Multiple sequence alignment - TraesCS4D01G093200

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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 TraesCS4D01G093200 chr4D 100.000 6300 0 0 1 6300 68659015 68665314 0.000000e+00 11635.0
1 TraesCS4D01G093200 chr4B 95.449 4373 130 30 389 4707 101263024 101267381 0.000000e+00 6909.0
2 TraesCS4D01G093200 chr4B 90.846 721 41 6 5188 5888 101268129 101268844 0.000000e+00 942.0
3 TraesCS4D01G093200 chr4B 97.835 231 2 1 4965 5192 101267861 101268091 4.580000e-106 396.0
4 TraesCS4D01G093200 chr4B 85.612 278 39 1 1 278 101262685 101262961 2.220000e-74 291.0
5 TraesCS4D01G093200 chr4B 96.914 162 4 1 4806 4966 483266379 483266540 2.890000e-68 270.0
6 TraesCS4D01G093200 chr4A 94.598 2462 81 17 1556 3993 519571344 519573777 0.000000e+00 3762.0
7 TraesCS4D01G093200 chr4A 92.378 879 50 4 683 1548 519570318 519571192 0.000000e+00 1236.0
8 TraesCS4D01G093200 chr4A 90.063 634 51 6 5188 5819 519574868 519575491 0.000000e+00 811.0
9 TraesCS4D01G093200 chr4A 93.970 398 20 3 5889 6284 558076177 558075782 3.250000e-167 599.0
10 TraesCS4D01G093200 chr4A 95.806 310 12 1 4498 4807 519574296 519574604 3.390000e-137 499.0
11 TraesCS4D01G093200 chr4A 86.173 405 51 2 1 404 519569236 519569636 3.490000e-117 433.0
12 TraesCS4D01G093200 chr4A 96.507 229 8 0 4964 5192 519574602 519574830 4.610000e-101 379.0
13 TraesCS4D01G093200 chr4A 88.715 319 14 7 4065 4380 519573958 519574257 2.770000e-98 370.0
14 TraesCS4D01G093200 chr4A 94.186 172 9 1 4806 4976 742467438 742467267 1.740000e-65 261.0
15 TraesCS4D01G093200 chr4A 98.425 127 2 0 6174 6300 558075797 558075671 2.290000e-54 224.0
16 TraesCS4D01G093200 chr4A 92.667 150 11 0 401 550 519570166 519570315 3.820000e-52 217.0
17 TraesCS4D01G093200 chr4A 90.741 108 10 0 5780 5887 519576697 519576804 1.830000e-30 145.0
18 TraesCS4D01G093200 chr4A 97.500 40 1 0 4402 4441 519574261 519574300 1.130000e-07 69.4
19 TraesCS4D01G093200 chr5D 95.377 411 15 4 5889 6298 45025017 45025424 0.000000e+00 651.0
20 TraesCS4D01G093200 chr5D 95.157 413 17 3 5889 6300 7641932 7642342 0.000000e+00 649.0
21 TraesCS4D01G093200 chr1D 94.915 413 18 2 5889 6300 401354144 401354554 1.480000e-180 643.0
22 TraesCS4D01G093200 chr7D 94.189 413 21 2 5889 6300 568468580 568468990 1.490000e-175 627.0
23 TraesCS4D01G093200 chr6D 93.947 413 20 2 5889 6300 121798140 121797732 2.490000e-173 619.0
24 TraesCS4D01G093200 chr6D 96.386 166 5 1 4804 4968 422936567 422936402 8.050000e-69 272.0
25 TraesCS4D01G093200 chr2D 95.763 354 9 4 5948 6300 644350352 644350700 3.300000e-157 566.0
26 TraesCS4D01G093200 chr2D 96.914 162 4 1 4806 4966 305515030 305514869 2.890000e-68 270.0
27 TraesCS4D01G093200 chr2D 97.222 36 1 0 5888 5923 644350310 644350345 1.900000e-05 62.1
28 TraesCS4D01G093200 chr5A 94.382 356 17 3 5947 6300 658507671 658507317 1.540000e-150 544.0
29 TraesCS4D01G093200 chr5A 97.297 37 1 0 5887 5923 658507714 658507678 5.270000e-06 63.9
30 TraesCS4D01G093200 chr6A 90.799 413 23 3 5889 6300 160471840 160472238 7.190000e-149 538.0
31 TraesCS4D01G093200 chr3D 96.970 165 4 1 4806 4969 410670224 410670060 6.220000e-70 276.0
32 TraesCS4D01G093200 chr3D 95.294 170 5 3 4804 4971 397162544 397162712 3.740000e-67 267.0
33 TraesCS4D01G093200 chr3D 94.186 172 8 2 4797 4966 571465538 571465367 1.740000e-65 261.0
34 TraesCS4D01G093200 chr3B 97.531 162 3 1 4806 4966 540175090 540174929 6.220000e-70 276.0
35 TraesCS4D01G093200 chr1A 94.186 172 9 1 4804 4974 588138671 588138500 1.740000e-65 261.0
36 TraesCS4D01G093200 chr3A 87.273 55 5 2 5831 5885 613529431 613529379 1.900000e-05 62.1
37 TraesCS4D01G093200 chr1B 84.375 64 8 2 5809 5871 587496734 587496796 1.900000e-05 62.1


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 TraesCS4D01G093200 chr4D 68659015 68665314 6299 False 11635.00 11635 100.0000 1 6300 1 chr4D.!!$F1 6299
1 TraesCS4D01G093200 chr4B 101262685 101268844 6159 False 2134.50 6909 92.4355 1 5888 4 chr4B.!!$F2 5887
2 TraesCS4D01G093200 chr4A 519569236 519576804 7568 False 792.14 3762 92.5148 1 5887 10 chr4A.!!$F1 5886
3 TraesCS4D01G093200 chr4A 558075671 558076177 506 True 411.50 599 96.1975 5889 6300 2 chr4A.!!$R2 411

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
141 142 0.035458 CGTCTTTGGTTCCTCTGGCT 59.965 55.0 0.00 0.00 0.00 4.75 F
1364 1930 0.038526 ACCGCCACTACATATAGCGC 60.039 55.0 0.00 0.00 45.17 5.92 F
1704 2418 0.398522 AGACGGCCAGGTGGATATCA 60.399 55.0 2.24 0.00 37.39 2.15 F
1782 2496 0.469917 ATTTCGCCGATCTGGACCAT 59.530 50.0 0.00 0.00 42.00 3.55 F
3665 4409 0.109735 CTGAGCTGCAGCATGTTGTG 60.110 55.0 38.24 17.39 45.16 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 2475 0.105039 GGTCCAGATCGGCGAAATCT 59.895 55.000 15.93 10.89 33.74 2.40 R
2716 3439 1.535028 CAAGGTATGTGACGCAAAGCA 59.465 47.619 0.00 0.00 0.00 3.91 R
3380 4123 1.490490 TGGACAACCAGATCCCTATGC 59.510 52.381 0.00 0.00 41.77 3.14 R
3850 4594 9.167311 GTAGATGTTAGGATGTTGAAGATGTTT 57.833 33.333 0.00 0.00 0.00 2.83 R
5594 6877 0.618458 TCATAGCCCAAAACGCTCCT 59.382 50.000 0.00 0.00 37.79 3.69 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
19 20 1.448985 GGTGATGAGTTAAAGGCGCA 58.551 50.000 10.83 0.00 0.00 6.09
106 107 2.050350 CCGCCTGTTCCGAGTCCTA 61.050 63.158 0.00 0.00 0.00 2.94
107 108 1.392710 CCGCCTGTTCCGAGTCCTAT 61.393 60.000 0.00 0.00 0.00 2.57
122 123 1.679680 TCCTATGGGACGACGAACATC 59.320 52.381 0.00 0.00 36.57 3.06
137 138 3.665190 GAACATCGTCTTTGGTTCCTCT 58.335 45.455 0.00 0.00 34.92 3.69
139 140 2.289694 ACATCGTCTTTGGTTCCTCTGG 60.290 50.000 0.00 0.00 0.00 3.86
141 142 0.035458 CGTCTTTGGTTCCTCTGGCT 59.965 55.000 0.00 0.00 0.00 4.75
146 147 3.782523 TCTTTGGTTCCTCTGGCTATCAT 59.217 43.478 0.00 0.00 0.00 2.45
147 148 3.565764 TTGGTTCCTCTGGCTATCATG 57.434 47.619 0.00 0.00 0.00 3.07
177 178 3.503827 GTCAAAATGACGGGGGATTTC 57.496 47.619 0.00 0.00 37.67 2.17
188 189 1.032114 GGGGATTTCGGTGAAGCCAG 61.032 60.000 4.33 0.00 36.97 4.85
195 196 2.753029 GGTGAAGCCAGCAGGAGT 59.247 61.111 0.00 0.00 40.34 3.85
268 269 0.820871 GCTCGATTCTGAGTGGGTCT 59.179 55.000 0.00 0.00 38.28 3.85
271 272 0.176680 CGATTCTGAGTGGGTCTGGG 59.823 60.000 0.00 0.00 0.00 4.45
279 280 1.561542 GAGTGGGTCTGGGATGTCAAT 59.438 52.381 0.00 0.00 0.00 2.57
291 292 3.817647 GGGATGTCAATCTCTAACATGGC 59.182 47.826 0.00 0.00 33.91 4.40
293 294 4.514441 GGATGTCAATCTCTAACATGGCAG 59.486 45.833 0.00 0.00 33.91 4.85
300 301 2.826128 TCTCTAACATGGCAGACGTCTT 59.174 45.455 17.26 1.59 0.00 3.01
301 302 4.014406 TCTCTAACATGGCAGACGTCTTA 58.986 43.478 17.26 5.83 0.00 2.10
321 322 1.400941 ACTCCCCTACACCTTCCCTA 58.599 55.000 0.00 0.00 0.00 3.53
347 349 3.244146 TGGTACCGGTTTCTCGAATTTCA 60.244 43.478 15.04 0.00 0.00 2.69
365 367 7.319380 CGAATTTCAAACGTTCATTTTAGACGA 59.681 33.333 0.00 0.00 0.00 4.20
366 368 8.488979 AATTTCAAACGTTCATTTTAGACGAG 57.511 30.769 0.00 0.00 0.00 4.18
367 369 5.013861 TCAAACGTTCATTTTAGACGAGC 57.986 39.130 0.00 0.00 0.00 5.03
368 370 4.084223 TCAAACGTTCATTTTAGACGAGCC 60.084 41.667 0.00 0.00 0.00 4.70
369 371 3.034721 ACGTTCATTTTAGACGAGCCA 57.965 42.857 1.90 0.00 0.00 4.75
370 372 2.993899 ACGTTCATTTTAGACGAGCCAG 59.006 45.455 1.90 0.00 0.00 4.85
371 373 2.222819 CGTTCATTTTAGACGAGCCAGC 60.223 50.000 0.00 0.00 0.00 4.85
372 374 2.024176 TCATTTTAGACGAGCCAGCC 57.976 50.000 0.00 0.00 0.00 4.85
373 375 0.652592 CATTTTAGACGAGCCAGCCG 59.347 55.000 0.00 0.00 0.00 5.52
374 376 0.535335 ATTTTAGACGAGCCAGCCGA 59.465 50.000 7.38 0.00 0.00 5.54
375 377 0.319083 TTTTAGACGAGCCAGCCGAA 59.681 50.000 7.38 0.00 0.00 4.30
376 378 0.535335 TTTAGACGAGCCAGCCGAAT 59.465 50.000 7.38 0.00 0.00 3.34
377 379 0.535335 TTAGACGAGCCAGCCGAATT 59.465 50.000 7.38 0.00 0.00 2.17
378 380 0.179111 TAGACGAGCCAGCCGAATTG 60.179 55.000 7.38 0.00 0.00 2.32
379 381 2.436646 ACGAGCCAGCCGAATTGG 60.437 61.111 7.38 0.00 42.50 3.16
380 382 2.125147 CGAGCCAGCCGAATTGGA 60.125 61.111 4.30 0.00 42.00 3.53
381 383 1.524621 CGAGCCAGCCGAATTGGAT 60.525 57.895 4.30 0.00 42.00 3.41
387 389 4.898607 GCCGAATTGGATGGGCTA 57.101 55.556 0.00 0.00 42.29 3.93
393 395 2.541588 CGAATTGGATGGGCTAAAAGCG 60.542 50.000 0.00 0.00 43.62 4.68
398 400 2.171659 TGGATGGGCTAAAAGCGTCATA 59.828 45.455 6.42 0.00 43.62 2.15
428 982 5.720371 ATTTTTGGTCGATTTGGTGATCA 57.280 34.783 0.00 0.00 0.00 2.92
477 1032 6.551736 ACTTCGTTGTATCAACAATATTGCC 58.448 36.000 15.48 0.00 46.84 4.52
480 1035 6.318628 TCGTTGTATCAACAATATTGCCAAC 58.681 36.000 15.48 15.06 46.84 3.77
487 1042 7.716799 ATCAACAATATTGCCAACCTTCTAA 57.283 32.000 15.48 0.00 0.00 2.10
536 1091 2.993264 GCTGCCCATGTGCCACTT 60.993 61.111 0.00 0.00 0.00 3.16
550 1105 1.609208 CCACTTCTTGACCACCCTTG 58.391 55.000 0.00 0.00 0.00 3.61
557 1112 1.421646 CTTGACCACCCTTGAGTCCTT 59.578 52.381 0.00 0.00 0.00 3.36
559 1114 2.696775 TGACCACCCTTGAGTCCTTTA 58.303 47.619 0.00 0.00 0.00 1.85
567 1122 4.254492 CCCTTGAGTCCTTTAACTGTAGC 58.746 47.826 0.00 0.00 0.00 3.58
655 1210 4.855388 CCGAAAGCAATTCTTCAATCAGTG 59.145 41.667 0.00 0.00 35.79 3.66
664 1219 0.322816 TTCAATCAGTGCCTGCTCCC 60.323 55.000 0.00 0.00 0.00 4.30
795 1350 9.219603 TCATGTATTCTTGAAGTCAAACTTAGG 57.780 33.333 0.00 0.00 38.80 2.69
998 1553 0.474660 AAGGAAGAGTGGTGGAGGCT 60.475 55.000 0.00 0.00 0.00 4.58
1020 1575 4.467107 GCGGAGGAGGGGAGGTCT 62.467 72.222 0.00 0.00 0.00 3.85
1331 1888 6.435428 AGCCGTTAATCTTAACACTGTTTTG 58.565 36.000 12.05 0.00 42.34 2.44
1358 1924 5.363292 TGTTTATTAGGACCGCCACTACATA 59.637 40.000 0.00 0.00 36.29 2.29
1364 1930 0.038526 ACCGCCACTACATATAGCGC 60.039 55.000 0.00 0.00 45.17 5.92
1379 1945 1.231221 AGCGCGGTTTACAAATGACA 58.769 45.000 4.23 0.00 0.00 3.58
1398 1964 1.197721 CAATGTTCACTCCAAGGTCGC 59.802 52.381 0.00 0.00 0.00 5.19
1425 1991 9.825972 CACGATTTGTAGTTTCATCACTTTTAT 57.174 29.630 0.00 0.00 0.00 1.40
1448 2014 9.793259 TTATTTATCAAGTGTCAAGGTCTTCTT 57.207 29.630 0.00 0.00 35.79 2.52
1475 2041 4.691216 GTCTGTCTGTATCTGTTTTGGGAC 59.309 45.833 0.00 0.00 0.00 4.46
1492 2061 5.975693 TGGGACATCCAACATTCTTTTAC 57.024 39.130 0.00 0.00 43.84 2.01
1582 2296 1.882623 GGGACTTCTCTTTTGCCACTG 59.117 52.381 0.00 0.00 0.00 3.66
1585 2299 3.381590 GGACTTCTCTTTTGCCACTGTTT 59.618 43.478 0.00 0.00 0.00 2.83
1704 2418 0.398522 AGACGGCCAGGTGGATATCA 60.399 55.000 2.24 0.00 37.39 2.15
1761 2475 7.337689 AGCAAATTCTATATGTGCACAGAGAAA 59.662 33.333 30.01 20.26 37.68 2.52
1782 2496 0.469917 ATTTCGCCGATCTGGACCAT 59.530 50.000 0.00 0.00 42.00 3.55
1791 2505 1.991070 GATCTGGACCATCATGGGGAT 59.009 52.381 9.04 6.06 43.37 3.85
1836 2550 1.413077 GCTAGAATCCTAGTTGGCGGT 59.587 52.381 0.00 0.00 43.35 5.68
1871 2585 4.699735 TGTTTGCGATGAGGTAAATGTCAT 59.300 37.500 0.00 0.00 36.07 3.06
1993 2707 1.018226 GTCTTGAGCAGCTGCATCGT 61.018 55.000 38.24 19.88 45.16 3.73
2136 2853 7.506114 TGGTCTCTAAGTGTCTAATGTGTTTT 58.494 34.615 0.00 0.00 0.00 2.43
2259 2977 6.555812 TGCTCGTTAGGTCATATAGTAGTG 57.444 41.667 0.00 0.00 0.00 2.74
2296 3014 9.853555 ATTCGCTTAATAATGATGTTTTGTTCA 57.146 25.926 0.00 0.00 0.00 3.18
2621 3339 3.504863 ACAAGTGCAAATGAATCGCATC 58.495 40.909 6.97 0.00 38.07 3.91
2622 3340 3.192001 ACAAGTGCAAATGAATCGCATCT 59.808 39.130 6.97 0.00 38.07 2.90
2623 3341 3.416119 AGTGCAAATGAATCGCATCTG 57.584 42.857 0.00 0.00 38.07 2.90
2624 3342 2.751259 AGTGCAAATGAATCGCATCTGT 59.249 40.909 0.00 0.00 38.07 3.41
2625 3343 3.940852 AGTGCAAATGAATCGCATCTGTA 59.059 39.130 0.00 0.00 38.07 2.74
2716 3439 2.817258 TCGATTTTCTCAACCCGCAAAT 59.183 40.909 0.00 0.00 0.00 2.32
2996 3739 3.462982 TCATAAGTTGCCGCATTCGTAT 58.537 40.909 0.00 0.00 0.00 3.06
3380 4123 7.162082 ACCTCCTTATTACTTTCTCACACAAG 58.838 38.462 0.00 0.00 0.00 3.16
3386 4129 6.992063 ATTACTTTCTCACACAAGCATAGG 57.008 37.500 0.00 0.00 0.00 2.57
3665 4409 0.109735 CTGAGCTGCAGCATGTTGTG 60.110 55.000 38.24 17.39 45.16 3.33
3850 4594 5.764487 TGATGTTGTGTTGTGATGCTTTA 57.236 34.783 0.00 0.00 0.00 1.85
4169 5022 9.463443 GTTGTTTACTACTTTGCATTCATCTTT 57.537 29.630 0.00 0.00 0.00 2.52
4277 5130 5.543714 ACCATGAATACGTTGTGAGTTACA 58.456 37.500 0.00 0.00 37.56 2.41
4354 5209 9.571810 TGCAACATATCAATTTTTACATCAGTC 57.428 29.630 0.00 0.00 0.00 3.51
4475 5330 6.727231 TGGTAGTAGACTAGTGAAAATTCCCA 59.273 38.462 0.00 0.00 0.00 4.37
4479 5334 4.911390 AGACTAGTGAAAATTCCCACCAG 58.089 43.478 0.00 5.64 34.00 4.00
4486 5341 4.160252 GTGAAAATTCCCACCAGCATATGT 59.840 41.667 4.29 0.00 0.00 2.29
4498 5353 7.147915 CCCACCAGCATATGTATTAAACACTTT 60.148 37.037 4.29 0.00 42.09 2.66
4517 5372 4.929808 ACTTTAAGAAGTGCATTCGATCGT 59.070 37.500 15.94 0.00 44.27 3.73
4665 5523 6.581171 AAACCTAAAAATCAAGAGAGCCAG 57.419 37.500 0.00 0.00 0.00 4.85
4809 6047 4.569943 TCCTCTTCATGCAGTTTGTACTC 58.430 43.478 0.00 0.00 30.26 2.59
4810 6048 3.686726 CCTCTTCATGCAGTTTGTACTCC 59.313 47.826 0.00 0.00 30.26 3.85
4811 6049 3.674997 TCTTCATGCAGTTTGTACTCCC 58.325 45.455 0.00 0.00 30.26 4.30
4812 6050 3.327757 TCTTCATGCAGTTTGTACTCCCT 59.672 43.478 0.00 0.00 30.26 4.20
4813 6051 3.334583 TCATGCAGTTTGTACTCCCTC 57.665 47.619 0.00 0.00 30.26 4.30
4814 6052 2.027192 TCATGCAGTTTGTACTCCCTCC 60.027 50.000 0.00 0.00 30.26 4.30
4815 6053 0.320374 TGCAGTTTGTACTCCCTCCG 59.680 55.000 0.00 0.00 30.26 4.63
4816 6054 0.320697 GCAGTTTGTACTCCCTCCGT 59.679 55.000 0.00 0.00 30.26 4.69
4817 6055 1.270678 GCAGTTTGTACTCCCTCCGTT 60.271 52.381 0.00 0.00 30.26 4.44
4818 6056 2.685100 CAGTTTGTACTCCCTCCGTTC 58.315 52.381 0.00 0.00 30.26 3.95
4819 6057 1.271656 AGTTTGTACTCCCTCCGTTCG 59.728 52.381 0.00 0.00 0.00 3.95
4820 6058 1.000171 GTTTGTACTCCCTCCGTTCGT 60.000 52.381 0.00 0.00 0.00 3.85
4821 6059 2.198827 TTGTACTCCCTCCGTTCGTA 57.801 50.000 0.00 0.00 0.00 3.43
4822 6060 2.198827 TGTACTCCCTCCGTTCGTAA 57.801 50.000 0.00 0.00 0.00 3.18
4823 6061 2.513753 TGTACTCCCTCCGTTCGTAAA 58.486 47.619 0.00 0.00 0.00 2.01
4824 6062 3.091545 TGTACTCCCTCCGTTCGTAAAT 58.908 45.455 0.00 0.00 0.00 1.40
4825 6063 4.269183 TGTACTCCCTCCGTTCGTAAATA 58.731 43.478 0.00 0.00 0.00 1.40
4826 6064 4.889409 TGTACTCCCTCCGTTCGTAAATAT 59.111 41.667 0.00 0.00 0.00 1.28
4827 6065 6.061441 TGTACTCCCTCCGTTCGTAAATATA 58.939 40.000 0.00 0.00 0.00 0.86
4828 6066 6.545666 TGTACTCCCTCCGTTCGTAAATATAA 59.454 38.462 0.00 0.00 0.00 0.98
4829 6067 6.081872 ACTCCCTCCGTTCGTAAATATAAG 57.918 41.667 0.00 0.00 0.00 1.73
4830 6068 5.595952 ACTCCCTCCGTTCGTAAATATAAGT 59.404 40.000 0.00 0.00 0.00 2.24
4831 6069 6.076981 TCCCTCCGTTCGTAAATATAAGTC 57.923 41.667 0.00 0.00 0.00 3.01
4832 6070 5.829924 TCCCTCCGTTCGTAAATATAAGTCT 59.170 40.000 0.00 0.00 0.00 3.24
4833 6071 6.322201 TCCCTCCGTTCGTAAATATAAGTCTT 59.678 38.462 0.00 0.00 0.00 3.01
4834 6072 6.982724 CCCTCCGTTCGTAAATATAAGTCTTT 59.017 38.462 0.00 0.00 0.00 2.52
4835 6073 7.042925 CCCTCCGTTCGTAAATATAAGTCTTTG 60.043 40.741 0.00 0.00 0.00 2.77
4836 6074 7.490402 CCTCCGTTCGTAAATATAAGTCTTTGT 59.510 37.037 0.00 0.00 0.00 2.83
4837 6075 9.507280 CTCCGTTCGTAAATATAAGTCTTTGTA 57.493 33.333 0.00 0.00 0.00 2.41
4838 6076 9.507280 TCCGTTCGTAAATATAAGTCTTTGTAG 57.493 33.333 0.00 0.00 0.00 2.74
4839 6077 9.507280 CCGTTCGTAAATATAAGTCTTTGTAGA 57.493 33.333 0.00 0.00 0.00 2.59
4852 6090 7.118496 AGTCTTTGTAGAGATTCCACTATGG 57.882 40.000 0.00 0.00 39.43 2.74
4853 6091 6.897966 AGTCTTTGTAGAGATTCCACTATGGA 59.102 38.462 0.00 0.00 46.61 3.41
4864 6102 4.442401 TCCACTATGGACTACATACGGA 57.558 45.455 0.00 0.00 42.67 4.69
4865 6103 4.395625 TCCACTATGGACTACATACGGAG 58.604 47.826 0.00 0.00 42.67 4.63
4866 6104 3.057456 CCACTATGGACTACATACGGAGC 60.057 52.174 0.00 0.00 40.96 4.70
4867 6105 3.568430 CACTATGGACTACATACGGAGCA 59.432 47.826 0.00 0.00 41.03 4.26
4868 6106 4.037565 CACTATGGACTACATACGGAGCAA 59.962 45.833 0.00 0.00 41.03 3.91
4869 6107 4.647853 ACTATGGACTACATACGGAGCAAA 59.352 41.667 0.00 0.00 41.03 3.68
4870 6108 3.965379 TGGACTACATACGGAGCAAAA 57.035 42.857 0.00 0.00 0.00 2.44
4871 6109 4.481368 TGGACTACATACGGAGCAAAAT 57.519 40.909 0.00 0.00 0.00 1.82
4872 6110 4.188462 TGGACTACATACGGAGCAAAATG 58.812 43.478 0.00 0.00 0.00 2.32
4873 6111 4.081365 TGGACTACATACGGAGCAAAATGA 60.081 41.667 0.00 0.00 0.00 2.57
4874 6112 4.508124 GGACTACATACGGAGCAAAATGAG 59.492 45.833 0.00 0.00 0.00 2.90
4875 6113 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
4876 6114 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
4877 6115 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
4878 6116 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
4879 6117 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
4880 6118 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
4881 6119 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
4882 6120 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
4883 6121 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
4884 6122 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
4885 6123 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
4898 6136 8.430801 AGTGAATCTACACTCTAAAATGCATC 57.569 34.615 0.00 0.00 46.36 3.91
4899 6137 8.263640 AGTGAATCTACACTCTAAAATGCATCT 58.736 33.333 0.00 0.00 46.36 2.90
4900 6138 9.534565 GTGAATCTACACTCTAAAATGCATCTA 57.465 33.333 0.00 0.00 37.73 1.98
4910 6148 9.809096 ACTCTAAAATGCATCTATATACATCCG 57.191 33.333 0.00 0.00 0.00 4.18
4911 6149 9.809096 CTCTAAAATGCATCTATATACATCCGT 57.191 33.333 0.00 0.00 0.00 4.69
4916 6154 8.877808 AATGCATCTATATACATCCGTATGTG 57.122 34.615 3.56 0.00 45.99 3.21
4917 6155 6.805713 TGCATCTATATACATCCGTATGTGG 58.194 40.000 3.56 0.00 45.99 4.17
4918 6156 6.379988 TGCATCTATATACATCCGTATGTGGT 59.620 38.462 3.56 0.00 45.99 4.16
4919 6157 6.918569 GCATCTATATACATCCGTATGTGGTC 59.081 42.308 3.56 0.00 45.99 4.02
4920 6158 7.426410 CATCTATATACATCCGTATGTGGTCC 58.574 42.308 3.56 0.00 45.99 4.46
4921 6159 6.486941 TCTATATACATCCGTATGTGGTCCA 58.513 40.000 3.56 0.00 45.99 4.02
4922 6160 7.123383 TCTATATACATCCGTATGTGGTCCAT 58.877 38.462 3.56 0.00 45.99 3.41
4923 6161 8.276477 TCTATATACATCCGTATGTGGTCCATA 58.724 37.037 3.56 0.00 45.99 2.74
4924 6162 7.914427 ATATACATCCGTATGTGGTCCATAT 57.086 36.000 3.56 6.35 45.99 1.78
4925 6163 4.271696 ACATCCGTATGTGGTCCATATG 57.728 45.455 11.21 0.00 44.79 1.78
4942 6180 7.921041 TCCATATGGAATCTCTACAAAGACT 57.079 36.000 22.52 0.00 42.18 3.24
4943 6181 8.324191 TCCATATGGAATCTCTACAAAGACTT 57.676 34.615 22.52 0.00 42.18 3.01
4944 6182 9.434275 TCCATATGGAATCTCTACAAAGACTTA 57.566 33.333 22.52 0.00 42.18 2.24
4957 6195 9.507280 TCTACAAAGACTTATATTTACGAACGG 57.493 33.333 0.00 0.00 0.00 4.44
4958 6196 9.507280 CTACAAAGACTTATATTTACGAACGGA 57.493 33.333 0.00 0.00 0.00 4.69
4959 6197 8.403606 ACAAAGACTTATATTTACGAACGGAG 57.596 34.615 0.00 0.00 0.00 4.63
4960 6198 7.490402 ACAAAGACTTATATTTACGAACGGAGG 59.510 37.037 0.00 0.00 0.00 4.30
4961 6199 6.081872 AGACTTATATTTACGAACGGAGGG 57.918 41.667 0.00 0.00 0.00 4.30
4962 6200 5.829924 AGACTTATATTTACGAACGGAGGGA 59.170 40.000 0.00 0.00 0.00 4.20
4963 6201 6.016443 AGACTTATATTTACGAACGGAGGGAG 60.016 42.308 0.00 0.00 0.00 4.30
5215 6498 3.948086 GAGGACTGTGTCGGCGTCG 62.948 68.421 1.15 1.15 32.65 5.12
5251 6534 3.180984 GACTGTGGTCACTGTCGAC 57.819 57.895 19.82 9.11 45.56 4.20
5371 6654 5.643379 ACTCTGCTGAACTTGAAAAACAA 57.357 34.783 0.00 0.00 36.97 2.83
5375 6658 4.757594 TGCTGAACTTGAAAAACAATGCT 58.242 34.783 0.00 0.00 37.88 3.79
5379 6662 6.018507 GCTGAACTTGAAAAACAATGCTCATT 60.019 34.615 0.00 0.00 37.88 2.57
5525 6808 3.793144 GACGCCTGCGCTTCAAGG 61.793 66.667 9.73 8.24 44.19 3.61
5531 6814 1.959042 CCTGCGCTTCAAGGTGATAT 58.041 50.000 9.73 0.00 0.00 1.63
5588 6871 8.873830 ACTAAATCATCAGAATTCACAACTACG 58.126 33.333 8.44 0.00 0.00 3.51
5590 6873 4.820897 TCATCAGAATTCACAACTACGCT 58.179 39.130 8.44 0.00 0.00 5.07
5594 6877 7.386573 TCATCAGAATTCACAACTACGCTTAAA 59.613 33.333 8.44 0.00 0.00 1.52
5598 6881 6.369065 AGAATTCACAACTACGCTTAAAGGAG 59.631 38.462 8.44 0.00 0.00 3.69
5609 6892 1.886542 CTTAAAGGAGCGTTTTGGGCT 59.113 47.619 0.00 0.00 45.00 5.19
5614 6897 1.212935 AGGAGCGTTTTGGGCTATGAT 59.787 47.619 0.00 0.00 41.72 2.45
5630 6914 5.973565 GGCTATGATAGTGTTTTTGCATCAC 59.026 40.000 0.92 0.00 0.00 3.06
5643 6927 3.138884 TGCATCACTACCTTGCTGAAA 57.861 42.857 0.00 0.00 37.28 2.69
5644 6928 3.485394 TGCATCACTACCTTGCTGAAAA 58.515 40.909 0.00 0.00 37.28 2.29
5706 6990 8.581578 GGATTTTACTTTTACTTGTTGGATCCA 58.418 33.333 11.44 11.44 0.00 3.41
5709 6993 7.504924 TTACTTTTACTTGTTGGATCCAGTG 57.495 36.000 15.53 8.92 0.00 3.66
5711 7003 5.531287 ACTTTTACTTGTTGGATCCAGTGAC 59.469 40.000 15.53 11.31 0.00 3.67
5718 7010 4.451150 GATCCAGTGACGGCGGCA 62.451 66.667 13.60 13.60 0.00 5.69
5780 7721 8.126700 TGAATAACCTTTCTCGTTTTCTTTGTC 58.873 33.333 0.00 0.00 0.00 3.18
5821 8367 6.937436 TCGCTTTAGAGTTTCTTTTTCCTT 57.063 33.333 0.00 0.00 0.00 3.36
5858 8404 6.879458 AGTTTCGGTCTTATATGACTTTGCTT 59.121 34.615 15.98 0.28 37.16 3.91
5863 8409 6.747280 CGGTCTTATATGACTTTGCTTTTTGG 59.253 38.462 15.98 0.00 37.16 3.28
5977 8523 8.658499 CCAAATTACTGGGTATTAGTAGTGTC 57.342 38.462 0.00 0.00 32.67 3.67
6003 8549 8.856153 TGTGTACCAATATAATCACACTTTGT 57.144 30.769 0.00 0.00 37.69 2.83
6039 8585 2.423577 CAAGGCCTAAGCAAAGTACGT 58.576 47.619 5.16 0.00 42.56 3.57
6058 8604 0.678950 TAGCAACAAAAAGCCAGCCC 59.321 50.000 0.00 0.00 0.00 5.19
6076 8622 2.373938 CGCGAGGCCTTCTTAAGTG 58.626 57.895 6.77 0.00 0.00 3.16
6078 8624 1.809684 GCGAGGCCTTCTTAAGTGTT 58.190 50.000 6.77 0.00 0.00 3.32
6088 8634 4.811557 CCTTCTTAAGTGTTCCCATCGATC 59.188 45.833 1.63 0.00 0.00 3.69
6102 8648 3.627218 GATCGCTAACACGCCGCC 61.627 66.667 0.00 0.00 0.00 6.13
6239 8882 4.717629 TGCTCGCCTGGAACGTCG 62.718 66.667 0.00 0.00 0.00 5.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.119459 TGTTTGTTTGCGCCTTTAACTCA 60.119 39.130 4.18 3.56 0.00 3.41
19 20 2.645802 TGGCGAAGGTAGTGTTTGTTT 58.354 42.857 0.00 0.00 0.00 2.83
82 83 1.601419 CTCGGAACAGGCGGAGGTAA 61.601 60.000 0.00 0.00 33.19 2.85
106 107 4.806571 CGATGTTCGTCGTCCCAT 57.193 55.556 6.30 0.00 36.88 4.00
122 123 0.035458 AGCCAGAGGAACCAAAGACG 59.965 55.000 0.00 0.00 0.00 4.18
131 132 0.394192 CGCCATGATAGCCAGAGGAA 59.606 55.000 0.00 0.00 0.00 3.36
137 138 0.035317 GTCCATCGCCATGATAGCCA 59.965 55.000 0.00 0.00 34.83 4.75
139 140 0.319900 ACGTCCATCGCCATGATAGC 60.320 55.000 0.00 0.00 44.19 2.97
141 142 1.036707 TGACGTCCATCGCCATGATA 58.963 50.000 14.12 0.00 44.19 2.15
146 147 0.801872 CATTTTGACGTCCATCGCCA 59.198 50.000 14.12 0.00 44.19 5.69
147 148 1.083489 TCATTTTGACGTCCATCGCC 58.917 50.000 14.12 0.00 44.19 5.54
177 178 2.435586 CTCCTGCTGGCTTCACCG 60.436 66.667 4.42 0.00 43.94 4.94
188 189 1.973812 GAAAGCCCACCACTCCTGC 60.974 63.158 0.00 0.00 0.00 4.85
257 258 0.539051 GACATCCCAGACCCACTCAG 59.461 60.000 0.00 0.00 0.00 3.35
268 269 4.686944 GCCATGTTAGAGATTGACATCCCA 60.687 45.833 0.00 0.00 34.08 4.37
271 272 5.236047 GTCTGCCATGTTAGAGATTGACATC 59.764 44.000 0.00 0.00 34.08 3.06
279 280 2.447443 AGACGTCTGCCATGTTAGAGA 58.553 47.619 19.30 0.00 0.00 3.10
291 292 3.087031 TGTAGGGGAGTTAAGACGTCTG 58.913 50.000 20.85 0.00 0.00 3.51
293 294 2.165234 GGTGTAGGGGAGTTAAGACGTC 59.835 54.545 7.70 7.70 0.00 4.34
300 301 1.726352 AGGGAAGGTGTAGGGGAGTTA 59.274 52.381 0.00 0.00 0.00 2.24
301 302 0.496841 AGGGAAGGTGTAGGGGAGTT 59.503 55.000 0.00 0.00 0.00 3.01
321 322 2.726821 TCGAGAAACCGGTACCATACT 58.273 47.619 8.00 0.82 0.00 2.12
347 349 3.810941 TGGCTCGTCTAAAATGAACGTTT 59.189 39.130 0.46 0.00 0.00 3.60
365 367 1.454479 CCATCCAATTCGGCTGGCT 60.454 57.895 0.00 0.00 44.03 4.75
366 368 3.122850 CCATCCAATTCGGCTGGC 58.877 61.111 0.00 0.00 44.03 4.85
368 370 3.122850 GCCCATCCAATTCGGCTG 58.877 61.111 0.00 0.00 38.41 4.85
369 371 3.010144 AGCCCATCCAATTCGGCT 58.990 55.556 0.00 0.00 46.96 5.52
370 372 1.398692 TTTAGCCCATCCAATTCGGC 58.601 50.000 0.00 0.00 41.96 5.54
371 373 2.223805 GCTTTTAGCCCATCCAATTCGG 60.224 50.000 0.00 0.00 34.48 4.30
372 374 2.541588 CGCTTTTAGCCCATCCAATTCG 60.542 50.000 0.00 0.00 38.18 3.34
373 375 2.427095 ACGCTTTTAGCCCATCCAATTC 59.573 45.455 0.00 0.00 38.18 2.17
374 376 2.427095 GACGCTTTTAGCCCATCCAATT 59.573 45.455 0.00 0.00 38.18 2.32
375 377 2.024414 GACGCTTTTAGCCCATCCAAT 58.976 47.619 0.00 0.00 38.18 3.16
376 378 1.271652 TGACGCTTTTAGCCCATCCAA 60.272 47.619 0.00 0.00 38.18 3.53
377 379 0.326595 TGACGCTTTTAGCCCATCCA 59.673 50.000 0.00 0.00 38.18 3.41
378 380 1.680338 ATGACGCTTTTAGCCCATCC 58.320 50.000 0.00 0.00 38.18 3.51
379 381 4.319177 AGATATGACGCTTTTAGCCCATC 58.681 43.478 0.00 0.00 38.18 3.51
380 382 4.357918 AGATATGACGCTTTTAGCCCAT 57.642 40.909 0.00 0.00 38.18 4.00
381 383 3.838244 AGATATGACGCTTTTAGCCCA 57.162 42.857 0.00 0.00 38.18 5.36
382 384 6.803154 ATTTAGATATGACGCTTTTAGCCC 57.197 37.500 0.00 0.00 38.18 5.19
398 400 9.801873 CACCAAATCGACCAAAAATATTTAGAT 57.198 29.630 0.01 0.00 0.00 1.98
411 965 1.001520 ACGTGATCACCAAATCGACCA 59.998 47.619 20.03 0.00 0.00 4.02
428 982 0.905357 AGATAAGGCAGCTCCAACGT 59.095 50.000 5.21 0.00 37.29 3.99
477 1032 9.810545 TTTGTCTTAATGGTTTTTAGAAGGTTG 57.189 29.630 0.00 0.00 0.00 3.77
480 1035 9.810545 TTGTTTGTCTTAATGGTTTTTAGAAGG 57.189 29.630 0.00 0.00 0.00 3.46
536 1091 1.056660 GGACTCAAGGGTGGTCAAGA 58.943 55.000 0.00 0.00 30.68 3.02
550 1105 5.185442 AGGTACTGCTACAGTTAAAGGACTC 59.815 44.000 5.44 0.00 42.59 3.36
557 1112 4.282449 TGAGCAAGGTACTGCTACAGTTAA 59.718 41.667 9.41 0.00 42.59 2.01
559 1114 2.632996 TGAGCAAGGTACTGCTACAGTT 59.367 45.455 9.41 0.00 42.59 3.16
567 1122 3.681897 GTGAGTGAATGAGCAAGGTACTG 59.318 47.826 0.00 0.00 40.86 2.74
624 1179 5.067936 TGAAGAATTGCTTTCGGGTTTAACA 59.932 36.000 0.00 0.00 39.46 2.41
655 1210 2.440980 GATTGGGTGGGAGCAGGC 60.441 66.667 0.00 0.00 0.00 4.85
664 1219 0.537188 AGTACGAGCTGGATTGGGTG 59.463 55.000 1.44 0.00 0.00 4.61
998 1553 4.088351 TCCCCTCCTCCGCCATCA 62.088 66.667 0.00 0.00 0.00 3.07
1253 1810 3.784701 TCAGAGTTTCTATCGTGAGGC 57.215 47.619 0.00 0.00 0.00 4.70
1256 1813 5.405571 GCAACTTTCAGAGTTTCTATCGTGA 59.594 40.000 0.00 0.00 46.34 4.35
1331 1888 2.934553 GTGGCGGTCCTAATAAACAGTC 59.065 50.000 0.00 0.00 0.00 3.51
1358 1924 3.004171 TGTCATTTGTAAACCGCGCTAT 58.996 40.909 5.56 0.00 0.00 2.97
1364 1930 6.205784 AGTGAACATTGTCATTTGTAAACCG 58.794 36.000 0.00 0.00 0.00 4.44
1379 1945 1.523758 GCGACCTTGGAGTGAACATT 58.476 50.000 0.00 0.00 0.00 2.71
1398 1964 5.862924 AGTGATGAAACTACAAATCGTGG 57.137 39.130 0.00 0.00 0.00 4.94
1425 1991 8.405531 CAAAAGAAGACCTTGACACTTGATAAA 58.594 33.333 0.00 0.00 34.79 1.40
1448 2014 5.530915 CCAAAACAGATACAGACAGACCAAA 59.469 40.000 0.00 0.00 0.00 3.28
1475 2041 7.661040 ACTGAAAGGTAAAAGAATGTTGGATG 58.339 34.615 0.00 0.00 39.30 3.51
1481 2050 7.990886 TGACACTACTGAAAGGTAAAAGAATGT 59.009 33.333 0.00 0.00 39.30 2.71
1492 2061 4.703897 TGAGGTTTGACACTACTGAAAGG 58.296 43.478 0.00 0.00 39.30 3.11
1582 2296 4.123497 ACACCTTCCAAGCAAGAAAAAC 57.877 40.909 0.00 0.00 0.00 2.43
1585 2299 3.766591 TCAAACACCTTCCAAGCAAGAAA 59.233 39.130 0.00 0.00 0.00 2.52
1704 2418 1.067084 CGATGGCACGCAGATCTCT 59.933 57.895 0.00 0.00 0.00 3.10
1761 2475 0.105039 GGTCCAGATCGGCGAAATCT 59.895 55.000 15.93 10.89 33.74 2.40
1782 2496 0.987613 TAGCAGTGCCATCCCCATGA 60.988 55.000 12.58 0.00 30.57 3.07
1791 2505 1.301401 GGTGTCGTTAGCAGTGCCA 60.301 57.895 12.58 0.00 0.00 4.92
1792 2506 2.033194 GGGTGTCGTTAGCAGTGCC 61.033 63.158 12.58 0.00 0.00 5.01
1795 2509 0.685097 ATGTGGGTGTCGTTAGCAGT 59.315 50.000 0.00 0.00 0.00 4.40
1797 2511 1.518325 CAATGTGGGTGTCGTTAGCA 58.482 50.000 0.00 0.00 0.00 3.49
1836 2550 0.443478 CGCAAACATGCATCGACTGA 59.557 50.000 0.00 0.00 34.41 3.41
1871 2585 1.788229 TGATGGGAGCCAGTCGATTA 58.212 50.000 0.00 0.00 36.75 1.75
2111 2828 6.665992 AACACATTAGACACTTAGAGACCA 57.334 37.500 0.00 0.00 0.00 4.02
2139 2856 9.363763 CCAGCTATATATCTGTAACAATCACAG 57.636 37.037 11.61 0.00 43.92 3.66
2296 3014 4.166144 TGAGAGGGAAAAACTTCTCAGGTT 59.834 41.667 4.23 0.00 31.60 3.50
2361 3079 1.886542 CATGGGTGAGATGCATGATGG 59.113 52.381 2.46 0.00 0.00 3.51
2595 3313 4.142816 GCGATTCATTTGCACTTGTAGTCT 60.143 41.667 0.00 0.00 34.56 3.24
2664 3387 1.895798 CAGAGAGCAGGTGTAGTTGGA 59.104 52.381 0.00 0.00 0.00 3.53
2716 3439 1.535028 CAAGGTATGTGACGCAAAGCA 59.465 47.619 0.00 0.00 0.00 3.91
2996 3739 4.932799 CGTACCATGTATTTGTGGAAGTCA 59.067 41.667 0.00 0.00 38.86 3.41
3380 4123 1.490490 TGGACAACCAGATCCCTATGC 59.510 52.381 0.00 0.00 41.77 3.14
3850 4594 9.167311 GTAGATGTTAGGATGTTGAAGATGTTT 57.833 33.333 0.00 0.00 0.00 2.83
4466 5321 8.546083 TTAATACATATGCTGGTGGGAATTTT 57.454 30.769 1.58 0.00 0.00 1.82
4470 5325 6.320164 GTGTTTAATACATATGCTGGTGGGAA 59.680 38.462 1.58 0.00 39.39 3.97
4498 5353 5.244785 AGTACGATCGAATGCACTTCTTA 57.755 39.130 24.34 0.00 0.00 2.10
4513 5368 4.402793 AGCTGTATGAGTCCAAAGTACGAT 59.597 41.667 0.00 0.00 0.00 3.73
4517 5372 5.483685 AACAGCTGTATGAGTCCAAAGTA 57.516 39.130 22.01 0.00 0.00 2.24
4653 5511 3.898123 AGTTCACTAACTGGCTCTCTTGA 59.102 43.478 0.00 0.00 44.40 3.02
4665 5523 7.117956 GGTGAAATAAGTGGAGAGTTCACTAAC 59.882 40.741 12.98 0.00 43.82 2.34
4755 5992 6.757897 AAAAGCTTCATAATCAATGACGGA 57.242 33.333 0.00 0.00 44.42 4.69
4794 6032 2.359900 GGAGGGAGTACAAACTGCATG 58.640 52.381 0.00 0.00 45.33 4.06
4809 6047 6.081872 AGACTTATATTTACGAACGGAGGG 57.918 41.667 0.00 0.00 0.00 4.30
4810 6048 7.490402 ACAAAGACTTATATTTACGAACGGAGG 59.510 37.037 0.00 0.00 0.00 4.30
4811 6049 8.403606 ACAAAGACTTATATTTACGAACGGAG 57.596 34.615 0.00 0.00 0.00 4.63
4812 6050 9.507280 CTACAAAGACTTATATTTACGAACGGA 57.493 33.333 0.00 0.00 0.00 4.69
4813 6051 9.507280 TCTACAAAGACTTATATTTACGAACGG 57.493 33.333 0.00 0.00 0.00 4.44
4826 6064 8.696374 CCATAGTGGAATCTCTACAAAGACTTA 58.304 37.037 0.00 0.00 40.96 2.24
4827 6065 7.400339 TCCATAGTGGAATCTCTACAAAGACTT 59.600 37.037 0.00 0.00 45.00 3.01
4828 6066 6.897966 TCCATAGTGGAATCTCTACAAAGACT 59.102 38.462 0.00 0.00 45.00 3.24
4829 6067 7.113658 TCCATAGTGGAATCTCTACAAAGAC 57.886 40.000 0.00 0.00 45.00 3.01
4843 6081 4.395625 CTCCGTATGTAGTCCATAGTGGA 58.604 47.826 0.00 0.00 45.98 4.02
4844 6082 3.057456 GCTCCGTATGTAGTCCATAGTGG 60.057 52.174 0.00 0.00 36.71 4.00
4845 6083 3.568430 TGCTCCGTATGTAGTCCATAGTG 59.432 47.826 0.00 0.00 36.71 2.74
4846 6084 3.828921 TGCTCCGTATGTAGTCCATAGT 58.171 45.455 0.00 0.00 36.71 2.12
4847 6085 4.848562 TTGCTCCGTATGTAGTCCATAG 57.151 45.455 0.00 0.00 36.71 2.23
4848 6086 5.601583 TTTTGCTCCGTATGTAGTCCATA 57.398 39.130 0.00 0.00 34.86 2.74
4849 6087 4.481368 TTTTGCTCCGTATGTAGTCCAT 57.519 40.909 0.00 0.00 37.58 3.41
4850 6088 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
4851 6089 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
4852 6090 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
4853 6091 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
4854 6092 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
4855 6093 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
4856 6094 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
4857 6095 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
4858 6096 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
4859 6097 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
4860 6098 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
4861 6099 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
4862 6100 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
4863 6101 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
4874 6112 8.430801 AGATGCATTTTAGAGTGTAGATTCAC 57.569 34.615 0.00 0.00 38.46 3.18
4884 6122 9.809096 CGGATGTATATAGATGCATTTTAGAGT 57.191 33.333 11.19 0.00 38.38 3.24
4885 6123 9.809096 ACGGATGTATATAGATGCATTTTAGAG 57.191 33.333 11.19 0.00 38.38 2.43
4889 6127 9.890629 ACATACGGATGTATATAGATGCATTTT 57.109 29.630 12.79 0.00 44.77 1.82
4890 6128 9.317936 CACATACGGATGTATATAGATGCATTT 57.682 33.333 14.23 0.00 44.82 2.32
4891 6129 7.928167 CCACATACGGATGTATATAGATGCATT 59.072 37.037 14.23 1.23 44.82 3.56
4892 6130 7.069950 ACCACATACGGATGTATATAGATGCAT 59.930 37.037 14.23 0.00 44.82 3.96
4893 6131 6.379988 ACCACATACGGATGTATATAGATGCA 59.620 38.462 14.23 0.00 44.82 3.96
4894 6132 6.806751 ACCACATACGGATGTATATAGATGC 58.193 40.000 14.23 0.00 44.82 3.91
4895 6133 7.068226 TGGACCACATACGGATGTATATAGATG 59.932 40.741 14.23 0.00 44.82 2.90
4896 6134 7.123383 TGGACCACATACGGATGTATATAGAT 58.877 38.462 14.23 0.00 44.82 1.98
4897 6135 6.486941 TGGACCACATACGGATGTATATAGA 58.513 40.000 14.23 0.00 44.82 1.98
4898 6136 6.769134 TGGACCACATACGGATGTATATAG 57.231 41.667 14.23 0.00 44.82 1.31
4899 6137 8.856103 CATATGGACCACATACGGATGTATATA 58.144 37.037 14.23 8.23 44.82 0.86
4900 6138 7.202001 CCATATGGACCACATACGGATGTATAT 60.202 40.741 17.49 9.84 45.95 0.86
4901 6139 6.097696 CCATATGGACCACATACGGATGTATA 59.902 42.308 17.49 7.78 45.95 1.47
4902 6140 5.104941 CCATATGGACCACATACGGATGTAT 60.105 44.000 17.49 4.48 45.95 2.29
4903 6141 4.221924 CCATATGGACCACATACGGATGTA 59.778 45.833 17.49 0.00 45.95 2.29
4904 6142 3.007940 CCATATGGACCACATACGGATGT 59.992 47.826 17.49 7.68 45.95 3.06
4905 6143 3.260632 TCCATATGGACCACATACGGATG 59.739 47.826 20.98 5.94 46.41 3.51
4906 6144 3.516586 TCCATATGGACCACATACGGAT 58.483 45.455 20.98 0.00 46.41 4.18
4908 6146 3.762407 TTCCATATGGACCACATACGG 57.238 47.619 24.47 0.00 44.76 4.02
4909 6147 5.047021 AGAGATTCCATATGGACCACATACG 60.047 44.000 24.47 0.00 44.41 3.06
4910 6148 6.365970 AGAGATTCCATATGGACCACATAC 57.634 41.667 24.47 11.87 44.41 2.39
4911 6149 7.016296 TGTAGAGATTCCATATGGACCACATA 58.984 38.462 24.47 9.01 45.39 2.29
4912 6150 5.846164 TGTAGAGATTCCATATGGACCACAT 59.154 40.000 24.47 14.77 45.39 3.21
4913 6151 5.215845 TGTAGAGATTCCATATGGACCACA 58.784 41.667 24.47 14.43 45.39 4.17
4914 6152 5.808366 TGTAGAGATTCCATATGGACCAC 57.192 43.478 24.47 16.88 45.39 4.16
4915 6153 6.615316 TCTTTGTAGAGATTCCATATGGACCA 59.385 38.462 24.47 11.37 45.39 4.02
4916 6154 6.931840 GTCTTTGTAGAGATTCCATATGGACC 59.068 42.308 24.47 17.88 45.39 4.46
4917 6155 7.731054 AGTCTTTGTAGAGATTCCATATGGAC 58.269 38.462 24.47 13.75 45.39 4.02
4918 6156 7.921041 AGTCTTTGTAGAGATTCCATATGGA 57.079 36.000 20.98 20.98 43.73 3.41
4931 6169 9.507280 CCGTTCGTAAATATAAGTCTTTGTAGA 57.493 33.333 0.00 0.00 0.00 2.59
4932 6170 9.507280 TCCGTTCGTAAATATAAGTCTTTGTAG 57.493 33.333 0.00 0.00 0.00 2.74
4933 6171 9.507280 CTCCGTTCGTAAATATAAGTCTTTGTA 57.493 33.333 0.00 0.00 0.00 2.41
4934 6172 7.490402 CCTCCGTTCGTAAATATAAGTCTTTGT 59.510 37.037 0.00 0.00 0.00 2.83
4935 6173 7.042925 CCCTCCGTTCGTAAATATAAGTCTTTG 60.043 40.741 0.00 0.00 0.00 2.77
4936 6174 6.982724 CCCTCCGTTCGTAAATATAAGTCTTT 59.017 38.462 0.00 0.00 0.00 2.52
4937 6175 6.322201 TCCCTCCGTTCGTAAATATAAGTCTT 59.678 38.462 0.00 0.00 0.00 3.01
4938 6176 5.829924 TCCCTCCGTTCGTAAATATAAGTCT 59.170 40.000 0.00 0.00 0.00 3.24
4939 6177 6.076981 TCCCTCCGTTCGTAAATATAAGTC 57.923 41.667 0.00 0.00 0.00 3.01
4940 6178 5.595952 ACTCCCTCCGTTCGTAAATATAAGT 59.404 40.000 0.00 0.00 0.00 2.24
4941 6179 6.081872 ACTCCCTCCGTTCGTAAATATAAG 57.918 41.667 0.00 0.00 0.00 1.73
4942 6180 6.772716 ACTACTCCCTCCGTTCGTAAATATAA 59.227 38.462 0.00 0.00 0.00 0.98
4943 6181 6.299141 ACTACTCCCTCCGTTCGTAAATATA 58.701 40.000 0.00 0.00 0.00 0.86
4944 6182 5.136105 ACTACTCCCTCCGTTCGTAAATAT 58.864 41.667 0.00 0.00 0.00 1.28
4945 6183 4.526970 ACTACTCCCTCCGTTCGTAAATA 58.473 43.478 0.00 0.00 0.00 1.40
4946 6184 3.359950 ACTACTCCCTCCGTTCGTAAAT 58.640 45.455 0.00 0.00 0.00 1.40
4947 6185 2.795329 ACTACTCCCTCCGTTCGTAAA 58.205 47.619 0.00 0.00 0.00 2.01
4948 6186 2.496899 ACTACTCCCTCCGTTCGTAA 57.503 50.000 0.00 0.00 0.00 3.18
4949 6187 2.766263 TCTACTACTCCCTCCGTTCGTA 59.234 50.000 0.00 0.00 0.00 3.43
4950 6188 1.556911 TCTACTACTCCCTCCGTTCGT 59.443 52.381 0.00 0.00 0.00 3.85
4951 6189 1.939255 GTCTACTACTCCCTCCGTTCG 59.061 57.143 0.00 0.00 0.00 3.95
4952 6190 2.996631 TGTCTACTACTCCCTCCGTTC 58.003 52.381 0.00 0.00 0.00 3.95
4953 6191 3.354467 CTTGTCTACTACTCCCTCCGTT 58.646 50.000 0.00 0.00 0.00 4.44
4954 6192 2.356947 CCTTGTCTACTACTCCCTCCGT 60.357 54.545 0.00 0.00 0.00 4.69
4955 6193 2.299521 CCTTGTCTACTACTCCCTCCG 58.700 57.143 0.00 0.00 0.00 4.63
4956 6194 3.385314 ACCTTGTCTACTACTCCCTCC 57.615 52.381 0.00 0.00 0.00 4.30
4957 6195 4.165758 TCCTACCTTGTCTACTACTCCCTC 59.834 50.000 0.00 0.00 0.00 4.30
4958 6196 4.117632 TCCTACCTTGTCTACTACTCCCT 58.882 47.826 0.00 0.00 0.00 4.20
4959 6197 4.516652 TCCTACCTTGTCTACTACTCCC 57.483 50.000 0.00 0.00 0.00 4.30
4960 6198 4.888823 CCTTCCTACCTTGTCTACTACTCC 59.111 50.000 0.00 0.00 0.00 3.85
4961 6199 5.508567 ACCTTCCTACCTTGTCTACTACTC 58.491 45.833 0.00 0.00 0.00 2.59
4962 6200 5.533333 ACCTTCCTACCTTGTCTACTACT 57.467 43.478 0.00 0.00 0.00 2.57
4963 6201 7.894753 ATTACCTTCCTACCTTGTCTACTAC 57.105 40.000 0.00 0.00 0.00 2.73
5215 6498 3.474570 AGCGCCTCATCCAGGGAC 61.475 66.667 2.29 0.00 43.70 4.46
5224 6507 3.226429 GACCACAGTCAGCGCCTCA 62.226 63.158 2.29 0.00 42.99 3.86
5251 6534 1.202592 TGAGAGATCTCCTCCTCGTCG 60.203 57.143 19.30 0.00 42.97 5.12
5257 6540 2.857483 TCGATGTGAGAGATCTCCTCC 58.143 52.381 19.30 9.44 42.97 4.30
5371 6654 1.493871 AGCTTAGGCAGGAATGAGCAT 59.506 47.619 0.00 0.00 41.70 3.79
5375 6658 3.439857 ACAAAGCTTAGGCAGGAATGA 57.560 42.857 0.00 0.00 41.70 2.57
5379 6662 3.197116 GGTACTACAAAGCTTAGGCAGGA 59.803 47.826 0.00 0.00 41.70 3.86
5515 6798 5.641209 AGATGATAATATCACCTTGAAGCGC 59.359 40.000 4.93 0.00 43.01 5.92
5588 6871 1.668919 GCCCAAAACGCTCCTTTAAGC 60.669 52.381 0.00 0.00 38.97 3.09
5590 6873 1.989706 AGCCCAAAACGCTCCTTTAA 58.010 45.000 0.00 0.00 0.00 1.52
5594 6877 0.618458 TCATAGCCCAAAACGCTCCT 59.382 50.000 0.00 0.00 37.79 3.69
5598 6881 2.943033 ACACTATCATAGCCCAAAACGC 59.057 45.455 0.00 0.00 0.00 4.84
5609 6892 8.046708 AGGTAGTGATGCAAAAACACTATCATA 58.953 33.333 24.50 9.26 45.20 2.15
5614 6897 5.278266 GCAAGGTAGTGATGCAAAAACACTA 60.278 40.000 16.54 16.54 43.27 2.74
5630 6914 4.479619 GAGCAATGTTTTCAGCAAGGTAG 58.520 43.478 0.00 0.00 0.00 3.18
5643 6927 6.313905 CCTGAAGATAAAGTACGAGCAATGTT 59.686 38.462 0.00 0.00 0.00 2.71
5644 6928 5.812642 CCTGAAGATAAAGTACGAGCAATGT 59.187 40.000 0.00 0.00 0.00 2.71
5696 6980 1.003839 GCCGTCACTGGATCCAACA 60.004 57.895 17.00 0.00 0.00 3.33
5706 6990 4.988598 CCAAGTGCCGCCGTCACT 62.989 66.667 0.00 0.00 45.83 3.41
5718 7010 1.270678 GGAAGCGAACTACACCCAAGT 60.271 52.381 0.00 0.00 0.00 3.16
5725 7017 0.895530 CCTCCAGGAAGCGAACTACA 59.104 55.000 0.00 0.00 37.39 2.74
5780 7721 1.721489 CGATCAAAACAGCGACCAACG 60.721 52.381 0.00 0.00 45.66 4.10
5821 8367 0.895530 CCGAAACTCTGCCTAGGTGA 59.104 55.000 11.31 8.44 0.00 4.02
5858 8404 4.081752 ACACAAAGAATCACACTGCCAAAA 60.082 37.500 0.00 0.00 0.00 2.44
5863 8409 3.365832 CACACACAAAGAATCACACTGC 58.634 45.455 0.00 0.00 0.00 4.40
5953 8499 9.314321 CAGACACTACTAATACCCAGTAATTTG 57.686 37.037 0.00 0.00 0.00 2.32
5976 8522 9.161629 CAAAGTGTGATTATATTGGTACACAGA 57.838 33.333 0.00 0.00 39.29 3.41
5977 8523 8.946085 ACAAAGTGTGATTATATTGGTACACAG 58.054 33.333 0.00 0.00 39.29 3.66
6003 8549 2.023673 CCTTGCCGCTGGATTAAATGA 58.976 47.619 0.00 0.00 0.00 2.57
6039 8585 0.678950 GGGCTGGCTTTTTGTTGCTA 59.321 50.000 0.00 0.00 0.00 3.49
6058 8604 0.389948 ACACTTAAGAAGGCCTCGCG 60.390 55.000 5.23 0.00 0.00 5.87
6076 8622 1.859080 GTGTTAGCGATCGATGGGAAC 59.141 52.381 21.57 14.69 0.00 3.62
6078 8624 0.030235 CGTGTTAGCGATCGATGGGA 59.970 55.000 21.57 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.