Multiple sequence alignment - TraesCS7D01G233800

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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 TraesCS7D01G233800 chr7D 100.000 7988 0 0 1 7988 195622132 195630119 0.000000e+00 14752.0
1 TraesCS7D01G233800 chr7D 88.679 53 2 4 1775 1827 431918848 431918896 2.410000e-05 62.1
2 TraesCS7D01G233800 chr7A 94.307 3162 153 13 4050 7197 205462089 205465237 0.000000e+00 4817.0
3 TraesCS7D01G233800 chr7A 92.875 2737 135 21 1278 3969 205459370 205462091 0.000000e+00 3919.0
4 TraesCS7D01G233800 chr7A 85.210 1217 76 31 1 1171 205458161 205459319 0.000000e+00 1155.0
5 TraesCS7D01G233800 chr7A 93.137 408 20 5 7212 7616 205465222 205465624 6.900000e-165 592.0
6 TraesCS7D01G233800 chr7A 93.458 321 20 1 7616 7936 205465716 205466035 7.250000e-130 475.0
7 TraesCS7D01G233800 chr7B 95.025 3055 112 15 4050 7098 159512838 159515858 0.000000e+00 4763.0
8 TraesCS7D01G233800 chr7B 94.126 2162 87 19 1827 3969 159510700 159512840 0.000000e+00 3253.0
9 TraesCS7D01G233800 chr7B 85.335 1432 100 46 7 1382 159508891 159510268 0.000000e+00 1380.0
10 TraesCS7D01G233800 chr7B 93.425 730 37 10 7212 7936 159516028 159516751 0.000000e+00 1072.0
11 TraesCS7D01G233800 chr7B 89.941 169 15 2 1620 1787 159510414 159510581 4.850000e-52 217.0
12 TraesCS7D01G233800 chr7B 97.059 102 3 0 7096 7197 159515942 159516043 1.070000e-38 172.0
13 TraesCS7D01G233800 chr7B 96.739 92 3 0 3960 4051 84214181 84214272 3.860000e-33 154.0
14 TraesCS7D01G233800 chr2B 98.851 87 1 0 3966 4052 354879124 354879210 1.070000e-33 156.0
15 TraesCS7D01G233800 chr2B 91.509 106 7 2 3954 4058 136175702 136175806 2.320000e-30 145.0
16 TraesCS7D01G233800 chr2B 100.000 35 0 0 1793 1827 136176058 136176092 1.860000e-06 65.8
17 TraesCS7D01G233800 chr2A 96.774 93 3 0 3960 4052 699439202 699439294 1.070000e-33 156.0
18 TraesCS7D01G233800 chr2A 90.909 110 6 4 3962 4069 617636030 617636137 2.320000e-30 145.0
19 TraesCS7D01G233800 chr2A 100.000 35 0 0 1793 1827 84959112 84959146 1.860000e-06 65.8
20 TraesCS7D01G233800 chr2A 100.000 35 0 0 1793 1827 84974333 84974367 1.860000e-06 65.8
21 TraesCS7D01G233800 chr5B 93.269 104 5 2 3953 4056 411034874 411034773 1.390000e-32 152.0
22 TraesCS7D01G233800 chr5B 91.304 46 4 0 1782 1827 635464460 635464505 6.690000e-06 63.9
23 TraesCS7D01G233800 chr5A 93.269 104 5 2 3953 4056 450750804 450750703 1.390000e-32 152.0
24 TraesCS7D01G233800 chr1A 96.703 91 3 0 3963 4053 530756663 530756573 1.390000e-32 152.0
25 TraesCS7D01G233800 chr6B 94.000 100 5 1 3954 4052 13827512 13827611 4.990000e-32 150.0
26 TraesCS7D01G233800 chrUn 100.000 34 0 0 1794 1827 50304284 50304251 6.690000e-06 63.9
27 TraesCS7D01G233800 chrUn 100.000 34 0 0 1794 1827 462835140 462835107 6.690000e-06 63.9
28 TraesCS7D01G233800 chr5D 91.304 46 4 0 1782 1827 505402860 505402905 6.690000e-06 63.9


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 TraesCS7D01G233800 chr7D 195622132 195630119 7987 False 14752.0 14752 100.000000 1 7988 1 chr7D.!!$F1 7987
1 TraesCS7D01G233800 chr7A 205458161 205466035 7874 False 2191.6 4817 91.797400 1 7936 5 chr7A.!!$F1 7935
2 TraesCS7D01G233800 chr7B 159508891 159516751 7860 False 1809.5 4763 92.485167 7 7936 6 chr7B.!!$F2 7929

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
539 556 0.319727 ACCGATTCCGCAACAACGTA 60.320 50.000 0.00 0.00 0.00 3.57 F
1558 1691 0.249955 TGTGATCATGCGCTCTTCCA 59.750 50.000 9.73 0.00 0.00 3.53 F
3514 3757 0.238289 CGTGCACAGGGAACATGAAC 59.762 55.000 18.64 0.00 0.00 3.18 F
3550 3793 1.063469 GAAATAATGACCACACGGCCG 59.937 52.381 26.86 26.86 34.57 6.13 F
3585 3828 1.334384 AAAACTTGGCAAACCCGGCT 61.334 50.000 0.00 0.00 35.87 5.52 F
4520 4765 1.466856 TGGTGGATGCATTCTTGAGC 58.533 50.000 6.53 0.00 0.00 4.26 F
5383 5634 1.895798 TCAGCTGCTACTAAGTGCACT 59.104 47.619 15.25 15.25 35.20 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1916 2132 1.202031 CCGAGTTGGCGCAGAAAATAC 60.202 52.381 10.83 0.00 0.00 1.89 R
3536 3779 0.250793 TAATTCGGCCGTGTGGTCAT 59.749 50.000 27.15 6.60 41.18 3.06 R
4496 4741 1.033746 AGAATGCATCCACCAAGGCG 61.034 55.000 0.00 0.00 37.29 5.52 R
5538 5789 1.274167 GTGGTATCACGTGAGGGTTCA 59.726 52.381 24.41 13.79 33.87 3.18 R
5677 5928 7.229506 AGTGTAAGCAATTAGAATCATTAGGGC 59.770 37.037 0.00 0.00 0.00 5.19 R
5823 6074 0.178992 CAACCCCACCAGCTTCTTCA 60.179 55.000 0.00 0.00 0.00 3.02 R
7030 7292 0.176910 TGACAACAACCTGACGAGCA 59.823 50.000 0.00 0.00 0.00 4.26 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
39 40 6.550854 TCATCCTATAAAATGCCCTTCCTTTG 59.449 38.462 0.00 0.00 0.00 2.77
61 62 6.926630 TGTAACCTTCCAAATTAGCCAAAT 57.073 33.333 0.00 0.00 0.00 2.32
62 63 7.309770 TGTAACCTTCCAAATTAGCCAAATT 57.690 32.000 0.00 0.00 39.56 1.82
111 120 2.858644 AGACCAGATCAAACCCCCATA 58.141 47.619 0.00 0.00 0.00 2.74
112 121 3.197983 AGACCAGATCAAACCCCCATAA 58.802 45.455 0.00 0.00 0.00 1.90
113 122 3.596046 AGACCAGATCAAACCCCCATAAA 59.404 43.478 0.00 0.00 0.00 1.40
114 123 4.045334 AGACCAGATCAAACCCCCATAAAA 59.955 41.667 0.00 0.00 0.00 1.52
115 124 4.959080 ACCAGATCAAACCCCCATAAAAT 58.041 39.130 0.00 0.00 0.00 1.82
116 125 5.349690 ACCAGATCAAACCCCCATAAAATT 58.650 37.500 0.00 0.00 0.00 1.82
117 126 6.507568 ACCAGATCAAACCCCCATAAAATTA 58.492 36.000 0.00 0.00 0.00 1.40
118 127 7.138934 ACCAGATCAAACCCCCATAAAATTAT 58.861 34.615 0.00 0.00 0.00 1.28
213 230 9.515226 TTTTCTTCATAACCTATGTAAAGTGCT 57.485 29.630 0.00 0.00 37.45 4.40
295 312 6.208007 TCAGATTAGCCTTATGATGCCAAATG 59.792 38.462 0.00 0.00 0.00 2.32
346 363 5.799827 TTTCTTCCGATTTGTGGGAATTT 57.200 34.783 0.00 0.00 41.26 1.82
355 372 1.209127 GTGGGAATTTGGACGTGCG 59.791 57.895 1.60 0.00 0.00 5.34
359 376 0.589223 GGAATTTGGACGTGCGAACA 59.411 50.000 12.36 0.00 0.00 3.18
370 387 2.737376 GCGAACAGGTCCGTGGAC 60.737 66.667 10.65 10.65 43.87 4.02
372 389 2.911484 CGAACAGGTCCGTGGACGA 61.911 63.158 12.65 0.00 45.41 4.20
378 395 0.612732 AGGTCCGTGGACGATTGGTA 60.613 55.000 12.65 0.00 45.41 3.25
389 406 1.265568 CGATTGGTAGACGACGTTGG 58.734 55.000 7.90 0.00 0.00 3.77
443 460 2.347452 ACGTTTACGAGCGATTTGATGG 59.653 45.455 9.53 0.00 43.02 3.51
444 461 2.601314 CGTTTACGAGCGATTTGATGGA 59.399 45.455 0.00 0.00 43.02 3.41
445 462 3.301835 CGTTTACGAGCGATTTGATGGAG 60.302 47.826 0.00 0.00 43.02 3.86
462 479 2.041206 GAGGGCGTTGGAGATACCCC 62.041 65.000 0.00 0.00 41.86 4.95
537 554 0.724453 CAACCGATTCCGCAACAACG 60.724 55.000 0.00 0.00 0.00 4.10
539 556 0.319727 ACCGATTCCGCAACAACGTA 60.320 50.000 0.00 0.00 0.00 3.57
540 557 1.003851 CCGATTCCGCAACAACGTAT 58.996 50.000 0.00 0.00 0.00 3.06
543 560 2.004017 GATTCCGCAACAACGTATGGA 58.996 47.619 0.00 0.00 0.00 3.41
635 660 9.709495 TTTCAATGAGATTTGATGGTAAAAAGG 57.291 29.630 0.00 0.00 35.64 3.11
636 661 8.421249 TCAATGAGATTTGATGGTAAAAAGGT 57.579 30.769 0.00 0.00 30.82 3.50
637 662 8.869109 TCAATGAGATTTGATGGTAAAAAGGTT 58.131 29.630 0.00 0.00 30.82 3.50
638 663 9.492973 CAATGAGATTTGATGGTAAAAAGGTTT 57.507 29.630 0.00 0.00 0.00 3.27
643 668 7.719193 AGATTTGATGGTAAAAAGGTTTTTGGG 59.281 33.333 10.12 0.00 40.33 4.12
654 679 8.480133 AAAAAGGTTTTTGGGGTAAAGTTTTT 57.520 26.923 0.00 0.00 38.81 1.94
655 680 7.455641 AAAGGTTTTTGGGGTAAAGTTTTTG 57.544 32.000 0.00 0.00 0.00 2.44
667 692 6.280643 GGTAAAGTTTTTGAAGCCTGTCAAT 58.719 36.000 0.00 0.00 37.36 2.57
712 746 0.389426 TTTAGGCGAACGGCAGAGAC 60.389 55.000 21.28 0.00 46.16 3.36
720 754 1.241990 AACGGCAGAGACGCTCTACA 61.242 55.000 8.70 0.00 38.99 2.74
724 758 0.798771 GCAGAGACGCTCTACAACGG 60.799 60.000 8.70 0.00 38.99 4.44
893 941 2.672996 CTGTTTGCCCGTCCCCAG 60.673 66.667 0.00 0.00 0.00 4.45
894 942 4.966787 TGTTTGCCCGTCCCCAGC 62.967 66.667 0.00 0.00 0.00 4.85
895 943 4.660938 GTTTGCCCGTCCCCAGCT 62.661 66.667 0.00 0.00 0.00 4.24
896 944 4.659172 TTTGCCCGTCCCCAGCTG 62.659 66.667 6.78 6.78 0.00 4.24
911 959 3.231298 CTGCCTACCAGCCTACCC 58.769 66.667 0.00 0.00 34.21 3.69
953 1001 2.010412 GCCATGATCCACCCATCCCA 62.010 60.000 0.00 0.00 0.00 4.37
1109 1189 0.743345 GCCCCAAAGGTACTGCTACG 60.743 60.000 0.00 0.00 40.86 3.51
1119 1199 2.527100 GTACTGCTACGCTTACACTGG 58.473 52.381 0.00 0.00 0.00 4.00
1193 1273 6.261158 TCCGCAATTTGATTTCCATTCGTATA 59.739 34.615 0.00 0.00 0.00 1.47
1217 1297 4.470876 GCGATCGTCGGTTCTCAA 57.529 55.556 17.81 0.00 40.84 3.02
1219 1299 0.847035 GCGATCGTCGGTTCTCAATC 59.153 55.000 17.81 0.00 40.84 2.67
1241 1329 3.125316 CCAGAAAGGAGTTAACACGCATC 59.875 47.826 8.61 0.84 41.22 3.91
1252 1340 6.112734 AGTTAACACGCATCCATTCTATTCA 58.887 36.000 8.61 0.00 0.00 2.57
1267 1355 6.588719 TTCTATTCATTTGTTCCCACAAGG 57.411 37.500 0.00 0.00 43.92 3.61
1271 1359 4.399004 TCATTTGTTCCCACAAGGTTTG 57.601 40.909 0.00 0.00 43.92 2.93
1272 1360 3.133721 TCATTTGTTCCCACAAGGTTTGG 59.866 43.478 0.00 0.00 43.92 3.28
1273 1361 0.827368 TTGTTCCCACAAGGTTTGGC 59.173 50.000 0.00 0.00 38.03 4.52
1275 1363 1.076632 TTCCCACAAGGTTTGGCGT 60.077 52.632 0.00 0.00 36.75 5.68
1276 1364 0.684805 TTCCCACAAGGTTTGGCGTT 60.685 50.000 0.00 0.00 36.75 4.84
1294 1382 4.694037 GGCGTTGTCACCTACTTTAGAAAT 59.306 41.667 0.00 0.00 0.00 2.17
1414 1547 7.232127 GGAACTACAGTAGCAGGGTAACATATA 59.768 40.741 7.57 0.00 39.74 0.86
1419 1552 7.671302 ACAGTAGCAGGGTAACATATAGATTG 58.329 38.462 0.00 0.00 39.74 2.67
1421 1554 8.803235 CAGTAGCAGGGTAACATATAGATTGTA 58.197 37.037 0.00 0.00 39.74 2.41
1514 1647 5.755375 TCATAAAAAGAGCGATGCTTCTAGG 59.245 40.000 0.00 0.00 39.88 3.02
1519 1652 2.497675 AGAGCGATGCTTCTAGGTTTGA 59.502 45.455 0.00 0.00 39.88 2.69
1520 1653 2.863137 GAGCGATGCTTCTAGGTTTGAG 59.137 50.000 0.00 0.00 39.88 3.02
1521 1654 2.497675 AGCGATGCTTCTAGGTTTGAGA 59.502 45.455 0.00 0.00 33.89 3.27
1522 1655 2.605366 GCGATGCTTCTAGGTTTGAGAC 59.395 50.000 0.00 0.00 0.00 3.36
1558 1691 0.249955 TGTGATCATGCGCTCTTCCA 59.750 50.000 9.73 0.00 0.00 3.53
1567 1700 1.156736 GCGCTCTTCCAGTTTAGCAA 58.843 50.000 0.00 0.00 34.60 3.91
1569 1702 2.223135 GCGCTCTTCCAGTTTAGCAATC 60.223 50.000 0.00 0.00 34.60 2.67
1576 1709 2.811431 TCCAGTTTAGCAATCGTGTTGG 59.189 45.455 5.68 0.00 0.00 3.77
1580 1713 3.252458 AGTTTAGCAATCGTGTTGGGTTC 59.748 43.478 5.68 0.00 0.00 3.62
1598 1731 5.044476 TGGGTTCTTAGCCTATGGAAATTCA 60.044 40.000 0.00 0.00 42.60 2.57
1603 1736 7.432148 TCTTAGCCTATGGAAATTCACTGTA 57.568 36.000 0.00 0.00 0.00 2.74
1616 1749 6.674694 AATTCACTGTAGCTGCTTATTGAG 57.325 37.500 7.79 0.00 0.00 3.02
1677 1810 7.360101 CCAAGGAGTTCTTATACAACTTTCACG 60.360 40.741 0.00 0.00 34.10 4.35
1707 1840 0.539051 TCCTGCTTAAGGCTCAGAGC 59.461 55.000 14.69 14.69 46.92 4.09
1838 2054 3.811083 TGTCGTGGTTAAACATTGGAGT 58.189 40.909 0.00 0.00 0.00 3.85
1916 2132 6.109359 CCTTGGAGTTGTCCTGTAGATTTAG 58.891 44.000 0.00 0.00 44.30 1.85
1929 2145 6.292919 CCTGTAGATTTAGTATTTTCTGCGCC 60.293 42.308 4.18 0.00 0.00 6.53
2518 2734 1.782044 ATGTGCAAATGCGGTCAAAC 58.218 45.000 0.35 0.00 45.83 2.93
2722 2938 4.813750 TTCAGCTCATGAACTCTGATGA 57.186 40.909 17.42 8.70 43.09 2.92
2738 2954 5.128205 TCTGATGATAAACTCATTGCCAGG 58.872 41.667 0.00 0.00 44.83 4.45
2813 3030 1.614996 TTGGTTGCATGTAGGGTGTG 58.385 50.000 0.00 0.00 0.00 3.82
2855 3072 2.029649 AGTTGCAGATCACATTGTTGGC 60.030 45.455 0.00 0.00 0.00 4.52
3029 3248 8.623903 CATAATGAACAGGTTACACATAGCATT 58.376 33.333 0.00 0.00 0.00 3.56
3056 3275 6.800072 TTCCTATTTTGGACCTTGTTTTGT 57.200 33.333 0.00 0.00 35.58 2.83
3084 3303 7.234577 TCCTAAATTTACTTGGTCTTTGCCAAT 59.765 33.333 0.00 0.00 46.22 3.16
3325 3568 4.524714 TGTCCTTCTAAACAGGAGTCTCTG 59.475 45.833 0.00 6.98 41.36 3.35
3373 3616 8.021973 ACGTAGTCTAGTCAAACACTATTTCTG 58.978 37.037 0.00 0.00 29.74 3.02
3460 3703 4.235079 ACTATTCTTATGCACTGCCCAA 57.765 40.909 0.00 0.00 0.00 4.12
3506 3749 2.046988 CATGAGCGTGCACAGGGA 60.047 61.111 18.64 0.00 0.00 4.20
3514 3757 0.238289 CGTGCACAGGGAACATGAAC 59.762 55.000 18.64 0.00 0.00 3.18
3536 3779 6.080648 ACGTGATAGAGCATACCGAAATAA 57.919 37.500 0.00 0.00 0.00 1.40
3541 3784 7.063544 GTGATAGAGCATACCGAAATAATGACC 59.936 40.741 0.00 0.00 0.00 4.02
3542 3785 5.290493 AGAGCATACCGAAATAATGACCA 57.710 39.130 0.00 0.00 0.00 4.02
3550 3793 1.063469 GAAATAATGACCACACGGCCG 59.937 52.381 26.86 26.86 34.57 6.13
3570 3813 3.596562 CCGAATTACGCAAACGAGAAAAC 59.403 43.478 0.00 0.00 43.93 2.43
3579 3822 3.241963 GCAAACGAGAAAACTTGGCAAAC 60.242 43.478 0.00 0.00 0.00 2.93
3585 3828 1.334384 AAAACTTGGCAAACCCGGCT 61.334 50.000 0.00 0.00 35.87 5.52
3588 3831 4.912395 TTGGCAAACCCGGCTGCT 62.912 61.111 17.59 0.00 38.65 4.24
3629 3872 4.081752 AGCATGACCTCAGAAGAGTACAAG 60.082 45.833 0.00 0.00 40.40 3.16
3642 3885 4.160329 AGAGTACAAGGGATTGTCACTCA 58.840 43.478 20.23 0.00 37.65 3.41
3643 3886 4.221703 AGAGTACAAGGGATTGTCACTCAG 59.778 45.833 20.23 2.36 37.65 3.35
3646 3889 2.082231 CAAGGGATTGTCACTCAGCAG 58.918 52.381 0.00 0.00 0.00 4.24
3648 3891 1.701847 AGGGATTGTCACTCAGCAGTT 59.298 47.619 0.00 0.00 0.00 3.16
3666 3909 2.982488 AGTTTCCACAACCCTCTCAGAT 59.018 45.455 0.00 0.00 0.00 2.90
3699 3942 5.367060 ACCCTTGGATCCTGTCTCTATAAAC 59.633 44.000 14.23 0.00 0.00 2.01
3744 3987 5.770685 AGCACCTAATCCTCTCTTTCTTT 57.229 39.130 0.00 0.00 0.00 2.52
3752 3995 4.357918 TCCTCTCTTTCTTTGACCTTGG 57.642 45.455 0.00 0.00 0.00 3.61
3785 4028 3.168963 CAATTGCTTGCGTTGAGATCAG 58.831 45.455 0.00 0.00 0.00 2.90
3786 4029 1.882912 TTGCTTGCGTTGAGATCAGT 58.117 45.000 0.00 0.00 0.00 3.41
3822 4065 5.307196 TCAAGAGTTTATATAGGCTCCCACC 59.693 44.000 0.00 0.00 0.00 4.61
3823 4066 3.833070 AGAGTTTATATAGGCTCCCACCG 59.167 47.826 0.00 0.00 33.69 4.94
3857 4100 2.488545 AGCAAGTAGACTACGTGTCCTG 59.511 50.000 23.70 10.33 46.46 3.86
3858 4101 2.486982 GCAAGTAGACTACGTGTCCTGA 59.513 50.000 23.70 0.00 46.46 3.86
3859 4102 3.670091 GCAAGTAGACTACGTGTCCTGAC 60.670 52.174 23.70 7.75 46.46 3.51
3903 4147 6.934645 CACACCTGTTTGAGTCCTAATAAGAA 59.065 38.462 0.00 0.00 0.00 2.52
3950 4194 7.173218 TCAGTTGAGAAAATCCATCTGTTACAC 59.827 37.037 0.00 0.00 33.87 2.90
3966 4210 4.992319 TGTTACACGCAAGCTGTAATTACT 59.008 37.500 16.33 0.00 41.87 2.24
3967 4211 6.157904 TGTTACACGCAAGCTGTAATTACTA 58.842 36.000 16.33 2.90 41.87 1.82
3968 4212 6.089820 TGTTACACGCAAGCTGTAATTACTAC 59.910 38.462 16.33 8.46 41.87 2.73
3969 4213 4.817517 ACACGCAAGCTGTAATTACTACT 58.182 39.130 16.33 10.46 45.62 2.57
3970 4214 4.863131 ACACGCAAGCTGTAATTACTACTC 59.137 41.667 16.33 3.63 45.62 2.59
3971 4215 4.267928 CACGCAAGCTGTAATTACTACTCC 59.732 45.833 16.33 7.67 45.62 3.85
3972 4216 3.802685 CGCAAGCTGTAATTACTACTCCC 59.197 47.826 16.33 7.40 0.00 4.30
3973 4217 4.441634 CGCAAGCTGTAATTACTACTCCCT 60.442 45.833 16.33 1.87 0.00 4.20
3974 4218 5.051153 GCAAGCTGTAATTACTACTCCCTC 58.949 45.833 16.33 2.00 0.00 4.30
3975 4219 5.163395 GCAAGCTGTAATTACTACTCCCTCT 60.163 44.000 16.33 0.46 0.00 3.69
3976 4220 6.630638 GCAAGCTGTAATTACTACTCCCTCTT 60.631 42.308 16.33 5.63 0.00 2.85
3977 4221 7.331791 CAAGCTGTAATTACTACTCCCTCTTT 58.668 38.462 16.33 0.00 0.00 2.52
3978 4222 8.475639 CAAGCTGTAATTACTACTCCCTCTTTA 58.524 37.037 16.33 0.00 0.00 1.85
3979 4223 8.605325 AGCTGTAATTACTACTCCCTCTTTAA 57.395 34.615 16.33 0.00 0.00 1.52
3980 4224 9.043548 AGCTGTAATTACTACTCCCTCTTTAAA 57.956 33.333 16.33 0.00 0.00 1.52
3981 4225 9.315525 GCTGTAATTACTACTCCCTCTTTAAAG 57.684 37.037 16.33 9.04 0.00 1.85
3993 4237 9.839817 ACTCCCTCTTTAAAGAAATATAAGAGC 57.160 33.333 18.25 0.00 40.13 4.09
3994 4238 8.888579 TCCCTCTTTAAAGAAATATAAGAGCG 57.111 34.615 18.25 3.08 40.13 5.03
3995 4239 8.483758 TCCCTCTTTAAAGAAATATAAGAGCGT 58.516 33.333 18.25 0.00 40.13 5.07
3996 4240 9.110502 CCCTCTTTAAAGAAATATAAGAGCGTT 57.889 33.333 18.25 0.00 40.13 4.84
4012 4256 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
4013 4257 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
4027 4271 7.393841 ACTACTTTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 40.05 4.09
4028 4272 7.828712 ACTACTTTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 40.05 2.85
4029 4273 8.954350 ACTACTTTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 40.05 2.10
4030 4274 9.953697 CTACTTTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 40.05 1.73
4042 4286 9.241317 TCTAAACGCTCTTATATTTCTTTACGG 57.759 33.333 0.00 0.00 0.00 4.02
4043 4287 9.241317 CTAAACGCTCTTATATTTCTTTACGGA 57.759 33.333 0.00 0.00 0.00 4.69
4044 4288 7.695869 AACGCTCTTATATTTCTTTACGGAG 57.304 36.000 0.00 0.00 0.00 4.63
4045 4289 6.214399 ACGCTCTTATATTTCTTTACGGAGG 58.786 40.000 0.00 0.00 0.00 4.30
4046 4290 5.634020 CGCTCTTATATTTCTTTACGGAGGG 59.366 44.000 0.00 0.00 0.00 4.30
4047 4291 6.516194 CGCTCTTATATTTCTTTACGGAGGGA 60.516 42.308 0.00 0.00 34.63 4.20
4048 4292 6.869388 GCTCTTATATTTCTTTACGGAGGGAG 59.131 42.308 0.00 0.00 0.00 4.30
4079 4324 5.064707 ACAAGTATGTACTTTATTGCCGCTG 59.935 40.000 2.77 0.00 43.57 5.18
4131 4376 2.695359 TGCGGTGAGTAAAAGACCATC 58.305 47.619 0.00 0.00 0.00 3.51
4137 4382 6.093633 GCGGTGAGTAAAAGACCATCTAATTT 59.906 38.462 0.00 0.00 0.00 1.82
4400 4645 8.590470 CATAATATGTTAGTTGCATCGCTAGAG 58.410 37.037 0.00 0.00 0.00 2.43
4405 4650 3.377346 AGTTGCATCGCTAGAGTATGG 57.623 47.619 0.00 0.00 0.00 2.74
4433 4678 5.422214 AAGGGTCATCGAATGAACTAAGT 57.578 39.130 11.11 0.00 46.18 2.24
4496 4741 3.575965 AACGATCCTGAATTTGCCAAC 57.424 42.857 0.00 0.00 0.00 3.77
4520 4765 1.466856 TGGTGGATGCATTCTTGAGC 58.533 50.000 6.53 0.00 0.00 4.26
4533 4778 6.091437 GCATTCTTGAGCATGGATATAAAGC 58.909 40.000 0.00 0.00 0.00 3.51
4546 4791 7.241042 TGGATATAAAGCCATCTAGTACCAC 57.759 40.000 0.00 0.00 35.85 4.16
4599 4844 7.529880 AAGCAAGACACAAATGAAAAAGAAG 57.470 32.000 0.00 0.00 0.00 2.85
4738 4983 2.071778 ATGCCCACACAAACAGACTT 57.928 45.000 0.00 0.00 0.00 3.01
4900 5145 5.453567 ACCTAGGCTTTTGTCACAATTTC 57.546 39.130 9.30 0.00 0.00 2.17
5189 5436 6.459066 TCATGTAGTCCTCAAGAAACTCAAG 58.541 40.000 0.00 0.00 0.00 3.02
5324 5571 2.869801 GTGCCGGATCATAAATGTTCGA 59.130 45.455 5.05 0.00 0.00 3.71
5382 5633 2.266554 CTCAGCTGCTACTAAGTGCAC 58.733 52.381 9.40 9.40 35.20 4.57
5383 5634 1.895798 TCAGCTGCTACTAAGTGCACT 59.104 47.619 15.25 15.25 35.20 4.40
5384 5635 3.089284 TCAGCTGCTACTAAGTGCACTA 58.911 45.455 22.01 2.85 35.20 2.74
5385 5636 3.509967 TCAGCTGCTACTAAGTGCACTAA 59.490 43.478 22.01 5.38 35.20 2.24
5437 5688 4.599047 TTTACAAAGGGGCAATGTCAAG 57.401 40.909 0.00 0.00 0.00 3.02
5449 5700 6.291377 GGGCAATGTCAAGACTCTAATGATA 58.709 40.000 1.53 0.00 0.00 2.15
5506 5757 7.497925 AATAACTGTGAAAGGTCAGAAGTTC 57.502 36.000 0.00 0.00 39.45 3.01
5524 5775 2.062971 TCGGCGTTAGATTCTAGGGT 57.937 50.000 6.85 0.00 0.00 4.34
5701 5952 7.059788 TGCCCTAATGATTCTAATTGCTTACA 58.940 34.615 0.00 0.00 0.00 2.41
5854 6105 1.474077 GTGGGGTTGATCTGATTGTGC 59.526 52.381 0.00 0.00 0.00 4.57
5869 6120 0.958382 TGTGCTGTACAATTCCGGGC 60.958 55.000 0.00 0.00 36.06 6.13
5892 6143 2.124151 CGAATGGCTGGAAGGGGG 60.124 66.667 0.00 0.00 0.00 5.40
5972 6223 4.836125 ATGAAGTGTTGCCTGTAAGTTG 57.164 40.909 0.00 0.00 0.00 3.16
6038 6289 7.321153 TGACTTGAGTATAGCTGGAAGTTAAC 58.679 38.462 0.00 0.00 31.88 2.01
6261 6512 6.657117 TCGATTCACCACATCCTTATTTTTCA 59.343 34.615 0.00 0.00 0.00 2.69
6286 6537 4.442401 ACATGTTCTATCCATGCCATGA 57.558 40.909 6.18 0.00 42.74 3.07
6287 6538 4.795469 ACATGTTCTATCCATGCCATGAA 58.205 39.130 6.18 0.00 42.74 2.57
6288 6539 4.581824 ACATGTTCTATCCATGCCATGAAC 59.418 41.667 6.18 2.83 42.74 3.18
6289 6540 4.233632 TGTTCTATCCATGCCATGAACA 57.766 40.909 6.18 5.56 40.58 3.18
6290 6541 4.795469 TGTTCTATCCATGCCATGAACAT 58.205 39.130 6.18 0.00 38.81 2.71
6296 6552 8.741603 TCTATCCATGCCATGAACATATAATG 57.258 34.615 6.18 0.00 0.00 1.90
6301 6557 3.058085 TGCCATGAACATATAATGCGCAG 60.058 43.478 18.32 2.85 0.00 5.18
6421 6683 5.225899 TGCATGTCTGAATTCTGAAATCG 57.774 39.130 15.70 11.62 0.00 3.34
6428 6690 6.128553 TGTCTGAATTCTGAAATCGTGCTAAC 60.129 38.462 15.70 1.97 0.00 2.34
6444 6706 2.729156 GCTAACTTCCGCATTTGAGTGC 60.729 50.000 0.00 0.00 41.65 4.40
6456 6718 1.581934 TTGAGTGCGTGTTCAAGGAG 58.418 50.000 0.00 0.00 0.00 3.69
6468 6730 6.741358 GCGTGTTCAAGGAGATTATGTTAAAC 59.259 38.462 0.00 0.00 0.00 2.01
6555 6817 0.725117 CGACCCCGTATGCTTTCAAC 59.275 55.000 0.00 0.00 0.00 3.18
6921 7183 4.838152 GGCGCCTCGAGCATGGAA 62.838 66.667 22.15 0.00 44.04 3.53
7022 7284 3.329889 AGGTGGGCGGATGAAGCA 61.330 61.111 0.00 0.00 36.08 3.91
7030 7292 4.778143 GGATGAAGCACGCCCGGT 62.778 66.667 0.00 0.00 0.00 5.28
7195 7542 5.774102 TGCCCATCAATGAGATATGATCT 57.226 39.130 0.00 0.00 43.70 2.75
7196 7543 6.135819 TGCCCATCAATGAGATATGATCTT 57.864 37.500 0.00 0.00 40.38 2.40
7197 7544 7.261688 TGCCCATCAATGAGATATGATCTTA 57.738 36.000 0.00 0.00 40.38 2.10
7198 7545 7.868974 TGCCCATCAATGAGATATGATCTTAT 58.131 34.615 0.89 0.89 40.38 1.73
7199 7546 7.773690 TGCCCATCAATGAGATATGATCTTATG 59.226 37.037 5.88 0.00 40.38 1.90
7200 7547 7.774157 GCCCATCAATGAGATATGATCTTATGT 59.226 37.037 5.88 2.15 40.38 2.29
7201 7548 9.682465 CCCATCAATGAGATATGATCTTATGTT 57.318 33.333 5.88 0.00 40.38 2.71
7346 7693 5.908106 CATGTGCTTCATGCTAAACAAAAC 58.092 37.500 8.88 0.00 45.69 2.43
7398 7745 6.220201 GCTATGAGAAGCTCTACCCTAAAAG 58.780 44.000 0.00 0.00 39.50 2.27
7399 7746 4.473477 TGAGAAGCTCTACCCTAAAAGC 57.527 45.455 0.00 0.00 34.95 3.51
7445 7794 1.749634 AGTCCAGGAATTCCGTACTCG 59.250 52.381 18.82 4.74 42.08 4.18
7458 7807 2.339418 CGTACTCGGGCACACATAAAA 58.661 47.619 0.00 0.00 0.00 1.52
7465 7814 2.544694 CGGGCACACATAAAAGCAACAA 60.545 45.455 0.00 0.00 0.00 2.83
7492 7841 3.332493 AACGCGCGACACGGATACT 62.332 57.895 39.36 6.60 43.93 2.12
7493 7842 1.980951 AACGCGCGACACGGATACTA 61.981 55.000 39.36 0.00 43.93 1.82
7494 7843 2.002401 CGCGCGACACGGATACTAC 61.002 63.158 28.94 0.00 43.93 2.73
7523 7872 6.177610 AGAGCGTACCCTCAATTTGAAATAA 58.822 36.000 10.10 0.00 34.26 1.40
7529 7878 5.793817 ACCCTCAATTTGAAATAACAAGCC 58.206 37.500 0.01 0.00 0.00 4.35
7594 7944 7.844653 GGATTAATAATTCGTCAACTGTCGAAC 59.155 37.037 12.68 0.51 45.03 3.95
7623 8065 4.359706 CAATGCTACGTGCTAGTACATCA 58.640 43.478 11.70 3.33 43.37 3.07
7637 8079 7.151308 GCTAGTACATCAGAGAAAGCATACAT 58.849 38.462 0.00 0.00 0.00 2.29
7647 8089 7.172703 TCAGAGAAAGCATACATCATATTGCTG 59.827 37.037 0.00 0.00 44.26 4.41
7663 8105 1.005805 TGCTGGCTAATCCCACAATGT 59.994 47.619 0.00 0.00 0.00 2.71
7727 8169 2.238084 TGTAGGAGCAGACCTGACAT 57.762 50.000 0.47 0.00 40.81 3.06
7733 8175 2.636893 GGAGCAGACCTGACATGGATAT 59.363 50.000 0.00 0.00 0.00 1.63
7744 8186 6.959954 ACCTGACATGGATATTAGGCATACTA 59.040 38.462 0.00 0.00 0.00 1.82
7791 8233 6.299805 ACATATTGTCAGAGGCAAGTAAGA 57.700 37.500 0.00 0.00 0.00 2.10
7888 8330 4.802248 GCATATCTAGGGGAAGCAAGAGTG 60.802 50.000 0.00 0.00 0.00 3.51
7920 8362 3.078837 ACAAGTGTGTGAAACGAGGTTT 58.921 40.909 0.00 0.00 42.39 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 6.248433 GCATTTTATAGGATGATCTTGGGGA 58.752 40.000 0.00 0.00 0.00 4.81
39 40 8.308207 TGTAATTTGGCTAATTTGGAAGGTTAC 58.692 33.333 11.93 2.53 37.60 2.50
111 120 8.248904 TGGCATATGAAAGCTACCATAATTTT 57.751 30.769 6.97 0.00 0.00 1.82
112 121 7.838079 TGGCATATGAAAGCTACCATAATTT 57.162 32.000 6.97 0.00 0.00 1.82
113 122 9.705103 ATATGGCATATGAAAGCTACCATAATT 57.295 29.630 18.87 3.31 40.86 1.40
116 125 9.836864 CTTATATGGCATATGAAAGCTACCATA 57.163 33.333 26.37 11.89 41.51 2.74
117 126 8.551440 TCTTATATGGCATATGAAAGCTACCAT 58.449 33.333 26.37 10.08 39.62 3.55
118 127 7.917003 TCTTATATGGCATATGAAAGCTACCA 58.083 34.615 26.37 2.52 0.00 3.25
295 312 2.605823 CGAGCTTCCTACCATCGATCAC 60.606 54.545 0.00 0.00 35.47 3.06
346 363 2.028484 GACCTGTTCGCACGTCCA 59.972 61.111 0.00 0.00 30.35 4.02
355 372 0.037605 AATCGTCCACGGACCTGTTC 60.038 55.000 10.61 0.00 41.76 3.18
359 376 0.612732 TACCAATCGTCCACGGACCT 60.613 55.000 10.61 0.00 41.76 3.85
370 387 1.135603 TCCAACGTCGTCTACCAATCG 60.136 52.381 0.00 0.00 0.00 3.34
372 389 1.203994 CCTCCAACGTCGTCTACCAAT 59.796 52.381 0.00 0.00 0.00 3.16
378 395 2.600769 AGCCCTCCAACGTCGTCT 60.601 61.111 0.00 0.00 0.00 4.18
389 406 0.034896 TCCGAACACTTTGAGCCCTC 59.965 55.000 0.00 0.00 0.00 4.30
418 435 0.168788 AATCGCTCGTAAACGTCCGA 59.831 50.000 17.19 17.19 42.69 4.55
424 441 3.001330 CCTCCATCAAATCGCTCGTAAAC 59.999 47.826 0.00 0.00 0.00 2.01
443 460 1.446366 GGGTATCTCCAACGCCCTC 59.554 63.158 0.00 0.00 38.11 4.30
444 461 2.070650 GGGGTATCTCCAACGCCCT 61.071 63.158 0.00 0.00 42.53 5.19
445 462 2.509422 GGGGTATCTCCAACGCCC 59.491 66.667 0.00 0.00 42.53 6.13
508 525 5.057819 TGCGGAATCGGTTGCTATTATTTA 58.942 37.500 0.00 0.00 36.79 1.40
516 533 1.169661 TTGTTGCGGAATCGGTTGCT 61.170 50.000 0.00 0.00 36.79 3.91
609 634 9.709495 CCTTTTTACCATCAAATCTCATTGAAA 57.291 29.630 0.00 0.00 42.22 2.69
610 635 8.869109 ACCTTTTTACCATCAAATCTCATTGAA 58.131 29.630 0.00 0.00 42.22 2.69
611 636 8.421249 ACCTTTTTACCATCAAATCTCATTGA 57.579 30.769 0.00 0.00 43.03 2.57
612 637 9.492973 AAACCTTTTTACCATCAAATCTCATTG 57.507 29.630 0.00 0.00 0.00 2.82
615 640 9.323985 CAAAAACCTTTTTACCATCAAATCTCA 57.676 29.630 0.00 0.00 38.23 3.27
616 641 8.773645 CCAAAAACCTTTTTACCATCAAATCTC 58.226 33.333 0.00 0.00 38.23 2.75
617 642 7.719193 CCCAAAAACCTTTTTACCATCAAATCT 59.281 33.333 0.00 0.00 38.23 2.40
618 643 7.040755 CCCCAAAAACCTTTTTACCATCAAATC 60.041 37.037 0.00 0.00 38.23 2.17
619 644 6.775142 CCCCAAAAACCTTTTTACCATCAAAT 59.225 34.615 0.00 0.00 38.23 2.32
620 645 6.122964 CCCCAAAAACCTTTTTACCATCAAA 58.877 36.000 0.00 0.00 38.23 2.69
621 646 5.191921 ACCCCAAAAACCTTTTTACCATCAA 59.808 36.000 0.00 0.00 38.23 2.57
622 647 4.722279 ACCCCAAAAACCTTTTTACCATCA 59.278 37.500 0.00 0.00 38.23 3.07
623 648 5.298989 ACCCCAAAAACCTTTTTACCATC 57.701 39.130 0.00 0.00 38.23 3.51
624 649 6.826632 TTACCCCAAAAACCTTTTTACCAT 57.173 33.333 0.00 0.00 38.23 3.55
625 650 6.215023 ACTTTACCCCAAAAACCTTTTTACCA 59.785 34.615 0.00 0.00 38.23 3.25
626 651 6.652053 ACTTTACCCCAAAAACCTTTTTACC 58.348 36.000 0.00 0.00 38.23 2.85
627 652 8.564509 AAACTTTACCCCAAAAACCTTTTTAC 57.435 30.769 0.00 0.00 38.23 2.01
628 653 9.584008 AAAAACTTTACCCCAAAAACCTTTTTA 57.416 25.926 0.00 0.00 38.23 1.52
629 654 8.361139 CAAAAACTTTACCCCAAAAACCTTTTT 58.639 29.630 0.00 0.00 40.75 1.94
630 655 7.724506 TCAAAAACTTTACCCCAAAAACCTTTT 59.275 29.630 0.00 0.00 0.00 2.27
631 656 7.232188 TCAAAAACTTTACCCCAAAAACCTTT 58.768 30.769 0.00 0.00 0.00 3.11
632 657 6.780901 TCAAAAACTTTACCCCAAAAACCTT 58.219 32.000 0.00 0.00 0.00 3.50
633 658 6.375830 TCAAAAACTTTACCCCAAAAACCT 57.624 33.333 0.00 0.00 0.00 3.50
634 659 6.403855 GCTTCAAAAACTTTACCCCAAAAACC 60.404 38.462 0.00 0.00 0.00 3.27
635 660 6.403855 GGCTTCAAAAACTTTACCCCAAAAAC 60.404 38.462 0.00 0.00 0.00 2.43
636 661 5.648526 GGCTTCAAAAACTTTACCCCAAAAA 59.351 36.000 0.00 0.00 0.00 1.94
637 662 5.045505 AGGCTTCAAAAACTTTACCCCAAAA 60.046 36.000 0.00 0.00 0.00 2.44
638 663 4.471747 AGGCTTCAAAAACTTTACCCCAAA 59.528 37.500 0.00 0.00 0.00 3.28
639 664 4.034410 AGGCTTCAAAAACTTTACCCCAA 58.966 39.130 0.00 0.00 0.00 4.12
640 665 3.386402 CAGGCTTCAAAAACTTTACCCCA 59.614 43.478 0.00 0.00 0.00 4.96
643 668 5.257082 TGACAGGCTTCAAAAACTTTACC 57.743 39.130 0.00 0.00 0.00 2.85
692 723 0.535335 TCTCTGCCGTTCGCCTAAAT 59.465 50.000 0.00 0.00 36.24 1.40
699 730 1.978712 TAGAGCGTCTCTGCCGTTCG 61.979 60.000 16.48 0.00 41.37 3.95
703 737 0.798771 GTTGTAGAGCGTCTCTGCCG 60.799 60.000 16.48 0.00 41.40 5.69
720 754 2.690778 GCTGGCGATTTGCTCCGTT 61.691 57.895 0.00 0.00 45.43 4.44
724 758 3.127533 ACGGCTGGCGATTTGCTC 61.128 61.111 30.58 0.00 45.43 4.26
833 867 2.646175 ATAGCGGTGTCGTGTGCCT 61.646 57.895 0.00 0.00 38.89 4.75
893 941 2.506472 GGTAGGCTGGTAGGCAGC 59.494 66.667 0.00 0.00 44.19 5.25
894 942 1.056700 ATGGGTAGGCTGGTAGGCAG 61.057 60.000 0.00 0.00 44.19 4.85
895 943 0.266453 TATGGGTAGGCTGGTAGGCA 59.734 55.000 0.00 0.00 44.19 4.75
896 944 1.657804 ATATGGGTAGGCTGGTAGGC 58.342 55.000 0.00 0.00 41.73 3.93
909 957 1.305201 GGTTGGTGCGTGTATATGGG 58.695 55.000 0.00 0.00 0.00 4.00
911 959 2.031258 TGGGTTGGTGCGTGTATATG 57.969 50.000 0.00 0.00 0.00 1.78
1109 1189 0.880718 GATAGGCGGCCAGTGTAAGC 60.881 60.000 23.09 0.00 0.00 3.09
1119 1199 1.007154 GGACGAGAAGATAGGCGGC 60.007 63.158 0.00 0.00 0.00 6.53
1193 1273 0.038526 AACCGACGATCGCTTCAAGT 60.039 50.000 16.60 3.93 38.82 3.16
1216 1296 3.751698 GCGTGTTAACTCCTTTCTGGATT 59.248 43.478 7.22 0.00 45.16 3.01
1217 1297 3.244422 TGCGTGTTAACTCCTTTCTGGAT 60.244 43.478 7.22 0.00 45.16 3.41
1219 1299 2.489971 TGCGTGTTAACTCCTTTCTGG 58.510 47.619 7.22 0.00 37.10 3.86
1231 1319 7.066887 ACAAATGAATAGAATGGATGCGTGTTA 59.933 33.333 0.00 0.00 0.00 2.41
1241 1329 6.528537 TGTGGGAACAAATGAATAGAATGG 57.471 37.500 0.00 0.00 46.06 3.16
1252 1340 2.158827 GCCAAACCTTGTGGGAACAAAT 60.159 45.455 0.00 0.00 46.06 2.32
1271 1359 3.308438 TCTAAAGTAGGTGACAACGCC 57.692 47.619 0.00 0.00 46.05 5.68
1272 1360 5.857822 ATTTCTAAAGTAGGTGACAACGC 57.142 39.130 0.00 0.00 0.00 4.84
1273 1361 8.752766 TCTAATTTCTAAAGTAGGTGACAACG 57.247 34.615 9.34 0.00 37.23 4.10
1294 1382 5.758296 CCTCAAAACTGCACTGTAGTTCTAA 59.242 40.000 12.33 1.76 37.39 2.10
1414 1547 9.507329 AACACAAGATGACAAATAGTACAATCT 57.493 29.630 0.00 0.00 0.00 2.40
1419 1552 8.230486 CCAAGAACACAAGATGACAAATAGTAC 58.770 37.037 0.00 0.00 0.00 2.73
1421 1554 6.998074 TCCAAGAACACAAGATGACAAATAGT 59.002 34.615 0.00 0.00 0.00 2.12
1514 1647 8.682016 CATGATTTCGTTAAACTTGTCTCAAAC 58.318 33.333 0.00 0.00 0.00 2.93
1519 1652 7.490962 TCACATGATTTCGTTAAACTTGTCT 57.509 32.000 0.00 0.00 0.00 3.41
1520 1653 8.015087 TGATCACATGATTTCGTTAAACTTGTC 58.985 33.333 0.00 0.00 34.37 3.18
1521 1654 7.870826 TGATCACATGATTTCGTTAAACTTGT 58.129 30.769 0.00 0.00 34.37 3.16
1522 1655 8.900511 ATGATCACATGATTTCGTTAAACTTG 57.099 30.769 0.00 0.00 35.21 3.16
1558 1691 2.858745 ACCCAACACGATTGCTAAACT 58.141 42.857 0.00 0.00 0.00 2.66
1567 1700 1.628846 AGGCTAAGAACCCAACACGAT 59.371 47.619 0.00 0.00 0.00 3.73
1569 1702 2.754946 TAGGCTAAGAACCCAACACG 57.245 50.000 0.00 0.00 0.00 4.49
1576 1709 6.038714 CAGTGAATTTCCATAGGCTAAGAACC 59.961 42.308 9.22 4.40 0.00 3.62
1580 1713 6.203723 GCTACAGTGAATTTCCATAGGCTAAG 59.796 42.308 0.00 0.00 0.00 2.18
1616 1749 2.404995 GGCATCTGCTGTCACCTGC 61.405 63.158 1.70 0.00 41.70 4.85
1626 1759 4.644103 AAACATTAGACATGGCATCTGC 57.356 40.909 0.00 0.00 41.14 4.26
1707 1840 7.596494 ACACAAATTAATGAAGGACTCATGTG 58.404 34.615 0.00 0.00 44.43 3.21
1763 1896 9.634021 ATGATTGTCTATTACTGAGAGTAGACA 57.366 33.333 16.24 16.24 46.62 3.41
1838 2054 4.041567 TGTCCTGCTTCAGAAGTTTGGATA 59.958 41.667 17.75 14.36 32.44 2.59
1916 2132 1.202031 CCGAGTTGGCGCAGAAAATAC 60.202 52.381 10.83 0.00 0.00 1.89
1929 2145 1.401552 CCACATGTTATGCCCGAGTTG 59.598 52.381 0.00 0.00 0.00 3.16
2518 2734 7.331026 TCATACCCTTCTTTGTTCAGTCTATG 58.669 38.462 0.00 0.00 0.00 2.23
2722 2938 3.370840 TCTGCCTGGCAATGAGTTTAT 57.629 42.857 23.51 0.00 38.41 1.40
2738 2954 5.438761 AATTAACACCAGTGAGTTTCTGC 57.561 39.130 4.48 0.00 0.00 4.26
2787 3004 3.451902 CCCTACATGCAACCAAATGGAAT 59.548 43.478 6.42 0.00 38.94 3.01
2813 3030 6.131544 ACTTCTGTTGTTGTTATGTCCAAC 57.868 37.500 0.00 0.00 41.97 3.77
2844 3061 2.223548 CCATGATACCGCCAACAATGTG 60.224 50.000 0.00 0.00 0.00 3.21
2855 3072 2.740447 CTCATCACATGCCATGATACCG 59.260 50.000 12.53 0.00 34.99 4.02
3029 3248 9.771534 CAAAACAAGGTCCAAAATAGGAAAATA 57.228 29.630 0.00 0.00 39.92 1.40
3056 3275 7.070074 TGGCAAAGACCAAGTAAATTTAGGAAA 59.930 33.333 8.55 0.00 36.55 3.13
3134 3369 9.944376 AGCGTATTAATCTGGTAAACATATCAT 57.056 29.630 0.00 0.00 0.00 2.45
3190 3425 4.884668 TCCACAACCTTACTCTTGGTAG 57.115 45.455 0.00 0.00 35.17 3.18
3325 3568 6.746364 ACGTCTCGTCTATTGATTTACTTGTC 59.254 38.462 0.00 0.00 33.69 3.18
3373 3616 4.579647 TTTAGGGATAGGTTGGGTTGTC 57.420 45.455 0.00 0.00 0.00 3.18
3442 3685 3.370840 TCTTGGGCAGTGCATAAGAAT 57.629 42.857 23.11 0.00 32.28 2.40
3460 3703 7.713734 ATCTCACAAATTTGGATCACATTCT 57.286 32.000 21.74 0.00 0.00 2.40
3506 3749 5.050490 GGTATGCTCTATCACGTTCATGTT 58.950 41.667 0.00 0.00 0.00 2.71
3514 3757 6.806739 TCATTATTTCGGTATGCTCTATCACG 59.193 38.462 0.00 0.00 0.00 4.35
3536 3779 0.250793 TAATTCGGCCGTGTGGTCAT 59.749 50.000 27.15 6.60 41.18 3.06
3541 3784 1.902716 TTGCGTAATTCGGCCGTGTG 61.903 55.000 27.15 11.32 40.26 3.82
3542 3785 1.229315 TTTGCGTAATTCGGCCGTGT 61.229 50.000 27.15 12.43 40.26 4.49
3550 3793 5.115021 CCAAGTTTTCTCGTTTGCGTAATTC 59.885 40.000 0.00 0.00 39.49 2.17
3570 3813 4.362476 GCAGCCGGGTTTGCCAAG 62.362 66.667 1.64 0.00 36.17 3.61
3579 3822 0.602562 TTGAAAAATCAGCAGCCGGG 59.397 50.000 2.18 0.00 0.00 5.73
3585 3828 4.613944 CTCTTGTGCTTGAAAAATCAGCA 58.386 39.130 0.00 0.00 0.00 4.41
3588 3831 4.652421 TGCTCTTGTGCTTGAAAAATCA 57.348 36.364 0.00 0.00 0.00 2.57
3589 3832 5.118203 GTCATGCTCTTGTGCTTGAAAAATC 59.882 40.000 12.49 0.99 44.68 2.17
3629 3872 2.191128 AACTGCTGAGTGACAATCCC 57.809 50.000 0.00 0.00 30.61 3.85
3642 3885 0.846693 AGAGGGTTGTGGAAACTGCT 59.153 50.000 0.00 0.00 0.00 4.24
3643 3886 1.239347 GAGAGGGTTGTGGAAACTGC 58.761 55.000 0.00 0.00 0.00 4.40
3646 3889 2.930826 TCTGAGAGGGTTGTGGAAAC 57.069 50.000 0.00 0.00 0.00 2.78
3648 3891 2.907892 AGATCTGAGAGGGTTGTGGAA 58.092 47.619 0.00 0.00 0.00 3.53
3666 3909 1.357761 GGATCCAAGGGTCCCAAAAGA 59.642 52.381 11.55 1.29 0.00 2.52
3699 3942 7.118245 TGCTATGTTCCATTAGCTCAATATTCG 59.882 37.037 0.00 0.00 41.13 3.34
3726 3969 6.306643 AGGTCAAAGAAAGAGAGGATTAGG 57.693 41.667 0.00 0.00 0.00 2.69
3744 3987 1.269517 GCGCAAATCAAACCAAGGTCA 60.270 47.619 0.30 0.00 0.00 4.02
3775 4018 2.941720 GAGATGGCCAACTGATCTCAAC 59.058 50.000 21.78 0.00 41.19 3.18
3785 4028 1.280421 ACTCTTGAGGAGATGGCCAAC 59.720 52.381 10.96 7.42 44.45 3.77
3786 4029 1.661463 ACTCTTGAGGAGATGGCCAA 58.339 50.000 10.96 0.00 44.45 4.52
3822 4065 3.320673 ACTTGCTTTAGAAGAGGACCG 57.679 47.619 0.00 0.00 0.00 4.79
3823 4066 5.186215 AGTCTACTTGCTTTAGAAGAGGACC 59.814 44.000 0.00 0.00 31.96 4.46
3857 4100 3.232662 GGTACCCAGAGGAATCCTAGTC 58.767 54.545 0.00 0.00 31.76 2.59
3858 4101 2.590611 TGGTACCCAGAGGAATCCTAGT 59.409 50.000 10.07 0.23 31.76 2.57
3859 4102 2.966516 GTGGTACCCAGAGGAATCCTAG 59.033 54.545 10.07 0.00 32.34 3.02
3903 4147 7.524290 ACTGAACATGATGATTCCAATCCTAT 58.476 34.615 0.00 0.00 34.50 2.57
3911 4155 6.748333 TTCTCAACTGAACATGATGATTCC 57.252 37.500 0.00 0.00 0.00 3.01
3917 4161 7.614583 AGATGGATTTTCTCAACTGAACATGAT 59.385 33.333 0.00 0.00 0.00 2.45
3918 4162 6.944290 AGATGGATTTTCTCAACTGAACATGA 59.056 34.615 0.00 0.00 0.00 3.07
3922 4166 6.566197 ACAGATGGATTTTCTCAACTGAAC 57.434 37.500 0.00 0.00 0.00 3.18
3950 4194 3.802685 GGGAGTAGTAATTACAGCTTGCG 59.197 47.826 17.65 0.00 34.56 4.85
3967 4211 9.839817 GCTCTTATATTTCTTTAAAGAGGGAGT 57.160 33.333 17.05 3.73 42.13 3.85
3986 4230 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
3987 4231 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
3988 4232 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
3989 4233 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
4003 4247 7.393841 AGAGCGTTTAGATCACTAAAGTAGT 57.606 36.000 0.00 0.00 45.42 2.73
4004 4248 9.953697 ATAAGAGCGTTTAGATCACTAAAGTAG 57.046 33.333 0.00 0.00 45.42 2.57
4016 4260 9.241317 CCGTAAAGAAATATAAGAGCGTTTAGA 57.759 33.333 0.00 0.00 0.00 2.10
4017 4261 9.241317 TCCGTAAAGAAATATAAGAGCGTTTAG 57.759 33.333 0.00 0.00 0.00 1.85
4018 4262 9.241317 CTCCGTAAAGAAATATAAGAGCGTTTA 57.759 33.333 0.00 0.00 0.00 2.01
4019 4263 7.224167 CCTCCGTAAAGAAATATAAGAGCGTTT 59.776 37.037 0.00 0.00 0.00 3.60
4020 4264 6.700520 CCTCCGTAAAGAAATATAAGAGCGTT 59.299 38.462 0.00 0.00 0.00 4.84
4021 4265 6.214399 CCTCCGTAAAGAAATATAAGAGCGT 58.786 40.000 0.00 0.00 0.00 5.07
4022 4266 5.634020 CCCTCCGTAAAGAAATATAAGAGCG 59.366 44.000 0.00 0.00 0.00 5.03
4023 4267 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
4024 4268 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
4025 4269 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
4026 4270 8.087136 GGTACTCCCTCCGTAAAGAAATATAAG 58.913 40.741 0.00 0.00 0.00 1.73
4027 4271 7.786464 AGGTACTCCCTCCGTAAAGAAATATAA 59.214 37.037 0.00 0.00 40.71 0.98
4028 4272 7.300658 AGGTACTCCCTCCGTAAAGAAATATA 58.699 38.462 0.00 0.00 40.71 0.86
4029 4273 6.141790 AGGTACTCCCTCCGTAAAGAAATAT 58.858 40.000 0.00 0.00 40.71 1.28
4030 4274 5.522641 AGGTACTCCCTCCGTAAAGAAATA 58.477 41.667 0.00 0.00 40.71 1.40
4031 4275 4.359996 AGGTACTCCCTCCGTAAAGAAAT 58.640 43.478 0.00 0.00 40.71 2.17
4032 4276 3.782992 AGGTACTCCCTCCGTAAAGAAA 58.217 45.455 0.00 0.00 40.71 2.52
4033 4277 3.463048 AGGTACTCCCTCCGTAAAGAA 57.537 47.619 0.00 0.00 40.71 2.52
4034 4278 3.463048 AAGGTACTCCCTCCGTAAAGA 57.537 47.619 0.00 0.00 45.47 2.52
4035 4279 4.019174 TGTAAGGTACTCCCTCCGTAAAG 58.981 47.826 0.00 0.00 45.47 1.85
4036 4280 4.046286 TGTAAGGTACTCCCTCCGTAAA 57.954 45.455 0.00 0.00 45.47 2.01
4037 4281 3.737559 TGTAAGGTACTCCCTCCGTAA 57.262 47.619 0.00 0.00 45.47 3.18
4038 4282 3.010584 ACTTGTAAGGTACTCCCTCCGTA 59.989 47.826 0.00 0.00 45.47 4.02
4039 4283 2.225217 ACTTGTAAGGTACTCCCTCCGT 60.225 50.000 0.00 0.00 45.47 4.69
4040 4284 2.454538 ACTTGTAAGGTACTCCCTCCG 58.545 52.381 0.00 0.00 45.47 4.63
4041 4285 4.961099 ACATACTTGTAAGGTACTCCCTCC 59.039 45.833 0.00 0.00 45.47 4.30
4042 4286 6.832900 AGTACATACTTGTAAGGTACTCCCTC 59.167 42.308 16.11 0.55 40.25 4.30
4043 4287 6.739664 AGTACATACTTGTAAGGTACTCCCT 58.260 40.000 16.11 0.00 40.25 4.20
4044 4288 7.415592 AAGTACATACTTGTAAGGTACTCCC 57.584 40.000 19.36 0.00 44.30 4.30
4079 4324 9.178758 ACTAGGAAATGTGAAATCCTCATAAAC 57.821 33.333 0.00 0.00 42.53 2.01
4137 4382 3.500299 TCCGCATCAACGAAATCTGAAAA 59.500 39.130 0.00 0.00 34.06 2.29
4266 4511 1.452651 CGGCATTCCAGGTGCATCT 60.453 57.895 0.00 0.00 44.25 2.90
4400 4645 5.209818 TCGATGACCCTTTGTATCCATAC 57.790 43.478 0.00 0.00 0.00 2.39
4405 4650 5.817816 AGTTCATTCGATGACCCTTTGTATC 59.182 40.000 0.00 0.00 39.39 2.24
4433 4678 2.361757 CACCTGTCAACAAGCCAATCAA 59.638 45.455 0.00 0.00 0.00 2.57
4496 4741 1.033746 AGAATGCATCCACCAAGGCG 61.034 55.000 0.00 0.00 37.29 5.52
4520 4765 7.766278 GTGGTACTAGATGGCTTTATATCCATG 59.234 40.741 0.00 0.00 42.74 3.66
4533 4778 5.661056 TTCTGAGTTGTGGTACTAGATGG 57.339 43.478 0.00 0.00 0.00 3.51
4535 4780 7.506114 TGTTTTTCTGAGTTGTGGTACTAGAT 58.494 34.615 0.00 0.00 0.00 1.98
4542 4787 5.410067 CATGTTGTTTTTCTGAGTTGTGGT 58.590 37.500 0.00 0.00 0.00 4.16
4546 4791 5.043248 GGACCATGTTGTTTTTCTGAGTTG 58.957 41.667 0.00 0.00 0.00 3.16
4900 5145 2.428530 TCTTGGATCATCGGAGACACAG 59.571 50.000 0.00 0.00 42.51 3.66
5189 5436 3.978164 AGCTCATCCCCAGCTACC 58.022 61.111 0.00 0.00 45.76 3.18
5384 5635 9.338622 ACTGTACTGCAAAATAGACTAAAACTT 57.661 29.630 0.00 0.00 0.00 2.66
5385 5636 8.904099 ACTGTACTGCAAAATAGACTAAAACT 57.096 30.769 0.00 0.00 0.00 2.66
5449 5700 5.987347 GCACACCGGTACTATAATGTGTAAT 59.013 40.000 6.87 0.00 39.65 1.89
5506 5757 5.633830 TTATACCCTAGAATCTAACGCCG 57.366 43.478 0.00 0.00 0.00 6.46
5524 5775 6.929049 CGTGAGGGTTCAGAATGCTTATTATA 59.071 38.462 0.00 0.00 34.76 0.98
5538 5789 1.274167 GTGGTATCACGTGAGGGTTCA 59.726 52.381 24.41 13.79 33.87 3.18
5677 5928 7.229506 AGTGTAAGCAATTAGAATCATTAGGGC 59.770 37.037 0.00 0.00 0.00 5.19
5701 5952 5.585390 CAAAGTTTCTGTCAGCATTGAAGT 58.415 37.500 0.00 0.00 34.49 3.01
5802 6053 0.530650 ACTTCGCAGATATGCCCGTG 60.531 55.000 6.76 0.00 35.04 4.94
5823 6074 0.178992 CAACCCCACCAGCTTCTTCA 60.179 55.000 0.00 0.00 0.00 3.02
5854 6105 0.675522 AACCGCCCGGAATTGTACAG 60.676 55.000 14.44 0.00 38.96 2.74
5869 6120 1.369091 CTTCCAGCCATTCGGAACCG 61.369 60.000 6.94 6.94 36.36 4.44
5877 6128 1.224003 ATGACCCCCTTCCAGCCATT 61.224 55.000 0.00 0.00 0.00 3.16
5892 6143 1.070914 GGTAGGAGCCCTGCTAATGAC 59.929 57.143 8.72 0.00 39.88 3.06
5972 6223 9.726232 AAAAGAATGAACTCCGTTACTAAAAAC 57.274 29.630 0.00 0.00 0.00 2.43
6038 6289 7.434307 TCTTTAACGACCTAAATTAGCATCTCG 59.566 37.037 0.00 1.29 0.00 4.04
6131 6382 4.463891 CCACAAAATCCAATGGCTTCTAGT 59.536 41.667 0.00 0.00 0.00 2.57
6261 6512 5.830799 TGGCATGGATAGAACATGTATCT 57.169 39.130 0.00 7.25 45.68 1.98
6272 6523 7.423199 GCATTATATGTTCATGGCATGGATAG 58.577 38.462 26.15 5.34 0.00 2.08
6286 6537 8.876275 AATTTTTCATCTGCGCATTATATGTT 57.124 26.923 12.24 0.47 0.00 2.71
6287 6538 7.596248 GGAATTTTTCATCTGCGCATTATATGT 59.404 33.333 12.24 0.00 0.00 2.29
6288 6539 7.201291 CGGAATTTTTCATCTGCGCATTATATG 60.201 37.037 12.24 12.82 0.00 1.78
6289 6540 6.803320 CGGAATTTTTCATCTGCGCATTATAT 59.197 34.615 12.24 0.00 0.00 0.86
6290 6541 6.142139 CGGAATTTTTCATCTGCGCATTATA 58.858 36.000 12.24 0.00 0.00 0.98
6296 6552 2.262572 ACGGAATTTTTCATCTGCGC 57.737 45.000 0.00 0.00 0.00 6.09
6383 6645 0.677731 TGCAAATCTTCCCCTCAGCG 60.678 55.000 0.00 0.00 0.00 5.18
6421 6683 2.484264 ACTCAAATGCGGAAGTTAGCAC 59.516 45.455 7.54 0.00 46.83 4.40
6444 6706 7.957484 CAGTTTAACATAATCTCCTTGAACACG 59.043 37.037 0.00 0.00 0.00 4.49
6468 6730 3.442625 TGCTGGCAAAAGATCAAGATCAG 59.557 43.478 12.21 1.47 40.22 2.90
6477 6739 2.232941 CACTTCCATGCTGGCAAAAGAT 59.767 45.455 16.69 4.92 37.47 2.40
6555 6817 3.130160 GCAGCGCCTTCTTCTGGG 61.130 66.667 2.29 0.00 0.00 4.45
6585 6847 1.138883 GACTACGATGTGCGCTCCA 59.861 57.895 9.73 5.79 46.04 3.86
6764 7026 2.837591 TCTGTTACTTGAGGCCTGCATA 59.162 45.455 12.00 0.00 0.00 3.14
6921 7183 4.269523 TGCTCAACCGGCAGCCTT 62.270 61.111 10.54 0.00 34.47 4.35
7030 7292 0.176910 TGACAACAACCTGACGAGCA 59.823 50.000 0.00 0.00 0.00 4.26
7032 7294 1.934589 TGTGACAACAACCTGACGAG 58.065 50.000 0.00 0.00 31.82 4.18
7113 7460 2.573915 TGCCACATCACACACCCTATAA 59.426 45.455 0.00 0.00 0.00 0.98
7149 7496 1.152984 TAATGCATGACCGCCTGGG 60.153 57.895 0.00 0.00 40.75 4.45
7222 7569 2.570415 TGTATGACCGCCTGGAAAAA 57.430 45.000 0.00 0.00 39.21 1.94
7329 7676 3.900941 AGCGGTTTTGTTTAGCATGAAG 58.099 40.909 0.00 0.00 0.00 3.02
7346 7693 1.762708 ACCCAATGTTATTGGAGCGG 58.237 50.000 19.41 7.38 42.06 5.52
7398 7745 4.023963 GGGAGCCTCTCGTATTTTTATTGC 60.024 45.833 0.00 0.00 0.00 3.56
7399 7746 5.123227 TGGGAGCCTCTCGTATTTTTATTG 58.877 41.667 0.00 0.00 0.00 1.90
7445 7794 2.799978 GTTGTTGCTTTTATGTGTGCCC 59.200 45.455 0.00 0.00 0.00 5.36
7458 7807 1.002468 GCGTTCTGTCATGTTGTTGCT 60.002 47.619 0.00 0.00 0.00 3.91
7465 7814 2.049526 TCGCGCGTTCTGTCATGT 60.050 55.556 30.98 0.00 0.00 3.21
7486 7835 4.357996 GGTACGCTCTTTGTGTAGTATCC 58.642 47.826 0.00 0.00 41.66 2.59
7492 7841 2.241160 TGAGGGTACGCTCTTTGTGTA 58.759 47.619 32.33 13.95 40.30 2.90
7493 7842 1.045407 TGAGGGTACGCTCTTTGTGT 58.955 50.000 32.33 2.82 42.68 3.72
7494 7843 2.163818 TTGAGGGTACGCTCTTTGTG 57.836 50.000 32.33 0.00 0.00 3.33
7523 7872 3.838244 TGACTGTTTCTGTAGGCTTGT 57.162 42.857 0.00 0.00 0.00 3.16
7529 7878 2.731976 GCGTCCTTGACTGTTTCTGTAG 59.268 50.000 0.00 0.00 0.00 2.74
7594 7944 0.921347 GCACGTAGCATTGGTCGTAG 59.079 55.000 11.14 8.36 44.79 3.51
7623 8065 6.430308 CCAGCAATATGATGTATGCTTTCTCT 59.570 38.462 0.00 0.00 46.36 3.10
7637 8079 3.138098 TGTGGGATTAGCCAGCAATATGA 59.862 43.478 0.00 0.00 38.95 2.15
7647 8089 6.006449 AGATGATAACATTGTGGGATTAGCC 58.994 40.000 0.00 0.00 36.82 3.93
7663 8105 8.807118 CCTTTATAGCTACAGTCCAGATGATAA 58.193 37.037 0.00 0.00 0.00 1.75
7702 8144 3.840666 TCAGGTCTGCTCCTACAAGAAAT 59.159 43.478 0.00 0.00 35.87 2.17
7727 8169 5.020795 TCGCCTTAGTATGCCTAATATCCA 58.979 41.667 0.00 0.00 35.14 3.41
7733 8175 4.038402 GGTAGTTCGCCTTAGTATGCCTAA 59.962 45.833 0.00 0.00 34.47 2.69
7744 8186 5.007682 ACAAATGTAATGGTAGTTCGCCTT 58.992 37.500 0.00 0.00 0.00 4.35
7791 8233 1.507141 CTTGAACGCCGCTGAAAGGT 61.507 55.000 0.00 0.00 0.00 3.50
7888 8330 5.611796 TCACACACTTGTATTGATCAAGC 57.388 39.130 14.54 9.72 43.97 4.01


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

AutoCloner maintained by Alex Coulton.