Multiple sequence alignment - TraesCS4A01G297900

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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 TraesCS4A01G297900 chr4A 100.000 2441 0 0 1 2441 596829380 596826940 0.000000e+00 4508.0
1 TraesCS4A01G297900 chr4D 91.094 932 53 15 827 1737 6573154 6574076 0.000000e+00 1234.0
2 TraesCS4A01G297900 chr4D 89.983 599 46 7 1846 2441 6574073 6574660 0.000000e+00 761.0
3 TraesCS4A01G297900 chr4D 96.610 118 4 0 1735 1852 5086814 5086931 1.910000e-46 196.0
4 TraesCS4A01G297900 chr4B 85.812 881 53 33 802 1658 11734773 11735605 0.000000e+00 869.0
5 TraesCS4A01G297900 chr4B 87.833 600 52 12 1850 2441 11735711 11736297 0.000000e+00 684.0
6 TraesCS4A01G297900 chr4B 73.477 558 100 30 34 562 40777988 40777450 1.500000e-37 167.0
7 TraesCS4A01G297900 chr4B 80.085 236 37 8 34 265 426777056 426776827 1.500000e-37 167.0
8 TraesCS4A01G297900 chr2D 78.732 710 110 27 34 717 631169227 631168533 1.040000e-118 436.0
9 TraesCS4A01G297900 chr2D 78.997 638 106 18 34 653 650236572 650235945 6.280000e-111 411.0
10 TraesCS4A01G297900 chr2D 78.816 642 101 19 34 653 621451207 621451835 1.360000e-107 399.0
11 TraesCS4A01G297900 chr2D 80.253 395 66 7 232 615 592397740 592397347 1.100000e-73 287.0
12 TraesCS4A01G297900 chr2D 81.481 297 54 1 232 527 605383646 605383942 2.420000e-60 243.0
13 TraesCS4A01G297900 chr2D 95.833 120 5 0 1736 1855 38627606 38627487 6.890000e-46 195.0
14 TraesCS4A01G297900 chr2D 75.000 200 39 6 464 653 563152339 563152537 5.590000e-12 82.4
15 TraesCS4A01G297900 chr2D 95.000 40 2 0 1 40 629422679 629422640 2.030000e-06 63.9
16 TraesCS4A01G297900 chr1A 79.006 624 105 15 34 639 163377435 163376820 1.050000e-108 403.0
17 TraesCS4A01G297900 chr5D 76.369 694 140 17 38 714 501071612 501070926 3.860000e-93 351.0
18 TraesCS4A01G297900 chr5D 82.857 140 13 8 450 580 560149340 560149203 5.520000e-22 115.0
19 TraesCS4A01G297900 chr3A 77.138 643 123 19 34 664 635539285 635539915 3.860000e-93 351.0
20 TraesCS4A01G297900 chr3A 93.939 132 6 2 1728 1859 455782949 455782820 5.320000e-47 198.0
21 TraesCS4A01G297900 chr3A 74.035 570 102 34 34 592 729483482 729484016 8.910000e-45 191.0
22 TraesCS4A01G297900 chr1D 76.444 658 115 25 34 655 235581496 235582149 1.090000e-83 320.0
23 TraesCS4A01G297900 chr1D 93.130 131 6 3 1723 1852 408872391 408872519 3.200000e-44 189.0
24 TraesCS4A01G297900 chr5B 78.656 506 86 16 34 527 390542189 390542684 1.410000e-82 316.0
25 TraesCS4A01G297900 chr2B 81.351 370 58 6 230 588 718217533 718217164 8.540000e-75 291.0
26 TraesCS4A01G297900 chr2B 95.833 120 5 0 1734 1853 209075693 209075812 6.890000e-46 195.0
27 TraesCS4A01G297900 chr3B 77.256 554 78 15 34 578 416267152 416267666 5.140000e-72 281.0
28 TraesCS4A01G297900 chr3B 75.777 611 103 29 5 578 160686158 160685556 1.440000e-67 267.0
29 TraesCS4A01G297900 chr3B 75.822 426 64 16 1 388 545065844 545065420 1.930000e-41 180.0
30 TraesCS4A01G297900 chr3B 73.284 539 106 24 34 562 807153474 807152964 1.940000e-36 163.0
31 TraesCS4A01G297900 chr5A 75.331 604 118 21 1 578 394263741 394263143 6.690000e-66 261.0
32 TraesCS4A01G297900 chr5A 74.727 550 107 20 40 578 333403481 333404009 1.470000e-52 217.0
33 TraesCS4A01G297900 chr2A 76.168 428 90 6 299 717 529935586 529935162 5.290000e-52 215.0
34 TraesCS4A01G297900 chr6D 96.000 125 4 1 1736 1860 366701222 366701099 4.120000e-48 202.0
35 TraesCS4A01G297900 chr6D 93.382 136 6 3 1719 1853 147675702 147675569 5.320000e-47 198.0
36 TraesCS4A01G297900 chr6D 73.429 557 94 31 1 518 45617605 45618146 2.510000e-35 159.0
37 TraesCS4A01G297900 chr7B 77.067 375 67 13 230 590 502692577 502692208 5.320000e-47 198.0
38 TraesCS4A01G297900 chr6B 95.868 121 5 0 1733 1853 260542969 260542849 1.910000e-46 196.0
39 TraesCS4A01G297900 chr7D 94.444 126 6 1 1736 1861 199358587 199358711 2.480000e-45 193.0
40 TraesCS4A01G297900 chr3D 76.689 296 50 11 1 283 290817421 290817132 1.960000e-31 147.0
41 TraesCS4A01G297900 chr7A 84.247 146 22 1 67 211 434733502 434733357 9.100000e-30 141.0


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 TraesCS4A01G297900 chr4A 596826940 596829380 2440 True 4508.0 4508 100.0000 1 2441 1 chr4A.!!$R1 2440
1 TraesCS4A01G297900 chr4D 6573154 6574660 1506 False 997.5 1234 90.5385 827 2441 2 chr4D.!!$F2 1614
2 TraesCS4A01G297900 chr4B 11734773 11736297 1524 False 776.5 869 86.8225 802 2441 2 chr4B.!!$F1 1639
3 TraesCS4A01G297900 chr2D 631168533 631169227 694 True 436.0 436 78.7320 34 717 1 chr2D.!!$R4 683
4 TraesCS4A01G297900 chr2D 650235945 650236572 627 True 411.0 411 78.9970 34 653 1 chr2D.!!$R5 619
5 TraesCS4A01G297900 chr2D 621451207 621451835 628 False 399.0 399 78.8160 34 653 1 chr2D.!!$F3 619
6 TraesCS4A01G297900 chr1A 163376820 163377435 615 True 403.0 403 79.0060 34 639 1 chr1A.!!$R1 605
7 TraesCS4A01G297900 chr5D 501070926 501071612 686 True 351.0 351 76.3690 38 714 1 chr5D.!!$R1 676
8 TraesCS4A01G297900 chr3A 635539285 635539915 630 False 351.0 351 77.1380 34 664 1 chr3A.!!$F1 630
9 TraesCS4A01G297900 chr1D 235581496 235582149 653 False 320.0 320 76.4440 34 655 1 chr1D.!!$F1 621
10 TraesCS4A01G297900 chr3B 416267152 416267666 514 False 281.0 281 77.2560 34 578 1 chr3B.!!$F1 544
11 TraesCS4A01G297900 chr3B 160685556 160686158 602 True 267.0 267 75.7770 5 578 1 chr3B.!!$R1 573
12 TraesCS4A01G297900 chr5A 394263143 394263741 598 True 261.0 261 75.3310 1 578 1 chr5A.!!$R1 577
13 TraesCS4A01G297900 chr5A 333403481 333404009 528 False 217.0 217 74.7270 40 578 1 chr5A.!!$F1 538

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
740 821 0.169451 GTATTTTTGTGACCGGGCCG 59.831 55.0 21.46 21.46 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1738 1889 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.0 13.64 4.95 46.06 4.2 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
62 63 1.602311 GCTTCCACATAGGCCTCATG 58.398 55.000 9.68 14.27 37.29 3.07
63 64 1.141657 GCTTCCACATAGGCCTCATGA 59.858 52.381 9.68 0.00 37.29 3.07
140 141 1.137086 GAACTCTGCCTTCGCATCCTA 59.863 52.381 0.00 0.00 46.11 2.94
185 207 3.330720 CGCCAGTTCCCCCTCCTT 61.331 66.667 0.00 0.00 0.00 3.36
188 210 1.612442 CCAGTTCCCCCTCCTTCGA 60.612 63.158 0.00 0.00 0.00 3.71
191 213 0.905337 AGTTCCCCCTCCTTCGACTG 60.905 60.000 0.00 0.00 0.00 3.51
192 214 2.291043 TTCCCCCTCCTTCGACTGC 61.291 63.158 0.00 0.00 0.00 4.40
235 275 1.144936 CCATCGAAGCCACCTCCTC 59.855 63.158 0.00 0.00 0.00 3.71
254 297 1.292941 CCTCCTCCTCCTCCTCCTCA 61.293 65.000 0.00 0.00 0.00 3.86
260 306 0.859760 CCTCCTCCTCCTCATCCTCT 59.140 60.000 0.00 0.00 0.00 3.69
296 345 4.884257 GGCAAGTCGGCCGCGATA 62.884 66.667 23.51 0.00 45.40 2.92
380 439 2.644798 AGCATAGGTGGTCTTCCTTTGT 59.355 45.455 0.00 0.00 36.74 2.83
382 441 3.559171 GCATAGGTGGTCTTCCTTTGTCA 60.559 47.826 0.00 0.00 36.74 3.58
438 501 1.003646 AGAGCAGGAGAGAGGTGGTA 58.996 55.000 0.00 0.00 0.00 3.25
448 511 0.639392 AGAGGTGGTAGATGGGCTCT 59.361 55.000 0.00 0.00 38.06 4.09
454 517 1.050988 GGTAGATGGGCTCTGGCTGA 61.051 60.000 0.00 0.00 38.73 4.26
589 666 1.070786 GGAGACGCCTGTTGAACCA 59.929 57.895 0.00 0.00 0.00 3.67
595 672 0.817634 CGCCTGTTGAACCACCAGAA 60.818 55.000 0.00 0.00 0.00 3.02
601 678 2.158740 TGTTGAACCACCAGAATTCCGA 60.159 45.455 0.65 0.00 0.00 4.55
602 679 2.882137 GTTGAACCACCAGAATTCCGAA 59.118 45.455 0.65 0.00 0.00 4.30
608 685 2.747446 CCACCAGAATTCCGAACGATTT 59.253 45.455 0.65 0.00 0.00 2.17
666 747 2.874457 GCGCCCGGACATCCTATATTTT 60.874 50.000 0.73 0.00 0.00 1.82
669 750 3.497942 GCCCGGACATCCTATATTTTGGT 60.498 47.826 0.73 0.00 0.00 3.67
675 756 7.362662 CGGACATCCTATATTTTGGTTGAATG 58.637 38.462 0.00 0.00 0.00 2.67
676 757 7.228507 CGGACATCCTATATTTTGGTTGAATGA 59.771 37.037 0.00 0.00 0.00 2.57
677 758 8.352942 GGACATCCTATATTTTGGTTGAATGAC 58.647 37.037 2.68 0.00 0.00 3.06
683 764 2.940994 TTTGGTTGAATGACGAGGGA 57.059 45.000 0.00 0.00 0.00 4.20
685 766 4.561500 TTTGGTTGAATGACGAGGGATA 57.438 40.909 0.00 0.00 0.00 2.59
717 798 2.742372 CGTTTGAGGCCCGTCTGG 60.742 66.667 0.00 0.00 37.09 3.86
718 799 2.747686 GTTTGAGGCCCGTCTGGA 59.252 61.111 0.00 0.00 37.49 3.86
719 800 1.299976 GTTTGAGGCCCGTCTGGAT 59.700 57.895 0.00 0.00 37.49 3.41
720 801 0.322546 GTTTGAGGCCCGTCTGGATT 60.323 55.000 0.00 0.00 37.49 3.01
721 802 0.322456 TTTGAGGCCCGTCTGGATTG 60.322 55.000 0.00 0.00 37.49 2.67
722 803 1.488705 TTGAGGCCCGTCTGGATTGT 61.489 55.000 0.00 0.00 37.49 2.71
723 804 0.616395 TGAGGCCCGTCTGGATTGTA 60.616 55.000 0.00 0.00 37.49 2.41
724 805 0.759346 GAGGCCCGTCTGGATTGTAT 59.241 55.000 0.00 0.00 37.49 2.29
725 806 1.141053 GAGGCCCGTCTGGATTGTATT 59.859 52.381 0.00 0.00 37.49 1.89
726 807 1.564348 AGGCCCGTCTGGATTGTATTT 59.436 47.619 0.00 0.00 37.49 1.40
727 808 2.025321 AGGCCCGTCTGGATTGTATTTT 60.025 45.455 0.00 0.00 37.49 1.82
728 809 2.758423 GGCCCGTCTGGATTGTATTTTT 59.242 45.455 0.00 0.00 37.49 1.94
729 810 3.428862 GGCCCGTCTGGATTGTATTTTTG 60.429 47.826 0.00 0.00 37.49 2.44
730 811 3.192633 GCCCGTCTGGATTGTATTTTTGT 59.807 43.478 0.00 0.00 37.49 2.83
731 812 4.732784 CCCGTCTGGATTGTATTTTTGTG 58.267 43.478 0.00 0.00 37.49 3.33
732 813 4.457603 CCCGTCTGGATTGTATTTTTGTGA 59.542 41.667 0.00 0.00 37.49 3.58
733 814 5.390613 CCGTCTGGATTGTATTTTTGTGAC 58.609 41.667 0.00 0.00 37.49 3.67
734 815 5.390613 CGTCTGGATTGTATTTTTGTGACC 58.609 41.667 0.00 0.00 0.00 4.02
735 816 5.390613 GTCTGGATTGTATTTTTGTGACCG 58.609 41.667 0.00 0.00 0.00 4.79
736 817 4.457603 TCTGGATTGTATTTTTGTGACCGG 59.542 41.667 0.00 0.00 0.00 5.28
737 818 3.508012 TGGATTGTATTTTTGTGACCGGG 59.492 43.478 6.32 0.00 0.00 5.73
738 819 3.507786 GATTGTATTTTTGTGACCGGGC 58.492 45.455 6.32 1.57 0.00 6.13
739 820 1.249407 TGTATTTTTGTGACCGGGCC 58.751 50.000 3.83 0.00 0.00 5.80
740 821 0.169451 GTATTTTTGTGACCGGGCCG 59.831 55.000 21.46 21.46 0.00 6.13
741 822 0.250814 TATTTTTGTGACCGGGCCGT 60.251 50.000 26.32 13.20 0.00 5.68
742 823 1.520600 ATTTTTGTGACCGGGCCGTC 61.521 55.000 26.32 21.30 0.00 4.79
743 824 4.629523 TTTGTGACCGGGCCGTCC 62.630 66.667 26.32 16.18 31.35 4.79
779 860 2.281276 GCCCGGCGGTATTAAGGG 60.281 66.667 26.32 7.75 44.72 3.95
780 861 2.428622 CCCGGCGGTATTAAGGGG 59.571 66.667 26.32 1.35 38.44 4.79
781 862 2.428622 CCGGCGGTATTAAGGGGG 59.571 66.667 19.97 0.00 0.00 5.40
812 893 1.117150 GGGAGGCAGTTCGGTACATA 58.883 55.000 0.00 0.00 0.00 2.29
817 898 4.035208 GGAGGCAGTTCGGTACATAAAATG 59.965 45.833 0.00 0.00 0.00 2.32
830 911 9.058174 CGGTACATAAAATGTATGTATTTCCCA 57.942 33.333 6.57 0.00 46.39 4.37
861 942 2.557056 TCTAGCGGGTAAGAATGGATCG 59.443 50.000 0.00 0.00 0.00 3.69
868 949 3.388350 GGGTAAGAATGGATCGAGGAAGT 59.612 47.826 0.00 0.00 0.00 3.01
869 950 4.587684 GGGTAAGAATGGATCGAGGAAGTA 59.412 45.833 0.00 0.00 0.00 2.24
880 961 1.300481 GAGGAAGTAAATGAGCGGCC 58.700 55.000 0.00 0.00 0.00 6.13
916 997 0.940126 AAAGCGAGACAACACAGCAG 59.060 50.000 0.00 0.00 0.00 4.24
988 1086 4.368808 CCGCACACAAACGCCGAG 62.369 66.667 0.00 0.00 0.00 4.63
1047 1148 4.124126 ACCCCCATCTCCTCCCCC 62.124 72.222 0.00 0.00 0.00 5.40
1067 1168 2.503061 CCTCCATCTCGGCCACAG 59.497 66.667 2.24 0.00 33.14 3.66
1092 1199 3.842923 ATCCTGCTCGGCCGTCAG 61.843 66.667 29.80 29.80 0.00 3.51
1095 1202 4.827087 CTGCTCGGCCGTCAGCAT 62.827 66.667 33.63 0.00 44.60 3.79
1103 1210 2.434884 CCGTCAGCATCCGCAAGT 60.435 61.111 0.00 0.00 42.27 3.16
1206 1319 1.227089 CGAGAACATCCTGGAGCGG 60.227 63.158 1.52 0.00 0.00 5.52
1454 1572 2.005960 GACTGACCGACCCCTCATCG 62.006 65.000 0.00 0.00 39.33 3.84
1523 1641 1.086634 GTTCATGTGCTCCGAGGCTC 61.087 60.000 3.87 3.87 0.00 4.70
1549 1667 6.887002 TGTACAATGTATTTCACCAGCCATTA 59.113 34.615 0.00 0.00 0.00 1.90
1560 1678 4.580167 TCACCAGCCATTACAATAAGATGC 59.420 41.667 0.00 0.00 0.00 3.91
1561 1679 3.891366 ACCAGCCATTACAATAAGATGCC 59.109 43.478 0.00 0.00 0.00 4.40
1563 1681 4.147321 CAGCCATTACAATAAGATGCCCT 58.853 43.478 0.00 0.00 0.00 5.19
1615 1735 3.096489 TGTTGCCTGAACAATCTTTGC 57.904 42.857 0.00 0.00 41.80 3.68
1616 1736 2.053627 GTTGCCTGAACAATCTTTGCG 58.946 47.619 0.00 0.00 34.35 4.85
1628 1750 1.388547 TCTTTGCGTTCCTGCTTGTT 58.611 45.000 0.00 0.00 35.36 2.83
1648 1770 6.154203 TGTTATGCTTGAAACATTGGTTCA 57.846 33.333 13.07 13.07 35.82 3.18
1718 1869 3.684908 TCGAAAGATTTGATGGGCAAGA 58.315 40.909 0.00 0.00 34.32 3.02
1738 1889 6.128172 GCAAGAAGCACATCATTTGTAGTACT 60.128 38.462 0.00 0.00 44.79 2.73
1739 1890 7.459486 CAAGAAGCACATCATTTGTAGTACTC 58.541 38.462 0.00 0.00 36.57 2.59
1740 1891 6.109359 AGAAGCACATCATTTGTAGTACTCC 58.891 40.000 0.00 0.00 36.57 3.85
1741 1892 4.770795 AGCACATCATTTGTAGTACTCCC 58.229 43.478 0.00 0.00 36.57 4.30
1742 1893 4.471386 AGCACATCATTTGTAGTACTCCCT 59.529 41.667 0.00 0.00 36.57 4.20
1743 1894 4.811557 GCACATCATTTGTAGTACTCCCTC 59.188 45.833 0.00 0.00 36.57 4.30
1744 1895 5.360591 CACATCATTTGTAGTACTCCCTCC 58.639 45.833 0.00 0.00 36.57 4.30
1745 1896 4.099573 ACATCATTTGTAGTACTCCCTCCG 59.900 45.833 0.00 0.00 36.57 4.63
1746 1897 3.705051 TCATTTGTAGTACTCCCTCCGT 58.295 45.455 0.00 0.00 0.00 4.69
1747 1898 3.698040 TCATTTGTAGTACTCCCTCCGTC 59.302 47.826 0.00 0.00 0.00 4.79
1748 1899 2.134789 TTGTAGTACTCCCTCCGTCC 57.865 55.000 0.00 0.00 0.00 4.79
1749 1900 0.107508 TGTAGTACTCCCTCCGTCCG 60.108 60.000 0.00 0.00 0.00 4.79
1750 1901 0.817229 GTAGTACTCCCTCCGTCCGG 60.817 65.000 0.00 0.00 0.00 5.14
1751 1902 0.982852 TAGTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
1752 1903 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
1753 1904 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
1754 1905 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
1755 1906 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
1756 1907 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
1757 1908 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
1758 1909 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
1759 1910 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
1760 1911 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
1761 1912 2.354403 CCTCCGTCCGGAAATACTTGTT 60.354 50.000 5.23 0.00 44.66 2.83
1762 1913 3.119029 CCTCCGTCCGGAAATACTTGTTA 60.119 47.826 5.23 0.00 44.66 2.41
1763 1914 4.110482 CTCCGTCCGGAAATACTTGTTAG 58.890 47.826 5.23 0.00 44.66 2.34
1764 1915 3.763360 TCCGTCCGGAAATACTTGTTAGA 59.237 43.478 5.23 0.00 42.05 2.10
1765 1916 4.110482 CCGTCCGGAAATACTTGTTAGAG 58.890 47.826 5.23 0.00 37.50 2.43
1766 1917 4.142315 CCGTCCGGAAATACTTGTTAGAGA 60.142 45.833 5.23 0.00 37.50 3.10
1767 1918 5.404946 CGTCCGGAAATACTTGTTAGAGAA 58.595 41.667 5.23 0.00 0.00 2.87
1768 1919 5.865552 CGTCCGGAAATACTTGTTAGAGAAA 59.134 40.000 5.23 0.00 0.00 2.52
1769 1920 6.534079 CGTCCGGAAATACTTGTTAGAGAAAT 59.466 38.462 5.23 0.00 0.00 2.17
1770 1921 7.464178 CGTCCGGAAATACTTGTTAGAGAAATG 60.464 40.741 5.23 0.00 0.00 2.32
1771 1922 6.821665 TCCGGAAATACTTGTTAGAGAAATGG 59.178 38.462 0.00 0.00 0.00 3.16
1772 1923 6.821665 CCGGAAATACTTGTTAGAGAAATGGA 59.178 38.462 0.00 0.00 0.00 3.41
1773 1924 7.499232 CCGGAAATACTTGTTAGAGAAATGGAT 59.501 37.037 0.00 0.00 0.00 3.41
1774 1925 8.338259 CGGAAATACTTGTTAGAGAAATGGATG 58.662 37.037 0.00 0.00 0.00 3.51
1775 1926 9.178758 GGAAATACTTGTTAGAGAAATGGATGT 57.821 33.333 0.00 0.00 0.00 3.06
1784 1935 8.568794 TGTTAGAGAAATGGATGTATCTAGACG 58.431 37.037 0.00 0.00 0.00 4.18
1785 1936 6.019779 AGAGAAATGGATGTATCTAGACGC 57.980 41.667 0.00 0.00 0.00 5.19
1786 1937 4.799678 AGAAATGGATGTATCTAGACGCG 58.200 43.478 3.53 3.53 0.00 6.01
1787 1938 4.278669 AGAAATGGATGTATCTAGACGCGT 59.721 41.667 13.85 13.85 0.00 6.01
1788 1939 4.585955 AATGGATGTATCTAGACGCGTT 57.414 40.909 15.53 6.16 0.00 4.84
1789 1940 4.585955 ATGGATGTATCTAGACGCGTTT 57.414 40.909 15.53 11.28 0.00 3.60
1790 1941 4.380841 TGGATGTATCTAGACGCGTTTT 57.619 40.909 15.53 7.94 0.00 2.43
1791 1942 5.503662 TGGATGTATCTAGACGCGTTTTA 57.496 39.130 15.53 8.78 0.00 1.52
1792 1943 5.516996 TGGATGTATCTAGACGCGTTTTAG 58.483 41.667 15.53 18.28 0.00 1.85
1793 1944 5.066893 TGGATGTATCTAGACGCGTTTTAGT 59.933 40.000 15.53 11.43 0.00 2.24
1794 1945 5.975939 GGATGTATCTAGACGCGTTTTAGTT 59.024 40.000 15.53 15.30 0.00 2.24
1795 1946 6.474751 GGATGTATCTAGACGCGTTTTAGTTT 59.525 38.462 15.53 12.60 0.00 2.66
1796 1947 7.009907 GGATGTATCTAGACGCGTTTTAGTTTT 59.990 37.037 15.53 10.46 0.00 2.43
1797 1948 8.915871 ATGTATCTAGACGCGTTTTAGTTTTA 57.084 30.769 15.53 9.61 0.00 1.52
1798 1949 8.385789 TGTATCTAGACGCGTTTTAGTTTTAG 57.614 34.615 15.53 0.00 0.00 1.85
1799 1950 8.236586 TGTATCTAGACGCGTTTTAGTTTTAGA 58.763 33.333 15.53 5.87 0.00 2.10
1800 1951 9.230932 GTATCTAGACGCGTTTTAGTTTTAGAT 57.769 33.333 15.53 13.20 34.73 1.98
1802 1953 8.606727 TCTAGACGCGTTTTAGTTTTAGATAC 57.393 34.615 15.53 0.00 0.00 2.24
1803 1954 8.236586 TCTAGACGCGTTTTAGTTTTAGATACA 58.763 33.333 15.53 0.00 0.00 2.29
1804 1955 7.823149 AGACGCGTTTTAGTTTTAGATACAT 57.177 32.000 15.53 0.00 0.00 2.29
1805 1956 7.892803 AGACGCGTTTTAGTTTTAGATACATC 58.107 34.615 15.53 0.00 0.00 3.06
1806 1957 6.997222 ACGCGTTTTAGTTTTAGATACATCC 58.003 36.000 5.58 0.00 0.00 3.51
1807 1958 6.591062 ACGCGTTTTAGTTTTAGATACATCCA 59.409 34.615 5.58 0.00 0.00 3.41
1808 1959 7.279313 ACGCGTTTTAGTTTTAGATACATCCAT 59.721 33.333 5.58 0.00 0.00 3.41
1809 1960 8.120465 CGCGTTTTAGTTTTAGATACATCCATT 58.880 33.333 0.00 0.00 0.00 3.16
1810 1961 9.783256 GCGTTTTAGTTTTAGATACATCCATTT 57.217 29.630 0.00 0.00 0.00 2.32
1817 1968 9.762381 AGTTTTAGATACATCCATTTTTACCCA 57.238 29.630 0.00 0.00 0.00 4.51
1823 1974 9.492730 AGATACATCCATTTTTACCCATTTCTT 57.507 29.630 0.00 0.00 0.00 2.52
1824 1975 9.750125 GATACATCCATTTTTACCCATTTCTTC 57.250 33.333 0.00 0.00 0.00 2.87
1825 1976 6.630071 ACATCCATTTTTACCCATTTCTTCG 58.370 36.000 0.00 0.00 0.00 3.79
1826 1977 6.435904 ACATCCATTTTTACCCATTTCTTCGA 59.564 34.615 0.00 0.00 0.00 3.71
1827 1978 6.262193 TCCATTTTTACCCATTTCTTCGAC 57.738 37.500 0.00 0.00 0.00 4.20
1828 1979 5.770663 TCCATTTTTACCCATTTCTTCGACA 59.229 36.000 0.00 0.00 0.00 4.35
1829 1980 6.265649 TCCATTTTTACCCATTTCTTCGACAA 59.734 34.615 0.00 0.00 0.00 3.18
1830 1981 6.586082 CCATTTTTACCCATTTCTTCGACAAG 59.414 38.462 0.00 0.00 0.00 3.16
1831 1982 6.702716 TTTTTACCCATTTCTTCGACAAGT 57.297 33.333 0.00 0.00 0.00 3.16
1832 1983 7.804843 TTTTTACCCATTTCTTCGACAAGTA 57.195 32.000 0.00 0.00 0.00 2.24
1833 1984 7.989416 TTTTACCCATTTCTTCGACAAGTAT 57.011 32.000 0.00 0.00 0.00 2.12
1834 1985 7.989416 TTTACCCATTTCTTCGACAAGTATT 57.011 32.000 0.00 0.00 0.00 1.89
1835 1986 7.989416 TTACCCATTTCTTCGACAAGTATTT 57.011 32.000 0.00 0.00 0.00 1.40
1836 1987 6.496338 ACCCATTTCTTCGACAAGTATTTC 57.504 37.500 0.00 0.00 0.00 2.17
1837 1988 5.414765 ACCCATTTCTTCGACAAGTATTTCC 59.585 40.000 0.00 0.00 0.00 3.13
1838 1989 5.447279 CCCATTTCTTCGACAAGTATTTCCG 60.447 44.000 0.00 0.00 0.00 4.30
1839 1990 5.447279 CCATTTCTTCGACAAGTATTTCCGG 60.447 44.000 0.00 0.00 0.00 5.14
1840 1991 4.524316 TTCTTCGACAAGTATTTCCGGA 57.476 40.909 0.00 0.00 0.00 5.14
1841 1992 3.841643 TCTTCGACAAGTATTTCCGGAC 58.158 45.455 1.83 0.00 0.00 4.79
1842 1993 2.267188 TCGACAAGTATTTCCGGACG 57.733 50.000 1.83 0.27 0.00 4.79
1843 1994 1.135315 TCGACAAGTATTTCCGGACGG 60.135 52.381 1.83 3.96 0.00 4.79
1844 1995 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
1845 1996 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
1846 1997 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
1847 1998 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
1848 1999 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
1855 2006 0.534652 CCGGACGGAGGGAGTACTAG 60.535 65.000 4.40 0.00 37.50 2.57
1893 2044 2.009774 ACACACAGCACAAGTTCAGTC 58.990 47.619 0.00 0.00 0.00 3.51
1896 2047 2.679837 ACACAGCACAAGTTCAGTCTTG 59.320 45.455 5.12 5.12 46.89 3.02
1897 2048 2.938451 CACAGCACAAGTTCAGTCTTGA 59.062 45.455 12.38 0.00 45.11 3.02
1898 2049 3.002042 CACAGCACAAGTTCAGTCTTGAG 59.998 47.826 12.38 6.50 45.11 3.02
1901 2052 2.564771 CACAAGTTCAGTCTTGAGCCA 58.435 47.619 12.38 0.00 45.11 4.75
1902 2053 2.547211 CACAAGTTCAGTCTTGAGCCAG 59.453 50.000 12.38 0.00 45.11 4.85
1925 2077 6.932960 CAGAGACATGCATATCCAGATTACAA 59.067 38.462 0.16 0.00 0.00 2.41
1948 2104 5.283763 AGCATGGGGAGCAGATAGATATAA 58.716 41.667 0.00 0.00 0.00 0.98
1953 2109 7.045693 TGGGGAGCAGATAGATATAAGTAGT 57.954 40.000 0.00 0.00 0.00 2.73
1960 2116 9.689501 AGCAGATAGATATAAGTAGTAAGGTCC 57.310 37.037 0.00 0.00 0.00 4.46
2000 2156 1.404583 GCATGGCACTGGATGTTTTCC 60.405 52.381 0.00 0.00 45.69 3.13
2005 2161 2.238521 GCACTGGATGTTTTCCCTCAA 58.761 47.619 0.00 0.00 44.77 3.02
2031 2187 2.026542 TGCAGCTTCCATCATCTTCAGT 60.027 45.455 0.00 0.00 0.00 3.41
2062 2219 1.885887 GCATCACTACCTGCAACCAAA 59.114 47.619 0.00 0.00 38.28 3.28
2073 2230 4.125703 CCTGCAACCAAACAAGCAAAATA 58.874 39.130 0.00 0.00 36.44 1.40
2074 2231 4.211794 CCTGCAACCAAACAAGCAAAATAG 59.788 41.667 0.00 0.00 36.44 1.73
2075 2232 5.016051 TGCAACCAAACAAGCAAAATAGA 57.984 34.783 0.00 0.00 33.48 1.98
2077 2234 6.753180 TGCAACCAAACAAGCAAAATAGATA 58.247 32.000 0.00 0.00 33.48 1.98
2078 2235 7.212976 TGCAACCAAACAAGCAAAATAGATAA 58.787 30.769 0.00 0.00 33.48 1.75
2079 2236 7.877097 TGCAACCAAACAAGCAAAATAGATAAT 59.123 29.630 0.00 0.00 33.48 1.28
2080 2237 8.170553 GCAACCAAACAAGCAAAATAGATAATG 58.829 33.333 0.00 0.00 0.00 1.90
2096 2254 5.601662 AGATAATGTGGATCAGTGTAACCG 58.398 41.667 0.00 0.00 37.80 4.44
2104 2262 3.383825 GGATCAGTGTAACCGGTACTCAT 59.616 47.826 8.00 0.00 37.80 2.90
2105 2263 3.861276 TCAGTGTAACCGGTACTCATG 57.139 47.619 8.00 4.99 37.80 3.07
2109 2267 1.619332 TGTAACCGGTACTCATGTGCA 59.381 47.619 8.00 0.00 33.46 4.57
2128 2286 4.266265 GTGCAAGAAAGAAAAACTGACAGC 59.734 41.667 1.25 0.00 0.00 4.40
2129 2287 4.082300 TGCAAGAAAGAAAAACTGACAGCA 60.082 37.500 1.25 0.00 0.00 4.41
2140 2298 2.969990 ACTGACAGCACTTCAGCATAG 58.030 47.619 1.25 0.00 43.79 2.23
2141 2299 1.664659 CTGACAGCACTTCAGCATAGC 59.335 52.381 0.00 0.00 34.41 2.97
2142 2300 1.002315 TGACAGCACTTCAGCATAGCA 59.998 47.619 0.00 0.00 36.85 3.49
2143 2301 2.286872 GACAGCACTTCAGCATAGCAT 58.713 47.619 0.00 0.00 36.85 3.79
2144 2302 3.118665 TGACAGCACTTCAGCATAGCATA 60.119 43.478 0.00 0.00 36.85 3.14
2153 2311 2.634453 TCAGCATAGCATAGCAGCCTAA 59.366 45.455 0.00 0.00 34.23 2.69
2175 2334 1.898574 CTCCCTGCTTGTTTGCCGT 60.899 57.895 0.00 0.00 0.00 5.68
2176 2335 2.133742 CTCCCTGCTTGTTTGCCGTG 62.134 60.000 0.00 0.00 0.00 4.94
2220 2379 4.493547 TGCAATTTAAGCTCGGGAAATTG 58.506 39.130 20.69 20.69 46.30 2.32
2221 2380 3.865164 GCAATTTAAGCTCGGGAAATTGG 59.135 43.478 23.44 13.55 44.85 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 2.107031 CCATCATGAGGCCTATGTGGAA 59.893 50.000 22.11 9.14 38.35 3.53
140 141 1.675641 GCTCCGGGCTTCAACATGT 60.676 57.895 0.00 0.00 38.06 3.21
167 174 4.658786 AGGAGGGGGAACTGGCGT 62.659 66.667 0.00 0.00 0.00 5.68
174 196 2.291043 GCAGTCGAAGGAGGGGGAA 61.291 63.158 0.00 0.00 0.00 3.97
178 200 3.003173 TGGGCAGTCGAAGGAGGG 61.003 66.667 0.00 0.00 0.00 4.30
179 201 2.266055 GTGGGCAGTCGAAGGAGG 59.734 66.667 0.00 0.00 0.00 4.30
185 207 2.680352 GAGGAGGTGGGCAGTCGA 60.680 66.667 0.00 0.00 0.00 4.20
191 213 4.554036 GATGCGGAGGAGGTGGGC 62.554 72.222 0.00 0.00 0.00 5.36
192 214 3.866582 GGATGCGGAGGAGGTGGG 61.867 72.222 0.00 0.00 0.00 4.61
216 238 2.190578 GGAGGTGGCTTCGATGGG 59.809 66.667 0.00 0.00 0.00 4.00
235 275 1.292941 TGAGGAGGAGGAGGAGGAGG 61.293 65.000 0.00 0.00 0.00 4.30
254 297 1.142748 CTCGCCGAAGCAAGAGGAT 59.857 57.895 0.00 0.00 39.83 3.24
260 306 2.048222 CTGGACTCGCCGAAGCAA 60.048 61.111 0.00 0.00 40.66 3.91
296 345 2.819595 GTGATCCGTGCCGCATGT 60.820 61.111 11.61 0.00 0.00 3.21
321 379 2.503356 ACCAGTTCTAGATTGAGCAGGG 59.497 50.000 0.00 0.00 30.39 4.45
438 501 2.729479 CGTCAGCCAGAGCCCATCT 61.729 63.158 0.00 0.00 41.25 2.90
469 532 1.700042 CCTAGCCACATCCACCTCCC 61.700 65.000 0.00 0.00 0.00 4.30
518 582 3.207669 CAGCTCATCGCCCAAGCC 61.208 66.667 0.00 0.00 40.39 4.35
583 660 2.500229 GTTCGGAATTCTGGTGGTTCA 58.500 47.619 14.33 0.00 0.00 3.18
608 685 4.133820 ACTGACAATGGAATTTCACACGA 58.866 39.130 0.00 0.00 31.22 4.35
655 736 7.445402 CCTCGTCATTCAACCAAAATATAGGAT 59.555 37.037 0.00 0.00 0.00 3.24
666 747 2.169769 GGTATCCCTCGTCATTCAACCA 59.830 50.000 0.00 0.00 0.00 3.67
669 750 3.104512 ACAGGTATCCCTCGTCATTCAA 58.895 45.455 0.00 0.00 39.89 2.69
675 756 1.677052 GTCTGACAGGTATCCCTCGTC 59.323 57.143 1.81 1.59 39.89 4.20
676 757 1.685491 GGTCTGACAGGTATCCCTCGT 60.685 57.143 10.38 0.00 39.89 4.18
677 758 1.033574 GGTCTGACAGGTATCCCTCG 58.966 60.000 10.38 0.00 39.89 4.63
683 764 2.217510 ACGTCTGGTCTGACAGGTAT 57.782 50.000 10.38 0.00 38.98 2.73
685 766 1.120530 AAACGTCTGGTCTGACAGGT 58.879 50.000 10.38 0.00 38.98 4.00
688 769 1.068588 CCTCAAACGTCTGGTCTGACA 59.931 52.381 10.38 0.00 36.82 3.58
694 775 2.430367 GGGCCTCAAACGTCTGGT 59.570 61.111 0.84 0.00 0.00 4.00
699 780 2.030562 CAGACGGGCCTCAAACGT 59.969 61.111 0.84 2.39 44.35 3.99
714 795 4.380444 CCCGGTCACAAAAATACAATCCAG 60.380 45.833 0.00 0.00 0.00 3.86
717 798 3.507786 GCCCGGTCACAAAAATACAATC 58.492 45.455 0.00 0.00 0.00 2.67
718 799 2.232696 GGCCCGGTCACAAAAATACAAT 59.767 45.455 0.00 0.00 0.00 2.71
719 800 1.614413 GGCCCGGTCACAAAAATACAA 59.386 47.619 0.00 0.00 0.00 2.41
720 801 1.249407 GGCCCGGTCACAAAAATACA 58.751 50.000 0.00 0.00 0.00 2.29
721 802 0.169451 CGGCCCGGTCACAAAAATAC 59.831 55.000 0.00 0.00 0.00 1.89
722 803 0.250814 ACGGCCCGGTCACAAAAATA 60.251 50.000 8.57 0.00 0.00 1.40
723 804 1.520600 GACGGCCCGGTCACAAAAAT 61.521 55.000 8.57 0.00 36.91 1.82
724 805 2.124236 ACGGCCCGGTCACAAAAA 60.124 55.556 8.57 0.00 0.00 1.94
725 806 2.592287 GACGGCCCGGTCACAAAA 60.592 61.111 8.57 0.00 36.91 2.44
726 807 4.629523 GGACGGCCCGGTCACAAA 62.630 66.667 8.57 0.00 38.70 2.83
762 843 2.281276 CCCTTAATACCGCCGGGC 60.281 66.667 8.57 9.54 36.48 6.13
763 844 2.428622 CCCCTTAATACCGCCGGG 59.571 66.667 8.57 0.00 40.11 5.73
764 845 2.428622 CCCCCTTAATACCGCCGG 59.571 66.667 0.00 0.00 0.00 6.13
791 872 2.686106 TACCGAACTGCCTCCCCC 60.686 66.667 0.00 0.00 0.00 5.40
792 873 1.623542 ATGTACCGAACTGCCTCCCC 61.624 60.000 0.00 0.00 0.00 4.81
793 874 1.117150 TATGTACCGAACTGCCTCCC 58.883 55.000 0.00 0.00 0.00 4.30
794 875 2.973694 TTATGTACCGAACTGCCTCC 57.026 50.000 0.00 0.00 0.00 4.30
795 876 4.634443 ACATTTTATGTACCGAACTGCCTC 59.366 41.667 0.00 0.00 42.78 4.70
796 877 4.585879 ACATTTTATGTACCGAACTGCCT 58.414 39.130 0.00 0.00 42.78 4.75
797 878 4.957759 ACATTTTATGTACCGAACTGCC 57.042 40.909 0.00 0.00 42.78 4.85
812 893 6.239008 CGCCTCATGGGAAATACATACATTTT 60.239 38.462 0.00 0.00 37.23 1.82
817 898 3.074412 CCGCCTCATGGGAAATACATAC 58.926 50.000 0.00 0.00 37.23 2.39
830 911 2.279069 CCCGCTAGATCCGCCTCAT 61.279 63.158 0.00 0.00 0.00 2.90
861 942 1.300481 GGCCGCTCATTTACTTCCTC 58.700 55.000 0.00 0.00 0.00 3.71
868 949 2.206750 GTAATCACGGCCGCTCATTTA 58.793 47.619 28.58 13.37 0.00 1.40
869 950 1.014352 GTAATCACGGCCGCTCATTT 58.986 50.000 28.58 14.43 0.00 2.32
880 961 2.668279 GCTTTGCCTTGGTGTAATCACG 60.668 50.000 0.00 0.00 44.68 4.35
916 997 1.770085 GATAAGGCGCTGTGCTGCTC 61.770 60.000 13.46 0.00 45.43 4.26
1011 1112 4.742201 GCGAGGTGGAGCAGCGAA 62.742 66.667 0.00 0.00 36.92 4.70
1289 1402 3.374402 CGTCGCTCTGGTCCACCT 61.374 66.667 0.00 0.00 36.82 4.00
1523 1641 4.699735 TGGCTGGTGAAATACATTGTACAG 59.300 41.667 0.00 2.53 0.00 2.74
1615 1735 2.483877 TCAAGCATAACAAGCAGGAACG 59.516 45.455 0.00 0.00 0.00 3.95
1616 1736 4.503741 TTCAAGCATAACAAGCAGGAAC 57.496 40.909 0.00 0.00 0.00 3.62
1628 1750 4.615682 CGCTGAACCAATGTTTCAAGCATA 60.616 41.667 12.39 0.00 36.38 3.14
1648 1770 1.806623 GCTGATGTTCCGGTTATCGCT 60.807 52.381 0.00 0.00 37.59 4.93
1686 1834 4.635765 TCAAATCTTTCGATTCGCCTTCAT 59.364 37.500 0.00 0.00 38.89 2.57
1718 1869 5.045578 AGGGAGTACTACAAATGATGTGCTT 60.046 40.000 7.57 0.00 43.77 3.91
1733 1884 1.856539 TTCCGGACGGAGGGAGTACT 61.857 60.000 13.64 0.00 46.06 2.73
1738 1889 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
1739 1890 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
1740 1891 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
1741 1892 2.667473 ACAAGTATTTCCGGACGGAG 57.333 50.000 13.64 3.15 46.06 4.63
1742 1893 3.763360 TCTAACAAGTATTTCCGGACGGA 59.237 43.478 1.83 9.76 43.52 4.69
1743 1894 4.110482 CTCTAACAAGTATTTCCGGACGG 58.890 47.826 1.83 3.96 0.00 4.79
1744 1895 4.990257 TCTCTAACAAGTATTTCCGGACG 58.010 43.478 1.83 0.00 0.00 4.79
1745 1896 7.201617 CCATTTCTCTAACAAGTATTTCCGGAC 60.202 40.741 1.83 0.00 0.00 4.79
1746 1897 6.821665 CCATTTCTCTAACAAGTATTTCCGGA 59.178 38.462 0.00 0.00 0.00 5.14
1747 1898 6.821665 TCCATTTCTCTAACAAGTATTTCCGG 59.178 38.462 0.00 0.00 0.00 5.14
1748 1899 7.843490 TCCATTTCTCTAACAAGTATTTCCG 57.157 36.000 0.00 0.00 0.00 4.30
1749 1900 9.178758 ACATCCATTTCTCTAACAAGTATTTCC 57.821 33.333 0.00 0.00 0.00 3.13
1758 1909 8.568794 CGTCTAGATACATCCATTTCTCTAACA 58.431 37.037 0.00 0.00 0.00 2.41
1759 1910 7.539366 GCGTCTAGATACATCCATTTCTCTAAC 59.461 40.741 0.00 0.00 0.00 2.34
1760 1911 7.573283 CGCGTCTAGATACATCCATTTCTCTAA 60.573 40.741 0.00 0.00 0.00 2.10
1761 1912 6.128254 CGCGTCTAGATACATCCATTTCTCTA 60.128 42.308 0.00 0.00 0.00 2.43
1762 1913 5.335269 CGCGTCTAGATACATCCATTTCTCT 60.335 44.000 0.00 0.00 0.00 3.10
1763 1914 4.854291 CGCGTCTAGATACATCCATTTCTC 59.146 45.833 0.00 0.00 0.00 2.87
1764 1915 4.278669 ACGCGTCTAGATACATCCATTTCT 59.721 41.667 5.58 0.00 0.00 2.52
1765 1916 4.547532 ACGCGTCTAGATACATCCATTTC 58.452 43.478 5.58 0.00 0.00 2.17
1766 1917 4.585955 ACGCGTCTAGATACATCCATTT 57.414 40.909 5.58 0.00 0.00 2.32
1767 1918 4.585955 AACGCGTCTAGATACATCCATT 57.414 40.909 14.44 0.00 0.00 3.16
1768 1919 4.585955 AAACGCGTCTAGATACATCCAT 57.414 40.909 14.44 0.00 0.00 3.41
1769 1920 4.380841 AAAACGCGTCTAGATACATCCA 57.619 40.909 14.44 0.00 0.00 3.41
1770 1921 5.517904 ACTAAAACGCGTCTAGATACATCC 58.482 41.667 26.32 0.00 0.00 3.51
1771 1922 7.447243 AAACTAAAACGCGTCTAGATACATC 57.553 36.000 26.32 0.00 0.00 3.06
1772 1923 7.823149 AAAACTAAAACGCGTCTAGATACAT 57.177 32.000 26.32 8.33 0.00 2.29
1773 1924 8.236586 TCTAAAACTAAAACGCGTCTAGATACA 58.763 33.333 26.32 12.74 0.00 2.29
1774 1925 8.606727 TCTAAAACTAAAACGCGTCTAGATAC 57.393 34.615 26.32 0.00 0.00 2.24
1776 1927 9.230932 GTATCTAAAACTAAAACGCGTCTAGAT 57.769 33.333 26.32 20.01 0.00 1.98
1777 1928 8.236586 TGTATCTAAAACTAAAACGCGTCTAGA 58.763 33.333 26.32 16.13 0.00 2.43
1778 1929 8.385789 TGTATCTAAAACTAAAACGCGTCTAG 57.614 34.615 14.44 18.66 0.00 2.43
1779 1930 8.915871 ATGTATCTAAAACTAAAACGCGTCTA 57.084 30.769 14.44 6.52 0.00 2.59
1780 1931 7.009907 GGATGTATCTAAAACTAAAACGCGTCT 59.990 37.037 14.44 5.48 0.00 4.18
1781 1932 7.115553 GGATGTATCTAAAACTAAAACGCGTC 58.884 38.462 14.44 0.00 0.00 5.19
1782 1933 6.591062 TGGATGTATCTAAAACTAAAACGCGT 59.409 34.615 5.58 5.58 0.00 6.01
1783 1934 6.996106 TGGATGTATCTAAAACTAAAACGCG 58.004 36.000 3.53 3.53 0.00 6.01
1784 1935 9.783256 AAATGGATGTATCTAAAACTAAAACGC 57.217 29.630 0.00 0.00 0.00 4.84
1791 1942 9.762381 TGGGTAAAAATGGATGTATCTAAAACT 57.238 29.630 0.00 0.00 0.00 2.66
1797 1948 9.492730 AAGAAATGGGTAAAAATGGATGTATCT 57.507 29.630 0.00 0.00 0.00 1.98
1798 1949 9.750125 GAAGAAATGGGTAAAAATGGATGTATC 57.250 33.333 0.00 0.00 0.00 2.24
1799 1950 8.413229 CGAAGAAATGGGTAAAAATGGATGTAT 58.587 33.333 0.00 0.00 0.00 2.29
1800 1951 7.612244 TCGAAGAAATGGGTAAAAATGGATGTA 59.388 33.333 0.00 0.00 0.00 2.29
1801 1952 6.435904 TCGAAGAAATGGGTAAAAATGGATGT 59.564 34.615 0.00 0.00 0.00 3.06
1802 1953 6.751888 GTCGAAGAAATGGGTAAAAATGGATG 59.248 38.462 0.00 0.00 39.69 3.51
1803 1954 6.435904 TGTCGAAGAAATGGGTAAAAATGGAT 59.564 34.615 0.00 0.00 39.69 3.41
1804 1955 5.770663 TGTCGAAGAAATGGGTAAAAATGGA 59.229 36.000 0.00 0.00 39.69 3.41
1805 1956 6.019779 TGTCGAAGAAATGGGTAAAAATGG 57.980 37.500 0.00 0.00 39.69 3.16
1806 1957 7.145323 ACTTGTCGAAGAAATGGGTAAAAATG 58.855 34.615 0.00 0.00 39.69 2.32
1807 1958 7.284919 ACTTGTCGAAGAAATGGGTAAAAAT 57.715 32.000 0.00 0.00 39.69 1.82
1808 1959 6.702716 ACTTGTCGAAGAAATGGGTAAAAA 57.297 33.333 0.00 0.00 39.69 1.94
1809 1960 7.989416 ATACTTGTCGAAGAAATGGGTAAAA 57.011 32.000 0.00 0.00 39.69 1.52
1810 1961 7.989416 AATACTTGTCGAAGAAATGGGTAAA 57.011 32.000 0.00 0.00 39.69 2.01
1811 1962 7.120138 GGAAATACTTGTCGAAGAAATGGGTAA 59.880 37.037 0.00 0.00 39.69 2.85
1812 1963 6.596497 GGAAATACTTGTCGAAGAAATGGGTA 59.404 38.462 0.00 0.00 39.69 3.69
1813 1964 5.414765 GGAAATACTTGTCGAAGAAATGGGT 59.585 40.000 0.00 0.00 39.69 4.51
1814 1965 5.447279 CGGAAATACTTGTCGAAGAAATGGG 60.447 44.000 0.00 0.00 39.69 4.00
1815 1966 5.447279 CCGGAAATACTTGTCGAAGAAATGG 60.447 44.000 0.00 0.00 39.69 3.16
1816 1967 5.350365 TCCGGAAATACTTGTCGAAGAAATG 59.650 40.000 0.00 0.00 39.69 2.32
1817 1968 5.350640 GTCCGGAAATACTTGTCGAAGAAAT 59.649 40.000 5.23 0.00 39.69 2.17
1818 1969 4.687483 GTCCGGAAATACTTGTCGAAGAAA 59.313 41.667 5.23 0.00 39.69 2.52
1819 1970 4.240096 GTCCGGAAATACTTGTCGAAGAA 58.760 43.478 5.23 0.00 39.69 2.52
1820 1971 3.671433 CGTCCGGAAATACTTGTCGAAGA 60.671 47.826 5.23 0.00 32.98 2.87
1821 1972 2.597305 CGTCCGGAAATACTTGTCGAAG 59.403 50.000 5.23 0.00 35.07 3.79
1822 1973 2.598589 CGTCCGGAAATACTTGTCGAA 58.401 47.619 5.23 0.00 0.00 3.71
1823 1974 1.135315 CCGTCCGGAAATACTTGTCGA 60.135 52.381 5.23 0.00 37.50 4.20
1824 1975 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
1825 1976 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
1826 1977 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
1827 1978 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
1828 1979 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
1829 1980 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
1830 1981 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
1831 1982 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
1832 1983 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
1833 1984 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
1834 1985 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
1835 1986 0.982852 TAGTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
1836 1987 0.534652 CTAGTACTCCCTCCGTCCGG 60.535 65.000 0.00 0.00 0.00 5.14
1837 1988 0.179936 ACTAGTACTCCCTCCGTCCG 59.820 60.000 0.00 0.00 0.00 4.79
1838 1989 2.433662 AACTAGTACTCCCTCCGTCC 57.566 55.000 0.00 0.00 0.00 4.79
1839 1990 4.946772 AGTTAAACTAGTACTCCCTCCGTC 59.053 45.833 0.00 0.00 0.00 4.79
1840 1991 4.928263 AGTTAAACTAGTACTCCCTCCGT 58.072 43.478 0.00 0.00 0.00 4.69
1841 1992 5.416952 TCAAGTTAAACTAGTACTCCCTCCG 59.583 44.000 0.00 0.00 0.00 4.63
1842 1993 6.847421 TCAAGTTAAACTAGTACTCCCTCC 57.153 41.667 0.00 0.00 0.00 4.30
1843 1994 7.838884 ACATCAAGTTAAACTAGTACTCCCTC 58.161 38.462 0.00 0.00 0.00 4.30
1844 1995 7.793948 ACATCAAGTTAAACTAGTACTCCCT 57.206 36.000 0.00 0.00 0.00 4.20
1845 1996 8.312564 AGAACATCAAGTTAAACTAGTACTCCC 58.687 37.037 0.00 0.00 41.51 4.30
1855 2006 7.376072 GCTGTGTGTTAGAACATCAAGTTAAAC 59.624 37.037 0.00 0.00 41.51 2.01
1893 2044 2.039818 ATGCATGTCTCTGGCTCAAG 57.960 50.000 0.00 0.00 0.00 3.02
1896 2047 2.038164 TGGATATGCATGTCTCTGGCTC 59.962 50.000 21.04 5.26 0.00 4.70
1897 2048 2.038689 CTGGATATGCATGTCTCTGGCT 59.961 50.000 21.04 0.00 0.00 4.75
1898 2049 2.038164 TCTGGATATGCATGTCTCTGGC 59.962 50.000 21.04 6.56 0.00 4.85
1899 2050 4.554960 ATCTGGATATGCATGTCTCTGG 57.445 45.455 21.04 10.12 0.00 3.86
1900 2051 6.461640 TGTAATCTGGATATGCATGTCTCTG 58.538 40.000 21.04 14.83 0.00 3.35
1901 2052 6.676990 TGTAATCTGGATATGCATGTCTCT 57.323 37.500 21.04 6.10 0.00 3.10
1902 2053 6.128336 GCTTGTAATCTGGATATGCATGTCTC 60.128 42.308 21.04 12.65 0.00 3.36
1925 2077 2.041824 ATCTATCTGCTCCCCATGCT 57.958 50.000 0.00 0.00 0.00 3.79
1948 2104 9.205513 TCCGAAATAAATAAGGACCTTACTACT 57.794 33.333 16.35 0.00 0.00 2.57
1953 2109 9.822185 GTTACTCCGAAATAAATAAGGACCTTA 57.178 33.333 16.35 16.35 0.00 2.69
1960 2116 7.069569 CCATGCGTTACTCCGAAATAAATAAG 58.930 38.462 0.00 0.00 0.00 1.73
1971 2127 1.447838 AGTGCCATGCGTTACTCCG 60.448 57.895 0.00 0.00 0.00 4.63
2000 2156 2.165167 TGGAAGCTGCAGAATTTGAGG 58.835 47.619 20.43 0.00 0.00 3.86
2005 2161 3.899726 AGATGATGGAAGCTGCAGAATT 58.100 40.909 20.43 11.40 0.00 2.17
2031 2187 0.033503 TAGTGATGCCCACCTCGAGA 60.034 55.000 15.71 0.00 46.87 4.04
2062 2219 8.523915 TGATCCACATTATCTATTTTGCTTGT 57.476 30.769 0.00 0.00 0.00 3.16
2073 2230 5.453339 CCGGTTACACTGATCCACATTATCT 60.453 44.000 0.00 0.00 0.00 1.98
2074 2231 4.750098 CCGGTTACACTGATCCACATTATC 59.250 45.833 0.00 0.00 0.00 1.75
2075 2232 4.163458 ACCGGTTACACTGATCCACATTAT 59.837 41.667 0.00 0.00 0.00 1.28
2077 2234 2.304761 ACCGGTTACACTGATCCACATT 59.695 45.455 0.00 0.00 0.00 2.71
2078 2235 1.906574 ACCGGTTACACTGATCCACAT 59.093 47.619 0.00 0.00 0.00 3.21
2079 2236 1.344065 ACCGGTTACACTGATCCACA 58.656 50.000 0.00 0.00 0.00 4.17
2080 2237 2.494870 AGTACCGGTTACACTGATCCAC 59.505 50.000 15.04 0.00 32.41 4.02
2096 2254 5.689383 TTTCTTTCTTGCACATGAGTACC 57.311 39.130 0.00 0.00 0.00 3.34
2104 2262 5.384063 TGTCAGTTTTTCTTTCTTGCACA 57.616 34.783 0.00 0.00 0.00 4.57
2105 2263 4.266265 GCTGTCAGTTTTTCTTTCTTGCAC 59.734 41.667 0.93 0.00 0.00 4.57
2109 2267 5.904362 AGTGCTGTCAGTTTTTCTTTCTT 57.096 34.783 0.93 0.00 0.00 2.52
2128 2286 2.223611 GCTGCTATGCTATGCTGAAGTG 59.776 50.000 0.00 0.00 0.00 3.16
2129 2287 2.492012 GCTGCTATGCTATGCTGAAGT 58.508 47.619 0.00 0.00 0.00 3.01
2175 2334 2.727544 GGTTTTTCGCAGCTGCCA 59.272 55.556 32.07 18.81 37.91 4.92
2176 2335 2.429069 CGGTTTTTCGCAGCTGCC 60.429 61.111 32.07 16.90 37.91 4.85
2186 2345 2.162319 AAATTGCATCGGCGGTTTTT 57.838 40.000 7.21 0.00 45.35 1.94
2197 2356 5.111293 CAATTTCCCGAGCTTAAATTGCAT 58.889 37.500 17.17 0.00 41.20 3.96
2220 2379 0.730840 CGCCTACCATTTCCGAAACC 59.269 55.000 0.00 0.00 0.00 3.27
2221 2380 0.098200 GCGCCTACCATTTCCGAAAC 59.902 55.000 0.00 0.00 0.00 2.78
2283 2442 1.078709 CTGCGACACCCATGTAAGTG 58.921 55.000 6.30 6.30 39.95 3.16
2389 2548 3.119602 CCATCATTGACAGCTTGGTTCTG 60.120 47.826 0.00 0.00 37.56 3.02


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

AutoCloner maintained by Alex Coulton.