Multiple sequence alignment - TraesCS1D01G142600

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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 TraesCS1D01G142600 chr1D 100.000 2631 0 0 2578 5208 198023309 198020679 0.000000e+00 4859.0
1 TraesCS1D01G142600 chr1D 100.000 2199 0 0 1 2199 198025886 198023688 0.000000e+00 4061.0
2 TraesCS1D01G142600 chr1A 86.842 1482 89 54 3755 5208 248614538 248613135 0.000000e+00 1559.0
3 TraesCS1D01G142600 chr1A 92.308 858 53 11 2594 3446 248615565 248614716 0.000000e+00 1206.0
4 TraesCS1D01G142600 chr1A 92.867 701 26 5 880 1559 248617005 248616308 0.000000e+00 996.0
5 TraesCS1D01G142600 chr1A 94.249 626 32 4 1555 2178 248616187 248615564 0.000000e+00 953.0
6 TraesCS1D01G142600 chr1A 89.058 722 69 3 80 792 248620644 248619924 0.000000e+00 887.0
7 TraesCS1D01G142600 chr1B 94.340 848 35 5 1 841 277966396 277965555 0.000000e+00 1288.0
8 TraesCS1D01G142600 chr1B 93.123 887 39 14 4335 5208 277960614 277959737 0.000000e+00 1280.0
9 TraesCS1D01G142600 chr1B 89.880 919 54 11 2590 3488 277963268 277962369 0.000000e+00 1146.0
10 TraesCS1D01G142600 chr1B 90.354 622 26 16 925 1521 277964542 277963930 0.000000e+00 785.0
11 TraesCS1D01G142600 chr1B 87.616 541 27 14 3755 4294 277962260 277961759 4.490000e-165 592.0
12 TraesCS1D01G142600 chr1B 88.645 273 19 2 1905 2177 277963531 277963271 6.510000e-84 322.0
13 TraesCS1D01G142600 chr1B 94.527 201 8 3 1572 1770 277963911 277963712 1.820000e-79 307.0
14 TraesCS1D01G142600 chr1B 96.341 82 3 0 853 934 277965076 277964995 9.100000e-28 135.0
15 TraesCS1D01G142600 chr1B 93.750 80 5 0 1827 1906 277963692 277963613 2.550000e-23 121.0
16 TraesCS1D01G142600 chr5D 77.857 280 44 15 458 723 9341226 9341501 1.940000e-34 158.0
17 TraesCS1D01G142600 chr3B 78.899 218 36 7 568 775 74276823 74277040 7.030000e-29 139.0
18 TraesCS1D01G142600 chr3B 100.000 33 0 0 845 877 752233746 752233714 1.570000e-05 62.1
19 TraesCS1D01G142600 chr4B 75.405 309 59 13 490 788 639253637 639253938 3.270000e-27 134.0
20 TraesCS1D01G142600 chr4B 75.524 286 50 13 460 733 561896228 561895951 7.080000e-24 122.0


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 TraesCS1D01G142600 chr1D 198020679 198025886 5207 True 4460.0 4859 100.0000 1 5208 2 chr1D.!!$R1 5207
1 TraesCS1D01G142600 chr1A 248613135 248620644 7509 True 1120.2 1559 91.0648 80 5208 5 chr1A.!!$R1 5128
2 TraesCS1D01G142600 chr1B 277959737 277966396 6659 True 664.0 1288 92.0640 1 5208 9 chr1B.!!$R1 5207

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
75 76 1.077501 TGCCCAGCTAGTTGCATCC 60.078 57.895 0.17 0.0 45.94 3.51 F
1621 5326 1.066605 GATGATGACATGTGCCCTTGC 59.933 52.381 1.15 0.0 36.82 4.01 F
1896 5617 0.042731 TGGGAGGTAGGAAGTCCAGG 59.957 60.000 0.00 0.0 38.89 4.45 F
1897 5618 0.338814 GGGAGGTAGGAAGTCCAGGA 59.661 60.000 0.00 0.0 38.89 3.86 F
3363 7178 0.401738 CCCTTGCTCTTGGACCAGAA 59.598 55.000 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1879 5600 2.480642 ATCCTGGACTTCCTACCTCC 57.519 55.0 0.00 0.00 36.82 4.30 R
3492 7323 0.824109 TTCTGGATGTAGGCCGACTG 59.176 55.0 17.46 2.94 0.00 3.51 R
3496 7327 0.947244 GCAATTCTGGATGTAGGCCG 59.053 55.0 0.00 0.00 0.00 6.13 R
3587 7419 1.086696 GCCGACAGAATTTAGCTGCA 58.913 50.0 1.02 0.00 36.86 4.41 R
4438 9437 0.030638 GGTGTGTGTGATTGTGGTGC 59.969 55.0 0.00 0.00 0.00 5.01 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
66 67 1.123077 CTACTCATGGTGCCCAGCTA 58.877 55.000 0.00 0.00 36.75 3.32
74 75 1.379642 GGTGCCCAGCTAGTTGCATC 61.380 60.000 0.17 0.00 45.94 3.91
75 76 1.077501 TGCCCAGCTAGTTGCATCC 60.078 57.895 0.17 0.00 45.94 3.51
95 96 5.946942 TCCAGAGAAATCACTGCTATCTT 57.053 39.130 2.74 0.00 33.98 2.40
150 157 4.498241 GGCAAAAGGAACAAGATCAATCC 58.502 43.478 0.00 0.00 0.00 3.01
157 164 3.181520 GGAACAAGATCAATCCGTTGTCG 60.182 47.826 0.00 0.00 36.69 4.35
175 182 1.647545 CGGCATGACACCAGCGAAAT 61.648 55.000 0.00 0.00 0.00 2.17
257 264 8.654230 AACTGTAATAGAGCAACTCATGTATG 57.346 34.615 0.00 0.00 32.06 2.39
479 487 6.272792 TCTTAAACTAAAGGATACCCCACACA 59.727 38.462 0.00 0.00 37.41 3.72
486 494 2.777692 AGGATACCCCACACATTACTGG 59.222 50.000 0.00 0.00 37.41 4.00
536 544 6.912051 GCGATTGCATGAAACATGAATAGTTA 59.088 34.615 14.65 0.00 42.15 2.24
844 855 4.872357 CAGCATGCTGGTCCCTAG 57.128 61.111 35.39 11.25 40.17 3.02
845 856 1.147824 CAGCATGCTGGTCCCTAGG 59.852 63.158 35.39 10.51 40.17 3.02
846 857 2.074948 AGCATGCTGGTCCCTAGGG 61.075 63.158 23.22 23.22 0.00 3.53
847 858 3.125376 GCATGCTGGTCCCTAGGGG 62.125 68.421 28.19 12.69 46.11 4.79
848 859 2.774351 ATGCTGGTCCCTAGGGGC 60.774 66.667 28.19 26.87 43.94 5.80
849 860 3.658346 ATGCTGGTCCCTAGGGGCA 62.658 63.158 33.24 29.18 43.94 5.36
851 862 2.823758 GCTGGTCCCTAGGGGCATC 61.824 68.421 33.24 17.77 43.94 3.91
918 4012 8.568794 CGAAGAAAAGGGAAAAGAAGTCTAATT 58.431 33.333 0.00 0.00 0.00 1.40
942 4498 2.290071 GGCCCTAAAACTAGTCACAGCA 60.290 50.000 0.00 0.00 0.00 4.41
1372 4952 8.043710 ACTCCTATTTGACTTTGTTATCTGGAG 58.956 37.037 0.00 0.00 40.21 3.86
1505 5085 8.475639 TCTCCTACTGTTTTAGCTTAATCGAAT 58.524 33.333 0.00 0.00 0.00 3.34
1519 5099 3.543680 ATCGAATCATCCGTTTCCACT 57.456 42.857 0.00 0.00 0.00 4.00
1564 5269 7.235606 TGTTTTCCATGTTTAATATTCACCCCA 59.764 33.333 0.00 0.00 0.00 4.96
1621 5326 1.066605 GATGATGACATGTGCCCTTGC 59.933 52.381 1.15 0.00 36.82 4.01
1635 5340 2.639065 CCCTTGCTGTTCCGCTTATTA 58.361 47.619 0.00 0.00 0.00 0.98
1714 5420 6.264832 TGACTTTCTATGCCAAAATTATGCG 58.735 36.000 0.00 0.00 0.00 4.73
1764 5471 3.011708 AGGTGGGAATGCAATAGGAGTTT 59.988 43.478 0.00 0.00 0.00 2.66
1766 5473 3.381590 GTGGGAATGCAATAGGAGTTTCC 59.618 47.826 3.33 3.33 36.58 3.13
1767 5474 3.011144 TGGGAATGCAATAGGAGTTTCCA 59.989 43.478 12.26 2.29 39.61 3.53
1768 5475 3.633986 GGGAATGCAATAGGAGTTTCCAG 59.366 47.826 12.26 0.00 39.61 3.86
1769 5476 4.273318 GGAATGCAATAGGAGTTTCCAGT 58.727 43.478 6.58 0.00 39.61 4.00
1770 5477 4.706962 GGAATGCAATAGGAGTTTCCAGTT 59.293 41.667 6.58 0.00 39.61 3.16
1771 5478 5.885912 GGAATGCAATAGGAGTTTCCAGTTA 59.114 40.000 6.58 0.00 39.61 2.24
1772 5479 6.377146 GGAATGCAATAGGAGTTTCCAGTTAA 59.623 38.462 6.58 0.00 39.61 2.01
1773 5480 7.093945 GGAATGCAATAGGAGTTTCCAGTTAAA 60.094 37.037 6.58 0.00 39.61 1.52
1774 5481 7.961326 ATGCAATAGGAGTTTCCAGTTAAAT 57.039 32.000 0.00 0.00 39.61 1.40
1775 5482 9.474313 AATGCAATAGGAGTTTCCAGTTAAATA 57.526 29.630 0.00 0.00 39.61 1.40
1776 5483 8.276252 TGCAATAGGAGTTTCCAGTTAAATAC 57.724 34.615 0.00 0.00 39.61 1.89
1777 5484 7.885922 TGCAATAGGAGTTTCCAGTTAAATACA 59.114 33.333 0.00 0.00 39.61 2.29
1778 5485 8.398665 GCAATAGGAGTTTCCAGTTAAATACAG 58.601 37.037 0.00 0.00 39.61 2.74
1779 5486 9.449719 CAATAGGAGTTTCCAGTTAAATACAGT 57.550 33.333 0.00 0.00 39.61 3.55
1879 5600 5.934402 ATTCTGGTAGTAGTACTGGTTGG 57.066 43.478 13.29 0.31 0.00 3.77
1896 5617 0.042731 TGGGAGGTAGGAAGTCCAGG 59.957 60.000 0.00 0.00 38.89 4.45
1897 5618 0.338814 GGGAGGTAGGAAGTCCAGGA 59.661 60.000 0.00 0.00 38.89 3.86
1988 5792 6.986231 TGTTATGATTCATAGCAGTGACGAAT 59.014 34.615 16.46 0.00 33.79 3.34
2013 5817 5.443283 CTCTGATGGAATTGGAATCTGGAA 58.557 41.667 0.00 0.00 0.00 3.53
2025 5829 4.044065 TGGAATCTGGAACCCATACACTTT 59.956 41.667 0.00 0.00 30.82 2.66
2034 5838 7.343357 TGGAACCCATACACTTTAATTAGGAG 58.657 38.462 0.00 0.00 0.00 3.69
2050 5854 2.045524 AGGAGTCTGATGCCCTACATG 58.954 52.381 0.00 0.00 39.84 3.21
2052 5856 2.224161 GGAGTCTGATGCCCTACATGTC 60.224 54.545 0.00 0.00 39.84 3.06
2074 5878 2.725221 AATTCAGCTGGAGATGGACC 57.275 50.000 15.13 0.00 31.33 4.46
2078 5882 0.617413 CAGCTGGAGATGGACCAAGT 59.383 55.000 5.57 0.00 36.95 3.16
2154 5958 5.508567 TGATGGAAATCATGCAAGTTCCTA 58.491 37.500 16.27 5.92 42.49 2.94
2160 5964 7.615365 TGGAAATCATGCAAGTTCCTATAAGTT 59.385 33.333 16.27 0.00 42.49 2.66
2181 5985 7.992180 AGTTTGTGATTTCAGTTTTGATGTC 57.008 32.000 0.00 0.00 32.27 3.06
2182 5986 7.775120 AGTTTGTGATTTCAGTTTTGATGTCT 58.225 30.769 0.00 0.00 32.27 3.41
2183 5987 7.917505 AGTTTGTGATTTCAGTTTTGATGTCTC 59.082 33.333 0.00 0.00 32.27 3.36
2184 5988 6.940831 TGTGATTTCAGTTTTGATGTCTCA 57.059 33.333 0.00 0.00 32.27 3.27
2185 5989 6.728200 TGTGATTTCAGTTTTGATGTCTCAC 58.272 36.000 0.00 0.00 33.21 3.51
2186 5990 6.145535 GTGATTTCAGTTTTGATGTCTCACC 58.854 40.000 0.00 0.00 32.27 4.02
2187 5991 5.827267 TGATTTCAGTTTTGATGTCTCACCA 59.173 36.000 0.00 0.00 32.27 4.17
2188 5992 6.320926 TGATTTCAGTTTTGATGTCTCACCAA 59.679 34.615 0.00 0.00 32.27 3.67
2189 5993 6.713762 TTTCAGTTTTGATGTCTCACCAAT 57.286 33.333 0.00 0.00 32.27 3.16
2190 5994 5.947228 TCAGTTTTGATGTCTCACCAATC 57.053 39.130 0.00 0.00 0.00 2.67
2191 5995 5.375773 TCAGTTTTGATGTCTCACCAATCA 58.624 37.500 0.00 0.00 0.00 2.57
2192 5996 5.239306 TCAGTTTTGATGTCTCACCAATCAC 59.761 40.000 0.00 0.00 0.00 3.06
2193 5997 4.520492 AGTTTTGATGTCTCACCAATCACC 59.480 41.667 0.00 0.00 0.00 4.02
2194 5998 4.371624 TTTGATGTCTCACCAATCACCT 57.628 40.909 0.00 0.00 0.00 4.00
2195 5999 5.497464 TTTGATGTCTCACCAATCACCTA 57.503 39.130 0.00 0.00 0.00 3.08
2196 6000 5.497464 TTGATGTCTCACCAATCACCTAA 57.503 39.130 0.00 0.00 0.00 2.69
2197 6001 4.832248 TGATGTCTCACCAATCACCTAAC 58.168 43.478 0.00 0.00 0.00 2.34
2198 6002 4.285775 TGATGTCTCACCAATCACCTAACA 59.714 41.667 0.00 0.00 0.00 2.41
2602 6406 7.619965 CCTCCTCTCAGAAAAAGAGAAGTAAT 58.380 38.462 1.78 0.00 42.39 1.89
2631 6443 8.665685 GTCATAAAATGAGTAACACCGAAGAAT 58.334 33.333 0.00 0.00 40.53 2.40
2646 6458 7.148656 ACACCGAAGAATTTCTTGTTGTTTTTG 60.149 33.333 16.17 4.97 36.73 2.44
2760 6573 5.303078 TGCATCTCAGGTACCTCTATCTTTC 59.697 44.000 12.84 0.00 0.00 2.62
2766 6580 8.290277 TCTCAGGTACCTCTATCTTTCCTAATT 58.710 37.037 12.84 0.00 0.00 1.40
2833 6647 6.209192 ACACTTGTTAATGAATCTGCATTCCA 59.791 34.615 0.00 0.00 38.14 3.53
2834 6648 7.093640 ACACTTGTTAATGAATCTGCATTCCAT 60.094 33.333 0.00 0.00 38.14 3.41
2835 6649 8.407832 CACTTGTTAATGAATCTGCATTCCATA 58.592 33.333 0.00 0.00 38.14 2.74
2836 6650 8.408601 ACTTGTTAATGAATCTGCATTCCATAC 58.591 33.333 0.00 0.00 38.14 2.39
2837 6651 7.275888 TGTTAATGAATCTGCATTCCATACC 57.724 36.000 0.00 0.00 38.14 2.73
2842 6656 5.508567 TGAATCTGCATTCCATACCTTGAA 58.491 37.500 0.00 0.00 38.14 2.69
2916 6730 4.394729 CTCAAAGGTTTGCCAGGTAACTA 58.605 43.478 0.00 0.00 41.12 2.24
2964 6778 9.158233 CAATTCCTAAATGAATTCAATGTGCTT 57.842 29.630 13.09 0.00 41.74 3.91
2986 6800 9.748708 TGCTTAATATGACATAATTTGCTTTCC 57.251 29.630 0.00 0.00 0.00 3.13
3014 6828 4.020128 CAGGGCCCTATATGTAAGTCCTTC 60.020 50.000 28.13 0.00 0.00 3.46
3036 6850 4.402793 TCTCTTCTCCAGGCACTATAACAC 59.597 45.833 0.00 0.00 36.02 3.32
3043 6857 4.634004 TCCAGGCACTATAACACATTTTCG 59.366 41.667 0.00 0.00 36.02 3.46
3051 6865 8.605746 GCACTATAACACATTTTCGTATTACCA 58.394 33.333 0.00 0.00 0.00 3.25
3126 6940 8.198109 TGCTTTCAGATATCCAGTCTAACTAAC 58.802 37.037 0.00 0.00 0.00 2.34
3223 7038 8.150945 TGAAGGTAATATGGCTACTCAATTCTC 58.849 37.037 0.00 0.00 0.00 2.87
3228 7043 7.865706 AATATGGCTACTCAATTCTCGTTTT 57.134 32.000 0.00 0.00 0.00 2.43
3295 7110 9.638239 TTTCTGCAATTATAGGTTTGAACAATC 57.362 29.630 0.00 0.00 0.00 2.67
3298 7113 7.035004 TGCAATTATAGGTTTGAACAATCTGC 58.965 34.615 0.00 0.00 0.00 4.26
3363 7178 0.401738 CCCTTGCTCTTGGACCAGAA 59.598 55.000 0.00 0.00 0.00 3.02
3431 7249 7.745620 ACTTGGAATTTTCGTCTGAAGTATT 57.254 32.000 0.00 0.00 35.06 1.89
3442 7261 7.430992 TCGTCTGAAGTATTACGTATATGCT 57.569 36.000 0.00 0.00 36.73 3.79
3472 7303 3.677121 CACTGTACAATGAGAGTGAGCAC 59.323 47.826 0.00 0.00 38.49 4.40
3475 7306 4.498241 TGTACAATGAGAGTGAGCACATC 58.502 43.478 3.19 1.67 0.00 3.06
3486 7317 2.606725 GTGAGCACATCTGTCAGTATGC 59.393 50.000 14.14 14.14 34.76 3.14
3487 7318 2.208431 GAGCACATCTGTCAGTATGCC 58.792 52.381 16.77 8.91 34.76 4.40
3488 7319 0.933097 GCACATCTGTCAGTATGCCG 59.067 55.000 12.06 6.34 34.76 5.69
3489 7320 0.933097 CACATCTGTCAGTATGCCGC 59.067 55.000 0.00 0.00 34.76 6.53
3490 7321 0.826715 ACATCTGTCAGTATGCCGCT 59.173 50.000 0.00 0.00 34.76 5.52
3491 7322 1.215244 CATCTGTCAGTATGCCGCTG 58.785 55.000 0.00 0.00 34.76 5.18
3492 7323 0.531532 ATCTGTCAGTATGCCGCTGC 60.532 55.000 0.00 0.00 34.76 5.25
3512 7343 1.414181 CAGTCGGCCTACATCCAGAAT 59.586 52.381 10.45 0.00 0.00 2.40
3527 7358 5.489792 TCCAGAATTGCATATCCCTCTAC 57.510 43.478 0.00 0.00 0.00 2.59
3534 7365 2.705658 TGCATATCCCTCTACAACCTGG 59.294 50.000 0.00 0.00 0.00 4.45
3546 7378 3.434940 ACAACCTGGATACCTTGAACC 57.565 47.619 0.00 0.00 0.00 3.62
3558 7390 8.217799 TGGATACCTTGAACCTATATTTTCTGG 58.782 37.037 0.00 0.00 0.00 3.86
3568 7400 9.516314 GAACCTATATTTTCTGGTGTATTTTGC 57.484 33.333 0.00 0.00 32.53 3.68
3582 7414 8.726988 TGGTGTATTTTGCTTATAAGTGAGTTC 58.273 33.333 13.91 0.00 0.00 3.01
3585 7417 9.719355 TGTATTTTGCTTATAAGTGAGTTCAGA 57.281 29.630 13.91 0.00 0.00 3.27
3587 7419 8.854614 ATTTTGCTTATAAGTGAGTTCAGAGT 57.145 30.769 13.91 0.00 0.00 3.24
3588 7420 7.658179 TTTGCTTATAAGTGAGTTCAGAGTG 57.342 36.000 13.91 0.00 0.00 3.51
3589 7421 5.171476 TGCTTATAAGTGAGTTCAGAGTGC 58.829 41.667 13.91 0.00 0.00 4.40
3590 7422 5.171476 GCTTATAAGTGAGTTCAGAGTGCA 58.829 41.667 13.91 0.00 0.00 4.57
3591 7423 5.290643 GCTTATAAGTGAGTTCAGAGTGCAG 59.709 44.000 13.91 0.00 0.00 4.41
3592 7424 1.876322 AAGTGAGTTCAGAGTGCAGC 58.124 50.000 0.00 0.00 0.00 5.25
3593 7425 1.047002 AGTGAGTTCAGAGTGCAGCT 58.953 50.000 0.00 0.00 0.00 4.24
3594 7426 2.242926 AGTGAGTTCAGAGTGCAGCTA 58.757 47.619 0.00 0.00 0.00 3.32
3595 7427 2.630098 AGTGAGTTCAGAGTGCAGCTAA 59.370 45.455 0.00 0.00 0.00 3.09
3596 7428 3.070159 AGTGAGTTCAGAGTGCAGCTAAA 59.930 43.478 0.00 0.00 0.00 1.85
3597 7429 3.999663 GTGAGTTCAGAGTGCAGCTAAAT 59.000 43.478 0.00 0.00 0.00 1.40
3598 7430 4.453819 GTGAGTTCAGAGTGCAGCTAAATT 59.546 41.667 0.00 0.00 0.00 1.82
3599 7431 4.692625 TGAGTTCAGAGTGCAGCTAAATTC 59.307 41.667 0.00 0.00 0.00 2.17
3600 7432 4.904241 AGTTCAGAGTGCAGCTAAATTCT 58.096 39.130 0.00 0.00 0.00 2.40
3601 7433 4.694509 AGTTCAGAGTGCAGCTAAATTCTG 59.305 41.667 11.86 11.86 34.76 3.02
3602 7434 4.277515 TCAGAGTGCAGCTAAATTCTGT 57.722 40.909 15.58 0.00 34.97 3.41
3603 7435 4.248859 TCAGAGTGCAGCTAAATTCTGTC 58.751 43.478 15.58 0.00 34.97 3.51
3604 7436 3.061831 CAGAGTGCAGCTAAATTCTGTCG 59.938 47.826 10.51 0.00 34.21 4.35
3605 7437 2.349886 GAGTGCAGCTAAATTCTGTCGG 59.650 50.000 0.00 0.00 34.21 4.79
3606 7438 1.086696 TGCAGCTAAATTCTGTCGGC 58.913 50.000 0.00 0.00 34.21 5.54
3607 7439 1.086696 GCAGCTAAATTCTGTCGGCA 58.913 50.000 0.00 0.00 34.21 5.69
3608 7440 1.672881 GCAGCTAAATTCTGTCGGCAT 59.327 47.619 0.00 0.00 34.21 4.40
3609 7441 2.286654 GCAGCTAAATTCTGTCGGCATC 60.287 50.000 0.00 0.00 34.21 3.91
3610 7442 2.938451 CAGCTAAATTCTGTCGGCATCA 59.062 45.455 0.00 0.00 0.00 3.07
3611 7443 3.002042 CAGCTAAATTCTGTCGGCATCAG 59.998 47.826 0.00 0.34 0.00 2.90
3612 7444 2.286654 GCTAAATTCTGTCGGCATCAGC 60.287 50.000 0.00 0.00 41.10 4.26
3613 7445 1.825090 AAATTCTGTCGGCATCAGCA 58.175 45.000 0.00 0.00 44.61 4.41
3614 7446 2.048444 AATTCTGTCGGCATCAGCAT 57.952 45.000 0.00 0.00 44.61 3.79
3615 7447 2.916702 ATTCTGTCGGCATCAGCATA 57.083 45.000 0.00 0.00 44.61 3.14
3616 7448 2.916702 TTCTGTCGGCATCAGCATAT 57.083 45.000 0.00 0.00 44.61 1.78
3617 7449 2.916702 TCTGTCGGCATCAGCATATT 57.083 45.000 0.00 0.00 44.61 1.28
3618 7450 2.759191 TCTGTCGGCATCAGCATATTC 58.241 47.619 0.00 0.00 44.61 1.75
3619 7451 1.458445 CTGTCGGCATCAGCATATTCG 59.542 52.381 0.00 0.00 44.61 3.34
3620 7452 1.202521 TGTCGGCATCAGCATATTCGT 60.203 47.619 0.00 0.00 44.61 3.85
3621 7453 2.035321 TGTCGGCATCAGCATATTCGTA 59.965 45.455 0.00 0.00 44.61 3.43
3622 7454 3.254060 GTCGGCATCAGCATATTCGTAT 58.746 45.455 0.00 0.00 44.61 3.06
3623 7455 3.679980 GTCGGCATCAGCATATTCGTATT 59.320 43.478 0.00 0.00 44.61 1.89
3624 7456 4.152402 GTCGGCATCAGCATATTCGTATTT 59.848 41.667 0.00 0.00 44.61 1.40
3625 7457 4.754618 TCGGCATCAGCATATTCGTATTTT 59.245 37.500 0.00 0.00 44.61 1.82
3626 7458 5.238432 TCGGCATCAGCATATTCGTATTTTT 59.762 36.000 0.00 0.00 44.61 1.94
3649 7481 8.943594 TTTTTAGGGGAACATATTAGTGTTGT 57.056 30.769 0.00 0.00 42.08 3.32
3650 7482 8.943594 TTTTAGGGGAACATATTAGTGTTGTT 57.056 30.769 0.00 0.00 42.08 2.83
3651 7483 7.931578 TTAGGGGAACATATTAGTGTTGTTG 57.068 36.000 0.00 0.00 42.08 3.33
3652 7484 5.261216 AGGGGAACATATTAGTGTTGTTGG 58.739 41.667 0.00 0.00 42.08 3.77
3653 7485 5.014755 AGGGGAACATATTAGTGTTGTTGGA 59.985 40.000 0.00 0.00 42.08 3.53
3654 7486 5.891551 GGGGAACATATTAGTGTTGTTGGAT 59.108 40.000 0.00 0.00 42.08 3.41
3655 7487 7.057894 GGGGAACATATTAGTGTTGTTGGATA 58.942 38.462 0.00 0.00 42.08 2.59
3656 7488 7.012989 GGGGAACATATTAGTGTTGTTGGATAC 59.987 40.741 0.00 0.00 42.08 2.24
3657 7489 7.554835 GGGAACATATTAGTGTTGTTGGATACA 59.445 37.037 0.00 0.00 43.69 2.29
3727 7589 8.261492 AGAAGCACTGTTATCTTGTTAGATTG 57.739 34.615 0.00 0.00 41.38 2.67
3730 7592 6.595716 AGCACTGTTATCTTGTTAGATTGTCC 59.404 38.462 0.00 0.00 41.38 4.02
3731 7593 6.455646 GCACTGTTATCTTGTTAGATTGTCCG 60.456 42.308 0.00 0.00 41.38 4.79
3743 7605 3.589988 AGATTGTCCGTCTTCATGTGTC 58.410 45.455 0.00 0.00 0.00 3.67
3745 7607 1.338107 TGTCCGTCTTCATGTGTCCT 58.662 50.000 0.00 0.00 0.00 3.85
3746 7608 1.272490 TGTCCGTCTTCATGTGTCCTC 59.728 52.381 0.00 0.00 0.00 3.71
3747 7609 1.272490 GTCCGTCTTCATGTGTCCTCA 59.728 52.381 0.00 0.00 0.00 3.86
3748 7610 1.967779 TCCGTCTTCATGTGTCCTCAA 59.032 47.619 0.00 0.00 0.00 3.02
3749 7611 2.567169 TCCGTCTTCATGTGTCCTCAAT 59.433 45.455 0.00 0.00 0.00 2.57
3751 7613 3.372206 CCGTCTTCATGTGTCCTCAATTC 59.628 47.826 0.00 0.00 0.00 2.17
3752 7614 3.372206 CGTCTTCATGTGTCCTCAATTCC 59.628 47.826 0.00 0.00 0.00 3.01
3753 7615 4.583871 GTCTTCATGTGTCCTCAATTCCT 58.416 43.478 0.00 0.00 0.00 3.36
3776 7645 6.238402 CCTCATCATAGCACTTTGATCTGTTG 60.238 42.308 1.20 0.00 30.62 3.33
3786 7655 1.674359 TGATCTGTTGTGGTGCGTTT 58.326 45.000 0.00 0.00 0.00 3.60
3791 7660 4.640789 TCTGTTGTGGTGCGTTTATTTT 57.359 36.364 0.00 0.00 0.00 1.82
3792 7661 4.355437 TCTGTTGTGGTGCGTTTATTTTG 58.645 39.130 0.00 0.00 0.00 2.44
3802 7671 3.181475 TGCGTTTATTTTGGCAAGGACAA 60.181 39.130 0.00 0.00 31.50 3.18
3849 7718 7.277174 AGTAAGAAAAATGAGAGTGGTTTGG 57.723 36.000 0.00 0.00 0.00 3.28
3850 7719 4.590850 AGAAAAATGAGAGTGGTTTGGC 57.409 40.909 0.00 0.00 0.00 4.52
3851 7720 4.218312 AGAAAAATGAGAGTGGTTTGGCT 58.782 39.130 0.00 0.00 0.00 4.75
3852 7721 4.651045 AGAAAAATGAGAGTGGTTTGGCTT 59.349 37.500 0.00 0.00 0.00 4.35
3853 7722 4.590850 AAAATGAGAGTGGTTTGGCTTC 57.409 40.909 0.00 0.00 0.00 3.86
3854 7723 3.515602 AATGAGAGTGGTTTGGCTTCT 57.484 42.857 0.00 0.00 0.00 2.85
3855 7724 3.515602 ATGAGAGTGGTTTGGCTTCTT 57.484 42.857 0.00 0.00 0.00 2.52
3883 7752 5.874810 CGTGTTTGAGATTTCCTTCTCCATA 59.125 40.000 0.00 0.00 41.24 2.74
3988 7857 7.076842 ACGTGAGTTTCATAATGATTTCCAG 57.923 36.000 0.00 0.00 46.40 3.86
3990 7859 7.174946 ACGTGAGTTTCATAATGATTTCCAGTT 59.825 33.333 0.00 0.00 46.40 3.16
4037 7907 4.487714 ACTGACAGGTGGGTATGTAATG 57.512 45.455 7.51 0.00 0.00 1.90
4038 7908 3.844211 ACTGACAGGTGGGTATGTAATGT 59.156 43.478 7.51 0.00 0.00 2.71
4039 7909 5.027460 ACTGACAGGTGGGTATGTAATGTA 58.973 41.667 7.51 0.00 0.00 2.29
4040 7910 5.105064 ACTGACAGGTGGGTATGTAATGTAC 60.105 44.000 7.51 0.00 0.00 2.90
4041 7911 4.778427 TGACAGGTGGGTATGTAATGTACA 59.222 41.667 0.00 0.00 43.80 2.90
4042 7912 5.248705 TGACAGGTGGGTATGTAATGTACAA 59.751 40.000 0.00 0.00 42.76 2.41
4043 7913 6.069905 TGACAGGTGGGTATGTAATGTACAAT 60.070 38.462 0.00 0.00 42.76 2.71
4067 7937 0.950116 GTATGCTGAGATGCCCAAGC 59.050 55.000 0.00 0.00 40.48 4.01
4069 7939 1.934459 ATGCTGAGATGCCCAAGCCT 61.934 55.000 0.00 0.00 38.69 4.58
4079 7949 1.895131 TGCCCAAGCCTGAAAAGAATC 59.105 47.619 0.00 0.00 38.69 2.52
4095 7965 9.578576 TGAAAAGAATCAAATATCTCATAGGGG 57.421 33.333 0.00 0.00 0.00 4.79
4151 8021 5.678107 GCTTCTGCCAATTATGAAGTTCAGG 60.678 44.000 11.91 7.65 38.41 3.86
4170 8040 1.471287 GGGTGACGGATTGGCTTAAAC 59.529 52.381 0.00 0.00 0.00 2.01
4200 8070 6.601741 TTCAAGCACCAAATGAACAAAATC 57.398 33.333 0.00 0.00 0.00 2.17
4225 8095 9.187996 TCTAATGGAATATGTGCAAAAGATTCA 57.812 29.630 15.85 6.52 0.00 2.57
4226 8096 9.976511 CTAATGGAATATGTGCAAAAGATTCAT 57.023 29.630 15.85 5.04 0.00 2.57
4229 8099 7.259882 TGGAATATGTGCAAAAGATTCATGTC 58.740 34.615 15.85 4.99 0.00 3.06
4230 8100 7.123098 TGGAATATGTGCAAAAGATTCATGTCT 59.877 33.333 15.85 0.00 0.00 3.41
4231 8101 7.646922 GGAATATGTGCAAAAGATTCATGTCTC 59.353 37.037 15.85 0.00 0.00 3.36
4232 8102 7.876936 ATATGTGCAAAAGATTCATGTCTCT 57.123 32.000 0.00 0.00 0.00 3.10
4233 8103 5.366829 TGTGCAAAAGATTCATGTCTCTG 57.633 39.130 0.00 0.00 0.00 3.35
4234 8104 4.823442 TGTGCAAAAGATTCATGTCTCTGT 59.177 37.500 0.00 0.00 0.00 3.41
4235 8105 5.300034 TGTGCAAAAGATTCATGTCTCTGTT 59.700 36.000 0.00 0.00 0.00 3.16
4236 8106 6.486320 TGTGCAAAAGATTCATGTCTCTGTTA 59.514 34.615 0.00 0.00 0.00 2.41
4237 8107 7.175467 TGTGCAAAAGATTCATGTCTCTGTTAT 59.825 33.333 0.00 0.00 0.00 1.89
4238 8108 8.668353 GTGCAAAAGATTCATGTCTCTGTTATA 58.332 33.333 0.00 0.00 0.00 0.98
4265 8145 4.284490 ACAGAATCTTCCAAGCTGTACTCA 59.716 41.667 0.00 0.00 37.98 3.41
4298 9268 5.008613 GCAACTTTTGGTGACTGTTATGAGA 59.991 40.000 0.00 0.00 40.19 3.27
4299 9269 6.294176 GCAACTTTTGGTGACTGTTATGAGAT 60.294 38.462 0.00 0.00 40.19 2.75
4300 9270 7.651808 CAACTTTTGGTGACTGTTATGAGATT 58.348 34.615 0.00 0.00 40.19 2.40
4301 9271 7.206981 ACTTTTGGTGACTGTTATGAGATTG 57.793 36.000 0.00 0.00 0.00 2.67
4303 9273 6.558771 TTTGGTGACTGTTATGAGATTGTG 57.441 37.500 0.00 0.00 0.00 3.33
4305 9275 4.285775 TGGTGACTGTTATGAGATTGTGGA 59.714 41.667 0.00 0.00 0.00 4.02
4306 9276 5.045651 TGGTGACTGTTATGAGATTGTGGAT 60.046 40.000 0.00 0.00 0.00 3.41
4308 9278 5.877012 GTGACTGTTATGAGATTGTGGATGT 59.123 40.000 0.00 0.00 0.00 3.06
4309 9279 7.041721 GTGACTGTTATGAGATTGTGGATGTA 58.958 38.462 0.00 0.00 0.00 2.29
4326 9320 9.123902 TGTGGATGTATTCTAGATGAATTTTGG 57.876 33.333 0.00 0.00 42.28 3.28
4327 9321 9.125026 GTGGATGTATTCTAGATGAATTTTGGT 57.875 33.333 0.00 0.00 42.28 3.67
4328 9322 9.123902 TGGATGTATTCTAGATGAATTTTGGTG 57.876 33.333 0.00 0.00 42.28 4.17
4329 9323 9.342308 GGATGTATTCTAGATGAATTTTGGTGA 57.658 33.333 0.00 0.00 42.28 4.02
4331 9325 9.911788 ATGTATTCTAGATGAATTTTGGTGACT 57.088 29.630 0.00 0.00 42.28 3.41
4332 9326 9.166173 TGTATTCTAGATGAATTTTGGTGACTG 57.834 33.333 0.00 0.00 42.28 3.51
4333 9327 9.167311 GTATTCTAGATGAATTTTGGTGACTGT 57.833 33.333 0.00 0.00 42.28 3.55
4351 9345 3.008813 ACTGTCATCATGTCTCTTTGCCT 59.991 43.478 0.00 0.00 0.00 4.75
4354 9348 5.121105 TGTCATCATGTCTCTTTGCCTATG 58.879 41.667 0.00 0.00 0.00 2.23
4356 9350 5.819379 GTCATCATGTCTCTTTGCCTATGAA 59.181 40.000 0.00 0.00 0.00 2.57
4377 9376 5.412594 TGAAGCAGAGTGATGGACAAATTAC 59.587 40.000 0.00 0.00 0.00 1.89
4385 9384 7.884877 AGAGTGATGGACAAATTACTTGAATCA 59.115 33.333 0.00 0.00 38.50 2.57
4416 9415 2.722094 TGAACCTCAACACCATATGGC 58.278 47.619 22.18 1.76 39.32 4.40
4417 9416 2.308570 TGAACCTCAACACCATATGGCT 59.691 45.455 22.18 6.34 39.32 4.75
4418 9417 3.521531 TGAACCTCAACACCATATGGCTA 59.478 43.478 22.18 2.04 39.32 3.93
4419 9418 3.845781 ACCTCAACACCATATGGCTAG 57.154 47.619 22.18 14.02 39.32 3.42
4420 9419 2.158755 ACCTCAACACCATATGGCTAGC 60.159 50.000 22.18 6.04 39.32 3.42
4421 9420 2.105477 CCTCAACACCATATGGCTAGCT 59.895 50.000 22.18 0.00 39.32 3.32
4422 9421 3.434167 CCTCAACACCATATGGCTAGCTT 60.434 47.826 22.18 5.30 39.32 3.74
4423 9422 3.808728 TCAACACCATATGGCTAGCTTC 58.191 45.455 22.18 0.00 39.32 3.86
4424 9423 3.455910 TCAACACCATATGGCTAGCTTCT 59.544 43.478 22.18 2.07 39.32 2.85
4425 9424 3.482156 ACACCATATGGCTAGCTTCTG 57.518 47.619 22.18 11.93 39.32 3.02
4426 9425 2.774234 ACACCATATGGCTAGCTTCTGT 59.226 45.455 22.18 12.58 39.32 3.41
4427 9426 3.136763 CACCATATGGCTAGCTTCTGTG 58.863 50.000 22.18 10.78 39.32 3.66
4428 9427 2.149578 CCATATGGCTAGCTTCTGTGC 58.850 52.381 15.72 0.00 0.00 4.57
4429 9428 2.149578 CATATGGCTAGCTTCTGTGCC 58.850 52.381 15.72 0.00 45.10 5.01
4431 9430 4.972875 GGCTAGCTTCTGTGCCAT 57.027 55.556 15.72 0.00 44.34 4.40
4438 9437 1.808945 AGCTTCTGTGCCATTCTTTCG 59.191 47.619 0.00 0.00 0.00 3.46
4442 9441 4.868195 GTGCCATTCTTTCGCACC 57.132 55.556 0.00 0.00 45.64 5.01
4449 9448 2.228582 CCATTCTTTCGCACCACAATCA 59.771 45.455 0.00 0.00 0.00 2.57
4450 9449 3.236816 CATTCTTTCGCACCACAATCAC 58.763 45.455 0.00 0.00 0.00 3.06
4451 9450 1.960417 TCTTTCGCACCACAATCACA 58.040 45.000 0.00 0.00 0.00 3.58
4452 9451 1.601903 TCTTTCGCACCACAATCACAC 59.398 47.619 0.00 0.00 0.00 3.82
4453 9452 1.333308 CTTTCGCACCACAATCACACA 59.667 47.619 0.00 0.00 0.00 3.72
4454 9453 0.660488 TTCGCACCACAATCACACAC 59.340 50.000 0.00 0.00 0.00 3.82
4455 9454 0.462759 TCGCACCACAATCACACACA 60.463 50.000 0.00 0.00 0.00 3.72
4456 9455 0.316937 CGCACCACAATCACACACAC 60.317 55.000 0.00 0.00 0.00 3.82
4457 9456 0.030638 GCACCACAATCACACACACC 59.969 55.000 0.00 0.00 0.00 4.16
4458 9457 0.307453 CACCACAATCACACACACCG 59.693 55.000 0.00 0.00 0.00 4.94
4459 9458 1.282570 CCACAATCACACACACCGC 59.717 57.895 0.00 0.00 0.00 5.68
4460 9459 1.165907 CCACAATCACACACACCGCT 61.166 55.000 0.00 0.00 0.00 5.52
4461 9460 0.041047 CACAATCACACACACCGCTG 60.041 55.000 0.00 0.00 0.00 5.18
4462 9461 1.165907 ACAATCACACACACCGCTGG 61.166 55.000 0.00 0.00 0.00 4.85
4464 9463 2.680974 AATCACACACACCGCTGGCT 62.681 55.000 0.00 0.00 0.00 4.75
4465 9464 3.653009 CACACACACCGCTGGCTG 61.653 66.667 0.00 0.00 0.00 4.85
4468 9467 4.569180 ACACACCGCTGGCTGCTT 62.569 61.111 14.58 0.00 40.11 3.91
4497 9516 4.280677 CAGAAGGCCACCAAAGAATAAACA 59.719 41.667 5.01 0.00 0.00 2.83
4673 9692 1.973281 CCTGCGTGGGAATTGCACT 60.973 57.895 0.00 0.00 34.42 4.40
4717 9736 2.043664 TCTCCTTCCTGTCATCTCCACT 59.956 50.000 0.00 0.00 0.00 4.00
4869 9888 5.509272 CGAACATTTGATGATTTTGACGAGG 59.491 40.000 0.00 0.00 0.00 4.63
4870 9889 4.737054 ACATTTGATGATTTTGACGAGGC 58.263 39.130 0.00 0.00 0.00 4.70
5000 10019 2.048444 ATCAGTTAGCATGGCCACAG 57.952 50.000 8.16 4.78 0.00 3.66
5019 10038 5.349061 ACAGATGTGAAGAGATGTATGCA 57.651 39.130 0.00 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 6.769822 CCATGAGTAGAAGCCAATATTTCAGT 59.230 38.462 0.00 0.00 0.00 3.41
66 67 4.008330 CAGTGATTTCTCTGGATGCAACT 58.992 43.478 0.00 0.00 34.75 3.16
74 75 5.916318 AGAAGATAGCAGTGATTTCTCTGG 58.084 41.667 1.72 0.00 37.79 3.86
75 76 6.198778 CGAAGAAGATAGCAGTGATTTCTCTG 59.801 42.308 1.72 5.49 39.66 3.35
95 96 1.347707 ACATGGAGCCAGTTTCGAAGA 59.652 47.619 0.00 0.00 0.00 2.87
157 164 0.527565 AATTTCGCTGGTGTCATGCC 59.472 50.000 0.00 0.00 0.00 4.40
257 264 3.838244 TGTAACATCTCATACCTGCCC 57.162 47.619 0.00 0.00 0.00 5.36
319 326 4.421948 CTCGTCGGTAAAGCTTCTACATT 58.578 43.478 0.00 0.00 0.00 2.71
386 393 9.599322 CTAATTAATGCACATCGAAATAACTCC 57.401 33.333 0.00 0.00 0.00 3.85
479 487 5.827797 ACATTGCAATCGATTACCCAGTAAT 59.172 36.000 9.53 6.62 40.82 1.89
486 494 7.096477 GCTCAATAAACATTGCAATCGATTACC 60.096 37.037 9.53 5.71 0.00 2.85
676 684 3.327757 ACTTCATACCTCACCACACATGT 59.672 43.478 0.00 0.00 0.00 3.21
751 762 2.815503 CACACATGTCACACCATCACAT 59.184 45.455 0.00 0.00 0.00 3.21
792 803 3.566130 GCATCCTGCAGAAGAACCT 57.434 52.632 17.39 0.00 44.26 3.50
811 822 0.242825 GCTGCTTGCAGATCAAAGCA 59.757 50.000 24.67 21.81 38.05 3.91
841 852 0.179073 CCGTGAAGTGATGCCCCTAG 60.179 60.000 0.00 0.00 0.00 3.02
842 853 0.907704 ACCGTGAAGTGATGCCCCTA 60.908 55.000 0.00 0.00 0.00 3.53
844 855 2.040544 CACCGTGAAGTGATGCCCC 61.041 63.158 0.00 0.00 40.34 5.80
845 856 2.040544 CCACCGTGAAGTGATGCCC 61.041 63.158 0.00 0.00 40.34 5.36
846 857 1.003839 TCCACCGTGAAGTGATGCC 60.004 57.895 0.00 0.00 40.34 4.40
847 858 1.639298 GCTCCACCGTGAAGTGATGC 61.639 60.000 0.00 0.00 40.34 3.91
848 859 0.320683 TGCTCCACCGTGAAGTGATG 60.321 55.000 0.00 0.00 40.34 3.07
849 860 0.615331 ATGCTCCACCGTGAAGTGAT 59.385 50.000 0.00 0.00 40.34 3.06
851 862 0.518636 CAATGCTCCACCGTGAAGTG 59.481 55.000 0.00 0.00 37.51 3.16
918 4012 1.631898 GTGACTAGTTTTAGGGCCCCA 59.368 52.381 21.43 0.00 0.00 4.96
1472 5052 7.483580 AGCTAAAACAGTAGGAGACAGTAAT 57.516 36.000 0.00 0.00 0.00 1.89
1505 5085 5.351948 TCATTATCAGTGGAAACGGATGA 57.648 39.130 2.36 0.00 0.00 2.92
1621 5326 6.927294 AAGAAGGAATAATAAGCGGAACAG 57.073 37.500 0.00 0.00 0.00 3.16
1635 5340 6.659242 ACATCGACACCATTTAAAGAAGGAAT 59.341 34.615 10.16 0.00 0.00 3.01
1714 5420 3.492337 TCCAAACATACCCCAAACTGTC 58.508 45.455 0.00 0.00 0.00 3.51
1764 5471 5.790593 GTCCACTGACTGTATTTAACTGGA 58.209 41.667 0.00 0.00 38.53 3.86
1778 5485 4.067896 ACATGAATCACAAGTCCACTGAC 58.932 43.478 0.00 0.00 42.09 3.51
1779 5486 4.067192 CACATGAATCACAAGTCCACTGA 58.933 43.478 0.00 0.00 0.00 3.41
1866 5587 3.029570 CCTACCTCCCAACCAGTACTAC 58.970 54.545 0.00 0.00 0.00 2.73
1879 5600 2.480642 ATCCTGGACTTCCTACCTCC 57.519 55.000 0.00 0.00 36.82 4.30
1913 5717 3.366679 CCCAGAATGCAAATGCGATATCC 60.367 47.826 0.00 0.00 45.83 2.59
1988 5792 4.141321 CCAGATTCCAATTCCATCAGAGGA 60.141 45.833 0.00 0.00 35.41 3.71
2013 5817 7.402071 TCAGACTCCTAATTAAAGTGTATGGGT 59.598 37.037 5.20 0.00 0.00 4.51
2025 5829 5.464069 TGTAGGGCATCAGACTCCTAATTA 58.536 41.667 0.00 0.00 34.12 1.40
2034 5838 2.988010 TGACATGTAGGGCATCAGAC 57.012 50.000 0.00 0.00 35.19 3.51
2050 5854 4.754114 GTCCATCTCCAGCTGAATTATGAC 59.246 45.833 17.39 11.02 0.00 3.06
2052 5856 4.070716 GGTCCATCTCCAGCTGAATTATG 58.929 47.826 17.39 12.53 0.00 1.90
2074 5878 6.389091 TGCCTATTTAAAATGAGCACACTTG 58.611 36.000 0.00 0.00 0.00 3.16
2078 5882 8.190122 CACTATTGCCTATTTAAAATGAGCACA 58.810 33.333 0.00 0.00 0.00 4.57
2111 5915 9.033711 TCCATCAGAACCATATTTTGAAATTGA 57.966 29.630 0.00 0.00 0.00 2.57
2160 5964 7.195646 GTGAGACATCAAAACTGAAATCACAA 58.804 34.615 0.00 0.00 37.14 3.33
2176 5980 4.832248 TGTTAGGTGATTGGTGAGACATC 58.168 43.478 0.00 0.00 0.00 3.06
2177 5981 4.908601 TGTTAGGTGATTGGTGAGACAT 57.091 40.909 0.00 0.00 0.00 3.06
2577 6381 5.482163 ACTTCTCTTTTTCTGAGAGGAGG 57.518 43.478 12.66 2.43 46.73 4.30
2580 6384 9.936759 ACTTATTACTTCTCTTTTTCTGAGAGG 57.063 33.333 0.00 0.00 40.99 3.69
2602 6406 9.146984 CTTCGGTGTTACTCATTTTATGACTTA 57.853 33.333 0.00 0.00 35.06 2.24
2614 6426 6.053005 ACAAGAAATTCTTCGGTGTTACTCA 58.947 36.000 5.09 0.00 33.78 3.41
2615 6427 6.541111 ACAAGAAATTCTTCGGTGTTACTC 57.459 37.500 5.09 0.00 33.78 2.59
2685 6498 1.572085 CTGGCTCACCTTGCAACTCG 61.572 60.000 0.00 0.00 36.63 4.18
2810 6624 6.839124 TGGAATGCAGATTCATTAACAAGT 57.161 33.333 2.65 0.00 39.98 3.16
2837 6651 4.848357 ACAGGACCATTCACCTATTCAAG 58.152 43.478 0.00 0.00 34.87 3.02
2842 6656 4.783227 ACAAGTACAGGACCATTCACCTAT 59.217 41.667 0.00 0.00 34.87 2.57
2854 6668 2.367567 GGTGTCCTCAACAAGTACAGGA 59.632 50.000 0.00 0.00 40.31 3.86
2986 6800 1.376424 CATATAGGGCCCTGCAGCG 60.376 63.158 35.81 14.86 0.00 5.18
3014 6828 4.160439 TGTGTTATAGTGCCTGGAGAAGAG 59.840 45.833 0.00 0.00 0.00 2.85
3126 6940 5.365021 ACATCCAGATAAGGAACAAGAGG 57.635 43.478 0.00 0.00 41.92 3.69
3250 7065 7.067251 TGCAGAAATAATATGCATGAGTTCACA 59.933 33.333 10.16 9.03 44.56 3.58
3295 7110 8.239314 TGATTTGTCTTCATAAGCTTTTAGCAG 58.761 33.333 3.20 0.00 45.56 4.24
3298 7113 8.457261 AGCTGATTTGTCTTCATAAGCTTTTAG 58.543 33.333 3.20 0.00 0.00 1.85
3302 7117 6.830873 AAGCTGATTTGTCTTCATAAGCTT 57.169 33.333 3.48 3.48 31.26 3.74
3345 7160 1.349026 TCTTCTGGTCCAAGAGCAAGG 59.651 52.381 0.00 0.00 39.59 3.61
3363 7178 3.703001 ACAAATGTGATCGGTTCCTCT 57.297 42.857 0.00 0.00 0.00 3.69
3406 7221 8.842358 AATACTTCAGACGAAAATTCCAAGTA 57.158 30.769 0.00 0.00 31.50 2.24
3442 7261 9.457436 TCACTCTCATTGTACAGTGTTAGTATA 57.543 33.333 16.89 10.38 37.97 1.47
3454 7285 4.565962 CAGATGTGCTCACTCTCATTGTAC 59.434 45.833 1.47 0.00 0.00 2.90
3472 7303 1.215244 CAGCGGCATACTGACAGATG 58.785 55.000 10.08 9.60 37.32 2.90
3475 7306 3.403277 GCAGCGGCATACTGACAG 58.597 61.111 3.18 0.00 40.72 3.51
3487 7318 3.723235 ATGTAGGCCGACTGCAGCG 62.723 63.158 15.27 17.81 45.17 5.18
3488 7319 1.884926 GATGTAGGCCGACTGCAGC 60.885 63.158 15.27 5.81 45.17 5.25
3489 7320 1.227380 GGATGTAGGCCGACTGCAG 60.227 63.158 17.46 13.48 45.17 4.41
3490 7321 1.960040 CTGGATGTAGGCCGACTGCA 61.960 60.000 17.46 12.31 46.03 4.41
3491 7322 1.227380 CTGGATGTAGGCCGACTGC 60.227 63.158 17.46 8.63 40.16 4.40
3492 7323 0.824109 TTCTGGATGTAGGCCGACTG 59.176 55.000 17.46 2.94 0.00 3.51
3493 7324 1.794714 ATTCTGGATGTAGGCCGACT 58.205 50.000 17.46 2.65 0.00 4.18
3494 7325 2.213499 CAATTCTGGATGTAGGCCGAC 58.787 52.381 9.38 9.38 0.00 4.79
3495 7326 1.475034 GCAATTCTGGATGTAGGCCGA 60.475 52.381 0.00 0.00 0.00 5.54
3496 7327 0.947244 GCAATTCTGGATGTAGGCCG 59.053 55.000 0.00 0.00 0.00 6.13
3497 7328 2.057137 TGCAATTCTGGATGTAGGCC 57.943 50.000 0.00 0.00 0.00 5.19
3498 7329 4.397417 GGATATGCAATTCTGGATGTAGGC 59.603 45.833 0.00 0.00 34.98 3.93
3512 7343 3.136443 CCAGGTTGTAGAGGGATATGCAA 59.864 47.826 0.00 0.00 0.00 4.08
3527 7358 3.721087 AGGTTCAAGGTATCCAGGTTG 57.279 47.619 0.00 0.00 0.00 3.77
3534 7365 9.057089 CACCAGAAAATATAGGTTCAAGGTATC 57.943 37.037 11.62 0.00 34.56 2.24
3558 7390 9.760660 CTGAACTCACTTATAAGCAAAATACAC 57.239 33.333 12.54 0.00 0.00 2.90
3568 7400 5.290643 GCTGCACTCTGAACTCACTTATAAG 59.709 44.000 11.05 11.05 0.00 1.73
3582 7414 3.061831 CGACAGAATTTAGCTGCACTCTG 59.938 47.826 1.02 13.21 36.86 3.35
3585 7417 2.350522 CCGACAGAATTTAGCTGCACT 58.649 47.619 1.02 0.00 36.86 4.40
3586 7418 1.202076 GCCGACAGAATTTAGCTGCAC 60.202 52.381 1.02 0.00 36.86 4.57
3587 7419 1.086696 GCCGACAGAATTTAGCTGCA 58.913 50.000 1.02 0.00 36.86 4.41
3588 7420 1.086696 TGCCGACAGAATTTAGCTGC 58.913 50.000 0.00 0.00 36.86 5.25
3589 7421 2.938451 TGATGCCGACAGAATTTAGCTG 59.062 45.455 0.00 0.00 39.26 4.24
3590 7422 3.201290 CTGATGCCGACAGAATTTAGCT 58.799 45.455 0.00 0.00 37.54 3.32
3591 7423 2.286654 GCTGATGCCGACAGAATTTAGC 60.287 50.000 0.00 0.00 37.54 3.09
3592 7424 2.938451 TGCTGATGCCGACAGAATTTAG 59.062 45.455 0.00 0.00 37.54 1.85
3593 7425 2.984562 TGCTGATGCCGACAGAATTTA 58.015 42.857 0.00 0.00 37.54 1.40
3594 7426 1.825090 TGCTGATGCCGACAGAATTT 58.175 45.000 0.00 0.00 37.54 1.82
3595 7427 2.048444 ATGCTGATGCCGACAGAATT 57.952 45.000 0.00 0.00 37.54 2.17
3596 7428 2.916702 TATGCTGATGCCGACAGAAT 57.083 45.000 0.00 0.00 37.41 2.40
3597 7429 2.916702 ATATGCTGATGCCGACAGAA 57.083 45.000 0.00 0.00 37.54 3.02
3598 7430 2.759191 GAATATGCTGATGCCGACAGA 58.241 47.619 0.00 0.00 37.54 3.41
3599 7431 1.458445 CGAATATGCTGATGCCGACAG 59.542 52.381 0.00 0.00 38.71 3.51
3600 7432 1.202521 ACGAATATGCTGATGCCGACA 60.203 47.619 0.00 0.00 38.71 4.35
3601 7433 1.502231 ACGAATATGCTGATGCCGAC 58.498 50.000 0.00 0.00 38.71 4.79
3602 7434 3.592898 ATACGAATATGCTGATGCCGA 57.407 42.857 0.00 0.00 38.71 5.54
3603 7435 4.668576 AAATACGAATATGCTGATGCCG 57.331 40.909 0.00 0.00 38.71 5.69
3624 7456 8.943594 ACAACACTAATATGTTCCCCTAAAAA 57.056 30.769 0.00 0.00 40.89 1.94
3625 7457 8.798402 CAACAACACTAATATGTTCCCCTAAAA 58.202 33.333 0.00 0.00 40.89 1.52
3626 7458 7.394923 CCAACAACACTAATATGTTCCCCTAAA 59.605 37.037 0.00 0.00 40.89 1.85
3627 7459 6.887545 CCAACAACACTAATATGTTCCCCTAA 59.112 38.462 0.00 0.00 40.89 2.69
3628 7460 6.215841 TCCAACAACACTAATATGTTCCCCTA 59.784 38.462 0.00 0.00 40.89 3.53
3629 7461 5.014755 TCCAACAACACTAATATGTTCCCCT 59.985 40.000 0.00 0.00 40.89 4.79
3630 7462 5.258051 TCCAACAACACTAATATGTTCCCC 58.742 41.667 0.00 0.00 40.89 4.81
3631 7463 7.554835 TGTATCCAACAACACTAATATGTTCCC 59.445 37.037 0.00 0.00 40.89 3.97
3632 7464 8.500753 TGTATCCAACAACACTAATATGTTCC 57.499 34.615 0.00 0.00 40.89 3.62
3695 7527 3.433615 AGATAACAGTGCTTCTTTGCGTC 59.566 43.478 0.00 0.00 35.36 5.19
3698 7530 5.113502 ACAAGATAACAGTGCTTCTTTGC 57.886 39.130 0.00 0.00 0.00 3.68
3701 7533 8.725148 CAATCTAACAAGATAACAGTGCTTCTT 58.275 33.333 0.00 0.00 0.00 2.52
3706 7538 6.455646 CGGACAATCTAACAAGATAACAGTGC 60.456 42.308 0.00 0.00 0.00 4.40
3727 7589 1.272490 TGAGGACACATGAAGACGGAC 59.728 52.381 0.00 0.00 0.00 4.79
3730 7592 3.372206 GGAATTGAGGACACATGAAGACG 59.628 47.826 0.00 0.00 0.00 4.18
3731 7593 4.583871 AGGAATTGAGGACACATGAAGAC 58.416 43.478 0.00 0.00 0.00 3.01
3743 7605 4.970711 AGTGCTATGATGAGGAATTGAGG 58.029 43.478 0.00 0.00 0.00 3.86
3745 7607 6.417258 TCAAAGTGCTATGATGAGGAATTGA 58.583 36.000 0.00 0.00 0.00 2.57
3746 7608 6.688637 TCAAAGTGCTATGATGAGGAATTG 57.311 37.500 0.00 0.00 0.00 2.32
3747 7609 7.228906 CAGATCAAAGTGCTATGATGAGGAATT 59.771 37.037 0.00 0.00 36.45 2.17
3748 7610 6.711194 CAGATCAAAGTGCTATGATGAGGAAT 59.289 38.462 0.00 0.00 36.45 3.01
3749 7611 6.053650 CAGATCAAAGTGCTATGATGAGGAA 58.946 40.000 0.00 0.00 36.45 3.36
3751 7613 5.366460 ACAGATCAAAGTGCTATGATGAGG 58.634 41.667 0.00 0.00 36.45 3.86
3752 7614 6.315642 ACAACAGATCAAAGTGCTATGATGAG 59.684 38.462 0.00 0.00 36.45 2.90
3753 7615 6.093082 CACAACAGATCAAAGTGCTATGATGA 59.907 38.462 0.00 0.00 36.45 2.92
3776 7645 2.141535 TGCCAAAATAAACGCACCAC 57.858 45.000 0.00 0.00 0.00 4.16
3786 7655 8.811017 TCAGATTTTATTGTCCTTGCCAAAATA 58.189 29.630 0.00 0.00 0.00 1.40
3791 7660 4.155826 CGTCAGATTTTATTGTCCTTGCCA 59.844 41.667 0.00 0.00 0.00 4.92
3792 7661 4.662145 CGTCAGATTTTATTGTCCTTGCC 58.338 43.478 0.00 0.00 0.00 4.52
3802 7671 7.826690 ACTAAAAACATGGCGTCAGATTTTAT 58.173 30.769 12.74 7.50 0.00 1.40
3842 7711 1.403679 CACGTTCAAGAAGCCAAACCA 59.596 47.619 0.00 0.00 0.00 3.67
3843 7712 1.404035 ACACGTTCAAGAAGCCAAACC 59.596 47.619 0.00 0.00 0.00 3.27
3844 7713 2.844122 ACACGTTCAAGAAGCCAAAC 57.156 45.000 0.00 0.00 0.00 2.93
3845 7714 3.191581 TCAAACACGTTCAAGAAGCCAAA 59.808 39.130 0.00 0.00 0.00 3.28
3846 7715 2.750166 TCAAACACGTTCAAGAAGCCAA 59.250 40.909 0.00 0.00 0.00 4.52
3847 7716 2.354510 CTCAAACACGTTCAAGAAGCCA 59.645 45.455 0.00 0.00 0.00 4.75
3848 7717 2.612212 TCTCAAACACGTTCAAGAAGCC 59.388 45.455 0.00 0.00 0.00 4.35
3849 7718 3.944422 TCTCAAACACGTTCAAGAAGC 57.056 42.857 0.00 0.00 0.00 3.86
3850 7719 5.909610 GGAAATCTCAAACACGTTCAAGAAG 59.090 40.000 0.00 0.00 0.00 2.85
3851 7720 5.588648 AGGAAATCTCAAACACGTTCAAGAA 59.411 36.000 0.00 0.00 0.00 2.52
3852 7721 5.123227 AGGAAATCTCAAACACGTTCAAGA 58.877 37.500 0.00 0.00 0.00 3.02
3853 7722 5.424121 AGGAAATCTCAAACACGTTCAAG 57.576 39.130 0.00 0.00 0.00 3.02
3854 7723 5.588648 AGAAGGAAATCTCAAACACGTTCAA 59.411 36.000 0.00 0.00 0.00 2.69
3855 7724 5.123227 AGAAGGAAATCTCAAACACGTTCA 58.877 37.500 0.00 0.00 0.00 3.18
3883 7752 3.099141 CAGGTACAATTTTCCCCTGCAT 58.901 45.455 0.00 0.00 36.58 3.96
3977 7846 6.349243 TGCATGAAAGAACTGGAAATCATT 57.651 33.333 0.00 0.00 0.00 2.57
4037 7907 5.406780 GCATCTCAGCATACCTGTATTGTAC 59.593 44.000 0.00 0.00 42.38 2.90
4038 7908 5.511373 GGCATCTCAGCATACCTGTATTGTA 60.511 44.000 0.00 0.00 42.38 2.41
4039 7909 4.384056 GCATCTCAGCATACCTGTATTGT 58.616 43.478 0.00 0.00 42.38 2.71
4040 7910 3.750130 GGCATCTCAGCATACCTGTATTG 59.250 47.826 0.00 0.00 42.38 1.90
4041 7911 3.244700 GGGCATCTCAGCATACCTGTATT 60.245 47.826 0.00 0.00 42.38 1.89
4042 7912 2.304180 GGGCATCTCAGCATACCTGTAT 59.696 50.000 0.00 0.00 42.38 2.29
4043 7913 1.694150 GGGCATCTCAGCATACCTGTA 59.306 52.381 0.00 0.00 42.38 2.74
4069 7939 9.578576 CCCCTATGAGATATTTGATTCTTTTCA 57.421 33.333 0.00 0.00 0.00 2.69
4079 7949 4.782156 AGCTCTCCCCCTATGAGATATTTG 59.218 45.833 0.00 0.00 38.16 2.32
4095 7965 0.673022 CACCAGTGCAAGAGCTCTCC 60.673 60.000 18.55 11.90 42.28 3.71
4120 7990 6.040209 TCATAATTGGCAGAAGCAAAATGT 57.960 33.333 0.00 0.00 44.61 2.71
4151 8021 2.433436 AGTTTAAGCCAATCCGTCACC 58.567 47.619 0.00 0.00 0.00 4.02
4170 8040 4.358851 TCATTTGGTGCTTGAAAACGAAG 58.641 39.130 0.00 0.00 0.00 3.79
4200 8070 9.976511 ATGAATCTTTTGCACATATTCCATTAG 57.023 29.630 0.00 0.00 0.00 1.73
4213 8083 7.692460 ATAACAGAGACATGAATCTTTTGCA 57.308 32.000 0.00 0.00 0.00 4.08
4231 8101 8.821894 GCTTGGAAGATTCTGTAACTATAACAG 58.178 37.037 0.00 0.00 44.66 3.16
4232 8102 8.540388 AGCTTGGAAGATTCTGTAACTATAACA 58.460 33.333 0.00 0.00 0.00 2.41
4233 8103 8.821894 CAGCTTGGAAGATTCTGTAACTATAAC 58.178 37.037 0.00 0.00 0.00 1.89
4234 8104 8.540388 ACAGCTTGGAAGATTCTGTAACTATAA 58.460 33.333 0.00 0.00 36.37 0.98
4235 8105 8.079211 ACAGCTTGGAAGATTCTGTAACTATA 57.921 34.615 0.00 0.00 36.37 1.31
4236 8106 6.951971 ACAGCTTGGAAGATTCTGTAACTAT 58.048 36.000 0.00 0.00 36.37 2.12
4237 8107 6.360370 ACAGCTTGGAAGATTCTGTAACTA 57.640 37.500 0.00 0.00 36.37 2.24
4238 8108 5.234466 ACAGCTTGGAAGATTCTGTAACT 57.766 39.130 0.00 0.00 36.37 2.24
4265 8145 3.960102 TCACCAAAAGTTGCAGGAGAAAT 59.040 39.130 0.00 0.00 0.00 2.17
4300 9270 9.123902 CCAAAATTCATCTAGAATACATCCACA 57.876 33.333 0.00 0.00 46.09 4.17
4301 9271 9.125026 ACCAAAATTCATCTAGAATACATCCAC 57.875 33.333 0.00 0.00 46.09 4.02
4303 9273 9.342308 TCACCAAAATTCATCTAGAATACATCC 57.658 33.333 0.00 0.00 46.09 3.51
4305 9275 9.911788 AGTCACCAAAATTCATCTAGAATACAT 57.088 29.630 0.00 0.00 46.09 2.29
4306 9276 9.166173 CAGTCACCAAAATTCATCTAGAATACA 57.834 33.333 0.00 0.00 46.09 2.29
4308 9278 9.383519 GACAGTCACCAAAATTCATCTAGAATA 57.616 33.333 0.00 0.00 46.09 1.75
4325 9319 3.883830 AGAGACATGATGACAGTCACC 57.116 47.619 5.05 0.00 34.80 4.02
4326 9320 4.142945 GCAAAGAGACATGATGACAGTCAC 60.143 45.833 5.05 0.80 34.80 3.67
4327 9321 3.999001 GCAAAGAGACATGATGACAGTCA 59.001 43.478 5.50 5.50 34.80 3.41
4328 9322 3.373439 GGCAAAGAGACATGATGACAGTC 59.627 47.826 0.00 0.00 0.00 3.51
4329 9323 3.008813 AGGCAAAGAGACATGATGACAGT 59.991 43.478 0.00 0.00 0.00 3.55
4330 9324 3.607741 AGGCAAAGAGACATGATGACAG 58.392 45.455 0.00 0.00 0.00 3.51
4331 9325 3.708403 AGGCAAAGAGACATGATGACA 57.292 42.857 0.00 0.00 0.00 3.58
4332 9326 5.363101 TCATAGGCAAAGAGACATGATGAC 58.637 41.667 0.00 0.00 0.00 3.06
4333 9327 5.619132 TCATAGGCAAAGAGACATGATGA 57.381 39.130 0.00 0.00 0.00 2.92
4351 9345 4.824479 TTGTCCATCACTCTGCTTCATA 57.176 40.909 0.00 0.00 0.00 2.15
4354 9348 5.645497 AGTAATTTGTCCATCACTCTGCTTC 59.355 40.000 0.00 0.00 0.00 3.86
4356 9350 5.171339 AGTAATTTGTCCATCACTCTGCT 57.829 39.130 0.00 0.00 0.00 4.24
4377 9376 4.572985 TCAACTGGCAAACTGATTCAAG 57.427 40.909 0.00 0.00 0.00 3.02
4385 9384 2.435372 TGAGGTTCAACTGGCAAACT 57.565 45.000 0.34 0.00 0.00 2.66
4412 9411 4.972875 GGCACAGAAGCTAGCCAT 57.027 55.556 12.13 0.00 46.26 4.40
4426 9425 0.821301 TGTGGTGCGAAAGAATGGCA 60.821 50.000 0.00 0.00 40.78 4.92
4427 9426 0.313672 TTGTGGTGCGAAAGAATGGC 59.686 50.000 0.00 0.00 0.00 4.40
4428 9427 2.228582 TGATTGTGGTGCGAAAGAATGG 59.771 45.455 0.00 0.00 0.00 3.16
4429 9428 3.236816 GTGATTGTGGTGCGAAAGAATG 58.763 45.455 0.00 0.00 0.00 2.67
4430 9429 2.884012 TGTGATTGTGGTGCGAAAGAAT 59.116 40.909 0.00 0.00 0.00 2.40
4431 9430 2.032799 GTGTGATTGTGGTGCGAAAGAA 59.967 45.455 0.00 0.00 0.00 2.52
4438 9437 0.030638 GGTGTGTGTGATTGTGGTGC 59.969 55.000 0.00 0.00 0.00 5.01
4442 9441 0.041047 CAGCGGTGTGTGTGATTGTG 60.041 55.000 6.41 0.00 0.00 3.33
4466 9465 1.003580 TGGTGGCCTTCTGCTTCTAAG 59.996 52.381 3.32 0.00 40.92 2.18
4467 9466 1.064003 TGGTGGCCTTCTGCTTCTAA 58.936 50.000 3.32 0.00 40.92 2.10
4468 9467 1.064003 TTGGTGGCCTTCTGCTTCTA 58.936 50.000 3.32 0.00 40.92 2.10
4481 9500 7.543868 TGCGATTATTTGTTTATTCTTTGGTGG 59.456 33.333 0.00 0.00 0.00 4.61
4667 9686 0.035317 AGCTGGATTCGTCAGTGCAA 59.965 50.000 0.00 0.00 34.89 4.08
4673 9692 1.596934 GTGGGAGCTGGATTCGTCA 59.403 57.895 0.00 0.00 0.00 4.35
4778 9797 1.970917 GCAAGTCCATGAGAACGCCG 61.971 60.000 0.00 0.00 0.00 6.46
4869 9888 1.270465 ACGGTAAGTAACACCCACAGC 60.270 52.381 0.00 0.00 31.96 4.40
4870 9889 2.298163 AGACGGTAAGTAACACCCACAG 59.702 50.000 0.00 0.00 31.96 3.66
5000 10019 4.445453 TGGTGCATACATCTCTTCACATC 58.555 43.478 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.