Multiple sequence alignment - TraesCS3D01G098500

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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 TraesCS3D01G098500 chr3D 100.000 3333 0 0 1 3333 50074832 50078164 0.000000e+00 6156.0
1 TraesCS3D01G098500 chr3D 90.786 1769 117 24 721 2472 50381177 50382916 0.000000e+00 2322.0
2 TraesCS3D01G098500 chr3D 93.750 128 8 0 1 128 50381162 50381289 3.390000e-45 193.0
3 TraesCS3D01G098500 chr3B 94.429 1777 64 15 718 2485 79560112 79561862 0.000000e+00 2700.0
4 TraesCS3D01G098500 chr3B 90.602 1777 121 21 721 2472 79781572 79783327 0.000000e+00 2314.0
5 TraesCS3D01G098500 chr3B 91.667 240 20 0 1 240 79559871 79560110 1.920000e-87 333.0
6 TraesCS3D01G098500 chr3B 79.381 291 37 11 379 654 750156146 750155864 2.040000e-42 183.0
7 TraesCS3D01G098500 chr3B 88.971 136 6 2 1 128 79781557 79781691 3.440000e-35 159.0
8 TraesCS3D01G098500 chr3B 91.228 114 8 2 721 833 79559886 79559998 1.600000e-33 154.0
9 TraesCS3D01G098500 chr3A 93.908 1428 66 4 910 2336 63434171 63435578 0.000000e+00 2135.0
10 TraesCS3D01G098500 chr3A 92.364 1362 91 6 976 2333 63389194 63390546 0.000000e+00 1927.0
11 TraesCS3D01G098500 chr3A 96.610 59 2 0 2331 2389 63390579 63390637 7.610000e-17 99.0
12 TraesCS3D01G098500 chr3A 90.141 71 6 1 1320 1390 63387379 63387448 1.270000e-14 91.6
13 TraesCS3D01G098500 chr3A 79.688 128 12 4 1 128 63426603 63426716 2.760000e-11 80.5
14 TraesCS3D01G098500 chr3A 86.364 66 9 0 2350 2415 59424007 59423942 4.610000e-09 73.1
15 TraesCS3D01G098500 chr5D 93.401 788 50 1 2548 3333 324410470 324409683 0.000000e+00 1166.0
16 TraesCS3D01G098500 chr7D 93.139 787 50 4 2548 3333 598310750 598309967 0.000000e+00 1151.0
17 TraesCS3D01G098500 chr7D 92.149 777 58 3 2548 3322 576645031 576644256 0.000000e+00 1094.0
18 TraesCS3D01G098500 chr7D 91.414 792 60 5 2547 3333 616465906 616465118 0.000000e+00 1079.0
19 TraesCS3D01G098500 chr7D 87.745 408 43 7 126 531 65530084 65529682 1.400000e-128 470.0
20 TraesCS3D01G098500 chr7D 80.702 114 15 5 475 584 503324744 503324634 7.660000e-12 82.4
21 TraesCS3D01G098500 chr6D 93.020 788 51 4 2548 3333 147887411 147888196 0.000000e+00 1147.0
22 TraesCS3D01G098500 chr6D 81.000 500 62 17 119 618 131930955 131930489 1.890000e-97 366.0
23 TraesCS3D01G098500 chr2D 92.308 793 53 6 2548 3333 276936748 276935957 0.000000e+00 1120.0
24 TraesCS3D01G098500 chr2D 91.508 789 61 5 2546 3330 285349012 285349798 0.000000e+00 1081.0
25 TraesCS3D01G098500 chr2B 92.005 788 59 3 2547 3333 548930992 548930208 0.000000e+00 1103.0
26 TraesCS3D01G098500 chr7B 91.878 788 60 3 2547 3333 616548544 616549328 0.000000e+00 1098.0
27 TraesCS3D01G098500 chr1B 80.045 887 163 13 1455 2334 101527996 101527117 0.000000e+00 645.0
28 TraesCS3D01G098500 chr1B 79.303 889 166 14 1455 2334 101271325 101270446 1.020000e-169 606.0
29 TraesCS3D01G098500 chr1B 85.890 326 46 0 124 449 141108141 141107816 6.840000e-92 348.0
30 TraesCS3D01G098500 chr1B 82.392 301 38 7 1083 1374 101271621 101271327 7.140000e-62 248.0
31 TraesCS3D01G098500 chr1B 82.392 301 35 7 1083 1374 101528289 101527998 2.570000e-61 246.0
32 TraesCS3D01G098500 chr1B 80.447 179 18 7 379 541 59498523 59498700 1.620000e-23 121.0
33 TraesCS3D01G098500 chr1B 80.447 179 18 7 379 541 59518225 59518402 1.620000e-23 121.0
34 TraesCS3D01G098500 chr1D 79.682 881 165 12 1461 2334 63429254 63428381 1.020000e-174 623.0
35 TraesCS3D01G098500 chr1D 79.839 124 19 5 475 594 473344925 473344804 5.920000e-13 86.1
36 TraesCS3D01G098500 chr1D 80.000 120 16 6 475 590 80654281 80654396 7.660000e-12 82.4
37 TraesCS3D01G098500 chr4B 84.672 548 69 9 125 663 545450430 545450971 1.760000e-147 532.0
38 TraesCS3D01G098500 chr4B 81.801 533 87 6 130 653 545492846 545492315 3.950000e-119 438.0
39 TraesCS3D01G098500 chr1A 76.776 887 192 13 1455 2334 62009654 62010533 5.000000e-133 484.0
40 TraesCS3D01G098500 chr1A 82.500 520 86 3 132 651 21082293 21081779 5.070000e-123 451.0
41 TraesCS3D01G098500 chr1A 80.488 205 25 8 1083 1284 61718531 61718339 3.470000e-30 143.0
42 TraesCS3D01G098500 chr6B 83.000 500 69 9 119 618 229517278 229516795 3.950000e-119 438.0
43 TraesCS3D01G098500 chr6A 83.607 427 57 9 125 540 542231096 542231520 4.030000e-104 388.0
44 TraesCS3D01G098500 chr4A 80.037 546 90 13 123 657 5710085 5709548 1.450000e-103 387.0
45 TraesCS3D01G098500 chr4A 82.203 118 17 4 475 590 618932577 618932692 7.610000e-17 99.0
46 TraesCS3D01G098500 chr5B 84.431 167 15 3 2330 2485 77588109 77588275 1.600000e-33 154.0
47 TraesCS3D01G098500 chr5B 89.610 77 7 1 2330 2406 77651820 77651895 2.740000e-16 97.1
48 TraesCS3D01G098500 chr5A 85.484 124 16 2 549 671 600065087 600065209 9.710000e-26 128.0
49 TraesCS3D01G098500 chr5A 80.000 165 21 5 2330 2485 70171748 70171587 9.770000e-21 111.0
50 TraesCS3D01G098500 chr7A 83.146 89 15 0 565 653 19461967 19461879 7.660000e-12 82.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G098500 chr3D 50074832 50078164 3332 False 6156.000000 6156 100.000000 1 3333 1 chr3D.!!$F1 3332
1 TraesCS3D01G098500 chr3D 50381162 50382916 1754 False 1257.500000 2322 92.268000 1 2472 2 chr3D.!!$F2 2471
2 TraesCS3D01G098500 chr3B 79781557 79783327 1770 False 1236.500000 2314 89.786500 1 2472 2 chr3B.!!$F2 2471
3 TraesCS3D01G098500 chr3B 79559871 79561862 1991 False 1062.333333 2700 92.441333 1 2485 3 chr3B.!!$F1 2484
4 TraesCS3D01G098500 chr3A 63434171 63435578 1407 False 2135.000000 2135 93.908000 910 2336 1 chr3A.!!$F2 1426
5 TraesCS3D01G098500 chr3A 63387379 63390637 3258 False 705.866667 1927 93.038333 976 2389 3 chr3A.!!$F3 1413
6 TraesCS3D01G098500 chr5D 324409683 324410470 787 True 1166.000000 1166 93.401000 2548 3333 1 chr5D.!!$R1 785
7 TraesCS3D01G098500 chr7D 598309967 598310750 783 True 1151.000000 1151 93.139000 2548 3333 1 chr7D.!!$R4 785
8 TraesCS3D01G098500 chr7D 576644256 576645031 775 True 1094.000000 1094 92.149000 2548 3322 1 chr7D.!!$R3 774
9 TraesCS3D01G098500 chr7D 616465118 616465906 788 True 1079.000000 1079 91.414000 2547 3333 1 chr7D.!!$R5 786
10 TraesCS3D01G098500 chr6D 147887411 147888196 785 False 1147.000000 1147 93.020000 2548 3333 1 chr6D.!!$F1 785
11 TraesCS3D01G098500 chr2D 276935957 276936748 791 True 1120.000000 1120 92.308000 2548 3333 1 chr2D.!!$R1 785
12 TraesCS3D01G098500 chr2D 285349012 285349798 786 False 1081.000000 1081 91.508000 2546 3330 1 chr2D.!!$F1 784
13 TraesCS3D01G098500 chr2B 548930208 548930992 784 True 1103.000000 1103 92.005000 2547 3333 1 chr2B.!!$R1 786
14 TraesCS3D01G098500 chr7B 616548544 616549328 784 False 1098.000000 1098 91.878000 2547 3333 1 chr7B.!!$F1 786
15 TraesCS3D01G098500 chr1B 101527117 101528289 1172 True 445.500000 645 81.218500 1083 2334 2 chr1B.!!$R3 1251
16 TraesCS3D01G098500 chr1B 101270446 101271621 1175 True 427.000000 606 80.847500 1083 2334 2 chr1B.!!$R2 1251
17 TraesCS3D01G098500 chr1D 63428381 63429254 873 True 623.000000 623 79.682000 1461 2334 1 chr1D.!!$R1 873
18 TraesCS3D01G098500 chr4B 545450430 545450971 541 False 532.000000 532 84.672000 125 663 1 chr4B.!!$F1 538
19 TraesCS3D01G098500 chr4B 545492315 545492846 531 True 438.000000 438 81.801000 130 653 1 chr4B.!!$R1 523
20 TraesCS3D01G098500 chr1A 62009654 62010533 879 False 484.000000 484 76.776000 1455 2334 1 chr1A.!!$F1 879
21 TraesCS3D01G098500 chr1A 21081779 21082293 514 True 451.000000 451 82.500000 132 651 1 chr1A.!!$R1 519
22 TraesCS3D01G098500 chr4A 5709548 5710085 537 True 387.000000 387 80.037000 123 657 1 chr4A.!!$R1 534

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
666 912 0.178984 GGGAGGGTTTTGTTTCGGGA 60.179 55.0 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2489 3479 0.310854 CCTCGCCAAACCAAACTCAC 59.689 55.0 0.0 0.0 0.0 3.51 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
61 63 8.581578 GGGGATTTTTAGAATACACTCAACAAA 58.418 33.333 0.00 0.00 0.00 2.83
126 363 4.366684 CCCCTTGGGCCTCCACAC 62.367 72.222 4.53 0.00 43.94 3.82
127 364 3.579302 CCCTTGGGCCTCCACACA 61.579 66.667 4.53 0.00 43.94 3.72
152 389 0.321919 CACTGCCTACATGTGCCACT 60.322 55.000 9.11 0.00 0.00 4.00
157 394 1.207089 GCCTACATGTGCCACTACTGA 59.793 52.381 9.11 0.00 0.00 3.41
198 435 2.436646 CCATCTCGCCAAACCGCT 60.437 61.111 0.00 0.00 0.00 5.52
265 502 4.282195 CCCGATCCAATCTAGAGCTAAAGT 59.718 45.833 0.00 0.00 0.00 2.66
346 583 2.953648 GAGAGGCCTAGACTTCACCTAC 59.046 54.545 4.42 0.00 0.00 3.18
353 590 2.097110 AGACTTCACCTACCACCACA 57.903 50.000 0.00 0.00 0.00 4.17
367 605 2.819595 CACATTCCAGGGACGCCG 60.820 66.667 0.00 0.00 0.00 6.46
396 634 2.432628 CACCGCCACGAAGTCCTC 60.433 66.667 0.00 0.00 41.61 3.71
401 639 2.109126 GCCACGAAGTCCTCCATGC 61.109 63.158 0.00 0.00 41.61 4.06
403 641 1.811266 CACGAAGTCCTCCATGCCG 60.811 63.158 0.00 0.00 41.61 5.69
513 759 1.671742 GCGTGAGGGGAAGAAGACA 59.328 57.895 0.00 0.00 0.00 3.41
521 767 2.434359 GAAGAAGACACCCCGCCG 60.434 66.667 0.00 0.00 0.00 6.46
523 769 3.236003 AAGAAGACACCCCGCCGAC 62.236 63.158 0.00 0.00 0.00 4.79
594 840 4.423209 GGGGAGGCAGGAGGAGGT 62.423 72.222 0.00 0.00 0.00 3.85
597 843 2.363172 GGAGGCAGGAGGAGGTGAC 61.363 68.421 0.00 0.00 0.00 3.67
599 845 0.980231 GAGGCAGGAGGAGGTGACAT 60.980 60.000 0.00 0.00 0.00 3.06
602 848 1.985614 CAGGAGGAGGTGACATGCA 59.014 57.895 0.00 0.00 0.00 3.96
604 850 0.326264 AGGAGGAGGTGACATGCAAC 59.674 55.000 0.00 0.00 0.00 4.17
608 854 1.514678 GGAGGTGACATGCAACGCAA 61.515 55.000 10.07 0.00 43.62 4.85
612 858 0.976963 GTGACATGCAACGCAAATCG 59.023 50.000 0.00 0.00 43.62 3.34
660 906 3.292159 GCGCGGGAGGGTTTTGTT 61.292 61.111 8.83 0.00 45.69 2.83
663 909 1.284715 GCGGGAGGGTTTTGTTTCG 59.715 57.895 0.00 0.00 0.00 3.46
664 910 1.953772 CGGGAGGGTTTTGTTTCGG 59.046 57.895 0.00 0.00 0.00 4.30
665 911 1.520600 CGGGAGGGTTTTGTTTCGGG 61.521 60.000 0.00 0.00 0.00 5.14
666 912 0.178984 GGGAGGGTTTTGTTTCGGGA 60.179 55.000 0.00 0.00 0.00 5.14
667 913 1.244816 GGAGGGTTTTGTTTCGGGAG 58.755 55.000 0.00 0.00 0.00 4.30
669 915 0.848053 AGGGTTTTGTTTCGGGAGGA 59.152 50.000 0.00 0.00 0.00 3.71
670 916 1.202891 AGGGTTTTGTTTCGGGAGGAG 60.203 52.381 0.00 0.00 0.00 3.69
671 917 1.202842 GGGTTTTGTTTCGGGAGGAGA 60.203 52.381 0.00 0.00 0.00 3.71
672 918 2.578786 GGTTTTGTTTCGGGAGGAGAA 58.421 47.619 0.00 0.00 0.00 2.87
673 919 2.292569 GGTTTTGTTTCGGGAGGAGAAC 59.707 50.000 0.00 0.00 0.00 3.01
676 922 3.502123 TTGTTTCGGGAGGAGAACAAT 57.498 42.857 0.00 0.00 0.00 2.71
678 924 4.202245 TGTTTCGGGAGGAGAACAATAG 57.798 45.455 0.00 0.00 0.00 1.73
679 925 3.581332 TGTTTCGGGAGGAGAACAATAGT 59.419 43.478 0.00 0.00 0.00 2.12
680 926 4.182339 GTTTCGGGAGGAGAACAATAGTC 58.818 47.826 0.00 0.00 0.00 2.59
681 927 3.383698 TCGGGAGGAGAACAATAGTCT 57.616 47.619 0.00 0.00 0.00 3.24
682 928 3.709587 TCGGGAGGAGAACAATAGTCTT 58.290 45.455 0.00 0.00 0.00 3.01
684 930 4.643784 TCGGGAGGAGAACAATAGTCTTAC 59.356 45.833 0.00 0.00 0.00 2.34
685 931 4.401519 CGGGAGGAGAACAATAGTCTTACA 59.598 45.833 0.00 0.00 0.00 2.41
687 933 6.573680 CGGGAGGAGAACAATAGTCTTACAAA 60.574 42.308 0.00 0.00 0.00 2.83
688 934 6.594547 GGGAGGAGAACAATAGTCTTACAAAC 59.405 42.308 0.00 0.00 0.00 2.93
690 936 7.546316 GGAGGAGAACAATAGTCTTACAAACTC 59.454 40.741 0.00 0.00 0.00 3.01
691 937 7.963532 AGGAGAACAATAGTCTTACAAACTCA 58.036 34.615 0.00 0.00 0.00 3.41
692 938 7.873505 AGGAGAACAATAGTCTTACAAACTCAC 59.126 37.037 0.00 0.00 0.00 3.51
694 940 8.366671 AGAACAATAGTCTTACAAACTCACAC 57.633 34.615 0.00 0.00 0.00 3.82
695 941 6.764877 ACAATAGTCTTACAAACTCACACG 57.235 37.500 0.00 0.00 0.00 4.49
697 943 7.428020 ACAATAGTCTTACAAACTCACACGTA 58.572 34.615 0.00 0.00 0.00 3.57
698 944 8.086522 ACAATAGTCTTACAAACTCACACGTAT 58.913 33.333 0.00 0.00 0.00 3.06
699 945 8.922676 CAATAGTCTTACAAACTCACACGTATT 58.077 33.333 0.00 0.00 0.00 1.89
701 947 7.864307 AGTCTTACAAACTCACACGTATTAC 57.136 36.000 0.00 0.00 0.00 1.89
703 949 7.922278 AGTCTTACAAACTCACACGTATTACAA 59.078 33.333 0.00 0.00 0.00 2.41
704 950 8.000435 GTCTTACAAACTCACACGTATTACAAC 59.000 37.037 0.00 0.00 0.00 3.32
705 951 5.662211 ACAAACTCACACGTATTACAACC 57.338 39.130 0.00 0.00 0.00 3.77
706 952 5.117584 ACAAACTCACACGTATTACAACCA 58.882 37.500 0.00 0.00 0.00 3.67
707 953 5.006941 ACAAACTCACACGTATTACAACCAC 59.993 40.000 0.00 0.00 0.00 4.16
708 954 3.656559 ACTCACACGTATTACAACCACC 58.343 45.455 0.00 0.00 0.00 4.61
709 955 3.322828 ACTCACACGTATTACAACCACCT 59.677 43.478 0.00 0.00 0.00 4.00
710 956 4.523943 ACTCACACGTATTACAACCACCTA 59.476 41.667 0.00 0.00 0.00 3.08
712 958 5.653507 TCACACGTATTACAACCACCTATC 58.346 41.667 0.00 0.00 0.00 2.08
714 960 4.467082 ACACGTATTACAACCACCTATCCA 59.533 41.667 0.00 0.00 0.00 3.41
716 962 5.875910 CACGTATTACAACCACCTATCCAAA 59.124 40.000 0.00 0.00 0.00 3.28
717 963 6.372103 CACGTATTACAACCACCTATCCAAAA 59.628 38.462 0.00 0.00 0.00 2.44
718 964 7.066525 CACGTATTACAACCACCTATCCAAAAT 59.933 37.037 0.00 0.00 0.00 1.82
719 965 7.281549 ACGTATTACAACCACCTATCCAAAATC 59.718 37.037 0.00 0.00 0.00 2.17
723 969 8.801882 TTACAACCACCTATCCAAAATCTTAG 57.198 34.615 0.00 0.00 0.00 2.18
726 972 8.387813 ACAACCACCTATCCAAAATCTTAGTTA 58.612 33.333 0.00 0.00 0.00 2.24
727 973 9.238368 CAACCACCTATCCAAAATCTTAGTTAA 57.762 33.333 0.00 0.00 0.00 2.01
728 974 9.816787 AACCACCTATCCAAAATCTTAGTTAAA 57.183 29.630 0.00 0.00 0.00 1.52
737 983 9.016438 TCCAAAATCTTAGTTAAATGTGTACCC 57.984 33.333 0.00 0.00 0.00 3.69
741 987 8.575649 AATCTTAGTTAAATGTGTACCCAAGG 57.424 34.615 0.00 0.00 0.00 3.61
742 988 6.478129 TCTTAGTTAAATGTGTACCCAAGGG 58.522 40.000 2.91 2.91 42.03 3.95
760 1006 7.348080 CCAAGGGGATTTTTAGAATAGGTTC 57.652 40.000 0.00 0.00 35.59 3.62
762 1008 7.398904 CCAAGGGGATTTTTAGAATAGGTTCAA 59.601 37.037 0.00 0.00 34.67 2.69
764 1010 7.475299 AGGGGATTTTTAGAATAGGTTCAACA 58.525 34.615 0.00 0.00 36.79 3.33
765 1011 7.953493 AGGGGATTTTTAGAATAGGTTCAACAA 59.047 33.333 0.00 0.00 36.79 2.83
766 1012 8.033038 GGGGATTTTTAGAATAGGTTCAACAAC 58.967 37.037 0.00 0.00 36.79 3.32
789 1035 6.531503 CCAGTAGGTTGAAGTTATCTCTCA 57.468 41.667 0.00 0.00 0.00 3.27
791 1037 6.378564 CCAGTAGGTTGAAGTTATCTCTCAGA 59.621 42.308 0.00 0.00 0.00 3.27
792 1038 7.093727 CCAGTAGGTTGAAGTTATCTCTCAGAA 60.094 40.741 0.00 0.00 0.00 3.02
793 1039 7.973388 CAGTAGGTTGAAGTTATCTCTCAGAAG 59.027 40.741 0.00 0.00 0.00 2.85
794 1040 7.891183 AGTAGGTTGAAGTTATCTCTCAGAAGA 59.109 37.037 0.00 0.00 0.00 2.87
795 1041 7.546250 AGGTTGAAGTTATCTCTCAGAAGAA 57.454 36.000 0.00 0.00 0.00 2.52
796 1042 7.610865 AGGTTGAAGTTATCTCTCAGAAGAAG 58.389 38.462 0.00 0.00 0.00 2.85
798 1044 8.257306 GGTTGAAGTTATCTCTCAGAAGAAGAT 58.743 37.037 0.00 0.00 0.00 2.40
799 1045 9.301153 GTTGAAGTTATCTCTCAGAAGAAGATC 57.699 37.037 0.00 0.00 0.00 2.75
800 1046 7.702386 TGAAGTTATCTCTCAGAAGAAGATCG 58.298 38.462 0.00 0.00 0.00 3.69
801 1047 7.338196 TGAAGTTATCTCTCAGAAGAAGATCGT 59.662 37.037 0.00 0.00 0.00 3.73
802 1048 7.259290 AGTTATCTCTCAGAAGAAGATCGTC 57.741 40.000 0.00 0.00 0.00 4.20
803 1049 6.262273 AGTTATCTCTCAGAAGAAGATCGTCC 59.738 42.308 4.93 0.00 0.00 4.79
804 1050 3.956744 TCTCTCAGAAGAAGATCGTCCA 58.043 45.455 4.93 0.00 0.00 4.02
805 1051 3.692101 TCTCTCAGAAGAAGATCGTCCAC 59.308 47.826 4.93 0.30 0.00 4.02
806 1052 3.421844 TCTCAGAAGAAGATCGTCCACA 58.578 45.455 4.93 0.00 0.00 4.17
807 1053 4.019858 TCTCAGAAGAAGATCGTCCACAT 58.980 43.478 4.93 0.00 0.00 3.21
809 1055 3.131223 TCAGAAGAAGATCGTCCACATCC 59.869 47.826 4.93 0.00 0.00 3.51
810 1056 3.099905 AGAAGAAGATCGTCCACATCCA 58.900 45.455 4.93 0.00 0.00 3.41
811 1057 3.131933 AGAAGAAGATCGTCCACATCCAG 59.868 47.826 4.93 0.00 0.00 3.86
821 1067 2.864114 CACATCCAGTGCCTCTTGG 58.136 57.895 0.00 0.00 42.15 3.61
886 1136 6.992063 ACTCAATCATCCACATTGACTAAC 57.008 37.500 0.00 0.00 35.71 2.34
892 1142 2.778299 TCCACATTGACTAACTGGTGC 58.222 47.619 0.00 0.00 0.00 5.01
911 1161 3.798380 CATTGTGGATGCGAGCGA 58.202 55.556 0.00 0.00 0.00 4.93
912 1162 1.640069 CATTGTGGATGCGAGCGAG 59.360 57.895 0.00 0.00 0.00 5.03
913 1163 2.176273 ATTGTGGATGCGAGCGAGC 61.176 57.895 0.00 0.00 37.71 5.03
915 1165 4.854784 GTGGATGCGAGCGAGCGA 62.855 66.667 1.41 0.00 40.67 4.93
916 1166 4.559229 TGGATGCGAGCGAGCGAG 62.559 66.667 1.41 0.00 40.67 5.03
922 1172 4.896028 CGAGCGAGCGAGCGACAT 62.896 66.667 1.41 0.00 43.00 3.06
923 1173 3.318555 GAGCGAGCGAGCGACATG 61.319 66.667 1.41 0.00 43.00 3.21
924 1174 4.862092 AGCGAGCGAGCGACATGG 62.862 66.667 0.00 0.00 43.00 3.66
926 1176 4.193334 CGAGCGAGCGACATGGGA 62.193 66.667 0.00 0.00 0.00 4.37
927 1177 2.419198 GAGCGAGCGACATGGGAT 59.581 61.111 0.00 0.00 0.00 3.85
928 1178 1.953138 GAGCGAGCGACATGGGATG 60.953 63.158 0.00 0.00 0.00 3.51
931 1181 1.522355 CGAGCGACATGGGATGCTT 60.522 57.895 0.00 0.00 37.91 3.91
932 1182 1.493950 CGAGCGACATGGGATGCTTC 61.494 60.000 0.00 0.00 37.91 3.86
933 1183 1.493950 GAGCGACATGGGATGCTTCG 61.494 60.000 0.00 0.00 37.91 3.79
934 1184 3.017323 CGACATGGGATGCTTCGC 58.983 61.111 9.44 9.44 35.46 4.70
935 1185 2.874694 CGACATGGGATGCTTCGCG 61.875 63.158 0.00 0.00 37.62 5.87
936 1186 1.815421 GACATGGGATGCTTCGCGT 60.815 57.895 5.77 8.59 37.62 6.01
940 1190 2.224185 ACATGGGATGCTTCGCGTATAA 60.224 45.455 5.77 0.00 37.62 0.98
942 1192 2.907634 TGGGATGCTTCGCGTATAAAA 58.092 42.857 5.77 0.00 37.62 1.52
943 1193 3.472652 TGGGATGCTTCGCGTATAAAAT 58.527 40.909 5.77 0.00 37.62 1.82
944 1194 3.249799 TGGGATGCTTCGCGTATAAAATG 59.750 43.478 5.77 0.00 37.62 2.32
946 1196 4.211389 GGATGCTTCGCGTATAAAATGTG 58.789 43.478 5.77 0.00 0.00 3.21
947 1197 3.046285 TGCTTCGCGTATAAAATGTGC 57.954 42.857 5.77 0.00 0.00 4.57
948 1198 2.675844 TGCTTCGCGTATAAAATGTGCT 59.324 40.909 5.77 0.00 0.00 4.40
949 1199 3.029074 GCTTCGCGTATAAAATGTGCTG 58.971 45.455 5.77 0.00 0.00 4.41
950 1200 2.730183 TCGCGTATAAAATGTGCTGC 57.270 45.000 5.77 0.00 0.00 5.25
951 1201 2.003301 TCGCGTATAAAATGTGCTGCA 58.997 42.857 5.77 0.00 0.00 4.41
952 1202 2.416893 TCGCGTATAAAATGTGCTGCAA 59.583 40.909 2.77 0.00 0.00 4.08
954 1204 3.790820 CGCGTATAAAATGTGCTGCAAAT 59.209 39.130 2.77 0.11 0.00 2.32
955 1205 4.265085 CGCGTATAAAATGTGCTGCAAATT 59.735 37.500 12.22 12.22 0.00 1.82
956 1206 5.483213 GCGTATAAAATGTGCTGCAAATTG 58.517 37.500 18.23 6.40 0.00 2.32
957 1207 5.500610 GCGTATAAAATGTGCTGCAAATTGG 60.501 40.000 18.23 5.90 0.00 3.16
958 1208 5.005586 CGTATAAAATGTGCTGCAAATTGGG 59.994 40.000 18.23 2.02 0.00 4.12
959 1209 1.525941 AAATGTGCTGCAAATTGGGC 58.474 45.000 18.23 0.00 0.00 5.36
960 1210 0.397187 AATGTGCTGCAAATTGGGCA 59.603 45.000 16.93 3.29 39.32 5.36
963 1213 1.307097 GTGCTGCAAATTGGGCAAAA 58.693 45.000 2.77 0.00 41.39 2.44
964 1214 1.264826 GTGCTGCAAATTGGGCAAAAG 59.735 47.619 2.77 0.00 41.39 2.27
965 1215 0.876399 GCTGCAAATTGGGCAAAAGG 59.124 50.000 6.52 0.00 41.39 3.11
966 1216 1.542987 GCTGCAAATTGGGCAAAAGGA 60.543 47.619 6.52 0.00 41.39 3.36
967 1217 2.419667 CTGCAAATTGGGCAAAAGGAG 58.580 47.619 6.52 0.00 41.39 3.69
969 1219 2.968574 TGCAAATTGGGCAAAAGGAGTA 59.031 40.909 2.79 0.00 38.54 2.59
970 1220 3.244044 TGCAAATTGGGCAAAAGGAGTAC 60.244 43.478 2.79 0.00 38.54 2.73
971 1221 3.006859 GCAAATTGGGCAAAAGGAGTACT 59.993 43.478 0.00 0.00 0.00 2.73
972 1222 4.809673 CAAATTGGGCAAAAGGAGTACTC 58.190 43.478 14.87 14.87 0.00 2.59
974 1224 2.859165 TGGGCAAAAGGAGTACTCAG 57.141 50.000 23.91 9.20 0.00 3.35
978 1228 3.149981 GGCAAAAGGAGTACTCAGCTTT 58.850 45.455 23.91 19.84 0.00 3.51
979 1229 3.057946 GGCAAAAGGAGTACTCAGCTTTG 60.058 47.826 23.91 24.50 32.20 2.77
986 1827 6.798427 AGGAGTACTCAGCTTTGATCATTA 57.202 37.500 23.91 0.00 0.00 1.90
1032 1873 2.199652 CCCGTTGCTTCTTGCCCAA 61.200 57.895 0.00 0.00 42.00 4.12
1036 1877 2.595386 CGTTGCTTCTTGCCCAATTAC 58.405 47.619 0.00 0.00 42.00 1.89
1037 1878 2.228822 CGTTGCTTCTTGCCCAATTACT 59.771 45.455 0.00 0.00 42.00 2.24
1038 1879 3.670627 CGTTGCTTCTTGCCCAATTACTC 60.671 47.826 0.00 0.00 42.00 2.59
1406 2259 1.808411 ATCGGTTGCTCAATCGTGTT 58.192 45.000 13.97 0.10 44.60 3.32
1451 2305 4.340894 TCGGCTGAATTTCTCGATTTTG 57.659 40.909 0.00 0.00 0.00 2.44
1614 2533 0.322322 TTCTTCCGGGCGCTTAAGAA 59.678 50.000 17.70 17.70 36.02 2.52
2239 3191 2.500229 CACCGTGGTGTGGATTTTAGT 58.500 47.619 10.94 0.00 40.91 2.24
2390 3378 2.005451 AGCATGCTGAGATTCGTGTTC 58.995 47.619 21.98 0.00 0.00 3.18
2392 3380 3.118992 AGCATGCTGAGATTCGTGTTCTA 60.119 43.478 21.98 0.00 0.00 2.10
2406 3394 2.793232 GTGTTCTAGTGTCGTTGTCCAC 59.207 50.000 0.00 0.00 0.00 4.02
2449 3439 1.291132 GTGCAGCCCTCTCGTTAATC 58.709 55.000 0.00 0.00 0.00 1.75
2451 3441 0.179108 GCAGCCCTCTCGTTAATCGT 60.179 55.000 0.00 0.00 40.80 3.73
2452 3442 1.739371 GCAGCCCTCTCGTTAATCGTT 60.739 52.381 0.00 0.00 40.80 3.85
2453 3443 2.618053 CAGCCCTCTCGTTAATCGTTT 58.382 47.619 0.00 0.00 40.80 3.60
2454 3444 3.000727 CAGCCCTCTCGTTAATCGTTTT 58.999 45.455 0.00 0.00 40.80 2.43
2485 3475 1.134280 TCTATTGCCAGGCTGAGCTTC 60.134 52.381 17.94 0.02 0.00 3.86
2486 3476 0.620030 TATTGCCAGGCTGAGCTTCA 59.380 50.000 17.94 6.78 0.00 3.02
2487 3477 0.033405 ATTGCCAGGCTGAGCTTCAT 60.033 50.000 17.94 8.64 0.00 2.57
2488 3478 0.251474 TTGCCAGGCTGAGCTTCATT 60.251 50.000 17.94 0.00 0.00 2.57
2489 3479 0.963856 TGCCAGGCTGAGCTTCATTG 60.964 55.000 17.94 0.00 0.00 2.82
2490 3480 0.964358 GCCAGGCTGAGCTTCATTGT 60.964 55.000 17.94 0.00 0.00 2.71
2491 3481 0.809385 CCAGGCTGAGCTTCATTGTG 59.191 55.000 17.94 0.00 0.00 3.33
2492 3482 1.612462 CCAGGCTGAGCTTCATTGTGA 60.612 52.381 17.94 0.00 0.00 3.58
2493 3483 1.738350 CAGGCTGAGCTTCATTGTGAG 59.262 52.381 9.42 0.00 0.00 3.51
2494 3484 1.350351 AGGCTGAGCTTCATTGTGAGT 59.650 47.619 3.72 0.00 0.00 3.41
2495 3485 2.157738 GGCTGAGCTTCATTGTGAGTT 58.842 47.619 3.72 0.00 0.00 3.01
2496 3486 2.555757 GGCTGAGCTTCATTGTGAGTTT 59.444 45.455 3.72 0.00 0.00 2.66
2497 3487 3.562505 GCTGAGCTTCATTGTGAGTTTG 58.437 45.455 0.00 0.00 0.00 2.93
2498 3488 3.611057 GCTGAGCTTCATTGTGAGTTTGG 60.611 47.826 0.00 0.00 0.00 3.28
2499 3489 3.554934 TGAGCTTCATTGTGAGTTTGGT 58.445 40.909 0.00 0.00 0.00 3.67
2500 3490 3.953612 TGAGCTTCATTGTGAGTTTGGTT 59.046 39.130 0.00 0.00 0.00 3.67
2501 3491 4.402155 TGAGCTTCATTGTGAGTTTGGTTT 59.598 37.500 0.00 0.00 0.00 3.27
2502 3492 4.685924 AGCTTCATTGTGAGTTTGGTTTG 58.314 39.130 0.00 0.00 0.00 2.93
2503 3493 3.803778 GCTTCATTGTGAGTTTGGTTTGG 59.196 43.478 0.00 0.00 0.00 3.28
2504 3494 3.451141 TCATTGTGAGTTTGGTTTGGC 57.549 42.857 0.00 0.00 0.00 4.52
2505 3495 2.126467 CATTGTGAGTTTGGTTTGGCG 58.874 47.619 0.00 0.00 0.00 5.69
2506 3496 1.464734 TTGTGAGTTTGGTTTGGCGA 58.535 45.000 0.00 0.00 0.00 5.54
2507 3497 1.021202 TGTGAGTTTGGTTTGGCGAG 58.979 50.000 0.00 0.00 0.00 5.03
2508 3498 0.310854 GTGAGTTTGGTTTGGCGAGG 59.689 55.000 0.00 0.00 0.00 4.63
2509 3499 1.285950 GAGTTTGGTTTGGCGAGGC 59.714 57.895 0.00 0.00 0.00 4.70
2510 3500 1.152756 AGTTTGGTTTGGCGAGGCT 60.153 52.632 0.00 0.00 0.00 4.58
2511 3501 1.007387 GTTTGGTTTGGCGAGGCTG 60.007 57.895 0.00 0.00 0.00 4.85
2512 3502 1.152860 TTTGGTTTGGCGAGGCTGA 60.153 52.632 0.00 0.00 0.00 4.26
2513 3503 0.539438 TTTGGTTTGGCGAGGCTGAT 60.539 50.000 0.00 0.00 0.00 2.90
2514 3504 1.243342 TTGGTTTGGCGAGGCTGATG 61.243 55.000 0.00 0.00 0.00 3.07
2515 3505 1.675641 GGTTTGGCGAGGCTGATGT 60.676 57.895 0.00 0.00 0.00 3.06
2516 3506 1.244019 GGTTTGGCGAGGCTGATGTT 61.244 55.000 0.00 0.00 0.00 2.71
2517 3507 0.598065 GTTTGGCGAGGCTGATGTTT 59.402 50.000 0.00 0.00 0.00 2.83
2518 3508 1.000274 GTTTGGCGAGGCTGATGTTTT 60.000 47.619 0.00 0.00 0.00 2.43
2519 3509 1.327303 TTGGCGAGGCTGATGTTTTT 58.673 45.000 0.00 0.00 0.00 1.94
2540 3530 4.902443 TTTTAAACATTGTGACGGCTCA 57.098 36.364 0.00 0.00 0.00 4.26
2541 3531 4.902443 TTTAAACATTGTGACGGCTCAA 57.098 36.364 8.42 8.42 32.70 3.02
2542 3532 5.446143 TTTAAACATTGTGACGGCTCAAT 57.554 34.783 12.70 12.70 38.39 2.57
2543 3533 6.561737 TTTAAACATTGTGACGGCTCAATA 57.438 33.333 17.63 0.30 36.41 1.90
2544 3534 6.561737 TTAAACATTGTGACGGCTCAATAA 57.438 33.333 17.63 6.56 36.41 1.40
2560 3550 5.290158 GCTCAATAAAAGGACGTCGATAACA 59.710 40.000 9.92 0.00 0.00 2.41
2657 3647 0.666374 GTGGGCAAAACAACTAGCGT 59.334 50.000 0.00 0.00 0.00 5.07
2661 3651 1.539827 GGCAAAACAACTAGCGTCCAT 59.460 47.619 0.00 0.00 0.00 3.41
2752 3749 1.621072 CCTCTCTCAGCCACCTACCTT 60.621 57.143 0.00 0.00 0.00 3.50
2792 3789 1.389555 TGATAGTCATCACGCGTCCT 58.610 50.000 9.86 2.79 36.22 3.85
2804 3801 2.664851 CGTCCTCGCAGTTGCCAA 60.665 61.111 0.00 0.00 37.91 4.52
2824 3821 0.618981 GGTCCGGACCCTCTTCAATT 59.381 55.000 39.24 0.00 45.68 2.32
2826 3823 2.554564 GGTCCGGACCCTCTTCAATTTT 60.555 50.000 39.24 0.00 45.68 1.82
3009 4007 5.541868 TGCCATGATTTGAAAACTTTAGGGA 59.458 36.000 0.00 0.00 0.00 4.20
3096 4095 1.145571 AACCTTAGGAGTTGCCACCA 58.854 50.000 4.77 0.00 40.02 4.17
3152 4153 8.121305 ACAAAGAGACATGGCAAAATAACATA 57.879 30.769 0.00 0.00 0.00 2.29
3228 4232 2.621055 GTGTACCCTGCAAAACACATGA 59.379 45.455 0.00 0.00 41.43 3.07
3323 4335 1.479730 TGCAAAACACATGGCAACTGA 59.520 42.857 0.00 0.00 32.54 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.615986 AAAATCCCCTTGGGTACACC 57.384 50.000 4.84 0.00 44.74 4.16
52 54 5.497474 ACTTCAACCTACTGTTTGTTGAGT 58.503 37.500 18.09 15.90 46.27 3.41
61 63 6.948886 TCTGAGAGATAACTTCAACCTACTGT 59.051 38.462 0.00 0.00 0.00 3.55
119 356 3.941188 AGTGGCCGGTGTGTGGAG 61.941 66.667 1.90 0.00 0.00 3.86
120 357 4.248842 CAGTGGCCGGTGTGTGGA 62.249 66.667 1.90 0.00 0.00 4.02
141 378 1.611673 GGCTTCAGTAGTGGCACATGT 60.612 52.381 21.41 1.16 44.52 3.21
143 380 0.987294 AGGCTTCAGTAGTGGCACAT 59.013 50.000 21.41 7.59 44.52 3.21
152 389 0.325671 CCTCCTCCCAGGCTTCAGTA 60.326 60.000 0.00 0.00 34.61 2.74
184 421 1.511305 CTCTAGCGGTTTGGCGAGA 59.489 57.895 0.00 0.00 41.44 4.04
198 435 1.152735 ATTCCTCTCGGCGGCTCTA 60.153 57.895 7.21 0.00 0.00 2.43
331 568 2.496470 GTGGTGGTAGGTGAAGTCTAGG 59.504 54.545 0.00 0.00 0.00 3.02
346 583 1.377202 CGTCCCTGGAATGTGGTGG 60.377 63.158 0.00 0.00 0.00 4.61
382 620 1.811266 CATGGAGGACTTCGTGGCG 60.811 63.158 0.00 0.00 0.00 5.69
383 621 2.109126 GCATGGAGGACTTCGTGGC 61.109 63.158 2.21 0.00 0.00 5.01
497 743 0.325272 GGGTGTCTTCTTCCCCTCAC 59.675 60.000 0.00 0.00 35.52 3.51
498 744 2.773458 GGGTGTCTTCTTCCCCTCA 58.227 57.895 0.00 0.00 35.52 3.86
579 825 2.039624 TCACCTCCTCCTGCCTCC 59.960 66.667 0.00 0.00 0.00 4.30
581 827 1.081833 ATGTCACCTCCTCCTGCCT 59.918 57.895 0.00 0.00 0.00 4.75
584 830 0.325933 TTGCATGTCACCTCCTCCTG 59.674 55.000 0.00 0.00 0.00 3.86
590 836 0.310543 TTTGCGTTGCATGTCACCTC 59.689 50.000 0.00 0.00 38.76 3.85
594 840 0.871057 TCGATTTGCGTTGCATGTCA 59.129 45.000 0.00 0.00 38.76 3.58
597 843 1.261989 CCTTCGATTTGCGTTGCATG 58.738 50.000 0.00 0.00 38.76 4.06
599 845 1.081509 GCCTTCGATTTGCGTTGCA 60.082 52.632 0.00 0.00 41.80 4.08
602 848 2.340328 GGGGCCTTCGATTTGCGTT 61.340 57.895 0.84 0.00 41.80 4.84
604 850 2.438434 AGGGGCCTTCGATTTGCG 60.438 61.111 0.84 0.00 42.69 4.85
608 854 3.097162 GGGGAGGGGCCTTCGATT 61.097 66.667 9.80 0.00 36.66 3.34
645 891 1.284715 CGAAACAAAACCCTCCCGC 59.715 57.895 0.00 0.00 0.00 6.13
654 900 3.284793 TGTTCTCCTCCCGAAACAAAA 57.715 42.857 0.00 0.00 0.00 2.44
657 903 3.581332 ACTATTGTTCTCCTCCCGAAACA 59.419 43.478 0.00 0.00 0.00 2.83
658 904 4.081586 AGACTATTGTTCTCCTCCCGAAAC 60.082 45.833 0.00 0.00 0.00 2.78
659 905 4.094476 AGACTATTGTTCTCCTCCCGAAA 58.906 43.478 0.00 0.00 0.00 3.46
660 906 3.709587 AGACTATTGTTCTCCTCCCGAA 58.290 45.455 0.00 0.00 0.00 4.30
663 909 5.934402 TGTAAGACTATTGTTCTCCTCCC 57.066 43.478 0.00 0.00 0.00 4.30
664 910 7.387643 AGTTTGTAAGACTATTGTTCTCCTCC 58.612 38.462 0.00 0.00 0.00 4.30
665 911 8.088981 TGAGTTTGTAAGACTATTGTTCTCCTC 58.911 37.037 0.00 0.00 0.00 3.71
666 912 7.873505 GTGAGTTTGTAAGACTATTGTTCTCCT 59.126 37.037 0.00 0.00 0.00 3.69
667 913 7.656137 TGTGAGTTTGTAAGACTATTGTTCTCC 59.344 37.037 0.00 0.00 0.00 3.71
669 915 7.169308 CGTGTGAGTTTGTAAGACTATTGTTCT 59.831 37.037 0.00 0.00 0.00 3.01
670 916 7.042925 ACGTGTGAGTTTGTAAGACTATTGTTC 60.043 37.037 0.00 0.00 0.00 3.18
671 917 6.759827 ACGTGTGAGTTTGTAAGACTATTGTT 59.240 34.615 0.00 0.00 0.00 2.83
672 918 6.278363 ACGTGTGAGTTTGTAAGACTATTGT 58.722 36.000 0.00 0.00 0.00 2.71
673 919 6.764877 ACGTGTGAGTTTGTAAGACTATTG 57.235 37.500 0.00 0.00 0.00 1.90
676 922 8.567104 TGTAATACGTGTGAGTTTGTAAGACTA 58.433 33.333 0.00 0.00 0.00 2.59
678 924 7.627585 TGTAATACGTGTGAGTTTGTAAGAC 57.372 36.000 0.00 0.00 0.00 3.01
679 925 7.169645 GGTTGTAATACGTGTGAGTTTGTAAGA 59.830 37.037 0.00 0.00 0.00 2.10
680 926 7.042590 TGGTTGTAATACGTGTGAGTTTGTAAG 60.043 37.037 0.00 0.00 0.00 2.34
681 927 6.760298 TGGTTGTAATACGTGTGAGTTTGTAA 59.240 34.615 0.00 0.00 0.00 2.41
682 928 6.200665 GTGGTTGTAATACGTGTGAGTTTGTA 59.799 38.462 0.00 0.00 0.00 2.41
684 930 5.437263 GTGGTTGTAATACGTGTGAGTTTG 58.563 41.667 0.00 0.00 0.00 2.93
685 931 4.512571 GGTGGTTGTAATACGTGTGAGTTT 59.487 41.667 0.00 0.00 0.00 2.66
687 933 3.322828 AGGTGGTTGTAATACGTGTGAGT 59.677 43.478 0.00 0.00 0.00 3.41
688 934 3.921677 AGGTGGTTGTAATACGTGTGAG 58.078 45.455 0.00 0.00 0.00 3.51
690 936 4.807304 GGATAGGTGGTTGTAATACGTGTG 59.193 45.833 0.00 0.00 0.00 3.82
691 937 4.467082 TGGATAGGTGGTTGTAATACGTGT 59.533 41.667 0.00 0.00 0.00 4.49
692 938 5.013568 TGGATAGGTGGTTGTAATACGTG 57.986 43.478 0.00 0.00 0.00 4.49
694 940 6.988622 TTTTGGATAGGTGGTTGTAATACG 57.011 37.500 0.00 0.00 0.00 3.06
695 941 8.747538 AGATTTTGGATAGGTGGTTGTAATAC 57.252 34.615 0.00 0.00 0.00 1.89
697 943 9.408648 CTAAGATTTTGGATAGGTGGTTGTAAT 57.591 33.333 0.00 0.00 0.00 1.89
698 944 8.387813 ACTAAGATTTTGGATAGGTGGTTGTAA 58.612 33.333 0.00 0.00 0.00 2.41
699 945 7.924541 ACTAAGATTTTGGATAGGTGGTTGTA 58.075 34.615 0.00 0.00 0.00 2.41
700 946 6.790319 ACTAAGATTTTGGATAGGTGGTTGT 58.210 36.000 0.00 0.00 0.00 3.32
701 947 7.703058 AACTAAGATTTTGGATAGGTGGTTG 57.297 36.000 0.00 0.00 0.00 3.77
703 949 9.990868 ATTTAACTAAGATTTTGGATAGGTGGT 57.009 29.630 0.00 0.00 0.00 4.16
712 958 8.798402 TGGGTACACATTTAACTAAGATTTTGG 58.202 33.333 0.00 0.00 0.00 3.28
716 962 7.614192 CCCTTGGGTACACATTTAACTAAGATT 59.386 37.037 0.00 0.00 0.00 2.40
717 963 7.116736 CCCTTGGGTACACATTTAACTAAGAT 58.883 38.462 0.00 0.00 0.00 2.40
718 964 6.478129 CCCTTGGGTACACATTTAACTAAGA 58.522 40.000 0.00 0.00 0.00 2.10
719 965 5.650703 CCCCTTGGGTACACATTTAACTAAG 59.349 44.000 0.00 0.00 38.25 2.18
722 968 3.658705 TCCCCTTGGGTACACATTTAACT 59.341 43.478 0.00 0.00 44.74 2.24
723 969 4.036941 TCCCCTTGGGTACACATTTAAC 57.963 45.455 0.00 0.00 44.74 2.01
726 972 3.845109 AATCCCCTTGGGTACACATTT 57.155 42.857 0.00 0.00 44.74 2.32
727 973 3.845109 AAATCCCCTTGGGTACACATT 57.155 42.857 0.00 0.00 44.74 2.71
728 974 3.845109 AAAATCCCCTTGGGTACACAT 57.155 42.857 0.00 0.00 44.74 3.21
730 976 4.925836 TCTAAAAATCCCCTTGGGTACAC 58.074 43.478 4.84 0.00 44.74 2.90
732 978 6.776116 CCTATTCTAAAAATCCCCTTGGGTAC 59.224 42.308 4.84 0.00 44.74 3.34
734 980 5.257816 ACCTATTCTAAAAATCCCCTTGGGT 59.742 40.000 4.84 0.00 44.74 4.51
735 981 5.777449 ACCTATTCTAAAAATCCCCTTGGG 58.223 41.667 0.00 0.00 46.11 4.12
736 982 6.895204 TGAACCTATTCTAAAAATCCCCTTGG 59.105 38.462 0.00 0.00 35.69 3.61
737 983 7.954666 TGAACCTATTCTAAAAATCCCCTTG 57.045 36.000 0.00 0.00 35.69 3.61
739 985 7.475299 TGTTGAACCTATTCTAAAAATCCCCT 58.525 34.615 0.00 0.00 35.69 4.79
740 986 7.712204 TGTTGAACCTATTCTAAAAATCCCC 57.288 36.000 0.00 0.00 35.69 4.81
741 987 8.981724 GTTGTTGAACCTATTCTAAAAATCCC 57.018 34.615 0.00 0.00 35.69 3.85
766 1012 6.378564 TCTGAGAGATAACTTCAACCTACTGG 59.621 42.308 0.00 0.00 39.83 4.00
767 1013 7.397892 TCTGAGAGATAACTTCAACCTACTG 57.602 40.000 0.00 0.00 0.00 2.74
768 1014 7.891183 TCTTCTGAGAGATAACTTCAACCTACT 59.109 37.037 0.00 0.00 0.00 2.57
769 1015 8.057536 TCTTCTGAGAGATAACTTCAACCTAC 57.942 38.462 0.00 0.00 0.00 3.18
772 1018 7.607250 TCTTCTTCTGAGAGATAACTTCAACC 58.393 38.462 0.00 0.00 32.44 3.77
773 1019 9.301153 GATCTTCTTCTGAGAGATAACTTCAAC 57.699 37.037 0.00 0.00 32.44 3.18
774 1020 8.187480 CGATCTTCTTCTGAGAGATAACTTCAA 58.813 37.037 0.00 0.00 32.44 2.69
775 1021 7.338196 ACGATCTTCTTCTGAGAGATAACTTCA 59.662 37.037 0.00 0.00 32.44 3.02
777 1023 7.201785 GGACGATCTTCTTCTGAGAGATAACTT 60.202 40.741 0.00 0.00 32.44 2.66
778 1024 6.262273 GGACGATCTTCTTCTGAGAGATAACT 59.738 42.308 0.00 0.00 32.44 2.24
779 1025 6.038825 TGGACGATCTTCTTCTGAGAGATAAC 59.961 42.308 0.00 0.00 32.44 1.89
780 1026 6.038825 GTGGACGATCTTCTTCTGAGAGATAA 59.961 42.308 0.00 0.00 32.44 1.75
781 1027 5.529430 GTGGACGATCTTCTTCTGAGAGATA 59.471 44.000 0.00 0.00 32.44 1.98
782 1028 4.338118 GTGGACGATCTTCTTCTGAGAGAT 59.662 45.833 0.00 1.49 32.44 2.75
783 1029 3.692101 GTGGACGATCTTCTTCTGAGAGA 59.308 47.826 0.00 0.00 32.44 3.10
784 1030 3.441922 TGTGGACGATCTTCTTCTGAGAG 59.558 47.826 0.00 0.00 32.44 3.20
785 1031 3.421844 TGTGGACGATCTTCTTCTGAGA 58.578 45.455 0.00 0.00 0.00 3.27
786 1032 3.857549 TGTGGACGATCTTCTTCTGAG 57.142 47.619 0.00 0.00 0.00 3.35
787 1033 3.131223 GGATGTGGACGATCTTCTTCTGA 59.869 47.826 0.00 0.00 0.00 3.27
789 1035 3.099905 TGGATGTGGACGATCTTCTTCT 58.900 45.455 0.00 0.00 0.00 2.85
791 1037 2.834549 ACTGGATGTGGACGATCTTCTT 59.165 45.455 0.00 0.00 0.00 2.52
792 1038 2.167281 CACTGGATGTGGACGATCTTCT 59.833 50.000 0.00 0.00 42.68 2.85
793 1039 2.544685 CACTGGATGTGGACGATCTTC 58.455 52.381 0.00 0.00 42.68 2.87
794 1040 1.406069 GCACTGGATGTGGACGATCTT 60.406 52.381 0.00 0.00 46.27 2.40
795 1041 0.176680 GCACTGGATGTGGACGATCT 59.823 55.000 0.00 0.00 46.27 2.75
796 1042 0.811616 GGCACTGGATGTGGACGATC 60.812 60.000 0.00 0.00 46.27 3.69
798 1044 1.888436 GAGGCACTGGATGTGGACGA 61.888 60.000 0.00 0.00 46.27 4.20
799 1045 1.448540 GAGGCACTGGATGTGGACG 60.449 63.158 0.00 0.00 46.27 4.79
800 1046 0.326264 AAGAGGCACTGGATGTGGAC 59.674 55.000 0.00 0.00 46.27 4.02
801 1047 0.325933 CAAGAGGCACTGGATGTGGA 59.674 55.000 0.00 0.00 46.27 4.02
802 1048 0.679002 CCAAGAGGCACTGGATGTGG 60.679 60.000 0.00 0.00 46.27 4.17
804 1050 1.687612 CCCAAGAGGCACTGGATGT 59.312 57.895 1.48 0.00 41.55 3.06
805 1051 4.651867 CCCAAGAGGCACTGGATG 57.348 61.111 1.48 0.00 41.55 3.51
814 1060 2.067932 TTGTGTGGAGGCCCAAGAGG 62.068 60.000 0.00 0.00 45.59 3.69
815 1061 0.607489 CTTGTGTGGAGGCCCAAGAG 60.607 60.000 10.65 0.00 45.59 2.85
818 1064 2.203480 GCTTGTGTGGAGGCCCAA 60.203 61.111 0.00 0.00 45.59 4.12
820 1066 1.398958 TTTTGCTTGTGTGGAGGCCC 61.399 55.000 0.00 0.00 0.00 5.80
821 1067 0.681175 ATTTTGCTTGTGTGGAGGCC 59.319 50.000 0.00 0.00 0.00 5.19
886 1136 1.138036 CATCCACAATGCGCACCAG 59.862 57.895 14.90 8.32 0.00 4.00
910 1160 1.953138 CATCCCATGTCGCTCGCTC 60.953 63.158 0.00 0.00 0.00 5.03
911 1161 2.107750 CATCCCATGTCGCTCGCT 59.892 61.111 0.00 0.00 0.00 4.93
912 1162 3.643978 GCATCCCATGTCGCTCGC 61.644 66.667 0.00 0.00 0.00 5.03
913 1163 1.493950 GAAGCATCCCATGTCGCTCG 61.494 60.000 0.00 0.00 32.37 5.03
914 1164 1.493950 CGAAGCATCCCATGTCGCTC 61.494 60.000 0.00 0.00 32.37 5.03
915 1165 1.522355 CGAAGCATCCCATGTCGCT 60.522 57.895 0.00 0.00 35.90 4.93
916 1166 3.017323 CGAAGCATCCCATGTCGC 58.983 61.111 0.00 0.00 0.00 5.19
931 1181 2.003301 TGCAGCACATTTTATACGCGA 58.997 42.857 15.93 0.00 0.00 5.87
932 1182 2.450365 TGCAGCACATTTTATACGCG 57.550 45.000 3.53 3.53 0.00 6.01
933 1183 5.483213 CAATTTGCAGCACATTTTATACGC 58.517 37.500 3.90 0.00 0.00 4.42
934 1184 5.005586 CCCAATTTGCAGCACATTTTATACG 59.994 40.000 3.90 0.00 0.00 3.06
935 1185 5.220643 GCCCAATTTGCAGCACATTTTATAC 60.221 40.000 3.90 0.00 0.00 1.47
936 1186 4.874966 GCCCAATTTGCAGCACATTTTATA 59.125 37.500 3.90 0.00 0.00 0.98
940 1190 1.202782 TGCCCAATTTGCAGCACATTT 60.203 42.857 3.90 0.00 34.05 2.32
942 1192 0.397187 TTGCCCAATTTGCAGCACAT 59.603 45.000 10.72 0.00 40.35 3.21
943 1193 0.179702 TTTGCCCAATTTGCAGCACA 59.820 45.000 10.72 0.00 40.35 4.57
944 1194 1.264826 CTTTTGCCCAATTTGCAGCAC 59.735 47.619 10.72 0.00 40.35 4.40
946 1196 0.876399 CCTTTTGCCCAATTTGCAGC 59.124 50.000 0.20 3.44 40.35 5.25
947 1197 2.224354 ACTCCTTTTGCCCAATTTGCAG 60.224 45.455 0.20 0.00 40.35 4.41
948 1198 1.767681 ACTCCTTTTGCCCAATTTGCA 59.232 42.857 0.00 0.00 36.84 4.08
949 1199 2.549064 ACTCCTTTTGCCCAATTTGC 57.451 45.000 0.00 0.00 0.00 3.68
950 1200 4.280677 TGAGTACTCCTTTTGCCCAATTTG 59.719 41.667 20.11 0.00 0.00 2.32
951 1201 4.479158 TGAGTACTCCTTTTGCCCAATTT 58.521 39.130 20.11 0.00 0.00 1.82
952 1202 4.082125 CTGAGTACTCCTTTTGCCCAATT 58.918 43.478 20.11 0.00 0.00 2.32
954 1204 2.814097 GCTGAGTACTCCTTTTGCCCAA 60.814 50.000 20.11 0.00 0.00 4.12
955 1205 1.271379 GCTGAGTACTCCTTTTGCCCA 60.271 52.381 20.11 0.00 0.00 5.36
956 1206 1.003696 AGCTGAGTACTCCTTTTGCCC 59.996 52.381 20.11 0.20 0.00 5.36
957 1207 2.481289 AGCTGAGTACTCCTTTTGCC 57.519 50.000 20.11 1.18 0.00 4.52
958 1208 3.815401 TCAAAGCTGAGTACTCCTTTTGC 59.185 43.478 24.51 18.53 0.00 3.68
959 1209 5.702670 TGATCAAAGCTGAGTACTCCTTTTG 59.297 40.000 23.91 23.91 34.23 2.44
960 1210 5.869579 TGATCAAAGCTGAGTACTCCTTTT 58.130 37.500 20.11 13.82 34.23 2.27
963 1213 5.690464 AATGATCAAAGCTGAGTACTCCT 57.310 39.130 20.11 8.07 34.23 3.69
964 1214 6.341316 TGTAATGATCAAAGCTGAGTACTCC 58.659 40.000 20.11 5.74 34.23 3.85
965 1215 7.708322 TGATGTAATGATCAAAGCTGAGTACTC 59.292 37.037 16.32 16.32 34.23 2.59
966 1216 7.559486 TGATGTAATGATCAAAGCTGAGTACT 58.441 34.615 0.00 0.00 34.23 2.73
967 1217 7.518052 GCTGATGTAATGATCAAAGCTGAGTAC 60.518 40.741 0.00 0.00 34.23 2.73
969 1219 5.296283 GCTGATGTAATGATCAAAGCTGAGT 59.704 40.000 0.00 0.00 34.23 3.41
970 1220 5.277876 GGCTGATGTAATGATCAAAGCTGAG 60.278 44.000 0.00 0.00 34.23 3.35
971 1221 4.577693 GGCTGATGTAATGATCAAAGCTGA 59.422 41.667 0.00 0.00 31.90 4.26
972 1222 4.261489 GGGCTGATGTAATGATCAAAGCTG 60.261 45.833 0.00 0.00 31.90 4.24
974 1224 3.633525 TGGGCTGATGTAATGATCAAAGC 59.366 43.478 0.00 0.85 31.90 3.51
978 1228 5.051409 TGAATGGGCTGATGTAATGATCA 57.949 39.130 0.00 0.00 0.00 2.92
979 1229 5.105877 CCATGAATGGGCTGATGTAATGATC 60.106 44.000 1.01 0.00 44.31 2.92
1032 1873 1.486726 GCCACTGCCAGTAGGAGTAAT 59.513 52.381 14.90 0.00 36.89 1.89
1036 1877 1.078848 GTGCCACTGCCAGTAGGAG 60.079 63.158 14.90 0.00 36.89 3.69
1037 1878 0.252057 TAGTGCCACTGCCAGTAGGA 60.252 55.000 7.83 0.00 36.89 2.94
1038 1879 0.176680 CTAGTGCCACTGCCAGTAGG 59.823 60.000 7.83 2.91 36.33 3.18
1406 2259 3.438216 TGATTCAGAATTGGGAGCACA 57.562 42.857 0.00 0.00 0.00 4.57
1609 2528 2.652590 GCCCTCTCGACTAGGTTCTTA 58.347 52.381 8.01 0.00 31.70 2.10
1614 2533 1.153127 CTCGCCCTCTCGACTAGGT 60.153 63.158 8.01 0.00 34.46 3.08
1810 2729 2.524148 GGCAGGCCCAGGTTGTTT 60.524 61.111 0.00 0.00 0.00 2.83
2239 3191 3.073798 ACATGTTGGACACCTTGACCATA 59.926 43.478 0.00 0.00 41.46 2.74
2472 3462 0.809385 CACAATGAAGCTCAGCCTGG 59.191 55.000 0.00 0.00 0.00 4.45
2473 3463 1.738350 CTCACAATGAAGCTCAGCCTG 59.262 52.381 0.00 0.00 0.00 4.85
2485 3475 2.126467 CGCCAAACCAAACTCACAATG 58.874 47.619 0.00 0.00 0.00 2.82
2486 3476 2.028130 TCGCCAAACCAAACTCACAAT 58.972 42.857 0.00 0.00 0.00 2.71
2487 3477 1.403679 CTCGCCAAACCAAACTCACAA 59.596 47.619 0.00 0.00 0.00 3.33
2488 3478 1.021202 CTCGCCAAACCAAACTCACA 58.979 50.000 0.00 0.00 0.00 3.58
2489 3479 0.310854 CCTCGCCAAACCAAACTCAC 59.689 55.000 0.00 0.00 0.00 3.51
2490 3480 1.452145 GCCTCGCCAAACCAAACTCA 61.452 55.000 0.00 0.00 0.00 3.41
2491 3481 1.172812 AGCCTCGCCAAACCAAACTC 61.173 55.000 0.00 0.00 0.00 3.01
2492 3482 1.152756 AGCCTCGCCAAACCAAACT 60.153 52.632 0.00 0.00 0.00 2.66
2493 3483 1.007387 CAGCCTCGCCAAACCAAAC 60.007 57.895 0.00 0.00 0.00 2.93
2494 3484 0.539438 ATCAGCCTCGCCAAACCAAA 60.539 50.000 0.00 0.00 0.00 3.28
2495 3485 1.074775 ATCAGCCTCGCCAAACCAA 59.925 52.632 0.00 0.00 0.00 3.67
2496 3486 1.675310 CATCAGCCTCGCCAAACCA 60.675 57.895 0.00 0.00 0.00 3.67
2497 3487 1.244019 AACATCAGCCTCGCCAAACC 61.244 55.000 0.00 0.00 0.00 3.27
2498 3488 0.598065 AAACATCAGCCTCGCCAAAC 59.402 50.000 0.00 0.00 0.00 2.93
2499 3489 1.327303 AAAACATCAGCCTCGCCAAA 58.673 45.000 0.00 0.00 0.00 3.28
2500 3490 1.327303 AAAAACATCAGCCTCGCCAA 58.673 45.000 0.00 0.00 0.00 4.52
2501 3491 3.034924 AAAAACATCAGCCTCGCCA 57.965 47.368 0.00 0.00 0.00 5.69
2518 3508 5.250235 TGAGCCGTCACAATGTTTAAAAA 57.750 34.783 0.00 0.00 0.00 1.94
2519 3509 4.902443 TGAGCCGTCACAATGTTTAAAA 57.098 36.364 0.00 0.00 0.00 1.52
2520 3510 4.902443 TTGAGCCGTCACAATGTTTAAA 57.098 36.364 0.00 0.00 30.10 1.52
2521 3511 6.561737 TTATTGAGCCGTCACAATGTTTAA 57.438 33.333 0.00 0.00 37.32 1.52
2522 3512 6.561737 TTTATTGAGCCGTCACAATGTTTA 57.438 33.333 0.00 0.00 37.32 2.01
2523 3513 5.446143 TTTATTGAGCCGTCACAATGTTT 57.554 34.783 0.00 0.00 37.32 2.83
2524 3514 5.446143 TTTTATTGAGCCGTCACAATGTT 57.554 34.783 0.00 0.00 37.32 2.71
2525 3515 4.082787 CCTTTTATTGAGCCGTCACAATGT 60.083 41.667 0.00 0.00 37.32 2.71
2526 3516 4.155826 TCCTTTTATTGAGCCGTCACAATG 59.844 41.667 0.00 0.00 37.32 2.82
2527 3517 4.156008 GTCCTTTTATTGAGCCGTCACAAT 59.844 41.667 0.00 0.00 39.53 2.71
2528 3518 3.500680 GTCCTTTTATTGAGCCGTCACAA 59.499 43.478 0.00 0.00 30.10 3.33
2529 3519 3.071479 GTCCTTTTATTGAGCCGTCACA 58.929 45.455 0.00 0.00 30.10 3.58
2530 3520 2.093783 CGTCCTTTTATTGAGCCGTCAC 59.906 50.000 0.00 0.00 30.10 3.67
2531 3521 2.289195 ACGTCCTTTTATTGAGCCGTCA 60.289 45.455 0.00 0.00 0.00 4.35
2532 3522 2.344025 ACGTCCTTTTATTGAGCCGTC 58.656 47.619 0.00 0.00 0.00 4.79
2533 3523 2.344025 GACGTCCTTTTATTGAGCCGT 58.656 47.619 3.51 0.00 0.00 5.68
2534 3524 1.323534 CGACGTCCTTTTATTGAGCCG 59.676 52.381 10.58 0.00 0.00 5.52
2535 3525 2.613691 TCGACGTCCTTTTATTGAGCC 58.386 47.619 10.58 0.00 0.00 4.70
2536 3526 5.290158 TGTTATCGACGTCCTTTTATTGAGC 59.710 40.000 10.58 0.00 0.00 4.26
2537 3527 6.237755 GGTGTTATCGACGTCCTTTTATTGAG 60.238 42.308 10.58 0.00 0.00 3.02
2538 3528 5.577945 GGTGTTATCGACGTCCTTTTATTGA 59.422 40.000 10.58 0.00 0.00 2.57
2539 3529 5.220529 GGGTGTTATCGACGTCCTTTTATTG 60.221 44.000 10.58 0.00 0.00 1.90
2540 3530 4.872124 GGGTGTTATCGACGTCCTTTTATT 59.128 41.667 10.58 0.00 0.00 1.40
2541 3531 4.081531 TGGGTGTTATCGACGTCCTTTTAT 60.082 41.667 10.58 0.00 0.00 1.40
2542 3532 3.257873 TGGGTGTTATCGACGTCCTTTTA 59.742 43.478 10.58 0.00 0.00 1.52
2543 3533 2.037511 TGGGTGTTATCGACGTCCTTTT 59.962 45.455 10.58 0.00 0.00 2.27
2544 3534 1.619827 TGGGTGTTATCGACGTCCTTT 59.380 47.619 10.58 0.00 0.00 3.11
2573 3563 1.271840 TGGCCAGATCCCTTAACGCT 61.272 55.000 0.00 0.00 0.00 5.07
2633 3623 2.888834 AGTTGTTTTGCCCACACATC 57.111 45.000 0.00 0.00 0.00 3.06
2680 3677 3.681835 GCGTGTGAGAGGGACCGT 61.682 66.667 0.00 0.00 0.00 4.83
2776 3773 1.719709 CGAGGACGCGTGATGACTA 59.280 57.895 20.70 0.00 0.00 2.59
2792 3789 2.281484 GGACCTTGGCAACTGCGA 60.281 61.111 0.00 0.00 43.26 5.10
2824 3821 4.948608 TGACAACTGCAGTTAAACGAAA 57.051 36.364 30.67 10.39 36.32 3.46
2826 3823 3.874543 ACATGACAACTGCAGTTAAACGA 59.125 39.130 30.67 13.89 36.32 3.85
2865 3862 3.746045 AACTGTAGTTGTCCGACATGT 57.254 42.857 0.00 0.00 36.80 3.21
3009 4007 3.118371 GCCTAGTGTTAGTAGGTGGCAAT 60.118 47.826 10.53 0.00 42.16 3.56
3117 4116 3.868757 TGTCTCTTTGTAGCGCTACAT 57.131 42.857 41.71 11.81 44.54 2.29
3152 4153 4.254492 GCAACTCTCTCTTTACCCGAAAT 58.746 43.478 0.00 0.00 0.00 2.17
3199 4201 1.599797 GCAGGGTACACGGCAACTT 60.600 57.895 15.80 0.00 0.00 2.66
3228 4232 3.478857 TTACCCGAACATGTCAGTTGT 57.521 42.857 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.