Multiple sequence alignment - TraesCS2A01G400400

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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 TraesCS2A01G400400 chr2A 100.000 4531 0 0 1 4531 653685219 653689749 0.000000e+00 8368.0
1 TraesCS2A01G400400 chr2A 93.863 277 14 1 1938 2211 676346603 676346327 9.070000e-112 414.0
2 TraesCS2A01G400400 chr2D 95.034 2356 72 22 2219 4531 509954662 509957015 0.000000e+00 3661.0
3 TraesCS2A01G400400 chr2D 92.910 677 27 12 974 1638 509953601 509954268 0.000000e+00 965.0
4 TraesCS2A01G400400 chr2D 86.377 668 56 17 1 659 509951098 509951739 0.000000e+00 697.0
5 TraesCS2A01G400400 chr2D 93.333 195 6 2 1680 1871 509954414 509954604 9.600000e-72 281.0
6 TraesCS2A01G400400 chr2D 86.667 165 21 1 3800 3963 336511295 336511131 1.000000e-41 182.0
7 TraesCS2A01G400400 chr2D 87.037 162 20 1 3800 3960 571079119 571078958 1.000000e-41 182.0
8 TraesCS2A01G400400 chr2B 94.450 937 39 6 2207 3134 599666595 599667527 0.000000e+00 1430.0
9 TraesCS2A01G400400 chr2B 91.139 948 64 10 991 1935 599665665 599666595 0.000000e+00 1267.0
10 TraesCS2A01G400400 chr2B 96.019 628 22 1 3180 3807 599667536 599668160 0.000000e+00 1018.0
11 TraesCS2A01G400400 chr2B 86.131 411 33 12 5 406 599664718 599665113 5.420000e-114 422.0
12 TraesCS2A01G400400 chr2B 91.837 294 18 4 1919 2209 164086332 164086622 5.460000e-109 405.0
13 TraesCS2A01G400400 chr2B 83.200 375 37 10 1 367 599624746 599625102 2.030000e-83 320.0
14 TraesCS2A01G400400 chr2B 96.875 128 4 0 779 906 599665405 599665532 9.870000e-52 215.0
15 TraesCS2A01G400400 chr2B 85.465 172 9 9 671 827 599663523 599663693 1.010000e-36 165.0
16 TraesCS2A01G400400 chr2B 97.727 44 1 0 363 406 599663333 599663376 4.860000e-10 76.8
17 TraesCS2A01G400400 chr5A 94.891 274 11 1 1937 2207 611640130 611639857 4.190000e-115 425.0
18 TraesCS2A01G400400 chr5A 93.333 285 16 1 1933 2214 379363626 379363342 7.010000e-113 418.0
19 TraesCS2A01G400400 chr7A 93.403 288 15 2 1924 2207 681096429 681096716 1.510000e-114 424.0
20 TraesCS2A01G400400 chr7A 100.000 29 0 0 4397 4425 39217470 39217498 2.000000e-03 54.7
21 TraesCS2A01G400400 chr3A 94.565 276 12 1 1937 2209 37506000 37506275 1.510000e-114 424.0
22 TraesCS2A01G400400 chr6B 93.950 281 14 1 1932 2209 518679772 518680052 5.420000e-114 422.0
23 TraesCS2A01G400400 chr6B 91.973 299 15 7 1935 2228 218975637 218975343 1.170000e-110 411.0
24 TraesCS2A01G400400 chr1A 93.571 280 14 2 1937 2212 436890198 436890477 9.070000e-112 414.0
25 TraesCS2A01G400400 chr5D 88.272 162 17 2 3800 3960 495547271 495547111 4.630000e-45 193.0
26 TraesCS2A01G400400 chr3D 87.425 167 20 1 3800 3965 549066952 549066786 1.660000e-44 191.0
27 TraesCS2A01G400400 chr3D 87.059 170 21 1 3799 3967 552772517 552772348 1.660000e-44 191.0
28 TraesCS2A01G400400 chr3D 85.799 169 21 3 3793 3960 87925995 87926161 4.660000e-40 176.0
29 TraesCS2A01G400400 chr7B 87.273 165 20 1 3800 3963 102234317 102234481 2.150000e-43 187.0
30 TraesCS2A01G400400 chr4D 86.550 171 21 2 3792 3960 117421182 117421352 2.150000e-43 187.0


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 TraesCS2A01G400400 chr2A 653685219 653689749 4530 False 8368.000000 8368 100.000000 1 4531 1 chr2A.!!$F1 4530
1 TraesCS2A01G400400 chr2D 509951098 509957015 5917 False 1401.000000 3661 91.913500 1 4531 4 chr2D.!!$F1 4530
2 TraesCS2A01G400400 chr2B 599663333 599668160 4827 False 656.257143 1430 92.543714 5 3807 7 chr2B.!!$F3 3802

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
39 1423 0.114364 AAACCTGCCACCCCCTTTAG 59.886 55.0 0.00 0.0 0.00 1.85 F
1217 4201 0.750546 AGGCTCACGAGGTACGCATA 60.751 55.0 0.00 0.0 46.94 3.14 F
1955 5062 0.332632 AGGGCATGTACAATGGTGCT 59.667 50.0 16.47 0.0 37.70 4.40 F
2287 5394 0.919710 TGGAGGAGAGGACGAGATCA 59.080 55.0 0.00 0.0 0.00 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1608 4604 0.321671 TGGAGACGGCTTCTTTGAGG 59.678 55.000 0.0 0.0 33.22 3.86 R
2622 5752 0.528017 GTCTGTCGCCATCAGTCTCA 59.472 55.000 0.0 0.0 34.86 3.27 R
3364 6511 2.397044 AATTTTGGGCTCCAAGTGGA 57.603 45.000 0.0 0.0 44.84 4.02 R
3967 7115 1.472904 GGAGAAACTTACTAGGCCGCC 60.473 57.143 0.0 0.0 0.00 6.13 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
30 1414 0.179018 AGGTGAGACAAACCTGCCAC 60.179 55.000 0.00 0.00 46.51 5.01
39 1423 0.114364 AAACCTGCCACCCCCTTTAG 59.886 55.000 0.00 0.00 0.00 1.85
40 1424 1.071909 AACCTGCCACCCCCTTTAGT 61.072 55.000 0.00 0.00 0.00 2.24
49 1433 4.216708 CCACCCCCTTTAGTAGTAGAGAG 58.783 52.174 0.00 0.00 0.00 3.20
50 1434 4.325974 CCACCCCCTTTAGTAGTAGAGAGT 60.326 50.000 0.00 0.00 0.00 3.24
51 1435 5.103771 CCACCCCCTTTAGTAGTAGAGAGTA 60.104 48.000 0.00 0.00 0.00 2.59
52 1436 6.411789 CCACCCCCTTTAGTAGTAGAGAGTAT 60.412 46.154 0.00 0.00 0.00 2.12
53 1437 6.716173 CACCCCCTTTAGTAGTAGAGAGTATC 59.284 46.154 0.00 0.00 0.00 2.24
114 1500 9.025041 TCCTTTTCTTCTTTCTCTTTCACTTTT 57.975 29.630 0.00 0.00 0.00 2.27
215 1606 8.608844 TTCACCTTATTTGTGTTTGTTTTTGT 57.391 26.923 0.00 0.00 35.25 2.83
217 1608 7.872993 TCACCTTATTTGTGTTTGTTTTTGTCA 59.127 29.630 0.00 0.00 35.25 3.58
274 1665 7.981225 GCACATGAATAATTTTTGTGGGATACT 59.019 33.333 0.00 0.00 38.44 2.12
275 1666 9.520204 CACATGAATAATTTTTGTGGGATACTC 57.480 33.333 0.00 0.00 35.25 2.59
276 1667 9.479549 ACATGAATAATTTTTGTGGGATACTCT 57.520 29.630 0.00 0.00 0.00 3.24
440 1831 7.760794 TGAATATTATTTTGCAGCACTTGAAGG 59.239 33.333 0.00 0.00 0.00 3.46
441 1832 4.935352 TTATTTTGCAGCACTTGAAGGT 57.065 36.364 0.00 0.00 0.00 3.50
554 1950 6.290605 AGGTGAAACATTATTTTTGCAGCTT 58.709 32.000 0.00 0.00 39.98 3.74
560 1956 6.543430 ACATTATTTTTGCAGCTTATGGGA 57.457 33.333 0.00 0.00 0.00 4.37
571 1967 6.630071 TGCAGCTTATGGGAATTTTTCTTAC 58.370 36.000 0.00 0.00 0.00 2.34
644 2041 8.974060 ACTGAAAAGGAAAATGTAGACTTACA 57.026 30.769 0.00 0.00 43.55 2.41
645 2042 9.057089 ACTGAAAAGGAAAATGTAGACTTACAG 57.943 33.333 0.00 0.00 42.72 2.74
646 2043 8.974060 TGAAAAGGAAAATGTAGACTTACAGT 57.026 30.769 0.00 0.00 42.72 3.55
651 2048 9.490379 AAGGAAAATGTAGACTTACAGTAACTG 57.510 33.333 0.00 0.00 42.72 3.16
652 2049 7.603024 AGGAAAATGTAGACTTACAGTAACTGC 59.397 37.037 0.00 0.00 42.72 4.40
653 2050 7.386848 GGAAAATGTAGACTTACAGTAACTGCA 59.613 37.037 4.78 4.78 42.72 4.41
654 2051 8.671384 AAAATGTAGACTTACAGTAACTGCAA 57.329 30.769 6.01 0.00 42.72 4.08
655 2052 8.848474 AAATGTAGACTTACAGTAACTGCAAT 57.152 30.769 6.01 0.00 42.72 3.56
656 2053 9.938280 AAATGTAGACTTACAGTAACTGCAATA 57.062 29.630 6.01 0.00 42.72 1.90
664 2061 9.338622 ACTTACAGTAACTGCAATATTATTCCC 57.661 33.333 0.00 0.00 34.37 3.97
665 2062 9.561069 CTTACAGTAACTGCAATATTATTCCCT 57.439 33.333 0.00 0.00 34.37 4.20
668 2065 9.914834 ACAGTAACTGCAATATTATTCCCTAAA 57.085 29.630 0.00 0.00 34.37 1.85
711 2108 2.037687 CCCATGGCAGCCCAAAGA 59.962 61.111 9.64 0.00 46.14 2.52
741 2138 3.796504 GCATGAATGAACGGCCCAATAAG 60.797 47.826 0.00 0.00 0.00 1.73
757 2154 7.147776 GGCCCAATAAGAAAGAGTACAGTAGTA 60.148 40.741 0.00 0.00 0.00 1.82
758 2155 7.921745 GCCCAATAAGAAAGAGTACAGTAGTAG 59.078 40.741 0.00 0.00 0.00 2.57
759 2156 8.968969 CCCAATAAGAAAGAGTACAGTAGTAGT 58.031 37.037 0.00 0.00 36.60 2.73
807 3717 0.884704 CACCAACCCCAACGAGTCAG 60.885 60.000 0.00 0.00 0.00 3.51
895 3809 1.742411 GCCCGCTGCTCTTTACATACA 60.742 52.381 0.00 0.00 36.87 2.29
906 3820 5.581085 GCTCTTTACATACAGATTGACCGTT 59.419 40.000 0.00 0.00 0.00 4.44
907 3821 6.092259 GCTCTTTACATACAGATTGACCGTTT 59.908 38.462 0.00 0.00 0.00 3.60
908 3822 7.591006 TCTTTACATACAGATTGACCGTTTC 57.409 36.000 0.00 0.00 0.00 2.78
911 3851 8.470040 TTTACATACAGATTGACCGTTTCTAC 57.530 34.615 0.00 0.00 0.00 2.59
918 3858 2.723124 TGACCGTTTCTACCCGTTAC 57.277 50.000 0.00 0.00 0.00 2.50
927 3867 3.429080 TACCCGTTACCCGATGCGC 62.429 63.158 0.00 0.00 39.56 6.09
944 3886 4.326255 CCTGGCTGGCTTTCGATT 57.674 55.556 2.00 0.00 0.00 3.34
971 3913 3.069016 ACACGAGACATGTAGAAACCACA 59.931 43.478 0.00 0.00 0.00 4.17
972 3914 4.245660 CACGAGACATGTAGAAACCACAT 58.754 43.478 0.00 0.00 37.09 3.21
988 3972 2.151202 CACATGCGTTTCCAACCTAGT 58.849 47.619 0.00 0.00 0.00 2.57
993 3977 4.546829 TGCGTTTCCAACCTAGTTAGAT 57.453 40.909 0.00 0.00 0.00 1.98
995 3979 5.657474 TGCGTTTCCAACCTAGTTAGATAG 58.343 41.667 0.00 0.00 0.00 2.08
996 3980 5.419788 TGCGTTTCCAACCTAGTTAGATAGA 59.580 40.000 0.00 0.00 0.00 1.98
997 3981 6.071221 TGCGTTTCCAACCTAGTTAGATAGAA 60.071 38.462 0.00 0.00 0.00 2.10
998 3982 6.476053 GCGTTTCCAACCTAGTTAGATAGAAG 59.524 42.308 0.00 0.00 0.00 2.85
1177 4161 4.796231 CGGACGCCTCCTTGGACG 62.796 72.222 0.07 0.00 39.83 4.79
1217 4201 0.750546 AGGCTCACGAGGTACGCATA 60.751 55.000 0.00 0.00 46.94 3.14
1272 4256 2.479560 GCGAATTACATGGGCCAGTTTC 60.480 50.000 13.78 10.57 0.00 2.78
1278 4262 3.287867 ACATGGGCCAGTTTCTCATAG 57.712 47.619 13.78 0.00 0.00 2.23
1290 4274 2.698855 TCTCATAGAGGCTTTGGTGC 57.301 50.000 0.00 0.00 0.00 5.01
1291 4275 1.134699 TCTCATAGAGGCTTTGGTGCG 60.135 52.381 0.00 0.00 0.00 5.34
1292 4276 0.901827 TCATAGAGGCTTTGGTGCGA 59.098 50.000 0.00 0.00 0.00 5.10
1293 4277 1.134699 TCATAGAGGCTTTGGTGCGAG 60.135 52.381 0.00 0.00 0.00 5.03
1294 4278 1.134699 CATAGAGGCTTTGGTGCGAGA 60.135 52.381 0.00 0.00 0.00 4.04
1297 4281 1.168714 GAGGCTTTGGTGCGAGATTT 58.831 50.000 0.00 0.00 0.00 2.17
1638 4634 1.033746 CCGTCTCCACCGTAAGCCTA 61.034 60.000 0.00 0.00 0.00 3.93
1644 4640 1.822990 TCCACCGTAAGCCTAGTCTTG 59.177 52.381 0.00 0.00 0.00 3.02
1645 4641 1.549170 CCACCGTAAGCCTAGTCTTGT 59.451 52.381 0.00 0.00 0.00 3.16
1646 4642 2.607187 CACCGTAAGCCTAGTCTTGTG 58.393 52.381 0.00 0.00 0.00 3.33
1666 4773 3.486108 GTGACGCTCTGGATTATTACACG 59.514 47.826 0.00 0.00 0.00 4.49
1699 4806 4.575885 TGTTCAGGTTATGTTGCTACCTC 58.424 43.478 0.00 0.00 40.24 3.85
1738 4845 3.243035 TGCAGATGGTGTTTGAACTTTCG 60.243 43.478 0.00 0.00 0.00 3.46
1835 4942 0.676736 CATCTCCTTCCCGCTCTACC 59.323 60.000 0.00 0.00 0.00 3.18
1877 4984 0.736636 ATGCATGCAGGTGATCAACG 59.263 50.000 26.69 1.54 0.00 4.10
1895 5002 1.443194 GCGAACGCTAAGTCGGTCA 60.443 57.895 11.97 0.00 45.74 4.02
1935 5042 1.878088 CATGCATGCACTAGGGTCATC 59.122 52.381 25.37 0.00 0.00 2.92
1937 5044 1.134310 TGCATGCACTAGGGTCATCAG 60.134 52.381 18.46 0.00 0.00 2.90
1938 5045 1.813092 GCATGCACTAGGGTCATCAGG 60.813 57.143 14.21 0.00 0.00 3.86
1939 5046 1.135094 ATGCACTAGGGTCATCAGGG 58.865 55.000 0.00 0.00 0.00 4.45
1940 5047 1.147153 GCACTAGGGTCATCAGGGC 59.853 63.158 0.00 0.00 0.00 5.19
1941 5048 1.626356 GCACTAGGGTCATCAGGGCA 61.626 60.000 0.00 0.00 38.61 5.36
1943 5050 1.135094 ACTAGGGTCATCAGGGCATG 58.865 55.000 0.00 0.00 0.00 4.06
1944 5051 1.135094 CTAGGGTCATCAGGGCATGT 58.865 55.000 0.00 0.00 0.00 3.21
1945 5052 2.329267 CTAGGGTCATCAGGGCATGTA 58.671 52.381 0.00 0.00 0.00 2.29
1946 5053 0.839946 AGGGTCATCAGGGCATGTAC 59.160 55.000 0.00 0.00 0.00 2.90
1948 5055 1.064758 GGGTCATCAGGGCATGTACAA 60.065 52.381 0.00 0.00 0.00 2.41
1950 5057 2.620115 GGTCATCAGGGCATGTACAATG 59.380 50.000 0.00 0.00 0.00 2.82
1951 5058 2.620115 GTCATCAGGGCATGTACAATGG 59.380 50.000 0.00 0.00 0.00 3.16
1952 5059 2.241941 TCATCAGGGCATGTACAATGGT 59.758 45.455 0.00 0.00 0.00 3.55
1953 5060 2.127271 TCAGGGCATGTACAATGGTG 57.873 50.000 0.00 0.00 0.00 4.17
1954 5061 0.457035 CAGGGCATGTACAATGGTGC 59.543 55.000 10.12 10.12 36.88 5.01
1955 5062 0.332632 AGGGCATGTACAATGGTGCT 59.667 50.000 16.47 0.00 37.70 4.40
1956 5063 1.563879 AGGGCATGTACAATGGTGCTA 59.436 47.619 16.47 0.00 37.70 3.49
1957 5064 2.175499 AGGGCATGTACAATGGTGCTAT 59.825 45.455 16.47 5.35 37.70 2.97
1958 5065 2.554032 GGGCATGTACAATGGTGCTATC 59.446 50.000 16.47 3.12 37.70 2.08
1959 5066 3.480470 GGCATGTACAATGGTGCTATCT 58.520 45.455 16.47 0.00 37.70 1.98
1960 5067 3.885297 GGCATGTACAATGGTGCTATCTT 59.115 43.478 16.47 0.00 37.70 2.40
1961 5068 5.063204 GGCATGTACAATGGTGCTATCTTA 58.937 41.667 16.47 0.00 37.70 2.10
1962 5069 5.180117 GGCATGTACAATGGTGCTATCTTAG 59.820 44.000 16.47 0.00 37.70 2.18
1963 5070 5.991606 GCATGTACAATGGTGCTATCTTAGA 59.008 40.000 11.12 0.00 34.85 2.10
1964 5071 6.483307 GCATGTACAATGGTGCTATCTTAGAA 59.517 38.462 11.12 0.00 34.85 2.10
1965 5072 7.307632 GCATGTACAATGGTGCTATCTTAGAAG 60.308 40.741 11.12 0.00 34.85 2.85
1966 5073 7.182817 TGTACAATGGTGCTATCTTAGAAGT 57.817 36.000 0.00 0.00 0.00 3.01
1967 5074 7.041721 TGTACAATGGTGCTATCTTAGAAGTG 58.958 38.462 0.00 0.00 0.00 3.16
1968 5075 4.878397 ACAATGGTGCTATCTTAGAAGTGC 59.122 41.667 0.00 0.00 0.00 4.40
1969 5076 3.543680 TGGTGCTATCTTAGAAGTGCC 57.456 47.619 0.00 0.00 0.00 5.01
1970 5077 2.837591 TGGTGCTATCTTAGAAGTGCCA 59.162 45.455 0.00 0.00 0.00 4.92
1971 5078 3.198872 GGTGCTATCTTAGAAGTGCCAC 58.801 50.000 0.00 0.00 0.00 5.01
1972 5079 2.860735 GTGCTATCTTAGAAGTGCCACG 59.139 50.000 0.00 0.00 0.00 4.94
1973 5080 2.496070 TGCTATCTTAGAAGTGCCACGT 59.504 45.455 0.00 0.00 0.00 4.49
1974 5081 3.697542 TGCTATCTTAGAAGTGCCACGTA 59.302 43.478 0.00 0.00 0.00 3.57
1975 5082 4.158949 TGCTATCTTAGAAGTGCCACGTAA 59.841 41.667 0.00 0.00 0.00 3.18
1977 5084 5.450137 GCTATCTTAGAAGTGCCACGTAAGA 60.450 44.000 15.24 15.24 43.62 2.10
1978 5085 5.599999 ATCTTAGAAGTGCCACGTAAGAT 57.400 39.130 17.39 17.39 43.62 2.40
1979 5086 6.710597 ATCTTAGAAGTGCCACGTAAGATA 57.289 37.500 19.79 4.51 38.22 1.98
1980 5087 6.519679 TCTTAGAAGTGCCACGTAAGATAA 57.480 37.500 11.15 0.00 43.62 1.75
1981 5088 6.927416 TCTTAGAAGTGCCACGTAAGATAAA 58.073 36.000 11.15 0.00 43.62 1.40
1982 5089 7.553334 TCTTAGAAGTGCCACGTAAGATAAAT 58.447 34.615 11.15 0.00 43.62 1.40
1983 5090 7.491372 TCTTAGAAGTGCCACGTAAGATAAATG 59.509 37.037 11.15 0.00 43.62 2.32
1984 5091 5.730550 AGAAGTGCCACGTAAGATAAATGA 58.269 37.500 0.00 0.00 43.62 2.57
1985 5092 6.349300 AGAAGTGCCACGTAAGATAAATGAT 58.651 36.000 0.00 0.00 43.62 2.45
1986 5093 5.991328 AGTGCCACGTAAGATAAATGATG 57.009 39.130 0.00 0.00 43.62 3.07
1987 5094 5.670485 AGTGCCACGTAAGATAAATGATGA 58.330 37.500 0.00 0.00 43.62 2.92
1988 5095 5.755375 AGTGCCACGTAAGATAAATGATGAG 59.245 40.000 0.00 0.00 43.62 2.90
1989 5096 5.753438 GTGCCACGTAAGATAAATGATGAGA 59.247 40.000 0.00 0.00 43.62 3.27
1990 5097 6.425114 GTGCCACGTAAGATAAATGATGAGAT 59.575 38.462 0.00 0.00 43.62 2.75
1991 5098 6.424812 TGCCACGTAAGATAAATGATGAGATG 59.575 38.462 0.00 0.00 43.62 2.90
1992 5099 6.128445 GCCACGTAAGATAAATGATGAGATGG 60.128 42.308 0.00 0.00 43.62 3.51
1993 5100 7.154656 CCACGTAAGATAAATGATGAGATGGA 58.845 38.462 0.00 0.00 43.62 3.41
1994 5101 7.330454 CCACGTAAGATAAATGATGAGATGGAG 59.670 40.741 0.00 0.00 43.62 3.86
1995 5102 7.330454 CACGTAAGATAAATGATGAGATGGAGG 59.670 40.741 0.00 0.00 43.62 4.30
1996 5103 7.233553 ACGTAAGATAAATGATGAGATGGAGGA 59.766 37.037 0.00 0.00 43.62 3.71
1997 5104 7.758980 CGTAAGATAAATGATGAGATGGAGGAG 59.241 40.741 0.00 0.00 43.02 3.69
1998 5105 7.868792 AAGATAAATGATGAGATGGAGGAGA 57.131 36.000 0.00 0.00 0.00 3.71
1999 5106 7.484993 AGATAAATGATGAGATGGAGGAGAG 57.515 40.000 0.00 0.00 0.00 3.20
2000 5107 7.247500 AGATAAATGATGAGATGGAGGAGAGA 58.753 38.462 0.00 0.00 0.00 3.10
2001 5108 5.811796 AAATGATGAGATGGAGGAGAGAG 57.188 43.478 0.00 0.00 0.00 3.20
2002 5109 4.745484 ATGATGAGATGGAGGAGAGAGA 57.255 45.455 0.00 0.00 0.00 3.10
2003 5110 4.533001 TGATGAGATGGAGGAGAGAGAA 57.467 45.455 0.00 0.00 0.00 2.87
2004 5111 4.214310 TGATGAGATGGAGGAGAGAGAAC 58.786 47.826 0.00 0.00 0.00 3.01
2005 5112 4.079269 TGATGAGATGGAGGAGAGAGAACT 60.079 45.833 0.00 0.00 0.00 3.01
2006 5113 3.897239 TGAGATGGAGGAGAGAGAACTC 58.103 50.000 0.00 0.00 42.90 3.01
2007 5114 3.268072 TGAGATGGAGGAGAGAGAACTCA 59.732 47.826 4.64 0.00 44.79 3.41
2008 5115 4.079269 TGAGATGGAGGAGAGAGAACTCAT 60.079 45.833 4.64 0.00 44.79 2.90
2009 5116 5.133491 TGAGATGGAGGAGAGAGAACTCATA 59.867 44.000 4.64 0.00 44.79 2.15
2010 5117 6.024563 AGATGGAGGAGAGAGAACTCATAA 57.975 41.667 4.64 0.00 44.79 1.90
2011 5118 6.070656 AGATGGAGGAGAGAGAACTCATAAG 58.929 44.000 4.64 0.00 44.79 1.73
2012 5119 5.458451 TGGAGGAGAGAGAACTCATAAGA 57.542 43.478 4.64 0.00 44.79 2.10
2013 5120 5.832221 TGGAGGAGAGAGAACTCATAAGAA 58.168 41.667 4.64 0.00 44.79 2.52
2014 5121 6.256819 TGGAGGAGAGAGAACTCATAAGAAA 58.743 40.000 4.64 0.00 44.79 2.52
2015 5122 6.726299 TGGAGGAGAGAGAACTCATAAGAAAA 59.274 38.462 4.64 0.00 44.79 2.29
2016 5123 7.093552 TGGAGGAGAGAGAACTCATAAGAAAAG 60.094 40.741 4.64 0.00 44.79 2.27
2017 5124 7.123547 GGAGGAGAGAGAACTCATAAGAAAAGA 59.876 40.741 4.64 0.00 44.79 2.52
2018 5125 8.608185 AGGAGAGAGAACTCATAAGAAAAGAT 57.392 34.615 4.64 0.00 44.79 2.40
2019 5126 9.045745 AGGAGAGAGAACTCATAAGAAAAGATT 57.954 33.333 4.64 0.00 44.79 2.40
2020 5127 9.665719 GGAGAGAGAACTCATAAGAAAAGATTT 57.334 33.333 4.64 0.00 44.79 2.17
2072 5179 5.911752 GAGGATCTCTTAGCACAATTCTCA 58.088 41.667 0.00 0.00 0.00 3.27
2073 5180 5.669477 AGGATCTCTTAGCACAATTCTCAC 58.331 41.667 0.00 0.00 0.00 3.51
2074 5181 4.813697 GGATCTCTTAGCACAATTCTCACC 59.186 45.833 0.00 0.00 0.00 4.02
2075 5182 4.890158 TCTCTTAGCACAATTCTCACCA 57.110 40.909 0.00 0.00 0.00 4.17
2076 5183 5.426689 TCTCTTAGCACAATTCTCACCAT 57.573 39.130 0.00 0.00 0.00 3.55
2077 5184 5.181009 TCTCTTAGCACAATTCTCACCATG 58.819 41.667 0.00 0.00 0.00 3.66
2078 5185 4.910195 TCTTAGCACAATTCTCACCATGT 58.090 39.130 0.00 0.00 0.00 3.21
2079 5186 5.316167 TCTTAGCACAATTCTCACCATGTT 58.684 37.500 0.00 0.00 0.00 2.71
2080 5187 5.769662 TCTTAGCACAATTCTCACCATGTTT 59.230 36.000 0.00 0.00 0.00 2.83
2081 5188 4.942761 AGCACAATTCTCACCATGTTTT 57.057 36.364 0.00 0.00 0.00 2.43
2082 5189 7.446931 TCTTAGCACAATTCTCACCATGTTTTA 59.553 33.333 0.00 0.00 0.00 1.52
2083 5190 6.403866 AGCACAATTCTCACCATGTTTTAA 57.596 33.333 0.00 0.00 0.00 1.52
2084 5191 6.449698 AGCACAATTCTCACCATGTTTTAAG 58.550 36.000 0.00 0.00 0.00 1.85
2085 5192 5.634859 GCACAATTCTCACCATGTTTTAAGG 59.365 40.000 0.00 0.00 0.00 2.69
2086 5193 6.516527 GCACAATTCTCACCATGTTTTAAGGA 60.517 38.462 0.00 0.00 0.00 3.36
2087 5194 7.432869 CACAATTCTCACCATGTTTTAAGGAA 58.567 34.615 0.00 0.00 0.00 3.36
2088 5195 8.090214 CACAATTCTCACCATGTTTTAAGGAAT 58.910 33.333 0.00 0.00 0.00 3.01
2089 5196 8.650490 ACAATTCTCACCATGTTTTAAGGAATT 58.350 29.630 0.00 0.00 33.15 2.17
2092 5199 8.934023 TTCTCACCATGTTTTAAGGAATTACT 57.066 30.769 0.00 0.00 0.00 2.24
2094 5201 9.667107 TCTCACCATGTTTTAAGGAATTACTAG 57.333 33.333 0.00 0.00 0.00 2.57
2095 5202 9.449719 CTCACCATGTTTTAAGGAATTACTAGT 57.550 33.333 0.00 0.00 0.00 2.57
2096 5203 9.802039 TCACCATGTTTTAAGGAATTACTAGTT 57.198 29.630 0.00 0.00 0.00 2.24
2127 5234 9.965902 AAGATAAGGCTAAGATATAACCCATTG 57.034 33.333 0.00 0.00 0.00 2.82
2128 5235 9.117223 AGATAAGGCTAAGATATAACCCATTGT 57.883 33.333 0.00 0.00 0.00 2.71
2132 5239 8.919777 AGGCTAAGATATAACCCATTGTAAAC 57.080 34.615 0.00 0.00 0.00 2.01
2133 5240 8.499406 AGGCTAAGATATAACCCATTGTAAACA 58.501 33.333 0.00 0.00 0.00 2.83
2134 5241 9.297037 GGCTAAGATATAACCCATTGTAAACAT 57.703 33.333 0.00 0.00 0.00 2.71
2162 5269 7.585286 TTTTTGTCATCTCTAAATTGCATGC 57.415 32.000 11.82 11.82 0.00 4.06
2163 5270 5.900865 TTGTCATCTCTAAATTGCATGCA 57.099 34.783 18.46 18.46 0.00 3.96
2164 5271 5.900865 TGTCATCTCTAAATTGCATGCAA 57.099 34.783 33.57 33.57 40.47 4.08
2165 5272 5.886992 TGTCATCTCTAAATTGCATGCAAG 58.113 37.500 34.15 22.53 39.47 4.01
2166 5273 5.648960 TGTCATCTCTAAATTGCATGCAAGA 59.351 36.000 34.15 25.56 39.47 3.02
2167 5274 5.970023 GTCATCTCTAAATTGCATGCAAGAC 59.030 40.000 34.15 26.57 39.47 3.01
2168 5275 5.884232 TCATCTCTAAATTGCATGCAAGACT 59.116 36.000 34.15 23.32 39.47 3.24
2169 5276 6.376299 TCATCTCTAAATTGCATGCAAGACTT 59.624 34.615 34.15 27.05 39.47 3.01
2170 5277 7.553760 TCATCTCTAAATTGCATGCAAGACTTA 59.446 33.333 34.15 26.78 39.47 2.24
2171 5278 7.686438 TCTCTAAATTGCATGCAAGACTTAA 57.314 32.000 34.15 18.32 39.47 1.85
2172 5279 7.755591 TCTCTAAATTGCATGCAAGACTTAAG 58.244 34.615 34.15 24.96 39.47 1.85
2173 5280 7.607607 TCTCTAAATTGCATGCAAGACTTAAGA 59.392 33.333 34.15 26.42 39.47 2.10
2174 5281 8.284945 TCTAAATTGCATGCAAGACTTAAGAT 57.715 30.769 34.15 14.63 39.47 2.40
2175 5282 9.394767 TCTAAATTGCATGCAAGACTTAAGATA 57.605 29.630 34.15 14.30 39.47 1.98
2177 5284 8.922058 AAATTGCATGCAAGACTTAAGATAAG 57.078 30.769 34.15 0.00 39.47 1.73
2178 5285 7.870509 ATTGCATGCAAGACTTAAGATAAGA 57.129 32.000 34.15 9.52 39.47 2.10
2179 5286 6.668541 TGCATGCAAGACTTAAGATAAGAC 57.331 37.500 20.30 0.00 0.00 3.01
2180 5287 6.409704 TGCATGCAAGACTTAAGATAAGACT 58.590 36.000 20.30 0.83 0.00 3.24
2181 5288 6.314648 TGCATGCAAGACTTAAGATAAGACTG 59.685 38.462 20.30 0.74 0.00 3.51
2182 5289 6.314896 GCATGCAAGACTTAAGATAAGACTGT 59.685 38.462 14.21 0.00 0.00 3.55
2183 5290 7.465245 GCATGCAAGACTTAAGATAAGACTGTC 60.465 40.741 14.21 0.00 0.00 3.51
2184 5291 7.233389 TGCAAGACTTAAGATAAGACTGTCT 57.767 36.000 10.09 4.06 35.20 3.41
2185 5292 7.671302 TGCAAGACTTAAGATAAGACTGTCTT 58.329 34.615 24.80 24.80 41.90 3.01
2186 5293 8.803235 TGCAAGACTTAAGATAAGACTGTCTTA 58.197 33.333 27.13 27.13 42.49 2.10
2202 5309 9.770097 AGACTGTCTTATCAACCATTGTATATG 57.230 33.333 4.06 0.00 0.00 1.78
2203 5310 8.383318 ACTGTCTTATCAACCATTGTATATGC 57.617 34.615 0.00 0.00 0.00 3.14
2204 5311 7.445402 ACTGTCTTATCAACCATTGTATATGCC 59.555 37.037 0.00 0.00 0.00 4.40
2205 5312 6.714810 TGTCTTATCAACCATTGTATATGCCC 59.285 38.462 0.00 0.00 0.00 5.36
2206 5313 6.942576 GTCTTATCAACCATTGTATATGCCCT 59.057 38.462 0.00 0.00 0.00 5.19
2207 5314 7.448469 GTCTTATCAACCATTGTATATGCCCTT 59.552 37.037 0.00 0.00 0.00 3.95
2208 5315 8.664992 TCTTATCAACCATTGTATATGCCCTTA 58.335 33.333 0.00 0.00 0.00 2.69
2216 5323 7.071950 ACCATTGTATATGCCCTTAACTGACTA 59.928 37.037 0.00 0.00 0.00 2.59
2221 5328 7.509318 TGTATATGCCCTTAACTGACTATGAGT 59.491 37.037 0.00 0.00 0.00 3.41
2287 5394 0.919710 TGGAGGAGAGGACGAGATCA 59.080 55.000 0.00 0.00 0.00 2.92
2347 5454 1.130186 GACTTCCTGGACTACGTCGTC 59.870 57.143 11.56 11.56 32.65 4.20
2534 5664 4.441792 TGTATGATCTTTACGTGCATGCT 58.558 39.130 20.33 0.40 0.00 3.79
2539 5669 1.081892 CTTTACGTGCATGCTGAGCT 58.918 50.000 20.33 0.00 0.00 4.09
2626 5756 3.695606 GTGAGGCAGGCGGTGAGA 61.696 66.667 0.00 0.00 0.00 3.27
2754 5891 2.671130 TGCTGTCATAATCAGACGCA 57.329 45.000 0.00 0.00 40.44 5.24
2764 5901 1.963172 ATCAGACGCACATGCATCAT 58.037 45.000 2.46 0.00 42.21 2.45
2765 5902 1.292992 TCAGACGCACATGCATCATC 58.707 50.000 2.46 0.00 42.21 2.92
2768 5905 1.938577 AGACGCACATGCATCATCTTC 59.061 47.619 2.46 0.00 42.21 2.87
2857 5994 7.907389 TGAAAGATGTACAGTTCAGAGGTAAT 58.093 34.615 12.84 0.00 0.00 1.89
2934 6073 2.102420 TCCTGCGAAAACAGAAGAGACA 59.898 45.455 0.00 0.00 40.25 3.41
2936 6075 3.126831 CTGCGAAAACAGAAGAGACAGT 58.873 45.455 0.00 0.00 40.25 3.55
2938 6077 4.299155 TGCGAAAACAGAAGAGACAGTAG 58.701 43.478 0.00 0.00 0.00 2.57
2948 6090 7.798071 ACAGAAGAGACAGTAGCTAGTAGTAT 58.202 38.462 0.00 0.00 0.00 2.12
2977 6120 1.742831 TGACAATTATTGGCGACAGGC 59.257 47.619 9.88 0.00 43.38 4.85
3079 6222 4.803452 TCACCTTCAATCCTTCAAGGTTT 58.197 39.130 2.50 0.00 46.48 3.27
3135 6278 3.152341 CAAGATCAAACAGCTCAACCCT 58.848 45.455 0.00 0.00 0.00 4.34
3143 6290 3.199880 ACAGCTCAACCCTATGTATGC 57.800 47.619 0.00 0.00 0.00 3.14
3364 6511 6.351286 GGTGCCTCCATTGTTTTCTAATGAAT 60.351 38.462 0.00 0.00 37.65 2.57
3515 6662 5.429762 TCCTGATGGTTACCTCATTCAGATT 59.570 40.000 18.48 0.00 34.23 2.40
3641 6788 6.787085 ACAGTTGTGCAGAAGTATTTCTAC 57.213 37.500 3.23 0.00 41.71 2.59
3649 6796 7.038659 GTGCAGAAGTATTTCTACTCTGTCAT 58.961 38.462 0.00 0.00 41.71 3.06
3697 6844 8.266392 ACATCTTCAGAGATTTTCAAGCTTAG 57.734 34.615 0.00 0.00 40.67 2.18
3776 6923 4.410743 GCTTTGCTGAGGTGGCGC 62.411 66.667 0.00 0.00 0.00 6.53
3967 7115 8.248945 TCTAGAAACGAAGGGAGTACAAAATAG 58.751 37.037 0.00 0.00 0.00 1.73
3993 7141 3.363627 CCTAGTAAGTTTCTCCCCTCGT 58.636 50.000 0.00 0.00 0.00 4.18
4034 7182 7.113658 TGAAATCTATAAACTCCGAAGCTCT 57.886 36.000 0.00 0.00 0.00 4.09
4094 7242 6.685403 TCTTCGTTTGCTAAAAGAAAGTTTCG 59.315 34.615 9.91 0.00 38.16 3.46
4163 7311 9.836864 AGCAAAAGGAAACAAGAAATTTAGATT 57.163 25.926 0.00 0.00 0.00 2.40
4290 7442 5.904362 AAGAGATTCAATTAGCAACACCC 57.096 39.130 0.00 0.00 0.00 4.61
4321 7473 1.208052 CATCCCATGGAGAACACGAGT 59.792 52.381 15.22 0.00 34.05 4.18
4327 7479 0.468226 TGGAGAACACGAGTGCCTTT 59.532 50.000 2.76 0.00 0.00 3.11
4342 7494 7.724061 ACGAGTGCCTTTAAATATTTGGGATAT 59.276 33.333 11.05 0.00 0.00 1.63
4407 7559 1.564348 AGCATCACGGACCCCTAAAAT 59.436 47.619 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 1414 7.093965 AGATACTCTCTACTACTAAAGGGGG 57.906 44.000 0.00 0.00 30.26 5.40
39 1423 8.685838 ATGGAAGACAAGATACTCTCTACTAC 57.314 38.462 0.00 0.00 32.41 2.73
40 1424 9.702253 AAATGGAAGACAAGATACTCTCTACTA 57.298 33.333 0.00 0.00 32.41 1.82
89 1475 9.295214 GAAAAGTGAAAGAGAAAGAAGAAAAGG 57.705 33.333 0.00 0.00 0.00 3.11
215 1606 9.844257 AAAAAGGTAAAAATGATTGGACATTGA 57.156 25.926 0.00 0.00 39.88 2.57
280 1671 9.545105 TGTTATAAAAGAAGTGTTCGACCTAAA 57.455 29.630 0.00 0.00 34.02 1.85
281 1672 9.715121 ATGTTATAAAAGAAGTGTTCGACCTAA 57.285 29.630 0.00 0.00 34.02 2.69
282 1673 9.146984 CATGTTATAAAAGAAGTGTTCGACCTA 57.853 33.333 0.00 0.00 34.02 3.08
283 1674 7.660208 ACATGTTATAAAAGAAGTGTTCGACCT 59.340 33.333 0.00 0.00 34.02 3.85
284 1675 7.744715 CACATGTTATAAAAGAAGTGTTCGACC 59.255 37.037 0.00 0.00 34.02 4.79
285 1676 7.744715 CCACATGTTATAAAAGAAGTGTTCGAC 59.255 37.037 0.00 0.00 28.55 4.20
406 1797 9.465985 TGCTGCAAAATAATATTCACATGTATG 57.534 29.630 0.00 0.00 0.00 2.39
418 1809 6.588719 ACCTTCAAGTGCTGCAAAATAATA 57.411 33.333 2.77 0.00 0.00 0.98
504 1900 6.419980 TTTGCACACATTTCAAGAAAAAGG 57.580 33.333 0.00 0.00 33.56 3.11
505 1901 9.640974 CTATTTTGCACACATTTCAAGAAAAAG 57.359 29.630 0.00 0.00 33.56 2.27
519 1915 8.532977 AATAATGTTTCACCTATTTTGCACAC 57.467 30.769 0.00 0.00 0.00 3.82
642 2039 9.914834 TTTAGGGAATAATATTGCAGTTACTGT 57.085 29.630 14.23 0.00 33.43 3.55
702 2099 2.262915 CGTCGCTCTCTTTGGGCT 59.737 61.111 0.00 0.00 0.00 5.19
711 2108 1.002366 GTTCATTCATGCGTCGCTCT 58.998 50.000 19.50 2.69 0.00 4.09
757 2154 4.322349 GCTGTGGTCTCTCTGAATTACACT 60.322 45.833 0.00 0.00 0.00 3.55
758 2155 3.929610 GCTGTGGTCTCTCTGAATTACAC 59.070 47.826 0.00 0.00 0.00 2.90
759 2156 3.578282 TGCTGTGGTCTCTCTGAATTACA 59.422 43.478 0.00 0.00 0.00 2.41
807 3717 0.108585 TGAGGAGAACAGTGGTTGCC 59.891 55.000 0.00 0.00 37.36 4.52
895 3809 1.897802 ACGGGTAGAAACGGTCAATCT 59.102 47.619 0.00 0.00 0.00 2.40
906 3820 0.461135 GCATCGGGTAACGGGTAGAA 59.539 55.000 0.00 0.00 44.45 2.10
907 3821 1.727511 CGCATCGGGTAACGGGTAGA 61.728 60.000 0.00 0.00 44.45 2.59
908 3822 1.299620 CGCATCGGGTAACGGGTAG 60.300 63.158 0.00 0.00 44.45 3.18
927 3867 0.677731 TCAATCGAAAGCCAGCCAGG 60.678 55.000 0.00 0.00 41.84 4.45
928 3868 1.332997 GATCAATCGAAAGCCAGCCAG 59.667 52.381 0.00 0.00 0.00 4.85
944 3886 5.161358 GTTTCTACATGTCTCGTGTGATCA 58.839 41.667 0.00 0.00 35.12 2.92
988 3972 3.845860 AGGCGTCCATCCTTCTATCTAA 58.154 45.455 0.00 0.00 0.00 2.10
993 3977 0.830648 CCAAGGCGTCCATCCTTCTA 59.169 55.000 0.00 0.00 41.73 2.10
995 3979 2.115291 GCCAAGGCGTCCATCCTTC 61.115 63.158 0.00 0.00 41.73 3.46
996 3980 2.044946 GCCAAGGCGTCCATCCTT 60.045 61.111 0.00 0.00 44.31 3.36
1046 4030 1.140589 CTGTACAGCAGGAGGAGCG 59.859 63.158 10.54 0.00 41.42 5.03
1177 4161 1.066587 CTCGGATGAAGCGAGGGAC 59.933 63.158 0.00 0.00 0.00 4.46
1272 4256 1.134699 TCGCACCAAAGCCTCTATGAG 60.135 52.381 0.00 0.00 0.00 2.90
1278 4262 1.168714 AAATCTCGCACCAAAGCCTC 58.831 50.000 0.00 0.00 0.00 4.70
1290 4274 3.985925 GGCCGTACCTATACAAAATCTCG 59.014 47.826 0.00 0.00 34.51 4.04
1291 4275 4.313282 GGGCCGTACCTATACAAAATCTC 58.687 47.826 0.00 0.00 39.10 2.75
1292 4276 3.243975 CGGGCCGTACCTATACAAAATCT 60.244 47.826 19.97 0.00 39.10 2.40
1293 4277 3.062042 CGGGCCGTACCTATACAAAATC 58.938 50.000 19.97 0.00 39.10 2.17
1294 4278 2.699846 TCGGGCCGTACCTATACAAAAT 59.300 45.455 27.32 0.00 39.10 1.82
1297 4281 1.888512 GATCGGGCCGTACCTATACAA 59.111 52.381 27.32 1.79 39.10 2.41
1608 4604 0.321671 TGGAGACGGCTTCTTTGAGG 59.678 55.000 0.00 0.00 33.22 3.86
1638 4634 1.261480 ATCCAGAGCGTCACAAGACT 58.739 50.000 0.00 0.00 42.73 3.24
1644 4640 3.486108 CGTGTAATAATCCAGAGCGTCAC 59.514 47.826 0.00 0.00 0.00 3.67
1645 4641 3.129813 ACGTGTAATAATCCAGAGCGTCA 59.870 43.478 0.00 0.00 0.00 4.35
1646 4642 3.486108 CACGTGTAATAATCCAGAGCGTC 59.514 47.826 7.58 0.00 0.00 5.19
1666 4773 5.938125 ACATAACCTGAACAGTGAATACCAC 59.062 40.000 0.00 0.00 46.03 4.16
1699 4806 0.787908 GCAATCAAACACCGTACGCG 60.788 55.000 10.49 3.53 37.95 6.01
1835 4942 1.134670 GTAGTAGGCTGTTCCTGGCAG 60.135 57.143 7.75 7.75 46.98 4.85
1877 4984 1.403972 CTGACCGACTTAGCGTTCGC 61.404 60.000 9.24 9.24 0.00 4.70
1883 4990 3.427773 CCTTCACTACTGACCGACTTAGC 60.428 52.174 0.00 0.00 0.00 3.09
1935 5042 0.457035 GCACCATTGTACATGCCCTG 59.543 55.000 7.77 0.00 31.71 4.45
1937 5044 2.051334 TAGCACCATTGTACATGCCC 57.949 50.000 14.08 0.00 38.92 5.36
1938 5045 3.480470 AGATAGCACCATTGTACATGCC 58.520 45.455 14.08 1.71 38.92 4.40
1939 5046 5.991606 TCTAAGATAGCACCATTGTACATGC 59.008 40.000 10.53 10.53 38.39 4.06
1940 5047 7.712639 ACTTCTAAGATAGCACCATTGTACATG 59.287 37.037 0.00 0.00 0.00 3.21
1941 5048 7.712639 CACTTCTAAGATAGCACCATTGTACAT 59.287 37.037 0.00 0.00 0.00 2.29
1943 5050 6.018669 GCACTTCTAAGATAGCACCATTGTAC 60.019 42.308 0.00 0.00 0.00 2.90
1944 5051 6.049149 GCACTTCTAAGATAGCACCATTGTA 58.951 40.000 0.00 0.00 0.00 2.41
1945 5052 4.878397 GCACTTCTAAGATAGCACCATTGT 59.122 41.667 0.00 0.00 0.00 2.71
1946 5053 4.274459 GGCACTTCTAAGATAGCACCATTG 59.726 45.833 0.00 0.00 0.00 2.82
1948 5055 3.455910 TGGCACTTCTAAGATAGCACCAT 59.544 43.478 0.00 0.00 0.00 3.55
1950 5057 3.198872 GTGGCACTTCTAAGATAGCACC 58.801 50.000 11.13 0.00 0.00 5.01
1951 5058 2.860735 CGTGGCACTTCTAAGATAGCAC 59.139 50.000 16.72 0.00 0.00 4.40
1952 5059 2.496070 ACGTGGCACTTCTAAGATAGCA 59.504 45.455 16.72 0.00 0.00 3.49
1953 5060 3.166489 ACGTGGCACTTCTAAGATAGC 57.834 47.619 16.72 0.00 0.00 2.97
1954 5061 6.132791 TCTTACGTGGCACTTCTAAGATAG 57.867 41.667 16.72 0.00 0.00 2.08
1955 5062 6.710597 ATCTTACGTGGCACTTCTAAGATA 57.289 37.500 25.27 11.89 34.05 1.98
1956 5063 5.599999 ATCTTACGTGGCACTTCTAAGAT 57.400 39.130 23.10 23.10 31.94 2.40
1957 5064 6.519679 TTATCTTACGTGGCACTTCTAAGA 57.480 37.500 21.53 21.53 0.00 2.10
1958 5065 7.491372 TCATTTATCTTACGTGGCACTTCTAAG 59.509 37.037 16.72 15.80 0.00 2.18
1959 5066 7.324935 TCATTTATCTTACGTGGCACTTCTAA 58.675 34.615 16.72 7.46 0.00 2.10
1960 5067 6.869695 TCATTTATCTTACGTGGCACTTCTA 58.130 36.000 16.72 0.00 0.00 2.10
1961 5068 5.730550 TCATTTATCTTACGTGGCACTTCT 58.269 37.500 16.72 0.21 0.00 2.85
1962 5069 6.257849 TCATCATTTATCTTACGTGGCACTTC 59.742 38.462 16.72 0.00 0.00 3.01
1963 5070 6.112734 TCATCATTTATCTTACGTGGCACTT 58.887 36.000 16.72 9.21 0.00 3.16
1964 5071 5.670485 TCATCATTTATCTTACGTGGCACT 58.330 37.500 16.72 5.47 0.00 4.40
1965 5072 5.753438 TCTCATCATTTATCTTACGTGGCAC 59.247 40.000 7.79 7.79 0.00 5.01
1966 5073 5.912892 TCTCATCATTTATCTTACGTGGCA 58.087 37.500 0.00 0.00 0.00 4.92
1967 5074 6.128445 CCATCTCATCATTTATCTTACGTGGC 60.128 42.308 0.00 0.00 0.00 5.01
1968 5075 7.154656 TCCATCTCATCATTTATCTTACGTGG 58.845 38.462 0.00 0.00 0.00 4.94
1969 5076 7.330454 CCTCCATCTCATCATTTATCTTACGTG 59.670 40.741 0.00 0.00 0.00 4.49
1970 5077 7.233553 TCCTCCATCTCATCATTTATCTTACGT 59.766 37.037 0.00 0.00 0.00 3.57
1971 5078 7.606349 TCCTCCATCTCATCATTTATCTTACG 58.394 38.462 0.00 0.00 0.00 3.18
1972 5079 8.811017 TCTCCTCCATCTCATCATTTATCTTAC 58.189 37.037 0.00 0.00 0.00 2.34
1973 5080 8.962912 TCTCCTCCATCTCATCATTTATCTTA 57.037 34.615 0.00 0.00 0.00 2.10
1974 5081 7.733955 TCTCTCCTCCATCTCATCATTTATCTT 59.266 37.037 0.00 0.00 0.00 2.40
1975 5082 7.247500 TCTCTCCTCCATCTCATCATTTATCT 58.753 38.462 0.00 0.00 0.00 1.98
1976 5083 7.396907 TCTCTCTCCTCCATCTCATCATTTATC 59.603 40.741 0.00 0.00 0.00 1.75
1977 5084 7.247500 TCTCTCTCCTCCATCTCATCATTTAT 58.753 38.462 0.00 0.00 0.00 1.40
1978 5085 6.618501 TCTCTCTCCTCCATCTCATCATTTA 58.381 40.000 0.00 0.00 0.00 1.40
1979 5086 5.465901 TCTCTCTCCTCCATCTCATCATTT 58.534 41.667 0.00 0.00 0.00 2.32
1980 5087 5.077369 TCTCTCTCCTCCATCTCATCATT 57.923 43.478 0.00 0.00 0.00 2.57
1981 5088 4.745484 TCTCTCTCCTCCATCTCATCAT 57.255 45.455 0.00 0.00 0.00 2.45
1982 5089 4.079269 AGTTCTCTCTCCTCCATCTCATCA 60.079 45.833 0.00 0.00 0.00 3.07
1983 5090 4.473444 AGTTCTCTCTCCTCCATCTCATC 58.527 47.826 0.00 0.00 0.00 2.92
1984 5091 4.079269 TGAGTTCTCTCTCCTCCATCTCAT 60.079 45.833 1.53 0.00 40.98 2.90
1985 5092 3.268072 TGAGTTCTCTCTCCTCCATCTCA 59.732 47.826 1.53 0.00 40.98 3.27
1986 5093 3.897239 TGAGTTCTCTCTCCTCCATCTC 58.103 50.000 1.53 0.00 40.98 2.75
1987 5094 4.541250 ATGAGTTCTCTCTCCTCCATCT 57.459 45.455 1.53 0.00 40.98 2.90
1988 5095 6.068010 TCTTATGAGTTCTCTCTCCTCCATC 58.932 44.000 1.53 0.00 40.98 3.51
1989 5096 6.024563 TCTTATGAGTTCTCTCTCCTCCAT 57.975 41.667 1.53 0.00 40.98 3.41
1990 5097 5.458451 TCTTATGAGTTCTCTCTCCTCCA 57.542 43.478 1.53 0.00 40.98 3.86
1991 5098 6.783708 TTTCTTATGAGTTCTCTCTCCTCC 57.216 41.667 1.53 0.00 40.98 4.30
1992 5099 8.062065 TCTTTTCTTATGAGTTCTCTCTCCTC 57.938 38.462 1.53 0.00 40.98 3.71
1993 5100 8.608185 ATCTTTTCTTATGAGTTCTCTCTCCT 57.392 34.615 1.53 0.00 40.98 3.69
1994 5101 9.665719 AAATCTTTTCTTATGAGTTCTCTCTCC 57.334 33.333 1.53 0.00 40.98 3.71
2047 5154 6.160576 AGAATTGTGCTAAGAGATCCTCTC 57.839 41.667 0.00 0.00 40.28 3.20
2048 5155 5.660417 TGAGAATTGTGCTAAGAGATCCTCT 59.340 40.000 0.00 0.00 43.37 3.69
2049 5156 5.752955 GTGAGAATTGTGCTAAGAGATCCTC 59.247 44.000 0.00 0.00 0.00 3.71
2050 5157 5.396213 GGTGAGAATTGTGCTAAGAGATCCT 60.396 44.000 0.00 0.00 0.00 3.24
2051 5158 4.813697 GGTGAGAATTGTGCTAAGAGATCC 59.186 45.833 0.00 0.00 0.00 3.36
2052 5159 5.423015 TGGTGAGAATTGTGCTAAGAGATC 58.577 41.667 0.00 0.00 0.00 2.75
2053 5160 5.426689 TGGTGAGAATTGTGCTAAGAGAT 57.573 39.130 0.00 0.00 0.00 2.75
2054 5161 4.890158 TGGTGAGAATTGTGCTAAGAGA 57.110 40.909 0.00 0.00 0.00 3.10
2055 5162 4.940046 ACATGGTGAGAATTGTGCTAAGAG 59.060 41.667 0.00 0.00 0.00 2.85
2056 5163 4.910195 ACATGGTGAGAATTGTGCTAAGA 58.090 39.130 0.00 0.00 0.00 2.10
2057 5164 5.633830 AACATGGTGAGAATTGTGCTAAG 57.366 39.130 0.00 0.00 0.00 2.18
2058 5165 6.403866 AAAACATGGTGAGAATTGTGCTAA 57.596 33.333 0.00 0.00 0.00 3.09
2059 5166 7.309133 CCTTAAAACATGGTGAGAATTGTGCTA 60.309 37.037 0.00 0.00 0.00 3.49
2060 5167 4.942761 AAAACATGGTGAGAATTGTGCT 57.057 36.364 0.00 0.00 0.00 4.40
2061 5168 5.634859 CCTTAAAACATGGTGAGAATTGTGC 59.365 40.000 0.00 0.00 0.00 4.57
2062 5169 6.980593 TCCTTAAAACATGGTGAGAATTGTG 58.019 36.000 0.00 0.00 0.00 3.33
2063 5170 7.595819 TTCCTTAAAACATGGTGAGAATTGT 57.404 32.000 0.00 0.00 0.00 2.71
2066 5173 9.533831 AGTAATTCCTTAAAACATGGTGAGAAT 57.466 29.630 0.00 0.00 0.00 2.40
2067 5174 8.934023 AGTAATTCCTTAAAACATGGTGAGAA 57.066 30.769 0.00 0.00 0.00 2.87
2068 5175 9.667107 CTAGTAATTCCTTAAAACATGGTGAGA 57.333 33.333 0.00 0.00 0.00 3.27
2069 5176 9.449719 ACTAGTAATTCCTTAAAACATGGTGAG 57.550 33.333 0.00 0.00 0.00 3.51
2070 5177 9.802039 AACTAGTAATTCCTTAAAACATGGTGA 57.198 29.630 0.00 0.00 0.00 4.02
2101 5208 9.965902 CAATGGGTTATATCTTAGCCTTATCTT 57.034 33.333 0.00 0.00 33.15 2.40
2102 5209 9.117223 ACAATGGGTTATATCTTAGCCTTATCT 57.883 33.333 0.00 0.00 33.15 1.98
2106 5213 9.350951 GTTTACAATGGGTTATATCTTAGCCTT 57.649 33.333 0.00 0.00 33.15 4.35
2107 5214 8.499406 TGTTTACAATGGGTTATATCTTAGCCT 58.501 33.333 0.00 0.00 33.15 4.58
2108 5215 8.685838 TGTTTACAATGGGTTATATCTTAGCC 57.314 34.615 0.00 0.00 0.00 3.93
2138 5245 7.153315 TGCATGCAATTTAGAGATGACAAAAA 58.847 30.769 20.30 0.00 0.00 1.94
2139 5246 6.689554 TGCATGCAATTTAGAGATGACAAAA 58.310 32.000 20.30 0.00 0.00 2.44
2140 5247 6.270156 TGCATGCAATTTAGAGATGACAAA 57.730 33.333 20.30 0.00 0.00 2.83
2141 5248 5.900865 TGCATGCAATTTAGAGATGACAA 57.099 34.783 20.30 0.00 0.00 3.18
2142 5249 5.648960 TCTTGCATGCAATTTAGAGATGACA 59.351 36.000 31.96 6.17 35.20 3.58
2143 5250 5.970023 GTCTTGCATGCAATTTAGAGATGAC 59.030 40.000 31.96 25.31 35.20 3.06
2144 5251 5.884232 AGTCTTGCATGCAATTTAGAGATGA 59.116 36.000 31.96 19.28 35.20 2.92
2145 5252 6.132791 AGTCTTGCATGCAATTTAGAGATG 57.867 37.500 31.96 17.36 35.20 2.90
2146 5253 6.770746 AAGTCTTGCATGCAATTTAGAGAT 57.229 33.333 31.96 14.64 35.20 2.75
2147 5254 7.607607 TCTTAAGTCTTGCATGCAATTTAGAGA 59.392 33.333 31.96 24.43 35.20 3.10
2148 5255 7.755591 TCTTAAGTCTTGCATGCAATTTAGAG 58.244 34.615 31.96 22.88 35.20 2.43
2149 5256 7.686438 TCTTAAGTCTTGCATGCAATTTAGA 57.314 32.000 31.96 25.57 35.20 2.10
2152 5259 8.742777 TCTTATCTTAAGTCTTGCATGCAATTT 58.257 29.630 31.96 25.44 35.20 1.82
2153 5260 8.186821 GTCTTATCTTAAGTCTTGCATGCAATT 58.813 33.333 31.96 24.59 35.20 2.32
2154 5261 7.555554 AGTCTTATCTTAAGTCTTGCATGCAAT 59.444 33.333 31.96 20.06 35.20 3.56
2155 5262 6.881065 AGTCTTATCTTAAGTCTTGCATGCAA 59.119 34.615 30.12 30.12 0.00 4.08
2156 5263 6.314648 CAGTCTTATCTTAAGTCTTGCATGCA 59.685 38.462 18.46 18.46 0.00 3.96
2157 5264 6.314896 ACAGTCTTATCTTAAGTCTTGCATGC 59.685 38.462 11.82 11.82 0.00 4.06
2158 5265 7.763528 AGACAGTCTTATCTTAAGTCTTGCATG 59.236 37.037 0.00 0.00 31.38 4.06
2159 5266 7.846066 AGACAGTCTTATCTTAAGTCTTGCAT 58.154 34.615 0.00 0.00 31.38 3.96
2160 5267 7.233389 AGACAGTCTTATCTTAAGTCTTGCA 57.767 36.000 0.00 0.00 31.38 4.08
2161 5268 9.810545 ATAAGACAGTCTTATCTTAAGTCTTGC 57.189 33.333 24.76 0.00 44.03 4.01
2176 5283 9.770097 CATATACAATGGTTGATAAGACAGTCT 57.230 33.333 0.00 0.00 0.00 3.24
2177 5284 8.499162 GCATATACAATGGTTGATAAGACAGTC 58.501 37.037 0.00 0.00 0.00 3.51
2178 5285 7.445402 GGCATATACAATGGTTGATAAGACAGT 59.555 37.037 0.00 0.00 0.00 3.55
2179 5286 7.094634 GGGCATATACAATGGTTGATAAGACAG 60.095 40.741 0.00 0.00 0.00 3.51
2180 5287 6.714810 GGGCATATACAATGGTTGATAAGACA 59.285 38.462 0.00 0.00 0.00 3.41
2181 5288 6.942576 AGGGCATATACAATGGTTGATAAGAC 59.057 38.462 0.00 0.00 0.00 3.01
2182 5289 7.090319 AGGGCATATACAATGGTTGATAAGA 57.910 36.000 0.00 0.00 0.00 2.10
2183 5290 7.765695 AAGGGCATATACAATGGTTGATAAG 57.234 36.000 0.00 0.00 0.00 1.73
2184 5291 9.073475 GTTAAGGGCATATACAATGGTTGATAA 57.927 33.333 0.00 0.00 0.00 1.75
2185 5292 8.444783 AGTTAAGGGCATATACAATGGTTGATA 58.555 33.333 0.00 0.00 0.00 2.15
2186 5293 7.231317 CAGTTAAGGGCATATACAATGGTTGAT 59.769 37.037 0.00 0.00 0.00 2.57
2187 5294 6.545666 CAGTTAAGGGCATATACAATGGTTGA 59.454 38.462 0.00 0.00 0.00 3.18
2188 5295 6.545666 TCAGTTAAGGGCATATACAATGGTTG 59.454 38.462 0.00 0.00 0.00 3.77
2189 5296 6.546034 GTCAGTTAAGGGCATATACAATGGTT 59.454 38.462 0.00 0.00 0.00 3.67
2190 5297 6.062095 GTCAGTTAAGGGCATATACAATGGT 58.938 40.000 0.00 0.00 0.00 3.55
2191 5298 6.299141 AGTCAGTTAAGGGCATATACAATGG 58.701 40.000 0.00 0.00 0.00 3.16
2192 5299 8.939929 CATAGTCAGTTAAGGGCATATACAATG 58.060 37.037 0.00 0.00 0.00 2.82
2193 5300 8.880244 TCATAGTCAGTTAAGGGCATATACAAT 58.120 33.333 0.00 0.00 0.00 2.71
2194 5301 8.257602 TCATAGTCAGTTAAGGGCATATACAA 57.742 34.615 0.00 0.00 0.00 2.41
2195 5302 7.509318 ACTCATAGTCAGTTAAGGGCATATACA 59.491 37.037 0.00 0.00 0.00 2.29
2196 5303 7.897864 ACTCATAGTCAGTTAAGGGCATATAC 58.102 38.462 0.00 0.00 0.00 1.47
2197 5304 9.596308 TTACTCATAGTCAGTTAAGGGCATATA 57.404 33.333 0.00 0.00 0.00 0.86
2198 5305 8.368668 GTTACTCATAGTCAGTTAAGGGCATAT 58.631 37.037 0.00 0.00 0.00 1.78
2199 5306 7.563924 AGTTACTCATAGTCAGTTAAGGGCATA 59.436 37.037 0.00 0.00 0.00 3.14
2200 5307 6.384305 AGTTACTCATAGTCAGTTAAGGGCAT 59.616 38.462 0.00 0.00 0.00 4.40
2201 5308 5.720041 AGTTACTCATAGTCAGTTAAGGGCA 59.280 40.000 0.00 0.00 0.00 5.36
2202 5309 6.223351 AGTTACTCATAGTCAGTTAAGGGC 57.777 41.667 0.00 0.00 0.00 5.19
2203 5310 8.311836 TGAAAGTTACTCATAGTCAGTTAAGGG 58.688 37.037 0.00 0.00 0.00 3.95
2204 5311 9.360093 CTGAAAGTTACTCATAGTCAGTTAAGG 57.640 37.037 0.00 0.00 0.00 2.69
2205 5312 9.360093 CCTGAAAGTTACTCATAGTCAGTTAAG 57.640 37.037 0.00 0.00 31.21 1.85
2206 5313 8.311836 CCCTGAAAGTTACTCATAGTCAGTTAA 58.688 37.037 0.00 0.00 31.21 2.01
2207 5314 7.672660 TCCCTGAAAGTTACTCATAGTCAGTTA 59.327 37.037 0.00 0.00 31.21 2.24
2208 5315 6.497259 TCCCTGAAAGTTACTCATAGTCAGTT 59.503 38.462 0.00 0.00 31.21 3.16
2216 5323 3.170717 TCCGTCCCTGAAAGTTACTCAT 58.829 45.455 0.00 0.00 0.00 2.90
2221 5328 3.056107 CACTCATCCGTCCCTGAAAGTTA 60.056 47.826 0.00 0.00 0.00 2.24
2267 5374 1.285078 TGATCTCGTCCTCTCCTCCAA 59.715 52.381 0.00 0.00 0.00 3.53
2347 5454 1.871418 TCTCCTTGGTGATCTCCTGG 58.129 55.000 14.65 15.20 0.00 4.45
2514 5644 4.692228 TCAGCATGCACGTAAAGATCATA 58.308 39.130 21.98 0.00 34.76 2.15
2534 5664 5.157940 AGATTTAGAAGTTGCTCAGCTCA 57.842 39.130 0.00 0.00 0.00 4.26
2539 5669 7.750229 ATCACAAAGATTTAGAAGTTGCTCA 57.250 32.000 0.00 0.00 31.20 4.26
2622 5752 0.528017 GTCTGTCGCCATCAGTCTCA 59.472 55.000 0.00 0.00 34.86 3.27
2626 5756 1.893137 TGTAAGTCTGTCGCCATCAGT 59.107 47.619 0.00 0.00 34.86 3.41
2641 5771 7.921786 TGGATTTGTACTCTTTCCATGTAAG 57.078 36.000 0.00 0.00 31.67 2.34
2740 5873 2.903798 TGCATGTGCGTCTGATTATGA 58.096 42.857 0.01 0.00 45.83 2.15
2741 5874 3.891056 ATGCATGTGCGTCTGATTATG 57.109 42.857 0.00 0.00 45.83 1.90
2754 5891 4.162888 TCACCTGTAGAAGATGATGCATGT 59.837 41.667 2.46 0.00 0.00 3.21
2764 5901 5.163784 CGTCTCGTTTATCACCTGTAGAAGA 60.164 44.000 0.00 0.00 0.00 2.87
2765 5902 5.029014 CGTCTCGTTTATCACCTGTAGAAG 58.971 45.833 0.00 0.00 0.00 2.85
2768 5905 3.128242 ACCGTCTCGTTTATCACCTGTAG 59.872 47.826 0.00 0.00 0.00 2.74
2926 6065 8.365647 AGAGATACTACTAGCTACTGTCTCTTC 58.634 40.741 7.80 0.00 37.27 2.87
2934 6073 9.280174 GTCATTTGAGAGATACTACTAGCTACT 57.720 37.037 0.00 0.00 0.00 2.57
2936 6075 9.628500 TTGTCATTTGAGAGATACTACTAGCTA 57.372 33.333 0.00 0.00 0.00 3.32
2938 6077 9.757227 AATTGTCATTTGAGAGATACTACTAGC 57.243 33.333 0.00 0.00 0.00 3.42
2948 6090 5.879777 TCGCCAATAATTGTCATTTGAGAGA 59.120 36.000 0.00 0.00 0.00 3.10
3079 6222 5.556915 CATTGAGGTCCAGTACAAACCTTA 58.443 41.667 13.21 8.06 43.43 2.69
3143 6290 9.517609 GTTGTCCTAGATAAAGTGTACTATGTG 57.482 37.037 0.00 0.00 0.00 3.21
3364 6511 2.397044 AATTTTGGGCTCCAAGTGGA 57.603 45.000 0.00 0.00 44.84 4.02
3515 6662 6.375736 CAGGTGTTGATTAGTCTCTCTGTCTA 59.624 42.308 0.00 0.00 0.00 2.59
3641 6788 6.963796 ACTTAACTGCAGAAAAATGACAGAG 58.036 36.000 23.35 2.06 32.32 3.35
3776 6923 8.580720 AGTAGTACTAATCTATCCATGCAACTG 58.419 37.037 3.61 0.00 0.00 3.16
3967 7115 1.472904 GGAGAAACTTACTAGGCCGCC 60.473 57.143 0.00 0.00 0.00 6.13
4026 7174 9.817365 CATGGTTTGATAAAATATAGAGCTTCG 57.183 33.333 0.00 0.00 0.00 3.79
4045 7193 7.673926 AGAAAGGGTACAAATGTATCATGGTTT 59.326 33.333 6.20 0.84 33.39 3.27
4094 7242 9.962783 ATTATAGAAGAAAGCAATGAAAGATGC 57.037 29.630 0.00 0.00 42.87 3.91
4163 7311 7.624360 AAATGAGTTTTGCGATAATAGGTCA 57.376 32.000 0.00 0.00 0.00 4.02
4271 7423 3.950397 TCGGGTGTTGCTAATTGAATCT 58.050 40.909 0.00 0.00 0.00 2.40
4290 7442 1.382522 CATGGGATGGGAGTGTTTCG 58.617 55.000 0.00 0.00 0.00 3.46
4321 7473 9.881773 AAGAGATATCCCAAATATTTAAAGGCA 57.118 29.630 0.00 0.00 0.00 4.75
4342 7494 0.685131 TTACGCGGATGGGGAAGAGA 60.685 55.000 12.47 0.00 0.00 3.10
4503 7655 7.649533 ATCAGGTTTGCATGAAATTCATCTA 57.350 32.000 5.36 0.00 38.97 1.98
4507 7659 5.964758 GGTATCAGGTTTGCATGAAATTCA 58.035 37.500 0.00 0.00 38.97 2.57


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

AutoCloner maintained by Alex Coulton.