Multiple sequence alignment - TraesCS7A01G422000

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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 TraesCS7A01G422000 chr7A 100.000 3569 0 0 1 3569 612758602 612755034 0.000000e+00 6591.0
1 TraesCS7A01G422000 chr7A 86.016 901 109 6 1666 2562 6803082 6803969 0.000000e+00 950.0
2 TraesCS7A01G422000 chr7D 95.879 1626 59 3 1016 2638 532612977 532611357 0.000000e+00 2625.0
3 TraesCS7A01G422000 chr7D 86.298 905 114 6 1666 2562 5352008 5351106 0.000000e+00 976.0
4 TraesCS7A01G422000 chr7D 85.246 549 35 21 458 979 532613780 532613251 1.140000e-144 523.0
5 TraesCS7A01G422000 chr7D 85.106 517 52 13 3071 3569 532610054 532609545 4.110000e-139 505.0
6 TraesCS7A01G422000 chr7D 77.219 338 54 15 2952 3269 37296066 37295732 3.660000e-40 176.0
7 TraesCS7A01G422000 chr7D 89.899 99 7 2 2660 2755 532610734 532610636 1.350000e-24 124.0
8 TraesCS7A01G422000 chr7B 95.831 1631 55 7 1016 2638 572959629 572958004 0.000000e+00 2623.0
9 TraesCS7A01G422000 chr7B 81.569 510 60 15 111 588 572962807 572962300 1.200000e-104 390.0
10 TraesCS7A01G422000 chr7B 94.444 72 2 1 2686 2755 572952917 572952846 3.770000e-20 110.0
11 TraesCS7A01G422000 chr7B 94.366 71 3 1 2686 2755 572953228 572953158 1.350000e-19 108.0
12 TraesCS7A01G422000 chr7B 97.674 43 1 0 923 965 572960321 572960279 1.370000e-09 75.0
13 TraesCS7A01G422000 chr1B 91.587 939 79 0 1659 2597 62723374 62724312 0.000000e+00 1297.0
14 TraesCS7A01G422000 chr1B 91.652 563 45 2 1008 1569 62722626 62723187 0.000000e+00 778.0
15 TraesCS7A01G422000 chr1B 82.264 530 79 14 1034 1555 62720035 62720557 9.090000e-121 444.0
16 TraesCS7A01G422000 chr1D 91.267 939 76 1 1659 2597 42762962 42763894 0.000000e+00 1275.0
17 TraesCS7A01G422000 chr1D 91.155 554 49 0 1016 1569 42762218 42762771 0.000000e+00 752.0
18 TraesCS7A01G422000 chr1D 89.944 537 54 0 1659 2195 42711539 42711003 0.000000e+00 693.0
19 TraesCS7A01G422000 chr1D 87.792 557 63 2 1016 1569 42625342 42624788 0.000000e+00 647.0
20 TraesCS7A01G422000 chr1D 87.253 557 66 2 1016 1569 42712253 42711699 6.500000e-177 630.0
21 TraesCS7A01G422000 chr1D 89.136 405 44 0 2191 2595 42614193 42613789 4.110000e-139 505.0
22 TraesCS7A01G422000 chr1D 78.466 339 45 14 2953 3269 94411491 94411159 2.810000e-46 196.0
23 TraesCS7A01G422000 chr1A 90.889 922 84 0 1659 2580 42255305 42256226 0.000000e+00 1238.0
24 TraesCS7A01G422000 chr1A 90.305 557 51 1 1016 1569 42254572 42255128 0.000000e+00 726.0
25 TraesCS7A01G422000 chr1A 87.814 558 63 4 1016 1569 42220780 42220224 0.000000e+00 649.0
26 TraesCS7A01G422000 chr1A 91.608 286 23 1 1723 2008 42218496 42218212 9.290000e-106 394.0
27 TraesCS7A01G422000 chr1A 88.889 72 8 0 1659 1730 42220048 42219977 4.910000e-14 89.8
28 TraesCS7A01G422000 chr4A 86.630 905 111 6 1666 2562 737139924 737140826 0.000000e+00 992.0
29 TraesCS7A01G422000 chr4A 78.571 336 47 12 2953 3269 330519682 330519353 7.820000e-47 198.0
30 TraesCS7A01G422000 chr3A 76.647 334 54 11 2950 3269 492057535 492057212 2.850000e-36 163.0
31 TraesCS7A01G422000 chr4D 75.953 341 53 20 2952 3269 474974158 474973824 7.980000e-32 148.0
32 TraesCS7A01G422000 chr2A 78.926 242 33 13 3270 3503 97304902 97305133 7.980000e-32 148.0
33 TraesCS7A01G422000 chr5D 75.221 339 52 18 2953 3269 58154469 58154797 8.040000e-27 132.0
34 TraesCS7A01G422000 chr2D 75.305 328 52 19 2963 3269 67480786 67480467 2.890000e-26 130.0
35 TraesCS7A01G422000 chr6B 87.059 85 11 0 3185 3269 320423839 320423923 2.930000e-16 97.1


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 TraesCS7A01G422000 chr7A 612755034 612758602 3568 True 6591.000000 6591 100.000000 1 3569 1 chr7A.!!$R1 3568
1 TraesCS7A01G422000 chr7A 6803082 6803969 887 False 950.000000 950 86.016000 1666 2562 1 chr7A.!!$F1 896
2 TraesCS7A01G422000 chr7D 5351106 5352008 902 True 976.000000 976 86.298000 1666 2562 1 chr7D.!!$R1 896
3 TraesCS7A01G422000 chr7D 532609545 532613780 4235 True 944.250000 2625 89.032500 458 3569 4 chr7D.!!$R3 3111
4 TraesCS7A01G422000 chr7B 572958004 572962807 4803 True 1029.333333 2623 91.691333 111 2638 3 chr7B.!!$R2 2527
5 TraesCS7A01G422000 chr1B 62720035 62724312 4277 False 839.666667 1297 88.501000 1008 2597 3 chr1B.!!$F1 1589
6 TraesCS7A01G422000 chr1D 42762218 42763894 1676 False 1013.500000 1275 91.211000 1016 2597 2 chr1D.!!$F1 1581
7 TraesCS7A01G422000 chr1D 42711003 42712253 1250 True 661.500000 693 88.598500 1016 2195 2 chr1D.!!$R4 1179
8 TraesCS7A01G422000 chr1D 42624788 42625342 554 True 647.000000 647 87.792000 1016 1569 1 chr1D.!!$R2 553
9 TraesCS7A01G422000 chr1A 42254572 42256226 1654 False 982.000000 1238 90.597000 1016 2580 2 chr1A.!!$F1 1564
10 TraesCS7A01G422000 chr1A 42218212 42220780 2568 True 377.600000 649 89.437000 1016 2008 3 chr1A.!!$R1 992
11 TraesCS7A01G422000 chr4A 737139924 737140826 902 False 992.000000 992 86.630000 1666 2562 1 chr4A.!!$F1 896

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
981 3008 0.03563 AAGAAGCGAATCTGCAGCCT 60.036 50.0 9.47 0.0 37.31 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2887 7699 1.140161 CTCCATTGCAATGCACGGG 59.86 57.895 30.15 18.3 38.71 5.28 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
20 21 2.686558 TGCATGCTTTGAAGTTCGTC 57.313 45.000 20.33 0.00 0.00 4.20
21 22 1.069973 TGCATGCTTTGAAGTTCGTCG 60.070 47.619 20.33 0.00 0.00 5.12
22 23 1.194547 GCATGCTTTGAAGTTCGTCGA 59.805 47.619 11.37 0.00 0.00 4.20
24 25 0.859232 TGCTTTGAAGTTCGTCGAGC 59.141 50.000 0.13 0.13 32.74 5.03
25 26 0.164002 GCTTTGAAGTTCGTCGAGCC 59.836 55.000 5.38 0.00 0.00 4.70
26 27 1.497991 CTTTGAAGTTCGTCGAGCCA 58.502 50.000 5.38 0.00 0.00 4.75
28 29 0.319555 TTGAAGTTCGTCGAGCCAGG 60.320 55.000 5.38 0.00 0.00 4.45
29 30 1.289380 GAAGTTCGTCGAGCCAGGT 59.711 57.895 5.38 0.00 0.00 4.00
30 31 0.319641 GAAGTTCGTCGAGCCAGGTT 60.320 55.000 5.38 0.00 0.00 3.50
31 32 0.106149 AAGTTCGTCGAGCCAGGTTT 59.894 50.000 5.38 0.00 0.00 3.27
32 33 0.106149 AGTTCGTCGAGCCAGGTTTT 59.894 50.000 5.38 0.00 0.00 2.43
43 44 2.679996 AGGTTTTGGATGCGGCCC 60.680 61.111 0.00 0.00 0.00 5.80
44 45 2.994417 GGTTTTGGATGCGGCCCA 60.994 61.111 0.00 0.00 0.00 5.36
45 46 2.573340 GTTTTGGATGCGGCCCAG 59.427 61.111 0.00 0.00 34.77 4.45
46 47 1.976474 GTTTTGGATGCGGCCCAGA 60.976 57.895 0.00 0.00 34.77 3.86
47 48 1.976474 TTTTGGATGCGGCCCAGAC 60.976 57.895 0.00 0.00 34.77 3.51
48 49 2.705312 TTTTGGATGCGGCCCAGACA 62.705 55.000 0.00 0.00 34.77 3.41
49 50 2.705312 TTTGGATGCGGCCCAGACAA 62.705 55.000 0.00 3.45 34.77 3.18
50 51 3.134127 GGATGCGGCCCAGACAAC 61.134 66.667 0.00 0.00 0.00 3.32
51 52 3.134127 GATGCGGCCCAGACAACC 61.134 66.667 0.00 0.00 0.00 3.77
53 54 3.505790 ATGCGGCCCAGACAACCAA 62.506 57.895 0.00 0.00 0.00 3.67
56 57 1.826054 CGGCCCAGACAACCAAACA 60.826 57.895 0.00 0.00 0.00 2.83
57 58 1.178534 CGGCCCAGACAACCAAACAT 61.179 55.000 0.00 0.00 0.00 2.71
58 59 1.884497 CGGCCCAGACAACCAAACATA 60.884 52.381 0.00 0.00 0.00 2.29
59 60 2.456577 GGCCCAGACAACCAAACATAT 58.543 47.619 0.00 0.00 0.00 1.78
61 62 3.088532 GCCCAGACAACCAAACATATCA 58.911 45.455 0.00 0.00 0.00 2.15
62 63 3.129287 GCCCAGACAACCAAACATATCAG 59.871 47.826 0.00 0.00 0.00 2.90
63 64 4.588899 CCCAGACAACCAAACATATCAGA 58.411 43.478 0.00 0.00 0.00 3.27
64 65 5.195940 CCCAGACAACCAAACATATCAGAT 58.804 41.667 0.00 0.00 0.00 2.90
67 68 6.600822 CCAGACAACCAAACATATCAGATTCT 59.399 38.462 0.00 0.00 0.00 2.40
68 69 7.121759 CCAGACAACCAAACATATCAGATTCTT 59.878 37.037 0.00 0.00 0.00 2.52
69 70 8.180267 CAGACAACCAAACATATCAGATTCTTC 58.820 37.037 0.00 0.00 0.00 2.87
70 71 8.105829 AGACAACCAAACATATCAGATTCTTCT 58.894 33.333 0.00 0.00 0.00 2.85
71 72 8.273780 ACAACCAAACATATCAGATTCTTCTC 57.726 34.615 0.00 0.00 0.00 2.87
72 73 7.065085 ACAACCAAACATATCAGATTCTTCTCG 59.935 37.037 0.00 0.00 0.00 4.04
73 74 6.644347 ACCAAACATATCAGATTCTTCTCGT 58.356 36.000 0.00 0.00 0.00 4.18
74 75 6.536582 ACCAAACATATCAGATTCTTCTCGTG 59.463 38.462 0.00 0.00 0.00 4.35
77 78 2.215907 ATCAGATTCTTCTCGTGCGG 57.784 50.000 0.00 0.00 0.00 5.69
78 79 0.458543 TCAGATTCTTCTCGTGCGGC 60.459 55.000 0.00 0.00 0.00 6.53
79 80 1.153549 AGATTCTTCTCGTGCGGCC 60.154 57.895 0.00 0.00 0.00 6.13
80 81 2.125106 ATTCTTCTCGTGCGGCCC 60.125 61.111 0.00 0.00 0.00 5.80
81 82 2.579684 GATTCTTCTCGTGCGGCCCT 62.580 60.000 0.00 0.00 0.00 5.19
82 83 2.859273 ATTCTTCTCGTGCGGCCCTG 62.859 60.000 0.00 0.00 0.00 4.45
97 98 1.307309 CCTGGTTGGGATGGATGCA 59.693 57.895 0.00 0.00 0.00 3.96
99 100 1.378382 TGGTTGGGATGGATGCACG 60.378 57.895 0.00 0.00 0.00 5.34
101 102 2.045708 GTTGGGATGGATGCACGCA 61.046 57.895 0.00 0.00 0.00 5.24
102 103 1.303970 TTGGGATGGATGCACGCAA 60.304 52.632 12.40 12.40 34.95 4.85
103 104 0.683828 TTGGGATGGATGCACGCAAT 60.684 50.000 12.40 0.00 33.06 3.56
104 105 1.102809 TGGGATGGATGCACGCAATC 61.103 55.000 0.00 0.00 0.00 2.67
105 106 1.102809 GGGATGGATGCACGCAATCA 61.103 55.000 7.78 0.00 0.00 2.57
106 107 0.740149 GGATGGATGCACGCAATCAA 59.260 50.000 7.78 0.00 0.00 2.57
107 108 1.134753 GGATGGATGCACGCAATCAAA 59.865 47.619 7.78 0.00 0.00 2.69
108 109 2.187707 GATGGATGCACGCAATCAAAC 58.812 47.619 0.00 0.00 0.00 2.93
118 119 0.109504 GCAATCAAACGCGCCCTTAA 60.110 50.000 5.73 0.00 0.00 1.85
160 163 8.950007 TTTCCTACTTGATATTTTTGGGAACT 57.050 30.769 0.00 0.00 31.30 3.01
162 165 6.821665 TCCTACTTGATATTTTTGGGAACTCG 59.178 38.462 0.00 0.00 0.00 4.18
172 175 3.637184 GGGAACTCGCCCTAAAACA 57.363 52.632 0.00 0.00 45.12 2.83
174 177 0.794473 GGAACTCGCCCTAAAACACG 59.206 55.000 0.00 0.00 0.00 4.49
188 198 3.773860 AAACACGTGAAACTTCATGCA 57.226 38.095 25.01 0.00 45.75 3.96
192 202 2.030893 CACGTGAAACTTCATGCATGGT 60.031 45.455 25.97 14.33 45.75 3.55
194 204 2.226200 CGTGAAACTTCATGCATGGTCA 59.774 45.455 25.97 17.31 39.73 4.02
247 257 2.357517 CACCACACCGCTGTCTCC 60.358 66.667 0.00 0.00 0.00 3.71
248 258 2.842462 ACCACACCGCTGTCTCCA 60.842 61.111 0.00 0.00 0.00 3.86
251 261 1.532604 CCACACCGCTGTCTCCACTA 61.533 60.000 0.00 0.00 0.00 2.74
257 282 1.251527 CGCTGTCTCCACTACCCACT 61.252 60.000 0.00 0.00 0.00 4.00
291 316 2.407340 GGATACTGTCTGATCCCCCT 57.593 55.000 0.00 0.00 36.39 4.79
298 323 2.040043 CTGATCCCCCTGCCTCCT 60.040 66.667 0.00 0.00 0.00 3.69
300 325 3.237741 GATCCCCCTGCCTCCTCG 61.238 72.222 0.00 0.00 0.00 4.63
304 329 3.003173 CCCCTGCCTCCTCGTTGA 61.003 66.667 0.00 0.00 0.00 3.18
330 355 3.647590 GGATATTAGGGGTCCGGTTGTAA 59.352 47.826 0.00 0.00 0.00 2.41
350 375 9.169592 GTTGTAAATACCCTAACATCTTTGCTA 57.830 33.333 0.00 0.00 0.00 3.49
355 380 8.682936 AATACCCTAACATCTTTGCTATTCAG 57.317 34.615 0.00 0.00 0.00 3.02
369 394 2.380064 ATTCAGCCCCAACACTTTGA 57.620 45.000 0.00 0.00 34.24 2.69
380 405 5.351189 CCCCAACACTTTGAAAAGACAAAAG 59.649 40.000 9.71 0.00 38.90 2.27
414 441 2.880770 CACCCAATATGCCGGTGTT 58.119 52.632 1.90 0.00 41.80 3.32
416 443 0.329931 ACCCAATATGCCGGTGTTGA 59.670 50.000 1.90 0.00 0.00 3.18
418 445 2.173782 ACCCAATATGCCGGTGTTGATA 59.826 45.455 1.90 0.00 0.00 2.15
419 446 2.552315 CCCAATATGCCGGTGTTGATAC 59.448 50.000 1.90 0.00 0.00 2.24
420 447 3.210227 CCAATATGCCGGTGTTGATACA 58.790 45.455 1.90 0.00 0.00 2.29
421 448 3.250762 CCAATATGCCGGTGTTGATACAG 59.749 47.826 1.90 0.00 34.24 2.74
445 472 2.973694 AAATTGCCTATTGCCAGCAG 57.026 45.000 0.00 0.00 40.16 4.24
477 504 5.489792 TTTACCAAATTGCCTATTGCCAA 57.510 34.783 0.00 0.00 40.16 4.52
523 550 5.859495 AGGATAAGATAAACTGCTACCAGC 58.141 41.667 0.00 0.00 43.02 4.85
542 570 1.300388 GGTTGGCTGCTGCTGTTTG 60.300 57.895 15.64 0.00 39.59 2.93
543 571 1.438814 GTTGGCTGCTGCTGTTTGT 59.561 52.632 15.64 0.00 39.59 2.83
585 881 8.254508 GGAACCTAGGTGTCATCTTATATCATC 58.745 40.741 17.14 2.76 0.00 2.92
609 910 8.001881 TCTTACTCTTCAGAACCATCTACATC 57.998 38.462 0.00 0.00 33.50 3.06
658 961 3.863142 ATTGTTCAAAGATGCTCTGCC 57.137 42.857 0.00 0.00 0.00 4.85
687 992 4.860802 AACCTATCAACATGTCCCATCA 57.139 40.909 0.00 0.00 0.00 3.07
717 1025 3.243771 ACAGGAAGAACAACTCTACGGTG 60.244 47.826 0.00 0.00 32.46 4.94
751 1059 5.706916 CCAAAGAACTTCTCCATGACAATG 58.293 41.667 0.00 0.00 0.00 2.82
775 1084 2.818751 TCCCATTGATGGTGGTTACC 57.181 50.000 9.07 0.00 46.65 2.85
787 1096 4.906065 GGTGGTTACCGTTTCTTCTTTT 57.094 40.909 0.00 0.00 37.19 2.27
790 1099 5.066893 GGTGGTTACCGTTTCTTCTTTTTCT 59.933 40.000 0.00 0.00 37.19 2.52
791 1100 6.405065 GGTGGTTACCGTTTCTTCTTTTTCTT 60.405 38.462 0.00 0.00 37.19 2.52
793 1102 7.543172 GTGGTTACCGTTTCTTCTTTTTCTTTT 59.457 33.333 0.00 0.00 0.00 2.27
794 1103 8.089597 TGGTTACCGTTTCTTCTTTTTCTTTTT 58.910 29.630 0.00 0.00 0.00 1.94
819 1128 1.370810 CAATGGTGGTTGTTGGGCC 59.629 57.895 0.00 0.00 0.00 5.80
846 1155 4.794439 CATGTGCGCGACGGAGGA 62.794 66.667 12.10 0.00 0.00 3.71
887 1408 2.031870 GCGCTTGGGAGGGAATATTTT 58.968 47.619 0.00 0.00 38.03 1.82
888 1409 2.223805 GCGCTTGGGAGGGAATATTTTG 60.224 50.000 0.00 0.00 38.03 2.44
890 1411 3.699038 CGCTTGGGAGGGAATATTTTGAA 59.301 43.478 0.00 0.00 38.03 2.69
901 1422 7.450074 AGGGAATATTTTGAAAACCACTTTCC 58.550 34.615 0.00 2.17 42.51 3.13
951 2655 1.275573 ACCTACCTTTGAGCCGAGTTC 59.724 52.381 0.00 0.00 0.00 3.01
965 2669 2.400399 CGAGTTCAAGCACGGTTAAGA 58.600 47.619 0.00 0.00 0.00 2.10
979 3006 2.223135 GGTTAAGAAGCGAATCTGCAGC 60.223 50.000 9.47 0.00 37.31 5.25
980 3007 1.656652 TAAGAAGCGAATCTGCAGCC 58.343 50.000 9.47 0.00 37.31 4.85
981 3008 0.035630 AAGAAGCGAATCTGCAGCCT 60.036 50.000 9.47 0.00 37.31 4.58
983 3010 2.320339 GAAGCGAATCTGCAGCCTGC 62.320 60.000 10.45 10.45 45.29 4.85
1000 3027 3.625897 CAGGGACGTGCCAGGTCA 61.626 66.667 28.90 0.00 38.95 4.02
1001 3028 2.607750 AGGGACGTGCCAGGTCAT 60.608 61.111 28.90 2.69 38.95 3.06
1002 3029 2.436646 GGGACGTGCCAGGTCATG 60.437 66.667 22.60 0.00 38.95 3.07
1005 3032 1.965930 GACGTGCCAGGTCATGCAA 60.966 57.895 12.39 0.00 39.57 4.08
1006 3033 1.514678 GACGTGCCAGGTCATGCAAA 61.515 55.000 12.39 0.00 39.57 3.68
1009 3036 1.337074 CGTGCCAGGTCATGCAAAAAT 60.337 47.619 0.00 0.00 39.57 1.82
1011 3038 2.481185 GTGCCAGGTCATGCAAAAATTG 59.519 45.455 0.00 0.00 39.57 2.32
1029 3564 1.448985 TGACTATGGCGCAAAAGGAC 58.551 50.000 10.83 2.58 0.00 3.85
1446 3987 4.388499 TTCTTCTCGTGGCCGGCC 62.388 66.667 39.40 39.40 33.95 6.13
1512 4053 2.182842 GCCCGCGCTCATCTTCAAT 61.183 57.895 5.56 0.00 0.00 2.57
1590 4149 2.038952 GCACCTCCCATATGCTCATGTA 59.961 50.000 0.00 0.00 36.40 2.29
1614 4269 6.327177 TCAATTCAACGTAGCGAAATAGTC 57.673 37.500 0.00 0.00 0.00 2.59
1615 4270 6.097356 TCAATTCAACGTAGCGAAATAGTCT 58.903 36.000 0.00 0.00 0.00 3.24
1616 4271 5.950965 ATTCAACGTAGCGAAATAGTCTG 57.049 39.130 0.00 0.00 0.00 3.51
1617 4272 3.176708 TCAACGTAGCGAAATAGTCTGC 58.823 45.455 0.00 0.00 0.00 4.26
1686 4343 0.811915 CTCGGAAGGACACGATCACT 59.188 55.000 0.00 0.00 38.56 3.41
1698 4355 0.033504 CGATCACTTACATCCCGGGG 59.966 60.000 23.50 6.77 0.00 5.73
1747 5892 1.002990 TCGTACCTGCAGGAGACGA 60.003 57.895 39.38 39.38 46.44 4.20
1964 6115 4.180946 CGAGTCCGACTGCTCCCG 62.181 72.222 5.57 0.00 38.22 5.14
2473 6642 0.036388 GGCGGTGAAGAATGTGAGGA 60.036 55.000 0.00 0.00 0.00 3.71
2580 6749 1.079127 ATGTTAAGCTGCGCCGACT 60.079 52.632 4.18 0.00 0.00 4.18
2597 6766 4.838152 TGATCGGCCTGAAGCGCC 62.838 66.667 2.29 0.00 45.17 6.53
2638 6807 5.536554 AACGAATGCAGTTCAGTTCATAG 57.463 39.130 0.00 0.00 36.60 2.23
2639 6808 3.935203 ACGAATGCAGTTCAGTTCATAGG 59.065 43.478 0.00 0.00 36.60 2.57
2640 6809 4.183865 CGAATGCAGTTCAGTTCATAGGA 58.816 43.478 0.00 0.00 36.60 2.94
2646 7182 6.913170 TGCAGTTCAGTTCATAGGATTTTTC 58.087 36.000 0.00 0.00 0.00 2.29
2654 7190 8.786898 TCAGTTCATAGGATTTTTCTGTCTTTG 58.213 33.333 0.00 0.00 0.00 2.77
2656 7192 9.793259 AGTTCATAGGATTTTTCTGTCTTTGTA 57.207 29.630 0.00 0.00 0.00 2.41
2669 7439 8.589335 TTCTGTCTTTGTATGTCTTTGTACTC 57.411 34.615 0.00 0.00 0.00 2.59
2673 7443 7.652105 TGTCTTTGTATGTCTTTGTACTCTGTC 59.348 37.037 0.00 0.00 0.00 3.51
2674 7444 7.652105 GTCTTTGTATGTCTTTGTACTCTGTCA 59.348 37.037 0.00 0.00 0.00 3.58
2681 7451 6.447162 TGTCTTTGTACTCTGTCATGTGTAG 58.553 40.000 0.00 0.00 0.00 2.74
2688 7458 5.122512 ACTCTGTCATGTGTAGTGTGTAC 57.877 43.478 0.00 0.00 0.00 2.90
2689 7459 4.022242 ACTCTGTCATGTGTAGTGTGTACC 60.022 45.833 0.00 0.00 0.00 3.34
2694 7467 6.999950 TGTCATGTGTAGTGTGTACCTAATT 58.000 36.000 0.00 0.00 0.00 1.40
2710 7483 5.324409 ACCTAATTGCCATCAAAAGTCAGA 58.676 37.500 0.00 0.00 35.56 3.27
2773 7584 4.259690 GGCTAACACGTTATCAACACGATC 60.260 45.833 0.00 0.00 40.20 3.69
2789 7600 1.678627 CGATCCTCTCAAGACCGTCAT 59.321 52.381 0.40 0.00 0.00 3.06
2798 7609 1.462283 CAAGACCGTCATGAAGTGCAG 59.538 52.381 7.88 0.00 0.00 4.41
2810 7621 5.583457 TCATGAAGTGCAGTTACATCATCAG 59.417 40.000 6.80 0.00 37.01 2.90
2833 7644 7.665145 TCAGAGAACATTTTATTCACCACATCA 59.335 33.333 0.00 0.00 0.00 3.07
2834 7645 8.464404 CAGAGAACATTTTATTCACCACATCAT 58.536 33.333 0.00 0.00 0.00 2.45
2835 7646 9.028284 AGAGAACATTTTATTCACCACATCATT 57.972 29.630 0.00 0.00 0.00 2.57
2904 7716 3.004326 GCCCGTGCATTGCAATGGA 62.004 57.895 34.23 31.05 41.47 3.41
2906 7718 1.597797 CCCGTGCATTGCAATGGAGT 61.598 55.000 34.23 2.32 41.47 3.85
2907 7719 1.093972 CCGTGCATTGCAATGGAGTA 58.906 50.000 34.23 11.24 41.47 2.59
2908 7720 1.677576 CCGTGCATTGCAATGGAGTAT 59.322 47.619 34.23 0.72 41.47 2.12
2909 7721 2.877786 CCGTGCATTGCAATGGAGTATA 59.122 45.455 34.23 0.00 41.47 1.47
2910 7722 3.058708 CCGTGCATTGCAATGGAGTATAG 60.059 47.826 34.23 21.27 41.47 1.31
2915 7727 5.413523 TGCATTGCAATGGAGTATAGCATAG 59.586 40.000 34.23 9.90 34.76 2.23
2919 7913 9.170734 CATTGCAATGGAGTATAGCATAGTATT 57.829 33.333 28.34 0.00 34.87 1.89
2935 7929 9.672673 AGCATAGTATTATATTGGTCCAACATC 57.327 33.333 6.41 0.00 0.00 3.06
2936 7930 9.448438 GCATAGTATTATATTGGTCCAACATCA 57.552 33.333 6.41 0.00 0.00 3.07
2949 7943 5.347342 GTCCAACATCAATTGTGTTTGACA 58.653 37.500 28.64 12.68 44.82 3.58
2951 7945 7.144661 GTCCAACATCAATTGTGTTTGACATA 58.855 34.615 28.64 12.05 44.82 2.29
2953 7947 9.018582 TCCAACATCAATTGTGTTTGACATATA 57.981 29.630 17.97 2.75 38.37 0.86
2957 8008 9.230122 ACATCAATTGTGTTTGACATATACTCA 57.770 29.630 5.13 0.00 38.37 3.41
2961 8012 8.720562 CAATTGTGTTTGACATATACTCACTCA 58.279 33.333 0.00 0.00 33.40 3.41
2981 8032 7.233962 TCACTCAGTTCCTTTATACAAGGTGTA 59.766 37.037 11.23 0.00 38.55 2.90
3054 8108 6.321945 TCCCCGTAATTTTATTTTTAGCCCTC 59.678 38.462 0.00 0.00 0.00 4.30
3055 8109 6.322969 CCCCGTAATTTTATTTTTAGCCCTCT 59.677 38.462 0.00 0.00 0.00 3.69
3068 8122 8.721133 TTTTTAGCCCTCTAGAAAAAGGAAAT 57.279 30.769 0.00 0.00 34.35 2.17
3098 8159 9.433153 CTGATTACATGTATATCTCATTGCAGT 57.567 33.333 19.63 0.00 0.00 4.40
3131 8192 8.722622 AAGGAAAAGTATCTCTATCCCGATTA 57.277 34.615 0.00 0.00 34.65 1.75
3133 8194 7.728981 AGGAAAAGTATCTCTATCCCGATTACA 59.271 37.037 0.00 0.00 34.65 2.41
3136 8197 8.423906 AAAGTATCTCTATCCCGATTACATGT 57.576 34.615 2.69 2.69 0.00 3.21
3148 8209 6.326583 TCCCGATTACATGTATCTCTTCCTTT 59.673 38.462 6.36 0.00 0.00 3.11
3150 8211 6.647067 CCGATTACATGTATCTCTTCCTTTCC 59.353 42.308 6.36 0.00 0.00 3.13
3151 8212 6.647067 CGATTACATGTATCTCTTCCTTTCCC 59.353 42.308 6.36 0.00 0.00 3.97
3152 8213 6.884472 TTACATGTATCTCTTCCTTTCCCA 57.116 37.500 6.36 0.00 0.00 4.37
3153 8214 5.983333 ACATGTATCTCTTCCTTTCCCAT 57.017 39.130 0.00 0.00 0.00 4.00
3154 8215 5.688807 ACATGTATCTCTTCCTTTCCCATG 58.311 41.667 0.00 0.00 34.75 3.66
3156 8217 5.779241 TGTATCTCTTCCTTTCCCATGTT 57.221 39.130 0.00 0.00 0.00 2.71
3157 8218 6.139679 TGTATCTCTTCCTTTCCCATGTTT 57.860 37.500 0.00 0.00 0.00 2.83
3162 8223 6.552008 TCTCTTCCTTTCCCATGTTTAATGT 58.448 36.000 0.00 0.00 0.00 2.71
3167 8228 9.203421 CTTCCTTTCCCATGTTTAATGTTTTAC 57.797 33.333 0.00 0.00 0.00 2.01
3186 8247 8.447833 TGTTTTACTTGCCGATAATCAACTAAG 58.552 33.333 0.00 0.00 0.00 2.18
3187 8248 7.548196 TTTACTTGCCGATAATCAACTAAGG 57.452 36.000 0.00 0.00 0.00 2.69
3193 8262 6.228258 TGCCGATAATCAACTAAGGGTAATC 58.772 40.000 0.00 0.00 0.00 1.75
3198 8267 8.509690 CGATAATCAACTAAGGGTAATCTCGTA 58.490 37.037 0.00 0.00 0.00 3.43
3199 8268 9.623350 GATAATCAACTAAGGGTAATCTCGTAC 57.377 37.037 0.00 0.00 0.00 3.67
3201 8270 8.757982 AATCAACTAAGGGTAATCTCGTACTA 57.242 34.615 0.00 0.00 0.00 1.82
3206 8275 8.393671 ACTAAGGGTAATCTCGTACTAGATTG 57.606 38.462 25.27 13.41 44.15 2.67
3229 8298 7.360113 TGTCTATAGTTATGTGCCTTGATCA 57.640 36.000 0.00 0.00 0.00 2.92
3235 8304 2.519771 ATGTGCCTTGATCACCATGT 57.480 45.000 0.00 0.00 33.71 3.21
3237 8306 1.073603 TGTGCCTTGATCACCATGTCA 59.926 47.619 0.00 0.00 33.71 3.58
3269 8338 9.975218 AATACACCTTACATAAAGAAATGGAGT 57.025 29.630 0.00 0.00 37.38 3.85
3271 8340 8.788325 ACACCTTACATAAAGAAATGGAGTAC 57.212 34.615 0.00 0.00 37.38 2.73
3272 8341 7.827729 ACACCTTACATAAAGAAATGGAGTACC 59.172 37.037 0.00 0.00 37.38 3.34
3280 8354 9.462606 CATAAAGAAATGGAGTACCTTAAACCT 57.537 33.333 0.00 0.00 37.04 3.50
3289 8363 8.396619 TGGAGTACCTTAAACCTACCATATTT 57.603 34.615 0.00 0.00 37.04 1.40
3341 8415 3.910627 AGTATGGCTAGGGGAATACAAGG 59.089 47.826 0.00 0.00 0.00 3.61
3346 8420 3.202373 GGCTAGGGGAATACAAGGAAAGT 59.798 47.826 0.00 0.00 0.00 2.66
3347 8421 4.325109 GGCTAGGGGAATACAAGGAAAGTT 60.325 45.833 0.00 0.00 0.00 2.66
3356 8430 9.990360 GGGAATACAAGGAAAGTTTTGATTTAA 57.010 29.630 0.00 0.00 0.00 1.52
3400 8474 7.493499 TGATTTGATTTGATTTGGGTATGGT 57.507 32.000 0.00 0.00 0.00 3.55
3408 8482 3.461831 TGATTTGGGTATGGTAGGGAAGG 59.538 47.826 0.00 0.00 0.00 3.46
3414 8488 1.002087 GTATGGTAGGGAAGGCGATGG 59.998 57.143 0.00 0.00 0.00 3.51
3420 8494 2.103153 AGGGAAGGCGATGGAAGATA 57.897 50.000 0.00 0.00 0.00 1.98
3421 8495 1.974236 AGGGAAGGCGATGGAAGATAG 59.026 52.381 0.00 0.00 0.00 2.08
3439 8515 2.100605 AGCTAAGGTTTGAGGCTTCG 57.899 50.000 0.00 0.00 0.00 3.79
3446 8522 2.074576 GGTTTGAGGCTTCGGTAAGAC 58.925 52.381 0.00 0.00 41.53 3.01
3454 8530 4.342352 GGCTTCGGTAAGACTTGATTTG 57.658 45.455 0.00 0.00 37.79 2.32
3474 8550 8.525316 TGATTTGATTTGACTGAGTTAATGCAT 58.475 29.630 0.00 0.00 0.00 3.96
3487 8563 7.828712 TGAGTTAATGCATGACATGATTTTCA 58.171 30.769 19.76 14.48 39.60 2.69
3525 8601 7.514721 AGTAGGACAAGGAAATGAAAGTAACA 58.485 34.615 0.00 0.00 0.00 2.41
3554 8630 7.647827 TGGTTTAGATTATTCCAAATCAGGGA 58.352 34.615 0.00 0.00 38.16 4.20
3555 8631 7.779798 TGGTTTAGATTATTCCAAATCAGGGAG 59.220 37.037 0.00 0.00 38.16 4.30
3559 8635 2.000290 ATTCCAAATCAGGGAGGGGA 58.000 50.000 0.00 0.00 35.46 4.81
3560 8636 1.766951 TTCCAAATCAGGGAGGGGAA 58.233 50.000 0.00 0.00 35.46 3.97
3561 8637 2.000290 TCCAAATCAGGGAGGGGAAT 58.000 50.000 0.00 0.00 0.00 3.01
3563 8639 1.412074 CCAAATCAGGGAGGGGAATGG 60.412 57.143 0.00 0.00 0.00 3.16
3564 8640 1.570501 CAAATCAGGGAGGGGAATGGA 59.429 52.381 0.00 0.00 0.00 3.41
3567 8643 0.421495 TCAGGGAGGGGAATGGAGAA 59.579 55.000 0.00 0.00 0.00 2.87
3568 8644 0.842635 CAGGGAGGGGAATGGAGAAG 59.157 60.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.413239 CGACGAACTTCAAAGCATGCAT 60.413 45.455 21.98 4.57 0.00 3.96
1 2 1.069973 CGACGAACTTCAAAGCATGCA 60.070 47.619 21.98 0.00 0.00 3.96
2 3 1.194547 TCGACGAACTTCAAAGCATGC 59.805 47.619 10.51 10.51 0.00 4.06
3 4 2.723010 GCTCGACGAACTTCAAAGCATG 60.723 50.000 0.00 0.00 0.00 4.06
4 5 1.461127 GCTCGACGAACTTCAAAGCAT 59.539 47.619 0.00 0.00 0.00 3.79
5 6 0.859232 GCTCGACGAACTTCAAAGCA 59.141 50.000 0.00 0.00 0.00 3.91
6 7 0.164002 GGCTCGACGAACTTCAAAGC 59.836 55.000 0.00 0.00 0.00 3.51
7 8 1.457303 CTGGCTCGACGAACTTCAAAG 59.543 52.381 0.00 0.00 0.00 2.77
8 9 1.497991 CTGGCTCGACGAACTTCAAA 58.502 50.000 0.00 0.00 0.00 2.69
9 10 0.319555 CCTGGCTCGACGAACTTCAA 60.320 55.000 0.00 0.00 0.00 2.69
10 11 1.289066 CCTGGCTCGACGAACTTCA 59.711 57.895 0.00 0.00 0.00 3.02
12 13 0.106149 AAACCTGGCTCGACGAACTT 59.894 50.000 0.00 0.00 0.00 2.66
14 15 0.234884 CAAAACCTGGCTCGACGAAC 59.765 55.000 0.00 0.00 0.00 3.95
15 16 0.882927 CCAAAACCTGGCTCGACGAA 60.883 55.000 0.00 0.00 38.76 3.85
16 17 1.301401 CCAAAACCTGGCTCGACGA 60.301 57.895 0.00 0.00 38.76 4.20
17 18 0.673644 ATCCAAAACCTGGCTCGACG 60.674 55.000 0.00 0.00 45.98 5.12
18 19 0.804989 CATCCAAAACCTGGCTCGAC 59.195 55.000 0.00 0.00 45.98 4.20
19 20 0.960364 GCATCCAAAACCTGGCTCGA 60.960 55.000 0.00 0.00 45.98 4.04
20 21 1.508088 GCATCCAAAACCTGGCTCG 59.492 57.895 0.00 0.00 45.98 5.03
21 22 1.508088 CGCATCCAAAACCTGGCTC 59.492 57.895 0.00 0.00 45.98 4.70
22 23 1.978617 CCGCATCCAAAACCTGGCT 60.979 57.895 0.00 0.00 45.98 4.75
25 26 2.573340 GGCCGCATCCAAAACCTG 59.427 61.111 0.00 0.00 0.00 4.00
26 27 2.679996 GGGCCGCATCCAAAACCT 60.680 61.111 0.00 0.00 0.00 3.50
28 29 1.976474 TCTGGGCCGCATCCAAAAC 60.976 57.895 0.00 0.00 33.36 2.43
29 30 1.976474 GTCTGGGCCGCATCCAAAA 60.976 57.895 0.00 0.00 33.36 2.44
30 31 2.361104 GTCTGGGCCGCATCCAAA 60.361 61.111 0.00 0.00 33.36 3.28
31 32 3.203086 TTGTCTGGGCCGCATCCAA 62.203 57.895 0.00 0.00 33.36 3.53
32 33 3.645660 TTGTCTGGGCCGCATCCA 61.646 61.111 0.00 0.00 0.00 3.41
34 35 3.134127 GGTTGTCTGGGCCGCATC 61.134 66.667 0.00 0.00 0.00 3.91
36 37 3.723097 TTTGGTTGTCTGGGCCGCA 62.723 57.895 0.00 0.00 0.00 5.69
37 38 2.909965 TTTGGTTGTCTGGGCCGC 60.910 61.111 0.00 0.00 0.00 6.53
40 41 3.088532 TGATATGTTTGGTTGTCTGGGC 58.911 45.455 0.00 0.00 0.00 5.36
41 42 4.588899 TCTGATATGTTTGGTTGTCTGGG 58.411 43.478 0.00 0.00 0.00 4.45
43 44 7.621428 AGAATCTGATATGTTTGGTTGTCTG 57.379 36.000 0.00 0.00 0.00 3.51
44 45 8.105829 AGAAGAATCTGATATGTTTGGTTGTCT 58.894 33.333 0.00 0.00 33.59 3.41
45 46 8.273780 AGAAGAATCTGATATGTTTGGTTGTC 57.726 34.615 0.00 0.00 33.59 3.18
46 47 7.065085 CGAGAAGAATCTGATATGTTTGGTTGT 59.935 37.037 0.00 0.00 35.54 3.32
47 48 7.065085 ACGAGAAGAATCTGATATGTTTGGTTG 59.935 37.037 0.00 0.00 35.54 3.77
48 49 7.065085 CACGAGAAGAATCTGATATGTTTGGTT 59.935 37.037 0.00 0.00 35.54 3.67
49 50 6.536582 CACGAGAAGAATCTGATATGTTTGGT 59.463 38.462 0.00 0.00 35.54 3.67
50 51 6.510799 GCACGAGAAGAATCTGATATGTTTGG 60.511 42.308 0.00 0.00 35.54 3.28
51 52 6.417327 GCACGAGAAGAATCTGATATGTTTG 58.583 40.000 0.00 0.00 35.54 2.93
53 54 4.742167 CGCACGAGAAGAATCTGATATGTT 59.258 41.667 0.00 0.00 35.54 2.71
56 57 3.858877 GCCGCACGAGAAGAATCTGATAT 60.859 47.826 0.00 0.00 35.54 1.63
57 58 2.543861 GCCGCACGAGAAGAATCTGATA 60.544 50.000 0.00 0.00 35.54 2.15
58 59 1.804372 GCCGCACGAGAAGAATCTGAT 60.804 52.381 0.00 0.00 35.54 2.90
59 60 0.458543 GCCGCACGAGAAGAATCTGA 60.459 55.000 0.00 0.00 35.54 3.27
61 62 1.153549 GGCCGCACGAGAAGAATCT 60.154 57.895 0.00 0.00 39.10 2.40
62 63 2.174319 GGGCCGCACGAGAAGAATC 61.174 63.158 0.00 0.00 0.00 2.52
63 64 2.125106 GGGCCGCACGAGAAGAAT 60.125 61.111 0.00 0.00 0.00 2.40
64 65 3.311110 AGGGCCGCACGAGAAGAA 61.311 61.111 0.00 0.00 0.00 2.52
79 80 1.039233 GTGCATCCATCCCAACCAGG 61.039 60.000 0.00 0.00 37.03 4.45
80 81 1.378882 CGTGCATCCATCCCAACCAG 61.379 60.000 0.00 0.00 0.00 4.00
81 82 1.378382 CGTGCATCCATCCCAACCA 60.378 57.895 0.00 0.00 0.00 3.67
82 83 2.774799 GCGTGCATCCATCCCAACC 61.775 63.158 0.00 0.00 0.00 3.77
83 84 1.594194 TTGCGTGCATCCATCCCAAC 61.594 55.000 0.00 0.00 0.00 3.77
84 85 0.683828 ATTGCGTGCATCCATCCCAA 60.684 50.000 0.00 0.00 0.00 4.12
85 86 1.076850 ATTGCGTGCATCCATCCCA 60.077 52.632 0.00 0.00 0.00 4.37
86 87 1.102809 TGATTGCGTGCATCCATCCC 61.103 55.000 0.00 0.00 0.00 3.85
89 90 1.467883 CGTTTGATTGCGTGCATCCAT 60.468 47.619 0.00 0.00 0.00 3.41
90 91 0.109827 CGTTTGATTGCGTGCATCCA 60.110 50.000 0.00 0.00 0.00 3.41
91 92 1.405469 GCGTTTGATTGCGTGCATCC 61.405 55.000 0.00 0.00 0.00 3.51
92 93 1.983160 GCGTTTGATTGCGTGCATC 59.017 52.632 0.00 0.00 0.00 3.91
93 94 4.151417 GCGTTTGATTGCGTGCAT 57.849 50.000 0.00 0.00 0.00 3.96
99 100 0.109504 TTAAGGGCGCGTTTGATTGC 60.110 50.000 8.43 0.00 0.00 3.56
101 102 1.883926 ACTTTAAGGGCGCGTTTGATT 59.116 42.857 8.43 0.00 0.00 2.57
102 103 1.530323 ACTTTAAGGGCGCGTTTGAT 58.470 45.000 8.43 0.00 0.00 2.57
103 104 2.166821 TACTTTAAGGGCGCGTTTGA 57.833 45.000 8.43 0.00 0.00 2.69
104 105 2.676342 AGATACTTTAAGGGCGCGTTTG 59.324 45.455 8.43 0.00 0.00 2.93
105 106 2.934553 GAGATACTTTAAGGGCGCGTTT 59.065 45.455 8.43 0.00 0.00 3.60
106 107 2.167900 AGAGATACTTTAAGGGCGCGTT 59.832 45.455 8.43 0.00 0.00 4.84
107 108 1.755380 AGAGATACTTTAAGGGCGCGT 59.245 47.619 8.43 0.00 0.00 6.01
108 109 2.510768 AGAGATACTTTAAGGGCGCG 57.489 50.000 0.00 0.00 0.00 6.86
142 143 4.440112 GGGCGAGTTCCCAAAAATATCAAG 60.440 45.833 0.00 0.00 45.82 3.02
143 144 3.445805 GGGCGAGTTCCCAAAAATATCAA 59.554 43.478 0.00 0.00 45.82 2.57
144 145 3.020984 GGGCGAGTTCCCAAAAATATCA 58.979 45.455 0.00 0.00 45.82 2.15
154 157 1.162698 GTGTTTTAGGGCGAGTTCCC 58.837 55.000 0.00 0.00 46.93 3.97
160 163 1.598601 GTTTCACGTGTTTTAGGGCGA 59.401 47.619 16.51 0.00 0.00 5.54
162 165 3.065648 TGAAGTTTCACGTGTTTTAGGGC 59.934 43.478 16.51 0.69 31.01 5.19
172 175 2.226437 GACCATGCATGAAGTTTCACGT 59.774 45.455 28.31 13.29 40.49 4.49
174 177 3.568538 GTGACCATGCATGAAGTTTCAC 58.431 45.455 28.31 22.94 40.49 3.18
239 249 0.247736 CAGTGGGTAGTGGAGACAGC 59.752 60.000 0.00 0.00 44.46 4.40
298 323 2.969950 CCCCTAATATCCACCTCAACGA 59.030 50.000 0.00 0.00 0.00 3.85
300 325 3.072622 GGACCCCTAATATCCACCTCAAC 59.927 52.174 0.00 0.00 32.35 3.18
304 329 1.484446 CCGGACCCCTAATATCCACCT 60.484 57.143 0.00 0.00 32.35 4.00
307 332 2.051692 CAACCGGACCCCTAATATCCA 58.948 52.381 9.46 0.00 32.35 3.41
314 339 2.771372 GGTATTTACAACCGGACCCCTA 59.229 50.000 9.46 0.00 0.00 3.53
330 355 8.682936 CTGAATAGCAAAGATGTTAGGGTATT 57.317 34.615 9.79 9.79 35.55 1.89
350 375 2.380064 TCAAAGTGTTGGGGCTGAAT 57.620 45.000 0.00 0.00 35.29 2.57
355 380 2.167487 TGTCTTTTCAAAGTGTTGGGGC 59.833 45.455 0.00 0.00 37.31 5.80
356 381 4.464069 TTGTCTTTTCAAAGTGTTGGGG 57.536 40.909 0.00 0.00 37.31 4.96
414 441 8.378172 GCAATAGGCAATTTAGTACTGTATCA 57.622 34.615 5.39 0.00 43.97 2.15
445 472 4.627035 GGCAATTTGGTAAAATCAGTCAGC 59.373 41.667 0.00 0.00 34.84 4.26
477 504 6.876257 CCTTAAGTCTAAAATCACTCTGCTGT 59.124 38.462 0.97 0.00 0.00 4.40
523 550 2.848858 AAACAGCAGCAGCCAACCG 61.849 57.895 0.00 0.00 43.56 4.44
542 570 3.993736 GGTTCCATATTTGCCAAACACAC 59.006 43.478 0.00 0.00 0.00 3.82
543 571 3.900601 AGGTTCCATATTTGCCAAACACA 59.099 39.130 0.00 0.00 0.00 3.72
585 881 8.006298 AGATGTAGATGGTTCTGAAGAGTAAG 57.994 38.462 0.00 0.00 33.17 2.34
609 910 6.702329 ACTCACACTAGGTAAATCCTTCAAG 58.298 40.000 0.00 0.00 45.67 3.02
658 961 7.106239 GGGACATGTTGATAGGTTATCTATGG 58.894 42.308 0.00 0.00 38.71 2.74
687 992 5.782845 AGAGTTGTTCTTCCTGTCCTAGAAT 59.217 40.000 0.00 0.00 29.61 2.40
793 1102 2.472029 ACAACCACCATTGTCCCAAAA 58.528 42.857 0.00 0.00 38.44 2.44
794 1103 2.166907 ACAACCACCATTGTCCCAAA 57.833 45.000 0.00 0.00 38.44 3.28
795 1104 1.759445 CAACAACCACCATTGTCCCAA 59.241 47.619 0.00 0.00 42.01 4.12
796 1105 1.407936 CAACAACCACCATTGTCCCA 58.592 50.000 0.00 0.00 42.01 4.37
797 1106 0.678950 CCAACAACCACCATTGTCCC 59.321 55.000 0.00 0.00 42.01 4.46
798 1107 0.678950 CCCAACAACCACCATTGTCC 59.321 55.000 0.00 0.00 42.01 4.02
799 1108 0.033366 GCCCAACAACCACCATTGTC 59.967 55.000 0.00 0.00 42.01 3.18
800 1109 1.406860 GGCCCAACAACCACCATTGT 61.407 55.000 0.00 0.00 44.76 2.71
812 1121 0.390209 ATGTACGTACACGGCCCAAC 60.390 55.000 29.54 0.22 44.95 3.77
819 1128 1.339134 GCGCACATGTACGTACACG 59.661 57.895 29.54 26.35 46.33 4.49
846 1155 0.907704 TATCGACAGCCAACCACCCT 60.908 55.000 0.00 0.00 0.00 4.34
887 1408 3.558033 GGTACAGGGAAAGTGGTTTTCA 58.442 45.455 0.00 0.00 45.70 2.69
888 1409 2.889045 GGGTACAGGGAAAGTGGTTTTC 59.111 50.000 0.00 0.00 43.64 2.29
890 1411 2.141067 AGGGTACAGGGAAAGTGGTTT 58.859 47.619 0.00 0.00 0.00 3.27
901 1422 2.158370 ACCAAAGGGAAAAGGGTACAGG 60.158 50.000 0.00 0.00 38.05 4.00
951 2655 1.144969 TCGCTTCTTAACCGTGCTTG 58.855 50.000 0.00 0.00 0.00 4.01
965 2669 2.404995 GCAGGCTGCAGATTCGCTT 61.405 57.895 33.33 0.00 44.26 4.68
983 3010 2.959484 ATGACCTGGCACGTCCCTG 61.959 63.158 12.99 0.00 0.00 4.45
984 3011 2.607750 ATGACCTGGCACGTCCCT 60.608 61.111 12.99 0.00 0.00 4.20
986 3013 3.127533 GCATGACCTGGCACGTCC 61.128 66.667 12.99 0.00 0.00 4.79
987 3014 1.514678 TTTGCATGACCTGGCACGTC 61.515 55.000 9.35 9.35 40.23 4.34
988 3015 1.106351 TTTTGCATGACCTGGCACGT 61.106 50.000 0.00 0.00 40.23 4.49
989 3016 0.031857 TTTTTGCATGACCTGGCACG 59.968 50.000 0.00 0.00 40.23 5.34
990 3017 2.460757 ATTTTTGCATGACCTGGCAC 57.539 45.000 0.00 0.00 40.23 5.01
992 3019 2.738314 GTCAATTTTTGCATGACCTGGC 59.262 45.455 6.17 0.00 37.97 4.85
994 3021 5.808540 CCATAGTCAATTTTTGCATGACCTG 59.191 40.000 12.60 10.65 43.46 4.00
995 3022 5.625197 GCCATAGTCAATTTTTGCATGACCT 60.625 40.000 12.60 4.77 43.46 3.85
998 3025 4.422840 CGCCATAGTCAATTTTTGCATGA 58.577 39.130 0.00 0.00 0.00 3.07
999 3026 3.000523 GCGCCATAGTCAATTTTTGCATG 59.999 43.478 0.00 0.00 0.00 4.06
1000 3027 3.189285 GCGCCATAGTCAATTTTTGCAT 58.811 40.909 0.00 0.00 0.00 3.96
1001 3028 2.029560 TGCGCCATAGTCAATTTTTGCA 60.030 40.909 4.18 0.00 0.00 4.08
1002 3029 2.605030 TGCGCCATAGTCAATTTTTGC 58.395 42.857 4.18 0.00 0.00 3.68
1005 3032 4.021544 TCCTTTTGCGCCATAGTCAATTTT 60.022 37.500 4.18 0.00 0.00 1.82
1006 3033 3.509575 TCCTTTTGCGCCATAGTCAATTT 59.490 39.130 4.18 0.00 0.00 1.82
1009 3036 1.810151 GTCCTTTTGCGCCATAGTCAA 59.190 47.619 4.18 0.00 0.00 3.18
1011 3038 0.373716 CGTCCTTTTGCGCCATAGTC 59.626 55.000 4.18 0.00 0.00 2.59
1108 3649 4.131088 GAGGTGCGTCTCGGGGAC 62.131 72.222 0.00 0.00 41.28 4.46
1468 4009 0.109412 CAGAAGGACACGTACGGGAC 60.109 60.000 27.01 18.96 0.00 4.46
1512 4053 1.632409 AGGTGGACGTGGTAGTAGAGA 59.368 52.381 0.00 0.00 0.00 3.10
1590 4149 6.757010 AGACTATTTCGCTACGTTGAATTGAT 59.243 34.615 0.00 0.00 0.00 2.57
1686 4343 3.413300 GGCACCCCCGGGATGTAA 61.413 66.667 26.32 0.00 38.96 2.41
1727 5872 1.136984 GTCTCCTGCAGGTACGACG 59.863 63.158 31.58 14.06 36.34 5.12
2580 6749 4.838152 GGCGCTTCAGGCCGATCA 62.838 66.667 7.64 0.00 41.39 2.92
2623 6792 7.025963 CAGAAAAATCCTATGAACTGAACTGC 58.974 38.462 0.00 0.00 0.00 4.40
2634 6803 9.994432 GACATACAAAGACAGAAAAATCCTATG 57.006 33.333 0.00 0.00 0.00 2.23
2638 6807 9.185192 CAAAGACATACAAAGACAGAAAAATCC 57.815 33.333 0.00 0.00 0.00 3.01
2639 6808 9.736023 ACAAAGACATACAAAGACAGAAAAATC 57.264 29.630 0.00 0.00 0.00 2.17
2646 7182 7.653713 ACAGAGTACAAAGACATACAAAGACAG 59.346 37.037 0.00 0.00 0.00 3.51
2654 7190 6.868864 ACACATGACAGAGTACAAAGACATAC 59.131 38.462 0.00 0.00 0.00 2.39
2656 7192 5.858381 ACACATGACAGAGTACAAAGACAT 58.142 37.500 0.00 0.00 0.00 3.06
2657 7193 5.276461 ACACATGACAGAGTACAAAGACA 57.724 39.130 0.00 0.00 0.00 3.41
2658 7194 6.363626 CACTACACATGACAGAGTACAAAGAC 59.636 42.308 0.00 0.00 0.00 3.01
2669 7439 4.521130 AGGTACACACTACACATGACAG 57.479 45.455 0.00 0.00 0.00 3.51
2673 7443 5.064707 GGCAATTAGGTACACACTACACATG 59.935 44.000 0.00 0.00 0.00 3.21
2674 7444 5.183228 GGCAATTAGGTACACACTACACAT 58.817 41.667 0.00 0.00 0.00 3.21
2681 7451 5.637006 TTTGATGGCAATTAGGTACACAC 57.363 39.130 0.00 0.00 33.25 3.82
2688 7458 5.902613 TCTGACTTTTGATGGCAATTAGG 57.097 39.130 0.00 0.00 33.25 2.69
2689 7459 8.767478 AAAATCTGACTTTTGATGGCAATTAG 57.233 30.769 0.00 0.00 33.25 1.73
2694 7467 6.183360 ACAGAAAAATCTGACTTTTGATGGCA 60.183 34.615 12.46 0.00 39.99 4.92
2773 7584 2.232452 ACTTCATGACGGTCTTGAGAGG 59.768 50.000 21.27 17.80 33.06 3.69
2789 7600 5.047092 TCTCTGATGATGTAACTGCACTTCA 60.047 40.000 0.00 0.00 37.11 3.02
2810 7621 9.643693 AAATGATGTGGTGAATAAAATGTTCTC 57.356 29.630 0.00 0.00 0.00 2.87
2887 7699 1.140161 CTCCATTGCAATGCACGGG 59.860 57.895 30.15 18.30 38.71 5.28
2909 7721 9.672673 GATGTTGGACCAATATAATACTATGCT 57.327 33.333 15.72 0.00 0.00 3.79
2910 7722 9.448438 TGATGTTGGACCAATATAATACTATGC 57.552 33.333 15.72 2.27 0.00 3.14
2919 7913 7.953005 ACACAATTGATGTTGGACCAATATA 57.047 32.000 15.72 2.94 41.46 0.86
2921 7915 6.662865 AACACAATTGATGTTGGACCAATA 57.337 33.333 13.59 8.36 41.46 1.90
2922 7916 5.549742 AACACAATTGATGTTGGACCAAT 57.450 34.783 13.59 0.00 41.46 3.16
2929 7923 9.844790 AGTATATGTCAAACACAATTGATGTTG 57.155 29.630 19.95 15.62 41.46 3.33
2935 7929 8.720562 TGAGTGAGTATATGTCAAACACAATTG 58.279 33.333 3.24 3.24 38.97 2.32
2936 7930 8.846943 TGAGTGAGTATATGTCAAACACAATT 57.153 30.769 0.00 0.00 38.97 2.32
2938 7932 7.441836 ACTGAGTGAGTATATGTCAAACACAA 58.558 34.615 0.00 0.00 33.35 3.33
2939 7933 6.993079 ACTGAGTGAGTATATGTCAAACACA 58.007 36.000 0.00 0.00 33.94 3.72
2940 7934 7.063544 GGAACTGAGTGAGTATATGTCAAACAC 59.936 40.741 0.00 0.00 33.09 3.32
2951 7945 8.478877 CCTTGTATAAAGGAACTGAGTGAGTAT 58.521 37.037 0.00 0.00 40.86 2.12
2953 7947 6.270231 ACCTTGTATAAAGGAACTGAGTGAGT 59.730 38.462 11.02 0.00 40.86 3.41
2957 8008 6.435292 ACACCTTGTATAAAGGAACTGAGT 57.565 37.500 11.02 0.00 40.86 3.41
2974 8025 9.995003 TGCAATTTTATCAGAAAAATACACCTT 57.005 25.926 0.00 0.00 37.93 3.50
2988 8042 8.033626 TGCATCTTACATTGTGCAATTTTATCA 58.966 29.630 0.00 0.00 43.83 2.15
3026 8080 7.988599 GGGCTAAAAATAAAATTACGGGGAATT 59.011 33.333 0.00 0.00 0.00 2.17
3027 8081 7.346175 AGGGCTAAAAATAAAATTACGGGGAAT 59.654 33.333 0.00 0.00 0.00 3.01
3028 8082 6.668718 AGGGCTAAAAATAAAATTACGGGGAA 59.331 34.615 0.00 0.00 0.00 3.97
3029 8083 6.196434 AGGGCTAAAAATAAAATTACGGGGA 58.804 36.000 0.00 0.00 0.00 4.81
3030 8084 6.322969 AGAGGGCTAAAAATAAAATTACGGGG 59.677 38.462 0.00 0.00 0.00 5.73
3031 8085 7.342769 AGAGGGCTAAAAATAAAATTACGGG 57.657 36.000 0.00 0.00 0.00 5.28
3032 8086 9.333724 TCTAGAGGGCTAAAAATAAAATTACGG 57.666 33.333 0.00 0.00 0.00 4.02
3039 8093 9.816787 TCCTTTTTCTAGAGGGCTAAAAATAAA 57.183 29.630 0.00 0.00 33.73 1.40
3040 8094 9.816787 TTCCTTTTTCTAGAGGGCTAAAAATAA 57.183 29.630 0.00 0.00 33.73 1.40
3041 8095 9.816787 TTTCCTTTTTCTAGAGGGCTAAAAATA 57.183 29.630 0.00 0.00 33.73 1.40
3042 8096 8.721133 TTTCCTTTTTCTAGAGGGCTAAAAAT 57.279 30.769 0.00 0.00 33.73 1.82
3043 8097 8.721133 ATTTCCTTTTTCTAGAGGGCTAAAAA 57.279 30.769 0.00 0.00 33.73 1.94
3044 8098 8.721133 AATTTCCTTTTTCTAGAGGGCTAAAA 57.279 30.769 0.00 0.00 33.73 1.52
3045 8099 9.990868 ATAATTTCCTTTTTCTAGAGGGCTAAA 57.009 29.630 0.00 0.00 33.73 1.85
3049 8103 7.775561 TCAGATAATTTCCTTTTTCTAGAGGGC 59.224 37.037 0.00 0.00 33.73 5.19
3078 8139 8.510243 TTTTCACTGCAATGAGATATACATGT 57.490 30.769 2.69 2.69 0.00 3.21
3108 8169 7.893658 TGTAATCGGGATAGAGATACTTTTCC 58.106 38.462 0.00 0.00 0.00 3.13
3120 8181 7.340743 AGGAAGAGATACATGTAATCGGGATAG 59.659 40.741 10.14 0.00 0.00 2.08
3131 8192 5.192522 ACATGGGAAAGGAAGAGATACATGT 59.807 40.000 2.69 2.69 40.84 3.21
3133 8194 5.983333 ACATGGGAAAGGAAGAGATACAT 57.017 39.130 0.00 0.00 0.00 2.29
3136 8197 8.336235 ACATTAAACATGGGAAAGGAAGAGATA 58.664 33.333 0.00 0.00 0.00 1.98
3148 8209 6.459923 GGCAAGTAAAACATTAAACATGGGA 58.540 36.000 0.00 0.00 0.00 4.37
3150 8211 6.153067 TCGGCAAGTAAAACATTAAACATGG 58.847 36.000 0.00 0.00 0.00 3.66
3151 8212 7.810766 ATCGGCAAGTAAAACATTAAACATG 57.189 32.000 0.00 0.00 0.00 3.21
3153 8214 9.562583 GATTATCGGCAAGTAAAACATTAAACA 57.437 29.630 0.00 0.00 0.00 2.83
3154 8215 9.562583 TGATTATCGGCAAGTAAAACATTAAAC 57.437 29.630 0.00 0.00 0.00 2.01
3156 8217 9.562583 GTTGATTATCGGCAAGTAAAACATTAA 57.437 29.630 0.00 0.00 0.00 1.40
3157 8218 8.952278 AGTTGATTATCGGCAAGTAAAACATTA 58.048 29.630 0.00 0.00 0.00 1.90
3162 8223 7.066525 CCCTTAGTTGATTATCGGCAAGTAAAA 59.933 37.037 0.00 0.00 38.62 1.52
3167 8228 4.451900 ACCCTTAGTTGATTATCGGCAAG 58.548 43.478 0.00 0.00 0.00 4.01
3186 8247 6.880942 AGACAATCTAGTACGAGATTACCC 57.119 41.667 25.04 17.78 42.96 3.69
3198 8267 8.713708 AGGCACATAACTATAGACAATCTAGT 57.286 34.615 6.78 0.00 31.67 2.57
3199 8268 9.416794 CAAGGCACATAACTATAGACAATCTAG 57.583 37.037 6.78 0.00 31.67 2.43
3201 8270 8.023021 TCAAGGCACATAACTATAGACAATCT 57.977 34.615 6.78 0.00 0.00 2.40
3206 8275 6.647067 GGTGATCAAGGCACATAACTATAGAC 59.353 42.308 6.78 0.00 37.99 2.59
3213 8282 3.696051 ACATGGTGATCAAGGCACATAAC 59.304 43.478 0.00 0.00 37.99 1.89
3220 8289 3.940209 TTTTGACATGGTGATCAAGGC 57.060 42.857 0.00 0.00 36.26 4.35
3229 8298 9.303116 TGTAAGGTGTATTATTTTTGACATGGT 57.697 29.630 0.00 0.00 0.00 3.55
3382 8456 5.701224 TCCCTACCATACCCAAATCAAATC 58.299 41.667 0.00 0.00 0.00 2.17
3388 8462 2.177016 GCCTTCCCTACCATACCCAAAT 59.823 50.000 0.00 0.00 0.00 2.32
3389 8463 1.567175 GCCTTCCCTACCATACCCAAA 59.433 52.381 0.00 0.00 0.00 3.28
3391 8465 1.052124 CGCCTTCCCTACCATACCCA 61.052 60.000 0.00 0.00 0.00 4.51
3392 8466 0.761702 TCGCCTTCCCTACCATACCC 60.762 60.000 0.00 0.00 0.00 3.69
3394 8468 1.002087 CCATCGCCTTCCCTACCATAC 59.998 57.143 0.00 0.00 0.00 2.39
3395 8469 1.132977 TCCATCGCCTTCCCTACCATA 60.133 52.381 0.00 0.00 0.00 2.74
3396 8470 0.399949 TCCATCGCCTTCCCTACCAT 60.400 55.000 0.00 0.00 0.00 3.55
3397 8471 0.619255 TTCCATCGCCTTCCCTACCA 60.619 55.000 0.00 0.00 0.00 3.25
3400 8474 2.103153 ATCTTCCATCGCCTTCCCTA 57.897 50.000 0.00 0.00 0.00 3.53
3408 8482 3.669251 ACCTTAGCTATCTTCCATCGC 57.331 47.619 0.00 0.00 0.00 4.58
3414 8488 5.029807 AGCCTCAAACCTTAGCTATCTTC 57.970 43.478 0.00 0.00 30.46 2.87
3420 8494 1.339151 CCGAAGCCTCAAACCTTAGCT 60.339 52.381 0.00 0.00 34.64 3.32
3421 8495 1.087501 CCGAAGCCTCAAACCTTAGC 58.912 55.000 0.00 0.00 0.00 3.09
3439 8515 8.099364 TCAGTCAAATCAAATCAAGTCTTACC 57.901 34.615 0.00 0.00 0.00 2.85
3446 8522 8.857216 GCATTAACTCAGTCAAATCAAATCAAG 58.143 33.333 0.00 0.00 0.00 3.02
3450 8526 8.525316 TCATGCATTAACTCAGTCAAATCAAAT 58.475 29.630 0.00 0.00 0.00 2.32
3454 8530 6.845302 TGTCATGCATTAACTCAGTCAAATC 58.155 36.000 0.00 0.00 0.00 2.17
3548 8624 0.421495 TTCTCCATTCCCCTCCCTGA 59.579 55.000 0.00 0.00 0.00 3.86
3549 8625 0.842635 CTTCTCCATTCCCCTCCCTG 59.157 60.000 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.