Multiple sequence alignment - TraesCS1B01G426200

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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 TraesCS1B01G426200 chr1B 100.000 4936 0 0 1 4936 652452863 652457798 0.000000e+00 9116.0
1 TraesCS1B01G426200 chr1A 93.237 4924 202 58 77 4936 563679881 563684737 0.000000e+00 7127.0
2 TraesCS1B01G426200 chr1A 91.667 48 4 0 2321 2368 563681991 563682038 3.190000e-07 67.6
3 TraesCS1B01G426200 chr1D 94.812 2236 99 10 77 2309 470070576 470072797 0.000000e+00 3470.0
4 TraesCS1B01G426200 chr1D 94.176 1202 45 16 3107 4298 470073647 470074833 0.000000e+00 1808.0
5 TraesCS1B01G426200 chr1D 95.890 876 31 4 2237 3109 470072671 470073544 0.000000e+00 1413.0
6 TraesCS1B01G426200 chr1D 86.925 696 26 15 4288 4936 470074853 470075530 0.000000e+00 721.0
7 TraesCS1B01G426200 chr1D 89.487 390 35 3 77 461 354747532 354747920 5.740000e-134 488.0
8 TraesCS1B01G426200 chr1D 88.608 79 9 0 2294 2372 470072674 470072752 4.070000e-16 97.1
9 TraesCS1B01G426200 chr1D 90.385 52 5 0 2321 2372 470072674 470072725 8.870000e-08 69.4
10 TraesCS1B01G426200 chr3D 90.513 390 31 3 77 461 549966087 549966475 1.230000e-140 510.0
11 TraesCS1B01G426200 chr3D 89.231 390 36 3 77 461 550030377 550029989 2.670000e-132 483.0
12 TraesCS1B01G426200 chr5D 89.744 390 34 3 77 461 563497481 563497093 1.230000e-135 494.0
13 TraesCS1B01G426200 chr2D 88.718 390 38 3 77 461 496894572 496894960 5.780000e-129 472.0
14 TraesCS1B01G426200 chr7D 92.784 97 7 0 196 292 134508547 134508643 1.850000e-29 141.0
15 TraesCS1B01G426200 chr7D 92.208 77 5 1 77 153 134508476 134508551 1.880000e-19 108.0
16 TraesCS1B01G426200 chr5A 91.753 97 8 0 196 292 296678721 296678817 8.620000e-28 135.0
17 TraesCS1B01G426200 chr6B 83.696 92 12 3 4322 4413 4295805 4295717 3.170000e-12 84.2
18 TraesCS1B01G426200 chr3A 96.078 51 2 0 103 153 458178304 458178254 3.170000e-12 84.2


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 TraesCS1B01G426200 chr1B 652452863 652457798 4935 False 9116.000000 9116 100.000000 1 4936 1 chr1B.!!$F1 4935
1 TraesCS1B01G426200 chr1A 563679881 563684737 4856 False 3597.300000 7127 92.452000 77 4936 2 chr1A.!!$F1 4859
2 TraesCS1B01G426200 chr1D 470070576 470075530 4954 False 1263.083333 3470 91.799333 77 4936 6 chr1D.!!$F2 4859

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
73 74 0.029300 CCGTGTTTCTGCAACTGTGG 59.971 55.0 0.00 0.0 36.21 4.17 F
431 437 0.037590 ACGCAAGGGTATTGCCTGAA 59.962 50.0 6.98 0.0 42.10 3.02 F
2297 2312 0.040058 AATCCTGCTGGAATGGTGCA 59.960 50.0 17.04 0.0 46.80 4.57 F
2298 2313 0.040058 ATCCTGCTGGAATGGTGCAA 59.960 50.0 17.04 0.0 46.80 4.08 F
2299 2314 0.609957 TCCTGCTGGAATGGTGCAAG 60.610 55.0 10.32 0.0 39.87 4.01 F
2301 2316 0.896940 CTGCTGGAATGGTGCAAGGT 60.897 55.0 0.00 0.0 36.22 3.50 F
3831 3964 0.741915 GGCGAGAGACCTTGTAGGAG 59.258 60.0 0.00 0.0 37.67 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1157 1169 3.185246 GTGAATCACGGACTCCATCAT 57.815 47.619 0.00 0.00 0.00 2.45 R
2309 2324 0.178953 ACCTTGCACCATTCCAGCTT 60.179 50.000 0.00 0.00 0.00 3.74 R
3462 3593 0.039035 GCCCTGGGAACAACATACCA 59.961 55.000 19.27 0.00 42.06 3.25 R
3747 3879 0.671472 CAGAGACGGCATTGACAGCA 60.671 55.000 0.00 0.00 0.00 4.41 R
3779 3912 1.202087 TGCAAAGACACGGAACAAACG 60.202 47.619 0.00 0.00 37.36 3.60 R
3921 4054 1.299562 CTGCTTCACTCTGCTGGCAG 61.300 60.000 10.94 10.94 44.86 4.85 R
4654 4874 1.354368 TCTTACAGGCCTTTCCTTGGG 59.646 52.381 0.00 0.00 44.75 4.12 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
22 23 4.893795 GTTAACGGATTTCACGAGATTGG 58.106 43.478 0.00 0.00 34.93 3.16
23 24 2.762535 ACGGATTTCACGAGATTGGT 57.237 45.000 0.00 0.00 34.93 3.67
24 25 3.053831 ACGGATTTCACGAGATTGGTT 57.946 42.857 0.00 0.00 34.93 3.67
25 26 2.742053 ACGGATTTCACGAGATTGGTTG 59.258 45.455 0.00 0.00 34.93 3.77
26 27 2.476185 CGGATTTCACGAGATTGGTTGC 60.476 50.000 0.00 0.00 0.00 4.17
27 28 2.159379 GGATTTCACGAGATTGGTTGCC 60.159 50.000 0.00 0.00 0.00 4.52
28 29 2.270352 TTTCACGAGATTGGTTGCCT 57.730 45.000 0.00 0.00 0.00 4.75
29 30 3.410631 TTTCACGAGATTGGTTGCCTA 57.589 42.857 0.00 0.00 0.00 3.93
30 31 2.672961 TCACGAGATTGGTTGCCTAG 57.327 50.000 0.00 0.00 0.00 3.02
31 32 2.176045 TCACGAGATTGGTTGCCTAGA 58.824 47.619 0.00 0.00 0.00 2.43
32 33 2.166459 TCACGAGATTGGTTGCCTAGAG 59.834 50.000 0.00 0.00 0.00 2.43
33 34 1.482593 ACGAGATTGGTTGCCTAGAGG 59.517 52.381 0.00 0.00 38.53 3.69
34 35 1.482593 CGAGATTGGTTGCCTAGAGGT 59.517 52.381 0.00 0.00 37.57 3.85
35 36 2.093447 CGAGATTGGTTGCCTAGAGGTT 60.093 50.000 0.00 0.00 37.57 3.50
36 37 3.619979 CGAGATTGGTTGCCTAGAGGTTT 60.620 47.826 0.00 0.00 37.57 3.27
37 38 4.336280 GAGATTGGTTGCCTAGAGGTTTT 58.664 43.478 0.00 0.00 37.57 2.43
38 39 4.336280 AGATTGGTTGCCTAGAGGTTTTC 58.664 43.478 0.00 0.00 37.57 2.29
39 40 2.579410 TGGTTGCCTAGAGGTTTTCC 57.421 50.000 0.00 0.00 41.05 3.13
40 41 1.777878 TGGTTGCCTAGAGGTTTTCCA 59.222 47.619 0.00 0.00 43.73 3.53
41 42 2.378547 TGGTTGCCTAGAGGTTTTCCAT 59.621 45.455 0.00 0.00 43.73 3.41
42 43 3.181423 TGGTTGCCTAGAGGTTTTCCATT 60.181 43.478 0.00 0.00 43.73 3.16
43 44 3.444034 GGTTGCCTAGAGGTTTTCCATTC 59.556 47.826 0.00 0.00 43.73 2.67
44 45 3.366052 TGCCTAGAGGTTTTCCATTCC 57.634 47.619 0.00 0.00 43.73 3.01
45 46 2.647299 TGCCTAGAGGTTTTCCATTCCA 59.353 45.455 0.00 0.00 43.73 3.53
46 47 3.269381 TGCCTAGAGGTTTTCCATTCCAT 59.731 43.478 0.00 0.00 43.73 3.41
47 48 3.885901 GCCTAGAGGTTTTCCATTCCATC 59.114 47.826 0.00 0.00 43.73 3.51
48 49 4.464947 CCTAGAGGTTTTCCATTCCATCC 58.535 47.826 0.00 0.00 43.73 3.51
49 50 4.166919 CCTAGAGGTTTTCCATTCCATCCT 59.833 45.833 0.00 0.00 43.73 3.24
50 51 4.682021 AGAGGTTTTCCATTCCATCCTT 57.318 40.909 0.00 0.00 43.73 3.36
51 52 4.347607 AGAGGTTTTCCATTCCATCCTTG 58.652 43.478 0.00 0.00 43.73 3.61
52 53 3.444029 AGGTTTTCCATTCCATCCTTGG 58.556 45.455 0.00 0.00 42.93 3.61
53 54 3.077391 AGGTTTTCCATTCCATCCTTGGA 59.923 43.478 0.00 0.00 46.04 3.53
54 55 3.195610 GGTTTTCCATTCCATCCTTGGAC 59.804 47.826 0.00 0.00 45.06 4.02
55 56 5.896295 GGTTTTCCATTCCATCCTTGGACC 61.896 50.000 0.00 0.00 45.06 4.46
61 62 3.339547 CCATCCTTGGACCGTGTTT 57.660 52.632 0.00 0.00 46.92 2.83
62 63 1.165270 CCATCCTTGGACCGTGTTTC 58.835 55.000 0.00 0.00 46.92 2.78
63 64 1.271379 CCATCCTTGGACCGTGTTTCT 60.271 52.381 0.00 0.00 46.92 2.52
64 65 1.806542 CATCCTTGGACCGTGTTTCTG 59.193 52.381 0.00 0.00 0.00 3.02
65 66 0.534203 TCCTTGGACCGTGTTTCTGC 60.534 55.000 0.00 0.00 0.00 4.26
66 67 0.817634 CCTTGGACCGTGTTTCTGCA 60.818 55.000 0.00 0.00 0.00 4.41
67 68 1.021202 CTTGGACCGTGTTTCTGCAA 58.979 50.000 0.00 0.00 0.00 4.08
68 69 0.736053 TTGGACCGTGTTTCTGCAAC 59.264 50.000 0.00 0.00 35.71 4.17
69 70 0.107410 TGGACCGTGTTTCTGCAACT 60.107 50.000 0.00 0.00 36.21 3.16
70 71 0.307760 GGACCGTGTTTCTGCAACTG 59.692 55.000 0.00 0.00 36.21 3.16
71 72 1.014352 GACCGTGTTTCTGCAACTGT 58.986 50.000 0.00 0.00 36.21 3.55
72 73 0.732571 ACCGTGTTTCTGCAACTGTG 59.267 50.000 0.00 0.00 36.21 3.66
73 74 0.029300 CCGTGTTTCTGCAACTGTGG 59.971 55.000 0.00 0.00 36.21 4.17
74 75 0.732571 CGTGTTTCTGCAACTGTGGT 59.267 50.000 0.00 0.00 36.21 4.16
75 76 1.531677 CGTGTTTCTGCAACTGTGGTG 60.532 52.381 0.00 0.00 36.21 4.17
76 77 1.472480 GTGTTTCTGCAACTGTGGTGT 59.528 47.619 0.00 0.00 36.21 4.16
77 78 1.472082 TGTTTCTGCAACTGTGGTGTG 59.528 47.619 0.00 0.00 36.21 3.82
78 79 1.102154 TTTCTGCAACTGTGGTGTGG 58.898 50.000 0.00 0.00 0.00 4.17
79 80 0.254462 TTCTGCAACTGTGGTGTGGA 59.746 50.000 0.00 0.00 0.00 4.02
80 81 0.463654 TCTGCAACTGTGGTGTGGAC 60.464 55.000 0.00 0.00 0.00 4.02
81 82 0.747644 CTGCAACTGTGGTGTGGACA 60.748 55.000 0.00 0.00 0.00 4.02
82 83 0.747644 TGCAACTGTGGTGTGGACAG 60.748 55.000 0.00 0.00 45.39 3.51
101 102 0.920664 GTTTGTTTTCACAGCGTGCC 59.079 50.000 4.15 0.00 33.22 5.01
180 183 4.457496 ATGTGCCTGGACGAGCGG 62.457 66.667 0.00 0.00 0.00 5.52
195 198 3.445096 ACGAGCGGGTGTAGTTAATTAGT 59.555 43.478 0.00 0.00 0.00 2.24
237 240 1.599071 CTTTTTGCAGTGAGCTGTCGA 59.401 47.619 0.00 0.00 45.94 4.20
238 241 0.937304 TTTTGCAGTGAGCTGTCGAC 59.063 50.000 9.11 9.11 45.94 4.20
259 262 4.324267 ACACAGGGTACAACTGCTTAATC 58.676 43.478 14.55 0.00 39.55 1.75
268 271 7.409697 GGTACAACTGCTTAATCATACACATG 58.590 38.462 0.00 0.00 0.00 3.21
314 320 6.980051 ACACTCTTGTTTTTACTCTTCGTT 57.020 33.333 0.00 0.00 28.43 3.85
387 393 7.284034 CCCTCATCTTGATTTTATTACTGCAGT 59.716 37.037 25.12 25.12 0.00 4.40
431 437 0.037590 ACGCAAGGGTATTGCCTGAA 59.962 50.000 6.98 0.00 42.10 3.02
437 443 1.065126 AGGGTATTGCCTGAACAGAGC 60.065 52.381 3.19 5.97 37.43 4.09
446 452 2.095364 GCCTGAACAGAGCAATTGAGTG 60.095 50.000 10.34 5.14 0.00 3.51
546 552 2.811431 TGTGCAGGAAATTTACACCTCG 59.189 45.455 2.58 0.00 31.06 4.63
566 572 7.645340 CACCTCGTTTCCATTTTTATGATGATC 59.355 37.037 0.00 0.00 0.00 2.92
605 611 7.433425 GCAAACTATTCCAAAATGCTATGAGAC 59.567 37.037 0.00 0.00 0.00 3.36
638 644 6.128035 TGTGAAACTCATATGTCCCGATTTTG 60.128 38.462 1.90 0.00 38.04 2.44
660 666 8.578308 TTTGTTCATTTAATGCTCTGTTGAAG 57.422 30.769 0.00 0.00 0.00 3.02
661 667 7.275888 TGTTCATTTAATGCTCTGTTGAAGT 57.724 32.000 0.00 0.00 0.00 3.01
743 755 7.448228 CACAATTAGTGTACAATCTTCTGTCG 58.552 38.462 0.00 0.00 43.40 4.35
744 756 6.090898 ACAATTAGTGTACAATCTTCTGTCGC 59.909 38.462 0.00 0.00 39.29 5.19
745 757 2.960819 AGTGTACAATCTTCTGTCGCC 58.039 47.619 0.00 0.00 0.00 5.54
746 758 2.299013 AGTGTACAATCTTCTGTCGCCA 59.701 45.455 0.00 0.00 0.00 5.69
747 759 3.055819 AGTGTACAATCTTCTGTCGCCAT 60.056 43.478 0.00 0.00 0.00 4.40
760 772 4.332543 TCTGTCGCCATTATGTTCATCAAC 59.667 41.667 0.00 0.00 0.00 3.18
786 798 4.590647 TGCTCATGCTAAGCCTTATCTACT 59.409 41.667 2.70 0.00 39.05 2.57
850 862 4.142038 AGTTTTTGTCCTGTACCATGACC 58.858 43.478 0.00 0.00 30.02 4.02
851 863 2.871096 TTTGTCCTGTACCATGACCC 57.129 50.000 0.00 0.00 30.02 4.46
855 867 2.225675 TGTCCTGTACCATGACCCCTTA 60.226 50.000 0.00 0.00 30.02 2.69
894 906 1.645265 CGCATTTTGCATGTCGACTTG 59.355 47.619 23.22 23.22 45.36 3.16
1157 1169 5.525484 TGGAGCTCCAGGAAATACTACTAA 58.475 41.667 32.00 2.41 42.01 2.24
1294 1306 4.022589 CGACTATGTACAATCCCGGTATGT 60.023 45.833 0.00 4.91 0.00 2.29
1463 1475 5.163622 CCATGAAAACGAGGAATGCTGTAAT 60.164 40.000 0.00 0.00 0.00 1.89
1983 1995 2.359531 GAGATGTGGAGAGGTAACCGAG 59.640 54.545 0.00 0.00 37.17 4.63
1996 2008 4.695928 AGGTAACCGAGAATCTTGCTTTTC 59.304 41.667 0.00 0.00 37.17 2.29
2075 2090 0.322816 CAAGCTGGCCCTTCTGCTAA 60.323 55.000 0.00 0.00 40.28 3.09
2209 2224 2.490903 CAAGGTGCAAATCCTTCTGGAG 59.509 50.000 4.16 0.00 46.91 3.86
2235 2250 3.402355 GCAAGGTGCAAATCCTTCTGGA 61.402 50.000 4.16 0.00 44.60 3.86
2236 2251 2.490903 CAAGGTGCAAATCCTTCTGGAG 59.509 50.000 4.16 0.00 46.91 3.86
2247 2262 0.109342 CTTCTGGAGTGGTGCAAGGT 59.891 55.000 0.00 0.00 0.00 3.50
2248 2263 0.179020 TTCTGGAGTGGTGCAAGGTG 60.179 55.000 0.00 0.00 0.00 4.00
2296 2311 1.134907 CAAATCCTGCTGGAATGGTGC 60.135 52.381 17.04 0.00 46.80 5.01
2297 2312 0.040058 AATCCTGCTGGAATGGTGCA 59.960 50.000 17.04 0.00 46.80 4.57
2298 2313 0.040058 ATCCTGCTGGAATGGTGCAA 59.960 50.000 17.04 0.00 46.80 4.08
2299 2314 0.609957 TCCTGCTGGAATGGTGCAAG 60.610 55.000 10.32 0.00 39.87 4.01
2300 2315 1.601419 CCTGCTGGAATGGTGCAAGG 61.601 60.000 2.92 0.00 36.22 3.61
2301 2316 0.896940 CTGCTGGAATGGTGCAAGGT 60.897 55.000 0.00 0.00 36.22 3.50
2302 2317 1.180456 TGCTGGAATGGTGCAAGGTG 61.180 55.000 0.00 0.00 33.48 4.00
2303 2318 1.588082 CTGGAATGGTGCAAGGTGC 59.412 57.895 0.00 0.00 45.29 5.01
2313 2328 3.900446 GCAAGGTGCAAATCAAGCT 57.100 47.368 0.00 0.00 44.26 3.74
2314 2329 1.425412 GCAAGGTGCAAATCAAGCTG 58.575 50.000 0.00 0.00 44.26 4.24
2315 2330 1.938016 GCAAGGTGCAAATCAAGCTGG 60.938 52.381 0.00 0.00 44.26 4.85
2316 2331 1.614903 CAAGGTGCAAATCAAGCTGGA 59.385 47.619 0.00 0.00 0.00 3.86
2317 2332 1.999648 AGGTGCAAATCAAGCTGGAA 58.000 45.000 0.00 0.00 0.00 3.53
2318 2333 2.532843 AGGTGCAAATCAAGCTGGAAT 58.467 42.857 0.00 0.00 0.00 3.01
2319 2334 2.232941 AGGTGCAAATCAAGCTGGAATG 59.767 45.455 0.00 0.00 0.00 2.67
2320 2335 2.613691 GTGCAAATCAAGCTGGAATGG 58.386 47.619 0.00 0.00 0.00 3.16
2321 2336 2.028748 GTGCAAATCAAGCTGGAATGGT 60.029 45.455 0.00 0.00 0.00 3.55
2322 2337 2.028839 TGCAAATCAAGCTGGAATGGTG 60.029 45.455 0.00 0.00 0.00 4.17
2508 2523 5.882000 TCAGGTGATTCACATTTCCATACAG 59.118 40.000 18.09 0.00 35.86 2.74
2616 2632 2.143122 CTACCTGCTGTTTCTTGCGAA 58.857 47.619 0.00 0.00 0.00 4.70
2944 2961 2.380064 TTCCCCTGCAATCTGTGTTT 57.620 45.000 0.00 0.00 0.00 2.83
3029 3048 5.631026 ACGTGATTATCATGTTTCTGTTGC 58.369 37.500 13.71 0.00 43.56 4.17
3083 3102 6.357579 ACAGACATTAAAATTTGCCATCCA 57.642 33.333 0.00 0.00 0.00 3.41
3266 3391 4.767928 GGGATATGGGGCTAGATATAGACG 59.232 50.000 0.00 0.00 0.00 4.18
3305 3430 1.002430 GGAGCAGATGACCAACTCACA 59.998 52.381 0.00 0.00 0.00 3.58
3306 3431 2.550855 GGAGCAGATGACCAACTCACAA 60.551 50.000 0.00 0.00 0.00 3.33
3307 3432 3.341823 GAGCAGATGACCAACTCACAAT 58.658 45.455 0.00 0.00 0.00 2.71
3315 3446 7.173907 CAGATGACCAACTCACAATAGTTTCTT 59.826 37.037 0.00 0.00 37.61 2.52
3328 3459 6.318648 ACAATAGTTTCTTGCAGACACTTTCA 59.681 34.615 9.29 0.00 36.69 2.69
3357 3488 9.072294 GGTTTGCATGTATGTAACTGATAAAAC 57.928 33.333 0.00 0.00 32.15 2.43
3359 3490 7.603963 TGCATGTATGTAACTGATAAAACGT 57.396 32.000 0.00 0.00 0.00 3.99
3441 3572 3.421844 GGTTTGCCAGAAAGGTACATCT 58.578 45.455 0.00 0.00 40.61 2.90
3462 3593 6.126863 TCTGTCAAAATCTGAGGGTACATT 57.873 37.500 0.00 0.00 33.60 2.71
3463 3594 5.939883 TCTGTCAAAATCTGAGGGTACATTG 59.060 40.000 0.00 0.00 33.60 2.82
3546 3677 8.455903 CATTATATGCCAGGTATTATCCCTTG 57.544 38.462 0.00 0.00 0.00 3.61
3567 3698 6.402983 CCTTGCACATTCTATCTCTTGTGTTC 60.403 42.308 4.11 0.00 41.14 3.18
3677 3809 6.116126 TCCTTATCCTTTTTAGAAGCAGCTC 58.884 40.000 0.00 0.00 0.00 4.09
3700 3832 7.764443 GCTCATTTACCTAGAACAGTCAATACA 59.236 37.037 0.00 0.00 0.00 2.29
3712 3844 3.753272 CAGTCAATACACCCCTTTGTCAG 59.247 47.826 0.00 0.00 0.00 3.51
3739 3871 5.096169 CGACGGCTAGATTAACCAGATATG 58.904 45.833 0.00 0.00 0.00 1.78
3747 3879 8.624776 GCTAGATTAACCAGATATGCAGTTTTT 58.375 33.333 0.00 0.00 0.00 1.94
3778 3911 2.870435 GCCGTCTCTGGTTTCTAAAGCA 60.870 50.000 7.09 7.09 43.36 3.91
3779 3912 2.737252 CCGTCTCTGGTTTCTAAAGCAC 59.263 50.000 3.33 0.00 41.03 4.40
3831 3964 0.741915 GGCGAGAGACCTTGTAGGAG 59.258 60.000 0.00 0.00 37.67 3.69
3896 4029 3.327757 AGTGGCTGATGGTGAAGAACTTA 59.672 43.478 0.00 0.00 0.00 2.24
3921 4054 0.170561 CATCTGCAAGGCAACAGCTC 59.829 55.000 0.00 0.00 38.41 4.09
3947 4080 2.031163 GAGTGAAGCAGCGGGTGT 59.969 61.111 9.16 0.00 0.00 4.16
3990 4123 1.082679 CCGCAGCAGTGACTGAGATG 61.083 60.000 18.18 12.14 39.55 2.90
3991 4124 0.108945 CGCAGCAGTGACTGAGATGA 60.109 55.000 18.18 0.00 39.55 2.92
3992 4125 1.471153 CGCAGCAGTGACTGAGATGAT 60.471 52.381 18.18 0.00 39.55 2.45
4030 4163 8.708378 TCTTGTACATAAGAGATGTTGGATGAT 58.292 33.333 0.00 0.00 33.08 2.45
4103 4236 3.876156 GCCCCAAAACTGTATAGCCAGAA 60.876 47.826 0.00 0.00 36.30 3.02
4104 4237 4.536765 CCCCAAAACTGTATAGCCAGAAT 58.463 43.478 0.00 0.00 36.30 2.40
4105 4238 4.339247 CCCCAAAACTGTATAGCCAGAATG 59.661 45.833 0.00 0.00 36.30 2.67
4106 4239 4.202050 CCCAAAACTGTATAGCCAGAATGC 60.202 45.833 0.00 0.00 36.30 3.56
4169 4304 3.204526 CCTGAACTTCTCTCATCATGGC 58.795 50.000 0.00 0.00 0.00 4.40
4176 4311 3.555527 TCTCTCATCATGGCTTTCCTG 57.444 47.619 0.00 0.00 0.00 3.86
4177 4312 2.172082 TCTCTCATCATGGCTTTCCTGG 59.828 50.000 0.00 0.00 0.00 4.45
4178 4313 2.172082 CTCTCATCATGGCTTTCCTGGA 59.828 50.000 0.00 0.00 0.00 3.86
4179 4314 2.781757 TCTCATCATGGCTTTCCTGGAT 59.218 45.455 0.00 0.00 0.00 3.41
4180 4315 3.203710 TCTCATCATGGCTTTCCTGGATT 59.796 43.478 0.00 0.00 0.00 3.01
4181 4316 3.293337 TCATCATGGCTTTCCTGGATTG 58.707 45.455 0.00 0.00 0.00 2.67
4182 4317 2.905415 TCATGGCTTTCCTGGATTGT 57.095 45.000 0.00 0.00 0.00 2.71
4183 4318 2.726821 TCATGGCTTTCCTGGATTGTC 58.273 47.619 0.00 0.00 0.00 3.18
4189 4324 0.039618 TTTCCTGGATTGTCTGCCCC 59.960 55.000 0.00 0.00 0.00 5.80
4248 4383 4.605640 TTCCCTTTGCCAAAAATCAGAG 57.394 40.909 0.00 0.00 0.00 3.35
4317 4482 2.611518 TGGTTTTGCAGTTTCGGTTTG 58.388 42.857 0.00 0.00 0.00 2.93
4318 4483 1.326245 GGTTTTGCAGTTTCGGTTTGC 59.674 47.619 0.00 0.00 38.30 3.68
4367 4539 6.926630 TGGCTTTTGGAGTTTGGTTTATAT 57.073 33.333 0.00 0.00 0.00 0.86
4368 4540 8.423906 TTGGCTTTTGGAGTTTGGTTTATATA 57.576 30.769 0.00 0.00 0.00 0.86
4369 4541 8.423906 TGGCTTTTGGAGTTTGGTTTATATAA 57.576 30.769 0.00 0.00 0.00 0.98
4371 4543 8.528643 GGCTTTTGGAGTTTGGTTTATATAACT 58.471 33.333 0.00 0.00 33.78 2.24
4372 4544 9.569167 GCTTTTGGAGTTTGGTTTATATAACTC 57.431 33.333 0.00 0.00 43.50 3.01
4412 4584 1.202557 TGCTCTTGGCTTTGGCTTTTG 60.203 47.619 0.00 0.00 42.39 2.44
4413 4585 1.069049 GCTCTTGGCTTTGGCTTTTGA 59.931 47.619 0.00 0.00 38.73 2.69
4416 4588 2.101249 TCTTGGCTTTGGCTTTTGACTG 59.899 45.455 0.00 0.00 38.73 3.51
4417 4589 0.752054 TGGCTTTGGCTTTTGACTGG 59.248 50.000 0.00 0.00 38.73 4.00
4418 4590 1.039856 GGCTTTGGCTTTTGACTGGA 58.960 50.000 0.00 0.00 38.73 3.86
4419 4591 1.620323 GGCTTTGGCTTTTGACTGGAT 59.380 47.619 0.00 0.00 38.73 3.41
4439 4616 8.585881 ACTGGATATACTGTTACATGATGGTAC 58.414 37.037 0.00 0.00 0.00 3.34
4542 4759 5.249393 ACTGTAGTTTTCATGATGGGAGTCT 59.751 40.000 0.00 0.00 0.00 3.24
4545 4762 3.084039 GTTTTCATGATGGGAGTCTGCA 58.916 45.455 0.00 0.00 0.00 4.41
4642 4862 5.105146 ACTCAGGAATACACAGATCCAAGAC 60.105 44.000 0.00 0.00 35.62 3.01
4654 4874 5.869888 ACAGATCCAAGACGTAGAAAACATC 59.130 40.000 0.00 0.00 0.00 3.06
4727 4947 7.556275 TCAAATCCCTAAACTATACCAGCAAAG 59.444 37.037 0.00 0.00 0.00 2.77
4753 4973 4.391830 TGTAGTCCTGAACGAATCAAATGC 59.608 41.667 0.00 0.00 37.67 3.56
4862 5082 5.162637 TCCCCTACAGTATAAGATGCCAAT 58.837 41.667 0.00 0.00 0.00 3.16
4863 5083 5.013079 TCCCCTACAGTATAAGATGCCAATG 59.987 44.000 0.00 0.00 0.00 2.82
4864 5084 4.697352 CCCTACAGTATAAGATGCCAATGC 59.303 45.833 0.00 0.00 38.26 3.56
4869 5089 2.457813 ATAAGATGCCAATGCCCACA 57.542 45.000 0.00 0.00 36.33 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.390909 ACCAATCTCGTGAAATCCGTTAAC 59.609 41.667 0.00 0.00 0.00 2.01
1 2 4.571919 ACCAATCTCGTGAAATCCGTTAA 58.428 39.130 0.00 0.00 0.00 2.01
2 3 4.196626 ACCAATCTCGTGAAATCCGTTA 57.803 40.909 0.00 0.00 0.00 3.18
3 4 3.053831 ACCAATCTCGTGAAATCCGTT 57.946 42.857 0.00 0.00 0.00 4.44
4 5 2.742053 CAACCAATCTCGTGAAATCCGT 59.258 45.455 0.00 0.00 0.00 4.69
5 6 2.476185 GCAACCAATCTCGTGAAATCCG 60.476 50.000 0.00 0.00 0.00 4.18
6 7 2.159379 GGCAACCAATCTCGTGAAATCC 60.159 50.000 0.00 0.00 0.00 3.01
7 8 2.749621 AGGCAACCAATCTCGTGAAATC 59.250 45.455 0.00 0.00 37.17 2.17
8 9 2.795329 AGGCAACCAATCTCGTGAAAT 58.205 42.857 0.00 0.00 37.17 2.17
9 10 2.270352 AGGCAACCAATCTCGTGAAA 57.730 45.000 0.00 0.00 37.17 2.69
10 11 2.565391 TCTAGGCAACCAATCTCGTGAA 59.435 45.455 0.00 0.00 37.17 3.18
11 12 2.166459 CTCTAGGCAACCAATCTCGTGA 59.834 50.000 0.00 0.00 37.17 4.35
12 13 2.544685 CTCTAGGCAACCAATCTCGTG 58.455 52.381 0.00 0.00 37.17 4.35
13 14 1.482593 CCTCTAGGCAACCAATCTCGT 59.517 52.381 0.00 0.00 37.17 4.18
14 15 1.482593 ACCTCTAGGCAACCAATCTCG 59.517 52.381 0.00 0.00 39.32 4.04
15 16 3.636153 AACCTCTAGGCAACCAATCTC 57.364 47.619 0.00 0.00 39.32 2.75
16 17 4.336280 GAAAACCTCTAGGCAACCAATCT 58.664 43.478 0.00 0.00 39.32 2.40
17 18 3.444034 GGAAAACCTCTAGGCAACCAATC 59.556 47.826 0.00 0.00 39.32 2.67
18 19 3.181423 TGGAAAACCTCTAGGCAACCAAT 60.181 43.478 0.00 0.00 39.32 3.16
19 20 2.175931 TGGAAAACCTCTAGGCAACCAA 59.824 45.455 0.00 0.00 39.32 3.67
20 21 1.777878 TGGAAAACCTCTAGGCAACCA 59.222 47.619 0.00 0.00 39.32 3.67
21 22 2.579410 TGGAAAACCTCTAGGCAACC 57.421 50.000 0.00 0.00 39.32 3.77
22 23 3.444034 GGAATGGAAAACCTCTAGGCAAC 59.556 47.826 0.00 0.00 39.32 4.17
23 24 3.075283 TGGAATGGAAAACCTCTAGGCAA 59.925 43.478 0.00 0.00 39.32 4.52
24 25 2.647299 TGGAATGGAAAACCTCTAGGCA 59.353 45.455 0.00 0.00 39.32 4.75
25 26 3.366052 TGGAATGGAAAACCTCTAGGC 57.634 47.619 0.00 0.00 39.32 3.93
26 27 4.166919 AGGATGGAATGGAAAACCTCTAGG 59.833 45.833 0.00 0.00 42.17 3.02
27 28 5.379706 AGGATGGAATGGAAAACCTCTAG 57.620 43.478 0.00 0.00 0.00 2.43
28 29 5.509498 CAAGGATGGAATGGAAAACCTCTA 58.491 41.667 0.00 0.00 0.00 2.43
29 30 4.347607 CAAGGATGGAATGGAAAACCTCT 58.652 43.478 0.00 0.00 0.00 3.69
30 31 4.725790 CAAGGATGGAATGGAAAACCTC 57.274 45.455 0.00 0.00 0.00 3.85
44 45 1.806542 CAGAAACACGGTCCAAGGATG 59.193 52.381 0.00 0.00 0.00 3.51
45 46 1.882352 GCAGAAACACGGTCCAAGGAT 60.882 52.381 0.00 0.00 0.00 3.24
46 47 0.534203 GCAGAAACACGGTCCAAGGA 60.534 55.000 0.00 0.00 0.00 3.36
47 48 0.817634 TGCAGAAACACGGTCCAAGG 60.818 55.000 0.00 0.00 0.00 3.61
48 49 1.021202 TTGCAGAAACACGGTCCAAG 58.979 50.000 0.00 0.00 0.00 3.61
49 50 0.736053 GTTGCAGAAACACGGTCCAA 59.264 50.000 0.00 0.00 38.75 3.53
50 51 0.107410 AGTTGCAGAAACACGGTCCA 60.107 50.000 0.00 0.00 41.61 4.02
51 52 0.307760 CAGTTGCAGAAACACGGTCC 59.692 55.000 0.00 0.00 41.61 4.46
52 53 1.014352 ACAGTTGCAGAAACACGGTC 58.986 50.000 0.00 0.00 41.61 4.79
53 54 0.732571 CACAGTTGCAGAAACACGGT 59.267 50.000 0.00 0.00 41.61 4.83
54 55 0.029300 CCACAGTTGCAGAAACACGG 59.971 55.000 0.00 0.00 41.61 4.94
55 56 0.732571 ACCACAGTTGCAGAAACACG 59.267 50.000 0.00 0.00 41.61 4.49
56 57 1.472480 ACACCACAGTTGCAGAAACAC 59.528 47.619 0.00 0.00 41.61 3.32
57 58 1.472082 CACACCACAGTTGCAGAAACA 59.528 47.619 0.00 0.00 41.61 2.83
58 59 1.202290 CCACACCACAGTTGCAGAAAC 60.202 52.381 0.00 0.00 39.24 2.78
59 60 1.102154 CCACACCACAGTTGCAGAAA 58.898 50.000 0.00 0.00 0.00 2.52
60 61 0.254462 TCCACACCACAGTTGCAGAA 59.746 50.000 0.00 0.00 0.00 3.02
61 62 0.463654 GTCCACACCACAGTTGCAGA 60.464 55.000 0.00 0.00 0.00 4.26
62 63 0.747644 TGTCCACACCACAGTTGCAG 60.748 55.000 0.00 0.00 0.00 4.41
63 64 0.747644 CTGTCCACACCACAGTTGCA 60.748 55.000 0.00 0.00 37.15 4.08
64 65 2.024918 CTGTCCACACCACAGTTGC 58.975 57.895 0.00 0.00 37.15 4.17
68 69 1.750193 ACAAACTGTCCACACCACAG 58.250 50.000 0.00 0.00 45.86 3.66
69 70 2.208132 AACAAACTGTCCACACCACA 57.792 45.000 0.00 0.00 0.00 4.17
70 71 3.057174 TGAAAACAAACTGTCCACACCAC 60.057 43.478 0.00 0.00 0.00 4.16
71 72 3.057174 GTGAAAACAAACTGTCCACACCA 60.057 43.478 0.00 0.00 0.00 4.17
72 73 3.057174 TGTGAAAACAAACTGTCCACACC 60.057 43.478 0.00 0.00 31.02 4.16
73 74 4.165779 CTGTGAAAACAAACTGTCCACAC 58.834 43.478 0.00 0.00 31.91 3.82
74 75 3.366883 GCTGTGAAAACAAACTGTCCACA 60.367 43.478 0.00 0.00 0.00 4.17
75 76 3.179048 GCTGTGAAAACAAACTGTCCAC 58.821 45.455 0.00 0.00 0.00 4.02
76 77 2.159448 CGCTGTGAAAACAAACTGTCCA 60.159 45.455 0.00 0.00 0.00 4.02
77 78 2.159435 ACGCTGTGAAAACAAACTGTCC 60.159 45.455 0.00 0.00 0.00 4.02
78 79 2.845967 CACGCTGTGAAAACAAACTGTC 59.154 45.455 3.04 0.00 35.23 3.51
79 80 2.862512 CACGCTGTGAAAACAAACTGT 58.137 42.857 3.04 0.00 35.23 3.55
80 81 1.583404 GCACGCTGTGAAAACAAACTG 59.417 47.619 11.94 0.00 35.23 3.16
81 82 1.469079 GGCACGCTGTGAAAACAAACT 60.469 47.619 11.94 0.00 35.23 2.66
82 83 0.920664 GGCACGCTGTGAAAACAAAC 59.079 50.000 11.94 0.00 35.23 2.93
101 102 7.203910 AGTTCATCAGTAACTAATCTAAGCCG 58.796 38.462 0.00 0.00 35.44 5.52
195 198 5.792741 AGCCAAAAACAGCAGCATTAATAA 58.207 33.333 0.00 0.00 0.00 1.40
237 240 3.849563 TTAAGCAGTTGTACCCTGTGT 57.150 42.857 10.34 3.28 32.41 3.72
238 241 4.323417 TGATTAAGCAGTTGTACCCTGTG 58.677 43.478 10.34 0.00 32.41 3.66
247 250 7.279536 AGACTCATGTGTATGATTAAGCAGTTG 59.720 37.037 0.00 0.00 42.19 3.16
337 343 6.403309 GGAGAGAACATACGGAAATTGGAAAC 60.403 42.308 0.00 0.00 0.00 2.78
340 346 4.383770 GGGAGAGAACATACGGAAATTGGA 60.384 45.833 0.00 0.00 0.00 3.53
347 353 2.820728 TGAGGGAGAGAACATACGGA 57.179 50.000 0.00 0.00 0.00 4.69
349 355 4.339530 TCAAGATGAGGGAGAGAACATACG 59.660 45.833 0.00 0.00 0.00 3.06
387 393 9.063615 GTCTTGGTAATCTTCCAGACTTAAAAA 57.936 33.333 0.00 0.00 36.28 1.94
414 420 1.474077 CTGTTCAGGCAATACCCTTGC 59.526 52.381 1.38 1.38 44.22 4.01
437 443 7.080353 TGATGACAGATTTAGCACTCAATTG 57.920 36.000 0.00 0.00 0.00 2.32
566 572 7.999679 TGGAATAGTTTGCAGAGGAATAAATG 58.000 34.615 0.00 0.00 0.00 2.32
605 611 8.184192 GGGACATATGAGTTTCACATGTTTTAG 58.816 37.037 10.38 0.00 43.77 1.85
638 644 8.579682 AAACTTCAACAGAGCATTAAATGAAC 57.420 30.769 0.00 0.00 0.00 3.18
735 741 6.945016 GTTGATGAACATAATGGCGACAGAAG 60.945 42.308 0.00 0.00 36.37 2.85
746 758 7.417456 AGCATGAGCAATGTTGATGAACATAAT 60.417 33.333 11.09 0.51 46.02 1.28
747 759 6.127563 AGCATGAGCAATGTTGATGAACATAA 60.128 34.615 11.09 0.00 46.02 1.90
760 772 4.760715 AGATAAGGCTTAGCATGAGCAATG 59.239 41.667 23.06 0.00 45.49 2.82
767 779 4.689812 CAGCAGTAGATAAGGCTTAGCATG 59.310 45.833 23.06 18.08 33.60 4.06
786 798 2.555325 CAAGAACAGGCATTCTTCAGCA 59.445 45.455 12.33 0.00 45.19 4.41
894 906 0.871057 GCAGTCAGTCCAAACTCTGC 59.129 55.000 0.00 0.00 42.58 4.26
898 910 1.202698 GGTCAGCAGTCAGTCCAAACT 60.203 52.381 0.00 0.00 35.60 2.66
1139 1151 8.195165 TCCATCATTAGTAGTATTTCCTGGAG 57.805 38.462 0.00 0.00 0.00 3.86
1157 1169 3.185246 GTGAATCACGGACTCCATCAT 57.815 47.619 0.00 0.00 0.00 2.45
1211 1223 5.065914 GGTATAAATTCTGAGCATGCTGGA 58.934 41.667 28.27 19.59 0.00 3.86
1254 1266 4.618920 AGTCGATGGGTAGACAAAACTT 57.381 40.909 0.00 0.00 39.67 2.66
1463 1475 3.765381 TCAAAATGATGGCCACTCTCAA 58.235 40.909 8.16 0.00 0.00 3.02
1760 1772 6.697641 AGGTTTACTTACCTGAAGGATTGA 57.302 37.500 2.62 0.00 46.71 2.57
1807 1819 7.599998 GTGCCTTGAATCATCACTTAACAAAAT 59.400 33.333 4.38 0.00 34.61 1.82
1813 1825 6.899393 AAAGTGCCTTGAATCATCACTTAA 57.101 33.333 18.93 0.00 44.35 1.85
1928 1940 7.805083 ATTATATCCTATAGCCAGGCCATAG 57.195 40.000 17.69 17.69 35.49 2.23
1983 1995 6.205658 ACTGACCTGTTAGAAAAGCAAGATTC 59.794 38.462 0.00 0.00 0.00 2.52
1996 2008 3.438087 CCATGAGCAAACTGACCTGTTAG 59.562 47.826 0.00 0.00 0.00 2.34
2075 2090 4.059773 TGAGGTAAAGGCCCATGAAAAT 57.940 40.909 0.00 0.00 0.00 1.82
2196 2211 1.425066 TGCACCACTCCAGAAGGATTT 59.575 47.619 0.00 0.00 44.70 2.17
2199 2214 0.397941 CTTGCACCACTCCAGAAGGA 59.602 55.000 0.00 0.00 43.21 3.36
2226 2241 0.397941 CTTGCACCACTCCAGAAGGA 59.602 55.000 0.00 0.00 43.21 3.36
2257 2272 1.588082 CACCTTGCACCATTCCAGC 59.412 57.895 0.00 0.00 0.00 4.85
2280 2295 0.609957 CTTGCACCATTCCAGCAGGA 60.610 55.000 0.00 0.00 43.93 3.86
2284 2299 1.588082 CACCTTGCACCATTCCAGC 59.412 57.895 0.00 0.00 0.00 4.85
2296 2311 1.614903 TCCAGCTTGATTTGCACCTTG 59.385 47.619 0.00 0.00 0.00 3.61
2297 2312 1.999648 TCCAGCTTGATTTGCACCTT 58.000 45.000 0.00 0.00 0.00 3.50
2298 2313 1.999648 TTCCAGCTTGATTTGCACCT 58.000 45.000 0.00 0.00 0.00 4.00
2299 2314 2.613691 CATTCCAGCTTGATTTGCACC 58.386 47.619 0.00 0.00 0.00 5.01
2300 2315 2.028748 ACCATTCCAGCTTGATTTGCAC 60.029 45.455 0.00 0.00 0.00 4.57
2301 2316 2.028839 CACCATTCCAGCTTGATTTGCA 60.029 45.455 0.00 0.00 0.00 4.08
2302 2317 2.613691 CACCATTCCAGCTTGATTTGC 58.386 47.619 0.00 0.00 0.00 3.68
2303 2318 2.028839 TGCACCATTCCAGCTTGATTTG 60.029 45.455 0.00 0.00 0.00 2.32
2304 2319 2.250031 TGCACCATTCCAGCTTGATTT 58.750 42.857 0.00 0.00 0.00 2.17
2305 2320 1.927487 TGCACCATTCCAGCTTGATT 58.073 45.000 0.00 0.00 0.00 2.57
2306 2321 1.822990 CTTGCACCATTCCAGCTTGAT 59.177 47.619 0.00 0.00 0.00 2.57
2307 2322 1.250328 CTTGCACCATTCCAGCTTGA 58.750 50.000 0.00 0.00 0.00 3.02
2308 2323 0.245539 CCTTGCACCATTCCAGCTTG 59.754 55.000 0.00 0.00 0.00 4.01
2309 2324 0.178953 ACCTTGCACCATTCCAGCTT 60.179 50.000 0.00 0.00 0.00 3.74
2310 2325 0.610232 GACCTTGCACCATTCCAGCT 60.610 55.000 0.00 0.00 0.00 4.24
2311 2326 1.598701 GGACCTTGCACCATTCCAGC 61.599 60.000 0.00 0.00 0.00 4.85
2312 2327 0.251297 TGGACCTTGCACCATTCCAG 60.251 55.000 2.13 0.00 32.45 3.86
2313 2328 0.187117 TTGGACCTTGCACCATTCCA 59.813 50.000 2.13 2.13 36.02 3.53
2314 2329 1.000843 GTTTGGACCTTGCACCATTCC 59.999 52.381 0.00 0.00 36.02 3.01
2315 2330 1.000843 GGTTTGGACCTTGCACCATTC 59.999 52.381 0.00 0.00 42.99 2.67
2316 2331 1.047801 GGTTTGGACCTTGCACCATT 58.952 50.000 0.00 0.00 42.99 3.16
2317 2332 0.831711 GGGTTTGGACCTTGCACCAT 60.832 55.000 0.00 0.00 45.75 3.55
2318 2333 1.456705 GGGTTTGGACCTTGCACCA 60.457 57.895 0.00 0.00 45.75 4.17
2319 2334 0.759060 AAGGGTTTGGACCTTGCACC 60.759 55.000 0.00 0.00 46.21 5.01
2320 2335 2.820845 AAGGGTTTGGACCTTGCAC 58.179 52.632 0.00 0.00 46.21 4.57
2338 2353 0.895100 GCACCTTGCACCATTCCAGA 60.895 55.000 0.00 0.00 44.26 3.86
2508 2523 3.603532 TGCTGTCATTCCATGAGAAGAC 58.396 45.455 0.00 6.86 40.53 3.01
2525 2540 4.784329 CAATTAGAGCTACATGCATGCTG 58.216 43.478 26.53 19.09 45.94 4.41
2569 2584 6.570378 CGCAAACAAAGTATCCAAGGAAGATT 60.570 38.462 0.00 0.00 0.00 2.40
2616 2632 6.420913 AACGGGTAATACATCTTCTATGCT 57.579 37.500 0.00 0.00 0.00 3.79
2683 2699 3.566742 CCAGCATAAGTATGAAGCATGCA 59.433 43.478 21.98 0.00 35.75 3.96
2745 2761 8.992349 TCCCAGAGATCTTTATGACTAAATTCA 58.008 33.333 0.00 0.00 0.00 2.57
2780 2797 7.821846 GGGTAATAATTGGCAATGTTTTCTTGA 59.178 33.333 14.47 0.00 0.00 3.02
2803 2820 1.109323 GCACTTCAGCAACCAAGGGT 61.109 55.000 0.00 0.00 37.65 4.34
2911 2928 5.630121 TGCAGGGGAAAATACATATGGTAG 58.370 41.667 7.80 0.00 34.92 3.18
3146 3271 9.833917 CAGATTGATTACATCAGATAGCCATAT 57.166 33.333 0.00 0.00 40.94 1.78
3315 3446 0.107410 AACCCGTGAAAGTGTCTGCA 60.107 50.000 0.00 0.00 0.00 4.41
3328 3459 3.438781 CAGTTACATACATGCAAACCCGT 59.561 43.478 0.00 0.00 31.18 5.28
3357 3488 2.575993 CAGGAGAGCAGGACCACG 59.424 66.667 0.00 0.00 0.00 4.94
3359 3490 2.203832 TGCAGGAGAGCAGGACCA 60.204 61.111 0.00 0.00 40.11 4.02
3380 3511 3.438087 TCTGTTCTTGCAATGCTAGAAGC 59.562 43.478 27.07 21.44 46.76 3.86
3441 3572 5.009631 CCAATGTACCCTCAGATTTTGACA 58.990 41.667 0.00 0.00 0.00 3.58
3462 3593 0.039035 GCCCTGGGAACAACATACCA 59.961 55.000 19.27 0.00 42.06 3.25
3463 3594 0.039035 TGCCCTGGGAACAACATACC 59.961 55.000 19.27 0.00 42.06 2.73
3539 3670 5.104193 ACAAGAGATAGAATGTGCAAGGGAT 60.104 40.000 0.00 0.00 0.00 3.85
3546 3677 6.674694 ATGAACACAAGAGATAGAATGTGC 57.325 37.500 4.78 0.00 0.00 4.57
3651 3783 6.370433 CTGCTTCTAAAAAGGATAAGGAGC 57.630 41.667 0.00 0.00 40.41 4.70
3677 3809 7.280205 GGGTGTATTGACTGTTCTAGGTAAATG 59.720 40.741 0.00 0.00 0.00 2.32
3712 3844 2.295349 TGGTTAATCTAGCCGTCGATCC 59.705 50.000 0.00 0.00 0.00 3.36
3717 3849 4.865365 GCATATCTGGTTAATCTAGCCGTC 59.135 45.833 0.00 0.00 0.00 4.79
3747 3879 0.671472 CAGAGACGGCATTGACAGCA 60.671 55.000 0.00 0.00 0.00 4.41
3778 3911 1.202098 GCAAAGACACGGAACAAACGT 60.202 47.619 0.00 0.00 46.82 3.99
3779 3912 1.202087 TGCAAAGACACGGAACAAACG 60.202 47.619 0.00 0.00 37.36 3.60
3871 4004 1.303561 TTCACCATCAGCCACTGCC 60.304 57.895 0.00 0.00 38.69 4.85
3896 4029 2.443390 GCCTTGCAGATGGGGCAT 60.443 61.111 10.36 0.00 43.59 4.40
3921 4054 1.299562 CTGCTTCACTCTGCTGGCAG 61.300 60.000 10.94 10.94 44.86 4.85
3947 4080 2.515057 ATTTATTGGCGCGGCGGA 60.515 55.556 28.22 19.23 0.00 5.54
3951 4084 1.522258 GCAAATGATTTATTGGCGCGG 59.478 47.619 8.83 0.00 36.06 6.46
3952 4085 1.522258 GGCAAATGATTTATTGGCGCG 59.478 47.619 0.00 0.00 45.12 6.86
3990 4123 6.734104 ATGTACAAGAAACTGAGCTGAATC 57.266 37.500 0.00 0.00 0.00 2.52
3991 4124 8.097038 TCTTATGTACAAGAAACTGAGCTGAAT 58.903 33.333 0.00 0.00 31.63 2.57
3992 4125 7.441836 TCTTATGTACAAGAAACTGAGCTGAA 58.558 34.615 0.00 0.00 31.63 3.02
4103 4236 5.359009 CAGTCTAGGAAATGAAACCATGCAT 59.641 40.000 0.00 0.00 0.00 3.96
4104 4237 4.701651 CAGTCTAGGAAATGAAACCATGCA 59.298 41.667 0.00 0.00 0.00 3.96
4105 4238 4.439289 GCAGTCTAGGAAATGAAACCATGC 60.439 45.833 0.00 0.00 0.00 4.06
4106 4239 4.946157 AGCAGTCTAGGAAATGAAACCATG 59.054 41.667 0.00 0.00 0.00 3.66
4141 4276 2.289882 TGAGAGAAGTTCAGGCACCATG 60.290 50.000 5.50 0.00 0.00 3.66
4169 4304 1.467920 GGGCAGACAATCCAGGAAAG 58.532 55.000 0.00 0.00 0.00 2.62
4176 4311 3.903467 AGATAAAAGGGGCAGACAATCC 58.097 45.455 0.00 0.00 0.00 3.01
4177 4312 7.068716 ACAAATAGATAAAAGGGGCAGACAATC 59.931 37.037 0.00 0.00 0.00 2.67
4178 4313 6.897413 ACAAATAGATAAAAGGGGCAGACAAT 59.103 34.615 0.00 0.00 0.00 2.71
4179 4314 6.252995 ACAAATAGATAAAAGGGGCAGACAA 58.747 36.000 0.00 0.00 0.00 3.18
4180 4315 5.826643 ACAAATAGATAAAAGGGGCAGACA 58.173 37.500 0.00 0.00 0.00 3.41
4181 4316 6.826741 TGTACAAATAGATAAAAGGGGCAGAC 59.173 38.462 0.00 0.00 0.00 3.51
4182 4317 6.964464 TGTACAAATAGATAAAAGGGGCAGA 58.036 36.000 0.00 0.00 0.00 4.26
4183 4318 7.823745 ATGTACAAATAGATAAAAGGGGCAG 57.176 36.000 0.00 0.00 0.00 4.85
4216 4351 8.616799 TTTTGGCAAAGGGAAATATATAGGTT 57.383 30.769 13.04 0.00 0.00 3.50
4317 4482 1.953772 CCTAACCAAACACCCGTGC 59.046 57.895 0.00 0.00 0.00 5.34
4318 4483 0.536460 AGCCTAACCAAACACCCGTG 60.536 55.000 0.00 0.00 0.00 4.94
4412 4584 7.671302 ACCATCATGTAACAGTATATCCAGTC 58.329 38.462 0.00 0.00 0.00 3.51
4413 4585 7.618019 ACCATCATGTAACAGTATATCCAGT 57.382 36.000 0.00 0.00 0.00 4.00
4416 4588 9.424319 CTTGTACCATCATGTAACAGTATATCC 57.576 37.037 0.00 0.00 0.00 2.59
4417 4589 8.926710 GCTTGTACCATCATGTAACAGTATATC 58.073 37.037 0.00 0.00 0.00 1.63
4418 4590 7.878127 GGCTTGTACCATCATGTAACAGTATAT 59.122 37.037 0.00 0.00 0.00 0.86
4419 4591 7.147637 TGGCTTGTACCATCATGTAACAGTATA 60.148 37.037 0.00 0.00 33.75 1.47
4439 4616 9.807649 ATAGTATATTTTTCTGCTTTTGGCTTG 57.192 29.630 0.00 0.00 42.39 4.01
4489 4679 8.581253 AAGCCAAAAACTATTGCTAGACTATT 57.419 30.769 0.00 0.00 0.00 1.73
4542 4759 8.634444 ACTGTTACTGTACCAAATATTTTTGCA 58.366 29.630 0.00 0.00 40.77 4.08
4572 4789 2.807676 GTTCAGGGGATTTGTCATGGT 58.192 47.619 0.00 0.00 0.00 3.55
4573 4790 1.745087 CGTTCAGGGGATTTGTCATGG 59.255 52.381 0.00 0.00 0.00 3.66
4642 4862 4.156008 CCTTTCCTTGGGATGTTTTCTACG 59.844 45.833 0.00 0.00 0.00 3.51
4654 4874 1.354368 TCTTACAGGCCTTTCCTTGGG 59.646 52.381 0.00 0.00 44.75 4.12
4727 4947 2.094182 TGATTCGTTCAGGACTACAGCC 60.094 50.000 0.00 0.00 0.00 4.85
4753 4973 5.467399 AGTGTTCATTTTGCCATGTTTGATG 59.533 36.000 0.00 0.00 0.00 3.07
4862 5082 2.305635 TCTTAGCTCAAGATTGTGGGCA 59.694 45.455 0.00 0.00 38.39 5.36
4863 5083 2.941720 CTCTTAGCTCAAGATTGTGGGC 59.058 50.000 0.00 0.00 42.44 5.36
4864 5084 3.198635 TCCTCTTAGCTCAAGATTGTGGG 59.801 47.826 0.00 0.00 42.44 4.61
4869 5089 5.869579 TGTTGTTCCTCTTAGCTCAAGATT 58.130 37.500 0.00 0.00 42.44 2.40
4884 5104 5.281727 GTGAAGAAATCCAACTGTTGTTCC 58.718 41.667 18.38 5.94 33.52 3.62


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

AutoCloner maintained by Alex Coulton.