Multiple sequence alignment - TraesCS3D01G061500

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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 TraesCS3D01G061500 chr3D 100.000 4047 0 0 1 4047 26680655 26684701 0.000000e+00 7474.0
1 TraesCS3D01G061500 chr3D 92.027 2521 167 17 740 3252 26816225 26813731 0.000000e+00 3511.0
2 TraesCS3D01G061500 chr3D 94.255 1497 74 8 1803 3289 27056919 27055425 0.000000e+00 2278.0
3 TraesCS3D01G061500 chr3D 83.543 1434 203 20 1871 3284 27060338 27058918 0.000000e+00 1310.0
4 TraesCS3D01G061500 chr3D 84.422 199 10 8 102 280 26816751 26816554 4.160000e-40 176.0
5 TraesCS3D01G061500 chr3D 92.647 68 3 1 289 356 26816425 26816360 3.330000e-16 97.1
6 TraesCS3D01G061500 chr3D 86.792 53 7 0 3925 3977 373853580 373853632 4.370000e-05 60.2
7 TraesCS3D01G061500 chr3A 92.418 2572 153 18 718 3265 37301539 37304092 0.000000e+00 3631.0
8 TraesCS3D01G061500 chr3A 94.595 1665 89 1 1441 3105 37234025 37235688 0.000000e+00 2575.0
9 TraesCS3D01G061500 chr3A 93.085 1287 79 6 962 2242 36940898 36942180 0.000000e+00 1875.0
10 TraesCS3D01G061500 chr3A 94.161 959 54 1 2274 3230 36942592 36943550 0.000000e+00 1459.0
11 TraesCS3D01G061500 chr3A 84.842 1326 184 9 1864 3182 36921086 36922401 0.000000e+00 1319.0
12 TraesCS3D01G061500 chr3A 88.602 737 70 8 718 1449 37231495 37232222 0.000000e+00 883.0
13 TraesCS3D01G061500 chr3A 87.415 294 12 9 1 277 37193932 37194217 8.440000e-82 315.0
14 TraesCS3D01G061500 chr3A 96.341 164 6 0 408 571 37194565 37194728 1.850000e-68 270.0
15 TraesCS3D01G061500 chr3A 92.973 185 7 4 404 586 37300905 37301085 8.620000e-67 265.0
16 TraesCS3D01G061500 chr3A 90.050 201 12 3 1 198 37298757 37298952 1.870000e-63 254.0
17 TraesCS3D01G061500 chr3A 89.941 169 11 2 3103 3265 37241207 37241375 3.170000e-51 213.0
18 TraesCS3D01G061500 chr3A 96.581 117 4 0 126 242 36923865 36923981 1.150000e-45 195.0
19 TraesCS3D01G061500 chr3A 98.507 67 1 0 290 356 36924359 36924425 7.110000e-23 119.0
20 TraesCS3D01G061500 chr3A 95.918 49 2 0 360 408 37300845 37300893 3.350000e-11 80.5
21 TraesCS3D01G061500 chr3A 92.593 54 4 0 441 494 36924485 36924538 1.210000e-10 78.7
22 TraesCS3D01G061500 chr3A 100.000 32 0 0 325 356 37194430 37194461 4.370000e-05 60.2
23 TraesCS3D01G061500 chrUn 94.739 2338 108 7 882 3210 38671586 38669255 0.000000e+00 3622.0
24 TraesCS3D01G061500 chrUn 93.218 1504 83 11 1803 3287 39209101 39210604 0.000000e+00 2194.0
25 TraesCS3D01G061500 chrUn 93.152 1504 84 11 1803 3287 311243888 311242385 0.000000e+00 2189.0
26 TraesCS3D01G061500 chrUn 87.397 968 91 19 718 1672 287695049 287695998 0.000000e+00 1083.0
27 TraesCS3D01G061500 chrUn 87.397 968 91 19 718 1672 287707253 287708202 0.000000e+00 1083.0
28 TraesCS3D01G061500 chrUn 87.397 968 91 19 718 1672 294703266 294704215 0.000000e+00 1083.0
29 TraesCS3D01G061500 chrUn 89.988 819 44 11 3259 4044 38665762 38664949 0.000000e+00 1024.0
30 TraesCS3D01G061500 chrUn 89.300 243 10 8 1 238 374338891 374338660 1.420000e-74 291.0
31 TraesCS3D01G061500 chrUn 90.393 229 10 6 1 228 412629422 412629205 1.420000e-74 291.0
32 TraesCS3D01G061500 chrUn 90.393 229 10 6 1 228 412691679 412691462 1.420000e-74 291.0
33 TraesCS3D01G061500 chrUn 90.393 229 10 6 1 228 465071992 465072209 1.420000e-74 291.0
34 TraesCS3D01G061500 chrUn 90.604 149 9 2 449 596 287694536 287694680 4.130000e-45 193.0
35 TraesCS3D01G061500 chrUn 90.604 149 9 2 449 596 287706740 287706884 4.130000e-45 193.0
36 TraesCS3D01G061500 chrUn 90.604 149 9 2 449 596 294702753 294702897 4.130000e-45 193.0
37 TraesCS3D01G061500 chrUn 96.364 110 4 0 136 245 38672168 38672059 8.940000e-42 182.0
38 TraesCS3D01G061500 chrUn 97.368 38 0 1 813 850 38671617 38671581 3.380000e-06 63.9
39 TraesCS3D01G061500 chrUn 100.000 28 0 0 561 588 326861583 326861610 7.000000e-03 52.8
40 TraesCS3D01G061500 chrUn 100.000 28 0 0 561 588 326864614 326864641 7.000000e-03 52.8
41 TraesCS3D01G061500 chrUn 100.000 28 0 0 561 588 371911714 371911687 7.000000e-03 52.8
42 TraesCS3D01G061500 chrUn 100.000 28 0 0 561 588 458243494 458243521 7.000000e-03 52.8
43 TraesCS3D01G061500 chr5D 84.777 381 55 1 1133 1513 523454809 523454432 2.950000e-101 379.0
44 TraesCS3D01G061500 chr4B 90.476 42 0 4 556 595 427498448 427498487 7.000000e-03 52.8


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 TraesCS3D01G061500 chr3D 26680655 26684701 4046 False 7474.000000 7474 100.000000 1 4047 1 chr3D.!!$F1 4046
1 TraesCS3D01G061500 chr3D 27055425 27060338 4913 True 1794.000000 2278 88.899000 1803 3289 2 chr3D.!!$R2 1486
2 TraesCS3D01G061500 chr3D 26813731 26816751 3020 True 1261.366667 3511 89.698667 102 3252 3 chr3D.!!$R1 3150
3 TraesCS3D01G061500 chr3A 37231495 37235688 4193 False 1729.000000 2575 91.598500 718 3105 2 chr3A.!!$F5 2387
4 TraesCS3D01G061500 chr3A 36940898 36943550 2652 False 1667.000000 1875 93.623000 962 3230 2 chr3A.!!$F3 2268
5 TraesCS3D01G061500 chr3A 37298757 37304092 5335 False 1057.625000 3631 92.839750 1 3265 4 chr3A.!!$F6 3264
6 TraesCS3D01G061500 chr3A 36921086 36924538 3452 False 427.925000 1319 93.130750 126 3182 4 chr3A.!!$F2 3056
7 TraesCS3D01G061500 chr3A 37193932 37194728 796 False 215.066667 315 94.585333 1 571 3 chr3A.!!$F4 570
8 TraesCS3D01G061500 chrUn 39209101 39210604 1503 False 2194.000000 2194 93.218000 1803 3287 1 chrUn.!!$F1 1484
9 TraesCS3D01G061500 chrUn 311242385 311243888 1503 True 2189.000000 2189 93.152000 1803 3287 1 chrUn.!!$R1 1484
10 TraesCS3D01G061500 chrUn 38664949 38672168 7219 True 1222.975000 3622 94.614750 136 4044 4 chrUn.!!$R6 3908
11 TraesCS3D01G061500 chrUn 287694536 287695998 1462 False 638.000000 1083 89.000500 449 1672 2 chrUn.!!$F4 1223
12 TraesCS3D01G061500 chrUn 287706740 287708202 1462 False 638.000000 1083 89.000500 449 1672 2 chrUn.!!$F5 1223
13 TraesCS3D01G061500 chrUn 294702753 294704215 1462 False 638.000000 1083 89.000500 449 1672 2 chrUn.!!$F6 1223

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
394 2163 0.603707 TCCTGCTTTTCCTGCGTGAG 60.604 55.0 0.00 0.0 0.00 3.51 F
1662 3911 0.252742 ATTTCTCCCTCCGTCTGGGT 60.253 55.0 0.00 0.0 44.84 4.51 F
1792 4041 0.174845 CGGATCCAGCGGTAGTTGAA 59.825 55.0 13.41 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1766 4015 0.828022 ACCGCTGGATCCGTATTCAA 59.172 50.0 7.39 0.00 0.00 2.69 R
2478 8197 0.986527 TGGCTTCCTCATGAGCTCAA 59.013 50.0 22.50 3.88 0.00 3.02 R
3731 14628 0.587768 GCAACTGGCACAAAATTGGC 59.412 50.0 0.00 0.00 43.97 4.52 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
26 27 3.316308 GGTGGCTGTAATTCCTATGCTTG 59.684 47.826 0.00 0.00 0.00 4.01
52 56 2.762327 GGATGCAACCAACCATTCTGAT 59.238 45.455 8.36 0.00 34.28 2.90
277 1836 1.106944 AAAACTTGGAGTGCCGTGGG 61.107 55.000 0.00 0.00 36.79 4.61
356 2090 4.292186 AGTTCAGTGCACCACAGATATT 57.708 40.909 14.63 0.00 36.74 1.28
358 2092 5.178797 AGTTCAGTGCACCACAGATATTAC 58.821 41.667 14.63 2.42 36.74 1.89
394 2163 0.603707 TCCTGCTTTTCCTGCGTGAG 60.604 55.000 0.00 0.00 0.00 3.51
538 2335 2.159037 CAGCACCAATATATCGCTGCAG 59.841 50.000 10.11 10.11 43.09 4.41
588 2389 1.962100 CTACTCCCTCCGTCCCATAAC 59.038 57.143 0.00 0.00 0.00 1.89
596 2398 1.958579 TCCGTCCCATAACGTAGGATG 59.041 52.381 3.41 6.22 41.01 3.51
598 2400 2.886523 CCGTCCCATAACGTAGGATGTA 59.113 50.000 12.43 0.00 41.01 2.29
601 2403 5.183713 CCGTCCCATAACGTAGGATGTATTA 59.816 44.000 12.43 0.00 41.01 0.98
602 2404 6.088824 CGTCCCATAACGTAGGATGTATTAC 58.911 44.000 3.41 0.00 37.86 1.89
679 2833 7.177498 TCATCCGAATATTGAATTCAAGACG 57.823 36.000 24.17 22.26 39.47 4.18
688 2842 9.840427 AATATTGAATTCAAGACGTGGTTTTAG 57.160 29.630 24.17 0.00 39.47 1.85
696 2850 7.692460 TCAAGACGTGGTTTTAGATAGAGTA 57.308 36.000 0.00 0.00 0.00 2.59
702 2856 8.297470 ACGTGGTTTTAGATAGAGTATGGTTA 57.703 34.615 0.00 0.00 0.00 2.85
726 2880 1.896183 CACCCACGGACATTGCACA 60.896 57.895 0.00 0.00 0.00 4.57
727 2881 1.074775 ACCCACGGACATTGCACAT 59.925 52.632 0.00 0.00 0.00 3.21
728 2882 0.960364 ACCCACGGACATTGCACATC 60.960 55.000 0.00 0.00 0.00 3.06
758 2974 1.804151 GCAAACGTATGCTGGTTGAGA 59.196 47.619 7.39 0.00 43.06 3.27
771 2987 3.154710 TGGTTGAGAACGAAGCTAGAGA 58.845 45.455 0.00 0.00 0.00 3.10
803 3019 3.515502 TGGAAGACTAGACATGACTTGGG 59.484 47.826 2.34 0.00 0.00 4.12
863 3099 8.970020 AGTTCATTGCTCCAAACATATTCATAA 58.030 29.630 0.00 0.00 0.00 1.90
864 3100 9.754382 GTTCATTGCTCCAAACATATTCATAAT 57.246 29.630 0.00 0.00 0.00 1.28
938 3174 1.135257 ACTGAGCTCGTCATTTCTCCG 60.135 52.381 9.64 0.00 33.51 4.63
976 3214 4.013728 CAGAGTGAGTACTTACAGAGCCT 58.986 47.826 18.91 5.90 37.25 4.58
985 3223 0.888619 TTACAGAGCCTGTCACTCCG 59.111 55.000 10.60 0.00 41.21 4.63
1043 3281 1.198759 TTGCCAGAGACCCTACCACC 61.199 60.000 0.00 0.00 0.00 4.61
1068 3306 4.320788 GCATGGTTGTTTCTCTTCCTCTTG 60.321 45.833 0.00 0.00 0.00 3.02
1108 3349 1.154197 GTACTGGTTCACCGGAAAGC 58.846 55.000 9.46 12.52 45.36 3.51
1227 3468 2.359230 AGCCTCGCAAGGAAGCAC 60.359 61.111 0.00 0.00 46.67 4.40
1251 3493 1.735973 CGACATGATGCTCCTCCGA 59.264 57.895 0.00 0.00 0.00 4.55
1284 3529 1.154263 GACCCTCGTCGTGTCTTCG 60.154 63.158 0.00 0.00 0.00 3.79
1285 3530 2.504244 CCCTCGTCGTGTCTTCGC 60.504 66.667 0.00 0.00 0.00 4.70
1538 3787 7.568199 TTTAAATTTCTAGGTGCTGATAGCC 57.432 36.000 0.00 0.00 41.51 3.93
1539 3788 5.379706 AAATTTCTAGGTGCTGATAGCCT 57.620 39.130 0.00 0.00 41.51 4.58
1540 3789 5.379706 AATTTCTAGGTGCTGATAGCCTT 57.620 39.130 0.00 0.00 41.51 4.35
1541 3790 4.844349 TTTCTAGGTGCTGATAGCCTTT 57.156 40.909 0.00 0.00 41.51 3.11
1542 3791 4.408182 TTCTAGGTGCTGATAGCCTTTC 57.592 45.455 0.00 0.00 41.51 2.62
1543 3792 3.647636 TCTAGGTGCTGATAGCCTTTCT 58.352 45.455 0.00 0.00 41.51 2.52
1544 3793 4.033709 TCTAGGTGCTGATAGCCTTTCTT 58.966 43.478 0.00 0.00 41.51 2.52
1545 3794 3.728385 AGGTGCTGATAGCCTTTCTTT 57.272 42.857 0.00 0.00 41.51 2.52
1546 3795 4.039603 AGGTGCTGATAGCCTTTCTTTT 57.960 40.909 0.00 0.00 41.51 2.27
1547 3796 5.179452 AGGTGCTGATAGCCTTTCTTTTA 57.821 39.130 0.00 0.00 41.51 1.52
1548 3797 5.570320 AGGTGCTGATAGCCTTTCTTTTAA 58.430 37.500 0.00 0.00 41.51 1.52
1549 3798 5.649831 AGGTGCTGATAGCCTTTCTTTTAAG 59.350 40.000 0.00 0.00 41.51 1.85
1550 3799 5.648092 GGTGCTGATAGCCTTTCTTTTAAGA 59.352 40.000 0.00 0.00 41.51 2.10
1551 3800 6.319911 GGTGCTGATAGCCTTTCTTTTAAGAT 59.680 38.462 0.00 0.00 41.51 2.40
1552 3801 7.413644 GTGCTGATAGCCTTTCTTTTAAGATC 58.586 38.462 0.00 0.00 41.51 2.75
1553 3802 7.281999 GTGCTGATAGCCTTTCTTTTAAGATCT 59.718 37.037 0.00 0.00 41.51 2.75
1554 3803 7.831193 TGCTGATAGCCTTTCTTTTAAGATCTT 59.169 33.333 13.56 13.56 41.51 2.40
1555 3804 8.127954 GCTGATAGCCTTTCTTTTAAGATCTTG 58.872 37.037 18.47 1.05 34.48 3.02
1556 3805 7.989826 TGATAGCCTTTCTTTTAAGATCTTGC 58.010 34.615 18.47 9.15 34.49 4.01
1559 3808 6.244654 AGCCTTTCTTTTAAGATCTTGCTCT 58.755 36.000 18.47 0.00 34.49 4.09
1561 3810 6.150140 GCCTTTCTTTTAAGATCTTGCTCTCA 59.850 38.462 18.47 0.00 34.49 3.27
1562 3811 7.148103 GCCTTTCTTTTAAGATCTTGCTCTCAT 60.148 37.037 18.47 0.00 34.49 2.90
1563 3812 8.738106 CCTTTCTTTTAAGATCTTGCTCTCATT 58.262 33.333 18.47 0.00 34.49 2.57
1570 3819 6.419980 AAGATCTTGCTCTCATTTTTCTCG 57.580 37.500 7.30 0.00 0.00 4.04
1572 3821 6.634805 AGATCTTGCTCTCATTTTTCTCGTA 58.365 36.000 0.00 0.00 0.00 3.43
1574 3823 5.784177 TCTTGCTCTCATTTTTCTCGTACT 58.216 37.500 0.00 0.00 0.00 2.73
1576 3825 5.134202 TGCTCTCATTTTTCTCGTACTGA 57.866 39.130 0.00 0.00 0.00 3.41
1577 3826 5.538118 TGCTCTCATTTTTCTCGTACTGAA 58.462 37.500 0.00 0.00 0.00 3.02
1579 3828 6.650807 TGCTCTCATTTTTCTCGTACTGAATT 59.349 34.615 0.00 0.00 0.00 2.17
1581 3830 7.364522 TCTCATTTTTCTCGTACTGAATTGG 57.635 36.000 0.00 0.00 0.00 3.16
1582 3831 7.158697 TCTCATTTTTCTCGTACTGAATTGGA 58.841 34.615 0.00 0.00 0.00 3.53
1583 3832 7.117812 TCTCATTTTTCTCGTACTGAATTGGAC 59.882 37.037 0.00 0.00 0.00 4.02
1585 3834 6.780706 TTTTTCTCGTACTGAATTGGACTC 57.219 37.500 0.00 0.00 0.00 3.36
1586 3835 5.723672 TTTCTCGTACTGAATTGGACTCT 57.276 39.130 0.00 0.00 0.00 3.24
1588 3837 4.332828 TCTCGTACTGAATTGGACTCTCA 58.667 43.478 0.00 0.00 0.00 3.27
1590 3839 4.079970 TCGTACTGAATTGGACTCTCACT 58.920 43.478 0.00 0.00 0.00 3.41
1591 3840 4.523173 TCGTACTGAATTGGACTCTCACTT 59.477 41.667 0.00 0.00 0.00 3.16
1592 3841 4.859798 CGTACTGAATTGGACTCTCACTTC 59.140 45.833 0.00 0.00 0.00 3.01
1593 3842 4.278975 ACTGAATTGGACTCTCACTTCC 57.721 45.455 0.00 0.00 0.00 3.46
1594 3843 3.257393 CTGAATTGGACTCTCACTTCCG 58.743 50.000 0.00 0.00 34.24 4.30
1595 3844 2.632996 TGAATTGGACTCTCACTTCCGT 59.367 45.455 0.00 0.00 34.24 4.69
1596 3845 3.254892 GAATTGGACTCTCACTTCCGTC 58.745 50.000 0.00 0.00 34.24 4.79
1598 3847 1.248486 TGGACTCTCACTTCCGTCAG 58.752 55.000 0.00 0.00 34.24 3.51
1599 3848 1.202891 TGGACTCTCACTTCCGTCAGA 60.203 52.381 0.00 0.00 34.24 3.27
1601 3850 2.296471 GGACTCTCACTTCCGTCAGAAA 59.704 50.000 0.00 0.00 32.88 2.52
1602 3851 3.310246 GACTCTCACTTCCGTCAGAAAC 58.690 50.000 0.00 0.00 32.88 2.78
1603 3852 2.693591 ACTCTCACTTCCGTCAGAAACA 59.306 45.455 0.00 0.00 32.88 2.83
1604 3853 3.132289 ACTCTCACTTCCGTCAGAAACAA 59.868 43.478 0.00 0.00 32.88 2.83
1605 3854 4.119862 CTCTCACTTCCGTCAGAAACAAA 58.880 43.478 0.00 0.00 32.88 2.83
1606 3855 4.509616 TCTCACTTCCGTCAGAAACAAAA 58.490 39.130 0.00 0.00 32.88 2.44
1607 3856 5.123227 TCTCACTTCCGTCAGAAACAAAAT 58.877 37.500 0.00 0.00 32.88 1.82
1608 3857 6.285224 TCTCACTTCCGTCAGAAACAAAATA 58.715 36.000 0.00 0.00 32.88 1.40
1609 3858 6.764085 TCTCACTTCCGTCAGAAACAAAATAA 59.236 34.615 0.00 0.00 32.88 1.40
1610 3859 6.721321 TCACTTCCGTCAGAAACAAAATAAC 58.279 36.000 0.00 0.00 32.88 1.89
1611 3860 5.619607 CACTTCCGTCAGAAACAAAATAACG 59.380 40.000 0.00 0.00 32.88 3.18
1616 3865 6.654519 CGTCAGAAACAAAATAACGGAAAG 57.345 37.500 0.00 0.00 0.00 2.62
1617 3866 5.623673 CGTCAGAAACAAAATAACGGAAAGG 59.376 40.000 0.00 0.00 0.00 3.11
1619 3868 6.635641 GTCAGAAACAAAATAACGGAAAGGAC 59.364 38.462 0.00 0.00 0.00 3.85
1621 3870 7.067737 TCAGAAACAAAATAACGGAAAGGACTT 59.932 33.333 0.00 0.00 0.00 3.01
1623 3872 7.919091 AGAAACAAAATAACGGAAAGGACTTTC 59.081 33.333 14.76 14.76 46.03 2.62
1636 3885 2.704572 GGACTTTCATGTGGTCCTCTG 58.295 52.381 19.38 0.00 44.21 3.35
1637 3886 2.079925 GACTTTCATGTGGTCCTCTGC 58.920 52.381 0.00 0.00 0.00 4.26
1638 3887 1.701847 ACTTTCATGTGGTCCTCTGCT 59.298 47.619 0.00 0.00 0.00 4.24
1642 3891 2.540383 TCATGTGGTCCTCTGCTAACT 58.460 47.619 0.00 0.00 0.00 2.24
1644 3893 4.290093 TCATGTGGTCCTCTGCTAACTAT 58.710 43.478 0.00 0.00 0.00 2.12
1645 3894 4.716784 TCATGTGGTCCTCTGCTAACTATT 59.283 41.667 0.00 0.00 0.00 1.73
1647 3896 5.086104 TGTGGTCCTCTGCTAACTATTTC 57.914 43.478 0.00 0.00 0.00 2.17
1648 3897 4.777896 TGTGGTCCTCTGCTAACTATTTCT 59.222 41.667 0.00 0.00 0.00 2.52
1649 3898 5.105310 TGTGGTCCTCTGCTAACTATTTCTC 60.105 44.000 0.00 0.00 0.00 2.87
1650 3899 4.406003 TGGTCCTCTGCTAACTATTTCTCC 59.594 45.833 0.00 0.00 0.00 3.71
1651 3900 4.202274 GGTCCTCTGCTAACTATTTCTCCC 60.202 50.000 0.00 0.00 0.00 4.30
1652 3901 4.651962 GTCCTCTGCTAACTATTTCTCCCT 59.348 45.833 0.00 0.00 0.00 4.20
1655 3904 3.637229 TCTGCTAACTATTTCTCCCTCCG 59.363 47.826 0.00 0.00 0.00 4.63
1656 3905 3.371965 TGCTAACTATTTCTCCCTCCGT 58.628 45.455 0.00 0.00 0.00 4.69
1657 3906 3.383825 TGCTAACTATTTCTCCCTCCGTC 59.616 47.826 0.00 0.00 0.00 4.79
1658 3907 3.637694 GCTAACTATTTCTCCCTCCGTCT 59.362 47.826 0.00 0.00 0.00 4.18
1659 3908 4.500035 GCTAACTATTTCTCCCTCCGTCTG 60.500 50.000 0.00 0.00 0.00 3.51
1661 3910 1.689273 CTATTTCTCCCTCCGTCTGGG 59.311 57.143 0.00 0.00 45.90 4.45
1662 3911 0.252742 ATTTCTCCCTCCGTCTGGGT 60.253 55.000 0.00 0.00 44.84 4.51
1663 3912 0.473117 TTTCTCCCTCCGTCTGGGTT 60.473 55.000 0.00 0.00 44.84 4.11
1666 3915 1.007963 TCTCCCTCCGTCTGGGTTTAT 59.992 52.381 0.00 0.00 44.84 1.40
1669 3918 3.036091 TCCCTCCGTCTGGGTTTATTAG 58.964 50.000 0.00 0.00 44.84 1.73
1670 3919 2.770232 CCCTCCGTCTGGGTTTATTAGT 59.230 50.000 0.00 0.00 39.82 2.24
1671 3920 3.199289 CCCTCCGTCTGGGTTTATTAGTT 59.801 47.826 0.00 0.00 39.82 2.24
1672 3921 4.324022 CCCTCCGTCTGGGTTTATTAGTTT 60.324 45.833 0.00 0.00 39.82 2.66
1673 3922 4.874396 CCTCCGTCTGGGTTTATTAGTTTC 59.126 45.833 0.00 0.00 37.00 2.78
1674 3923 5.484715 CTCCGTCTGGGTTTATTAGTTTCA 58.515 41.667 0.00 0.00 37.00 2.69
1675 3924 5.240121 TCCGTCTGGGTTTATTAGTTTCAC 58.760 41.667 0.00 0.00 37.00 3.18
1676 3925 5.012354 TCCGTCTGGGTTTATTAGTTTCACT 59.988 40.000 0.00 0.00 37.00 3.41
1677 3926 5.350640 CCGTCTGGGTTTATTAGTTTCACTC 59.649 44.000 0.00 0.00 0.00 3.51
1678 3927 5.929992 CGTCTGGGTTTATTAGTTTCACTCA 59.070 40.000 0.00 0.00 0.00 3.41
1680 3929 7.762615 CGTCTGGGTTTATTAGTTTCACTCATA 59.237 37.037 0.00 0.00 0.00 2.15
1681 3930 9.099454 GTCTGGGTTTATTAGTTTCACTCATAG 57.901 37.037 0.00 0.00 0.00 2.23
1682 3931 8.822805 TCTGGGTTTATTAGTTTCACTCATAGT 58.177 33.333 0.00 0.00 0.00 2.12
1683 3932 9.449719 CTGGGTTTATTAGTTTCACTCATAGTT 57.550 33.333 0.00 0.00 0.00 2.24
1696 3945 9.997482 TTTCACTCATAGTTTGTGTTTAACTTC 57.003 29.630 0.00 0.00 37.12 3.01
1697 3946 8.958119 TCACTCATAGTTTGTGTTTAACTTCT 57.042 30.769 0.00 0.00 37.12 2.85
1765 4014 8.706322 AAAAATGATACCACCTGAAACTACTT 57.294 30.769 0.00 0.00 0.00 2.24
1766 4015 8.706322 AAAATGATACCACCTGAAACTACTTT 57.294 30.769 0.00 0.00 0.00 2.66
1767 4016 8.706322 AAATGATACCACCTGAAACTACTTTT 57.294 30.769 0.00 0.00 0.00 2.27
1768 4017 7.687941 ATGATACCACCTGAAACTACTTTTG 57.312 36.000 0.00 0.00 0.00 2.44
1769 4018 6.833041 TGATACCACCTGAAACTACTTTTGA 58.167 36.000 0.00 0.00 0.00 2.69
1770 4019 7.284074 TGATACCACCTGAAACTACTTTTGAA 58.716 34.615 0.00 0.00 0.00 2.69
1772 4021 9.444600 GATACCACCTGAAACTACTTTTGAATA 57.555 33.333 0.00 0.00 0.00 1.75
1775 4024 6.348213 CCACCTGAAACTACTTTTGAATACGG 60.348 42.308 0.00 0.00 0.00 4.02
1776 4025 6.425721 CACCTGAAACTACTTTTGAATACGGA 59.574 38.462 0.00 0.00 0.00 4.69
1777 4026 7.119262 CACCTGAAACTACTTTTGAATACGGAT 59.881 37.037 0.00 0.00 0.00 4.18
1781 4030 7.333423 TGAAACTACTTTTGAATACGGATCCAG 59.667 37.037 13.41 7.30 0.00 3.86
1782 4031 5.116882 ACTACTTTTGAATACGGATCCAGC 58.883 41.667 13.41 0.00 0.00 4.85
1784 4033 1.948104 TTTGAATACGGATCCAGCGG 58.052 50.000 13.41 0.00 0.00 5.52
1785 4034 0.828022 TTGAATACGGATCCAGCGGT 59.172 50.000 13.41 3.78 0.00 5.68
1786 4035 1.694844 TGAATACGGATCCAGCGGTA 58.305 50.000 13.41 6.12 0.00 4.02
1788 4037 1.612463 GAATACGGATCCAGCGGTAGT 59.388 52.381 13.41 4.86 0.00 2.73
1789 4038 1.700955 ATACGGATCCAGCGGTAGTT 58.299 50.000 13.41 0.00 0.00 2.24
1790 4039 0.742505 TACGGATCCAGCGGTAGTTG 59.257 55.000 13.41 0.00 0.00 3.16
1791 4040 0.968901 ACGGATCCAGCGGTAGTTGA 60.969 55.000 13.41 0.00 0.00 3.18
1792 4041 0.174845 CGGATCCAGCGGTAGTTGAA 59.825 55.000 13.41 0.00 0.00 2.69
1794 4043 2.484889 GGATCCAGCGGTAGTTGAATC 58.515 52.381 6.95 0.00 0.00 2.52
1796 4045 3.321111 GGATCCAGCGGTAGTTGAATCTA 59.679 47.826 6.95 0.00 0.00 1.98
1797 4046 4.021016 GGATCCAGCGGTAGTTGAATCTAT 60.021 45.833 6.95 0.00 0.00 1.98
1799 4048 6.127310 GGATCCAGCGGTAGTTGAATCTATAT 60.127 42.308 6.95 0.00 0.00 0.86
1800 4049 7.068348 GGATCCAGCGGTAGTTGAATCTATATA 59.932 40.741 6.95 0.00 0.00 0.86
2351 8064 2.160205 CTCTCCTGACCGTGAGTACAA 58.840 52.381 0.00 0.00 0.00 2.41
2459 8178 5.874810 GGTTCAATAGACACATCAGCTAACA 59.125 40.000 0.00 0.00 0.00 2.41
2478 8197 1.064825 ACCCTCGAATTCACCTTGGT 58.935 50.000 6.22 1.61 0.00 3.67
2521 8240 3.265791 CCTGATGGTGAAGCTACAAGAC 58.734 50.000 0.00 0.00 0.00 3.01
2965 8687 1.160137 CGCTTGGGGTTGAGAGAAAG 58.840 55.000 0.00 0.00 0.00 2.62
3088 8816 7.639162 AGCTAAATAGTGTGTTATATCGCAC 57.361 36.000 16.37 16.37 45.57 5.34
3105 8833 4.536065 TCGCACAATGCTTTTCTTTGTAG 58.464 39.130 0.00 0.00 42.25 2.74
3309 12487 5.763444 ATCGGATTTACTAAATCGCATCG 57.237 39.130 13.18 11.32 46.45 3.84
3343 12521 9.562408 TTTTAACTATGTCACATCCAAGTTGTA 57.438 29.630 12.82 1.34 0.00 2.41
3354 12532 9.104713 TCACATCCAAGTTGTATATCATAGGAT 57.895 33.333 1.45 0.00 37.55 3.24
3487 14354 4.705023 GGCCACTAGTCCATTTGTTGTATT 59.295 41.667 0.00 0.00 0.00 1.89
3488 14355 5.393027 GGCCACTAGTCCATTTGTTGTATTG 60.393 44.000 0.00 0.00 0.00 1.90
3491 14358 5.710099 CACTAGTCCATTTGTTGTATTGGGT 59.290 40.000 0.00 0.00 0.00 4.51
3492 14359 5.944007 ACTAGTCCATTTGTTGTATTGGGTC 59.056 40.000 0.00 0.00 0.00 4.46
3496 14363 6.603201 AGTCCATTTGTTGTATTGGGTCATAG 59.397 38.462 0.00 0.00 0.00 2.23
3497 14364 5.359576 TCCATTTGTTGTATTGGGTCATAGC 59.640 40.000 0.00 0.00 0.00 2.97
3498 14365 5.360714 CCATTTGTTGTATTGGGTCATAGCT 59.639 40.000 0.00 0.00 0.00 3.32
3499 14366 6.127366 CCATTTGTTGTATTGGGTCATAGCTT 60.127 38.462 0.00 0.00 0.00 3.74
3500 14367 6.509418 TTTGTTGTATTGGGTCATAGCTTC 57.491 37.500 0.00 0.00 0.00 3.86
3502 14369 5.815581 TGTTGTATTGGGTCATAGCTTCTT 58.184 37.500 0.00 0.00 0.00 2.52
3504 14371 7.398829 TGTTGTATTGGGTCATAGCTTCTTAA 58.601 34.615 0.00 0.00 0.00 1.85
3570 14437 9.090103 ACTTTTTCCTATCATCGATGGTATAGA 57.910 33.333 25.02 19.09 0.00 1.98
3575 14442 9.562408 TTCCTATCATCGATGGTATAGAGATAC 57.438 37.037 25.02 0.00 37.75 2.24
3579 14446 8.815565 ATCATCGATGGTATAGAGATACAACT 57.184 34.615 24.61 0.00 39.91 3.16
3719 14616 1.359848 CAAGTCCACCATCAGTACGC 58.640 55.000 0.00 0.00 0.00 4.42
3721 14618 0.973632 AGTCCACCATCAGTACGCAA 59.026 50.000 0.00 0.00 0.00 4.85
3731 14628 2.746277 GTACGCAACTGGGCCTGG 60.746 66.667 15.36 5.47 0.00 4.45
3743 14640 3.970721 GCCTGGCCAATTTTGTGC 58.029 55.556 7.01 0.00 0.00 4.57
3760 14657 3.886044 GCCAGTTGCAACTTTACCC 57.114 52.632 29.23 11.83 40.77 3.69
3762 14659 1.269723 GCCAGTTGCAACTTTACCCTC 59.730 52.381 29.23 9.50 40.77 4.30
3809 14706 0.467290 TTGTCCCAGTTGCAAGTCCC 60.467 55.000 3.08 0.00 0.00 4.46
3836 14733 1.466856 TACGCAACTAGGTGGTCGAT 58.533 50.000 10.43 0.00 0.00 3.59
3854 14751 4.800471 GTCGATCATTTTTCCTCCAATTGC 59.200 41.667 0.00 0.00 0.00 3.56
3887 14784 0.544833 ACATGCATTTGGGGGCTTCA 60.545 50.000 0.00 0.00 0.00 3.02
4023 14920 2.517650 TTCCCGGTTTGCAAATCAAC 57.482 45.000 21.77 6.84 33.73 3.18
4044 14941 0.687354 ATTGACTCGCAACTGGGTCT 59.313 50.000 0.00 0.00 39.78 3.85
4045 14942 0.249868 TTGACTCGCAACTGGGTCTG 60.250 55.000 0.00 0.00 0.00 3.51
4046 14943 1.112916 TGACTCGCAACTGGGTCTGA 61.113 55.000 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.220602 AGAATGGTTGGTTGCATCCTTTAC 59.779 41.667 14.81 9.74 0.00 2.01
35 36 6.397272 TCATTTAATCAGAATGGTTGGTTGC 58.603 36.000 0.00 0.00 41.38 4.17
36 37 7.871973 TGTTCATTTAATCAGAATGGTTGGTTG 59.128 33.333 0.00 0.00 41.38 3.77
38 39 7.537596 TGTTCATTTAATCAGAATGGTTGGT 57.462 32.000 0.00 0.00 41.38 3.67
39 40 8.830201 TTTGTTCATTTAATCAGAATGGTTGG 57.170 30.769 0.00 0.00 41.38 3.77
52 56 9.364989 CACTTCAAACCTTCTTTGTTCATTTAA 57.635 29.630 0.00 0.00 0.00 1.52
93 97 7.406553 CACACATATATTCATCGTCGGTTTTT 58.593 34.615 0.00 0.00 0.00 1.94
277 1836 1.427819 CACGTTTAATCAGGCGGCC 59.572 57.895 12.11 12.11 0.00 6.13
280 1839 1.127951 GTGTCCACGTTTAATCAGGCG 59.872 52.381 0.00 0.00 0.00 5.52
281 1840 2.423577 AGTGTCCACGTTTAATCAGGC 58.576 47.619 0.00 0.00 36.20 4.85
282 1841 4.817517 AGTAGTGTCCACGTTTAATCAGG 58.182 43.478 0.00 0.00 36.20 3.86
283 1842 6.384224 TGTAGTAGTGTCCACGTTTAATCAG 58.616 40.000 0.00 0.00 36.20 2.90
284 1843 6.330004 TGTAGTAGTGTCCACGTTTAATCA 57.670 37.500 0.00 0.00 36.20 2.57
356 2090 1.080772 CAGCTTCGGTGAGCACGTA 60.081 57.895 8.62 0.00 45.12 3.57
358 2092 2.356313 ACAGCTTCGGTGAGCACG 60.356 61.111 8.62 0.00 45.12 5.34
387 2156 2.527671 CGTGGAATTCACTCACGCA 58.472 52.632 18.38 0.00 45.56 5.24
538 2335 7.100458 ACTAATATCTTTGGTGCAATGAACC 57.900 36.000 2.67 2.67 38.26 3.62
588 2389 9.537192 TTATTGACCAAAGTAATACATCCTACG 57.463 33.333 0.00 0.00 0.00 3.51
660 2814 6.106877 ACCACGTCTTGAATTCAATATTCG 57.893 37.500 20.76 21.04 35.02 3.34
688 2842 8.305317 GTGGGTGTAGAATAACCATACTCTATC 58.695 40.741 0.00 0.00 38.27 2.08
696 2850 3.109151 TCCGTGGGTGTAGAATAACCAT 58.891 45.455 0.00 0.00 38.27 3.55
702 2856 2.939640 GCAATGTCCGTGGGTGTAGAAT 60.940 50.000 0.00 0.00 0.00 2.40
726 2880 2.961526 ACGTTTGCTCATAGTCGGAT 57.038 45.000 0.00 0.00 0.00 4.18
727 2881 3.702330 CATACGTTTGCTCATAGTCGGA 58.298 45.455 0.00 0.00 0.00 4.55
728 2882 2.218759 GCATACGTTTGCTCATAGTCGG 59.781 50.000 21.65 0.00 39.57 4.79
758 2974 4.832266 AGATGGATGATCTCTAGCTTCGTT 59.168 41.667 0.00 0.00 36.63 3.85
771 2987 5.462240 TGTCTAGTCTTCCAGATGGATGAT 58.538 41.667 17.55 10.81 46.03 2.45
794 3010 0.607489 GACTGCTGTGCCCAAGTCAT 60.607 55.000 0.00 0.00 0.00 3.06
803 3019 1.580845 GGTGATGGTGACTGCTGTGC 61.581 60.000 0.00 0.00 0.00 4.57
863 3099 4.396166 GGACAAAAGCATGTGCAGTACTAT 59.604 41.667 7.83 0.00 45.16 2.12
864 3100 3.751175 GGACAAAAGCATGTGCAGTACTA 59.249 43.478 7.83 0.00 45.16 1.82
865 3101 2.554032 GGACAAAAGCATGTGCAGTACT 59.446 45.455 7.83 0.00 45.16 2.73
866 3102 2.554032 AGGACAAAAGCATGTGCAGTAC 59.446 45.455 7.83 1.49 43.32 2.73
867 3103 2.862541 AGGACAAAAGCATGTGCAGTA 58.137 42.857 7.83 0.00 43.32 2.74
868 3104 1.696063 AGGACAAAAGCATGTGCAGT 58.304 45.000 7.83 0.36 43.32 4.40
869 3105 2.806608 AAGGACAAAAGCATGTGCAG 57.193 45.000 7.83 0.00 43.32 4.41
918 3154 1.135257 CGGAGAAATGACGAGCTCAGT 60.135 52.381 15.40 12.55 30.20 3.41
985 3223 3.186047 CATGGCGAACCGACGTCC 61.186 66.667 10.58 0.00 37.93 4.79
1043 3281 1.200020 GGAAGAGAAACAACCATGCCG 59.800 52.381 0.00 0.00 0.00 5.69
1068 3306 1.276145 GCACAGACACGACGAGGAAC 61.276 60.000 0.00 0.00 0.00 3.62
1108 3349 2.870372 CCTCCTTTTTGCGCCGAG 59.130 61.111 4.18 0.00 0.00 4.63
1113 3354 2.126734 CGCTGCCTCCTTTTTGCG 60.127 61.111 0.00 0.00 37.57 4.85
1164 3405 1.997874 GATGAGGTGGAGGTGCCCT 60.998 63.158 0.00 0.00 36.03 5.19
1227 3468 4.552365 AGCATCATGTCGGGGCCG 62.552 66.667 0.00 0.00 41.35 6.13
1237 3479 1.406065 CCCAGTCGGAGGAGCATCAT 61.406 60.000 0.00 0.00 36.25 2.45
1268 3513 2.504244 GCGAAGACACGACGAGGG 60.504 66.667 0.00 0.00 35.09 4.30
1481 3730 0.965866 CAGTACCTCCTCCACAGCGA 60.966 60.000 0.00 0.00 0.00 4.93
1524 3773 4.844349 AAAGAAAGGCTATCAGCACCTA 57.156 40.909 0.00 0.00 44.75 3.08
1528 3777 7.341805 AGATCTTAAAAGAAAGGCTATCAGCA 58.658 34.615 0.00 0.00 39.95 4.41
1529 3778 7.800155 AGATCTTAAAAGAAAGGCTATCAGC 57.200 36.000 0.00 0.00 38.45 4.26
1530 3779 8.127954 GCAAGATCTTAAAAGAAAGGCTATCAG 58.872 37.037 7.86 0.00 38.77 2.90
1533 3782 8.052141 AGAGCAAGATCTTAAAAGAAAGGCTAT 58.948 33.333 7.86 3.91 38.77 2.97
1534 3783 7.398024 AGAGCAAGATCTTAAAAGAAAGGCTA 58.602 34.615 7.86 0.00 38.77 3.93
1535 3784 6.244654 AGAGCAAGATCTTAAAAGAAAGGCT 58.755 36.000 7.86 9.15 38.77 4.58
1536 3785 6.150140 TGAGAGCAAGATCTTAAAAGAAAGGC 59.850 38.462 7.86 4.11 38.77 4.35
1537 3786 7.678947 TGAGAGCAAGATCTTAAAAGAAAGG 57.321 36.000 7.86 0.00 38.77 3.11
1544 3793 8.446273 CGAGAAAAATGAGAGCAAGATCTTAAA 58.554 33.333 7.86 0.00 0.00 1.52
1545 3794 7.604164 ACGAGAAAAATGAGAGCAAGATCTTAA 59.396 33.333 7.86 0.00 0.00 1.85
1546 3795 7.099764 ACGAGAAAAATGAGAGCAAGATCTTA 58.900 34.615 7.86 0.00 0.00 2.10
1547 3796 5.936956 ACGAGAAAAATGAGAGCAAGATCTT 59.063 36.000 0.88 0.88 0.00 2.40
1548 3797 5.486526 ACGAGAAAAATGAGAGCAAGATCT 58.513 37.500 0.00 0.00 0.00 2.75
1549 3798 5.793026 ACGAGAAAAATGAGAGCAAGATC 57.207 39.130 0.00 0.00 0.00 2.75
1550 3799 6.312426 CAGTACGAGAAAAATGAGAGCAAGAT 59.688 38.462 0.00 0.00 0.00 2.40
1551 3800 5.635280 CAGTACGAGAAAAATGAGAGCAAGA 59.365 40.000 0.00 0.00 0.00 3.02
1552 3801 5.635280 TCAGTACGAGAAAAATGAGAGCAAG 59.365 40.000 0.00 0.00 0.00 4.01
1553 3802 5.538118 TCAGTACGAGAAAAATGAGAGCAA 58.462 37.500 0.00 0.00 0.00 3.91
1554 3803 5.134202 TCAGTACGAGAAAAATGAGAGCA 57.866 39.130 0.00 0.00 0.00 4.26
1555 3804 6.654793 ATTCAGTACGAGAAAAATGAGAGC 57.345 37.500 7.68 0.00 0.00 4.09
1556 3805 7.331934 TCCAATTCAGTACGAGAAAAATGAGAG 59.668 37.037 7.68 0.00 0.00 3.20
1559 3808 6.934645 AGTCCAATTCAGTACGAGAAAAATGA 59.065 34.615 7.68 1.77 0.00 2.57
1561 3810 7.162082 AGAGTCCAATTCAGTACGAGAAAAAT 58.838 34.615 7.68 0.00 0.00 1.82
1562 3811 6.522054 AGAGTCCAATTCAGTACGAGAAAAA 58.478 36.000 7.68 0.00 0.00 1.94
1563 3812 6.097915 AGAGTCCAATTCAGTACGAGAAAA 57.902 37.500 7.68 0.00 0.00 2.29
1566 3815 4.156190 GTGAGAGTCCAATTCAGTACGAGA 59.844 45.833 0.00 0.00 0.00 4.04
1567 3816 4.156922 AGTGAGAGTCCAATTCAGTACGAG 59.843 45.833 0.00 0.00 0.00 4.18
1569 3818 4.442375 AGTGAGAGTCCAATTCAGTACG 57.558 45.455 0.00 0.00 0.00 3.67
1570 3819 5.172205 GGAAGTGAGAGTCCAATTCAGTAC 58.828 45.833 17.56 0.00 41.35 2.73
1572 3821 3.306364 CGGAAGTGAGAGTCCAATTCAGT 60.306 47.826 17.56 3.73 41.35 3.41
1574 3823 2.632996 ACGGAAGTGAGAGTCCAATTCA 59.367 45.455 17.56 1.09 46.97 2.57
1593 3842 5.623673 CCTTTCCGTTATTTTGTTTCTGACG 59.376 40.000 0.00 0.00 0.00 4.35
1594 3843 6.635641 GTCCTTTCCGTTATTTTGTTTCTGAC 59.364 38.462 0.00 0.00 0.00 3.51
1595 3844 6.544564 AGTCCTTTCCGTTATTTTGTTTCTGA 59.455 34.615 0.00 0.00 0.00 3.27
1596 3845 6.735130 AGTCCTTTCCGTTATTTTGTTTCTG 58.265 36.000 0.00 0.00 0.00 3.02
1598 3847 7.703197 TGAAAGTCCTTTCCGTTATTTTGTTTC 59.297 33.333 15.25 0.00 46.15 2.78
1599 3848 7.548967 TGAAAGTCCTTTCCGTTATTTTGTTT 58.451 30.769 15.25 0.00 46.15 2.83
1601 3850 6.702716 TGAAAGTCCTTTCCGTTATTTTGT 57.297 33.333 15.25 0.00 46.15 2.83
1602 3851 7.114811 CACATGAAAGTCCTTTCCGTTATTTTG 59.885 37.037 15.25 5.13 46.15 2.44
1603 3852 7.145323 CACATGAAAGTCCTTTCCGTTATTTT 58.855 34.615 15.25 0.00 46.15 1.82
1604 3853 6.294508 CCACATGAAAGTCCTTTCCGTTATTT 60.295 38.462 15.25 0.00 46.15 1.40
1605 3854 5.183140 CCACATGAAAGTCCTTTCCGTTATT 59.817 40.000 15.25 0.00 46.15 1.40
1606 3855 4.700213 CCACATGAAAGTCCTTTCCGTTAT 59.300 41.667 15.25 1.97 46.15 1.89
1607 3856 4.069304 CCACATGAAAGTCCTTTCCGTTA 58.931 43.478 15.25 0.00 46.15 3.18
1608 3857 2.884639 CCACATGAAAGTCCTTTCCGTT 59.115 45.455 15.25 0.67 46.15 4.44
1609 3858 2.158667 ACCACATGAAAGTCCTTTCCGT 60.159 45.455 15.25 10.46 46.15 4.69
1610 3859 2.484264 GACCACATGAAAGTCCTTTCCG 59.516 50.000 15.25 9.93 46.15 4.30
1611 3860 2.820197 GGACCACATGAAAGTCCTTTCC 59.180 50.000 19.57 0.81 46.15 3.13
1617 3866 2.079925 GCAGAGGACCACATGAAAGTC 58.920 52.381 0.00 2.76 0.00 3.01
1619 3868 2.486472 AGCAGAGGACCACATGAAAG 57.514 50.000 0.00 0.00 0.00 2.62
1621 3870 2.906389 AGTTAGCAGAGGACCACATGAA 59.094 45.455 0.00 0.00 0.00 2.57
1623 3872 4.679373 ATAGTTAGCAGAGGACCACATG 57.321 45.455 0.00 0.00 0.00 3.21
1625 3874 4.777896 AGAAATAGTTAGCAGAGGACCACA 59.222 41.667 0.00 0.00 0.00 4.17
1626 3875 5.346181 AGAAATAGTTAGCAGAGGACCAC 57.654 43.478 0.00 0.00 0.00 4.16
1627 3876 4.406003 GGAGAAATAGTTAGCAGAGGACCA 59.594 45.833 0.00 0.00 0.00 4.02
1628 3877 4.202274 GGGAGAAATAGTTAGCAGAGGACC 60.202 50.000 0.00 0.00 0.00 4.46
1629 3878 4.651962 AGGGAGAAATAGTTAGCAGAGGAC 59.348 45.833 0.00 0.00 0.00 3.85
1630 3879 4.884961 AGGGAGAAATAGTTAGCAGAGGA 58.115 43.478 0.00 0.00 0.00 3.71
1632 3881 4.261825 CGGAGGGAGAAATAGTTAGCAGAG 60.262 50.000 0.00 0.00 0.00 3.35
1633 3882 3.637229 CGGAGGGAGAAATAGTTAGCAGA 59.363 47.826 0.00 0.00 0.00 4.26
1634 3883 3.385111 ACGGAGGGAGAAATAGTTAGCAG 59.615 47.826 0.00 0.00 0.00 4.24
1635 3884 3.371965 ACGGAGGGAGAAATAGTTAGCA 58.628 45.455 0.00 0.00 0.00 3.49
1636 3885 3.637694 AGACGGAGGGAGAAATAGTTAGC 59.362 47.826 0.00 0.00 0.00 3.09
1637 3886 4.038162 CCAGACGGAGGGAGAAATAGTTAG 59.962 50.000 0.00 0.00 0.00 2.34
1638 3887 3.958798 CCAGACGGAGGGAGAAATAGTTA 59.041 47.826 0.00 0.00 0.00 2.24
1650 3899 4.482952 AACTAATAAACCCAGACGGAGG 57.517 45.455 0.00 0.00 34.64 4.30
1651 3900 5.350640 GTGAAACTAATAAACCCAGACGGAG 59.649 44.000 0.00 0.00 34.64 4.63
1652 3901 5.240121 GTGAAACTAATAAACCCAGACGGA 58.760 41.667 0.00 0.00 34.64 4.69
1669 3918 9.783256 AAGTTAAACACAAACTATGAGTGAAAC 57.217 29.630 0.00 0.00 36.17 2.78
1670 3919 9.997482 GAAGTTAAACACAAACTATGAGTGAAA 57.003 29.630 0.00 0.00 36.17 2.69
1671 3920 9.391006 AGAAGTTAAACACAAACTATGAGTGAA 57.609 29.630 0.00 0.00 36.17 3.18
1672 3921 8.958119 AGAAGTTAAACACAAACTATGAGTGA 57.042 30.769 0.00 0.00 36.17 3.41
1740 3989 8.706322 AAGTAGTTTCAGGTGGTATCATTTTT 57.294 30.769 0.00 0.00 0.00 1.94
1741 3990 8.706322 AAAGTAGTTTCAGGTGGTATCATTTT 57.294 30.769 0.00 0.00 0.00 1.82
1743 3992 7.942341 TCAAAAGTAGTTTCAGGTGGTATCATT 59.058 33.333 0.00 0.00 0.00 2.57
1744 3993 7.458397 TCAAAAGTAGTTTCAGGTGGTATCAT 58.542 34.615 0.00 0.00 0.00 2.45
1745 3994 6.833041 TCAAAAGTAGTTTCAGGTGGTATCA 58.167 36.000 0.00 0.00 0.00 2.15
1746 3995 7.739498 TTCAAAAGTAGTTTCAGGTGGTATC 57.261 36.000 0.00 0.00 0.00 2.24
1747 3996 9.227777 GTATTCAAAAGTAGTTTCAGGTGGTAT 57.772 33.333 0.00 0.00 0.00 2.73
1748 3997 7.385752 CGTATTCAAAAGTAGTTTCAGGTGGTA 59.614 37.037 0.00 0.00 0.00 3.25
1749 3998 6.204108 CGTATTCAAAAGTAGTTTCAGGTGGT 59.796 38.462 0.00 0.00 0.00 4.16
1750 3999 6.348213 CCGTATTCAAAAGTAGTTTCAGGTGG 60.348 42.308 0.00 0.00 0.00 4.61
1751 4000 6.425721 TCCGTATTCAAAAGTAGTTTCAGGTG 59.574 38.462 0.00 0.00 0.00 4.00
1752 4001 6.527423 TCCGTATTCAAAAGTAGTTTCAGGT 58.473 36.000 0.00 0.00 0.00 4.00
1753 4002 7.201617 GGATCCGTATTCAAAAGTAGTTTCAGG 60.202 40.741 0.00 0.00 0.00 3.86
1754 4003 7.333423 TGGATCCGTATTCAAAAGTAGTTTCAG 59.667 37.037 7.39 0.00 0.00 3.02
1756 4005 7.605410 TGGATCCGTATTCAAAAGTAGTTTC 57.395 36.000 7.39 0.00 0.00 2.78
1757 4006 6.093633 GCTGGATCCGTATTCAAAAGTAGTTT 59.906 38.462 7.39 0.00 0.00 2.66
1758 4007 5.585047 GCTGGATCCGTATTCAAAAGTAGTT 59.415 40.000 7.39 0.00 0.00 2.24
1759 4008 5.116882 GCTGGATCCGTATTCAAAAGTAGT 58.883 41.667 7.39 0.00 0.00 2.73
1762 4011 2.936498 CGCTGGATCCGTATTCAAAAGT 59.064 45.455 7.39 0.00 0.00 2.66
1764 4013 2.285083 CCGCTGGATCCGTATTCAAAA 58.715 47.619 7.39 0.00 0.00 2.44
1765 4014 1.208535 ACCGCTGGATCCGTATTCAAA 59.791 47.619 7.39 0.00 0.00 2.69
1766 4015 0.828022 ACCGCTGGATCCGTATTCAA 59.172 50.000 7.39 0.00 0.00 2.69
1767 4016 1.611977 CTACCGCTGGATCCGTATTCA 59.388 52.381 7.39 0.00 0.00 2.57
1768 4017 1.612463 ACTACCGCTGGATCCGTATTC 59.388 52.381 7.39 0.00 0.00 1.75
1769 4018 1.700955 ACTACCGCTGGATCCGTATT 58.299 50.000 7.39 0.00 0.00 1.89
1770 4019 1.340248 CAACTACCGCTGGATCCGTAT 59.660 52.381 7.39 0.00 0.00 3.06
1772 4021 0.968901 TCAACTACCGCTGGATCCGT 60.969 55.000 7.39 0.89 0.00 4.69
1775 4024 3.460857 AGATTCAACTACCGCTGGATC 57.539 47.619 1.50 0.00 0.00 3.36
1776 4025 6.859112 ATATAGATTCAACTACCGCTGGAT 57.141 37.500 1.50 0.00 0.00 3.41
1777 4026 6.377429 CCTATATAGATTCAACTACCGCTGGA 59.623 42.308 11.53 0.00 0.00 3.86
1781 4030 6.405619 GGACCCTATATAGATTCAACTACCGC 60.406 46.154 11.53 0.00 0.00 5.68
1782 4031 6.662234 TGGACCCTATATAGATTCAACTACCG 59.338 42.308 11.53 0.00 0.00 4.02
1784 4033 7.674772 AGGTGGACCCTATATAGATTCAACTAC 59.325 40.741 11.53 4.85 43.87 2.73
1785 4034 7.776745 AGGTGGACCCTATATAGATTCAACTA 58.223 38.462 11.53 0.00 43.87 2.24
1786 4035 6.635021 AGGTGGACCCTATATAGATTCAACT 58.365 40.000 11.53 8.82 43.87 3.16
1788 4037 7.570982 TCAAAGGTGGACCCTATATAGATTCAA 59.429 37.037 11.53 0.00 45.47 2.69
1789 4038 7.016268 GTCAAAGGTGGACCCTATATAGATTCA 59.984 40.741 11.53 1.43 45.47 2.57
1790 4039 7.387643 GTCAAAGGTGGACCCTATATAGATTC 58.612 42.308 11.53 6.66 45.47 2.52
1791 4040 7.317722 GTCAAAGGTGGACCCTATATAGATT 57.682 40.000 11.53 0.00 45.47 2.40
1792 4041 6.936968 GTCAAAGGTGGACCCTATATAGAT 57.063 41.667 11.53 0.00 45.47 1.98
2438 8157 5.419542 GGTGTTAGCTGATGTGTCTATTGA 58.580 41.667 0.00 0.00 0.00 2.57
2459 8178 1.064825 ACCAAGGTGAATTCGAGGGT 58.935 50.000 0.04 1.46 0.00 4.34
2478 8197 0.986527 TGGCTTCCTCATGAGCTCAA 59.013 50.000 22.50 3.88 0.00 3.02
2521 8240 1.411612 GGTACAATACCCCTCACCTCG 59.588 57.143 0.00 0.00 43.18 4.63
2704 8426 2.183478 AAGCATTGATGACCACACGA 57.817 45.000 0.00 0.00 0.00 4.35
2965 8687 5.028549 ACACCTCTGTCATATCAATGTCC 57.971 43.478 0.00 0.00 34.50 4.02
3003 8725 6.049955 TCAACAATAGTTTCTCCTTCCGAT 57.950 37.500 0.00 0.00 35.28 4.18
3088 8816 6.860023 CACCTTCTCTACAAAGAAAAGCATTG 59.140 38.462 0.00 0.00 34.95 2.82
3290 12468 6.586463 TCATCTCGATGCGATTTAGTAAATCC 59.414 38.462 23.71 18.02 39.53 3.01
3308 12486 9.855361 GATGTGACATAGTTAAAAATCATCTCG 57.145 33.333 0.00 0.00 0.00 4.04
3448 12627 2.961768 CCACGCATTGAACACCCC 59.038 61.111 0.00 0.00 0.00 4.95
3555 14422 9.734984 TTAGTTGTATCTCTATACCATCGATGA 57.265 33.333 26.86 8.19 37.72 2.92
3693 14590 2.361757 CTGATGGTGGACTTGCAACAAA 59.638 45.455 0.00 0.00 0.00 2.83
3731 14628 0.587768 GCAACTGGCACAAAATTGGC 59.412 50.000 0.00 0.00 43.97 4.52
3743 14640 1.535462 CGAGGGTAAAGTTGCAACTGG 59.465 52.381 31.73 6.61 39.66 4.00
3760 14657 0.883833 GGGCCCAATTGCATATCGAG 59.116 55.000 19.95 0.00 0.00 4.04
3762 14659 1.580942 CGGGCCCAATTGCATATCG 59.419 57.895 24.92 0.00 0.00 2.92
3794 14691 2.283173 GGGGGACTTGCAACTGGG 60.283 66.667 0.00 0.00 0.00 4.45
3809 14706 1.485066 ACCTAGTTGCGTATTGAGGGG 59.515 52.381 0.00 0.00 0.00 4.79
3836 14733 5.511202 GGAGTTGCAATTGGAGGAAAAATGA 60.511 40.000 0.59 0.00 0.00 2.57
3854 14751 1.278985 TGCATGTCTAGGGTGGAGTTG 59.721 52.381 0.00 0.00 0.00 3.16
3927 14824 0.114954 ATGGATTGGGCCACAGTTGT 59.885 50.000 5.23 0.00 41.56 3.32
3931 14828 1.856629 AAGAATGGATTGGGCCACAG 58.143 50.000 5.23 0.00 41.56 3.66
3943 14840 5.335976 GGACTTGCAACTAGGAAAAGAATGG 60.336 44.000 0.00 0.00 0.00 3.16
4007 14904 2.453983 ATGGTTGATTTGCAAACCGG 57.546 45.000 15.41 0.00 43.74 5.28
4008 14905 3.184178 GTCAATGGTTGATTTGCAAACCG 59.816 43.478 15.41 0.00 43.74 4.44
4011 14908 4.297510 CGAGTCAATGGTTGATTTGCAAA 58.702 39.130 15.44 15.44 42.47 3.68
4023 14920 0.606401 ACCCAGTTGCGAGTCAATGG 60.606 55.000 0.00 0.00 36.99 3.16


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

AutoCloner maintained by Alex Coulton.