Multiple sequence alignment - TraesCS5D01G312200

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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 TraesCS5D01G312200 chr5D 100.000 5695 0 0 1 5695 408299619 408305313 0.000000e+00 10517.0
1 TraesCS5D01G312200 chr5B 91.027 2619 158 32 1 2559 489611545 489614146 0.000000e+00 3463.0
2 TraesCS5D01G312200 chr5B 91.825 1737 99 22 3290 5002 489614894 489616611 0.000000e+00 2381.0
3 TraesCS5D01G312200 chr5B 94.747 514 24 2 2683 3193 489614140 489614653 0.000000e+00 797.0
4 TraesCS5D01G312200 chr5B 90.411 365 31 4 5219 5580 489616615 489616978 1.440000e-130 477.0
5 TraesCS5D01G312200 chr5B 93.274 223 11 3 5002 5220 184283965 184284187 5.500000e-85 326.0
6 TraesCS5D01G312200 chr5B 92.241 232 12 5 5003 5230 270054065 270053836 1.980000e-84 324.0
7 TraesCS5D01G312200 chr5B 91.489 235 14 5 5000 5230 421542777 421543009 9.210000e-83 318.0
8 TraesCS5D01G312200 chr5B 97.403 77 1 1 3431 3507 489617179 489617104 4.630000e-26 130.0
9 TraesCS5D01G312200 chr5A 92.687 1805 104 15 1507 3294 514093168 514094961 0.000000e+00 2577.0
10 TraesCS5D01G312200 chr5A 95.356 1615 63 9 3397 5004 514095076 514096685 0.000000e+00 2556.0
11 TraesCS5D01G312200 chr5A 88.867 1527 110 26 2 1517 514091421 514092898 0.000000e+00 1823.0
12 TraesCS5D01G312200 chr5A 88.410 673 62 9 2 668 514040071 514040733 0.000000e+00 797.0
13 TraesCS5D01G312200 chr5A 86.991 638 80 3 2627 3264 548605212 548605846 0.000000e+00 715.0
14 TraesCS5D01G312200 chr5A 92.105 494 26 5 5215 5695 514096683 514097176 0.000000e+00 684.0
15 TraesCS5D01G312200 chr5A 80.317 442 61 14 3291 3724 548606290 548606713 1.540000e-80 311.0
16 TraesCS5D01G312200 chr3A 94.118 221 9 3 5001 5217 535225743 535225523 3.290000e-87 333.0
17 TraesCS5D01G312200 chr2D 94.091 220 9 3 5002 5217 293524835 293525054 1.180000e-86 331.0
18 TraesCS5D01G312200 chr2D 100.000 39 0 0 5652 5690 92913420 92913458 7.920000e-09 73.1
19 TraesCS5D01G312200 chr6B 94.064 219 9 3 5003 5217 623382001 623382219 4.250000e-86 329.0
20 TraesCS5D01G312200 chr2A 94.064 219 9 3 5003 5217 258346747 258346965 4.250000e-86 329.0
21 TraesCS5D01G312200 chr2A 79.564 367 51 14 1397 1746 296494544 296494903 2.050000e-59 241.0
22 TraesCS5D01G312200 chr7B 91.667 240 13 6 5000 5235 692158948 692159184 5.500000e-85 326.0
23 TraesCS5D01G312200 chr7B 86.765 68 9 0 1545 1612 229869500 229869567 6.120000e-10 76.8
24 TraesCS5D01G312200 chr7D 91.845 233 13 5 5003 5231 5480152 5479922 2.560000e-83 320.0
25 TraesCS5D01G312200 chr7D 87.692 65 8 0 1539 1603 252557279 252557343 6.120000e-10 76.8
26 TraesCS5D01G312200 chr4A 79.564 367 51 12 1397 1746 525579058 525578699 2.050000e-59 241.0
27 TraesCS5D01G312200 chr3B 79.235 366 56 13 1397 1746 341297037 341296676 2.650000e-58 237.0
28 TraesCS5D01G312200 chr6A 78.630 365 58 12 1397 1746 462412398 462412039 2.060000e-54 224.0
29 TraesCS5D01G312200 chr7A 86.486 74 10 0 1539 1612 267433199 267433126 1.320000e-11 82.4


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 TraesCS5D01G312200 chr5D 408299619 408305313 5694 False 10517.0 10517 100.00000 1 5695 1 chr5D.!!$F1 5694
1 TraesCS5D01G312200 chr5B 489611545 489616978 5433 False 1779.5 3463 92.00250 1 5580 4 chr5B.!!$F3 5579
2 TraesCS5D01G312200 chr5A 514091421 514097176 5755 False 1910.0 2577 92.25375 2 5695 4 chr5A.!!$F2 5693
3 TraesCS5D01G312200 chr5A 514040071 514040733 662 False 797.0 797 88.41000 2 668 1 chr5A.!!$F1 666
4 TraesCS5D01G312200 chr5A 548605212 548606713 1501 False 513.0 715 83.65400 2627 3724 2 chr5A.!!$F3 1097

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
909 947 0.603569 GCAGAGAAGACCGAAGACCA 59.396 55.000 0.0 0.0 0.00 4.02 F
1148 1193 0.251165 TTGCTTCCCCAGTAGTTGGC 60.251 55.000 0.0 0.0 46.32 4.52 F
1558 1886 1.383803 GGGGATGGAGAGGCAGTCT 60.384 63.158 0.0 0.0 38.71 3.24 F
2604 2964 1.843851 TGGAGGAGAACAAACCACAGT 59.156 47.619 0.0 0.0 0.00 3.55 F
3767 4670 0.734942 ACTCCAATACCGTTGTCGCG 60.735 55.000 0.0 0.0 35.54 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2572 2932 1.639108 TCTCCTCCACTGCCTACTACA 59.361 52.381 0.00 0.00 0.00 2.74 R
3037 3399 0.809241 CTGAGACATCGGGCTTCAGC 60.809 60.000 0.00 0.00 41.14 4.26 R
3094 3456 1.442520 CTTCCGCGTTGCAACATGG 60.443 57.895 28.01 25.94 0.00 3.66 R
4466 5371 0.239347 CTTGTGCAAAGGAGGCTTCG 59.761 55.000 0.00 0.00 0.00 3.79 R
5217 6147 0.039618 TGGGGATTTGGAAGGAGTGC 59.960 55.000 0.00 0.00 0.00 4.40 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
112 118 6.925610 TTTTAGAAGGAATCCATCGATGTG 57.074 37.500 23.27 14.77 0.00 3.21
122 128 5.720371 ATCCATCGATGTGAAAAACCAAA 57.280 34.783 23.27 0.00 0.00 3.28
171 178 4.404507 TTTCTTTTGGAGAAATCGCTCG 57.595 40.909 0.00 0.00 46.69 5.03
239 246 1.374758 CCACGCAGACAGAGGAACC 60.375 63.158 0.00 0.00 0.00 3.62
287 294 4.157289 GGTCTCAAACATTGATGCTCACAT 59.843 41.667 0.00 0.00 39.30 3.21
294 301 6.519679 AACATTGATGCTCACATACATTGT 57.480 33.333 0.00 0.00 39.91 2.71
401 408 2.722094 TGATTATGGTGCCTGGAACAC 58.278 47.619 7.23 1.33 37.31 3.32
523 535 5.001232 TGTTACAGGTGAAATGCTTAGGTC 58.999 41.667 0.00 0.00 0.00 3.85
529 566 5.922544 CAGGTGAAATGCTTAGGTCTTTTTG 59.077 40.000 0.00 0.00 0.00 2.44
536 573 8.962884 AAATGCTTAGGTCTTTTTGTTCAATT 57.037 26.923 0.00 0.00 0.00 2.32
641 679 8.819974 GGACAAATATTAGCATTCCACAAATTG 58.180 33.333 0.00 0.00 0.00 2.32
653 691 6.968263 TTCCACAAATTGAACCATCACTTA 57.032 33.333 0.00 0.00 34.61 2.24
663 701 2.632377 ACCATCACTTATGTGGCGAAG 58.368 47.619 8.74 0.00 43.94 3.79
679 717 6.151985 TGTGGCGAAGAATAAACATAAATGGT 59.848 34.615 0.00 0.00 0.00 3.55
680 718 6.472163 GTGGCGAAGAATAAACATAAATGGTG 59.528 38.462 0.00 0.00 0.00 4.17
683 721 5.977129 CGAAGAATAAACATAAATGGTGCCC 59.023 40.000 0.00 0.00 0.00 5.36
692 730 4.949856 ACATAAATGGTGCCCTAGAAAGTG 59.050 41.667 0.00 0.00 0.00 3.16
717 755 2.430332 GAGACAGTAGCTCTTGCATCCT 59.570 50.000 0.00 0.00 42.74 3.24
720 758 2.770802 ACAGTAGCTCTTGCATCCTCAT 59.229 45.455 0.00 0.00 42.74 2.90
764 802 3.214328 TGAAGGAAGAACAGGTCAAAGC 58.786 45.455 0.00 0.00 0.00 3.51
772 810 6.599638 GGAAGAACAGGTCAAAGCTATATGTT 59.400 38.462 0.00 0.00 32.46 2.71
797 835 7.496346 TTTGGTCATCTAGTCCAGAGTAAAT 57.504 36.000 0.00 0.00 36.77 1.40
798 836 6.716934 TGGTCATCTAGTCCAGAGTAAATC 57.283 41.667 0.00 0.00 36.48 2.17
799 837 6.194967 TGGTCATCTAGTCCAGAGTAAATCA 58.805 40.000 0.00 0.00 36.48 2.57
800 838 6.841229 TGGTCATCTAGTCCAGAGTAAATCAT 59.159 38.462 0.00 0.00 36.48 2.45
801 839 8.004801 TGGTCATCTAGTCCAGAGTAAATCATA 58.995 37.037 0.00 0.00 36.48 2.15
878 916 2.157668 TCGCGTGAGAAAAAGATCAAGC 59.842 45.455 5.77 3.50 44.26 4.01
882 920 2.157668 GTGAGAAAAAGATCAAGCGCGA 59.842 45.455 12.10 0.00 0.00 5.87
909 947 0.603569 GCAGAGAAGACCGAAGACCA 59.396 55.000 0.00 0.00 0.00 4.02
910 948 1.670380 GCAGAGAAGACCGAAGACCAC 60.670 57.143 0.00 0.00 0.00 4.16
911 949 1.067495 CAGAGAAGACCGAAGACCACC 60.067 57.143 0.00 0.00 0.00 4.61
912 950 0.966920 GAGAAGACCGAAGACCACCA 59.033 55.000 0.00 0.00 0.00 4.17
913 951 1.343465 GAGAAGACCGAAGACCACCAA 59.657 52.381 0.00 0.00 0.00 3.67
1139 1184 1.925455 CTCCCCTCTTGCTTCCCCA 60.925 63.158 0.00 0.00 0.00 4.96
1148 1193 0.251165 TTGCTTCCCCAGTAGTTGGC 60.251 55.000 0.00 0.00 46.32 4.52
1191 1236 2.514458 TGGGATTTTTCCAGCTCTCC 57.486 50.000 0.00 0.00 0.00 3.71
1275 1323 1.600413 GCTGGTTGCTTCGTTTCTTGG 60.600 52.381 0.00 0.00 38.95 3.61
1276 1324 1.676006 CTGGTTGCTTCGTTTCTTGGT 59.324 47.619 0.00 0.00 0.00 3.67
1371 1419 3.642705 GGTGTTGCTGATTTTCTTGACC 58.357 45.455 0.00 0.00 0.00 4.02
1373 1421 3.319122 GTGTTGCTGATTTTCTTGACCCT 59.681 43.478 0.00 0.00 0.00 4.34
1375 1423 2.795329 TGCTGATTTTCTTGACCCTCC 58.205 47.619 0.00 0.00 0.00 4.30
1463 1511 6.817765 TTCCTCATCAATTTCAAGTGTACC 57.182 37.500 0.00 0.00 0.00 3.34
1464 1512 6.126863 TCCTCATCAATTTCAAGTGTACCT 57.873 37.500 0.00 0.00 0.00 3.08
1465 1513 5.939883 TCCTCATCAATTTCAAGTGTACCTG 59.060 40.000 0.00 0.00 0.00 4.00
1466 1514 5.124457 CCTCATCAATTTCAAGTGTACCTGG 59.876 44.000 0.00 0.00 0.00 4.45
1467 1515 5.875224 TCATCAATTTCAAGTGTACCTGGA 58.125 37.500 0.00 0.00 0.00 3.86
1468 1516 5.705441 TCATCAATTTCAAGTGTACCTGGAC 59.295 40.000 0.00 0.00 0.00 4.02
1469 1517 5.304686 TCAATTTCAAGTGTACCTGGACT 57.695 39.130 0.00 0.00 0.00 3.85
1520 1848 5.841957 AGAACAAGATCTTGCAGTTTTGT 57.158 34.783 30.95 15.49 44.03 2.83
1526 1854 8.396272 ACAAGATCTTGCAGTTTTGTATACTT 57.604 30.769 30.95 6.79 44.03 2.24
1558 1886 1.383803 GGGGATGGAGAGGCAGTCT 60.384 63.158 0.00 0.00 38.71 3.24
1976 2304 4.999310 TCTGGGTTAGTTCTCTTCTCTGA 58.001 43.478 0.00 0.00 0.00 3.27
2038 2374 2.628178 TGGTCACGATGAACTCTGTCTT 59.372 45.455 0.00 0.00 34.53 3.01
2093 2429 8.825745 GTTTGAACCTTGAATTGCAATTCTTTA 58.174 29.630 38.33 26.67 43.97 1.85
2112 2448 2.727123 AAGTGTGTGGATGTGGTGAA 57.273 45.000 0.00 0.00 0.00 3.18
2113 2449 2.957402 AGTGTGTGGATGTGGTGAAT 57.043 45.000 0.00 0.00 0.00 2.57
2131 2467 5.404946 GTGAATTGATCAGTGGAACCATTG 58.595 41.667 9.56 9.56 39.19 2.82
2299 2635 7.430502 GCTAGAGCATTTACTTGTGCATTAAAG 59.569 37.037 0.00 0.00 43.63 1.85
2418 2762 7.068593 ACCATGGATTCACAGTTTTATGTATGG 59.931 37.037 21.47 0.00 37.63 2.74
2466 2810 2.040947 TGTATCCAAACCAGTGCATCCA 59.959 45.455 0.00 0.00 0.00 3.41
2508 2852 7.412853 AGATAATGAAATGTTGCTTCATCGTC 58.587 34.615 0.00 1.96 41.56 4.20
2512 2856 4.218200 TGAAATGTTGCTTCATCGTCCATT 59.782 37.500 0.00 0.00 0.00 3.16
2514 2858 4.789012 ATGTTGCTTCATCGTCCATTTT 57.211 36.364 0.00 0.00 0.00 1.82
2517 2861 5.639757 TGTTGCTTCATCGTCCATTTTATG 58.360 37.500 0.00 0.00 0.00 1.90
2559 2919 4.032786 GTGTTGAAACAAACCAACTCATGC 59.967 41.667 0.00 0.00 42.16 4.06
2569 2929 6.534793 ACAAACCAACTCATGCAACTTTTAAG 59.465 34.615 0.00 0.00 0.00 1.85
2570 2930 6.463995 AACCAACTCATGCAACTTTTAAGA 57.536 33.333 0.00 0.00 0.00 2.10
2571 2931 5.831997 ACCAACTCATGCAACTTTTAAGAC 58.168 37.500 0.00 0.00 0.00 3.01
2572 2932 5.594317 ACCAACTCATGCAACTTTTAAGACT 59.406 36.000 0.00 0.00 0.00 3.24
2573 2933 5.916883 CCAACTCATGCAACTTTTAAGACTG 59.083 40.000 0.00 0.00 0.00 3.51
2593 2953 2.042569 TGTAGTAGGCAGTGGAGGAGAA 59.957 50.000 0.00 0.00 0.00 2.87
2602 2962 2.341846 GTGGAGGAGAACAAACCACA 57.658 50.000 0.00 0.00 46.75 4.17
2604 2964 1.843851 TGGAGGAGAACAAACCACAGT 59.156 47.619 0.00 0.00 0.00 3.55
2699 3061 9.646427 GTCATTTAGACTCATATAGATGTTCCC 57.354 37.037 0.00 0.00 44.09 3.97
2700 3062 8.816894 TCATTTAGACTCATATAGATGTTCCCC 58.183 37.037 0.00 0.00 34.41 4.81
2707 3069 5.376625 TCATATAGATGTTCCCCACTTTGC 58.623 41.667 0.00 0.00 34.41 3.68
3004 3366 2.177531 GCACTGCACATGGCTTCG 59.822 61.111 0.00 0.00 45.15 3.79
3037 3399 2.228103 TGCTGAAATTCTGCTTGAGCTG 59.772 45.455 22.04 4.07 41.21 4.24
3094 3456 1.303643 CAAGGGGAACAGGGCACTC 60.304 63.158 0.00 0.00 0.00 3.51
3128 3490 3.283751 CGGAAGGGCAATACCATTGTAA 58.716 45.455 1.24 0.00 44.17 2.41
3151 3513 9.255304 GTAAGTTCTCATATCTCAGAAACATCC 57.745 37.037 0.00 0.00 30.38 3.51
3196 3561 8.430063 TCTTTCTTCACGTGTTAATAATTCGTC 58.570 33.333 16.51 0.00 32.47 4.20
3201 3566 6.290643 TCACGTGTTAATAATTCGTCGTTTG 58.709 36.000 16.51 0.00 32.47 2.93
3203 3568 5.074134 CGTGTTAATAATTCGTCGTTTGCA 58.926 37.500 0.00 0.00 0.00 4.08
3204 3569 5.560751 CGTGTTAATAATTCGTCGTTTGCAA 59.439 36.000 0.00 0.00 0.00 4.08
3205 3570 6.085198 CGTGTTAATAATTCGTCGTTTGCAAA 59.915 34.615 8.05 8.05 0.00 3.68
3214 3689 7.630470 ATTCGTCGTTTGCAAAATTATTTCA 57.370 28.000 14.67 0.00 0.00 2.69
3227 3702 9.768662 GCAAAATTATTTCATGTCCATCCTATT 57.231 29.630 0.00 0.00 0.00 1.73
3276 3751 4.141883 GCAATGCTGCGTGTTCTG 57.858 55.556 0.00 0.00 39.20 3.02
3329 4228 9.626045 CATAAACTTAGAAAACCATGAAGTTCC 57.374 33.333 0.00 0.00 38.94 3.62
3333 4232 6.833933 ACTTAGAAAACCATGAAGTTCCAAGT 59.166 34.615 0.00 2.63 0.00 3.16
3336 4235 5.770162 AGAAAACCATGAAGTTCCAAGTAGG 59.230 40.000 0.00 0.00 39.47 3.18
3339 4238 5.061721 ACCATGAAGTTCCAAGTAGGTTT 57.938 39.130 0.00 0.00 39.02 3.27
3352 4251 8.173542 TCCAAGTAGGTTTAACCAGAATTTTC 57.826 34.615 17.10 0.00 41.95 2.29
3353 4252 8.002459 TCCAAGTAGGTTTAACCAGAATTTTCT 58.998 33.333 17.10 0.00 41.95 2.52
3358 4257 7.290110 AGGTTTAACCAGAATTTTCTTGGAG 57.710 36.000 17.10 0.00 41.95 3.86
3393 4292 8.644374 TGTACTTAGCCATTTAGGAATTTTGT 57.356 30.769 0.00 0.00 41.22 2.83
3409 4308 8.149647 AGGAATTTTGTTTCATAACTTGCATCA 58.850 29.630 0.00 0.00 35.24 3.07
3554 4457 2.028112 AGAGCTTGTTAACATCCTGCGA 60.028 45.455 9.56 0.00 0.00 5.10
3563 4466 0.904865 ACATCCTGCGAGAGGTTGGA 60.905 55.000 13.60 0.00 43.54 3.53
3566 4469 2.581354 CTGCGAGAGGTTGGAGGG 59.419 66.667 0.00 0.00 0.00 4.30
3767 4670 0.734942 ACTCCAATACCGTTGTCGCG 60.735 55.000 0.00 0.00 35.54 5.87
3779 4682 1.997606 GTTGTCGCGGTACTTATTGCT 59.002 47.619 6.13 0.00 0.00 3.91
3782 4685 2.122564 GTCGCGGTACTTATTGCTACC 58.877 52.381 6.13 0.00 0.00 3.18
3842 4745 3.445008 TCTGGAGAGTATGGACAAAGCT 58.555 45.455 0.00 0.00 0.00 3.74
3859 4762 2.355717 GCTACTGAGCCCGATATGAC 57.644 55.000 0.00 0.00 43.49 3.06
3938 4841 3.697190 TCCCTGGCTCTCTTTATCTCT 57.303 47.619 0.00 0.00 0.00 3.10
3971 4874 1.135333 GTCGTCCAGACTTCCCTGATC 59.865 57.143 0.00 0.00 46.13 2.92
4457 5362 6.257411 GCAGCTGTATGTATCATGGATGTATC 59.743 42.308 16.64 0.00 0.00 2.24
4460 5365 8.911965 AGCTGTATGTATCATGGATGTATCTAG 58.088 37.037 0.00 0.00 0.00 2.43
4462 5367 8.539117 TGTATGTATCATGGATGTATCTAGGG 57.461 38.462 0.00 0.00 0.00 3.53
4463 5368 5.939764 TGTATCATGGATGTATCTAGGGC 57.060 43.478 0.00 0.00 0.00 5.19
4464 5369 4.716784 TGTATCATGGATGTATCTAGGGCC 59.283 45.833 0.00 0.00 0.00 5.80
4465 5370 2.551270 TCATGGATGTATCTAGGGCCC 58.449 52.381 16.46 16.46 0.00 5.80
4466 5371 1.561542 CATGGATGTATCTAGGGCCCC 59.438 57.143 21.43 1.37 0.00 5.80
4485 5395 0.239347 CGAAGCCTCCTTTGCACAAG 59.761 55.000 0.00 0.00 0.00 3.16
4573 5485 8.103660 AGGCACTATATATAGGAGTAGTAGCA 57.896 38.462 21.20 0.00 36.02 3.49
4574 5486 7.994334 AGGCACTATATATAGGAGTAGTAGCAC 59.006 40.741 21.20 8.03 36.02 4.40
4883 5807 6.211515 GTTGACATGAGAAAGCAAGAACAAT 58.788 36.000 0.00 0.00 0.00 2.71
4897 5821 6.770076 GCAAGAACAATTTTTGCAACTGTTA 58.230 32.000 0.00 0.00 44.88 2.41
4899 5823 7.216130 GCAAGAACAATTTTTGCAACTGTTAAC 59.784 33.333 0.00 0.00 44.88 2.01
4940 5865 0.604780 ACACAGCGATTGAGCAGCTT 60.605 50.000 0.00 0.00 39.48 3.74
4941 5866 0.520404 CACAGCGATTGAGCAGCTTT 59.480 50.000 0.00 0.00 39.48 3.51
4942 5867 0.801251 ACAGCGATTGAGCAGCTTTC 59.199 50.000 0.00 0.00 39.48 2.62
4943 5868 0.800631 CAGCGATTGAGCAGCTTTCA 59.199 50.000 0.00 0.00 39.48 2.69
4944 5869 1.400846 CAGCGATTGAGCAGCTTTCAT 59.599 47.619 0.00 0.00 39.48 2.57
4983 5913 4.215399 TGCCTTTTATTGTCTGAACGGAAG 59.785 41.667 0.00 0.00 0.00 3.46
4985 5915 5.001232 CCTTTTATTGTCTGAACGGAAGGA 58.999 41.667 0.00 0.00 34.49 3.36
4986 5916 5.648092 CCTTTTATTGTCTGAACGGAAGGAT 59.352 40.000 0.00 0.00 34.49 3.24
5004 5934 6.294010 GGAAGGATGTCAAAACTTTCAGGTAC 60.294 42.308 0.00 0.00 0.00 3.34
5005 5935 5.941788 AGGATGTCAAAACTTTCAGGTACT 58.058 37.500 0.00 0.00 43.88 2.73
5006 5936 7.074653 AGGATGTCAAAACTTTCAGGTACTA 57.925 36.000 0.00 0.00 36.02 1.82
5007 5937 6.935208 AGGATGTCAAAACTTTCAGGTACTAC 59.065 38.462 0.00 0.00 36.02 2.73
5008 5938 6.148976 GGATGTCAAAACTTTCAGGTACTACC 59.851 42.308 0.00 0.00 36.02 3.18
5021 5951 3.813443 GGTACTACCTCCGTCTATGTGA 58.187 50.000 0.00 0.00 34.73 3.58
5022 5952 3.814283 GGTACTACCTCCGTCTATGTGAG 59.186 52.174 0.00 0.00 34.73 3.51
5023 5953 3.648507 ACTACCTCCGTCTATGTGAGT 57.351 47.619 0.00 0.00 0.00 3.41
5024 5954 4.767578 ACTACCTCCGTCTATGTGAGTA 57.232 45.455 0.00 0.00 0.00 2.59
5025 5955 5.108187 ACTACCTCCGTCTATGTGAGTAA 57.892 43.478 0.00 0.00 0.00 2.24
5026 5956 5.124645 ACTACCTCCGTCTATGTGAGTAAG 58.875 45.833 0.00 0.00 0.00 2.34
5027 5957 3.965694 ACCTCCGTCTATGTGAGTAAGT 58.034 45.455 0.00 0.00 0.00 2.24
5028 5958 3.946558 ACCTCCGTCTATGTGAGTAAGTC 59.053 47.826 0.00 0.00 0.00 3.01
5029 5959 3.945921 CCTCCGTCTATGTGAGTAAGTCA 59.054 47.826 0.00 0.00 0.00 3.41
5030 5960 4.580995 CCTCCGTCTATGTGAGTAAGTCAT 59.419 45.833 0.00 0.00 37.56 3.06
5031 5961 5.067936 CCTCCGTCTATGTGAGTAAGTCATT 59.932 44.000 0.00 0.00 37.56 2.57
5032 5962 6.132791 TCCGTCTATGTGAGTAAGTCATTC 57.867 41.667 0.00 0.00 37.56 2.67
5033 5963 4.970611 CCGTCTATGTGAGTAAGTCATTCG 59.029 45.833 0.00 0.00 37.56 3.34
5034 5964 4.438145 CGTCTATGTGAGTAAGTCATTCGC 59.562 45.833 0.00 0.00 37.56 4.70
5035 5965 4.438145 GTCTATGTGAGTAAGTCATTCGCG 59.562 45.833 0.00 0.00 37.56 5.87
5036 5966 2.717580 TGTGAGTAAGTCATTCGCGT 57.282 45.000 5.77 0.00 37.56 6.01
5037 5967 3.835378 TGTGAGTAAGTCATTCGCGTA 57.165 42.857 5.77 0.00 37.56 4.42
5038 5968 3.754955 TGTGAGTAAGTCATTCGCGTAG 58.245 45.455 5.77 0.00 37.56 3.51
5039 5969 3.189910 TGTGAGTAAGTCATTCGCGTAGT 59.810 43.478 5.77 0.00 37.56 2.73
5040 5970 4.164294 GTGAGTAAGTCATTCGCGTAGTT 58.836 43.478 5.77 2.59 37.56 2.24
5041 5971 4.620184 GTGAGTAAGTCATTCGCGTAGTTT 59.380 41.667 5.77 0.00 37.56 2.66
5042 5972 5.118203 GTGAGTAAGTCATTCGCGTAGTTTT 59.882 40.000 5.77 0.00 37.56 2.43
5043 5973 6.306356 GTGAGTAAGTCATTCGCGTAGTTTTA 59.694 38.462 5.77 0.00 37.56 1.52
5044 5974 6.525628 TGAGTAAGTCATTCGCGTAGTTTTAG 59.474 38.462 5.77 0.00 0.00 1.85
5045 5975 6.615088 AGTAAGTCATTCGCGTAGTTTTAGA 58.385 36.000 5.77 0.00 0.00 2.10
5046 5976 7.256286 AGTAAGTCATTCGCGTAGTTTTAGAT 58.744 34.615 5.77 0.00 0.00 1.98
5047 5977 6.570690 AAGTCATTCGCGTAGTTTTAGATC 57.429 37.500 5.77 0.00 0.00 2.75
5048 5978 5.647589 AGTCATTCGCGTAGTTTTAGATCA 58.352 37.500 5.77 0.00 0.00 2.92
5049 5979 6.273825 AGTCATTCGCGTAGTTTTAGATCAT 58.726 36.000 5.77 0.00 0.00 2.45
5050 5980 6.418226 AGTCATTCGCGTAGTTTTAGATCATC 59.582 38.462 5.77 0.00 0.00 2.92
5051 5981 5.398416 TCATTCGCGTAGTTTTAGATCATCG 59.602 40.000 5.77 0.00 0.00 3.84
5052 5982 4.541085 TCGCGTAGTTTTAGATCATCGA 57.459 40.909 5.77 0.00 0.00 3.59
5053 5983 5.104562 TCGCGTAGTTTTAGATCATCGAT 57.895 39.130 5.77 0.00 0.00 3.59
5054 5984 5.516996 TCGCGTAGTTTTAGATCATCGATT 58.483 37.500 5.77 0.00 0.00 3.34
5055 5985 5.975344 TCGCGTAGTTTTAGATCATCGATTT 59.025 36.000 5.77 0.00 0.00 2.17
5056 5986 6.058905 CGCGTAGTTTTAGATCATCGATTTG 58.941 40.000 0.00 0.00 0.00 2.32
5057 5987 6.075046 CGCGTAGTTTTAGATCATCGATTTGA 60.075 38.462 0.00 0.00 0.00 2.69
5058 5988 7.277205 GCGTAGTTTTAGATCATCGATTTGAG 58.723 38.462 0.00 0.00 0.00 3.02
5059 5989 7.567771 GCGTAGTTTTAGATCATCGATTTGAGG 60.568 40.741 0.00 0.00 0.00 3.86
5060 5990 6.610741 AGTTTTAGATCATCGATTTGAGGC 57.389 37.500 0.00 0.00 0.00 4.70
5061 5991 6.115446 AGTTTTAGATCATCGATTTGAGGCA 58.885 36.000 0.00 0.00 0.00 4.75
5062 5992 6.769822 AGTTTTAGATCATCGATTTGAGGCAT 59.230 34.615 0.00 0.00 0.00 4.40
5063 5993 7.284034 AGTTTTAGATCATCGATTTGAGGCATT 59.716 33.333 0.00 0.00 0.00 3.56
5064 5994 8.559536 GTTTTAGATCATCGATTTGAGGCATTA 58.440 33.333 0.00 0.00 0.00 1.90
5065 5995 8.675705 TTTAGATCATCGATTTGAGGCATTAA 57.324 30.769 0.00 0.00 0.00 1.40
5066 5996 8.675705 TTAGATCATCGATTTGAGGCATTAAA 57.324 30.769 0.00 0.00 0.00 1.52
5067 5997 7.756395 AGATCATCGATTTGAGGCATTAAAT 57.244 32.000 0.27 0.27 0.00 1.40
5068 5998 8.853077 AGATCATCGATTTGAGGCATTAAATA 57.147 30.769 0.74 0.00 0.00 1.40
5069 5999 9.458727 AGATCATCGATTTGAGGCATTAAATAT 57.541 29.630 0.74 0.00 0.00 1.28
5070 6000 9.499585 GATCATCGATTTGAGGCATTAAATATG 57.500 33.333 0.74 3.57 0.00 1.78
5071 6001 8.394971 TCATCGATTTGAGGCATTAAATATGT 57.605 30.769 0.74 0.00 0.00 2.29
5072 6002 8.291740 TCATCGATTTGAGGCATTAAATATGTG 58.708 33.333 0.74 1.73 0.00 3.21
5073 6003 7.566760 TCGATTTGAGGCATTAAATATGTGT 57.433 32.000 0.74 0.00 0.00 3.72
5074 6004 7.995289 TCGATTTGAGGCATTAAATATGTGTT 58.005 30.769 0.74 0.00 0.00 3.32
5075 6005 9.114952 TCGATTTGAGGCATTAAATATGTGTTA 57.885 29.630 0.74 0.00 0.00 2.41
5076 6006 9.897744 CGATTTGAGGCATTAAATATGTGTTAT 57.102 29.630 0.74 0.00 0.00 1.89
5113 6043 9.570468 AAGTATATCACTAGATTTCTACACGGA 57.430 33.333 0.00 0.00 36.04 4.69
5114 6044 9.742144 AGTATATCACTAGATTTCTACACGGAT 57.258 33.333 0.00 0.00 34.98 4.18
5115 6045 9.776158 GTATATCACTAGATTTCTACACGGATG 57.224 37.037 0.00 0.00 35.67 3.51
5116 6046 6.716934 ATCACTAGATTTCTACACGGATGT 57.283 37.500 0.00 0.00 43.30 3.06
5117 6047 7.818997 ATCACTAGATTTCTACACGGATGTA 57.181 36.000 0.00 0.00 40.48 2.29
5118 6048 9.000486 TATCACTAGATTTCTACACGGATGTAG 58.000 37.037 7.95 7.95 45.22 2.74
5182 6112 8.893219 TTAGATAGTTAAATCGTCGACCTAGA 57.107 34.615 10.58 1.59 0.00 2.43
5183 6113 7.798596 AGATAGTTAAATCGTCGACCTAGAA 57.201 36.000 10.58 0.00 0.00 2.10
5184 6114 7.638134 AGATAGTTAAATCGTCGACCTAGAAC 58.362 38.462 10.58 8.24 0.00 3.01
5185 6115 5.893897 AGTTAAATCGTCGACCTAGAACT 57.106 39.130 10.58 10.32 0.00 3.01
5186 6116 6.992063 AGTTAAATCGTCGACCTAGAACTA 57.008 37.500 10.58 0.00 0.00 2.24
5187 6117 6.780127 AGTTAAATCGTCGACCTAGAACTAC 58.220 40.000 10.58 0.00 0.00 2.73
5188 6118 3.940657 AATCGTCGACCTAGAACTACG 57.059 47.619 10.58 0.00 0.00 3.51
5189 6119 2.370281 TCGTCGACCTAGAACTACGT 57.630 50.000 10.58 0.00 0.00 3.57
5190 6120 1.995484 TCGTCGACCTAGAACTACGTG 59.005 52.381 10.58 0.00 0.00 4.49
5191 6121 1.995484 CGTCGACCTAGAACTACGTGA 59.005 52.381 10.58 0.00 0.00 4.35
5192 6122 2.413112 CGTCGACCTAGAACTACGTGAA 59.587 50.000 10.58 0.00 0.00 3.18
5193 6123 3.063180 CGTCGACCTAGAACTACGTGAAT 59.937 47.826 10.58 0.00 0.00 2.57
5194 6124 4.341099 GTCGACCTAGAACTACGTGAATG 58.659 47.826 3.51 0.00 0.00 2.67
5195 6125 4.093998 GTCGACCTAGAACTACGTGAATGA 59.906 45.833 3.51 0.00 0.00 2.57
5196 6126 4.093998 TCGACCTAGAACTACGTGAATGAC 59.906 45.833 0.00 0.00 0.00 3.06
5197 6127 4.094590 CGACCTAGAACTACGTGAATGACT 59.905 45.833 0.00 0.00 0.00 3.41
5198 6128 5.391736 CGACCTAGAACTACGTGAATGACTT 60.392 44.000 0.00 0.00 0.00 3.01
5199 6129 6.183360 CGACCTAGAACTACGTGAATGACTTA 60.183 42.308 0.00 0.00 0.00 2.24
5200 6130 6.850555 ACCTAGAACTACGTGAATGACTTAC 58.149 40.000 0.00 0.00 0.00 2.34
5201 6131 6.127786 ACCTAGAACTACGTGAATGACTTACC 60.128 42.308 0.00 0.00 0.00 2.85
5202 6132 5.979288 AGAACTACGTGAATGACTTACCT 57.021 39.130 0.00 0.00 0.00 3.08
5203 6133 6.342338 AGAACTACGTGAATGACTTACCTT 57.658 37.500 0.00 0.00 0.00 3.50
5204 6134 6.157211 AGAACTACGTGAATGACTTACCTTG 58.843 40.000 0.00 0.00 0.00 3.61
5205 6135 5.717078 ACTACGTGAATGACTTACCTTGA 57.283 39.130 0.00 0.00 0.00 3.02
5206 6136 5.467705 ACTACGTGAATGACTTACCTTGAC 58.532 41.667 0.00 0.00 0.00 3.18
5207 6137 3.314553 ACGTGAATGACTTACCTTGACG 58.685 45.455 0.00 0.00 38.86 4.35
5208 6138 2.666508 CGTGAATGACTTACCTTGACGG 59.333 50.000 0.00 0.00 32.62 4.79
5209 6139 3.613193 CGTGAATGACTTACCTTGACGGA 60.613 47.826 0.00 0.00 32.62 4.69
5210 6140 3.927142 GTGAATGACTTACCTTGACGGAG 59.073 47.826 0.00 0.00 36.31 4.63
5211 6141 3.056107 TGAATGACTTACCTTGACGGAGG 60.056 47.826 0.78 0.78 42.75 4.30
5225 6155 1.005687 ACGGAGGTAGTAGCACTCCTT 59.994 52.381 8.17 0.00 46.74 3.36
5243 6173 3.597868 TCCTTCCAAATCCCCAGAATTCT 59.402 43.478 0.88 0.88 0.00 2.40
5246 6176 5.957774 CCTTCCAAATCCCCAGAATTCTAAA 59.042 40.000 7.86 0.00 0.00 1.85
5247 6177 6.127338 CCTTCCAAATCCCCAGAATTCTAAAC 60.127 42.308 7.86 0.00 0.00 2.01
5321 6251 3.129502 CGTAGAGCGACCGGACCA 61.130 66.667 9.46 0.00 44.77 4.02
5345 6276 4.873129 CGGATCGTCAGCCGGTGG 62.873 72.222 1.90 0.00 43.67 4.61
5383 6314 2.159142 GCCAAATCAGATGCCAAGAAGG 60.159 50.000 0.00 0.00 41.84 3.46
5445 6376 1.827969 ACACCTACTGTCTCCATCTGC 59.172 52.381 0.00 0.00 0.00 4.26
5449 6380 2.382882 CTACTGTCTCCATCTGCTCCA 58.617 52.381 0.00 0.00 0.00 3.86
5458 6390 1.004044 CCATCTGCTCCAAGTTCCAGT 59.996 52.381 0.00 0.00 0.00 4.00
5589 6523 5.801380 TGTTACAAAAGATACACTCCCTCC 58.199 41.667 0.00 0.00 0.00 4.30
5594 6528 1.898902 AGATACACTCCCTCCGATCG 58.101 55.000 8.51 8.51 0.00 3.69
5616 6563 9.715121 GATCGTAAATAATTAGATGGGGTTGTA 57.285 33.333 0.00 0.00 0.00 2.41
5642 6589 7.315142 TGGAGCTGTTTGACATTTCATAAATC 58.685 34.615 0.00 0.00 0.00 2.17
5644 6591 7.699812 GGAGCTGTTTGACATTTCATAAATCTC 59.300 37.037 0.00 0.00 0.00 2.75
5662 6609 2.280592 ACTCGGTGCGAACCAACC 60.281 61.111 14.51 0.00 34.74 3.77
5691 6638 1.628846 GATGGTTAGGTGGACAGTGGT 59.371 52.381 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 118 2.272678 CCCCACACGTTTTGGTTTTTC 58.727 47.619 11.25 0.00 31.46 2.29
122 128 2.594592 GCAAGAGCCCCACACGTT 60.595 61.111 0.00 0.00 33.58 3.99
165 172 0.599991 AACATCACAAGTGCGAGCGA 60.600 50.000 0.00 0.00 0.00 4.93
171 178 2.749076 TGGCTATCAACATCACAAGTGC 59.251 45.455 0.00 0.00 0.00 4.40
239 246 2.126618 CAGTGGCACATGCTTGCG 60.127 61.111 21.41 0.00 44.52 4.85
287 294 1.700186 TGGTAGTGGTGGCACAATGTA 59.300 47.619 20.82 1.29 44.16 2.29
294 301 0.180642 TTCGTTTGGTAGTGGTGGCA 59.819 50.000 0.00 0.00 0.00 4.92
416 423 4.452455 AGCATTGAGTAGTGTTTTTCGGAG 59.548 41.667 0.00 0.00 0.00 4.63
501 513 5.246307 AGACCTAAGCATTTCACCTGTAAC 58.754 41.667 0.00 0.00 0.00 2.50
569 607 3.049912 GCGGGAAAAACAAGATGTTGTC 58.950 45.455 8.90 0.00 46.68 3.18
583 621 8.719560 AAAAATAACTTAGTTTTTGCGGGAAA 57.280 26.923 1.94 0.00 36.48 3.13
632 670 6.690530 ACATAAGTGATGGTTCAATTTGTGG 58.309 36.000 0.00 0.00 40.41 4.17
653 691 7.147915 ACCATTTATGTTTATTCTTCGCCACAT 60.148 33.333 0.00 0.00 0.00 3.21
679 717 2.567615 GTCTCTTCCACTTTCTAGGGCA 59.432 50.000 0.00 0.00 0.00 5.36
680 718 2.567615 TGTCTCTTCCACTTTCTAGGGC 59.432 50.000 0.00 0.00 0.00 5.19
683 721 5.417580 AGCTACTGTCTCTTCCACTTTCTAG 59.582 44.000 0.00 0.00 0.00 2.43
692 730 2.232452 TGCAAGAGCTACTGTCTCTTCC 59.768 50.000 8.36 2.02 46.01 3.46
754 792 6.924111 ACCAAAAACATATAGCTTTGACCTG 58.076 36.000 0.00 0.00 31.77 4.00
764 802 9.265901 CTGGACTAGATGACCAAAAACATATAG 57.734 37.037 0.00 0.00 41.27 1.31
772 810 6.928348 TTACTCTGGACTAGATGACCAAAA 57.072 37.500 0.00 0.00 39.78 2.44
878 916 2.263771 TTCTCTGCTCTGCTCTCGCG 62.264 60.000 0.00 0.00 39.65 5.87
882 920 1.185315 GGTCTTCTCTGCTCTGCTCT 58.815 55.000 0.00 0.00 0.00 4.09
892 930 1.258676 GGTGGTCTTCGGTCTTCTCT 58.741 55.000 0.00 0.00 0.00 3.10
909 947 1.619332 ACACGTTTGGTTTGGTTTGGT 59.381 42.857 0.00 0.00 0.00 3.67
910 948 1.996191 CACACGTTTGGTTTGGTTTGG 59.004 47.619 0.00 0.00 0.00 3.28
911 949 1.391826 GCACACGTTTGGTTTGGTTTG 59.608 47.619 3.53 0.00 0.00 2.93
912 950 1.715993 GCACACGTTTGGTTTGGTTT 58.284 45.000 3.53 0.00 0.00 3.27
913 951 0.456995 CGCACACGTTTGGTTTGGTT 60.457 50.000 3.53 0.00 33.53 3.67
1041 1085 3.407967 GGTCTCAATCCCCGGCCA 61.408 66.667 2.24 0.00 0.00 5.36
1263 1311 2.833794 TCCTCACACCAAGAAACGAAG 58.166 47.619 0.00 0.00 0.00 3.79
1371 1419 1.351017 TCACCTAAAACTGCAGGGAGG 59.649 52.381 19.93 19.10 36.15 4.30
1373 1421 1.073284 GGTCACCTAAAACTGCAGGGA 59.927 52.381 19.93 0.00 36.15 4.20
1375 1423 2.154462 CAGGTCACCTAAAACTGCAGG 58.846 52.381 19.93 1.64 37.97 4.85
1462 1510 1.382420 CCCTCTCCAGGAGTCCAGG 60.382 68.421 16.65 14.49 43.65 4.45
1463 1511 1.382420 CCCCTCTCCAGGAGTCCAG 60.382 68.421 16.65 2.60 43.65 3.86
1464 1512 2.169590 GACCCCTCTCCAGGAGTCCA 62.170 65.000 16.65 0.00 40.90 4.02
1465 1513 1.382009 GACCCCTCTCCAGGAGTCC 60.382 68.421 16.65 0.00 40.90 3.85
1466 1514 0.927767 TAGACCCCTCTCCAGGAGTC 59.072 60.000 16.65 7.01 45.97 3.36
1467 1515 0.632294 GTAGACCCCTCTCCAGGAGT 59.368 60.000 16.65 0.00 43.65 3.85
1468 1516 0.105913 GGTAGACCCCTCTCCAGGAG 60.106 65.000 10.70 10.70 43.65 3.69
1469 1517 0.854039 TGGTAGACCCCTCTCCAGGA 60.854 60.000 0.00 0.00 43.65 3.86
1517 1565 5.184864 CCAAATCCAGTGGCAAAGTATACAA 59.815 40.000 3.51 0.00 0.00 2.41
1520 1848 4.277476 CCCAAATCCAGTGGCAAAGTATA 58.723 43.478 3.51 0.00 34.56 1.47
1526 1854 0.413037 ATCCCCAAATCCAGTGGCAA 59.587 50.000 3.51 0.00 34.56 4.52
1976 2304 4.334759 CCATCAGCGATGAACTGAAAGAAT 59.665 41.667 7.76 0.00 46.63 2.40
2093 2429 2.727123 TTCACCACATCCACACACTT 57.273 45.000 0.00 0.00 0.00 3.16
2112 2448 3.691118 CGTCAATGGTTCCACTGATCAAT 59.309 43.478 6.28 0.00 0.00 2.57
2113 2449 3.073678 CGTCAATGGTTCCACTGATCAA 58.926 45.455 6.28 0.00 0.00 2.57
2131 2467 6.013689 GTGCAACTATAAACAAGCTAACGTC 58.986 40.000 0.00 0.00 0.00 4.34
2181 2517 5.452078 TTGCCAAAGTCAAAGGAATACAG 57.548 39.130 0.00 0.00 0.00 2.74
2289 2625 4.688021 TGTGGACCAAAACTTTAATGCAC 58.312 39.130 0.00 0.00 0.00 4.57
2299 2635 4.599047 TGATTGGAATGTGGACCAAAAC 57.401 40.909 0.00 0.00 46.87 2.43
2508 2852 3.432933 GCTGGCACAACAACATAAAATGG 59.567 43.478 0.00 0.00 38.70 3.16
2512 2856 3.808466 TTGCTGGCACAACAACATAAA 57.192 38.095 0.00 0.00 39.68 1.40
2559 2919 6.929606 ACTGCCTACTACAGTCTTAAAAGTTG 59.070 38.462 0.00 0.00 45.06 3.16
2569 2929 1.751924 CCTCCACTGCCTACTACAGTC 59.248 57.143 0.00 0.00 45.06 3.51
2571 2931 2.028130 CTCCTCCACTGCCTACTACAG 58.972 57.143 0.00 0.00 41.08 2.74
2572 2932 1.639108 TCTCCTCCACTGCCTACTACA 59.361 52.381 0.00 0.00 0.00 2.74
2573 2933 2.427812 GTTCTCCTCCACTGCCTACTAC 59.572 54.545 0.00 0.00 0.00 2.73
2602 2962 2.024464 AGTCAGGATCAGCAGTAGGACT 60.024 50.000 0.00 0.00 0.00 3.85
2604 2964 2.836636 AGTCAGGATCAGCAGTAGGA 57.163 50.000 0.00 0.00 0.00 2.94
2644 3004 7.850193 ACAATAACATTAAGCCAAACATCCAT 58.150 30.769 0.00 0.00 0.00 3.41
2680 3040 5.721225 AGTGGGGAACATCTATATGAGTCT 58.279 41.667 0.00 0.00 36.54 3.24
3004 3366 3.881937 ATTTCAGCATTCTGGCCTTTC 57.118 42.857 3.32 0.00 40.69 2.62
3037 3399 0.809241 CTGAGACATCGGGCTTCAGC 60.809 60.000 0.00 0.00 41.14 4.26
3094 3456 1.442520 CTTCCGCGTTGCAACATGG 60.443 57.895 28.01 25.94 0.00 3.66
3118 3480 9.421399 TCTGAGATATGAGAACTTACAATGGTA 57.579 33.333 0.00 0.00 0.00 3.25
3128 3490 7.564660 AGAGGATGTTTCTGAGATATGAGAACT 59.435 37.037 0.00 0.00 0.00 3.01
3147 3509 8.503458 AGACATAATGAAGAAAACAGAGGATG 57.497 34.615 0.00 0.00 0.00 3.51
3193 3558 6.806246 ACATGAAATAATTTTGCAAACGACG 58.194 32.000 12.39 0.00 0.00 5.12
3196 3561 7.114882 TGGACATGAAATAATTTTGCAAACG 57.885 32.000 12.39 0.00 0.00 3.60
3201 3566 9.768662 AATAGGATGGACATGAAATAATTTTGC 57.231 29.630 0.00 0.00 0.00 3.68
3214 3689 6.795144 TGCAAATGAAAATAGGATGGACAT 57.205 33.333 0.00 0.00 0.00 3.06
3276 3751 9.764363 AAAAGAAACCTTTCAGAATTATGTTCC 57.236 29.630 0.00 0.00 39.61 3.62
3307 4205 7.342026 ACTTGGAACTTCATGGTTTTCTAAGTT 59.658 33.333 18.42 13.34 43.31 2.66
3329 4228 9.463443 CAAGAAAATTCTGGTTAAACCTACTTG 57.537 33.333 0.00 0.00 39.58 3.16
3333 4232 8.002459 ACTCCAAGAAAATTCTGGTTAAACCTA 58.998 33.333 0.00 0.00 39.58 3.08
3336 4235 9.678941 CTAACTCCAAGAAAATTCTGGTTAAAC 57.321 33.333 0.00 0.00 37.65 2.01
3339 4238 7.523415 ACCTAACTCCAAGAAAATTCTGGTTA 58.477 34.615 0.00 4.51 37.65 2.85
3352 4251 8.305317 GGCTAAGTACATATACCTAACTCCAAG 58.695 40.741 0.00 0.00 30.88 3.61
3353 4252 7.785985 TGGCTAAGTACATATACCTAACTCCAA 59.214 37.037 0.00 0.00 30.88 3.53
3384 4283 8.309163 TGATGCAAGTTATGAAACAAAATTCC 57.691 30.769 0.00 0.00 38.12 3.01
3554 4457 1.840635 GCAGTTATCCCTCCAACCTCT 59.159 52.381 0.00 0.00 0.00 3.69
3563 4466 3.439857 TGCTCTTTTGCAGTTATCCCT 57.560 42.857 0.00 0.00 38.12 4.20
3566 4469 4.164822 TGCTTGCTCTTTTGCAGTTATC 57.835 40.909 0.00 0.00 44.27 1.75
3767 4670 2.610833 GGCAACGGTAGCAATAAGTACC 59.389 50.000 0.00 0.00 36.15 3.34
3796 4699 6.655078 AATTACCAGGAATGGTGAATATGC 57.345 37.500 10.17 0.00 43.03 3.14
3824 4727 4.402793 TCAGTAGCTTTGTCCATACTCTCC 59.597 45.833 0.00 0.00 0.00 3.71
3842 4745 2.677542 AGGTCATATCGGGCTCAGTA 57.322 50.000 0.00 0.00 0.00 2.74
3852 4755 3.142174 GTGCTTGCCCTAAGGTCATATC 58.858 50.000 0.00 0.00 36.87 1.63
3859 4762 0.618458 TACCAGTGCTTGCCCTAAGG 59.382 55.000 0.00 0.00 36.87 2.69
3938 4841 3.584250 GACGACGACGACCGCAAGA 62.584 63.158 15.32 0.00 43.32 3.02
3971 4874 0.662619 TTGCCTTCTGCTCAACAACG 59.337 50.000 0.00 0.00 42.00 4.10
3989 4892 3.953612 TCACAAACACCATCTTCTGCTTT 59.046 39.130 0.00 0.00 0.00 3.51
4130 5033 4.889409 CCAATGGTGGTTAGCATAATCACT 59.111 41.667 11.55 0.00 43.81 3.41
4193 5096 2.040939 CTGATCCTCCTCATGCTCTGT 58.959 52.381 0.00 0.00 0.00 3.41
4395 5300 4.655440 AGATACATCTCGAGTCGAATCG 57.345 45.455 27.75 27.75 44.07 3.34
4462 5367 2.751837 CAAAGGAGGCTTCGGGGC 60.752 66.667 0.00 0.00 41.20 5.80
4463 5368 2.751837 GCAAAGGAGGCTTCGGGG 60.752 66.667 0.00 0.00 0.00 5.73
4464 5369 2.034066 TGCAAAGGAGGCTTCGGG 59.966 61.111 0.00 0.00 0.00 5.14
4465 5370 1.172180 TTGTGCAAAGGAGGCTTCGG 61.172 55.000 0.00 0.00 0.00 4.30
4466 5371 0.239347 CTTGTGCAAAGGAGGCTTCG 59.761 55.000 0.00 0.00 0.00 3.79
4485 5395 0.685458 ATCCACATGCCTCCCTTTGC 60.685 55.000 0.00 0.00 0.00 3.68
4572 5484 7.393327 CAAAACATTTTGCTTCACAAGTAGTG 58.607 34.615 4.25 0.00 43.68 2.74
4573 5485 7.524294 CAAAACATTTTGCTTCACAAGTAGT 57.476 32.000 4.25 0.00 40.76 2.73
4601 5514 4.683832 GTCCACAGTGGTAGTAAGCATAG 58.316 47.826 19.65 0.00 39.03 2.23
4708 5629 6.320418 TGCAAAGATCAAGATGAGCATACATT 59.680 34.615 0.00 0.00 34.77 2.71
4712 5633 6.059484 TGATGCAAAGATCAAGATGAGCATA 58.941 36.000 0.00 0.00 41.07 3.14
4883 5807 5.344743 TGATGGGTTAACAGTTGCAAAAA 57.655 34.783 8.10 0.00 0.00 1.94
4899 5823 1.171308 CTTGAGCACAACCTGATGGG 58.829 55.000 0.00 0.00 41.89 4.00
4927 5852 3.850273 GTGAAATGAAAGCTGCTCAATCG 59.150 43.478 1.00 0.00 0.00 3.34
4940 5865 5.246656 AGGCAGAATTTGATGGTGAAATGAA 59.753 36.000 0.00 0.00 0.00 2.57
4941 5866 4.773674 AGGCAGAATTTGATGGTGAAATGA 59.226 37.500 0.00 0.00 0.00 2.57
4942 5867 5.080969 AGGCAGAATTTGATGGTGAAATG 57.919 39.130 0.00 0.00 0.00 2.32
4943 5868 5.750352 AAGGCAGAATTTGATGGTGAAAT 57.250 34.783 0.00 0.00 0.00 2.17
4944 5869 5.549742 AAAGGCAGAATTTGATGGTGAAA 57.450 34.783 0.00 0.00 0.00 2.69
4983 5913 6.148976 GGTAGTACCTGAAAGTTTTGACATCC 59.851 42.308 12.41 0.00 34.73 3.51
5004 5934 5.124645 ACTTACTCACATAGACGGAGGTAG 58.875 45.833 0.00 0.00 32.98 3.18
5005 5935 5.108187 ACTTACTCACATAGACGGAGGTA 57.892 43.478 0.00 0.00 32.98 3.08
5006 5936 3.946558 GACTTACTCACATAGACGGAGGT 59.053 47.826 0.00 0.00 32.98 3.85
5007 5937 3.945921 TGACTTACTCACATAGACGGAGG 59.054 47.826 0.00 0.00 32.98 4.30
5008 5938 5.759506 ATGACTTACTCACATAGACGGAG 57.240 43.478 0.00 0.00 34.85 4.63
5009 5939 5.220796 CGAATGACTTACTCACATAGACGGA 60.221 44.000 0.00 0.00 0.00 4.69
5010 5940 4.970611 CGAATGACTTACTCACATAGACGG 59.029 45.833 0.00 0.00 0.00 4.79
5011 5941 4.438145 GCGAATGACTTACTCACATAGACG 59.562 45.833 0.00 0.00 0.00 4.18
5012 5942 4.438145 CGCGAATGACTTACTCACATAGAC 59.562 45.833 0.00 0.00 0.00 2.59
5013 5943 4.095932 ACGCGAATGACTTACTCACATAGA 59.904 41.667 15.93 0.00 0.00 1.98
5014 5944 4.352039 ACGCGAATGACTTACTCACATAG 58.648 43.478 15.93 0.00 0.00 2.23
5015 5945 4.365899 ACGCGAATGACTTACTCACATA 57.634 40.909 15.93 0.00 0.00 2.29
5016 5946 3.232213 ACGCGAATGACTTACTCACAT 57.768 42.857 15.93 0.00 0.00 3.21
5017 5947 2.717580 ACGCGAATGACTTACTCACA 57.282 45.000 15.93 0.00 0.00 3.58
5018 5948 3.756069 ACTACGCGAATGACTTACTCAC 58.244 45.455 15.93 0.00 0.00 3.51
5019 5949 4.430137 AACTACGCGAATGACTTACTCA 57.570 40.909 15.93 0.00 0.00 3.41
5020 5950 5.758570 AAAACTACGCGAATGACTTACTC 57.241 39.130 15.93 0.00 0.00 2.59
5021 5951 6.615088 TCTAAAACTACGCGAATGACTTACT 58.385 36.000 15.93 0.00 0.00 2.24
5022 5952 6.859715 TCTAAAACTACGCGAATGACTTAC 57.140 37.500 15.93 0.00 0.00 2.34
5023 5953 7.252708 TGATCTAAAACTACGCGAATGACTTA 58.747 34.615 15.93 2.18 0.00 2.24
5024 5954 6.097356 TGATCTAAAACTACGCGAATGACTT 58.903 36.000 15.93 0.94 0.00 3.01
5025 5955 5.647589 TGATCTAAAACTACGCGAATGACT 58.352 37.500 15.93 0.00 0.00 3.41
5026 5956 5.944049 TGATCTAAAACTACGCGAATGAC 57.056 39.130 15.93 0.00 0.00 3.06
5027 5957 5.398416 CGATGATCTAAAACTACGCGAATGA 59.602 40.000 15.93 0.00 0.00 2.57
5028 5958 5.398416 TCGATGATCTAAAACTACGCGAATG 59.602 40.000 15.93 4.47 0.00 2.67
5029 5959 5.516996 TCGATGATCTAAAACTACGCGAAT 58.483 37.500 15.93 0.00 0.00 3.34
5030 5960 4.912214 TCGATGATCTAAAACTACGCGAA 58.088 39.130 15.93 0.00 0.00 4.70
5031 5961 4.541085 TCGATGATCTAAAACTACGCGA 57.459 40.909 15.93 0.00 0.00 5.87
5032 5962 5.807730 AATCGATGATCTAAAACTACGCG 57.192 39.130 3.53 3.53 0.00 6.01
5033 5963 7.161829 TCAAATCGATGATCTAAAACTACGC 57.838 36.000 0.00 0.00 0.00 4.42
5034 5964 7.567771 GCCTCAAATCGATGATCTAAAACTACG 60.568 40.741 0.00 0.00 0.00 3.51
5035 5965 7.224753 TGCCTCAAATCGATGATCTAAAACTAC 59.775 37.037 0.00 0.00 0.00 2.73
5036 5966 7.272244 TGCCTCAAATCGATGATCTAAAACTA 58.728 34.615 0.00 0.00 0.00 2.24
5037 5967 6.115446 TGCCTCAAATCGATGATCTAAAACT 58.885 36.000 0.00 0.00 0.00 2.66
5038 5968 6.363577 TGCCTCAAATCGATGATCTAAAAC 57.636 37.500 0.00 0.00 0.00 2.43
5039 5969 7.572523 AATGCCTCAAATCGATGATCTAAAA 57.427 32.000 0.00 0.00 0.00 1.52
5040 5970 8.675705 TTAATGCCTCAAATCGATGATCTAAA 57.324 30.769 0.00 0.00 0.00 1.85
5041 5971 8.675705 TTTAATGCCTCAAATCGATGATCTAA 57.324 30.769 0.00 0.00 0.00 2.10
5042 5972 8.853077 ATTTAATGCCTCAAATCGATGATCTA 57.147 30.769 0.00 0.00 0.00 1.98
5043 5973 7.756395 ATTTAATGCCTCAAATCGATGATCT 57.244 32.000 0.00 0.00 0.00 2.75
5044 5974 9.499585 CATATTTAATGCCTCAAATCGATGATC 57.500 33.333 0.00 0.00 0.00 2.92
5045 5975 9.017509 ACATATTTAATGCCTCAAATCGATGAT 57.982 29.630 0.00 0.00 0.00 2.45
5046 5976 8.291740 CACATATTTAATGCCTCAAATCGATGA 58.708 33.333 0.00 0.00 0.00 2.92
5047 5977 8.077991 ACACATATTTAATGCCTCAAATCGATG 58.922 33.333 0.00 0.00 0.00 3.84
5048 5978 8.169977 ACACATATTTAATGCCTCAAATCGAT 57.830 30.769 0.00 0.00 0.00 3.59
5049 5979 7.566760 ACACATATTTAATGCCTCAAATCGA 57.433 32.000 0.00 0.00 0.00 3.59
5050 5980 9.897744 ATAACACATATTTAATGCCTCAAATCG 57.102 29.630 0.00 0.00 0.00 3.34
5087 6017 9.570468 TCCGTGTAGAAATCTAGTGATATACTT 57.430 33.333 0.00 0.00 40.89 2.24
5088 6018 9.742144 ATCCGTGTAGAAATCTAGTGATATACT 57.258 33.333 0.00 0.00 43.56 2.12
5089 6019 9.776158 CATCCGTGTAGAAATCTAGTGATATAC 57.224 37.037 0.00 0.00 31.70 1.47
5090 6020 9.516546 ACATCCGTGTAGAAATCTAGTGATATA 57.483 33.333 0.00 0.00 36.63 0.86
5091 6021 8.410673 ACATCCGTGTAGAAATCTAGTGATAT 57.589 34.615 0.00 0.00 36.63 1.63
5092 6022 7.818997 ACATCCGTGTAGAAATCTAGTGATA 57.181 36.000 0.00 0.00 36.63 2.15
5093 6023 6.716934 ACATCCGTGTAGAAATCTAGTGAT 57.283 37.500 0.00 0.00 36.63 3.06
5156 6086 9.330063 TCTAGGTCGACGATTTAACTATCTAAA 57.670 33.333 9.92 0.00 0.00 1.85
5157 6087 8.893219 TCTAGGTCGACGATTTAACTATCTAA 57.107 34.615 9.92 0.00 0.00 2.10
5158 6088 8.768955 GTTCTAGGTCGACGATTTAACTATCTA 58.231 37.037 9.92 0.00 0.00 1.98
5159 6089 7.498570 AGTTCTAGGTCGACGATTTAACTATCT 59.501 37.037 9.92 0.00 0.00 1.98
5160 6090 7.638134 AGTTCTAGGTCGACGATTTAACTATC 58.362 38.462 9.92 0.00 0.00 2.08
5161 6091 7.565323 AGTTCTAGGTCGACGATTTAACTAT 57.435 36.000 9.92 0.00 0.00 2.12
5162 6092 6.992063 AGTTCTAGGTCGACGATTTAACTA 57.008 37.500 9.92 2.53 0.00 2.24
5163 6093 5.893897 AGTTCTAGGTCGACGATTTAACT 57.106 39.130 9.92 11.88 0.00 2.24
5164 6094 5.674580 CGTAGTTCTAGGTCGACGATTTAAC 59.325 44.000 9.92 9.89 35.42 2.01
5165 6095 5.351465 ACGTAGTTCTAGGTCGACGATTTAA 59.649 40.000 19.87 0.00 37.78 1.52
5166 6096 4.870426 ACGTAGTTCTAGGTCGACGATTTA 59.130 41.667 19.87 0.00 37.78 1.40
5167 6097 3.686726 ACGTAGTTCTAGGTCGACGATTT 59.313 43.478 19.87 0.00 37.78 2.17
5168 6098 3.063180 CACGTAGTTCTAGGTCGACGATT 59.937 47.826 19.87 0.07 41.61 3.34
5169 6099 2.606725 CACGTAGTTCTAGGTCGACGAT 59.393 50.000 19.87 3.12 41.61 3.73
5170 6100 1.995484 CACGTAGTTCTAGGTCGACGA 59.005 52.381 19.87 0.00 41.61 4.20
5171 6101 1.995484 TCACGTAGTTCTAGGTCGACG 59.005 52.381 9.92 14.67 41.61 5.12
5172 6102 4.093998 TCATTCACGTAGTTCTAGGTCGAC 59.906 45.833 7.13 7.13 41.61 4.20
5173 6103 4.093998 GTCATTCACGTAGTTCTAGGTCGA 59.906 45.833 0.00 0.00 41.61 4.20
5174 6104 4.094590 AGTCATTCACGTAGTTCTAGGTCG 59.905 45.833 0.00 0.00 41.61 4.79
5175 6105 5.564048 AGTCATTCACGTAGTTCTAGGTC 57.436 43.478 0.00 0.00 41.61 3.85
5176 6106 5.979288 AAGTCATTCACGTAGTTCTAGGT 57.021 39.130 0.00 0.20 41.61 3.08
5177 6107 6.095160 AGGTAAGTCATTCACGTAGTTCTAGG 59.905 42.308 0.00 0.00 41.61 3.02
5178 6108 7.086230 AGGTAAGTCATTCACGTAGTTCTAG 57.914 40.000 0.00 0.00 41.61 2.43
5179 6109 7.175467 TCAAGGTAAGTCATTCACGTAGTTCTA 59.825 37.037 0.00 0.00 41.61 2.10
5180 6110 5.979288 AGGTAAGTCATTCACGTAGTTCT 57.021 39.130 0.00 0.00 41.61 3.01
5181 6111 6.089150 GTCAAGGTAAGTCATTCACGTAGTTC 59.911 42.308 0.00 0.00 41.61 3.01
5182 6112 5.924825 GTCAAGGTAAGTCATTCACGTAGTT 59.075 40.000 0.00 0.00 41.61 2.24
5183 6113 8.707781 CCGTCAAGGTAAGTCATTCACGTAGT 62.708 46.154 0.00 0.00 36.55 2.73
5184 6114 4.557690 CGTCAAGGTAAGTCATTCACGTAG 59.442 45.833 0.00 0.00 0.00 3.51
5185 6115 4.478699 CGTCAAGGTAAGTCATTCACGTA 58.521 43.478 0.00 0.00 0.00 3.57
5186 6116 3.314553 CGTCAAGGTAAGTCATTCACGT 58.685 45.455 0.00 0.00 0.00 4.49
5187 6117 2.666508 CCGTCAAGGTAAGTCATTCACG 59.333 50.000 0.00 0.00 34.51 4.35
5188 6118 3.921677 TCCGTCAAGGTAAGTCATTCAC 58.078 45.455 0.00 0.00 41.99 3.18
5189 6119 3.056107 CCTCCGTCAAGGTAAGTCATTCA 60.056 47.826 0.00 0.00 41.99 2.57
5190 6120 3.522553 CCTCCGTCAAGGTAAGTCATTC 58.477 50.000 0.00 0.00 41.99 2.67
5191 6121 3.611766 CCTCCGTCAAGGTAAGTCATT 57.388 47.619 0.00 0.00 41.99 2.57
5200 6130 1.134560 GTGCTACTACCTCCGTCAAGG 59.865 57.143 0.00 0.00 42.55 3.61
5201 6131 2.093106 AGTGCTACTACCTCCGTCAAG 58.907 52.381 0.00 0.00 0.00 3.02
5202 6132 2.089980 GAGTGCTACTACCTCCGTCAA 58.910 52.381 0.00 0.00 0.00 3.18
5203 6133 1.681166 GGAGTGCTACTACCTCCGTCA 60.681 57.143 0.00 0.00 0.00 4.35
5204 6134 1.023502 GGAGTGCTACTACCTCCGTC 58.976 60.000 0.00 0.00 0.00 4.79
5205 6135 0.624785 AGGAGTGCTACTACCTCCGT 59.375 55.000 0.00 0.00 39.07 4.69
5206 6136 1.677052 GAAGGAGTGCTACTACCTCCG 59.323 57.143 0.00 0.00 39.07 4.63
5207 6137 2.033372 GGAAGGAGTGCTACTACCTCC 58.967 57.143 0.00 0.00 29.53 4.30
5208 6138 2.736347 TGGAAGGAGTGCTACTACCTC 58.264 52.381 0.00 0.00 29.53 3.85
5209 6139 2.921834 TGGAAGGAGTGCTACTACCT 57.078 50.000 0.00 0.00 25.63 3.08
5210 6140 3.975168 TTTGGAAGGAGTGCTACTACC 57.025 47.619 0.00 0.00 25.63 3.18
5211 6141 4.443621 GGATTTGGAAGGAGTGCTACTAC 58.556 47.826 0.00 0.00 0.00 2.73
5212 6142 3.454812 GGGATTTGGAAGGAGTGCTACTA 59.545 47.826 0.00 0.00 0.00 1.82
5213 6143 2.239907 GGGATTTGGAAGGAGTGCTACT 59.760 50.000 0.00 0.00 0.00 2.57
5214 6144 2.644676 GGGATTTGGAAGGAGTGCTAC 58.355 52.381 0.00 0.00 0.00 3.58
5215 6145 1.564348 GGGGATTTGGAAGGAGTGCTA 59.436 52.381 0.00 0.00 0.00 3.49
5216 6146 0.332972 GGGGATTTGGAAGGAGTGCT 59.667 55.000 0.00 0.00 0.00 4.40
5217 6147 0.039618 TGGGGATTTGGAAGGAGTGC 59.960 55.000 0.00 0.00 0.00 4.40
5225 6155 5.222442 TGGTTTAGAATTCTGGGGATTTGGA 60.222 40.000 18.47 0.00 0.00 3.53
5243 6173 7.504403 TGGCTTCAAGATGAAATTTTGGTTTA 58.496 30.769 0.00 0.00 38.80 2.01
5246 6176 5.511888 CCTGGCTTCAAGATGAAATTTTGGT 60.512 40.000 0.00 0.00 38.80 3.67
5247 6177 4.933400 CCTGGCTTCAAGATGAAATTTTGG 59.067 41.667 0.00 0.00 38.80 3.28
5345 6276 4.864334 CACCATCAGGCCGGCTCC 62.864 72.222 28.56 11.04 39.06 4.70
5383 6314 1.133025 CAAGAATTCCACATCCGTGCC 59.867 52.381 0.65 0.00 42.17 5.01
5386 6317 2.039746 TCCACAAGAATTCCACATCCGT 59.960 45.455 0.65 0.00 0.00 4.69
5445 6376 1.625818 AGGCACTACTGGAACTTGGAG 59.374 52.381 0.00 0.00 36.02 3.86
5449 6380 2.047061 TGTCAGGCACTACTGGAACTT 58.953 47.619 0.00 0.00 38.98 2.66
5458 6390 4.065088 GTGATCAGTTTTGTCAGGCACTA 58.935 43.478 0.00 0.00 36.02 2.74
5589 6523 7.386848 ACAACCCCATCTAATTATTTACGATCG 59.613 37.037 14.88 14.88 0.00 3.69
5594 6528 9.802039 TCCATACAACCCCATCTAATTATTTAC 57.198 33.333 0.00 0.00 0.00 2.01
5616 6563 6.839124 TTATGAAATGTCAAACAGCTCCAT 57.161 33.333 0.00 0.00 37.30 3.41
5662 6609 2.355108 CCACCTAACCATCCAGTCACAG 60.355 54.545 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.