Multiple sequence alignment - TraesCS7A01G525400

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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 TraesCS7A01G525400 chr7A 100.000 4834 0 0 1 4834 707970154 707965321 0.000000e+00 8927.0
1 TraesCS7A01G525400 chr7A 95.205 146 4 3 3161 3306 707966849 707966707 1.350000e-55 228.0
2 TraesCS7A01G525400 chr7A 95.205 146 4 3 3306 3448 707966994 707966849 1.350000e-55 228.0
3 TraesCS7A01G525400 chr7B 89.721 2792 151 52 556 3306 708001233 707998537 0.000000e+00 3441.0
4 TraesCS7A01G525400 chr7B 95.471 1126 41 8 3306 4424 707998679 707997557 0.000000e+00 1788.0
5 TraesCS7A01G525400 chr7B 97.943 389 8 0 4446 4834 707997410 707997022 0.000000e+00 675.0
6 TraesCS7A01G525400 chr7B 82.627 236 27 7 4613 4834 712844769 712844534 3.820000e-46 196.0
7 TraesCS7A01G525400 chr7B 84.459 148 13 5 2147 2290 708102590 708102449 2.350000e-28 137.0
8 TraesCS7A01G525400 chr7D 88.435 1911 105 48 556 2428 615466535 615464703 0.000000e+00 2198.0
9 TraesCS7A01G525400 chr7D 94.381 783 36 7 3388 4165 615462243 615461464 0.000000e+00 1195.0
10 TraesCS7A01G525400 chr7D 91.625 800 40 15 2433 3219 615463025 615462240 0.000000e+00 1081.0
11 TraesCS7A01G525400 chr7D 94.188 499 26 3 1 498 41370678 41370182 0.000000e+00 758.0
12 TraesCS7A01G525400 chr7D 95.169 414 18 2 4421 4834 615461098 615460687 0.000000e+00 652.0
13 TraesCS7A01G525400 chr7D 97.692 260 6 0 4165 4424 615461384 615461125 9.540000e-122 448.0
14 TraesCS7A01G525400 chr7D 90.870 230 18 3 3333 3559 614702781 614703010 6.080000e-79 305.0
15 TraesCS7A01G525400 chr7D 95.082 61 2 1 3246 3306 615462243 615462184 1.430000e-15 95.3
16 TraesCS7A01G525400 chr1A 95.179 560 21 5 1 556 563186890 563187447 0.000000e+00 880.0
17 TraesCS7A01G525400 chr1A 94.414 555 25 2 1 555 97260806 97260258 0.000000e+00 848.0
18 TraesCS7A01G525400 chr1A 93.705 556 28 3 1 555 353279029 353278480 0.000000e+00 826.0
19 TraesCS7A01G525400 chr2A 93.525 556 27 5 1 555 702408968 702408421 0.000000e+00 819.0
20 TraesCS7A01G525400 chr1B 88.989 554 42 8 9 555 497826087 497825546 0.000000e+00 667.0
21 TraesCS7A01G525400 chr6A 96.078 255 9 1 1 255 610214692 610214439 9.680000e-112 414.0
22 TraesCS7A01G525400 chr3B 91.235 251 15 6 308 555 485537754 485538000 7.750000e-88 335.0
23 TraesCS7A01G525400 chr3B 89.151 212 23 0 3 214 485537537 485537748 1.030000e-66 265.0
24 TraesCS7A01G525400 chr4A 87.226 274 17 8 283 556 491458882 491459137 3.660000e-76 296.0
25 TraesCS7A01G525400 chr1D 93.865 163 10 0 3 165 417749114 417749276 3.740000e-61 246.0
26 TraesCS7A01G525400 chr2B 83.630 281 18 18 283 555 232837985 232838245 6.250000e-59 239.0
27 TraesCS7A01G525400 chr2B 84.127 252 17 8 3 231 232837728 232837979 6.300000e-54 222.0


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 TraesCS7A01G525400 chr7A 707965321 707970154 4833 True 3127.666667 8927 96.803333 1 4834 3 chr7A.!!$R1 4833
1 TraesCS7A01G525400 chr7B 707997022 708001233 4211 True 1968.000000 3441 94.378333 556 4834 3 chr7B.!!$R3 4278
2 TraesCS7A01G525400 chr7D 615460687 615466535 5848 True 944.883333 2198 93.730667 556 4834 6 chr7D.!!$R2 4278
3 TraesCS7A01G525400 chr1A 563186890 563187447 557 False 880.000000 880 95.179000 1 556 1 chr1A.!!$F1 555
4 TraesCS7A01G525400 chr1A 97260258 97260806 548 True 848.000000 848 94.414000 1 555 1 chr1A.!!$R1 554
5 TraesCS7A01G525400 chr1A 353278480 353279029 549 True 826.000000 826 93.705000 1 555 1 chr1A.!!$R2 554
6 TraesCS7A01G525400 chr2A 702408421 702408968 547 True 819.000000 819 93.525000 1 555 1 chr2A.!!$R1 554
7 TraesCS7A01G525400 chr1B 497825546 497826087 541 True 667.000000 667 88.989000 9 555 1 chr1B.!!$R1 546
8 TraesCS7A01G525400 chr2B 232837728 232838245 517 False 230.500000 239 83.878500 3 555 2 chr2B.!!$F1 552

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
747 794 1.384525 GCACCACCACCGCAAATATA 58.615 50.000 0.00 0.0 0.00 0.86 F
1429 1502 1.065102 GGCGCATCTCTTCTGTACGTA 59.935 52.381 10.83 0.0 0.00 3.57 F
2322 2420 0.179048 CTGATATGGCTGGCCGTTGA 60.179 55.000 11.79 0.0 39.42 3.18 F
2738 4513 0.540365 ACATGGGAACTTGGCAGGTG 60.540 55.000 1.91 0.0 39.68 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1553 1630 0.106116 TTTACCAAACCCACCGGCTT 60.106 50.0 0.00 0.0 0.00 4.35 R
3183 4973 0.693622 TCAGGTACCCGATTTGGCAA 59.306 50.0 8.74 0.0 35.87 4.52 R
3657 5450 0.036010 AACTTCCCACATGAGAGGCG 60.036 55.0 0.00 0.0 0.00 5.52 R
3834 5629 0.178998 CAGCTCCTAGCATTGGCCAT 60.179 55.0 6.09 0.0 45.56 4.40 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
56 63 1.920835 GACCAAGACTGAGGGCCCT 60.921 63.158 29.18 29.18 0.00 5.19
289 319 7.442364 GTGAAGCTGTGAAAGGATAGCATATTA 59.558 37.037 0.00 0.00 38.59 0.98
422 464 3.478540 GGCTGATAAAAGGCCTCGT 57.521 52.632 5.23 0.00 42.31 4.18
488 530 7.233632 ACGTATATACCTTGTACATACCTGGA 58.766 38.462 7.30 0.00 0.00 3.86
577 621 6.863275 TGGACATAGGCACATATTATACTCG 58.137 40.000 0.00 0.00 0.00 4.18
578 622 6.127451 TGGACATAGGCACATATTATACTCGG 60.127 42.308 0.00 0.00 0.00 4.63
580 624 7.241042 ACATAGGCACATATTATACTCGGTT 57.759 36.000 0.00 0.00 0.00 4.44
591 635 5.850557 TTATACTCGGTTCGTCCCATAAA 57.149 39.130 0.00 0.00 0.00 1.40
604 649 7.258022 TCGTCCCATAAAATGACATGTTATG 57.742 36.000 23.51 23.51 35.77 1.90
662 709 7.775053 AAATTAGGTTGGCTGATTTACTCAA 57.225 32.000 0.00 0.00 32.14 3.02
747 794 1.384525 GCACCACCACCGCAAATATA 58.615 50.000 0.00 0.00 0.00 0.86
777 824 6.211184 TCCACTGGACATTGCAAAATAGATTT 59.789 34.615 1.71 0.00 0.00 2.17
778 825 6.532657 CCACTGGACATTGCAAAATAGATTTC 59.467 38.462 1.71 0.00 0.00 2.17
822 874 7.899973 AGATTTTACAGTGGATGCTTTTCATT 58.100 30.769 0.00 0.00 35.05 2.57
833 885 8.650714 GTGGATGCTTTTCATTATGAAAGAAAC 58.349 33.333 18.09 10.84 45.77 2.78
839 891 9.428097 GCTTTTCATTATGAAAGAAACAGGAAT 57.572 29.630 18.09 0.00 45.77 3.01
898 950 3.960755 ACCAAGGGGACAAGAAAAGAAAG 59.039 43.478 0.00 0.00 38.05 2.62
899 951 4.215109 CCAAGGGGACAAGAAAAGAAAGA 58.785 43.478 0.00 0.00 35.59 2.52
902 954 6.276091 CAAGGGGACAAGAAAAGAAAGAAAG 58.724 40.000 0.00 0.00 0.00 2.62
903 955 4.895889 AGGGGACAAGAAAAGAAAGAAAGG 59.104 41.667 0.00 0.00 0.00 3.11
905 957 5.362717 GGGGACAAGAAAAGAAAGAAAGGAA 59.637 40.000 0.00 0.00 0.00 3.36
908 960 7.822334 GGGACAAGAAAAGAAAGAAAGGAAAAA 59.178 33.333 0.00 0.00 0.00 1.94
910 962 9.203421 GACAAGAAAAGAAAGAAAGGAAAAACA 57.797 29.630 0.00 0.00 0.00 2.83
912 964 8.987890 CAAGAAAAGAAAGAAAGGAAAAACACA 58.012 29.630 0.00 0.00 0.00 3.72
913 965 9.554395 AAGAAAAGAAAGAAAGGAAAAACACAA 57.446 25.926 0.00 0.00 0.00 3.33
914 966 9.208022 AGAAAAGAAAGAAAGGAAAAACACAAG 57.792 29.630 0.00 0.00 0.00 3.16
1055 1113 2.364961 CGTCCTCCTCCCCCTCTT 59.635 66.667 0.00 0.00 0.00 2.85
1236 1303 1.450848 CGGCTGCCACATCATCACT 60.451 57.895 20.29 0.00 0.00 3.41
1293 1366 2.831333 CCACTGTCATGCCTCTGTATC 58.169 52.381 0.00 0.00 0.00 2.24
1296 1369 4.511527 CACTGTCATGCCTCTGTATCTTT 58.488 43.478 0.00 0.00 0.00 2.52
1297 1370 4.331992 CACTGTCATGCCTCTGTATCTTTG 59.668 45.833 0.00 0.00 0.00 2.77
1298 1371 3.875727 CTGTCATGCCTCTGTATCTTTGG 59.124 47.826 0.00 0.00 0.00 3.28
1299 1372 3.264193 TGTCATGCCTCTGTATCTTTGGT 59.736 43.478 0.00 0.00 0.00 3.67
1300 1373 4.469586 TGTCATGCCTCTGTATCTTTGGTA 59.530 41.667 0.00 0.00 0.00 3.25
1301 1374 5.130975 TGTCATGCCTCTGTATCTTTGGTAT 59.869 40.000 0.00 0.00 0.00 2.73
1302 1375 5.698545 GTCATGCCTCTGTATCTTTGGTATC 59.301 44.000 0.00 0.00 0.00 2.24
1303 1376 5.366477 TCATGCCTCTGTATCTTTGGTATCA 59.634 40.000 0.00 0.00 0.00 2.15
1304 1377 5.282055 TGCCTCTGTATCTTTGGTATCAG 57.718 43.478 0.00 0.00 0.00 2.90
1305 1378 4.716784 TGCCTCTGTATCTTTGGTATCAGT 59.283 41.667 0.00 0.00 0.00 3.41
1306 1379 5.897250 TGCCTCTGTATCTTTGGTATCAGTA 59.103 40.000 0.00 0.00 0.00 2.74
1307 1380 6.183360 TGCCTCTGTATCTTTGGTATCAGTAC 60.183 42.308 0.00 0.00 0.00 2.73
1308 1381 6.041069 GCCTCTGTATCTTTGGTATCAGTACT 59.959 42.308 0.00 0.00 0.00 2.73
1309 1382 7.429633 CCTCTGTATCTTTGGTATCAGTACTG 58.570 42.308 17.17 17.17 0.00 2.74
1429 1502 1.065102 GGCGCATCTCTTCTGTACGTA 59.935 52.381 10.83 0.00 0.00 3.57
1450 1523 8.280909 ACGTAATGCAGTTTTATGTTCTTTTG 57.719 30.769 0.00 0.00 0.00 2.44
1451 1524 7.918562 ACGTAATGCAGTTTTATGTTCTTTTGT 59.081 29.630 0.00 0.00 0.00 2.83
1452 1525 8.751335 CGTAATGCAGTTTTATGTTCTTTTGTT 58.249 29.630 0.00 0.00 0.00 2.83
1521 1594 9.019764 ACAATCTTGTGTCGTTTCTTAAAATTG 57.980 29.630 0.00 0.00 40.49 2.32
1553 1630 2.666190 GGCGCTGCTCAGTGTCAA 60.666 61.111 7.64 0.00 42.66 3.18
1579 1656 3.181474 CGGTGGGTTTGGTAAATGTTGTT 60.181 43.478 0.00 0.00 0.00 2.83
1613 1690 5.065914 AGCTCTGTTCTGAAAGCATGTTTA 58.934 37.500 13.35 0.00 37.22 2.01
1637 1721 6.182039 TCATGGAAACTAAAGCAGATTTCG 57.818 37.500 0.00 0.00 32.87 3.46
1673 1757 8.794553 ACGATGAGTAAATTATCTCGGAACTAT 58.205 33.333 0.00 0.00 33.88 2.12
1674 1758 9.627395 CGATGAGTAAATTATCTCGGAACTATT 57.373 33.333 5.67 0.00 33.88 1.73
1799 1893 1.812571 CAATTTGCTCCGCTGTAAGGT 59.187 47.619 0.00 0.00 0.00 3.50
1800 1894 1.739067 ATTTGCTCCGCTGTAAGGTC 58.261 50.000 0.00 0.00 0.00 3.85
1816 1910 2.171840 AGGTCTCTTGTCTGTGCGTAT 58.828 47.619 0.00 0.00 0.00 3.06
1827 1921 5.474825 TGTCTGTGCGTATGTCAAATTAGA 58.525 37.500 0.00 0.00 0.00 2.10
1905 1999 3.003689 ACTGAGTGCACAAAATGTACAGC 59.996 43.478 21.04 0.00 45.74 4.40
1911 2005 4.788100 GTGCACAAAATGTACAGCTAATCG 59.212 41.667 13.17 0.00 43.03 3.34
1965 2059 3.196901 TGTATCCGCAGAACTTATGGTGT 59.803 43.478 0.00 0.00 0.00 4.16
1968 2062 1.732259 CCGCAGAACTTATGGTGTCAC 59.268 52.381 0.00 0.00 0.00 3.67
1983 2078 5.197451 TGGTGTCACTGGTTTAGTTTTGAT 58.803 37.500 2.35 0.00 37.60 2.57
2035 2132 4.730949 ATCAGAATGCAGTTTCCATTGG 57.269 40.909 0.00 0.00 33.34 3.16
2192 2290 6.018669 GGTGAACGATGTGATATTTCCTTCTC 60.019 42.308 0.00 0.00 0.00 2.87
2239 2337 4.953940 AGATTGGTCTCCTAATCTCTGC 57.046 45.455 0.00 0.00 38.86 4.26
2322 2420 0.179048 CTGATATGGCTGGCCGTTGA 60.179 55.000 11.79 0.00 39.42 3.18
2382 2480 3.197549 TCATGTATACTGCTGCACCTTCA 59.802 43.478 0.00 0.00 0.00 3.02
2415 2513 8.423906 TCCATTAGTTCTCTAAGACTGAAGTT 57.576 34.615 0.00 0.00 39.17 2.66
2488 4260 4.070716 CCTGAGCTGTTTCTTGACTTGAT 58.929 43.478 0.00 0.00 0.00 2.57
2495 4267 5.180117 GCTGTTTCTTGACTTGATAAGCAGA 59.820 40.000 0.00 0.00 0.00 4.26
2504 4276 8.579850 TTGACTTGATAAGCAGAAACCATAAT 57.420 30.769 0.00 0.00 0.00 1.28
2534 4308 9.920946 ACATGATTAAATCACCCACTAATACTT 57.079 29.630 0.00 0.00 43.01 2.24
2619 4394 1.457831 GACGTATGCCCTCCCTCCT 60.458 63.158 0.00 0.00 0.00 3.69
2624 4399 2.372172 CGTATGCCCTCCCTCCTTAATT 59.628 50.000 0.00 0.00 0.00 1.40
2738 4513 0.540365 ACATGGGAACTTGGCAGGTG 60.540 55.000 1.91 0.00 39.68 4.00
2758 4533 5.938125 AGGTGCGTAAAGACATTTTACTCAT 59.062 36.000 5.96 0.00 33.80 2.90
2859 4634 8.691661 TTATGGTTCTATTTTCTTGATAGGCC 57.308 34.615 0.00 0.00 0.00 5.19
2861 4636 4.515567 GGTTCTATTTTCTTGATAGGCCCG 59.484 45.833 0.00 0.00 0.00 6.13
2870 4645 1.271856 TGATAGGCCCGACTGAACAA 58.728 50.000 0.00 0.00 0.00 2.83
2932 4716 6.931838 TGTAACAGAACTATAGGAAGTGGTG 58.068 40.000 4.43 0.00 0.00 4.17
2939 4723 8.258007 CAGAACTATAGGAAGTGGTGTATTCAA 58.742 37.037 4.43 0.00 0.00 2.69
2947 4731 6.319658 AGGAAGTGGTGTATTCAATGCATAAG 59.680 38.462 0.00 0.00 0.00 1.73
2948 4732 6.318648 GGAAGTGGTGTATTCAATGCATAAGA 59.681 38.462 0.00 0.00 0.00 2.10
2949 4733 7.013655 GGAAGTGGTGTATTCAATGCATAAGAT 59.986 37.037 0.00 0.00 0.00 2.40
2950 4734 7.502120 AGTGGTGTATTCAATGCATAAGATC 57.498 36.000 0.00 0.00 0.00 2.75
2979 4769 6.929049 CAGTATCCATCTATGCCGAGTTTAAA 59.071 38.462 0.00 0.00 0.00 1.52
2986 4776 5.790593 TCTATGCCGAGTTTAAACTTGACT 58.209 37.500 29.64 18.16 41.97 3.41
2987 4777 5.867716 TCTATGCCGAGTTTAAACTTGACTC 59.132 40.000 29.64 19.84 41.97 3.36
2988 4778 4.067972 TGCCGAGTTTAAACTTGACTCT 57.932 40.909 29.64 5.53 41.97 3.24
2989 4779 4.448210 TGCCGAGTTTAAACTTGACTCTT 58.552 39.130 29.64 4.83 41.97 2.85
2990 4780 5.603596 TGCCGAGTTTAAACTTGACTCTTA 58.396 37.500 29.64 6.40 41.97 2.10
2991 4781 6.050432 TGCCGAGTTTAAACTTGACTCTTAA 58.950 36.000 29.64 6.08 41.97 1.85
2992 4782 6.018507 TGCCGAGTTTAAACTTGACTCTTAAC 60.019 38.462 29.64 10.65 41.97 2.01
2993 4783 6.202379 GCCGAGTTTAAACTTGACTCTTAACT 59.798 38.462 29.64 2.51 41.97 2.24
3009 4799 6.926272 ACTCTTAACTTCTTAAGTCTGTGCAG 59.074 38.462 1.63 0.00 41.91 4.41
3013 4803 5.152623 ACTTCTTAAGTCTGTGCAGCATA 57.847 39.130 0.00 0.00 37.02 3.14
3065 4855 7.050377 ACATAATGTCAGTATTAGCAGCAACT 58.950 34.615 0.00 0.00 0.00 3.16
3087 4877 3.976793 AATGTTATTCAGGCATCTGCG 57.023 42.857 0.00 0.00 43.26 5.18
3124 4914 1.341531 CTGAGTCGAACACCTGAACCT 59.658 52.381 0.00 0.00 0.00 3.50
3146 4936 5.231265 TGACTTGTACTACGTCAGCTATG 57.769 43.478 0.00 0.00 33.15 2.23
3167 4957 5.118729 TGTCCATATCCGGGTAACATTTT 57.881 39.130 0.00 0.00 39.74 1.82
3168 4958 4.884744 TGTCCATATCCGGGTAACATTTTG 59.115 41.667 0.00 0.00 39.74 2.44
3169 4959 4.885325 GTCCATATCCGGGTAACATTTTGT 59.115 41.667 0.00 0.00 39.74 2.83
3170 4960 5.008316 GTCCATATCCGGGTAACATTTTGTC 59.992 44.000 0.00 0.00 39.74 3.18
3171 4961 4.884744 CCATATCCGGGTAACATTTTGTCA 59.115 41.667 0.00 0.00 39.74 3.58
3172 4962 5.534654 CCATATCCGGGTAACATTTTGTCAT 59.465 40.000 0.00 0.00 39.74 3.06
3173 4963 4.981806 ATCCGGGTAACATTTTGTCATG 57.018 40.909 0.00 0.00 39.74 3.07
3174 4964 4.022413 TCCGGGTAACATTTTGTCATGA 57.978 40.909 0.00 0.00 39.74 3.07
3175 4965 4.594970 TCCGGGTAACATTTTGTCATGAT 58.405 39.130 0.00 0.00 39.74 2.45
3176 4966 5.013547 TCCGGGTAACATTTTGTCATGATT 58.986 37.500 0.00 0.00 39.74 2.57
3177 4967 5.478679 TCCGGGTAACATTTTGTCATGATTT 59.521 36.000 0.00 0.00 39.74 2.17
3178 4968 6.015010 TCCGGGTAACATTTTGTCATGATTTT 60.015 34.615 0.00 0.00 39.74 1.82
3179 4969 7.176865 TCCGGGTAACATTTTGTCATGATTTTA 59.823 33.333 0.00 0.00 39.74 1.52
3180 4970 7.815068 CCGGGTAACATTTTGTCATGATTTTAA 59.185 33.333 0.00 0.00 39.74 1.52
3181 4971 9.364989 CGGGTAACATTTTGTCATGATTTTAAT 57.635 29.630 0.00 0.00 39.74 1.40
3187 4977 9.896263 ACATTTTGTCATGATTTTAATTTTGCC 57.104 25.926 0.00 0.00 0.00 4.52
3188 4978 9.894783 CATTTTGTCATGATTTTAATTTTGCCA 57.105 25.926 0.00 0.00 0.00 4.92
3193 4983 8.441608 TGTCATGATTTTAATTTTGCCAAATCG 58.558 29.630 0.00 0.00 38.12 3.34
3194 4984 7.904461 GTCATGATTTTAATTTTGCCAAATCGG 59.096 33.333 0.00 0.00 38.12 4.18
3195 4985 6.734104 TGATTTTAATTTTGCCAAATCGGG 57.266 33.333 0.00 0.00 38.12 5.14
3196 4986 6.234177 TGATTTTAATTTTGCCAAATCGGGT 58.766 32.000 0.00 0.00 38.12 5.28
3197 4987 7.386851 TGATTTTAATTTTGCCAAATCGGGTA 58.613 30.769 0.00 0.00 38.12 3.69
3198 4988 7.332182 TGATTTTAATTTTGCCAAATCGGGTAC 59.668 33.333 0.00 0.00 38.12 3.34
3199 4989 3.603158 AATTTTGCCAAATCGGGTACC 57.397 42.857 2.17 2.17 36.98 3.34
3200 4990 3.169908 AATTTTGCCAAATCGGGTACCT 58.830 40.909 12.72 0.00 37.84 3.08
3201 4991 3.056179 AATTTTGCCAAATCGGGTACCTG 60.056 43.478 15.21 15.21 37.84 4.00
3202 4992 5.297162 AATTTTGCCAAATCGGGTACCTGA 61.297 41.667 25.65 25.65 37.84 3.86
3203 4993 6.739675 AATTTTGCCAAATCGGGTACCTGAA 61.740 40.000 27.07 11.10 37.84 3.02
3204 4994 7.985162 AATTTTGCCAAATCGGGTACCTGAAT 61.985 38.462 27.07 16.77 37.84 2.57
3205 4995 9.667866 AATTTTGCCAAATCGGGTACCTGAATC 62.668 40.741 27.07 14.03 37.84 2.52
3217 5007 6.250344 GGTACCTGAATCCAGTTTTGTTAC 57.750 41.667 4.06 0.00 38.74 2.50
3218 5008 5.182570 GGTACCTGAATCCAGTTTTGTTACC 59.817 44.000 4.06 0.00 38.74 2.85
3219 5009 4.798882 ACCTGAATCCAGTTTTGTTACCA 58.201 39.130 0.00 0.00 38.74 3.25
3220 5010 5.205056 ACCTGAATCCAGTTTTGTTACCAA 58.795 37.500 0.00 0.00 38.74 3.67
3221 5011 5.068591 ACCTGAATCCAGTTTTGTTACCAAC 59.931 40.000 0.00 0.00 38.74 3.77
3222 5012 5.068460 CCTGAATCCAGTTTTGTTACCAACA 59.932 40.000 0.00 0.00 38.74 3.33
3223 5013 5.897050 TGAATCCAGTTTTGTTACCAACAC 58.103 37.500 0.00 0.00 41.97 3.32
3224 5014 4.929819 ATCCAGTTTTGTTACCAACACC 57.070 40.909 0.00 0.00 41.97 4.16
3225 5015 3.970842 TCCAGTTTTGTTACCAACACCT 58.029 40.909 0.00 0.00 41.97 4.00
3226 5016 3.697045 TCCAGTTTTGTTACCAACACCTG 59.303 43.478 0.00 0.00 41.97 4.00
3239 5029 3.813166 CCAACACCTGGGTATATTTAGCG 59.187 47.826 0.00 0.00 42.17 4.26
3240 5030 3.121738 ACACCTGGGTATATTTAGCGC 57.878 47.619 0.00 0.00 0.00 5.92
3241 5031 2.436542 ACACCTGGGTATATTTAGCGCA 59.563 45.455 11.47 0.00 0.00 6.09
3242 5032 3.072476 ACACCTGGGTATATTTAGCGCAT 59.928 43.478 11.47 0.00 0.00 4.73
3243 5033 4.285003 ACACCTGGGTATATTTAGCGCATA 59.715 41.667 11.47 0.00 0.00 3.14
3244 5034 5.221762 ACACCTGGGTATATTTAGCGCATAA 60.222 40.000 11.47 2.88 0.00 1.90
3245 5035 5.351465 CACCTGGGTATATTTAGCGCATAAG 59.649 44.000 11.47 0.00 0.00 1.73
3246 5036 5.247564 ACCTGGGTATATTTAGCGCATAAGA 59.752 40.000 11.47 0.00 0.00 2.10
3247 5037 5.581085 CCTGGGTATATTTAGCGCATAAGAC 59.419 44.000 11.47 1.94 0.00 3.01
3248 5038 5.484715 TGGGTATATTTAGCGCATAAGACC 58.515 41.667 11.47 10.55 0.00 3.85
3249 5039 4.874396 GGGTATATTTAGCGCATAAGACCC 59.126 45.833 11.47 15.37 0.00 4.46
3250 5040 5.484715 GGTATATTTAGCGCATAAGACCCA 58.515 41.667 11.47 0.00 0.00 4.51
3251 5041 5.935789 GGTATATTTAGCGCATAAGACCCAA 59.064 40.000 11.47 0.00 0.00 4.12
3252 5042 6.598064 GGTATATTTAGCGCATAAGACCCAAT 59.402 38.462 11.47 0.00 0.00 3.16
3253 5043 7.767198 GGTATATTTAGCGCATAAGACCCAATA 59.233 37.037 11.47 0.37 0.00 1.90
3254 5044 9.326413 GTATATTTAGCGCATAAGACCCAATAT 57.674 33.333 11.47 7.17 0.00 1.28
3255 5045 6.743575 ATTTAGCGCATAAGACCCAATATC 57.256 37.500 11.47 0.00 0.00 1.63
3256 5046 3.059352 AGCGCATAAGACCCAATATCC 57.941 47.619 11.47 0.00 0.00 2.59
3257 5047 2.084546 GCGCATAAGACCCAATATCCC 58.915 52.381 0.30 0.00 0.00 3.85
3258 5048 2.552155 GCGCATAAGACCCAATATCCCA 60.552 50.000 0.30 0.00 0.00 4.37
3259 5049 3.873801 GCGCATAAGACCCAATATCCCAT 60.874 47.826 0.30 0.00 0.00 4.00
3260 5050 3.941483 CGCATAAGACCCAATATCCCATC 59.059 47.826 0.00 0.00 0.00 3.51
3261 5051 4.323792 CGCATAAGACCCAATATCCCATCT 60.324 45.833 0.00 0.00 0.00 2.90
3262 5052 5.574188 GCATAAGACCCAATATCCCATCTT 58.426 41.667 0.00 0.00 0.00 2.40
3263 5053 6.012745 GCATAAGACCCAATATCCCATCTTT 58.987 40.000 0.00 0.00 0.00 2.52
3264 5054 6.071728 GCATAAGACCCAATATCCCATCTTTG 60.072 42.308 0.00 0.00 0.00 2.77
3265 5055 3.837355 AGACCCAATATCCCATCTTTGC 58.163 45.455 0.00 0.00 0.00 3.68
3266 5056 2.893489 GACCCAATATCCCATCTTTGCC 59.107 50.000 0.00 0.00 0.00 4.52
3267 5057 2.247111 ACCCAATATCCCATCTTTGCCA 59.753 45.455 0.00 0.00 0.00 4.92
3268 5058 3.116629 ACCCAATATCCCATCTTTGCCAT 60.117 43.478 0.00 0.00 0.00 4.40
3269 5059 4.107798 ACCCAATATCCCATCTTTGCCATA 59.892 41.667 0.00 0.00 0.00 2.74
3270 5060 5.222610 ACCCAATATCCCATCTTTGCCATAT 60.223 40.000 0.00 0.00 0.00 1.78
3271 5061 6.010828 ACCCAATATCCCATCTTTGCCATATA 60.011 38.462 0.00 0.00 0.00 0.86
3272 5062 7.071273 CCCAATATCCCATCTTTGCCATATAT 58.929 38.462 0.00 0.00 0.00 0.86
3273 5063 8.226810 CCCAATATCCCATCTTTGCCATATATA 58.773 37.037 0.00 0.00 0.00 0.86
3274 5064 9.645128 CCAATATCCCATCTTTGCCATATATAA 57.355 33.333 0.00 0.00 0.00 0.98
3279 5069 8.408043 TCCCATCTTTGCCATATATAAGTTTG 57.592 34.615 0.00 0.00 0.00 2.93
3280 5070 8.224025 TCCCATCTTTGCCATATATAAGTTTGA 58.776 33.333 0.00 0.00 0.00 2.69
3281 5071 8.859090 CCCATCTTTGCCATATATAAGTTTGAA 58.141 33.333 0.00 0.00 0.00 2.69
3282 5072 9.903682 CCATCTTTGCCATATATAAGTTTGAAG 57.096 33.333 0.00 0.00 0.00 3.02
3288 5078 9.461312 TTGCCATATATAAGTTTGAAGTTCACT 57.539 29.630 4.68 0.00 0.00 3.41
3289 5079 9.109393 TGCCATATATAAGTTTGAAGTTCACTC 57.891 33.333 4.68 1.79 0.00 3.51
3290 5080 9.331282 GCCATATATAAGTTTGAAGTTCACTCT 57.669 33.333 4.68 4.20 0.00 3.24
3299 5089 9.614792 AAGTTTGAAGTTCACTCTTAAGTATGT 57.385 29.630 4.68 0.00 33.25 2.29
3300 5090 9.046296 AGTTTGAAGTTCACTCTTAAGTATGTG 57.954 33.333 4.68 14.90 33.25 3.21
3301 5091 7.421530 TTGAAGTTCACTCTTAAGTATGTGC 57.578 36.000 4.68 7.67 33.25 4.57
3302 5092 6.521162 TGAAGTTCACTCTTAAGTATGTGCA 58.479 36.000 0.08 7.35 33.25 4.57
3303 5093 6.646653 TGAAGTTCACTCTTAAGTATGTGCAG 59.353 38.462 0.08 3.36 33.25 4.41
3304 5094 4.932200 AGTTCACTCTTAAGTATGTGCAGC 59.068 41.667 15.70 0.00 33.25 5.25
3305 5095 4.535526 TCACTCTTAAGTATGTGCAGCA 57.464 40.909 15.70 0.00 33.25 4.41
3306 5096 4.893608 TCACTCTTAAGTATGTGCAGCAA 58.106 39.130 0.00 0.00 33.25 3.91
3307 5097 4.690748 TCACTCTTAAGTATGTGCAGCAAC 59.309 41.667 0.00 0.00 33.25 4.17
3308 5098 4.452114 CACTCTTAAGTATGTGCAGCAACA 59.548 41.667 0.00 0.00 33.25 3.33
3309 5099 5.122869 CACTCTTAAGTATGTGCAGCAACAT 59.877 40.000 0.00 6.19 43.21 2.71
3310 5100 5.707298 ACTCTTAAGTATGTGCAGCAACATT 59.293 36.000 13.51 1.57 41.09 2.71
3311 5101 6.207417 ACTCTTAAGTATGTGCAGCAACATTT 59.793 34.615 13.51 7.53 41.09 2.32
3318 5108 2.361438 TGTGCAGCAACATTTGTCATGA 59.639 40.909 0.00 0.00 0.00 3.07
3422 5213 7.775093 TCCCATCTATGCCATATATAAGTTTGC 59.225 37.037 0.00 0.00 0.00 3.68
3439 5230 9.726438 ATAAGTTTGCAGTTCACTCTTAAGTAT 57.274 29.630 1.63 0.00 33.25 2.12
3440 5231 7.426929 AGTTTGCAGTTCACTCTTAAGTATG 57.573 36.000 1.63 2.59 33.25 2.39
3497 5290 8.877779 CCAAGACATACTATCAATATTAGCAGC 58.122 37.037 0.00 0.00 0.00 5.25
3505 5298 8.469309 ACTATCAATATTAGCAGCAACCAAAT 57.531 30.769 0.00 0.00 0.00 2.32
3512 5305 9.889128 AATATTAGCAGCAACCAAATGTTATTT 57.111 25.926 0.00 0.00 34.69 1.40
3516 5309 5.480073 AGCAGCAACCAAATGTTATTTAGGA 59.520 36.000 0.00 0.00 34.69 2.94
3538 5331 8.506168 AGGAATCTGCGTTCTTAATTTTATCA 57.494 30.769 0.00 0.00 0.00 2.15
3581 5374 5.507482 CCCAAGTCGTACTATGACACCTATG 60.507 48.000 10.45 2.71 36.61 2.23
3657 5450 4.681074 TCCAATTCTTTTTCCAACACCC 57.319 40.909 0.00 0.00 0.00 4.61
3677 5470 1.457346 GCCTCTCATGTGGGAAGTTG 58.543 55.000 0.00 0.00 0.00 3.16
3686 5479 1.133730 TGTGGGAAGTTGGGGTAACAC 60.134 52.381 0.00 0.00 41.88 3.32
3700 5493 3.363627 GGTAACACCCTGCTAGTACTCT 58.636 50.000 0.00 0.00 30.04 3.24
3712 5505 0.910088 AGTACTCTGGGCCCAACCTC 60.910 60.000 28.29 15.03 39.10 3.85
3714 5507 4.101448 CTCTGGGCCCAACCTCGG 62.101 72.222 28.29 13.52 39.10 4.63
3725 5518 3.305335 GCCCAACCTCGGCATTATATTTG 60.305 47.826 0.00 0.00 46.27 2.32
3791 5586 3.262420 GCTCTGTGAACACCGTGATTAT 58.738 45.455 5.28 0.00 0.00 1.28
3834 5629 6.611236 TGTGATTACTCTCAGTGGGATATGAA 59.389 38.462 0.00 0.00 0.00 2.57
3838 5633 3.072184 ACTCTCAGTGGGATATGAATGGC 59.928 47.826 0.00 0.00 0.00 4.40
3846 5641 3.075732 TGGGATATGAATGGCCAATGCTA 59.924 43.478 10.96 0.00 37.74 3.49
3852 5647 0.554792 AATGGCCAATGCTAGGAGCT 59.445 50.000 10.96 0.00 42.97 4.09
3924 5719 2.880890 CAACTGTTATATGAGCTGCCCC 59.119 50.000 0.00 0.00 0.00 5.80
3944 5739 7.001674 TGCCCCGACATATCTTATTTGTAATT 58.998 34.615 0.00 0.00 0.00 1.40
3945 5740 7.040755 TGCCCCGACATATCTTATTTGTAATTG 60.041 37.037 0.00 0.00 0.00 2.32
3947 5742 8.846211 CCCCGACATATCTTATTTGTAATTGTT 58.154 33.333 0.00 0.00 0.00 2.83
3966 5763 5.738118 TGTTTCCGTAGTTTTGTACAAGG 57.262 39.130 8.56 5.72 0.00 3.61
4005 5802 0.394762 CTAAGCTCCCATGCAAGCCA 60.395 55.000 12.42 2.80 39.39 4.75
4029 5826 3.551846 CCTATGTGGGCCGTCTAATTTT 58.448 45.455 0.00 0.00 0.00 1.82
4076 5873 5.050702 GCTATCTTCACCTTCGTAGAAATGC 60.051 44.000 0.00 0.00 45.90 3.56
4482 6484 0.699399 TGGTGGAGCCCGGAAATAAA 59.301 50.000 0.73 0.00 36.04 1.40
4484 6486 1.340697 GGTGGAGCCCGGAAATAAACT 60.341 52.381 0.73 0.00 0.00 2.66
4539 6541 8.204836 ACCTAGTCCAAGTGTCATACAATATTC 58.795 37.037 0.00 0.00 0.00 1.75
4541 6543 6.873997 AGTCCAAGTGTCATACAATATTCGA 58.126 36.000 0.00 0.00 0.00 3.71
4544 6546 6.097696 TCCAAGTGTCATACAATATTCGAGGA 59.902 38.462 0.00 0.00 0.00 3.71
4672 6674 3.119388 TGCCATGAAAGCTTCAACTATGC 60.119 43.478 0.00 0.00 43.95 3.14
4724 6726 4.142600 GCCAGTAAGCAATAGTTCACAAGG 60.143 45.833 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 63 7.572523 AGTTCACAACTGATTTCAATTCAGA 57.427 32.000 14.84 0.00 41.01 3.27
262 292 3.008375 TGCTATCCTTTCACAGCTTCACT 59.992 43.478 0.00 0.00 35.05 3.41
342 376 0.530650 CGGCAGGATTAGCGACATGT 60.531 55.000 0.00 0.00 0.00 3.21
392 434 2.401583 TATCAGCCTTTCACGCACAT 57.598 45.000 0.00 0.00 0.00 3.21
411 453 2.341452 GCCAAAGACGAGGCCTTTT 58.659 52.632 6.77 0.00 45.18 2.27
422 464 6.222389 CCATGTCAAACAAAATAGCCAAAGA 58.778 36.000 0.00 0.00 0.00 2.52
577 621 4.398044 ACATGTCATTTTATGGGACGAACC 59.602 41.667 0.00 0.00 34.32 3.62
578 622 5.560966 ACATGTCATTTTATGGGACGAAC 57.439 39.130 0.00 0.00 34.32 3.95
580 624 7.051000 TCATAACATGTCATTTTATGGGACGA 58.949 34.615 22.71 8.18 35.02 4.20
630 677 5.782047 TCAGCCAACCTAATTTTCAATGTG 58.218 37.500 0.00 0.00 0.00 3.21
636 683 7.826690 TGAGTAAATCAGCCAACCTAATTTTC 58.173 34.615 0.00 0.00 32.77 2.29
641 688 5.626142 TGTTGAGTAAATCAGCCAACCTAA 58.374 37.500 0.00 0.00 39.68 2.69
646 693 6.707440 TCTTTTGTTGAGTAAATCAGCCAA 57.293 33.333 0.00 0.00 39.68 4.52
662 709 9.778993 CATCAATCGTTATCTCATTTCTTTTGT 57.221 29.630 0.00 0.00 0.00 2.83
747 794 4.686191 TTGCAATGTCCAGTGGAAAAAT 57.314 36.364 15.09 5.41 34.03 1.82
777 824 6.916360 ATCTATTTTGCCCACTCAAAAAGA 57.084 33.333 5.87 9.57 45.50 2.52
778 825 7.967890 AAATCTATTTTGCCCACTCAAAAAG 57.032 32.000 5.87 5.69 45.50 2.27
822 874 9.912634 GTGAATTTGATTCCTGTTTCTTTCATA 57.087 29.630 0.00 0.00 38.50 2.15
833 885 2.827322 TGCTGGGTGAATTTGATTCCTG 59.173 45.455 0.00 0.00 38.50 3.86
839 891 7.448420 TGAATTTTATTGCTGGGTGAATTTGA 58.552 30.769 0.00 0.00 0.00 2.69
898 950 3.305897 CGGTTGCTTGTGTTTTTCCTTTC 59.694 43.478 0.00 0.00 0.00 2.62
899 951 3.258228 CGGTTGCTTGTGTTTTTCCTTT 58.742 40.909 0.00 0.00 0.00 3.11
902 954 0.927537 GCGGTTGCTTGTGTTTTTCC 59.072 50.000 0.00 0.00 38.39 3.13
1236 1303 4.980805 GTCGGGCGCACCTTGTGA 62.981 66.667 10.83 0.00 35.23 3.58
1263 1336 0.956633 ATGACAGTGGCAAAGCTGTG 59.043 50.000 13.26 0.00 44.89 3.66
1293 1366 7.065803 CCATACCAAACAGTACTGATACCAAAG 59.934 40.741 29.30 12.28 30.88 2.77
1296 1369 5.486063 ACCATACCAAACAGTACTGATACCA 59.514 40.000 29.30 9.67 30.88 3.25
1297 1370 5.985911 ACCATACCAAACAGTACTGATACC 58.014 41.667 29.30 0.00 30.88 2.73
1298 1371 7.779073 ACTACCATACCAAACAGTACTGATAC 58.221 38.462 29.30 0.00 0.00 2.24
1299 1372 7.966339 ACTACCATACCAAACAGTACTGATA 57.034 36.000 29.30 12.61 0.00 2.15
1300 1373 6.869206 ACTACCATACCAAACAGTACTGAT 57.131 37.500 29.30 15.34 0.00 2.90
1301 1374 7.779754 TTACTACCATACCAAACAGTACTGA 57.220 36.000 29.30 5.99 0.00 3.41
1302 1375 9.444600 AATTTACTACCATACCAAACAGTACTG 57.555 33.333 21.44 21.44 0.00 2.74
1303 1376 9.444600 CAATTTACTACCATACCAAACAGTACT 57.555 33.333 0.00 0.00 0.00 2.73
1304 1377 8.671028 CCAATTTACTACCATACCAAACAGTAC 58.329 37.037 0.00 0.00 0.00 2.73
1305 1378 8.384718 ACCAATTTACTACCATACCAAACAGTA 58.615 33.333 0.00 0.00 0.00 2.74
1306 1379 7.175990 CACCAATTTACTACCATACCAAACAGT 59.824 37.037 0.00 0.00 0.00 3.55
1307 1380 7.392113 TCACCAATTTACTACCATACCAAACAG 59.608 37.037 0.00 0.00 0.00 3.16
1308 1381 7.232188 TCACCAATTTACTACCATACCAAACA 58.768 34.615 0.00 0.00 0.00 2.83
1309 1382 7.690952 TCACCAATTTACTACCATACCAAAC 57.309 36.000 0.00 0.00 0.00 2.93
1450 1523 7.568433 ACAACAACAACAACAACAACAATAAC 58.432 30.769 0.00 0.00 0.00 1.89
1451 1524 7.715265 ACAACAACAACAACAACAACAATAA 57.285 28.000 0.00 0.00 0.00 1.40
1452 1525 7.224753 ACAACAACAACAACAACAACAACAATA 59.775 29.630 0.00 0.00 0.00 1.90
1453 1526 6.037610 ACAACAACAACAACAACAACAACAAT 59.962 30.769 0.00 0.00 0.00 2.71
1521 1594 3.727970 GCAGCGCCATAAAACTTACTGAC 60.728 47.826 2.29 0.00 0.00 3.51
1553 1630 0.106116 TTTACCAAACCCACCGGCTT 60.106 50.000 0.00 0.00 0.00 4.35
1566 1643 5.674525 TCCAATGCAAAACAACATTTACCA 58.325 33.333 0.00 0.00 34.32 3.25
1579 1656 3.005050 CAGAACAGAGCTTCCAATGCAAA 59.995 43.478 0.00 0.00 0.00 3.68
1613 1690 6.599244 TCGAAATCTGCTTTAGTTTCCATGAT 59.401 34.615 0.00 0.00 0.00 2.45
1627 1704 4.451096 TCGTTTAAAGCTTCGAAATCTGCT 59.549 37.500 0.00 3.95 37.37 4.24
1628 1705 4.708601 TCGTTTAAAGCTTCGAAATCTGC 58.291 39.130 0.00 0.00 0.00 4.26
1645 1729 7.980099 AGTTCCGAGATAATTTACTCATCGTTT 59.020 33.333 10.60 0.00 33.86 3.60
1799 1893 2.556622 TGACATACGCACAGACAAGAGA 59.443 45.455 0.00 0.00 0.00 3.10
1800 1894 2.946564 TGACATACGCACAGACAAGAG 58.053 47.619 0.00 0.00 0.00 2.85
1905 1999 5.845985 TTTCAAGTTCTGCTGTCGATTAG 57.154 39.130 0.00 0.00 0.00 1.73
1911 2005 4.516698 TCAGGAATTTCAAGTTCTGCTGTC 59.483 41.667 0.00 0.00 0.00 3.51
1965 2059 7.338196 TCACTTCAATCAAAACTAAACCAGTGA 59.662 33.333 0.00 0.00 37.63 3.41
1968 2062 7.930217 TCTCACTTCAATCAAAACTAAACCAG 58.070 34.615 0.00 0.00 0.00 4.00
1983 2078 7.397221 ACCATCATCAAATACTCTCACTTCAA 58.603 34.615 0.00 0.00 0.00 2.69
1998 2093 7.720515 TGCATTCTGATAACATACCATCATCAA 59.279 33.333 0.00 0.00 31.05 2.57
2239 2337 6.000219 CAGATGGACCCTAATTACAATCAGG 59.000 44.000 0.00 0.00 0.00 3.86
2322 2420 9.574516 AAATAAGAACACTGTAACAAGGAAGAT 57.425 29.630 0.00 0.00 0.00 2.40
2382 2480 4.500499 AGAGAACTAATGGAGCATTGCT 57.500 40.909 11.79 11.79 43.88 3.91
2456 4228 1.342074 ACAGCTCAGGCAGTCTTGTA 58.658 50.000 0.00 0.00 41.70 2.41
2481 4253 9.860898 AAAATTATGGTTTCTGCTTATCAAGTC 57.139 29.630 0.00 0.00 0.00 3.01
2534 4308 5.889289 TCATCAGATCCTGCAATCAAAATCA 59.111 36.000 1.40 0.00 0.00 2.57
2535 4309 6.183360 TGTCATCAGATCCTGCAATCAAAATC 60.183 38.462 1.40 0.00 0.00 2.17
2536 4310 5.655090 TGTCATCAGATCCTGCAATCAAAAT 59.345 36.000 1.40 0.00 0.00 1.82
2537 4311 5.011586 TGTCATCAGATCCTGCAATCAAAA 58.988 37.500 1.40 0.00 0.00 2.44
2624 4399 8.626526 GTCACCCATAGTTTGTAAAAGAGAAAA 58.373 33.333 0.00 0.00 0.00 2.29
2813 4588 8.530311 CCATAAATACTGAGAGTAGATGCATCT 58.470 37.037 30.85 30.85 40.86 2.90
2814 4589 8.310382 ACCATAAATACTGAGAGTAGATGCATC 58.690 37.037 19.37 19.37 33.66 3.91
2837 4612 5.445964 GGGCCTATCAAGAAAATAGAACCA 58.554 41.667 0.84 0.00 30.40 3.67
2859 4634 7.596749 AATATTCTACTGTTTGTTCAGTCGG 57.403 36.000 2.59 0.00 45.79 4.79
2861 4636 8.784043 ACCAAATATTCTACTGTTTGTTCAGTC 58.216 33.333 2.59 0.00 45.79 3.51
2932 4716 6.146837 ACTGCTCGATCTTATGCATTGAATAC 59.853 38.462 3.54 0.53 34.79 1.89
2939 4723 4.221482 TGGATACTGCTCGATCTTATGCAT 59.779 41.667 3.79 3.79 34.79 3.96
2947 4731 4.358851 GCATAGATGGATACTGCTCGATC 58.641 47.826 0.00 0.00 32.37 3.69
2948 4732 3.131933 GGCATAGATGGATACTGCTCGAT 59.868 47.826 0.00 0.00 33.43 3.59
2949 4733 2.493675 GGCATAGATGGATACTGCTCGA 59.506 50.000 0.00 0.00 33.43 4.04
2950 4734 2.733542 CGGCATAGATGGATACTGCTCG 60.734 54.545 0.00 0.00 33.43 5.03
2979 4769 8.697292 ACAGACTTAAGAAGTTAAGAGTCAAGT 58.303 33.333 10.09 0.00 45.67 3.16
2986 4776 5.696724 GCTGCACAGACTTAAGAAGTTAAGA 59.303 40.000 10.09 0.00 45.67 2.10
2988 4778 5.364778 TGCTGCACAGACTTAAGAAGTTAA 58.635 37.500 10.09 0.00 43.03 2.01
2989 4779 4.956085 TGCTGCACAGACTTAAGAAGTTA 58.044 39.130 10.09 0.00 43.03 2.24
2990 4780 3.808728 TGCTGCACAGACTTAAGAAGTT 58.191 40.909 10.09 0.00 43.03 2.66
2991 4781 3.475566 TGCTGCACAGACTTAAGAAGT 57.524 42.857 10.09 1.47 46.38 3.01
2992 4782 6.674694 AATATGCTGCACAGACTTAAGAAG 57.325 37.500 10.09 0.82 0.00 2.85
2993 4783 7.452880 AAAATATGCTGCACAGACTTAAGAA 57.547 32.000 10.09 0.00 0.00 2.52
3009 4799 6.312672 GTGGTTGACACCCAAATAAAATATGC 59.687 38.462 0.00 0.00 43.49 3.14
3058 4848 5.953183 TGCCTGAATAACATTTAGTTGCTG 58.047 37.500 0.00 0.00 41.50 4.41
3065 4855 4.881273 ACGCAGATGCCTGAATAACATTTA 59.119 37.500 0.00 0.00 43.02 1.40
3087 4877 8.390854 TCGACTCAGACGATAAAATTTAGAAC 57.609 34.615 0.00 0.00 34.85 3.01
3141 4931 3.259876 TGTTACCCGGATATGGACATAGC 59.740 47.826 0.73 0.00 0.00 2.97
3146 4936 4.885325 ACAAAATGTTACCCGGATATGGAC 59.115 41.667 0.73 0.00 0.00 4.02
3167 4957 8.441608 CGATTTGGCAAAATTAAAATCATGACA 58.558 29.630 17.70 0.00 38.40 3.58
3168 4958 7.904461 CCGATTTGGCAAAATTAAAATCATGAC 59.096 33.333 17.70 0.00 38.40 3.06
3169 4959 7.065563 CCCGATTTGGCAAAATTAAAATCATGA 59.934 33.333 17.70 0.00 38.40 3.07
3170 4960 7.148272 ACCCGATTTGGCAAAATTAAAATCATG 60.148 33.333 17.70 4.59 38.40 3.07
3171 4961 6.883756 ACCCGATTTGGCAAAATTAAAATCAT 59.116 30.769 17.70 0.00 38.40 2.45
3172 4962 6.234177 ACCCGATTTGGCAAAATTAAAATCA 58.766 32.000 17.70 0.00 38.40 2.57
3173 4963 6.735678 ACCCGATTTGGCAAAATTAAAATC 57.264 33.333 17.70 7.06 36.10 2.17
3174 4964 6.596106 GGTACCCGATTTGGCAAAATTAAAAT 59.404 34.615 17.70 0.00 36.10 1.82
3175 4965 5.932883 GGTACCCGATTTGGCAAAATTAAAA 59.067 36.000 17.70 0.00 36.10 1.52
3176 4966 5.246429 AGGTACCCGATTTGGCAAAATTAAA 59.754 36.000 17.70 0.00 36.10 1.52
3177 4967 4.773149 AGGTACCCGATTTGGCAAAATTAA 59.227 37.500 17.70 0.00 36.10 1.40
3178 4968 4.158764 CAGGTACCCGATTTGGCAAAATTA 59.841 41.667 17.70 0.00 36.10 1.40
3179 4969 3.056179 CAGGTACCCGATTTGGCAAAATT 60.056 43.478 17.70 0.46 36.10 1.82
3180 4970 2.495669 CAGGTACCCGATTTGGCAAAAT 59.504 45.455 17.70 0.00 38.74 1.82
3181 4971 1.889829 CAGGTACCCGATTTGGCAAAA 59.110 47.619 17.70 0.44 35.87 2.44
3182 4972 1.074084 TCAGGTACCCGATTTGGCAAA 59.926 47.619 16.01 16.01 35.87 3.68
3183 4973 0.693622 TCAGGTACCCGATTTGGCAA 59.306 50.000 8.74 0.00 35.87 4.52
3184 4974 0.693622 TTCAGGTACCCGATTTGGCA 59.306 50.000 8.74 0.00 35.87 4.92
3185 4975 1.947456 GATTCAGGTACCCGATTTGGC 59.053 52.381 8.74 0.00 35.87 4.52
3186 4976 2.092646 TGGATTCAGGTACCCGATTTGG 60.093 50.000 8.74 0.00 37.55 3.28
3187 4977 3.206150 CTGGATTCAGGTACCCGATTTG 58.794 50.000 8.74 0.00 37.36 2.32
3188 4978 2.844348 ACTGGATTCAGGTACCCGATTT 59.156 45.455 8.74 0.00 44.99 2.17
3189 4979 2.478292 ACTGGATTCAGGTACCCGATT 58.522 47.619 8.74 0.00 44.99 3.34
3190 4980 2.176247 ACTGGATTCAGGTACCCGAT 57.824 50.000 8.74 0.00 44.99 4.18
3191 4981 1.946984 AACTGGATTCAGGTACCCGA 58.053 50.000 8.74 0.00 44.99 5.14
3192 4982 2.747446 CAAAACTGGATTCAGGTACCCG 59.253 50.000 8.74 0.00 40.66 5.28
3193 4983 3.763057 ACAAAACTGGATTCAGGTACCC 58.237 45.455 8.74 0.00 40.66 3.69
3194 4984 5.182570 GGTAACAAAACTGGATTCAGGTACC 59.817 44.000 5.84 2.73 40.66 3.34
3195 4985 6.250344 GGTAACAAAACTGGATTCAGGTAC 57.750 41.667 5.84 0.00 40.66 3.34
3213 5003 6.261603 GCTAAATATACCCAGGTGTTGGTAAC 59.738 42.308 0.00 0.00 46.25 2.50
3214 5004 6.358991 GCTAAATATACCCAGGTGTTGGTAA 58.641 40.000 0.00 0.00 46.25 2.85
3215 5005 5.453621 CGCTAAATATACCCAGGTGTTGGTA 60.454 44.000 0.00 0.00 46.25 3.25
3216 5006 4.685030 CGCTAAATATACCCAGGTGTTGGT 60.685 45.833 0.00 0.00 46.25 3.67
3218 5008 3.250040 GCGCTAAATATACCCAGGTGTTG 59.750 47.826 0.00 0.00 0.00 3.33
3219 5009 3.118186 TGCGCTAAATATACCCAGGTGTT 60.118 43.478 9.73 0.00 0.00 3.32
3220 5010 2.436542 TGCGCTAAATATACCCAGGTGT 59.563 45.455 9.73 0.00 0.00 4.16
3221 5011 3.120321 TGCGCTAAATATACCCAGGTG 57.880 47.619 9.73 0.00 0.00 4.00
3222 5012 5.247564 TCTTATGCGCTAAATATACCCAGGT 59.752 40.000 9.73 0.00 0.00 4.00
3223 5013 5.581085 GTCTTATGCGCTAAATATACCCAGG 59.419 44.000 9.73 0.00 0.00 4.45
3224 5014 5.581085 GGTCTTATGCGCTAAATATACCCAG 59.419 44.000 9.73 0.00 0.00 4.45
3225 5015 5.484715 GGTCTTATGCGCTAAATATACCCA 58.515 41.667 9.73 0.00 0.00 4.51
3226 5016 4.874396 GGGTCTTATGCGCTAAATATACCC 59.126 45.833 9.73 13.78 32.87 3.69
3227 5017 5.484715 TGGGTCTTATGCGCTAAATATACC 58.515 41.667 9.73 8.96 0.00 2.73
3228 5018 7.611213 ATTGGGTCTTATGCGCTAAATATAC 57.389 36.000 9.73 0.31 0.00 1.47
3229 5019 9.542462 GATATTGGGTCTTATGCGCTAAATATA 57.458 33.333 9.73 0.00 0.00 0.86
3230 5020 7.499232 GGATATTGGGTCTTATGCGCTAAATAT 59.501 37.037 9.73 5.11 0.00 1.28
3231 5021 6.821665 GGATATTGGGTCTTATGCGCTAAATA 59.178 38.462 9.73 0.00 0.00 1.40
3232 5022 5.648092 GGATATTGGGTCTTATGCGCTAAAT 59.352 40.000 9.73 0.00 0.00 1.40
3233 5023 5.001232 GGATATTGGGTCTTATGCGCTAAA 58.999 41.667 9.73 1.38 0.00 1.85
3234 5024 4.564821 GGGATATTGGGTCTTATGCGCTAA 60.565 45.833 9.73 4.03 0.00 3.09
3235 5025 3.055385 GGGATATTGGGTCTTATGCGCTA 60.055 47.826 9.73 0.00 0.00 4.26
3236 5026 2.290323 GGGATATTGGGTCTTATGCGCT 60.290 50.000 9.73 0.00 0.00 5.92
3237 5027 2.084546 GGGATATTGGGTCTTATGCGC 58.915 52.381 0.00 0.00 0.00 6.09
3238 5028 3.417069 TGGGATATTGGGTCTTATGCG 57.583 47.619 0.00 0.00 0.00 4.73
3239 5029 5.184892 AGATGGGATATTGGGTCTTATGC 57.815 43.478 0.00 0.00 0.00 3.14
3240 5030 6.071728 GCAAAGATGGGATATTGGGTCTTATG 60.072 42.308 0.00 0.00 0.00 1.90
3241 5031 6.012745 GCAAAGATGGGATATTGGGTCTTAT 58.987 40.000 0.00 0.00 0.00 1.73
3242 5032 5.385198 GCAAAGATGGGATATTGGGTCTTA 58.615 41.667 0.00 0.00 0.00 2.10
3243 5033 4.218312 GCAAAGATGGGATATTGGGTCTT 58.782 43.478 0.00 0.00 0.00 3.01
3244 5034 3.437052 GGCAAAGATGGGATATTGGGTCT 60.437 47.826 0.00 0.00 0.00 3.85
3245 5035 2.893489 GGCAAAGATGGGATATTGGGTC 59.107 50.000 0.00 0.00 0.00 4.46
3246 5036 2.247111 TGGCAAAGATGGGATATTGGGT 59.753 45.455 0.00 0.00 0.00 4.51
3247 5037 2.961510 TGGCAAAGATGGGATATTGGG 58.038 47.619 0.00 0.00 0.00 4.12
3248 5038 9.645128 TTATATATGGCAAAGATGGGATATTGG 57.355 33.333 0.00 0.00 0.00 3.16
3253 5043 9.028284 CAAACTTATATATGGCAAAGATGGGAT 57.972 33.333 3.04 0.00 0.00 3.85
3254 5044 8.224025 TCAAACTTATATATGGCAAAGATGGGA 58.776 33.333 3.04 0.00 0.00 4.37
3255 5045 8.408043 TCAAACTTATATATGGCAAAGATGGG 57.592 34.615 3.04 0.00 0.00 4.00
3256 5046 9.903682 CTTCAAACTTATATATGGCAAAGATGG 57.096 33.333 3.04 0.00 0.00 3.51
3262 5052 9.461312 AGTGAACTTCAAACTTATATATGGCAA 57.539 29.630 0.00 0.00 0.00 4.52
3263 5053 9.109393 GAGTGAACTTCAAACTTATATATGGCA 57.891 33.333 0.00 0.00 0.00 4.92
3264 5054 9.331282 AGAGTGAACTTCAAACTTATATATGGC 57.669 33.333 0.00 0.00 0.00 4.40
3273 5063 9.614792 ACATACTTAAGAGTGAACTTCAAACTT 57.385 29.630 10.09 12.98 36.60 2.66
3274 5064 9.046296 CACATACTTAAGAGTGAACTTCAAACT 57.954 33.333 10.09 0.00 36.60 2.66
3275 5065 7.798982 GCACATACTTAAGAGTGAACTTCAAAC 59.201 37.037 22.32 6.17 36.60 2.93
3276 5066 7.497579 TGCACATACTTAAGAGTGAACTTCAAA 59.502 33.333 22.32 0.00 36.60 2.69
3277 5067 6.989759 TGCACATACTTAAGAGTGAACTTCAA 59.010 34.615 22.32 4.78 36.60 2.69
3278 5068 6.521162 TGCACATACTTAAGAGTGAACTTCA 58.479 36.000 22.32 12.43 36.60 3.02
3279 5069 6.401581 GCTGCACATACTTAAGAGTGAACTTC 60.402 42.308 22.32 10.77 36.60 3.01
3280 5070 5.409826 GCTGCACATACTTAAGAGTGAACTT 59.590 40.000 22.32 0.00 36.60 2.66
3281 5071 4.932200 GCTGCACATACTTAAGAGTGAACT 59.068 41.667 22.32 0.00 36.60 3.01
3282 5072 4.690748 TGCTGCACATACTTAAGAGTGAAC 59.309 41.667 22.32 14.27 36.60 3.18
3283 5073 4.893608 TGCTGCACATACTTAAGAGTGAA 58.106 39.130 22.32 15.30 36.60 3.18
3284 5074 4.535526 TGCTGCACATACTTAAGAGTGA 57.464 40.909 22.32 11.88 36.60 3.41
3285 5075 4.452114 TGTTGCTGCACATACTTAAGAGTG 59.548 41.667 10.09 14.72 36.60 3.51
3286 5076 4.641396 TGTTGCTGCACATACTTAAGAGT 58.359 39.130 10.09 1.85 39.97 3.24
3287 5077 5.808042 ATGTTGCTGCACATACTTAAGAG 57.192 39.130 10.09 1.19 35.51 2.85
3288 5078 6.016360 ACAAATGTTGCTGCACATACTTAAGA 60.016 34.615 10.09 0.00 36.30 2.10
3289 5079 6.151691 ACAAATGTTGCTGCACATACTTAAG 58.848 36.000 0.00 0.00 36.30 1.85
3290 5080 6.083098 ACAAATGTTGCTGCACATACTTAA 57.917 33.333 0.00 0.00 36.30 1.85
3291 5081 5.240403 TGACAAATGTTGCTGCACATACTTA 59.760 36.000 0.00 0.00 36.30 2.24
3292 5082 4.037803 TGACAAATGTTGCTGCACATACTT 59.962 37.500 0.00 0.00 36.30 2.24
3293 5083 3.569277 TGACAAATGTTGCTGCACATACT 59.431 39.130 0.00 0.00 36.30 2.12
3294 5084 3.899734 TGACAAATGTTGCTGCACATAC 58.100 40.909 0.00 0.00 36.30 2.39
3295 5085 4.217983 TCATGACAAATGTTGCTGCACATA 59.782 37.500 0.00 0.00 36.30 2.29
3296 5086 3.006003 TCATGACAAATGTTGCTGCACAT 59.994 39.130 0.00 6.86 39.17 3.21
3297 5087 2.361438 TCATGACAAATGTTGCTGCACA 59.639 40.909 0.00 4.51 0.00 4.57
3298 5088 3.015934 TCATGACAAATGTTGCTGCAC 57.984 42.857 0.00 0.00 0.00 4.57
3299 5089 3.945981 ATCATGACAAATGTTGCTGCA 57.054 38.095 0.00 0.00 0.00 4.41
3300 5090 5.600908 AAAATCATGACAAATGTTGCTGC 57.399 34.783 0.00 0.00 0.00 5.25
3311 5101 9.138062 CCGATTGACAAAATTAAAATCATGACA 57.862 29.630 0.00 0.00 0.00 3.58
3318 5108 8.032451 CAGGTACCCGATTGACAAAATTAAAAT 58.968 33.333 8.74 0.00 0.00 1.82
3330 5120 2.473070 TGGATTCAGGTACCCGATTGA 58.527 47.619 8.74 2.46 0.00 2.57
3422 5213 5.163913 GCTGCACATACTTAAGAGTGAACTG 60.164 44.000 22.32 14.99 36.60 3.16
3439 5230 2.483363 CCCAAAAGAAACATGCTGCACA 60.483 45.455 3.57 0.00 0.00 4.57
3440 5231 2.137523 CCCAAAAGAAACATGCTGCAC 58.862 47.619 3.57 0.00 0.00 4.57
3497 5290 7.220683 CGCAGATTCCTAAATAACATTTGGTTG 59.779 37.037 0.00 0.00 40.73 3.77
3505 5298 8.780846 TTAAGAACGCAGATTCCTAAATAACA 57.219 30.769 0.00 0.00 0.00 2.41
3512 5305 9.607988 TGATAAAATTAAGAACGCAGATTCCTA 57.392 29.630 0.00 0.00 0.00 2.94
3535 5328 4.142138 GGTTCAGGTGTTCGACTCTATGAT 60.142 45.833 0.00 0.00 0.00 2.45
3537 5330 3.512680 GGTTCAGGTGTTCGACTCTATG 58.487 50.000 0.00 0.00 0.00 2.23
3538 5331 2.496470 GGGTTCAGGTGTTCGACTCTAT 59.504 50.000 0.00 0.00 0.00 1.98
3540 5333 0.680061 GGGTTCAGGTGTTCGACTCT 59.320 55.000 0.00 0.00 0.00 3.24
3549 5342 1.343465 AGTACGACTTGGGTTCAGGTG 59.657 52.381 0.00 0.00 33.12 4.00
3581 5374 3.248602 GCAAATGTCACTCGGATATGGAC 59.751 47.826 0.00 0.00 0.00 4.02
3645 5438 0.536460 GAGAGGCGGGTGTTGGAAAA 60.536 55.000 0.00 0.00 0.00 2.29
3657 5450 0.036010 AACTTCCCACATGAGAGGCG 60.036 55.000 0.00 0.00 0.00 5.52
3686 5479 1.403687 GGCCCAGAGTACTAGCAGGG 61.404 65.000 14.12 14.12 39.33 4.45
3691 5484 0.831307 GGTTGGGCCCAGAGTACTAG 59.169 60.000 26.87 0.00 0.00 2.57
3694 5487 1.602771 GAGGTTGGGCCCAGAGTAC 59.397 63.158 26.87 20.31 38.26 2.73
3791 5586 1.001974 ACAATTGTGCGAGGAGTAGCA 59.998 47.619 11.07 0.00 41.55 3.49
3818 5613 2.373169 GGCCATTCATATCCCACTGAGA 59.627 50.000 0.00 0.00 0.00 3.27
3834 5629 0.178998 CAGCTCCTAGCATTGGCCAT 60.179 55.000 6.09 0.00 45.56 4.40
3838 5633 1.466856 TTTGCAGCTCCTAGCATTGG 58.533 50.000 1.22 0.00 45.56 3.16
3846 5641 2.816087 CAACACTGTATTTGCAGCTCCT 59.184 45.455 0.00 0.00 39.96 3.69
3852 5647 5.530543 TCAGAATCACAACACTGTATTTGCA 59.469 36.000 0.00 0.00 33.22 4.08
3944 5739 4.575645 CCCTTGTACAAAACTACGGAAACA 59.424 41.667 10.03 0.00 0.00 2.83
3945 5740 4.023792 CCCCTTGTACAAAACTACGGAAAC 60.024 45.833 10.03 0.00 0.00 2.78
3947 5742 3.390639 TCCCCTTGTACAAAACTACGGAA 59.609 43.478 10.03 0.00 0.00 4.30
3949 5744 3.405823 TCCCCTTGTACAAAACTACGG 57.594 47.619 10.03 6.07 0.00 4.02
3950 5745 7.437793 TTTATTCCCCTTGTACAAAACTACG 57.562 36.000 10.03 0.00 0.00 3.51
3988 5785 1.001248 ATGGCTTGCATGGGAGCTT 59.999 52.632 7.97 0.00 38.89 3.74
4029 5826 4.313282 GAGCTAGCACATATCTTGATGCA 58.687 43.478 18.83 0.00 40.63 3.96
4076 5873 7.857885 GTGTTGTTTGAGATAACAAAAGAGAGG 59.142 37.037 3.75 0.00 46.27 3.69
4482 6484 1.055849 TATGTGTGCACACCCTCAGT 58.944 50.000 39.34 22.83 45.88 3.41
4484 6486 2.647683 TTTATGTGTGCACACCCTCA 57.352 45.000 39.34 25.49 45.88 3.86
4601 6603 9.410556 AGTGTTGCATTTTCTATGTTGTAAATC 57.589 29.630 0.00 0.00 0.00 2.17
4672 6674 5.027293 TGAGTGATATGTGTTGAGGATGG 57.973 43.478 0.00 0.00 0.00 3.51
4724 6726 7.275920 AGTTGAGAAATAGTATGGGTGATGAC 58.724 38.462 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.