Multiple sequence alignment - TraesCS2B01G242800

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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 TraesCS2B01G242800 chr2B 100.000 6530 0 0 1 6530 246958772 246952243 0.000000e+00 12059.0
1 TraesCS2B01G242800 chr2B 91.488 1351 97 10 4729 6070 247363817 247362476 0.000000e+00 1842.0
2 TraesCS2B01G242800 chr2B 85.781 858 106 14 3664 4509 150341224 150340371 0.000000e+00 894.0
3 TraesCS2B01G242800 chr2B 93.846 585 27 2 228 811 247372936 247372360 0.000000e+00 872.0
4 TraesCS2B01G242800 chr2B 89.522 649 42 3 805 1451 247372029 247371405 0.000000e+00 798.0
5 TraesCS2B01G242800 chr2B 87.417 604 53 9 2262 2860 247368541 247367956 0.000000e+00 673.0
6 TraesCS2B01G242800 chr2B 88.256 579 37 17 1693 2265 247369174 247368621 0.000000e+00 664.0
7 TraesCS2B01G242800 chr2B 93.750 176 10 1 1 176 247373111 247372937 5.020000e-66 263.0
8 TraesCS2B01G242800 chr2B 94.156 154 9 0 4575 4728 247363999 247363846 1.090000e-57 235.0
9 TraesCS2B01G242800 chr2B 81.735 219 15 16 1441 1651 247369369 247369168 6.780000e-35 159.0
10 TraesCS2B01G242800 chr2B 96.842 95 2 1 2981 3075 247365882 247365789 2.440000e-34 158.0
11 TraesCS2B01G242800 chr2B 92.308 91 3 4 1557 1645 246957183 246957095 6.870000e-25 126.0
12 TraesCS2B01G242800 chr2B 92.308 91 3 4 1590 1678 246957216 246957128 6.870000e-25 126.0
13 TraesCS2B01G242800 chr2B 95.349 43 2 0 1636 1678 247369216 247369174 1.170000e-07 69.4
14 TraesCS2B01G242800 chr2D 93.971 1808 86 12 4729 6530 190213978 190212188 0.000000e+00 2713.0
15 TraesCS2B01G242800 chr2D 95.223 1235 42 3 1 1226 190221506 190220280 0.000000e+00 1938.0
16 TraesCS2B01G242800 chr2D 90.970 1351 104 10 4729 6070 190326888 190325547 0.000000e+00 1803.0
17 TraesCS2B01G242800 chr2D 88.990 1435 91 22 228 1651 190330740 190329362 0.000000e+00 1712.0
18 TraesCS2B01G242800 chr2D 94.951 1030 42 5 2041 3065 190219767 190218743 0.000000e+00 1605.0
19 TraesCS2B01G242800 chr2D 86.131 858 102 14 3664 4510 98710783 98709932 0.000000e+00 909.0
20 TraesCS2B01G242800 chr2D 84.972 905 112 17 3622 4511 388478703 388477808 0.000000e+00 896.0
21 TraesCS2B01G242800 chr2D 85.882 850 102 16 3671 4511 108630624 108629784 0.000000e+00 889.0
22 TraesCS2B01G242800 chr2D 90.054 372 30 6 1228 1595 190220183 190219815 5.920000e-130 475.0
23 TraesCS2B01G242800 chr2D 96.648 179 5 1 4550 4727 190214186 190214008 4.950000e-76 296.0
24 TraesCS2B01G242800 chr2D 94.805 154 8 0 4575 4728 190327070 190326917 2.350000e-59 241.0
25 TraesCS2B01G242800 chr2D 93.960 149 9 0 28 176 190330889 190330741 6.590000e-55 226.0
26 TraesCS2B01G242800 chr2D 89.655 145 14 1 2931 3075 190329352 190329209 4.020000e-42 183.0
27 TraesCS2B01G242800 chr2D 95.349 43 2 0 1636 1678 190329410 190329368 1.170000e-07 69.4
28 TraesCS2B01G242800 chr4A 90.424 1462 93 17 3071 4513 19578102 19579535 0.000000e+00 1881.0
29 TraesCS2B01G242800 chr4A 85.507 138 7 6 1853 1979 458244736 458244601 1.480000e-26 132.0
30 TraesCS2B01G242800 chr4A 85.507 138 7 6 1853 1979 458528660 458528525 1.480000e-26 132.0
31 TraesCS2B01G242800 chr2A 91.266 1351 102 8 4729 6070 204816432 204815089 0.000000e+00 1827.0
32 TraesCS2B01G242800 chr2A 95.365 1122 49 2 1946 3064 204627648 204626527 0.000000e+00 1781.0
33 TraesCS2B01G242800 chr2A 94.466 1012 33 11 4549 5541 204626092 204625085 0.000000e+00 1537.0
34 TraesCS2B01G242800 chr2A 94.487 907 39 3 101 1005 204628918 204628021 0.000000e+00 1387.0
35 TraesCS2B01G242800 chr2A 97.476 515 13 0 101 615 204832100 204831586 0.000000e+00 880.0
36 TraesCS2B01G242800 chr2A 90.868 219 16 4 2857 3075 204820613 204820399 2.300000e-74 291.0
37 TraesCS2B01G242800 chr2A 93.590 156 8 2 4575 4728 204816616 204816461 1.420000e-56 231.0
38 TraesCS2B01G242800 chr2A 92.437 119 5 3 1831 1946 204627860 204627743 4.050000e-37 167.0
39 TraesCS2B01G242800 chr4D 86.054 882 99 16 3643 4512 203646186 203645317 0.000000e+00 926.0
40 TraesCS2B01G242800 chr4D 87.432 183 14 4 1806 1979 117423881 117424063 1.110000e-47 202.0
41 TraesCS2B01G242800 chr3D 86.642 816 98 9 3704 4512 526262474 526261663 0.000000e+00 893.0
42 TraesCS2B01G242800 chr7B 85.798 852 102 15 3672 4511 104218781 104219625 0.000000e+00 885.0
43 TraesCS2B01G242800 chr5D 84.555 887 118 15 3643 4519 30592896 30593773 0.000000e+00 861.0
44 TraesCS2B01G242800 chr3B 84.134 895 121 15 3630 4512 584975464 584976349 0.000000e+00 846.0
45 TraesCS2B01G242800 chr7A 85.816 141 16 3 3098 3234 1445064 1444924 5.280000e-31 147.0
46 TraesCS2B01G242800 chr7A 78.243 239 28 17 1782 2013 270279636 270279857 1.480000e-26 132.0
47 TraesCS2B01G242800 chr1B 95.385 65 3 0 1946 2010 157285738 157285802 3.220000e-18 104.0


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 TraesCS2B01G242800 chr2B 246952243 246958772 6529 True 4103.666667 12059 94.872000 1 6530 3 chr2B.!!$R2 6529
1 TraesCS2B01G242800 chr2B 150340371 150341224 853 True 894.000000 894 85.781000 3664 4509 1 chr2B.!!$R1 845
2 TraesCS2B01G242800 chr2B 247362476 247373111 10635 True 573.340000 1842 91.236100 1 6070 10 chr2B.!!$R3 6069
3 TraesCS2B01G242800 chr2D 190212188 190214186 1998 True 1504.500000 2713 95.309500 4550 6530 2 chr2D.!!$R4 1980
4 TraesCS2B01G242800 chr2D 190218743 190221506 2763 True 1339.333333 1938 93.409333 1 3065 3 chr2D.!!$R5 3064
5 TraesCS2B01G242800 chr2D 98709932 98710783 851 True 909.000000 909 86.131000 3664 4510 1 chr2D.!!$R1 846
6 TraesCS2B01G242800 chr2D 388477808 388478703 895 True 896.000000 896 84.972000 3622 4511 1 chr2D.!!$R3 889
7 TraesCS2B01G242800 chr2D 108629784 108630624 840 True 889.000000 889 85.882000 3671 4511 1 chr2D.!!$R2 840
8 TraesCS2B01G242800 chr2D 190325547 190330889 5342 True 705.733333 1803 92.288167 28 6070 6 chr2D.!!$R6 6042
9 TraesCS2B01G242800 chr4A 19578102 19579535 1433 False 1881.000000 1881 90.424000 3071 4513 1 chr4A.!!$F1 1442
10 TraesCS2B01G242800 chr2A 204625085 204628918 3833 True 1218.000000 1781 94.188750 101 5541 4 chr2A.!!$R2 5440
11 TraesCS2B01G242800 chr2A 204831586 204832100 514 True 880.000000 880 97.476000 101 615 1 chr2A.!!$R1 514
12 TraesCS2B01G242800 chr2A 204815089 204820613 5524 True 783.000000 1827 91.908000 2857 6070 3 chr2A.!!$R3 3213
13 TraesCS2B01G242800 chr4D 203645317 203646186 869 True 926.000000 926 86.054000 3643 4512 1 chr4D.!!$R1 869
14 TraesCS2B01G242800 chr3D 526261663 526262474 811 True 893.000000 893 86.642000 3704 4512 1 chr3D.!!$R1 808
15 TraesCS2B01G242800 chr7B 104218781 104219625 844 False 885.000000 885 85.798000 3672 4511 1 chr7B.!!$F1 839
16 TraesCS2B01G242800 chr5D 30592896 30593773 877 False 861.000000 861 84.555000 3643 4519 1 chr5D.!!$F1 876
17 TraesCS2B01G242800 chr3B 584975464 584976349 885 False 846.000000 846 84.134000 3630 4512 1 chr3B.!!$F1 882

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
758 762 0.391793 CTTGAGCGGGAAGGAAGTCC 60.392 60.0 0.00 0.00 36.90 3.85 F
1320 1765 0.687354 TGGTGGAGAAGCCTGAAGAC 59.313 55.0 0.00 0.00 37.63 3.01 F
1687 4195 0.105593 CAGCTCCTCTGTGTGTGTGT 59.894 55.0 0.00 0.00 38.02 3.72 F
2550 5251 0.395311 TGACCGCTCGACCTTCCTAT 60.395 55.0 0.00 0.00 0.00 2.57 F
3111 7784 0.461693 TAATAAACCGAACGGCCCCG 60.462 55.0 13.32 4.96 46.03 5.73 F
3467 8158 0.538584 TCGATCTGCTCATTGGTGCT 59.461 50.0 0.00 0.00 34.68 4.40 F
4742 13643 0.180406 ACCAGAGGTGTTCGCAACTT 59.820 50.0 0.00 0.00 46.84 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1601 4104 0.116143 AACAGAGAGAGGGAGGCTGT 59.884 55.000 0.00 0.00 41.19 4.40 R
3152 7826 0.244994 AGATGAGAAACGCGCTGAGT 59.755 50.000 5.73 0.00 0.00 3.41 R
3435 8126 0.107945 AGATCGAAGAAGTGCTGCCC 60.108 55.000 0.00 0.00 43.58 5.36 R
3914 8613 0.468226 TTCTTCACCACCTCAACGCT 59.532 50.000 0.00 0.00 0.00 5.07 R
3966 8667 0.516877 CGCAATCAAAACTCCTCGCA 59.483 50.000 0.00 0.00 0.00 5.10 R
5220 14134 1.134068 GGAATCACTTGACCTAGGGCC 60.134 57.143 13.60 4.15 0.00 5.80 R
6292 15215 0.169009 GAGGGCATTCGACAACAAGC 59.831 55.000 0.00 0.00 0.00 4.01 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
291 293 7.721402 TCTGTTTCTTAATCTCCAGCTCTATC 58.279 38.462 0.00 0.00 0.00 2.08
302 304 5.934625 TCTCCAGCTCTATCTTGTTGTTTTC 59.065 40.000 0.00 0.00 0.00 2.29
600 602 2.807837 GCAATCAAGGGCTGTTTTGCTT 60.808 45.455 0.00 0.00 39.76 3.91
618 620 5.912360 TGCTTTGCAGATATATCTTCACG 57.088 39.130 13.74 9.62 34.22 4.35
619 621 5.600696 TGCTTTGCAGATATATCTTCACGA 58.399 37.500 13.74 6.14 34.22 4.35
620 622 5.463392 TGCTTTGCAGATATATCTTCACGAC 59.537 40.000 13.74 7.42 34.22 4.34
621 623 5.694006 GCTTTGCAGATATATCTTCACGACT 59.306 40.000 13.74 0.00 34.22 4.18
622 624 6.201806 GCTTTGCAGATATATCTTCACGACTT 59.798 38.462 13.74 0.00 34.22 3.01
623 625 7.568497 GCTTTGCAGATATATCTTCACGACTTC 60.568 40.741 13.74 0.00 34.22 3.01
624 626 6.391227 TGCAGATATATCTTCACGACTTCA 57.609 37.500 12.75 0.00 34.22 3.02
625 627 6.209361 TGCAGATATATCTTCACGACTTCAC 58.791 40.000 12.75 0.00 34.22 3.18
697 701 5.795441 GTGTATTTCGAAATCCTTGTCTTGC 59.205 40.000 25.89 5.19 0.00 4.01
758 762 0.391793 CTTGAGCGGGAAGGAAGTCC 60.392 60.000 0.00 0.00 36.90 3.85
848 1189 1.346068 ACACTGACCTTCTGCCTTCTC 59.654 52.381 0.00 0.00 0.00 2.87
849 1190 1.345741 CACTGACCTTCTGCCTTCTCA 59.654 52.381 0.00 0.00 0.00 3.27
868 1211 9.014297 CCTTCTCACATAATAAACCTTGTCTTT 57.986 33.333 0.00 0.00 0.00 2.52
897 1240 6.749139 TCTGATACTTGCATATGTACTGACC 58.251 40.000 4.29 0.00 0.00 4.02
918 1261 4.074259 CCAACAACATGTTCTGATCAGGA 58.926 43.478 22.42 11.83 38.77 3.86
953 1296 1.070134 AGCGAGGTTAGCAACAGTGAA 59.930 47.619 0.00 0.00 37.01 3.18
966 1309 4.799586 GCAACAGTGAAGGCTCTGTAACTA 60.800 45.833 7.66 0.00 45.29 2.24
970 1313 3.452627 AGTGAAGGCTCTGTAACTATGGG 59.547 47.826 0.00 0.00 0.00 4.00
981 1324 5.778241 TCTGTAACTATGGGTCTGTCAGAAA 59.222 40.000 3.51 0.00 0.00 2.52
982 1325 6.440647 TCTGTAACTATGGGTCTGTCAGAAAT 59.559 38.462 3.51 1.94 0.00 2.17
1007 1350 1.506493 CCCTAGCGCTGAATGACATC 58.494 55.000 22.90 0.00 0.00 3.06
1008 1351 1.069823 CCCTAGCGCTGAATGACATCT 59.930 52.381 22.90 0.00 0.00 2.90
1015 1358 3.305950 GCGCTGAATGACATCTCTCCTAT 60.306 47.826 0.00 0.00 0.00 2.57
1108 1451 7.787904 TGGATACTTATTATGACCCACAGTACT 59.212 37.037 0.00 0.00 37.61 2.73
1111 1454 7.113658 ACTTATTATGACCCACAGTACTCTG 57.886 40.000 0.00 0.00 46.18 3.35
1214 1564 3.370840 TGCCAGGAAGCTGAACATTAT 57.629 42.857 0.00 0.00 0.00 1.28
1296 1741 1.135731 CAGCGAGAGTGAGTCGGAC 59.864 63.158 0.00 0.00 37.91 4.79
1320 1765 0.687354 TGGTGGAGAAGCCTGAAGAC 59.313 55.000 0.00 0.00 37.63 3.01
1411 1856 5.130350 TGTAACTTTTAAGTCTTGGCTGCT 58.870 37.500 0.00 0.00 38.57 4.24
1419 1864 9.294030 CTTTTAAGTCTTGGCTGCTTTAATATG 57.706 33.333 0.00 0.00 0.00 1.78
1438 1883 3.451141 TGGCAAGTGTTGGAATTGAAC 57.549 42.857 0.00 0.00 0.00 3.18
1451 1896 3.756117 GAATTGAACCACTCAACTCCCT 58.244 45.455 0.00 0.00 46.80 4.20
1474 3967 4.343526 TCCTCTTCCTGAGATATGCTTCAC 59.656 45.833 0.00 0.00 45.39 3.18
1494 3989 1.670811 CCCACTCTCAAACACACACAC 59.329 52.381 0.00 0.00 0.00 3.82
1495 3990 2.355197 CCACTCTCAAACACACACACA 58.645 47.619 0.00 0.00 0.00 3.72
1496 3991 2.095853 CCACTCTCAAACACACACACAC 59.904 50.000 0.00 0.00 0.00 3.82
1497 3992 2.741517 CACTCTCAAACACACACACACA 59.258 45.455 0.00 0.00 0.00 3.72
1498 3993 3.002791 ACTCTCAAACACACACACACAG 58.997 45.455 0.00 0.00 0.00 3.66
1499 3994 2.352651 CTCTCAAACACACACACACAGG 59.647 50.000 0.00 0.00 0.00 4.00
1500 3995 2.027653 TCTCAAACACACACACACAGGA 60.028 45.455 0.00 0.00 0.00 3.86
1501 3996 2.080693 TCAAACACACACACACAGGAC 58.919 47.619 0.00 0.00 0.00 3.85
1502 3997 2.083774 CAAACACACACACACAGGACT 58.916 47.619 0.00 0.00 0.00 3.85
1503 3998 3.055747 TCAAACACACACACACAGGACTA 60.056 43.478 0.00 0.00 0.00 2.59
1504 3999 2.890808 ACACACACACACAGGACTAG 57.109 50.000 0.00 0.00 0.00 2.57
1505 4000 2.108168 ACACACACACACAGGACTAGT 58.892 47.619 0.00 0.00 0.00 2.57
1506 4001 3.293337 ACACACACACACAGGACTAGTA 58.707 45.455 0.00 0.00 0.00 1.82
1521 4016 4.440802 GGACTAGTACAGTGAGGCTTGATG 60.441 50.000 0.00 0.00 37.72 3.07
1537 4034 5.063944 GGCTTGATGTCTTATACACACACAG 59.936 44.000 0.00 0.00 42.09 3.66
1566 4067 2.233431 ACCTGAAGCTTAGCTGAGTCAG 59.767 50.000 21.19 21.19 39.40 3.51
1595 4098 1.477700 CCTCTCTCTGTTGGAGCTGAG 59.522 57.143 0.00 0.00 41.60 3.35
1596 4099 2.170166 CTCTCTCTGTTGGAGCTGAGT 58.830 52.381 0.00 0.00 41.60 3.41
1597 4100 2.164219 CTCTCTCTGTTGGAGCTGAGTC 59.836 54.545 0.00 0.00 41.60 3.36
1598 4101 1.891811 CTCTCTGTTGGAGCTGAGTCA 59.108 52.381 0.00 0.00 41.60 3.41
1599 4102 1.615883 TCTCTGTTGGAGCTGAGTCAC 59.384 52.381 0.00 0.00 41.60 3.67
1600 4103 1.617850 CTCTGTTGGAGCTGAGTCACT 59.382 52.381 0.00 0.00 35.08 3.41
1601 4104 2.822561 CTCTGTTGGAGCTGAGTCACTA 59.177 50.000 0.00 0.00 35.08 2.74
1602 4105 2.558795 TCTGTTGGAGCTGAGTCACTAC 59.441 50.000 0.00 0.00 0.00 2.73
1603 4106 2.297315 CTGTTGGAGCTGAGTCACTACA 59.703 50.000 0.00 4.16 0.00 2.74
1604 4107 2.297315 TGTTGGAGCTGAGTCACTACAG 59.703 50.000 0.00 0.00 37.22 2.74
1610 4113 0.820871 CTGAGTCACTACAGCCTCCC 59.179 60.000 0.00 0.00 0.00 4.30
1611 4114 0.409876 TGAGTCACTACAGCCTCCCT 59.590 55.000 0.00 0.00 0.00 4.20
1612 4115 1.107945 GAGTCACTACAGCCTCCCTC 58.892 60.000 0.00 0.00 0.00 4.30
1613 4116 0.707616 AGTCACTACAGCCTCCCTCT 59.292 55.000 0.00 0.00 0.00 3.69
1614 4117 1.107945 GTCACTACAGCCTCCCTCTC 58.892 60.000 0.00 0.00 0.00 3.20
1615 4118 1.003646 TCACTACAGCCTCCCTCTCT 58.996 55.000 0.00 0.00 0.00 3.10
1616 4119 1.064314 TCACTACAGCCTCCCTCTCTC 60.064 57.143 0.00 0.00 0.00 3.20
1617 4120 1.064017 CACTACAGCCTCCCTCTCTCT 60.064 57.143 0.00 0.00 0.00 3.10
1618 4121 1.064017 ACTACAGCCTCCCTCTCTCTG 60.064 57.143 0.00 0.00 0.00 3.35
1619 4122 1.003646 TACAGCCTCCCTCTCTCTGT 58.996 55.000 0.00 0.00 40.60 3.41
1620 4123 0.116143 ACAGCCTCCCTCTCTCTGTT 59.884 55.000 0.00 0.00 34.69 3.16
1621 4124 0.536260 CAGCCTCCCTCTCTCTGTTG 59.464 60.000 0.00 0.00 0.00 3.33
1622 4125 0.617249 AGCCTCCCTCTCTCTGTTGG 60.617 60.000 0.00 0.00 0.00 3.77
1665 4173 4.958581 TCTATCTCTGTTGGAGCTGAATCA 59.041 41.667 0.00 0.00 41.60 2.57
1678 4186 3.167921 CTGAATCACTCAGCTCCTCTG 57.832 52.381 0.00 0.00 45.11 3.35
1679 4187 2.496871 CTGAATCACTCAGCTCCTCTGT 59.503 50.000 0.00 0.00 45.11 3.41
1680 4188 2.233186 TGAATCACTCAGCTCCTCTGTG 59.767 50.000 0.00 0.00 43.32 3.66
1681 4189 1.935799 ATCACTCAGCTCCTCTGTGT 58.064 50.000 0.00 0.00 46.89 3.72
1683 4191 3.139810 ACTCAGCTCCTCTGTGTGT 57.860 52.632 0.00 0.00 44.94 3.72
1684 4192 0.678395 ACTCAGCTCCTCTGTGTGTG 59.322 55.000 0.00 0.00 44.94 3.82
1685 4193 0.678395 CTCAGCTCCTCTGTGTGTGT 59.322 55.000 0.00 0.00 43.32 3.72
1686 4194 0.390492 TCAGCTCCTCTGTGTGTGTG 59.610 55.000 0.00 0.00 43.32 3.82
1687 4195 0.105593 CAGCTCCTCTGTGTGTGTGT 59.894 55.000 0.00 0.00 38.02 3.72
1688 4196 0.833287 AGCTCCTCTGTGTGTGTGTT 59.167 50.000 0.00 0.00 0.00 3.32
1689 4197 0.940126 GCTCCTCTGTGTGTGTGTTG 59.060 55.000 0.00 0.00 0.00 3.33
1690 4198 1.743772 GCTCCTCTGTGTGTGTGTTGT 60.744 52.381 0.00 0.00 0.00 3.32
1691 4199 2.632377 CTCCTCTGTGTGTGTGTTGTT 58.368 47.619 0.00 0.00 0.00 2.83
1696 4204 3.669536 TCTGTGTGTGTGTTGTTTCTCA 58.330 40.909 0.00 0.00 0.00 3.27
1698 4206 3.142174 TGTGTGTGTGTTGTTTCTCACA 58.858 40.909 0.00 0.00 41.37 3.58
1720 4228 3.904571 ACATGCACAAATACACAAGCTG 58.095 40.909 0.00 0.00 0.00 4.24
1740 4248 0.463620 TTTTTGGTGACTTGCTGCCC 59.536 50.000 0.00 0.00 0.00 5.36
1748 4256 2.203394 CTTGCTGCCCCACACAGT 60.203 61.111 0.00 0.00 37.47 3.55
1758 4266 1.402787 CCCACACAGTCAAAGCCTTT 58.597 50.000 0.00 0.00 0.00 3.11
1761 4269 2.689983 CCACACAGTCAAAGCCTTTTCT 59.310 45.455 0.00 0.00 0.00 2.52
1762 4270 3.243201 CCACACAGTCAAAGCCTTTTCTC 60.243 47.826 0.00 0.00 0.00 2.87
1931 4441 7.450634 TGACTTCTAGCCTAAGACAAAGACTTA 59.549 37.037 0.00 0.00 0.00 2.24
1932 4442 7.604549 ACTTCTAGCCTAAGACAAAGACTTAC 58.395 38.462 0.00 0.00 0.00 2.34
2013 4619 8.807948 ACAACAAGGATTATAACTAACAGCAT 57.192 30.769 0.00 0.00 0.00 3.79
2020 4626 7.934120 AGGATTATAACTAACAGCATGAAGTCC 59.066 37.037 0.00 0.00 39.69 3.85
2139 4746 5.735892 CGACAAATGTGAGTGCTATGAATTG 59.264 40.000 0.00 0.00 0.00 2.32
2373 5074 9.746457 TTGCATTATGTAAACTATATGGGCATA 57.254 29.630 0.00 0.00 0.00 3.14
2460 5161 5.580691 CACTGTAAGCGAAGTGATGGATAAA 59.419 40.000 5.52 0.00 45.43 1.40
2550 5251 0.395311 TGACCGCTCGACCTTCCTAT 60.395 55.000 0.00 0.00 0.00 2.57
2685 5396 1.528161 CGTCGACAACCAAGGTAAACC 59.472 52.381 17.16 0.00 0.00 3.27
2686 5397 2.563702 GTCGACAACCAAGGTAAACCA 58.436 47.619 11.55 0.00 38.89 3.67
2687 5398 3.143728 GTCGACAACCAAGGTAAACCAT 58.856 45.455 11.55 0.00 38.89 3.55
2688 5399 3.187842 GTCGACAACCAAGGTAAACCATC 59.812 47.826 11.55 0.00 38.89 3.51
2689 5400 3.071892 TCGACAACCAAGGTAAACCATCT 59.928 43.478 1.26 0.00 38.89 2.90
2690 5401 4.283978 TCGACAACCAAGGTAAACCATCTA 59.716 41.667 1.26 0.00 38.89 1.98
2691 5402 4.390909 CGACAACCAAGGTAAACCATCTAC 59.609 45.833 1.26 0.00 38.89 2.59
2966 5755 1.002430 GATCTGACTGGCAACTGGTCA 59.998 52.381 7.05 7.05 43.63 4.02
3065 7738 5.960704 TCCTATCACCCTTGTATGCTACTA 58.039 41.667 0.00 0.00 0.00 1.82
3066 7739 5.773680 TCCTATCACCCTTGTATGCTACTAC 59.226 44.000 0.00 0.00 0.00 2.73
3067 7740 5.538813 CCTATCACCCTTGTATGCTACTACA 59.461 44.000 0.00 0.00 0.00 2.74
3068 7741 6.211584 CCTATCACCCTTGTATGCTACTACAT 59.788 42.308 0.00 0.00 31.94 2.29
3069 7742 5.276461 TCACCCTTGTATGCTACTACATG 57.724 43.478 0.00 0.00 31.94 3.21
3111 7784 0.461693 TAATAAACCGAACGGCCCCG 60.462 55.000 13.32 4.96 46.03 5.73
3152 7826 1.621992 GGGTGGCGATCTCATCTCTA 58.378 55.000 0.00 0.00 0.00 2.43
3153 7827 1.271102 GGGTGGCGATCTCATCTCTAC 59.729 57.143 0.00 0.00 0.00 2.59
3154 7828 2.235016 GGTGGCGATCTCATCTCTACT 58.765 52.381 0.00 0.00 0.00 2.57
3180 7856 2.034053 GCGTTTCTCATCTCCGATCTCT 59.966 50.000 0.00 0.00 0.00 3.10
3181 7857 3.626977 CGTTTCTCATCTCCGATCTCTG 58.373 50.000 0.00 0.00 0.00 3.35
3214 7893 1.539124 AGGACACCCCTGGGAGAAC 60.539 63.158 16.20 2.86 45.61 3.01
3256 7935 2.032681 GGCCTTTGCTGTCGTCCT 59.967 61.111 0.00 0.00 37.74 3.85
3318 7999 2.971598 CGGCCCCAGACCTGTTCAT 61.972 63.158 0.00 0.00 0.00 2.57
3398 8089 3.060000 GGCTGCCCGGTTTGGTAC 61.060 66.667 7.66 0.00 35.15 3.34
3435 8126 0.936764 CGCGGTGGATCTCGAAGATG 60.937 60.000 0.00 0.00 34.53 2.90
3459 8150 1.547820 AGCACTTCTTCGATCTGCTCA 59.452 47.619 0.00 0.00 32.68 4.26
3461 8152 2.935201 GCACTTCTTCGATCTGCTCATT 59.065 45.455 0.00 0.00 0.00 2.57
3467 8158 0.538584 TCGATCTGCTCATTGGTGCT 59.461 50.000 0.00 0.00 34.68 4.40
3531 8222 2.666190 CCGGCGGGCACATATCTG 60.666 66.667 20.56 0.00 0.00 2.90
3658 8350 2.844348 GTCCAATCCAGGGGAGTTCTAA 59.156 50.000 0.00 0.00 34.05 2.10
3668 8360 4.286291 CAGGGGAGTTCTAAGTTAGTTGGT 59.714 45.833 9.71 0.00 0.00 3.67
3914 8613 8.421784 GGACATGTCTAAGTATAGATTTCCACA 58.578 37.037 24.50 0.00 40.21 4.17
3966 8667 4.130118 GCTGTGATCGGAGAATTAATGGT 58.870 43.478 0.00 0.00 43.58 3.55
4238 8954 5.478332 GGGTGAAAACTCAAGATCCTTGATT 59.522 40.000 9.51 2.32 0.00 2.57
4275 8993 4.866486 GCTTATGCATTGTTTCCTTCTTGG 59.134 41.667 3.54 0.00 39.41 3.61
4433 9156 2.358957 GCTGTGTGCATCCTTGATGTA 58.641 47.619 6.01 0.00 41.60 2.29
4742 13643 0.180406 ACCAGAGGTGTTCGCAACTT 59.820 50.000 0.00 0.00 46.84 2.66
4743 13644 1.308998 CCAGAGGTGTTCGCAACTTT 58.691 50.000 0.00 0.00 46.84 2.66
4872 13785 8.948631 TGACATCATATTCTGGTTTCTACTTC 57.051 34.615 0.00 0.00 0.00 3.01
4882 13795 8.701908 TTCTGGTTTCTACTTCTTCTACTACA 57.298 34.615 0.00 0.00 0.00 2.74
4911 13824 3.986442 AAATGCAATTTTGTGTTGGCC 57.014 38.095 0.00 0.00 46.10 5.36
5004 13917 5.288472 GGTGATGTTGGCATTCGAAAAATAC 59.712 40.000 0.00 0.00 35.07 1.89
5090 14004 4.157656 CACAAGAAAGTGACCAGGAAAACA 59.842 41.667 0.00 0.00 42.05 2.83
5323 14237 4.335416 TGCCCTCTAGAACCAAATGAAAG 58.665 43.478 0.00 0.00 0.00 2.62
5516 14430 6.065976 TCTGGATATCGCATTCCCATTTAT 57.934 37.500 0.00 0.00 0.00 1.40
5645 14559 5.940617 TCCATTATGGGTTTGATACTGAGG 58.059 41.667 11.76 0.00 38.32 3.86
5746 14660 6.805271 GGTTGTCATTGTGATGAGAAGAATTG 59.195 38.462 0.00 0.00 43.64 2.32
5754 14668 5.302568 TGTGATGAGAAGAATTGGCAACTTT 59.697 36.000 0.00 0.00 37.61 2.66
5894 14815 0.442699 CTTACGCCCGAAGAAAGCAC 59.557 55.000 0.00 0.00 0.00 4.40
5956 14877 8.879427 AAAATGCACTATAGGTCCTAAAAGTT 57.121 30.769 12.50 0.00 0.00 2.66
6044 14965 0.693049 GGTTCACCATGGGTCTGACT 59.307 55.000 18.09 0.00 31.02 3.41
6045 14966 1.611673 GGTTCACCATGGGTCTGACTG 60.612 57.143 18.09 3.05 31.02 3.51
6052 14973 2.439409 CATGGGTCTGACTGCATTTGA 58.561 47.619 7.85 0.00 0.00 2.69
6070 14992 5.605564 TTTGACCACGTAGATGTCATTTG 57.394 39.130 9.32 0.00 40.00 2.32
6077 14999 5.111989 CACGTAGATGTCATTTGTGATCCT 58.888 41.667 0.00 0.00 0.00 3.24
6102 15024 1.408822 CCCCCTCTACTCATGGTTTGC 60.409 57.143 0.00 0.00 0.00 3.68
6135 15057 0.607489 GACTGGTTGCTGGCATCAGT 60.607 55.000 22.14 22.14 42.78 3.41
6136 15058 0.892358 ACTGGTTGCTGGCATCAGTG 60.892 55.000 21.67 8.64 42.78 3.66
6137 15059 0.892358 CTGGTTGCTGGCATCAGTGT 60.892 55.000 13.99 0.00 42.78 3.55
6168 15090 9.841880 GGAAGGAAAGAATAGTTTGAATACAAC 57.158 33.333 0.00 0.00 35.63 3.32
6169 15091 9.841880 GAAGGAAAGAATAGTTTGAATACAACC 57.158 33.333 0.00 0.00 35.63 3.77
6212 15134 9.770097 ACATGTACAAGATTAATCGAGATCATT 57.230 29.630 9.78 0.00 0.00 2.57
6226 15148 4.562789 CGAGATCATTGTTCGCAACTCTAA 59.437 41.667 0.00 0.00 40.27 2.10
6227 15149 5.276114 CGAGATCATTGTTCGCAACTCTAAG 60.276 44.000 0.00 0.00 40.27 2.18
6283 15206 1.270625 TGTGCCTACTACCACAGCAAC 60.271 52.381 0.00 0.00 37.07 4.17
6289 15212 2.411628 ACTACCACAGCAACAACACA 57.588 45.000 0.00 0.00 0.00 3.72
6292 15215 2.582728 ACCACAGCAACAACACAATG 57.417 45.000 0.00 0.00 0.00 2.82
6305 15228 3.988379 ACACAATGCTTGTTGTCGAAT 57.012 38.095 0.00 0.00 43.23 3.34
6306 15229 3.631144 ACACAATGCTTGTTGTCGAATG 58.369 40.909 0.00 0.00 43.23 2.67
6318 15241 2.917933 TGTCGAATGCCCTCCTATTTG 58.082 47.619 0.00 0.00 0.00 2.32
6335 15258 7.661968 TCCTATTTGTCTCACACTAGATATGC 58.338 38.462 0.00 0.00 0.00 3.14
6344 15267 5.604565 TCACACTAGATATGCCAGAATGTG 58.395 41.667 0.00 0.00 36.99 3.21
6345 15268 5.129320 TCACACTAGATATGCCAGAATGTGT 59.871 40.000 0.00 0.00 36.98 3.72
6346 15269 6.323739 TCACACTAGATATGCCAGAATGTGTA 59.676 38.462 0.00 0.00 36.98 2.90
6349 15272 8.213679 ACACTAGATATGCCAGAATGTGTAATT 58.786 33.333 0.00 0.00 34.88 1.40
6358 15281 5.523916 GCCAGAATGTGTAATTAGTGACGAT 59.476 40.000 0.00 0.00 0.00 3.73
6359 15282 6.510157 GCCAGAATGTGTAATTAGTGACGATG 60.510 42.308 0.00 0.00 0.00 3.84
6382 15305 3.118149 CCATCAATCACATGTCTGGAGGA 60.118 47.826 0.00 0.00 0.00 3.71
6383 15306 4.445879 CCATCAATCACATGTCTGGAGGAT 60.446 45.833 0.00 0.00 0.00 3.24
6399 15323 0.538977 GGATGATCACCAGGGCCATG 60.539 60.000 11.33 11.33 0.00 3.66
6403 15327 0.251077 GATCACCAGGGCCATGGATC 60.251 60.000 41.60 29.22 43.57 3.36
6412 15336 2.123428 GCCATGGATCTGGTGCCAC 61.123 63.158 18.40 0.00 38.63 5.01
6437 15361 1.277557 CAGGGAAGGAGGTTGTCTCTG 59.722 57.143 0.00 0.00 42.10 3.35
6441 15365 2.289133 GGAAGGAGGTTGTCTCTGTCAC 60.289 54.545 0.00 0.00 42.10 3.67
6442 15366 2.088104 AGGAGGTTGTCTCTGTCACA 57.912 50.000 0.00 0.00 42.10 3.58
6468 15392 1.596895 GGTGAGACAGAGGGACGGTC 61.597 65.000 0.00 0.00 42.42 4.79
6502 15426 4.060038 GCATGCCACACCTGGTGC 62.060 66.667 26.20 13.47 46.50 5.01
6517 15441 0.928229 GGTGCGCGAAACTATACCTG 59.072 55.000 12.10 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.730612 GTGGCGTTAGTGTTAGAAGCC 59.269 52.381 0.00 0.00 43.05 4.35
600 602 6.697455 GTGAAGTCGTGAAGATATATCTGCAA 59.303 38.462 22.77 7.86 43.85 4.08
618 620 8.648968 GTTACTTAGTATTGAGCAAGTGAAGTC 58.351 37.037 0.00 0.00 33.47 3.01
619 621 8.148351 TGTTACTTAGTATTGAGCAAGTGAAGT 58.852 33.333 0.00 0.00 33.47 3.01
620 622 8.534333 TGTTACTTAGTATTGAGCAAGTGAAG 57.466 34.615 0.00 0.00 33.47 3.02
621 623 8.770828 GTTGTTACTTAGTATTGAGCAAGTGAA 58.229 33.333 0.00 0.00 33.47 3.18
622 624 7.115805 CGTTGTTACTTAGTATTGAGCAAGTGA 59.884 37.037 0.00 0.00 33.47 3.41
623 625 7.115805 TCGTTGTTACTTAGTATTGAGCAAGTG 59.884 37.037 0.00 0.00 33.47 3.16
624 626 7.149973 TCGTTGTTACTTAGTATTGAGCAAGT 58.850 34.615 0.00 0.00 35.50 3.16
625 627 7.576750 TCGTTGTTACTTAGTATTGAGCAAG 57.423 36.000 0.00 0.00 0.00 4.01
657 659 6.558252 CGAAATACACAATGTTATGCAATGCG 60.558 38.462 0.00 0.00 31.33 4.73
697 701 6.851222 AGACAGACATACACAGAAACAAAG 57.149 37.500 0.00 0.00 0.00 2.77
758 762 4.150627 CAGACATACACAGAAACAAGACGG 59.849 45.833 0.00 0.00 0.00 4.79
759 763 4.745125 ACAGACATACACAGAAACAAGACG 59.255 41.667 0.00 0.00 0.00 4.18
889 1232 4.814234 TCAGAACATGTTGTTGGTCAGTAC 59.186 41.667 17.58 0.00 41.28 2.73
897 1240 5.892160 ATCCTGATCAGAACATGTTGTTG 57.108 39.130 24.62 13.92 41.28 3.33
918 1261 0.755079 TCGCTAGCATGCTCCTCAAT 59.245 50.000 26.57 0.00 0.00 2.57
946 1289 4.081420 CCATAGTTACAGAGCCTTCACTGT 60.081 45.833 0.00 0.00 46.81 3.55
953 1296 3.034635 CAGACCCATAGTTACAGAGCCT 58.965 50.000 0.00 0.00 0.00 4.58
966 1309 3.871463 GCAGTGATTTCTGACAGACCCAT 60.871 47.826 4.15 0.00 37.61 4.00
970 1313 2.079925 GGGCAGTGATTTCTGACAGAC 58.920 52.381 4.15 0.00 44.56 3.51
981 1324 1.617018 TTCAGCGCTAGGGCAGTGAT 61.617 55.000 30.70 9.50 36.86 3.06
982 1325 1.617018 ATTCAGCGCTAGGGCAGTGA 61.617 55.000 30.70 23.29 36.86 3.41
1007 1350 4.710324 AGGTCGACTGAAGTATAGGAGAG 58.290 47.826 16.46 0.00 0.00 3.20
1008 1351 4.774660 AGGTCGACTGAAGTATAGGAGA 57.225 45.455 16.46 0.00 0.00 3.71
1076 1419 9.349713 GTGGGTCATAATAAGTATCCATTTCAA 57.650 33.333 0.00 0.00 0.00 2.69
1108 1451 4.123506 TGATGTGCAAAACGTAAGACAGA 58.876 39.130 0.00 0.00 43.62 3.41
1111 1454 4.616802 CCAATGATGTGCAAAACGTAAGAC 59.383 41.667 0.00 0.00 43.62 3.01
1117 1460 5.342433 ACATATCCAATGATGTGCAAAACG 58.658 37.500 0.00 0.00 42.16 3.60
1286 1731 0.597637 CACCACAGTGTCCGACTCAC 60.598 60.000 0.00 0.00 39.30 3.51
1296 1741 0.604780 CAGGCTTCTCCACCACAGTG 60.605 60.000 0.00 0.00 44.12 3.66
1385 1830 6.198403 GCAGCCAAGACTTAAAAGTTACAAAC 59.802 38.462 0.00 0.00 39.88 2.93
1405 1850 3.131046 ACACTTGCCATATTAAAGCAGCC 59.869 43.478 0.00 0.00 37.89 4.85
1411 1856 7.901029 TCAATTCCAACACTTGCCATATTAAA 58.099 30.769 0.00 0.00 0.00 1.52
1419 1864 2.102252 TGGTTCAATTCCAACACTTGCC 59.898 45.455 0.40 0.00 31.50 4.52
1438 1883 1.552792 GAAGAGGAGGGAGTTGAGTGG 59.447 57.143 0.00 0.00 0.00 4.00
1451 1896 4.343526 GTGAAGCATATCTCAGGAAGAGGA 59.656 45.833 0.00 0.00 44.81 3.71
1474 3967 1.670811 GTGTGTGTGTTTGAGAGTGGG 59.329 52.381 0.00 0.00 0.00 4.61
1494 3989 2.164624 GCCTCACTGTACTAGTCCTGTG 59.835 54.545 16.29 16.29 37.60 3.66
1495 3990 2.041891 AGCCTCACTGTACTAGTCCTGT 59.958 50.000 0.00 0.00 37.60 4.00
1496 3991 2.729194 AGCCTCACTGTACTAGTCCTG 58.271 52.381 0.00 0.00 37.60 3.86
1497 3992 3.093057 CAAGCCTCACTGTACTAGTCCT 58.907 50.000 0.00 0.00 37.60 3.85
1498 3993 3.090037 TCAAGCCTCACTGTACTAGTCC 58.910 50.000 0.00 0.00 37.60 3.85
1499 3994 4.158764 ACATCAAGCCTCACTGTACTAGTC 59.841 45.833 0.00 0.00 37.60 2.59
1500 3995 4.090090 ACATCAAGCCTCACTGTACTAGT 58.910 43.478 0.00 0.00 41.36 2.57
1501 3996 4.400884 AGACATCAAGCCTCACTGTACTAG 59.599 45.833 0.00 0.00 0.00 2.57
1502 3997 4.344978 AGACATCAAGCCTCACTGTACTA 58.655 43.478 0.00 0.00 0.00 1.82
1503 3998 3.169099 AGACATCAAGCCTCACTGTACT 58.831 45.455 0.00 0.00 0.00 2.73
1504 3999 3.601443 AGACATCAAGCCTCACTGTAC 57.399 47.619 0.00 0.00 0.00 2.90
1505 4000 5.939764 ATAAGACATCAAGCCTCACTGTA 57.060 39.130 0.00 0.00 0.00 2.74
1506 4001 4.833478 ATAAGACATCAAGCCTCACTGT 57.167 40.909 0.00 0.00 0.00 3.55
1521 4016 4.563184 GCTAGTGCTGTGTGTGTATAAGAC 59.437 45.833 0.00 0.00 36.03 3.01
1537 4034 2.275318 CTAAGCTTCAGGTGCTAGTGC 58.725 52.381 0.00 0.00 40.22 4.40
1566 4067 0.324275 ACAGAGAGAGGGAGGCTGAC 60.324 60.000 0.00 0.00 0.00 3.51
1595 4098 1.107945 GAGAGGGAGGCTGTAGTGAC 58.892 60.000 0.00 0.00 0.00 3.67
1596 4099 1.003646 AGAGAGGGAGGCTGTAGTGA 58.996 55.000 0.00 0.00 0.00 3.41
1597 4100 1.064017 AGAGAGAGGGAGGCTGTAGTG 60.064 57.143 0.00 0.00 0.00 2.74
1598 4101 1.064017 CAGAGAGAGGGAGGCTGTAGT 60.064 57.143 0.00 0.00 0.00 2.73
1599 4102 1.064017 ACAGAGAGAGGGAGGCTGTAG 60.064 57.143 0.00 0.00 37.98 2.74
1600 4103 1.003646 ACAGAGAGAGGGAGGCTGTA 58.996 55.000 0.00 0.00 37.98 2.74
1601 4104 0.116143 AACAGAGAGAGGGAGGCTGT 59.884 55.000 0.00 0.00 41.19 4.40
1602 4105 0.536260 CAACAGAGAGAGGGAGGCTG 59.464 60.000 0.00 0.00 0.00 4.85
1603 4106 0.617249 CCAACAGAGAGAGGGAGGCT 60.617 60.000 0.00 0.00 0.00 4.58
1604 4107 0.616111 TCCAACAGAGAGAGGGAGGC 60.616 60.000 0.00 0.00 0.00 4.70
1605 4108 1.484038 CTCCAACAGAGAGAGGGAGG 58.516 60.000 0.00 0.00 46.50 4.30
1606 4109 0.823460 GCTCCAACAGAGAGAGGGAG 59.177 60.000 0.00 0.00 46.50 4.30
1607 4110 0.411452 AGCTCCAACAGAGAGAGGGA 59.589 55.000 0.00 0.00 46.50 4.20
1608 4111 0.536260 CAGCTCCAACAGAGAGAGGG 59.464 60.000 0.00 0.00 46.50 4.30
1609 4112 1.477700 CTCAGCTCCAACAGAGAGAGG 59.522 57.143 0.00 0.00 46.50 3.69
1610 4113 2.164219 GACTCAGCTCCAACAGAGAGAG 59.836 54.545 3.69 9.60 46.50 3.20
1611 4114 2.166829 GACTCAGCTCCAACAGAGAGA 58.833 52.381 3.69 0.00 46.50 3.10
1612 4115 1.891811 TGACTCAGCTCCAACAGAGAG 59.108 52.381 3.69 0.00 46.50 3.20
1613 4116 1.615883 GTGACTCAGCTCCAACAGAGA 59.384 52.381 3.69 0.00 46.50 3.10
1614 4117 1.617850 AGTGACTCAGCTCCAACAGAG 59.382 52.381 0.00 0.00 46.29 3.35
1615 4118 1.615883 GAGTGACTCAGCTCCAACAGA 59.384 52.381 7.90 0.00 0.00 3.41
1616 4119 1.342496 TGAGTGACTCAGCTCCAACAG 59.658 52.381 11.93 0.00 35.39 3.16
1617 4120 1.413118 TGAGTGACTCAGCTCCAACA 58.587 50.000 11.93 0.00 35.39 3.33
1671 4179 2.315925 ACAACACACACACAGAGGAG 57.684 50.000 0.00 0.00 0.00 3.69
1677 4185 3.142174 TGTGAGAAACAACACACACACA 58.858 40.909 0.00 0.00 41.19 3.72
1678 4186 3.822594 TGTGAGAAACAACACACACAC 57.177 42.857 0.00 0.00 41.19 3.82
1687 4195 4.446994 TTGTGCATGTTGTGAGAAACAA 57.553 36.364 0.00 0.00 46.66 2.83
1688 4196 4.446994 TTTGTGCATGTTGTGAGAAACA 57.553 36.364 0.00 0.00 43.82 2.83
1689 4197 5.976534 TGTATTTGTGCATGTTGTGAGAAAC 59.023 36.000 0.00 0.00 0.00 2.78
1690 4198 5.976534 GTGTATTTGTGCATGTTGTGAGAAA 59.023 36.000 0.00 0.00 0.00 2.52
1691 4199 5.067023 TGTGTATTTGTGCATGTTGTGAGAA 59.933 36.000 0.00 0.00 0.00 2.87
1696 4204 4.050553 GCTTGTGTATTTGTGCATGTTGT 58.949 39.130 0.00 0.00 0.00 3.32
1698 4206 4.202141 ACAGCTTGTGTATTTGTGCATGTT 60.202 37.500 0.00 0.00 37.75 2.71
1720 4228 1.570813 GGCAGCAAGTCACCAAAAAC 58.429 50.000 0.00 0.00 0.00 2.43
1740 4248 2.689983 AGAAAAGGCTTTGACTGTGTGG 59.310 45.455 14.19 0.00 0.00 4.17
1748 4256 6.209192 TGCATCAATAAGAGAAAAGGCTTTGA 59.791 34.615 14.19 4.05 0.00 2.69
1838 4346 6.285990 GTGGTTCTGTACTAGTTCCTTTCAA 58.714 40.000 0.00 0.00 0.00 2.69
1931 4441 5.044698 AGTCTTAGGGAGTAAGCTAGTGAGT 60.045 44.000 0.00 0.00 38.48 3.41
1932 4442 5.442391 AGTCTTAGGGAGTAAGCTAGTGAG 58.558 45.833 0.00 0.00 38.48 3.51
2013 4619 4.532834 AGTTTTAGTGCTTTGGGACTTCA 58.467 39.130 0.00 0.00 41.32 3.02
2020 4626 7.448748 AACAGGTATAGTTTTAGTGCTTTGG 57.551 36.000 0.00 0.00 0.00 3.28
2234 4849 1.908344 TGCTTATTTGCAGGTGCTGA 58.092 45.000 3.18 0.00 42.66 4.26
2242 4857 8.885494 AAATACTTTTTGTCTGCTTATTTGCA 57.115 26.923 0.00 0.00 41.05 4.08
2373 5074 5.302823 CAGTTCCTTGTCCCTGAAGAAAATT 59.697 40.000 0.00 0.00 0.00 1.82
2460 5161 3.151554 GGAACACCCTACACCGAAAATT 58.848 45.455 0.00 0.00 0.00 1.82
2526 5227 0.311165 AAGGTCGAGCGGTCATATCG 59.689 55.000 15.89 0.34 37.79 2.92
2550 5251 1.422402 ACGGGAGGCCTCTTACAAAAA 59.578 47.619 31.36 0.00 0.00 1.94
2580 5284 5.184711 GTTTCTGAATCAGCTGGAGAAGAT 58.815 41.667 15.13 0.00 0.00 2.40
2685 5396 3.640498 TGCAAGAGAGAGGATGGTAGATG 59.360 47.826 0.00 0.00 0.00 2.90
2686 5397 3.896888 CTGCAAGAGAGAGGATGGTAGAT 59.103 47.826 0.00 0.00 34.07 1.98
2687 5398 3.295093 CTGCAAGAGAGAGGATGGTAGA 58.705 50.000 0.00 0.00 34.07 2.59
2688 5399 2.364970 CCTGCAAGAGAGAGGATGGTAG 59.635 54.545 0.00 0.00 34.07 3.18
2689 5400 2.292521 ACCTGCAAGAGAGAGGATGGTA 60.293 50.000 0.00 0.00 34.07 3.25
2690 5401 1.202330 CCTGCAAGAGAGAGGATGGT 58.798 55.000 0.00 0.00 34.07 3.55
2691 5402 1.202330 ACCTGCAAGAGAGAGGATGG 58.798 55.000 0.00 0.00 34.07 3.51
2798 5517 7.260558 TGACTATACAAGATACAGTTCCTCG 57.739 40.000 0.00 0.00 0.00 4.63
2894 5683 4.221924 ACCCACTTAAAACAGCTTTTGTGT 59.778 37.500 0.00 0.00 40.74 3.72
2898 5687 6.989759 CCAATAACCCACTTAAAACAGCTTTT 59.010 34.615 0.00 0.00 33.92 2.27
2966 5755 2.281761 CAGGCAACCTCGGCAGTT 60.282 61.111 0.00 0.00 37.17 3.16
3152 7826 0.244994 AGATGAGAAACGCGCTGAGT 59.755 50.000 5.73 0.00 0.00 3.41
3153 7827 0.919981 GAGATGAGAAACGCGCTGAG 59.080 55.000 5.73 0.00 0.00 3.35
3154 7828 0.458543 GGAGATGAGAAACGCGCTGA 60.459 55.000 5.73 0.00 0.00 4.26
3256 7935 2.577059 GCCAGATCGTCCAACCGA 59.423 61.111 0.00 0.00 41.73 4.69
3307 7988 0.321671 CCACCGTCATGAACAGGTCT 59.678 55.000 13.85 0.00 34.09 3.85
3309 7990 1.302511 GCCACCGTCATGAACAGGT 60.303 57.895 11.65 11.65 35.88 4.00
3318 7999 3.680786 CAGGAGTCGCCACCGTCA 61.681 66.667 0.00 0.00 40.02 4.35
3352 8033 4.988716 TCCAGGCCAGACCGTCGT 62.989 66.667 5.01 0.00 46.52 4.34
3355 8036 4.316823 TCCTCCAGGCCAGACCGT 62.317 66.667 5.01 0.00 46.52 4.83
3392 8083 1.376683 GCGCCATGGACAGTACCAA 60.377 57.895 18.40 0.00 43.47 3.67
3398 8089 3.136123 CCCTTGCGCCATGGACAG 61.136 66.667 18.40 6.95 31.33 3.51
3419 8110 0.250081 GCCCATCTTCGAGATCCACC 60.250 60.000 0.00 0.00 31.32 4.61
3435 8126 0.107945 AGATCGAAGAAGTGCTGCCC 60.108 55.000 0.00 0.00 43.58 5.36
3478 8169 2.440247 CCTCCCCGCCAATTGGAC 60.440 66.667 29.02 17.45 37.39 4.02
3531 8222 1.603739 GTTCCAGCCACTCCCAACC 60.604 63.158 0.00 0.00 0.00 3.77
3658 8350 4.423625 AGAACAGCAGAACCAACTAACT 57.576 40.909 0.00 0.00 0.00 2.24
3668 8360 1.502231 GAGCACGAAGAACAGCAGAA 58.498 50.000 0.00 0.00 0.00 3.02
3692 8384 2.939103 AGGTCGACATGCAGATTAAAGC 59.061 45.455 18.91 0.00 0.00 3.51
3914 8613 0.468226 TTCTTCACCACCTCAACGCT 59.532 50.000 0.00 0.00 0.00 5.07
3966 8667 0.516877 CGCAATCAAAACTCCTCGCA 59.483 50.000 0.00 0.00 0.00 5.10
4012 8721 1.414550 TCAACATCCGACACACAGGAA 59.585 47.619 0.00 0.00 40.32 3.36
4013 8722 1.000843 CTCAACATCCGACACACAGGA 59.999 52.381 0.00 0.00 41.30 3.86
4275 8993 1.195674 GCTCTTCAAAAGCGACACCTC 59.804 52.381 0.00 0.00 0.00 3.85
4357 9076 1.477553 AAGACCCCGTCGCAGTAATA 58.522 50.000 0.00 0.00 37.67 0.98
4433 9156 6.127535 CCTCTGCACCAACAAGATATCAAAAT 60.128 38.462 5.32 0.00 0.00 1.82
4528 9251 6.426980 TCTGCAAACACAAAGATGCTATAG 57.573 37.500 0.00 0.00 39.49 1.31
4742 13643 9.845740 AATTAACTAGATATATGTGTGGTGCAA 57.154 29.630 0.00 0.00 0.00 4.08
4743 13644 9.845740 AAATTAACTAGATATATGTGTGGTGCA 57.154 29.630 0.00 0.00 0.00 4.57
4872 13785 8.032952 TGCATTTTCTGTTCATGTAGTAGAAG 57.967 34.615 0.00 0.00 0.00 2.85
4882 13795 7.556733 ACACAAAATTGCATTTTCTGTTCAT 57.443 28.000 7.01 1.66 37.88 2.57
4911 13824 4.572389 GGAACTTCACACCTGTATGCATAG 59.428 45.833 6.67 0.00 0.00 2.23
5004 13917 7.278868 ACCTTGAGATTAGTATTTCTTTCAGCG 59.721 37.037 0.00 0.00 0.00 5.18
5129 14043 2.289945 ACAGAGTTCCTCAATCTGCCAC 60.290 50.000 1.50 0.00 43.42 5.01
5220 14134 1.134068 GGAATCACTTGACCTAGGGCC 60.134 57.143 13.60 4.15 0.00 5.80
5323 14237 2.753452 TGAAGACGAGGATCAGTACCAC 59.247 50.000 0.00 0.00 33.17 4.16
5516 14430 9.126151 TCAACAACTTTCACTAATCCATACAAA 57.874 29.630 0.00 0.00 0.00 2.83
5623 14537 5.694995 ACCTCAGTATCAAACCCATAATGG 58.305 41.667 0.00 0.00 37.25 3.16
5645 14559 6.611381 TGCAGAAACAATATTAGCACAGAAC 58.389 36.000 0.00 0.00 0.00 3.01
5730 14644 4.401022 AGTTGCCAATTCTTCTCATCACA 58.599 39.130 0.00 0.00 0.00 3.58
5746 14660 9.399403 CTTTCTTGATAGTTTAGAAAAGTTGCC 57.601 33.333 0.00 0.00 37.42 4.52
5824 14745 4.188247 TGATCAGGTTTAGTTCCAGTCG 57.812 45.455 0.00 0.00 0.00 4.18
5894 14815 1.749033 GGAGCGAACTATCCCAGGG 59.251 63.158 0.00 0.00 0.00 4.45
5956 14877 5.721000 AGGATTCAATTGGCATACCTCAAAA 59.279 36.000 5.42 0.00 36.63 2.44
6044 14965 3.000041 GACATCTACGTGGTCAAATGCA 59.000 45.455 0.00 0.00 0.00 3.96
6045 14966 3.000041 TGACATCTACGTGGTCAAATGC 59.000 45.455 0.00 0.00 38.50 3.56
6052 14973 4.265904 TCACAAATGACATCTACGTGGT 57.734 40.909 0.00 0.00 0.00 4.16
6070 14992 3.523972 AGTAGAGGGGGAAAAAGGATCAC 59.476 47.826 0.00 0.00 0.00 3.06
6077 14999 3.265489 ACCATGAGTAGAGGGGGAAAAA 58.735 45.455 0.00 0.00 0.00 1.94
6102 15024 4.790962 AGTCCAGCGGCCATGCAG 62.791 66.667 2.24 0.00 37.31 4.41
6135 15057 2.978156 ATTCTTTCCTTCCAGGCACA 57.022 45.000 0.00 0.00 34.61 4.57
6136 15058 3.956744 ACTATTCTTTCCTTCCAGGCAC 58.043 45.455 0.00 0.00 34.61 5.01
6137 15059 4.657814 AACTATTCTTTCCTTCCAGGCA 57.342 40.909 0.00 0.00 34.61 4.75
6168 15090 6.006759 ACATGTGTTTTTGTTGGTTTTTGG 57.993 33.333 0.00 0.00 0.00 3.28
6169 15091 7.576236 TGTACATGTGTTTTTGTTGGTTTTTG 58.424 30.769 9.11 0.00 0.00 2.44
6203 15125 2.926200 AGAGTTGCGAACAATGATCTCG 59.074 45.455 0.00 0.00 38.27 4.04
6212 15134 2.870435 GCCTTCCTTAGAGTTGCGAACA 60.870 50.000 0.00 0.00 0.00 3.18
6226 15148 3.083997 CCGTGCCCTAGCCTTCCT 61.084 66.667 0.00 0.00 38.69 3.36
6227 15149 4.176752 CCCGTGCCCTAGCCTTCC 62.177 72.222 0.00 0.00 38.69 3.46
6264 15186 1.270625 TGTTGCTGTGGTAGTAGGCAC 60.271 52.381 0.00 0.00 32.47 5.01
6275 15198 2.212869 AGCATTGTGTTGTTGCTGTG 57.787 45.000 0.00 0.00 44.63 3.66
6276 15199 2.542597 CAAGCATTGTGTTGTTGCTGT 58.457 42.857 0.00 0.00 45.54 4.40
6289 15212 1.067635 GGGCATTCGACAACAAGCATT 60.068 47.619 0.00 0.00 0.00 3.56
6292 15215 0.169009 GAGGGCATTCGACAACAAGC 59.831 55.000 0.00 0.00 0.00 4.01
6305 15228 2.027192 GTGTGAGACAAATAGGAGGGCA 60.027 50.000 0.00 0.00 0.00 5.36
6306 15229 2.237392 AGTGTGAGACAAATAGGAGGGC 59.763 50.000 0.00 0.00 0.00 5.19
6318 15241 5.521906 TTCTGGCATATCTAGTGTGAGAC 57.478 43.478 0.00 0.00 0.00 3.36
6335 15258 6.510157 GCATCGTCACTAATTACACATTCTGG 60.510 42.308 0.00 0.00 0.00 3.86
6344 15267 5.984233 TTGATGGCATCGTCACTAATTAC 57.016 39.130 21.65 0.00 38.52 1.89
6345 15268 6.202762 GTGATTGATGGCATCGTCACTAATTA 59.797 38.462 34.61 19.80 40.92 1.40
6346 15269 5.008019 GTGATTGATGGCATCGTCACTAATT 59.992 40.000 34.61 13.83 40.92 1.40
6349 15272 3.118811 TGTGATTGATGGCATCGTCACTA 60.119 43.478 37.42 28.89 42.78 2.74
6358 15281 2.026075 TCCAGACATGTGATTGATGGCA 60.026 45.455 1.15 0.00 30.41 4.92
6359 15282 2.617308 CTCCAGACATGTGATTGATGGC 59.383 50.000 1.15 0.00 31.41 4.40
6382 15305 0.995132 TCCATGGCCCTGGTGATCAT 60.995 55.000 24.62 0.00 37.57 2.45
6383 15306 0.995132 ATCCATGGCCCTGGTGATCA 60.995 55.000 24.62 7.36 37.57 2.92
6412 15336 0.326264 CAACCTCCTTCCCTGAGTGG 59.674 60.000 0.00 0.00 0.00 4.00
6437 15361 1.964223 TGTCTCACCTCCTTCTGTGAC 59.036 52.381 0.00 0.00 36.62 3.67
6441 15365 1.824230 CCTCTGTCTCACCTCCTTCTG 59.176 57.143 0.00 0.00 0.00 3.02
6442 15366 1.272985 CCCTCTGTCTCACCTCCTTCT 60.273 57.143 0.00 0.00 0.00 2.85
6502 15426 5.104562 TCATACTCAGGTATAGTTTCGCG 57.895 43.478 0.00 0.00 36.60 5.87


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

AutoCloner maintained by Alex Coulton.