAATGCGCGGAGTTA 58.927 34.615 5.57 0.00 30.88 2.24
786 1636 1.626825 ACTTACTTGCCGGGCTTCTTA 59.373 47.619 21.46 3.44 0.00 2.10
901 3596 1.726853 GGTCATCACCAAACTCCTCG 58.273 55.000 0.00 0.00 43.17 4.63
904 3599 0.321564 CATCACCAAACTCCTCGGCA 60.322 55.000 0.00 0.00 0.00 5.69
909 3604 1.301677 CCAAACTCCTCGGCAGAAGC 61.302 60.000 0.00 0.00 41.10 3.86
1389 4092 2.996631 AGTGAGTCCATTCTGGCATTC 58.003 47.619 0.00 0.00 37.47 2.67
1391 4094 2.941720 GTGAGTCCATTCTGGCATTCTC 59.058 50.000 0.00 0.00 37.47 2.87
1563 4288 8.095937 AGAACCTGCAGTTAGTGTTTTATTAC 57.904 34.615 13.81 0.00 39.40 1.89
1629 4361 5.645497 AGCTGTAGATGCAAAAGGTTTCTAG 59.355 40.000 0.00 0.00 0.00 2.43
1684 4416 4.522405 CACCACCATTGTGTTAGGATTGAA 59.478 41.667 0.00 0.00 41.09 2.69
1900 4632 1.098050 GGTGTGATGTCTTGCCCATC 58.902 55.000 0.00 0.00 39.32 3.51
1919 4651 1.893137 TCTAGTGGCACGACAATCTGT 59.107 47.619 12.71 0.00 0.00 3.41
1986 4718 5.540337 ACTGCGGGAAGAAGATATAGATGAA 59.460 40.000 0.00 0.00 0.00 2.57
2114 4846 7.539712 TCTTGCCTTAATTTTCTAGATCACG 57.460 36.000 0.00 0.00 0.00 4.35
2278 5011 4.863152 AAAAACTGCAAACTGAATGTGC 57.137 36.364 0.00 0.00 38.78 4.57
2279 5012 2.514205 AACTGCAAACTGAATGTGCC 57.486 45.000 0.00 0.00 37.48 5.01
2280 5013 1.401761 ACTGCAAACTGAATGTGCCA 58.598 45.000 0.00 0.00 37.48 4.92
2282 5015 3.156293 ACTGCAAACTGAATGTGCCATA 58.844 40.909 0.00 0.00 37.48 2.74
2283 5016 3.765511 ACTGCAAACTGAATGTGCCATAT 59.234 39.130 0.00 0.00 37.48 1.78
2284 5017 4.949238 ACTGCAAACTGAATGTGCCATATA 59.051 37.500 0.00 0.00 37.48 0.86
2285 5018 5.595542 ACTGCAAACTGAATGTGCCATATAT 59.404 36.000 0.00 0.00 37.48 0.86
2288 5021 6.207221 TGCAAACTGAATGTGCCATATATAGG 59.793 38.462 0.00 0.00 37.48 2.57
2289 5022 6.349611 GCAAACTGAATGTGCCATATATAGGG 60.350 42.308 9.14 9.14 31.94 3.53
2290 5023 6.702449 AACTGAATGTGCCATATATAGGGA 57.298 37.500 17.56 3.24 0.00 4.20
2291 5024 6.702449 ACTGAATGTGCCATATATAGGGAA 57.298 37.500 17.56 3.42 0.00 3.97
2292 5025 7.090319 ACTGAATGTGCCATATATAGGGAAA 57.910 36.000 17.56 1.50 0.00 3.13
2294 5027 8.004215 ACTGAATGTGCCATATATAGGGAAAAA 58.996 33.333 17.56 0.00 0.00 1.94
2338 5247 5.916661 TCGTAAGGAATCTTAGTTGCTCT 57.083 39.130 0.00 0.00 36.27 4.09
2654 5577 3.189287 CCTTTTCCTTTCACTGGATGTCG 59.811 47.826 0.00 0.00 33.09 4.35
2695 5618 4.174411 TGGAGATATATTTCCGCTCACG 57.826 45.455 15.59 0.00 36.22 4.35
2732 5655 6.677781 TTTTACTGCTACTGACAATATGGC 57.322 37.500 0.00 0.00 0.00 4.40
2808 5933 5.985911 TGCTCTAATTTGACCTTACCTACC 58.014 41.667 0.00 0.00 0.00 3.18
2862 5987 9.729023 CTATACTTGACTTCATTCACTAGACAG 57.271 37.037 0.00 0.00 0.00 3.51
2924 6053 1.812571 CTGTTGCCGAATACCTTGCTT 59.187 47.619 0.00 0.00 0.00 3.91
2984 6118 9.199982 GATCAATTGACATTTGATGTTCAAGTT 57.800 29.630 23.54 4.22 45.03 2.66
2987 6121 8.819015 CAATTGACATTTGATGTTCAAGTTTCA 58.181 29.630 0.00 0.00 45.03 2.69
3005 6139 8.445493 CAAGTTTCATAATTCAAATTTCCCTGC 58.555 33.333 0.00 0.00 0.00 4.85
3141 6275 0.898320 ACTGCGCAGAAGAGGTATGT 59.102 50.000 42.03 15.20 0.00 2.29
3445 6581 7.536622 GTCAGTATGCAATGAGCTAATTAATGC 59.463 37.037 0.00 0.00 45.94 3.56
3485 6621 7.230510 TCCCTTCCAAATAACATGCATACATAC 59.769 37.037 0.00 0.00 33.67 2.39
3959 7095 4.833478 ATGGTCACTTAGAGATGCAACT 57.167 40.909 0.00 0.00 0.00 3.16
4025 7161 2.890808 TGCGATATCCTCCACTTGTC 57.109 50.000 0.00 0.00 0.00 3.18
4073 7209 2.158081 AGTGAGGGAGGGAGTTTCTCTT 60.158 50.000 0.00 0.00 0.00 2.85
4181 7317 8.540388 GCAATACTGGATCCTATAATTCAGGTA 58.460 37.037 14.23 1.76 36.69 3.08
4283 7419 6.458342 CGATCTGACTAATTTTTACCCTTGGC 60.458 42.308 0.00 0.00 0.00 4.52
4308 7444 7.010367 GCGCAATTTTGAATTTTGATCCTATCA 59.990 33.333 0.30 0.00 37.55 2.15
4383 7519 8.507582 TCTTCCTATCCTCTATGTCTACAGTA 57.492 38.462 0.00 0.00 0.00 2.74
4432 7568 8.314751 ACTAGCAGTATTTCAGTGTCTGTATTT 58.685 33.333 0.00 0.00 32.61 1.40
4468 7617 1.066215 TCCGCTCAAGCAAGCTATCAA 60.066 47.619 2.50 0.00 42.21 2.57
4715 7870 8.890410 TTAGTACTCCCTCTGTAAACTAATGT 57.110 34.615 0.00 0.00 0.00 2.71
4716 7871 9.979897 TTAGTACTCCCTCTGTAAACTAATGTA 57.020 33.333 0.00 0.00 0.00 2.29
4717 7872 8.890410 AGTACTCCCTCTGTAAACTAATGTAA 57.110 34.615 0.00 0.00 0.00 2.41
4718 7873 8.968969 AGTACTCCCTCTGTAAACTAATGTAAG 58.031 37.037 0.00 0.00 0.00 2.34
4719 7874 8.964772 GTACTCCCTCTGTAAACTAATGTAAGA 58.035 37.037 0.00 0.00 0.00 2.10
4720 7875 8.068892 ACTCCCTCTGTAAACTAATGTAAGAG 57.931 38.462 0.00 0.00 0.00 2.85
4721 7876 7.674772 ACTCCCTCTGTAAACTAATGTAAGAGT 59.325 37.037 0.00 0.00 0.00 3.24
4722 7877 7.837863 TCCCTCTGTAAACTAATGTAAGAGTG 58.162 38.462 0.00 0.00 0.00 3.51
4723 7878 7.453752 TCCCTCTGTAAACTAATGTAAGAGTGT 59.546 37.037 0.00 0.00 0.00 3.55
4724 7879 8.095169 CCCTCTGTAAACTAATGTAAGAGTGTT 58.905 37.037 0.00 0.00 0.00 3.32
4725 7880 9.141400 CCTCTGTAAACTAATGTAAGAGTGTTC 57.859 37.037 0.00 0.00 0.00 3.18
4726 7881 9.692749 CTCTGTAAACTAATGTAAGAGTGTTCA 57.307 33.333 0.00 0.00 0.00 3.18
4727 7882 9.692749 TCTGTAAACTAATGTAAGAGTGTTCAG 57.307 33.333 0.00 0.00 0.00 3.02
4728 7883 9.692749 CTGTAAACTAATGTAAGAGTGTTCAGA 57.307 33.333 0.00 0.00 0.00 3.27
4732 7887 8.764524 AACTAATGTAAGAGTGTTCAGATCAC 57.235 34.615 3.68 3.68 36.22 3.06
4733 7888 8.128322 ACTAATGTAAGAGTGTTCAGATCACT 57.872 34.615 13.13 13.13 46.86 3.41
4734 7889 9.244292 ACTAATGTAAGAGTGTTCAGATCACTA 57.756 33.333 13.22 0.00 44.68 2.74
4735 7890 9.509855 CTAATGTAAGAGTGTTCAGATCACTAC 57.490 37.037 13.22 9.32 44.68 2.73
4736 7891 7.710676 ATGTAAGAGTGTTCAGATCACTACT 57.289 36.000 13.22 9.80 44.68 2.57
4737 7892 7.526142 TGTAAGAGTGTTCAGATCACTACTT 57.474 36.000 13.22 17.14 44.68 2.24
4738 7893 7.952671 TGTAAGAGTGTTCAGATCACTACTTT 58.047 34.615 20.08 14.82 44.68 2.66
4739 7894 9.074576 TGTAAGAGTGTTCAGATCACTACTTTA 57.925 33.333 20.08 14.19 44.68 1.85
4740 7895 9.562583 GTAAGAGTGTTCAGATCACTACTTTAG 57.437 37.037 20.08 0.00 44.68 1.85
4741 7896 7.768807 AGAGTGTTCAGATCACTACTTTAGT 57.231 36.000 13.22 0.00 44.68 2.24
4742 7897 8.865420 AGAGTGTTCAGATCACTACTTTAGTA 57.135 34.615 13.22 0.00 44.68 1.82
4743 7898 9.469097 AGAGTGTTCAGATCACTACTTTAGTAT 57.531 33.333 13.22 0.00 44.68 2.12
4752 7907 9.733219 AGATCACTACTTTAGTATTCTAAACGC 57.267 33.333 0.76 0.00 40.05 4.84
4753 7908 9.733219 GATCACTACTTTAGTATTCTAAACGCT 57.267 33.333 0.76 0.00 40.05 5.07
4754 7909 9.733219 ATCACTACTTTAGTATTCTAAACGCTC 57.267 33.333 0.76 0.00 40.05 5.03
4755 7910 8.954350 TCACTACTTTAGTATTCTAAACGCTCT 58.046 33.333 0.76 0.00 40.05 4.09
4756 7911 9.570488 CACTACTTTAGTATTCTAAACGCTCTT 57.430 33.333 0.76 0.00 40.05 2.85
4770 7925 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
4771 7926 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
4772 7927 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
4773 7928 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
4774 7929 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
4775 7930 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
4776 7931 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
4777 7932 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
4778 7933 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
4781 7936 4.660789 TTAGTTTACGGAGGGAGTATGC 57.339 45.455 0.00 0.00 0.00 3.14
4782 7937 2.463752 AGTTTACGGAGGGAGTATGCA 58.536 47.619 0.00 0.00 0.00 3.96
4783 7938 2.835764 AGTTTACGGAGGGAGTATGCAA 59.164 45.455 0.00 0.00 0.00 4.08
4829 7986 0.740737 ATGCTATCGGTGCAAAAGGC 59.259 50.000 0.00 0.00 44.01 4.35
4850 8007 4.119862 GCGTTCCATATCTGCTGTTCTTA 58.880 43.478 0.00 0.00 0.00 2.10
4938 8095 2.698797 TGGTTTATCGGGAGTCCTCATC 59.301 50.000 9.58 0.00 0.00 2.92
5003 8160 2.038164 TCTTCAGATGTGTGAGCAAGCT 59.962 45.455 0.00 0.00 0.00 3.74
5250 8407 7.907389 TCTGGTCATGAACTGAACTAGTAAAT 58.093 34.615 17.09 0.00 42.49 1.40
5284 8442 2.708216 TCTTTCTGTTGCCAGTCACA 57.292 45.000 0.00 0.00 39.82 3.58
5354 8512 9.487790 ACAAGTCAAGAAATTTCAAAAAGTTCA 57.512 25.926 19.99 0.00 0.00 3.18
5362 8520 7.706607 AGAAATTTCAAAAAGTTCACTGTAGCC 59.293 33.333 19.99 0.00 0.00 3.93
5471 8637 2.752354 CACTTCCATTCATTTGGCGGTA 59.248 45.455 0.00 0.00 36.66 4.02
5502 8669 6.228616 TCGACATGGGAAACACTTATGATA 57.771 37.500 0.00 0.00 0.00 2.15
5529 8696 8.899427 AGTAATTGATGAACTGATCCTACATG 57.101 34.615 0.00 0.00 0.00 3.21
5565 8763 5.867330 TGCAATTCCAATTCACATTCCTTT 58.133 33.333 0.00 0.00 0.00 3.11
5594 8792 6.126409 TCGCTTTATGGTCCCAGAATAAAAT 58.874 36.000 0.00 0.00 0.00 1.82
5627 8827 2.032681 GAGGAGCAGCCGGTGTTT 59.967 61.111 1.90 0.00 43.43 2.83
5753 8956 3.713826 TTAAGCCTTTGACTGGGTAGG 57.286 47.619 0.00 0.00 34.56 3.18
5784 8988 5.154222 GCTTTAGCTGCGTAAATCAACTTT 58.846 37.500 0.00 0.00 38.21 2.66
5815 9019 9.421806 CATTTGCTTACATCCAAGTAATTTCAA 57.578 29.630 0.00 0.00 33.82 2.69
5850 9071 2.628178 ACAGAGTGGTGAATCTTCGTCA 59.372 45.455 0.00 0.00 0.00 4.35
5956 9177 2.214244 CGCTCTATGATCGAAACACACG 59.786 50.000 0.00 0.00 0.00 4.49
6204 9425 2.354805 GGTTCCAAGGTTACGCTCAGAT 60.355 50.000 0.00 0.00 0.00 2.90
6530 9763 8.447833 TCGAATACAGGTTTGCTTGTTTATAAG 58.552 33.333 0.00 0.00 36.32 1.73
6531 9764 8.447833 CGAATACAGGTTTGCTTGTTTATAAGA 58.552 33.333 0.00 0.00 36.32 2.10
6594 9829 7.829706 GGTATACCAGAGAAGAAAAACATTCCT 59.170 37.037 17.44 0.00 35.64 3.36
6631 9874 5.713861 AGATTTGAAGAAACCAGATTCCAGG 59.286 40.000 0.00 0.00 0.00 4.45
6639 9882 2.196595 ACCAGATTCCAGGATTTCCGA 58.803 47.619 0.00 0.00 42.08 4.55
6640 9883 2.576191 ACCAGATTCCAGGATTTCCGAA 59.424 45.455 0.00 0.00 42.08 4.30
6652 9895 5.123820 CAGGATTTCCGAATTCTTGCTTGTA 59.876 40.000 3.52 0.00 42.08 2.41
6673 9916 2.485122 GGTTGAAAGCGATGCCGG 59.515 61.111 0.00 0.00 36.06 6.13
6692 9935 2.355756 CGGATAACTGCATCCAACTTGG 59.644 50.000 0.74 0.74 44.16 3.61
6704 9947 2.069273 CCAACTTGGCAACTAGAGTCG 58.931 52.381 0.00 0.00 42.51 4.18
6880 10123 5.398603 TTTTGATGGAACTTTGTGTGTGT 57.601 34.783 0.00 0.00 0.00 3.72
6881 10124 4.368874 TTGATGGAACTTTGTGTGTGTG 57.631 40.909 0.00 0.00 0.00 3.82
6888 10133 3.302685 TTTGTGTGTGTGGCCCCCA 62.303 57.895 0.00 0.00 0.00 4.96
6906 10152 5.691167 GCCCCCATATCTGATCTCTTTTTCA 60.691 44.000 0.00 0.00 0.00 2.69
7215 10469 4.556942 TCGGCAGCTGAAAAATATGATG 57.443 40.909 20.43 0.00 0.00 3.07
7286 10540 3.003068 GTGGCTTGTAATAGCAGCATCAG 59.997 47.826 0.00 0.00 43.02 2.90
7288 10542 2.615447 GCTTGTAATAGCAGCATCAGCA 59.385 45.455 0.00 0.00 45.49 4.41
7296 10550 0.027716 GCAGCATCAGCATCGTTGAG 59.972 55.000 0.00 0.00 45.49 3.02
7306 10560 2.002586 GCATCGTTGAGTACTGCACAT 58.997 47.619 0.00 0.00 33.13 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
139 140 6.354080 CGACGCATGTTTCAATTTTCAAAAT 58.646 32.000 0.00 0.00 0.00 1.82
176 177 2.877168 GAGCATTTGAGCCCTGATGTAG 59.123 50.000 0.00 0.00 34.23 2.74
181 182 1.615116 CCAAGAGCATTTGAGCCCTGA 60.615 52.381 2.15 0.00 34.23 3.86
260 269 6.491745 TGCATACACTCCAAACATTCCTTAAA 59.508 34.615 0.00 0.00 0.00 1.52
276 285 4.032960 TGATGGGAGTTTTGCATACACT 57.967 40.909 0.00 0.00 0.00 3.55
279 288 3.130869 TGCATGATGGGAGTTTTGCATAC 59.869 43.478 0.00 0.00 35.36 2.39
280 289 3.363627 TGCATGATGGGAGTTTTGCATA 58.636 40.909 0.00 0.00 35.36 3.14
281 290 2.181125 TGCATGATGGGAGTTTTGCAT 58.819 42.857 0.00 0.00 35.36 3.96
282 291 1.630223 TGCATGATGGGAGTTTTGCA 58.370 45.000 0.00 0.00 37.73 4.08
283 292 2.747396 TTGCATGATGGGAGTTTTGC 57.253 45.000 0.00 0.00 0.00 3.68
284 293 4.178540 GTGATTGCATGATGGGAGTTTTG 58.821 43.478 0.00 0.00 0.00 2.44
287 296 3.090210 TGTGATTGCATGATGGGAGTT 57.910 42.857 0.00 0.00 0.00 3.01
288 297 2.812836 TGTGATTGCATGATGGGAGT 57.187 45.000 0.00 0.00 0.00 3.85
289 298 3.243737 CCAATGTGATTGCATGATGGGAG 60.244 47.826 0.00 0.00 38.92 4.30
290 299 2.696187 CCAATGTGATTGCATGATGGGA 59.304 45.455 0.00 0.00 38.92 4.37
291 300 2.805295 GCCAATGTGATTGCATGATGGG 60.805 50.000 0.00 0.00 38.92 4.00
292 301 2.479837 GCCAATGTGATTGCATGATGG 58.520 47.619 0.00 0.00 38.92 3.51
332 341 9.907576 GTAACATTTTCAGAGTATCGATTTCAG 57.092 33.333 1.71 0.00 42.67 3.02
333 342 9.653287 AGTAACATTTTCAGAGTATCGATTTCA 57.347 29.630 1.71 0.00 42.67 2.69
343 352 7.758495 ACGTTTGAAAGTAACATTTTCAGAGT 58.242 30.769 1.37 1.59 43.22 3.24
423 432 5.721232 TGTTGTGCATGCAAAATATCATCA 58.279 33.333 25.58 17.41 0.00 3.07
429 438 6.615264 AATGTTTGTTGTGCATGCAAAATA 57.385 29.167 25.58 20.46 34.47 1.40
516 525 1.131928 ACCTTTCTACACCCGGGCTT 61.132 55.000 24.08 10.59 0.00 4.35
517 526 0.252375 TACCTTTCTACACCCGGGCT 60.252 55.000 24.08 8.77 0.00 5.19
520 529 3.593096 GAAAGTACCTTTCTACACCCGG 58.407 50.000 9.00 0.00 44.33 5.73
521 530 3.057315 TCGAAAGTACCTTTCTACACCCG 60.057 47.826 13.19 1.64 45.19 5.28
522 531 4.240888 GTCGAAAGTACCTTTCTACACCC 58.759 47.826 13.40 0.00 45.19 4.61
580 590 9.587772 GCTAGTTGTAGTATCAGAATTTCTCAA 57.412 33.333 0.00 0.00 0.00 3.02
631 1470 2.354821 GGATTTTCTAACTCCGCGCATT 59.645 45.455 8.75 0.00 0.00 3.56
644 1483 6.178607 AGGCAAGAATGTTTTGGATTTTCT 57.821 33.333 0.00 0.00 0.00 2.52
688 1528 4.932200 CACTGTCAGTGGAAAGAGGTTATC 59.068 45.833 23.09 0.00 42.35 1.75
690 1530 4.336889 CACTGTCAGTGGAAAGAGGTTA 57.663 45.455 23.09 0.00 42.35 2.85
692 1532 2.918712 CACTGTCAGTGGAAAGAGGT 57.081 50.000 23.09 0.00 42.35 3.85
703 1543 3.753272 CCACATTTTCCTACCACTGTCAG 59.247 47.826 0.00 0.00 0.00 3.51
731 1581 2.173519 CACAGATGGGCCACAATTCTT 58.826 47.619 9.28 0.00 0.00 2.52
901 3596 2.124942 CCTCCCTTCGCTTCTGCC 60.125 66.667 0.00 0.00 35.36 4.85
904 3599 1.687493 CCCTCCTCCCTTCGCTTCT 60.687 63.158 0.00 0.00 0.00 2.85
909 3604 0.399233 ATCTTCCCCTCCTCCCTTCG 60.399 60.000 0.00 0.00 0.00 3.79
1221 3922 2.282391 AGCAATGCGGCAACAGGA 60.282 55.556 6.82 0.00 35.83 3.86
1222 3923 2.126228 CAGCAATGCGGCAACAGG 60.126 61.111 6.82 0.00 35.83 4.00
1361 4064 3.999663 CAGAATGGACTCACTTCTTCCAC 59.000 47.826 0.00 0.00 42.26 4.02
1501 4204 5.750067 ACAAAGATTGAGTGAAAACATGTGC 59.250 36.000 0.00 0.00 0.00 4.57
1563 4288 5.187967 ACTCCAATGTCTTAGTTAGGACCAG 59.812 44.000 0.00 0.00 31.98 4.00
1602 4334 5.886960 AACCTTTTGCATCTACAGCTTAG 57.113 39.130 0.00 0.00 0.00 2.18
1629 4361 2.433436 AGTTAAACCGGTTGATCCTGC 58.567 47.619 23.08 7.33 0.00 4.85
1684 4416 2.027377 ACTACAGCTGCTCAATGCTTCT 60.027 45.455 15.27 0.00 43.37 2.85
1900 4632 2.370281 ACAGATTGTCGTGCCACTAG 57.630 50.000 0.00 0.00 0.00 2.57
1945 4677 5.106948 CCCGCAGTGCATGTATCTATTAAAG 60.107 44.000 16.83 0.00 0.00 1.85
1965 4697 7.730364 TTTTTCATCTATATCTTCTTCCCGC 57.270 36.000 0.00 0.00 0.00 6.13
2114 4846 5.403466 GGCAAGAGAAAATGTTGATGTTGTC 59.597 40.000 0.00 0.00 34.07 3.18
2257 4990 3.622612 GGCACATTCAGTTTGCAGTTTTT 59.377 39.130 0.00 0.00 38.04 1.94
2258 4991 3.197265 GGCACATTCAGTTTGCAGTTTT 58.803 40.909 0.00 0.00 38.04 2.43
2259 4992 2.168106 TGGCACATTCAGTTTGCAGTTT 59.832 40.909 0.00 0.00 38.04 2.66
2260 4993 1.755959 TGGCACATTCAGTTTGCAGTT 59.244 42.857 0.00 0.00 38.04 3.16
2272 5005 8.815912 GGAATTTTTCCCTATATATGGCACATT 58.184 33.333 0.00 0.00 43.99 2.71
2273 5006 8.366359 GGAATTTTTCCCTATATATGGCACAT 57.634 34.615 0.00 0.00 43.99 3.21
2302 5035 9.715121 AGATTCCTTACGATTGTGTAGTTTTTA 57.285 29.630 0.00 0.00 0.00 1.52
2304 5037 8.617290 AAGATTCCTTACGATTGTGTAGTTTT 57.383 30.769 0.00 0.00 0.00 2.43
2305 5038 9.367444 CTAAGATTCCTTACGATTGTGTAGTTT 57.633 33.333 0.00 0.00 33.94 2.66
2306 5039 8.529476 ACTAAGATTCCTTACGATTGTGTAGTT 58.471 33.333 0.00 0.00 33.94 2.24
2308 5041 8.808529 CAACTAAGATTCCTTACGATTGTGTAG 58.191 37.037 0.00 0.00 33.94 2.74
2338 5247 3.680490 TGGCATTCGTTTCATAGGAACA 58.320 40.909 0.00 0.00 33.80 3.18
2386 5306 0.598065 GGCTCATTCGGTTTGCAGTT 59.402 50.000 0.00 0.00 0.00 3.16
2732 5655 4.344104 ACATCCCAAGGAAATGTTAGGTG 58.656 43.478 2.45 0.00 34.34 4.00
2808 5933 3.603857 CGTTGAACACTAGCTTTGGAACG 60.604 47.826 0.00 3.52 0.00 3.95
2924 6053 6.980593 AGAACACAGCACAATAGCAAATTTA 58.019 32.000 0.00 0.00 36.85 1.40
2984 6118 6.617782 TGGCAGGGAAATTTGAATTATGAA 57.382 33.333 0.00 0.00 0.00 2.57
2987 6121 6.811634 TGATGGCAGGGAAATTTGAATTAT 57.188 33.333 0.00 0.00 0.00 1.28
3485 6621 2.836479 TGTTGCAGATGAATGATGCG 57.164 45.000 0.00 0.00 42.92 4.73
3959 7095 2.542020 TGTTGAAGAATGTCCGCTGA 57.458 45.000 0.00 0.00 0.00 4.26
4025 7161 2.182030 GGAGAGAGGTCAACCGCG 59.818 66.667 0.00 0.00 40.98 6.46
4073 7209 5.165961 AGGTACTTATGAGCTCAAGCAAA 57.834 39.130 22.50 11.65 38.97 3.68
4181 7317 4.256920 AGTACATCGAATGCAGAAAGCTT 58.743 39.130 0.00 0.00 45.94 3.74
4283 7419 8.410030 TGATAGGATCAAAATTCAAAATTGCG 57.590 30.769 0.00 0.00 36.11 4.85
4308 7444 7.847711 AATATAGAGTGCTCAGTGGATACTT 57.152 36.000 1.82 0.00 34.07 2.24
4432 7568 2.092968 AGCGGAAGATAACTTGATGGCA 60.093 45.455 0.00 0.00 36.39 4.92
4604 7754 6.830912 ACTTCATATTAGGTGCAATCTAGCA 58.169 36.000 0.00 0.00 43.35 3.49
4696 7851 7.976734 CACTCTTACATTAGTTTACAGAGGGAG 59.023 40.741 0.00 0.00 0.00 4.30
4697 7852 7.453752 ACACTCTTACATTAGTTTACAGAGGGA 59.546 37.037 2.59 0.00 0.00 4.20
4698 7853 7.612677 ACACTCTTACATTAGTTTACAGAGGG 58.387 38.462 0.00 0.00 0.00 4.30
4699 7854 9.141400 GAACACTCTTACATTAGTTTACAGAGG 57.859 37.037 0.00 0.00 0.00 3.69
4701 7856 9.692749 CTGAACACTCTTACATTAGTTTACAGA 57.307 33.333 0.00 0.00 0.00 3.41
4702 7857 9.692749 TCTGAACACTCTTACATTAGTTTACAG 57.307 33.333 0.00 0.00 0.00 2.74
4706 7861 9.209175 GTGATCTGAACACTCTTACATTAGTTT 57.791 33.333 10.42 0.00 35.66 2.66
4707 7862 8.589338 AGTGATCTGAACACTCTTACATTAGTT 58.411 33.333 14.01 0.00 43.84 2.24
4708 7863 8.128322 AGTGATCTGAACACTCTTACATTAGT 57.872 34.615 14.01 0.00 43.84 2.24
4709 7864 9.509855 GTAGTGATCTGAACACTCTTACATTAG 57.490 37.037 21.68 0.00 45.58 1.73
4710 7865 9.244292 AGTAGTGATCTGAACACTCTTACATTA 57.756 33.333 21.68 1.90 45.58 1.90
4711 7866 8.128322 AGTAGTGATCTGAACACTCTTACATT 57.872 34.615 21.68 1.20 45.58 2.71
4712 7867 7.710676 AGTAGTGATCTGAACACTCTTACAT 57.289 36.000 21.68 2.04 45.58 2.29
4713 7868 7.526142 AAGTAGTGATCTGAACACTCTTACA 57.474 36.000 21.68 3.92 45.58 2.41
4714 7869 9.562583 CTAAAGTAGTGATCTGAACACTCTTAC 57.437 37.037 21.68 15.21 45.58 2.34
4715 7870 9.298250 ACTAAAGTAGTGATCTGAACACTCTTA 57.702 33.333 21.68 16.01 45.58 2.10
4716 7871 8.184304 ACTAAAGTAGTGATCTGAACACTCTT 57.816 34.615 21.68 19.46 45.58 2.85
4717 7872 7.768807 ACTAAAGTAGTGATCTGAACACTCT 57.231 36.000 21.68 15.71 45.58 3.24
4726 7881 9.733219 GCGTTTAGAATACTAAAGTAGTGATCT 57.267 33.333 0.00 4.67 45.42 2.75
4727 7882 9.733219 AGCGTTTAGAATACTAAAGTAGTGATC 57.267 33.333 0.00 0.00 45.42 2.92
4728 7883 9.733219 GAGCGTTTAGAATACTAAAGTAGTGAT 57.267 33.333 0.00 0.00 45.42 3.06
4729 7884 8.954350 AGAGCGTTTAGAATACTAAAGTAGTGA 58.046 33.333 0.00 0.00 45.42 3.41
4730 7885 9.570488 AAGAGCGTTTAGAATACTAAAGTAGTG 57.430 33.333 0.00 0.00 45.42 2.74
4744 7899 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
4745 7900 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
4746 7901 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
4747 7902 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
4748 7903 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
4749 7904 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
4750 7905 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
4751 7906 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
4752 7907 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
4755 7910 8.526147 GCATACTCCCTCCGTAAACTAATATAA 58.474 37.037 0.00 0.00 0.00 0.98
4756 7911 7.670979 TGCATACTCCCTCCGTAAACTAATATA 59.329 37.037 0.00 0.00 0.00 0.86
4757 7912 6.495872 TGCATACTCCCTCCGTAAACTAATAT 59.504 38.462 0.00 0.00 0.00 1.28
4758 7913 5.834742 TGCATACTCCCTCCGTAAACTAATA 59.165 40.000 0.00 0.00 0.00 0.98
4759 7914 4.652421 TGCATACTCCCTCCGTAAACTAAT 59.348 41.667 0.00 0.00 0.00 1.73
4760 7915 4.025360 TGCATACTCCCTCCGTAAACTAA 58.975 43.478 0.00 0.00 0.00 2.24
4761 7916 3.634504 TGCATACTCCCTCCGTAAACTA 58.365 45.455 0.00 0.00 0.00 2.24
4762 7917 2.463752 TGCATACTCCCTCCGTAAACT 58.536 47.619 0.00 0.00 0.00 2.66
4763 7918 2.973694 TGCATACTCCCTCCGTAAAC 57.026 50.000 0.00 0.00 0.00 2.01
4764 7919 4.652421 ACTATTGCATACTCCCTCCGTAAA 59.348 41.667 0.00 0.00 0.00 2.01
4765 7920 4.038763 CACTATTGCATACTCCCTCCGTAA 59.961 45.833 0.00 0.00 0.00 3.18
4766 7921 3.572682 CACTATTGCATACTCCCTCCGTA 59.427 47.826 0.00 0.00 0.00 4.02
4767 7922 2.365617 CACTATTGCATACTCCCTCCGT 59.634 50.000 0.00 0.00 0.00 4.69
4768 7923 2.289072 CCACTATTGCATACTCCCTCCG 60.289 54.545 0.00 0.00 0.00 4.63
4769 7924 2.972713 TCCACTATTGCATACTCCCTCC 59.027 50.000 0.00 0.00 0.00 4.30
4770 7925 3.556004 GCTCCACTATTGCATACTCCCTC 60.556 52.174 0.00 0.00 0.00 4.30
4771 7926 2.370189 GCTCCACTATTGCATACTCCCT 59.630 50.000 0.00 0.00 0.00 4.20
4772 7927 2.551071 GGCTCCACTATTGCATACTCCC 60.551 54.545 0.00 0.00 0.00 4.30
4773 7928 2.104792 TGGCTCCACTATTGCATACTCC 59.895 50.000 0.00 0.00 0.00 3.85
4774 7929 3.181461 ACTGGCTCCACTATTGCATACTC 60.181 47.826 0.00 0.00 0.00 2.59
4775 7930 2.774234 ACTGGCTCCACTATTGCATACT 59.226 45.455 0.00 0.00 0.00 2.12
4776 7931 3.199880 ACTGGCTCCACTATTGCATAC 57.800 47.619 0.00 0.00 0.00 2.39
4777 7932 3.931907 AACTGGCTCCACTATTGCATA 57.068 42.857 0.00 0.00 0.00 3.14
4778 7933 2.814805 AACTGGCTCCACTATTGCAT 57.185 45.000 0.00 0.00 0.00 3.96
4779 7934 2.571653 AGTAACTGGCTCCACTATTGCA 59.428 45.455 0.00 0.00 0.00 4.08
4780 7935 3.268023 AGTAACTGGCTCCACTATTGC 57.732 47.619 0.00 0.00 0.00 3.56
4781 7936 5.127194 TCTGTAGTAACTGGCTCCACTATTG 59.873 44.000 0.00 0.00 0.00 1.90
4782 7937 5.269991 TCTGTAGTAACTGGCTCCACTATT 58.730 41.667 0.00 0.00 0.00 1.73
4783 7938 4.868268 TCTGTAGTAACTGGCTCCACTAT 58.132 43.478 0.00 0.00 0.00 2.12
4829 7986 6.219473 AGATAAGAACAGCAGATATGGAACG 58.781 40.000 0.00 0.00 0.00 3.95
4839 7996 9.209175 ACTACTTGTAAAAGATAAGAACAGCAG 57.791 33.333 0.00 0.00 31.03 4.24
4903 8060 5.197549 CGATAAACCACAATGCAGATAACG 58.802 41.667 0.00 0.00 0.00 3.18
4938 8095 5.073311 AGCACTAACAGTACCACATGTAG 57.927 43.478 0.00 0.00 0.00 2.74
5284 8442 6.877322 GTCTAATAACTGTATGGTGTGTGGTT 59.123 38.462 0.00 0.00 0.00 3.67
5362 8520 0.592247 GTGCCAGTTTCACTGTTGCG 60.592 55.000 3.30 0.00 44.50 4.85
5471 8637 4.454504 GTGTTTCCCATGTCGAATAGTGTT 59.545 41.667 0.00 0.00 0.00 3.32
5529 8696 2.484264 GGAATTGCATGCCTATCGGTAC 59.516 50.000 16.68 0.00 0.00 3.34
5565 8763 4.476297 TCTGGGACCATAAAGCGAGTATA 58.524 43.478 0.00 0.00 0.00 1.47
5594 8792 6.207417 GCTGCTCCTCATAAAGCCAATTATAA 59.793 38.462 0.00 0.00 37.73 0.98
5613 8811 1.244019 ATCCAAAACACCGGCTGCTC 61.244 55.000 0.00 0.00 0.00 4.26
5615 8813 0.033366 AAATCCAAAACACCGGCTGC 59.967 50.000 0.00 0.00 0.00 5.25
5627 8827 5.011840 TGAACAAGGCAATCATGAAATCCAA 59.988 36.000 0.00 0.00 0.00 3.53
5712 8915 5.612725 AAAGCAAAAAGGTTTCTGATCCA 57.387 34.783 0.00 0.00 44.10 3.41
5771 8975 8.728088 AGCAAATGTCTAAAAGTTGATTTACG 57.272 30.769 0.00 0.00 0.00 3.18
5784 8988 8.856153 TTACTTGGATGTAAGCAAATGTCTAA 57.144 30.769 0.00 0.00 0.00 2.10
5815 9019 7.508687 TCACCACTCTGTACATTGCATAATAT 58.491 34.615 0.00 0.00 0.00 1.28
5818 9022 5.159273 TCACCACTCTGTACATTGCATAA 57.841 39.130 0.00 0.00 0.00 1.90
5850 9071 6.715347 AAGCAGTTGATGAGGTAAACTTTT 57.285 33.333 0.00 0.00 31.88 2.27
5956 9177 0.808453 TTATCTACCAAGGCACGCGC 60.808 55.000 5.73 0.00 37.44 6.86
6204 9425 3.350612 GCCAAACCGTAGCACGCA 61.351 61.111 3.56 0.00 40.91 5.24
6508 9731 9.908152 GTTTCTTATAAACAAGCAAACCTGTAT 57.092 29.630 0.00 0.00 0.00 2.29
6530 9763 3.120199 CCGACAATGACTCATGTGGTTTC 60.120 47.826 0.00 0.00 0.00 2.78
6531 9764 2.813754 CCGACAATGACTCATGTGGTTT 59.186 45.455 0.00 0.00 0.00 3.27
6608 9851 5.711976 TCCTGGAATCTGGTTTCTTCAAATC 59.288 40.000 0.00 0.00 34.13 2.17
6614 9857 5.019470 GGAAATCCTGGAATCTGGTTTCTT 58.981 41.667 14.48 0.00 35.32 2.52
6631 9874 7.355778 CCTATACAAGCAAGAATTCGGAAATC 58.644 38.462 0.00 0.00 0.00 2.17
6639 9882 7.577616 GCTTTCAACCCTATACAAGCAAGAATT 60.578 37.037 0.00 0.00 37.24 2.17
6640 9883 6.127619 GCTTTCAACCCTATACAAGCAAGAAT 60.128 38.462 0.00 0.00 37.24 2.40
6652 9895 1.680338 GGCATCGCTTTCAACCCTAT 58.320 50.000 0.00 0.00 0.00 2.57
6673 9916 2.754552 TGCCAAGTTGGATGCAGTTATC 59.245 45.455 26.52 4.04 40.96 1.75
6692 9935 1.989165 CAGTTGCTCGACTCTAGTTGC 59.011 52.381 0.00 0.00 0.00 4.17
6722 9965 3.648507 ATTTGCTGATGAGAGCCTCTT 57.351 42.857 0.00 0.00 38.28 2.85
6835 10078 4.067192 TCAACTGCTCGTGTGTAGTACTA 58.933 43.478 0.00 0.00 32.76 1.82
6836 10079 2.882761 TCAACTGCTCGTGTGTAGTACT 59.117 45.455 0.00 0.00 32.76 2.73
6837 10080 3.278367 TCAACTGCTCGTGTGTAGTAC 57.722 47.619 0.00 0.00 32.76 2.73
6880 10123 1.152917 AGAGATCAGATATGGGGGCCA 59.847 52.381 4.39 0.00 38.19 5.36
6881 10124 1.963985 AGAGATCAGATATGGGGGCC 58.036 55.000 0.00 0.00 0.00 5.80
6906 10152 1.038681 TGCATCCGCCAAATCAGCAT 61.039 50.000 0.00 0.00 37.32 3.79
7144 10398 4.758688 AGAGGAAAACTGTTGCCAAAAAG 58.241 39.130 13.19 0.00 34.29 2.27
7166 10420 8.391075 AGGAGAAAATTTGATCACGAAGTAAA 57.609 30.769 0.00 0.00 41.61 2.01
7286 10540 1.428448 TGTGCAGTACTCAACGATGC 58.572 50.000 0.00 0.00 37.40 3.91
7288 10542 2.418746 GGGATGTGCAGTACTCAACGAT 60.419 50.000 0.00 0.00 0.00 3.73
7296 10550 2.645838 ATGGATGGGATGTGCAGTAC 57.354 50.000 0.00 0.00 0.00 2.73
7306 10560 1.510492 TGAGCAGCTAATGGATGGGA 58.490 50.000 0.00 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.