Multiple sequence alignment - TraesCS5B01G383400

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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 TraesCS5B01G383400 chr5B 100.000 3245 0 0 1 3245 562224657 562227901 0.000000e+00 5993.0
1 TraesCS5B01G383400 chr5D 86.610 1994 139 64 702 2610 458679568 458681518 0.000000e+00 2085.0
2 TraesCS5B01G383400 chr5D 84.314 102 9 4 2634 2735 458685812 458685906 3.450000e-15 93.5
3 TraesCS5B01G383400 chr5A 86.678 1734 128 61 674 2336 577707899 577709600 0.000000e+00 1827.0
4 TraesCS5B01G383400 chr5A 89.764 381 34 3 2865 3244 577709980 577710356 1.750000e-132 483.0
5 TraesCS5B01G383400 chr5A 91.304 253 14 1 2357 2609 577709675 577709919 4.010000e-89 339.0
6 TraesCS5B01G383400 chr5A 100.000 37 0 0 3208 3244 522768218 522768254 5.810000e-08 69.4
7 TraesCS5B01G383400 chr5A 100.000 28 0 0 908 935 668148934 668148907 6.000000e-03 52.8
8 TraesCS5B01G383400 chr3B 93.632 691 33 5 1 680 588409908 588410598 0.000000e+00 1022.0
9 TraesCS5B01G383400 chr7B 92.764 691 39 6 1 680 648091864 648092554 0.000000e+00 989.0
10 TraesCS5B01G383400 chr7B 92.722 687 41 4 1 678 592779898 592779212 0.000000e+00 983.0
11 TraesCS5B01G383400 chr6B 92.619 691 40 5 1 680 688940762 688941452 0.000000e+00 983.0
12 TraesCS5B01G383400 chr6B 92.464 690 41 6 1 680 654634722 654635410 0.000000e+00 976.0
13 TraesCS5B01G383400 chr4A 92.722 687 34 6 1 678 615529454 615528775 0.000000e+00 977.0
14 TraesCS5B01G383400 chr4A 100.000 37 0 0 3208 3244 417052760 417052796 5.810000e-08 69.4
15 TraesCS5B01G383400 chr4A 97.436 39 1 0 3206 3244 55032761 55032799 2.090000e-07 67.6
16 TraesCS5B01G383400 chr3A 92.453 689 34 6 1 680 737389406 737390085 0.000000e+00 968.0
17 TraesCS5B01G383400 chr1B 92.453 689 35 7 1 678 576146615 576147297 0.000000e+00 968.0
18 TraesCS5B01G383400 chr1B 91.489 705 43 11 1 689 357471921 357471218 0.000000e+00 953.0
19 TraesCS5B01G383400 chr7D 97.500 40 1 0 3205 3244 305877803 305877764 5.810000e-08 69.4
20 TraesCS5B01G383400 chr6A 97.436 39 1 0 3206 3244 475088495 475088533 2.090000e-07 67.6
21 TraesCS5B01G383400 chr4D 100.000 36 0 0 3210 3245 242426477 242426442 2.090000e-07 67.6
22 TraesCS5B01G383400 chr1D 100.000 36 0 0 3209 3244 138259364 138259399 2.090000e-07 67.6
23 TraesCS5B01G383400 chr1D 100.000 36 0 0 3209 3244 395800592 395800627 2.090000e-07 67.6


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 TraesCS5B01G383400 chr5B 562224657 562227901 3244 False 5993 5993 100.000000 1 3245 1 chr5B.!!$F1 3244
1 TraesCS5B01G383400 chr5D 458679568 458681518 1950 False 2085 2085 86.610000 702 2610 1 chr5D.!!$F1 1908
2 TraesCS5B01G383400 chr5A 577707899 577710356 2457 False 883 1827 89.248667 674 3244 3 chr5A.!!$F2 2570
3 TraesCS5B01G383400 chr3B 588409908 588410598 690 False 1022 1022 93.632000 1 680 1 chr3B.!!$F1 679
4 TraesCS5B01G383400 chr7B 648091864 648092554 690 False 989 989 92.764000 1 680 1 chr7B.!!$F1 679
5 TraesCS5B01G383400 chr7B 592779212 592779898 686 True 983 983 92.722000 1 678 1 chr7B.!!$R1 677
6 TraesCS5B01G383400 chr6B 688940762 688941452 690 False 983 983 92.619000 1 680 1 chr6B.!!$F2 679
7 TraesCS5B01G383400 chr6B 654634722 654635410 688 False 976 976 92.464000 1 680 1 chr6B.!!$F1 679
8 TraesCS5B01G383400 chr4A 615528775 615529454 679 True 977 977 92.722000 1 678 1 chr4A.!!$R1 677
9 TraesCS5B01G383400 chr3A 737389406 737390085 679 False 968 968 92.453000 1 680 1 chr3A.!!$F1 679
10 TraesCS5B01G383400 chr1B 576146615 576147297 682 False 968 968 92.453000 1 678 1 chr1B.!!$F1 677
11 TraesCS5B01G383400 chr1B 357471218 357471921 703 True 953 953 91.489000 1 689 1 chr1B.!!$R1 688

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
907 954 0.165944 CGCCACGGTTCATTCAACTC 59.834 55.0 0.0 0.0 35.06 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2620 2843 0.033366 AAAAATTCACCAGCACGCCC 59.967 50.0 0.0 0.0 0.0 6.13 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
46 47 2.876892 GCATTTGGGATTTTGCAAGCCT 60.877 45.455 12.81 0.00 38.65 4.58
66 67 4.884164 GCCTAATTTGCTATTGTGAGAGGT 59.116 41.667 0.00 0.00 0.00 3.85
74 75 1.568504 ATTGTGAGAGGTCCGGCTAA 58.431 50.000 0.00 0.00 0.00 3.09
122 124 0.518636 ATCATGCACGCTTGTGTGAC 59.481 50.000 17.16 9.39 45.65 3.67
322 328 0.994247 AGAGTGGCATGGAATGGACA 59.006 50.000 0.00 0.00 46.86 4.02
330 336 3.006752 GGCATGGAATGGACAACAAAGAA 59.993 43.478 0.00 0.00 46.86 2.52
367 376 7.433131 GCATTCGACATTGTATTGTTCATGAAT 59.567 33.333 12.12 0.00 0.00 2.57
498 518 9.940166 GTTTGATCATTTTTGCTTTTCTTTGAT 57.060 25.926 0.00 0.00 0.00 2.57
582 608 1.904852 CTGCATTATAGCGCGGCTGG 61.905 60.000 8.83 0.00 40.10 4.85
617 643 3.358707 GCCGCGCTAAACCAACCA 61.359 61.111 5.56 0.00 0.00 3.67
682 710 3.181516 GGCTGTTGAAGATGCTCTTAACG 60.182 47.826 0.00 0.00 36.73 3.18
753 787 2.858158 GGAAAAAGTACGCGCGCT 59.142 55.556 32.58 17.79 0.00 5.92
843 881 2.338620 CACAGGAACGAGACGCCA 59.661 61.111 0.00 0.00 0.00 5.69
844 882 1.079819 CACAGGAACGAGACGCCAT 60.080 57.895 0.00 0.00 0.00 4.40
845 883 0.670546 CACAGGAACGAGACGCCATT 60.671 55.000 0.00 0.00 0.00 3.16
846 884 0.389948 ACAGGAACGAGACGCCATTC 60.390 55.000 0.00 0.00 0.00 2.67
847 885 1.153823 AGGAACGAGACGCCATTCG 60.154 57.895 0.00 0.00 45.38 3.34
904 951 3.661911 CCGCCACGGTTCATTCAA 58.338 55.556 0.00 0.00 42.73 2.69
905 952 1.209127 CCGCCACGGTTCATTCAAC 59.791 57.895 0.00 0.00 42.73 3.18
906 953 1.234615 CCGCCACGGTTCATTCAACT 61.235 55.000 0.00 0.00 42.73 3.16
907 954 0.165944 CGCCACGGTTCATTCAACTC 59.834 55.000 0.00 0.00 35.06 3.01
908 955 0.521735 GCCACGGTTCATTCAACTCC 59.478 55.000 0.00 0.00 35.06 3.85
909 956 0.796312 CCACGGTTCATTCAACTCCG 59.204 55.000 0.00 0.00 45.53 4.63
910 957 0.796312 CACGGTTCATTCAACTCCGG 59.204 55.000 0.00 0.00 44.54 5.14
911 958 0.953960 ACGGTTCATTCAACTCCGGC 60.954 55.000 0.00 0.00 44.54 6.13
912 959 1.644786 CGGTTCATTCAACTCCGGCC 61.645 60.000 0.00 0.00 37.92 6.13
913 960 1.313091 GGTTCATTCAACTCCGGCCC 61.313 60.000 0.00 0.00 35.06 5.80
914 961 0.322546 GTTCATTCAACTCCGGCCCT 60.323 55.000 0.00 0.00 31.50 5.19
915 962 0.322456 TTCATTCAACTCCGGCCCTG 60.322 55.000 0.00 0.00 0.00 4.45
916 963 2.044946 ATTCAACTCCGGCCCTGC 60.045 61.111 0.00 0.00 0.00 4.85
917 964 3.645268 ATTCAACTCCGGCCCTGCC 62.645 63.158 0.00 0.00 46.75 4.85
1059 1112 6.094742 TGCACAGTCAATACTTCAACTTCAAA 59.905 34.615 0.00 0.00 31.97 2.69
1161 1216 4.057428 GCTCAGAGCGACCACCGT 62.057 66.667 6.67 0.00 41.15 4.83
1168 1223 2.227089 GAGCGACCACCGTCAAGGAT 62.227 60.000 0.00 0.00 45.00 3.24
1175 1230 0.742505 CACCGTCAAGGATAGCCGTA 59.257 55.000 0.00 0.00 45.00 4.02
1249 1334 2.045926 GACACCAAGGCGAGGCAT 60.046 61.111 0.00 0.00 0.00 4.40
1261 1346 0.250209 CGAGGCATGGGAAGATCAGG 60.250 60.000 0.00 0.00 0.00 3.86
1531 1616 4.286320 ATCGGCGTCGCAGGATCC 62.286 66.667 20.50 2.48 36.13 3.36
1552 1637 1.450312 CCTCGGTTCAGTCCCATGC 60.450 63.158 0.00 0.00 0.00 4.06
1561 1646 0.460987 CAGTCCCATGCTTCCTCGAC 60.461 60.000 0.00 0.00 0.00 4.20
1571 1656 4.445452 TGCTTCCTCGACGTAATTAACT 57.555 40.909 0.00 0.00 0.00 2.24
1577 1662 6.199937 TCCTCGACGTAATTAACTTAAGCT 57.800 37.500 1.29 0.00 0.00 3.74
1585 1670 8.476657 ACGTAATTAACTTAAGCTCTTCTTCC 57.523 34.615 1.29 0.00 36.25 3.46
1592 1677 2.334006 AAGCTCTTCTTCCTCCTCCA 57.666 50.000 0.00 0.00 0.00 3.86
1593 1678 2.566708 AGCTCTTCTTCCTCCTCCAT 57.433 50.000 0.00 0.00 0.00 3.41
1596 1681 2.503356 GCTCTTCTTCCTCCTCCATTCA 59.497 50.000 0.00 0.00 0.00 2.57
1597 1682 3.681313 GCTCTTCTTCCTCCTCCATTCAC 60.681 52.174 0.00 0.00 0.00 3.18
1598 1683 2.497675 TCTTCTTCCTCCTCCATTCACG 59.502 50.000 0.00 0.00 0.00 4.35
1599 1684 0.537188 TCTTCCTCCTCCATTCACGC 59.463 55.000 0.00 0.00 0.00 5.34
1602 1687 1.817099 CCTCCTCCATTCACGCTGC 60.817 63.158 0.00 0.00 0.00 5.25
1603 1688 1.078918 CTCCTCCATTCACGCTGCA 60.079 57.895 0.00 0.00 0.00 4.41
1604 1689 0.674581 CTCCTCCATTCACGCTGCAA 60.675 55.000 0.00 0.00 0.00 4.08
1605 1690 0.955428 TCCTCCATTCACGCTGCAAC 60.955 55.000 0.00 0.00 0.00 4.17
1606 1691 1.503542 CTCCATTCACGCTGCAACC 59.496 57.895 0.00 0.00 0.00 3.77
1607 1692 0.957395 CTCCATTCACGCTGCAACCT 60.957 55.000 0.00 0.00 0.00 3.50
1609 1694 0.109597 CCATTCACGCTGCAACCTTC 60.110 55.000 0.00 0.00 0.00 3.46
1625 1735 2.948979 ACCTTCGTTGCAAATCAAGTCA 59.051 40.909 0.00 0.00 34.91 3.41
1626 1736 3.243068 ACCTTCGTTGCAAATCAAGTCAC 60.243 43.478 0.00 0.00 34.91 3.67
1629 1739 2.290367 TCGTTGCAAATCAAGTCACCAG 59.710 45.455 0.00 0.00 34.91 4.00
1685 1798 0.242017 GTGGCATTGTTCTGCAGTCC 59.758 55.000 14.67 6.02 44.12 3.85
1745 1858 2.002586 CACGCCGAGATCATCAAACTT 58.997 47.619 0.00 0.00 0.00 2.66
1766 1879 5.837437 CTTCTCATCGAAGCATTAGGTACT 58.163 41.667 0.00 0.00 42.39 2.73
1771 1884 6.504398 TCATCGAAGCATTAGGTACTTACTG 58.496 40.000 0.00 0.00 41.75 2.74
1775 1888 5.163540 CGAAGCATTAGGTACTTACTGGTCT 60.164 44.000 7.37 0.27 41.75 3.85
1776 1889 6.039047 CGAAGCATTAGGTACTTACTGGTCTA 59.961 42.308 7.37 0.00 41.75 2.59
1777 1890 7.415989 CGAAGCATTAGGTACTTACTGGTCTAA 60.416 40.741 7.37 0.00 41.75 2.10
1788 1909 5.045578 ACTTACTGGTCTAATCACAAGGCAT 60.046 40.000 0.00 0.00 0.00 4.40
1796 1917 0.035152 ATCACAAGGCATCCTTCGCA 60.035 50.000 0.00 0.00 42.67 5.10
1801 1922 1.679680 CAAGGCATCCTTCGCATCAAT 59.320 47.619 0.00 0.00 42.67 2.57
1802 1923 1.602311 AGGCATCCTTCGCATCAATC 58.398 50.000 0.00 0.00 0.00 2.67
1820 1946 2.724977 TCCGAGTCTGTTGCTAACTG 57.275 50.000 0.00 0.00 0.00 3.16
1821 1947 1.272490 TCCGAGTCTGTTGCTAACTGG 59.728 52.381 0.00 0.00 0.00 4.00
1829 1955 6.534634 AGTCTGTTGCTAACTGGAGTATTTT 58.465 36.000 0.00 0.00 0.00 1.82
1835 1961 7.387948 TGTTGCTAACTGGAGTATTTTCTCTTC 59.612 37.037 0.00 0.00 35.11 2.87
1836 1962 7.246171 TGCTAACTGGAGTATTTTCTCTTCT 57.754 36.000 0.00 0.00 35.11 2.85
1838 1964 7.604164 TGCTAACTGGAGTATTTTCTCTTCTTG 59.396 37.037 0.00 0.00 35.11 3.02
1839 1965 6.809630 AACTGGAGTATTTTCTCTTCTTGC 57.190 37.500 0.00 0.00 35.11 4.01
1840 1966 5.869579 ACTGGAGTATTTTCTCTTCTTGCA 58.130 37.500 0.00 0.00 35.11 4.08
1954 2107 0.898320 CGAGAGGCTGAAGAAAGGGA 59.102 55.000 0.00 0.00 0.00 4.20
2288 2453 3.525268 AAACCAAAACCTGTGAAGCTG 57.475 42.857 0.00 0.00 0.00 4.24
2289 2454 1.402787 ACCAAAACCTGTGAAGCTGG 58.597 50.000 0.00 0.00 41.41 4.85
2320 2485 1.063806 CGTCTTTTCTCTCACTGCCG 58.936 55.000 0.00 0.00 0.00 5.69
2336 2501 2.925578 GCCGGTAGCGGTTTATTTTT 57.074 45.000 31.92 0.00 0.00 1.94
2338 2503 4.556942 GCCGGTAGCGGTTTATTTTTAT 57.443 40.909 31.92 0.00 0.00 1.40
2339 2504 4.923893 GCCGGTAGCGGTTTATTTTTATT 58.076 39.130 31.92 0.00 0.00 1.40
2340 2505 5.342433 GCCGGTAGCGGTTTATTTTTATTT 58.658 37.500 31.92 0.00 0.00 1.40
2369 2592 2.191128 TTTTGGCTCTCCTGCTCTTC 57.809 50.000 0.00 0.00 0.00 2.87
2406 2629 4.712122 AAAAACTCGTGGTGTGTTTCAT 57.288 36.364 0.00 0.00 41.92 2.57
2432 2655 1.265635 CGTTGCCTCACGAAATTCCAA 59.734 47.619 0.00 0.00 43.15 3.53
2439 2662 0.525761 CACGAAATTCCAATGGCCGT 59.474 50.000 0.00 0.00 0.00 5.68
2610 2833 1.043673 TTAGGAGAGGGAAGAGGCGC 61.044 60.000 0.00 0.00 0.00 6.53
2611 2834 2.930777 TAGGAGAGGGAAGAGGCGCC 62.931 65.000 21.89 21.89 0.00 6.53
2612 2835 3.077556 GAGAGGGAAGAGGCGCCA 61.078 66.667 31.54 0.00 0.00 5.69
2613 2836 3.080121 AGAGGGAAGAGGCGCCAG 61.080 66.667 31.54 0.00 0.00 4.85
2615 2838 4.722535 AGGGAAGAGGCGCCAGGA 62.723 66.667 31.54 0.00 0.00 3.86
2616 2839 4.168291 GGGAAGAGGCGCCAGGAG 62.168 72.222 31.54 0.00 0.00 3.69
2618 2841 3.394836 GAAGAGGCGCCAGGAGGT 61.395 66.667 31.54 6.18 37.19 3.85
2619 2842 3.378399 GAAGAGGCGCCAGGAGGTC 62.378 68.421 31.54 16.55 37.19 3.85
2634 2857 4.980805 GTCGGGCGTGCTGGTGAA 62.981 66.667 0.00 0.00 0.00 3.18
2635 2858 4.015406 TCGGGCGTGCTGGTGAAT 62.015 61.111 0.00 0.00 0.00 2.57
2636 2859 3.055719 CGGGCGTGCTGGTGAATT 61.056 61.111 0.00 0.00 0.00 2.17
2637 2860 2.625823 CGGGCGTGCTGGTGAATTT 61.626 57.895 0.00 0.00 0.00 1.82
2638 2861 1.665442 GGGCGTGCTGGTGAATTTT 59.335 52.632 0.00 0.00 0.00 1.82
2639 2862 0.033366 GGGCGTGCTGGTGAATTTTT 59.967 50.000 0.00 0.00 0.00 1.94
2640 2863 1.271102 GGGCGTGCTGGTGAATTTTTA 59.729 47.619 0.00 0.00 0.00 1.52
2641 2864 2.324860 GGCGTGCTGGTGAATTTTTAC 58.675 47.619 0.00 0.00 0.00 2.01
2642 2865 1.976045 GCGTGCTGGTGAATTTTTACG 59.024 47.619 0.00 0.00 0.00 3.18
2643 2866 2.580589 CGTGCTGGTGAATTTTTACGG 58.419 47.619 0.00 0.00 0.00 4.02
2644 2867 2.324860 GTGCTGGTGAATTTTTACGGC 58.675 47.619 0.00 0.00 0.00 5.68
2645 2868 1.271102 TGCTGGTGAATTTTTACGGCC 59.729 47.619 0.00 0.00 0.00 6.13
2646 2869 1.731098 GCTGGTGAATTTTTACGGCCG 60.731 52.381 26.86 26.86 0.00 6.13
2647 2870 1.538075 CTGGTGAATTTTTACGGCCGT 59.462 47.619 36.01 36.01 0.00 5.68
2648 2871 1.955080 TGGTGAATTTTTACGGCCGTT 59.045 42.857 38.94 18.38 0.00 4.44
2649 2872 2.361438 TGGTGAATTTTTACGGCCGTTT 59.639 40.909 38.94 24.62 0.00 3.60
2650 2873 3.181478 TGGTGAATTTTTACGGCCGTTTT 60.181 39.130 38.94 21.21 0.00 2.43
2651 2874 3.803231 GGTGAATTTTTACGGCCGTTTTT 59.197 39.130 38.94 21.56 0.00 1.94
2652 2875 4.084952 GGTGAATTTTTACGGCCGTTTTTC 60.085 41.667 38.94 27.55 0.00 2.29
2653 2876 4.503370 GTGAATTTTTACGGCCGTTTTTCA 59.497 37.500 38.94 29.49 0.00 2.69
2654 2877 4.740695 TGAATTTTTACGGCCGTTTTTCAG 59.259 37.500 38.94 1.29 0.00 3.02
2655 2878 3.779271 TTTTTACGGCCGTTTTTCAGT 57.221 38.095 38.94 11.55 0.00 3.41
2656 2879 3.779271 TTTTACGGCCGTTTTTCAGTT 57.221 38.095 38.94 10.68 0.00 3.16
2657 2880 3.337301 TTTACGGCCGTTTTTCAGTTC 57.663 42.857 38.94 0.00 0.00 3.01
2658 2881 2.243602 TACGGCCGTTTTTCAGTTCT 57.756 45.000 38.94 9.19 0.00 3.01
2659 2882 0.942252 ACGGCCGTTTTTCAGTTCTC 59.058 50.000 28.70 0.00 0.00 2.87
2660 2883 0.237498 CGGCCGTTTTTCAGTTCTCC 59.763 55.000 19.50 0.00 0.00 3.71
2661 2884 1.314730 GGCCGTTTTTCAGTTCTCCA 58.685 50.000 0.00 0.00 0.00 3.86
2662 2885 1.001706 GGCCGTTTTTCAGTTCTCCAC 60.002 52.381 0.00 0.00 0.00 4.02
2663 2886 1.001706 GCCGTTTTTCAGTTCTCCACC 60.002 52.381 0.00 0.00 0.00 4.61
2664 2887 1.263217 CCGTTTTTCAGTTCTCCACCG 59.737 52.381 0.00 0.00 0.00 4.94
2665 2888 1.263217 CGTTTTTCAGTTCTCCACCGG 59.737 52.381 0.00 0.00 0.00 5.28
2666 2889 1.607148 GTTTTTCAGTTCTCCACCGGG 59.393 52.381 6.32 0.00 0.00 5.73
2667 2890 0.109723 TTTTCAGTTCTCCACCGGGG 59.890 55.000 6.32 0.00 38.37 5.73
2668 2891 2.406002 TTTCAGTTCTCCACCGGGGC 62.406 60.000 6.32 0.00 36.21 5.80
2669 2892 4.410400 CAGTTCTCCACCGGGGCC 62.410 72.222 6.32 0.00 36.21 5.80
2680 2903 2.523412 CGGGGCCGGGAGAATCTA 60.523 66.667 2.18 0.00 35.56 1.98
2681 2904 2.574955 CGGGGCCGGGAGAATCTAG 61.575 68.421 2.18 0.00 35.56 2.43
2682 2905 1.459730 GGGGCCGGGAGAATCTAGT 60.460 63.158 2.18 0.00 33.73 2.57
2683 2906 0.178941 GGGGCCGGGAGAATCTAGTA 60.179 60.000 2.18 0.00 33.73 1.82
2684 2907 1.713297 GGGCCGGGAGAATCTAGTAA 58.287 55.000 2.18 0.00 33.73 2.24
2685 2908 2.044758 GGGCCGGGAGAATCTAGTAAA 58.955 52.381 2.18 0.00 33.73 2.01
2686 2909 2.436911 GGGCCGGGAGAATCTAGTAAAA 59.563 50.000 2.18 0.00 33.73 1.52
2687 2910 3.118149 GGGCCGGGAGAATCTAGTAAAAA 60.118 47.826 2.18 0.00 33.73 1.94
2688 2911 4.445879 GGGCCGGGAGAATCTAGTAAAAAT 60.446 45.833 2.18 0.00 33.73 1.82
2689 2912 5.221783 GGGCCGGGAGAATCTAGTAAAAATA 60.222 44.000 2.18 0.00 33.73 1.40
2690 2913 6.293698 GGCCGGGAGAATCTAGTAAAAATAA 58.706 40.000 2.18 0.00 33.73 1.40
2691 2914 6.769341 GGCCGGGAGAATCTAGTAAAAATAAA 59.231 38.462 2.18 0.00 33.73 1.40
2692 2915 7.447545 GGCCGGGAGAATCTAGTAAAAATAAAT 59.552 37.037 2.18 0.00 33.73 1.40
2693 2916 9.498176 GCCGGGAGAATCTAGTAAAAATAAATA 57.502 33.333 2.18 0.00 33.73 1.40
2723 2946 6.927933 AACCGAAGCAAAATATTTTTCTCG 57.072 33.333 19.57 19.57 0.00 4.04
2724 2947 6.009115 ACCGAAGCAAAATATTTTTCTCGT 57.991 33.333 22.17 13.78 0.00 4.18
2725 2948 6.084277 ACCGAAGCAAAATATTTTTCTCGTC 58.916 36.000 22.17 14.03 0.00 4.20
2726 2949 5.511729 CCGAAGCAAAATATTTTTCTCGTCC 59.488 40.000 22.17 10.77 0.00 4.79
2727 2950 5.511729 CGAAGCAAAATATTTTTCTCGTCCC 59.488 40.000 12.55 1.97 0.00 4.46
2728 2951 4.981794 AGCAAAATATTTTTCTCGTCCCG 58.018 39.130 10.77 0.00 0.00 5.14
2729 2952 4.457949 AGCAAAATATTTTTCTCGTCCCGT 59.542 37.500 10.77 0.00 0.00 5.28
2730 2953 5.048294 AGCAAAATATTTTTCTCGTCCCGTT 60.048 36.000 10.77 0.00 0.00 4.44
2731 2954 6.149807 AGCAAAATATTTTTCTCGTCCCGTTA 59.850 34.615 10.77 0.00 0.00 3.18
2732 2955 6.802834 GCAAAATATTTTTCTCGTCCCGTTAA 59.197 34.615 10.77 0.00 0.00 2.01
2733 2956 7.486870 GCAAAATATTTTTCTCGTCCCGTTAAT 59.513 33.333 10.77 0.00 0.00 1.40
2734 2957 9.349145 CAAAATATTTTTCTCGTCCCGTTAATT 57.651 29.630 10.77 0.00 0.00 1.40
2735 2958 9.563898 AAAATATTTTTCTCGTCCCGTTAATTC 57.436 29.630 7.64 0.00 0.00 2.17
2736 2959 7.852971 ATATTTTTCTCGTCCCGTTAATTCA 57.147 32.000 0.00 0.00 0.00 2.57
2737 2960 6.753107 ATTTTTCTCGTCCCGTTAATTCAT 57.247 33.333 0.00 0.00 0.00 2.57
2738 2961 5.789710 TTTTCTCGTCCCGTTAATTCATC 57.210 39.130 0.00 0.00 0.00 2.92
2739 2962 4.730949 TTCTCGTCCCGTTAATTCATCT 57.269 40.909 0.00 0.00 0.00 2.90
2740 2963 4.303086 TCTCGTCCCGTTAATTCATCTC 57.697 45.455 0.00 0.00 0.00 2.75
2741 2964 3.697542 TCTCGTCCCGTTAATTCATCTCA 59.302 43.478 0.00 0.00 0.00 3.27
2742 2965 4.341235 TCTCGTCCCGTTAATTCATCTCAT 59.659 41.667 0.00 0.00 0.00 2.90
2743 2966 5.018539 TCGTCCCGTTAATTCATCTCATT 57.981 39.130 0.00 0.00 0.00 2.57
2744 2967 6.040054 TCTCGTCCCGTTAATTCATCTCATTA 59.960 38.462 0.00 0.00 0.00 1.90
2745 2968 6.575267 TCGTCCCGTTAATTCATCTCATTAA 58.425 36.000 0.00 0.00 0.00 1.40
2746 2969 7.214381 TCGTCCCGTTAATTCATCTCATTAAT 58.786 34.615 0.00 0.00 30.62 1.40
2747 2970 7.713507 TCGTCCCGTTAATTCATCTCATTAATT 59.286 33.333 0.00 0.00 30.62 1.40
2748 2971 8.342634 CGTCCCGTTAATTCATCTCATTAATTT 58.657 33.333 0.00 0.00 30.62 1.82
2774 2997 7.308435 AGAAGATGTAGAATTTTTCTTTGCCG 58.692 34.615 0.00 0.00 41.14 5.69
2775 2998 5.402398 AGATGTAGAATTTTTCTTTGCCGC 58.598 37.500 0.00 0.00 41.14 6.53
2776 2999 4.846779 TGTAGAATTTTTCTTTGCCGCT 57.153 36.364 0.00 0.00 41.14 5.52
2777 3000 5.950758 TGTAGAATTTTTCTTTGCCGCTA 57.049 34.783 0.00 0.00 41.14 4.26
2778 3001 6.320494 TGTAGAATTTTTCTTTGCCGCTAA 57.680 33.333 0.00 0.00 41.14 3.09
2779 3002 6.378582 TGTAGAATTTTTCTTTGCCGCTAAG 58.621 36.000 8.12 8.12 41.14 2.18
2780 3003 5.705609 AGAATTTTTCTTTGCCGCTAAGA 57.294 34.783 12.47 12.47 36.36 2.10
2781 3004 6.272822 AGAATTTTTCTTTGCCGCTAAGAT 57.727 33.333 16.40 3.20 36.36 2.40
2782 3005 6.095377 AGAATTTTTCTTTGCCGCTAAGATG 58.905 36.000 16.40 0.00 36.36 2.90
2783 3006 4.846779 TTTTTCTTTGCCGCTAAGATGT 57.153 36.364 16.40 0.00 32.09 3.06
2784 3007 5.950758 TTTTTCTTTGCCGCTAAGATGTA 57.049 34.783 16.40 1.41 32.09 2.29
2785 3008 5.545658 TTTTCTTTGCCGCTAAGATGTAG 57.454 39.130 16.40 0.00 32.09 2.74
2786 3009 4.465632 TTCTTTGCCGCTAAGATGTAGA 57.534 40.909 16.40 0.74 32.09 2.59
2787 3010 4.465632 TCTTTGCCGCTAAGATGTAGAA 57.534 40.909 12.47 0.00 0.00 2.10
2788 3011 5.023533 TCTTTGCCGCTAAGATGTAGAAT 57.976 39.130 12.47 0.00 0.00 2.40
2789 3012 5.428253 TCTTTGCCGCTAAGATGTAGAATT 58.572 37.500 12.47 0.00 0.00 2.17
2790 3013 5.294306 TCTTTGCCGCTAAGATGTAGAATTG 59.706 40.000 12.47 0.00 0.00 2.32
2791 3014 4.137116 TGCCGCTAAGATGTAGAATTGT 57.863 40.909 0.00 0.00 0.00 2.71
2792 3015 4.119862 TGCCGCTAAGATGTAGAATTGTC 58.880 43.478 0.00 0.00 0.00 3.18
2793 3016 4.141937 TGCCGCTAAGATGTAGAATTGTCT 60.142 41.667 0.00 0.00 37.95 3.41
2794 3017 5.068591 TGCCGCTAAGATGTAGAATTGTCTA 59.931 40.000 0.00 0.00 35.12 2.59
2795 3018 5.631512 GCCGCTAAGATGTAGAATTGTCTAG 59.368 44.000 0.00 0.00 37.02 2.43
2796 3019 6.736243 GCCGCTAAGATGTAGAATTGTCTAGT 60.736 42.308 0.00 0.00 37.02 2.57
2797 3020 7.203910 CCGCTAAGATGTAGAATTGTCTAGTT 58.796 38.462 0.00 0.00 37.02 2.24
2798 3021 8.350722 CCGCTAAGATGTAGAATTGTCTAGTTA 58.649 37.037 0.00 0.00 37.02 2.24
2799 3022 9.731819 CGCTAAGATGTAGAATTGTCTAGTTAA 57.268 33.333 0.00 0.00 37.02 2.01
2815 3038 9.042008 TGTCTAGTTAATTAGCGAAAATCATCC 57.958 33.333 0.24 0.00 0.00 3.51
2816 3039 8.215132 GTCTAGTTAATTAGCGAAAATCATCCG 58.785 37.037 0.24 0.00 0.00 4.18
2817 3040 6.920569 AGTTAATTAGCGAAAATCATCCGT 57.079 33.333 0.00 0.00 0.00 4.69
2818 3041 7.316544 AGTTAATTAGCGAAAATCATCCGTT 57.683 32.000 0.00 0.00 0.00 4.44
2819 3042 7.186804 AGTTAATTAGCGAAAATCATCCGTTG 58.813 34.615 0.00 0.00 0.00 4.10
2820 3043 3.398954 TTAGCGAAAATCATCCGTTGC 57.601 42.857 0.00 0.00 0.00 4.17
2821 3044 1.164411 AGCGAAAATCATCCGTTGCA 58.836 45.000 0.00 0.00 0.00 4.08
2822 3045 1.539388 AGCGAAAATCATCCGTTGCAA 59.461 42.857 0.00 0.00 0.00 4.08
2823 3046 1.648681 GCGAAAATCATCCGTTGCAAC 59.351 47.619 19.89 19.89 0.00 4.17
2824 3047 2.920227 GCGAAAATCATCCGTTGCAACA 60.920 45.455 28.01 11.20 0.00 3.33
2825 3048 2.910482 CGAAAATCATCCGTTGCAACAG 59.090 45.455 28.01 18.12 0.00 3.16
2826 3049 2.352503 AAATCATCCGTTGCAACAGC 57.647 45.000 28.01 2.77 0.00 4.40
2827 3050 0.527565 AATCATCCGTTGCAACAGCC 59.472 50.000 28.01 2.38 0.00 4.85
2828 3051 1.315257 ATCATCCGTTGCAACAGCCC 61.315 55.000 28.01 1.98 0.00 5.19
2829 3052 2.115052 ATCCGTTGCAACAGCCCA 59.885 55.556 28.01 7.77 0.00 5.36
2830 3053 1.304381 ATCCGTTGCAACAGCCCAT 60.304 52.632 28.01 9.66 0.00 4.00
2831 3054 0.899717 ATCCGTTGCAACAGCCCATT 60.900 50.000 28.01 3.66 0.00 3.16
2832 3055 1.112315 TCCGTTGCAACAGCCCATTT 61.112 50.000 28.01 0.00 0.00 2.32
2833 3056 0.600557 CCGTTGCAACAGCCCATTTA 59.399 50.000 28.01 0.00 0.00 1.40
2834 3057 1.668628 CCGTTGCAACAGCCCATTTAC 60.669 52.381 28.01 0.00 0.00 2.01
2835 3058 1.696988 GTTGCAACAGCCCATTTACG 58.303 50.000 24.52 0.00 0.00 3.18
2836 3059 1.268352 GTTGCAACAGCCCATTTACGA 59.732 47.619 24.52 0.00 0.00 3.43
2842 3065 4.380023 GCAACAGCCCATTTACGATAACAA 60.380 41.667 0.00 0.00 0.00 2.83
2843 3066 5.331902 CAACAGCCCATTTACGATAACAAG 58.668 41.667 0.00 0.00 0.00 3.16
2852 3075 0.402504 ACGATAACAAGGGCCAACCA 59.597 50.000 6.18 0.00 43.89 3.67
2862 3085 1.000359 GGCCAACCAAGCTACCCAT 60.000 57.895 0.00 0.00 35.26 4.00
2865 3088 0.323725 CCAACCAAGCTACCCATGCT 60.324 55.000 0.00 0.00 43.32 3.79
2866 3089 0.813184 CAACCAAGCTACCCATGCTG 59.187 55.000 0.00 0.00 41.03 4.41
2871 3106 1.741706 CAAGCTACCCATGCTGTTGAG 59.258 52.381 0.00 0.00 41.03 3.02
2894 3129 5.582665 AGAAGAAAGCATTGTCGAGGTTATC 59.417 40.000 0.00 0.00 0.00 1.75
2921 3156 5.495926 ACCAATATCATCATCACTCCTCC 57.504 43.478 0.00 0.00 0.00 4.30
2924 3159 1.417288 ATCATCATCACTCCTCCGCA 58.583 50.000 0.00 0.00 0.00 5.69
2964 3199 1.225376 GCATTGACGACCACCAACGA 61.225 55.000 0.00 0.00 0.00 3.85
2976 3211 2.226330 CACCAACGAAACCCTCATCAA 58.774 47.619 0.00 0.00 0.00 2.57
2982 3217 3.551846 ACGAAACCCTCATCAAACAGTT 58.448 40.909 0.00 0.00 0.00 3.16
2983 3218 3.315191 ACGAAACCCTCATCAAACAGTTG 59.685 43.478 0.00 0.00 35.95 3.16
2989 3224 3.213506 CCTCATCAAACAGTTGACCACA 58.786 45.455 0.00 0.00 46.40 4.17
3002 3237 3.896133 CCACATGCGCTGGCCATC 61.896 66.667 5.51 0.00 38.85 3.51
3047 3282 4.828939 TGATGAACCTTGCATGAGAAAAGT 59.171 37.500 0.00 0.00 0.00 2.66
3056 3291 2.352127 GCATGAGAAAAGTGTTGAGCCC 60.352 50.000 0.00 0.00 0.00 5.19
3065 3300 2.904866 GTTGAGCCCGCACCAACA 60.905 61.111 15.48 0.00 39.74 3.33
3083 3319 2.555547 AAGCCCTGCAAGCGAACAC 61.556 57.895 2.93 0.00 34.64 3.32
3084 3320 2.965716 AAGCCCTGCAAGCGAACACT 62.966 55.000 2.93 0.00 34.64 3.55
3091 3327 0.368227 GCAAGCGAACACTGATCTCG 59.632 55.000 0.00 0.00 35.70 4.04
3104 3340 0.101399 GATCTCGTGCCATCGTCACT 59.899 55.000 0.00 0.00 32.54 3.41
3105 3341 0.101399 ATCTCGTGCCATCGTCACTC 59.899 55.000 0.00 0.00 32.54 3.51
3125 3361 2.890847 CTAACGCACCTCCTCCGCAG 62.891 65.000 0.00 0.00 0.00 5.18
3133 3369 2.759973 TCCTCCGCAGCTCCGATT 60.760 61.111 0.00 0.00 0.00 3.34
3145 3381 1.939838 GCTCCGATTCCACAAAGACGT 60.940 52.381 0.00 0.00 0.00 4.34
3155 3391 2.079158 CACAAAGACGTGATGAGGCAT 58.921 47.619 0.00 0.00 39.34 4.40
3165 3401 1.487976 TGATGAGGCATGAGAACTCCC 59.512 52.381 0.00 0.00 0.00 4.30
3166 3402 1.767681 GATGAGGCATGAGAACTCCCT 59.232 52.381 0.00 0.00 0.00 4.20
3176 3412 3.242867 TGAGAACTCCCTGAACACATCT 58.757 45.455 0.00 0.00 0.00 2.90
3201 3437 1.257055 TACCGACTACCAAACCCCCG 61.257 60.000 0.00 0.00 0.00 5.73
3211 3447 2.457323 AAACCCCCGCCTCAACTGA 61.457 57.895 0.00 0.00 0.00 3.41
3239 3475 1.416401 ACCACAACCATCGACAAGTCT 59.584 47.619 0.00 0.00 0.00 3.24
3244 3480 3.244561 ACAACCATCGACAAGTCTCCAAT 60.245 43.478 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.078411 TGCTCTCTCCACATCTTTTCTAC 57.922 43.478 0.00 0.00 0.00 2.59
46 47 5.116180 CGGACCTCTCACAATAGCAAATTA 58.884 41.667 0.00 0.00 0.00 1.40
66 67 3.374042 TGATCCCAAAATTTAGCCGGA 57.626 42.857 5.05 0.00 0.00 5.14
95 97 2.042686 AGCGTGCATGATGTACCAAT 57.957 45.000 10.93 0.00 28.65 3.16
322 328 6.805271 CGAATGCAGAAATCATCTTCTTTGTT 59.195 34.615 0.00 0.00 35.73 2.83
330 336 5.356190 ACAATGTCGAATGCAGAAATCATCT 59.644 36.000 0.00 0.00 39.68 2.90
498 518 4.034626 GCACGCACAAACCACATATACATA 59.965 41.667 0.00 0.00 0.00 2.29
682 710 3.330267 AGAAACTCTGAAACGATGCCTC 58.670 45.455 0.00 0.00 0.00 4.70
735 769 2.569812 GCGCGCGTACTTTTTCCG 60.570 61.111 32.35 0.00 0.00 4.30
753 787 0.598158 GTTGACGTGTTAGTGCCCGA 60.598 55.000 0.00 0.00 0.00 5.14
816 854 0.250295 CGTTCCTGTGGCTGGAGAAA 60.250 55.000 0.00 0.00 33.24 2.52
843 881 1.308998 GACGATTCCAATGGCCGAAT 58.691 50.000 13.47 0.00 0.00 3.34
844 882 0.746563 GGACGATTCCAATGGCCGAA 60.747 55.000 13.47 0.00 42.30 4.30
845 883 1.153249 GGACGATTCCAATGGCCGA 60.153 57.895 13.47 0.00 42.30 5.54
846 884 2.534019 CGGACGATTCCAATGGCCG 61.534 63.158 0.00 0.00 43.00 6.13
847 885 2.834618 GCGGACGATTCCAATGGCC 61.835 63.158 0.00 0.00 43.00 5.36
922 969 2.666596 GAATAGACGGGCAGGGCAGG 62.667 65.000 0.00 0.00 0.00 4.85
923 970 1.227674 GAATAGACGGGCAGGGCAG 60.228 63.158 0.00 0.00 0.00 4.85
924 971 1.271840 AAGAATAGACGGGCAGGGCA 61.272 55.000 0.00 0.00 0.00 5.36
925 972 0.815615 CAAGAATAGACGGGCAGGGC 60.816 60.000 0.00 0.00 0.00 5.19
926 973 0.179045 CCAAGAATAGACGGGCAGGG 60.179 60.000 0.00 0.00 0.00 4.45
927 974 0.830648 TCCAAGAATAGACGGGCAGG 59.169 55.000 0.00 0.00 0.00 4.85
928 975 2.280628 GTTCCAAGAATAGACGGGCAG 58.719 52.381 0.00 0.00 0.00 4.85
929 976 1.065709 GGTTCCAAGAATAGACGGGCA 60.066 52.381 0.00 0.00 0.00 5.36
930 977 1.209747 AGGTTCCAAGAATAGACGGGC 59.790 52.381 0.00 0.00 0.00 6.13
1020 1072 1.294780 GTGCAGAGGACCTGTGGAG 59.705 63.158 19.62 0.00 44.71 3.86
1023 1075 0.320247 GACTGTGCAGAGGACCTGTG 60.320 60.000 16.19 14.33 44.71 3.66
1161 1216 0.317160 CGGCATACGGCTATCCTTGA 59.683 55.000 0.00 0.00 44.01 3.02
1207 1292 1.896465 AGGAACGGGAACTTGAGAGAG 59.104 52.381 0.00 0.00 0.00 3.20
1249 1334 4.838152 GCGCGCCTGATCTTCCCA 62.838 66.667 23.24 0.00 0.00 4.37
1310 1395 3.314331 CTCCTCCGTGGTGCTGGT 61.314 66.667 0.00 0.00 37.07 4.00
1552 1637 6.750963 AGCTTAAGTTAATTACGTCGAGGAAG 59.249 38.462 12.85 2.14 0.00 3.46
1561 1646 8.705048 AGGAAGAAGAGCTTAAGTTAATTACG 57.295 34.615 4.02 0.00 36.83 3.18
1571 1656 3.791320 TGGAGGAGGAAGAAGAGCTTAA 58.209 45.455 0.00 0.00 36.83 1.85
1577 1662 2.497675 CGTGAATGGAGGAGGAAGAAGA 59.502 50.000 0.00 0.00 0.00 2.87
1585 1670 0.674581 TTGCAGCGTGAATGGAGGAG 60.675 55.000 0.00 0.00 0.00 3.69
1592 1677 0.884704 ACGAAGGTTGCAGCGTGAAT 60.885 50.000 0.00 0.00 35.44 2.57
1593 1678 1.092921 AACGAAGGTTGCAGCGTGAA 61.093 50.000 0.00 0.00 37.03 3.18
1596 1681 3.022287 CAACGAAGGTTGCAGCGT 58.978 55.556 0.00 0.00 46.22 5.07
1603 1688 3.380004 TGACTTGATTTGCAACGAAGGTT 59.620 39.130 0.00 0.00 36.63 3.50
1604 1689 2.948979 TGACTTGATTTGCAACGAAGGT 59.051 40.909 0.00 0.00 31.96 3.50
1605 1690 3.300009 GTGACTTGATTTGCAACGAAGG 58.700 45.455 0.00 0.00 31.96 3.46
1606 1691 3.243035 TGGTGACTTGATTTGCAACGAAG 60.243 43.478 0.00 4.17 31.96 3.79
1607 1692 2.685388 TGGTGACTTGATTTGCAACGAA 59.315 40.909 0.00 0.00 31.96 3.85
1609 1694 2.290367 TCTGGTGACTTGATTTGCAACG 59.710 45.455 0.00 0.00 31.96 4.10
1625 1735 5.684704 TGAAAAGTTTGATCAGTCTCTGGT 58.315 37.500 0.00 0.00 31.51 4.00
1626 1736 6.609533 CATGAAAAGTTTGATCAGTCTCTGG 58.390 40.000 0.00 0.00 31.51 3.86
1629 1739 5.084722 CGCATGAAAAGTTTGATCAGTCTC 58.915 41.667 0.00 0.00 0.00 3.36
1685 1798 1.151668 CACGGAACTGCAAGGAGAAG 58.848 55.000 0.00 0.00 39.30 2.85
1745 1858 5.854010 AAGTACCTAATGCTTCGATGAGA 57.146 39.130 1.89 0.00 0.00 3.27
1766 1879 4.901197 TGCCTTGTGATTAGACCAGTAA 57.099 40.909 0.00 0.00 0.00 2.24
1771 1884 3.567478 AGGATGCCTTGTGATTAGACC 57.433 47.619 0.00 0.00 0.00 3.85
1775 1888 2.288666 GCGAAGGATGCCTTGTGATTA 58.711 47.619 2.98 0.00 44.82 1.75
1776 1889 1.098050 GCGAAGGATGCCTTGTGATT 58.902 50.000 2.98 0.00 44.82 2.57
1777 1890 0.035152 TGCGAAGGATGCCTTGTGAT 60.035 50.000 2.98 0.00 44.82 3.06
1796 1917 4.081420 AGTTAGCAACAGACTCGGATTGAT 60.081 41.667 0.00 0.00 0.00 2.57
1801 1922 1.272490 CCAGTTAGCAACAGACTCGGA 59.728 52.381 0.00 0.00 0.00 4.55
1802 1923 1.272490 TCCAGTTAGCAACAGACTCGG 59.728 52.381 0.00 0.00 0.00 4.63
1820 1946 5.934625 TCTGTGCAAGAAGAGAAAATACTCC 59.065 40.000 0.00 0.00 37.60 3.85
1821 1947 6.425114 TGTCTGTGCAAGAAGAGAAAATACTC 59.575 38.462 0.00 0.00 36.40 2.59
1829 1955 3.758755 ACATGTCTGTGCAAGAAGAGA 57.241 42.857 0.00 0.00 36.40 3.10
1835 1961 4.668431 CGATCAGAAACATGTCTGTGCAAG 60.668 45.833 12.77 0.00 44.56 4.01
1836 1962 3.187022 CGATCAGAAACATGTCTGTGCAA 59.813 43.478 12.77 0.00 44.56 4.08
1838 1964 2.094894 CCGATCAGAAACATGTCTGTGC 59.905 50.000 12.77 6.81 44.56 4.57
1839 1965 2.094894 GCCGATCAGAAACATGTCTGTG 59.905 50.000 12.77 2.36 44.56 3.66
1840 1966 2.289631 TGCCGATCAGAAACATGTCTGT 60.290 45.455 12.77 2.98 44.56 3.41
1954 2107 2.827642 GACGGACCGGATCCTCGT 60.828 66.667 20.00 13.72 46.69 4.18
1973 2126 2.731691 GAACCTCGACTTGGCCTGCA 62.732 60.000 3.32 0.00 0.00 4.41
2164 2317 2.049433 CGTTCACGCGAAGGAGGT 60.049 61.111 15.93 0.00 38.95 3.85
2185 2338 3.646611 CATGTTTTGCAGTGACATGGA 57.353 42.857 21.77 0.00 44.19 3.41
2233 2398 9.974750 GTAAGTACTATTTCTTGCTTTGCTAAG 57.025 33.333 3.31 3.31 34.36 2.18
2288 2453 2.863401 AAAGACGAAAAAGGCACACC 57.137 45.000 0.00 0.00 0.00 4.16
2289 2454 4.028852 AGAAAAGACGAAAAAGGCACAC 57.971 40.909 0.00 0.00 0.00 3.82
2349 2514 2.107204 AGAAGAGCAGGAGAGCCAAAAA 59.893 45.455 0.00 0.00 36.29 1.94
2350 2515 1.701847 AGAAGAGCAGGAGAGCCAAAA 59.298 47.619 0.00 0.00 36.29 2.44
2352 2517 0.612229 CAGAAGAGCAGGAGAGCCAA 59.388 55.000 0.00 0.00 36.29 4.52
2354 2519 0.108233 CACAGAAGAGCAGGAGAGCC 60.108 60.000 0.00 0.00 34.23 4.70
2355 2520 0.894141 TCACAGAAGAGCAGGAGAGC 59.106 55.000 0.00 0.00 0.00 4.09
2361 2584 2.740981 GTGGTTGATCACAGAAGAGCAG 59.259 50.000 0.00 0.00 35.10 4.24
2369 2592 5.418310 AGTTTTTACGTGGTTGATCACAG 57.582 39.130 0.00 0.00 37.50 3.66
2406 2629 1.370609 TTCGTGAGGCAACGTGAAAA 58.629 45.000 11.67 0.00 43.96 2.29
2439 2662 2.264480 CCAGTCGATGCCGGAACA 59.736 61.111 5.05 0.00 36.24 3.18
2473 2696 3.093278 CCATCGAAAGCACTCGGC 58.907 61.111 7.50 0.00 45.30 5.54
2474 2697 2.802667 CGCCATCGAAAGCACTCGG 61.803 63.158 10.25 0.00 39.35 4.63
2475 2698 1.805539 TCGCCATCGAAAGCACTCG 60.806 57.895 10.25 1.30 42.44 4.18
2476 2699 4.185413 TCGCCATCGAAAGCACTC 57.815 55.556 10.25 0.00 42.44 3.51
2618 2841 3.545124 AATTCACCAGCACGCCCGA 62.545 57.895 0.00 0.00 0.00 5.14
2619 2842 2.141122 AAAATTCACCAGCACGCCCG 62.141 55.000 0.00 0.00 0.00 6.13
2620 2843 0.033366 AAAAATTCACCAGCACGCCC 59.967 50.000 0.00 0.00 0.00 6.13
2622 2845 1.976045 CGTAAAAATTCACCAGCACGC 59.024 47.619 0.00 0.00 0.00 5.34
2623 2846 2.580589 CCGTAAAAATTCACCAGCACG 58.419 47.619 0.00 0.00 0.00 5.34
2624 2847 2.324860 GCCGTAAAAATTCACCAGCAC 58.675 47.619 0.00 0.00 0.00 4.40
2625 2848 1.271102 GGCCGTAAAAATTCACCAGCA 59.729 47.619 0.00 0.00 0.00 4.41
2626 2849 1.731098 CGGCCGTAAAAATTCACCAGC 60.731 52.381 19.50 0.00 0.00 4.85
2627 2850 1.538075 ACGGCCGTAAAAATTCACCAG 59.462 47.619 33.34 0.00 0.00 4.00
2628 2851 1.606903 ACGGCCGTAAAAATTCACCA 58.393 45.000 33.34 0.00 0.00 4.17
2630 2853 4.503370 TGAAAAACGGCCGTAAAAATTCAC 59.497 37.500 34.44 17.81 0.00 3.18
2631 2854 4.679662 TGAAAAACGGCCGTAAAAATTCA 58.320 34.783 34.44 29.14 0.00 2.57
2632 2855 4.741185 ACTGAAAAACGGCCGTAAAAATTC 59.259 37.500 34.44 27.16 0.00 2.17
2633 2856 4.684877 ACTGAAAAACGGCCGTAAAAATT 58.315 34.783 34.44 19.50 0.00 1.82
2634 2857 4.310357 ACTGAAAAACGGCCGTAAAAAT 57.690 36.364 34.44 13.45 0.00 1.82
2635 2858 3.779271 ACTGAAAAACGGCCGTAAAAA 57.221 38.095 34.44 15.49 0.00 1.94
2636 2859 3.377798 AGAACTGAAAAACGGCCGTAAAA 59.622 39.130 34.44 14.73 0.00 1.52
2637 2860 2.944349 AGAACTGAAAAACGGCCGTAAA 59.056 40.909 34.44 14.34 0.00 2.01
2638 2861 2.545106 GAGAACTGAAAAACGGCCGTAA 59.455 45.455 34.44 13.97 0.00 3.18
2639 2862 2.137523 GAGAACTGAAAAACGGCCGTA 58.862 47.619 34.44 15.21 0.00 4.02
2640 2863 0.942252 GAGAACTGAAAAACGGCCGT 59.058 50.000 28.70 28.70 0.00 5.68
2641 2864 0.237498 GGAGAACTGAAAAACGGCCG 59.763 55.000 26.86 26.86 0.00 6.13
2642 2865 1.001706 GTGGAGAACTGAAAAACGGCC 60.002 52.381 0.00 0.00 0.00 6.13
2643 2866 1.001706 GGTGGAGAACTGAAAAACGGC 60.002 52.381 0.00 0.00 0.00 5.68
2644 2867 1.263217 CGGTGGAGAACTGAAAAACGG 59.737 52.381 0.00 0.00 37.33 4.44
2645 2868 1.263217 CCGGTGGAGAACTGAAAAACG 59.737 52.381 0.00 0.00 37.33 3.60
2646 2869 1.607148 CCCGGTGGAGAACTGAAAAAC 59.393 52.381 0.00 0.00 37.33 2.43
2647 2870 1.477923 CCCCGGTGGAGAACTGAAAAA 60.478 52.381 0.00 0.00 37.33 1.94
2648 2871 0.109723 CCCCGGTGGAGAACTGAAAA 59.890 55.000 0.00 0.00 37.33 2.29
2649 2872 1.758592 CCCCGGTGGAGAACTGAAA 59.241 57.895 0.00 0.00 37.33 2.69
2650 2873 2.890766 GCCCCGGTGGAGAACTGAA 61.891 63.158 12.67 0.00 37.33 3.02
2651 2874 3.319198 GCCCCGGTGGAGAACTGA 61.319 66.667 12.67 0.00 37.33 3.41
2652 2875 4.410400 GGCCCCGGTGGAGAACTG 62.410 72.222 12.67 0.00 35.39 3.16
2663 2886 2.523412 TAGATTCTCCCGGCCCCG 60.523 66.667 0.00 0.00 39.44 5.73
2664 2887 0.178941 TACTAGATTCTCCCGGCCCC 60.179 60.000 0.00 0.00 0.00 5.80
2665 2888 1.713297 TTACTAGATTCTCCCGGCCC 58.287 55.000 0.00 0.00 0.00 5.80
2666 2889 3.832615 TTTTACTAGATTCTCCCGGCC 57.167 47.619 0.00 0.00 0.00 6.13
2667 2890 7.797038 TTTATTTTTACTAGATTCTCCCGGC 57.203 36.000 0.00 0.00 0.00 6.13
2697 2920 8.907685 CGAGAAAAATATTTTGCTTCGGTTTAA 58.092 29.630 20.28 0.00 36.18 1.52
2698 2921 8.077386 ACGAGAAAAATATTTTGCTTCGGTTTA 58.923 29.630 26.72 0.00 36.18 2.01
2699 2922 6.921307 ACGAGAAAAATATTTTGCTTCGGTTT 59.079 30.769 26.72 14.63 36.18 3.27
2700 2923 6.443792 ACGAGAAAAATATTTTGCTTCGGTT 58.556 32.000 26.72 15.06 36.18 4.44
2701 2924 6.009115 ACGAGAAAAATATTTTGCTTCGGT 57.991 33.333 26.72 20.17 36.18 4.69
2702 2925 5.511729 GGACGAGAAAAATATTTTGCTTCGG 59.488 40.000 26.72 19.76 36.18 4.30
2703 2926 5.511729 GGGACGAGAAAAATATTTTGCTTCG 59.488 40.000 20.28 22.69 36.18 3.79
2704 2927 6.871044 GGGACGAGAAAAATATTTTGCTTC 57.129 37.500 20.28 14.93 36.18 3.86
2748 2971 8.450964 CGGCAAAGAAAAATTCTACATCTTCTA 58.549 33.333 0.00 0.00 39.61 2.10
2749 2972 7.308435 CGGCAAAGAAAAATTCTACATCTTCT 58.692 34.615 0.00 0.00 39.61 2.85
2750 2973 6.033937 GCGGCAAAGAAAAATTCTACATCTTC 59.966 38.462 0.00 0.00 39.61 2.87
2751 2974 5.863935 GCGGCAAAGAAAAATTCTACATCTT 59.136 36.000 0.00 0.00 39.61 2.40
2752 2975 5.183904 AGCGGCAAAGAAAAATTCTACATCT 59.816 36.000 1.45 0.00 39.61 2.90
2753 2976 5.402398 AGCGGCAAAGAAAAATTCTACATC 58.598 37.500 1.45 0.00 39.61 3.06
2754 2977 5.391312 AGCGGCAAAGAAAAATTCTACAT 57.609 34.783 1.45 0.00 39.61 2.29
2755 2978 4.846779 AGCGGCAAAGAAAAATTCTACA 57.153 36.364 1.45 0.00 39.61 2.74
2756 2979 6.608610 TCTTAGCGGCAAAGAAAAATTCTAC 58.391 36.000 1.45 0.00 39.61 2.59
2757 2980 6.811253 TCTTAGCGGCAAAGAAAAATTCTA 57.189 33.333 1.45 0.00 39.61 2.10
2758 2981 5.705609 TCTTAGCGGCAAAGAAAAATTCT 57.294 34.783 1.45 0.00 43.15 2.40
2759 2982 5.863935 ACATCTTAGCGGCAAAGAAAAATTC 59.136 36.000 1.45 0.00 36.60 2.17
2760 2983 5.783111 ACATCTTAGCGGCAAAGAAAAATT 58.217 33.333 1.45 0.00 36.60 1.82
2761 2984 5.391312 ACATCTTAGCGGCAAAGAAAAAT 57.609 34.783 1.45 0.00 36.60 1.82
2762 2985 4.846779 ACATCTTAGCGGCAAAGAAAAA 57.153 36.364 1.45 0.00 36.60 1.94
2763 2986 5.242434 TCTACATCTTAGCGGCAAAGAAAA 58.758 37.500 1.45 0.00 36.60 2.29
2764 2987 4.827692 TCTACATCTTAGCGGCAAAGAAA 58.172 39.130 1.45 0.00 36.60 2.52
2765 2988 4.465632 TCTACATCTTAGCGGCAAAGAA 57.534 40.909 1.45 0.00 36.60 2.52
2766 2989 4.465632 TTCTACATCTTAGCGGCAAAGA 57.534 40.909 1.45 0.00 37.38 2.52
2767 2990 5.065218 ACAATTCTACATCTTAGCGGCAAAG 59.935 40.000 1.45 0.00 0.00 2.77
2768 2991 4.941263 ACAATTCTACATCTTAGCGGCAAA 59.059 37.500 1.45 0.00 0.00 3.68
2769 2992 4.513442 ACAATTCTACATCTTAGCGGCAA 58.487 39.130 1.45 0.00 0.00 4.52
2770 2993 4.119862 GACAATTCTACATCTTAGCGGCA 58.880 43.478 1.45 0.00 0.00 5.69
2771 2994 4.372656 AGACAATTCTACATCTTAGCGGC 58.627 43.478 0.00 0.00 0.00 6.53
2772 2995 6.740110 ACTAGACAATTCTACATCTTAGCGG 58.260 40.000 0.00 0.00 32.75 5.52
2773 2996 9.731819 TTAACTAGACAATTCTACATCTTAGCG 57.268 33.333 0.00 0.00 32.75 4.26
2789 3012 9.042008 GGATGATTTTCGCTAATTAACTAGACA 57.958 33.333 0.00 0.00 0.00 3.41
2790 3013 8.215132 CGGATGATTTTCGCTAATTAACTAGAC 58.785 37.037 0.00 0.00 0.00 2.59
2791 3014 7.924412 ACGGATGATTTTCGCTAATTAACTAGA 59.076 33.333 0.00 0.00 0.00 2.43
2792 3015 8.073355 ACGGATGATTTTCGCTAATTAACTAG 57.927 34.615 0.00 0.00 0.00 2.57
2793 3016 8.332464 CAACGGATGATTTTCGCTAATTAACTA 58.668 33.333 0.00 0.00 0.00 2.24
2794 3017 6.920569 ACGGATGATTTTCGCTAATTAACT 57.079 33.333 0.00 0.00 0.00 2.24
2795 3018 6.075572 GCAACGGATGATTTTCGCTAATTAAC 60.076 38.462 0.00 0.00 0.00 2.01
2796 3019 5.968848 GCAACGGATGATTTTCGCTAATTAA 59.031 36.000 0.00 0.00 0.00 1.40
2797 3020 5.065346 TGCAACGGATGATTTTCGCTAATTA 59.935 36.000 0.00 0.00 0.00 1.40
2798 3021 4.142491 TGCAACGGATGATTTTCGCTAATT 60.142 37.500 0.00 0.00 0.00 1.40
2799 3022 3.376859 TGCAACGGATGATTTTCGCTAAT 59.623 39.130 0.00 0.00 0.00 1.73
2800 3023 2.744741 TGCAACGGATGATTTTCGCTAA 59.255 40.909 0.00 0.00 0.00 3.09
2801 3024 2.351455 TGCAACGGATGATTTTCGCTA 58.649 42.857 0.00 0.00 0.00 4.26
2802 3025 1.164411 TGCAACGGATGATTTTCGCT 58.836 45.000 0.00 0.00 0.00 4.93
2803 3026 1.648681 GTTGCAACGGATGATTTTCGC 59.351 47.619 14.90 0.00 0.00 4.70
2804 3027 2.910482 CTGTTGCAACGGATGATTTTCG 59.090 45.455 30.72 1.37 37.48 3.46
2805 3028 2.663119 GCTGTTGCAACGGATGATTTTC 59.337 45.455 36.72 15.97 37.48 2.29
2806 3029 2.610232 GGCTGTTGCAACGGATGATTTT 60.610 45.455 36.72 0.00 41.91 1.82
2807 3030 1.067635 GGCTGTTGCAACGGATGATTT 60.068 47.619 36.72 0.00 41.91 2.17
2808 3031 0.527565 GGCTGTTGCAACGGATGATT 59.472 50.000 36.72 0.00 41.91 2.57
2809 3032 1.315257 GGGCTGTTGCAACGGATGAT 61.315 55.000 36.72 0.00 41.91 2.45
2810 3033 1.971167 GGGCTGTTGCAACGGATGA 60.971 57.895 36.72 13.92 41.91 2.92
2811 3034 1.597797 ATGGGCTGTTGCAACGGATG 61.598 55.000 36.72 21.04 41.91 3.51
2812 3035 0.899717 AATGGGCTGTTGCAACGGAT 60.900 50.000 36.72 21.10 41.91 4.18
2813 3036 1.112315 AAATGGGCTGTTGCAACGGA 61.112 50.000 36.72 19.84 41.91 4.69
2814 3037 0.600557 TAAATGGGCTGTTGCAACGG 59.399 50.000 30.22 30.22 41.91 4.44
2815 3038 1.696988 GTAAATGGGCTGTTGCAACG 58.303 50.000 23.79 18.61 41.91 4.10
2816 3039 1.268352 TCGTAAATGGGCTGTTGCAAC 59.732 47.619 22.83 22.83 41.91 4.17
2817 3040 1.610363 TCGTAAATGGGCTGTTGCAA 58.390 45.000 0.00 0.00 41.91 4.08
2818 3041 1.832883 ATCGTAAATGGGCTGTTGCA 58.167 45.000 0.00 0.00 41.91 4.08
2819 3042 3.127895 TGTTATCGTAAATGGGCTGTTGC 59.872 43.478 0.00 0.00 38.76 4.17
2820 3043 4.955925 TGTTATCGTAAATGGGCTGTTG 57.044 40.909 0.00 0.00 0.00 3.33
2821 3044 4.398044 CCTTGTTATCGTAAATGGGCTGTT 59.602 41.667 0.00 0.00 0.00 3.16
2822 3045 3.945285 CCTTGTTATCGTAAATGGGCTGT 59.055 43.478 0.00 0.00 0.00 4.40
2823 3046 3.315191 CCCTTGTTATCGTAAATGGGCTG 59.685 47.826 0.00 0.00 0.00 4.85
2824 3047 3.551846 CCCTTGTTATCGTAAATGGGCT 58.448 45.455 0.00 0.00 0.00 5.19
2825 3048 3.982576 CCCTTGTTATCGTAAATGGGC 57.017 47.619 0.00 0.00 0.00 5.36
2826 3049 2.621526 GGCCCTTGTTATCGTAAATGGG 59.378 50.000 0.00 0.00 36.63 4.00
2827 3050 3.283751 TGGCCCTTGTTATCGTAAATGG 58.716 45.455 0.00 0.00 0.00 3.16
2828 3051 4.439563 GGTTGGCCCTTGTTATCGTAAATG 60.440 45.833 0.00 0.00 0.00 2.32
2829 3052 3.697542 GGTTGGCCCTTGTTATCGTAAAT 59.302 43.478 0.00 0.00 0.00 1.40
2830 3053 3.083293 GGTTGGCCCTTGTTATCGTAAA 58.917 45.455 0.00 0.00 0.00 2.01
2831 3054 2.040012 TGGTTGGCCCTTGTTATCGTAA 59.960 45.455 0.00 0.00 0.00 3.18
2832 3055 1.629353 TGGTTGGCCCTTGTTATCGTA 59.371 47.619 0.00 0.00 0.00 3.43
2833 3056 0.402504 TGGTTGGCCCTTGTTATCGT 59.597 50.000 0.00 0.00 0.00 3.73
2834 3057 1.472480 CTTGGTTGGCCCTTGTTATCG 59.528 52.381 0.00 0.00 0.00 2.92
2835 3058 1.204704 GCTTGGTTGGCCCTTGTTATC 59.795 52.381 0.00 0.00 0.00 1.75
2836 3059 1.203174 AGCTTGGTTGGCCCTTGTTAT 60.203 47.619 0.00 0.00 0.00 1.89
2842 3065 2.763902 GGTAGCTTGGTTGGCCCT 59.236 61.111 0.00 0.00 0.00 5.19
2843 3066 2.362503 GGGTAGCTTGGTTGGCCC 60.363 66.667 0.00 0.00 0.00 5.80
2852 3075 1.630369 TCTCAACAGCATGGGTAGCTT 59.370 47.619 0.00 0.00 43.62 3.74
2862 3085 3.633525 ACAATGCTTTCTTCTCAACAGCA 59.366 39.130 0.00 0.00 44.32 4.41
2865 3088 4.126437 TCGACAATGCTTTCTTCTCAACA 58.874 39.130 0.00 0.00 0.00 3.33
2866 3089 4.377841 CCTCGACAATGCTTTCTTCTCAAC 60.378 45.833 0.00 0.00 0.00 3.18
2871 3106 5.351465 TGATAACCTCGACAATGCTTTCTTC 59.649 40.000 0.00 0.00 0.00 2.87
2882 3117 2.754946 GGTTGGTGATAACCTCGACA 57.245 50.000 0.00 0.00 45.29 4.35
2894 3129 5.240183 GGAGTGATGATGATATTGGTTGGTG 59.760 44.000 0.00 0.00 0.00 4.17
2903 3138 3.168292 TGCGGAGGAGTGATGATGATAT 58.832 45.455 0.00 0.00 0.00 1.63
2907 3142 1.579698 CTTGCGGAGGAGTGATGATG 58.420 55.000 0.00 0.00 0.00 3.07
2908 3143 0.179062 GCTTGCGGAGGAGTGATGAT 60.179 55.000 0.00 0.00 0.00 2.45
2921 3156 2.480224 ATCGAAATTGATGGCTTGCG 57.520 45.000 0.00 0.00 0.00 4.85
2924 3159 4.082081 TGCTGAAATCGAAATTGATGGCTT 60.082 37.500 0.00 0.00 0.00 4.35
2964 3199 3.636764 GGTCAACTGTTTGATGAGGGTTT 59.363 43.478 0.00 0.00 43.72 3.27
2976 3211 0.819259 AGCGCATGTGGTCAACTGTT 60.819 50.000 11.47 0.00 0.00 3.16
2989 3224 2.515523 GTCTGATGGCCAGCGCAT 60.516 61.111 17.68 0.00 42.62 4.73
3002 3237 2.625314 TCTGAGTCAAGTCAGGTGTCTG 59.375 50.000 13.51 0.00 43.69 3.51
3013 3248 4.094590 GCAAGGTTCATCATCTGAGTCAAG 59.905 45.833 0.00 0.00 34.68 3.02
3014 3249 4.005650 GCAAGGTTCATCATCTGAGTCAA 58.994 43.478 0.00 0.00 34.68 3.18
3015 3250 3.008266 TGCAAGGTTCATCATCTGAGTCA 59.992 43.478 0.00 0.00 34.68 3.41
3020 3255 4.196971 TCTCATGCAAGGTTCATCATCTG 58.803 43.478 0.00 0.00 0.00 2.90
3047 3282 2.904866 GTTGGTGCGGGCTCAACA 60.905 61.111 18.26 0.00 40.11 3.33
3056 3291 4.347453 GCAGGGCTTGTTGGTGCG 62.347 66.667 0.00 0.00 0.00 5.34
3065 3300 2.203337 TGTTCGCTTGCAGGGCTT 60.203 55.556 11.04 0.00 0.00 4.35
3083 3319 0.101219 TGACGATGGCACGAGATCAG 59.899 55.000 14.63 0.00 37.03 2.90
3084 3320 0.179137 GTGACGATGGCACGAGATCA 60.179 55.000 14.63 6.77 37.03 2.92
3091 3327 1.641577 GTTAGGAGTGACGATGGCAC 58.358 55.000 0.00 0.00 36.53 5.01
3104 3340 2.050350 CGGAGGAGGTGCGTTAGGA 61.050 63.158 0.00 0.00 34.79 2.94
3105 3341 2.494918 CGGAGGAGGTGCGTTAGG 59.505 66.667 0.00 0.00 34.79 2.69
3125 3361 0.721718 CGTCTTTGTGGAATCGGAGC 59.278 55.000 0.00 0.00 0.00 4.70
3133 3369 1.608025 GCCTCATCACGTCTTTGTGGA 60.608 52.381 11.97 0.00 40.31 4.02
3145 3381 1.487976 GGGAGTTCTCATGCCTCATCA 59.512 52.381 2.24 0.00 0.00 3.07
3155 3391 3.007290 CAGATGTGTTCAGGGAGTTCTCA 59.993 47.826 2.24 0.00 0.00 3.27
3165 3401 4.742167 GTCGGTATCATCAGATGTGTTCAG 59.258 45.833 10.34 0.93 35.67 3.02
3166 3402 4.402474 AGTCGGTATCATCAGATGTGTTCA 59.598 41.667 10.34 0.00 35.67 3.18
3176 3412 3.133362 GGGTTTGGTAGTCGGTATCATCA 59.867 47.826 0.00 0.00 0.00 3.07
3211 3447 1.339055 CGATGGTTGTGGTGTCCTCAT 60.339 52.381 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.