Multiple sequence alignment - TraesCS4B01G208000

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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 TraesCS4B01G208000 chr4B 100.000 4477 0 0 1 4477 445227689 445232165 0.000000e+00 8268
1 TraesCS4B01G208000 chr4D 92.664 1554 91 13 2237 3771 360451910 360453459 0.000000e+00 2217
2 TraesCS4B01G208000 chr4D 91.018 1592 84 24 1 1572 360449842 360451394 0.000000e+00 2093
3 TraesCS4B01G208000 chr4D 94.646 523 17 6 1694 2206 360451397 360451918 0.000000e+00 800
4 TraesCS4B01G208000 chr4D 88.032 493 37 10 4004 4477 360453636 360454125 8.410000e-157 564
5 TraesCS4B01G208000 chr4D 90.780 141 11 1 3806 3944 360453464 360453604 2.130000e-43 187
6 TraesCS4B01G208000 chr4D 90.769 130 12 0 1566 1695 23352727 23352598 1.660000e-39 174
7 TraesCS4B01G208000 chr4A 90.951 1503 84 25 2264 3742 104410537 104409063 0.000000e+00 1975
8 TraesCS4B01G208000 chr4A 86.569 1303 104 32 4 1276 104413121 104411860 0.000000e+00 1371
9 TraesCS4B01G208000 chr4A 95.844 409 16 1 1774 2182 104410991 104410584 0.000000e+00 660
10 TraesCS4B01G208000 chr4A 94.203 276 16 0 1284 1559 104411595 104411320 5.350000e-114 422
11 TraesCS4B01G208000 chr4A 86.197 355 21 11 4006 4350 104408855 104408519 4.260000e-95 359
12 TraesCS4B01G208000 chr4A 90.370 135 12 1 1566 1700 734470655 734470522 4.600000e-40 176
13 TraesCS4B01G208000 chr4A 88.889 144 11 3 3806 3944 104409032 104408889 5.950000e-39 172
14 TraesCS4B01G208000 chr1A 76.947 976 169 41 2301 3242 481674509 481675462 5.170000e-139 505
15 TraesCS4B01G208000 chr1A 73.615 1209 246 56 2299 3468 480935160 480933986 9.020000e-107 398
16 TraesCS4B01G208000 chr1D 76.139 1010 177 40 2301 3266 381019561 381020550 5.240000e-129 472
17 TraesCS4B01G208000 chr1D 73.719 1210 243 60 2299 3468 379911999 379910825 1.940000e-108 403
18 TraesCS4B01G208000 chr1B 75.964 1011 177 44 2301 3266 510809344 510810333 1.130000e-125 460
19 TraesCS4B01G208000 chr1B 74.303 1004 200 49 2299 3277 509902338 509901368 5.470000e-99 372
20 TraesCS4B01G208000 chr3A 74.444 990 204 41 2299 3268 608751173 608752133 9.090000e-102 381
21 TraesCS4B01G208000 chr3A 83.534 249 37 3 1807 2053 608347931 608347685 3.480000e-56 230
22 TraesCS4B01G208000 chr3A 90.698 129 12 0 1567 1695 13008823 13008951 5.950000e-39 172
23 TraesCS4B01G208000 chr7D 72.286 1216 258 58 2297 3468 149181891 149183071 5.630000e-79 305
24 TraesCS4B01G208000 chr3D 83.401 247 41 0 1807 2053 465027713 465027467 3.480000e-56 230
25 TraesCS4B01G208000 chr3B 91.473 129 11 0 1568 1696 279692043 279692171 1.280000e-40 178
26 TraesCS4B01G208000 chr3B 87.755 147 17 1 1552 1697 51909533 51909679 2.140000e-38 171
27 TraesCS4B01G208000 chr3B 88.571 140 15 1 1566 1704 636123109 636122970 7.700000e-38 169
28 TraesCS4B01G208000 chr3B 80.000 200 34 5 2299 2495 618870681 618870877 4.670000e-30 143
29 TraesCS4B01G208000 chr5B 91.406 128 11 0 1568 1695 567933081 567933208 4.600000e-40 176
30 TraesCS4B01G208000 chr2B 90.769 130 12 0 1567 1696 620640849 620640720 1.660000e-39 174
31 TraesCS4B01G208000 chr6B 90.152 132 11 2 1565 1695 101745917 101745787 2.140000e-38 171
32 TraesCS4B01G208000 chrUn 76.533 375 44 21 377 726 113190404 113190759 9.960000e-37 165
33 TraesCS4B01G208000 chr7B 81.395 129 17 7 3343 3468 111944149 111944273 1.020000e-16 99
34 TraesCS4B01G208000 chr7A 80.576 139 18 8 3334 3468 150023580 150023713 1.020000e-16 99


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 TraesCS4B01G208000 chr4B 445227689 445232165 4476 False 8268.0 8268 100.000000 1 4477 1 chr4B.!!$F1 4476
1 TraesCS4B01G208000 chr4D 360449842 360454125 4283 False 1172.2 2217 91.428000 1 4477 5 chr4D.!!$F1 4476
2 TraesCS4B01G208000 chr4A 104408519 104413121 4602 True 826.5 1975 90.442167 4 4350 6 chr4A.!!$R2 4346
3 TraesCS4B01G208000 chr1A 481674509 481675462 953 False 505.0 505 76.947000 2301 3242 1 chr1A.!!$F1 941
4 TraesCS4B01G208000 chr1A 480933986 480935160 1174 True 398.0 398 73.615000 2299 3468 1 chr1A.!!$R1 1169
5 TraesCS4B01G208000 chr1D 381019561 381020550 989 False 472.0 472 76.139000 2301 3266 1 chr1D.!!$F1 965
6 TraesCS4B01G208000 chr1D 379910825 379911999 1174 True 403.0 403 73.719000 2299 3468 1 chr1D.!!$R1 1169
7 TraesCS4B01G208000 chr1B 510809344 510810333 989 False 460.0 460 75.964000 2301 3266 1 chr1B.!!$F1 965
8 TraesCS4B01G208000 chr1B 509901368 509902338 970 True 372.0 372 74.303000 2299 3277 1 chr1B.!!$R1 978
9 TraesCS4B01G208000 chr3A 608751173 608752133 960 False 381.0 381 74.444000 2299 3268 1 chr3A.!!$F2 969
10 TraesCS4B01G208000 chr7D 149181891 149183071 1180 False 305.0 305 72.286000 2297 3468 1 chr7D.!!$F1 1171

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
777 816 0.166814 GCTTCGCTGATCACGCTTTT 59.833 50.0 13.06 0.00 0.00 2.27 F
941 990 0.249741 GTTATGGTACGAGCGGGCAT 60.250 55.0 0.00 0.00 0.00 4.40 F
1188 1238 0.450583 ATCTCAAGCAAGCGCACATG 59.549 50.0 11.47 6.85 42.27 3.21 F
1190 1240 0.728129 CTCAAGCAAGCGCACATGTG 60.728 55.0 21.83 21.83 42.27 3.21 F
2173 2756 0.737715 GCCCACTCTACAACTGCTCG 60.738 60.0 0.00 0.00 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1778 2103 0.035439 CATCAACGCCAGTTACCCCT 60.035 55.000 0.00 0.00 38.79 4.79 R
1779 2104 0.322187 ACATCAACGCCAGTTACCCC 60.322 55.000 0.00 0.00 38.79 4.95 R
2175 2758 0.948678 TGTTACGAACCAGCCTTTGC 59.051 50.000 0.00 0.00 37.95 3.68 R
2320 2903 1.073199 GTACCACTTGCCTGGCTGT 59.927 57.895 21.03 15.41 34.20 4.40 R
3998 4679 0.036164 TTCACTTGGTCGGACATGGG 59.964 55.000 10.76 0.53 0.00 4.00 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
124 125 0.737219 GGATGTGCAGGTCATTCAGC 59.263 55.000 0.00 0.00 0.00 4.26
128 129 1.672030 TGCAGGTCATTCAGCCACG 60.672 57.895 0.00 0.00 0.00 4.94
142 143 3.006430 TCAGCCACGAATCTTAACTGTCA 59.994 43.478 0.00 0.00 0.00 3.58
161 162 0.329931 ATTGGGGTACGTGCAATGGA 59.670 50.000 5.86 0.00 0.00 3.41
166 167 1.084289 GGTACGTGCAATGGAGGAAC 58.916 55.000 5.86 0.00 0.00 3.62
184 185 6.774170 GGAGGAACTTAGGAACTTAAACCAAA 59.226 38.462 0.00 0.00 41.55 3.28
287 310 7.162082 CAGAACCCTATAAGTTGAAGTGTTCT 58.838 38.462 9.72 9.72 40.17 3.01
405 432 2.033550 GCTACCGAACTGACGAGATGAT 59.966 50.000 0.00 0.00 35.09 2.45
415 442 5.380900 ACTGACGAGATGATAAGGAGATCA 58.619 41.667 0.00 0.00 40.08 2.92
416 443 6.009589 ACTGACGAGATGATAAGGAGATCAT 58.990 40.000 0.00 0.00 46.89 2.45
495 528 1.144936 GCTAGGCACGGCAGATTCT 59.855 57.895 0.00 0.00 32.95 2.40
500 533 0.530870 GGCACGGCAGATTCTAGTCC 60.531 60.000 0.00 0.00 0.00 3.85
529 566 2.158856 TCGCATCATGATTCTTGAGGCT 60.159 45.455 26.33 0.00 45.87 4.58
538 575 3.131223 TGATTCTTGAGGCTTACTCCGAG 59.869 47.826 0.00 0.00 46.01 4.63
540 577 1.819288 TCTTGAGGCTTACTCCGAGTG 59.181 52.381 11.52 0.00 46.01 3.51
564 601 4.481463 ACCAACTGTTCAAAAGTGAAACG 58.519 39.130 0.00 0.00 45.29 3.60
565 602 4.216687 ACCAACTGTTCAAAAGTGAAACGA 59.783 37.500 0.00 0.00 45.29 3.85
566 603 5.105917 ACCAACTGTTCAAAAGTGAAACGAT 60.106 36.000 0.00 0.00 45.29 3.73
567 604 5.455525 CCAACTGTTCAAAAGTGAAACGATC 59.544 40.000 0.00 0.00 45.29 3.69
569 606 6.189677 ACTGTTCAAAAGTGAAACGATCAA 57.810 33.333 0.00 0.00 45.29 2.57
570 607 6.258160 ACTGTTCAAAAGTGAAACGATCAAG 58.742 36.000 0.00 0.00 45.29 3.02
571 608 6.128007 ACTGTTCAAAAGTGAAACGATCAAGT 60.128 34.615 0.00 0.00 45.29 3.16
572 609 6.616947 TGTTCAAAAGTGAAACGATCAAGTT 58.383 32.000 0.00 0.00 45.29 2.66
573 610 6.745450 TGTTCAAAAGTGAAACGATCAAGTTC 59.255 34.615 0.00 0.00 45.29 3.01
592 629 1.066858 TCGTTCTGGCTCCTGATGTTC 60.067 52.381 0.00 0.00 0.00 3.18
598 635 1.066858 TGGCTCCTGATGTTCGAGAAC 60.067 52.381 8.89 8.89 41.50 3.01
683 722 3.119096 GCGCGACCCAACTCTTCC 61.119 66.667 12.10 0.00 0.00 3.46
777 816 0.166814 GCTTCGCTGATCACGCTTTT 59.833 50.000 13.06 0.00 0.00 2.27
778 817 1.393539 GCTTCGCTGATCACGCTTTTA 59.606 47.619 13.06 0.00 0.00 1.52
830 869 7.775093 CCTAACACTTCTCATATTTCCCATCAA 59.225 37.037 0.00 0.00 0.00 2.57
881 923 5.826643 TCTTCACCTAATAAATTGCACCCT 58.173 37.500 0.00 0.00 0.00 4.34
937 982 2.034179 TCTCATGTTATGGTACGAGCGG 59.966 50.000 0.00 0.00 0.00 5.52
941 990 0.249741 GTTATGGTACGAGCGGGCAT 60.250 55.000 0.00 0.00 0.00 4.40
963 1012 1.533625 CTCCTCCCATTTGCGAAACA 58.466 50.000 0.00 0.00 0.00 2.83
970 1019 2.417651 CCCATTTGCGAAACATCTGCAT 60.418 45.455 0.00 0.00 38.60 3.96
995 1044 2.171448 AGATCGATCAAAGGGTTGGGAG 59.829 50.000 26.47 0.00 35.29 4.30
1119 1168 4.823442 ACTGTGTTCATGCATTTTCTCTCA 59.177 37.500 0.00 0.00 0.00 3.27
1139 1188 7.989741 TCTCTCAATCTCTCTTTTCTTTTGTGT 59.010 33.333 0.00 0.00 0.00 3.72
1159 1209 4.029520 TGTTTATGGGGTTATGCTGCATT 58.970 39.130 21.56 3.08 0.00 3.56
1187 1237 0.731417 GATCTCAAGCAAGCGCACAT 59.269 50.000 11.47 0.00 42.27 3.21
1188 1238 0.450583 ATCTCAAGCAAGCGCACATG 59.549 50.000 11.47 6.85 42.27 3.21
1190 1240 0.728129 CTCAAGCAAGCGCACATGTG 60.728 55.000 21.83 21.83 42.27 3.21
1260 1310 1.229975 TTGAGACCATGCTGCGTGTG 61.230 55.000 19.58 13.43 0.00 3.82
1275 1327 1.603802 CGTGTGTTTGTTCTGGCAGAT 59.396 47.619 19.50 0.00 0.00 2.90
1276 1328 2.805671 CGTGTGTTTGTTCTGGCAGATA 59.194 45.455 19.50 7.98 0.00 1.98
1277 1329 3.363970 CGTGTGTTTGTTCTGGCAGATAC 60.364 47.826 19.50 18.19 0.00 2.24
1278 1330 2.805671 TGTGTTTGTTCTGGCAGATACG 59.194 45.455 19.50 0.00 0.00 3.06
1296 1609 1.449601 GTACCGCCTGATGTGTGGG 60.450 63.158 0.00 0.00 37.71 4.61
1304 1617 3.692101 CGCCTGATGTGTGGGTTAATTTA 59.308 43.478 0.00 0.00 0.00 1.40
1410 1723 4.697756 CAAGGGAAGGCGACCGCA 62.698 66.667 16.47 0.00 44.11 5.69
1507 1823 5.353394 TGCTCTTACTTAATTCCATCGGT 57.647 39.130 0.00 0.00 0.00 4.69
1559 1875 4.836125 AACAAAGTCATGGTCATCACAC 57.164 40.909 0.00 0.00 0.00 3.82
1572 1888 4.381718 GGTCATCACACTTGGGTAGTACTC 60.382 50.000 0.00 0.00 34.56 2.59
1574 1890 2.532843 TCACACTTGGGTAGTACTCCC 58.467 52.381 18.49 18.49 44.81 4.30
1575 1891 2.111255 TCACACTTGGGTAGTACTCCCT 59.889 50.000 23.01 7.87 44.84 4.20
1576 1892 2.496470 CACACTTGGGTAGTACTCCCTC 59.504 54.545 23.01 8.25 44.84 4.30
1577 1893 2.108970 CACTTGGGTAGTACTCCCTCC 58.891 57.143 23.01 12.44 44.84 4.30
1578 1894 1.720533 ACTTGGGTAGTACTCCCTCCA 59.279 52.381 23.01 14.02 44.84 3.86
1579 1895 2.318207 ACTTGGGTAGTACTCCCTCCAT 59.682 50.000 23.01 9.81 44.84 3.41
1580 1896 2.769602 TGGGTAGTACTCCCTCCATC 57.230 55.000 23.01 2.34 44.84 3.51
1581 1897 1.219724 TGGGTAGTACTCCCTCCATCC 59.780 57.143 23.01 7.49 44.84 3.51
1582 1898 1.618487 GGTAGTACTCCCTCCATCCG 58.382 60.000 0.00 0.00 0.00 4.18
1583 1899 1.144503 GGTAGTACTCCCTCCATCCGA 59.855 57.143 0.00 0.00 0.00 4.55
1584 1900 2.423947 GGTAGTACTCCCTCCATCCGAA 60.424 54.545 0.00 0.00 0.00 4.30
1585 1901 2.544844 AGTACTCCCTCCATCCGAAA 57.455 50.000 0.00 0.00 0.00 3.46
1586 1902 2.829023 AGTACTCCCTCCATCCGAAAA 58.171 47.619 0.00 0.00 0.00 2.29
1587 1903 3.385115 AGTACTCCCTCCATCCGAAAAT 58.615 45.455 0.00 0.00 0.00 1.82
1588 1904 4.553678 AGTACTCCCTCCATCCGAAAATA 58.446 43.478 0.00 0.00 0.00 1.40
1589 1905 3.840124 ACTCCCTCCATCCGAAAATAC 57.160 47.619 0.00 0.00 0.00 1.89
1590 1906 3.385115 ACTCCCTCCATCCGAAAATACT 58.615 45.455 0.00 0.00 0.00 2.12
1591 1907 3.780850 ACTCCCTCCATCCGAAAATACTT 59.219 43.478 0.00 0.00 0.00 2.24
1592 1908 4.130118 CTCCCTCCATCCGAAAATACTTG 58.870 47.826 0.00 0.00 0.00 3.16
1593 1909 3.521937 TCCCTCCATCCGAAAATACTTGT 59.478 43.478 0.00 0.00 0.00 3.16
1594 1910 3.877508 CCCTCCATCCGAAAATACTTGTC 59.122 47.826 0.00 0.00 0.00 3.18
1595 1911 4.513442 CCTCCATCCGAAAATACTTGTCA 58.487 43.478 0.00 0.00 0.00 3.58
1596 1912 5.126067 CCTCCATCCGAAAATACTTGTCAT 58.874 41.667 0.00 0.00 0.00 3.06
1597 1913 5.237344 CCTCCATCCGAAAATACTTGTCATC 59.763 44.000 0.00 0.00 0.00 2.92
1598 1914 5.739959 TCCATCCGAAAATACTTGTCATCA 58.260 37.500 0.00 0.00 0.00 3.07
1599 1915 6.176896 TCCATCCGAAAATACTTGTCATCAA 58.823 36.000 0.00 0.00 0.00 2.57
1600 1916 6.657117 TCCATCCGAAAATACTTGTCATCAAA 59.343 34.615 0.00 0.00 32.87 2.69
1601 1917 6.747280 CCATCCGAAAATACTTGTCATCAAAC 59.253 38.462 0.00 0.00 32.87 2.93
1602 1918 7.362056 CCATCCGAAAATACTTGTCATCAAACT 60.362 37.037 0.00 0.00 32.87 2.66
1603 1919 8.664798 CATCCGAAAATACTTGTCATCAAACTA 58.335 33.333 0.00 0.00 32.87 2.24
1604 1920 8.251750 TCCGAAAATACTTGTCATCAAACTAG 57.748 34.615 0.00 0.00 32.87 2.57
1605 1921 8.092068 TCCGAAAATACTTGTCATCAAACTAGA 58.908 33.333 0.00 0.00 32.87 2.43
1606 1922 8.883731 CCGAAAATACTTGTCATCAAACTAGAT 58.116 33.333 0.00 0.00 32.87 1.98
1689 2005 9.632807 TTGATAACAAATATTTTCAAACGGAGG 57.367 29.630 9.54 0.00 29.91 4.30
1690 2006 8.247562 TGATAACAAATATTTTCAAACGGAGGG 58.752 33.333 0.00 0.00 0.00 4.30
1691 2007 6.658188 AACAAATATTTTCAAACGGAGGGA 57.342 33.333 0.00 0.00 0.00 4.20
1692 2008 6.267496 ACAAATATTTTCAAACGGAGGGAG 57.733 37.500 0.00 0.00 0.00 4.30
1715 2031 1.202452 GCAACTGCAGCCACTTTTCTT 60.202 47.619 15.27 0.00 41.59 2.52
1722 2038 2.095718 GCAGCCACTTTTCTTAAGACGG 60.096 50.000 4.18 2.51 0.00 4.79
1730 2046 5.007724 CACTTTTCTTAAGACGGCTCAGTTT 59.992 40.000 4.18 0.00 0.00 2.66
1764 2083 5.291371 GCGAAAAATTACTCCACCTCTAGTC 59.709 44.000 0.00 0.00 0.00 2.59
1778 2103 8.609483 TCCACCTCTAGTCTACTCTTTTACTAA 58.391 37.037 0.00 0.00 0.00 2.24
1779 2104 8.895737 CCACCTCTAGTCTACTCTTTTACTAAG 58.104 40.741 0.00 0.00 0.00 2.18
1982 2565 4.647615 CGCTCTACGGCCCCATCG 62.648 72.222 0.00 0.00 38.44 3.84
2065 2648 2.344025 GTCTTCGGCGAGTGGTTTAAT 58.656 47.619 10.46 0.00 0.00 1.40
2173 2756 0.737715 GCCCACTCTACAACTGCTCG 60.738 60.000 0.00 0.00 0.00 5.03
2175 2758 1.135257 CCCACTCTACAACTGCTCGAG 60.135 57.143 8.45 8.45 0.00 4.04
2200 2783 1.003223 GGCTGGTTCGTAACACACAAC 60.003 52.381 0.00 0.00 0.00 3.32
2203 2786 3.787476 GCTGGTTCGTAACACACAACAAG 60.787 47.826 0.00 0.00 0.00 3.16
2215 2798 1.879380 CACAACAAGAGGCCGAATTCA 59.121 47.619 6.22 0.00 0.00 2.57
2216 2799 2.293122 CACAACAAGAGGCCGAATTCAA 59.707 45.455 6.22 0.00 0.00 2.69
2218 2801 2.270352 ACAAGAGGCCGAATTCAACA 57.730 45.000 6.22 0.00 0.00 3.33
2220 2803 2.154462 CAAGAGGCCGAATTCAACACT 58.846 47.619 6.22 0.00 0.00 3.55
2221 2804 2.100605 AGAGGCCGAATTCAACACTC 57.899 50.000 6.22 7.21 0.00 3.51
2222 2805 1.347707 AGAGGCCGAATTCAACACTCA 59.652 47.619 6.22 0.00 0.00 3.41
2225 2808 2.955660 AGGCCGAATTCAACACTCAAAA 59.044 40.909 6.22 0.00 0.00 2.44
2269 2852 5.122082 GGGTTACGGTTTTCATGTCGATTTA 59.878 40.000 0.00 0.00 0.00 1.40
2272 2855 7.751793 GGTTACGGTTTTCATGTCGATTTATTT 59.248 33.333 0.00 0.00 0.00 1.40
2280 2863 9.554724 TTTTCATGTCGATTTATTTTAGCTCAC 57.445 29.630 0.00 0.00 0.00 3.51
2286 2869 5.530915 TCGATTTATTTTAGCTCACCATGGG 59.469 40.000 18.09 5.22 0.00 4.00
2353 2936 1.522569 GTACCTGCTCCGGCTGATT 59.477 57.895 0.00 0.00 39.31 2.57
2578 3166 2.125269 GGACGCGTTGGCACCTAT 60.125 61.111 15.53 0.00 39.92 2.57
3004 3635 1.489070 CGCCCAACAACACGAACGTA 61.489 55.000 0.00 0.00 0.00 3.57
3037 3668 2.046314 GTGGTGGTGCTGCCGTAT 60.046 61.111 0.00 0.00 41.21 3.06
3064 3695 2.203337 GTGGAGGTGGTGCTGCAA 60.203 61.111 2.77 0.00 0.00 4.08
3127 3758 1.937899 CACGGGTTCGACTTCTTTGTT 59.062 47.619 0.00 0.00 40.11 2.83
3249 3880 0.616395 TGGGTCGCCATCAGGTTCTA 60.616 55.000 0.00 0.00 37.19 2.10
3337 3992 5.072055 TGATTCACTCTTTTCCTTGCATGA 58.928 37.500 0.00 0.00 0.00 3.07
3488 4143 1.139095 CTGTTAGACTCCGGCCGTC 59.861 63.158 26.12 15.65 0.00 4.79
3495 4150 1.880819 GACTCCGGCCGTCAACCTTA 61.881 60.000 26.12 0.00 0.00 2.69
3582 4238 4.968626 TCGCACATACATAAGCACAAAAG 58.031 39.130 0.00 0.00 0.00 2.27
3584 4240 4.379394 CGCACATACATAAGCACAAAAGGT 60.379 41.667 0.00 0.00 0.00 3.50
3587 4243 6.423604 GCACATACATAAGCACAAAAGGTTTT 59.576 34.615 0.00 0.00 0.00 2.43
3590 4246 9.691362 ACATACATAAGCACAAAAGGTTTTAAG 57.309 29.630 0.00 0.00 0.00 1.85
3598 4254 9.830975 AAGCACAAAAGGTTTTAAGAATTGTAT 57.169 25.926 0.00 0.00 0.00 2.29
3635 4302 4.952262 TTTCTCATGCTCATTCTTTCCG 57.048 40.909 0.00 0.00 0.00 4.30
3654 4321 3.441222 TCCGATGTTACGCTCTGTTCTTA 59.559 43.478 0.00 0.00 0.00 2.10
3663 4330 2.926200 CGCTCTGTTCTTATCACAGGTG 59.074 50.000 0.40 0.00 41.83 4.00
3671 4338 1.406539 CTTATCACAGGTGGCCATTGC 59.593 52.381 9.72 0.00 0.00 3.56
3673 4340 0.251922 ATCACAGGTGGCCATTGCTT 60.252 50.000 9.72 0.00 37.74 3.91
3675 4342 1.153524 ACAGGTGGCCATTGCTTCA 59.846 52.632 9.72 0.00 37.74 3.02
3676 4343 1.181098 ACAGGTGGCCATTGCTTCAC 61.181 55.000 9.72 0.00 37.74 3.18
3678 4345 0.178953 AGGTGGCCATTGCTTCACTT 60.179 50.000 9.72 0.00 37.74 3.16
3679 4346 0.037975 GGTGGCCATTGCTTCACTTG 60.038 55.000 9.72 0.00 37.74 3.16
3699 4375 7.816995 TCACTTGCTTTTACTTGACATTGTTTT 59.183 29.630 0.00 0.00 0.00 2.43
3702 4378 7.754069 TGCTTTTACTTGACATTGTTTTGAG 57.246 32.000 0.00 0.00 0.00 3.02
3718 4394 5.107298 TGTTTTGAGGCTTTTGTTTGAAACG 60.107 36.000 3.37 0.00 0.00 3.60
3723 4399 2.284798 GGCTTTTGTTTGAAACGCGAAC 60.285 45.455 15.93 6.93 40.65 3.95
3738 4414 1.518515 GCGAACGGTTTATACGCTACC 59.481 52.381 14.87 0.00 44.67 3.18
3739 4415 2.796304 CGAACGGTTTATACGCTACCA 58.204 47.619 0.00 0.00 34.00 3.25
3740 4416 2.785477 CGAACGGTTTATACGCTACCAG 59.215 50.000 0.00 0.00 34.00 4.00
3743 4419 2.951642 ACGGTTTATACGCTACCAGCTA 59.048 45.455 0.00 0.00 39.60 3.32
3746 4422 3.553715 GGTTTATACGCTACCAGCTACCC 60.554 52.174 0.00 0.00 39.60 3.69
3763 4439 1.005450 ACCCATGGTTCGGCATAAAGT 59.995 47.619 11.73 0.00 27.29 2.66
3787 4463 8.571461 GTCGGATGACTAAATATAAGACGTTT 57.429 34.615 0.00 0.00 42.08 3.60
3788 4464 9.028185 GTCGGATGACTAAATATAAGACGTTTT 57.972 33.333 0.00 0.00 42.08 2.43
3789 4465 9.590451 TCGGATGACTAAATATAAGACGTTTTT 57.410 29.630 0.00 0.00 0.00 1.94
3810 4486 2.634639 TCACACTGGGGGTACTACAT 57.365 50.000 0.00 0.00 0.00 2.29
3817 4493 4.040461 CACTGGGGGTACTACATTAGGATG 59.960 50.000 0.00 0.00 39.25 3.51
3834 4510 3.442273 AGGATGAGAACAGTCGAGAGAAC 59.558 47.826 0.00 0.00 45.01 3.01
3836 4512 4.438200 GGATGAGAACAGTCGAGAGAACTC 60.438 50.000 0.00 0.00 45.01 3.01
3841 4517 4.282195 AGAACAGTCGAGAGAACTCCATTT 59.718 41.667 0.00 0.00 45.01 2.32
3843 4519 2.670414 CAGTCGAGAGAACTCCATTTGC 59.330 50.000 0.00 0.00 45.01 3.68
3849 4527 2.909006 AGAGAACTCCATTTGCAGAGGA 59.091 45.455 5.76 4.93 34.27 3.71
3944 4625 3.376935 ATCTCCTCGGTGCGCTTGG 62.377 63.158 9.73 3.62 0.00 3.61
3956 4637 2.190578 GCTTGGCGGGACATAGCT 59.809 61.111 0.00 0.00 0.00 3.32
3957 4638 1.889573 GCTTGGCGGGACATAGCTC 60.890 63.158 0.00 0.00 0.00 4.09
3958 4639 1.592669 CTTGGCGGGACATAGCTCG 60.593 63.158 0.00 0.00 0.00 5.03
3959 4640 3.733344 TTGGCGGGACATAGCTCGC 62.733 63.158 6.67 6.67 46.35 5.03
3961 4642 4.266070 GCGGGACATAGCTCGCGA 62.266 66.667 9.26 9.26 46.53 5.87
3962 4643 2.050895 CGGGACATAGCTCGCGAG 60.051 66.667 31.37 31.37 46.53 5.03
3963 4644 2.543802 CGGGACATAGCTCGCGAGA 61.544 63.158 38.74 20.29 46.53 4.04
3982 4663 4.640690 AGGGACTCCACGGCCTGT 62.641 66.667 0.00 0.00 34.83 4.00
3983 4664 4.083862 GGGACTCCACGGCCTGTC 62.084 72.222 0.00 1.21 0.00 3.51
3984 4665 4.436998 GGACTCCACGGCCTGTCG 62.437 72.222 0.00 0.00 0.00 4.35
3987 4668 4.803426 CTCCACGGCCTGTCGCTC 62.803 72.222 0.00 0.00 37.74 5.03
3995 4676 3.461773 CCTGTCGCTCCCCGTCAT 61.462 66.667 0.00 0.00 34.67 3.06
3996 4677 2.125326 CCTGTCGCTCCCCGTCATA 61.125 63.158 0.00 0.00 34.67 2.15
3997 4678 1.360551 CTGTCGCTCCCCGTCATAG 59.639 63.158 0.00 0.00 34.67 2.23
3998 4679 2.027751 GTCGCTCCCCGTCATAGC 59.972 66.667 0.00 0.00 38.35 2.97
3999 4680 3.224324 TCGCTCCCCGTCATAGCC 61.224 66.667 0.00 0.00 38.35 3.93
4000 4681 4.301027 CGCTCCCCGTCATAGCCC 62.301 72.222 0.00 0.00 32.50 5.19
4001 4682 3.161450 GCTCCCCGTCATAGCCCA 61.161 66.667 0.00 0.00 0.00 5.36
4002 4683 2.520536 GCTCCCCGTCATAGCCCAT 61.521 63.158 0.00 0.00 0.00 4.00
4014 4695 0.907704 TAGCCCATGTCCGACCAAGT 60.908 55.000 0.00 0.00 0.00 3.16
4017 4698 0.036164 CCCATGTCCGACCAAGTGAA 59.964 55.000 0.00 0.00 0.00 3.18
4024 4705 1.374252 CGACCAAGTGAAGGGGACG 60.374 63.158 0.00 0.00 34.02 4.79
4025 4706 1.812686 CGACCAAGTGAAGGGGACGA 61.813 60.000 0.00 0.00 41.23 4.20
4026 4707 0.613777 GACCAAGTGAAGGGGACGAT 59.386 55.000 0.00 0.00 0.00 3.73
4184 4884 2.218066 CCTGTATGTAGGCCGGGTT 58.782 57.895 2.18 0.00 0.00 4.11
4203 4903 5.635280 CGGGTTATGTGTTGATCAGCTATAG 59.365 44.000 11.09 0.00 0.00 1.31
4235 4935 8.194104 ACTGCACAATTTATCTCTCTACACTAG 58.806 37.037 0.00 0.00 0.00 2.57
4236 4936 6.980978 TGCACAATTTATCTCTCTACACTAGC 59.019 38.462 0.00 0.00 0.00 3.42
4247 4952 2.026542 TCTACACTAGCTCAGTTCCGGA 60.027 50.000 0.00 0.00 34.26 5.14
4259 4964 0.387929 GTTCCGGATGGCTGTCGATA 59.612 55.000 4.15 0.00 34.14 2.92
4268 4973 4.890158 ATGGCTGTCGATACCATCAATA 57.110 40.909 10.13 0.00 40.14 1.90
4274 4979 5.276461 TGTCGATACCATCAATAGCAGTT 57.724 39.130 0.00 0.00 0.00 3.16
4275 4980 6.399639 TGTCGATACCATCAATAGCAGTTA 57.600 37.500 0.00 0.00 0.00 2.24
4276 4981 6.811954 TGTCGATACCATCAATAGCAGTTAA 58.188 36.000 0.00 0.00 0.00 2.01
4277 4982 6.923508 TGTCGATACCATCAATAGCAGTTAAG 59.076 38.462 0.00 0.00 0.00 1.85
4278 4983 6.924060 GTCGATACCATCAATAGCAGTTAAGT 59.076 38.462 0.00 0.00 0.00 2.24
4291 4996 5.881447 AGCAGTTAAGTAGTACATGACTCG 58.119 41.667 0.00 0.53 39.81 4.18
4360 5065 1.489649 TGGTTTCTGTTGGTAACCCGA 59.510 47.619 0.00 0.00 40.44 5.14
4362 5067 2.551032 GGTTTCTGTTGGTAACCCGAAG 59.449 50.000 0.00 0.00 36.21 3.79
4384 5089 0.608640 AGTTCCTGTCATCGACCACC 59.391 55.000 0.00 0.00 0.00 4.61
4386 5091 1.884075 TTCCTGTCATCGACCACCGG 61.884 60.000 0.00 0.00 39.14 5.28
4391 5096 1.343789 TGTCATCGACCACCGGTTAAA 59.656 47.619 2.97 0.00 35.25 1.52
4399 5104 1.094785 CCACCGGTTAAATGCAGAGG 58.905 55.000 2.97 0.00 0.00 3.69
4405 5110 1.737793 GGTTAAATGCAGAGGTGGACG 59.262 52.381 0.00 0.00 0.00 4.79
4419 5124 3.755628 GACGGCCTGCGGTGTCTA 61.756 66.667 7.09 0.00 31.12 2.59
4420 5125 3.075005 ACGGCCTGCGGTGTCTAT 61.075 61.111 0.00 0.00 0.00 1.98
4421 5126 2.186903 CGGCCTGCGGTGTCTATT 59.813 61.111 0.00 0.00 0.00 1.73
4423 5128 1.883084 GGCCTGCGGTGTCTATTCG 60.883 63.158 0.00 0.00 0.00 3.34
4424 5129 1.141019 GCCTGCGGTGTCTATTCGA 59.859 57.895 0.00 0.00 0.00 3.71
4425 5130 1.146358 GCCTGCGGTGTCTATTCGAC 61.146 60.000 0.00 0.00 43.14 4.20
4426 5131 0.866061 CCTGCGGTGTCTATTCGACG 60.866 60.000 0.00 0.00 45.87 5.12
4429 5134 0.591741 GCGGTGTCTATTCGACGGAG 60.592 60.000 0.00 0.00 45.87 4.63
4430 5135 0.591741 CGGTGTCTATTCGACGGAGC 60.592 60.000 0.00 0.00 45.87 4.70
4431 5136 0.739561 GGTGTCTATTCGACGGAGCT 59.260 55.000 0.00 0.00 45.87 4.09
4432 5137 1.134560 GGTGTCTATTCGACGGAGCTT 59.865 52.381 0.00 0.00 45.87 3.74
4433 5138 2.452105 GTGTCTATTCGACGGAGCTTC 58.548 52.381 0.00 0.00 45.87 3.86
4434 5139 1.063616 TGTCTATTCGACGGAGCTTCG 59.936 52.381 14.32 14.32 45.87 3.79
4435 5140 0.029035 TCTATTCGACGGAGCTTCGC 59.971 55.000 16.11 6.54 36.40 4.70
4436 5141 0.935366 CTATTCGACGGAGCTTCGCC 60.935 60.000 16.11 1.09 36.40 5.54
4443 5152 4.201951 GGAGCTTCGCCGATGAAA 57.798 55.556 3.96 0.00 0.00 2.69
4448 5157 1.067142 AGCTTCGCCGATGAAAGTGTA 60.067 47.619 3.96 0.00 0.00 2.90
4472 5181 1.000955 GTGGAATGACTCGGTGAGTGT 59.999 52.381 3.85 0.00 43.53 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
124 125 4.094887 CCCAATGACAGTTAAGATTCGTGG 59.905 45.833 0.00 0.00 0.00 4.94
128 129 5.293569 CGTACCCCAATGACAGTTAAGATTC 59.706 44.000 0.00 0.00 0.00 2.52
142 143 0.329931 TCCATTGCACGTACCCCAAT 59.670 50.000 0.00 0.00 0.00 3.16
161 162 7.351952 AGTTTGGTTTAAGTTCCTAAGTTCCT 58.648 34.615 0.00 0.00 0.00 3.36
166 167 6.695713 GTGCAAGTTTGGTTTAAGTTCCTAAG 59.304 38.462 0.00 0.00 0.00 2.18
184 185 6.068670 ACCTAAAACAAGATAAGGTGCAAGT 58.931 36.000 0.00 0.00 39.10 3.16
287 310 5.248248 TGGAGTGACTGATGAAACTGGATTA 59.752 40.000 0.00 0.00 0.00 1.75
358 382 5.121811 CCTTAAGGACAATGTGGAGATGAG 58.878 45.833 17.21 0.00 37.39 2.90
389 416 4.273724 TCTCCTTATCATCTCGTCAGTTCG 59.726 45.833 0.00 0.00 0.00 3.95
405 432 7.658982 CAGCTAGCATTTGTTATGATCTCCTTA 59.341 37.037 18.83 0.00 0.00 2.69
415 442 4.096984 GCCTTGACAGCTAGCATTTGTTAT 59.903 41.667 18.83 0.00 0.00 1.89
416 443 3.440173 GCCTTGACAGCTAGCATTTGTTA 59.560 43.478 18.83 6.73 0.00 2.41
476 503 1.144936 GAATCTGCCGTGCCTAGCT 59.855 57.895 0.00 0.00 0.00 3.32
495 528 1.679153 TGATGCGAAGTATGCGGACTA 59.321 47.619 0.00 0.00 43.86 2.59
500 533 3.431233 AGAATCATGATGCGAAGTATGCG 59.569 43.478 9.46 0.00 43.07 4.73
529 566 2.696707 ACAGTTGGTTCACTCGGAGTAA 59.303 45.455 10.87 0.00 0.00 2.24
564 601 2.003301 GGAGCCAGAACGAACTTGATC 58.997 52.381 0.00 0.00 0.00 2.92
565 602 1.625818 AGGAGCCAGAACGAACTTGAT 59.374 47.619 0.00 0.00 0.00 2.57
566 603 1.048601 AGGAGCCAGAACGAACTTGA 58.951 50.000 0.00 0.00 0.00 3.02
567 604 1.151668 CAGGAGCCAGAACGAACTTG 58.848 55.000 0.00 0.00 0.00 3.16
569 606 1.066573 CATCAGGAGCCAGAACGAACT 60.067 52.381 0.00 0.00 0.00 3.01
570 607 1.338200 ACATCAGGAGCCAGAACGAAC 60.338 52.381 0.00 0.00 0.00 3.95
571 608 0.976641 ACATCAGGAGCCAGAACGAA 59.023 50.000 0.00 0.00 0.00 3.85
572 609 0.976641 AACATCAGGAGCCAGAACGA 59.023 50.000 0.00 0.00 0.00 3.85
573 610 1.363744 GAACATCAGGAGCCAGAACG 58.636 55.000 0.00 0.00 0.00 3.95
592 629 1.068541 TCACTCACACGGATGTTCTCG 60.069 52.381 0.00 0.00 36.72 4.04
598 635 0.037882 ACTGCTCACTCACACGGATG 60.038 55.000 0.00 0.00 0.00 3.51
683 722 3.829948 CTTTTTGCTGGTGATGCAGTAG 58.170 45.455 0.00 0.00 41.71 2.57
713 752 5.034152 CGAGAAAAGAGAGTTGCTAGCTAG 58.966 45.833 16.84 16.84 0.00 3.42
714 753 4.459685 ACGAGAAAAGAGAGTTGCTAGCTA 59.540 41.667 17.23 5.31 0.00 3.32
715 754 3.257127 ACGAGAAAAGAGAGTTGCTAGCT 59.743 43.478 17.23 0.00 0.00 3.32
716 755 3.366422 CACGAGAAAAGAGAGTTGCTAGC 59.634 47.826 8.10 8.10 0.00 3.42
717 756 4.551388 ACACGAGAAAAGAGAGTTGCTAG 58.449 43.478 0.00 0.00 0.00 3.42
718 757 4.037565 TGACACGAGAAAAGAGAGTTGCTA 59.962 41.667 0.00 0.00 0.00 3.49
719 758 3.181475 TGACACGAGAAAAGAGAGTTGCT 60.181 43.478 0.00 0.00 0.00 3.91
720 759 3.123804 TGACACGAGAAAAGAGAGTTGC 58.876 45.455 0.00 0.00 0.00 4.17
721 760 5.226396 AGATGACACGAGAAAAGAGAGTTG 58.774 41.667 0.00 0.00 0.00 3.16
777 816 5.255687 TGATGATCAGCCAAGCTTTTTCTA 58.744 37.500 8.78 0.00 36.40 2.10
778 817 4.084287 TGATGATCAGCCAAGCTTTTTCT 58.916 39.130 8.78 0.00 36.40 2.52
844 886 4.579869 AGGTGAAGATACGATGTTTTGCT 58.420 39.130 0.00 0.00 0.00 3.91
881 923 0.397254 GGAGGCCACTAGCTAGGTGA 60.397 60.000 24.35 0.00 43.05 4.02
937 982 1.152881 AAATGGGAGGAGCGATGCC 60.153 57.895 0.00 0.00 0.00 4.40
970 1019 2.749076 CAACCCTTTGATCGATCTGCAA 59.251 45.455 25.02 14.18 34.24 4.08
995 1044 2.679996 GGTGTGCCCCCATTGTCC 60.680 66.667 0.00 0.00 0.00 4.02
1119 1168 9.971922 CCATAAACACAAAAGAAAAGAGAGATT 57.028 29.630 0.00 0.00 0.00 2.40
1139 1188 4.713814 TGAAATGCAGCATAACCCCATAAA 59.286 37.500 8.75 0.00 0.00 1.40
1159 1209 3.125829 GCTTGCTTGAGATCGATGTTGAA 59.874 43.478 0.54 0.00 0.00 2.69
1190 1240 4.449870 TTTCGTGCATTTGAAAATGTGC 57.550 36.364 15.27 6.13 45.77 4.57
1230 1280 2.620251 TGGTCTCAACTGGACAACTG 57.380 50.000 0.00 0.00 35.61 3.16
1260 1310 3.370061 GGTACGTATCTGCCAGAACAAAC 59.630 47.826 0.00 0.48 0.00 2.93
1278 1330 1.449601 CCCACACATCAGGCGGTAC 60.450 63.158 0.00 0.00 0.00 3.34
1296 1609 6.908825 TCTGCATTGTCACCTGTAAATTAAC 58.091 36.000 0.00 0.00 0.00 2.01
1304 1617 1.143684 ACCTTCTGCATTGTCACCTGT 59.856 47.619 0.00 0.00 0.00 4.00
1382 1695 2.095212 GCCTTCCCTTGTGACGATTTTC 60.095 50.000 0.00 0.00 0.00 2.29
1410 1723 3.811083 TGTTAACCACCTTGACGACAAT 58.189 40.909 2.48 0.00 35.37 2.71
1412 1725 2.983907 TGTTAACCACCTTGACGACA 57.016 45.000 2.48 0.00 0.00 4.35
1507 1823 4.201657 TGTAGCTAGCAGTACGGTTATCA 58.798 43.478 18.83 0.00 0.00 2.15
1572 1888 3.877508 GACAAGTATTTTCGGATGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
1574 1890 5.817296 TGATGACAAGTATTTTCGGATGGAG 59.183 40.000 0.00 0.00 0.00 3.86
1575 1891 5.739959 TGATGACAAGTATTTTCGGATGGA 58.260 37.500 0.00 0.00 0.00 3.41
1576 1892 6.435430 TTGATGACAAGTATTTTCGGATGG 57.565 37.500 0.00 0.00 0.00 3.51
1577 1893 7.530010 AGTTTGATGACAAGTATTTTCGGATG 58.470 34.615 0.00 0.00 37.32 3.51
1578 1894 7.687941 AGTTTGATGACAAGTATTTTCGGAT 57.312 32.000 0.00 0.00 37.32 4.18
1579 1895 8.092068 TCTAGTTTGATGACAAGTATTTTCGGA 58.908 33.333 0.00 0.00 37.32 4.55
1580 1896 8.251750 TCTAGTTTGATGACAAGTATTTTCGG 57.748 34.615 0.00 0.00 37.32 4.30
1663 1979 9.632807 CCTCCGTTTGAAAATATTTGTTATCAA 57.367 29.630 0.39 5.31 0.00 2.57
1664 1980 8.247562 CCCTCCGTTTGAAAATATTTGTTATCA 58.752 33.333 0.39 0.00 0.00 2.15
1665 1981 8.463607 TCCCTCCGTTTGAAAATATTTGTTATC 58.536 33.333 0.39 0.00 0.00 1.75
1666 1982 8.356000 TCCCTCCGTTTGAAAATATTTGTTAT 57.644 30.769 0.39 0.00 0.00 1.89
1667 1983 7.449086 ACTCCCTCCGTTTGAAAATATTTGTTA 59.551 33.333 0.39 0.00 0.00 2.41
1668 1984 6.266786 ACTCCCTCCGTTTGAAAATATTTGTT 59.733 34.615 0.39 0.00 0.00 2.83
1669 1985 5.773176 ACTCCCTCCGTTTGAAAATATTTGT 59.227 36.000 0.39 0.00 0.00 2.83
1670 1986 6.267496 ACTCCCTCCGTTTGAAAATATTTG 57.733 37.500 0.39 0.00 0.00 2.32
1671 1987 6.095021 GCTACTCCCTCCGTTTGAAAATATTT 59.905 38.462 0.00 0.00 0.00 1.40
1672 1988 5.589050 GCTACTCCCTCCGTTTGAAAATATT 59.411 40.000 0.00 0.00 0.00 1.28
1673 1989 5.123936 GCTACTCCCTCCGTTTGAAAATAT 58.876 41.667 0.00 0.00 0.00 1.28
1674 1990 4.020039 TGCTACTCCCTCCGTTTGAAAATA 60.020 41.667 0.00 0.00 0.00 1.40
1675 1991 3.244770 TGCTACTCCCTCCGTTTGAAAAT 60.245 43.478 0.00 0.00 0.00 1.82
1676 1992 2.105134 TGCTACTCCCTCCGTTTGAAAA 59.895 45.455 0.00 0.00 0.00 2.29
1677 1993 1.695242 TGCTACTCCCTCCGTTTGAAA 59.305 47.619 0.00 0.00 0.00 2.69
1678 1994 1.344065 TGCTACTCCCTCCGTTTGAA 58.656 50.000 0.00 0.00 0.00 2.69
1679 1995 1.001633 GTTGCTACTCCCTCCGTTTGA 59.998 52.381 0.00 0.00 0.00 2.69
1680 1996 1.002087 AGTTGCTACTCCCTCCGTTTG 59.998 52.381 0.00 0.00 0.00 2.93
1681 1997 1.002087 CAGTTGCTACTCCCTCCGTTT 59.998 52.381 0.00 0.00 30.26 3.60
1682 1998 0.608640 CAGTTGCTACTCCCTCCGTT 59.391 55.000 0.00 0.00 30.26 4.44
1683 1999 1.889530 GCAGTTGCTACTCCCTCCGT 61.890 60.000 0.00 0.00 38.21 4.69
1684 2000 1.153549 GCAGTTGCTACTCCCTCCG 60.154 63.158 0.00 0.00 38.21 4.63
1685 2001 0.107945 CTGCAGTTGCTACTCCCTCC 60.108 60.000 5.25 0.00 42.66 4.30
1686 2002 0.742635 GCTGCAGTTGCTACTCCCTC 60.743 60.000 16.64 0.00 42.66 4.30
1687 2003 1.298014 GCTGCAGTTGCTACTCCCT 59.702 57.895 16.64 0.00 42.66 4.20
1688 2004 1.746991 GGCTGCAGTTGCTACTCCC 60.747 63.158 16.64 0.04 42.66 4.30
1689 2005 1.003355 TGGCTGCAGTTGCTACTCC 60.003 57.895 16.64 5.67 42.66 3.85
1690 2006 0.321122 AGTGGCTGCAGTTGCTACTC 60.321 55.000 16.64 0.00 46.66 2.59
1691 2007 1.757306 AGTGGCTGCAGTTGCTACT 59.243 52.632 16.64 12.51 45.18 2.57
1692 2008 0.954452 AAAGTGGCTGCAGTTGCTAC 59.046 50.000 16.64 10.22 42.66 3.58
1715 2031 6.590292 CAGAAAGATAAAACTGAGCCGTCTTA 59.410 38.462 0.00 0.00 32.90 2.10
1722 2038 4.928661 TCGCAGAAAGATAAAACTGAGC 57.071 40.909 0.00 0.00 32.11 4.26
1730 2046 8.234546 GTGGAGTAATTTTTCGCAGAAAGATAA 58.765 33.333 7.22 0.69 45.90 1.75
1764 2083 7.554211 CCAGTTACCCCTTAGTAAAAGAGTAG 58.446 42.308 0.00 0.00 34.13 2.57
1778 2103 0.035439 CATCAACGCCAGTTACCCCT 60.035 55.000 0.00 0.00 38.79 4.79
1779 2104 0.322187 ACATCAACGCCAGTTACCCC 60.322 55.000 0.00 0.00 38.79 4.95
1852 2435 1.521457 CGGGCACTGCGTGATGTAT 60.521 57.895 11.94 0.00 35.23 2.29
1871 2454 4.459089 GCTCTGCCCCGTCTGGAC 62.459 72.222 0.00 0.00 37.49 4.02
1982 2565 1.522569 CGGACTTGGGGAGGATGAC 59.477 63.158 0.00 0.00 0.00 3.06
2175 2758 0.948678 TGTTACGAACCAGCCTTTGC 59.051 50.000 0.00 0.00 37.95 3.68
2182 2765 3.619483 TCTTGTTGTGTGTTACGAACCAG 59.381 43.478 0.00 0.00 0.00 4.00
2188 2771 1.263217 GGCCTCTTGTTGTGTGTTACG 59.737 52.381 0.00 0.00 0.00 3.18
2200 2783 2.154462 AGTGTTGAATTCGGCCTCTTG 58.846 47.619 0.00 0.00 0.00 3.02
2203 2786 1.808411 TGAGTGTTGAATTCGGCCTC 58.192 50.000 0.00 4.44 0.00 4.70
2241 2824 4.070009 GACATGAAAACCGTAACCCTTCT 58.930 43.478 0.00 0.00 0.00 2.85
2242 2825 3.120442 CGACATGAAAACCGTAACCCTTC 60.120 47.826 0.00 0.00 0.00 3.46
2243 2826 2.809696 CGACATGAAAACCGTAACCCTT 59.190 45.455 0.00 0.00 0.00 3.95
2245 2828 2.415776 TCGACATGAAAACCGTAACCC 58.584 47.619 0.00 0.00 0.00 4.11
2250 2833 7.483691 GCTAAAATAAATCGACATGAAAACCGT 59.516 33.333 0.00 0.00 0.00 4.83
2254 2837 9.554724 GTGAGCTAAAATAAATCGACATGAAAA 57.445 29.630 0.00 0.00 0.00 2.29
2257 2840 6.821160 TGGTGAGCTAAAATAAATCGACATGA 59.179 34.615 0.00 0.00 0.00 3.07
2269 2852 4.046286 TCAACCCATGGTGAGCTAAAAT 57.954 40.909 11.73 0.00 35.34 1.82
2272 2855 2.107378 TGTTCAACCCATGGTGAGCTAA 59.893 45.455 16.69 0.00 35.34 3.09
2280 2863 2.299582 TCTGCAAATGTTCAACCCATGG 59.700 45.455 4.14 4.14 0.00 3.66
2286 2869 3.065019 ACGTGTCTGCAAATGTTCAAC 57.935 42.857 0.00 0.00 0.00 3.18
2320 2903 1.073199 GTACCACTTGCCTGGCTGT 59.927 57.895 21.03 15.41 34.20 4.40
2578 3166 2.586635 GCGACGGTGGTGTTGTCA 60.587 61.111 0.00 0.00 32.91 3.58
3004 3635 1.214589 CACCTTCGTCCCGTTCGAT 59.785 57.895 0.00 0.00 37.18 3.59
3037 3668 1.287815 CACCTCCACGCTCGTGTTA 59.712 57.895 19.25 7.83 44.02 2.41
3064 3695 3.023949 GCCCTGGATGCTCGTGTCT 62.024 63.158 0.00 0.00 0.00 3.41
3249 3880 2.185387 ACTTACCAGGGTTATCAGCGT 58.815 47.619 0.00 0.00 0.00 5.07
3337 3992 2.193087 GAACCATACACCTGCCCCGT 62.193 60.000 0.00 0.00 0.00 5.28
3488 4143 6.686630 TGAATAGCAATGTTGGTTAAGGTTG 58.313 36.000 2.53 0.00 39.88 3.77
3495 4150 7.603784 GGAAAGAAATGAATAGCAATGTTGGTT 59.396 33.333 2.53 0.00 39.88 3.67
3560 4216 4.142708 CCTTTTGTGCTTATGTATGTGCGA 60.143 41.667 0.00 0.00 0.00 5.10
3599 4255 9.270640 GAGCATGAGAAAATACATGTAAGATCT 57.729 33.333 10.14 12.62 43.67 2.75
3600 4256 9.049523 TGAGCATGAGAAAATACATGTAAGATC 57.950 33.333 10.14 8.16 43.67 2.75
3606 4273 7.876936 AGAATGAGCATGAGAAAATACATGT 57.123 32.000 2.69 2.69 43.67 3.21
3607 4274 9.234384 GAAAGAATGAGCATGAGAAAATACATG 57.766 33.333 0.00 0.00 44.32 3.21
3618 4285 3.877559 ACATCGGAAAGAATGAGCATGA 58.122 40.909 0.00 0.00 0.00 3.07
3622 4289 3.544244 GCGTAACATCGGAAAGAATGAGC 60.544 47.826 0.00 0.00 0.00 4.26
3635 4302 5.805486 TGTGATAAGAACAGAGCGTAACATC 59.195 40.000 0.00 0.00 0.00 3.06
3654 4321 0.251922 AAGCAATGGCCACCTGTGAT 60.252 50.000 8.16 0.00 42.56 3.06
3663 4330 0.319405 AAGCAAGTGAAGCAATGGCC 59.681 50.000 0.00 0.00 42.56 5.36
3671 4338 6.974622 ACAATGTCAAGTAAAAGCAAGTGAAG 59.025 34.615 0.00 0.00 0.00 3.02
3673 4340 6.449635 ACAATGTCAAGTAAAAGCAAGTGA 57.550 33.333 0.00 0.00 0.00 3.41
3675 4342 7.816995 TCAAAACAATGTCAAGTAAAAGCAAGT 59.183 29.630 0.00 0.00 0.00 3.16
3676 4343 8.183830 TCAAAACAATGTCAAGTAAAAGCAAG 57.816 30.769 0.00 0.00 0.00 4.01
3678 4345 6.756074 CCTCAAAACAATGTCAAGTAAAAGCA 59.244 34.615 0.00 0.00 0.00 3.91
3679 4346 6.292328 GCCTCAAAACAATGTCAAGTAAAAGC 60.292 38.462 0.00 0.00 0.00 3.51
3699 4375 2.535331 GCGTTTCAAACAAAAGCCTCA 58.465 42.857 0.22 0.00 0.00 3.86
3702 4378 1.551145 TCGCGTTTCAAACAAAAGCC 58.449 45.000 5.77 0.00 32.35 4.35
3718 4394 1.518515 GGTAGCGTATAAACCGTTCGC 59.481 52.381 6.90 6.90 45.82 4.70
3738 4414 1.819632 GCCGAACCATGGGTAGCTG 60.820 63.158 18.09 0.00 33.12 4.24
3739 4415 1.635817 ATGCCGAACCATGGGTAGCT 61.636 55.000 21.57 7.79 33.12 3.32
3740 4416 0.107831 TATGCCGAACCATGGGTAGC 59.892 55.000 18.09 16.83 33.12 3.58
3743 4419 1.005450 ACTTTATGCCGAACCATGGGT 59.995 47.619 18.09 10.33 37.65 4.51
3746 4422 1.330521 CCGACTTTATGCCGAACCATG 59.669 52.381 0.00 0.00 0.00 3.66
3763 4439 9.590451 AAAAACGTCTTATATTTAGTCATCCGA 57.410 29.630 0.00 0.00 0.00 4.55
3787 4463 3.458857 TGTAGTACCCCCAGTGTGAAAAA 59.541 43.478 0.00 0.00 0.00 1.94
3788 4464 3.047115 TGTAGTACCCCCAGTGTGAAAA 58.953 45.455 0.00 0.00 0.00 2.29
3789 4465 2.692024 TGTAGTACCCCCAGTGTGAAA 58.308 47.619 0.00 0.00 0.00 2.69
3790 4466 2.402182 TGTAGTACCCCCAGTGTGAA 57.598 50.000 0.00 0.00 0.00 3.18
3791 4467 2.634639 ATGTAGTACCCCCAGTGTGA 57.365 50.000 0.00 0.00 0.00 3.58
3792 4468 3.134081 CCTAATGTAGTACCCCCAGTGTG 59.866 52.174 0.00 0.00 0.00 3.82
3793 4469 3.013188 TCCTAATGTAGTACCCCCAGTGT 59.987 47.826 0.00 0.00 0.00 3.55
3794 4470 3.649843 TCCTAATGTAGTACCCCCAGTG 58.350 50.000 0.00 0.00 0.00 3.66
3795 4471 4.078219 TCATCCTAATGTAGTACCCCCAGT 60.078 45.833 0.00 0.00 34.32 4.00
3796 4472 4.489737 TCATCCTAATGTAGTACCCCCAG 58.510 47.826 0.00 0.00 34.32 4.45
3797 4473 4.171243 TCTCATCCTAATGTAGTACCCCCA 59.829 45.833 0.00 0.00 34.32 4.96
3798 4474 4.748701 TCTCATCCTAATGTAGTACCCCC 58.251 47.826 0.00 0.00 34.32 5.40
3799 4475 5.601313 TGTTCTCATCCTAATGTAGTACCCC 59.399 44.000 0.00 0.00 34.32 4.95
3800 4476 6.324254 ACTGTTCTCATCCTAATGTAGTACCC 59.676 42.308 0.00 0.00 34.32 3.69
3801 4477 7.349412 ACTGTTCTCATCCTAATGTAGTACC 57.651 40.000 0.00 0.00 34.32 3.34
3802 4478 7.012138 TCGACTGTTCTCATCCTAATGTAGTAC 59.988 40.741 0.00 0.00 34.32 2.73
3803 4479 7.052248 TCGACTGTTCTCATCCTAATGTAGTA 58.948 38.462 0.00 0.00 34.32 1.82
3804 4480 5.886474 TCGACTGTTCTCATCCTAATGTAGT 59.114 40.000 0.00 0.00 34.32 2.73
3810 4486 4.844884 TCTCTCGACTGTTCTCATCCTAA 58.155 43.478 0.00 0.00 0.00 2.69
3817 4493 2.814919 TGGAGTTCTCTCGACTGTTCTC 59.185 50.000 0.00 0.00 41.26 2.87
3834 4510 2.089980 CTGGTTCCTCTGCAAATGGAG 58.910 52.381 0.00 0.00 34.56 3.86
3836 4512 2.089980 CTCTGGTTCCTCTGCAAATGG 58.910 52.381 0.00 0.00 0.00 3.16
3841 4517 1.123861 ACTGCTCTGGTTCCTCTGCA 61.124 55.000 0.00 0.00 0.00 4.41
3843 4519 3.902881 AATACTGCTCTGGTTCCTCTG 57.097 47.619 0.00 0.00 0.00 3.35
3849 4527 6.490381 TGATATCGACTAATACTGCTCTGGTT 59.510 38.462 0.00 0.00 0.00 3.67
3900 4581 2.747177 ACAAGATCCAGTATGTCCCGA 58.253 47.619 0.00 0.00 0.00 5.14
3944 4625 4.266070 TCGCGAGCTATGTCCCGC 62.266 66.667 3.71 5.24 43.68 6.13
3946 4627 1.167155 TCTCTCGCGAGCTATGTCCC 61.167 60.000 30.97 0.00 37.19 4.46
3948 4629 0.237235 CCTCTCTCGCGAGCTATGTC 59.763 60.000 30.97 0.00 37.19 3.06
3949 4630 1.169661 CCCTCTCTCGCGAGCTATGT 61.170 60.000 30.97 0.00 37.19 2.29
3950 4631 0.886938 TCCCTCTCTCGCGAGCTATG 60.887 60.000 30.97 19.10 37.19 2.23
3952 4633 1.524165 GTCCCTCTCTCGCGAGCTA 60.524 63.158 30.97 19.20 37.19 3.32
3953 4634 2.826738 GTCCCTCTCTCGCGAGCT 60.827 66.667 30.97 0.00 37.19 4.09
3954 4635 2.826738 AGTCCCTCTCTCGCGAGC 60.827 66.667 30.97 14.98 37.19 5.03
3956 4637 2.124653 GGAGTCCCTCTCTCGCGA 60.125 66.667 9.26 9.26 42.40 5.87
3957 4638 2.438614 TGGAGTCCCTCTCTCGCG 60.439 66.667 6.74 0.00 42.40 5.87
3958 4639 2.766400 CGTGGAGTCCCTCTCTCGC 61.766 68.421 6.74 0.00 42.40 5.03
3959 4640 2.115911 CCGTGGAGTCCCTCTCTCG 61.116 68.421 6.74 2.29 42.40 4.04
3960 4641 2.419739 GCCGTGGAGTCCCTCTCTC 61.420 68.421 6.74 0.00 42.40 3.20
3961 4642 2.363147 GCCGTGGAGTCCCTCTCT 60.363 66.667 6.74 0.00 42.40 3.10
3962 4643 3.462678 GGCCGTGGAGTCCCTCTC 61.463 72.222 6.74 0.00 42.07 3.20
3963 4644 3.999285 AGGCCGTGGAGTCCCTCT 61.999 66.667 6.74 0.00 0.00 3.69
3964 4645 3.775654 CAGGCCGTGGAGTCCCTC 61.776 72.222 6.74 0.00 0.00 4.30
3965 4646 4.640690 ACAGGCCGTGGAGTCCCT 62.641 66.667 6.74 0.00 0.00 4.20
3966 4647 4.083862 GACAGGCCGTGGAGTCCC 62.084 72.222 6.74 0.00 0.00 4.46
3970 4651 4.803426 GAGCGACAGGCCGTGGAG 62.803 72.222 12.44 4.92 45.17 3.86
3978 4659 2.076622 CTATGACGGGGAGCGACAGG 62.077 65.000 0.00 0.00 0.00 4.00
3979 4660 1.360551 CTATGACGGGGAGCGACAG 59.639 63.158 0.00 0.00 0.00 3.51
3980 4661 2.782222 GCTATGACGGGGAGCGACA 61.782 63.158 0.00 0.00 0.00 4.35
3981 4662 2.027751 GCTATGACGGGGAGCGAC 59.972 66.667 0.00 0.00 0.00 5.19
3982 4663 3.224324 GGCTATGACGGGGAGCGA 61.224 66.667 0.00 0.00 37.07 4.93
3983 4664 4.301027 GGGCTATGACGGGGAGCG 62.301 72.222 0.00 0.00 37.07 5.03
3984 4665 2.520536 ATGGGCTATGACGGGGAGC 61.521 63.158 0.00 0.00 35.39 4.70
3985 4666 1.372683 CATGGGCTATGACGGGGAG 59.627 63.158 4.63 0.00 39.21 4.30
3986 4667 1.383943 ACATGGGCTATGACGGGGA 60.384 57.895 18.36 0.00 39.21 4.81
3987 4668 1.071471 GACATGGGCTATGACGGGG 59.929 63.158 18.36 0.00 39.21 5.73
3988 4669 1.071471 GGACATGGGCTATGACGGG 59.929 63.158 18.36 0.00 39.21 5.28
3989 4670 1.300931 CGGACATGGGCTATGACGG 60.301 63.158 18.36 11.72 39.21 4.79
3990 4671 0.597637 GTCGGACATGGGCTATGACG 60.598 60.000 18.36 19.25 39.21 4.35
3991 4672 0.249911 GGTCGGACATGGGCTATGAC 60.250 60.000 18.36 11.31 39.21 3.06
3992 4673 0.689412 TGGTCGGACATGGGCTATGA 60.689 55.000 18.36 0.00 39.21 2.15
3993 4674 0.180171 TTGGTCGGACATGGGCTATG 59.820 55.000 9.52 9.52 42.68 2.23
3994 4675 0.469917 CTTGGTCGGACATGGGCTAT 59.530 55.000 10.76 0.00 0.00 2.97
3995 4676 0.907704 ACTTGGTCGGACATGGGCTA 60.908 55.000 10.76 0.00 0.00 3.93
3996 4677 2.224159 ACTTGGTCGGACATGGGCT 61.224 57.895 10.76 0.00 0.00 5.19
3997 4678 2.040544 CACTTGGTCGGACATGGGC 61.041 63.158 10.76 0.00 0.00 5.36
3998 4679 0.036164 TTCACTTGGTCGGACATGGG 59.964 55.000 10.76 0.53 0.00 4.00
3999 4680 1.442769 CTTCACTTGGTCGGACATGG 58.557 55.000 10.76 1.55 0.00 3.66
4000 4681 1.442769 CCTTCACTTGGTCGGACATG 58.557 55.000 10.76 2.86 0.00 3.21
4001 4682 0.324943 CCCTTCACTTGGTCGGACAT 59.675 55.000 10.76 0.00 0.00 3.06
4002 4683 1.752198 CCCTTCACTTGGTCGGACA 59.248 57.895 10.76 0.00 0.00 4.02
4014 4695 1.065491 CATGTTGGATCGTCCCCTTCA 60.065 52.381 2.23 0.00 35.03 3.02
4017 4698 0.833287 CTCATGTTGGATCGTCCCCT 59.167 55.000 0.00 0.00 35.03 4.79
4024 4705 3.612860 GTGACGTGTACTCATGTTGGATC 59.387 47.826 0.00 0.00 42.94 3.36
4025 4706 3.585862 GTGACGTGTACTCATGTTGGAT 58.414 45.455 0.00 0.00 42.94 3.41
4026 4707 2.606065 CGTGACGTGTACTCATGTTGGA 60.606 50.000 0.00 0.00 42.94 3.53
4203 4903 6.705381 AGAGAGATAAATTGTGCAGTGATAGC 59.295 38.462 0.00 0.00 0.00 2.97
4216 4916 8.760980 ACTGAGCTAGTGTAGAGAGATAAATT 57.239 34.615 0.00 0.00 38.49 1.82
4235 4935 1.817099 CAGCCATCCGGAACTGAGC 60.817 63.158 21.75 15.33 31.67 4.26
4236 4936 0.460987 GACAGCCATCCGGAACTGAG 60.461 60.000 28.99 14.89 34.25 3.35
4247 4952 3.777106 ATTGATGGTATCGACAGCCAT 57.223 42.857 14.64 14.64 44.82 4.40
4259 4964 8.074613 TGTACTACTTAACTGCTATTGATGGT 57.925 34.615 0.00 0.00 0.00 3.55
4265 4970 8.129840 CGAGTCATGTACTACTTAACTGCTATT 58.870 37.037 0.00 0.00 39.07 1.73
4268 4973 5.415077 ACGAGTCATGTACTACTTAACTGCT 59.585 40.000 0.00 0.00 39.07 4.24
4274 4979 5.353400 CCTGTCACGAGTCATGTACTACTTA 59.647 44.000 0.00 0.00 39.07 2.24
4275 4980 4.156190 CCTGTCACGAGTCATGTACTACTT 59.844 45.833 0.00 0.00 39.07 2.24
4276 4981 3.690139 CCTGTCACGAGTCATGTACTACT 59.310 47.826 0.00 0.00 39.07 2.57
4277 4982 3.731264 GCCTGTCACGAGTCATGTACTAC 60.731 52.174 0.00 0.00 39.07 2.73
4278 4983 2.422479 GCCTGTCACGAGTCATGTACTA 59.578 50.000 0.00 0.00 39.07 1.82
4360 5065 2.028930 GGTCGATGACAGGAACTCACTT 60.029 50.000 0.00 0.00 34.60 3.16
4362 5067 1.272490 TGGTCGATGACAGGAACTCAC 59.728 52.381 0.00 0.00 34.60 3.51
4384 5089 1.737793 GTCCACCTCTGCATTTAACCG 59.262 52.381 0.00 0.00 0.00 4.44
4386 5091 1.737793 CCGTCCACCTCTGCATTTAAC 59.262 52.381 0.00 0.00 0.00 2.01
4391 5096 4.101448 GGCCGTCCACCTCTGCAT 62.101 66.667 0.00 0.00 0.00 3.96
4430 5135 1.927174 CCTACACTTTCATCGGCGAAG 59.073 52.381 15.93 10.47 0.00 3.79
4431 5136 1.404986 CCCTACACTTTCATCGGCGAA 60.405 52.381 15.93 0.00 0.00 4.70
4432 5137 0.174845 CCCTACACTTTCATCGGCGA 59.825 55.000 13.87 13.87 0.00 5.54
4433 5138 0.810031 CCCCTACACTTTCATCGGCG 60.810 60.000 0.00 0.00 0.00 6.46
4434 5139 0.252197 ACCCCTACACTTTCATCGGC 59.748 55.000 0.00 0.00 0.00 5.54
4435 5140 1.406887 CCACCCCTACACTTTCATCGG 60.407 57.143 0.00 0.00 0.00 4.18
4436 5141 1.553248 TCCACCCCTACACTTTCATCG 59.447 52.381 0.00 0.00 0.00 3.84
4439 5148 2.983192 TCATTCCACCCCTACACTTTCA 59.017 45.455 0.00 0.00 0.00 2.69
4443 5152 2.188817 GAGTCATTCCACCCCTACACT 58.811 52.381 0.00 0.00 0.00 3.55
4448 5157 1.229529 ACCGAGTCATTCCACCCCT 60.230 57.895 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.