Multiple sequence alignment - TraesCS1A01G319400

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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 TraesCS1A01G319400 chr1A 100.000 3029 0 0 1 3029 510368420 510365392 0.000000e+00 5594.0
1 TraesCS1A01G319400 chr1A 95.767 874 32 2 3 871 381129077 381128204 0.000000e+00 1404.0
2 TraesCS1A01G319400 chr1A 86.395 147 19 1 1909 2055 512453403 512453258 3.130000e-35 159.0
3 TraesCS1A01G319400 chr1A 84.416 154 17 4 2468 2621 492022765 492022619 8.750000e-31 145.0
4 TraesCS1A01G319400 chr1B 92.766 1410 65 16 870 2251 557919402 557918002 0.000000e+00 2004.0
5 TraesCS1A01G319400 chr1B 87.857 140 17 0 1916 2055 557544025 557543886 6.720000e-37 165.0
6 TraesCS1A01G319400 chr1B 77.907 172 24 11 2435 2605 128020769 128020927 8.940000e-16 95.3
7 TraesCS1A01G319400 chr1D 92.379 1404 73 17 873 2251 413413020 413411626 0.000000e+00 1969.0
8 TraesCS1A01G319400 chr1D 94.020 301 18 0 1659 1959 413410475 413410175 9.900000e-125 457.0
9 TraesCS1A01G319400 chr1D 90.141 142 12 2 2288 2427 112352033 112352174 1.850000e-42 183.0
10 TraesCS1A01G319400 chr1D 90.714 140 10 3 2289 2427 349470997 349471134 1.850000e-42 183.0
11 TraesCS1A01G319400 chr1D 83.251 203 26 5 1948 2145 413335263 413335064 2.400000e-41 180.0
12 TraesCS1A01G319400 chr1D 88.435 147 15 2 1909 2055 413406419 413406275 3.100000e-40 176.0
13 TraesCS1A01G319400 chr1D 97.778 45 1 0 1960 2004 413297316 413297272 9.000000e-11 78.7
14 TraesCS1A01G319400 chr4A 87.351 419 35 9 81 489 676923446 676923856 5.910000e-127 464.0
15 TraesCS1A01G319400 chr4A 87.436 390 35 6 490 876 676924579 676924957 1.290000e-118 436.0
16 TraesCS1A01G319400 chr5D 91.358 162 14 0 1295 1456 561621245 561621084 3.930000e-54 222.0
17 TraesCS1A01G319400 chrUn 86.592 179 14 4 2443 2621 87719807 87719639 3.990000e-44 189.0
18 TraesCS1A01G319400 chr4B 91.852 135 9 1 2288 2420 406463702 406463836 1.430000e-43 187.0
19 TraesCS1A01G319400 chr4B 82.394 142 17 7 2480 2621 599169207 599169074 1.910000e-22 117.0
20 TraesCS1A01G319400 chr2D 90.780 141 11 2 2287 2427 486333015 486333153 1.430000e-43 187.0
21 TraesCS1A01G319400 chr2D 89.583 144 11 2 2287 2427 101884248 101884106 2.400000e-41 180.0
22 TraesCS1A01G319400 chr5A 90.210 143 12 2 2287 2427 491964579 491964721 5.160000e-43 185.0
23 TraesCS1A01G319400 chr5A 86.765 136 11 3 2474 2609 593601345 593601473 8.750000e-31 145.0
24 TraesCS1A01G319400 chr5A 85.000 100 15 0 772 871 28858028 28858127 5.340000e-18 102.0
25 TraesCS1A01G319400 chr6D 89.510 143 14 1 2286 2427 395525763 395525621 2.400000e-41 180.0
26 TraesCS1A01G319400 chr6D 90.385 52 4 1 1285 1336 19349008 19349058 1.950000e-07 67.6
27 TraesCS1A01G319400 chr7B 89.510 143 11 3 2287 2427 130896545 130896405 8.630000e-41 178.0
28 TraesCS1A01G319400 chr7B 82.550 149 23 2 550 698 331057187 331057042 8.810000e-26 128.0
29 TraesCS1A01G319400 chr7B 84.466 103 14 2 774 875 591455800 591455699 1.920000e-17 100.0
30 TraesCS1A01G319400 chr4D 84.831 178 17 7 2259 2427 418740237 418740413 1.440000e-38 171.0
31 TraesCS1A01G319400 chr4D 84.302 172 20 3 2263 2427 50424220 50424391 8.690000e-36 161.0
32 TraesCS1A01G319400 chr7A 82.888 187 22 6 2435 2621 448731161 448731337 3.130000e-35 159.0
33 TraesCS1A01G319400 chr7A 81.967 183 23 8 2439 2621 40893965 40894137 2.430000e-31 147.0
34 TraesCS1A01G319400 chr3B 85.161 155 14 7 2468 2621 344273591 344273737 1.880000e-32 150.0
35 TraesCS1A01G319400 chr3A 80.110 181 25 6 2443 2621 475726753 475726582 1.140000e-24 124.0
36 TraesCS1A01G319400 chr3A 85.149 101 10 4 2439 2538 263221 263317 6.910000e-17 99.0
37 TraesCS1A01G319400 chr2B 88.000 100 10 2 773 871 218403880 218403782 1.910000e-22 117.0
38 TraesCS1A01G319400 chr2B 83.168 101 17 0 772 872 694299824 694299724 3.220000e-15 93.5
39 TraesCS1A01G319400 chr2A 87.129 101 11 2 772 871 723584561 723584660 2.470000e-21 113.0
40 TraesCS1A01G319400 chr2A 100.000 30 0 0 1350 1379 553282775 553282746 4.220000e-04 56.5
41 TraesCS1A01G319400 chr7D 84.112 107 14 3 770 874 445481663 445481768 1.920000e-17 100.0
42 TraesCS1A01G319400 chr7D 97.222 36 0 1 1350 1384 579054097 579054132 3.260000e-05 60.2
43 TraesCS1A01G319400 chr6B 84.848 99 11 3 775 871 618094439 618094343 2.490000e-16 97.1
44 TraesCS1A01G319400 chr6A 100.000 30 0 0 2258 2287 551628033 551628062 4.220000e-04 56.5


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 TraesCS1A01G319400 chr1A 510365392 510368420 3028 True 5594.000000 5594 100.000000 1 3029 1 chr1A.!!$R3 3028
1 TraesCS1A01G319400 chr1A 381128204 381129077 873 True 1404.000000 1404 95.767000 3 871 1 chr1A.!!$R1 868
2 TraesCS1A01G319400 chr1B 557918002 557919402 1400 True 2004.000000 2004 92.766000 870 2251 1 chr1B.!!$R2 1381
3 TraesCS1A01G319400 chr1D 413406275 413413020 6745 True 867.333333 1969 91.611333 873 2251 3 chr1D.!!$R3 1378
4 TraesCS1A01G319400 chr4A 676923446 676924957 1511 False 450.000000 464 87.393500 81 876 2 chr4A.!!$F1 795

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
546 1279 0.254747 GATGTCGGGGTGGGATTGAA 59.745 55.0 0.0 0.0 0.0 2.69 F
1059 1798 0.319900 TCGCACTCAAAGCTCCAGTC 60.320 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1737 2476 0.471617 CCAGCCCCATGAAGGAGTAG 59.528 60.0 5.96 0.0 41.22 2.57 R
2717 5392 0.174162 AATCCCAATGAAAGCAGCGC 59.826 50.0 0.00 0.0 0.00 5.92 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
60 61 2.096248 CCTAGCGACTTTCCAGACTCT 58.904 52.381 0.00 0.00 0.00 3.24
140 141 1.569493 CTTGTGGACGCGGACAAAG 59.431 57.895 12.47 10.96 31.83 2.77
180 181 1.523938 GGAGCCCCAGTCAATACGC 60.524 63.158 0.00 0.00 0.00 4.42
546 1279 0.254747 GATGTCGGGGTGGGATTGAA 59.745 55.000 0.00 0.00 0.00 2.69
644 1377 1.077429 GGCTTTCGATTCTGCCCCT 60.077 57.895 7.09 0.00 39.49 4.79
801 1535 0.745845 GCCAGGAACATCTGCATCGT 60.746 55.000 0.00 0.00 33.64 3.73
807 1541 4.012374 AGGAACATCTGCATCGTCAAAAT 58.988 39.130 0.00 0.00 0.00 1.82
828 1562 9.471084 CAAAATGGACGGTTAAAAACTCTAATT 57.529 29.630 0.00 0.00 0.00 1.40
880 1614 0.521291 TGTCCTTAATTGCACGCAGC 59.479 50.000 0.00 0.00 45.96 5.25
920 1654 2.674380 GCCAGTGTCCAAGCCCAG 60.674 66.667 0.00 0.00 0.00 4.45
921 1655 2.674380 CCAGTGTCCAAGCCCAGC 60.674 66.667 0.00 0.00 0.00 4.85
922 1656 2.433446 CAGTGTCCAAGCCCAGCT 59.567 61.111 0.00 0.00 42.56 4.24
923 1657 1.673665 CAGTGTCCAAGCCCAGCTC 60.674 63.158 0.00 0.00 38.25 4.09
924 1658 1.845205 AGTGTCCAAGCCCAGCTCT 60.845 57.895 0.00 0.00 38.25 4.09
934 1668 2.268280 CCAGCTCTGCTCCACCAG 59.732 66.667 0.00 0.00 36.40 4.00
1024 1763 0.676151 GCTCAGCCTCTTGAACCCTG 60.676 60.000 0.00 0.00 0.00 4.45
1059 1798 0.319900 TCGCACTCAAAGCTCCAGTC 60.320 55.000 0.00 0.00 0.00 3.51
1614 2353 2.435586 CAGGTGGAGAAGCTGCGG 60.436 66.667 0.00 0.00 46.71 5.69
1737 2476 1.671379 GGGCTCCTTCAACGTGGTC 60.671 63.158 0.00 0.00 0.00 4.02
2024 2763 2.684104 GGGAAGGAAGGGGAAGCC 59.316 66.667 0.00 0.00 0.00 4.35
2039 2778 1.606668 GAAGCCGTGACATTGGTTTCA 59.393 47.619 16.33 0.00 42.85 2.69
2044 2783 2.327568 CGTGACATTGGTTTCATTGGC 58.672 47.619 0.00 0.00 33.97 4.52
2076 2815 0.319555 CGGCGTCTCCTGAACTTTCA 60.320 55.000 0.00 0.00 35.57 2.69
2077 2816 1.872237 CGGCGTCTCCTGAACTTTCAA 60.872 52.381 0.00 0.00 36.64 2.69
2079 2818 2.210116 GCGTCTCCTGAACTTTCAACA 58.790 47.619 0.00 0.00 36.64 3.33
2080 2819 2.032808 GCGTCTCCTGAACTTTCAACAC 60.033 50.000 0.00 0.00 36.64 3.32
2082 2821 3.871594 CGTCTCCTGAACTTTCAACACTT 59.128 43.478 0.00 0.00 36.64 3.16
2086 2825 5.710099 TCTCCTGAACTTTCAACACTTTGTT 59.290 36.000 0.00 0.00 42.08 2.83
2130 2876 1.403679 GTTGTAGTGGTGCAGCAACAA 59.596 47.619 24.83 24.83 39.17 2.83
2154 2918 2.990774 GCATTTGCAATGCATCTTCG 57.009 45.000 21.39 0.00 44.00 3.79
2157 2921 3.513662 CATTTGCAATGCATCTTCGGAA 58.486 40.909 9.39 0.00 38.76 4.30
2178 2942 6.655003 CGGAATATGATAGGCAATGTTAACCT 59.345 38.462 2.48 0.00 37.61 3.50
2180 2944 9.686683 GGAATATGATAGGCAATGTTAACCTAT 57.313 33.333 2.48 2.26 46.98 2.57
2187 2951 9.686683 GATAGGCAATGTTAACCTATGGATAAT 57.313 33.333 5.55 0.00 44.88 1.28
2200 2964 6.204882 ACCTATGGATAATAGAAGTTTTGCGC 59.795 38.462 0.00 0.00 40.83 6.09
2206 2970 0.719465 TAGAAGTTTTGCGCGCTAGC 59.281 50.000 33.29 21.04 40.74 3.42
2213 2977 2.784596 TGCGCGCTAGCAAATGAC 59.215 55.556 33.29 0.00 45.06 3.06
2227 2991 4.022589 AGCAAATGACAGAAATCAGGTGTG 60.023 41.667 0.00 0.00 30.46 3.82
2229 2993 2.636647 TGACAGAAATCAGGTGTGCA 57.363 45.000 0.00 0.00 0.00 4.57
2231 2995 2.618241 TGACAGAAATCAGGTGTGCAAC 59.382 45.455 0.00 0.00 37.35 4.17
2233 2997 6.670869 ATGACAGAAATCAGGTGTGCAACAA 61.671 40.000 0.00 0.00 39.75 2.83
2270 3034 8.764558 ACACCCATTGTTGATAATACTAGTGTA 58.235 33.333 5.39 0.00 33.09 2.90
2271 3035 9.778741 CACCCATTGTTGATAATACTAGTGTAT 57.221 33.333 5.39 3.11 40.79 2.29
2272 3036 9.778741 ACCCATTGTTGATAATACTAGTGTATG 57.221 33.333 5.39 0.00 39.16 2.39
2273 3037 9.996554 CCCATTGTTGATAATACTAGTGTATGA 57.003 33.333 5.39 0.00 39.16 2.15
2339 3103 8.814038 ATTTTTAAGGACATCACATCTAAGCT 57.186 30.769 0.00 0.00 0.00 3.74
2340 3104 7.849804 TTTTAAGGACATCACATCTAAGCTC 57.150 36.000 0.00 0.00 0.00 4.09
2342 3106 2.703007 AGGACATCACATCTAAGCTCCC 59.297 50.000 0.00 0.00 0.00 4.30
2343 3107 2.435805 GGACATCACATCTAAGCTCCCA 59.564 50.000 0.00 0.00 0.00 4.37
2345 3109 2.840038 ACATCACATCTAAGCTCCCACA 59.160 45.455 0.00 0.00 0.00 4.17
2346 3110 3.264193 ACATCACATCTAAGCTCCCACAA 59.736 43.478 0.00 0.00 0.00 3.33
2347 3111 4.263462 ACATCACATCTAAGCTCCCACAAA 60.263 41.667 0.00 0.00 0.00 2.83
2348 3112 4.574674 TCACATCTAAGCTCCCACAAAT 57.425 40.909 0.00 0.00 0.00 2.32
2349 3113 5.692115 TCACATCTAAGCTCCCACAAATA 57.308 39.130 0.00 0.00 0.00 1.40
2350 3114 6.252599 TCACATCTAAGCTCCCACAAATAT 57.747 37.500 0.00 0.00 0.00 1.28
2351 3115 7.373617 TCACATCTAAGCTCCCACAAATATA 57.626 36.000 0.00 0.00 0.00 0.86
2353 3117 9.100197 TCACATCTAAGCTCCCACAAATATATA 57.900 33.333 0.00 0.00 0.00 0.86
2354 3118 9.725019 CACATCTAAGCTCCCACAAATATATAA 57.275 33.333 0.00 0.00 0.00 0.98
2357 3121 8.792830 TCTAAGCTCCCACAAATATATAATGC 57.207 34.615 0.00 0.00 0.00 3.56
2358 3122 8.382405 TCTAAGCTCCCACAAATATATAATGCA 58.618 33.333 0.00 0.00 0.00 3.96
2361 3125 5.183713 GCTCCCACAAATATATAATGCAGCA 59.816 40.000 0.00 0.00 0.00 4.41
2363 3127 6.980593 TCCCACAAATATATAATGCAGCAAC 58.019 36.000 0.00 0.00 0.00 4.17
2364 3128 6.548993 TCCCACAAATATATAATGCAGCAACA 59.451 34.615 0.00 0.00 0.00 3.33
2366 3130 7.383029 CCCACAAATATATAATGCAGCAACAAG 59.617 37.037 0.00 0.00 0.00 3.16
2368 3132 9.518906 CACAAATATATAATGCAGCAACAAGAA 57.481 29.630 0.00 0.00 0.00 2.52
2377 3141 7.790823 AATGCAGCAACAAGAAATAAAAACT 57.209 28.000 0.00 0.00 0.00 2.66
2378 3142 8.885494 AATGCAGCAACAAGAAATAAAAACTA 57.115 26.923 0.00 0.00 0.00 2.24
2379 3143 7.928908 TGCAGCAACAAGAAATAAAAACTAG 57.071 32.000 0.00 0.00 0.00 2.57
2381 3145 7.145323 GCAGCAACAAGAAATAAAAACTAGGA 58.855 34.615 0.00 0.00 0.00 2.94
2382 3146 7.114953 GCAGCAACAAGAAATAAAAACTAGGAC 59.885 37.037 0.00 0.00 0.00 3.85
2383 3147 8.134895 CAGCAACAAGAAATAAAAACTAGGACA 58.865 33.333 0.00 0.00 0.00 4.02
2384 3148 8.691797 AGCAACAAGAAATAAAAACTAGGACAA 58.308 29.630 0.00 0.00 0.00 3.18
2385 3149 9.308318 GCAACAAGAAATAAAAACTAGGACAAA 57.692 29.630 0.00 0.00 0.00 2.83
2416 3180 7.092716 AGACCACAAACAAAATGAATATCAGC 58.907 34.615 0.00 0.00 0.00 4.26
2417 3181 6.996509 ACCACAAACAAAATGAATATCAGCT 58.003 32.000 0.00 0.00 0.00 4.24
2418 3182 7.444299 ACCACAAACAAAATGAATATCAGCTT 58.556 30.769 0.00 0.00 0.00 3.74
2419 3183 8.584157 ACCACAAACAAAATGAATATCAGCTTA 58.416 29.630 0.00 0.00 0.00 3.09
2421 3185 9.844790 CACAAACAAAATGAATATCAGCTTAGA 57.155 29.630 0.00 0.00 0.00 2.10
2426 3190 9.399797 ACAAAATGAATATCAGCTTAGATGTGA 57.600 29.630 0.00 0.00 0.00 3.58
2429 3193 9.570468 AAATGAATATCAGCTTAGATGTGATGT 57.430 29.630 0.00 0.00 33.05 3.06
2430 3194 8.774890 ATGAATATCAGCTTAGATGTGATGTC 57.225 34.615 0.00 0.00 33.05 3.06
2431 3195 7.729116 TGAATATCAGCTTAGATGTGATGTCA 58.271 34.615 0.00 1.88 33.05 3.58
2432 3196 7.654923 TGAATATCAGCTTAGATGTGATGTCAC 59.345 37.037 6.21 6.21 46.59 3.67
2472 3236 9.007252 GCATAGTATCGTAGTATTTTGGTATCG 57.993 37.037 0.00 0.00 0.00 2.92
2482 3904 9.277783 GTAGTATTTTGGTATCGTAGAGGACTA 57.722 37.037 0.00 0.00 43.63 2.59
2497 4428 9.077674 CGTAGAGGACTATATTTATTGACATGC 57.922 37.037 0.00 0.00 0.00 4.06
2511 4442 9.838975 TTTATTGACATGCATAACACAAAGTAG 57.161 29.630 0.00 0.00 0.00 2.57
2515 4446 4.518590 ACATGCATAACACAAAGTAGCACA 59.481 37.500 0.00 0.00 36.10 4.57
2521 4452 6.623549 GCATAACACAAAGTAGCACATCATGT 60.624 38.462 0.00 0.00 0.00 3.21
2522 4453 7.413988 GCATAACACAAAGTAGCACATCATGTA 60.414 37.037 0.00 0.00 0.00 2.29
2523 4454 6.875948 AACACAAAGTAGCACATCATGTAA 57.124 33.333 0.00 0.00 0.00 2.41
2524 4455 7.452880 AACACAAAGTAGCACATCATGTAAT 57.547 32.000 0.00 0.00 0.00 1.89
2525 4456 8.560355 AACACAAAGTAGCACATCATGTAATA 57.440 30.769 0.00 0.00 0.00 0.98
2526 4457 8.737168 ACACAAAGTAGCACATCATGTAATAT 57.263 30.769 0.00 0.00 0.00 1.28
2590 4521 9.973661 TCTCTTTCTTCATTTAATTCCATACCA 57.026 29.630 0.00 0.00 0.00 3.25
2593 4524 8.893563 TTTCTTCATTTAATTCCATACCACCT 57.106 30.769 0.00 0.00 0.00 4.00
2595 4526 7.638444 TCTTCATTTAATTCCATACCACCTCA 58.362 34.615 0.00 0.00 0.00 3.86
2596 4527 8.281531 TCTTCATTTAATTCCATACCACCTCAT 58.718 33.333 0.00 0.00 0.00 2.90
2597 4528 8.463930 TTCATTTAATTCCATACCACCTCATC 57.536 34.615 0.00 0.00 0.00 2.92
2601 4924 8.657387 TTTAATTCCATACCACCTCATCAAAA 57.343 30.769 0.00 0.00 0.00 2.44
2606 4929 6.015918 TCCATACCACCTCATCAAAATTGTT 58.984 36.000 0.00 0.00 0.00 2.83
2614 4937 7.382218 CCACCTCATCAAAATTGTTTAGTTGTC 59.618 37.037 0.00 0.00 0.00 3.18
2615 4938 7.920151 CACCTCATCAAAATTGTTTAGTTGTCA 59.080 33.333 0.00 0.00 0.00 3.58
2616 4939 8.641541 ACCTCATCAAAATTGTTTAGTTGTCAT 58.358 29.630 0.00 0.00 0.00 3.06
2617 4940 8.918658 CCTCATCAAAATTGTTTAGTTGTCATG 58.081 33.333 0.00 0.00 0.00 3.07
2619 4942 7.924947 TCATCAAAATTGTTTAGTTGTCATGCA 59.075 29.630 0.00 0.00 0.00 3.96
2621 4944 8.296799 TCAAAATTGTTTAGTTGTCATGCATC 57.703 30.769 0.00 0.00 0.00 3.91
2622 4945 7.384660 TCAAAATTGTTTAGTTGTCATGCATCC 59.615 33.333 0.00 0.00 0.00 3.51
2623 4946 5.981088 ATTGTTTAGTTGTCATGCATCCA 57.019 34.783 0.00 0.00 0.00 3.41
2624 4947 5.981088 TTGTTTAGTTGTCATGCATCCAT 57.019 34.783 0.00 0.00 0.00 3.41
2625 4948 5.981088 TGTTTAGTTGTCATGCATCCATT 57.019 34.783 0.00 0.00 0.00 3.16
2627 4950 6.851609 TGTTTAGTTGTCATGCATCCATTAC 58.148 36.000 0.00 0.00 0.00 1.89
2628 4951 5.733226 TTAGTTGTCATGCATCCATTACG 57.267 39.130 0.00 0.00 30.00 3.18
2630 4953 4.260985 AGTTGTCATGCATCCATTACGAA 58.739 39.130 0.00 0.00 30.00 3.85
2631 4954 4.094887 AGTTGTCATGCATCCATTACGAAC 59.905 41.667 0.00 0.00 30.00 3.95
2635 5310 4.094887 GTCATGCATCCATTACGAACAACT 59.905 41.667 0.00 0.00 0.00 3.16
2636 5311 4.699735 TCATGCATCCATTACGAACAACTT 59.300 37.500 0.00 0.00 0.00 2.66
2639 5314 6.561737 TGCATCCATTACGAACAACTTTAA 57.438 33.333 0.00 0.00 0.00 1.52
2669 5344 6.653526 TTGTTCATCATGACCATTTTCAGT 57.346 33.333 0.00 0.00 0.00 3.41
2670 5345 6.016213 TGTTCATCATGACCATTTTCAGTG 57.984 37.500 0.00 0.00 0.00 3.66
2671 5346 4.707030 TCATCATGACCATTTTCAGTGC 57.293 40.909 0.00 0.00 0.00 4.40
2677 5352 3.819368 TGACCATTTTCAGTGCTCAGAA 58.181 40.909 0.00 0.00 0.00 3.02
2679 5354 2.549754 ACCATTTTCAGTGCTCAGAACG 59.450 45.455 0.00 0.00 0.00 3.95
2680 5355 2.095567 CCATTTTCAGTGCTCAGAACGG 60.096 50.000 0.00 0.00 0.00 4.44
2681 5356 2.613026 TTTTCAGTGCTCAGAACGGA 57.387 45.000 0.00 0.00 0.00 4.69
2692 5367 3.674997 CTCAGAACGGAATTGAAGGGAA 58.325 45.455 0.00 0.00 0.00 3.97
2695 5370 5.811190 TCAGAACGGAATTGAAGGGAATTA 58.189 37.500 0.00 0.00 0.00 1.40
2698 5373 7.396055 TCAGAACGGAATTGAAGGGAATTATTT 59.604 33.333 0.00 0.00 0.00 1.40
2700 5375 8.251026 AGAACGGAATTGAAGGGAATTATTTTC 58.749 33.333 0.00 0.00 0.00 2.29
2701 5376 7.718334 ACGGAATTGAAGGGAATTATTTTCT 57.282 32.000 0.00 0.00 0.00 2.52
2702 5377 7.547227 ACGGAATTGAAGGGAATTATTTTCTG 58.453 34.615 0.00 0.00 0.00 3.02
2703 5378 6.980397 CGGAATTGAAGGGAATTATTTTCTGG 59.020 38.462 0.00 0.00 0.00 3.86
2704 5379 6.763135 GGAATTGAAGGGAATTATTTTCTGGC 59.237 38.462 0.00 0.00 0.00 4.85
2705 5380 4.981806 TGAAGGGAATTATTTTCTGGCG 57.018 40.909 0.00 0.00 0.00 5.69
2706 5381 4.340617 TGAAGGGAATTATTTTCTGGCGT 58.659 39.130 0.00 0.00 0.00 5.68
2732 5407 2.202518 CGGCGCTGCTTTCATTGG 60.203 61.111 7.64 0.00 0.00 3.16
2736 5411 0.174162 GCGCTGCTTTCATTGGGATT 59.826 50.000 0.00 0.00 0.00 3.01
2742 5417 3.887716 CTGCTTTCATTGGGATTAGAGGG 59.112 47.826 0.00 0.00 0.00 4.30
2743 5418 3.225940 GCTTTCATTGGGATTAGAGGGG 58.774 50.000 0.00 0.00 0.00 4.79
2744 5419 3.117512 GCTTTCATTGGGATTAGAGGGGA 60.118 47.826 0.00 0.00 0.00 4.81
2746 5421 5.518865 CTTTCATTGGGATTAGAGGGGAAA 58.481 41.667 0.00 0.00 0.00 3.13
2747 5422 5.749422 TTCATTGGGATTAGAGGGGAAAT 57.251 39.130 0.00 0.00 0.00 2.17
2748 5423 6.857083 TTCATTGGGATTAGAGGGGAAATA 57.143 37.500 0.00 0.00 0.00 1.40
2749 5424 6.454223 TCATTGGGATTAGAGGGGAAATAG 57.546 41.667 0.00 0.00 0.00 1.73
2750 5425 5.917087 TCATTGGGATTAGAGGGGAAATAGT 59.083 40.000 0.00 0.00 0.00 2.12
2751 5426 6.392842 TCATTGGGATTAGAGGGGAAATAGTT 59.607 38.462 0.00 0.00 0.00 2.24
2752 5427 7.574750 TCATTGGGATTAGAGGGGAAATAGTTA 59.425 37.037 0.00 0.00 0.00 2.24
2753 5428 6.758806 TGGGATTAGAGGGGAAATAGTTAC 57.241 41.667 0.00 0.00 0.00 2.50
2754 5429 6.214278 TGGGATTAGAGGGGAAATAGTTACA 58.786 40.000 0.00 0.00 0.00 2.41
2756 5431 6.239915 GGGATTAGAGGGGAAATAGTTACAGG 60.240 46.154 0.00 0.00 0.00 4.00
2757 5432 6.557633 GGATTAGAGGGGAAATAGTTACAGGA 59.442 42.308 0.00 0.00 0.00 3.86
2758 5433 7.237887 GGATTAGAGGGGAAATAGTTACAGGAT 59.762 40.741 0.00 0.00 0.00 3.24
2759 5434 5.896073 AGAGGGGAAATAGTTACAGGATG 57.104 43.478 0.00 0.00 46.00 3.51
2760 5435 4.660771 AGAGGGGAAATAGTTACAGGATGG 59.339 45.833 0.00 0.00 43.62 3.51
2761 5436 4.380791 AGGGGAAATAGTTACAGGATGGT 58.619 43.478 0.00 0.00 43.62 3.55
2762 5437 5.544682 AGGGGAAATAGTTACAGGATGGTA 58.455 41.667 0.00 0.00 43.62 3.25
2763 5438 5.368816 AGGGGAAATAGTTACAGGATGGTAC 59.631 44.000 0.00 0.00 43.62 3.34
2771 5446 6.388619 AGTTACAGGATGGTACAAATTCCT 57.611 37.500 0.00 0.00 45.28 3.36
2772 5447 7.504926 AGTTACAGGATGGTACAAATTCCTA 57.495 36.000 0.00 0.00 42.83 2.94
2773 5448 7.924541 AGTTACAGGATGGTACAAATTCCTAA 58.075 34.615 0.00 0.00 42.83 2.69
2774 5449 8.047310 AGTTACAGGATGGTACAAATTCCTAAG 58.953 37.037 0.00 0.00 42.83 2.18
2777 5452 6.058183 CAGGATGGTACAAATTCCTAAGAGG 58.942 44.000 0.00 0.00 42.83 3.69
2780 5455 8.469147 AGGATGGTACAAATTCCTAAGAGGTGA 61.469 40.741 0.00 0.00 42.88 4.02
2781 5456 6.636454 TGGTACAAATTCCTAAGAGGTGAT 57.364 37.500 0.00 0.00 33.05 3.06
2785 5733 5.574188 ACAAATTCCTAAGAGGTGATGCTT 58.426 37.500 0.00 0.00 36.53 3.91
2796 5744 9.565213 CTAAGAGGTGATGCTTAATTTTGAAAG 57.435 33.333 0.00 0.00 0.00 2.62
2826 6342 2.507886 TCCCGATGCTTCTTATTCCCAA 59.492 45.455 0.00 0.00 0.00 4.12
2827 6343 2.880890 CCCGATGCTTCTTATTCCCAAG 59.119 50.000 0.00 0.00 0.00 3.61
2832 6348 5.407995 CGATGCTTCTTATTCCCAAGAGATC 59.592 44.000 0.00 0.00 35.99 2.75
2833 6349 5.698741 TGCTTCTTATTCCCAAGAGATCA 57.301 39.130 0.00 0.00 35.99 2.92
2834 6350 6.065976 TGCTTCTTATTCCCAAGAGATCAA 57.934 37.500 0.00 0.00 35.99 2.57
2835 6351 6.666678 TGCTTCTTATTCCCAAGAGATCAAT 58.333 36.000 0.00 0.00 35.99 2.57
2836 6352 6.769822 TGCTTCTTATTCCCAAGAGATCAATC 59.230 38.462 0.00 0.00 35.99 2.67
2843 6359 2.353889 CCCAAGAGATCAATCACGCTTG 59.646 50.000 0.00 0.00 34.96 4.01
2847 6363 0.749454 AGATCAATCACGCTTGGGCC 60.749 55.000 0.00 0.00 34.44 5.80
2849 6365 4.481112 CAATCACGCTTGGGCCGC 62.481 66.667 0.00 0.00 34.44 6.53
2869 6385 2.159435 GCTCCGACGCCACATTTTATTT 60.159 45.455 0.00 0.00 0.00 1.40
2870 6386 3.672241 GCTCCGACGCCACATTTTATTTT 60.672 43.478 0.00 0.00 0.00 1.82
2874 6390 4.089351 CCGACGCCACATTTTATTTTTCAC 59.911 41.667 0.00 0.00 0.00 3.18
2878 6394 5.689961 ACGCCACATTTTATTTTTCACTGTC 59.310 36.000 0.00 0.00 0.00 3.51
2879 6395 5.164196 CGCCACATTTTATTTTTCACTGTCG 60.164 40.000 0.00 0.00 0.00 4.35
2885 6401 4.759516 TTATTTTTCACTGTCGCCCTTC 57.240 40.909 0.00 0.00 0.00 3.46
2901 6417 2.234908 CCCTTCTCAATCACTTCTCGGT 59.765 50.000 0.00 0.00 0.00 4.69
2905 6421 4.553756 TCTCAATCACTTCTCGGTATCG 57.446 45.455 0.00 0.00 37.82 2.92
2906 6422 3.046390 CTCAATCACTTCTCGGTATCGC 58.954 50.000 0.00 0.00 36.13 4.58
2934 6450 3.424962 GGCATGCTTCGTTTTGACTACTC 60.425 47.826 18.92 0.00 0.00 2.59
2936 6452 1.790623 TGCTTCGTTTTGACTACTCGC 59.209 47.619 0.00 0.00 0.00 5.03
2941 6457 2.792674 TCGTTTTGACTACTCGCTGTTG 59.207 45.455 0.00 0.00 0.00 3.33
2945 6461 3.570926 TTGACTACTCGCTGTTGGTAG 57.429 47.619 0.00 0.00 38.89 3.18
2949 6465 2.228343 ACTACTCGCTGTTGGTAGACAC 59.772 50.000 0.00 0.00 37.11 3.67
2951 6467 0.732880 CTCGCTGTTGGTAGACACGG 60.733 60.000 0.00 0.00 0.00 4.94
2962 6478 2.434428 GTAGACACGGAGAAGGTCAGA 58.566 52.381 0.00 0.00 34.04 3.27
2996 6513 7.798596 ATAAACAAGATCAGTAGAGCCATTG 57.201 36.000 0.00 0.00 0.00 2.82
3005 6522 5.604565 TCAGTAGAGCCATTGATACATGTG 58.395 41.667 9.11 0.00 0.00 3.21
3008 6525 3.828921 AGAGCCATTGATACATGTGCAT 58.171 40.909 9.11 0.00 0.00 3.96
3009 6526 3.568430 AGAGCCATTGATACATGTGCATG 59.432 43.478 9.11 10.31 44.15 4.06
3028 6553 9.184523 TGTGCATGTTTTATTATAGGCTTTAGT 57.815 29.630 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.473677 TGCTGGCAATTCCTTCAATCG 59.526 47.619 0.00 0.00 35.26 3.34
1 2 2.159142 CCTGCTGGCAATTCCTTCAATC 60.159 50.000 0.00 0.00 35.26 2.67
72 73 0.397941 TCTGCACTCCCTTGACCTTG 59.602 55.000 0.00 0.00 0.00 3.61
117 118 3.049674 CCGCGTCCACAAGCACAT 61.050 61.111 4.92 0.00 0.00 3.21
140 141 4.154918 CCTCCTCTTGTTTCACAGTATTGC 59.845 45.833 0.00 0.00 0.00 3.56
180 181 6.884096 CAGACTGCTTCTGTTTACATCTAG 57.116 41.667 7.53 0.00 46.12 2.43
291 299 4.675114 CGCTGAATTTGTTCAACCTTGTAC 59.325 41.667 0.00 0.00 0.00 2.90
367 375 0.386476 TGTATCGGTGTATGGCGTCC 59.614 55.000 0.00 0.00 0.00 4.79
546 1279 2.774351 GCCACCTCCTAGCCCCAT 60.774 66.667 0.00 0.00 0.00 4.00
644 1377 1.613332 TCCTTGGGCTGCTGCTCTA 60.613 57.895 17.02 8.25 41.13 2.43
801 1535 6.702716 AGAGTTTTTAACCGTCCATTTTGA 57.297 33.333 0.00 0.00 0.00 2.69
807 1541 5.766174 AGCAATTAGAGTTTTTAACCGTCCA 59.234 36.000 0.00 0.00 0.00 4.02
880 1614 4.748144 GGCCCCACTGCCCAGAAG 62.748 72.222 1.69 0.00 46.11 2.85
899 1633 2.282040 GCTTGGACACTGGCTGCT 60.282 61.111 0.00 0.00 0.00 4.24
902 1636 3.177884 TGGGCTTGGACACTGGCT 61.178 61.111 0.00 0.00 0.00 4.75
904 1638 2.674380 GCTGGGCTTGGACACTGG 60.674 66.667 0.00 0.00 0.00 4.00
1016 1755 1.613630 GAGGAGGGAGCAGGGTTCA 60.614 63.158 0.00 0.00 0.00 3.18
1024 1763 1.745264 CGATCTTGGAGGAGGGAGC 59.255 63.158 0.00 0.00 0.00 4.70
1737 2476 0.471617 CCAGCCCCATGAAGGAGTAG 59.528 60.000 5.96 0.00 41.22 2.57
2004 2743 1.299976 CTTCCCCTTCCTTCCCGTG 59.700 63.158 0.00 0.00 0.00 4.94
2024 2763 2.327568 GCCAATGAAACCAATGTCACG 58.672 47.619 0.00 0.00 0.00 4.35
2039 2778 0.667993 CGTGAACACACAAGGCCAAT 59.332 50.000 5.01 0.00 34.59 3.16
2044 2783 2.101209 GACGCCGTGAACACACAAGG 62.101 60.000 0.00 0.00 41.13 3.61
2076 2815 4.734398 TTCAGGCAATCAACAAAGTGTT 57.266 36.364 0.00 0.00 42.08 3.32
2077 2816 4.734398 TTTCAGGCAATCAACAAAGTGT 57.266 36.364 0.00 0.00 0.00 3.55
2079 2818 5.127682 AGAGTTTTCAGGCAATCAACAAAGT 59.872 36.000 0.00 0.00 0.00 2.66
2080 2819 5.461078 CAGAGTTTTCAGGCAATCAACAAAG 59.539 40.000 0.00 0.00 0.00 2.77
2082 2821 4.644234 TCAGAGTTTTCAGGCAATCAACAA 59.356 37.500 0.00 0.00 0.00 2.83
2086 2825 5.279106 CCATTTCAGAGTTTTCAGGCAATCA 60.279 40.000 0.00 0.00 0.00 2.57
2087 2826 5.166398 CCATTTCAGAGTTTTCAGGCAATC 58.834 41.667 0.00 0.00 0.00 2.67
2144 2908 5.121811 GCCTATCATATTCCGAAGATGCAT 58.878 41.667 10.35 0.00 30.39 3.96
2145 2909 4.020307 TGCCTATCATATTCCGAAGATGCA 60.020 41.667 10.35 2.89 30.39 3.96
2152 2916 6.653320 GGTTAACATTGCCTATCATATTCCGA 59.347 38.462 8.10 0.00 0.00 4.55
2154 2918 9.686683 ATAGGTTAACATTGCCTATCATATTCC 57.313 33.333 8.10 0.00 40.47 3.01
2157 2921 8.835734 TCCATAGGTTAACATTGCCTATCATAT 58.164 33.333 8.10 0.00 42.00 1.78
2178 2942 5.333798 GCGCGCAAAACTTCTATTATCCATA 60.334 40.000 29.10 0.00 0.00 2.74
2180 2944 3.242608 GCGCGCAAAACTTCTATTATCCA 60.243 43.478 29.10 0.00 0.00 3.41
2187 2951 0.719465 GCTAGCGCGCAAAACTTCTA 59.281 50.000 35.10 13.12 0.00 2.10
2188 2952 1.227999 TGCTAGCGCGCAAAACTTCT 61.228 50.000 35.10 12.60 39.65 2.85
2198 2962 0.721154 TTCTGTCATTTGCTAGCGCG 59.279 50.000 10.77 0.00 39.65 6.86
2200 2964 4.495349 CCTGATTTCTGTCATTTGCTAGCG 60.495 45.833 10.77 0.00 0.00 4.26
2206 2970 4.232221 GCACACCTGATTTCTGTCATTTG 58.768 43.478 0.00 0.00 0.00 2.32
2213 2977 3.067180 AGTTGTTGCACACCTGATTTCTG 59.933 43.478 0.00 0.00 0.00 3.02
2227 2991 3.554129 GGGTGTTAATCCCAAGTTGTTGC 60.554 47.826 12.10 0.00 44.05 4.17
2280 3044 9.959749 ATGTGAATTAAACAAACTGTTACGAAT 57.040 25.926 0.00 0.00 40.14 3.34
2313 3077 8.897752 AGCTTAGATGTGATGTCCTTAAAAATC 58.102 33.333 0.00 0.00 0.00 2.17
2314 3078 8.814038 AGCTTAGATGTGATGTCCTTAAAAAT 57.186 30.769 0.00 0.00 0.00 1.82
2320 3084 3.135530 GGGAGCTTAGATGTGATGTCCTT 59.864 47.826 0.00 0.00 0.00 3.36
2321 3085 2.703007 GGGAGCTTAGATGTGATGTCCT 59.297 50.000 0.00 0.00 0.00 3.85
2322 3086 2.435805 TGGGAGCTTAGATGTGATGTCC 59.564 50.000 0.00 0.00 0.00 4.02
2323 3087 3.118629 TGTGGGAGCTTAGATGTGATGTC 60.119 47.826 0.00 0.00 0.00 3.06
2324 3088 2.840038 TGTGGGAGCTTAGATGTGATGT 59.160 45.455 0.00 0.00 0.00 3.06
2325 3089 3.548745 TGTGGGAGCTTAGATGTGATG 57.451 47.619 0.00 0.00 0.00 3.07
2327 3091 4.574674 ATTTGTGGGAGCTTAGATGTGA 57.425 40.909 0.00 0.00 0.00 3.58
2328 3092 9.725019 TTATATATTTGTGGGAGCTTAGATGTG 57.275 33.333 0.00 0.00 0.00 3.21
2332 3096 8.382405 TGCATTATATATTTGTGGGAGCTTAGA 58.618 33.333 0.00 0.00 0.00 2.10
2333 3097 8.565896 TGCATTATATATTTGTGGGAGCTTAG 57.434 34.615 0.00 0.00 0.00 2.18
2336 3100 5.416952 GCTGCATTATATATTTGTGGGAGCT 59.583 40.000 0.00 0.00 0.00 4.09
2339 3103 6.548993 TGTTGCTGCATTATATATTTGTGGGA 59.451 34.615 1.84 0.00 0.00 4.37
2340 3104 6.747125 TGTTGCTGCATTATATATTTGTGGG 58.253 36.000 1.84 0.00 0.00 4.61
2342 3106 9.518906 TTCTTGTTGCTGCATTATATATTTGTG 57.481 29.630 1.84 0.00 0.00 3.33
2351 3115 9.492973 AGTTTTTATTTCTTGTTGCTGCATTAT 57.507 25.926 1.84 0.00 0.00 1.28
2353 3117 7.790823 AGTTTTTATTTCTTGTTGCTGCATT 57.209 28.000 1.84 0.00 0.00 3.56
2354 3118 7.599998 CCTAGTTTTTATTTCTTGTTGCTGCAT 59.400 33.333 1.84 0.00 0.00 3.96
2355 3119 6.922957 CCTAGTTTTTATTTCTTGTTGCTGCA 59.077 34.615 0.00 0.00 0.00 4.41
2356 3120 7.114953 GTCCTAGTTTTTATTTCTTGTTGCTGC 59.885 37.037 0.00 0.00 0.00 5.25
2357 3121 8.134895 TGTCCTAGTTTTTATTTCTTGTTGCTG 58.865 33.333 0.00 0.00 0.00 4.41
2358 3122 8.232913 TGTCCTAGTTTTTATTTCTTGTTGCT 57.767 30.769 0.00 0.00 0.00 3.91
2390 3154 8.243426 GCTGATATTCATTTTGTTTGTGGTCTA 58.757 33.333 0.00 0.00 0.00 2.59
2392 3156 7.092716 AGCTGATATTCATTTTGTTTGTGGTC 58.907 34.615 0.00 0.00 0.00 4.02
2394 3158 7.894376 AAGCTGATATTCATTTTGTTTGTGG 57.106 32.000 0.00 0.00 0.00 4.17
2395 3159 9.844790 TCTAAGCTGATATTCATTTTGTTTGTG 57.155 29.630 0.00 0.00 0.00 3.33
2400 3164 9.399797 TCACATCTAAGCTGATATTCATTTTGT 57.600 29.630 0.00 0.00 0.00 2.83
2403 3167 9.570468 ACATCACATCTAAGCTGATATTCATTT 57.430 29.630 0.00 0.00 0.00 2.32
2407 3171 8.016497 GTGACATCACATCTAAGCTGATATTC 57.984 38.462 7.15 0.00 45.75 1.75
2408 3172 7.959689 GTGACATCACATCTAAGCTGATATT 57.040 36.000 7.15 0.00 45.75 1.28
2445 3209 9.850628 GATACCAAAATACTACGATACTATGCA 57.149 33.333 0.00 0.00 0.00 3.96
2446 3210 9.007252 CGATACCAAAATACTACGATACTATGC 57.993 37.037 0.00 0.00 0.00 3.14
2451 3215 9.752274 CTCTACGATACCAAAATACTACGATAC 57.248 37.037 0.00 0.00 0.00 2.24
2452 3216 8.939929 CCTCTACGATACCAAAATACTACGATA 58.060 37.037 0.00 0.00 0.00 2.92
2453 3217 7.663081 TCCTCTACGATACCAAAATACTACGAT 59.337 37.037 0.00 0.00 0.00 3.73
2454 3218 6.992123 TCCTCTACGATACCAAAATACTACGA 59.008 38.462 0.00 0.00 0.00 3.43
2455 3219 7.041508 AGTCCTCTACGATACCAAAATACTACG 60.042 40.741 0.00 0.00 0.00 3.51
2456 3220 8.164058 AGTCCTCTACGATACCAAAATACTAC 57.836 38.462 0.00 0.00 0.00 2.73
2458 3222 8.937207 ATAGTCCTCTACGATACCAAAATACT 57.063 34.615 0.00 0.00 0.00 2.12
2472 3236 9.929180 TGCATGTCAATAAATATAGTCCTCTAC 57.071 33.333 0.00 0.00 0.00 2.59
2488 3910 6.072008 TGCTACTTTGTGTTATGCATGTCAAT 60.072 34.615 10.16 0.00 0.00 2.57
2489 3911 5.240403 TGCTACTTTGTGTTATGCATGTCAA 59.760 36.000 10.16 6.53 0.00 3.18
2490 3912 4.759183 TGCTACTTTGTGTTATGCATGTCA 59.241 37.500 10.16 5.48 0.00 3.58
2493 4424 5.045668 TGTGCTACTTTGTGTTATGCATG 57.954 39.130 10.16 0.00 33.48 4.06
2494 4425 5.415389 TGATGTGCTACTTTGTGTTATGCAT 59.585 36.000 3.79 3.79 33.48 3.96
2497 4428 6.845302 ACATGATGTGCTACTTTGTGTTATG 58.155 36.000 0.00 0.00 0.00 1.90
2499 4430 7.971183 TTACATGATGTGCTACTTTGTGTTA 57.029 32.000 8.61 0.00 0.00 2.41
2564 4495 9.973661 TGGTATGGAATTAAATGAAGAAAGAGA 57.026 29.630 0.00 0.00 0.00 3.10
2566 4497 8.966868 GGTGGTATGGAATTAAATGAAGAAAGA 58.033 33.333 0.00 0.00 0.00 2.52
2569 4500 8.112822 TGAGGTGGTATGGAATTAAATGAAGAA 58.887 33.333 0.00 0.00 0.00 2.52
2570 4501 7.638444 TGAGGTGGTATGGAATTAAATGAAGA 58.362 34.615 0.00 0.00 0.00 2.87
2572 4503 8.058235 TGATGAGGTGGTATGGAATTAAATGAA 58.942 33.333 0.00 0.00 0.00 2.57
2573 4504 7.581814 TGATGAGGTGGTATGGAATTAAATGA 58.418 34.615 0.00 0.00 0.00 2.57
2574 4505 7.822161 TGATGAGGTGGTATGGAATTAAATG 57.178 36.000 0.00 0.00 0.00 2.32
2575 4506 8.837099 TTTGATGAGGTGGTATGGAATTAAAT 57.163 30.769 0.00 0.00 0.00 1.40
2576 4507 8.657387 TTTTGATGAGGTGGTATGGAATTAAA 57.343 30.769 0.00 0.00 0.00 1.52
2577 4508 8.837099 ATTTTGATGAGGTGGTATGGAATTAA 57.163 30.769 0.00 0.00 0.00 1.40
2578 4509 8.694540 CAATTTTGATGAGGTGGTATGGAATTA 58.305 33.333 0.00 0.00 0.00 1.40
2579 4510 7.180766 ACAATTTTGATGAGGTGGTATGGAATT 59.819 33.333 0.00 0.00 0.00 2.17
2581 4512 6.015918 ACAATTTTGATGAGGTGGTATGGAA 58.984 36.000 0.00 0.00 0.00 3.53
2582 4513 5.579047 ACAATTTTGATGAGGTGGTATGGA 58.421 37.500 0.00 0.00 0.00 3.41
2586 4517 8.356657 CAACTAAACAATTTTGATGAGGTGGTA 58.643 33.333 0.00 0.00 0.00 3.25
2587 4518 6.976934 ACTAAACAATTTTGATGAGGTGGT 57.023 33.333 0.00 0.00 0.00 4.16
2590 4521 8.006298 TGACAACTAAACAATTTTGATGAGGT 57.994 30.769 0.00 0.00 0.00 3.85
2591 4522 8.918658 CATGACAACTAAACAATTTTGATGAGG 58.081 33.333 0.00 0.00 0.00 3.86
2593 4524 7.924947 TGCATGACAACTAAACAATTTTGATGA 59.075 29.630 0.00 0.00 0.00 2.92
2595 4526 8.836268 ATGCATGACAACTAAACAATTTTGAT 57.164 26.923 0.00 0.00 0.00 2.57
2596 4527 7.384660 GGATGCATGACAACTAAACAATTTTGA 59.615 33.333 2.46 0.00 0.00 2.69
2597 4528 7.171167 TGGATGCATGACAACTAAACAATTTTG 59.829 33.333 2.46 0.00 0.00 2.44
2601 4924 5.981088 TGGATGCATGACAACTAAACAAT 57.019 34.783 2.46 0.00 0.00 2.71
2606 4929 5.423886 TCGTAATGGATGCATGACAACTAA 58.576 37.500 14.52 0.00 0.00 2.24
2614 4937 4.621068 AGTTGTTCGTAATGGATGCATG 57.379 40.909 2.46 0.00 0.00 4.06
2615 4938 5.643379 AAAGTTGTTCGTAATGGATGCAT 57.357 34.783 0.00 0.00 0.00 3.96
2616 4939 6.561737 TTAAAGTTGTTCGTAATGGATGCA 57.438 33.333 0.00 0.00 0.00 3.96
2617 4940 9.730420 ATATTTAAAGTTGTTCGTAATGGATGC 57.270 29.630 0.00 0.00 0.00 3.91
2658 5333 2.549754 CGTTCTGAGCACTGAAAATGGT 59.450 45.455 5.11 0.00 36.16 3.55
2661 5336 3.126001 TCCGTTCTGAGCACTGAAAAT 57.874 42.857 5.11 0.00 36.16 1.82
2669 5344 2.426522 CCTTCAATTCCGTTCTGAGCA 58.573 47.619 0.00 0.00 0.00 4.26
2670 5345 1.740025 CCCTTCAATTCCGTTCTGAGC 59.260 52.381 0.00 0.00 0.00 4.26
2671 5346 3.334583 TCCCTTCAATTCCGTTCTGAG 57.665 47.619 0.00 0.00 0.00 3.35
2677 5352 7.363793 CCAGAAAATAATTCCCTTCAATTCCGT 60.364 37.037 0.00 0.00 0.00 4.69
2679 5354 6.763135 GCCAGAAAATAATTCCCTTCAATTCC 59.237 38.462 0.00 0.00 0.00 3.01
2680 5355 6.476706 CGCCAGAAAATAATTCCCTTCAATTC 59.523 38.462 0.00 0.00 0.00 2.17
2681 5356 6.070824 ACGCCAGAAAATAATTCCCTTCAATT 60.071 34.615 0.00 0.00 0.00 2.32
2692 5367 3.632145 CCTGCCTTACGCCAGAAAATAAT 59.368 43.478 0.00 0.00 36.24 1.28
2695 5370 1.463674 CCTGCCTTACGCCAGAAAAT 58.536 50.000 0.00 0.00 36.24 1.82
2698 5373 2.046314 GCCTGCCTTACGCCAGAA 60.046 61.111 0.00 0.00 36.24 3.02
2716 5391 1.669999 ATCCCAATGAAAGCAGCGCC 61.670 55.000 2.29 0.00 0.00 6.53
2717 5392 0.174162 AATCCCAATGAAAGCAGCGC 59.826 50.000 0.00 0.00 0.00 5.92
2732 5407 6.557633 TCCTGTAACTATTTCCCCTCTAATCC 59.442 42.308 0.00 0.00 0.00 3.01
2736 5411 5.844516 CCATCCTGTAACTATTTCCCCTCTA 59.155 44.000 0.00 0.00 0.00 2.43
2742 5417 8.747538 ATTTGTACCATCCTGTAACTATTTCC 57.252 34.615 0.00 0.00 0.00 3.13
2744 5419 9.185680 GGAATTTGTACCATCCTGTAACTATTT 57.814 33.333 0.00 0.00 0.00 1.40
2746 5421 8.102484 AGGAATTTGTACCATCCTGTAACTAT 57.898 34.615 5.38 0.00 40.73 2.12
2747 5422 7.504926 AGGAATTTGTACCATCCTGTAACTA 57.495 36.000 5.38 0.00 40.73 2.24
2748 5423 6.388619 AGGAATTTGTACCATCCTGTAACT 57.611 37.500 5.38 0.00 40.73 2.24
2749 5424 8.044908 TCTTAGGAATTTGTACCATCCTGTAAC 58.955 37.037 13.23 0.00 42.20 2.50
2750 5425 8.153221 TCTTAGGAATTTGTACCATCCTGTAA 57.847 34.615 13.23 3.64 42.20 2.41
2751 5426 7.147549 CCTCTTAGGAATTTGTACCATCCTGTA 60.148 40.741 13.23 4.21 42.20 2.74
2752 5427 6.353082 CCTCTTAGGAATTTGTACCATCCTGT 60.353 42.308 13.23 0.00 42.20 4.00
2753 5428 6.058183 CCTCTTAGGAATTTGTACCATCCTG 58.942 44.000 13.23 2.12 42.20 3.86
2754 5429 5.731678 ACCTCTTAGGAATTTGTACCATCCT 59.268 40.000 0.00 9.79 44.34 3.24
2756 5431 6.650120 TCACCTCTTAGGAATTTGTACCATC 58.350 40.000 0.00 0.00 37.67 3.51
2757 5432 6.636454 TCACCTCTTAGGAATTTGTACCAT 57.364 37.500 0.00 0.00 37.67 3.55
2758 5433 6.414732 CATCACCTCTTAGGAATTTGTACCA 58.585 40.000 0.00 0.00 37.67 3.25
2759 5434 5.297029 GCATCACCTCTTAGGAATTTGTACC 59.703 44.000 0.00 0.00 37.67 3.34
2760 5435 6.116126 AGCATCACCTCTTAGGAATTTGTAC 58.884 40.000 0.00 0.00 37.67 2.90
2761 5436 6.313519 AGCATCACCTCTTAGGAATTTGTA 57.686 37.500 0.00 0.00 37.67 2.41
2762 5437 5.184892 AGCATCACCTCTTAGGAATTTGT 57.815 39.130 0.00 0.00 37.67 2.83
2763 5438 7.630242 TTAAGCATCACCTCTTAGGAATTTG 57.370 36.000 0.00 0.00 37.67 2.32
2765 5440 8.829373 AAATTAAGCATCACCTCTTAGGAATT 57.171 30.769 0.00 0.00 37.67 2.17
2766 5441 8.689972 CAAAATTAAGCATCACCTCTTAGGAAT 58.310 33.333 0.00 0.00 37.67 3.01
2767 5442 7.888021 TCAAAATTAAGCATCACCTCTTAGGAA 59.112 33.333 0.00 0.00 37.67 3.36
2768 5443 7.402054 TCAAAATTAAGCATCACCTCTTAGGA 58.598 34.615 0.00 0.00 37.67 2.94
2769 5444 7.630242 TCAAAATTAAGCATCACCTCTTAGG 57.370 36.000 0.00 0.00 42.49 2.69
2770 5445 9.565213 CTTTCAAAATTAAGCATCACCTCTTAG 57.435 33.333 0.00 0.00 0.00 2.18
2771 5446 8.522830 CCTTTCAAAATTAAGCATCACCTCTTA 58.477 33.333 0.00 0.00 0.00 2.10
2772 5447 7.233348 TCCTTTCAAAATTAAGCATCACCTCTT 59.767 33.333 0.00 0.00 0.00 2.85
2773 5448 6.721208 TCCTTTCAAAATTAAGCATCACCTCT 59.279 34.615 0.00 0.00 0.00 3.69
2774 5449 6.924111 TCCTTTCAAAATTAAGCATCACCTC 58.076 36.000 0.00 0.00 0.00 3.85
2807 6323 3.808728 TCTTGGGAATAAGAAGCATCGG 58.191 45.455 0.00 0.00 33.96 4.18
2808 6324 4.697514 TCTCTTGGGAATAAGAAGCATCG 58.302 43.478 0.00 0.00 36.34 3.84
2814 6330 6.763135 CGTGATTGATCTCTTGGGAATAAGAA 59.237 38.462 0.00 0.00 36.34 2.52
2817 6333 4.816385 GCGTGATTGATCTCTTGGGAATAA 59.184 41.667 0.00 0.00 0.00 1.40
2826 6342 1.745141 GCCCAAGCGTGATTGATCTCT 60.745 52.381 0.00 0.00 31.55 3.10
2827 6343 0.659957 GCCCAAGCGTGATTGATCTC 59.340 55.000 0.00 0.00 31.55 2.75
2832 6348 4.481112 GCGGCCCAAGCGTGATTG 62.481 66.667 0.00 0.00 41.24 2.67
2833 6349 4.722700 AGCGGCCCAAGCGTGATT 62.723 61.111 0.00 0.00 41.24 2.57
2847 6363 1.355796 TAAAATGTGGCGTCGGAGCG 61.356 55.000 0.00 0.00 38.18 5.03
2849 6365 3.757745 AAATAAAATGTGGCGTCGGAG 57.242 42.857 0.00 0.00 0.00 4.63
2853 6369 5.689961 ACAGTGAAAAATAAAATGTGGCGTC 59.310 36.000 0.00 0.00 0.00 5.19
2857 6373 5.118510 GGCGACAGTGAAAAATAAAATGTGG 59.881 40.000 0.00 0.00 0.00 4.17
2869 6385 0.756294 TGAGAAGGGCGACAGTGAAA 59.244 50.000 0.00 0.00 0.00 2.69
2870 6386 0.756294 TTGAGAAGGGCGACAGTGAA 59.244 50.000 0.00 0.00 0.00 3.18
2874 6390 1.066573 AGTGATTGAGAAGGGCGACAG 60.067 52.381 0.00 0.00 0.00 3.51
2878 6394 2.275318 GAGAAGTGATTGAGAAGGGCG 58.725 52.381 0.00 0.00 0.00 6.13
2879 6395 2.275318 CGAGAAGTGATTGAGAAGGGC 58.725 52.381 0.00 0.00 0.00 5.19
2885 6401 3.046390 GCGATACCGAGAAGTGATTGAG 58.954 50.000 0.00 0.00 38.22 3.02
2923 6439 3.188159 ACCAACAGCGAGTAGTCAAAA 57.812 42.857 0.00 0.00 0.00 2.44
2934 6450 0.732880 CTCCGTGTCTACCAACAGCG 60.733 60.000 0.00 0.00 0.00 5.18
2936 6452 2.352814 CCTTCTCCGTGTCTACCAACAG 60.353 54.545 0.00 0.00 0.00 3.16
2941 6457 1.473278 CTGACCTTCTCCGTGTCTACC 59.527 57.143 0.00 0.00 0.00 3.18
2945 6461 3.444388 ACTTATCTGACCTTCTCCGTGTC 59.556 47.826 0.00 0.00 0.00 3.67
2976 6493 5.627182 ATCAATGGCTCTACTGATCTTGT 57.373 39.130 0.00 0.00 0.00 3.16
2977 6494 6.519382 TGTATCAATGGCTCTACTGATCTTG 58.481 40.000 0.00 0.00 31.20 3.02
2983 6500 4.212847 GCACATGTATCAATGGCTCTACTG 59.787 45.833 0.00 0.00 31.46 2.74
2986 6503 4.420522 TGCACATGTATCAATGGCTCTA 57.579 40.909 0.00 0.00 31.46 2.43


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

AutoCloner maintained by Alex Coulton.