Multiple sequence alignment - TraesCS2D01G239500

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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 TraesCS2D01G239500 chr2D 100.000 6815 0 0 1830 8644 254982953 254976139 0.000000e+00 12586.0
1 TraesCS2D01G239500 chr2D 100.000 1588 0 0 1 1588 254984782 254983195 0.000000e+00 2933.0
2 TraesCS2D01G239500 chr2D 85.614 570 65 12 7822 8381 277781367 277781929 4.500000e-162 582.0
3 TraesCS2D01G239500 chr2D 85.269 577 66 8 7822 8381 107485518 107486092 2.090000e-160 577.0
4 TraesCS2D01G239500 chr2D 80.339 295 41 13 8035 8318 147001026 147001314 3.160000e-49 207.0
5 TraesCS2D01G239500 chr2A 97.297 3145 58 7 4505 7647 323014028 323010909 0.000000e+00 5312.0
6 TraesCS2D01G239500 chr2A 98.148 1512 26 2 2936 4445 323015559 323014048 0.000000e+00 2636.0
7 TraesCS2D01G239500 chr2A 95.660 1129 28 9 1830 2937 323016772 323015644 0.000000e+00 1794.0
8 TraesCS2D01G239500 chr2A 96.751 554 17 1 1035 1588 323017450 323016898 0.000000e+00 922.0
9 TraesCS2D01G239500 chr2A 80.099 1010 173 23 3 994 487697156 487698155 0.000000e+00 726.0
10 TraesCS2D01G239500 chr2A 84.629 579 71 8 7822 8383 103827415 103827992 2.110000e-155 560.0
11 TraesCS2D01G239500 chr2A 80.423 189 34 3 13 200 191717117 191717303 3.250000e-29 141.0
12 TraesCS2D01G239500 chr2A 98.734 79 1 0 7633 7711 322996196 322996118 3.250000e-29 141.0
13 TraesCS2D01G239500 chr2A 100.000 59 0 0 4449 4507 642931141 642931083 9.170000e-20 110.0
14 TraesCS2D01G239500 chr2A 98.361 61 1 0 4447 4507 242231728 242231668 3.300000e-19 108.0
15 TraesCS2D01G239500 chr2B 97.206 1718 45 3 2733 4449 325848338 325846623 0.000000e+00 2904.0
16 TraesCS2D01G239500 chr2B 96.983 928 26 2 5219 6146 325845759 325844834 0.000000e+00 1557.0
17 TraesCS2D01G239500 chr2B 95.553 877 37 2 1857 2732 325849245 325848370 0.000000e+00 1402.0
18 TraesCS2D01G239500 chr2B 96.379 718 15 2 4505 5221 325846589 325845882 0.000000e+00 1171.0
19 TraesCS2D01G239500 chr2B 96.552 551 17 1 7228 7776 325844809 325844259 0.000000e+00 911.0
20 TraesCS2D01G239500 chr2B 95.062 567 24 3 1025 1588 325849823 325849258 0.000000e+00 889.0
21 TraesCS2D01G239500 chr2B 89.423 624 40 10 7783 8381 325844211 325843589 0.000000e+00 763.0
22 TraesCS2D01G239500 chr2B 85.614 570 75 4 7821 8383 326843396 326842827 7.470000e-165 592.0
23 TraesCS2D01G239500 chr2B 79.608 868 111 46 7821 8644 275233868 275234713 5.860000e-156 562.0
24 TraesCS2D01G239500 chr2B 91.228 285 21 2 8363 8644 325843569 325843286 1.360000e-102 385.0
25 TraesCS2D01G239500 chr1D 82.500 1000 155 16 1 987 259434228 259433236 0.000000e+00 859.0
26 TraesCS2D01G239500 chr4B 82.596 994 150 18 6 994 441109760 441108785 0.000000e+00 856.0
27 TraesCS2D01G239500 chr4B 100.000 59 0 0 4449 4507 115099379 115099437 9.170000e-20 110.0
28 TraesCS2D01G239500 chr4B 80.769 104 18 2 8280 8382 669579841 669579943 7.190000e-11 80.5
29 TraesCS2D01G239500 chr5D 81.033 1007 169 19 1 994 356504665 356503668 0.000000e+00 782.0
30 TraesCS2D01G239500 chr5D 77.496 671 132 15 4752 5412 492562896 492562235 1.360000e-102 385.0
31 TraesCS2D01G239500 chr5D 82.184 174 31 0 6595 6768 492560812 492560639 5.410000e-32 150.0
32 TraesCS2D01G239500 chr5D 83.099 142 24 0 6595 6736 493313466 493313607 7.040000e-26 130.0
33 TraesCS2D01G239500 chr7D 80.896 1005 166 20 1 994 346256188 346257177 0.000000e+00 769.0
34 TraesCS2D01G239500 chr7D 80.220 1001 175 20 4 994 344910089 344909102 0.000000e+00 730.0
35 TraesCS2D01G239500 chr7D 84.263 502 60 10 8155 8644 326048993 326049487 1.020000e-128 472.0
36 TraesCS2D01G239500 chr7D 74.721 538 80 49 7870 8381 177890927 177891434 1.150000e-43 189.0
37 TraesCS2D01G239500 chr7D 98.305 59 1 0 4449 4507 519265613 519265555 4.270000e-18 104.0
38 TraesCS2D01G239500 chr3D 82.123 895 143 14 109 994 225137858 225138744 0.000000e+00 750.0
39 TraesCS2D01G239500 chr3D 81.550 271 33 12 8388 8643 227120915 227120647 3.160000e-49 207.0
40 TraesCS2D01G239500 chr7A 80.339 1002 174 18 5 994 528547424 528546434 0.000000e+00 737.0
41 TraesCS2D01G239500 chr1A 80.241 997 178 18 3 987 207118942 207117953 0.000000e+00 732.0
42 TraesCS2D01G239500 chr4D 88.817 465 43 5 7882 8338 109084089 109083626 5.860000e-156 562.0
43 TraesCS2D01G239500 chr4D 83.624 458 65 6 7931 8379 176702461 176702005 1.040000e-113 422.0
44 TraesCS2D01G239500 chr4D 81.787 291 35 8 8369 8644 260773956 260774243 2.430000e-55 228.0
45 TraesCS2D01G239500 chr4D 96.667 60 2 0 4448 4507 385745179 385745120 5.520000e-17 100.0
46 TraesCS2D01G239500 chr5A 77.761 670 120 23 4752 5412 615315436 615316085 1.360000e-102 385.0
47 TraesCS2D01G239500 chr5A 82.738 168 29 0 6592 6759 615317507 615317674 5.410000e-32 150.0
48 TraesCS2D01G239500 chr5A 82.877 146 25 0 6592 6737 616358835 616358980 1.960000e-26 132.0
49 TraesCS2D01G239500 chr5A 87.778 90 11 0 6647 6736 616432736 616432825 1.190000e-18 106.0
50 TraesCS2D01G239500 chr5A 100.000 29 0 0 7152 7180 395692622 395692594 4.000000e-03 54.7
51 TraesCS2D01G239500 chr7B 78.454 608 78 29 8057 8644 293163345 293162771 1.790000e-91 348.0
52 TraesCS2D01G239500 chr6A 84.638 345 40 12 7815 8150 268998279 268997939 1.800000e-86 331.0
53 TraesCS2D01G239500 chr3B 85.417 288 30 4 8369 8644 308185812 308185525 1.100000e-73 289.0
54 TraesCS2D01G239500 chr3B 100.000 59 0 0 4449 4507 290321202 290321144 9.170000e-20 110.0
55 TraesCS2D01G239500 chr6D 80.139 287 40 11 8362 8644 172012129 172012402 1.900000e-46 198.0
56 TraesCS2D01G239500 chr6B 92.373 118 9 0 8527 8644 293110399 293110516 1.490000e-37 169.0
57 TraesCS2D01G239500 chr6B 100.000 59 0 0 4449 4507 626047587 626047645 9.170000e-20 110.0
58 TraesCS2D01G239500 chr5B 83.333 168 28 0 6592 6759 607875156 607875323 1.160000e-33 156.0
59 TraesCS2D01G239500 chr5B 80.137 146 29 0 6592 6737 608637628 608637773 9.170000e-20 110.0
60 TraesCS2D01G239500 chr4A 98.333 60 0 1 4449 4507 477060050 477059991 4.270000e-18 104.0
61 TraesCS2D01G239500 chr4A 96.667 60 2 0 4448 4507 67184480 67184421 5.520000e-17 100.0


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 TraesCS2D01G239500 chr2D 254976139 254984782 8643 True 7759.50 12586 100.00000 1 8644 2 chr2D.!!$R1 8643
1 TraesCS2D01G239500 chr2D 277781367 277781929 562 False 582.00 582 85.61400 7822 8381 1 chr2D.!!$F3 559
2 TraesCS2D01G239500 chr2D 107485518 107486092 574 False 577.00 577 85.26900 7822 8381 1 chr2D.!!$F1 559
3 TraesCS2D01G239500 chr2A 323010909 323017450 6541 True 2666.00 5312 96.96400 1035 7647 4 chr2A.!!$R4 6612
4 TraesCS2D01G239500 chr2A 487697156 487698155 999 False 726.00 726 80.09900 3 994 1 chr2A.!!$F3 991
5 TraesCS2D01G239500 chr2A 103827415 103827992 577 False 560.00 560 84.62900 7822 8383 1 chr2A.!!$F1 561
6 TraesCS2D01G239500 chr2B 325843286 325849823 6537 True 1247.75 2904 94.79825 1025 8644 8 chr2B.!!$R2 7619
7 TraesCS2D01G239500 chr2B 326842827 326843396 569 True 592.00 592 85.61400 7821 8383 1 chr2B.!!$R1 562
8 TraesCS2D01G239500 chr2B 275233868 275234713 845 False 562.00 562 79.60800 7821 8644 1 chr2B.!!$F1 823
9 TraesCS2D01G239500 chr1D 259433236 259434228 992 True 859.00 859 82.50000 1 987 1 chr1D.!!$R1 986
10 TraesCS2D01G239500 chr4B 441108785 441109760 975 True 856.00 856 82.59600 6 994 1 chr4B.!!$R1 988
11 TraesCS2D01G239500 chr5D 356503668 356504665 997 True 782.00 782 81.03300 1 994 1 chr5D.!!$R1 993
12 TraesCS2D01G239500 chr5D 492560639 492562896 2257 True 267.50 385 79.84000 4752 6768 2 chr5D.!!$R2 2016
13 TraesCS2D01G239500 chr7D 346256188 346257177 989 False 769.00 769 80.89600 1 994 1 chr7D.!!$F3 993
14 TraesCS2D01G239500 chr7D 344909102 344910089 987 True 730.00 730 80.22000 4 994 1 chr7D.!!$R1 990
15 TraesCS2D01G239500 chr3D 225137858 225138744 886 False 750.00 750 82.12300 109 994 1 chr3D.!!$F1 885
16 TraesCS2D01G239500 chr7A 528546434 528547424 990 True 737.00 737 80.33900 5 994 1 chr7A.!!$R1 989
17 TraesCS2D01G239500 chr1A 207117953 207118942 989 True 732.00 732 80.24100 3 987 1 chr1A.!!$R1 984
18 TraesCS2D01G239500 chr5A 615315436 615317674 2238 False 267.50 385 80.24950 4752 6759 2 chr5A.!!$F3 2007
19 TraesCS2D01G239500 chr7B 293162771 293163345 574 True 348.00 348 78.45400 8057 8644 1 chr7B.!!$R1 587

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
856 889 0.112995 TTGGGCTGATGAGGCACTTT 59.887 50.000 8.23 0.0 46.80 2.66 F
1012 1050 0.034186 CATACACCACCACCCTGCAT 60.034 55.000 0.00 0.0 0.00 3.96 F
1013 1051 0.034186 ATACACCACCACCCTGCATG 60.034 55.000 0.00 0.0 0.00 4.06 F
2055 2096 0.481567 CATGGGGAGAGGATGCCATT 59.518 55.000 0.00 0.0 42.44 3.16 F
2165 2206 1.078567 CCACAGAGAGCAGGGAAGC 60.079 63.158 0.00 0.0 0.00 3.86 F
3025 3186 1.202855 CCTCTTGCATCCGGAATCCAT 60.203 52.381 9.01 0.0 0.00 3.41 F
4479 4642 3.066203 ACAACAACAAAGCCTTTAGTCCG 59.934 43.478 0.00 0.0 0.00 4.79 F
4493 4656 0.549469 AGTCCGAAACAAGTTGGGGT 59.451 50.000 7.96 0.0 35.83 4.95 F
4497 4660 0.879090 CGAAACAAGTTGGGGTAGGC 59.121 55.000 7.96 0.0 0.00 3.93 F
4503 4666 1.486726 CAAGTTGGGGTAGGCTAGAGG 59.513 57.143 0.00 0.0 0.00 3.69 F
6193 6755 2.143925 CTGGTTTCGGTTCTCAGGTTC 58.856 52.381 0.00 0.0 0.00 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2614 2655 0.668535 GAAGGTCCTTTTGCTTGCGT 59.331 50.000 5.36 0.0 0.00 5.24 R
2756 2829 1.001633 GGACAAAGCGAAGTACTCCCA 59.998 52.381 0.00 0.0 0.00 4.37 R
2764 2837 1.433534 GACAGAGGGACAAAGCGAAG 58.566 55.000 0.00 0.0 0.00 3.79 R
3896 4059 1.887707 GGTACACCATAGCAGCCGC 60.888 63.158 0.00 0.0 35.36 6.53 R
4451 4614 3.676291 AGGCTTTGTTGTTGTTGTTGT 57.324 38.095 0.00 0.0 0.00 3.32 R
4488 4651 0.032416 GTCACCTCTAGCCTACCCCA 60.032 60.000 0.00 0.0 0.00 4.96 R
6429 6991 4.450082 AATTTAAGTGGCAAACCCGATC 57.550 40.909 0.00 0.0 35.87 3.69 R
6527 7104 6.071447 CCTGTGAACAATGACATTTATGGGAA 60.071 38.462 0.00 0.0 0.00 3.97 R
6750 7690 6.341316 TGCTAATCAAGTATTCTGACCTGTC 58.659 40.000 0.00 0.0 0.00 3.51 R
6771 7711 7.116075 ACAATTTCATATGGCTAACAATGCT 57.884 32.000 2.13 0.0 0.00 3.79 R
7862 8845 0.481128 TCTTCCCCTTTTCGCCCTTT 59.519 50.000 0.00 0.0 0.00 3.11 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
36 38 1.144057 ACTTGTCATCGGATCGCCC 59.856 57.895 0.00 0.00 0.00 6.13
45 47 2.511600 GGATCGCCCACCAGTTCG 60.512 66.667 0.00 0.00 34.14 3.95
52 54 1.449601 CCCACCAGTTCGCGCTTAT 60.450 57.895 5.56 0.00 0.00 1.73
76 78 2.494073 TGACGGTCAGTTTTTGGCTTTT 59.506 40.909 6.76 0.00 0.00 2.27
80 82 3.430236 CGGTCAGTTTTTGGCTTTTTCCT 60.430 43.478 0.00 0.00 0.00 3.36
128 130 2.463752 AGTACAATCGCAGGGGTTCTA 58.536 47.619 0.00 0.00 0.00 2.10
211 213 5.014755 ACCCAACTATTGACCCAAGACATAA 59.985 40.000 0.00 0.00 0.00 1.90
259 261 1.733041 CGAGACGCCGAACACACAT 60.733 57.895 0.00 0.00 0.00 3.21
272 274 0.250295 CACACATCGGGAAGTGGTGT 60.250 55.000 8.66 0.00 42.94 4.16
286 288 0.523072 TGGTGTCGGACTTAGTACGC 59.477 55.000 12.76 8.20 40.05 4.42
327 329 2.025321 AGCCCTTGGTCAATTAACCGAT 60.025 45.455 0.00 0.00 42.62 4.18
360 363 0.171007 ACAATGTATGCGTGCCAAGC 59.829 50.000 0.00 0.00 0.00 4.01
412 433 3.312890 AGGGCTAGACAATACAGATGCT 58.687 45.455 0.00 0.00 0.00 3.79
476 499 6.425114 GGTGCATCTATCTGTACAATTCGAAT 59.575 38.462 4.39 4.39 33.90 3.34
568 594 0.606604 GGGTCGAAGCCTCAACTGTA 59.393 55.000 0.00 0.00 31.81 2.74
570 596 1.000506 GGTCGAAGCCTCAACTGTACA 59.999 52.381 0.00 0.00 0.00 2.90
571 597 2.353803 GGTCGAAGCCTCAACTGTACAT 60.354 50.000 0.00 0.00 0.00 2.29
605 631 1.668919 CGTCTTTGCTTCTGCGAGGTA 60.669 52.381 0.00 0.00 43.34 3.08
610 637 1.815840 GCTTCTGCGAGGTAAGGGC 60.816 63.158 0.00 0.00 0.00 5.19
703 732 2.590575 CCGTGCCGTCACACCTTT 60.591 61.111 0.00 0.00 43.28 3.11
725 754 3.649277 CTGGGCAAGTCCGGAGTCG 62.649 68.421 13.41 1.49 35.18 4.18
777 807 1.459592 CGTGGTTCGGTTAAGCTGAAG 59.540 52.381 10.66 0.00 42.63 3.02
783 813 3.953712 TCGGTTAAGCTGAAGACATGA 57.046 42.857 0.00 0.00 0.00 3.07
802 835 9.618890 AGACATGATGCACTTGTTTAATATAGT 57.381 29.630 0.00 0.00 37.08 2.12
818 851 4.091939 GTCCCCACGGCTACCCAC 62.092 72.222 0.00 0.00 0.00 4.61
819 852 4.642488 TCCCCACGGCTACCCACA 62.642 66.667 0.00 0.00 0.00 4.17
826 859 2.304092 CACGGCTACCCACAGTATCTA 58.696 52.381 0.00 0.00 0.00 1.98
840 873 2.033550 AGTATCTAGAGCGCGAAGTTGG 59.966 50.000 12.10 0.00 0.00 3.77
846 879 3.127533 GCGCGAAGTTGGGCTGAT 61.128 61.111 12.10 0.00 43.75 2.90
854 887 1.001641 GTTGGGCTGATGAGGCACT 60.002 57.895 8.23 0.00 46.80 4.40
856 889 0.112995 TTGGGCTGATGAGGCACTTT 59.887 50.000 8.23 0.00 46.80 2.66
866 899 3.044305 GGCACTTTGAGCGCGACT 61.044 61.111 12.10 6.51 0.00 4.18
922 959 1.625616 CGACGAACGTAGGCAGATTT 58.374 50.000 0.00 0.00 37.22 2.17
923 960 1.990563 CGACGAACGTAGGCAGATTTT 59.009 47.619 0.00 0.00 37.22 1.82
967 1005 5.548406 AGCTCGTTTAGTTGTATCTTTGGT 58.452 37.500 0.00 0.00 0.00 3.67
998 1036 2.257207 GGCTGATACCTAGGCCATACA 58.743 52.381 9.30 1.76 43.59 2.29
999 1037 2.028020 GGCTGATACCTAGGCCATACAC 60.028 54.545 9.30 0.00 43.59 2.90
1000 1038 2.028020 GCTGATACCTAGGCCATACACC 60.028 54.545 9.30 0.00 0.00 4.16
1001 1039 3.239449 CTGATACCTAGGCCATACACCA 58.761 50.000 9.30 0.00 0.00 4.17
1002 1040 2.969950 TGATACCTAGGCCATACACCAC 59.030 50.000 9.30 0.00 0.00 4.16
1003 1041 1.797320 TACCTAGGCCATACACCACC 58.203 55.000 9.30 0.00 0.00 4.61
1004 1042 0.252974 ACCTAGGCCATACACCACCA 60.253 55.000 9.30 0.00 0.00 4.17
1005 1043 0.180406 CCTAGGCCATACACCACCAC 59.820 60.000 5.01 0.00 0.00 4.16
1006 1044 0.180406 CTAGGCCATACACCACCACC 59.820 60.000 5.01 0.00 0.00 4.61
1007 1045 1.276140 TAGGCCATACACCACCACCC 61.276 60.000 5.01 0.00 0.00 4.61
1008 1046 2.612493 GGCCATACACCACCACCCT 61.612 63.158 0.00 0.00 0.00 4.34
1009 1047 1.378514 GCCATACACCACCACCCTG 60.379 63.158 0.00 0.00 0.00 4.45
1010 1048 1.378514 CCATACACCACCACCCTGC 60.379 63.158 0.00 0.00 0.00 4.85
1011 1049 1.378378 CATACACCACCACCCTGCA 59.622 57.895 0.00 0.00 0.00 4.41
1012 1050 0.034186 CATACACCACCACCCTGCAT 60.034 55.000 0.00 0.00 0.00 3.96
1013 1051 0.034186 ATACACCACCACCCTGCATG 60.034 55.000 0.00 0.00 0.00 4.06
1014 1052 1.130678 TACACCACCACCCTGCATGA 61.131 55.000 0.00 0.00 0.00 3.07
1015 1053 1.973281 CACCACCACCCTGCATGAC 60.973 63.158 0.00 0.00 0.00 3.06
1016 1054 2.747460 CCACCACCCTGCATGACG 60.747 66.667 0.00 0.00 0.00 4.35
1017 1055 3.434319 CACCACCCTGCATGACGC 61.434 66.667 0.00 0.00 42.89 5.19
1051 1089 2.508891 GCTCACACGGCGAGATTCG 61.509 63.158 16.62 0.00 43.89 3.34
1158 1196 0.609131 CAATTCGTGTGCCTTCCCCT 60.609 55.000 0.00 0.00 0.00 4.79
1200 1240 3.154473 CGAATCGGGCCTCCTCCA 61.154 66.667 0.84 0.00 0.00 3.86
1213 1253 1.075226 CCTCCATCTCCCCTTCCGA 60.075 63.158 0.00 0.00 0.00 4.55
1241 1281 1.333791 CGCTACGTCGATGTGAGCATA 60.334 52.381 25.27 7.47 35.07 3.14
1258 1298 2.658321 ATACCCGCACCCCGATCTCT 62.658 60.000 0.00 0.00 40.02 3.10
1259 1299 4.227134 CCCGCACCCCGATCTCTG 62.227 72.222 0.00 0.00 40.02 3.35
1275 1315 2.178580 CTCTGGCTTCCTCTCTCTGTT 58.821 52.381 0.00 0.00 0.00 3.16
1929 1970 4.380233 GCTCCAGATTTCCATTTGTGTCTG 60.380 45.833 0.00 0.00 34.39 3.51
2054 2095 2.077842 GCATGGGGAGAGGATGCCAT 62.078 60.000 0.00 0.00 42.44 4.40
2055 2096 0.481567 CATGGGGAGAGGATGCCATT 59.518 55.000 0.00 0.00 42.44 3.16
2165 2206 1.078567 CCACAGAGAGCAGGGAAGC 60.079 63.158 0.00 0.00 0.00 3.86
2166 2207 1.675801 CACAGAGAGCAGGGAAGCA 59.324 57.895 0.00 0.00 36.85 3.91
2475 2516 5.070580 CGGAGAGGGTACTTCTTTTCCATAT 59.929 44.000 14.70 0.00 0.00 1.78
2616 2657 7.706607 TCTGTTTTAGATTGATCACATAGGACG 59.293 37.037 0.00 0.00 0.00 4.79
2690 2731 2.134201 TATGCTGTATGTTCGGAGCG 57.866 50.000 0.00 0.00 33.97 5.03
2756 2829 3.181445 TGCGCCACTTATTATGGATCCTT 60.181 43.478 14.23 9.56 39.87 3.36
2764 2837 7.162082 CACTTATTATGGATCCTTGGGAGTAC 58.838 42.308 14.23 0.00 34.05 2.73
3025 3186 1.202855 CCTCTTGCATCCGGAATCCAT 60.203 52.381 9.01 0.00 0.00 3.41
3066 3227 5.887598 TGACATGCTACAGCTAAATCCATTT 59.112 36.000 2.44 0.00 42.66 2.32
3221 3382 7.295322 TGATCCAATCCAATACACAAAACAA 57.705 32.000 0.00 0.00 0.00 2.83
3264 3425 6.998673 ACATGCTACTTCTTTAAGTCCTTGTT 59.001 34.615 0.00 0.00 42.42 2.83
3796 3959 3.994392 AGTGGCAAGTTTATCAGTACGTG 59.006 43.478 0.00 0.00 0.00 4.49
3896 4059 6.017852 GGTTTTTCTGTAACAAGGACTCTCAG 60.018 42.308 0.00 0.00 0.00 3.35
3950 4113 3.771160 CCGGCAGGGCGACTACTT 61.771 66.667 17.24 0.00 0.00 2.24
4122 4285 6.385033 CATCCTCTTGTTCCTTTTGACATTC 58.615 40.000 0.00 0.00 0.00 2.67
4465 4628 9.862371 AATTCTTATACAACAACAACAACAACA 57.138 25.926 0.00 0.00 0.00 3.33
4466 4629 9.862371 ATTCTTATACAACAACAACAACAACAA 57.138 25.926 0.00 0.00 0.00 2.83
4467 4630 9.692749 TTCTTATACAACAACAACAACAACAAA 57.307 25.926 0.00 0.00 0.00 2.83
4468 4631 9.347934 TCTTATACAACAACAACAACAACAAAG 57.652 29.630 0.00 0.00 0.00 2.77
4469 4632 4.723879 ACAACAACAACAACAACAAAGC 57.276 36.364 0.00 0.00 0.00 3.51
4471 4634 3.676291 ACAACAACAACAACAAAGCCT 57.324 38.095 0.00 0.00 0.00 4.58
4472 4635 4.001618 ACAACAACAACAACAAAGCCTT 57.998 36.364 0.00 0.00 0.00 4.35
4473 4636 4.384940 ACAACAACAACAACAAAGCCTTT 58.615 34.783 0.00 0.00 0.00 3.11
4475 4638 5.637387 ACAACAACAACAACAAAGCCTTTAG 59.363 36.000 0.00 0.00 0.00 1.85
4476 4639 5.400066 ACAACAACAACAAAGCCTTTAGT 57.600 34.783 0.00 0.00 0.00 2.24
4477 4640 5.407502 ACAACAACAACAAAGCCTTTAGTC 58.592 37.500 0.00 0.00 0.00 2.59
4478 4641 4.649088 ACAACAACAAAGCCTTTAGTCC 57.351 40.909 0.00 0.00 0.00 3.85
4479 4642 3.066203 ACAACAACAAAGCCTTTAGTCCG 59.934 43.478 0.00 0.00 0.00 4.79
4480 4643 3.202829 ACAACAAAGCCTTTAGTCCGA 57.797 42.857 0.00 0.00 0.00 4.55
4482 4645 3.949113 ACAACAAAGCCTTTAGTCCGAAA 59.051 39.130 0.00 0.00 0.00 3.46
4483 4646 4.201980 ACAACAAAGCCTTTAGTCCGAAAC 60.202 41.667 0.00 0.00 0.00 2.78
4484 4647 3.547746 ACAAAGCCTTTAGTCCGAAACA 58.452 40.909 0.00 0.00 0.00 2.83
4485 4648 3.949113 ACAAAGCCTTTAGTCCGAAACAA 59.051 39.130 0.00 0.00 0.00 2.83
4486 4649 4.036380 ACAAAGCCTTTAGTCCGAAACAAG 59.964 41.667 0.00 0.00 0.00 3.16
4487 4650 3.487120 AGCCTTTAGTCCGAAACAAGT 57.513 42.857 0.00 0.00 0.00 3.16
4488 4651 3.816994 AGCCTTTAGTCCGAAACAAGTT 58.183 40.909 0.00 0.00 0.00 2.66
4489 4652 3.564225 AGCCTTTAGTCCGAAACAAGTTG 59.436 43.478 0.00 0.00 0.00 3.16
4490 4653 3.304458 GCCTTTAGTCCGAAACAAGTTGG 60.304 47.826 7.96 0.00 0.00 3.77
4491 4654 3.252458 CCTTTAGTCCGAAACAAGTTGGG 59.748 47.826 7.96 0.00 36.45 4.12
4492 4655 2.554370 TAGTCCGAAACAAGTTGGGG 57.446 50.000 7.96 3.22 35.83 4.96
4493 4656 0.549469 AGTCCGAAACAAGTTGGGGT 59.451 50.000 7.96 0.00 35.83 4.95
4494 4657 1.770061 AGTCCGAAACAAGTTGGGGTA 59.230 47.619 7.96 0.00 35.83 3.69
4495 4658 2.148768 GTCCGAAACAAGTTGGGGTAG 58.851 52.381 7.96 0.00 35.83 3.18
4496 4659 1.072648 TCCGAAACAAGTTGGGGTAGG 59.927 52.381 7.96 4.28 35.83 3.18
4497 4660 0.879090 CGAAACAAGTTGGGGTAGGC 59.121 55.000 7.96 0.00 0.00 3.93
4498 4661 1.544759 CGAAACAAGTTGGGGTAGGCT 60.545 52.381 7.96 0.00 0.00 4.58
4499 4662 2.289819 CGAAACAAGTTGGGGTAGGCTA 60.290 50.000 7.96 0.00 0.00 3.93
4500 4663 3.344515 GAAACAAGTTGGGGTAGGCTAG 58.655 50.000 7.96 0.00 0.00 3.42
4501 4664 2.337359 ACAAGTTGGGGTAGGCTAGA 57.663 50.000 7.96 0.00 0.00 2.43
4502 4665 2.188817 ACAAGTTGGGGTAGGCTAGAG 58.811 52.381 7.96 0.00 0.00 2.43
4503 4666 1.486726 CAAGTTGGGGTAGGCTAGAGG 59.513 57.143 0.00 0.00 0.00 3.69
4521 4685 3.100671 GAGGTGACATAACTCAGGGTCT 58.899 50.000 0.00 0.00 0.00 3.85
4615 4779 3.499537 TGTCTAAACTGTGCAGCATCAAG 59.500 43.478 0.00 0.00 0.00 3.02
4698 4862 5.120399 TGGTTATTTTCCCTATGCGTACTG 58.880 41.667 0.00 0.00 0.00 2.74
4756 4920 5.694231 TTTTCTTCGTTTTTACTAGGGGC 57.306 39.130 0.00 0.00 0.00 5.80
4896 5060 7.173390 GCAAGGCTACCAGGTAGATTTAATTAG 59.827 40.741 28.47 10.74 38.29 1.73
5224 5513 6.368791 GCTGTACTTTCACTGTCATGTATTGA 59.631 38.462 0.00 0.00 0.00 2.57
5627 5916 2.875933 CGACTGAAGTTTAGCAAACCCA 59.124 45.455 7.77 6.34 42.34 4.51
5638 5927 3.866883 AGCAAACCCATTAATTGTCGG 57.133 42.857 0.00 0.00 0.00 4.79
6193 6755 2.143925 CTGGTTTCGGTTCTCAGGTTC 58.856 52.381 0.00 0.00 0.00 3.62
6219 6781 6.591935 TGAACTCTCACCTGTTTTTCTACAT 58.408 36.000 0.00 0.00 0.00 2.29
6415 6977 3.618690 ATGTCTAAAGGTCTGTGGCTC 57.381 47.619 0.00 0.00 0.00 4.70
6429 6991 4.982295 TCTGTGGCTCACGATTTTATATCG 59.018 41.667 3.68 3.68 46.02 2.92
6464 7026 7.127917 CCACTTAAATTTGTATTTTGTGGCC 57.872 36.000 15.58 0.00 42.78 5.36
6527 7104 7.153985 TGTTTGTACGTATTTAGCTTGGTACT 58.846 34.615 0.00 0.00 33.31 2.73
6750 7690 3.198635 TCAAGGAACTCTGGCTATTCTGG 59.801 47.826 0.00 0.00 38.49 3.86
6771 7711 6.667848 TCTGGACAGGTCAGAATACTTGATTA 59.332 38.462 1.41 0.00 38.20 1.75
6811 7751 8.861033 ATGAAATTGTCCATTCGATTAATGTG 57.139 30.769 0.00 0.00 43.03 3.21
6830 7770 9.764363 TTAATGTGCCAGTATAGATTTCTGTAG 57.236 33.333 0.00 0.00 0.00 2.74
6932 7872 2.905415 TCCAAGTGAAGGCATCCATT 57.095 45.000 0.00 0.00 0.00 3.16
7086 8026 4.156008 CAGCAACCATGTAAAGGTACCTTC 59.844 45.833 27.24 16.15 38.76 3.46
7090 8030 2.676342 CCATGTAAAGGTACCTTCGCAC 59.324 50.000 27.24 22.69 34.84 5.34
7168 8108 5.152306 AGTATTACATACCACTCCCTCCA 57.848 43.478 0.00 0.00 36.40 3.86
7363 8303 4.156556 GCCAAGAATCTGTACATTGCTTCA 59.843 41.667 0.00 0.00 0.00 3.02
7403 8343 3.619483 TGTCAGTTGACCAACGTAACTTG 59.381 43.478 9.60 0.39 45.50 3.16
7517 8457 7.575532 GCAGAAGTTGATGTGATGGTTAATTCA 60.576 37.037 0.00 0.00 0.00 2.57
7749 8691 2.996734 CCCCACCCCAACATGCAC 60.997 66.667 0.00 0.00 0.00 4.57
7777 8719 4.936685 ATAGGGATTTTCCTATGAGGGC 57.063 45.455 2.91 0.00 45.58 5.19
7780 8722 3.913163 AGGGATTTTCCTATGAGGGCTAG 59.087 47.826 0.00 0.00 36.57 3.42
7793 8776 1.361543 AGGGCTAGGGTGTCTAGTTGA 59.638 52.381 0.00 0.00 45.55 3.18
7802 8785 6.380079 AGGGTGTCTAGTTGATTGATCTTT 57.620 37.500 0.00 0.00 0.00 2.52
7814 8797 7.555554 AGTTGATTGATCTTTTGGATGAGTAGG 59.444 37.037 0.00 0.00 34.33 3.18
7847 8830 5.036916 TGTAGGGTGGAATCCTAGTTCATT 58.963 41.667 0.00 0.00 37.53 2.57
7876 8876 4.888917 TCAAATTTAAAGGGCGAAAAGGG 58.111 39.130 0.00 0.00 0.00 3.95
7920 8931 5.128499 TCACTCAAACAAACCCAAATCACAT 59.872 36.000 0.00 0.00 0.00 3.21
7924 8935 7.233348 ACTCAAACAAACCCAAATCACATATCT 59.767 33.333 0.00 0.00 0.00 1.98
7958 8969 6.536582 AGCACACATGAGATTCACAAGTATAC 59.463 38.462 0.00 0.00 0.00 1.47
8016 9028 7.511959 AAGGTTCTTCTCAAATCCAAAGTAC 57.488 36.000 0.00 0.00 0.00 2.73
8055 9069 2.629909 GGTAGATCCTTCTCCCTTGGGT 60.630 54.545 5.51 0.00 33.17 4.51
8078 9093 5.012458 GTGGTCTTGATGATCCTATGATGGA 59.988 44.000 0.00 0.00 40.82 3.41
8134 9149 2.567615 GAGGAGGTACAAGGAGCAAAGA 59.432 50.000 0.00 0.00 0.00 2.52
8215 9237 2.602267 TGGAGGCGAGGGACGAAA 60.602 61.111 0.00 0.00 45.77 3.46
8360 9382 2.903855 CATGCGCATGGGGTCCTC 60.904 66.667 37.09 0.00 35.24 3.71
8391 9450 1.454539 CACGGGGTCCAAAAGAGGT 59.545 57.895 0.00 0.00 0.00 3.85
8393 9452 1.057851 ACGGGGTCCAAAAGAGGTCA 61.058 55.000 0.00 0.00 0.00 4.02
8450 9510 1.310933 GCTGGTCTCCGTCTTCCGTA 61.311 60.000 0.00 0.00 33.66 4.02
8467 9530 2.414293 CCGTACAGTCTTCTCGTCCTTG 60.414 54.545 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 38 2.863740 TCATAATAAGCGCGAACTGGTG 59.136 45.455 12.10 0.00 0.00 4.17
45 47 2.470821 ACTGACCGTCATAATAAGCGC 58.529 47.619 0.00 0.00 0.00 5.92
52 54 3.482436 AGCCAAAAACTGACCGTCATAA 58.518 40.909 0.62 0.00 0.00 1.90
76 78 3.308402 CCCAATTAAGCACCTCAGAGGAA 60.308 47.826 24.45 6.74 37.67 3.36
80 82 1.635487 AGCCCAATTAAGCACCTCAGA 59.365 47.619 2.11 0.00 0.00 3.27
128 130 4.279420 ACGTTCGTCTAAGAAGGTAAAGGT 59.721 41.667 3.66 0.00 44.30 3.50
259 261 2.203523 TCCGACACCACTTCCCGA 60.204 61.111 0.00 0.00 0.00 5.14
272 274 1.709147 GCTCCGCGTACTAAGTCCGA 61.709 60.000 4.92 0.00 0.00 4.55
286 288 1.372748 GATCTGCTCATCGGCTCCG 60.373 63.158 1.14 1.14 41.35 4.63
292 294 0.106335 AGGGCTTGATCTGCTCATCG 59.894 55.000 12.37 0.00 32.72 3.84
299 301 2.205022 TTGACCAAGGGCTTGATCTG 57.795 50.000 0.00 0.00 42.93 2.90
348 351 1.286880 GAACAAGCTTGGCACGCAT 59.713 52.632 29.18 2.85 0.00 4.73
352 355 2.735823 CTCTTTGAACAAGCTTGGCAC 58.264 47.619 29.18 19.10 0.00 5.01
389 410 3.812053 GCATCTGTATTGTCTAGCCCTTG 59.188 47.826 0.00 0.00 0.00 3.61
423 444 9.489084 AGCTTATGGAAAATAAAAACACCTTTC 57.511 29.630 0.00 0.00 0.00 2.62
476 499 4.444536 ACTTATAATAAACGCCTCCGCAA 58.555 39.130 0.00 0.00 38.22 4.85
480 503 9.926751 GTTTTCTTACTTATAATAAACGCCTCC 57.073 33.333 0.00 0.00 0.00 4.30
508 531 8.809478 TGCGTAAACCTTTCTTTTGTAAAATTC 58.191 29.630 0.00 0.00 0.00 2.17
548 574 1.738099 CAGTTGAGGCTTCGACCCG 60.738 63.158 12.39 1.07 38.31 5.28
620 647 0.314935 TTTCTACACGGACGTCCACC 59.685 55.000 32.80 8.66 35.14 4.61
621 648 2.138596 TTTTCTACACGGACGTCCAC 57.861 50.000 32.80 8.60 35.14 4.02
703 732 1.971505 CTCCGGACTTGCCCAGCATA 61.972 60.000 0.00 0.00 38.76 3.14
744 773 2.223317 CGAACCACGGTATCATCACGTA 60.223 50.000 0.00 0.00 39.02 3.57
777 807 9.869844 GACTATATTAAACAAGTGCATCATGTC 57.130 33.333 0.00 0.00 0.00 3.06
783 813 6.546034 GTGGGGACTATATTAAACAAGTGCAT 59.454 38.462 0.00 0.00 32.53 3.96
802 835 4.642488 TGTGGGTAGCCGTGGGGA 62.642 66.667 6.45 0.00 34.06 4.81
818 851 3.039405 CAACTTCGCGCTCTAGATACTG 58.961 50.000 5.56 0.00 0.00 2.74
819 852 2.033550 CCAACTTCGCGCTCTAGATACT 59.966 50.000 5.56 0.00 0.00 2.12
826 859 4.008933 AGCCCAACTTCGCGCTCT 62.009 61.111 5.56 0.00 0.00 4.09
840 873 1.093159 CTCAAAGTGCCTCATCAGCC 58.907 55.000 0.00 0.00 0.00 4.85
854 887 1.641140 CAACACAGTCGCGCTCAAA 59.359 52.632 5.56 0.00 0.00 2.69
856 889 2.661537 CCAACACAGTCGCGCTCA 60.662 61.111 5.56 0.00 0.00 4.26
900 937 2.126618 TGCCTACGTTCGTCGCAG 60.127 61.111 13.31 2.34 44.19 5.18
922 959 1.002624 GCCCGGTCCTTGTCATGAA 60.003 57.895 0.00 0.00 0.00 2.57
923 960 1.899437 GAGCCCGGTCCTTGTCATGA 61.899 60.000 0.00 0.00 0.00 3.07
947 985 8.981647 GTAAAGACCAAAGATACAACTAAACGA 58.018 33.333 0.00 0.00 0.00 3.85
967 1005 0.103572 GTATCAGCCCGCCGTAAAGA 59.896 55.000 0.00 0.00 0.00 2.52
994 1032 0.034186 CATGCAGGGTGGTGGTGTAT 60.034 55.000 0.00 0.00 0.00 2.29
995 1033 1.130678 TCATGCAGGGTGGTGGTGTA 61.131 55.000 0.00 0.00 0.00 2.90
996 1034 2.115910 CATGCAGGGTGGTGGTGT 59.884 61.111 0.00 0.00 0.00 4.16
997 1035 1.973281 GTCATGCAGGGTGGTGGTG 60.973 63.158 0.00 0.00 0.00 4.17
998 1036 2.436109 GTCATGCAGGGTGGTGGT 59.564 61.111 0.00 0.00 0.00 4.16
999 1037 2.747460 CGTCATGCAGGGTGGTGG 60.747 66.667 0.00 0.00 0.00 4.61
1000 1038 3.434319 GCGTCATGCAGGGTGGTG 61.434 66.667 0.00 0.00 45.45 4.17
1009 1047 2.703409 GTCCGTCATGCGTCATGC 59.297 61.111 13.00 8.64 41.18 4.06
1010 1048 1.474648 CTCGTCCGTCATGCGTCATG 61.475 60.000 11.97 11.97 42.60 3.07
1011 1049 1.226688 CTCGTCCGTCATGCGTCAT 60.227 57.895 8.37 0.00 39.32 3.06
1012 1050 2.178273 CTCGTCCGTCATGCGTCA 59.822 61.111 8.37 0.00 39.32 4.35
1013 1051 2.579787 CCTCGTCCGTCATGCGTC 60.580 66.667 8.37 1.98 39.32 5.19
1014 1052 3.371063 ACCTCGTCCGTCATGCGT 61.371 61.111 8.37 0.00 39.32 5.24
1015 1053 2.880879 CACCTCGTCCGTCATGCG 60.881 66.667 3.02 3.02 40.95 4.73
1016 1054 2.509336 CCACCTCGTCCGTCATGC 60.509 66.667 0.00 0.00 0.00 4.06
1017 1055 2.509336 GCCACCTCGTCCGTCATG 60.509 66.667 0.00 0.00 0.00 3.07
1018 1056 2.680352 AGCCACCTCGTCCGTCAT 60.680 61.111 0.00 0.00 0.00 3.06
1019 1057 3.371063 GAGCCACCTCGTCCGTCA 61.371 66.667 0.00 0.00 0.00 4.35
1020 1058 3.371063 TGAGCCACCTCGTCCGTC 61.371 66.667 0.00 0.00 41.13 4.79
1021 1059 3.681835 GTGAGCCACCTCGTCCGT 61.682 66.667 0.00 0.00 41.13 4.69
1022 1060 3.680786 TGTGAGCCACCTCGTCCG 61.681 66.667 3.33 0.00 41.13 4.79
1023 1061 2.048127 GTGTGAGCCACCTCGTCC 60.048 66.667 3.33 0.00 41.13 4.79
1200 1240 2.210711 GGCGATCGGAAGGGGAGAT 61.211 63.158 18.30 0.00 0.00 2.75
1241 1281 4.779733 AGAGATCGGGGTGCGGGT 62.780 66.667 0.00 0.00 0.00 5.28
1258 1298 2.301296 CAGAAACAGAGAGAGGAAGCCA 59.699 50.000 0.00 0.00 0.00 4.75
1259 1299 2.934801 GCAGAAACAGAGAGAGGAAGCC 60.935 54.545 0.00 0.00 0.00 4.35
1486 1527 0.953960 GTTCTGTCGCCCAAATCCGT 60.954 55.000 0.00 0.00 0.00 4.69
1855 1896 1.008995 CCCAACGTGGCAAAAGTCG 60.009 57.895 0.00 0.00 35.79 4.18
1907 1948 4.380233 GCAGACACAAATGGAAATCTGGAG 60.380 45.833 0.00 0.00 35.25 3.86
2165 2206 1.867233 GGCAGCAGGTATATGAACGTG 59.133 52.381 0.00 0.00 38.09 4.49
2166 2207 1.484653 TGGCAGCAGGTATATGAACGT 59.515 47.619 0.00 0.00 0.00 3.99
2484 2525 1.271934 TCACAAAATGGCGGTTCATGG 59.728 47.619 0.00 0.00 0.00 3.66
2614 2655 0.668535 GAAGGTCCTTTTGCTTGCGT 59.331 50.000 5.36 0.00 0.00 5.24
2616 2657 2.560105 AGATGAAGGTCCTTTTGCTTGC 59.440 45.455 5.36 0.00 0.00 4.01
2671 2712 1.868109 GCGCTCCGAACATACAGCATA 60.868 52.381 0.00 0.00 0.00 3.14
2756 2829 1.001633 GGACAAAGCGAAGTACTCCCA 59.998 52.381 0.00 0.00 0.00 4.37
2764 2837 1.433534 GACAGAGGGACAAAGCGAAG 58.566 55.000 0.00 0.00 0.00 3.79
2985 3145 3.502211 AGGGTAATTCTGCAGTTCGTTTG 59.498 43.478 14.67 0.00 0.00 2.93
3090 3251 5.322754 CATCATCTAGGGCAGAATTTCCAT 58.677 41.667 0.00 0.00 36.67 3.41
3221 3382 6.866480 AGCATGTTTTTCCATGATAATTCGT 58.134 32.000 5.39 0.00 43.99 3.85
3264 3425 4.035091 GCCATGTGCAACTATATTCGAACA 59.965 41.667 0.00 0.00 40.77 3.18
3667 3830 4.935352 TTAATGTGACAAAAAGCTGCCT 57.065 36.364 0.00 0.00 0.00 4.75
3708 3871 7.517614 TCAAACTTCAATGCAACCTACATAA 57.482 32.000 0.00 0.00 0.00 1.90
3796 3959 2.262423 AGGAGTTGACTGTCCAAAGC 57.738 50.000 5.17 0.00 35.02 3.51
3896 4059 1.887707 GGTACACCATAGCAGCCGC 60.888 63.158 0.00 0.00 35.36 6.53
4449 4612 3.745458 AGGCTTTGTTGTTGTTGTTGTTG 59.255 39.130 0.00 0.00 0.00 3.33
4450 4613 4.001618 AGGCTTTGTTGTTGTTGTTGTT 57.998 36.364 0.00 0.00 0.00 2.83
4451 4614 3.676291 AGGCTTTGTTGTTGTTGTTGT 57.324 38.095 0.00 0.00 0.00 3.32
4452 4615 5.637387 ACTAAAGGCTTTGTTGTTGTTGTTG 59.363 36.000 22.32 0.00 0.00 3.33
4453 4616 5.789521 ACTAAAGGCTTTGTTGTTGTTGTT 58.210 33.333 22.32 0.00 0.00 2.83
4455 4618 4.803613 GGACTAAAGGCTTTGTTGTTGTTG 59.196 41.667 22.32 0.00 0.00 3.33
4458 4621 3.314080 TCGGACTAAAGGCTTTGTTGTTG 59.686 43.478 22.32 13.36 0.00 3.33
4459 4622 3.547746 TCGGACTAAAGGCTTTGTTGTT 58.452 40.909 22.32 1.84 0.00 2.83
4460 4623 3.202829 TCGGACTAAAGGCTTTGTTGT 57.797 42.857 22.32 16.69 0.00 3.32
4462 4625 3.949113 TGTTTCGGACTAAAGGCTTTGTT 59.051 39.130 22.32 8.73 0.00 2.83
4464 4627 4.036380 ACTTGTTTCGGACTAAAGGCTTTG 59.964 41.667 22.32 13.97 0.00 2.77
4465 4628 4.204799 ACTTGTTTCGGACTAAAGGCTTT 58.795 39.130 17.76 17.76 0.00 3.51
4466 4629 3.816994 ACTTGTTTCGGACTAAAGGCTT 58.183 40.909 0.00 0.00 0.00 4.35
4467 4630 3.487120 ACTTGTTTCGGACTAAAGGCT 57.513 42.857 0.00 0.00 0.00 4.58
4468 4631 3.304458 CCAACTTGTTTCGGACTAAAGGC 60.304 47.826 0.00 0.00 0.00 4.35
4469 4632 3.252458 CCCAACTTGTTTCGGACTAAAGG 59.748 47.826 0.00 0.00 0.00 3.11
4471 4634 3.215975 CCCCAACTTGTTTCGGACTAAA 58.784 45.455 0.00 0.00 0.00 1.85
4472 4635 2.173143 ACCCCAACTTGTTTCGGACTAA 59.827 45.455 3.47 0.00 0.00 2.24
4473 4636 1.770061 ACCCCAACTTGTTTCGGACTA 59.230 47.619 3.47 0.00 0.00 2.59
4475 4638 2.148768 CTACCCCAACTTGTTTCGGAC 58.851 52.381 3.47 0.00 0.00 4.79
4476 4639 1.072648 CCTACCCCAACTTGTTTCGGA 59.927 52.381 3.47 0.00 0.00 4.55
4477 4640 1.530323 CCTACCCCAACTTGTTTCGG 58.470 55.000 0.00 0.00 0.00 4.30
4478 4641 0.879090 GCCTACCCCAACTTGTTTCG 59.121 55.000 0.00 0.00 0.00 3.46
4479 4642 2.287977 AGCCTACCCCAACTTGTTTC 57.712 50.000 0.00 0.00 0.00 2.78
4480 4643 2.983898 TCTAGCCTACCCCAACTTGTTT 59.016 45.455 0.00 0.00 0.00 2.83
4482 4645 2.188817 CTCTAGCCTACCCCAACTTGT 58.811 52.381 0.00 0.00 0.00 3.16
4483 4646 1.486726 CCTCTAGCCTACCCCAACTTG 59.513 57.143 0.00 0.00 0.00 3.16
4484 4647 1.080666 ACCTCTAGCCTACCCCAACTT 59.919 52.381 0.00 0.00 0.00 2.66
4485 4648 0.717196 ACCTCTAGCCTACCCCAACT 59.283 55.000 0.00 0.00 0.00 3.16
4486 4649 0.831307 CACCTCTAGCCTACCCCAAC 59.169 60.000 0.00 0.00 0.00 3.77
4487 4650 0.714180 TCACCTCTAGCCTACCCCAA 59.286 55.000 0.00 0.00 0.00 4.12
4488 4651 0.032416 GTCACCTCTAGCCTACCCCA 60.032 60.000 0.00 0.00 0.00 4.96
4489 4652 0.032416 TGTCACCTCTAGCCTACCCC 60.032 60.000 0.00 0.00 0.00 4.95
4490 4653 2.089600 ATGTCACCTCTAGCCTACCC 57.910 55.000 0.00 0.00 0.00 3.69
4491 4654 4.216708 AGTTATGTCACCTCTAGCCTACC 58.783 47.826 0.00 0.00 0.00 3.18
4492 4655 4.888239 TGAGTTATGTCACCTCTAGCCTAC 59.112 45.833 0.00 0.00 0.00 3.18
4493 4656 5.125367 TGAGTTATGTCACCTCTAGCCTA 57.875 43.478 0.00 0.00 0.00 3.93
4494 4657 3.957497 CTGAGTTATGTCACCTCTAGCCT 59.043 47.826 0.00 0.00 0.00 4.58
4495 4658 3.068873 CCTGAGTTATGTCACCTCTAGCC 59.931 52.174 0.00 0.00 0.00 3.93
4496 4659 3.068873 CCCTGAGTTATGTCACCTCTAGC 59.931 52.174 0.00 0.00 0.00 3.42
4497 4660 4.282496 ACCCTGAGTTATGTCACCTCTAG 58.718 47.826 0.00 0.00 0.00 2.43
4498 4661 4.017407 AGACCCTGAGTTATGTCACCTCTA 60.017 45.833 0.00 0.00 0.00 2.43
4499 4662 3.100671 GACCCTGAGTTATGTCACCTCT 58.899 50.000 0.00 0.00 0.00 3.69
4500 4663 3.100671 AGACCCTGAGTTATGTCACCTC 58.899 50.000 0.00 0.00 0.00 3.85
4501 4664 3.191888 AGACCCTGAGTTATGTCACCT 57.808 47.619 0.00 0.00 0.00 4.00
4502 4665 3.983044 AAGACCCTGAGTTATGTCACC 57.017 47.619 0.00 0.00 0.00 4.02
4503 4666 5.419471 AGACTAAGACCCTGAGTTATGTCAC 59.581 44.000 0.00 0.00 0.00 3.67
4615 4779 1.135333 GACCTGACGAATCTCTCCACC 59.865 57.143 0.00 0.00 0.00 4.61
4756 4920 6.367686 TGAGCACTTGCATATCTAATTGTG 57.632 37.500 3.62 0.00 45.16 3.33
4896 5060 8.758633 ATATAGTGATGTTAACGCAATAGGTC 57.241 34.615 12.01 0.00 0.00 3.85
5224 5513 4.904241 AGACACAGAAGAAGCAAGCTAAT 58.096 39.130 0.00 0.00 0.00 1.73
5627 5916 5.531287 GGGAAGCAGTAATCCGACAATTAAT 59.469 40.000 0.00 0.00 36.54 1.40
5941 6493 6.210584 ACCAATGTATTAAACAAAGGGACTGG 59.789 38.462 12.17 0.00 42.70 4.00
6193 6755 6.483307 TGTAGAAAAACAGGTGAGAGTTCATG 59.517 38.462 0.00 0.00 35.39 3.07
6219 6781 7.907841 TGCTTTATGAGACTACCATACCTTA 57.092 36.000 0.00 0.00 0.00 2.69
6415 6977 6.296605 CAAACCCGATCGATATAAAATCGTG 58.703 40.000 18.66 0.00 40.41 4.35
6429 6991 4.450082 AATTTAAGTGGCAAACCCGATC 57.550 40.909 0.00 0.00 35.87 3.69
6527 7104 6.071447 CCTGTGAACAATGACATTTATGGGAA 60.071 38.462 0.00 0.00 0.00 3.97
6750 7690 6.341316 TGCTAATCAAGTATTCTGACCTGTC 58.659 40.000 0.00 0.00 0.00 3.51
6771 7711 7.116075 ACAATTTCATATGGCTAACAATGCT 57.884 32.000 2.13 0.00 0.00 3.79
6811 7751 8.994170 GGAAAATCTACAGAAATCTATACTGGC 58.006 37.037 0.00 0.00 36.17 4.85
6830 7770 5.049129 GCCATGCTATAGTCACTGGAAAATC 60.049 44.000 18.40 6.88 0.00 2.17
6932 7872 1.631071 TAACCATGCTCCCATCGCCA 61.631 55.000 0.00 0.00 0.00 5.69
7086 8026 5.348986 AGTAACACTATTGTATGAGGTGCG 58.651 41.667 0.00 0.00 33.55 5.34
7168 8108 8.800332 GTCAAAAATGCTCTGATATTATGGGAT 58.200 33.333 0.00 0.00 0.00 3.85
7214 8154 2.168728 GCTCCCTCCGTCCCATAATATC 59.831 54.545 0.00 0.00 0.00 1.63
7363 8303 2.166664 GACAGTTCTCCCGTAGCAGATT 59.833 50.000 0.00 0.00 0.00 2.40
7403 8343 2.677848 GTCCCTCCCTTGGGCTTC 59.322 66.667 0.00 0.00 46.67 3.86
7517 8457 6.334102 TGCATTCGGTTTTACAATTAGGTT 57.666 33.333 0.00 0.00 0.00 3.50
7749 8691 3.249481 AGGAAAATCCCTATGCATGGG 57.751 47.619 21.68 21.68 45.90 4.00
7776 8718 4.737855 TCAATCAACTAGACACCCTAGC 57.262 45.455 0.00 0.00 46.98 3.42
7780 8722 6.127897 CCAAAAGATCAATCAACTAGACACCC 60.128 42.308 0.00 0.00 0.00 4.61
7793 8776 6.360618 GGTCCTACTCATCCAAAAGATCAAT 58.639 40.000 0.00 0.00 30.59 2.57
7802 8785 4.552883 TCATAGGGTCCTACTCATCCAA 57.447 45.455 0.00 0.00 0.00 3.53
7847 8830 9.765795 TTTTCGCCCTTTAAATTTGAAAAGATA 57.234 25.926 12.91 0.00 35.19 1.98
7862 8845 0.481128 TCTTCCCCTTTTCGCCCTTT 59.519 50.000 0.00 0.00 0.00 3.11
7863 8846 0.481128 TTCTTCCCCTTTTCGCCCTT 59.519 50.000 0.00 0.00 0.00 3.95
7868 8859 3.630312 TCTTTGTGTTCTTCCCCTTTTCG 59.370 43.478 0.00 0.00 0.00 3.46
7876 8876 5.532779 AGTGATTTCCTCTTTGTGTTCTTCC 59.467 40.000 0.00 0.00 0.00 3.46
7920 8931 9.746457 ATCTCATGTGTGCTATTCTAGTAGATA 57.254 33.333 0.00 0.00 0.00 1.98
7924 8935 8.138074 GTGAATCTCATGTGTGCTATTCTAGTA 58.862 37.037 0.00 0.00 32.22 1.82
7958 8969 6.044682 GCTATTTTCCCTTGATTGTTCATGG 58.955 40.000 0.00 1.89 43.55 3.66
8055 9069 5.157395 TCCATCATAGGATCATCAAGACCA 58.843 41.667 0.00 0.00 31.23 4.02
8134 9149 6.428083 AGCAGATGAGATCATTTGAGAGAT 57.572 37.500 15.41 0.00 39.88 2.75
8193 9215 4.804420 TCCCTCGCCTCCAGCCAT 62.804 66.667 0.00 0.00 38.78 4.40
8215 9237 1.075601 TGTCTCTTTTGCCCCTCCAT 58.924 50.000 0.00 0.00 0.00 3.41
8285 9307 4.973055 GCGTGTACCGTGCCCACA 62.973 66.667 5.79 0.00 39.32 4.17
8405 9464 4.373116 GAAGACGTGCCCAGGCGA 62.373 66.667 3.83 0.00 45.51 5.54
8415 9475 1.506493 CAGCAGCAAGAAGAAGACGT 58.494 50.000 0.00 0.00 0.00 4.34
8450 9510 2.224066 CCAACAAGGACGAGAAGACTGT 60.224 50.000 0.00 0.00 41.22 3.55
8467 9530 1.235281 GGAACCTCGCCAAGTCCAAC 61.235 60.000 0.00 0.00 0.00 3.77
8551 9620 3.508793 GCTTGACATGAATATGGATGGGG 59.491 47.826 0.00 0.00 38.66 4.96


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

AutoCloner maintained by Alex Coulton.