Multiple sequence alignment - TraesCS3A01G357200

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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 TraesCS3A01G357200 chr3A 100.000 4679 0 0 1 4679 605167754 605172432 0.000000e+00 8641.0
1 TraesCS3A01G357200 chr3A 93.284 134 9 0 1687 1820 28447534 28447401 1.030000e-46 198.0
2 TraesCS3A01G357200 chr3A 100.000 106 0 0 4060 4165 701224907 701224802 3.690000e-46 196.0
3 TraesCS3A01G357200 chr3A 94.340 106 5 1 4060 4165 572680951 572681055 1.350000e-35 161.0
4 TraesCS3A01G357200 chr3A 95.455 44 2 0 2540 2583 150715893 150715936 2.340000e-08 71.3
5 TraesCS3A01G357200 chr3A 86.441 59 6 2 2582 2638 42218544 42218486 3.910000e-06 63.9
6 TraesCS3A01G357200 chr3A 86.441 59 6 2 2582 2638 42247972 42247914 3.910000e-06 63.9
7 TraesCS3A01G357200 chr3B 84.975 1817 140 61 1 1730 613801407 613803177 0.000000e+00 1720.0
8 TraesCS3A01G357200 chr3B 92.430 753 36 9 1779 2526 613803193 613803929 0.000000e+00 1055.0
9 TraesCS3A01G357200 chr3B 95.198 479 23 0 4201 4679 613805579 613806057 0.000000e+00 758.0
10 TraesCS3A01G357200 chr3B 91.196 443 32 6 2979 3420 613804439 613804875 3.120000e-166 595.0
11 TraesCS3A01G357200 chr3B 80.000 665 69 32 3421 4049 613804909 613805545 2.590000e-117 433.0
12 TraesCS3A01G357200 chr3B 85.366 451 23 14 2533 2972 613803982 613804400 1.200000e-115 427.0
13 TraesCS3A01G357200 chr3B 99.057 106 1 0 4060 4165 740517064 740517169 1.720000e-44 191.0
14 TraesCS3A01G357200 chr3B 97.170 106 3 0 4060 4165 517859574 517859469 3.720000e-41 180.0
15 TraesCS3A01G357200 chr3B 90.909 44 3 1 2540 2583 609305088 609305046 1.820000e-04 58.4
16 TraesCS3A01G357200 chr3D 92.054 818 61 3 1 815 462232474 462233290 0.000000e+00 1147.0
17 TraesCS3A01G357200 chr3D 87.019 701 53 19 1812 2502 462234159 462234831 0.000000e+00 756.0
18 TraesCS3A01G357200 chr3D 94.480 471 25 1 4209 4679 462236472 462236941 0.000000e+00 725.0
19 TraesCS3A01G357200 chr3D 85.100 698 57 29 845 1519 462233288 462233961 0.000000e+00 669.0
20 TraesCS3A01G357200 chr3D 85.540 657 56 9 3419 4039 462235762 462236415 0.000000e+00 651.0
21 TraesCS3A01G357200 chr3D 85.045 448 54 9 2979 3423 462235292 462235729 1.190000e-120 444.0
22 TraesCS3A01G357200 chr3D 81.509 265 29 9 2625 2874 462234932 462235191 2.860000e-47 200.0
23 TraesCS3A01G357200 chr7A 95.455 132 6 0 1683 1814 121932675 121932806 1.320000e-50 211.0
24 TraesCS3A01G357200 chr7A 90.909 44 3 1 2540 2583 375916029 375915987 1.820000e-04 58.4
25 TraesCS3A01G357200 chr2A 95.455 132 6 0 1687 1818 773232177 773232308 1.320000e-50 211.0
26 TraesCS3A01G357200 chr2A 94.074 135 8 0 1679 1813 65193125 65192991 6.140000e-49 206.0
27 TraesCS3A01G357200 chr5B 94.776 134 7 0 1687 1820 224325662 224325529 4.740000e-50 209.0
28 TraesCS3A01G357200 chr4B 95.420 131 6 0 1686 1816 576982569 576982439 4.740000e-50 209.0
29 TraesCS3A01G357200 chr4B 98.113 106 2 0 4060 4165 187551768 187551663 8.000000e-43 185.0
30 TraesCS3A01G357200 chr4B 97.222 108 3 0 4058 4165 420967687 420967794 2.880000e-42 183.0
31 TraesCS3A01G357200 chr4B 98.077 104 2 0 4060 4163 142848198 142848095 1.030000e-41 182.0
32 TraesCS3A01G357200 chr4A 94.737 133 7 0 1684 1816 177639141 177639009 1.710000e-49 207.0
33 TraesCS3A01G357200 chr4A 94.776 134 5 2 1682 1813 477881749 477881882 1.710000e-49 207.0
34 TraesCS3A01G357200 chr4A 98.113 106 2 0 4060 4165 209311237 209311342 8.000000e-43 185.0
35 TraesCS3A01G357200 chr6B 94.074 135 6 2 1682 1814 674714630 674714764 2.210000e-48 204.0
36 TraesCS3A01G357200 chr6B 90.566 53 4 1 2530 2582 477221920 477221971 8.400000e-08 69.4
37 TraesCS3A01G357200 chr6B 88.889 54 1 2 2570 2618 567471555 567471502 1.410000e-05 62.1
38 TraesCS3A01G357200 chr1D 97.170 106 2 1 4060 4165 89988043 89988147 1.340000e-40 178.0
39 TraesCS3A01G357200 chr1D 98.438 64 1 0 1276 1339 382725853 382725790 3.830000e-21 113.0
40 TraesCS3A01G357200 chr1D 92.000 50 4 0 2535 2584 413584624 413584575 2.340000e-08 71.3
41 TraesCS3A01G357200 chr1D 82.051 78 12 1 2546 2623 225554717 225554642 1.090000e-06 65.8
42 TraesCS3A01G357200 chr1B 100.000 61 0 0 1279 1339 512636952 512636892 3.830000e-21 113.0
43 TraesCS3A01G357200 chr1B 95.000 60 3 0 1412 1471 512636779 512636720 1.390000e-15 95.3
44 TraesCS3A01G357200 chr1A 100.000 61 0 0 1279 1339 482780061 482780001 3.830000e-21 113.0
45 TraesCS3A01G357200 chr1A 96.721 61 2 0 1411 1471 482779886 482779826 8.280000e-18 102.0
46 TraesCS3A01G357200 chr6D 90.566 53 4 1 2530 2582 309584387 309584438 8.400000e-08 69.4
47 TraesCS3A01G357200 chr5A 93.478 46 2 1 2590 2635 536890438 536890394 3.020000e-07 67.6
48 TraesCS3A01G357200 chr5A 80.000 105 10 6 2540 2635 552064928 552064826 3.020000e-07 67.6
49 TraesCS3A01G357200 chr4D 97.297 37 1 0 2582 2618 312868341 312868377 3.910000e-06 63.9
50 TraesCS3A01G357200 chr2B 92.683 41 2 1 2589 2628 51797602 51797642 1.820000e-04 58.4


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 TraesCS3A01G357200 chr3A 605167754 605172432 4678 False 8641.000000 8641 100.000000 1 4679 1 chr3A.!!$F3 4678
1 TraesCS3A01G357200 chr3B 613801407 613806057 4650 False 831.333333 1720 88.194167 1 4679 6 chr3B.!!$F2 4678
2 TraesCS3A01G357200 chr3D 462232474 462236941 4467 False 656.000000 1147 87.249571 1 4679 7 chr3D.!!$F1 4678

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
357 359 0.317103 GATCGTCATCGTCCGACCTG 60.317 60.0 0.0 0.0 35.69 4.00 F
1072 1116 0.034896 TCGCAAACCTCTCCTCAACC 59.965 55.0 0.0 0.0 0.00 3.77 F
1601 1692 0.174162 GTGGCATTCATTGTCCCAGC 59.826 55.0 0.0 0.0 0.00 4.85 F
2527 2636 0.333312 GAGAGGTCTGTCAGGAGGGA 59.667 60.0 0.0 0.0 0.00 4.20 F
3519 3780 0.175760 AGCGAATACAGATGCGGTGT 59.824 50.0 0.0 0.0 43.31 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1794 1889 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.0 5.23 0.0 44.66 3.13 R
2082 2184 0.175760 GAGGCTTGAGGTCGCATACA 59.824 55.0 0.00 0.0 0.00 2.29 R
3516 3777 0.179225 CATACTTGCGCGGACAACAC 60.179 55.0 8.83 0.0 0.00 3.32 R
3642 3920 0.034477 ACCTTTTATGGAGGCCGTGG 60.034 55.0 0.00 0.0 37.84 4.94 R
4385 4712 1.518056 TTCCGTCGAGCAGGTTACGT 61.518 55.0 0.00 0.0 33.63 3.57 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
184 185 2.266055 GAAGCCAGTCGTCCAGGG 59.734 66.667 0.00 0.00 0.00 4.45
207 208 1.673808 GAGACAACCGCCCGAGGTAT 61.674 60.000 0.00 0.00 45.21 2.73
332 333 3.545481 CGCGCGGTACTGCTTCTG 61.545 66.667 24.84 9.80 0.00 3.02
356 358 1.445716 GGATCGTCATCGTCCGACCT 61.446 60.000 0.00 0.00 35.69 3.85
357 359 0.317103 GATCGTCATCGTCCGACCTG 60.317 60.000 0.00 0.00 35.69 4.00
358 360 1.030488 ATCGTCATCGTCCGACCTGT 61.030 55.000 0.00 0.00 35.69 4.00
359 361 1.211969 CGTCATCGTCCGACCTGTT 59.788 57.895 0.00 0.00 0.00 3.16
361 363 0.526662 GTCATCGTCCGACCTGTTCT 59.473 55.000 0.00 0.00 0.00 3.01
362 364 0.809385 TCATCGTCCGACCTGTTCTC 59.191 55.000 0.00 0.00 0.00 2.87
364 366 0.959372 ATCGTCCGACCTGTTCTCGT 60.959 55.000 0.00 0.00 0.00 4.18
421 423 4.785453 GCCTGGGGGAGTGCTTCG 62.785 72.222 0.00 0.00 33.58 3.79
481 483 4.749310 CCTGCTTCGCGTCCAGCT 62.749 66.667 22.02 0.00 45.59 4.24
589 600 2.255252 GTGCGTGTTGGTGATGGC 59.745 61.111 0.00 0.00 0.00 4.40
601 612 4.796231 GATGGCTCGTCGCGTGGT 62.796 66.667 5.77 0.00 40.44 4.16
658 669 3.127533 GTGATGAGCACGGTGGCC 61.128 66.667 10.60 0.00 37.83 5.36
772 783 2.024414 GTTGTGGTTCAGGTTTCAGCT 58.976 47.619 0.00 0.00 0.00 4.24
776 794 2.023673 TGGTTCAGGTTTCAGCTGTTG 58.976 47.619 14.67 6.15 43.70 3.33
824 842 1.098712 TTGGACACCAACGGAGCAAC 61.099 55.000 0.00 0.00 38.75 4.17
825 843 2.604174 GGACACCAACGGAGCAACG 61.604 63.158 0.00 0.00 40.31 4.10
826 844 3.236618 GACACCAACGGAGCAACGC 62.237 63.158 0.00 0.00 37.37 4.84
827 845 4.368808 CACCAACGGAGCAACGCG 62.369 66.667 3.53 3.53 37.37 6.01
828 846 4.903010 ACCAACGGAGCAACGCGT 62.903 61.111 5.58 5.58 37.37 6.01
829 847 2.735478 CCAACGGAGCAACGCGTA 60.735 61.111 14.46 0.00 37.37 4.42
830 848 2.098233 CCAACGGAGCAACGCGTAT 61.098 57.895 14.46 0.50 37.37 3.06
831 849 1.343821 CAACGGAGCAACGCGTATC 59.656 57.895 14.46 11.49 37.37 2.24
832 850 1.076533 CAACGGAGCAACGCGTATCT 61.077 55.000 14.46 13.06 37.37 1.98
833 851 1.076533 AACGGAGCAACGCGTATCTG 61.077 55.000 14.46 18.31 37.37 2.90
834 852 2.860628 CGGAGCAACGCGTATCTGC 61.861 63.158 23.24 23.24 36.29 4.26
835 853 2.526120 GGAGCAACGCGTATCTGCC 61.526 63.158 26.00 18.33 36.73 4.85
836 854 1.519455 GAGCAACGCGTATCTGCCT 60.519 57.895 26.00 15.72 36.73 4.75
851 869 0.394216 TGCCTTATGCTGCCACGATT 60.394 50.000 0.00 0.00 42.00 3.34
921 939 2.666207 GTGTATCCACGGGCCACA 59.334 61.111 4.39 0.00 0.00 4.17
959 977 0.813184 TAAGGCCCACGTAGAACGAG 59.187 55.000 6.44 0.00 46.05 4.18
973 991 4.932789 CGAGATTTCGGGCCAGAA 57.067 55.556 14.85 14.85 43.05 3.02
974 992 3.153024 CGAGATTTCGGGCCAGAAA 57.847 52.632 29.38 29.38 43.05 2.52
976 994 1.676014 CGAGATTTCGGGCCAGAAAGT 60.676 52.381 30.27 21.92 42.52 2.66
978 996 0.727398 GATTTCGGGCCAGAAAGTCG 59.273 55.000 30.27 12.54 42.52 4.18
983 1010 2.041115 GGGCCAGAAAGTCGAAGGC 61.041 63.158 4.39 0.00 44.48 4.35
1039 1083 4.185059 GTCCGAGCGGTACCGACC 62.185 72.222 37.62 24.53 42.83 4.79
1062 1106 1.961277 CGAGCACCTTCGCAAACCT 60.961 57.895 0.00 0.00 33.39 3.50
1066 1110 1.578206 GCACCTTCGCAAACCTCTCC 61.578 60.000 0.00 0.00 0.00 3.71
1067 1111 0.035458 CACCTTCGCAAACCTCTCCT 59.965 55.000 0.00 0.00 0.00 3.69
1069 1113 0.321671 CCTTCGCAAACCTCTCCTCA 59.678 55.000 0.00 0.00 0.00 3.86
1070 1114 1.270839 CCTTCGCAAACCTCTCCTCAA 60.271 52.381 0.00 0.00 0.00 3.02
1071 1115 1.801178 CTTCGCAAACCTCTCCTCAAC 59.199 52.381 0.00 0.00 0.00 3.18
1072 1116 0.034896 TCGCAAACCTCTCCTCAACC 59.965 55.000 0.00 0.00 0.00 3.77
1073 1117 0.955919 CGCAAACCTCTCCTCAACCC 60.956 60.000 0.00 0.00 0.00 4.11
1074 1118 0.402121 GCAAACCTCTCCTCAACCCT 59.598 55.000 0.00 0.00 0.00 4.34
1075 1119 1.611936 GCAAACCTCTCCTCAACCCTC 60.612 57.143 0.00 0.00 0.00 4.30
1076 1120 0.977395 AAACCTCTCCTCAACCCTCG 59.023 55.000 0.00 0.00 0.00 4.63
1077 1121 1.545706 AACCTCTCCTCAACCCTCGC 61.546 60.000 0.00 0.00 0.00 5.03
1078 1122 2.726351 CCTCTCCTCAACCCTCGCC 61.726 68.421 0.00 0.00 0.00 5.54
1079 1123 3.068691 TCTCCTCAACCCTCGCCG 61.069 66.667 0.00 0.00 0.00 6.46
1080 1124 4.821589 CTCCTCAACCCTCGCCGC 62.822 72.222 0.00 0.00 0.00 6.53
1237 1284 1.331447 TGTGATGAATATGTGCTGCGC 59.669 47.619 6.19 6.19 0.00 6.09
1257 1304 2.252260 CCGTGCGGCTGACTTTTG 59.748 61.111 0.00 0.00 0.00 2.44
1261 1308 0.317854 GTGCGGCTGACTTTTGTTCC 60.318 55.000 0.00 0.00 0.00 3.62
1351 1398 0.721718 CCAAGGTGCGTCTTTCGATC 59.278 55.000 0.00 0.00 42.86 3.69
1353 1400 0.736325 AAGGTGCGTCTTTCGATCGG 60.736 55.000 16.41 0.00 42.86 4.18
1355 1402 1.683790 GGTGCGTCTTTCGATCGGTG 61.684 60.000 16.41 5.95 42.86 4.94
1357 1404 0.522626 TGCGTCTTTCGATCGGTGTA 59.477 50.000 16.41 0.00 42.86 2.90
1380 1442 3.154589 GGAACGGAATCTGTGGGTC 57.845 57.895 0.00 0.00 0.00 4.46
1419 1481 0.603065 GGTGATTGGTGTTTCAGGCC 59.397 55.000 0.00 0.00 0.00 5.19
1474 1536 2.084546 AGCTCGGCAAAGATGTAAACC 58.915 47.619 0.00 0.00 0.00 3.27
1477 1539 2.420022 CTCGGCAAAGATGTAAACCCAG 59.580 50.000 0.00 0.00 0.00 4.45
1565 1655 3.609103 CTGCACACACAGTTTAGAACC 57.391 47.619 0.00 0.00 32.78 3.62
1585 1676 4.344104 ACCAGTTAAATCCAGGAATGTGG 58.656 43.478 0.00 0.00 39.19 4.17
1590 1681 5.127682 AGTTAAATCCAGGAATGTGGCATTC 59.872 40.000 12.04 12.04 37.53 2.67
1601 1692 0.174162 GTGGCATTCATTGTCCCAGC 59.826 55.000 0.00 0.00 0.00 4.85
1617 1708 3.774766 TCCCAGCTCTGTTCTATTAGCAA 59.225 43.478 0.00 0.00 37.44 3.91
1671 1763 6.741109 ACCTTATAACTTTGGGTTGTTTTCG 58.259 36.000 0.00 0.00 38.75 3.46
1679 1771 2.925724 TGGGTTGTTTTCGTCATGAGT 58.074 42.857 0.00 0.00 0.00 3.41
1680 1772 4.074627 TGGGTTGTTTTCGTCATGAGTA 57.925 40.909 0.00 0.00 0.00 2.59
1682 1774 4.454161 TGGGTTGTTTTCGTCATGAGTATG 59.546 41.667 0.00 0.00 35.57 2.39
1701 1796 0.962356 GTGTTACTCCCTCCGTCCGA 60.962 60.000 0.00 0.00 0.00 4.55
1704 1799 1.273327 GTTACTCCCTCCGTCCGAAAA 59.727 52.381 0.00 0.00 0.00 2.29
1715 1810 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
1723 1818 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
1732 1827 8.096414 ACTTGTCATCAAAATGGATAAAAAGGG 58.904 33.333 0.00 0.00 33.42 3.95
1733 1828 7.789202 TGTCATCAAAATGGATAAAAAGGGA 57.211 32.000 0.00 0.00 33.42 4.20
1734 1829 8.378115 TGTCATCAAAATGGATAAAAAGGGAT 57.622 30.769 0.00 0.00 33.42 3.85
1735 1830 8.259411 TGTCATCAAAATGGATAAAAAGGGATG 58.741 33.333 0.00 0.00 33.42 3.51
1737 1832 9.486123 TCATCAAAATGGATAAAAAGGGATGTA 57.514 29.630 0.00 0.00 33.42 2.29
1740 1835 9.713684 TCAAAATGGATAAAAAGGGATGTATCT 57.286 29.630 0.00 0.00 0.00 1.98
1770 1865 9.845214 ACTAAAATACATCTAGATATGTCCCCT 57.155 33.333 4.54 0.00 40.52 4.79
1835 1930 9.474313 AGTATTTCCCAGCAGAATAAAATGTTA 57.526 29.630 0.00 0.00 0.00 2.41
1934 2034 7.708752 AGTCTATTTTTCAGCATAGTGACTAGC 59.291 37.037 0.00 2.49 0.00 3.42
1968 2068 5.676532 TTTTGCCTGCTCAAAATTCATTG 57.323 34.783 7.61 0.00 39.99 2.82
1994 2094 2.872858 GCCAAAGATCCCTTCGATACAC 59.127 50.000 0.00 0.00 0.00 2.90
2044 2146 4.546570 GTTGGTTCAACATAAGTTCCTGC 58.453 43.478 5.97 0.00 43.09 4.85
2056 2158 0.947244 GTTCCTGCTGGTGTTCTGTG 59.053 55.000 9.73 0.00 34.23 3.66
2058 2160 0.546122 TCCTGCTGGTGTTCTGTGTT 59.454 50.000 9.73 0.00 34.23 3.32
2059 2161 0.947244 CCTGCTGGTGTTCTGTGTTC 59.053 55.000 0.51 0.00 0.00 3.18
2061 2163 2.292267 CTGCTGGTGTTCTGTGTTCTT 58.708 47.619 0.00 0.00 0.00 2.52
2069 2171 5.941058 TGGTGTTCTGTGTTCTTTCTGTAAA 59.059 36.000 0.00 0.00 0.00 2.01
2126 2228 4.941263 TGTTATCTACCCAAGATGTTGCAC 59.059 41.667 0.00 0.00 44.95 4.57
2143 2245 6.954944 TGTTGCACTGATTTGTTAGTCTTAC 58.045 36.000 0.00 0.00 0.00 2.34
2191 2296 5.781210 TGCTCTTGTTATCTGATCGAGAT 57.219 39.130 10.99 10.99 44.24 2.75
2192 2297 6.154203 TGCTCTTGTTATCTGATCGAGATT 57.846 37.500 11.34 0.41 41.94 2.40
2193 2298 6.577103 TGCTCTTGTTATCTGATCGAGATTT 58.423 36.000 11.34 0.00 41.94 2.17
2194 2299 7.044181 TGCTCTTGTTATCTGATCGAGATTTT 58.956 34.615 11.34 0.00 41.94 1.82
2519 2627 3.181480 GCTAGACAATGGAGAGGTCTGTC 60.181 52.174 0.00 0.00 41.66 3.51
2520 2628 2.894731 AGACAATGGAGAGGTCTGTCA 58.105 47.619 3.61 0.00 40.21 3.58
2526 2635 0.686112 GGAGAGGTCTGTCAGGAGGG 60.686 65.000 0.00 0.00 0.00 4.30
2527 2636 0.333312 GAGAGGTCTGTCAGGAGGGA 59.667 60.000 0.00 0.00 0.00 4.20
2528 2637 0.334676 AGAGGTCTGTCAGGAGGGAG 59.665 60.000 0.00 0.00 0.00 4.30
2530 2639 1.285373 GAGGTCTGTCAGGAGGGAGTA 59.715 57.143 0.00 0.00 0.00 2.59
2531 2640 1.286553 AGGTCTGTCAGGAGGGAGTAG 59.713 57.143 0.00 0.00 0.00 2.57
2563 2718 3.380320 CCCTCCGACCCAAATTAATTGAC 59.620 47.826 0.39 0.00 41.85 3.18
2576 2731 7.483691 CCAAATTAATTGACGCTGGTTTAGTAC 59.516 37.037 0.39 0.00 41.85 2.73
2580 2735 5.607119 ATTGACGCTGGTTTAGTACAAAG 57.393 39.130 0.00 0.00 0.00 2.77
2581 2736 4.062677 TGACGCTGGTTTAGTACAAAGT 57.937 40.909 0.00 0.00 0.00 2.66
2623 2788 6.901615 TTTGGATTGGAGGGAGTAGAATAA 57.098 37.500 0.00 0.00 0.00 1.40
2727 2892 0.452184 ATCGAGCAGGCGGATATACG 59.548 55.000 1.93 1.93 0.00 3.06
2796 2961 7.398829 TGGCATACATTGAGTAAGTTCCTTTA 58.601 34.615 0.00 0.00 36.05 1.85
2874 3054 3.325293 TTGCCTTTGTGTTTGCTTGAA 57.675 38.095 0.00 0.00 0.00 2.69
2877 3057 3.445450 TGCCTTTGTGTTTGCTTGAAGTA 59.555 39.130 0.00 0.00 0.00 2.24
2881 3068 5.973565 CCTTTGTGTTTGCTTGAAGTAGAAG 59.026 40.000 0.00 0.00 0.00 2.85
2900 3087 1.341531 AGGTCTGACTGGTTGAGAACG 59.658 52.381 7.85 0.00 0.00 3.95
2903 3090 2.795470 GTCTGACTGGTTGAGAACGAAC 59.205 50.000 0.00 0.00 0.00 3.95
2904 3091 2.693591 TCTGACTGGTTGAGAACGAACT 59.306 45.455 0.00 0.00 0.00 3.01
2921 3108 4.864247 ACGAACTTTATTTTCATGGCATGC 59.136 37.500 22.56 9.90 0.00 4.06
2931 3118 6.932356 TTTTCATGGCATGCTTTGTTTTAA 57.068 29.167 22.56 5.53 0.00 1.52
2942 3129 7.693536 GCATGCTTTGTTTTAATGAAATAAGCC 59.306 33.333 11.37 1.58 41.77 4.35
2943 3130 8.719648 CATGCTTTGTTTTAATGAAATAAGCCA 58.280 29.630 13.45 6.47 41.77 4.75
2946 3133 8.773645 GCTTTGTTTTAATGAAATAAGCCACTT 58.226 29.630 8.20 0.00 39.40 3.16
2991 3212 9.388506 CCATGAATAATCTAGGCTATTAACTGG 57.611 37.037 0.00 0.00 0.00 4.00
3012 3233 2.550180 GTGAAGAAAGCTGGTCAGTTCC 59.450 50.000 0.00 0.00 0.00 3.62
3013 3234 2.172505 TGAAGAAAGCTGGTCAGTTCCA 59.827 45.455 0.00 0.00 36.00 3.53
3015 3236 2.787994 AGAAAGCTGGTCAGTTCCATG 58.212 47.619 0.00 0.00 36.84 3.66
3020 3241 3.378512 AGCTGGTCAGTTCCATGATAGA 58.621 45.455 0.00 0.00 36.84 1.98
3033 3254 8.713036 AGTTCCATGATAGATCTAGAGCTTTTT 58.287 33.333 16.99 1.56 0.00 1.94
3067 3288 6.655078 AGTCCAATATTCTGCTGTGTTTTT 57.345 33.333 0.00 0.00 0.00 1.94
3087 3308 3.766068 TGCAAATTTGGCCAAGATTGA 57.234 38.095 32.82 21.36 0.00 2.57
3088 3309 4.289238 TGCAAATTTGGCCAAGATTGAT 57.711 36.364 32.82 18.24 0.00 2.57
3089 3310 4.004314 TGCAAATTTGGCCAAGATTGATG 58.996 39.130 32.82 23.15 0.00 3.07
3090 3311 4.004982 GCAAATTTGGCCAAGATTGATGT 58.995 39.130 32.82 14.55 0.00 3.06
3093 3314 2.905415 TTGGCCAAGATTGATGTCCT 57.095 45.000 16.05 0.00 0.00 3.85
3095 3316 2.449464 TGGCCAAGATTGATGTCCTTG 58.551 47.619 0.61 0.00 37.58 3.61
3104 3327 7.309990 CCAAGATTGATGTCCTTGTACCAAAAT 60.310 37.037 0.00 0.00 36.47 1.82
3115 3338 5.245075 CCTTGTACCAAAATTTTGCTCCCTA 59.755 40.000 22.90 8.18 36.86 3.53
3119 3342 7.740805 TGTACCAAAATTTTGCTCCCTAAAAT 58.259 30.769 22.90 0.00 38.88 1.82
3192 3415 1.518367 TCAACAGGACTTTCCACCCT 58.482 50.000 0.00 0.00 39.61 4.34
3280 3503 3.910490 GCCAAACCTGCAACGCCA 61.910 61.111 0.00 0.00 0.00 5.69
3325 3548 0.982852 ATCCATGGGCCAAGTCTCGA 60.983 55.000 11.89 0.00 0.00 4.04
3365 3588 3.305608 CGGACCTAAAGTTACCGTGAACT 60.306 47.826 0.00 0.00 41.50 3.01
3391 3614 4.978438 ATCAGAAGGCTTATGAGAGCAT 57.022 40.909 26.38 9.55 44.49 3.79
3396 3619 5.642919 CAGAAGGCTTATGAGAGCATTATCC 59.357 44.000 16.61 0.00 45.54 2.59
3436 3697 0.815734 AATGAGGCTTGTCATGCAGC 59.184 50.000 12.33 0.00 37.24 5.25
3448 3709 2.991190 GTCATGCAGCAGGATTTTTGTG 59.009 45.455 13.86 0.00 0.00 3.33
3449 3710 2.629137 TCATGCAGCAGGATTTTTGTGT 59.371 40.909 5.43 0.00 0.00 3.72
3453 3714 2.608752 GCAGCAGGATTTTTGTGTCAGG 60.609 50.000 0.00 0.00 0.00 3.86
3459 3720 5.066505 GCAGGATTTTTGTGTCAGGGTATAG 59.933 44.000 0.00 0.00 0.00 1.31
3465 3726 3.861276 TGTGTCAGGGTATAGTTGTCG 57.139 47.619 0.00 0.00 0.00 4.35
3499 3760 5.601662 TCAACTTAGATTTGCTATCCCTCG 58.398 41.667 0.00 0.00 0.00 4.63
3512 3773 1.982660 TCCCTCGAGCGAATACAGAT 58.017 50.000 6.99 0.00 0.00 2.90
3513 3774 1.609072 TCCCTCGAGCGAATACAGATG 59.391 52.381 6.99 0.00 0.00 2.90
3514 3775 1.413382 CCTCGAGCGAATACAGATGC 58.587 55.000 6.99 0.00 0.00 3.91
3516 3777 0.317854 TCGAGCGAATACAGATGCGG 60.318 55.000 0.00 0.00 34.32 5.69
3518 3779 0.855349 GAGCGAATACAGATGCGGTG 59.145 55.000 0.00 0.00 44.98 4.94
3519 3780 0.175760 AGCGAATACAGATGCGGTGT 59.824 50.000 0.00 0.00 43.31 4.16
3520 3781 1.006832 GCGAATACAGATGCGGTGTT 58.993 50.000 0.00 0.00 34.32 3.32
3521 3782 1.267532 GCGAATACAGATGCGGTGTTG 60.268 52.381 0.00 0.00 34.32 3.33
3523 3784 2.029244 CGAATACAGATGCGGTGTTGTC 59.971 50.000 0.00 0.00 29.51 3.18
3524 3785 2.024176 ATACAGATGCGGTGTTGTCC 57.976 50.000 0.00 0.00 0.00 4.02
3531 3792 4.368808 CGGTGTTGTCCGCGCAAG 62.369 66.667 8.75 0.00 43.96 4.01
3533 3794 1.957186 GGTGTTGTCCGCGCAAGTA 60.957 57.895 8.75 0.00 41.68 2.24
3551 3826 0.179032 TATGGTGGTATGGCGCAAGG 60.179 55.000 10.83 0.00 38.28 3.61
3556 3831 1.377987 GGTATGGCGCAAGGGTCAA 60.378 57.895 10.83 0.00 38.28 3.18
3557 3832 0.963355 GGTATGGCGCAAGGGTCAAA 60.963 55.000 10.83 0.00 38.28 2.69
3561 3836 1.243342 TGGCGCAAGGGTCAAAGATG 61.243 55.000 10.83 0.00 38.28 2.90
3566 3843 2.811431 CGCAAGGGTCAAAGATGTGTTA 59.189 45.455 0.00 0.00 0.00 2.41
3567 3844 3.252215 CGCAAGGGTCAAAGATGTGTTAA 59.748 43.478 0.00 0.00 0.00 2.01
3572 3849 7.870445 GCAAGGGTCAAAGATGTGTTAATTTTA 59.130 33.333 0.00 0.00 0.00 1.52
3575 3852 7.507616 AGGGTCAAAGATGTGTTAATTTTACCA 59.492 33.333 0.00 0.00 0.00 3.25
3640 3918 1.834996 GAGCCTGGATCTCATGCCA 59.165 57.895 4.35 0.00 37.67 4.92
3642 3920 0.400975 AGCCTGGATCTCATGCCATC 59.599 55.000 0.00 0.00 37.67 3.51
3659 3937 1.949525 CATCCACGGCCTCCATAAAAG 59.050 52.381 0.00 0.00 0.00 2.27
3666 3944 2.092914 CGGCCTCCATAAAAGGTCTCTT 60.093 50.000 0.00 0.00 36.32 2.85
3713 4004 1.670295 TGTGTGTGTTTACTGCAGCTG 59.330 47.619 15.27 10.11 0.00 4.24
3718 4009 0.182537 TGTTTACTGCAGCTGGTGGT 59.817 50.000 17.12 1.66 0.00 4.16
3813 4109 2.422597 TCTGTTACGGTGGAATTGCTG 58.577 47.619 0.00 0.00 0.00 4.41
3823 4119 2.923020 GTGGAATTGCTGCCATTTAACG 59.077 45.455 0.15 0.00 36.41 3.18
3890 4192 3.377172 CCATTCTATGAACCAAACGACCC 59.623 47.826 0.00 0.00 0.00 4.46
3901 4204 4.403734 ACCAAACGACCCACATAGAAAAT 58.596 39.130 0.00 0.00 0.00 1.82
3907 4210 8.696175 CAAACGACCCACATAGAAAATAAAAAC 58.304 33.333 0.00 0.00 0.00 2.43
3909 4212 6.717997 ACGACCCACATAGAAAATAAAAACCT 59.282 34.615 0.00 0.00 0.00 3.50
3961 4284 2.155732 CGAACAAGTGGAGATTGACGTG 59.844 50.000 0.00 0.00 0.00 4.49
3981 4304 2.857152 TGCGTGCTTGTCATTTCAAAAC 59.143 40.909 0.00 0.00 0.00 2.43
3987 4310 5.057819 TGCTTGTCATTTCAAAACATGCAT 58.942 33.333 10.11 0.00 44.27 3.96
3995 4318 7.531534 GTCATTTCAAAACATGCATTAACAAGC 59.468 33.333 0.00 0.00 0.00 4.01
4022 4346 8.528643 TCTATAATTTTCAAACTCCGTCTCTGA 58.471 33.333 0.00 0.00 0.00 3.27
4039 4363 7.307989 CCGTCTCTGAATTTTACACATCACTTT 60.308 37.037 0.00 0.00 0.00 2.66
4040 4364 8.070171 CGTCTCTGAATTTTACACATCACTTTT 58.930 33.333 0.00 0.00 0.00 2.27
4051 4375 8.918961 TTACACATCACTTTTACAAACTTTGG 57.081 30.769 6.47 0.00 34.12 3.28
4052 4376 7.164230 ACACATCACTTTTACAAACTTTGGA 57.836 32.000 6.47 0.00 34.12 3.53
4053 4377 7.607250 ACACATCACTTTTACAAACTTTGGAA 58.393 30.769 6.47 0.63 34.12 3.53
4054 4378 8.091449 ACACATCACTTTTACAAACTTTGGAAA 58.909 29.630 7.69 7.69 41.55 3.13
4060 4384 6.976636 TTTTACAAACTTTGGAAAAGCTGG 57.023 33.333 17.34 0.00 45.81 4.85
4061 4385 3.541996 ACAAACTTTGGAAAAGCTGGG 57.458 42.857 6.47 0.00 34.12 4.45
4062 4386 3.103742 ACAAACTTTGGAAAAGCTGGGA 58.896 40.909 6.47 0.00 34.12 4.37
4063 4387 3.517500 ACAAACTTTGGAAAAGCTGGGAA 59.482 39.130 6.47 0.00 34.12 3.97
4064 4388 4.122046 CAAACTTTGGAAAAGCTGGGAAG 58.878 43.478 0.00 0.00 0.00 3.46
4065 4389 1.688735 ACTTTGGAAAAGCTGGGAAGC 59.311 47.619 0.00 0.00 0.00 3.86
4066 4390 1.688197 CTTTGGAAAAGCTGGGAAGCA 59.312 47.619 0.00 0.00 37.25 3.91
4067 4391 1.039856 TTGGAAAAGCTGGGAAGCAC 58.960 50.000 0.00 0.00 37.25 4.40
4068 4392 0.185901 TGGAAAAGCTGGGAAGCACT 59.814 50.000 0.00 0.00 37.25 4.40
4069 4393 1.423541 TGGAAAAGCTGGGAAGCACTA 59.576 47.619 0.00 0.00 37.25 2.74
4070 4394 2.087646 GGAAAAGCTGGGAAGCACTAG 58.912 52.381 0.00 0.00 37.25 2.57
4071 4395 1.470494 GAAAAGCTGGGAAGCACTAGC 59.530 52.381 0.00 3.77 42.56 3.42
4099 4423 5.355467 CAACTTCTGCTTCTCTTTTCTCC 57.645 43.478 0.00 0.00 0.00 3.71
4100 4424 4.014569 ACTTCTGCTTCTCTTTTCTCCC 57.985 45.455 0.00 0.00 0.00 4.30
4101 4425 3.244735 ACTTCTGCTTCTCTTTTCTCCCC 60.245 47.826 0.00 0.00 0.00 4.81
4102 4426 1.630878 TCTGCTTCTCTTTTCTCCCCC 59.369 52.381 0.00 0.00 0.00 5.40
4103 4427 1.632920 CTGCTTCTCTTTTCTCCCCCT 59.367 52.381 0.00 0.00 0.00 4.79
4104 4428 2.040947 CTGCTTCTCTTTTCTCCCCCTT 59.959 50.000 0.00 0.00 0.00 3.95
4105 4429 2.447047 TGCTTCTCTTTTCTCCCCCTTT 59.553 45.455 0.00 0.00 0.00 3.11
4106 4430 2.822561 GCTTCTCTTTTCTCCCCCTTTG 59.177 50.000 0.00 0.00 0.00 2.77
4107 4431 3.425659 CTTCTCTTTTCTCCCCCTTTGG 58.574 50.000 0.00 0.00 0.00 3.28
4108 4432 2.428901 TCTCTTTTCTCCCCCTTTGGT 58.571 47.619 0.00 0.00 0.00 3.67
4109 4433 2.789399 TCTCTTTTCTCCCCCTTTGGTT 59.211 45.455 0.00 0.00 0.00 3.67
4110 4434 3.984770 TCTCTTTTCTCCCCCTTTGGTTA 59.015 43.478 0.00 0.00 0.00 2.85
4111 4435 4.042934 TCTCTTTTCTCCCCCTTTGGTTAG 59.957 45.833 0.00 0.00 0.00 2.34
4112 4436 2.597578 TTTCTCCCCCTTTGGTTAGC 57.402 50.000 0.00 0.00 0.00 3.09
4113 4437 1.755200 TTCTCCCCCTTTGGTTAGCT 58.245 50.000 0.00 0.00 0.00 3.32
4114 4438 1.755200 TCTCCCCCTTTGGTTAGCTT 58.245 50.000 0.00 0.00 0.00 3.74
4115 4439 2.923908 TCTCCCCCTTTGGTTAGCTTA 58.076 47.619 0.00 0.00 0.00 3.09
4116 4440 3.470868 TCTCCCCCTTTGGTTAGCTTAT 58.529 45.455 0.00 0.00 0.00 1.73
4117 4441 4.637600 TCTCCCCCTTTGGTTAGCTTATA 58.362 43.478 0.00 0.00 0.00 0.98
4118 4442 4.658901 TCTCCCCCTTTGGTTAGCTTATAG 59.341 45.833 0.00 0.00 0.00 1.31
4119 4443 3.137728 TCCCCCTTTGGTTAGCTTATAGC 59.862 47.826 0.00 0.00 42.84 2.97
4146 4470 3.767816 CCAGAAGCTGGCTGCAAA 58.232 55.556 18.84 0.00 45.13 3.68
4147 4471 2.043625 CCAGAAGCTGGCTGCAAAA 58.956 52.632 18.84 0.00 45.13 2.44
4148 4472 0.038526 CCAGAAGCTGGCTGCAAAAG 60.039 55.000 18.84 5.65 45.13 2.27
4160 4484 2.891112 CTGCAAAAGCTCAACCAAACA 58.109 42.857 0.00 0.00 0.00 2.83
4161 4485 2.604462 CTGCAAAAGCTCAACCAAACAC 59.396 45.455 0.00 0.00 0.00 3.32
4162 4486 2.028658 TGCAAAAGCTCAACCAAACACA 60.029 40.909 0.00 0.00 0.00 3.72
4163 4487 2.604462 GCAAAAGCTCAACCAAACACAG 59.396 45.455 0.00 0.00 0.00 3.66
4164 4488 2.584492 AAAGCTCAACCAAACACAGC 57.416 45.000 0.00 0.00 0.00 4.40
4170 4494 2.184167 AACCAAACACAGCGTCCGG 61.184 57.895 0.00 0.00 0.00 5.14
4172 4499 1.301087 CCAAACACAGCGTCCGGTA 60.301 57.895 0.00 0.00 0.00 4.02
4183 4510 0.235144 CGTCCGGTACTGCTATCTCG 59.765 60.000 0.00 0.00 0.00 4.04
4185 4512 1.170919 TCCGGTACTGCTATCTCGGC 61.171 60.000 0.00 0.00 37.65 5.54
4188 4515 1.113517 GGTACTGCTATCTCGGCCCA 61.114 60.000 0.00 0.00 0.00 5.36
4189 4516 0.750850 GTACTGCTATCTCGGCCCAA 59.249 55.000 0.00 0.00 0.00 4.12
4190 4517 1.040646 TACTGCTATCTCGGCCCAAG 58.959 55.000 0.00 0.00 0.00 3.61
4191 4518 0.687757 ACTGCTATCTCGGCCCAAGA 60.688 55.000 5.02 5.02 0.00 3.02
4192 4519 0.465705 CTGCTATCTCGGCCCAAGAA 59.534 55.000 6.58 0.00 0.00 2.52
4193 4520 0.465705 TGCTATCTCGGCCCAAGAAG 59.534 55.000 6.58 6.98 0.00 2.85
4195 4522 0.755686 CTATCTCGGCCCAAGAAGCT 59.244 55.000 6.58 0.00 0.00 3.74
4196 4523 0.753262 TATCTCGGCCCAAGAAGCTC 59.247 55.000 6.58 0.00 0.00 4.09
4197 4524 2.303549 ATCTCGGCCCAAGAAGCTCG 62.304 60.000 6.58 0.00 0.00 5.03
4198 4525 4.082523 TCGGCCCAAGAAGCTCGG 62.083 66.667 0.00 0.00 0.00 4.63
4213 4540 4.100084 CGGCATCCTCAGCACCCA 62.100 66.667 0.00 0.00 0.00 4.51
4248 4575 0.827089 CACCAAATCCCTGCACCACA 60.827 55.000 0.00 0.00 0.00 4.17
4254 4581 0.251341 ATCCCTGCACCACAAAGACC 60.251 55.000 0.00 0.00 0.00 3.85
4258 4585 1.785041 CTGCACCACAAAGACCCACG 61.785 60.000 0.00 0.00 0.00 4.94
4409 4736 2.892425 CTGCTCGACGGAATGCCC 60.892 66.667 0.00 0.00 0.00 5.36
4412 4739 1.367840 GCTCGACGGAATGCCCTAT 59.632 57.895 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.827925 TTCACCTCTCCTGCGTGTCT 60.828 55.000 0.00 0.00 0.00 3.41
9 10 1.079543 CCTTCACCTCTCCTGCGTG 60.080 63.158 0.00 0.00 0.00 5.34
540 542 2.661537 CGACACGCAGCAGGACAA 60.662 61.111 0.00 0.00 0.00 3.18
572 580 2.187599 GAGCCATCACCAACACGCAC 62.188 60.000 0.00 0.00 0.00 5.34
578 586 2.740714 GCGACGAGCCATCACCAAC 61.741 63.158 0.00 0.00 40.81 3.77
580 588 4.794439 CGCGACGAGCCATCACCA 62.794 66.667 0.00 0.00 44.76 4.17
582 593 3.545481 CACGCGACGAGCCATCAC 61.545 66.667 15.93 0.00 44.76 3.06
608 619 1.107538 CCCAGCCTGATCTGCCATTG 61.108 60.000 0.00 0.00 32.87 2.82
609 620 1.229359 CCCAGCCTGATCTGCCATT 59.771 57.895 0.00 0.00 32.87 3.16
693 704 1.689582 AATCTGACCGGTCCTCCCC 60.690 63.158 31.19 6.98 0.00 4.81
703 714 1.209504 TCGATGGGGAACAATCTGACC 59.790 52.381 0.00 0.00 0.00 4.02
756 767 2.023673 CAACAGCTGAAACCTGAACCA 58.976 47.619 23.35 0.00 34.47 3.67
772 783 4.228567 TCGTGCCTGTCGCCAACA 62.229 61.111 0.00 0.00 36.24 3.33
782 800 0.179062 GATGATCTTGCCTCGTGCCT 60.179 55.000 0.00 0.00 40.16 4.75
783 801 1.493950 CGATGATCTTGCCTCGTGCC 61.494 60.000 0.00 0.00 40.16 5.01
785 803 2.145958 ATCGATGATCTTGCCTCGTG 57.854 50.000 0.00 0.00 33.10 4.35
792 810 3.940852 TGGTGTCCAAATCGATGATCTTG 59.059 43.478 0.00 0.00 0.00 3.02
833 851 1.593196 TAATCGTGGCAGCATAAGGC 58.407 50.000 0.00 0.00 45.30 4.35
834 852 2.413112 CGATAATCGTGGCAGCATAAGG 59.587 50.000 0.00 0.00 34.72 2.69
835 853 3.712162 CGATAATCGTGGCAGCATAAG 57.288 47.619 0.00 0.00 34.72 1.73
959 977 0.727398 CGACTTTCTGGCCCGAAATC 59.273 55.000 20.94 17.71 32.90 2.17
971 989 3.565516 GAAATGTTGGCCTTCGACTTTC 58.434 45.455 3.32 2.51 0.00 2.62
973 991 1.886542 GGAAATGTTGGCCTTCGACTT 59.113 47.619 3.32 0.00 0.00 3.01
974 992 1.534729 GGAAATGTTGGCCTTCGACT 58.465 50.000 3.32 0.00 0.00 4.18
976 994 0.958382 CCGGAAATGTTGGCCTTCGA 60.958 55.000 3.32 0.00 0.00 3.71
978 996 1.215382 GCCGGAAATGTTGGCCTTC 59.785 57.895 5.05 0.00 43.06 3.46
983 1010 2.126502 GCGTGCCGGAAATGTTGG 60.127 61.111 5.05 0.00 0.00 3.77
1062 1106 3.068691 CGGCGAGGGTTGAGGAGA 61.069 66.667 0.00 0.00 0.00 3.71
1170 1217 3.260380 GCACTAGATACCTGAGCATGGAT 59.740 47.826 0.00 0.00 0.00 3.41
1256 1303 0.250124 AAGCACACGAATCCGGAACA 60.250 50.000 9.01 0.00 40.78 3.18
1257 1304 0.442699 GAAGCACACGAATCCGGAAC 59.557 55.000 9.01 4.92 40.78 3.62
1261 1308 3.081133 CCGAAGCACACGAATCCG 58.919 61.111 0.00 0.00 42.50 4.18
1315 1362 2.278013 GCGACGGTGGTCTCGATC 60.278 66.667 0.00 0.00 41.16 3.69
1339 1386 1.517276 CATACACCGATCGAAAGACGC 59.483 52.381 18.66 0.00 46.97 5.19
1365 1427 1.056660 AACAGACCCACAGATTCCGT 58.943 50.000 0.00 0.00 0.00 4.69
1380 1442 3.181454 ACCAGAAAGGGTCAGTACAACAG 60.181 47.826 0.00 0.00 43.89 3.16
1474 1536 1.755179 CACTAGGGAAATGGTGCTGG 58.245 55.000 0.00 0.00 0.00 4.85
1565 1655 3.763360 TGCCACATTCCTGGATTTAACTG 59.237 43.478 0.00 0.00 32.30 3.16
1585 1676 1.404391 CAGAGCTGGGACAATGAATGC 59.596 52.381 0.00 0.00 38.70 3.56
1590 1681 2.486472 AGAACAGAGCTGGGACAATG 57.514 50.000 0.00 0.00 38.70 2.82
1601 1692 6.703607 ACGGATTGATTGCTAATAGAACAGAG 59.296 38.462 0.00 0.00 0.00 3.35
1617 1708 2.783135 AGTGACTGCAAACGGATTGAT 58.217 42.857 1.83 0.00 41.85 2.57
1679 1771 2.381911 GGACGGAGGGAGTAACACATA 58.618 52.381 0.00 0.00 0.00 2.29
1680 1772 1.192428 GGACGGAGGGAGTAACACAT 58.808 55.000 0.00 0.00 0.00 3.21
1682 1774 0.962356 TCGGACGGAGGGAGTAACAC 60.962 60.000 0.00 0.00 0.00 3.32
1744 1839 9.845214 AGGGGACATATCTAGATGTATTTTAGT 57.155 33.333 15.79 1.73 40.18 2.24
1762 1857 9.136323 GTCATCAAGATTAATAAAAGGGGACAT 57.864 33.333 0.00 0.00 0.00 3.06
1763 1858 8.112822 TGTCATCAAGATTAATAAAAGGGGACA 58.887 33.333 0.00 0.00 0.00 4.02
1764 1859 8.519799 TGTCATCAAGATTAATAAAAGGGGAC 57.480 34.615 0.00 0.00 0.00 4.46
1779 1874 8.994207 CCGTCCGGAAATACTTGTCATCAAGA 62.994 46.154 5.23 0.31 44.37 3.02
1780 1875 6.918800 CCGTCCGGAAATACTTGTCATCAAG 61.919 48.000 5.23 6.44 45.65 3.02
1781 1876 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
1782 1877 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
1783 1878 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
1794 1889 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
1957 2057 5.792741 TCTTTGGCCCTACAATGAATTTTG 58.207 37.500 0.00 0.00 33.33 2.44
1994 2094 4.222336 AGAGTGATAATCAGGACTCCCAG 58.778 47.826 0.00 0.00 36.31 4.45
2044 2146 3.941483 ACAGAAAGAACACAGAACACCAG 59.059 43.478 0.00 0.00 0.00 4.00
2069 2171 5.305644 AGGTCGCATACAGAAGGAGATAATT 59.694 40.000 0.00 0.00 0.00 1.40
2078 2180 1.929836 GCTTGAGGTCGCATACAGAAG 59.070 52.381 0.00 0.00 0.00 2.85
2082 2184 0.175760 GAGGCTTGAGGTCGCATACA 59.824 55.000 0.00 0.00 0.00 2.29
2083 2185 0.461961 AGAGGCTTGAGGTCGCATAC 59.538 55.000 0.00 0.00 0.00 2.39
2126 2228 7.444183 TGAAACCTGGTAAGACTAACAAATCAG 59.556 37.037 0.00 0.00 0.00 2.90
2232 2337 6.003326 TGACATGAGGTTCTGAATTTTAGCA 58.997 36.000 0.00 0.00 0.00 3.49
2489 2595 5.338381 CCTCTCCATTGTCTAGCAAGGTTAA 60.338 44.000 9.55 0.00 40.86 2.01
2519 2627 3.571590 AGCAGTATTCTACTCCCTCCTG 58.428 50.000 0.00 0.00 36.76 3.86
2520 2628 3.437344 GGAGCAGTATTCTACTCCCTCCT 60.437 52.174 7.27 0.00 44.46 3.69
2526 2635 2.554893 CGGAGGGAGCAGTATTCTACTC 59.445 54.545 0.00 0.00 36.76 2.59
2527 2636 2.175069 TCGGAGGGAGCAGTATTCTACT 59.825 50.000 0.00 0.00 40.28 2.57
2528 2637 2.293955 GTCGGAGGGAGCAGTATTCTAC 59.706 54.545 0.00 0.00 0.00 2.59
2530 2639 1.404843 GTCGGAGGGAGCAGTATTCT 58.595 55.000 0.00 0.00 0.00 2.40
2531 2640 0.389757 GGTCGGAGGGAGCAGTATTC 59.610 60.000 0.00 0.00 42.75 1.75
2538 2693 0.544697 TAATTTGGGTCGGAGGGAGC 59.455 55.000 0.00 0.00 42.48 4.70
2576 2731 7.867445 ATTAATTGACGCTGGTTTAACTTTG 57.133 32.000 0.00 0.00 0.00 2.77
2580 2735 6.864165 TCCAAATTAATTGACGCTGGTTTAAC 59.136 34.615 13.18 0.00 41.85 2.01
2581 2736 6.982852 TCCAAATTAATTGACGCTGGTTTAA 58.017 32.000 13.18 0.00 41.85 1.52
2591 2756 6.381133 ACTCCCTCCAATCCAAATTAATTGAC 59.619 38.462 0.39 0.00 41.85 3.18
2727 2892 4.499758 CGTATCCTAGTTCGCAAAAGTCTC 59.500 45.833 0.00 0.00 0.00 3.36
2809 2974 7.418025 GGTGAGTAACAGATAGTAGGAAATGCT 60.418 40.741 0.00 0.00 0.00 3.79
2810 2975 6.702282 GGTGAGTAACAGATAGTAGGAAATGC 59.298 42.308 0.00 0.00 0.00 3.56
2822 2987 9.574516 AACAGAAATAAAAGGTGAGTAACAGAT 57.425 29.630 0.00 0.00 0.00 2.90
2823 2988 8.974060 AACAGAAATAAAAGGTGAGTAACAGA 57.026 30.769 0.00 0.00 0.00 3.41
2824 2989 9.450807 CAAACAGAAATAAAAGGTGAGTAACAG 57.549 33.333 0.00 0.00 0.00 3.16
2825 2990 9.179909 TCAAACAGAAATAAAAGGTGAGTAACA 57.820 29.630 0.00 0.00 0.00 2.41
2826 2991 9.447040 GTCAAACAGAAATAAAAGGTGAGTAAC 57.553 33.333 0.00 0.00 0.00 2.50
2874 3054 3.829601 CTCAACCAGTCAGACCTTCTACT 59.170 47.826 0.00 0.00 0.00 2.57
2877 3057 2.964209 TCTCAACCAGTCAGACCTTCT 58.036 47.619 0.00 0.00 0.00 2.85
2881 3068 1.340248 TCGTTCTCAACCAGTCAGACC 59.660 52.381 0.00 0.00 0.00 3.85
2900 3087 6.973229 AAGCATGCCATGAAAATAAAGTTC 57.027 33.333 15.66 0.00 0.00 3.01
2903 3090 6.730960 ACAAAGCATGCCATGAAAATAAAG 57.269 33.333 22.87 0.00 0.00 1.85
2904 3091 7.507733 AAACAAAGCATGCCATGAAAATAAA 57.492 28.000 22.87 0.00 0.00 1.40
2931 3118 4.591321 TCCTGGAAGTGGCTTATTTCAT 57.409 40.909 0.00 0.00 0.00 2.57
2973 3160 7.676683 TCTTCACCAGTTAATAGCCTAGATT 57.323 36.000 0.00 0.00 0.00 2.40
2976 3163 6.258947 GCTTTCTTCACCAGTTAATAGCCTAG 59.741 42.308 0.00 0.00 0.00 3.02
2991 3212 2.550180 GGAACTGACCAGCTTTCTTCAC 59.450 50.000 0.00 0.00 0.00 3.18
3012 3233 8.881743 GGCATAAAAAGCTCTAGATCTATCATG 58.118 37.037 2.11 0.96 0.00 3.07
3013 3234 8.600668 TGGCATAAAAAGCTCTAGATCTATCAT 58.399 33.333 2.11 0.00 0.00 2.45
3015 3236 8.839310 TTGGCATAAAAAGCTCTAGATCTATC 57.161 34.615 2.11 0.00 0.00 2.08
3020 3241 8.049721 ACTAACTTGGCATAAAAAGCTCTAGAT 58.950 33.333 0.00 0.00 0.00 1.98
3033 3254 6.486657 GCAGAATATTGGACTAACTTGGCATA 59.513 38.462 0.00 0.00 0.00 3.14
3067 3288 3.766068 TCAATCTTGGCCAAATTTGCA 57.234 38.095 25.06 15.92 0.00 4.08
3095 3316 9.062524 AAATTTTAGGGAGCAAAATTTTGGTAC 57.937 29.630 29.29 29.29 46.04 3.34
3104 3327 6.739331 TCTGGAAAATTTTAGGGAGCAAAA 57.261 33.333 2.75 0.00 0.00 2.44
3192 3415 3.081061 AGATACAACATCCGCAAAAGCA 58.919 40.909 0.00 0.00 0.00 3.91
3201 3424 6.260936 CAGGGAACATGTTAGATACAACATCC 59.739 42.308 11.95 3.61 45.18 3.51
3202 3425 6.823689 ACAGGGAACATGTTAGATACAACATC 59.176 38.462 11.95 0.00 45.18 3.06
3325 3548 2.352805 GCCCACTGTTGGCTAGCT 59.647 61.111 15.72 0.00 45.70 3.32
3343 3566 2.989166 GTTCACGGTAACTTTAGGTCCG 59.011 50.000 0.00 0.00 45.53 4.79
3365 3588 5.678583 CTCTCATAAGCCTTCTGATTTGGA 58.321 41.667 0.00 0.00 0.00 3.53
3391 3614 5.070001 CCAGAAAGAAACACAGTGGGATAA 58.930 41.667 0.00 0.00 0.00 1.75
3392 3615 4.104102 ACCAGAAAGAAACACAGTGGGATA 59.896 41.667 0.00 0.00 0.00 2.59
3396 3619 3.278574 TCACCAGAAAGAAACACAGTGG 58.721 45.455 5.31 0.00 0.00 4.00
3436 3697 6.180472 ACTATACCCTGACACAAAAATCCTG 58.820 40.000 0.00 0.00 0.00 3.86
3448 3709 6.630444 TTCTATCGACAACTATACCCTGAC 57.370 41.667 0.00 0.00 0.00 3.51
3449 3710 8.929260 TTATTCTATCGACAACTATACCCTGA 57.071 34.615 0.00 0.00 0.00 3.86
3499 3760 0.855349 CACCGCATCTGTATTCGCTC 59.145 55.000 0.00 0.00 0.00 5.03
3516 3777 0.179225 CATACTTGCGCGGACAACAC 60.179 55.000 8.83 0.00 0.00 3.32
3517 3778 1.295357 CCATACTTGCGCGGACAACA 61.295 55.000 8.83 0.00 0.00 3.33
3518 3779 1.296056 ACCATACTTGCGCGGACAAC 61.296 55.000 8.83 0.00 0.00 3.32
3519 3780 1.004320 ACCATACTTGCGCGGACAA 60.004 52.632 8.83 3.25 0.00 3.18
3520 3781 1.739929 CACCATACTTGCGCGGACA 60.740 57.895 8.83 0.00 0.00 4.02
3521 3782 2.461110 CCACCATACTTGCGCGGAC 61.461 63.158 8.83 0.00 0.00 4.79
3523 3784 0.531974 ATACCACCATACTTGCGCGG 60.532 55.000 8.83 0.00 0.00 6.46
3524 3785 0.581529 CATACCACCATACTTGCGCG 59.418 55.000 0.00 0.00 0.00 6.86
3525 3786 0.944386 CCATACCACCATACTTGCGC 59.056 55.000 0.00 0.00 0.00 6.09
3526 3787 0.944386 GCCATACCACCATACTTGCG 59.056 55.000 0.00 0.00 0.00 4.85
3528 3789 0.944386 GCGCCATACCACCATACTTG 59.056 55.000 0.00 0.00 0.00 3.16
3529 3790 0.544223 TGCGCCATACCACCATACTT 59.456 50.000 4.18 0.00 0.00 2.24
3530 3791 0.544223 TTGCGCCATACCACCATACT 59.456 50.000 4.18 0.00 0.00 2.12
3531 3792 0.944386 CTTGCGCCATACCACCATAC 59.056 55.000 4.18 0.00 0.00 2.39
3533 3794 1.453745 CCTTGCGCCATACCACCAT 60.454 57.895 4.18 0.00 0.00 3.55
3551 3826 9.705290 ATTGGTAAAATTAACACATCTTTGACC 57.295 29.630 0.00 0.00 28.35 4.02
3556 3831 9.206870 CAGCAATTGGTAAAATTAACACATCTT 57.793 29.630 10.31 0.00 28.35 2.40
3557 3832 8.584157 TCAGCAATTGGTAAAATTAACACATCT 58.416 29.630 10.31 0.00 28.35 2.90
3561 3836 8.532977 ACATCAGCAATTGGTAAAATTAACAC 57.467 30.769 10.31 0.00 28.35 3.32
3566 3843 9.537192 CATGATACATCAGCAATTGGTAAAATT 57.463 29.630 10.31 0.00 40.64 1.82
3567 3844 8.916062 TCATGATACATCAGCAATTGGTAAAAT 58.084 29.630 10.31 1.90 40.64 1.82
3572 3849 6.778834 TTTCATGATACATCAGCAATTGGT 57.221 33.333 3.82 3.82 40.64 3.67
3575 3852 9.093970 CAAACATTTCATGATACATCAGCAATT 57.906 29.630 0.00 0.00 40.64 2.32
3640 3918 1.133792 CCTTTTATGGAGGCCGTGGAT 60.134 52.381 0.00 0.00 0.00 3.41
3642 3920 0.034477 ACCTTTTATGGAGGCCGTGG 60.034 55.000 0.00 0.00 37.84 4.94
3659 3937 3.507622 AGCAAGCAATTAACCAAGAGACC 59.492 43.478 0.00 0.00 0.00 3.85
3666 3944 5.009631 ACATCAGTAGCAAGCAATTAACCA 58.990 37.500 0.00 0.00 0.00 3.67
3713 4004 3.380320 AGTCTAAACAAAAGCACACCACC 59.620 43.478 0.00 0.00 0.00 4.61
3718 4009 4.710423 TTGCAGTCTAAACAAAAGCACA 57.290 36.364 0.00 0.00 0.00 4.57
3813 4109 2.223479 ACAATGCGATCCGTTAAATGGC 60.223 45.455 0.00 0.00 0.00 4.40
3907 4210 6.431234 GTGCTTATAGGATTTGGATGGTTAGG 59.569 42.308 0.00 0.00 0.00 2.69
3909 4212 7.149202 AGTGCTTATAGGATTTGGATGGTTA 57.851 36.000 0.00 0.00 0.00 2.85
3961 4284 2.857152 TGTTTTGAAATGACAAGCACGC 59.143 40.909 0.00 0.00 0.00 5.34
4039 4363 4.712337 TCCCAGCTTTTCCAAAGTTTGTAA 59.288 37.500 14.36 2.03 0.00 2.41
4040 4364 4.282496 TCCCAGCTTTTCCAAAGTTTGTA 58.718 39.130 14.36 0.00 0.00 2.41
4064 4388 3.303406 CAGAAGTTGCAAAAGCTAGTGC 58.697 45.455 13.32 13.32 41.29 4.40
4077 4401 4.215185 GGGAGAAAAGAGAAGCAGAAGTTG 59.785 45.833 0.00 0.00 0.00 3.16
4078 4402 4.393834 GGGAGAAAAGAGAAGCAGAAGTT 58.606 43.478 0.00 0.00 0.00 2.66
4079 4403 3.244735 GGGGAGAAAAGAGAAGCAGAAGT 60.245 47.826 0.00 0.00 0.00 3.01
4080 4404 3.342719 GGGGAGAAAAGAGAAGCAGAAG 58.657 50.000 0.00 0.00 0.00 2.85
4081 4405 2.040412 GGGGGAGAAAAGAGAAGCAGAA 59.960 50.000 0.00 0.00 0.00 3.02
4082 4406 1.630878 GGGGGAGAAAAGAGAAGCAGA 59.369 52.381 0.00 0.00 0.00 4.26
4083 4407 1.632920 AGGGGGAGAAAAGAGAAGCAG 59.367 52.381 0.00 0.00 0.00 4.24
4084 4408 1.747444 AGGGGGAGAAAAGAGAAGCA 58.253 50.000 0.00 0.00 0.00 3.91
4085 4409 2.822561 CAAAGGGGGAGAAAAGAGAAGC 59.177 50.000 0.00 0.00 0.00 3.86
4086 4410 3.181428 ACCAAAGGGGGAGAAAAGAGAAG 60.181 47.826 0.00 0.00 42.91 2.85
4087 4411 2.789399 ACCAAAGGGGGAGAAAAGAGAA 59.211 45.455 0.00 0.00 42.91 2.87
4088 4412 2.428901 ACCAAAGGGGGAGAAAAGAGA 58.571 47.619 0.00 0.00 42.91 3.10
4089 4413 2.980246 ACCAAAGGGGGAGAAAAGAG 57.020 50.000 0.00 0.00 42.91 2.85
4090 4414 3.499745 GCTAACCAAAGGGGGAGAAAAGA 60.500 47.826 0.00 0.00 42.91 2.52
4091 4415 2.826128 GCTAACCAAAGGGGGAGAAAAG 59.174 50.000 0.00 0.00 42.91 2.27
4092 4416 2.449345 AGCTAACCAAAGGGGGAGAAAA 59.551 45.455 0.00 0.00 42.91 2.29
4093 4417 2.070573 AGCTAACCAAAGGGGGAGAAA 58.929 47.619 0.00 0.00 42.91 2.52
4094 4418 1.755200 AGCTAACCAAAGGGGGAGAA 58.245 50.000 0.00 0.00 42.91 2.87
4095 4419 1.755200 AAGCTAACCAAAGGGGGAGA 58.245 50.000 0.00 0.00 42.91 3.71
4096 4420 3.953542 ATAAGCTAACCAAAGGGGGAG 57.046 47.619 0.00 0.00 42.91 4.30
4097 4421 3.137728 GCTATAAGCTAACCAAAGGGGGA 59.862 47.826 0.00 0.00 38.66 4.81
4098 4422 3.487372 GCTATAAGCTAACCAAAGGGGG 58.513 50.000 0.00 0.00 38.66 5.40
4130 4454 0.666577 GCTTTTGCAGCCAGCTTCTG 60.667 55.000 8.09 8.09 43.65 3.02
4131 4455 1.664306 GCTTTTGCAGCCAGCTTCT 59.336 52.632 6.60 0.00 43.65 2.85
4132 4456 4.256813 GCTTTTGCAGCCAGCTTC 57.743 55.556 6.60 0.00 43.65 3.86
4143 4467 2.604462 GCTGTGTTTGGTTGAGCTTTTG 59.396 45.455 0.00 0.00 0.00 2.44
4144 4468 2.735126 CGCTGTGTTTGGTTGAGCTTTT 60.735 45.455 0.00 0.00 0.00 2.27
4145 4469 1.202290 CGCTGTGTTTGGTTGAGCTTT 60.202 47.619 0.00 0.00 0.00 3.51
4146 4470 0.381801 CGCTGTGTTTGGTTGAGCTT 59.618 50.000 0.00 0.00 0.00 3.74
4147 4471 0.748005 ACGCTGTGTTTGGTTGAGCT 60.748 50.000 0.00 0.00 0.00 4.09
4148 4472 0.317020 GACGCTGTGTTTGGTTGAGC 60.317 55.000 0.00 0.00 0.00 4.26
4149 4473 0.307760 GGACGCTGTGTTTGGTTGAG 59.692 55.000 0.00 0.00 0.00 3.02
4150 4474 1.433053 CGGACGCTGTGTTTGGTTGA 61.433 55.000 0.00 0.00 0.00 3.18
4151 4475 1.010125 CGGACGCTGTGTTTGGTTG 60.010 57.895 0.00 0.00 0.00 3.77
4152 4476 2.184167 CCGGACGCTGTGTTTGGTT 61.184 57.895 0.00 0.00 0.00 3.67
4153 4477 2.030490 TACCGGACGCTGTGTTTGGT 62.030 55.000 9.46 18.29 40.32 3.67
4154 4478 1.301087 TACCGGACGCTGTGTTTGG 60.301 57.895 9.46 10.19 0.00 3.28
4155 4479 0.599204 AGTACCGGACGCTGTGTTTG 60.599 55.000 9.46 0.00 0.00 2.93
4156 4480 0.599204 CAGTACCGGACGCTGTGTTT 60.599 55.000 9.46 0.00 0.00 2.83
4157 4481 1.006571 CAGTACCGGACGCTGTGTT 60.007 57.895 9.46 0.00 0.00 3.32
4158 4482 2.649034 CAGTACCGGACGCTGTGT 59.351 61.111 9.46 0.00 0.00 3.72
4159 4483 1.929806 TAGCAGTACCGGACGCTGTG 61.930 60.000 9.46 0.00 38.06 3.66
4160 4484 1.035932 ATAGCAGTACCGGACGCTGT 61.036 55.000 9.46 10.61 38.06 4.40
4161 4485 0.317938 GATAGCAGTACCGGACGCTG 60.318 60.000 9.46 14.13 38.06 5.18
4162 4486 0.465824 AGATAGCAGTACCGGACGCT 60.466 55.000 9.46 16.27 39.88 5.07
4163 4487 0.040246 GAGATAGCAGTACCGGACGC 60.040 60.000 9.46 10.15 0.00 5.19
4164 4488 0.235144 CGAGATAGCAGTACCGGACG 59.765 60.000 9.46 0.24 0.00 4.79
4170 4494 0.750850 TTGGGCCGAGATAGCAGTAC 59.249 55.000 0.00 0.00 0.00 2.73
4172 4499 0.687757 TCTTGGGCCGAGATAGCAGT 60.688 55.000 19.96 0.00 0.00 4.40
4183 4510 4.722700 TGCCGAGCTTCTTGGGCC 62.723 66.667 0.00 0.00 44.96 5.80
4185 4512 1.821332 GGATGCCGAGCTTCTTGGG 60.821 63.158 10.18 0.00 35.62 4.12
4188 4515 0.177604 CTGAGGATGCCGAGCTTCTT 59.822 55.000 10.18 4.59 33.95 2.52
4189 4516 1.821936 CTGAGGATGCCGAGCTTCT 59.178 57.895 10.18 0.98 33.95 2.85
4190 4517 1.886777 GCTGAGGATGCCGAGCTTC 60.887 63.158 0.00 0.00 33.19 3.86
4191 4518 2.188994 GCTGAGGATGCCGAGCTT 59.811 61.111 0.00 0.00 33.19 3.74
4192 4519 3.079478 TGCTGAGGATGCCGAGCT 61.079 61.111 6.63 0.00 35.72 4.09
4193 4520 2.894387 GTGCTGAGGATGCCGAGC 60.894 66.667 0.00 0.00 35.42 5.03
4195 4522 3.785859 GGGTGCTGAGGATGCCGA 61.786 66.667 0.00 0.00 0.00 5.54
4196 4523 4.100084 TGGGTGCTGAGGATGCCG 62.100 66.667 0.00 0.00 0.00 5.69
4197 4524 2.124403 CTGGGTGCTGAGGATGCC 60.124 66.667 0.00 0.00 0.00 4.40
4198 4525 2.124403 CCTGGGTGCTGAGGATGC 60.124 66.667 0.00 0.00 0.00 3.91
4199 4526 2.593978 CCCTGGGTGCTGAGGATG 59.406 66.667 3.97 0.00 0.00 3.51
4248 4575 0.036671 GGAACGATCCGTGGGTCTTT 60.037 55.000 0.00 0.00 39.99 2.52
4385 4712 1.518056 TTCCGTCGAGCAGGTTACGT 61.518 55.000 0.00 0.00 33.63 3.57
4409 4736 2.052414 GCGACGACGTCCCGATAG 60.052 66.667 21.63 8.06 41.98 2.08
4484 4811 3.708220 GAGCACGCGGGAGAAGAGG 62.708 68.421 15.48 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.