Multiple sequence alignment - TraesCS4D01G090300

Loading Multiple Alignment...

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 TraesCS4D01G090300 chr4D 100.000 5407 0 0 1 5407 65180905 65175499 0.000000e+00 9985.0
1 TraesCS4D01G090300 chr4D 82.963 270 31 10 1471 1739 294346471 294346216 4.210000e-56 230.0
2 TraesCS4D01G090300 chr4A 93.273 2646 87 38 1 2627 530814843 530817416 0.000000e+00 3816.0
3 TraesCS4D01G090300 chr4A 94.244 2241 56 21 2572 4769 530817414 530819624 0.000000e+00 3356.0
4 TraesCS4D01G090300 chr4A 92.806 139 4 3 5088 5221 530819919 530820056 4.270000e-46 196.0
5 TraesCS4D01G090300 chr4A 93.590 78 2 2 5242 5316 530820045 530820122 4.430000e-21 113.0
6 TraesCS4D01G090300 chr4A 88.636 88 10 0 2377 2464 524285372 524285459 2.060000e-19 108.0
7 TraesCS4D01G090300 chr4A 94.286 70 4 0 4790 4859 621883894 621883963 2.060000e-19 108.0
8 TraesCS4D01G090300 chr4A 91.489 47 1 3 2754 2797 34671468 34671422 1.630000e-05 62.1
9 TraesCS4D01G090300 chr4B 87.755 2254 129 61 1761 3954 95861117 95858951 0.000000e+00 2497.0
10 TraesCS4D01G090300 chr4B 89.891 1741 98 30 1 1690 95862836 95861123 0.000000e+00 2169.0
11 TraesCS4D01G090300 chr4B 89.554 718 49 17 4070 4773 95858932 95858227 0.000000e+00 887.0
12 TraesCS4D01G090300 chr4B 90.556 360 20 8 4875 5224 95858200 95857845 1.060000e-126 464.0
13 TraesCS4D01G090300 chr4B 83.137 255 31 9 1486 1739 362144220 362143977 7.050000e-54 222.0
14 TraesCS4D01G090300 chr4B 90.000 90 9 0 2377 2466 65499667 65499756 3.420000e-22 117.0
15 TraesCS4D01G090300 chr6A 87.611 452 42 5 2867 3313 9585551 9585109 3.740000e-141 512.0
16 TraesCS4D01G090300 chr6A 94.030 67 3 1 4790 4856 90754118 90754053 3.450000e-17 100.0
17 TraesCS4D01G090300 chr3A 87.583 451 45 6 2867 3313 712304945 712305388 3.740000e-141 512.0
18 TraesCS4D01G090300 chr3A 97.101 69 2 0 4790 4858 701344635 701344567 3.420000e-22 117.0
19 TraesCS4D01G090300 chr3A 95.588 68 3 0 4790 4857 750541569 750541502 5.730000e-20 110.0
20 TraesCS4D01G090300 chr3B 87.061 456 47 9 2867 3313 370958803 370958351 6.250000e-139 505.0
21 TraesCS4D01G090300 chr3B 97.015 67 1 1 4790 4856 556870055 556870120 1.590000e-20 111.0
22 TraesCS4D01G090300 chr7B 86.344 454 46 8 2867 3313 10685298 10685742 1.050000e-131 481.0
23 TraesCS4D01G090300 chr7B 83.333 168 25 2 1475 1641 375201292 375201127 9.380000e-33 152.0
24 TraesCS4D01G090300 chr3D 86.510 341 32 6 2867 3202 112759816 112759485 3.980000e-96 363.0
25 TraesCS4D01G090300 chr3D 93.277 119 8 0 3195 3313 112758250 112758132 5.570000e-40 176.0
26 TraesCS4D01G090300 chr3D 88.235 85 8 1 4773 4857 523616565 523616647 3.450000e-17 100.0
27 TraesCS4D01G090300 chr3D 94.286 35 2 0 2754 2788 608334836 608334870 3.000000e-03 54.7
28 TraesCS4D01G090300 chr6B 85.955 178 20 4 2377 2551 471229663 471229838 9.250000e-43 185.0
29 TraesCS4D01G090300 chr6D 82.629 213 30 6 1471 1681 310399519 310399726 1.200000e-41 182.0
30 TraesCS4D01G090300 chr2D 80.861 209 30 8 1484 1688 599209004 599208802 7.250000e-34 156.0
31 TraesCS4D01G090300 chr2D 100.000 33 0 0 2754 2786 160193510 160193542 1.630000e-05 62.1
32 TraesCS4D01G090300 chr5B 94.444 90 5 0 2377 2466 18337548 18337637 7.300000e-29 139.0
33 TraesCS4D01G090300 chr5B 82.558 86 11 2 1654 1739 8269059 8268978 7.510000e-09 73.1
34 TraesCS4D01G090300 chr5B 78.889 90 13 3 1651 1739 591529804 591529888 7.570000e-04 56.5
35 TraesCS4D01G090300 chr7D 92.308 91 6 1 2377 2466 58205116 58205026 1.580000e-25 128.0
36 TraesCS4D01G090300 chr7D 74.638 276 43 18 1472 1745 365319901 365319651 4.460000e-16 97.1
37 TraesCS4D01G090300 chr7D 84.444 90 9 4 1654 1743 610922374 610922458 3.470000e-12 84.2
38 TraesCS4D01G090300 chr7D 94.444 36 1 1 2754 2788 611753669 611753704 3.000000e-03 54.7
39 TraesCS4D01G090300 chr5A 97.101 69 2 0 4790 4858 600952998 600952930 3.420000e-22 117.0
40 TraesCS4D01G090300 chr5A 94.366 71 3 1 4790 4859 703180665 703180735 2.060000e-19 108.0
41 TraesCS4D01G090300 chr5A 91.549 71 5 1 4790 4859 556176377 556176447 4.460000e-16 97.1
42 TraesCS4D01G090300 chr5D 82.569 109 18 1 1474 1581 267617435 267617543 1.600000e-15 95.3
43 TraesCS4D01G090300 chr5D 96.970 33 1 0 2753 2785 335051211 335051243 7.570000e-04 56.5
44 TraesCS4D01G090300 chr7A 83.333 90 11 4 1657 1744 166738647 166738560 4.490000e-11 80.5
45 TraesCS4D01G090300 chr2B 96.970 33 1 0 2754 2786 257534834 257534866 7.570000e-04 56.5
46 TraesCS4D01G090300 chr1D 96.970 33 1 0 2754 2786 433036812 433036844 7.570000e-04 56.5
47 TraesCS4D01G090300 chrUn 92.105 38 2 1 2754 2791 81701305 81701341 1.000000e-02 52.8


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 TraesCS4D01G090300 chr4D 65175499 65180905 5406 True 9985.00 9985 100.00000 1 5407 1 chr4D.!!$R1 5406
1 TraesCS4D01G090300 chr4A 530814843 530820122 5279 False 1870.25 3816 93.47825 1 5316 4 chr4A.!!$F3 5315
2 TraesCS4D01G090300 chr4B 95857845 95862836 4991 True 1504.25 2497 89.43900 1 5224 4 chr4B.!!$R2 5223
3 TraesCS4D01G090300 chr3D 112758132 112759816 1684 True 269.50 363 89.89350 2867 3313 2 chr3D.!!$R1 446

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
687 741 0.174845 TGGCCAGTGTAGATACGCAC 59.825 55.000 0.00 0.0 39.08 5.34 F
966 1035 0.323725 TCATTTCCCTTGCAGGAGCC 60.324 55.000 0.00 0.0 37.67 4.70 F
2317 2394 1.137479 CTCCTCCGGGCGTATACAAAA 59.863 52.381 0.00 0.0 0.00 2.44 F
3959 5403 0.038166 TGGGGGAAGTTCTGTCATGC 59.962 55.000 2.25 0.0 0.00 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1631 1705 1.169661 TGCAAAGGGCTACAACACCG 61.170 55.000 0.00 0.00 45.15 4.94 R
2515 2592 2.028748 GCCACCTCAATTGAATTGTGCT 60.029 45.455 16.62 0.35 41.02 4.40 R
4011 5455 1.275010 TCGTGCATAACCAGAAGCAGA 59.725 47.619 0.00 0.00 37.72 4.26 R
5383 7010 0.255318 GGACCGGACTCTACCTCTGA 59.745 60.000 9.46 0.00 0.00 3.27 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
134 137 0.688087 TGGGCTGGGTTTCGGTTTTT 60.688 50.000 0.00 0.00 0.00 1.94
205 241 0.869454 GTCGATTCCGCTCTGCTCTG 60.869 60.000 0.00 0.00 35.37 3.35
255 291 4.627284 TCCGGTGAACTTTCCTGAAATA 57.373 40.909 0.00 0.00 0.00 1.40
276 312 0.815734 TACAGCCTTCCTAGTCACGC 59.184 55.000 0.00 0.00 0.00 5.34
473 516 1.840635 GGTTATGAGCTCTTCACCCCT 59.159 52.381 18.06 0.00 38.99 4.79
474 517 2.158885 GGTTATGAGCTCTTCACCCCTC 60.159 54.545 18.06 0.00 38.99 4.30
475 518 2.769095 GTTATGAGCTCTTCACCCCTCT 59.231 50.000 16.19 0.00 38.99 3.69
476 519 2.856760 ATGAGCTCTTCACCCCTCTA 57.143 50.000 16.19 0.00 38.99 2.43
477 520 2.151502 TGAGCTCTTCACCCCTCTAG 57.848 55.000 16.19 0.00 0.00 2.43
478 521 1.359474 TGAGCTCTTCACCCCTCTAGT 59.641 52.381 16.19 0.00 0.00 2.57
479 522 2.028876 GAGCTCTTCACCCCTCTAGTC 58.971 57.143 6.43 0.00 0.00 2.59
480 523 1.643811 AGCTCTTCACCCCTCTAGTCT 59.356 52.381 0.00 0.00 0.00 3.24
481 524 2.853707 AGCTCTTCACCCCTCTAGTCTA 59.146 50.000 0.00 0.00 0.00 2.59
482 525 3.117663 AGCTCTTCACCCCTCTAGTCTAG 60.118 52.174 0.00 0.00 0.00 2.43
660 710 1.503542 CACCAGCACCGATTCTTGC 59.496 57.895 0.00 0.10 39.16 4.01
676 726 1.733402 TTGCTTTCCGTTGGCCAGTG 61.733 55.000 5.11 1.77 0.00 3.66
687 741 0.174845 TGGCCAGTGTAGATACGCAC 59.825 55.000 0.00 0.00 39.08 5.34
706 760 0.814010 CCCCCTTAATCGTTGGAGCG 60.814 60.000 0.00 0.00 0.00 5.03
708 762 1.436983 CCCTTAATCGTTGGAGCGCC 61.437 60.000 2.29 0.00 0.00 6.53
761 815 6.689554 ACTAGTACTCCAGTTTAGTTGCTTC 58.310 40.000 0.00 0.00 29.05 3.86
914 983 3.068732 TCTCTGCACCTTAATCATCCTCG 59.931 47.826 0.00 0.00 0.00 4.63
919 988 4.065088 GCACCTTAATCATCCTCGCAATA 58.935 43.478 0.00 0.00 0.00 1.90
920 989 4.515191 GCACCTTAATCATCCTCGCAATAA 59.485 41.667 0.00 0.00 0.00 1.40
927 996 2.437651 TCATCCTCGCAATAACATGGGA 59.562 45.455 0.00 0.00 39.62 4.37
939 1008 6.407299 GCAATAACATGGGATTGAACCTGAAT 60.407 38.462 20.21 0.00 35.46 2.57
948 1017 8.010733 TGGGATTGAACCTGAATTGATATTTC 57.989 34.615 0.00 0.00 0.00 2.17
966 1035 0.323725 TCATTTCCCTTGCAGGAGCC 60.324 55.000 0.00 0.00 37.67 4.70
1056 1125 4.121317 CAGAGGCAGAGATCAATCTTGAC 58.879 47.826 0.00 0.00 40.49 3.18
1101 1170 1.598130 AAGGTTCACACTGGAGCGC 60.598 57.895 0.00 0.00 0.00 5.92
1149 1218 2.583593 GACCTCTCGCATCGGCAC 60.584 66.667 0.00 0.00 41.24 5.01
1341 1410 1.421410 CCGTTGCTGCGGTAGATCAC 61.421 60.000 10.61 0.00 46.11 3.06
1396 1466 6.591834 GGTAAAATCCATCGTCTCATATCTGG 59.408 42.308 0.00 0.00 0.00 3.86
1484 1558 1.825474 GGTTGCCTAGTACTCTCTGCA 59.175 52.381 0.00 1.28 0.00 4.41
1654 1728 2.035832 GTGTTGTAGCCCTTTGCATGTT 59.964 45.455 0.00 0.00 44.83 2.71
1746 1820 8.698973 TTTTGAAATGGAGGTAGTGATAAACA 57.301 30.769 0.00 0.00 0.00 2.83
1848 1925 4.697828 TGAACTACAAAGTGTTCACTTGCA 59.302 37.500 17.16 6.50 44.89 4.08
1887 1964 9.504708 TGAAACTAATTGATGCAATTTTCCATT 57.495 25.926 10.26 0.00 40.60 3.16
1957 2034 4.256110 TCACATTCATCGTTCTCTTGCAT 58.744 39.130 0.00 0.00 0.00 3.96
2317 2394 1.137479 CTCCTCCGGGCGTATACAAAA 59.863 52.381 0.00 0.00 0.00 2.44
2501 2578 9.489084 ACCTTTATTTGCTTTAAATTCAGAACC 57.511 29.630 0.00 0.00 39.61 3.62
3005 3187 6.601332 AGTTTCCTGATTCCTTGTTCAACTA 58.399 36.000 0.00 0.00 0.00 2.24
3653 5081 5.670361 AGGATCTTGGCCAGGTAATTTACTA 59.330 40.000 15.41 0.00 0.00 1.82
3662 5090 5.123979 GCCAGGTAATTTACTATATGCCAGC 59.876 44.000 6.52 0.00 0.00 4.85
3704 5136 4.989279 TCTTTGCTGCCCAATATTCTTC 57.011 40.909 0.00 0.00 32.49 2.87
3956 5400 0.110486 GCTTGGGGGAAGTTCTGTCA 59.890 55.000 2.25 0.00 33.73 3.58
3958 5402 2.440409 CTTGGGGGAAGTTCTGTCATG 58.560 52.381 2.25 0.00 0.00 3.07
3959 5403 0.038166 TGGGGGAAGTTCTGTCATGC 59.962 55.000 2.25 0.00 0.00 4.06
3962 5406 2.087646 GGGGAAGTTCTGTCATGCTTC 58.912 52.381 2.25 0.00 37.27 3.86
4007 5451 3.081061 TGGCTTTGTATGCTCAATCGTT 58.919 40.909 0.00 0.00 0.00 3.85
4008 5452 3.505680 TGGCTTTGTATGCTCAATCGTTT 59.494 39.130 0.00 0.00 0.00 3.60
4009 5453 3.853671 GGCTTTGTATGCTCAATCGTTTG 59.146 43.478 0.00 0.00 0.00 2.93
4010 5454 4.475944 GCTTTGTATGCTCAATCGTTTGT 58.524 39.130 6.14 0.00 34.32 2.83
4011 5455 4.917415 GCTTTGTATGCTCAATCGTTTGTT 59.083 37.500 6.14 0.00 34.32 2.83
4020 5464 4.461405 CTCAATCGTTTGTTCTGCTTCTG 58.539 43.478 6.14 0.00 34.32 3.02
4021 5465 3.250762 TCAATCGTTTGTTCTGCTTCTGG 59.749 43.478 6.14 0.00 34.32 3.86
4077 5529 2.128771 TCTTGGGATGCAAAGCCTAC 57.871 50.000 0.00 0.00 0.00 3.18
4097 5549 6.741358 GCCTACGAATTTTAACATTCTCACAC 59.259 38.462 11.52 0.00 31.81 3.82
4328 5780 1.348008 TGATGCTGGAGGACCCATCC 61.348 60.000 5.52 0.00 45.57 3.51
4409 5861 1.202222 GCGTCATGGAATGCTTGAAGG 60.202 52.381 5.89 0.00 46.21 3.46
4417 5871 3.157087 GGAATGCTTGAAGGAAGGTTGA 58.843 45.455 0.00 0.00 31.56 3.18
4528 5983 5.302059 ACAGAAGTGTATACCGTAGATGCAT 59.698 40.000 0.00 0.00 34.05 3.96
4559 6014 4.333372 TCGCACTACGTTTTCTTCCTTTTT 59.667 37.500 0.00 0.00 44.19 1.94
4604 6060 3.003480 GTGCTTTGGTGATACCTCAGTC 58.997 50.000 0.00 0.00 39.58 3.51
4621 6077 6.986817 ACCTCAGTCTCGGAATAATATGTTTG 59.013 38.462 0.00 0.00 0.00 2.93
4652 6142 3.748048 CAGTGACACCTTGGATAGTTGTG 59.252 47.826 0.84 0.00 0.00 3.33
4653 6143 2.484264 GTGACACCTTGGATAGTTGTGC 59.516 50.000 0.00 0.00 0.00 4.57
4704 6194 4.525996 ACTTGTTTTAACCAAGTACCCGT 58.474 39.130 14.90 0.00 37.39 5.28
4793 6290 5.371115 TTTTTGCTAAAGCGCATCTAAGT 57.629 34.783 11.47 0.00 45.83 2.24
4794 6291 6.489127 TTTTTGCTAAAGCGCATCTAAGTA 57.511 33.333 11.47 0.00 45.83 2.24
4795 6292 6.677781 TTTTGCTAAAGCGCATCTAAGTAT 57.322 33.333 11.47 0.00 45.83 2.12
4796 6293 6.677781 TTTGCTAAAGCGCATCTAAGTATT 57.322 33.333 11.47 0.00 45.83 1.89
4797 6294 5.657470 TGCTAAAGCGCATCTAAGTATTG 57.343 39.130 11.47 0.00 45.83 1.90
4798 6295 4.024893 TGCTAAAGCGCATCTAAGTATTGC 60.025 41.667 11.47 0.00 45.83 3.56
4799 6296 4.024893 GCTAAAGCGCATCTAAGTATTGCA 60.025 41.667 11.47 0.00 36.15 4.08
4800 6297 3.951979 AAGCGCATCTAAGTATTGCAC 57.048 42.857 11.47 0.00 36.15 4.57
4801 6298 1.860950 AGCGCATCTAAGTATTGCACG 59.139 47.619 11.47 0.00 36.15 5.34
4802 6299 1.593006 GCGCATCTAAGTATTGCACGT 59.407 47.619 0.30 0.00 36.15 4.49
4803 6300 2.347661 GCGCATCTAAGTATTGCACGTC 60.348 50.000 0.30 0.00 36.15 4.34
4804 6301 3.116300 CGCATCTAAGTATTGCACGTCT 58.884 45.455 0.00 0.00 36.15 4.18
4805 6302 4.287720 CGCATCTAAGTATTGCACGTCTA 58.712 43.478 0.00 0.00 36.15 2.59
4806 6303 4.738252 CGCATCTAAGTATTGCACGTCTAA 59.262 41.667 0.00 0.00 36.15 2.10
4807 6304 5.108217 CGCATCTAAGTATTGCACGTCTAAG 60.108 44.000 0.00 0.00 36.15 2.18
4808 6305 5.749109 GCATCTAAGTATTGCACGTCTAAGT 59.251 40.000 0.00 0.00 36.40 2.24
4809 6306 6.074782 GCATCTAAGTATTGCACGTCTAAGTC 60.075 42.308 0.00 0.00 36.40 3.01
4810 6307 5.888105 TCTAAGTATTGCACGTCTAAGTCC 58.112 41.667 0.00 0.00 0.00 3.85
4811 6308 4.803098 AAGTATTGCACGTCTAAGTCCT 57.197 40.909 0.00 0.00 0.00 3.85
4812 6309 4.111375 AGTATTGCACGTCTAAGTCCTG 57.889 45.455 0.00 0.00 0.00 3.86
4813 6310 3.510360 AGTATTGCACGTCTAAGTCCTGT 59.490 43.478 0.00 0.00 0.00 4.00
4814 6311 2.148916 TTGCACGTCTAAGTCCTGTG 57.851 50.000 0.00 0.00 0.00 3.66
4815 6312 1.037493 TGCACGTCTAAGTCCTGTGT 58.963 50.000 0.00 0.00 33.23 3.72
4816 6313 1.000607 TGCACGTCTAAGTCCTGTGTC 60.001 52.381 0.00 0.00 33.23 3.67
4817 6314 1.000607 GCACGTCTAAGTCCTGTGTCA 60.001 52.381 0.00 0.00 33.23 3.58
4818 6315 2.352814 GCACGTCTAAGTCCTGTGTCAT 60.353 50.000 0.00 0.00 33.23 3.06
4819 6316 3.861131 GCACGTCTAAGTCCTGTGTCATT 60.861 47.826 0.00 0.00 33.23 2.57
4820 6317 3.675225 CACGTCTAAGTCCTGTGTCATTG 59.325 47.826 0.00 0.00 0.00 2.82
4821 6318 3.572682 ACGTCTAAGTCCTGTGTCATTGA 59.427 43.478 0.00 0.00 0.00 2.57
4822 6319 4.220821 ACGTCTAAGTCCTGTGTCATTGAT 59.779 41.667 0.00 0.00 0.00 2.57
4823 6320 4.800993 CGTCTAAGTCCTGTGTCATTGATC 59.199 45.833 0.00 0.00 0.00 2.92
4824 6321 5.393569 CGTCTAAGTCCTGTGTCATTGATCT 60.394 44.000 0.00 0.00 0.00 2.75
4825 6322 6.402222 GTCTAAGTCCTGTGTCATTGATCTT 58.598 40.000 0.00 0.00 0.00 2.40
4826 6323 7.548097 GTCTAAGTCCTGTGTCATTGATCTTA 58.452 38.462 0.00 0.00 0.00 2.10
4827 6324 7.489757 GTCTAAGTCCTGTGTCATTGATCTTAC 59.510 40.741 0.00 0.00 0.00 2.34
4828 6325 4.748892 AGTCCTGTGTCATTGATCTTACG 58.251 43.478 0.00 0.00 0.00 3.18
4829 6326 4.220821 AGTCCTGTGTCATTGATCTTACGT 59.779 41.667 0.00 0.00 0.00 3.57
4830 6327 4.563184 GTCCTGTGTCATTGATCTTACGTC 59.437 45.833 0.00 0.00 0.00 4.34
4831 6328 3.547868 CCTGTGTCATTGATCTTACGTCG 59.452 47.826 0.00 0.00 0.00 5.12
4832 6329 4.412207 CTGTGTCATTGATCTTACGTCGA 58.588 43.478 0.00 0.00 0.00 4.20
4833 6330 4.412207 TGTGTCATTGATCTTACGTCGAG 58.588 43.478 0.00 0.00 0.00 4.04
4834 6331 4.155280 TGTGTCATTGATCTTACGTCGAGA 59.845 41.667 0.00 0.00 0.00 4.04
4835 6332 5.163652 TGTGTCATTGATCTTACGTCGAGAT 60.164 40.000 12.62 12.62 36.60 2.75
4836 6333 5.744345 GTGTCATTGATCTTACGTCGAGATT 59.256 40.000 13.64 0.00 34.13 2.40
4837 6334 5.971792 TGTCATTGATCTTACGTCGAGATTC 59.028 40.000 13.64 8.91 34.13 2.52
4838 6335 5.971792 GTCATTGATCTTACGTCGAGATTCA 59.028 40.000 13.64 10.72 34.13 2.57
4839 6336 6.638873 GTCATTGATCTTACGTCGAGATTCAT 59.361 38.462 13.64 7.81 34.13 2.57
4840 6337 6.638468 TCATTGATCTTACGTCGAGATTCATG 59.362 38.462 13.64 15.95 34.13 3.07
4841 6338 5.500645 TGATCTTACGTCGAGATTCATGT 57.499 39.130 13.64 0.00 34.13 3.21
4842 6339 5.273944 TGATCTTACGTCGAGATTCATGTG 58.726 41.667 13.64 0.00 34.13 3.21
4843 6340 4.028852 TCTTACGTCGAGATTCATGTGG 57.971 45.455 0.00 0.00 0.00 4.17
4844 6341 3.692593 TCTTACGTCGAGATTCATGTGGA 59.307 43.478 0.00 0.00 0.00 4.02
4845 6342 4.338400 TCTTACGTCGAGATTCATGTGGAT 59.662 41.667 0.00 0.00 0.00 3.41
4846 6343 5.529800 TCTTACGTCGAGATTCATGTGGATA 59.470 40.000 0.00 0.00 0.00 2.59
4847 6344 4.855715 ACGTCGAGATTCATGTGGATAT 57.144 40.909 0.00 0.00 0.00 1.63
4848 6345 5.201713 ACGTCGAGATTCATGTGGATATT 57.798 39.130 0.00 0.00 0.00 1.28
4849 6346 5.601662 ACGTCGAGATTCATGTGGATATTT 58.398 37.500 0.00 0.00 0.00 1.40
4850 6347 6.049149 ACGTCGAGATTCATGTGGATATTTT 58.951 36.000 0.00 0.00 0.00 1.82
4851 6348 6.201044 ACGTCGAGATTCATGTGGATATTTTC 59.799 38.462 0.00 0.00 0.00 2.29
4852 6349 6.422100 CGTCGAGATTCATGTGGATATTTTCT 59.578 38.462 0.00 0.00 0.00 2.52
4853 6350 7.042456 CGTCGAGATTCATGTGGATATTTTCTT 60.042 37.037 0.00 0.00 0.00 2.52
4854 6351 8.616076 GTCGAGATTCATGTGGATATTTTCTTT 58.384 33.333 0.00 0.00 0.00 2.52
4855 6352 9.177608 TCGAGATTCATGTGGATATTTTCTTTT 57.822 29.630 0.00 0.00 0.00 2.27
4911 6425 5.871465 TTTTTGCAAGAAAAGACCAAACC 57.129 34.783 0.00 0.00 0.00 3.27
4950 6464 1.311859 TCCAGCTTTGACTGTTGCAG 58.688 50.000 0.00 0.00 35.83 4.41
5007 6522 4.278170 TGTAATTGCTTGAAGTGTTCCCTG 59.722 41.667 0.00 0.00 0.00 4.45
5008 6523 1.032014 TTGCTTGAAGTGTTCCCTGC 58.968 50.000 0.00 0.00 0.00 4.85
5120 6739 8.926715 AAGAAAGTTTGTTTTAGCTTACTTGG 57.073 30.769 0.00 0.00 0.00 3.61
5133 6760 3.193479 GCTTACTTGGTTGATTGAAGGGG 59.807 47.826 0.00 0.00 0.00 4.79
5221 6848 3.792956 CGGCATCATCATAAACAACAAGC 59.207 43.478 0.00 0.00 0.00 4.01
5222 6849 4.674885 CGGCATCATCATAAACAACAAGCA 60.675 41.667 0.00 0.00 0.00 3.91
5223 6850 4.563976 GGCATCATCATAAACAACAAGCAC 59.436 41.667 0.00 0.00 0.00 4.40
5224 6851 5.404946 GCATCATCATAAACAACAAGCACT 58.595 37.500 0.00 0.00 0.00 4.40
5225 6852 5.865552 GCATCATCATAAACAACAAGCACTT 59.134 36.000 0.00 0.00 0.00 3.16
5226 6853 6.183360 GCATCATCATAAACAACAAGCACTTG 60.183 38.462 8.82 8.82 45.58 3.16
5306 6933 0.109226 GAGCACTTCGTAAGTCGGCT 60.109 55.000 10.28 10.28 41.70 5.52
5308 6935 1.145803 GCACTTCGTAAGTCGGCTTT 58.854 50.000 7.97 0.00 40.46 3.51
5309 6936 1.529865 GCACTTCGTAAGTCGGCTTTT 59.470 47.619 7.97 0.00 40.46 2.27
5335 6962 2.975732 GGGGGAGTAACTTAAGTCGG 57.024 55.000 8.95 0.00 0.00 4.79
5336 6963 1.134580 GGGGGAGTAACTTAAGTCGGC 60.135 57.143 8.95 2.44 0.00 5.54
5337 6964 1.829849 GGGGAGTAACTTAAGTCGGCT 59.170 52.381 8.95 7.36 0.00 5.52
5338 6965 2.235650 GGGGAGTAACTTAAGTCGGCTT 59.764 50.000 7.72 7.72 38.66 4.35
5339 6966 3.259902 GGGAGTAACTTAAGTCGGCTTG 58.740 50.000 13.69 0.00 36.22 4.01
5340 6967 2.671888 GGAGTAACTTAAGTCGGCTTGC 59.328 50.000 13.69 0.00 36.22 4.01
5341 6968 3.586892 GAGTAACTTAAGTCGGCTTGCT 58.413 45.455 13.69 1.38 36.22 3.91
5342 6969 3.586892 AGTAACTTAAGTCGGCTTGCTC 58.413 45.455 13.69 0.00 36.22 4.26
5343 6970 2.543777 AACTTAAGTCGGCTTGCTCA 57.456 45.000 13.69 0.00 36.22 4.26
5344 6971 2.543777 ACTTAAGTCGGCTTGCTCAA 57.456 45.000 13.69 0.00 36.22 3.02
5345 6972 2.143925 ACTTAAGTCGGCTTGCTCAAC 58.856 47.619 13.69 0.00 36.22 3.18
5346 6973 1.126846 CTTAAGTCGGCTTGCTCAACG 59.873 52.381 13.69 0.00 36.22 4.10
5347 6974 0.315886 TAAGTCGGCTTGCTCAACGA 59.684 50.000 13.69 0.00 36.22 3.85
5348 6975 0.320771 AAGTCGGCTTGCTCAACGAT 60.321 50.000 0.00 0.00 37.69 3.73
5349 6976 0.530744 AGTCGGCTTGCTCAACGATA 59.469 50.000 0.00 0.00 37.69 2.92
5350 6977 1.067142 AGTCGGCTTGCTCAACGATAA 60.067 47.619 0.00 0.00 37.69 1.75
5351 6978 1.730064 GTCGGCTTGCTCAACGATAAA 59.270 47.619 0.00 0.00 37.69 1.40
5352 6979 2.158841 GTCGGCTTGCTCAACGATAAAA 59.841 45.455 0.00 0.00 37.69 1.52
5353 6980 2.415168 TCGGCTTGCTCAACGATAAAAG 59.585 45.455 0.00 0.00 0.00 2.27
5354 6981 2.476185 CGGCTTGCTCAACGATAAAAGG 60.476 50.000 0.00 0.00 0.00 3.11
5355 6982 2.519963 GCTTGCTCAACGATAAAAGGC 58.480 47.619 0.00 0.00 0.00 4.35
5356 6983 2.095263 GCTTGCTCAACGATAAAAGGCA 60.095 45.455 0.00 0.00 0.00 4.75
5357 6984 3.751621 CTTGCTCAACGATAAAAGGCAG 58.248 45.455 0.00 0.00 0.00 4.85
5358 6985 3.052455 TGCTCAACGATAAAAGGCAGA 57.948 42.857 0.00 0.00 0.00 4.26
5359 6986 3.002791 TGCTCAACGATAAAAGGCAGAG 58.997 45.455 0.00 0.00 0.00 3.35
5360 6987 3.003480 GCTCAACGATAAAAGGCAGAGT 58.997 45.455 0.00 0.00 0.00 3.24
5361 6988 4.181578 GCTCAACGATAAAAGGCAGAGTA 58.818 43.478 0.00 0.00 0.00 2.59
5362 6989 4.268884 GCTCAACGATAAAAGGCAGAGTAG 59.731 45.833 0.00 0.00 0.00 2.57
5363 6990 5.401531 TCAACGATAAAAGGCAGAGTAGT 57.598 39.130 0.00 0.00 0.00 2.73
5364 6991 5.790593 TCAACGATAAAAGGCAGAGTAGTT 58.209 37.500 0.00 0.00 0.00 2.24
5365 6992 6.228258 TCAACGATAAAAGGCAGAGTAGTTT 58.772 36.000 0.00 0.00 0.00 2.66
5366 6993 6.708949 TCAACGATAAAAGGCAGAGTAGTTTT 59.291 34.615 0.00 0.00 0.00 2.43
5367 6994 6.723131 ACGATAAAAGGCAGAGTAGTTTTC 57.277 37.500 0.00 0.00 0.00 2.29
5368 6995 6.228258 ACGATAAAAGGCAGAGTAGTTTTCA 58.772 36.000 0.00 0.00 0.00 2.69
5369 6996 6.708949 ACGATAAAAGGCAGAGTAGTTTTCAA 59.291 34.615 0.00 0.00 0.00 2.69
5370 6997 7.015877 CGATAAAAGGCAGAGTAGTTTTCAAC 58.984 38.462 0.00 0.00 0.00 3.18
5371 6998 5.515797 AAAAGGCAGAGTAGTTTTCAACC 57.484 39.130 0.00 0.00 0.00 3.77
5372 6999 3.857157 AGGCAGAGTAGTTTTCAACCA 57.143 42.857 0.00 0.00 0.00 3.67
5373 7000 3.744660 AGGCAGAGTAGTTTTCAACCAG 58.255 45.455 0.00 0.00 0.00 4.00
5374 7001 3.391296 AGGCAGAGTAGTTTTCAACCAGA 59.609 43.478 0.00 0.00 0.00 3.86
5375 7002 3.748568 GGCAGAGTAGTTTTCAACCAGAG 59.251 47.826 0.00 0.00 0.00 3.35
5376 7003 4.381411 GCAGAGTAGTTTTCAACCAGAGT 58.619 43.478 0.00 0.00 0.00 3.24
5377 7004 5.510861 GGCAGAGTAGTTTTCAACCAGAGTA 60.511 44.000 0.00 0.00 0.00 2.59
5378 7005 5.405873 GCAGAGTAGTTTTCAACCAGAGTAC 59.594 44.000 0.00 0.00 0.00 2.73
5379 7006 6.513180 CAGAGTAGTTTTCAACCAGAGTACA 58.487 40.000 0.00 0.00 0.00 2.90
5380 7007 6.984474 CAGAGTAGTTTTCAACCAGAGTACAA 59.016 38.462 0.00 0.00 0.00 2.41
5381 7008 7.494625 CAGAGTAGTTTTCAACCAGAGTACAAA 59.505 37.037 0.00 0.00 0.00 2.83
5382 7009 8.044908 AGAGTAGTTTTCAACCAGAGTACAAAA 58.955 33.333 0.00 0.00 0.00 2.44
5383 7010 8.747538 AGTAGTTTTCAACCAGAGTACAAAAT 57.252 30.769 0.00 0.00 0.00 1.82
5384 7011 8.837389 AGTAGTTTTCAACCAGAGTACAAAATC 58.163 33.333 0.00 0.00 0.00 2.17
5385 7012 7.639113 AGTTTTCAACCAGAGTACAAAATCA 57.361 32.000 0.00 0.00 0.00 2.57
5386 7013 7.707104 AGTTTTCAACCAGAGTACAAAATCAG 58.293 34.615 0.00 0.00 0.00 2.90
5387 7014 7.556275 AGTTTTCAACCAGAGTACAAAATCAGA 59.444 33.333 0.00 0.00 0.00 3.27
5388 7015 7.496529 TTTCAACCAGAGTACAAAATCAGAG 57.503 36.000 0.00 0.00 0.00 3.35
5389 7016 5.551233 TCAACCAGAGTACAAAATCAGAGG 58.449 41.667 0.00 0.00 0.00 3.69
5390 7017 5.071788 TCAACCAGAGTACAAAATCAGAGGT 59.928 40.000 0.00 0.00 0.00 3.85
5391 7018 6.269077 TCAACCAGAGTACAAAATCAGAGGTA 59.731 38.462 0.00 0.00 0.00 3.08
5392 7019 6.287589 ACCAGAGTACAAAATCAGAGGTAG 57.712 41.667 0.00 0.00 0.00 3.18
5393 7020 6.017192 ACCAGAGTACAAAATCAGAGGTAGA 58.983 40.000 0.00 0.00 0.00 2.59
5394 7021 6.153680 ACCAGAGTACAAAATCAGAGGTAGAG 59.846 42.308 0.00 0.00 0.00 2.43
5395 7022 6.153680 CCAGAGTACAAAATCAGAGGTAGAGT 59.846 42.308 0.00 0.00 0.00 3.24
5396 7023 7.254852 CAGAGTACAAAATCAGAGGTAGAGTC 58.745 42.308 0.00 0.00 0.00 3.36
5397 7024 6.378848 AGAGTACAAAATCAGAGGTAGAGTCC 59.621 42.308 0.00 0.00 0.00 3.85
5398 7025 4.457834 ACAAAATCAGAGGTAGAGTCCG 57.542 45.455 0.00 0.00 0.00 4.79
5399 7026 3.195825 ACAAAATCAGAGGTAGAGTCCGG 59.804 47.826 0.00 0.00 0.00 5.14
5400 7027 2.830651 AATCAGAGGTAGAGTCCGGT 57.169 50.000 0.00 0.00 0.00 5.28
5401 7028 2.351706 ATCAGAGGTAGAGTCCGGTC 57.648 55.000 0.00 0.00 0.00 4.79
5402 7029 0.255318 TCAGAGGTAGAGTCCGGTCC 59.745 60.000 0.00 0.00 0.00 4.46
5403 7030 1.096386 CAGAGGTAGAGTCCGGTCCG 61.096 65.000 3.60 3.60 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 137 2.460275 CCGATTTCGTGCGGCATCA 61.460 57.895 5.72 0.00 41.17 3.07
212 248 3.184683 GCTCTGCTGCGACGGAAG 61.185 66.667 0.00 0.00 0.00 3.46
218 254 1.638388 CGGATTTTGCTCTGCTGCGA 61.638 55.000 0.00 0.00 35.36 5.10
221 257 0.169672 CACCGGATTTTGCTCTGCTG 59.830 55.000 9.46 0.00 0.00 4.41
255 291 2.159085 GCGTGACTAGGAAGGCTGTATT 60.159 50.000 0.00 0.00 0.00 1.89
474 517 6.816640 CCGGATCTGAATCTAGACTAGACTAG 59.183 46.154 19.43 19.43 40.59 2.57
475 518 6.703319 CCGGATCTGAATCTAGACTAGACTA 58.297 44.000 14.47 0.00 37.69 2.59
476 519 5.556915 CCGGATCTGAATCTAGACTAGACT 58.443 45.833 14.47 3.42 37.69 3.24
477 520 4.155280 GCCGGATCTGAATCTAGACTAGAC 59.845 50.000 14.47 3.94 37.69 2.59
478 521 4.202472 TGCCGGATCTGAATCTAGACTAGA 60.202 45.833 14.53 14.53 39.50 2.43
479 522 4.075682 TGCCGGATCTGAATCTAGACTAG 58.924 47.826 5.05 2.81 32.12 2.57
480 523 4.100279 TGCCGGATCTGAATCTAGACTA 57.900 45.455 5.05 0.00 32.12 2.59
481 524 2.950781 TGCCGGATCTGAATCTAGACT 58.049 47.619 5.05 0.00 32.12 3.24
482 525 3.951775 ATGCCGGATCTGAATCTAGAC 57.048 47.619 5.05 0.00 32.12 2.59
660 710 1.156736 CTACACTGGCCAACGGAAAG 58.843 55.000 7.01 0.00 0.00 2.62
676 726 3.613432 CGATTAAGGGGGTGCGTATCTAC 60.613 52.174 0.00 0.00 0.00 2.59
687 741 0.814010 CGCTCCAACGATTAAGGGGG 60.814 60.000 0.00 0.00 34.06 5.40
706 760 4.994852 TGTATACTATTGGCAGAAATCGGC 59.005 41.667 4.17 0.00 36.32 5.54
708 762 7.017645 GCAATGTATACTATTGGCAGAAATCG 58.982 38.462 20.15 0.00 36.33 3.34
818 874 7.858382 CACAAACAGATTTACGGTGAATAAACA 59.142 33.333 0.00 0.00 0.00 2.83
827 883 4.274950 CCAGTTCACAAACAGATTTACGGT 59.725 41.667 0.00 0.00 37.88 4.83
914 983 4.402155 TCAGGTTCAATCCCATGTTATTGC 59.598 41.667 10.81 1.44 33.91 3.56
919 988 5.085920 TCAATTCAGGTTCAATCCCATGTT 58.914 37.500 0.00 0.00 0.00 2.71
920 989 4.676109 TCAATTCAGGTTCAATCCCATGT 58.324 39.130 0.00 0.00 0.00 3.21
966 1035 6.471233 TCTGGTCAACTACTATTCAGATGG 57.529 41.667 0.00 0.00 0.00 3.51
1056 1125 5.068234 TGTCAATTAGTAACCGTGAGAGG 57.932 43.478 0.00 0.00 37.30 3.69
1101 1170 5.471116 TGACTGTTCATCAAATGACCTCTTG 59.529 40.000 0.00 0.00 39.39 3.02
1149 1218 3.181507 CCACACTATCAAAGCCGTCATTG 60.182 47.826 0.00 0.00 0.00 2.82
1200 1269 1.001974 CCCGTTGAGAATGGTGACTCA 59.998 52.381 0.00 0.00 40.66 3.41
1293 1362 1.609555 GGTTGGCCACGAAAATACACA 59.390 47.619 3.88 0.00 34.09 3.72
1341 1410 1.227205 GAGCACCTCCTCTGATGCG 60.227 63.158 0.00 0.00 42.98 4.73
1631 1705 1.169661 TGCAAAGGGCTACAACACCG 61.170 55.000 0.00 0.00 45.15 4.94
1654 1728 8.754991 TTAAGTTTGACCAACTCCATAGAAAA 57.245 30.769 0.00 0.00 45.77 2.29
2317 2394 9.760926 TCTGATAAACTAGCATCTCCAGTATAT 57.239 33.333 0.00 0.00 0.00 0.86
2513 2590 4.737054 CCACCTCAATTGAATTGTGCTAC 58.263 43.478 16.62 0.00 41.02 3.58
2515 2592 2.028748 GCCACCTCAATTGAATTGTGCT 60.029 45.455 16.62 0.35 41.02 4.40
2696 2856 7.417797 GCATGGTCTTGGTAAATTAATGGTCAT 60.418 37.037 0.00 0.00 0.00 3.06
2756 2916 7.127955 ACATACTCCCTCCATCTCAAAATAAGT 59.872 37.037 0.00 0.00 0.00 2.24
2761 2921 4.536090 ACACATACTCCCTCCATCTCAAAA 59.464 41.667 0.00 0.00 0.00 2.44
2762 2922 4.104086 ACACATACTCCCTCCATCTCAAA 58.896 43.478 0.00 0.00 0.00 2.69
3005 3187 6.150140 GCTCCAACTGAAATTGTAACTCAGAT 59.850 38.462 10.37 0.00 39.15 2.90
3653 5081 5.049198 CACTGAAATAATGACGCTGGCATAT 60.049 40.000 0.00 0.00 0.00 1.78
3662 5090 6.355397 AGAATGCTCACTGAAATAATGACG 57.645 37.500 0.00 0.00 0.00 4.35
3862 5301 6.007076 TCCTGACAAACTATGTTGCCATTTA 58.993 36.000 0.00 0.00 44.12 1.40
3956 5400 4.036518 ACTCCTCAAGTGATAGGAAGCAT 58.963 43.478 0.00 0.00 41.33 3.79
4007 5451 3.253188 GTGCATAACCAGAAGCAGAACAA 59.747 43.478 0.00 0.00 37.72 2.83
4008 5452 2.813754 GTGCATAACCAGAAGCAGAACA 59.186 45.455 0.00 0.00 37.72 3.18
4009 5453 2.159653 CGTGCATAACCAGAAGCAGAAC 60.160 50.000 0.00 0.00 37.72 3.01
4010 5454 2.076100 CGTGCATAACCAGAAGCAGAA 58.924 47.619 0.00 0.00 37.72 3.02
4011 5455 1.275010 TCGTGCATAACCAGAAGCAGA 59.725 47.619 0.00 0.00 37.72 4.26
4077 5529 7.374754 TGAAACGTGTGAGAATGTTAAAATTCG 59.625 33.333 11.85 3.61 40.75 3.34
4097 5549 5.220548 CCATAGAAGAACTGCAGATGAAACG 60.221 44.000 23.35 0.59 0.00 3.60
4328 5780 2.521105 TGGAGATCATCATGAGCGTG 57.479 50.000 0.09 0.00 37.94 5.34
4446 5901 4.610333 ACTCCTTTTTCTGTTGAACCCTT 58.390 39.130 0.00 0.00 31.02 3.95
4528 5983 2.105006 AACGTAGTGCGACCTCTAGA 57.895 50.000 7.88 0.00 45.00 2.43
4559 6014 3.193267 AGCTTCACTTGCTGTTTTTGACA 59.807 39.130 0.00 0.00 39.56 3.58
4604 6060 9.498307 GGTACAAAACAAACATATTATTCCGAG 57.502 33.333 0.00 0.00 0.00 4.63
4621 6077 3.066203 CCAAGGTGTCACTGGTACAAAAC 59.934 47.826 2.35 0.00 38.70 2.43
4652 6142 5.401550 TCATAATTGTGTGCTAAAGCTTGC 58.598 37.500 0.00 0.00 42.66 4.01
4653 6143 7.307694 TCTTCATAATTGTGTGCTAAAGCTTG 58.692 34.615 0.00 0.00 42.66 4.01
4685 6175 3.876320 GTGACGGGTACTTGGTTAAAACA 59.124 43.478 0.00 0.00 0.00 2.83
4776 6273 4.024893 TGCAATACTTAGATGCGCTTTAGC 60.025 41.667 9.73 0.00 42.91 3.09
4777 6274 5.435557 GTGCAATACTTAGATGCGCTTTAG 58.564 41.667 9.73 4.32 44.79 1.85
4778 6275 4.026062 CGTGCAATACTTAGATGCGCTTTA 60.026 41.667 9.73 0.00 45.73 1.85
4779 6276 3.242413 CGTGCAATACTTAGATGCGCTTT 60.242 43.478 9.73 0.00 45.73 3.51
4780 6277 2.285220 CGTGCAATACTTAGATGCGCTT 59.715 45.455 9.73 0.55 45.73 4.68
4781 6278 1.860950 CGTGCAATACTTAGATGCGCT 59.139 47.619 9.73 0.00 45.73 5.92
4782 6279 1.593006 ACGTGCAATACTTAGATGCGC 59.407 47.619 0.00 0.00 44.77 6.09
4783 6280 3.116300 AGACGTGCAATACTTAGATGCG 58.884 45.455 0.00 0.00 42.91 4.73
4784 6281 5.749109 ACTTAGACGTGCAATACTTAGATGC 59.251 40.000 0.00 0.00 40.45 3.91
4785 6282 6.418226 GGACTTAGACGTGCAATACTTAGATG 59.582 42.308 0.00 0.00 0.00 2.90
4786 6283 6.321690 AGGACTTAGACGTGCAATACTTAGAT 59.678 38.462 0.00 0.00 0.00 1.98
4787 6284 5.651139 AGGACTTAGACGTGCAATACTTAGA 59.349 40.000 0.00 0.00 0.00 2.10
4788 6285 5.744345 CAGGACTTAGACGTGCAATACTTAG 59.256 44.000 0.00 0.00 0.00 2.18
4789 6286 5.184479 ACAGGACTTAGACGTGCAATACTTA 59.816 40.000 0.00 0.00 0.00 2.24
4790 6287 4.021368 ACAGGACTTAGACGTGCAATACTT 60.021 41.667 0.00 0.00 0.00 2.24
4791 6288 3.510360 ACAGGACTTAGACGTGCAATACT 59.490 43.478 0.00 0.00 0.00 2.12
4792 6289 3.612860 CACAGGACTTAGACGTGCAATAC 59.387 47.826 0.00 0.00 0.00 1.89
4793 6290 3.257375 ACACAGGACTTAGACGTGCAATA 59.743 43.478 0.00 0.00 0.00 1.90
4794 6291 2.037251 ACACAGGACTTAGACGTGCAAT 59.963 45.455 0.00 0.00 0.00 3.56
4795 6292 1.411246 ACACAGGACTTAGACGTGCAA 59.589 47.619 0.00 0.00 0.00 4.08
4796 6293 1.000607 GACACAGGACTTAGACGTGCA 60.001 52.381 0.00 0.00 0.00 4.57
4797 6294 1.000607 TGACACAGGACTTAGACGTGC 60.001 52.381 0.00 0.00 0.00 5.34
4798 6295 3.577649 ATGACACAGGACTTAGACGTG 57.422 47.619 0.00 3.21 0.00 4.49
4799 6296 3.572682 TCAATGACACAGGACTTAGACGT 59.427 43.478 0.00 0.00 0.00 4.34
4800 6297 4.174411 TCAATGACACAGGACTTAGACG 57.826 45.455 0.00 0.00 0.00 4.18
4801 6298 5.971763 AGATCAATGACACAGGACTTAGAC 58.028 41.667 0.00 0.00 0.00 2.59
4802 6299 6.611613 AAGATCAATGACACAGGACTTAGA 57.388 37.500 0.00 0.00 0.00 2.10
4803 6300 6.473778 CGTAAGATCAATGACACAGGACTTAG 59.526 42.308 0.00 0.00 43.02 2.18
4804 6301 6.071560 ACGTAAGATCAATGACACAGGACTTA 60.072 38.462 0.00 0.00 43.62 2.24
4805 6302 5.171476 CGTAAGATCAATGACACAGGACTT 58.829 41.667 0.00 0.00 43.02 3.01
4806 6303 4.220821 ACGTAAGATCAATGACACAGGACT 59.779 41.667 0.00 0.00 43.62 3.85
4807 6304 4.495422 ACGTAAGATCAATGACACAGGAC 58.505 43.478 0.00 0.00 43.62 3.85
4808 6305 4.674362 CGACGTAAGATCAATGACACAGGA 60.674 45.833 0.00 0.00 43.62 3.86
4809 6306 3.547868 CGACGTAAGATCAATGACACAGG 59.452 47.826 0.00 0.00 43.62 4.00
4810 6307 4.412207 TCGACGTAAGATCAATGACACAG 58.588 43.478 0.00 0.00 43.62 3.66
4811 6308 4.155280 TCTCGACGTAAGATCAATGACACA 59.845 41.667 0.00 0.00 43.62 3.72
4812 6309 4.659088 TCTCGACGTAAGATCAATGACAC 58.341 43.478 0.00 0.00 43.62 3.67
4813 6310 4.957759 TCTCGACGTAAGATCAATGACA 57.042 40.909 0.00 0.00 43.62 3.58
4814 6311 5.971792 TGAATCTCGACGTAAGATCAATGAC 59.028 40.000 12.04 3.61 43.62 3.06
4815 6312 6.131544 TGAATCTCGACGTAAGATCAATGA 57.868 37.500 12.04 0.00 43.62 2.57
4816 6313 6.419116 ACATGAATCTCGACGTAAGATCAATG 59.581 38.462 20.31 20.31 43.62 2.82
4817 6314 6.419116 CACATGAATCTCGACGTAAGATCAAT 59.581 38.462 12.04 7.37 43.62 2.57
4818 6315 5.743872 CACATGAATCTCGACGTAAGATCAA 59.256 40.000 12.04 5.73 43.62 2.57
4819 6316 5.273944 CACATGAATCTCGACGTAAGATCA 58.726 41.667 12.04 11.67 43.62 2.92
4820 6317 4.677378 CCACATGAATCTCGACGTAAGATC 59.323 45.833 12.04 7.67 43.62 2.75
4821 6318 4.338400 TCCACATGAATCTCGACGTAAGAT 59.662 41.667 0.00 7.03 43.62 2.40
4822 6319 3.692593 TCCACATGAATCTCGACGTAAGA 59.307 43.478 0.00 2.87 43.62 2.10
4824 6321 4.649088 ATCCACATGAATCTCGACGTAA 57.351 40.909 0.00 0.00 0.00 3.18
4825 6322 5.959618 ATATCCACATGAATCTCGACGTA 57.040 39.130 0.00 0.00 0.00 3.57
4826 6323 4.855715 ATATCCACATGAATCTCGACGT 57.144 40.909 0.00 0.00 0.00 4.34
4827 6324 6.422100 AGAAAATATCCACATGAATCTCGACG 59.578 38.462 0.00 0.00 0.00 5.12
4828 6325 7.721286 AGAAAATATCCACATGAATCTCGAC 57.279 36.000 0.00 0.00 0.00 4.20
4829 6326 8.737168 AAAGAAAATATCCACATGAATCTCGA 57.263 30.769 0.00 0.00 0.00 4.04
4830 6327 9.793252 AAAAAGAAAATATCCACATGAATCTCG 57.207 29.630 0.00 0.00 0.00 4.04
4905 6419 9.550406 AATATTTGCATCATTAATCTGGTTTGG 57.450 29.630 0.00 0.00 0.00 3.28
4911 6425 8.304596 AGCTGGAATATTTGCATCATTAATCTG 58.695 33.333 10.25 0.00 0.00 2.90
4950 6464 2.502213 AAAGCGTGCCCTTGTTTTAC 57.498 45.000 0.00 0.00 0.00 2.01
4979 6493 3.498397 ACACTTCAAGCAATTACAGTCGG 59.502 43.478 0.00 0.00 0.00 4.79
4980 6494 4.732285 ACACTTCAAGCAATTACAGTCG 57.268 40.909 0.00 0.00 0.00 4.18
4981 6495 5.452777 GGAACACTTCAAGCAATTACAGTC 58.547 41.667 0.00 0.00 0.00 3.51
4983 6497 4.520492 AGGGAACACTTCAAGCAATTACAG 59.480 41.667 0.00 0.00 0.00 2.74
4991 6506 0.312102 GTGCAGGGAACACTTCAAGC 59.688 55.000 0.00 0.00 35.12 4.01
5007 6522 0.928451 GTGTTTTCGACTTGCGGTGC 60.928 55.000 0.00 0.00 41.33 5.01
5008 6523 0.653323 CGTGTTTTCGACTTGCGGTG 60.653 55.000 0.00 0.00 41.33 4.94
5112 6731 3.193479 GCCCCTTCAATCAACCAAGTAAG 59.807 47.826 0.00 0.00 0.00 2.34
5120 6739 3.959535 TTTGATGCCCCTTCAATCAAC 57.040 42.857 0.00 0.00 33.37 3.18
5133 6760 2.187707 GTGGTCGATGCAATTTGATGC 58.812 47.619 0.00 0.00 46.58 3.91
5236 6863 9.691362 ACGAAATGTGCTTGTTCTTTATTTATT 57.309 25.926 0.00 0.00 0.00 1.40
5237 6864 9.341899 GACGAAATGTGCTTGTTCTTTATTTAT 57.658 29.630 0.00 0.00 0.00 1.40
5238 6865 8.346300 TGACGAAATGTGCTTGTTCTTTATTTA 58.654 29.630 0.00 0.00 0.00 1.40
5239 6866 7.199766 TGACGAAATGTGCTTGTTCTTTATTT 58.800 30.769 0.00 0.00 0.00 1.40
5240 6867 6.734137 TGACGAAATGTGCTTGTTCTTTATT 58.266 32.000 0.00 0.00 0.00 1.40
5241 6868 6.312399 TGACGAAATGTGCTTGTTCTTTAT 57.688 33.333 0.00 0.00 0.00 1.40
5242 6869 5.743026 TGACGAAATGTGCTTGTTCTTTA 57.257 34.783 0.00 0.00 0.00 1.85
5243 6870 4.630894 TGACGAAATGTGCTTGTTCTTT 57.369 36.364 0.00 0.00 0.00 2.52
5244 6871 4.096382 ACTTGACGAAATGTGCTTGTTCTT 59.904 37.500 0.00 0.00 0.00 2.52
5245 6872 3.627577 ACTTGACGAAATGTGCTTGTTCT 59.372 39.130 0.00 0.00 0.00 3.01
5246 6873 3.952535 ACTTGACGAAATGTGCTTGTTC 58.047 40.909 0.00 0.00 0.00 3.18
5247 6874 3.546020 CGACTTGACGAAATGTGCTTGTT 60.546 43.478 0.00 0.00 35.09 2.83
5248 6875 2.032894 CGACTTGACGAAATGTGCTTGT 60.033 45.455 0.00 0.00 35.09 3.16
5249 6876 2.563976 CGACTTGACGAAATGTGCTTG 58.436 47.619 0.00 0.00 35.09 4.01
5250 6877 1.531149 CCGACTTGACGAAATGTGCTT 59.469 47.619 0.00 0.00 35.09 3.91
5251 6878 1.148310 CCGACTTGACGAAATGTGCT 58.852 50.000 0.00 0.00 35.09 4.40
5252 6879 0.865769 ACCGACTTGACGAAATGTGC 59.134 50.000 0.00 0.00 35.09 4.57
5253 6880 3.985279 TCTAACCGACTTGACGAAATGTG 59.015 43.478 0.00 0.00 35.09 3.21
5316 6943 1.134580 GCCGACTTAAGTTACTCCCCC 60.135 57.143 10.02 0.00 0.00 5.40
5317 6944 1.829849 AGCCGACTTAAGTTACTCCCC 59.170 52.381 10.02 0.00 0.00 4.81
5319 6946 2.671888 GCAAGCCGACTTAAGTTACTCC 59.328 50.000 10.02 0.00 33.74 3.85
5320 6947 3.586892 AGCAAGCCGACTTAAGTTACTC 58.413 45.455 10.02 0.00 33.74 2.59
5321 6948 3.006537 TGAGCAAGCCGACTTAAGTTACT 59.993 43.478 10.02 4.95 33.74 2.24
5322 6949 3.323243 TGAGCAAGCCGACTTAAGTTAC 58.677 45.455 10.02 2.59 33.74 2.50
5323 6950 3.671008 TGAGCAAGCCGACTTAAGTTA 57.329 42.857 10.02 0.00 33.74 2.24
5324 6951 2.543777 TGAGCAAGCCGACTTAAGTT 57.456 45.000 10.02 0.00 33.74 2.66
5325 6952 2.143925 GTTGAGCAAGCCGACTTAAGT 58.856 47.619 8.13 8.13 33.74 2.24
5326 6953 1.126846 CGTTGAGCAAGCCGACTTAAG 59.873 52.381 0.00 0.00 33.74 1.85
5327 6954 1.144969 CGTTGAGCAAGCCGACTTAA 58.855 50.000 0.00 0.00 33.74 1.85
5328 6955 0.315886 TCGTTGAGCAAGCCGACTTA 59.684 50.000 0.00 0.00 33.74 2.24
5329 6956 0.320771 ATCGTTGAGCAAGCCGACTT 60.321 50.000 0.00 0.00 36.19 3.01
5330 6957 0.530744 TATCGTTGAGCAAGCCGACT 59.469 50.000 0.00 0.00 31.43 4.18
5331 6958 1.355971 TTATCGTTGAGCAAGCCGAC 58.644 50.000 0.00 0.00 31.43 4.79
5332 6959 2.087501 TTTATCGTTGAGCAAGCCGA 57.912 45.000 0.00 0.00 0.00 5.54
5333 6960 2.476185 CCTTTTATCGTTGAGCAAGCCG 60.476 50.000 0.00 0.00 0.00 5.52
5334 6961 2.732282 GCCTTTTATCGTTGAGCAAGCC 60.732 50.000 0.00 0.00 0.00 4.35
5335 6962 2.095263 TGCCTTTTATCGTTGAGCAAGC 60.095 45.455 0.00 0.00 0.00 4.01
5336 6963 3.436704 TCTGCCTTTTATCGTTGAGCAAG 59.563 43.478 0.00 0.00 0.00 4.01
5337 6964 3.407698 TCTGCCTTTTATCGTTGAGCAA 58.592 40.909 0.00 0.00 0.00 3.91
5338 6965 3.002791 CTCTGCCTTTTATCGTTGAGCA 58.997 45.455 0.00 0.00 0.00 4.26
5339 6966 3.003480 ACTCTGCCTTTTATCGTTGAGC 58.997 45.455 0.00 0.00 0.00 4.26
5340 6967 5.411781 ACTACTCTGCCTTTTATCGTTGAG 58.588 41.667 0.00 0.00 0.00 3.02
5341 6968 5.401531 ACTACTCTGCCTTTTATCGTTGA 57.598 39.130 0.00 0.00 0.00 3.18
5342 6969 6.481954 AAACTACTCTGCCTTTTATCGTTG 57.518 37.500 0.00 0.00 0.00 4.10
5343 6970 6.708949 TGAAAACTACTCTGCCTTTTATCGTT 59.291 34.615 0.00 0.00 0.00 3.85
5344 6971 6.228258 TGAAAACTACTCTGCCTTTTATCGT 58.772 36.000 0.00 0.00 0.00 3.73
5345 6972 6.721571 TGAAAACTACTCTGCCTTTTATCG 57.278 37.500 0.00 0.00 0.00 2.92
5363 6990 7.013274 CCTCTGATTTTGTACTCTGGTTGAAAA 59.987 37.037 0.00 0.00 0.00 2.29
5364 6991 6.486657 CCTCTGATTTTGTACTCTGGTTGAAA 59.513 38.462 0.00 0.00 0.00 2.69
5365 6992 5.997746 CCTCTGATTTTGTACTCTGGTTGAA 59.002 40.000 0.00 0.00 0.00 2.69
5366 6993 5.071788 ACCTCTGATTTTGTACTCTGGTTGA 59.928 40.000 0.00 0.00 0.00 3.18
5367 6994 5.308825 ACCTCTGATTTTGTACTCTGGTTG 58.691 41.667 0.00 0.00 0.00 3.77
5368 6995 5.568620 ACCTCTGATTTTGTACTCTGGTT 57.431 39.130 0.00 0.00 0.00 3.67
5369 6996 6.017192 TCTACCTCTGATTTTGTACTCTGGT 58.983 40.000 0.00 0.00 0.00 4.00
5370 6997 6.153680 ACTCTACCTCTGATTTTGTACTCTGG 59.846 42.308 0.00 0.00 0.00 3.86
5371 6998 7.164230 ACTCTACCTCTGATTTTGTACTCTG 57.836 40.000 0.00 0.00 0.00 3.35
5372 6999 6.378848 GGACTCTACCTCTGATTTTGTACTCT 59.621 42.308 0.00 0.00 0.00 3.24
5373 7000 6.566141 GGACTCTACCTCTGATTTTGTACTC 58.434 44.000 0.00 0.00 0.00 2.59
5374 7001 5.125739 CGGACTCTACCTCTGATTTTGTACT 59.874 44.000 0.00 0.00 0.00 2.73
5375 7002 5.341617 CGGACTCTACCTCTGATTTTGTAC 58.658 45.833 0.00 0.00 0.00 2.90
5376 7003 4.401519 CCGGACTCTACCTCTGATTTTGTA 59.598 45.833 0.00 0.00 0.00 2.41
5377 7004 3.195825 CCGGACTCTACCTCTGATTTTGT 59.804 47.826 0.00 0.00 0.00 2.83
5378 7005 3.195825 ACCGGACTCTACCTCTGATTTTG 59.804 47.826 9.46 0.00 0.00 2.44
5379 7006 3.442076 ACCGGACTCTACCTCTGATTTT 58.558 45.455 9.46 0.00 0.00 1.82
5380 7007 3.025262 GACCGGACTCTACCTCTGATTT 58.975 50.000 9.46 0.00 0.00 2.17
5381 7008 2.657143 GACCGGACTCTACCTCTGATT 58.343 52.381 9.46 0.00 0.00 2.57
5382 7009 1.133730 GGACCGGACTCTACCTCTGAT 60.134 57.143 9.46 0.00 0.00 2.90
5383 7010 0.255318 GGACCGGACTCTACCTCTGA 59.745 60.000 9.46 0.00 0.00 3.27
5384 7011 1.096386 CGGACCGGACTCTACCTCTG 61.096 65.000 9.46 0.00 0.00 3.35
5385 7012 1.224039 CGGACCGGACTCTACCTCT 59.776 63.158 9.46 0.00 0.00 3.69
5386 7013 3.824810 CGGACCGGACTCTACCTC 58.175 66.667 9.46 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.