Multiple sequence alignment - TraesCS4A01G224400

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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 TraesCS4A01G224400 chr4A 100.000 2338 0 0 758 3095 532208154 532210491 0.000000e+00 4318.0
1 TraesCS4A01G224400 chr4A 100.000 522 0 0 1 522 532207397 532207918 0.000000e+00 965.0
2 TraesCS4A01G224400 chr4A 94.038 520 29 1 1 518 597316498 597315979 0.000000e+00 787.0
3 TraesCS4A01G224400 chr4A 90.141 71 2 5 863 933 600979463 600979528 1.530000e-13 87.9
4 TraesCS4A01G224400 chr4A 89.394 66 5 2 868 933 624285554 624285491 7.110000e-12 82.4
5 TraesCS4A01G224400 chr2A 96.645 775 23 1 2321 3095 82982711 82981940 0.000000e+00 1284.0
6 TraesCS4A01G224400 chr2A 78.846 260 40 12 2315 2567 2810532 2810783 8.880000e-36 161.0
7 TraesCS4A01G224400 chr5D 94.942 514 24 1 1 512 450524357 450524870 0.000000e+00 804.0
8 TraesCS4A01G224400 chr5D 78.026 537 96 17 1563 2094 5823881 5823362 4.980000e-83 318.0
9 TraesCS4A01G224400 chr5D 93.370 181 12 0 2915 3095 17245054 17245234 5.090000e-68 268.0
10 TraesCS4A01G224400 chr6D 94.747 514 25 1 1 512 262276793 262277306 0.000000e+00 798.0
11 TraesCS4A01G224400 chr6D 88.406 69 4 4 866 933 303461146 303461081 2.560000e-11 80.5
12 TraesCS4A01G224400 chr1A 94.423 520 27 1 1 518 504104756 504104237 0.000000e+00 798.0
13 TraesCS4A01G224400 chr1A 94.084 524 29 1 1 522 515234897 515235420 0.000000e+00 795.0
14 TraesCS4A01G224400 chr7D 94.242 521 27 2 1 518 63815108 63814588 0.000000e+00 793.0
15 TraesCS4A01G224400 chr7D 94.061 522 28 3 1 520 543096239 543095719 0.000000e+00 789.0
16 TraesCS4A01G224400 chr7D 86.111 72 7 3 867 938 593885386 593885318 1.190000e-09 75.0
17 TraesCS4A01G224400 chr7D 86.567 67 5 4 867 933 33649287 33649349 1.540000e-08 71.3
18 TraesCS4A01G224400 chr7D 83.562 73 10 2 868 940 156176097 156176167 1.990000e-07 67.6
19 TraesCS4A01G224400 chr1D 94.061 522 29 1 1 520 435761560 435761039 0.000000e+00 791.0
20 TraesCS4A01G224400 chr2B 93.893 524 30 2 1 522 68251792 68252315 0.000000e+00 789.0
21 TraesCS4A01G224400 chr2B 87.097 62 3 4 867 926 247626342 247626400 7.160000e-07 65.8
22 TraesCS4A01G224400 chr5A 84.262 610 89 5 939 1545 3384951 3385556 3.440000e-164 588.0
23 TraesCS4A01G224400 chr5A 86.747 83 5 6 853 933 75047650 75047572 1.530000e-13 87.9
24 TraesCS4A01G224400 chr4D 86.681 458 52 8 945 1400 64364678 64364228 1.660000e-137 499.0
25 TraesCS4A01G224400 chr4D 80.000 490 80 12 1607 2090 64364034 64363557 2.280000e-91 346.0
26 TraesCS4A01G224400 chr4B 82.979 564 83 10 945 1506 94840912 94840360 5.960000e-137 497.0
27 TraesCS4A01G224400 chr4B 86.250 80 10 1 777 856 94840987 94840909 5.500000e-13 86.1
28 TraesCS4A01G224400 chr2D 91.562 320 27 0 2776 3095 32425075 32425394 2.830000e-120 442.0
29 TraesCS4A01G224400 chr2D 83.486 109 9 8 2385 2490 68006505 68006403 3.290000e-15 93.5
30 TraesCS4A01G224400 chrUn 87.109 256 18 7 2314 2561 78830444 78830692 3.040000e-70 276.0
31 TraesCS4A01G224400 chrUn 87.109 256 18 7 2314 2561 332275693 332275941 3.040000e-70 276.0
32 TraesCS4A01G224400 chrUn 87.109 256 18 7 2314 2561 332356332 332356084 3.040000e-70 276.0
33 TraesCS4A01G224400 chr1B 71.709 1223 268 54 971 2141 1953278 1954474 1.410000e-68 270.0
34 TraesCS4A01G224400 chr1B 73.116 491 105 19 1640 2111 2307084 2306602 1.920000e-32 150.0
35 TraesCS4A01G224400 chr7A 73.200 500 115 16 1335 1829 54853141 54852656 2.470000e-36 163.0
36 TraesCS4A01G224400 chr7A 83.146 89 9 6 847 933 54984680 54984596 3.310000e-10 76.8
37 TraesCS4A01G224400 chr3D 77.612 268 44 9 2315 2576 153856676 153856933 6.910000e-32 148.0
38 TraesCS4A01G224400 chr7B 78.744 207 40 4 1302 1506 747598527 747598323 5.380000e-28 135.0


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 TraesCS4A01G224400 chr4A 532207397 532210491 3094 False 2641.50 4318 100.0000 1 3095 2 chr4A.!!$F2 3094
1 TraesCS4A01G224400 chr4A 597315979 597316498 519 True 787.00 787 94.0380 1 518 1 chr4A.!!$R1 517
2 TraesCS4A01G224400 chr2A 82981940 82982711 771 True 1284.00 1284 96.6450 2321 3095 1 chr2A.!!$R1 774
3 TraesCS4A01G224400 chr5D 450524357 450524870 513 False 804.00 804 94.9420 1 512 1 chr5D.!!$F2 511
4 TraesCS4A01G224400 chr5D 5823362 5823881 519 True 318.00 318 78.0260 1563 2094 1 chr5D.!!$R1 531
5 TraesCS4A01G224400 chr6D 262276793 262277306 513 False 798.00 798 94.7470 1 512 1 chr6D.!!$F1 511
6 TraesCS4A01G224400 chr1A 504104237 504104756 519 True 798.00 798 94.4230 1 518 1 chr1A.!!$R1 517
7 TraesCS4A01G224400 chr1A 515234897 515235420 523 False 795.00 795 94.0840 1 522 1 chr1A.!!$F1 521
8 TraesCS4A01G224400 chr7D 63814588 63815108 520 True 793.00 793 94.2420 1 518 1 chr7D.!!$R1 517
9 TraesCS4A01G224400 chr7D 543095719 543096239 520 True 789.00 789 94.0610 1 520 1 chr7D.!!$R2 519
10 TraesCS4A01G224400 chr1D 435761039 435761560 521 True 791.00 791 94.0610 1 520 1 chr1D.!!$R1 519
11 TraesCS4A01G224400 chr2B 68251792 68252315 523 False 789.00 789 93.8930 1 522 1 chr2B.!!$F1 521
12 TraesCS4A01G224400 chr5A 3384951 3385556 605 False 588.00 588 84.2620 939 1545 1 chr5A.!!$F1 606
13 TraesCS4A01G224400 chr4D 64363557 64364678 1121 True 422.50 499 83.3405 945 2090 2 chr4D.!!$R1 1145
14 TraesCS4A01G224400 chr4B 94840360 94840987 627 True 291.55 497 84.6145 777 1506 2 chr4B.!!$R1 729
15 TraesCS4A01G224400 chr1B 1953278 1954474 1196 False 270.00 270 71.7090 971 2141 1 chr1B.!!$F1 1170

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
267 271 0.529555 GATCTGGCGAAGGAGAGCAC 60.530 60.0 0.00 0.0 34.54 4.4 F
926 930 0.761187 AGAGTGATGCATACGGCCAT 59.239 50.0 2.24 0.0 43.89 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1636 1683 2.544267 CGTTTTCTCCAGTCAAGTCCAC 59.456 50.0 0.0 0.0 0.00 4.02 R
2306 2374 0.036875 CGGGAGGCAGTTTTCCTTCT 59.963 55.0 0.0 0.0 33.24 2.85 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
103 106 1.603802 CTTCAAGAAGGAAACAGCGCA 59.396 47.619 11.47 0.00 34.87 6.09
223 226 0.961358 CGGACTGACGAGGAGGAAGT 60.961 60.000 0.00 0.00 35.47 3.01
267 271 0.529555 GATCTGGCGAAGGAGAGCAC 60.530 60.000 0.00 0.00 34.54 4.40
268 272 0.975040 ATCTGGCGAAGGAGAGCACT 60.975 55.000 0.00 0.00 34.54 4.40
398 402 4.040645 CCTCACTAGCAGAGGCCA 57.959 61.111 16.37 0.00 45.51 5.36
787 791 2.963599 GGGGGTTCTACCTTTCAACA 57.036 50.000 0.00 0.00 38.64 3.33
802 806 4.751767 TTCAACAATTTTCTGGCCACTT 57.248 36.364 0.00 0.00 0.00 3.16
804 808 5.860941 TCAACAATTTTCTGGCCACTTAA 57.139 34.783 0.00 0.00 0.00 1.85
805 809 6.227298 TCAACAATTTTCTGGCCACTTAAA 57.773 33.333 0.00 2.69 0.00 1.52
809 813 6.591001 ACAATTTTCTGGCCACTTAAAATGT 58.409 32.000 21.03 17.30 33.16 2.71
810 814 7.053498 ACAATTTTCTGGCCACTTAAAATGTT 58.947 30.769 21.03 12.76 33.16 2.71
890 894 9.725019 ATTTTTATTTTGGAAAAGGAGGACATC 57.275 29.630 0.00 0.00 0.00 3.06
891 895 8.491045 TTTTATTTTGGAAAAGGAGGACATCT 57.509 30.769 0.00 0.00 0.00 2.90
892 896 7.703058 TTATTTTGGAAAAGGAGGACATCTC 57.297 36.000 0.00 0.00 41.71 2.75
899 903 2.444895 GAGGACATCTCCCGGCCT 60.445 66.667 0.00 0.00 37.25 5.19
900 904 2.444895 AGGACATCTCCCGGCCTC 60.445 66.667 0.00 0.00 37.25 4.70
901 905 2.444895 GGACATCTCCCGGCCTCT 60.445 66.667 0.00 0.00 0.00 3.69
902 906 2.801631 GGACATCTCCCGGCCTCTG 61.802 68.421 0.00 0.00 0.00 3.35
903 907 3.453070 GACATCTCCCGGCCTCTGC 62.453 68.421 0.00 0.00 0.00 4.26
904 908 3.473647 CATCTCCCGGCCTCTGCA 61.474 66.667 0.00 0.00 40.13 4.41
905 909 2.447379 ATCTCCCGGCCTCTGCAT 60.447 61.111 0.00 0.00 40.13 3.96
906 910 2.074948 ATCTCCCGGCCTCTGCATT 61.075 57.895 0.00 0.00 40.13 3.56
907 911 0.764369 ATCTCCCGGCCTCTGCATTA 60.764 55.000 0.00 0.00 40.13 1.90
908 912 1.070445 CTCCCGGCCTCTGCATTAG 59.930 63.158 0.00 0.00 40.13 1.73
909 913 1.382557 TCCCGGCCTCTGCATTAGA 60.383 57.895 0.00 0.00 40.13 2.10
923 927 2.158449 GCATTAGAGTGATGCATACGGC 59.842 50.000 0.00 0.00 46.96 5.68
924 928 2.526304 TTAGAGTGATGCATACGGCC 57.474 50.000 0.00 0.00 43.89 6.13
925 929 1.408969 TAGAGTGATGCATACGGCCA 58.591 50.000 2.24 0.00 43.89 5.36
926 930 0.761187 AGAGTGATGCATACGGCCAT 59.239 50.000 2.24 0.00 43.89 4.40
927 931 1.141657 AGAGTGATGCATACGGCCATT 59.858 47.619 2.24 0.00 43.89 3.16
928 932 1.949525 GAGTGATGCATACGGCCATTT 59.050 47.619 2.24 0.00 43.89 2.32
929 933 2.358898 GAGTGATGCATACGGCCATTTT 59.641 45.455 2.24 0.00 43.89 1.82
930 934 3.550820 AGTGATGCATACGGCCATTTTA 58.449 40.909 2.24 0.00 43.89 1.52
931 935 4.144297 AGTGATGCATACGGCCATTTTAT 58.856 39.130 2.24 0.00 43.89 1.40
932 936 4.584325 AGTGATGCATACGGCCATTTTATT 59.416 37.500 2.24 0.00 43.89 1.40
933 937 5.068987 AGTGATGCATACGGCCATTTTATTT 59.931 36.000 2.24 0.00 43.89 1.40
934 938 6.264292 AGTGATGCATACGGCCATTTTATTTA 59.736 34.615 2.24 0.00 43.89 1.40
935 939 6.920758 GTGATGCATACGGCCATTTTATTTAA 59.079 34.615 2.24 0.00 43.89 1.52
936 940 7.436673 GTGATGCATACGGCCATTTTATTTAAA 59.563 33.333 2.24 0.00 43.89 1.52
937 941 8.147058 TGATGCATACGGCCATTTTATTTAAAT 58.853 29.630 2.24 5.89 43.89 1.40
940 944 7.651304 TGCATACGGCCATTTTATTTAAATCAG 59.349 33.333 3.39 0.00 43.89 2.90
981 985 8.055181 TGCTCTTATTTTCACTTTCCAGGATAT 58.945 33.333 0.00 0.00 0.00 1.63
996 1000 8.579850 TTCCAGGATATTGTGGCATATAATTC 57.420 34.615 0.00 0.00 33.43 2.17
1008 1012 6.009589 TGGCATATAATTCCAAATGGATCGT 58.990 36.000 2.38 0.00 44.98 3.73
1025 1029 3.211803 TCGTCATTCAACTCCTACACG 57.788 47.619 0.00 0.00 0.00 4.49
1167 1171 3.359033 TGCAGTGGTCTATAAGGTACGT 58.641 45.455 0.00 0.00 0.00 3.57
1176 1180 5.277250 GGTCTATAAGGTACGTCAACTCTCG 60.277 48.000 0.00 0.00 0.00 4.04
1178 1182 6.036517 GTCTATAAGGTACGTCAACTCTCGAA 59.963 42.308 0.00 0.00 0.00 3.71
1184 1188 3.577649 ACGTCAACTCTCGAATGTCAT 57.422 42.857 0.00 0.00 0.00 3.06
1223 1231 8.402472 AGTTGATCTCGAGACTTTAGTTGATAG 58.598 37.037 19.30 0.00 0.00 2.08
1232 1240 7.466455 CGAGACTTTAGTTGATAGCATGCAAAT 60.466 37.037 21.98 13.00 0.00 2.32
1286 1294 2.342279 CCGTTGCGGTGAAGAGGA 59.658 61.111 0.00 0.00 42.73 3.71
1293 1301 2.329267 TGCGGTGAAGAGGATATCCAT 58.671 47.619 23.81 9.05 38.89 3.41
1294 1302 3.506398 TGCGGTGAAGAGGATATCCATA 58.494 45.455 23.81 2.23 38.89 2.74
1295 1303 3.258372 TGCGGTGAAGAGGATATCCATAC 59.742 47.826 23.81 13.78 38.89 2.39
1305 1313 9.965902 GAAGAGGATATCCATACCATTTATGTT 57.034 33.333 23.81 3.66 38.89 2.71
1347 1356 5.189180 AGAGGTTGAATGTCTGATAAAGGC 58.811 41.667 0.00 0.00 0.00 4.35
1348 1357 4.922206 AGGTTGAATGTCTGATAAAGGCA 58.078 39.130 0.00 0.00 46.81 4.75
1350 1359 5.416952 AGGTTGAATGTCTGATAAAGGCAAG 59.583 40.000 0.00 0.00 45.62 4.01
1355 1364 3.674997 TGTCTGATAAAGGCAAGTCACC 58.325 45.455 0.00 0.00 37.65 4.02
1401 1410 0.836606 TGTGCTGACTCACAAGGGAA 59.163 50.000 0.00 0.00 43.27 3.97
1405 1414 1.544314 GCTGACTCACAAGGGAAAGCT 60.544 52.381 0.00 0.00 0.00 3.74
1429 1438 8.181487 CTGAAAGCTATGATGGAAAATTTGTG 57.819 34.615 0.00 0.00 0.00 3.33
1453 1462 6.883756 TGATGGCAGATGTACAACAAAGATTA 59.116 34.615 0.00 0.00 0.00 1.75
1474 1483 8.371699 AGATTACTCTGCTTTGAATATCTACCC 58.628 37.037 0.00 0.00 0.00 3.69
1518 1527 2.562738 TCACTGGTAGGATCATATGGCG 59.437 50.000 2.13 0.00 0.00 5.69
1519 1528 2.562738 CACTGGTAGGATCATATGGCGA 59.437 50.000 2.13 0.00 0.00 5.54
1525 1534 6.774673 TGGTAGGATCATATGGCGAATAAAA 58.225 36.000 2.13 0.00 0.00 1.52
1602 1649 9.806203 TGAATGAATGTGAAATGATATTGAACC 57.194 29.630 0.00 0.00 0.00 3.62
1618 1665 3.318313 TGAACCACCTTTCTCTTCTCCT 58.682 45.455 0.00 0.00 0.00 3.69
1619 1666 3.325135 TGAACCACCTTTCTCTTCTCCTC 59.675 47.826 0.00 0.00 0.00 3.71
1620 1667 2.261729 ACCACCTTTCTCTTCTCCTCC 58.738 52.381 0.00 0.00 0.00 4.30
1630 1677 5.136068 TCTCTTCTCCTCCACATAGATGT 57.864 43.478 0.00 0.00 42.84 3.06
1635 1682 7.301420 TCTTCTCCTCCACATAGATGTATCTT 58.699 38.462 0.00 0.00 39.39 2.40
1636 1683 6.907853 TCTCCTCCACATAGATGTATCTTG 57.092 41.667 0.00 2.05 39.39 3.02
1655 1702 3.924114 TGTGGACTTGACTGGAGAAAA 57.076 42.857 0.00 0.00 0.00 2.29
1663 1710 4.809426 ACTTGACTGGAGAAAACGTTACAG 59.191 41.667 0.00 8.12 0.00 2.74
1664 1711 3.724374 TGACTGGAGAAAACGTTACAGG 58.276 45.455 0.00 0.00 0.00 4.00
1704 1751 4.708177 CAAGGGATTACACTACCTCCATG 58.292 47.826 0.00 0.00 31.69 3.66
1722 1769 6.194796 TCCATGAAAATCGAATTCTTCACC 57.805 37.500 9.33 0.00 31.00 4.02
1755 1802 5.213891 ACCTCCAAACATTTTGTTGGATC 57.786 39.130 5.63 0.00 40.14 3.36
1796 1843 9.558396 AAAATTGCTGATTTTGGTTTATCAAGA 57.442 25.926 9.55 0.00 44.26 3.02
1797 1844 8.538409 AATTGCTGATTTTGGTTTATCAAGAC 57.462 30.769 0.00 0.00 30.90 3.01
1820 1867 2.437200 TTGATGAAAAGCAAAGCCGG 57.563 45.000 0.00 0.00 0.00 6.13
1824 1871 0.538516 TGAAAAGCAAAGCCGGGCTA 60.539 50.000 24.16 0.00 40.01 3.93
1829 1876 0.546598 AGCAAAGCCGGGCTATTACT 59.453 50.000 24.16 14.44 38.25 2.24
1835 1882 0.602905 GCCGGGCTATTACTGCGAAT 60.603 55.000 12.87 0.00 0.00 3.34
1838 1885 2.930040 CCGGGCTATTACTGCGAATATG 59.070 50.000 0.00 0.00 0.00 1.78
1864 1911 6.544197 TGTGGAACATTGTAAGTTTGCTAAGA 59.456 34.615 0.00 0.00 45.67 2.10
1867 1914 7.284489 TGGAACATTGTAAGTTTGCTAAGACTT 59.716 33.333 0.00 0.00 39.32 3.01
1868 1915 7.803659 GGAACATTGTAAGTTTGCTAAGACTTC 59.196 37.037 0.00 0.00 37.32 3.01
1872 1919 7.715265 TTGTAAGTTTGCTAAGACTTCTGAG 57.285 36.000 0.00 0.00 37.32 3.35
1874 1921 7.148641 TGTAAGTTTGCTAAGACTTCTGAGAG 58.851 38.462 0.00 0.00 37.32 3.20
1876 1923 5.778862 AGTTTGCTAAGACTTCTGAGAGTC 58.221 41.667 10.20 10.20 45.05 3.36
1879 1926 5.384063 TGCTAAGACTTCTGAGAGTCAAG 57.616 43.478 16.66 14.40 46.69 3.02
1880 1927 4.173256 GCTAAGACTTCTGAGAGTCAAGC 58.827 47.826 18.95 18.95 46.69 4.01
1883 1930 4.519540 AGACTTCTGAGAGTCAAGCTTC 57.480 45.455 16.66 0.00 46.69 3.86
1886 1934 5.011943 AGACTTCTGAGAGTCAAGCTTCATT 59.988 40.000 16.66 0.00 46.69 2.57
1887 1935 5.619220 ACTTCTGAGAGTCAAGCTTCATTT 58.381 37.500 0.00 0.00 0.00 2.32
1889 1937 6.204495 ACTTCTGAGAGTCAAGCTTCATTTTC 59.796 38.462 0.00 0.00 0.00 2.29
1891 1940 4.717877 TGAGAGTCAAGCTTCATTTTCCA 58.282 39.130 0.00 0.00 0.00 3.53
1925 1975 3.907221 AGCATTGTATTCCCTTGCTCAT 58.093 40.909 0.00 0.00 39.32 2.90
1926 1976 4.284178 AGCATTGTATTCCCTTGCTCATT 58.716 39.130 0.00 0.00 39.32 2.57
1931 1981 7.712205 GCATTGTATTCCCTTGCTCATTTTAAT 59.288 33.333 0.00 0.00 0.00 1.40
1938 1988 7.664552 TCCCTTGCTCATTTTAATCAATCAT 57.335 32.000 0.00 0.00 0.00 2.45
1986 2037 5.659440 ATTTGGCACCAGAATTCGTTAAT 57.341 34.783 0.00 0.00 0.00 1.40
1987 2038 4.433186 TTGGCACCAGAATTCGTTAATG 57.567 40.909 0.00 0.00 0.00 1.90
2011 2077 4.032104 GTGTAATCACGTACCGGTTTGATC 59.968 45.833 15.04 8.57 34.79 2.92
2028 2094 4.257267 TGATCTGTACAGTCTTGGTGTG 57.743 45.455 21.99 0.00 0.00 3.82
2064 2130 0.978907 TCACCGGAAAGAAGGGGTAC 59.021 55.000 9.46 0.00 31.54 3.34
2094 2160 7.800155 TGTTGATGATGTAAGAACAGTTTGA 57.200 32.000 0.00 0.00 39.49 2.69
2098 2164 6.650807 TGATGATGTAAGAACAGTTTGAGTCC 59.349 38.462 0.00 0.00 39.49 3.85
2104 2170 6.761714 TGTAAGAACAGTTTGAGTCCTCTTTC 59.238 38.462 0.00 0.00 0.00 2.62
2105 2171 5.359194 AGAACAGTTTGAGTCCTCTTTCA 57.641 39.130 0.00 0.00 0.00 2.69
2106 2172 5.363939 AGAACAGTTTGAGTCCTCTTTCAG 58.636 41.667 0.00 0.00 0.00 3.02
2110 2176 6.180472 ACAGTTTGAGTCCTCTTTCAGAAAA 58.820 36.000 0.00 0.00 0.00 2.29
2111 2177 6.317391 ACAGTTTGAGTCCTCTTTCAGAAAAG 59.683 38.462 0.00 0.00 42.77 2.27
2112 2178 6.540189 CAGTTTGAGTCCTCTTTCAGAAAAGA 59.460 38.462 0.00 1.10 46.72 2.52
2123 2191 4.322080 TTCAGAAAAGAGCTCGACTTCA 57.678 40.909 20.47 5.37 0.00 3.02
2128 2196 5.007136 CAGAAAAGAGCTCGACTTCAAAACT 59.993 40.000 20.47 5.70 0.00 2.66
2141 2209 8.564574 TCGACTTCAAAACTAATGCATTACTTT 58.435 29.630 15.21 14.88 0.00 2.66
2142 2210 8.840867 CGACTTCAAAACTAATGCATTACTTTC 58.159 33.333 15.21 5.72 0.00 2.62
2143 2211 9.899226 GACTTCAAAACTAATGCATTACTTTCT 57.101 29.630 15.21 7.44 0.00 2.52
2172 2240 8.922738 TTGTAGTTTTTCTATTTTTAGACGCG 57.077 30.769 3.53 3.53 0.00 6.01
2173 2241 8.296799 TGTAGTTTTTCTATTTTTAGACGCGA 57.703 30.769 15.93 0.00 0.00 5.87
2174 2242 8.216453 TGTAGTTTTTCTATTTTTAGACGCGAC 58.784 33.333 15.93 6.86 0.00 5.19
2175 2243 7.181143 AGTTTTTCTATTTTTAGACGCGACA 57.819 32.000 15.93 0.00 0.00 4.35
2176 2244 7.803724 AGTTTTTCTATTTTTAGACGCGACAT 58.196 30.769 15.93 0.00 0.00 3.06
2177 2245 8.928733 AGTTTTTCTATTTTTAGACGCGACATA 58.071 29.630 15.93 0.00 0.00 2.29
2178 2246 9.532697 GTTTTTCTATTTTTAGACGCGACATAA 57.467 29.630 15.93 5.68 0.00 1.90
2183 2251 9.902196 TCTATTTTTAGACGCGACATAATATCA 57.098 29.630 15.93 0.00 0.00 2.15
2184 2252 9.939047 CTATTTTTAGACGCGACATAATATCAC 57.061 33.333 15.93 0.00 0.00 3.06
2185 2253 7.997107 TTTTTAGACGCGACATAATATCACT 57.003 32.000 15.93 0.00 0.00 3.41
2186 2254 7.618964 TTTTAGACGCGACATAATATCACTC 57.381 36.000 15.93 0.00 0.00 3.51
2187 2255 4.830826 AGACGCGACATAATATCACTCA 57.169 40.909 15.93 0.00 0.00 3.41
2188 2256 5.378292 AGACGCGACATAATATCACTCAT 57.622 39.130 15.93 0.00 0.00 2.90
2189 2257 5.773575 AGACGCGACATAATATCACTCATT 58.226 37.500 15.93 0.00 0.00 2.57
2190 2258 6.216569 AGACGCGACATAATATCACTCATTT 58.783 36.000 15.93 0.00 0.00 2.32
2191 2259 7.368059 AGACGCGACATAATATCACTCATTTA 58.632 34.615 15.93 0.00 0.00 1.40
2192 2260 8.029522 AGACGCGACATAATATCACTCATTTAT 58.970 33.333 15.93 0.00 0.00 1.40
2193 2261 8.534333 ACGCGACATAATATCACTCATTTATT 57.466 30.769 15.93 0.00 0.00 1.40
2194 2262 8.988934 ACGCGACATAATATCACTCATTTATTT 58.011 29.630 15.93 0.00 0.00 1.40
2195 2263 9.811655 CGCGACATAATATCACTCATTTATTTT 57.188 29.630 0.00 0.00 0.00 1.82
2231 2299 7.921786 ACATTATGGACCATATATTTGACCG 57.078 36.000 15.05 2.74 0.00 4.79
2232 2300 7.685481 ACATTATGGACCATATATTTGACCGA 58.315 34.615 15.05 0.00 0.00 4.69
2233 2301 8.160765 ACATTATGGACCATATATTTGACCGAA 58.839 33.333 15.05 0.00 0.00 4.30
2234 2302 9.008965 CATTATGGACCATATATTTGACCGAAA 57.991 33.333 15.05 0.00 0.00 3.46
2235 2303 8.615878 TTATGGACCATATATTTGACCGAAAG 57.384 34.615 15.05 0.00 0.00 2.62
2236 2304 6.241882 TGGACCATATATTTGACCGAAAGA 57.758 37.500 0.00 0.00 0.00 2.52
2237 2305 6.053005 TGGACCATATATTTGACCGAAAGAC 58.947 40.000 0.00 0.00 0.00 3.01
2238 2306 6.126883 TGGACCATATATTTGACCGAAAGACT 60.127 38.462 0.00 0.00 0.00 3.24
2239 2307 6.766467 GGACCATATATTTGACCGAAAGACTT 59.234 38.462 0.00 0.00 0.00 3.01
2240 2308 7.929785 GGACCATATATTTGACCGAAAGACTTA 59.070 37.037 0.00 0.00 0.00 2.24
2241 2309 9.321562 GACCATATATTTGACCGAAAGACTTAA 57.678 33.333 0.00 0.00 0.00 1.85
2242 2310 9.326413 ACCATATATTTGACCGAAAGACTTAAG 57.674 33.333 0.00 0.00 0.00 1.85
2243 2311 9.542462 CCATATATTTGACCGAAAGACTTAAGA 57.458 33.333 10.09 0.00 0.00 2.10
2246 2314 8.934507 ATATTTGACCGAAAGACTTAAGAGAG 57.065 34.615 10.09 0.00 0.00 3.20
2247 2315 4.175787 TGACCGAAAGACTTAAGAGAGC 57.824 45.455 10.09 0.00 0.00 4.09
2248 2316 3.056749 TGACCGAAAGACTTAAGAGAGCC 60.057 47.826 10.09 0.00 0.00 4.70
2249 2317 3.166679 ACCGAAAGACTTAAGAGAGCCT 58.833 45.455 10.09 0.00 0.00 4.58
2250 2318 4.342359 ACCGAAAGACTTAAGAGAGCCTA 58.658 43.478 10.09 0.00 0.00 3.93
2251 2319 4.158209 ACCGAAAGACTTAAGAGAGCCTAC 59.842 45.833 10.09 0.00 0.00 3.18
2252 2320 4.344448 CGAAAGACTTAAGAGAGCCTACG 58.656 47.826 10.09 1.27 0.00 3.51
2253 2321 4.674475 GAAAGACTTAAGAGAGCCTACGG 58.326 47.826 10.09 0.00 0.00 4.02
2254 2322 3.648507 AGACTTAAGAGAGCCTACGGA 57.351 47.619 10.09 0.00 0.00 4.69
2255 2323 3.965694 AGACTTAAGAGAGCCTACGGAA 58.034 45.455 10.09 0.00 0.00 4.30
2256 2324 4.538738 AGACTTAAGAGAGCCTACGGAAT 58.461 43.478 10.09 0.00 0.00 3.01
2257 2325 4.957327 AGACTTAAGAGAGCCTACGGAATT 59.043 41.667 10.09 0.00 0.00 2.17
2258 2326 6.127793 AGACTTAAGAGAGCCTACGGAATTA 58.872 40.000 10.09 0.00 0.00 1.40
2259 2327 6.778559 AGACTTAAGAGAGCCTACGGAATTAT 59.221 38.462 10.09 0.00 0.00 1.28
2260 2328 7.943447 AGACTTAAGAGAGCCTACGGAATTATA 59.057 37.037 10.09 0.00 0.00 0.98
2261 2329 8.474710 ACTTAAGAGAGCCTACGGAATTATAA 57.525 34.615 10.09 0.00 0.00 0.98
2262 2330 8.921205 ACTTAAGAGAGCCTACGGAATTATAAA 58.079 33.333 10.09 0.00 0.00 1.40
2263 2331 9.930693 CTTAAGAGAGCCTACGGAATTATAAAT 57.069 33.333 0.00 0.00 0.00 1.40
2264 2332 9.706691 TTAAGAGAGCCTACGGAATTATAAATG 57.293 33.333 0.00 0.00 0.00 2.32
2265 2333 7.304497 AGAGAGCCTACGGAATTATAAATGT 57.696 36.000 0.00 0.00 0.00 2.71
2266 2334 8.418597 AGAGAGCCTACGGAATTATAAATGTA 57.581 34.615 0.00 0.00 0.00 2.29
2267 2335 9.036980 AGAGAGCCTACGGAATTATAAATGTAT 57.963 33.333 0.00 0.00 0.00 2.29
2268 2336 9.088512 GAGAGCCTACGGAATTATAAATGTATG 57.911 37.037 0.00 0.00 0.00 2.39
2269 2337 8.812972 AGAGCCTACGGAATTATAAATGTATGA 58.187 33.333 0.00 0.00 0.00 2.15
2270 2338 9.431887 GAGCCTACGGAATTATAAATGTATGAA 57.568 33.333 0.00 0.00 0.00 2.57
2271 2339 9.787435 AGCCTACGGAATTATAAATGTATGAAA 57.213 29.630 0.00 0.00 0.00 2.69
2298 2366 7.979444 TTGAAAAGTAGGATTTGTACCTCTG 57.021 36.000 0.00 0.00 38.76 3.35
2299 2367 6.472887 TGAAAAGTAGGATTTGTACCTCTGG 58.527 40.000 0.00 0.00 38.76 3.86
2300 2368 6.043938 TGAAAAGTAGGATTTGTACCTCTGGT 59.956 38.462 0.00 0.00 38.76 4.00
2301 2369 5.422214 AAGTAGGATTTGTACCTCTGGTG 57.578 43.478 0.00 0.00 36.19 4.17
2302 2370 3.775316 AGTAGGATTTGTACCTCTGGTGG 59.225 47.826 0.00 0.00 36.19 4.61
2303 2371 1.916181 AGGATTTGTACCTCTGGTGGG 59.084 52.381 0.00 0.00 36.19 4.61
2304 2372 1.913419 GGATTTGTACCTCTGGTGGGA 59.087 52.381 0.00 0.00 36.19 4.37
2305 2373 2.509964 GGATTTGTACCTCTGGTGGGAT 59.490 50.000 0.00 0.00 36.19 3.85
2306 2374 3.714798 GGATTTGTACCTCTGGTGGGATA 59.285 47.826 0.00 0.00 36.19 2.59
2307 2375 4.202367 GGATTTGTACCTCTGGTGGGATAG 60.202 50.000 0.00 0.00 36.19 2.08
2308 2376 3.769189 TTGTACCTCTGGTGGGATAGA 57.231 47.619 0.00 0.00 36.19 1.98
2309 2377 3.769189 TGTACCTCTGGTGGGATAGAA 57.231 47.619 0.00 0.00 36.19 2.10
2310 2378 3.643237 TGTACCTCTGGTGGGATAGAAG 58.357 50.000 0.00 0.00 36.19 2.85
2311 2379 2.182516 ACCTCTGGTGGGATAGAAGG 57.817 55.000 0.00 0.00 32.98 3.46
2312 2380 1.651770 ACCTCTGGTGGGATAGAAGGA 59.348 52.381 0.00 0.00 32.98 3.36
2313 2381 2.045885 ACCTCTGGTGGGATAGAAGGAA 59.954 50.000 0.00 0.00 32.98 3.36
2314 2382 3.115390 CCTCTGGTGGGATAGAAGGAAA 58.885 50.000 0.00 0.00 0.00 3.13
2315 2383 3.523564 CCTCTGGTGGGATAGAAGGAAAA 59.476 47.826 0.00 0.00 0.00 2.29
2316 2384 4.518249 CTCTGGTGGGATAGAAGGAAAAC 58.482 47.826 0.00 0.00 0.00 2.43
2317 2385 4.175962 TCTGGTGGGATAGAAGGAAAACT 58.824 43.478 0.00 0.00 0.00 2.66
2318 2386 4.019321 TCTGGTGGGATAGAAGGAAAACTG 60.019 45.833 0.00 0.00 0.00 3.16
2319 2387 3.017442 GGTGGGATAGAAGGAAAACTGC 58.983 50.000 0.00 0.00 0.00 4.40
2400 2468 3.698289 TCCTTCCAAGATCTGTACTCGT 58.302 45.455 0.00 0.00 0.00 4.18
2401 2469 4.087182 TCCTTCCAAGATCTGTACTCGTT 58.913 43.478 0.00 0.00 0.00 3.85
2408 2476 0.179171 ATCTGTACTCGTTGCCGTCG 60.179 55.000 0.00 0.00 35.01 5.12
2512 2580 2.556287 GAGCGCAAAGGACAACGG 59.444 61.111 11.47 0.00 0.00 4.44
2664 2732 1.228063 CCGCCCAAGGATCTGGATG 60.228 63.158 2.56 0.00 38.96 3.51
2679 2747 1.076485 GATGTGCTGGCCCCTGATT 60.076 57.895 0.00 0.00 0.00 2.57
2684 2752 1.607467 GCTGGCCCCTGATTTGTGT 60.607 57.895 0.00 0.00 0.00 3.72
2725 2793 2.279517 GGCATGACCGACGGCTAG 60.280 66.667 15.39 2.63 0.00 3.42
2744 2812 1.202770 AGTGGTAATCCGGCTAATGGC 60.203 52.381 0.00 0.00 40.90 4.40
2891 2959 1.140407 CTTCGGCGTCCTTCGTGATC 61.140 60.000 6.85 0.00 42.13 2.92
2898 2966 0.381089 GTCCTTCGTGATCGATCCGT 59.619 55.000 25.27 0.00 45.65 4.69
2917 2985 3.679980 CCGTTGTGACTACCTTGATTCAG 59.320 47.826 0.00 0.00 0.00 3.02
3028 3096 7.175990 TCAAAACGTCTATTTTCCAGGCTAATT 59.824 33.333 0.00 0.00 29.17 1.40
3058 3126 4.496360 TCGACGGTGAAATGCAAACTATA 58.504 39.130 0.00 0.00 0.00 1.31
3087 3155 3.482436 ACTTGACGCAAAGGAATGGTTA 58.518 40.909 3.08 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 60 0.260230 TCGAGATCCAGCTCCCTCTT 59.740 55.000 0.00 0.00 0.00 2.85
134 137 1.677820 CGGAGTAATTTCTTGGCCGGT 60.678 52.381 1.90 0.00 34.08 5.28
238 241 0.965866 TCGCCAGATCTGAAGACGGT 60.966 55.000 24.62 0.00 0.00 4.83
323 327 4.790962 AGGGCCGCGTCTACTCGA 62.791 66.667 4.92 0.00 0.00 4.04
375 379 3.774528 CTGCTAGTGAGGGCGGCA 61.775 66.667 12.47 0.00 0.00 5.69
398 402 3.400188 CCTAGGGTTTGAGGCGGT 58.600 61.111 0.00 0.00 0.00 5.68
768 772 2.963599 TGTTGAAAGGTAGAACCCCC 57.036 50.000 0.00 0.00 39.75 5.40
769 773 5.801531 AAATTGTTGAAAGGTAGAACCCC 57.198 39.130 0.00 0.00 39.75 4.95
770 774 6.923508 CAGAAAATTGTTGAAAGGTAGAACCC 59.076 38.462 0.00 0.00 39.75 4.11
771 775 6.923508 CCAGAAAATTGTTGAAAGGTAGAACC 59.076 38.462 0.00 0.00 38.99 3.62
772 776 6.420903 GCCAGAAAATTGTTGAAAGGTAGAAC 59.579 38.462 0.00 0.00 0.00 3.01
773 777 6.462347 GGCCAGAAAATTGTTGAAAGGTAGAA 60.462 38.462 0.00 0.00 0.00 2.10
774 778 5.010617 GGCCAGAAAATTGTTGAAAGGTAGA 59.989 40.000 0.00 0.00 0.00 2.59
775 779 5.221422 TGGCCAGAAAATTGTTGAAAGGTAG 60.221 40.000 0.00 0.00 0.00 3.18
787 791 8.518430 AAAACATTTTAAGTGGCCAGAAAATT 57.482 26.923 21.87 12.30 30.91 1.82
864 868 9.725019 GATGTCCTCCTTTTCCAAAATAAAAAT 57.275 29.630 0.00 0.00 0.00 1.82
865 869 8.933653 AGATGTCCTCCTTTTCCAAAATAAAAA 58.066 29.630 0.00 0.00 0.00 1.94
866 870 8.491045 AGATGTCCTCCTTTTCCAAAATAAAA 57.509 30.769 0.00 0.00 0.00 1.52
867 871 8.122472 GAGATGTCCTCCTTTTCCAAAATAAA 57.878 34.615 0.00 0.00 35.87 1.40
868 872 7.703058 GAGATGTCCTCCTTTTCCAAAATAA 57.297 36.000 0.00 0.00 35.87 1.40
882 886 2.444895 AGGCCGGGAGATGTCCTC 60.445 66.667 9.08 0.00 43.36 3.71
883 887 2.444895 GAGGCCGGGAGATGTCCT 60.445 66.667 9.08 0.00 43.36 3.85
884 888 2.444895 AGAGGCCGGGAGATGTCC 60.445 66.667 2.18 0.00 43.05 4.02
885 889 2.818132 CAGAGGCCGGGAGATGTC 59.182 66.667 2.18 0.00 0.00 3.06
886 890 3.474570 GCAGAGGCCGGGAGATGT 61.475 66.667 2.18 0.00 0.00 3.06
887 891 2.335092 AATGCAGAGGCCGGGAGATG 62.335 60.000 2.18 0.00 40.13 2.90
888 892 0.764369 TAATGCAGAGGCCGGGAGAT 60.764 55.000 2.18 0.00 40.13 2.75
889 893 1.382557 TAATGCAGAGGCCGGGAGA 60.383 57.895 2.18 0.00 40.13 3.71
890 894 1.070445 CTAATGCAGAGGCCGGGAG 59.930 63.158 2.18 0.00 40.13 4.30
891 895 1.382557 TCTAATGCAGAGGCCGGGA 60.383 57.895 2.18 0.00 40.13 5.14
892 896 1.070445 CTCTAATGCAGAGGCCGGG 59.930 63.158 2.18 0.00 46.21 5.73
893 897 4.766970 CTCTAATGCAGAGGCCGG 57.233 61.111 0.00 0.00 46.21 6.13
903 907 2.738846 GGCCGTATGCATCACTCTAATG 59.261 50.000 0.19 0.00 43.89 1.90
904 908 2.368548 TGGCCGTATGCATCACTCTAAT 59.631 45.455 0.19 0.00 43.89 1.73
905 909 1.760029 TGGCCGTATGCATCACTCTAA 59.240 47.619 0.19 0.00 43.89 2.10
906 910 1.408969 TGGCCGTATGCATCACTCTA 58.591 50.000 0.19 0.00 43.89 2.43
907 911 0.761187 ATGGCCGTATGCATCACTCT 59.239 50.000 0.19 0.00 43.89 3.24
908 912 1.597742 AATGGCCGTATGCATCACTC 58.402 50.000 0.19 0.00 43.89 3.51
909 913 2.057137 AAATGGCCGTATGCATCACT 57.943 45.000 0.19 0.00 43.89 3.41
910 914 2.869233 AAAATGGCCGTATGCATCAC 57.131 45.000 0.19 0.00 43.89 3.06
911 915 5.528043 AAATAAAATGGCCGTATGCATCA 57.472 34.783 0.19 0.00 43.89 3.07
912 916 7.938563 TTTAAATAAAATGGCCGTATGCATC 57.061 32.000 0.19 0.00 43.89 3.91
913 917 8.147058 TGATTTAAATAAAATGGCCGTATGCAT 58.853 29.630 3.79 3.79 38.76 3.96
914 918 7.492524 TGATTTAAATAAAATGGCCGTATGCA 58.507 30.769 0.00 0.00 38.76 3.96
915 919 7.651704 ACTGATTTAAATAAAATGGCCGTATGC 59.348 33.333 0.00 0.00 37.93 3.14
916 920 8.967218 CACTGATTTAAATAAAATGGCCGTATG 58.033 33.333 0.00 0.00 37.93 2.39
917 921 8.908903 TCACTGATTTAAATAAAATGGCCGTAT 58.091 29.630 0.00 0.00 37.93 3.06
918 922 8.282455 TCACTGATTTAAATAAAATGGCCGTA 57.718 30.769 0.00 0.00 37.93 4.02
919 923 7.164230 TCACTGATTTAAATAAAATGGCCGT 57.836 32.000 0.00 0.00 37.93 5.68
920 924 8.647143 AATCACTGATTTAAATAAAATGGCCG 57.353 30.769 0.00 0.00 37.93 6.13
934 938 8.964772 AGAGCAAGCTTATTAAATCACTGATTT 58.035 29.630 18.76 18.76 43.49 2.17
935 939 8.517062 AGAGCAAGCTTATTAAATCACTGATT 57.483 30.769 0.00 0.00 33.25 2.57
936 940 8.517062 AAGAGCAAGCTTATTAAATCACTGAT 57.483 30.769 0.00 0.00 0.00 2.90
937 941 7.928307 AAGAGCAAGCTTATTAAATCACTGA 57.072 32.000 0.00 0.00 0.00 3.41
953 957 6.207417 TCCTGGAAAGTGAAAATAAGAGCAAG 59.793 38.462 0.00 0.00 0.00 4.01
996 1000 4.201950 GGAGTTGAATGACGATCCATTTGG 60.202 45.833 0.00 0.00 36.93 3.28
1008 1012 3.585862 GCTTCGTGTAGGAGTTGAATGA 58.414 45.455 0.00 0.00 0.00 2.57
1025 1029 1.078848 ATGCACTCCAGGTCGCTTC 60.079 57.895 0.00 0.00 0.00 3.86
1167 1171 8.922676 GTTAAAACTATGACATTCGAGAGTTGA 58.077 33.333 0.00 0.00 0.00 3.18
1176 1180 8.564574 TCAACTGTGGTTAAAACTATGACATTC 58.435 33.333 0.00 0.00 33.88 2.67
1178 1182 8.635765 ATCAACTGTGGTTAAAACTATGACAT 57.364 30.769 0.00 0.00 33.88 3.06
1184 1188 6.751157 TCGAGATCAACTGTGGTTAAAACTA 58.249 36.000 0.00 0.00 33.88 2.24
1232 1240 6.154192 TCAAGCATTCCCTACATTTGCAATAA 59.846 34.615 0.00 0.00 35.79 1.40
1239 1247 5.361857 CCATTCTCAAGCATTCCCTACATTT 59.638 40.000 0.00 0.00 0.00 2.32
1276 1284 6.380079 AATGGTATGGATATCCTCTTCACC 57.620 41.667 22.35 19.12 36.82 4.02
1294 1302 8.869109 TGGAATTCTTTCTCAAACATAAATGGT 58.131 29.630 5.23 0.00 32.16 3.55
1295 1303 9.143631 GTGGAATTCTTTCTCAAACATAAATGG 57.856 33.333 5.23 0.00 32.16 3.16
1305 1313 4.563580 CCTCTCGGTGGAATTCTTTCTCAA 60.564 45.833 5.23 0.00 32.16 3.02
1405 1414 7.894708 TCACAAATTTTCCATCATAGCTTTCA 58.105 30.769 0.00 0.00 0.00 2.69
1414 1423 4.527427 TCTGCCATCACAAATTTTCCATCA 59.473 37.500 0.00 0.00 0.00 3.07
1415 1424 5.075858 TCTGCCATCACAAATTTTCCATC 57.924 39.130 0.00 0.00 0.00 3.51
1429 1438 5.824904 ATCTTTGTTGTACATCTGCCATC 57.175 39.130 0.00 0.00 0.00 3.51
1453 1462 4.721776 TGGGGTAGATATTCAAAGCAGAGT 59.278 41.667 0.00 0.00 0.00 3.24
1474 1483 4.832590 ATACTTATCGAGAGTTCCGTGG 57.167 45.455 9.22 0.00 0.00 4.94
1534 1543 6.675413 TGGCCGGTAGTAGAAATAATATGT 57.325 37.500 1.90 0.00 0.00 2.29
1542 1551 3.985019 TTGAATGGCCGGTAGTAGAAA 57.015 42.857 1.90 0.00 0.00 2.52
1545 1554 6.877611 AATATTTTGAATGGCCGGTAGTAG 57.122 37.500 1.90 0.00 0.00 2.57
1553 1596 8.785329 TCAAACCTTAAATATTTTGAATGGCC 57.215 30.769 5.91 0.00 35.54 5.36
1582 1629 7.722949 AGGTGGTTCAATATCATTTCACATT 57.277 32.000 0.00 0.00 0.00 2.71
1587 1634 8.286191 AGAGAAAGGTGGTTCAATATCATTTC 57.714 34.615 0.00 0.00 0.00 2.17
1592 1639 6.540551 GGAGAAGAGAAAGGTGGTTCAATATC 59.459 42.308 0.00 0.00 0.00 1.63
1596 1643 3.716872 AGGAGAAGAGAAAGGTGGTTCAA 59.283 43.478 0.00 0.00 0.00 2.69
1598 1645 3.307129 GGAGGAGAAGAGAAAGGTGGTTC 60.307 52.174 0.00 0.00 0.00 3.62
1602 1649 2.634940 TGTGGAGGAGAAGAGAAAGGTG 59.365 50.000 0.00 0.00 0.00 4.00
1620 1667 7.223582 GTCAAGTCCACAAGATACATCTATGTG 59.776 40.741 18.02 18.02 41.89 3.21
1630 1677 4.416516 TCTCCAGTCAAGTCCACAAGATA 58.583 43.478 0.00 0.00 0.00 1.98
1635 1682 3.541632 GTTTTCTCCAGTCAAGTCCACA 58.458 45.455 0.00 0.00 0.00 4.17
1636 1683 2.544267 CGTTTTCTCCAGTCAAGTCCAC 59.456 50.000 0.00 0.00 0.00 4.02
1655 1702 5.623956 TCCCATTGATTATCCTGTAACGT 57.376 39.130 0.00 0.00 0.00 3.99
1663 1710 5.511888 CCCTTGCAAATCCCATTGATTATCC 60.512 44.000 0.00 0.00 42.97 2.59
1664 1711 5.305128 TCCCTTGCAAATCCCATTGATTATC 59.695 40.000 0.00 0.00 42.97 1.75
1722 1769 6.840780 AATGTTTGGAGGTTTAAGATCCAG 57.159 37.500 5.76 0.00 43.71 3.86
1755 1802 9.701098 ATCAGCAATTTTTGGTAGCATATTATG 57.299 29.630 0.00 0.00 39.79 1.90
1820 1867 4.152402 CCACACATATTCGCAGTAATAGCC 59.848 45.833 0.00 0.00 0.00 3.93
1824 1871 5.182487 TGTTCCACACATATTCGCAGTAAT 58.818 37.500 0.00 0.00 0.00 1.89
1829 1876 3.755905 ACAATGTTCCACACATATTCGCA 59.244 39.130 0.00 0.00 46.23 5.10
1835 1882 6.264292 AGCAAACTTACAATGTTCCACACATA 59.736 34.615 0.00 0.00 46.23 2.29
1838 1885 4.932146 AGCAAACTTACAATGTTCCACAC 58.068 39.130 0.00 0.00 0.00 3.82
1848 1895 7.497595 TCTCAGAAGTCTTAGCAAACTTACAA 58.502 34.615 0.00 0.00 35.90 2.41
1864 1911 4.888326 ATGAAGCTTGACTCTCAGAAGT 57.112 40.909 2.10 0.00 0.00 3.01
1867 1914 4.999950 GGAAAATGAAGCTTGACTCTCAGA 59.000 41.667 2.10 0.00 0.00 3.27
1868 1915 4.758674 TGGAAAATGAAGCTTGACTCTCAG 59.241 41.667 2.10 0.00 0.00 3.35
1872 1919 6.017400 TCATTGGAAAATGAAGCTTGACTC 57.983 37.500 2.10 0.00 36.34 3.36
1903 1952 3.700538 TGAGCAAGGGAATACAATGCTT 58.299 40.909 0.00 0.00 46.58 3.91
1905 1954 4.660789 AATGAGCAAGGGAATACAATGC 57.339 40.909 0.00 0.00 37.28 3.56
1908 1957 8.359875 TGATTAAAATGAGCAAGGGAATACAA 57.640 30.769 0.00 0.00 0.00 2.41
1911 1961 9.199645 TGATTGATTAAAATGAGCAAGGGAATA 57.800 29.630 0.00 0.00 0.00 1.75
1915 1965 9.419297 CATATGATTGATTAAAATGAGCAAGGG 57.581 33.333 0.00 0.00 0.00 3.95
2011 2077 8.948631 ATAATTATCACACCAAGACTGTACAG 57.051 34.615 21.44 21.44 0.00 2.74
2064 2130 5.351189 TGTTCTTACATCATCAACATCGTGG 59.649 40.000 0.00 0.00 0.00 4.94
2076 2142 6.042093 AGAGGACTCAAACTGTTCTTACATCA 59.958 38.462 1.75 0.00 32.86 3.07
2104 2170 5.007136 AGTTTTGAAGTCGAGCTCTTTTCTG 59.993 40.000 12.85 0.00 0.00 3.02
2105 2171 5.119694 AGTTTTGAAGTCGAGCTCTTTTCT 58.880 37.500 12.85 1.79 0.00 2.52
2106 2172 5.411083 AGTTTTGAAGTCGAGCTCTTTTC 57.589 39.130 12.85 12.47 0.00 2.29
2110 2176 4.390297 GCATTAGTTTTGAAGTCGAGCTCT 59.610 41.667 12.85 0.00 0.00 4.09
2111 2177 4.152402 TGCATTAGTTTTGAAGTCGAGCTC 59.848 41.667 2.73 2.73 0.00 4.09
2112 2178 4.065088 TGCATTAGTTTTGAAGTCGAGCT 58.935 39.130 0.00 0.00 0.00 4.09
2113 2179 4.404507 TGCATTAGTTTTGAAGTCGAGC 57.595 40.909 0.00 0.00 0.00 5.03
2114 2180 7.743104 AGTAATGCATTAGTTTTGAAGTCGAG 58.257 34.615 19.41 0.00 0.00 4.04
2115 2181 7.667043 AGTAATGCATTAGTTTTGAAGTCGA 57.333 32.000 19.41 0.00 0.00 4.20
2116 2182 8.728088 AAAGTAATGCATTAGTTTTGAAGTCG 57.272 30.769 32.55 0.00 40.92 4.18
2117 2183 9.899226 AGAAAGTAATGCATTAGTTTTGAAGTC 57.101 29.630 35.71 26.88 42.70 3.01
2146 2214 9.537848 CGCGTCTAAAAATAGAAAAACTACAAT 57.462 29.630 0.00 0.00 33.62 2.71
2147 2215 8.763356 TCGCGTCTAAAAATAGAAAAACTACAA 58.237 29.630 5.77 0.00 33.62 2.41
2148 2216 8.216453 GTCGCGTCTAAAAATAGAAAAACTACA 58.784 33.333 5.77 0.00 33.62 2.74
2149 2217 8.216453 TGTCGCGTCTAAAAATAGAAAAACTAC 58.784 33.333 5.77 0.00 33.62 2.73
2150 2218 8.296799 TGTCGCGTCTAAAAATAGAAAAACTA 57.703 30.769 5.77 0.00 35.42 2.24
2151 2219 7.181143 TGTCGCGTCTAAAAATAGAAAAACT 57.819 32.000 5.77 0.00 0.00 2.66
2152 2220 9.532697 TTATGTCGCGTCTAAAAATAGAAAAAC 57.467 29.630 5.77 0.00 0.00 2.43
2157 2225 9.902196 TGATATTATGTCGCGTCTAAAAATAGA 57.098 29.630 5.77 0.00 0.00 1.98
2158 2226 9.939047 GTGATATTATGTCGCGTCTAAAAATAG 57.061 33.333 5.77 0.00 0.00 1.73
2159 2227 9.687210 AGTGATATTATGTCGCGTCTAAAAATA 57.313 29.630 5.77 5.07 0.00 1.40
2160 2228 8.589335 AGTGATATTATGTCGCGTCTAAAAAT 57.411 30.769 5.77 2.91 0.00 1.82
2161 2229 7.703197 TGAGTGATATTATGTCGCGTCTAAAAA 59.297 33.333 5.77 0.00 0.00 1.94
2162 2230 7.197703 TGAGTGATATTATGTCGCGTCTAAAA 58.802 34.615 5.77 0.00 0.00 1.52
2163 2231 6.731164 TGAGTGATATTATGTCGCGTCTAAA 58.269 36.000 5.77 0.00 0.00 1.85
2164 2232 6.308371 TGAGTGATATTATGTCGCGTCTAA 57.692 37.500 5.77 3.09 0.00 2.10
2165 2233 5.934935 TGAGTGATATTATGTCGCGTCTA 57.065 39.130 5.77 0.00 0.00 2.59
2166 2234 4.830826 TGAGTGATATTATGTCGCGTCT 57.169 40.909 5.77 0.00 0.00 4.18
2167 2235 6.453643 AAATGAGTGATATTATGTCGCGTC 57.546 37.500 5.77 0.00 0.00 5.19
2168 2236 8.534333 AATAAATGAGTGATATTATGTCGCGT 57.466 30.769 5.77 0.00 0.00 6.01
2169 2237 9.811655 AAAATAAATGAGTGATATTATGTCGCG 57.188 29.630 0.00 0.00 0.00 5.87
2205 2273 9.613428 CGGTCAAATATATGGTCCATAATGTAT 57.387 33.333 15.64 6.66 29.74 2.29
2206 2274 8.817876 TCGGTCAAATATATGGTCCATAATGTA 58.182 33.333 15.64 4.57 29.74 2.29
2207 2275 7.685481 TCGGTCAAATATATGGTCCATAATGT 58.315 34.615 15.64 2.35 29.74 2.71
2208 2276 8.560355 TTCGGTCAAATATATGGTCCATAATG 57.440 34.615 15.64 11.88 29.74 1.90
2209 2277 9.231297 CTTTCGGTCAAATATATGGTCCATAAT 57.769 33.333 15.64 7.93 29.74 1.28
2210 2278 8.433599 TCTTTCGGTCAAATATATGGTCCATAA 58.566 33.333 15.64 6.03 29.74 1.90
2211 2279 7.876068 GTCTTTCGGTCAAATATATGGTCCATA 59.124 37.037 14.08 14.08 0.00 2.74
2212 2280 6.710744 GTCTTTCGGTCAAATATATGGTCCAT 59.289 38.462 9.88 9.88 0.00 3.41
2213 2281 6.053005 GTCTTTCGGTCAAATATATGGTCCA 58.947 40.000 0.00 0.00 0.00 4.02
2214 2282 6.289064 AGTCTTTCGGTCAAATATATGGTCC 58.711 40.000 0.00 0.00 0.00 4.46
2215 2283 7.787725 AAGTCTTTCGGTCAAATATATGGTC 57.212 36.000 0.00 0.00 0.00 4.02
2216 2284 9.326413 CTTAAGTCTTTCGGTCAAATATATGGT 57.674 33.333 0.00 0.00 0.00 3.55
2217 2285 9.542462 TCTTAAGTCTTTCGGTCAAATATATGG 57.458 33.333 1.63 0.00 0.00 2.74
2221 2289 7.492994 GCTCTCTTAAGTCTTTCGGTCAAATAT 59.507 37.037 1.63 0.00 0.00 1.28
2222 2290 6.812160 GCTCTCTTAAGTCTTTCGGTCAAATA 59.188 38.462 1.63 0.00 0.00 1.40
2223 2291 5.639931 GCTCTCTTAAGTCTTTCGGTCAAAT 59.360 40.000 1.63 0.00 0.00 2.32
2224 2292 4.989168 GCTCTCTTAAGTCTTTCGGTCAAA 59.011 41.667 1.63 0.00 0.00 2.69
2225 2293 4.557205 GCTCTCTTAAGTCTTTCGGTCAA 58.443 43.478 1.63 0.00 0.00 3.18
2226 2294 3.056749 GGCTCTCTTAAGTCTTTCGGTCA 60.057 47.826 1.63 0.00 0.00 4.02
2227 2295 3.193903 AGGCTCTCTTAAGTCTTTCGGTC 59.806 47.826 1.63 0.00 0.00 4.79
2228 2296 3.166679 AGGCTCTCTTAAGTCTTTCGGT 58.833 45.455 1.63 0.00 0.00 4.69
2229 2297 3.878160 AGGCTCTCTTAAGTCTTTCGG 57.122 47.619 1.63 0.00 0.00 4.30
2230 2298 4.344448 CGTAGGCTCTCTTAAGTCTTTCG 58.656 47.826 1.63 0.00 32.35 3.46
2231 2299 4.674475 CCGTAGGCTCTCTTAAGTCTTTC 58.326 47.826 1.63 0.00 46.14 2.62
2232 2300 4.722361 CCGTAGGCTCTCTTAAGTCTTT 57.278 45.455 1.63 0.00 46.14 2.52
2268 2336 9.459640 GGTACAAATCCTACTTTTCAAGTTTTC 57.540 33.333 0.00 0.00 42.81 2.29
2269 2337 9.197306 AGGTACAAATCCTACTTTTCAAGTTTT 57.803 29.630 0.00 0.00 42.81 2.43
2270 2338 8.762481 AGGTACAAATCCTACTTTTCAAGTTT 57.238 30.769 0.00 0.00 42.81 2.66
2271 2339 8.218488 AGAGGTACAAATCCTACTTTTCAAGTT 58.782 33.333 0.00 0.00 42.81 2.66
2272 2340 7.661847 CAGAGGTACAAATCCTACTTTTCAAGT 59.338 37.037 0.00 0.00 45.40 3.16
2273 2341 7.119846 CCAGAGGTACAAATCCTACTTTTCAAG 59.880 40.741 0.00 0.00 35.20 3.02
2274 2342 6.940298 CCAGAGGTACAAATCCTACTTTTCAA 59.060 38.462 0.00 0.00 35.20 2.69
2275 2343 6.043938 ACCAGAGGTACAAATCCTACTTTTCA 59.956 38.462 0.00 0.00 35.20 2.69
2276 2344 6.371825 CACCAGAGGTACAAATCCTACTTTTC 59.628 42.308 0.00 0.00 35.20 2.29
2277 2345 6.238648 CACCAGAGGTACAAATCCTACTTTT 58.761 40.000 0.00 0.00 35.20 2.27
2278 2346 5.280521 CCACCAGAGGTACAAATCCTACTTT 60.281 44.000 0.00 0.00 35.20 2.66
2279 2347 4.225267 CCACCAGAGGTACAAATCCTACTT 59.775 45.833 0.00 0.00 35.20 2.24
2280 2348 3.775316 CCACCAGAGGTACAAATCCTACT 59.225 47.826 0.00 0.00 35.20 2.57
2281 2349 3.118371 CCCACCAGAGGTACAAATCCTAC 60.118 52.174 0.00 0.00 35.20 3.18
2282 2350 3.112263 CCCACCAGAGGTACAAATCCTA 58.888 50.000 0.00 0.00 35.20 2.94
2283 2351 1.916181 CCCACCAGAGGTACAAATCCT 59.084 52.381 0.00 0.00 38.09 3.24
2284 2352 1.913419 TCCCACCAGAGGTACAAATCC 59.087 52.381 0.00 0.00 32.11 3.01
2285 2353 3.933861 ATCCCACCAGAGGTACAAATC 57.066 47.619 0.00 0.00 32.11 2.17
2286 2354 4.631234 TCTATCCCACCAGAGGTACAAAT 58.369 43.478 0.00 0.00 32.11 2.32
2287 2355 4.069312 TCTATCCCACCAGAGGTACAAA 57.931 45.455 0.00 0.00 32.11 2.83
2288 2356 3.769189 TCTATCCCACCAGAGGTACAA 57.231 47.619 0.00 0.00 32.11 2.41
2289 2357 3.630054 CCTTCTATCCCACCAGAGGTACA 60.630 52.174 0.00 0.00 32.11 2.90
2290 2358 2.966516 CCTTCTATCCCACCAGAGGTAC 59.033 54.545 0.00 0.00 32.11 3.34
2291 2359 2.863238 TCCTTCTATCCCACCAGAGGTA 59.137 50.000 0.00 0.00 32.11 3.08
2292 2360 1.651770 TCCTTCTATCCCACCAGAGGT 59.348 52.381 0.00 0.00 35.62 3.85
2293 2361 2.478872 TCCTTCTATCCCACCAGAGG 57.521 55.000 0.00 0.00 0.00 3.69
2294 2362 4.226168 AGTTTTCCTTCTATCCCACCAGAG 59.774 45.833 0.00 0.00 0.00 3.35
2295 2363 4.019321 CAGTTTTCCTTCTATCCCACCAGA 60.019 45.833 0.00 0.00 0.00 3.86
2296 2364 4.265073 CAGTTTTCCTTCTATCCCACCAG 58.735 47.826 0.00 0.00 0.00 4.00
2297 2365 3.561313 GCAGTTTTCCTTCTATCCCACCA 60.561 47.826 0.00 0.00 0.00 4.17
2298 2366 3.017442 GCAGTTTTCCTTCTATCCCACC 58.983 50.000 0.00 0.00 0.00 4.61
2299 2367 3.017442 GGCAGTTTTCCTTCTATCCCAC 58.983 50.000 0.00 0.00 0.00 4.61
2300 2368 2.919602 AGGCAGTTTTCCTTCTATCCCA 59.080 45.455 0.00 0.00 0.00 4.37
2301 2369 3.546724 GAGGCAGTTTTCCTTCTATCCC 58.453 50.000 0.00 0.00 33.24 3.85
2302 2370 3.546724 GGAGGCAGTTTTCCTTCTATCC 58.453 50.000 0.00 0.00 33.24 2.59
2303 2371 3.546724 GGGAGGCAGTTTTCCTTCTATC 58.453 50.000 0.00 0.00 33.24 2.08
2304 2372 2.092914 CGGGAGGCAGTTTTCCTTCTAT 60.093 50.000 0.00 0.00 33.24 1.98
2305 2373 1.278127 CGGGAGGCAGTTTTCCTTCTA 59.722 52.381 0.00 0.00 33.24 2.10
2306 2374 0.036875 CGGGAGGCAGTTTTCCTTCT 59.963 55.000 0.00 0.00 33.24 2.85
2307 2375 2.556286 CGGGAGGCAGTTTTCCTTC 58.444 57.895 0.00 0.00 33.24 3.46
2308 2376 4.821935 CGGGAGGCAGTTTTCCTT 57.178 55.556 0.00 0.00 33.24 3.36
2502 2570 1.545582 CCATTTGATGCCGTTGTCCTT 59.454 47.619 0.00 0.00 0.00 3.36
2512 2580 2.613691 CCAAACAGCTCCATTTGATGC 58.386 47.619 13.68 0.00 37.91 3.91
2561 2629 0.322277 ATCCAAGCCACAGCACAGAG 60.322 55.000 0.00 0.00 43.56 3.35
2664 2732 1.607467 ACAAATCAGGGGCCAGCAC 60.607 57.895 4.39 0.00 0.00 4.40
2679 2747 2.830827 CCCACCCGCACAACACAA 60.831 61.111 0.00 0.00 0.00 3.33
2725 2793 1.202770 AGCCATTAGCCGGATTACCAC 60.203 52.381 5.05 0.00 45.47 4.16
2854 2922 2.870372 CTGCGGCTGCCTAACAAC 59.130 61.111 16.57 0.00 41.78 3.32
2891 2959 2.094906 TCAAGGTAGTCACAACGGATCG 60.095 50.000 0.00 0.00 0.00 3.69
2898 2966 6.401394 CAGATCTGAATCAAGGTAGTCACAA 58.599 40.000 18.34 0.00 34.07 3.33
2917 2985 1.869767 CGCAACCAAGCTATCCAGATC 59.130 52.381 0.00 0.00 0.00 2.75
3028 3096 2.296831 TTTCACCGTCGAAGTCAACA 57.703 45.000 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.