Multiple sequence alignment - TraesCS6B01G366900

Loading Multiple Alignment...

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 TraesCS6B01G366900 chr6B 100.000 8824 0 0 1 8824 640574797 640583620 0.000000e+00 16295
1 TraesCS6B01G366900 chr6B 75.811 339 46 20 7729 8042 640678595 640678922 1.190000e-28 139
2 TraesCS6B01G366900 chr6D 94.982 7154 241 47 1175 8279 424824731 424831815 0.000000e+00 11114
3 TraesCS6B01G366900 chr6D 84.130 523 27 23 617 1119 424824227 424824713 1.040000e-123 455
4 TraesCS6B01G366900 chr6D 89.401 217 18 2 8465 8678 424832184 424832398 1.460000e-67 268
5 TraesCS6B01G366900 chr6D 90.608 181 13 4 8269 8446 424831927 424832106 4.120000e-58 237
6 TraesCS6B01G366900 chr6D 92.000 125 6 1 8700 8824 424832390 424832510 1.180000e-38 172
7 TraesCS6B01G366900 chr6A 96.305 5684 155 24 1595 7243 569687083 569692746 0.000000e+00 9282
8 TraesCS6B01G366900 chr6A 94.730 778 28 5 7240 8011 569692829 569693599 0.000000e+00 1197
9 TraesCS6B01G366900 chr6A 83.959 586 50 24 614 1189 569686108 569686659 1.020000e-143 521
10 TraesCS6B01G366900 chr6A 85.071 422 22 13 1153 1543 569686673 569687084 8.300000e-105 392
11 TraesCS6B01G366900 chr6A 88.496 226 14 3 8056 8280 569693752 569693966 6.790000e-66 263
12 TraesCS6B01G366900 chr6A 81.915 188 18 6 8492 8678 569695545 569695717 2.570000e-30 145
13 TraesCS6B01G366900 chr4A 99.003 602 4 2 1 602 595420534 595421133 0.000000e+00 1077
14 TraesCS6B01G366900 chr4A 98.500 600 7 2 1 599 606793311 606793909 0.000000e+00 1057
15 TraesCS6B01G366900 chr3B 98.682 607 7 1 1 607 201349796 201349191 0.000000e+00 1075
16 TraesCS6B01G366900 chr4B 98.835 601 6 1 1 601 551260662 551260063 0.000000e+00 1070
17 TraesCS6B01G366900 chr7B 98.331 599 9 1 1 599 503494917 503495514 0.000000e+00 1050
18 TraesCS6B01G366900 chr7A 98.451 581 7 2 1 581 679160364 679159786 0.000000e+00 1022
19 TraesCS6B01G366900 chr7A 97.762 581 11 2 1 581 597472105 597472683 0.000000e+00 1000
20 TraesCS6B01G366900 chr5B 97.935 581 10 2 1 581 226430970 226431548 0.000000e+00 1005
21 TraesCS6B01G366900 chr5A 95.826 599 22 3 1 599 452435552 452434957 0.000000e+00 965
22 TraesCS6B01G366900 chr7D 85.255 373 55 0 6563 6935 116471892 116471520 1.390000e-102 385


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 TraesCS6B01G366900 chr6B 640574797 640583620 8823 False 16295.000000 16295 100.000000 1 8824 1 chr6B.!!$F1 8823
1 TraesCS6B01G366900 chr6D 424824227 424832510 8283 False 2449.200000 11114 90.224200 617 8824 5 chr6D.!!$F1 8207
2 TraesCS6B01G366900 chr6A 569686108 569695717 9609 False 1966.666667 9282 88.412667 614 8678 6 chr6A.!!$F1 8064
3 TraesCS6B01G366900 chr4A 595420534 595421133 599 False 1077.000000 1077 99.003000 1 602 1 chr4A.!!$F1 601
4 TraesCS6B01G366900 chr4A 606793311 606793909 598 False 1057.000000 1057 98.500000 1 599 1 chr4A.!!$F2 598
5 TraesCS6B01G366900 chr3B 201349191 201349796 605 True 1075.000000 1075 98.682000 1 607 1 chr3B.!!$R1 606
6 TraesCS6B01G366900 chr4B 551260063 551260662 599 True 1070.000000 1070 98.835000 1 601 1 chr4B.!!$R1 600
7 TraesCS6B01G366900 chr7B 503494917 503495514 597 False 1050.000000 1050 98.331000 1 599 1 chr7B.!!$F1 598
8 TraesCS6B01G366900 chr7A 679159786 679160364 578 True 1022.000000 1022 98.451000 1 581 1 chr7A.!!$R1 580
9 TraesCS6B01G366900 chr7A 597472105 597472683 578 False 1000.000000 1000 97.762000 1 581 1 chr7A.!!$F1 580
10 TraesCS6B01G366900 chr5B 226430970 226431548 578 False 1005.000000 1005 97.935000 1 581 1 chr5B.!!$F1 580
11 TraesCS6B01G366900 chr5A 452434957 452435552 595 True 965.000000 965 95.826000 1 599 1 chr5A.!!$R1 598

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
637 642 0.042188 CACGAGTTTGACGGCACTTG 60.042 55.000 0.00 0.0 34.93 3.16 F
1564 1683 0.097674 GTGCTATTCGTGCAAGCCAG 59.902 55.000 4.93 0.0 42.41 4.85 F
1594 1713 0.250901 ATGGCGAGCTGGAAACTTGT 60.251 50.000 0.00 0.0 0.00 3.16 F
1680 1799 0.455410 TTTGCAAGCAACGCTCAAGT 59.545 45.000 7.03 0.0 38.25 3.16 F
2453 2594 0.593128 CTTCTTGCCGGAACTTGGTG 59.407 55.000 5.05 0.0 0.00 4.17 F
2563 2704 2.612471 CCACACTCTCTCAGCTTCCAAG 60.612 54.545 0.00 0.0 0.00 3.61 F
3515 3662 3.063861 CGCTTGCAGTGCTGTATGATAAA 59.936 43.478 17.60 0.0 0.00 1.40 F
5050 5208 1.053264 ATGGGTTTTGCCTTGCACCA 61.053 50.000 0.00 0.0 38.71 4.17 F
6768 6927 1.021390 GCATCTCCAAGACCCACACG 61.021 60.000 0.00 0.0 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2183 2319 0.462759 GATCTGCCCGGAAAGTCCAG 60.463 60.000 0.73 0.0 35.91 3.86 R
3252 3394 0.107945 AACAGCGGAAGATCAGGAGC 60.108 55.000 0.00 0.0 0.00 4.70 R
3515 3662 8.143835 CAGTCACCATAAACCAAGAAAAGAATT 58.856 33.333 0.00 0.0 0.00 2.17 R
3744 3894 5.777732 AGAGGGCTAGAATATCAGTTAGTGG 59.222 44.000 0.00 0.0 0.00 4.00 R
3842 3992 1.202927 GGCCCAGATAGCTTATTGCCA 60.203 52.381 0.00 0.0 44.23 4.92 R
4043 4198 1.268079 GCTGTGAGTTTTCCAAGCTCC 59.732 52.381 0.00 0.0 0.00 4.70 R
5471 5629 1.225704 GACTGGAGGAAGGGCATGG 59.774 63.158 0.00 0.0 0.00 3.66 R
6822 6981 0.108138 ATTTCTCGTTGAGGCGGGAG 60.108 55.000 0.00 0.0 42.69 4.30 R
8489 10348 0.743345 GAGGGTCGCCGCAGTTTTAT 60.743 55.000 0.00 0.0 0.00 1.40 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
58 59 0.818445 TTCGCCGGTGGTAGCAAAAA 60.818 50.000 16.49 0.00 0.00 1.94
85 86 1.382629 GGTTGCAGCTTCCCCCTTA 59.617 57.895 0.00 0.00 0.00 2.69
607 609 6.363088 CGGAAAACGTTTCCCTTATTTTTACC 59.637 38.462 14.77 0.00 37.93 2.85
608 610 6.363088 GGAAAACGTTTCCCTTATTTTTACCG 59.637 38.462 15.01 0.00 32.48 4.02
609 611 5.375417 AACGTTTCCCTTATTTTTACCGG 57.625 39.130 0.00 0.00 0.00 5.28
610 612 4.650734 ACGTTTCCCTTATTTTTACCGGA 58.349 39.130 9.46 0.00 0.00 5.14
611 613 5.069318 ACGTTTCCCTTATTTTTACCGGAA 58.931 37.500 9.46 0.00 0.00 4.30
612 614 5.048782 ACGTTTCCCTTATTTTTACCGGAAC 60.049 40.000 9.46 0.00 0.00 3.62
613 615 5.048852 CGTTTCCCTTATTTTTACCGGAACA 60.049 40.000 9.46 0.00 0.00 3.18
614 616 6.514705 CGTTTCCCTTATTTTTACCGGAACAA 60.515 38.462 9.46 0.00 0.00 2.83
615 617 6.973460 TTCCCTTATTTTTACCGGAACAAA 57.027 33.333 9.46 3.56 0.00 2.83
637 642 0.042188 CACGAGTTTGACGGCACTTG 60.042 55.000 0.00 0.00 34.93 3.16
641 646 2.662791 CGAGTTTGACGGCACTTGAATG 60.663 50.000 0.00 0.00 0.00 2.67
722 727 0.468226 AAGTGAAACCGACTGGCTGA 59.532 50.000 0.00 0.00 37.80 4.26
734 739 4.509737 GGCTGACTCGCCGGGTAC 62.510 72.222 2.18 0.00 40.79 3.34
735 740 3.755628 GCTGACTCGCCGGGTACA 61.756 66.667 2.18 0.00 0.00 2.90
746 751 2.586914 GGGTACATACACGCGGCC 60.587 66.667 12.47 0.00 0.00 6.13
844 850 1.151450 AAACCACAGCACAGGAGGG 59.849 57.895 0.00 0.00 0.00 4.30
845 851 1.645402 AAACCACAGCACAGGAGGGT 61.645 55.000 0.00 0.00 0.00 4.34
872 889 3.917760 CGCACGAGATCCTCCCCC 61.918 72.222 0.00 0.00 0.00 5.40
873 890 2.444895 GCACGAGATCCTCCCCCT 60.445 66.667 0.00 0.00 0.00 4.79
874 891 2.503382 GCACGAGATCCTCCCCCTC 61.503 68.421 0.00 0.00 0.00 4.30
875 892 1.834822 CACGAGATCCTCCCCCTCC 60.835 68.421 0.00 0.00 0.00 4.30
876 893 2.325364 ACGAGATCCTCCCCCTCCA 61.325 63.158 0.00 0.00 0.00 3.86
877 894 1.157276 CGAGATCCTCCCCCTCCAT 59.843 63.158 0.00 0.00 0.00 3.41
878 895 0.902516 CGAGATCCTCCCCCTCCATC 60.903 65.000 0.00 0.00 0.00 3.51
879 896 0.546507 GAGATCCTCCCCCTCCATCC 60.547 65.000 0.00 0.00 0.00 3.51
880 897 1.540118 GATCCTCCCCCTCCATCCC 60.540 68.421 0.00 0.00 0.00 3.85
881 898 2.346715 GATCCTCCCCCTCCATCCCA 62.347 65.000 0.00 0.00 0.00 4.37
892 909 1.073474 CCATCCCATCCCTCCCTCA 60.073 63.158 0.00 0.00 0.00 3.86
893 910 0.698886 CCATCCCATCCCTCCCTCAA 60.699 60.000 0.00 0.00 0.00 3.02
899 916 1.063183 CATCCCTCCCTCAATCCCTC 58.937 60.000 0.00 0.00 0.00 4.30
908 926 1.407989 CCTCAATCCCTCCTTCAGCAC 60.408 57.143 0.00 0.00 0.00 4.40
955 973 1.529010 AAAACCCCGAACCCCGTTC 60.529 57.895 0.00 0.00 38.97 3.95
1125 1161 3.112709 GGTTCGTGCTCGTGCTCC 61.113 66.667 11.19 0.61 40.48 4.70
1276 1378 1.302993 TTTTCTAGTGGGGCGTGGC 60.303 57.895 0.00 0.00 0.00 5.01
1316 1418 3.524095 TGGTGATTTGGTGTTCCATCT 57.476 42.857 0.00 0.00 43.91 2.90
1437 1545 1.893137 TCCGTTCACTGCTACATCTGT 59.107 47.619 0.00 0.00 0.00 3.41
1516 1632 4.318263 GCACAAATGCGGCATATTTCATTC 60.318 41.667 17.00 0.00 43.33 2.67
1544 1663 2.091885 TGTTTCCCCTTCTCAAGTTGCT 60.092 45.455 0.00 0.00 0.00 3.91
1546 1665 1.140312 TCCCCTTCTCAAGTTGCTGT 58.860 50.000 0.00 0.00 0.00 4.40
1554 1673 2.995939 TCTCAAGTTGCTGTGCTATTCG 59.004 45.455 0.00 0.00 0.00 3.34
1564 1683 0.097674 GTGCTATTCGTGCAAGCCAG 59.902 55.000 4.93 0.00 42.41 4.85
1594 1713 0.250901 ATGGCGAGCTGGAAACTTGT 60.251 50.000 0.00 0.00 0.00 3.16
1595 1714 1.165907 TGGCGAGCTGGAAACTTGTG 61.166 55.000 0.00 0.00 0.00 3.33
1633 1752 8.387354 GTTTTTGGTTTGGTTATCTGAACTTTG 58.613 33.333 0.00 0.00 0.00 2.77
1637 1756 5.069914 GGTTTGGTTATCTGAACTTTGGGTT 59.930 40.000 0.00 0.00 41.40 4.11
1665 1784 3.672310 CAAGTTTGTGTTGTGCATTTGC 58.328 40.909 0.00 0.00 42.50 3.68
1680 1799 0.455410 TTTGCAAGCAACGCTCAAGT 59.545 45.000 7.03 0.00 38.25 3.16
1725 1858 1.272490 TCGTGGCGTCAGATTCTTCTT 59.728 47.619 0.00 0.00 0.00 2.52
1728 1861 3.330267 GTGGCGTCAGATTCTTCTTCTT 58.670 45.455 0.00 0.00 0.00 2.52
1730 1863 2.933260 GGCGTCAGATTCTTCTTCTTCC 59.067 50.000 0.00 0.00 0.00 3.46
1740 1873 1.731160 CTTCTTCTTCCGCTTCTGCTG 59.269 52.381 0.00 0.00 36.97 4.41
1743 1876 1.664659 CTTCTTCCGCTTCTGCTGATG 59.335 52.381 0.00 0.00 36.97 3.07
1973 2106 1.647545 TTGCTGGCTGTAATGAGCGC 61.648 55.000 0.00 0.00 40.13 5.92
2123 2258 7.487829 TGAAATTTAAGTGCTTTTGTCTGTGTC 59.512 33.333 0.00 0.00 0.00 3.67
2133 2268 1.616159 TGTCTGTGTCATGAGTCCGA 58.384 50.000 0.00 0.00 0.00 4.55
2181 2317 5.496387 GTCATATGCAGTGATTTTCAGTCG 58.504 41.667 7.72 0.00 0.00 4.18
2183 2319 5.291858 TCATATGCAGTGATTTTCAGTCGAC 59.708 40.000 7.70 7.70 0.00 4.20
2203 2339 0.909610 TGGACTTTCCGGGCAGATCT 60.910 55.000 0.00 0.00 40.17 2.75
2258 2394 3.735591 TGTTGTAAGTGGGCTTCAGTAC 58.264 45.455 0.00 0.00 36.22 2.73
2340 2480 8.437742 CAAGTAATGCCTGTTTCAATTTTCATC 58.562 33.333 0.00 0.00 0.00 2.92
2429 2569 3.798889 GCACCTTGAAAACTTGTAAGGGC 60.799 47.826 0.00 0.00 43.07 5.19
2453 2594 0.593128 CTTCTTGCCGGAACTTGGTG 59.407 55.000 5.05 0.00 0.00 4.17
2531 2672 4.016444 TGAAGAATAATCAGTTGGTGGGC 58.984 43.478 0.00 0.00 0.00 5.36
2563 2704 2.612471 CCACACTCTCTCAGCTTCCAAG 60.612 54.545 0.00 0.00 0.00 3.61
3104 3246 5.681954 GCCATTTATTCTGCTAACAATGCCA 60.682 40.000 0.00 0.00 0.00 4.92
3130 3272 3.075148 TGTTTGGTTCAGTGACGTGAAA 58.925 40.909 0.00 0.00 38.17 2.69
3218 3360 5.320549 TGTACATTCGTTCTACTCCCTTC 57.679 43.478 0.00 0.00 0.00 3.46
3230 3372 6.540438 TCTACTCCCTTCGAATAATGTTGT 57.460 37.500 0.00 0.00 0.00 3.32
3252 3394 8.892905 GTTGTTCATTTTCTAGCTTTTAGAACG 58.107 33.333 0.00 0.00 36.54 3.95
3515 3662 3.063861 CGCTTGCAGTGCTGTATGATAAA 59.936 43.478 17.60 0.00 0.00 1.40
3578 3725 8.266473 TCAGCCCTTAAATGCAAAATTATGATT 58.734 29.630 0.00 0.00 0.00 2.57
3821 3971 9.477484 CAAGTAGTTACTGATACCACAATATCC 57.523 37.037 0.00 0.00 36.50 2.59
3842 3992 6.202202 TCCTGTACTACTAGATACCTGCAT 57.798 41.667 0.00 0.00 0.00 3.96
3931 4082 4.617959 GCATGTAGCCTTTGTACTATCGA 58.382 43.478 0.00 0.00 37.23 3.59
3932 4083 5.047847 GCATGTAGCCTTTGTACTATCGAA 58.952 41.667 0.00 0.00 37.23 3.71
3933 4084 5.522460 GCATGTAGCCTTTGTACTATCGAAA 59.478 40.000 0.00 0.00 37.23 3.46
3934 4085 6.036735 GCATGTAGCCTTTGTACTATCGAAAA 59.963 38.462 0.00 0.00 37.23 2.29
3935 4086 7.254795 GCATGTAGCCTTTGTACTATCGAAAAT 60.255 37.037 0.00 0.00 37.23 1.82
3936 4087 7.766219 TGTAGCCTTTGTACTATCGAAAATC 57.234 36.000 0.00 0.00 0.00 2.17
4043 4198 1.450312 GACTGGGCTCATTCCACCG 60.450 63.158 0.00 0.00 0.00 4.94
4134 4289 6.296026 TCTTATCAACAGTGCTAGTTTGGTT 58.704 36.000 0.00 0.00 0.00 3.67
4135 4290 7.446769 TCTTATCAACAGTGCTAGTTTGGTTA 58.553 34.615 0.00 0.00 0.00 2.85
4139 4294 4.682778 ACAGTGCTAGTTTGGTTAGTGA 57.317 40.909 0.00 0.00 0.00 3.41
4182 4337 6.880484 TGCAGGAATCTTGCAAATAATGAAT 58.120 32.000 17.75 0.00 35.46 2.57
4246 4401 6.260271 AGTCTTGTTAGCTTGTAAGTTTCACC 59.740 38.462 0.00 0.00 0.00 4.02
4395 4553 6.714810 AGCATGACTTATTTGTAAGTGGTTCA 59.285 34.615 5.64 0.00 40.09 3.18
4454 4612 3.616956 TCTTGTTCTGGACTGCCATAG 57.383 47.619 0.00 0.00 44.91 2.23
4906 5064 3.198068 TGCGCTCAAATCTGTATCCTTC 58.802 45.455 9.73 0.00 0.00 3.46
4921 5079 9.607333 TCTGTATCCTTCAAGAGTAATATGGAT 57.393 33.333 0.00 0.00 36.99 3.41
5050 5208 1.053264 ATGGGTTTTGCCTTGCACCA 61.053 50.000 0.00 0.00 38.71 4.17
5171 5329 3.244561 TGACTGGGGATGTTTCTTCACTC 60.245 47.826 0.00 0.00 0.00 3.51
5207 5365 9.778741 TTCAGTCTCAATGTCTTGTAAGTTAAT 57.221 29.630 0.00 0.00 33.87 1.40
5208 5366 9.778741 TCAGTCTCAATGTCTTGTAAGTTAATT 57.221 29.630 0.00 0.00 33.87 1.40
5398 5556 9.264719 CTTCAAAAAGATTTGTTCTGGCTAAAT 57.735 29.630 1.69 0.00 45.02 1.40
5471 5629 2.435059 GCTCCTGGCGTGGTTCTC 60.435 66.667 0.00 0.00 0.00 2.87
5552 5710 6.692849 TGCTCTGGAATATGACCTCATTAT 57.307 37.500 0.00 0.00 37.76 1.28
5634 5792 3.181493 GGCTGTCATTCTTGGTATTGCTG 60.181 47.826 0.00 0.00 0.00 4.41
5674 5832 2.038952 TGTTGTTGATCCTAGCAGCTGT 59.961 45.455 16.64 4.79 0.00 4.40
5779 5937 6.975197 TGTTGCTTTAACACATCAATTTCGAA 59.025 30.769 0.00 0.00 44.07 3.71
5780 5938 7.167302 TGTTGCTTTAACACATCAATTTCGAAG 59.833 33.333 0.00 0.00 44.07 3.79
5781 5939 5.629020 TGCTTTAACACATCAATTTCGAAGC 59.371 36.000 0.00 0.00 37.04 3.86
5782 5940 5.858581 GCTTTAACACATCAATTTCGAAGCT 59.141 36.000 0.00 0.00 34.54 3.74
5783 5941 7.021196 GCTTTAACACATCAATTTCGAAGCTA 58.979 34.615 0.00 0.00 34.54 3.32
5784 5942 7.217070 GCTTTAACACATCAATTTCGAAGCTAG 59.783 37.037 0.00 0.00 34.54 3.42
6304 6463 1.154197 GCCTCTGGGACGTTTTACAC 58.846 55.000 0.00 0.00 33.58 2.90
6358 6517 1.956477 GGGCACAGTTTCACTTCATGT 59.044 47.619 0.00 0.00 0.00 3.21
6519 6678 9.865321 ACATATGATTTGAGAATTTTCCACAAG 57.135 29.630 10.38 0.00 0.00 3.16
6522 6681 5.984926 TGATTTGAGAATTTTCCACAAGCAC 59.015 36.000 0.00 0.00 0.00 4.40
6544 6703 2.991250 TGCTAATCTGGAGGTCTTTGC 58.009 47.619 0.00 0.00 0.00 3.68
6609 6768 2.035832 GGCTAGACTCCAGATTGCTCTC 59.964 54.545 0.00 0.00 0.00 3.20
6657 6816 3.129502 CATGACTGCAGCCCACGG 61.130 66.667 15.27 4.86 0.00 4.94
6768 6927 1.021390 GCATCTCCAAGACCCACACG 61.021 60.000 0.00 0.00 0.00 4.49
6822 6981 3.264897 CCTGAGTATGCGCGCACC 61.265 66.667 39.05 28.89 0.00 5.01
6906 7065 1.609072 GGGAAGAAGCCAGTTGACAAC 59.391 52.381 10.47 10.47 0.00 3.32
6995 7154 6.111382 TGATTCTGAGGCTCAATAAGTTCAG 58.889 40.000 19.29 3.45 38.82 3.02
7110 7270 1.949525 GCGATTCATTGTATGGCTGGT 59.050 47.619 3.57 0.00 0.00 4.00
7276 7522 9.982651 GTACCTTCTGCTTTGATCACTAATATA 57.017 33.333 0.00 0.00 0.00 0.86
7291 7540 9.726438 ATCACTAATATACTGGTAATTTGGCTC 57.274 33.333 0.00 0.00 0.00 4.70
7311 7560 3.343617 TCGAGCATTTTACTTTCCCCTG 58.656 45.455 0.00 0.00 0.00 4.45
7327 7576 3.330701 TCCCCTGCTCTGTCAAAATTAGT 59.669 43.478 0.00 0.00 0.00 2.24
7368 7617 0.388659 TGTTGTGCAGGGAACAATGC 59.611 50.000 3.90 0.00 39.57 3.56
7400 7649 7.534239 GCTGTGCATAGTTAGTTTTAACTGTTC 59.466 37.037 12.41 0.06 46.80 3.18
7415 7664 4.236527 ACTGTTCAACTTCCCTGTCTTT 57.763 40.909 0.00 0.00 0.00 2.52
7424 7673 1.909700 TCCCTGTCTTTCACCAATGC 58.090 50.000 0.00 0.00 0.00 3.56
7458 7708 0.034670 GTTGCTCCCCTTGCAGATCT 60.035 55.000 0.00 0.00 41.71 2.75
7470 7720 3.650281 TGCAGATCTTATCCAAAGCCA 57.350 42.857 0.00 0.00 0.00 4.75
7472 7722 3.282021 GCAGATCTTATCCAAAGCCACA 58.718 45.455 0.00 0.00 0.00 4.17
7481 7731 1.102154 CCAAAGCCACAGACAACACA 58.898 50.000 0.00 0.00 0.00 3.72
7898 8148 3.721706 CAGAGGGGGACACTGGGC 61.722 72.222 0.00 0.00 34.28 5.36
7914 8164 2.046285 GGCTTGGGGATGTGTTCGG 61.046 63.158 0.00 0.00 0.00 4.30
7994 8251 1.524008 CCTTCCCTTTTGCGACCACC 61.524 60.000 0.00 0.00 0.00 4.61
8015 8272 3.074412 CGTTGGGCTGGGATCATAATAC 58.926 50.000 0.00 0.00 0.00 1.89
8018 8275 2.976185 TGGGCTGGGATCATAATACGAA 59.024 45.455 0.00 0.00 0.00 3.85
8042 8299 3.951037 TGTGCTAAAACAGAAAGGAAGCA 59.049 39.130 0.00 0.00 36.23 3.91
8045 8302 4.887071 TGCTAAAACAGAAAGGAAGCAGAA 59.113 37.500 0.00 0.00 33.84 3.02
8047 8304 5.860716 GCTAAAACAGAAAGGAAGCAGAATG 59.139 40.000 0.00 0.00 40.87 2.67
8048 8305 6.294176 GCTAAAACAGAAAGGAAGCAGAATGA 60.294 38.462 0.00 0.00 39.69 2.57
8050 8307 4.630644 ACAGAAAGGAAGCAGAATGAGA 57.369 40.909 0.00 0.00 39.69 3.27
8053 8310 4.575645 CAGAAAGGAAGCAGAATGAGATCC 59.424 45.833 0.00 0.00 39.69 3.36
8061 8438 4.378774 AGCAGAATGAGATCCAAATCGAG 58.621 43.478 0.00 0.00 39.69 4.04
8064 8441 5.120519 GCAGAATGAGATCCAAATCGAGATC 59.879 44.000 4.62 4.62 39.69 2.75
8079 8456 2.672098 GAGATCCTGCTGGGTAGAAGA 58.328 52.381 10.07 0.00 30.28 2.87
8112 8489 1.953231 CTGCACTCTGCCCAGATCGA 61.953 60.000 0.00 0.00 44.23 3.59
8155 8532 3.688235 TCATGCCACTGTGATTGATTCA 58.312 40.909 9.86 0.00 0.00 2.57
8176 8553 9.190858 GATTCACTGATTACTGCTAGATAAGTG 57.809 37.037 0.00 0.00 35.07 3.16
8184 8561 0.750850 GCTAGATAAGTGGCCACGGA 59.249 55.000 29.68 21.56 36.20 4.69
8229 8607 1.203287 GGAATTCCCACTCTTTGCAGC 59.797 52.381 14.03 0.00 34.14 5.25
8241 8619 4.145876 TCTTTGCAGCAAAATCTACGTG 57.854 40.909 20.95 7.48 32.75 4.49
8270 8648 1.134175 TGTCATTCTGTGCGAGCGATA 59.866 47.619 0.00 0.00 0.00 2.92
8309 10098 0.250252 GCTTATCTCTCTGCCAGCCC 60.250 60.000 0.00 0.00 0.00 5.19
8409 10200 3.941188 CTGGTGTGGGGAGCACGT 61.941 66.667 0.00 0.00 37.70 4.49
8454 10313 2.279252 AGAGAACGTGCGTTGCGT 60.279 55.556 14.89 0.00 45.07 5.24
8489 10348 2.250646 CGATACAGTCGGCGGGATA 58.749 57.895 7.21 0.00 46.47 2.59
8490 10349 0.809385 CGATACAGTCGGCGGGATAT 59.191 55.000 7.21 0.04 46.47 1.63
8496 10379 2.433239 ACAGTCGGCGGGATATAAAACT 59.567 45.455 7.21 0.00 0.00 2.66
8498 10381 1.529865 GTCGGCGGGATATAAAACTGC 59.470 52.381 7.21 0.00 35.80 4.40
8533 10416 2.943199 GCCAAGGTTCAGGAATCAGGAG 60.943 54.545 7.67 0.00 0.00 3.69
8564 10450 0.662619 CAGCAGCGTTCCAGACAAAA 59.337 50.000 0.00 0.00 0.00 2.44
8596 10482 3.827625 TCAACACAACAAGAAAACCACG 58.172 40.909 0.00 0.00 0.00 4.94
8597 10483 3.502595 TCAACACAACAAGAAAACCACGA 59.497 39.130 0.00 0.00 0.00 4.35
8614 10500 2.677836 CACGATGGATGGTTGTTTCGAT 59.322 45.455 0.00 0.00 0.00 3.59
8674 10560 6.691508 ACTTTGTTCCTAATTTTGCCAGATC 58.308 36.000 0.00 0.00 0.00 2.75
8675 10561 6.267471 ACTTTGTTCCTAATTTTGCCAGATCA 59.733 34.615 0.00 0.00 0.00 2.92
8676 10562 6.855763 TTGTTCCTAATTTTGCCAGATCAT 57.144 33.333 0.00 0.00 0.00 2.45
8677 10563 6.455360 TGTTCCTAATTTTGCCAGATCATC 57.545 37.500 0.00 0.00 0.00 2.92
8678 10564 5.360714 TGTTCCTAATTTTGCCAGATCATCC 59.639 40.000 0.00 0.00 0.00 3.51
8679 10565 5.128033 TCCTAATTTTGCCAGATCATCCA 57.872 39.130 0.00 0.00 0.00 3.41
8680 10566 5.517924 TCCTAATTTTGCCAGATCATCCAA 58.482 37.500 0.00 0.00 0.00 3.53
8681 10567 5.360714 TCCTAATTTTGCCAGATCATCCAAC 59.639 40.000 0.00 0.00 0.00 3.77
8682 10568 3.788333 ATTTTGCCAGATCATCCAACG 57.212 42.857 0.00 0.00 0.00 4.10
8683 10569 0.810648 TTTGCCAGATCATCCAACGC 59.189 50.000 0.00 0.00 0.00 4.84
8684 10570 1.031571 TTGCCAGATCATCCAACGCC 61.032 55.000 0.00 0.00 0.00 5.68
8685 10571 2.189499 GCCAGATCATCCAACGCCC 61.189 63.158 0.00 0.00 0.00 6.13
8686 10572 1.526917 CCAGATCATCCAACGCCCC 60.527 63.158 0.00 0.00 0.00 5.80
8687 10573 1.526917 CAGATCATCCAACGCCCCC 60.527 63.158 0.00 0.00 0.00 5.40
8688 10574 2.000701 AGATCATCCAACGCCCCCA 61.001 57.895 0.00 0.00 0.00 4.96
8689 10575 1.526917 GATCATCCAACGCCCCCAG 60.527 63.158 0.00 0.00 0.00 4.45
8690 10576 3.721370 ATCATCCAACGCCCCCAGC 62.721 63.158 0.00 0.00 38.52 4.85
8760 10646 3.585289 AGAAAACCCAACCAACCAAACTT 59.415 39.130 0.00 0.00 0.00 2.66
8771 10657 3.490761 CCAACCAAACTTCGCAACTCAAT 60.491 43.478 0.00 0.00 0.00 2.57
8778 10664 2.948979 ACTTCGCAACTCAATCAACCAA 59.051 40.909 0.00 0.00 0.00 3.67
8779 10665 3.243068 ACTTCGCAACTCAATCAACCAAC 60.243 43.478 0.00 0.00 0.00 3.77
8780 10666 1.606668 TCGCAACTCAATCAACCAACC 59.393 47.619 0.00 0.00 0.00 3.77
8781 10667 1.336440 CGCAACTCAATCAACCAACCA 59.664 47.619 0.00 0.00 0.00 3.67
8800 10686 2.618709 CCACACAGTTCAAGAACCTTCC 59.381 50.000 9.20 0.00 42.06 3.46
8811 10697 1.346722 AGAACCTTCCGTTACCACTGG 59.653 52.381 0.00 0.00 33.74 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 1.337447 GCTTCAATGGCACTGCACAAT 60.337 47.619 2.82 0.00 0.00 2.71
208 209 1.378514 CGCCCACCATAACTGCCTT 60.379 57.895 0.00 0.00 0.00 4.35
607 609 2.096174 TCAAACTCGTGGTTTTGTTCCG 59.904 45.455 6.55 0.00 44.77 4.30
608 610 3.431856 GTCAAACTCGTGGTTTTGTTCC 58.568 45.455 6.55 0.00 44.77 3.62
609 611 3.095738 CGTCAAACTCGTGGTTTTGTTC 58.904 45.455 6.55 0.42 44.77 3.18
610 612 2.159490 CCGTCAAACTCGTGGTTTTGTT 60.159 45.455 6.55 0.00 44.77 2.83
611 613 1.399089 CCGTCAAACTCGTGGTTTTGT 59.601 47.619 6.55 0.00 44.77 2.83
612 614 1.858399 GCCGTCAAACTCGTGGTTTTG 60.858 52.381 6.55 1.58 44.77 2.44
613 615 0.379316 GCCGTCAAACTCGTGGTTTT 59.621 50.000 6.55 0.00 44.77 2.43
615 617 1.153329 TGCCGTCAAACTCGTGGTT 60.153 52.632 0.00 0.00 40.28 3.67
631 636 1.226773 GGCGATGGCATTCAAGTGC 60.227 57.895 0.00 0.00 44.31 4.40
637 642 1.198637 GATAAGCTGGCGATGGCATTC 59.801 52.381 0.00 0.00 42.47 2.67
641 646 2.320587 CGGATAAGCTGGCGATGGC 61.321 63.158 0.00 0.00 38.90 4.40
643 648 3.957260 CCGGATAAGCTGGCGATG 58.043 61.111 0.00 0.00 35.91 3.84
674 679 1.759236 ACTTCCCCAAGTTCGTCCC 59.241 57.895 0.00 0.00 40.16 4.46
682 687 2.691011 TCCGTTTTTCAACTTCCCCAAG 59.309 45.455 0.00 0.00 35.50 3.61
685 690 2.691526 ACTTCCGTTTTTCAACTTCCCC 59.308 45.455 0.00 0.00 0.00 4.81
718 723 1.731433 TATGTACCCGGCGAGTCAGC 61.731 60.000 9.30 0.00 0.00 4.26
722 727 1.811860 GTGTATGTACCCGGCGAGT 59.188 57.895 9.30 2.81 0.00 4.18
732 737 1.153529 CTTGGGCCGCGTGTATGTA 60.154 57.895 4.92 0.00 0.00 2.29
733 738 2.435938 CTTGGGCCGCGTGTATGT 60.436 61.111 4.92 0.00 0.00 2.29
734 739 2.435938 ACTTGGGCCGCGTGTATG 60.436 61.111 4.92 0.00 0.00 2.39
735 740 2.435938 CACTTGGGCCGCGTGTAT 60.436 61.111 14.72 0.00 0.00 2.29
746 751 4.034258 CGCAGCAGCACCACTTGG 62.034 66.667 0.82 0.00 42.27 3.61
872 889 0.839853 GAGGGAGGGATGGGATGGAG 60.840 65.000 0.00 0.00 0.00 3.86
873 890 1.240129 GAGGGAGGGATGGGATGGA 59.760 63.158 0.00 0.00 0.00 3.41
874 891 0.698886 TTGAGGGAGGGATGGGATGG 60.699 60.000 0.00 0.00 0.00 3.51
875 892 1.353694 GATTGAGGGAGGGATGGGATG 59.646 57.143 0.00 0.00 0.00 3.51
876 893 1.752608 GATTGAGGGAGGGATGGGAT 58.247 55.000 0.00 0.00 0.00 3.85
877 894 0.401979 GGATTGAGGGAGGGATGGGA 60.402 60.000 0.00 0.00 0.00 4.37
878 895 1.430369 GGGATTGAGGGAGGGATGGG 61.430 65.000 0.00 0.00 0.00 4.00
879 896 0.402566 AGGGATTGAGGGAGGGATGG 60.403 60.000 0.00 0.00 0.00 3.51
880 897 1.063183 GAGGGATTGAGGGAGGGATG 58.937 60.000 0.00 0.00 0.00 3.51
881 898 0.104197 GGAGGGATTGAGGGAGGGAT 60.104 60.000 0.00 0.00 0.00 3.85
892 909 0.622665 CTGGTGCTGAAGGAGGGATT 59.377 55.000 0.00 0.00 0.00 3.01
893 910 1.919600 GCTGGTGCTGAAGGAGGGAT 61.920 60.000 0.00 0.00 36.03 3.85
899 916 2.281970 TGCTGCTGGTGCTGAAGG 60.282 61.111 0.00 0.00 40.01 3.46
955 973 0.037605 AAGTGCCTCCCGTTTAGTCG 60.038 55.000 0.00 0.00 0.00 4.18
958 976 0.605319 TGCAAGTGCCTCCCGTTTAG 60.605 55.000 0.00 0.00 41.18 1.85
1239 1338 6.192360 AGAAAAGCGCGCACTAATAAAATAG 58.808 36.000 35.10 0.00 0.00 1.73
1276 1378 3.056607 CCAAGCCATAAACAAAGACCTGG 60.057 47.826 0.00 0.00 0.00 4.45
1278 1380 3.573967 CACCAAGCCATAAACAAAGACCT 59.426 43.478 0.00 0.00 0.00 3.85
1316 1418 2.661537 CAGTCGGCGTGAACAGCA 60.662 61.111 6.85 0.00 36.08 4.41
1437 1545 2.066262 GACGACAGGAAAAAGATGCGA 58.934 47.619 0.00 0.00 0.00 5.10
1516 1632 5.770162 ACTTGAGAAGGGGAAACAAATACTG 59.230 40.000 0.00 0.00 0.00 2.74
1544 1663 0.605050 TGGCTTGCACGAATAGCACA 60.605 50.000 9.41 2.74 42.54 4.57
1546 1665 1.647545 GCTGGCTTGCACGAATAGCA 61.648 55.000 9.41 0.00 40.85 3.49
1554 1673 1.957695 GCAAAAGGCTGGCTTGCAC 60.958 57.895 17.73 5.97 43.89 4.57
1564 1683 0.595825 GCTCGCCATATGCAAAAGGC 60.596 55.000 14.58 14.58 43.61 4.35
1583 1702 2.158971 CCCCCAAAACACAAGTTTCCAG 60.159 50.000 0.00 0.00 46.79 3.86
1605 1724 4.612943 TCAGATAACCAAACCAAAAACGC 58.387 39.130 0.00 0.00 0.00 4.84
1633 1752 2.100749 ACACAAACTTGCTTGCTAACCC 59.899 45.455 0.00 0.00 0.00 4.11
1637 1756 3.768406 CACAACACAAACTTGCTTGCTA 58.232 40.909 0.00 0.00 0.00 3.49
1665 1784 1.370900 GGCACTTGAGCGTTGCTTG 60.371 57.895 0.00 0.00 39.88 4.01
1673 1792 2.039405 CAGGCAGAGGCACTTGAGC 61.039 63.158 0.00 0.00 41.55 4.26
1680 1799 2.926779 AGTCAGCAGGCAGAGGCA 60.927 61.111 0.00 0.00 43.71 4.75
1740 1873 3.262420 ACACGCATAAGAACACTCCATC 58.738 45.455 0.00 0.00 0.00 3.51
1743 1876 3.120304 GGAAACACGCATAAGAACACTCC 60.120 47.826 0.00 0.00 0.00 3.85
1821 1954 2.433664 GTCGCCGGACCAATCGTT 60.434 61.111 5.05 0.00 37.19 3.85
1973 2106 4.213906 TGCACACATGAACACATCAGTAAG 59.786 41.667 0.00 0.00 42.53 2.34
2107 2242 3.313526 ACTCATGACACAGACAAAAGCAC 59.686 43.478 0.00 0.00 0.00 4.40
2123 2258 2.732412 AAGTGTGACTCGGACTCATG 57.268 50.000 0.00 0.00 0.00 3.07
2133 2268 6.332630 CAAACAATCAGGAAAAAGTGTGACT 58.667 36.000 0.00 0.00 0.00 3.41
2181 2317 1.376037 CTGCCCGGAAAGTCCAGTC 60.376 63.158 0.73 0.00 35.91 3.51
2183 2319 0.462759 GATCTGCCCGGAAAGTCCAG 60.463 60.000 0.73 0.00 35.91 3.86
2203 2339 4.449131 GAGCAATCACCAATCTCATCAGA 58.551 43.478 0.00 0.00 0.00 3.27
2304 2444 3.804325 CAGGCATTACTTGTACAGATCCG 59.196 47.826 0.00 0.00 0.00 4.18
2429 2569 3.375299 CCAAGTTCCGGCAAGAAGAATAG 59.625 47.826 0.00 0.00 0.00 1.73
2462 2603 4.883585 GCAGGGATTATGATGAGTGAAACA 59.116 41.667 0.00 0.00 41.43 2.83
2531 2672 1.153823 GAGTGTGGACGGGATCACG 60.154 63.158 17.58 17.58 36.74 4.35
2543 2684 2.036992 ACTTGGAAGCTGAGAGAGTGTG 59.963 50.000 0.00 0.00 0.00 3.82
2563 2704 9.760660 CAGCACTAACTTACAATATCTTCAAAC 57.239 33.333 0.00 0.00 0.00 2.93
2666 2807 8.050930 AGTATATTAACCTTGGAATTTCACCGT 58.949 33.333 0.00 0.00 0.00 4.83
3104 3246 3.504520 ACGTCACTGAACCAAACAAAAGT 59.495 39.130 0.00 0.00 0.00 2.66
3130 3272 3.164268 TGTGCCCATCAAGCTATTGTTT 58.836 40.909 0.00 0.00 37.68 2.83
3218 3360 9.559958 AAGCTAGAAAATGAACAACATTATTCG 57.440 29.630 0.00 0.00 46.90 3.34
3230 3372 7.360946 GGAGCGTTCTAAAAGCTAGAAAATGAA 60.361 37.037 0.00 0.00 41.84 2.57
3252 3394 0.107945 AACAGCGGAAGATCAGGAGC 60.108 55.000 0.00 0.00 0.00 4.70
3515 3662 8.143835 CAGTCACCATAAACCAAGAAAAGAATT 58.856 33.333 0.00 0.00 0.00 2.17
3744 3894 5.777732 AGAGGGCTAGAATATCAGTTAGTGG 59.222 44.000 0.00 0.00 0.00 4.00
3821 3971 5.336055 GCCATGCAGGTATCTAGTAGTACAG 60.336 48.000 2.52 0.00 40.61 2.74
3842 3992 1.202927 GGCCCAGATAGCTTATTGCCA 60.203 52.381 0.00 0.00 44.23 4.92
3966 4117 9.539825 GATCGTAGCATATCAAATGGATAGAAT 57.460 33.333 0.00 0.00 41.64 2.40
4043 4198 1.268079 GCTGTGAGTTTTCCAAGCTCC 59.732 52.381 0.00 0.00 0.00 4.70
4127 4282 7.649306 GCAAATGATATGGATCACTAACCAAAC 59.351 37.037 0.00 0.00 44.90 2.93
4134 4289 7.040892 GCAAGAAGCAAATGATATGGATCACTA 60.041 37.037 0.00 0.00 43.38 2.74
4135 4290 6.238953 GCAAGAAGCAAATGATATGGATCACT 60.239 38.462 0.00 0.00 43.38 3.41
4219 4374 8.182227 GTGAAACTTACAAGCTAACAAGACTTT 58.818 33.333 7.81 0.78 0.00 2.66
4274 4432 7.621991 CAAACAAGTTAAGTATCCAGCTATCG 58.378 38.462 0.00 0.00 0.00 2.92
4349 4507 3.216800 TCTGAAGCTTGTGCAATGAACT 58.783 40.909 2.10 0.00 42.74 3.01
4662 4820 1.945819 GCTGAAGGAATCGAACCAGCA 60.946 52.381 13.17 9.54 44.40 4.41
4906 5064 8.682936 AGCAAAAGGTATCCATATTACTCTTG 57.317 34.615 0.00 0.00 0.00 3.02
4921 5079 6.274157 TCACTGAAACAAAAGCAAAAGGTA 57.726 33.333 0.00 0.00 0.00 3.08
5171 5329 4.993584 ACATTGAGACTGAAGCAGTTAGTG 59.006 41.667 1.18 2.57 45.44 2.74
5207 5365 6.228258 ACAGTTCGAATAGCTTTTCAGGTAA 58.772 36.000 15.83 3.23 36.57 2.85
5208 5366 5.790593 ACAGTTCGAATAGCTTTTCAGGTA 58.209 37.500 15.83 0.00 37.40 3.08
5322 5480 3.506455 TGTCAGGTGAAAACCGTGAAAAA 59.494 39.130 0.00 0.00 34.28 1.94
5471 5629 1.225704 GACTGGAGGAAGGGCATGG 59.774 63.158 0.00 0.00 0.00 3.66
5542 5700 7.336396 AGGTTTGTTAGTGGTATAATGAGGTC 58.664 38.462 0.00 0.00 0.00 3.85
5552 5710 7.016858 AGAGTATTGGAAGGTTTGTTAGTGGTA 59.983 37.037 0.00 0.00 0.00 3.25
5634 5792 2.125952 GATTGCAAGCCCGCCAAC 60.126 61.111 2.49 0.00 0.00 3.77
5674 5832 2.499214 GGACTGTGTGGCCAACAAA 58.501 52.632 7.24 2.08 45.54 2.83
5779 5937 5.730296 ACATCACTTGTCAAGTACTAGCT 57.270 39.130 17.76 0.00 40.46 3.32
5847 6006 0.590195 CAAGTTGAGCAGACTGGCAC 59.410 55.000 4.26 0.00 35.83 5.01
5930 6089 8.571461 AACACATCATGAATCTCTGTAACAAT 57.429 30.769 0.00 0.00 0.00 2.71
5949 6108 4.517285 AGGAACATTGCTCGATAACACAT 58.483 39.130 0.00 0.00 0.00 3.21
6100 6259 0.879765 CTGGCTTGCAGTTCTTCAGG 59.120 55.000 0.00 0.00 0.00 3.86
6304 6463 1.472728 GCCTGGTATGTCCACTTACCG 60.473 57.143 14.10 10.07 44.86 4.02
6358 6517 7.231467 AGGAAAAGGTTCTAAATACTGAGCAA 58.769 34.615 0.00 0.00 33.92 3.91
6460 6619 6.359804 CAGACATCCCAATCCAAGAGAATAA 58.640 40.000 0.00 0.00 0.00 1.40
6519 6678 2.158842 AGACCTCCAGATTAGCATGTGC 60.159 50.000 0.00 0.00 42.49 4.57
6522 6681 3.314635 GCAAAGACCTCCAGATTAGCATG 59.685 47.826 0.00 0.00 0.00 4.06
6544 6703 3.002791 TGGACGAAGCTGCTGAAATAAG 58.997 45.455 1.35 0.00 0.00 1.73
6556 6715 3.312697 AGTTTTGTCTTCTTGGACGAAGC 59.687 43.478 0.00 0.00 39.73 3.86
6657 6816 8.378172 TCGATTTTACATCCCTGTGAATTATC 57.622 34.615 0.00 0.00 36.79 1.75
6768 6927 2.017049 GTGCCCATCACATAGGTTGAC 58.983 52.381 0.00 0.00 44.98 3.18
6822 6981 0.108138 ATTTCTCGTTGAGGCGGGAG 60.108 55.000 0.00 0.00 42.69 4.30
6831 6990 5.445142 GCTGTACACATCAGATTTCTCGTTG 60.445 44.000 0.00 0.00 35.20 4.10
6906 7065 1.021390 GGTGATGGAGGTTGCACTCG 61.021 60.000 0.00 0.00 38.39 4.18
6995 7154 2.213499 CGAACCTAATGCCCATGACTC 58.787 52.381 0.00 0.00 0.00 3.36
7058 7217 2.028930 GTGCAGATAGATCTAACCCCCG 60.029 54.545 6.52 0.00 34.85 5.73
7110 7270 5.744171 TGCCAGTGATAATAGAGCTTTCAA 58.256 37.500 0.00 0.00 0.00 2.69
7276 7522 1.003118 TGCTCGAGCCAAATTACCAGT 59.997 47.619 33.23 0.00 41.18 4.00
7291 7540 2.159379 GCAGGGGAAAGTAAAATGCTCG 60.159 50.000 0.00 0.00 0.00 5.03
7311 7560 6.978080 TCCAAACAAACTAATTTTGACAGAGC 59.022 34.615 3.81 0.00 46.76 4.09
7327 7576 3.838565 TGGGCATCTTACTCCAAACAAA 58.161 40.909 0.00 0.00 0.00 2.83
7371 7620 4.425577 AAAACTAACTATGCACAGCTGC 57.574 40.909 15.27 1.39 44.52 5.25
7400 7649 2.930950 TGGTGAAAGACAGGGAAGTTG 58.069 47.619 0.00 0.00 0.00 3.16
7415 7664 1.339535 TGAGCATAACGGCATTGGTGA 60.340 47.619 0.00 0.00 35.83 4.02
7424 7673 1.745087 AGCAACCAATGAGCATAACGG 59.255 47.619 0.00 0.00 0.00 4.44
7458 7708 3.568007 GTGTTGTCTGTGGCTTTGGATAA 59.432 43.478 0.00 0.00 0.00 1.75
7470 7720 2.700371 TCTCCATCACTGTGTTGTCTGT 59.300 45.455 15.51 0.00 0.00 3.41
7472 7722 3.307269 CCATCTCCATCACTGTGTTGTCT 60.307 47.826 15.51 0.00 0.00 3.41
7481 7731 1.115467 GGTCGACCATCTCCATCACT 58.885 55.000 29.75 0.00 35.64 3.41
7843 8093 6.404712 AACAGTTAGCGAAAATGCTACTAC 57.595 37.500 2.78 0.00 46.57 2.73
7844 8094 7.429636 AAAACAGTTAGCGAAAATGCTACTA 57.570 32.000 2.78 0.00 46.57 1.82
7845 8095 5.941948 AAACAGTTAGCGAAAATGCTACT 57.058 34.783 2.78 0.00 46.57 2.57
7898 8148 1.165270 GAACCGAACACATCCCCAAG 58.835 55.000 0.00 0.00 0.00 3.61
7914 8164 4.095483 AGCAGCAGCATATTTACAGTGAAC 59.905 41.667 3.17 0.00 45.49 3.18
7994 8251 2.276732 ATTATGATCCCAGCCCAACG 57.723 50.000 0.00 0.00 0.00 4.10
8015 8272 4.272504 TCCTTTCTGTTTTAGCACAGTTCG 59.727 41.667 2.24 0.00 44.10 3.95
8018 8275 4.036852 GCTTCCTTTCTGTTTTAGCACAGT 59.963 41.667 2.24 0.00 44.10 3.55
8042 8299 5.543405 AGGATCTCGATTTGGATCTCATTCT 59.457 40.000 10.99 0.00 38.56 2.40
8045 8302 4.563168 GCAGGATCTCGATTTGGATCTCAT 60.563 45.833 10.99 0.00 38.56 2.90
8047 8304 3.006752 AGCAGGATCTCGATTTGGATCTC 59.993 47.826 10.99 3.68 38.56 2.75
8048 8305 2.971330 AGCAGGATCTCGATTTGGATCT 59.029 45.455 10.99 0.00 38.56 2.75
8050 8307 2.224475 CCAGCAGGATCTCGATTTGGAT 60.224 50.000 0.00 0.00 36.89 3.41
8053 8310 1.134280 ACCCAGCAGGATCTCGATTTG 60.134 52.381 0.00 0.00 39.89 2.32
8061 8438 3.006752 CAGATCTTCTACCCAGCAGGATC 59.993 52.174 0.00 0.00 39.89 3.36
8064 8441 2.392662 TCAGATCTTCTACCCAGCAGG 58.607 52.381 0.00 0.00 43.78 4.85
8155 8532 5.221541 GGCCACTTATCTAGCAGTAATCAGT 60.222 44.000 0.00 0.00 0.00 3.41
8156 8533 5.221521 TGGCCACTTATCTAGCAGTAATCAG 60.222 44.000 0.00 0.00 0.00 2.90
8157 8534 4.653801 TGGCCACTTATCTAGCAGTAATCA 59.346 41.667 0.00 0.00 0.00 2.57
8158 8535 4.991687 GTGGCCACTTATCTAGCAGTAATC 59.008 45.833 29.12 0.00 0.00 1.75
8159 8536 4.501571 CGTGGCCACTTATCTAGCAGTAAT 60.502 45.833 32.28 0.00 0.00 1.89
8200 8577 0.890683 GTGGGAATTCCTTGGCACTG 59.109 55.000 23.63 0.00 36.20 3.66
8207 8584 3.160269 CTGCAAAGAGTGGGAATTCCTT 58.840 45.455 23.63 10.10 36.20 3.36
8229 8607 4.452455 ACAGAAAGGAGCACGTAGATTTTG 59.548 41.667 0.00 0.00 0.00 2.44
8241 8619 2.161211 GCACAGAATGACAGAAAGGAGC 59.839 50.000 0.00 0.00 39.69 4.70
8270 8648 2.738743 CTTTGGCCCCATGTATCAGTT 58.261 47.619 0.00 0.00 0.00 3.16
8309 10098 4.778415 CAGTCGACTCGCGTGGGG 62.778 72.222 16.96 0.00 41.80 4.96
8317 10106 2.349275 CGAGGAACTAGACAGTCGACTC 59.651 54.545 16.96 5.83 41.55 3.36
8359 10150 1.372499 GATCCGCGGCGCATTACTA 60.372 57.895 32.61 9.91 0.00 1.82
8370 10161 1.572941 CAATGGCATCTGATCCGCG 59.427 57.895 0.00 0.00 0.00 6.46
8445 10268 1.068832 CGTTAGAGCTACGCAACGCA 61.069 55.000 8.17 0.00 36.01 5.24
8478 10337 1.529865 GCAGTTTTATATCCCGCCGAC 59.470 52.381 0.00 0.00 0.00 4.79
8481 10340 0.872388 CCGCAGTTTTATATCCCGCC 59.128 55.000 0.00 0.00 0.00 6.13
8489 10348 0.743345 GAGGGTCGCCGCAGTTTTAT 60.743 55.000 0.00 0.00 0.00 1.40
8490 10349 1.375013 GAGGGTCGCCGCAGTTTTA 60.375 57.895 0.00 0.00 0.00 1.52
8533 10416 2.338785 GCTGCTGGTGAGGAAAGGC 61.339 63.158 0.00 0.00 0.00 4.35
8574 10460 4.023107 TCGTGGTTTTCTTGTTGTGTTGAA 60.023 37.500 0.00 0.00 0.00 2.69
8596 10482 4.157656 TGGAAATCGAAACAACCATCCATC 59.842 41.667 0.00 0.00 31.12 3.51
8597 10483 4.085733 TGGAAATCGAAACAACCATCCAT 58.914 39.130 0.00 0.00 31.12 3.41
8614 10500 4.764172 CAAGGTGTTGGTTTGAATGGAAA 58.236 39.130 0.00 0.00 0.00 3.13
8687 10573 2.792890 CGATCTTCTGTACCAGACGCTG 60.793 54.545 0.00 0.52 40.46 5.18
8688 10574 1.402259 CGATCTTCTGTACCAGACGCT 59.598 52.381 0.00 0.00 40.46 5.07
8689 10575 1.132643 ACGATCTTCTGTACCAGACGC 59.867 52.381 0.00 0.00 40.46 5.19
8690 10576 3.489180 AACGATCTTCTGTACCAGACG 57.511 47.619 0.00 0.00 40.46 4.18
8691 10577 4.439837 GGGTAACGATCTTCTGTACCAGAC 60.440 50.000 0.00 0.00 37.65 3.51
8692 10578 3.698040 GGGTAACGATCTTCTGTACCAGA 59.302 47.826 0.00 0.00 36.50 3.86
8693 10579 4.043037 GGGTAACGATCTTCTGTACCAG 57.957 50.000 0.00 0.00 37.60 4.00
8711 10597 4.324991 GTTTGGAGGCGGACGGGT 62.325 66.667 0.00 0.00 0.00 5.28
8713 10599 2.742372 CAGTTTGGAGGCGGACGG 60.742 66.667 0.00 0.00 0.00 4.79
8760 10646 1.606668 GGTTGGTTGATTGAGTTGCGA 59.393 47.619 0.00 0.00 0.00 5.10
8771 10657 2.498644 TGAACTGTGTGGTTGGTTGA 57.501 45.000 0.00 0.00 0.00 3.18
8778 10664 3.279434 GAAGGTTCTTGAACTGTGTGGT 58.721 45.455 12.44 0.00 0.00 4.16
8779 10665 2.618709 GGAAGGTTCTTGAACTGTGTGG 59.381 50.000 12.44 0.00 0.00 4.17
8780 10666 2.287915 CGGAAGGTTCTTGAACTGTGTG 59.712 50.000 12.44 0.00 0.00 3.82
8781 10667 2.093128 ACGGAAGGTTCTTGAACTGTGT 60.093 45.455 12.44 3.53 0.00 3.72
8800 10686 2.448926 TCATGTGACCAGTGGTAACG 57.551 50.000 22.65 11.15 39.89 3.18


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

AutoCloner maintained by Alex Coulton.