Multiple sequence alignment - TraesCS7B01G405200

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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 TraesCS7B01G405200 chr7B 100.000 4847 0 0 1 4847 673517795 673522641 0.000000e+00 8951.0
1 TraesCS7B01G405200 chr7B 96.912 680 20 1 1 680 687966652 687965974 0.000000e+00 1138.0
2 TraesCS7B01G405200 chr7B 94.265 680 36 3 1 679 48452236 48452913 0.000000e+00 1037.0
3 TraesCS7B01G405200 chr2B 86.511 3766 419 52 998 4719 793165600 793161880 0.000000e+00 4058.0
4 TraesCS7B01G405200 chr2B 95.175 684 28 3 1 679 411512066 411512749 0.000000e+00 1075.0
5 TraesCS7B01G405200 chr2B 94.721 682 33 3 1 679 631108563 631107882 0.000000e+00 1057.0
6 TraesCS7B01G405200 chr6B 82.775 3913 547 88 949 4803 471170860 471167017 0.000000e+00 3374.0
7 TraesCS7B01G405200 chr1A 82.822 3452 485 69 949 4359 530707159 530703775 0.000000e+00 2990.0
8 TraesCS7B01G405200 chr1A 83.465 381 56 7 4371 4747 530694441 530694064 9.980000e-92 348.0
9 TraesCS7B01G405200 chr6A 82.015 3642 531 86 729 4316 100260940 100257369 0.000000e+00 2983.0
10 TraesCS7B01G405200 chr6A 82.965 452 66 10 4313 4760 100247979 100247535 9.770000e-107 398.0
11 TraesCS7B01G405200 chr4B 86.178 2033 221 29 695 2684 127724226 127722211 0.000000e+00 2143.0
12 TraesCS7B01G405200 chr4B 83.460 2110 294 38 2736 4819 127722181 127720101 0.000000e+00 1912.0
13 TraesCS7B01G405200 chr4B 94.315 686 35 3 1 683 519575293 519574609 0.000000e+00 1048.0
14 TraesCS7B01G405200 chr5A 86.129 2033 221 30 695 2684 603383374 603381360 0.000000e+00 2135.0
15 TraesCS7B01G405200 chr5A 83.555 2110 292 38 2736 4819 603381330 603379250 0.000000e+00 1923.0
16 TraesCS7B01G405200 chr5A 76.673 523 99 17 1869 2375 414011554 414012069 8.000000e-68 268.0
17 TraesCS7B01G405200 chr5A 93.023 43 3 0 2820 2862 414012474 414012516 4.050000e-06 63.9
18 TraesCS7B01G405200 chrUn 85.681 1306 146 15 1410 2684 391667332 391668627 0.000000e+00 1338.0
19 TraesCS7B01G405200 chrUn 90.148 203 19 1 2736 2938 391668657 391668858 3.720000e-66 263.0
20 TraesCS7B01G405200 chr1B 95.448 681 26 4 1 679 482338245 482338922 0.000000e+00 1081.0
21 TraesCS7B01G405200 chr3B 94.444 684 32 4 1 679 813730762 813730080 0.000000e+00 1048.0
22 TraesCS7B01G405200 chr4A 94.667 675 31 3 1 671 531072090 531072763 0.000000e+00 1042.0
23 TraesCS7B01G405200 chr4A 94.290 683 34 4 1 679 740136929 740136248 0.000000e+00 1040.0
24 TraesCS7B01G405200 chr2A 80.976 799 130 16 948 1727 705787273 705788068 8.920000e-172 614.0
25 TraesCS7B01G405200 chr2A 76.259 278 51 9 2105 2376 705788459 705788727 3.040000e-27 134.0


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 TraesCS7B01G405200 chr7B 673517795 673522641 4846 False 8951.0 8951 100.0000 1 4847 1 chr7B.!!$F2 4846
1 TraesCS7B01G405200 chr7B 687965974 687966652 678 True 1138.0 1138 96.9120 1 680 1 chr7B.!!$R1 679
2 TraesCS7B01G405200 chr7B 48452236 48452913 677 False 1037.0 1037 94.2650 1 679 1 chr7B.!!$F1 678
3 TraesCS7B01G405200 chr2B 793161880 793165600 3720 True 4058.0 4058 86.5110 998 4719 1 chr2B.!!$R2 3721
4 TraesCS7B01G405200 chr2B 411512066 411512749 683 False 1075.0 1075 95.1750 1 679 1 chr2B.!!$F1 678
5 TraesCS7B01G405200 chr2B 631107882 631108563 681 True 1057.0 1057 94.7210 1 679 1 chr2B.!!$R1 678
6 TraesCS7B01G405200 chr6B 471167017 471170860 3843 True 3374.0 3374 82.7750 949 4803 1 chr6B.!!$R1 3854
7 TraesCS7B01G405200 chr1A 530703775 530707159 3384 True 2990.0 2990 82.8220 949 4359 1 chr1A.!!$R2 3410
8 TraesCS7B01G405200 chr6A 100257369 100260940 3571 True 2983.0 2983 82.0150 729 4316 1 chr6A.!!$R2 3587
9 TraesCS7B01G405200 chr4B 127720101 127724226 4125 True 2027.5 2143 84.8190 695 4819 2 chr4B.!!$R2 4124
10 TraesCS7B01G405200 chr4B 519574609 519575293 684 True 1048.0 1048 94.3150 1 683 1 chr4B.!!$R1 682
11 TraesCS7B01G405200 chr5A 603379250 603383374 4124 True 2029.0 2135 84.8420 695 4819 2 chr5A.!!$R1 4124
12 TraesCS7B01G405200 chrUn 391667332 391668858 1526 False 800.5 1338 87.9145 1410 2938 2 chrUn.!!$F1 1528
13 TraesCS7B01G405200 chr1B 482338245 482338922 677 False 1081.0 1081 95.4480 1 679 1 chr1B.!!$F1 678
14 TraesCS7B01G405200 chr3B 813730080 813730762 682 True 1048.0 1048 94.4440 1 679 1 chr3B.!!$R1 678
15 TraesCS7B01G405200 chr4A 531072090 531072763 673 False 1042.0 1042 94.6670 1 671 1 chr4A.!!$F1 670
16 TraesCS7B01G405200 chr4A 740136248 740136929 681 True 1040.0 1040 94.2900 1 679 1 chr4A.!!$R1 678
17 TraesCS7B01G405200 chr2A 705787273 705788727 1454 False 374.0 614 78.6175 948 2376 2 chr2A.!!$F1 1428

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
689 700 0.680921 ATTTCTGCCCACCATGTCCG 60.681 55.0 0.0 0.0 0.00 4.79 F
1275 1306 0.033228 GCATCATCCTGAGAGACGGG 59.967 60.0 0.0 0.0 45.93 5.28 F
2270 2410 0.036765 GGGCGGACTACATCAACACA 60.037 55.0 0.0 0.0 0.00 3.72 F
2439 2615 0.911769 TGGAGTCTGCTATGGGGTTG 59.088 55.0 0.0 0.0 0.00 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2098 2237 0.453390 GTGTCTTGCCTGCATTAGCC 59.547 55.0 0.00 0.0 41.13 3.93 R
3175 3367 0.395311 CTGCCCTACTAGGTGGTCGA 60.395 60.0 1.25 0.0 31.93 4.20 R
3472 3668 0.037232 GCTTTAGCGACTGGAGGTGT 60.037 55.0 0.00 0.0 0.00 4.16 R
4129 4342 0.617535 ATGATGTGTCCCCCGTCTGA 60.618 55.0 0.00 0.0 0.00 3.27 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
274 276 2.903135 GGAGGGATTGGAGATCGAATCT 59.097 50.000 14.62 0.00 43.70 2.40
287 289 3.973206 TCGAATCTAGGCCTCAAAACA 57.027 42.857 9.68 0.00 0.00 2.83
450 458 1.520564 CGGGCGCTGCACTATACAA 60.521 57.895 7.64 0.00 0.00 2.41
483 491 1.374758 GCCTTAGACGCTGCAGTGT 60.375 57.895 31.99 31.99 42.13 3.55
542 550 3.141488 AGGAGGTGCGACGCCTAG 61.141 66.667 18.69 0.00 45.19 3.02
683 694 3.668141 ATATGTGATTTCTGCCCACCA 57.332 42.857 0.00 0.00 0.00 4.17
684 695 2.537633 ATGTGATTTCTGCCCACCAT 57.462 45.000 0.00 0.00 0.00 3.55
685 696 1.548081 TGTGATTTCTGCCCACCATG 58.452 50.000 0.00 0.00 0.00 3.66
686 697 1.203038 TGTGATTTCTGCCCACCATGT 60.203 47.619 0.00 0.00 0.00 3.21
687 698 1.474077 GTGATTTCTGCCCACCATGTC 59.526 52.381 0.00 0.00 0.00 3.06
688 699 1.106285 GATTTCTGCCCACCATGTCC 58.894 55.000 0.00 0.00 0.00 4.02
689 700 0.680921 ATTTCTGCCCACCATGTCCG 60.681 55.000 0.00 0.00 0.00 4.79
690 701 2.762969 TTTCTGCCCACCATGTCCGG 62.763 60.000 0.00 0.00 0.00 5.14
691 702 3.716195 CTGCCCACCATGTCCGGA 61.716 66.667 0.00 0.00 0.00 5.14
692 703 3.976701 CTGCCCACCATGTCCGGAC 62.977 68.421 28.17 28.17 0.00 4.79
693 704 3.717294 GCCCACCATGTCCGGACT 61.717 66.667 33.39 17.38 0.00 3.85
697 708 1.406887 CCCACCATGTCCGGACTTAAG 60.407 57.143 33.39 22.78 0.00 1.85
702 713 5.183228 CACCATGTCCGGACTTAAGTAATT 58.817 41.667 33.39 7.06 0.00 1.40
722 733 4.942761 TTAAAACTCTGTACCCACTCGT 57.057 40.909 0.00 0.00 0.00 4.18
732 743 3.953775 CCACTCGTTGGGCCACCT 61.954 66.667 5.23 0.00 42.54 4.00
736 747 3.316573 CTCGTTGGGCCACCTCTCC 62.317 68.421 5.23 0.00 37.76 3.71
762 773 1.738365 GCACAGACACTGCAGATCGAT 60.738 52.381 23.35 0.00 34.37 3.59
783 794 3.228188 AGCAGTCTCCATCACCAAAAA 57.772 42.857 0.00 0.00 0.00 1.94
814 826 2.037772 GAGGATATCGTGGTGCCTTCAT 59.962 50.000 1.92 0.00 0.00 2.57
859 871 1.402259 CACGTAGCGAGGTGAGATCTT 59.598 52.381 13.55 0.00 42.83 2.40
860 872 2.093106 ACGTAGCGAGGTGAGATCTTT 58.907 47.619 0.00 0.00 0.00 2.52
868 880 4.202121 GCGAGGTGAGATCTTTACCACATA 60.202 45.833 23.99 0.00 36.94 2.29
875 887 6.753180 TGAGATCTTTACCACATATCTCAGC 58.247 40.000 8.78 0.00 44.59 4.26
878 890 6.552725 AGATCTTTACCACATATCTCAGCTCA 59.447 38.462 0.00 0.00 0.00 4.26
879 891 5.907207 TCTTTACCACATATCTCAGCTCAC 58.093 41.667 0.00 0.00 0.00 3.51
896 908 2.228582 CTCACCGGCACATCAATCAAAA 59.771 45.455 0.00 0.00 0.00 2.44
898 910 3.119531 TCACCGGCACATCAATCAAAATC 60.120 43.478 0.00 0.00 0.00 2.17
899 911 2.159393 ACCGGCACATCAATCAAAATCG 60.159 45.455 0.00 0.00 0.00 3.34
902 914 3.670359 CGGCACATCAATCAAAATCGTGT 60.670 43.478 0.00 0.00 0.00 4.49
977 993 6.817765 AGAAAAAGAACAACAACTCAGACA 57.182 33.333 0.00 0.00 0.00 3.41
995 1011 2.764128 GGAGATCCAGACCCCGCA 60.764 66.667 0.00 0.00 35.64 5.69
1062 1093 2.202892 GCTCCGTCGGGATCAACC 60.203 66.667 12.29 0.00 42.83 3.77
1197 1228 1.280133 CTGCGTATCCCCATGATCCAT 59.720 52.381 0.00 0.00 34.76 3.41
1275 1306 0.033228 GCATCATCCTGAGAGACGGG 59.967 60.000 0.00 0.00 45.93 5.28
1327 1358 4.481930 TTCCACAAAGTGTTTAGCATCG 57.518 40.909 0.00 0.00 0.00 3.84
1383 1414 3.376234 CAGACATCACATCCGAAGCAATT 59.624 43.478 0.00 0.00 0.00 2.32
1467 1498 3.157087 AGTGTTCATCGGCAAGGAAATT 58.843 40.909 0.00 0.00 0.00 1.82
1543 1576 5.241506 GTCTTTGTGATGGGAAATCTGTTCA 59.758 40.000 0.00 0.00 0.00 3.18
1638 1672 7.098477 CCCTCTTCAATTGTGCAAATATTCAA 58.902 34.615 5.13 0.00 0.00 2.69
1640 1674 9.806203 CCTCTTCAATTGTGCAAATATTCAATA 57.194 29.630 5.13 0.00 31.54 1.90
1728 1763 0.107831 CTCCGGGTGTCACCTTTTCA 59.892 55.000 21.40 1.35 38.64 2.69
1729 1764 0.179040 TCCGGGTGTCACCTTTTCAC 60.179 55.000 21.40 2.91 38.64 3.18
1735 1770 4.041740 GGTGTCACCTTTTCACCTTTTC 57.958 45.455 15.22 0.00 45.46 2.29
1762 1797 5.622233 GCAGGTAAATCCCTCAAAATCACAC 60.622 44.000 0.00 0.00 36.75 3.82
1897 2010 2.079158 TCGACAGGTGTTCGTACTAGG 58.921 52.381 0.00 0.00 0.00 3.02
1907 2020 4.091509 GTGTTCGTACTAGGCAATGTTGAG 59.908 45.833 0.00 0.00 0.00 3.02
1959 2072 5.592282 ACAATGCCACGGATACAATTATTCA 59.408 36.000 0.00 0.00 0.00 2.57
2031 2144 6.408662 GCTAGGGAAAACCATCTTCATAGTCT 60.409 42.308 0.00 0.00 43.89 3.24
2044 2163 2.092753 TCATAGTCTCCGAGGTAACCGT 60.093 50.000 0.00 0.00 37.17 4.83
2049 2168 2.813908 CCGAGGTAACCGTGCTGC 60.814 66.667 0.00 0.00 37.17 5.25
2054 2175 0.673644 AGGTAACCGTGCTGCATGTC 60.674 55.000 19.58 7.78 37.17 3.06
2061 2182 2.196749 CCGTGCTGCATGTCTAACTAG 58.803 52.381 19.58 0.00 0.00 2.57
2089 2228 6.088217 CGATAAGATCACGGCACATACTAAAG 59.912 42.308 0.00 0.00 0.00 1.85
2098 2237 5.351465 ACGGCACATACTAAAGTTTCAGATG 59.649 40.000 0.00 0.00 0.00 2.90
2132 2272 3.751767 ACACTGGAATGCCATGTGT 57.248 47.368 17.59 17.59 44.91 3.72
2167 2307 5.932303 ACAACTACATAAACGAGAAGCATGT 59.068 36.000 0.00 0.00 34.40 3.21
2187 2327 6.349944 GCATGTCAAGAAGAAATCAATGGAGT 60.350 38.462 0.00 0.00 0.00 3.85
2220 2360 4.081406 AGGTTCAGCAAATCAGTATGCAA 58.919 39.130 0.00 0.00 44.95 4.08
2249 2389 1.669115 CAACCCAGACAGCACTCGG 60.669 63.158 0.00 0.00 0.00 4.63
2270 2410 0.036765 GGGCGGACTACATCAACACA 60.037 55.000 0.00 0.00 0.00 3.72
2305 2445 2.891112 CAACCTTGCACACACACAAAT 58.109 42.857 0.00 0.00 0.00 2.32
2314 2454 3.242712 GCACACACACAAATAAGCAACAC 59.757 43.478 0.00 0.00 0.00 3.32
2389 2539 2.092699 TGGTGAGACACAAATCCACACA 60.093 45.455 0.00 0.00 35.86 3.72
2405 2555 3.446799 CACACAAACCACACATCAAAGG 58.553 45.455 0.00 0.00 0.00 3.11
2413 2573 6.923928 AACCACACATCAAAGGAATTTTTG 57.076 33.333 0.00 0.00 38.97 2.44
2433 2595 2.234661 TGGTCTTGTGGAGTCTGCTATG 59.765 50.000 0.00 0.00 0.00 2.23
2439 2615 0.911769 TGGAGTCTGCTATGGGGTTG 59.088 55.000 0.00 0.00 0.00 3.77
2470 2648 7.847711 AACCTAGAGTCTATCTACATTGCAT 57.152 36.000 0.00 0.00 39.64 3.96
2485 2663 1.065273 GCATGCCGCTTCTCCATTG 59.935 57.895 6.36 0.00 37.77 2.82
2504 2682 2.274542 TGGGATGGGCACTAAAAGAGA 58.725 47.619 0.00 0.00 0.00 3.10
2652 2830 2.359792 CGTCTTATCGCGCTGTTGT 58.640 52.632 5.56 0.00 0.00 3.32
2686 2864 1.822613 CGGCGGCTCAGGTACTCTA 60.823 63.158 7.61 0.00 34.60 2.43
2690 2868 1.460504 CGGCTCAGGTACTCTACACA 58.539 55.000 0.00 0.00 34.60 3.72
2697 2875 1.148446 AGGTACTCTACACACACCCCA 59.852 52.381 0.00 0.00 0.00 4.96
2770 2956 7.746475 GCATACATGTCTGAAGTTACAAGTTTC 59.254 37.037 14.90 0.00 30.85 2.78
2784 2970 1.235724 AGTTTCTTTACGCAGGCCAC 58.764 50.000 5.01 0.00 0.00 5.01
2921 3107 2.951642 CTGACCAATTGTCCACAACACT 59.048 45.455 4.43 0.00 43.78 3.55
3259 3451 2.285083 TGTCTTTGGTCAAGTGAACGG 58.715 47.619 0.00 0.00 33.57 4.44
3411 3605 5.601313 ACACCCTATGATCTTGTACGGTAAT 59.399 40.000 0.00 0.00 0.00 1.89
3457 3653 2.362077 CCAATATAAGCAAGGGTGGCAC 59.638 50.000 9.70 9.70 0.00 5.01
3483 3679 1.188219 TGAGCCTGACACCTCCAGTC 61.188 60.000 0.00 0.00 36.55 3.51
3485 3681 2.262915 CCTGACACCTCCAGTCGC 59.737 66.667 0.00 0.00 38.83 5.19
3497 3693 3.385577 CTCCAGTCGCTAAAGCTAATCC 58.614 50.000 0.00 0.00 39.32 3.01
3504 3700 2.104963 CGCTAAAGCTAATCCCCTTCCT 59.895 50.000 0.00 0.00 39.32 3.36
3506 3702 3.804063 GCTAAAGCTAATCCCCTTCCTCG 60.804 52.174 0.00 0.00 38.21 4.63
3507 3703 1.132500 AAGCTAATCCCCTTCCTCGG 58.868 55.000 0.00 0.00 0.00 4.63
3509 3705 1.411651 GCTAATCCCCTTCCTCGGCT 61.412 60.000 0.00 0.00 0.00 5.52
3538 3736 3.526899 TCTTAGGGATTGGGTCTCACAA 58.473 45.455 0.00 0.00 0.00 3.33
3549 3747 0.468226 GTCTCACAACCTGACCCACA 59.532 55.000 0.00 0.00 0.00 4.17
3560 3758 2.583024 TGACCCACAGATCATTGCAA 57.417 45.000 0.00 0.00 0.00 4.08
3592 3790 6.682113 GCAATGCCATCAAGTCTCAATTATGT 60.682 38.462 0.00 0.00 0.00 2.29
3631 3829 1.201429 ACGAGCTTGGGTCCCTGATT 61.201 55.000 10.00 0.00 0.00 2.57
3639 3837 1.550130 GGGTCCCTGATTGTCCGTCA 61.550 60.000 0.00 0.00 0.00 4.35
3647 3845 3.081061 CTGATTGTCCGTCAAATTGGGA 58.919 45.455 0.00 0.00 39.62 4.37
3657 3855 3.758554 CGTCAAATTGGGAAGATGGAGTT 59.241 43.478 0.00 0.00 0.00 3.01
3658 3856 4.379813 CGTCAAATTGGGAAGATGGAGTTG 60.380 45.833 0.00 0.00 0.00 3.16
3741 3939 4.992951 GGTACGAAAGGTCAAGTACAACAT 59.007 41.667 0.00 0.00 40.66 2.71
3746 3945 6.147164 ACGAAAGGTCAAGTACAACATATGTG 59.853 38.462 9.63 6.45 43.77 3.21
3801 4003 1.400494 CTCGTTCTTTTTATGGGGCGG 59.600 52.381 0.00 0.00 0.00 6.13
3805 4007 0.252479 TCTTTTTATGGGGCGGCGTA 59.748 50.000 9.37 0.00 0.00 4.42
3835 4037 0.614812 GCCATTGCAGGGGAAAACAT 59.385 50.000 9.70 0.00 37.47 2.71
3845 4047 4.462483 GCAGGGGAAAACATCACAAGAATA 59.538 41.667 0.00 0.00 30.77 1.75
3903 4111 1.122849 GTGCAACATCGCAAACTGTG 58.877 50.000 0.00 0.00 45.14 3.66
3946 4155 7.061094 GGACTTGCTTTTCATTTCAATAGTTCG 59.939 37.037 0.00 0.00 0.00 3.95
3960 4170 7.972832 TCAATAGTTCGGTTCTTACATTTGT 57.027 32.000 0.00 0.00 0.00 2.83
3985 4195 6.548321 TCAAAAATACATCAGTACCCCAAGT 58.452 36.000 0.00 0.00 31.96 3.16
3993 4203 5.163131 ACATCAGTACCCCAAGTAAAGTTGT 60.163 40.000 0.00 0.00 31.05 3.32
4008 4218 5.520376 AAAGTTGTTGCTTGACATAAGCT 57.480 34.783 12.24 0.00 43.38 3.74
4053 4266 3.206957 GGTTACAATCCCCGCCGC 61.207 66.667 0.00 0.00 0.00 6.53
4087 4300 0.610232 GGTGCTGCTTCAACTGGGAT 60.610 55.000 0.00 0.00 0.00 3.85
4098 4311 0.401738 AACTGGGATATGATGGCCCG 59.598 55.000 0.00 0.00 45.08 6.13
4129 4342 4.202814 ACCATAATGGACCCAATGGCATAT 60.203 41.667 16.05 0.00 40.96 1.78
4137 4350 1.527034 CCAATGGCATATCAGACGGG 58.473 55.000 0.00 0.00 0.00 5.28
4148 4361 0.617535 TCAGACGGGGGACACATCAT 60.618 55.000 0.00 0.00 0.00 2.45
4158 4371 3.244181 GGGGACACATCATGCAAAACTTT 60.244 43.478 0.00 0.00 0.00 2.66
4171 4384 4.163552 GCAAAACTTTCCTTATGTACGCC 58.836 43.478 0.00 0.00 0.00 5.68
4195 4408 3.986572 CCGACAAGATACATGATGCTCTC 59.013 47.826 0.00 0.00 0.00 3.20
4234 4447 1.069765 CTTCACCGAGTGGCACTGT 59.930 57.895 27.45 15.13 39.70 3.55
4251 4464 1.410517 CTGTAGCCGACTGTCATGGAT 59.589 52.381 8.73 3.25 0.00 3.41
4257 4470 2.819115 CCGACTGTCATGGATGAAGAG 58.181 52.381 8.73 0.00 38.75 2.85
4316 4529 4.939439 ACACATACCGAACCCAAAATACTC 59.061 41.667 0.00 0.00 0.00 2.59
4318 4531 4.019141 ACATACCGAACCCAAAATACTCCA 60.019 41.667 0.00 0.00 0.00 3.86
4321 4534 2.486592 CCGAACCCAAAATACTCCACAC 59.513 50.000 0.00 0.00 0.00 3.82
4323 4536 3.058501 CGAACCCAAAATACTCCACACAC 60.059 47.826 0.00 0.00 0.00 3.82
4324 4537 3.876309 ACCCAAAATACTCCACACACT 57.124 42.857 0.00 0.00 0.00 3.55
4365 4580 5.067273 TGTCAATCTTGTGTTCCGGTATTT 58.933 37.500 0.00 0.00 0.00 1.40
4385 4600 1.996786 CTGCCCGCTAGCCACATTTG 61.997 60.000 9.66 0.00 0.00 2.32
4406 4624 7.630470 TTTGTATTTTCGACAATGCGATTTT 57.370 28.000 7.06 0.00 40.35 1.82
4407 4625 8.729529 TTTGTATTTTCGACAATGCGATTTTA 57.270 26.923 7.06 0.00 40.35 1.52
4437 4655 0.874175 CGAGAGTGCCGTTTGTGTCA 60.874 55.000 0.00 0.00 0.00 3.58
4493 4711 2.036387 GCAAAACCACTTACCAGGGTT 58.964 47.619 0.00 0.00 46.43 4.11
4497 4715 5.623169 CAAAACCACTTACCAGGGTTAGTA 58.377 41.667 9.56 0.00 43.82 1.82
4498 4716 4.897509 AACCACTTACCAGGGTTAGTAC 57.102 45.455 9.56 0.00 42.84 2.73
4499 4717 2.827921 ACCACTTACCAGGGTTAGTACG 59.172 50.000 9.56 6.18 36.07 3.67
4500 4718 2.827921 CCACTTACCAGGGTTAGTACGT 59.172 50.000 9.56 0.00 36.07 3.57
4501 4719 3.119352 CCACTTACCAGGGTTAGTACGTC 60.119 52.174 9.56 0.00 36.07 4.34
4502 4720 3.507233 CACTTACCAGGGTTAGTACGTCA 59.493 47.826 9.56 0.00 36.07 4.35
4503 4721 3.760684 ACTTACCAGGGTTAGTACGTCAG 59.239 47.826 8.27 0.00 36.41 3.51
4504 4722 0.893447 ACCAGGGTTAGTACGTCAGC 59.107 55.000 0.00 0.00 0.00 4.26
4505 4723 0.892755 CCAGGGTTAGTACGTCAGCA 59.107 55.000 0.00 0.00 0.00 4.41
4596 4823 1.812571 CAGCTATTGCCAACGAAAGGT 59.187 47.619 0.00 0.00 40.80 3.50
4614 4841 2.506231 AGGTACTCACTCCTCATCGAGA 59.494 50.000 0.00 0.00 33.83 4.04
4670 4898 2.496070 CTGGAAGGATTAGACACCGTCA 59.504 50.000 0.00 0.00 36.64 4.35
4690 4918 0.039074 CCAACGCTCTGAACGAGACT 60.039 55.000 7.54 0.00 42.62 3.24
4699 4927 5.034152 GCTCTGAACGAGACTATGAAAGAG 58.966 45.833 0.00 0.00 42.62 2.85
4701 4929 6.183360 GCTCTGAACGAGACTATGAAAGAGTA 60.183 42.308 0.00 0.00 42.62 2.59
4702 4930 7.310072 TCTGAACGAGACTATGAAAGAGTAG 57.690 40.000 0.00 0.00 0.00 2.57
4709 4937 6.320672 CGAGACTATGAAAGAGTAGGGGTTTA 59.679 42.308 0.00 0.00 0.00 2.01
4710 4938 7.468906 CGAGACTATGAAAGAGTAGGGGTTTAG 60.469 44.444 0.00 0.00 0.00 1.85
4711 4939 7.190501 AGACTATGAAAGAGTAGGGGTTTAGT 58.809 38.462 0.00 0.00 0.00 2.24
4714 4942 5.479124 TGAAAGAGTAGGGGTTTAGTGTC 57.521 43.478 0.00 0.00 0.00 3.67
4715 4943 4.903049 TGAAAGAGTAGGGGTTTAGTGTCA 59.097 41.667 0.00 0.00 0.00 3.58
4717 4945 4.399483 AGAGTAGGGGTTTAGTGTCAGA 57.601 45.455 0.00 0.00 0.00 3.27
4734 4963 5.010213 GTGTCAGAGAAGAGTGTTAGTTCCT 59.990 44.000 0.00 0.00 0.00 3.36
4768 4997 2.430694 GGGTTCTGGAAAACAAAGCAGT 59.569 45.455 0.00 0.00 0.00 4.40
4769 4998 3.447742 GGTTCTGGAAAACAAAGCAGTG 58.552 45.455 0.00 0.00 0.00 3.66
4770 4999 3.119137 GGTTCTGGAAAACAAAGCAGTGT 60.119 43.478 0.00 0.00 0.00 3.55
4785 5022 0.506932 AGTGTCGTTGTCGCGAATTG 59.493 50.000 12.06 0.74 42.82 2.32
4821 5059 9.653067 TTTAACTACAATGTGTAATGAACAACG 57.347 29.630 0.00 0.00 40.63 4.10
4822 5060 7.485418 AACTACAATGTGTAATGAACAACGA 57.515 32.000 0.00 0.00 40.63 3.85
4823 5061 6.884187 ACTACAATGTGTAATGAACAACGAC 58.116 36.000 0.00 0.00 40.63 4.34
4824 5062 6.704493 ACTACAATGTGTAATGAACAACGACT 59.296 34.615 0.00 0.00 40.63 4.18
4825 5063 6.371809 ACAATGTGTAATGAACAACGACTT 57.628 33.333 0.00 0.00 40.63 3.01
4826 5064 6.791303 ACAATGTGTAATGAACAACGACTTT 58.209 32.000 0.00 0.00 40.63 2.66
4827 5065 7.254852 ACAATGTGTAATGAACAACGACTTTT 58.745 30.769 0.00 0.00 40.63 2.27
4828 5066 7.757624 ACAATGTGTAATGAACAACGACTTTTT 59.242 29.630 0.00 0.00 40.63 1.94
4845 5083 2.499214 TTTTTGCTGAACCCGCAGT 58.501 47.368 0.00 0.00 38.80 4.40
4846 5084 0.102120 TTTTTGCTGAACCCGCAGTG 59.898 50.000 0.00 0.00 38.80 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
274 276 4.471025 TCAGATCTGATGTTTTGAGGCCTA 59.529 41.667 21.67 0.00 34.14 3.93
287 289 1.293458 ACACCCCCTCTCAGATCTGAT 59.707 52.381 25.30 6.40 39.13 2.90
472 480 1.153369 ACAGACAACACTGCAGCGT 60.153 52.632 15.27 7.82 41.06 5.07
483 491 4.196778 TTGCGGCCCCACAGACAA 62.197 61.111 0.00 0.00 0.00 3.18
683 694 9.159364 GAGTTTTAATTACTTAAGTCCGGACAT 57.841 33.333 35.00 26.66 0.00 3.06
684 695 8.370182 AGAGTTTTAATTACTTAAGTCCGGACA 58.630 33.333 35.00 14.29 0.00 4.02
685 696 8.654215 CAGAGTTTTAATTACTTAAGTCCGGAC 58.346 37.037 27.67 27.67 0.00 4.79
686 697 8.370182 ACAGAGTTTTAATTACTTAAGTCCGGA 58.630 33.333 12.39 0.00 0.00 5.14
687 698 8.543862 ACAGAGTTTTAATTACTTAAGTCCGG 57.456 34.615 12.39 0.00 0.00 5.14
697 708 6.870439 ACGAGTGGGTACAGAGTTTTAATTAC 59.130 38.462 0.00 0.00 0.00 1.89
702 713 4.501915 CCAACGAGTGGGTACAGAGTTTTA 60.502 45.833 0.00 0.00 44.64 1.52
719 730 3.319198 GGAGAGGTGGCCCAACGA 61.319 66.667 0.00 0.00 0.00 3.85
732 743 4.357947 GTCTGTGCGCGTGGGAGA 62.358 66.667 8.43 1.27 0.00 3.71
736 747 3.705638 CAGTGTCTGTGCGCGTGG 61.706 66.667 8.43 0.00 0.00 4.94
762 773 4.365514 TTTTTGGTGATGGAGACTGCTA 57.634 40.909 0.00 0.00 0.00 3.49
799 810 2.108514 CGCATGAAGGCACCACGAT 61.109 57.895 0.00 0.00 0.00 3.73
840 852 1.752683 AAGATCTCACCTCGCTACGT 58.247 50.000 0.00 0.00 0.00 3.57
843 855 3.380637 GTGGTAAAGATCTCACCTCGCTA 59.619 47.826 21.19 4.41 33.28 4.26
859 871 3.068165 CGGTGAGCTGAGATATGTGGTAA 59.932 47.826 0.00 0.00 0.00 2.85
860 872 2.623416 CGGTGAGCTGAGATATGTGGTA 59.377 50.000 0.00 0.00 0.00 3.25
868 880 1.620739 ATGTGCCGGTGAGCTGAGAT 61.621 55.000 1.90 0.00 0.00 2.75
875 887 1.452110 TTGATTGATGTGCCGGTGAG 58.548 50.000 1.90 0.00 0.00 3.51
878 890 2.159393 CGATTTTGATTGATGTGCCGGT 60.159 45.455 1.90 0.00 0.00 5.28
879 891 2.159393 ACGATTTTGATTGATGTGCCGG 60.159 45.455 0.00 0.00 0.00 6.13
932 944 3.740128 ATCACATGGCTCGCCGGTC 62.740 63.158 1.90 0.00 39.42 4.79
933 945 3.785859 ATCACATGGCTCGCCGGT 61.786 61.111 1.90 1.38 39.42 5.28
935 947 3.274586 CCATCACATGGCTCGCCG 61.275 66.667 3.14 0.00 44.70 6.46
944 956 7.111247 TGTTGTTCTTTTTCTTCCATCACAT 57.889 32.000 0.00 0.00 0.00 3.21
945 957 6.522625 TGTTGTTCTTTTTCTTCCATCACA 57.477 33.333 0.00 0.00 0.00 3.58
946 958 7.035612 AGTTGTTGTTCTTTTTCTTCCATCAC 58.964 34.615 0.00 0.00 0.00 3.06
958 974 4.843728 TCCTGTCTGAGTTGTTGTTCTTT 58.156 39.130 0.00 0.00 0.00 2.52
977 993 2.444895 GCGGGGTCTGGATCTCCT 60.445 66.667 0.00 0.00 36.82 3.69
995 1011 0.909610 TCCCTCTCTTTCCATGGCGT 60.910 55.000 6.96 0.00 0.00 5.68
1062 1093 2.942376 TGTGTGTTTAGTTGACCTGCTG 59.058 45.455 0.00 0.00 0.00 4.41
1112 1143 0.322456 TGACAATGCAGCTACCACCC 60.322 55.000 0.00 0.00 0.00 4.61
1158 1189 3.055385 GCAGTACACCCTCAAATCCAGTA 60.055 47.826 0.00 0.00 0.00 2.74
1160 1191 2.359900 GCAGTACACCCTCAAATCCAG 58.640 52.381 0.00 0.00 0.00 3.86
1275 1306 4.215613 GGATAGAATGTAATTGGCGTTCCC 59.784 45.833 11.00 4.93 36.07 3.97
1348 1379 3.665173 GATGTCTGCATCTTTTCCGTC 57.335 47.619 0.00 0.00 45.97 4.79
1374 1405 5.801350 TCCTAATGAACTCAATTGCTTCG 57.199 39.130 0.00 0.00 0.00 3.79
1467 1498 4.823442 TCTAATCGGCTGGATAGTTCGTTA 59.177 41.667 0.00 0.00 34.08 3.18
1506 1539 3.119316 TCACAAAGACAACAAACGCCATT 60.119 39.130 0.00 0.00 0.00 3.16
1543 1576 2.904866 ATGTTTGGTGCACGGCGT 60.905 55.556 6.77 6.77 0.00 5.68
1612 1645 3.967332 ATTTGCACAATTGAAGAGGGG 57.033 42.857 13.59 0.00 0.00 4.79
1729 1764 2.760650 GGGATTTACCTGCAGGAAAAGG 59.239 50.000 39.19 13.28 39.65 3.11
1730 1765 3.696548 GAGGGATTTACCTGCAGGAAAAG 59.303 47.826 39.19 12.80 42.10 2.27
1731 1766 3.075283 TGAGGGATTTACCTGCAGGAAAA 59.925 43.478 39.19 27.03 42.10 2.29
1732 1767 2.647299 TGAGGGATTTACCTGCAGGAAA 59.353 45.455 39.19 29.86 42.10 3.13
1733 1768 2.274542 TGAGGGATTTACCTGCAGGAA 58.725 47.619 39.19 23.84 42.10 3.36
1734 1769 1.965414 TGAGGGATTTACCTGCAGGA 58.035 50.000 39.19 18.02 42.10 3.86
1735 1770 2.806945 TTGAGGGATTTACCTGCAGG 57.193 50.000 31.60 31.60 42.10 4.85
1762 1797 8.945481 TCAACATTTTATTTGCCATATCCAAG 57.055 30.769 0.00 0.00 0.00 3.61
1829 1874 4.454678 AGTGCAGATCTTCAAACAAGACA 58.545 39.130 0.00 0.00 0.00 3.41
1843 1888 8.701908 ATCCATATGAAAATGTTAGTGCAGAT 57.298 30.769 3.65 0.00 0.00 2.90
1897 2010 0.459585 CATGCCCAGCTCAACATTGC 60.460 55.000 0.00 0.00 0.00 3.56
1907 2020 3.736126 GCTTTAAGTTCATCATGCCCAGC 60.736 47.826 0.00 0.00 0.00 4.85
1973 2086 2.684881 GCACACGAGGATCATCCATTTT 59.315 45.455 6.42 0.00 39.61 1.82
2031 2144 2.967397 CAGCACGGTTACCTCGGA 59.033 61.111 0.00 0.00 0.00 4.55
2044 2163 3.192633 TCGTTCTAGTTAGACATGCAGCA 59.807 43.478 0.00 0.00 30.81 4.41
2049 2168 9.388346 GTGATCTTATCGTTCTAGTTAGACATG 57.612 37.037 0.00 0.00 30.81 3.21
2054 2175 5.852229 GCCGTGATCTTATCGTTCTAGTTAG 59.148 44.000 0.00 0.00 0.00 2.34
2061 2182 2.536365 TGTGCCGTGATCTTATCGTTC 58.464 47.619 0.00 0.00 0.00 3.95
2089 2228 2.223665 GCCTGCATTAGCCATCTGAAAC 60.224 50.000 0.00 0.00 41.13 2.78
2098 2237 0.453390 GTGTCTTGCCTGCATTAGCC 59.547 55.000 0.00 0.00 41.13 3.93
2132 2272 6.347806 CGTTTATGTAGTTGTGCCATGTGTAA 60.348 38.462 0.00 0.00 0.00 2.41
2167 2307 7.391554 CCTTGTACTCCATTGATTTCTTCTTGA 59.608 37.037 0.00 0.00 0.00 3.02
2220 2360 2.172505 TGTCTGGGTTGTGTCTGACAAT 59.827 45.455 12.81 0.00 46.34 2.71
2249 2389 2.171725 GTTGATGTAGTCCGCCCGC 61.172 63.158 0.00 0.00 0.00 6.13
2254 2394 4.993905 TGTATCTGTGTTGATGTAGTCCG 58.006 43.478 0.00 0.00 0.00 4.79
2270 2410 1.831736 AGGTTGCTTACGGCTGTATCT 59.168 47.619 6.15 0.00 42.39 1.98
2305 2445 1.810151 GGCTGAATTCGGTGTTGCTTA 59.190 47.619 15.63 0.00 0.00 3.09
2314 2454 2.824041 CACCGGGGCTGAATTCGG 60.824 66.667 6.32 10.10 46.95 4.30
2389 2539 6.318396 CCAAAAATTCCTTTGATGTGTGGTTT 59.682 34.615 4.50 0.00 38.35 3.27
2405 2555 5.523369 CAGACTCCACAAGACCAAAAATTC 58.477 41.667 0.00 0.00 0.00 2.17
2413 2573 2.419297 CCATAGCAGACTCCACAAGACC 60.419 54.545 0.00 0.00 0.00 3.85
2433 2595 5.071923 AGACTCTAGGTTATTATGCAACCCC 59.928 44.000 0.76 0.00 45.55 4.95
2470 2648 1.925285 ATCCCAATGGAGAAGCGGCA 61.925 55.000 0.00 0.00 46.08 5.69
2485 2663 3.017442 GTTCTCTTTTAGTGCCCATCCC 58.983 50.000 0.00 0.00 0.00 3.85
2504 2682 1.138671 GCACACACTTGGCGTTGTT 59.861 52.632 0.00 0.00 0.00 2.83
2582 2760 4.041567 TCTGACAGAATAAACTTGGAGCCA 59.958 41.667 1.64 0.00 0.00 4.75
2583 2761 4.393371 GTCTGACAGAATAAACTTGGAGCC 59.607 45.833 6.76 0.00 0.00 4.70
2635 2813 2.664568 TGTTACAACAGCGCGATAAGAC 59.335 45.455 12.10 0.00 34.30 3.01
2650 2828 2.203401 CCGACACCTTTCGTTGTTACA 58.797 47.619 0.00 0.00 37.29 2.41
2652 2830 1.219646 GCCGACACCTTTCGTTGTTA 58.780 50.000 0.00 0.00 37.29 2.41
2770 2956 1.169661 TTGTGGTGGCCTGCGTAAAG 61.170 55.000 3.32 0.00 0.00 1.85
2784 2970 2.002586 CTCGGTGCTTCTACATTGTGG 58.997 52.381 0.00 0.00 0.00 4.17
2829 3015 2.235898 AGATGACAACTCCAGCCTTCTC 59.764 50.000 0.00 0.00 0.00 2.87
2938 3124 1.957562 CGTCGTCTGTCCTTGGTCT 59.042 57.895 0.00 0.00 0.00 3.85
3108 3300 3.555168 CCATCCTTCTTGATAGGCGTACC 60.555 52.174 0.00 0.00 32.59 3.34
3173 3365 1.188863 GCCCTACTAGGTGGTCGAAA 58.811 55.000 1.25 0.00 31.93 3.46
3175 3367 0.395311 CTGCCCTACTAGGTGGTCGA 60.395 60.000 1.25 0.00 31.93 4.20
3271 3463 4.023707 CGGTGTGAGAAGCTTTGATCTTTT 60.024 41.667 0.00 0.00 0.00 2.27
3285 3477 0.542333 TTTGTGAACCCGGTGTGAGA 59.458 50.000 0.00 0.00 0.00 3.27
3317 3509 0.747852 TGCGCACCATCCGATTACTA 59.252 50.000 5.66 0.00 0.00 1.82
3401 3595 2.613474 GGTGCTTGTGGATTACCGTACA 60.613 50.000 0.00 0.00 39.42 2.90
3403 3597 1.624312 TGGTGCTTGTGGATTACCGTA 59.376 47.619 0.00 0.00 39.42 4.02
3405 3599 1.086696 CTGGTGCTTGTGGATTACCG 58.913 55.000 0.00 0.00 39.42 4.02
3411 3605 2.848608 ACCTACTGGTGCTTGTGGA 58.151 52.632 0.00 0.00 46.51 4.02
3437 3633 2.033299 CGTGCCACCCTTGCTTATATTG 59.967 50.000 0.00 0.00 0.00 1.90
3464 3660 1.152247 ACTGGAGGTGTCAGGCTCA 60.152 57.895 0.00 0.00 36.62 4.26
3472 3668 0.037232 GCTTTAGCGACTGGAGGTGT 60.037 55.000 0.00 0.00 0.00 4.16
3485 3681 3.244249 CCGAGGAAGGGGATTAGCTTTAG 60.244 52.174 0.00 0.00 0.00 1.85
3497 3693 2.491675 AAAAAGTAGCCGAGGAAGGG 57.508 50.000 0.00 0.00 0.00 3.95
3518 3716 3.610911 GTTGTGAGACCCAATCCCTAAG 58.389 50.000 0.00 0.00 0.00 2.18
3520 3718 1.913419 GGTTGTGAGACCCAATCCCTA 59.087 52.381 0.00 0.00 33.41 3.53
3538 3736 1.340405 GCAATGATCTGTGGGTCAGGT 60.340 52.381 0.00 0.00 43.76 4.00
3549 3747 0.666913 GCCGCTGATTGCAATGATCT 59.333 50.000 18.59 0.00 43.06 2.75
3583 3781 7.665145 TCAAGTTCAGAACCATCACATAATTGA 59.335 33.333 9.85 6.46 0.00 2.57
3592 3790 3.476552 GTGGTCAAGTTCAGAACCATCA 58.523 45.455 9.85 0.00 0.00 3.07
3631 3829 2.940994 TCTTCCCAATTTGACGGACA 57.059 45.000 0.00 0.00 0.00 4.02
3639 3837 3.509442 TGCAACTCCATCTTCCCAATTT 58.491 40.909 0.00 0.00 0.00 1.82
3647 3845 1.805254 GCGCATGCAACTCCATCTT 59.195 52.632 19.57 0.00 42.15 2.40
3727 3925 5.049060 TGTTGCACATATGTTGTACTTGACC 60.049 40.000 5.37 0.00 36.57 4.02
3762 3961 9.298250 AGAACGAGGTTAGTATATGTGTATGAT 57.702 33.333 0.00 0.00 0.00 2.45
3801 4003 2.225068 ATGGCATGACACTAGTACGC 57.775 50.000 1.45 0.00 0.00 4.42
3845 4047 9.426837 CCAATGAATTGTCTTTGTATTGACATT 57.573 29.630 2.55 0.00 41.93 2.71
3960 4170 7.007723 ACTTGGGGTACTGATGTATTTTTGAA 58.992 34.615 0.00 0.00 0.00 2.69
3978 4188 3.383185 TCAAGCAACAACTTTACTTGGGG 59.617 43.478 0.00 0.00 38.56 4.96
3985 4195 6.633500 AGCTTATGTCAAGCAACAACTTTA 57.367 33.333 11.24 0.00 45.30 1.85
3993 4203 5.178797 GGAAGAGTAGCTTATGTCAAGCAA 58.821 41.667 11.24 0.00 45.30 3.91
4008 4218 4.593206 ACAGTTGGTGAGAATGGAAGAGTA 59.407 41.667 0.00 0.00 0.00 2.59
4053 4266 1.592743 CACCACCCATGTTGCATGG 59.407 57.895 18.43 18.43 38.88 3.66
4087 4300 0.682292 TTATCACGCGGGCCATCATA 59.318 50.000 12.47 0.00 0.00 2.15
4098 4311 2.812011 GGGTCCATTATGGTTATCACGC 59.188 50.000 11.39 6.26 39.03 5.34
4129 4342 0.617535 ATGATGTGTCCCCCGTCTGA 60.618 55.000 0.00 0.00 0.00 3.27
4137 4350 3.665745 AAGTTTTGCATGATGTGTCCC 57.334 42.857 0.00 0.00 0.00 4.46
4148 4361 4.320641 GGCGTACATAAGGAAAGTTTTGCA 60.321 41.667 0.00 0.00 0.00 4.08
4158 4371 2.120282 TCGGCGGCGTACATAAGGA 61.120 57.895 31.06 5.27 0.00 3.36
4171 4384 1.193203 GCATCATGTATCTTGTCGGCG 59.807 52.381 0.00 0.00 0.00 6.46
4234 4447 1.775385 TCATCCATGACAGTCGGCTA 58.225 50.000 0.00 0.00 0.00 3.93
4238 4451 2.428530 TCCTCTTCATCCATGACAGTCG 59.571 50.000 0.00 0.00 36.36 4.18
4243 4456 2.503356 AGGTGTCCTCTTCATCCATGAC 59.497 50.000 0.00 0.00 36.36 3.06
4257 4470 3.767673 TGTGGTAGACAATAGAGGTGTCC 59.232 47.826 1.08 0.00 45.39 4.02
4316 4529 4.637483 AACTGATGAACAAAGTGTGTGG 57.363 40.909 0.00 0.00 40.60 4.17
4385 4600 8.192396 CGAATAAAATCGCATTGTCGAAAATAC 58.808 33.333 0.00 0.00 42.15 1.89
4406 4624 1.756950 ACTCTCGGGCCTGCGAATA 60.757 57.895 6.73 0.00 0.00 1.75
4407 4625 3.077556 ACTCTCGGGCCTGCGAAT 61.078 61.111 6.73 0.00 0.00 3.34
4437 4655 6.295916 CCTTTGAAGTGTCTTAGTAGGTGGAT 60.296 42.308 0.00 0.00 0.00 3.41
4493 4711 6.263516 AGTATGTTTTCTGCTGACGTACTA 57.736 37.500 11.64 0.00 41.71 1.82
4497 4715 8.033038 TCTATTTAGTATGTTTTCTGCTGACGT 58.967 33.333 0.00 0.00 0.00 4.34
4498 4716 8.321716 GTCTATTTAGTATGTTTTCTGCTGACG 58.678 37.037 0.00 0.00 0.00 4.35
4499 4717 9.151471 TGTCTATTTAGTATGTTTTCTGCTGAC 57.849 33.333 0.00 0.00 0.00 3.51
4500 4718 9.151471 GTGTCTATTTAGTATGTTTTCTGCTGA 57.849 33.333 0.00 0.00 0.00 4.26
4501 4719 8.391106 GGTGTCTATTTAGTATGTTTTCTGCTG 58.609 37.037 0.00 0.00 0.00 4.41
4502 4720 8.322091 AGGTGTCTATTTAGTATGTTTTCTGCT 58.678 33.333 0.00 0.00 0.00 4.24
4503 4721 8.494016 AGGTGTCTATTTAGTATGTTTTCTGC 57.506 34.615 0.00 0.00 0.00 4.26
4538 4765 8.470002 GGCCAGTCATAAAATTAGATTTGTCTT 58.530 33.333 0.00 0.00 31.77 3.01
4596 4823 4.423625 TCATCTCGATGAGGAGTGAGTA 57.576 45.455 5.53 0.00 42.42 2.59
4614 4841 2.291735 TGTTGCCTTCCATGTGGATCAT 60.292 45.455 1.98 0.00 44.98 2.45
4646 4874 2.693591 CGGTGTCTAATCCTTCCAGCTA 59.306 50.000 0.00 0.00 0.00 3.32
4670 4898 0.318784 GTCTCGTTCAGAGCGTTGGT 60.319 55.000 6.56 0.00 46.44 3.67
4690 4918 6.727231 TGACACTAAACCCCTACTCTTTCATA 59.273 38.462 0.00 0.00 0.00 2.15
4699 4927 4.771054 TCTTCTCTGACACTAAACCCCTAC 59.229 45.833 0.00 0.00 0.00 3.18
4701 4929 3.835395 CTCTTCTCTGACACTAAACCCCT 59.165 47.826 0.00 0.00 0.00 4.79
4702 4930 3.579151 ACTCTTCTCTGACACTAAACCCC 59.421 47.826 0.00 0.00 0.00 4.95
4709 4937 5.010213 GGAACTAACACTCTTCTCTGACACT 59.990 44.000 0.00 0.00 0.00 3.55
4710 4938 5.010213 AGGAACTAACACTCTTCTCTGACAC 59.990 44.000 0.00 0.00 36.02 3.67
4711 4939 5.141182 AGGAACTAACACTCTTCTCTGACA 58.859 41.667 0.00 0.00 36.02 3.58
4734 4963 5.942977 TCCAGAACCCTCCTAGATACATA 57.057 43.478 0.00 0.00 0.00 2.29
4768 4997 0.931702 AACAATTCGCGACAACGACA 59.068 45.000 9.15 0.00 42.78 4.35
4769 4998 2.013286 AAACAATTCGCGACAACGAC 57.987 45.000 9.15 0.00 42.78 4.34
4770 4999 3.676172 AGATAAACAATTCGCGACAACGA 59.324 39.130 9.15 0.00 42.66 3.85
4827 5065 0.102120 CACTGCGGGTTCAGCAAAAA 59.898 50.000 0.00 0.00 44.67 1.94
4828 5066 1.732917 CACTGCGGGTTCAGCAAAA 59.267 52.632 0.00 0.00 44.67 2.44
4829 5067 3.431055 CACTGCGGGTTCAGCAAA 58.569 55.556 0.00 0.00 44.67 3.68


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

AutoCloner maintained by Alex Coulton.