Multiple sequence alignment - TraesCS4D01G118600

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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 TraesCS4D01G118600 chr4D 100.000 7506 0 0 2083 9588 99665021 99657516 0.000000e+00 13862.0
1 TraesCS4D01G118600 chr4D 100.000 1737 0 0 1 1737 99667103 99665367 0.000000e+00 3208.0
2 TraesCS4D01G118600 chr4D 94.340 265 15 0 1473 1737 99665019 99664755 3.220000e-109 407.0
3 TraesCS4D01G118600 chr4D 94.340 265 15 0 2085 2349 99665631 99665367 3.220000e-109 407.0
4 TraesCS4D01G118600 chr4D 100.000 85 0 0 4234 4318 99662786 99662702 3.580000e-34 158.0
5 TraesCS4D01G118600 chr4D 100.000 85 0 0 4318 4402 99662870 99662786 3.580000e-34 158.0
6 TraesCS4D01G118600 chr4D 95.745 94 4 0 4604 4697 252173797 252173704 1.670000e-32 152.0
7 TraesCS4D01G118600 chr4A 95.941 4040 86 25 4318 8338 476748371 476752351 0.000000e+00 6481.0
8 TraesCS4D01G118600 chr4A 95.603 2047 62 8 2083 4110 476746062 476748099 0.000000e+00 3256.0
9 TraesCS4D01G118600 chr4A 92.628 1777 54 34 1 1737 476743798 476745537 0.000000e+00 2484.0
10 TraesCS4D01G118600 chr4A 93.870 832 25 13 8337 9167 476752421 476753227 0.000000e+00 1230.0
11 TraesCS4D01G118600 chr4A 91.354 347 16 2 2083 2415 476745257 476745603 6.780000e-126 462.0
12 TraesCS4D01G118600 chr4A 97.642 212 5 0 4107 4318 476748244 476748455 1.970000e-96 364.0
13 TraesCS4D01G118600 chr4A 87.986 283 17 3 1468 1734 476746059 476746340 1.550000e-82 318.0
14 TraesCS4D01G118600 chr4A 90.404 198 12 3 9191 9387 476753373 476753564 4.440000e-63 254.0
15 TraesCS4D01G118600 chr4A 81.651 218 33 4 2295 2507 476745136 476745351 3.560000e-39 174.0
16 TraesCS4D01G118600 chr4A 91.000 100 9 0 2408 2507 476746057 476746156 1.680000e-27 135.0
17 TraesCS4D01G118600 chr4B 97.728 2509 44 3 4720 7227 142056351 142053855 0.000000e+00 4305.0
18 TraesCS4D01G118600 chr4B 92.644 1645 55 31 129 1737 142060692 142059078 0.000000e+00 2307.0
19 TraesCS4D01G118600 chr4B 96.393 1109 33 4 7231 8338 142048908 142047806 0.000000e+00 1820.0
20 TraesCS4D01G118600 chr4B 95.354 861 23 4 3459 4318 142057941 142057097 0.000000e+00 1352.0
21 TraesCS4D01G118600 chr4B 95.689 835 27 6 8337 9169 142047701 142046874 0.000000e+00 1334.0
22 TraesCS4D01G118600 chr4B 95.480 708 21 6 2562 3263 142058700 142057998 0.000000e+00 1120.0
23 TraesCS4D01G118600 chr4B 92.430 502 21 5 2083 2569 142059357 142058858 0.000000e+00 701.0
24 TraesCS4D01G118600 chr4B 94.089 406 11 8 4318 4720 142057181 142056786 1.070000e-168 604.0
25 TraesCS4D01G118600 chr4B 85.885 418 26 6 9178 9588 142046713 142046322 1.930000e-111 414.0
26 TraesCS4D01G118600 chr4B 81.967 122 8 9 7 127 142062905 142062797 3.690000e-14 91.6
27 TraesCS4D01G118600 chr1D 95.067 446 20 2 729 1174 427313069 427312626 0.000000e+00 701.0
28 TraesCS4D01G118600 chr5D 81.723 766 118 15 4725 5471 231738122 231738884 3.800000e-173 619.0
29 TraesCS4D01G118600 chr5D 78.723 329 57 10 3489 3808 231736911 231737235 3.510000e-49 207.0
30 TraesCS4D01G118600 chr5D 94.845 97 5 0 4602 4698 310705361 310705265 1.670000e-32 152.0
31 TraesCS4D01G118600 chr5D 92.929 99 6 1 4600 4697 452219495 452219397 1.000000e-29 143.0
32 TraesCS4D01G118600 chr5A 81.769 746 113 16 4745 5471 325383112 325382371 3.830000e-168 603.0
33 TraesCS4D01G118600 chr5A 79.027 329 55 12 3489 3808 325384342 325384019 7.540000e-51 213.0
34 TraesCS4D01G118600 chr5B 81.682 737 114 15 4725 5445 273726262 273725531 2.310000e-165 593.0
35 TraesCS4D01G118600 chr5B 79.091 330 53 12 3489 3808 273727463 273727140 7.540000e-51 213.0
36 TraesCS4D01G118600 chr2B 98.824 85 1 0 4614 4698 354879208 354879124 1.670000e-32 152.0
37 TraesCS4D01G118600 chr2B 96.703 91 3 0 4614 4704 483453036 483452946 1.670000e-32 152.0
38 TraesCS4D01G118600 chr2B 94.737 95 2 1 4603 4697 239852604 239852695 2.790000e-30 145.0
39 TraesCS4D01G118600 chr7D 95.604 91 4 0 4614 4704 195626181 195626091 7.760000e-31 147.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G118600 chr4D 99657516 99667103 9587 True 3033.333333 13862 98.113333 1 9588 6 chr4D.!!$R2 9587
1 TraesCS4D01G118600 chr4A 476743798 476753564 9766 False 1515.800000 6481 91.807900 1 9387 10 chr4A.!!$F1 9386
2 TraesCS4D01G118600 chr4B 142053855 142062905 9050 True 1497.228571 4305 92.813143 7 7227 7 chr4B.!!$R2 7220
3 TraesCS4D01G118600 chr4B 142046322 142048908 2586 True 1189.333333 1820 92.655667 7231 9588 3 chr4B.!!$R1 2357
4 TraesCS4D01G118600 chr5D 231736911 231738884 1973 False 413.000000 619 80.223000 3489 5471 2 chr5D.!!$F1 1982
5 TraesCS4D01G118600 chr5A 325382371 325384342 1971 True 408.000000 603 80.398000 3489 5471 2 chr5A.!!$R1 1982
6 TraesCS4D01G118600 chr5B 273725531 273727463 1932 True 403.000000 593 80.386500 3489 5445 2 chr5B.!!$R1 1956

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
295 2401 1.274712 AGGCAAGAGAGAAGACCCAG 58.725 55.000 0.00 0.00 0.00 4.45 F
1632 3776 0.538746 TCCCCGACTTCCCTTTTTGC 60.539 55.000 0.00 0.00 0.00 3.68 F
1685 3843 0.176219 TTTCCTATGGGTGCCGTACG 59.824 55.000 8.69 8.69 0.00 3.67 F
2291 4628 1.379527 CCCGACTTTCCTATTGGTGC 58.620 55.000 0.00 0.00 34.23 5.01 F
3812 6348 0.613260 TATCCACGCTGAGGTTTGCT 59.387 50.000 0.00 0.00 0.00 3.91 F
4332 7318 0.114954 AATGGGGATTGTGCAGTGGT 59.885 50.000 0.00 0.00 0.00 4.16 F
4333 7319 0.612732 ATGGGGATTGTGCAGTGGTG 60.613 55.000 0.00 0.00 0.00 4.17 F
5597 9038 0.179150 GTGAGTAGCACTGCCTCTCG 60.179 60.000 14.36 0.00 44.27 4.04 F
5598 9039 0.322546 TGAGTAGCACTGCCTCTCGA 60.323 55.000 14.36 0.00 33.79 4.04 F
7018 10473 1.391577 TCGATCACCAAATGGCCATG 58.608 50.000 21.63 9.54 39.32 3.66 F
8115 11571 2.818432 AGGTCAGAGCTTCTGCAAAATG 59.182 45.455 0.00 0.00 43.95 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1661 3805 0.463833 GGCACCCATAGGAAAGTCGG 60.464 60.000 0.00 0.0 36.73 4.79 R
2612 5129 1.830477 TGGGCCCAATTAAAGCATGAC 59.170 47.619 26.33 0.0 0.00 3.06 R
3275 5800 1.882623 GAGGACCCTGAAAGTGCAAAG 59.117 52.381 0.00 0.0 0.00 2.77 R
3864 6400 1.867233 CGCAGCAACTTAGAAGTGTGT 59.133 47.619 0.00 0.0 39.66 3.72 R
5412 8850 1.878953 AACCTTTGCTGACACTACGG 58.121 50.000 0.00 0.0 0.00 4.02 R
5598 9039 3.395941 AGAAGTCAACCCACATTCTTCCT 59.604 43.478 0.00 0.0 33.94 3.36 R
5672 9114 4.041815 AGCTGATGGTGAGATGATTATGCT 59.958 41.667 0.00 0.0 0.00 3.79 R
7002 10457 0.618107 TGCCATGGCCATTTGGTGAT 60.618 50.000 33.44 0.0 41.09 3.06 R
7442 10897 1.680338 AACACAAGACAGACAAGCCC 58.320 50.000 0.00 0.0 0.00 5.19 R
8164 11639 0.178903 AGTAAGGGCAGACCACCAGA 60.179 55.000 0.00 0.0 43.89 3.86 R
9213 12953 0.252881 TCACAGCCTCCATCCTCCTT 60.253 55.000 0.00 0.0 0.00 3.36 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
50 52 6.380274 TCCATAGAAAATCTAGAGTCGTTGGT 59.620 38.462 16.22 0.00 31.67 3.67
52 54 5.723672 AGAAAATCTAGAGTCGTTGGTCA 57.276 39.130 0.00 0.00 0.00 4.02
54 56 4.866508 AAATCTAGAGTCGTTGGTCACA 57.133 40.909 0.00 0.00 0.00 3.58
134 2239 6.314896 GGTGGCTATTACTATGATCATGAAGC 59.685 42.308 18.72 15.20 0.00 3.86
295 2401 1.274712 AGGCAAGAGAGAAGACCCAG 58.725 55.000 0.00 0.00 0.00 4.45
328 2434 3.381272 TCCATTAGCATTAGCAGCAAACC 59.619 43.478 0.00 0.00 45.49 3.27
495 2604 2.204401 TTCCCCTTTCCCCCTCCC 60.204 66.667 0.00 0.00 0.00 4.30
496 2605 2.807599 CTTCCCCTTTCCCCCTCCCT 62.808 65.000 0.00 0.00 0.00 4.20
497 2606 2.204464 CCCCTTTCCCCCTCCCTT 60.204 66.667 0.00 0.00 0.00 3.95
511 2627 2.124942 CCTTCTTCCTCCGCTGCC 60.125 66.667 0.00 0.00 0.00 4.85
798 2931 3.917760 CCCAGATCGCGACCCCTC 61.918 72.222 12.93 4.84 0.00 4.30
799 2932 3.917760 CCAGATCGCGACCCCTCC 61.918 72.222 12.93 0.00 0.00 4.30
1368 3509 2.478894 CGCTGTACCCTTGTTAGTTGTG 59.521 50.000 0.00 0.00 0.00 3.33
1372 3513 4.952460 TGTACCCTTGTTAGTTGTGTCTC 58.048 43.478 0.00 0.00 0.00 3.36
1446 3590 2.423892 TCCTCTCAGTTCTTCGGATTCG 59.576 50.000 0.00 0.00 37.82 3.34
1471 3615 6.708054 GTCCTCTAGGTCATGGAAATATTGTG 59.292 42.308 0.00 0.00 36.34 3.33
1525 3669 3.861840 TGCTGCTCAGTTCATACTTACC 58.138 45.455 0.00 0.00 30.26 2.85
1535 3679 4.227300 AGTTCATACTTACCATGCTTCCCA 59.773 41.667 0.00 0.00 0.00 4.37
1567 3711 3.508793 GCTCTACCATAATGCCCTACGTA 59.491 47.826 0.00 0.00 0.00 3.57
1568 3712 4.159879 GCTCTACCATAATGCCCTACGTAT 59.840 45.833 0.00 0.00 0.00 3.06
1623 3767 2.033194 CGCCAAACTCCCCGACTTC 61.033 63.158 0.00 0.00 0.00 3.01
1632 3776 0.538746 TCCCCGACTTCCCTTTTTGC 60.539 55.000 0.00 0.00 0.00 3.68
1643 3787 1.001378 CCCTTTTTGCGTCAAGGACAG 60.001 52.381 8.78 0.00 42.11 3.51
1681 3839 0.810031 CGACTTTCCTATGGGTGCCG 60.810 60.000 0.00 0.00 0.00 5.69
1685 3843 0.176219 TTTCCTATGGGTGCCGTACG 59.824 55.000 8.69 8.69 0.00 3.67
1730 3888 1.961394 TCCGGGTCATGTCTATGTAGC 59.039 52.381 0.00 0.00 35.73 3.58
2132 4469 2.681848 AGTGCTGCTGCTCATTTCATAC 59.318 45.455 17.00 3.17 40.48 2.39
2137 4474 4.260948 GCTGCTGCTCATTTCATACTTACC 60.261 45.833 8.53 0.00 36.03 2.85
2146 4483 6.662755 TCATTTCATACTTACCATGCTTCCT 58.337 36.000 0.00 0.00 0.00 3.36
2176 4513 2.637872 TGGCTCTACCATAATGCCCTAC 59.362 50.000 0.00 0.00 46.36 3.18
2177 4514 2.637872 GGCTCTACCATAATGCCCTACA 59.362 50.000 0.00 0.00 37.81 2.74
2186 4523 6.819284 ACCATAATGCCCTACATGATTTTTG 58.181 36.000 0.00 0.00 39.60 2.44
2206 4543 6.710692 TTTGTATGCTATATCATGCTGTCG 57.289 37.500 6.28 0.00 31.58 4.35
2222 4559 2.963854 CGCTAGTGATGCCGCCAG 60.964 66.667 0.00 0.00 0.00 4.85
2229 4566 3.474570 GATGCCGCCAGACTCCCT 61.475 66.667 0.00 0.00 0.00 4.20
2284 4621 1.626825 CCAAACTCCCCGACTTTCCTA 59.373 52.381 0.00 0.00 0.00 2.94
2286 4623 3.308188 CCAAACTCCCCGACTTTCCTATT 60.308 47.826 0.00 0.00 0.00 1.73
2287 4624 3.629142 AACTCCCCGACTTTCCTATTG 57.371 47.619 0.00 0.00 0.00 1.90
2289 4626 1.838077 CTCCCCGACTTTCCTATTGGT 59.162 52.381 0.00 0.00 34.23 3.67
2291 4628 1.379527 CCCGACTTTCCTATTGGTGC 58.620 55.000 0.00 0.00 34.23 5.01
2573 5090 7.606456 ACCAAACTGATGTACAAGTTGGTATAG 59.394 37.037 20.91 8.71 45.61 1.31
2612 5129 2.093288 TGGTGCTGGAGAGCTAGATTTG 60.093 50.000 0.00 0.00 46.39 2.32
3173 5698 1.724582 GGCACTTCTGGCACGTGTTT 61.725 55.000 18.38 0.00 42.66 2.83
3275 5800 7.331193 CAGTACAACTTCCTATACACCTTGAAC 59.669 40.741 0.00 0.00 0.00 3.18
3405 5931 5.104259 AGTTCTTCAAGAGGTTCACAGTT 57.896 39.130 0.00 0.00 0.00 3.16
3461 5987 6.959606 AGGTATCAACATGGCCTTAGATAT 57.040 37.500 3.32 0.00 0.00 1.63
3670 6206 7.050377 TGAAAACATATCTTCCTGATGGAGAC 58.950 38.462 0.00 0.00 44.24 3.36
3812 6348 0.613260 TATCCACGCTGAGGTTTGCT 59.387 50.000 0.00 0.00 0.00 3.91
3862 6398 9.802039 TTACCAATTAGACCTAATTCACAGTTT 57.198 29.630 11.01 0.00 42.11 2.66
3863 6399 8.336801 ACCAATTAGACCTAATTCACAGTTTC 57.663 34.615 11.01 0.00 42.11 2.78
3864 6400 7.942341 ACCAATTAGACCTAATTCACAGTTTCA 59.058 33.333 11.01 0.00 42.11 2.69
3884 6420 1.867233 ACACACTTCTAAGTTGCTGCG 59.133 47.619 0.00 0.00 37.08 5.18
4081 6617 7.333528 ACACATGTGAATATCCCAATGTTAC 57.666 36.000 31.94 0.00 0.00 2.50
4082 6618 6.321181 ACACATGTGAATATCCCAATGTTACC 59.679 38.462 31.94 0.00 0.00 2.85
4306 7292 5.748152 CGTCCAAATGTTTCAAATGACAAGT 59.252 36.000 0.00 0.00 0.00 3.16
4307 7293 6.074888 CGTCCAAATGTTTCAAATGACAAGTC 60.075 38.462 0.00 0.00 0.00 3.01
4308 7294 6.980397 GTCCAAATGTTTCAAATGACAAGTCT 59.020 34.615 1.53 0.00 0.00 3.24
4309 7295 7.492344 GTCCAAATGTTTCAAATGACAAGTCTT 59.508 33.333 1.53 0.00 0.00 3.01
4310 7296 8.040132 TCCAAATGTTTCAAATGACAAGTCTTT 58.960 29.630 1.53 0.00 0.00 2.52
4311 7297 8.330302 CCAAATGTTTCAAATGACAAGTCTTTC 58.670 33.333 1.53 0.00 0.00 2.62
4312 7298 8.330302 CAAATGTTTCAAATGACAAGTCTTTCC 58.670 33.333 1.53 0.00 0.00 3.13
4313 7299 6.522625 TGTTTCAAATGACAAGTCTTTCCA 57.477 33.333 1.53 0.00 0.00 3.53
4314 7300 6.929625 TGTTTCAAATGACAAGTCTTTCCAA 58.070 32.000 1.53 0.00 0.00 3.53
4315 7301 7.555087 TGTTTCAAATGACAAGTCTTTCCAAT 58.445 30.769 1.53 0.00 0.00 3.16
4316 7302 7.492020 TGTTTCAAATGACAAGTCTTTCCAATG 59.508 33.333 1.53 0.00 0.00 2.82
4317 7303 6.088016 TCAAATGACAAGTCTTTCCAATGG 57.912 37.500 0.00 0.00 0.00 3.16
4318 7304 5.010922 TCAAATGACAAGTCTTTCCAATGGG 59.989 40.000 0.00 0.00 0.00 4.00
4319 7305 2.875296 TGACAAGTCTTTCCAATGGGG 58.125 47.619 0.00 0.00 38.37 4.96
4320 7306 2.445145 TGACAAGTCTTTCCAATGGGGA 59.555 45.455 0.00 0.00 46.61 4.81
4328 7314 3.286404 TCCAATGGGGATTGTGCAG 57.714 52.632 0.00 0.00 42.15 4.41
4329 7315 0.409092 TCCAATGGGGATTGTGCAGT 59.591 50.000 0.00 0.00 42.15 4.40
4330 7316 0.533491 CCAATGGGGATTGTGCAGTG 59.467 55.000 0.00 0.00 40.01 3.66
4331 7317 0.533491 CAATGGGGATTGTGCAGTGG 59.467 55.000 0.00 0.00 0.00 4.00
4332 7318 0.114954 AATGGGGATTGTGCAGTGGT 59.885 50.000 0.00 0.00 0.00 4.16
4333 7319 0.612732 ATGGGGATTGTGCAGTGGTG 60.613 55.000 0.00 0.00 0.00 4.17
4334 7320 1.978617 GGGGATTGTGCAGTGGTGG 60.979 63.158 0.00 0.00 0.00 4.61
4335 7321 1.074775 GGGATTGTGCAGTGGTGGA 59.925 57.895 0.00 0.00 0.00 4.02
4336 7322 1.244019 GGGATTGTGCAGTGGTGGAC 61.244 60.000 0.00 0.00 44.99 4.02
4340 7326 2.956987 GTGCAGTGGTGGACATGC 59.043 61.111 0.00 0.00 44.20 4.06
4341 7327 1.601759 GTGCAGTGGTGGACATGCT 60.602 57.895 0.00 0.00 44.20 3.79
4342 7328 1.601477 TGCAGTGGTGGACATGCTG 60.601 57.895 0.00 0.00 35.78 4.41
4343 7329 1.601759 GCAGTGGTGGACATGCTGT 60.602 57.895 0.00 0.00 33.59 4.40
4344 7330 1.580845 GCAGTGGTGGACATGCTGTC 61.581 60.000 7.52 7.52 46.23 3.51
4357 7343 6.187125 GACATGCTGTCACATAACAATTCT 57.813 37.500 10.30 0.00 46.22 2.40
4358 7344 5.946298 ACATGCTGTCACATAACAATTCTG 58.054 37.500 0.00 0.00 0.00 3.02
4359 7345 5.474532 ACATGCTGTCACATAACAATTCTGT 59.525 36.000 0.00 0.00 37.39 3.41
4360 7346 6.654582 ACATGCTGTCACATAACAATTCTGTA 59.345 34.615 0.00 0.00 33.45 2.74
4361 7347 7.337689 ACATGCTGTCACATAACAATTCTGTAT 59.662 33.333 0.00 0.00 33.45 2.29
4362 7348 7.686438 TGCTGTCACATAACAATTCTGTATT 57.314 32.000 0.00 0.00 33.45 1.89
4363 7349 8.109705 TGCTGTCACATAACAATTCTGTATTT 57.890 30.769 0.00 0.00 33.45 1.40
4364 7350 9.225436 TGCTGTCACATAACAATTCTGTATTTA 57.775 29.630 0.00 0.00 33.45 1.40
4370 7356 9.864034 CACATAACAATTCTGTATTTATCGTCC 57.136 33.333 0.00 0.00 33.45 4.79
4371 7357 9.607988 ACATAACAATTCTGTATTTATCGTCCA 57.392 29.630 0.00 0.00 33.45 4.02
4375 7361 9.787532 AACAATTCTGTATTTATCGTCCAAATG 57.212 29.630 0.00 0.00 33.45 2.32
4376 7362 8.956426 ACAATTCTGTATTTATCGTCCAAATGT 58.044 29.630 0.00 0.00 32.54 2.71
4377 7363 9.787532 CAATTCTGTATTTATCGTCCAAATGTT 57.212 29.630 0.00 0.00 0.00 2.71
4380 7366 8.554835 TCTGTATTTATCGTCCAAATGTTTCA 57.445 30.769 0.00 0.00 0.00 2.69
4381 7367 9.004717 TCTGTATTTATCGTCCAAATGTTTCAA 57.995 29.630 0.00 0.00 0.00 2.69
4382 7368 9.619316 CTGTATTTATCGTCCAAATGTTTCAAA 57.381 29.630 0.00 0.00 0.00 2.69
4386 7372 8.514136 TTTATCGTCCAAATGTTTCAAATGAC 57.486 30.769 0.00 0.00 0.00 3.06
4387 7373 5.506686 TCGTCCAAATGTTTCAAATGACA 57.493 34.783 0.00 0.00 0.00 3.58
4388 7374 5.895928 TCGTCCAAATGTTTCAAATGACAA 58.104 33.333 0.00 0.00 0.00 3.18
4389 7375 5.976534 TCGTCCAAATGTTTCAAATGACAAG 59.023 36.000 0.00 0.00 0.00 3.16
4397 7383 6.522625 TGTTTCAAATGACAAGTCTTTCCA 57.477 33.333 1.53 0.00 0.00 3.53
4658 7646 9.953697 ATAAGAGCGTTTAGATCACTAAAGTAG 57.046 33.333 0.00 0.00 45.42 2.57
4717 7706 4.368565 AGGACTTAGGGTGAAAGGTTTC 57.631 45.455 0.00 0.00 37.69 2.78
4733 8158 2.504367 GTTTCCTTAAGTCAGCCTGCA 58.496 47.619 0.97 0.00 0.00 4.41
5412 8850 3.054878 CAAGCAGAACAACAATCTTGGC 58.945 45.455 0.00 0.00 0.00 4.52
5513 8954 5.300539 TGCCATGCAACTTTAGTCAACTTAA 59.699 36.000 0.00 0.00 34.76 1.85
5597 9038 0.179150 GTGAGTAGCACTGCCTCTCG 60.179 60.000 14.36 0.00 44.27 4.04
5598 9039 0.322546 TGAGTAGCACTGCCTCTCGA 60.323 55.000 14.36 0.00 33.79 4.04
5945 9400 4.320788 GCACAGAAGCAAACTTTCAGCTAT 60.321 41.667 0.00 0.00 37.70 2.97
6109 9564 5.261209 ACTTTTGTGCATTAAGCTGTTGA 57.739 34.783 0.00 0.00 45.94 3.18
6480 9935 3.245052 ACCATGGGTCTCTGAAGGAAAAG 60.245 47.826 18.09 0.00 0.00 2.27
6491 9946 7.013750 GTCTCTGAAGGAAAAGGAACAAAATCT 59.986 37.037 0.00 0.00 0.00 2.40
6692 10147 7.141363 GTCAATCATGATATAAACTTGGCACC 58.859 38.462 9.04 0.00 38.01 5.01
6798 10253 7.500227 CCATCTAAAAACTCAGATAGCAATGGA 59.500 37.037 0.00 0.00 30.32 3.41
6804 10259 2.871022 CTCAGATAGCAATGGAGCACAC 59.129 50.000 0.00 0.00 36.85 3.82
6825 10280 2.859165 TTAAAGAGGCAGGTGGTGAG 57.141 50.000 0.00 0.00 0.00 3.51
6987 10442 2.670934 GCTCCACCACCTGCACAG 60.671 66.667 0.00 0.00 0.00 3.66
7002 10457 4.176271 CTGCACAGTATCAGAACAATCGA 58.824 43.478 0.00 0.00 32.26 3.59
7018 10473 1.391577 TCGATCACCAAATGGCCATG 58.608 50.000 21.63 9.54 39.32 3.66
7353 10808 7.735326 ATTGGAGTTACTGTACCTTCTGTAT 57.265 36.000 0.00 0.00 0.00 2.29
7382 10837 6.884836 AGGCTGAAAAATAACCCTACTACTTG 59.115 38.462 0.00 0.00 0.00 3.16
7442 10897 3.589061 AATGCGCATTTGTGTTGTTTG 57.411 38.095 29.36 0.00 0.00 2.93
7988 11443 9.316730 ACTTTAGTCGTCAAAAGTATTAACACA 57.683 29.630 9.08 0.00 42.57 3.72
8002 11457 7.907389 AGTATTAACACAGTCTCTTTCATGGA 58.093 34.615 0.00 0.00 0.00 3.41
8115 11571 2.818432 AGGTCAGAGCTTCTGCAAAATG 59.182 45.455 0.00 0.00 43.95 2.32
8181 11656 2.561209 TATCTGGTGGTCTGCCCTTA 57.439 50.000 0.00 0.00 0.00 2.69
8197 11672 3.432326 GCCCTTACTCTCCCACATTACTG 60.432 52.174 0.00 0.00 0.00 2.74
8285 11761 7.385205 GCTTCTGTCTTGTCTGTTATGTCTTTA 59.615 37.037 0.00 0.00 0.00 1.85
8286 11762 9.429359 CTTCTGTCTTGTCTGTTATGTCTTTAT 57.571 33.333 0.00 0.00 0.00 1.40
8313 11789 4.226168 GGGATACTCCTAATTAGCATGGCT 59.774 45.833 6.99 0.00 38.57 4.75
8392 11975 3.414759 TCCCCTGTAGGCTTCTGATTA 57.585 47.619 0.00 0.00 0.00 1.75
8393 11976 3.941629 TCCCCTGTAGGCTTCTGATTAT 58.058 45.455 0.00 0.00 0.00 1.28
8394 11977 4.307259 TCCCCTGTAGGCTTCTGATTATT 58.693 43.478 0.00 0.00 0.00 1.40
8395 11978 5.473273 TCCCCTGTAGGCTTCTGATTATTA 58.527 41.667 0.00 0.00 0.00 0.98
8437 12020 4.260985 TCTCTTCTGTCTTGTTTGTTGCA 58.739 39.130 0.00 0.00 0.00 4.08
8443 12026 3.188492 TGTCTTGTTTGTTGCAGCATTG 58.812 40.909 3.36 0.00 0.00 2.82
8447 12030 1.479730 TGTTTGTTGCAGCATTGACCA 59.520 42.857 3.36 0.00 0.00 4.02
8478 12061 0.524414 GCTCAGTTCACATGCATGCA 59.476 50.000 26.53 25.04 0.00 3.96
8515 12098 2.598589 TCACAGTTGGTAATCGCGTAC 58.401 47.619 5.77 1.51 0.00 3.67
8560 12143 5.074929 TGGGCCATATCATCTTAAGGACAAT 59.925 40.000 0.00 0.00 0.00 2.71
8723 12306 4.033009 TCACCATCATGTACATCCTGACT 58.967 43.478 5.07 0.00 0.00 3.41
8861 12445 7.371126 AGAAGAGGAAAAGAAAGAATAAGCG 57.629 36.000 0.00 0.00 0.00 4.68
9044 12628 8.141298 TGATGAAATTGGTAGGTACAGAGTTA 57.859 34.615 0.00 0.00 0.00 2.24
9045 12629 8.598916 TGATGAAATTGGTAGGTACAGAGTTAA 58.401 33.333 0.00 0.00 0.00 2.01
9118 12702 6.212235 AGATAGTCATAGTTGTGCTTCATCG 58.788 40.000 0.00 0.00 0.00 3.84
9124 12708 0.040425 GTTGTGCTTCATCGCCGTTT 60.040 50.000 0.00 0.00 0.00 3.60
9127 12711 2.276680 GCTTCATCGCCGTTTCGC 60.277 61.111 0.00 0.00 0.00 4.70
9169 12754 9.074443 GTTCTTGTGCTTGTATTCTACTACTAC 57.926 37.037 0.00 0.00 0.00 2.73
9170 12755 7.769220 TCTTGTGCTTGTATTCTACTACTACC 58.231 38.462 0.00 0.00 0.00 3.18
9171 12756 6.461110 TGTGCTTGTATTCTACTACTACCC 57.539 41.667 0.00 0.00 0.00 3.69
9174 12759 5.597182 TGCTTGTATTCTACTACTACCCCTG 59.403 44.000 0.00 0.00 0.00 4.45
9189 12929 1.597027 CCTGTTCTTGGACGGCGTT 60.597 57.895 16.19 0.00 0.00 4.84
9213 12953 3.106827 TCCAGTCCATGCTTATCACAGA 58.893 45.455 0.00 0.00 0.00 3.41
9282 13022 2.278596 CCGGTAGTCCACGATGCG 60.279 66.667 0.00 0.00 0.00 4.73
9284 13024 1.153901 CGGTAGTCCACGATGCGTT 60.154 57.895 0.00 0.00 38.32 4.84
9285 13025 0.734942 CGGTAGTCCACGATGCGTTT 60.735 55.000 0.00 0.00 38.32 3.60
9287 13027 0.094730 GTAGTCCACGATGCGTTTGC 59.905 55.000 0.00 0.00 38.32 3.68
9289 13029 0.037697 AGTCCACGATGCGTTTGCTA 60.038 50.000 0.00 0.00 43.34 3.49
9351 13092 0.395311 GTAAGCTTTGGTAGGCCCCC 60.395 60.000 3.20 0.00 0.00 5.40
9356 13097 2.831894 CTTTGGTAGGCCCCCGGAAC 62.832 65.000 0.73 0.00 0.00 3.62
9398 13139 1.630244 ATGTGCTGAAAGTCTCGCGC 61.630 55.000 0.00 0.00 35.30 6.86
9403 13144 1.423395 CTGAAAGTCTCGCGCTTCTT 58.577 50.000 5.56 2.22 0.00 2.52
9410 13151 0.097674 TCTCGCGCTTCTTACCGTAC 59.902 55.000 5.56 0.00 0.00 3.67
9444 13185 4.511454 CAGCTTTAATAGACCAAGCGCATA 59.489 41.667 11.47 0.00 46.30 3.14
9445 13186 5.007626 CAGCTTTAATAGACCAAGCGCATAA 59.992 40.000 11.47 0.00 46.30 1.90
9446 13187 5.237344 AGCTTTAATAGACCAAGCGCATAAG 59.763 40.000 11.47 0.00 46.30 1.73
9447 13188 5.560953 GCTTTAATAGACCAAGCGCATAAGG 60.561 44.000 11.47 8.12 34.01 2.69
9448 13189 3.838244 AATAGACCAAGCGCATAAGGA 57.162 42.857 11.47 0.00 0.00 3.36
9449 13190 3.838244 ATAGACCAAGCGCATAAGGAA 57.162 42.857 11.47 0.00 0.00 3.36
9450 13191 2.029838 AGACCAAGCGCATAAGGAAG 57.970 50.000 11.47 0.00 0.00 3.46
9451 13192 1.555075 AGACCAAGCGCATAAGGAAGA 59.445 47.619 11.47 0.00 0.00 2.87
9452 13193 1.936547 GACCAAGCGCATAAGGAAGAG 59.063 52.381 11.47 0.00 0.00 2.85
9453 13194 1.303309 CCAAGCGCATAAGGAAGAGG 58.697 55.000 11.47 0.00 0.00 3.69
9454 13195 1.134401 CCAAGCGCATAAGGAAGAGGA 60.134 52.381 11.47 0.00 0.00 3.71
9455 13196 2.632377 CAAGCGCATAAGGAAGAGGAA 58.368 47.619 11.47 0.00 0.00 3.36
9456 13197 2.611225 AGCGCATAAGGAAGAGGAAG 57.389 50.000 11.47 0.00 0.00 3.46
9457 13198 1.139853 AGCGCATAAGGAAGAGGAAGG 59.860 52.381 11.47 0.00 0.00 3.46
9458 13199 1.587547 CGCATAAGGAAGAGGAAGGC 58.412 55.000 0.00 0.00 0.00 4.35
9459 13200 1.134401 CGCATAAGGAAGAGGAAGGCA 60.134 52.381 0.00 0.00 0.00 4.75
9460 13201 2.570135 GCATAAGGAAGAGGAAGGCAG 58.430 52.381 0.00 0.00 0.00 4.85
9461 13202 2.570135 CATAAGGAAGAGGAAGGCAGC 58.430 52.381 0.00 0.00 0.00 5.25
9462 13203 1.656587 TAAGGAAGAGGAAGGCAGCA 58.343 50.000 0.00 0.00 0.00 4.41
9463 13204 0.998145 AAGGAAGAGGAAGGCAGCAT 59.002 50.000 0.00 0.00 0.00 3.79
9464 13205 0.255318 AGGAAGAGGAAGGCAGCATG 59.745 55.000 0.00 0.00 40.87 4.06
9465 13206 0.750911 GGAAGAGGAAGGCAGCATGG 60.751 60.000 0.00 0.00 35.86 3.66
9466 13207 0.254178 GAAGAGGAAGGCAGCATGGA 59.746 55.000 0.00 0.00 35.86 3.41
9467 13208 0.924823 AAGAGGAAGGCAGCATGGAT 59.075 50.000 0.00 0.00 35.86 3.41
9468 13209 0.924823 AGAGGAAGGCAGCATGGATT 59.075 50.000 0.00 0.00 35.86 3.01
9469 13210 1.030457 GAGGAAGGCAGCATGGATTG 58.970 55.000 0.00 0.00 35.86 2.67
9513 13254 5.281727 CAAACTGGTAGTGGAAAAAGAAGC 58.718 41.667 0.00 0.00 0.00 3.86
9515 13256 3.181458 ACTGGTAGTGGAAAAAGAAGCGA 60.181 43.478 0.00 0.00 0.00 4.93
9517 13258 3.181458 TGGTAGTGGAAAAAGAAGCGACT 60.181 43.478 0.00 0.00 0.00 4.18
9543 13289 6.569610 GCTGAAAGACCAAACCGAAATCATTA 60.570 38.462 0.00 0.00 34.07 1.90
9556 13303 4.318333 CGAAATCATTATGGAGTGCGTCAG 60.318 45.833 0.00 0.00 29.69 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 52 0.538746 TCCGTACTCTGTGGCTGTGA 60.539 55.000 0.00 0.00 0.00 3.58
52 54 1.251527 CCTCCGTACTCTGTGGCTGT 61.252 60.000 0.00 0.00 0.00 4.40
54 56 1.682684 CCCTCCGTACTCTGTGGCT 60.683 63.158 0.00 0.00 0.00 4.75
134 2239 5.396484 CACCAAAATAGAATGCACTGACAG 58.604 41.667 0.00 0.00 0.00 3.51
495 2604 2.510238 CGGCAGCGGAGGAAGAAG 60.510 66.667 0.00 0.00 0.00 2.85
496 2605 4.760047 GCGGCAGCGGAGGAAGAA 62.760 66.667 3.69 0.00 0.00 2.52
651 2784 1.610886 GGGTCAGGTTTTTCTCCCTCG 60.611 57.143 0.00 0.00 32.89 4.63
1368 3509 3.119316 ACATGATCTGGAGAACGTGAGAC 60.119 47.826 11.81 0.00 37.31 3.36
1372 3513 3.516981 AGACATGATCTGGAGAACGTG 57.483 47.619 0.00 4.95 39.04 4.49
1446 3590 6.708054 CACAATATTTCCATGACCTAGAGGAC 59.292 42.308 1.60 0.00 38.94 3.85
1513 3657 4.523083 TGGGAAGCATGGTAAGTATGAAC 58.477 43.478 0.00 0.00 0.00 3.18
1525 3669 2.675889 GCCAAACAGAATGGGAAGCATG 60.676 50.000 0.00 0.00 43.62 4.06
1623 3767 1.001378 CTGTCCTTGACGCAAAAAGGG 60.001 52.381 8.09 0.00 42.77 3.95
1632 3776 2.358737 GCACCCCTGTCCTTGACG 60.359 66.667 0.00 0.00 34.95 4.35
1661 3805 0.463833 GGCACCCATAGGAAAGTCGG 60.464 60.000 0.00 0.00 36.73 4.79
1681 3839 5.967674 ACGTCACATATAACTACAAGCGTAC 59.032 40.000 0.00 0.00 0.00 3.67
1685 3843 7.416022 AGACTACGTCACATATAACTACAAGC 58.584 38.462 0.00 0.00 34.60 4.01
2132 4469 3.679389 ACAGAACAGGAAGCATGGTAAG 58.321 45.455 0.00 0.00 0.00 2.34
2137 4474 2.608752 GCCAAACAGAACAGGAAGCATG 60.609 50.000 0.00 0.00 0.00 4.06
2186 4523 4.768659 GCGACAGCATGATATAGCATAC 57.231 45.455 2.57 0.00 44.35 2.39
2203 4540 2.962253 GGCGGCATCACTAGCGAC 60.962 66.667 3.07 0.00 0.00 5.19
2206 4543 1.884926 GTCTGGCGGCATCACTAGC 60.885 63.158 13.85 0.00 0.00 3.42
2222 4559 3.004839 GCAAAAAGGAAAGTCAGGGAGTC 59.995 47.826 0.00 0.00 0.00 3.36
2229 4566 3.181491 CCTTGACGCAAAAAGGAAAGTCA 60.181 43.478 2.81 0.00 44.93 3.41
2291 4628 6.087687 CGTCACATATAACTACAAGCGTATGG 59.912 42.308 0.00 0.00 0.00 2.74
2324 4676 5.458595 AGACATCTACATAGACATGACCCA 58.541 41.667 0.00 0.00 34.72 4.51
2573 5090 3.005684 CACCATGAGAGCAGGATCTCTAC 59.994 52.174 14.81 0.00 45.03 2.59
2612 5129 1.830477 TGGGCCCAATTAAAGCATGAC 59.170 47.619 26.33 0.00 0.00 3.06
2655 5172 6.402118 GCAACGTGAGAAACTAGAATGCATAA 60.402 38.462 0.00 0.00 0.00 1.90
2656 5173 5.063438 GCAACGTGAGAAACTAGAATGCATA 59.937 40.000 0.00 0.00 0.00 3.14
2788 5305 9.110617 CGGTCACTAATTTACATACGTATACAG 57.889 37.037 7.96 0.00 0.00 2.74
3275 5800 1.882623 GAGGACCCTGAAAGTGCAAAG 59.117 52.381 0.00 0.00 0.00 2.77
3436 5962 5.808366 TCTAAGGCCATGTTGATACCTAG 57.192 43.478 5.01 0.00 0.00 3.02
3461 5987 8.992349 TGAAGAAATCTGAGATTCCAGGTTATA 58.008 33.333 8.32 0.00 36.55 0.98
3670 6206 2.485426 ACCAAATGCAGTCAAGTCGATG 59.515 45.455 0.00 0.00 0.00 3.84
3858 6394 5.065218 CAGCAACTTAGAAGTGTGTGAAACT 59.935 40.000 0.00 0.00 39.66 2.66
3859 6395 5.266242 CAGCAACTTAGAAGTGTGTGAAAC 58.734 41.667 0.00 0.00 39.66 2.78
3860 6396 4.201910 GCAGCAACTTAGAAGTGTGTGAAA 60.202 41.667 0.00 0.00 39.66 2.69
3862 6398 2.872245 GCAGCAACTTAGAAGTGTGTGA 59.128 45.455 0.00 0.00 39.66 3.58
3863 6399 2.348872 CGCAGCAACTTAGAAGTGTGTG 60.349 50.000 0.00 0.00 39.66 3.82
3864 6400 1.867233 CGCAGCAACTTAGAAGTGTGT 59.133 47.619 0.00 0.00 39.66 3.72
3884 6420 3.393089 AAGCATATGTCGGGAGTCATC 57.607 47.619 4.29 0.00 39.30 2.92
4311 7297 0.533491 CACTGCACAATCCCCATTGG 59.467 55.000 0.00 0.00 43.47 3.16
4312 7298 0.533491 CCACTGCACAATCCCCATTG 59.467 55.000 0.00 0.00 44.57 2.82
4313 7299 0.114954 ACCACTGCACAATCCCCATT 59.885 50.000 0.00 0.00 0.00 3.16
4314 7300 0.612732 CACCACTGCACAATCCCCAT 60.613 55.000 0.00 0.00 0.00 4.00
4315 7301 1.228521 CACCACTGCACAATCCCCA 60.229 57.895 0.00 0.00 0.00 4.96
4316 7302 1.978617 CCACCACTGCACAATCCCC 60.979 63.158 0.00 0.00 0.00 4.81
4317 7303 1.074775 TCCACCACTGCACAATCCC 59.925 57.895 0.00 0.00 0.00 3.85
4318 7304 0.537143 TGTCCACCACTGCACAATCC 60.537 55.000 0.00 0.00 0.00 3.01
4319 7305 1.200716 CATGTCCACCACTGCACAATC 59.799 52.381 0.00 0.00 0.00 2.67
4320 7306 1.250328 CATGTCCACCACTGCACAAT 58.750 50.000 0.00 0.00 0.00 2.71
4321 7307 1.454572 GCATGTCCACCACTGCACAA 61.455 55.000 0.00 0.00 34.77 3.33
4322 7308 1.898094 GCATGTCCACCACTGCACA 60.898 57.895 0.00 0.00 34.77 4.57
4323 7309 1.601759 AGCATGTCCACCACTGCAC 60.602 57.895 0.00 0.00 37.09 4.57
4324 7310 1.601477 CAGCATGTCCACCACTGCA 60.601 57.895 0.00 0.00 37.09 4.41
4325 7311 3.271014 CAGCATGTCCACCACTGC 58.729 61.111 0.00 0.00 34.85 4.40
4335 7321 5.474532 ACAGAATTGTTATGTGACAGCATGT 59.525 36.000 0.00 0.00 44.96 3.21
4336 7322 5.946298 ACAGAATTGTTATGTGACAGCATG 58.054 37.500 0.00 0.00 36.34 4.06
4337 7323 7.870509 ATACAGAATTGTTATGTGACAGCAT 57.129 32.000 0.00 0.00 38.76 3.79
4338 7324 7.686438 AATACAGAATTGTTATGTGACAGCA 57.314 32.000 0.00 0.00 38.76 4.41
4344 7330 9.864034 GGACGATAAATACAGAATTGTTATGTG 57.136 33.333 0.00 0.00 38.76 3.21
4345 7331 9.607988 TGGACGATAAATACAGAATTGTTATGT 57.392 29.630 0.00 0.00 38.76 2.29
4349 7335 9.787532 CATTTGGACGATAAATACAGAATTGTT 57.212 29.630 0.00 0.00 38.76 2.83
4350 7336 8.956426 ACATTTGGACGATAAATACAGAATTGT 58.044 29.630 0.00 0.00 41.39 2.71
4351 7337 9.787532 AACATTTGGACGATAAATACAGAATTG 57.212 29.630 0.00 0.00 0.00 2.32
4354 7340 9.004717 TGAAACATTTGGACGATAAATACAGAA 57.995 29.630 0.00 0.00 0.00 3.02
4355 7341 8.554835 TGAAACATTTGGACGATAAATACAGA 57.445 30.769 0.00 0.00 0.00 3.41
4356 7342 9.619316 TTTGAAACATTTGGACGATAAATACAG 57.381 29.630 0.00 0.00 0.00 2.74
4360 7346 9.139174 GTCATTTGAAACATTTGGACGATAAAT 57.861 29.630 0.00 0.00 0.00 1.40
4361 7347 8.138074 TGTCATTTGAAACATTTGGACGATAAA 58.862 29.630 0.00 0.00 0.00 1.40
4362 7348 7.652727 TGTCATTTGAAACATTTGGACGATAA 58.347 30.769 0.00 0.00 0.00 1.75
4363 7349 7.208225 TGTCATTTGAAACATTTGGACGATA 57.792 32.000 0.00 0.00 0.00 2.92
4364 7350 6.083098 TGTCATTTGAAACATTTGGACGAT 57.917 33.333 0.00 0.00 0.00 3.73
4365 7351 5.506686 TGTCATTTGAAACATTTGGACGA 57.493 34.783 0.00 0.00 0.00 4.20
4366 7352 5.748152 ACTTGTCATTTGAAACATTTGGACG 59.252 36.000 0.00 0.00 0.00 4.79
4367 7353 6.980397 AGACTTGTCATTTGAAACATTTGGAC 59.020 34.615 3.49 0.00 0.00 4.02
4368 7354 7.111247 AGACTTGTCATTTGAAACATTTGGA 57.889 32.000 3.49 0.00 0.00 3.53
4369 7355 7.775397 AAGACTTGTCATTTGAAACATTTGG 57.225 32.000 3.49 0.00 0.00 3.28
4370 7356 8.330302 GGAAAGACTTGTCATTTGAAACATTTG 58.670 33.333 3.49 0.00 0.00 2.32
4371 7357 8.040132 TGGAAAGACTTGTCATTTGAAACATTT 58.960 29.630 3.49 0.00 0.00 2.32
4372 7358 7.555087 TGGAAAGACTTGTCATTTGAAACATT 58.445 30.769 3.49 0.00 0.00 2.71
4373 7359 7.111247 TGGAAAGACTTGTCATTTGAAACAT 57.889 32.000 3.49 0.00 0.00 2.71
4374 7360 6.522625 TGGAAAGACTTGTCATTTGAAACA 57.477 33.333 3.49 0.00 0.00 2.83
4375 7361 7.042523 CCATTGGAAAGACTTGTCATTTGAAAC 60.043 37.037 0.00 0.00 0.00 2.78
4376 7362 6.985645 CCATTGGAAAGACTTGTCATTTGAAA 59.014 34.615 0.00 0.00 0.00 2.69
4377 7363 6.514947 CCATTGGAAAGACTTGTCATTTGAA 58.485 36.000 0.00 0.00 0.00 2.69
4378 7364 5.509501 GCCATTGGAAAGACTTGTCATTTGA 60.510 40.000 6.95 0.00 0.00 2.69
4379 7365 4.687483 GCCATTGGAAAGACTTGTCATTTG 59.313 41.667 6.95 0.00 0.00 2.32
4380 7366 4.344679 TGCCATTGGAAAGACTTGTCATTT 59.655 37.500 6.95 1.67 0.00 2.32
4381 7367 3.896888 TGCCATTGGAAAGACTTGTCATT 59.103 39.130 6.95 0.00 0.00 2.57
4382 7368 3.499338 TGCCATTGGAAAGACTTGTCAT 58.501 40.909 6.95 0.00 0.00 3.06
4383 7369 2.886523 CTGCCATTGGAAAGACTTGTCA 59.113 45.455 6.95 0.00 0.00 3.58
4384 7370 2.229784 CCTGCCATTGGAAAGACTTGTC 59.770 50.000 6.95 0.00 0.00 3.18
4385 7371 2.242043 CCTGCCATTGGAAAGACTTGT 58.758 47.619 6.95 0.00 0.00 3.16
4386 7372 2.029649 CACCTGCCATTGGAAAGACTTG 60.030 50.000 6.95 0.00 0.00 3.16
4387 7373 2.158475 TCACCTGCCATTGGAAAGACTT 60.158 45.455 6.95 0.00 0.00 3.01
4388 7374 1.425066 TCACCTGCCATTGGAAAGACT 59.575 47.619 6.95 0.00 0.00 3.24
4389 7375 1.909700 TCACCTGCCATTGGAAAGAC 58.090 50.000 6.95 0.00 0.00 3.01
4397 7383 0.610232 GACCAGCTTCACCTGCCATT 60.610 55.000 0.00 0.00 0.00 3.16
4596 7584 3.691609 GGGAGTGCCACATAAGAAAAGAG 59.308 47.826 0.00 0.00 35.15 2.85
4597 7585 3.330701 AGGGAGTGCCACATAAGAAAAGA 59.669 43.478 2.50 0.00 35.15 2.52
4599 7587 3.330701 AGAGGGAGTGCCACATAAGAAAA 59.669 43.478 2.50 0.00 35.15 2.29
4717 7706 2.119801 ATGTGCAGGCTGACTTAAGG 57.880 50.000 20.86 0.00 0.00 2.69
4733 8158 5.105023 TGGTTATAAACATGCATGCCAATGT 60.105 36.000 26.53 16.18 36.08 2.71
5391 8829 3.054878 GCCAAGATTGTTGTTCTGCTTG 58.945 45.455 0.00 0.00 34.18 4.01
5412 8850 1.878953 AACCTTTGCTGACACTACGG 58.121 50.000 0.00 0.00 0.00 4.02
5597 9038 3.425162 AGTCAACCCACATTCTTCCTC 57.575 47.619 0.00 0.00 0.00 3.71
5598 9039 3.395941 AGAAGTCAACCCACATTCTTCCT 59.604 43.478 0.00 0.00 33.94 3.36
5672 9114 4.041815 AGCTGATGGTGAGATGATTATGCT 59.958 41.667 0.00 0.00 0.00 3.79
6109 9564 5.870978 GCATCTTGGACAATAAACAGCAAAT 59.129 36.000 0.00 0.00 0.00 2.32
6480 9935 6.024552 TGCTCAACCATAAGATTTTGTTCC 57.975 37.500 0.00 0.00 0.00 3.62
6491 9946 3.464720 TTTCCCCATGCTCAACCATAA 57.535 42.857 0.00 0.00 0.00 1.90
6692 10147 2.696707 CCTTTTGATGTCATCCCATGGG 59.303 50.000 26.30 26.30 0.00 4.00
6798 10253 2.224867 ACCTGCCTCTTTAATGTGTGCT 60.225 45.455 0.00 0.00 0.00 4.40
6804 10259 3.012518 CTCACCACCTGCCTCTTTAATG 58.987 50.000 0.00 0.00 0.00 1.90
6825 10280 1.838112 TGTCATTGATTGCACCTCCC 58.162 50.000 0.00 0.00 0.00 4.30
6987 10442 6.662414 TTTGGTGATCGATTGTTCTGATAC 57.338 37.500 0.00 0.00 0.00 2.24
7002 10457 0.618107 TGCCATGGCCATTTGGTGAT 60.618 50.000 33.44 0.00 41.09 3.06
7353 10808 7.208064 AGTAGGGTTATTTTTCAGCCTCATA 57.792 36.000 0.00 0.00 41.31 2.15
7442 10897 1.680338 AACACAAGACAGACAAGCCC 58.320 50.000 0.00 0.00 0.00 5.19
7750 11205 5.036737 GGTGAATAAAACCATTGCGATGAG 58.963 41.667 15.98 8.05 37.65 2.90
7988 11443 1.283321 GGCCCTTCCATGAAAGAGACT 59.717 52.381 0.00 0.00 34.01 3.24
8002 11457 1.771255 CTATCAGCTAGGTTGGCCCTT 59.229 52.381 0.00 0.00 42.73 3.95
8010 11465 9.320295 ATCTAAAGATAAAGCTATCAGCTAGGT 57.680 33.333 0.24 0.00 41.25 3.08
8152 11627 6.043411 GCAGACCACCAGATAAAGTAAGTAG 58.957 44.000 0.00 0.00 0.00 2.57
8153 11628 5.105064 GGCAGACCACCAGATAAAGTAAGTA 60.105 44.000 0.00 0.00 35.26 2.24
8154 11629 4.323562 GGCAGACCACCAGATAAAGTAAGT 60.324 45.833 0.00 0.00 35.26 2.24
8155 11630 4.192317 GGCAGACCACCAGATAAAGTAAG 58.808 47.826 0.00 0.00 35.26 2.34
8156 11631 3.054655 GGGCAGACCACCAGATAAAGTAA 60.055 47.826 0.00 0.00 39.85 2.24
8157 11632 2.504175 GGGCAGACCACCAGATAAAGTA 59.496 50.000 0.00 0.00 39.85 2.24
8158 11633 1.282157 GGGCAGACCACCAGATAAAGT 59.718 52.381 0.00 0.00 39.85 2.66
8159 11634 1.561542 AGGGCAGACCACCAGATAAAG 59.438 52.381 0.00 0.00 43.89 1.85
8160 11635 1.668826 AGGGCAGACCACCAGATAAA 58.331 50.000 0.00 0.00 43.89 1.40
8161 11636 1.668826 AAGGGCAGACCACCAGATAA 58.331 50.000 0.00 0.00 43.89 1.75
8162 11637 2.116238 GTAAGGGCAGACCACCAGATA 58.884 52.381 0.00 0.00 43.89 1.98
8163 11638 0.912486 GTAAGGGCAGACCACCAGAT 59.088 55.000 0.00 0.00 43.89 2.90
8164 11639 0.178903 AGTAAGGGCAGACCACCAGA 60.179 55.000 0.00 0.00 43.89 3.86
8165 11640 0.250513 GAGTAAGGGCAGACCACCAG 59.749 60.000 0.00 0.00 43.89 4.00
8166 11641 0.178903 AGAGTAAGGGCAGACCACCA 60.179 55.000 0.00 0.00 43.89 4.17
8167 11642 0.537653 GAGAGTAAGGGCAGACCACC 59.462 60.000 0.00 0.00 43.89 4.61
8168 11643 0.537653 GGAGAGTAAGGGCAGACCAC 59.462 60.000 0.00 0.00 43.89 4.16
8169 11644 0.617820 GGGAGAGTAAGGGCAGACCA 60.618 60.000 0.00 0.00 43.89 4.02
8170 11645 0.617820 TGGGAGAGTAAGGGCAGACC 60.618 60.000 0.00 0.00 40.67 3.85
8181 11656 4.104102 TGGTTTTCAGTAATGTGGGAGAGT 59.896 41.667 0.00 0.00 0.00 3.24
8197 11672 2.231716 AATAGGGGGCACTGGTTTTC 57.768 50.000 0.00 0.00 0.00 2.29
8313 11789 1.707106 TAAGAGTGTGGACGGGTTCA 58.293 50.000 0.00 0.00 0.00 3.18
8437 12020 5.653769 AGCATACAAGTTAATGGTCAATGCT 59.346 36.000 0.00 0.00 35.90 3.79
8443 12026 6.371548 TGAACTGAGCATACAAGTTAATGGTC 59.628 38.462 16.84 16.84 46.07 4.02
8447 12030 7.627088 GCATGTGAACTGAGCATACAAGTTAAT 60.627 37.037 0.00 0.00 0.00 1.40
8500 12083 3.500982 TGTACAGTACGCGATTACCAAC 58.499 45.455 15.93 5.13 0.00 3.77
8515 12098 4.487948 CACCATTCCTGCAAATTGTACAG 58.512 43.478 0.00 0.00 0.00 2.74
8861 12445 2.351111 GCACAGACAGAGATTAAGCTGC 59.649 50.000 0.00 0.00 35.57 5.25
9127 12711 0.395724 GAACAGGGGTAGCCATTGGG 60.396 60.000 14.06 0.00 37.18 4.12
9169 12754 2.359975 GCCGTCCAAGAACAGGGG 60.360 66.667 0.00 0.00 0.00 4.79
9170 12755 2.742372 CGCCGTCCAAGAACAGGG 60.742 66.667 0.00 0.00 0.00 4.45
9171 12756 1.597027 AACGCCGTCCAAGAACAGG 60.597 57.895 0.00 0.00 0.00 4.00
9174 12759 1.838568 GACCAACGCCGTCCAAGAAC 61.839 60.000 0.00 0.00 0.00 3.01
9189 12929 2.092968 GTGATAAGCATGGACTGGACCA 60.093 50.000 0.00 0.00 44.41 4.02
9213 12953 0.252881 TCACAGCCTCCATCCTCCTT 60.253 55.000 0.00 0.00 0.00 3.36
9351 13092 2.754472 TCATATCTGAATGGCGTTCCG 58.246 47.619 16.44 10.52 35.91 4.30
9388 13129 0.456312 CGGTAAGAAGCGCGAGACTT 60.456 55.000 12.10 13.51 40.09 3.01
9398 13139 1.734707 CGCCTGGTGTACGGTAAGAAG 60.735 57.143 0.00 0.00 0.00 2.85
9410 13151 3.918253 TAAAGCTGGCCGCCTGGTG 62.918 63.158 20.24 0.00 40.39 4.17
9427 13168 4.948341 TCCTTATGCGCTTGGTCTATTA 57.052 40.909 9.73 0.00 0.00 0.98
9444 13185 0.998145 ATGCTGCCTTCCTCTTCCTT 59.002 50.000 0.00 0.00 0.00 3.36
9445 13186 0.255318 CATGCTGCCTTCCTCTTCCT 59.745 55.000 0.00 0.00 0.00 3.36
9446 13187 0.750911 CCATGCTGCCTTCCTCTTCC 60.751 60.000 0.00 0.00 0.00 3.46
9447 13188 0.254178 TCCATGCTGCCTTCCTCTTC 59.746 55.000 0.00 0.00 0.00 2.87
9448 13189 0.924823 ATCCATGCTGCCTTCCTCTT 59.075 50.000 0.00 0.00 0.00 2.85
9449 13190 0.924823 AATCCATGCTGCCTTCCTCT 59.075 50.000 0.00 0.00 0.00 3.69
9450 13191 1.030457 CAATCCATGCTGCCTTCCTC 58.970 55.000 0.00 0.00 0.00 3.71
9451 13192 3.202548 CAATCCATGCTGCCTTCCT 57.797 52.632 0.00 0.00 0.00 3.36
9461 13202 5.327616 TGGTCAGTAAAATGCAATCCATG 57.672 39.130 0.00 0.00 33.49 3.66
9462 13203 5.999205 TTGGTCAGTAAAATGCAATCCAT 57.001 34.783 0.00 0.00 35.06 3.41
9463 13204 5.479724 TGATTGGTCAGTAAAATGCAATCCA 59.520 36.000 0.00 0.00 32.84 3.41
9464 13205 5.964758 TGATTGGTCAGTAAAATGCAATCC 58.035 37.500 0.00 0.00 32.84 3.01
9513 13254 1.264288 GGTTTGGTCTTTCAGCAGTCG 59.736 52.381 0.00 0.00 32.85 4.18
9515 13256 1.134220 TCGGTTTGGTCTTTCAGCAGT 60.134 47.619 0.00 0.00 32.85 4.40
9517 13258 2.045561 TTCGGTTTGGTCTTTCAGCA 57.954 45.000 0.00 0.00 0.00 4.41
9556 13303 1.154580 GACTCTTTGCAAGACGCGC 60.155 57.895 5.73 0.00 46.97 6.86


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

AutoCloner maintained by Alex Coulton.