Multiple sequence alignment - TraesCS1B01G090700

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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 TraesCS1B01G090700 chr1B 100.000 4273 0 0 1 4273 91883340 91879068 0.000000e+00 7891.0
1 TraesCS1B01G090700 chr1B 87.833 263 25 4 143 399 547249276 547249015 6.940000e-78 302.0
2 TraesCS1B01G090700 chr1D 93.443 2120 91 12 2052 4141 56429128 56427027 0.000000e+00 3101.0
3 TraesCS1B01G090700 chr1D 94.860 1323 44 8 2519 3819 56529582 56528262 0.000000e+00 2045.0
4 TraesCS1B01G090700 chr1D 90.823 1471 91 19 2052 3492 56874363 56872907 0.000000e+00 1929.0
5 TraesCS1B01G090700 chr1D 93.351 1128 60 7 2202 3323 56609375 56608257 0.000000e+00 1653.0
6 TraesCS1B01G090700 chr1D 91.515 931 54 14 1 912 56876298 56875374 0.000000e+00 1258.0
7 TraesCS1B01G090700 chr1D 92.716 810 39 7 941 1740 56875299 56874500 0.000000e+00 1151.0
8 TraesCS1B01G090700 chr1D 90.498 863 58 9 973 1821 56430058 56429206 0.000000e+00 1118.0
9 TraesCS1B01G090700 chr1D 93.099 768 40 4 968 1734 56530856 56530101 0.000000e+00 1112.0
10 TraesCS1B01G090700 chr1D 92.555 779 40 5 967 1740 56610392 56609627 0.000000e+00 1101.0
11 TraesCS1B01G090700 chr1D 91.418 536 24 8 3742 4273 56869027 56868510 0.000000e+00 715.0
12 TraesCS1B01G090700 chr1D 88.841 466 28 5 469 912 56610981 56610518 6.240000e-153 551.0
13 TraesCS1B01G090700 chr1D 86.476 525 35 14 404 906 56531512 56531002 1.040000e-150 544.0
14 TraesCS1B01G090700 chr1D 84.906 583 37 17 403 949 56430705 56430138 3.760000e-150 542.0
15 TraesCS1B01G090700 chr1D 85.321 436 28 10 442 864 56618430 56618018 6.610000e-113 418.0
16 TraesCS1B01G090700 chr1D 85.500 400 45 7 2052 2447 56529964 56529574 5.140000e-109 405.0
17 TraesCS1B01G090700 chr1D 84.367 371 36 9 1449 1808 57200749 57200390 1.140000e-90 344.0
18 TraesCS1B01G090700 chr1D 89.919 248 23 1 985 1232 57219350 57219105 6.890000e-83 318.0
19 TraesCS1B01G090700 chr1D 85.069 288 33 6 404 685 56612625 56612342 6.990000e-73 285.0
20 TraesCS1B01G090700 chr1D 90.452 199 19 0 1255 1453 57212907 57212709 3.280000e-66 263.0
21 TraesCS1B01G090700 chr1D 95.152 165 8 0 3489 3653 56869549 56869385 1.180000e-65 261.0
22 TraesCS1B01G090700 chr1D 78.016 514 43 25 2055 2519 57073748 57073256 4.240000e-65 259.0
23 TraesCS1B01G090700 chr1D 88.095 126 11 2 1 126 56430813 56430692 3.440000e-31 147.0
24 TraesCS1B01G090700 chr1D 90.909 88 8 0 1 88 56611146 56611059 7.510000e-23 119.0
25 TraesCS1B01G090700 chr1D 91.111 45 3 1 906 949 56875362 56875318 4.610000e-05 60.2
26 TraesCS1B01G090700 chr1A 92.553 2068 110 17 2085 4141 54459845 54461879 0.000000e+00 2926.0
27 TraesCS1B01G090700 chr1A 90.006 1761 105 17 2054 3780 56370221 56371944 0.000000e+00 2211.0
28 TraesCS1B01G090700 chr1A 91.385 1300 86 15 2052 3341 56338314 56339597 0.000000e+00 1757.0
29 TraesCS1B01G090700 chr1A 90.614 831 63 4 3340 4170 56340308 56341123 0.000000e+00 1088.0
30 TraesCS1B01G090700 chr1A 92.298 766 50 6 968 1731 54458913 54459671 0.000000e+00 1079.0
31 TraesCS1B01G090700 chr1A 88.901 883 63 22 968 1822 56337367 56338242 0.000000e+00 1055.0
32 TraesCS1B01G090700 chr1A 85.745 940 83 29 1007 1906 56369273 56370201 0.000000e+00 946.0
33 TraesCS1B01G090700 chr1A 91.250 560 35 3 360 906 56336659 56337217 0.000000e+00 750.0
34 TraesCS1B01G090700 chr1A 90.057 523 32 8 404 906 54458241 54458763 0.000000e+00 660.0
35 TraesCS1B01G090700 chr1A 89.433 388 25 4 533 906 56368136 56368521 3.870000e-130 475.0
36 TraesCS1B01G090700 chr1A 86.849 365 45 3 1 364 56326302 56326664 5.140000e-109 405.0
37 TraesCS1B01G090700 chr1A 90.458 262 25 0 1 262 56365432 56365693 3.160000e-91 346.0
38 TraesCS1B01G090700 chr5A 89.231 260 23 4 143 399 545568138 545567881 1.920000e-83 320.0
39 TraesCS1B01G090700 chr5A 88.258 264 25 4 143 401 334341428 334341690 1.150000e-80 311.0
40 TraesCS1B01G090700 chr5A 87.833 263 27 3 143 400 299295058 299294796 1.930000e-78 303.0
41 TraesCS1B01G090700 chr5A 79.381 388 57 20 1305 1681 365253857 365254232 7.090000e-63 252.0
42 TraesCS1B01G090700 chr3D 88.123 261 26 2 143 399 527520285 527520544 5.370000e-79 305.0
43 TraesCS1B01G090700 chr6A 87.452 263 27 5 143 399 46549115 46548853 8.980000e-77 298.0
44 TraesCS1B01G090700 chr3B 87.500 264 25 5 143 399 776503356 776503094 8.980000e-77 298.0
45 TraesCS1B01G090700 chr7B 77.540 374 63 17 1305 1669 409712036 409711675 5.600000e-49 206.0
46 TraesCS1B01G090700 chr5D 85.135 74 9 2 1109 1181 315485471 315485399 1.650000e-09 75.0
47 TraesCS1B01G090700 chr6D 100.000 29 0 0 3019 3047 426337313 426337341 2.000000e-03 54.7
48 TraesCS1B01G090700 chr6B 100.000 29 0 0 3019 3047 641911658 641911686 2.000000e-03 54.7


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 TraesCS1B01G090700 chr1B 91879068 91883340 4272 True 7891.0 7891 100.00000 1 4273 1 chr1B.!!$R1 4272
1 TraesCS1B01G090700 chr1D 56427027 56430813 3786 True 1227.0 3101 89.23550 1 4141 4 chr1D.!!$R6 4140
2 TraesCS1B01G090700 chr1D 56528262 56531512 3250 True 1026.5 2045 89.98375 404 3819 4 chr1D.!!$R7 3415
3 TraesCS1B01G090700 chr1D 56868510 56876298 7788 True 895.7 1929 92.12250 1 4273 6 chr1D.!!$R9 4272
4 TraesCS1B01G090700 chr1D 56608257 56612625 4368 True 741.8 1653 90.14500 1 3323 5 chr1D.!!$R8 3322
5 TraesCS1B01G090700 chr1A 54458241 54461879 3638 False 1555.0 2926 91.63600 404 4141 3 chr1A.!!$F2 3737
6 TraesCS1B01G090700 chr1A 56336659 56341123 4464 False 1162.5 1757 90.53750 360 4170 4 chr1A.!!$F3 3810
7 TraesCS1B01G090700 chr1A 56365432 56371944 6512 False 994.5 2211 88.91050 1 3780 4 chr1A.!!$F4 3779

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
237 238 0.689623 CAGTGGGAGGAGACTTTGCT 59.310 55.0 0.00 0.00 44.43 3.91 F
1235 4273 0.037046 TCGGCGATGCATATGCTGAT 60.037 50.0 27.13 14.27 38.99 2.90 F
1983 5135 0.109964 GCACGCGAAATAGGCAAACA 60.110 50.0 15.93 0.00 0.00 2.83 F
2210 5455 0.504384 CTGAACGTGCACAGACGAAG 59.496 55.0 18.64 0.40 42.10 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1964 5116 0.109964 TGTTTGCCTATTTCGCGTGC 60.110 50.0 5.77 1.25 0.0 5.34 R
2660 5930 0.540454 CTTGGAGGATGAGCTGCAGA 59.460 55.0 20.43 0.00 0.0 4.26 R
3061 6338 0.743345 GATCTTCCCCGGGTTGTTCG 60.743 60.0 21.85 2.11 0.0 3.95 R
3900 11541 1.856629 AGGTTGCTGCAGCCATAAAT 58.143 45.0 34.64 13.79 37.2 1.40 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
105 106 2.504175 TCTATGAGGCCCAACAACTACC 59.496 50.000 0.00 0.00 0.00 3.18
127 128 5.372661 ACCACTAATCTATTGGCTATTGGGT 59.627 40.000 0.00 0.00 32.17 4.51
195 196 7.648908 TGCTCGCATTTATCCTGAATTTATTTG 59.351 33.333 0.00 0.00 0.00 2.32
212 213 4.104143 GACGATTTCCGGCGATGT 57.896 55.556 9.30 0.00 43.93 3.06
214 215 2.324477 CGATTTCCGGCGATGTGC 59.676 61.111 9.30 0.00 45.38 4.57
235 236 2.772287 GTTCAGTGGGAGGAGACTTTG 58.228 52.381 0.00 0.00 44.43 2.77
237 238 0.689623 CAGTGGGAGGAGACTTTGCT 59.310 55.000 0.00 0.00 44.43 3.91
238 239 0.689623 AGTGGGAGGAGACTTTGCTG 59.310 55.000 0.00 0.00 44.43 4.41
244 245 2.485479 GGAGGAGACTTTGCTGTCAACA 60.485 50.000 7.56 0.00 44.43 3.33
278 279 4.817517 ACGGTGACTTCGTAAAATCTCAT 58.182 39.130 0.00 0.00 39.22 2.90
283 284 6.535150 GGTGACTTCGTAAAATCTCATGATGA 59.465 38.462 0.00 0.00 32.44 2.92
288 289 9.770097 ACTTCGTAAAATCTCATGATGATATGT 57.230 29.630 0.00 0.00 32.44 2.29
299 300 2.958355 TGATGATATGTCGGCTCAGTCA 59.042 45.455 0.00 0.00 0.00 3.41
320 321 2.832498 GGAGGTGCTCATAGGGGC 59.168 66.667 0.00 0.00 31.08 5.80
323 324 2.049627 GAGGTGCTCATAGGGGCAGG 62.050 65.000 0.00 0.00 39.22 4.85
326 327 2.377810 TGCTCATAGGGGCAGGGTG 61.378 63.158 0.00 0.00 34.22 4.61
336 337 3.209097 GCAGGGTGTGTGTGCGTT 61.209 61.111 0.00 0.00 0.00 4.84
337 338 3.022287 CAGGGTGTGTGTGCGTTC 58.978 61.111 0.00 0.00 0.00 3.95
341 342 1.003118 AGGGTGTGTGTGCGTTCATAT 59.997 47.619 0.00 0.00 0.00 1.78
424 2702 8.211629 ACCTAATTGGCTATTGGAGTAGTAAAG 58.788 37.037 6.60 0.00 40.22 1.85
438 2717 7.451877 TGGAGTAGTAAAGACCCATCTCATATC 59.548 40.741 0.00 0.00 32.34 1.63
439 2718 7.451877 GGAGTAGTAAAGACCCATCTCATATCA 59.548 40.741 0.00 0.00 32.34 2.15
466 2759 4.840716 AAGAGCTCAGTCATTGATTCCT 57.159 40.909 17.77 0.00 34.68 3.36
485 2806 7.958016 TGATTCCTAGATATCCATCCTTTCTCA 59.042 37.037 0.00 0.00 0.00 3.27
547 2896 7.807907 GTGTGACGTTTTTCATTATCCATCTTT 59.192 33.333 0.00 0.00 0.00 2.52
622 2971 9.168451 TCAATACAGTCCTTTTATTCGCAAATA 57.832 29.630 0.00 0.00 0.00 1.40
749 3099 4.891992 ATAAGTTCAGATACGGGGATGG 57.108 45.455 0.00 0.00 0.00 3.51
775 3126 1.705873 TACATTTGGCACCCGGTTTT 58.294 45.000 0.00 0.00 0.00 2.43
977 3449 6.309737 CGGTGGTACAATACAAGAAACTACTC 59.690 42.308 0.00 0.00 44.16 2.59
981 3453 7.383029 TGGTACAATACAAGAAACTACTCGTTG 59.617 37.037 0.00 0.00 32.34 4.10
1023 4060 2.203126 GCTAGCGCCAGGATGCTT 60.203 61.111 11.55 0.00 42.48 3.91
1228 4266 2.899345 AAGCACGTCGGCGATGCATA 62.899 55.000 30.10 0.00 42.82 3.14
1229 4267 2.310233 GCACGTCGGCGATGCATAT 61.310 57.895 27.66 6.58 41.33 1.78
1230 4268 1.488525 CACGTCGGCGATGCATATG 59.511 57.895 27.66 15.12 42.00 1.78
1231 4269 2.310233 ACGTCGGCGATGCATATGC 61.310 57.895 27.66 21.09 42.00 3.14
1232 4270 2.023771 CGTCGGCGATGCATATGCT 61.024 57.895 27.13 13.57 40.42 3.79
1233 4271 1.494628 GTCGGCGATGCATATGCTG 59.505 57.895 27.13 20.84 42.66 4.41
1234 4272 0.945743 GTCGGCGATGCATATGCTGA 60.946 55.000 27.13 23.94 41.46 4.26
1235 4273 0.037046 TCGGCGATGCATATGCTGAT 60.037 50.000 27.13 14.27 38.99 2.90
1236 4274 1.204467 TCGGCGATGCATATGCTGATA 59.796 47.619 27.13 8.58 38.99 2.15
1237 4275 2.159057 TCGGCGATGCATATGCTGATAT 60.159 45.455 27.13 13.17 38.99 1.63
1275 4346 0.736053 ACGTGTTTGGTTCGTGCATT 59.264 45.000 0.00 0.00 36.46 3.56
1290 4364 3.002553 CGTGCATTATGCTGACATGCTTA 59.997 43.478 18.44 0.00 45.31 3.09
1315 4389 1.079819 CGACGTGCAGGTGGATCTT 60.080 57.895 18.18 0.00 0.00 2.40
1734 4828 2.109739 ACGCGAAACAGGTGCACAA 61.110 52.632 20.43 0.00 0.00 3.33
1740 4834 3.554524 CGAAACAGGTGCACAATACTTG 58.445 45.455 20.43 8.88 0.00 3.16
1743 4837 2.154462 ACAGGTGCACAATACTTGCTC 58.846 47.619 20.43 0.00 40.86 4.26
1744 4838 2.224621 ACAGGTGCACAATACTTGCTCT 60.225 45.455 20.43 0.00 40.86 4.09
1751 4872 6.093495 GGTGCACAATACTTGCTCTTACATTA 59.907 38.462 20.43 0.00 40.86 1.90
1754 4875 7.390440 TGCACAATACTTGCTCTTACATTACTT 59.610 33.333 0.00 0.00 40.86 2.24
1766 4887 8.721478 GCTCTTACATTACTTCATGTTTTGAGA 58.279 33.333 0.00 0.00 38.40 3.27
1768 4889 9.554395 TCTTACATTACTTCATGTTTTGAGACA 57.446 29.630 0.00 0.00 38.40 3.41
1784 4908 4.111916 TGAGACACACACGTATGCATATG 58.888 43.478 21.85 21.85 0.00 1.78
1810 4934 1.469703 GCATGCACAGCACACAGATTA 59.530 47.619 14.21 0.00 43.04 1.75
1811 4935 2.730090 GCATGCACAGCACACAGATTAC 60.730 50.000 14.21 0.00 43.04 1.89
1812 4936 2.252976 TGCACAGCACACAGATTACA 57.747 45.000 0.00 0.00 31.71 2.41
1813 4937 1.872952 TGCACAGCACACAGATTACAC 59.127 47.619 0.00 0.00 31.71 2.90
1814 4938 1.872952 GCACAGCACACAGATTACACA 59.127 47.619 0.00 0.00 0.00 3.72
1815 4939 2.290367 GCACAGCACACAGATTACACAA 59.710 45.455 0.00 0.00 0.00 3.33
1816 4940 3.058016 GCACAGCACACAGATTACACAAT 60.058 43.478 0.00 0.00 0.00 2.71
1817 4941 4.715896 CACAGCACACAGATTACACAATC 58.284 43.478 0.00 0.00 40.85 2.67
1818 4942 3.433274 ACAGCACACAGATTACACAATCG 59.567 43.478 0.00 0.00 44.51 3.34
1819 4943 3.679502 CAGCACACAGATTACACAATCGA 59.320 43.478 0.00 0.00 44.51 3.59
1820 4944 4.330894 CAGCACACAGATTACACAATCGAT 59.669 41.667 0.00 0.00 44.51 3.59
1821 4945 4.937620 AGCACACAGATTACACAATCGATT 59.062 37.500 4.39 4.39 44.51 3.34
1822 4946 5.063944 AGCACACAGATTACACAATCGATTC 59.936 40.000 7.92 0.00 44.51 2.52
1823 4947 5.063944 GCACACAGATTACACAATCGATTCT 59.936 40.000 7.92 0.00 44.51 2.40
1824 4948 6.255670 GCACACAGATTACACAATCGATTCTA 59.744 38.462 7.92 0.00 44.51 2.10
1825 4949 7.042456 GCACACAGATTACACAATCGATTCTAT 60.042 37.037 7.92 0.00 44.51 1.98
1826 4950 9.463443 CACACAGATTACACAATCGATTCTATA 57.537 33.333 7.92 0.00 44.51 1.31
1827 4951 9.464714 ACACAGATTACACAATCGATTCTATAC 57.535 33.333 7.92 0.00 44.51 1.47
1828 4952 9.463443 CACAGATTACACAATCGATTCTATACA 57.537 33.333 7.92 0.00 44.51 2.29
1858 4982 5.163281 TGGATGGTCCAAAAATCATTTGG 57.837 39.130 12.62 12.62 45.00 3.28
1859 4983 4.596643 TGGATGGTCCAAAAATCATTTGGT 59.403 37.500 16.98 1.11 45.00 3.67
1860 4984 4.937015 GGATGGTCCAAAAATCATTTGGTG 59.063 41.667 16.98 2.71 46.75 4.17
1865 4989 8.195165 TGGTCCAAAAATCATTTGGTGTAATA 57.805 30.769 16.98 0.00 46.75 0.98
1867 4991 7.763985 GGTCCAAAAATCATTTGGTGTAATAGG 59.236 37.037 16.98 0.00 46.75 2.57
1868 4992 8.311109 GTCCAAAAATCATTTGGTGTAATAGGT 58.689 33.333 16.98 0.00 46.75 3.08
1869 4993 9.535170 TCCAAAAATCATTTGGTGTAATAGGTA 57.465 29.630 16.98 0.00 46.75 3.08
1898 5050 0.589729 GAGCGGCGCACATGTTAATG 60.590 55.000 35.02 0.00 39.89 1.90
1914 5066 8.965819 ACATGTTAATGTGCCATTCTAATTACA 58.034 29.630 0.00 0.00 45.51 2.41
1948 5100 7.377766 ACAATCATAATGTTCCATATACGCC 57.622 36.000 0.00 0.00 0.00 5.68
1949 5101 7.168219 ACAATCATAATGTTCCATATACGCCT 58.832 34.615 0.00 0.00 0.00 5.52
1950 5102 7.665559 ACAATCATAATGTTCCATATACGCCTT 59.334 33.333 0.00 0.00 0.00 4.35
1951 5103 8.514594 CAATCATAATGTTCCATATACGCCTTT 58.485 33.333 0.00 0.00 0.00 3.11
1952 5104 7.433708 TCATAATGTTCCATATACGCCTTTG 57.566 36.000 0.00 0.00 0.00 2.77
1953 5105 6.429692 TCATAATGTTCCATATACGCCTTTGG 59.570 38.462 0.00 0.00 0.00 3.28
1954 5106 2.294074 TGTTCCATATACGCCTTTGGC 58.706 47.619 0.00 0.00 46.75 4.52
1963 5115 2.563427 GCCTTTGGCGCTTCTGAC 59.437 61.111 7.64 0.00 39.62 3.51
1964 5116 2.863153 CCTTTGGCGCTTCTGACG 59.137 61.111 7.64 0.00 0.00 4.35
1972 5124 3.403057 GCTTCTGACGCACGCGAA 61.403 61.111 19.66 4.94 42.83 4.70
1973 5125 2.938823 GCTTCTGACGCACGCGAAA 61.939 57.895 19.66 4.56 42.83 3.46
1974 5126 1.781555 CTTCTGACGCACGCGAAAT 59.218 52.632 19.66 0.00 42.83 2.17
1975 5127 0.989164 CTTCTGACGCACGCGAAATA 59.011 50.000 19.66 0.00 42.83 1.40
1976 5128 0.989164 TTCTGACGCACGCGAAATAG 59.011 50.000 19.66 9.98 42.83 1.73
1977 5129 0.800683 TCTGACGCACGCGAAATAGG 60.801 55.000 19.66 0.00 42.83 2.57
1978 5130 2.320044 GACGCACGCGAAATAGGC 59.680 61.111 19.66 5.32 42.83 3.93
1979 5131 2.433491 ACGCACGCGAAATAGGCA 60.433 55.556 19.66 0.00 42.83 4.75
1980 5132 1.962092 GACGCACGCGAAATAGGCAA 61.962 55.000 19.66 0.00 42.83 4.52
1981 5133 1.133664 CGCACGCGAAATAGGCAAA 59.866 52.632 15.93 0.00 42.83 3.68
1982 5134 1.125847 CGCACGCGAAATAGGCAAAC 61.126 55.000 15.93 0.00 42.83 2.93
1983 5135 0.109964 GCACGCGAAATAGGCAAACA 60.110 50.000 15.93 0.00 0.00 2.83
1984 5136 1.467374 GCACGCGAAATAGGCAAACAT 60.467 47.619 15.93 0.00 0.00 2.71
1985 5137 2.176369 CACGCGAAATAGGCAAACATG 58.824 47.619 15.93 0.00 0.00 3.21
1986 5138 1.810151 ACGCGAAATAGGCAAACATGT 59.190 42.857 15.93 0.00 0.00 3.21
1987 5139 3.004171 ACGCGAAATAGGCAAACATGTA 58.996 40.909 15.93 0.00 0.00 2.29
1988 5140 3.437395 ACGCGAAATAGGCAAACATGTAA 59.563 39.130 15.93 0.00 0.00 2.41
1989 5141 3.783943 CGCGAAATAGGCAAACATGTAAC 59.216 43.478 0.00 0.00 0.00 2.50
1990 5142 4.436852 CGCGAAATAGGCAAACATGTAACT 60.437 41.667 0.00 0.00 0.00 2.24
1991 5143 4.793216 GCGAAATAGGCAAACATGTAACTG 59.207 41.667 0.00 0.00 0.00 3.16
1992 5144 5.619086 GCGAAATAGGCAAACATGTAACTGT 60.619 40.000 0.00 0.00 0.00 3.55
1993 5145 5.794945 CGAAATAGGCAAACATGTAACTGTG 59.205 40.000 0.00 0.00 0.00 3.66
1994 5146 4.701956 ATAGGCAAACATGTAACTGTGC 57.298 40.909 0.00 4.38 0.00 4.57
1995 5147 2.586425 AGGCAAACATGTAACTGTGCT 58.414 42.857 0.00 0.00 0.00 4.40
1996 5148 2.958355 AGGCAAACATGTAACTGTGCTT 59.042 40.909 0.00 0.00 0.00 3.91
1997 5149 3.384467 AGGCAAACATGTAACTGTGCTTT 59.616 39.130 0.00 0.00 0.00 3.51
1998 5150 3.490526 GGCAAACATGTAACTGTGCTTTG 59.509 43.478 0.00 0.00 0.00 2.77
1999 5151 3.060339 GCAAACATGTAACTGTGCTTTGC 60.060 43.478 9.56 9.56 36.37 3.68
2000 5152 4.111198 CAAACATGTAACTGTGCTTTGCA 58.889 39.130 0.00 0.00 35.60 4.08
2001 5153 4.589216 AACATGTAACTGTGCTTTGCAT 57.411 36.364 0.00 0.00 41.91 3.96
2002 5154 3.904571 ACATGTAACTGTGCTTTGCATG 58.095 40.909 0.00 10.44 46.55 4.06
2003 5155 3.569277 ACATGTAACTGTGCTTTGCATGA 59.431 39.130 16.73 0.00 45.00 3.07
2004 5156 4.037803 ACATGTAACTGTGCTTTGCATGAA 59.962 37.500 16.73 0.00 45.00 2.57
2005 5157 4.227512 TGTAACTGTGCTTTGCATGAAG 57.772 40.909 0.00 0.00 41.91 3.02
2006 5158 3.882288 TGTAACTGTGCTTTGCATGAAGA 59.118 39.130 0.00 0.00 41.91 2.87
2007 5159 3.637998 AACTGTGCTTTGCATGAAGAG 57.362 42.857 0.00 0.00 41.91 2.85
2008 5160 2.854963 ACTGTGCTTTGCATGAAGAGA 58.145 42.857 0.00 0.00 41.91 3.10
2009 5161 3.418995 ACTGTGCTTTGCATGAAGAGAT 58.581 40.909 0.00 0.00 41.91 2.75
2010 5162 4.582869 ACTGTGCTTTGCATGAAGAGATA 58.417 39.130 0.00 0.00 41.91 1.98
2011 5163 4.634883 ACTGTGCTTTGCATGAAGAGATAG 59.365 41.667 0.00 0.00 41.91 2.08
2012 5164 4.582869 TGTGCTTTGCATGAAGAGATAGT 58.417 39.130 0.00 0.00 41.91 2.12
2013 5165 5.733676 TGTGCTTTGCATGAAGAGATAGTA 58.266 37.500 0.00 0.00 41.91 1.82
2014 5166 5.582269 TGTGCTTTGCATGAAGAGATAGTAC 59.418 40.000 0.00 0.00 41.91 2.73
2015 5167 5.814705 GTGCTTTGCATGAAGAGATAGTACT 59.185 40.000 0.00 0.00 41.91 2.73
2016 5168 6.980978 GTGCTTTGCATGAAGAGATAGTACTA 59.019 38.462 4.77 4.77 41.91 1.82
2017 5169 6.980978 TGCTTTGCATGAAGAGATAGTACTAC 59.019 38.462 4.31 0.00 31.71 2.73
2018 5170 6.422400 GCTTTGCATGAAGAGATAGTACTACC 59.578 42.308 4.31 0.00 0.00 3.18
2019 5171 7.418337 TTTGCATGAAGAGATAGTACTACCA 57.582 36.000 4.31 0.00 0.00 3.25
2020 5172 6.641169 TGCATGAAGAGATAGTACTACCAG 57.359 41.667 4.31 0.00 0.00 4.00
2021 5173 6.129874 TGCATGAAGAGATAGTACTACCAGT 58.870 40.000 4.31 0.00 0.00 4.00
2022 5174 6.263392 TGCATGAAGAGATAGTACTACCAGTC 59.737 42.308 4.31 0.00 0.00 3.51
2023 5175 6.488683 GCATGAAGAGATAGTACTACCAGTCT 59.511 42.308 4.31 4.04 0.00 3.24
2024 5176 7.662258 GCATGAAGAGATAGTACTACCAGTCTA 59.338 40.741 4.31 0.00 0.00 2.59
2025 5177 8.995220 CATGAAGAGATAGTACTACCAGTCTAC 58.005 40.741 4.31 1.39 0.00 2.59
2026 5178 7.507829 TGAAGAGATAGTACTACCAGTCTACC 58.492 42.308 4.31 2.59 0.00 3.18
2027 5179 7.126879 TGAAGAGATAGTACTACCAGTCTACCA 59.873 40.741 4.31 4.73 0.00 3.25
2028 5180 6.829849 AGAGATAGTACTACCAGTCTACCAC 58.170 44.000 4.31 0.00 0.00 4.16
2029 5181 6.616548 AGAGATAGTACTACCAGTCTACCACT 59.383 42.308 4.31 0.00 34.67 4.00
2042 5194 7.182361 CAGTCTACCACTGCATAATTACATG 57.818 40.000 0.00 0.00 46.30 3.21
2043 5195 6.293081 CAGTCTACCACTGCATAATTACATGC 60.293 42.308 6.28 6.28 46.30 4.06
2078 5230 2.292016 CACAGCACAAATTGGACGGTTA 59.708 45.455 0.00 0.00 0.00 2.85
2080 5232 1.883926 AGCACAAATTGGACGGTTACC 59.116 47.619 0.00 0.00 0.00 2.85
2101 5317 2.867429 GTGGGCACGATCAATTTGAAG 58.133 47.619 2.68 3.69 0.00 3.02
2108 5324 5.400485 GGCACGATCAATTTGAAGATAATGC 59.600 40.000 2.68 7.75 35.80 3.56
2112 5328 6.479990 ACGATCAATTTGAAGATAATGCGAGA 59.520 34.615 2.68 0.00 0.00 4.04
2126 5342 8.491152 AGATAATGCGAGAGAATTAATTTGACG 58.509 33.333 1.43 7.65 44.46 4.35
2154 5370 7.226720 ACCATTTCATAAAGTCGTGGTCATATC 59.773 37.037 0.00 0.00 33.47 1.63
2155 5371 7.226523 CCATTTCATAAAGTCGTGGTCATATCA 59.773 37.037 0.00 0.00 0.00 2.15
2196 5420 8.816144 TGTCAAATTATTGCTTGAAAACTGAAC 58.184 29.630 0.00 0.00 36.45 3.18
2200 5424 2.187351 TGCTTGAAAACTGAACGTGC 57.813 45.000 0.00 0.00 0.00 5.34
2210 5455 0.504384 CTGAACGTGCACAGACGAAG 59.496 55.000 18.64 0.40 42.10 3.79
2238 5486 8.097038 TGTATCAGCTAATTTCTTCAGTCACTT 58.903 33.333 0.00 0.00 0.00 3.16
2239 5487 6.791887 TCAGCTAATTTCTTCAGTCACTTG 57.208 37.500 0.00 0.00 0.00 3.16
2240 5488 5.180117 TCAGCTAATTTCTTCAGTCACTTGC 59.820 40.000 0.00 0.00 0.00 4.01
2364 5625 8.487970 GGTATCACATCACTAATTAATGTCACG 58.512 37.037 0.00 0.00 31.43 4.35
2660 5930 2.972713 ACTGATGACTATACCGGCCATT 59.027 45.455 0.00 0.00 0.00 3.16
2942 6212 2.876645 CAGCTCGTCTCGTTCGCC 60.877 66.667 0.00 0.00 0.00 5.54
3005 6275 1.959710 TGAGCTACATGGTTGGGGTA 58.040 50.000 0.00 0.00 0.00 3.69
3021 6298 1.342374 GGGTAGGAAAGAGGTACCCGA 60.342 57.143 8.74 0.00 45.06 5.14
3254 6531 1.737735 CATCGTCGGAGTGCTTGCA 60.738 57.895 0.00 0.00 0.00 4.08
3528 10885 5.081728 TGTTTACACTAAGAGGTAGAGGCA 58.918 41.667 0.00 0.00 33.61 4.75
3556 10913 3.322254 AGCAGGTAGACATTCCCTTATCG 59.678 47.826 0.00 0.00 0.00 2.92
3761 11402 1.003696 AGGGTTTCCACTCAGCTTAGC 59.996 52.381 0.00 0.00 34.83 3.09
3900 11541 1.057471 TGGTTCCATGGTCACCGTAA 58.943 50.000 23.07 9.65 32.71 3.18
3936 11577 1.574428 CTTTTCCGTGACCAAGGCG 59.426 57.895 0.00 0.00 0.00 5.52
4074 11716 6.020971 TGCGTTTCAGACAGTAGATTAGAA 57.979 37.500 0.00 0.00 0.00 2.10
4075 11717 6.452242 TGCGTTTCAGACAGTAGATTAGAAA 58.548 36.000 0.00 0.00 0.00 2.52
4174 11816 4.579454 TGGGTAGTATTACGATGCAGAC 57.421 45.455 0.00 0.00 0.00 3.51
4176 11818 4.277672 TGGGTAGTATTACGATGCAGACTC 59.722 45.833 0.00 0.00 0.00 3.36
4202 11844 1.856920 GGGGTATTTCCTTCATGGGGA 59.143 52.381 4.58 4.58 36.20 4.81
4207 11849 2.619697 TTTCCTTCATGGGGATGCAA 57.380 45.000 8.70 0.00 36.20 4.08
4208 11850 2.619697 TTCCTTCATGGGGATGCAAA 57.380 45.000 8.70 0.00 36.20 3.68
4209 11851 2.619697 TCCTTCATGGGGATGCAAAA 57.380 45.000 0.00 0.00 36.20 2.44
4210 11852 3.119009 TCCTTCATGGGGATGCAAAAT 57.881 42.857 0.00 0.00 36.20 1.82
4211 11853 4.262891 TCCTTCATGGGGATGCAAAATA 57.737 40.909 0.00 0.00 36.20 1.40
4212 11854 4.217510 TCCTTCATGGGGATGCAAAATAG 58.782 43.478 0.00 0.00 36.20 1.73
4213 11855 3.962718 CCTTCATGGGGATGCAAAATAGT 59.037 43.478 0.00 0.00 0.00 2.12
4214 11856 4.202182 CCTTCATGGGGATGCAAAATAGTG 60.202 45.833 0.00 0.00 0.00 2.74
4215 11857 4.248174 TCATGGGGATGCAAAATAGTGA 57.752 40.909 0.00 0.00 0.00 3.41
4216 11858 4.608269 TCATGGGGATGCAAAATAGTGAA 58.392 39.130 0.00 0.00 0.00 3.18
4240 11882 8.567285 AAAATACATTCCCAGTCTTGAACTAG 57.433 34.615 0.00 0.00 36.07 2.57
4241 11883 6.875972 ATACATTCCCAGTCTTGAACTAGT 57.124 37.500 0.00 0.00 36.07 2.57
4242 11884 7.973048 ATACATTCCCAGTCTTGAACTAGTA 57.027 36.000 0.00 0.00 36.07 1.82
4259 11901 2.826488 AGTACCACTGAGCAATCTCCT 58.174 47.619 0.00 0.00 38.58 3.69
4263 11905 2.027377 ACCACTGAGCAATCTCCTGAAG 60.027 50.000 0.00 0.00 38.58 3.02
4264 11906 2.630158 CACTGAGCAATCTCCTGAAGG 58.370 52.381 0.00 0.00 38.58 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 6.976636 TTGGCAACTTTTCTTTTAGTTTGG 57.023 33.333 0.00 0.00 32.50 3.28
105 106 6.533730 TCACCCAATAGCCAATAGATTAGTG 58.466 40.000 0.00 0.00 0.00 2.74
195 196 1.636340 CACATCGCCGGAAATCGTC 59.364 57.895 5.05 0.00 37.11 4.20
212 213 1.533033 TCTCCTCCCACTGAACGCA 60.533 57.895 0.00 0.00 0.00 5.24
214 215 0.969894 AAGTCTCCTCCCACTGAACG 59.030 55.000 0.00 0.00 0.00 3.95
221 222 0.687354 GACAGCAAAGTCTCCTCCCA 59.313 55.000 0.00 0.00 35.65 4.37
232 233 0.380378 GCCTCGTTGTTGACAGCAAA 59.620 50.000 6.27 0.00 35.42 3.68
235 236 2.551270 CGCCTCGTTGTTGACAGC 59.449 61.111 0.00 0.00 0.00 4.40
237 238 2.089887 TAGGCGCCTCGTTGTTGACA 62.090 55.000 36.73 8.49 0.00 3.58
238 239 1.373748 TAGGCGCCTCGTTGTTGAC 60.374 57.895 36.73 0.00 0.00 3.18
262 263 9.770097 ACATATCATCATGAGATTTTACGAAGT 57.230 29.630 0.09 0.00 37.06 3.01
278 279 2.958355 TGACTGAGCCGACATATCATCA 59.042 45.455 0.00 0.00 0.00 3.07
283 284 1.335182 CGAGTGACTGAGCCGACATAT 59.665 52.381 0.00 0.00 0.00 1.78
288 289 2.033602 TCCGAGTGACTGAGCCGA 59.966 61.111 0.00 0.00 0.00 5.54
299 300 0.757188 CCCTATGAGCACCTCCGAGT 60.757 60.000 0.00 0.00 0.00 4.18
320 321 1.165907 ATGAACGCACACACACCCTG 61.166 55.000 0.00 0.00 0.00 4.45
323 324 1.130373 CCATATGAACGCACACACACC 59.870 52.381 3.65 0.00 0.00 4.16
326 327 1.130373 CACCCATATGAACGCACACAC 59.870 52.381 3.65 0.00 0.00 3.82
333 334 3.494626 GCATACACTCACCCATATGAACG 59.505 47.826 3.65 0.00 0.00 3.95
335 336 4.769345 TGCATACACTCACCCATATGAA 57.231 40.909 3.65 0.00 0.00 2.57
336 337 4.102996 ACATGCATACACTCACCCATATGA 59.897 41.667 3.65 0.00 0.00 2.15
337 338 4.392047 ACATGCATACACTCACCCATATG 58.608 43.478 0.00 0.00 0.00 1.78
341 342 2.877097 AACATGCATACACTCACCCA 57.123 45.000 0.00 0.00 0.00 4.51
399 948 8.429641 TCTTTACTACTCCAATAGCCAATTAGG 58.570 37.037 0.00 0.00 41.84 2.69
402 951 7.054751 GGTCTTTACTACTCCAATAGCCAATT 58.945 38.462 0.00 0.00 0.00 2.32
424 2702 6.705302 TCTTTAGCATGATATGAGATGGGTC 58.295 40.000 0.00 0.00 0.00 4.46
466 2759 6.207614 CGAGTGTGAGAAAGGATGGATATCTA 59.792 42.308 2.05 0.00 33.68 1.98
485 2806 3.365465 CGTGAGTTGATCTTCTCGAGTGT 60.365 47.826 13.13 0.00 33.88 3.55
547 2896 8.528643 TCTTTGGAGATCGAAGAGTTAACATAA 58.471 33.333 8.61 0.00 43.63 1.90
749 3099 2.413108 CGGGTGCCAAATGTAAACGTAC 60.413 50.000 0.00 0.00 0.00 3.67
775 3126 1.804151 CGGAGATTTTGCGACCTTCAA 59.196 47.619 0.00 0.00 44.18 2.69
934 3324 0.458543 CGCGTTATGTGTGCTCCTCT 60.459 55.000 0.00 0.00 0.00 3.69
994 3469 1.524621 CGCTAGCCACCATCTTGGG 60.525 63.158 9.66 0.00 43.37 4.12
996 3471 3.414272 GCGCTAGCCACCATCTTG 58.586 61.111 9.66 0.00 37.42 3.02
1014 4050 2.093216 GGCAACGAGAAGCATCCTG 58.907 57.895 0.00 0.00 0.00 3.86
1230 4268 2.221749 CGTACCACACATGCATATCAGC 59.778 50.000 0.00 0.00 0.00 4.26
1231 4269 3.457234 ACGTACCACACATGCATATCAG 58.543 45.455 0.00 0.00 0.00 2.90
1232 4270 3.535280 ACGTACCACACATGCATATCA 57.465 42.857 0.00 0.00 0.00 2.15
1233 4271 3.621268 ACAACGTACCACACATGCATATC 59.379 43.478 0.00 0.00 0.00 1.63
1234 4272 3.605634 ACAACGTACCACACATGCATAT 58.394 40.909 0.00 0.00 0.00 1.78
1235 4273 3.046968 ACAACGTACCACACATGCATA 57.953 42.857 0.00 0.00 0.00 3.14
1236 4274 1.890876 ACAACGTACCACACATGCAT 58.109 45.000 0.00 0.00 0.00 3.96
1237 4275 2.136728 GTACAACGTACCACACATGCA 58.863 47.619 0.00 0.00 0.00 3.96
1275 4346 4.622740 CGATCGATTAAGCATGTCAGCATA 59.377 41.667 10.26 0.00 36.85 3.14
1290 4364 0.802222 CACCTGCACGTCGATCGATT 60.802 55.000 22.50 8.80 42.86 3.34
1315 4389 2.180204 GTCGTAGTAGCCGCCGGTA 61.180 63.158 4.45 0.00 0.00 4.02
1688 4782 3.195002 CGTAGACGCGTACCGGGA 61.195 66.667 13.97 0.00 42.31 5.14
1734 4828 9.672673 AACATGAAGTAATGTAAGAGCAAGTAT 57.327 29.630 0.00 0.00 39.89 2.12
1740 4834 8.721478 TCTCAAAACATGAAGTAATGTAAGAGC 58.279 33.333 0.00 0.00 39.89 4.09
1743 4837 9.599322 GTGTCTCAAAACATGAAGTAATGTAAG 57.401 33.333 0.00 0.00 39.89 2.34
1744 4838 9.114952 TGTGTCTCAAAACATGAAGTAATGTAA 57.885 29.630 0.00 0.00 39.89 2.41
1751 4872 4.201812 CGTGTGTGTCTCAAAACATGAAGT 60.202 41.667 0.00 0.00 37.67 3.01
1754 4875 3.266636 ACGTGTGTGTCTCAAAACATGA 58.733 40.909 0.00 0.00 34.40 3.07
1766 4887 1.939934 GCCATATGCATACGTGTGTGT 59.060 47.619 8.99 5.60 40.77 3.72
1767 4888 2.668617 GCCATATGCATACGTGTGTG 57.331 50.000 8.99 2.06 40.77 3.82
1810 4934 8.731275 TTGGATTTGTATAGAATCGATTGTGT 57.269 30.769 16.96 12.68 34.97 3.72
1811 4935 9.603298 CATTGGATTTGTATAGAATCGATTGTG 57.397 33.333 16.96 0.00 34.97 3.33
1812 4936 8.786898 CCATTGGATTTGTATAGAATCGATTGT 58.213 33.333 16.96 14.71 34.97 2.71
1813 4937 9.002600 TCCATTGGATTTGTATAGAATCGATTG 57.997 33.333 16.96 0.00 34.97 2.67
1814 4938 9.745018 ATCCATTGGATTTGTATAGAATCGATT 57.255 29.630 11.20 11.20 39.79 3.34
1815 4939 9.170734 CATCCATTGGATTTGTATAGAATCGAT 57.829 33.333 15.75 0.00 39.79 3.59
1816 4940 8.552083 CATCCATTGGATTTGTATAGAATCGA 57.448 34.615 15.75 0.00 39.79 3.59
1856 4980 9.609346 GCTCTATTTTTCTTACCTATTACACCA 57.391 33.333 0.00 0.00 0.00 4.17
1858 4982 8.762426 CCGCTCTATTTTTCTTACCTATTACAC 58.238 37.037 0.00 0.00 0.00 2.90
1859 4983 7.440255 GCCGCTCTATTTTTCTTACCTATTACA 59.560 37.037 0.00 0.00 0.00 2.41
1860 4984 7.359014 CGCCGCTCTATTTTTCTTACCTATTAC 60.359 40.741 0.00 0.00 0.00 1.89
1865 4989 3.195661 CGCCGCTCTATTTTTCTTACCT 58.804 45.455 0.00 0.00 0.00 3.08
1867 4991 2.350498 TGCGCCGCTCTATTTTTCTTAC 59.650 45.455 11.67 0.00 0.00 2.34
1868 4992 2.350498 GTGCGCCGCTCTATTTTTCTTA 59.650 45.455 11.67 0.00 0.00 2.10
1869 4993 1.130561 GTGCGCCGCTCTATTTTTCTT 59.869 47.619 11.67 0.00 0.00 2.52
1928 5080 8.913419 GCCAAAGGCGTATATGGAACATTATGA 61.913 40.741 0.00 0.00 41.24 2.15
1929 5081 6.842121 GCCAAAGGCGTATATGGAACATTATG 60.842 42.308 9.28 0.00 41.24 1.90
1930 5082 5.183140 GCCAAAGGCGTATATGGAACATTAT 59.817 40.000 9.28 0.00 41.24 1.28
1931 5083 4.517453 GCCAAAGGCGTATATGGAACATTA 59.483 41.667 9.28 0.00 41.24 1.90
1932 5084 3.317993 GCCAAAGGCGTATATGGAACATT 59.682 43.478 9.28 0.00 41.24 2.71
1933 5085 2.884639 GCCAAAGGCGTATATGGAACAT 59.115 45.455 9.28 0.00 41.24 2.71
1934 5086 2.294074 GCCAAAGGCGTATATGGAACA 58.706 47.619 9.28 0.00 41.19 3.18
1946 5098 2.563427 GTCAGAAGCGCCAAAGGC 59.437 61.111 2.29 0.00 46.75 4.35
1947 5099 2.863153 CGTCAGAAGCGCCAAAGG 59.137 61.111 2.29 0.00 0.00 3.11
1955 5107 2.227968 ATTTCGCGTGCGTCAGAAGC 62.228 55.000 14.47 0.65 40.74 3.86
1956 5108 0.989164 TATTTCGCGTGCGTCAGAAG 59.011 50.000 14.47 0.00 40.74 2.85
1957 5109 0.989164 CTATTTCGCGTGCGTCAGAA 59.011 50.000 14.47 5.96 40.74 3.02
1958 5110 0.800683 CCTATTTCGCGTGCGTCAGA 60.801 55.000 14.47 0.00 40.74 3.27
1959 5111 1.631072 CCTATTTCGCGTGCGTCAG 59.369 57.895 14.47 7.07 40.74 3.51
1960 5112 2.449525 GCCTATTTCGCGTGCGTCA 61.450 57.895 14.47 2.39 40.74 4.35
1961 5113 1.962092 TTGCCTATTTCGCGTGCGTC 61.962 55.000 14.47 0.00 40.74 5.19
1962 5114 1.570347 TTTGCCTATTTCGCGTGCGT 61.570 50.000 14.47 0.00 40.74 5.24
1963 5115 1.125847 GTTTGCCTATTTCGCGTGCG 61.126 55.000 5.77 8.14 41.35 5.34
1964 5116 0.109964 TGTTTGCCTATTTCGCGTGC 60.110 50.000 5.77 1.25 0.00 5.34
1965 5117 2.176369 CATGTTTGCCTATTTCGCGTG 58.824 47.619 5.77 0.00 0.00 5.34
1966 5118 1.810151 ACATGTTTGCCTATTTCGCGT 59.190 42.857 5.77 0.00 0.00 6.01
1967 5119 2.542766 ACATGTTTGCCTATTTCGCG 57.457 45.000 0.00 0.00 0.00 5.87
1968 5120 4.793216 CAGTTACATGTTTGCCTATTTCGC 59.207 41.667 2.30 0.00 0.00 4.70
1969 5121 5.794945 CACAGTTACATGTTTGCCTATTTCG 59.205 40.000 2.30 0.00 0.00 3.46
1970 5122 5.572896 GCACAGTTACATGTTTGCCTATTTC 59.427 40.000 2.30 0.00 0.00 2.17
1971 5123 5.243730 AGCACAGTTACATGTTTGCCTATTT 59.756 36.000 2.30 0.00 0.00 1.40
1972 5124 4.766891 AGCACAGTTACATGTTTGCCTATT 59.233 37.500 2.30 0.00 0.00 1.73
1973 5125 4.335416 AGCACAGTTACATGTTTGCCTAT 58.665 39.130 2.30 0.00 0.00 2.57
1974 5126 3.750371 AGCACAGTTACATGTTTGCCTA 58.250 40.909 2.30 0.00 0.00 3.93
1975 5127 2.586425 AGCACAGTTACATGTTTGCCT 58.414 42.857 2.30 0.00 0.00 4.75
1976 5128 3.369546 AAGCACAGTTACATGTTTGCC 57.630 42.857 2.30 0.00 0.00 4.52
1977 5129 3.060339 GCAAAGCACAGTTACATGTTTGC 60.060 43.478 2.30 7.02 37.31 3.68
1978 5130 4.111198 TGCAAAGCACAGTTACATGTTTG 58.889 39.130 2.30 3.33 31.71 2.93
1979 5131 4.383850 TGCAAAGCACAGTTACATGTTT 57.616 36.364 2.30 0.00 31.71 2.83
1980 5132 4.037803 TCATGCAAAGCACAGTTACATGTT 59.962 37.500 2.30 0.00 43.04 2.71
1981 5133 3.569277 TCATGCAAAGCACAGTTACATGT 59.431 39.130 2.69 2.69 43.04 3.21
1982 5134 4.163458 TCATGCAAAGCACAGTTACATG 57.837 40.909 0.00 0.00 43.04 3.21
1983 5135 4.520111 TCTTCATGCAAAGCACAGTTACAT 59.480 37.500 0.00 0.00 43.04 2.29
1984 5136 3.882288 TCTTCATGCAAAGCACAGTTACA 59.118 39.130 0.00 0.00 43.04 2.41
1985 5137 4.214119 TCTCTTCATGCAAAGCACAGTTAC 59.786 41.667 0.00 0.00 43.04 2.50
1986 5138 4.388485 TCTCTTCATGCAAAGCACAGTTA 58.612 39.130 0.00 0.00 43.04 2.24
1987 5139 3.216800 TCTCTTCATGCAAAGCACAGTT 58.783 40.909 0.00 0.00 43.04 3.16
1988 5140 2.854963 TCTCTTCATGCAAAGCACAGT 58.145 42.857 0.00 0.00 43.04 3.55
1989 5141 4.634883 ACTATCTCTTCATGCAAAGCACAG 59.365 41.667 0.00 0.00 43.04 3.66
1990 5142 4.582869 ACTATCTCTTCATGCAAAGCACA 58.417 39.130 0.00 0.00 43.04 4.57
1991 5143 5.814705 AGTACTATCTCTTCATGCAAAGCAC 59.185 40.000 0.00 0.00 43.04 4.40
1992 5144 5.982356 AGTACTATCTCTTCATGCAAAGCA 58.018 37.500 0.00 0.00 44.86 3.91
1993 5145 6.422400 GGTAGTACTATCTCTTCATGCAAAGC 59.578 42.308 5.75 0.00 0.00 3.51
1994 5146 7.492524 TGGTAGTACTATCTCTTCATGCAAAG 58.507 38.462 14.21 0.00 0.00 2.77
1995 5147 7.124298 ACTGGTAGTACTATCTCTTCATGCAAA 59.876 37.037 14.21 0.00 0.00 3.68
1996 5148 6.607600 ACTGGTAGTACTATCTCTTCATGCAA 59.392 38.462 14.21 0.00 0.00 4.08
1997 5149 6.129874 ACTGGTAGTACTATCTCTTCATGCA 58.870 40.000 14.21 0.00 0.00 3.96
1998 5150 6.488683 AGACTGGTAGTACTATCTCTTCATGC 59.511 42.308 14.21 0.00 0.00 4.06
1999 5151 8.995220 GTAGACTGGTAGTACTATCTCTTCATG 58.005 40.741 14.21 0.00 0.00 3.07
2000 5152 8.158789 GGTAGACTGGTAGTACTATCTCTTCAT 58.841 40.741 14.21 0.00 0.00 2.57
2001 5153 7.126879 TGGTAGACTGGTAGTACTATCTCTTCA 59.873 40.741 14.21 8.63 0.00 3.02
2002 5154 7.442062 GTGGTAGACTGGTAGTACTATCTCTTC 59.558 44.444 14.21 7.42 0.00 2.87
2003 5155 7.127647 AGTGGTAGACTGGTAGTACTATCTCTT 59.872 40.741 14.21 0.00 31.75 2.85
2004 5156 6.616548 AGTGGTAGACTGGTAGTACTATCTCT 59.383 42.308 14.21 11.46 31.75 3.10
2005 5157 6.829849 AGTGGTAGACTGGTAGTACTATCTC 58.170 44.000 14.21 4.70 31.75 2.75
2006 5158 6.828307 AGTGGTAGACTGGTAGTACTATCT 57.172 41.667 14.21 11.04 31.75 1.98
2049 5201 2.465860 ATTTGTGCTGTGCATGCAAT 57.534 40.000 24.58 6.69 41.91 3.56
2050 5202 1.867865 CAATTTGTGCTGTGCATGCAA 59.132 42.857 24.58 11.95 41.91 4.08
2085 5301 5.114572 CGCATTATCTTCAAATTGATCGTGC 59.885 40.000 0.00 2.07 33.65 5.34
2086 5302 6.421405 TCGCATTATCTTCAAATTGATCGTG 58.579 36.000 0.00 0.00 0.00 4.35
2089 5305 8.081208 TCTCTCGCATTATCTTCAAATTGATC 57.919 34.615 0.00 0.00 0.00 2.92
2101 5317 8.487970 TCGTCAAATTAATTCTCTCGCATTATC 58.512 33.333 0.10 0.00 0.00 1.75
2108 5324 6.403333 TGGTTCGTCAAATTAATTCTCTCG 57.597 37.500 0.10 5.19 0.00 4.04
2118 5334 7.537306 CGACTTTATGAAATGGTTCGTCAAATT 59.463 33.333 0.00 0.00 36.46 1.82
2123 5339 5.313623 CACGACTTTATGAAATGGTTCGTC 58.686 41.667 0.00 0.00 36.46 4.20
2124 5340 4.153475 CCACGACTTTATGAAATGGTTCGT 59.847 41.667 0.00 0.00 36.46 3.85
2126 5342 5.180492 TGACCACGACTTTATGAAATGGTTC 59.820 40.000 0.00 0.00 39.06 3.62
2185 5409 2.095213 GTCTGTGCACGTTCAGTTTTCA 59.905 45.455 13.13 0.00 33.89 2.69
2196 5420 0.663269 TACAGCTTCGTCTGTGCACG 60.663 55.000 13.13 7.36 45.95 5.34
2273 5521 0.834687 TTCTGGTAGAGGCCACGGTT 60.835 55.000 5.01 0.00 34.36 4.44
2342 5599 9.810545 TTATCGTGACATTAATTAGTGATGTGA 57.189 29.630 14.28 7.36 34.38 3.58
2473 5742 1.864435 GCGATGTAGGCCTTGTACTCG 60.864 57.143 12.58 14.81 0.00 4.18
2660 5930 0.540454 CTTGGAGGATGAGCTGCAGA 59.460 55.000 20.43 0.00 0.00 4.26
2924 6194 2.126812 GCGAACGAGACGAGCTGT 60.127 61.111 0.00 0.00 0.00 4.40
2942 6212 3.066190 TAGTCCGCCTGTGACCGG 61.066 66.667 0.00 0.00 45.64 5.28
3057 6334 2.358247 CCCCGGGTTGTTCGTGAG 60.358 66.667 21.85 0.00 0.00 3.51
3061 6338 0.743345 GATCTTCCCCGGGTTGTTCG 60.743 60.000 21.85 2.11 0.00 3.95
3254 6531 3.960571 ACATCAGTTATGCAGAAGCCTT 58.039 40.909 0.00 0.00 39.39 4.35
3528 10885 3.135530 GGGAATGTCTACCTGCTCTTGAT 59.864 47.826 0.00 0.00 0.00 2.57
3900 11541 1.856629 AGGTTGCTGCAGCCATAAAT 58.143 45.000 34.64 13.79 37.20 1.40
4074 11716 7.587037 TCTGTCAATTTGAAAAGTGGAGATT 57.413 32.000 0.00 0.00 34.95 2.40
4075 11717 7.286316 ACTTCTGTCAATTTGAAAAGTGGAGAT 59.714 33.333 16.29 0.00 34.95 2.75
4174 11816 3.459598 TGAAGGAAATACCCCATGAGGAG 59.540 47.826 0.00 0.00 40.05 3.69
4176 11818 3.951563 TGAAGGAAATACCCCATGAGG 57.048 47.619 0.00 0.00 40.05 3.86
4188 11830 2.619697 TTGCATCCCCATGAAGGAAA 57.380 45.000 8.33 0.00 41.22 3.13
4202 11844 8.538701 TGGGAATGTATTTTCACTATTTTGCAT 58.461 29.630 0.00 0.00 30.08 3.96
4207 11849 9.533831 AAGACTGGGAATGTATTTTCACTATTT 57.466 29.630 0.00 0.00 30.08 1.40
4208 11850 8.960591 CAAGACTGGGAATGTATTTTCACTATT 58.039 33.333 0.00 0.00 30.08 1.73
4209 11851 8.328758 TCAAGACTGGGAATGTATTTTCACTAT 58.671 33.333 0.00 0.00 30.08 2.12
4210 11852 7.685481 TCAAGACTGGGAATGTATTTTCACTA 58.315 34.615 0.00 0.00 30.08 2.74
4211 11853 6.542821 TCAAGACTGGGAATGTATTTTCACT 58.457 36.000 0.00 0.00 30.08 3.41
4212 11854 6.817765 TCAAGACTGGGAATGTATTTTCAC 57.182 37.500 0.00 0.00 0.00 3.18
4213 11855 7.004086 AGTTCAAGACTGGGAATGTATTTTCA 58.996 34.615 0.00 0.00 37.17 2.69
4214 11856 7.454260 AGTTCAAGACTGGGAATGTATTTTC 57.546 36.000 0.00 0.00 37.17 2.29
4215 11857 8.164070 ACTAGTTCAAGACTGGGAATGTATTTT 58.836 33.333 0.00 0.00 40.87 1.82
4216 11858 7.690256 ACTAGTTCAAGACTGGGAATGTATTT 58.310 34.615 0.00 0.00 40.87 1.40
4240 11882 2.497675 TCAGGAGATTGCTCAGTGGTAC 59.502 50.000 0.00 0.00 43.14 3.34
4241 11883 2.820178 TCAGGAGATTGCTCAGTGGTA 58.180 47.619 0.00 0.00 43.14 3.25
4242 11884 1.649321 TCAGGAGATTGCTCAGTGGT 58.351 50.000 0.00 0.00 43.14 4.16


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

AutoCloner maintained by Alex Coulton.