Multiple sequence alignment - TraesCS4B01G286500

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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 TraesCS4B01G286500 chr4B 100.000 3352 0 0 1 3352 570092643 570089292 0.000000e+00 6191
1 TraesCS4B01G286500 chr4B 88.751 889 75 9 1 873 119383373 119382494 0.000000e+00 1064
2 TraesCS4B01G286500 chr4B 86.364 110 10 3 2705 2810 5725518 5725410 7.600000e-22 115
3 TraesCS4B01G286500 chr4D 91.879 1884 90 21 873 2709 455898995 455897128 0.000000e+00 2573
4 TraesCS4B01G286500 chr4D 93.056 504 15 10 2850 3352 455897121 455896637 0.000000e+00 719
5 TraesCS4B01G286500 chr4A 93.157 1739 94 17 981 2709 11711768 11713491 0.000000e+00 2529
6 TraesCS4B01G286500 chr4A 92.857 532 18 3 2822 3352 11713499 11714011 0.000000e+00 754
7 TraesCS4B01G286500 chr4A 85.321 109 6 2 873 981 11711641 11711739 1.650000e-18 104
8 TraesCS4B01G286500 chr3B 90.522 823 66 8 1 820 767244832 767245645 0.000000e+00 1077
9 TraesCS4B01G286500 chr7A 90.511 822 66 8 1 819 648083419 648084231 0.000000e+00 1075
10 TraesCS4B01G286500 chr7D 90.291 824 66 10 1 820 449521479 449520666 0.000000e+00 1066
11 TraesCS4B01G286500 chr7D 90.024 822 71 7 1 820 590148903 590148091 0.000000e+00 1053
12 TraesCS4B01G286500 chrUn 89.903 822 70 8 1 820 119077355 119076545 0.000000e+00 1046
13 TraesCS4B01G286500 chr5B 89.793 823 72 8 1 820 273865024 273864211 0.000000e+00 1044
14 TraesCS4B01G286500 chr6A 89.806 824 69 10 1 820 592595267 592596079 0.000000e+00 1042
15 TraesCS4B01G286500 chr6B 90.392 791 63 9 1 788 569881679 569880899 0.000000e+00 1027
16 TraesCS4B01G286500 chr6B 88.889 99 9 2 2705 2803 46875029 46875125 1.630000e-23 121
17 TraesCS4B01G286500 chr6B 88.660 97 10 1 2727 2823 534932104 534932199 2.110000e-22 117
18 TraesCS4B01G286500 chr6B 85.849 106 12 3 2709 2814 716590351 716590453 3.540000e-20 110
19 TraesCS4B01G286500 chr6B 84.685 111 14 3 2704 2814 27822059 27822166 1.270000e-19 108
20 TraesCS4B01G286500 chr1A 88.450 329 29 7 494 820 62676924 62677245 4.060000e-104 388
21 TraesCS4B01G286500 chr1B 93.023 86 5 1 2726 2810 592045610 592045695 1.260000e-24 124
22 TraesCS4B01G286500 chr1B 86.111 108 15 0 2707 2814 642916611 642916718 2.110000e-22 117
23 TraesCS4B01G286500 chr1B 91.566 83 7 0 2721 2803 658730680 658730598 7.600000e-22 115
24 TraesCS4B01G286500 chr2D 86.408 103 13 1 2710 2812 85687173 85687274 9.830000e-21 111


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 TraesCS4B01G286500 chr4B 570089292 570092643 3351 True 6191 6191 100.0000 1 3352 1 chr4B.!!$R3 3351
1 TraesCS4B01G286500 chr4B 119382494 119383373 879 True 1064 1064 88.7510 1 873 1 chr4B.!!$R2 872
2 TraesCS4B01G286500 chr4D 455896637 455898995 2358 True 1646 2573 92.4675 873 3352 2 chr4D.!!$R1 2479
3 TraesCS4B01G286500 chr4A 11711641 11714011 2370 False 1129 2529 90.4450 873 3352 3 chr4A.!!$F1 2479
4 TraesCS4B01G286500 chr3B 767244832 767245645 813 False 1077 1077 90.5220 1 820 1 chr3B.!!$F1 819
5 TraesCS4B01G286500 chr7A 648083419 648084231 812 False 1075 1075 90.5110 1 819 1 chr7A.!!$F1 818
6 TraesCS4B01G286500 chr7D 449520666 449521479 813 True 1066 1066 90.2910 1 820 1 chr7D.!!$R1 819
7 TraesCS4B01G286500 chr7D 590148091 590148903 812 True 1053 1053 90.0240 1 820 1 chr7D.!!$R2 819
8 TraesCS4B01G286500 chrUn 119076545 119077355 810 True 1046 1046 89.9030 1 820 1 chrUn.!!$R1 819
9 TraesCS4B01G286500 chr5B 273864211 273865024 813 True 1044 1044 89.7930 1 820 1 chr5B.!!$R1 819
10 TraesCS4B01G286500 chr6A 592595267 592596079 812 False 1042 1042 89.8060 1 820 1 chr6A.!!$F1 819
11 TraesCS4B01G286500 chr6B 569880899 569881679 780 True 1027 1027 90.3920 1 788 1 chr6B.!!$R1 787

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
835 855 0.180642 TGTGACCGCCCTACACAAAA 59.819 50.0 0.0 0.0 40.72 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2757 2841 0.321996 ACCGGGCAACTCTCTTCTTC 59.678 55.0 6.32 0.0 0.0 2.87 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
112 116 6.937457 ACATGATTAAAATCTGACGACATCG 58.063 36.000 0.00 0.00 39.59 3.84
113 117 6.535150 ACATGATTAAAATCTGACGACATCGT 59.465 34.615 6.64 6.64 44.59 3.73
220 224 0.656259 CACGATCTTGCTGCATCCAG 59.344 55.000 1.84 0.00 42.13 3.86
263 267 2.071778 AATATGACCGCCAATGCCTT 57.928 45.000 0.00 0.00 0.00 4.35
325 329 2.348362 GCTGCCACAATAAATTTTCCGC 59.652 45.455 0.00 0.00 0.00 5.54
348 352 1.507140 AATCTCGGATTACTGCCCCA 58.493 50.000 0.00 0.00 0.00 4.96
350 354 1.146263 CTCGGATTACTGCCCCACC 59.854 63.158 0.00 0.00 0.00 4.61
355 361 0.600255 GATTACTGCCCCACCGATCG 60.600 60.000 8.51 8.51 0.00 3.69
376 382 3.309138 CGCTCAAGAAGATCATGGTCAAG 59.691 47.826 9.06 0.00 0.00 3.02
383 389 1.442526 GATCATGGTCAAGGCCAGCG 61.443 60.000 5.01 0.00 42.47 5.18
391 397 0.613260 TCAAGGCCAGCGTCTACATT 59.387 50.000 5.01 0.00 0.00 2.71
431 437 2.037144 GCATTTGGCTTCTCCCATGAT 58.963 47.619 0.00 0.00 40.25 2.45
436 442 3.008835 TGGCTTCTCCCATGATTCAAG 57.991 47.619 0.00 0.00 0.00 3.02
442 448 4.386867 TCTCCCATGATTCAAGACGTAC 57.613 45.455 0.00 0.00 0.00 3.67
468 474 3.756434 TGCCTTAGTGGAACAAGCAATAC 59.244 43.478 0.00 0.00 44.16 1.89
489 495 9.930693 CAATACTAAAGTTAGTTGAGAGTCCTT 57.069 33.333 8.92 0.00 40.96 3.36
522 528 2.555199 CAATTTGTGCGGGTTTTTGGA 58.445 42.857 0.00 0.00 0.00 3.53
545 551 6.039829 GGATGTCCTCTCCATGGTAATTTTTC 59.960 42.308 12.58 1.86 32.72 2.29
563 569 2.483014 TCCGGTGTTCAAACCATAGG 57.517 50.000 0.00 0.00 40.53 2.57
573 579 2.578480 TCAAACCATAGGTACCATGCCA 59.422 45.455 15.94 0.00 33.12 4.92
593 599 0.468029 CAGTGGCCACAACCTCCTTT 60.468 55.000 36.39 10.81 0.00 3.11
595 601 1.497286 AGTGGCCACAACCTCCTTTAA 59.503 47.619 36.39 0.00 0.00 1.52
605 611 4.838423 ACAACCTCCTTTAATTTGGGAAGG 59.162 41.667 0.00 0.00 41.01 3.46
610 616 5.269189 CTCCTTTAATTTGGGAAGGCCTAA 58.731 41.667 5.16 0.00 39.78 2.69
620 626 2.119495 GGAAGGCCTAAGATCTGGACA 58.881 52.381 5.16 0.00 32.68 4.02
628 634 5.189180 GCCTAAGATCTGGACATCAGTTTT 58.811 41.667 0.00 0.00 43.76 2.43
632 638 6.371595 AAGATCTGGACATCAGTTTTCTCT 57.628 37.500 0.00 0.00 43.76 3.10
634 640 7.111247 AGATCTGGACATCAGTTTTCTCTAG 57.889 40.000 0.00 0.00 43.76 2.43
635 641 5.667539 TCTGGACATCAGTTTTCTCTAGG 57.332 43.478 0.00 0.00 43.76 3.02
636 642 5.333581 TCTGGACATCAGTTTTCTCTAGGA 58.666 41.667 0.00 0.00 43.76 2.94
637 643 5.780282 TCTGGACATCAGTTTTCTCTAGGAA 59.220 40.000 0.00 0.00 43.76 3.36
638 644 6.270000 TCTGGACATCAGTTTTCTCTAGGAAA 59.730 38.462 3.19 3.19 43.76 3.13
639 645 6.936900 CTGGACATCAGTTTTCTCTAGGAAAA 59.063 38.462 12.40 12.40 41.18 2.29
656 662 9.745880 TCTAGGAAAAGCTTAATAGTTCATACG 57.254 33.333 0.00 0.00 0.00 3.06
669 675 3.006967 AGTTCATACGCCACTTCTTCACT 59.993 43.478 0.00 0.00 0.00 3.41
691 697 8.849168 TCACTTGATTTGAATTGTGTACATCTT 58.151 29.630 0.00 0.00 0.00 2.40
713 719 4.903054 TCTCTTGACAACATCAATCAGCT 58.097 39.130 0.00 0.00 46.37 4.24
742 749 5.105106 TGTCGCCATACCTCTTTTGATCTTA 60.105 40.000 0.00 0.00 0.00 2.10
756 763 7.502226 TCTTTTGATCTTAGGCACTCAAAAAGA 59.498 33.333 9.69 0.00 43.25 2.52
762 769 8.870075 ATCTTAGGCACTCAAAAAGAAAGTAT 57.130 30.769 0.00 0.00 41.75 2.12
781 788 0.472471 TTTGATGCTATCCGGTCCCC 59.528 55.000 0.00 0.00 0.00 4.81
810 817 3.980646 TTCCGGACAATGTGTTTTCAG 57.019 42.857 1.83 0.00 0.00 3.02
832 852 1.188871 TCATGTGACCGCCCTACACA 61.189 55.000 0.00 0.00 46.04 3.72
833 853 0.321210 CATGTGACCGCCCTACACAA 60.321 55.000 0.00 0.00 45.34 3.33
834 854 0.398696 ATGTGACCGCCCTACACAAA 59.601 50.000 0.00 0.00 45.34 2.83
835 855 0.180642 TGTGACCGCCCTACACAAAA 59.819 50.000 0.00 0.00 40.72 2.44
836 856 1.202830 TGTGACCGCCCTACACAAAAT 60.203 47.619 0.00 0.00 40.72 1.82
837 857 2.038689 TGTGACCGCCCTACACAAAATA 59.961 45.455 0.00 0.00 40.72 1.40
838 858 2.676342 GTGACCGCCCTACACAAAATAG 59.324 50.000 0.00 0.00 35.06 1.73
839 859 1.669265 GACCGCCCTACACAAAATAGC 59.331 52.381 0.00 0.00 0.00 2.97
840 860 1.003812 ACCGCCCTACACAAAATAGCA 59.996 47.619 0.00 0.00 0.00 3.49
841 861 1.400494 CCGCCCTACACAAAATAGCAC 59.600 52.381 0.00 0.00 0.00 4.40
842 862 2.356135 CGCCCTACACAAAATAGCACT 58.644 47.619 0.00 0.00 0.00 4.40
843 863 3.527533 CGCCCTACACAAAATAGCACTA 58.472 45.455 0.00 0.00 0.00 2.74
844 864 4.127171 CGCCCTACACAAAATAGCACTAT 58.873 43.478 0.00 0.00 0.00 2.12
845 865 5.294356 CGCCCTACACAAAATAGCACTATA 58.706 41.667 0.00 0.00 0.00 1.31
846 866 5.405571 CGCCCTACACAAAATAGCACTATAG 59.594 44.000 0.00 0.00 0.00 1.31
847 867 6.522054 GCCCTACACAAAATAGCACTATAGA 58.478 40.000 6.78 0.00 0.00 1.98
848 868 6.990349 GCCCTACACAAAATAGCACTATAGAA 59.010 38.462 6.78 0.00 0.00 2.10
849 869 7.497909 GCCCTACACAAAATAGCACTATAGAAA 59.502 37.037 6.78 0.00 0.00 2.52
850 870 9.391006 CCCTACACAAAATAGCACTATAGAAAA 57.609 33.333 6.78 0.00 0.00 2.29
857 877 9.869844 CAAAATAGCACTATAGAAAAATCTCCG 57.130 33.333 6.78 0.00 0.00 4.63
858 878 9.832445 AAAATAGCACTATAGAAAAATCTCCGA 57.168 29.630 6.78 0.00 0.00 4.55
859 879 9.832445 AAATAGCACTATAGAAAAATCTCCGAA 57.168 29.630 6.78 0.00 0.00 4.30
863 883 9.832445 AGCACTATAGAAAAATCTCCGAATAAA 57.168 29.630 6.78 0.00 0.00 1.40
871 891 9.243105 AGAAAAATCTCCGAATAAAAATCTGGA 57.757 29.630 0.00 0.00 0.00 3.86
900 920 1.018226 CAGACCCTTTGCTCGAGCTG 61.018 60.000 35.27 24.18 42.66 4.24
914 934 2.038426 TCGAGCTGTTCCCATCTTTTCA 59.962 45.455 0.00 0.00 0.00 2.69
921 941 3.009473 TGTTCCCATCTTTTCAGGAGAGG 59.991 47.826 0.00 0.00 0.00 3.69
922 942 1.561542 TCCCATCTTTTCAGGAGAGGC 59.438 52.381 0.00 0.00 0.00 4.70
947 967 3.053455 GCCTCGAAGTATCTCGGAAATG 58.947 50.000 0.00 0.00 39.35 2.32
1287 1336 2.022129 CGTCTTCCGCAAGCTCGTT 61.022 57.895 0.00 0.00 0.00 3.85
1384 1462 5.277683 CGCTTGCTATTTGCTTGATACATCT 60.278 40.000 0.00 0.00 43.37 2.90
1385 1463 5.913514 GCTTGCTATTTGCTTGATACATCTG 59.086 40.000 0.00 0.00 43.37 2.90
1386 1464 6.238566 GCTTGCTATTTGCTTGATACATCTGA 60.239 38.462 0.00 0.00 43.37 3.27
1411 1489 0.179015 TTCCGTAGTGCTTTTGCCCA 60.179 50.000 0.00 0.00 46.87 5.36
1452 1532 4.150627 CCTGAACTTGTTGTATCACTGACG 59.849 45.833 0.00 0.00 0.00 4.35
1545 1625 3.256879 TGATCACTCCAGTCTCTGTTGTC 59.743 47.826 0.00 0.00 0.00 3.18
1551 1631 1.202582 CCAGTCTCTGTTGTCTACCCG 59.797 57.143 0.00 0.00 0.00 5.28
1565 1645 5.353938 TGTCTACCCGAAAATGTACTATGC 58.646 41.667 0.00 0.00 0.00 3.14
1568 1648 3.805207 ACCCGAAAATGTACTATGCCTC 58.195 45.455 0.00 0.00 0.00 4.70
1588 1668 5.406649 CCTCGAGCAAGATAATGGATACTC 58.593 45.833 6.99 0.00 37.61 2.59
1610 1691 5.449553 TCTCATGCTGGTTATGTCTAGAGA 58.550 41.667 0.00 0.00 0.00 3.10
1618 1699 8.928448 TGCTGGTTATGTCTAGAGAAAGATAAT 58.072 33.333 0.00 0.00 0.00 1.28
1619 1700 9.202273 GCTGGTTATGTCTAGAGAAAGATAATG 57.798 37.037 0.00 0.00 0.00 1.90
1628 1709 9.084533 GTCTAGAGAAAGATAATGGATACCACT 57.915 37.037 0.00 0.00 35.80 4.00
1644 1725 1.134580 CCACTATGGTCCAGCAGACTG 60.135 57.143 9.70 0.00 45.54 3.51
1677 1758 3.388024 TGCTTATAGGCAACCGAGAGAAT 59.612 43.478 7.13 0.00 39.43 2.40
1719 1800 5.566627 GCCTACCTGTTTGCATATTGTTTGT 60.567 40.000 0.00 0.00 0.00 2.83
1725 1806 4.083961 TGTTTGCATATTGTTTGTGCATGC 60.084 37.500 11.82 11.82 46.90 4.06
1766 1847 4.926238 CACAGATCTTTCAAAGTAGTCGCT 59.074 41.667 0.00 0.00 0.00 4.93
1793 1874 2.571548 CAGATCCCTGTTTGGCCAC 58.428 57.895 3.88 0.00 35.70 5.01
1794 1875 0.038744 CAGATCCCTGTTTGGCCACT 59.961 55.000 3.88 0.00 35.70 4.00
1795 1876 0.329596 AGATCCCTGTTTGGCCACTC 59.670 55.000 3.88 1.33 0.00 3.51
1796 1877 0.681243 GATCCCTGTTTGGCCACTCC 60.681 60.000 3.88 0.00 0.00 3.85
1797 1878 1.434513 ATCCCTGTTTGGCCACTCCA 61.435 55.000 3.88 0.64 44.85 3.86
1809 1891 2.024414 GCCACTCCAGTCTGTTGTTTT 58.976 47.619 0.00 0.00 0.00 2.43
1858 1940 6.692486 CAAGATAGTGGATACTACCATGGTC 58.308 44.000 23.76 6.28 41.92 4.02
1863 1945 3.038280 TGGATACTACCATGGTCCAGTG 58.962 50.000 23.76 10.16 34.23 3.66
1867 1949 0.541863 CTACCATGGTCCAGTGGTCC 59.458 60.000 23.76 17.70 45.30 4.46
1869 1951 1.300963 CCATGGTCCAGTGGTCCAG 59.699 63.158 28.40 20.42 43.41 3.86
1870 1952 1.377725 CATGGTCCAGTGGTCCAGC 60.378 63.158 28.40 12.18 43.41 4.85
1872 1954 1.845627 ATGGTCCAGTGGTCCAGCTG 61.846 60.000 28.40 6.78 43.41 4.24
1875 1957 3.644606 CCAGTGGTCCAGCTGGCT 61.645 66.667 28.91 16.28 44.65 4.75
1876 1958 2.293318 CCAGTGGTCCAGCTGGCTA 61.293 63.158 28.91 17.71 44.65 3.93
1878 1960 0.254178 CAGTGGTCCAGCTGGCTATT 59.746 55.000 28.91 14.47 34.44 1.73
1879 1961 0.543749 AGTGGTCCAGCTGGCTATTC 59.456 55.000 28.91 15.81 34.44 1.75
1880 1962 0.543749 GTGGTCCAGCTGGCTATTCT 59.456 55.000 28.91 0.00 34.44 2.40
1881 1963 0.543277 TGGTCCAGCTGGCTATTCTG 59.457 55.000 28.91 1.49 34.44 3.02
1882 1964 0.543749 GGTCCAGCTGGCTATTCTGT 59.456 55.000 28.91 0.00 34.44 3.41
1883 1965 1.065126 GGTCCAGCTGGCTATTCTGTT 60.065 52.381 28.91 0.00 34.44 3.16
1884 1966 2.619074 GGTCCAGCTGGCTATTCTGTTT 60.619 50.000 28.91 0.00 34.44 2.83
1885 1967 3.370527 GGTCCAGCTGGCTATTCTGTTTA 60.371 47.826 28.91 2.69 34.44 2.01
1888 1970 3.817647 CCAGCTGGCTATTCTGTTTATCC 59.182 47.826 22.33 0.00 0.00 2.59
1899 1981 7.118971 GCTATTCTGTTTATCCTCATAGGCAAG 59.881 40.741 0.00 0.00 34.61 4.01
1934 2016 8.695456 CCAAACTTCATATTTTATGCCTACCTT 58.305 33.333 0.00 0.00 0.00 3.50
1935 2017 9.736023 CAAACTTCATATTTTATGCCTACCTTC 57.264 33.333 0.00 0.00 0.00 3.46
1982 2064 3.064900 ACTTTCTTCAGCCACAGATCC 57.935 47.619 0.00 0.00 0.00 3.36
2118 2200 7.072263 AGGGAACAATACTGAGATATCCAAG 57.928 40.000 0.00 0.00 0.00 3.61
2243 2325 1.620822 ATTCAGACACCCAACTTGCC 58.379 50.000 0.00 0.00 0.00 4.52
2394 2476 4.081406 TGATGTTAACCAGCTTTGAGCAT 58.919 39.130 2.48 0.00 45.56 3.79
2398 2480 4.099266 TGTTAACCAGCTTTGAGCATTTGT 59.901 37.500 2.48 0.00 45.56 2.83
2416 2498 3.857549 TGTCTCGAATCTGTGAAGAGG 57.142 47.619 0.00 0.00 0.00 3.69
2429 2511 2.550180 GTGAAGAGGAAGCTTGGTTGAC 59.450 50.000 2.10 0.00 0.00 3.18
2432 2514 1.578206 GAGGAAGCTTGGTTGACGGC 61.578 60.000 2.10 0.00 0.00 5.68
2477 2559 7.698836 ATTTGTCTGTAATTTGACACTTTGC 57.301 32.000 7.74 0.00 42.06 3.68
2488 2570 5.940192 TTGACACTTTGCGTGAATTATCT 57.060 34.783 0.00 0.00 46.81 1.98
2489 2571 5.281693 TGACACTTTGCGTGAATTATCTG 57.718 39.130 0.00 0.00 46.81 2.90
2536 2618 3.006940 GCCCGATATCTGTTGTGTTCAA 58.993 45.455 0.34 0.00 0.00 2.69
2730 2814 9.784531 TTTTATTTTATTGTTGAAATGGAGGCA 57.215 25.926 0.00 0.00 0.00 4.75
2731 2815 9.784531 TTTATTTTATTGTTGAAATGGAGGCAA 57.215 25.926 0.00 0.00 0.00 4.52
2732 2816 9.784531 TTATTTTATTGTTGAAATGGAGGCAAA 57.215 25.926 0.00 0.00 0.00 3.68
2733 2817 8.688747 ATTTTATTGTTGAAATGGAGGCAAAA 57.311 26.923 0.00 0.00 0.00 2.44
2734 2818 8.688747 TTTTATTGTTGAAATGGAGGCAAAAT 57.311 26.923 0.00 0.00 0.00 1.82
2735 2819 9.784531 TTTTATTGTTGAAATGGAGGCAAAATA 57.215 25.926 0.00 0.00 0.00 1.40
2736 2820 9.956640 TTTATTGTTGAAATGGAGGCAAAATAT 57.043 25.926 0.00 0.00 0.00 1.28
2737 2821 9.956640 TTATTGTTGAAATGGAGGCAAAATATT 57.043 25.926 0.00 0.00 0.00 1.28
2738 2822 8.866970 ATTGTTGAAATGGAGGCAAAATATTT 57.133 26.923 0.00 0.00 0.00 1.40
2739 2823 7.670009 TGTTGAAATGGAGGCAAAATATTTG 57.330 32.000 0.39 0.00 0.00 2.32
2740 2824 6.149142 TGTTGAAATGGAGGCAAAATATTTGC 59.851 34.615 17.18 17.18 44.22 3.68
2754 2838 9.463443 GCAAAATATTTGCCTCGTCTATTAATT 57.537 29.630 15.12 0.00 39.38 1.40
2761 2845 9.832445 ATTTGCCTCGTCTATTAATTAAGAAGA 57.168 29.630 3.94 6.52 0.00 2.87
2762 2846 9.661563 TTTGCCTCGTCTATTAATTAAGAAGAA 57.338 29.630 12.33 1.68 31.35 2.52
2763 2847 8.873215 TGCCTCGTCTATTAATTAAGAAGAAG 57.127 34.615 12.33 13.61 31.35 2.85
2764 2848 8.692710 TGCCTCGTCTATTAATTAAGAAGAAGA 58.307 33.333 18.91 18.91 31.35 2.87
2765 2849 9.187455 GCCTCGTCTATTAATTAAGAAGAAGAG 57.813 37.037 27.52 27.52 37.42 2.85
2773 2857 7.923414 TTAATTAAGAAGAAGAGAGTTGCCC 57.077 36.000 0.00 0.00 0.00 5.36
2774 2858 2.464157 AAGAAGAAGAGAGTTGCCCG 57.536 50.000 0.00 0.00 0.00 6.13
2775 2859 0.610687 AGAAGAAGAGAGTTGCCCGG 59.389 55.000 0.00 0.00 0.00 5.73
2776 2860 0.321996 GAAGAAGAGAGTTGCCCGGT 59.678 55.000 0.00 0.00 0.00 5.28
2777 2861 0.765510 AAGAAGAGAGTTGCCCGGTT 59.234 50.000 0.00 0.00 0.00 4.44
2778 2862 1.640917 AGAAGAGAGTTGCCCGGTTA 58.359 50.000 0.00 0.00 0.00 2.85
2779 2863 1.975680 AGAAGAGAGTTGCCCGGTTAA 59.024 47.619 0.00 0.00 0.00 2.01
2780 2864 2.572104 AGAAGAGAGTTGCCCGGTTAAT 59.428 45.455 0.00 0.00 0.00 1.40
2781 2865 3.009143 AGAAGAGAGTTGCCCGGTTAATT 59.991 43.478 0.00 0.00 0.00 1.40
2782 2866 3.434940 AGAGAGTTGCCCGGTTAATTT 57.565 42.857 0.00 0.00 0.00 1.82
2783 2867 4.563140 AGAGAGTTGCCCGGTTAATTTA 57.437 40.909 0.00 0.00 0.00 1.40
2784 2868 4.913784 AGAGAGTTGCCCGGTTAATTTAA 58.086 39.130 0.00 0.00 0.00 1.52
2785 2869 4.941873 AGAGAGTTGCCCGGTTAATTTAAG 59.058 41.667 0.00 0.00 0.00 1.85
2786 2870 4.014406 AGAGTTGCCCGGTTAATTTAAGG 58.986 43.478 0.00 0.00 0.00 2.69
2787 2871 4.011698 GAGTTGCCCGGTTAATTTAAGGA 58.988 43.478 0.00 0.00 0.00 3.36
2788 2872 4.409187 AGTTGCCCGGTTAATTTAAGGAA 58.591 39.130 0.00 0.00 0.00 3.36
2789 2873 4.833938 AGTTGCCCGGTTAATTTAAGGAAA 59.166 37.500 0.00 0.00 0.00 3.13
2790 2874 5.304871 AGTTGCCCGGTTAATTTAAGGAAAA 59.695 36.000 0.00 0.00 0.00 2.29
2791 2875 5.136816 TGCCCGGTTAATTTAAGGAAAAC 57.863 39.130 0.00 0.00 0.00 2.43
2792 2876 4.587684 TGCCCGGTTAATTTAAGGAAAACA 59.412 37.500 0.00 0.00 0.00 2.83
2793 2877 5.165676 GCCCGGTTAATTTAAGGAAAACAG 58.834 41.667 0.00 0.00 0.00 3.16
2794 2878 5.716094 CCCGGTTAATTTAAGGAAAACAGG 58.284 41.667 0.00 0.00 35.83 4.00
2795 2879 5.336929 CCCGGTTAATTTAAGGAAAACAGGG 60.337 44.000 0.00 8.28 45.01 4.45
2796 2880 5.165676 CGGTTAATTTAAGGAAAACAGGGC 58.834 41.667 0.00 0.00 0.00 5.19
2797 2881 5.165676 GGTTAATTTAAGGAAAACAGGGCG 58.834 41.667 0.00 0.00 0.00 6.13
2798 2882 5.047872 GGTTAATTTAAGGAAAACAGGGCGA 60.048 40.000 0.00 0.00 0.00 5.54
2799 2883 6.448852 GTTAATTTAAGGAAAACAGGGCGAA 58.551 36.000 0.00 0.00 0.00 4.70
2800 2884 5.538849 AATTTAAGGAAAACAGGGCGAAA 57.461 34.783 0.00 0.00 0.00 3.46
2801 2885 5.538849 ATTTAAGGAAAACAGGGCGAAAA 57.461 34.783 0.00 0.00 0.00 2.29
2802 2886 2.882927 AAGGAAAACAGGGCGAAAAC 57.117 45.000 0.00 0.00 0.00 2.43
2803 2887 2.067365 AGGAAAACAGGGCGAAAACT 57.933 45.000 0.00 0.00 0.00 2.66
2804 2888 1.681264 AGGAAAACAGGGCGAAAACTG 59.319 47.619 0.00 0.00 40.48 3.16
2805 2889 1.679153 GGAAAACAGGGCGAAAACTGA 59.321 47.619 0.00 0.00 38.09 3.41
2806 2890 2.296190 GGAAAACAGGGCGAAAACTGAT 59.704 45.455 0.00 0.00 38.09 2.90
2807 2891 3.504520 GGAAAACAGGGCGAAAACTGATA 59.495 43.478 0.00 0.00 38.09 2.15
2808 2892 4.473199 GAAAACAGGGCGAAAACTGATAC 58.527 43.478 0.00 0.00 38.09 2.24
2809 2893 2.851263 ACAGGGCGAAAACTGATACA 57.149 45.000 0.00 0.00 38.09 2.29
2810 2894 3.134574 ACAGGGCGAAAACTGATACAA 57.865 42.857 0.00 0.00 38.09 2.41
2811 2895 2.812011 ACAGGGCGAAAACTGATACAAC 59.188 45.455 0.00 0.00 38.09 3.32
2812 2896 2.161609 CAGGGCGAAAACTGATACAACC 59.838 50.000 0.00 0.00 36.86 3.77
2813 2897 2.156098 GGGCGAAAACTGATACAACCA 58.844 47.619 0.00 0.00 0.00 3.67
2814 2898 2.554893 GGGCGAAAACTGATACAACCAA 59.445 45.455 0.00 0.00 0.00 3.67
2815 2899 3.561503 GGCGAAAACTGATACAACCAAC 58.438 45.455 0.00 0.00 0.00 3.77
2816 2900 3.561503 GCGAAAACTGATACAACCAACC 58.438 45.455 0.00 0.00 0.00 3.77
2817 2901 3.610821 GCGAAAACTGATACAACCAACCC 60.611 47.826 0.00 0.00 0.00 4.11
2818 2902 3.566322 CGAAAACTGATACAACCAACCCA 59.434 43.478 0.00 0.00 0.00 4.51
2819 2903 4.217550 CGAAAACTGATACAACCAACCCAT 59.782 41.667 0.00 0.00 0.00 4.00
2820 2904 5.413213 CGAAAACTGATACAACCAACCCATA 59.587 40.000 0.00 0.00 0.00 2.74
2825 2909 3.451540 TGATACAACCAACCCATACGCTA 59.548 43.478 0.00 0.00 0.00 4.26
2871 2955 8.880878 ATGGTGACTTGTTTTTGTAAAATACC 57.119 30.769 0.00 0.00 0.00 2.73
2876 2960 9.804758 TGACTTGTTTTTGTAAAATACCGAATT 57.195 25.926 0.00 0.00 0.00 2.17
2925 3009 4.341806 TGTGCATTCTTTTGTCCACAATCT 59.658 37.500 0.00 0.00 35.55 2.40
2946 3030 7.959658 ATCTAGAGGATTGACTATCAGGATG 57.040 40.000 0.00 0.00 34.77 3.51
2947 3031 8.176105 AATCTAGAGGATTGACTATCAGGATGA 58.824 37.037 0.00 0.00 45.97 2.92
2958 3042 1.637338 TCAGGATGAGCTGTGTGACT 58.363 50.000 0.00 0.00 42.56 3.41
2959 3043 1.973515 TCAGGATGAGCTGTGTGACTT 59.026 47.619 0.00 0.00 42.56 3.01
2960 3044 3.165071 TCAGGATGAGCTGTGTGACTTA 58.835 45.455 0.00 0.00 42.56 2.24
2961 3045 3.056536 TCAGGATGAGCTGTGTGACTTAC 60.057 47.826 0.00 0.00 42.56 2.34
2962 3046 2.094494 AGGATGAGCTGTGTGACTTACG 60.094 50.000 0.00 0.00 0.00 3.18
3077 3162 0.110486 ATGCCCCAGTTCGAAAGTGT 59.890 50.000 0.00 0.00 0.00 3.55
3078 3163 0.817634 TGCCCCAGTTCGAAAGTGTG 60.818 55.000 0.00 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
160 164 2.173569 AGGTTGTGGAAGCTTTGAGAGT 59.826 45.455 0.00 0.00 36.48 3.24
220 224 2.680339 GCTTGAATCTAGCCAGAACCAC 59.320 50.000 5.39 0.00 33.50 4.16
247 251 0.611618 TCAAAGGCATTGGCGGTCAT 60.612 50.000 4.38 0.00 42.47 3.06
263 267 7.495606 ACATATGCTATGATTCGTTCACTTCAA 59.504 33.333 1.58 0.00 37.11 2.69
325 329 3.555168 GGGGCAGTAATCCGAGATTACAG 60.555 52.174 25.43 21.34 37.05 2.74
348 352 1.751351 TGATCTTCTTGAGCGATCGGT 59.249 47.619 21.42 21.42 37.07 4.69
350 354 2.730404 CCATGATCTTCTTGAGCGATCG 59.270 50.000 11.69 11.69 37.07 3.69
355 361 3.626670 CCTTGACCATGATCTTCTTGAGC 59.373 47.826 0.00 0.00 0.00 4.26
376 382 4.632538 AATTAAAATGTAGACGCTGGCC 57.367 40.909 0.00 0.00 0.00 5.36
406 412 1.188863 GGAGAAGCCAAATGCATGGT 58.811 50.000 0.00 0.00 44.83 3.55
409 415 1.760613 CATGGGAGAAGCCAAATGCAT 59.239 47.619 0.00 0.00 44.83 3.96
410 416 1.187974 CATGGGAGAAGCCAAATGCA 58.812 50.000 0.00 0.00 44.83 3.96
411 417 1.477553 TCATGGGAGAAGCCAAATGC 58.522 50.000 0.00 0.00 38.95 3.56
412 418 3.702548 TGAATCATGGGAGAAGCCAAATG 59.297 43.478 0.00 0.00 38.95 2.32
413 419 3.985127 TGAATCATGGGAGAAGCCAAAT 58.015 40.909 0.00 0.00 38.95 2.32
414 420 3.454719 TGAATCATGGGAGAAGCCAAA 57.545 42.857 0.00 0.00 38.95 3.28
415 421 3.010472 TCTTGAATCATGGGAGAAGCCAA 59.990 43.478 0.00 0.00 38.95 4.52
416 422 2.577563 TCTTGAATCATGGGAGAAGCCA 59.422 45.455 0.00 0.00 38.95 4.75
431 437 2.922740 AGGCAAAGGTACGTCTTGAA 57.077 45.000 0.00 0.00 0.00 2.69
436 442 2.028748 TCCACTAAGGCAAAGGTACGTC 60.029 50.000 0.00 0.00 37.29 4.34
442 448 2.029918 GCTTGTTCCACTAAGGCAAAGG 60.030 50.000 0.00 0.00 37.29 3.11
468 474 6.994221 TCCAAGGACTCTCAACTAACTTTAG 58.006 40.000 0.00 0.00 36.82 1.85
489 495 2.938451 CACAAATTGCTCTCGCTATCCA 59.062 45.455 0.00 0.00 36.97 3.41
511 517 2.084546 GAGAGGACATCCAAAAACCCG 58.915 52.381 0.00 0.00 38.89 5.28
522 528 5.893824 GGAAAAATTACCATGGAGAGGACAT 59.106 40.000 21.47 0.00 0.00 3.06
545 551 2.194201 ACCTATGGTTTGAACACCGG 57.806 50.000 0.00 0.00 40.09 5.28
573 579 1.645402 AAGGAGGTTGTGGCCACTGT 61.645 55.000 34.75 17.39 0.00 3.55
593 599 5.399038 CCAGATCTTAGGCCTTCCCAAATTA 60.399 44.000 12.58 0.00 35.39 1.40
595 601 3.117360 CCAGATCTTAGGCCTTCCCAAAT 60.117 47.826 12.58 0.00 35.39 2.32
605 611 4.414337 AACTGATGTCCAGATCTTAGGC 57.586 45.455 0.00 0.00 45.78 3.93
610 616 6.098124 CCTAGAGAAAACTGATGTCCAGATCT 59.902 42.308 0.00 0.00 45.78 2.75
620 626 9.746457 ATTAAGCTTTTCCTAGAGAAAACTGAT 57.254 29.630 3.20 4.06 47.00 2.90
632 638 7.440255 GGCGTATGAACTATTAAGCTTTTCCTA 59.560 37.037 3.20 0.00 0.00 2.94
634 640 6.037830 TGGCGTATGAACTATTAAGCTTTTCC 59.962 38.462 3.20 0.00 0.00 3.13
635 641 6.905609 GTGGCGTATGAACTATTAAGCTTTTC 59.094 38.462 3.20 2.20 0.00 2.29
636 642 6.598064 AGTGGCGTATGAACTATTAAGCTTTT 59.402 34.615 3.20 0.00 0.00 2.27
637 643 6.113411 AGTGGCGTATGAACTATTAAGCTTT 58.887 36.000 3.20 0.00 0.00 3.51
638 644 5.671493 AGTGGCGTATGAACTATTAAGCTT 58.329 37.500 3.48 3.48 0.00 3.74
639 645 5.277857 AGTGGCGTATGAACTATTAAGCT 57.722 39.130 0.00 0.00 0.00 3.74
654 660 2.550830 ATCAAGTGAAGAAGTGGCGT 57.449 45.000 0.00 0.00 0.00 5.68
656 662 4.836125 TCAAATCAAGTGAAGAAGTGGC 57.164 40.909 0.00 0.00 0.00 5.01
669 675 9.288576 AGAGAAGATGTACACAATTCAAATCAA 57.711 29.630 15.18 0.00 31.77 2.57
742 749 7.346751 TCAAATACTTTCTTTTTGAGTGCCT 57.653 32.000 0.00 0.00 35.16 4.75
756 763 5.063880 GGACCGGATAGCATCAAATACTTT 58.936 41.667 9.46 0.00 0.00 2.66
762 769 0.472471 GGGGACCGGATAGCATCAAA 59.528 55.000 9.46 0.00 40.86 2.69
781 788 2.354510 ACATTGTCCGGAATGCAATACG 59.645 45.455 16.04 0.00 36.89 3.06
782 789 3.128589 ACACATTGTCCGGAATGCAATAC 59.871 43.478 16.04 0.00 36.89 1.89
810 817 1.084289 GTAGGGCGGTCACATGAAAC 58.916 55.000 0.00 0.00 0.00 2.78
832 852 9.832445 TCGGAGATTTTTCTATAGTGCTATTTT 57.168 29.630 0.00 0.00 0.00 1.82
833 853 9.832445 TTCGGAGATTTTTCTATAGTGCTATTT 57.168 29.630 0.00 0.00 35.04 1.40
837 857 9.832445 TTTATTCGGAGATTTTTCTATAGTGCT 57.168 29.630 0.00 0.00 35.04 4.40
845 865 9.243105 TCCAGATTTTTATTCGGAGATTTTTCT 57.757 29.630 0.00 0.00 35.04 2.52
849 869 9.853177 ACTATCCAGATTTTTATTCGGAGATTT 57.147 29.630 0.00 0.00 35.04 2.17
850 870 9.277783 CACTATCCAGATTTTTATTCGGAGATT 57.722 33.333 0.00 0.00 35.04 2.40
851 871 7.389053 GCACTATCCAGATTTTTATTCGGAGAT 59.611 37.037 0.00 0.00 35.04 2.75
852 872 6.706270 GCACTATCCAGATTTTTATTCGGAGA 59.294 38.462 0.00 0.00 0.00 3.71
853 873 6.346919 CGCACTATCCAGATTTTTATTCGGAG 60.347 42.308 0.00 0.00 0.00 4.63
854 874 5.465390 CGCACTATCCAGATTTTTATTCGGA 59.535 40.000 0.00 0.00 0.00 4.55
855 875 5.465390 TCGCACTATCCAGATTTTTATTCGG 59.535 40.000 0.00 0.00 0.00 4.30
856 876 6.525121 TCGCACTATCCAGATTTTTATTCG 57.475 37.500 0.00 0.00 0.00 3.34
857 877 6.017934 TGCTCGCACTATCCAGATTTTTATTC 60.018 38.462 0.00 0.00 0.00 1.75
858 878 5.822519 TGCTCGCACTATCCAGATTTTTATT 59.177 36.000 0.00 0.00 0.00 1.40
859 879 5.368145 TGCTCGCACTATCCAGATTTTTAT 58.632 37.500 0.00 0.00 0.00 1.40
860 880 4.765273 TGCTCGCACTATCCAGATTTTTA 58.235 39.130 0.00 0.00 0.00 1.52
861 881 3.609853 TGCTCGCACTATCCAGATTTTT 58.390 40.909 0.00 0.00 0.00 1.94
862 882 3.118629 TCTGCTCGCACTATCCAGATTTT 60.119 43.478 0.00 0.00 0.00 1.82
863 883 2.432146 TCTGCTCGCACTATCCAGATTT 59.568 45.455 0.00 0.00 0.00 2.17
864 884 2.034878 TCTGCTCGCACTATCCAGATT 58.965 47.619 0.00 0.00 0.00 2.40
865 885 1.339610 GTCTGCTCGCACTATCCAGAT 59.660 52.381 0.00 0.00 35.30 2.90
866 886 0.741326 GTCTGCTCGCACTATCCAGA 59.259 55.000 0.00 0.00 0.00 3.86
867 887 0.249238 GGTCTGCTCGCACTATCCAG 60.249 60.000 0.00 0.00 0.00 3.86
868 888 1.676678 GGGTCTGCTCGCACTATCCA 61.677 60.000 0.00 0.00 0.00 3.41
869 889 1.068250 GGGTCTGCTCGCACTATCC 59.932 63.158 0.00 0.00 0.00 2.59
870 890 0.461961 AAGGGTCTGCTCGCACTATC 59.538 55.000 0.00 0.00 0.00 2.08
871 891 0.905357 AAAGGGTCTGCTCGCACTAT 59.095 50.000 0.00 0.00 0.00 2.12
900 920 3.615155 CCTCTCCTGAAAAGATGGGAAC 58.385 50.000 0.00 0.00 0.00 3.62
921 941 0.032815 GAGATACTTCGAGGCAGGGC 59.967 60.000 0.00 0.00 0.00 5.19
922 942 0.312416 CGAGATACTTCGAGGCAGGG 59.688 60.000 0.00 0.00 43.03 4.45
926 946 2.865343 TTTCCGAGATACTTCGAGGC 57.135 50.000 0.00 0.00 43.03 4.70
933 953 2.431057 AGCCGTTCATTTCCGAGATACT 59.569 45.455 0.00 0.00 0.00 2.12
947 967 2.414957 CGGGGTTTATTTTGAGCCGTTC 60.415 50.000 0.00 0.00 34.29 3.95
1126 1175 0.612174 TAGAGCAGCTCGTCCAGGTT 60.612 55.000 16.99 0.00 35.36 3.50
1384 1462 5.698832 CAAAAGCACTACGGAAATTCATCA 58.301 37.500 0.00 0.00 0.00 3.07
1385 1463 4.558860 GCAAAAGCACTACGGAAATTCATC 59.441 41.667 0.00 0.00 0.00 2.92
1386 1464 4.485163 GCAAAAGCACTACGGAAATTCAT 58.515 39.130 0.00 0.00 0.00 2.57
1411 1489 1.741145 AGGAAACAAAAACGTGCGAGT 59.259 42.857 0.00 0.00 0.00 4.18
1452 1532 1.669795 CCGCCCTGTCAATTGAAAAGC 60.670 52.381 10.35 9.75 0.00 3.51
1545 1625 4.957296 AGGCATAGTACATTTTCGGGTAG 58.043 43.478 0.00 0.00 0.00 3.18
1551 1631 4.717188 GCTCGAGGCATAGTACATTTTC 57.283 45.455 15.58 0.00 41.35 2.29
1565 1645 5.184864 AGAGTATCCATTATCTTGCTCGAGG 59.815 44.000 15.58 0.00 33.66 4.63
1568 1648 6.018589 TGAGAGTATCCATTATCTTGCTCG 57.981 41.667 0.00 0.00 33.66 5.03
1574 1654 5.784390 ACCAGCATGAGAGTATCCATTATCT 59.216 40.000 0.00 0.00 39.69 1.98
1588 1668 5.781210 TCTCTAGACATAACCAGCATGAG 57.219 43.478 0.00 0.00 39.69 2.90
1628 1709 2.906389 AGAAACAGTCTGCTGGACCATA 59.094 45.455 0.00 0.00 46.62 2.74
1644 1725 6.972901 GGTTGCCTATAAGCATAAACAGAAAC 59.027 38.462 0.00 0.00 43.64 2.78
1677 1758 7.556275 CAGGTAGGCATAAAATAGGAAGTTTGA 59.444 37.037 0.00 0.00 0.00 2.69
1725 1806 3.381045 TGTGTCTGAAGAAAGTAGCACG 58.619 45.455 0.00 0.00 0.00 5.34
1791 1872 3.313526 CAGGAAAACAACAGACTGGAGTG 59.686 47.826 7.51 4.59 0.00 3.51
1792 1873 3.199946 TCAGGAAAACAACAGACTGGAGT 59.800 43.478 7.51 1.72 0.00 3.85
1793 1874 3.808728 TCAGGAAAACAACAGACTGGAG 58.191 45.455 7.51 1.04 0.00 3.86
1794 1875 3.924114 TCAGGAAAACAACAGACTGGA 57.076 42.857 7.51 0.00 0.00 3.86
1795 1876 4.981806 TTTCAGGAAAACAACAGACTGG 57.018 40.909 7.51 0.00 0.00 4.00
1796 1877 6.254157 CACATTTTCAGGAAAACAACAGACTG 59.746 38.462 9.19 0.00 42.32 3.51
1797 1878 6.332630 CACATTTTCAGGAAAACAACAGACT 58.667 36.000 9.19 0.00 42.32 3.24
1798 1879 5.005682 GCACATTTTCAGGAAAACAACAGAC 59.994 40.000 9.19 0.00 42.32 3.51
1809 1891 6.544928 TCTAGACATAGCACATTTTCAGGA 57.455 37.500 0.00 0.00 0.00 3.86
1863 1945 0.543749 ACAGAATAGCCAGCTGGACC 59.456 55.000 37.21 19.60 37.39 4.46
1865 1947 4.444876 GGATAAACAGAATAGCCAGCTGGA 60.445 45.833 37.21 17.52 37.39 3.86
1867 1949 4.712476 AGGATAAACAGAATAGCCAGCTG 58.288 43.478 6.78 6.78 31.17 4.24
1869 1951 4.708177 TGAGGATAAACAGAATAGCCAGC 58.292 43.478 0.00 0.00 31.17 4.85
1870 1952 7.102346 CCTATGAGGATAAACAGAATAGCCAG 58.898 42.308 0.00 0.00 37.67 4.85
1872 1954 5.877564 GCCTATGAGGATAAACAGAATAGCC 59.122 44.000 0.00 0.00 37.67 3.93
1873 1955 6.467677 TGCCTATGAGGATAAACAGAATAGC 58.532 40.000 0.00 0.00 37.67 2.97
1874 1956 8.153550 ACTTGCCTATGAGGATAAACAGAATAG 58.846 37.037 0.00 0.00 37.67 1.73
1875 1957 7.933577 CACTTGCCTATGAGGATAAACAGAATA 59.066 37.037 0.00 0.00 37.67 1.75
1876 1958 6.769822 CACTTGCCTATGAGGATAAACAGAAT 59.230 38.462 0.00 0.00 37.67 2.40
1878 1960 5.425217 TCACTTGCCTATGAGGATAAACAGA 59.575 40.000 0.00 0.00 37.67 3.41
1879 1961 5.674525 TCACTTGCCTATGAGGATAAACAG 58.325 41.667 0.00 0.00 37.67 3.16
1880 1962 5.425217 TCTCACTTGCCTATGAGGATAAACA 59.575 40.000 7.98 0.00 42.25 2.83
1881 1963 5.918608 TCTCACTTGCCTATGAGGATAAAC 58.081 41.667 7.98 0.00 42.25 2.01
1882 1964 5.899547 TCTCTCACTTGCCTATGAGGATAAA 59.100 40.000 7.98 0.00 42.25 1.40
1883 1965 5.458595 TCTCTCACTTGCCTATGAGGATAA 58.541 41.667 7.98 0.00 42.25 1.75
1884 1966 5.066913 TCTCTCACTTGCCTATGAGGATA 57.933 43.478 7.98 0.00 42.25 2.59
1885 1967 3.921104 TCTCTCACTTGCCTATGAGGAT 58.079 45.455 7.98 0.00 42.25 3.24
1888 1970 3.196469 TGGTTCTCTCACTTGCCTATGAG 59.804 47.826 2.57 2.57 43.16 2.90
1956 2038 1.807142 GTGGCTGAAGAAAGTAGCACC 59.193 52.381 0.00 0.00 39.15 5.01
2118 2200 3.249917 GCTTCTCTGTGCTAGTTCAGAC 58.750 50.000 12.58 3.33 36.04 3.51
2243 2325 6.459066 TGAGGAAATCAGACAGAGTTACTTG 58.541 40.000 0.00 0.00 45.10 3.16
2394 2476 4.280929 TCCTCTTCACAGATTCGAGACAAA 59.719 41.667 0.00 0.00 0.00 2.83
2398 2480 3.119316 GCTTCCTCTTCACAGATTCGAGA 60.119 47.826 0.00 0.00 0.00 4.04
2416 2498 1.166531 ACAGCCGTCAACCAAGCTTC 61.167 55.000 0.00 0.00 31.93 3.86
2429 2511 5.991328 ACTGATAATATTTGACACAGCCG 57.009 39.130 0.00 0.00 0.00 5.52
2477 2559 8.887717 AGATTCTTTTTCCTCAGATAATTCACG 58.112 33.333 0.00 0.00 0.00 4.35
2488 2570 7.092716 GCAAAATAGCAGATTCTTTTTCCTCA 58.907 34.615 0.00 0.00 0.00 3.86
2489 2571 7.092716 TGCAAAATAGCAGATTCTTTTTCCTC 58.907 34.615 0.00 0.00 40.11 3.71
2571 2653 9.887629 AATTGTATGATTGTAAAATTGCCATGA 57.112 25.926 0.00 0.00 0.00 3.07
2654 2736 7.981789 GTCAGTAGATTATCTGGATCACAACAA 59.018 37.037 4.78 0.00 33.13 2.83
2677 2759 5.913137 ACAAACAAAATTCAGGTCAGTCA 57.087 34.783 0.00 0.00 0.00 3.41
2709 2793 8.688747 ATTTTGCCTCCATTTCAACAATAAAA 57.311 26.923 0.00 0.00 0.00 1.52
2710 2794 9.956640 ATATTTTGCCTCCATTTCAACAATAAA 57.043 25.926 0.00 0.00 0.00 1.40
2711 2795 9.956640 AATATTTTGCCTCCATTTCAACAATAA 57.043 25.926 0.00 0.00 0.00 1.40
2713 2797 8.732531 CAAATATTTTGCCTCCATTTCAACAAT 58.267 29.630 0.00 0.00 0.00 2.71
2715 2799 6.149142 GCAAATATTTTGCCTCCATTTCAACA 59.851 34.615 12.74 0.00 39.38 3.33
2716 2800 6.545508 GCAAATATTTTGCCTCCATTTCAAC 58.454 36.000 12.74 0.00 39.38 3.18
2717 2801 6.740411 GCAAATATTTTGCCTCCATTTCAA 57.260 33.333 12.74 0.00 39.38 2.69
2728 2812 9.463443 AATTAATAGACGAGGCAAATATTTTGC 57.537 29.630 14.88 14.88 44.22 3.68
2735 2819 9.832445 TCTTCTTAATTAATAGACGAGGCAAAT 57.168 29.630 0.00 0.00 0.00 2.32
2736 2820 9.661563 TTCTTCTTAATTAATAGACGAGGCAAA 57.338 29.630 0.00 0.00 0.00 3.68
2737 2821 9.314321 CTTCTTCTTAATTAATAGACGAGGCAA 57.686 33.333 0.00 0.00 0.00 4.52
2738 2822 8.692710 TCTTCTTCTTAATTAATAGACGAGGCA 58.307 33.333 0.00 0.00 0.00 4.75
2739 2823 9.187455 CTCTTCTTCTTAATTAATAGACGAGGC 57.813 37.037 21.53 0.00 31.39 4.70
2747 2831 9.614792 GGGCAACTCTCTTCTTCTTAATTAATA 57.385 33.333 0.00 0.00 0.00 0.98
2748 2832 7.281100 CGGGCAACTCTCTTCTTCTTAATTAAT 59.719 37.037 0.00 0.00 0.00 1.40
2749 2833 6.594159 CGGGCAACTCTCTTCTTCTTAATTAA 59.406 38.462 0.00 0.00 0.00 1.40
2750 2834 6.106673 CGGGCAACTCTCTTCTTCTTAATTA 58.893 40.000 0.00 0.00 0.00 1.40
2751 2835 4.938226 CGGGCAACTCTCTTCTTCTTAATT 59.062 41.667 0.00 0.00 0.00 1.40
2752 2836 4.508662 CGGGCAACTCTCTTCTTCTTAAT 58.491 43.478 0.00 0.00 0.00 1.40
2753 2837 3.306780 CCGGGCAACTCTCTTCTTCTTAA 60.307 47.826 0.00 0.00 0.00 1.85
2754 2838 2.233922 CCGGGCAACTCTCTTCTTCTTA 59.766 50.000 0.00 0.00 0.00 2.10
2755 2839 1.002544 CCGGGCAACTCTCTTCTTCTT 59.997 52.381 0.00 0.00 0.00 2.52
2756 2840 0.610687 CCGGGCAACTCTCTTCTTCT 59.389 55.000 0.00 0.00 0.00 2.85
2757 2841 0.321996 ACCGGGCAACTCTCTTCTTC 59.678 55.000 6.32 0.00 0.00 2.87
2758 2842 0.765510 AACCGGGCAACTCTCTTCTT 59.234 50.000 6.32 0.00 0.00 2.52
2759 2843 1.640917 TAACCGGGCAACTCTCTTCT 58.359 50.000 6.32 0.00 0.00 2.85
2760 2844 2.467566 TTAACCGGGCAACTCTCTTC 57.532 50.000 6.32 0.00 0.00 2.87
2761 2845 3.434940 AATTAACCGGGCAACTCTCTT 57.565 42.857 6.32 0.00 0.00 2.85
2762 2846 3.434940 AAATTAACCGGGCAACTCTCT 57.565 42.857 6.32 0.00 0.00 3.10
2763 2847 4.095932 CCTTAAATTAACCGGGCAACTCTC 59.904 45.833 6.32 0.00 0.00 3.20
2764 2848 4.014406 CCTTAAATTAACCGGGCAACTCT 58.986 43.478 6.32 0.00 0.00 3.24
2765 2849 4.011698 TCCTTAAATTAACCGGGCAACTC 58.988 43.478 6.32 0.00 0.00 3.01
2766 2850 4.036941 TCCTTAAATTAACCGGGCAACT 57.963 40.909 6.32 0.00 0.00 3.16
2767 2851 4.787260 TTCCTTAAATTAACCGGGCAAC 57.213 40.909 6.32 0.00 0.00 4.17
2768 2852 5.070047 TGTTTTCCTTAAATTAACCGGGCAA 59.930 36.000 6.32 0.00 0.00 4.52
2769 2853 4.587684 TGTTTTCCTTAAATTAACCGGGCA 59.412 37.500 6.32 0.00 0.00 5.36
2770 2854 5.136816 TGTTTTCCTTAAATTAACCGGGC 57.863 39.130 6.32 0.00 0.00 6.13
2771 2855 5.336929 CCCTGTTTTCCTTAAATTAACCGGG 60.337 44.000 6.32 0.00 37.06 5.73
2772 2856 5.716094 CCCTGTTTTCCTTAAATTAACCGG 58.284 41.667 0.00 0.00 0.00 5.28
2773 2857 5.165676 GCCCTGTTTTCCTTAAATTAACCG 58.834 41.667 0.00 0.00 0.00 4.44
2774 2858 5.047872 TCGCCCTGTTTTCCTTAAATTAACC 60.048 40.000 0.00 0.00 0.00 2.85
2775 2859 6.016213 TCGCCCTGTTTTCCTTAAATTAAC 57.984 37.500 0.00 0.00 0.00 2.01
2776 2860 6.651975 TTCGCCCTGTTTTCCTTAAATTAA 57.348 33.333 0.00 0.00 0.00 1.40
2777 2861 6.651975 TTTCGCCCTGTTTTCCTTAAATTA 57.348 33.333 0.00 0.00 0.00 1.40
2778 2862 5.538849 TTTCGCCCTGTTTTCCTTAAATT 57.461 34.783 0.00 0.00 0.00 1.82
2779 2863 5.069914 AGTTTTCGCCCTGTTTTCCTTAAAT 59.930 36.000 0.00 0.00 0.00 1.40
2780 2864 4.403113 AGTTTTCGCCCTGTTTTCCTTAAA 59.597 37.500 0.00 0.00 0.00 1.52
2781 2865 3.955551 AGTTTTCGCCCTGTTTTCCTTAA 59.044 39.130 0.00 0.00 0.00 1.85
2782 2866 3.316868 CAGTTTTCGCCCTGTTTTCCTTA 59.683 43.478 0.00 0.00 0.00 2.69
2783 2867 2.100749 CAGTTTTCGCCCTGTTTTCCTT 59.899 45.455 0.00 0.00 0.00 3.36
2784 2868 1.681264 CAGTTTTCGCCCTGTTTTCCT 59.319 47.619 0.00 0.00 0.00 3.36
2785 2869 1.679153 TCAGTTTTCGCCCTGTTTTCC 59.321 47.619 0.00 0.00 0.00 3.13
2786 2870 3.643159 ATCAGTTTTCGCCCTGTTTTC 57.357 42.857 0.00 0.00 0.00 2.29
2787 2871 3.886505 TGTATCAGTTTTCGCCCTGTTTT 59.113 39.130 0.00 0.00 0.00 2.43
2788 2872 3.482436 TGTATCAGTTTTCGCCCTGTTT 58.518 40.909 0.00 0.00 0.00 2.83
2789 2873 3.134574 TGTATCAGTTTTCGCCCTGTT 57.865 42.857 0.00 0.00 0.00 3.16
2790 2874 2.812011 GTTGTATCAGTTTTCGCCCTGT 59.188 45.455 0.00 0.00 0.00 4.00
2791 2875 2.161609 GGTTGTATCAGTTTTCGCCCTG 59.838 50.000 0.00 0.00 0.00 4.45
2792 2876 2.224670 TGGTTGTATCAGTTTTCGCCCT 60.225 45.455 0.00 0.00 0.00 5.19
2793 2877 2.156098 TGGTTGTATCAGTTTTCGCCC 58.844 47.619 0.00 0.00 0.00 6.13
2794 2878 3.561503 GTTGGTTGTATCAGTTTTCGCC 58.438 45.455 0.00 0.00 0.00 5.54
2795 2879 3.561503 GGTTGGTTGTATCAGTTTTCGC 58.438 45.455 0.00 0.00 0.00 4.70
2796 2880 3.566322 TGGGTTGGTTGTATCAGTTTTCG 59.434 43.478 0.00 0.00 0.00 3.46
2797 2881 5.722021 ATGGGTTGGTTGTATCAGTTTTC 57.278 39.130 0.00 0.00 0.00 2.29
2798 2882 5.182380 CGTATGGGTTGGTTGTATCAGTTTT 59.818 40.000 0.00 0.00 0.00 2.43
2799 2883 4.698304 CGTATGGGTTGGTTGTATCAGTTT 59.302 41.667 0.00 0.00 0.00 2.66
2800 2884 4.258543 CGTATGGGTTGGTTGTATCAGTT 58.741 43.478 0.00 0.00 0.00 3.16
2801 2885 3.869065 CGTATGGGTTGGTTGTATCAGT 58.131 45.455 0.00 0.00 0.00 3.41
2802 2886 2.612212 GCGTATGGGTTGGTTGTATCAG 59.388 50.000 0.00 0.00 0.00 2.90
2803 2887 2.237643 AGCGTATGGGTTGGTTGTATCA 59.762 45.455 0.00 0.00 0.00 2.15
2804 2888 2.914059 AGCGTATGGGTTGGTTGTATC 58.086 47.619 0.00 0.00 0.00 2.24
2805 2889 4.699925 ATAGCGTATGGGTTGGTTGTAT 57.300 40.909 0.00 0.00 0.00 2.29
2806 2890 4.193090 CAATAGCGTATGGGTTGGTTGTA 58.807 43.478 0.00 0.00 0.00 2.41
2807 2891 3.013921 CAATAGCGTATGGGTTGGTTGT 58.986 45.455 0.00 0.00 0.00 3.32
2808 2892 3.013921 ACAATAGCGTATGGGTTGGTTG 58.986 45.455 0.00 0.00 0.00 3.77
2809 2893 3.359695 ACAATAGCGTATGGGTTGGTT 57.640 42.857 0.00 0.00 0.00 3.67
2810 2894 4.699925 ATACAATAGCGTATGGGTTGGT 57.300 40.909 0.00 0.00 30.82 3.67
2811 2895 7.553334 AGTATATACAATAGCGTATGGGTTGG 58.447 38.462 15.18 0.00 34.03 3.77
2812 2896 8.997621 AAGTATATACAATAGCGTATGGGTTG 57.002 34.615 15.18 0.00 34.03 3.77
2876 2960 9.905713 AAAGCTTCTCAATACATGATAACCTTA 57.094 29.630 0.00 0.00 37.44 2.69
2925 3009 5.714333 GCTCATCCTGATAGTCAATCCTCTA 59.286 44.000 0.00 0.00 33.22 2.43
2957 3041 8.760538 AGCTAAGATGACACAGCTCACGTAAG 62.761 46.154 0.00 0.00 40.25 2.34
2958 3042 3.660501 AAGATGACACAGCTCACGTAA 57.339 42.857 0.00 0.00 0.00 3.18
2959 3043 3.427638 GCTAAGATGACACAGCTCACGTA 60.428 47.826 0.00 0.00 0.00 3.57
2960 3044 2.672478 GCTAAGATGACACAGCTCACGT 60.672 50.000 0.00 0.00 0.00 4.49
2961 3045 1.923204 GCTAAGATGACACAGCTCACG 59.077 52.381 0.00 0.00 0.00 4.35
2962 3046 2.928757 CAGCTAAGATGACACAGCTCAC 59.071 50.000 0.00 0.00 42.33 3.51
2995 3079 2.592861 GCCCATCATCCTGGCGTC 60.593 66.667 0.00 0.00 35.08 5.19
3056 3141 1.200020 CACTTTCGAACTGGGGCATTC 59.800 52.381 0.00 0.00 0.00 2.67
3060 3145 1.515521 CCACACTTTCGAACTGGGGC 61.516 60.000 9.81 0.00 0.00 5.80
3077 3162 4.509616 CAAAATCCTGTATACGGTGACCA 58.490 43.478 10.79 0.00 0.00 4.02
3078 3163 3.311596 GCAAAATCCTGTATACGGTGACC 59.688 47.826 10.79 0.00 0.00 4.02
3210 3295 6.127703 CCTTGGATCTGGATATTGCATCATTC 60.128 42.308 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.