Multiple sequence alignment - TraesCS2A01G486600

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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 TraesCS2A01G486600 chr2A 100.000 6725 0 0 1 6725 721730682 721723958 0.000000e+00 12419.0
1 TraesCS2A01G486600 chr2A 85.519 1319 160 21 1112 2416 749385158 749386459 0.000000e+00 1349.0
2 TraesCS2A01G486600 chr2A 84.512 1343 163 26 1088 2420 748910516 748909209 0.000000e+00 1286.0
3 TraesCS2A01G486600 chr2A 79.348 276 56 1 4785 5059 749388498 749388773 6.880000e-45 193.0
4 TraesCS2A01G486600 chr2A 82.014 139 22 1 2288 2423 748871279 748871141 1.530000e-21 115.0
5 TraesCS2A01G486600 chr2A 97.917 48 1 0 2561 2608 721727934 721727887 4.320000e-12 84.2
6 TraesCS2A01G486600 chr2A 97.917 48 1 0 2749 2796 721728122 721728075 4.320000e-12 84.2
7 TraesCS2A01G486600 chr2D 94.662 3297 104 17 910 4141 586961882 586958593 0.000000e+00 5048.0
8 TraesCS2A01G486600 chr2D 93.343 2103 107 22 4202 6292 586958607 586956526 0.000000e+00 3077.0
9 TraesCS2A01G486600 chr2D 85.444 1319 161 20 1112 2416 618333434 618334735 0.000000e+00 1343.0
10 TraesCS2A01G486600 chr2D 84.903 1338 158 26 1088 2415 618143197 618141894 0.000000e+00 1312.0
11 TraesCS2A01G486600 chr2D 94.199 793 32 8 1 788 586964375 586963592 0.000000e+00 1197.0
12 TraesCS2A01G486600 chr2D 81.947 1274 179 29 1191 2431 586846885 586845630 0.000000e+00 1031.0
13 TraesCS2A01G486600 chr2D 79.859 1276 202 39 1167 2414 618660290 618659042 0.000000e+00 881.0
14 TraesCS2A01G486600 chr2D 88.980 245 26 1 3859 4103 586843175 586842932 1.100000e-77 302.0
15 TraesCS2A01G486600 chr2D 95.455 154 6 1 6277 6429 586951017 586950864 1.870000e-60 244.0
16 TraesCS2A01G486600 chr2D 79.710 276 55 1 4785 5059 618336907 618337182 1.480000e-46 198.0
17 TraesCS2A01G486600 chr2D 88.514 148 17 0 3945 4092 586803992 586803845 5.360000e-41 180.0
18 TraesCS2A01G486600 chr2D 82.589 224 5 4 6534 6725 586950867 586950646 4.170000e-37 167.0
19 TraesCS2A01G486600 chr2D 94.545 55 3 0 4144 4198 334538500 334538446 1.200000e-12 86.1
20 TraesCS2A01G486600 chr2D 97.872 47 1 0 799 845 586963607 586963561 1.550000e-11 82.4
21 TraesCS2A01G486600 chr2D 95.833 48 2 0 2561 2608 586960040 586959993 2.010000e-10 78.7
22 TraesCS2A01G486600 chr2D 95.745 47 2 0 4152 4198 241495465 241495419 7.230000e-10 76.8
23 TraesCS2A01G486600 chr2B 91.741 2458 120 33 14 2423 708717400 708714978 0.000000e+00 3338.0
24 TraesCS2A01G486600 chr2B 92.090 1239 89 8 4633 5869 708710947 708709716 0.000000e+00 1736.0
25 TraesCS2A01G486600 chr2B 91.537 1028 42 12 3150 4141 708712168 708711150 0.000000e+00 1375.0
26 TraesCS2A01G486600 chr2B 85.323 1315 166 14 1112 2416 755150784 755149487 0.000000e+00 1334.0
27 TraesCS2A01G486600 chr2B 84.673 1344 160 28 1088 2420 754654635 754653327 0.000000e+00 1299.0
28 TraesCS2A01G486600 chr2B 88.151 557 49 10 6130 6674 708704292 708703741 0.000000e+00 647.0
29 TraesCS2A01G486600 chr2B 85.000 480 34 16 2665 3121 708714958 708714494 2.860000e-123 453.0
30 TraesCS2A01G486600 chr2B 90.265 226 20 2 4195 4420 708711170 708710947 1.830000e-75 294.0
31 TraesCS2A01G486600 chr2B 79.930 284 53 4 4785 5066 755148070 755147789 8.840000e-49 206.0
32 TraesCS2A01G486600 chr2B 77.818 275 58 3 4793 5066 755032302 755032574 4.170000e-37 167.0
33 TraesCS2A01G486600 chr2B 97.468 79 2 0 5916 5994 708709712 708709634 1.180000e-27 135.0
34 TraesCS2A01G486600 chr2B 97.959 49 1 0 2560 2608 708714879 708714831 1.200000e-12 86.1
35 TraesCS2A01G486600 chr2B 92.857 56 3 1 4143 4198 298841437 298841491 5.590000e-11 80.5
36 TraesCS2A01G486600 chr3D 92.857 56 2 2 4143 4198 87508678 87508731 5.590000e-11 80.5
37 TraesCS2A01G486600 chr7B 94.118 51 2 1 6675 6725 49352437 49352388 7.230000e-10 76.8
38 TraesCS2A01G486600 chr7B 94.118 51 2 1 6675 6725 49623658 49623707 7.230000e-10 76.8
39 TraesCS2A01G486600 chr6B 91.228 57 3 2 4143 4199 698672187 698672133 7.230000e-10 76.8
40 TraesCS2A01G486600 chr7D 91.071 56 3 2 4143 4198 60523736 60523789 2.600000e-09 75.0
41 TraesCS2A01G486600 chr5D 91.071 56 3 2 4143 4198 271172233 271172180 2.600000e-09 75.0
42 TraesCS2A01G486600 chr3B 91.071 56 3 2 4143 4198 468543128 468543075 2.600000e-09 75.0
43 TraesCS2A01G486600 chr3B 100.000 29 0 0 875 903 7335779 7335807 3.000000e-03 54.7
44 TraesCS2A01G486600 chr1B 91.071 56 3 2 4143 4198 674750415 674750362 2.600000e-09 75.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G486600 chr2A 721723958 721730682 6724 True 4195.800000 12419 98.611333 1 6725 3 chr2A.!!$R3 6724
1 TraesCS2A01G486600 chr2A 748909209 748910516 1307 True 1286.000000 1286 84.512000 1088 2420 1 chr2A.!!$R2 1332
2 TraesCS2A01G486600 chr2A 749385158 749388773 3615 False 771.000000 1349 82.433500 1112 5059 2 chr2A.!!$F1 3947
3 TraesCS2A01G486600 chr2D 586956526 586964375 7849 True 1896.620000 5048 95.181800 1 6292 5 chr2D.!!$R8 6291
4 TraesCS2A01G486600 chr2D 618141894 618143197 1303 True 1312.000000 1312 84.903000 1088 2415 1 chr2D.!!$R4 1327
5 TraesCS2A01G486600 chr2D 618659042 618660290 1248 True 881.000000 881 79.859000 1167 2414 1 chr2D.!!$R5 1247
6 TraesCS2A01G486600 chr2D 618333434 618337182 3748 False 770.500000 1343 82.577000 1112 5059 2 chr2D.!!$F1 3947
7 TraesCS2A01G486600 chr2D 586842932 586846885 3953 True 666.500000 1031 85.463500 1191 4103 2 chr2D.!!$R6 2912
8 TraesCS2A01G486600 chr2B 754653327 754654635 1308 True 1299.000000 1299 84.673000 1088 2420 1 chr2B.!!$R2 1332
9 TraesCS2A01G486600 chr2B 708709634 708717400 7766 True 1059.585714 3338 92.294286 14 5994 7 chr2B.!!$R3 5980
10 TraesCS2A01G486600 chr2B 755147789 755150784 2995 True 770.000000 1334 82.626500 1112 5066 2 chr2B.!!$R4 3954
11 TraesCS2A01G486600 chr2B 708703741 708704292 551 True 647.000000 647 88.151000 6130 6674 1 chr2B.!!$R1 544

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
76 77 0.734889 GCCACATCACCTACATGCAC 59.265 55.0 0.00 0.0 0.00 4.57 F
1053 2709 0.403271 ATGGCCCATGTATGAGCTCC 59.597 55.0 12.15 0.0 31.62 4.70 F
1189 2846 0.528924 CGGTGTCCGTGATAGGTTCA 59.471 55.0 0.00 0.0 42.73 3.18 F
1546 3237 1.231958 GCAATCGTTCGACCACCCAA 61.232 55.0 0.00 0.0 0.00 4.12 F
3181 10589 0.108019 GGGATACAAACCGGGCTAGG 59.892 60.0 6.32 0.0 39.74 3.02 F
4197 11766 0.037160 ACCCGTTTATTCCAAGCGGT 59.963 50.0 10.64 0.0 40.70 5.68 F
5170 12773 0.036388 GAGGGGACATGACGCTGAAA 60.036 55.0 14.24 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1189 2846 0.402121 GTGAGGTTCTGGCCCTTCTT 59.598 55.000 0.00 0.00 30.60 2.52 R
2718 7569 4.233123 ACTGTGAGTTCAAACATGCATG 57.767 40.909 25.09 25.09 0.00 4.06 R
3161 10569 0.108019 CTAGCCCGGTTTGTATCCCC 59.892 60.000 0.00 0.00 0.00 4.81 R
3207 10615 1.000646 GACCTCCCTCTCTGACGGT 60.001 63.158 0.00 0.00 0.00 4.83 R
4827 12430 0.670546 TCCAGCTCAGTAAAGCACGC 60.671 55.000 0.00 0.00 45.00 5.34 R
5210 12813 0.106519 CCATTCCTTTCCCCGCTGAT 60.107 55.000 0.00 0.00 0.00 2.90 R
6615 14233 0.036010 ACTTTAGCCACGCTGCTCAT 60.036 50.000 2.14 0.00 41.68 2.90 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
76 77 0.734889 GCCACATCACCTACATGCAC 59.265 55.000 0.00 0.00 0.00 4.57
101 102 2.952978 ACTTGCTATGAGACCTACTCCG 59.047 50.000 0.00 0.00 44.34 4.63
156 176 4.706842 AGAGCCTTTCCTTTTCACTGTA 57.293 40.909 0.00 0.00 0.00 2.74
284 305 3.309954 GGAGAGTATTCAACCAATGACGC 59.690 47.826 0.00 0.00 37.92 5.19
322 350 5.182001 ACAAAAGTATGTGCTTAGAGCCTTG 59.818 40.000 0.00 0.00 41.51 3.61
340 368 4.599047 CTTGAGACTGACAAGGACTCTT 57.401 45.455 0.00 0.00 40.39 2.85
397 425 3.068024 TGACCAATCAACCACTTCAAAGC 59.932 43.478 0.00 0.00 0.00 3.51
437 465 6.303259 GCTTCAGTTACATCACGTTGAAAATC 59.697 38.462 0.00 0.00 0.00 2.17
447 475 0.872388 GTTGAAAATCACCTCGCCGT 59.128 50.000 0.00 0.00 0.00 5.68
452 480 0.806102 AAATCACCTCGCCGTCATCG 60.806 55.000 0.00 0.00 0.00 3.84
554 582 4.987912 GTCTAATGACTCTAGAAGCATGCC 59.012 45.833 15.66 0.00 39.94 4.40
598 626 2.248248 ACCACTCGTTTGAGATGGAGA 58.752 47.619 15.81 0.00 45.57 3.71
659 688 4.129380 CCTGTCACATCAACAACTGAAGA 58.871 43.478 0.00 0.00 37.67 2.87
778 808 7.672122 GGAAGTTTCCCTCCTTCTAATAGTA 57.328 40.000 0.00 0.00 41.62 1.82
779 809 8.087303 GGAAGTTTCCCTCCTTCTAATAGTAA 57.913 38.462 0.00 0.00 41.62 2.24
780 810 8.546322 GGAAGTTTCCCTCCTTCTAATAGTAAA 58.454 37.037 0.00 0.00 41.62 2.01
781 811 9.955102 GAAGTTTCCCTCCTTCTAATAGTAAAA 57.045 33.333 0.00 0.00 35.33 1.52
785 815 8.747538 TTCCCTCCTTCTAATAGTAAAATTGC 57.252 34.615 0.00 0.00 0.00 3.56
786 816 7.867921 TCCCTCCTTCTAATAGTAAAATTGCA 58.132 34.615 0.00 0.00 0.00 4.08
787 817 7.993183 TCCCTCCTTCTAATAGTAAAATTGCAG 59.007 37.037 0.00 0.00 0.00 4.41
788 818 7.255277 CCCTCCTTCTAATAGTAAAATTGCAGC 60.255 40.741 0.00 0.00 0.00 5.25
789 819 7.255277 CCTCCTTCTAATAGTAAAATTGCAGCC 60.255 40.741 0.00 0.00 0.00 4.85
790 820 6.546034 TCCTTCTAATAGTAAAATTGCAGCCC 59.454 38.462 0.00 0.00 0.00 5.19
791 821 6.547510 CCTTCTAATAGTAAAATTGCAGCCCT 59.452 38.462 0.00 0.00 0.00 5.19
792 822 7.719633 CCTTCTAATAGTAAAATTGCAGCCCTA 59.280 37.037 0.00 0.00 0.00 3.53
793 823 9.120538 CTTCTAATAGTAAAATTGCAGCCCTAA 57.879 33.333 0.00 0.00 0.00 2.69
794 824 9.469097 TTCTAATAGTAAAATTGCAGCCCTAAA 57.531 29.630 0.00 0.00 0.00 1.85
795 825 9.469097 TCTAATAGTAAAATTGCAGCCCTAAAA 57.531 29.630 0.00 0.00 0.00 1.52
796 826 9.736023 CTAATAGTAAAATTGCAGCCCTAAAAG 57.264 33.333 0.00 0.00 0.00 2.27
797 827 7.954666 ATAGTAAAATTGCAGCCCTAAAAGA 57.045 32.000 0.00 0.00 0.00 2.52
798 828 6.664428 AGTAAAATTGCAGCCCTAAAAGAA 57.336 33.333 0.00 0.00 0.00 2.52
799 829 7.061566 AGTAAAATTGCAGCCCTAAAAGAAA 57.938 32.000 0.00 0.00 0.00 2.52
800 830 7.679783 AGTAAAATTGCAGCCCTAAAAGAAAT 58.320 30.769 0.00 0.00 0.00 2.17
801 831 8.811994 AGTAAAATTGCAGCCCTAAAAGAAATA 58.188 29.630 0.00 0.00 0.00 1.40
873 920 8.777865 AAGCTTATTTCCATCTTTAAAAAGGC 57.222 30.769 0.00 0.00 36.67 4.35
1044 2700 5.253798 ACTGTATATATTCCATGGCCCATGT 59.746 40.000 21.88 6.76 39.94 3.21
1053 2709 0.403271 ATGGCCCATGTATGAGCTCC 59.597 55.000 12.15 0.00 31.62 4.70
1054 2710 1.302033 GGCCCATGTATGAGCTCCG 60.302 63.158 12.15 0.00 31.62 4.63
1065 2721 3.596066 GAGCTCCGCTGTGCAAGGA 62.596 63.158 0.87 0.00 39.88 3.36
1068 2724 1.597854 CTCCGCTGTGCAAGGACAA 60.598 57.895 0.00 0.00 0.00 3.18
1085 2742 1.972795 ACAATGCAAAGCAATGAGGGT 59.027 42.857 13.41 0.00 41.42 4.34
1149 2806 4.420206 TGATCACTCTCTTCCTCCTTTCA 58.580 43.478 0.00 0.00 0.00 2.69
1182 2839 3.771160 GCCTCCGGTGTCCGTGAT 61.771 66.667 0.00 0.00 46.80 3.06
1189 2846 0.528924 CGGTGTCCGTGATAGGTTCA 59.471 55.000 0.00 0.00 42.73 3.18
1545 3236 1.669760 GCAATCGTTCGACCACCCA 60.670 57.895 0.00 0.00 0.00 4.51
1546 3237 1.231958 GCAATCGTTCGACCACCCAA 61.232 55.000 0.00 0.00 0.00 4.12
1599 3290 3.827898 GACCTCTGGACCGGAGCG 61.828 72.222 23.23 18.10 35.69 5.03
2478 4200 5.879237 TGTCTTGACACAAATTGACTCAAC 58.121 37.500 0.00 0.00 0.00 3.18
2566 5543 2.129607 CATGTTTGAACTGGTTGCTGC 58.870 47.619 0.00 0.00 0.00 5.25
2584 5561 3.877559 CTGCCATAACAGATGACCAGAA 58.122 45.455 0.00 0.00 40.25 3.02
2901 7987 2.959030 TCTACTCTGATGGGATGGTTCG 59.041 50.000 0.00 0.00 0.00 3.95
2919 8005 5.703592 TGGTTCGCTGTTACTGTTATTTCAT 59.296 36.000 0.00 0.00 0.00 2.57
3021 8113 4.567971 ACGGTTGGTGACATATAAAACGA 58.432 39.130 0.00 0.00 42.32 3.85
3114 8225 8.603242 TCTAGAATTTTAACACTCAAGTCCAC 57.397 34.615 0.00 0.00 0.00 4.02
3181 10589 0.108019 GGGATACAAACCGGGCTAGG 59.892 60.000 6.32 0.00 39.74 3.02
3210 10618 1.738700 GCAAACCAAATATGCCCACCG 60.739 52.381 0.00 0.00 34.03 4.94
3242 10650 4.304939 GAGGTCACAAACTTAACTAGCGT 58.695 43.478 0.00 0.00 0.00 5.07
3246 10654 5.636543 GGTCACAAACTTAACTAGCGTATGT 59.363 40.000 0.00 0.00 0.00 2.29
3326 10734 2.128771 TAGGCTGCCATGAAACTTCC 57.871 50.000 22.65 0.00 0.00 3.46
3331 10739 0.825425 TGCCATGAAACTTCCGGCAA 60.825 50.000 16.29 0.00 45.83 4.52
3332 10740 0.388520 GCCATGAAACTTCCGGCAAC 60.389 55.000 12.70 0.00 41.70 4.17
3333 10741 0.958091 CCATGAAACTTCCGGCAACA 59.042 50.000 0.00 0.00 0.00 3.33
3334 10742 1.339610 CCATGAAACTTCCGGCAACAA 59.660 47.619 0.00 0.00 0.00 2.83
3335 10743 2.607771 CCATGAAACTTCCGGCAACAAG 60.608 50.000 0.00 0.00 0.00 3.16
3336 10744 1.028905 TGAAACTTCCGGCAACAAGG 58.971 50.000 0.00 0.00 0.00 3.61
3337 10745 0.318699 GAAACTTCCGGCAACAAGGC 60.319 55.000 0.00 0.00 39.93 4.35
3372 10780 5.368989 CCAAGTCTTGGTCTAGTGAACTTT 58.631 41.667 21.76 0.00 45.93 2.66
3378 10787 4.948341 TGGTCTAGTGAACTTTGCACTA 57.052 40.909 0.00 0.00 44.27 2.74
3438 10848 8.346300 TCGCATGTAACTTATTTTCTTTTGTCA 58.654 29.630 0.00 0.00 0.00 3.58
3476 10886 7.437713 TGGAGATCCAACAACTCACTATTAT 57.562 36.000 0.00 0.00 44.35 1.28
3483 10893 7.327975 TCCAACAACTCACTATTATTCGTGAT 58.672 34.615 0.00 0.00 39.23 3.06
3521 10931 1.033746 ATTCCACTGATGCCTTGCCG 61.034 55.000 0.00 0.00 0.00 5.69
3525 10935 2.825836 CTGATGCCTTGCCGGACC 60.826 66.667 5.05 0.00 33.16 4.46
3774 11263 6.874134 GTGTGTGGATCTATCTTGTACTGTTT 59.126 38.462 0.00 0.00 0.00 2.83
3815 11365 9.330063 TGACTATATCCTTCACATGATTTTCAC 57.670 33.333 0.00 0.00 0.00 3.18
4125 11694 3.181479 ACACTGCTACAAGAACACGAGAA 60.181 43.478 0.00 0.00 0.00 2.87
4126 11695 3.802139 CACTGCTACAAGAACACGAGAAA 59.198 43.478 0.00 0.00 0.00 2.52
4128 11697 5.050091 CACTGCTACAAGAACACGAGAAATT 60.050 40.000 0.00 0.00 0.00 1.82
4129 11698 5.527582 ACTGCTACAAGAACACGAGAAATTT 59.472 36.000 0.00 0.00 0.00 1.82
4130 11699 5.985781 TGCTACAAGAACACGAGAAATTTC 58.014 37.500 10.33 10.33 0.00 2.17
4131 11700 5.758296 TGCTACAAGAACACGAGAAATTTCT 59.242 36.000 20.60 20.60 41.00 2.52
4132 11701 6.260050 TGCTACAAGAACACGAGAAATTTCTT 59.740 34.615 21.33 5.61 38.55 2.52
4136 11705 6.927294 AAGAACACGAGAAATTTCTTGACT 57.073 33.333 32.97 23.12 40.46 3.41
4137 11706 6.927294 AGAACACGAGAAATTTCTTGACTT 57.073 33.333 32.97 23.77 40.46 3.01
4138 11707 8.433421 AAGAACACGAGAAATTTCTTGACTTA 57.567 30.769 32.97 0.00 40.46 2.24
4139 11708 8.608844 AGAACACGAGAAATTTCTTGACTTAT 57.391 30.769 32.97 20.10 40.46 1.73
4140 11709 8.713271 AGAACACGAGAAATTTCTTGACTTATC 58.287 33.333 32.97 22.90 40.46 1.75
4141 11710 8.608844 AACACGAGAAATTTCTTGACTTATCT 57.391 30.769 32.97 12.88 40.46 1.98
4142 11711 8.608844 ACACGAGAAATTTCTTGACTTATCTT 57.391 30.769 32.97 12.26 40.46 2.40
4143 11712 9.057089 ACACGAGAAATTTCTTGACTTATCTTT 57.943 29.630 32.97 11.65 40.46 2.52
4144 11713 9.884465 CACGAGAAATTTCTTGACTTATCTTTT 57.116 29.630 32.97 11.03 40.46 2.27
4191 11760 3.825143 GGTAGCTACCCGTTTATTCCA 57.175 47.619 29.68 0.00 40.53 3.53
4192 11761 4.141233 GGTAGCTACCCGTTTATTCCAA 57.859 45.455 29.68 0.00 40.53 3.53
4193 11762 4.124970 GGTAGCTACCCGTTTATTCCAAG 58.875 47.826 29.68 0.00 40.53 3.61
4194 11763 2.640184 AGCTACCCGTTTATTCCAAGC 58.360 47.619 0.00 0.00 0.00 4.01
4195 11764 1.329599 GCTACCCGTTTATTCCAAGCG 59.670 52.381 0.00 0.00 0.00 4.68
4196 11765 1.937899 CTACCCGTTTATTCCAAGCGG 59.062 52.381 5.43 5.43 41.82 5.52
4197 11766 0.037160 ACCCGTTTATTCCAAGCGGT 59.963 50.000 10.64 0.00 40.70 5.68
4207 11777 4.616181 ATTCCAAGCGGTAAATTTCTCG 57.384 40.909 0.00 1.18 0.00 4.04
4247 11817 4.026804 CGACCGTCTAATTCTTGTGTATGC 60.027 45.833 0.00 0.00 0.00 3.14
4316 11913 6.351317 TCCTAAGTCCACTCTTCCCTTATA 57.649 41.667 0.00 0.00 0.00 0.98
4317 11914 6.935036 TCCTAAGTCCACTCTTCCCTTATAT 58.065 40.000 0.00 0.00 0.00 0.86
4318 11915 7.011382 TCCTAAGTCCACTCTTCCCTTATATC 58.989 42.308 0.00 0.00 0.00 1.63
4325 11922 5.248705 CCACTCTTCCCTTATATCCCCTAAC 59.751 48.000 0.00 0.00 0.00 2.34
4327 11924 7.246763 CACTCTTCCCTTATATCCCCTAACTA 58.753 42.308 0.00 0.00 0.00 2.24
4389 11986 8.679100 TCAAATTATATTTGAACCCACCTAACG 58.321 33.333 11.31 0.00 35.69 3.18
4393 11990 0.250553 TTGAACCCACCTAACGCCAG 60.251 55.000 0.00 0.00 0.00 4.85
4414 12011 3.509575 AGAAGCTATCACATCCGAGATCC 59.490 47.826 0.00 0.00 0.00 3.36
4421 12018 4.551702 TCACATCCGAGATCCTTTTTCA 57.448 40.909 0.00 0.00 0.00 2.69
4477 12078 9.262358 GGTTACAAAATAGCAACCAATGTAAAA 57.738 29.630 0.00 0.00 40.17 1.52
4511 12112 8.652810 TTAAATAAGTCCGTTAGGTCATAAGC 57.347 34.615 0.00 0.00 39.05 3.09
4514 12115 3.097614 AGTCCGTTAGGTCATAAGCTGT 58.902 45.455 0.00 0.00 39.05 4.40
4518 12119 2.852413 CGTTAGGTCATAAGCTGTCGTG 59.148 50.000 0.00 0.00 34.40 4.35
4668 12269 1.066303 GTGCTCTAGGATGGACAGTCG 59.934 57.143 0.00 0.00 0.00 4.18
4699 12300 6.262193 AGTGAGCTAGAAACAACTAGAGAC 57.738 41.667 0.00 0.00 41.42 3.36
4706 12307 9.863845 AGCTAGAAACAACTAGAGACTTAAATC 57.136 33.333 0.00 0.00 41.42 2.17
4783 12386 8.691661 ATGAATATTATCAAAGTGGGTGTACC 57.308 34.615 0.00 0.00 34.35 3.34
4791 12394 6.290294 TCAAAGTGGGTGTACCTATCTAAC 57.710 41.667 0.44 0.00 41.11 2.34
4827 12430 5.109903 GCACTCACAGGTATACCTAAACTG 58.890 45.833 24.15 14.54 46.65 3.16
4841 12444 3.123621 CCTAAACTGCGTGCTTTACTGAG 59.876 47.826 0.00 0.00 0.00 3.35
4846 12449 0.670546 GCGTGCTTTACTGAGCTGGA 60.671 55.000 0.00 0.00 43.11 3.86
5074 12677 9.856488 CACCGTAAGTAGTCAAATATATATGCT 57.144 33.333 0.00 0.00 0.00 3.79
5158 12761 1.043673 AGTATGCACGGAGAGGGGAC 61.044 60.000 0.00 0.00 0.00 4.46
5170 12773 0.036388 GAGGGGACATGACGCTGAAA 60.036 55.000 14.24 0.00 0.00 2.69
5210 12813 0.036448 AGTTGTCCTCCTCGAGACGA 59.964 55.000 15.71 2.20 0.00 4.20
5239 12842 1.551883 GAAAGGAATGGTGGCTTGCAT 59.448 47.619 0.00 0.00 0.00 3.96
5304 12908 9.407380 TCATATTTATCACAAACTAAGGCATGT 57.593 29.630 0.00 0.00 0.00 3.21
5352 12957 0.946221 GTGTTCCGGCACTCAGTCTG 60.946 60.000 5.66 0.00 36.51 3.51
5398 13003 2.483877 TGAAGCAAGACATAACTTGGCG 59.516 45.455 0.00 0.00 44.87 5.69
5410 13016 5.010617 ACATAACTTGGCGAATCTTTTTGGT 59.989 36.000 0.00 0.00 0.00 3.67
5443 13049 1.267121 GTGGGAGCAGAACAGGACTA 58.733 55.000 0.00 0.00 0.00 2.59
5664 13270 1.476833 GGAGGAGTTGTGCAACCTTCA 60.477 52.381 11.00 0.00 42.06 3.02
5665 13271 1.876156 GAGGAGTTGTGCAACCTTCAG 59.124 52.381 11.00 0.00 42.06 3.02
5670 13276 3.554934 AGTTGTGCAACCTTCAGATTCA 58.445 40.909 11.00 0.00 42.06 2.57
5675 13281 3.503363 GTGCAACCTTCAGATTCATCACA 59.497 43.478 0.00 0.00 0.00 3.58
5728 13334 9.916397 CCACTACTATTGATTTGACGTAAATTC 57.084 33.333 0.00 0.00 39.06 2.17
5767 13373 4.631247 TGCTGCAGCCTCGCTTGT 62.631 61.111 34.64 0.00 36.40 3.16
5885 13491 4.038642 GTGAAGCAAACACTAAAATGGGGA 59.961 41.667 0.00 0.00 35.66 4.81
5945 13553 4.148696 GCGCAGTGTAAAACGTAGTCTAAA 59.851 41.667 0.30 0.00 45.00 1.85
5998 13606 5.047872 TGGTTATTCTTGAGTACACGCAGTA 60.048 40.000 0.00 0.00 41.61 2.74
6042 13650 4.831741 GACATCGATTTGTCTGTCAGTC 57.168 45.455 11.13 1.43 42.22 3.51
6043 13651 4.489810 GACATCGATTTGTCTGTCAGTCT 58.510 43.478 11.13 0.00 42.22 3.24
6044 13652 4.887748 ACATCGATTTGTCTGTCAGTCTT 58.112 39.130 0.00 0.00 0.00 3.01
6139 13747 4.607293 TTCATCCAGTGAATCCTATCCG 57.393 45.455 0.00 0.00 41.79 4.18
6180 13788 1.777030 TTTTTCGGCGAGCGAGCAAA 61.777 50.000 10.46 3.68 39.27 3.68
6306 13915 0.974010 AATAGTTGTCGGCCCGAGGA 60.974 55.000 5.82 0.00 36.23 3.71
6310 13919 3.365291 TTGTCGGCCCGAGGAATCG 62.365 63.158 5.82 0.00 36.23 3.34
6313 13922 4.830765 CGGCCCGAGGAATCGCAA 62.831 66.667 0.00 0.00 0.00 4.85
6323 13932 1.447317 GGAATCGCAACGGATGGCAT 61.447 55.000 0.00 0.00 0.00 4.40
6326 13935 2.340453 ATCGCAACGGATGGCATTGC 62.340 55.000 12.36 12.36 44.21 3.56
6353 13966 5.537188 TCCAATGTATCTGGTTGTTTTTGC 58.463 37.500 0.00 0.00 35.30 3.68
6391 14009 0.600255 AACGAACCCGAAGTGCTCTG 60.600 55.000 0.00 0.00 39.50 3.35
6392 14010 1.006102 CGAACCCGAAGTGCTCTGT 60.006 57.895 0.00 0.00 38.22 3.41
6394 14012 1.149148 GAACCCGAAGTGCTCTGTTC 58.851 55.000 0.00 0.00 0.00 3.18
6399 14017 1.634702 CGAAGTGCTCTGTTCTAGCC 58.365 55.000 0.00 0.00 39.30 3.93
6402 14020 1.650528 AGTGCTCTGTTCTAGCCCTT 58.349 50.000 0.00 0.00 39.30 3.95
6426 14044 3.516586 TGACTTGATTCCTAGACCACCA 58.483 45.455 0.00 0.00 0.00 4.17
6439 14057 2.572104 AGACCACCAACCTTAGATGACC 59.428 50.000 0.00 0.00 0.00 4.02
6443 14061 2.039746 CACCAACCTTAGATGACCCACA 59.960 50.000 0.00 0.00 0.00 4.17
6445 14063 2.356125 CCAACCTTAGATGACCCACAGG 60.356 54.545 0.00 0.00 40.04 4.00
6468 14086 6.013466 AGGTTCTTTTCCAATTAACATGGCAT 60.013 34.615 0.00 0.00 37.88 4.40
6533 14151 5.239525 CCTATAGGGTAATGCAGCAGAAAAC 59.760 44.000 11.33 0.00 0.00 2.43
6535 14153 3.230134 AGGGTAATGCAGCAGAAAACAA 58.770 40.909 0.00 0.00 0.00 2.83
6536 14154 3.256631 AGGGTAATGCAGCAGAAAACAAG 59.743 43.478 0.00 0.00 0.00 3.16
6537 14155 3.255642 GGGTAATGCAGCAGAAAACAAGA 59.744 43.478 0.00 0.00 0.00 3.02
6539 14157 5.288804 GGTAATGCAGCAGAAAACAAGAAA 58.711 37.500 0.00 0.00 0.00 2.52
6541 14159 6.257630 GGTAATGCAGCAGAAAACAAGAAAAA 59.742 34.615 0.00 0.00 0.00 1.94
6542 14160 6.930667 AATGCAGCAGAAAACAAGAAAAAT 57.069 29.167 0.00 0.00 0.00 1.82
6543 14161 5.971895 TGCAGCAGAAAACAAGAAAAATC 57.028 34.783 0.00 0.00 0.00 2.17
6545 14163 4.084900 GCAGCAGAAAACAAGAAAAATCCG 60.085 41.667 0.00 0.00 0.00 4.18
6546 14164 5.043248 CAGCAGAAAACAAGAAAAATCCGT 58.957 37.500 0.00 0.00 0.00 4.69
6547 14165 6.205784 CAGCAGAAAACAAGAAAAATCCGTA 58.794 36.000 0.00 0.00 0.00 4.02
6548 14166 6.863126 CAGCAGAAAACAAGAAAAATCCGTAT 59.137 34.615 0.00 0.00 0.00 3.06
6549 14167 7.382218 CAGCAGAAAACAAGAAAAATCCGTATT 59.618 33.333 0.00 0.00 0.00 1.89
6550 14168 8.573035 AGCAGAAAACAAGAAAAATCCGTATTA 58.427 29.630 0.00 0.00 0.00 0.98
6551 14169 8.635983 GCAGAAAACAAGAAAAATCCGTATTAC 58.364 33.333 0.00 0.00 0.00 1.89
6552 14170 9.672086 CAGAAAACAAGAAAAATCCGTATTACA 57.328 29.630 0.00 0.00 0.00 2.41
6561 14179 5.917541 AAATCCGTATTACATACAAGCCG 57.082 39.130 0.00 0.00 35.48 5.52
6567 14185 2.973694 TTACATACAAGCCGAGGACC 57.026 50.000 0.00 0.00 0.00 4.46
6573 14191 2.154567 ACAAGCCGAGGACCACTATA 57.845 50.000 0.00 0.00 0.00 1.31
6606 14224 4.225942 ACAGATAATGACTTTGCCAGGAGA 59.774 41.667 0.00 0.00 0.00 3.71
6623 14241 2.278854 GAGACTTCCTTGATGAGCAGC 58.721 52.381 0.00 0.00 0.00 5.25
6631 14249 0.036483 TTGATGAGCAGCGTGGCTAA 60.036 50.000 2.92 0.00 45.99 3.09
6655 14273 1.112113 TCTTCAGCCCTCGTATCACC 58.888 55.000 0.00 0.00 0.00 4.02
6658 14276 1.112113 TCAGCCCTCGTATCACCTTC 58.888 55.000 0.00 0.00 0.00 3.46
6659 14277 0.105039 CAGCCCTCGTATCACCTTCC 59.895 60.000 0.00 0.00 0.00 3.46
6662 14280 1.756690 GCCCTCGTATCACCTTCCCTA 60.757 57.143 0.00 0.00 0.00 3.53
6674 14292 5.332743 TCACCTTCCCTAATTCATTTGCTT 58.667 37.500 0.00 0.00 0.00 3.91
6675 14293 6.489603 TCACCTTCCCTAATTCATTTGCTTA 58.510 36.000 0.00 0.00 0.00 3.09
6676 14294 6.603201 TCACCTTCCCTAATTCATTTGCTTAG 59.397 38.462 0.00 0.00 0.00 2.18
6677 14295 6.378280 CACCTTCCCTAATTCATTTGCTTAGT 59.622 38.462 0.00 0.00 0.00 2.24
6678 14296 6.954102 ACCTTCCCTAATTCATTTGCTTAGTT 59.046 34.615 0.00 0.00 0.00 2.24
6679 14297 8.113462 ACCTTCCCTAATTCATTTGCTTAGTTA 58.887 33.333 0.00 0.00 0.00 2.24
6680 14298 8.966868 CCTTCCCTAATTCATTTGCTTAGTTAA 58.033 33.333 0.00 0.00 0.00 2.01
6690 14308 9.809096 TTCATTTGCTTAGTTAAAATGTTCACA 57.191 25.926 12.94 0.00 40.53 3.58
6691 14309 9.979578 TCATTTGCTTAGTTAAAATGTTCACAT 57.020 25.926 12.94 0.00 40.53 3.21
6693 14311 9.762933 ATTTGCTTAGTTAAAATGTTCACATGT 57.237 25.926 0.00 0.00 36.56 3.21
6694 14312 8.795786 TTGCTTAGTTAAAATGTTCACATGTC 57.204 30.769 0.00 0.00 36.56 3.06
6695 14313 7.935520 TGCTTAGTTAAAATGTTCACATGTCA 58.064 30.769 0.00 0.00 36.56 3.58
6696 14314 8.575589 TGCTTAGTTAAAATGTTCACATGTCAT 58.424 29.630 0.00 0.00 36.56 3.06
6705 14323 9.985730 AAAATGTTCACATGTCATATTTCTTGT 57.014 25.926 0.00 0.00 36.56 3.16
6706 14324 9.630098 AAATGTTCACATGTCATATTTCTTGTC 57.370 29.630 0.00 0.00 36.56 3.18
6707 14325 7.742556 TGTTCACATGTCATATTTCTTGTCA 57.257 32.000 0.00 0.00 0.00 3.58
6708 14326 8.164058 TGTTCACATGTCATATTTCTTGTCAA 57.836 30.769 0.00 0.00 0.00 3.18
6709 14327 8.628280 TGTTCACATGTCATATTTCTTGTCAAA 58.372 29.630 0.00 0.00 0.00 2.69
6710 14328 9.630098 GTTCACATGTCATATTTCTTGTCAAAT 57.370 29.630 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 2.969628 AGGTCTCATAGCAAGTTCCG 57.030 50.000 0.00 0.00 0.00 4.30
156 176 5.358160 GCTTGGAGCCTATAGTGTTTCAATT 59.642 40.000 0.00 0.00 34.48 2.32
284 305 9.694520 CACATACTTTTGTCTCGATTCTTATTG 57.305 33.333 0.00 0.00 0.00 1.90
340 368 1.071542 TCCAGTTCAAGTGGATTCGCA 59.928 47.619 10.19 0.00 42.54 5.10
397 425 4.551388 ACTGAAGCTACTCTCGTTCAAAG 58.449 43.478 0.00 0.00 0.00 2.77
437 465 2.126071 AACGATGACGGCGAGGTG 60.126 61.111 16.62 1.19 44.46 4.00
447 475 3.449377 TGCTACTGGAATACCAACGATGA 59.551 43.478 0.00 0.00 46.32 2.92
452 480 4.120589 GCTACTGCTACTGGAATACCAAC 58.879 47.826 0.00 0.00 39.95 3.77
548 576 2.493278 AGAACAATGTAAGTGGGCATGC 59.507 45.455 9.90 9.90 35.33 4.06
554 582 5.551233 TCCTCTCAAGAACAATGTAAGTGG 58.449 41.667 0.00 0.00 35.33 4.00
598 626 4.562143 GCAATCATGGAGCCAAGAAAACTT 60.562 41.667 0.00 0.00 0.00 2.66
659 688 5.464030 AAGTTGCAATCTCAGCTGATTTT 57.536 34.783 18.63 11.03 34.77 1.82
666 695 1.471684 CCAGGAAGTTGCAATCTCAGC 59.528 52.381 0.59 0.00 0.00 4.26
766 796 6.547510 AGGGCTGCAATTTTACTATTAGAAGG 59.452 38.462 0.50 0.00 0.00 3.46
778 808 7.679783 ACTATTTCTTTTAGGGCTGCAATTTT 58.320 30.769 0.50 0.00 0.00 1.82
779 809 7.244886 ACTATTTCTTTTAGGGCTGCAATTT 57.755 32.000 0.50 0.00 0.00 1.82
780 810 6.857437 ACTATTTCTTTTAGGGCTGCAATT 57.143 33.333 0.50 0.00 0.00 2.32
781 811 7.954666 TTACTATTTCTTTTAGGGCTGCAAT 57.045 32.000 0.50 0.00 0.00 3.56
782 812 7.768807 TTTACTATTTCTTTTAGGGCTGCAA 57.231 32.000 0.50 0.00 0.00 4.08
783 813 7.768807 TTTTACTATTTCTTTTAGGGCTGCA 57.231 32.000 0.50 0.00 0.00 4.41
784 814 9.087424 CAATTTTACTATTTCTTTTAGGGCTGC 57.913 33.333 0.00 0.00 0.00 5.25
785 815 9.087424 GCAATTTTACTATTTCTTTTAGGGCTG 57.913 33.333 0.00 0.00 0.00 4.85
786 816 8.811994 TGCAATTTTACTATTTCTTTTAGGGCT 58.188 29.630 0.00 0.00 0.00 5.19
787 817 8.996024 TGCAATTTTACTATTTCTTTTAGGGC 57.004 30.769 0.00 0.00 0.00 5.19
793 823 9.626045 GTAGCACTGCAATTTTACTATTTCTTT 57.374 29.630 3.30 0.00 0.00 2.52
794 824 9.014297 AGTAGCACTGCAATTTTACTATTTCTT 57.986 29.630 3.30 0.00 0.00 2.52
795 825 8.454106 CAGTAGCACTGCAATTTTACTATTTCT 58.546 33.333 3.30 0.00 39.62 2.52
796 826 8.606727 CAGTAGCACTGCAATTTTACTATTTC 57.393 34.615 3.30 0.00 39.62 2.17
871 918 8.376270 ACTACCTCTGTATCAAAATATAAGGCC 58.624 37.037 0.00 0.00 0.00 5.19
960 2616 2.354805 GGCTTGGACCGAGAACATAACT 60.355 50.000 13.45 0.00 0.00 2.24
987 2643 2.346766 TGGTCATGCACTGAAGTTGT 57.653 45.000 0.00 0.00 35.07 3.32
1053 2709 1.443194 GCATTGTCCTTGCACAGCG 60.443 57.895 0.00 0.00 39.90 5.18
1054 2710 1.661480 TGCATTGTCCTTGCACAGC 59.339 52.632 0.00 0.00 44.73 4.40
1065 2721 1.972795 ACCCTCATTGCTTTGCATTGT 59.027 42.857 12.19 0.00 39.79 2.71
1068 2724 2.497273 GGTTACCCTCATTGCTTTGCAT 59.503 45.455 0.00 0.00 38.76 3.96
1182 2839 2.038863 TCTGGCCCTTCTTGAACCTA 57.961 50.000 0.00 0.00 0.00 3.08
1189 2846 0.402121 GTGAGGTTCTGGCCCTTCTT 59.598 55.000 0.00 0.00 30.60 2.52
1521 3212 0.949105 GGTCGAACGATTGCCACAGT 60.949 55.000 0.00 0.00 0.00 3.55
1545 3236 2.594592 GGCAGCAAGGTGTCCGTT 60.595 61.111 0.00 0.00 0.00 4.44
1546 3237 4.643387 GGGCAGCAAGGTGTCCGT 62.643 66.667 7.18 0.00 30.98 4.69
2478 4200 9.525409 AATCAAGTCAATTTGTCTCTCAAAAAG 57.475 29.630 0.00 0.00 46.97 2.27
2566 5543 5.738909 ACTCTTTCTGGTCATCTGTTATGG 58.261 41.667 0.00 0.00 0.00 2.74
2718 7569 4.233123 ACTGTGAGTTCAAACATGCATG 57.767 40.909 25.09 25.09 0.00 4.06
2901 7987 8.662781 TCTCCATATGAAATAACAGTAACAGC 57.337 34.615 3.65 0.00 29.06 4.40
3161 10569 0.108019 CTAGCCCGGTTTGTATCCCC 59.892 60.000 0.00 0.00 0.00 4.81
3181 10589 4.990426 GCATATTTGGTTTGCCACATATCC 59.010 41.667 3.17 0.00 42.92 2.59
3207 10615 1.000646 GACCTCCCTCTCTGACGGT 60.001 63.158 0.00 0.00 0.00 4.83
3210 10618 1.633774 TTGTGACCTCCCTCTCTGAC 58.366 55.000 0.00 0.00 0.00 3.51
3242 10650 5.372343 AGAACATGTTAGGGATGCACATA 57.628 39.130 11.95 0.00 29.78 2.29
3246 10654 2.754552 GCAAGAACATGTTAGGGATGCA 59.245 45.455 11.95 0.00 0.00 3.96
3304 10712 2.062971 AGTTTCATGGCAGCCTATGG 57.937 50.000 14.15 0.00 0.00 2.74
3331 10739 1.988107 TGGAGAAATCTCAGGCCTTGT 59.012 47.619 0.00 0.00 44.60 3.16
3332 10740 2.795231 TGGAGAAATCTCAGGCCTTG 57.205 50.000 0.00 0.00 44.60 3.61
3333 10741 2.646798 ACTTGGAGAAATCTCAGGCCTT 59.353 45.455 0.00 0.00 44.60 4.35
3334 10742 2.238395 GACTTGGAGAAATCTCAGGCCT 59.762 50.000 0.00 0.00 44.60 5.19
3335 10743 2.238395 AGACTTGGAGAAATCTCAGGCC 59.762 50.000 12.21 0.00 44.60 5.19
3336 10744 3.625649 AGACTTGGAGAAATCTCAGGC 57.374 47.619 12.21 4.41 44.60 4.85
3372 10780 7.854557 TTTACGAGACTAATCTAGTAGTGCA 57.145 36.000 0.00 0.00 42.05 4.57
3425 10835 7.973388 TCGAACAATCACTTGACAAAAGAAAAT 59.027 29.630 0.00 0.00 36.20 1.82
3438 10848 4.080919 TGGATCTCCATCGAACAATCACTT 60.081 41.667 0.00 0.00 42.01 3.16
3496 10906 3.947612 AGGCATCAGTGGAATGAGATT 57.052 42.857 0.00 0.00 31.44 2.40
3504 10914 2.046023 CGGCAAGGCATCAGTGGA 60.046 61.111 0.00 0.00 0.00 4.02
3521 10931 7.859325 ATTGTGTTACAACATGTATAGGTCC 57.141 36.000 0.00 0.00 41.40 4.46
3774 11263 7.015974 AGGATATAGTCATGCATGAGTTTCTCA 59.984 37.037 35.40 21.14 44.99 3.27
3815 11365 7.230108 AGAGTTTGCAATGGATGGTTCTATATG 59.770 37.037 0.00 0.00 0.00 1.78
4164 11733 3.775261 AACGGGTAGCTACCTCAAAAA 57.225 42.857 35.80 0.00 45.72 1.94
4165 11734 3.775261 AAACGGGTAGCTACCTCAAAA 57.225 42.857 35.80 0.00 45.72 2.44
4166 11735 5.422145 GAATAAACGGGTAGCTACCTCAAA 58.578 41.667 35.80 20.91 45.72 2.69
4167 11736 4.141869 GGAATAAACGGGTAGCTACCTCAA 60.142 45.833 35.80 20.30 45.72 3.02
4168 11737 3.385755 GGAATAAACGGGTAGCTACCTCA 59.614 47.826 35.80 19.73 45.72 3.86
4169 11738 3.385755 TGGAATAAACGGGTAGCTACCTC 59.614 47.826 35.80 25.85 45.72 3.85
4170 11739 3.377573 TGGAATAAACGGGTAGCTACCT 58.622 45.455 35.80 22.08 45.72 3.08
4171 11740 3.825143 TGGAATAAACGGGTAGCTACC 57.175 47.619 31.50 31.50 45.71 3.18
4172 11741 3.558829 GCTTGGAATAAACGGGTAGCTAC 59.441 47.826 15.88 15.88 0.00 3.58
4173 11742 3.738899 CGCTTGGAATAAACGGGTAGCTA 60.739 47.826 0.00 0.00 0.00 3.32
4174 11743 2.640184 GCTTGGAATAAACGGGTAGCT 58.360 47.619 0.00 0.00 0.00 3.32
4175 11744 1.329599 CGCTTGGAATAAACGGGTAGC 59.670 52.381 0.00 0.00 0.00 3.58
4176 11745 1.937899 CCGCTTGGAATAAACGGGTAG 59.062 52.381 0.00 0.00 40.18 3.18
4177 11746 2.027003 CCGCTTGGAATAAACGGGTA 57.973 50.000 0.00 0.00 40.18 3.69
4178 11747 2.862738 CCGCTTGGAATAAACGGGT 58.137 52.632 0.00 0.00 40.18 5.28
4181 11750 6.319399 AGAAATTTACCGCTTGGAATAAACG 58.681 36.000 0.00 0.00 36.26 3.60
4182 11751 6.468000 CGAGAAATTTACCGCTTGGAATAAAC 59.532 38.462 0.00 0.00 36.26 2.01
4183 11752 6.372103 TCGAGAAATTTACCGCTTGGAATAAA 59.628 34.615 6.77 0.00 36.26 1.40
4184 11753 5.875910 TCGAGAAATTTACCGCTTGGAATAA 59.124 36.000 6.77 0.00 36.26 1.40
4185 11754 5.292589 GTCGAGAAATTTACCGCTTGGAATA 59.707 40.000 6.77 0.00 36.26 1.75
4186 11755 4.094442 GTCGAGAAATTTACCGCTTGGAAT 59.906 41.667 6.77 0.00 36.26 3.01
4187 11756 3.434299 GTCGAGAAATTTACCGCTTGGAA 59.566 43.478 6.77 0.00 36.26 3.53
4188 11757 2.997986 GTCGAGAAATTTACCGCTTGGA 59.002 45.455 6.77 0.00 36.26 3.53
4189 11758 3.000727 AGTCGAGAAATTTACCGCTTGG 58.999 45.455 6.77 0.00 39.35 3.61
4190 11759 4.663636 AAGTCGAGAAATTTACCGCTTG 57.336 40.909 14.27 4.18 0.00 4.01
4191 11760 6.103997 TGATAAGTCGAGAAATTTACCGCTT 58.896 36.000 16.81 16.81 0.00 4.68
4192 11761 5.657474 TGATAAGTCGAGAAATTTACCGCT 58.343 37.500 6.77 5.36 0.00 5.52
4193 11762 5.961395 TGATAAGTCGAGAAATTTACCGC 57.039 39.130 6.77 3.64 0.00 5.68
4194 11763 7.694388 TCATGATAAGTCGAGAAATTTACCG 57.306 36.000 0.00 0.00 0.00 4.02
4207 11777 4.863131 ACGGTCGAGTTTTCATGATAAGTC 59.137 41.667 18.59 18.59 0.00 3.01
4224 11794 4.026804 GCATACACAAGAATTAGACGGTCG 60.027 45.833 1.89 0.00 0.00 4.79
4273 11870 1.280133 AGGTGCATGCATGTAGACAGT 59.720 47.619 25.64 10.22 0.00 3.55
4316 11913 3.212397 AGTCAGGGGAATAGTTAGGGGAT 59.788 47.826 0.00 0.00 0.00 3.85
4317 11914 2.595380 AGTCAGGGGAATAGTTAGGGGA 59.405 50.000 0.00 0.00 0.00 4.81
4318 11915 3.061909 AGTCAGGGGAATAGTTAGGGG 57.938 52.381 0.00 0.00 0.00 4.79
4325 11922 6.931840 GTCAAGCTAATAAGTCAGGGGAATAG 59.068 42.308 0.00 0.00 0.00 1.73
4327 11924 5.430089 AGTCAAGCTAATAAGTCAGGGGAAT 59.570 40.000 0.00 0.00 0.00 3.01
4378 11975 1.677552 CTTCTGGCGTTAGGTGGGT 59.322 57.895 0.00 0.00 0.00 4.51
4389 11986 1.069204 TCGGATGTGATAGCTTCTGGC 59.931 52.381 0.00 0.00 42.19 4.85
4393 11990 3.509575 AGGATCTCGGATGTGATAGCTTC 59.490 47.826 0.00 0.00 0.00 3.86
4414 12011 3.490348 ACTGACCCCATGACTGAAAAAG 58.510 45.455 0.00 0.00 0.00 2.27
4421 12018 4.523173 CACGTATATACTGACCCCATGACT 59.477 45.833 11.05 0.00 0.00 3.41
4490 12091 5.363005 ACAGCTTATGACCTAACGGACTTAT 59.637 40.000 0.00 0.00 0.00 1.73
4493 12094 3.097614 ACAGCTTATGACCTAACGGACT 58.902 45.455 0.00 0.00 0.00 3.85
4618 12219 7.988028 ACCCTTTAACCAATTTTCGAAATGAAA 59.012 29.630 12.12 1.38 44.70 2.69
4619 12220 7.439655 CACCCTTTAACCAATTTTCGAAATGAA 59.560 33.333 12.12 0.00 33.85 2.57
4622 12223 7.056844 TCACCCTTTAACCAATTTTCGAAAT 57.943 32.000 12.12 0.00 0.00 2.17
4623 12224 6.466885 TCACCCTTTAACCAATTTTCGAAA 57.533 33.333 6.47 6.47 0.00 3.46
4624 12225 6.041069 ACATCACCCTTTAACCAATTTTCGAA 59.959 34.615 0.00 0.00 0.00 3.71
4625 12226 5.536916 ACATCACCCTTTAACCAATTTTCGA 59.463 36.000 0.00 0.00 0.00 3.71
4626 12227 5.633182 CACATCACCCTTTAACCAATTTTCG 59.367 40.000 0.00 0.00 0.00 3.46
4627 12228 5.408299 GCACATCACCCTTTAACCAATTTTC 59.592 40.000 0.00 0.00 0.00 2.29
4629 12230 4.592778 AGCACATCACCCTTTAACCAATTT 59.407 37.500 0.00 0.00 0.00 1.82
4631 12232 3.763897 GAGCACATCACCCTTTAACCAAT 59.236 43.478 0.00 0.00 0.00 3.16
4668 12269 3.008704 TGTTTCTAGCTCACTTAACCCCC 59.991 47.826 0.00 0.00 0.00 5.40
4706 12307 8.674607 GTTCATTTTACTCCCCTAATTGTACAG 58.325 37.037 0.00 0.00 0.00 2.74
4771 12372 6.886178 ATTGTTAGATAGGTACACCCACTT 57.114 37.500 0.00 0.00 36.42 3.16
4782 12385 9.507329 AGTGCCAAATATGTATTGTTAGATAGG 57.493 33.333 0.00 0.00 0.00 2.57
4791 12394 5.357878 ACCTGTGAGTGCCAAATATGTATTG 59.642 40.000 0.00 0.00 0.00 1.90
4827 12430 0.670546 TCCAGCTCAGTAAAGCACGC 60.671 55.000 0.00 0.00 45.00 5.34
4841 12444 1.202818 ACTCCAACCTTCTTGTCCAGC 60.203 52.381 0.00 0.00 0.00 4.85
4846 12449 3.118038 TGCAGTAACTCCAACCTTCTTGT 60.118 43.478 0.00 0.00 0.00 3.16
4933 12536 2.357569 GGAGAATGTTCCCAGGCTTGAT 60.358 50.000 0.00 0.00 0.00 2.57
5074 12677 9.305555 GTTAGGTATATATCTGGTGGTGAAGTA 57.694 37.037 5.73 0.00 0.00 2.24
5158 12761 3.373130 AGACATCACATTTCAGCGTCATG 59.627 43.478 0.00 0.00 0.00 3.07
5170 12773 4.830046 ACTCCGAAGCTATAGACATCACAT 59.170 41.667 3.21 0.00 0.00 3.21
5210 12813 0.106519 CCATTCCTTTCCCCGCTGAT 60.107 55.000 0.00 0.00 0.00 2.90
5239 12842 4.033709 AGCTTACATGAGAAAGGAGCCTA 58.966 43.478 0.00 0.00 0.00 3.93
5288 12891 3.504863 GATGCACATGCCTTAGTTTGTG 58.495 45.455 0.49 0.00 41.80 3.33
5289 12892 2.493278 GGATGCACATGCCTTAGTTTGT 59.507 45.455 0.49 0.00 41.18 2.83
5371 12976 6.583806 CCAAGTTATGTCTTGCTTCATTTCAC 59.416 38.462 6.29 0.00 42.16 3.18
5375 12980 4.379813 CGCCAAGTTATGTCTTGCTTCATT 60.380 41.667 6.29 0.00 42.16 2.57
5398 13003 4.023291 TCCCATGCCTACCAAAAAGATTC 58.977 43.478 0.00 0.00 0.00 2.52
5410 13016 0.548926 TCCCACAGTTCCCATGCCTA 60.549 55.000 0.00 0.00 0.00 3.93
5443 13049 0.674895 GCGGTGTCAAGAAGCTCCAT 60.675 55.000 0.00 0.00 0.00 3.41
5664 13270 3.201487 TCTCAAGCCCATGTGATGAATCT 59.799 43.478 0.00 0.00 0.00 2.40
5665 13271 3.314635 GTCTCAAGCCCATGTGATGAATC 59.685 47.826 0.00 0.00 0.00 2.52
5670 13276 0.107508 CCGTCTCAAGCCCATGTGAT 60.108 55.000 0.00 0.00 0.00 3.06
5675 13281 1.207791 AAGATCCGTCTCAAGCCCAT 58.792 50.000 0.00 0.00 32.15 4.00
5728 13334 3.686016 ACAACTAGTTGCACCCAATAGG 58.314 45.455 30.97 7.47 44.03 2.57
5767 13373 4.202284 ACCGAGCCTTTAATAAATCGCCTA 60.202 41.667 2.69 0.00 0.00 3.93
5885 13491 1.550072 CGATTGCCCAACCAATTTCCT 59.450 47.619 0.00 0.00 35.67 3.36
5945 13553 7.611467 TGAACAAAGACAACTCCTATATGCAAT 59.389 33.333 0.00 0.00 0.00 3.56
6026 13634 5.914085 AAGAAAGACTGACAGACAAATCG 57.086 39.130 10.08 0.00 0.00 3.34
6139 13747 2.104963 ACTTGACAGTCAAAGAGGACCC 59.895 50.000 16.85 0.00 35.73 4.46
6180 13788 1.887301 CTTGCGCCGGGGTTATTTT 59.113 52.632 20.83 0.00 0.00 1.82
6306 13915 0.101040 CAATGCCATCCGTTGCGATT 59.899 50.000 0.00 0.00 33.98 3.34
6323 13932 4.046286 ACCAGATACATTGGAAAGGCAA 57.954 40.909 0.00 0.00 39.08 4.52
6326 13935 5.982890 AACAACCAGATACATTGGAAAGG 57.017 39.130 0.00 0.00 39.08 3.11
6353 13966 1.218316 GGGCTTGGTACGAGTGGAG 59.782 63.158 0.00 0.00 0.00 3.86
6391 14009 4.207891 TCAAGTCATCAAGGGCTAGAAC 57.792 45.455 0.00 0.00 0.00 3.01
6392 14010 5.431765 GAATCAAGTCATCAAGGGCTAGAA 58.568 41.667 0.00 0.00 0.00 2.10
6394 14012 4.133078 GGAATCAAGTCATCAAGGGCTAG 58.867 47.826 0.00 0.00 0.00 3.42
6399 14017 5.104776 TGGTCTAGGAATCAAGTCATCAAGG 60.105 44.000 0.00 0.00 0.00 3.61
6402 14020 4.162320 GGTGGTCTAGGAATCAAGTCATCA 59.838 45.833 0.00 0.00 0.00 3.07
6426 14044 2.632537 ACCTGTGGGTCATCTAAGGTT 58.367 47.619 0.00 0.00 43.38 3.50
6439 14057 6.155475 TGTTAATTGGAAAAGAACCTGTGG 57.845 37.500 0.00 0.00 0.00 4.17
6443 14061 5.306678 TGCCATGTTAATTGGAAAAGAACCT 59.693 36.000 10.68 0.00 36.26 3.50
6445 14063 7.671495 AATGCCATGTTAATTGGAAAAGAAC 57.329 32.000 10.68 0.00 36.26 3.01
6512 14130 4.599041 TGTTTTCTGCTGCATTACCCTAT 58.401 39.130 1.31 0.00 0.00 2.57
6522 14140 4.084900 CGGATTTTTCTTGTTTTCTGCTGC 60.085 41.667 0.00 0.00 0.00 5.25
6546 14164 3.962063 TGGTCCTCGGCTTGTATGTAATA 59.038 43.478 0.00 0.00 0.00 0.98
6547 14165 2.769663 TGGTCCTCGGCTTGTATGTAAT 59.230 45.455 0.00 0.00 0.00 1.89
6548 14166 2.093869 GTGGTCCTCGGCTTGTATGTAA 60.094 50.000 0.00 0.00 0.00 2.41
6549 14167 1.479323 GTGGTCCTCGGCTTGTATGTA 59.521 52.381 0.00 0.00 0.00 2.29
6550 14168 0.249398 GTGGTCCTCGGCTTGTATGT 59.751 55.000 0.00 0.00 0.00 2.29
6551 14169 0.537188 AGTGGTCCTCGGCTTGTATG 59.463 55.000 0.00 0.00 0.00 2.39
6552 14170 2.154567 TAGTGGTCCTCGGCTTGTAT 57.845 50.000 0.00 0.00 0.00 2.29
6561 14179 6.759272 TGTATGCATCTTTATAGTGGTCCTC 58.241 40.000 0.19 0.00 0.00 3.71
6573 14191 8.133627 GCAAAGTCATTATCTGTATGCATCTTT 58.866 33.333 0.19 0.00 0.00 2.52
6591 14209 1.072331 GGAAGTCTCCTGGCAAAGTCA 59.928 52.381 0.00 0.00 38.88 3.41
6606 14224 0.322975 ACGCTGCTCATCAAGGAAGT 59.677 50.000 0.00 0.00 0.00 3.01
6615 14233 0.036010 ACTTTAGCCACGCTGCTCAT 60.036 50.000 2.14 0.00 41.68 2.90
6623 14241 3.188895 GCTGAAGAAACTTTAGCCACG 57.811 47.619 14.41 0.00 0.00 4.94
6629 14247 3.764237 ACGAGGGCTGAAGAAACTTTA 57.236 42.857 0.00 0.00 0.00 1.85
6631 14249 3.260884 TGATACGAGGGCTGAAGAAACTT 59.739 43.478 0.00 0.00 0.00 2.66
6679 14297 9.985730 ACAAGAAATATGACATGTGAACATTTT 57.014 25.926 1.15 0.00 33.61 1.82
6680 14298 9.630098 GACAAGAAATATGACATGTGAACATTT 57.370 29.630 1.15 5.51 33.61 2.32
6681 14299 8.795513 TGACAAGAAATATGACATGTGAACATT 58.204 29.630 1.15 0.00 33.61 2.71
6682 14300 8.339344 TGACAAGAAATATGACATGTGAACAT 57.661 30.769 1.15 3.11 36.96 2.71
6683 14301 7.742556 TGACAAGAAATATGACATGTGAACA 57.257 32.000 1.15 0.00 0.00 3.18
6684 14302 9.630098 ATTTGACAAGAAATATGACATGTGAAC 57.370 29.630 1.15 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.