Multiple sequence alignment - TraesCS5D01G504600

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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 TraesCS5D01G504600 chr5D 100.000 4031 0 0 1 4031 530868968 530872998 0.000000e+00 7444.0
1 TraesCS5D01G504600 chr5D 84.173 139 15 4 3105 3243 531880254 531880123 1.180000e-25 128.0
2 TraesCS5D01G504600 chr5D 100.000 34 0 0 1488 1521 530921412 530921445 3.360000e-06 63.9
3 TraesCS5D01G504600 chr5B 86.013 1816 136 60 1720 3481 670114750 670116501 0.000000e+00 1838.0
4 TraesCS5D01G504600 chr5B 89.730 740 66 4 4 736 670111245 670111981 0.000000e+00 937.0
5 TraesCS5D01G504600 chr5B 86.465 761 74 17 785 1518 670113860 670114618 0.000000e+00 808.0
6 TraesCS5D01G504600 chr5B 93.289 149 9 1 3805 3952 670116887 670117035 6.780000e-53 219.0
7 TraesCS5D01G504600 chr4A 86.411 1538 125 42 769 2247 641405204 641403692 0.000000e+00 1605.0
8 TraesCS5D01G504600 chr4A 84.173 1112 123 32 2397 3484 641403609 641402527 0.000000e+00 1029.0
9 TraesCS5D01G504600 chr4A 88.710 248 18 3 3688 3927 641402353 641402108 1.100000e-75 294.0
10 TraesCS5D01G504600 chr4A 100.000 37 0 0 3995 4031 641402072 641402036 7.230000e-08 69.4
11 TraesCS5D01G504600 chr4B 86.927 742 84 7 1 730 187364498 187365238 0.000000e+00 821.0
12 TraesCS5D01G504600 chr2A 77.895 760 136 22 4 743 652862811 652862064 1.030000e-120 444.0
13 TraesCS5D01G504600 chr5A 89.730 185 19 0 3485 3669 578233471 578233655 1.870000e-58 237.0
14 TraesCS5D01G504600 chr5A 89.247 186 18 2 3485 3669 631470287 631470103 8.710000e-57 231.0
15 TraesCS5D01G504600 chr5A 93.103 58 3 1 3427 3484 104242967 104242911 2.580000e-12 84.2
16 TraesCS5D01G504600 chr4D 90.000 180 16 2 3491 3669 69179571 69179749 8.710000e-57 231.0
17 TraesCS5D01G504600 chr4D 88.649 185 21 0 3485 3669 16920428 16920612 4.050000e-55 226.0
18 TraesCS5D01G504600 chr4D 88.649 185 21 0 3485 3669 69178044 69178228 4.050000e-55 226.0
19 TraesCS5D01G504600 chr3A 89.189 185 20 0 3485 3669 743686137 743686321 8.710000e-57 231.0
20 TraesCS5D01G504600 chr3A 88.398 181 21 0 3489 3669 729764564 729764384 6.780000e-53 219.0
21 TraesCS5D01G504600 chr1D 89.189 185 20 0 3485 3669 339743476 339743292 8.710000e-57 231.0
22 TraesCS5D01G504600 chr1D 93.220 59 3 1 3427 3485 170206395 170206338 7.180000e-13 86.1
23 TraesCS5D01G504600 chr3D 89.071 183 20 0 3485 3667 588164401 588164219 1.130000e-55 228.0
24 TraesCS5D01G504600 chr7A 84.211 133 13 6 3102 3233 402123002 402123127 5.470000e-24 122.0
25 TraesCS5D01G504600 chr7A 94.828 58 2 1 3427 3484 721736951 721736895 5.550000e-14 89.8
26 TraesCS5D01G504600 chr7D 94.828 58 2 1 3427 3484 157472987 157472931 5.550000e-14 89.8
27 TraesCS5D01G504600 chr7D 94.828 58 2 1 3427 3484 525006959 525007015 5.550000e-14 89.8
28 TraesCS5D01G504600 chr3B 94.828 58 2 1 3427 3484 417235976 417236032 5.550000e-14 89.8
29 TraesCS5D01G504600 chr6D 93.220 59 3 1 3427 3485 357239140 357239083 7.180000e-13 86.1
30 TraesCS5D01G504600 chr2D 93.220 59 3 1 3427 3485 20551983 20551926 7.180000e-13 86.1
31 TraesCS5D01G504600 chr2D 93.220 59 3 1 3427 3485 395183700 395183757 7.180000e-13 86.1


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 TraesCS5D01G504600 chr5D 530868968 530872998 4030 False 7444.00 7444 100.00000 1 4031 1 chr5D.!!$F1 4030
1 TraesCS5D01G504600 chr5B 670111245 670117035 5790 False 950.50 1838 88.87425 4 3952 4 chr5B.!!$F1 3948
2 TraesCS5D01G504600 chr4A 641402036 641405204 3168 True 749.35 1605 89.82350 769 4031 4 chr4A.!!$R1 3262
3 TraesCS5D01G504600 chr4B 187364498 187365238 740 False 821.00 821 86.92700 1 730 1 chr4B.!!$F1 729
4 TraesCS5D01G504600 chr2A 652862064 652862811 747 True 444.00 444 77.89500 4 743 1 chr2A.!!$R1 739
5 TraesCS5D01G504600 chr4D 69178044 69179749 1705 False 228.50 231 89.32450 3485 3669 2 chr4D.!!$F2 184

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
741 760 0.108520 AGAAACACCGTCACACGTGT 60.109 50.0 17.22 17.22 40.58 4.49 F
1297 3160 0.098552 TTGATTGCAAGTATGGCGCG 59.901 50.0 4.94 0.00 38.51 6.86 F
1351 3217 0.238289 ATGCCGTTGAAGCGTTTGAG 59.762 50.0 0.00 0.00 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2375 4354 0.038166 ATGACCATCCACGGCAAACT 59.962 50.000 0.00 0.0 0.00 2.66 R
2488 4481 0.834612 TACTTCCCTGCCAATACGGG 59.165 55.000 0.00 0.0 39.41 5.28 R
3230 5225 1.074775 AAGGTCGCATGGGCAGAAA 59.925 52.632 4.59 0.0 41.24 2.52 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.490490 TGCCATAAGCTCTAACCCAGG 59.510 52.381 0.00 0.00 44.23 4.45
177 178 9.140286 GCCTTTTGTTGGAAGATAAATAGAAAC 57.860 33.333 0.00 0.00 0.00 2.78
194 195 5.466127 AGAAACCTATTCCTGCCCAAATA 57.534 39.130 0.00 0.00 0.00 1.40
225 228 4.651867 CCACAATGGGCTCCAGAG 57.348 61.111 0.41 0.00 36.75 3.35
233 237 3.957919 GGCTCCAGAGTCCCCTAC 58.042 66.667 0.00 0.00 0.00 3.18
245 249 1.555533 GTCCCCTACAGTTCTTCCCAG 59.444 57.143 0.00 0.00 0.00 4.45
300 304 0.401738 TGCCTACTGCCTGAAGCTTT 59.598 50.000 0.00 0.00 44.23 3.51
307 311 0.473755 TGCCTGAAGCTTTCTCACCA 59.526 50.000 0.00 0.00 44.23 4.17
366 370 3.556004 CCTTCTTTTCCGCTTCAGAGAGT 60.556 47.826 0.00 0.00 0.00 3.24
400 411 3.264450 CCCTTCACTCCTTCAAGGTATGT 59.736 47.826 2.50 0.00 35.77 2.29
405 416 2.572104 ACTCCTTCAAGGTATGTGGTCC 59.428 50.000 2.50 0.00 36.53 4.46
466 478 4.431131 CACCGCAGCCCCCTTCAT 62.431 66.667 0.00 0.00 0.00 2.57
480 492 2.029623 CCTTCATGCCTCCAAATCTGG 58.970 52.381 0.00 0.00 45.08 3.86
500 517 2.826287 CCGCCACACACCACAACA 60.826 61.111 0.00 0.00 0.00 3.33
520 537 3.011032 ACATGCTCCCAAAATCCTCTCTT 59.989 43.478 0.00 0.00 0.00 2.85
545 562 3.684788 CCTCACCAGGTTGTTCTAAATCG 59.315 47.826 0.00 0.00 34.60 3.34
555 572 5.237344 GGTTGTTCTAAATCGGATCTGGATG 59.763 44.000 0.62 0.00 0.00 3.51
575 592 1.673665 GGCTCTCACACTTGCTGGG 60.674 63.158 0.00 0.00 0.00 4.45
606 623 3.493350 GGAATCTATGCACGAGATGGTGT 60.493 47.826 12.53 0.00 40.08 4.16
674 693 0.393808 GGATTGAGCGGCAAGGGTTA 60.394 55.000 1.45 0.00 40.42 2.85
681 700 4.296265 GGCAAGGGTTACCGACAG 57.704 61.111 0.00 0.00 43.47 3.51
686 705 0.472352 AAGGGTTACCGACAGGGACA 60.472 55.000 0.00 0.00 43.47 4.02
705 724 2.029666 GCACTGAGTCGCCACACT 59.970 61.111 0.00 0.00 0.00 3.55
721 740 2.357881 CTGTCGCCAGAAGCAGCA 60.358 61.111 0.00 0.00 44.04 4.41
736 755 1.013596 CAGCAAGAAACACCGTCACA 58.986 50.000 0.00 0.00 0.00 3.58
739 758 1.003851 CAAGAAACACCGTCACACGT 58.996 50.000 0.00 0.00 40.58 4.49
741 760 0.108520 AGAAACACCGTCACACGTGT 60.109 50.000 17.22 17.22 40.58 4.49
743 762 1.519758 GAAACACCGTCACACGTGTAG 59.480 52.381 22.90 15.62 40.58 2.74
761 800 3.396276 TGTAGGGGGAAATGAAGTTGTGA 59.604 43.478 0.00 0.00 0.00 3.58
781 820 5.766670 TGTGAAGCTTGAAGATTGATGAAGT 59.233 36.000 2.10 0.00 0.00 3.01
802 2651 5.902051 GTCATAAGACGCCTTGTTATACC 57.098 43.478 0.00 0.00 34.60 2.73
820 2669 8.781196 TGTTATACCGTGTGTATTTTGCTTTTA 58.219 29.630 0.00 0.00 40.64 1.52
872 2726 4.451900 TGACAAAGTCTGAGGTCTTTTCC 58.548 43.478 0.00 0.00 32.52 3.13
922 2778 2.722100 GCAGCTTAAAGAAACGCGAGAC 60.722 50.000 15.93 2.72 0.00 3.36
1085 2945 3.075005 CATCCACCTCCCGTCCGT 61.075 66.667 0.00 0.00 0.00 4.69
1086 2946 3.075005 ATCCACCTCCCGTCCGTG 61.075 66.667 0.00 0.00 0.00 4.94
1207 3067 1.471153 GCCTCCGCAAGAAGGTACTAC 60.471 57.143 0.00 0.00 36.17 2.73
1208 3068 1.136500 CCTCCGCAAGAAGGTACTACC 59.864 57.143 0.00 0.00 38.49 3.18
1222 3085 1.218316 CTACCAGTGAACCTCCGGC 59.782 63.158 0.00 0.00 0.00 6.13
1237 3100 4.002797 GGCACGAAGATTGGGCTT 57.997 55.556 0.00 0.00 0.00 4.35
1248 3111 3.222603 AGATTGGGCTTCGTTGTTTTCT 58.777 40.909 0.00 0.00 0.00 2.52
1249 3112 3.636764 AGATTGGGCTTCGTTGTTTTCTT 59.363 39.130 0.00 0.00 0.00 2.52
1256 3119 4.201920 GGCTTCGTTGTTTTCTTGTCTCTT 60.202 41.667 0.00 0.00 0.00 2.85
1258 3121 5.228012 GCTTCGTTGTTTTCTTGTCTCTTTG 59.772 40.000 0.00 0.00 0.00 2.77
1280 3143 1.343510 AATGCGCGGCGATTTGTTTG 61.344 50.000 28.54 0.00 0.00 2.93
1282 3145 1.514014 GCGCGGCGATTTGTTTGAT 60.514 52.632 28.54 0.00 0.00 2.57
1285 3148 0.366534 GCGGCGATTTGTTTGATTGC 59.633 50.000 12.98 0.00 33.92 3.56
1289 3152 3.059166 GGCGATTTGTTTGATTGCAAGT 58.941 40.909 4.94 0.00 35.94 3.16
1290 3153 4.233789 GGCGATTTGTTTGATTGCAAGTA 58.766 39.130 4.94 0.00 35.94 2.24
1291 3154 4.864247 GGCGATTTGTTTGATTGCAAGTAT 59.136 37.500 4.94 0.00 35.94 2.12
1293 3156 5.220265 GCGATTTGTTTGATTGCAAGTATGG 60.220 40.000 4.94 0.00 35.04 2.74
1294 3157 5.220265 CGATTTGTTTGATTGCAAGTATGGC 60.220 40.000 4.94 0.00 35.04 4.40
1295 3158 3.214697 TGTTTGATTGCAAGTATGGCG 57.785 42.857 4.94 0.00 38.51 5.69
1296 3159 1.919918 GTTTGATTGCAAGTATGGCGC 59.080 47.619 4.94 0.00 38.51 6.53
1297 3160 0.098552 TTGATTGCAAGTATGGCGCG 59.901 50.000 4.94 0.00 38.51 6.86
1298 3161 1.655350 GATTGCAAGTATGGCGCGC 60.655 57.895 25.94 25.94 38.51 6.86
1301 3164 4.241999 GCAAGTATGGCGCGCCTG 62.242 66.667 45.79 35.82 36.94 4.85
1351 3217 0.238289 ATGCCGTTGAAGCGTTTGAG 59.762 50.000 0.00 0.00 0.00 3.02
1360 3226 3.476552 TGAAGCGTTTGAGGAAATGTCT 58.523 40.909 0.00 0.00 31.59 3.41
1371 3237 9.366216 GTTTGAGGAAATGTCTTTAGTTTGTTT 57.634 29.630 0.00 0.00 0.00 2.83
1384 3250 2.548480 AGTTTGTTTCGGCAGTAGCTTC 59.452 45.455 0.00 0.00 41.70 3.86
1385 3251 2.543777 TTGTTTCGGCAGTAGCTTCT 57.456 45.000 0.00 0.00 41.70 2.85
1386 3252 2.543777 TGTTTCGGCAGTAGCTTCTT 57.456 45.000 0.00 0.00 41.70 2.52
1388 3254 3.997762 TGTTTCGGCAGTAGCTTCTTTA 58.002 40.909 0.00 0.00 41.70 1.85
1413 3293 2.263077 CTGAACGTCTGCAGTATGTCC 58.737 52.381 14.67 0.81 39.31 4.02
1420 3300 0.940126 CTGCAGTATGTCCGATTGGC 59.060 55.000 5.25 0.00 39.31 4.52
1479 3391 8.786826 TTACAGAGAAGTATTTGTACCAATGG 57.213 34.615 0.00 0.00 0.00 3.16
1495 3407 0.625316 ATGGCTGCCACTGGATACAA 59.375 50.000 25.99 0.00 40.72 2.41
1522 3434 2.016318 TCAAGGGATTGCAATGTAGCG 58.984 47.619 18.59 2.53 37.31 4.26
1538 3450 3.981416 TGTAGCGAGCGCATCTATAAAAG 59.019 43.478 17.68 0.00 44.88 2.27
1540 3452 1.461127 GCGAGCGCATCTATAAAAGGG 59.539 52.381 11.47 0.00 41.49 3.95
1555 3467 1.767759 AAGGGCATGCCACTTGTATC 58.232 50.000 36.56 17.44 37.98 2.24
1562 3474 3.503748 GCATGCCACTTGTATCTAATCCC 59.496 47.826 6.36 0.00 0.00 3.85
1569 3481 4.758674 CACTTGTATCTAATCCCATGCCAG 59.241 45.833 0.00 0.00 0.00 4.85
1580 3492 1.309950 CCATGCCAGCTCAGATTCTG 58.690 55.000 7.38 7.38 0.00 3.02
1587 3499 1.829849 CAGCTCAGATTCTGGGTGAGA 59.170 52.381 20.45 0.90 40.21 3.27
1618 3530 8.470805 TGATGTAGAAGAGAGATGGTTAACTTC 58.529 37.037 5.42 3.48 35.47 3.01
1651 3571 1.747355 GATGCAAGCTTAGGCACACAT 59.253 47.619 13.15 0.00 43.75 3.21
1659 3579 5.614324 AGCTTAGGCACACATATCAAGTA 57.386 39.130 0.00 0.00 41.70 2.24
1665 3585 6.683974 AGGCACACATATCAAGTATTTGAC 57.316 37.500 2.38 0.00 45.54 3.18
1667 3587 6.094048 AGGCACACATATCAAGTATTTGACAC 59.906 38.462 2.38 0.00 45.54 3.67
1693 3615 9.904647 CAAAAATATATGCATCGGAAAACTTTG 57.095 29.630 0.19 1.15 0.00 2.77
1706 3629 3.518634 AAACTTTGCACACGAACCAAT 57.481 38.095 0.00 0.00 0.00 3.16
1707 3630 3.518634 AACTTTGCACACGAACCAATT 57.481 38.095 0.00 0.00 0.00 2.32
1756 3683 6.554334 AATGGTGTGATGTTTACACTGTAC 57.446 37.500 8.01 0.00 45.82 2.90
1791 3718 8.398665 GTTATTGTCAATGGAATCAGGACTTAC 58.601 37.037 8.39 0.00 34.33 2.34
2011 3943 6.801575 TGGTTTTGAGTTGTCATACCTTTTC 58.198 36.000 0.00 0.00 38.07 2.29
2012 3944 6.378564 TGGTTTTGAGTTGTCATACCTTTTCA 59.621 34.615 0.00 0.00 38.07 2.69
2039 3978 6.230472 TCATATTAAGCTAACATGGTCGCAT 58.770 36.000 10.21 0.00 0.00 4.73
2069 4015 4.305989 TCAACTTGTTTTGTGATCCTGC 57.694 40.909 0.00 0.00 0.00 4.85
2093 4051 6.554334 GCTCCCTTGCGTATATAAATGAAA 57.446 37.500 0.00 0.00 0.00 2.69
2094 4052 6.371389 GCTCCCTTGCGTATATAAATGAAAC 58.629 40.000 0.00 0.00 0.00 2.78
2095 4053 6.204882 GCTCCCTTGCGTATATAAATGAAACT 59.795 38.462 0.00 0.00 0.00 2.66
2096 4054 7.490962 TCCCTTGCGTATATAAATGAAACTG 57.509 36.000 0.00 0.00 0.00 3.16
2097 4055 7.051623 TCCCTTGCGTATATAAATGAAACTGT 58.948 34.615 0.00 0.00 0.00 3.55
2113 4071 7.764141 TGAAACTGTACAGTACTGTATACCA 57.236 36.000 32.53 24.88 46.36 3.25
2114 4072 8.357290 TGAAACTGTACAGTACTGTATACCAT 57.643 34.615 32.53 20.99 46.36 3.55
2115 4073 8.809066 TGAAACTGTACAGTACTGTATACCATT 58.191 33.333 32.53 23.57 46.36 3.16
2116 4074 9.649167 GAAACTGTACAGTACTGTATACCATTT 57.351 33.333 32.53 25.32 46.36 2.32
2138 4096 6.902771 TTATTTTAACTGGCAGCACCTTTA 57.097 33.333 15.89 2.19 40.22 1.85
2150 4108 5.991606 GGCAGCACCTTTAGAAAAGAAATTT 59.008 36.000 0.00 0.00 34.51 1.82
2154 4112 8.542953 CAGCACCTTTAGAAAAGAAATTTGTTC 58.457 33.333 0.45 0.08 0.00 3.18
2200 4159 8.128322 ACTGGCTGTCTATTATACTTCCTATG 57.872 38.462 0.00 0.00 0.00 2.23
2255 4231 7.543359 TGAGTCAAAGAAAATTCCATCCAAT 57.457 32.000 0.00 0.00 0.00 3.16
2277 4253 8.413229 CCAATAATATGACTAAACCCAGGTTTG 58.587 37.037 22.26 14.87 46.34 2.93
2278 4254 8.413229 CAATAATATGACTAAACCCAGGTTTGG 58.587 37.037 22.26 21.29 46.34 3.28
2285 4261 5.855740 CTAAACCCAGGTTTGGTTAAACA 57.144 39.130 22.26 0.00 45.23 2.83
2287 4263 5.702065 AAACCCAGGTTTGGTTAAACAAT 57.298 34.783 13.94 0.00 45.23 2.71
2288 4264 6.809976 AAACCCAGGTTTGGTTAAACAATA 57.190 33.333 13.94 0.00 45.23 1.90
2308 4284 7.177878 ACAATAAGAGATTTTGAGTGGTGGAT 58.822 34.615 0.00 0.00 0.00 3.41
2312 4288 5.006386 AGAGATTTTGAGTGGTGGATCAAC 58.994 41.667 0.00 0.00 35.25 3.18
2318 4294 1.197721 GAGTGGTGGATCAACAAAGCG 59.802 52.381 1.86 0.00 30.77 4.68
2337 4315 1.407258 CGCCTCTCTCTGTTTCCCTAG 59.593 57.143 0.00 0.00 0.00 3.02
2353 4331 8.215050 TGTTTCCCTAGTTATATGTGGGTAATG 58.785 37.037 0.00 0.00 38.95 1.90
2360 4338 5.304614 AGTTATATGTGGGTAATGCGACTCT 59.695 40.000 0.00 0.00 0.00 3.24
2361 4339 2.315925 ATGTGGGTAATGCGACTCTG 57.684 50.000 0.00 0.00 0.00 3.35
2375 4354 5.972935 TGCGACTCTGGTTCATAAATAGAA 58.027 37.500 0.00 0.00 0.00 2.10
2383 4362 6.093495 TCTGGTTCATAAATAGAAGTTTGCCG 59.907 38.462 0.00 0.00 0.00 5.69
2385 4364 6.027749 GGTTCATAAATAGAAGTTTGCCGTG 58.972 40.000 0.00 0.00 0.00 4.94
2390 4369 2.107950 TAGAAGTTTGCCGTGGATGG 57.892 50.000 0.00 0.00 0.00 3.51
2401 4381 1.942657 CCGTGGATGGTCATGATTGTC 59.057 52.381 0.00 0.00 0.00 3.18
2421 4401 0.927537 CAATTGCTGGCATTGCGATG 59.072 50.000 9.80 9.80 35.00 3.84
2429 4409 3.058450 CTGGCATTGCGATGTTTTTCAA 58.942 40.909 15.45 0.00 35.63 2.69
2436 4417 6.183360 GCATTGCGATGTTTTTCAATCAATCT 60.183 34.615 15.45 0.00 35.63 2.40
2488 4481 4.744795 ACACTAGGTGAGATGATTGGAC 57.255 45.455 4.62 0.00 36.96 4.02
2491 4484 0.833287 AGGTGAGATGATTGGACCCG 59.167 55.000 0.00 0.00 0.00 5.28
2516 4509 2.112190 GGCAGGGAAGTAGCTTCTAGT 58.888 52.381 8.52 0.00 40.07 2.57
2520 4513 4.202172 GCAGGGAAGTAGCTTCTAGTTAGG 60.202 50.000 8.52 0.00 40.07 2.69
2556 4549 5.853936 TGATAATCCGAGGGAACATTGTAG 58.146 41.667 0.00 0.00 34.34 2.74
2558 4551 6.551975 TGATAATCCGAGGGAACATTGTAGTA 59.448 38.462 0.00 0.00 34.34 1.82
2559 4552 4.667519 ATCCGAGGGAACATTGTAGTAC 57.332 45.455 0.00 0.00 34.34 2.73
2561 4554 4.858850 TCCGAGGGAACATTGTAGTACTA 58.141 43.478 0.00 0.00 0.00 1.82
2562 4555 5.263599 TCCGAGGGAACATTGTAGTACTAA 58.736 41.667 3.61 0.00 0.00 2.24
2563 4556 5.126061 TCCGAGGGAACATTGTAGTACTAAC 59.874 44.000 3.61 0.09 0.00 2.34
2564 4557 5.032863 CGAGGGAACATTGTAGTACTAACG 58.967 45.833 3.61 0.00 0.00 3.18
2565 4558 5.163723 CGAGGGAACATTGTAGTACTAACGA 60.164 44.000 3.61 0.00 0.00 3.85
2584 4577 6.463483 AACGAATCTCCGAAGAAAACTTAC 57.537 37.500 0.00 0.00 34.49 2.34
2588 4581 6.531948 CGAATCTCCGAAGAAAACTTACAGAT 59.468 38.462 0.00 0.00 34.49 2.90
2850 4844 5.128919 AGGCTTATGCTTAGTTTCTGATGG 58.871 41.667 0.13 0.00 39.59 3.51
3084 5079 8.857694 TGTAATATTCTCTTTTCTTTCCCGTT 57.142 30.769 0.00 0.00 0.00 4.44
3135 5130 0.242017 GGTTGTTCTGCAGACATGGC 59.758 55.000 18.03 5.94 0.00 4.40
3136 5131 0.242017 GTTGTTCTGCAGACATGGCC 59.758 55.000 18.03 0.00 0.00 5.36
3137 5132 0.895100 TTGTTCTGCAGACATGGCCC 60.895 55.000 18.03 0.00 0.00 5.80
3138 5133 2.048603 GTTCTGCAGACATGGCCCC 61.049 63.158 18.03 0.00 0.00 5.80
3139 5134 2.233566 TTCTGCAGACATGGCCCCT 61.234 57.895 18.03 0.00 0.00 4.79
3230 5225 6.174720 TCTGTCTATTTCTGACACTTTGGT 57.825 37.500 0.00 0.00 39.23 3.67
3243 5238 0.388907 CTTTGGTTTCTGCCCATGCG 60.389 55.000 0.00 0.00 41.78 4.73
3250 5245 3.818787 CTGCCCATGCGACCTTGC 61.819 66.667 0.00 0.00 41.78 4.01
3257 5253 3.431055 TGCGACCTTGCAAACCAG 58.569 55.556 0.00 0.00 43.02 4.00
3261 5257 1.363807 GACCTTGCAAACCAGCACC 59.636 57.895 0.00 0.00 45.61 5.01
3304 5300 2.422127 GCGAGCTTGGGCAAAATAACTA 59.578 45.455 2.37 0.00 41.70 2.24
3305 5301 3.487544 GCGAGCTTGGGCAAAATAACTAG 60.488 47.826 2.37 0.00 41.70 2.57
3307 5303 3.365472 AGCTTGGGCAAAATAACTAGGG 58.635 45.455 0.00 0.00 41.70 3.53
3309 5305 3.960755 GCTTGGGCAAAATAACTAGGGAT 59.039 43.478 0.00 0.00 38.54 3.85
3324 5328 3.847671 AGGGATACTTTAGCAGCTTCC 57.152 47.619 0.00 0.00 0.00 3.46
3327 5331 3.817647 GGGATACTTTAGCAGCTTCCATG 59.182 47.826 0.00 0.00 31.11 3.66
3348 5352 7.937942 TCCATGCTTTAGTACTACTAGTAGGAG 59.062 40.741 29.05 17.85 37.49 3.69
3349 5353 7.720515 CCATGCTTTAGTACTACTAGTAGGAGT 59.279 40.741 29.05 26.13 37.49 3.85
3368 5372 9.727859 GTAGGAGTAGATAACAGATACAGATGA 57.272 37.037 0.00 0.00 0.00 2.92
3421 5425 8.623903 GCATGTCAAATCCTGATTACAGAATTA 58.376 33.333 0.00 0.00 46.03 1.40
3447 5451 4.437239 AGCACTACACAGTAATGCATCTC 58.563 43.478 12.30 0.00 32.21 2.75
3506 5513 4.765856 ACTCTGTCCGTGAATAAGTGTACT 59.234 41.667 0.00 0.00 0.00 2.73
3511 5518 7.338703 TCTGTCCGTGAATAAGTGTACTTCTAT 59.661 37.037 0.00 0.00 37.40 1.98
3512 5519 8.510243 TGTCCGTGAATAAGTGTACTTCTATA 57.490 34.615 0.00 0.00 37.40 1.31
3516 5523 9.961265 CCGTGAATAAGTGTACTTCTATATTCA 57.039 33.333 12.95 12.95 36.05 2.57
3660 5667 5.404466 TGCCATAAATGCTGCTACTTTTT 57.596 34.783 0.00 0.00 0.00 1.94
3671 7154 6.795399 TGCTGCTACTTTTTCCTATAAATGC 58.205 36.000 0.00 0.00 0.00 3.56
3673 7156 6.914757 GCTGCTACTTTTTCCTATAAATGCTG 59.085 38.462 0.00 0.00 0.00 4.41
3677 7160 8.070769 GCTACTTTTTCCTATAAATGCTGCTAC 58.929 37.037 0.00 0.00 0.00 3.58
3727 7210 2.047179 GCACCGTCCTCTTGGTCC 60.047 66.667 0.00 0.00 35.96 4.46
3772 7263 4.655762 TCTGCAGCAAATAGATACGAGT 57.344 40.909 9.47 0.00 0.00 4.18
3773 7264 4.611943 TCTGCAGCAAATAGATACGAGTC 58.388 43.478 9.47 0.00 0.00 3.36
3809 7300 7.566760 CAAAAGGTGCCACATGTATTATCTA 57.433 36.000 0.00 0.00 0.00 1.98
3814 7379 8.435931 AGGTGCCACATGTATTATCTAGATTA 57.564 34.615 11.25 1.48 0.00 1.75
3875 7440 8.223100 GCAAATGATCAACAAATCCAAGTAAAC 58.777 33.333 0.00 0.00 0.00 2.01
3900 7465 5.222048 TGGGGGCTAATCATGTAATCCTAAC 60.222 44.000 0.00 0.00 0.00 2.34
3905 7470 9.569122 GGGCTAATCATGTAATCCTAACTAAAA 57.431 33.333 0.00 0.00 0.00 1.52
3954 7519 1.136695 TGCGGGGCAAATGATCAAATC 59.863 47.619 0.00 0.00 34.76 2.17
3958 7523 3.303049 GGGGCAAATGATCAAATCTCCT 58.697 45.455 0.00 0.00 0.00 3.69
3963 7528 5.338365 GCAAATGATCAAATCTCCTGACAC 58.662 41.667 0.00 0.00 0.00 3.67
3973 7538 1.214175 TCTCCTGACACCAAAAGGCAA 59.786 47.619 0.00 0.00 0.00 4.52
3974 7539 2.158475 TCTCCTGACACCAAAAGGCAAT 60.158 45.455 0.00 0.00 0.00 3.56
3975 7540 3.073798 TCTCCTGACACCAAAAGGCAATA 59.926 43.478 0.00 0.00 0.00 1.90
3976 7541 4.019174 CTCCTGACACCAAAAGGCAATAT 58.981 43.478 0.00 0.00 0.00 1.28
3977 7542 3.763360 TCCTGACACCAAAAGGCAATATG 59.237 43.478 0.00 0.00 0.00 1.78
3978 7543 3.514645 CTGACACCAAAAGGCAATATGC 58.485 45.455 0.00 0.00 44.08 3.14
3989 7554 2.124011 GCAATATGCACCGACAATGG 57.876 50.000 0.00 0.00 44.26 3.16
3990 7555 1.865248 GCAATATGCACCGACAATGGC 60.865 52.381 0.00 0.00 44.26 4.40
3991 7556 1.677576 CAATATGCACCGACAATGGCT 59.322 47.619 0.00 0.00 0.00 4.75
3992 7557 1.597742 ATATGCACCGACAATGGCTC 58.402 50.000 0.00 0.00 0.00 4.70
3993 7558 0.809636 TATGCACCGACAATGGCTCG 60.810 55.000 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
177 178 7.595819 TTGTAAATATTTGGGCAGGAATAGG 57.404 36.000 11.05 0.00 0.00 2.57
194 195 3.774216 CCATTGTGGGGTGGATTGTAAAT 59.226 43.478 0.00 0.00 37.72 1.40
225 228 1.555533 CTGGGAAGAACTGTAGGGGAC 59.444 57.143 0.00 0.00 0.00 4.46
233 237 3.503748 GGTTGAACATCTGGGAAGAACTG 59.496 47.826 0.00 0.00 0.00 3.16
245 249 2.237392 AGACCTGCTAGGGTTGAACATC 59.763 50.000 0.00 0.00 40.58 3.06
307 311 2.157738 GAAACAAGCATGCTCCTCACT 58.842 47.619 22.93 0.00 0.00 3.41
500 517 4.328118 AAAGAGAGGATTTTGGGAGCAT 57.672 40.909 0.00 0.00 0.00 3.79
520 537 4.781775 TTAGAACAACCTGGTGAGGAAA 57.218 40.909 0.00 0.00 42.93 3.13
545 562 0.765903 TGAGAGCCCCATCCAGATCC 60.766 60.000 0.00 0.00 0.00 3.36
555 572 1.673665 CAGCAAGTGTGAGAGCCCC 60.674 63.158 0.00 0.00 0.00 5.80
575 592 2.050144 TGCATAGATTCCAGTCCTCCC 58.950 52.381 0.00 0.00 0.00 4.30
606 623 1.500474 ATCGCCCTGATTCTCCTTCA 58.500 50.000 0.00 0.00 31.57 3.02
650 669 1.000233 TTGCCGCTCAATCCCCATT 60.000 52.632 0.00 0.00 0.00 3.16
674 693 4.295119 GTGCGTGTCCCTGTCGGT 62.295 66.667 0.00 0.00 0.00 4.69
680 699 2.920645 CGACTCAGTGCGTGTCCCT 61.921 63.158 0.00 0.00 35.17 4.20
681 700 2.430921 CGACTCAGTGCGTGTCCC 60.431 66.667 0.00 0.00 35.17 4.46
686 705 3.911698 TGTGGCGACTCAGTGCGT 61.912 61.111 0.00 0.00 0.00 5.24
705 724 1.962822 CTTGCTGCTTCTGGCGACA 60.963 57.895 0.00 0.00 45.43 4.35
736 755 1.982958 ACTTCATTTCCCCCTACACGT 59.017 47.619 0.00 0.00 0.00 4.49
739 758 3.396276 TCACAACTTCATTTCCCCCTACA 59.604 43.478 0.00 0.00 0.00 2.74
741 760 4.662278 CTTCACAACTTCATTTCCCCCTA 58.338 43.478 0.00 0.00 0.00 3.53
743 762 2.029020 GCTTCACAACTTCATTTCCCCC 60.029 50.000 0.00 0.00 0.00 5.40
761 800 8.571461 TTATGACTTCATCAATCTTCAAGCTT 57.429 30.769 0.00 0.00 41.93 3.74
781 820 4.098349 ACGGTATAACAAGGCGTCTTATGA 59.902 41.667 0.00 0.00 0.00 2.15
802 2651 8.751335 AGAACAAATAAAAGCAAAATACACACG 58.249 29.630 0.00 0.00 0.00 4.49
835 2686 8.708742 CAGACTTTGTCATTTTTCTACGTATCA 58.291 33.333 0.00 0.00 34.60 2.15
841 2692 7.442666 AGACCTCAGACTTTGTCATTTTTCTAC 59.557 37.037 0.46 0.00 34.60 2.59
859 2713 4.842139 CGAATTACGGAAAAGACCTCAG 57.158 45.455 0.00 0.00 38.46 3.35
872 2726 1.560923 CTCTGCTGGACCGAATTACG 58.439 55.000 0.00 0.00 42.18 3.18
922 2778 1.202582 CTCGCCTTATCCTATCCACCG 59.797 57.143 0.00 0.00 0.00 4.94
1069 2929 3.075005 CACGGACGGGAGGTGGAT 61.075 66.667 0.00 0.00 0.00 3.41
1234 3097 4.537936 AGAGACAAGAAAACAACGAAGC 57.462 40.909 0.00 0.00 0.00 3.86
1237 3100 4.438200 GGCAAAGAGACAAGAAAACAACGA 60.438 41.667 0.00 0.00 0.00 3.85
1249 3112 1.580942 GCGCATTGGCAAAGAGACA 59.419 52.632 10.34 0.00 41.24 3.41
1270 3133 5.220265 GCCATACTTGCAATCAAACAAATCG 60.220 40.000 0.00 0.00 0.00 3.34
1271 3134 5.220265 CGCCATACTTGCAATCAAACAAATC 60.220 40.000 0.00 0.00 0.00 2.17
1273 3136 3.986572 CGCCATACTTGCAATCAAACAAA 59.013 39.130 0.00 0.00 0.00 2.83
1280 3143 1.655350 GCGCGCCATACTTGCAATC 60.655 57.895 23.24 0.00 0.00 2.67
1282 3145 3.809775 GGCGCGCCATACTTGCAA 61.810 61.111 43.55 0.00 35.81 4.08
1293 3156 3.206211 ATAGAGAGAGCAGGCGCGC 62.206 63.158 25.94 25.94 45.49 6.86
1294 3157 1.371512 CATAGAGAGAGCAGGCGCG 60.372 63.158 0.00 0.00 45.49 6.86
1295 3158 1.006337 CCATAGAGAGAGCAGGCGC 60.006 63.158 0.00 0.00 38.99 6.53
1296 3159 0.597568 CTCCATAGAGAGAGCAGGCG 59.402 60.000 0.00 0.00 43.39 5.52
1297 3160 1.703411 ACTCCATAGAGAGAGCAGGC 58.297 55.000 0.00 0.00 43.39 4.85
1298 3161 3.295093 TCAACTCCATAGAGAGAGCAGG 58.705 50.000 0.00 0.00 43.39 4.85
1301 3164 4.462483 CCCTATCAACTCCATAGAGAGAGC 59.538 50.000 0.00 0.00 43.39 4.09
1340 3206 4.489679 AAGACATTTCCTCAAACGCTTC 57.510 40.909 0.00 0.00 0.00 3.86
1351 3217 5.401376 GCCGAAACAAACTAAAGACATTTCC 59.599 40.000 0.00 0.00 0.00 3.13
1360 3226 4.131596 AGCTACTGCCGAAACAAACTAAA 58.868 39.130 0.00 0.00 40.80 1.85
1371 3237 3.585862 CAACTAAAGAAGCTACTGCCGA 58.414 45.455 0.00 0.00 40.80 5.54
1384 3250 2.543848 TGCAGACGTTCAGCAACTAAAG 59.456 45.455 7.86 0.00 35.94 1.85
1385 3251 2.543848 CTGCAGACGTTCAGCAACTAAA 59.456 45.455 8.42 0.00 38.42 1.85
1386 3252 2.135139 CTGCAGACGTTCAGCAACTAA 58.865 47.619 8.42 0.00 38.42 2.24
1388 3254 0.179073 ACTGCAGACGTTCAGCAACT 60.179 50.000 23.35 0.00 38.42 3.16
1413 3293 1.372087 GGAGCTCAAGTGGCCAATCG 61.372 60.000 17.19 0.00 0.00 3.34
1420 3300 2.082231 CATCAACAGGAGCTCAAGTGG 58.918 52.381 17.19 10.77 0.00 4.00
1479 3391 0.677731 TGCTTGTATCCAGTGGCAGC 60.678 55.000 3.51 7.18 0.00 5.25
1495 3407 0.694771 TGCAATCCCTTGACTCTGCT 59.305 50.000 0.00 0.00 34.04 4.24
1522 3434 2.494059 TGCCCTTTTATAGATGCGCTC 58.506 47.619 9.73 3.60 0.00 5.03
1538 3450 2.638480 TAGATACAAGTGGCATGCCC 57.362 50.000 33.44 23.56 34.56 5.36
1540 3452 3.503748 GGGATTAGATACAAGTGGCATGC 59.496 47.826 9.90 9.90 0.00 4.06
1555 3467 1.419012 TCTGAGCTGGCATGGGATTAG 59.581 52.381 0.00 0.00 0.00 1.73
1562 3474 1.309950 CCAGAATCTGAGCTGGCATG 58.690 55.000 12.53 0.00 44.53 4.06
1569 3481 3.204526 CAATCTCACCCAGAATCTGAGC 58.795 50.000 12.53 0.00 33.62 4.26
1580 3492 4.162320 TCTTCTACATCACCAATCTCACCC 59.838 45.833 0.00 0.00 0.00 4.61
1587 3499 5.664908 ACCATCTCTCTTCTACATCACCAAT 59.335 40.000 0.00 0.00 0.00 3.16
1640 3560 7.826744 TGTCAAATACTTGATATGTGTGCCTAA 59.173 33.333 0.00 0.00 43.39 2.69
1659 3579 8.412456 TCCGATGCATATATTTTTGTGTCAAAT 58.588 29.630 0.00 0.00 0.00 2.32
1665 3585 8.633075 AGTTTTCCGATGCATATATTTTTGTG 57.367 30.769 0.00 0.00 0.00 3.33
1667 3587 9.904647 CAAAGTTTTCCGATGCATATATTTTTG 57.095 29.630 0.00 0.60 0.00 2.44
1693 3615 3.500680 TCCTTCTAAATTGGTTCGTGTGC 59.499 43.478 0.00 0.00 0.00 4.57
1706 3629 5.076873 CACCCTTTGAACCATCCTTCTAAA 58.923 41.667 0.00 0.00 0.00 1.85
1707 3630 4.352595 TCACCCTTTGAACCATCCTTCTAA 59.647 41.667 0.00 0.00 0.00 2.10
1756 3683 9.241317 GATTCCATTGACAATAACATAAGCTTG 57.759 33.333 9.86 0.00 0.00 4.01
1791 3718 7.871973 TGAAAGGAAAAATGTGTAATGACCATG 59.128 33.333 0.00 0.00 0.00 3.66
2011 3943 7.535258 GCGACCATGTTAGCTTAATATGAAATG 59.465 37.037 0.00 0.00 38.93 2.32
2012 3944 7.228507 TGCGACCATGTTAGCTTAATATGAAAT 59.771 33.333 0.00 0.00 38.93 2.17
2029 3968 9.333497 CAAGTTGATAAATATTATGCGACCATG 57.667 33.333 0.00 0.00 32.85 3.66
2113 4071 6.358974 AAGGTGCTGCCAGTTAAAATAAAT 57.641 33.333 0.00 0.00 40.61 1.40
2114 4072 5.799827 AAGGTGCTGCCAGTTAAAATAAA 57.200 34.783 0.00 0.00 40.61 1.40
2115 4073 5.799827 AAAGGTGCTGCCAGTTAAAATAA 57.200 34.783 0.00 0.00 40.61 1.40
2116 4074 6.242396 TCTAAAGGTGCTGCCAGTTAAAATA 58.758 36.000 0.00 0.00 40.61 1.40
2138 4096 8.533569 TCCTTACTGGAACAAATTTCTTTTCT 57.466 30.769 0.00 0.00 42.94 2.52
2167 4125 4.357918 AATAGACAGCCAGTTTGACAGT 57.642 40.909 0.00 0.00 0.00 3.55
2247 4207 7.394359 CCTGGGTTTAGTCATATTATTGGATGG 59.606 40.741 0.00 0.00 0.00 3.51
2255 4231 7.471890 AACCAAACCTGGGTTTAGTCATATTA 58.528 34.615 16.13 0.00 41.17 0.98
2259 4235 4.193240 AACCAAACCTGGGTTTAGTCAT 57.807 40.909 16.13 0.77 41.17 3.06
2264 4240 6.809976 ATTGTTTAACCAAACCTGGGTTTA 57.190 33.333 16.13 0.04 41.17 2.01
2277 4253 9.626045 CCACTCAAAATCTCTTATTGTTTAACC 57.374 33.333 0.00 0.00 0.00 2.85
2281 4257 7.505585 TCCACCACTCAAAATCTCTTATTGTTT 59.494 33.333 0.00 0.00 0.00 2.83
2285 4261 7.405292 TGATCCACCACTCAAAATCTCTTATT 58.595 34.615 0.00 0.00 0.00 1.40
2287 4263 6.373005 TGATCCACCACTCAAAATCTCTTA 57.627 37.500 0.00 0.00 0.00 2.10
2288 4264 5.246981 TGATCCACCACTCAAAATCTCTT 57.753 39.130 0.00 0.00 0.00 2.85
2301 4277 1.523154 GGCGCTTTGTTGATCCACCA 61.523 55.000 7.64 0.00 0.00 4.17
2308 4284 0.681733 AGAGAGAGGCGCTTTGTTGA 59.318 50.000 7.64 0.00 0.00 3.18
2312 4288 1.462670 GAAACAGAGAGAGGCGCTTTG 59.537 52.381 7.64 0.00 0.00 2.77
2318 4294 2.462723 ACTAGGGAAACAGAGAGAGGC 58.537 52.381 0.00 0.00 0.00 4.70
2337 4315 5.405571 CAGAGTCGCATTACCCACATATAAC 59.594 44.000 0.00 0.00 0.00 1.89
2353 4331 6.043411 ACTTCTATTTATGAACCAGAGTCGC 58.957 40.000 0.00 0.00 0.00 5.19
2360 4338 5.708230 ACGGCAAACTTCTATTTATGAACCA 59.292 36.000 0.00 0.00 0.00 3.67
2361 4339 6.027749 CACGGCAAACTTCTATTTATGAACC 58.972 40.000 0.00 0.00 0.00 3.62
2375 4354 0.038166 ATGACCATCCACGGCAAACT 59.962 50.000 0.00 0.00 0.00 2.66
2383 4362 3.003394 TGGACAATCATGACCATCCAC 57.997 47.619 16.16 0.00 44.67 4.02
2421 4401 8.538409 AATGGCTGTTAGATTGATTGAAAAAC 57.462 30.769 0.00 0.00 0.00 2.43
2429 4409 5.533903 GTGGATGAATGGCTGTTAGATTGAT 59.466 40.000 0.00 0.00 0.00 2.57
2436 4417 3.245229 ACTTGGTGGATGAATGGCTGTTA 60.245 43.478 0.00 0.00 0.00 2.41
2488 4481 0.834612 TACTTCCCTGCCAATACGGG 59.165 55.000 0.00 0.00 39.41 5.28
2491 4484 3.118223 AGAAGCTACTTCCCTGCCAATAC 60.118 47.826 3.77 0.00 40.98 1.89
2503 4496 6.839657 TCCAATAGCCTAACTAGAAGCTACTT 59.160 38.462 0.00 0.00 40.41 2.24
2516 4509 7.525526 CGGATTATCAGAGTTCCAATAGCCTAA 60.526 40.741 0.00 0.00 0.00 2.69
2520 4513 5.784177 TCGGATTATCAGAGTTCCAATAGC 58.216 41.667 0.00 0.00 0.00 2.97
2556 4549 6.805760 AGTTTTCTTCGGAGATTCGTTAGTAC 59.194 38.462 0.00 0.00 35.04 2.73
2558 4551 5.780984 AGTTTTCTTCGGAGATTCGTTAGT 58.219 37.500 0.00 0.00 35.04 2.24
2559 4552 6.707599 AAGTTTTCTTCGGAGATTCGTTAG 57.292 37.500 0.00 0.00 34.76 2.34
2561 4554 5.987347 TGTAAGTTTTCTTCGGAGATTCGTT 59.013 36.000 0.00 0.00 40.91 3.85
2562 4555 5.535333 TGTAAGTTTTCTTCGGAGATTCGT 58.465 37.500 0.00 0.00 40.91 3.85
2563 4556 5.862323 TCTGTAAGTTTTCTTCGGAGATTCG 59.138 40.000 0.00 0.00 40.91 3.34
2564 4557 7.332182 ACATCTGTAAGTTTTCTTCGGAGATTC 59.668 37.037 0.00 0.00 40.91 2.52
2565 4558 7.162082 ACATCTGTAAGTTTTCTTCGGAGATT 58.838 34.615 0.00 0.00 40.91 2.40
2725 4719 3.640029 CAGAAAGCATCATGGGCCTTTAT 59.360 43.478 4.53 0.00 0.00 1.40
2850 4844 1.956477 AGCACCACAACATTGAACTCC 59.044 47.619 0.00 0.00 0.00 3.85
3084 5079 8.882415 ACTACAGAAAGAACTTCGTTCAATAA 57.118 30.769 16.66 2.58 44.11 1.40
3093 5088 6.486993 ACCCAAATGACTACAGAAAGAACTTC 59.513 38.462 0.00 0.00 0.00 3.01
3135 5130 4.665483 AGATAACATTAAAGAGGGGAGGGG 59.335 45.833 0.00 0.00 0.00 4.79
3136 5131 5.369699 TCAGATAACATTAAAGAGGGGAGGG 59.630 44.000 0.00 0.00 0.00 4.30
3137 5132 6.500589 TCAGATAACATTAAAGAGGGGAGG 57.499 41.667 0.00 0.00 0.00 4.30
3138 5133 7.972301 AGATCAGATAACATTAAAGAGGGGAG 58.028 38.462 0.00 0.00 0.00 4.30
3139 5134 7.937700 AGATCAGATAACATTAAAGAGGGGA 57.062 36.000 0.00 0.00 0.00 4.81
3221 5216 1.688197 CATGGGCAGAAACCAAAGTGT 59.312 47.619 0.00 0.00 42.17 3.55
3230 5225 1.074775 AAGGTCGCATGGGCAGAAA 59.925 52.632 4.59 0.00 41.24 2.52
3243 5238 1.109323 AGGTGCTGGTTTGCAAGGTC 61.109 55.000 0.00 0.00 45.12 3.85
3257 5253 3.620488 TGAATACTCCATTTCCAGGTGC 58.380 45.455 0.00 0.00 0.00 5.01
3261 5257 4.574013 GCAGACTGAATACTCCATTTCCAG 59.426 45.833 6.65 0.00 0.00 3.86
3304 5300 3.115390 TGGAAGCTGCTAAAGTATCCCT 58.885 45.455 0.90 0.00 33.92 4.20
3305 5301 3.560636 TGGAAGCTGCTAAAGTATCCC 57.439 47.619 0.90 0.00 33.92 3.85
3307 5303 4.480386 GCATGGAAGCTGCTAAAGTATC 57.520 45.455 0.90 0.00 36.68 2.24
3324 5328 8.680039 ACTCCTACTAGTAGTACTAAAGCATG 57.320 38.462 24.84 8.22 29.00 4.06
3360 5364 7.465960 AGAGGCTTATAGACATCTCATCTGTA 58.534 38.462 0.00 0.00 0.00 2.74
3365 5369 7.372260 ACAAAGAGGCTTATAGACATCTCAT 57.628 36.000 0.00 0.00 0.00 2.90
3368 5372 9.553064 CAATAACAAAGAGGCTTATAGACATCT 57.447 33.333 0.00 0.00 0.00 2.90
3372 5376 6.542370 TGCCAATAACAAAGAGGCTTATAGAC 59.458 38.462 0.00 0.00 45.42 2.59
3376 5380 5.658190 ACATGCCAATAACAAAGAGGCTTAT 59.342 36.000 0.00 0.00 45.42 1.73
3421 5425 7.050377 AGATGCATTACTGTGTAGTGCTTATT 58.950 34.615 20.16 8.32 37.78 1.40
3425 5429 4.161189 AGAGATGCATTACTGTGTAGTGCT 59.839 41.667 20.16 10.11 37.78 4.40
3427 5431 4.269603 GCAGAGATGCATTACTGTGTAGTG 59.730 45.833 24.40 8.44 35.14 2.74
3428 5432 4.161189 AGCAGAGATGCATTACTGTGTAGT 59.839 41.667 24.40 6.97 37.86 2.73
3429 5433 4.691175 AGCAGAGATGCATTACTGTGTAG 58.309 43.478 24.40 8.82 37.25 2.74
3487 5494 5.717078 AGAAGTACACTTATTCACGGACA 57.283 39.130 0.00 0.00 36.11 4.02
3564 5571 9.578576 ACCAATTTGATGTCATATATGCTACTT 57.421 29.630 7.92 0.78 0.00 2.24
3577 5584 8.730680 ACTTTCACAGTATACCAATTTGATGTC 58.269 33.333 0.00 0.00 31.97 3.06
3632 5639 6.742109 AGTAGCAGCATTTATGGCATTAAAG 58.258 36.000 4.78 0.51 0.00 1.85
3637 5644 5.603170 AAAAGTAGCAGCATTTATGGCAT 57.397 34.783 4.88 4.88 0.00 4.40
3660 5667 7.174946 GGCATTAAAGTAGCAGCATTTATAGGA 59.825 37.037 0.00 0.00 0.00 2.94
3671 7154 8.623903 TCTTCATTTATGGCATTAAAGTAGCAG 58.376 33.333 4.78 0.00 0.00 4.24
3727 7210 5.061179 TGATGCACAGATATGATTGACAGG 58.939 41.667 0.00 0.00 0.00 4.00
3772 7263 1.203001 ACCTTTTGCAATTCCTCCCGA 60.203 47.619 0.00 0.00 0.00 5.14
3773 7264 1.067635 CACCTTTTGCAATTCCTCCCG 60.068 52.381 0.00 0.00 0.00 5.14
3846 7411 3.055240 TGGATTTGTTGATCATTTGCCCC 60.055 43.478 0.00 0.00 0.00 5.80
3875 7440 3.331889 AGGATTACATGATTAGCCCCCAG 59.668 47.826 0.00 0.00 0.00 4.45
3900 7465 6.405176 GGACTTGATCATTTGCTCCCTTTTAG 60.405 42.308 0.00 0.00 0.00 1.85
3905 7470 2.357569 GGGACTTGATCATTTGCTCCCT 60.358 50.000 12.97 0.00 34.15 4.20
3908 7473 2.726821 TGGGGACTTGATCATTTGCTC 58.273 47.619 0.00 0.00 0.00 4.26
3954 7519 1.691196 TTGCCTTTTGGTGTCAGGAG 58.309 50.000 0.00 0.00 42.99 3.69
3958 7523 2.896044 TGCATATTGCCTTTTGGTGTCA 59.104 40.909 0.00 0.00 44.23 3.58
3963 7528 1.476085 TCGGTGCATATTGCCTTTTGG 59.524 47.619 0.00 0.00 44.23 3.28
3973 7538 1.597742 GAGCCATTGTCGGTGCATAT 58.402 50.000 0.00 0.00 0.00 1.78
3974 7539 0.809636 CGAGCCATTGTCGGTGCATA 60.810 55.000 0.00 0.00 33.66 3.14
3975 7540 2.108514 CGAGCCATTGTCGGTGCAT 61.109 57.895 0.00 0.00 33.66 3.96
3976 7541 2.723586 TTCGAGCCATTGTCGGTGCA 62.724 55.000 0.00 0.00 38.02 4.57
3977 7542 1.573829 TTTCGAGCCATTGTCGGTGC 61.574 55.000 0.00 0.00 38.02 5.01
3978 7543 0.165944 GTTTCGAGCCATTGTCGGTG 59.834 55.000 0.00 0.00 38.02 4.94
3979 7544 0.250124 TGTTTCGAGCCATTGTCGGT 60.250 50.000 0.00 0.00 38.02 4.69
3980 7545 0.165944 GTGTTTCGAGCCATTGTCGG 59.834 55.000 0.00 0.00 38.02 4.79
3981 7546 0.865111 TGTGTTTCGAGCCATTGTCG 59.135 50.000 0.00 0.00 38.84 4.35
3982 7547 1.069227 GGTGTGTTTCGAGCCATTGTC 60.069 52.381 0.00 0.00 0.00 3.18
3983 7548 0.951558 GGTGTGTTTCGAGCCATTGT 59.048 50.000 0.00 0.00 0.00 2.71
3984 7549 0.240945 GGGTGTGTTTCGAGCCATTG 59.759 55.000 0.00 0.00 0.00 2.82
3985 7550 0.110486 AGGGTGTGTTTCGAGCCATT 59.890 50.000 0.00 0.00 31.76 3.16
3986 7551 0.110486 AAGGGTGTGTTTCGAGCCAT 59.890 50.000 0.00 0.00 31.76 4.40
3987 7552 0.534203 GAAGGGTGTGTTTCGAGCCA 60.534 55.000 0.00 0.00 31.76 4.75
3988 7553 0.250338 AGAAGGGTGTGTTTCGAGCC 60.250 55.000 0.00 0.00 0.00 4.70
3989 7554 0.868406 CAGAAGGGTGTGTTTCGAGC 59.132 55.000 0.00 0.00 0.00 5.03
3990 7555 2.526304 TCAGAAGGGTGTGTTTCGAG 57.474 50.000 0.00 0.00 0.00 4.04
3991 7556 2.992124 TTCAGAAGGGTGTGTTTCGA 57.008 45.000 0.00 0.00 0.00 3.71
3992 7557 3.563808 TCATTTCAGAAGGGTGTGTTTCG 59.436 43.478 0.00 0.00 0.00 3.46
3993 7558 4.557496 GCTCATTTCAGAAGGGTGTGTTTC 60.557 45.833 0.00 0.00 0.00 2.78


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

AutoCloner maintained by Alex Coulton.