Multiple sequence alignment - TraesCS7D01G164900

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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 TraesCS7D01G164900 chr7D 100.000 3614 0 0 1 3614 114151645 114148032 0.000000e+00 6674.0
1 TraesCS7D01G164900 chr7D 87.983 466 22 4 800 1264 114468585 114469017 1.490000e-143 520.0
2 TraesCS7D01G164900 chr7D 81.329 632 78 25 1977 2579 104226588 104225968 9.080000e-131 477.0
3 TraesCS7D01G164900 chr7D 80.000 635 88 25 1977 2585 104365979 104365358 1.990000e-117 433.0
4 TraesCS7D01G164900 chr7D 86.735 392 37 9 1794 2173 114469290 114469678 4.310000e-114 422.0
5 TraesCS7D01G164900 chr7D 78.163 664 136 9 53 711 523124666 523125325 7.220000e-112 414.0
6 TraesCS7D01G164900 chr7D 93.818 275 12 3 1459 1733 114469019 114469288 3.360000e-110 409.0
7 TraesCS7D01G164900 chr7D 81.629 528 43 21 885 1392 104366708 104366215 4.380000e-104 388.0
8 TraesCS7D01G164900 chr7D 77.190 662 146 5 53 711 555169885 555169226 7.320000e-102 381.0
9 TraesCS7D01G164900 chr7D 80.925 346 23 16 891 1231 104227293 104226986 2.170000e-57 233.0
10 TraesCS7D01G164900 chr7D 95.683 139 6 0 1253 1391 114150250 114150112 1.310000e-54 224.0
11 TraesCS7D01G164900 chr7D 95.683 139 6 0 1396 1534 114150393 114150255 1.310000e-54 224.0
12 TraesCS7D01G164900 chr7D 84.247 146 16 3 3466 3610 549645183 549645322 6.290000e-28 135.0
13 TraesCS7D01G164900 chr7D 94.030 67 4 0 2790 2856 226113628 226113562 6.380000e-18 102.0
14 TraesCS7D01G164900 chr7D 91.667 60 5 0 1819 1878 114469144 114469203 2.310000e-12 84.2
15 TraesCS7D01G164900 chr7D 91.304 46 4 0 1730 1775 403810547 403810502 3.010000e-06 63.9
16 TraesCS7D01G164900 chr7D 97.059 34 1 0 799 832 104366805 104366772 1.400000e-04 58.4
17 TraesCS7D01G164900 chr7A 89.631 1842 96 26 1794 3614 119306399 119304632 0.000000e+00 2255.0
18 TraesCS7D01G164900 chr7A 91.789 475 26 7 800 1264 119307143 119306672 0.000000e+00 649.0
19 TraesCS7D01G164900 chr7A 92.289 402 29 2 865 1264 119461803 119462204 1.460000e-158 569.0
20 TraesCS7D01G164900 chr7A 85.447 481 34 20 928 1396 108547848 108547392 5.460000e-128 468.0
21 TraesCS7D01G164900 chr7A 92.364 275 16 3 1459 1733 119306670 119306401 1.570000e-103 387.0
22 TraesCS7D01G164900 chr7A 90.545 275 21 3 1459 1733 119462206 119462475 3.430000e-95 359.0
23 TraesCS7D01G164900 chr7A 81.292 449 54 17 2028 2463 108547067 108546636 1.610000e-88 337.0
24 TraesCS7D01G164900 chr7A 81.818 352 36 17 2061 2392 108565763 108565420 1.650000e-68 270.0
25 TraesCS7D01G164900 chr7A 89.320 103 9 2 1799 1901 119462483 119462583 1.050000e-25 128.0
26 TraesCS7D01G164900 chr7A 78.182 220 28 12 1180 1392 108566334 108566128 4.900000e-24 122.0
27 TraesCS7D01G164900 chr7A 91.111 90 4 2 3487 3575 99589727 99589641 6.340000e-23 119.0
28 TraesCS7D01G164900 chr7A 88.333 60 7 0 1819 1878 119306545 119306486 5.010000e-09 73.1
29 TraesCS7D01G164900 chr7B 93.524 1436 49 14 1794 3219 73935018 73933617 0.000000e+00 2097.0
30 TraesCS7D01G164900 chr7B 92.373 944 50 5 795 1733 73989863 73990789 0.000000e+00 1325.0
31 TraesCS7D01G164900 chr7B 94.039 822 41 3 795 1611 73936802 73935984 0.000000e+00 1240.0
32 TraesCS7D01G164900 chr7B 84.510 510 51 16 898 1396 62479715 62479223 2.520000e-131 479.0
33 TraesCS7D01G164900 chr7B 87.406 397 22 12 1794 2173 73990791 73991176 7.170000e-117 431.0
34 TraesCS7D01G164900 chr7B 80.855 538 72 19 2068 2585 62483530 62483004 9.410000e-106 394.0
35 TraesCS7D01G164900 chr7B 78.191 619 129 6 62 676 174049544 174050160 1.220000e-104 390.0
36 TraesCS7D01G164900 chr7B 82.276 457 50 15 2028 2463 62478822 62478376 2.050000e-97 366.0
37 TraesCS7D01G164900 chr7B 86.290 248 21 4 3285 3522 73921723 73921479 1.290000e-64 257.0
38 TraesCS7D01G164900 chr7B 97.902 143 3 0 1392 1534 73936350 73936208 7.750000e-62 248.0
39 TraesCS7D01G164900 chr7B 95.804 143 6 0 1250 1392 73990445 73990587 7.800000e-57 231.0
40 TraesCS7D01G164900 chr7B 95.000 140 7 0 1253 1392 73936203 73936064 1.690000e-53 220.0
41 TraesCS7D01G164900 chr7B 93.846 130 8 0 1604 1733 73935149 73935020 2.850000e-46 196.0
42 TraesCS7D01G164900 chr7B 88.166 169 13 4 1421 1585 62484168 62484003 1.020000e-45 195.0
43 TraesCS7D01G164900 chr7B 83.505 194 30 1 1392 1585 62479368 62479177 2.870000e-41 180.0
44 TraesCS7D01G164900 chr7B 97.938 97 2 0 1392 1488 73990315 73990411 6.210000e-38 169.0
45 TraesCS7D01G164900 chr7B 100.000 43 0 0 3201 3243 73926646 73926604 2.990000e-11 80.5
46 TraesCS7D01G164900 chr5D 79.020 653 124 13 63 708 351954497 351955143 5.540000e-118 435.0
47 TraesCS7D01G164900 chr5D 77.946 662 141 5 53 711 479883265 479882606 3.360000e-110 409.0
48 TraesCS7D01G164900 chr5D 92.391 92 3 2 3487 3577 346975 347063 1.050000e-25 128.0
49 TraesCS7D01G164900 chr3B 78.443 668 137 7 63 726 53914129 53914793 2.580000e-116 429.0
50 TraesCS7D01G164900 chr2A 78.571 658 128 12 65 716 677553596 677552946 4.310000e-114 422.0
51 TraesCS7D01G164900 chr2A 88.889 198 19 2 2584 2778 117393211 117393014 1.300000e-59 241.0
52 TraesCS7D01G164900 chr3D 78.053 647 130 11 65 705 120320768 120320128 7.270000e-107 398.0
53 TraesCS7D01G164900 chr3D 90.306 196 17 2 2588 2782 436020077 436020271 4.630000e-64 255.0
54 TraesCS7D01G164900 chr1B 79.310 580 109 11 138 711 493732144 493731570 2.620000e-106 396.0
55 TraesCS7D01G164900 chr1B 88.406 207 21 3 2580 2784 665505175 665504970 2.790000e-61 246.0
56 TraesCS7D01G164900 chr2D 89.904 208 19 2 2579 2784 128025763 128025970 2.140000e-67 267.0
57 TraesCS7D01G164900 chr1A 89.796 196 19 1 2584 2778 440899065 440899260 2.150000e-62 250.0
58 TraesCS7D01G164900 chr1A 89.691 194 18 2 2584 2777 542817605 542817796 2.790000e-61 246.0
59 TraesCS7D01G164900 chr1A 93.617 47 3 0 1730 1776 351880424 351880378 1.800000e-08 71.3
60 TraesCS7D01G164900 chr4B 88.177 203 21 3 2584 2784 173325480 173325279 4.660000e-59 239.0
61 TraesCS7D01G164900 chr4B 95.000 40 1 1 3538 3576 665158337 665158298 1.080000e-05 62.1
62 TraesCS7D01G164900 chr3A 88.095 84 6 3 3483 3564 164398124 164398043 2.970000e-16 97.1
63 TraesCS7D01G164900 chr6B 83.784 74 8 2 3538 3610 681427149 681427219 2.330000e-07 67.6
64 TraesCS7D01G164900 chr6B 95.122 41 1 1 3537 3576 560634394 560634354 3.010000e-06 63.9
65 TraesCS7D01G164900 chr5A 93.333 45 3 0 1732 1776 643451304 643451260 2.330000e-07 67.6
66 TraesCS7D01G164900 chr2B 93.478 46 1 2 3482 3527 198422460 198422503 2.330000e-07 67.6
67 TraesCS7D01G164900 chr2B 91.489 47 3 1 3531 3576 255855566 255855612 3.010000e-06 63.9
68 TraesCS7D01G164900 chr1D 93.182 44 3 0 1732 1775 409914447 409914490 8.380000e-07 65.8
69 TraesCS7D01G164900 chr4D 91.304 46 4 0 1730 1775 492602238 492602193 3.010000e-06 63.9
70 TraesCS7D01G164900 chr4A 91.304 46 4 0 1730 1775 743181557 743181512 3.010000e-06 63.9
71 TraesCS7D01G164900 chr4A 91.304 46 4 0 1730 1775 743224702 743224657 3.010000e-06 63.9
72 TraesCS7D01G164900 chr6A 91.111 45 4 0 1732 1776 585176382 585176426 1.080000e-05 62.1
73 TraesCS7D01G164900 chr6A 91.111 45 4 0 1732 1776 585181157 585181201 1.080000e-05 62.1


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 TraesCS7D01G164900 chr7D 114148032 114151645 3613 True 2374.000000 6674 97.122000 1 3614 3 chr7D.!!$R6 3613
1 TraesCS7D01G164900 chr7D 523124666 523125325 659 False 414.000000 414 78.163000 53 711 1 chr7D.!!$F1 658
2 TraesCS7D01G164900 chr7D 555169226 555169885 659 True 381.000000 381 77.190000 53 711 1 chr7D.!!$R3 658
3 TraesCS7D01G164900 chr7D 114468585 114469678 1093 False 358.800000 520 90.050750 800 2173 4 chr7D.!!$F3 1373
4 TraesCS7D01G164900 chr7D 104225968 104227293 1325 True 355.000000 477 81.127000 891 2579 2 chr7D.!!$R4 1688
5 TraesCS7D01G164900 chr7D 104365358 104366805 1447 True 293.133333 433 86.229333 799 2585 3 chr7D.!!$R5 1786
6 TraesCS7D01G164900 chr7A 119304632 119307143 2511 True 841.025000 2255 90.529250 800 3614 4 chr7A.!!$R4 2814
7 TraesCS7D01G164900 chr7A 108546636 108547848 1212 True 402.500000 468 83.369500 928 2463 2 chr7A.!!$R2 1535
8 TraesCS7D01G164900 chr7A 119461803 119462583 780 False 352.000000 569 90.718000 865 1901 3 chr7A.!!$F1 1036
9 TraesCS7D01G164900 chr7B 73933617 73936802 3185 True 800.200000 2097 94.862200 795 3219 5 chr7B.!!$R4 2424
10 TraesCS7D01G164900 chr7B 73989863 73991176 1313 False 539.000000 1325 93.380250 795 2173 4 chr7B.!!$F2 1378
11 TraesCS7D01G164900 chr7B 174049544 174050160 616 False 390.000000 390 78.191000 62 676 1 chr7B.!!$F1 614
12 TraesCS7D01G164900 chr7B 62478376 62484168 5792 True 322.800000 479 83.862400 898 2585 5 chr7B.!!$R3 1687
13 TraesCS7D01G164900 chr5D 351954497 351955143 646 False 435.000000 435 79.020000 63 708 1 chr5D.!!$F2 645
14 TraesCS7D01G164900 chr5D 479882606 479883265 659 True 409.000000 409 77.946000 53 711 1 chr5D.!!$R1 658
15 TraesCS7D01G164900 chr3B 53914129 53914793 664 False 429.000000 429 78.443000 63 726 1 chr3B.!!$F1 663
16 TraesCS7D01G164900 chr2A 677552946 677553596 650 True 422.000000 422 78.571000 65 716 1 chr2A.!!$R2 651
17 TraesCS7D01G164900 chr3D 120320128 120320768 640 True 398.000000 398 78.053000 65 705 1 chr3D.!!$R1 640
18 TraesCS7D01G164900 chr1B 493731570 493732144 574 True 396.000000 396 79.310000 138 711 1 chr1B.!!$R1 573

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
48 49 0.106708 ATACCGCGCACTCCATCAAT 59.893 50.0 8.75 0.0 0.00 2.57 F
772 774 0.243907 CGACTCCCTGAAGCGAGAAA 59.756 55.0 0.00 0.0 0.00 2.52 F
1742 6203 0.251653 TTGCAGAGTACTCCCTCGGT 60.252 55.0 19.38 0.0 36.56 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1097 4671 0.905839 CGATCGAACGAGAACGGAAC 59.094 55.000 10.26 0.0 44.46 3.62 R
2207 6882 1.077930 GCTCTGGCTCCATTGCTGA 60.078 57.895 6.18 0.0 35.22 4.26 R
3291 8007 0.034186 TAGCACCCCAGCATCCTTTG 60.034 55.000 0.00 0.0 36.85 2.77 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 3.885814 ACCTCGGGTGCAGAAGAA 58.114 55.556 0.00 0.00 32.98 2.52
20 21 1.674057 ACCTCGGGTGCAGAAGAAG 59.326 57.895 0.00 0.00 32.98 2.85
21 22 1.743252 CCTCGGGTGCAGAAGAAGC 60.743 63.158 0.00 0.00 0.00 3.86
22 23 1.743252 CTCGGGTGCAGAAGAAGCC 60.743 63.158 0.00 0.00 37.61 4.35
23 24 2.032528 CGGGTGCAGAAGAAGCCA 59.967 61.111 0.00 0.00 41.37 4.75
24 25 2.328099 CGGGTGCAGAAGAAGCCAC 61.328 63.158 0.00 0.00 41.37 5.01
25 26 1.973812 GGGTGCAGAAGAAGCCACC 60.974 63.158 0.00 0.00 40.94 4.61
26 27 1.073897 GGTGCAGAAGAAGCCACCT 59.926 57.895 0.00 0.00 33.38 4.00
27 28 0.538287 GGTGCAGAAGAAGCCACCTT 60.538 55.000 0.00 0.00 33.38 3.50
30 31 1.074405 TGCAGAAGAAGCCACCTTGAT 59.926 47.619 0.00 0.00 0.00 2.57
31 32 2.305635 TGCAGAAGAAGCCACCTTGATA 59.694 45.455 0.00 0.00 0.00 2.15
32 33 2.680339 GCAGAAGAAGCCACCTTGATAC 59.320 50.000 0.00 0.00 0.00 2.24
33 34 3.274288 CAGAAGAAGCCACCTTGATACC 58.726 50.000 0.00 0.00 0.00 2.73
34 35 2.093447 AGAAGAAGCCACCTTGATACCG 60.093 50.000 0.00 0.00 0.00 4.02
35 36 0.107654 AGAAGCCACCTTGATACCGC 60.108 55.000 0.00 0.00 0.00 5.68
37 38 3.573491 GCCACCTTGATACCGCGC 61.573 66.667 0.00 0.00 0.00 6.86
39 40 2.461110 CCACCTTGATACCGCGCAC 61.461 63.158 8.75 0.00 0.00 5.34
41 42 1.153628 ACCTTGATACCGCGCACTC 60.154 57.895 8.75 0.00 0.00 3.51
42 43 1.883084 CCTTGATACCGCGCACTCC 60.883 63.158 8.75 0.00 0.00 3.85
43 44 1.153647 CTTGATACCGCGCACTCCA 60.154 57.895 8.75 0.00 0.00 3.86
44 45 0.530650 CTTGATACCGCGCACTCCAT 60.531 55.000 8.75 0.00 0.00 3.41
45 46 0.529773 TTGATACCGCGCACTCCATC 60.530 55.000 8.75 2.86 0.00 3.51
46 47 1.067416 GATACCGCGCACTCCATCA 59.933 57.895 8.75 0.00 0.00 3.07
47 48 0.529773 GATACCGCGCACTCCATCAA 60.530 55.000 8.75 0.00 0.00 2.57
48 49 0.106708 ATACCGCGCACTCCATCAAT 59.893 50.000 8.75 0.00 0.00 2.57
50 51 0.106708 ACCGCGCACTCCATCAATAT 59.893 50.000 8.75 0.00 0.00 1.28
51 52 0.514255 CCGCGCACTCCATCAATATG 59.486 55.000 8.75 0.00 0.00 1.78
55 56 3.679502 CGCGCACTCCATCAATATGATTA 59.320 43.478 8.75 0.00 34.28 1.75
58 59 6.025896 GCGCACTCCATCAATATGATTATTG 58.974 40.000 0.30 0.32 44.05 1.90
81 82 3.525199 AGGAAACATGATAGCCCTTCTGT 59.475 43.478 0.00 0.00 0.00 3.41
113 114 6.126739 GGGAAACAGATATGGGGATATAGGAC 60.127 46.154 0.00 0.00 0.00 3.85
158 159 2.356125 GGCCTGAAAGCATCCAGACTTA 60.356 50.000 0.00 0.00 32.37 2.24
172 173 5.630121 TCCAGACTTACACCATTGAACAAT 58.370 37.500 0.00 0.00 0.00 2.71
185 186 7.114811 CACCATTGAACAATACCGAAAAAGAAG 59.885 37.037 0.00 0.00 0.00 2.85
196 197 3.561725 CCGAAAAAGAAGCTGAAGTCACT 59.438 43.478 0.00 0.00 0.00 3.41
232 233 2.849942 TCCGTGAATCATGGGCTAATG 58.150 47.619 20.36 0.00 40.65 1.90
271 272 3.694072 CCGCTTTCAAATAGGACCATTCA 59.306 43.478 0.00 0.00 0.00 2.57
333 334 5.525378 CACATAACCTATTGCTCTTCACTCC 59.475 44.000 0.00 0.00 0.00 3.85
335 336 4.917906 AACCTATTGCTCTTCACTCCTT 57.082 40.909 0.00 0.00 0.00 3.36
344 345 4.949856 TGCTCTTCACTCCTTTTGTTTTCT 59.050 37.500 0.00 0.00 0.00 2.52
397 398 3.940209 TTGTCCGTAATAACACGTCCT 57.060 42.857 0.00 0.00 40.31 3.85
398 399 5.581126 ATTGTCCGTAATAACACGTCCTA 57.419 39.130 0.00 0.00 40.31 2.94
421 422 1.668151 AAACGCCGACTGCTCTTCC 60.668 57.895 0.00 0.00 38.05 3.46
430 431 3.304257 CGACTGCTCTTCCGAGATTATG 58.696 50.000 0.00 0.00 39.74 1.90
433 434 3.068873 ACTGCTCTTCCGAGATTATGTCC 59.931 47.826 0.00 0.00 39.74 4.02
437 438 2.885266 TCTTCCGAGATTATGTCCGGAG 59.115 50.000 3.06 0.00 44.66 4.63
595 597 0.749649 CTCCGGTGAATCCTCTCCAG 59.250 60.000 0.00 0.00 35.31 3.86
602 604 2.027745 GTGAATCCTCTCCAGTGAGCAA 60.028 50.000 0.00 0.00 38.58 3.91
648 650 4.894705 TCATCACCACATAAATCCCAATGG 59.105 41.667 0.00 0.00 0.00 3.16
728 730 4.870363 TGGAACAAAGCATCTTAAACAGC 58.130 39.130 0.00 0.00 31.92 4.40
729 731 4.237724 GGAACAAAGCATCTTAAACAGCC 58.762 43.478 0.00 0.00 0.00 4.85
730 732 3.559238 ACAAAGCATCTTAAACAGCCG 57.441 42.857 0.00 0.00 0.00 5.52
731 733 2.228822 ACAAAGCATCTTAAACAGCCGG 59.771 45.455 0.00 0.00 0.00 6.13
733 735 1.032114 AGCATCTTAAACAGCCGGCC 61.032 55.000 26.15 5.07 0.00 6.13
737 739 1.969589 CTTAAACAGCCGGCCCGTT 60.970 57.895 26.15 24.03 0.00 4.44
738 740 0.674269 CTTAAACAGCCGGCCCGTTA 60.674 55.000 26.84 17.98 0.00 3.18
739 741 0.954938 TTAAACAGCCGGCCCGTTAC 60.955 55.000 26.84 0.00 0.00 2.50
741 743 3.894547 AACAGCCGGCCCGTTACTG 62.895 63.158 25.80 17.45 0.00 2.74
742 744 4.388499 CAGCCGGCCCGTTACTGT 62.388 66.667 26.15 0.00 0.00 3.55
743 745 4.388499 AGCCGGCCCGTTACTGTG 62.388 66.667 26.15 0.00 0.00 3.66
746 748 1.153706 CCGGCCCGTTACTGTGTAG 60.154 63.158 0.85 0.00 0.00 2.74
747 749 1.153706 CGGCCCGTTACTGTGTAGG 60.154 63.158 0.00 0.00 0.00 3.18
748 750 1.449070 GGCCCGTTACTGTGTAGGC 60.449 63.158 0.00 0.00 39.73 3.93
749 751 1.595357 GCCCGTTACTGTGTAGGCT 59.405 57.895 0.00 0.00 37.42 4.58
752 754 2.159000 GCCCGTTACTGTGTAGGCTATT 60.159 50.000 0.00 0.00 37.42 1.73
753 755 3.714391 CCCGTTACTGTGTAGGCTATTC 58.286 50.000 0.00 0.00 0.00 1.75
754 756 3.369385 CCGTTACTGTGTAGGCTATTCG 58.631 50.000 0.00 0.00 0.00 3.34
756 758 4.033684 CGTTACTGTGTAGGCTATTCGAC 58.966 47.826 0.00 0.00 0.00 4.20
758 760 5.272397 GTTACTGTGTAGGCTATTCGACTC 58.728 45.833 0.00 0.00 29.76 3.36
759 761 2.688958 ACTGTGTAGGCTATTCGACTCC 59.311 50.000 0.00 0.00 29.76 3.85
760 762 2.029623 TGTGTAGGCTATTCGACTCCC 58.970 52.381 0.00 0.00 29.76 4.30
762 764 2.034812 GTGTAGGCTATTCGACTCCCTG 59.965 54.545 0.00 0.00 29.76 4.45
764 766 2.160721 AGGCTATTCGACTCCCTGAA 57.839 50.000 0.00 0.00 0.00 3.02
765 767 2.035632 AGGCTATTCGACTCCCTGAAG 58.964 52.381 0.00 0.00 0.00 3.02
766 768 1.539280 GGCTATTCGACTCCCTGAAGC 60.539 57.143 0.00 0.00 0.00 3.86
767 769 1.866063 GCTATTCGACTCCCTGAAGCG 60.866 57.143 0.00 0.00 0.00 4.68
768 770 1.676529 CTATTCGACTCCCTGAAGCGA 59.323 52.381 0.00 0.00 0.00 4.93
769 771 0.457851 ATTCGACTCCCTGAAGCGAG 59.542 55.000 0.00 0.00 32.22 5.03
772 774 0.243907 CGACTCCCTGAAGCGAGAAA 59.756 55.000 0.00 0.00 0.00 2.52
775 777 3.712187 GACTCCCTGAAGCGAGAAATAG 58.288 50.000 0.00 0.00 0.00 1.73
776 778 2.159028 ACTCCCTGAAGCGAGAAATAGC 60.159 50.000 0.00 0.00 0.00 2.97
777 779 2.102252 CTCCCTGAAGCGAGAAATAGCT 59.898 50.000 0.00 0.00 46.97 3.32
778 780 2.101582 TCCCTGAAGCGAGAAATAGCTC 59.898 50.000 0.00 0.00 43.78 4.09
785 787 3.949031 GAGAAATAGCTCTCGCGGT 57.051 52.632 6.13 0.00 42.32 5.68
786 788 1.482278 GAGAAATAGCTCTCGCGGTG 58.518 55.000 6.13 0.00 42.32 4.94
787 789 1.065701 GAGAAATAGCTCTCGCGGTGA 59.934 52.381 6.13 4.24 42.32 4.02
791 793 1.038130 ATAGCTCTCGCGGTGAGGTT 61.038 55.000 28.63 18.25 45.32 3.50
840 842 4.554036 GCCAGCCCATCCGAGTCC 62.554 72.222 0.00 0.00 0.00 3.85
841 843 4.227134 CCAGCCCATCCGAGTCCG 62.227 72.222 0.00 0.00 0.00 4.79
842 844 3.461773 CAGCCCATCCGAGTCCGT 61.462 66.667 0.00 0.00 0.00 4.69
896 927 2.133742 CTCGGCTGCCACAACAAAGG 62.134 60.000 20.29 0.00 0.00 3.11
977 4551 1.857583 TCCTCCTCCTCCGGATTCTTA 59.142 52.381 3.57 0.00 31.43 2.10
978 4552 2.246588 TCCTCCTCCTCCGGATTCTTAA 59.753 50.000 3.57 0.00 31.43 1.85
1127 4709 1.332686 CGTTCGATCGATCCACCTACA 59.667 52.381 20.18 0.00 0.00 2.74
1133 4715 0.468226 TCGATCCACCTACAATGCCC 59.532 55.000 0.00 0.00 0.00 5.36
1146 4728 1.876497 AATGCCCGCAATTCGCTGTT 61.876 50.000 0.00 0.00 39.08 3.16
1186 4769 5.924356 ACTTTTTCACCAAATTAACCCCAG 58.076 37.500 0.00 0.00 0.00 4.45
1248 4844 0.900182 GCCCTGACCTTTTTCCCAGG 60.900 60.000 0.00 0.00 44.29 4.45
1321 4924 3.974642 AGGAGAGGGTTTCTGTACTTTGT 59.025 43.478 0.00 0.00 35.87 2.83
1333 4936 4.947388 TCTGTACTTTGTCCCAATAATGGC 59.053 41.667 0.00 0.00 46.09 4.40
1738 6199 2.481289 GCTTTTGCAGAGTACTCCCT 57.519 50.000 19.38 0.00 46.58 4.20
1739 6200 2.351455 GCTTTTGCAGAGTACTCCCTC 58.649 52.381 19.38 9.16 46.58 4.30
1740 6201 2.611518 CTTTTGCAGAGTACTCCCTCG 58.388 52.381 19.38 7.01 36.56 4.63
1741 6202 0.895530 TTTGCAGAGTACTCCCTCGG 59.104 55.000 19.38 5.62 36.56 4.63
1742 6203 0.251653 TTGCAGAGTACTCCCTCGGT 60.252 55.000 19.38 0.00 36.56 4.69
1743 6204 0.680280 TGCAGAGTACTCCCTCGGTC 60.680 60.000 19.38 2.11 36.56 4.79
1744 6205 0.394625 GCAGAGTACTCCCTCGGTCT 60.395 60.000 19.38 0.00 36.56 3.85
1745 6206 1.134159 GCAGAGTACTCCCTCGGTCTA 60.134 57.143 19.38 0.00 36.56 2.59
1746 6207 2.841215 CAGAGTACTCCCTCGGTCTAG 58.159 57.143 19.38 0.00 36.56 2.43
1747 6208 2.171027 CAGAGTACTCCCTCGGTCTAGT 59.829 54.545 19.38 0.00 36.56 2.57
1748 6209 3.387374 CAGAGTACTCCCTCGGTCTAGTA 59.613 52.174 19.38 0.00 36.56 1.82
1749 6210 4.036518 AGAGTACTCCCTCGGTCTAGTAA 58.963 47.826 19.38 0.00 36.56 2.24
1750 6211 4.659835 AGAGTACTCCCTCGGTCTAGTAAT 59.340 45.833 19.38 0.00 36.56 1.89
1751 6212 5.843421 AGAGTACTCCCTCGGTCTAGTAATA 59.157 44.000 19.38 0.00 36.56 0.98
1752 6213 6.501453 AGAGTACTCCCTCGGTCTAGTAATAT 59.499 42.308 19.38 0.00 36.56 1.28
1753 6214 7.677745 AGAGTACTCCCTCGGTCTAGTAATATA 59.322 40.741 19.38 0.00 36.56 0.86
1754 6215 8.212259 AGTACTCCCTCGGTCTAGTAATATAA 57.788 38.462 0.00 0.00 0.00 0.98
1755 6216 8.320617 AGTACTCCCTCGGTCTAGTAATATAAG 58.679 40.741 0.00 0.00 0.00 1.73
1756 6217 7.327064 ACTCCCTCGGTCTAGTAATATAAGA 57.673 40.000 0.00 0.00 0.00 2.10
1757 6218 7.753630 ACTCCCTCGGTCTAGTAATATAAGAA 58.246 38.462 0.00 0.00 0.00 2.52
1758 6219 7.665145 ACTCCCTCGGTCTAGTAATATAAGAAC 59.335 40.741 0.00 0.00 0.00 3.01
1776 6237 5.813080 AGAACGTTTTTCAAGCTAACAGT 57.187 34.783 0.46 0.00 0.00 3.55
1777 6238 6.913873 AGAACGTTTTTCAAGCTAACAGTA 57.086 33.333 0.46 0.00 0.00 2.74
1778 6239 7.492352 AGAACGTTTTTCAAGCTAACAGTAT 57.508 32.000 0.46 0.00 0.00 2.12
1779 6240 7.927048 AGAACGTTTTTCAAGCTAACAGTATT 58.073 30.769 0.46 0.00 0.00 1.89
1780 6241 9.048446 AGAACGTTTTTCAAGCTAACAGTATTA 57.952 29.630 0.46 0.00 0.00 0.98
1781 6242 9.821662 GAACGTTTTTCAAGCTAACAGTATTAT 57.178 29.630 0.46 0.00 0.00 1.28
1782 6243 9.607285 AACGTTTTTCAAGCTAACAGTATTATG 57.393 29.630 0.00 0.00 0.00 1.90
1783 6244 8.234546 ACGTTTTTCAAGCTAACAGTATTATGG 58.765 33.333 0.00 0.00 0.00 2.74
1784 6245 7.696453 CGTTTTTCAAGCTAACAGTATTATGGG 59.304 37.037 0.00 0.00 0.00 4.00
1785 6246 8.736244 GTTTTTCAAGCTAACAGTATTATGGGA 58.264 33.333 0.00 0.00 0.00 4.37
1786 6247 7.859325 TTTCAAGCTAACAGTATTATGGGAC 57.141 36.000 0.00 0.00 0.00 4.46
1787 6248 5.597806 TCAAGCTAACAGTATTATGGGACG 58.402 41.667 0.00 0.00 0.00 4.79
1788 6249 4.602340 AGCTAACAGTATTATGGGACGG 57.398 45.455 0.00 0.00 0.00 4.79
1789 6250 4.220724 AGCTAACAGTATTATGGGACGGA 58.779 43.478 0.00 0.00 0.00 4.69
1790 6251 4.281182 AGCTAACAGTATTATGGGACGGAG 59.719 45.833 0.00 0.00 0.00 4.63
1791 6252 4.280174 GCTAACAGTATTATGGGACGGAGA 59.720 45.833 0.00 0.00 0.00 3.71
1792 6253 5.221382 GCTAACAGTATTATGGGACGGAGAA 60.221 44.000 0.00 0.00 0.00 2.87
1908 6372 7.674772 TGATTCCATGATATATGGGCATTTGAA 59.325 33.333 6.13 0.00 39.60 2.69
2130 6794 2.568696 TGCTCTGTCGTTAGCATCTC 57.431 50.000 0.00 0.00 43.56 2.75
2207 6882 6.068498 TCCAATTAATCTTACCAGGGTGGATT 60.068 38.462 18.40 18.40 40.96 3.01
2374 7053 3.876914 TGCTGCGAGGTAATTAATTCTGG 59.123 43.478 3.39 0.00 0.00 3.86
2397 7076 6.948886 TGGGGCACTACAACTTATTTGATTTA 59.051 34.615 0.00 0.00 38.73 1.40
2499 7187 1.490574 AGAGGATTAGACGGCTGCTT 58.509 50.000 0.00 0.00 0.00 3.91
2529 7217 0.381801 CTGCTGCTGTTGGTTTCGTT 59.618 50.000 0.00 0.00 0.00 3.85
2569 7257 8.027189 GTGAAATGAATAGGTACCAAAAGGAAC 58.973 37.037 15.94 0.00 0.00 3.62
2608 7296 5.382618 ACAGATCTTTTGGCAGCTTAAAG 57.617 39.130 11.39 11.39 0.00 1.85
2627 7315 1.423161 AGAATAAGCTGCATCCTCCCC 59.577 52.381 1.02 0.00 0.00 4.81
2657 7345 3.330267 CCATAAGCCGCCTCTCTTATTC 58.670 50.000 0.00 0.00 34.33 1.75
2718 7406 5.325239 AGAAGTCTCAACAAATTTAGGGGG 58.675 41.667 0.00 0.00 0.00 5.40
2719 7407 4.741928 AGTCTCAACAAATTTAGGGGGT 57.258 40.909 0.00 0.00 0.00 4.95
2738 7426 7.658260 AGGGGGTGGTTTATTTATTAATCTGT 58.342 34.615 0.00 0.00 0.00 3.41
2950 7640 0.034186 TGCTCCATTAAGTGCCCCTG 60.034 55.000 0.00 0.00 0.00 4.45
3024 7725 7.012894 GTGGACCGATGGTGATAATTTATGAAA 59.987 37.037 0.00 0.00 35.25 2.69
3025 7726 7.723616 TGGACCGATGGTGATAATTTATGAAAT 59.276 33.333 0.00 0.00 35.25 2.17
3026 7727 9.226606 GGACCGATGGTGATAATTTATGAAATA 57.773 33.333 0.00 0.00 35.25 1.40
3028 7729 9.793259 ACCGATGGTGATAATTTATGAAATAGT 57.207 29.630 0.00 0.00 32.98 2.12
3232 7948 0.952984 AGCTGAGCGTCCAAAGAAGC 60.953 55.000 0.00 0.00 46.55 3.86
3255 7971 7.198390 AGCAATTCGGATGTTCATATTTGAAG 58.802 34.615 0.00 0.00 42.41 3.02
3279 7995 2.046892 CCCAGCCTGTCGTCCAAG 60.047 66.667 0.00 0.00 0.00 3.61
3280 7996 2.046892 CCAGCCTGTCGTCCAAGG 60.047 66.667 0.00 0.00 0.00 3.61
3291 8007 5.350640 CCTGTCGTCCAAGGATTTTACTTAC 59.649 44.000 0.00 0.00 0.00 2.34
3311 8027 0.929244 AAAGGATGCTGGGGTGCTAT 59.071 50.000 0.00 0.00 0.00 2.97
3312 8028 0.184451 AAGGATGCTGGGGTGCTATG 59.816 55.000 0.00 0.00 0.00 2.23
3331 8047 4.409218 AGCCGCGTTCGCTTCGTA 62.409 61.111 14.92 0.00 0.00 3.43
3332 8048 4.187498 GCCGCGTTCGCTTCGTAC 62.187 66.667 14.92 0.00 0.00 3.67
3333 8049 2.801996 CCGCGTTCGCTTCGTACA 60.802 61.111 14.92 0.00 0.00 2.90
3334 8050 2.681666 CGCGTTCGCTTCGTACAG 59.318 61.111 14.92 0.00 0.00 2.74
3335 8051 2.390670 GCGTTCGCTTCGTACAGC 59.609 61.111 9.99 0.00 36.33 4.40
3336 8052 3.067846 GCGTTCGCTTCGTACAGCC 62.068 63.158 9.99 0.00 36.31 4.85
3421 8137 2.828661 AAATGAGGGGGTTTCTAGGC 57.171 50.000 0.00 0.00 0.00 3.93
3422 8138 1.681229 AATGAGGGGGTTTCTAGGCA 58.319 50.000 0.00 0.00 0.00 4.75
3423 8139 0.919710 ATGAGGGGGTTTCTAGGCAC 59.080 55.000 0.00 0.00 0.00 5.01
3424 8140 0.178873 TGAGGGGGTTTCTAGGCACT 60.179 55.000 0.00 0.00 46.37 4.40
3425 8141 0.542333 GAGGGGGTTTCTAGGCACTC 59.458 60.000 0.00 0.00 41.75 3.51
3426 8142 0.914902 AGGGGGTTTCTAGGCACTCC 60.915 60.000 3.11 3.11 41.75 3.85
3431 8147 1.271217 GGTTTCTAGGCACTCCCGTTT 60.271 52.381 0.00 0.00 41.75 3.60
3448 8164 3.551496 TTGCAAGGGGAGCGAGTGG 62.551 63.158 0.00 0.00 33.85 4.00
3463 8179 0.469892 AGTGGGCAGTGGGGAAAAAG 60.470 55.000 0.00 0.00 0.00 2.27
3483 8199 1.521681 CCAATCCTCGCTCGAACCC 60.522 63.158 0.00 0.00 0.00 4.11
3524 8240 1.532794 CTCCTCCTCCATCCTCCCG 60.533 68.421 0.00 0.00 0.00 5.14
3526 8242 3.610669 CTCCTCCATCCTCCCGCG 61.611 72.222 0.00 0.00 0.00 6.46
3532 8248 2.579201 CATCCTCCCGCGTCAGTT 59.421 61.111 4.92 0.00 0.00 3.16
3533 8249 1.811266 CATCCTCCCGCGTCAGTTG 60.811 63.158 4.92 0.00 0.00 3.16
3567 8283 3.461773 CCGCATCTCGTCCACCCT 61.462 66.667 0.00 0.00 36.19 4.34
3574 8290 2.365105 TCGTCCACCCTGGGATCC 60.365 66.667 22.23 1.92 39.62 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.032528 TGGCTTCTTCTGCACCCG 59.967 61.111 0.00 0.00 0.00 5.28
8 9 0.538287 AAGGTGGCTTCTTCTGCACC 60.538 55.000 0.00 0.00 34.33 5.01
9 10 0.595095 CAAGGTGGCTTCTTCTGCAC 59.405 55.000 0.00 0.00 0.00 4.57
10 11 0.473755 TCAAGGTGGCTTCTTCTGCA 59.526 50.000 0.00 0.00 0.00 4.41
11 12 1.831580 ATCAAGGTGGCTTCTTCTGC 58.168 50.000 0.00 0.00 0.00 4.26
12 13 3.274288 GGTATCAAGGTGGCTTCTTCTG 58.726 50.000 0.00 0.00 0.00 3.02
14 15 2.280628 CGGTATCAAGGTGGCTTCTTC 58.719 52.381 0.00 0.00 0.00 2.87
15 16 1.679032 GCGGTATCAAGGTGGCTTCTT 60.679 52.381 0.00 0.00 0.00 2.52
16 17 0.107654 GCGGTATCAAGGTGGCTTCT 60.108 55.000 0.00 0.00 0.00 2.85
17 18 1.429148 CGCGGTATCAAGGTGGCTTC 61.429 60.000 0.00 0.00 0.00 3.86
18 19 1.449601 CGCGGTATCAAGGTGGCTT 60.450 57.895 0.00 0.00 0.00 4.35
19 20 2.186903 CGCGGTATCAAGGTGGCT 59.813 61.111 0.00 0.00 0.00 4.75
20 21 3.573491 GCGCGGTATCAAGGTGGC 61.573 66.667 8.83 0.00 0.00 5.01
21 22 2.125310 TGCGCGGTATCAAGGTGG 60.125 61.111 8.83 0.00 0.00 4.61
22 23 1.421410 GAGTGCGCGGTATCAAGGTG 61.421 60.000 8.83 0.00 0.00 4.00
23 24 1.153628 GAGTGCGCGGTATCAAGGT 60.154 57.895 8.83 0.00 0.00 3.50
24 25 1.883084 GGAGTGCGCGGTATCAAGG 60.883 63.158 8.83 0.00 0.00 3.61
25 26 0.530650 ATGGAGTGCGCGGTATCAAG 60.531 55.000 8.83 0.00 0.00 3.02
26 27 0.529773 GATGGAGTGCGCGGTATCAA 60.530 55.000 8.83 0.00 0.00 2.57
27 28 1.067416 GATGGAGTGCGCGGTATCA 59.933 57.895 8.83 0.00 0.00 2.15
30 31 0.747852 TATTGATGGAGTGCGCGGTA 59.252 50.000 8.83 0.00 0.00 4.02
31 32 0.106708 ATATTGATGGAGTGCGCGGT 59.893 50.000 8.83 0.00 0.00 5.68
32 33 0.514255 CATATTGATGGAGTGCGCGG 59.486 55.000 8.83 0.00 0.00 6.46
33 34 1.501169 TCATATTGATGGAGTGCGCG 58.499 50.000 0.00 0.00 33.49 6.86
34 35 5.808042 ATAATCATATTGATGGAGTGCGC 57.192 39.130 0.00 0.00 37.15 6.09
48 49 9.453572 GGCTATCATGTTTCCTCAATAATCATA 57.546 33.333 0.00 0.00 0.00 2.15
50 51 6.716628 GGGCTATCATGTTTCCTCAATAATCA 59.283 38.462 0.00 0.00 0.00 2.57
51 52 6.944862 AGGGCTATCATGTTTCCTCAATAATC 59.055 38.462 0.00 0.00 0.00 1.75
55 56 4.803329 AGGGCTATCATGTTTCCTCAAT 57.197 40.909 0.00 0.00 0.00 2.57
58 59 4.133078 CAGAAGGGCTATCATGTTTCCTC 58.867 47.826 0.00 0.00 0.00 3.71
61 62 4.513318 GCTACAGAAGGGCTATCATGTTTC 59.487 45.833 0.00 0.00 0.00 2.78
81 82 4.168101 CCCATATCTGTTTCCCCTAGCTA 58.832 47.826 0.00 0.00 0.00 3.32
89 90 6.126739 GGTCCTATATCCCCATATCTGTTTCC 60.127 46.154 0.00 0.00 0.00 3.13
130 131 0.539438 ATGCTTTCAGGCCGTCCAAA 60.539 50.000 0.00 0.00 33.74 3.28
158 159 5.776173 TTTTCGGTATTGTTCAATGGTGT 57.224 34.783 8.11 0.00 0.00 4.16
172 173 4.510340 GTGACTTCAGCTTCTTTTTCGGTA 59.490 41.667 0.00 0.00 0.00 4.02
185 186 2.028658 TCATGAGGTGAGTGACTTCAGC 60.029 50.000 0.54 6.25 43.40 4.26
196 197 2.427095 CACGGATACAGTCATGAGGTGA 59.573 50.000 11.21 0.00 0.00 4.02
208 209 1.768275 AGCCCATGATTCACGGATACA 59.232 47.619 0.00 0.00 0.00 2.29
232 233 0.451783 CGGTGATGCTTAAGTTGGGC 59.548 55.000 4.02 0.00 0.00 5.36
284 285 9.342308 TGCTTTAAAGTTAGATATGATGAAGGG 57.658 33.333 16.38 0.00 0.00 3.95
306 307 5.355350 GTGAAGAGCAATAGGTTATGTGCTT 59.645 40.000 0.00 0.00 46.99 3.91
333 334 8.442384 AGTGTTTGCATTACAAGAAAACAAAAG 58.558 29.630 3.97 0.00 41.06 2.27
335 336 7.600375 TGAGTGTTTGCATTACAAGAAAACAAA 59.400 29.630 3.97 0.00 41.06 2.83
344 345 6.016360 ACAGCTTATGAGTGTTTGCATTACAA 60.016 34.615 3.97 0.00 36.13 2.41
397 398 1.373748 GCAGTCGGCGTTTGTCCTA 60.374 57.895 6.85 0.00 0.00 2.94
398 399 2.665185 GCAGTCGGCGTTTGTCCT 60.665 61.111 6.85 0.00 0.00 3.85
421 422 3.944055 ATTCCTCCGGACATAATCTCG 57.056 47.619 0.00 0.00 0.00 4.04
430 431 3.128764 GGTTGAAATCAATTCCTCCGGAC 59.871 47.826 0.00 0.00 38.24 4.79
433 434 3.758554 ACAGGTTGAAATCAATTCCTCCG 59.241 43.478 0.00 0.00 38.24 4.63
437 438 8.655651 TTAACAAACAGGTTGAAATCAATTCC 57.344 30.769 4.81 0.00 39.87 3.01
442 443 7.616313 AGGTTTTAACAAACAGGTTGAAATCA 58.384 30.769 4.81 0.00 43.76 2.57
534 536 3.975035 TCGTTATGATTCTCAAGATCGCG 59.025 43.478 0.00 0.00 0.00 5.87
595 597 6.933521 ACTGGTATGATCATTAGATTGCTCAC 59.066 38.462 14.65 1.42 33.72 3.51
648 650 0.110644 CGGCGCACTTCTTTCAGAAC 60.111 55.000 10.83 0.00 29.89 3.01
722 724 2.670592 GTAACGGGCCGGCTGTTT 60.671 61.111 32.00 22.04 0.00 2.83
726 728 4.388499 CACAGTAACGGGCCGGCT 62.388 66.667 31.78 21.27 0.00 5.52
727 729 3.299524 TACACAGTAACGGGCCGGC 62.300 63.158 31.78 21.18 0.00 6.13
728 730 1.153706 CTACACAGTAACGGGCCGG 60.154 63.158 31.78 14.51 0.00 6.13
729 731 1.153706 CCTACACAGTAACGGGCCG 60.154 63.158 27.06 27.06 0.00 6.13
730 732 1.449070 GCCTACACAGTAACGGGCC 60.449 63.158 0.00 0.00 34.19 5.80
731 733 0.819582 TAGCCTACACAGTAACGGGC 59.180 55.000 0.00 0.00 39.82 6.13
733 735 3.065786 TCGAATAGCCTACACAGTAACGG 59.934 47.826 0.00 0.00 0.00 4.44
737 739 3.881688 GGAGTCGAATAGCCTACACAGTA 59.118 47.826 0.00 0.00 0.00 2.74
738 740 2.688958 GGAGTCGAATAGCCTACACAGT 59.311 50.000 0.00 0.00 0.00 3.55
739 741 2.034812 GGGAGTCGAATAGCCTACACAG 59.965 54.545 0.00 0.00 0.00 3.66
741 743 2.034812 CAGGGAGTCGAATAGCCTACAC 59.965 54.545 0.00 0.00 0.00 2.90
742 744 2.092049 TCAGGGAGTCGAATAGCCTACA 60.092 50.000 0.00 0.00 0.00 2.74
743 745 2.584236 TCAGGGAGTCGAATAGCCTAC 58.416 52.381 0.00 0.00 0.00 3.18
746 748 1.539280 GCTTCAGGGAGTCGAATAGCC 60.539 57.143 0.00 0.00 0.00 3.93
747 749 1.859383 GCTTCAGGGAGTCGAATAGC 58.141 55.000 0.00 0.00 0.00 2.97
748 750 1.676529 TCGCTTCAGGGAGTCGAATAG 59.323 52.381 0.00 0.00 32.93 1.73
749 751 1.676529 CTCGCTTCAGGGAGTCGAATA 59.323 52.381 11.79 0.00 46.26 1.75
752 754 3.592070 CTCGCTTCAGGGAGTCGA 58.408 61.111 11.79 0.00 46.26 4.20
758 760 2.102252 AGAGCTATTTCTCGCTTCAGGG 59.898 50.000 0.00 0.00 38.12 4.45
759 761 3.380142 GAGAGCTATTTCTCGCTTCAGG 58.620 50.000 0.00 0.00 38.12 3.86
776 778 1.153939 CTCAACCTCACCGCGAGAG 60.154 63.158 8.23 14.73 45.45 3.20
777 779 2.636412 CCTCAACCTCACCGCGAGA 61.636 63.158 8.23 4.02 45.45 4.04
778 780 2.125912 CCTCAACCTCACCGCGAG 60.126 66.667 8.23 0.00 41.89 5.03
781 783 3.050275 GCACCTCAACCTCACCGC 61.050 66.667 0.00 0.00 0.00 5.68
782 784 2.709125 TTCGCACCTCAACCTCACCG 62.709 60.000 0.00 0.00 0.00 4.94
783 785 0.951040 CTTCGCACCTCAACCTCACC 60.951 60.000 0.00 0.00 0.00 4.02
784 786 1.569479 GCTTCGCACCTCAACCTCAC 61.569 60.000 0.00 0.00 0.00 3.51
785 787 1.301716 GCTTCGCACCTCAACCTCA 60.302 57.895 0.00 0.00 0.00 3.86
786 788 1.294659 CTGCTTCGCACCTCAACCTC 61.295 60.000 0.00 0.00 33.79 3.85
787 789 1.302033 CTGCTTCGCACCTCAACCT 60.302 57.895 0.00 0.00 33.79 3.50
791 793 4.704833 GGCCTGCTTCGCACCTCA 62.705 66.667 0.00 0.00 33.79 3.86
840 842 1.009389 GCTCTTCTTGGTGGACGACG 61.009 60.000 0.00 0.00 0.00 5.12
841 843 0.318762 AGCTCTTCTTGGTGGACGAC 59.681 55.000 0.00 0.00 0.00 4.34
842 844 1.544691 GTAGCTCTTCTTGGTGGACGA 59.455 52.381 0.00 0.00 0.00 4.20
1097 4671 0.905839 CGATCGAACGAGAACGGAAC 59.094 55.000 10.26 0.00 44.46 3.62
1146 4728 1.040646 AGTCAGAACAAGGCAGTCGA 58.959 50.000 0.00 0.00 0.00 4.20
1186 4769 3.842732 ACTAGCATAAAACCCGTTTGC 57.157 42.857 0.00 0.00 32.36 3.68
1248 4844 7.009540 GCATCAAACCAATATCTTTGTTACTGC 59.990 37.037 0.00 0.00 0.00 4.40
1321 4924 4.782019 GCAATATTCGCCATTATTGGGA 57.218 40.909 5.82 0.00 43.84 4.37
1333 4936 3.792956 GCACATTTCAGTGGCAATATTCG 59.207 43.478 0.00 0.00 39.87 3.34
1614 6075 2.035961 ACTGTGTAGTCAATGTGCGAGT 59.964 45.455 0.00 0.00 28.79 4.18
1733 6194 7.148440 CGTTCTTATATTACTAGACCGAGGGAG 60.148 44.444 0.00 0.00 0.00 4.30
1734 6195 6.652481 CGTTCTTATATTACTAGACCGAGGGA 59.348 42.308 0.00 0.00 0.00 4.20
1735 6196 6.429385 ACGTTCTTATATTACTAGACCGAGGG 59.571 42.308 0.00 0.00 29.90 4.30
1736 6197 7.432350 ACGTTCTTATATTACTAGACCGAGG 57.568 40.000 0.00 0.00 29.90 4.63
1737 6198 9.727627 AAAACGTTCTTATATTACTAGACCGAG 57.272 33.333 0.00 0.00 29.90 4.63
1750 6211 9.048446 ACTGTTAGCTTGAAAAACGTTCTTATA 57.952 29.630 0.00 0.00 0.00 0.98
1751 6212 7.927048 ACTGTTAGCTTGAAAAACGTTCTTAT 58.073 30.769 0.00 0.00 0.00 1.73
1752 6213 7.311364 ACTGTTAGCTTGAAAAACGTTCTTA 57.689 32.000 0.00 0.00 0.00 2.10
1753 6214 6.190954 ACTGTTAGCTTGAAAAACGTTCTT 57.809 33.333 0.00 0.00 0.00 2.52
1754 6215 5.813080 ACTGTTAGCTTGAAAAACGTTCT 57.187 34.783 0.00 0.00 0.00 3.01
1755 6216 9.821662 ATAATACTGTTAGCTTGAAAAACGTTC 57.178 29.630 0.00 0.00 0.00 3.95
1756 6217 9.607285 CATAATACTGTTAGCTTGAAAAACGTT 57.393 29.630 0.00 0.00 0.00 3.99
1757 6218 8.234546 CCATAATACTGTTAGCTTGAAAAACGT 58.765 33.333 0.00 0.00 0.00 3.99
1758 6219 7.696453 CCCATAATACTGTTAGCTTGAAAAACG 59.304 37.037 0.00 0.00 0.00 3.60
1759 6220 8.736244 TCCCATAATACTGTTAGCTTGAAAAAC 58.264 33.333 0.00 0.00 0.00 2.43
1760 6221 8.736244 GTCCCATAATACTGTTAGCTTGAAAAA 58.264 33.333 0.00 0.00 0.00 1.94
1761 6222 7.065324 CGTCCCATAATACTGTTAGCTTGAAAA 59.935 37.037 0.00 0.00 0.00 2.29
1762 6223 6.537301 CGTCCCATAATACTGTTAGCTTGAAA 59.463 38.462 0.00 0.00 0.00 2.69
1763 6224 6.046593 CGTCCCATAATACTGTTAGCTTGAA 58.953 40.000 0.00 0.00 0.00 2.69
1764 6225 5.452776 CCGTCCCATAATACTGTTAGCTTGA 60.453 44.000 0.00 0.00 0.00 3.02
1765 6226 4.750098 CCGTCCCATAATACTGTTAGCTTG 59.250 45.833 0.00 0.00 0.00 4.01
1766 6227 4.652421 TCCGTCCCATAATACTGTTAGCTT 59.348 41.667 0.00 0.00 0.00 3.74
1767 6228 4.220724 TCCGTCCCATAATACTGTTAGCT 58.779 43.478 0.00 0.00 0.00 3.32
1768 6229 4.280174 TCTCCGTCCCATAATACTGTTAGC 59.720 45.833 0.00 0.00 0.00 3.09
1769 6230 6.401047 TTCTCCGTCCCATAATACTGTTAG 57.599 41.667 0.00 0.00 0.00 2.34
1770 6231 6.381994 ACTTTCTCCGTCCCATAATACTGTTA 59.618 38.462 0.00 0.00 0.00 2.41
1771 6232 5.189145 ACTTTCTCCGTCCCATAATACTGTT 59.811 40.000 0.00 0.00 0.00 3.16
1772 6233 4.715297 ACTTTCTCCGTCCCATAATACTGT 59.285 41.667 0.00 0.00 0.00 3.55
1773 6234 5.277857 ACTTTCTCCGTCCCATAATACTG 57.722 43.478 0.00 0.00 0.00 2.74
1774 6235 6.134754 ACTACTTTCTCCGTCCCATAATACT 58.865 40.000 0.00 0.00 0.00 2.12
1775 6236 6.402456 ACTACTTTCTCCGTCCCATAATAC 57.598 41.667 0.00 0.00 0.00 1.89
1776 6237 7.427989 AAACTACTTTCTCCGTCCCATAATA 57.572 36.000 0.00 0.00 0.00 0.98
1777 6238 5.952347 AACTACTTTCTCCGTCCCATAAT 57.048 39.130 0.00 0.00 0.00 1.28
1778 6239 5.750352 AAACTACTTTCTCCGTCCCATAA 57.250 39.130 0.00 0.00 0.00 1.90
1779 6240 5.750352 AAAACTACTTTCTCCGTCCCATA 57.250 39.130 0.00 0.00 0.00 2.74
1780 6241 4.635699 AAAACTACTTTCTCCGTCCCAT 57.364 40.909 0.00 0.00 0.00 4.00
1781 6242 4.426736 AAAAACTACTTTCTCCGTCCCA 57.573 40.909 0.00 0.00 0.00 4.37
1782 6243 5.407691 CAGTAAAAACTACTTTCTCCGTCCC 59.592 44.000 0.00 0.00 0.00 4.46
1783 6244 6.218746 TCAGTAAAAACTACTTTCTCCGTCC 58.781 40.000 0.00 0.00 0.00 4.79
1784 6245 7.569043 GCTTCAGTAAAAACTACTTTCTCCGTC 60.569 40.741 0.00 0.00 0.00 4.79
1785 6246 6.202379 GCTTCAGTAAAAACTACTTTCTCCGT 59.798 38.462 0.00 0.00 0.00 4.69
1786 6247 6.202188 TGCTTCAGTAAAAACTACTTTCTCCG 59.798 38.462 0.00 0.00 0.00 4.63
1787 6248 7.492352 TGCTTCAGTAAAAACTACTTTCTCC 57.508 36.000 0.00 0.00 0.00 3.71
1788 6249 9.600646 GATTGCTTCAGTAAAAACTACTTTCTC 57.399 33.333 0.00 0.00 0.00 2.87
1789 6250 9.343539 AGATTGCTTCAGTAAAAACTACTTTCT 57.656 29.630 0.00 0.00 0.00 2.52
1790 6251 9.387123 CAGATTGCTTCAGTAAAAACTACTTTC 57.613 33.333 0.00 0.00 0.00 2.62
1791 6252 8.903820 ACAGATTGCTTCAGTAAAAACTACTTT 58.096 29.630 0.00 0.00 0.00 2.66
1792 6253 8.451908 ACAGATTGCTTCAGTAAAAACTACTT 57.548 30.769 0.00 0.00 0.00 2.24
1908 6372 7.044798 GCATACTCTTCTTCACTCCAAGTAAT 58.955 38.462 0.00 0.00 0.00 1.89
2130 6794 2.159170 GCAGCTAGTCCTGAGTGTTAGG 60.159 54.545 1.89 0.00 34.77 2.69
2184 6856 6.833416 TGAATCCACCCTGGTAAGATTAATTG 59.167 38.462 11.65 0.00 39.03 2.32
2207 6882 1.077930 GCTCTGGCTCCATTGCTGA 60.078 57.895 6.18 0.00 35.22 4.26
2529 7217 3.956848 TCATTTCACATTTCACACCCACA 59.043 39.130 0.00 0.00 0.00 4.17
2569 7257 2.239654 TCTGTCCCCTATTCTTGGCAAG 59.760 50.000 21.17 21.17 0.00 4.01
2579 7267 2.852449 TGCCAAAAGATCTGTCCCCTAT 59.148 45.455 0.00 0.00 0.00 2.57
2608 7296 1.143684 TGGGGAGGATGCAGCTTATTC 59.856 52.381 0.22 0.00 0.00 1.75
2657 7345 3.329929 ACTAGTTTAGAAGCCCCAACG 57.670 47.619 0.00 0.00 0.00 4.10
2767 7456 2.689983 ACAAGCTTGGACCAGTTCTTTG 59.310 45.455 29.18 0.84 0.00 2.77
2895 7585 0.391130 TAGAGCCGCAACATGGTGTC 60.391 55.000 13.35 1.44 0.00 3.67
2950 7640 8.736244 TCTTCAATTACCAAACATTAGCTAACC 58.264 33.333 8.70 0.00 0.00 2.85
3025 7726 9.104713 ACCATCTGATTGTCATATTATGGACTA 57.895 33.333 0.00 0.03 36.86 2.59
3026 7727 7.881751 CACCATCTGATTGTCATATTATGGACT 59.118 37.037 0.00 0.00 36.86 3.85
3027 7728 7.120285 CCACCATCTGATTGTCATATTATGGAC 59.880 40.741 0.00 2.53 36.86 4.02
3028 7729 7.170277 CCACCATCTGATTGTCATATTATGGA 58.830 38.462 0.00 0.00 36.86 3.41
3029 7730 6.944290 ACCACCATCTGATTGTCATATTATGG 59.056 38.462 3.89 0.00 38.84 2.74
3030 7731 7.991084 ACCACCATCTGATTGTCATATTATG 57.009 36.000 0.00 0.00 0.00 1.90
3032 7733 9.559732 CTAAACCACCATCTGATTGTCATATTA 57.440 33.333 0.00 0.00 0.00 0.98
3033 7734 7.503566 CCTAAACCACCATCTGATTGTCATATT 59.496 37.037 0.00 0.00 0.00 1.28
3034 7735 7.000472 CCTAAACCACCATCTGATTGTCATAT 59.000 38.462 0.00 0.00 0.00 1.78
3211 7927 0.392706 TTCTTTGGACGCTCAGCTGA 59.607 50.000 17.19 17.19 0.00 4.26
3216 7932 1.896220 ATTGCTTCTTTGGACGCTCA 58.104 45.000 0.00 0.00 37.57 4.26
3232 7948 7.166970 CAGCTTCAAATATGAACATCCGAATTG 59.833 37.037 0.00 0.00 40.59 2.32
3270 7986 6.790285 TTGTAAGTAAAATCCTTGGACGAC 57.210 37.500 0.00 0.00 0.00 4.34
3279 7995 6.405842 CCCAGCATCCTTTGTAAGTAAAATCC 60.406 42.308 0.00 0.00 0.00 3.01
3280 7996 6.405842 CCCCAGCATCCTTTGTAAGTAAAATC 60.406 42.308 0.00 0.00 0.00 2.17
3291 8007 0.034186 TAGCACCCCAGCATCCTTTG 60.034 55.000 0.00 0.00 36.85 2.77
3327 8043 2.882761 ACTATTCATAGCGGCTGTACGA 59.117 45.455 13.86 0.00 33.68 3.43
3328 8044 2.980476 CACTATTCATAGCGGCTGTACG 59.020 50.000 13.86 0.00 33.68 3.67
3329 8045 2.731976 GCACTATTCATAGCGGCTGTAC 59.268 50.000 13.86 0.00 33.66 2.90
3330 8046 2.364002 TGCACTATTCATAGCGGCTGTA 59.636 45.455 13.86 0.00 35.94 2.74
3331 8047 1.138859 TGCACTATTCATAGCGGCTGT 59.861 47.619 13.86 2.17 35.94 4.40
3332 8048 1.797046 CTGCACTATTCATAGCGGCTG 59.203 52.381 13.86 0.00 35.94 4.85
3333 8049 2.160822 CTGCACTATTCATAGCGGCT 57.839 50.000 7.98 7.98 35.94 5.52
3335 8051 1.151668 GGCTGCACTATTCATAGCGG 58.848 55.000 0.50 0.00 35.31 5.52
3336 8052 1.797046 CTGGCTGCACTATTCATAGCG 59.203 52.381 0.50 0.00 35.31 4.26
3404 8120 0.919710 GTGCCTAGAAACCCCCTCAT 59.080 55.000 0.00 0.00 0.00 2.90
3405 8121 0.178873 AGTGCCTAGAAACCCCCTCA 60.179 55.000 0.00 0.00 0.00 3.86
3411 8127 0.323957 AACGGGAGTGCCTAGAAACC 59.676 55.000 0.00 0.00 46.69 3.27
3412 8128 1.804748 CAAACGGGAGTGCCTAGAAAC 59.195 52.381 0.00 0.00 46.69 2.78
3414 8130 0.321298 GCAAACGGGAGTGCCTAGAA 60.321 55.000 0.00 0.00 46.69 2.10
3415 8131 1.295423 GCAAACGGGAGTGCCTAGA 59.705 57.895 0.00 0.00 46.69 2.43
3416 8132 0.605319 TTGCAAACGGGAGTGCCTAG 60.605 55.000 0.00 0.00 46.69 3.02
3417 8133 0.605319 CTTGCAAACGGGAGTGCCTA 60.605 55.000 0.00 0.00 46.69 3.93
3418 8134 1.898574 CTTGCAAACGGGAGTGCCT 60.899 57.895 0.00 0.00 46.69 4.75
3419 8135 2.644992 CTTGCAAACGGGAGTGCC 59.355 61.111 0.00 0.00 46.69 5.01
3420 8136 2.644992 CCTTGCAAACGGGAGTGC 59.355 61.111 0.00 0.00 46.69 4.40
3421 8137 2.268076 CCCCTTGCAAACGGGAGTG 61.268 63.158 22.35 4.99 43.97 3.51
3422 8138 2.115266 CCCCTTGCAAACGGGAGT 59.885 61.111 22.35 0.00 43.97 3.85
3423 8139 2.434331 TCCCCTTGCAAACGGGAG 59.566 61.111 24.00 14.77 44.73 4.30
3424 8140 2.434331 CTCCCCTTGCAAACGGGA 59.566 61.111 25.38 25.38 46.94 5.14
3425 8141 3.373565 GCTCCCCTTGCAAACGGG 61.374 66.667 20.76 20.76 42.77 5.28
3426 8142 3.737172 CGCTCCCCTTGCAAACGG 61.737 66.667 0.00 2.57 0.00 4.44
3431 8147 4.020617 CCACTCGCTCCCCTTGCA 62.021 66.667 0.00 0.00 0.00 4.08
3439 8155 4.767255 CCCACTGCCCACTCGCTC 62.767 72.222 0.00 0.00 0.00 5.03
3448 8164 2.583441 GGCCTTTTTCCCCACTGCC 61.583 63.158 0.00 0.00 0.00 4.85
3453 8169 3.081048 GGATTGGCCTTTTTCCCCA 57.919 52.632 3.32 0.00 0.00 4.96
3463 8179 2.174319 GTTCGAGCGAGGATTGGCC 61.174 63.158 0.00 0.00 0.00 5.36
3483 8199 4.577246 GAGCGTGGAGGCGGCTAG 62.577 72.222 13.24 5.11 38.18 3.42
3504 8220 1.669927 GGGAGGATGGAGGAGGAGGA 61.670 65.000 0.00 0.00 0.00 3.71
3505 8221 1.152139 GGGAGGATGGAGGAGGAGG 60.152 68.421 0.00 0.00 0.00 4.30
3506 8222 1.532794 CGGGAGGATGGAGGAGGAG 60.533 68.421 0.00 0.00 0.00 3.69
3567 8283 2.825982 CGCATAACCCGGATCCCA 59.174 61.111 0.73 0.00 0.00 4.37
3574 8290 4.215742 TCGCCTCCGCATAACCCG 62.216 66.667 0.00 0.00 34.03 5.28


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

AutoCloner maintained by Alex Coulton.