Multiple sequence alignment - TraesCS4B01G223700

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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 TraesCS4B01G223700 chr4B 100.000 3735 0 0 1 3735 468052994 468049260 0.000000e+00 6898
1 TraesCS4B01G223700 chr4D 93.553 3366 114 45 203 3510 380798189 380794869 0.000000e+00 4918
2 TraesCS4B01G223700 chr4A 92.535 2840 71 39 538 3280 82846297 82849092 0.000000e+00 3940
3 TraesCS4B01G223700 chr4A 91.509 212 10 3 1 210 82843560 82843765 6.110000e-73 285
4 TraesCS4B01G223700 chr4A 85.932 263 24 8 204 464 82845944 82846195 6.150000e-68 268
5 TraesCS4B01G223700 chr4A 91.753 97 7 1 3218 3313 82849093 82849189 2.340000e-27 134


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 TraesCS4B01G223700 chr4B 468049260 468052994 3734 True 6898.00 6898 100.00000 1 3735 1 chr4B.!!$R1 3734
1 TraesCS4B01G223700 chr4D 380794869 380798189 3320 True 4918.00 4918 93.55300 203 3510 1 chr4D.!!$R1 3307
2 TraesCS4B01G223700 chr4A 82843560 82849189 5629 False 1156.75 3940 90.43225 1 3313 4 chr4A.!!$F1 3312

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
568 2803 0.248621 GATCCTCAAATTTGCCGGCG 60.249 55.0 23.90 6.13 0.0 6.46 F
841 3100 0.984995 AACGGAGGAGAAAGGAAGGG 59.015 55.0 0.00 0.00 0.0 3.95 F
2104 4434 0.445043 GTCGGCCAATCACGGTTTAC 59.555 55.0 2.24 0.00 0.0 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 4194 0.971447 GGGAGTTGAGCCCGTAGACT 60.971 60.000 0.00 0.0 35.5 3.24 R
2191 4521 1.077787 CCGCCCAGCTGTATCCAAA 60.078 57.895 13.81 0.0 0.0 3.28 R
3635 6042 0.179119 GCCATGCAGATTGAAGCCAC 60.179 55.000 0.00 0.0 0.0 5.01 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
46 47 1.000739 TTATCCCGTGACCCGACCT 59.999 57.895 0.00 0.00 39.56 3.85
85 86 0.585357 CCGTACGTAGGACCATCGAG 59.415 60.000 16.52 6.03 0.00 4.04
147 150 0.321671 ATCCCGCCAGATGATAACGG 59.678 55.000 0.00 0.00 43.44 4.44
155 158 3.861131 GCCAGATGATAACGGTTAGCGAT 60.861 47.826 11.70 0.24 0.00 4.58
156 159 3.675225 CCAGATGATAACGGTTAGCGATG 59.325 47.826 11.70 9.12 0.00 3.84
157 160 4.546570 CAGATGATAACGGTTAGCGATGA 58.453 43.478 11.70 0.00 0.00 2.92
158 161 5.164233 CAGATGATAACGGTTAGCGATGAT 58.836 41.667 11.70 0.07 0.00 2.45
159 162 5.287274 CAGATGATAACGGTTAGCGATGATC 59.713 44.000 11.70 10.06 0.00 2.92
160 163 3.561503 TGATAACGGTTAGCGATGATCG 58.438 45.455 11.70 11.02 43.89 3.69
186 189 4.883083 TCGTGAGCACTAATCTGAACTTT 58.117 39.130 0.00 0.00 0.00 2.66
189 192 6.073765 TCGTGAGCACTAATCTGAACTTTTTC 60.074 38.462 0.00 0.00 0.00 2.29
193 196 7.283127 TGAGCACTAATCTGAACTTTTTCTTGT 59.717 33.333 0.00 0.00 32.36 3.16
200 203 3.436243 TGAACTTTTTCTTGTGGGGTGT 58.564 40.909 0.00 0.00 32.36 4.16
201 204 4.601084 TGAACTTTTTCTTGTGGGGTGTA 58.399 39.130 0.00 0.00 32.36 2.90
211 2399 3.799432 TGTGGGGTGTAAGCACTAATT 57.201 42.857 0.00 0.00 44.65 1.40
215 2403 4.705023 GTGGGGTGTAAGCACTAATTTGAT 59.295 41.667 0.00 0.00 44.65 2.57
260 2448 1.446272 CGAAGTCTCGGTTCCTGGC 60.446 63.158 0.00 0.00 41.57 4.85
319 2508 3.375699 TGGTTACAAAAGGCCCAAAAGA 58.624 40.909 0.00 0.00 0.00 2.52
379 2569 0.598065 CTACTTTGCAACCACCCTGC 59.402 55.000 0.00 0.00 40.35 4.85
391 2581 2.025037 ACCACCCTGCAATCACATGTAT 60.025 45.455 0.00 0.00 0.00 2.29
443 2633 1.661463 TGAGATGAAGAAGCCCACCT 58.339 50.000 0.00 0.00 0.00 4.00
464 2655 0.887247 TGTAAACACGCCGGCTACTA 59.113 50.000 26.68 5.68 0.00 1.82
466 2657 2.687425 TGTAAACACGCCGGCTACTATA 59.313 45.455 26.68 9.43 0.00 1.31
467 2658 2.965572 AAACACGCCGGCTACTATAA 57.034 45.000 26.68 0.00 0.00 0.98
468 2659 2.503920 AACACGCCGGCTACTATAAG 57.496 50.000 26.68 8.67 0.00 1.73
470 2661 2.236766 ACACGCCGGCTACTATAAGAT 58.763 47.619 26.68 0.00 0.00 2.40
471 2662 2.228343 ACACGCCGGCTACTATAAGATC 59.772 50.000 26.68 0.00 0.00 2.75
472 2663 2.228103 CACGCCGGCTACTATAAGATCA 59.772 50.000 26.68 0.00 0.00 2.92
476 2667 5.184479 ACGCCGGCTACTATAAGATCATTTA 59.816 40.000 26.68 0.00 0.00 1.40
477 2668 5.744345 CGCCGGCTACTATAAGATCATTTAG 59.256 44.000 26.68 0.00 0.00 1.85
478 2669 6.404403 CGCCGGCTACTATAAGATCATTTAGA 60.404 42.308 26.68 0.00 0.00 2.10
563 2798 7.542025 AGTTACAGATTGATCCTCAAATTTGC 58.458 34.615 13.54 0.00 40.12 3.68
564 2799 5.334724 ACAGATTGATCCTCAAATTTGCC 57.665 39.130 13.54 1.23 40.12 4.52
565 2800 4.142315 ACAGATTGATCCTCAAATTTGCCG 60.142 41.667 13.54 6.80 40.12 5.69
568 2803 0.248621 GATCCTCAAATTTGCCGGCG 60.249 55.000 23.90 6.13 0.00 6.46
662 2897 5.098893 CGTTCCAAATTTGAAATGCGGATA 58.901 37.500 19.86 0.00 0.00 2.59
758 3016 3.102052 TCGTCAAAAGTACGAAAGCCT 57.898 42.857 0.00 0.00 45.62 4.58
769 3027 1.279271 ACGAAAGCCTAGGCAGTCATT 59.721 47.619 34.70 20.02 44.88 2.57
770 3028 1.667724 CGAAAGCCTAGGCAGTCATTG 59.332 52.381 34.70 15.24 44.88 2.82
771 3029 2.019984 GAAAGCCTAGGCAGTCATTGG 58.980 52.381 34.70 0.00 44.88 3.16
811 3069 4.158579 GTGGGCTCCTGGAAAATCTAAAAG 59.841 45.833 0.00 0.00 0.00 2.27
839 3098 2.388310 GGAACGGAGGAGAAAGGAAG 57.612 55.000 0.00 0.00 0.00 3.46
840 3099 1.066071 GGAACGGAGGAGAAAGGAAGG 60.066 57.143 0.00 0.00 0.00 3.46
841 3100 0.984995 AACGGAGGAGAAAGGAAGGG 59.015 55.000 0.00 0.00 0.00 3.95
858 3128 2.203209 GATCCATCCCCACGCCAC 60.203 66.667 0.00 0.00 0.00 5.01
940 3231 2.355197 AGCAAGCAAACAAACAAACCC 58.645 42.857 0.00 0.00 0.00 4.11
963 3254 2.992114 AACCGAGGAGAGCACGCT 60.992 61.111 0.00 0.00 0.00 5.07
964 3255 1.654954 GAACCGAGGAGAGCACGCTA 61.655 60.000 0.00 0.00 0.00 4.26
965 3256 1.935327 AACCGAGGAGAGCACGCTAC 61.935 60.000 0.00 0.00 0.00 3.58
966 3257 2.115911 CCGAGGAGAGCACGCTACT 61.116 63.158 0.00 0.00 0.00 2.57
967 3258 1.063327 CGAGGAGAGCACGCTACTG 59.937 63.158 0.00 0.00 0.00 2.74
968 3259 1.226831 GAGGAGAGCACGCTACTGC 60.227 63.158 0.00 0.00 37.44 4.40
970 3261 2.202810 GAGAGCACGCTACTGCCC 60.203 66.667 0.00 0.00 37.96 5.36
971 3262 3.724914 GAGAGCACGCTACTGCCCC 62.725 68.421 0.00 0.00 37.96 5.80
1648 3978 2.034066 TCGGGGGTCTACGTCGTT 59.966 61.111 1.78 0.00 0.00 3.85
1864 4194 0.614697 TCTGGGCATCCTCGTCTTCA 60.615 55.000 0.00 0.00 0.00 3.02
2104 4434 0.445043 GTCGGCCAATCACGGTTTAC 59.555 55.000 2.24 0.00 0.00 2.01
2110 4440 2.929592 GCCAATCACGGTTTACGAGAGT 60.930 50.000 0.00 0.00 45.00 3.24
2191 4521 2.311542 TGTGAAAGGATGTATTGGGGCT 59.688 45.455 0.00 0.00 0.00 5.19
2467 4797 0.661483 GGCTCAAGAAGTTTGTGCGC 60.661 55.000 0.00 0.00 39.13 6.09
2569 4899 2.033141 AATGGCAGCACGAGCAGT 59.967 55.556 7.77 0.00 45.49 4.40
2866 5196 7.757097 TTGCAAAGACTACGATAGATTCTTC 57.243 36.000 0.00 0.00 41.38 2.87
3048 5378 5.048364 TGCACTTGTGGTATAAAACATGTCC 60.048 40.000 0.00 0.00 33.75 4.02
3104 5434 4.045636 TGTGGATACGACTCATGTGATG 57.954 45.455 0.94 0.00 42.51 3.07
3192 5531 2.792674 TCGTGAGTGCTACAACTTTTCG 59.207 45.455 0.00 0.00 0.00 3.46
3193 5532 2.792674 CGTGAGTGCTACAACTTTTCGA 59.207 45.455 0.00 0.00 0.00 3.71
3205 5544 8.443937 GCTACAACTTTTCGAAGACAGATTAAT 58.556 33.333 0.00 0.00 34.32 1.40
3211 5550 8.027771 ACTTTTCGAAGACAGATTAATCGTACT 58.972 33.333 9.78 7.48 34.32 2.73
3299 5703 5.775686 TGAATTGTCTGATTTGGCTTTCTG 58.224 37.500 0.00 0.00 0.00 3.02
3300 5704 3.648339 TTGTCTGATTTGGCTTTCTGC 57.352 42.857 0.00 0.00 41.94 4.26
3318 5722 8.141268 GCTTTCTGCTTATGAACTACTAGATCT 58.859 37.037 0.00 0.00 38.95 2.75
3384 5788 5.539955 GGTTGAATGCTATGGTATGGGAATT 59.460 40.000 0.00 0.00 0.00 2.17
3398 5802 6.715264 GGTATGGGAATTACCAATTGTCTAGG 59.285 42.308 14.99 0.00 45.13 3.02
3402 5806 6.661805 TGGGAATTACCAATTGTCTAGGAAAC 59.338 38.462 7.04 0.00 41.20 2.78
3422 5826 8.571336 AGGAAACAGAAACATAATTTCAGACTG 58.429 33.333 0.00 0.00 32.13 3.51
3460 5864 4.281941 CGGATGGGAAGATCTGATCACTTA 59.718 45.833 19.12 2.86 31.19 2.24
3481 5888 9.632807 CACTTATTACTATAGCAATCCAGTCTC 57.367 37.037 1.28 0.00 0.00 3.36
3492 5899 5.936956 AGCAATCCAGTCTCTTTCTTTACTG 59.063 40.000 0.00 0.00 39.22 2.74
3493 5900 5.391416 GCAATCCAGTCTCTTTCTTTACTGC 60.391 44.000 0.00 0.00 38.39 4.40
3499 5906 2.038557 TCTCTTTCTTTACTGCGGGCTT 59.961 45.455 0.00 0.00 0.00 4.35
3531 5938 9.443323 TTTGTCGGACTTTTATTCATAGAATGA 57.557 29.630 9.88 0.00 37.55 2.57
3532 5939 8.648557 TGTCGGACTTTTATTCATAGAATGAG 57.351 34.615 9.88 1.66 40.94 2.90
3533 5940 8.258007 TGTCGGACTTTTATTCATAGAATGAGT 58.742 33.333 9.88 4.36 40.94 3.41
3534 5941 9.099454 GTCGGACTTTTATTCATAGAATGAGTT 57.901 33.333 0.00 0.00 40.94 3.01
3535 5942 9.667107 TCGGACTTTTATTCATAGAATGAGTTT 57.333 29.630 2.65 0.00 40.94 2.66
3536 5943 9.708222 CGGACTTTTATTCATAGAATGAGTTTG 57.292 33.333 2.65 0.00 40.94 2.93
3551 5958 9.125026 AGAATGAGTTTGTGAGTAAAAATGTCT 57.875 29.630 0.00 0.00 0.00 3.41
3554 5961 9.778741 ATGAGTTTGTGAGTAAAAATGTCTAGA 57.221 29.630 0.00 0.00 0.00 2.43
3555 5962 9.607988 TGAGTTTGTGAGTAAAAATGTCTAGAA 57.392 29.630 0.00 0.00 0.00 2.10
3556 5963 9.865484 GAGTTTGTGAGTAAAAATGTCTAGAAC 57.135 33.333 0.00 0.00 0.00 3.01
3557 5964 9.614792 AGTTTGTGAGTAAAAATGTCTAGAACT 57.385 29.630 0.00 0.00 0.00 3.01
3558 5965 9.651718 GTTTGTGAGTAAAAATGTCTAGAACTG 57.348 33.333 0.00 0.00 0.00 3.16
3559 5966 7.962964 TGTGAGTAAAAATGTCTAGAACTGG 57.037 36.000 0.00 0.00 0.00 4.00
3560 5967 7.732025 TGTGAGTAAAAATGTCTAGAACTGGA 58.268 34.615 0.00 0.00 0.00 3.86
3561 5968 8.208224 TGTGAGTAAAAATGTCTAGAACTGGAA 58.792 33.333 0.00 0.00 0.00 3.53
3562 5969 9.052759 GTGAGTAAAAATGTCTAGAACTGGAAA 57.947 33.333 0.00 0.00 0.00 3.13
3563 5970 9.793259 TGAGTAAAAATGTCTAGAACTGGAAAT 57.207 29.630 0.00 0.00 0.00 2.17
3565 5972 8.515414 AGTAAAAATGTCTAGAACTGGAAATGC 58.485 33.333 0.00 0.00 0.00 3.56
3566 5973 6.899393 AAAATGTCTAGAACTGGAAATGCA 57.101 33.333 0.00 0.00 0.00 3.96
3567 5974 7.472334 AAAATGTCTAGAACTGGAAATGCAT 57.528 32.000 0.00 0.00 0.00 3.96
3568 5975 7.472334 AAATGTCTAGAACTGGAAATGCATT 57.528 32.000 5.99 5.99 0.00 3.56
3569 5976 7.472334 AATGTCTAGAACTGGAAATGCATTT 57.528 32.000 24.33 24.33 0.00 2.32
3570 5977 6.899393 TGTCTAGAACTGGAAATGCATTTT 57.101 33.333 24.81 9.49 0.00 1.82
3571 5978 6.913170 TGTCTAGAACTGGAAATGCATTTTC 58.087 36.000 24.81 23.17 42.57 2.29
3572 5979 6.716628 TGTCTAGAACTGGAAATGCATTTTCT 59.283 34.615 26.87 23.71 42.83 2.52
3573 5980 7.025963 GTCTAGAACTGGAAATGCATTTTCTG 58.974 38.462 27.04 27.04 42.83 3.02
3574 5981 6.942005 TCTAGAACTGGAAATGCATTTTCTGA 59.058 34.615 32.43 21.72 42.83 3.27
3575 5982 6.600882 AGAACTGGAAATGCATTTTCTGAT 57.399 33.333 32.43 24.97 42.83 2.90
3576 5983 7.001099 AGAACTGGAAATGCATTTTCTGATT 57.999 32.000 32.43 24.12 42.83 2.57
3577 5984 7.447594 AGAACTGGAAATGCATTTTCTGATTT 58.552 30.769 32.43 21.69 42.83 2.17
3578 5985 7.386848 AGAACTGGAAATGCATTTTCTGATTTG 59.613 33.333 32.43 17.58 42.83 2.32
3579 5986 5.935789 ACTGGAAATGCATTTTCTGATTTGG 59.064 36.000 32.43 16.24 42.83 3.28
3580 5987 5.867330 TGGAAATGCATTTTCTGATTTGGT 58.133 33.333 26.87 1.95 42.83 3.67
3581 5988 5.933463 TGGAAATGCATTTTCTGATTTGGTC 59.067 36.000 26.87 10.60 42.83 4.02
3582 5989 5.062558 GGAAATGCATTTTCTGATTTGGTCG 59.937 40.000 24.81 0.00 42.83 4.79
3583 5990 4.789012 ATGCATTTTCTGATTTGGTCGT 57.211 36.364 0.00 0.00 0.00 4.34
3584 5991 4.582701 TGCATTTTCTGATTTGGTCGTT 57.417 36.364 0.00 0.00 0.00 3.85
3585 5992 4.297510 TGCATTTTCTGATTTGGTCGTTG 58.702 39.130 0.00 0.00 0.00 4.10
3586 5993 3.674753 GCATTTTCTGATTTGGTCGTTGG 59.325 43.478 0.00 0.00 0.00 3.77
3587 5994 3.363341 TTTTCTGATTTGGTCGTTGGC 57.637 42.857 0.00 0.00 0.00 4.52
3588 5995 1.974265 TTCTGATTTGGTCGTTGGCA 58.026 45.000 0.00 0.00 0.00 4.92
3589 5996 1.234821 TCTGATTTGGTCGTTGGCAC 58.765 50.000 0.00 0.00 0.00 5.01
3590 5997 1.202758 TCTGATTTGGTCGTTGGCACT 60.203 47.619 0.00 0.00 0.00 4.40
3591 5998 0.950836 TGATTTGGTCGTTGGCACTG 59.049 50.000 0.00 0.00 0.00 3.66
3592 5999 0.951558 GATTTGGTCGTTGGCACTGT 59.048 50.000 0.00 0.00 0.00 3.55
3593 6000 0.667993 ATTTGGTCGTTGGCACTGTG 59.332 50.000 2.76 2.76 0.00 3.66
3594 6001 0.393132 TTTGGTCGTTGGCACTGTGA 60.393 50.000 12.86 0.00 0.00 3.58
3595 6002 0.393132 TTGGTCGTTGGCACTGTGAA 60.393 50.000 12.86 0.00 0.00 3.18
3596 6003 1.092921 TGGTCGTTGGCACTGTGAAC 61.093 55.000 12.86 7.12 0.00 3.18
3597 6004 1.275657 GTCGTTGGCACTGTGAACG 59.724 57.895 21.64 21.64 42.96 3.95
3598 6005 1.153529 TCGTTGGCACTGTGAACGT 60.154 52.632 24.56 0.00 42.37 3.99
3599 6006 0.741574 TCGTTGGCACTGTGAACGTT 60.742 50.000 24.56 0.00 42.37 3.99
3600 6007 0.588730 CGTTGGCACTGTGAACGTTG 60.589 55.000 20.21 0.00 38.10 4.10
3601 6008 0.865639 GTTGGCACTGTGAACGTTGC 60.866 55.000 12.86 1.40 0.00 4.17
3602 6009 1.029408 TTGGCACTGTGAACGTTGCT 61.029 50.000 12.86 0.00 0.00 3.91
3603 6010 1.009675 GGCACTGTGAACGTTGCTG 60.010 57.895 12.86 5.18 0.00 4.41
3604 6011 1.436195 GGCACTGTGAACGTTGCTGA 61.436 55.000 12.86 0.00 0.00 4.26
3605 6012 0.588252 GCACTGTGAACGTTGCTGAT 59.412 50.000 12.86 0.00 0.00 2.90
3606 6013 1.798223 GCACTGTGAACGTTGCTGATA 59.202 47.619 12.86 0.00 0.00 2.15
3607 6014 2.416547 GCACTGTGAACGTTGCTGATAT 59.583 45.455 12.86 0.00 0.00 1.63
3608 6015 3.484229 GCACTGTGAACGTTGCTGATATC 60.484 47.826 12.86 0.00 0.00 1.63
3609 6016 3.928992 CACTGTGAACGTTGCTGATATCT 59.071 43.478 5.00 0.00 0.00 1.98
3610 6017 4.389992 CACTGTGAACGTTGCTGATATCTT 59.610 41.667 5.00 0.00 0.00 2.40
3611 6018 4.389992 ACTGTGAACGTTGCTGATATCTTG 59.610 41.667 5.00 0.00 0.00 3.02
3612 6019 3.684305 TGTGAACGTTGCTGATATCTTGG 59.316 43.478 5.00 0.00 0.00 3.61
3613 6020 3.063997 GTGAACGTTGCTGATATCTTGGG 59.936 47.826 5.00 0.00 0.00 4.12
3614 6021 3.055458 TGAACGTTGCTGATATCTTGGGA 60.055 43.478 5.00 0.00 0.00 4.37
3615 6022 3.845781 ACGTTGCTGATATCTTGGGAT 57.154 42.857 3.98 0.00 36.07 3.85
3616 6023 3.470709 ACGTTGCTGATATCTTGGGATG 58.529 45.455 3.98 0.00 33.71 3.51
3617 6024 2.225019 CGTTGCTGATATCTTGGGATGC 59.775 50.000 3.98 0.00 33.71 3.91
3618 6025 2.555757 GTTGCTGATATCTTGGGATGCC 59.444 50.000 3.98 0.00 33.71 4.40
3619 6026 1.776063 TGCTGATATCTTGGGATGCCA 59.224 47.619 0.00 0.00 33.71 4.92
3620 6027 2.377531 TGCTGATATCTTGGGATGCCAT 59.622 45.455 6.84 0.00 33.71 4.40
3621 6028 2.753452 GCTGATATCTTGGGATGCCATG 59.247 50.000 6.84 10.11 33.71 3.66
3622 6029 3.353557 CTGATATCTTGGGATGCCATGG 58.646 50.000 17.49 7.63 33.71 3.66
3623 6030 2.718062 TGATATCTTGGGATGCCATGGT 59.282 45.455 17.49 13.84 33.71 3.55
3624 6031 3.915711 TGATATCTTGGGATGCCATGGTA 59.084 43.478 17.49 15.50 33.71 3.25
3625 6032 4.541310 TGATATCTTGGGATGCCATGGTAT 59.459 41.667 20.61 20.61 33.71 2.73
3626 6033 2.957402 TCTTGGGATGCCATGGTATC 57.043 50.000 29.14 29.14 36.67 2.24
3627 6034 2.134354 TCTTGGGATGCCATGGTATCA 58.866 47.619 34.80 19.56 38.66 2.15
3628 6035 2.718062 TCTTGGGATGCCATGGTATCAT 59.282 45.455 34.80 21.01 38.66 2.45
3629 6036 3.140707 TCTTGGGATGCCATGGTATCATT 59.859 43.478 34.80 9.18 38.66 2.57
3630 6037 2.879154 TGGGATGCCATGGTATCATTG 58.121 47.619 34.80 1.23 38.66 2.82
3631 6038 1.547372 GGGATGCCATGGTATCATTGC 59.453 52.381 34.80 21.56 41.00 3.56
3632 6039 2.522185 GGATGCCATGGTATCATTGCT 58.478 47.619 34.80 7.33 41.14 3.91
3633 6040 3.561960 GGGATGCCATGGTATCATTGCTA 60.562 47.826 34.80 1.03 41.14 3.49
3634 6041 4.275810 GGATGCCATGGTATCATTGCTAT 58.724 43.478 34.80 5.86 41.14 2.97
3635 6042 4.097437 GGATGCCATGGTATCATTGCTATG 59.903 45.833 34.80 1.30 41.14 2.23
3636 6043 4.103013 TGCCATGGTATCATTGCTATGT 57.897 40.909 14.67 0.00 41.14 2.29
3637 6044 3.822167 TGCCATGGTATCATTGCTATGTG 59.178 43.478 14.67 0.00 41.14 3.21
3638 6045 3.192001 GCCATGGTATCATTGCTATGTGG 59.808 47.826 14.67 8.16 38.54 4.17
3639 6046 3.192001 CCATGGTATCATTGCTATGTGGC 59.808 47.826 2.57 0.20 33.34 5.01
3640 6047 3.862877 TGGTATCATTGCTATGTGGCT 57.137 42.857 8.01 0.00 33.34 4.75
3641 6048 4.169059 TGGTATCATTGCTATGTGGCTT 57.831 40.909 8.01 0.00 33.34 4.35
3642 6049 4.136796 TGGTATCATTGCTATGTGGCTTC 58.863 43.478 8.01 0.00 33.34 3.86
3643 6050 4.136796 GGTATCATTGCTATGTGGCTTCA 58.863 43.478 8.01 0.00 33.34 3.02
3644 6051 4.580167 GGTATCATTGCTATGTGGCTTCAA 59.420 41.667 8.01 0.00 33.34 2.69
3645 6052 5.242393 GGTATCATTGCTATGTGGCTTCAAT 59.758 40.000 8.01 0.00 33.34 2.57
3646 6053 4.906065 TCATTGCTATGTGGCTTCAATC 57.094 40.909 8.01 0.00 33.34 2.67
3647 6054 4.529897 TCATTGCTATGTGGCTTCAATCT 58.470 39.130 8.01 0.00 33.34 2.40
3648 6055 4.337274 TCATTGCTATGTGGCTTCAATCTG 59.663 41.667 8.01 0.00 33.34 2.90
3649 6056 2.019249 TGCTATGTGGCTTCAATCTGC 58.981 47.619 0.00 0.00 0.00 4.26
3650 6057 2.019249 GCTATGTGGCTTCAATCTGCA 58.981 47.619 0.00 0.00 0.00 4.41
3651 6058 2.621998 GCTATGTGGCTTCAATCTGCAT 59.378 45.455 0.00 0.00 0.00 3.96
3652 6059 3.550233 GCTATGTGGCTTCAATCTGCATG 60.550 47.826 0.00 0.00 0.00 4.06
3653 6060 1.179152 TGTGGCTTCAATCTGCATGG 58.821 50.000 0.00 0.00 0.00 3.66
3654 6061 0.179119 GTGGCTTCAATCTGCATGGC 60.179 55.000 0.00 0.00 0.00 4.40
3655 6062 1.324740 TGGCTTCAATCTGCATGGCC 61.325 55.000 0.00 0.00 38.67 5.36
3656 6063 1.324740 GGCTTCAATCTGCATGGCCA 61.325 55.000 8.56 8.56 38.16 5.36
3657 6064 0.750850 GCTTCAATCTGCATGGCCAT 59.249 50.000 14.09 14.09 0.00 4.40
3658 6065 1.138266 GCTTCAATCTGCATGGCCATT 59.862 47.619 17.92 0.00 0.00 3.16
3659 6066 2.419574 GCTTCAATCTGCATGGCCATTT 60.420 45.455 17.92 4.34 0.00 2.32
3660 6067 3.869065 CTTCAATCTGCATGGCCATTTT 58.131 40.909 17.92 2.10 0.00 1.82
3661 6068 3.254470 TCAATCTGCATGGCCATTTTG 57.746 42.857 17.92 14.37 0.00 2.44
3662 6069 2.832733 TCAATCTGCATGGCCATTTTGA 59.167 40.909 17.92 16.31 0.00 2.69
3663 6070 3.452990 TCAATCTGCATGGCCATTTTGAT 59.547 39.130 17.92 15.90 0.00 2.57
3664 6071 4.080807 TCAATCTGCATGGCCATTTTGATT 60.081 37.500 17.92 20.45 0.00 2.57
3665 6072 3.254470 TCTGCATGGCCATTTTGATTG 57.746 42.857 17.92 5.56 0.00 2.67
3666 6073 2.568062 TCTGCATGGCCATTTTGATTGT 59.432 40.909 17.92 0.00 0.00 2.71
3667 6074 3.008157 TCTGCATGGCCATTTTGATTGTT 59.992 39.130 17.92 0.00 0.00 2.83
3668 6075 3.752665 TGCATGGCCATTTTGATTGTTT 58.247 36.364 17.92 0.00 0.00 2.83
3669 6076 3.502595 TGCATGGCCATTTTGATTGTTTG 59.497 39.130 17.92 2.36 0.00 2.93
3670 6077 3.752222 GCATGGCCATTTTGATTGTTTGA 59.248 39.130 17.92 0.00 0.00 2.69
3671 6078 4.378666 GCATGGCCATTTTGATTGTTTGAC 60.379 41.667 17.92 0.00 0.00 3.18
3672 6079 4.412796 TGGCCATTTTGATTGTTTGACA 57.587 36.364 0.00 0.00 0.00 3.58
3673 6080 4.970711 TGGCCATTTTGATTGTTTGACAT 58.029 34.783 0.00 0.00 0.00 3.06
3674 6081 5.374921 TGGCCATTTTGATTGTTTGACATT 58.625 33.333 0.00 0.00 0.00 2.71
3675 6082 5.238868 TGGCCATTTTGATTGTTTGACATTG 59.761 36.000 0.00 0.00 0.00 2.82
3676 6083 5.239087 GGCCATTTTGATTGTTTGACATTGT 59.761 36.000 0.00 0.00 0.00 2.71
3677 6084 6.365050 GCCATTTTGATTGTTTGACATTGTC 58.635 36.000 9.93 9.93 0.00 3.18
3678 6085 6.018098 GCCATTTTGATTGTTTGACATTGTCA 60.018 34.615 15.41 15.41 41.09 3.58
3679 6086 7.308109 GCCATTTTGATTGTTTGACATTGTCAT 60.308 33.333 19.63 4.97 42.40 3.06
3680 6087 8.012809 CCATTTTGATTGTTTGACATTGTCATG 58.987 33.333 19.63 10.21 42.40 3.07
3681 6088 8.766151 CATTTTGATTGTTTGACATTGTCATGA 58.234 29.630 19.63 9.40 42.40 3.07
3682 6089 7.697352 TTTGATTGTTTGACATTGTCATGAC 57.303 32.000 19.63 19.27 42.40 3.06
3683 6090 6.638096 TGATTGTTTGACATTGTCATGACT 57.362 33.333 25.55 6.21 42.40 3.41
3684 6091 7.742556 TGATTGTTTGACATTGTCATGACTA 57.257 32.000 25.55 19.23 42.40 2.59
3685 6092 8.164058 TGATTGTTTGACATTGTCATGACTAA 57.836 30.769 25.55 17.74 42.40 2.24
3686 6093 8.075574 TGATTGTTTGACATTGTCATGACTAAC 58.924 33.333 25.55 18.73 42.40 2.34
3687 6094 6.934048 TGTTTGACATTGTCATGACTAACA 57.066 33.333 25.55 21.49 43.03 2.41
3688 6095 6.958255 TGTTTGACATTGTCATGACTAACAG 58.042 36.000 25.55 14.68 41.69 3.16
3689 6096 6.542005 TGTTTGACATTGTCATGACTAACAGT 59.458 34.615 25.55 17.39 41.69 3.55
3690 6097 7.066887 TGTTTGACATTGTCATGACTAACAGTT 59.933 33.333 25.55 1.03 41.69 3.16
3691 6098 8.556194 GTTTGACATTGTCATGACTAACAGTTA 58.444 33.333 25.55 12.59 42.40 2.24
3692 6099 8.669946 TTGACATTGTCATGACTAACAGTTAA 57.330 30.769 25.55 16.76 42.40 2.01
3693 6100 8.669946 TGACATTGTCATGACTAACAGTTAAA 57.330 30.769 25.55 9.37 37.67 1.52
3694 6101 8.556194 TGACATTGTCATGACTAACAGTTAAAC 58.444 33.333 25.55 8.28 37.67 2.01
3695 6102 8.445275 ACATTGTCATGACTAACAGTTAAACA 57.555 30.769 25.55 0.00 34.11 2.83
3696 6103 8.559536 ACATTGTCATGACTAACAGTTAAACAG 58.440 33.333 25.55 8.04 34.11 3.16
3697 6104 8.773645 CATTGTCATGACTAACAGTTAAACAGA 58.226 33.333 25.55 0.00 31.07 3.41
3698 6105 7.946655 TGTCATGACTAACAGTTAAACAGAG 57.053 36.000 25.55 0.00 0.00 3.35
3699 6106 6.929049 TGTCATGACTAACAGTTAAACAGAGG 59.071 38.462 25.55 0.00 0.00 3.69
3700 6107 6.929606 GTCATGACTAACAGTTAAACAGAGGT 59.070 38.462 18.83 0.00 0.00 3.85
3701 6108 8.086522 GTCATGACTAACAGTTAAACAGAGGTA 58.913 37.037 18.83 0.00 0.00 3.08
3702 6109 8.644216 TCATGACTAACAGTTAAACAGAGGTAA 58.356 33.333 0.00 0.00 0.00 2.85
3703 6110 8.709646 CATGACTAACAGTTAAACAGAGGTAAC 58.290 37.037 0.00 0.00 0.00 2.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 0.988832 CCCTACACTGCCCTACCAAA 59.011 55.000 0.00 0.00 0.00 3.28
115 118 2.026729 TGGCGGGATTTTCAGATGTGTA 60.027 45.455 0.00 0.00 0.00 2.90
147 150 2.402049 CACGATCACGATCATCGCTAAC 59.598 50.000 7.05 0.00 45.83 2.34
155 158 0.811281 AGTGCTCACGATCACGATCA 59.189 50.000 7.75 0.00 42.66 2.92
156 159 2.757686 TAGTGCTCACGATCACGATC 57.242 50.000 0.00 0.00 42.66 3.69
157 160 3.316588 AGATTAGTGCTCACGATCACGAT 59.683 43.478 16.06 0.00 42.66 3.73
158 161 2.683362 AGATTAGTGCTCACGATCACGA 59.317 45.455 16.06 0.00 42.66 4.35
159 162 2.786027 CAGATTAGTGCTCACGATCACG 59.214 50.000 16.06 0.00 45.75 4.35
160 163 4.033990 TCAGATTAGTGCTCACGATCAC 57.966 45.455 16.06 0.00 33.90 3.06
186 189 2.303175 GTGCTTACACCCCACAAGAAA 58.697 47.619 0.00 0.00 41.21 2.52
201 204 5.904362 GGAACCTCATCAAATTAGTGCTT 57.096 39.130 0.00 0.00 0.00 3.91
260 2448 4.186715 CCCTAGCTGGCTGGCCTG 62.187 72.222 13.05 13.06 37.98 4.85
319 2508 4.796038 TCTCCCTATCGTTCGTTTCTTT 57.204 40.909 0.00 0.00 0.00 2.52
379 2569 7.095565 TGCAAAAGCAGAAAATACATGTGATTG 60.096 33.333 9.11 0.00 0.00 2.67
443 2633 0.945265 GTAGCCGGCGTGTTTACACA 60.945 55.000 23.20 0.00 46.75 3.72
454 2645 6.864342 TCTAAATGATCTTATAGTAGCCGGC 58.136 40.000 21.89 21.89 0.00 6.13
549 2784 0.248621 CGCCGGCAAATTTGAGGATC 60.249 55.000 28.98 14.75 31.83 3.36
563 2798 0.800631 GGTTTACTTTCTTCCGCCGG 59.199 55.000 0.00 0.00 0.00 6.13
564 2799 1.463444 CAGGTTTACTTTCTTCCGCCG 59.537 52.381 0.00 0.00 0.00 6.46
565 2800 2.501261 ACAGGTTTACTTTCTTCCGCC 58.499 47.619 0.00 0.00 0.00 6.13
568 2803 3.434641 GCCGTACAGGTTTACTTTCTTCC 59.565 47.826 0.00 0.00 43.70 3.46
610 2845 4.320057 CGCTACTGGTACTAGATTTACGGG 60.320 50.000 13.86 0.00 0.00 5.28
758 3016 1.077501 GCCAGCCAATGACTGCCTA 60.078 57.895 0.00 0.00 33.65 3.93
811 3069 1.529865 CTCCTCCGTTCCGTTTGTTTC 59.470 52.381 0.00 0.00 0.00 2.78
840 3099 3.488569 TGGCGTGGGGATGGATCC 61.489 66.667 4.20 4.20 46.41 3.36
841 3100 2.203209 GTGGCGTGGGGATGGATC 60.203 66.667 0.00 0.00 0.00 3.36
869 3139 1.739035 CGGCGCTACATTTGAGGAGAA 60.739 52.381 7.64 0.00 0.00 2.87
940 3231 0.319555 TGCTCTCCTCGGTTCGTTTG 60.320 55.000 0.00 0.00 0.00 2.93
968 3259 2.112815 GTTTCGATTCGCCTGGGGG 61.113 63.158 11.17 0.78 0.00 5.40
970 3261 0.748005 ATGGTTTCGATTCGCCTGGG 60.748 55.000 0.00 0.00 0.00 4.45
971 3262 0.657840 GATGGTTTCGATTCGCCTGG 59.342 55.000 0.00 0.00 0.00 4.45
1046 3364 3.076916 GGATTGGTTGGGGGCTGC 61.077 66.667 0.00 0.00 0.00 5.25
1047 3365 2.364186 GGGATTGGTTGGGGGCTG 60.364 66.667 0.00 0.00 0.00 4.85
1048 3366 4.060667 CGGGATTGGTTGGGGGCT 62.061 66.667 0.00 0.00 0.00 5.19
1049 3367 4.055227 TCGGGATTGGTTGGGGGC 62.055 66.667 0.00 0.00 0.00 5.80
1864 4194 0.971447 GGGAGTTGAGCCCGTAGACT 60.971 60.000 0.00 0.00 35.50 3.24
2104 4434 2.885861 CCTCCACCGGAACTCTCG 59.114 66.667 9.46 0.00 0.00 4.04
2110 4440 3.164977 TGTGTGCCTCCACCGGAA 61.165 61.111 9.46 0.00 41.35 4.30
2191 4521 1.077787 CCGCCCAGCTGTATCCAAA 60.078 57.895 13.81 0.00 0.00 3.28
2467 4797 7.285629 TCAGGATTGTAGTACTCAAGATACCAG 59.714 40.741 0.00 4.71 0.00 4.00
2866 5196 5.055642 TCTCGTGGTACAAATGTCACTAG 57.944 43.478 0.00 0.00 44.16 2.57
3048 5378 7.646922 GCTAGATTTTAAGATTGTCATGGCAAG 59.353 37.037 18.95 0.64 0.00 4.01
3104 5434 9.813080 GATCAGTACAGACAAAACAAATACTTC 57.187 33.333 0.00 0.00 0.00 3.01
3192 5531 5.512473 AGCGAGTACGATTAATCTGTCTTC 58.488 41.667 13.45 11.57 42.66 2.87
3193 5532 5.502153 AGCGAGTACGATTAATCTGTCTT 57.498 39.130 13.45 5.46 42.66 3.01
3205 5544 1.610038 TGACCAAAGAAGCGAGTACGA 59.390 47.619 0.00 0.00 42.66 3.43
3211 5550 0.468226 ACCAGTGACCAAAGAAGCGA 59.532 50.000 0.00 0.00 0.00 4.93
3257 5661 5.970317 TTCAAACAGATGAACATGAGCAT 57.030 34.783 0.00 1.82 34.50 3.79
3274 5678 6.702723 CAGAAAGCCAAATCAGACAATTCAAA 59.297 34.615 0.00 0.00 0.00 2.69
3276 5680 5.775686 CAGAAAGCCAAATCAGACAATTCA 58.224 37.500 0.00 0.00 0.00 2.57
3355 5759 5.535783 CCATACCATAGCATTCAACCATCAA 59.464 40.000 0.00 0.00 0.00 2.57
3356 5760 5.072055 CCATACCATAGCATTCAACCATCA 58.928 41.667 0.00 0.00 0.00 3.07
3384 5788 7.284074 TGTTTCTGTTTCCTAGACAATTGGTA 58.716 34.615 10.83 0.04 0.00 3.25
3398 5802 9.387123 GACAGTCTGAAATTATGTTTCTGTTTC 57.613 33.333 6.91 0.00 34.49 2.78
3402 5806 6.368791 TCGGACAGTCTGAAATTATGTTTCTG 59.631 38.462 9.87 6.50 0.00 3.02
3422 5826 3.520187 TCCGCTTAAACCTTCGGAC 57.480 52.632 0.00 0.00 44.99 4.79
3433 5837 2.677914 TCAGATCTTCCCATCCGCTTA 58.322 47.619 0.00 0.00 0.00 3.09
3435 5839 1.622811 GATCAGATCTTCCCATCCGCT 59.377 52.381 2.81 0.00 0.00 5.52
3436 5840 1.345741 TGATCAGATCTTCCCATCCGC 59.654 52.381 11.83 0.00 0.00 5.54
3438 5842 4.703379 AAGTGATCAGATCTTCCCATCC 57.297 45.455 11.83 0.00 0.00 3.51
3460 5864 9.153479 AGAAAGAGACTGGATTGCTATAGTAAT 57.847 33.333 15.03 15.03 33.06 1.89
3481 5888 4.965119 ATTAAGCCCGCAGTAAAGAAAG 57.035 40.909 0.00 0.00 0.00 2.62
3510 5917 9.708222 CAAACTCATTCTATGAATAAAAGTCCG 57.292 33.333 0.00 0.00 39.11 4.79
3525 5932 9.125026 AGACATTTTTACTCACAAACTCATTCT 57.875 29.630 0.00 0.00 0.00 2.40
3528 5935 9.778741 TCTAGACATTTTTACTCACAAACTCAT 57.221 29.630 0.00 0.00 0.00 2.90
3529 5936 9.607988 TTCTAGACATTTTTACTCACAAACTCA 57.392 29.630 0.00 0.00 0.00 3.41
3530 5937 9.865484 GTTCTAGACATTTTTACTCACAAACTC 57.135 33.333 0.00 0.00 0.00 3.01
3531 5938 9.614792 AGTTCTAGACATTTTTACTCACAAACT 57.385 29.630 0.00 0.00 0.00 2.66
3532 5939 9.651718 CAGTTCTAGACATTTTTACTCACAAAC 57.348 33.333 0.00 0.00 0.00 2.93
3533 5940 8.836413 CCAGTTCTAGACATTTTTACTCACAAA 58.164 33.333 0.00 0.00 0.00 2.83
3534 5941 8.208224 TCCAGTTCTAGACATTTTTACTCACAA 58.792 33.333 0.00 0.00 0.00 3.33
3535 5942 7.732025 TCCAGTTCTAGACATTTTTACTCACA 58.268 34.615 0.00 0.00 0.00 3.58
3536 5943 8.603242 TTCCAGTTCTAGACATTTTTACTCAC 57.397 34.615 0.00 0.00 0.00 3.51
3537 5944 9.793259 ATTTCCAGTTCTAGACATTTTTACTCA 57.207 29.630 0.00 0.00 0.00 3.41
3539 5946 8.515414 GCATTTCCAGTTCTAGACATTTTTACT 58.485 33.333 0.00 0.00 0.00 2.24
3540 5947 8.296713 TGCATTTCCAGTTCTAGACATTTTTAC 58.703 33.333 0.00 0.00 0.00 2.01
3541 5948 8.402798 TGCATTTCCAGTTCTAGACATTTTTA 57.597 30.769 0.00 0.00 0.00 1.52
3542 5949 7.288810 TGCATTTCCAGTTCTAGACATTTTT 57.711 32.000 0.00 0.00 0.00 1.94
3543 5950 6.899393 TGCATTTCCAGTTCTAGACATTTT 57.101 33.333 0.00 0.00 0.00 1.82
3544 5951 7.472334 AATGCATTTCCAGTTCTAGACATTT 57.528 32.000 5.99 0.00 0.00 2.32
3545 5952 7.472334 AAATGCATTTCCAGTTCTAGACATT 57.528 32.000 18.99 0.00 0.00 2.71
3546 5953 7.472334 AAAATGCATTTCCAGTTCTAGACAT 57.528 32.000 24.28 1.41 0.00 3.06
3547 5954 6.899393 AAAATGCATTTCCAGTTCTAGACA 57.101 33.333 24.28 0.00 0.00 3.41
3559 5966 5.634859 ACGACCAAATCAGAAAATGCATTTC 59.365 36.000 24.28 16.84 46.45 2.17
3560 5967 5.540911 ACGACCAAATCAGAAAATGCATTT 58.459 33.333 18.99 18.99 0.00 2.32
3561 5968 5.138125 ACGACCAAATCAGAAAATGCATT 57.862 34.783 5.99 5.99 0.00 3.56
3562 5969 4.789012 ACGACCAAATCAGAAAATGCAT 57.211 36.364 0.00 0.00 0.00 3.96
3563 5970 4.297510 CAACGACCAAATCAGAAAATGCA 58.702 39.130 0.00 0.00 0.00 3.96
3564 5971 3.674753 CCAACGACCAAATCAGAAAATGC 59.325 43.478 0.00 0.00 0.00 3.56
3565 5972 3.674753 GCCAACGACCAAATCAGAAAATG 59.325 43.478 0.00 0.00 0.00 2.32
3566 5973 3.320541 TGCCAACGACCAAATCAGAAAAT 59.679 39.130 0.00 0.00 0.00 1.82
3567 5974 2.690497 TGCCAACGACCAAATCAGAAAA 59.310 40.909 0.00 0.00 0.00 2.29
3568 5975 2.034053 GTGCCAACGACCAAATCAGAAA 59.966 45.455 0.00 0.00 0.00 2.52
3569 5976 1.606668 GTGCCAACGACCAAATCAGAA 59.393 47.619 0.00 0.00 0.00 3.02
3570 5977 1.202758 AGTGCCAACGACCAAATCAGA 60.203 47.619 0.00 0.00 0.00 3.27
3571 5978 1.069022 CAGTGCCAACGACCAAATCAG 60.069 52.381 0.00 0.00 0.00 2.90
3572 5979 0.950836 CAGTGCCAACGACCAAATCA 59.049 50.000 0.00 0.00 0.00 2.57
3573 5980 0.951558 ACAGTGCCAACGACCAAATC 59.048 50.000 0.00 0.00 0.00 2.17
3574 5981 0.667993 CACAGTGCCAACGACCAAAT 59.332 50.000 0.00 0.00 0.00 2.32
3575 5982 0.393132 TCACAGTGCCAACGACCAAA 60.393 50.000 0.00 0.00 0.00 3.28
3576 5983 0.393132 TTCACAGTGCCAACGACCAA 60.393 50.000 0.00 0.00 0.00 3.67
3577 5984 1.092921 GTTCACAGTGCCAACGACCA 61.093 55.000 0.00 0.00 0.00 4.02
3578 5985 1.647084 GTTCACAGTGCCAACGACC 59.353 57.895 0.00 0.00 0.00 4.79
3579 5986 1.275657 CGTTCACAGTGCCAACGAC 59.724 57.895 18.26 0.93 44.51 4.34
3580 5987 0.741574 AACGTTCACAGTGCCAACGA 60.742 50.000 26.01 0.00 44.51 3.85
3581 5988 0.588730 CAACGTTCACAGTGCCAACG 60.589 55.000 20.39 20.39 46.57 4.10
3582 5989 0.865639 GCAACGTTCACAGTGCCAAC 60.866 55.000 0.00 0.00 0.00 3.77
3583 5990 1.029408 AGCAACGTTCACAGTGCCAA 61.029 50.000 0.00 0.00 0.00 4.52
3584 5991 1.451207 AGCAACGTTCACAGTGCCA 60.451 52.632 0.00 0.00 0.00 4.92
3585 5992 1.009675 CAGCAACGTTCACAGTGCC 60.010 57.895 0.00 0.00 0.00 5.01
3586 5993 0.588252 ATCAGCAACGTTCACAGTGC 59.412 50.000 0.00 0.00 0.00 4.40
3587 5994 3.928992 AGATATCAGCAACGTTCACAGTG 59.071 43.478 5.32 0.00 0.00 3.66
3588 5995 4.193826 AGATATCAGCAACGTTCACAGT 57.806 40.909 5.32 0.00 0.00 3.55
3589 5996 4.201753 CCAAGATATCAGCAACGTTCACAG 60.202 45.833 5.32 0.00 0.00 3.66
3590 5997 3.684305 CCAAGATATCAGCAACGTTCACA 59.316 43.478 5.32 0.00 0.00 3.58
3591 5998 3.063997 CCCAAGATATCAGCAACGTTCAC 59.936 47.826 5.32 0.00 0.00 3.18
3592 5999 3.055458 TCCCAAGATATCAGCAACGTTCA 60.055 43.478 5.32 0.00 0.00 3.18
3593 6000 3.531538 TCCCAAGATATCAGCAACGTTC 58.468 45.455 5.32 0.00 0.00 3.95
3594 6001 3.627395 TCCCAAGATATCAGCAACGTT 57.373 42.857 5.32 0.00 0.00 3.99
3595 6002 3.470709 CATCCCAAGATATCAGCAACGT 58.529 45.455 5.32 0.00 0.00 3.99
3596 6003 2.225019 GCATCCCAAGATATCAGCAACG 59.775 50.000 5.32 0.00 0.00 4.10
3597 6004 2.555757 GGCATCCCAAGATATCAGCAAC 59.444 50.000 5.32 0.00 0.00 4.17
3598 6005 2.175284 TGGCATCCCAAGATATCAGCAA 59.825 45.455 5.32 0.00 38.46 3.91
3599 6006 1.776063 TGGCATCCCAAGATATCAGCA 59.224 47.619 5.32 0.00 38.46 4.41
3600 6007 2.574006 TGGCATCCCAAGATATCAGC 57.426 50.000 5.32 0.00 38.46 4.26
3601 6008 3.245158 ACCATGGCATCCCAAGATATCAG 60.245 47.826 13.04 0.00 46.14 2.90
3602 6009 2.718062 ACCATGGCATCCCAAGATATCA 59.282 45.455 13.04 0.00 46.14 2.15
3603 6010 3.446442 ACCATGGCATCCCAAGATATC 57.554 47.619 13.04 0.00 46.14 1.63
3604 6011 4.541310 TGATACCATGGCATCCCAAGATAT 59.459 41.667 20.30 3.48 46.14 1.63
3605 6012 3.915711 TGATACCATGGCATCCCAAGATA 59.084 43.478 20.30 0.00 46.14 1.98
3606 6013 2.718062 TGATACCATGGCATCCCAAGAT 59.282 45.455 20.30 0.00 46.14 2.40
3607 6014 2.134354 TGATACCATGGCATCCCAAGA 58.866 47.619 20.30 0.53 46.14 3.02
3608 6015 2.662535 TGATACCATGGCATCCCAAG 57.337 50.000 20.30 0.00 46.14 3.61
3609 6016 3.232662 CAATGATACCATGGCATCCCAA 58.767 45.455 20.30 4.41 46.14 4.12
3610 6017 3.082191 GCAATGATACCATGGCATCCCA 61.082 50.000 20.30 5.73 46.61 4.37
3611 6018 1.547372 GCAATGATACCATGGCATCCC 59.453 52.381 20.30 4.78 46.61 3.85
3617 6024 3.192001 GCCACATAGCAATGATACCATGG 59.808 47.826 11.19 11.19 36.54 3.66
3618 6025 4.077108 AGCCACATAGCAATGATACCATG 58.923 43.478 0.00 0.00 36.54 3.66
3619 6026 4.377762 AGCCACATAGCAATGATACCAT 57.622 40.909 0.00 0.00 36.54 3.55
3620 6027 3.862877 AGCCACATAGCAATGATACCA 57.137 42.857 0.00 0.00 36.54 3.25
3621 6028 4.136796 TGAAGCCACATAGCAATGATACC 58.863 43.478 0.00 0.00 36.54 2.73
3622 6029 5.756195 TTGAAGCCACATAGCAATGATAC 57.244 39.130 0.00 0.00 36.54 2.24
3623 6030 6.206048 CAGATTGAAGCCACATAGCAATGATA 59.794 38.462 0.00 0.00 36.54 2.15
3624 6031 5.009710 CAGATTGAAGCCACATAGCAATGAT 59.990 40.000 0.00 0.00 36.54 2.45
3625 6032 4.337274 CAGATTGAAGCCACATAGCAATGA 59.663 41.667 0.00 0.00 36.54 2.57
3626 6033 4.607955 CAGATTGAAGCCACATAGCAATG 58.392 43.478 0.00 0.00 39.17 2.82
3627 6034 3.067742 GCAGATTGAAGCCACATAGCAAT 59.932 43.478 0.00 0.00 34.23 3.56
3628 6035 2.424601 GCAGATTGAAGCCACATAGCAA 59.575 45.455 0.00 0.00 34.23 3.91
3629 6036 2.019249 GCAGATTGAAGCCACATAGCA 58.981 47.619 0.00 0.00 34.23 3.49
3630 6037 2.019249 TGCAGATTGAAGCCACATAGC 58.981 47.619 0.00 0.00 0.00 2.97
3631 6038 3.004419 CCATGCAGATTGAAGCCACATAG 59.996 47.826 0.00 0.00 0.00 2.23
3632 6039 2.953648 CCATGCAGATTGAAGCCACATA 59.046 45.455 0.00 0.00 0.00 2.29
3633 6040 1.754803 CCATGCAGATTGAAGCCACAT 59.245 47.619 0.00 0.00 0.00 3.21
3634 6041 1.179152 CCATGCAGATTGAAGCCACA 58.821 50.000 0.00 0.00 0.00 4.17
3635 6042 0.179119 GCCATGCAGATTGAAGCCAC 60.179 55.000 0.00 0.00 0.00 5.01
3636 6043 1.324740 GGCCATGCAGATTGAAGCCA 61.325 55.000 0.00 0.00 38.79 4.75
3637 6044 1.324740 TGGCCATGCAGATTGAAGCC 61.325 55.000 0.00 0.00 39.41 4.35
3638 6045 0.750850 ATGGCCATGCAGATTGAAGC 59.249 50.000 20.04 0.00 0.00 3.86
3639 6046 3.536956 AAATGGCCATGCAGATTGAAG 57.463 42.857 21.63 0.00 0.00 3.02
3640 6047 3.261137 TCAAAATGGCCATGCAGATTGAA 59.739 39.130 21.63 7.50 0.00 2.69
3641 6048 2.832733 TCAAAATGGCCATGCAGATTGA 59.167 40.909 21.63 19.96 0.00 2.57
3642 6049 3.254470 TCAAAATGGCCATGCAGATTG 57.746 42.857 21.63 18.16 0.00 2.67
3643 6050 4.196193 CAATCAAAATGGCCATGCAGATT 58.804 39.130 21.63 22.95 0.00 2.40
3644 6051 3.199071 ACAATCAAAATGGCCATGCAGAT 59.801 39.130 21.63 18.68 0.00 2.90
3645 6052 2.568062 ACAATCAAAATGGCCATGCAGA 59.432 40.909 21.63 17.20 0.00 4.26
3646 6053 2.980568 ACAATCAAAATGGCCATGCAG 58.019 42.857 21.63 12.06 0.00 4.41
3647 6054 3.420300 AACAATCAAAATGGCCATGCA 57.580 38.095 21.63 3.62 0.00 3.96
3648 6055 3.752222 TCAAACAATCAAAATGGCCATGC 59.248 39.130 21.63 0.00 0.00 4.06
3649 6056 4.755629 TGTCAAACAATCAAAATGGCCATG 59.244 37.500 21.63 9.06 0.00 3.66
3650 6057 4.970711 TGTCAAACAATCAAAATGGCCAT 58.029 34.783 14.09 14.09 0.00 4.40
3651 6058 4.412796 TGTCAAACAATCAAAATGGCCA 57.587 36.364 8.56 8.56 0.00 5.36
3652 6059 5.239087 ACAATGTCAAACAATCAAAATGGCC 59.761 36.000 0.00 0.00 0.00 5.36
3653 6060 6.018098 TGACAATGTCAAACAATCAAAATGGC 60.018 34.615 14.37 0.00 39.78 4.40
3654 6061 7.479897 TGACAATGTCAAACAATCAAAATGG 57.520 32.000 14.37 0.00 39.78 3.16
3655 6062 8.766151 TCATGACAATGTCAAACAATCAAAATG 58.234 29.630 20.64 9.23 45.96 2.32
3656 6063 8.767085 GTCATGACAATGTCAAACAATCAAAAT 58.233 29.630 20.64 0.00 45.96 1.82
3657 6064 7.980662 AGTCATGACAATGTCAAACAATCAAAA 59.019 29.630 27.02 0.00 45.96 2.44
3658 6065 7.490840 AGTCATGACAATGTCAAACAATCAAA 58.509 30.769 27.02 0.00 45.96 2.69
3659 6066 7.041635 AGTCATGACAATGTCAAACAATCAA 57.958 32.000 27.02 0.00 45.96 2.57
3660 6067 6.638096 AGTCATGACAATGTCAAACAATCA 57.362 33.333 27.02 0.00 45.96 2.57
3661 6068 8.075574 TGTTAGTCATGACAATGTCAAACAATC 58.924 33.333 27.02 13.83 45.96 2.67
3662 6069 7.939782 TGTTAGTCATGACAATGTCAAACAAT 58.060 30.769 27.02 8.69 45.96 2.71
3663 6070 7.066887 ACTGTTAGTCATGACAATGTCAAACAA 59.933 33.333 27.02 16.00 45.96 2.83
3664 6071 6.542005 ACTGTTAGTCATGACAATGTCAAACA 59.458 34.615 27.02 21.35 45.96 2.83
3665 6072 6.959361 ACTGTTAGTCATGACAATGTCAAAC 58.041 36.000 27.02 19.44 45.96 2.93
3666 6073 7.566760 AACTGTTAGTCATGACAATGTCAAA 57.433 32.000 27.02 8.85 45.96 2.69
3667 6074 8.669946 TTAACTGTTAGTCATGACAATGTCAA 57.330 30.769 27.02 1.47 45.96 3.18
3668 6075 8.556194 GTTTAACTGTTAGTCATGACAATGTCA 58.444 33.333 27.02 19.08 46.90 3.58
3669 6076 8.556194 TGTTTAACTGTTAGTCATGACAATGTC 58.444 33.333 27.02 6.41 35.15 3.06
3670 6077 8.445275 TGTTTAACTGTTAGTCATGACAATGT 57.555 30.769 27.02 14.58 35.15 2.71
3671 6078 8.773645 TCTGTTTAACTGTTAGTCATGACAATG 58.226 33.333 27.02 14.00 34.88 2.82
3672 6079 8.902540 TCTGTTTAACTGTTAGTCATGACAAT 57.097 30.769 27.02 10.59 0.00 2.71
3673 6080 7.441157 CCTCTGTTTAACTGTTAGTCATGACAA 59.559 37.037 27.02 15.88 0.00 3.18
3674 6081 6.929049 CCTCTGTTTAACTGTTAGTCATGACA 59.071 38.462 27.02 10.87 0.00 3.58
3675 6082 6.929606 ACCTCTGTTTAACTGTTAGTCATGAC 59.070 38.462 18.47 18.47 0.00 3.06
3676 6083 7.062749 ACCTCTGTTTAACTGTTAGTCATGA 57.937 36.000 0.00 0.00 0.00 3.07
3677 6084 8.709646 GTTACCTCTGTTTAACTGTTAGTCATG 58.290 37.037 0.00 0.00 0.00 3.07
3678 6085 8.648693 AGTTACCTCTGTTTAACTGTTAGTCAT 58.351 33.333 0.00 0.00 37.19 3.06
3679 6086 8.015185 AGTTACCTCTGTTTAACTGTTAGTCA 57.985 34.615 0.00 4.04 37.19 3.41
3684 6091 9.708092 GAAGATAGTTACCTCTGTTTAACTGTT 57.292 33.333 0.00 0.00 38.65 3.16
3685 6092 8.867097 TGAAGATAGTTACCTCTGTTTAACTGT 58.133 33.333 4.60 0.00 38.65 3.55
3686 6093 9.706691 TTGAAGATAGTTACCTCTGTTTAACTG 57.293 33.333 4.60 0.00 38.65 3.16
3687 6094 9.930693 CTTGAAGATAGTTACCTCTGTTTAACT 57.069 33.333 0.00 0.00 40.74 2.24
3688 6095 8.657729 GCTTGAAGATAGTTACCTCTGTTTAAC 58.342 37.037 0.00 0.00 0.00 2.01
3689 6096 8.372459 TGCTTGAAGATAGTTACCTCTGTTTAA 58.628 33.333 0.00 0.00 0.00 1.52
3690 6097 7.817962 GTGCTTGAAGATAGTTACCTCTGTTTA 59.182 37.037 0.00 0.00 0.00 2.01
3691 6098 6.651225 GTGCTTGAAGATAGTTACCTCTGTTT 59.349 38.462 0.00 0.00 0.00 2.83
3692 6099 6.166982 GTGCTTGAAGATAGTTACCTCTGTT 58.833 40.000 0.00 0.00 0.00 3.16
3693 6100 5.246203 TGTGCTTGAAGATAGTTACCTCTGT 59.754 40.000 0.00 0.00 0.00 3.41
3694 6101 5.724328 TGTGCTTGAAGATAGTTACCTCTG 58.276 41.667 0.00 0.00 0.00 3.35
3695 6102 6.552445 ATGTGCTTGAAGATAGTTACCTCT 57.448 37.500 0.00 0.00 0.00 3.69
3696 6103 7.617041 AAATGTGCTTGAAGATAGTTACCTC 57.383 36.000 0.00 0.00 0.00 3.85
3697 6104 8.409358 AAAAATGTGCTTGAAGATAGTTACCT 57.591 30.769 0.00 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.