Multiple sequence alignment - TraesCS7D01G554000

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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 TraesCS7D01G554000 chr7D 100.000 2597 0 0 1 2597 638269573 638266977 0.000000e+00 4796.0
1 TraesCS7D01G554000 chr7D 80.000 445 43 22 124 540 478316834 478317260 1.180000e-73 287.0
2 TraesCS7D01G554000 chr7D 76.755 413 58 23 1112 1490 638288387 638287979 2.040000e-46 196.0
3 TraesCS7D01G554000 chr7D 77.374 358 63 14 1116 1455 638354482 638354125 2.040000e-46 196.0
4 TraesCS7D01G554000 chr7D 85.340 191 24 2 635 821 478317747 478317937 7.330000e-46 195.0
5 TraesCS7D01G554000 chr7D 80.402 199 27 8 1116 1302 638382089 638381891 9.690000e-30 141.0
6 TraesCS7D01G554000 chr7D 83.740 123 18 1 2100 2222 221982697 221982577 5.870000e-22 115.0
7 TraesCS7D01G554000 chr7A 87.696 894 47 28 1164 2015 727821021 727821893 0.000000e+00 983.0
8 TraesCS7D01G554000 chr7A 84.615 858 81 28 868 1699 727832885 727833717 0.000000e+00 806.0
9 TraesCS7D01G554000 chr7A 94.410 322 15 1 848 1166 727815504 727815825 2.320000e-135 492.0
10 TraesCS7D01G554000 chr7A 94.466 253 13 1 570 821 727815198 727815450 3.130000e-104 388.0
11 TraesCS7D01G554000 chr7A 79.318 440 51 20 123 540 699092204 699092625 3.290000e-69 272.0
12 TraesCS7D01G554000 chr7A 88.718 195 13 6 2036 2222 727821882 727822075 2.010000e-56 230.0
13 TraesCS7D01G554000 chr7A 91.892 148 12 0 2228 2375 727822108 727822255 9.420000e-50 207.0
14 TraesCS7D01G554000 chr7A 93.805 113 6 1 8 120 727814742 727814853 4.440000e-38 169.0
15 TraesCS7D01G554000 chr7B 90.650 738 60 5 868 1600 734430154 734430887 0.000000e+00 972.0
16 TraesCS7D01G554000 chr7B 92.578 256 13 3 1764 2015 734431393 734431646 1.900000e-96 363.0
17 TraesCS7D01G554000 chr7B 77.410 363 62 15 1112 1455 734366236 734366597 5.670000e-47 198.0
18 TraesCS7D01G554000 chr7B 88.235 119 8 3 6 124 734430037 734430149 1.250000e-28 137.0
19 TraesCS7D01G554000 chr7B 82.166 157 16 8 663 812 614343876 614343725 9.760000e-25 124.0
20 TraesCS7D01G554000 chr3A 88.696 345 31 4 202 540 700757911 700757569 5.170000e-112 414.0
21 TraesCS7D01G554000 chr3A 92.188 256 19 1 570 824 700756232 700755977 6.830000e-96 361.0
22 TraesCS7D01G554000 chr4A 78.864 440 53 19 123 540 564699811 564700232 7.130000e-66 261.0
23 TraesCS7D01G554000 chr4A 94.872 39 2 0 2556 2594 712271417 712271455 7.760000e-06 62.1
24 TraesCS7D01G554000 chr4A 94.872 39 2 0 2556 2594 712307566 712307604 7.760000e-06 62.1
25 TraesCS7D01G554000 chr3B 77.419 372 27 28 123 467 90739419 90739078 4.440000e-38 169.0
26 TraesCS7D01G554000 chr3B 86.567 67 7 2 123 188 771625372 771625307 3.580000e-09 73.1
27 TraesCS7D01G554000 chr2A 79.216 255 41 9 2256 2501 249789226 249789477 1.600000e-37 167.0
28 TraesCS7D01G554000 chr1B 79.902 204 24 12 635 821 209565323 209565526 1.620000e-27 134.0
29 TraesCS7D01G554000 chr6B 84.091 132 16 3 659 787 159367205 159367334 3.510000e-24 122.0
30 TraesCS7D01G554000 chr6B 82.432 74 10 3 123 195 713465832 713465761 7.760000e-06 62.1
31 TraesCS7D01G554000 chr2D 87.879 99 12 0 2119 2217 633347908 633347810 1.630000e-22 117.0
32 TraesCS7D01G554000 chr2D 85.135 74 8 3 123 195 626271478 626271407 3.580000e-09 73.1
33 TraesCS7D01G554000 chr5D 88.889 45 5 0 123 167 64138668 64138624 3.610000e-04 56.5
34 TraesCS7D01G554000 chr4B 96.875 32 1 0 2556 2587 493332388 493332357 1.000000e-03 54.7
35 TraesCS7D01G554000 chr5B 100.000 28 0 0 123 150 122419609 122419636 5.000000e-03 52.8


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 TraesCS7D01G554000 chr7D 638266977 638269573 2596 True 4796.000000 4796 100.000000 1 2597 1 chr7D.!!$R2 2596
1 TraesCS7D01G554000 chr7D 478316834 478317937 1103 False 241.000000 287 82.670000 124 821 2 chr7D.!!$F1 697
2 TraesCS7D01G554000 chr7A 727832885 727833717 832 False 806.000000 806 84.615000 868 1699 1 chr7A.!!$F2 831
3 TraesCS7D01G554000 chr7A 727821021 727822255 1234 False 473.333333 983 89.435333 1164 2375 3 chr7A.!!$F4 1211
4 TraesCS7D01G554000 chr7A 727814742 727815825 1083 False 349.666667 492 94.227000 8 1166 3 chr7A.!!$F3 1158
5 TraesCS7D01G554000 chr7B 734430037 734431646 1609 False 490.666667 972 90.487667 6 2015 3 chr7B.!!$F2 2009
6 TraesCS7D01G554000 chr3A 700755977 700757911 1934 True 387.500000 414 90.442000 202 824 2 chr3A.!!$R1 622

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
664 2078 0.03601 CTCTTTGCAGATGTCCCCGT 60.036 55.0 0.0 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2445 4362 0.030235 TGACTCTTCGTCCACACGTG 59.97 55.0 15.48 15.48 46.76 4.49 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
22 23 4.062293 CAAAAGTGGAATCGACTGTACCA 58.938 43.478 0.00 0.00 0.00 3.25
91 92 2.303311 GTTGCTCCTTCCTTCCACTACT 59.697 50.000 0.00 0.00 0.00 2.57
97 98 2.352814 CCTTCCTTCCACTACTGTGACG 60.353 54.545 0.00 0.00 46.55 4.35
120 121 5.475220 CGACATCCTCTATCTATCCACAAGT 59.525 44.000 0.00 0.00 0.00 3.16
173 174 2.046285 GGATTGGCCGGTTGACCTG 61.046 63.158 1.90 0.00 0.00 4.00
178 179 3.637273 GCCGGTTGACCTGGGACT 61.637 66.667 1.90 0.00 32.69 3.85
192 193 2.623889 CTGGGACTGTACGATTCCTAGG 59.376 54.545 0.82 0.82 35.03 3.02
197 198 2.553172 ACTGTACGATTCCTAGGCGATC 59.447 50.000 13.38 12.91 0.00 3.69
198 199 2.552743 CTGTACGATTCCTAGGCGATCA 59.447 50.000 19.06 13.30 0.00 2.92
200 201 3.572682 TGTACGATTCCTAGGCGATCAAT 59.427 43.478 19.06 8.55 0.00 2.57
215 217 4.726021 GCGATCAATAATTGCTAGCCATCG 60.726 45.833 13.29 12.21 41.04 3.84
378 404 2.690778 GCCGCCATCACACAACCTC 61.691 63.158 0.00 0.00 0.00 3.85
387 413 0.758734 CACACAACCTCCTCCTCACA 59.241 55.000 0.00 0.00 0.00 3.58
390 416 1.051812 ACAACCTCCTCCTCACACTG 58.948 55.000 0.00 0.00 0.00 3.66
393 419 0.188587 ACCTCCTCCTCACACTGTGA 59.811 55.000 15.86 11.44 40.50 3.58
419 445 2.758736 ATCGATCCATGGAGCTTAGC 57.241 50.000 26.56 1.77 0.00 3.09
458 484 3.192422 CACCGGTTCCAGCATGAAAAATA 59.808 43.478 2.97 0.00 39.69 1.40
466 492 5.508567 TCCAGCATGAAAAATACTCATCCA 58.491 37.500 0.00 0.00 39.69 3.41
467 493 6.131264 TCCAGCATGAAAAATACTCATCCAT 58.869 36.000 0.00 0.00 39.69 3.41
472 498 6.736794 GCATGAAAAATACTCATCCATGGGTC 60.737 42.308 13.02 0.00 41.45 4.46
545 747 2.447887 CGTCGCAGCAGTGATGACC 61.448 63.158 13.68 0.00 42.55 4.02
550 752 1.230635 GCAGCAGTGATGACCGTTGT 61.231 55.000 13.68 0.00 0.00 3.32
552 754 2.621338 CAGCAGTGATGACCGTTGTAT 58.379 47.619 0.98 0.00 0.00 2.29
555 757 2.348666 GCAGTGATGACCGTTGTATCAC 59.651 50.000 8.17 8.17 46.83 3.06
558 760 3.585862 GTGATGACCGTTGTATCACTGT 58.414 45.455 8.81 0.00 44.43 3.55
563 765 4.740268 TGACCGTTGTATCACTGTATCAC 58.260 43.478 0.00 0.00 0.00 3.06
564 766 4.461431 TGACCGTTGTATCACTGTATCACT 59.539 41.667 0.00 0.00 0.00 3.41
567 769 5.416639 ACCGTTGTATCACTGTATCACTGTA 59.583 40.000 0.00 0.00 0.00 2.74
568 770 6.096423 ACCGTTGTATCACTGTATCACTGTAT 59.904 38.462 0.00 0.00 0.00 2.29
610 1946 0.106569 TGGGCACATCCATGATGACC 60.107 55.000 10.84 10.61 42.09 4.02
664 2078 0.036010 CTCTTTGCAGATGTCCCCGT 60.036 55.000 0.00 0.00 0.00 5.28
676 2090 2.178521 CCCCGTCGTCGTCTTCTG 59.821 66.667 0.71 0.00 35.01 3.02
817 2234 5.164090 CGTGAAGAAAACGATTCGATTGAGA 60.164 40.000 13.95 0.00 43.68 3.27
818 2235 6.237073 GTGAAGAAAACGATTCGATTGAGAG 58.763 40.000 13.95 0.00 0.00 3.20
819 2236 4.849111 AGAAAACGATTCGATTGAGAGC 57.151 40.909 13.95 0.00 0.00 4.09
820 2237 3.304559 AGAAAACGATTCGATTGAGAGCG 59.695 43.478 13.95 0.00 35.66 5.03
821 2238 2.561733 AACGATTCGATTGAGAGCGA 57.438 45.000 13.95 0.00 42.66 4.93
823 2240 2.656085 ACGATTCGATTGAGAGCGATC 58.344 47.619 13.95 0.00 43.92 3.69
830 2247 2.055100 GATTGAGAGCGATCGTAAGGC 58.945 52.381 17.81 0.00 38.47 4.35
832 2249 1.963172 TGAGAGCGATCGTAAGGCTA 58.037 50.000 17.81 0.00 37.10 3.93
833 2250 1.874231 TGAGAGCGATCGTAAGGCTAG 59.126 52.381 17.81 0.00 37.10 3.42
834 2251 0.594110 AGAGCGATCGTAAGGCTAGC 59.406 55.000 17.81 6.04 37.10 3.42
835 2252 0.726452 GAGCGATCGTAAGGCTAGCG 60.726 60.000 17.81 4.54 37.10 4.26
836 2253 1.164662 AGCGATCGTAAGGCTAGCGA 61.165 55.000 17.81 14.09 39.02 4.93
837 2254 0.997726 GCGATCGTAAGGCTAGCGAC 60.998 60.000 17.81 5.83 37.47 5.19
839 2256 1.797046 CGATCGTAAGGCTAGCGACTA 59.203 52.381 9.00 0.00 37.47 2.59
928 2376 1.903877 CGGCCAGGTCCAGAGTCAAT 61.904 60.000 2.24 0.00 0.00 2.57
973 2421 2.202623 GCAGAGCGTCCACCGTAG 60.203 66.667 0.00 0.00 39.32 3.51
1101 2572 1.808799 CGAGCAGCAGACATCGCTT 60.809 57.895 0.00 0.00 37.72 4.68
1520 3006 1.604308 TAGTCGTCGTGGCAGGGAA 60.604 57.895 7.42 0.00 0.00 3.97
1618 3104 3.985925 GTCAGGTTTGTAGGTACTGTTCG 59.014 47.826 0.00 0.00 41.52 3.95
1619 3105 2.735134 CAGGTTTGTAGGTACTGTTCGC 59.265 50.000 0.00 0.00 41.52 4.70
1653 3179 1.131883 CTCGGCCTCTGCTTCATTTTG 59.868 52.381 0.00 0.00 37.74 2.44
1702 3264 5.049954 TGTGGTGTTTAAGATTTCAGTACGC 60.050 40.000 0.00 0.00 0.00 4.42
1829 3707 1.138464 TCAGTCTCCATCAGCATCAGC 59.862 52.381 0.00 0.00 42.56 4.26
1875 3753 0.461548 TAGCAGCTTGACGGATGGAG 59.538 55.000 0.00 0.00 0.00 3.86
1926 3804 7.498900 ACAAACTCATCATTGTCTCTGTTGTTA 59.501 33.333 0.00 0.00 34.84 2.41
2015 3898 4.074970 CCATGTATAACTGGCAGGATTCC 58.925 47.826 20.34 4.18 0.00 3.01
2016 3899 4.446167 CCATGTATAACTGGCAGGATTCCA 60.446 45.833 20.34 9.95 0.00 3.53
2017 3900 4.150897 TGTATAACTGGCAGGATTCCAC 57.849 45.455 20.34 9.06 0.00 4.02
2018 3901 2.736670 ATAACTGGCAGGATTCCACC 57.263 50.000 20.34 6.65 0.00 4.61
2019 3902 0.623723 TAACTGGCAGGATTCCACCC 59.376 55.000 20.34 5.15 0.00 4.61
2020 3903 2.124570 CTGGCAGGATTCCACCCG 60.125 66.667 6.61 0.00 0.00 5.28
2021 3904 2.609299 TGGCAGGATTCCACCCGA 60.609 61.111 5.29 0.00 0.00 5.14
2022 3905 2.190578 GGCAGGATTCCACCCGAG 59.809 66.667 5.29 0.00 0.00 4.63
2023 3906 2.367202 GGCAGGATTCCACCCGAGA 61.367 63.158 5.29 0.00 0.00 4.04
2024 3907 1.602237 GCAGGATTCCACCCGAGAA 59.398 57.895 5.29 0.00 0.00 2.87
2025 3908 0.035439 GCAGGATTCCACCCGAGAAA 60.035 55.000 5.29 0.00 0.00 2.52
2026 3909 1.613255 GCAGGATTCCACCCGAGAAAA 60.613 52.381 5.29 0.00 0.00 2.29
2027 3910 2.790433 CAGGATTCCACCCGAGAAAAA 58.210 47.619 5.29 0.00 0.00 1.94
2051 3934 2.373169 AGAAACTGGCAGGATTCAGACA 59.627 45.455 26.63 0.00 35.20 3.41
2055 3938 1.277273 CTGGCAGGATTCAGACAGTCA 59.723 52.381 6.61 0.00 33.11 3.41
2059 3942 2.935201 GCAGGATTCAGACAGTCATGAC 59.065 50.000 18.47 18.47 0.00 3.06
2065 3948 2.242043 TCAGACAGTCATGACAGAGCA 58.758 47.619 27.02 4.12 0.00 4.26
2077 3960 2.035193 TGACAGAGCAAGTCAGTCTCAC 59.965 50.000 2.30 0.00 41.26 3.51
2088 3971 3.118738 AGTCAGTCTCACGGTTCTTGTTT 60.119 43.478 0.00 0.00 0.00 2.83
2089 3972 3.621715 GTCAGTCTCACGGTTCTTGTTTT 59.378 43.478 0.00 0.00 0.00 2.43
2146 4036 7.816945 ATTAATTGCAAAATTTCTCACCGAG 57.183 32.000 1.71 0.00 0.00 4.63
2152 4042 2.380084 AATTTCTCACCGAGCGCTAA 57.620 45.000 11.50 0.00 0.00 3.09
2180 4070 4.260375 GCTTGCGGTAGTCAATGTAGATTG 60.260 45.833 6.25 6.25 40.47 2.67
2209 4099 3.665745 AATTTGTCCTCCACAATGCAC 57.334 42.857 0.00 0.00 44.77 4.57
2218 4108 2.743664 CTCCACAATGCACGATTCAAGA 59.256 45.455 0.00 0.00 0.00 3.02
2222 4112 3.684305 CACAATGCACGATTCAAGAGGTA 59.316 43.478 0.00 0.00 0.00 3.08
2223 4113 4.333649 CACAATGCACGATTCAAGAGGTAT 59.666 41.667 0.00 0.00 0.00 2.73
2224 4114 4.572389 ACAATGCACGATTCAAGAGGTATC 59.428 41.667 0.00 0.00 0.00 2.24
2225 4115 2.809446 TGCACGATTCAAGAGGTATCG 58.191 47.619 0.00 0.00 44.86 2.92
2226 4116 2.425668 TGCACGATTCAAGAGGTATCGA 59.574 45.455 10.27 0.00 42.70 3.59
2241 4158 4.554363 CGAGGTCCTAGTGGCGCG 62.554 72.222 0.00 0.00 0.00 6.86
2289 4206 5.237344 GGTGTATAAAGGATGTGCTTGCTAG 59.763 44.000 0.00 0.00 0.00 3.42
2299 4216 0.253044 TGCTTGCTAGGTGGATGTCC 59.747 55.000 0.00 0.00 0.00 4.02
2313 4230 2.887152 GGATGTCCACTCTTGCTTTGTT 59.113 45.455 0.00 0.00 35.64 2.83
2315 4232 4.518970 GGATGTCCACTCTTGCTTTGTTAA 59.481 41.667 0.00 0.00 35.64 2.01
2361 4278 7.406031 TGTAGACCCACTCTTTGTCTATTAG 57.594 40.000 0.00 0.00 41.96 1.73
2371 4288 7.759886 CACTCTTTGTCTATTAGATGGACGAAA 59.240 37.037 8.02 5.71 41.66 3.46
2375 4292 6.288941 TGTCTATTAGATGGACGAAAACCA 57.711 37.500 0.00 0.00 42.92 3.67
2376 4293 6.103997 TGTCTATTAGATGGACGAAAACCAC 58.896 40.000 0.00 0.00 42.92 4.16
2377 4294 6.070995 TGTCTATTAGATGGACGAAAACCACT 60.071 38.462 0.00 0.00 42.92 4.00
2378 4295 6.476053 GTCTATTAGATGGACGAAAACCACTC 59.524 42.308 0.00 0.00 40.36 3.51
2379 4296 4.610605 TTAGATGGACGAAAACCACTCA 57.389 40.909 0.00 0.00 40.36 3.41
2380 4297 3.703001 AGATGGACGAAAACCACTCAT 57.297 42.857 0.00 0.00 40.36 2.90
2381 4298 3.600388 AGATGGACGAAAACCACTCATC 58.400 45.455 0.00 0.00 40.36 2.92
2382 4299 2.178912 TGGACGAAAACCACTCATCC 57.821 50.000 0.00 0.00 32.03 3.51
2383 4300 1.076332 GGACGAAAACCACTCATCCG 58.924 55.000 0.00 0.00 0.00 4.18
2384 4301 1.607251 GGACGAAAACCACTCATCCGT 60.607 52.381 0.00 0.00 0.00 4.69
2385 4302 1.725164 GACGAAAACCACTCATCCGTC 59.275 52.381 0.00 0.00 38.17 4.79
2386 4303 1.343465 ACGAAAACCACTCATCCGTCT 59.657 47.619 0.00 0.00 0.00 4.18
2387 4304 2.224209 ACGAAAACCACTCATCCGTCTT 60.224 45.455 0.00 0.00 0.00 3.01
2388 4305 2.806244 CGAAAACCACTCATCCGTCTTT 59.194 45.455 0.00 0.00 0.00 2.52
2389 4306 3.120649 CGAAAACCACTCATCCGTCTTTC 60.121 47.826 0.00 0.00 0.00 2.62
2390 4307 3.485463 AAACCACTCATCCGTCTTTCA 57.515 42.857 0.00 0.00 0.00 2.69
2391 4308 3.485463 AACCACTCATCCGTCTTTCAA 57.515 42.857 0.00 0.00 0.00 2.69
2392 4309 3.045601 ACCACTCATCCGTCTTTCAAG 57.954 47.619 0.00 0.00 0.00 3.02
2393 4310 2.289694 ACCACTCATCCGTCTTTCAAGG 60.290 50.000 0.00 0.00 0.00 3.61
2394 4311 2.028112 CCACTCATCCGTCTTTCAAGGA 60.028 50.000 0.00 0.00 38.56 3.36
2395 4312 3.557054 CCACTCATCCGTCTTTCAAGGAA 60.557 47.826 0.00 0.00 37.62 3.36
2396 4313 3.433615 CACTCATCCGTCTTTCAAGGAAC 59.566 47.826 0.00 0.00 37.62 3.62
2397 4314 2.668457 CTCATCCGTCTTTCAAGGAACG 59.332 50.000 0.00 0.00 37.62 3.95
2398 4315 2.297880 TCATCCGTCTTTCAAGGAACGA 59.702 45.455 0.00 0.00 37.62 3.85
2399 4316 2.894763 TCCGTCTTTCAAGGAACGAA 57.105 45.000 0.00 0.00 0.00 3.85
2400 4317 3.396260 TCCGTCTTTCAAGGAACGAAT 57.604 42.857 0.00 0.00 0.00 3.34
2401 4318 3.735591 TCCGTCTTTCAAGGAACGAATT 58.264 40.909 0.00 0.00 0.00 2.17
2402 4319 3.496884 TCCGTCTTTCAAGGAACGAATTG 59.503 43.478 0.00 0.00 0.00 2.32
2403 4320 3.250040 CCGTCTTTCAAGGAACGAATTGT 59.750 43.478 0.00 0.00 0.00 2.71
2404 4321 4.211389 CGTCTTTCAAGGAACGAATTGTG 58.789 43.478 0.00 0.00 0.00 3.33
2405 4322 4.025229 CGTCTTTCAAGGAACGAATTGTGA 60.025 41.667 0.00 0.00 0.00 3.58
2406 4323 5.334105 CGTCTTTCAAGGAACGAATTGTGAT 60.334 40.000 0.00 0.00 0.00 3.06
2407 4324 6.080406 GTCTTTCAAGGAACGAATTGTGATC 58.920 40.000 0.00 0.00 0.00 2.92
2408 4325 5.997746 TCTTTCAAGGAACGAATTGTGATCT 59.002 36.000 0.00 0.00 0.00 2.75
2409 4326 6.486657 TCTTTCAAGGAACGAATTGTGATCTT 59.513 34.615 0.00 0.00 0.00 2.40
2410 4327 5.862924 TCAAGGAACGAATTGTGATCTTC 57.137 39.130 0.00 0.00 0.00 2.87
2411 4328 4.695455 TCAAGGAACGAATTGTGATCTTCC 59.305 41.667 0.00 0.00 0.00 3.46
2412 4329 3.262420 AGGAACGAATTGTGATCTTCCG 58.738 45.455 0.00 0.00 33.28 4.30
2413 4330 2.223044 GGAACGAATTGTGATCTTCCGC 60.223 50.000 0.00 0.00 0.00 5.54
2414 4331 1.369625 ACGAATTGTGATCTTCCGCC 58.630 50.000 0.00 0.00 0.00 6.13
2415 4332 0.657840 CGAATTGTGATCTTCCGCCC 59.342 55.000 0.00 0.00 0.00 6.13
2416 4333 1.750193 GAATTGTGATCTTCCGCCCA 58.250 50.000 0.00 0.00 0.00 5.36
2417 4334 2.091541 GAATTGTGATCTTCCGCCCAA 58.908 47.619 0.00 0.00 0.00 4.12
2418 4335 2.214376 ATTGTGATCTTCCGCCCAAA 57.786 45.000 0.00 0.00 0.00 3.28
2419 4336 1.243902 TTGTGATCTTCCGCCCAAAC 58.756 50.000 0.00 0.00 0.00 2.93
2420 4337 0.953471 TGTGATCTTCCGCCCAAACG 60.953 55.000 0.00 0.00 0.00 3.60
2421 4338 0.953960 GTGATCTTCCGCCCAAACGT 60.954 55.000 0.00 0.00 0.00 3.99
2422 4339 0.953471 TGATCTTCCGCCCAAACGTG 60.953 55.000 0.00 0.00 0.00 4.49
2423 4340 0.672401 GATCTTCCGCCCAAACGTGA 60.672 55.000 0.00 0.00 0.00 4.35
2424 4341 0.250553 ATCTTCCGCCCAAACGTGAA 60.251 50.000 0.00 0.00 0.00 3.18
2425 4342 1.161563 TCTTCCGCCCAAACGTGAAC 61.162 55.000 0.00 0.00 0.00 3.18
2426 4343 2.438385 CTTCCGCCCAAACGTGAACG 62.438 60.000 0.40 0.40 46.33 3.95
2427 4344 2.919960 TTCCGCCCAAACGTGAACGA 62.920 55.000 10.26 0.00 43.02 3.85
2428 4345 2.535788 CCGCCCAAACGTGAACGAA 61.536 57.895 10.26 0.00 43.02 3.85
2429 4346 1.083015 CGCCCAAACGTGAACGAAG 60.083 57.895 10.26 0.00 43.02 3.79
2430 4347 1.492319 CGCCCAAACGTGAACGAAGA 61.492 55.000 10.26 0.00 43.02 2.87
2431 4348 0.234884 GCCCAAACGTGAACGAAGAG 59.765 55.000 10.26 0.00 43.02 2.85
2432 4349 0.865769 CCCAAACGTGAACGAAGAGG 59.134 55.000 10.26 5.75 43.02 3.69
2433 4350 1.578583 CCAAACGTGAACGAAGAGGT 58.421 50.000 10.26 0.00 43.02 3.85
2434 4351 1.525619 CCAAACGTGAACGAAGAGGTC 59.474 52.381 10.26 0.00 43.02 3.85
2435 4352 1.525619 CAAACGTGAACGAAGAGGTCC 59.474 52.381 10.26 0.00 43.02 4.46
2436 4353 1.038280 AACGTGAACGAAGAGGTCCT 58.962 50.000 10.26 0.00 43.02 3.85
2437 4354 0.597072 ACGTGAACGAAGAGGTCCTC 59.403 55.000 11.31 11.31 43.02 3.71
2438 4355 0.882474 CGTGAACGAAGAGGTCCTCT 59.118 55.000 16.28 16.28 43.37 3.69
2444 4361 4.876752 AAGAGGTCCTCTTCGGCT 57.123 55.556 25.96 6.27 46.42 5.52
2445 4362 2.585876 AAGAGGTCCTCTTCGGCTC 58.414 57.895 25.96 0.00 46.42 4.70
2446 4363 0.251832 AAGAGGTCCTCTTCGGCTCA 60.252 55.000 25.96 0.00 46.42 4.26
2447 4364 0.968393 AGAGGTCCTCTTCGGCTCAC 60.968 60.000 16.28 0.00 37.60 3.51
2448 4365 2.182030 GGTCCTCTTCGGCTCACG 59.818 66.667 0.00 0.00 46.11 4.35
2449 4366 2.637383 GGTCCTCTTCGGCTCACGT 61.637 63.158 0.00 0.00 44.69 4.49
2450 4367 1.444553 GTCCTCTTCGGCTCACGTG 60.445 63.158 9.94 9.94 44.69 4.49
2451 4368 1.901948 TCCTCTTCGGCTCACGTGT 60.902 57.895 16.51 0.00 44.69 4.49
2452 4369 1.734477 CCTCTTCGGCTCACGTGTG 60.734 63.158 16.51 14.71 44.69 3.82
2453 4370 1.734477 CTCTTCGGCTCACGTGTGG 60.734 63.158 16.51 10.89 44.69 4.17
2454 4371 2.142357 CTCTTCGGCTCACGTGTGGA 62.142 60.000 16.51 3.98 44.69 4.02
2455 4372 2.022129 CTTCGGCTCACGTGTGGAC 61.022 63.158 16.51 11.02 44.69 4.02
2474 4391 2.828933 GAAGAGTCACACTTCGGCC 58.171 57.895 0.00 0.00 35.25 6.13
2475 4392 0.318762 GAAGAGTCACACTTCGGCCT 59.681 55.000 0.00 0.00 35.25 5.19
2476 4393 1.544691 GAAGAGTCACACTTCGGCCTA 59.455 52.381 0.00 0.00 35.25 3.93
2477 4394 1.178276 AGAGTCACACTTCGGCCTAG 58.822 55.000 0.00 0.00 0.00 3.02
2478 4395 0.173708 GAGTCACACTTCGGCCTAGG 59.826 60.000 3.67 3.67 0.00 3.02
2479 4396 1.218316 GTCACACTTCGGCCTAGGG 59.782 63.158 11.72 1.09 0.00 3.53
2480 4397 1.987855 TCACACTTCGGCCTAGGGG 60.988 63.158 11.72 0.00 0.00 4.79
2481 4398 1.987855 CACACTTCGGCCTAGGGGA 60.988 63.158 11.72 0.00 33.58 4.81
2482 4399 1.686110 ACACTTCGGCCTAGGGGAG 60.686 63.158 11.72 0.91 33.58 4.30
2491 4408 4.925311 CTAGGGGAGGACTACCGG 57.075 66.667 0.00 0.00 41.83 5.28
2492 4409 1.153292 CTAGGGGAGGACTACCGGG 59.847 68.421 6.32 0.00 41.83 5.73
2493 4410 2.369022 CTAGGGGAGGACTACCGGGG 62.369 70.000 6.32 0.00 41.83 5.73
2494 4411 4.085546 GGGGAGGACTACCGGGGT 62.086 72.222 6.32 3.78 41.83 4.95
2495 4412 2.704424 GGGGAGGACTACCGGGGTA 61.704 68.421 6.32 0.00 41.83 3.69
2496 4413 1.545719 GGGAGGACTACCGGGGTAT 59.454 63.158 6.32 0.00 41.83 2.73
2497 4414 0.779997 GGGAGGACTACCGGGGTATA 59.220 60.000 6.32 0.00 41.83 1.47
2498 4415 1.272369 GGGAGGACTACCGGGGTATAG 60.272 61.905 6.32 0.00 41.83 1.31
2499 4416 1.707427 GGAGGACTACCGGGGTATAGA 59.293 57.143 6.32 0.00 41.83 1.98
2500 4417 2.108952 GGAGGACTACCGGGGTATAGAA 59.891 54.545 6.32 0.00 41.83 2.10
2501 4418 3.245550 GGAGGACTACCGGGGTATAGAAT 60.246 52.174 6.32 0.00 41.83 2.40
2502 4419 4.414677 GAGGACTACCGGGGTATAGAATT 58.585 47.826 6.32 0.00 41.83 2.17
2503 4420 4.158015 AGGACTACCGGGGTATAGAATTG 58.842 47.826 6.32 0.00 41.83 2.32
2504 4421 4.140853 AGGACTACCGGGGTATAGAATTGA 60.141 45.833 6.32 0.00 41.83 2.57
2505 4422 4.590222 GGACTACCGGGGTATAGAATTGAA 59.410 45.833 6.32 0.00 0.00 2.69
2506 4423 5.070847 GGACTACCGGGGTATAGAATTGAAA 59.929 44.000 6.32 0.00 0.00 2.69
2507 4424 6.239800 GGACTACCGGGGTATAGAATTGAAAT 60.240 42.308 6.32 0.00 0.00 2.17
2508 4425 7.038799 GGACTACCGGGGTATAGAATTGAAATA 60.039 40.741 6.32 0.00 0.00 1.40
2509 4426 8.266363 ACTACCGGGGTATAGAATTGAAATAA 57.734 34.615 6.32 0.00 0.00 1.40
2510 4427 8.887393 ACTACCGGGGTATAGAATTGAAATAAT 58.113 33.333 6.32 0.00 0.00 1.28
2542 4459 8.819152 AAAATCGCAAAAGTTTTATGTGTTTG 57.181 26.923 0.00 0.00 33.35 2.93
2543 4460 5.382573 TCGCAAAAGTTTTATGTGTTTGC 57.617 34.783 0.00 8.90 46.63 3.68
2550 4467 9.719279 CAAAAGTTTTATGTGTTTGCATTTCAT 57.281 25.926 0.00 0.00 0.00 2.57
2553 4470 9.979578 AAGTTTTATGTGTTTGCATTTCATAGA 57.020 25.926 0.00 0.00 0.00 1.98
2554 4471 9.630098 AGTTTTATGTGTTTGCATTTCATAGAG 57.370 29.630 0.00 0.00 0.00 2.43
2555 4472 9.624697 GTTTTATGTGTTTGCATTTCATAGAGA 57.375 29.630 0.00 0.00 0.00 3.10
2557 4474 9.844790 TTTATGTGTTTGCATTTCATAGAGAAG 57.155 29.630 0.00 0.00 37.57 2.85
2558 4475 6.882610 TGTGTTTGCATTTCATAGAGAAGT 57.117 33.333 0.00 0.00 37.57 3.01
2559 4476 7.275888 TGTGTTTGCATTTCATAGAGAAGTT 57.724 32.000 0.00 0.00 37.57 2.66
2560 4477 7.140705 TGTGTTTGCATTTCATAGAGAAGTTG 58.859 34.615 0.00 0.00 37.57 3.16
2561 4478 7.141363 GTGTTTGCATTTCATAGAGAAGTTGT 58.859 34.615 0.00 0.00 37.57 3.32
2562 4479 8.289618 GTGTTTGCATTTCATAGAGAAGTTGTA 58.710 33.333 0.00 0.00 37.57 2.41
2563 4480 8.506437 TGTTTGCATTTCATAGAGAAGTTGTAG 58.494 33.333 0.00 0.00 37.57 2.74
2564 4481 6.668541 TGCATTTCATAGAGAAGTTGTAGC 57.331 37.500 0.00 0.00 37.57 3.58
2565 4482 6.172630 TGCATTTCATAGAGAAGTTGTAGCA 58.827 36.000 0.00 0.00 37.57 3.49
2566 4483 6.314648 TGCATTTCATAGAGAAGTTGTAGCAG 59.685 38.462 0.00 0.00 37.57 4.24
2567 4484 6.314896 GCATTTCATAGAGAAGTTGTAGCAGT 59.685 38.462 0.00 0.00 37.57 4.40
2568 4485 7.148340 GCATTTCATAGAGAAGTTGTAGCAGTT 60.148 37.037 0.00 0.00 37.57 3.16
2569 4486 8.725148 CATTTCATAGAGAAGTTGTAGCAGTTT 58.275 33.333 0.00 0.00 37.57 2.66
2570 4487 8.677148 TTTCATAGAGAAGTTGTAGCAGTTTT 57.323 30.769 0.00 0.00 37.57 2.43
2571 4488 7.891183 TCATAGAGAAGTTGTAGCAGTTTTC 57.109 36.000 0.00 0.00 0.00 2.29
2572 4489 7.441836 TCATAGAGAAGTTGTAGCAGTTTTCA 58.558 34.615 0.00 0.00 0.00 2.69
2573 4490 8.097038 TCATAGAGAAGTTGTAGCAGTTTTCAT 58.903 33.333 0.00 0.00 0.00 2.57
2574 4491 8.725148 CATAGAGAAGTTGTAGCAGTTTTCATT 58.275 33.333 0.00 0.00 0.00 2.57
2575 4492 6.963796 AGAGAAGTTGTAGCAGTTTTCATTG 58.036 36.000 0.00 0.00 0.00 2.82
2576 4493 6.543831 AGAGAAGTTGTAGCAGTTTTCATTGT 59.456 34.615 0.00 0.00 0.00 2.71
2577 4494 7.715249 AGAGAAGTTGTAGCAGTTTTCATTGTA 59.285 33.333 0.00 0.00 0.00 2.41
2578 4495 8.220755 AGAAGTTGTAGCAGTTTTCATTGTAA 57.779 30.769 0.00 0.00 0.00 2.41
2579 4496 8.129211 AGAAGTTGTAGCAGTTTTCATTGTAAC 58.871 33.333 0.00 0.00 0.00 2.50
2580 4497 7.328277 AGTTGTAGCAGTTTTCATTGTAACA 57.672 32.000 0.00 0.00 0.00 2.41
2581 4498 7.767261 AGTTGTAGCAGTTTTCATTGTAACAA 58.233 30.769 0.00 0.00 0.00 2.83
2582 4499 8.247562 AGTTGTAGCAGTTTTCATTGTAACAAA 58.752 29.630 0.00 0.00 0.00 2.83
2583 4500 9.030301 GTTGTAGCAGTTTTCATTGTAACAAAT 57.970 29.630 0.00 0.00 0.00 2.32
2588 4505 9.683069 AGCAGTTTTCATTGTAACAAATAAGAG 57.317 29.630 0.00 0.00 0.00 2.85
2589 4506 8.915654 GCAGTTTTCATTGTAACAAATAAGAGG 58.084 33.333 0.00 0.00 0.00 3.69
2596 4513 9.177608 TCATTGTAACAAATAAGAGGAATCTGG 57.822 33.333 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.062293 TGGTACAGTCGATTCCACTTTTG 58.938 43.478 0.00 0.00 0.00 2.44
1 2 4.345859 TGGTACAGTCGATTCCACTTTT 57.654 40.909 0.00 0.00 0.00 2.27
51 52 2.436115 GGCCCGCAGACAGGTAAC 60.436 66.667 0.00 0.00 0.00 2.50
91 92 5.004448 GGATAGATAGAGGATGTCGTCACA 58.996 45.833 5.62 0.00 36.78 3.58
97 98 6.295011 CCACTTGTGGATAGATAGAGGATGTC 60.295 46.154 14.15 0.00 0.00 3.06
120 121 4.082523 GCGCAGAGTAGTGCCCCA 62.083 66.667 0.30 0.00 40.62 4.96
156 157 2.046285 CCAGGTCAACCGGCCAATC 61.046 63.158 0.00 0.00 42.08 2.67
157 158 2.035626 CCAGGTCAACCGGCCAAT 59.964 61.111 0.00 0.00 42.08 3.16
162 163 1.189524 TACAGTCCCAGGTCAACCGG 61.190 60.000 0.00 0.00 42.08 5.28
164 165 0.037605 CGTACAGTCCCAGGTCAACC 60.038 60.000 0.00 0.00 0.00 3.77
167 168 1.822990 GAATCGTACAGTCCCAGGTCA 59.177 52.381 0.00 0.00 0.00 4.02
170 171 1.486211 AGGAATCGTACAGTCCCAGG 58.514 55.000 7.78 0.00 31.25 4.45
173 174 1.340568 GCCTAGGAATCGTACAGTCCC 59.659 57.143 14.75 0.00 31.25 4.46
178 179 2.578786 TGATCGCCTAGGAATCGTACA 58.421 47.619 14.75 8.65 0.00 2.90
192 193 4.656041 GATGGCTAGCAATTATTGATCGC 58.344 43.478 18.24 10.55 37.07 4.58
197 198 4.456911 ACATCCGATGGCTAGCAATTATTG 59.543 41.667 18.24 9.86 33.60 1.90
198 199 4.456911 CACATCCGATGGCTAGCAATTATT 59.543 41.667 18.24 0.00 33.60 1.40
200 201 3.181455 ACACATCCGATGGCTAGCAATTA 60.181 43.478 18.24 1.04 33.60 1.40
215 217 1.338200 ACAAAGCGAGGAGACACATCC 60.338 52.381 0.00 0.00 39.89 3.51
274 284 3.146913 GCAGCCTCCTCTCGCTCT 61.147 66.667 0.00 0.00 31.40 4.09
297 307 2.885644 CGCTCACGGGGATTGACG 60.886 66.667 0.00 0.00 34.97 4.35
308 333 2.852431 CTTCGGACTCGGTCGCTCAC 62.852 65.000 0.00 0.00 36.95 3.51
366 392 1.625818 GTGAGGAGGAGGTTGTGTGAT 59.374 52.381 0.00 0.00 0.00 3.06
419 445 1.402984 GGTGAGGAGTCGTGCTACAAG 60.403 57.143 0.00 0.00 0.00 3.16
458 484 1.524002 CTGCGACCCATGGATGAGT 59.476 57.895 15.22 1.30 0.00 3.41
494 520 3.808656 GGGACGAGGACGACGACC 61.809 72.222 8.37 8.37 42.58 4.79
545 747 6.417930 CCATACAGTGATACAGTGATACAACG 59.582 42.308 12.56 0.00 38.11 4.10
550 752 7.654022 TTCACCATACAGTGATACAGTGATA 57.346 36.000 12.56 3.49 45.80 2.15
552 754 5.624509 GCTTCACCATACAGTGATACAGTGA 60.625 44.000 12.56 0.44 45.80 3.41
555 757 5.016051 AGCTTCACCATACAGTGATACAG 57.984 43.478 0.00 0.00 45.80 2.74
556 758 4.711846 AGAGCTTCACCATACAGTGATACA 59.288 41.667 0.00 0.00 45.80 2.29
557 759 5.046529 CAGAGCTTCACCATACAGTGATAC 58.953 45.833 0.00 0.00 45.80 2.24
558 760 4.711846 ACAGAGCTTCACCATACAGTGATA 59.288 41.667 0.00 0.00 45.80 2.15
563 765 5.046529 GTGATACAGAGCTTCACCATACAG 58.953 45.833 4.43 0.00 34.95 2.74
564 766 4.711846 AGTGATACAGAGCTTCACCATACA 59.288 41.667 11.06 0.00 40.46 2.29
567 769 3.517100 ACAGTGATACAGAGCTTCACCAT 59.483 43.478 11.06 0.00 40.46 3.55
568 770 2.899900 ACAGTGATACAGAGCTTCACCA 59.100 45.455 11.06 0.00 40.46 4.17
610 1946 1.406219 CTGGAGACGTCGATGCAACG 61.406 60.000 10.48 10.48 45.37 4.10
643 2057 0.329596 GGGGACATCTGCAAAGAGGT 59.670 55.000 0.00 0.00 35.39 3.85
664 2078 4.415332 GGGCGCAGAAGACGACGA 62.415 66.667 10.83 0.00 40.28 4.20
782 2199 4.506217 GTTTTCTTCACGTCGTCTTCTTG 58.494 43.478 0.00 0.00 0.00 3.02
817 2234 1.164662 TCGCTAGCCTTACGATCGCT 61.165 55.000 16.60 6.13 36.63 4.93
818 2235 0.997726 GTCGCTAGCCTTACGATCGC 60.998 60.000 16.60 0.00 38.22 4.58
819 2236 0.587285 AGTCGCTAGCCTTACGATCG 59.413 55.000 14.88 14.88 38.22 3.69
820 2237 3.458779 CTAGTCGCTAGCCTTACGATC 57.541 52.381 9.66 0.00 38.22 3.69
830 2247 1.083273 GACGCTCGCTAGTCGCTAG 60.083 63.158 8.87 8.87 37.16 3.42
832 2249 3.878519 GGACGCTCGCTAGTCGCT 61.879 66.667 2.24 0.00 38.20 4.93
834 2251 4.592936 CCGGACGCTCGCTAGTCG 62.593 72.222 0.00 0.00 38.20 4.18
835 2252 4.908877 GCCGGACGCTCGCTAGTC 62.909 72.222 5.05 0.00 36.70 2.59
1101 2572 2.108157 GAGTGCACGGTGACCACA 59.892 61.111 13.29 0.00 32.09 4.17
1206 2677 2.045131 GTAGCGGTCAGAGGGTCGT 61.045 63.158 0.00 0.00 0.00 4.34
1520 3006 1.750930 CATCTCCCGCACCTGCTAT 59.249 57.895 0.00 0.00 39.32 2.97
1585 3071 3.477530 ACAAACCTGACTAAGCCAAGAC 58.522 45.455 0.00 0.00 0.00 3.01
1618 3104 1.790481 GCCGAGTAAAATGAAGCACGC 60.790 52.381 0.00 0.00 0.00 5.34
1619 3105 1.202031 GGCCGAGTAAAATGAAGCACG 60.202 52.381 0.00 0.00 0.00 5.34
1750 3600 5.645497 AGAGCACCATAAACAAACTCAGATC 59.355 40.000 0.00 0.00 0.00 2.75
1755 3605 3.503748 AGCAGAGCACCATAAACAAACTC 59.496 43.478 0.00 0.00 0.00 3.01
1760 3610 2.568956 AGAGAGCAGAGCACCATAAACA 59.431 45.455 0.00 0.00 0.00 2.83
1918 3796 8.850454 TTTCGAAGAAGGAAAAATAACAACAG 57.150 30.769 0.00 0.00 45.90 3.16
1992 3875 4.446311 GGAATCCTGCCAGTTATACATGGT 60.446 45.833 0.00 0.00 38.91 3.55
2026 3909 4.895297 TCTGAATCCTGCCAGTTTCTTTTT 59.105 37.500 6.30 0.00 0.00 1.94
2027 3910 4.279420 GTCTGAATCCTGCCAGTTTCTTTT 59.721 41.667 6.30 0.00 0.00 2.27
2028 3911 3.823304 GTCTGAATCCTGCCAGTTTCTTT 59.177 43.478 6.30 0.00 0.00 2.52
2029 3912 3.181440 TGTCTGAATCCTGCCAGTTTCTT 60.181 43.478 6.30 0.00 0.00 2.52
2030 3913 2.373169 TGTCTGAATCCTGCCAGTTTCT 59.627 45.455 6.30 0.00 0.00 2.52
2031 3914 2.746362 CTGTCTGAATCCTGCCAGTTTC 59.254 50.000 0.00 0.00 0.00 2.78
2032 3915 2.107204 ACTGTCTGAATCCTGCCAGTTT 59.893 45.455 0.00 0.00 29.32 2.66
2033 3916 1.701847 ACTGTCTGAATCCTGCCAGTT 59.298 47.619 0.00 0.00 29.32 3.16
2034 3917 1.277557 GACTGTCTGAATCCTGCCAGT 59.722 52.381 0.00 0.00 35.97 4.00
2035 3918 1.277273 TGACTGTCTGAATCCTGCCAG 59.723 52.381 9.51 0.00 0.00 4.85
2036 3919 1.351076 TGACTGTCTGAATCCTGCCA 58.649 50.000 9.51 0.00 0.00 4.92
2037 3920 2.093288 TCATGACTGTCTGAATCCTGCC 60.093 50.000 9.51 0.00 0.00 4.85
2038 3921 2.935201 GTCATGACTGTCTGAATCCTGC 59.065 50.000 18.83 0.00 0.00 4.85
2039 3922 4.081807 TCTGTCATGACTGTCTGAATCCTG 60.082 45.833 25.55 0.34 0.00 3.86
2040 3923 4.092279 TCTGTCATGACTGTCTGAATCCT 58.908 43.478 25.55 0.00 0.00 3.24
2041 3924 4.431809 CTCTGTCATGACTGTCTGAATCC 58.568 47.826 25.55 0.00 0.00 3.01
2042 3925 3.864583 GCTCTGTCATGACTGTCTGAATC 59.135 47.826 25.55 2.50 0.00 2.52
2043 3926 3.260128 TGCTCTGTCATGACTGTCTGAAT 59.740 43.478 25.55 0.00 0.00 2.57
2044 3927 2.629617 TGCTCTGTCATGACTGTCTGAA 59.370 45.455 25.55 12.04 0.00 3.02
2045 3928 2.242043 TGCTCTGTCATGACTGTCTGA 58.758 47.619 25.55 14.21 0.00 3.27
2046 3929 2.738013 TGCTCTGTCATGACTGTCTG 57.262 50.000 25.55 18.44 0.00 3.51
2051 3934 2.632028 ACTGACTTGCTCTGTCATGACT 59.368 45.455 25.55 3.48 42.57 3.41
2055 3938 2.896044 TGAGACTGACTTGCTCTGTCAT 59.104 45.455 12.07 3.18 45.80 3.06
2059 3942 1.668337 CCGTGAGACTGACTTGCTCTG 60.668 57.143 0.00 0.00 0.00 3.35
2065 3948 2.431057 ACAAGAACCGTGAGACTGACTT 59.569 45.455 0.00 0.00 0.00 3.01
2146 4036 2.526120 CCGCAAGCCTACTTAGCGC 61.526 63.158 0.00 0.00 44.62 5.92
2152 4042 1.263356 TTGACTACCGCAAGCCTACT 58.737 50.000 0.00 0.00 0.00 2.57
2180 4070 4.058124 GTGGAGGACAAATTTTGCCTTTC 58.942 43.478 19.39 16.03 37.33 2.62
2209 4099 3.304794 GGACCTCGATACCTCTTGAATCG 60.305 52.174 0.00 0.00 42.90 3.34
2218 4108 1.479021 GCCACTAGGACCTCGATACCT 60.479 57.143 0.00 9.49 36.89 3.08
2222 4112 2.491022 GCGCCACTAGGACCTCGAT 61.491 63.158 0.00 0.00 36.89 3.59
2223 4113 3.138798 GCGCCACTAGGACCTCGA 61.139 66.667 0.00 0.00 36.89 4.04
2224 4114 4.554363 CGCGCCACTAGGACCTCG 62.554 72.222 0.00 0.00 36.89 4.63
2225 4115 3.138798 TCGCGCCACTAGGACCTC 61.139 66.667 0.00 0.00 36.89 3.85
2226 4116 3.450115 GTCGCGCCACTAGGACCT 61.450 66.667 0.00 0.00 36.89 3.85
2241 4158 0.248843 CTCCTCTTGGTCAGGCTGTC 59.751 60.000 15.27 8.99 34.23 3.51
2247 4164 1.417890 ACCACAACTCCTCTTGGTCAG 59.582 52.381 0.00 0.00 37.90 3.51
2299 4216 6.363577 TGAAGACTTAACAAAGCAAGAGTG 57.636 37.500 0.00 0.00 0.00 3.51
2331 4248 3.983044 AAGAGTGGGTCTACATTCACC 57.017 47.619 0.00 0.00 32.65 4.02
2337 4254 7.179966 TCTAATAGACAAAGAGTGGGTCTACA 58.820 38.462 0.00 0.00 44.32 2.74
2339 4256 7.287927 CCATCTAATAGACAAAGAGTGGGTCTA 59.712 40.741 0.00 0.00 45.24 2.59
2361 4278 2.678336 GGATGAGTGGTTTTCGTCCATC 59.322 50.000 8.28 0.00 45.86 3.51
2371 4288 3.403038 CTTGAAAGACGGATGAGTGGTT 58.597 45.455 0.00 0.00 0.00 3.67
2375 4292 3.665190 GTTCCTTGAAAGACGGATGAGT 58.335 45.455 0.00 0.00 0.00 3.41
2376 4293 2.668457 CGTTCCTTGAAAGACGGATGAG 59.332 50.000 0.00 0.00 32.29 2.90
2377 4294 2.297880 TCGTTCCTTGAAAGACGGATGA 59.702 45.455 4.95 0.00 36.27 2.92
2378 4295 2.683968 TCGTTCCTTGAAAGACGGATG 58.316 47.619 4.95 0.00 36.27 3.51
2379 4296 3.396260 TTCGTTCCTTGAAAGACGGAT 57.604 42.857 4.95 0.00 36.27 4.18
2380 4297 2.894763 TTCGTTCCTTGAAAGACGGA 57.105 45.000 4.95 0.00 36.27 4.69
2381 4298 3.250040 ACAATTCGTTCCTTGAAAGACGG 59.750 43.478 4.95 0.00 36.27 4.79
2382 4299 4.025229 TCACAATTCGTTCCTTGAAAGACG 60.025 41.667 0.00 0.00 30.67 4.18
2383 4300 5.418310 TCACAATTCGTTCCTTGAAAGAC 57.582 39.130 0.00 0.00 30.67 3.01
2384 4301 5.997746 AGATCACAATTCGTTCCTTGAAAGA 59.002 36.000 0.00 0.00 0.00 2.52
2385 4302 6.246420 AGATCACAATTCGTTCCTTGAAAG 57.754 37.500 0.00 0.00 0.00 2.62
2386 4303 6.293955 GGAAGATCACAATTCGTTCCTTGAAA 60.294 38.462 0.00 0.00 32.33 2.69
2387 4304 5.181245 GGAAGATCACAATTCGTTCCTTGAA 59.819 40.000 0.00 0.00 32.33 2.69
2388 4305 4.695455 GGAAGATCACAATTCGTTCCTTGA 59.305 41.667 0.00 0.00 32.33 3.02
2389 4306 4.436050 CGGAAGATCACAATTCGTTCCTTG 60.436 45.833 0.00 0.00 32.79 3.61
2390 4307 3.684788 CGGAAGATCACAATTCGTTCCTT 59.315 43.478 0.00 0.00 32.79 3.36
2391 4308 3.262420 CGGAAGATCACAATTCGTTCCT 58.738 45.455 0.00 0.00 32.79 3.36
2392 4309 2.223044 GCGGAAGATCACAATTCGTTCC 60.223 50.000 0.00 0.00 0.00 3.62
2393 4310 2.223044 GGCGGAAGATCACAATTCGTTC 60.223 50.000 0.00 0.00 0.00 3.95
2394 4311 1.737793 GGCGGAAGATCACAATTCGTT 59.262 47.619 0.00 0.00 0.00 3.85
2395 4312 1.369625 GGCGGAAGATCACAATTCGT 58.630 50.000 0.00 0.00 0.00 3.85
2396 4313 0.657840 GGGCGGAAGATCACAATTCG 59.342 55.000 0.00 0.00 0.00 3.34
2397 4314 1.750193 TGGGCGGAAGATCACAATTC 58.250 50.000 0.00 0.00 0.00 2.17
2398 4315 2.214376 TTGGGCGGAAGATCACAATT 57.786 45.000 0.00 0.00 0.00 2.32
2399 4316 1.818674 GTTTGGGCGGAAGATCACAAT 59.181 47.619 0.00 0.00 0.00 2.71
2400 4317 1.243902 GTTTGGGCGGAAGATCACAA 58.756 50.000 0.00 0.00 0.00 3.33
2401 4318 0.953471 CGTTTGGGCGGAAGATCACA 60.953 55.000 0.00 0.00 0.00 3.58
2402 4319 0.953960 ACGTTTGGGCGGAAGATCAC 60.954 55.000 0.00 0.00 35.98 3.06
2403 4320 0.953471 CACGTTTGGGCGGAAGATCA 60.953 55.000 0.00 0.00 35.98 2.92
2404 4321 0.672401 TCACGTTTGGGCGGAAGATC 60.672 55.000 0.00 0.00 35.98 2.75
2405 4322 0.250553 TTCACGTTTGGGCGGAAGAT 60.251 50.000 0.00 0.00 35.98 2.40
2406 4323 1.146485 TTCACGTTTGGGCGGAAGA 59.854 52.632 0.00 0.00 35.98 2.87
2407 4324 1.281656 GTTCACGTTTGGGCGGAAG 59.718 57.895 0.00 0.00 35.98 3.46
2408 4325 2.535788 CGTTCACGTTTGGGCGGAA 61.536 57.895 0.00 0.00 35.98 4.30
2409 4326 2.919960 TTCGTTCACGTTTGGGCGGA 62.920 55.000 0.00 0.00 40.80 5.54
2410 4327 2.438385 CTTCGTTCACGTTTGGGCGG 62.438 60.000 0.00 0.00 40.80 6.13
2411 4328 1.083015 CTTCGTTCACGTTTGGGCG 60.083 57.895 0.00 0.00 40.80 6.13
2412 4329 0.234884 CTCTTCGTTCACGTTTGGGC 59.765 55.000 0.00 0.00 40.80 5.36
2413 4330 0.865769 CCTCTTCGTTCACGTTTGGG 59.134 55.000 0.00 0.00 40.80 4.12
2414 4331 1.525619 GACCTCTTCGTTCACGTTTGG 59.474 52.381 0.00 1.41 40.80 3.28
2415 4332 1.525619 GGACCTCTTCGTTCACGTTTG 59.474 52.381 0.00 0.00 40.80 2.93
2416 4333 1.411612 AGGACCTCTTCGTTCACGTTT 59.588 47.619 0.00 0.00 40.80 3.60
2417 4334 1.000496 GAGGACCTCTTCGTTCACGTT 60.000 52.381 14.72 0.00 40.80 3.99
2418 4335 0.597072 GAGGACCTCTTCGTTCACGT 59.403 55.000 14.72 0.00 40.80 4.49
2419 4336 0.882474 AGAGGACCTCTTCGTTCACG 59.118 55.000 18.94 0.00 37.60 4.35
2428 4345 0.968393 GTGAGCCGAAGAGGACCTCT 60.968 60.000 18.94 18.94 43.37 3.69
2429 4346 1.513622 GTGAGCCGAAGAGGACCTC 59.486 63.158 14.15 14.15 45.00 3.85
2430 4347 2.344203 CGTGAGCCGAAGAGGACCT 61.344 63.158 0.00 0.00 45.00 3.85
2431 4348 2.182030 CGTGAGCCGAAGAGGACC 59.818 66.667 0.00 0.00 45.00 4.46
2432 4349 1.444553 CACGTGAGCCGAAGAGGAC 60.445 63.158 10.90 0.00 45.00 3.85
2433 4350 1.901948 ACACGTGAGCCGAAGAGGA 60.902 57.895 25.01 0.00 45.00 3.71
2434 4351 1.734477 CACACGTGAGCCGAAGAGG 60.734 63.158 25.01 0.00 44.97 3.69
2435 4352 1.734477 CCACACGTGAGCCGAAGAG 60.734 63.158 25.01 0.00 40.70 2.85
2436 4353 2.197605 TCCACACGTGAGCCGAAGA 61.198 57.895 25.01 3.53 40.70 2.87
2437 4354 2.022129 GTCCACACGTGAGCCGAAG 61.022 63.158 25.01 0.82 40.70 3.79
2438 4355 2.028484 GTCCACACGTGAGCCGAA 59.972 61.111 25.01 0.00 40.70 4.30
2439 4356 4.337060 CGTCCACACGTGAGCCGA 62.337 66.667 25.01 5.13 41.42 5.54
2440 4357 3.834447 TTCGTCCACACGTGAGCCG 62.834 63.158 25.01 18.21 46.76 5.52
2441 4358 2.022129 CTTCGTCCACACGTGAGCC 61.022 63.158 25.01 6.68 46.76 4.70
2442 4359 1.004277 CTCTTCGTCCACACGTGAGC 61.004 60.000 25.01 7.87 46.76 4.26
2443 4360 0.311165 ACTCTTCGTCCACACGTGAG 59.689 55.000 25.01 15.20 46.76 3.51
2444 4361 0.309922 GACTCTTCGTCCACACGTGA 59.690 55.000 25.01 0.00 46.76 4.35
2445 4362 0.030235 TGACTCTTCGTCCACACGTG 59.970 55.000 15.48 15.48 46.76 4.49
2446 4363 0.030369 GTGACTCTTCGTCCACACGT 59.970 55.000 0.00 0.00 46.76 4.49
2447 4364 4.456883 AGTGTGACTCTTCGTCCACACG 62.457 54.545 15.76 0.00 46.87 4.49
2448 4365 1.067212 AGTGTGACTCTTCGTCCACAC 59.933 52.381 14.43 14.43 45.08 3.82
2449 4366 1.399714 AGTGTGACTCTTCGTCCACA 58.600 50.000 12.67 0.00 41.89 4.17
2450 4367 2.395654 GAAGTGTGACTCTTCGTCCAC 58.604 52.381 11.08 0.00 42.13 4.02
2451 4368 2.795175 GAAGTGTGACTCTTCGTCCA 57.205 50.000 11.08 0.00 42.13 4.02
2456 4373 0.318762 AGGCCGAAGTGTGACTCTTC 59.681 55.000 15.34 15.34 38.22 2.87
2457 4374 1.546476 CTAGGCCGAAGTGTGACTCTT 59.454 52.381 0.00 0.00 0.00 2.85
2458 4375 1.178276 CTAGGCCGAAGTGTGACTCT 58.822 55.000 0.00 0.00 0.00 3.24
2459 4376 0.173708 CCTAGGCCGAAGTGTGACTC 59.826 60.000 0.00 0.00 0.00 3.36
2460 4377 1.258445 CCCTAGGCCGAAGTGTGACT 61.258 60.000 2.05 0.00 0.00 3.41
2461 4378 1.218316 CCCTAGGCCGAAGTGTGAC 59.782 63.158 2.05 0.00 0.00 3.67
2462 4379 1.987855 CCCCTAGGCCGAAGTGTGA 60.988 63.158 2.05 0.00 0.00 3.58
2463 4380 1.961180 CTCCCCTAGGCCGAAGTGTG 61.961 65.000 2.05 0.00 0.00 3.82
2464 4381 1.686110 CTCCCCTAGGCCGAAGTGT 60.686 63.158 2.05 0.00 0.00 3.55
2465 4382 2.435693 CCTCCCCTAGGCCGAAGTG 61.436 68.421 2.05 0.00 38.97 3.16
2466 4383 2.041819 CCTCCCCTAGGCCGAAGT 60.042 66.667 2.05 0.00 38.97 3.01
2467 4384 2.134933 GTCCTCCCCTAGGCCGAAG 61.135 68.421 2.05 0.00 46.10 3.79
2468 4385 1.291459 TAGTCCTCCCCTAGGCCGAA 61.291 60.000 2.05 0.00 46.10 4.30
2469 4386 1.698840 TAGTCCTCCCCTAGGCCGA 60.699 63.158 2.05 0.00 46.10 5.54
2470 4387 1.531128 GTAGTCCTCCCCTAGGCCG 60.531 68.421 2.05 0.00 46.10 6.13
2471 4388 1.152290 GGTAGTCCTCCCCTAGGCC 60.152 68.421 2.05 0.00 46.10 5.19
2472 4389 1.531128 CGGTAGTCCTCCCCTAGGC 60.531 68.421 2.05 0.00 46.10 3.93
2474 4391 1.153292 CCCGGTAGTCCTCCCCTAG 59.847 68.421 0.00 0.00 0.00 3.02
2475 4392 2.397902 CCCCGGTAGTCCTCCCCTA 61.398 68.421 0.00 0.00 0.00 3.53
2476 4393 3.763757 CCCCGGTAGTCCTCCCCT 61.764 72.222 0.00 0.00 0.00 4.79
2477 4394 2.028662 ATACCCCGGTAGTCCTCCCC 62.029 65.000 0.00 0.00 33.77 4.81
2478 4395 0.779997 TATACCCCGGTAGTCCTCCC 59.220 60.000 0.00 0.00 33.77 4.30
2479 4396 1.707427 TCTATACCCCGGTAGTCCTCC 59.293 57.143 0.00 0.00 33.77 4.30
2480 4397 3.515602 TTCTATACCCCGGTAGTCCTC 57.484 52.381 0.00 0.00 33.77 3.71
2481 4398 4.140853 TCAATTCTATACCCCGGTAGTCCT 60.141 45.833 0.00 0.00 33.77 3.85
2482 4399 4.154942 TCAATTCTATACCCCGGTAGTCC 58.845 47.826 0.00 0.00 33.77 3.85
2483 4400 5.796424 TTCAATTCTATACCCCGGTAGTC 57.204 43.478 0.00 0.00 33.77 2.59
2484 4401 6.758806 ATTTCAATTCTATACCCCGGTAGT 57.241 37.500 0.00 0.00 33.77 2.73
2516 4433 9.271738 CAAACACATAAAACTTTTGCGATTTTT 57.728 25.926 0.00 0.00 0.00 1.94
2517 4434 7.427895 GCAAACACATAAAACTTTTGCGATTTT 59.572 29.630 1.94 0.00 41.73 1.82
2518 4435 6.904543 GCAAACACATAAAACTTTTGCGATTT 59.095 30.769 1.94 0.00 41.73 2.17
2519 4436 6.418141 GCAAACACATAAAACTTTTGCGATT 58.582 32.000 1.94 0.00 41.73 3.34
2520 4437 5.973158 GCAAACACATAAAACTTTTGCGAT 58.027 33.333 1.94 0.00 41.73 4.58
2521 4438 5.382573 GCAAACACATAAAACTTTTGCGA 57.617 34.783 1.94 0.00 41.73 5.10
2524 4441 9.719279 ATGAAATGCAAACACATAAAACTTTTG 57.281 25.926 0.00 0.00 0.00 2.44
2527 4444 9.979578 TCTATGAAATGCAAACACATAAAACTT 57.020 25.926 0.00 0.00 0.00 2.66
2528 4445 9.630098 CTCTATGAAATGCAAACACATAAAACT 57.370 29.630 0.00 0.00 0.00 2.66
2529 4446 9.624697 TCTCTATGAAATGCAAACACATAAAAC 57.375 29.630 0.00 0.00 0.00 2.43
2531 4448 9.844790 CTTCTCTATGAAATGCAAACACATAAA 57.155 29.630 0.00 0.00 33.79 1.40
2532 4449 9.013229 ACTTCTCTATGAAATGCAAACACATAA 57.987 29.630 0.00 0.00 33.79 1.90
2533 4450 8.565896 ACTTCTCTATGAAATGCAAACACATA 57.434 30.769 0.00 0.00 33.79 2.29
2534 4451 7.458409 ACTTCTCTATGAAATGCAAACACAT 57.542 32.000 0.00 0.00 33.79 3.21
2535 4452 6.882610 ACTTCTCTATGAAATGCAAACACA 57.117 33.333 0.00 0.00 33.79 3.72
2536 4453 7.141363 ACAACTTCTCTATGAAATGCAAACAC 58.859 34.615 0.00 0.00 33.79 3.32
2537 4454 7.275888 ACAACTTCTCTATGAAATGCAAACA 57.724 32.000 0.00 0.00 33.79 2.83
2538 4455 7.483059 GCTACAACTTCTCTATGAAATGCAAAC 59.517 37.037 0.00 0.00 33.79 2.93
2539 4456 7.174772 TGCTACAACTTCTCTATGAAATGCAAA 59.825 33.333 0.00 0.00 33.79 3.68
2540 4457 6.654582 TGCTACAACTTCTCTATGAAATGCAA 59.345 34.615 0.00 0.00 33.79 4.08
2541 4458 6.172630 TGCTACAACTTCTCTATGAAATGCA 58.827 36.000 0.00 0.00 33.79 3.96
2542 4459 6.314896 ACTGCTACAACTTCTCTATGAAATGC 59.685 38.462 0.00 0.00 33.79 3.56
2543 4460 7.840342 ACTGCTACAACTTCTCTATGAAATG 57.160 36.000 0.00 0.00 33.79 2.32
2544 4461 8.854614 AAACTGCTACAACTTCTCTATGAAAT 57.145 30.769 0.00 0.00 33.79 2.17
2545 4462 8.677148 AAAACTGCTACAACTTCTCTATGAAA 57.323 30.769 0.00 0.00 33.79 2.69
2546 4463 7.931407 TGAAAACTGCTACAACTTCTCTATGAA 59.069 33.333 0.00 0.00 0.00 2.57
2547 4464 7.441836 TGAAAACTGCTACAACTTCTCTATGA 58.558 34.615 0.00 0.00 0.00 2.15
2548 4465 7.658179 TGAAAACTGCTACAACTTCTCTATG 57.342 36.000 0.00 0.00 0.00 2.23
2549 4466 8.725148 CAATGAAAACTGCTACAACTTCTCTAT 58.275 33.333 0.00 0.00 0.00 1.98
2550 4467 7.715249 ACAATGAAAACTGCTACAACTTCTCTA 59.285 33.333 0.00 0.00 0.00 2.43
2551 4468 6.543831 ACAATGAAAACTGCTACAACTTCTCT 59.456 34.615 0.00 0.00 0.00 3.10
2552 4469 6.729187 ACAATGAAAACTGCTACAACTTCTC 58.271 36.000 0.00 0.00 0.00 2.87
2553 4470 6.699575 ACAATGAAAACTGCTACAACTTCT 57.300 33.333 0.00 0.00 0.00 2.85
2554 4471 7.913297 TGTTACAATGAAAACTGCTACAACTTC 59.087 33.333 0.00 0.00 0.00 3.01
2555 4472 7.767261 TGTTACAATGAAAACTGCTACAACTT 58.233 30.769 0.00 0.00 0.00 2.66
2556 4473 7.328277 TGTTACAATGAAAACTGCTACAACT 57.672 32.000 0.00 0.00 0.00 3.16
2557 4474 7.979115 TTGTTACAATGAAAACTGCTACAAC 57.021 32.000 0.00 0.00 0.00 3.32
2562 4479 9.683069 CTCTTATTTGTTACAATGAAAACTGCT 57.317 29.630 0.00 0.00 0.00 4.24
2563 4480 8.915654 CCTCTTATTTGTTACAATGAAAACTGC 58.084 33.333 0.00 0.00 0.00 4.40
2570 4487 9.177608 CCAGATTCCTCTTATTTGTTACAATGA 57.822 33.333 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.