Multiple sequence alignment - TraesCS1B01G407000

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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 TraesCS1B01G407000 chr1B 100.000 2344 0 0 1 2344 634146479 634144136 0.000000e+00 4329.0
1 TraesCS1B01G407000 chr1B 100.000 399 0 0 2632 3030 634143848 634143450 0.000000e+00 737.0
2 TraesCS1B01G407000 chr1B 78.358 938 173 21 88 1022 634241769 634240859 5.630000e-162 580.0
3 TraesCS1B01G407000 chr1B 75.646 271 56 9 1123 1386 633980165 633979898 3.170000e-25 126.0
4 TraesCS1B01G407000 chr1B 77.500 200 29 8 1133 1321 636064805 636064999 4.130000e-19 106.0
5 TraesCS1B01G407000 chr1D 92.642 1427 72 6 85 1510 461380080 461378686 0.000000e+00 2023.0
6 TraesCS1B01G407000 chr1D 92.083 821 42 14 1524 2344 461377637 461376840 0.000000e+00 1134.0
7 TraesCS1B01G407000 chr1D 78.965 908 157 23 108 1009 461398254 461397375 3.370000e-164 588.0
8 TraesCS1B01G407000 chr1D 77.376 663 133 13 128 780 461952429 461953084 7.930000e-101 377.0
9 TraesCS1B01G407000 chr1D 75.200 250 58 4 440 687 461755416 461755663 6.860000e-22 115.0
10 TraesCS1B01G407000 chr1D 91.549 71 6 0 2960 3030 321929005 321929075 6.910000e-17 99.0
11 TraesCS1B01G407000 chr1A 93.552 822 50 1 69 890 552526405 552525587 0.000000e+00 1221.0
12 TraesCS1B01G407000 chr1A 81.510 1298 193 17 881 2176 552503406 552502154 0.000000e+00 1024.0
13 TraesCS1B01G407000 chr1A 79.383 907 155 21 108 1009 552892050 552891171 7.180000e-171 610.0
14 TraesCS1B01G407000 chr1A 75.212 944 190 27 84 1008 552387508 552386590 1.010000e-109 407.0
15 TraesCS1B01G407000 chr7D 77.971 345 59 9 2700 3030 3901986 3902327 1.840000e-47 200.0
16 TraesCS1B01G407000 chr4B 77.326 344 55 14 2701 3028 114484276 114484612 6.670000e-42 182.0
17 TraesCS1B01G407000 chr3D 85.393 89 7 6 2857 2941 536326251 536326165 1.500000e-13 87.9
18 TraesCS1B01G407000 chr6B 84.211 76 7 5 2873 2945 681360108 681360035 5.420000e-08 69.4
19 TraesCS1B01G407000 chr6B 85.714 56 6 2 2876 2930 165465740 165465794 1.170000e-04 58.4
20 TraesCS1B01G407000 chr3A 93.333 45 1 2 2898 2941 434923134 434923177 7.010000e-07 65.8
21 TraesCS1B01G407000 chr4A 83.077 65 9 2 2876 2939 724503775 724503712 1.170000e-04 58.4


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 TraesCS1B01G407000 chr1B 634143450 634146479 3029 True 2533.0 4329 100.0000 1 3030 2 chr1B.!!$R3 3029
1 TraesCS1B01G407000 chr1B 634240859 634241769 910 True 580.0 580 78.3580 88 1022 1 chr1B.!!$R2 934
2 TraesCS1B01G407000 chr1D 461376840 461380080 3240 True 1578.5 2023 92.3625 85 2344 2 chr1D.!!$R2 2259
3 TraesCS1B01G407000 chr1D 461397375 461398254 879 True 588.0 588 78.9650 108 1009 1 chr1D.!!$R1 901
4 TraesCS1B01G407000 chr1D 461952429 461953084 655 False 377.0 377 77.3760 128 780 1 chr1D.!!$F3 652
5 TraesCS1B01G407000 chr1A 552525587 552526405 818 True 1221.0 1221 93.5520 69 890 1 chr1A.!!$R3 821
6 TraesCS1B01G407000 chr1A 552502154 552503406 1252 True 1024.0 1024 81.5100 881 2176 1 chr1A.!!$R2 1295
7 TraesCS1B01G407000 chr1A 552891171 552892050 879 True 610.0 610 79.3830 108 1009 1 chr1A.!!$R4 901
8 TraesCS1B01G407000 chr1A 552386590 552387508 918 True 407.0 407 75.2120 84 1008 1 chr1A.!!$R1 924

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
856 893 0.320374 CTGCTCCTTCCGTTGTGGTA 59.68 55.0 0.0 0.0 39.52 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2290 3365 0.405852 AAAGGGGGAGGGGAAGGAAA 60.406 55.0 0.0 0.0 0.0 3.13 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
20 21 2.091541 ACAACAAGGCAATATGTCCCG 58.908 47.619 0.00 0.00 0.00 5.14
21 22 2.290641 ACAACAAGGCAATATGTCCCGA 60.291 45.455 0.00 0.00 0.00 5.14
22 23 2.332063 ACAAGGCAATATGTCCCGAG 57.668 50.000 0.00 0.00 0.00 4.63
23 24 1.837439 ACAAGGCAATATGTCCCGAGA 59.163 47.619 0.00 0.00 0.00 4.04
24 25 2.439507 ACAAGGCAATATGTCCCGAGAT 59.560 45.455 0.00 0.00 0.00 2.75
25 26 2.810274 CAAGGCAATATGTCCCGAGATG 59.190 50.000 0.00 0.00 0.00 2.90
26 27 1.160137 GGCAATATGTCCCGAGATGC 58.840 55.000 0.00 0.00 0.00 3.91
27 28 1.160137 GCAATATGTCCCGAGATGCC 58.840 55.000 0.00 0.00 0.00 4.40
28 29 1.813513 CAATATGTCCCGAGATGCCC 58.186 55.000 0.00 0.00 0.00 5.36
29 30 1.072173 CAATATGTCCCGAGATGCCCA 59.928 52.381 0.00 0.00 0.00 5.36
30 31 0.979665 ATATGTCCCGAGATGCCCAG 59.020 55.000 0.00 0.00 0.00 4.45
31 32 1.758440 TATGTCCCGAGATGCCCAGC 61.758 60.000 0.00 0.00 0.00 4.85
32 33 3.785859 GTCCCGAGATGCCCAGCA 61.786 66.667 0.00 0.00 44.86 4.41
33 34 3.008517 TCCCGAGATGCCCAGCAA 61.009 61.111 0.00 0.00 43.62 3.91
34 35 2.045045 CCCGAGATGCCCAGCAAA 60.045 61.111 0.00 0.00 43.62 3.68
35 36 1.678635 CCCGAGATGCCCAGCAAAA 60.679 57.895 0.00 0.00 43.62 2.44
36 37 1.039233 CCCGAGATGCCCAGCAAAAT 61.039 55.000 0.00 0.00 43.62 1.82
37 38 1.679139 CCGAGATGCCCAGCAAAATA 58.321 50.000 0.00 0.00 43.62 1.40
38 39 2.233271 CCGAGATGCCCAGCAAAATAT 58.767 47.619 0.00 0.00 43.62 1.28
39 40 2.030540 CCGAGATGCCCAGCAAAATATG 60.031 50.000 0.00 0.00 43.62 1.78
40 41 2.030540 CGAGATGCCCAGCAAAATATGG 60.031 50.000 0.00 0.00 43.62 2.74
41 42 3.225104 GAGATGCCCAGCAAAATATGGA 58.775 45.455 0.00 0.00 43.62 3.41
42 43 3.638160 GAGATGCCCAGCAAAATATGGAA 59.362 43.478 0.00 0.00 43.62 3.53
43 44 3.385755 AGATGCCCAGCAAAATATGGAAC 59.614 43.478 0.00 0.00 43.62 3.62
44 45 2.533916 TGCCCAGCAAAATATGGAACA 58.466 42.857 0.00 0.00 38.31 3.18
45 46 2.902486 TGCCCAGCAAAATATGGAACAA 59.098 40.909 0.00 0.00 37.54 2.83
46 47 3.055963 TGCCCAGCAAAATATGGAACAAG 60.056 43.478 0.00 0.00 37.54 3.16
47 48 5.298994 TGCCCAGCAAAATATGGAACAAGA 61.299 41.667 0.00 0.00 37.54 3.02
48 49 6.742132 TGCCCAGCAAAATATGGAACAAGAA 61.742 40.000 0.00 0.00 37.54 2.52
49 50 8.683360 TGCCCAGCAAAATATGGAACAAGAAC 62.683 42.308 0.00 0.00 37.54 3.01
63 64 1.605710 CAAGAACTTGTCTGCCACAGG 59.394 52.381 6.41 0.00 36.40 4.00
65 66 2.047061 AGAACTTGTCTGCCACAGGTA 58.953 47.619 1.65 0.00 44.34 3.08
66 67 2.639839 AGAACTTGTCTGCCACAGGTAT 59.360 45.455 1.65 0.00 44.34 2.73
67 68 3.838317 AGAACTTGTCTGCCACAGGTATA 59.162 43.478 1.65 0.00 44.34 1.47
81 82 7.180587 TGCCACAGGTATAATATTAATACGGGA 59.819 37.037 0.00 0.17 0.00 5.14
113 117 1.725164 GTGTTTGCCGTCAGCTACTAC 59.275 52.381 0.00 0.00 44.23 2.73
255 259 2.223829 ACGTTCCTGGAGATGCTATTCG 60.224 50.000 0.00 0.00 0.00 3.34
276 280 7.502177 TTCGAAACTTATACTCAACGATGAC 57.498 36.000 0.00 0.00 0.00 3.06
320 324 7.830099 AGAAATTTGAGAACAGAGAACCATT 57.170 32.000 0.00 0.00 0.00 3.16
798 814 5.056480 TCCTTGTGTATTATCGAATGCCTG 58.944 41.667 0.00 0.00 0.00 4.85
856 893 0.320374 CTGCTCCTTCCGTTGTGGTA 59.680 55.000 0.00 0.00 39.52 3.25
857 894 0.320374 TGCTCCTTCCGTTGTGGTAG 59.680 55.000 0.00 0.00 39.52 3.18
861 898 3.737355 GCTCCTTCCGTTGTGGTAGTATC 60.737 52.174 0.00 0.00 39.52 2.24
866 903 4.829872 TCCGTTGTGGTAGTATCCATTT 57.170 40.909 0.00 0.00 39.81 2.32
868 905 4.938832 TCCGTTGTGGTAGTATCCATTTTG 59.061 41.667 0.00 0.00 39.81 2.44
869 906 4.938832 CCGTTGTGGTAGTATCCATTTTGA 59.061 41.667 0.00 0.00 39.81 2.69
873 910 5.984725 TGTGGTAGTATCCATTTTGATCGT 58.015 37.500 0.00 0.00 39.81 3.73
892 929 7.691213 TGATCGTACCTAGATAGAAATCTCCT 58.309 38.462 0.00 0.00 41.71 3.69
1009 1046 1.153289 AGGCTTACCATGCGCTCTG 60.153 57.895 9.73 6.24 39.06 3.35
1048 1085 9.073475 GCCCTCTCCTACTATATATATTGTCAG 57.927 40.741 12.26 8.19 0.00 3.51
1049 1086 9.073475 CCCTCTCCTACTATATATATTGTCAGC 57.927 40.741 12.26 0.00 0.00 4.26
1050 1087 9.073475 CCTCTCCTACTATATATATTGTCAGCC 57.927 40.741 12.26 0.00 0.00 4.85
1051 1088 8.998277 TCTCCTACTATATATATTGTCAGCCC 57.002 38.462 12.26 0.00 0.00 5.19
1052 1089 8.792734 TCTCCTACTATATATATTGTCAGCCCT 58.207 37.037 12.26 0.00 0.00 5.19
1053 1090 9.427821 CTCCTACTATATATATTGTCAGCCCTT 57.572 37.037 12.26 0.00 0.00 3.95
1054 1091 9.784376 TCCTACTATATATATTGTCAGCCCTTT 57.216 33.333 12.26 0.00 0.00 3.11
1058 1095 8.812972 ACTATATATATTGTCAGCCCTTTTCGA 58.187 33.333 0.00 0.00 0.00 3.71
1059 1096 9.653287 CTATATATATTGTCAGCCCTTTTCGAA 57.347 33.333 0.00 0.00 0.00 3.71
1060 1097 8.918202 ATATATATTGTCAGCCCTTTTCGAAA 57.082 30.769 6.47 6.47 0.00 3.46
1061 1098 5.975693 ATATTGTCAGCCCTTTTCGAAAA 57.024 34.783 21.35 21.35 0.00 2.29
1062 1099 4.664150 ATTGTCAGCCCTTTTCGAAAAA 57.336 36.364 22.67 5.62 0.00 1.94
1143 1180 4.399934 ACAAACACAACGTTAATCTTGGGT 59.600 37.500 0.00 0.00 36.59 4.51
1251 1289 1.217882 CGGTCATATTCCCAAGCGAC 58.782 55.000 0.00 0.00 34.79 5.19
1334 1372 8.088365 CCTTCGTGTAAGTTGATATCCATATCA 58.912 37.037 5.32 5.32 39.01 2.15
1356 1394 5.877564 TCACTCGGAGCTATATATGTCTCTG 59.122 44.000 4.58 14.16 34.21 3.35
1376 1414 5.852827 TCTGTGTTGATGTATCACACTTGA 58.147 37.500 18.91 15.66 38.47 3.02
1391 1429 2.749621 CACTTGACAATGACTTAGGGGC 59.250 50.000 0.00 0.00 0.00 5.80
1409 1447 3.555586 GGGGCATTATGGCATCAATGTTC 60.556 47.826 20.08 15.78 45.76 3.18
1429 1467 6.601264 TGTTCATGTTACATATGCATATGCG 58.399 36.000 35.84 20.60 42.98 4.73
1430 1468 5.220557 TCATGTTACATATGCATATGCGC 57.779 39.130 35.84 27.15 42.98 6.09
1435 1473 2.507484 ACATATGCATATGCGCAGGTT 58.493 42.857 35.84 18.74 46.99 3.50
1443 1481 3.772932 CATATGCGCAGGTTCAACATTT 58.227 40.909 18.32 0.00 0.00 2.32
1446 1484 1.001487 TGCGCAGGTTCAACATTTCAG 60.001 47.619 5.66 0.00 0.00 3.02
1495 1533 3.005554 CAGTGGTGATGACAATGAGGAC 58.994 50.000 0.00 0.00 36.11 3.85
1520 1603 0.247537 TGACGATGATGACGACGACG 60.248 55.000 5.58 5.58 45.75 5.12
1522 1605 1.062047 CGATGATGACGACGACGGT 59.938 57.895 12.58 0.00 44.46 4.83
1542 2615 1.554617 TGGTGATGATGACGGTGACAT 59.445 47.619 0.00 0.00 0.00 3.06
1563 2636 1.369091 GACGATGATGGTGGTGGTGC 61.369 60.000 0.00 0.00 0.00 5.01
1565 2638 1.371337 CGATGATGGTGGTGGTGCTG 61.371 60.000 0.00 0.00 0.00 4.41
1566 2639 1.660560 GATGATGGTGGTGGTGCTGC 61.661 60.000 0.00 0.00 0.00 5.25
1567 2640 2.034687 GATGGTGGTGGTGCTGCT 59.965 61.111 0.00 0.00 0.00 4.24
1568 2641 2.282674 ATGGTGGTGGTGCTGCTG 60.283 61.111 0.00 0.00 0.00 4.41
1570 2643 4.962836 GGTGGTGGTGCTGCTGCT 62.963 66.667 17.00 0.00 40.48 4.24
1571 2644 3.667282 GTGGTGGTGCTGCTGCTG 61.667 66.667 17.00 0.77 40.48 4.41
1572 2645 4.960866 TGGTGGTGCTGCTGCTGG 62.961 66.667 17.00 0.00 40.48 4.85
1573 2646 4.648626 GGTGGTGCTGCTGCTGGA 62.649 66.667 17.00 2.36 40.48 3.86
1588 2661 2.631545 TGCTGGAGATGATGATGACGAT 59.368 45.455 0.00 0.00 0.00 3.73
1594 2667 4.447054 GGAGATGATGATGACGATGACAAC 59.553 45.833 0.00 0.00 0.00 3.32
1600 2673 2.159435 TGATGACGATGACAACGACGAT 60.159 45.455 12.41 2.80 34.70 3.73
1601 2674 1.613270 TGACGATGACAACGACGATG 58.387 50.000 12.41 1.72 34.70 3.84
1602 2675 1.198178 TGACGATGACAACGACGATGA 59.802 47.619 12.41 0.00 34.70 2.92
1610 2683 0.561593 CAACGACGATGACGATGACG 59.438 55.000 0.00 0.00 42.66 4.35
1613 2686 1.247261 CGACGATGACGATGACGACG 61.247 60.000 0.00 0.00 42.66 5.12
1615 2688 0.247576 ACGATGACGATGACGACGAC 60.248 55.000 0.00 0.00 42.66 4.34
1626 2699 1.329599 TGACGACGACGATGGTGATAG 59.670 52.381 15.32 0.00 42.66 2.08
1627 2700 0.029035 ACGACGACGATGGTGATAGC 59.971 55.000 15.32 0.00 42.66 2.97
1628 2701 0.992263 CGACGACGATGGTGATAGCG 60.992 60.000 0.00 0.00 42.66 4.26
1639 2712 3.230976 TGGTGATAGCGATAGTGATGGT 58.769 45.455 0.00 0.00 39.35 3.55
1640 2713 3.005791 TGGTGATAGCGATAGTGATGGTG 59.994 47.826 0.00 0.00 39.35 4.17
1641 2714 3.255888 GGTGATAGCGATAGTGATGGTGA 59.744 47.826 0.00 0.00 39.35 4.02
1642 2715 4.081972 GGTGATAGCGATAGTGATGGTGAT 60.082 45.833 0.00 0.00 39.35 3.06
1643 2716 4.861462 GTGATAGCGATAGTGATGGTGATG 59.139 45.833 0.00 0.00 39.35 3.07
1644 2717 2.827800 AGCGATAGTGATGGTGATGG 57.172 50.000 0.00 0.00 39.35 3.51
1685 2758 3.243737 CCATGACGACAAATATCCGAGGA 60.244 47.826 0.00 0.00 0.00 3.71
1779 2852 2.502947 TCACCATCCACATCCTCAAGAG 59.497 50.000 0.00 0.00 0.00 2.85
1910 2983 3.097877 TGAGCAATACGGCTATCACAG 57.902 47.619 0.00 0.00 45.99 3.66
2034 3107 0.037975 AACCGCCGACGTTAGATTGT 60.038 50.000 0.00 0.00 37.70 2.71
2137 3210 5.332355 GCACGTCTACTGTTTAAAGTCTGTG 60.332 44.000 0.00 0.00 0.00 3.66
2198 3273 2.222027 AGCTTGGACGACCTTTTCTTG 58.778 47.619 5.33 0.00 37.04 3.02
2229 3304 3.765026 TGCTGAAAACAGAACGAAAACC 58.235 40.909 0.00 0.00 0.00 3.27
2243 3318 1.668751 GAAAACCGCTGCCATCGATAA 59.331 47.619 0.00 0.00 0.00 1.75
2249 3324 1.602920 CGCTGCCATCGATAACTGCTA 60.603 52.381 19.48 4.76 0.00 3.49
2257 3332 2.888594 TCGATAACTGCTACAACTGGC 58.111 47.619 0.00 0.00 0.00 4.85
2268 3343 3.782443 AACTGGCGGACCGGATCC 61.782 66.667 17.22 10.97 46.41 3.36
2275 3350 3.367725 GGACCGGATCCGATCTCC 58.632 66.667 35.42 27.58 42.83 3.71
2276 3351 1.228613 GGACCGGATCCGATCTCCT 60.229 63.158 35.42 9.72 42.83 3.69
2277 3352 1.245376 GGACCGGATCCGATCTCCTC 61.245 65.000 35.42 11.40 42.83 3.71
2280 3355 1.979693 CGGATCCGATCTCCTCCCC 60.980 68.421 30.62 0.00 42.83 4.81
2307 3382 1.230314 CTTTCCTTCCCCTCCCCCT 60.230 63.158 0.00 0.00 0.00 4.79
2315 3390 0.503805 TCCCCTCCCCCTTTTTCCTA 59.496 55.000 0.00 0.00 0.00 2.94
2648 3723 2.445654 CTCTCCCAGCCCTCCTCC 60.446 72.222 0.00 0.00 0.00 4.30
2649 3724 4.095400 TCTCCCAGCCCTCCTCCC 62.095 72.222 0.00 0.00 0.00 4.30
2650 3725 4.101077 CTCCCAGCCCTCCTCCCT 62.101 72.222 0.00 0.00 0.00 4.20
2651 3726 4.421554 TCCCAGCCCTCCTCCCTG 62.422 72.222 0.00 0.00 0.00 4.45
2652 3727 4.748798 CCCAGCCCTCCTCCCTGT 62.749 72.222 0.00 0.00 0.00 4.00
2653 3728 3.086600 CCAGCCCTCCTCCCTGTC 61.087 72.222 0.00 0.00 0.00 3.51
2654 3729 3.465403 CAGCCCTCCTCCCTGTCG 61.465 72.222 0.00 0.00 0.00 4.35
2655 3730 3.673597 AGCCCTCCTCCCTGTCGA 61.674 66.667 0.00 0.00 0.00 4.20
2656 3731 2.444895 GCCCTCCTCCCTGTCGAT 60.445 66.667 0.00 0.00 0.00 3.59
2657 3732 2.503382 GCCCTCCTCCCTGTCGATC 61.503 68.421 0.00 0.00 0.00 3.69
2658 3733 1.834822 CCCTCCTCCCTGTCGATCC 60.835 68.421 0.00 0.00 0.00 3.36
2659 3734 1.834822 CCTCCTCCCTGTCGATCCC 60.835 68.421 0.00 0.00 0.00 3.85
2660 3735 1.834822 CTCCTCCCTGTCGATCCCC 60.835 68.421 0.00 0.00 0.00 4.81
2661 3736 2.844839 CCTCCCTGTCGATCCCCC 60.845 72.222 0.00 0.00 0.00 5.40
2685 3760 2.681064 CCGTTCCACCGGGTCCTA 60.681 66.667 6.32 0.00 44.32 2.94
2686 3761 2.575461 CGTTCCACCGGGTCCTAC 59.425 66.667 6.32 0.00 34.93 3.18
2687 3762 2.984623 GTTCCACCGGGTCCTACC 59.015 66.667 6.32 0.00 37.60 3.18
2696 3771 4.091939 GGTCCTACCCGTGCCACC 62.092 72.222 0.00 0.00 30.04 4.61
2697 3772 4.091939 GTCCTACCCGTGCCACCC 62.092 72.222 0.00 0.00 0.00 4.61
2698 3773 4.326227 TCCTACCCGTGCCACCCT 62.326 66.667 0.00 0.00 0.00 4.34
2699 3774 4.096003 CCTACCCGTGCCACCCTG 62.096 72.222 0.00 0.00 0.00 4.45
2700 3775 4.096003 CTACCCGTGCCACCCTGG 62.096 72.222 0.00 0.00 41.55 4.45
2768 3843 4.778415 CCTCTGACGACGGCGGTG 62.778 72.222 18.49 7.05 43.17 4.94
2769 3844 4.039357 CTCTGACGACGGCGGTGT 62.039 66.667 18.49 9.22 43.17 4.16
2770 3845 3.553437 CTCTGACGACGGCGGTGTT 62.553 63.158 18.49 0.00 43.17 3.32
2771 3846 3.403057 CTGACGACGGCGGTGTTG 61.403 66.667 18.49 0.00 43.17 3.33
2776 3851 3.414700 GACGGCGGTGTTGCTCAG 61.415 66.667 13.24 0.00 34.52 3.35
2779 3854 3.730761 GGCGGTGTTGCTCAGCTG 61.731 66.667 7.63 7.63 41.76 4.24
2780 3855 3.730761 GCGGTGTTGCTCAGCTGG 61.731 66.667 15.13 5.82 41.76 4.85
2781 3856 3.730761 CGGTGTTGCTCAGCTGGC 61.731 66.667 15.13 16.41 41.76 4.85
2782 3857 2.595463 GGTGTTGCTCAGCTGGCA 60.595 61.111 21.35 21.35 40.87 4.92
2783 3858 2.623915 GGTGTTGCTCAGCTGGCAG 61.624 63.158 23.11 10.94 40.90 4.85
2784 3859 2.981909 TGTTGCTCAGCTGGCAGC 60.982 61.111 31.56 31.56 42.84 5.25
2820 3895 2.815211 CGATCCCGTGTGCCACAG 60.815 66.667 0.00 0.00 33.40 3.66
2821 3896 2.436646 GATCCCGTGTGCCACAGG 60.437 66.667 10.48 10.48 33.55 4.00
2822 3897 3.249189 ATCCCGTGTGCCACAGGT 61.249 61.111 15.61 0.00 33.93 4.00
2823 3898 3.551496 ATCCCGTGTGCCACAGGTG 62.551 63.158 15.61 5.27 33.93 4.00
2827 3902 4.586235 GTGTGCCACAGGTGCCCT 62.586 66.667 0.00 0.00 34.08 5.19
2828 3903 3.819652 TGTGCCACAGGTGCCCTT 61.820 61.111 0.00 0.00 0.00 3.95
2829 3904 3.297620 GTGCCACAGGTGCCCTTG 61.298 66.667 0.00 0.00 0.00 3.61
2830 3905 3.497115 TGCCACAGGTGCCCTTGA 61.497 61.111 0.00 0.00 0.00 3.02
2831 3906 2.985847 GCCACAGGTGCCCTTGAC 60.986 66.667 0.00 0.00 0.00 3.18
2832 3907 2.669569 CCACAGGTGCCCTTGACG 60.670 66.667 0.00 0.00 0.00 4.35
2833 3908 3.357079 CACAGGTGCCCTTGACGC 61.357 66.667 0.00 0.00 0.00 5.19
2834 3909 4.988598 ACAGGTGCCCTTGACGCG 62.989 66.667 3.53 3.53 0.00 6.01
2838 3913 4.980805 GTGCCCTTGACGCGGTGA 62.981 66.667 12.47 0.00 0.00 4.02
2839 3914 4.980805 TGCCCTTGACGCGGTGAC 62.981 66.667 12.47 0.00 0.00 3.67
2905 3980 4.598894 CCGCTCGGGCCAGATCTG 62.599 72.222 16.24 16.24 34.44 2.90
2915 3990 2.892025 CCAGATCTGGGCCCTTTTG 58.108 57.895 31.14 12.87 46.81 2.44
2916 3991 0.685458 CCAGATCTGGGCCCTTTTGG 60.685 60.000 31.14 17.87 46.81 3.28
2928 4003 1.780503 CCTTTTGGGCCCAATCTAGG 58.219 55.000 37.41 33.48 35.70 3.02
2929 4004 1.007118 CCTTTTGGGCCCAATCTAGGT 59.993 52.381 37.41 0.00 35.70 3.08
2930 4005 2.559705 CCTTTTGGGCCCAATCTAGGTT 60.560 50.000 37.41 0.00 35.70 3.50
2931 4006 2.230130 TTTGGGCCCAATCTAGGTTG 57.770 50.000 37.41 8.89 35.70 3.77
2932 4007 0.334676 TTGGGCCCAATCTAGGTTGG 59.665 55.000 34.07 25.61 46.58 3.77
2937 4012 3.780624 CCAATCTAGGTTGGGACGG 57.219 57.895 24.99 0.61 43.94 4.79
2938 4013 0.180406 CCAATCTAGGTTGGGACGGG 59.820 60.000 24.99 0.00 43.94 5.28
2939 4014 0.463833 CAATCTAGGTTGGGACGGGC 60.464 60.000 7.93 0.00 0.00 6.13
2940 4015 1.632965 AATCTAGGTTGGGACGGGCC 61.633 60.000 0.00 0.00 0.00 5.80
2941 4016 4.157120 CTAGGTTGGGACGGGCCG 62.157 72.222 27.06 27.06 37.63 6.13
2957 4032 4.260355 CGGCGGCATTGCTCCATG 62.260 66.667 10.53 0.00 34.52 3.66
2958 4033 3.908081 GGCGGCATTGCTCCATGG 61.908 66.667 4.97 4.97 34.52 3.66
2959 4034 3.142838 GCGGCATTGCTCCATGGT 61.143 61.111 12.58 0.00 0.00 3.55
2960 4035 2.802792 CGGCATTGCTCCATGGTG 59.197 61.111 12.58 10.95 0.00 4.17
2961 4036 2.777972 CGGCATTGCTCCATGGTGG 61.778 63.158 12.58 7.36 39.43 4.61
2962 4037 1.683365 GGCATTGCTCCATGGTGGT 60.683 57.895 12.58 0.00 39.03 4.16
2963 4038 1.514087 GCATTGCTCCATGGTGGTG 59.486 57.895 12.58 6.35 39.03 4.17
2964 4039 1.952102 GCATTGCTCCATGGTGGTGG 61.952 60.000 12.58 0.00 39.03 4.61
2965 4040 0.612732 CATTGCTCCATGGTGGTGGT 60.613 55.000 12.58 0.00 39.03 4.16
2966 4041 0.612732 ATTGCTCCATGGTGGTGGTG 60.613 55.000 12.58 0.00 39.03 4.17
2967 4042 2.361610 GCTCCATGGTGGTGGTGG 60.362 66.667 12.58 0.00 39.03 4.61
2968 4043 2.361610 CTCCATGGTGGTGGTGGC 60.362 66.667 12.58 0.00 39.03 5.01
2969 4044 4.343323 TCCATGGTGGTGGTGGCG 62.343 66.667 12.58 0.00 39.03 5.69
2970 4045 4.343323 CCATGGTGGTGGTGGCGA 62.343 66.667 2.57 0.00 34.46 5.54
2971 4046 2.747460 CATGGTGGTGGTGGCGAG 60.747 66.667 0.00 0.00 0.00 5.03
2972 4047 4.033776 ATGGTGGTGGTGGCGAGG 62.034 66.667 0.00 0.00 0.00 4.63
2985 4060 4.778415 CGAGGCGTCGGTGGTCTG 62.778 72.222 20.58 0.00 42.87 3.51
3003 4078 3.726517 CAGGCGGTGCAGGTTTCG 61.727 66.667 0.00 0.00 0.00 3.46
3004 4079 4.250305 AGGCGGTGCAGGTTTCGT 62.250 61.111 0.00 0.00 0.00 3.85
3005 4080 3.284449 GGCGGTGCAGGTTTCGTT 61.284 61.111 0.00 0.00 0.00 3.85
3006 4081 2.051345 GCGGTGCAGGTTTCGTTG 60.051 61.111 0.00 0.00 0.00 4.10
3007 4082 2.637025 CGGTGCAGGTTTCGTTGG 59.363 61.111 0.00 0.00 0.00 3.77
3008 4083 2.335011 GGTGCAGGTTTCGTTGGC 59.665 61.111 0.00 0.00 0.00 4.52
3009 4084 2.335011 GTGCAGGTTTCGTTGGCC 59.665 61.111 0.00 0.00 0.00 5.36
3010 4085 2.124109 TGCAGGTTTCGTTGGCCA 60.124 55.556 0.00 0.00 0.00 5.36
3011 4086 2.192861 TGCAGGTTTCGTTGGCCAG 61.193 57.895 5.11 0.00 0.00 4.85
3012 4087 2.644992 CAGGTTTCGTTGGCCAGC 59.355 61.111 10.00 10.00 0.00 4.85
3013 4088 2.978010 AGGTTTCGTTGGCCAGCG 60.978 61.111 33.34 33.34 36.35 5.18
3014 4089 3.284449 GGTTTCGTTGGCCAGCGT 61.284 61.111 36.06 0.00 36.41 5.07
3015 4090 2.051345 GTTTCGTTGGCCAGCGTG 60.051 61.111 36.06 14.49 36.41 5.34
3016 4091 3.959975 TTTCGTTGGCCAGCGTGC 61.960 61.111 36.06 11.74 36.41 5.34
3017 4092 4.927782 TTCGTTGGCCAGCGTGCT 62.928 61.111 36.06 0.00 36.41 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.091541 CGGGACATATTGCCTTGTTGT 58.908 47.619 0.00 0.00 31.97 3.32
1 2 2.355756 CTCGGGACATATTGCCTTGTTG 59.644 50.000 0.00 0.00 31.97 3.33
3 4 1.837439 TCTCGGGACATATTGCCTTGT 59.163 47.619 0.00 0.00 31.97 3.16
4 5 2.620251 TCTCGGGACATATTGCCTTG 57.380 50.000 0.00 0.00 31.97 3.61
5 6 2.811873 GCATCTCGGGACATATTGCCTT 60.812 50.000 0.00 0.00 31.97 4.35
6 7 1.271054 GCATCTCGGGACATATTGCCT 60.271 52.381 0.00 0.00 31.97 4.75
8 9 1.160137 GGCATCTCGGGACATATTGC 58.840 55.000 0.00 0.00 0.00 3.56
9 10 1.072173 TGGGCATCTCGGGACATATTG 59.928 52.381 0.00 0.00 0.00 1.90
10 11 1.349026 CTGGGCATCTCGGGACATATT 59.651 52.381 0.00 0.00 0.00 1.28
11 12 0.979665 CTGGGCATCTCGGGACATAT 59.020 55.000 0.00 0.00 0.00 1.78
12 13 1.758440 GCTGGGCATCTCGGGACATA 61.758 60.000 0.00 0.00 0.00 2.29
13 14 3.112205 GCTGGGCATCTCGGGACAT 62.112 63.158 0.00 0.00 0.00 3.06
14 15 3.785859 GCTGGGCATCTCGGGACA 61.786 66.667 0.00 0.00 0.00 4.02
15 16 2.819984 TTTGCTGGGCATCTCGGGAC 62.820 60.000 0.00 0.00 38.76 4.46
16 17 2.135903 TTTTGCTGGGCATCTCGGGA 62.136 55.000 0.00 0.00 38.76 5.14
17 18 1.039233 ATTTTGCTGGGCATCTCGGG 61.039 55.000 0.00 0.00 38.76 5.14
18 19 1.679139 TATTTTGCTGGGCATCTCGG 58.321 50.000 0.00 0.00 38.76 4.63
19 20 2.030540 CCATATTTTGCTGGGCATCTCG 60.031 50.000 0.00 0.00 38.76 4.04
20 21 3.225104 TCCATATTTTGCTGGGCATCTC 58.775 45.455 0.00 0.00 38.76 2.75
21 22 3.317455 TCCATATTTTGCTGGGCATCT 57.683 42.857 0.00 0.00 38.76 2.90
22 23 3.132646 TGTTCCATATTTTGCTGGGCATC 59.867 43.478 0.00 0.00 38.76 3.91
23 24 3.106054 TGTTCCATATTTTGCTGGGCAT 58.894 40.909 0.00 0.00 38.76 4.40
24 25 2.533916 TGTTCCATATTTTGCTGGGCA 58.466 42.857 0.00 0.00 36.47 5.36
25 26 3.195396 TCTTGTTCCATATTTTGCTGGGC 59.805 43.478 0.00 0.00 33.13 5.36
26 27 5.047092 AGTTCTTGTTCCATATTTTGCTGGG 60.047 40.000 0.00 0.00 33.13 4.45
27 28 6.029346 AGTTCTTGTTCCATATTTTGCTGG 57.971 37.500 0.00 0.00 0.00 4.85
28 29 6.925165 ACAAGTTCTTGTTCCATATTTTGCTG 59.075 34.615 11.75 0.00 0.00 4.41
29 30 7.014615 AGACAAGTTCTTGTTCCATATTTTGCT 59.985 33.333 17.44 4.95 34.90 3.91
30 31 7.115378 CAGACAAGTTCTTGTTCCATATTTTGC 59.885 37.037 17.44 3.03 34.90 3.68
31 32 7.115378 GCAGACAAGTTCTTGTTCCATATTTTG 59.885 37.037 17.44 7.97 34.90 2.44
32 33 7.147976 GCAGACAAGTTCTTGTTCCATATTTT 58.852 34.615 17.44 0.00 34.90 1.82
33 34 6.294731 GGCAGACAAGTTCTTGTTCCATATTT 60.295 38.462 17.44 0.00 34.90 1.40
34 35 5.183904 GGCAGACAAGTTCTTGTTCCATATT 59.816 40.000 17.44 0.00 34.90 1.28
35 36 4.702131 GGCAGACAAGTTCTTGTTCCATAT 59.298 41.667 17.44 0.00 34.90 1.78
36 37 4.072131 GGCAGACAAGTTCTTGTTCCATA 58.928 43.478 17.44 0.00 34.90 2.74
37 38 2.887152 GGCAGACAAGTTCTTGTTCCAT 59.113 45.455 17.44 4.40 34.90 3.41
38 39 2.297701 GGCAGACAAGTTCTTGTTCCA 58.702 47.619 17.44 0.00 34.90 3.53
39 40 2.033424 GTGGCAGACAAGTTCTTGTTCC 59.967 50.000 17.44 17.32 34.90 3.62
40 41 2.682856 TGTGGCAGACAAGTTCTTGTTC 59.317 45.455 17.44 11.46 34.90 3.18
41 42 2.684881 CTGTGGCAGACAAGTTCTTGTT 59.315 45.455 17.44 6.98 34.90 2.83
42 43 2.292267 CTGTGGCAGACAAGTTCTTGT 58.708 47.619 16.56 16.56 37.97 3.16
43 44 1.605710 CCTGTGGCAGACAAGTTCTTG 59.394 52.381 10.50 10.50 32.80 3.02
44 45 1.212935 ACCTGTGGCAGACAAGTTCTT 59.787 47.619 0.00 0.00 32.80 2.52
45 46 0.839946 ACCTGTGGCAGACAAGTTCT 59.160 50.000 0.00 0.00 32.80 3.01
46 47 2.543777 TACCTGTGGCAGACAAGTTC 57.456 50.000 0.00 0.00 31.38 3.01
47 48 4.634012 TTATACCTGTGGCAGACAAGTT 57.366 40.909 0.00 0.00 31.38 2.66
48 49 4.844349 ATTATACCTGTGGCAGACAAGT 57.156 40.909 0.00 0.00 33.58 3.16
49 50 8.902540 TTAATATTATACCTGTGGCAGACAAG 57.097 34.615 0.00 0.00 32.80 3.16
51 52 9.938280 GTATTAATATTATACCTGTGGCAGACA 57.062 33.333 0.00 0.00 32.44 3.41
52 53 9.084164 CGTATTAATATTATACCTGTGGCAGAC 57.916 37.037 0.00 0.00 32.44 3.51
53 54 8.255206 CCGTATTAATATTATACCTGTGGCAGA 58.745 37.037 0.00 0.00 32.44 4.26
54 55 7.494625 CCCGTATTAATATTATACCTGTGGCAG 59.505 40.741 0.00 0.00 0.00 4.85
55 56 7.180587 TCCCGTATTAATATTATACCTGTGGCA 59.819 37.037 0.00 0.00 0.00 4.92
56 57 7.493645 GTCCCGTATTAATATTATACCTGTGGC 59.506 40.741 0.00 0.00 0.00 5.01
57 58 8.755977 AGTCCCGTATTAATATTATACCTGTGG 58.244 37.037 0.00 0.00 0.00 4.17
58 59 9.582431 CAGTCCCGTATTAATATTATACCTGTG 57.418 37.037 0.00 0.00 0.00 3.66
59 60 9.537852 TCAGTCCCGTATTAATATTATACCTGT 57.462 33.333 0.00 0.00 0.00 4.00
76 77 2.650322 ACACAACAAAATCAGTCCCGT 58.350 42.857 0.00 0.00 0.00 5.28
81 82 3.186119 CGGCAAACACAACAAAATCAGT 58.814 40.909 0.00 0.00 0.00 3.41
255 259 7.328737 AGTGTGTCATCGTTGAGTATAAGTTTC 59.671 37.037 0.00 0.00 30.85 2.78
290 294 7.251704 TCTCTGTTCTCAAATTTCTTGTCAC 57.748 36.000 0.00 0.00 0.00 3.67
320 324 3.680490 TGGCCAACTTTGTCGATGATAA 58.320 40.909 0.61 0.00 0.00 1.75
393 397 2.747855 CCGCAAGAGCCAAGGTCC 60.748 66.667 0.00 0.00 43.02 4.46
798 814 0.103208 CTACCACCTGGAGCATCGTC 59.897 60.000 0.00 0.00 38.94 4.20
856 893 7.834881 TCTAGGTACGATCAAAATGGATACT 57.165 36.000 0.00 0.00 37.61 2.12
857 894 9.790389 CTATCTAGGTACGATCAAAATGGATAC 57.210 37.037 0.00 0.00 0.00 2.24
861 898 9.712305 ATTTCTATCTAGGTACGATCAAAATGG 57.288 33.333 0.00 0.00 0.00 3.16
866 903 8.164733 AGGAGATTTCTATCTAGGTACGATCAA 58.835 37.037 0.00 0.00 41.23 2.57
868 905 7.281549 GGAGGAGATTTCTATCTAGGTACGATC 59.718 44.444 0.00 0.00 41.23 3.69
869 906 7.114095 GGAGGAGATTTCTATCTAGGTACGAT 58.886 42.308 0.00 0.00 41.23 3.73
873 910 6.566870 TCCTGGAGGAGATTTCTATCTAGGTA 59.433 42.308 17.20 0.00 41.23 3.08
1334 1372 5.645929 CACAGAGACATATATAGCTCCGAGT 59.354 44.000 0.00 5.20 0.00 4.18
1356 1394 5.922739 TGTCAAGTGTGATACATCAACAC 57.077 39.130 12.86 12.86 38.75 3.32
1376 1414 4.473444 CCATAATGCCCCTAAGTCATTGT 58.527 43.478 0.00 0.00 33.13 2.71
1391 1429 7.921745 TGTAACATGAACATTGATGCCATAATG 59.078 33.333 0.00 0.00 39.55 1.90
1409 1447 4.972201 TGCGCATATGCATATGTAACATG 58.028 39.130 35.50 23.02 41.63 3.21
1429 1467 4.874970 ACAATCTGAAATGTTGAACCTGC 58.125 39.130 0.00 0.00 0.00 4.85
1430 1468 7.206981 AGTACAATCTGAAATGTTGAACCTG 57.793 36.000 5.03 0.00 0.00 4.00
1487 1525 3.119137 TCATCGTCATTGTCGTCCTCATT 60.119 43.478 3.38 0.00 0.00 2.57
1495 1533 2.214244 GTCGTCATCATCGTCATTGTCG 59.786 50.000 0.00 0.00 0.00 4.35
1520 1603 0.249120 TCACCGTCATCATCACCACC 59.751 55.000 0.00 0.00 0.00 4.61
1522 1605 0.972883 TGTCACCGTCATCATCACCA 59.027 50.000 0.00 0.00 0.00 4.17
1542 2615 1.254975 ACCACCACCATCATCGTCGA 61.255 55.000 0.00 0.00 0.00 4.20
1563 2636 2.147150 CATCATCATCTCCAGCAGCAG 58.853 52.381 0.00 0.00 0.00 4.24
1565 2638 2.144730 GTCATCATCATCTCCAGCAGC 58.855 52.381 0.00 0.00 0.00 5.25
1566 2639 2.035576 TCGTCATCATCATCTCCAGCAG 59.964 50.000 0.00 0.00 0.00 4.24
1567 2640 2.034124 TCGTCATCATCATCTCCAGCA 58.966 47.619 0.00 0.00 0.00 4.41
1568 2641 2.808523 TCGTCATCATCATCTCCAGC 57.191 50.000 0.00 0.00 0.00 4.85
1569 2642 4.236147 GTCATCGTCATCATCATCTCCAG 58.764 47.826 0.00 0.00 0.00 3.86
1570 2643 3.638160 TGTCATCGTCATCATCATCTCCA 59.362 43.478 0.00 0.00 0.00 3.86
1571 2644 4.248691 TGTCATCGTCATCATCATCTCC 57.751 45.455 0.00 0.00 0.00 3.71
1572 2645 4.147826 CGTTGTCATCGTCATCATCATCTC 59.852 45.833 0.00 0.00 0.00 2.75
1573 2646 4.047142 CGTTGTCATCGTCATCATCATCT 58.953 43.478 0.00 0.00 0.00 2.90
1588 2661 1.198178 TCATCGTCATCGTCGTTGTCA 59.802 47.619 3.38 0.00 38.33 3.58
1594 2667 1.247261 CGTCGTCATCGTCATCGTCG 61.247 60.000 0.00 0.00 38.33 5.12
1600 2673 0.247537 CATCGTCGTCGTCATCGTCA 60.248 55.000 1.33 0.00 38.33 4.35
1601 2674 0.924363 CCATCGTCGTCGTCATCGTC 60.924 60.000 1.33 0.00 38.33 4.20
1602 2675 1.062047 CCATCGTCGTCGTCATCGT 59.938 57.895 1.33 0.00 38.33 3.73
1610 2683 0.306840 TCGCTATCACCATCGTCGTC 59.693 55.000 0.00 0.00 0.00 4.20
1613 2686 3.188667 TCACTATCGCTATCACCATCGTC 59.811 47.826 0.00 0.00 0.00 4.20
1615 2688 3.831715 TCACTATCGCTATCACCATCG 57.168 47.619 0.00 0.00 0.00 3.84
1626 2699 2.138320 CACCATCACCATCACTATCGC 58.862 52.381 0.00 0.00 0.00 4.58
1627 2700 3.733443 TCACCATCACCATCACTATCG 57.267 47.619 0.00 0.00 0.00 2.92
1628 2701 5.219343 TCATCACCATCACCATCACTATC 57.781 43.478 0.00 0.00 0.00 2.08
1639 2712 6.882678 GGTCATCATTATCATCATCACCATCA 59.117 38.462 0.00 0.00 0.00 3.07
1640 2713 6.882678 TGGTCATCATTATCATCATCACCATC 59.117 38.462 0.00 0.00 0.00 3.51
1641 2714 6.786122 TGGTCATCATTATCATCATCACCAT 58.214 36.000 0.00 0.00 0.00 3.55
1642 2715 6.190346 TGGTCATCATTATCATCATCACCA 57.810 37.500 0.00 0.00 0.00 4.17
1643 2716 6.882678 TCATGGTCATCATTATCATCATCACC 59.117 38.462 0.00 0.00 32.92 4.02
1644 2717 7.412672 CGTCATGGTCATCATTATCATCATCAC 60.413 40.741 0.00 0.00 32.92 3.06
1685 2758 0.969149 TGCTGACACTCCATCTTCGT 59.031 50.000 0.00 0.00 0.00 3.85
1738 2811 1.377366 GCTCGATCAGGGAGTGTCGA 61.377 60.000 0.00 0.00 36.79 4.20
1779 2852 3.558411 GCTCGAGTGATGGTGCGC 61.558 66.667 15.13 0.00 0.00 6.09
1813 2886 3.069729 ACCTCCTATCATAGCCGTTTGTC 59.930 47.826 0.00 0.00 0.00 3.18
1825 2898 1.891933 TGCCATCCAACCTCCTATCA 58.108 50.000 0.00 0.00 0.00 2.15
1858 2931 2.892640 CCAATCTCCGTCGAGGCA 59.107 61.111 0.00 0.00 40.77 4.75
1944 3017 1.303317 GGAACCCTCGGTGCAATGT 60.303 57.895 0.00 0.00 35.34 2.71
2023 3096 1.153353 CACCGGCAACAATCTAACGT 58.847 50.000 0.00 0.00 0.00 3.99
2034 3107 2.083774 GATGAAGAATCACACCGGCAA 58.916 47.619 0.00 0.00 38.69 4.52
2137 3210 7.985634 AATATTATTGTTCAACATTGCGGTC 57.014 32.000 0.00 0.00 0.00 4.79
2198 3273 1.134848 TGTTTTCAGCAAGCCAACCAC 60.135 47.619 0.00 0.00 0.00 4.16
2229 3304 0.877649 AGCAGTTATCGATGGCAGCG 60.878 55.000 20.57 20.57 0.00 5.18
2243 3318 1.004918 GTCCGCCAGTTGTAGCAGT 60.005 57.895 0.00 0.00 0.00 4.40
2249 3324 3.310860 GATCCGGTCCGCCAGTTGT 62.311 63.158 5.50 0.00 34.09 3.32
2287 3362 1.230182 GGGGAGGGGAAGGAAAGGA 60.230 63.158 0.00 0.00 0.00 3.36
2290 3365 0.405852 AAAGGGGGAGGGGAAGGAAA 60.406 55.000 0.00 0.00 0.00 3.13
2307 3382 2.010043 GCGAGCGGACCATAGGAAAAA 61.010 52.381 0.00 0.00 0.00 1.94
2631 3706 2.445654 GGAGGAGGGCTGGGAGAG 60.446 72.222 0.00 0.00 0.00 3.20
2632 3707 4.095400 GGGAGGAGGGCTGGGAGA 62.095 72.222 0.00 0.00 0.00 3.71
2633 3708 4.101077 AGGGAGGAGGGCTGGGAG 62.101 72.222 0.00 0.00 0.00 4.30
2634 3709 4.421554 CAGGGAGGAGGGCTGGGA 62.422 72.222 0.00 0.00 0.00 4.37
2635 3710 4.748798 ACAGGGAGGAGGGCTGGG 62.749 72.222 0.00 0.00 0.00 4.45
2636 3711 3.086600 GACAGGGAGGAGGGCTGG 61.087 72.222 0.00 0.00 0.00 4.85
2637 3712 3.465403 CGACAGGGAGGAGGGCTG 61.465 72.222 0.00 0.00 0.00 4.85
2638 3713 2.937959 GATCGACAGGGAGGAGGGCT 62.938 65.000 0.00 0.00 0.00 5.19
2639 3714 2.444895 ATCGACAGGGAGGAGGGC 60.445 66.667 0.00 0.00 0.00 5.19
2640 3715 1.834822 GGATCGACAGGGAGGAGGG 60.835 68.421 0.00 0.00 0.00 4.30
2641 3716 1.834822 GGGATCGACAGGGAGGAGG 60.835 68.421 0.00 0.00 0.00 4.30
2642 3717 1.834822 GGGGATCGACAGGGAGGAG 60.835 68.421 0.00 0.00 0.00 3.69
2643 3718 2.282446 GGGGATCGACAGGGAGGA 59.718 66.667 0.00 0.00 0.00 3.71
2644 3719 2.844839 GGGGGATCGACAGGGAGG 60.845 72.222 0.00 0.00 0.00 4.30
2669 3744 2.575461 GTAGGACCCGGTGGAACG 59.425 66.667 0.00 0.00 38.12 3.95
2670 3745 2.984623 GGTAGGACCCGGTGGAAC 59.015 66.667 0.00 0.00 34.81 3.62
2679 3754 4.091939 GGTGGCACGGGTAGGACC 62.092 72.222 12.17 0.00 37.60 4.46
2680 3755 4.091939 GGGTGGCACGGGTAGGAC 62.092 72.222 12.17 0.00 0.00 3.85
2681 3756 4.326227 AGGGTGGCACGGGTAGGA 62.326 66.667 12.17 0.00 0.00 2.94
2682 3757 4.096003 CAGGGTGGCACGGGTAGG 62.096 72.222 12.17 0.00 0.00 3.18
2683 3758 4.096003 CCAGGGTGGCACGGGTAG 62.096 72.222 12.17 0.00 0.00 3.18
2751 3826 4.778415 CACCGCCGTCGTCAGAGG 62.778 72.222 0.00 0.00 0.00 3.69
2752 3827 3.553437 AACACCGCCGTCGTCAGAG 62.553 63.158 0.00 0.00 0.00 3.35
2753 3828 3.598715 AACACCGCCGTCGTCAGA 61.599 61.111 0.00 0.00 0.00 3.27
2754 3829 3.403057 CAACACCGCCGTCGTCAG 61.403 66.667 0.00 0.00 0.00 3.51
2759 3834 3.414700 CTGAGCAACACCGCCGTC 61.415 66.667 0.00 0.00 0.00 4.79
2762 3837 3.730761 CAGCTGAGCAACACCGCC 61.731 66.667 8.42 0.00 0.00 6.13
2763 3838 3.730761 CCAGCTGAGCAACACCGC 61.731 66.667 17.39 0.00 0.00 5.68
2764 3839 3.730761 GCCAGCTGAGCAACACCG 61.731 66.667 17.39 0.00 0.00 4.94
2765 3840 2.595463 TGCCAGCTGAGCAACACC 60.595 61.111 22.49 0.53 37.28 4.16
2766 3841 2.952245 CTGCCAGCTGAGCAACAC 59.048 61.111 24.02 4.34 40.35 3.32
2767 3842 2.981909 GCTGCCAGCTGAGCAACA 60.982 61.111 24.02 10.83 40.35 3.33
2768 3843 4.099170 CGCTGCCAGCTGAGCAAC 62.099 66.667 24.02 20.02 40.35 4.17
2772 3847 4.694233 ACACCGCTGCCAGCTGAG 62.694 66.667 17.39 9.51 39.60 3.35
2773 3848 4.994471 CACACCGCTGCCAGCTGA 62.994 66.667 17.39 0.00 39.60 4.26
2821 3896 4.980805 TCACCGCGTCAAGGGCAC 62.981 66.667 4.92 0.00 0.00 5.01
2822 3897 4.980805 GTCACCGCGTCAAGGGCA 62.981 66.667 4.92 0.00 0.00 5.36
2834 3909 4.955774 ACCAACGGTCGCGTCACC 62.956 66.667 5.77 6.43 0.00 4.02
2835 3910 3.400590 GACCAACGGTCGCGTCAC 61.401 66.667 5.77 0.00 43.14 3.67
2888 3963 4.598894 CAGATCTGGCCCGAGCGG 62.599 72.222 15.38 2.19 41.24 5.52
2889 3964 4.598894 CCAGATCTGGCCCGAGCG 62.599 72.222 28.45 2.83 44.73 5.03
2898 3973 0.685458 CCCAAAAGGGCCCAGATCTG 60.685 60.000 27.56 16.24 34.21 2.90
2899 3974 1.699752 CCCAAAAGGGCCCAGATCT 59.300 57.895 27.56 0.00 34.21 2.75
2900 3975 4.362479 CCCAAAAGGGCCCAGATC 57.638 61.111 27.56 0.00 34.21 2.75
2908 3983 1.689258 CCTAGATTGGGCCCAAAAGGG 60.689 57.143 40.00 30.78 39.55 3.95
2909 3984 1.007118 ACCTAGATTGGGCCCAAAAGG 59.993 52.381 38.18 38.18 39.55 3.11
2910 3985 2.497273 CAACCTAGATTGGGCCCAAAAG 59.503 50.000 40.00 32.06 39.55 2.27
2911 3986 2.534990 CAACCTAGATTGGGCCCAAAA 58.465 47.619 40.00 25.93 39.55 2.44
2912 3987 1.272985 CCAACCTAGATTGGGCCCAAA 60.273 52.381 40.00 23.51 44.74 3.28
2913 3988 0.334676 CCAACCTAGATTGGGCCCAA 59.665 55.000 38.72 38.72 44.74 4.12
2914 3989 2.006748 CCAACCTAGATTGGGCCCA 58.993 57.895 24.45 24.45 44.74 5.36
2920 3995 0.463833 GCCCGTCCCAACCTAGATTG 60.464 60.000 0.00 0.00 0.00 2.67
2921 3996 1.632965 GGCCCGTCCCAACCTAGATT 61.633 60.000 0.00 0.00 0.00 2.40
2922 3997 2.070650 GGCCCGTCCCAACCTAGAT 61.071 63.158 0.00 0.00 0.00 1.98
2923 3998 2.686106 GGCCCGTCCCAACCTAGA 60.686 66.667 0.00 0.00 0.00 2.43
2924 3999 4.157120 CGGCCCGTCCCAACCTAG 62.157 72.222 0.00 0.00 0.00 3.02
2940 4015 4.260355 CATGGAGCAATGCCGCCG 62.260 66.667 0.00 0.00 0.00 6.46
2941 4016 3.908081 CCATGGAGCAATGCCGCC 61.908 66.667 5.56 4.53 0.00 6.13
2942 4017 3.142838 ACCATGGAGCAATGCCGC 61.143 61.111 21.47 0.00 0.00 6.53
2943 4018 2.777972 CCACCATGGAGCAATGCCG 61.778 63.158 21.47 0.00 40.96 5.69
2944 4019 1.683365 ACCACCATGGAGCAATGCC 60.683 57.895 21.47 0.00 40.96 4.40
2945 4020 1.514087 CACCACCATGGAGCAATGC 59.486 57.895 21.47 0.00 40.96 3.56
2946 4021 0.612732 ACCACCACCATGGAGCAATG 60.613 55.000 21.47 5.41 43.02 2.82
2947 4022 0.612732 CACCACCACCATGGAGCAAT 60.613 55.000 21.47 0.00 43.02 3.56
2948 4023 1.228521 CACCACCACCATGGAGCAA 60.229 57.895 21.47 0.00 43.02 3.91
2949 4024 2.435663 CACCACCACCATGGAGCA 59.564 61.111 21.47 0.00 43.02 4.26
2950 4025 2.361610 CCACCACCACCATGGAGC 60.362 66.667 21.47 0.00 43.02 4.70
2951 4026 2.361610 GCCACCACCACCATGGAG 60.362 66.667 21.47 11.19 43.02 3.86
2952 4027 4.343323 CGCCACCACCACCATGGA 62.343 66.667 21.47 0.00 43.02 3.41
2953 4028 4.343323 TCGCCACCACCACCATGG 62.343 66.667 11.19 11.19 46.10 3.66
2954 4029 2.747460 CTCGCCACCACCACCATG 60.747 66.667 0.00 0.00 0.00 3.66
2955 4030 4.033776 CCTCGCCACCACCACCAT 62.034 66.667 0.00 0.00 0.00 3.55
2968 4043 4.778415 CAGACCACCGACGCCTCG 62.778 72.222 0.00 0.00 39.83 4.63
2986 4061 3.726517 CGAAACCTGCACCGCCTG 61.727 66.667 0.00 0.00 0.00 4.85
2987 4062 3.767630 AACGAAACCTGCACCGCCT 62.768 57.895 0.00 0.00 0.00 5.52
2988 4063 3.284449 AACGAAACCTGCACCGCC 61.284 61.111 0.00 0.00 0.00 6.13
2989 4064 2.051345 CAACGAAACCTGCACCGC 60.051 61.111 0.00 0.00 0.00 5.68
2990 4065 2.637025 CCAACGAAACCTGCACCG 59.363 61.111 0.00 0.00 0.00 4.94
2991 4066 2.335011 GCCAACGAAACCTGCACC 59.665 61.111 0.00 0.00 0.00 5.01
2992 4067 2.335011 GGCCAACGAAACCTGCAC 59.665 61.111 0.00 0.00 0.00 4.57
2993 4068 2.124109 TGGCCAACGAAACCTGCA 60.124 55.556 0.61 0.00 0.00 4.41
2994 4069 2.644992 CTGGCCAACGAAACCTGC 59.355 61.111 7.01 0.00 0.00 4.85
2995 4070 2.644992 GCTGGCCAACGAAACCTG 59.355 61.111 7.01 0.00 0.00 4.00
2996 4071 2.978010 CGCTGGCCAACGAAACCT 60.978 61.111 24.03 0.00 0.00 3.50
2997 4072 3.284449 ACGCTGGCCAACGAAACC 61.284 61.111 33.68 2.69 0.00 3.27
2998 4073 2.051345 CACGCTGGCCAACGAAAC 60.051 61.111 33.68 5.56 0.00 2.78
2999 4074 3.959975 GCACGCTGGCCAACGAAA 61.960 61.111 33.68 0.00 0.00 3.46
3000 4075 4.927782 AGCACGCTGGCCAACGAA 62.928 61.111 33.68 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.