Multiple sequence alignment - TraesCS4D01G058200

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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 TraesCS4D01G058200 chr4D 100.000 3804 0 0 1 3804 34088062 34091865 0.000000e+00 7025.0
1 TraesCS4D01G058200 chr4B 92.055 2530 101 30 722 3174 48991289 48993795 0.000000e+00 3467.0
2 TraesCS4D01G058200 chr4B 83.974 468 44 20 259 721 48990714 48991155 1.630000e-113 420.0
3 TraesCS4D01G058200 chr4B 89.041 292 11 4 3223 3503 48993911 48994192 3.640000e-90 342.0
4 TraesCS4D01G058200 chr4B 89.506 162 16 1 81 241 48990488 48990649 1.790000e-48 204.0
5 TraesCS4D01G058200 chr4B 87.324 142 15 3 3665 3804 48994600 48994740 3.930000e-35 159.0
6 TraesCS4D01G058200 chr4A 91.700 2506 112 49 789 3229 568192690 568195164 0.000000e+00 3387.0
7 TraesCS4D01G058200 chr4A 85.354 396 18 11 3223 3588 568195191 568195576 1.290000e-99 374.0
8 TraesCS4D01G058200 chr4A 81.047 401 24 26 259 649 568192141 568192499 4.840000e-69 272.0
9 TraesCS4D01G058200 chr4A 89.216 102 7 4 3587 3684 511040486 511040587 1.430000e-24 124.0
10 TraesCS4D01G058200 chr2D 72.449 686 149 32 1941 2612 505815778 505816437 2.330000e-42 183.0
11 TraesCS4D01G058200 chr2D 91.209 91 5 3 3585 3672 302248099 302248009 1.860000e-23 121.0
12 TraesCS4D01G058200 chr2D 82.906 117 18 2 1060 1175 505814510 505814625 1.870000e-18 104.0
13 TraesCS4D01G058200 chr3B 71.463 827 190 36 1806 2612 99501419 99502219 1.090000e-40 178.0
14 TraesCS4D01G058200 chr3B 93.258 89 3 3 3586 3671 39349864 39349952 1.110000e-25 128.0
15 TraesCS4D01G058200 chr3B 82.051 117 17 3 1059 1173 99500820 99500934 3.130000e-16 97.1
16 TraesCS4D01G058200 chr3D 71.135 828 191 37 1806 2612 61803401 61804201 1.090000e-35 161.0
17 TraesCS4D01G058200 chr3D 90.526 95 6 3 3581 3672 74446992 74446898 5.160000e-24 122.0
18 TraesCS4D01G058200 chr3A 71.309 833 181 42 1806 2612 70849130 70849930 1.090000e-35 161.0
19 TraesCS4D01G058200 chr1B 95.122 82 1 3 3590 3668 675980636 675980555 3.990000e-25 126.0
20 TraesCS4D01G058200 chr7D 89.474 95 6 4 3580 3670 218418297 218418391 2.400000e-22 117.0
21 TraesCS4D01G058200 chr7D 88.776 98 6 5 3586 3679 540570509 540570413 8.640000e-22 115.0
22 TraesCS4D01G058200 chr5B 87.500 104 7 4 3580 3679 662596818 662596919 8.640000e-22 115.0
23 TraesCS4D01G058200 chr1D 88.776 98 6 5 3586 3679 469153916 469154012 8.640000e-22 115.0
24 TraesCS4D01G058200 chr2A 79.730 148 28 2 1029 1175 650243646 650243792 5.200000e-19 106.0


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 TraesCS4D01G058200 chr4D 34088062 34091865 3803 False 7025.000000 7025 100.000000 1 3804 1 chr4D.!!$F1 3803
1 TraesCS4D01G058200 chr4B 48990488 48994740 4252 False 918.400000 3467 88.380000 81 3804 5 chr4B.!!$F1 3723
2 TraesCS4D01G058200 chr4A 568192141 568195576 3435 False 1344.333333 3387 86.033667 259 3588 3 chr4A.!!$F2 3329

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
40 41 0.109342 ACCAGTTTCAGTCCCAGCTG 59.891 55.0 6.78 6.78 37.81 4.24 F
1089 1354 0.324460 ACTCGTCCTACTTCCTGGGG 60.324 60.0 0.00 0.00 0.00 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1943 2236 0.745845 GTGATGAGCACGCCCTTGAT 60.746 55.0 0.0 0.0 37.83 2.57 R
2871 3164 0.176680 CATGGCCGTAAGCTGTCTCT 59.823 55.0 0.0 0.0 43.05 3.10 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
17 18 2.563942 GTTTGCCCGCGTGCATAA 59.436 55.556 18.85 11.69 41.70 1.90
18 19 1.081108 GTTTGCCCGCGTGCATAAA 60.081 52.632 18.85 6.86 41.70 1.40
19 20 0.457681 GTTTGCCCGCGTGCATAAAT 60.458 50.000 18.85 0.00 41.70 1.40
20 21 1.095600 TTTGCCCGCGTGCATAAATA 58.904 45.000 18.85 0.00 41.70 1.40
21 22 1.095600 TTGCCCGCGTGCATAAATAA 58.904 45.000 18.85 0.00 41.70 1.40
22 23 0.378962 TGCCCGCGTGCATAAATAAC 59.621 50.000 13.54 0.00 36.04 1.89
23 24 0.317519 GCCCGCGTGCATAAATAACC 60.318 55.000 9.21 0.00 0.00 2.85
24 25 1.018148 CCCGCGTGCATAAATAACCA 58.982 50.000 4.92 0.00 0.00 3.67
25 26 1.002900 CCCGCGTGCATAAATAACCAG 60.003 52.381 4.92 0.00 0.00 4.00
26 27 1.668751 CCGCGTGCATAAATAACCAGT 59.331 47.619 4.92 0.00 0.00 4.00
27 28 2.096819 CCGCGTGCATAAATAACCAGTT 59.903 45.455 4.92 0.00 0.00 3.16
28 29 3.426963 CCGCGTGCATAAATAACCAGTTT 60.427 43.478 4.92 0.00 0.00 2.66
29 30 3.783943 CGCGTGCATAAATAACCAGTTTC 59.216 43.478 0.00 0.00 0.00 2.78
30 31 4.670478 CGCGTGCATAAATAACCAGTTTCA 60.670 41.667 0.00 0.00 0.00 2.69
31 32 4.793216 GCGTGCATAAATAACCAGTTTCAG 59.207 41.667 0.00 0.00 0.00 3.02
32 33 5.619086 GCGTGCATAAATAACCAGTTTCAGT 60.619 40.000 0.00 0.00 0.00 3.41
33 34 6.021596 CGTGCATAAATAACCAGTTTCAGTC 58.978 40.000 0.00 0.00 0.00 3.51
34 35 6.322491 GTGCATAAATAACCAGTTTCAGTCC 58.678 40.000 0.00 0.00 0.00 3.85
35 36 5.417580 TGCATAAATAACCAGTTTCAGTCCC 59.582 40.000 0.00 0.00 0.00 4.46
36 37 5.417580 GCATAAATAACCAGTTTCAGTCCCA 59.582 40.000 0.00 0.00 0.00 4.37
37 38 6.404734 GCATAAATAACCAGTTTCAGTCCCAG 60.405 42.308 0.00 0.00 0.00 4.45
38 39 2.561478 TAACCAGTTTCAGTCCCAGC 57.439 50.000 0.00 0.00 0.00 4.85
39 40 0.846693 AACCAGTTTCAGTCCCAGCT 59.153 50.000 0.00 0.00 0.00 4.24
40 41 0.109342 ACCAGTTTCAGTCCCAGCTG 59.891 55.000 6.78 6.78 37.81 4.24
41 42 0.607489 CCAGTTTCAGTCCCAGCTGG 60.607 60.000 26.87 26.87 37.71 4.85
42 43 1.073897 AGTTTCAGTCCCAGCTGGC 59.926 57.895 28.39 14.93 37.12 4.85
43 44 1.973812 GTTTCAGTCCCAGCTGGCC 60.974 63.158 28.39 19.09 37.12 5.36
44 45 2.459969 TTTCAGTCCCAGCTGGCCA 61.460 57.895 28.39 13.11 37.12 5.36
45 46 2.005606 TTTCAGTCCCAGCTGGCCAA 62.006 55.000 28.39 11.93 37.12 4.52
46 47 2.360852 CAGTCCCAGCTGGCCAAG 60.361 66.667 28.39 13.92 33.11 3.61
73 74 3.498927 CTGCTTAACAGCCAAGGATTG 57.501 47.619 0.00 0.00 46.74 2.67
74 75 2.416431 CTGCTTAACAGCCAAGGATTGC 60.416 50.000 0.00 0.00 46.74 3.56
75 76 4.925691 CTGCTTAACAGCCAAGGATTGCA 61.926 47.826 0.00 0.00 46.74 4.08
76 77 6.915370 CTGCTTAACAGCCAAGGATTGCAC 62.915 50.000 0.00 0.00 46.74 4.57
102 103 7.521509 ACACACGCACTAATAAAATACTCTC 57.478 36.000 0.00 0.00 0.00 3.20
103 104 7.094631 ACACACGCACTAATAAAATACTCTCA 58.905 34.615 0.00 0.00 0.00 3.27
147 148 2.444351 GCGAATGCAGTTCACATAAGC 58.556 47.619 0.00 0.00 42.15 3.09
150 151 3.728864 CGAATGCAGTTCACATAAGCCAC 60.729 47.826 0.00 0.00 36.60 5.01
151 152 2.268762 TGCAGTTCACATAAGCCACA 57.731 45.000 0.00 0.00 0.00 4.17
152 153 2.794103 TGCAGTTCACATAAGCCACAT 58.206 42.857 0.00 0.00 0.00 3.21
204 205 3.319122 GGCATATCCTGATTGGGTGAAAC 59.681 47.826 0.00 0.00 36.20 2.78
207 208 5.827797 GCATATCCTGATTGGGTGAAACTAA 59.172 40.000 0.00 0.00 36.74 2.24
209 210 7.014615 GCATATCCTGATTGGGTGAAACTAAAT 59.985 37.037 0.00 0.00 36.74 1.40
221 222 5.523552 GGTGAAACTAAATTGCAAAGTTGCT 59.476 36.000 17.50 4.74 46.01 3.91
241 243 4.675510 GCTTACTACACCAAGCACGTATA 58.324 43.478 1.62 0.00 45.20 1.47
243 245 5.449588 GCTTACTACACCAAGCACGTATAGA 60.450 44.000 1.62 0.00 45.20 1.98
246 248 6.315091 ACTACACCAAGCACGTATAGATAG 57.685 41.667 0.00 0.00 0.00 2.08
247 249 3.978687 ACACCAAGCACGTATAGATAGC 58.021 45.455 0.00 0.00 0.00 2.97
248 250 3.637229 ACACCAAGCACGTATAGATAGCT 59.363 43.478 0.00 0.00 37.08 3.32
249 251 4.099573 ACACCAAGCACGTATAGATAGCTT 59.900 41.667 0.00 1.57 45.54 3.74
253 255 4.775058 AGCACGTATAGATAGCTTGAGG 57.225 45.455 0.00 0.00 29.98 3.86
255 257 4.827835 AGCACGTATAGATAGCTTGAGGAA 59.172 41.667 0.00 0.00 29.98 3.36
256 258 5.048364 AGCACGTATAGATAGCTTGAGGAAG 60.048 44.000 0.00 0.00 29.98 3.46
320 369 2.465813 CCTCCAGTTGATCCTGTCTCT 58.534 52.381 0.00 0.00 0.00 3.10
329 378 0.394488 ATCCTGTCTCTCGCTTCGGA 60.394 55.000 0.00 0.00 0.00 4.55
354 403 3.044059 GCTGGCTTGTCCACATCGC 62.044 63.158 0.00 0.00 40.72 4.58
404 453 1.606606 CGCATGTCGGCTTTTCTTTC 58.393 50.000 0.00 0.00 33.78 2.62
405 454 1.197721 CGCATGTCGGCTTTTCTTTCT 59.802 47.619 0.00 0.00 33.78 2.52
406 455 2.350772 CGCATGTCGGCTTTTCTTTCTT 60.351 45.455 0.00 0.00 33.78 2.52
407 456 3.642705 GCATGTCGGCTTTTCTTTCTTT 58.357 40.909 0.00 0.00 0.00 2.52
408 457 4.051237 GCATGTCGGCTTTTCTTTCTTTT 58.949 39.130 0.00 0.00 0.00 2.27
409 458 4.084900 GCATGTCGGCTTTTCTTTCTTTTG 60.085 41.667 0.00 0.00 0.00 2.44
411 460 4.668289 TGTCGGCTTTTCTTTCTTTTGAC 58.332 39.130 0.00 0.00 0.00 3.18
413 462 5.099575 GTCGGCTTTTCTTTCTTTTGACAA 58.900 37.500 0.00 0.00 0.00 3.18
447 496 5.345702 TGTACTGCACCGTAGTATTTCATC 58.654 41.667 0.00 0.00 33.60 2.92
451 500 3.181469 TGCACCGTAGTATTTCATCTCCC 60.181 47.826 0.00 0.00 0.00 4.30
461 510 6.750148 AGTATTTCATCTCCCTAACGTGATC 58.250 40.000 0.00 0.00 0.00 2.92
463 512 1.954382 TCATCTCCCTAACGTGATCCG 59.046 52.381 0.00 2.55 44.03 4.18
465 514 2.359981 TCTCCCTAACGTGATCCGAT 57.640 50.000 10.05 1.86 40.70 4.18
467 516 2.621998 TCTCCCTAACGTGATCCGATTC 59.378 50.000 10.05 0.00 40.70 2.52
468 517 2.361119 CTCCCTAACGTGATCCGATTCA 59.639 50.000 10.05 0.00 40.70 2.57
469 518 2.963101 TCCCTAACGTGATCCGATTCAT 59.037 45.455 10.05 0.00 40.70 2.57
470 519 3.005472 TCCCTAACGTGATCCGATTCATC 59.995 47.826 10.05 0.00 40.70 2.92
472 521 3.983988 CCTAACGTGATCCGATTCATCTG 59.016 47.826 10.05 0.00 40.70 2.90
481 532 4.655762 TCCGATTCATCTGTCCTTACTG 57.344 45.455 0.00 0.00 0.00 2.74
532 587 3.211963 GCGTGGATCCCATGTGCC 61.212 66.667 9.90 0.00 42.15 5.01
574 630 5.411781 AGCTACAGTTCAGAAGGTAAATCG 58.588 41.667 0.00 0.00 0.00 3.34
580 636 4.159879 AGTTCAGAAGGTAAATCGGTCGAT 59.840 41.667 0.00 0.00 36.23 3.59
588 644 1.567504 AAATCGGTCGATTACGGCAG 58.432 50.000 17.30 0.00 46.58 4.85
597 653 1.077716 ATTACGGCAGAGGCAACCC 60.078 57.895 0.00 0.00 43.71 4.11
598 654 2.552231 ATTACGGCAGAGGCAACCCC 62.552 60.000 0.00 0.00 43.71 4.95
624 684 4.645535 TCCAAACAGAAGAGATTCCAGTG 58.354 43.478 0.00 0.00 0.00 3.66
637 697 3.634397 TTCCAGTGCCAAGATTAGAGG 57.366 47.619 0.00 0.00 0.00 3.69
640 700 2.158842 CCAGTGCCAAGATTAGAGGGAG 60.159 54.545 0.00 0.00 0.00 4.30
649 709 4.273300 AGATTAGAGGGAGCCTACACTT 57.727 45.455 0.00 0.00 31.76 3.16
650 710 3.964031 AGATTAGAGGGAGCCTACACTTG 59.036 47.826 0.00 0.00 31.76 3.16
651 711 2.921834 TAGAGGGAGCCTACACTTGT 57.078 50.000 0.00 0.00 31.76 3.16
652 712 2.921834 AGAGGGAGCCTACACTTGTA 57.078 50.000 0.00 0.00 31.76 2.41
653 713 2.458620 AGAGGGAGCCTACACTTGTAC 58.541 52.381 0.00 0.00 31.76 2.90
654 714 2.043252 AGAGGGAGCCTACACTTGTACT 59.957 50.000 0.00 0.00 31.76 2.73
655 715 2.427812 GAGGGAGCCTACACTTGTACTC 59.572 54.545 0.00 0.44 31.76 2.59
656 716 1.481363 GGGAGCCTACACTTGTACTCC 59.519 57.143 13.90 13.90 40.39 3.85
657 717 2.458620 GGAGCCTACACTTGTACTCCT 58.541 52.381 14.59 0.70 39.14 3.69
658 718 2.832733 GGAGCCTACACTTGTACTCCTT 59.167 50.000 14.59 0.00 39.14 3.36
659 719 3.119065 GGAGCCTACACTTGTACTCCTTC 60.119 52.174 14.59 0.00 39.14 3.46
660 720 3.764972 GAGCCTACACTTGTACTCCTTCT 59.235 47.826 0.00 0.00 0.00 2.85
661 721 3.764972 AGCCTACACTTGTACTCCTTCTC 59.235 47.826 0.00 0.00 0.00 2.87
662 722 3.764972 GCCTACACTTGTACTCCTTCTCT 59.235 47.826 0.00 0.00 0.00 3.10
663 723 4.381079 GCCTACACTTGTACTCCTTCTCTG 60.381 50.000 0.00 0.00 0.00 3.35
664 724 3.669251 ACACTTGTACTCCTTCTCTGC 57.331 47.619 0.00 0.00 0.00 4.26
665 725 3.235200 ACACTTGTACTCCTTCTCTGCT 58.765 45.455 0.00 0.00 0.00 4.24
666 726 4.408276 ACACTTGTACTCCTTCTCTGCTA 58.592 43.478 0.00 0.00 0.00 3.49
667 727 4.218852 ACACTTGTACTCCTTCTCTGCTAC 59.781 45.833 0.00 0.00 0.00 3.58
668 728 4.461081 CACTTGTACTCCTTCTCTGCTACT 59.539 45.833 0.00 0.00 0.00 2.57
669 729 5.648526 CACTTGTACTCCTTCTCTGCTACTA 59.351 44.000 0.00 0.00 0.00 1.82
670 730 5.648960 ACTTGTACTCCTTCTCTGCTACTAC 59.351 44.000 0.00 0.00 0.00 2.73
671 731 5.438698 TGTACTCCTTCTCTGCTACTACT 57.561 43.478 0.00 0.00 0.00 2.57
672 732 5.186942 TGTACTCCTTCTCTGCTACTACTG 58.813 45.833 0.00 0.00 0.00 2.74
673 733 4.310022 ACTCCTTCTCTGCTACTACTGT 57.690 45.455 0.00 0.00 0.00 3.55
674 734 4.668636 ACTCCTTCTCTGCTACTACTGTT 58.331 43.478 0.00 0.00 0.00 3.16
675 735 4.461081 ACTCCTTCTCTGCTACTACTGTTG 59.539 45.833 0.00 0.00 0.00 3.33
676 736 4.663334 TCCTTCTCTGCTACTACTGTTGA 58.337 43.478 0.00 0.00 0.00 3.18
677 737 5.077564 TCCTTCTCTGCTACTACTGTTGAA 58.922 41.667 0.00 0.00 0.00 2.69
678 738 5.047943 TCCTTCTCTGCTACTACTGTTGAAC 60.048 44.000 0.00 0.00 0.00 3.18
679 739 4.785511 TCTCTGCTACTACTGTTGAACC 57.214 45.455 0.00 0.00 0.00 3.62
680 740 3.190744 TCTCTGCTACTACTGTTGAACCG 59.809 47.826 0.00 0.00 0.00 4.44
681 741 1.993370 CTGCTACTACTGTTGAACCGC 59.007 52.381 0.00 0.00 0.00 5.68
682 742 0.989890 GCTACTACTGTTGAACCGCG 59.010 55.000 0.00 0.00 0.00 6.46
683 743 1.625616 CTACTACTGTTGAACCGCGG 58.374 55.000 26.86 26.86 0.00 6.46
684 744 0.388907 TACTACTGTTGAACCGCGGC 60.389 55.000 28.58 11.02 0.00 6.53
685 745 2.357760 TACTGTTGAACCGCGGCC 60.358 61.111 28.58 18.55 0.00 6.13
740 959 1.139256 TGCTGTTCTGACGTTAACCCA 59.861 47.619 0.00 0.00 0.00 4.51
743 962 1.142474 GTTCTGACGTTAACCCACCG 58.858 55.000 0.00 0.00 0.00 4.94
745 964 2.030862 TGACGTTAACCCACCGCC 59.969 61.111 0.00 0.00 0.00 6.13
749 969 3.969119 GTTAACCCACCGCCCCCA 61.969 66.667 0.00 0.00 0.00 4.96
750 970 3.969119 TTAACCCACCGCCCCCAC 61.969 66.667 0.00 0.00 0.00 4.61
751 971 4.986774 TAACCCACCGCCCCCACT 62.987 66.667 0.00 0.00 0.00 4.00
806 1043 2.426023 GTGACGCCACCTTCACCT 59.574 61.111 0.00 0.00 35.00 4.00
807 1044 1.668151 GTGACGCCACCTTCACCTC 60.668 63.158 0.00 0.00 35.00 3.85
808 1045 2.137528 TGACGCCACCTTCACCTCA 61.138 57.895 0.00 0.00 0.00 3.86
809 1046 1.668151 GACGCCACCTTCACCTCAC 60.668 63.158 0.00 0.00 0.00 3.51
811 1048 2.358737 GCCACCTTCACCTCACCG 60.359 66.667 0.00 0.00 0.00 4.94
816 1053 3.636231 CTTCACCTCACCGCCCCA 61.636 66.667 0.00 0.00 0.00 4.96
887 1124 2.166254 CTGCCTCTTCACTCCTCTTCTC 59.834 54.545 0.00 0.00 0.00 2.87
888 1125 2.225242 TGCCTCTTCACTCCTCTTCTCT 60.225 50.000 0.00 0.00 0.00 3.10
889 1126 3.010696 TGCCTCTTCACTCCTCTTCTCTA 59.989 47.826 0.00 0.00 0.00 2.43
890 1127 4.020543 GCCTCTTCACTCCTCTTCTCTAA 58.979 47.826 0.00 0.00 0.00 2.10
891 1128 4.097892 GCCTCTTCACTCCTCTTCTCTAAG 59.902 50.000 0.00 0.00 0.00 2.18
892 1129 4.097892 CCTCTTCACTCCTCTTCTCTAAGC 59.902 50.000 0.00 0.00 32.36 3.09
893 1130 4.929479 TCTTCACTCCTCTTCTCTAAGCT 58.071 43.478 0.00 0.00 32.36 3.74
894 1131 6.068461 TCTTCACTCCTCTTCTCTAAGCTA 57.932 41.667 0.00 0.00 32.36 3.32
895 1132 6.119536 TCTTCACTCCTCTTCTCTAAGCTAG 58.880 44.000 0.00 0.00 32.36 3.42
896 1133 4.204012 TCACTCCTCTTCTCTAAGCTAGC 58.796 47.826 6.62 6.62 32.36 3.42
897 1134 4.080015 TCACTCCTCTTCTCTAAGCTAGCT 60.080 45.833 12.68 12.68 32.36 3.32
898 1135 4.036734 CACTCCTCTTCTCTAAGCTAGCTG 59.963 50.000 20.16 6.89 32.36 4.24
899 1136 2.955660 TCCTCTTCTCTAAGCTAGCTGC 59.044 50.000 20.16 0.00 43.29 5.25
912 1150 3.132801 GCTGCTGCTTGCTCTCCC 61.133 66.667 8.53 0.00 43.37 4.30
926 1164 1.204467 CTCTCCCAGCTCAGTCTTGAC 59.796 57.143 0.00 0.00 0.00 3.18
944 1186 2.224042 TGACAACACTCGATCACAGCTT 60.224 45.455 0.00 0.00 0.00 3.74
1089 1354 0.324460 ACTCGTCCTACTTCCTGGGG 60.324 60.000 0.00 0.00 0.00 4.96
1107 1372 2.478292 GGGTGGGAGGAGTATGAGAAA 58.522 52.381 0.00 0.00 0.00 2.52
1182 1447 3.637229 CCGAGAACCAGGTACATACAGAT 59.363 47.826 0.00 0.00 0.00 2.90
1186 1451 3.827008 ACCAGGTACATACAGATGCAG 57.173 47.619 0.00 0.00 36.43 4.41
1187 1452 2.435805 ACCAGGTACATACAGATGCAGG 59.564 50.000 0.00 0.00 36.43 4.85
1188 1453 2.224378 CCAGGTACATACAGATGCAGGG 60.224 54.545 0.00 0.00 36.43 4.45
1193 1458 4.344102 GGTACATACAGATGCAGGGTTCTA 59.656 45.833 0.00 0.00 36.43 2.10
1196 1461 1.279496 ACAGATGCAGGGTTCTAGCA 58.721 50.000 0.00 0.00 43.14 3.49
1228 1504 1.023513 CAGCTAGCTTGCCACTGTCC 61.024 60.000 16.46 0.00 0.00 4.02
1232 1510 2.167398 TAGCTTGCCACTGTCCGTCC 62.167 60.000 0.00 0.00 0.00 4.79
1310 1588 1.463214 TGGCTGGAGAAGAACCCCA 60.463 57.895 0.00 0.00 0.00 4.96
1404 1682 3.231818 TCCCGGCCTTCAAAAATGTAAA 58.768 40.909 0.00 0.00 0.00 2.01
1697 1979 1.079405 TGCCGTCCCTCGACATTTC 60.079 57.895 0.00 0.00 42.86 2.17
1775 2065 8.842358 TCCATCACTAACCTTTTAACAGTAAG 57.158 34.615 0.00 0.00 0.00 2.34
2191 2484 0.888619 TCGTGTACAGCCTCTCCAAG 59.111 55.000 0.00 0.00 0.00 3.61
2240 2533 0.249073 CGCCATCTACTCCTCCAACG 60.249 60.000 0.00 0.00 0.00 4.10
2317 2610 4.208686 CAGTACCTCCTCGCGGCC 62.209 72.222 6.13 0.00 0.00 6.13
2804 3097 4.222847 GGAAGGCCGAGCGGTAGG 62.223 72.222 9.64 9.64 37.65 3.18
2814 3107 2.125512 GCGGTAGGCAGACCACAG 60.126 66.667 9.03 0.00 42.87 3.66
2826 3119 0.876342 GACCACAGCCGCATAGCTAC 60.876 60.000 0.00 0.00 42.61 3.58
2829 3122 0.179100 CACAGCCGCATAGCTACTGT 60.179 55.000 7.86 7.86 42.61 3.55
2832 3125 1.065928 GCCGCATAGCTACTGTCGT 59.934 57.895 0.00 0.00 0.00 4.34
2835 3128 2.852748 CCGCATAGCTACTGTCGTATC 58.147 52.381 0.00 0.00 0.00 2.24
2836 3129 2.496926 CGCATAGCTACTGTCGTATCG 58.503 52.381 0.00 0.00 0.00 2.92
2851 3144 0.394938 TATCGCCGCCACATTACCAT 59.605 50.000 0.00 0.00 0.00 3.55
2853 3146 2.833533 CGCCGCCACATTACCATGG 61.834 63.158 11.19 11.19 39.16 3.66
2854 3147 1.453015 GCCGCCACATTACCATGGA 60.453 57.895 21.47 0.00 38.34 3.41
2855 3148 0.823356 GCCGCCACATTACCATGGAT 60.823 55.000 21.47 5.32 38.34 3.41
2871 3164 1.552792 TGGATGATCACGTGCACCTTA 59.447 47.619 11.67 0.00 0.00 2.69
2875 3168 2.167662 TGATCACGTGCACCTTAGAGA 58.832 47.619 11.67 1.49 0.00 3.10
2883 3176 3.254892 GTGCACCTTAGAGACAGCTTAC 58.745 50.000 5.22 0.00 0.00 2.34
2961 3270 8.644374 AATTCCTTTAGTTTTGCTGTATACCA 57.356 30.769 0.00 0.00 0.00 3.25
2991 3300 4.838152 CGGAGCACCATCCACGGG 62.838 72.222 0.00 0.00 39.53 5.28
3100 3409 0.318762 ACTGGAGTGTTCTTCGGAGC 59.681 55.000 0.00 0.00 30.38 4.70
3143 3455 9.426837 GTATTATTGTTGCCGGTTACTATATGA 57.573 33.333 1.90 0.00 0.00 2.15
3193 3540 3.545481 CATCGGTCGCTGTCACGC 61.545 66.667 0.00 0.00 0.00 5.34
3204 3551 0.111704 CTGTCACGCGAAGTCAAACG 60.112 55.000 15.93 0.00 0.00 3.60
3214 3561 2.427506 GAAGTCAAACGGCTTGGAGAT 58.572 47.619 0.33 0.00 35.56 2.75
3216 3563 1.347707 AGTCAAACGGCTTGGAGATCA 59.652 47.619 0.00 0.00 35.56 2.92
3245 3624 2.491693 CAATGTTGCTAAACCGGTCCAT 59.508 45.455 8.04 0.00 35.25 3.41
3349 3734 2.167398 TAGCGGCTGTGACCACCTTC 62.167 60.000 13.86 0.00 0.00 3.46
3350 3735 2.738521 CGGCTGTGACCACCTTCG 60.739 66.667 0.00 0.00 0.00 3.79
3351 3736 3.050275 GGCTGTGACCACCTTCGC 61.050 66.667 0.00 0.00 0.00 4.70
3352 3737 2.031163 GCTGTGACCACCTTCGCT 59.969 61.111 0.00 0.00 0.00 4.93
3353 3738 1.598130 GCTGTGACCACCTTCGCTT 60.598 57.895 0.00 0.00 0.00 4.68
3354 3739 1.166531 GCTGTGACCACCTTCGCTTT 61.167 55.000 0.00 0.00 0.00 3.51
3355 3740 0.588252 CTGTGACCACCTTCGCTTTG 59.412 55.000 0.00 0.00 0.00 2.77
3356 3741 1.282875 GTGACCACCTTCGCTTTGC 59.717 57.895 0.00 0.00 0.00 3.68
3373 3758 0.029567 TGCGTGCTTAAACAAACGGG 59.970 50.000 0.00 0.00 36.57 5.28
3503 3913 1.569493 CCGGAGCACGTTGTTTCTG 59.431 57.895 0.00 0.00 42.24 3.02
3532 4277 8.076178 TCTTCTTCTTCTCCTTTTATTTTTGCG 58.924 33.333 0.00 0.00 0.00 4.85
3533 4278 7.504924 TCTTCTTCTCCTTTTATTTTTGCGA 57.495 32.000 0.00 0.00 0.00 5.10
3534 4279 7.584987 TCTTCTTCTCCTTTTATTTTTGCGAG 58.415 34.615 0.00 0.00 0.00 5.03
3535 4280 6.877611 TCTTCTCCTTTTATTTTTGCGAGT 57.122 33.333 0.00 0.00 0.00 4.18
3536 4281 7.972832 TCTTCTCCTTTTATTTTTGCGAGTA 57.027 32.000 0.00 0.00 0.00 2.59
3537 4282 7.803724 TCTTCTCCTTTTATTTTTGCGAGTAC 58.196 34.615 0.00 0.00 0.00 2.73
3538 4283 7.660208 TCTTCTCCTTTTATTTTTGCGAGTACT 59.340 33.333 0.00 0.00 0.00 2.73
3539 4284 7.739498 TCTCCTTTTATTTTTGCGAGTACTT 57.261 32.000 0.00 0.00 0.00 2.24
3540 4285 7.803724 TCTCCTTTTATTTTTGCGAGTACTTC 58.196 34.615 0.00 0.00 0.00 3.01
3541 4286 7.660208 TCTCCTTTTATTTTTGCGAGTACTTCT 59.340 33.333 0.00 0.00 0.00 2.85
3542 4287 8.161699 TCCTTTTATTTTTGCGAGTACTTCTT 57.838 30.769 0.00 0.00 0.00 2.52
3588 4336 6.069847 TCGGGGGACAAGAAAGAAATTAGTAT 60.070 38.462 0.00 0.00 0.00 2.12
3590 4338 7.201705 CGGGGGACAAGAAAGAAATTAGTATTC 60.202 40.741 0.00 0.00 0.00 1.75
3591 4339 7.068348 GGGGGACAAGAAAGAAATTAGTATTCC 59.932 40.741 0.00 0.00 0.00 3.01
3592 4340 7.068348 GGGGACAAGAAAGAAATTAGTATTCCC 59.932 40.741 0.00 0.00 0.00 3.97
3593 4341 7.834681 GGGACAAGAAAGAAATTAGTATTCCCT 59.165 37.037 0.00 0.00 0.00 4.20
3594 4342 9.244292 GGACAAGAAAGAAATTAGTATTCCCTT 57.756 33.333 0.00 0.00 0.00 3.95
3739 4489 0.505231 GTGCATTGACGACGACGAAA 59.495 50.000 15.32 8.35 42.66 3.46
3744 4494 3.663233 GCATTGACGACGACGAAAAATGA 60.663 43.478 24.46 5.26 42.66 2.57
3746 4496 2.461903 TGACGACGACGAAAAATGACA 58.538 42.857 15.32 0.00 42.66 3.58
3750 4500 3.152983 CGACGACGAAAAATGACAATGG 58.847 45.455 0.00 0.00 42.66 3.16
3752 4502 4.143284 CGACGACGAAAAATGACAATGGTA 60.143 41.667 0.00 0.00 42.66 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 0.317519 GGTTATTTATGCACGCGGGC 60.318 55.000 29.97 29.97 0.00 6.13
5 6 1.002900 CTGGTTATTTATGCACGCGGG 60.003 52.381 12.47 7.92 0.00 6.13
6 7 1.668751 ACTGGTTATTTATGCACGCGG 59.331 47.619 12.47 0.00 0.00 6.46
7 8 3.398954 AACTGGTTATTTATGCACGCG 57.601 42.857 3.53 3.53 0.00 6.01
8 9 4.728534 TGAAACTGGTTATTTATGCACGC 58.271 39.130 0.00 0.00 0.00 5.34
9 10 5.938322 ACTGAAACTGGTTATTTATGCACG 58.062 37.500 0.00 0.00 0.00 5.34
10 11 6.322491 GGACTGAAACTGGTTATTTATGCAC 58.678 40.000 0.00 0.00 0.00 4.57
11 12 5.417580 GGGACTGAAACTGGTTATTTATGCA 59.582 40.000 0.00 0.00 0.00 3.96
12 13 5.417580 TGGGACTGAAACTGGTTATTTATGC 59.582 40.000 0.00 0.00 0.00 3.14
13 14 6.404734 GCTGGGACTGAAACTGGTTATTTATG 60.405 42.308 0.00 0.00 0.00 1.90
14 15 5.652452 GCTGGGACTGAAACTGGTTATTTAT 59.348 40.000 0.00 0.00 0.00 1.40
15 16 5.007682 GCTGGGACTGAAACTGGTTATTTA 58.992 41.667 0.00 0.00 0.00 1.40
16 17 3.826729 GCTGGGACTGAAACTGGTTATTT 59.173 43.478 0.00 0.00 0.00 1.40
17 18 3.074538 AGCTGGGACTGAAACTGGTTATT 59.925 43.478 0.00 0.00 0.00 1.40
18 19 2.644798 AGCTGGGACTGAAACTGGTTAT 59.355 45.455 0.00 0.00 0.00 1.89
19 20 2.054799 AGCTGGGACTGAAACTGGTTA 58.945 47.619 0.00 0.00 0.00 2.85
20 21 0.846693 AGCTGGGACTGAAACTGGTT 59.153 50.000 0.00 0.00 0.00 3.67
21 22 0.109342 CAGCTGGGACTGAAACTGGT 59.891 55.000 5.57 0.00 40.25 4.00
22 23 0.607489 CCAGCTGGGACTGAAACTGG 60.607 60.000 26.14 0.00 40.25 4.00
23 24 1.239968 GCCAGCTGGGACTGAAACTG 61.240 60.000 33.46 4.31 40.25 3.16
24 25 1.073897 GCCAGCTGGGACTGAAACT 59.926 57.895 33.46 0.00 40.25 2.66
25 26 1.973812 GGCCAGCTGGGACTGAAAC 60.974 63.158 33.46 14.17 43.78 2.78
26 27 2.436109 GGCCAGCTGGGACTGAAA 59.564 61.111 33.46 0.00 43.78 2.69
38 39 3.429141 CAGCTGACGCTTGGCCAG 61.429 66.667 8.42 1.08 46.47 4.85
44 45 1.151668 CTGTTAAGCAGCTGACGCTT 58.848 50.000 20.43 16.37 46.47 4.68
56 57 2.821969 AGTGCAATCCTTGGCTGTTAAG 59.178 45.455 0.00 0.00 0.00 1.85
57 58 2.875296 AGTGCAATCCTTGGCTGTTAA 58.125 42.857 0.00 0.00 0.00 2.01
58 59 2.584835 AGTGCAATCCTTGGCTGTTA 57.415 45.000 0.00 0.00 0.00 2.41
59 60 2.162681 GTAGTGCAATCCTTGGCTGTT 58.837 47.619 0.00 0.00 0.00 3.16
60 61 1.073763 TGTAGTGCAATCCTTGGCTGT 59.926 47.619 0.00 0.00 0.00 4.40
61 62 1.470098 GTGTAGTGCAATCCTTGGCTG 59.530 52.381 0.00 0.00 0.00 4.85
62 63 1.073763 TGTGTAGTGCAATCCTTGGCT 59.926 47.619 0.00 0.00 0.00 4.75
63 64 1.200020 GTGTGTAGTGCAATCCTTGGC 59.800 52.381 0.00 0.00 0.00 4.52
64 65 1.464608 CGTGTGTAGTGCAATCCTTGG 59.535 52.381 0.00 0.00 0.00 3.61
65 66 1.135972 GCGTGTGTAGTGCAATCCTTG 60.136 52.381 0.00 0.00 0.00 3.61
66 67 1.156736 GCGTGTGTAGTGCAATCCTT 58.843 50.000 0.00 0.00 0.00 3.36
67 68 0.034756 TGCGTGTGTAGTGCAATCCT 59.965 50.000 0.00 0.00 35.33 3.24
68 69 0.165944 GTGCGTGTGTAGTGCAATCC 59.834 55.000 0.00 0.00 40.83 3.01
69 70 1.148310 AGTGCGTGTGTAGTGCAATC 58.852 50.000 0.00 0.00 40.83 2.67
70 71 2.448926 TAGTGCGTGTGTAGTGCAAT 57.551 45.000 0.00 0.00 40.83 3.56
71 72 2.226602 TTAGTGCGTGTGTAGTGCAA 57.773 45.000 0.00 0.00 40.83 4.08
72 73 2.448926 ATTAGTGCGTGTGTAGTGCA 57.551 45.000 0.00 0.00 36.02 4.57
73 74 4.914312 TTTATTAGTGCGTGTGTAGTGC 57.086 40.909 0.00 0.00 0.00 4.40
74 75 8.181487 AGTATTTTATTAGTGCGTGTGTAGTG 57.819 34.615 0.00 0.00 0.00 2.74
75 76 8.248945 AGAGTATTTTATTAGTGCGTGTGTAGT 58.751 33.333 0.00 0.00 0.00 2.73
76 77 8.630278 AGAGTATTTTATTAGTGCGTGTGTAG 57.370 34.615 0.00 0.00 0.00 2.74
77 78 8.245491 TGAGAGTATTTTATTAGTGCGTGTGTA 58.755 33.333 0.00 0.00 0.00 2.90
78 79 7.063074 GTGAGAGTATTTTATTAGTGCGTGTGT 59.937 37.037 0.00 0.00 0.00 3.72
79 80 7.062956 TGTGAGAGTATTTTATTAGTGCGTGTG 59.937 37.037 0.00 0.00 0.00 3.82
102 103 1.681264 GGTTCAGGAAAAGGTGGTGTG 59.319 52.381 0.00 0.00 0.00 3.82
103 104 1.286553 TGGTTCAGGAAAAGGTGGTGT 59.713 47.619 0.00 0.00 0.00 4.16
138 139 2.779755 AACGGATGTGGCTTATGTGA 57.220 45.000 0.00 0.00 0.00 3.58
141 142 5.120830 GCTCTAATAACGGATGTGGCTTATG 59.879 44.000 0.00 0.00 0.00 1.90
147 148 3.997021 GGATGCTCTAATAACGGATGTGG 59.003 47.826 0.00 0.00 0.00 4.17
150 151 3.997021 GGTGGATGCTCTAATAACGGATG 59.003 47.826 0.00 0.00 0.00 3.51
151 152 3.008049 GGGTGGATGCTCTAATAACGGAT 59.992 47.826 0.00 0.00 0.00 4.18
152 153 2.367567 GGGTGGATGCTCTAATAACGGA 59.632 50.000 0.00 0.00 0.00 4.69
178 179 1.446907 CCAATCAGGATATGCCTCGC 58.553 55.000 0.00 0.00 46.97 5.03
221 222 6.704289 ATCTATACGTGCTTGGTGTAGTAA 57.296 37.500 0.00 0.00 32.76 2.24
224 225 5.048643 AGCTATCTATACGTGCTTGGTGTAG 60.049 44.000 0.00 0.00 32.35 2.74
246 248 7.181364 TTTTCAAGAAAATGGCTTCCTCAAGC 61.181 38.462 3.98 0.00 43.07 4.01
247 249 5.458041 TTCAAGAAAATGGCTTCCTCAAG 57.542 39.130 0.00 0.00 0.00 3.02
248 250 5.867903 TTTCAAGAAAATGGCTTCCTCAA 57.132 34.783 0.00 0.00 0.00 3.02
249 251 5.867903 TTTTCAAGAAAATGGCTTCCTCA 57.132 34.783 3.98 0.00 35.57 3.86
250 252 6.707608 ACATTTTTCAAGAAAATGGCTTCCTC 59.292 34.615 21.38 0.00 46.44 3.71
252 254 6.866010 ACATTTTTCAAGAAAATGGCTTCC 57.134 33.333 21.38 0.00 46.44 3.46
253 255 8.490355 CAGTACATTTTTCAAGAAAATGGCTTC 58.510 33.333 21.38 12.05 46.44 3.86
255 257 7.500141 ACAGTACATTTTTCAAGAAAATGGCT 58.500 30.769 21.38 16.90 46.44 4.75
256 258 7.653311 AGACAGTACATTTTTCAAGAAAATGGC 59.347 33.333 21.38 15.55 46.44 4.40
257 259 9.185192 GAGACAGTACATTTTTCAAGAAAATGG 57.815 33.333 21.38 11.94 46.44 3.16
320 369 4.547905 GCCGATCGTCCGAAGCGA 62.548 66.667 15.09 0.00 42.75 4.93
329 378 2.125512 GACAAGCCAGCCGATCGT 60.126 61.111 15.09 0.00 0.00 3.73
354 403 3.610669 CCGCCCTGGATCTCGAGG 61.611 72.222 13.56 1.51 42.00 4.63
413 462 6.079424 ACGGTGCAGTACATTTACATTTTT 57.921 33.333 0.00 0.00 0.00 1.94
417 466 5.080969 ACTACGGTGCAGTACATTTACAT 57.919 39.130 0.00 0.00 0.00 2.29
418 467 4.524316 ACTACGGTGCAGTACATTTACA 57.476 40.909 0.00 0.00 0.00 2.41
419 468 7.276218 TGAAATACTACGGTGCAGTACATTTAC 59.724 37.037 0.00 0.00 31.53 2.01
420 469 7.321908 TGAAATACTACGGTGCAGTACATTTA 58.678 34.615 0.00 0.00 31.53 1.40
424 473 4.787260 TGAAATACTACGGTGCAGTACA 57.213 40.909 0.00 0.00 31.53 2.90
431 480 4.939052 AGGGAGATGAAATACTACGGTG 57.061 45.455 0.00 0.00 0.00 4.94
434 483 5.913514 CACGTTAGGGAGATGAAATACTACG 59.086 44.000 0.00 0.00 0.00 3.51
447 496 2.361119 TGAATCGGATCACGTTAGGGAG 59.639 50.000 0.00 0.00 44.69 4.30
451 500 4.611943 ACAGATGAATCGGATCACGTTAG 58.388 43.478 0.00 0.00 44.69 2.34
461 510 3.133003 ACCAGTAAGGACAGATGAATCGG 59.867 47.826 0.00 0.00 41.22 4.18
463 512 5.091261 ACACCAGTAAGGACAGATGAATC 57.909 43.478 0.00 0.00 41.22 2.52
465 514 3.901222 TGACACCAGTAAGGACAGATGAA 59.099 43.478 0.00 0.00 41.22 2.57
467 516 3.854666 CTGACACCAGTAAGGACAGATG 58.145 50.000 0.00 0.00 41.22 2.90
481 532 3.495001 GCTGTTGTCTCTTTACTGACACC 59.505 47.826 0.00 0.00 42.06 4.16
493 544 1.846648 CGACGTGTGCTGTTGTCTC 59.153 57.895 0.00 0.00 0.00 3.36
499 550 3.640000 GCTTGCGACGTGTGCTGT 61.640 61.111 10.37 0.00 0.00 4.40
552 607 4.567159 CCGATTTACCTTCTGAACTGTAGC 59.433 45.833 0.00 0.00 0.00 3.58
553 608 5.721232 ACCGATTTACCTTCTGAACTGTAG 58.279 41.667 0.00 0.00 0.00 2.74
554 609 5.620654 CGACCGATTTACCTTCTGAACTGTA 60.621 44.000 0.00 0.00 0.00 2.74
555 610 4.566987 GACCGATTTACCTTCTGAACTGT 58.433 43.478 0.00 0.00 0.00 3.55
574 630 1.591863 GCCTCTGCCGTAATCGACC 60.592 63.158 0.00 0.00 39.71 4.79
580 636 2.349755 GGGTTGCCTCTGCCGTAA 59.650 61.111 0.00 0.00 36.33 3.18
597 653 2.847327 TCTCTTCTGTTTGGAGCAGG 57.153 50.000 0.00 0.00 34.89 4.85
598 654 3.688673 GGAATCTCTTCTGTTTGGAGCAG 59.311 47.826 0.00 0.00 35.43 4.24
599 655 3.072915 TGGAATCTCTTCTGTTTGGAGCA 59.927 43.478 0.00 0.00 0.00 4.26
600 656 3.679389 TGGAATCTCTTCTGTTTGGAGC 58.321 45.455 0.00 0.00 0.00 4.70
608 664 2.775911 TGGCACTGGAATCTCTTCTG 57.224 50.000 0.00 0.00 0.00 3.02
624 684 1.135960 AGGCTCCCTCTAATCTTGGC 58.864 55.000 0.00 0.00 0.00 4.52
637 697 2.458620 AGGAGTACAAGTGTAGGCTCC 58.541 52.381 15.49 15.49 40.94 4.70
640 700 3.764972 AGAGAAGGAGTACAAGTGTAGGC 59.235 47.826 0.00 0.00 0.00 3.93
649 709 5.186942 CAGTAGTAGCAGAGAAGGAGTACA 58.813 45.833 0.00 0.00 0.00 2.90
650 710 5.187687 ACAGTAGTAGCAGAGAAGGAGTAC 58.812 45.833 0.00 0.00 0.00 2.73
651 711 5.438698 ACAGTAGTAGCAGAGAAGGAGTA 57.561 43.478 0.00 0.00 0.00 2.59
652 712 4.310022 ACAGTAGTAGCAGAGAAGGAGT 57.690 45.455 0.00 0.00 0.00 3.85
653 713 4.702612 TCAACAGTAGTAGCAGAGAAGGAG 59.297 45.833 0.00 0.00 0.00 3.69
654 714 4.663334 TCAACAGTAGTAGCAGAGAAGGA 58.337 43.478 0.00 0.00 0.00 3.36
655 715 5.164954 GTTCAACAGTAGTAGCAGAGAAGG 58.835 45.833 0.00 0.00 0.00 3.46
656 716 5.164954 GGTTCAACAGTAGTAGCAGAGAAG 58.835 45.833 0.00 0.00 0.00 2.85
657 717 4.321008 CGGTTCAACAGTAGTAGCAGAGAA 60.321 45.833 0.00 0.00 0.00 2.87
658 718 3.190744 CGGTTCAACAGTAGTAGCAGAGA 59.809 47.826 0.00 0.00 0.00 3.10
659 719 3.502920 CGGTTCAACAGTAGTAGCAGAG 58.497 50.000 0.00 0.00 0.00 3.35
660 720 2.352421 GCGGTTCAACAGTAGTAGCAGA 60.352 50.000 0.00 0.00 0.00 4.26
661 721 1.993370 GCGGTTCAACAGTAGTAGCAG 59.007 52.381 0.00 0.00 0.00 4.24
662 722 1.667756 CGCGGTTCAACAGTAGTAGCA 60.668 52.381 0.00 0.00 0.00 3.49
663 723 0.989890 CGCGGTTCAACAGTAGTAGC 59.010 55.000 0.00 0.00 0.00 3.58
664 724 1.625616 CCGCGGTTCAACAGTAGTAG 58.374 55.000 19.50 0.00 0.00 2.57
665 725 0.388907 GCCGCGGTTCAACAGTAGTA 60.389 55.000 28.70 0.00 0.00 1.82
666 726 1.666872 GCCGCGGTTCAACAGTAGT 60.667 57.895 28.70 0.00 0.00 2.73
667 727 2.388232 GGCCGCGGTTCAACAGTAG 61.388 63.158 28.70 0.00 0.00 2.57
668 728 2.357760 GGCCGCGGTTCAACAGTA 60.358 61.111 28.70 0.00 0.00 2.74
686 746 3.200593 CTCATGGCGCAGACCAGC 61.201 66.667 10.83 0.00 44.71 4.85
687 747 2.513204 CCTCATGGCGCAGACCAG 60.513 66.667 10.83 0.00 44.71 4.00
696 782 3.508840 CCGCGGTTTCCTCATGGC 61.509 66.667 19.50 0.00 0.00 4.40
697 783 1.153168 ATCCGCGGTTTCCTCATGG 60.153 57.895 27.15 0.00 0.00 3.66
700 786 2.267642 CCATCCGCGGTTTCCTCA 59.732 61.111 27.15 3.40 0.00 3.86
740 959 2.599757 GGAGTTAAGTGGGGGCGGT 61.600 63.158 0.00 0.00 0.00 5.68
743 962 1.376812 CACGGAGTTAAGTGGGGGC 60.377 63.158 0.00 0.00 41.61 5.80
745 964 2.933928 GCTAACACGGAGTTAAGTGGGG 60.934 54.545 4.62 0.00 41.61 4.96
749 969 2.094854 CGGAGCTAACACGGAGTTAAGT 60.095 50.000 0.00 0.00 41.61 2.24
750 970 2.527100 CGGAGCTAACACGGAGTTAAG 58.473 52.381 0.00 1.62 41.61 1.85
751 971 2.642139 CGGAGCTAACACGGAGTTAA 57.358 50.000 0.00 0.00 41.61 2.01
912 1150 2.799412 GAGTGTTGTCAAGACTGAGCTG 59.201 50.000 19.30 0.00 34.82 4.24
926 1164 1.728971 GGAAGCTGTGATCGAGTGTTG 59.271 52.381 0.00 0.00 0.00 3.33
944 1186 0.469144 GGCTGGGTTTGAAACTGGGA 60.469 55.000 8.09 0.00 0.00 4.37
983 1248 1.078759 CATCTCGTCAGCCGGTCAAC 61.079 60.000 1.90 0.00 37.11 3.18
1089 1354 4.262617 GGTTTTTCTCATACTCCTCCCAC 58.737 47.826 0.00 0.00 0.00 4.61
1107 1372 2.164967 GGTGGGGTGGTAGGGGTTT 61.165 63.158 0.00 0.00 0.00 3.27
1182 1447 1.065926 CAGACATGCTAGAACCCTGCA 60.066 52.381 0.00 0.00 41.13 4.41
1223 1499 1.235281 TGTCAGAGACGGACGGACAG 61.235 60.000 0.00 0.00 38.10 3.51
1228 1504 2.672714 TGAATTTGTCAGAGACGGACG 58.327 47.619 0.00 0.00 38.10 4.79
1517 1795 1.203287 TCTCTGCTCTGACATGAACCG 59.797 52.381 0.00 0.00 0.00 4.44
1686 1964 1.202582 ACGTGGAGAGAAATGTCGAGG 59.797 52.381 0.00 0.00 0.00 4.63
1775 2065 3.127030 GCAAGGTTAGCCATGTGTACTTC 59.873 47.826 2.71 0.00 35.98 3.01
1943 2236 0.745845 GTGATGAGCACGCCCTTGAT 60.746 55.000 0.00 0.00 37.83 2.57
2317 2610 2.038975 TCCTTGTCCCCGAGGAGG 59.961 66.667 0.00 0.00 44.94 4.30
2652 2945 1.374758 CTGCTGGTCTGGACGAACC 60.375 63.158 0.00 0.00 39.54 3.62
2804 3097 2.125147 TATGCGGCTGTGGTCTGC 60.125 61.111 0.00 0.00 37.71 4.26
2814 3107 0.309922 TACGACAGTAGCTATGCGGC 59.690 55.000 0.00 0.00 0.00 6.53
2829 3122 0.595567 GTAATGTGGCGGCGATACGA 60.596 55.000 12.98 0.00 35.47 3.43
2832 3125 0.394938 ATGGTAATGTGGCGGCGATA 59.605 50.000 12.98 0.00 0.00 2.92
2835 3128 2.715005 CATGGTAATGTGGCGGCG 59.285 61.111 0.51 0.51 0.00 6.46
2836 3129 0.823356 ATCCATGGTAATGTGGCGGC 60.823 55.000 12.58 0.00 35.43 6.53
2851 3144 0.324614 AAGGTGCACGTGATCATCCA 59.675 50.000 22.23 3.06 0.00 3.41
2853 3146 3.119291 CTCTAAGGTGCACGTGATCATC 58.881 50.000 22.23 9.18 0.00 2.92
2854 3147 2.760650 TCTCTAAGGTGCACGTGATCAT 59.239 45.455 22.23 5.69 0.00 2.45
2855 3148 2.094700 GTCTCTAAGGTGCACGTGATCA 60.095 50.000 22.23 5.63 0.00 2.92
2871 3164 0.176680 CATGGCCGTAAGCTGTCTCT 59.823 55.000 0.00 0.00 43.05 3.10
2875 3168 2.438434 GCCATGGCCGTAAGCTGT 60.438 61.111 27.24 0.00 43.05 4.40
2925 3221 7.563888 AAACTAAAGGAATTAATCGGCTACC 57.436 36.000 0.00 0.00 0.00 3.18
2995 3304 2.447443 AGATACAACAGTGCTCCTCGA 58.553 47.619 0.00 0.00 0.00 4.04
3100 3409 0.250124 TACAGCGAACAACTGGGGTG 60.250 55.000 0.00 0.00 39.55 4.61
3193 3540 0.512952 CTCCAAGCCGTTTGACTTCG 59.487 55.000 0.00 0.00 39.21 3.79
3204 3551 1.078143 AACCGCTGATCTCCAAGCC 60.078 57.895 0.00 0.00 0.00 4.35
3214 3561 0.537143 AGCAACATTGGAACCGCTGA 60.537 50.000 0.00 0.00 0.00 4.26
3216 3563 1.904287 TTAGCAACATTGGAACCGCT 58.096 45.000 0.00 0.00 0.00 5.52
3245 3624 1.905637 TATTAGCCCGAGATCGAGCA 58.094 50.000 11.33 0.00 45.77 4.26
3350 3735 2.346285 CGTTTGTTTAAGCACGCAAAGC 60.346 45.455 0.00 0.00 32.44 3.51
3351 3736 2.215363 CCGTTTGTTTAAGCACGCAAAG 59.785 45.455 0.00 0.00 32.44 2.77
3352 3737 2.186076 CCGTTTGTTTAAGCACGCAAA 58.814 42.857 0.00 0.00 0.00 3.68
3353 3738 1.534175 CCCGTTTGTTTAAGCACGCAA 60.534 47.619 0.00 0.00 0.00 4.85
3354 3739 0.029567 CCCGTTTGTTTAAGCACGCA 59.970 50.000 0.00 0.00 0.00 5.24
3355 3740 0.662077 CCCCGTTTGTTTAAGCACGC 60.662 55.000 0.00 0.00 0.00 5.34
3356 3741 0.662077 GCCCCGTTTGTTTAAGCACG 60.662 55.000 0.00 0.00 0.00 5.34
3357 3742 0.662077 CGCCCCGTTTGTTTAAGCAC 60.662 55.000 0.00 0.00 0.00 4.40
3373 3758 2.686816 CCGAATGTCCACCAACGCC 61.687 63.158 0.00 0.00 0.00 5.68
3503 3913 9.973450 AAAAATAAAAGGAGAAGAAGAAGAAGC 57.027 29.630 0.00 0.00 0.00 3.86
3564 4312 4.332828 ACTAATTTCTTTCTTGTCCCCCG 58.667 43.478 0.00 0.00 0.00 5.73
3651 4399 5.324409 TCACTACTACTCCCTCCGTAAAAA 58.676 41.667 0.00 0.00 0.00 1.94
3652 4400 4.922206 TCACTACTACTCCCTCCGTAAAA 58.078 43.478 0.00 0.00 0.00 1.52
3653 4401 4.574674 TCACTACTACTCCCTCCGTAAA 57.425 45.455 0.00 0.00 0.00 2.01
3654 4402 4.574674 TTCACTACTACTCCCTCCGTAA 57.425 45.455 0.00 0.00 0.00 3.18
3655 4403 4.785346 ATTCACTACTACTCCCTCCGTA 57.215 45.455 0.00 0.00 0.00 4.02
3656 4404 3.666345 ATTCACTACTACTCCCTCCGT 57.334 47.619 0.00 0.00 0.00 4.69
3657 4405 4.401519 TGAAATTCACTACTACTCCCTCCG 59.598 45.833 0.00 0.00 0.00 4.63
3658 4406 5.662456 GTGAAATTCACTACTACTCCCTCC 58.338 45.833 18.03 0.00 43.73 4.30
3690 4438 6.272320 CCCCCTATCCCTGATATTCTTCTAA 58.728 44.000 0.00 0.00 0.00 2.10
3692 4440 4.704403 CCCCCTATCCCTGATATTCTTCT 58.296 47.826 0.00 0.00 0.00 2.85
3739 4489 3.852578 ACCTCCTCCTACCATTGTCATTT 59.147 43.478 0.00 0.00 0.00 2.32
3744 4494 1.584724 CCACCTCCTCCTACCATTGT 58.415 55.000 0.00 0.00 0.00 2.71
3746 4496 0.253160 TGCCACCTCCTCCTACCATT 60.253 55.000 0.00 0.00 0.00 3.16
3750 4500 1.147153 GCATGCCACCTCCTCCTAC 59.853 63.158 6.36 0.00 0.00 3.18
3752 4502 3.790437 CGCATGCCACCTCCTCCT 61.790 66.667 13.15 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.