Multiple sequence alignment - TraesCS3D01G225100

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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 TraesCS3D01G225100 chr3D 100.000 2868 0 0 1 2868 306075045 306072178 0.000000e+00 5297
1 TraesCS3D01G225100 chr3D 98.194 720 13 0 2149 2868 306048420 306047701 0.000000e+00 1258
2 TraesCS3D01G225100 chr3B 92.785 1483 72 15 473 1928 415044710 415046184 0.000000e+00 2113
3 TraesCS3D01G225100 chr3A 89.398 1179 79 21 4 1162 424537750 424536598 0.000000e+00 1443
4 TraesCS3D01G225100 chr3A 94.000 50 2 1 1773 1822 424536557 424536509 1.100000e-09 75
5 TraesCS3D01G225100 chr1D 97.222 720 19 1 2149 2868 99309837 99310555 0.000000e+00 1218
6 TraesCS3D01G225100 chrUn 96.944 720 21 1 2149 2868 44881254 44881972 0.000000e+00 1206
7 TraesCS3D01G225100 chrUn 96.806 720 23 0 2149 2868 358153095 358153814 0.000000e+00 1203
8 TraesCS3D01G225100 chrUn 81.614 223 37 2 1930 2148 108464946 108464724 6.310000e-42 182
9 TraesCS3D01G225100 chr6D 96.667 720 24 0 2149 2868 138295891 138296610 0.000000e+00 1197
10 TraesCS3D01G225100 chr6D 96.394 721 25 1 2148 2868 73450052 73450771 0.000000e+00 1186
11 TraesCS3D01G225100 chr6D 75.481 779 103 49 857 1596 17485428 17486157 1.670000e-77 300
12 TraesCS3D01G225100 chr7D 96.528 720 25 0 2149 2868 484444184 484444903 0.000000e+00 1192
13 TraesCS3D01G225100 chr7D 96.404 723 25 1 2146 2868 444290820 444290099 0.000000e+00 1190
14 TraesCS3D01G225100 chr7D 88.485 165 16 3 1987 2148 413129011 413129175 2.250000e-46 196
15 TraesCS3D01G225100 chr5D 96.389 720 26 0 2149 2868 473278687 473277968 0.000000e+00 1186
16 TraesCS3D01G225100 chr5D 86.878 221 19 4 1930 2148 436204322 436204110 3.690000e-59 239
17 TraesCS3D01G225100 chr5D 83.111 225 33 4 1929 2148 487597837 487597613 1.740000e-47 200
18 TraesCS3D01G225100 chr6B 76.628 599 92 31 1036 1596 31278430 31279018 1.300000e-73 287
19 TraesCS3D01G225100 chr6B 76.501 583 89 34 1083 1646 31714238 31713685 1.010000e-69 274
20 TraesCS3D01G225100 chr6B 91.333 150 12 1 1452 1600 30654558 30654707 1.350000e-48 204
21 TraesCS3D01G225100 chr6B 91.333 150 12 1 1452 1600 30656379 30656528 1.350000e-48 204
22 TraesCS3D01G225100 chr6B 91.333 150 12 1 1452 1600 30735657 30735806 1.350000e-48 204
23 TraesCS3D01G225100 chr6B 91.333 150 12 1 1452 1600 30814317 30814466 1.350000e-48 204
24 TraesCS3D01G225100 chr6B 90.667 150 13 1 1452 1600 30652466 30652615 6.270000e-47 198
25 TraesCS3D01G225100 chr2D 86.486 222 20 4 1929 2148 351048383 351048170 4.780000e-58 235
26 TraesCS3D01G225100 chr2D 82.819 227 34 4 1926 2148 620162757 620162532 6.270000e-47 198
27 TraesCS3D01G225100 chr5A 88.679 159 15 3 1993 2148 480178562 480178404 1.050000e-44 191
28 TraesCS3D01G225100 chr1A 82.629 213 29 7 1942 2148 574508102 574507892 6.310000e-42 182
29 TraesCS3D01G225100 chr7B 82.199 191 30 3 1962 2148 709083878 709083688 8.220000e-36 161


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 TraesCS3D01G225100 chr3D 306072178 306075045 2867 True 5297 5297 100.000 1 2868 1 chr3D.!!$R2 2867
1 TraesCS3D01G225100 chr3D 306047701 306048420 719 True 1258 1258 98.194 2149 2868 1 chr3D.!!$R1 719
2 TraesCS3D01G225100 chr3B 415044710 415046184 1474 False 2113 2113 92.785 473 1928 1 chr3B.!!$F1 1455
3 TraesCS3D01G225100 chr3A 424536509 424537750 1241 True 759 1443 91.699 4 1822 2 chr3A.!!$R1 1818
4 TraesCS3D01G225100 chr1D 99309837 99310555 718 False 1218 1218 97.222 2149 2868 1 chr1D.!!$F1 719
5 TraesCS3D01G225100 chrUn 44881254 44881972 718 False 1206 1206 96.944 2149 2868 1 chrUn.!!$F1 719
6 TraesCS3D01G225100 chrUn 358153095 358153814 719 False 1203 1203 96.806 2149 2868 1 chrUn.!!$F2 719
7 TraesCS3D01G225100 chr6D 138295891 138296610 719 False 1197 1197 96.667 2149 2868 1 chr6D.!!$F3 719
8 TraesCS3D01G225100 chr6D 73450052 73450771 719 False 1186 1186 96.394 2148 2868 1 chr6D.!!$F2 720
9 TraesCS3D01G225100 chr6D 17485428 17486157 729 False 300 300 75.481 857 1596 1 chr6D.!!$F1 739
10 TraesCS3D01G225100 chr7D 484444184 484444903 719 False 1192 1192 96.528 2149 2868 1 chr7D.!!$F2 719
11 TraesCS3D01G225100 chr7D 444290099 444290820 721 True 1190 1190 96.404 2146 2868 1 chr7D.!!$R1 722
12 TraesCS3D01G225100 chr5D 473277968 473278687 719 True 1186 1186 96.389 2149 2868 1 chr5D.!!$R2 719
13 TraesCS3D01G225100 chr6B 31278430 31279018 588 False 287 287 76.628 1036 1596 1 chr6B.!!$F3 560
14 TraesCS3D01G225100 chr6B 31713685 31714238 553 True 274 274 76.501 1083 1646 1 chr6B.!!$R1 563
15 TraesCS3D01G225100 chr6B 30652466 30656528 4062 False 202 204 91.111 1452 1600 3 chr6B.!!$F4 148

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
412 426 0.043637 ATGTTTAGGGTCTCGGGGGA 59.956 55.0 0.0 0.0 0.0 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1931 4409 0.102481 ACGTGTCCGGATGTAGATGC 59.898 55.0 7.81 0.0 38.78 3.91 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
34 35 1.160137 GCTTCGACACTGGAGCAAAT 58.840 50.000 0.00 0.00 0.00 2.32
35 36 1.135859 GCTTCGACACTGGAGCAAATG 60.136 52.381 0.00 0.00 0.00 2.32
36 37 1.466167 CTTCGACACTGGAGCAAATGG 59.534 52.381 0.00 0.00 0.00 3.16
48 49 1.405469 GCAAATGGCATCGCAACGAC 61.405 55.000 14.88 0.00 43.97 4.34
49 50 1.127571 CAAATGGCATCGCAACGACG 61.128 55.000 0.00 0.00 39.18 5.12
51 52 3.657448 ATGGCATCGCAACGACGGA 62.657 57.895 0.00 0.00 39.18 4.69
53 54 4.210304 GCATCGCAACGACGGAGC 62.210 66.667 0.00 1.34 39.18 4.70
64 65 1.901085 GACGGAGCCTGAGGACATT 59.099 57.895 0.65 0.00 0.00 2.71
72 73 2.846206 AGCCTGAGGACATTAATCCACA 59.154 45.455 0.65 0.00 41.73 4.17
94 95 4.045781 TGATGCCGCCACCACCAT 62.046 61.111 0.00 0.00 0.00 3.55
100 101 1.525995 CCGCCACCACCATACATCC 60.526 63.158 0.00 0.00 0.00 3.51
107 108 2.507886 CACCACCATACATCCCCACTTA 59.492 50.000 0.00 0.00 0.00 2.24
122 123 5.724854 TCCCCACTTAAATAGACTAGCAAGT 59.275 40.000 0.00 2.03 39.21 3.16
137 139 3.959573 GCAAGTAGCAACCAGATCATC 57.040 47.619 0.00 0.00 44.79 2.92
157 159 1.003545 CACTCACCAACAAGCAGAACG 60.004 52.381 0.00 0.00 0.00 3.95
169 171 3.973516 AGAACGCCGTGTCGCAGA 61.974 61.111 0.00 0.00 0.00 4.26
175 177 3.084579 CCGTGTCGCAGAAGCATC 58.915 61.111 0.00 0.00 39.69 3.91
195 197 5.455392 CATCTGAAGCTTTATTATTGGGCG 58.545 41.667 0.00 0.00 0.00 6.13
196 198 4.523083 TCTGAAGCTTTATTATTGGGCGT 58.477 39.130 0.00 0.00 0.00 5.68
200 202 2.949644 AGCTTTATTATTGGGCGTCACC 59.050 45.455 0.00 0.00 37.93 4.02
211 213 3.041940 CGTCACCGTCACCCTTGC 61.042 66.667 0.00 0.00 0.00 4.01
222 224 1.914764 ACCCTTGCCAAAGCCATGG 60.915 57.895 7.63 7.63 43.70 3.66
274 283 3.373130 GCCCTAAAACCTAAAGCTACACG 59.627 47.826 0.00 0.00 0.00 4.49
282 291 2.360165 CCTAAAGCTACACGACCCGTAT 59.640 50.000 0.00 0.00 38.32 3.06
298 307 1.693467 GTATGCGCGTATTCCGATGA 58.307 50.000 16.54 0.00 39.56 2.92
311 321 1.450312 CGATGACCCCCTTCAGCAC 60.450 63.158 0.00 0.00 31.01 4.40
317 327 1.628846 GACCCCCTTCAGCACTAAAGA 59.371 52.381 0.00 0.00 0.00 2.52
329 339 2.229302 GCACTAAAGACTGAGAGGTCGT 59.771 50.000 0.00 0.00 40.76 4.34
330 340 3.671164 GCACTAAAGACTGAGAGGTCGTC 60.671 52.174 0.00 0.00 40.76 4.20
331 341 2.743126 ACTAAAGACTGAGAGGTCGTCG 59.257 50.000 0.00 0.00 40.76 5.12
340 350 1.753463 GAGGTCGTCGGTGGAGGAT 60.753 63.158 0.00 0.00 39.10 3.24
348 358 4.195334 GGTGGAGGATGGCGCCAT 62.195 66.667 41.16 41.16 39.69 4.40
357 367 1.680338 GATGGCGCCATAAGAAGGTT 58.320 50.000 40.56 18.23 36.70 3.50
359 369 0.393808 TGGCGCCATAAGAAGGTTCC 60.394 55.000 29.03 0.00 0.00 3.62
361 371 1.101635 GCGCCATAAGAAGGTTCCCC 61.102 60.000 0.00 0.00 0.00 4.81
376 386 1.272807 TCCCCTTGAAACCCTAGTCG 58.727 55.000 0.00 0.00 0.00 4.18
387 397 1.442148 CCTAGTCGCCTTAGCCACC 59.558 63.158 0.00 0.00 34.57 4.61
389 399 2.351336 CTAGTCGCCTTAGCCACCGG 62.351 65.000 0.00 0.00 34.57 5.28
404 414 0.322187 ACCGGCACATGTTTAGGGTC 60.322 55.000 0.00 0.00 0.00 4.46
412 426 0.043637 ATGTTTAGGGTCTCGGGGGA 59.956 55.000 0.00 0.00 0.00 4.81
449 463 1.107114 AGACCATCGTGAGCTACCTG 58.893 55.000 0.00 0.00 0.00 4.00
515 529 3.050619 GTGTACCGTAGCATAGCATCAC 58.949 50.000 0.00 0.00 0.00 3.06
526 540 0.550914 TAGCATCACCCCATTCCCAC 59.449 55.000 0.00 0.00 0.00 4.61
626 640 7.040494 TCAGAGATTCTCACAGCAAGAAATAG 58.960 38.462 15.83 0.00 36.41 1.73
630 644 9.539825 GAGATTCTCACAGCAAGAAATAGATTA 57.460 33.333 8.84 0.00 36.41 1.75
670 689 7.471721 TCAGAGTCAAACAATGTTTTGTAGTG 58.528 34.615 8.85 5.02 45.30 2.74
672 691 5.960113 AGTCAAACAATGTTTTGTAGTGCA 58.040 33.333 8.85 0.00 45.30 4.57
674 693 6.697019 AGTCAAACAATGTTTTGTAGTGCATC 59.303 34.615 8.85 0.00 45.30 3.91
675 694 5.685068 TCAAACAATGTTTTGTAGTGCATCG 59.315 36.000 8.85 0.00 45.30 3.84
680 702 3.937814 TGTTTTGTAGTGCATCGGAGAT 58.062 40.909 0.00 0.00 45.12 2.75
696 718 2.805099 GGAGATGATGAAGCGATCAACC 59.195 50.000 0.00 2.12 42.54 3.77
703 725 4.507756 TGATGAAGCGATCAACCGAATAAG 59.492 41.667 0.00 0.00 42.54 1.73
720 742 5.277779 CGAATAAGTTTGACTTGAGCACCAA 60.278 40.000 3.70 0.00 39.11 3.67
728 750 4.577677 TGAGCACCAAGGCGGCAA 62.578 61.111 13.08 0.00 39.03 4.52
729 751 3.064324 GAGCACCAAGGCGGCAAT 61.064 61.111 13.08 0.00 39.03 3.56
731 753 3.064324 GCACCAAGGCGGCAATCT 61.064 61.111 13.08 0.00 39.03 2.40
739 764 0.618458 AGGCGGCAATCTTCCACTAA 59.382 50.000 13.08 0.00 0.00 2.24
744 769 3.305064 GCGGCAATCTTCCACTAACAAAA 60.305 43.478 0.00 0.00 0.00 2.44
777 802 4.796369 AGCTCAACTAACTAACGAGACAC 58.204 43.478 0.00 0.00 0.00 3.67
787 812 6.630444 AACTAACGAGACACTTCTAGTCAA 57.370 37.500 0.00 0.00 36.75 3.18
1015 1040 2.135933 GCGTCTTCCTATCCATTTCCG 58.864 52.381 0.00 0.00 0.00 4.30
1020 1045 3.778075 TCTTCCTATCCATTTCCGTCCAA 59.222 43.478 0.00 0.00 0.00 3.53
1022 1047 3.112263 TCCTATCCATTTCCGTCCAAGT 58.888 45.455 0.00 0.00 0.00 3.16
1162 1218 5.505654 GCAAGCAACAAGAAGCAACTTACTA 60.506 40.000 0.00 0.00 0.00 1.82
1164 1220 6.305693 AGCAACAAGAAGCAACTTACTAAG 57.694 37.500 0.00 0.00 0.00 2.18
1611 4081 1.069823 CTGAGCTCACCCGATGCTATT 59.930 52.381 13.74 0.00 37.16 1.73
1614 4086 0.533755 GCTCACCCGATGCTATTGCT 60.534 55.000 0.00 0.00 40.48 3.91
1698 4176 0.600255 CGTTCCGTTTCCTCTGTGCT 60.600 55.000 0.00 0.00 0.00 4.40
1699 4177 0.868406 GTTCCGTTTCCTCTGTGCTG 59.132 55.000 0.00 0.00 0.00 4.41
1701 4179 0.756294 TCCGTTTCCTCTGTGCTGAA 59.244 50.000 0.00 0.00 0.00 3.02
1703 4181 2.565391 TCCGTTTCCTCTGTGCTGAATA 59.435 45.455 0.00 0.00 0.00 1.75
1706 4184 3.614616 CGTTTCCTCTGTGCTGAATAGTC 59.385 47.826 0.00 0.00 0.00 2.59
1714 4192 1.661112 GTGCTGAATAGTCTGCCGTTC 59.339 52.381 17.66 4.36 45.50 3.95
1718 4196 2.854777 CTGAATAGTCTGCCGTTCTTCG 59.145 50.000 0.00 0.00 39.52 3.79
1739 4217 0.899720 AGGCTTCCGATCCGTAACAA 59.100 50.000 0.00 0.00 0.00 2.83
1759 4237 3.788227 AGTTGTAAATGCCCTCACTCA 57.212 42.857 0.00 0.00 0.00 3.41
1771 4249 0.673022 CTCACTCAGCCCTCTTGTGC 60.673 60.000 0.00 0.00 0.00 4.57
1789 4267 6.642131 TCTTGTGCATAAAGAAATTTCTGTGC 59.358 34.615 28.69 28.69 39.43 4.57
1819 4297 5.049060 CCTGTTTAACGGAAATGTCATGACA 60.049 40.000 29.67 29.67 46.44 3.58
1846 4324 7.671495 AAGATGTTGGGCATTTTTAATCAAC 57.329 32.000 0.00 0.00 38.06 3.18
1850 4328 1.923864 GGGCATTTTTAATCAACCGCG 59.076 47.619 0.00 0.00 0.00 6.46
1875 4353 2.724977 TTGAGCTCTGACGTAAGGTG 57.275 50.000 16.19 0.00 46.39 4.00
1877 4355 0.458716 GAGCTCTGACGTAAGGTGCC 60.459 60.000 6.43 4.33 46.39 5.01
1892 4370 0.234106 GTGCCTTCATGCGATCGATG 59.766 55.000 21.57 18.39 0.00 3.84
1928 4406 2.269562 CCGGTTCCGGGTGCATAA 59.730 61.111 21.10 0.00 44.99 1.90
1929 4407 1.817941 CCGGTTCCGGGTGCATAAG 60.818 63.158 21.10 0.00 44.99 1.73
1930 4408 1.219664 CGGTTCCGGGTGCATAAGA 59.780 57.895 0.00 0.00 0.00 2.10
1931 4409 0.810031 CGGTTCCGGGTGCATAAGAG 60.810 60.000 0.00 0.00 0.00 2.85
1932 4410 1.095807 GGTTCCGGGTGCATAAGAGC 61.096 60.000 0.00 0.00 0.00 4.09
1933 4411 0.392461 GTTCCGGGTGCATAAGAGCA 60.392 55.000 0.00 0.00 43.35 4.26
1948 4426 2.141535 GAGCATCTACATCCGGACAC 57.858 55.000 6.12 0.00 0.00 3.67
1949 4427 0.385751 AGCATCTACATCCGGACACG 59.614 55.000 6.12 0.00 40.55 4.49
1950 4428 0.102481 GCATCTACATCCGGACACGT 59.898 55.000 6.12 7.34 38.78 4.49
1951 4429 1.864435 GCATCTACATCCGGACACGTC 60.864 57.143 6.12 0.00 38.78 4.34
1952 4430 1.404035 CATCTACATCCGGACACGTCA 59.596 52.381 6.12 0.00 38.78 4.35
1953 4431 1.536940 TCTACATCCGGACACGTCAA 58.463 50.000 6.12 0.00 38.78 3.18
1954 4432 1.887854 TCTACATCCGGACACGTCAAA 59.112 47.619 6.12 0.00 38.78 2.69
1955 4433 2.494471 TCTACATCCGGACACGTCAAAT 59.506 45.455 6.12 0.00 38.78 2.32
1956 4434 3.695556 TCTACATCCGGACACGTCAAATA 59.304 43.478 6.12 0.00 38.78 1.40
1957 4435 3.536956 ACATCCGGACACGTCAAATAT 57.463 42.857 6.12 0.00 38.78 1.28
1958 4436 4.659111 ACATCCGGACACGTCAAATATA 57.341 40.909 6.12 0.00 38.78 0.86
1959 4437 4.617959 ACATCCGGACACGTCAAATATAG 58.382 43.478 6.12 0.00 38.78 1.31
1960 4438 3.088194 TCCGGACACGTCAAATATAGC 57.912 47.619 0.00 0.00 38.78 2.97
1961 4439 2.132762 CCGGACACGTCAAATATAGCC 58.867 52.381 0.00 0.00 38.78 3.93
1962 4440 2.132762 CGGACACGTCAAATATAGCCC 58.867 52.381 0.00 0.00 34.81 5.19
1963 4441 2.490991 GGACACGTCAAATATAGCCCC 58.509 52.381 0.00 0.00 0.00 5.80
1964 4442 2.104281 GGACACGTCAAATATAGCCCCT 59.896 50.000 0.00 0.00 0.00 4.79
1965 4443 3.391049 GACACGTCAAATATAGCCCCTC 58.609 50.000 0.00 0.00 0.00 4.30
1966 4444 2.769663 ACACGTCAAATATAGCCCCTCA 59.230 45.455 0.00 0.00 0.00 3.86
1967 4445 3.199071 ACACGTCAAATATAGCCCCTCAA 59.801 43.478 0.00 0.00 0.00 3.02
1968 4446 4.196193 CACGTCAAATATAGCCCCTCAAA 58.804 43.478 0.00 0.00 0.00 2.69
1969 4447 4.035208 CACGTCAAATATAGCCCCTCAAAC 59.965 45.833 0.00 0.00 0.00 2.93
1970 4448 3.247648 CGTCAAATATAGCCCCTCAAACG 59.752 47.826 0.00 0.00 0.00 3.60
1971 4449 4.196971 GTCAAATATAGCCCCTCAAACGT 58.803 43.478 0.00 0.00 0.00 3.99
1972 4450 4.272748 GTCAAATATAGCCCCTCAAACGTC 59.727 45.833 0.00 0.00 0.00 4.34
1973 4451 4.163458 TCAAATATAGCCCCTCAAACGTCT 59.837 41.667 0.00 0.00 0.00 4.18
1974 4452 3.753294 ATATAGCCCCTCAAACGTCTG 57.247 47.619 0.00 0.00 0.00 3.51
1975 4453 0.107654 ATAGCCCCTCAAACGTCTGC 60.108 55.000 0.00 0.00 0.00 4.26
1976 4454 2.501223 TAGCCCCTCAAACGTCTGCG 62.501 60.000 0.00 0.00 44.93 5.18
1977 4455 2.742372 CCCCTCAAACGTCTGCGG 60.742 66.667 0.00 0.00 43.45 5.69
1978 4456 2.342279 CCCTCAAACGTCTGCGGA 59.658 61.111 0.00 0.00 43.45 5.54
1979 4457 2.027625 CCCTCAAACGTCTGCGGAC 61.028 63.158 16.12 16.12 43.45 4.79
1980 4458 1.300620 CCTCAAACGTCTGCGGACA 60.301 57.895 24.91 4.50 42.21 4.02
1981 4459 1.557443 CCTCAAACGTCTGCGGACAC 61.557 60.000 24.91 0.00 42.21 3.67
1982 4460 0.874175 CTCAAACGTCTGCGGACACA 60.874 55.000 24.91 3.02 42.21 3.72
1983 4461 0.249699 TCAAACGTCTGCGGACACAT 60.250 50.000 24.91 7.35 42.21 3.21
1984 4462 0.163788 CAAACGTCTGCGGACACATC 59.836 55.000 24.91 0.00 42.21 3.06
1985 4463 0.949105 AAACGTCTGCGGACACATCC 60.949 55.000 24.91 0.00 42.21 3.51
2006 4484 3.437795 CGTCCGCGGGTAGTGACT 61.438 66.667 27.83 0.00 0.00 3.41
2007 4485 2.181021 GTCCGCGGGTAGTGACTG 59.819 66.667 27.83 0.00 0.00 3.51
2008 4486 2.034532 TCCGCGGGTAGTGACTGA 59.965 61.111 27.83 0.00 0.00 3.41
2009 4487 2.044555 TCCGCGGGTAGTGACTGAG 61.045 63.158 27.83 0.00 0.00 3.35
2010 4488 2.202623 CGCGGGTAGTGACTGAGC 60.203 66.667 0.00 0.00 0.00 4.26
2011 4489 2.970639 GCGGGTAGTGACTGAGCA 59.029 61.111 0.00 0.00 0.00 4.26
2012 4490 1.446272 GCGGGTAGTGACTGAGCAC 60.446 63.158 0.00 0.00 39.05 4.40
2013 4491 1.154016 CGGGTAGTGACTGAGCACG 60.154 63.158 0.00 0.00 43.42 5.34
2014 4492 1.863662 CGGGTAGTGACTGAGCACGT 61.864 60.000 0.00 0.00 43.42 4.49
2015 4493 0.109226 GGGTAGTGACTGAGCACGTC 60.109 60.000 0.00 0.00 43.42 4.34
2016 4494 0.882474 GGTAGTGACTGAGCACGTCT 59.118 55.000 0.00 0.00 43.42 4.18
2017 4495 1.269998 GGTAGTGACTGAGCACGTCTT 59.730 52.381 0.00 0.00 43.42 3.01
2018 4496 2.486982 GGTAGTGACTGAGCACGTCTTA 59.513 50.000 0.00 0.00 43.42 2.10
2019 4497 3.057736 GGTAGTGACTGAGCACGTCTTAA 60.058 47.826 0.00 0.00 43.42 1.85
2020 4498 3.728076 AGTGACTGAGCACGTCTTAAA 57.272 42.857 0.00 0.00 43.42 1.52
2021 4499 4.258702 AGTGACTGAGCACGTCTTAAAT 57.741 40.909 0.00 0.00 43.42 1.40
2022 4500 4.632153 AGTGACTGAGCACGTCTTAAATT 58.368 39.130 0.00 0.00 43.42 1.82
2023 4501 5.057149 AGTGACTGAGCACGTCTTAAATTT 58.943 37.500 0.00 0.00 43.42 1.82
2024 4502 5.177696 AGTGACTGAGCACGTCTTAAATTTC 59.822 40.000 0.00 0.00 43.42 2.17
2025 4503 5.050363 GTGACTGAGCACGTCTTAAATTTCA 60.050 40.000 0.00 0.00 32.70 2.69
2026 4504 5.050363 TGACTGAGCACGTCTTAAATTTCAC 60.050 40.000 0.00 0.00 32.70 3.18
2027 4505 5.057149 ACTGAGCACGTCTTAAATTTCACT 58.943 37.500 0.00 0.00 0.00 3.41
2028 4506 5.527582 ACTGAGCACGTCTTAAATTTCACTT 59.472 36.000 0.00 0.00 0.00 3.16
2029 4507 5.747565 TGAGCACGTCTTAAATTTCACTTG 58.252 37.500 0.00 0.00 0.00 3.16
2030 4508 5.295787 TGAGCACGTCTTAAATTTCACTTGT 59.704 36.000 0.00 0.00 0.00 3.16
2031 4509 6.131544 AGCACGTCTTAAATTTCACTTGTT 57.868 33.333 0.00 0.00 0.00 2.83
2032 4510 5.971202 AGCACGTCTTAAATTTCACTTGTTG 59.029 36.000 0.00 0.00 0.00 3.33
2033 4511 5.331532 GCACGTCTTAAATTTCACTTGTTGC 60.332 40.000 0.00 0.00 0.00 4.17
2034 4512 5.741510 CACGTCTTAAATTTCACTTGTTGCA 59.258 36.000 0.00 0.00 0.00 4.08
2035 4513 6.417635 CACGTCTTAAATTTCACTTGTTGCAT 59.582 34.615 0.00 0.00 0.00 3.96
2036 4514 6.636850 ACGTCTTAAATTTCACTTGTTGCATC 59.363 34.615 0.00 0.00 0.00 3.91
2037 4515 6.857964 CGTCTTAAATTTCACTTGTTGCATCT 59.142 34.615 0.00 0.00 0.00 2.90
2038 4516 7.149080 CGTCTTAAATTTCACTTGTTGCATCTG 60.149 37.037 0.00 0.00 0.00 2.90
2039 4517 7.115378 GTCTTAAATTTCACTTGTTGCATCTGG 59.885 37.037 0.00 0.00 0.00 3.86
2040 4518 5.534207 AAATTTCACTTGTTGCATCTGGA 57.466 34.783 0.00 0.00 0.00 3.86
2041 4519 3.988379 TTTCACTTGTTGCATCTGGAC 57.012 42.857 0.00 0.00 0.00 4.02
2042 4520 2.636647 TCACTTGTTGCATCTGGACA 57.363 45.000 0.00 0.00 0.00 4.02
2043 4521 3.144657 TCACTTGTTGCATCTGGACAT 57.855 42.857 0.00 0.00 0.00 3.06
2044 4522 3.076621 TCACTTGTTGCATCTGGACATC 58.923 45.455 0.00 0.00 0.00 3.06
2045 4523 3.079578 CACTTGTTGCATCTGGACATCT 58.920 45.455 0.00 0.00 0.00 2.90
2046 4524 3.126514 CACTTGTTGCATCTGGACATCTC 59.873 47.826 0.00 0.00 0.00 2.75
2047 4525 3.244665 ACTTGTTGCATCTGGACATCTCA 60.245 43.478 0.00 0.00 0.00 3.27
2048 4526 3.639672 TGTTGCATCTGGACATCTCAT 57.360 42.857 0.00 0.00 0.00 2.90
2049 4527 4.758773 TGTTGCATCTGGACATCTCATA 57.241 40.909 0.00 0.00 0.00 2.15
2050 4528 4.445453 TGTTGCATCTGGACATCTCATAC 58.555 43.478 0.00 0.00 0.00 2.39
2051 4529 4.162888 TGTTGCATCTGGACATCTCATACT 59.837 41.667 0.00 0.00 0.00 2.12
2052 4530 5.363580 TGTTGCATCTGGACATCTCATACTA 59.636 40.000 0.00 0.00 0.00 1.82
2053 4531 5.718724 TGCATCTGGACATCTCATACTAG 57.281 43.478 0.00 0.00 0.00 2.57
2054 4532 5.388654 TGCATCTGGACATCTCATACTAGA 58.611 41.667 0.00 0.00 0.00 2.43
2055 4533 6.015282 TGCATCTGGACATCTCATACTAGAT 58.985 40.000 0.00 0.00 36.64 1.98
2056 4534 6.496218 TGCATCTGGACATCTCATACTAGATT 59.504 38.462 0.00 0.00 33.87 2.40
2057 4535 7.015974 TGCATCTGGACATCTCATACTAGATTT 59.984 37.037 0.00 0.00 33.87 2.17
2058 4536 7.877097 GCATCTGGACATCTCATACTAGATTTT 59.123 37.037 0.00 0.00 33.87 1.82
2059 4537 9.775854 CATCTGGACATCTCATACTAGATTTTT 57.224 33.333 0.00 0.00 33.87 1.94
2077 4555 8.937634 AGATTTTTAAATCCATCAAGACATGC 57.062 30.769 10.71 0.00 44.55 4.06
2078 4556 8.533657 AGATTTTTAAATCCATCAAGACATGCA 58.466 29.630 10.71 0.00 44.55 3.96
2079 4557 9.153721 GATTTTTAAATCCATCAAGACATGCAA 57.846 29.630 0.00 0.00 39.04 4.08
2080 4558 8.899427 TTTTTAAATCCATCAAGACATGCAAA 57.101 26.923 0.00 0.00 0.00 3.68
2081 4559 7.887996 TTTAAATCCATCAAGACATGCAAAC 57.112 32.000 0.00 0.00 0.00 2.93
2082 4560 5.471556 AAATCCATCAAGACATGCAAACA 57.528 34.783 0.00 0.00 0.00 2.83
2083 4561 5.471556 AATCCATCAAGACATGCAAACAA 57.528 34.783 0.00 0.00 0.00 2.83
2084 4562 4.933505 TCCATCAAGACATGCAAACAAA 57.066 36.364 0.00 0.00 0.00 2.83
2085 4563 5.273674 TCCATCAAGACATGCAAACAAAA 57.726 34.783 0.00 0.00 0.00 2.44
2086 4564 5.856156 TCCATCAAGACATGCAAACAAAAT 58.144 33.333 0.00 0.00 0.00 1.82
2087 4565 6.990798 TCCATCAAGACATGCAAACAAAATA 58.009 32.000 0.00 0.00 0.00 1.40
2088 4566 7.440198 TCCATCAAGACATGCAAACAAAATAA 58.560 30.769 0.00 0.00 0.00 1.40
2089 4567 7.384660 TCCATCAAGACATGCAAACAAAATAAC 59.615 33.333 0.00 0.00 0.00 1.89
2090 4568 7.360269 CCATCAAGACATGCAAACAAAATAACC 60.360 37.037 0.00 0.00 0.00 2.85
2091 4569 6.815089 TCAAGACATGCAAACAAAATAACCT 58.185 32.000 0.00 0.00 0.00 3.50
2092 4570 7.946207 TCAAGACATGCAAACAAAATAACCTA 58.054 30.769 0.00 0.00 0.00 3.08
2093 4571 7.865385 TCAAGACATGCAAACAAAATAACCTAC 59.135 33.333 0.00 0.00 0.00 3.18
2094 4572 7.524717 AGACATGCAAACAAAATAACCTACT 57.475 32.000 0.00 0.00 0.00 2.57
2095 4573 7.951591 AGACATGCAAACAAAATAACCTACTT 58.048 30.769 0.00 0.00 0.00 2.24
2096 4574 9.073475 AGACATGCAAACAAAATAACCTACTTA 57.927 29.630 0.00 0.00 0.00 2.24
2097 4575 9.124807 GACATGCAAACAAAATAACCTACTTAC 57.875 33.333 0.00 0.00 0.00 2.34
2098 4576 8.856103 ACATGCAAACAAAATAACCTACTTACT 58.144 29.630 0.00 0.00 0.00 2.24
2101 4579 8.497554 TGCAAACAAAATAACCTACTTACTACG 58.502 33.333 0.00 0.00 0.00 3.51
2102 4580 8.498358 GCAAACAAAATAACCTACTTACTACGT 58.502 33.333 0.00 0.00 0.00 3.57
2104 4582 8.452989 AACAAAATAACCTACTTACTACGTCG 57.547 34.615 0.00 0.00 0.00 5.12
2105 4583 7.816640 ACAAAATAACCTACTTACTACGTCGA 58.183 34.615 0.00 0.00 0.00 4.20
2106 4584 8.462016 ACAAAATAACCTACTTACTACGTCGAT 58.538 33.333 0.00 0.00 0.00 3.59
2107 4585 8.951969 CAAAATAACCTACTTACTACGTCGATC 58.048 37.037 0.00 0.00 0.00 3.69
2108 4586 7.792374 AATAACCTACTTACTACGTCGATCA 57.208 36.000 0.00 0.00 0.00 2.92
2109 4587 5.476752 AACCTACTTACTACGTCGATCAC 57.523 43.478 0.00 0.00 0.00 3.06
2110 4588 3.873952 ACCTACTTACTACGTCGATCACC 59.126 47.826 0.00 0.00 0.00 4.02
2111 4589 4.125703 CCTACTTACTACGTCGATCACCT 58.874 47.826 0.00 0.00 0.00 4.00
2112 4590 5.163405 ACCTACTTACTACGTCGATCACCTA 60.163 44.000 0.00 0.00 0.00 3.08
2113 4591 5.404968 CCTACTTACTACGTCGATCACCTAG 59.595 48.000 0.00 0.00 0.00 3.02
2114 4592 3.559242 ACTTACTACGTCGATCACCTAGC 59.441 47.826 0.00 0.00 0.00 3.42
2115 4593 2.328819 ACTACGTCGATCACCTAGCT 57.671 50.000 0.00 0.00 0.00 3.32
2116 4594 3.465742 ACTACGTCGATCACCTAGCTA 57.534 47.619 0.00 0.00 0.00 3.32
2117 4595 3.129871 ACTACGTCGATCACCTAGCTAC 58.870 50.000 0.00 0.00 0.00 3.58
2118 4596 2.328819 ACGTCGATCACCTAGCTACT 57.671 50.000 0.00 0.00 0.00 2.57
2119 4597 3.465742 ACGTCGATCACCTAGCTACTA 57.534 47.619 0.00 0.00 0.00 1.82
2120 4598 3.801698 ACGTCGATCACCTAGCTACTAA 58.198 45.455 0.00 0.00 0.00 2.24
2121 4599 4.387598 ACGTCGATCACCTAGCTACTAAT 58.612 43.478 0.00 0.00 0.00 1.73
2122 4600 4.451774 ACGTCGATCACCTAGCTACTAATC 59.548 45.833 0.00 0.00 0.00 1.75
2123 4601 4.434461 CGTCGATCACCTAGCTACTAATCG 60.434 50.000 13.10 13.10 36.71 3.34
2124 4602 4.451774 GTCGATCACCTAGCTACTAATCGT 59.548 45.833 16.40 0.00 36.73 3.73
2125 4603 4.689812 TCGATCACCTAGCTACTAATCGTC 59.310 45.833 16.40 0.83 36.73 4.20
2126 4604 4.434461 CGATCACCTAGCTACTAATCGTCG 60.434 50.000 11.87 0.00 32.21 5.12
2127 4605 3.136763 TCACCTAGCTACTAATCGTCGG 58.863 50.000 0.00 0.00 0.00 4.79
2128 4606 3.136763 CACCTAGCTACTAATCGTCGGA 58.863 50.000 0.00 0.00 0.00 4.55
2129 4607 3.186817 CACCTAGCTACTAATCGTCGGAG 59.813 52.174 0.00 0.00 0.00 4.63
2130 4608 3.070734 ACCTAGCTACTAATCGTCGGAGA 59.929 47.826 0.00 0.00 0.00 3.71
2131 4609 4.255301 CCTAGCTACTAATCGTCGGAGAT 58.745 47.826 0.00 0.00 40.67 2.75
2132 4610 4.093703 CCTAGCTACTAATCGTCGGAGATG 59.906 50.000 0.00 0.00 46.63 2.90
2133 4611 3.478509 AGCTACTAATCGTCGGAGATGT 58.521 45.455 0.00 0.00 45.22 3.06
2134 4612 3.499157 AGCTACTAATCGTCGGAGATGTC 59.501 47.826 0.00 0.00 45.22 3.06
2135 4613 3.664798 GCTACTAATCGTCGGAGATGTCG 60.665 52.174 0.00 0.00 45.22 4.35
2136 4614 2.558378 ACTAATCGTCGGAGATGTCGA 58.442 47.619 0.00 0.00 45.22 4.20
2141 4619 3.441246 GTCGGAGATGTCGACGATC 57.559 57.895 11.62 14.19 45.53 3.69
2142 4620 0.938713 GTCGGAGATGTCGACGATCT 59.061 55.000 22.31 22.31 45.53 2.75
2143 4621 1.070443 GTCGGAGATGTCGACGATCTC 60.070 57.143 29.97 29.97 45.53 2.75
2234 4712 3.116300 CTCACGGGAAGATATCACAACG 58.884 50.000 5.32 6.89 0.00 4.10
2247 4725 7.212976 AGATATCACAACGCAATTCTAGACAT 58.787 34.615 5.32 0.00 0.00 3.06
2332 4810 5.043903 GCTCGAATATACAAGAGTCAGCAA 58.956 41.667 0.00 0.00 33.57 3.91
2628 5106 4.800993 GGATCTACACTACATATGCATCGC 59.199 45.833 0.19 0.00 0.00 4.58
2741 5220 1.636148 AACCACCATCTTGCAGCAAT 58.364 45.000 8.67 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.304713 AAGCGGAACTCGGGAGGTA 60.305 57.895 0.00 0.00 39.69 3.08
1 2 2.603776 AAGCGGAACTCGGGAGGT 60.604 61.111 0.00 0.00 39.69 3.85
2 3 2.184579 GAAGCGGAACTCGGGAGG 59.815 66.667 0.00 0.00 39.69 4.30
34 35 4.365505 TCCGTCGTTGCGATGCCA 62.366 61.111 5.34 0.00 40.97 4.92
35 36 3.554692 CTCCGTCGTTGCGATGCC 61.555 66.667 5.34 0.00 40.97 4.40
36 37 4.210304 GCTCCGTCGTTGCGATGC 62.210 66.667 5.34 0.55 40.97 3.91
43 44 2.282958 TCCTCAGGCTCCGTCGTT 60.283 61.111 0.00 0.00 0.00 3.85
48 49 2.548920 GGATTAATGTCCTCAGGCTCCG 60.549 54.545 0.00 0.00 35.32 4.63
49 50 2.439507 TGGATTAATGTCCTCAGGCTCC 59.560 50.000 0.00 0.00 39.12 4.70
51 52 2.846206 TGTGGATTAATGTCCTCAGGCT 59.154 45.455 0.00 0.00 36.98 4.58
53 54 6.484643 CACTATTGTGGATTAATGTCCTCAGG 59.515 42.308 0.00 0.00 41.31 3.86
64 65 3.138304 GCGGCATCACTATTGTGGATTA 58.862 45.455 7.45 0.00 43.94 1.75
72 73 0.748005 GTGGTGGCGGCATCACTATT 60.748 55.000 39.16 0.00 33.64 1.73
94 95 6.842280 TGCTAGTCTATTTAAGTGGGGATGTA 59.158 38.462 0.00 0.00 0.00 2.29
100 101 6.702282 GCTACTTGCTAGTCTATTTAAGTGGG 59.298 42.308 3.45 7.19 38.95 4.61
107 108 6.049955 TGGTTGCTACTTGCTAGTCTATTT 57.950 37.500 3.45 0.00 43.37 1.40
122 123 3.118629 GGTGAGTGATGATCTGGTTGCTA 60.119 47.826 0.00 0.00 0.00 3.49
137 139 1.003545 CGTTCTGCTTGTTGGTGAGTG 60.004 52.381 0.00 0.00 0.00 3.51
157 159 3.088500 GATGCTTCTGCGACACGGC 62.089 63.158 0.00 0.00 43.34 5.68
172 174 5.009010 ACGCCCAATAATAAAGCTTCAGATG 59.991 40.000 0.00 0.00 0.00 2.90
175 177 4.335315 TGACGCCCAATAATAAAGCTTCAG 59.665 41.667 0.00 0.00 29.64 3.02
195 197 2.668550 GGCAAGGGTGACGGTGAC 60.669 66.667 0.00 0.00 0.00 3.67
196 198 2.272230 TTTGGCAAGGGTGACGGTGA 62.272 55.000 0.00 0.00 34.30 4.02
200 202 2.644992 GCTTTGGCAAGGGTGACG 59.355 61.111 11.55 0.00 34.30 4.35
211 213 2.331893 TTCGACGCCATGGCTTTGG 61.332 57.895 33.07 20.33 39.94 3.28
222 224 2.007114 GTTTTTGGCCGTTCGACGC 61.007 57.895 0.00 0.00 40.91 5.19
282 291 1.590525 GGTCATCGGAATACGCGCA 60.591 57.895 5.73 0.00 43.86 6.09
298 307 1.351350 GTCTTTAGTGCTGAAGGGGGT 59.649 52.381 4.30 0.00 0.00 4.95
311 321 2.096174 CCGACGACCTCTCAGTCTTTAG 59.904 54.545 0.00 0.00 34.46 1.85
317 327 1.972223 CCACCGACGACCTCTCAGT 60.972 63.158 0.00 0.00 0.00 3.41
331 341 2.337879 TTATGGCGCCATCCTCCACC 62.338 60.000 43.60 5.49 37.82 4.61
340 350 0.393808 GGAACCTTCTTATGGCGCCA 60.394 55.000 34.80 34.80 0.00 5.69
357 367 1.272807 CGACTAGGGTTTCAAGGGGA 58.727 55.000 0.00 0.00 0.00 4.81
359 369 0.392595 GGCGACTAGGGTTTCAAGGG 60.393 60.000 0.00 0.00 0.00 3.95
361 371 2.474410 AAGGCGACTAGGGTTTCAAG 57.526 50.000 0.00 0.00 42.68 3.02
363 373 1.206371 GCTAAGGCGACTAGGGTTTCA 59.794 52.381 0.00 0.00 42.68 2.69
387 397 1.369625 GAGACCCTAAACATGTGCCG 58.630 55.000 0.00 0.00 0.00 5.69
389 399 1.369625 CCGAGACCCTAAACATGTGC 58.630 55.000 0.00 0.00 0.00 4.57
394 404 0.178897 TTCCCCCGAGACCCTAAACA 60.179 55.000 0.00 0.00 0.00 2.83
418 432 0.522915 GATGGTCTTCGTCGTCGTCC 60.523 60.000 1.33 2.41 38.33 4.79
420 434 1.134075 CGATGGTCTTCGTCGTCGT 59.866 57.895 1.33 0.00 46.56 4.34
427 441 1.534175 GGTAGCTCACGATGGTCTTCG 60.534 57.143 0.00 4.99 44.56 3.79
439 453 1.767654 TTGCACAGCCAGGTAGCTCA 61.768 55.000 0.00 0.00 42.61 4.26
444 458 1.209504 GGTATCTTGCACAGCCAGGTA 59.790 52.381 0.00 0.00 0.00 3.08
449 463 3.885297 ACATAATGGTATCTTGCACAGCC 59.115 43.478 0.00 0.00 0.00 4.85
515 529 1.000896 AAAGCTCGTGGGAATGGGG 60.001 57.895 0.00 0.00 0.00 4.96
526 540 5.907197 TTCTGTTTCTAGAACAAAGCTCG 57.093 39.130 4.18 0.00 32.02 5.03
558 572 1.939974 TGCAAGTGGCTGATCGTATC 58.060 50.000 0.00 0.00 45.15 2.24
670 689 0.788995 CGCTTCATCATCTCCGATGC 59.211 55.000 0.00 0.00 42.15 3.91
672 691 2.560105 TGATCGCTTCATCATCTCCGAT 59.440 45.455 0.00 0.00 38.03 4.18
674 693 2.428888 TGATCGCTTCATCATCTCCG 57.571 50.000 0.00 0.00 0.00 4.63
675 694 2.805099 GGTTGATCGCTTCATCATCTCC 59.195 50.000 0.00 0.00 32.69 3.71
680 702 2.378445 TTCGGTTGATCGCTTCATCA 57.622 45.000 0.00 0.00 33.34 3.07
696 718 4.213270 TGGTGCTCAAGTCAAACTTATTCG 59.787 41.667 0.00 0.00 36.03 3.34
720 742 0.618458 TTAGTGGAAGATTGCCGCCT 59.382 50.000 0.00 0.00 36.58 5.52
777 802 6.149973 TCAGCAATGTTTGGATTGACTAGAAG 59.850 38.462 0.00 0.00 35.65 2.85
787 812 4.246712 AGGAGATCAGCAATGTTTGGAT 57.753 40.909 0.00 0.00 0.00 3.41
1015 1040 3.050275 GCTCGGGTGCACTTGGAC 61.050 66.667 17.98 0.00 35.50 4.02
1020 1045 4.320456 CCACAGCTCGGGTGCACT 62.320 66.667 17.98 0.00 34.04 4.40
1162 1218 2.761208 ACGGATTTCCACTCGATCTCTT 59.239 45.455 0.00 0.00 35.14 2.85
1164 1220 2.873133 ACGGATTTCCACTCGATCTC 57.127 50.000 0.00 0.00 35.14 2.75
1294 1387 1.874872 GCGTCTCTTAGTATCGGCTCT 59.125 52.381 0.00 0.00 0.00 4.09
1556 2199 1.663135 GAAGCGCATGAGGAAGAAGAC 59.337 52.381 11.47 0.00 0.00 3.01
1611 4081 2.687200 ACCCTCCACGCCATAGCA 60.687 61.111 0.00 0.00 39.83 3.49
1614 4086 2.285069 ACCACCCTCCACGCCATA 60.285 61.111 0.00 0.00 0.00 2.74
1684 4162 3.589988 ACTATTCAGCACAGAGGAAACG 58.410 45.455 0.00 0.00 0.00 3.60
1698 4176 2.876091 CGAAGAACGGCAGACTATTCA 58.124 47.619 0.00 0.00 38.46 2.57
1718 4196 0.249363 GTTACGGATCGGAAGCCTCC 60.249 60.000 7.35 0.00 38.52 4.30
1739 4217 3.679389 CTGAGTGAGGGCATTTACAACT 58.321 45.455 0.00 0.00 0.00 3.16
1759 4237 3.439857 TTCTTTATGCACAAGAGGGCT 57.560 42.857 9.53 0.00 31.84 5.19
1771 4249 6.587608 GGAACCAGCACAGAAATTTCTTTATG 59.412 38.462 18.16 16.33 39.06 1.90
1789 4267 4.277423 ACATTTCCGTTAAACAGGAACCAG 59.723 41.667 7.56 4.65 45.23 4.00
1819 4297 9.956640 TTGATTAAAAATGCCCAACATCTTATT 57.043 25.926 0.00 0.00 38.34 1.40
1846 4324 3.175152 GTCAGAGCTCAATATATCGCGG 58.825 50.000 17.77 0.00 0.00 6.46
1850 4328 6.804295 CACCTTACGTCAGAGCTCAATATATC 59.196 42.308 17.77 0.00 0.00 1.63
1875 4353 0.882042 ACCATCGATCGCATGAAGGC 60.882 55.000 21.46 0.00 0.00 4.35
1877 4355 0.863799 CCACCATCGATCGCATGAAG 59.136 55.000 21.46 15.10 0.00 3.02
1899 4377 2.436646 AACCGGAAGCGATGGCAG 60.437 61.111 9.46 0.00 43.41 4.85
1928 4406 1.683917 GTGTCCGGATGTAGATGCTCT 59.316 52.381 7.81 0.00 0.00 4.09
1929 4407 1.600663 CGTGTCCGGATGTAGATGCTC 60.601 57.143 7.81 0.00 0.00 4.26
1930 4408 0.385751 CGTGTCCGGATGTAGATGCT 59.614 55.000 7.81 0.00 0.00 3.79
1931 4409 0.102481 ACGTGTCCGGATGTAGATGC 59.898 55.000 7.81 0.00 38.78 3.91
1932 4410 1.404035 TGACGTGTCCGGATGTAGATG 59.596 52.381 7.81 0.00 38.78 2.90
1933 4411 1.758936 TGACGTGTCCGGATGTAGAT 58.241 50.000 7.81 0.00 38.78 1.98
1934 4412 1.536940 TTGACGTGTCCGGATGTAGA 58.463 50.000 7.81 0.00 38.78 2.59
1935 4413 2.357327 TTTGACGTGTCCGGATGTAG 57.643 50.000 7.81 2.18 38.78 2.74
1936 4414 4.659111 ATATTTGACGTGTCCGGATGTA 57.341 40.909 7.81 0.00 38.78 2.29
1937 4415 3.536956 ATATTTGACGTGTCCGGATGT 57.463 42.857 7.81 7.10 38.78 3.06
1938 4416 3.428870 GCTATATTTGACGTGTCCGGATG 59.571 47.826 7.81 3.20 38.78 3.51
1939 4417 3.554337 GGCTATATTTGACGTGTCCGGAT 60.554 47.826 7.81 0.00 38.78 4.18
1940 4418 2.223876 GGCTATATTTGACGTGTCCGGA 60.224 50.000 0.00 0.00 38.78 5.14
1941 4419 2.132762 GGCTATATTTGACGTGTCCGG 58.867 52.381 0.00 0.00 38.78 5.14
1942 4420 2.132762 GGGCTATATTTGACGTGTCCG 58.867 52.381 0.00 0.00 40.83 4.79
1943 4421 2.104281 AGGGGCTATATTTGACGTGTCC 59.896 50.000 0.00 0.00 0.00 4.02
1944 4422 3.181469 TGAGGGGCTATATTTGACGTGTC 60.181 47.826 0.00 0.00 0.00 3.67
1945 4423 2.769663 TGAGGGGCTATATTTGACGTGT 59.230 45.455 0.00 0.00 0.00 4.49
1946 4424 3.469008 TGAGGGGCTATATTTGACGTG 57.531 47.619 0.00 0.00 0.00 4.49
1947 4425 4.196971 GTTTGAGGGGCTATATTTGACGT 58.803 43.478 0.00 0.00 0.00 4.34
1948 4426 3.247648 CGTTTGAGGGGCTATATTTGACG 59.752 47.826 0.00 0.00 0.00 4.35
1949 4427 4.196971 ACGTTTGAGGGGCTATATTTGAC 58.803 43.478 0.00 0.00 0.00 3.18
1950 4428 4.163458 AGACGTTTGAGGGGCTATATTTGA 59.837 41.667 0.00 0.00 0.00 2.69
1951 4429 4.273480 CAGACGTTTGAGGGGCTATATTTG 59.727 45.833 0.00 0.00 0.00 2.32
1952 4430 4.451900 CAGACGTTTGAGGGGCTATATTT 58.548 43.478 0.00 0.00 0.00 1.40
1953 4431 3.744530 GCAGACGTTTGAGGGGCTATATT 60.745 47.826 10.75 0.00 0.00 1.28
1954 4432 2.224305 GCAGACGTTTGAGGGGCTATAT 60.224 50.000 10.75 0.00 0.00 0.86
1955 4433 1.138266 GCAGACGTTTGAGGGGCTATA 59.862 52.381 10.75 0.00 0.00 1.31
1956 4434 0.107654 GCAGACGTTTGAGGGGCTAT 60.108 55.000 10.75 0.00 0.00 2.97
1957 4435 1.295423 GCAGACGTTTGAGGGGCTA 59.705 57.895 10.75 0.00 0.00 3.93
1958 4436 2.032681 GCAGACGTTTGAGGGGCT 59.967 61.111 10.75 0.00 0.00 5.19
1959 4437 3.423154 CGCAGACGTTTGAGGGGC 61.423 66.667 10.75 0.00 33.53 5.80
1960 4438 2.742372 CCGCAGACGTTTGAGGGG 60.742 66.667 19.35 8.59 34.75 4.79
1961 4439 2.027625 GTCCGCAGACGTTTGAGGG 61.028 63.158 24.99 17.07 38.42 4.30
1962 4440 1.300620 TGTCCGCAGACGTTTGAGG 60.301 57.895 20.76 20.76 46.74 3.86
1963 4441 0.874175 TGTGTCCGCAGACGTTTGAG 60.874 55.000 10.75 6.55 46.74 3.02
1964 4442 0.249699 ATGTGTCCGCAGACGTTTGA 60.250 50.000 10.75 0.00 46.74 2.69
1965 4443 0.163788 GATGTGTCCGCAGACGTTTG 59.836 55.000 0.86 0.86 46.74 2.93
1966 4444 0.949105 GGATGTGTCCGCAGACGTTT 60.949 55.000 0.00 0.00 46.74 3.60
1967 4445 1.374252 GGATGTGTCCGCAGACGTT 60.374 57.895 0.00 0.00 46.74 3.99
1968 4446 2.261671 GGATGTGTCCGCAGACGT 59.738 61.111 0.00 0.00 46.74 4.34
1989 4467 3.437795 AGTCACTACCCGCGGACG 61.438 66.667 30.73 14.21 35.49 4.79
1990 4468 2.181021 CAGTCACTACCCGCGGAC 59.819 66.667 30.73 16.22 0.00 4.79
1991 4469 2.034532 TCAGTCACTACCCGCGGA 59.965 61.111 30.73 6.52 0.00 5.54
1992 4470 2.490217 CTCAGTCACTACCCGCGG 59.510 66.667 21.04 21.04 0.00 6.46
1993 4471 2.202623 GCTCAGTCACTACCCGCG 60.203 66.667 0.00 0.00 0.00 6.46
1994 4472 1.446272 GTGCTCAGTCACTACCCGC 60.446 63.158 0.00 0.00 34.29 6.13
1995 4473 1.154016 CGTGCTCAGTCACTACCCG 60.154 63.158 0.00 0.00 34.92 5.28
1996 4474 0.109226 GACGTGCTCAGTCACTACCC 60.109 60.000 0.00 0.00 38.42 3.69
1997 4475 0.882474 AGACGTGCTCAGTCACTACC 59.118 55.000 0.00 0.00 40.84 3.18
1998 4476 2.708386 AAGACGTGCTCAGTCACTAC 57.292 50.000 0.00 0.00 40.84 2.73
1999 4477 4.841443 TTTAAGACGTGCTCAGTCACTA 57.159 40.909 0.00 2.92 40.84 2.74
2000 4478 3.728076 TTTAAGACGTGCTCAGTCACT 57.272 42.857 0.00 3.60 40.84 3.41
2001 4479 4.992381 AATTTAAGACGTGCTCAGTCAC 57.008 40.909 0.00 0.00 40.84 3.67
2002 4480 5.050363 GTGAAATTTAAGACGTGCTCAGTCA 60.050 40.000 0.00 0.00 40.84 3.41
2003 4481 5.177696 AGTGAAATTTAAGACGTGCTCAGTC 59.822 40.000 0.00 3.59 38.81 3.51
2004 4482 5.057149 AGTGAAATTTAAGACGTGCTCAGT 58.943 37.500 0.00 0.00 0.00 3.41
2005 4483 5.597813 AGTGAAATTTAAGACGTGCTCAG 57.402 39.130 0.00 0.00 0.00 3.35
2006 4484 5.295787 ACAAGTGAAATTTAAGACGTGCTCA 59.704 36.000 0.00 0.00 0.00 4.26
2007 4485 5.748592 ACAAGTGAAATTTAAGACGTGCTC 58.251 37.500 0.00 0.00 0.00 4.26
2008 4486 5.751243 ACAAGTGAAATTTAAGACGTGCT 57.249 34.783 0.00 0.00 0.00 4.40
2009 4487 5.331532 GCAACAAGTGAAATTTAAGACGTGC 60.332 40.000 0.00 0.00 0.00 5.34
2010 4488 5.741510 TGCAACAAGTGAAATTTAAGACGTG 59.258 36.000 0.00 0.24 0.00 4.49
2011 4489 5.885881 TGCAACAAGTGAAATTTAAGACGT 58.114 33.333 0.00 0.00 0.00 4.34
2012 4490 6.857964 AGATGCAACAAGTGAAATTTAAGACG 59.142 34.615 0.00 0.00 0.00 4.18
2013 4491 7.115378 CCAGATGCAACAAGTGAAATTTAAGAC 59.885 37.037 0.00 0.00 0.00 3.01
2014 4492 7.014134 TCCAGATGCAACAAGTGAAATTTAAGA 59.986 33.333 0.00 0.00 0.00 2.10
2015 4493 7.115378 GTCCAGATGCAACAAGTGAAATTTAAG 59.885 37.037 0.00 0.00 0.00 1.85
2016 4494 6.922957 GTCCAGATGCAACAAGTGAAATTTAA 59.077 34.615 0.00 0.00 0.00 1.52
2017 4495 6.040278 TGTCCAGATGCAACAAGTGAAATTTA 59.960 34.615 0.00 0.00 0.00 1.40
2018 4496 5.163426 TGTCCAGATGCAACAAGTGAAATTT 60.163 36.000 0.00 0.00 0.00 1.82
2019 4497 4.341806 TGTCCAGATGCAACAAGTGAAATT 59.658 37.500 0.00 0.00 0.00 1.82
2020 4498 3.890756 TGTCCAGATGCAACAAGTGAAAT 59.109 39.130 0.00 0.00 0.00 2.17
2021 4499 3.286353 TGTCCAGATGCAACAAGTGAAA 58.714 40.909 0.00 0.00 0.00 2.69
2022 4500 2.929641 TGTCCAGATGCAACAAGTGAA 58.070 42.857 0.00 0.00 0.00 3.18
2023 4501 2.636647 TGTCCAGATGCAACAAGTGA 57.363 45.000 0.00 0.00 0.00 3.41
2024 4502 3.079578 AGATGTCCAGATGCAACAAGTG 58.920 45.455 0.00 0.00 0.00 3.16
2025 4503 3.244665 TGAGATGTCCAGATGCAACAAGT 60.245 43.478 0.00 0.00 0.00 3.16
2026 4504 3.340928 TGAGATGTCCAGATGCAACAAG 58.659 45.455 0.00 0.00 0.00 3.16
2027 4505 3.421919 TGAGATGTCCAGATGCAACAA 57.578 42.857 0.00 0.00 0.00 2.83
2028 4506 3.639672 ATGAGATGTCCAGATGCAACA 57.360 42.857 0.00 0.00 0.00 3.33
2029 4507 4.701765 AGTATGAGATGTCCAGATGCAAC 58.298 43.478 0.00 0.00 0.00 4.17
2030 4508 5.835280 TCTAGTATGAGATGTCCAGATGCAA 59.165 40.000 0.00 0.00 0.00 4.08
2031 4509 5.388654 TCTAGTATGAGATGTCCAGATGCA 58.611 41.667 0.00 0.00 0.00 3.96
2032 4510 5.973899 TCTAGTATGAGATGTCCAGATGC 57.026 43.478 0.00 0.00 0.00 3.91
2033 4511 9.775854 AAAAATCTAGTATGAGATGTCCAGATG 57.224 33.333 0.00 0.00 36.28 2.90
2052 4530 8.533657 TGCATGTCTTGATGGATTTAAAAATCT 58.466 29.630 13.57 0.00 43.33 2.40
2053 4531 8.706492 TGCATGTCTTGATGGATTTAAAAATC 57.294 30.769 6.85 6.85 43.12 2.17
2054 4532 9.504708 TTTGCATGTCTTGATGGATTTAAAAAT 57.495 25.926 0.00 0.00 0.00 1.82
2055 4533 8.772705 GTTTGCATGTCTTGATGGATTTAAAAA 58.227 29.630 0.00 0.00 0.00 1.94
2056 4534 7.930325 TGTTTGCATGTCTTGATGGATTTAAAA 59.070 29.630 0.00 0.00 0.00 1.52
2057 4535 7.440198 TGTTTGCATGTCTTGATGGATTTAAA 58.560 30.769 0.00 0.00 0.00 1.52
2058 4536 6.990798 TGTTTGCATGTCTTGATGGATTTAA 58.009 32.000 0.00 0.00 0.00 1.52
2059 4537 6.587206 TGTTTGCATGTCTTGATGGATTTA 57.413 33.333 0.00 0.00 0.00 1.40
2060 4538 5.471556 TGTTTGCATGTCTTGATGGATTT 57.528 34.783 0.00 0.00 0.00 2.17
2061 4539 5.471556 TTGTTTGCATGTCTTGATGGATT 57.528 34.783 0.00 0.00 0.00 3.01
2062 4540 5.471556 TTTGTTTGCATGTCTTGATGGAT 57.528 34.783 0.00 0.00 0.00 3.41
2063 4541 4.933505 TTTGTTTGCATGTCTTGATGGA 57.066 36.364 0.00 0.00 0.00 3.41
2064 4542 7.360269 GGTTATTTTGTTTGCATGTCTTGATGG 60.360 37.037 0.00 0.00 0.00 3.51
2065 4543 7.385752 AGGTTATTTTGTTTGCATGTCTTGATG 59.614 33.333 0.00 0.00 0.00 3.07
2066 4544 7.444299 AGGTTATTTTGTTTGCATGTCTTGAT 58.556 30.769 0.00 0.00 0.00 2.57
2067 4545 6.815089 AGGTTATTTTGTTTGCATGTCTTGA 58.185 32.000 0.00 0.00 0.00 3.02
2068 4546 7.867403 AGTAGGTTATTTTGTTTGCATGTCTTG 59.133 33.333 0.00 0.00 0.00 3.02
2069 4547 7.951591 AGTAGGTTATTTTGTTTGCATGTCTT 58.048 30.769 0.00 0.00 0.00 3.01
2070 4548 7.524717 AGTAGGTTATTTTGTTTGCATGTCT 57.475 32.000 0.00 0.00 0.00 3.41
2071 4549 9.124807 GTAAGTAGGTTATTTTGTTTGCATGTC 57.875 33.333 0.00 0.00 0.00 3.06
2072 4550 8.856103 AGTAAGTAGGTTATTTTGTTTGCATGT 58.144 29.630 0.00 0.00 0.00 3.21
2075 4553 8.497554 CGTAGTAAGTAGGTTATTTTGTTTGCA 58.502 33.333 0.00 0.00 0.00 4.08
2076 4554 8.498358 ACGTAGTAAGTAGGTTATTTTGTTTGC 58.502 33.333 0.00 0.00 41.94 3.68
2097 4575 3.391965 AGTAGCTAGGTGATCGACGTAG 58.608 50.000 4.27 15.04 43.25 3.51
2098 4576 3.465742 AGTAGCTAGGTGATCGACGTA 57.534 47.619 4.27 0.00 0.00 3.57
2099 4577 2.328819 AGTAGCTAGGTGATCGACGT 57.671 50.000 4.27 0.00 0.00 4.34
2100 4578 4.434461 CGATTAGTAGCTAGGTGATCGACG 60.434 50.000 18.47 9.55 37.64 5.12
2101 4579 4.451774 ACGATTAGTAGCTAGGTGATCGAC 59.548 45.833 25.25 10.04 38.49 4.20
2102 4580 4.639334 ACGATTAGTAGCTAGGTGATCGA 58.361 43.478 25.25 0.00 38.49 3.59
2103 4581 4.434461 CGACGATTAGTAGCTAGGTGATCG 60.434 50.000 20.32 20.32 40.30 3.69
2104 4582 4.142859 CCGACGATTAGTAGCTAGGTGATC 60.143 50.000 4.27 2.58 0.00 2.92
2105 4583 3.752222 CCGACGATTAGTAGCTAGGTGAT 59.248 47.826 4.27 0.00 0.00 3.06
2106 4584 3.136763 CCGACGATTAGTAGCTAGGTGA 58.863 50.000 4.27 0.00 0.00 4.02
2107 4585 3.136763 TCCGACGATTAGTAGCTAGGTG 58.863 50.000 4.27 0.00 0.00 4.00
2108 4586 3.070734 TCTCCGACGATTAGTAGCTAGGT 59.929 47.826 0.00 0.00 0.00 3.08
2109 4587 3.661944 TCTCCGACGATTAGTAGCTAGG 58.338 50.000 0.00 0.00 0.00 3.02
2110 4588 4.691685 ACATCTCCGACGATTAGTAGCTAG 59.308 45.833 0.00 0.00 0.00 3.42
2111 4589 4.639334 ACATCTCCGACGATTAGTAGCTA 58.361 43.478 0.00 0.00 0.00 3.32
2112 4590 3.478509 ACATCTCCGACGATTAGTAGCT 58.521 45.455 0.00 0.00 0.00 3.32
2113 4591 3.664798 CGACATCTCCGACGATTAGTAGC 60.665 52.174 0.00 0.00 0.00 3.58
2114 4592 3.739810 TCGACATCTCCGACGATTAGTAG 59.260 47.826 0.00 0.00 0.00 2.57
2115 4593 3.492383 GTCGACATCTCCGACGATTAGTA 59.508 47.826 11.55 0.00 45.23 1.82
2116 4594 2.287373 GTCGACATCTCCGACGATTAGT 59.713 50.000 11.55 0.00 45.23 2.24
2117 4595 2.906153 GTCGACATCTCCGACGATTAG 58.094 52.381 11.55 0.00 45.23 1.73
2119 4597 3.920144 GTCGACATCTCCGACGATT 57.080 52.632 11.55 0.00 45.23 3.34
2124 4602 1.218763 GAGATCGTCGACATCTCCGA 58.781 55.000 28.85 17.26 40.30 4.55
2125 4603 3.738482 GAGATCGTCGACATCTCCG 57.262 57.895 28.85 13.38 40.30 4.63
2127 4605 3.738482 CGGAGATCGTCGACATCTC 57.262 57.895 29.97 29.97 43.93 2.75
2137 4615 1.148157 GGCATCACACACGGAGATCG 61.148 60.000 0.00 0.00 45.88 3.69
2138 4616 0.811616 GGGCATCACACACGGAGATC 60.812 60.000 0.00 0.00 0.00 2.75
2139 4617 1.221840 GGGCATCACACACGGAGAT 59.778 57.895 0.00 0.00 0.00 2.75
2140 4618 1.888436 GAGGGCATCACACACGGAGA 61.888 60.000 0.00 0.00 0.00 3.71
2141 4619 1.448540 GAGGGCATCACACACGGAG 60.449 63.158 0.00 0.00 0.00 4.63
2142 4620 2.662596 GAGGGCATCACACACGGA 59.337 61.111 0.00 0.00 0.00 4.69
2143 4621 2.578163 ATCGAGGGCATCACACACGG 62.578 60.000 0.00 0.00 0.00 4.94
2144 4622 0.740868 AATCGAGGGCATCACACACG 60.741 55.000 0.00 0.00 0.00 4.49
2332 4810 9.618890 ATGTATGTACTCAGATAATGTTGCTTT 57.381 29.630 0.00 0.00 0.00 3.51
2471 4949 1.174783 CCGCCGATGCCTACTACTAT 58.825 55.000 0.00 0.00 0.00 2.12
2628 5106 8.400947 CACAGATACAACCCTTTTCATTGATAG 58.599 37.037 0.00 0.00 0.00 2.08
2741 5220 6.102910 ACTTTATGCTACTCTACTCCCTCCTA 59.897 42.308 0.00 0.00 0.00 2.94


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

AutoCloner maintained by Alex Coulton.