Multiple sequence alignment - TraesCS2B01G604500

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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 TraesCS2B01G604500 chr2B 100.000 4984 0 0 1 4984 786101567 786106550 0.000000e+00 9204.0
1 TraesCS2B01G604500 chr2B 79.684 822 154 6 3355 4176 559422336 559421528 9.300000e-162 580.0
2 TraesCS2B01G604500 chr2B 100.000 62 0 0 4689 4750 786106195 786106256 1.130000e-21 115.0
3 TraesCS2B01G604500 chr2B 100.000 62 0 0 4629 4690 786106255 786106316 1.130000e-21 115.0
4 TraesCS2B01G604500 chr2D 96.376 1297 44 3 3227 4522 650078862 650080156 0.000000e+00 2132.0
5 TraesCS2B01G604500 chr2D 94.160 1250 61 4 670 1913 650076553 650077796 0.000000e+00 1893.0
6 TraesCS2B01G604500 chr2D 86.755 1057 105 7 2145 3186 650077821 650078857 0.000000e+00 1144.0
7 TraesCS2B01G604500 chr2D 78.986 947 170 22 3238 4176 477425627 477424702 1.970000e-173 619.0
8 TraesCS2B01G604500 chr2D 94.611 167 9 0 4524 4690 650080207 650080373 4.950000e-65 259.0
9 TraesCS2B01G604500 chr2D 94.656 131 6 1 4690 4820 650080313 650080442 8.460000e-48 202.0
10 TraesCS2B01G604500 chr2D 95.833 120 5 0 4857 4976 650190645 650190764 1.420000e-45 195.0
11 TraesCS2B01G604500 chr2A 95.227 1299 59 3 3227 4524 774815533 774814237 0.000000e+00 2052.0
12 TraesCS2B01G604500 chr2A 86.938 1424 117 33 1806 3186 774816935 774815538 0.000000e+00 1535.0
13 TraesCS2B01G604500 chr2A 93.527 1035 49 5 670 1686 774831956 774830922 0.000000e+00 1524.0
14 TraesCS2B01G604500 chr2A 83.519 1256 175 19 3237 4475 619771360 619770120 0.000000e+00 1144.0
15 TraesCS2B01G604500 chr2A 94.178 292 15 1 4690 4979 774814082 774813791 1.270000e-120 444.0
16 TraesCS2B01G604500 chr2A 75.597 922 161 38 996 1888 619809166 619808280 1.010000e-106 398.0
17 TraesCS2B01G604500 chr2A 94.340 159 9 0 4532 4690 774814180 774814022 1.390000e-60 244.0
18 TraesCS2B01G604500 chr2A 93.056 144 7 1 1667 1810 774829076 774828936 1.820000e-49 207.0
19 TraesCS2B01G604500 chr3B 83.307 1264 171 21 3237 4475 723459797 723461045 0.000000e+00 1129.0
20 TraesCS2B01G604500 chr3B 83.055 1257 181 16 3237 4476 723466652 723467893 0.000000e+00 1112.0
21 TraesCS2B01G604500 chr3B 76.199 584 102 24 1272 1840 723456954 723457515 1.770000e-69 274.0
22 TraesCS2B01G604500 chr3A 83.280 1256 179 16 3237 4475 683214768 683216009 0.000000e+00 1127.0
23 TraesCS2B01G604500 chr3D 83.214 1257 179 15 3237 4476 546388405 546389646 0.000000e+00 1123.0
24 TraesCS2B01G604500 chr7B 91.577 653 50 2 1 649 616641416 616640765 0.000000e+00 896.0
25 TraesCS2B01G604500 chr7B 89.790 666 68 0 1 666 327740010 327740675 0.000000e+00 854.0
26 TraesCS2B01G604500 chr7B 89.640 666 69 0 1 666 327721767 327722432 0.000000e+00 848.0
27 TraesCS2B01G604500 chr7B 89.489 666 70 0 1 666 327704015 327704680 0.000000e+00 843.0
28 TraesCS2B01G604500 chr7B 89.355 667 70 1 1 666 327757716 327758382 0.000000e+00 837.0
29 TraesCS2B01G604500 chr7B 86.667 195 18 6 2908 3101 688738560 688738373 5.060000e-50 209.0
30 TraesCS2B01G604500 chr5D 89.790 666 63 4 1 666 110435736 110436396 0.000000e+00 848.0
31 TraesCS2B01G604500 chr4A 78.250 1246 248 16 3237 4471 18012662 18013895 0.000000e+00 778.0
32 TraesCS2B01G604500 chr4A 86.166 253 28 4 2854 3105 572560709 572560955 2.960000e-67 267.0
33 TraesCS2B01G604500 chr4A 89.474 95 10 0 2727 2821 18012452 18012546 2.440000e-23 121.0
34 TraesCS2B01G604500 chr7D 87.519 649 81 0 1 649 540874418 540875066 0.000000e+00 750.0
35 TraesCS2B01G604500 chr7D 87.281 228 24 3 2838 3065 98399218 98398996 6.400000e-64 255.0
36 TraesCS2B01G604500 chr7D 85.034 147 13 7 2846 2989 58105696 58105836 1.870000e-29 141.0
37 TraesCS2B01G604500 chr6A 86.057 667 88 3 1 667 27468792 27469453 0.000000e+00 712.0
38 TraesCS2B01G604500 chr1D 85.800 669 91 3 1 668 258506492 258507157 0.000000e+00 706.0
39 TraesCS2B01G604500 chr1D 87.925 265 25 4 2838 3101 485415858 485416116 6.270000e-79 305.0
40 TraesCS2B01G604500 chr4D 89.167 240 20 5 2854 3093 30414587 30414354 1.360000e-75 294.0
41 TraesCS2B01G604500 chr6B 82.166 157 19 7 2835 2989 135836858 135837007 5.240000e-25 126.0
42 TraesCS2B01G604500 chr6B 71.805 266 63 7 3442 3701 73073798 73074057 1.160000e-06 65.8
43 TraesCS2B01G604500 chr6D 81.818 154 20 7 2838 2989 291222631 291222484 6.780000e-24 122.0
44 TraesCS2B01G604500 chr5B 89.474 95 10 0 2727 2821 7070619 7070525 2.440000e-23 121.0


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 TraesCS2B01G604500 chr2B 786101567 786106550 4983 False 3144.666667 9204 100.00000 1 4984 3 chr2B.!!$F1 4983
1 TraesCS2B01G604500 chr2B 559421528 559422336 808 True 580.000000 580 79.68400 3355 4176 1 chr2B.!!$R1 821
2 TraesCS2B01G604500 chr2D 650076553 650080442 3889 False 1126.000000 2132 93.31160 670 4820 5 chr2D.!!$F2 4150
3 TraesCS2B01G604500 chr2D 477424702 477425627 925 True 619.000000 619 78.98600 3238 4176 1 chr2D.!!$R1 938
4 TraesCS2B01G604500 chr2A 619770120 619771360 1240 True 1144.000000 1144 83.51900 3237 4475 1 chr2A.!!$R1 1238
5 TraesCS2B01G604500 chr2A 774813791 774816935 3144 True 1068.750000 2052 92.67075 1806 4979 4 chr2A.!!$R3 3173
6 TraesCS2B01G604500 chr2A 774828936 774831956 3020 True 865.500000 1524 93.29150 670 1810 2 chr2A.!!$R4 1140
7 TraesCS2B01G604500 chr2A 619808280 619809166 886 True 398.000000 398 75.59700 996 1888 1 chr2A.!!$R2 892
8 TraesCS2B01G604500 chr3B 723466652 723467893 1241 False 1112.000000 1112 83.05500 3237 4476 1 chr3B.!!$F1 1239
9 TraesCS2B01G604500 chr3B 723456954 723461045 4091 False 701.500000 1129 79.75300 1272 4475 2 chr3B.!!$F2 3203
10 TraesCS2B01G604500 chr3A 683214768 683216009 1241 False 1127.000000 1127 83.28000 3237 4475 1 chr3A.!!$F1 1238
11 TraesCS2B01G604500 chr3D 546388405 546389646 1241 False 1123.000000 1123 83.21400 3237 4476 1 chr3D.!!$F1 1239
12 TraesCS2B01G604500 chr7B 616640765 616641416 651 True 896.000000 896 91.57700 1 649 1 chr7B.!!$R1 648
13 TraesCS2B01G604500 chr7B 327740010 327740675 665 False 854.000000 854 89.79000 1 666 1 chr7B.!!$F3 665
14 TraesCS2B01G604500 chr7B 327721767 327722432 665 False 848.000000 848 89.64000 1 666 1 chr7B.!!$F2 665
15 TraesCS2B01G604500 chr7B 327704015 327704680 665 False 843.000000 843 89.48900 1 666 1 chr7B.!!$F1 665
16 TraesCS2B01G604500 chr7B 327757716 327758382 666 False 837.000000 837 89.35500 1 666 1 chr7B.!!$F4 665
17 TraesCS2B01G604500 chr5D 110435736 110436396 660 False 848.000000 848 89.79000 1 666 1 chr5D.!!$F1 665
18 TraesCS2B01G604500 chr4A 18012452 18013895 1443 False 449.500000 778 83.86200 2727 4471 2 chr4A.!!$F2 1744
19 TraesCS2B01G604500 chr7D 540874418 540875066 648 False 750.000000 750 87.51900 1 649 1 chr7D.!!$F2 648
20 TraesCS2B01G604500 chr6A 27468792 27469453 661 False 712.000000 712 86.05700 1 667 1 chr6A.!!$F1 666
21 TraesCS2B01G604500 chr1D 258506492 258507157 665 False 706.000000 706 85.80000 1 668 1 chr1D.!!$F1 667

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
519 526 0.108615 GTCACACCGTCTCATGGAGG 60.109 60.0 0.0 0.0 0.00 4.30 F
1447 1489 0.389948 GTTCATCGGCAACTCGACCT 60.390 55.0 0.0 0.0 42.21 3.85 F
2706 5576 0.035458 ATCTGGTTAGCATAGCGGCC 59.965 55.0 0.0 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1455 1497 0.251653 AGAGGACGTAGCAGTTCCCA 60.252 55.0 0.0 0.0 0.00 4.37 R
2820 6010 0.179225 GATTACCGTGCTTGTGCGTG 60.179 55.0 0.0 0.0 43.34 5.34 R
4092 7326 0.035317 TCTTGCCATGCTCGTTCTGT 59.965 50.0 0.0 0.0 0.00 3.41 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
106 108 1.487976 TCTCATTGCACCCCTCATCTC 59.512 52.381 0.00 0.00 0.00 2.75
113 115 2.765807 CCCCTCATCTCGGGCACT 60.766 66.667 0.00 0.00 40.54 4.40
163 165 1.434188 TGGCTTCTCTTCAAGGACCA 58.566 50.000 0.00 0.00 0.00 4.02
205 207 5.117355 CTTGCCCACAAGCATATAATCTG 57.883 43.478 0.00 0.00 46.38 2.90
223 225 2.421314 CTCCGATGTATGCCCGCA 59.579 61.111 0.00 0.00 0.00 5.69
229 231 0.461870 GATGTATGCCCGCAGTGTGA 60.462 55.000 4.93 0.00 0.00 3.58
252 254 1.829222 GGTTACCCGAAGACTCCATGA 59.171 52.381 0.00 0.00 0.00 3.07
262 264 1.827969 AGACTCCATGAACCTCTTCGG 59.172 52.381 0.00 0.00 39.35 4.30
338 344 2.449548 CGACATCGCTGAGCTTTGT 58.550 52.632 1.78 5.82 0.00 2.83
439 446 6.541969 CAGCACGTAATGATATGTTGTTCAA 58.458 36.000 0.00 0.00 0.00 2.69
472 479 8.877864 AATCAATGTTCTGTAATAACCCTCAA 57.122 30.769 0.00 0.00 0.00 3.02
519 526 0.108615 GTCACACCGTCTCATGGAGG 60.109 60.000 0.00 0.00 0.00 4.30
544 551 2.036089 GTGACAAGGAGGACGTCTTCTT 59.964 50.000 24.68 16.49 41.94 2.52
714 725 1.407656 TATCTAACAGGCGGGGCTGG 61.408 60.000 23.70 8.57 0.00 4.85
769 783 1.231221 GCGCGAGAGAGATAAGAGGA 58.769 55.000 12.10 0.00 0.00 3.71
770 784 1.069500 GCGCGAGAGAGATAAGAGGAC 60.069 57.143 12.10 0.00 0.00 3.85
771 785 1.193650 CGCGAGAGAGATAAGAGGACG 59.806 57.143 0.00 0.00 0.00 4.79
772 786 2.485903 GCGAGAGAGATAAGAGGACGA 58.514 52.381 0.00 0.00 0.00 4.20
773 787 2.478894 GCGAGAGAGATAAGAGGACGAG 59.521 54.545 0.00 0.00 0.00 4.18
775 789 3.493699 CGAGAGAGATAAGAGGACGAGGT 60.494 52.174 0.00 0.00 0.00 3.85
776 790 3.813166 GAGAGAGATAAGAGGACGAGGTG 59.187 52.174 0.00 0.00 0.00 4.00
777 791 2.882137 GAGAGATAAGAGGACGAGGTGG 59.118 54.545 0.00 0.00 0.00 4.61
778 792 1.338655 GAGATAAGAGGACGAGGTGGC 59.661 57.143 0.00 0.00 0.00 5.01
810 830 3.448934 AGTGACTGAGAAGGGATGTGAT 58.551 45.455 0.00 0.00 0.00 3.06
832 852 2.703007 GAGATAAGGCTGATGTGGAGGT 59.297 50.000 0.00 0.00 0.00 3.85
838 858 1.153489 CTGATGTGGAGGTGAGCGG 60.153 63.158 0.00 0.00 0.00 5.52
840 860 1.296715 GATGTGGAGGTGAGCGGTT 59.703 57.895 0.00 0.00 0.00 4.44
863 883 2.185310 GAAGCCCTCGGACATGTGGT 62.185 60.000 1.15 0.00 0.00 4.16
896 916 1.092348 GGGGGATGCGTGAGTTTTAC 58.908 55.000 0.00 0.00 0.00 2.01
977 1000 5.164233 CACAGTAGTATCCAACACAGACAG 58.836 45.833 0.00 0.00 0.00 3.51
1238 1277 3.329386 TCGAGAGCTTTGACATCTTTGG 58.671 45.455 0.00 0.00 0.00 3.28
1330 1369 2.587322 GATGATTCCCGGTGTCCGCA 62.587 60.000 0.00 0.00 46.86 5.69
1447 1489 0.389948 GTTCATCGGCAACTCGACCT 60.390 55.000 0.00 0.00 42.21 3.85
1466 1508 2.224769 CCTTTGAGGTTGGGAACTGCTA 60.225 50.000 0.00 0.00 0.00 3.49
1471 1513 0.672711 GGTTGGGAACTGCTACGTCC 60.673 60.000 0.00 0.00 0.00 4.79
1662 1713 3.756082 AAGGACCAAATATTCTGGCCA 57.244 42.857 4.71 4.71 37.48 5.36
1746 3677 1.761822 GGCTATTCCCTACCAGCCC 59.238 63.158 0.00 0.00 46.47 5.19
1749 3680 1.425448 GCTATTCCCTACCAGCCCAAT 59.575 52.381 0.00 0.00 0.00 3.16
1784 3715 0.543749 GAGGACAGGGCAAGCTATGT 59.456 55.000 0.00 3.08 0.00 2.29
1841 3772 0.249489 ATCGGTGGATACTTCTGCGC 60.249 55.000 0.00 0.00 37.61 6.09
1876 3807 3.698820 ACGGCAACCCCTACGTCC 61.699 66.667 0.00 0.00 33.92 4.79
1950 3908 1.407437 CCGGCAGGTCAGCTCTAAATT 60.407 52.381 0.00 0.00 34.17 1.82
1951 3909 2.158957 CCGGCAGGTCAGCTCTAAATTA 60.159 50.000 0.00 0.00 34.17 1.40
1953 3911 3.938963 CGGCAGGTCAGCTCTAAATTAAA 59.061 43.478 0.00 0.00 34.17 1.52
2063 4298 6.958752 GCCAAAATAAACCAATTGTATTTCGC 59.041 34.615 4.43 9.45 29.37 4.70
2146 4583 4.020573 ACAGTCGTTTATGACTCCATCCAA 60.021 41.667 1.66 0.00 45.97 3.53
2163 4600 1.732259 CCAACCGAAGAAGGATTGTCG 59.268 52.381 0.00 0.00 33.40 4.35
2255 4692 8.190888 ACAATTCTATCTCAAATGTCTTCGAC 57.809 34.615 0.00 0.00 0.00 4.20
2263 4700 0.400213 AATGTCTTCGACCCTTGCCA 59.600 50.000 0.00 0.00 0.00 4.92
2277 4714 0.772124 TTGCCAGGGACCCTTCTTCT 60.772 55.000 11.56 0.00 0.00 2.85
2289 4726 2.751806 CCCTTCTTCTGGTGCTTGAATC 59.248 50.000 0.00 0.00 0.00 2.52
2296 4733 3.673902 TCTGGTGCTTGAATCGAATGAA 58.326 40.909 0.00 0.00 0.00 2.57
2340 4777 2.798834 ATTGACGACGGTATTTTGCG 57.201 45.000 0.00 0.00 0.00 4.85
2342 4779 1.059838 GACGACGGTATTTTGCGCC 59.940 57.895 4.18 0.00 0.00 6.53
2344 4781 1.060308 CGACGGTATTTTGCGCCTG 59.940 57.895 4.18 0.00 0.00 4.85
2346 4783 1.644786 GACGGTATTTTGCGCCTGCT 61.645 55.000 4.18 0.00 43.34 4.24
2414 4860 0.107831 CGCCTTATCCGGGAAATGGA 59.892 55.000 0.00 0.00 40.46 3.41
2450 4896 1.653114 CCGTTGTTAAAATGCCATGCG 59.347 47.619 0.00 0.00 0.00 4.73
2472 4918 3.003480 AGCATGGAAAGCTAAACGAGAC 58.997 45.455 0.00 0.00 41.32 3.36
2474 4920 3.334691 CATGGAAAGCTAAACGAGACCA 58.665 45.455 0.00 0.00 0.00 4.02
2475 4921 3.040147 TGGAAAGCTAAACGAGACCAG 57.960 47.619 0.00 0.00 0.00 4.00
2497 4943 0.917533 ACAGATGCTTCAGCTCCCAT 59.082 50.000 2.07 0.00 42.66 4.00
2545 4991 1.149148 GAACACTCCAACTTCTCGGC 58.851 55.000 0.00 0.00 0.00 5.54
2573 5019 1.268079 GCAAGTGCTCTTCTGGTTTCC 59.732 52.381 0.00 0.00 38.21 3.13
2604 5050 8.537728 AATCCTTACATTAAAGATGGATGCAA 57.462 30.769 0.00 0.00 33.68 4.08
2688 5190 7.624549 TGAGTTTTATCACTTCAGAGCCTAAT 58.375 34.615 0.00 0.00 0.00 1.73
2706 5576 0.035458 ATCTGGTTAGCATAGCGGCC 59.965 55.000 0.00 0.00 0.00 6.13
2728 5915 3.371273 CCTGGATCACCACTGATGTCATT 60.371 47.826 0.00 0.00 41.77 2.57
2815 6005 5.331902 CACAATAAATTTGGGAGCTACACG 58.668 41.667 0.00 0.00 0.00 4.49
2817 6007 5.106317 ACAATAAATTTGGGAGCTACACGTG 60.106 40.000 15.48 15.48 0.00 4.49
2818 6008 1.165270 AATTTGGGAGCTACACGTGC 58.835 50.000 17.22 0.86 0.00 5.34
2819 6009 0.036164 ATTTGGGAGCTACACGTGCA 59.964 50.000 17.22 0.49 0.00 4.57
2820 6010 0.882927 TTTGGGAGCTACACGTGCAC 60.883 55.000 17.22 6.82 0.00 4.57
2821 6011 2.034048 TTGGGAGCTACACGTGCACA 62.034 55.000 17.22 2.74 0.00 4.57
2822 6012 2.027625 GGGAGCTACACGTGCACAC 61.028 63.158 17.22 2.65 0.00 3.82
2843 6033 1.130561 GCACAAGCACGGTAATCTTCC 59.869 52.381 0.00 0.00 41.58 3.46
2870 6060 7.624360 TCTTAAATAGTTGCAACCCACTATG 57.376 36.000 25.62 13.73 0.00 2.23
2892 6082 6.899393 TGTAATTTTCCTCTTCATGCAACT 57.101 33.333 0.00 0.00 0.00 3.16
2920 6110 5.526111 TCACATCATCAAGTCATGCATGTAG 59.474 40.000 25.43 13.81 30.19 2.74
2923 6113 5.280654 TCATCAAGTCATGCATGTAGCTA 57.719 39.130 25.43 10.80 45.94 3.32
2935 6125 8.084684 TCATGCATGTAGCTAGTCATAAGTTAG 58.915 37.037 25.43 0.00 45.94 2.34
2964 6154 9.499479 TTTGCATTAATTTATTCCTTCAAAGCA 57.501 25.926 0.00 0.00 0.00 3.91
2974 6164 1.250328 CTTCAAAGCATGCCACCTCA 58.750 50.000 15.66 0.00 0.00 3.86
3072 6277 5.869344 GCACTTCATTTTTAACAGGATTCCC 59.131 40.000 0.00 0.00 0.00 3.97
3073 6278 6.518200 GCACTTCATTTTTAACAGGATTCCCA 60.518 38.462 0.00 0.00 33.88 4.37
3074 6279 6.868339 CACTTCATTTTTAACAGGATTCCCAC 59.132 38.462 0.00 0.00 33.88 4.61
3075 6280 6.553100 ACTTCATTTTTAACAGGATTCCCACA 59.447 34.615 0.00 0.00 33.88 4.17
3076 6281 6.588719 TCATTTTTAACAGGATTCCCACAG 57.411 37.500 0.00 0.00 33.88 3.66
3077 6282 4.864704 TTTTTAACAGGATTCCCACAGC 57.135 40.909 0.00 0.00 33.88 4.40
3078 6283 3.517296 TTTAACAGGATTCCCACAGCA 57.483 42.857 0.00 0.00 33.88 4.41
3079 6284 3.517296 TTAACAGGATTCCCACAGCAA 57.483 42.857 0.00 0.00 33.88 3.91
3080 6285 2.610438 AACAGGATTCCCACAGCAAT 57.390 45.000 0.00 0.00 33.88 3.56
3081 6286 2.134789 ACAGGATTCCCACAGCAATC 57.865 50.000 0.00 0.00 33.88 2.67
3082 6287 1.019673 CAGGATTCCCACAGCAATCG 58.980 55.000 0.00 0.00 30.82 3.34
3083 6288 0.749454 AGGATTCCCACAGCAATCGC 60.749 55.000 0.00 0.00 34.43 4.58
3084 6289 1.353103 GATTCCCACAGCAATCGCG 59.647 57.895 0.00 0.00 45.49 5.87
3135 6340 4.336889 TCTATACCGCTTGAAATCCTGG 57.663 45.455 0.00 0.00 0.00 4.45
3138 6343 0.539438 ACCGCTTGAAATCCTGGCAA 60.539 50.000 0.00 0.00 0.00 4.52
3140 6345 2.023673 CCGCTTGAAATCCTGGCAATA 58.976 47.619 0.00 0.00 0.00 1.90
3141 6346 2.033801 CCGCTTGAAATCCTGGCAATAG 59.966 50.000 0.00 0.00 0.00 1.73
3142 6347 2.684881 CGCTTGAAATCCTGGCAATAGT 59.315 45.455 0.00 0.00 0.00 2.12
3143 6348 3.488047 CGCTTGAAATCCTGGCAATAGTG 60.488 47.826 0.00 0.00 0.00 2.74
3145 6350 4.640201 GCTTGAAATCCTGGCAATAGTGTA 59.360 41.667 0.00 0.00 0.00 2.90
3186 6391 2.611974 ATCGTTCGGTTGCATTGTTC 57.388 45.000 0.00 0.00 0.00 3.18
3190 6395 1.606668 GTTCGGTTGCATTGTTCCTGA 59.393 47.619 0.00 0.00 0.00 3.86
3191 6396 2.198827 TCGGTTGCATTGTTCCTGAT 57.801 45.000 0.00 0.00 0.00 2.90
3192 6397 2.513753 TCGGTTGCATTGTTCCTGATT 58.486 42.857 0.00 0.00 0.00 2.57
3193 6398 2.487762 TCGGTTGCATTGTTCCTGATTC 59.512 45.455 0.00 0.00 0.00 2.52
3194 6399 2.415893 CGGTTGCATTGTTCCTGATTCC 60.416 50.000 0.00 0.00 0.00 3.01
3196 6401 4.016444 GGTTGCATTGTTCCTGATTCCTA 58.984 43.478 0.00 0.00 0.00 2.94
3197 6402 4.096984 GGTTGCATTGTTCCTGATTCCTAG 59.903 45.833 0.00 0.00 0.00 3.02
3198 6403 3.282021 TGCATTGTTCCTGATTCCTAGC 58.718 45.455 0.00 0.00 0.00 3.42
3200 6405 3.563390 GCATTGTTCCTGATTCCTAGCTC 59.437 47.826 0.00 0.00 0.00 4.09
3201 6406 3.526931 TTGTTCCTGATTCCTAGCTCG 57.473 47.619 0.00 0.00 0.00 5.03
3203 6408 1.069358 GTTCCTGATTCCTAGCTCGGG 59.931 57.143 4.14 1.70 38.98 5.14
3204 6409 0.470080 TCCTGATTCCTAGCTCGGGG 60.470 60.000 4.14 0.00 38.30 5.73
3205 6410 1.476007 CCTGATTCCTAGCTCGGGGG 61.476 65.000 4.14 0.00 34.76 5.40
3206 6411 0.760945 CTGATTCCTAGCTCGGGGGT 60.761 60.000 4.14 0.00 0.00 4.95
3207 6412 0.326238 TGATTCCTAGCTCGGGGGTT 60.326 55.000 4.14 0.00 0.00 4.11
3208 6413 0.837940 GATTCCTAGCTCGGGGGTTT 59.162 55.000 4.14 0.00 0.00 3.27
3209 6414 2.044758 GATTCCTAGCTCGGGGGTTTA 58.955 52.381 4.14 0.00 0.00 2.01
3210 6415 1.955451 TTCCTAGCTCGGGGGTTTAA 58.045 50.000 4.14 0.00 0.00 1.52
3211 6416 1.955451 TCCTAGCTCGGGGGTTTAAA 58.045 50.000 4.14 0.00 0.00 1.52
3212 6417 2.484602 TCCTAGCTCGGGGGTTTAAAT 58.515 47.619 4.14 0.00 0.00 1.40
3213 6418 3.656496 TCCTAGCTCGGGGGTTTAAATA 58.344 45.455 4.14 0.00 0.00 1.40
3214 6419 3.389002 TCCTAGCTCGGGGGTTTAAATAC 59.611 47.826 4.14 0.00 0.00 1.89
3215 6420 2.723322 AGCTCGGGGGTTTAAATACC 57.277 50.000 0.00 0.00 37.47 2.73
3216 6421 2.202707 AGCTCGGGGGTTTAAATACCT 58.797 47.619 10.55 0.00 38.30 3.08
3217 6422 2.579400 AGCTCGGGGGTTTAAATACCTT 59.421 45.455 10.55 0.00 38.30 3.50
3225 6430 6.179756 GGGGGTTTAAATACCTTTAACTCGA 58.820 40.000 10.55 0.00 36.73 4.04
3349 6570 4.836125 TTCAGAAGCGCTTGAGAAAAAT 57.164 36.364 30.47 0.00 0.00 1.82
3406 6627 8.831550 AGAACAACTTATCTCTTCAGACAAAAC 58.168 33.333 0.00 0.00 0.00 2.43
3408 6629 9.832445 AACAACTTATCTCTTCAGACAAAACTA 57.168 29.630 0.00 0.00 0.00 2.24
3473 6700 6.993902 AGAAGGCAACAAACAATTTTGATCAT 59.006 30.769 0.00 0.00 44.38 2.45
3887 7121 1.278985 TCCATGAACGTGCTCCTGAAT 59.721 47.619 0.00 0.00 0.00 2.57
3890 7124 2.768253 TGAACGTGCTCCTGAATGAT 57.232 45.000 0.00 0.00 0.00 2.45
3981 7215 1.223417 CGCCGTTCAGGGTACGTTTT 61.223 55.000 0.00 0.00 41.48 2.43
3982 7216 1.794512 GCCGTTCAGGGTACGTTTTA 58.205 50.000 0.00 0.00 41.48 1.52
4092 7326 2.494888 TGAGGAGGAAGCCCATCATA 57.505 50.000 0.00 0.00 33.88 2.15
4108 7342 1.206849 TCATACAGAACGAGCATGGCA 59.793 47.619 0.00 0.00 0.00 4.92
4136 7370 5.755861 AGCAGAACTTGTCAAACTACTTCTC 59.244 40.000 0.00 0.00 0.00 2.87
4140 7374 5.007385 ACTTGTCAAACTACTTCTCGTGT 57.993 39.130 0.00 0.00 0.00 4.49
4312 7558 1.675801 CTGCAGCTCCTCACAGGAA 59.324 57.895 0.00 0.00 45.28 3.36
4313 7559 0.252479 CTGCAGCTCCTCACAGGAAT 59.748 55.000 0.00 0.00 45.28 3.01
4352 7618 0.327591 AGGCAAGAAGAAGAGGCAGG 59.672 55.000 0.00 0.00 0.00 4.85
4387 7653 3.771160 GACATGGCGGGGTCGACT 61.771 66.667 16.46 0.00 46.40 4.18
4494 7760 4.380023 GGCACACCTTATTTACATTTCGCA 60.380 41.667 0.00 0.00 0.00 5.10
4514 7780 6.682746 TCGCACTTGCCAGAAAAATAATTTA 58.317 32.000 0.00 0.00 37.91 1.40
4593 7908 8.746530 AGTGTCAATGATTAATGCTTCTCAAAT 58.253 29.630 0.00 0.00 0.00 2.32
4613 7928 8.737168 TCAAATAATAGGACTGGATGAAACTG 57.263 34.615 0.00 0.00 0.00 3.16
4664 7979 8.124199 GTCGATAAGGTGTTTTTGTCTTAAACA 58.876 33.333 0.00 0.00 41.69 2.83
4670 7985 9.744468 AAGGTGTTTTTGTCTTAAACATATCAC 57.256 29.630 0.00 0.00 44.52 3.06
4671 7986 8.908903 AGGTGTTTTTGTCTTAAACATATCACA 58.091 29.630 0.00 0.00 44.52 3.58
4672 7987 9.691362 GGTGTTTTTGTCTTAAACATATCACAT 57.309 29.630 0.00 0.00 44.52 3.21
4698 8013 6.387041 TCTAAAGATGATAGTGTACGGTGG 57.613 41.667 0.00 0.00 0.00 4.61
4699 8014 5.889853 TCTAAAGATGATAGTGTACGGTGGT 59.110 40.000 0.00 0.00 0.00 4.16
4700 8015 4.650754 AAGATGATAGTGTACGGTGGTC 57.349 45.455 0.00 0.00 0.00 4.02
4701 8016 2.617308 AGATGATAGTGTACGGTGGTCG 59.383 50.000 0.00 0.00 45.88 4.79
4702 8017 2.112380 TGATAGTGTACGGTGGTCGA 57.888 50.000 0.00 0.00 42.43 4.20
4703 8018 2.646930 TGATAGTGTACGGTGGTCGAT 58.353 47.619 0.00 0.00 42.43 3.59
4704 8019 3.807553 TGATAGTGTACGGTGGTCGATA 58.192 45.455 0.00 0.00 42.43 2.92
4705 8020 4.198530 TGATAGTGTACGGTGGTCGATAA 58.801 43.478 0.00 0.00 42.43 1.75
4706 8021 4.274214 TGATAGTGTACGGTGGTCGATAAG 59.726 45.833 0.00 0.00 42.43 1.73
4707 8022 1.747355 AGTGTACGGTGGTCGATAAGG 59.253 52.381 0.00 0.00 42.43 2.69
4708 8023 1.474077 GTGTACGGTGGTCGATAAGGT 59.526 52.381 0.00 0.00 42.43 3.50
4709 8024 1.473677 TGTACGGTGGTCGATAAGGTG 59.526 52.381 0.00 0.00 42.43 4.00
4710 8025 1.474077 GTACGGTGGTCGATAAGGTGT 59.526 52.381 0.00 0.00 42.43 4.16
4711 8026 0.971386 ACGGTGGTCGATAAGGTGTT 59.029 50.000 0.00 0.00 42.43 3.32
4712 8027 1.345415 ACGGTGGTCGATAAGGTGTTT 59.655 47.619 0.00 0.00 42.43 2.83
4713 8028 2.224354 ACGGTGGTCGATAAGGTGTTTT 60.224 45.455 0.00 0.00 42.43 2.43
4714 8029 2.809696 CGGTGGTCGATAAGGTGTTTTT 59.190 45.455 0.00 0.00 42.43 1.94
4715 8030 3.364565 CGGTGGTCGATAAGGTGTTTTTG 60.365 47.826 0.00 0.00 42.43 2.44
4716 8031 3.566742 GGTGGTCGATAAGGTGTTTTTGT 59.433 43.478 0.00 0.00 0.00 2.83
4717 8032 4.319984 GGTGGTCGATAAGGTGTTTTTGTC 60.320 45.833 0.00 0.00 0.00 3.18
4718 8033 4.514066 GTGGTCGATAAGGTGTTTTTGTCT 59.486 41.667 0.00 0.00 0.00 3.41
4719 8034 5.008316 GTGGTCGATAAGGTGTTTTTGTCTT 59.992 40.000 0.00 0.00 0.00 3.01
4720 8035 6.203338 GTGGTCGATAAGGTGTTTTTGTCTTA 59.797 38.462 0.00 0.00 0.00 2.10
4721 8036 6.766944 TGGTCGATAAGGTGTTTTTGTCTTAA 59.233 34.615 0.00 0.00 0.00 1.85
4722 8037 7.282675 TGGTCGATAAGGTGTTTTTGTCTTAAA 59.717 33.333 0.00 0.00 0.00 1.52
4723 8038 7.588854 GGTCGATAAGGTGTTTTTGTCTTAAAC 59.411 37.037 0.00 0.00 36.32 2.01
4724 8039 8.124199 GTCGATAAGGTGTTTTTGTCTTAAACA 58.876 33.333 0.00 0.00 41.69 2.83
4725 8040 8.842280 TCGATAAGGTGTTTTTGTCTTAAACAT 58.158 29.630 0.00 0.00 44.52 2.71
4820 8136 5.970692 AGGTATTCCTAGGGGTCTATCTT 57.029 43.478 9.46 0.00 43.12 2.40
4825 8141 1.353091 CTAGGGGTCTATCTTGGGCC 58.647 60.000 0.00 0.00 0.00 5.80
4826 8142 0.104620 TAGGGGTCTATCTTGGGCCC 60.105 60.000 17.59 17.59 38.61 5.80
4830 8146 1.420514 GGGTCTATCTTGGGCCCTAAC 59.579 57.143 25.70 10.02 36.49 2.34
4838 8154 2.310349 TCTTGGGCCCTAACTATTGCAA 59.690 45.455 25.70 0.00 0.00 4.08
4860 8176 8.043113 TGCAAATCTAAGTGACTCAATCATACT 58.957 33.333 0.00 0.00 40.28 2.12
4868 8184 5.769662 AGTGACTCAATCATACTGGCAAAAA 59.230 36.000 0.00 0.00 40.28 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 1.288188 TGAGGGGTGCAATGAGATCA 58.712 50.000 0.00 0.00 0.00 2.92
106 108 2.501610 GAGGAGCCTTAGTGCCCG 59.498 66.667 0.00 0.00 0.00 6.13
163 165 3.595021 AGGTTAACCCTAGTGTTGAGGT 58.405 45.455 21.30 0.00 43.87 3.85
205 207 3.044305 GCGGGCATACATCGGAGC 61.044 66.667 0.00 0.00 0.00 4.70
252 254 0.321653 GGACATGTGCCGAAGAGGTT 60.322 55.000 1.15 0.00 43.70 3.50
262 264 0.318955 GTTGGCAAGTGGACATGTGC 60.319 55.000 10.90 10.90 31.62 4.57
295 301 1.065199 TCTGCGGCAGAATCCTGATTT 60.065 47.619 29.13 0.00 43.02 2.17
300 306 2.586792 GGTCTGCGGCAGAATCCT 59.413 61.111 32.30 0.00 42.46 3.24
338 344 1.748403 GTGAGGCAGTGGAGTGTCA 59.252 57.895 0.00 0.00 0.00 3.58
447 454 8.877864 TTGAGGGTTATTACAGAACATTGATT 57.122 30.769 0.00 0.00 0.00 2.57
472 479 5.372066 AGATCCAAATCAGAGATAAGGGCTT 59.628 40.000 0.00 0.00 34.07 4.35
519 526 0.320771 ACGTCCTCCTTGTCACATGC 60.321 55.000 0.00 0.00 0.00 4.06
544 551 2.248248 CAGAGAGGTAGGAACACCACA 58.752 52.381 0.00 0.00 41.40 4.17
575 582 5.274718 CGAGTACAGAATCACATAGACACC 58.725 45.833 0.00 0.00 0.00 4.16
579 586 4.498177 GCAGCGAGTACAGAATCACATAGA 60.498 45.833 0.00 0.00 0.00 1.98
668 675 5.009510 CAGTACTCTACTCACATCATCAGGG 59.990 48.000 0.00 0.00 36.76 4.45
714 725 3.825160 TTCACCTGCTCACCACCGC 62.825 63.158 0.00 0.00 0.00 5.68
778 792 4.400251 AGTCACTCCCCTCCCCGG 62.400 72.222 0.00 0.00 0.00 5.73
810 830 2.702478 CCTCCACATCAGCCTTATCTCA 59.298 50.000 0.00 0.00 0.00 3.27
896 916 2.936498 ACGATAAAAATCTGCCGGTCAG 59.064 45.455 16.84 16.84 44.21 3.51
910 933 9.656040 TTCTTAAGCATGGTAGTAAACGATAAA 57.344 29.630 0.00 0.00 0.00 1.40
1077 1107 1.795286 GTGTCGGAGCAGTTTCTTCTG 59.205 52.381 0.00 0.00 38.35 3.02
1238 1277 0.589708 GGCGTACAGGTTGTTGGAAC 59.410 55.000 0.00 0.00 0.00 3.62
1330 1369 3.244249 GCTTCCCAGTGAACAGAGTAGTT 60.244 47.826 0.00 0.00 0.00 2.24
1447 1489 2.808933 CGTAGCAGTTCCCAACCTCAAA 60.809 50.000 0.00 0.00 0.00 2.69
1455 1497 0.251653 AGAGGACGTAGCAGTTCCCA 60.252 55.000 0.00 0.00 0.00 4.37
1466 1508 2.651361 CTTCCGCACAGAGGACGT 59.349 61.111 0.00 0.00 37.53 4.34
1471 1513 0.459237 ATTCGAGCTTCCGCACAGAG 60.459 55.000 0.00 0.00 39.10 3.35
1662 1713 3.012518 CAAAGATCTCAGGGCGTCAATT 58.987 45.455 0.00 0.00 0.00 2.32
1746 3677 0.866906 CCATGGCGCGCTTACAATTG 60.867 55.000 32.29 15.65 0.00 2.32
1749 3680 2.046796 TCCATGGCGCGCTTACAA 60.047 55.556 32.29 11.53 0.00 2.41
1784 3715 3.855858 TCACTGTGATTAGCAACGCATA 58.144 40.909 6.36 0.00 0.00 3.14
1841 3772 1.227823 TCGTCACCCCACTTGCAAG 60.228 57.895 24.84 24.84 0.00 4.01
1888 3819 0.392060 GGTTCGTATTCACCCCGCTT 60.392 55.000 0.00 0.00 0.00 4.68
1889 3820 1.219935 GGTTCGTATTCACCCCGCT 59.780 57.895 0.00 0.00 0.00 5.52
1891 3822 0.741927 GGTGGTTCGTATTCACCCCG 60.742 60.000 0.00 0.00 43.65 5.73
1892 3823 3.164026 GGTGGTTCGTATTCACCCC 57.836 57.895 0.00 0.00 43.65 4.95
1895 3826 2.344025 GTGGAGGTGGTTCGTATTCAC 58.656 52.381 0.00 0.00 0.00 3.18
1896 3827 1.276989 GGTGGAGGTGGTTCGTATTCA 59.723 52.381 0.00 0.00 0.00 2.57
1950 3908 3.368739 GGTGAACGCCCTTAGCTAGTTTA 60.369 47.826 0.00 0.00 40.39 2.01
1951 3909 2.614734 GGTGAACGCCCTTAGCTAGTTT 60.615 50.000 0.00 0.00 40.39 2.66
1953 3911 0.535797 GGTGAACGCCCTTAGCTAGT 59.464 55.000 0.00 0.00 40.39 2.57
2146 4583 0.320374 TGCGACAATCCTTCTTCGGT 59.680 50.000 0.00 0.00 32.04 4.69
2211 4648 0.386476 TTCAGTTGCAAAGCAGCCTG 59.614 50.000 0.00 3.16 40.57 4.85
2263 4700 1.492993 GCACCAGAAGAAGGGTCCCT 61.493 60.000 3.85 3.85 34.45 4.20
2269 4706 2.417933 CGATTCAAGCACCAGAAGAAGG 59.582 50.000 0.00 0.00 0.00 3.46
2277 4714 2.159430 CGTTCATTCGATTCAAGCACCA 59.841 45.455 0.00 0.00 0.00 4.17
2289 4726 3.186409 AGTGACAACCAATCGTTCATTCG 59.814 43.478 0.00 0.00 29.93 3.34
2296 4733 2.613026 TGTCAGTGACAACCAATCGT 57.387 45.000 23.55 0.00 39.78 3.73
2305 4742 6.495706 GTCGTCAATAGATATGTCAGTGACA 58.504 40.000 27.35 27.35 46.90 3.58
2340 4777 1.569708 CTCTGATTTCTCGAGCAGGC 58.430 55.000 7.81 0.00 0.00 4.85
2342 4779 1.134877 TGGCTCTGATTTCTCGAGCAG 60.135 52.381 7.81 9.46 43.56 4.24
2344 4781 1.663135 GTTGGCTCTGATTTCTCGAGC 59.337 52.381 7.81 11.48 42.31 5.03
2346 4783 2.562738 TCAGTTGGCTCTGATTTCTCGA 59.437 45.455 8.41 0.00 39.20 4.04
2364 4801 4.342378 TCTCCGGATTAGAAAGGACATCAG 59.658 45.833 3.57 0.00 0.00 2.90
2369 4806 2.686915 TCGTCTCCGGATTAGAAAGGAC 59.313 50.000 3.57 5.29 33.95 3.85
2372 4809 5.398711 CGTAAATCGTCTCCGGATTAGAAAG 59.601 44.000 3.57 0.00 34.52 2.62
2390 4836 3.564053 TTTCCCGGATAAGGCGTAAAT 57.436 42.857 0.73 0.00 0.00 1.40
2392 4838 2.485835 CCATTTCCCGGATAAGGCGTAA 60.486 50.000 0.73 0.00 0.00 3.18
2414 4860 4.643387 GGCCCACTTCACCACGCT 62.643 66.667 0.00 0.00 0.00 5.07
2450 4896 3.062774 GTCTCGTTTAGCTTTCCATGCTC 59.937 47.826 0.00 0.00 41.46 4.26
2457 4903 2.689646 AGCTGGTCTCGTTTAGCTTTC 58.310 47.619 0.00 0.00 43.49 2.62
2472 4918 1.134461 AGCTGAAGCATCTGTAGCTGG 60.134 52.381 4.90 0.00 42.63 4.85
2474 4920 1.138661 GGAGCTGAAGCATCTGTAGCT 59.861 52.381 4.90 2.28 46.50 3.32
2475 4921 1.580815 GGAGCTGAAGCATCTGTAGC 58.419 55.000 4.90 0.00 45.16 3.58
2545 4991 0.671781 AAGAGCACTTGCAGCGGTAG 60.672 55.000 3.62 0.00 45.16 3.18
2663 5165 5.489792 AGGCTCTGAAGTGATAAAACTCA 57.510 39.130 0.00 0.00 0.00 3.41
2669 5171 5.663106 ACCAGATTAGGCTCTGAAGTGATAA 59.337 40.000 3.97 0.00 44.48 1.75
2688 5190 1.445942 GGCCGCTATGCTAACCAGA 59.554 57.895 0.00 0.00 0.00 3.86
2706 5576 1.556451 TGACATCAGTGGTGATCCAGG 59.444 52.381 11.21 0.00 45.24 4.45
2728 5915 6.976349 ACTCGTTTATATCTGTAATTCGCACA 59.024 34.615 0.00 0.00 0.00 4.57
2817 6007 4.962122 CCGTGCTTGTGCGTGTGC 62.962 66.667 0.00 0.00 43.34 4.57
2818 6008 1.767127 TTACCGTGCTTGTGCGTGTG 61.767 55.000 0.00 0.00 43.34 3.82
2819 6009 0.882927 ATTACCGTGCTTGTGCGTGT 60.883 50.000 0.00 0.00 43.34 4.49
2820 6010 0.179225 GATTACCGTGCTTGTGCGTG 60.179 55.000 0.00 0.00 43.34 5.34
2821 6011 0.320421 AGATTACCGTGCTTGTGCGT 60.320 50.000 0.00 0.00 43.34 5.24
2822 6012 0.796312 AAGATTACCGTGCTTGTGCG 59.204 50.000 0.00 0.00 43.34 5.34
2843 6033 6.924111 AGTGGGTTGCAACTATTTAAGAATG 58.076 36.000 27.64 0.00 0.00 2.67
2870 6060 8.462016 ACATAGTTGCATGAAGAGGAAAATTAC 58.538 33.333 0.00 0.00 0.00 1.89
2892 6082 5.430007 TGCATGACTTGATGATGTGACATA 58.570 37.500 0.00 0.00 0.00 2.29
2955 6145 1.250328 TGAGGTGGCATGCTTTGAAG 58.750 50.000 18.92 0.00 0.00 3.02
2957 6147 1.272037 TGATGAGGTGGCATGCTTTGA 60.272 47.619 18.92 0.00 0.00 2.69
2964 6154 2.651455 CATGAGTTGATGAGGTGGCAT 58.349 47.619 0.00 0.00 0.00 4.40
3044 6249 9.346725 GAATCCTGTTAAAAATGAAGTGCTAAG 57.653 33.333 0.00 0.00 0.00 2.18
3078 6283 4.935495 ATGATGCCCCGCGCGATT 62.935 61.111 34.63 10.68 42.08 3.34
3081 6286 4.662961 TAGATGATGCCCCGCGCG 62.663 66.667 25.67 25.67 42.08 6.86
3082 6287 2.154798 TACTAGATGATGCCCCGCGC 62.155 60.000 0.00 0.00 38.31 6.86
3083 6288 0.532573 ATACTAGATGATGCCCCGCG 59.467 55.000 0.00 0.00 0.00 6.46
3084 6289 2.770164 AATACTAGATGATGCCCCGC 57.230 50.000 0.00 0.00 0.00 6.13
3135 6340 9.793252 ATTTCAAGACATTGATTACACTATTGC 57.207 29.630 0.00 0.00 44.75 3.56
3186 6391 1.476007 CCCCCGAGCTAGGAATCAGG 61.476 65.000 15.38 6.29 0.00 3.86
3190 6395 2.185663 TAAACCCCCGAGCTAGGAAT 57.814 50.000 15.38 0.00 0.00 3.01
3191 6396 1.955451 TTAAACCCCCGAGCTAGGAA 58.045 50.000 15.38 0.00 0.00 3.36
3192 6397 1.955451 TTTAAACCCCCGAGCTAGGA 58.045 50.000 15.38 0.00 0.00 2.94
3193 6398 3.495629 GGTATTTAAACCCCCGAGCTAGG 60.496 52.174 5.78 5.78 33.02 3.02
3194 6399 3.390311 AGGTATTTAAACCCCCGAGCTAG 59.610 47.826 0.00 0.00 40.71 3.42
3196 6401 2.202707 AGGTATTTAAACCCCCGAGCT 58.797 47.619 0.00 0.00 40.71 4.09
3197 6402 2.723322 AGGTATTTAAACCCCCGAGC 57.277 50.000 0.00 0.00 40.71 5.03
3198 6403 6.182627 AGTTAAAGGTATTTAAACCCCCGAG 58.817 40.000 0.00 0.00 41.36 4.63
3200 6405 5.065090 CGAGTTAAAGGTATTTAAACCCCCG 59.935 44.000 0.00 0.00 41.36 5.73
3201 6406 6.094048 GTCGAGTTAAAGGTATTTAAACCCCC 59.906 42.308 0.00 0.00 41.36 5.40
3203 6408 7.912056 AGTCGAGTTAAAGGTATTTAAACCC 57.088 36.000 0.00 0.00 41.36 4.11
3208 6413 9.643693 CCAGTTAAGTCGAGTTAAAGGTATTTA 57.356 33.333 23.50 0.00 0.00 1.40
3209 6414 7.118825 GCCAGTTAAGTCGAGTTAAAGGTATTT 59.881 37.037 28.49 11.31 0.00 1.40
3210 6415 6.592994 GCCAGTTAAGTCGAGTTAAAGGTATT 59.407 38.462 28.49 12.47 0.00 1.89
3211 6416 6.070938 AGCCAGTTAAGTCGAGTTAAAGGTAT 60.071 38.462 28.49 21.02 0.00 2.73
3212 6417 5.244626 AGCCAGTTAAGTCGAGTTAAAGGTA 59.755 40.000 28.49 10.65 0.00 3.08
3213 6418 4.040095 AGCCAGTTAAGTCGAGTTAAAGGT 59.960 41.667 28.49 21.54 0.00 3.50
3214 6419 4.389077 CAGCCAGTTAAGTCGAGTTAAAGG 59.611 45.833 26.32 26.32 0.00 3.11
3215 6420 4.143094 GCAGCCAGTTAAGTCGAGTTAAAG 60.143 45.833 23.50 18.61 0.00 1.85
3216 6421 3.744426 GCAGCCAGTTAAGTCGAGTTAAA 59.256 43.478 23.50 8.45 0.00 1.52
3217 6422 3.243941 TGCAGCCAGTTAAGTCGAGTTAA 60.244 43.478 19.20 19.20 0.00 2.01
3225 6430 2.571653 TGATACCTGCAGCCAGTTAAGT 59.428 45.455 8.66 0.25 37.38 2.24
3349 6570 4.580995 TGCCTTTGTTCTTCCGAAAATACA 59.419 37.500 0.00 0.00 0.00 2.29
3375 6596 7.815068 GTCTGAAGAGATAAGTTGTTCTAGCAA 59.185 37.037 0.00 0.00 0.00 3.91
3386 6607 7.963532 TGGTAGTTTTGTCTGAAGAGATAAGT 58.036 34.615 0.00 0.00 31.62 2.24
3406 6627 2.422597 TCTTTGTGCCATCGTTGGTAG 58.577 47.619 13.90 4.87 45.57 3.18
3408 6629 1.909700 ATCTTTGTGCCATCGTTGGT 58.090 45.000 13.90 0.00 45.57 3.67
3473 6700 4.920112 CGTCCAACCACACGGGCA 62.920 66.667 0.00 0.00 42.05 5.36
3887 7121 1.553248 ACCTTTGCGGTGTAGCTATCA 59.447 47.619 0.00 0.00 46.80 2.15
3981 7215 1.229131 ACTCCGGATCCAGGTACCTA 58.771 55.000 15.80 0.00 0.00 3.08
3982 7216 1.229131 TACTCCGGATCCAGGTACCT 58.771 55.000 9.21 9.21 0.00 3.08
4092 7326 0.035317 TCTTGCCATGCTCGTTCTGT 59.965 50.000 0.00 0.00 0.00 3.41
4108 7342 6.116126 AGTAGTTTGACAAGTTCTGCTTCTT 58.884 36.000 0.00 0.00 34.69 2.52
4371 7637 3.771160 GAGTCGACCCCGCCATGT 61.771 66.667 13.01 0.00 35.37 3.21
4387 7653 1.663379 CCATGCTGACCGACTACCGA 61.663 60.000 0.00 0.00 41.76 4.69
4440 7706 3.713936 CGGTACACGCAGAGATGAA 57.286 52.632 0.00 0.00 34.82 2.57
4491 7757 5.844301 AAATTATTTTTCTGGCAAGTGCG 57.156 34.783 0.00 0.00 43.26 5.34
4525 7840 7.551262 TGTGACTCACATAATAATAACCGCTTT 59.449 33.333 7.84 0.00 39.62 3.51
4536 7851 6.262273 TGCTATCGACTGTGACTCACATAATA 59.738 38.462 12.34 7.31 43.71 0.98
4593 7908 9.396022 GAAAATCAGTTTCATCCAGTCCTATTA 57.604 33.333 0.00 0.00 44.42 0.98
4613 7928 3.001939 CCGTACACGCCCTTATGAAAATC 59.998 47.826 0.00 0.00 38.18 2.17
4628 7943 1.474077 ACCTTATCGACCACCGTACAC 59.526 52.381 0.00 0.00 39.75 2.90
4674 7989 6.550108 ACCACCGTACACTATCATCTTTAGAT 59.450 38.462 0.00 0.00 34.56 1.98
4675 7990 5.889853 ACCACCGTACACTATCATCTTTAGA 59.110 40.000 0.00 0.00 0.00 2.10
4676 7991 6.145338 ACCACCGTACACTATCATCTTTAG 57.855 41.667 0.00 0.00 0.00 1.85
4677 7992 5.220912 CGACCACCGTACACTATCATCTTTA 60.221 44.000 0.00 0.00 0.00 1.85
4678 7993 4.439700 CGACCACCGTACACTATCATCTTT 60.440 45.833 0.00 0.00 0.00 2.52
4679 7994 3.066342 CGACCACCGTACACTATCATCTT 59.934 47.826 0.00 0.00 0.00 2.40
4680 7995 2.617308 CGACCACCGTACACTATCATCT 59.383 50.000 0.00 0.00 0.00 2.90
4681 7996 2.615447 TCGACCACCGTACACTATCATC 59.385 50.000 0.00 0.00 39.75 2.92
4682 7997 2.646930 TCGACCACCGTACACTATCAT 58.353 47.619 0.00 0.00 39.75 2.45
4683 7998 2.112380 TCGACCACCGTACACTATCA 57.888 50.000 0.00 0.00 39.75 2.15
4684 7999 4.320057 CCTTATCGACCACCGTACACTATC 60.320 50.000 0.00 0.00 39.75 2.08
4685 8000 3.567164 CCTTATCGACCACCGTACACTAT 59.433 47.826 0.00 0.00 39.75 2.12
4686 8001 2.945008 CCTTATCGACCACCGTACACTA 59.055 50.000 0.00 0.00 39.75 2.74
4687 8002 1.747355 CCTTATCGACCACCGTACACT 59.253 52.381 0.00 0.00 39.75 3.55
4688 8003 1.474077 ACCTTATCGACCACCGTACAC 59.526 52.381 0.00 0.00 39.75 2.90
4689 8004 1.473677 CACCTTATCGACCACCGTACA 59.526 52.381 0.00 0.00 39.75 2.90
4690 8005 1.474077 ACACCTTATCGACCACCGTAC 59.526 52.381 0.00 0.00 39.75 3.67
4691 8006 1.838112 ACACCTTATCGACCACCGTA 58.162 50.000 0.00 0.00 39.75 4.02
4692 8007 0.971386 AACACCTTATCGACCACCGT 59.029 50.000 0.00 0.00 39.75 4.83
4693 8008 2.088950 AAACACCTTATCGACCACCG 57.911 50.000 0.00 0.00 40.25 4.94
4694 8009 3.566742 ACAAAAACACCTTATCGACCACC 59.433 43.478 0.00 0.00 0.00 4.61
4695 8010 4.514066 AGACAAAAACACCTTATCGACCAC 59.486 41.667 0.00 0.00 0.00 4.16
4696 8011 4.710324 AGACAAAAACACCTTATCGACCA 58.290 39.130 0.00 0.00 0.00 4.02
4697 8012 5.684550 AAGACAAAAACACCTTATCGACC 57.315 39.130 0.00 0.00 0.00 4.79
4698 8013 8.124199 TGTTTAAGACAAAAACACCTTATCGAC 58.876 33.333 0.00 0.00 40.83 4.20
4699 8014 8.211116 TGTTTAAGACAAAAACACCTTATCGA 57.789 30.769 0.00 0.00 40.83 3.59
4704 8019 9.744468 GTGATATGTTTAAGACAAAAACACCTT 57.256 29.630 3.72 0.00 46.40 3.50
4705 8020 8.908903 TGTGATATGTTTAAGACAAAAACACCT 58.091 29.630 3.72 0.00 46.40 4.00
4706 8021 9.691362 ATGTGATATGTTTAAGACAAAAACACC 57.309 29.630 3.72 0.00 46.40 4.16
4796 8111 7.246763 CAAGATAGACCCCTAGGAATACCTAA 58.753 42.308 11.48 0.00 46.59 2.69
4799 8114 4.778427 CCAAGATAGACCCCTAGGAATACC 59.222 50.000 11.48 0.00 36.73 2.73
4820 8136 2.909504 TTTGCAATAGTTAGGGCCCA 57.090 45.000 27.56 7.27 0.00 5.36
4825 8141 8.723942 AGTCACTTAGATTTGCAATAGTTAGG 57.276 34.615 0.00 0.00 0.00 2.69
4826 8142 9.371136 TGAGTCACTTAGATTTGCAATAGTTAG 57.629 33.333 0.00 0.00 0.00 2.34
4830 8146 8.886719 TGATTGAGTCACTTAGATTTGCAATAG 58.113 33.333 0.00 0.00 0.00 1.73
4838 8154 6.989169 GCCAGTATGATTGAGTCACTTAGATT 59.011 38.462 0.00 0.00 40.28 2.40
4860 8176 5.947228 TGTTTGATTGTTTGTTTTTGCCA 57.053 30.435 0.00 0.00 0.00 4.92


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

AutoCloner maintained by Alex Coulton.