Multiple sequence alignment - TraesCS5D01G105500

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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 TraesCS5D01G105500 chr5D 100.000 7162 0 0 1 7162 119490529 119483368 0.000000e+00 13226.0
1 TraesCS5D01G105500 chr5D 88.966 145 13 1 2790 2931 119487662 119487518 7.380000e-40 176.0
2 TraesCS5D01G105500 chr5D 88.966 145 13 1 2868 3012 119487740 119487599 7.380000e-40 176.0
3 TraesCS5D01G105500 chr5A 94.348 6387 235 63 820 7162 129604598 129598294 0.000000e+00 9679.0
4 TraesCS5D01G105500 chr5A 85.412 473 33 15 3 442 129605642 129605173 6.550000e-125 459.0
5 TraesCS5D01G105500 chr5A 88.650 326 32 3 512 833 129604944 129604620 6.740000e-105 392.0
6 TraesCS5D01G105500 chr5A 91.724 145 9 1 2791 2932 129602540 129602396 1.580000e-46 198.0
7 TraesCS5D01G105500 chr5B 93.762 5050 203 60 818 5810 132291085 132286091 0.000000e+00 7478.0
8 TraesCS5D01G105500 chr5B 94.389 1408 40 19 5758 7162 132286088 132284717 0.000000e+00 2126.0
9 TraesCS5D01G105500 chr5B 86.946 429 24 19 3 406 132293365 132292944 3.050000e-123 453.0
10 TraesCS5D01G105500 chr5B 86.076 237 22 10 506 733 132292631 132292397 2.000000e-60 244.0
11 TraesCS5D01G105500 chr5B 90.647 139 10 1 2790 2925 132289016 132288878 1.590000e-41 182.0
12 TraesCS5D01G105500 chr5B 90.141 71 6 1 360 430 105767657 105767588 2.750000e-14 91.6
13 TraesCS5D01G105500 chr2D 87.624 202 21 2 6558 6759 500811759 500811956 1.550000e-56 231.0
14 TraesCS5D01G105500 chr3A 85.922 206 23 5 6558 6759 25032143 25031940 1.560000e-51 215.0
15 TraesCS5D01G105500 chr3A 88.158 76 7 2 360 435 35991304 35991377 9.900000e-14 89.8
16 TraesCS5D01G105500 chr7D 84.906 106 10 6 359 461 182608444 182608342 1.270000e-17 102.0
17 TraesCS5D01G105500 chr4A 87.952 83 9 1 360 442 472670444 472670525 5.910000e-16 97.1
18 TraesCS5D01G105500 chr2B 87.059 85 10 1 358 442 796178775 796178858 2.130000e-15 95.3
19 TraesCS5D01G105500 chr4D 86.905 84 10 1 359 442 51078993 51079075 7.650000e-15 93.5
20 TraesCS5D01G105500 chr1D 87.342 79 8 2 370 447 14741241 14741164 9.900000e-14 89.8


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 TraesCS5D01G105500 chr5D 119483368 119490529 7161 True 4526.0 13226 92.6440 1 7162 3 chr5D.!!$R1 7161
1 TraesCS5D01G105500 chr5A 129598294 129605642 7348 True 2682.0 9679 90.0335 3 7162 4 chr5A.!!$R1 7159
2 TraesCS5D01G105500 chr5B 132284717 132293365 8648 True 2096.6 7478 90.3640 3 7162 5 chr5B.!!$R2 7159

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
252 294 0.109597 GTTGCGAGCCCTGTTGAATG 60.110 55.000 0.00 0.0 0.00 2.67 F
944 2478 0.184933 AGTCTATCGCCTCTGCTCCT 59.815 55.000 0.00 0.0 34.43 3.69 F
1977 3535 0.101399 CACGTAAGAGCGAGATGCCT 59.899 55.000 0.00 0.0 43.91 4.75 F
2451 4009 0.037303 CAAGGGAAGAGGAAGCAGCA 59.963 55.000 0.00 0.0 0.00 4.41 F
3533 5099 0.105453 ATCTCATCCGCCCCTGTACT 60.105 55.000 0.00 0.0 0.00 2.73 F
4193 5785 0.042131 TCCTCCGGAAGAAAGGGCTA 59.958 55.000 5.23 0.0 35.38 3.93 F
5168 6761 1.216977 CCACGACAACCGCATAGGA 59.783 57.895 0.00 0.0 45.00 2.94 F
5411 7004 1.202818 GGGCGGATATCAAAGAGGCTT 60.203 52.381 4.83 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1307 2849 0.039326 ACAGCGAGTACCACCCTAGT 59.961 55.000 0.00 0.00 0.00 2.57 R
2451 4009 1.066143 CCGATAAGGGTGAACAGTGCT 60.066 52.381 0.00 0.00 35.97 4.40 R
3441 5006 0.179097 CCCTTTGAGCTAGCGAGGAC 60.179 60.000 22.72 10.13 0.00 3.85 R
4091 5683 0.952497 CTGCTCCAGTTGCATCACGT 60.952 55.000 0.00 0.00 39.86 4.49 R
5144 6737 0.248012 TGCGGTTGTCGTGGATGTAT 59.752 50.000 0.00 0.00 41.72 2.29 R
5201 6794 0.729116 ATTTCTCATTGCGAGCCACG 59.271 50.000 0.00 0.00 41.98 4.94 R
6104 7752 1.220206 CGCTGGATGTGGAAGCTCT 59.780 57.895 0.00 0.00 34.72 4.09 R
6227 7875 2.699846 GAGAGTCTGGGCATCATCTCTT 59.300 50.000 0.00 2.49 37.01 2.85 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
53 54 3.068590 AGTGTTGGCATGGAAGAAACTTG 59.931 43.478 0.00 0.00 0.00 3.16
76 77 7.540474 TGTGTAGAGATGTCTTTCTTAACCT 57.460 36.000 0.00 0.00 33.84 3.50
78 79 9.085645 TGTGTAGAGATGTCTTTCTTAACCTTA 57.914 33.333 0.00 0.00 33.84 2.69
83 84 5.875359 AGATGTCTTTCTTAACCTTAAGGCG 59.125 40.000 21.92 7.79 40.35 5.52
222 264 4.903054 TGAATCTATGATGCAGGTGGATC 58.097 43.478 4.61 4.61 42.33 3.36
252 294 0.109597 GTTGCGAGCCCTGTTGAATG 60.110 55.000 0.00 0.00 0.00 2.67
295 337 3.050619 GGAATGCTTAGACCATACGACG 58.949 50.000 0.00 0.00 0.00 5.12
483 698 3.297620 CGGGGCAAAAGCTGTGCT 61.298 61.111 19.06 0.00 42.56 4.40
510 772 3.657350 CGGTGGGGTGTTGGGGAT 61.657 66.667 0.00 0.00 0.00 3.85
555 817 1.928503 GCGGAAAATACGGTCGATTCA 59.071 47.619 0.00 0.00 0.00 2.57
562 824 4.316205 AATACGGTCGATTCACAGCATA 57.684 40.909 0.00 0.00 0.00 3.14
760 1031 1.338655 CCACGGTTTTTACAAGGTGGG 59.661 52.381 0.16 0.00 40.86 4.61
764 1035 2.894765 CGGTTTTTACAAGGTGGGGAAT 59.105 45.455 0.00 0.00 0.00 3.01
784 1056 2.150809 CTGCACACGCACGACTTGAG 62.151 60.000 0.00 0.00 45.36 3.02
794 1066 2.223249 GCACGACTTGAGAAAACTTGCA 60.223 45.455 0.00 0.00 0.00 4.08
811 1083 2.124901 ACACACACACACACGGGG 60.125 61.111 0.00 0.00 0.00 5.73
816 1088 2.826287 CACACACACGGGGCACAA 60.826 61.111 0.00 0.00 0.00 3.33
843 2371 1.164041 ACGGAACTCAAAGGCAACCG 61.164 55.000 0.00 0.00 43.61 4.44
844 2372 1.164041 CGGAACTCAAAGGCAACCGT 61.164 55.000 0.00 0.00 35.21 4.83
845 2373 0.591659 GGAACTCAAAGGCAACCGTC 59.408 55.000 0.00 0.00 37.17 4.79
846 2374 0.234884 GAACTCAAAGGCAACCGTCG 59.765 55.000 0.00 0.00 37.17 5.12
847 2375 0.463116 AACTCAAAGGCAACCGTCGT 60.463 50.000 0.00 0.00 37.17 4.34
850 2378 3.284449 AAAGGCAACCGTCGTGGC 61.284 61.111 1.64 1.64 43.94 5.01
933 2467 3.304996 CCACTGCTACCATCAGTCTATCG 60.305 52.174 0.00 0.00 42.38 2.92
943 2477 0.313672 CAGTCTATCGCCTCTGCTCC 59.686 60.000 0.00 0.00 34.43 4.70
944 2478 0.184933 AGTCTATCGCCTCTGCTCCT 59.815 55.000 0.00 0.00 34.43 3.69
945 2479 1.036707 GTCTATCGCCTCTGCTCCTT 58.963 55.000 0.00 0.00 34.43 3.36
984 2521 5.604231 CAGATAAGGCTATATATCCCCAGCA 59.396 44.000 7.37 0.00 35.69 4.41
1017 2558 2.445654 CCTCAGCCTCCCTCTCCC 60.446 72.222 0.00 0.00 0.00 4.30
1183 2724 4.521062 CCTTGCTCCGCCCTCTCG 62.521 72.222 0.00 0.00 0.00 4.04
1287 2828 4.351054 CCAGCCCGCTTTCCCACT 62.351 66.667 0.00 0.00 0.00 4.00
1306 2848 4.929808 CCACTCTGTAAAGCGATAAGTTGT 59.070 41.667 0.00 0.00 0.00 3.32
1307 2849 6.097356 CCACTCTGTAAAGCGATAAGTTGTA 58.903 40.000 0.00 0.00 0.00 2.41
1308 2850 6.034683 CCACTCTGTAAAGCGATAAGTTGTAC 59.965 42.308 0.00 0.00 0.00 2.90
1405 2947 0.399833 TCCCCCAAAATTTTGCTGGC 59.600 50.000 22.90 0.00 36.86 4.85
1408 2950 1.348696 CCCCAAAATTTTGCTGGCTCT 59.651 47.619 22.90 0.00 36.86 4.09
1409 2951 2.566724 CCCCAAAATTTTGCTGGCTCTA 59.433 45.455 22.90 0.00 36.86 2.43
1411 2953 4.323715 CCCCAAAATTTTGCTGGCTCTAAT 60.324 41.667 22.90 0.00 36.86 1.73
1422 2964 3.007398 GCTGGCTCTAATACTGCCTATGT 59.993 47.826 0.00 0.00 46.23 2.29
1423 2965 4.503991 GCTGGCTCTAATACTGCCTATGTT 60.504 45.833 0.00 0.00 46.23 2.71
1429 2975 7.148069 GGCTCTAATACTGCCTATGTTTGTTTT 60.148 37.037 0.00 0.00 43.05 2.43
1430 2976 8.244113 GCTCTAATACTGCCTATGTTTGTTTTT 58.756 33.333 0.00 0.00 0.00 1.94
1465 3021 1.325943 GCTCTTTCGCAGCATCTGTAC 59.674 52.381 0.00 0.00 36.82 2.90
1481 3037 3.244345 TCTGTACTGCTTTTTGTTCGTCG 59.756 43.478 0.00 0.00 0.00 5.12
1558 3116 6.093357 GGTTCTCAAGGAATCAAGATTCTGAC 59.907 42.308 19.04 6.20 44.90 3.51
1573 3131 2.111384 TCTGACATAGCTCCCCTGAAC 58.889 52.381 0.00 0.00 0.00 3.18
1692 3250 2.479730 CCGTGGTTCAGAGAGGTATTCG 60.480 54.545 0.00 0.00 0.00 3.34
1846 3404 3.307906 TCACGGTGGAGGGTTCGG 61.308 66.667 8.50 0.00 0.00 4.30
1977 3535 0.101399 CACGTAAGAGCGAGATGCCT 59.899 55.000 0.00 0.00 43.91 4.75
2019 3577 2.644798 AGTTCCTGGTGCATCCTTTACT 59.355 45.455 0.00 0.00 37.07 2.24
2118 3676 2.220133 CCGAGTAAGTGACGGTTTTGTG 59.780 50.000 0.00 0.00 41.47 3.33
2451 4009 0.037303 CAAGGGAAGAGGAAGCAGCA 59.963 55.000 0.00 0.00 0.00 4.41
2761 4319 1.001378 CAACTTCTGGGGTTGAAAGCG 60.001 52.381 0.00 0.00 44.58 4.68
2764 4322 0.753479 TTCTGGGGTTGAAAGCGCAA 60.753 50.000 11.47 0.00 46.34 4.85
2769 4327 1.066929 GGGGTTGAAAGCGCAATTGAT 60.067 47.619 11.47 0.00 38.94 2.57
2830 4388 8.784043 GCAAAGAGGATAGTTCTTTAACAGAAA 58.216 33.333 0.43 0.00 43.52 2.52
2882 4443 6.183360 ACAGTTTCTGCTACTGAAGTTGAAAC 60.183 38.462 9.74 15.32 44.52 2.78
2926 4487 4.254709 AAGCTGTCACTGGCGCCA 62.255 61.111 30.59 30.59 0.00 5.69
2963 4524 6.183360 ACAGTTTCTGCTACTGAAGTTGAAAC 60.183 38.462 9.74 15.32 44.52 2.78
2976 4537 4.731313 AGTTGAAACCAAAGAGGAGGAT 57.269 40.909 0.00 0.00 41.22 3.24
2994 4555 2.356125 GGATAGCCCTTCAACAGAAGCA 60.356 50.000 0.00 0.00 37.92 3.91
3003 4564 1.486310 TCAACAGAAGCAGTCACTGGT 59.514 47.619 2.86 2.86 44.48 4.00
3012 4573 0.813610 CAGTCACTGGTGCCGTTGAA 60.814 55.000 0.00 0.00 0.00 2.69
3025 4586 2.160417 GCCGTTGAAGAAATCACTCCTG 59.840 50.000 0.00 0.00 37.92 3.86
3057 4618 3.703556 CTGAGGAGCCAGAAGAATCAGTA 59.296 47.826 0.00 0.00 36.29 2.74
3059 4620 3.445008 AGGAGCCAGAAGAATCAGTACA 58.555 45.455 0.00 0.00 0.00 2.90
3084 4645 7.255331 GGAGGTTCCTACAACTGCAAGTAGT 62.255 48.000 15.41 3.74 39.26 2.73
3152 4713 1.874562 CAGAGGTTTCTGCTGCTGC 59.125 57.895 8.89 8.89 43.98 5.25
3196 4757 4.037923 CCACAGGTCAGCAGTAATTTTGTT 59.962 41.667 0.00 0.00 0.00 2.83
3258 4819 6.550938 ATTTGATCAGTCACATCCTGTCTA 57.449 37.500 0.00 0.00 33.11 2.59
3300 4861 8.862085 GCAACTCTACCTAATTAGGAAGAGTAT 58.138 37.037 33.60 14.74 46.63 2.12
3358 4923 5.901552 TCCTTTTGCCAGTTCTTTTTACAG 58.098 37.500 0.00 0.00 0.00 2.74
3361 4926 6.593770 CCTTTTGCCAGTTCTTTTTACAGTTT 59.406 34.615 0.00 0.00 0.00 2.66
3365 4930 5.802956 TGCCAGTTCTTTTTACAGTTTTTCG 59.197 36.000 0.00 0.00 0.00 3.46
3369 4934 7.964011 CCAGTTCTTTTTACAGTTTTTCGTGTA 59.036 33.333 0.00 0.00 0.00 2.90
3382 4947 7.586300 CAGTTTTTCGTGTAGTATTGTTCCTTG 59.414 37.037 0.00 0.00 0.00 3.61
3396 4961 6.418057 TTGTTCCTTGCTTTGGTAAATGAT 57.582 33.333 0.00 0.00 0.00 2.45
3399 4964 4.023291 TCCTTGCTTTGGTAAATGATCCC 58.977 43.478 0.00 0.00 0.00 3.85
3400 4965 3.132824 CCTTGCTTTGGTAAATGATCCCC 59.867 47.826 0.00 0.00 0.00 4.81
3401 4966 3.756082 TGCTTTGGTAAATGATCCCCT 57.244 42.857 0.00 0.00 0.00 4.79
3402 4967 4.059773 TGCTTTGGTAAATGATCCCCTT 57.940 40.909 0.00 0.00 0.00 3.95
3404 4969 4.953579 TGCTTTGGTAAATGATCCCCTTAC 59.046 41.667 0.00 0.00 0.00 2.34
3405 4970 4.953579 GCTTTGGTAAATGATCCCCTTACA 59.046 41.667 9.56 0.00 0.00 2.41
3406 4971 5.067805 GCTTTGGTAAATGATCCCCTTACAG 59.932 44.000 9.56 2.71 0.00 2.74
3407 4972 6.395780 TTTGGTAAATGATCCCCTTACAGA 57.604 37.500 9.56 0.00 0.00 3.41
3408 4973 6.590656 TTGGTAAATGATCCCCTTACAGAT 57.409 37.500 9.56 0.00 0.00 2.90
3409 4974 6.590656 TGGTAAATGATCCCCTTACAGATT 57.409 37.500 9.56 0.00 0.00 2.40
3410 4975 6.364701 TGGTAAATGATCCCCTTACAGATTG 58.635 40.000 9.56 0.00 0.00 2.67
3411 4976 5.241728 GGTAAATGATCCCCTTACAGATTGC 59.758 44.000 9.56 0.00 0.00 3.56
3412 4977 4.524802 AATGATCCCCTTACAGATTGCA 57.475 40.909 0.00 0.00 0.00 4.08
3413 4978 4.736611 ATGATCCCCTTACAGATTGCAT 57.263 40.909 0.00 0.00 0.00 3.96
3414 4979 3.824133 TGATCCCCTTACAGATTGCATG 58.176 45.455 0.00 0.00 0.00 4.06
3415 4980 3.202818 TGATCCCCTTACAGATTGCATGT 59.797 43.478 0.00 0.00 34.62 3.21
3416 4981 4.411869 TGATCCCCTTACAGATTGCATGTA 59.588 41.667 0.00 0.00 32.02 2.29
3417 4982 4.853468 TCCCCTTACAGATTGCATGTAA 57.147 40.909 10.20 10.20 40.03 2.41
3418 4983 5.186256 TCCCCTTACAGATTGCATGTAAA 57.814 39.130 11.44 0.00 41.31 2.01
3419 4984 4.947388 TCCCCTTACAGATTGCATGTAAAC 59.053 41.667 11.44 0.00 41.31 2.01
3420 4985 4.949856 CCCCTTACAGATTGCATGTAAACT 59.050 41.667 11.44 0.00 41.31 2.66
3421 4986 5.163622 CCCCTTACAGATTGCATGTAAACTG 60.164 44.000 25.15 25.15 41.31 3.16
3422 4987 5.415701 CCCTTACAGATTGCATGTAAACTGT 59.584 40.000 31.25 31.25 43.33 3.55
3436 5001 7.168972 GCATGTAAACTGTTCAATGCACTTAAA 59.831 33.333 20.77 0.00 34.31 1.52
3437 5002 8.693504 CATGTAAACTGTTCAATGCACTTAAAG 58.306 33.333 0.00 0.00 0.00 1.85
3440 5005 9.083080 GTAAACTGTTCAATGCACTTAAAGTTT 57.917 29.630 15.32 15.32 38.49 2.66
3441 5006 7.524294 AACTGTTCAATGCACTTAAAGTTTG 57.476 32.000 0.00 0.00 0.00 2.93
3460 5026 0.179097 GTCCTCGCTAGCTCAAAGGG 60.179 60.000 13.93 5.76 0.00 3.95
3461 5027 1.522580 CCTCGCTAGCTCAAAGGGC 60.523 63.158 13.93 0.00 0.00 5.19
3463 5029 0.529555 CTCGCTAGCTCAAAGGGCTC 60.530 60.000 13.93 0.00 40.74 4.70
3472 5038 0.110486 TCAAAGGGCTCAGTTGGTCC 59.890 55.000 0.64 0.00 0.00 4.46
3474 5040 1.705997 AAAGGGCTCAGTTGGTCCGT 61.706 55.000 0.00 0.00 0.00 4.69
3475 5041 0.834687 AAGGGCTCAGTTGGTCCGTA 60.835 55.000 0.00 0.00 0.00 4.02
3476 5042 0.617820 AGGGCTCAGTTGGTCCGTAT 60.618 55.000 0.00 0.00 0.00 3.06
3477 5043 0.252197 GGGCTCAGTTGGTCCGTATT 59.748 55.000 0.00 0.00 0.00 1.89
3479 5045 1.338769 GGCTCAGTTGGTCCGTATTGT 60.339 52.381 0.00 0.00 0.00 2.71
3480 5046 2.423577 GCTCAGTTGGTCCGTATTGTT 58.576 47.619 0.00 0.00 0.00 2.83
3482 5048 3.364964 GCTCAGTTGGTCCGTATTGTTTG 60.365 47.826 0.00 0.00 0.00 2.93
3483 5049 3.811083 TCAGTTGGTCCGTATTGTTTGT 58.189 40.909 0.00 0.00 0.00 2.83
3484 5050 3.810941 TCAGTTGGTCCGTATTGTTTGTC 59.189 43.478 0.00 0.00 0.00 3.18
3485 5051 2.803956 AGTTGGTCCGTATTGTTTGTCG 59.196 45.455 0.00 0.00 0.00 4.35
3486 5052 1.149987 TGGTCCGTATTGTTTGTCGC 58.850 50.000 0.00 0.00 0.00 5.19
3488 5054 2.029200 TGGTCCGTATTGTTTGTCGCTA 60.029 45.455 0.00 0.00 0.00 4.26
3489 5055 2.601763 GGTCCGTATTGTTTGTCGCTAG 59.398 50.000 0.00 0.00 0.00 3.42
3490 5056 2.601763 GTCCGTATTGTTTGTCGCTAGG 59.398 50.000 0.00 0.00 0.00 3.02
3491 5057 1.931172 CCGTATTGTTTGTCGCTAGGG 59.069 52.381 0.00 0.00 0.00 3.53
3492 5058 1.931172 CGTATTGTTTGTCGCTAGGGG 59.069 52.381 6.99 0.00 0.00 4.79
3493 5059 2.417651 CGTATTGTTTGTCGCTAGGGGA 60.418 50.000 6.99 0.00 0.00 4.81
3494 5060 3.740141 CGTATTGTTTGTCGCTAGGGGAT 60.740 47.826 6.99 0.00 0.00 3.85
3495 5061 2.396590 TTGTTTGTCGCTAGGGGATC 57.603 50.000 6.99 0.00 0.00 3.36
3496 5062 1.271856 TGTTTGTCGCTAGGGGATCA 58.728 50.000 6.99 2.03 0.00 2.92
3497 5063 1.837439 TGTTTGTCGCTAGGGGATCAT 59.163 47.619 6.99 0.00 0.00 2.45
3498 5064 3.035363 TGTTTGTCGCTAGGGGATCATA 58.965 45.455 6.99 0.00 0.00 2.15
3499 5065 3.646162 TGTTTGTCGCTAGGGGATCATAT 59.354 43.478 6.99 0.00 0.00 1.78
3500 5066 3.961480 TTGTCGCTAGGGGATCATATG 57.039 47.619 6.99 0.00 0.00 1.78
3515 5081 7.232188 GGGATCATATGCAATCCAGATATCAT 58.768 38.462 19.80 0.00 42.78 2.45
3526 5092 2.158986 CCAGATATCATCTCATCCGCCC 60.159 54.545 5.32 0.00 37.58 6.13
3533 5099 0.105453 ATCTCATCCGCCCCTGTACT 60.105 55.000 0.00 0.00 0.00 2.73
3540 5106 1.241315 CCGCCCCTGTACTGTTTTGG 61.241 60.000 0.00 0.00 0.00 3.28
3549 5115 5.514136 CCCTGTACTGTTTTGGACTATGGAA 60.514 44.000 0.00 0.00 0.00 3.53
3558 5124 5.708736 TTTGGACTATGGAAGATAAGCCA 57.291 39.130 0.00 0.00 38.78 4.75
3608 5174 4.963276 TTTTGGAACATCGCATTAGGAG 57.037 40.909 0.00 0.00 39.30 3.69
3617 5183 2.632377 TCGCATTAGGAGGCTTTCTTG 58.368 47.619 0.00 0.00 0.00 3.02
3618 5184 2.027192 TCGCATTAGGAGGCTTTCTTGT 60.027 45.455 0.00 0.00 0.00 3.16
3619 5185 2.749621 CGCATTAGGAGGCTTTCTTGTT 59.250 45.455 0.00 0.00 0.00 2.83
3620 5186 3.181506 CGCATTAGGAGGCTTTCTTGTTC 60.182 47.826 0.00 0.00 0.00 3.18
3621 5187 4.013050 GCATTAGGAGGCTTTCTTGTTCT 58.987 43.478 0.00 0.00 0.00 3.01
3625 5191 3.749226 AGGAGGCTTTCTTGTTCTTCTG 58.251 45.455 0.00 0.00 0.00 3.02
3646 5212 4.100707 GCATTTGCATAGCTTTGTCTGA 57.899 40.909 6.03 0.00 41.59 3.27
3651 5224 7.360607 GCATTTGCATAGCTTTGTCTGATTTTT 60.361 33.333 6.03 0.00 41.59 1.94
3670 5243 2.566833 TTGTCTTGTGGCAGCTACAT 57.433 45.000 13.03 0.00 0.00 2.29
3671 5244 2.099141 TGTCTTGTGGCAGCTACATC 57.901 50.000 13.03 7.27 0.00 3.06
3702 5275 5.104374 ACAAATTTGTTGACAGCACTGAAG 58.896 37.500 18.13 0.00 38.47 3.02
3714 5287 5.650543 ACAGCACTGAAGGTTTTAAGTTTG 58.349 37.500 4.31 0.00 0.00 2.93
3719 5292 6.034577 GCACTGAAGGTTTTAAGTTTGTTGTC 59.965 38.462 0.00 0.00 0.00 3.18
3750 5323 6.949352 TCAAGATGGCATAAAGAGATTTCC 57.051 37.500 0.00 0.00 0.00 3.13
3751 5324 6.666678 TCAAGATGGCATAAAGAGATTTCCT 58.333 36.000 0.00 0.00 0.00 3.36
3752 5325 6.544931 TCAAGATGGCATAAAGAGATTTCCTG 59.455 38.462 0.00 0.00 0.00 3.86
3771 5344 3.305403 CCTGATGACGTGTAACTGTGTCT 60.305 47.826 0.00 0.00 32.64 3.41
3773 5346 3.316868 TGATGACGTGTAACTGTGTCTCA 59.683 43.478 0.00 0.00 32.64 3.27
3781 5354 5.348724 CGTGTAACTGTGTCTCATAAATGCT 59.651 40.000 0.00 0.00 31.75 3.79
3794 5367 9.548208 GTCTCATAAATGCTTTTAGAAAGTGAC 57.452 33.333 10.20 10.96 31.07 3.67
3800 5373 4.968259 TGCTTTTAGAAAGTGACTGCCTA 58.032 39.130 0.00 0.00 0.00 3.93
3803 5376 7.165485 TGCTTTTAGAAAGTGACTGCCTAATA 58.835 34.615 7.47 3.76 0.00 0.98
3817 5390 9.638239 TGACTGCCTAATACAAATTTTGATTTC 57.362 29.630 15.81 5.70 0.00 2.17
3882 5455 5.652452 ACATGGTCCTAAAGCTTTTATGGAC 59.348 40.000 30.16 30.16 42.11 4.02
3883 5456 5.249780 TGGTCCTAAAGCTTTTATGGACA 57.750 39.130 33.97 25.28 43.94 4.02
3896 5469 7.172703 AGCTTTTATGGACACAGTGTAAGTTAC 59.827 37.037 6.06 6.06 0.00 2.50
3905 5497 8.780249 GGACACAGTGTAAGTTACAATTAACAT 58.220 33.333 17.16 0.48 40.25 2.71
3931 5523 9.741647 TTTCCATTATTTGCAATTTGTTTTTCC 57.258 25.926 0.00 0.00 0.00 3.13
3932 5524 8.688747 TCCATTATTTGCAATTTGTTTTTCCT 57.311 26.923 0.00 0.00 0.00 3.36
3933 5525 9.129532 TCCATTATTTGCAATTTGTTTTTCCTT 57.870 25.926 0.00 0.00 0.00 3.36
3934 5526 9.747293 CCATTATTTGCAATTTGTTTTTCCTTT 57.253 25.926 0.00 0.00 0.00 3.11
3972 5564 0.899720 CCCCACATTTTCTGCAGCAT 59.100 50.000 9.47 0.00 0.00 3.79
3999 5591 8.677300 AGTTCACTGCATATTGTACTTTATTGG 58.323 33.333 0.00 0.00 0.00 3.16
4014 5606 9.048446 GTACTTTATTGGTGAACTGTTGTTAGA 57.952 33.333 0.00 0.00 36.39 2.10
4019 5611 3.118408 TGGTGAACTGTTGTTAGAGCAGT 60.118 43.478 0.00 0.00 44.31 4.40
4097 5689 3.990092 TCTTGTCAAGCAGTTACGTGAT 58.010 40.909 7.78 0.00 30.78 3.06
4193 5785 0.042131 TCCTCCGGAAGAAAGGGCTA 59.958 55.000 5.23 0.00 35.38 3.93
4229 5821 3.123620 GCTGGAAGAGCCACTGCG 61.124 66.667 0.00 0.00 43.33 5.18
4319 5911 3.909430 TGACTTTGTATCACGAGGTGAC 58.091 45.455 0.00 0.00 45.65 3.67
4403 5995 1.732941 TTTCCATTGACGATGTCCCG 58.267 50.000 1.96 0.00 33.71 5.14
4568 6160 3.882888 TCAAGAATGACAAGGTCACAACC 59.117 43.478 0.49 0.00 45.65 3.77
4728 6320 2.359602 CACCACCAGCTGCTCCTG 60.360 66.667 8.66 0.00 0.00 3.86
4893 6486 9.657121 GCATTTCTAACTTCTAATTGCATAGAC 57.343 33.333 0.00 0.00 31.78 2.59
4928 6521 7.865706 AAAGTCAACACTCAATCTAACTTGT 57.134 32.000 0.00 0.00 29.93 3.16
5144 6737 1.339438 GCTGAAGGTCTGATTGGCTCA 60.339 52.381 0.00 0.00 0.00 4.26
5168 6761 1.216977 CCACGACAACCGCATAGGA 59.783 57.895 0.00 0.00 45.00 2.94
5201 6794 6.219473 TGAAATCAACTCTGAGACTGACTTC 58.781 40.000 19.23 19.23 34.23 3.01
5384 6977 4.265073 CCGAAAACATCAGGGAGAAGATT 58.735 43.478 0.00 0.00 0.00 2.40
5411 7004 1.202818 GGGCGGATATCAAAGAGGCTT 60.203 52.381 4.83 0.00 0.00 4.35
5733 7326 4.256110 TGCACACCTTCAATGTAGATGAG 58.744 43.478 0.00 0.00 0.00 2.90
6002 7649 6.215121 TGCTCAAAAACTATGACAATTGGTG 58.785 36.000 10.83 0.00 0.00 4.17
6079 7727 8.970691 ATTTACATGCTACAAACAAGATGTTC 57.029 30.769 0.00 0.00 40.14 3.18
6104 7752 6.426633 CCACTACATGTTCATGTGAGTTACAA 59.573 38.462 23.33 5.06 43.77 2.41
6130 7778 0.099968 CCACATCCAGCGCAATTCAG 59.900 55.000 11.47 0.00 0.00 3.02
6170 7818 2.159490 CGCCCGACGTTAAAATCCAAAT 60.159 45.455 0.00 0.00 36.87 2.32
6227 7875 0.249868 CACCAAGAGACACGGAAGCA 60.250 55.000 0.00 0.00 0.00 3.91
6265 7913 4.922206 ACTCTCATGTTTATGGCTCCAAA 58.078 39.130 0.00 0.00 34.97 3.28
6377 8025 1.448893 GGCGTGCCGGAAGTATTGA 60.449 57.895 5.05 0.00 0.00 2.57
6438 8086 7.014422 GGAAGAAGAACGAGAATATCCTTAGGA 59.986 40.741 2.37 2.37 35.55 2.94
6722 8370 8.421784 TGATCTAACAATCATACTGGTTAGGTC 58.578 37.037 13.83 13.83 46.59 3.85
6737 8385 8.768397 ACTGGTTAGGTCATAGTAAAATGATGA 58.232 33.333 0.00 0.00 38.13 2.92
6752 8400 9.013490 GTAAAATGATGACAATTACATCTGTGC 57.987 33.333 18.83 7.50 42.89 4.57
6753 8401 6.762702 AATGATGACAATTACATCTGTGCA 57.237 33.333 18.83 0.00 42.89 4.57
6754 8402 6.954487 ATGATGACAATTACATCTGTGCAT 57.046 33.333 18.83 7.64 42.89 3.96
6755 8403 8.454570 AATGATGACAATTACATCTGTGCATA 57.545 30.769 18.83 0.00 42.89 3.14
6756 8404 8.631480 ATGATGACAATTACATCTGTGCATAT 57.369 30.769 18.83 6.25 42.89 1.78
6757 8405 8.454570 TGATGACAATTACATCTGTGCATATT 57.545 30.769 18.83 0.00 42.89 1.28
6758 8406 8.905850 TGATGACAATTACATCTGTGCATATTT 58.094 29.630 18.83 0.00 42.89 1.40
6759 8407 9.740239 GATGACAATTACATCTGTGCATATTTT 57.260 29.630 13.91 0.00 40.36 1.82
6969 8618 7.012704 CACAGTAGCCATTATTTGCTAATCACT 59.987 37.037 0.00 0.00 41.42 3.41
6970 8619 8.210946 ACAGTAGCCATTATTTGCTAATCACTA 58.789 33.333 0.00 0.00 41.42 2.74
6971 8620 9.224267 CAGTAGCCATTATTTGCTAATCACTAT 57.776 33.333 0.00 0.00 41.42 2.12
6996 8645 2.762535 ATCAGGTGGGTTACAACTCG 57.237 50.000 0.00 0.00 46.59 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.111277 GTCAGCAAAACAACCCAGGT 58.889 50.000 0.00 0.00 0.00 4.00
1 2 1.110442 TGTCAGCAAAACAACCCAGG 58.890 50.000 0.00 0.00 0.00 4.45
53 54 9.924650 TTAAGGTTAAGAAAGACATCTCTACAC 57.075 33.333 0.00 0.00 0.00 2.90
76 77 2.813754 GCATGAAGATATGCCGCCTTAA 59.186 45.455 0.00 0.00 45.93 1.85
78 79 1.242076 GCATGAAGATATGCCGCCTT 58.758 50.000 0.00 0.00 45.93 4.35
189 203 4.790765 TCATAGATTCAGCCGTATCCAG 57.209 45.455 0.00 0.00 0.00 3.86
233 275 0.109597 CATTCAACAGGGCTCGCAAC 60.110 55.000 0.00 0.00 0.00 4.17
295 337 1.358759 CCAGGACAACAAACGTGGC 59.641 57.895 0.00 0.00 35.76 5.01
389 471 9.567776 TTTACATCTTCTGTTTTACATCTCCAA 57.432 29.630 0.00 0.00 39.39 3.53
434 516 5.925969 CGCCCTGATTTTGAAGTAAAAACAT 59.074 36.000 0.00 0.00 41.29 2.71
442 524 1.586154 CGCCGCCCTGATTTTGAAGT 61.586 55.000 0.00 0.00 0.00 3.01
443 525 1.137404 CGCCGCCCTGATTTTGAAG 59.863 57.895 0.00 0.00 0.00 3.02
444 526 2.339556 CCGCCGCCCTGATTTTGAA 61.340 57.895 0.00 0.00 0.00 2.69
445 527 2.749839 CCGCCGCCCTGATTTTGA 60.750 61.111 0.00 0.00 0.00 2.69
446 528 4.496927 GCCGCCGCCCTGATTTTG 62.497 66.667 0.00 0.00 0.00 2.44
500 715 1.677633 CCCGGTTCATCCCCAACAC 60.678 63.158 0.00 0.00 0.00 3.32
501 716 2.760477 CCCGGTTCATCCCCAACA 59.240 61.111 0.00 0.00 0.00 3.33
502 717 2.754254 GCCCGGTTCATCCCCAAC 60.754 66.667 0.00 0.00 0.00 3.77
503 718 4.418328 CGCCCGGTTCATCCCCAA 62.418 66.667 0.00 0.00 0.00 4.12
526 788 1.201877 CGTATTTTCCGCCACTCAACG 60.202 52.381 0.00 0.00 0.00 4.10
529 791 0.322322 ACCGTATTTTCCGCCACTCA 59.678 50.000 0.00 0.00 0.00 3.41
555 817 4.530857 GCTCCGCCCGTATGCTGT 62.531 66.667 0.00 0.00 0.00 4.40
577 839 2.438434 AAGCATACGGCCAGCCAC 60.438 61.111 9.78 0.00 46.50 5.01
588 858 1.677300 CACCCAACCGCCAAGCATA 60.677 57.895 0.00 0.00 0.00 3.14
656 926 1.886886 TTTGAGCGTTTACTCCACCC 58.113 50.000 0.00 0.00 35.72 4.61
664 934 3.488384 CCAGTGCTGTTTTTGAGCGTTTA 60.488 43.478 0.00 0.00 39.47 2.01
784 1056 2.661195 GTGTGTGTGTGTGCAAGTTTTC 59.339 45.455 0.00 0.00 0.00 2.29
794 1066 2.124901 CCCCGTGTGTGTGTGTGT 60.125 61.111 0.00 0.00 0.00 3.72
811 1083 1.593209 TTCCGTCGGTCAGTTGTGC 60.593 57.895 11.88 0.00 0.00 4.57
816 1088 0.748450 TTTGAGTTCCGTCGGTCAGT 59.252 50.000 11.88 2.08 0.00 3.41
933 2467 1.893919 AACGGAGAAGGAGCAGAGGC 61.894 60.000 0.00 0.00 41.61 4.70
943 2477 2.750948 TCTGGAAACGAAACGGAGAAG 58.249 47.619 0.00 0.00 0.00 2.85
944 2478 2.894763 TCTGGAAACGAAACGGAGAA 57.105 45.000 0.00 0.00 0.00 2.87
945 2479 4.491676 CTTATCTGGAAACGAAACGGAGA 58.508 43.478 0.00 0.00 0.00 3.71
1098 2639 2.535788 CGCCGACGAGCTAGCTACT 61.536 63.158 19.38 5.12 43.93 2.57
1099 2640 2.052060 CGCCGACGAGCTAGCTAC 60.052 66.667 19.38 11.29 43.93 3.58
1100 2641 2.202974 TCGCCGACGAGCTAGCTA 60.203 61.111 19.38 0.00 45.12 3.32
1134 2675 1.366854 CGAGAGACATGGACGACGGA 61.367 60.000 0.00 0.00 0.00 4.69
1183 2724 0.942962 CGATGGCAAAGGAGATGCTC 59.057 55.000 0.00 0.00 43.34 4.26
1287 2828 7.415989 CCCTAGTACAACTTATCGCTTTACAGA 60.416 40.741 0.00 0.00 0.00 3.41
1306 2848 1.283029 ACAGCGAGTACCACCCTAGTA 59.717 52.381 0.00 0.00 0.00 1.82
1307 2849 0.039326 ACAGCGAGTACCACCCTAGT 59.961 55.000 0.00 0.00 0.00 2.57
1308 2850 0.456221 CACAGCGAGTACCACCCTAG 59.544 60.000 0.00 0.00 0.00 3.02
1409 2951 9.908152 GAACTAAAAACAAACATAGGCAGTATT 57.092 29.630 0.00 0.00 0.00 1.89
1411 2953 8.685838 AGAACTAAAAACAAACATAGGCAGTA 57.314 30.769 0.00 0.00 0.00 2.74
1422 2964 7.771183 AGCATCAGTTGAGAACTAAAAACAAA 58.229 30.769 0.00 0.00 40.46 2.83
1423 2965 7.283127 AGAGCATCAGTTGAGAACTAAAAACAA 59.717 33.333 0.00 0.00 40.46 2.83
1429 2975 5.635280 CGAAAGAGCATCAGTTGAGAACTAA 59.365 40.000 0.00 0.00 40.46 2.24
1430 2976 5.164233 CGAAAGAGCATCAGTTGAGAACTA 58.836 41.667 0.00 0.00 40.46 2.24
1432 2978 3.424170 GCGAAAGAGCATCAGTTGAGAAC 60.424 47.826 0.00 0.00 37.82 3.01
1465 3021 2.969443 ATCCGACGAACAAAAAGCAG 57.031 45.000 0.00 0.00 0.00 4.24
1470 3026 4.693566 AGCAAGATAATCCGACGAACAAAA 59.306 37.500 0.00 0.00 0.00 2.44
1481 3037 3.303659 GCGCAAGAAGAGCAAGATAATCC 60.304 47.826 0.30 0.00 43.16 3.01
1558 3116 1.202627 GCTGAGTTCAGGGGAGCTATG 60.203 57.143 10.88 0.00 43.94 2.23
1692 3250 1.064946 CGAGGGCGATGTGACTCTC 59.935 63.158 0.00 0.00 40.82 3.20
1977 3535 2.187958 AGATCACCATCCTTCAACGGA 58.812 47.619 0.00 0.00 37.50 4.69
2019 3577 3.055094 GCTTGATAGACCTGACTTTCCCA 60.055 47.826 0.00 0.00 0.00 4.37
2118 3676 7.672239 ACAGTGAAGAGGGTAGATATATCTTCC 59.328 40.741 23.64 23.64 43.29 3.46
2451 4009 1.066143 CCGATAAGGGTGAACAGTGCT 60.066 52.381 0.00 0.00 35.97 4.40
2761 4319 2.907910 ACGAGCTTGTCATCAATTGC 57.092 45.000 0.00 0.00 32.82 3.56
2830 4388 1.523711 CAACGGTGCCAGTGACAGT 60.524 57.895 0.00 0.00 0.00 3.55
2882 4443 1.743252 GCGCTGTCCTCCTCTTTGG 60.743 63.158 0.00 0.00 37.10 3.28
2926 4487 3.620966 GCAGAAACTGTAGGAGGCTCAAT 60.621 47.826 17.69 6.77 33.43 2.57
2963 4524 1.813102 AGGGCTATCCTCCTCTTTGG 58.187 55.000 0.00 0.00 44.06 3.28
2994 4555 0.532862 CTTCAACGGCACCAGTGACT 60.533 55.000 0.99 0.00 36.16 3.41
3003 4564 2.151202 GGAGTGATTTCTTCAACGGCA 58.849 47.619 0.00 0.00 35.70 5.69
3012 4573 5.045286 AGCCTTATCAACAGGAGTGATTTCT 60.045 40.000 0.00 0.00 32.41 2.52
3070 4631 3.722147 CAGACTCACTACTTGCAGTTGT 58.278 45.455 0.00 0.00 34.63 3.32
3084 4645 2.297315 CTCAGTTACCACAGCAGACTCA 59.703 50.000 0.00 0.00 0.00 3.41
3300 4861 9.461312 AACAGTTTACATGCAATCTATCCTAAA 57.539 29.630 0.00 0.00 0.00 1.85
3358 4923 6.358822 GCAAGGAACAATACTACACGAAAAAC 59.641 38.462 0.00 0.00 0.00 2.43
3361 4926 5.302360 AGCAAGGAACAATACTACACGAAA 58.698 37.500 0.00 0.00 0.00 3.46
3365 4930 5.240844 ACCAAAGCAAGGAACAATACTACAC 59.759 40.000 0.00 0.00 0.00 2.90
3369 4934 6.969993 TTTACCAAAGCAAGGAACAATACT 57.030 33.333 0.00 0.00 0.00 2.12
3382 4947 4.953579 TGTAAGGGGATCATTTACCAAAGC 59.046 41.667 0.00 0.00 0.00 3.51
3396 4961 4.853468 TTACATGCAATCTGTAAGGGGA 57.147 40.909 7.19 0.00 34.90 4.81
3399 4964 6.500684 ACAGTTTACATGCAATCTGTAAGG 57.499 37.500 17.19 7.90 39.51 2.69
3400 4965 7.584108 TGAACAGTTTACATGCAATCTGTAAG 58.416 34.615 18.45 4.06 39.51 2.34
3401 4966 7.503521 TGAACAGTTTACATGCAATCTGTAA 57.496 32.000 18.45 7.19 37.43 2.41
3402 4967 7.503521 TTGAACAGTTTACATGCAATCTGTA 57.496 32.000 18.45 5.80 37.43 2.74
3404 4969 6.183360 GCATTGAACAGTTTACATGCAATCTG 60.183 38.462 13.10 13.10 34.31 2.90
3405 4970 5.865552 GCATTGAACAGTTTACATGCAATCT 59.134 36.000 15.51 0.00 34.31 2.40
3406 4971 5.634439 TGCATTGAACAGTTTACATGCAATC 59.366 36.000 18.73 5.96 40.27 2.67
3407 4972 5.406175 GTGCATTGAACAGTTTACATGCAAT 59.594 36.000 21.06 8.85 43.95 3.56
3408 4973 4.744137 GTGCATTGAACAGTTTACATGCAA 59.256 37.500 21.06 7.23 43.95 4.08
3409 4974 4.037803 AGTGCATTGAACAGTTTACATGCA 59.962 37.500 17.75 17.75 40.84 3.96
3410 4975 4.549458 AGTGCATTGAACAGTTTACATGC 58.451 39.130 14.28 14.28 0.00 4.06
3411 4976 8.572828 TTTAAGTGCATTGAACAGTTTACATG 57.427 30.769 0.00 0.00 32.96 3.21
3412 4977 8.413229 ACTTTAAGTGCATTGAACAGTTTACAT 58.587 29.630 0.00 0.00 32.96 2.29
3413 4978 7.767261 ACTTTAAGTGCATTGAACAGTTTACA 58.233 30.769 0.00 0.00 32.96 2.41
3414 4979 8.628882 AACTTTAAGTGCATTGAACAGTTTAC 57.371 30.769 0.00 0.00 32.96 2.01
3415 4980 9.081997 CAAACTTTAAGTGCATTGAACAGTTTA 57.918 29.630 13.89 0.00 32.96 2.01
3416 4981 7.602265 ACAAACTTTAAGTGCATTGAACAGTTT 59.398 29.630 13.03 10.85 32.96 2.66
3417 4982 7.096551 ACAAACTTTAAGTGCATTGAACAGTT 58.903 30.769 13.03 0.00 35.02 3.16
3418 4983 6.630071 ACAAACTTTAAGTGCATTGAACAGT 58.370 32.000 13.03 0.00 0.00 3.55
3419 4984 6.198966 GGACAAACTTTAAGTGCATTGAACAG 59.801 38.462 13.03 0.00 0.00 3.16
3420 4985 6.039616 GGACAAACTTTAAGTGCATTGAACA 58.960 36.000 13.03 0.00 0.00 3.18
3421 4986 6.273071 AGGACAAACTTTAAGTGCATTGAAC 58.727 36.000 13.03 6.74 0.00 3.18
3422 4987 6.463995 AGGACAAACTTTAAGTGCATTGAA 57.536 33.333 13.03 0.00 0.00 2.69
3436 5001 1.257743 TGAGCTAGCGAGGACAAACT 58.742 50.000 9.55 0.00 0.00 2.66
3437 5002 2.080286 TTGAGCTAGCGAGGACAAAC 57.920 50.000 9.55 0.00 0.00 2.93
3440 5005 0.532573 CCTTTGAGCTAGCGAGGACA 59.467 55.000 18.68 9.55 0.00 4.02
3441 5006 0.179097 CCCTTTGAGCTAGCGAGGAC 60.179 60.000 22.72 10.13 0.00 3.85
3460 5026 2.094762 ACAATACGGACCAACTGAGC 57.905 50.000 0.00 0.00 0.00 4.26
3461 5027 3.813166 ACAAACAATACGGACCAACTGAG 59.187 43.478 0.00 0.00 0.00 3.35
3463 5029 3.363575 CGACAAACAATACGGACCAACTG 60.364 47.826 0.00 0.00 0.00 3.16
3472 5038 1.931172 CCCCTAGCGACAAACAATACG 59.069 52.381 0.00 0.00 0.00 3.06
3474 5040 3.452990 TGATCCCCTAGCGACAAACAATA 59.547 43.478 0.00 0.00 0.00 1.90
3475 5041 2.238646 TGATCCCCTAGCGACAAACAAT 59.761 45.455 0.00 0.00 0.00 2.71
3476 5042 1.626321 TGATCCCCTAGCGACAAACAA 59.374 47.619 0.00 0.00 0.00 2.83
3477 5043 1.271856 TGATCCCCTAGCGACAAACA 58.728 50.000 0.00 0.00 0.00 2.83
3479 5045 3.557054 GCATATGATCCCCTAGCGACAAA 60.557 47.826 6.97 0.00 0.00 2.83
3480 5046 2.028112 GCATATGATCCCCTAGCGACAA 60.028 50.000 6.97 0.00 0.00 3.18
3482 5048 1.550524 TGCATATGATCCCCTAGCGAC 59.449 52.381 6.97 0.00 0.00 5.19
3483 5049 1.937191 TGCATATGATCCCCTAGCGA 58.063 50.000 6.97 0.00 0.00 4.93
3484 5050 2.768253 TTGCATATGATCCCCTAGCG 57.232 50.000 6.97 0.00 0.00 4.26
3485 5051 3.054139 TGGATTGCATATGATCCCCTAGC 60.054 47.826 16.88 0.00 40.92 3.42
3486 5052 4.472470 TCTGGATTGCATATGATCCCCTAG 59.528 45.833 16.88 10.26 40.92 3.02
3488 5054 3.262842 TCTGGATTGCATATGATCCCCT 58.737 45.455 16.88 0.00 40.92 4.79
3489 5055 3.726557 TCTGGATTGCATATGATCCCC 57.273 47.619 16.88 8.64 40.92 4.81
3490 5056 6.598503 TGATATCTGGATTGCATATGATCCC 58.401 40.000 16.88 8.35 40.92 3.85
3491 5057 8.158132 AGATGATATCTGGATTGCATATGATCC 58.842 37.037 14.00 14.00 41.78 3.36
3492 5058 9.210329 GAGATGATATCTGGATTGCATATGATC 57.790 37.037 6.97 1.20 40.38 2.92
3493 5059 8.714906 TGAGATGATATCTGGATTGCATATGAT 58.285 33.333 6.97 0.00 40.38 2.45
3494 5060 8.086143 TGAGATGATATCTGGATTGCATATGA 57.914 34.615 6.97 0.00 40.38 2.15
3495 5061 8.910351 ATGAGATGATATCTGGATTGCATATG 57.090 34.615 3.98 0.00 40.38 1.78
3496 5062 8.158132 GGATGAGATGATATCTGGATTGCATAT 58.842 37.037 3.98 0.00 40.38 1.78
3497 5063 7.506971 GGATGAGATGATATCTGGATTGCATA 58.493 38.462 3.98 0.00 40.38 3.14
3498 5064 6.358178 GGATGAGATGATATCTGGATTGCAT 58.642 40.000 3.98 0.00 40.38 3.96
3499 5065 5.626116 CGGATGAGATGATATCTGGATTGCA 60.626 44.000 3.98 0.00 40.38 4.08
3500 5066 4.809958 CGGATGAGATGATATCTGGATTGC 59.190 45.833 3.98 0.00 40.38 3.56
3515 5081 1.043116 CAGTACAGGGGCGGATGAGA 61.043 60.000 0.00 0.00 0.00 3.27
3526 5092 5.160607 TCCATAGTCCAAAACAGTACAGG 57.839 43.478 0.00 0.00 0.00 4.00
3533 5099 5.885912 GGCTTATCTTCCATAGTCCAAAACA 59.114 40.000 0.00 0.00 0.00 2.83
3540 5106 5.428253 TGTTGTGGCTTATCTTCCATAGTC 58.572 41.667 0.00 0.00 34.47 2.59
3549 5115 6.319658 CCAAAGTATCATGTTGTGGCTTATCT 59.680 38.462 0.00 0.00 0.00 1.98
3558 5124 4.588528 AGCCAAACCAAAGTATCATGTTGT 59.411 37.500 0.00 0.00 0.00 3.32
3608 5174 3.930634 ATGCAGAAGAACAAGAAAGCC 57.069 42.857 0.00 0.00 0.00 4.35
3625 5191 4.100707 TCAGACAAAGCTATGCAAATGC 57.899 40.909 0.00 0.00 42.50 3.56
3651 5224 2.038952 AGATGTAGCTGCCACAAGACAA 59.961 45.455 4.77 0.00 0.00 3.18
3653 5226 2.393271 AGATGTAGCTGCCACAAGAC 57.607 50.000 4.77 0.75 0.00 3.01
3656 5229 2.819608 GGAAAAGATGTAGCTGCCACAA 59.180 45.455 4.77 0.00 0.00 3.33
3664 5237 8.915654 CAACAAATTTGTAGGAAAAGATGTAGC 58.084 33.333 23.53 0.00 41.31 3.58
3670 5243 6.978080 GCTGTCAACAAATTTGTAGGAAAAGA 59.022 34.615 23.53 10.38 41.31 2.52
3671 5244 6.756074 TGCTGTCAACAAATTTGTAGGAAAAG 59.244 34.615 23.53 21.08 41.31 2.27
3726 5299 7.067859 CAGGAAATCTCTTTATGCCATCTTGAA 59.932 37.037 0.00 0.00 0.00 2.69
3727 5300 6.544931 CAGGAAATCTCTTTATGCCATCTTGA 59.455 38.462 0.00 0.00 0.00 3.02
3728 5301 6.544931 TCAGGAAATCTCTTTATGCCATCTTG 59.455 38.462 0.00 0.00 0.00 3.02
3729 5302 6.666678 TCAGGAAATCTCTTTATGCCATCTT 58.333 36.000 0.00 0.00 0.00 2.40
3730 5303 6.257994 TCAGGAAATCTCTTTATGCCATCT 57.742 37.500 0.00 0.00 0.00 2.90
3731 5304 6.713903 TCATCAGGAAATCTCTTTATGCCATC 59.286 38.462 0.00 0.00 0.00 3.51
3750 5323 3.902150 AGACACAGTTACACGTCATCAG 58.098 45.455 0.00 0.00 0.00 2.90
3751 5324 3.316868 TGAGACACAGTTACACGTCATCA 59.683 43.478 0.00 0.00 0.00 3.07
3752 5325 3.897325 TGAGACACAGTTACACGTCATC 58.103 45.455 0.00 0.00 0.00 2.92
3771 5344 8.023128 GCAGTCACTTTCTAAAAGCATTTATGA 58.977 33.333 0.00 0.00 37.28 2.15
3773 5346 7.177392 AGGCAGTCACTTTCTAAAAGCATTTAT 59.823 33.333 0.00 0.00 37.28 1.40
3781 5354 8.911918 TTGTATTAGGCAGTCACTTTCTAAAA 57.088 30.769 1.88 0.00 0.00 1.52
3794 5367 9.434420 TTGGAAATCAAAATTTGTATTAGGCAG 57.566 29.630 5.56 0.00 35.21 4.85
3840 5413 6.668541 CCATGTACTGGTGTCTCATTTTAG 57.331 41.667 0.00 0.00 40.49 1.85
3858 5431 5.652452 GTCCATAAAAGCTTTAGGACCATGT 59.348 40.000 29.82 11.54 39.61 3.21
3859 5432 5.652014 TGTCCATAAAAGCTTTAGGACCATG 59.348 40.000 33.10 20.87 43.68 3.66
3905 5497 9.741647 GGAAAAACAAATTGCAAATAATGGAAA 57.258 25.926 1.71 0.00 43.03 3.13
3906 5498 9.129532 AGGAAAAACAAATTGCAAATAATGGAA 57.870 25.926 1.71 0.00 43.98 3.53
3947 5539 1.337167 GCAGAAAATGTGGGGACAAGC 60.337 52.381 0.00 0.00 46.06 4.01
3949 5541 1.962807 CTGCAGAAAATGTGGGGACAA 59.037 47.619 8.42 0.00 46.06 3.18
3956 5548 4.855388 GTGAACTATGCTGCAGAAAATGTG 59.145 41.667 20.43 7.63 0.00 3.21
3957 5549 4.763793 AGTGAACTATGCTGCAGAAAATGT 59.236 37.500 20.43 4.75 0.00 2.71
3999 5591 5.529791 TCTACTGCTCTAACAACAGTTCAC 58.470 41.667 0.00 0.00 41.78 3.18
4014 5606 6.944862 ACCATCAAAATCTTTCTTCTACTGCT 59.055 34.615 0.00 0.00 0.00 4.24
4091 5683 0.952497 CTGCTCCAGTTGCATCACGT 60.952 55.000 0.00 0.00 39.86 4.49
4097 5689 1.974875 CATGCCTGCTCCAGTTGCA 60.975 57.895 0.00 0.00 34.36 4.08
4319 5911 3.293311 TCGACCAACTCCTTAAAGACG 57.707 47.619 0.00 0.00 0.00 4.18
4403 5995 1.978580 TCCTTCTTCACAACCTCCTCC 59.021 52.381 0.00 0.00 0.00 4.30
4568 6160 0.958091 TTTGCTTCACCCATTCACCG 59.042 50.000 0.00 0.00 0.00 4.94
4601 6193 2.417924 CCTCACCTTCATGTTCTCTCCG 60.418 54.545 0.00 0.00 0.00 4.63
4728 6320 2.354259 CTCAGGCTTGTCATCCTTCAC 58.646 52.381 0.00 0.00 0.00 3.18
4893 6486 4.407365 AGTGTTGACTTTAGGGGAAATGG 58.593 43.478 0.00 0.00 0.00 3.16
5132 6725 3.493176 CGTGGATGTATGAGCCAATCAGA 60.493 47.826 0.00 0.00 43.52 3.27
5144 6737 0.248012 TGCGGTTGTCGTGGATGTAT 59.752 50.000 0.00 0.00 41.72 2.29
5168 6761 6.602009 TCTCAGAGTTGATTTCAATCATGCAT 59.398 34.615 3.06 0.00 44.27 3.96
5195 6788 1.005037 ATTGCGAGCCACGAAGTCA 60.005 52.632 5.11 0.00 41.61 3.41
5201 6794 0.729116 ATTTCTCATTGCGAGCCACG 59.271 50.000 0.00 0.00 41.98 4.94
5384 6977 1.208706 TTGATATCCGCCCTTCCACA 58.791 50.000 0.00 0.00 0.00 4.17
5733 7326 8.756927 TCATGGACAATATATTGATCTCTCCTC 58.243 37.037 28.13 14.07 40.14 3.71
6002 7649 7.065085 AGACACACTGTAACATTAATCATGAGC 59.935 37.037 0.09 0.00 36.24 4.26
6104 7752 1.220206 CGCTGGATGTGGAAGCTCT 59.780 57.895 0.00 0.00 34.72 4.09
6130 7778 2.894387 GAGAGCATGCGGGCTGTC 60.894 66.667 13.01 8.62 45.99 3.51
6170 7818 4.639334 GAGCTGCTAGATTGGATTGATGA 58.361 43.478 0.15 0.00 0.00 2.92
6227 7875 2.699846 GAGAGTCTGGGCATCATCTCTT 59.300 50.000 0.00 2.49 37.01 2.85
6265 7913 3.994165 AGCAAATGGAGGCTCATGT 57.006 47.368 17.69 0.33 34.76 3.21
6664 8312 5.877012 CACTATCATTAGCTGGTCACACTTT 59.123 40.000 0.00 0.00 0.00 2.66
6758 8406 5.053811 TGCACAGATGTTACTCTCGAAAAA 58.946 37.500 0.00 0.00 0.00 1.94
6759 8407 4.627058 TGCACAGATGTTACTCTCGAAAA 58.373 39.130 0.00 0.00 0.00 2.29
6760 8408 4.251543 TGCACAGATGTTACTCTCGAAA 57.748 40.909 0.00 0.00 0.00 3.46
6761 8409 3.934457 TGCACAGATGTTACTCTCGAA 57.066 42.857 0.00 0.00 0.00 3.71
6762 8410 5.774498 ATATGCACAGATGTTACTCTCGA 57.226 39.130 0.00 0.00 0.00 4.04
6763 8411 6.834959 AAATATGCACAGATGTTACTCTCG 57.165 37.500 0.00 0.00 0.00 4.04
6764 8412 9.098355 TGTTAAATATGCACAGATGTTACTCTC 57.902 33.333 0.00 0.00 0.00 3.20
6765 8413 9.618890 ATGTTAAATATGCACAGATGTTACTCT 57.381 29.630 0.00 0.00 0.00 3.24
6766 8414 9.869844 GATGTTAAATATGCACAGATGTTACTC 57.130 33.333 0.00 0.00 0.00 2.59
6767 8415 8.840321 GGATGTTAAATATGCACAGATGTTACT 58.160 33.333 0.00 0.00 0.00 2.24
6768 8416 8.620416 TGGATGTTAAATATGCACAGATGTTAC 58.380 33.333 0.00 0.00 0.00 2.50
6769 8417 8.744568 TGGATGTTAAATATGCACAGATGTTA 57.255 30.769 0.00 0.00 0.00 2.41
6770 8418 7.643569 TGGATGTTAAATATGCACAGATGTT 57.356 32.000 0.00 0.00 0.00 2.71
6771 8419 7.828508 ATGGATGTTAAATATGCACAGATGT 57.171 32.000 0.00 0.00 0.00 3.06
6806 8454 6.763610 AGTAATTCTCTGGAGGAAAAATAGCG 59.236 38.462 0.00 0.00 0.00 4.26
6809 8457 9.231297 CAACAGTAATTCTCTGGAGGAAAAATA 57.769 33.333 12.90 0.00 37.25 1.40
6814 8462 4.565652 GGCAACAGTAATTCTCTGGAGGAA 60.566 45.833 12.90 0.00 37.25 3.36
6950 8599 8.792830 TCCTATAGTGATTAGCAAATAATGGC 57.207 34.615 0.00 0.00 34.10 4.40
6969 8618 7.310634 AGTTGTAACCCACCTGATATCCTATA 58.689 38.462 0.00 0.00 0.00 1.31
6970 8619 6.151049 AGTTGTAACCCACCTGATATCCTAT 58.849 40.000 0.00 0.00 0.00 2.57
6971 8620 5.535029 AGTTGTAACCCACCTGATATCCTA 58.465 41.667 0.00 0.00 0.00 2.94


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

AutoCloner maintained by Alex Coulton.