Multiple sequence alignment - TraesCS7B01G424300

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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 TraesCS7B01G424300 chr7B 100.000 3194 0 0 1 3194 693259635 693256442 0.000000e+00 5899.0
1 TraesCS7B01G424300 chr7B 95.971 1241 37 5 1955 3194 696906807 696905579 0.000000e+00 2002.0
2 TraesCS7B01G424300 chr7B 91.427 1458 95 11 1269 2711 697265105 697263663 0.000000e+00 1973.0
3 TraesCS7B01G424300 chr7B 95.747 964 41 0 987 1950 696909510 696908547 0.000000e+00 1554.0
4 TraesCS7B01G424300 chr7B 90.379 738 50 11 1980 2711 697227756 697227034 0.000000e+00 950.0
5 TraesCS7B01G424300 chr7B 90.257 739 51 11 1979 2711 697230266 697229543 0.000000e+00 946.0
6 TraesCS7B01G424300 chr7B 90.923 672 54 4 1565 2231 700731675 700732344 0.000000e+00 896.0
7 TraesCS7B01G424300 chr7B 91.667 540 45 0 1565 2104 700679183 700679722 0.000000e+00 749.0
8 TraesCS7B01G424300 chr7B 91.716 338 27 1 942 1279 697277408 697277072 4.820000e-128 468.0
9 TraesCS7B01G424300 chr7B 79.717 636 90 24 2386 3004 700731095 700730482 1.060000e-114 424.0
10 TraesCS7B01G424300 chr7B 80.874 549 72 21 2477 3004 700678364 700677828 4.960000e-108 401.0
11 TraesCS7B01G424300 chr7B 82.658 444 59 10 2272 2705 696905645 696905210 8.360000e-101 377.0
12 TraesCS7B01G424300 chr7B 93.220 236 12 2 2963 3194 697263432 697263197 8.480000e-91 344.0
13 TraesCS7B01G424300 chr7B 80.711 394 70 4 1067 1457 695366318 695366708 5.180000e-78 302.0
14 TraesCS7B01G424300 chr7B 93.401 197 13 0 2718 2914 693954522 693954326 3.120000e-75 292.0
15 TraesCS7B01G424300 chr7B 90.547 201 13 4 2712 2909 697263628 697263431 8.790000e-66 261.0
16 TraesCS7B01G424300 chr7B 93.396 106 6 1 2606 2711 693954667 693954563 4.270000e-34 156.0
17 TraesCS7B01G424300 chrUn 87.133 1873 179 28 869 2711 83447909 83446069 0.000000e+00 2067.0
18 TraesCS7B01G424300 chrUn 90.881 647 56 3 44 688 225680649 225680004 0.000000e+00 865.0
19 TraesCS7B01G424300 chrUn 90.867 646 57 2 44 688 269607924 269607280 0.000000e+00 865.0
20 TraesCS7B01G424300 chrUn 90.712 646 58 2 44 688 287109366 287108722 0.000000e+00 859.0
21 TraesCS7B01G424300 chrUn 90.712 646 58 2 44 688 347579457 347578813 0.000000e+00 859.0
22 TraesCS7B01G424300 chrUn 90.557 646 58 3 44 688 195663309 195663952 0.000000e+00 852.0
23 TraesCS7B01G424300 chrUn 93.878 49 3 0 1 49 306480289 306480241 1.230000e-09 75.0
24 TraesCS7B01G424300 chrUn 91.837 49 4 0 1 49 306479028 306478980 5.720000e-08 69.4
25 TraesCS7B01G424300 chrUn 93.478 46 3 0 1 46 390436931 390436976 5.720000e-08 69.4
26 TraesCS7B01G424300 chrUn 91.837 49 4 0 1 49 423964344 423964296 5.720000e-08 69.4
27 TraesCS7B01G424300 chr7A 91.942 1452 102 7 962 2409 699865865 699864425 0.000000e+00 2019.0
28 TraesCS7B01G424300 chr7A 87.327 1594 148 22 869 2434 700421612 700423179 0.000000e+00 1775.0
29 TraesCS7B01G424300 chr7A 86.141 368 28 11 2762 3127 700423243 700423589 3.010000e-100 375.0
30 TraesCS7B01G424300 chr7A 93.023 43 3 0 687 729 699898382 699898340 2.660000e-06 63.9
31 TraesCS7B01G424300 chr1B 88.650 1533 147 11 890 2406 455356171 455357692 0.000000e+00 1842.0
32 TraesCS7B01G424300 chr1B 90.615 650 56 4 44 689 8844964 8844316 0.000000e+00 857.0
33 TraesCS7B01G424300 chr1B 89.398 415 39 3 2718 3128 455357754 455358167 4.720000e-143 518.0
34 TraesCS7B01G424300 chr7D 87.829 1594 155 19 865 2434 608422395 608423973 0.000000e+00 1832.0
35 TraesCS7B01G424300 chr7D 88.953 1213 101 13 1509 2711 607622345 607621156 0.000000e+00 1467.0
36 TraesCS7B01G424300 chr7D 88.384 1145 100 13 1577 2711 610203362 610204483 0.000000e+00 1347.0
37 TraesCS7B01G424300 chr7D 88.836 421 41 4 2712 3128 608424002 608424420 2.200000e-141 512.0
38 TraesCS7B01G424300 chr7D 93.162 234 13 2 2963 3194 607620928 607620696 1.100000e-89 340.0
39 TraesCS7B01G424300 chr7D 94.118 221 10 2 2963 3181 610204711 610204930 1.840000e-87 333.0
40 TraesCS7B01G424300 chr7D 92.424 198 12 2 2712 2909 607621121 607620927 2.430000e-71 279.0
41 TraesCS7B01G424300 chr7D 92.424 198 12 2 2712 2909 610204518 610204712 2.430000e-71 279.0
42 TraesCS7B01G424300 chr2A 91.008 645 55 3 44 687 1104809 1104167 0.000000e+00 867.0
43 TraesCS7B01G424300 chr3A 90.712 646 58 2 44 688 48653486 48654130 0.000000e+00 859.0
44 TraesCS7B01G424300 chr1A 90.367 654 57 5 44 695 507231797 507232446 0.000000e+00 854.0
45 TraesCS7B01G424300 chr4D 93.878 49 3 0 1 49 60166379 60166331 1.230000e-09 75.0
46 TraesCS7B01G424300 chr2D 93.878 49 3 0 1 49 637213574 637213526 1.230000e-09 75.0
47 TraesCS7B01G424300 chr2D 92.000 50 4 0 1 50 637243648 637243599 1.590000e-08 71.3
48 TraesCS7B01G424300 chr2D 91.837 49 4 0 1 49 637190166 637190118 5.720000e-08 69.4
49 TraesCS7B01G424300 chr1D 93.478 46 3 0 1 46 265132710 265132755 5.720000e-08 69.4


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 TraesCS7B01G424300 chr7B 693256442 693259635 3193 True 5899.000000 5899 100.000000 1 3194 1 chr7B.!!$R1 3193
1 TraesCS7B01G424300 chr7B 696905210 696909510 4300 True 1311.000000 2002 91.458667 987 3194 3 chr7B.!!$R6 2207
2 TraesCS7B01G424300 chr7B 697227034 697230266 3232 True 948.000000 950 90.318000 1979 2711 2 chr7B.!!$R7 732
3 TraesCS7B01G424300 chr7B 700731675 700732344 669 False 896.000000 896 90.923000 1565 2231 1 chr7B.!!$F3 666
4 TraesCS7B01G424300 chr7B 697263197 697265105 1908 True 859.333333 1973 91.731333 1269 3194 3 chr7B.!!$R8 1925
5 TraesCS7B01G424300 chr7B 700679183 700679722 539 False 749.000000 749 91.667000 1565 2104 1 chr7B.!!$F2 539
6 TraesCS7B01G424300 chr7B 700730482 700731095 613 True 424.000000 424 79.717000 2386 3004 1 chr7B.!!$R4 618
7 TraesCS7B01G424300 chr7B 700677828 700678364 536 True 401.000000 401 80.874000 2477 3004 1 chr7B.!!$R3 527
8 TraesCS7B01G424300 chrUn 83446069 83447909 1840 True 2067.000000 2067 87.133000 869 2711 1 chrUn.!!$R1 1842
9 TraesCS7B01G424300 chrUn 225680004 225680649 645 True 865.000000 865 90.881000 44 688 1 chrUn.!!$R2 644
10 TraesCS7B01G424300 chrUn 269607280 269607924 644 True 865.000000 865 90.867000 44 688 1 chrUn.!!$R3 644
11 TraesCS7B01G424300 chrUn 287108722 287109366 644 True 859.000000 859 90.712000 44 688 1 chrUn.!!$R4 644
12 TraesCS7B01G424300 chrUn 347578813 347579457 644 True 859.000000 859 90.712000 44 688 1 chrUn.!!$R5 644
13 TraesCS7B01G424300 chrUn 195663309 195663952 643 False 852.000000 852 90.557000 44 688 1 chrUn.!!$F1 644
14 TraesCS7B01G424300 chr7A 699864425 699865865 1440 True 2019.000000 2019 91.942000 962 2409 1 chr7A.!!$R1 1447
15 TraesCS7B01G424300 chr7A 700421612 700423589 1977 False 1075.000000 1775 86.734000 869 3127 2 chr7A.!!$F1 2258
16 TraesCS7B01G424300 chr1B 455356171 455358167 1996 False 1180.000000 1842 89.024000 890 3128 2 chr1B.!!$F1 2238
17 TraesCS7B01G424300 chr1B 8844316 8844964 648 True 857.000000 857 90.615000 44 689 1 chr1B.!!$R1 645
18 TraesCS7B01G424300 chr7D 608422395 608424420 2025 False 1172.000000 1832 88.332500 865 3128 2 chr7D.!!$F1 2263
19 TraesCS7B01G424300 chr7D 607620696 607622345 1649 True 695.333333 1467 91.513000 1509 3194 3 chr7D.!!$R1 1685
20 TraesCS7B01G424300 chr7D 610203362 610204930 1568 False 653.000000 1347 91.642000 1577 3181 3 chr7D.!!$F2 1604
21 TraesCS7B01G424300 chr2A 1104167 1104809 642 True 867.000000 867 91.008000 44 687 1 chr2A.!!$R1 643
22 TraesCS7B01G424300 chr3A 48653486 48654130 644 False 859.000000 859 90.712000 44 688 1 chr3A.!!$F1 644
23 TraesCS7B01G424300 chr1A 507231797 507232446 649 False 854.000000 854 90.367000 44 695 1 chr1A.!!$F1 651

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
822 828 0.035915 GGAGAAGCCAAGGAGTCCAC 60.036 60.0 12.86 0.00 36.34 4.02 F
853 859 0.447801 GCACACAAATACTCGGCCAG 59.552 55.0 2.24 1.58 0.00 4.85 F
1789 1832 0.262876 TGCTGAGCTCCCATCCTCTA 59.737 55.0 12.15 0.00 0.00 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1648 1691 0.677288 TAAGTATGGTCCATCGGCGG 59.323 55.000 7.92 0.0 0.00 6.13 R
1953 3737 0.710588 TCAGGCCCTCAGAACCTAGA 59.289 55.000 0.00 0.0 30.84 2.43 R
2676 7281 7.224557 ACAACATCAGCACAATAAAAGGAAAAC 59.775 33.333 0.00 0.0 0.00 2.43 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
19 20 1.841450 CTCTACGCGGATTGGTCTTC 58.159 55.000 12.47 0.00 0.00 2.87
20 21 0.099968 TCTACGCGGATTGGTCTTCG 59.900 55.000 12.47 0.00 0.00 3.79
21 22 1.480219 CTACGCGGATTGGTCTTCGC 61.480 60.000 12.47 0.00 44.04 4.70
23 24 2.813908 GCGGATTGGTCTTCGCGT 60.814 61.111 5.77 0.00 38.82 6.01
24 25 3.081133 CGGATTGGTCTTCGCGTG 58.919 61.111 5.77 0.00 0.00 5.34
25 26 1.736645 CGGATTGGTCTTCGCGTGT 60.737 57.895 5.77 0.00 0.00 4.49
26 27 1.683790 CGGATTGGTCTTCGCGTGTC 61.684 60.000 5.77 0.00 0.00 3.67
27 28 0.389948 GGATTGGTCTTCGCGTGTCT 60.390 55.000 5.77 0.00 0.00 3.41
28 29 1.135199 GGATTGGTCTTCGCGTGTCTA 60.135 52.381 5.77 0.00 0.00 2.59
29 30 1.918609 GATTGGTCTTCGCGTGTCTAC 59.081 52.381 5.77 0.00 0.00 2.59
41 42 2.624316 GTGTCTACGATTGTGACCGA 57.376 50.000 11.05 0.00 0.00 4.69
42 43 2.248487 GTGTCTACGATTGTGACCGAC 58.752 52.381 11.05 6.51 0.00 4.79
46 47 1.588824 TACGATTGTGACCGACGGCT 61.589 55.000 15.39 0.48 0.00 5.52
54 55 1.134560 GTGACCGACGGCTTCTTAGAT 59.865 52.381 15.39 0.00 0.00 1.98
65 66 6.120905 ACGGCTTCTTAGATGTCTAGAAGTA 58.879 40.000 19.07 0.00 36.80 2.24
91 92 2.103736 GGTACGCTAGGGTGTCGC 59.896 66.667 21.79 9.31 37.38 5.19
94 95 0.388907 GTACGCTAGGGTGTCGCAAA 60.389 55.000 21.79 0.00 37.38 3.68
106 107 4.109050 GGTGTCGCAAAAGTCATGAAAAA 58.891 39.130 0.00 0.00 0.00 1.94
110 111 7.201350 GGTGTCGCAAAAGTCATGAAAAATATC 60.201 37.037 0.00 0.00 0.00 1.63
119 121 7.230849 AGTCATGAAAAATATCAAAGTGGCA 57.769 32.000 0.00 0.00 32.06 4.92
163 165 3.611766 AGACCCATGAAAACTAGTCGG 57.388 47.619 0.00 0.00 0.00 4.79
348 350 0.315886 TGTATGCTTCGGACACACGT 59.684 50.000 0.00 0.00 34.94 4.49
385 387 2.811317 GAGTGCCTGCTTCGGACG 60.811 66.667 0.00 0.00 0.00 4.79
401 403 0.313043 GACGCACGGCTTATAGGCTA 59.687 55.000 6.81 0.00 38.85 3.93
405 407 1.614413 GCACGGCTTATAGGCTACTCT 59.386 52.381 6.81 0.00 38.85 3.24
413 415 2.438800 ATAGGCTACTCTGTGACGGT 57.561 50.000 0.00 0.00 0.00 4.83
417 419 1.964448 CTACTCTGTGACGGTGCCA 59.036 57.895 0.00 0.00 0.00 4.92
426 428 2.282180 ACGGTGCCATCAACCACC 60.282 61.111 0.00 0.00 46.25 4.61
462 464 1.796796 GCAGATGTCTTTGCCGACC 59.203 57.895 0.00 0.00 34.28 4.79
490 492 2.158579 TGTAAGCCGGGTTCCTTTTTCT 60.159 45.455 24.52 0.00 0.00 2.52
491 493 2.963599 AAGCCGGGTTCCTTTTTCTA 57.036 45.000 14.44 0.00 0.00 2.10
497 499 4.515567 GCCGGGTTCCTTTTTCTATAGATG 59.484 45.833 2.18 0.00 0.00 2.90
506 508 5.220662 CCTTTTTCTATAGATGCCGTGTGTG 60.221 44.000 2.58 0.00 0.00 3.82
508 510 4.465632 TTCTATAGATGCCGTGTGTGTT 57.534 40.909 2.58 0.00 0.00 3.32
518 520 3.199677 GCCGTGTGTGTTATATAAGCCA 58.800 45.455 0.00 0.00 0.00 4.75
548 550 2.218953 TGCGAAACTCGGCTTATAGG 57.781 50.000 0.00 0.00 40.84 2.57
625 630 1.972660 GAGGAGCATAAGCCGGGTGT 61.973 60.000 7.07 0.00 43.56 4.16
689 695 4.226620 ACCGGGATTTACCTGTAGTGATTT 59.773 41.667 6.32 0.00 43.20 2.17
690 696 5.426185 ACCGGGATTTACCTGTAGTGATTTA 59.574 40.000 6.32 0.00 43.20 1.40
691 697 6.070078 ACCGGGATTTACCTGTAGTGATTTAA 60.070 38.462 6.32 0.00 43.20 1.52
692 698 6.482308 CCGGGATTTACCTGTAGTGATTTAAG 59.518 42.308 0.00 0.00 43.20 1.85
693 699 6.018180 CGGGATTTACCTGTAGTGATTTAAGC 60.018 42.308 0.00 0.00 40.03 3.09
694 700 6.262496 GGGATTTACCTGTAGTGATTTAAGCC 59.738 42.308 0.00 0.00 38.98 4.35
695 701 7.054751 GGATTTACCTGTAGTGATTTAAGCCT 58.945 38.462 0.00 0.00 35.41 4.58
696 702 8.208903 GGATTTACCTGTAGTGATTTAAGCCTA 58.791 37.037 0.00 0.00 35.41 3.93
697 703 9.609346 GATTTACCTGTAGTGATTTAAGCCTAA 57.391 33.333 0.00 0.00 0.00 2.69
698 704 8.782339 TTTACCTGTAGTGATTTAAGCCTAAC 57.218 34.615 0.00 0.00 0.00 2.34
699 705 5.742063 ACCTGTAGTGATTTAAGCCTAACC 58.258 41.667 0.00 0.00 0.00 2.85
700 706 5.249852 ACCTGTAGTGATTTAAGCCTAACCA 59.750 40.000 0.00 0.00 0.00 3.67
701 707 6.177610 CCTGTAGTGATTTAAGCCTAACCAA 58.822 40.000 0.00 0.00 0.00 3.67
702 708 6.657541 CCTGTAGTGATTTAAGCCTAACCAAA 59.342 38.462 0.00 0.00 0.00 3.28
703 709 7.361799 CCTGTAGTGATTTAAGCCTAACCAAAC 60.362 40.741 0.00 0.00 0.00 2.93
704 710 6.999272 TGTAGTGATTTAAGCCTAACCAAACA 59.001 34.615 0.00 0.00 0.00 2.83
705 711 6.327279 AGTGATTTAAGCCTAACCAAACAC 57.673 37.500 0.00 0.00 0.00 3.32
706 712 5.243060 AGTGATTTAAGCCTAACCAAACACC 59.757 40.000 0.00 0.00 0.00 4.16
707 713 4.525100 TGATTTAAGCCTAACCAAACACCC 59.475 41.667 0.00 0.00 0.00 4.61
708 714 3.887916 TTAAGCCTAACCAAACACCCT 57.112 42.857 0.00 0.00 0.00 4.34
709 715 2.287977 AAGCCTAACCAAACACCCTC 57.712 50.000 0.00 0.00 0.00 4.30
710 716 0.404426 AGCCTAACCAAACACCCTCC 59.596 55.000 0.00 0.00 0.00 4.30
711 717 0.404426 GCCTAACCAAACACCCTCCT 59.596 55.000 0.00 0.00 0.00 3.69
712 718 1.631898 GCCTAACCAAACACCCTCCTA 59.368 52.381 0.00 0.00 0.00 2.94
713 719 2.040679 GCCTAACCAAACACCCTCCTAA 59.959 50.000 0.00 0.00 0.00 2.69
714 720 3.308904 GCCTAACCAAACACCCTCCTAAT 60.309 47.826 0.00 0.00 0.00 1.73
715 721 4.813133 GCCTAACCAAACACCCTCCTAATT 60.813 45.833 0.00 0.00 0.00 1.40
716 722 5.574120 GCCTAACCAAACACCCTCCTAATTA 60.574 44.000 0.00 0.00 0.00 1.40
717 723 6.486941 CCTAACCAAACACCCTCCTAATTAA 58.513 40.000 0.00 0.00 0.00 1.40
718 724 6.602009 CCTAACCAAACACCCTCCTAATTAAG 59.398 42.308 0.00 0.00 0.00 1.85
719 725 4.341487 ACCAAACACCCTCCTAATTAAGC 58.659 43.478 0.00 0.00 0.00 3.09
720 726 4.202631 ACCAAACACCCTCCTAATTAAGCA 60.203 41.667 0.00 0.00 0.00 3.91
721 727 4.770010 CCAAACACCCTCCTAATTAAGCAA 59.230 41.667 0.00 0.00 0.00 3.91
722 728 5.245075 CCAAACACCCTCCTAATTAAGCAAA 59.755 40.000 0.00 0.00 0.00 3.68
723 729 6.389906 CAAACACCCTCCTAATTAAGCAAAG 58.610 40.000 0.00 0.00 0.00 2.77
724 730 4.600062 ACACCCTCCTAATTAAGCAAAGG 58.400 43.478 0.00 0.00 0.00 3.11
725 731 4.291249 ACACCCTCCTAATTAAGCAAAGGA 59.709 41.667 0.00 0.00 36.69 3.36
731 737 5.193679 TCCTAATTAAGCAAAGGAGAAGCC 58.806 41.667 0.00 0.00 33.18 4.35
732 738 4.949856 CCTAATTAAGCAAAGGAGAAGCCA 59.050 41.667 0.00 0.00 40.02 4.75
733 739 5.418840 CCTAATTAAGCAAAGGAGAAGCCAA 59.581 40.000 0.00 0.00 40.02 4.52
734 740 5.397142 AATTAAGCAAAGGAGAAGCCAAG 57.603 39.130 0.00 0.00 40.02 3.61
735 741 2.664402 AAGCAAAGGAGAAGCCAAGA 57.336 45.000 0.00 0.00 40.02 3.02
736 742 2.664402 AGCAAAGGAGAAGCCAAGAA 57.336 45.000 0.00 0.00 40.02 2.52
737 743 2.234143 AGCAAAGGAGAAGCCAAGAAC 58.766 47.619 0.00 0.00 40.02 3.01
738 744 1.956477 GCAAAGGAGAAGCCAAGAACA 59.044 47.619 0.00 0.00 40.02 3.18
739 745 2.362077 GCAAAGGAGAAGCCAAGAACAA 59.638 45.455 0.00 0.00 40.02 2.83
740 746 3.551659 GCAAAGGAGAAGCCAAGAACAAG 60.552 47.826 0.00 0.00 40.02 3.16
741 747 1.902938 AGGAGAAGCCAAGAACAAGC 58.097 50.000 0.00 0.00 40.02 4.01
742 748 0.884514 GGAGAAGCCAAGAACAAGCC 59.115 55.000 0.00 0.00 36.34 4.35
743 749 0.519077 GAGAAGCCAAGAACAAGCCG 59.481 55.000 0.00 0.00 0.00 5.52
744 750 0.890996 AGAAGCCAAGAACAAGCCGG 60.891 55.000 0.00 0.00 0.00 6.13
745 751 2.477972 GAAGCCAAGAACAAGCCGGC 62.478 60.000 21.89 21.89 43.31 6.13
746 752 3.294493 GCCAAGAACAAGCCGGCA 61.294 61.111 31.54 0.00 42.50 5.69
747 753 2.855514 GCCAAGAACAAGCCGGCAA 61.856 57.895 31.54 0.00 42.50 4.52
748 754 1.966762 CCAAGAACAAGCCGGCAAT 59.033 52.632 31.54 14.96 0.00 3.56
749 755 0.318120 CCAAGAACAAGCCGGCAATT 59.682 50.000 31.54 19.49 0.00 2.32
750 756 1.543802 CCAAGAACAAGCCGGCAATTA 59.456 47.619 31.54 0.00 0.00 1.40
751 757 2.595386 CAAGAACAAGCCGGCAATTAC 58.405 47.619 31.54 16.56 0.00 1.89
752 758 2.200373 AGAACAAGCCGGCAATTACT 57.800 45.000 31.54 18.62 0.00 2.24
753 759 1.812571 AGAACAAGCCGGCAATTACTG 59.187 47.619 31.54 16.98 0.00 2.74
766 772 4.352600 CAATTACTGCTCTTGGCTCTTG 57.647 45.455 0.00 0.00 42.39 3.02
767 773 2.479566 TTACTGCTCTTGGCTCTTGG 57.520 50.000 0.00 0.00 42.39 3.61
768 774 0.615331 TACTGCTCTTGGCTCTTGGG 59.385 55.000 0.00 0.00 42.39 4.12
769 775 2.034687 TGCTCTTGGCTCTTGGGC 59.965 61.111 0.00 0.00 42.39 5.36
775 781 3.899371 TGGCTCTTGGGCAGTGTA 58.101 55.556 0.00 0.00 45.79 2.90
776 782 1.679311 TGGCTCTTGGGCAGTGTAG 59.321 57.895 0.00 0.00 45.79 2.74
777 783 1.746991 GGCTCTTGGGCAGTGTAGC 60.747 63.158 0.00 0.00 40.53 3.58
778 784 1.003355 GCTCTTGGGCAGTGTAGCA 60.003 57.895 0.00 0.00 35.83 3.49
779 785 1.023513 GCTCTTGGGCAGTGTAGCAG 61.024 60.000 0.00 0.00 35.83 4.24
780 786 1.003355 TCTTGGGCAGTGTAGCAGC 60.003 57.895 0.00 0.00 35.83 5.25
784 790 3.121030 GGCAGTGTAGCAGCCGTG 61.121 66.667 0.00 0.00 39.98 4.94
785 791 2.048222 GCAGTGTAGCAGCCGTGA 60.048 61.111 0.00 0.00 0.00 4.35
786 792 1.667830 GCAGTGTAGCAGCCGTGAA 60.668 57.895 0.00 0.00 0.00 3.18
787 793 1.901650 GCAGTGTAGCAGCCGTGAAC 61.902 60.000 0.00 0.00 0.00 3.18
788 794 0.319900 CAGTGTAGCAGCCGTGAACT 60.320 55.000 0.00 0.00 0.00 3.01
789 795 1.067846 CAGTGTAGCAGCCGTGAACTA 60.068 52.381 0.00 0.00 0.00 2.24
790 796 1.202582 AGTGTAGCAGCCGTGAACTAG 59.797 52.381 0.00 0.00 0.00 2.57
791 797 1.067776 GTGTAGCAGCCGTGAACTAGT 60.068 52.381 0.00 0.00 0.00 2.57
792 798 1.616865 TGTAGCAGCCGTGAACTAGTT 59.383 47.619 8.13 8.13 0.00 2.24
793 799 2.821378 TGTAGCAGCCGTGAACTAGTTA 59.179 45.455 8.42 0.00 0.00 2.24
794 800 2.365408 AGCAGCCGTGAACTAGTTAC 57.635 50.000 8.42 6.62 0.00 2.50
795 801 1.616865 AGCAGCCGTGAACTAGTTACA 59.383 47.619 8.42 5.92 0.00 2.41
796 802 2.233922 AGCAGCCGTGAACTAGTTACAT 59.766 45.455 8.42 0.00 0.00 2.29
797 803 3.000727 GCAGCCGTGAACTAGTTACATT 58.999 45.455 8.42 0.00 0.00 2.71
798 804 3.181520 GCAGCCGTGAACTAGTTACATTG 60.182 47.826 8.42 4.32 0.00 2.82
799 805 3.370978 CAGCCGTGAACTAGTTACATTGG 59.629 47.826 8.42 13.90 0.00 3.16
800 806 2.095372 GCCGTGAACTAGTTACATTGGC 59.905 50.000 22.66 22.66 33.47 4.52
801 807 3.596214 CCGTGAACTAGTTACATTGGCT 58.404 45.455 8.42 0.00 0.00 4.75
802 808 4.751060 CCGTGAACTAGTTACATTGGCTA 58.249 43.478 8.42 0.00 0.00 3.93
803 809 4.804139 CCGTGAACTAGTTACATTGGCTAG 59.196 45.833 8.42 9.26 38.43 3.42
804 810 4.804139 CGTGAACTAGTTACATTGGCTAGG 59.196 45.833 8.42 0.00 37.20 3.02
805 811 5.393787 CGTGAACTAGTTACATTGGCTAGGA 60.394 44.000 8.42 0.51 37.20 2.94
806 812 6.043411 GTGAACTAGTTACATTGGCTAGGAG 58.957 44.000 8.42 0.00 37.20 3.69
807 813 5.955959 TGAACTAGTTACATTGGCTAGGAGA 59.044 40.000 8.42 0.04 37.20 3.71
808 814 6.439375 TGAACTAGTTACATTGGCTAGGAGAA 59.561 38.462 8.42 0.00 37.20 2.87
809 815 6.472686 ACTAGTTACATTGGCTAGGAGAAG 57.527 41.667 13.12 0.00 37.20 2.85
810 816 4.143986 AGTTACATTGGCTAGGAGAAGC 57.856 45.455 0.00 0.00 41.99 3.86
818 824 1.199615 GCTAGGAGAAGCCAAGGAGT 58.800 55.000 0.00 0.00 40.02 3.85
819 825 1.138069 GCTAGGAGAAGCCAAGGAGTC 59.862 57.143 0.00 0.00 40.02 3.36
820 826 1.760029 CTAGGAGAAGCCAAGGAGTCC 59.240 57.143 0.00 0.00 40.02 3.85
821 827 0.178891 AGGAGAAGCCAAGGAGTCCA 60.179 55.000 12.86 0.00 40.02 4.02
822 828 0.035915 GGAGAAGCCAAGGAGTCCAC 60.036 60.000 12.86 0.00 36.34 4.02
823 829 0.980423 GAGAAGCCAAGGAGTCCACT 59.020 55.000 12.86 0.00 0.00 4.00
824 830 2.180276 GAGAAGCCAAGGAGTCCACTA 58.820 52.381 12.86 0.00 0.00 2.74
825 831 2.769095 GAGAAGCCAAGGAGTCCACTAT 59.231 50.000 12.86 0.00 0.00 2.12
826 832 2.503356 AGAAGCCAAGGAGTCCACTATG 59.497 50.000 12.86 4.70 0.00 2.23
827 833 0.543749 AGCCAAGGAGTCCACTATGC 59.456 55.000 12.86 6.51 0.00 3.14
828 834 0.464554 GCCAAGGAGTCCACTATGCC 60.465 60.000 12.86 0.00 0.00 4.40
829 835 0.911769 CCAAGGAGTCCACTATGCCA 59.088 55.000 12.86 0.00 0.00 4.92
830 836 1.492176 CCAAGGAGTCCACTATGCCAT 59.508 52.381 12.86 0.00 0.00 4.40
831 837 2.092212 CCAAGGAGTCCACTATGCCATT 60.092 50.000 12.86 0.00 0.00 3.16
832 838 2.947652 CAAGGAGTCCACTATGCCATTG 59.052 50.000 12.86 0.00 0.00 2.82
833 839 1.492176 AGGAGTCCACTATGCCATTGG 59.508 52.381 12.86 0.00 0.00 3.16
834 840 1.477558 GGAGTCCACTATGCCATTGGG 60.478 57.143 3.60 0.00 37.18 4.12
847 853 3.508744 CCATTGGGCACACAAATACTC 57.491 47.619 0.00 0.00 33.48 2.59
848 854 2.159393 CCATTGGGCACACAAATACTCG 60.159 50.000 0.00 0.00 33.48 4.18
849 855 1.529226 TTGGGCACACAAATACTCGG 58.471 50.000 0.00 0.00 0.00 4.63
850 856 0.958382 TGGGCACACAAATACTCGGC 60.958 55.000 0.00 0.00 0.00 5.54
851 857 1.654023 GGGCACACAAATACTCGGCC 61.654 60.000 0.00 0.00 39.18 6.13
852 858 0.958382 GGCACACAAATACTCGGCCA 60.958 55.000 2.24 0.00 39.66 5.36
853 859 0.447801 GCACACAAATACTCGGCCAG 59.552 55.000 2.24 1.58 0.00 4.85
854 860 1.086696 CACACAAATACTCGGCCAGG 58.913 55.000 2.24 0.00 0.00 4.45
855 861 0.981183 ACACAAATACTCGGCCAGGA 59.019 50.000 2.24 0.00 0.00 3.86
856 862 1.338769 ACACAAATACTCGGCCAGGAC 60.339 52.381 2.24 0.00 0.00 3.85
857 863 1.066143 CACAAATACTCGGCCAGGACT 60.066 52.381 2.24 0.00 0.00 3.85
858 864 1.066143 ACAAATACTCGGCCAGGACTG 60.066 52.381 2.24 0.57 0.00 3.51
877 883 3.170672 ACTGGACTGCAGCACCCA 61.171 61.111 22.27 20.31 0.00 4.51
879 885 3.480679 CTGGACTGCAGCACCCACA 62.481 63.158 22.27 9.40 0.00 4.17
881 887 2.203195 GACTGCAGCACCCACACA 60.203 61.111 15.27 0.00 0.00 3.72
882 888 2.203252 ACTGCAGCACCCACACAG 60.203 61.111 15.27 0.00 0.00 3.66
883 889 2.981909 CTGCAGCACCCACACAGG 60.982 66.667 0.00 0.00 37.03 4.00
888 897 2.191908 GCACCCACACAGGACACA 59.808 61.111 0.00 0.00 41.22 3.72
923 932 1.609783 CTTCCACCCCACCATCTCC 59.390 63.158 0.00 0.00 0.00 3.71
934 943 2.092968 CCACCATCTCCTCCGATTTTCA 60.093 50.000 0.00 0.00 0.00 2.69
954 966 4.104183 GGATTCCGCCCCCGTCAA 62.104 66.667 0.00 0.00 0.00 3.18
966 978 1.554042 CCCGTCAACGACAACTTCCG 61.554 60.000 3.71 0.00 43.02 4.30
967 979 0.595567 CCGTCAACGACAACTTCCGA 60.596 55.000 3.71 0.00 43.02 4.55
982 994 2.202797 CGATCCAGTCCACGCCAG 60.203 66.667 0.00 0.00 0.00 4.85
1380 1395 2.108566 CCGATCTGCAGGGAGCTG 59.891 66.667 15.13 0.00 45.94 4.24
1707 1750 1.289160 ATGGCTGCTTCTACTGGGAA 58.711 50.000 0.00 0.00 0.00 3.97
1789 1832 0.262876 TGCTGAGCTCCCATCCTCTA 59.737 55.000 12.15 0.00 0.00 2.43
1917 1966 4.586841 ACAGTTAGGCATAACAAAGGCAAA 59.413 37.500 22.06 0.00 43.21 3.68
1953 3737 3.370315 GGCAGATGGTGAAGACATTCTCT 60.370 47.826 0.00 0.00 36.33 3.10
1997 3781 1.160137 ATCAAAGCCGCAACAGAGAC 58.840 50.000 0.00 0.00 0.00 3.36
2256 6564 8.649973 ATGTTATATCTTTCACTTCGAAGGTC 57.350 34.615 27.86 4.73 34.32 3.85
2277 6585 3.195610 TCTCACACGGATTGTCTAATGCT 59.804 43.478 0.00 0.00 35.67 3.79
2592 7188 8.666821 AGTTTCACCCCTAGAAAGTTAATTACT 58.333 33.333 0.00 0.00 35.66 2.24
2676 7281 4.154737 TCTTTTGGTCATCTTCGCATTCAG 59.845 41.667 0.00 0.00 0.00 3.02
2940 7585 5.409826 CCTAAGATTTTCAGTGCTCGTTTCT 59.590 40.000 0.00 0.00 0.00 2.52
3033 7679 3.165890 CACAACAGCACTGCATATTTCG 58.834 45.455 3.30 0.00 0.00 3.46
3093 7741 7.953005 TGCTATTCTGCTTCTATATCTAGCT 57.047 36.000 0.00 0.00 35.93 3.32
3189 7839 6.699642 TGTTAACACGGTTTAGTAGTGGTTAC 59.300 38.462 3.59 0.00 39.95 2.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.841450 GAAGACCAATCCGCGTAGAG 58.159 55.000 4.92 0.00 0.00 2.43
4 5 2.813908 GCGAAGACCAATCCGCGT 60.814 61.111 4.92 0.00 38.27 6.01
6 7 2.813908 ACGCGAAGACCAATCCGC 60.814 61.111 15.93 0.00 43.68 5.54
7 8 1.683790 GACACGCGAAGACCAATCCG 61.684 60.000 15.93 0.00 0.00 4.18
8 9 0.389948 AGACACGCGAAGACCAATCC 60.390 55.000 15.93 0.00 0.00 3.01
9 10 1.918609 GTAGACACGCGAAGACCAATC 59.081 52.381 15.93 0.00 0.00 2.67
10 11 1.731424 CGTAGACACGCGAAGACCAAT 60.731 52.381 15.93 0.00 42.05 3.16
11 12 0.386352 CGTAGACACGCGAAGACCAA 60.386 55.000 15.93 0.00 42.05 3.67
12 13 1.208358 CGTAGACACGCGAAGACCA 59.792 57.895 15.93 0.00 42.05 4.02
13 14 4.053067 CGTAGACACGCGAAGACC 57.947 61.111 15.93 2.91 42.05 3.85
22 23 2.248487 GTCGGTCACAATCGTAGACAC 58.752 52.381 0.00 0.00 42.51 3.67
23 24 1.135888 CGTCGGTCACAATCGTAGACA 60.136 52.381 0.00 0.00 42.51 3.41
24 25 1.531912 CGTCGGTCACAATCGTAGAC 58.468 55.000 0.00 0.00 42.51 2.59
25 26 0.448990 CCGTCGGTCACAATCGTAGA 59.551 55.000 2.08 0.00 45.75 2.59
26 27 1.138047 GCCGTCGGTCACAATCGTAG 61.138 60.000 13.94 0.00 0.00 3.51
27 28 1.153978 GCCGTCGGTCACAATCGTA 60.154 57.895 13.94 0.00 0.00 3.43
28 29 2.430382 AAGCCGTCGGTCACAATCGT 62.430 55.000 13.94 0.00 0.00 3.73
29 30 1.683790 GAAGCCGTCGGTCACAATCG 61.684 60.000 13.94 0.00 0.00 3.34
30 31 0.389948 AGAAGCCGTCGGTCACAATC 60.390 55.000 13.94 2.94 0.00 2.67
31 32 0.034896 AAGAAGCCGTCGGTCACAAT 59.965 50.000 13.94 0.00 0.00 2.71
32 33 0.675083 TAAGAAGCCGTCGGTCACAA 59.325 50.000 13.94 0.00 0.00 3.33
33 34 0.242825 CTAAGAAGCCGTCGGTCACA 59.757 55.000 13.94 0.00 0.00 3.58
34 35 0.524862 TCTAAGAAGCCGTCGGTCAC 59.475 55.000 13.94 4.47 0.00 3.67
35 36 1.134367 CATCTAAGAAGCCGTCGGTCA 59.866 52.381 13.94 0.00 0.00 4.02
36 37 1.134560 ACATCTAAGAAGCCGTCGGTC 59.865 52.381 13.94 3.22 0.00 4.79
37 38 1.134560 GACATCTAAGAAGCCGTCGGT 59.865 52.381 13.94 0.00 0.00 4.69
38 39 1.405821 AGACATCTAAGAAGCCGTCGG 59.594 52.381 6.99 6.99 32.12 4.79
39 40 2.853731 AGACATCTAAGAAGCCGTCG 57.146 50.000 0.00 0.00 32.12 5.12
40 41 5.066764 ACTTCTAGACATCTAAGAAGCCGTC 59.933 44.000 18.29 0.00 37.30 4.79
41 42 4.951094 ACTTCTAGACATCTAAGAAGCCGT 59.049 41.667 18.29 6.75 37.30 5.68
42 43 5.508200 ACTTCTAGACATCTAAGAAGCCG 57.492 43.478 18.29 6.36 37.30 5.52
46 47 7.201920 GCCACCATACTTCTAGACATCTAAGAA 60.202 40.741 0.00 1.40 0.00 2.52
54 55 1.754803 CCGCCACCATACTTCTAGACA 59.245 52.381 0.00 0.00 0.00 3.41
94 95 7.669427 TGCCACTTTGATATTTTTCATGACTT 58.331 30.769 0.00 0.00 0.00 3.01
239 241 1.747956 CAACGCGTAACATTTGTGCA 58.252 45.000 14.46 0.00 0.00 4.57
325 327 1.616374 TGTGTCCGAAGCATACACTCA 59.384 47.619 0.00 0.00 0.00 3.41
331 333 0.885879 AGACGTGTGTCCGAAGCATA 59.114 50.000 0.00 0.00 46.74 3.14
332 334 0.033504 AAGACGTGTGTCCGAAGCAT 59.966 50.000 0.00 0.00 46.74 3.79
385 387 1.614413 AGAGTAGCCTATAAGCCGTGC 59.386 52.381 0.00 0.00 0.00 5.34
401 403 1.293498 GATGGCACCGTCACAGAGT 59.707 57.895 3.95 0.00 32.55 3.24
405 407 1.599518 GGTTGATGGCACCGTCACA 60.600 57.895 11.15 1.10 41.12 3.58
417 419 3.361977 GCAACGGCGGTGGTTGAT 61.362 61.111 27.92 0.00 45.85 2.57
426 428 4.354212 CACGTGTCTGCAACGGCG 62.354 66.667 13.50 4.80 45.35 6.46
461 463 3.118454 CCGGCTTACAGCACACGG 61.118 66.667 0.00 0.00 44.75 4.94
462 464 3.118454 CCCGGCTTACAGCACACG 61.118 66.667 0.00 0.00 44.75 4.49
481 483 5.116180 CACACGGCATCTATAGAAAAAGGA 58.884 41.667 6.52 0.00 0.00 3.36
490 492 7.758076 GCTTATATAACACACACGGCATCTATA 59.242 37.037 0.00 0.00 0.00 1.31
491 493 6.590292 GCTTATATAACACACACGGCATCTAT 59.410 38.462 0.00 0.00 0.00 1.98
497 499 3.199677 TGGCTTATATAACACACACGGC 58.800 45.455 0.00 0.00 0.00 5.68
548 550 0.824759 AGGACTCGGCTTATGGTCAC 59.175 55.000 0.00 0.00 0.00 3.67
602 607 1.416401 CCCGGCTTATGCTCCTCTAAA 59.584 52.381 0.00 0.00 39.59 1.85
625 630 0.949105 GCCGAGTGCTTTTCTTCGGA 60.949 55.000 15.18 0.00 42.63 4.55
676 682 5.249852 TGGTTAGGCTTAAATCACTACAGGT 59.750 40.000 0.00 0.00 0.00 4.00
689 695 2.040679 GGAGGGTGTTTGGTTAGGCTTA 59.959 50.000 0.00 0.00 0.00 3.09
690 696 1.203013 GGAGGGTGTTTGGTTAGGCTT 60.203 52.381 0.00 0.00 0.00 4.35
691 697 0.404426 GGAGGGTGTTTGGTTAGGCT 59.596 55.000 0.00 0.00 0.00 4.58
692 698 0.404426 AGGAGGGTGTTTGGTTAGGC 59.596 55.000 0.00 0.00 0.00 3.93
693 699 4.586306 ATTAGGAGGGTGTTTGGTTAGG 57.414 45.455 0.00 0.00 0.00 2.69
694 700 6.095021 GCTTAATTAGGAGGGTGTTTGGTTAG 59.905 42.308 0.00 0.00 0.00 2.34
695 701 5.947566 GCTTAATTAGGAGGGTGTTTGGTTA 59.052 40.000 0.00 0.00 0.00 2.85
696 702 4.770531 GCTTAATTAGGAGGGTGTTTGGTT 59.229 41.667 0.00 0.00 0.00 3.67
697 703 4.202631 TGCTTAATTAGGAGGGTGTTTGGT 60.203 41.667 0.00 0.00 0.00 3.67
698 704 4.340617 TGCTTAATTAGGAGGGTGTTTGG 58.659 43.478 0.00 0.00 0.00 3.28
699 705 5.975693 TTGCTTAATTAGGAGGGTGTTTG 57.024 39.130 0.00 0.00 0.00 2.93
700 706 5.480422 CCTTTGCTTAATTAGGAGGGTGTTT 59.520 40.000 0.00 0.00 0.00 2.83
701 707 5.016831 CCTTTGCTTAATTAGGAGGGTGTT 58.983 41.667 0.00 0.00 0.00 3.32
702 708 4.291249 TCCTTTGCTTAATTAGGAGGGTGT 59.709 41.667 0.00 0.00 33.08 4.16
703 709 4.855340 TCCTTTGCTTAATTAGGAGGGTG 58.145 43.478 0.00 0.00 33.08 4.61
704 710 5.117406 CTCCTTTGCTTAATTAGGAGGGT 57.883 43.478 10.69 0.00 46.51 4.34
708 714 5.193679 GGCTTCTCCTTTGCTTAATTAGGA 58.806 41.667 0.00 0.00 35.57 2.94
709 715 4.949856 TGGCTTCTCCTTTGCTTAATTAGG 59.050 41.667 0.00 0.00 35.26 2.69
710 716 6.375455 TCTTGGCTTCTCCTTTGCTTAATTAG 59.625 38.462 0.00 0.00 35.26 1.73
711 717 6.245408 TCTTGGCTTCTCCTTTGCTTAATTA 58.755 36.000 0.00 0.00 35.26 1.40
712 718 5.079643 TCTTGGCTTCTCCTTTGCTTAATT 58.920 37.500 0.00 0.00 35.26 1.40
713 719 4.666512 TCTTGGCTTCTCCTTTGCTTAAT 58.333 39.130 0.00 0.00 35.26 1.40
714 720 4.098914 TCTTGGCTTCTCCTTTGCTTAA 57.901 40.909 0.00 0.00 35.26 1.85
715 721 3.788227 TCTTGGCTTCTCCTTTGCTTA 57.212 42.857 0.00 0.00 35.26 3.09
716 722 2.625314 GTTCTTGGCTTCTCCTTTGCTT 59.375 45.455 0.00 0.00 35.26 3.91
717 723 2.234143 GTTCTTGGCTTCTCCTTTGCT 58.766 47.619 0.00 0.00 35.26 3.91
718 724 1.956477 TGTTCTTGGCTTCTCCTTTGC 59.044 47.619 0.00 0.00 35.26 3.68
719 725 3.551659 GCTTGTTCTTGGCTTCTCCTTTG 60.552 47.826 0.00 0.00 35.26 2.77
720 726 2.625314 GCTTGTTCTTGGCTTCTCCTTT 59.375 45.455 0.00 0.00 35.26 3.11
721 727 2.234143 GCTTGTTCTTGGCTTCTCCTT 58.766 47.619 0.00 0.00 35.26 3.36
722 728 1.546548 GGCTTGTTCTTGGCTTCTCCT 60.547 52.381 0.00 0.00 35.26 3.69
723 729 0.884514 GGCTTGTTCTTGGCTTCTCC 59.115 55.000 0.00 0.00 0.00 3.71
724 730 0.519077 CGGCTTGTTCTTGGCTTCTC 59.481 55.000 0.00 0.00 0.00 2.87
725 731 0.890996 CCGGCTTGTTCTTGGCTTCT 60.891 55.000 0.00 0.00 0.00 2.85
726 732 1.581447 CCGGCTTGTTCTTGGCTTC 59.419 57.895 0.00 0.00 0.00 3.86
727 733 2.564721 GCCGGCTTGTTCTTGGCTT 61.565 57.895 22.15 0.00 42.44 4.35
728 734 2.985847 GCCGGCTTGTTCTTGGCT 60.986 61.111 22.15 0.00 42.44 4.75
729 735 2.158561 ATTGCCGGCTTGTTCTTGGC 62.159 55.000 29.70 0.00 45.91 4.52
730 736 0.318120 AATTGCCGGCTTGTTCTTGG 59.682 50.000 29.70 0.00 0.00 3.61
731 737 2.228822 AGTAATTGCCGGCTTGTTCTTG 59.771 45.455 29.70 0.00 0.00 3.02
732 738 2.228822 CAGTAATTGCCGGCTTGTTCTT 59.771 45.455 29.70 13.51 0.00 2.52
733 739 1.812571 CAGTAATTGCCGGCTTGTTCT 59.187 47.619 29.70 17.07 0.00 3.01
734 740 2.262572 CAGTAATTGCCGGCTTGTTC 57.737 50.000 29.70 15.04 0.00 3.18
753 759 2.034687 TGCCCAAGAGCCAAGAGC 59.965 61.111 0.00 0.00 44.25 4.09
754 760 0.959372 CACTGCCCAAGAGCCAAGAG 60.959 60.000 0.00 0.00 0.00 2.85
755 761 1.073722 CACTGCCCAAGAGCCAAGA 59.926 57.895 0.00 0.00 0.00 3.02
756 762 0.036732 TACACTGCCCAAGAGCCAAG 59.963 55.000 0.00 0.00 0.00 3.61
757 763 0.036732 CTACACTGCCCAAGAGCCAA 59.963 55.000 0.00 0.00 0.00 4.52
758 764 1.679311 CTACACTGCCCAAGAGCCA 59.321 57.895 0.00 0.00 0.00 4.75
759 765 1.746991 GCTACACTGCCCAAGAGCC 60.747 63.158 0.00 0.00 0.00 4.70
760 766 1.003355 TGCTACACTGCCCAAGAGC 60.003 57.895 0.00 0.00 0.00 4.09
761 767 1.023513 GCTGCTACACTGCCCAAGAG 61.024 60.000 0.00 0.00 37.26 2.85
762 768 1.003355 GCTGCTACACTGCCCAAGA 60.003 57.895 0.00 0.00 37.26 3.02
763 769 3.583383 GCTGCTACACTGCCCAAG 58.417 61.111 0.00 0.00 37.26 3.61
768 774 1.667830 TTCACGGCTGCTACACTGC 60.668 57.895 0.00 0.00 42.19 4.40
769 775 0.319900 AGTTCACGGCTGCTACACTG 60.320 55.000 0.00 0.00 0.00 3.66
770 776 1.202582 CTAGTTCACGGCTGCTACACT 59.797 52.381 0.00 0.00 0.00 3.55
771 777 1.067776 ACTAGTTCACGGCTGCTACAC 60.068 52.381 0.00 0.00 0.00 2.90
772 778 1.254026 ACTAGTTCACGGCTGCTACA 58.746 50.000 0.00 0.00 0.00 2.74
773 779 2.365408 AACTAGTTCACGGCTGCTAC 57.635 50.000 1.12 0.00 0.00 3.58
774 780 2.821378 TGTAACTAGTTCACGGCTGCTA 59.179 45.455 12.39 0.00 0.00 3.49
775 781 1.616865 TGTAACTAGTTCACGGCTGCT 59.383 47.619 12.39 0.00 0.00 4.24
776 782 2.074547 TGTAACTAGTTCACGGCTGC 57.925 50.000 12.39 0.00 0.00 5.25
777 783 3.370978 CCAATGTAACTAGTTCACGGCTG 59.629 47.826 12.39 3.70 0.00 4.85
778 784 3.596214 CCAATGTAACTAGTTCACGGCT 58.404 45.455 12.39 0.00 0.00 5.52
779 785 2.095372 GCCAATGTAACTAGTTCACGGC 59.905 50.000 12.39 18.55 0.00 5.68
780 786 3.596214 AGCCAATGTAACTAGTTCACGG 58.404 45.455 12.39 13.84 0.00 4.94
781 787 4.804139 CCTAGCCAATGTAACTAGTTCACG 59.196 45.833 12.39 5.60 0.00 4.35
782 788 5.974108 TCCTAGCCAATGTAACTAGTTCAC 58.026 41.667 12.39 9.44 0.00 3.18
783 789 5.955959 TCTCCTAGCCAATGTAACTAGTTCA 59.044 40.000 12.39 10.46 0.00 3.18
784 790 6.466885 TCTCCTAGCCAATGTAACTAGTTC 57.533 41.667 12.39 4.83 0.00 3.01
785 791 6.630638 GCTTCTCCTAGCCAATGTAACTAGTT 60.631 42.308 13.68 13.68 35.06 2.24
786 792 5.163395 GCTTCTCCTAGCCAATGTAACTAGT 60.163 44.000 0.00 0.00 35.06 2.57
787 793 5.293560 GCTTCTCCTAGCCAATGTAACTAG 58.706 45.833 0.00 0.00 35.06 2.57
788 794 5.277857 GCTTCTCCTAGCCAATGTAACTA 57.722 43.478 0.00 0.00 35.06 2.24
789 795 4.143986 GCTTCTCCTAGCCAATGTAACT 57.856 45.455 0.00 0.00 35.06 2.24
799 805 1.138069 GACTCCTTGGCTTCTCCTAGC 59.862 57.143 0.00 0.00 36.53 3.42
800 806 1.760029 GGACTCCTTGGCTTCTCCTAG 59.240 57.143 0.00 0.00 37.43 3.02
801 807 1.078823 TGGACTCCTTGGCTTCTCCTA 59.921 52.381 0.00 0.00 35.26 2.94
802 808 0.178891 TGGACTCCTTGGCTTCTCCT 60.179 55.000 0.00 0.00 35.26 3.69
803 809 0.035915 GTGGACTCCTTGGCTTCTCC 60.036 60.000 0.00 0.00 0.00 3.71
804 810 0.980423 AGTGGACTCCTTGGCTTCTC 59.020 55.000 0.00 0.00 0.00 2.87
805 811 2.327325 TAGTGGACTCCTTGGCTTCT 57.673 50.000 0.00 0.00 0.00 2.85
806 812 2.911484 CATAGTGGACTCCTTGGCTTC 58.089 52.381 0.00 0.00 0.00 3.86
807 813 1.065126 GCATAGTGGACTCCTTGGCTT 60.065 52.381 0.00 0.00 0.00 4.35
808 814 0.543749 GCATAGTGGACTCCTTGGCT 59.456 55.000 0.00 0.00 0.00 4.75
809 815 0.464554 GGCATAGTGGACTCCTTGGC 60.465 60.000 0.00 0.00 0.00 4.52
810 816 0.911769 TGGCATAGTGGACTCCTTGG 59.088 55.000 0.00 0.00 0.00 3.61
811 817 2.947652 CAATGGCATAGTGGACTCCTTG 59.052 50.000 0.00 0.00 0.00 3.61
812 818 3.287867 CAATGGCATAGTGGACTCCTT 57.712 47.619 0.00 0.00 0.00 3.36
827 833 2.159393 CGAGTATTTGTGTGCCCAATGG 60.159 50.000 0.00 0.00 0.00 3.16
828 834 2.159393 CCGAGTATTTGTGTGCCCAATG 60.159 50.000 0.00 0.00 0.00 2.82
829 835 2.091541 CCGAGTATTTGTGTGCCCAAT 58.908 47.619 0.00 0.00 0.00 3.16
830 836 1.529226 CCGAGTATTTGTGTGCCCAA 58.471 50.000 0.00 0.00 0.00 4.12
831 837 0.958382 GCCGAGTATTTGTGTGCCCA 60.958 55.000 0.00 0.00 0.00 5.36
832 838 1.654023 GGCCGAGTATTTGTGTGCCC 61.654 60.000 0.00 0.00 0.00 5.36
833 839 0.958382 TGGCCGAGTATTTGTGTGCC 60.958 55.000 0.00 0.00 37.90 5.01
834 840 0.447801 CTGGCCGAGTATTTGTGTGC 59.552 55.000 0.00 0.00 0.00 4.57
835 841 1.086696 CCTGGCCGAGTATTTGTGTG 58.913 55.000 0.00 0.00 0.00 3.82
836 842 0.981183 TCCTGGCCGAGTATTTGTGT 59.019 50.000 0.00 0.00 0.00 3.72
837 843 1.066143 AGTCCTGGCCGAGTATTTGTG 60.066 52.381 0.00 0.00 0.00 3.33
838 844 1.066143 CAGTCCTGGCCGAGTATTTGT 60.066 52.381 0.00 0.00 0.00 2.83
839 845 1.656652 CAGTCCTGGCCGAGTATTTG 58.343 55.000 0.00 0.00 0.00 2.32
840 846 0.541863 CCAGTCCTGGCCGAGTATTT 59.458 55.000 0.00 0.00 44.73 1.40
841 847 2.212327 CCAGTCCTGGCCGAGTATT 58.788 57.895 0.00 0.00 44.73 1.89
842 848 3.956377 CCAGTCCTGGCCGAGTAT 58.044 61.111 0.00 0.00 44.73 2.12
851 857 1.294780 GCAGTCCAGTCCAGTCCTG 59.705 63.158 0.00 0.00 0.00 3.86
852 858 1.152247 TGCAGTCCAGTCCAGTCCT 60.152 57.895 0.00 0.00 0.00 3.85
853 859 1.294780 CTGCAGTCCAGTCCAGTCC 59.705 63.158 5.25 0.00 36.79 3.85
854 860 1.375268 GCTGCAGTCCAGTCCAGTC 60.375 63.158 16.64 0.00 43.71 3.51
855 861 2.142761 TGCTGCAGTCCAGTCCAGT 61.143 57.895 16.64 0.00 43.71 4.00
856 862 1.670406 GTGCTGCAGTCCAGTCCAG 60.670 63.158 16.64 0.00 43.71 3.86
857 863 2.427320 GTGCTGCAGTCCAGTCCA 59.573 61.111 16.64 0.00 43.71 4.02
858 864 2.359230 GGTGCTGCAGTCCAGTCC 60.359 66.667 16.64 5.52 43.71 3.85
859 865 2.359230 GGGTGCTGCAGTCCAGTC 60.359 66.667 23.94 6.19 43.71 3.51
860 866 3.170672 TGGGTGCTGCAGTCCAGT 61.171 61.111 23.94 0.00 43.71 4.00
861 867 2.670934 GTGGGTGCTGCAGTCCAG 60.671 66.667 23.94 0.00 44.67 3.86
862 868 3.487626 TGTGGGTGCTGCAGTCCA 61.488 61.111 23.94 20.84 0.00 4.02
863 869 2.980233 GTGTGGGTGCTGCAGTCC 60.980 66.667 16.64 17.26 0.00 3.85
877 883 4.626081 GGCGGCTGTGTCCTGTGT 62.626 66.667 0.00 0.00 0.00 3.72
899 908 2.861974 GTGGGGTGGAAGGGGGAA 60.862 66.667 0.00 0.00 0.00 3.97
938 947 2.822701 GTTGACGGGGGCGGAATC 60.823 66.667 0.00 0.00 0.00 2.52
939 948 4.770874 CGTTGACGGGGGCGGAAT 62.771 66.667 0.00 0.00 35.37 3.01
946 955 1.226030 GGAAGTTGTCGTTGACGGGG 61.226 60.000 3.48 0.00 40.29 5.73
953 962 1.343465 ACTGGATCGGAAGTTGTCGTT 59.657 47.619 0.00 0.00 0.00 3.85
954 966 0.966920 ACTGGATCGGAAGTTGTCGT 59.033 50.000 0.00 0.00 0.00 4.34
959 971 0.246635 CGTGGACTGGATCGGAAGTT 59.753 55.000 0.00 0.00 0.00 2.66
966 978 2.512515 GCTGGCGTGGACTGGATC 60.513 66.667 0.00 0.00 0.00 3.36
967 979 4.457496 CGCTGGCGTGGACTGGAT 62.457 66.667 6.83 0.00 34.35 3.41
985 997 2.590007 CATCTGGTAGCAGGCCGC 60.590 66.667 21.22 11.02 42.91 6.53
1648 1691 0.677288 TAAGTATGGTCCATCGGCGG 59.323 55.000 7.92 0.00 0.00 6.13
1707 1750 2.022625 TCTCCTCTTGATCAGGGTGGAT 60.023 50.000 16.39 0.00 0.00 3.41
1789 1832 1.616628 CCCCTAGAGTGCCCCAACT 60.617 63.158 0.00 0.00 0.00 3.16
1953 3737 0.710588 TCAGGCCCTCAGAACCTAGA 59.289 55.000 0.00 0.00 30.84 2.43
1997 3781 4.683320 CAGAACATATCAGGAGCACATACG 59.317 45.833 0.00 0.00 0.00 3.06
2238 6546 4.039245 TGTGAGACCTTCGAAGTGAAAGAT 59.961 41.667 23.03 2.58 35.79 2.40
2250 6558 2.028930 AGACAATCCGTGTGAGACCTTC 60.029 50.000 0.00 0.00 41.96 3.46
2254 6562 3.307242 GCATTAGACAATCCGTGTGAGAC 59.693 47.826 0.00 0.00 41.96 3.36
2256 6564 3.525537 AGCATTAGACAATCCGTGTGAG 58.474 45.455 0.00 0.00 41.96 3.51
2277 6585 7.271511 ACCAATTGCAACTCTGAACAATTAAA 58.728 30.769 0.00 0.00 39.92 1.52
2341 6649 5.159209 GTTCACTTTTCCATGATTGAGCAG 58.841 41.667 0.00 0.00 0.00 4.24
2676 7281 7.224557 ACAACATCAGCACAATAAAAGGAAAAC 59.775 33.333 0.00 0.00 0.00 2.43
2888 7527 9.715121 CATTCTAAACTGGTACCTTAGTGTTTA 57.285 33.333 14.36 16.58 0.00 2.01
2940 7585 8.050778 ACAAGACAGAGAAATGTACACAAAAA 57.949 30.769 0.00 0.00 32.25 1.94


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

AutoCloner maintained by Alex Coulton.