Multiple sequence alignment - TraesCS3D01G515700

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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 TraesCS3D01G515700 chr3D 100.000 4204 0 0 1 4204 599162848 599167051 0.000000e+00 7764.0
1 TraesCS3D01G515700 chr3D 87.580 314 39 0 1920 2233 599322742 599322429 8.590000e-97 364.0
2 TraesCS3D01G515700 chr3A 95.756 919 32 3 2303 3221 729184415 729185326 0.000000e+00 1474.0
3 TraesCS3D01G515700 chr3A 95.405 914 35 3 2313 3226 729576915 729576009 0.000000e+00 1448.0
4 TraesCS3D01G515700 chr3A 95.539 807 29 3 2303 3109 729353444 729354243 0.000000e+00 1284.0
5 TraesCS3D01G515700 chr3A 86.937 888 75 20 1407 2268 729182987 729183859 0.000000e+00 959.0
6 TraesCS3D01G515700 chr3A 95.455 572 15 2 3314 3876 729359052 729359621 0.000000e+00 902.0
7 TraesCS3D01G515700 chr3A 91.956 547 29 5 843 1375 729182365 729182910 0.000000e+00 752.0
8 TraesCS3D01G515700 chr3A 93.333 510 30 2 1763 2268 729577983 729577474 0.000000e+00 750.0
9 TraesCS3D01G515700 chr3A 80.630 857 97 23 1 827 729181500 729182317 2.160000e-167 599.0
10 TraesCS3D01G515700 chr3A 95.115 348 14 1 3860 4204 729359638 729359985 2.860000e-151 545.0
11 TraesCS3D01G515700 chr3A 92.089 316 19 4 1060 1375 729578710 729578401 1.390000e-119 440.0
12 TraesCS3D01G515700 chr3A 96.190 210 8 0 3107 3316 729356330 729356539 1.120000e-90 344.0
13 TraesCS3D01G515700 chr3A 90.135 223 17 2 1410 1627 729578321 729578099 6.880000e-73 285.0
14 TraesCS3D01G515700 chr3A 90.909 187 16 1 3942 4128 686990466 686990281 2.510000e-62 250.0
15 TraesCS3D01G515700 chr3A 100.000 28 0 0 1705 1732 729183254 729183281 8.000000e-03 52.8
16 TraesCS3D01G515700 chr3B 95.548 921 34 3 2303 3223 807080749 807081662 0.000000e+00 1467.0
17 TraesCS3D01G515700 chr3B 88.466 893 56 25 1410 2268 807079301 807080180 0.000000e+00 1035.0
18 TraesCS3D01G515700 chr3B 86.122 526 43 8 853 1374 807078721 807079220 1.330000e-149 540.0
19 TraesCS3D01G515700 chr3B 73.434 399 75 17 866 1240 807187209 807186818 2.050000e-23 121.0
20 TraesCS3D01G515700 chr1D 93.846 195 10 1 3283 3475 416845226 416845032 4.110000e-75 292.0
21 TraesCS3D01G515700 chr1D 91.795 195 12 2 3283 3475 328875582 328875774 6.930000e-68 268.0
22 TraesCS3D01G515700 chr2B 93.401 197 8 4 3283 3475 800132992 800132797 1.910000e-73 287.0
23 TraesCS3D01G515700 chr2B 91.795 195 14 1 3283 3475 587341509 587341315 1.930000e-68 270.0
24 TraesCS3D01G515700 chr2B 88.421 190 18 2 3942 4128 795121548 795121360 4.230000e-55 226.0
25 TraesCS3D01G515700 chr6B 91.919 198 15 1 3931 4128 684435635 684435831 4.140000e-70 276.0
26 TraesCS3D01G515700 chr6B 100.000 28 0 0 194 221 153361326 153361299 8.000000e-03 52.8
27 TraesCS3D01G515700 chr2D 92.347 196 12 2 3282 3475 540321321 540321515 4.140000e-70 276.0
28 TraesCS3D01G515700 chr6D 91.878 197 15 1 3932 4128 450687228 450687423 1.490000e-69 274.0
29 TraesCS3D01G515700 chr6D 89.899 198 19 1 3931 4128 298645060 298645256 1.940000e-63 254.0
30 TraesCS3D01G515700 chr4D 91.045 201 15 3 3276 3475 310115558 310115756 6.930000e-68 268.0
31 TraesCS3D01G515700 chr1A 91.414 198 13 2 3280 3475 425710668 425710863 6.930000e-68 268.0
32 TraesCS3D01G515700 chr1A 91.710 193 13 2 3283 3473 514139144 514138953 8.960000e-67 265.0
33 TraesCS3D01G515700 chr7D 90.909 198 17 1 3931 4128 130107832 130108028 8.960000e-67 265.0
34 TraesCS3D01G515700 chr5D 87.245 196 24 1 3933 4128 357495005 357494811 5.470000e-54 222.0
35 TraesCS3D01G515700 chr5D 95.192 104 5 0 4025 4128 10650276 10650379 9.350000e-37 165.0
36 TraesCS3D01G515700 chr1B 80.711 197 32 3 3741 3935 146939002 146938810 9.420000e-32 148.0
37 TraesCS3D01G515700 chr1B 84.106 151 22 2 3741 3889 116259218 116259368 1.220000e-30 145.0
38 TraesCS3D01G515700 chr5B 89.744 78 7 1 4127 4204 709190477 709190553 9.620000e-17 99.0
39 TraesCS3D01G515700 chr5B 89.610 77 7 1 4128 4204 709015447 709015522 3.460000e-16 97.1
40 TraesCS3D01G515700 chr5B 89.610 77 7 1 4128 4204 709036222 709036297 3.460000e-16 97.1
41 TraesCS3D01G515700 chrUn 89.610 77 7 1 4128 4204 252895646 252895571 3.460000e-16 97.1
42 TraesCS3D01G515700 chrUn 89.610 77 7 1 4128 4204 281107203 281107278 3.460000e-16 97.1
43 TraesCS3D01G515700 chrUn 89.610 77 7 1 4128 4204 368651107 368651032 3.460000e-16 97.1
44 TraesCS3D01G515700 chrUn 89.610 77 7 1 4128 4204 368660827 368660752 3.460000e-16 97.1
45 TraesCS3D01G515700 chr4B 89.610 77 7 1 4127 4203 467099753 467099678 3.460000e-16 97.1


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 TraesCS3D01G515700 chr3D 599162848 599167051 4203 False 7764.00 7764 100.000000 1 4204 1 chr3D.!!$F1 4203
1 TraesCS3D01G515700 chr3A 729353444 729359985 6541 False 768.75 1284 95.574750 2303 4204 4 chr3A.!!$F2 1901
2 TraesCS3D01G515700 chr3A 729181500 729185326 3826 False 767.36 1474 91.055800 1 3221 5 chr3A.!!$F1 3220
3 TraesCS3D01G515700 chr3A 729576009 729578710 2701 True 730.75 1448 92.740500 1060 3226 4 chr3A.!!$R2 2166
4 TraesCS3D01G515700 chr3B 807078721 807081662 2941 False 1014.00 1467 90.045333 853 3223 3 chr3B.!!$F1 2370

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
624 650 0.032267 GACTATAGCCGCCAGTGGTC 59.968 60.0 11.74 2.09 0.00 4.02 F
1306 1387 0.319555 TCCTTTCGAAGCCGTCAGTG 60.320 55.0 0.00 0.00 37.05 3.66 F
1307 1388 0.319555 CCTTTCGAAGCCGTCAGTGA 60.320 55.0 0.00 0.00 37.05 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2002 2211 0.243365 TTGGTAAAGCGCATGCAAGG 59.757 50.0 19.57 2.17 46.23 3.61 R
3109 5946 0.947244 AGTGCTTGTTTCAGCTTCCG 59.053 50.0 0.00 0.00 40.79 4.30 R
3228 6065 2.737252 GACTGTGACTTCCAACGATTCC 59.263 50.0 0.00 0.00 0.00 3.01 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
46 47 7.596494 TGGAAACAATCACAATTTTGCAAAAA 58.404 26.923 27.10 11.87 37.44 1.94
47 48 7.754027 TGGAAACAATCACAATTTTGCAAAAAG 59.246 29.630 27.10 22.99 37.44 2.27
48 49 7.754475 GGAAACAATCACAATTTTGCAAAAAGT 59.246 29.630 27.10 23.58 0.00 2.66
52 53 7.067251 ACAATCACAATTTTGCAAAAAGTCCAT 59.933 29.630 27.10 17.71 0.00 3.41
56 57 7.282675 TCACAATTTTGCAAAAAGTCCATGAAT 59.717 29.630 27.10 5.17 0.00 2.57
58 59 7.916450 ACAATTTTGCAAAAAGTCCATGAATTG 59.084 29.630 27.10 22.07 37.02 2.32
65 66 6.513230 GCAAAAAGTCCATGAATTGGGAAAAC 60.513 38.462 0.00 0.00 46.45 2.43
66 67 4.519540 AAGTCCATGAATTGGGAAAACG 57.480 40.909 0.00 0.00 46.45 3.60
177 178 4.776795 AAGTCCGCGGATTTTGTAAAAT 57.223 36.364 33.58 6.22 41.06 1.82
178 179 4.776795 AGTCCGCGGATTTTGTAAAATT 57.223 36.364 33.58 0.00 38.64 1.82
179 180 5.128992 AGTCCGCGGATTTTGTAAAATTT 57.871 34.783 33.58 1.01 38.64 1.82
186 202 9.894439 CCGCGGATTTTGTAAAATTTATAAAAG 57.106 29.630 24.07 11.27 38.64 2.27
214 230 8.155821 TGTTGATTTGAAAAACAATCATGCAT 57.844 26.923 0.00 0.00 38.36 3.96
363 383 9.996554 AAAACAGAAAAGGAAAAGAAGAAAAGA 57.003 25.926 0.00 0.00 0.00 2.52
445 471 2.295349 CCAGAAGCTGCTCAAAACATGT 59.705 45.455 1.00 0.00 0.00 3.21
450 476 1.881973 GCTGCTCAAAACATGTCCAGA 59.118 47.619 0.00 0.00 33.22 3.86
476 502 0.512952 CTGTGAGCTTCCGAAAACCG 59.487 55.000 0.00 0.00 38.18 4.44
477 503 1.206831 GTGAGCTTCCGAAAACCGC 59.793 57.895 0.00 0.00 36.84 5.68
478 504 2.314647 TGAGCTTCCGAAAACCGCG 61.315 57.895 0.00 0.00 36.84 6.46
481 507 0.953960 AGCTTCCGAAAACCGCGAAT 60.954 50.000 8.23 0.00 36.84 3.34
492 518 2.187946 CGCGAATGGGAGCTTCCT 59.812 61.111 13.68 0.00 36.57 3.36
500 526 1.059584 TGGGAGCTTCCTGTTGGTGA 61.060 55.000 13.68 0.00 36.57 4.02
506 532 4.081087 GGAGCTTCCTGTTGGTGACTTATA 60.081 45.833 0.00 0.00 32.53 0.98
510 536 5.794894 CTTCCTGTTGGTGACTTATACAGT 58.205 41.667 0.00 0.00 35.58 3.55
511 537 5.818678 TCCTGTTGGTGACTTATACAGTT 57.181 39.130 0.00 0.00 35.58 3.16
513 539 5.305902 TCCTGTTGGTGACTTATACAGTTCA 59.694 40.000 0.00 0.00 35.58 3.18
514 540 5.995282 CCTGTTGGTGACTTATACAGTTCAA 59.005 40.000 0.00 0.00 35.01 2.69
517 543 4.901868 TGGTGACTTATACAGTTCAACCC 58.098 43.478 0.00 0.00 35.01 4.11
532 558 8.328758 ACAGTTCAACCCATAAAGATTCTATGA 58.671 33.333 0.00 0.00 0.00 2.15
562 588 1.231221 TGTGCGCCTTGTACGAAAAT 58.769 45.000 4.18 0.00 35.72 1.82
568 594 2.727916 CGCCTTGTACGAAAATGCCTTC 60.728 50.000 0.00 0.00 0.00 3.46
573 599 4.902443 TGTACGAAAATGCCTTCAAACA 57.098 36.364 0.00 0.00 0.00 2.83
576 602 2.100584 ACGAAAATGCCTTCAAACAGCA 59.899 40.909 0.00 0.00 41.50 4.41
586 612 0.518636 TCAAACAGCATCTGAAGCGC 59.481 50.000 0.00 0.00 35.18 5.92
596 622 2.779755 TCTGAAGCGCCAAATAGGAA 57.220 45.000 2.29 0.00 41.22 3.36
597 623 3.281727 TCTGAAGCGCCAAATAGGAAT 57.718 42.857 2.29 0.00 41.22 3.01
613 639 4.092116 AGGAATTGGCCTTGACTATAGC 57.908 45.455 3.32 0.00 33.46 2.97
614 640 3.149981 GGAATTGGCCTTGACTATAGCC 58.850 50.000 3.32 0.00 45.96 3.93
616 642 4.363034 GGCCTTGACTATAGCCGC 57.637 61.111 0.00 0.00 35.30 6.53
617 643 1.301795 GGCCTTGACTATAGCCGCC 60.302 63.158 0.00 0.23 35.30 6.13
618 644 1.445942 GCCTTGACTATAGCCGCCA 59.554 57.895 0.00 0.00 0.00 5.69
619 645 0.601311 GCCTTGACTATAGCCGCCAG 60.601 60.000 0.00 0.00 0.00 4.85
620 646 0.753262 CCTTGACTATAGCCGCCAGT 59.247 55.000 0.00 0.00 0.00 4.00
621 647 1.539065 CCTTGACTATAGCCGCCAGTG 60.539 57.143 0.00 0.00 0.00 3.66
622 648 0.464036 TTGACTATAGCCGCCAGTGG 59.536 55.000 4.20 4.20 0.00 4.00
623 649 0.686441 TGACTATAGCCGCCAGTGGT 60.686 55.000 11.74 0.00 0.00 4.16
624 650 0.032267 GACTATAGCCGCCAGTGGTC 59.968 60.000 11.74 2.09 0.00 4.02
625 651 1.007271 CTATAGCCGCCAGTGGTCG 60.007 63.158 11.74 14.40 0.00 4.79
640 666 1.449778 GTCGAGGTTAGCAAGGGCC 60.450 63.158 0.00 0.00 42.56 5.80
641 667 1.916273 TCGAGGTTAGCAAGGGCCA 60.916 57.895 6.18 0.00 42.56 5.36
642 668 1.002624 CGAGGTTAGCAAGGGCCAA 60.003 57.895 6.18 0.00 42.56 4.52
656 682 1.456331 GCCAACCTATGCCATGCCT 60.456 57.895 0.00 0.00 0.00 4.75
709 735 7.066307 TGCCTATGCATGTAAGAGATTTCTA 57.934 36.000 10.16 0.00 44.23 2.10
728 754 9.764363 GATTTCTACACTGTATTCATGGATGTA 57.236 33.333 0.00 0.00 0.00 2.29
804 833 7.721286 AATCGATAATCATCTTCACACCTTC 57.279 36.000 0.00 0.00 0.00 3.46
848 877 4.287766 ACATCTTTACACCCTCTTGTCC 57.712 45.455 0.00 0.00 0.00 4.02
850 879 4.351111 ACATCTTTACACCCTCTTGTCCTT 59.649 41.667 0.00 0.00 0.00 3.36
854 916 4.618920 TTACACCCTCTTGTCCTTTCTC 57.381 45.455 0.00 0.00 0.00 2.87
890 952 1.243342 TTCAAGAACGCCAGCCCATG 61.243 55.000 0.00 0.00 0.00 3.66
893 955 2.359850 GAACGCCAGCCCATGTGA 60.360 61.111 0.00 0.00 0.00 3.58
897 959 1.973281 CGCCAGCCCATGTGAGTTT 60.973 57.895 0.00 0.00 0.00 2.66
919 981 1.749063 GGCCCGGAGAATAAAACCAAG 59.251 52.381 0.73 0.00 0.00 3.61
1170 1251 2.438434 AAGGCGGCTGAATTCCGG 60.438 61.111 14.21 0.00 46.51 5.14
1247 1328 1.533731 CGCGTGGGAAAAGTACAACAT 59.466 47.619 0.00 0.00 0.00 2.71
1286 1367 1.685224 GGGACAACTGGATCTGGCA 59.315 57.895 0.00 0.00 0.00 4.92
1290 1371 1.211457 GACAACTGGATCTGGCATCCT 59.789 52.381 8.51 0.00 38.95 3.24
1301 1382 1.745489 GGCATCCTTTCGAAGCCGT 60.745 57.895 9.32 0.00 44.92 5.68
1306 1387 0.319555 TCCTTTCGAAGCCGTCAGTG 60.320 55.000 0.00 0.00 37.05 3.66
1307 1388 0.319555 CCTTTCGAAGCCGTCAGTGA 60.320 55.000 0.00 0.00 37.05 3.41
1350 1435 7.066404 CCCTCTATCTTTAGTTTCTTTCTTGCC 59.934 40.741 0.00 0.00 0.00 4.52
1354 1439 7.689446 ATCTTTAGTTTCTTTCTTGCCCTAC 57.311 36.000 0.00 0.00 0.00 3.18
1403 1511 1.638467 GGCACGATCACGATCAAGC 59.362 57.895 7.75 9.34 42.66 4.01
1405 1513 0.574454 GCACGATCACGATCAAGCTC 59.426 55.000 7.75 0.00 42.66 4.09
1408 1551 1.202348 ACGATCACGATCAAGCTCCTG 60.202 52.381 7.75 0.00 42.66 3.86
1432 1575 5.927954 ATCACCAATTCAAACATTTGTGC 57.072 34.783 4.36 0.00 39.18 4.57
1445 1588 9.770097 TCAAACATTTGTGCTCCAATAAAAATA 57.230 25.926 4.36 0.00 39.18 1.40
1496 1643 7.736447 AAACATAAGTGAAAAGGACAGAGAG 57.264 36.000 0.00 0.00 0.00 3.20
1505 1652 6.094186 GTGAAAAGGACAGAGAGTTTGTCTTT 59.906 38.462 5.49 1.74 43.85 2.52
1531 1678 9.620259 TTGTAAAATTTGCAGGTTTTTCCTAAT 57.380 25.926 13.93 0.00 46.24 1.73
1532 1679 9.050601 TGTAAAATTTGCAGGTTTTTCCTAATG 57.949 29.630 13.93 0.00 46.24 1.90
1579 1730 9.498176 CAAATATGGATACTGATGACTTCATGA 57.502 33.333 0.00 0.00 35.03 3.07
1632 1784 8.306680 TGTTATTGTACTACTCAAAAGCTGAC 57.693 34.615 0.00 0.00 0.00 3.51
1657 1809 2.022195 CTCTCCTCATTGCCATGTTGG 58.978 52.381 0.00 2.54 41.55 3.77
1658 1810 1.634973 TCTCCTCATTGCCATGTTGGA 59.365 47.619 12.12 12.12 40.96 3.53
1659 1811 2.242965 TCTCCTCATTGCCATGTTGGAT 59.757 45.455 12.75 0.00 40.96 3.41
1660 1812 2.361119 CTCCTCATTGCCATGTTGGATG 59.639 50.000 12.75 0.00 40.96 3.51
1661 1813 2.104967 CCTCATTGCCATGTTGGATGT 58.895 47.619 0.00 0.00 40.96 3.06
1662 1814 2.498481 CCTCATTGCCATGTTGGATGTT 59.502 45.455 0.00 0.00 40.96 2.71
1663 1815 3.517602 CTCATTGCCATGTTGGATGTTG 58.482 45.455 0.00 0.00 40.96 3.33
1675 1827 2.037901 TGGATGTTGCCACACAATTGT 58.962 42.857 4.92 4.92 41.27 2.71
1692 1844 7.955502 CACAATTGTGTCATGATGGTATTTTG 58.044 34.615 27.08 0.94 40.96 2.44
1693 1845 7.599621 CACAATTGTGTCATGATGGTATTTTGT 59.400 33.333 27.08 1.55 40.96 2.83
1694 1846 7.599621 ACAATTGTGTCATGATGGTATTTTGTG 59.400 33.333 11.07 0.00 29.49 3.33
1695 1847 6.890979 TTGTGTCATGATGGTATTTTGTGA 57.109 33.333 0.00 0.00 0.00 3.58
1696 1848 7.465353 TTGTGTCATGATGGTATTTTGTGAT 57.535 32.000 0.00 0.00 0.00 3.06
1697 1849 7.465353 TGTGTCATGATGGTATTTTGTGATT 57.535 32.000 0.00 0.00 0.00 2.57
1698 1850 7.314393 TGTGTCATGATGGTATTTTGTGATTG 58.686 34.615 0.00 0.00 0.00 2.67
1699 1851 7.176340 TGTGTCATGATGGTATTTTGTGATTGA 59.824 33.333 0.00 0.00 0.00 2.57
1700 1852 7.485913 GTGTCATGATGGTATTTTGTGATTGAC 59.514 37.037 0.00 0.00 0.00 3.18
1701 1853 7.394077 TGTCATGATGGTATTTTGTGATTGACT 59.606 33.333 0.00 0.00 32.09 3.41
1702 1854 8.892723 GTCATGATGGTATTTTGTGATTGACTA 58.107 33.333 0.00 0.00 0.00 2.59
1703 1855 8.892723 TCATGATGGTATTTTGTGATTGACTAC 58.107 33.333 0.00 0.00 0.00 2.73
1734 1886 6.153756 GCGGTTTACCTGTATTTGTTTCATT 58.846 36.000 0.00 0.00 0.00 2.57
1735 1887 7.040617 TGCGGTTTACCTGTATTTGTTTCATTA 60.041 33.333 0.00 0.00 0.00 1.90
1736 1888 7.971722 GCGGTTTACCTGTATTTGTTTCATTAT 59.028 33.333 0.00 0.00 0.00 1.28
1737 1889 9.849166 CGGTTTACCTGTATTTGTTTCATTATT 57.151 29.630 0.00 0.00 0.00 1.40
1772 1976 4.331108 TGAGTTGCCATGCTATTTACACA 58.669 39.130 0.00 0.00 0.00 3.72
1789 1993 2.634940 ACACACACTTGTCTGGATAGCT 59.365 45.455 0.00 0.00 31.66 3.32
1792 1996 2.234661 CACACTTGTCTGGATAGCTGGA 59.765 50.000 0.00 0.00 0.00 3.86
1802 2006 4.063689 CTGGATAGCTGGATGTGATTGTC 58.936 47.826 0.00 0.00 0.00 3.18
1814 2021 9.787532 CTGGATGTGATTGTCGTTTTAATTATT 57.212 29.630 0.00 0.00 0.00 1.40
1861 2068 6.785076 TCCCTTGTATGTTTACTTCCATTCA 58.215 36.000 0.00 0.00 0.00 2.57
1975 2184 4.225267 CCACCATCCCTCTTGTAACTAACT 59.775 45.833 0.00 0.00 0.00 2.24
1998 2207 2.987413 TTGTATTTGTTGCAGCGGAG 57.013 45.000 0.00 0.00 0.00 4.63
2002 2211 1.098050 ATTTGTTGCAGCGGAGATCC 58.902 50.000 0.00 0.00 0.00 3.36
2025 2234 0.793104 GCATGCGCTTTACCAACGAC 60.793 55.000 9.73 0.00 34.30 4.34
2029 2238 1.069568 TGCGCTTTACCAACGACAATG 60.070 47.619 9.73 0.00 0.00 2.82
2059 2268 3.139077 CCTAATTATCCACGCCTTGTCC 58.861 50.000 0.00 0.00 0.00 4.02
2068 2277 4.120331 GCCTTGTCCGCACCATGC 62.120 66.667 0.00 0.00 40.69 4.06
2073 2282 3.747976 GTCCGCACCATGCCAACC 61.748 66.667 0.00 0.00 41.12 3.77
2127 2336 2.921972 GGTGGGTTGCATTGGCCA 60.922 61.111 0.00 0.00 40.13 5.36
2177 2386 1.164411 GATGTGGTGGATCGCAAACA 58.836 50.000 0.00 0.00 0.00 2.83
2191 2400 4.222886 TCGCAAACACATTATGGTTTTCG 58.777 39.130 17.31 17.31 42.25 3.46
2280 2571 9.539825 CACTCTAATACATAGATATGAATGGCC 57.460 37.037 6.84 0.00 39.88 5.36
2286 2577 6.560003 ACATAGATATGAATGGCCGGAATA 57.440 37.500 5.05 0.00 37.15 1.75
2300 2591 3.193691 GCCGGAATAGAATAGCAGCTAGA 59.806 47.826 5.05 0.00 0.00 2.43
2306 3054 7.523052 CGGAATAGAATAGCAGCTAGAGAGTTT 60.523 40.741 8.43 0.00 0.00 2.66
2348 3096 6.016777 CCTGCAAGCTGAAGGGTTATAAATAG 60.017 42.308 0.16 0.00 39.67 1.73
2407 3155 3.584733 AATCCTGCTAATGGGGAAGTC 57.415 47.619 0.00 0.00 32.53 3.01
2409 3157 2.492025 TCCTGCTAATGGGGAAGTCAT 58.508 47.619 0.00 0.00 0.00 3.06
2413 3161 5.134339 TCCTGCTAATGGGGAAGTCATATTT 59.866 40.000 0.00 0.00 0.00 1.40
2414 3162 5.835280 CCTGCTAATGGGGAAGTCATATTTT 59.165 40.000 0.00 0.00 0.00 1.82
2415 3163 7.004086 CCTGCTAATGGGGAAGTCATATTTTA 58.996 38.462 0.00 0.00 0.00 1.52
2416 3164 7.175641 CCTGCTAATGGGGAAGTCATATTTTAG 59.824 40.741 0.00 0.00 0.00 1.85
2417 3165 7.811282 TGCTAATGGGGAAGTCATATTTTAGA 58.189 34.615 0.00 0.00 0.00 2.10
2447 3195 4.630894 TTGTCATCGGCATATTTTGGAC 57.369 40.909 0.00 0.00 0.00 4.02
2448 3196 3.884895 TGTCATCGGCATATTTTGGACT 58.115 40.909 0.00 0.00 0.00 3.85
3019 3767 3.311322 TCACGCCAAGTTGTTTCTGTTAG 59.689 43.478 1.45 0.00 0.00 2.34
3053 3801 2.031333 GCTGAAAGTTTCTGTCTGGCAG 60.031 50.000 19.81 8.58 40.91 4.85
3102 3850 6.261603 CCAAGAGATAACTGCTGCATCATTTA 59.738 38.462 1.31 3.26 0.00 1.40
3103 3851 6.857777 AGAGATAACTGCTGCATCATTTAC 57.142 37.500 1.31 0.00 0.00 2.01
3228 6065 5.404466 AAGAAGACCAAGAGAGAGATGTG 57.596 43.478 0.00 0.00 0.00 3.21
3276 6113 2.884639 GTGGCATATACCCAACACATCC 59.115 50.000 0.00 0.00 33.39 3.51
3349 8701 0.321996 GAGCCTCCCGGATACAATCC 59.678 60.000 0.73 0.00 46.22 3.01
3368 8720 6.096282 ACAATCCGGGGTTACATGAAAAATAG 59.904 38.462 0.00 0.00 0.00 1.73
3369 8721 5.438698 TCCGGGGTTACATGAAAAATAGA 57.561 39.130 0.00 0.00 0.00 1.98
3410 8762 4.505313 TCTAGCTAGAATATGTGCCACG 57.495 45.455 21.26 0.00 0.00 4.94
3414 8766 3.070159 AGCTAGAATATGTGCCACGACAT 59.930 43.478 0.00 0.00 39.87 3.06
3430 8782 5.338559 CCACGACATTCAACAAACGATTTAC 59.661 40.000 0.00 0.00 0.00 2.01
3454 8806 4.689071 TGACTAAAGCGAACAGACAAGAA 58.311 39.130 0.00 0.00 0.00 2.52
3463 8815 3.654414 GAACAGACAAGAAGACCGACAT 58.346 45.455 0.00 0.00 0.00 3.06
3491 8843 4.015084 CCTTGACTTACGAGTAGAAGGGA 58.985 47.826 0.00 0.00 39.64 4.20
3839 9200 0.838122 AAGAGGATAGATGGGCCCGG 60.838 60.000 19.37 0.00 0.00 5.73
3855 9216 3.293337 GCCCGGGTAGTTAAATTCCAAT 58.707 45.455 24.63 0.00 0.00 3.16
3990 9387 1.834263 ACATCCCTCAGGTTAGCACTC 59.166 52.381 0.00 0.00 0.00 3.51
3991 9388 2.114616 CATCCCTCAGGTTAGCACTCT 58.885 52.381 0.00 0.00 0.00 3.24
3999 9396 3.256879 TCAGGTTAGCACTCTTGACTCAG 59.743 47.826 0.00 0.00 0.00 3.35
4098 9495 4.624015 CAACTGCTTTGTGGTTGAATCAT 58.376 39.130 0.00 0.00 41.71 2.45
4108 9505 7.778470 TTGTGGTTGAATCATTACAAAAACC 57.222 32.000 5.43 0.00 36.86 3.27
4136 9533 4.328169 GCTCATGCTGGACTTTTTATTTGC 59.672 41.667 0.00 0.00 36.03 3.68
4146 9543 9.271828 CTGGACTTTTTATTTGCAAAATAACCT 57.728 29.630 17.19 0.49 0.00 3.50
4147 9544 9.620259 TGGACTTTTTATTTGCAAAATAACCTT 57.380 25.926 17.19 0.00 0.00 3.50
4188 9585 3.564644 ACGGTTACATCGTCTATCAGAGG 59.435 47.826 0.00 0.00 35.87 3.69
4194 9591 7.415989 GGTTACATCGTCTATCAGAGGTTGTAA 60.416 40.741 18.97 18.97 44.37 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 6.748333 TTTGCAAAATTGTGATTGTTTCCA 57.252 29.167 10.02 0.00 0.00 3.53
24 25 7.754475 GGACTTTTTGCAAAATTGTGATTGTTT 59.246 29.630 24.39 3.67 0.00 2.83
27 28 6.783162 TGGACTTTTTGCAAAATTGTGATTG 58.217 32.000 24.39 10.13 0.00 2.67
31 32 6.360844 TCATGGACTTTTTGCAAAATTGTG 57.639 33.333 24.39 16.37 0.00 3.33
52 53 3.891977 TCATGAACCGTTTTCCCAATTCA 59.108 39.130 0.00 0.00 0.00 2.57
56 57 4.946478 AATTCATGAACCGTTTTCCCAA 57.054 36.364 11.07 0.00 0.00 4.12
58 59 7.899178 ATTTAAATTCATGAACCGTTTTCCC 57.101 32.000 11.07 0.00 0.00 3.97
127 128 8.940768 TCAAAATCGATGAACTTTTCCTTTTT 57.059 26.923 0.00 0.00 0.00 1.94
128 129 8.940768 TTCAAAATCGATGAACTTTTCCTTTT 57.059 26.923 0.00 0.00 32.10 2.27
129 130 8.940768 TTTCAAAATCGATGAACTTTTCCTTT 57.059 26.923 0.00 0.00 36.57 3.11
130 131 8.940768 TTTTCAAAATCGATGAACTTTTCCTT 57.059 26.923 0.00 0.00 36.57 3.36
131 132 8.940768 TTTTTCAAAATCGATGAACTTTTCCT 57.059 26.923 0.00 0.00 36.57 3.36
186 202 8.735837 GCATGATTGTTTTTCAAATCAACAAAC 58.264 29.630 4.60 3.38 42.22 2.93
192 208 8.837389 TCAAATGCATGATTGTTTTTCAAATCA 58.163 25.926 0.00 0.97 39.62 2.57
332 352 9.996554 TCTTCTTTTCCTTTTCTGTTTTTCTTT 57.003 25.926 0.00 0.00 0.00 2.52
333 353 9.996554 TTCTTCTTTTCCTTTTCTGTTTTTCTT 57.003 25.926 0.00 0.00 0.00 2.52
334 354 9.996554 TTTCTTCTTTTCCTTTTCTGTTTTTCT 57.003 25.926 0.00 0.00 0.00 2.52
337 357 9.996554 TCTTTTCTTCTTTTCCTTTTCTGTTTT 57.003 25.926 0.00 0.00 0.00 2.43
338 358 9.996554 TTCTTTTCTTCTTTTCCTTTTCTGTTT 57.003 25.926 0.00 0.00 0.00 2.83
339 359 9.996554 TTTCTTTTCTTCTTTTCCTTTTCTGTT 57.003 25.926 0.00 0.00 0.00 3.16
340 360 9.996554 TTTTCTTTTCTTCTTTTCCTTTTCTGT 57.003 25.926 0.00 0.00 0.00 3.41
367 387 2.649531 TGGACCGACTTTGATTGGTT 57.350 45.000 0.00 0.00 36.40 3.67
407 433 1.303282 GGAAGCTTCCATTCGGGGT 59.697 57.895 35.71 0.00 46.76 4.95
425 451 3.562505 GACATGTTTTGAGCAGCTTCTG 58.437 45.455 0.00 0.00 34.12 3.02
460 486 2.314647 CGCGGTTTTCGGAAGCTCA 61.315 57.895 0.00 0.00 39.69 4.26
463 489 0.793104 CATTCGCGGTTTTCGGAAGC 60.793 55.000 6.13 0.00 39.69 3.86
469 495 1.136774 GCTCCCATTCGCGGTTTTC 59.863 57.895 6.13 0.00 0.00 2.29
476 502 0.678048 AACAGGAAGCTCCCATTCGC 60.678 55.000 0.00 0.00 37.19 4.70
477 503 1.089920 CAACAGGAAGCTCCCATTCG 58.910 55.000 0.00 0.00 37.19 3.34
478 504 1.272147 ACCAACAGGAAGCTCCCATTC 60.272 52.381 0.00 0.00 37.19 2.67
481 507 1.059584 TCACCAACAGGAAGCTCCCA 61.060 55.000 0.00 0.00 37.19 4.37
492 518 5.761234 GGTTGAACTGTATAAGTCACCAACA 59.239 40.000 0.00 0.00 41.01 3.33
500 526 9.975218 AATCTTTATGGGTTGAACTGTATAAGT 57.025 29.630 0.00 0.00 42.60 2.24
506 532 8.328758 TCATAGAATCTTTATGGGTTGAACTGT 58.671 33.333 0.00 0.00 0.00 3.55
510 536 6.765989 CCGTCATAGAATCTTTATGGGTTGAA 59.234 38.462 0.00 0.00 0.00 2.69
511 537 6.288294 CCGTCATAGAATCTTTATGGGTTGA 58.712 40.000 0.00 0.00 0.00 3.18
513 539 5.368523 TCCCGTCATAGAATCTTTATGGGTT 59.631 40.000 13.02 0.00 0.00 4.11
514 540 4.905456 TCCCGTCATAGAATCTTTATGGGT 59.095 41.667 13.02 0.00 0.00 4.51
517 543 5.482908 CCCTCCCGTCATAGAATCTTTATG 58.517 45.833 0.00 0.00 0.00 1.90
549 575 4.497473 TTGAAGGCATTTTCGTACAAGG 57.503 40.909 0.00 0.00 0.00 3.61
562 588 2.275134 TCAGATGCTGTTTGAAGGCA 57.725 45.000 0.00 0.00 40.32 4.75
568 594 0.455633 GGCGCTTCAGATGCTGTTTG 60.456 55.000 7.64 0.00 32.61 2.93
573 599 1.945394 CTATTTGGCGCTTCAGATGCT 59.055 47.619 7.64 0.00 0.00 3.79
576 602 3.281727 TTCCTATTTGGCGCTTCAGAT 57.718 42.857 7.64 0.69 35.26 2.90
586 612 4.026052 AGTCAAGGCCAATTCCTATTTGG 58.974 43.478 5.01 0.00 45.30 3.28
596 622 1.543429 GCGGCTATAGTCAAGGCCAAT 60.543 52.381 5.01 0.00 44.27 3.16
597 623 0.179056 GCGGCTATAGTCAAGGCCAA 60.179 55.000 5.01 0.00 44.27 4.52
613 639 2.558554 CTAACCTCGACCACTGGCGG 62.559 65.000 10.69 0.00 0.00 6.13
614 640 1.153823 CTAACCTCGACCACTGGCG 60.154 63.158 0.00 0.20 0.00 5.69
615 641 1.448013 GCTAACCTCGACCACTGGC 60.448 63.158 0.00 0.00 0.00 4.85
616 642 0.320374 TTGCTAACCTCGACCACTGG 59.680 55.000 0.00 0.00 0.00 4.00
617 643 1.673033 CCTTGCTAACCTCGACCACTG 60.673 57.143 0.00 0.00 0.00 3.66
618 644 0.608640 CCTTGCTAACCTCGACCACT 59.391 55.000 0.00 0.00 0.00 4.00
619 645 0.391263 CCCTTGCTAACCTCGACCAC 60.391 60.000 0.00 0.00 0.00 4.16
620 646 1.980052 CCCTTGCTAACCTCGACCA 59.020 57.895 0.00 0.00 0.00 4.02
621 647 1.449778 GCCCTTGCTAACCTCGACC 60.450 63.158 0.00 0.00 33.53 4.79
622 648 1.449778 GGCCCTTGCTAACCTCGAC 60.450 63.158 0.00 0.00 37.74 4.20
623 649 1.485294 TTGGCCCTTGCTAACCTCGA 61.485 55.000 0.00 0.00 32.47 4.04
624 650 1.002624 TTGGCCCTTGCTAACCTCG 60.003 57.895 0.00 0.00 32.47 4.63
640 666 0.825010 GGGAGGCATGGCATAGGTTG 60.825 60.000 22.64 0.00 0.00 3.77
641 667 0.995675 AGGGAGGCATGGCATAGGTT 60.996 55.000 22.64 0.00 0.00 3.50
642 668 0.104462 TAGGGAGGCATGGCATAGGT 60.104 55.000 22.64 0.00 0.00 3.08
644 670 0.035630 GCTAGGGAGGCATGGCATAG 60.036 60.000 22.64 16.85 0.00 2.23
656 682 2.040144 GCATAGGTTCTGGGCTAGGGA 61.040 57.143 0.00 0.00 0.00 4.20
709 735 6.327365 TCTCCATACATCCATGAATACAGTGT 59.673 38.462 0.00 0.00 0.00 3.55
782 811 6.096846 TGAGAAGGTGTGAAGATGATTATCGA 59.903 38.462 0.00 0.00 38.38 3.59
783 812 6.276091 TGAGAAGGTGTGAAGATGATTATCG 58.724 40.000 0.00 0.00 38.38 2.92
789 818 5.752036 AAGATGAGAAGGTGTGAAGATGA 57.248 39.130 0.00 0.00 0.00 2.92
823 852 6.713450 GGACAAGAGGGTGTAAAGATGTAAAA 59.287 38.462 0.00 0.00 0.00 1.52
827 856 3.910627 AGGACAAGAGGGTGTAAAGATGT 59.089 43.478 0.00 0.00 0.00 3.06
829 858 5.310857 AGAAAGGACAAGAGGGTGTAAAGAT 59.689 40.000 0.00 0.00 0.00 2.40
831 860 4.974399 AGAAAGGACAAGAGGGTGTAAAG 58.026 43.478 0.00 0.00 0.00 1.85
832 861 4.658901 AGAGAAAGGACAAGAGGGTGTAAA 59.341 41.667 0.00 0.00 0.00 2.01
833 862 4.232091 AGAGAAAGGACAAGAGGGTGTAA 58.768 43.478 0.00 0.00 0.00 2.41
834 863 3.858135 AGAGAAAGGACAAGAGGGTGTA 58.142 45.455 0.00 0.00 0.00 2.90
836 865 3.181450 ACAAGAGAAAGGACAAGAGGGTG 60.181 47.826 0.00 0.00 0.00 4.61
838 867 3.778954 ACAAGAGAAAGGACAAGAGGG 57.221 47.619 0.00 0.00 0.00 4.30
839 868 4.708177 TCAACAAGAGAAAGGACAAGAGG 58.292 43.478 0.00 0.00 0.00 3.69
854 916 3.071874 TGAATGGGCTACCTCAACAAG 57.928 47.619 0.00 0.00 37.76 3.16
890 952 2.434359 CTCCGGGCCGAAACTCAC 60.434 66.667 30.79 0.00 0.00 3.51
893 955 0.906775 TTATTCTCCGGGCCGAAACT 59.093 50.000 30.79 10.33 0.00 2.66
897 959 0.107557 GGTTTTATTCTCCGGGCCGA 60.108 55.000 30.79 12.88 0.00 5.54
1025 1106 0.825840 GGACTCCCTCTCCATCTCCG 60.826 65.000 0.00 0.00 0.00 4.63
1026 1107 0.263172 TGGACTCCCTCTCCATCTCC 59.737 60.000 0.00 0.00 32.52 3.71
1027 1108 1.703411 CTGGACTCCCTCTCCATCTC 58.297 60.000 0.00 0.00 37.18 2.75
1028 1109 0.264359 CCTGGACTCCCTCTCCATCT 59.736 60.000 0.00 0.00 37.18 2.90
1029 1110 0.263172 TCCTGGACTCCCTCTCCATC 59.737 60.000 0.00 0.00 37.18 3.51
1030 1111 0.719015 TTCCTGGACTCCCTCTCCAT 59.281 55.000 0.00 0.00 37.18 3.41
1170 1251 0.729690 GATTCGCCAGCAGGTTCTTC 59.270 55.000 0.00 0.00 37.19 2.87
1247 1328 2.045242 CCCTCTCCCACGACTCGA 60.045 66.667 5.20 0.00 0.00 4.04
1269 1350 1.673168 GATGCCAGATCCAGTTGTCC 58.327 55.000 0.00 0.00 0.00 4.02
1286 1367 0.608640 ACTGACGGCTTCGAAAGGAT 59.391 50.000 0.00 0.00 37.63 3.24
1290 1371 0.319555 CCTCACTGACGGCTTCGAAA 60.320 55.000 0.00 0.00 37.63 3.46
1350 1435 3.063997 CAGCACGCTCCAAAATTAGTAGG 59.936 47.826 0.00 0.00 0.00 3.18
1354 1439 1.468054 GGCAGCACGCTCCAAAATTAG 60.468 52.381 0.00 0.00 41.91 1.73
1397 1505 3.726557 TTGGTGATTCAGGAGCTTGAT 57.273 42.857 0.00 0.00 0.00 2.57
1398 1506 3.726557 ATTGGTGATTCAGGAGCTTGA 57.273 42.857 0.00 0.00 0.00 3.02
1399 1507 3.760151 TGAATTGGTGATTCAGGAGCTTG 59.240 43.478 0.00 0.00 47.00 4.01
1400 1508 4.038271 TGAATTGGTGATTCAGGAGCTT 57.962 40.909 0.00 0.00 47.00 3.74
1401 1509 3.726557 TGAATTGGTGATTCAGGAGCT 57.273 42.857 0.00 0.00 47.00 4.09
1408 1551 6.203338 AGCACAAATGTTTGAATTGGTGATTC 59.797 34.615 12.09 0.00 42.00 2.52
1451 1594 6.127281 TGTTTAGATCTAAGACGCCAATGGTA 60.127 38.462 14.63 0.00 0.00 3.25
1496 1643 7.747888 ACCTGCAAATTTTACAAAAGACAAAC 58.252 30.769 0.00 0.00 0.00 2.93
1553 1704 9.498176 TCATGAAGTCATCAGTATCCATATTTG 57.502 33.333 0.00 0.00 42.53 2.32
1556 1707 8.661752 TCTCATGAAGTCATCAGTATCCATAT 57.338 34.615 0.00 0.00 42.53 1.78
1579 1730 4.504858 CCTGTAGCCGAAAAGTGTAATCT 58.495 43.478 0.00 0.00 0.00 2.40
1675 1827 7.394077 AGTCAATCACAAAATACCATCATGACA 59.606 33.333 0.00 0.00 35.85 3.58
1676 1828 7.765307 AGTCAATCACAAAATACCATCATGAC 58.235 34.615 0.00 0.00 34.14 3.06
1677 1829 7.943079 AGTCAATCACAAAATACCATCATGA 57.057 32.000 0.00 0.00 0.00 3.07
1678 1830 8.131100 GGTAGTCAATCACAAAATACCATCATG 58.869 37.037 0.00 0.00 33.08 3.07
1679 1831 8.055181 AGGTAGTCAATCACAAAATACCATCAT 58.945 33.333 0.00 0.00 34.86 2.45
1680 1832 7.402054 AGGTAGTCAATCACAAAATACCATCA 58.598 34.615 0.00 0.00 34.86 3.07
1681 1833 7.254455 CGAGGTAGTCAATCACAAAATACCATC 60.254 40.741 0.00 0.00 34.86 3.51
1682 1834 6.538742 CGAGGTAGTCAATCACAAAATACCAT 59.461 38.462 0.00 0.00 34.86 3.55
1684 1836 5.873164 ACGAGGTAGTCAATCACAAAATACC 59.127 40.000 0.00 0.00 33.02 2.73
1685 1837 6.963049 ACGAGGTAGTCAATCACAAAATAC 57.037 37.500 0.00 0.00 0.00 1.89
1687 1839 5.334879 GCAACGAGGTAGTCAATCACAAAAT 60.335 40.000 0.00 0.00 0.00 1.82
1688 1840 4.024387 GCAACGAGGTAGTCAATCACAAAA 60.024 41.667 0.00 0.00 0.00 2.44
1689 1841 3.496884 GCAACGAGGTAGTCAATCACAAA 59.503 43.478 0.00 0.00 0.00 2.83
1690 1842 3.064207 GCAACGAGGTAGTCAATCACAA 58.936 45.455 0.00 0.00 0.00 3.33
1691 1843 2.683968 GCAACGAGGTAGTCAATCACA 58.316 47.619 0.00 0.00 0.00 3.58
1692 1844 1.654105 CGCAACGAGGTAGTCAATCAC 59.346 52.381 0.00 0.00 0.00 3.06
1693 1845 1.403647 CCGCAACGAGGTAGTCAATCA 60.404 52.381 0.00 0.00 0.00 2.57
1694 1846 1.278238 CCGCAACGAGGTAGTCAATC 58.722 55.000 0.00 0.00 0.00 2.67
1695 1847 0.606604 ACCGCAACGAGGTAGTCAAT 59.393 50.000 0.00 0.00 40.80 2.57
1696 1848 0.390124 AACCGCAACGAGGTAGTCAA 59.610 50.000 0.00 0.00 41.95 3.18
1697 1849 0.390124 AAACCGCAACGAGGTAGTCA 59.610 50.000 0.00 0.00 41.95 3.41
1698 1850 1.988467 GTAAACCGCAACGAGGTAGTC 59.012 52.381 0.00 0.00 41.95 2.59
1699 1851 1.337167 GGTAAACCGCAACGAGGTAGT 60.337 52.381 0.00 0.00 41.95 2.73
1700 1852 1.067354 AGGTAAACCGCAACGAGGTAG 60.067 52.381 0.00 0.00 41.95 3.18
1701 1853 0.968405 AGGTAAACCGCAACGAGGTA 59.032 50.000 0.00 0.00 41.95 3.08
1702 1854 0.601841 CAGGTAAACCGCAACGAGGT 60.602 55.000 0.00 0.00 45.29 3.85
1703 1855 0.601841 ACAGGTAAACCGCAACGAGG 60.602 55.000 0.00 0.00 42.08 4.63
1734 1886 5.428253 GCAACTCAGGACAATCCAGTAATA 58.572 41.667 0.00 0.00 39.61 0.98
1735 1887 4.265073 GCAACTCAGGACAATCCAGTAAT 58.735 43.478 0.00 0.00 39.61 1.89
1736 1888 3.559171 GGCAACTCAGGACAATCCAGTAA 60.559 47.826 0.00 0.00 39.61 2.24
1737 1889 2.027192 GGCAACTCAGGACAATCCAGTA 60.027 50.000 0.00 0.00 39.61 2.74
1738 1890 1.271597 GGCAACTCAGGACAATCCAGT 60.272 52.381 0.00 0.00 39.61 4.00
1739 1891 1.271543 TGGCAACTCAGGACAATCCAG 60.272 52.381 0.00 0.00 36.70 3.86
1742 1894 1.133790 GCATGGCAACTCAGGACAATC 59.866 52.381 0.00 0.00 37.61 2.67
1772 1976 2.540383 TCCAGCTATCCAGACAAGTGT 58.460 47.619 0.00 0.00 0.00 3.55
1789 1993 9.781834 GAATAATTAAAACGACAATCACATCCA 57.218 29.630 0.00 0.00 0.00 3.41
1792 1996 8.670135 TCGGAATAATTAAAACGACAATCACAT 58.330 29.630 0.00 0.00 0.00 3.21
1861 2068 3.079578 CGCTGCATCAATCCTATCCAAT 58.920 45.455 0.00 0.00 0.00 3.16
1866 2073 5.068636 AGATTTTCGCTGCATCAATCCTAT 58.931 37.500 0.00 0.00 0.00 2.57
1975 2184 4.257731 TCCGCTGCAACAAATACAATCTA 58.742 39.130 0.00 0.00 0.00 1.98
1988 2197 1.078214 CAAGGGATCTCCGCTGCAA 60.078 57.895 0.00 0.00 41.52 4.08
1998 2207 1.024271 TAAAGCGCATGCAAGGGATC 58.976 50.000 19.57 0.00 46.23 3.36
2002 2211 0.243365 TTGGTAAAGCGCATGCAAGG 59.757 50.000 19.57 2.17 46.23 3.61
2025 2234 5.820423 TGGATAATTAGGGTCGTTGACATTG 59.180 40.000 0.00 0.00 33.68 2.82
2029 2238 3.800506 CGTGGATAATTAGGGTCGTTGAC 59.199 47.826 0.00 0.00 0.00 3.18
2059 2268 3.751246 CAGGGTTGGCATGGTGCG 61.751 66.667 0.00 0.00 46.21 5.34
2068 2277 1.962807 TGAAACAATCTGCAGGGTTGG 59.037 47.619 25.90 14.37 0.00 3.77
2073 2282 2.486982 CTGGACTGAAACAATCTGCAGG 59.513 50.000 15.13 0.00 32.82 4.85
2127 2336 4.320935 GCGACAAAACCATAAACATCCAGT 60.321 41.667 0.00 0.00 0.00 4.00
2191 2400 2.418334 GGTAGTCATCCCTTTCACGGTC 60.418 54.545 0.00 0.00 0.00 4.79
2278 2569 2.464157 AGCTGCTATTCTATTCCGGC 57.536 50.000 0.00 0.00 0.00 6.13
2280 2571 5.414454 ACTCTCTAGCTGCTATTCTATTCCG 59.586 44.000 10.23 0.00 0.00 4.30
2286 2577 9.898152 AAAATTAAACTCTCTAGCTGCTATTCT 57.102 29.630 10.23 0.00 0.00 2.40
2300 2591 9.546428 CAGGAACCAATTGAAAAATTAAACTCT 57.454 29.630 7.12 0.00 0.00 3.24
2306 3054 6.204495 GCTTGCAGGAACCAATTGAAAAATTA 59.796 34.615 7.12 0.00 0.00 1.40
2311 3059 2.699846 AGCTTGCAGGAACCAATTGAAA 59.300 40.909 7.12 0.00 0.00 2.69
2348 3096 8.506168 TTGAGATGGGAAGTAAACATGATAAC 57.494 34.615 0.00 0.00 0.00 1.89
2413 3161 5.414144 TGCCGATGACAAACATGAAATCTAA 59.586 36.000 0.00 0.00 39.56 2.10
2414 3162 4.940654 TGCCGATGACAAACATGAAATCTA 59.059 37.500 0.00 0.00 39.56 1.98
2415 3163 3.758023 TGCCGATGACAAACATGAAATCT 59.242 39.130 0.00 0.00 39.56 2.40
2416 3164 4.095410 TGCCGATGACAAACATGAAATC 57.905 40.909 0.00 0.00 39.56 2.17
2417 3165 4.724074 ATGCCGATGACAAACATGAAAT 57.276 36.364 0.00 0.00 39.56 2.17
2447 3195 4.829968 ACTTCATGATGGTGACTTGAGAG 58.170 43.478 12.76 0.00 0.00 3.20
2448 3196 4.897509 ACTTCATGATGGTGACTTGAGA 57.102 40.909 12.76 0.00 0.00 3.27
3032 3780 1.949525 TGCCAGACAGAAACTTTCAGC 59.050 47.619 4.34 0.00 0.00 4.26
3053 3801 1.507141 CTTCCTCACCAACACCGTGC 61.507 60.000 0.00 0.00 0.00 5.34
3109 5946 0.947244 AGTGCTTGTTTCAGCTTCCG 59.053 50.000 0.00 0.00 40.79 4.30
3228 6065 2.737252 GACTGTGACTTCCAACGATTCC 59.263 50.000 0.00 0.00 0.00 3.01
3298 6135 9.663904 TTTGATTATACTTGATCAATAAAGCGC 57.336 29.630 8.96 0.00 40.72 5.92
3349 8701 5.878116 TGACTCTATTTTTCATGTAACCCCG 59.122 40.000 0.00 0.00 0.00 5.73
3369 8721 5.387113 AGATCATGAGTCCTCTAGTGACT 57.613 43.478 14.71 14.71 45.47 3.41
3410 8762 7.803189 AGTCATGTAAATCGTTTGTTGAATGTC 59.197 33.333 0.00 0.00 0.00 3.06
3414 8766 9.658475 CTTTAGTCATGTAAATCGTTTGTTGAA 57.342 29.630 0.00 0.00 0.00 2.69
3430 8782 4.686091 TCTTGTCTGTTCGCTTTAGTCATG 59.314 41.667 0.00 0.00 0.00 3.07
3454 8806 2.028930 GTCAAGGAGTTGATGTCGGTCT 60.029 50.000 0.00 0.00 44.58 3.85
3463 8815 5.311265 TCTACTCGTAAGTCAAGGAGTTGA 58.689 41.667 4.74 5.83 40.69 3.18
3491 8843 2.352805 CAAGGCCCTCCGCTCTTT 59.647 61.111 0.00 0.00 37.74 2.52
3517 8869 1.594862 GCATTCTCCGTTGGAATCGAG 59.405 52.381 0.00 0.00 31.90 4.04
3798 9159 8.650143 TCTTATTCTCTGCTTGGGTAAAAATT 57.350 30.769 0.00 0.00 0.00 1.82
3839 9200 7.659799 ACCAGCAAAAATTGGAATTTAACTACC 59.340 33.333 0.00 0.00 37.62 3.18
3990 9387 0.735632 GCTGTCTCCGCTGAGTCAAG 60.736 60.000 4.97 3.21 36.45 3.02
3991 9388 1.290324 GCTGTCTCCGCTGAGTCAA 59.710 57.895 4.97 0.00 36.45 3.18
3999 9396 3.567797 GATTGCCGCTGTCTCCGC 61.568 66.667 0.00 0.00 0.00 5.54
4023 9420 1.141657 CTTCCCTGCTAAGCATAGGCA 59.858 52.381 0.67 0.00 44.61 4.75
4089 9486 6.183360 GCATCCGGTTTTTGTAATGATTCAAC 60.183 38.462 0.00 0.00 0.00 3.18
4098 9495 3.366883 GCATGAGCATCCGGTTTTTGTAA 60.367 43.478 0.00 0.00 41.58 2.41
4108 9505 0.463295 AAGTCCAGCATGAGCATCCG 60.463 55.000 0.00 0.00 45.49 4.18
4176 9573 7.274904 TCGAAATTTTACAACCTCTGATAGACG 59.725 37.037 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.