Multiple sequence alignment - TraesCS3B01G165400

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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 TraesCS3B01G165400 chr3B 100.000 5921 0 0 1 5921 163665980 163660060 0.000000e+00 10935
1 TraesCS3B01G165400 chr3D 93.651 3166 133 30 2804 5919 112696532 112693385 0.000000e+00 4671
2 TraesCS3B01G165400 chr3D 88.058 2395 153 52 23 2326 112699638 112697286 0.000000e+00 2715
3 TraesCS3B01G165400 chr3D 84.304 395 35 19 2340 2730 112696902 112696531 1.570000e-95 361
4 TraesCS3B01G165400 chr3A 93.356 873 49 6 3291 4155 108378134 108377263 0.000000e+00 1282
5 TraesCS3B01G165400 chr3A 91.381 905 59 13 4192 5095 108377179 108376293 0.000000e+00 1221
6 TraesCS3B01G165400 chr3A 93.064 793 38 13 676 1457 108381220 108380434 0.000000e+00 1144
7 TraesCS3B01G165400 chr3A 84.406 917 80 23 1459 2326 108380399 108379497 0.000000e+00 843
8 TraesCS3B01G165400 chr3A 84.666 763 76 18 5184 5921 108375957 108375211 0.000000e+00 723
9 TraesCS3B01G165400 chr3A 86.892 473 35 10 2774 3221 108378618 108378148 6.850000e-139 505
10 TraesCS3B01G165400 chr7D 87.354 427 26 8 2915 3340 453305509 453305908 1.160000e-126 464
11 TraesCS3B01G165400 chr7D 75.862 232 35 15 1196 1406 60079481 60079712 1.360000e-16 99
12 TraesCS3B01G165400 chr2D 87.294 425 26 8 2915 3338 442449190 442449587 1.500000e-125 460
13 TraesCS3B01G165400 chr7B 78.526 475 92 10 3635 4107 2494275 2494741 2.680000e-78 303
14 TraesCS3B01G165400 chr7B 78.105 475 95 9 3635 4107 2512627 2513094 5.800000e-75 292
15 TraesCS3B01G165400 chr7A 75.983 229 37 12 1196 1406 64466099 64466327 1.050000e-17 102


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 TraesCS3B01G165400 chr3B 163660060 163665980 5920 True 10935.000000 10935 100.000000 1 5921 1 chr3B.!!$R1 5920
1 TraesCS3B01G165400 chr3D 112693385 112699638 6253 True 2582.333333 4671 88.671000 23 5919 3 chr3D.!!$R1 5896
2 TraesCS3B01G165400 chr3A 108375211 108381220 6009 True 953.000000 1282 88.960833 676 5921 6 chr3A.!!$R1 5245

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
326 336 0.106268 TGGAGCACCAGCCAAGAAAA 60.106 50.000 0.00 0.0 41.77 2.29 F
348 358 0.525761 GCCTACATTTTGCTTCCGCA 59.474 50.000 0.00 0.0 46.24 5.69 F
409 424 0.528017 TGAACTGAGCTGAGTAGGCG 59.472 55.000 6.17 0.0 34.52 5.52 F
1911 2054 0.548031 TATGCCCTGCTTTCTCTGGG 59.452 55.000 0.00 0.0 45.09 4.45 F
2055 2201 0.675208 TTGTCCGCCGCACACATAAT 60.675 50.000 0.00 0.0 0.00 1.28 F
2854 3538 0.720027 CTGATGCTCTGCTCACAACG 59.280 55.000 0.00 0.0 0.00 4.10 F
3021 3728 1.550524 CAAAGTCAGGTCCTCATCGGA 59.449 52.381 0.00 0.0 40.30 4.55 F
3253 3961 1.931906 ATGCAGTACGATGCTGTCAG 58.068 50.000 8.39 0.0 46.63 3.51 F
4263 5033 2.159085 AGATAGGCACTTACCGAGTTGC 60.159 50.000 0.00 0.0 41.75 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2205 2363 0.034756 CCATCACCAAGACACCGACA 59.965 55.000 0.00 0.0 0.00 4.35 R
2206 2364 0.673644 CCCATCACCAAGACACCGAC 60.674 60.000 0.00 0.0 0.00 4.79 R
2247 2411 3.449737 CCGACTAATAGAACACCTTCCCA 59.550 47.826 0.00 0.0 0.00 4.37 R
3461 4170 0.839946 ATGAAGCGATTAGGGCCAGT 59.160 50.000 6.18 0.0 0.00 4.00 R
3592 4301 2.297033 GCTGGAAAACCTGATGCAAAGA 59.703 45.455 0.00 0.0 0.00 2.52 R
4245 5011 0.248289 GGCAACTCGGTAAGTGCCTA 59.752 55.000 6.28 0.0 43.32 3.93 R
4246 5012 1.003718 GGCAACTCGGTAAGTGCCT 60.004 57.895 6.28 0.0 43.32 4.75 R
4803 5590 1.048601 TCCGGAAGCTTGTGAAGAGT 58.951 50.000 2.10 0.0 0.00 3.24 R
5649 6763 0.467290 TGTGGAAGGGCTGACCAAAC 60.467 55.000 0.47 0.0 43.89 2.93 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
17 18 4.452733 AGCAACCGGTAGGAGCGC 62.453 66.667 8.00 0.00 43.26 5.92
18 19 4.452733 GCAACCGGTAGGAGCGCT 62.453 66.667 11.27 11.27 41.02 5.92
19 20 2.509336 CAACCGGTAGGAGCGCTG 60.509 66.667 18.48 0.00 41.02 5.18
20 21 4.452733 AACCGGTAGGAGCGCTGC 62.453 66.667 22.65 22.65 41.02 5.25
23 24 4.148825 CGGTAGGAGCGCTGCCTT 62.149 66.667 26.33 10.85 36.96 4.35
24 25 2.202946 GGTAGGAGCGCTGCCTTC 60.203 66.667 26.33 21.14 36.96 3.46
25 26 2.726351 GGTAGGAGCGCTGCCTTCT 61.726 63.158 26.33 9.63 36.96 2.85
26 27 1.392710 GGTAGGAGCGCTGCCTTCTA 61.393 60.000 26.33 8.49 36.96 2.10
27 28 0.460311 GTAGGAGCGCTGCCTTCTAA 59.540 55.000 26.33 8.45 36.96 2.10
28 29 1.134788 GTAGGAGCGCTGCCTTCTAAA 60.135 52.381 26.33 8.10 36.96 1.85
29 30 0.391793 AGGAGCGCTGCCTTCTAAAC 60.392 55.000 26.33 0.46 29.44 2.01
30 31 0.673644 GGAGCGCTGCCTTCTAAACA 60.674 55.000 18.48 0.00 0.00 2.83
31 32 1.373570 GAGCGCTGCCTTCTAAACAT 58.626 50.000 18.48 0.00 0.00 2.71
32 33 1.740025 GAGCGCTGCCTTCTAAACATT 59.260 47.619 18.48 0.00 0.00 2.71
33 34 1.740025 AGCGCTGCCTTCTAAACATTC 59.260 47.619 10.39 0.00 0.00 2.67
51 52 8.936070 AAACATTCCACATGATGTAAATGATG 57.064 30.769 26.39 16.48 36.75 3.07
54 55 7.776500 ACATTCCACATGATGTAAATGATGAGA 59.224 33.333 26.39 0.00 36.75 3.27
56 57 6.057533 TCCACATGATGTAAATGATGAGACC 58.942 40.000 0.00 0.00 0.00 3.85
58 59 5.525012 CACATGATGTAAATGATGAGACCGT 59.475 40.000 0.00 0.00 0.00 4.83
73 74 3.726517 CGTTGTGGCGCCTCTTGG 61.727 66.667 29.70 12.90 0.00 3.61
134 135 1.455822 TCAATGGGGGTGGAAGAAGT 58.544 50.000 0.00 0.00 0.00 3.01
139 140 1.152830 GGGGTGGAAGAAGTGGCAA 59.847 57.895 0.00 0.00 0.00 4.52
147 148 3.181440 TGGAAGAAGTGGCAAGATTCTGT 60.181 43.478 10.53 3.49 33.67 3.41
151 152 3.326006 AGAAGTGGCAAGATTCTGTCTCA 59.674 43.478 9.35 0.00 35.67 3.27
164 165 4.277515 TCTGTCTCAAATTGACTCCCTG 57.722 45.455 0.00 0.00 35.63 4.45
167 168 1.988107 TCTCAAATTGACTCCCTGCCT 59.012 47.619 0.00 0.00 0.00 4.75
176 177 3.005539 TCCCTGCCTGGAGAGCAC 61.006 66.667 0.00 0.00 38.35 4.40
210 211 1.595357 CACGGTGAAGGGGTAGTCC 59.405 63.158 0.74 0.00 0.00 3.85
218 219 3.056035 GTGAAGGGGTAGTCCTTACACAG 60.056 52.174 14.91 0.00 46.31 3.66
220 221 0.540454 GGGGTAGTCCTTACACAGGC 59.460 60.000 0.00 0.00 43.55 4.85
316 326 1.347707 GGATCCGATTATGGAGCACCA 59.652 52.381 4.98 4.98 46.29 4.17
324 334 3.249805 TGGAGCACCAGCCAAGAA 58.750 55.556 0.00 0.00 41.77 2.52
325 335 1.536180 TGGAGCACCAGCCAAGAAA 59.464 52.632 0.00 0.00 41.77 2.52
326 336 0.106268 TGGAGCACCAGCCAAGAAAA 60.106 50.000 0.00 0.00 41.77 2.29
341 351 4.925646 CCAAGAAAAGAGCCTACATTTTGC 59.074 41.667 0.00 0.00 0.00 3.68
346 356 2.359900 AGAGCCTACATTTTGCTTCCG 58.640 47.619 0.00 0.00 34.99 4.30
347 357 0.811281 AGCCTACATTTTGCTTCCGC 59.189 50.000 0.00 0.00 29.17 5.54
348 358 0.525761 GCCTACATTTTGCTTCCGCA 59.474 50.000 0.00 0.00 46.24 5.69
380 395 4.212847 CCATATCTGTCTCGAATTTGCCAG 59.787 45.833 0.00 0.00 0.00 4.85
383 398 0.690192 TGTCTCGAATTTGCCAGGGA 59.310 50.000 0.00 0.00 0.00 4.20
396 411 1.959042 CCAGGGAATCCGATGAACTG 58.041 55.000 4.88 0.09 38.33 3.16
400 415 1.139853 GGGAATCCGATGAACTGAGCT 59.860 52.381 0.00 0.00 0.00 4.09
409 424 0.528017 TGAACTGAGCTGAGTAGGCG 59.472 55.000 6.17 0.00 34.52 5.52
429 446 1.028905 GAGCTCACATAGTCTCCGCT 58.971 55.000 9.40 0.00 0.00 5.52
445 462 1.380380 GCTGGGGGTCCAAATCCAG 60.380 63.158 12.67 12.67 46.93 3.86
462 479 1.760086 AGGAGATGGAGTCTGGGCG 60.760 63.158 0.00 0.00 37.29 6.13
471 488 1.946475 GAGTCTGGGCGTAGGGTGTC 61.946 65.000 0.00 0.00 0.00 3.67
543 582 8.627487 TTTTGACATGATTGTGTTTAGTGAAC 57.373 30.769 0.00 0.00 35.79 3.18
545 584 5.825151 TGACATGATTGTGTTTAGTGAACCA 59.175 36.000 0.00 0.00 37.45 3.67
550 589 7.867305 TGATTGTGTTTAGTGAACCAACTTA 57.133 32.000 0.00 0.00 37.45 2.24
552 591 8.349245 TGATTGTGTTTAGTGAACCAACTTATG 58.651 33.333 0.00 0.00 37.45 1.90
568 607 6.992715 CCAACTTATGGTTAGATGGTTAGGAG 59.007 42.308 0.00 0.00 44.85 3.69
571 610 2.463752 TGGTTAGATGGTTAGGAGCGT 58.536 47.619 0.00 0.00 0.00 5.07
574 613 3.369157 GGTTAGATGGTTAGGAGCGTGTT 60.369 47.826 0.00 0.00 0.00 3.32
576 615 2.180276 AGATGGTTAGGAGCGTGTTCT 58.820 47.619 0.00 0.00 0.00 3.01
577 616 3.362706 AGATGGTTAGGAGCGTGTTCTA 58.637 45.455 0.00 0.00 0.00 2.10
613 667 8.954950 TGATTGTGTTCATAATTTTGGTGTTT 57.045 26.923 0.00 0.00 0.00 2.83
644 701 4.022849 AGCTAGGTTGCAATTTTGTGAGTC 60.023 41.667 0.59 0.00 34.99 3.36
651 708 2.156891 GCAATTTTGTGAGTCGAGCGTA 59.843 45.455 0.00 0.00 0.00 4.42
652 709 3.722123 CAATTTTGTGAGTCGAGCGTAC 58.278 45.455 0.00 0.00 0.00 3.67
658 715 0.956633 TGAGTCGAGCGTACAAAGGT 59.043 50.000 0.00 0.00 0.00 3.50
709 766 9.140286 GGAAAGAATATTTACAGCTCCAAAAAC 57.860 33.333 0.00 0.00 0.00 2.43
712 769 7.602753 AGAATATTTACAGCTCCAAAAACACC 58.397 34.615 0.00 0.00 0.00 4.16
781 847 7.670605 ATCATCATGGTTGGATTCTTTGAAT 57.329 32.000 0.00 0.00 0.00 2.57
783 849 5.664294 TCATGGTTGGATTCTTTGAATGG 57.336 39.130 0.00 0.00 0.00 3.16
844 912 4.999524 GCCACATGGATCCCAAAAGGAAG 62.000 52.174 9.90 0.00 41.62 3.46
1302 1374 4.980805 GCGGCCACGTTCCTGTCA 62.981 66.667 2.24 0.00 43.45 3.58
1368 1440 2.621115 GGCCTCCTCCTCCCCATA 59.379 66.667 0.00 0.00 0.00 2.74
1441 1513 7.172342 TGCTTCCTTGCTTAAATTCTACCTAA 58.828 34.615 0.00 0.00 0.00 2.69
1443 1515 7.553044 GCTTCCTTGCTTAAATTCTACCTAAGA 59.447 37.037 0.00 0.00 0.00 2.10
1445 1517 7.913789 TCCTTGCTTAAATTCTACCTAAGACA 58.086 34.615 0.00 0.00 32.51 3.41
1448 1520 6.412214 TGCTTAAATTCTACCTAAGACACCC 58.588 40.000 0.00 0.00 32.51 4.61
1507 1612 4.186926 TCTGAAGGAGAGAATGATTTGCG 58.813 43.478 0.00 0.00 0.00 4.85
1540 1645 4.158209 ACTCCCGAGCTACTCTTTAGAAAC 59.842 45.833 0.00 0.00 0.00 2.78
1620 1726 3.443681 AGCAAATCCTCCCGTTTATGTTG 59.556 43.478 0.00 0.00 0.00 3.33
1623 1729 0.988832 TCCTCCCGTTTATGTTGGCT 59.011 50.000 0.00 0.00 0.00 4.75
1626 1732 2.618045 CCTCCCGTTTATGTTGGCTCTT 60.618 50.000 0.00 0.00 0.00 2.85
1640 1746 3.074412 TGGCTCTTTTCGGTTCTTGATC 58.926 45.455 0.00 0.00 0.00 2.92
1697 1805 4.321718 TGGATCAGAGCATAATAAGCTGC 58.678 43.478 0.00 0.00 43.58 5.25
1715 1823 1.109323 GCTGTATGACCCCCATTGGC 61.109 60.000 0.00 0.00 36.71 4.52
1716 1824 0.819259 CTGTATGACCCCCATTGGCG 60.819 60.000 0.00 0.00 36.71 5.69
1787 1914 1.153706 GTTGGCACATGCATGGCTC 60.154 57.895 29.41 20.67 45.16 4.70
1801 1928 3.420893 CATGGCTCAACCCAAAAGTAGA 58.579 45.455 0.00 0.00 38.61 2.59
1818 1958 9.720769 CAAAAGTAGACTATTTGGAGACCTTTA 57.279 33.333 1.97 0.00 31.93 1.85
1881 2024 2.280524 CGCCCACGGACAAACAGA 60.281 61.111 0.00 0.00 34.97 3.41
1911 2054 0.548031 TATGCCCTGCTTTCTCTGGG 59.452 55.000 0.00 0.00 45.09 4.45
1915 2058 1.211456 CCCTGCTTTCTCTGGGATCT 58.789 55.000 0.01 0.00 45.12 2.75
1923 2066 1.475403 TCTCTGGGATCTGTCGGTTC 58.525 55.000 0.00 0.00 0.00 3.62
1928 2071 3.772572 TCTGGGATCTGTCGGTTCATTAA 59.227 43.478 0.00 0.00 0.00 1.40
1932 2075 4.941873 GGGATCTGTCGGTTCATTAACTTT 59.058 41.667 0.00 0.00 35.81 2.66
1960 2103 5.941948 AAGTTTCACCAGTATACTTGTGC 57.058 39.130 25.21 15.17 38.90 4.57
1995 2140 5.104277 TGACTTTCCCCACTTTCTGTTCTAA 60.104 40.000 0.00 0.00 0.00 2.10
1996 2141 5.762279 ACTTTCCCCACTTTCTGTTCTAAA 58.238 37.500 0.00 0.00 0.00 1.85
2042 2188 6.616947 TGCATAATTTACCTTTCTTTGTCCG 58.383 36.000 0.00 0.00 0.00 4.79
2044 2190 4.514781 AATTTACCTTTCTTTGTCCGCC 57.485 40.909 0.00 0.00 0.00 6.13
2046 2192 0.952010 TACCTTTCTTTGTCCGCCGC 60.952 55.000 0.00 0.00 0.00 6.53
2047 2193 2.258013 CCTTTCTTTGTCCGCCGCA 61.258 57.895 0.00 0.00 0.00 5.69
2055 2201 0.675208 TTGTCCGCCGCACACATAAT 60.675 50.000 0.00 0.00 0.00 1.28
2095 2242 5.578727 TCGAGCTGCTTTTCTCTCTAATTTC 59.421 40.000 2.53 0.00 0.00 2.17
2137 2284 9.498307 CTTTGATCGGTATTTTTGTATGGTAAC 57.502 33.333 0.00 0.00 0.00 2.50
2184 2331 7.077605 GCTTTTGAAATATTGTGGGAAAAAGC 58.922 34.615 17.27 17.27 46.05 3.51
2185 2332 6.777526 TTTGAAATATTGTGGGAAAAAGCG 57.222 33.333 0.00 0.00 0.00 4.68
2186 2333 4.241681 TGAAATATTGTGGGAAAAAGCGC 58.758 39.130 0.00 0.00 0.00 5.92
2188 2335 1.621992 TATTGTGGGAAAAAGCGCCA 58.378 45.000 2.29 0.00 0.00 5.69
2205 2363 2.545526 CGCCATAGTTCGCTGATCAATT 59.454 45.455 0.00 0.00 0.00 2.32
2206 2364 3.605461 CGCCATAGTTCGCTGATCAATTG 60.605 47.826 0.00 0.00 0.00 2.32
2247 2411 7.302948 TGGGTAGGTATCATCACTAGTGTATT 58.697 38.462 21.99 6.36 0.00 1.89
2248 2412 7.232737 TGGGTAGGTATCATCACTAGTGTATTG 59.767 40.741 21.99 17.00 0.00 1.90
2250 2414 6.672266 AGGTATCATCACTAGTGTATTGGG 57.328 41.667 21.99 7.19 0.00 4.12
2277 2441 6.435277 AGGTGTTCTATTAGTCGGTCAGTTAA 59.565 38.462 0.00 0.00 0.00 2.01
2282 2446 7.876936 TCTATTAGTCGGTCAGTTAATCAGT 57.123 36.000 0.00 0.00 0.00 3.41
2284 2448 8.188799 TCTATTAGTCGGTCAGTTAATCAGTTG 58.811 37.037 0.00 0.00 0.00 3.16
2285 2449 3.926616 AGTCGGTCAGTTAATCAGTTGG 58.073 45.455 0.00 0.00 0.00 3.77
2319 2483 9.689976 CAGTTAATTGTTTTGTGATATTGTGGA 57.310 29.630 0.00 0.00 0.00 4.02
2326 2490 6.072948 TGTTTTGTGATATTGTGGAACGGTAG 60.073 38.462 0.00 0.00 42.39 3.18
2327 2491 4.811969 TGTGATATTGTGGAACGGTAGT 57.188 40.909 0.00 0.00 42.39 2.73
2328 2492 5.918426 TGTGATATTGTGGAACGGTAGTA 57.082 39.130 0.00 0.00 42.39 1.82
2330 2494 5.419788 TGTGATATTGTGGAACGGTAGTACT 59.580 40.000 0.00 0.00 42.39 2.73
2331 2495 6.602803 TGTGATATTGTGGAACGGTAGTACTA 59.397 38.462 0.00 0.00 42.39 1.82
2332 2496 6.914757 GTGATATTGTGGAACGGTAGTACTAC 59.085 42.308 22.53 22.53 42.39 2.73
2333 2497 6.602803 TGATATTGTGGAACGGTAGTACTACA 59.397 38.462 29.38 10.58 42.39 2.74
2334 2498 5.927281 ATTGTGGAACGGTAGTACTACAT 57.073 39.130 29.38 16.96 42.39 2.29
2335 2499 4.970662 TGTGGAACGGTAGTACTACATC 57.029 45.455 29.38 22.88 42.39 3.06
2338 2502 6.121590 TGTGGAACGGTAGTACTACATCATA 58.878 40.000 29.38 16.22 42.39 2.15
2389 2923 4.574674 TGCATGTATCAGAAAGGACCTT 57.425 40.909 0.00 0.00 0.00 3.50
2408 2942 8.118600 AGGACCTTATTTCTCCAAAGATCAAAT 58.881 33.333 0.00 0.00 0.00 2.32
2421 2955 4.591321 AGATCAAATGCAAGGTTCCCTA 57.409 40.909 0.00 0.00 31.13 3.53
2422 2956 5.134725 AGATCAAATGCAAGGTTCCCTAT 57.865 39.130 0.00 0.00 31.13 2.57
2435 2969 8.914011 GCAAGGTTCCCTATTGAAATAAGTTAT 58.086 33.333 0.00 0.00 31.13 1.89
2507 3159 9.088512 CATTAGTAAAGGCTAGTACAAAGACAG 57.911 37.037 10.03 0.00 0.00 3.51
2573 3230 2.298729 ACATAACACGGCTGCCAATTTT 59.701 40.909 20.29 7.94 0.00 1.82
2584 3241 5.687285 CGGCTGCCAATTTTCTACATTATTC 59.313 40.000 20.29 0.00 0.00 1.75
2588 3245 7.646922 GCTGCCAATTTTCTACATTATTCTCAG 59.353 37.037 0.00 0.00 0.00 3.35
2591 3248 8.677300 GCCAATTTTCTACATTATTCTCAGTGA 58.323 33.333 0.00 0.00 0.00 3.41
2636 3293 9.778993 AATTGATCACTTCTAAATTCAACATCG 57.221 29.630 0.00 0.00 0.00 3.84
2638 3295 7.963981 TGATCACTTCTAAATTCAACATCGTC 58.036 34.615 0.00 0.00 0.00 4.20
2641 3298 8.322906 TCACTTCTAAATTCAACATCGTCAAT 57.677 30.769 0.00 0.00 0.00 2.57
2680 3364 4.974645 AAATGGTGTACTTCTCCTGTGA 57.025 40.909 0.00 0.00 0.00 3.58
2700 3384 5.698089 TGTGATCACTTCAAAGACTAGCTTG 59.302 40.000 25.55 0.00 36.80 4.01
2709 3393 5.710984 TCAAAGACTAGCTTGCTACAGTAC 58.289 41.667 0.00 0.00 36.80 2.73
2710 3394 5.477291 TCAAAGACTAGCTTGCTACAGTACT 59.523 40.000 0.00 0.00 36.80 2.73
2712 3396 5.317733 AGACTAGCTTGCTACAGTACTTG 57.682 43.478 0.00 0.00 0.00 3.16
2716 3400 5.696724 ACTAGCTTGCTACAGTACTTGTTTG 59.303 40.000 0.00 0.00 41.29 2.93
2717 3401 3.251004 AGCTTGCTACAGTACTTGTTTGC 59.749 43.478 0.00 4.78 41.29 3.68
2718 3402 3.003275 GCTTGCTACAGTACTTGTTTGCA 59.997 43.478 14.90 14.90 42.28 4.08
2719 3403 4.527564 CTTGCTACAGTACTTGTTTGCAC 58.472 43.478 16.79 0.00 43.04 4.57
2720 3404 3.536570 TGCTACAGTACTTGTTTGCACA 58.463 40.909 14.90 0.00 40.54 4.57
2721 3405 4.133820 TGCTACAGTACTTGTTTGCACAT 58.866 39.130 14.90 0.00 40.54 3.21
2722 3406 4.578516 TGCTACAGTACTTGTTTGCACATT 59.421 37.500 14.90 0.00 40.54 2.71
2723 3407 5.147162 GCTACAGTACTTGTTTGCACATTC 58.853 41.667 0.00 0.00 41.29 2.67
2724 3408 5.049405 GCTACAGTACTTGTTTGCACATTCT 60.049 40.000 0.00 0.00 41.29 2.40
2725 3409 5.835113 ACAGTACTTGTTTGCACATTCTT 57.165 34.783 0.00 0.00 36.31 2.52
2726 3410 6.935741 ACAGTACTTGTTTGCACATTCTTA 57.064 33.333 0.00 0.00 36.31 2.10
2731 3415 5.591099 ACTTGTTTGCACATTCTTACTTGG 58.409 37.500 0.00 0.00 31.06 3.61
2738 3422 6.325919 TGCACATTCTTACTTGGGTTTTAG 57.674 37.500 0.00 0.00 0.00 1.85
2749 3433 8.634335 TTACTTGGGTTTTAGGTGGTATAAAC 57.366 34.615 0.00 0.00 0.00 2.01
2750 3434 6.612741 ACTTGGGTTTTAGGTGGTATAAACA 58.387 36.000 0.00 0.00 33.33 2.83
2751 3435 7.243091 ACTTGGGTTTTAGGTGGTATAAACAT 58.757 34.615 0.00 0.00 33.33 2.71
2752 3436 7.731235 ACTTGGGTTTTAGGTGGTATAAACATT 59.269 33.333 0.00 0.00 33.33 2.71
2753 3437 8.493787 TTGGGTTTTAGGTGGTATAAACATTT 57.506 30.769 0.00 0.00 33.33 2.32
2754 3438 7.897864 TGGGTTTTAGGTGGTATAAACATTTG 58.102 34.615 0.00 0.00 33.33 2.32
2755 3439 7.509659 TGGGTTTTAGGTGGTATAAACATTTGT 59.490 33.333 0.00 0.00 33.33 2.83
2756 3440 9.022884 GGGTTTTAGGTGGTATAAACATTTGTA 57.977 33.333 0.00 0.00 33.33 2.41
2788 3472 8.729805 TTTTTGCACATTCTTACTTGGATTTT 57.270 26.923 0.00 0.00 0.00 1.82
2789 3473 9.823647 TTTTTGCACATTCTTACTTGGATTTTA 57.176 25.926 0.00 0.00 0.00 1.52
2790 3474 9.474920 TTTTGCACATTCTTACTTGGATTTTAG 57.525 29.630 0.00 0.00 0.00 1.85
2791 3475 7.156876 TGCACATTCTTACTTGGATTTTAGG 57.843 36.000 0.00 0.00 0.00 2.69
2792 3476 6.719370 TGCACATTCTTACTTGGATTTTAGGT 59.281 34.615 0.00 0.00 0.00 3.08
2793 3477 7.029563 GCACATTCTTACTTGGATTTTAGGTG 58.970 38.462 0.00 0.00 0.00 4.00
2794 3478 7.538575 CACATTCTTACTTGGATTTTAGGTGG 58.461 38.462 0.00 0.00 0.00 4.61
2795 3479 7.176690 CACATTCTTACTTGGATTTTAGGTGGT 59.823 37.037 0.00 0.00 0.00 4.16
2796 3480 8.387813 ACATTCTTACTTGGATTTTAGGTGGTA 58.612 33.333 0.00 0.00 0.00 3.25
2797 3481 9.408648 CATTCTTACTTGGATTTTAGGTGGTAT 57.591 33.333 0.00 0.00 0.00 2.73
2798 3482 8.801882 TTCTTACTTGGATTTTAGGTGGTATG 57.198 34.615 0.00 0.00 0.00 2.39
2799 3483 8.153221 TCTTACTTGGATTTTAGGTGGTATGA 57.847 34.615 0.00 0.00 0.00 2.15
2804 3488 7.673926 ACTTGGATTTTAGGTGGTATGAACATT 59.326 33.333 0.00 0.00 0.00 2.71
2814 3498 7.826690 AGGTGGTATGAACATTTTTATGTGAC 58.173 34.615 0.00 0.00 34.56 3.67
2815 3499 7.450014 AGGTGGTATGAACATTTTTATGTGACA 59.550 33.333 0.00 0.00 34.56 3.58
2854 3538 0.720027 CTGATGCTCTGCTCACAACG 59.280 55.000 0.00 0.00 0.00 4.10
2885 3569 6.412214 TGATGGTCCATATGCTAGAATCATG 58.588 40.000 3.72 0.00 0.00 3.07
2910 3617 9.618890 TGAAGCTATTTAATTTCTATGCAGACT 57.381 29.630 0.00 0.00 0.00 3.24
2912 3619 7.869800 AGCTATTTAATTTCTATGCAGACTGC 58.130 34.615 20.86 20.86 45.29 4.40
2924 3631 2.097160 GACTGCGCTTGATGCACG 59.903 61.111 9.73 0.00 43.06 5.34
3021 3728 1.550524 CAAAGTCAGGTCCTCATCGGA 59.449 52.381 0.00 0.00 40.30 4.55
3111 3818 3.244181 GCAAGTGTGATGTTGGGGAAAAT 60.244 43.478 0.00 0.00 0.00 1.82
3166 3873 2.977405 CAGCTTGACTGGTAAGTTGC 57.023 50.000 0.00 0.00 43.19 4.17
3170 3877 2.851195 CTTGACTGGTAAGTTGCCACT 58.149 47.619 8.83 0.00 36.52 4.00
3183 3890 5.932619 AGTTGCCACTCTGTATGTATGTA 57.067 39.130 0.00 0.00 0.00 2.29
3224 3932 7.388776 TCTGAAGATTTCTGATACTTGGTTGTG 59.611 37.037 0.00 0.00 33.45 3.33
3240 3948 6.398234 TGGTTGTGTTGTAAATTATGCAGT 57.602 33.333 0.00 0.00 0.00 4.40
3242 3950 7.364200 TGGTTGTGTTGTAAATTATGCAGTAC 58.636 34.615 0.00 0.00 0.00 2.73
3243 3951 6.521821 GGTTGTGTTGTAAATTATGCAGTACG 59.478 38.462 0.00 0.00 0.00 3.67
3247 3955 6.410914 GTGTTGTAAATTATGCAGTACGATGC 59.589 38.462 0.27 0.27 46.68 3.91
3253 3961 1.931906 ATGCAGTACGATGCTGTCAG 58.068 50.000 8.39 0.00 46.63 3.51
3267 3976 6.401047 CGATGCTGTCAGTTTTATCTCGAAAA 60.401 38.462 0.93 0.00 0.00 2.29
3272 3981 8.656849 GCTGTCAGTTTTATCTCGAAAAGAATA 58.343 33.333 0.93 0.00 37.61 1.75
3279 3988 9.052080 GTTTTATCTCGAAAAGAATACAACAGC 57.948 33.333 0.00 0.00 37.61 4.40
3280 3989 8.547967 TTTATCTCGAAAAGAATACAACAGCT 57.452 30.769 0.00 0.00 37.61 4.24
3281 3990 6.654793 ATCTCGAAAAGAATACAACAGCTC 57.345 37.500 0.00 0.00 37.61 4.09
3359 4068 4.549458 GCATTACAACTGATGTGCAAACT 58.451 39.130 0.34 0.00 43.77 2.66
3365 4074 4.452455 ACAACTGATGTGCAAACTAGCTAC 59.548 41.667 0.00 0.00 41.93 3.58
3496 4205 3.614616 GCTTCATTCTCACTTGTACTCGG 59.385 47.826 0.00 0.00 0.00 4.63
3568 4277 5.815740 GCTGCAAATGATGAAAAGATTGGAT 59.184 36.000 0.00 0.00 0.00 3.41
3642 4354 2.961741 TCAGAAGAGGAAGCTCGCATAT 59.038 45.455 0.00 0.00 0.00 1.78
4139 4855 9.117183 GTTTATTTACTTCCGATCCCTGTAAAT 57.883 33.333 17.13 17.13 42.60 1.40
4243 5009 4.710528 GTGTAACTTGGACACGAAAGAG 57.289 45.455 0.00 0.00 38.01 2.85
4244 5010 4.365723 GTGTAACTTGGACACGAAAGAGA 58.634 43.478 0.00 0.00 38.01 3.10
4245 5011 4.989168 GTGTAACTTGGACACGAAAGAGAT 59.011 41.667 0.00 0.00 38.01 2.75
4246 5012 6.154445 GTGTAACTTGGACACGAAAGAGATA 58.846 40.000 0.00 0.00 38.01 1.98
4263 5033 2.159085 AGATAGGCACTTACCGAGTTGC 60.159 50.000 0.00 0.00 41.75 4.17
4420 5190 2.964978 GCATTTGCAGACCCGCTT 59.035 55.556 0.00 0.00 41.59 4.68
4607 5392 5.608676 GTGAAACTCCTTAGCTTGTAACC 57.391 43.478 0.00 0.00 0.00 2.85
4608 5393 4.151867 GTGAAACTCCTTAGCTTGTAACCG 59.848 45.833 0.00 0.00 0.00 4.44
4609 5394 4.202284 TGAAACTCCTTAGCTTGTAACCGT 60.202 41.667 0.00 0.00 0.00 4.83
4610 5395 3.589495 ACTCCTTAGCTTGTAACCGTC 57.411 47.619 0.00 0.00 0.00 4.79
4611 5396 2.233186 ACTCCTTAGCTTGTAACCGTCC 59.767 50.000 0.00 0.00 0.00 4.79
4612 5397 2.232941 CTCCTTAGCTTGTAACCGTCCA 59.767 50.000 0.00 0.00 0.00 4.02
4613 5398 2.835764 TCCTTAGCTTGTAACCGTCCAT 59.164 45.455 0.00 0.00 0.00 3.41
4650 5437 5.485620 ACTAAGAACATCCTTCGGTAAACC 58.514 41.667 0.00 0.00 0.00 3.27
4683 5470 2.202960 TTGCAGGTATACGGCGGC 60.203 61.111 13.24 0.00 43.71 6.53
4803 5590 1.478105 CTCGTCTGTGTCATCATGGGA 59.522 52.381 0.00 0.00 0.00 4.37
4923 5710 1.227674 CTTCGGCTGGTCATAGGCC 60.228 63.158 0.00 0.00 39.88 5.19
4927 5714 1.538666 GGCTGGTCATAGGCCCATT 59.461 57.895 0.00 0.00 39.96 3.16
4959 5746 2.349817 GGACACACGCTTGAGTTTGATG 60.350 50.000 0.00 0.00 0.00 3.07
4965 5752 1.532437 CGCTTGAGTTTGATGCTGTCA 59.468 47.619 0.00 0.00 34.25 3.58
5110 5898 4.228317 GTGTGTTCTCTTCTCTTCGGTAC 58.772 47.826 0.00 0.00 0.00 3.34
5115 5903 4.564782 TCTCTTCTCTTCGGTACTGGTA 57.435 45.455 0.85 0.00 0.00 3.25
5121 5909 9.233649 CTCTTCTCTTCGGTACTGGTATATTAT 57.766 37.037 0.85 0.00 0.00 1.28
5168 5956 5.447573 GCTACATGCTAGAAATAAGCTTGC 58.552 41.667 9.86 2.12 44.62 4.01
5178 5969 6.124088 AGAAATAAGCTTGCGATTAACCTG 57.876 37.500 9.86 0.00 0.00 4.00
5199 6270 6.151817 ACCTGTTTTATCTGGATTTTGCTCTC 59.848 38.462 0.00 0.00 0.00 3.20
5200 6271 6.151648 CCTGTTTTATCTGGATTTTGCTCTCA 59.848 38.462 0.00 0.00 0.00 3.27
5203 6274 6.748333 TTTATCTGGATTTTGCTCTCAGTG 57.252 37.500 0.00 0.00 0.00 3.66
5249 6329 2.016318 AGGTTGTCATGTGTGTGTGTG 58.984 47.619 0.00 0.00 0.00 3.82
5250 6330 1.742831 GGTTGTCATGTGTGTGTGTGT 59.257 47.619 0.00 0.00 0.00 3.72
5251 6331 2.477694 GGTTGTCATGTGTGTGTGTGTG 60.478 50.000 0.00 0.00 0.00 3.82
5252 6332 2.106477 TGTCATGTGTGTGTGTGTGT 57.894 45.000 0.00 0.00 0.00 3.72
5253 6333 1.736681 TGTCATGTGTGTGTGTGTGTG 59.263 47.619 0.00 0.00 0.00 3.82
5254 6334 0.731994 TCATGTGTGTGTGTGTGTGC 59.268 50.000 0.00 0.00 0.00 4.57
5255 6335 0.589479 CATGTGTGTGTGTGTGTGCG 60.589 55.000 0.00 0.00 0.00 5.34
5256 6336 0.742635 ATGTGTGTGTGTGTGTGCGA 60.743 50.000 0.00 0.00 0.00 5.10
5278 6358 5.056894 AGAGAGAGAAAATTGCATTGTGC 57.943 39.130 0.00 0.00 45.29 4.57
5281 6361 3.921677 AGAGAAAATTGCATTGTGCCAG 58.078 40.909 0.00 0.00 44.23 4.85
5398 6481 5.491070 TCATCTACCCATCTCACACTTTTG 58.509 41.667 0.00 0.00 0.00 2.44
5558 6670 3.820467 TGGCAGTGAAAAACATGTCCTAG 59.180 43.478 0.00 0.00 0.00 3.02
5588 6701 6.111382 ACATCTCTTGATACATCTGGTGTTG 58.889 40.000 0.00 0.00 42.29 3.33
5649 6763 5.047802 ACAACTTCCTAATGTTCATTGCAGG 60.048 40.000 8.11 7.84 0.00 4.85
5667 6781 1.179174 GGTTTGGTCAGCCCTTCCAC 61.179 60.000 0.00 0.00 0.00 4.02
5777 6891 1.745653 GAAGTTGTAGAATGGCAGGGC 59.254 52.381 0.00 0.00 0.00 5.19
5859 6974 2.159234 GTCAGAGCAAGCTCACACATTC 59.841 50.000 22.68 3.90 44.99 2.67
5875 6990 4.256920 CACATTCTACAGGGTTCAGAAGG 58.743 47.826 0.00 0.00 36.45 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.452733 GCGCTCCTACCGGTTGCT 62.453 66.667 15.04 0.00 0.00 3.91
1 2 4.452733 AGCGCTCCTACCGGTTGC 62.453 66.667 15.04 11.89 31.77 4.17
7 8 1.392710 TAGAAGGCAGCGCTCCTACC 61.393 60.000 23.11 15.70 32.65 3.18
8 9 0.460311 TTAGAAGGCAGCGCTCCTAC 59.540 55.000 23.11 8.58 32.65 3.18
10 11 0.391793 GTTTAGAAGGCAGCGCTCCT 60.392 55.000 18.96 18.96 34.90 3.69
11 12 0.673644 TGTTTAGAAGGCAGCGCTCC 60.674 55.000 7.13 12.68 0.00 4.70
12 13 1.373570 ATGTTTAGAAGGCAGCGCTC 58.626 50.000 7.13 2.01 0.00 5.03
13 14 1.740025 GAATGTTTAGAAGGCAGCGCT 59.260 47.619 2.64 2.64 0.00 5.92
14 15 1.202188 GGAATGTTTAGAAGGCAGCGC 60.202 52.381 0.00 0.00 0.00 5.92
15 16 2.083774 TGGAATGTTTAGAAGGCAGCG 58.916 47.619 0.00 0.00 0.00 5.18
16 17 2.819608 TGTGGAATGTTTAGAAGGCAGC 59.180 45.455 0.00 0.00 0.00 5.25
17 18 4.701651 TCATGTGGAATGTTTAGAAGGCAG 59.298 41.667 0.00 0.00 0.00 4.85
18 19 4.661222 TCATGTGGAATGTTTAGAAGGCA 58.339 39.130 0.00 0.00 0.00 4.75
19 20 5.126061 ACATCATGTGGAATGTTTAGAAGGC 59.874 40.000 0.00 0.00 0.00 4.35
20 21 6.764308 ACATCATGTGGAATGTTTAGAAGG 57.236 37.500 0.00 0.00 0.00 3.46
23 24 9.460019 TCATTTACATCATGTGGAATGTTTAGA 57.540 29.630 19.86 6.07 36.96 2.10
26 27 8.751242 TCATCATTTACATCATGTGGAATGTTT 58.249 29.630 19.86 11.46 36.96 2.83
27 28 8.296211 TCATCATTTACATCATGTGGAATGTT 57.704 30.769 19.86 13.38 36.96 2.71
28 29 7.776500 TCTCATCATTTACATCATGTGGAATGT 59.224 33.333 19.86 11.70 36.96 2.71
29 30 8.074370 GTCTCATCATTTACATCATGTGGAATG 58.926 37.037 16.78 16.78 36.97 2.67
30 31 7.230108 GGTCTCATCATTTACATCATGTGGAAT 59.770 37.037 0.00 0.00 28.59 3.01
31 32 6.543465 GGTCTCATCATTTACATCATGTGGAA 59.457 38.462 0.00 0.00 0.00 3.53
32 33 6.057533 GGTCTCATCATTTACATCATGTGGA 58.942 40.000 0.00 0.00 0.00 4.02
33 34 5.049886 CGGTCTCATCATTTACATCATGTGG 60.050 44.000 0.00 0.00 0.00 4.17
51 52 4.681978 AGGCGCCACAACGGTCTC 62.682 66.667 31.54 0.00 36.97 3.36
54 55 4.250305 AAGAGGCGCCACAACGGT 62.250 61.111 31.54 5.22 36.97 4.83
56 57 3.726517 CCAAGAGGCGCCACAACG 61.727 66.667 31.54 14.39 0.00 4.10
58 59 2.594303 CACCAAGAGGCGCCACAA 60.594 61.111 31.54 0.00 39.06 3.33
73 74 0.607489 AGGCACTCCAGCAATGACAC 60.607 55.000 0.00 0.00 35.83 3.67
107 108 0.332632 CACCCCCATTGATGTCTGGT 59.667 55.000 0.00 0.00 0.00 4.00
112 113 1.381867 TCTTCCACCCCCATTGATGT 58.618 50.000 0.00 0.00 0.00 3.06
134 135 5.048504 GTCAATTTGAGACAGAATCTTGCCA 60.049 40.000 0.00 0.00 38.00 4.92
139 140 5.250313 AGGGAGTCAATTTGAGACAGAATCT 59.750 40.000 0.00 0.00 41.91 2.40
147 148 1.988107 AGGCAGGGAGTCAATTTGAGA 59.012 47.619 0.00 0.00 0.00 3.27
151 152 1.075601 TCCAGGCAGGGAGTCAATTT 58.924 50.000 0.00 0.00 38.24 1.82
164 165 2.124403 CCATGGTGCTCTCCAGGC 60.124 66.667 2.57 0.00 41.05 4.85
167 168 1.288188 TCATTCCATGGTGCTCTCCA 58.712 50.000 12.58 0.00 42.01 3.86
176 177 0.308684 CGTGCCGATTCATTCCATGG 59.691 55.000 4.97 4.97 0.00 3.66
191 192 1.079336 GACTACCCCTTCACCGTGC 60.079 63.158 0.00 0.00 0.00 5.34
193 194 0.178912 AAGGACTACCCCTTCACCGT 60.179 55.000 0.00 0.00 42.62 4.83
194 195 1.479730 GTAAGGACTACCCCTTCACCG 59.520 57.143 0.00 0.00 44.88 4.94
210 211 1.375523 GGTCACCCGCCTGTGTAAG 60.376 63.158 0.71 0.00 37.51 2.34
303 313 1.565759 TCTTGGCTGGTGCTCCATAAT 59.434 47.619 8.18 0.00 43.43 1.28
316 326 3.728385 ATGTAGGCTCTTTTCTTGGCT 57.272 42.857 0.00 0.00 39.84 4.75
324 334 3.191371 CGGAAGCAAAATGTAGGCTCTTT 59.809 43.478 0.00 0.00 36.76 2.52
325 335 2.749621 CGGAAGCAAAATGTAGGCTCTT 59.250 45.455 0.00 0.00 36.76 2.85
326 336 2.359900 CGGAAGCAAAATGTAGGCTCT 58.640 47.619 0.00 0.00 36.76 4.09
341 351 3.499737 GGTGCGTCCATGCGGAAG 61.500 66.667 0.00 0.00 45.20 3.46
352 362 1.389555 TCGAGACAGATATGGTGCGT 58.610 50.000 0.00 0.00 0.00 5.24
365 375 1.821216 TTCCCTGGCAAATTCGAGAC 58.179 50.000 0.00 0.00 0.00 3.36
380 395 1.139853 AGCTCAGTTCATCGGATTCCC 59.860 52.381 0.00 0.00 0.00 3.97
383 398 2.499289 ACTCAGCTCAGTTCATCGGATT 59.501 45.455 0.00 0.00 0.00 3.01
396 411 2.124693 AGCTCCGCCTACTCAGCTC 61.125 63.158 0.00 0.00 37.72 4.09
400 415 0.684479 ATGTGAGCTCCGCCTACTCA 60.684 55.000 12.15 0.00 38.09 3.41
409 424 0.031449 GCGGAGACTATGTGAGCTCC 59.969 60.000 12.15 3.09 41.47 4.70
415 430 1.443407 CCCCAGCGGAGACTATGTG 59.557 63.158 0.00 0.00 0.00 3.21
416 431 1.762460 CCCCCAGCGGAGACTATGT 60.762 63.158 0.00 0.00 0.00 2.29
418 433 1.457831 GACCCCCAGCGGAGACTAT 60.458 63.158 0.00 0.00 0.00 2.12
419 434 2.043248 GACCCCCAGCGGAGACTA 60.043 66.667 0.00 0.00 0.00 2.59
423 438 2.893682 GATTTGGACCCCCAGCGGAG 62.894 65.000 0.00 0.00 44.60 4.63
429 446 1.151474 TCCTGGATTTGGACCCCCA 60.151 57.895 0.00 0.00 41.64 4.96
445 462 0.755698 TACGCCCAGACTCCATCTCC 60.756 60.000 0.00 0.00 34.41 3.71
458 475 1.736365 GCTCTAGACACCCTACGCCC 61.736 65.000 0.00 0.00 0.00 6.13
462 479 5.637006 CATAGATGCTCTAGACACCCTAC 57.363 47.826 0.00 0.00 31.67 3.18
487 504 6.335471 TGATTCATGAACACAAGAGCAAAT 57.665 33.333 11.07 0.00 0.00 2.32
545 584 6.592870 GCTCCTAACCATCTAACCATAAGTT 58.407 40.000 0.00 0.00 42.83 2.66
550 589 3.039011 ACGCTCCTAACCATCTAACCAT 58.961 45.455 0.00 0.00 0.00 3.55
552 591 2.167900 ACACGCTCCTAACCATCTAACC 59.832 50.000 0.00 0.00 0.00 2.85
556 595 2.180276 AGAACACGCTCCTAACCATCT 58.820 47.619 0.00 0.00 0.00 2.90
557 596 2.674796 AGAACACGCTCCTAACCATC 57.325 50.000 0.00 0.00 0.00 3.51
602 656 4.842574 AGCTGGTTTTGAAACACCAAAAT 58.157 34.783 8.68 1.63 44.63 1.82
644 701 4.229096 TGTTACTTACCTTTGTACGCTCG 58.771 43.478 0.00 0.00 0.00 5.03
651 708 7.095355 CGTTGAGCTATTGTTACTTACCTTTGT 60.095 37.037 0.00 0.00 0.00 2.83
652 709 7.234384 CGTTGAGCTATTGTTACTTACCTTTG 58.766 38.462 0.00 0.00 0.00 2.77
658 715 3.861113 CGCCGTTGAGCTATTGTTACTTA 59.139 43.478 0.00 0.00 0.00 2.24
810 876 1.140852 CCATGTGGCGGGAATAGAAGA 59.859 52.381 0.00 0.00 0.00 2.87
892 960 6.483307 TGCGATCCGAGAGATATTTCAAAATT 59.517 34.615 0.00 0.00 34.42 1.82
893 961 5.991606 TGCGATCCGAGAGATATTTCAAAAT 59.008 36.000 0.00 0.00 34.42 1.82
1150 1219 1.671901 GAGGAGGAGTTGAGGCGGAG 61.672 65.000 0.00 0.00 0.00 4.63
1269 1341 1.089920 CCGCCTTGAACATGAGGAAG 58.910 55.000 0.00 0.00 34.91 3.46
1441 1513 2.430367 GCCTTGAACGGGGTGTCT 59.570 61.111 0.00 0.00 0.00 3.41
1443 1515 4.280019 GGGCCTTGAACGGGGTGT 62.280 66.667 0.84 0.00 0.00 4.16
1445 1517 2.591193 TTTTGGGCCTTGAACGGGGT 62.591 55.000 4.53 0.00 0.00 4.95
1507 1612 1.916697 GCTCGGGAGTTGCTTCAAGC 61.917 60.000 1.04 1.04 42.82 4.01
1540 1645 9.630098 TTACTCTTTGGTACGATACTACTTTTG 57.370 33.333 0.00 0.00 0.00 2.44
1553 1658 6.856426 GTCAACAAGCATTTACTCTTTGGTAC 59.144 38.462 0.00 0.00 0.00 3.34
1586 1692 5.712446 GGGAGGATTTGCTTTTTACTCTTCT 59.288 40.000 0.00 0.00 0.00 2.85
1603 1709 1.564348 AGCCAACATAAACGGGAGGAT 59.436 47.619 0.00 0.00 0.00 3.24
1620 1726 3.126000 CAGATCAAGAACCGAAAAGAGCC 59.874 47.826 0.00 0.00 0.00 4.70
1623 1729 5.820423 TGAAACAGATCAAGAACCGAAAAGA 59.180 36.000 0.00 0.00 0.00 2.52
1626 1732 5.364778 TCTGAAACAGATCAAGAACCGAAA 58.635 37.500 0.00 0.00 35.39 3.46
1640 1746 2.500910 AGAGGGCTCAGATCTGAAACAG 59.499 50.000 25.09 14.92 39.39 3.16
1655 1761 2.686915 CAATCAGATCAAACCAGAGGGC 59.313 50.000 0.00 0.00 37.90 5.19
1697 1805 0.819259 CGCCAATGGGGGTCATACAG 60.819 60.000 8.64 0.00 41.99 2.74
1698 1806 1.225983 CGCCAATGGGGGTCATACA 59.774 57.895 8.64 0.00 41.99 2.29
1699 1807 4.157607 CGCCAATGGGGGTCATAC 57.842 61.111 8.64 0.00 41.99 2.39
1715 1823 3.365265 GCACAAGCCCAAGGTCCG 61.365 66.667 0.00 0.00 33.58 4.79
1716 1824 2.203480 TGCACAAGCCCAAGGTCC 60.203 61.111 0.00 0.00 41.13 4.46
1787 1914 6.940298 TCTCCAAATAGTCTACTTTTGGGTTG 59.060 38.462 22.49 16.98 46.06 3.77
1840 1983 0.854218 TGGTTGGTTGGGGCTTAAGA 59.146 50.000 6.67 0.00 0.00 2.10
1952 2095 0.764890 AAGGCCAGTGAGCACAAGTA 59.235 50.000 5.01 0.00 0.00 2.24
1953 2096 0.820891 CAAGGCCAGTGAGCACAAGT 60.821 55.000 5.01 0.00 0.00 3.16
1954 2097 0.535780 TCAAGGCCAGTGAGCACAAG 60.536 55.000 5.01 0.00 0.00 3.16
1955 2098 0.819259 GTCAAGGCCAGTGAGCACAA 60.819 55.000 5.01 0.00 0.00 3.33
1960 2103 1.528129 GGAAAGTCAAGGCCAGTGAG 58.472 55.000 5.01 0.00 0.00 3.51
2042 2188 1.269206 CCAATCCATTATGTGTGCGGC 60.269 52.381 0.00 0.00 0.00 6.53
2044 2190 2.682352 TCACCAATCCATTATGTGTGCG 59.318 45.455 0.00 0.00 0.00 5.34
2046 2192 4.500205 GCCATCACCAATCCATTATGTGTG 60.500 45.833 0.00 0.00 0.00 3.82
2047 2193 3.638160 GCCATCACCAATCCATTATGTGT 59.362 43.478 0.00 0.00 0.00 3.72
2055 2201 0.617935 TCGAAGCCATCACCAATCCA 59.382 50.000 0.00 0.00 0.00 3.41
2095 2242 0.750249 AAAGGCAAGAAAACCCCACG 59.250 50.000 0.00 0.00 0.00 4.94
2137 2284 7.375106 AGCTATTCTCAAAGAATCACTGTTG 57.625 36.000 5.50 0.00 40.75 3.33
2184 2331 1.570813 TTGATCAGCGAACTATGGCG 58.429 50.000 0.00 0.00 35.13 5.69
2185 2332 3.313526 ACAATTGATCAGCGAACTATGGC 59.686 43.478 13.59 0.00 0.00 4.40
2186 2333 4.318333 CGACAATTGATCAGCGAACTATGG 60.318 45.833 13.59 0.00 0.00 2.74
2188 2335 3.804325 CCGACAATTGATCAGCGAACTAT 59.196 43.478 13.59 0.00 0.00 2.12
2205 2363 0.034756 CCATCACCAAGACACCGACA 59.965 55.000 0.00 0.00 0.00 4.35
2206 2364 0.673644 CCCATCACCAAGACACCGAC 60.674 60.000 0.00 0.00 0.00 4.79
2247 2411 3.449737 CCGACTAATAGAACACCTTCCCA 59.550 47.826 0.00 0.00 0.00 4.37
2248 2412 3.450096 ACCGACTAATAGAACACCTTCCC 59.550 47.826 0.00 0.00 0.00 3.97
2250 2414 5.105837 ACTGACCGACTAATAGAACACCTTC 60.106 44.000 0.00 0.00 0.00 3.46
2277 2441 7.394359 ACAATTAACTGTAAGATGCCAACTGAT 59.606 33.333 0.00 0.00 37.43 2.90
2282 2446 8.200792 ACAAAACAATTAACTGTAAGATGCCAA 58.799 29.630 0.00 0.00 37.43 4.52
2284 2448 7.865385 TCACAAAACAATTAACTGTAAGATGCC 59.135 33.333 0.00 0.00 37.43 4.40
2285 2449 8.795786 TCACAAAACAATTAACTGTAAGATGC 57.204 30.769 0.00 0.00 37.43 3.91
2319 2483 7.592885 AACCATATGATGTAGTACTACCGTT 57.407 36.000 26.41 13.70 35.26 4.44
2326 2490 6.973843 TGTCGGTAACCATATGATGTAGTAC 58.026 40.000 3.65 0.00 0.00 2.73
2327 2491 7.585579 TTGTCGGTAACCATATGATGTAGTA 57.414 36.000 3.65 0.00 0.00 1.82
2328 2492 6.474140 TTGTCGGTAACCATATGATGTAGT 57.526 37.500 3.65 0.00 0.00 2.73
2330 2494 8.422566 TGTTATTGTCGGTAACCATATGATGTA 58.577 33.333 3.65 0.00 32.40 2.29
2331 2495 7.225931 GTGTTATTGTCGGTAACCATATGATGT 59.774 37.037 3.65 0.00 32.40 3.06
2332 2496 7.225734 TGTGTTATTGTCGGTAACCATATGATG 59.774 37.037 3.65 0.00 32.40 3.07
2333 2497 7.276658 TGTGTTATTGTCGGTAACCATATGAT 58.723 34.615 3.65 0.00 32.40 2.45
2334 2498 6.641474 TGTGTTATTGTCGGTAACCATATGA 58.359 36.000 3.65 0.00 32.40 2.15
2335 2499 6.912203 TGTGTTATTGTCGGTAACCATATG 57.088 37.500 0.00 0.00 32.40 1.78
2338 2502 5.941058 TCAATGTGTTATTGTCGGTAACCAT 59.059 36.000 0.00 0.00 32.40 3.55
2389 2923 7.178983 ACCTTGCATTTGATCTTTGGAGAAATA 59.821 33.333 0.00 0.00 35.07 1.40
2573 3230 9.082313 TGCATATCTCACTGAGAATAATGTAGA 57.918 33.333 12.83 4.28 42.27 2.59
2611 3268 8.950210 ACGATGTTGAATTTAGAAGTGATCAAT 58.050 29.630 0.00 0.00 0.00 2.57
2680 3364 4.904241 AGCAAGCTAGTCTTTGAAGTGAT 58.096 39.130 0.00 0.00 31.27 3.06
2700 3384 4.749245 ATGTGCAAACAAGTACTGTAGC 57.251 40.909 0.00 6.10 37.23 3.58
2709 3393 4.984161 CCCAAGTAAGAATGTGCAAACAAG 59.016 41.667 0.00 0.00 0.00 3.16
2710 3394 4.404073 ACCCAAGTAAGAATGTGCAAACAA 59.596 37.500 0.00 0.00 0.00 2.83
2712 3396 4.584327 ACCCAAGTAAGAATGTGCAAAC 57.416 40.909 0.00 0.00 0.00 2.93
2716 3400 5.243060 ACCTAAAACCCAAGTAAGAATGTGC 59.757 40.000 0.00 0.00 0.00 4.57
2717 3401 6.294508 CCACCTAAAACCCAAGTAAGAATGTG 60.295 42.308 0.00 0.00 0.00 3.21
2718 3402 5.773176 CCACCTAAAACCCAAGTAAGAATGT 59.227 40.000 0.00 0.00 0.00 2.71
2719 3403 5.773176 ACCACCTAAAACCCAAGTAAGAATG 59.227 40.000 0.00 0.00 0.00 2.67
2720 3404 5.960704 ACCACCTAAAACCCAAGTAAGAAT 58.039 37.500 0.00 0.00 0.00 2.40
2721 3405 5.391577 ACCACCTAAAACCCAAGTAAGAA 57.608 39.130 0.00 0.00 0.00 2.52
2722 3406 6.707273 ATACCACCTAAAACCCAAGTAAGA 57.293 37.500 0.00 0.00 0.00 2.10
2723 3407 8.733458 GTTTATACCACCTAAAACCCAAGTAAG 58.267 37.037 0.00 0.00 0.00 2.34
2724 3408 8.223330 TGTTTATACCACCTAAAACCCAAGTAA 58.777 33.333 0.00 0.00 32.18 2.24
2725 3409 7.753630 TGTTTATACCACCTAAAACCCAAGTA 58.246 34.615 0.00 0.00 32.18 2.24
2726 3410 6.612741 TGTTTATACCACCTAAAACCCAAGT 58.387 36.000 0.00 0.00 32.18 3.16
2763 3447 8.729805 AAAATCCAAGTAAGAATGTGCAAAAA 57.270 26.923 0.00 0.00 0.00 1.94
2764 3448 9.474920 CTAAAATCCAAGTAAGAATGTGCAAAA 57.525 29.630 0.00 0.00 0.00 2.44
2765 3449 8.087750 CCTAAAATCCAAGTAAGAATGTGCAAA 58.912 33.333 0.00 0.00 0.00 3.68
2766 3450 7.232534 ACCTAAAATCCAAGTAAGAATGTGCAA 59.767 33.333 0.00 0.00 0.00 4.08
2787 3471 9.521841 TCACATAAAAATGTTCATACCACCTAA 57.478 29.630 0.00 0.00 31.37 2.69
2788 3472 8.952278 GTCACATAAAAATGTTCATACCACCTA 58.048 33.333 0.00 0.00 31.37 3.08
2789 3473 7.450014 TGTCACATAAAAATGTTCATACCACCT 59.550 33.333 0.00 0.00 31.37 4.00
2790 3474 7.598278 TGTCACATAAAAATGTTCATACCACC 58.402 34.615 0.00 0.00 31.37 4.61
2791 3475 8.511321 TCTGTCACATAAAAATGTTCATACCAC 58.489 33.333 0.00 0.00 31.37 4.16
2792 3476 8.628630 TCTGTCACATAAAAATGTTCATACCA 57.371 30.769 0.00 0.00 31.37 3.25
2793 3477 9.906660 TTTCTGTCACATAAAAATGTTCATACC 57.093 29.630 0.00 0.00 31.37 2.73
2796 3480 9.985730 ATGTTTCTGTCACATAAAAATGTTCAT 57.014 25.926 0.00 0.00 32.88 2.57
2797 3481 9.462174 GATGTTTCTGTCACATAAAAATGTTCA 57.538 29.630 0.00 0.00 34.89 3.18
2798 3482 9.683069 AGATGTTTCTGTCACATAAAAATGTTC 57.317 29.630 0.00 0.00 34.89 3.18
2854 3538 5.171339 AGCATATGGACCATCATAACTCC 57.829 43.478 11.17 0.00 33.86 3.85
2885 3569 9.875675 CAGTCTGCATAGAAATTAAATAGCTTC 57.124 33.333 0.00 0.00 34.01 3.86
2924 3631 5.063944 ACAGATCAGAATTATGTGTGAACGC 59.936 40.000 0.00 0.00 30.37 4.84
3111 3818 5.048782 GTCAGTTGAATCAATAGCAACACCA 60.049 40.000 0.00 0.00 43.15 4.17
3166 3873 9.031360 GTAACAACATACATACATACAGAGTGG 57.969 37.037 0.00 0.00 0.00 4.00
3170 3877 8.254508 TGCAGTAACAACATACATACATACAGA 58.745 33.333 0.00 0.00 0.00 3.41
3183 3890 4.960938 TCTTCAGACTGCAGTAACAACAT 58.039 39.130 21.73 0.00 0.00 2.71
3224 3932 6.628856 CAGCATCGTACTGCATAATTTACAAC 59.371 38.462 9.50 0.00 44.77 3.32
3240 3948 5.034797 CGAGATAAAACTGACAGCATCGTA 58.965 41.667 1.25 0.00 0.00 3.43
3242 3950 4.105486 TCGAGATAAAACTGACAGCATCG 58.895 43.478 1.25 2.75 0.00 3.84
3243 3951 6.408858 TTTCGAGATAAAACTGACAGCATC 57.591 37.500 1.25 1.00 0.00 3.91
3247 3955 9.959775 GTATTCTTTTCGAGATAAAACTGACAG 57.040 33.333 0.00 0.00 33.49 3.51
3253 3961 9.052080 GCTGTTGTATTCTTTTCGAGATAAAAC 57.948 33.333 0.00 0.00 33.49 2.43
3267 3976 8.798859 ATTCAATAACTGAGCTGTTGTATTCT 57.201 30.769 0.00 0.00 34.81 2.40
3302 4011 3.002656 CAGGGTGCGATCATATCAAACAC 59.997 47.826 0.00 0.00 0.00 3.32
3365 4074 2.023741 GCCATGATTCGTGCTGCG 59.976 61.111 0.00 0.00 43.01 5.18
3461 4170 0.839946 ATGAAGCGATTAGGGCCAGT 59.160 50.000 6.18 0.00 0.00 4.00
3473 4182 3.301906 CGAGTACAAGTGAGAATGAAGCG 59.698 47.826 0.00 0.00 0.00 4.68
3518 4227 9.667107 CCTCCTACAAATGAAACTGTCTAAATA 57.333 33.333 0.00 0.00 0.00 1.40
3522 4231 5.248477 AGCCTCCTACAAATGAAACTGTCTA 59.752 40.000 0.00 0.00 0.00 2.59
3583 4292 8.635765 AAAACCTGATGCAAAGAGTAGAATTA 57.364 30.769 0.00 0.00 0.00 1.40
3584 4293 7.309438 GGAAAACCTGATGCAAAGAGTAGAATT 60.309 37.037 0.00 0.00 0.00 2.17
3585 4294 6.151817 GGAAAACCTGATGCAAAGAGTAGAAT 59.848 38.462 0.00 0.00 0.00 2.40
3586 4295 5.473504 GGAAAACCTGATGCAAAGAGTAGAA 59.526 40.000 0.00 0.00 0.00 2.10
3587 4296 5.003804 GGAAAACCTGATGCAAAGAGTAGA 58.996 41.667 0.00 0.00 0.00 2.59
3588 4297 4.761739 TGGAAAACCTGATGCAAAGAGTAG 59.238 41.667 0.00 0.00 0.00 2.57
3590 4299 3.565307 TGGAAAACCTGATGCAAAGAGT 58.435 40.909 0.00 0.00 0.00 3.24
3592 4301 2.297033 GCTGGAAAACCTGATGCAAAGA 59.703 45.455 0.00 0.00 0.00 2.52
3593 4302 2.611224 GGCTGGAAAACCTGATGCAAAG 60.611 50.000 0.00 0.00 0.00 2.77
3642 4354 3.276021 CACATGCTTGTGCTTTGCA 57.724 47.368 18.52 0.00 46.20 4.08
3777 4490 7.416817 TGAATGCTGTGTTATTTGAATATCGG 58.583 34.615 0.00 0.00 0.00 4.18
4139 4855 5.265191 AGAGGTGTGCTCTGTCTATTTCTA 58.735 41.667 0.00 0.00 0.00 2.10
4186 4904 6.831868 ACTTGTTTTATGTGTTTCCCTAGTGT 59.168 34.615 0.00 0.00 0.00 3.55
4236 5002 3.066342 TCGGTAAGTGCCTATCTCTTTCG 59.934 47.826 0.00 0.00 31.62 3.46
4243 5009 2.202566 GCAACTCGGTAAGTGCCTATC 58.797 52.381 0.00 0.00 38.58 2.08
4244 5010 1.134491 GGCAACTCGGTAAGTGCCTAT 60.134 52.381 6.28 0.00 43.32 2.57
4245 5011 0.248289 GGCAACTCGGTAAGTGCCTA 59.752 55.000 6.28 0.00 43.32 3.93
4246 5012 1.003718 GGCAACTCGGTAAGTGCCT 60.004 57.895 6.28 0.00 43.32 4.75
4263 5033 4.440880 CCTAGTTCTCTGCAGAATTCAGG 58.559 47.826 18.85 15.60 40.88 3.86
4387 5157 1.992233 ATGCGGCACAAATGGTAGCG 61.992 55.000 4.03 0.00 0.00 4.26
4420 5190 2.346766 AGTTGTGGACAGCATCAACA 57.653 45.000 9.04 0.00 39.71 3.33
4606 5391 2.158740 TCCAGAGTAGAGAGATGGACGG 60.159 54.545 0.00 0.00 35.16 4.79
4607 5392 3.201353 TCCAGAGTAGAGAGATGGACG 57.799 52.381 0.00 0.00 35.16 4.79
4609 5394 5.668080 TCTTAGTCCAGAGTAGAGAGATGGA 59.332 44.000 0.00 0.00 37.71 3.41
4610 5395 5.935945 TCTTAGTCCAGAGTAGAGAGATGG 58.064 45.833 0.00 0.00 0.00 3.51
4611 5396 6.826231 TGTTCTTAGTCCAGAGTAGAGAGATG 59.174 42.308 0.00 0.00 0.00 2.90
4612 5397 6.964464 TGTTCTTAGTCCAGAGTAGAGAGAT 58.036 40.000 0.00 0.00 0.00 2.75
4613 5398 6.375830 TGTTCTTAGTCCAGAGTAGAGAGA 57.624 41.667 0.00 0.00 0.00 3.10
4683 5470 1.939934 AGTGTGTTGTTCATGGTCACG 59.060 47.619 0.00 0.00 32.55 4.35
4803 5590 1.048601 TCCGGAAGCTTGTGAAGAGT 58.951 50.000 2.10 0.00 0.00 3.24
4854 5641 1.751924 GTCAGAGGGTACAGCAGGTAG 59.248 57.143 0.00 0.00 31.13 3.18
4923 5710 4.499183 GTGTGTCCAGACTAGAAGAATGG 58.501 47.826 0.00 0.00 0.00 3.16
4927 5714 1.540267 GCGTGTGTCCAGACTAGAAGA 59.460 52.381 0.00 0.00 0.00 2.87
5086 5874 3.053455 CCGAAGAGAAGAGAACACACAC 58.947 50.000 0.00 0.00 0.00 3.82
5110 5898 8.638873 TCCTCCGCATTATGTATAATATACCAG 58.361 37.037 7.85 0.00 32.05 4.00
5115 5903 8.304596 CGGTATCCTCCGCATTATGTATAATAT 58.695 37.037 0.00 0.00 43.96 1.28
5121 5909 3.861276 CGGTATCCTCCGCATTATGTA 57.139 47.619 0.00 0.00 43.96 2.29
5168 5956 9.289303 CAAAATCCAGATAAAACAGGTTAATCG 57.711 33.333 0.00 0.00 0.00 3.34
5178 5969 7.025963 CACTGAGAGCAAAATCCAGATAAAAC 58.974 38.462 0.00 0.00 0.00 2.43
5199 6270 3.624861 GCCACTCCATAATCTTCACACTG 59.375 47.826 0.00 0.00 0.00 3.66
5200 6271 3.264193 TGCCACTCCATAATCTTCACACT 59.736 43.478 0.00 0.00 0.00 3.55
5203 6274 5.841957 AAATGCCACTCCATAATCTTCAC 57.158 39.130 0.00 0.00 0.00 3.18
5249 6329 3.424170 GCAATTTTCTCTCTCTCGCACAC 60.424 47.826 0.00 0.00 0.00 3.82
5250 6330 2.738846 GCAATTTTCTCTCTCTCGCACA 59.261 45.455 0.00 0.00 0.00 4.57
5251 6331 2.738846 TGCAATTTTCTCTCTCTCGCAC 59.261 45.455 0.00 0.00 0.00 5.34
5252 6332 3.044235 TGCAATTTTCTCTCTCTCGCA 57.956 42.857 0.00 0.00 0.00 5.10
5253 6333 4.142730 ACAATGCAATTTTCTCTCTCTCGC 60.143 41.667 0.00 0.00 31.22 5.03
5254 6334 5.322310 CACAATGCAATTTTCTCTCTCTCG 58.678 41.667 0.00 0.00 31.22 4.04
5255 6335 5.094134 GCACAATGCAATTTTCTCTCTCTC 58.906 41.667 0.00 0.00 44.26 3.20
5256 6336 5.056894 GCACAATGCAATTTTCTCTCTCT 57.943 39.130 0.00 0.00 44.26 3.10
5278 6358 1.736126 CTGTGCACATCTAGCAACTGG 59.264 52.381 22.00 0.00 44.64 4.00
5281 6361 2.005451 CTCCTGTGCACATCTAGCAAC 58.995 52.381 22.00 0.00 44.64 4.17
5398 6481 6.017440 TGCCAAATGTAGTAGAAACTCAACAC 60.017 38.462 0.00 0.00 37.15 3.32
5588 6701 4.815269 AGAGACAGATGTGTTCAAGTAGC 58.185 43.478 0.00 0.00 36.88 3.58
5649 6763 0.467290 TGTGGAAGGGCTGACCAAAC 60.467 55.000 0.47 0.00 43.89 2.93
5823 6937 4.991056 TGCTCTGACTGTAACTGATGAAAC 59.009 41.667 0.00 0.00 0.00 2.78
5859 6974 0.984230 TGCCCTTCTGAACCCTGTAG 59.016 55.000 0.00 0.00 0.00 2.74
5875 6990 1.734117 GCAAGTGAAACGCCATGCC 60.734 57.895 0.00 0.00 45.86 4.40


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

AutoCloner maintained by Alex Coulton.