Multiple sequence alignment - TraesCS3A01G482800

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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 TraesCS3A01G482800 chr3A 100.000 1786 0 0 662 2447 713343021 713341236 0.000000e+00 3299.0
1 TraesCS3A01G482800 chr3A 87.744 1534 159 20 904 2427 713308305 713306791 0.000000e+00 1764.0
2 TraesCS3A01G482800 chr3A 82.536 836 121 20 1341 2170 713417774 713416958 0.000000e+00 712.0
3 TraesCS3A01G482800 chr3A 100.000 317 0 0 1 317 713343682 713343366 9.750000e-164 586.0
4 TraesCS3A01G482800 chr3A 88.725 408 46 0 904 1311 713418178 713417771 1.310000e-137 499.0
5 TraesCS3A01G482800 chr3A 84.783 230 28 3 84 307 713308632 713308404 8.810000e-55 224.0
6 TraesCS3A01G482800 chr3A 89.922 129 12 1 80 208 713419085 713418958 5.410000e-37 165.0
7 TraesCS3A01G482800 chr3A 87.402 127 14 2 757 882 334690550 334690425 7.050000e-31 145.0
8 TraesCS3A01G482800 chr3A 88.571 105 9 1 206 307 713418381 713418277 9.190000e-25 124.0
9 TraesCS3A01G482800 chr3D 86.931 1561 171 25 904 2447 577668783 577667239 0.000000e+00 1722.0
10 TraesCS3A01G482800 chr3D 88.791 910 85 10 904 1811 578040999 578041893 0.000000e+00 1099.0
11 TraesCS3A01G482800 chr3D 86.616 919 89 12 904 1818 577752813 577751925 0.000000e+00 985.0
12 TraesCS3A01G482800 chr3D 86.196 920 92 14 904 1818 577779686 577778797 0.000000e+00 963.0
13 TraesCS3A01G482800 chr3D 83.025 595 83 13 1845 2435 578041894 578042474 7.750000e-145 523.0
14 TraesCS3A01G482800 chr3D 89.205 176 16 3 732 905 188626241 188626067 1.470000e-52 217.0
15 TraesCS3A01G482800 chr3D 91.589 107 9 0 206 312 577779880 577779774 5.450000e-32 148.0
16 TraesCS3A01G482800 chr3D 87.619 105 9 2 206 307 578040809 578040912 4.270000e-23 119.0
17 TraesCS3A01G482800 chr3B 85.973 1547 170 22 904 2435 771241944 771243458 0.000000e+00 1611.0
18 TraesCS3A01G482800 chr3B 89.157 913 85 12 904 1811 770964774 770963871 0.000000e+00 1125.0
19 TraesCS3A01G482800 chr3B 85.379 725 55 28 904 1622 771178410 771179089 0.000000e+00 704.0
20 TraesCS3A01G482800 chr3B 95.098 102 5 0 206 307 770964977 770964876 7.000000e-36 161.0
21 TraesCS3A01G482800 chr3B 95.098 102 5 0 206 307 771178207 771178308 7.000000e-36 161.0
22 TraesCS3A01G482800 chr3B 93.137 102 7 0 206 307 771241741 771241842 1.520000e-32 150.0
23 TraesCS3A01G482800 chr5A 92.025 163 11 2 750 912 706935246 706935086 6.810000e-56 228.0
24 TraesCS3A01G482800 chr4A 87.640 178 19 3 730 905 335689491 335689667 1.150000e-48 204.0
25 TraesCS3A01G482800 chr2A 90.260 154 13 2 732 884 239911655 239911503 1.480000e-47 200.0
26 TraesCS3A01G482800 chr7A 89.103 156 15 2 750 905 645406315 645406162 2.480000e-45 193.0
27 TraesCS3A01G482800 chr7D 83.146 178 28 2 730 907 379740494 379740669 7.000000e-36 161.0
28 TraesCS3A01G482800 chr6A 84.663 163 23 1 743 905 415388048 415388208 7.000000e-36 161.0
29 TraesCS3A01G482800 chr6D 90.909 110 9 1 796 905 173359074 173358966 1.960000e-31 147.0
30 TraesCS3A01G482800 chr4D 71.002 469 105 24 1897 2356 497237400 497236954 1.560000e-12 84.2


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 TraesCS3A01G482800 chr3A 713341236 713343682 2446 True 1942.500000 3299 100.000000 1 2447 2 chr3A.!!$R3 2446
1 TraesCS3A01G482800 chr3A 713306791 713308632 1841 True 994.000000 1764 86.263500 84 2427 2 chr3A.!!$R2 2343
2 TraesCS3A01G482800 chr3A 713416958 713419085 2127 True 375.000000 712 87.438500 80 2170 4 chr3A.!!$R4 2090
3 TraesCS3A01G482800 chr3D 577667239 577668783 1544 True 1722.000000 1722 86.931000 904 2447 1 chr3D.!!$R2 1543
4 TraesCS3A01G482800 chr3D 577751925 577752813 888 True 985.000000 985 86.616000 904 1818 1 chr3D.!!$R3 914
5 TraesCS3A01G482800 chr3D 578040809 578042474 1665 False 580.333333 1099 86.478333 206 2435 3 chr3D.!!$F1 2229
6 TraesCS3A01G482800 chr3D 577778797 577779880 1083 True 555.500000 963 88.892500 206 1818 2 chr3D.!!$R4 1612
7 TraesCS3A01G482800 chr3B 771241741 771243458 1717 False 880.500000 1611 89.555000 206 2435 2 chr3B.!!$F2 2229
8 TraesCS3A01G482800 chr3B 770963871 770964977 1106 True 643.000000 1125 92.127500 206 1811 2 chr3B.!!$R1 1605
9 TraesCS3A01G482800 chr3B 771178207 771179089 882 False 432.500000 704 90.238500 206 1622 2 chr3B.!!$F1 1416

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
698 1293 0.096976 GTGTGTGTGTCTGTGTGTGC 59.903 55.0 0.0 0.0 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1551 2217 0.172127 TTGCAAAACAAGCAGCGACA 59.828 45.0 0.0 0.0 43.75 4.35 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
18 19 2.612200 CACCAGTGTACACGTTGGG 58.388 57.895 28.39 24.28 32.66 4.12
19 20 0.179067 CACCAGTGTACACGTTGGGT 60.179 55.000 28.39 24.78 32.66 4.51
27 28 2.555782 CACGTTGGGTGTCATGCG 59.444 61.111 0.00 0.00 41.89 4.73
28 29 3.353836 ACGTTGGGTGTCATGCGC 61.354 61.111 0.00 0.00 0.00 6.09
29 30 3.049674 CGTTGGGTGTCATGCGCT 61.050 61.111 9.73 0.00 0.00 5.92
30 31 1.739929 CGTTGGGTGTCATGCGCTA 60.740 57.895 9.73 0.00 0.00 4.26
31 32 1.089481 CGTTGGGTGTCATGCGCTAT 61.089 55.000 9.73 0.00 0.00 2.97
32 33 1.804746 CGTTGGGTGTCATGCGCTATA 60.805 52.381 9.73 0.00 0.00 1.31
33 34 1.597663 GTTGGGTGTCATGCGCTATAC 59.402 52.381 9.73 4.17 0.00 1.47
34 35 0.827368 TGGGTGTCATGCGCTATACA 59.173 50.000 9.73 7.09 0.00 2.29
35 36 1.416030 TGGGTGTCATGCGCTATACAT 59.584 47.619 9.73 0.00 0.00 2.29
36 37 2.158827 TGGGTGTCATGCGCTATACATT 60.159 45.455 9.73 0.00 0.00 2.71
37 38 2.224079 GGGTGTCATGCGCTATACATTG 59.776 50.000 9.73 0.00 0.00 2.82
38 39 2.349817 GGTGTCATGCGCTATACATTGC 60.350 50.000 9.73 0.00 0.00 3.56
39 40 1.872952 TGTCATGCGCTATACATTGCC 59.127 47.619 9.73 0.00 0.00 4.52
40 41 1.136252 GTCATGCGCTATACATTGCCG 60.136 52.381 9.73 0.00 0.00 5.69
41 42 0.166597 CATGCGCTATACATTGCCGG 59.833 55.000 9.73 0.00 0.00 6.13
42 43 0.250295 ATGCGCTATACATTGCCGGT 60.250 50.000 9.73 0.00 0.00 5.28
43 44 0.389757 TGCGCTATACATTGCCGGTA 59.610 50.000 9.73 0.00 0.00 4.02
44 45 1.068474 GCGCTATACATTGCCGGTAG 58.932 55.000 1.90 0.00 0.00 3.18
45 46 1.604693 GCGCTATACATTGCCGGTAGT 60.605 52.381 1.90 0.00 0.00 2.73
46 47 2.325761 CGCTATACATTGCCGGTAGTC 58.674 52.381 1.90 0.00 0.00 2.59
47 48 2.325761 GCTATACATTGCCGGTAGTCG 58.674 52.381 1.90 0.00 38.88 4.18
56 57 3.429925 CGGTAGTCGGTAGAGGCC 58.570 66.667 0.00 0.00 34.75 5.19
57 58 1.452651 CGGTAGTCGGTAGAGGCCA 60.453 63.158 5.01 0.00 34.75 5.36
58 59 0.822532 CGGTAGTCGGTAGAGGCCAT 60.823 60.000 5.01 0.00 34.75 4.40
59 60 1.544093 CGGTAGTCGGTAGAGGCCATA 60.544 57.143 5.01 0.00 34.75 2.74
60 61 2.805194 GGTAGTCGGTAGAGGCCATAT 58.195 52.381 5.01 0.00 0.00 1.78
61 62 2.492484 GGTAGTCGGTAGAGGCCATATG 59.508 54.545 5.01 0.00 0.00 1.78
62 63 0.969894 AGTCGGTAGAGGCCATATGC 59.030 55.000 5.01 0.00 40.16 3.14
75 76 4.574599 GCCATATGCCAAGTTTTCCTAG 57.425 45.455 0.00 0.00 0.00 3.02
76 77 3.319122 GCCATATGCCAAGTTTTCCTAGG 59.681 47.826 0.82 0.82 0.00 3.02
77 78 3.891366 CCATATGCCAAGTTTTCCTAGGG 59.109 47.826 9.46 0.00 0.00 3.53
78 79 4.386312 CCATATGCCAAGTTTTCCTAGGGA 60.386 45.833 9.46 0.00 0.00 4.20
94 95 0.393808 GGGAATAGGTCGCCTTGCAA 60.394 55.000 0.00 0.00 34.61 4.08
110 111 5.934043 GCCTTGCAAGATTCAAAAGGTATTT 59.066 36.000 28.05 0.00 39.70 1.40
114 115 4.201618 GCAAGATTCAAAAGGTATTTGCGC 60.202 41.667 0.00 0.00 31.71 6.09
133 134 6.007936 TGCGCGCCAAGATAAATAATAATT 57.992 33.333 30.77 0.00 0.00 1.40
137 138 6.155827 GCGCCAAGATAAATAATAATTGCCA 58.844 36.000 0.00 0.00 0.00 4.92
139 140 7.331687 GCGCCAAGATAAATAATAATTGCCATT 59.668 33.333 0.00 0.00 0.00 3.16
186 187 9.968743 GGTGAATGTTATTAAAGTAGAAACTCG 57.031 33.333 0.00 0.00 33.75 4.18
202 203 6.546056 GAAACTCGATTTCTGCTAAAATGC 57.454 37.500 10.96 0.00 43.06 3.56
213 793 9.831737 ATTTCTGCTAAAATGCGATACATATTC 57.168 29.630 0.00 0.00 38.34 1.75
240 820 7.630242 TTCCACCTCAATGAATGTAAAGATC 57.370 36.000 0.00 0.00 0.00 2.75
243 832 7.554118 TCCACCTCAATGAATGTAAAGATCTTC 59.446 37.037 8.78 0.00 0.00 2.87
266 858 9.807649 CTTCTTGGAGGGAATTAAATGTTTATG 57.192 33.333 0.00 0.00 0.00 1.90
683 1278 2.695613 TTTGTGTGTGTGTGTGTGTG 57.304 45.000 0.00 0.00 0.00 3.82
684 1279 1.598882 TTGTGTGTGTGTGTGTGTGT 58.401 45.000 0.00 0.00 0.00 3.72
685 1280 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
686 1281 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
687 1282 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
688 1283 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
689 1284 1.136085 GTGTGTGTGTGTGTGTGTGTC 60.136 52.381 0.00 0.00 0.00 3.67
690 1285 1.270571 TGTGTGTGTGTGTGTGTGTCT 60.271 47.619 0.00 0.00 0.00 3.41
691 1286 1.128507 GTGTGTGTGTGTGTGTGTCTG 59.871 52.381 0.00 0.00 0.00 3.51
692 1287 1.270571 TGTGTGTGTGTGTGTGTCTGT 60.271 47.619 0.00 0.00 0.00 3.41
693 1288 1.128507 GTGTGTGTGTGTGTGTCTGTG 59.871 52.381 0.00 0.00 0.00 3.66
694 1289 1.270571 TGTGTGTGTGTGTGTCTGTGT 60.271 47.619 0.00 0.00 0.00 3.72
695 1290 1.128507 GTGTGTGTGTGTGTCTGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
696 1291 1.270571 TGTGTGTGTGTGTCTGTGTGT 60.271 47.619 0.00 0.00 0.00 3.72
697 1292 1.128507 GTGTGTGTGTGTCTGTGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
698 1293 0.096976 GTGTGTGTGTCTGTGTGTGC 59.903 55.000 0.00 0.00 0.00 4.57
699 1294 1.348250 GTGTGTGTCTGTGTGTGCG 59.652 57.895 0.00 0.00 0.00 5.34
700 1295 2.324477 GTGTGTCTGTGTGTGCGC 59.676 61.111 0.00 0.00 0.00 6.09
701 1296 2.125350 TGTGTCTGTGTGTGCGCA 60.125 55.556 5.66 5.66 0.00 6.09
702 1297 1.523484 TGTGTCTGTGTGTGCGCAT 60.523 52.632 15.91 0.00 34.29 4.73
703 1298 1.082561 GTGTCTGTGTGTGCGCATG 60.083 57.895 15.91 0.00 34.29 4.06
704 1299 1.523484 TGTCTGTGTGTGCGCATGT 60.523 52.632 15.91 0.00 34.29 3.21
705 1300 1.082561 GTCTGTGTGTGCGCATGTG 60.083 57.895 15.91 0.66 34.29 3.21
706 1301 1.523484 TCTGTGTGTGCGCATGTGT 60.523 52.632 15.91 0.00 34.29 3.72
707 1302 1.369568 CTGTGTGTGCGCATGTGTG 60.370 57.895 15.91 0.00 34.29 3.82
708 1303 2.050639 CTGTGTGTGCGCATGTGTGT 62.051 55.000 15.91 0.00 34.29 3.72
709 1304 0.811616 TGTGTGTGCGCATGTGTGTA 60.812 50.000 15.91 0.00 0.00 2.90
710 1305 0.516877 GTGTGTGCGCATGTGTGTAT 59.483 50.000 15.91 0.00 0.00 2.29
711 1306 1.729517 GTGTGTGCGCATGTGTGTATA 59.270 47.619 15.91 0.00 0.00 1.47
712 1307 1.999024 TGTGTGCGCATGTGTGTATAG 59.001 47.619 15.91 0.00 0.00 1.31
713 1308 1.999735 GTGTGCGCATGTGTGTATAGT 59.000 47.619 15.91 0.00 0.00 2.12
714 1309 2.415168 GTGTGCGCATGTGTGTATAGTT 59.585 45.455 15.91 0.00 0.00 2.24
715 1310 3.615056 GTGTGCGCATGTGTGTATAGTTA 59.385 43.478 15.91 0.00 0.00 2.24
716 1311 3.615056 TGTGCGCATGTGTGTATAGTTAC 59.385 43.478 15.91 0.00 0.00 2.50
717 1312 3.863424 GTGCGCATGTGTGTATAGTTACT 59.137 43.478 15.91 0.00 0.00 2.24
718 1313 3.862845 TGCGCATGTGTGTATAGTTACTG 59.137 43.478 5.66 0.00 0.00 2.74
719 1314 3.245284 GCGCATGTGTGTATAGTTACTGG 59.755 47.826 0.30 0.00 0.00 4.00
720 1315 3.802139 CGCATGTGTGTATAGTTACTGGG 59.198 47.826 0.00 0.00 0.00 4.45
721 1316 4.127171 GCATGTGTGTATAGTTACTGGGG 58.873 47.826 0.00 0.00 0.00 4.96
722 1317 4.383770 GCATGTGTGTATAGTTACTGGGGT 60.384 45.833 0.00 0.00 0.00 4.95
723 1318 4.811969 TGTGTGTATAGTTACTGGGGTG 57.188 45.455 0.00 0.00 0.00 4.61
724 1319 4.161876 TGTGTGTATAGTTACTGGGGTGT 58.838 43.478 0.00 0.00 0.00 4.16
725 1320 4.020928 TGTGTGTATAGTTACTGGGGTGTG 60.021 45.833 0.00 0.00 0.00 3.82
726 1321 4.020839 GTGTGTATAGTTACTGGGGTGTGT 60.021 45.833 0.00 0.00 0.00 3.72
727 1322 4.020928 TGTGTATAGTTACTGGGGTGTGTG 60.021 45.833 0.00 0.00 0.00 3.82
728 1323 4.020839 GTGTATAGTTACTGGGGTGTGTGT 60.021 45.833 0.00 0.00 0.00 3.72
729 1324 5.185635 GTGTATAGTTACTGGGGTGTGTGTA 59.814 44.000 0.00 0.00 0.00 2.90
730 1325 4.813750 ATAGTTACTGGGGTGTGTGTAC 57.186 45.455 0.00 0.00 0.00 2.90
731 1326 2.400573 AGTTACTGGGGTGTGTGTACA 58.599 47.619 0.00 0.00 0.00 2.90
732 1327 2.976882 AGTTACTGGGGTGTGTGTACAT 59.023 45.455 0.00 0.00 39.39 2.29
733 1328 4.161876 AGTTACTGGGGTGTGTGTACATA 58.838 43.478 0.00 0.00 39.39 2.29
734 1329 4.781087 AGTTACTGGGGTGTGTGTACATAT 59.219 41.667 0.00 0.00 39.39 1.78
735 1330 5.959594 AGTTACTGGGGTGTGTGTACATATA 59.040 40.000 0.00 0.00 39.39 0.86
736 1331 6.614087 AGTTACTGGGGTGTGTGTACATATAT 59.386 38.462 0.00 0.00 39.39 0.86
737 1332 5.290493 ACTGGGGTGTGTGTACATATATG 57.710 43.478 11.29 11.29 39.39 1.78
738 1333 4.719773 ACTGGGGTGTGTGTACATATATGT 59.280 41.667 21.57 21.57 44.48 2.29
739 1334 5.029807 TGGGGTGTGTGTACATATATGTG 57.970 43.478 25.48 0.00 41.89 3.21
740 1335 4.471747 TGGGGTGTGTGTACATATATGTGT 59.528 41.667 25.48 10.18 41.89 3.72
741 1336 4.814234 GGGGTGTGTGTACATATATGTGTG 59.186 45.833 25.48 0.00 41.89 3.82
742 1337 5.424757 GGGTGTGTGTACATATATGTGTGT 58.575 41.667 25.48 5.34 41.89 3.72
743 1338 6.407187 GGGGTGTGTGTACATATATGTGTGTA 60.407 42.308 25.48 5.35 41.89 2.90
744 1339 7.042950 GGGTGTGTGTACATATATGTGTGTAA 58.957 38.462 25.48 4.99 41.89 2.41
745 1340 7.549842 GGGTGTGTGTACATATATGTGTGTAAA 59.450 37.037 25.48 4.27 41.89 2.01
746 1341 9.104965 GGTGTGTGTACATATATGTGTGTAAAT 57.895 33.333 25.48 1.44 41.89 1.40
773 1368 9.794719 ATATGCTATACTAAGTGTGAGTGTAGA 57.205 33.333 9.84 0.00 39.64 2.59
774 1369 7.933215 TGCTATACTAAGTGTGAGTGTAGAA 57.067 36.000 9.84 0.00 39.64 2.10
775 1370 8.521170 TGCTATACTAAGTGTGAGTGTAGAAT 57.479 34.615 9.84 0.00 39.64 2.40
776 1371 9.623000 TGCTATACTAAGTGTGAGTGTAGAATA 57.377 33.333 9.84 0.00 39.64 1.75
779 1374 8.754991 ATACTAAGTGTGAGTGTAGAATAGCT 57.245 34.615 0.00 0.00 0.00 3.32
780 1375 7.469537 ACTAAGTGTGAGTGTAGAATAGCTT 57.530 36.000 0.00 0.00 0.00 3.74
781 1376 8.577048 ACTAAGTGTGAGTGTAGAATAGCTTA 57.423 34.615 0.00 0.00 0.00 3.09
782 1377 9.191479 ACTAAGTGTGAGTGTAGAATAGCTTAT 57.809 33.333 0.00 0.00 0.00 1.73
784 1379 8.934507 AAGTGTGAGTGTAGAATAGCTTATTC 57.065 34.615 0.00 0.00 43.77 1.75
795 1390 6.086785 GAATAGCTTATTCTACACCCGAGT 57.913 41.667 0.00 0.00 41.00 4.18
796 1391 7.211966 GAATAGCTTATTCTACACCCGAGTA 57.788 40.000 0.00 0.00 41.00 2.59
797 1392 7.592885 AATAGCTTATTCTACACCCGAGTAA 57.407 36.000 0.00 0.00 0.00 2.24
798 1393 5.259832 AGCTTATTCTACACCCGAGTAAC 57.740 43.478 0.00 0.00 0.00 2.50
799 1394 4.040376 GCTTATTCTACACCCGAGTAACG 58.960 47.826 0.00 0.00 42.18 3.18
800 1395 4.201950 GCTTATTCTACACCCGAGTAACGA 60.202 45.833 0.00 0.00 45.77 3.85
801 1396 5.506982 GCTTATTCTACACCCGAGTAACGAT 60.507 44.000 0.00 0.00 45.77 3.73
802 1397 6.293626 GCTTATTCTACACCCGAGTAACGATA 60.294 42.308 0.00 0.00 45.77 2.92
803 1398 4.882671 TTCTACACCCGAGTAACGATAC 57.117 45.455 0.00 0.00 45.77 2.24
804 1399 3.872696 TCTACACCCGAGTAACGATACA 58.127 45.455 5.59 0.00 45.77 2.29
805 1400 4.454678 TCTACACCCGAGTAACGATACAT 58.545 43.478 5.59 0.00 45.77 2.29
806 1401 5.610398 TCTACACCCGAGTAACGATACATA 58.390 41.667 5.59 0.00 45.77 2.29
807 1402 4.558538 ACACCCGAGTAACGATACATAC 57.441 45.455 5.59 0.00 45.77 2.39
808 1403 3.947196 ACACCCGAGTAACGATACATACA 59.053 43.478 5.59 0.00 45.77 2.29
809 1404 4.398988 ACACCCGAGTAACGATACATACAA 59.601 41.667 5.59 0.00 45.77 2.41
810 1405 5.105797 ACACCCGAGTAACGATACATACAAA 60.106 40.000 5.59 0.00 45.77 2.83
811 1406 5.806502 CACCCGAGTAACGATACATACAAAA 59.193 40.000 5.59 0.00 45.77 2.44
812 1407 6.477688 CACCCGAGTAACGATACATACAAAAT 59.522 38.462 5.59 0.00 45.77 1.82
813 1408 6.477688 ACCCGAGTAACGATACATACAAAATG 59.522 38.462 5.59 0.00 45.77 2.32
814 1409 6.477688 CCCGAGTAACGATACATACAAAATGT 59.522 38.462 5.59 0.00 45.77 2.71
815 1410 7.648908 CCCGAGTAACGATACATACAAAATGTA 59.351 37.037 5.59 0.69 45.77 2.29
816 1411 8.688184 CCGAGTAACGATACATACAAAATGTAG 58.312 37.037 5.59 0.00 45.77 2.74
817 1412 9.229784 CGAGTAACGATACATACAAAATGTAGT 57.770 33.333 5.59 0.00 45.77 2.73
822 1417 7.834529 ACGATACATACAAAATGTAGTAACGC 58.165 34.615 18.06 0.00 36.90 4.84
823 1418 7.488792 ACGATACATACAAAATGTAGTAACGCA 59.511 33.333 18.06 0.00 36.90 5.24
824 1419 8.322428 CGATACATACAAAATGTAGTAACGCAA 58.678 33.333 4.38 0.00 36.14 4.85
979 1641 2.946329 TCGGCAAAGCTTTAGTTGTCAA 59.054 40.909 12.25 0.00 29.64 3.18
1103 1768 4.473520 CCCCGCAGACAAGCCGAT 62.474 66.667 0.00 0.00 0.00 4.18
1173 1838 1.476891 GAGGGAGTGCATGACTACGAA 59.523 52.381 0.00 0.00 36.16 3.85
1206 1871 3.244582 TGGCTCCTTTGAGGTACACTTA 58.755 45.455 0.00 0.00 39.14 2.24
1224 1889 7.566760 ACACTTATCCGATGAATGCAAATTA 57.433 32.000 0.00 0.00 0.00 1.40
1234 1899 6.561350 CGATGAATGCAAATTACGTATCGACA 60.561 38.462 0.00 0.00 37.63 4.35
1267 1932 0.677288 CCACTACAACACTCGGGTCA 59.323 55.000 0.00 0.00 0.00 4.02
1303 1968 3.356639 GACACGATCAGCGGCCTCA 62.357 63.158 0.00 0.00 46.49 3.86
1418 2083 2.830704 AAGTCATTCCCGGTCGACGC 62.831 60.000 9.92 1.55 42.52 5.19
1502 2167 2.621055 CCGAGTCTTCCTCTTCGATCAT 59.379 50.000 0.00 0.00 38.11 2.45
1505 2170 4.439426 CGAGTCTTCCTCTTCGATCATGTT 60.439 45.833 0.00 0.00 38.11 2.71
1510 2175 4.736126 TCCTCTTCGATCATGTTGCTTA 57.264 40.909 0.00 0.00 0.00 3.09
1545 2211 6.988580 TCTTTCTTCGTAGATTGATGATGCAT 59.011 34.615 0.00 0.00 35.04 3.96
1546 2212 6.535274 TTCTTCGTAGATTGATGATGCATG 57.465 37.500 2.46 0.00 35.04 4.06
1547 2213 4.450080 TCTTCGTAGATTGATGATGCATGC 59.550 41.667 11.82 11.82 35.04 4.06
1548 2214 2.733026 TCGTAGATTGATGATGCATGCG 59.267 45.455 14.09 0.00 0.00 4.73
1549 2215 2.159747 CGTAGATTGATGATGCATGCGG 60.160 50.000 14.09 0.00 0.00 5.69
1550 2216 0.596577 AGATTGATGATGCATGCGGC 59.403 50.000 14.09 7.96 45.13 6.53
1551 2217 0.596577 GATTGATGATGCATGCGGCT 59.403 50.000 14.09 0.00 45.15 5.52
1554 2220 1.281960 GATGATGCATGCGGCTGTC 59.718 57.895 14.09 6.56 45.15 3.51
1575 2241 0.177604 CTGCTTGTTTTGCAACCCCA 59.822 50.000 0.00 0.00 40.13 4.96
1585 2251 1.259142 TGCAACCCCATGCCATCTTG 61.259 55.000 0.00 0.00 45.83 3.02
1646 2320 7.122715 ACCAAGTGATATTAAATGGTGCCTTA 58.877 34.615 5.06 0.00 39.57 2.69
1721 2396 3.555547 CGGTGAATGCGTTATCTGATCAA 59.444 43.478 0.00 0.00 0.00 2.57
1728 2403 4.832248 TGCGTTATCTGATCAAAGAAGGT 58.168 39.130 0.00 0.00 0.00 3.50
1750 2425 6.770785 AGGTATAATCGTATTGTGGCACAAAT 59.229 34.615 34.01 22.90 44.16 2.32
1776 2451 6.035112 GGAAACTGTCACTTAATTAGCTCTCG 59.965 42.308 0.00 0.00 0.00 4.04
1830 2506 5.520632 TCGATCTTGAAGATAGCTTTACCG 58.479 41.667 7.82 5.11 34.53 4.02
1881 2560 9.159470 GCGATAAAACTTTTGATCTATTAGTGC 57.841 33.333 0.00 0.00 0.00 4.40
1901 2580 0.038599 TGCCATGTCAGCATTGGAGT 59.961 50.000 0.00 0.00 34.69 3.85
1933 2612 2.882876 CCGTCGTCATCGTCCCTT 59.117 61.111 0.00 0.00 38.33 3.95
1939 2618 0.747255 CGTCATCGTCCCTTCCTCAT 59.253 55.000 0.00 0.00 0.00 2.90
1961 2640 1.963515 GGAGTCAGGCCAAACATGTTT 59.036 47.619 18.13 18.13 0.00 2.83
1987 2666 3.162666 AGACAGTCGGAAAGTCATGGTA 58.837 45.455 11.98 0.00 34.80 3.25
1988 2667 3.769844 AGACAGTCGGAAAGTCATGGTAT 59.230 43.478 11.98 0.00 34.80 2.73
2000 2680 1.142060 TCATGGTATTAAGGCCCCACG 59.858 52.381 0.00 0.00 0.00 4.94
2031 2711 2.066262 ACCAGAACAGTAAACATCGCG 58.934 47.619 0.00 0.00 0.00 5.87
2038 2718 5.636121 AGAACAGTAAACATCGCGTATGAAA 59.364 36.000 20.36 0.00 39.07 2.69
2137 2817 3.252215 CCAAACACTAGCACCGATTGAAA 59.748 43.478 0.00 0.00 0.00 2.69
2153 2833 3.986996 TGAAACTCATGAGATCTGCCA 57.013 42.857 29.27 13.65 0.00 4.92
2156 2836 4.019950 TGAAACTCATGAGATCTGCCAGAA 60.020 41.667 29.27 6.45 0.00 3.02
2174 2854 0.685785 AAACACACCACCACATGCCA 60.686 50.000 0.00 0.00 0.00 4.92
2177 2857 0.680618 CACACCACCACATGCCATTT 59.319 50.000 0.00 0.00 0.00 2.32
2183 2863 2.432874 CCACCACATGCCATTTGATGAT 59.567 45.455 0.00 0.00 0.00 2.45
2221 2901 1.508256 AATGGGCACTAGGTAGGGAC 58.492 55.000 0.00 0.00 32.54 4.46
2224 2904 1.282382 GGGCACTAGGTAGGGACAAA 58.718 55.000 0.00 0.00 36.07 2.83
2283 2966 4.380531 TCTGAGCAAGACACAAACCTAAG 58.619 43.478 0.00 0.00 0.00 2.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.179067 ACCCAACGTGTACACTGGTG 60.179 55.000 24.86 23.11 0.00 4.17
1 2 0.179067 CACCCAACGTGTACACTGGT 60.179 55.000 24.86 20.50 37.73 4.00
2 3 2.612200 CACCCAACGTGTACACTGG 58.388 57.895 23.01 22.32 37.73 4.00
11 12 2.443260 TAGCGCATGACACCCAACGT 62.443 55.000 11.47 0.00 32.88 3.99
12 13 1.089481 ATAGCGCATGACACCCAACG 61.089 55.000 11.47 0.00 0.00 4.10
13 14 1.597663 GTATAGCGCATGACACCCAAC 59.402 52.381 11.47 0.00 0.00 3.77
14 15 1.208293 TGTATAGCGCATGACACCCAA 59.792 47.619 11.47 0.00 0.00 4.12
15 16 0.827368 TGTATAGCGCATGACACCCA 59.173 50.000 11.47 0.00 0.00 4.51
16 17 2.169832 ATGTATAGCGCATGACACCC 57.830 50.000 11.47 0.00 0.00 4.61
17 18 2.349817 GCAATGTATAGCGCATGACACC 60.350 50.000 11.47 0.00 0.00 4.16
18 19 2.349817 GGCAATGTATAGCGCATGACAC 60.350 50.000 11.47 0.00 0.00 3.67
19 20 1.872952 GGCAATGTATAGCGCATGACA 59.127 47.619 11.47 10.67 0.00 3.58
20 21 1.136252 CGGCAATGTATAGCGCATGAC 60.136 52.381 11.47 4.17 0.00 3.06
21 22 1.147473 CGGCAATGTATAGCGCATGA 58.853 50.000 11.47 0.00 0.00 3.07
22 23 0.166597 CCGGCAATGTATAGCGCATG 59.833 55.000 11.47 0.00 0.00 4.06
23 24 0.250295 ACCGGCAATGTATAGCGCAT 60.250 50.000 11.47 3.63 0.00 4.73
24 25 0.389757 TACCGGCAATGTATAGCGCA 59.610 50.000 11.47 0.00 0.00 6.09
25 26 1.068474 CTACCGGCAATGTATAGCGC 58.932 55.000 0.00 0.00 0.00 5.92
26 27 2.325761 GACTACCGGCAATGTATAGCG 58.674 52.381 0.00 0.00 0.00 4.26
27 28 2.325761 CGACTACCGGCAATGTATAGC 58.674 52.381 0.00 0.00 33.91 2.97
39 40 0.822532 ATGGCCTCTACCGACTACCG 60.823 60.000 3.32 0.00 38.18 4.02
40 41 2.283145 TATGGCCTCTACCGACTACC 57.717 55.000 3.32 0.00 0.00 3.18
41 42 2.094649 GCATATGGCCTCTACCGACTAC 60.095 54.545 3.32 0.00 36.11 2.73
42 43 2.168496 GCATATGGCCTCTACCGACTA 58.832 52.381 3.32 0.00 36.11 2.59
43 44 0.969894 GCATATGGCCTCTACCGACT 59.030 55.000 3.32 0.00 36.11 4.18
44 45 3.516578 GCATATGGCCTCTACCGAC 57.483 57.895 3.32 0.00 36.11 4.79
54 55 3.319122 CCTAGGAAAACTTGGCATATGGC 59.681 47.826 21.76 21.76 43.74 4.40
55 56 3.891366 CCCTAGGAAAACTTGGCATATGG 59.109 47.826 11.48 0.00 40.30 2.74
56 57 4.792068 TCCCTAGGAAAACTTGGCATATG 58.208 43.478 11.48 0.00 40.30 1.78
57 58 5.466127 TTCCCTAGGAAAACTTGGCATAT 57.534 39.130 11.48 0.00 38.93 1.78
58 59 4.938575 TTCCCTAGGAAAACTTGGCATA 57.061 40.909 11.48 0.00 38.93 3.14
59 60 3.825908 TTCCCTAGGAAAACTTGGCAT 57.174 42.857 11.48 0.00 38.93 4.40
60 61 3.825908 ATTCCCTAGGAAAACTTGGCA 57.174 42.857 11.48 0.00 45.41 4.92
72 73 1.270358 GCAAGGCGACCTATTCCCTAG 60.270 57.143 0.00 0.00 31.13 3.02
73 74 0.756903 GCAAGGCGACCTATTCCCTA 59.243 55.000 0.00 0.00 31.13 3.53
74 75 1.271840 TGCAAGGCGACCTATTCCCT 61.272 55.000 0.00 0.00 31.13 4.20
75 76 0.393808 TTGCAAGGCGACCTATTCCC 60.394 55.000 0.00 0.00 31.13 3.97
76 77 1.017387 CTTGCAAGGCGACCTATTCC 58.983 55.000 19.14 0.00 31.13 3.01
77 78 2.024176 TCTTGCAAGGCGACCTATTC 57.976 50.000 25.73 0.00 31.13 1.75
78 79 2.717639 ATCTTGCAAGGCGACCTATT 57.282 45.000 25.73 0.00 31.13 1.73
94 95 3.758300 CGCGCAAATACCTTTTGAATCT 58.242 40.909 8.75 0.00 0.00 2.40
110 111 5.621197 ATTATTATTTATCTTGGCGCGCA 57.379 34.783 34.42 16.55 0.00 6.09
114 115 8.761575 AATGGCAATTATTATTTATCTTGGCG 57.238 30.769 0.00 0.00 37.37 5.69
137 138 5.420104 CCAAGTTCTTCTCAAAGGCCATAAT 59.580 40.000 5.01 0.00 33.03 1.28
139 140 4.202567 ACCAAGTTCTTCTCAAAGGCCATA 60.203 41.667 5.01 0.00 33.03 2.74
183 184 4.520743 TCGCATTTTAGCAGAAATCGAG 57.479 40.909 0.00 4.78 31.50 4.04
185 186 5.737353 TGTATCGCATTTTAGCAGAAATCG 58.263 37.500 0.00 0.00 0.00 3.34
186 187 9.831737 AATATGTATCGCATTTTAGCAGAAATC 57.168 29.630 0.00 0.00 38.94 2.17
201 202 5.700832 TGAGGTGGAATTGAATATGTATCGC 59.299 40.000 0.00 0.00 0.00 4.58
202 203 7.728847 TTGAGGTGGAATTGAATATGTATCG 57.271 36.000 0.00 0.00 0.00 2.92
213 793 7.829725 TCTTTACATTCATTGAGGTGGAATTG 58.170 34.615 3.98 0.93 0.00 2.32
240 820 9.807649 CATAAACATTTAATTCCCTCCAAGAAG 57.192 33.333 0.00 0.00 0.00 2.85
243 832 9.369904 CAACATAAACATTTAATTCCCTCCAAG 57.630 33.333 0.00 0.00 0.00 3.61
661 1256 4.397730 ACACACACACACACACACAAATAT 59.602 37.500 0.00 0.00 0.00 1.28
662 1257 3.753797 ACACACACACACACACACAAATA 59.246 39.130 0.00 0.00 0.00 1.40
663 1258 2.556189 ACACACACACACACACACAAAT 59.444 40.909 0.00 0.00 0.00 2.32
664 1259 1.950216 ACACACACACACACACACAAA 59.050 42.857 0.00 0.00 0.00 2.83
665 1260 1.265365 CACACACACACACACACACAA 59.735 47.619 0.00 0.00 0.00 3.33
666 1261 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
667 1262 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
668 1263 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
669 1264 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
670 1265 1.152510 GACACACACACACACACACA 58.847 50.000 0.00 0.00 0.00 3.72
671 1266 1.128507 CAGACACACACACACACACAC 59.871 52.381 0.00 0.00 0.00 3.82
672 1267 1.270571 ACAGACACACACACACACACA 60.271 47.619 0.00 0.00 0.00 3.72
673 1268 1.128507 CACAGACACACACACACACAC 59.871 52.381 0.00 0.00 0.00 3.82
674 1269 1.270571 ACACAGACACACACACACACA 60.271 47.619 0.00 0.00 0.00 3.72
675 1270 1.128507 CACACAGACACACACACACAC 59.871 52.381 0.00 0.00 0.00 3.82
676 1271 1.270571 ACACACAGACACACACACACA 60.271 47.619 0.00 0.00 0.00 3.72
677 1272 1.128507 CACACACAGACACACACACAC 59.871 52.381 0.00 0.00 0.00 3.82
678 1273 1.437625 CACACACAGACACACACACA 58.562 50.000 0.00 0.00 0.00 3.72
679 1274 0.096976 GCACACACAGACACACACAC 59.903 55.000 0.00 0.00 0.00 3.82
680 1275 1.357991 CGCACACACAGACACACACA 61.358 55.000 0.00 0.00 0.00 3.72
681 1276 1.348250 CGCACACACAGACACACAC 59.652 57.895 0.00 0.00 0.00 3.82
682 1277 2.460275 GCGCACACACAGACACACA 61.460 57.895 0.30 0.00 0.00 3.72
683 1278 1.775039 ATGCGCACACACAGACACAC 61.775 55.000 14.90 0.00 0.00 3.82
684 1279 1.523484 ATGCGCACACACAGACACA 60.523 52.632 14.90 0.00 0.00 3.72
685 1280 1.082561 CATGCGCACACACAGACAC 60.083 57.895 14.90 0.00 0.00 3.67
686 1281 1.523484 ACATGCGCACACACAGACA 60.523 52.632 14.90 0.00 0.00 3.41
687 1282 1.082561 CACATGCGCACACACAGAC 60.083 57.895 14.90 0.00 0.00 3.51
688 1283 1.523484 ACACATGCGCACACACAGA 60.523 52.632 14.90 0.00 0.00 3.41
689 1284 1.369568 CACACATGCGCACACACAG 60.370 57.895 14.90 1.98 0.00 3.66
690 1285 0.811616 TACACACATGCGCACACACA 60.812 50.000 14.90 0.00 0.00 3.72
691 1286 0.516877 ATACACACATGCGCACACAC 59.483 50.000 14.90 0.00 0.00 3.82
692 1287 1.999024 CTATACACACATGCGCACACA 59.001 47.619 14.90 0.00 0.00 3.72
693 1288 1.999735 ACTATACACACATGCGCACAC 59.000 47.619 14.90 0.00 0.00 3.82
694 1289 2.378445 ACTATACACACATGCGCACA 57.622 45.000 14.90 0.00 0.00 4.57
695 1290 3.863424 AGTAACTATACACACATGCGCAC 59.137 43.478 14.90 0.00 34.29 5.34
696 1291 3.862845 CAGTAACTATACACACATGCGCA 59.137 43.478 14.96 14.96 34.29 6.09
697 1292 3.245284 CCAGTAACTATACACACATGCGC 59.755 47.826 0.00 0.00 34.29 6.09
698 1293 3.802139 CCCAGTAACTATACACACATGCG 59.198 47.826 0.00 0.00 34.29 4.73
699 1294 4.127171 CCCCAGTAACTATACACACATGC 58.873 47.826 0.00 0.00 34.29 4.06
700 1295 5.116180 CACCCCAGTAACTATACACACATG 58.884 45.833 0.00 0.00 34.29 3.21
701 1296 4.781087 ACACCCCAGTAACTATACACACAT 59.219 41.667 0.00 0.00 34.29 3.21
702 1297 4.020928 CACACCCCAGTAACTATACACACA 60.021 45.833 0.00 0.00 34.29 3.72
703 1298 4.020839 ACACACCCCAGTAACTATACACAC 60.021 45.833 0.00 0.00 34.29 3.82
704 1299 4.020928 CACACACCCCAGTAACTATACACA 60.021 45.833 0.00 0.00 34.29 3.72
705 1300 4.020839 ACACACACCCCAGTAACTATACAC 60.021 45.833 0.00 0.00 34.29 2.90
706 1301 4.161876 ACACACACCCCAGTAACTATACA 58.838 43.478 0.00 0.00 34.29 2.29
707 1302 4.813750 ACACACACCCCAGTAACTATAC 57.186 45.455 0.00 0.00 0.00 1.47
708 1303 5.331906 TGTACACACACCCCAGTAACTATA 58.668 41.667 0.00 0.00 0.00 1.31
709 1304 4.161876 TGTACACACACCCCAGTAACTAT 58.838 43.478 0.00 0.00 0.00 2.12
710 1305 3.574749 TGTACACACACCCCAGTAACTA 58.425 45.455 0.00 0.00 0.00 2.24
711 1306 2.400573 TGTACACACACCCCAGTAACT 58.599 47.619 0.00 0.00 0.00 2.24
712 1307 2.914695 TGTACACACACCCCAGTAAC 57.085 50.000 0.00 0.00 0.00 2.50
713 1308 6.384595 ACATATATGTACACACACCCCAGTAA 59.615 38.462 16.85 0.00 39.68 2.24
714 1309 5.900699 ACATATATGTACACACACCCCAGTA 59.099 40.000 16.85 0.00 39.68 2.74
715 1310 4.719773 ACATATATGTACACACACCCCAGT 59.280 41.667 16.85 0.00 39.68 4.00
716 1311 5.056480 CACATATATGTACACACACCCCAG 58.944 45.833 17.86 0.00 39.39 4.45
717 1312 4.471747 ACACATATATGTACACACACCCCA 59.528 41.667 17.86 0.00 39.39 4.96
718 1313 4.814234 CACACATATATGTACACACACCCC 59.186 45.833 17.86 0.00 39.39 4.95
719 1314 5.424757 ACACACATATATGTACACACACCC 58.575 41.667 17.86 0.00 39.39 4.61
720 1315 8.481974 TTTACACACATATATGTACACACACC 57.518 34.615 17.86 0.00 39.39 4.16
747 1342 9.794719 TCTACACTCACACTTAGTATAGCATAT 57.205 33.333 0.00 0.00 0.00 1.78
748 1343 9.623000 TTCTACACTCACACTTAGTATAGCATA 57.377 33.333 0.00 0.00 0.00 3.14
749 1344 8.521170 TTCTACACTCACACTTAGTATAGCAT 57.479 34.615 0.00 0.00 0.00 3.79
750 1345 7.933215 TTCTACACTCACACTTAGTATAGCA 57.067 36.000 0.00 0.00 0.00 3.49
753 1348 9.848710 AGCTATTCTACACTCACACTTAGTATA 57.151 33.333 0.00 0.00 0.00 1.47
754 1349 8.754991 AGCTATTCTACACTCACACTTAGTAT 57.245 34.615 0.00 0.00 0.00 2.12
755 1350 8.577048 AAGCTATTCTACACTCACACTTAGTA 57.423 34.615 0.00 0.00 0.00 1.82
756 1351 7.469537 AAGCTATTCTACACTCACACTTAGT 57.530 36.000 0.00 0.00 0.00 2.24
759 1354 8.934507 GAATAAGCTATTCTACACTCACACTT 57.065 34.615 0.00 0.00 41.00 3.16
772 1367 6.086785 ACTCGGGTGTAGAATAAGCTATTC 57.913 41.667 0.00 0.00 43.77 1.75
773 1368 7.432059 GTTACTCGGGTGTAGAATAAGCTATT 58.568 38.462 0.00 0.00 0.00 1.73
774 1369 6.293845 CGTTACTCGGGTGTAGAATAAGCTAT 60.294 42.308 0.00 0.00 35.71 2.97
775 1370 5.008019 CGTTACTCGGGTGTAGAATAAGCTA 59.992 44.000 0.00 0.00 35.71 3.32
776 1371 4.201990 CGTTACTCGGGTGTAGAATAAGCT 60.202 45.833 0.00 0.00 35.71 3.74
777 1372 4.040376 CGTTACTCGGGTGTAGAATAAGC 58.960 47.826 0.00 0.00 35.71 3.09
778 1373 5.490139 TCGTTACTCGGGTGTAGAATAAG 57.510 43.478 0.00 0.00 40.32 1.73
779 1374 6.542005 TGTATCGTTACTCGGGTGTAGAATAA 59.458 38.462 0.00 0.00 40.32 1.40
780 1375 6.054941 TGTATCGTTACTCGGGTGTAGAATA 58.945 40.000 0.00 0.00 40.32 1.75
781 1376 4.883585 TGTATCGTTACTCGGGTGTAGAAT 59.116 41.667 0.00 0.00 40.32 2.40
782 1377 4.260985 TGTATCGTTACTCGGGTGTAGAA 58.739 43.478 0.00 0.00 40.32 2.10
783 1378 3.872696 TGTATCGTTACTCGGGTGTAGA 58.127 45.455 0.00 0.00 40.32 2.59
784 1379 4.825546 ATGTATCGTTACTCGGGTGTAG 57.174 45.455 0.00 0.00 40.32 2.74
785 1380 5.122519 TGTATGTATCGTTACTCGGGTGTA 58.877 41.667 0.00 0.00 40.32 2.90
786 1381 3.947196 TGTATGTATCGTTACTCGGGTGT 59.053 43.478 0.00 0.00 40.32 4.16
787 1382 4.556942 TGTATGTATCGTTACTCGGGTG 57.443 45.455 0.00 0.00 40.32 4.61
788 1383 5.581126 TTTGTATGTATCGTTACTCGGGT 57.419 39.130 0.00 0.00 40.32 5.28
789 1384 6.477688 ACATTTTGTATGTATCGTTACTCGGG 59.522 38.462 5.32 0.00 40.32 5.14
790 1385 7.459394 ACATTTTGTATGTATCGTTACTCGG 57.541 36.000 5.32 0.00 40.32 4.63
791 1386 9.229784 ACTACATTTTGTATGTATCGTTACTCG 57.770 33.333 5.32 0.00 34.42 4.18
796 1391 8.323140 GCGTTACTACATTTTGTATGTATCGTT 58.677 33.333 17.14 0.00 35.37 3.85
797 1392 7.488792 TGCGTTACTACATTTTGTATGTATCGT 59.511 33.333 17.14 0.00 35.37 3.73
798 1393 7.833539 TGCGTTACTACATTTTGTATGTATCG 58.166 34.615 14.70 14.70 35.62 2.92
947 1608 6.588348 AAAGCTTTGCCGATATATTTTTGC 57.412 33.333 11.80 0.00 0.00 3.68
950 1611 8.466798 ACAACTAAAGCTTTGCCGATATATTTT 58.533 29.630 22.02 0.00 0.00 1.82
960 1621 3.068165 AGGTTGACAACTAAAGCTTTGCC 59.932 43.478 22.02 9.06 30.18 4.52
979 1641 0.610687 GTTGGTGCTCTAGCTCAGGT 59.389 55.000 3.26 0.00 42.66 4.00
1007 1669 1.634960 GAGGAGGAGGGTAGTATGCC 58.365 60.000 0.00 0.00 41.82 4.40
1044 1706 4.664677 GCGGTGGCAGTGACGAGT 62.665 66.667 0.00 0.00 39.62 4.18
1103 1768 1.813862 GCCCTAGCATTTCGTATGCCA 60.814 52.381 17.44 7.24 45.59 4.92
1206 1871 6.401047 CGATACGTAATTTGCATTCATCGGAT 60.401 38.462 0.00 0.00 31.58 4.18
1224 1889 0.376152 CGTACTGGCTGTCGATACGT 59.624 55.000 0.00 0.00 35.17 3.57
1234 1899 0.321919 TAGTGGACGTCGTACTGGCT 60.322 55.000 25.41 7.09 0.00 4.75
1303 1968 2.108952 AGACCTTCACCTCAATGCCTTT 59.891 45.455 0.00 0.00 0.00 3.11
1312 1977 3.125316 CACGCAATAAAGACCTTCACCTC 59.875 47.826 0.00 0.00 0.00 3.85
1418 2083 2.104170 ACTTCGGGCTAGAGGAGAAAG 58.896 52.381 0.00 0.00 0.00 2.62
1489 2154 3.616956 AAGCAACATGATCGAAGAGGA 57.383 42.857 0.00 0.00 43.63 3.71
1502 2167 7.346751 AGAAAGAAGGAAACATTAAGCAACA 57.653 32.000 0.00 0.00 0.00 3.33
1505 2170 6.262273 ACGAAGAAAGAAGGAAACATTAAGCA 59.738 34.615 0.00 0.00 0.00 3.91
1510 2175 8.507249 CAATCTACGAAGAAAGAAGGAAACATT 58.493 33.333 0.00 0.00 34.73 2.71
1547 2213 2.392613 AAAACAAGCAGCGACAGCCG 62.393 55.000 0.00 0.00 46.67 5.52
1548 2214 0.936297 CAAAACAAGCAGCGACAGCC 60.936 55.000 0.00 0.00 46.67 4.85
1549 2215 1.543106 GCAAAACAAGCAGCGACAGC 61.543 55.000 0.00 0.00 45.58 4.40
1550 2216 0.248580 TGCAAAACAAGCAGCGACAG 60.249 50.000 0.00 0.00 37.02 3.51
1551 2217 0.172127 TTGCAAAACAAGCAGCGACA 59.828 45.000 0.00 0.00 43.75 4.35
1585 2251 3.701040 ACAATGGGAGTACATGAATTGGC 59.299 43.478 0.00 0.00 30.97 4.52
1616 2285 7.148086 GCACCATTTAATATCACTTGGTCTCAA 60.148 37.037 0.00 0.00 35.35 3.02
1624 2293 8.766994 ACATAAGGCACCATTTAATATCACTT 57.233 30.769 0.00 0.00 0.00 3.16
1626 2295 7.803189 CGAACATAAGGCACCATTTAATATCAC 59.197 37.037 0.00 0.00 0.00 3.06
1633 2302 4.580868 TCACGAACATAAGGCACCATTTA 58.419 39.130 0.00 0.00 0.00 1.40
1637 2311 2.746904 CAATCACGAACATAAGGCACCA 59.253 45.455 0.00 0.00 0.00 4.17
1638 2312 2.477863 GCAATCACGAACATAAGGCACC 60.478 50.000 0.00 0.00 0.00 5.01
1646 2320 7.292292 CAAATGAATTTTGCAATCACGAACAT 58.708 30.769 0.00 0.00 38.42 2.71
1721 2396 6.482308 GTGCCACAATACGATTATACCTTCTT 59.518 38.462 0.00 0.00 0.00 2.52
1728 2403 6.768381 TCCATTTGTGCCACAATACGATTATA 59.232 34.615 11.67 0.00 38.00 0.98
1734 2409 3.567576 TTCCATTTGTGCCACAATACG 57.432 42.857 11.67 2.96 38.00 3.06
1750 2425 6.769512 AGAGCTAATTAAGTGACAGTTTCCA 58.230 36.000 0.00 0.00 0.00 3.53
1804 2480 7.169982 CGGTAAAGCTATCTTCAAGATCGAAAT 59.830 37.037 2.18 0.00 36.20 2.17
1824 2500 1.821753 CCACATGGGAAATGCGGTAAA 59.178 47.619 0.00 0.00 40.01 2.01
1830 2506 5.343307 AAAAGATACCACATGGGAAATGC 57.657 39.130 0.00 0.00 41.15 3.56
1859 2538 8.458843 GGCAGCACTAATAGATCAAAAGTTTTA 58.541 33.333 0.00 0.00 0.00 1.52
1860 2539 7.039784 TGGCAGCACTAATAGATCAAAAGTTTT 60.040 33.333 0.00 0.00 0.00 2.43
1881 2560 0.738975 CTCCAATGCTGACATGGCAG 59.261 55.000 25.09 25.09 43.15 4.85
1939 2618 0.321564 CATGTTTGGCCTGACTCCGA 60.322 55.000 3.32 0.00 0.00 4.55
1961 2640 6.070995 ACCATGACTTTCCGACTGTCTAATAA 60.071 38.462 6.21 0.00 0.00 1.40
1987 2666 0.991355 TGATCCCGTGGGGCCTTAAT 60.991 55.000 0.84 0.00 43.94 1.40
1988 2667 1.208844 TTGATCCCGTGGGGCCTTAA 61.209 55.000 0.84 0.00 43.94 1.85
2000 2680 0.605319 TGTTCTGGTGCGTTGATCCC 60.605 55.000 0.00 0.00 0.00 3.85
2038 2718 9.620259 GTTGGATCCTTTCAATCTATAGTTCTT 57.380 33.333 14.23 0.00 0.00 2.52
2067 2747 3.649073 TCATCTTCGTTCGTGTGTCATT 58.351 40.909 0.00 0.00 0.00 2.57
2069 2749 2.785713 TCATCTTCGTTCGTGTGTCA 57.214 45.000 0.00 0.00 0.00 3.58
2137 2817 3.262660 TGTTTCTGGCAGATCTCATGAGT 59.737 43.478 19.50 9.83 0.00 3.41
2153 2833 1.032014 GCATGTGGTGGTGTGTTTCT 58.968 50.000 0.00 0.00 0.00 2.52
2156 2836 0.469705 ATGGCATGTGGTGGTGTGTT 60.470 50.000 0.00 0.00 0.00 3.32
2209 2889 6.027482 TGGAATAAGTTTGTCCCTACCTAGT 58.973 40.000 2.88 0.00 0.00 2.57
2215 2895 9.053472 TCTAAAGATGGAATAAGTTTGTCCCTA 57.947 33.333 2.88 0.00 0.00 3.53
2216 2896 7.928873 TCTAAAGATGGAATAAGTTTGTCCCT 58.071 34.615 2.88 0.00 0.00 4.20
2221 2901 9.219603 TGTCACTCTAAAGATGGAATAAGTTTG 57.780 33.333 0.00 0.00 0.00 2.93
2224 2904 7.331791 GGTGTCACTCTAAAGATGGAATAAGT 58.668 38.462 2.35 0.00 0.00 2.24
2261 2943 4.380531 CTTAGGTTTGTGTCTTGCTCAGA 58.619 43.478 0.00 0.00 0.00 3.27
2283 2966 3.843999 TCTGGTGTTTTTGTGAGTTTGC 58.156 40.909 0.00 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.